Multiple sequence alignment - TraesCS2D01G376000

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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 TraesCS2D01G376000 chr2D 100.000 4122 0 0 1 4122 480182671 480178550 0.000000e+00 7613.0
1 TraesCS2D01G376000 chr2D 84.628 1802 139 81 651 2424 480325868 480324177 0.000000e+00 1666.0
2 TraesCS2D01G376000 chr2D 95.000 660 27 6 3466 4122 35978398 35977742 0.000000e+00 1031.0
3 TraesCS2D01G376000 chr2D 94.954 654 23 8 3471 4122 160319641 160320286 0.000000e+00 1016.0
4 TraesCS2D01G376000 chr2D 87.986 591 71 0 1030 1620 159573843 159574433 0.000000e+00 699.0
5 TraesCS2D01G376000 chr2D 81.925 426 58 12 2756 3181 480323997 480323591 3.950000e-90 342.0
6 TraesCS2D01G376000 chr2D 80.786 229 27 11 163 379 480326362 480326139 3.300000e-36 163.0
7 TraesCS2D01G376000 chr2D 82.353 136 23 1 2590 2724 480324133 480323998 2.600000e-22 117.0
8 TraesCS2D01G376000 chr2B 95.414 1461 46 15 588 2041 563046858 563045412 0.000000e+00 2307.0
9 TraesCS2D01G376000 chr2B 88.441 1142 92 21 650 1788 563185302 563184198 0.000000e+00 1341.0
10 TraesCS2D01G376000 chr2B 87.228 1151 84 33 2332 3470 563044623 563043524 0.000000e+00 1253.0
11 TraesCS2D01G376000 chr2B 87.986 591 71 0 1030 1620 216708490 216709080 0.000000e+00 699.0
12 TraesCS2D01G376000 chr2B 90.976 410 16 6 1 399 563047338 563046939 2.180000e-147 532.0
13 TraesCS2D01G376000 chr2B 82.215 596 76 18 2590 3181 563183274 563182705 1.720000e-133 486.0
14 TraesCS2D01G376000 chr2B 94.561 239 8 3 2094 2331 563045312 563045078 8.420000e-97 364.0
15 TraesCS2D01G376000 chr2B 84.326 319 24 17 2112 2424 563183618 563183320 5.210000e-74 289.0
16 TraesCS2D01G376000 chr2B 88.435 147 17 0 2122 2268 216710516 216710662 1.180000e-40 178.0
17 TraesCS2D01G376000 chr2B 93.878 49 0 2 410 455 563046906 563046858 2.060000e-08 71.3
18 TraesCS2D01G376000 chr2A 93.004 1458 61 19 588 2041 622748471 622747051 0.000000e+00 2089.0
19 TraesCS2D01G376000 chr2A 89.867 1431 84 37 2054 3470 622747004 622745621 0.000000e+00 1783.0
20 TraesCS2D01G376000 chr2A 91.317 1048 76 7 596 1636 622854143 622853104 0.000000e+00 1417.0
21 TraesCS2D01G376000 chr2A 88.156 591 70 0 1030 1620 170602948 170603538 0.000000e+00 704.0
22 TraesCS2D01G376000 chr2A 90.201 398 22 6 1 397 622748935 622748554 1.710000e-138 503.0
23 TraesCS2D01G376000 chr2A 81.271 598 83 20 2590 3181 622852401 622851827 1.350000e-124 457.0
24 TraesCS2D01G376000 chr2A 84.665 313 23 17 2112 2424 622852732 622852445 5.210000e-74 289.0
25 TraesCS2D01G376000 chr2A 80.658 243 25 6 157 379 622855238 622854998 7.090000e-38 169.0
26 TraesCS2D01G376000 chr6D 95.890 657 19 7 3471 4122 147646485 147647138 0.000000e+00 1057.0
27 TraesCS2D01G376000 chr6D 91.892 148 12 0 2121 2268 302039302 302039449 1.500000e-49 207.0
28 TraesCS2D01G376000 chr6D 92.553 94 7 0 3001 3094 302040147 302040240 7.190000e-28 135.0
29 TraesCS2D01G376000 chr7D 94.776 670 24 11 3455 4122 50710893 50711553 0.000000e+00 1033.0
30 TraesCS2D01G376000 chr7D 95.115 655 26 5 3471 4122 434163855 434163204 0.000000e+00 1027.0
31 TraesCS2D01G376000 chr5D 94.977 657 27 6 3470 4122 498435958 498436612 0.000000e+00 1026.0
32 TraesCS2D01G376000 chr3D 94.962 655 26 6 3471 4122 566073598 566072948 0.000000e+00 1020.0
33 TraesCS2D01G376000 chr3D 94.817 656 28 6 3471 4122 535498312 535498965 0.000000e+00 1018.0
34 TraesCS2D01G376000 chr4D 94.648 654 30 4 3470 4122 468007785 468007136 0.000000e+00 1009.0
35 TraesCS2D01G376000 chr5A 86.819 569 72 3 1051 1619 143552900 143552335 2.090000e-177 632.0
36 TraesCS2D01G376000 chr6A 92.568 148 11 0 2121 2268 414876528 414876381 3.230000e-51 213.0
37 TraesCS2D01G376000 chr6A 90.722 97 9 0 3001 3097 414875608 414875512 3.340000e-26 130.0
38 TraesCS2D01G376000 chr6B 91.216 148 13 0 2121 2268 467449755 467449902 6.990000e-48 202.0
39 TraesCS2D01G376000 chr6B 93.258 89 6 0 3001 3089 467450593 467450681 9.300000e-27 132.0


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 TraesCS2D01G376000 chr2D 480178550 480182671 4121 True 7613.000000 7613 100.00000 1 4122 1 chr2D.!!$R2 4121
1 TraesCS2D01G376000 chr2D 35977742 35978398 656 True 1031.000000 1031 95.00000 3466 4122 1 chr2D.!!$R1 656
2 TraesCS2D01G376000 chr2D 160319641 160320286 645 False 1016.000000 1016 94.95400 3471 4122 1 chr2D.!!$F2 651
3 TraesCS2D01G376000 chr2D 159573843 159574433 590 False 699.000000 699 87.98600 1030 1620 1 chr2D.!!$F1 590
4 TraesCS2D01G376000 chr2D 480323591 480326362 2771 True 572.000000 1666 82.42300 163 3181 4 chr2D.!!$R3 3018
5 TraesCS2D01G376000 chr2B 563043524 563047338 3814 True 905.460000 2307 92.41140 1 3470 5 chr2B.!!$R1 3469
