Multiple sequence alignment - TraesCS2B01G128600

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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 TraesCS2B01G128600 chr2B 100.000 2339 0 0 1 2339 96096307 96093969 0.000000e+00 4320.0
1 TraesCS2B01G128600 chr2B 93.256 1379 77 9 1 1366 390803538 390802163 0.000000e+00 2017.0
2 TraesCS2B01G128600 chr2B 92.369 1376 88 8 1 1363 105898978 105897607 0.000000e+00 1943.0
3 TraesCS2B01G128600 chr2B 93.522 1096 60 4 278 1363 793363233 793364327 0.000000e+00 1620.0
4 TraesCS2B01G128600 chr2B 88.274 759 50 20 1428 2148 387059656 387060413 0.000000e+00 872.0
5 TraesCS2B01G128600 chr5D 93.309 1375 79 6 1 1363 383585968 383587341 0.000000e+00 2017.0
6 TraesCS2B01G128600 chr5D 93.106 1378 79 8 1 1366 473452333 473453706 0.000000e+00 2004.0
7 TraesCS2B01G128600 chr5D 88.844 744 55 12 1428 2144 385869714 385870456 0.000000e+00 889.0
8 TraesCS2B01G128600 chr5D 88.267 750 59 12 1428 2151 477172674 477171928 0.000000e+00 870.0
9 TraesCS2B01G128600 chr5D 77.551 98 20 2 2239 2334 241832357 241832260 9.030000e-05 58.4
10 TraesCS2B01G128600 chr3B 93.164 1375 81 6 1 1363 161678856 161677483 0.000000e+00 2006.0
11 TraesCS2B01G128600 chr3B 92.868 1374 85 6 1 1362 772414842 772413470 0.000000e+00 1982.0
12 TraesCS2B01G128600 chr3B 92.614 1381 88 7 1 1369 571263373 571261995 0.000000e+00 1973.0
13 TraesCS2B01G128600 chr3B 87.055 703 49 13 1428 2120 764800273 764800943 0.000000e+00 756.0
14 TraesCS2B01G128600 chr3B 100.000 31 0 0 1404 1434 704046986 704047016 9.030000e-05 58.4
15 TraesCS2B01G128600 chr1B 93.091 1375 81 9 1 1363 92336386 92337758 0.000000e+00 2001.0
16 TraesCS2B01G128600 chr1B 85.000 740 62 17 1428 2144 503450674 503449961 0.000000e+00 706.0
17 TraesCS2B01G128600 chr2A 92.945 1375 84 6 1 1363 89174051 89175424 0.000000e+00 1989.0
18 TraesCS2B01G128600 chr6D 92.727 1375 84 10 1 1363 338919663 338921033 0.000000e+00 1971.0
19 TraesCS2B01G128600 chr5B 92.975 1338 81 6 38 1363 677677435 677678771 0.000000e+00 1938.0
20 TraesCS2B01G128600 chr5B 91.117 743 36 13 1428 2144 664614237 664613499 0.000000e+00 979.0
21 TraesCS2B01G128600 chr5B 89.341 713 49 11 1433 2119 702851608 702850897 0.000000e+00 870.0
22 TraesCS2B01G128600 chr5B 86.116 605 59 12 1555 2144 252359290 252359884 1.530000e-176 628.0
23 TraesCS2B01G128600 chr5B 92.462 398 27 2 1747 2144 664649082 664648688 1.210000e-157 566.0
24 TraesCS2B01G128600 chr5B 94.286 35 2 0 1397 1431 634378592 634378626 1.000000e-03 54.7
25 TraesCS2B01G128600 chr5B 84.906 53 7 1 2265 2316 673988116 673988064 4.000000e-03 52.8
26 TraesCS2B01G128600 chr4D 92.869 1178 71 6 197 1363 469445645 469444470 0.000000e+00 1698.0
27 TraesCS2B01G128600 chr4B 92.510 721 49 3 1428 2146 6658467 6659184 0.000000e+00 1027.0
28 TraesCS2B01G128600 chr4B 100.000 30 0 0 1402 1431 604326004 604326033 3.250000e-04 56.5
29 TraesCS2B01G128600 chr7B 91.925 743 44 7 1428 2159 19102780 19102043 0.000000e+00 1026.0
30 TraesCS2B01G128600 chr7B 90.283 741 41 13 1430 2144 627907699 627908434 0.000000e+00 941.0
31 TraesCS2B01G128600 chr7B 91.832 404 32 1 1742 2145 337069365 337069767 1.570000e-156 562.0
32 TraesCS2B01G128600 chr7B 81.395 86 11 4 2240 2320 114415205 114415120 5.400000e-07 65.8
33 TraesCS2B01G128600 chrUn 90.040 753 38 7 1428 2144 17294900 17295651 0.000000e+00 941.0
34 TraesCS2B01G128600 chr7A 92.687 588 33 3 1 578 11062647 11063234 0.000000e+00 839.0
35 TraesCS2B01G128600 chr7A 95.639 321 10 2 1428 1745 68313968 68313649 1.600000e-141 512.0
36 TraesCS2B01G128600 chr4A 86.881 747 39 23 1429 2145 697307364 697306647 0.000000e+00 782.0
37 TraesCS2B01G128600 chr1A 86.557 729 68 16 1428 2129 209822183 209822908 0.000000e+00 776.0
38 TraesCS2B01G128600 chr7D 80.780 744 69 34 1428 2144 628633024 628633720 4.460000e-142 514.0
39 TraesCS2B01G128600 chr2D 97.222 36 0 1 1402 1436 427678430 427678395 2.510000e-05 60.2
40 TraesCS2B01G128600 chr1D 96.970 33 1 0 1403 1435 7113503 7113471 3.250000e-04 56.5
41 TraesCS2B01G128600 chr1D 100.000 30 0 0 1402 1431 29960259 29960230 3.250000e-04 56.5
42 TraesCS2B01G128600 chr1D 100.000 30 0 0 1402 1431 388799116 388799087 3.250000e-04 56.5
43 TraesCS2B01G128600 chr1D 94.444 36 1 1 1397 1431 443123822 443123787 1.000000e-03 54.7
44 TraesCS2B01G128600 chr1D 92.105 38 2 1 1401 1437 223948495 223948532 4.000000e-03 52.8


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 TraesCS2B01G128600 chr2B 96093969 96096307 2338 True 4320 4320 100.000 1 2339 1 chr2B.!!$R1 2338
1 TraesCS2B01G128600 chr2B 390802163 390803538 1375 True 2017 2017 93.256 1 1366 1 chr2B.!!$R3 1365
2 TraesCS2B01G128600 chr2B 105897607 105898978 1371 True 1943 1943 92.369 1 1363 1 chr2B.!!$R2 1362
3 TraesCS2B01G128600 chr2B 793363233 793364327 1094 False 1620 1620 93.522 278 1363 1 chr2B.!!$F2 1085
