Multiple sequence alignment - TraesCS4A01G151000

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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 TraesCS4A01G151000 chr4A 100.000 4793 0 0 1 4793 299603478 299598686 0.000000e+00 8852.0
1 TraesCS4A01G151000 chr4D 93.934 2753 99 21 1588 4305 209095904 209098623 0.000000e+00 4096.0
2 TraesCS4A01G151000 chr4D 94.737 722 20 8 752 1458 209095148 209095866 0.000000e+00 1107.0
3 TraesCS4A01G151000 chr4D 91.083 471 29 9 754 1215 209092006 209092472 4.070000e-175 625.0
4 TraesCS4A01G151000 chr4D 87.701 374 40 4 2041 2410 226256043 226255672 9.530000e-117 431.0
5 TraesCS4A01G151000 chr4D 94.466 253 7 4 4298 4547 209100295 209100543 2.710000e-102 383.0
6 TraesCS4A01G151000 chr4D 94.203 207 9 3 906 1111 209073205 209073409 3.600000e-81 313.0
7 TraesCS4A01G151000 chr4D 77.184 412 79 11 1015 1425 21888300 21887903 4.830000e-55 226.0
8 TraesCS4A01G151000 chr4D 93.846 130 6 2 4548 4675 209100589 209100718 1.360000e-45 195.0
9 TraesCS4A01G151000 chr4B 94.783 2377 89 9 1970 4342 310974676 310977021 0.000000e+00 3670.0
10 TraesCS4A01G151000 chr4B 97.155 703 11 5 765 1458 310973434 310974136 0.000000e+00 1179.0
11 TraesCS4A01G151000 chr4B 94.753 324 13 4 1652 1972 310974266 310974588 7.160000e-138 501.0
12 TraesCS4A01G151000 chr4B 93.956 182 4 4 4369 4547 310982604 310982781 7.910000e-68 268.0
13 TraesCS4A01G151000 chr4B 76.528 409 81 11 1015 1422 32806100 32806494 4.860000e-50 209.0
14 TraesCS4A01G151000 chr4B 95.522 67 3 0 4321 4387 310977022 310977088 1.820000e-19 108.0
15 TraesCS4A01G151000 chr4B 100.000 37 0 0 1623 1659 310974223 310974259 8.610000e-08 69.4
16 TraesCS4A01G151000 chr6A 91.184 760 47 5 8 750 488404960 488405716 0.000000e+00 1014.0
17 TraesCS4A01G151000 chr6A 95.522 134 5 1 1457 1590 64662250 64662382 3.760000e-51 213.0
18 TraesCS4A01G151000 chr2A 86.326 724 80 8 2038 2760 777208107 777207402 0.000000e+00 771.0
19 TraesCS4A01G151000 chr2A 85.480 427 46 5 2335 2760 777161851 777161440 9.530000e-117 431.0
20 TraesCS4A01G151000 chr2A 96.212 132 5 0 1459 1590 59720426 59720295 2.900000e-52 217.0
21 TraesCS4A01G151000 chr2A 94.776 134 5 2 1457 1590 59331095 59330964 1.750000e-49 207.0
22 TraesCS4A01G151000 chr2A 91.250 80 5 2 4676 4754 192192664 192192742 1.820000e-19 108.0
23 TraesCS4A01G151000 chr1A 85.714 427 46 4 334 745 562115450 562115876 2.050000e-118 436.0
24 TraesCS4A01G151000 chr1A 94.118 136 5 3 1458 1590 494886899 494887034 2.260000e-48 204.0
25 TraesCS4A01G151000 chr7D 86.898 374 40 7 2041 2410 575582181 575581813 1.240000e-110 411.0
26 TraesCS4A01G151000 chr7D 88.950 181 15 4 2580 2756 575581805 575581626 8.080000e-53 219.0
27 TraesCS4A01G151000 chrUn 87.645 259 30 2 2503 2760 478021377 478021120 2.800000e-77 300.0
28 TraesCS4A01G151000 chrUn 84.112 107 17 0 603 709 267848377 267848271 2.360000e-18 104.0
29 TraesCS4A01G151000 chrUn 84.112 107 17 0 603 709 267873356 267873462 2.360000e-18 104.0
30 TraesCS4A01G151000 chrUn 84.112 107 17 0 603 709 276829109 276829003 2.360000e-18 104.0
31 TraesCS4A01G151000 chrUn 84.112 107 17 0 603 709 282416646 282416540 2.360000e-18 104.0
32 TraesCS4A01G151000 chrUn 100.000 28 0 0 2463 2490 478021403 478021376 9.000000e-03 52.8
33 TraesCS4A01G151000 chr5A 94.203 138 4 2 1457 1590 469102500 469102637 1.750000e-49 207.0
34 TraesCS4A01G151000 chr5A 93.007 143 7 2 1448 1590 382961771 382961910 6.290000e-49 206.0
35 TraesCS4A01G151000 chr3A 93.151 146 3 5 1450 1590 674734175 674734032 1.750000e-49 207.0
36 TraesCS4A01G151000 chr1D 94.737 133 5 1 1458 1590 42271589 42271719 6.290000e-49 206.0
37 TraesCS4A01G151000 chr1D 94.074 135 7 1 1457 1590 192568560 192568426 2.260000e-48 204.0
38 TraesCS4A01G151000 chr7B 85.915 142 20 0 604 745 150835158 150835299 8.310000e-33 152.0
39 TraesCS4A01G151000 chr5B 84.112 107 17 0 603 709 595687843 595687949 2.360000e-18 104.0
40 TraesCS4A01G151000 chr5D 88.158 76 7 2 4676 4750 73513496 73513570 6.610000e-14 89.8


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 TraesCS4A01G151000 chr4A 299598686 299603478 4792 True 8852.00 8852 100.0000 1 4793 1 chr4A.!!$R1 4792
1 TraesCS4A01G151000 chr4D 209092006 209100718 8712 False 1281.20 4096 93.6132 752 4675 5 chr4D.!!$F2 3923
2 TraesCS4A01G151000 chr4B 310973434 310977088 3654 False 1105.48 3670 96.4426 765 4387 5 chr4B.!!$F3 3622
3 TraesCS4A01G151000 chr6A 488404960 488405716 756 False 1014.00 1014 91.1840 8 750 1 chr6A.!!$F2 742
4 TraesCS4A01G151000 chr2A 777207402 777208107 705 True 771.00 771 86.3260 2038 2760 1 chr2A.!!$R4 722
5 TraesCS4A01G151000 chr7D 575581626 575582181 555 True 315.00 411 87.9240 2041 2756 2 chr7D.!!$R1 715

