Multiple sequence alignment - TraesCS2B01G561200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G561200 chr2B 100.000 2273 0 0 1 2273 753996107 753998379 0.000000e+00 4198.0
1 TraesCS2B01G561200 chr2B 92.577 943 29 11 1365 2273 772838910 772837975 0.000000e+00 1315.0
2 TraesCS2B01G561200 chr2B 91.221 786 63 5 1 781 616457119 616457903 0.000000e+00 1064.0
3 TraesCS2B01G561200 chr2B 81.025 527 69 17 782 1295 754004433 754004941 7.610000e-105 390.0
4 TraesCS2B01G561200 chr2B 80.488 533 73 20 782 1302 753988306 753988819 1.650000e-101 379.0
5 TraesCS2B01G561200 chr2B 84.053 301 42 4 1009 1305 708863259 708862961 3.700000e-73 285.0
6 TraesCS2B01G561200 chr2B 84.151 265 39 1 1009 1273 753974099 753974360 1.040000e-63 254.0
7 TraesCS2B01G561200 chr2B 93.023 43 3 0 1323 1365 754014177 754014219 1.880000e-06 63.9
8 TraesCS2B01G561200 chr2B 92.683 41 3 0 1323 1363 754011382 754011422 2.440000e-05 60.2
9 TraesCS2B01G561200 chr3B 98.901 910 8 2 1365 2273 390497475 390496567 0.000000e+00 1624.0
10 TraesCS2B01G561200 chr3B 91.083 785 65 4 1 781 578618727 578617944 0.000000e+00 1057.0
11 TraesCS2B01G561200 chr3B 90.712 786 67 5 1 781 697857479 697856695 0.000000e+00 1042.0
12 TraesCS2B01G561200 chr1A 96.061 914 29 6 1364 2273 278083959 278084869 0.000000e+00 1482.0
13 TraesCS2B01G561200 chr2D 91.347 913 44 12 1365 2273 480219342 480218461 0.000000e+00 1216.0
14 TraesCS2B01G561200 chr2D 80.192 520 70 16 799 1292 618003885 618004397 2.150000e-95 359.0
15 TraesCS2B01G561200 chr2D 83.056 301 45 4 1009 1305 587111808 587111510 3.720000e-68 268.0
16 TraesCS2B01G561200 chr2D 84.962 266 38 2 1009 1273 617973060 617973324 3.720000e-68 268.0
17 TraesCS2B01G561200 chr7A 91.288 792 62 6 1 787 217583696 217582907 0.000000e+00 1074.0
18 TraesCS2B01G561200 chr7A 90.038 783 69 5 1 777 691471357 691472136 0.000000e+00 1005.0
19 TraesCS2B01G561200 chr1B 91.139 790 64 5 1 786 17618240 17617453 0.000000e+00 1066.0
20 TraesCS2B01G561200 chr1B 91.346 728 57 5 59 781 407307441 407306715 0.000000e+00 990.0
21 TraesCS2B01G561200 chr4B 91.013 790 64 6 1 785 3910100 3910887 0.000000e+00 1059.0
22 TraesCS2B01G561200 chr3A 90.840 786 66 5 1 781 742043257 742042473 0.000000e+00 1048.0
23 TraesCS2B01G561200 chr2A 82.667 525 69 9 782 1287 748550390 748550911 1.600000e-121 446.0
24 TraesCS2B01G561200 chr2A 79.477 497 86 15 782 1273 748775808 748776293 2.800000e-89 339.0
25 TraesCS2B01G561200 chr2A 83.784 296 39 7 1013 1307 748685262 748685549 2.880000e-69 272.0
26 TraesCS2B01G561200 chr2A 83.922 255 38 2 1009 1263 748524476 748524727 8.110000e-60 241.0
27 TraesCS2B01G561200 chr2A 87.879 99 10 2 782 879 748685104 748685201 5.130000e-22 115.0
28 TraesCS2B01G561200 chr2A 93.023 43 3 0 1323 1365 748529639 748529681 1.880000e-06 63.9
