Multiple sequence alignment - TraesCS3A01G076900

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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 TraesCS3A01G076900 chr3A 100.000 5404 0 0 1 5404 47820427 47825830 0.000000e+00 9980.0
1 TraesCS3A01G076900 chr3A 91.667 84 3 3 534 617 28451128 28451049 4.420000e-21 113.0
2 TraesCS3A01G076900 chr3A 80.870 115 18 3 506 617 12148064 12148177 2.680000e-13 87.9
3 TraesCS3A01G076900 chr3D 95.011 2305 85 14 2384 4670 37752995 37755287 0.000000e+00 3592.0
4 TraesCS3A01G076900 chr3D 91.723 1776 98 29 618 2376 37751157 37752900 0.000000e+00 2420.0
5 TraesCS3A01G076900 chr3D 84.021 751 61 25 4671 5404 37755326 37756034 0.000000e+00 667.0
6 TraesCS3A01G076900 chr3B 94.256 2211 86 19 2384 4576 60252419 60254606 0.000000e+00 3341.0
7 TraesCS3A01G076900 chr3B 89.504 867 58 17 701 1553 60250706 60251553 0.000000e+00 1066.0
8 TraesCS3A01G076900 chr3B 93.411 683 37 4 1552 2228 60251581 60252261 0.000000e+00 1005.0
9 TraesCS3A01G076900 chr3B 89.358 639 51 7 4728 5352 60254620 60255255 0.000000e+00 787.0
10 TraesCS3A01G076900 chr3B 91.209 91 4 3 531 618 660315398 660315487 2.640000e-23 121.0
11 TraesCS3A01G076900 chr3B 90.741 54 4 1 2312 2364 60252261 60252314 2.700000e-08 71.3
12 TraesCS3A01G076900 chr7B 98.606 502 5 1 2 501 311428805 311428304 0.000000e+00 887.0
13 TraesCS3A01G076900 chr7B 95.057 263 11 2 1 262 481112781 481113042 3.890000e-111 412.0
14 TraesCS3A01G076900 chr7B 94.650 243 11 2 257 497 481114253 481114495 5.110000e-100 375.0
15 TraesCS3A01G076900 chr7A 98.795 498 5 1 1 497 69979425 69978928 0.000000e+00 885.0
16 TraesCS3A01G076900 chr2D 84.848 363 38 9 3325 3684 645555705 645556053 3.100000e-92 350.0
17 TraesCS3A01G076900 chr2D 86.275 102 6 5 518 614 616138816 616138914 2.660000e-18 104.0
18 TraesCS3A01G076900 chr1A 75.194 516 66 29 1 487 361063709 361064191 2.570000e-43 187.0
19 TraesCS3A01G076900 chr1B 89.362 94 6 4 527 619 660817520 660817430 1.230000e-21 115.0
20 TraesCS3A01G076900 chr2B 87.879 99 5 3 528 619 25672188 25672286 5.720000e-20 110.0
21 TraesCS3A01G076900 chr2B 87.629 97 5 4 527 619 599993477 599993570 7.400000e-19 106.0
22 TraesCS3A01G076900 chr6B 87.640 89 5 4 527 612 645531122 645531207 1.240000e-16 99.0
23 TraesCS3A01G076900 chr6A 86.813 91 8 3 514 601 566529424 566529513 1.240000e-16 99.0
24 TraesCS3A01G076900 chr4B 95.000 40 2 0 188 227 226964144 226964183 4.520000e-06 63.9


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 TraesCS3A01G076900 chr3A 47820427 47825830 5403 False 9980.000000 9980 100.000000 1 5404 1 chr3A.!!$F2 5403
1 TraesCS3A01G076900 chr3D 37751157 37756034 4877 False 2226.333333 3592 90.251667 618 5404 3 chr3D.!!$F1 4786
2 TraesCS3A01G076900 chr3B 60250706 60255255 4549 False 1254.060000 3341 91.454000 701 5352 5 chr3B.!!$F2 4651
3 TraesCS3A01G076900 chr7B 311428304 311428805 501 True 887.000000 887 98.606000 2 501 1 chr7B.!!$R1 499
4 TraesCS3A01G076900 chr7B 481112781 481114495 1714 False 393.500000 412 94.853500 1 497 2 chr7B.!!$F1 496

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
863 2086 2.312436 GCGACCGCCTAAAACACGT 61.312 57.895 2.55 0.0 34.56 4.49 F
1172 2402 0.109342 ATTAATCCTGGGAGCTGGCG 59.891 55.000 0.00 0.0 0.00 5.69 F
1230 2460 0.693049 GCTCTTCTGTTTCCCCTCCA 59.307 55.000 0.00 0.0 0.00 3.86 F
2261 3538 0.951558 AAGAATGTGTTGCGTCACCC 59.048 50.000 8.26 0.0 37.51 4.61 F
2382 3660 1.094785 TTTCTAATCGCAAGCTGGCC 58.905 50.000 7.72 0.0 37.18 5.36 F
3449 4815 1.556911 AGGATGAGTACAAGCACCAGG 59.443 52.381 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 3520 0.889186 GGGGTGACGCAACACATTCT 60.889 55.000 1.14 0.00 43.99 2.40 R