4 TraesCS2B01G128600 chr2B 387059656 387060413 757 False 872 872 88.274 1428 2148 1 chr2B.!!$F1 720
5 TraesCS2B01G128600 chr5D 383585968 383587341 1373 False 2017 2017 93.309 1 1363 1 chr5D.!!$F1 1362
6 TraesCS2B01G128600 chr5D 473452333 473453706 1373 False 2004 2004 93.106 1 1366 1 chr5D.!!$F3 1365
7 TraesCS2B01G128600 chr5D 385869714 385870456 742 False 889 889 88.844 1428 2144 1 chr5D.!!$F2 716
8 TraesCS2B01G128600 chr5D 477171928 477172674 746 True 870 870 88.267 1428 2151 1 chr5D.!!$R2 723
9 TraesCS2B01G128600 chr3B 161677483 161678856 1373 True 2006 2006 93.164 1 1363 1 chr3B.!!$R1 1362
10 TraesCS2B01G128600 chr3B 772413470 772414842 1372 True 1982 1982 92.868 1 1362 1 chr3B.!!$R3 1361
11 TraesCS2B01G128600 chr3B 571261995 571263373 1378 True 1973 1973 92.614 1 1369 1 chr3B.!!$R2 1368
12 TraesCS2B01G128600 chr3B 764800273 764800943 670 False 756 756 87.055 1428 2120 1 chr3B.!!$F2 692
13 TraesCS2B01G128600 chr1B 92336386 92337758 1372 False 2001 2001 93.091 1 1363 1 chr1B.!!$F1 1362
14 TraesCS2B01G128600 chr1B 503449961 503450674 713 True 706 706 85.000 1428 2144 1 chr1B.!!$R1 716
15 TraesCS2B01G128600 chr2A 89174051 89175424 1373 False 1989 1989 92.945 1 1363 1 chr2A.!!$F1 1362
16 TraesCS2B01G128600 chr6D 338919663 338921033 1370 False 1971 1971 92.727 1 1363 1 chr6D.!!$F1 1362
17 TraesCS2B01G128600 chr5B 677677435 677678771 1336 False 1938 1938 92.975 38 1363 1 chr5B.!!$F3 1325
18 TraesCS2B01G128600 chr5B 664613499 664614237 738 True 979 979 91.117 1428 2144 1 chr5B.!!$R1 716
19 TraesCS2B01G128600 chr5B 702850897 702851608 711 True 870 870 89.341 1433 2119 1 chr5B.!!$R4 686
20 TraesCS2B01G128600 chr5B 252359290 252359884 594 False 628 628 86.116 1555 2144 1 chr5B.!!$F1 589
21 TraesCS2B01G128600 chr4D 469444470 469445645 1175 True 1698 1698 92.869 197 1363 1 chr4D.!!$R1 1166
22 TraesCS2B01G128600 chr4B 6658467 6659184 717 False 1027 1027 92.510 1428 2146 1 chr4B.!!$F1 718
23 TraesCS2B01G128600 chr7B 19102043 19102780 737 True 1026 1026 91.925 1428 2159 1 chr7B.!!$R1 731
24 TraesCS2B01G128600 chr7B 627907699 627908434 735 False 941 941 90.283 1430 2144 1 chr7B.!!$F2 714
25 TraesCS2B01G128600 chrUn 17294900 17295651 751 False 941 941 90.040 1428 2144 1 chrUn.!!$F1 716
26 TraesCS2B01G128600 chr7A 11062647 11063234 587 False 839 839 92.687 1 578 1 chr7A.!!$F1 577
27 TraesCS2B01G128600 chr4A 697306647 697307364 717 True 782 782 86.881 1429 2145 1 chr4A.!!$R1 716
28 TraesCS2B01G128600 chr1A 209822183 209822908 725 False 776 776 86.557 1428 2129 1 chr1A.!!$F1 701
29 TraesCS2B01G128600 chr7D 628633024 628633720 696 False 514 514 80.780 1428 2144 1 chr7D.!!$F1 716

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
737 749 0.321346 GGGAAGGTGGCAAATTGGTG 59.679 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2323 0.039346 CACCGCATGACAATGTGCAA 60.039 50.0 0.0 0.0 42.01 4.08 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
133 135 6.837568 AGGTAGCAGATTTGATTGATCCAATT 59.162 34.615 0.00 0.00 33.90 2.32
162 164 7.921041 ATAGTTGGGATGAAGATCTACTCAA 57.079 36.000 0.00 0.00 0.00 3.02
195 197 1.262683 GCCTATTGATGTTCAGCGAGC 59.737 52.381 0.00 0.00 0.00 5.03
236 238 4.023450 CGCAACATGATATGCCAGATTTCT 60.023 41.667 0.00 0.00 39.39 2.52
268 271 7.444792 TGGAATTTCACAAAAATGGGATCTTTG 59.555 33.333 0.00 3.53 36.37 2.77
339 342 6.126997 ACAAGTTACGACATACCAATGGGATA 60.127 38.462 3.55 0.00 37.43 2.59
344 347 3.323691 CGACATACCAATGGGATAGGACA 59.676 47.826 3.55 0.00 37.43 4.02
368 371 2.297701 CACGGTCAATCCTATTTGGGG 58.702 52.381 0.00 0.00 36.20 4.96
389 392 4.560128 GGGAGGATTTTGAAACTTGCTTC 58.440 43.478 0.00 0.00 0.00 3.86
453 456 2.724690 CACTCTTCCGTGTCGTGTTAAG 59.275 50.000 0.00 0.00 0.00 1.85
454 457 1.719780 CTCTTCCGTGTCGTGTTAAGC 59.280 52.381 0.00 0.00 0.00 3.09
505 508 0.826715 GTGTCCTGCCTGCTCATCTA 59.173 55.000 0.00 0.00 0.00 1.98
555 566 4.130118 GACAGAGCAAAAGAAGTCTGGAA 58.870 43.478 3.44 0.00 40.69 3.53
617 628 1.227380 GACTATGCGGGTGAGGCAG 60.227 63.158 0.00 0.00 44.71 4.85
629 641 3.471680 GGTGAGGCAGTCTTGGAATATC 58.528 50.000 0.00 0.00 0.00 1.63
673 685 5.801531 AACTATGTATTATGGGCACTCGA 57.198 39.130 0.00 0.00 0.00 4.04
677 689 7.224297 ACTATGTATTATGGGCACTCGAAATT 58.776 34.615 0.00 0.00 0.00 1.82
680 692 5.650266 TGTATTATGGGCACTCGAAATTTGT 59.350 36.000 0.00 0.00 0.00 2.83
692 704 6.638063 CACTCGAAATTTGTGTGACATGATTT 59.362 34.615 9.20 0.00 33.80 2.17
699 711 9.947433 AAATTTGTGTGACATGATTTCCATATT 57.053 25.926 0.00 0.00 33.31 1.28
700 712 8.936070 ATTTGTGTGACATGATTTCCATATTG 57.064 30.769 0.00 0.00 33.31 1.90
709 721 5.337956 TGATTTCCATATTGGCCTGGTAT 57.662 39.130 3.32 1.70 37.47 2.73
720 732 0.970427 GCCTGGTATTTGTGGTGGGG 60.970 60.000 0.00 0.00 0.00 4.96
726 738 2.167662 GTATTTGTGGTGGGGAAGGTG 58.832 52.381 0.00 0.00 0.00 4.00