29 TraesCS2B01G561200 chr2A 93.023 43 3 0 1323 1365 748542731 748542773 1.880000e-06 63.9
30 TraesCS2B01G561200 chr2A 92.857 42 3 0 1323 1364 748535377 748535418 6.780000e-06 62.1
31 TraesCS2B01G561200 chr7D 100.000 30 0 0 1365 1394 596090580 596090609 3.150000e-04 56.5
32 TraesCS2B01G561200 chrUn 92.308 39 2 1 1362 1400 17048154 17048191 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G561200 chr2B 753996107 753998379 2272 False 4198 4198 100.000 1 2273 1 chr2B.!!$F4 2272
1 TraesCS2B01G561200 chr2B 772837975 772838910 935 True 1315 1315 92.577 1365 2273 1 chr2B.!!$R2 908
2 TraesCS2B01G561200 chr2B 616457119 616457903 784 False 1064 1064 91.221 1 781 1 chr2B.!!$F1 780
3 TraesCS2B01G561200 chr2B 754004433 754004941 508 False 390 390 81.025 782 1295 1 chr2B.!!$F5 513
4 TraesCS2B01G561200 chr2B 753988306 753988819 513 False 379 379 80.488 782 1302 1 chr2B.!!$F3 520
5 TraesCS2B01G561200 chr3B 390496567 390497475 908 True 1624 1624 98.901 1365 2273 1 chr3B.!!$R1 908
6 TraesCS2B01G561200 chr3B 578617944 578618727 783 True 1057 1057 91.083 1 781 1 chr3B.!!$R2 780
7 TraesCS2B01G561200 chr3B 697856695 697857479 784 True 1042 1042 90.712 1 781 1 chr3B.!!$R3 780
8 TraesCS2B01G561200 chr1A 278083959 278084869 910 False 1482 1482 96.061 1364 2273 1 chr1A.!!$F1 909
9 TraesCS2B01G561200 chr2D 480218461 480219342 881 True 1216 1216 91.347 1365 2273 1 chr2D.!!$R1 908
10 TraesCS2B01G561200 chr2D 618003885 618004397 512 False 359 359 80.192 799 1292 1 chr2D.!!$F2 493
11 TraesCS2B01G561200 chr7A 217582907 217583696 789 True 1074 1074 91.288 1 787 1 chr7A.!!$R1 786
12 TraesCS2B01G561200 chr7A 691471357 691472136 779 False 1005 1005 90.038 1 777 1 chr7A.!!$F1 776
13 TraesCS2B01G561200 chr1B 17617453 17618240 787 True 1066 1066 91.139 1 786 1 chr1B.!!$R1 785
14 TraesCS2B01G561200 chr1B 407306715 407307441 726 True 990 990 91.346 59 781 1 chr1B.!!$R2 722
15 TraesCS2B01G561200 chr4B 3910100 3910887 787 False 1059 1059 91.013 1 785 1 chr4B.!!$F1 784
16 TraesCS2B01G561200 chr3A 742042473 742043257 784 True 1048 1048 90.840 1 781 1 chr3A.!!$R1 780
17 TraesCS2B01G561200 chr2A 748550390 748550911 521 False 446 446 82.667 782 1287 1 chr2A.!!$F5 505

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
464 466 0.396278 GCCTTTCCTTCCTGATGGGG 60.396 60.0 0.0 0.0 35.33 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1405 0.038744 AAGCACATGGACAAGGAGGG 59.961 55.0 0.0 0.0 0.0 4.3 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.667348 CTGGAGGTGTAGTTCGGGT 58.333 57.895 0.00 0.00 0.00 5.28
203 205 2.592861 GATGGCGATGGAGGTGGC 60.593 66.667 0.00 0.00 0.00 5.01
246 248 2.680370 GCCCCTCCCGATTTCTGGT 61.680 63.158 0.00 0.00 0.00 4.00