2848 4213 1.974265 TCCGTGCAGAGAGATAGAGG 58.026 55.000 0.00 0.00 0.00 3.69 R
3214 4580 1.070758 AGTCTGCAGAAACGATGTGGT 59.929 47.619 20.19 0.00 0.00 4.16 R
4217 5594 0.179043 TCTCCCAGATCGAGACGAGG 60.179 60.000 0.00 0.00 39.91 4.63 R
4300 5681 1.808411 ACACAACATTGTAGCCTCGG 58.192 50.000 0.00 0.00 39.91 4.63 R
4616 6003 0.108329 TGAGGTTCGAATCCTTCCGC 60.108 55.000 16.93 9.03 35.20 5.54 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
528 1750 8.252964 AGAAAAACTAACAGAATACCTAAGCG 57.747 34.615 0.00 0.00 0.00 4.68
529 1751 8.092687 AGAAAAACTAACAGAATACCTAAGCGA 58.907 33.333 0.00 0.00 0.00 4.93
530 1752 7.829378 AAAACTAACAGAATACCTAAGCGAG 57.171 36.000 0.00 0.00 0.00 5.03
531 1753 6.770746 AACTAACAGAATACCTAAGCGAGA 57.229 37.500 0.00 0.00 0.00 4.04
532 1754 6.963083 ACTAACAGAATACCTAAGCGAGAT 57.037 37.500 0.00 0.00 0.00 2.75
533 1755 6.740110 ACTAACAGAATACCTAAGCGAGATG 58.260 40.000 0.00 0.00 0.00 2.90
534 1756 5.854010 AACAGAATACCTAAGCGAGATGA 57.146 39.130 0.00 0.00 0.00 2.92
535 1757 5.854010 ACAGAATACCTAAGCGAGATGAA 57.146 39.130 0.00 0.00 0.00 2.57
536 1758 6.222038 ACAGAATACCTAAGCGAGATGAAA 57.778 37.500 0.00 0.00 0.00 2.69
537 1759 6.043411 ACAGAATACCTAAGCGAGATGAAAC 58.957 40.000 0.00 0.00 0.00 2.78
538 1760 5.463724 CAGAATACCTAAGCGAGATGAAACC 59.536 44.000 0.00 0.00 0.00 3.27
539 1761 5.128827 AGAATACCTAAGCGAGATGAAACCA 59.871 40.000 0.00 0.00 0.00 3.67
540 1762 3.695830 ACCTAAGCGAGATGAAACCAA 57.304 42.857 0.00 0.00 0.00 3.67
541 1763 3.600388 ACCTAAGCGAGATGAAACCAAG 58.400 45.455 0.00 0.00 0.00 3.61
542 1764 3.260884 ACCTAAGCGAGATGAAACCAAGA 59.739 43.478 0.00 0.00 0.00 3.02
543 1765 4.253685 CCTAAGCGAGATGAAACCAAGAA 58.746 43.478 0.00 0.00 0.00 2.52
544 1766 4.878397 CCTAAGCGAGATGAAACCAAGAAT 59.122 41.667 0.00 0.00 0.00 2.40
545 1767 6.049149 CCTAAGCGAGATGAAACCAAGAATA 58.951 40.000 0.00 0.00 0.00 1.75
546 1768 6.708054 CCTAAGCGAGATGAAACCAAGAATAT 59.292 38.462 0.00 0.00 0.00 1.28
547 1769 6.610741 AAGCGAGATGAAACCAAGAATATC 57.389 37.500 0.00 0.00 0.00 1.63
548 1770 5.674525 AGCGAGATGAAACCAAGAATATCA 58.325 37.500 0.00 0.00 0.00 2.15
549 1771 5.525378 AGCGAGATGAAACCAAGAATATCAC 59.475 40.000 0.00 0.00 0.00 3.06
550 1772 5.277538 GCGAGATGAAACCAAGAATATCACC 60.278 44.000 0.00 0.00 0.00 4.02
551 1773 6.051717 CGAGATGAAACCAAGAATATCACCT 58.948 40.000 0.00 0.00 0.00 4.00
552 1774 6.540189 CGAGATGAAACCAAGAATATCACCTT 59.460 38.462 0.00 0.00 0.00 3.50
553 1775 7.466455 CGAGATGAAACCAAGAATATCACCTTG 60.466 40.741 0.00 0.00 39.43 3.61
554 1776 5.643379 TGAAACCAAGAATATCACCTTGC 57.357 39.130 0.00 0.00 38.65 4.01
555 1777 5.324409 TGAAACCAAGAATATCACCTTGCT 58.676 37.500 0.00 0.00 38.65 3.91
556 1778 5.774690 TGAAACCAAGAATATCACCTTGCTT 59.225 36.000 0.00 0.00 38.65 3.91
557 1779 6.267471 TGAAACCAAGAATATCACCTTGCTTT 59.733 34.615 0.00 0.00 38.65 3.51
558 1780 7.450014 TGAAACCAAGAATATCACCTTGCTTTA 59.550 33.333 0.00 0.00 38.65 1.85
559 1781 7.961326 AACCAAGAATATCACCTTGCTTTAT 57.039 32.000 0.00 0.00 38.65 1.40
560 1782 7.961326 ACCAAGAATATCACCTTGCTTTATT 57.039 32.000 0.00 0.00 38.65 1.40
561 1783 9.474313 AACCAAGAATATCACCTTGCTTTATTA 57.526 29.630 0.00 0.00 38.65 0.98
562 1784 9.474313 ACCAAGAATATCACCTTGCTTTATTAA 57.526 29.630 0.00 0.00 38.65 1.40
637 1859 3.776417 AGATGGGCATGCCACTTTAATTT 59.224 39.130 36.56 12.78 37.98 1.82
863 2086 2.312436 GCGACCGCCTAAAACACGT 61.312 57.895 2.55 0.00 34.56 4.49
1102 2331 1.948508 CGCAAGCTGCACAAGGTTA 59.051 52.632 1.02 0.00 44.82 2.85
1128 2357 3.366739 ATTCGTTCCGACCCCTCGC 62.367 63.158 0.00 0.00 38.70 5.03
1150 2379 1.012841 CTCTCTTCATTCCTTGCGGC 58.987 55.000 0.00 0.00 0.00 6.53
1152 2381 0.731417 CTCTTCATTCCTTGCGGCTG 59.269 55.000 0.00 0.00 0.00 4.85