737 749 0.321346 GGGAAGGTGGCAAATTGGTG 59.679 55.000 0.00 0.00 0.00 4.17
821 833 3.517296 TTTGTTAATGCCTCCTCACCA 57.483 42.857 0.00 0.00 0.00 4.17
824 836 3.838565 TGTTAATGCCTCCTCACCAAAA 58.161 40.909 0.00 0.00 0.00 2.44
863 876 3.369410 ATGGTCTAGCCCCCGACGA 62.369 63.158 0.00 0.00 36.04 4.20
896 909 7.679659 AAACTTAACGTTGATGCTTCTTTTC 57.320 32.000 11.99 0.00 35.61 2.29
924 937 1.676746 CTTCTCAGGGGTACGATCGA 58.323 55.000 24.34 2.23 0.00 3.59
1004 1018 1.881973 GTGTGCAGATGTGTTGATGGT 59.118 47.619 0.00 0.00 0.00 3.55
1026 1040 5.333035 GGTTGAAGCTTTGGCGTTAAAATTC 60.333 40.000 0.00 0.00 44.37 2.17
1132 1146 3.912907 GACGATCGTCGGGGGCAT 61.913 66.667 30.46 0.00 45.59 4.40
1139 1153 4.101448 GTCGGGGGCATCAGCTGT 62.101 66.667 14.67 0.00 41.70 4.40
1263 1277 6.153510 AGTTGGCTAGATTTTCCTTCATTTCC 59.846 38.462 0.00 0.00 0.00 3.13
1265 1279 4.036852 GGCTAGATTTTCCTTCATTTCCGG 59.963 45.833 0.00 0.00 0.00 5.14
1379 1393 4.591321 AAAAATAGATGGCAGACTGGGA 57.409 40.909 4.26 0.00 0.00 4.37
1380 1394 3.853355 AAATAGATGGCAGACTGGGAG 57.147 47.619 4.26 0.00 0.00 4.30
1381 1395 2.485966 ATAGATGGCAGACTGGGAGT 57.514 50.000 4.26 0.00 0.00 3.85
1382 1396 1.489481 TAGATGGCAGACTGGGAGTG 58.511 55.000 4.26 0.00 0.00 3.51
1383 1397 1.451028 GATGGCAGACTGGGAGTGC 60.451 63.158 4.26 0.00 36.42 4.40
1398 1412 4.337177 TGCCCGCGATCCACCAAA 62.337 61.111 8.23 0.00 0.00 3.28
1399 1413 3.508840 GCCCGCGATCCACCAAAG 61.509 66.667 8.23 0.00 0.00 2.77
1400 1414 2.267642 CCCGCGATCCACCAAAGA 59.732 61.111 8.23 0.00 0.00 2.52
1401 1415 1.153168 CCCGCGATCCACCAAAGAT 60.153 57.895 8.23 0.00 0.00 2.40
1402 1416 1.160329 CCCGCGATCCACCAAAGATC 61.160 60.000 8.23 0.00 37.39 2.75
1403 1417 1.160329 CCGCGATCCACCAAAGATCC 61.160 60.000 8.23 0.00 37.45 3.36
1404 1418 0.461870 CGCGATCCACCAAAGATCCA 60.462 55.000 0.00 0.00 37.45 3.41
1405 1419 1.017387 GCGATCCACCAAAGATCCAC 58.983 55.000 0.00 0.00 37.45 4.02
1406 1420 1.407437 GCGATCCACCAAAGATCCACT 60.407 52.381 0.00 0.00 37.45 4.00
1407 1421 2.158957 GCGATCCACCAAAGATCCACTA 60.159 50.000 0.00 0.00 37.45 2.74
1408 1422 3.458189 CGATCCACCAAAGATCCACTAC 58.542 50.000 0.00 0.00 37.45 2.73
1409 1423 3.133003 CGATCCACCAAAGATCCACTACT 59.867 47.826 0.00 0.00 37.45 2.57
1410 1424 4.341235 CGATCCACCAAAGATCCACTACTA 59.659 45.833 0.00 0.00 37.45 1.82
1411 1425 5.508153 CGATCCACCAAAGATCCACTACTAG 60.508 48.000 0.00 0.00 37.45 2.57
1412 1426 4.030913 TCCACCAAAGATCCACTACTAGG 58.969 47.826 0.00 0.00 0.00 3.02
1413 1427 3.134804 CCACCAAAGATCCACTACTAGGG 59.865 52.174 0.00 0.00 0.00 3.53
1414 1428 4.030913 CACCAAAGATCCACTACTAGGGA 58.969 47.826 0.00 0.00 37.64 4.20
1415 1429 4.469945 CACCAAAGATCCACTACTAGGGAA 59.530 45.833 0.00 0.00 36.62 3.97
1416 1430 5.045869 CACCAAAGATCCACTACTAGGGAAA 60.046 44.000 0.00 0.00 36.62 3.13
1417 1431 5.731678 ACCAAAGATCCACTACTAGGGAAAT 59.268 40.000 0.00 0.00 36.62 2.17
1418 1432 6.058183 CCAAAGATCCACTACTAGGGAAATG 58.942 44.000 0.00 0.00 36.62 2.32
1419 1433 4.965200 AGATCCACTACTAGGGAAATGC 57.035 45.455 0.00 0.00 36.62 3.56
1420 1434 4.561752 AGATCCACTACTAGGGAAATGCT 58.438 43.478 0.00 0.00 36.62 3.79
1421 1435 4.971924 AGATCCACTACTAGGGAAATGCTT 59.028 41.667 0.00 0.00 36.62 3.91
1422 1436 6.143915 AGATCCACTACTAGGGAAATGCTTA 58.856 40.000 0.00 0.00 36.62 3.09
1423 1437 6.789959 AGATCCACTACTAGGGAAATGCTTAT 59.210 38.462 0.00 0.00 36.62 1.73
1424 1438 7.956315 AGATCCACTACTAGGGAAATGCTTATA 59.044 37.037 0.00 0.00 36.62 0.98
1425 1439 7.299246 TCCACTACTAGGGAAATGCTTATAC 57.701 40.000 0.00 0.00 0.00 1.47
1426 1440 6.842280 TCCACTACTAGGGAAATGCTTATACA 59.158 38.462 0.00 0.00 0.00 2.29
1447 1461 6.321821 ACACAGGGCCTATCTTGTTTTATA 57.678 37.500 5.28 0.00 0.00 0.98
1550 1612 5.489249 AGATGACTATGATGATGATGTGGC 58.511 41.667 0.00 0.00 0.00 5.01
1568 1631 3.858238 GTGGCATCGAGTAGAAGTTGTAC 59.142 47.826 1.96 1.96 0.00 2.90
1763 1888 8.298140 GCACGATCTAGTTTGGATTAGTAGTAT 58.702 37.037 0.00 0.00 0.00 2.12
1811 1936 4.039973 TCCACTTGAATCTACTCCACGTTT 59.960 41.667 0.00 0.00 0.00 3.60
2079 2228 4.158015 AGTTGTAGTGCCTTAGTGGTAGT 58.842 43.478 0.00 0.00 37.80 2.73
2086 2235 2.105821 TGCCTTAGTGGTAGTGCTTGTT 59.894 45.455 0.00 0.00 38.35 2.83
2133 2282 4.251268 CAAGCGCTACTACTAGGGTTTTT 58.749 43.478 12.05 0.00 35.14 1.94
2148 2297 5.816682 AGGGTTTTTCCTAGTAGTGATTGG 58.183 41.667 0.00 0.00 34.92 3.16
2152 2301 5.499004 TTTTCCTAGTAGTGATTGGTGCT 57.501 39.130 0.00 0.00 0.00 4.40
2153 2302 4.737855 TTCCTAGTAGTGATTGGTGCTC 57.262 45.455 0.00 0.00 0.00 4.26
2155 2304 4.093743 TCCTAGTAGTGATTGGTGCTCAA 58.906 43.478 0.00 0.00 40.01 3.02
2157 2306 5.189736 TCCTAGTAGTGATTGGTGCTCAATT 59.810 40.000 7.17 0.00 45.36 2.32
2158 2307 5.295292 CCTAGTAGTGATTGGTGCTCAATTG 59.705 44.000 0.00 0.00 45.36 2.32
2159 2308 3.441572 AGTAGTGATTGGTGCTCAATTGC 59.558 43.478 0.00 0.00 45.36 3.56
2160 2309 2.522185 AGTGATTGGTGCTCAATTGCT 58.478 42.857 0.00 6.23 45.36 3.91