6 TraesCS2D01G376000 chr2B 563182705 563185302 2597 True 705.333333 1341 84.99400 650 3181 3 chr2B.!!$R2 2531
7 TraesCS2D01G376000 chr2B 216708490 216710662 2172 False 438.500000 699 88.21050 1030 2268 2 chr2B.!!$F1 1238
8 TraesCS2D01G376000 chr2A 622745621 622748935 3314 True 1458.333333 2089 91.02400 1 3470 3 chr2A.!!$R1 3469
9 TraesCS2D01G376000 chr2A 170602948 170603538 590 False 704.000000 704 88.15600 1030 1620 1 chr2A.!!$F1 590
10 TraesCS2D01G376000 chr2A 622851827 622855238 3411 True 583.000000 1417 84.47775 157 3181 4 chr2A.!!$R2 3024
11 TraesCS2D01G376000 chr6D 147646485 147647138 653 False 1057.000000 1057 95.89000 3471 4122 1 chr6D.!!$F1 651
12 TraesCS2D01G376000 chr7D 50710893 50711553 660 False 1033.000000 1033 94.77600 3455 4122 1 chr7D.!!$F1 667
13 TraesCS2D01G376000 chr7D 434163204 434163855 651 True 1027.000000 1027 95.11500 3471 4122 1 chr7D.!!$R1 651
14 TraesCS2D01G376000 chr5D 498435958 498436612 654 False 1026.000000 1026 94.97700 3470 4122 1 chr5D.!!$F1 652
15 TraesCS2D01G376000 chr3D 566072948 566073598 650 True 1020.000000 1020 94.96200 3471 4122 1 chr3D.!!$R1 651
16 TraesCS2D01G376000 chr3D 535498312 535498965 653 False 1018.000000 1018 94.81700 3471 4122 1 chr3D.!!$F1 651
17 TraesCS2D01G376000 chr4D 468007136 468007785 649 True 1009.000000 1009 94.64800 3470 4122 1 chr4D.!!$R1 652
18 TraesCS2D01G376000 chr5A 143552335 143552900 565 True 632.000000 632 86.81900 1051 1619 1 chr5A.!!$R1 568

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
544 1369 0.036732 CAACCTCAGCTGCCCAGTTA 59.963 55.000 9.47 0.0 0.0 2.24 F
546 1371 0.036875 ACCTCAGCTGCCCAGTTAAC 59.963 55.000 9.47 0.0 0.0 2.01 F
555 1380 0.179200 GCCCAGTTAACGCATCAACG 60.179 55.000 0.00 0.0 39.5 4.10 F
719 1564 0.309922 GTGATGCAATGATGAGGGCG 59.690 55.000 0.00 0.0 0.0 6.13 F
2280 4381 1.065998 ACCACGTATGTACCGCCATTT 60.066 47.619 0.00 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 3483 0.820871 AGCTGGCTAGGAAGAAGACG 59.179 55.000 0.00 0.00 0.00 4.18 R
2281 4382 2.523412 AGATGCATGCATGGGGGC 60.523 61.111 36.73 21.46 36.70 5.80 R
2464 5031 7.751768 AATAAAGTTATCCTGGCTATCTTGC 57.248 36.000 2.55 0.00 0.00 4.01 R
2621 5229 0.032678 ATAATCGACCTGCTCAGCGG 59.967 55.000 0.00 0.00 34.23 5.52 R
3289 5921 1.015109 GCACACTCGATCGGTAGAGA 58.985 55.000 16.41 0.00 37.87 3.10 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
59 60 2.525248 CCATCATGCGGACGGTTCG 61.525 63.158 4.00 4.00 0.00 3.95
100 101 2.567049 GAGGGATATCGGGTCGCG 59.433 66.667 0.00 0.00 34.14 5.87
131 132 1.591059 CCTCGCGCATCTTCTGGAG 60.591 63.158 8.75 2.66 0.00 3.86
246 283 5.953571 ACTTTGATTAGAGGGTGGTTCTTT 58.046 37.500 0.00 0.00 0.00 2.52
247 284 5.770162 ACTTTGATTAGAGGGTGGTTCTTTG 59.230 40.000 0.00 0.00 0.00 2.77
248 285 3.686016 TGATTAGAGGGTGGTTCTTTGC 58.314 45.455 0.00 0.00 0.00 3.68
279 316 2.415893 GCGCATGATTAGCAACCAAACT 60.416 45.455 0.30 0.00 0.00 2.66
281 318 3.366273 CGCATGATTAGCAACCAAACTGT 60.366 43.478 0.00 0.00 0.00 3.55
293 330 4.853924 ACCAAACTGTTGATTAAGCAGG 57.146 40.909 0.00 0.00 36.83 4.85
299 336 3.498397 ACTGTTGATTAAGCAGGTGTTCG 59.502 43.478 0.00 0.00 34.79 3.95
314 351 0.458025 GTTCGTTAGTGGAGAGCCCG 60.458 60.000 0.00 0.00 37.93 6.13
331 368 2.926159 GCCCGGACAAATGTCAACAATG 60.926 50.000 14.93 0.00 46.47 2.82
341 378 6.973474 ACAAATGTCAACAATGCAAAATTTGG 59.027 30.769 7.89 0.00 31.77 3.28
348 385 1.158434 ATGCAAAATTTGGCGCCAAG 58.842 45.000 37.88 27.68 37.24 3.61
455 1280 4.776435 TCTGCCATCACCTCAAATCATA 57.224 40.909 0.00 0.00 0.00 2.15
456 1281 5.114764 TCTGCCATCACCTCAAATCATAA 57.885 39.130 0.00 0.00 0.00 1.90
458 1283 5.951148 TCTGCCATCACCTCAAATCATAAAA 59.049 36.000 0.00 0.00 0.00 1.52
459 1284 6.436847 TCTGCCATCACCTCAAATCATAAAAA 59.563 34.615 0.00 0.00 0.00 1.94
488 1313 8.541899 AAAAATAAGACCAACCCAAGAACTAA 57.458 30.769 0.00 0.00 0.00 2.24
489 1314 8.721133 AAAATAAGACCAACCCAAGAACTAAT 57.279 30.769 0.00 0.00 0.00 1.73
490 1315 7.939784 AATAAGACCAACCCAAGAACTAATC 57.060 36.000 0.00 0.00 0.00 1.75
491 1316 4.302559 AGACCAACCCAAGAACTAATCC 57.697 45.455 0.00 0.00 0.00 3.01
492 1317 3.916989 AGACCAACCCAAGAACTAATCCT 59.083 43.478 0.00 0.00 0.00 3.24
493 1318 4.010349 GACCAACCCAAGAACTAATCCTG 58.990 47.826 0.00 0.00 0.00 3.86
494 1319 3.655777 ACCAACCCAAGAACTAATCCTGA 59.344 43.478 0.00 0.00 0.00 3.86
495 1320 4.263506 ACCAACCCAAGAACTAATCCTGAG 60.264 45.833 0.00 0.00 0.00 3.35
496 1321 3.636153 ACCCAAGAACTAATCCTGAGC 57.364 47.619 0.00 0.00 0.00 4.26
497 1322 3.185455 ACCCAAGAACTAATCCTGAGCT 58.815 45.455 0.00 0.00 0.00 4.09
498 1323 4.362677 ACCCAAGAACTAATCCTGAGCTA 58.637 43.478 0.00 0.00 0.00 3.32
499 1324 4.407296 ACCCAAGAACTAATCCTGAGCTAG 59.593 45.833 0.00 0.00 0.00 3.42