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
755 773 0.099436 CAGTGATTTTAGCCCGCTGC 59.901 55.0 0.00 0.0 41.71 5.25 F
1320 4494 0.459237 CCGAGCTCGCAAAGATCTGT 60.459 55.0 30.49 0.0 38.30 3.41 F
2332 5640 0.471211 TCTTGAACTCCCCTGACCGT 60.471 55.0 0.00 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 4748 0.108138 GCCGGCACATCTAAGTGAGT 60.108 55.0 24.80 0.0 42.05 3.41 R
3207 6518 0.178995 TGTTTCTGACAGGCCATGCA 60.179 50.0 5.01 0.0 33.40 3.96 R
4104 7427 0.592637 TGCGCAAACCATCTTGTCAG 59.407 50.0 8.16 0.0 0.00 3.51 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
69 71 1.492176 CCTAGCATCCCACTGTTCCAT 59.508 52.381 0.00 0.00 0.00 3.41
111 113 1.608283 GCTATAACCGCCCAGTCATCC 60.608 57.143 0.00 0.00 0.00 3.51
144 146 3.190535 GTCGGGCTGCTATCAAAAGAAAA 59.809 43.478 0.00 0.00 0.00 2.29
178 180 1.150567 CTGACCGCTAGAGTGCATGC 61.151 60.000 11.82 11.82 0.00 4.06
393 396 2.125391 CCTTGCTGCTCGCTGCTA 60.125 61.111 19.07 12.19 43.37 3.49
436 454 7.907389 TGACTTGTACATAGGAACTCTGATTT 58.093 34.615 0.00 0.00 41.75 2.17
465 483 2.810274 CAGCACTGCATATGGTATGTCC 59.190 50.000 4.56 0.00 0.00 4.02
481 499 6.440010 TGGTATGTCCATTCAACCAAAATCAT 59.560 34.615 0.00 0.00 41.93 2.45
484 502 6.416631 TGTCCATTCAACCAAAATCATTGA 57.583 33.333 0.00 0.00 0.00 2.57
489 507 8.259411 TCCATTCAACCAAAATCATTGATTAGG 58.741 33.333 20.76 20.76 35.14 2.69
498 516 5.505173 AATCATTGATTAGGGCAGAAACG 57.495 39.130 10.16 0.00 29.72 3.60
509 527 1.373570 GCAGAAACGCCATAGCTCTT 58.626 50.000 0.00 0.00 36.60 2.85
573 591 4.288670 TCTAGAAACGTAATCTGGCTCG 57.711 45.455 12.66 0.00 0.00 5.03
583 601 2.463589 ATCTGGCTCGGCGTTTCCAA 62.464 55.000 6.85 4.83 34.01 3.53
587 605 1.154225 GCTCGGCGTTTCCAACATG 60.154 57.895 6.85 0.00 34.01 3.21
592 610 1.729131 GCGTTTCCAACATGCCACG 60.729 57.895 0.00 0.00 0.00 4.94
594 612 0.385473 CGTTTCCAACATGCCACGTC 60.385 55.000 0.00 0.00 0.00 4.34
598 616 2.174107 CAACATGCCACGTCAGCG 59.826 61.111 0.00 0.00 44.93 5.18
627 645 1.741770 CTGGCTAGCTCGGCGTTTT 60.742 57.895 15.72 0.00 0.00 2.43
636 654 1.264826 GCTCGGCGTTTTTAAGTTGGA 59.735 47.619 6.85 0.00 0.00 3.53
648 666 5.473796 TTTAAGTTGGACAGAAACGTCAC 57.526 39.130 0.00 0.00 37.66 3.67
650 668 1.135527 AGTTGGACAGAAACGTCACGA 59.864 47.619 2.91 0.00 37.66 4.35
652 670 2.519377 TGGACAGAAACGTCACGAAT 57.481 45.000 2.91 0.00 37.66 3.34
663 681 2.502510 CACGAATTGTGGCGCTGC 60.503 61.111 7.64 0.29 45.21 5.25
669 687 2.671596 GAATTGTGGCGCTGCTAAAAA 58.328 42.857 7.64 0.00 0.00 1.94
671 689 1.313772 TTGTGGCGCTGCTAAAAAGA 58.686 45.000 7.64 0.00 0.00 2.52
681 699 5.441543 CGCTGCTAAAAAGATCAGATCATG 58.558 41.667 13.14 0.00 0.00 3.07
720 738 9.176181 GTCAAGTTTAATTTGCGACAAAGATTA 57.824 29.630 10.06 3.84 0.00 1.75
721 739 9.906660 TCAAGTTTAATTTGCGACAAAGATTAT 57.093 25.926 10.06 0.00 0.00 1.28
746 764 9.739276 ATTGATAAGGTCAGAACAGTGATTTTA 57.261 29.630 0.00 0.00 38.29 1.52
750 768 3.440522 GGTCAGAACAGTGATTTTAGCCC 59.559 47.826 0.00 0.00 0.00 5.19
751 769 3.125316 GTCAGAACAGTGATTTTAGCCCG 59.875 47.826 0.00 0.00 0.00 6.13
752 770 2.084546 AGAACAGTGATTTTAGCCCGC 58.915 47.619 0.00 0.00 0.00 6.13
753 771 2.084546 GAACAGTGATTTTAGCCCGCT 58.915 47.619 0.00 0.00 0.00 5.52
754 772 1.453155 ACAGTGATTTTAGCCCGCTG 58.547 50.000 0.00 0.00 42.32 5.18
755 773 0.099436 CAGTGATTTTAGCCCGCTGC 59.901 55.000 0.00 0.00 41.71 5.25
829 3988 4.554363 CGCTACGTGGCTCTCCGG 62.554 72.222 22.04 0.00 34.14 5.14
831 3990 2.490217 CTACGTGGCTCTCCGGTG 59.510 66.667 0.00 0.00 34.14 4.94
832 3991 2.034532 TACGTGGCTCTCCGGTGA 59.965 61.111 6.00 6.00 34.14 4.02
835 3994 2.574399 GTGGCTCTCCGGTGACTC 59.426 66.667 0.00 0.00 34.14 3.36
836 3995 3.062466 TGGCTCTCCGGTGACTCG 61.062 66.667 0.00 0.00 34.14 4.18
1320 4494 0.459237 CCGAGCTCGCAAAGATCTGT 60.459 55.000 30.49 0.00 38.30 3.41
1458 4632 7.429340 CCTTATTTGCGACACAGATATTTCAAC 59.571 37.037 0.00 0.00 0.00 3.18
1459 4633 5.681337 TTTGCGACACAGATATTTCAACA 57.319 34.783 0.00 0.00 0.00 3.33
1460 4634 4.926860 TGCGACACAGATATTTCAACAG 57.073 40.909 0.00 0.00 0.00 3.16
1461 4635 4.314961 TGCGACACAGATATTTCAACAGT 58.685 39.130 0.00 0.00 0.00 3.55
1462 4636 4.754618 TGCGACACAGATATTTCAACAGTT 59.245 37.500 0.00 0.00 0.00 3.16
1464 4638 6.142817 GCGACACAGATATTTCAACAGTTTT 58.857 36.000 0.00 0.00 0.00 2.43
1465 4639 6.086765 GCGACACAGATATTTCAACAGTTTTG 59.913 38.462 0.00 0.00 0.00 2.44
1467 4641 7.042797 ACACAGATATTTCAACAGTTTTGCT 57.957 32.000 0.00 0.00 0.00 3.91
1468 4642 8.165239 ACACAGATATTTCAACAGTTTTGCTA 57.835 30.769 0.00 0.00 0.00 3.49
1469 4643 8.629158 ACACAGATATTTCAACAGTTTTGCTAA 58.371 29.630 0.00 0.00 0.00 3.09
1471 4645 9.683069 ACAGATATTTCAACAGTTTTGCTAAAG 57.317 29.630 0.00 0.00 0.00 1.85
