Multiple sequence alignment - TraesCS1D01G172400

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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 TraesCS1D01G172400 chr1D 100.000 3221 0 0 1 3221 246104932 246108152 0.000000e+00 5949.0
1 TraesCS1D01G172400 chr1D 91.209 182 10 5 631 806 41446426 41446245 3.210000e-60 243.0
2 TraesCS1D01G172400 chr1D 82.927 164 27 1 2495 2658 296543692 296543530 2.590000e-31 147.0
3 TraesCS1D01G172400 chr1A 92.825 1561 81 11 815 2353 307060298 307061849 0.000000e+00 2233.0
4 TraesCS1D01G172400 chr1A 92.135 178 14 0 632 809 298903920 298903743 5.330000e-63 252.0
5 TraesCS1D01G172400 chr1A 91.925 161 11 2 452 611 307060128 307060287 1.160000e-54 224.0
6 TraesCS1D01G172400 chr1A 81.230 309 25 15 2 309 307046865 307047141 5.410000e-53 219.0
7 TraesCS1D01G172400 chr1A 98.507 67 1 0 2422 2488 307061832 307061898 5.640000e-23 119.0
8 TraesCS1D01G172400 chr1A 96.364 55 1 1 2351 2404 15063812 15063758 4.430000e-14 89.8
9 TraesCS1D01G172400 chr1A 96.296 54 1 1 2352 2404 15011604 15011551 1.590000e-13 87.9
10 TraesCS1D01G172400 chr1A 94.444 54 2 1 2352 2404 15107550 15107497 7.410000e-12 82.4
11 TraesCS1D01G172400 chr1B 92.156 1517 81 16 807 2313 332073944 332072456 0.000000e+00 2108.0
12 TraesCS1D01G172400 chr1B 90.984 244 17 4 120 359 332074437 332074195 1.110000e-84 324.0
13 TraesCS1D01G172400 chr1B 94.475 181 8 2 452 631 332074114 332073935 8.800000e-71 278.0
14 TraesCS1D01G172400 chr1B 83.425 181 29 1 2489 2668 407901329 407901509 1.990000e-37 167.0
15 TraesCS1D01G172400 chr1B 89.516 124 13 0 2 125 332075600 332075477 1.200000e-34 158.0
16 TraesCS1D01G172400 chr1B 79.191 173 34 1 225 397 418054083 418053913 5.640000e-23 119.0
17 TraesCS1D01G172400 chr1B 94.030 67 4 0 2422 2488 332072415 332072349 5.680000e-18 102.0
18 TraesCS1D01G172400 chr5D 99.862 727 1 0 2495 3221 220706256 220706982 0.000000e+00 1338.0
19 TraesCS1D01G172400 chr5D 83.429 175 26 2 223 397 510907229 510907400 3.330000e-35 159.0
20 TraesCS1D01G172400 chr5D 90.217 92 9 0 2490 2581 220707524 220707433 1.570000e-23 121.0
21 TraesCS1D01G172400 chr2B 90.773 737 59 8 2490 3221 620646174 620645442 0.000000e+00 976.0
22 TraesCS1D01G172400 chr2B 98.077 52 0 1 2354 2404 37815745 37815796 4.430000e-14 89.8
23 TraesCS1D01G172400 chr2D 92.896 183 10 3 627 806 409579184 409579366 2.460000e-66 263.0
24 TraesCS1D01G172400 chr2D 91.713 181 10 5 627 805 636740645 636740468 2.480000e-61 246.0
25 TraesCS1D01G172400 chr2D 91.713 181 10 5 627 805 636887758 636887935 2.480000e-61 246.0
26 TraesCS1D01G172400 chr7D 90.816 196 15 3 621 813 574065510 574065705 3.190000e-65 259.0
27 TraesCS1D01G172400 chr7D 98.113 53 0 1 2353 2404 365389238 365389186 1.230000e-14 91.6
28 TraesCS1D01G172400 chrUn 91.061 179 14 2 630 806 70301794 70301616 1.150000e-59 241.0
29 TraesCS1D01G172400 chr4D 88.060 201 16 7 619 813 54289308 54289110 6.950000e-57 231.0
30 TraesCS1D01G172400 chr3D 87.940 199 20 4 618 812 429728336 429728138 6.950000e-57 231.0
31 TraesCS1D01G172400 chr5B 83.523 176 28 1 2494 2668 642597193 642597368 2.570000e-36 163.0
32 TraesCS1D01G172400 chr5A 82.514 183 31 1 2487 2668 534072724 534072906 3.330000e-35 159.0
33 TraesCS1D01G172400 chr4B 82.320 181 31 1 2495 2674 619367084 619366904 4.300000e-34 156.0
34 TraesCS1D01G172400 chr3A 74.750 400 76 19 2495 2884 607449923 607449539 4.300000e-34 156.0
35 TraesCS1D01G172400 chr3A 87.324 71 4 4 2353 2418 41640052 41639982 3.450000e-10 76.8
36 TraesCS1D01G172400 chr6D 79.096 177 24 10 223 396 389300869 389301035 3.400000e-20 110.0
37 TraesCS1D01G172400 chr6D 96.296 54 0 2 2353 2404 237352456 237352509 1.590000e-13 87.9
38 TraesCS1D01G172400 chr2A 96.154 52 1 1 2354 2404 71386384 71386333 2.060000e-12 84.2
39 TraesCS1D01G172400 chr7B 92.857 56 2 2 2350 2404 251156627 251156681 2.660000e-11 80.5
40 TraesCS1D01G172400 chr7B 75.776 161 22 8 226 382 416441539 416441392 7.460000e-07 65.8


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 TraesCS1D01G172400 chr1D 246104932 246108152 3220 False 5949.000000 5949 100.0000 1 3221 1 chr1D.!!$F1 3220
1 TraesCS1D01G172400 chr1A 307060128 307061898 1770 False 858.666667 2233 94.4190 452 2488 3 chr1A.!!$F2 2036
2 TraesCS1D01G172400 chr1B 332072349 332075600 3251 True 594.000000 2108 92.2322 2 2488 5 chr1B.!!$R2 2486
3 TraesCS1D01G172400 chr5D 220706256 220706982 726 False 1338.000000 1338 99.8620 2495 3221 1 chr5D.!!$F1 726
4 TraesCS1D01G172400 chr2B 620645442 620646174 732 True 976.000000 976 90.7730 2490 3221 1 chr2B.!!$R1 731

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
696 1746 0.032615 AACCTCCCACAAACAAGGCA 60.033 50.0 0.0 0.0 31.79 4.75 F
702 1752 0.175302 CCACAAACAAGGCAGCAACA 59.825 50.0 0.0 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 3201 0.615331 ACTCCATCTTGCCGTCATGT 59.385 50.000 0.0 0.0 0.0 3.21 R
2492 3575 1.066929 GCAAATCCTCAAATTGCCCGT 60.067 47.619 0.0 0.0 42.7 5.28 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