273 275 1.146774 CTCTCCATCCTCTAGGCCTCA 59.853 57.143 9.68 0.00 34.44 3.86
292 294 2.093021 TCATGATGGCGGTCTCAATGAA 60.093 45.455 0.00 0.00 0.00 2.57
314 316 1.809271 CGGCATGGATGACCTCAAGAG 60.809 57.143 0.00 0.00 37.04 2.85
334 336 2.046411 TGGTGGCGTATGCTGGTG 60.046 61.111 6.92 0.00 42.25 4.17
364 366 2.044946 GCTGGTTGGCTCCGGATT 60.045 61.111 3.57 0.00 36.02 3.01
390 392 0.998928 ATAGTGGTGGTTGGGATGCA 59.001 50.000 0.00 0.00 0.00 3.96
464 466 0.396278 GCCTTTCCTTCCTGATGGGG 60.396 60.000 0.00 0.00 35.33 4.96
465 467 1.298953 CCTTTCCTTCCTGATGGGGA 58.701 55.000 0.00 0.00 35.33 4.81
468 470 3.463329 CCTTTCCTTCCTGATGGGGATAA 59.537 47.826 0.00 0.00 35.07 1.75
470 472 2.057922 TCCTTCCTGATGGGGATAAGC 58.942 52.381 0.00 0.00 35.07 3.09
474 476 1.140852 TCCTGATGGGGATAAGCGTTG 59.859 52.381 0.00 0.00 35.33 4.10
484 486 0.546122 ATAAGCGTTGCCCATCCTCA 59.454 50.000 0.00 0.00 0.00 3.86
488 490 1.244019 GCGTTGCCCATCCTCAACTT 61.244 55.000 0.00 0.00 40.12 2.66
524 526 1.831736 CGGAAACCCTAGGACATGTCT 59.168 52.381 24.50 13.31 0.00 3.41
562 568 1.004745 ACGTTGCATCCCTTCTTGGAT 59.995 47.619 0.00 0.00 46.22 3.41
644 650 2.355986 AACGGTGGCGGCTCATCTA 61.356 57.895 11.43 0.00 0.00 1.98
686 692 6.248210 CGTTGTTGGCATTTTGTTTTTCTTTC 59.752 34.615 0.00 0.00 0.00 2.62
715 721 0.677731 TAGGCTTGATGTGCTGTGCC 60.678 55.000 0.00 0.00 40.54 5.01
734 742 1.359848 CCCAGCAGTTATCGTGTGAC 58.640 55.000 0.00 0.00 0.00 3.67
736 744 2.165641 CCCAGCAGTTATCGTGTGACTA 59.834 50.000 0.00 0.00 0.00 2.59
856 866 1.089978 TCCCACTCCCACTCTTCCTA 58.910 55.000 0.00 0.00 0.00 2.94
857 867 1.435563 TCCCACTCCCACTCTTCCTAA 59.564 52.381 0.00 0.00 0.00 2.69
871 881 5.236478 ACTCTTCCTAACATCAACACAAACG 59.764 40.000 0.00 0.00 0.00 3.60
880 890 3.332761 TCAACACAAACGAGCATCAAC 57.667 42.857 0.00 0.00 33.17 3.18
884 894 2.287915 ACACAAACGAGCATCAACTCAC 59.712 45.455 0.00 0.00 36.42 3.51
898 908 5.282055 TCAACTCACTGAGACAGTTCAAT 57.718 39.130 13.25 0.00 42.59 2.57
900 910 6.816136 TCAACTCACTGAGACAGTTCAATAA 58.184 36.000 13.25 0.00 42.59 1.40
901 911 7.272244 TCAACTCACTGAGACAGTTCAATAAA 58.728 34.615 13.25 0.00 42.59 1.40
902 912 7.768582 TCAACTCACTGAGACAGTTCAATAAAA 59.231 33.333 13.25 0.00 42.59 1.52
903 913 8.562892 CAACTCACTGAGACAGTTCAATAAAAT 58.437 33.333 13.25 0.00 42.59 1.82
904 914 8.316640 ACTCACTGAGACAGTTCAATAAAATC 57.683 34.615 13.25 0.00 42.59 2.17
947 980 1.065854 CAAGTCCACTCCAGGATCACC 60.066 57.143 0.00 0.00 40.42 4.02
955 988 1.905215 CTCCAGGATCACCAGTCAGTT 59.095 52.381 0.00 0.00 38.94 3.16
959 994 1.276421 AGGATCACCAGTCAGTTTCCG 59.724 52.381 0.00 0.00 38.94 4.30
977 1012 3.754068 CTCCAGCAGCACAGCAAA 58.246 55.556 0.00 0.00 36.85 3.68
983 1024 2.001159 CAGCAGCACAGCAAAAACAAA 58.999 42.857 0.00 0.00 36.85 2.83