1472 4646 8.642020 CAGATATTTCAACAGTTTTGCTAAAGC 58.358 33.333 0.00 0.00 42.50 3.51
1487 4661 5.793026 GCTAAAGCACATCTAGATATGCC 57.207 43.478 28.11 11.97 41.89 4.40
1488 4662 5.240891 GCTAAAGCACATCTAGATATGCCA 58.759 41.667 28.11 15.14 41.89 4.92
1490 4664 7.044181 GCTAAAGCACATCTAGATATGCCATA 58.956 38.462 28.11 20.39 41.89 2.74
1491 4665 7.550551 GCTAAAGCACATCTAGATATGCCATAA 59.449 37.037 28.11 13.25 41.89 1.90
1492 4666 7.918536 AAAGCACATCTAGATATGCCATAAG 57.081 36.000 28.11 5.94 41.89 1.73
1495 4669 8.316497 AGCACATCTAGATATGCCATAAGTAT 57.684 34.615 28.11 8.14 41.89 2.12
1496 4670 8.766476 AGCACATCTAGATATGCCATAAGTATT 58.234 33.333 28.11 7.46 41.89 1.89
1497 4671 8.824781 GCACATCTAGATATGCCATAAGTATTG 58.175 37.037 22.87 1.33 35.32 1.90
1498 4672 8.824781 CACATCTAGATATGCCATAAGTATTGC 58.175 37.037 4.54 0.00 0.00 3.56
1499 4673 8.542926 ACATCTAGATATGCCATAAGTATTGCA 58.457 33.333 4.54 0.09 38.48 4.08
1500 4674 8.824781 CATCTAGATATGCCATAAGTATTGCAC 58.175 37.037 4.54 0.00 37.20 4.57
1501 4675 7.906327 TCTAGATATGCCATAAGTATTGCACA 58.094 34.615 0.00 0.00 37.20 4.57
1502 4676 8.542926 TCTAGATATGCCATAAGTATTGCACAT 58.457 33.333 0.00 0.00 37.20 3.21
1503 4677 7.621428 AGATATGCCATAAGTATTGCACATC 57.379 36.000 7.30 7.30 38.07 3.06
1504 4678 7.400439 AGATATGCCATAAGTATTGCACATCT 58.600 34.615 10.73 10.73 41.15 2.90
1505 4679 8.542926 AGATATGCCATAAGTATTGCACATCTA 58.457 33.333 13.60 0.00 42.90 1.98
1506 4680 9.166173 GATATGCCATAAGTATTGCACATCTAA 57.834 33.333 7.89 0.00 36.14 2.10
1507 4681 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
1508 4682 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
1509 4683 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
1510 4684 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
1511 4685 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
1512 4686 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
1516 4690 8.824159 AGTATTGCACATCTAAGTCATATGTC 57.176 34.615 1.90 0.00 31.60 3.06
1517 4691 8.424133 AGTATTGCACATCTAAGTCATATGTCA 58.576 33.333 1.90 0.00 31.60 3.58
1518 4692 9.212641 GTATTGCACATCTAAGTCATATGTCAT 57.787 33.333 1.90 0.00 31.60 3.06
1519 4693 8.687292 ATTGCACATCTAAGTCATATGTCATT 57.313 30.769 1.90 0.00 31.60 2.57
1520 4694 7.486802 TGCACATCTAAGTCATATGTCATTG 57.513 36.000 1.90 0.00 31.60 2.82
1521 4695 7.274447 TGCACATCTAAGTCATATGTCATTGA 58.726 34.615 1.90 0.00 31.60 2.57
1522 4696 7.935210 TGCACATCTAAGTCATATGTCATTGAT 59.065 33.333 1.90 0.00 31.60 2.57
1523 4697 8.441608 GCACATCTAAGTCATATGTCATTGATC 58.558 37.037 1.90 0.00 31.60 2.92
1524 4698 9.708092 CACATCTAAGTCATATGTCATTGATCT 57.292 33.333 1.90 0.00 31.60 2.75
1538 4712 8.134905 TGTCATTGATCTTACATTGAGATTCG 57.865 34.615 0.00 0.00 34.13 3.34
1539 4713 7.765819 TGTCATTGATCTTACATTGAGATTCGT 59.234 33.333 0.00 0.00 34.13 3.85
1540 4714 8.060679 GTCATTGATCTTACATTGAGATTCGTG 58.939 37.037 0.00 0.00 34.13 4.35
1541 4715 7.765819 TCATTGATCTTACATTGAGATTCGTGT 59.234 33.333 0.00 0.00 34.13 4.49
1542 4716 6.892310 TGATCTTACATTGAGATTCGTGTG 57.108 37.500 0.00 0.00 34.13 3.82
1543 4717 6.630071 TGATCTTACATTGAGATTCGTGTGA 58.370 36.000 0.00 0.00 34.13 3.58
1544 4718 7.096551 TGATCTTACATTGAGATTCGTGTGAA 58.903 34.615 0.00 0.00 38.76 3.18
1546 4720 9.249457 GATCTTACATTGAGATTCGTGTGAATA 57.751 33.333 0.00 0.00 44.79 1.75
1547 4721 9.770097 ATCTTACATTGAGATTCGTGTGAATAT 57.230 29.630 0.00 0.00 44.79 1.28
1548 4722 9.599866 TCTTACATTGAGATTCGTGTGAATATT 57.400 29.630 0.00 0.00 44.79 1.28
1552 4726 8.950210 ACATTGAGATTCGTGTGAATATTTTCT 58.050 29.630 0.00 0.00 44.79 2.52
1553 4727 9.778993 CATTGAGATTCGTGTGAATATTTTCTT 57.221 29.630 0.00 0.00 44.79 2.52
1578 4752 9.814899 TTTTTCTTTTTATGCTTGATTCACTCA 57.185 25.926 0.00 0.00 0.00 3.41
1579 4753 8.801715 TTTCTTTTTATGCTTGATTCACTCAC 57.198 30.769 0.00 0.00 32.17 3.51
1580 4754 7.750229 TCTTTTTATGCTTGATTCACTCACT 57.250 32.000 0.00 0.00 32.17 3.41
1581 4755 8.169977 TCTTTTTATGCTTGATTCACTCACTT 57.830 30.769 0.00 0.00 32.17 3.16
1582 4756 9.283768 TCTTTTTATGCTTGATTCACTCACTTA 57.716 29.630 0.00 0.00 32.17 2.24
1583 4757 9.552114 CTTTTTATGCTTGATTCACTCACTTAG 57.448 33.333 0.00 0.00 32.17 2.18
1584 4758 8.846943 TTTTATGCTTGATTCACTCACTTAGA 57.153 30.769 0.00 0.00 32.17 2.10
1585 4759 9.453572 TTTTATGCTTGATTCACTCACTTAGAT 57.546 29.630 0.00 0.00 32.17 1.98
1586 4760 6.922247 ATGCTTGATTCACTCACTTAGATG 57.078 37.500 0.00 0.00 32.17 2.90
1689 4891 8.506168 TGCAGTAGTTTAGAAATTTATGAGGG 57.494 34.615 0.00 0.00 0.00 4.30
1721 4923 2.375174 TGTAGGCCAGGATTTGAGTTGT 59.625 45.455 5.01 0.00 0.00 3.32
1725 4927 1.915141 CCAGGATTTGAGTTGTGGCT 58.085 50.000 0.00 0.00 0.00 4.75