2161 2310 3.689347 AGTGATTGGTGCTCAATTGCTA 58.311 40.909 0.00 0.00 45.36 3.49
2162 2311 3.441572 AGTGATTGGTGCTCAATTGCTAC 59.558 43.478 0.00 0.00 45.36 3.58
2163 2312 2.419673 TGATTGGTGCTCAATTGCTACG 59.580 45.455 0.00 0.00 45.36 3.51
2164 2313 2.177394 TTGGTGCTCAATTGCTACGA 57.823 45.000 0.00 0.00 0.00 3.43
2165 2314 1.725641 TGGTGCTCAATTGCTACGAG 58.274 50.000 0.00 0.00 0.00 4.18
2166 2315 1.275010 TGGTGCTCAATTGCTACGAGA 59.725 47.619 0.00 0.00 0.00 4.04
2167 2316 1.661112 GGTGCTCAATTGCTACGAGAC 59.339 52.381 0.00 0.00 0.00 3.36
2168 2317 2.337583 GTGCTCAATTGCTACGAGACA 58.662 47.619 0.00 0.00 0.00 3.41
2169 2318 2.736721 GTGCTCAATTGCTACGAGACAA 59.263 45.455 0.00 0.00 0.00 3.18
2170 2319 3.186409 GTGCTCAATTGCTACGAGACAAA 59.814 43.478 0.00 0.00 0.00 2.83
2171 2320 4.002982 TGCTCAATTGCTACGAGACAAAT 58.997 39.130 0.00 0.00 0.00 2.32
2172 2321 5.063438 GTGCTCAATTGCTACGAGACAAATA 59.937 40.000 0.00 0.00 0.00 1.40
2173 2322 5.063438 TGCTCAATTGCTACGAGACAAATAC 59.937 40.000 0.00 0.00 0.00 1.89
2174 2323 5.292101 GCTCAATTGCTACGAGACAAATACT 59.708 40.000 0.00 0.00 0.00 2.12
2175 2324 6.183360 GCTCAATTGCTACGAGACAAATACTT 60.183 38.462 0.00 0.00 0.00 2.24
2176 2325 7.060600 TCAATTGCTACGAGACAAATACTTG 57.939 36.000 0.00 0.00 38.61 3.16
2177 2326 4.921470 TTGCTACGAGACAAATACTTGC 57.079 40.909 0.00 0.00 35.84 4.01
2178 2327 3.920446 TGCTACGAGACAAATACTTGCA 58.080 40.909 0.00 0.00 35.84 4.08
2179 2328 3.678072 TGCTACGAGACAAATACTTGCAC 59.322 43.478 0.00 0.00 35.84 4.57
2180 2329 3.678072 GCTACGAGACAAATACTTGCACA 59.322 43.478 0.00 0.00 35.84 4.57
2181 2330 4.330074 GCTACGAGACAAATACTTGCACAT 59.670 41.667 0.00 0.00 35.84 3.21
2182 2331 5.163854 GCTACGAGACAAATACTTGCACATT 60.164 40.000 0.00 0.00 35.84 2.71
2183 2332 5.034554 ACGAGACAAATACTTGCACATTG 57.965 39.130 0.00 0.00 35.84 2.82
2184 2333 4.515191 ACGAGACAAATACTTGCACATTGT 59.485 37.500 0.00 0.00 35.84 2.71
2185 2334 5.082059 CGAGACAAATACTTGCACATTGTC 58.918 41.667 15.79 15.79 46.31 3.18
2188 2337 6.621737 GACAAATACTTGCACATTGTCATG 57.378 37.500 17.45 0.00 45.63 3.07
2189 2338 4.925054 ACAAATACTTGCACATTGTCATGC 59.075 37.500 0.00 0.00 42.40 4.06
2190 2339 2.898181 TACTTGCACATTGTCATGCG 57.102 45.000 0.00 0.00 45.13 4.73
2191 2340 0.241749 ACTTGCACATTGTCATGCGG 59.758 50.000 0.00 0.00 45.13 5.69
2192 2341 0.241749 CTTGCACATTGTCATGCGGT 59.758 50.000 0.00 0.00 45.13 5.68
2193 2342 0.039346 TTGCACATTGTCATGCGGTG 60.039 50.000 0.00 0.00 45.13 4.94
2194 2343 0.888285 TGCACATTGTCATGCGGTGA 60.888 50.000 0.00 0.00 45.13 4.02
2195 2344 0.240678 GCACATTGTCATGCGGTGAA 59.759 50.000 0.00 0.00 38.90 3.18
2196 2345 1.335780 GCACATTGTCATGCGGTGAAA 60.336 47.619 0.00 0.00 38.90 2.69
2197 2346 2.861750 GCACATTGTCATGCGGTGAAAA 60.862 45.455 0.00 0.00 38.40 2.29
2198 2347 3.577667 CACATTGTCATGCGGTGAAAAT 58.422 40.909 2.38 2.38 44.02 1.82
2199 2348 4.731720 CACATTGTCATGCGGTGAAAATA 58.268 39.130 6.92 0.00 41.81 1.40
2200 2349 5.342433 CACATTGTCATGCGGTGAAAATAT 58.658 37.500 6.92 0.00 41.81 1.28
2201 2350 6.493978 CACATTGTCATGCGGTGAAAATATA 58.506 36.000 6.92 0.00 41.81 0.86
2202 2351 7.140705 CACATTGTCATGCGGTGAAAATATAT 58.859 34.615 6.92 0.00 41.81 0.86
2203 2352 8.288913 CACATTGTCATGCGGTGAAAATATATA 58.711 33.333 6.92 0.00 41.81 0.86
2204 2353 9.013229 ACATTGTCATGCGGTGAAAATATATAT 57.987 29.630 6.92 0.00 41.81 0.86
2205 2354 9.844790 CATTGTCATGCGGTGAAAATATATATT 57.155 29.630 1.91 1.91 41.81 1.28
2207 2356 9.891828 TTGTCATGCGGTGAAAATATATATTTC 57.108 29.630 18.72 13.22 38.90 2.17
2208 2357 8.227119 TGTCATGCGGTGAAAATATATATTTCG 58.773 33.333 18.72 17.57 39.17 3.46
2209 2358 7.692291 GTCATGCGGTGAAAATATATATTTCGG 59.308 37.037 18.72 12.47 39.17 4.30
2210 2359 6.489127 TGCGGTGAAAATATATATTTCGGG 57.511 37.500 18.72 9.55 39.17 5.14
2211 2360 6.231951 TGCGGTGAAAATATATATTTCGGGA 58.768 36.000 18.72 10.61 39.17 5.14
2212 2361 6.148150 TGCGGTGAAAATATATATTTCGGGAC 59.852 38.462 18.72 12.87 39.17 4.46
2213 2362 6.148150 GCGGTGAAAATATATATTTCGGGACA 59.852 38.462 18.72 11.98 39.17 4.02
2214 2363 7.148306 GCGGTGAAAATATATATTTCGGGACAT 60.148 37.037 18.72 4.04 39.17 3.06
2215 2364 8.726988 CGGTGAAAATATATATTTCGGGACATT 58.273 33.333 18.72 3.39 39.17 2.71
2225 2374 5.835113 ATTTCGGGACATTAATGTGGAAG 57.165 39.130 25.42 13.24 41.95 3.46
2226 2375 2.639065 TCGGGACATTAATGTGGAAGC 58.361 47.619 25.42 10.40 41.95 3.86
2227 2376 1.330521 CGGGACATTAATGTGGAAGCG 59.669 52.381 25.42 0.00 41.95 4.68
2228 2377 2.365582 GGGACATTAATGTGGAAGCGT 58.634 47.619 25.42 0.00 41.95 5.07
2229 2378 2.752903 GGGACATTAATGTGGAAGCGTT 59.247 45.455 25.42 0.00 41.95 4.84
2230 2379 3.192633 GGGACATTAATGTGGAAGCGTTT 59.807 43.478 25.42 0.00 41.95 3.60
2231 2380 4.321675 GGGACATTAATGTGGAAGCGTTTT 60.322 41.667 25.42 0.00 41.95 2.43
2232 2381 5.227152 GGACATTAATGTGGAAGCGTTTTT 58.773 37.500 25.42 0.00 41.95 1.94