511 1336 1.329292 CTGAGCTAGGACTCGAACTCG 59.671 57.143 0.00 0.00 39.68 4.18
512 1337 0.658897 GAGCTAGGACTCGAACTCGG 59.341 60.000 0.00 0.00 40.29 4.63
519 1344 3.382832 CTCGAACTCGGGTGGGCT 61.383 66.667 0.00 0.00 40.29 5.19
520 1345 3.358076 CTCGAACTCGGGTGGGCTC 62.358 68.421 0.00 0.00 40.29 4.70
521 1346 3.691342 CGAACTCGGGTGGGCTCA 61.691 66.667 0.00 0.00 35.37 4.26
522 1347 2.990479 GAACTCGGGTGGGCTCAT 59.010 61.111 0.00 0.00 0.00 2.90
523 1348 1.672854 CGAACTCGGGTGGGCTCATA 61.673 60.000 0.00 0.00 35.37 2.15
524 1349 0.105039 GAACTCGGGTGGGCTCATAG 59.895 60.000 0.00 0.00 0.00 2.23
525 1350 1.972660 AACTCGGGTGGGCTCATAGC 61.973 60.000 0.00 0.00 41.46 2.97
526 1351 2.364973 TCGGGTGGGCTCATAGCA 60.365 61.111 0.00 0.00 44.75 3.49
527 1352 1.971505 CTCGGGTGGGCTCATAGCAA 61.972 60.000 0.00 0.00 44.75 3.91
528 1353 1.819632 CGGGTGGGCTCATAGCAAC 60.820 63.158 0.00 0.00 44.75 4.17
529 1354 1.453928 GGGTGGGCTCATAGCAACC 60.454 63.158 12.29 12.29 44.75 3.77
530 1355 1.609783 GGTGGGCTCATAGCAACCT 59.390 57.895 13.06 0.00 44.75 3.50
531 1356 0.464554 GGTGGGCTCATAGCAACCTC 60.465 60.000 13.06 2.96 44.75 3.85
532 1357 0.253044 GTGGGCTCATAGCAACCTCA 59.747 55.000 0.00 0.00 44.75 3.86
533 1358 0.543277 TGGGCTCATAGCAACCTCAG 59.457 55.000 0.78 0.00 44.75 3.35
534 1359 0.817229 GGGCTCATAGCAACCTCAGC 60.817 60.000 0.78 0.00 44.75 4.26
535 1360 0.179936 GGCTCATAGCAACCTCAGCT 59.820 55.000 0.78 0.00 44.75 4.24
536 1361 1.297664 GCTCATAGCAACCTCAGCTG 58.702 55.000 7.63 7.63 43.33 4.24
537 1362 1.297664 CTCATAGCAACCTCAGCTGC 58.702 55.000 9.47 0.00 43.33 5.25
538 1363 0.107508 TCATAGCAACCTCAGCTGCC 60.108 55.000 9.47 0.00 43.33 4.85
539 1364 1.099879 CATAGCAACCTCAGCTGCCC 61.100 60.000 9.47 0.00 43.33 5.36
540 1365 1.565390 ATAGCAACCTCAGCTGCCCA 61.565 55.000 9.47 0.00 43.33 5.36
541 1366 2.189191 TAGCAACCTCAGCTGCCCAG 62.189 60.000 9.47 0.70 43.33 4.45
542 1367 2.433446 CAACCTCAGCTGCCCAGT 59.567 61.111 9.47 0.02 0.00 4.00
543 1368 1.228367 CAACCTCAGCTGCCCAGTT 60.228 57.895 9.47 6.75 0.00 3.16
544 1369 0.036732 CAACCTCAGCTGCCCAGTTA 59.963 55.000 9.47 0.00 0.00 2.24
545 1370 0.771127 AACCTCAGCTGCCCAGTTAA 59.229 50.000 9.47 0.00 0.00 2.01
546 1371 0.036875 ACCTCAGCTGCCCAGTTAAC 59.963 55.000 9.47 0.00 0.00 2.01
547 1372 1.021390 CCTCAGCTGCCCAGTTAACG 61.021 60.000 9.47 0.00 0.00 3.18
548 1373 1.639298 CTCAGCTGCCCAGTTAACGC 61.639 60.000 9.47 0.00 0.00 4.84
549 1374 1.965930 CAGCTGCCCAGTTAACGCA 60.966 57.895 0.00 6.51 0.00 5.24
550 1375 1.002134 AGCTGCCCAGTTAACGCAT 60.002 52.632 7.05 0.00 0.00 4.73
551 1376 1.026718 AGCTGCCCAGTTAACGCATC 61.027 55.000 7.05 3.95 0.00 3.91
552 1377 1.305219 GCTGCCCAGTTAACGCATCA 61.305 55.000 7.05 1.45 0.00 3.07
553 1378 1.164411 CTGCCCAGTTAACGCATCAA 58.836 50.000 7.05 0.00 0.00 2.57
554 1379 0.878416 TGCCCAGTTAACGCATCAAC 59.122 50.000 0.00 0.00 0.00 3.18
555 1380 0.179200 GCCCAGTTAACGCATCAACG 60.179 55.000 0.00 0.00 39.50 4.10
556 1381 0.179200 CCCAGTTAACGCATCAACGC 60.179 55.000 0.00 0.00 36.19 4.84
557 1382 0.179200 CCAGTTAACGCATCAACGCC 60.179 55.000 0.00 0.00 36.19 5.68
558 1383 0.179200 CAGTTAACGCATCAACGCCC 60.179 55.000 0.00 0.00 36.19 6.13
559 1384 1.135939 GTTAACGCATCAACGCCCC 59.864 57.895 0.00 0.00 36.19 5.80
560 1385 2.392181 TTAACGCATCAACGCCCCG 61.392 57.895 0.00 0.00 36.19 5.73
561 1386 3.592856 TAACGCATCAACGCCCCGT 62.593 57.895 0.00 0.00 43.97 5.28
564 1389 4.778143 GCATCAACGCCCCGTCCT 62.778 66.667 0.00 0.00 39.99 3.85
565 1390 2.511600 CATCAACGCCCCGTCCTC 60.512 66.667 0.00 0.00 39.99 3.71
566 1391 3.782443 ATCAACGCCCCGTCCTCC 61.782 66.667 0.00 0.00 39.99 4.30
568 1393 4.096003 CAACGCCCCGTCCTCCAT 62.096 66.667 0.00 0.00 39.99 3.41
569 1394 3.782443 AACGCCCCGTCCTCCATC 61.782 66.667 0.00 0.00 39.99 3.51
571 1396 4.530857 CGCCCCGTCCTCCATCAC 62.531 72.222 0.00 0.00 0.00 3.06
572 1397 4.176752 GCCCCGTCCTCCATCACC 62.177 72.222 0.00 0.00 0.00 4.02
573 1398 2.365635 CCCCGTCCTCCATCACCT 60.366 66.667 0.00 0.00 0.00 4.00
574 1399 2.435693 CCCCGTCCTCCATCACCTC 61.436 68.421 0.00 0.00 0.00 3.85
575 1400 1.685765 CCCGTCCTCCATCACCTCA 60.686 63.158 0.00 0.00 0.00 3.86
576 1401 1.264749 CCCGTCCTCCATCACCTCAA 61.265 60.000 0.00 0.00 0.00 3.02
577 1402 0.613260 CCGTCCTCCATCACCTCAAA 59.387 55.000 0.00 0.00 0.00 2.69
578 1403 1.210478 CCGTCCTCCATCACCTCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
579 1404 2.356125 CCGTCCTCCATCACCTCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
580 1405 3.347216 CGTCCTCCATCACCTCAAATTT 58.653 45.455 0.00 0.00 0.00 1.82
581 1406 3.758554 CGTCCTCCATCACCTCAAATTTT 59.241 43.478 0.00 0.00 0.00 1.82
582 1407 4.379813 CGTCCTCCATCACCTCAAATTTTG 60.380 45.833 2.59 2.59 0.00 2.44
583 1408 4.524328 GTCCTCCATCACCTCAAATTTTGT 59.476 41.667 8.89 0.00 0.00 2.83