38 39 4.148128 ACAGATCTAATGGTTGCTGAGG 57.852 45.455 0.00 0.00 0.00 3.86
39 40 2.877168 CAGATCTAATGGTTGCTGAGGC 59.123 50.000 0.00 0.00 39.26 4.70
109 110 8.697846 AATCTATAACACAATCTTCGTCGAAA 57.302 30.769 9.30 1.06 0.00 3.46
128 1174 6.018751 GTCGAAAATCTATGCAACATGAGCTA 60.019 38.462 14.16 3.90 0.00 3.32
199 1246 2.770130 GGCCCCCTGAATGAACCA 59.230 61.111 0.00 0.00 0.00 3.67
217 1264 3.926616 ACCAGATCTAACGGTTGTTGAG 58.073 45.455 3.07 0.00 39.12 3.02
234 1281 2.117941 GAGGCCGCGCAACATTATCC 62.118 60.000 8.75 0.00 0.00 2.59
315 1365 8.821147 TTTCTACAACACGAGCTCTATTTTAA 57.179 30.769 12.85 0.00 0.00 1.52
317 1367 8.407457 TCTACAACACGAGCTCTATTTTAATG 57.593 34.615 12.85 2.84 0.00 1.90
359 1409 0.916086 TGCAATAATGAGGACGGGGT 59.084 50.000 0.00 0.00 0.00 4.95
360 1410 1.283613 TGCAATAATGAGGACGGGGTT 59.716 47.619 0.00 0.00 0.00 4.11
361 1411 2.506231 TGCAATAATGAGGACGGGGTTA 59.494 45.455 0.00 0.00 0.00 2.85
362 1412 3.054287 TGCAATAATGAGGACGGGGTTAA 60.054 43.478 0.00 0.00 0.00 2.01
363 1413 3.564225 GCAATAATGAGGACGGGGTTAAG 59.436 47.826 0.00 0.00 0.00 1.85
364 1414 2.994186 TAATGAGGACGGGGTTAAGC 57.006 50.000 0.00 0.00 0.00 3.09
366 1416 0.912487 ATGAGGACGGGGTTAAGCCA 60.912 55.000 24.42 3.07 39.65 4.75
367 1417 1.078637 GAGGACGGGGTTAAGCCAC 60.079 63.158 24.42 14.43 39.65 5.01
368 1418 1.538135 AGGACGGGGTTAAGCCACT 60.538 57.895 24.42 13.48 38.96 4.00
369 1419 1.376812 GGACGGGGTTAAGCCACTG 60.377 63.158 24.42 15.50 38.96 3.66
370 1420 1.376812 GACGGGGTTAAGCCACTGG 60.377 63.158 24.42 12.69 38.96 4.00
372 1422 1.205460 ACGGGGTTAAGCCACTGGAT 61.205 55.000 24.42 0.00 38.96 3.41
373 1423 0.834612 CGGGGTTAAGCCACTGGATA 59.165 55.000 24.42 0.00 38.96 2.59
374 1424 1.202651 CGGGGTTAAGCCACTGGATAG 60.203 57.143 24.42 2.40 38.96 2.08
376 1426 2.158798 GGGGTTAAGCCACTGGATAGAC 60.159 54.545 24.42 0.01 37.78 2.59
377 1427 2.158798 GGGTTAAGCCACTGGATAGACC 60.159 54.545 18.84 4.44 39.65 3.85
378 1428 2.504175 GGTTAAGCCACTGGATAGACCA 59.496 50.000 11.38 0.00 41.08 4.02
388 1438 2.587522 TGGATAGACCAGATCTCACGG 58.412 52.381 0.00 0.00 44.64 4.94
390 1440 2.235016 GATAGACCAGATCTCACGGCT 58.765 52.381 0.00 0.00 39.04 5.52
391 1441 1.393603 TAGACCAGATCTCACGGCTG 58.606 55.000 0.00 0.00 39.04 4.85
393 1443 1.954362 GACCAGATCTCACGGCTGCT 61.954 60.000 0.00 0.00 0.00 4.24
395 1445 1.514553 CAGATCTCACGGCTGCTGA 59.485 57.895 16.72 3.23 0.00 4.26
396 1446 0.528033 CAGATCTCACGGCTGCTGAG 60.528 60.000 16.72 13.68 37.14 3.35
397 1447 0.682532 AGATCTCACGGCTGCTGAGA 60.683 55.000 19.75 19.75 46.39 3.27
399 1449 2.280835 TCTCACGGCTGCTGAGATT 58.719 52.632 16.72 0.00 39.41 2.40
400 1450 1.474330 TCTCACGGCTGCTGAGATTA 58.526 50.000 16.72 1.35 39.41 1.75
401 1451 1.824852 TCTCACGGCTGCTGAGATTAA 59.175 47.619 16.72 0.00 39.41 1.40
402 1452 1.929836 CTCACGGCTGCTGAGATTAAC 59.070 52.381 16.72 0.00 37.90 2.01
403 1453 1.550524 TCACGGCTGCTGAGATTAACT 59.449 47.619 16.72 0.00 0.00 2.24
404 1454 1.662629 CACGGCTGCTGAGATTAACTG 59.337 52.381 16.72 0.00 0.00 3.16
405 1455 0.654683 CGGCTGCTGAGATTAACTGC 59.345 55.000 1.17 0.00 0.00 4.40
406 1456 1.020437 GGCTGCTGAGATTAACTGCC 58.980 55.000 0.00 0.00 39.47 4.85
407 1457 0.654683 GCTGCTGAGATTAACTGCCG 59.345 55.000 0.00 0.00 0.00 5.69
408 1458 1.740380 GCTGCTGAGATTAACTGCCGA 60.740 52.381 0.00 0.00 0.00 5.54
409 1459 1.929836 CTGCTGAGATTAACTGCCGAC 59.070 52.381 0.00 0.00 0.00 4.79
410 1460 0.924090 GCTGAGATTAACTGCCGACG 59.076 55.000 0.00 0.00 0.00 5.12
411 1461 1.469251 GCTGAGATTAACTGCCGACGA 60.469 52.381 0.00 0.00 0.00 4.20
413 1463 1.189403 GAGATTAACTGCCGACGACG 58.811 55.000 0.00 0.00 39.43 5.12
440 1490 5.607858 CGTAGCGCTAAACAAAAACAAAA 57.392 34.783 20.73 0.00 0.00 2.44
442 1492 5.003590 CGTAGCGCTAAACAAAAACAAAACA 59.996 36.000 20.73 0.00 0.00 2.83
443 1493 6.291374 CGTAGCGCTAAACAAAAACAAAACAT 60.291 34.615 20.73 0.00 0.00 2.71
444 1494 6.415798 AGCGCTAAACAAAAACAAAACATT 57.584 29.167 8.99 0.00 0.00 2.71
445 1495 7.527084 AGCGCTAAACAAAAACAAAACATTA 57.473 28.000 8.99 0.00 0.00 1.90
446 1496 7.617557 AGCGCTAAACAAAAACAAAACATTAG 58.382 30.769 8.99 0.00 0.00 1.73
447 1497 6.843779 GCGCTAAACAAAAACAAAACATTAGG 59.156 34.615 0.00 0.00 0.00 2.69
448 1498 7.254151 GCGCTAAACAAAAACAAAACATTAGGA 60.254 33.333 0.00 0.00 0.00 2.94
449 1499 8.053653 CGCTAAACAAAAACAAAACATTAGGAC 58.946 33.333 0.00 0.00 0.00 3.85
450 1500 8.053653 GCTAAACAAAAACAAAACATTAGGACG 58.946 33.333 0.00 0.00 0.00 4.79
451 1501 6.895607 AACAAAAACAAAACATTAGGACGG 57.104 33.333 0.00 0.00 0.00 4.79
452 1502 4.806775 ACAAAAACAAAACATTAGGACGGC 59.193 37.500 0.00 0.00 0.00 5.68
453 1503 3.653539 AAACAAAACATTAGGACGGCC 57.346 42.857 0.00 0.00 0.00 6.13
498 1548 9.965824 AAAATGAAAAGAATTGTATCACGTCTT 57.034 25.926 0.00 0.00 0.00 3.01
560 1610 7.272144 AGGTTAGTGTGAATTTCTTCCCTAT 57.728 36.000 0.00 0.00 0.00 2.57
606 1656 3.536956 TCTCAGCCCCGTAGTTTTATG 57.463 47.619 0.00 0.00 0.00 1.90