1743 4945 7.701539 TGTGGCTTTTCTGTATGATTTATGT 57.298 32.000 0.00 0.00 0.00 2.29
1804 5006 4.142687 CGGATGCGAGTTTAATTTCTGGTT 60.143 41.667 0.00 0.00 0.00 3.67
1846 5050 9.693739 AACTTGTGGTATTTGTATATGGAATCA 57.306 29.630 0.00 0.00 0.00 2.57
1882 5086 7.657336 TCTCAATGGTGATGGAAAGTAAAAAC 58.343 34.615 0.00 0.00 31.85 2.43
1946 5158 6.691388 CGTTAGCTTATAATTTTCAAGGTGGC 59.309 38.462 0.00 0.00 32.63 5.01
2029 5331 0.610232 ACATGAGCTTCTGTTGCCCC 60.610 55.000 0.00 0.00 0.00 5.80
2224 5531 1.063031 GGCTGAGTTTTGCGAATTGC 58.937 50.000 0.00 0.00 46.70 3.56
2244 5552 1.620819 CTTGCAGGATATCGCCCTAGT 59.379 52.381 0.00 0.00 31.64 2.57
2260 5568 3.199946 CCCTAGTAGATTTGGCTCCAACA 59.800 47.826 0.00 0.00 35.46 3.33
2332 5640 0.471211 TCTTGAACTCCCCTGACCGT 60.471 55.000 0.00 0.00 0.00 4.83
2576 5884 2.811410 AGCTGCAGGAAATCAATCCAA 58.189 42.857 17.12 0.00 42.27 3.53
2624 5932 6.072342 GGGGAAAGTTGATAAAGCTTTCGTAA 60.072 38.462 16.57 6.41 45.19 3.18
2903 6214 1.369689 CTGTTCGTGCTTGTGCTGC 60.370 57.895 0.00 0.00 40.48 5.25
3054 6365 8.279970 TGTGCTGTCTACTTTGCATTAAATAT 57.720 30.769 0.00 0.00 37.76 1.28
3055 6366 8.183536 TGTGCTGTCTACTTTGCATTAAATATG 58.816 33.333 0.00 0.00 37.76 1.78
3057 6368 8.183536 TGCTGTCTACTTTGCATTAAATATGTG 58.816 33.333 0.00 0.00 0.00 3.21
3065 6376 9.467258 ACTTTGCATTAAATATGTGATATGCAC 57.533 29.630 7.03 0.00 45.44 4.57
3066 6377 9.687210 CTTTGCATTAAATATGTGATATGCACT 57.313 29.630 7.03 0.00 45.44 4.40
3068 6379 9.465985 TTGCATTAAATATGTGATATGCACTTG 57.534 29.630 7.03 0.00 45.44 3.16
3077 6388 5.376854 GTGATATGCACTTGTTGTTCCTT 57.623 39.130 0.00 0.00 44.27 3.36
3078 6389 5.772521 GTGATATGCACTTGTTGTTCCTTT 58.227 37.500 0.00 0.00 44.27 3.11
3079 6390 5.630680 GTGATATGCACTTGTTGTTCCTTTG 59.369 40.000 0.00 0.00 44.27 2.77
3207 6518 6.701340 TCAGTGTGCATGTAGACTAAGATTT 58.299 36.000 13.18 0.00 0.00 2.17
3208 6519 6.591448 TCAGTGTGCATGTAGACTAAGATTTG 59.409 38.462 13.18 1.12 0.00 2.32
3237 6548 7.121168 TGGCCTGTCAGAAACATAGATTTAAAG 59.879 37.037 3.32 0.00 37.23 1.85
3283 6597 2.306341 TTAGTCTCATGCTCTGCTGC 57.694 50.000 0.00 0.00 0.00 5.25
3320 6634 9.614792 GATGTTGTAGGTAAAGTGATTTATCCT 57.385 33.333 0.00 0.00 0.00 3.24
3349 6663 0.930310 CATGATAGTGTGAACCGCGG 59.070 55.000 26.86 26.86 0.00 6.46
3352 6666 0.997196 GATAGTGTGAACCGCGGAAC 59.003 55.000 35.90 25.54 0.00 3.62
3558 6872 2.896685 GGCTATATCAGAGCTGGACAGT 59.103 50.000 0.00 0.00 39.98 3.55
3654 6968 2.878406 CGACACCAATGTGAGTTTCCTT 59.122 45.455 0.00 0.00 45.76 3.36
3655 6969 3.303990 CGACACCAATGTGAGTTTCCTTG 60.304 47.826 0.00 0.00 45.76 3.61
3690 7004 5.869579 ACAGCTTTCCTTTCTGTCTTCATA 58.130 37.500 0.00 0.00 36.42 2.15
3701 7015 6.932356 TTCTGTCTTCATATTTCTCATGCC 57.068 37.500 0.00 0.00 0.00 4.40
3703 7017 6.417258 TCTGTCTTCATATTTCTCATGCCAA 58.583 36.000 0.00 0.00 0.00 4.52
3712 7026 0.179004 TCTCATGCCAACCGGTGTTT 60.179 50.000 8.52 0.00 30.42 2.83
3805 7119 3.753272 CGGACAGTGAGGTGAATGAAAAT 59.247 43.478 0.00 0.00 0.00 1.82
3898 7212 8.177663 CACTACCTCTGTTTAATTATGCACTTG 58.822 37.037 0.00 0.00 0.00 3.16
3930 7244 2.164422 GGGCTATGTTTTTCTGGTGCTC 59.836 50.000 0.00 0.00 0.00 4.26
4047 7361 1.872952 TGTTTGGTGAGACTTGATGCG 59.127 47.619 0.00 0.00 0.00 4.73
4057 7372 4.941873 TGAGACTTGATGCGACTAGACTAA 59.058 41.667 0.00 0.00 0.00 2.24
4071 7386 6.684555 CGACTAGACTAATTTGCTGAAATTGC 59.315 38.462 0.00 0.00 41.09 3.56
4104 7427 5.627499 TCATGTTTGGCTGAACTACATTC 57.373 39.130 0.00 0.00 37.88 2.67
4113 7436 5.181748 GGCTGAACTACATTCTGACAAGAT 58.818 41.667 0.00 0.00 42.48 2.40
4212 7535 3.056322 ACCTGATTGATGCTTTTCTTGGC 60.056 43.478 0.00 0.00 0.00 4.52
4213 7536 3.518590 CTGATTGATGCTTTTCTTGGCC 58.481 45.455 0.00 0.00 0.00 5.36
4265 7588 1.200020 GCTTTGCTGCGTTGTTCCTAT 59.800 47.619 0.00 0.00 0.00 2.57
4290 7613 3.433343 TCTTGGCATTGTCATGGTGATT 58.567 40.909 4.53 0.00 0.00 2.57
4360 9384 4.627467 CCTTCCTGAAGAATGTAACGTGAG 59.373 45.833 8.46 0.00 40.79 3.51
4375 9399 4.207891 ACGTGAGCTAAATGAGGAATGT 57.792 40.909 0.00 0.00 0.00 2.71
4376 9400 4.579869 ACGTGAGCTAAATGAGGAATGTT 58.420 39.130 0.00 0.00 0.00 2.71
4466 9490 2.099756 GTCAGTGTTTTCCTTGCAAGCT 59.900 45.455 21.43 7.77 0.00 3.74
4467 9491 2.099592 TCAGTGTTTTCCTTGCAAGCTG 59.900 45.455 21.43 18.81 0.00 4.24
4493 9517 6.925610 TTATAATAGCACCTTGAGCAACTG 57.074 37.500 0.00 0.00 0.00 3.16
4494 9518 2.119801 ATAGCACCTTGAGCAACTGG 57.880 50.000 0.00 0.00 0.00 4.00
4495 9519 1.055849 TAGCACCTTGAGCAACTGGA 58.944 50.000 0.00 0.00 0.00 3.86
4496 9520 0.183492 AGCACCTTGAGCAACTGGAA 59.817 50.000 0.00 0.00 0.00 3.53
4498 9522 0.595095 CACCTTGAGCAACTGGAAGC 59.405 55.000 0.00 0.00 37.60 3.86
4500 9524 1.321474 CCTTGAGCAACTGGAAGCAA 58.679 50.000 0.00 0.00 37.60 3.91