2233 2382 6.383415 GGACATTAATGTGGAAGCGTTTTTA 58.617 36.000 25.42 0.00 41.95 1.52
2234 2383 6.864165 GGACATTAATGTGGAAGCGTTTTTAA 59.136 34.615 25.42 0.00 41.95 1.52
2235 2384 7.544217 GGACATTAATGTGGAAGCGTTTTTAAT 59.456 33.333 25.42 0.00 41.95 1.40
2236 2385 8.238481 ACATTAATGTGGAAGCGTTTTTAATG 57.762 30.769 20.19 17.39 40.03 1.90
2237 2386 7.330700 ACATTAATGTGGAAGCGTTTTTAATGG 59.669 33.333 20.19 9.96 40.03 3.16
2238 2387 3.019933 TGTGGAAGCGTTTTTAATGGC 57.980 42.857 0.00 0.00 0.00 4.40
2239 2388 2.625790 TGTGGAAGCGTTTTTAATGGCT 59.374 40.909 0.00 0.00 37.33 4.75
2240 2389 3.821600 TGTGGAAGCGTTTTTAATGGCTA 59.178 39.130 0.00 0.00 34.82 3.93
2241 2390 4.083003 TGTGGAAGCGTTTTTAATGGCTAG 60.083 41.667 0.00 0.00 34.82 3.42
2242 2391 4.155280 GTGGAAGCGTTTTTAATGGCTAGA 59.845 41.667 0.00 0.00 34.82 2.43
2243 2392 4.947388 TGGAAGCGTTTTTAATGGCTAGAT 59.053 37.500 0.00 0.00 34.82 1.98
2244 2393 5.065988 TGGAAGCGTTTTTAATGGCTAGATC 59.934 40.000 0.00 0.00 34.82 2.75
2245 2394 5.297029 GGAAGCGTTTTTAATGGCTAGATCT 59.703 40.000 0.00 0.00 34.82 2.75
2246 2395 6.482308 GGAAGCGTTTTTAATGGCTAGATCTA 59.518 38.462 1.69 1.69 34.82 1.98
2247 2396 6.846325 AGCGTTTTTAATGGCTAGATCTAC 57.154 37.500 0.00 0.00 33.19 2.59
2248 2397 6.583562 AGCGTTTTTAATGGCTAGATCTACT 58.416 36.000 0.00 0.00 33.19 2.57
2249 2398 7.723324 AGCGTTTTTAATGGCTAGATCTACTA 58.277 34.615 0.00 0.00 33.19 1.82
2250 2399 8.368668 AGCGTTTTTAATGGCTAGATCTACTAT 58.631 33.333 0.00 0.00 33.19 2.12
2251 2400 9.635520 GCGTTTTTAATGGCTAGATCTACTATA 57.364 33.333 0.00 0.00 0.00 1.31
2259 2408 8.958060 ATGGCTAGATCTACTATAAAGGTTCA 57.042 34.615 0.00 0.00 0.00 3.18
2260 2409 8.179509 TGGCTAGATCTACTATAAAGGTTCAC 57.820 38.462 0.00 0.00 0.00 3.18
2261 2410 7.783119 TGGCTAGATCTACTATAAAGGTTCACA 59.217 37.037 0.00 0.00 0.00 3.58
2262 2411 8.639761 GGCTAGATCTACTATAAAGGTTCACAA 58.360 37.037 0.00 0.00 0.00 3.33
2263 2412 9.685828 GCTAGATCTACTATAAAGGTTCACAAG 57.314 37.037 0.00 0.00 0.00 3.16
2275 2424 7.817418 AAAGGTTCACAAGAAGTATAAAGCA 57.183 32.000 0.00 0.00 33.63 3.91
2276 2425 6.803154 AGGTTCACAAGAAGTATAAAGCAC 57.197 37.500 0.00 0.00 33.63 4.40
2277 2426 6.296026 AGGTTCACAAGAAGTATAAAGCACA 58.704 36.000 0.00 0.00 33.63 4.57
2278 2427 6.770785 AGGTTCACAAGAAGTATAAAGCACAA 59.229 34.615 0.00 0.00 33.63 3.33
2279 2428 6.856426 GGTTCACAAGAAGTATAAAGCACAAC 59.144 38.462 0.00 0.00 33.63 3.32
2280 2429 7.414436 GTTCACAAGAAGTATAAAGCACAACA 58.586 34.615 0.00 0.00 33.63 3.33
2281 2430 7.561021 TCACAAGAAGTATAAAGCACAACAA 57.439 32.000 0.00 0.00 0.00 2.83
2282 2431 7.990917 TCACAAGAAGTATAAAGCACAACAAA 58.009 30.769 0.00 0.00 0.00 2.83
2283 2432 8.629158 TCACAAGAAGTATAAAGCACAACAAAT 58.371 29.630 0.00 0.00 0.00 2.32
2284 2433 8.693504 CACAAGAAGTATAAAGCACAACAAATG 58.306 33.333 0.00 0.00 0.00 2.32
2285 2434 8.413229 ACAAGAAGTATAAAGCACAACAAATGT 58.587 29.630 0.00 0.00 45.34 2.71
2286 2435 9.248291 CAAGAAGTATAAAGCACAACAAATGTT 57.752 29.630 0.00 0.00 41.46 2.71
2312 2461 7.454260 AAAAATTACATCAAGGTCTCTGGAC 57.546 36.000 0.00 0.00 41.43 4.02
2321 2470 2.352817 GTCTCTGGACCACCGAAGT 58.647 57.895 0.00 0.00 39.42 3.01
2322 2471 1.542492 GTCTCTGGACCACCGAAGTA 58.458 55.000 0.00 0.00 39.42 2.24
2323 2472 1.201880 GTCTCTGGACCACCGAAGTAC 59.798 57.143 0.00 0.00 39.42 2.73
2324 2473 0.531200 CTCTGGACCACCGAAGTACC 59.469 60.000 0.00 0.00 39.42 3.34
2325 2474 0.178955 TCTGGACCACCGAAGTACCA 60.179 55.000 0.00 0.00 39.42 3.25
2326 2475 0.902531 CTGGACCACCGAAGTACCAT 59.097 55.000 0.00 0.00 39.42 3.55
2327 2476 1.278127 CTGGACCACCGAAGTACCATT 59.722 52.381 0.00 0.00 39.42 3.16
2328 2477 1.002659 TGGACCACCGAAGTACCATTG 59.997 52.381 0.00 0.00 39.42 2.82
2329 2478 1.276989 GGACCACCGAAGTACCATTGA 59.723 52.381 0.00 0.00 0.00 2.57
2330 2479 2.344025 GACCACCGAAGTACCATTGAC 58.656 52.381 0.00 0.00 0.00 3.18
2331 2480 1.695242 ACCACCGAAGTACCATTGACA 59.305 47.619 0.00 0.00 0.00 3.58
2332 2481 2.304761 ACCACCGAAGTACCATTGACAT 59.695 45.455 0.00 0.00 0.00 3.06
2333 2482 2.936498 CCACCGAAGTACCATTGACATC 59.064 50.000 0.00 0.00 0.00 3.06
2334 2483 2.603110 CACCGAAGTACCATTGACATCG 59.397 50.000 0.00 0.00 37.67 3.84
2335 2484 1.593006 CCGAAGTACCATTGACATCGC 59.407 52.381 0.00 0.00 36.86 4.58
2336 2485 2.540515 CGAAGTACCATTGACATCGCT 58.459 47.619 0.00 0.00 32.19 4.93
2337 2486 3.490249 CCGAAGTACCATTGACATCGCTA 60.490 47.826 0.00 0.00 36.86 4.26
2338 2487 4.109766 CGAAGTACCATTGACATCGCTAA 58.890 43.478 0.00 0.00 32.19 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 3.772572 TGCTACCTTCTGTATAACTGGCA 59.227 43.478 0.00 0.00 0.00 4.92
101 102 7.568349 TCAATCAAATCTGCTACCTTCTGTAT 58.432 34.615 0.00 0.00 0.00 2.29
133 135 9.661954 AGTAGATCTTCATCCCAACTATTTAGA 57.338 33.333 0.00 0.00 0.00 2.10
157 159 3.177228 AGGCCATAGAGTCTGTTTGAGT 58.823 45.455 5.01 0.00 0.00 3.41