655 1705 9.737427 ACAGTTTGTCTAATTCGTATCTAGATG 57.263 33.333 15.79 0.00 0.00 2.90
656 1706 9.737427 CAGTTTGTCTAATTCGTATCTAGATGT 57.263 33.333 15.79 0.00 0.00 3.06
682 1732 8.561738 TTTTTAAGGATGTCACATCTAACCTC 57.438 34.615 17.46 0.00 0.00 3.85
683 1733 4.762289 AAGGATGTCACATCTAACCTCC 57.238 45.455 17.46 0.18 32.24 4.30
684 1734 3.041946 AGGATGTCACATCTAACCTCCC 58.958 50.000 17.46 0.00 32.42 4.30
685 1735 2.771943 GGATGTCACATCTAACCTCCCA 59.228 50.000 17.46 0.00 0.00 4.37
686 1736 3.432326 GGATGTCACATCTAACCTCCCAC 60.432 52.174 17.46 0.00 0.00 4.61
687 1737 2.615391 TGTCACATCTAACCTCCCACA 58.385 47.619 0.00 0.00 0.00 4.17
688 1738 2.976185 TGTCACATCTAACCTCCCACAA 59.024 45.455 0.00 0.00 0.00 3.33
689 1739 3.392947 TGTCACATCTAACCTCCCACAAA 59.607 43.478 0.00 0.00 0.00 2.83
690 1740 3.751698 GTCACATCTAACCTCCCACAAAC 59.248 47.826 0.00 0.00 0.00 2.93
691 1741 3.392947 TCACATCTAACCTCCCACAAACA 59.607 43.478 0.00 0.00 0.00 2.83
692 1742 4.141287 CACATCTAACCTCCCACAAACAA 58.859 43.478 0.00 0.00 0.00 2.83
693 1743 4.216257 CACATCTAACCTCCCACAAACAAG 59.784 45.833 0.00 0.00 0.00 3.16
694 1744 3.502123 TCTAACCTCCCACAAACAAGG 57.498 47.619 0.00 0.00 34.94 3.61
695 1745 1.886542 CTAACCTCCCACAAACAAGGC 59.113 52.381 0.00 0.00 31.79 4.35
696 1746 0.032615 AACCTCCCACAAACAAGGCA 60.033 50.000 0.00 0.00 31.79 4.75
697 1747 0.468029 ACCTCCCACAAACAAGGCAG 60.468 55.000 0.00 0.00 31.79 4.85
698 1748 1.662044 CTCCCACAAACAAGGCAGC 59.338 57.895 0.00 0.00 0.00 5.25
699 1749 1.076412 TCCCACAAACAAGGCAGCA 60.076 52.632 0.00 0.00 0.00 4.41
700 1750 0.685785 TCCCACAAACAAGGCAGCAA 60.686 50.000 0.00 0.00 0.00 3.91
701 1751 0.530431 CCCACAAACAAGGCAGCAAC 60.530 55.000 0.00 0.00 0.00 4.17
702 1752 0.175302 CCACAAACAAGGCAGCAACA 59.825 50.000 0.00 0.00 0.00 3.33
703 1753 1.405256 CCACAAACAAGGCAGCAACAA 60.405 47.619 0.00 0.00 0.00 2.83
704 1754 2.344950 CACAAACAAGGCAGCAACAAA 58.655 42.857 0.00 0.00 0.00 2.83
705 1755 2.349275 CACAAACAAGGCAGCAACAAAG 59.651 45.455 0.00 0.00 0.00 2.77
706 1756 2.233431 ACAAACAAGGCAGCAACAAAGA 59.767 40.909 0.00 0.00 0.00 2.52
707 1757 3.260740 CAAACAAGGCAGCAACAAAGAA 58.739 40.909 0.00 0.00 0.00 2.52
708 1758 2.584492 ACAAGGCAGCAACAAAGAAC 57.416 45.000 0.00 0.00 0.00 3.01
709 1759 1.824230 ACAAGGCAGCAACAAAGAACA 59.176 42.857 0.00 0.00 0.00 3.18
710 1760 2.233431 ACAAGGCAGCAACAAAGAACAA 59.767 40.909 0.00 0.00 0.00 2.83
711 1761 3.260740 CAAGGCAGCAACAAAGAACAAA 58.739 40.909 0.00 0.00 0.00 2.83
712 1762 3.608316 AGGCAGCAACAAAGAACAAAA 57.392 38.095 0.00 0.00 0.00 2.44
713 1763 3.936564 AGGCAGCAACAAAGAACAAAAA 58.063 36.364 0.00 0.00 0.00 1.94
755 1805 7.581213 AAAACCACAAACATAGTGAAGATCA 57.419 32.000 0.00 0.00 39.30 2.92
756 1806 6.808008 AACCACAAACATAGTGAAGATCAG 57.192 37.500 0.00 0.00 39.30 2.90
757 1807 5.248640 ACCACAAACATAGTGAAGATCAGG 58.751 41.667 0.00 0.00 39.30 3.86
758 1808 5.221925 ACCACAAACATAGTGAAGATCAGGT 60.222 40.000 0.00 0.00 39.30 4.00
759 1809 5.707298 CCACAAACATAGTGAAGATCAGGTT 59.293 40.000 0.00 0.00 39.30 3.50
760 1810 6.878923 CCACAAACATAGTGAAGATCAGGTTA 59.121 38.462 0.00 0.00 39.30 2.85
761 1811 7.065085 CCACAAACATAGTGAAGATCAGGTTAG 59.935 40.741 0.00 0.00 39.30 2.34
762 1812 7.819415 CACAAACATAGTGAAGATCAGGTTAGA 59.181 37.037 0.00 0.00 39.30 2.10
763 1813 8.543774 ACAAACATAGTGAAGATCAGGTTAGAT 58.456 33.333 0.00 0.00 0.00 1.98
764 1814 8.824781 CAAACATAGTGAAGATCAGGTTAGATG 58.175 37.037 0.00 0.00 0.00 2.90
765 1815 7.667575 ACATAGTGAAGATCAGGTTAGATGT 57.332 36.000 0.00 0.00 0.00 3.06
766 1816 7.495901 ACATAGTGAAGATCAGGTTAGATGTG 58.504 38.462 0.00 0.00 0.00 3.21
767 1817 7.343057 ACATAGTGAAGATCAGGTTAGATGTGA 59.657 37.037 0.00 0.00 0.00 3.58
768 1818 6.805016 AGTGAAGATCAGGTTAGATGTGAT 57.195 37.500 0.00 0.00 33.53 3.06
769 1819 7.904558 AGTGAAGATCAGGTTAGATGTGATA 57.095 36.000 0.00 0.00 30.93 2.15
770 1820 8.489676 AGTGAAGATCAGGTTAGATGTGATAT 57.510 34.615 0.00 0.00 30.93 1.63
771 1821 9.593565 AGTGAAGATCAGGTTAGATGTGATATA 57.406 33.333 0.00 0.00 30.93 0.86
803 1853 5.764487 CATCTAGATGTGTGCTAGACAGA 57.236 43.478 22.42 0.00 44.98 3.41
804 1854 5.518812 CATCTAGATGTGTGCTAGACAGAC 58.481 45.833 22.42 0.55 44.98 3.51
805 1855 3.948473 TCTAGATGTGTGCTAGACAGACC 59.052 47.826 10.44 0.00 41.82 3.85
806 1856 2.529632 AGATGTGTGCTAGACAGACCA 58.470 47.619 10.44 1.36 41.82 4.02
807 1857 3.102972 AGATGTGTGCTAGACAGACCAT 58.897 45.455 10.44 5.03 41.82 3.55
808 1858 4.281657 AGATGTGTGCTAGACAGACCATA 58.718 43.478 10.44 0.00 41.82 2.74
809 1859 4.898265 AGATGTGTGCTAGACAGACCATAT 59.102 41.667 10.44 0.97 41.82 1.78
810 1860 6.071320 AGATGTGTGCTAGACAGACCATATA 58.929 40.000 10.44 0.00 41.82 0.86
811 1861 6.723515 AGATGTGTGCTAGACAGACCATATAT 59.276 38.462 10.44 0.43 41.82 0.86
821 1871 7.159322 AGACAGACCATATATTTACGCTAGG 57.841 40.000 0.00 0.00 0.00 3.02
916 1972 4.457834 AAGGAATCAGTTCGGACTACAG 57.542 45.455 0.00 0.00 35.10 2.74
917 1973 2.761208 AGGAATCAGTTCGGACTACAGG 59.239 50.000 0.00 0.00 35.10 4.00