584 1409 5.710099 GTCCTCCATCACCTCAAATTTTGTA 59.290 40.000 8.89 0.00 0.00 2.41
585 1410 5.710099 TCCTCCATCACCTCAAATTTTGTAC 59.290 40.000 8.89 0.00 0.00 2.90
586 1411 5.391950 CCTCCATCACCTCAAATTTTGTACG 60.392 44.000 8.89 1.26 0.00 3.67
587 1412 5.067273 TCCATCACCTCAAATTTTGTACGT 58.933 37.500 8.89 0.00 0.00 3.57
719 1564 0.309922 GTGATGCAATGATGAGGGCG 59.690 55.000 0.00 0.00 0.00 6.13
1023 1878 3.077556 AAGGACATCGAGGCGGCT 61.078 61.111 13.09 13.09 0.00 5.52
1634 2489 3.320256 CCGGTAAGTTATCACCCTCCTAC 59.680 52.174 0.00 0.00 0.00 3.18
1635 2490 4.213513 CGGTAAGTTATCACCCTCCTACT 58.786 47.826 0.00 0.00 0.00 2.57
1636 2491 4.277921 CGGTAAGTTATCACCCTCCTACTC 59.722 50.000 0.00 0.00 0.00 2.59
1688 2544 3.587797 TTGGTCCACGAACTAGTGATC 57.412 47.619 0.00 0.00 44.43 2.92
1690 2546 1.741706 GGTCCACGAACTAGTGATCGA 59.258 52.381 20.78 0.00 44.43 3.59
1692 2548 3.364062 GTCCACGAACTAGTGATCGATG 58.636 50.000 20.78 14.70 44.43 3.84
1693 2549 2.120232 CCACGAACTAGTGATCGATGC 58.880 52.381 20.78 0.00 44.43 3.91
1721 2728 7.309377 GCATGGAAATAGCTAGGCATGATAAAA 60.309 37.037 0.00 0.00 0.00 1.52
1723 2730 6.716628 TGGAAATAGCTAGGCATGATAAAAGG 59.283 38.462 0.00 0.00 0.00 3.11
1726 2733 3.749226 AGCTAGGCATGATAAAAGGAGC 58.251 45.455 0.00 0.00 0.00 4.70
1930 3389 5.212194 CGAAAGTCCAACATGAATTTTCGT 58.788 37.500 0.00 0.00 38.02 3.85
1982 3464 2.426738 CCTTTTCAAGGCGGCATATCAA 59.573 45.455 13.08 0.00 42.78 2.57
1988 3470 5.159273 TCAAGGCGGCATATCAACATATA 57.841 39.130 13.08 0.00 0.00 0.86
1989 3471 5.744171 TCAAGGCGGCATATCAACATATAT 58.256 37.500 13.08 0.00 0.00 0.86
2030 3512 2.237392 TCCTAGCCAGCTCTCCTTTTTC 59.763 50.000 0.00 0.00 0.00 2.29
2031 3513 2.238395 CCTAGCCAGCTCTCCTTTTTCT 59.762 50.000 0.00 0.00 0.00 2.52
2034 3516 1.067985 GCCAGCTCTCCTTTTTCTTGC 60.068 52.381 0.00 0.00 0.00 4.01
2035 3517 2.233271 CCAGCTCTCCTTTTTCTTGCA 58.767 47.619 0.00 0.00 0.00 4.08
2036 3518 2.824341 CCAGCTCTCCTTTTTCTTGCAT 59.176 45.455 0.00 0.00 0.00 3.96
2038 3520 4.142513 CCAGCTCTCCTTTTTCTTGCATAC 60.143 45.833 0.00 0.00 0.00 2.39
2039 3521 4.456911 CAGCTCTCCTTTTTCTTGCATACA 59.543 41.667 0.00 0.00 0.00 2.29
2042 3524 6.886459 AGCTCTCCTTTTTCTTGCATACATAA 59.114 34.615 0.00 0.00 0.00 1.90
2056 4141 8.518430 TTGCATACATAATTTGTAGATGGTGT 57.482 30.769 0.00 0.00 43.87 4.16
2074 4159 8.540388 AGATGGTGTTGAATTAAGCTAGAGTTA 58.460 33.333 0.00 0.00 0.00 2.24
2104 4205 6.560003 TGAGAAGTGGCTAAATAGATGGAA 57.440 37.500 0.00 0.00 0.00 3.53
2280 4381 1.065998 ACCACGTATGTACCGCCATTT 60.066 47.619 0.00 0.00 0.00 2.32
2281 4382 1.329292 CCACGTATGTACCGCCATTTG 59.671 52.381 0.00 0.00 0.00 2.32
2287 4388 3.662726 TACCGCCATTTGCCCCCA 61.663 61.111 0.00 0.00 36.24 4.96
2288 4389 3.002620 TACCGCCATTTGCCCCCAT 62.003 57.895 0.00 0.00 36.24 4.00
2289 4390 3.852307 CCGCCATTTGCCCCCATG 61.852 66.667 0.00 0.00 36.24 3.66
2376 4941 7.221067 GTCACAATCACCTCGAAGACTATTAAG 59.779 40.741 0.00 0.00 0.00 1.85
2424 4989 1.202758 TGTGTGGTGTTCCTCATCCAC 60.203 52.381 6.28 6.28 42.68 4.02
2464 5031 4.720090 ACTGTATATCTTATCGAACGGCG 58.280 43.478 4.80 4.80 42.69 6.46
2564 5172 4.960469 TGGTATTCCTCGTCCATAAGTTCT 59.040 41.667 0.00 0.00 34.23 3.01
2565 5173 5.424252 TGGTATTCCTCGTCCATAAGTTCTT 59.576 40.000 0.00 0.00 34.23 2.52
2566 5174 5.984323 GGTATTCCTCGTCCATAAGTTCTTC 59.016 44.000 0.00 0.00 0.00 2.87
2567 5175 5.941555 ATTCCTCGTCCATAAGTTCTTCT 57.058 39.130 0.00 0.00 0.00 2.85
2568 5176 5.740290 TTCCTCGTCCATAAGTTCTTCTT 57.260 39.130 0.00 0.00 39.89 2.52
2569 5177 5.326200 TCCTCGTCCATAAGTTCTTCTTC 57.674 43.478 0.00 0.00 37.56 2.87
2570 5178 5.017490 TCCTCGTCCATAAGTTCTTCTTCT 58.983 41.667 0.00 0.00 37.56 2.85
2571 5179 5.480772 TCCTCGTCCATAAGTTCTTCTTCTT 59.519 40.000 0.00 0.00 37.56 2.52
2572 5180 6.014499 TCCTCGTCCATAAGTTCTTCTTCTTT 60.014 38.462 0.00 0.00 37.56 2.52
2573 5181 6.651225 CCTCGTCCATAAGTTCTTCTTCTTTT 59.349 38.462 0.00 0.00 37.56 2.27
2574 5182 7.173390 CCTCGTCCATAAGTTCTTCTTCTTTTT 59.827 37.037 0.00 0.00 37.56 1.94
2619 5227 8.296713 GTCCATAAGTTCAAAAGTAGCAATCAA 58.703 33.333 0.00 0.00 0.00 2.57
2621 5229 8.915654 CCATAAGTTCAAAAGTAGCAATCAAAC 58.084 33.333 0.00 0.00 0.00 2.93
2646 5255 3.278574 TGAGCAGGTCGATTATTTTGGG 58.721 45.455 0.00 0.00 0.00 4.12
2727 5348 9.811655 GATTAGCCTTGAAGTTTTTATTTTTGC 57.188 29.630 0.00 0.00 0.00 3.68
2747 5368 3.996363 TGCACACTCTTGTAGCTTATGTG 59.004 43.478 0.00 0.00 39.13 3.21
2751 5372 5.230942 ACACTCTTGTAGCTTATGTGTGAC 58.769 41.667 17.58 0.49 36.10 3.67
2759 5380 6.872920 TGTAGCTTATGTGTGACATGACATA 58.127 36.000 0.00 0.00 39.53 2.29
2774 5397 8.355913 TGACATGACATATGCAAACAAAACTAA 58.644 29.630 1.58 0.00 0.00 2.24
2808 5431 1.038130 ACGCTGCCTAATCTCGTCCT 61.038 55.000 0.00 0.00 0.00 3.85