1155 2385 1.747355 CTTCATTCCTTGCGGCTGATT 59.253 47.619 0.00 0.00 0.00 2.57
1160 2390 1.967319 TCCTTGCGGCTGATTAATCC 58.033 50.000 12.90 0.00 0.00 3.01
1166 2396 1.879796 GCGGCTGATTAATCCTGGGAG 60.880 57.143 12.90 4.40 0.00 4.30
1167 2397 1.879796 CGGCTGATTAATCCTGGGAGC 60.880 57.143 12.90 13.32 0.00 4.70
1170 2400 2.813354 GCTGATTAATCCTGGGAGCTGG 60.813 54.545 12.90 0.00 0.00 4.85
1171 2401 1.143684 TGATTAATCCTGGGAGCTGGC 59.856 52.381 12.90 0.00 0.00 4.85
1172 2402 0.109342 ATTAATCCTGGGAGCTGGCG 59.891 55.000 0.00 0.00 0.00 5.69
1199 2429 1.019278 ATTTGACAATCGCGCCGTCT 61.019 50.000 18.64 1.83 0.00 4.18
1220 2450 2.995872 GCCCGTCGAGCTCTTCTGT 61.996 63.158 12.85 0.00 0.00 3.41
1230 2460 0.693049 GCTCTTCTGTTTCCCCTCCA 59.307 55.000 0.00 0.00 0.00 3.86
1264 2494 2.000447 GCTCTTAGCGGTCAATTTCGT 59.000 47.619 0.00 0.00 0.00 3.85
1304 2534 3.328382 TCGGAGTCAATCGATTGGTTT 57.672 42.857 32.03 20.01 38.30 3.27
1354 2585 6.650427 AAAGTAAAGGTGGATTCTGGTTTC 57.350 37.500 0.00 0.00 0.00 2.78
1377 2608 5.421693 TCATTCAAATGTCAAATGGTAGGGG 59.578 40.000 2.85 0.00 37.65 4.79
1378 2609 3.707316 TCAAATGTCAAATGGTAGGGGG 58.293 45.455 0.00 0.00 0.00 5.40
1412 2643 3.370840 AGATTCTATTGCAAGTGGGCA 57.629 42.857 4.94 0.00 43.19 5.36
1425 2656 4.580167 GCAAGTGGGCATACAATTGATAGA 59.420 41.667 13.59 0.00 46.10 1.98
1445 2684 4.678256 AGAGGGAAAAAGGAGGGATTTTC 58.322 43.478 0.00 0.00 42.19 2.29
1564 2831 7.624134 GCTTTAGGCTGAATTTTAATTGGTTGC 60.624 37.037 0.00 0.00 38.06 4.17
1597 2864 2.877300 GCAGGCTCTGAATTCCAACTCA 60.877 50.000 2.27 0.00 32.44 3.41
1646 2913 1.371758 GCCGATATCGCGCTCAAGA 60.372 57.895 19.78 0.00 38.18 3.02
1721 2988 7.234166 TGTTCTGCTAATCATCATCCTCTGATA 59.766 37.037 0.00 0.00 42.91 2.15
1723 2990 8.376803 TCTGCTAATCATCATCCTCTGATATT 57.623 34.615 0.00 0.00 42.91 1.28
1749 3016 4.125703 GTTGGTGCATTTCAAATGGTTGA 58.874 39.130 12.14 0.00 42.12 3.18
1775 3042 1.373748 GTTCGTGCCAGCTTACGGA 60.374 57.895 13.10 3.89 40.48 4.69
1975 3252 2.415491 CCAGTAGATGAACGCGAAGACA 60.415 50.000 15.93 7.45 0.00 3.41
2230 3507 7.872163 TTTTGACTTGGATGATTTCATTTCG 57.128 32.000 0.00 0.00 36.57 3.46
2243 3520 7.158697 TGATTTCATTTCGACTCTACCTGAAA 58.841 34.615 0.00 0.00 36.09 2.69
2254 3531 4.757149 ACTCTACCTGAAAGAATGTGTTGC 59.243 41.667 0.00 0.00 34.07 4.17
2261 3538 0.951558 AAGAATGTGTTGCGTCACCC 59.048 50.000 8.26 0.00 37.51 4.61
2264 3541 1.452145 AATGTGTTGCGTCACCCCAC 61.452 55.000 8.26 0.00 37.51 4.61
2282 3559 4.878397 CCCCACTTCTTTCTATAGCACTTG 59.122 45.833 0.00 0.00 0.00 3.16
2283 3560 5.491982 CCCACTTCTTTCTATAGCACTTGT 58.508 41.667 0.00 0.00 0.00 3.16
2284 3561 5.582665 CCCACTTCTTTCTATAGCACTTGTC 59.417 44.000 0.00 0.00 0.00 3.18
2290 3567 9.593134 CTTCTTTCTATAGCACTTGTCAGTAAT 57.407 33.333 0.00 0.00 0.00 1.89
2351 3628 2.115343 AACTACAAGCTGGCCTTAGC 57.885 50.000 3.32 5.44 44.01 3.09
2381 3659 2.919666 TTTTCTAATCGCAAGCTGGC 57.080 45.000 1.77 1.77 37.18 4.85
2382 3660 1.094785 TTTCTAATCGCAAGCTGGCC 58.905 50.000 7.72 0.00 37.18 5.36
2486 3851 5.357878 TCTTCATTGCAGTTGTTTGAAGTCT 59.642 36.000 9.91 0.00 42.36 3.24
2500 3865 3.587498 TGAAGTCTCTCTTGAGGGGAAA 58.413 45.455 0.00 0.00 40.58 3.13
2604 3969 2.224042 CCTTTTTGCCTCAAACTCCCAC 60.224 50.000 0.00 0.00 32.79 4.61
2648 4013 9.770097 TTTTATATCTCTGACAGGATTGACATC 57.230 33.333 1.81 0.00 0.00 3.06
2700 4065 7.579589 TTGTATCATGTAAGCATTTGTTTGC 57.420 32.000 0.00 0.00 43.09 3.68
2731 4096 5.617528 TTGTACCTCTGTTTGGAACTGTA 57.382 39.130 0.00 0.00 0.00 2.74
2733 4098 4.406326 TGTACCTCTGTTTGGAACTGTACA 59.594 41.667 0.00 0.00 34.17 2.90
2751 4116 4.279420 TGTACAGCATGCATTTTTACACCA 59.721 37.500 21.98 0.00 42.53 4.17
2797 4162 6.459066 TGAACAGTATCTCCTTGAAGAAGTG 58.541 40.000 0.00 0.00 0.00 3.16