162 164 5.367937 ACATCAATAGGCCATAGAGTCTGTT 59.632 40.000 5.01 0.00 0.00 3.16
195 197 1.406219 CGATATCGGGATCGCAAGCG 61.406 60.000 17.51 8.36 41.98 4.68
236 238 6.709846 CCCATTTTTGTGAAATTCCAAGCTAA 59.290 34.615 0.00 0.00 0.00 3.09
268 271 1.084289 AAATAAGCAGACCGAACCGC 58.916 50.000 0.00 0.00 0.00 5.68
339 342 1.485066 GGATTGACCGTGGTATGTCCT 59.515 52.381 0.00 0.00 37.07 3.85
344 347 4.445735 CCCAAATAGGATTGACCGTGGTAT 60.446 45.833 0.00 0.00 44.74 2.73
368 371 5.459536 AGAAGCAAGTTTCAAAATCCTCC 57.540 39.130 0.00 0.00 0.00 4.30
418 421 3.243301 GGAAGAGTGTCGTGAAGTGTACA 60.243 47.826 0.00 0.00 0.00 2.90
453 456 7.206687 AGACTTTCACATGTCTATTAGCTAGC 58.793 38.462 6.62 6.62 41.19 3.42
454 457 7.589587 CGAGACTTTCACATGTCTATTAGCTAG 59.410 40.741 0.00 0.00 42.79 3.42
505 508 0.839946 ACAACAGTGTCTTCTGGCCT 59.160 50.000 3.32 0.00 39.48 5.19
555 566 7.674348 TGATAATATCGTCCATCCCTAGTCTTT 59.326 37.037 0.00 0.00 0.00 2.52
617 628 9.832445 TGGTAATGAAAGTAGATATTCCAAGAC 57.168 33.333 0.00 0.00 0.00 3.01
650 662 6.169557 TCGAGTGCCCATAATACATAGTTT 57.830 37.500 0.00 0.00 0.00 2.66
673 685 9.947433 AATATGGAAATCATGTCACACAAATTT 57.053 25.926 0.00 0.00 37.30 1.82
677 689 6.627731 GCCAATATGGAAATCATGTCACACAA 60.628 38.462 0.00 0.00 40.96 3.33
680 692 4.341806 GGCCAATATGGAAATCATGTCACA 59.658 41.667 0.00 0.00 40.96 3.58
692 704 4.214310 CACAAATACCAGGCCAATATGGA 58.786 43.478 15.38 0.24 40.96 3.41
699 711 0.251564 CCACCACAAATACCAGGCCA 60.252 55.000 5.01 0.00 0.00 5.36
700 712 0.970427 CCCACCACAAATACCAGGCC 60.970 60.000 0.00 0.00 0.00 5.19
709 721 1.231641 CCACCTTCCCCACCACAAA 59.768 57.895 0.00 0.00 0.00 2.83
720 732 0.392336 TGCACCAATTTGCCACCTTC 59.608 50.000 0.00 0.00 42.25 3.46
726 738 2.070783 CTCATTGTGCACCAATTTGCC 58.929 47.619 15.69 0.00 41.93 4.52
821 833 4.525874 CCTCCTCTTTTCATGGAAGCTTTT 59.474 41.667 0.00 0.00 0.00 2.27
824 836 2.915604 TCCTCCTCTTTTCATGGAAGCT 59.084 45.455 0.00 0.00 0.00 3.74
863 876 8.349983 AGCATCAACGTTAAGTTTAACAAATCT 58.650 29.630 0.00 1.11 42.02 2.40
896 909 1.293498 CCCTGAGAAGGTCGTGGTG 59.707 63.158 0.00 0.00 0.00 4.17
924 937 2.457598 TGTCATCTCTTAAGACCGCCT 58.542 47.619 0.00 0.00 33.32 5.52
1004 1018 4.442733 CGAATTTTAACGCCAAAGCTTCAA 59.557 37.500 0.00 0.00 36.60 2.69
1082 1096 4.279420 TCATGGTCTCGATCACCTTCATAG 59.721 45.833 13.42 0.00 34.66 2.23
1087 1101 2.417379 CGTTCATGGTCTCGATCACCTT 60.417 50.000 13.42 5.91 34.66 3.50
1263 1277 2.434359 GGTTCCTCGAGCCAACCG 60.434 66.667 22.02 3.71 33.06 4.44
1265 1279 0.321653 ATGTGGTTCCTCGAGCCAAC 60.322 55.000 11.30 12.91 44.05 3.77
1363 1377 1.489481 CACTCCCAGTCTGCCATCTA 58.511 55.000 0.00 0.00 0.00 1.98
1381 1395 4.337177 TTTGGTGGATCGCGGGCA 62.337 61.111 6.13 0.00 0.00 5.36
1382 1396 3.508840 CTTTGGTGGATCGCGGGC 61.509 66.667 6.13 0.00 0.00 6.13
1383 1397 1.153168 ATCTTTGGTGGATCGCGGG 60.153 57.895 6.13 0.00 0.00 6.13
1384 1398 1.160329 GGATCTTTGGTGGATCGCGG 61.160 60.000 6.13 0.00 40.11 6.46
1385 1399 0.461870 TGGATCTTTGGTGGATCGCG 60.462 55.000 0.00 0.00 40.11 5.87
1386 1400 1.017387 GTGGATCTTTGGTGGATCGC 58.983 55.000 0.00 0.00 40.11 4.58
1387 1401 2.698855 AGTGGATCTTTGGTGGATCG 57.301 50.000 0.00 0.00 40.11 3.69
1388 1402 4.762289 AGTAGTGGATCTTTGGTGGATC 57.238 45.455 0.00 0.00 38.92 3.36
1389 1403 4.656112 CCTAGTAGTGGATCTTTGGTGGAT 59.344 45.833 0.00 0.00 0.00 3.41
1390 1404 4.030913 CCTAGTAGTGGATCTTTGGTGGA 58.969 47.826 0.00 0.00 0.00 4.02
1391 1405 3.134804 CCCTAGTAGTGGATCTTTGGTGG 59.865 52.174 0.00 0.00 0.00 4.61
1392 1406 4.030913 TCCCTAGTAGTGGATCTTTGGTG 58.969 47.826 3.89 0.00 0.00 4.17
1393 1407 4.348020 TCCCTAGTAGTGGATCTTTGGT 57.652 45.455 3.89 0.00 0.00 3.67
1394 1408 5.693769 TTTCCCTAGTAGTGGATCTTTGG 57.306 43.478 7.86 0.00 0.00 3.28
1395 1409 5.529060 GCATTTCCCTAGTAGTGGATCTTTG 59.471 44.000 7.86 5.75 0.00 2.77
1396 1410 5.430089 AGCATTTCCCTAGTAGTGGATCTTT 59.570 40.000 7.86 0.00 0.00 2.52
1397 1411 4.971924 AGCATTTCCCTAGTAGTGGATCTT 59.028 41.667 7.86 0.00 0.00 2.40
1398 1412 4.561752 AGCATTTCCCTAGTAGTGGATCT 58.438 43.478 7.86 2.75 0.00 2.75
1399 1413 4.965200 AGCATTTCCCTAGTAGTGGATC 57.035 45.455 7.86 0.00 0.00 3.36
1400 1414 7.512746 TGTATAAGCATTTCCCTAGTAGTGGAT 59.487 37.037 7.86 0.00 0.00 3.41
1401 1415 6.842280 TGTATAAGCATTTCCCTAGTAGTGGA 59.158 38.462 3.89 3.89 0.00 4.02
1402 1416 6.929606 GTGTATAAGCATTTCCCTAGTAGTGG 59.070 42.308 0.00 0.00 0.00 4.00
1403 1417 7.497595 TGTGTATAAGCATTTCCCTAGTAGTG 58.502 38.462 0.00 0.00 0.00 2.74
1404 1418 7.202011 CCTGTGTATAAGCATTTCCCTAGTAGT 60.202 40.741 0.00 0.00 0.00 2.73
1405 1419 7.155328 CCTGTGTATAAGCATTTCCCTAGTAG 58.845 42.308 0.00 0.00 0.00 2.57
1406 1420 6.042781 CCCTGTGTATAAGCATTTCCCTAGTA 59.957 42.308 0.00 0.00 0.00 1.82
1407 1421 5.163195 CCCTGTGTATAAGCATTTCCCTAGT 60.163 44.000 0.00 0.00 0.00 2.57
1408 1422 5.308825 CCCTGTGTATAAGCATTTCCCTAG 58.691 45.833 0.00 0.00 0.00 3.02