2822 5445 2.607750 TCCTGCTCCCACTCCCAC 60.608 66.667 0.00 0.00 0.00 4.61
2848 5471 0.106918 TCCAACCACGCCAGAAACTT 60.107 50.000 0.00 0.00 0.00 2.66
2850 5473 1.535860 CCAACCACGCCAGAAACTTTG 60.536 52.381 0.00 0.00 0.00 2.77
2854 5479 1.069227 CCACGCCAGAAACTTTGCTAC 60.069 52.381 0.00 0.00 0.00 3.58
2856 5487 1.234821 CGCCAGAAACTTTGCTACCA 58.765 50.000 0.00 0.00 0.00 3.25
2868 5499 5.488341 ACTTTGCTACCACTAATGTACCTG 58.512 41.667 0.00 0.00 0.00 4.00
2873 5504 5.953548 TGCTACCACTAATGTACCTGACTAA 59.046 40.000 0.00 0.00 0.00 2.24
2874 5505 6.096423 TGCTACCACTAATGTACCTGACTAAG 59.904 42.308 0.00 0.00 0.00 2.18
2876 5507 6.930068 ACCACTAATGTACCTGACTAAGTT 57.070 37.500 0.00 0.00 0.00 2.66
2878 5509 8.064336 ACCACTAATGTACCTGACTAAGTTAG 57.936 38.462 8.41 8.41 0.00 2.34
2879 5510 7.673082 ACCACTAATGTACCTGACTAAGTTAGT 59.327 37.037 15.48 15.48 42.86 2.24
2909 5541 3.873910 AGTTCTACATACACATGCCCAC 58.126 45.455 0.00 0.00 35.39 4.61
2912 5544 2.837591 TCTACATACACATGCCCACAGT 59.162 45.455 0.00 0.00 35.39 3.55
2919 5551 2.235898 ACACATGCCCACAGTTTTTGTT 59.764 40.909 0.00 0.00 38.16 2.83
2935 5567 6.096846 AGTTTTTGTTGAGAGTGCAATTAGGT 59.903 34.615 0.00 0.00 0.00 3.08
2938 5570 2.749621 GTTGAGAGTGCAATTAGGTGGG 59.250 50.000 0.00 0.00 0.00 4.61
2942 5574 4.263905 TGAGAGTGCAATTAGGTGGGAATT 60.264 41.667 0.00 0.00 0.00 2.17
2943 5575 5.045213 TGAGAGTGCAATTAGGTGGGAATTA 60.045 40.000 0.00 0.00 0.00 1.40
2944 5576 5.440610 AGAGTGCAATTAGGTGGGAATTAG 58.559 41.667 0.00 0.00 0.00 1.73
2945 5577 5.044846 AGAGTGCAATTAGGTGGGAATTAGT 60.045 40.000 0.00 0.00 0.00 2.24
2946 5578 6.157994 AGAGTGCAATTAGGTGGGAATTAGTA 59.842 38.462 0.00 0.00 0.00 1.82
2947 5579 6.120220 AGTGCAATTAGGTGGGAATTAGTAC 58.880 40.000 0.00 0.00 0.00 2.73
2971 5603 8.503458 ACTAATTCAAATTCCTCTGAGACATG 57.497 34.615 6.17 0.00 0.00 3.21
3100 5732 2.049433 ACCAAGTTCGGCTCGTCG 60.049 61.111 0.00 0.00 0.00 5.12
3289 5921 0.644843 CGCGTTTGCTGCTTGTTTTT 59.355 45.000 0.00 0.00 39.65 1.94
3306 5938 4.022589 TGTTTTTCTCTACCGATCGAGTGT 60.023 41.667 18.66 8.79 0.00 3.55
3307 5939 3.759527 TTTCTCTACCGATCGAGTGTG 57.240 47.619 18.66 10.18 0.00 3.82
3308 5940 1.015109 TCTCTACCGATCGAGTGTGC 58.985 55.000 18.66 0.00 0.00 4.57
3309 5941 0.316278 CTCTACCGATCGAGTGTGCG 60.316 60.000 18.66 0.00 0.00 5.34
3310 5942 1.022982 TCTACCGATCGAGTGTGCGT 61.023 55.000 18.66 6.42 0.00 5.24
3311 5943 0.589229 CTACCGATCGAGTGTGCGTC 60.589 60.000 18.66 0.00 0.00 5.19
3485 6118 7.370836 GCATGTTTCGTCGAAATCACTAATTAG 59.629 37.037 22.28 11.05 33.97 1.73
3511 6144 2.906354 ACTCGTTGCAAAGAACACTCT 58.094 42.857 15.91 0.00 0.00 3.24
3695 6329 7.505923 TCGAGATCTTCAAAACTAGATCCCATA 59.494 37.037 0.00 0.00 38.24 2.74
3843 6480 0.041312 CGTGGAAGCAAAACCGTGAG 60.041 55.000 0.00 0.00 0.00 3.51
3900 6540 0.991920 TCCCTTTCCGAAAGAGGCAT 59.008 50.000 20.43 0.00 41.02 4.40
4114 6761 4.707934 ACGAGTTTTCTTTTTCCCTTTCCA 59.292 37.500 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 0.749454 ATTTGCATGCCGGGAGACTC 60.749 55.000 16.68 0.00 0.00 3.36
131 132 3.755628 TACGCGGCTGGTCCAGAC 61.756 66.667 23.77 19.83 35.89 3.51
142 143 0.437295 GTGTAACAAGCTGTACGCGG 59.563 55.000 12.47 0.00 39.77 6.46
279 316 3.472652 ACGAACACCTGCTTAATCAACA 58.527 40.909 0.00 0.00 0.00 3.33
281 318 5.178623 CACTAACGAACACCTGCTTAATCAA 59.821 40.000 0.00 0.00 0.00 2.57
293 330 1.672145 GGGCTCTCCACTAACGAACAC 60.672 57.143 0.00 0.00 35.00 3.32
299 336 1.255667 TGTCCGGGCTCTCCACTAAC 61.256 60.000 7.97 0.00 34.36 2.34
314 351 5.731599 TTTTGCATTGTTGACATTTGTCC 57.268 34.783 8.16 0.00 44.15 4.02
331 368 0.235404 CACTTGGCGCCAAATTTTGC 59.765 50.000 38.96 5.37 35.33 3.68
406 601 1.453235 AGCTTTGCCTGCTGAGTGA 59.547 52.632 0.00 0.00 39.56 3.41
463 1288 8.541899 TTAGTTCTTGGGTTGGTCTTATTTTT 57.458 30.769 0.00 0.00 0.00 1.94
465 1290 7.396339 GGATTAGTTCTTGGGTTGGTCTTATTT 59.604 37.037 0.00 0.00 0.00 1.40
466 1291 6.890268 GGATTAGTTCTTGGGTTGGTCTTATT 59.110 38.462 0.00 0.00 0.00 1.40
467 1292 6.217693 AGGATTAGTTCTTGGGTTGGTCTTAT 59.782 38.462 0.00 0.00 0.00 1.73
468 1293 5.550403 AGGATTAGTTCTTGGGTTGGTCTTA 59.450 40.000 0.00 0.00 0.00 2.10
469 1294 4.354087 AGGATTAGTTCTTGGGTTGGTCTT 59.646 41.667 0.00 0.00 0.00 3.01
470 1295 3.916989 AGGATTAGTTCTTGGGTTGGTCT 59.083 43.478 0.00 0.00 0.00 3.85
471 1296 4.010349 CAGGATTAGTTCTTGGGTTGGTC 58.990 47.826 0.00 0.00 0.00 4.02
472 1297 3.655777 TCAGGATTAGTTCTTGGGTTGGT 59.344 43.478 0.00 0.00 32.47 3.67
473 1298 4.265073 CTCAGGATTAGTTCTTGGGTTGG 58.735 47.826 0.00 0.00 32.47 3.77
474 1299 3.691609 GCTCAGGATTAGTTCTTGGGTTG 59.308 47.826 0.00 0.00 34.44 3.77
475 1300 3.589288 AGCTCAGGATTAGTTCTTGGGTT 59.411 43.478 0.00 0.00 34.44 4.11