918 1974 2.541556 GAATCAGTTCGGACTACAGGC 58.458 52.381 0.00 0.00 33.90 4.85
919 1975 1.853963 ATCAGTTCGGACTACAGGCT 58.146 50.000 0.00 0.00 33.90 4.58
955 2011 2.124411 GGCTGGTTAGATTACAGGGGA 58.876 52.381 0.00 0.00 32.98 4.81
985 2047 1.694696 ACAGCGAAGGAAGGAAGAAGT 59.305 47.619 0.00 0.00 0.00 3.01
1049 2111 0.946221 AGAAACACAAGAGCGGCTCG 60.946 55.000 23.15 13.18 35.36 5.03
1127 2189 1.079543 GATCCCGCGATCCCATCAG 60.080 63.158 8.23 0.00 39.29 2.90
1394 2456 2.002586 CAAGACCATGTCCGACATCAC 58.997 52.381 11.24 6.12 36.53 3.06
1395 2457 1.561643 AGACCATGTCCGACATCACT 58.438 50.000 11.24 8.11 36.53 3.41
1443 2505 3.133014 CGCCAGATCCAGATCCGT 58.867 61.111 4.01 0.00 38.58 4.69
1519 2581 3.336814 TTCGCCATTCATGCCCCGA 62.337 57.895 0.00 0.00 0.00 5.14
1525 2587 2.067605 ATTCATGCCCCGACCGGTA 61.068 57.895 7.34 0.00 0.00 4.02
1531 2593 2.266689 CCCCGACCGGTACTTTGG 59.733 66.667 7.34 4.56 0.00 3.28
1537 2599 1.298859 GACCGGTACTTTGGCAGCAG 61.299 60.000 7.34 0.00 0.00 4.24
1546 2608 3.876236 TGGCAGCAGGCACAGACA 61.876 61.111 0.00 0.00 46.46 3.41
1548 2610 2.952245 GCAGCAGGCACAGACAAG 59.048 61.111 0.00 0.00 43.97 3.16
1570 2632 3.570912 TGATGATCATCATGTGCCACT 57.429 42.857 30.27 0.00 42.42 4.00
1574 2636 2.171027 TGATCATCATGTGCCACTGCTA 59.829 45.455 0.00 0.00 38.71 3.49
1628 2693 4.498520 AGACGCGGCATGGACGAG 62.499 66.667 17.71 0.00 40.30 4.18
1639 2704 2.747855 GGACGAGGCTGCCCAAAG 60.748 66.667 16.57 6.90 0.00 2.77
1653 2718 1.004918 CAAAGGCCCGTCTTCTCGT 60.005 57.895 0.00 0.00 0.00 4.18
1654 2719 1.014564 CAAAGGCCCGTCTTCTCGTC 61.015 60.000 0.00 0.00 0.00 4.20
1655 2720 1.469335 AAAGGCCCGTCTTCTCGTCA 61.469 55.000 0.00 0.00 0.00 4.35
1668 2733 5.800941 GTCTTCTCGTCACGACTATTTCATT 59.199 40.000 0.00 0.00 0.00 2.57
1671 2736 5.093457 TCTCGTCACGACTATTTCATTGAC 58.907 41.667 0.00 0.00 35.10 3.18
1692 2757 2.882137 CGTAACCTCTTTTCAGGGCAAA 59.118 45.455 0.00 0.00 37.96 3.68
1740 2805 1.748493 ACATTGGTGTTTGACGCAACT 59.252 42.857 0.00 0.00 34.01 3.16
1746 2811 2.353579 GGTGTTTGACGCAACTACACTT 59.646 45.455 18.31 0.00 39.16 3.16
1765 2830 2.949451 TGAGTTCCTCTGCTCGATTC 57.051 50.000 0.00 0.00 34.67 2.52
1769 2834 2.499289 AGTTCCTCTGCTCGATTCATGT 59.501 45.455 0.00 0.00 0.00 3.21
1788 2853 1.593209 GCCACAGTCGACGTCCAAA 60.593 57.895 10.58 0.00 0.00 3.28
1798 2863 1.717645 CGACGTCCAAACTTTACTCCG 59.282 52.381 10.58 0.00 0.00 4.63
1810 2875 7.041372 CCAAACTTTACTCCGTGATATATTGGG 60.041 40.741 0.00 0.00 0.00 4.12
1811 2876 5.548406 ACTTTACTCCGTGATATATTGGGC 58.452 41.667 0.00 0.00 0.00 5.36
1812 2877 5.307196 ACTTTACTCCGTGATATATTGGGCT 59.693 40.000 0.00 0.00 0.00 5.19
1813 2878 5.818678 TTACTCCGTGATATATTGGGCTT 57.181 39.130 0.00 0.00 0.00 4.35
1814 2879 4.273148 ACTCCGTGATATATTGGGCTTC 57.727 45.455 0.00 0.00 0.00 3.86
1815 2880 3.008049 ACTCCGTGATATATTGGGCTTCC 59.992 47.826 0.00 0.00 0.00 3.46
1816 2881 2.976185 TCCGTGATATATTGGGCTTCCA 59.024 45.455 0.00 0.00 39.13 3.53
1820 2885 4.452455 CGTGATATATTGGGCTTCCACTTC 59.548 45.833 0.00 0.00 40.91 3.01
1823 2888 2.806945 TATTGGGCTTCCACTTCCAG 57.193 50.000 0.00 0.00 40.91 3.86
1825 2890 0.401738 TTGGGCTTCCACTTCCAGAG 59.598 55.000 0.00 0.00 40.91 3.35
1830 2895 2.626840 GCTTCCACTTCCAGAGATGAC 58.373 52.381 0.00 0.00 0.00 3.06
1983 3048 1.153549 GCTCTCCTGGCGTAAGGTG 60.154 63.158 5.57 3.87 38.58 4.00
2055 3120 2.669434 TGCGACCTTTAGCGACAATAAC 59.331 45.455 0.00 0.00 35.87 1.89
2094 3159 6.692486 AGCTCGGGTATATTATGTTCTTCAG 58.308 40.000 0.00 0.00 0.00 3.02
2127 3192 2.769663 TCCCAAAGCATCCACGTACTAT 59.230 45.455 0.00 0.00 0.00 2.12
2136 3201 7.939784 AGCATCCACGTACTATTATGAGATA 57.060 36.000 0.00 0.00 0.00 1.98
2179 3244 1.816835 TGTACAGGTCACCAGACGATC 59.183 52.381 0.00 0.00 45.92 3.69
2377 3460 5.557891 TTTTTGAACCGAAAACCGTAGAA 57.442 34.783 0.00 0.00 36.31 2.10
2378 3461 4.534794 TTTGAACCGAAAACCGTAGAAC 57.465 40.909 0.00 0.00 36.31 3.01
2379 3462 3.176552 TGAACCGAAAACCGTAGAACA 57.823 42.857 0.00 0.00 36.31 3.18
2380 3463 3.529533 TGAACCGAAAACCGTAGAACAA 58.470 40.909 0.00 0.00 36.31 2.83
2381 3464 4.128643 TGAACCGAAAACCGTAGAACAAT 58.871 39.130 0.00 0.00 36.31 2.71
2382 3465 4.211794 TGAACCGAAAACCGTAGAACAATC 59.788 41.667 0.00 0.00 36.31 2.67
2383 3466 2.733026 ACCGAAAACCGTAGAACAATCG 59.267 45.455 0.00 0.00 36.31 3.34
2384 3467 2.733026 CCGAAAACCGTAGAACAATCGT 59.267 45.455 0.00 0.00 36.31 3.73
2385 3468 3.184986 CCGAAAACCGTAGAACAATCGTT 59.815 43.478 0.00 0.00 35.54 3.85
2386 3469 4.664891 CCGAAAACCGTAGAACAATCGTTC 60.665 45.833 0.00 0.00 43.35 3.95
2429 3512 9.213777 AGTATTTACAAGAGTCCCAAGATATCA 57.786 33.333 5.32 0.00 0.00 2.15
2430 3513 9.482627 GTATTTACAAGAGTCCCAAGATATCAG 57.517 37.037 5.32 0.00 0.00 2.90
2431 3514 7.496346 TTTACAAGAGTCCCAAGATATCAGT 57.504 36.000 5.32 0.00 0.00 3.41
2432 3515 7.496346 TTACAAGAGTCCCAAGATATCAGTT 57.504 36.000 5.32 0.00 0.00 3.16
2433 3516 5.983540 ACAAGAGTCCCAAGATATCAGTTC 58.016 41.667 5.32 0.00 0.00 3.01
2434 3517 5.723887 ACAAGAGTCCCAAGATATCAGTTCT 59.276 40.000 5.32 0.00 0.00 3.01