984 1025 2.415857 CAGCAGCACAGCAAAAACAAAA 59.584 40.909 0.00 0.00 36.85 2.44
987 1028 3.120234 GCAGCACAGCAAAAACAAAAAGT 60.120 39.130 0.00 0.00 0.00 2.66
988 1029 4.092675 GCAGCACAGCAAAAACAAAAAGTA 59.907 37.500 0.00 0.00 0.00 2.24
989 1030 5.220643 GCAGCACAGCAAAAACAAAAAGTAT 60.221 36.000 0.00 0.00 0.00 2.12
998 1039 7.867909 AGCAAAAACAAAAAGTATAGGAGAAGC 59.132 33.333 0.00 0.00 0.00 3.86
1032 1073 0.104120 CGAAGGCATCGTGGATGGTA 59.896 55.000 3.61 0.00 46.52 3.25
1116 1157 2.359169 GCTCAGGTCCATCCACCGA 61.359 63.158 0.00 0.00 41.90 4.69
1119 1160 2.039624 AGGTCCATCCACCGAGCT 59.960 61.111 0.00 0.00 41.90 4.09
1131 1178 3.437795 CGAGCTGCCAAGGCCAAG 61.438 66.667 5.01 1.13 41.09 3.61
1132 1179 3.066814 GAGCTGCCAAGGCCAAGG 61.067 66.667 5.01 7.44 41.09 3.61
1183 1230 2.932194 AGCAGCTTCTGGCCTCCA 60.932 61.111 3.32 0.00 43.05 3.86
1214 1261 4.539881 GGAGAGACGGCGAGCGAC 62.540 72.222 16.62 5.38 0.00 5.19
1227 1285 2.214181 GAGCGACGAAGGCTGAGGAA 62.214 60.000 0.00 0.00 41.72 3.36
1239 1297 0.617249 CTGAGGAAGGGCTGAGGACT 60.617 60.000 0.00 0.00 0.00 3.85
1258 1327 0.250234 TGTCATGTACCTCAGCTGCC 59.750 55.000 9.47 0.00 0.00 4.85
1298 1367 4.057063 ACTAGTAGCTTAGGGGTGTTGA 57.943 45.455 0.00 0.00 0.00 3.18
1302 1371 3.651423 AGTAGCTTAGGGGTGTTGAGTTT 59.349 43.478 0.00 0.00 0.00 2.66
1303 1372 2.863809 AGCTTAGGGGTGTTGAGTTTG 58.136 47.619 0.00 0.00 0.00 2.93
1304 1373 2.174854 AGCTTAGGGGTGTTGAGTTTGT 59.825 45.455 0.00 0.00 0.00 2.83
1305 1374 2.956333 GCTTAGGGGTGTTGAGTTTGTT 59.044 45.455 0.00 0.00 0.00 2.83
1306 1375 3.243401 GCTTAGGGGTGTTGAGTTTGTTG 60.243 47.826 0.00 0.00 0.00 3.33
1307 1376 2.818751 AGGGGTGTTGAGTTTGTTGA 57.181 45.000 0.00 0.00 0.00 3.18
1308 1377 3.312736 AGGGGTGTTGAGTTTGTTGAT 57.687 42.857 0.00 0.00 0.00 2.57
1309 1378 2.958355 AGGGGTGTTGAGTTTGTTGATG 59.042 45.455 0.00 0.00 0.00 3.07
1310 1379 2.955660 GGGGTGTTGAGTTTGTTGATGA 59.044 45.455 0.00 0.00 0.00 2.92
1311 1380 3.573967 GGGGTGTTGAGTTTGTTGATGAT 59.426 43.478 0.00 0.00 0.00 2.45
1312 1381 4.549458 GGGTGTTGAGTTTGTTGATGATG 58.451 43.478 0.00 0.00 0.00 3.07
1313 1382 4.278170 GGGTGTTGAGTTTGTTGATGATGA 59.722 41.667 0.00 0.00 0.00 2.92
1314 1383 5.047802 GGGTGTTGAGTTTGTTGATGATGAT 60.048 40.000 0.00 0.00 0.00 2.45
1315 1384 5.860182 GGTGTTGAGTTTGTTGATGATGATG 59.140 40.000 0.00 0.00 0.00 3.07
1316 1385 6.294120 GGTGTTGAGTTTGTTGATGATGATGA 60.294 38.462 0.00 0.00 0.00 2.92
1317 1386 7.310664 GTGTTGAGTTTGTTGATGATGATGAT 58.689 34.615 0.00 0.00 0.00 2.45
1318 1387 7.272731 GTGTTGAGTTTGTTGATGATGATGATG 59.727 37.037 0.00 0.00 0.00 3.07
1319 1388 7.175293 TGTTGAGTTTGTTGATGATGATGATGA 59.825 33.333 0.00 0.00 0.00 2.92
1320 1389 7.875327 TGAGTTTGTTGATGATGATGATGAT 57.125 32.000 0.00 0.00 0.00 2.45