476 1301 3.185455 AGCTCAGGATTAGTTCTTGGGT 58.815 45.455 0.00 0.00 34.44 4.51
477 1302 3.922171 AGCTCAGGATTAGTTCTTGGG 57.078 47.619 0.00 0.00 35.06 4.12
490 1315 3.882541 CGAGTTCGAGTCCTAGCTCAGG 61.883 59.091 0.00 0.00 43.58 3.86
491 1316 1.329292 CGAGTTCGAGTCCTAGCTCAG 59.671 57.143 0.00 0.00 43.02 3.35
492 1317 1.370609 CGAGTTCGAGTCCTAGCTCA 58.629 55.000 0.00 0.00 43.02 4.26
493 1318 0.658897 CCGAGTTCGAGTCCTAGCTC 59.341 60.000 2.59 0.00 43.02 4.09
494 1319 0.748729 CCCGAGTTCGAGTCCTAGCT 60.749 60.000 2.59 0.00 43.02 3.32
495 1320 1.031029 ACCCGAGTTCGAGTCCTAGC 61.031 60.000 2.59 0.00 43.02 3.42
496 1321 0.733729 CACCCGAGTTCGAGTCCTAG 59.266 60.000 2.59 0.00 43.02 3.02
497 1322 0.679002 CCACCCGAGTTCGAGTCCTA 60.679 60.000 2.59 0.00 43.02 2.94
498 1323 1.977544 CCACCCGAGTTCGAGTCCT 60.978 63.158 2.59 0.00 43.02 3.85
499 1324 2.572284 CCACCCGAGTTCGAGTCC 59.428 66.667 2.59 0.00 43.02 3.85
500 1325 2.572284 CCCACCCGAGTTCGAGTC 59.428 66.667 2.59 0.00 43.02 3.36
501 1326 3.692406 GCCCACCCGAGTTCGAGT 61.692 66.667 2.59 0.00 43.02 4.18
502 1327 3.358076 GAGCCCACCCGAGTTCGAG 62.358 68.421 2.59 0.00 43.02 4.04
503 1328 3.379445 GAGCCCACCCGAGTTCGA 61.379 66.667 2.59 0.00 43.02 3.71
504 1329 1.672854 TATGAGCCCACCCGAGTTCG 61.673 60.000 0.00 0.00 39.44 3.95
505 1330 0.105039 CTATGAGCCCACCCGAGTTC 59.895 60.000 0.00 0.00 0.00 3.01
506 1331 1.972660 GCTATGAGCCCACCCGAGTT 61.973 60.000 0.00 0.00 34.48 3.01
507 1332 2.435693 GCTATGAGCCCACCCGAGT 61.436 63.158 0.00 0.00 34.48 4.18
508 1333 1.971505 TTGCTATGAGCCCACCCGAG 61.972 60.000 0.00 0.00 41.51 4.63
509 1334 1.992834 TTGCTATGAGCCCACCCGA 60.993 57.895 0.00 0.00 41.51 5.14
510 1335 1.819632 GTTGCTATGAGCCCACCCG 60.820 63.158 0.00 0.00 41.51 5.28
511 1336 1.453928 GGTTGCTATGAGCCCACCC 60.454 63.158 5.87 0.00 41.51 4.61
512 1337 0.464554 GAGGTTGCTATGAGCCCACC 60.465 60.000 8.30 8.30 41.51 4.61
513 1338 0.253044 TGAGGTTGCTATGAGCCCAC 59.747 55.000 0.00 0.00 41.51 4.61
514 1339 0.543277 CTGAGGTTGCTATGAGCCCA 59.457 55.000 0.00 0.00 41.51 5.36
515 1340 0.817229 GCTGAGGTTGCTATGAGCCC 60.817 60.000 0.00 0.00 41.51 5.19
516 1341 0.179936 AGCTGAGGTTGCTATGAGCC 59.820 55.000 0.00 0.00 41.51 4.70
517 1342 1.297664 CAGCTGAGGTTGCTATGAGC 58.702 55.000 8.42 0.00 42.82 4.26
518 1343 1.297664 GCAGCTGAGGTTGCTATGAG 58.702 55.000 20.43 0.00 44.45 2.90
519 1344 0.107508 GGCAGCTGAGGTTGCTATGA 60.108 55.000 20.43 0.00 46.51 2.15
520 1345 1.099879 GGGCAGCTGAGGTTGCTATG 61.100 60.000 20.43 0.00 46.51 2.23
521 1346 1.225704 GGGCAGCTGAGGTTGCTAT 59.774 57.895 20.43 0.00 46.51 2.97
522 1347 2.189191 CTGGGCAGCTGAGGTTGCTA 62.189 60.000 20.43 0.00 46.51 3.49
523 1348 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
524 1349 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
525 1350 0.036732 TAACTGGGCAGCTGAGGTTG 59.963 55.000 20.43 5.27 0.00 3.77
526 1351 0.771127 TTAACTGGGCAGCTGAGGTT 59.229 50.000 20.43 16.69 0.00 3.50
527 1352 0.036875 GTTAACTGGGCAGCTGAGGT 59.963 55.000 20.43 7.37 0.00 3.85
528 1353 1.021390 CGTTAACTGGGCAGCTGAGG 61.021 60.000 20.43 6.01 0.00 3.86
529 1354 1.639298 GCGTTAACTGGGCAGCTGAG 61.639 60.000 20.43 8.80 0.00 3.35
530 1355 1.671054 GCGTTAACTGGGCAGCTGA 60.671 57.895 20.43 0.00 0.00 4.26
531 1356 1.308069 ATGCGTTAACTGGGCAGCTG 61.308 55.000 10.11 10.11 40.44 4.24
532 1357 1.002134 ATGCGTTAACTGGGCAGCT 60.002 52.632 11.46 0.00 40.44 4.24
533 1358 1.305219 TGATGCGTTAACTGGGCAGC 61.305 55.000 13.21 13.21 42.94 5.25
534 1359 1.135689 GTTGATGCGTTAACTGGGCAG 60.136 52.381 11.46 0.00 40.44 4.85
535 1360 0.878416 GTTGATGCGTTAACTGGGCA 59.122 50.000 8.76 8.76 41.48 5.36
536 1361 0.179200 CGTTGATGCGTTAACTGGGC 60.179 55.000 11.34 0.43 0.00 5.36
537 1362 0.179200 GCGTTGATGCGTTAACTGGG 60.179 55.000 11.34 0.00 0.00 4.45
538 1363 0.179200 GGCGTTGATGCGTTAACTGG 60.179 55.000 11.34 0.00 35.06 4.00
539 1364 0.179200 GGGCGTTGATGCGTTAACTG 60.179 55.000 11.34 6.55 35.06 3.16
540 1365 1.303091 GGGGCGTTGATGCGTTAACT 61.303 55.000 11.34 0.00 35.06 2.24
541 1366 1.135939 GGGGCGTTGATGCGTTAAC 59.864 57.895 3.54 3.54 35.06 2.01
542 1367 2.392181 CGGGGCGTTGATGCGTTAA 61.392 57.895 0.00 0.00 35.06 2.01
543 1368 2.816083 CGGGGCGTTGATGCGTTA 60.816 61.111 0.00 0.00 35.06 3.18
547 1372 4.778143 AGGACGGGGCGTTGATGC 62.778 66.667 0.00 0.00 41.37 3.91
548 1373 2.511600 GAGGACGGGGCGTTGATG 60.512 66.667 0.00 0.00 41.37 3.07
549 1374 3.782443 GGAGGACGGGGCGTTGAT 61.782 66.667 0.00 0.00 41.37 2.57
551 1376 4.096003 ATGGAGGACGGGGCGTTG 62.096 66.667 0.00 0.00 41.37 4.10
552 1377 3.782443 GATGGAGGACGGGGCGTT 61.782 66.667 0.00 0.00 41.37 4.84
554 1379 4.530857 GTGATGGAGGACGGGGCG 62.531 72.222 0.00 0.00 0.00 6.13
555 1380 4.176752 GGTGATGGAGGACGGGGC 62.177 72.222 0.00 0.00 0.00 5.80