2435 3518 6.214412 ACAAGAGTCCCAAGATATCAGTTCTT 59.786 38.462 5.32 1.98 33.75 2.52
2436 3519 6.882768 AGAGTCCCAAGATATCAGTTCTTT 57.117 37.500 5.32 0.00 31.11 2.52
2437 3520 7.264294 AGAGTCCCAAGATATCAGTTCTTTT 57.736 36.000 5.32 0.00 31.11 2.27
2438 3521 7.694093 AGAGTCCCAAGATATCAGTTCTTTTT 58.306 34.615 5.32 0.00 31.11 1.94
2488 3571 6.534793 GGTTTTGGTTAGGTTGATATGCATTG 59.465 38.462 3.54 0.00 0.00 2.82
2492 3575 7.473735 TGGTTAGGTTGATATGCATTGAAAA 57.526 32.000 3.54 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.321564 CTGTTCCATTCAGCGGTCCA 60.322 55.000 0.00 0.00 0.00 4.02
4 5 1.556911 AGATCTGTTCCATTCAGCGGT 59.443 47.619 0.00 0.00 33.48 5.68
7 8 5.128919 ACCATTAGATCTGTTCCATTCAGC 58.871 41.667 5.18 0.00 33.48 4.26
17 18 3.683847 GCCTCAGCAACCATTAGATCTGT 60.684 47.826 5.18 0.00 39.53 3.41
33 34 1.331756 GATAATGTTGTGCGGCCTCAG 59.668 52.381 0.00 0.00 0.00 3.35
89 90 7.596749 AGATTTTCGACGAAGATTGTGTTAT 57.403 32.000 14.08 0.00 0.00 1.89
101 102 4.867608 TCATGTTGCATAGATTTTCGACGA 59.132 37.500 0.00 0.00 0.00 4.20
103 104 4.966366 GCTCATGTTGCATAGATTTTCGAC 59.034 41.667 8.20 0.00 0.00 4.20
105 106 5.165911 AGCTCATGTTGCATAGATTTTCG 57.834 39.130 13.86 0.00 0.00 3.46
128 1174 3.450457 TGTTGCAGAACCCTTTGAAACAT 59.550 39.130 0.00 0.00 37.80 2.71
137 1183 3.214328 CAAAGTAGTGTTGCAGAACCCT 58.786 45.455 0.00 0.00 0.00 4.34
186 1233 4.122776 CGTTAGATCTGGTTCATTCAGGG 58.877 47.826 5.18 0.00 33.36 4.45
187 1234 4.122776 CCGTTAGATCTGGTTCATTCAGG 58.877 47.826 5.18 0.00 33.36 3.86
199 1246 2.354805 GGCCTCAACAACCGTTAGATCT 60.355 50.000 0.00 0.00 32.75 2.75
217 1264 1.795170 ATGGATAATGTTGCGCGGCC 61.795 55.000 8.83 0.00 0.00 6.13
260 1307 6.385649 ACGGACATTGTGTTGTAGATTTTT 57.614 33.333 0.00 0.00 0.00 1.94
264 1311 7.681939 ATTTAACGGACATTGTGTTGTAGAT 57.318 32.000 0.00 0.00 0.00 1.98
265 1312 8.780846 ATATTTAACGGACATTGTGTTGTAGA 57.219 30.769 0.00 0.00 0.00 2.59
266 1313 9.834628 AAATATTTAACGGACATTGTGTTGTAG 57.165 29.630 0.00 0.00 0.00 2.74
278 1328 7.952339 TCGTGTTGTAGAAATATTTAACGGAC 58.048 34.615 0.00 6.61 0.00 4.79
282 1332 8.870879 AGAGCTCGTGTTGTAGAAATATTTAAC 58.129 33.333 8.37 2.90 0.00 2.01
295 1345 5.354234 CCCATTAAAATAGAGCTCGTGTTGT 59.646 40.000 8.37 2.58 0.00 3.32
309 1359 5.806654 AGTGTTGCAGAACCCATTAAAAT 57.193 34.783 0.00 0.00 0.00 1.82
315 1365 3.508845 AGTTAGTGTTGCAGAACCCAT 57.491 42.857 0.00 0.00 0.00 4.00
317 1367 3.380320 ACAAAGTTAGTGTTGCAGAACCC 59.620 43.478 0.00 0.00 0.00 4.11
342 1392 3.564225 GCTTAACCCCGTCCTCATTATTG 59.436 47.826 0.00 0.00 0.00 1.90
349 1399 1.078637 GTGGCTTAACCCCGTCCTC 60.079 63.158 0.00 0.00 37.83 3.71
368 1418 2.587522 CCGTGAGATCTGGTCTATCCA 58.412 52.381 0.00 0.00 45.01 3.41
369 1419 1.271102 GCCGTGAGATCTGGTCTATCC 59.729 57.143 0.00 0.00 37.29 2.59
370 1420 2.030363 CAGCCGTGAGATCTGGTCTATC 60.030 54.545 0.00 0.00 37.29 2.08
372 1422 1.393603 CAGCCGTGAGATCTGGTCTA 58.606 55.000 0.00 0.00 37.29 2.59
373 1423 1.954362 GCAGCCGTGAGATCTGGTCT 61.954 60.000 0.00 0.00 40.81 3.85
374 1424 1.520342 GCAGCCGTGAGATCTGGTC 60.520 63.158 0.00 0.00 33.92 4.02
376 1426 1.521010 CAGCAGCCGTGAGATCTGG 60.521 63.158 0.00 0.00 33.92 3.86
377 1427 0.528033 CTCAGCAGCCGTGAGATCTG 60.528 60.000 0.00 0.00 43.65 2.90
378 1428 0.682532 TCTCAGCAGCCGTGAGATCT 60.683 55.000 9.74 0.00 44.43 2.75
379 1429 1.812525 TCTCAGCAGCCGTGAGATC 59.187 57.895 9.74 0.00 44.43 2.75
383 1433 1.550524 AGTTAATCTCAGCAGCCGTGA 59.449 47.619 0.00 0.00 0.00 4.35
384 1434 1.662629 CAGTTAATCTCAGCAGCCGTG 59.337 52.381 0.00 0.00 0.00 4.94
385 1435 2.009042 GCAGTTAATCTCAGCAGCCGT 61.009 52.381 0.00 0.00 0.00 5.68
387 1437 1.020437 GGCAGTTAATCTCAGCAGCC 58.980 55.000 0.00 0.00 0.00 4.85
388 1438 0.654683 CGGCAGTTAATCTCAGCAGC 59.345 55.000 0.00 0.00 0.00 5.25
390 1440 1.735700 CGTCGGCAGTTAATCTCAGCA 60.736 52.381 0.00 0.00 0.00 4.41
391 1441 0.924090 CGTCGGCAGTTAATCTCAGC 59.076 55.000 0.00 0.00 0.00 4.26
393 1443 1.466866 CGTCGTCGGCAGTTAATCTCA 60.467 52.381 0.00 0.00 0.00 3.27
395 1445 3.324170 CGTCGTCGGCAGTTAATCT 57.676 52.632 0.00 0.00 0.00 2.40
418 1468 5.003590 TGTTTTGTTTTTGTTTAGCGCTACG 59.996 36.000 18.63 0.00 0.00 3.51
420 1470 7.527084 AATGTTTTGTTTTTGTTTAGCGCTA 57.473 28.000 14.45 14.45 0.00 4.26
421 1471 6.415798 AATGTTTTGTTTTTGTTTAGCGCT 57.584 29.167 17.26 17.26 0.00 5.92
422 1472 6.843779 CCTAATGTTTTGTTTTTGTTTAGCGC 59.156 34.615 0.00 0.00 0.00 5.92
424 1474 8.053653 CGTCCTAATGTTTTGTTTTTGTTTAGC 58.946 33.333 0.00 0.00 0.00 3.09
425 1475 8.536407 CCGTCCTAATGTTTTGTTTTTGTTTAG 58.464 33.333 0.00 0.00 0.00 1.85
428 1478 5.292345 GCCGTCCTAATGTTTTGTTTTTGTT 59.708 36.000 0.00 0.00 0.00 2.83
429 1479 4.806775 GCCGTCCTAATGTTTTGTTTTTGT 59.193 37.500 0.00 0.00 0.00 2.83
430 1480 4.210328 GGCCGTCCTAATGTTTTGTTTTTG 59.790 41.667 0.00 0.00 0.00 2.44
431 1481 4.373527 GGCCGTCCTAATGTTTTGTTTTT 58.626 39.130 0.00 0.00 0.00 1.94
432 1482 3.243941 GGGCCGTCCTAATGTTTTGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