1321 1390 7.703328 TGAGTTTGTTGATGATGATGATGATG 58.297 34.615 0.00 0.00 0.00 3.07
1322 1391 7.554835 TGAGTTTGTTGATGATGATGATGATGA 59.445 33.333 0.00 0.00 0.00 2.92
1323 1392 8.465273 AGTTTGTTGATGATGATGATGATGAT 57.535 30.769 0.00 0.00 0.00 2.45
1324 1393 8.352942 AGTTTGTTGATGATGATGATGATGATG 58.647 33.333 0.00 0.00 0.00 3.07
1325 1394 8.349983 GTTTGTTGATGATGATGATGATGATGA 58.650 33.333 0.00 0.00 0.00 2.92
1326 1395 8.458573 TTGTTGATGATGATGATGATGATGAA 57.541 30.769 0.00 0.00 0.00 2.57
1327 1396 8.635765 TGTTGATGATGATGATGATGATGAAT 57.364 30.769 0.00 0.00 0.00 2.57
1328 1397 9.733556 TGTTGATGATGATGATGATGATGAATA 57.266 29.630 0.00 0.00 0.00 1.75
1341 1410 9.941325 GATGATGATGAATATATATCACCCTCC 57.059 37.037 0.00 0.00 36.26 4.30
1342 1411 9.686136 ATGATGATGAATATATATCACCCTCCT 57.314 33.333 0.00 0.00 36.26 3.69
1343 1412 9.511404 TGATGATGAATATATATCACCCTCCTT 57.489 33.333 0.00 0.00 36.26 3.36
1344 1413 9.775854 GATGATGAATATATATCACCCTCCTTG 57.224 37.037 0.00 0.00 36.26 3.61
1345 1414 8.685257 TGATGAATATATATCACCCTCCTTGT 57.315 34.615 0.00 0.00 0.00 3.16
1346 1415 8.762645 TGATGAATATATATCACCCTCCTTGTC 58.237 37.037 0.00 0.00 0.00 3.18
1347 1416 7.496346 TGAATATATATCACCCTCCTTGTCC 57.504 40.000 0.00 0.00 0.00 4.02
1348 1417 7.022496 TGAATATATATCACCCTCCTTGTCCA 58.978 38.462 0.00 0.00 0.00 4.02
1349 1418 7.684186 TGAATATATATCACCCTCCTTGTCCAT 59.316 37.037 0.00 0.00 0.00 3.41
1350 1419 5.768980 ATATATCACCCTCCTTGTCCATG 57.231 43.478 0.00 0.00 0.00 3.66
1351 1420 1.673767 ATCACCCTCCTTGTCCATGT 58.326 50.000 0.00 0.00 0.00 3.21
1352 1421 0.692476 TCACCCTCCTTGTCCATGTG 59.308 55.000 0.00 0.00 0.00 3.21
1353 1422 0.962356 CACCCTCCTTGTCCATGTGC 60.962 60.000 0.00 0.00 0.00 4.57
1354 1423 1.136329 ACCCTCCTTGTCCATGTGCT 61.136 55.000 0.00 0.00 0.00 4.40
1355 1424 0.038744 CCCTCCTTGTCCATGTGCTT 59.961 55.000 0.00 0.00 0.00 3.91
1356 1425 1.457346 CCTCCTTGTCCATGTGCTTC 58.543 55.000 0.00 0.00 0.00 3.86
1357 1426 1.457346 CTCCTTGTCCATGTGCTTCC 58.543 55.000 0.00 0.00 0.00 3.46
1358 1427 0.770499 TCCTTGTCCATGTGCTTCCA 59.230 50.000 0.00 0.00 0.00 3.53
1359 1428 1.355381 TCCTTGTCCATGTGCTTCCAT 59.645 47.619 0.00 0.00 0.00 3.41
1360 1429 1.475280 CCTTGTCCATGTGCTTCCATG 59.525 52.381 0.00 5.06 41.52 3.66
1361 1430 2.439409 CTTGTCCATGTGCTTCCATGA 58.561 47.619 11.54 0.00 43.99 3.07
1362 1431 1.825090 TGTCCATGTGCTTCCATGAC 58.175 50.000 11.54 8.90 43.99 3.06
1422 1499 8.163408 TGTCCCTAATGGTCAATAGAAATATGG 58.837 37.037 0.00 0.00 34.77 2.74
1558 1636 3.569701 TGTCAAGGATTTTTCTGTGCTCC 59.430 43.478 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.188863 GCCTTCCTACACCCGAACTA 58.811 55.000 0.00 0.00 0.00 2.24
18 19 1.923395 CCCACCCAGCCTTCCTACA 60.923 63.158 0.00 0.00 0.00 2.74
42 43 4.728110 AGCAAGCTGGCGATGGCA 62.728 61.111 7.63 0.00 42.47 4.92