556 1381 2.365635 AGGTGATGGAGGACGGGG 60.366 66.667 0.00 0.00 0.00 5.73
557 1382 1.264749 TTGAGGTGATGGAGGACGGG 61.265 60.000 0.00 0.00 0.00 5.28
558 1383 0.613260 TTTGAGGTGATGGAGGACGG 59.387 55.000 0.00 0.00 0.00 4.79
559 1384 2.698855 ATTTGAGGTGATGGAGGACG 57.301 50.000 0.00 0.00 0.00 4.79
560 1385 4.524328 ACAAAATTTGAGGTGATGGAGGAC 59.476 41.667 13.19 0.00 0.00 3.85
561 1386 4.739793 ACAAAATTTGAGGTGATGGAGGA 58.260 39.130 13.19 0.00 0.00 3.71
562 1387 5.391950 CGTACAAAATTTGAGGTGATGGAGG 60.392 44.000 13.19 0.00 0.00 4.30
563 1388 5.181245 ACGTACAAAATTTGAGGTGATGGAG 59.819 40.000 13.19 0.00 0.00 3.86
564 1389 5.049060 CACGTACAAAATTTGAGGTGATGGA 60.049 40.000 13.19 0.00 33.03 3.41
565 1390 5.153513 CACGTACAAAATTTGAGGTGATGG 58.846 41.667 13.19 0.00 33.03 3.51
566 1391 5.049060 TCCACGTACAAAATTTGAGGTGATG 60.049 40.000 21.00 12.17 33.03 3.07
567 1392 5.067273 TCCACGTACAAAATTTGAGGTGAT 58.933 37.500 21.00 2.49 33.03 3.06
568 1393 4.452825 TCCACGTACAAAATTTGAGGTGA 58.547 39.130 21.00 11.56 33.03 4.02
569 1394 4.822036 TCCACGTACAAAATTTGAGGTG 57.178 40.909 13.19 15.32 32.07 4.00
570 1395 5.768164 AGAATCCACGTACAAAATTTGAGGT 59.232 36.000 13.19 5.40 0.00 3.85
571 1396 6.086222 CAGAATCCACGTACAAAATTTGAGG 58.914 40.000 13.19 6.22 0.00 3.86
572 1397 6.668323 ACAGAATCCACGTACAAAATTTGAG 58.332 36.000 13.19 5.98 0.00 3.02
573 1398 6.627395 ACAGAATCCACGTACAAAATTTGA 57.373 33.333 13.19 0.00 0.00 2.69
574 1399 6.518395 CGTACAGAATCCACGTACAAAATTTG 59.482 38.462 3.89 3.89 36.18 2.32
575 1400 6.203338 ACGTACAGAATCCACGTACAAAATTT 59.797 34.615 3.92 0.00 46.23 1.82
576 1401 5.697633 ACGTACAGAATCCACGTACAAAATT 59.302 36.000 3.92 0.00 46.23 1.82
577 1402 5.119588 CACGTACAGAATCCACGTACAAAAT 59.880 40.000 5.24 0.00 46.34 1.82
578 1403 4.445052 CACGTACAGAATCCACGTACAAAA 59.555 41.667 5.24 0.00 46.34 2.44
579 1404 3.982701 CACGTACAGAATCCACGTACAAA 59.017 43.478 5.24 0.00 46.34 2.83
580 1405 3.567530 CACGTACAGAATCCACGTACAA 58.432 45.455 5.24 0.00 46.34 2.41
581 1406 2.669113 GCACGTACAGAATCCACGTACA 60.669 50.000 5.24 0.00 46.34 2.90
582 1407 1.916000 GCACGTACAGAATCCACGTAC 59.084 52.381 5.24 1.28 46.34 3.67
583 1408 1.540707 TGCACGTACAGAATCCACGTA 59.459 47.619 5.24 0.00 46.34 3.57
585 1410 1.640428 ATGCACGTACAGAATCCACG 58.360 50.000 0.00 0.00 41.32 4.94
586 1411 3.000041 TGAATGCACGTACAGAATCCAC 59.000 45.455 0.00 0.00 0.00 4.02
587 1412 3.000041 GTGAATGCACGTACAGAATCCA 59.000 45.455 0.00 0.00 34.94 3.41
719 1564 1.465794 TATAAACTTTGCCGCCCACC 58.534 50.000 0.00 0.00 0.00 4.61
946 1798 4.866224 TGTGTGTGGTGGTGCCCG 62.866 66.667 0.00 0.00 36.04 6.13
997 1852 3.425422 GATGTCCTTGGCCATCGC 58.575 61.111 6.09 0.00 0.00 4.58
1634 2489 1.078918 TTGGACGCATGCTGAGGAG 60.079 57.895 17.13 0.80 0.00 3.69
1635 2490 1.375908 GTTGGACGCATGCTGAGGA 60.376 57.895 17.13 0.00 0.00 3.71
1636 2491 1.376424 AGTTGGACGCATGCTGAGG 60.376 57.895 17.13 2.03 0.00 3.86
1688 2544 1.878088 AGCTATTTCCATGCAGCATCG 59.122 47.619 4.38 0.00 36.47 3.84
1690 2546 3.418995 CCTAGCTATTTCCATGCAGCAT 58.581 45.455 0.52 0.52 36.47 3.79
1692 2548 1.538950 GCCTAGCTATTTCCATGCAGC 59.461 52.381 0.00 0.00 0.00 5.25
1693 2549 2.854963 TGCCTAGCTATTTCCATGCAG 58.145 47.619 0.00 0.00 0.00 4.41
1723 2730 3.692593 GGTAGAGAATATCCGGAGAGCTC 59.307 52.174 18.86 18.86 0.00 4.09
1817 3229 6.379386 CCAGTTGCTGCATATAATGAATCAG 58.621 40.000 1.84 0.00 0.00 2.90
1982 3464 9.383519 AGAAGACGTGAATGTTTTCATATATGT 57.616 29.630 12.42 0.00 43.49 2.29
1988 3470 5.765182 AGGAAGAAGACGTGAATGTTTTCAT 59.235 36.000 0.00 0.00 43.49 2.57
1989 3471 5.123227 AGGAAGAAGACGTGAATGTTTTCA 58.877 37.500 0.00 0.00 39.54 2.69
2001 3483 0.820871 AGCTGGCTAGGAAGAAGACG 59.179 55.000 0.00 0.00 0.00 4.18
2030 3512 8.623903 ACACCATCTACAAATTATGTATGCAAG 58.376 33.333 0.00 0.00 43.42 4.01
2031 3513 8.518430 ACACCATCTACAAATTATGTATGCAA 57.482 30.769 0.00 0.00 43.42 4.08
2042 3524 8.353423 AGCTTAATTCAACACCATCTACAAAT 57.647 30.769 0.00 0.00 0.00 2.32
2048 4130 6.951971 ACTCTAGCTTAATTCAACACCATCT 58.048 36.000 0.00 0.00 0.00 2.90
2049 4131 7.617041 AACTCTAGCTTAATTCAACACCATC 57.383 36.000 0.00 0.00 0.00 3.51
2074 4159 9.638176 ATCTATTTAGCCACTTCTCAATGATTT 57.362 29.630 0.00 0.00 0.00 2.17
2104 4205 4.261741 GCACCTGAACAATTCATCACAACT 60.262 41.667 0.00 0.00 39.30 3.16
2281 4382 2.523412 AGATGCATGCATGGGGGC 60.523 61.111 36.73 21.46 36.70 5.80
2464 5031 7.751768 AATAAAGTTATCCTGGCTATCTTGC 57.248 36.000 2.55 0.00 0.00 4.01
2474 5041 8.137437 CAGCATGGGTTTAATAAAGTTATCCTG 58.863 37.037 0.00 0.00 0.00 3.86
2577 5185 1.598685 GACGAGGTCCCCGCAAAAA 60.599 57.895 0.00 0.00 0.00 1.94
2578 5186 2.031465 GACGAGGTCCCCGCAAAA 59.969 61.111 0.00 0.00 0.00 2.44