434 1484 1.890489 GGGCCGTCCTAATGTTTTGTT 59.110 47.619 0.00 0.00 0.00 2.83
435 1485 1.541379 GGGCCGTCCTAATGTTTTGT 58.459 50.000 0.00 0.00 0.00 2.83
437 1487 0.037160 ACGGGCCGTCCTAATGTTTT 59.963 50.000 28.83 0.00 33.69 2.43
438 1488 0.037160 AACGGGCCGTCCTAATGTTT 59.963 50.000 34.23 10.60 39.99 2.83
439 1489 0.037160 AAACGGGCCGTCCTAATGTT 59.963 50.000 34.23 18.26 39.99 2.71
440 1490 0.392060 GAAACGGGCCGTCCTAATGT 60.392 55.000 34.23 12.35 39.99 2.71
442 1492 1.222661 GGAAACGGGCCGTCCTAAT 59.777 57.895 34.23 14.11 39.99 1.73
443 1493 0.614415 TAGGAAACGGGCCGTCCTAA 60.614 55.000 32.60 20.94 39.99 2.69
444 1494 0.397535 ATAGGAAACGGGCCGTCCTA 60.398 55.000 34.94 34.94 39.99 2.94
445 1495 1.683418 GATAGGAAACGGGCCGTCCT 61.683 60.000 33.42 33.42 39.99 3.85
446 1496 1.227468 GATAGGAAACGGGCCGTCC 60.227 63.158 34.23 28.96 39.99 4.79
447 1497 0.106149 ATGATAGGAAACGGGCCGTC 59.894 55.000 34.23 20.92 39.99 4.79
448 1498 0.106149 GATGATAGGAAACGGGCCGT 59.894 55.000 28.83 28.83 43.97 5.68
449 1499 0.105964 TGATGATAGGAAACGGGCCG 59.894 55.000 27.06 27.06 0.00 6.13
450 1500 1.134220 TGTGATGATAGGAAACGGGCC 60.134 52.381 0.00 0.00 0.00 5.80
451 1501 2.325583 TGTGATGATAGGAAACGGGC 57.674 50.000 0.00 0.00 0.00 6.13
452 1502 5.637006 TTTTTGTGATGATAGGAAACGGG 57.363 39.130 0.00 0.00 0.00 5.28
475 1525 8.553459 AGAAGACGTGATACAATTCTTTTCAT 57.447 30.769 0.00 0.00 0.00 2.57
498 1548 5.213891 TGATTTTCGGCTGCATCTATAGA 57.786 39.130 4.57 4.57 0.00 1.98
507 1557 0.453390 CTCCCTTGATTTTCGGCTGC 59.547 55.000 0.00 0.00 0.00 5.25
629 1679 9.737427 CATCTAGATACGAATTAGACAAACTGT 57.263 33.333 4.54 0.00 0.00 3.55
630 1680 9.737427 ACATCTAGATACGAATTAGACAAACTG 57.263 33.333 4.54 0.00 0.00 3.16
657 1707 7.610305 GGAGGTTAGATGTGACATCCTTAAAAA 59.390 37.037 21.05 4.81 42.00 1.94
658 1708 7.110155 GGAGGTTAGATGTGACATCCTTAAAA 58.890 38.462 21.05 6.42 42.00 1.52
659 1709 6.352737 GGGAGGTTAGATGTGACATCCTTAAA 60.353 42.308 21.05 8.69 44.05 1.52
660 1710 5.130477 GGGAGGTTAGATGTGACATCCTTAA 59.870 44.000 21.05 11.73 44.05 1.85
661 1711 4.654262 GGGAGGTTAGATGTGACATCCTTA 59.346 45.833 21.05 6.22 44.05 2.69
662 1712 3.456277 GGGAGGTTAGATGTGACATCCTT 59.544 47.826 21.05 7.22 44.05 3.36
663 1713 3.041946 GGGAGGTTAGATGTGACATCCT 58.958 50.000 21.05 12.23 44.05 3.24
664 1714 2.771943 TGGGAGGTTAGATGTGACATCC 59.228 50.000 21.05 9.65 43.91 3.51
665 1715 3.197766 TGTGGGAGGTTAGATGTGACATC 59.802 47.826 17.46 17.46 0.00 3.06
666 1716 3.181329 TGTGGGAGGTTAGATGTGACAT 58.819 45.455 0.00 0.00 0.00 3.06
667 1717 2.615391 TGTGGGAGGTTAGATGTGACA 58.385 47.619 0.00 0.00 0.00 3.58
668 1718 3.695830 TTGTGGGAGGTTAGATGTGAC 57.304 47.619 0.00 0.00 0.00 3.67
669 1719 3.392947 TGTTTGTGGGAGGTTAGATGTGA 59.607 43.478 0.00 0.00 0.00 3.58
670 1720 3.750371 TGTTTGTGGGAGGTTAGATGTG 58.250 45.455 0.00 0.00 0.00 3.21
671 1721 4.398319 CTTGTTTGTGGGAGGTTAGATGT 58.602 43.478 0.00 0.00 0.00 3.06
672 1722 3.758554 CCTTGTTTGTGGGAGGTTAGATG 59.241 47.826 0.00 0.00 0.00 2.90
673 1723 3.814316 GCCTTGTTTGTGGGAGGTTAGAT 60.814 47.826 0.00 0.00 0.00 1.98
674 1724 2.488347 GCCTTGTTTGTGGGAGGTTAGA 60.488 50.000 0.00 0.00 0.00 2.10
675 1725 1.886542 GCCTTGTTTGTGGGAGGTTAG 59.113 52.381 0.00 0.00 0.00 2.34
676 1726 1.215673 TGCCTTGTTTGTGGGAGGTTA 59.784 47.619 0.00 0.00 0.00 2.85
677 1727 0.032615 TGCCTTGTTTGTGGGAGGTT 60.033 50.000 0.00 0.00 0.00 3.50
678 1728 0.468029 CTGCCTTGTTTGTGGGAGGT 60.468 55.000 0.00 0.00 38.01 3.85
679 1729 1.809567 GCTGCCTTGTTTGTGGGAGG 61.810 60.000 0.00 0.00 41.30 4.30
680 1730 1.108727 TGCTGCCTTGTTTGTGGGAG 61.109 55.000 0.00 0.00 43.41 4.30
681 1731 0.685785 TTGCTGCCTTGTTTGTGGGA 60.686 50.000 0.00 0.00 0.00 4.37
682 1732 0.530431 GTTGCTGCCTTGTTTGTGGG 60.530 55.000 0.00 0.00 0.00 4.61
683 1733 0.175302 TGTTGCTGCCTTGTTTGTGG 59.825 50.000 0.00 0.00 0.00 4.17
684 1734 2.007360 TTGTTGCTGCCTTGTTTGTG 57.993 45.000 0.00 0.00 0.00 3.33
685 1735 2.233431 TCTTTGTTGCTGCCTTGTTTGT 59.767 40.909 0.00 0.00 0.00 2.83
686 1736 2.891112 TCTTTGTTGCTGCCTTGTTTG 58.109 42.857 0.00 0.00 0.00 2.93
687 1737 3.261580 GTTCTTTGTTGCTGCCTTGTTT 58.738 40.909 0.00 0.00 0.00 2.83
688 1738 2.233431 TGTTCTTTGTTGCTGCCTTGTT 59.767 40.909 0.00 0.00 0.00 2.83
689 1739 1.824230 TGTTCTTTGTTGCTGCCTTGT 59.176 42.857 0.00 0.00 0.00 3.16
690 1740 2.582728 TGTTCTTTGTTGCTGCCTTG 57.417 45.000 0.00 0.00 0.00 3.61
691 1741 3.608316 TTTGTTCTTTGTTGCTGCCTT 57.392 38.095 0.00 0.00 0.00 4.35
692 1742 3.608316 TTTTGTTCTTTGTTGCTGCCT 57.392 38.095 0.00 0.00 0.00 4.75
730 1780 8.006298 TGATCTTCACTATGTTTGTGGTTTTT 57.994 30.769 0.00 0.00 36.21 1.94
731 1781 7.255590 CCTGATCTTCACTATGTTTGTGGTTTT 60.256 37.037 0.00 0.00 36.21 2.43
732 1782 6.207417 CCTGATCTTCACTATGTTTGTGGTTT 59.793 38.462 0.00 0.00 36.21 3.27
733 1783 5.707298 CCTGATCTTCACTATGTTTGTGGTT 59.293 40.000 0.00 0.00 36.21 3.67
734 1784 5.221925 ACCTGATCTTCACTATGTTTGTGGT 60.222 40.000 0.00 0.00 36.21 4.16
735 1785 5.248640 ACCTGATCTTCACTATGTTTGTGG 58.751 41.667 0.00 0.00 36.21 4.17