172 174 3.536917 CATCGTGCGGGAGGCCTA 61.537 66.667 4.42 0.00 42.61 3.93
246 248 0.932955 AGAGGATGGAGAGAGGAGCA 59.067 55.000 0.00 0.00 0.00 4.26
273 275 2.569059 CTTCATTGAGACCGCCATCAT 58.431 47.619 0.00 0.00 0.00 2.45
292 294 1.913951 TTGAGGTCATCCATGCCGCT 61.914 55.000 0.00 0.00 35.89 5.52
314 316 3.864686 CAGCATACGCCACCACGC 61.865 66.667 0.00 0.00 39.83 5.34
364 366 0.611200 CAACCACCACTATCCGTCCA 59.389 55.000 0.00 0.00 0.00 4.02
390 392 3.468850 AGAACCATCAGGGATTTCTCCT 58.531 45.455 0.00 0.00 41.74 3.69
443 445 0.749454 CCATCAGGAAGGAAAGGCGG 60.749 60.000 0.00 0.00 36.89 6.13
464 466 1.230324 GAGGATGGGCAACGCTTATC 58.770 55.000 0.00 0.00 37.60 1.75
465 467 0.546122 TGAGGATGGGCAACGCTTAT 59.454 50.000 0.00 0.00 37.60 1.73
468 470 1.675641 GTTGAGGATGGGCAACGCT 60.676 57.895 0.00 0.00 35.58 5.07
470 472 0.804989 GAAGTTGAGGATGGGCAACG 59.195 55.000 0.00 0.00 46.65 4.10
474 476 1.134250 GGAGAGAAGTTGAGGATGGGC 60.134 57.143 0.00 0.00 0.00 5.36
484 486 2.048127 GGCACGCGGAGAGAAGTT 60.048 61.111 12.47 0.00 0.00 2.66
504 506 1.831736 AGACATGTCCTAGGGTTTCCG 59.168 52.381 22.21 0.00 38.33 4.30
562 568 2.603247 CGCGTAACCAAGCAGCACA 61.603 57.895 0.00 0.00 0.00 4.57
627 633 2.134287 ATAGATGAGCCGCCACCGT 61.134 57.895 0.00 0.00 0.00 4.83
637 643 2.831333 ACTCGGCAAAGCATAGATGAG 58.169 47.619 0.00 0.00 0.00 2.90
644 650 2.964978 GGCAACTCGGCAAAGCAT 59.035 55.556 0.00 0.00 40.76 3.79
679 685 8.519799 TCAAGCCTAAAAGAGAAAGAAAGAAA 57.480 30.769 0.00 0.00 0.00 2.52
686 692 5.182760 AGCACATCAAGCCTAAAAGAGAAAG 59.817 40.000 0.00 0.00 0.00 2.62
697 703 1.975407 GGCACAGCACATCAAGCCT 60.975 57.895 0.00 0.00 39.02 4.58
715 721 1.066858 AGTCACACGATAACTGCTGGG 60.067 52.381 0.00 0.00 0.00 4.45
778 786 4.038080 CGGGCGCTGGTTTTCACC 62.038 66.667 7.64 0.00 44.56 4.02
779 787 1.908066 CTACGGGCGCTGGTTTTCAC 61.908 60.000 7.64 0.00 0.00 3.18
780 788 1.669760 CTACGGGCGCTGGTTTTCA 60.670 57.895 7.64 0.00 0.00 2.69
803 811 0.889186 GGAGAGCCGGAGCAAAACAA 60.889 55.000 5.05 0.00 43.56 2.83
856 866 3.314913 TGATGCTCGTTTGTGTTGATGTT 59.685 39.130 0.00 0.00 0.00 2.71
857 867 2.877786 TGATGCTCGTTTGTGTTGATGT 59.122 40.909 0.00 0.00 0.00 3.06
871 881 3.252400 CTGTCTCAGTGAGTTGATGCTC 58.748 50.000 19.53 3.16 36.12 4.26
880 890 8.315391 TGATTTTATTGAACTGTCTCAGTGAG 57.685 34.615 14.36 14.36 44.62 3.51
898 908 8.169977 AGTTGAACAGAGCTGATTTGATTTTA 57.830 30.769 4.21 0.00 0.00 1.52
900 910 6.645790 AGTTGAACAGAGCTGATTTGATTT 57.354 33.333 4.21 0.00 0.00 2.17
901 911 6.567321 CGAAGTTGAACAGAGCTGATTTGATT 60.567 38.462 4.21 0.00 0.00 2.57
902 912 5.106791 CGAAGTTGAACAGAGCTGATTTGAT 60.107 40.000 4.21 0.00 0.00 2.57
903 913 4.212004 CGAAGTTGAACAGAGCTGATTTGA 59.788 41.667 4.21 0.00 0.00 2.69
