From: Aligning coding sequences with frameshift extension penalties
fs_open_ cost | fs_extend_cost (# CDS pairs) | Method | Identity_ NT | Identity_ AA | Gap_ init | Gap_ length | FS_init (avg) | FS_ length |
---|---|---|---|---|---|---|---|---|
−10 | −1 (2127) | fse0 (862) | 1095102 | 1737105 | 24489 | 908218 | 1111 (1.28 ± 0.54) | 42730 |
fse | 1086546 | 1719774 | 23483 | 906540 | 0 | 0 | ||
macse_p (2076) | 1124316 | 1790199 | 45335 | 936002 | 12436 (5.99 \(\pm\,4.96\)) | 216772 | ||
needleprot | 1085007 | 1723950 | 25288 | 916518 | 0 | 0 | ||
−0.5 (1953) | fse0 (688) | 1008514 | 1597605 | 22984 | 854021 | 855 (1.24 \(\pm\,0.53\) ) | 31172 | |
fse (2) | 1003293 | 1587258 | 22102 | 853793 | 2 (1.0 \(\pm\,0\) ) | 80 | ||
macse_p (1902) | 1036768 | 1649604 | 42619 | 880399 | 11562 (6.07 \(\pm\,4.91\)) | 197772 | ||
needleprot | 1001957 | 1591134 | 23790 | 863199 | 0 | 0 | ||
−0.2 (1720) | fse0 (455) | 890042 | 1420569 | 20050 | 764510 | 532 (1.16 \(\pm\,0.48\)) | 19568 | |
fse (3) | 887372 | 1415403 | 19465 | 764162 | 3 (1.0 \(\pm\,0\)) | 92 | ||
macse_p (1669) | 915754 | 1468305 | 37472 | 789220 | 9975 (5.97 \(\pm\,4.75\)) | 167484 | ||
needleprot | 886178 | 1418748 | 20955 | 772272 | 0 | 0 | ||
−20 | −1 (409) | fse0 (100) | 219277 | 358554 | 3633 | 153487 | 120 (1.2 \(\pm\,0.40\)) | 6937 |
fse | 216936 | 353586 | 3619 | 152391 | 0 | 0 | ||
macse_p (403) | 225976 | 374391 | 6509 | 158165 | 1348 (3.34 \(\pm\,3.00\)) | 36179 | ||
needleprot | 216842 | 355656 | 4172 | 153957 | 0 | 0 | ||
−0.5 (381) | fse0 (72) | 195615 | 311757 | 3545 | 144317 | 91 (1.26 \(\pm\,0.44\)) | 5108 | |
fse | 194048 | 308448 | 3505 | 144045 | 0 | 0 | ||
macse_p (375) | 202374 | 327711 | 6380 | 148909 | 1311 (3.49 \(\pm\,3.05\)) | 34322 | ||
needleprot | 193980 | 310632 | 4051 | 145563 | 0 | 0 | ||
−0.2 (354) | fse0 (45) | 181185 | 284787 | 3371 | 138419 | 63 (1.4 \(\pm\,0.49\)) | 3407 | |
fse (1) | 180151 | 282693 | 3344 | 138217 | 1 (1.0 \(\pm\,0\)) | 40 | ||
macse_p (348) | 187895 | 300777 | 6157 | 143035 | 1265 (3.63 \(\pm\,3.11\)) | 32301 | ||
needleprot | 180116 | 284946 | 3883 | 139731 | 0 | 0 | ||
−30 | −1 (200) | fse0 (119) | 151090 | 289617 | 805 | 42437 | 120 (1.01 \(\pm\,0.09\)) | 6818 |
fse | 147590 | 282018 | 852 | 40221 | 0 | 0 | ||
macse_p (200) | 152626 | 292254 | 1309 | 43043 | 378 (1.89 \(\pm\,2.16\)) | 14515 | ||
needleprot | 147228 | 281472 | 933 | 40455 | 0 | 0 | ||
−0.5 (117) | fse0 (36) | 77603 | 143115 | 590 | 30765 | 37 (1.02 \(\pm\,0.16\)) | 2109 | |
fse | 76678 | 141108 | 626 | 29913 | 0 | 0 | ||
macse_p (117) | 79224 | 146046 | 990 | 31321 | 284 (2.42 \(\pm\,2.65\)) | 9731 | ||
needleprot | 76561 | 141036 | 703 | 30099 | 0 | 0 | ||
−0.2 (93) | fse0 (12) | 60710 | 109842 | 510 | 22691 | 12 (1.0 \(\pm\,0\)) | 668 | |
fse | 60407 | 109170 | 518 | 22491 | 0 | 0 | ||
macse_p (93) | 62387 | 112872 | 878 | 23181 | 252 (2.70 \(\pm\,2.89\)) | 8262 | ||
needleprot | 60270 | 109122 | 581 | 22677 | 0 | 0 |