736 1786 6.808008 AACCTGATCTTCACTATGTTTGTG 57.192 37.500 0.00 0.00 36.82 3.33
737 1787 7.907389 TCTAACCTGATCTTCACTATGTTTGT 58.093 34.615 0.00 0.00 0.00 2.83
738 1788 8.824781 CATCTAACCTGATCTTCACTATGTTTG 58.175 37.037 0.00 0.00 0.00 2.93
739 1789 8.543774 ACATCTAACCTGATCTTCACTATGTTT 58.456 33.333 0.00 0.00 0.00 2.83
740 1790 7.984050 CACATCTAACCTGATCTTCACTATGTT 59.016 37.037 0.00 0.00 0.00 2.71
741 1791 7.343057 TCACATCTAACCTGATCTTCACTATGT 59.657 37.037 0.00 0.00 0.00 2.29
742 1792 7.720442 TCACATCTAACCTGATCTTCACTATG 58.280 38.462 0.00 0.00 0.00 2.23
743 1793 7.904558 TCACATCTAACCTGATCTTCACTAT 57.095 36.000 0.00 0.00 0.00 2.12
744 1794 7.904558 ATCACATCTAACCTGATCTTCACTA 57.095 36.000 0.00 0.00 0.00 2.74
745 1795 6.805016 ATCACATCTAACCTGATCTTCACT 57.195 37.500 0.00 0.00 0.00 3.41
781 1831 5.507149 GGTCTGTCTAGCACACATCTAGATG 60.507 48.000 27.63 27.63 42.90 2.90
782 1832 4.582656 GGTCTGTCTAGCACACATCTAGAT 59.417 45.833 0.00 0.00 42.90 1.98
783 1833 3.948473 GGTCTGTCTAGCACACATCTAGA 59.052 47.826 0.00 0.00 39.94 2.43
784 1834 3.696548 TGGTCTGTCTAGCACACATCTAG 59.303 47.826 0.00 0.00 35.90 2.43
785 1835 3.697166 TGGTCTGTCTAGCACACATCTA 58.303 45.455 0.00 0.00 0.00 1.98
786 1836 2.529632 TGGTCTGTCTAGCACACATCT 58.470 47.619 0.00 0.00 0.00 2.90
787 1837 3.533606 ATGGTCTGTCTAGCACACATC 57.466 47.619 0.00 0.00 0.00 3.06
788 1838 6.924913 ATATATGGTCTGTCTAGCACACAT 57.075 37.500 0.00 0.00 0.00 3.21
789 1839 6.731292 AATATATGGTCTGTCTAGCACACA 57.269 37.500 0.00 0.00 0.00 3.72
790 1840 7.326305 CGTAAATATATGGTCTGTCTAGCACAC 59.674 40.741 0.00 0.00 0.00 3.82
791 1841 7.368059 CGTAAATATATGGTCTGTCTAGCACA 58.632 38.462 0.00 0.00 0.00 4.57
792 1842 6.308282 GCGTAAATATATGGTCTGTCTAGCAC 59.692 42.308 0.00 0.00 0.00 4.40
793 1843 6.208797 AGCGTAAATATATGGTCTGTCTAGCA 59.791 38.462 0.00 0.00 0.00 3.49
794 1844 6.622549 AGCGTAAATATATGGTCTGTCTAGC 58.377 40.000 0.00 0.00 0.00 3.42
795 1845 8.399425 CCTAGCGTAAATATATGGTCTGTCTAG 58.601 40.741 0.00 0.00 31.48 2.43
796 1846 7.148120 GCCTAGCGTAAATATATGGTCTGTCTA 60.148 40.741 0.00 0.00 31.48 2.59
797 1847 6.350277 GCCTAGCGTAAATATATGGTCTGTCT 60.350 42.308 0.00 0.00 31.48 3.41
798 1848 5.805994 GCCTAGCGTAAATATATGGTCTGTC 59.194 44.000 0.00 0.00 31.48 3.51
799 1849 5.337330 GGCCTAGCGTAAATATATGGTCTGT 60.337 44.000 0.00 0.00 31.48 3.41
800 1850 5.109903 GGCCTAGCGTAAATATATGGTCTG 58.890 45.833 0.00 0.00 31.48 3.51
801 1851 4.142227 CGGCCTAGCGTAAATATATGGTCT 60.142 45.833 0.00 0.00 31.48 3.85
802 1852 4.110482 CGGCCTAGCGTAAATATATGGTC 58.890 47.826 0.00 0.00 31.48 4.02
803 1853 3.512724 ACGGCCTAGCGTAAATATATGGT 59.487 43.478 0.00 0.00 33.51 3.55
804 1854 3.863424 CACGGCCTAGCGTAAATATATGG 59.137 47.826 0.00 0.00 0.00 2.74
805 1855 3.306166 GCACGGCCTAGCGTAAATATATG 59.694 47.826 0.00 0.00 0.00 1.78
806 1856 3.518590 GCACGGCCTAGCGTAAATATAT 58.481 45.455 0.00 0.00 0.00 0.86
807 1857 2.353011 GGCACGGCCTAGCGTAAATATA 60.353 50.000 0.00 0.00 46.69 0.86
808 1858 1.607251 GGCACGGCCTAGCGTAAATAT 60.607 52.381 0.00 0.00 46.69 1.28
809 1859 0.249573 GGCACGGCCTAGCGTAAATA 60.250 55.000 0.00 0.00 46.69 1.40
810 1860 1.523032 GGCACGGCCTAGCGTAAAT 60.523 57.895 0.00 0.00 46.69 1.40
811 1861 2.125431 GGCACGGCCTAGCGTAAA 60.125 61.111 0.00 0.00 46.69 2.01
916 1972 2.423577 CCCGTAATATAACCAGCAGCC 58.576 52.381 0.00 0.00 0.00 4.85
917 1973 1.804748 GCCCGTAATATAACCAGCAGC 59.195 52.381 0.00 0.00 0.00 5.25
918 1974 3.067106 CAGCCCGTAATATAACCAGCAG 58.933 50.000 0.00 0.00 0.00 4.24
919 1975 2.224426 CCAGCCCGTAATATAACCAGCA 60.224 50.000 0.00 0.00 0.00 4.41
955 2011 1.881973 TCCTTCGCTGTTACGTGTAGT 59.118 47.619 0.00 0.00 0.00 2.73
985 2047 1.449423 CCATTGTGATCACGGCCGA 60.449 57.895 35.90 11.57 0.00 5.54
1301 2363 3.749064 GCGAGAGACGGCAGGACA 61.749 66.667 0.00 0.00 42.83 4.02
1311 2373 2.626780 CGTGGTCAGGTGCGAGAGA 61.627 63.158 0.00 0.00 0.00 3.10
1394 2456 3.927656 GCATCGGTATGGTGCACGTAAG 61.928 54.545 11.45 4.83 38.68 2.34
1395 2457 1.929230 CATCGGTATGGTGCACGTAA 58.071 50.000 11.45 0.00 0.00 3.18
1429 2491 0.969894 GGGGTACGGATCTGGATCTG 59.030 60.000 15.47 15.47 46.89 2.90
1432 2494 0.267960 AAGGGGGTACGGATCTGGAT 59.732 55.000 6.47 0.00 0.00 3.41
1443 2505 5.633473 AGGATACATCATAGAAGGGGGTA 57.367 43.478 0.00 0.00 41.41 3.69
1519 2581 1.302511 CTGCTGCCAAAGTACCGGT 60.303 57.895 13.98 13.98 0.00 5.28
1525 2587 2.123769 TGTGCCTGCTGCCAAAGT 60.124 55.556 0.00 0.00 40.16 2.66
1531 2593 0.959372 ATCTTGTCTGTGCCTGCTGC 60.959 55.000 0.00 0.00 41.77 5.25
1537 2599 3.538591 TGATCATCATCTTGTCTGTGCC 58.461 45.455 0.00 0.00 0.00 5.01
1548 2610 7.549536 GCAGTGGCACATGATGATCATCATC 62.550 48.000 37.21 28.25 46.44 2.92
1570 2632 3.199438 TGCTCTCTCGTAGCAAGTAGCA 61.199 50.000 0.00 0.00 46.57 3.49
1620 2685 2.826777 CTTTGGGCAGCCTCGTCCAT 62.827 60.000 12.43 0.00 0.00 3.41
1635 2700 1.004918 ACGAGAAGACGGGCCTTTG 60.005 57.895 0.84 0.00 37.61 2.77
1639 2704 2.126031 GTGACGAGAAGACGGGCC 60.126 66.667 0.00 0.00 37.61 5.80