2579 5187 4.011517 GGACGAGGTCCCCGCAAA 62.012 66.667 3.36 0.00 46.19 3.68
2587 5195 4.995487 ACTTTTGAACTTATGGACGAGGTC 59.005 41.667 0.00 0.00 0.00 3.85
2588 5196 4.969484 ACTTTTGAACTTATGGACGAGGT 58.031 39.130 0.00 0.00 0.00 3.85
2589 5197 5.063564 GCTACTTTTGAACTTATGGACGAGG 59.936 44.000 0.00 0.00 0.00 4.63
2590 5198 5.637810 TGCTACTTTTGAACTTATGGACGAG 59.362 40.000 0.00 0.00 0.00 4.18
2591 5199 5.543714 TGCTACTTTTGAACTTATGGACGA 58.456 37.500 0.00 0.00 0.00 4.20
2592 5200 5.856126 TGCTACTTTTGAACTTATGGACG 57.144 39.130 0.00 0.00 0.00 4.79
2593 5201 7.816640 TGATTGCTACTTTTGAACTTATGGAC 58.183 34.615 0.00 0.00 0.00 4.02
2594 5202 7.994425 TGATTGCTACTTTTGAACTTATGGA 57.006 32.000 0.00 0.00 0.00 3.41
2595 5203 8.915654 GTTTGATTGCTACTTTTGAACTTATGG 58.084 33.333 0.00 0.00 0.00 2.74
2596 5204 8.915654 GGTTTGATTGCTACTTTTGAACTTATG 58.084 33.333 0.00 0.00 0.00 1.90
2597 5205 7.807907 CGGTTTGATTGCTACTTTTGAACTTAT 59.192 33.333 0.00 0.00 0.00 1.73
2598 5206 7.136119 CGGTTTGATTGCTACTTTTGAACTTA 58.864 34.615 0.00 0.00 0.00 2.24
2599 5207 5.977129 CGGTTTGATTGCTACTTTTGAACTT 59.023 36.000 0.00 0.00 0.00 2.66
2600 5208 5.519722 CGGTTTGATTGCTACTTTTGAACT 58.480 37.500 0.00 0.00 0.00 3.01
2601 5209 4.148174 GCGGTTTGATTGCTACTTTTGAAC 59.852 41.667 0.00 0.00 0.00 3.18
2602 5210 4.037446 AGCGGTTTGATTGCTACTTTTGAA 59.963 37.500 0.00 0.00 37.15 2.69
2603 5211 3.568007 AGCGGTTTGATTGCTACTTTTGA 59.432 39.130 0.00 0.00 37.15 2.69
2604 5212 3.670055 CAGCGGTTTGATTGCTACTTTTG 59.330 43.478 0.00 0.00 37.15 2.44
2619 5227 2.172483 AATCGACCTGCTCAGCGGTT 62.172 55.000 13.42 0.00 36.12 4.44
2621 5229 0.032678 ATAATCGACCTGCTCAGCGG 59.967 55.000 0.00 0.00 34.23 5.52
2646 5255 1.148498 CCTTATCCCGGGTCCTTGC 59.852 63.158 22.86 0.00 0.00 4.01
2727 5348 5.521516 CACACATAAGCTACAAGAGTGTG 57.478 43.478 15.43 15.43 45.95 3.82
2747 5368 6.642131 AGTTTTGTTTGCATATGTCATGTCAC 59.358 34.615 4.29 0.00 0.00 3.67
2774 5397 1.238439 AGCGTGTACTGCTGCAAAAT 58.762 45.000 11.61 0.00 42.14 1.82
2808 5431 1.612442 GTAGGTGGGAGTGGGAGCA 60.612 63.158 0.00 0.00 0.00 4.26
2822 5445 1.451387 GGCGTGGTTGGATGGTAGG 60.451 63.158 0.00 0.00 0.00 3.18
2848 5471 4.775780 AGTCAGGTACATTAGTGGTAGCAA 59.224 41.667 0.00 0.00 40.67 3.91
2850 5473 6.096564 ACTTAGTCAGGTACATTAGTGGTAGC 59.903 42.308 0.00 0.00 39.01 3.58
2854 5479 8.064336 ACTAACTTAGTCAGGTACATTAGTGG 57.936 38.462 0.00 0.00 32.47 4.00
2878 5509 9.885934 CATGTGTATGTAGAACTAGATAGTGAC 57.114 37.037 0.00 0.00 36.50 3.67
2879 5510 8.568794 GCATGTGTATGTAGAACTAGATAGTGA 58.431 37.037 0.00 0.00 35.22 3.41
2880 5511 7.810282 GGCATGTGTATGTAGAACTAGATAGTG 59.190 40.741 0.00 0.00 35.22 2.74
2881 5512 7.039644 GGGCATGTGTATGTAGAACTAGATAGT 60.040 40.741 0.00 0.00 35.94 2.12
2888 5520 3.263170 TGTGGGCATGTGTATGTAGAACT 59.737 43.478 0.00 0.00 36.65 3.01
2901 5533 3.125316 CTCAACAAAAACTGTGGGCATG 58.875 45.455 0.00 0.00 38.67 4.06
2909 5541 6.418819 CCTAATTGCACTCTCAACAAAAACTG 59.581 38.462 0.00 0.00 0.00 3.16
2912 5544 6.272318 CACCTAATTGCACTCTCAACAAAAA 58.728 36.000 0.00 0.00 0.00 1.94
2919 5551 2.265367 TCCCACCTAATTGCACTCTCA 58.735 47.619 0.00 0.00 0.00 3.27
2943 5575 8.816894 TGTCTCAGAGGAATTTGAATTAGTACT 58.183 33.333 0.00 0.00 0.00 2.73
2944 5576 9.606631 ATGTCTCAGAGGAATTTGAATTAGTAC 57.393 33.333 0.00 0.00 0.00 2.73
2945 5577 9.605275 CATGTCTCAGAGGAATTTGAATTAGTA 57.395 33.333 0.00 0.00 0.00 1.82
2946 5578 8.105829 ACATGTCTCAGAGGAATTTGAATTAGT 58.894 33.333 0.00 0.00 0.00 2.24
2947 5579 8.503458 ACATGTCTCAGAGGAATTTGAATTAG 57.497 34.615 0.00 0.00 0.00 1.73
2971 5603 4.448537 TGGCCACAAATGTAAGCATAAC 57.551 40.909 0.00 0.00 34.39 1.89
3115 5747 3.646976 CGGCCGTCGATCTAGCGA 61.647 66.667 19.50 0.00 42.43 4.93
3289 5921 1.015109 GCACACTCGATCGGTAGAGA 58.985 55.000 16.41 0.00 37.87 3.10
3306 5938 1.335810 ACACTAACGAAGACAGACGCA 59.664 47.619 0.00 0.00 0.00 5.24
3307 5939 2.047679 ACACTAACGAAGACAGACGC 57.952 50.000 0.00 0.00 0.00 5.19
3308 5940 3.361724 GCAAACACTAACGAAGACAGACG 60.362 47.826 0.00 0.00 0.00 4.18
3309 5941 3.802685 AGCAAACACTAACGAAGACAGAC 59.197 43.478 0.00 0.00 0.00 3.51
3310 5942 4.054780 AGCAAACACTAACGAAGACAGA 57.945 40.909 0.00 0.00 0.00 3.41
3311 5943 4.318831 GGAAGCAAACACTAACGAAGACAG 60.319 45.833 0.00 0.00 0.00 3.51
3485 6118 2.450609 TCTTTGCAACGAGTACTCCC 57.549 50.000 17.23 4.21 0.00 4.30
3511 6144 2.225382 TGTCGTGACCTGGGAAGATA 57.775 50.000 0.00 0.00 0.00 1.98
3585 6219 9.719279 AAACGTTTTGAATAAACAAATCTACGA 57.281 25.926 7.96 0.00 40.60 3.43
4050 6694 1.597663 CGAGAGTCACGGTTTTGCTTT 59.402 47.619 1.62 0.00 0.00 3.51
4094 6740 6.867519 TCTTGGAAAGGGAAAAAGAAAACT 57.132 33.333 0.00 0.00 46.24 2.66


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

AutoCloner maintained by Alex Coulton.