4501 9525 1.891150 CCTTGAGCAACTGGAAGCAAT 59.109 47.619 0.00 0.00 37.60 3.56
4502 9526 2.298163 CCTTGAGCAACTGGAAGCAATT 59.702 45.455 0.00 0.00 37.60 2.32
4503 9527 3.572584 CTTGAGCAACTGGAAGCAATTC 58.427 45.455 0.00 0.00 37.60 2.17
4518 9543 4.067192 AGCAATTCTTTTTGGGATGCAAC 58.933 39.130 0.00 0.00 34.89 4.17
4579 9649 5.863935 GGAACTGAATTTGTACAATCTTGCC 59.136 40.000 9.56 1.55 0.00 4.52
4613 9683 7.144000 GGATCTCAAATGGATGCAACTTATTC 58.856 38.462 0.00 0.00 32.90 1.75
4684 9756 9.959721 TTGCTACATTAAATCTCTAGGAAAACT 57.040 29.630 0.00 0.00 0.00 2.66
4713 9785 9.624373 AGAAAGTAAGATAACATGCATCTCAAT 57.376 29.630 10.07 0.00 31.45 2.57
4716 9788 8.388484 AGTAAGATAACATGCATCTCAATTCC 57.612 34.615 10.07 0.00 31.45 3.01
4717 9789 8.216423 AGTAAGATAACATGCATCTCAATTCCT 58.784 33.333 10.07 0.00 31.45 3.36
4718 9790 9.494271 GTAAGATAACATGCATCTCAATTCCTA 57.506 33.333 10.07 0.00 31.45 2.94
4721 9793 9.887629 AGATAACATGCATCTCAATTCCTATAG 57.112 33.333 0.00 0.00 0.00 1.31
4722 9794 9.107177 GATAACATGCATCTCAATTCCTATAGG 57.893 37.037 13.07 13.07 0.00 2.57
4723 9795 6.692849 ACATGCATCTCAATTCCTATAGGA 57.307 37.500 18.00 18.00 43.73 2.94
4766 9838 8.700145 TTCATAGGATAGGAATACCATGGAAT 57.300 34.615 21.47 3.22 36.32 3.01
4767 9839 9.797732 TTCATAGGATAGGAATACCATGGAATA 57.202 33.333 21.47 0.67 36.32 1.75
4768 9840 9.439461 TCATAGGATAGGAATACCATGGAATAG 57.561 37.037 21.47 0.00 38.94 1.73
4769 9841 8.654997 CATAGGATAGGAATACCATGGAATAGG 58.345 40.741 21.47 0.00 38.94 2.57
4770 9842 6.826727 AGGATAGGAATACCATGGAATAGGA 58.173 40.000 21.47 0.00 38.94 2.94
4771 9843 7.263901 AGGATAGGAATACCATGGAATAGGAA 58.736 38.462 21.47 0.00 38.94 3.36
4772 9844 7.744068 AGGATAGGAATACCATGGAATAGGAAA 59.256 37.037 21.47 0.00 38.94 3.13
4773 9845 8.390921 GGATAGGAATACCATGGAATAGGAAAA 58.609 37.037 21.47 0.00 38.94 2.29
4774 9846 9.232473 GATAGGAATACCATGGAATAGGAAAAC 57.768 37.037 21.47 0.00 38.94 2.43
4775 9847 7.226059 AGGAATACCATGGAATAGGAAAACT 57.774 36.000 21.47 0.14 38.94 2.66
4776 9848 8.344939 AGGAATACCATGGAATAGGAAAACTA 57.655 34.615 21.47 0.00 38.94 2.24
4777 9849 8.960064 AGGAATACCATGGAATAGGAAAACTAT 58.040 33.333 21.47 0.00 40.35 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.689345 GCTAGGCTAGACTCGTTTGAAAAA 59.311 41.667 25.37 0.00 0.00 1.94
40 41 0.885196 GGGATGCTAGGCTAGACTCG 59.115 60.000 25.37 0.00 0.00 4.18
69 71 0.261991 AGCTGGATTCTCCCCTACGA 59.738 55.000 0.00 0.00 35.03 3.43
91 93 1.608283 GGATGACTGGGCGGTTATAGC 60.608 57.143 0.00 0.00 0.00 2.97
94 96 1.046472 TCGGATGACTGGGCGGTTAT 61.046 55.000 0.00 0.00 0.00 1.89
111 113 0.374758 CAGCCCGACATGTCAATTCG 59.625 55.000 24.93 11.46 0.00 3.34
144 146 1.119684 GTCAGCCACCCCTTGTTTTT 58.880 50.000 0.00 0.00 0.00 1.94
159 161 1.150567 GCATGCACTCTAGCGGTCAG 61.151 60.000 14.21 0.00 37.31 3.51
178 180 0.873054 CACCTGCTGCTTCAGACAAG 59.127 55.000 0.00 0.00 36.19 3.16
226 229 6.461092 CGCTCACATAAGATCCCACTAAGTAA 60.461 42.308 0.00 0.00 0.00 2.24
352 355 0.817654 CGACTCCCTGACATGCAGTA 59.182 55.000 13.67 3.93 43.33 2.74
393 396 4.511527 AGTCAATTCGATGAGACAATGCT 58.488 39.130 12.29 0.00 33.56 3.79
465 483 7.011669 GCCCTAATCAATGATTTTGGTTGAATG 59.988 37.037 14.15 4.91 35.70 2.67
498 516 2.436417 TGAAACACCAAGAGCTATGGC 58.564 47.619 16.11 0.00 41.89 4.40
506 524 3.064207 GACACGCTATGAAACACCAAGA 58.936 45.455 0.00 0.00 0.00 3.02
509 527 2.535012 TGACACGCTATGAAACACCA 57.465 45.000 0.00 0.00 0.00 4.17
583 601 2.433145 CTCGCTGACGTGGCATGT 60.433 61.111 13.11 13.11 41.18 3.21
627 645 3.552699 CGTGACGTTTCTGTCCAACTTAA 59.447 43.478 0.00 0.00 38.11 1.85
648 666 0.167908 TTTAGCAGCGCCACAATTCG 59.832 50.000 2.29 0.00 0.00 3.34
650 668 2.295909 TCTTTTTAGCAGCGCCACAATT 59.704 40.909 2.29 0.00 0.00 2.32
652 670 1.313772 TCTTTTTAGCAGCGCCACAA 58.686 45.000 2.29 0.00 0.00 3.33
659 677 6.615264 TCATGATCTGATCTTTTTAGCAGC 57.385 37.500 17.82 0.00 32.90 5.25
687 705 7.489435 TGTCGCAAATTAAACTTGACATGAAAA 59.511 29.630 0.00 0.00 30.61 2.29
703 721 9.520204 CCTTATCAATAATCTTTGTCGCAAATT 57.480 29.630 5.66 2.36 0.00 1.82
704 722 8.686334 ACCTTATCAATAATCTTTGTCGCAAAT 58.314 29.630 5.66 0.00 0.00 2.32
709 727 8.648557 TCTGACCTTATCAATAATCTTTGTCG 57.351 34.615 0.00 0.00 36.69 4.35
720 738 8.641498 AAAATCACTGTTCTGACCTTATCAAT 57.359 30.769 0.00 0.00 36.69 2.57
721 739 9.219603 CTAAAATCACTGTTCTGACCTTATCAA 57.780 33.333 0.00 0.00 36.69 2.57
750 768 1.195347 CGTGAGTATCTTCAGCAGCG 58.805 55.000 0.00 0.00 34.92 5.18
751 769 0.926846 GCGTGAGTATCTTCAGCAGC 59.073 55.000 0.00 0.00 34.92 5.25
752 770 1.565305 GGCGTGAGTATCTTCAGCAG 58.435 55.000 0.00 0.00 34.92 4.24
753 771 0.175760 GGGCGTGAGTATCTTCAGCA 59.824 55.000 0.00 0.00 34.92 4.41