1409 1423 4.445735 GCCCTGTGTATAAGCATTTCCCTA 60.446 45.833 0.00 0.00 0.00 3.53
1410 1424 3.688414 GCCCTGTGTATAAGCATTTCCCT 60.688 47.826 0.00 0.00 0.00 4.20
1411 1425 2.623416 GCCCTGTGTATAAGCATTTCCC 59.377 50.000 0.00 0.00 0.00 3.97
1412 1426 2.623416 GGCCCTGTGTATAAGCATTTCC 59.377 50.000 0.00 0.00 0.00 3.13
1413 1427 3.555966 AGGCCCTGTGTATAAGCATTTC 58.444 45.455 0.00 0.00 0.00 2.17
1414 1428 3.669939 AGGCCCTGTGTATAAGCATTT 57.330 42.857 0.00 0.00 0.00 2.32
1415 1429 4.599241 AGATAGGCCCTGTGTATAAGCATT 59.401 41.667 0.00 0.00 0.00 3.56
1416 1430 4.171234 AGATAGGCCCTGTGTATAAGCAT 58.829 43.478 0.00 0.00 0.00 3.79
1417 1431 3.587498 AGATAGGCCCTGTGTATAAGCA 58.413 45.455 0.00 0.00 0.00 3.91
1418 1432 4.202367 ACAAGATAGGCCCTGTGTATAAGC 60.202 45.833 0.00 0.00 0.00 3.09
1419 1433 5.552870 ACAAGATAGGCCCTGTGTATAAG 57.447 43.478 0.00 0.00 0.00 1.73
1420 1434 5.968676 AACAAGATAGGCCCTGTGTATAA 57.031 39.130 0.00 0.00 0.00 0.98
1421 1435 5.968676 AAACAAGATAGGCCCTGTGTATA 57.031 39.130 0.00 0.00 0.00 1.47
1422 1436 4.862641 AAACAAGATAGGCCCTGTGTAT 57.137 40.909 0.00 0.00 0.00 2.29
1423 1437 4.650972 AAAACAAGATAGGCCCTGTGTA 57.349 40.909 0.00 0.00 0.00 2.90
1424 1438 3.525800 AAAACAAGATAGGCCCTGTGT 57.474 42.857 0.00 0.00 0.00 3.72
1425 1439 6.357367 AGTATAAAACAAGATAGGCCCTGTG 58.643 40.000 0.00 0.00 0.00 3.66
1426 1440 6.576778 AGTATAAAACAAGATAGGCCCTGT 57.423 37.500 0.00 0.00 0.00 4.00
1550 1612 6.255950 TCAATCGTACAACTTCTACTCGATG 58.744 40.000 0.00 0.00 36.82 3.84
1568 1631 6.023357 AGTCCTACTCATCATCATCAATCG 57.977 41.667 0.00 0.00 0.00 3.34
1783 1908 3.431486 GGAGTAGATTCAAGTGGAGGCAG 60.431 52.174 0.00 0.00 0.00 4.85
2065 2214 1.697432 ACAAGCACTACCACTAAGGCA 59.303 47.619 0.00 0.00 43.14 4.75
2092 2241 4.691216 GCTTGTTTTGTAGCTAGCAGTAGT 59.309 41.667 18.83 0.00 34.52 2.73
2133 2282 3.708451 TGAGCACCAATCACTACTAGGA 58.292 45.455 0.00 0.00 0.00 2.94
2148 2297 2.337583 TGTCTCGTAGCAATTGAGCAC 58.662 47.619 10.34 2.10 36.85 4.40
2152 2301 6.402118 GCAAGTATTTGTCTCGTAGCAATTGA 60.402 38.462 10.34 0.00 36.65 2.57
2153 2302 5.734498 GCAAGTATTTGTCTCGTAGCAATTG 59.266 40.000 0.00 0.00 36.65 2.32
2155 2304 4.935205 TGCAAGTATTTGTCTCGTAGCAAT 59.065 37.500 0.00 0.00 36.65 3.56
2157 2306 3.678072 GTGCAAGTATTTGTCTCGTAGCA 59.322 43.478 0.00 0.00 36.65 3.49
2158 2307 3.678072 TGTGCAAGTATTTGTCTCGTAGC 59.322 43.478 0.00 0.00 36.65 3.58
2159 2308 6.128553 ACAATGTGCAAGTATTTGTCTCGTAG 60.129 38.462 0.00 0.00 36.65 3.51
2160 2309 5.699001 ACAATGTGCAAGTATTTGTCTCGTA 59.301 36.000 0.00 0.00 36.65 3.43
2161 2310 4.515191 ACAATGTGCAAGTATTTGTCTCGT 59.485 37.500 0.00 0.00 36.65 4.18
2162 2311 5.034554 ACAATGTGCAAGTATTTGTCTCG 57.965 39.130 0.00 0.00 36.65 4.04
2163 2312 6.000891 TGACAATGTGCAAGTATTTGTCTC 57.999 37.500 19.96 5.69 36.65 3.36
2164 2313 6.384224 CATGACAATGTGCAAGTATTTGTCT 58.616 36.000 19.96 9.88 36.65 3.41
2165 2314 5.061311 GCATGACAATGTGCAAGTATTTGTC 59.939 40.000 15.78 15.78 40.94 3.18
2166 2315 4.925054 GCATGACAATGTGCAAGTATTTGT 59.075 37.500 0.00 0.00 40.94 2.83
2167 2316 4.030865 CGCATGACAATGTGCAAGTATTTG 59.969 41.667 0.00 0.00 41.32 2.32
2168 2317 4.168014 CGCATGACAATGTGCAAGTATTT 58.832 39.130 0.00 0.00 41.32 1.40
2169 2318 3.427909 CCGCATGACAATGTGCAAGTATT 60.428 43.478 0.00 0.00 42.01 1.89
2170 2319 2.097954 CCGCATGACAATGTGCAAGTAT 59.902 45.455 0.00 0.00 42.01 2.12
2171 2320 1.468127 CCGCATGACAATGTGCAAGTA 59.532 47.619 0.00 0.00 42.01 2.24
2172 2321 0.241749 CCGCATGACAATGTGCAAGT 59.758 50.000 0.00 0.00 42.01 3.16
2173 2322 0.241749 ACCGCATGACAATGTGCAAG 59.758 50.000 0.00 0.00 42.01 4.01
2174 2323 0.039346 CACCGCATGACAATGTGCAA 60.039 50.000 0.00 0.00 42.01 4.08
2175 2324 0.888285 TCACCGCATGACAATGTGCA 60.888 50.000 0.00 0.00 42.01 4.57
2176 2325 0.240678 TTCACCGCATGACAATGTGC 59.759 50.000 0.00 0.00 42.01 4.57
2177 2326 2.702898 TTTCACCGCATGACAATGTG 57.297 45.000 0.00 0.00 42.82 3.21
2178 2327 3.940209 ATTTTCACCGCATGACAATGT 57.060 38.095 0.00 0.00 36.54 2.71
2179 2328 9.844790 AATATATATTTTCACCGCATGACAATG 57.155 29.630 1.91 0.00 38.05 2.82
2181 2330 9.891828 GAAATATATATTTTCACCGCATGACAA 57.108 29.630 19.30 0.00 36.92 3.18
2182 2331 8.227119 CGAAATATATATTTTCACCGCATGACA 58.773 33.333 19.30 0.00 36.92 3.58
2183 2332 7.692291 CCGAAATATATATTTTCACCGCATGAC 59.308 37.037 19.30 4.29 36.92 3.06
2184 2333 7.148323 CCCGAAATATATATTTTCACCGCATGA 60.148 37.037 19.30 0.00 36.13 3.07
2185 2334 6.966632 CCCGAAATATATATTTTCACCGCATG 59.033 38.462 19.30 7.90 36.13 4.06
2186 2335 6.882140 TCCCGAAATATATATTTTCACCGCAT 59.118 34.615 19.30 0.00 36.13 4.73
2187 2336 6.148150 GTCCCGAAATATATATTTTCACCGCA 59.852 38.462 19.30 7.22 36.13 5.69
2188 2337 6.148150 TGTCCCGAAATATATATTTTCACCGC 59.852 38.462 19.30 7.07 36.13 5.68
2189 2338 7.661127 TGTCCCGAAATATATATTTTCACCG 57.339 36.000 19.30 16.95 36.13 4.94