2848 4213 1.606889 ACCACAGGTCGACCTCTCC 60.607 63.158 34.28 7.63 46.65 3.71
2884 4249 4.082949 GCACGGAAATGTACTAGCCTTTTT 60.083 41.667 0.00 0.00 0.00 1.94
3186 4552 9.948818 CCGATCAGGTTACCATCTGAATGGAAA 62.949 44.444 11.29 0.00 44.50 3.13
3214 4580 5.686387 CGTTGTTCCCCTTCCATATGACATA 60.686 44.000 3.65 0.00 0.00 2.29
3247 4613 8.447833 CGTTTCTGCAGACTAAATATTTGGTTA 58.552 33.333 18.03 5.52 31.69 2.85
3449 4815 1.556911 AGGATGAGTACAAGCACCAGG 59.443 52.381 0.00 0.00 0.00 4.45
3708 5075 7.114095 TGGTTTGTTCTACCTAACTGAAGTTT 58.886 34.615 0.21 0.00 36.60 2.66
3808 5175 3.261897 AGTTACCCTTGACATGGAGTGAG 59.738 47.826 8.93 0.00 0.00 3.51
4078 5455 8.559536 CGATTATGTTCAATGGCTTACTGTTAT 58.440 33.333 0.00 0.00 0.00 1.89
4081 5458 4.764308 TGTTCAATGGCTTACTGTTATGCA 59.236 37.500 0.00 0.00 31.36 3.96
4209 5586 5.533154 GTGAGCACCATCTACTACTACATCT 59.467 44.000 0.00 0.00 0.00 2.90
4217 5594 9.073475 ACCATCTACTACTACATCTTGAATCTC 57.927 37.037 0.00 0.00 0.00 2.75
4288 5665 3.614176 CACAGAGAATGAAGAAATCGCGA 59.386 43.478 13.09 13.09 0.00 5.87
4291 5668 2.930040 GAGAATGAAGAAATCGCGACCA 59.070 45.455 12.93 3.15 0.00 4.02
4300 5681 0.743345 AATCGCGACCAGGCCTAAAC 60.743 55.000 12.93 0.00 0.00 2.01
4328 5709 4.502645 GCTACAATGTTGTGTTGTTGTTCC 59.497 41.667 8.57 0.00 42.31 3.62
4331 5712 5.167845 ACAATGTTGTGTTGTTGTTCCTTC 58.832 37.500 0.00 0.00 40.49 3.46
4332 5713 5.047377 ACAATGTTGTGTTGTTGTTCCTTCT 60.047 36.000 0.00 0.00 40.49 2.85
4333 5714 4.433186 TGTTGTGTTGTTGTTCCTTCTG 57.567 40.909 0.00 0.00 0.00 3.02
4334 5715 3.823873 TGTTGTGTTGTTGTTCCTTCTGT 59.176 39.130 0.00 0.00 0.00 3.41
4356 5737 6.786122 TGTTTTACCTTTAGGATGGTTAGCT 58.214 36.000 2.06 0.00 37.74 3.32
4438 5819 1.556451 TGGACAGAGGATGTGATGTGG 59.444 52.381 0.00 0.00 44.17 4.17
4446 5827 0.254178 GATGTGATGTGGGGCAGAGT 59.746 55.000 0.00 0.00 0.00 3.24
4464 5845 0.681733 GTTGTGCAGTGAGAGAGGGA 59.318 55.000 0.00 0.00 0.00 4.20
4551 5932 3.903090 TCTCCAAATGCCATCAAAGGTTT 59.097 39.130 0.00 0.00 0.00 3.27
4552 5933 5.083122 TCTCCAAATGCCATCAAAGGTTTA 58.917 37.500 0.00 0.00 0.00 2.01
4566 5951 8.997323 CATCAAAGGTTTATATGCTCTAAGAGG 58.003 37.037 0.00 0.00 0.00 3.69
4567 5952 8.319057 TCAAAGGTTTATATGCTCTAAGAGGA 57.681 34.615 0.00 0.00 33.93 3.71
4568 5953 8.424918 TCAAAGGTTTATATGCTCTAAGAGGAG 58.575 37.037 0.00 0.00 32.71 3.69
4570 5955 7.922699 AGGTTTATATGCTCTAAGAGGAGTT 57.077 36.000 0.00 0.00 32.71 3.01
4572 5957 6.931840 GGTTTATATGCTCTAAGAGGAGTTGG 59.068 42.308 0.00 0.00 32.71 3.77
4573 5958 2.998316 ATGCTCTAAGAGGAGTTGGC 57.002 50.000 0.00 0.00 32.71 4.52
4574 5959 0.532573 TGCTCTAAGAGGAGTTGGCG 59.467 55.000 0.00 0.00 35.89 5.69
4575 5960 0.808060 GCTCTAAGAGGAGTTGGCGC 60.808 60.000 0.00 0.00 35.89 6.53
4580 5967 0.954452 AAGAGGAGTTGGCGCTTTTG 59.046 50.000 7.64 0.00 0.00 2.44
4590 5977 0.523335 GGCGCTTTTGCTGGAATACG 60.523 55.000 7.64 0.00 44.80 3.06
4593 5980 2.920647 GCGCTTTTGCTGGAATACGTTT 60.921 45.455 0.00 0.00 44.80 3.60
4609 5996 1.544724 GTTTTGCCCATACCAGCTCA 58.455 50.000 0.00 0.00 0.00 4.26
4616 6003 1.905215 CCCATACCAGCTCATCTAGGG 59.095 57.143 0.00 0.00 0.00 3.53
4623 6010 1.118356 AGCTCATCTAGGGCGGAAGG 61.118 60.000 0.00 0.00 0.00 3.46
4627 6014 1.971357 TCATCTAGGGCGGAAGGATTC 59.029 52.381 0.00 0.00 46.67 2.52
4646 6033 1.945394 TCGAACCTCACCGCTACTATC 59.055 52.381 0.00 0.00 0.00 2.08
4647 6034 1.948145 CGAACCTCACCGCTACTATCT 59.052 52.381 0.00 0.00 0.00 1.98
4653 6040 3.827302 CCTCACCGCTACTATCTGGTATT 59.173 47.826 0.00 0.00 32.29 1.89
4677 6102 3.312890 TGATTTTCCTTCCTGGCCAAAA 58.687 40.909 7.01 2.42 35.26 2.44
4678 6103 3.324556 TGATTTTCCTTCCTGGCCAAAAG 59.675 43.478 17.06 17.06 35.26 2.27
4680 6105 0.560688 TTCCTTCCTGGCCAAAAGGT 59.439 50.000 31.44 0.00 40.40 3.50