904 914 4.461405 CGAAGTTGAACAGAGCTGATTTG 58.539 43.478 4.21 0.00 0.00 2.32
947 980 1.294659 GCTGGAGCGGAAACTGACTG 61.295 60.000 0.00 0.00 0.00 3.51
977 1012 7.148239 CCATCGCTTCTCCTATACTTTTTGTTT 60.148 37.037 0.00 0.00 0.00 2.83
983 1024 3.643792 AGCCATCGCTTCTCCTATACTTT 59.356 43.478 0.00 0.00 45.55 2.66
984 1025 3.235200 AGCCATCGCTTCTCCTATACTT 58.765 45.455 0.00 0.00 45.55 2.24
987 1028 4.382040 GCAATAGCCATCGCTTCTCCTATA 60.382 45.833 0.00 0.00 45.55 1.31
988 1029 3.618507 GCAATAGCCATCGCTTCTCCTAT 60.619 47.826 0.00 0.00 45.55 2.57
989 1030 2.289072 GCAATAGCCATCGCTTCTCCTA 60.289 50.000 0.00 0.00 45.55 2.94
998 1039 2.162921 CTTCGCCGCAATAGCCATCG 62.163 60.000 0.00 0.00 37.52 3.84
1006 1047 3.576356 CGATGCCTTCGCCGCAAT 61.576 61.111 0.00 0.00 41.69 3.56
1059 1100 1.743252 CCTCGCTTGGTCCTTGAGC 60.743 63.158 0.00 0.00 0.00 4.26
1157 1204 4.704833 GAAGCTGCTCGGTGCCCA 62.705 66.667 1.00 0.00 42.00 5.36
1165 1212 2.124778 GGAGGCCAGAAGCTGCTC 60.125 66.667 5.01 0.00 43.05 4.26
1188 1235 4.056125 CGTCTCTCCGCCACAGCA 62.056 66.667 0.00 0.00 39.83 4.41
1213 1260 2.960688 GCCCTTCCTCAGCCTTCGT 61.961 63.158 0.00 0.00 0.00 3.85
1214 1261 2.124942 GCCCTTCCTCAGCCTTCG 60.125 66.667 0.00 0.00 0.00 3.79
1221 1268 0.906756 CAGTCCTCAGCCCTTCCTCA 60.907 60.000 0.00 0.00 0.00 3.86
1227 1285 0.546267 ACATGACAGTCCTCAGCCCT 60.546 55.000 0.00 0.00 0.00 5.19
1239 1297 0.250234 GGCAGCTGAGGTACATGACA 59.750 55.000 20.43 0.00 0.00 3.58
1258 1327 0.841289 TACTCCTAATTTGGCCCCCG 59.159 55.000 0.00 0.00 0.00 5.73
1298 1367 7.875327 TCATCATCATCATCATCAACAAACT 57.125 32.000 0.00 0.00 0.00 2.66
1302 1371 8.635765 ATTCATCATCATCATCATCATCAACA 57.364 30.769 0.00 0.00 0.00 3.33
1315 1384 9.941325 GGAGGGTGATATATATTCATCATCATC 57.059 37.037 12.15 12.15 40.59 2.92
1316 1385 9.686136 AGGAGGGTGATATATATTCATCATCAT 57.314 33.333 17.00 9.17 34.55 2.45
1317 1386 9.511404 AAGGAGGGTGATATATATTCATCATCA 57.489 33.333 17.00 7.63 34.55 3.07
1318 1387 9.775854 CAAGGAGGGTGATATATATTCATCATC 57.224 37.037 11.27 11.27 33.92 2.92
1319 1388 9.289049 ACAAGGAGGGTGATATATATTCATCAT 57.711 33.333 0.00 0.00 33.92 2.45
1320 1389 8.685257 ACAAGGAGGGTGATATATATTCATCA 57.315 34.615 0.00 0.00 0.00 3.07
1321 1390 8.207545 GGACAAGGAGGGTGATATATATTCATC 58.792 40.741 0.00 0.00 0.00 2.92
1322 1391 7.684186 TGGACAAGGAGGGTGATATATATTCAT 59.316 37.037 0.00 0.00 0.00 2.57
1323 1392 7.022496 TGGACAAGGAGGGTGATATATATTCA 58.978 38.462 0.00 0.00 0.00 2.57
1324 1393 7.496346 TGGACAAGGAGGGTGATATATATTC 57.504 40.000 0.00 0.00 0.00 1.75
1325 1394 7.462328 ACATGGACAAGGAGGGTGATATATATT 59.538 37.037 0.00 0.00 0.00 1.28
1326 1395 6.968248 ACATGGACAAGGAGGGTGATATATAT 59.032 38.462 0.00 0.00 0.00 0.86
1327 1396 6.213397 CACATGGACAAGGAGGGTGATATATA 59.787 42.308 0.00 0.00 0.00 0.86