1653 2718 5.574055 GGTTACGTCAATGAAATAGTCGTGA 59.426 40.000 0.00 0.00 31.05 4.35
1654 2719 5.575606 AGGTTACGTCAATGAAATAGTCGTG 59.424 40.000 0.00 0.00 31.05 4.35
1655 2720 5.717119 AGGTTACGTCAATGAAATAGTCGT 58.283 37.500 0.00 0.44 32.59 4.34
1668 2733 2.549349 GCCCTGAAAAGAGGTTACGTCA 60.549 50.000 7.80 0.00 0.00 4.35
1671 2736 2.178912 TGCCCTGAAAAGAGGTTACG 57.821 50.000 0.00 0.00 0.00 3.18
1692 2757 7.687592 GCACCATTAGATTCCAAGCCATAAATT 60.688 37.037 0.00 0.00 0.00 1.82
1765 2830 1.617755 GACGTCGACTGTGGCACATG 61.618 60.000 22.35 16.90 44.52 3.21
1769 2834 2.299503 TTTGGACGTCGACTGTGGCA 62.300 55.000 14.70 0.00 0.00 4.92
1788 2853 5.307196 AGCCCAATATATCACGGAGTAAAGT 59.693 40.000 0.00 0.00 41.61 2.66
1798 2863 4.762251 GGAAGTGGAAGCCCAATATATCAC 59.238 45.833 0.00 0.00 45.59 3.06
1810 2875 2.626840 GTCATCTCTGGAAGTGGAAGC 58.373 52.381 0.00 0.00 33.76 3.86
1811 2876 2.493675 TCGTCATCTCTGGAAGTGGAAG 59.506 50.000 0.00 0.00 33.76 3.46
1812 2877 2.525368 TCGTCATCTCTGGAAGTGGAA 58.475 47.619 0.00 0.00 33.76 3.53
1813 2878 2.215942 TCGTCATCTCTGGAAGTGGA 57.784 50.000 0.00 0.00 33.76 4.02
1814 2879 2.223923 GGATCGTCATCTCTGGAAGTGG 60.224 54.545 0.00 0.00 33.76 4.00
1815 2880 2.692557 AGGATCGTCATCTCTGGAAGTG 59.307 50.000 0.00 0.00 33.76 3.16
1816 2881 2.692557 CAGGATCGTCATCTCTGGAAGT 59.307 50.000 0.00 0.00 33.76 3.01
1820 2885 1.001924 CGACAGGATCGTCATCTCTGG 60.002 57.143 2.31 0.00 46.25 3.86
1983 3048 1.202580 CCACCGATTCCATCTCCTGTC 60.203 57.143 0.00 0.00 0.00 3.51
2127 3192 5.529581 TCTTGCCGTCATGTATCTCATAA 57.470 39.130 0.00 0.00 34.67 1.90
2136 3201 0.615331 ACTCCATCTTGCCGTCATGT 59.385 50.000 0.00 0.00 0.00 3.21
2171 3236 6.533012 AGTTGAGTATTCACAATGATCGTCTG 59.467 38.462 0.00 0.00 31.71 3.51
2179 3244 6.992063 AGGCTTAGTTGAGTATTCACAATG 57.008 37.500 0.00 0.00 31.71 2.82
2355 3438 5.106396 TGTTCTACGGTTTTCGGTTCAAAAA 60.106 36.000 0.00 0.00 44.45 1.94
2356 3439 4.394300 TGTTCTACGGTTTTCGGTTCAAAA 59.606 37.500 0.00 0.00 44.45 2.44
2357 3440 3.937706 TGTTCTACGGTTTTCGGTTCAAA 59.062 39.130 0.00 0.00 44.45 2.69
2358 3441 3.529533 TGTTCTACGGTTTTCGGTTCAA 58.470 40.909 0.00 0.00 44.45 2.69
2359 3442 3.176552 TGTTCTACGGTTTTCGGTTCA 57.823 42.857 0.00 0.00 44.45 3.18
2360 3443 4.664891 CGATTGTTCTACGGTTTTCGGTTC 60.665 45.833 0.00 0.00 44.45 3.62
2361 3444 3.184986 CGATTGTTCTACGGTTTTCGGTT 59.815 43.478 0.00 0.00 44.45 4.44
2362 3445 2.733026 CGATTGTTCTACGGTTTTCGGT 59.267 45.455 0.00 0.00 44.45 4.69
2363 3446 2.733026 ACGATTGTTCTACGGTTTTCGG 59.267 45.455 0.00 0.00 44.45 4.30
2364 3447 4.379374 AACGATTGTTCTACGGTTTTCG 57.621 40.909 0.00 0.00 38.28 3.46
2403 3486 9.213777 TGATATCTTGGGACTCTTGTAAATACT 57.786 33.333 3.98 0.00 0.00 2.12
2404 3487 9.482627 CTGATATCTTGGGACTCTTGTAAATAC 57.517 37.037 3.98 0.00 0.00 1.89
2405 3488 9.213777 ACTGATATCTTGGGACTCTTGTAAATA 57.786 33.333 3.98 0.00 0.00 1.40
2406 3489 8.095452 ACTGATATCTTGGGACTCTTGTAAAT 57.905 34.615 3.98 0.00 0.00 1.40
2407 3490 7.496346 ACTGATATCTTGGGACTCTTGTAAA 57.504 36.000 3.98 0.00 0.00 2.01
2408 3491 7.400339 AGAACTGATATCTTGGGACTCTTGTAA 59.600 37.037 3.98 0.00 0.00 2.41
2409 3492 6.897966 AGAACTGATATCTTGGGACTCTTGTA 59.102 38.462 3.98 0.00 0.00 2.41
2410 3493 5.723887 AGAACTGATATCTTGGGACTCTTGT 59.276 40.000 3.98 0.00 0.00 3.16
2411 3494 6.232581 AGAACTGATATCTTGGGACTCTTG 57.767 41.667 3.98 0.00 0.00 3.02
2412 3495 6.882768 AAGAACTGATATCTTGGGACTCTT 57.117 37.500 3.98 0.76 35.85 2.85
2413 3496 6.882768 AAAGAACTGATATCTTGGGACTCT 57.117 37.500 3.98 0.00 37.22 3.24
2414 3497 7.391833 ACAAAAAGAACTGATATCTTGGGACTC 59.608 37.037 3.98 0.00 37.22 3.36
2415 3498 7.234355 ACAAAAAGAACTGATATCTTGGGACT 58.766 34.615 3.98 0.00 37.22 3.85
2416 3499 7.454260 ACAAAAAGAACTGATATCTTGGGAC 57.546 36.000 3.98 0.00 37.22 4.46
2417 3500 7.723616 TGAACAAAAAGAACTGATATCTTGGGA 59.276 33.333 3.98 0.00 37.22 4.37
2418 3501 7.885297 TGAACAAAAAGAACTGATATCTTGGG 58.115 34.615 3.98 0.00 37.22 4.12
2419 3502 9.350357 CATGAACAAAAAGAACTGATATCTTGG 57.650 33.333 3.98 0.00 37.22 3.61
2431 3514 9.195411 GCAGTTTATCATCATGAACAAAAAGAA 57.805 29.630 0.00 0.00 32.13 2.52
2432 3515 8.358895 TGCAGTTTATCATCATGAACAAAAAGA 58.641 29.630 0.00 0.00 32.13 2.52
2433 3516 8.523523 TGCAGTTTATCATCATGAACAAAAAG 57.476 30.769 0.00 0.00 32.13 2.27
2434 3517 8.883954 TTGCAGTTTATCATCATGAACAAAAA 57.116 26.923 0.00 0.00 32.13 1.94
2435 3518 9.491675 AATTGCAGTTTATCATCATGAACAAAA 57.508 25.926 0.00 0.00 32.13 2.44
2436 3519 9.142515 GAATTGCAGTTTATCATCATGAACAAA 57.857 29.630 0.00 0.00 32.13 2.83
2437 3520 7.485595 CGAATTGCAGTTTATCATCATGAACAA 59.514 33.333 0.00 0.00 32.13 2.83
2438 3521 6.968335 CGAATTGCAGTTTATCATCATGAACA 59.032 34.615 0.00 0.00 32.13 3.18
2488 3571 3.592898 ATCCTCAAATTGCCCGTTTTC 57.407 42.857 0.00 0.00 0.00 2.29
2492 3575 1.066929 GCAAATCCTCAAATTGCCCGT 60.067 47.619 0.00 0.00 42.70 5.28


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

AutoCloner maintained by Alex Coulton.