4681 6106 0.560688 TCCTTCCTGGCCAAAAGGTT 59.439 50.000 31.44 0.00 40.40 3.50
4707 6132 8.386264 TGAGACTAGATTGATTTTCCTTCCTTT 58.614 33.333 0.00 0.00 0.00 3.11
4724 6149 5.249780 TCCTTTGGCTACTTGGATGTTTA 57.750 39.130 0.00 0.00 0.00 2.01
4730 6155 3.998341 GGCTACTTGGATGTTTACGTTCA 59.002 43.478 0.00 0.00 0.00 3.18
4744 6169 8.348983 TGTTTACGTTCACAAAGTTTGAAAAA 57.651 26.923 22.23 9.70 34.78 1.94
4759 6184 8.255111 AGTTTGAAAAATCCAAAAGAGAGGAT 57.745 30.769 0.00 0.00 46.33 3.24
4763 6188 5.656213 AAAATCCAAAAGAGAGGATGCTG 57.344 39.130 0.00 0.00 43.67 4.41
4768 6193 3.618351 CAAAAGAGAGGATGCTGGACAT 58.382 45.455 0.00 0.00 43.54 3.06
4775 6200 1.211457 AGGATGCTGGACATGGAACTC 59.789 52.381 0.00 0.00 39.84 3.01
4823 6248 1.682087 GGATCAAAAACCCTCTCCCCG 60.682 57.143 0.00 0.00 0.00 5.73
4848 6273 2.016318 CTTGCTGGACAGTGTTGTGAA 58.984 47.619 0.00 0.00 37.76 3.18
4865 6290 9.305925 GTGTTGTGAATTCTCAAAAAGAAAGAT 57.694 29.630 21.10 0.00 46.85 2.40
4896 6322 4.998672 CCCTGAATTGTGATGTGCAAATTT 59.001 37.500 0.00 0.00 0.00 1.82
4904 6330 6.141560 TGTGATGTGCAAATTTACACTTGA 57.858 33.333 19.68 7.60 37.68 3.02
4938 6367 7.603024 AGCATAAACTCTACTTACAACAGAACC 59.397 37.037 0.00 0.00 0.00 3.62
4966 6397 4.617253 ACCATAGTTACAGACTTGCACA 57.383 40.909 0.00 0.00 39.86 4.57
4980 6411 1.753930 TGCACAGTTATGAGGCATGG 58.246 50.000 0.00 0.00 36.08 3.66
4991 6422 4.637483 ATGAGGCATGGAAATTACAACG 57.363 40.909 0.00 0.00 0.00 4.10
4995 6426 3.941483 AGGCATGGAAATTACAACGAGAG 59.059 43.478 0.00 0.00 0.00 3.20
4998 6429 5.324697 GCATGGAAATTACAACGAGAGAAC 58.675 41.667 0.00 0.00 0.00 3.01
5001 6432 7.011482 GCATGGAAATTACAACGAGAGAACTAT 59.989 37.037 0.00 0.00 0.00 2.12
5004 6435 6.535508 GGAAATTACAACGAGAGAACTATGCT 59.464 38.462 0.00 0.00 0.00 3.79
5010 6441 4.539509 ACGAGAGAACTATGCTAAGACG 57.460 45.455 0.00 0.00 0.00 4.18
5070 6504 7.750229 AAACTGTGAACATGATGTAATGTCT 57.250 32.000 0.00 0.00 39.89 3.41
5120 6564 1.029408 GGTCCACATATGTGCCGCAA 61.029 55.000 27.27 9.12 44.34 4.85
5121 6565 0.808125 GTCCACATATGTGCCGCAAA 59.192 50.000 27.27 7.54 44.34 3.68
5172 6616 1.268899 GCCAAGTGCTCATCATATGCC 59.731 52.381 0.00 0.00 36.87 4.40
5271 6715 9.643735 TTTAATTTCCAACAAACTTAGGTAGGA 57.356 29.630 0.00 0.00 0.00 2.94
5291 6735 8.640651 GGTAGGATTAACTTTACAAAACCCAAA 58.359 33.333 0.00 0.00 0.00 3.28
5292 6736 9.687210 GTAGGATTAACTTTACAAAACCCAAAG 57.313 33.333 0.00 0.00 35.78 2.77
5348 6793 2.949963 GCCCCTAAATGTGATGGCAAGA 60.950 50.000 0.00 0.00 38.73 3.02
5352 6797 4.220382 CCCTAAATGTGATGGCAAGAAACA 59.780 41.667 0.00 0.00 0.00 2.83
5354 6799 5.865552 CCTAAATGTGATGGCAAGAAACAAG 59.134 40.000 0.00 0.00 0.00 3.16
5355 6800 5.534207 AAATGTGATGGCAAGAAACAAGA 57.466 34.783 0.00 0.00 0.00 3.02
5356 6801 3.988379 TGTGATGGCAAGAAACAAGAC 57.012 42.857 0.00 0.00 0.00 3.01
5357 6802 3.554934 TGTGATGGCAAGAAACAAGACT 58.445 40.909 0.00 0.00 0.00 3.24
5358 6803 3.316029 TGTGATGGCAAGAAACAAGACTG 59.684 43.478 0.00 0.00 0.00 3.51
5359 6804 2.886523 TGATGGCAAGAAACAAGACTGG 59.113 45.455 0.00 0.00 0.00 4.00
5376 6821 1.003545 CTGGCAACACAAGACTGAACG 60.004 52.381 0.00 0.00 46.17 3.95
5385 6830 5.734720 ACACAAGACTGAACGATGGATAAT 58.265 37.500 0.00 0.00 0.00 1.28
5389 6834 6.878923 ACAAGACTGAACGATGGATAATGAAA 59.121 34.615 0.00 0.00 0.00 2.69
5390 6835 7.554118 ACAAGACTGAACGATGGATAATGAAAT 59.446 33.333 0.00 0.00 0.00 2.17
5391 6836 7.488187 AGACTGAACGATGGATAATGAAATG 57.512 36.000 0.00 0.00 0.00 2.32
5392 6837 7.050377 AGACTGAACGATGGATAATGAAATGT 58.950 34.615 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
502 1724 8.718734 CGCTTAGGTATTCTGTTAGTTTTTCTT 58.281 33.333 0.00 0.00 0.00 2.52