754 772 0.461961 AGGGCGTGAGTATCTTCAGC 59.538 55.000 0.00 0.00 34.92 4.26
755 773 1.067821 GGAGGGCGTGAGTATCTTCAG 59.932 57.143 0.00 0.00 34.92 3.02
756 774 1.112113 GGAGGGCGTGAGTATCTTCA 58.888 55.000 0.00 0.00 34.92 3.02
757 775 0.389757 GGGAGGGCGTGAGTATCTTC 59.610 60.000 0.00 0.00 34.92 2.87
758 776 0.325296 TGGGAGGGCGTGAGTATCTT 60.325 55.000 0.00 0.00 34.92 2.40
853 4021 2.047061 CGATGGGGATTTGAGGAGGTA 58.953 52.381 0.00 0.00 0.00 3.08
907 4081 0.793861 GAGGCAATACGCGTTTGTGA 59.206 50.000 20.78 0.00 43.84 3.58
1011 4185 3.726631 CTCGTCTCGCGTCTGCTCC 62.727 68.421 5.77 0.00 42.13 4.70
1016 4190 3.855589 CGCTCTCGTCTCGCGTCT 61.856 66.667 5.77 0.00 41.78 4.18
1269 4443 2.198287 GCGGTAGGAGCGGATGGTA 61.198 63.158 0.00 0.00 39.82 3.25
1472 4646 8.824781 GCAATACTTATGGCATATCTAGATGTG 58.175 37.037 21.61 21.61 32.79 3.21
1474 4648 8.824781 GTGCAATACTTATGGCATATCTAGATG 58.175 37.037 15.79 2.00 43.91 2.90
1475 4649 8.542926 TGTGCAATACTTATGGCATATCTAGAT 58.457 33.333 10.73 10.73 43.91 1.98
1477 4651 8.728337 ATGTGCAATACTTATGGCATATCTAG 57.272 34.615 8.24 5.61 43.91 2.43
1481 4655 9.170734 CTTAGATGTGCAATACTTATGGCATAT 57.829 33.333 8.24 7.39 44.11 1.78
1484 4658 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
1485 4659 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
1486 4660 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
1490 4664 9.265901 GACATATGACTTAGATGTGCAATACTT 57.734 33.333 10.38 0.00 41.09 2.24
1491 4665 8.424133 TGACATATGACTTAGATGTGCAATACT 58.576 33.333 10.38 0.00 41.09 2.12
1492 4666 8.593492 TGACATATGACTTAGATGTGCAATAC 57.407 34.615 10.38 0.00 41.09 1.89
1495 4669 7.769970 TCAATGACATATGACTTAGATGTGCAA 59.230 33.333 10.38 0.00 41.09 4.08
1496 4670 7.274447 TCAATGACATATGACTTAGATGTGCA 58.726 34.615 10.38 0.00 41.09 4.57
1497 4671 7.719778 TCAATGACATATGACTTAGATGTGC 57.280 36.000 10.38 0.00 41.09 4.57
1498 4672 9.708092 AGATCAATGACATATGACTTAGATGTG 57.292 33.333 10.38 0.00 41.09 3.21
1512 4686 8.771766 CGAATCTCAATGTAAGATCAATGACAT 58.228 33.333 0.00 0.00 32.29 3.06
1513 4687 7.765819 ACGAATCTCAATGTAAGATCAATGACA 59.234 33.333 0.00 0.00 32.29 3.58
1514 4688 8.060679 CACGAATCTCAATGTAAGATCAATGAC 58.939 37.037 0.00 0.00 32.29 3.06
1515 4689 7.765819 ACACGAATCTCAATGTAAGATCAATGA 59.234 33.333 0.00 0.00 32.29 2.57
1516 4690 7.849515 CACACGAATCTCAATGTAAGATCAATG 59.150 37.037 0.00 0.00 32.29 2.82
1517 4691 7.765819 TCACACGAATCTCAATGTAAGATCAAT 59.234 33.333 0.00 0.00 32.29 2.57
1518 4692 7.096551 TCACACGAATCTCAATGTAAGATCAA 58.903 34.615 0.00 0.00 32.29 2.57
1519 4693 6.630071 TCACACGAATCTCAATGTAAGATCA 58.370 36.000 0.00 0.00 32.29 2.92
1520 4694 7.525688 TTCACACGAATCTCAATGTAAGATC 57.474 36.000 0.00 0.00 32.29 2.75
1521 4695 9.770097 ATATTCACACGAATCTCAATGTAAGAT 57.230 29.630 0.00 0.00 41.09 2.40
1522 4696 9.599866 AATATTCACACGAATCTCAATGTAAGA 57.400 29.630 0.00 0.00 41.09 2.10
1526 4700 8.950210 AGAAAATATTCACACGAATCTCAATGT 58.050 29.630 0.00 0.00 41.09 2.71
1527 4701 9.778993 AAGAAAATATTCACACGAATCTCAATG 57.221 29.630 0.00 0.00 41.09 2.82
1552 4726 9.814899 TGAGTGAATCAAGCATAAAAAGAAAAA 57.185 25.926 0.00 0.00 34.02 1.94
1553 4727 9.248291 GTGAGTGAATCAAGCATAAAAAGAAAA 57.752 29.630 0.00 0.00 40.43 2.29
1554 4728 8.632679 AGTGAGTGAATCAAGCATAAAAAGAAA 58.367 29.630 0.00 0.00 40.43 2.52
1555 4729 8.169977 AGTGAGTGAATCAAGCATAAAAAGAA 57.830 30.769 0.00 0.00 40.43 2.52
1556 4730 7.750229 AGTGAGTGAATCAAGCATAAAAAGA 57.250 32.000 0.00 0.00 40.43 2.52
1557 4731 9.552114 CTAAGTGAGTGAATCAAGCATAAAAAG 57.448 33.333 0.00 0.00 40.43 2.27
1558 4732 9.283768 TCTAAGTGAGTGAATCAAGCATAAAAA 57.716 29.630 0.00 0.00 40.43 1.94
1559 4733 8.846943 TCTAAGTGAGTGAATCAAGCATAAAA 57.153 30.769 0.00 0.00 40.43 1.52
1560 4734 8.886719 CATCTAAGTGAGTGAATCAAGCATAAA 58.113 33.333 0.00 0.00 40.43 1.40
1561 4735 8.043113 ACATCTAAGTGAGTGAATCAAGCATAA 58.957 33.333 0.00 0.00 40.43 1.90
1562 4736 7.493645 CACATCTAAGTGAGTGAATCAAGCATA 59.506 37.037 0.00 0.00 42.05 3.14
1563 4737 6.315642 CACATCTAAGTGAGTGAATCAAGCAT 59.684 38.462 0.00 0.00 42.05 3.79
1564 4738 5.640783 CACATCTAAGTGAGTGAATCAAGCA 59.359 40.000 0.00 0.00 42.05 3.91
1565 4739 5.447010 GCACATCTAAGTGAGTGAATCAAGC 60.447 44.000 0.00 0.00 42.05 4.01
1566 4740 5.064452 GGCACATCTAAGTGAGTGAATCAAG 59.936 44.000 0.00 0.00 42.05 3.02
1567 4741 4.937620 GGCACATCTAAGTGAGTGAATCAA 59.062 41.667 0.00 0.00 42.05 2.57
1568 4742 4.507710 GGCACATCTAAGTGAGTGAATCA 58.492 43.478 0.00 0.00 42.05 2.57
1569 4743 3.553511 CGGCACATCTAAGTGAGTGAATC 59.446 47.826 0.00 0.00 42.05 2.52
1570 4744 3.525537 CGGCACATCTAAGTGAGTGAAT 58.474 45.455 0.00 0.00 42.05 2.57