2199 2348 9.231297 CTTCCACATTAATGTCCCGAAATATAT 57.769 33.333 18.25 0.00 39.39 0.86
2200 2349 7.174253 GCTTCCACATTAATGTCCCGAAATATA 59.826 37.037 18.25 0.00 39.39 0.86
2201 2350 6.016276 GCTTCCACATTAATGTCCCGAAATAT 60.016 38.462 18.25 0.00 39.39 1.28
2202 2351 5.298276 GCTTCCACATTAATGTCCCGAAATA 59.702 40.000 18.25 0.17 39.39 1.40
2203 2352 4.097892 GCTTCCACATTAATGTCCCGAAAT 59.902 41.667 18.25 0.00 39.39 2.17
2204 2353 3.442273 GCTTCCACATTAATGTCCCGAAA 59.558 43.478 18.25 7.55 39.39 3.46
2205 2354 3.013921 GCTTCCACATTAATGTCCCGAA 58.986 45.455 18.25 16.85 39.39 4.30
2206 2355 2.639065 GCTTCCACATTAATGTCCCGA 58.361 47.619 18.25 11.04 39.39 5.14
2207 2356 1.330521 CGCTTCCACATTAATGTCCCG 59.669 52.381 18.25 11.92 39.39 5.14
2208 2357 2.365582 ACGCTTCCACATTAATGTCCC 58.634 47.619 18.25 4.64 39.39 4.46
2209 2358 4.434713 AAACGCTTCCACATTAATGTCC 57.565 40.909 18.25 4.32 39.39 4.02
2210 2359 7.861176 TTAAAAACGCTTCCACATTAATGTC 57.139 32.000 18.25 6.17 39.39 3.06
2211 2360 7.330700 CCATTAAAAACGCTTCCACATTAATGT 59.669 33.333 15.47 15.47 42.84 2.71
2212 2361 7.673776 GCCATTAAAAACGCTTCCACATTAATG 60.674 37.037 14.01 14.01 38.25 1.90
2213 2362 6.312672 GCCATTAAAAACGCTTCCACATTAAT 59.687 34.615 0.00 0.00 0.00 1.40
2214 2363 5.635700 GCCATTAAAAACGCTTCCACATTAA 59.364 36.000 0.00 0.00 0.00 1.40
2215 2364 5.047660 AGCCATTAAAAACGCTTCCACATTA 60.048 36.000 0.00 0.00 0.00 1.90
2216 2365 3.993736 GCCATTAAAAACGCTTCCACATT 59.006 39.130 0.00 0.00 0.00 2.71
2217 2366 3.258123 AGCCATTAAAAACGCTTCCACAT 59.742 39.130 0.00 0.00 0.00 3.21
2218 2367 2.625790 AGCCATTAAAAACGCTTCCACA 59.374 40.909 0.00 0.00 0.00 4.17
2219 2368 3.297830 AGCCATTAAAAACGCTTCCAC 57.702 42.857 0.00 0.00 0.00 4.02
2220 2369 4.328536 TCTAGCCATTAAAAACGCTTCCA 58.671 39.130 0.00 0.00 32.76 3.53
2221 2370 4.957759 TCTAGCCATTAAAAACGCTTCC 57.042 40.909 0.00 0.00 32.76 3.46
2222 2371 6.364945 AGATCTAGCCATTAAAAACGCTTC 57.635 37.500 0.00 0.00 32.76 3.86
2223 2372 7.048512 AGTAGATCTAGCCATTAAAAACGCTT 58.951 34.615 1.64 0.00 32.76 4.68
2224 2373 6.583562 AGTAGATCTAGCCATTAAAAACGCT 58.416 36.000 1.64 0.00 35.34 5.07
2225 2374 6.846325 AGTAGATCTAGCCATTAAAAACGC 57.154 37.500 1.64 0.00 0.00 4.84
2233 2382 9.381038 TGAACCTTTATAGTAGATCTAGCCATT 57.619 33.333 1.64 0.00 31.67 3.16
2234 2383 8.808092 GTGAACCTTTATAGTAGATCTAGCCAT 58.192 37.037 1.64 0.00 31.67 4.40
2235 2384 7.783119 TGTGAACCTTTATAGTAGATCTAGCCA 59.217 37.037 1.64 0.00 31.67 4.75
2236 2385 8.179509 TGTGAACCTTTATAGTAGATCTAGCC 57.820 38.462 1.64 0.00 31.67 3.93
2237 2386 9.685828 CTTGTGAACCTTTATAGTAGATCTAGC 57.314 37.037 1.64 0.00 31.67 3.42
2249 2398 9.515226 TGCTTTATACTTCTTGTGAACCTTTAT 57.485 29.630 0.00 0.00 0.00 1.40
2250 2399 8.780249 GTGCTTTATACTTCTTGTGAACCTTTA 58.220 33.333 0.00 0.00 0.00 1.85
2251 2400 7.284489 TGTGCTTTATACTTCTTGTGAACCTTT 59.716 33.333 0.00 0.00 0.00 3.11
2252 2401 6.770785 TGTGCTTTATACTTCTTGTGAACCTT 59.229 34.615 0.00 0.00 0.00 3.50
2253 2402 6.296026 TGTGCTTTATACTTCTTGTGAACCT 58.704 36.000 0.00 0.00 0.00 3.50
2254 2403 6.554334 TGTGCTTTATACTTCTTGTGAACC 57.446 37.500 0.00 0.00 0.00 3.62
2255 2404 7.414436 TGTTGTGCTTTATACTTCTTGTGAAC 58.586 34.615 0.00 0.00 0.00 3.18
2256 2405 7.561021 TGTTGTGCTTTATACTTCTTGTGAA 57.439 32.000 0.00 0.00 0.00 3.18
2257 2406 7.561021 TTGTTGTGCTTTATACTTCTTGTGA 57.439 32.000 0.00 0.00 0.00 3.58
2258 2407 8.693504 CATTTGTTGTGCTTTATACTTCTTGTG 58.306 33.333 0.00 0.00 0.00 3.33
2259 2408 8.413229 ACATTTGTTGTGCTTTATACTTCTTGT 58.587 29.630 0.00 0.00 37.11 3.16
2260 2409 8.801715 ACATTTGTTGTGCTTTATACTTCTTG 57.198 30.769 0.00 0.00 37.11 3.02
2288 2437 7.454260 GTCCAGAGACCTTGATGTAATTTTT 57.546 36.000 0.00 0.00 37.00 1.94
2303 2452 1.201880 GTACTTCGGTGGTCCAGAGAC 59.798 57.143 0.00 0.00 42.73 3.36
2304 2453 1.542492 GTACTTCGGTGGTCCAGAGA 58.458 55.000 0.00 0.00 0.00 3.10
2305 2454 0.531200 GGTACTTCGGTGGTCCAGAG 59.469 60.000 0.00 0.00 0.00 3.35
2306 2455 0.178955 TGGTACTTCGGTGGTCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
2307 2456 0.902531 ATGGTACTTCGGTGGTCCAG 59.097 55.000 0.00 0.00 32.04 3.86
2308 2457 1.002659 CAATGGTACTTCGGTGGTCCA 59.997 52.381 0.00 0.00 0.00 4.02
2309 2458 1.276989 TCAATGGTACTTCGGTGGTCC 59.723 52.381 0.00 0.00 0.00 4.46
2310 2459 2.289195 TGTCAATGGTACTTCGGTGGTC 60.289 50.000 0.00 0.00 0.00 4.02
2311 2460 1.695242 TGTCAATGGTACTTCGGTGGT 59.305 47.619 0.00 0.00 0.00 4.16
2312 2461 2.465860 TGTCAATGGTACTTCGGTGG 57.534 50.000 0.00 0.00 0.00 4.61
2313 2462 2.603110 CGATGTCAATGGTACTTCGGTG 59.397 50.000 0.00 0.00 39.49 4.94
2314 2463 2.888594 CGATGTCAATGGTACTTCGGT 58.111 47.619 0.00 0.00 39.49 4.69
2315 2464 1.593006 GCGATGTCAATGGTACTTCGG 59.407 52.381 11.72 0.00 41.89 4.30
2316 2465 2.540515 AGCGATGTCAATGGTACTTCG 58.459 47.619 0.00 0.00 43.45 3.79


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

AutoCloner maintained by Alex Coulton.