503 1725 8.092687 TCGCTTAGGTATTCTGTTAGTTTTTCT 58.907 33.333 0.00 0.00 0.00 2.52
504 1726 8.248117 TCGCTTAGGTATTCTGTTAGTTTTTC 57.752 34.615 0.00 0.00 0.00 2.29
505 1727 8.092687 TCTCGCTTAGGTATTCTGTTAGTTTTT 58.907 33.333 0.00 0.00 0.00 1.94
506 1728 7.609056 TCTCGCTTAGGTATTCTGTTAGTTTT 58.391 34.615 0.00 0.00 0.00 2.43
507 1729 7.166691 TCTCGCTTAGGTATTCTGTTAGTTT 57.833 36.000 0.00 0.00 0.00 2.66
508 1730 6.770746 TCTCGCTTAGGTATTCTGTTAGTT 57.229 37.500 0.00 0.00 0.00 2.24
509 1731 6.546403 TCATCTCGCTTAGGTATTCTGTTAGT 59.454 38.462 0.00 0.00 0.00 2.24
510 1732 6.971602 TCATCTCGCTTAGGTATTCTGTTAG 58.028 40.000 0.00 0.00 0.00 2.34
511 1733 6.954487 TCATCTCGCTTAGGTATTCTGTTA 57.046 37.500 0.00 0.00 0.00 2.41
512 1734 5.854010 TCATCTCGCTTAGGTATTCTGTT 57.146 39.130 0.00 0.00 0.00 3.16
513 1735 5.854010 TTCATCTCGCTTAGGTATTCTGT 57.146 39.130 0.00 0.00 0.00 3.41
514 1736 5.463724 GGTTTCATCTCGCTTAGGTATTCTG 59.536 44.000 0.00 0.00 0.00 3.02
515 1737 5.128827 TGGTTTCATCTCGCTTAGGTATTCT 59.871 40.000 0.00 0.00 0.00 2.40
516 1738 5.357257 TGGTTTCATCTCGCTTAGGTATTC 58.643 41.667 0.00 0.00 0.00 1.75
517 1739 5.353394 TGGTTTCATCTCGCTTAGGTATT 57.647 39.130 0.00 0.00 0.00 1.89
518 1740 5.128827 TCTTGGTTTCATCTCGCTTAGGTAT 59.871 40.000 0.00 0.00 0.00 2.73
519 1741 4.464951 TCTTGGTTTCATCTCGCTTAGGTA 59.535 41.667 0.00 0.00 0.00 3.08
520 1742 3.260884 TCTTGGTTTCATCTCGCTTAGGT 59.739 43.478 0.00 0.00 0.00 3.08
521 1743 3.861840 TCTTGGTTTCATCTCGCTTAGG 58.138 45.455 0.00 0.00 0.00 2.69
522 1744 7.439356 TGATATTCTTGGTTTCATCTCGCTTAG 59.561 37.037 0.00 0.00 0.00 2.18
523 1745 7.224753 GTGATATTCTTGGTTTCATCTCGCTTA 59.775 37.037 0.00 0.00 0.00 3.09
524 1746 6.037610 GTGATATTCTTGGTTTCATCTCGCTT 59.962 38.462 0.00 0.00 0.00 4.68
525 1747 5.525378 GTGATATTCTTGGTTTCATCTCGCT 59.475 40.000 0.00 0.00 0.00 4.93
526 1748 5.277538 GGTGATATTCTTGGTTTCATCTCGC 60.278 44.000 0.00 0.00 0.00 5.03
527 1749 6.051717 AGGTGATATTCTTGGTTTCATCTCG 58.948 40.000 0.00 0.00 0.00 4.04
528 1750 7.680588 GCAAGGTGATATTCTTGGTTTCATCTC 60.681 40.741 12.91 0.00 40.31 2.75
529 1751 6.096001 GCAAGGTGATATTCTTGGTTTCATCT 59.904 38.462 12.91 0.00 40.31 2.90
530 1752 6.096001 AGCAAGGTGATATTCTTGGTTTCATC 59.904 38.462 10.99 0.00 45.69 2.92
531 1753 5.954150 AGCAAGGTGATATTCTTGGTTTCAT 59.046 36.000 10.99 0.00 45.69 2.57
532 1754 5.324409 AGCAAGGTGATATTCTTGGTTTCA 58.676 37.500 10.99 0.00 45.69 2.69
533 1755 5.904362 AGCAAGGTGATATTCTTGGTTTC 57.096 39.130 10.99 0.64 45.69 2.78
601 1823 9.211410 GGCATGCCCATCTATATCTATATCTAT 57.789 37.037 27.24 0.00 0.00 1.98
602 1824 8.179487 TGGCATGCCCATCTATATCTATATCTA 58.821 37.037 33.44 5.03 39.18 1.98
603 1825 7.021251 TGGCATGCCCATCTATATCTATATCT 58.979 38.462 33.44 0.00 39.18 1.98
604 1826 7.250032 TGGCATGCCCATCTATATCTATATC 57.750 40.000 33.44 2.54 39.18 1.63
647 1869 7.388500 ACGATTCTAAAAACGTGGGAATAGAAA 59.612 33.333 11.20 0.88 41.58 2.52
660 1882 9.124807 CCCTTTGATTTGTACGATTCTAAAAAC 57.875 33.333 6.57 0.00 0.00 2.43
809 2032 1.276859 TGCCTGCTGGATGGATGTCT 61.277 55.000 14.77 0.00 34.57 3.41
840 2063 1.079875 GTTTTAGGCGGTCGCATCGA 61.080 55.000 17.21 0.00 44.11 3.59
863 2086 3.845259 GGTCGCATCTGGGCCGTA 61.845 66.667 0.00 0.00 0.00 4.02
994 2219 1.819632 CTCGCCGGGATTTGGGAAG 60.820 63.158 2.18 0.00 0.00 3.46
1016 2241 0.464735 CATCTCCTCTCCGTCCGACT 60.465 60.000 0.00 0.00 0.00 4.18
1128 2357 1.745141 CGCAAGGAATGAAGAGAGGGG 60.745 57.143 0.00 0.00 0.00 4.79
1150 2379 2.813354 GCCAGCTCCCAGGATTAATCAG 60.813 54.545 17.07 8.68 0.00 2.90
1152 2381 1.879796 CGCCAGCTCCCAGGATTAATC 60.880 57.143 6.93 6.93 0.00 1.75
1155 2385 2.443394 CCGCCAGCTCCCAGGATTA 61.443 63.158 0.00 0.00 0.00 1.75
1172 2402 1.064134 GATTGTCAAATCGGCGGCC 59.936 57.895 9.54 9.54 33.25 6.13