1571 4745 2.353704 CCGGCACATCTAAGTGAGTGAA 60.354 50.000 0.00 0.00 42.05 3.18
1572 4746 1.204704 CCGGCACATCTAAGTGAGTGA 59.795 52.381 0.00 0.00 42.05 3.41
1573 4747 1.645034 CCGGCACATCTAAGTGAGTG 58.355 55.000 0.00 0.00 42.05 3.51
1574 4748 0.108138 GCCGGCACATCTAAGTGAGT 60.108 55.000 24.80 0.00 42.05 3.41
1575 4749 1.148157 CGCCGGCACATCTAAGTGAG 61.148 60.000 28.98 0.12 42.05 3.51
1576 4750 1.153647 CGCCGGCACATCTAAGTGA 60.154 57.895 28.98 0.00 42.05 3.41
1577 4751 2.813179 GCGCCGGCACATCTAAGTG 61.813 63.158 28.98 6.77 42.37 3.16
1578 4752 2.511600 GCGCCGGCACATCTAAGT 60.512 61.111 28.98 0.00 39.62 2.24
1579 4753 3.272334 GGCGCCGGCACATCTAAG 61.272 66.667 28.98 8.44 42.47 2.18
1580 4754 4.849310 GGGCGCCGGCACATCTAA 62.849 66.667 28.98 0.00 44.02 2.10
1618 4792 4.838423 TCATATCACATCCCGTTACTCCAT 59.162 41.667 0.00 0.00 0.00 3.41
1619 4793 4.219919 TCATATCACATCCCGTTACTCCA 58.780 43.478 0.00 0.00 0.00 3.86
1620 4794 4.866508 TCATATCACATCCCGTTACTCC 57.133 45.455 0.00 0.00 0.00 3.85
1665 4867 8.507524 ACCCTCATAAATTTCTAAACTACTGC 57.492 34.615 0.00 0.00 0.00 4.40
1689 4891 0.821711 TGGCCTACACAGCACCAAAC 60.822 55.000 3.32 0.00 0.00 2.93
1804 5006 5.587043 CCACAAGTTAACTTACCAACAGACA 59.413 40.000 20.15 0.00 34.28 3.41
1846 5050 9.699410 TCCATCACCATTGAGAAAATAAACTAT 57.301 29.630 0.00 0.00 34.35 2.12
1882 5086 9.577110 AGCACTAACAAATATCACAATCATTTG 57.423 29.630 5.06 5.06 42.61 2.32
2029 5331 2.389059 AGAAATCAGATGTCGATCGCG 58.611 47.619 11.09 0.00 39.35 5.87
2204 5509 1.336240 GCAATTCGCAAAACTCAGCCT 60.336 47.619 0.00 0.00 41.79 4.58
2224 5531 1.620819 ACTAGGGCGATATCCTGCAAG 59.379 52.381 5.18 2.53 35.92 4.01
2244 5552 2.554344 GGGTGTGTTGGAGCCAAATCTA 60.554 50.000 3.05 0.00 37.70 1.98
2260 5568 2.765969 CCAAGCCTGATGGGGTGT 59.234 61.111 0.00 0.00 46.33 4.16
2522 5830 0.392461 GGTTGCCGCAGAACCTATCA 60.392 55.000 6.94 0.00 39.94 2.15
2652 5961 5.636903 AGCATAGTAACTTCCATGGTGAT 57.363 39.130 12.58 3.71 0.00 3.06
2696 6005 6.352016 AGATTGAGCAGTTCAGAAGTTAGA 57.648 37.500 0.00 0.00 37.07 2.10
2858 6169 0.312102 GCCAGCAGACAAACAACTCC 59.688 55.000 0.00 0.00 0.00 3.85
2889 6200 2.948323 CATGCAGCACAAGCACGA 59.052 55.556 0.00 0.00 45.95 4.35
3055 6366 5.376854 AAGGAACAACAAGTGCATATCAC 57.623 39.130 0.00 0.00 45.98 3.06
3057 6368 5.163513 CCAAAGGAACAACAAGTGCATATC 58.836 41.667 0.00 0.00 0.00 1.63
3059 6370 3.957497 ACCAAAGGAACAACAAGTGCATA 59.043 39.130 0.00 0.00 0.00 3.14
3060 6371 2.765699 ACCAAAGGAACAACAAGTGCAT 59.234 40.909 0.00 0.00 0.00 3.96
3061 6372 2.165437 GACCAAAGGAACAACAAGTGCA 59.835 45.455 0.00 0.00 0.00 4.57
3062 6373 2.481276 GGACCAAAGGAACAACAAGTGC 60.481 50.000 0.00 0.00 0.00 4.40
3063 6374 2.100749 GGGACCAAAGGAACAACAAGTG 59.899 50.000 0.00 0.00 0.00 3.16
3064 6375 2.024369 AGGGACCAAAGGAACAACAAGT 60.024 45.455 0.00 0.00 0.00 3.16
3065 6376 2.623416 GAGGGACCAAAGGAACAACAAG 59.377 50.000 0.00 0.00 0.00 3.16
3066 6377 2.024846 TGAGGGACCAAAGGAACAACAA 60.025 45.455 0.00 0.00 0.00 2.83
3067 6378 1.566703 TGAGGGACCAAAGGAACAACA 59.433 47.619 0.00 0.00 0.00 3.33
3068 6379 2.358322 TGAGGGACCAAAGGAACAAC 57.642 50.000 0.00 0.00 0.00 3.32
3069 6380 3.655777 ACTATGAGGGACCAAAGGAACAA 59.344 43.478 0.00 0.00 0.00 2.83
3070 6381 3.256704 ACTATGAGGGACCAAAGGAACA 58.743 45.455 0.00 0.00 0.00 3.18
3071 6382 3.519913 AGACTATGAGGGACCAAAGGAAC 59.480 47.826 0.00 0.00 0.00 3.62
3072 6383 3.519510 CAGACTATGAGGGACCAAAGGAA 59.480 47.826 0.00 0.00 0.00 3.36
3073 6384 3.107601 CAGACTATGAGGGACCAAAGGA 58.892 50.000 0.00 0.00 0.00 3.36
3074 6385 2.420687 GCAGACTATGAGGGACCAAAGG 60.421 54.545 0.00 0.00 0.00 3.11
3075 6386 2.503356 AGCAGACTATGAGGGACCAAAG 59.497 50.000 0.00 0.00 0.00 2.77
3076 6387 2.237143 CAGCAGACTATGAGGGACCAAA 59.763 50.000 0.00 0.00 0.00 3.28
3077 6388 1.833630 CAGCAGACTATGAGGGACCAA 59.166 52.381 0.00 0.00 0.00 3.67
3078 6389 1.007118 TCAGCAGACTATGAGGGACCA 59.993 52.381 0.00 0.00 0.00 4.02
3079 6390 1.781786 TCAGCAGACTATGAGGGACC 58.218 55.000 0.00 0.00 0.00 4.46
3207 6518 0.178995 TGTTTCTGACAGGCCATGCA 60.179 50.000 5.01 0.00 33.40 3.96
3208 6519 1.180029 ATGTTTCTGACAGGCCATGC 58.820 50.000 5.01 0.00 42.62 4.06
3320 6634 7.497595 GGTTCACACTATCATGGTAGACATTA 58.502 38.462 20.00 0.00 37.84 1.90
3349 6663 8.603242 TCTTATTGAGAAACCACTACAAGTTC 57.397 34.615 0.00 0.00 0.00 3.01
3352 6666 9.003658 ACATTCTTATTGAGAAACCACTACAAG 57.996 33.333 0.00 0.00 46.90 3.16
3534 6848 2.163412 GTCCAGCTCTGATATAGCCTCG 59.837 54.545 0.00 0.00 41.02 4.63
3558 6872 3.134081 CCTTGTAGGATTCCTCGCCTAAA 59.866 47.826 8.94 0.00 37.67 1.85
3671 6985 9.224267 TGAGAAATATGAAGACAGAAAGGAAAG 57.776 33.333 0.00 0.00 0.00 2.62
3690 7004 1.176527 CACCGGTTGGCATGAGAAAT 58.823 50.000 2.97 0.00 39.70 2.17