1328 1397 5.013495 CACATGGACAAGGAGGGTGATATAT 59.987 44.000 0.00 0.00 0.00 0.86
1329 1398 4.347876 CACATGGACAAGGAGGGTGATATA 59.652 45.833 0.00 0.00 0.00 0.86
1330 1399 3.137176 CACATGGACAAGGAGGGTGATAT 59.863 47.826 0.00 0.00 0.00 1.63
1331 1400 2.505407 CACATGGACAAGGAGGGTGATA 59.495 50.000 0.00 0.00 0.00 2.15
1332 1401 1.283029 CACATGGACAAGGAGGGTGAT 59.717 52.381 0.00 0.00 0.00 3.06
1333 1402 0.692476 CACATGGACAAGGAGGGTGA 59.308 55.000 0.00 0.00 0.00 4.02
1334 1403 0.962356 GCACATGGACAAGGAGGGTG 60.962 60.000 0.00 0.00 0.00 4.61
1335 1404 1.136329 AGCACATGGACAAGGAGGGT 61.136 55.000 0.00 0.00 0.00 4.34
1336 1405 0.038744 AAGCACATGGACAAGGAGGG 59.961 55.000 0.00 0.00 0.00 4.30
1337 1406 1.457346 GAAGCACATGGACAAGGAGG 58.543 55.000 0.00 0.00 0.00 4.30
1338 1407 1.271543 TGGAAGCACATGGACAAGGAG 60.272 52.381 0.00 0.00 0.00 3.69
1339 1408 0.770499 TGGAAGCACATGGACAAGGA 59.230 50.000 0.00 0.00 0.00 3.36
1340 1409 1.475280 CATGGAAGCACATGGACAAGG 59.525 52.381 0.00 0.00 43.44 3.61
1341 1410 2.163010 GTCATGGAAGCACATGGACAAG 59.837 50.000 13.71 0.00 46.33 3.16
1342 1411 2.161855 GTCATGGAAGCACATGGACAA 58.838 47.619 13.71 0.00 46.33 3.18
1343 1412 1.352017 AGTCATGGAAGCACATGGACA 59.648 47.619 13.71 0.00 46.33 4.02
1344 1413 2.119801 AGTCATGGAAGCACATGGAC 57.880 50.000 13.71 10.97 46.33 4.02
1345 1414 2.840038 AGTAGTCATGGAAGCACATGGA 59.160 45.455 13.71 1.94 46.33 3.41
1346 1415 3.272574 AGTAGTCATGGAAGCACATGG 57.727 47.619 13.71 0.00 46.33 3.66
1348 1417 5.187772 TGTTCTAGTAGTCATGGAAGCACAT 59.812 40.000 0.00 0.00 0.00 3.21
1349 1418 4.526650 TGTTCTAGTAGTCATGGAAGCACA 59.473 41.667 0.00 0.00 0.00 4.57
1350 1419 5.073311 TGTTCTAGTAGTCATGGAAGCAC 57.927 43.478 0.00 0.00 0.00 4.40
1351 1420 5.939764 ATGTTCTAGTAGTCATGGAAGCA 57.060 39.130 0.00 0.00 0.00 3.91
1352 1421 8.768955 CATTTATGTTCTAGTAGTCATGGAAGC 58.231 37.037 15.47 0.00 0.00 3.86
1353 1422 8.768955 GCATTTATGTTCTAGTAGTCATGGAAG 58.231 37.037 15.47 8.24 0.00 3.46
1354 1423 7.438160 CGCATTTATGTTCTAGTAGTCATGGAA 59.562 37.037 15.47 11.92 0.00 3.53
1355 1424 6.923508 CGCATTTATGTTCTAGTAGTCATGGA 59.076 38.462 15.47 8.20 0.00 3.41
1356 1425 6.346919 GCGCATTTATGTTCTAGTAGTCATGG 60.347 42.308 0.30 7.80 0.00 3.66
1357 1426 6.584954 GCGCATTTATGTTCTAGTAGTCATG 58.415 40.000 0.30 0.00 0.00 3.07
1358 1427 5.402568 CGCGCATTTATGTTCTAGTAGTCAT 59.597 40.000 8.75 12.46 0.00 3.06
1359 1428 4.738252 CGCGCATTTATGTTCTAGTAGTCA 59.262 41.667 8.75 0.00 0.00 3.41
1360 1429 4.375105 GCGCGCATTTATGTTCTAGTAGTC 60.375 45.833 29.10 0.00 0.00 2.59
1361 1430 3.489785 GCGCGCATTTATGTTCTAGTAGT 59.510 43.478 29.10 0.00 0.00 2.73
1362 1431 3.420544 CGCGCGCATTTATGTTCTAGTAG 60.421 47.826 32.61 3.88 0.00 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.