1199 2429 2.676822 AAGAGCTCGACGGGCAGA 60.677 61.111 23.83 0.00 0.00 4.26
1220 2450 4.995058 AGGCGGGTGGAGGGGAAA 62.995 66.667 0.00 0.00 0.00 3.13
1264 2494 4.496673 CCGAAAGAAATCAAACCAACACGA 60.497 41.667 0.00 0.00 0.00 4.35
1304 2534 0.757188 AACAATTCCCCACGTGGCAA 60.757 50.000 29.75 22.49 0.00 4.52
1339 2569 5.467035 TTTGAATGAAACCAGAATCCACC 57.533 39.130 0.00 0.00 0.00 4.61
1354 2585 5.395546 CCCCCTACCATTTGACATTTGAATG 60.396 44.000 2.29 2.29 42.10 2.67
1377 2608 8.144478 GCAATAGAATCTTTTTCCTATTTCCCC 58.856 37.037 0.00 0.00 31.59 4.81
1378 2609 8.695456 TGCAATAGAATCTTTTTCCTATTTCCC 58.305 33.333 0.00 0.00 31.59 3.97
1412 2643 8.001292 CCTCCTTTTTCCCTCTATCAATTGTAT 58.999 37.037 5.13 0.80 0.00 2.29
1425 2656 3.431415 CGAAAATCCCTCCTTTTTCCCT 58.569 45.455 0.00 0.00 38.17 4.20
1445 2684 4.036262 TGAATCTTTTGAAACAGACCACCG 59.964 41.667 0.00 0.00 0.00 4.94
1487 2726 2.990740 ACAGCCCCCAATTCTAAACA 57.009 45.000 0.00 0.00 0.00 2.83
1564 2831 1.406539 AGAGCCTGCACACAAAACAAG 59.593 47.619 0.00 0.00 0.00 3.16
1721 2988 3.472283 TTGAAATGCACCAACAGCAAT 57.528 38.095 0.00 0.00 46.27 3.56
1749 3016 1.525995 CTGGCACGAACTTGGGTGT 60.526 57.895 0.00 0.00 36.54 4.16
1975 3252 6.888632 AGAATCTCATAGAAACACAAATGGCT 59.111 34.615 0.00 0.00 0.00 4.75
2230 3507 5.106908 GCAACACATTCTTTCAGGTAGAGTC 60.107 44.000 0.00 0.00 0.00 3.36
2243 3520 0.889186 GGGGTGACGCAACACATTCT 60.889 55.000 1.14 0.00 43.99 2.40
2254 3531 3.611766 ATAGAAAGAAGTGGGGTGACG 57.388 47.619 0.00 0.00 0.00 4.35
2261 3538 6.166279 TGACAAGTGCTATAGAAAGAAGTGG 58.834 40.000 3.21 0.00 0.00 4.00
2264 3541 8.988064 TTACTGACAAGTGCTATAGAAAGAAG 57.012 34.615 3.21 0.00 37.19 2.85
2306 3583 8.662781 TCATTTTGAGCCTGATGTATAGTAAC 57.337 34.615 0.00 0.00 0.00 2.50
2310 3587 8.218338 AGTTTCATTTTGAGCCTGATGTATAG 57.782 34.615 0.00 0.00 0.00 1.31
2311 3588 9.109393 GTAGTTTCATTTTGAGCCTGATGTATA 57.891 33.333 0.00 0.00 0.00 1.47
2312 3589 7.611467 TGTAGTTTCATTTTGAGCCTGATGTAT 59.389 33.333 0.00 0.00 0.00 2.29
2313 3590 6.939730 TGTAGTTTCATTTTGAGCCTGATGTA 59.060 34.615 0.00 0.00 0.00 2.29
2314 3591 5.769662 TGTAGTTTCATTTTGAGCCTGATGT 59.230 36.000 0.00 0.00 0.00 3.06
2315 3592 6.258230 TGTAGTTTCATTTTGAGCCTGATG 57.742 37.500 0.00 0.00 0.00 3.07
2316 3593 6.571150 GCTTGTAGTTTCATTTTGAGCCTGAT 60.571 38.462 0.00 0.00 0.00 2.90
2317 3594 5.278463 GCTTGTAGTTTCATTTTGAGCCTGA 60.278 40.000 0.00 0.00 0.00 3.86
2318 3595 4.919754 GCTTGTAGTTTCATTTTGAGCCTG 59.080 41.667 0.00 0.00 0.00 4.85
2319 3596 4.829492 AGCTTGTAGTTTCATTTTGAGCCT 59.171 37.500 0.00 0.00 0.00 4.58
2320 3597 4.919754 CAGCTTGTAGTTTCATTTTGAGCC 59.080 41.667 0.00 0.00 0.00 4.70
2321 3598 4.919754 CCAGCTTGTAGTTTCATTTTGAGC 59.080 41.667 0.00 0.00 0.00 4.26
2322 3599 4.919754 GCCAGCTTGTAGTTTCATTTTGAG 59.080 41.667 0.00 0.00 0.00 3.02
2376 3654 5.880887 ACAAGACTAAATAACTAAGGCCAGC 59.119 40.000 5.01 0.00 0.00 4.85
2378 3656 7.455058 TCAACAAGACTAAATAACTAAGGCCA 58.545 34.615 5.01 0.00 0.00 5.36
2648 4013 5.638596 GGAAGTACCTTGTATTGGTTTGG 57.361 43.478 0.00 0.00 38.88 3.28
2700 4065 6.206634 TCCAAACAGAGGTACAAAAGCATAAG 59.793 38.462 0.00 0.00 0.00 1.73
2731 4096 4.540359 ATGGTGTAAAAATGCATGCTGT 57.460 36.364 20.33 4.66 0.00 4.40
2733 4098 6.284891 AGTAATGGTGTAAAAATGCATGCT 57.715 33.333 20.33 0.00 0.00 3.79
2751 4116 8.793592 GTTCAAGGAACAAAGGATGTTAGTAAT 58.206 33.333 4.33 0.00 45.86 1.89
2797 4162 4.579869 TGAGTTGATCTGGAACTAAAGCC 58.420 43.478 0.00 0.00 33.71 4.35
2848 4213 1.974265 TCCGTGCAGAGAGATAGAGG 58.026 55.000 0.00 0.00 0.00 3.69
2884 4249 8.791675 TCATTGATTACTGAACATGCTTACAAA 58.208 29.630 0.00 0.00 0.00 2.83
2927 4292 8.275040 AGAATAAATTTCTACCAGCCTGTACAT 58.725 33.333 0.00 0.00 0.00 2.29