3712 7026 4.735369 TCCTCCTGCAAAGTTGGATAAAA 58.265 39.130 0.00 0.00 0.00 1.52
3725 7039 0.904649 ATCAACGTCATCCTCCTGCA 59.095 50.000 0.00 0.00 0.00 4.41
3805 7119 2.884012 CCCAACAATGCACAGACTGTTA 59.116 45.455 5.04 0.00 31.00 2.41
3898 7212 5.966742 AAAACATAGCCCAGAAACTTCTC 57.033 39.130 0.00 0.00 34.74 2.87
3930 7244 2.620115 ACGAATCCAGCCAGCATTTATG 59.380 45.455 0.00 0.00 0.00 1.90
4034 7348 3.348119 AGTCTAGTCGCATCAAGTCTCA 58.652 45.455 0.00 0.00 0.00 3.27
4047 7361 6.684555 CGCAATTTCAGCAAATTAGTCTAGTC 59.315 38.462 0.00 0.00 39.75 2.59
4057 7372 3.701040 AGGATACCGCAATTTCAGCAAAT 59.299 39.130 0.00 0.00 32.34 2.32
4071 7386 2.097466 GCCAAACATGAACAGGATACCG 59.903 50.000 0.00 0.00 37.17 4.02
4104 7427 0.592637 TGCGCAAACCATCTTGTCAG 59.407 50.000 8.16 0.00 0.00 3.51
4113 7436 1.406898 TGAACATCTTTGCGCAAACCA 59.593 42.857 30.63 20.15 0.00 3.67
4165 7488 5.152623 ACCTTGACATTCTTCTCAATCGA 57.847 39.130 0.00 0.00 0.00 3.59
4212 7535 2.875933 TCTAGTTGCAACGAAAACTGGG 59.124 45.455 23.21 5.33 37.23 4.45
4213 7536 4.527564 CTTCTAGTTGCAACGAAAACTGG 58.472 43.478 23.21 7.43 37.23 4.00
4256 7579 5.716228 ACAATGCCAAGAATGATAGGAACAA 59.284 36.000 0.00 0.00 0.00 2.83
4257 7580 5.263599 ACAATGCCAAGAATGATAGGAACA 58.736 37.500 0.00 0.00 0.00 3.18
4265 7588 3.193903 CACCATGACAATGCCAAGAATGA 59.806 43.478 0.00 0.00 31.93 2.57
4290 7613 4.094739 CGCATCGGATTATTTGCCATATCA 59.905 41.667 0.00 0.00 0.00 2.15
4466 9490 8.210946 AGTTGCTCAAGGTGCTATTATAATACA 58.789 33.333 0.81 3.09 0.00 2.29
4467 9491 8.499162 CAGTTGCTCAAGGTGCTATTATAATAC 58.501 37.037 0.81 0.00 0.00 1.89
4493 9517 3.686241 GCATCCCAAAAAGAATTGCTTCC 59.314 43.478 0.00 0.00 35.24 3.46
4494 9518 4.317488 TGCATCCCAAAAAGAATTGCTTC 58.683 39.130 0.00 0.00 35.24 3.86
4495 9519 4.354893 TGCATCCCAAAAAGAATTGCTT 57.645 36.364 0.00 0.00 38.88 3.91
4496 9520 4.067192 GTTGCATCCCAAAAAGAATTGCT 58.933 39.130 0.00 0.00 34.68 3.91
4498 9522 6.374565 TTTGTTGCATCCCAAAAAGAATTG 57.625 33.333 4.73 0.00 32.43 2.32
4500 9524 7.427214 CAAATTTGTTGCATCCCAAAAAGAAT 58.573 30.769 10.15 0.00 32.43 2.40
4501 9525 6.183360 CCAAATTTGTTGCATCCCAAAAAGAA 60.183 34.615 16.73 0.00 32.43 2.52
4502 9526 5.298777 CCAAATTTGTTGCATCCCAAAAAGA 59.701 36.000 16.73 0.00 32.43 2.52
4503 9527 5.521544 CCAAATTTGTTGCATCCCAAAAAG 58.478 37.500 16.73 4.72 32.43 2.27
4518 9543 3.116079 ACCAAGAGCAAGCCAAATTTG 57.884 42.857 11.40 11.40 0.00 2.32
4579 9649 4.529897 TCCATTTGAGATCCAGGAATGTG 58.470 43.478 0.00 0.00 0.00 3.21
4658 9730 9.959721 AGTTTTCCTAGAGATTTAATGTAGCAA 57.040 29.630 0.00 0.00 0.00 3.91
4687 9759 9.624373 ATTGAGATGCATGTTATCTTACTTTCT 57.376 29.630 2.46 0.00 35.14 2.52
4690 9762 8.844244 GGAATTGAGATGCATGTTATCTTACTT 58.156 33.333 2.46 10.63 35.14 2.24
4691 9763 8.216423 AGGAATTGAGATGCATGTTATCTTACT 58.784 33.333 2.46 0.00 35.14 2.24
4692 9764 8.388484 AGGAATTGAGATGCATGTTATCTTAC 57.612 34.615 2.46 0.00 35.14 2.34
4695 9767 9.887629 CTATAGGAATTGAGATGCATGTTATCT 57.112 33.333 2.46 12.53 37.59 1.98
4696 9768 9.107177 CCTATAGGAATTGAGATGCATGTTATC 57.893 37.037 14.11 0.00 37.39 1.75
4697 9769 8.829746 TCCTATAGGAATTGAGATGCATGTTAT 58.170 33.333 19.59 0.00 42.18 1.89
4698 9770 8.206126 TCCTATAGGAATTGAGATGCATGTTA 57.794 34.615 19.59 0.00 42.18 2.41
4699 9771 7.083062 TCCTATAGGAATTGAGATGCATGTT 57.917 36.000 19.59 0.00 42.18 2.71
4700 9772 6.692849 TCCTATAGGAATTGAGATGCATGT 57.307 37.500 19.59 0.00 42.18 3.21
4738 9810 9.797732 TCCATGGTATTCCTATCCTATGAATAA 57.202 33.333 12.58 0.00 33.94 1.40
4739 9811 9.797732 TTCCATGGTATTCCTATCCTATGAATA 57.202 33.333 12.58 0.00 31.55 1.75
4740 9812 8.700145 TTCCATGGTATTCCTATCCTATGAAT 57.300 34.615 12.58 0.00 33.54 2.57
4741 9813 8.700145 ATTCCATGGTATTCCTATCCTATGAA 57.300 34.615 12.58 0.00 34.23 2.57
4742 9814 9.439461 CTATTCCATGGTATTCCTATCCTATGA 57.561 37.037 12.58 0.00 34.23 2.15
4743 9815 8.654997 CCTATTCCATGGTATTCCTATCCTATG 58.345 40.741 12.58 0.00 34.23 2.23
4744 9816 8.587244 TCCTATTCCATGGTATTCCTATCCTAT 58.413 37.037 12.58 0.00 34.23 2.57
4745 9817 7.961940 TCCTATTCCATGGTATTCCTATCCTA 58.038 38.462 12.58 0.00 34.23 2.94
4746 9818 6.826727 TCCTATTCCATGGTATTCCTATCCT 58.173 40.000 12.58 0.00 34.23 3.24
4747 9819 7.510675 TTCCTATTCCATGGTATTCCTATCC 57.489 40.000 12.58 0.00 34.23 2.59
4748 9820 9.232473 GTTTTCCTATTCCATGGTATTCCTATC 57.768 37.037 12.58 0.00 34.23 2.08
4749 9821 8.960064 AGTTTTCCTATTCCATGGTATTCCTAT 58.040 33.333 12.58 0.00 34.23 2.57
4750 9822 8.344939 AGTTTTCCTATTCCATGGTATTCCTA 57.655 34.615 12.58 0.00 34.23 2.94
4751 9823 7.226059 AGTTTTCCTATTCCATGGTATTCCT 57.774 36.000 12.58 0.00 34.23 3.36


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

AutoCloner maintained by Alex Coulton.