2947 4312 3.404869 TCTGGAGAGGAGGCAGAATAA 57.595 47.619 0.00 0.00 0.00 1.40
3186 4552 2.668144 TGGAAGGGGAACAACGAATT 57.332 45.000 0.00 0.00 0.00 2.17
3214 4580 1.070758 AGTCTGCAGAAACGATGTGGT 59.929 47.619 20.19 0.00 0.00 4.16
3449 4815 4.636249 AGCTATACAGGCATGACTTTAGC 58.364 43.478 20.20 20.20 0.00 3.09
3731 5098 7.500227 TCTCAAAATTGTCAGAATCTGTGTTCT 59.500 33.333 10.36 0.00 38.95 3.01
3768 5135 8.661345 AGGGTAACTAGAAAGAGAATTTCTTGT 58.339 33.333 8.05 9.31 45.41 3.16
3787 5154 3.600388 CTCACTCCATGTCAAGGGTAAC 58.400 50.000 0.00 0.00 0.00 2.50
3788 5155 2.571653 CCTCACTCCATGTCAAGGGTAA 59.428 50.000 0.00 0.00 0.00 2.85
3789 5156 2.187958 CCTCACTCCATGTCAAGGGTA 58.812 52.381 0.00 0.00 0.00 3.69
3808 5175 2.496899 TGAGCTCCCAATCTCAAACC 57.503 50.000 12.15 0.00 36.50 3.27
4078 5455 1.295101 CGACCCACCTGTACATGCA 59.705 57.895 0.00 0.00 0.00 3.96
4081 5458 1.687123 GATAGCGACCCACCTGTACAT 59.313 52.381 0.00 0.00 0.00 2.29
4209 5586 3.313803 CAGATCGAGACGAGGAGATTCAA 59.686 47.826 0.00 0.00 39.91 2.69
4217 5594 0.179043 TCTCCCAGATCGAGACGAGG 60.179 60.000 0.00 0.00 39.91 4.63
4288 5665 3.400188 CCTCGGTTTAGGCCTGGT 58.600 61.111 17.99 0.00 0.00 4.00
4300 5681 1.808411 ACACAACATTGTAGCCTCGG 58.192 50.000 0.00 0.00 39.91 4.63
4309 5690 5.289193 CAGAAGGAACAACAACACAACATTG 59.711 40.000 0.00 0.00 0.00 2.82
4328 5709 7.761038 AACCATCCTAAAGGTAAAACAGAAG 57.239 36.000 0.00 0.00 37.07 2.85
4331 5712 6.884836 AGCTAACCATCCTAAAGGTAAAACAG 59.115 38.462 0.00 0.00 37.07 3.16
4332 5713 6.786122 AGCTAACCATCCTAAAGGTAAAACA 58.214 36.000 0.00 0.00 37.07 2.83
4333 5714 7.392393 TGAAGCTAACCATCCTAAAGGTAAAAC 59.608 37.037 0.00 0.00 37.07 2.43
4334 5715 7.463431 TGAAGCTAACCATCCTAAAGGTAAAA 58.537 34.615 0.00 0.00 37.07 1.52
4438 5819 1.227943 TCACTGCACAACTCTGCCC 60.228 57.895 0.00 0.00 36.21 5.36
4446 5827 1.345741 CTTCCCTCTCTCACTGCACAA 59.654 52.381 0.00 0.00 0.00 3.33
4464 5845 2.567169 GCATAAAAACTGCCCCTTCCTT 59.433 45.455 0.00 0.00 33.44 3.36
4551 5932 4.218635 CGCCAACTCCTCTTAGAGCATATA 59.781 45.833 3.26 0.00 37.39 0.86
4552 5933 3.006323 CGCCAACTCCTCTTAGAGCATAT 59.994 47.826 3.26 0.00 37.39 1.78
4566 5951 1.372128 CCAGCAAAAGCGCCAACTC 60.372 57.895 2.29 0.00 0.00 3.01
4567 5952 1.391157 TTCCAGCAAAAGCGCCAACT 61.391 50.000 2.29 0.00 0.00 3.16
4568 5953 0.319813 ATTCCAGCAAAAGCGCCAAC 60.320 50.000 2.29 0.00 0.00 3.77
4570 5955 0.525761 GTATTCCAGCAAAAGCGCCA 59.474 50.000 2.29 0.00 0.00 5.69
4572 5957 0.168128 ACGTATTCCAGCAAAAGCGC 59.832 50.000 0.00 0.00 0.00 5.92
4573 5958 2.611974 AACGTATTCCAGCAAAAGCG 57.388 45.000 0.00 0.00 0.00 4.68
4574 5959 3.121025 GCAAAACGTATTCCAGCAAAAGC 60.121 43.478 0.00 0.00 0.00 3.51
4575 5960 3.428534 GGCAAAACGTATTCCAGCAAAAG 59.571 43.478 0.00 0.00 0.00 2.27
4580 5967 0.885196 TGGGCAAAACGTATTCCAGC 59.115 50.000 0.00 0.00 0.00 4.85
4590 5977 1.544724 TGAGCTGGTATGGGCAAAAC 58.455 50.000 0.00 0.00 0.00 2.43
4593 5980 1.216064 AGATGAGCTGGTATGGGCAA 58.784 50.000 0.00 0.00 0.00 4.52
4609 5996 0.969894 CGAATCCTTCCGCCCTAGAT 59.030 55.000 0.00 0.00 0.00 1.98
4616 6003 0.108329 TGAGGTTCGAATCCTTCCGC 60.108 55.000 16.93 9.03 35.20 5.54
4623 6010 1.134560 AGTAGCGGTGAGGTTCGAATC 59.865 52.381 0.00 0.00 0.00 2.52
4627 6014 1.948145 AGATAGTAGCGGTGAGGTTCG 59.052 52.381 0.00 0.00 0.00 3.95
4629 6016 2.032620 CCAGATAGTAGCGGTGAGGTT 58.967 52.381 0.00 0.00 0.00 3.50
4635 6022 7.719871 ATCAATAATACCAGATAGTAGCGGT 57.280 36.000 7.04 7.04 35.46 5.68
4646 6033 7.470563 GCCAGGAAGGAAAATCAATAATACCAG 60.471 40.741 0.00 0.00 41.22 4.00
4647 6034 6.323739 GCCAGGAAGGAAAATCAATAATACCA 59.676 38.462 0.00 0.00 41.22 3.25
4653 6040 4.329638 TGGCCAGGAAGGAAAATCAATA 57.670 40.909 0.00 0.00 41.22 1.90
4677 6102 7.264294 AGGAAAATCAATCTAGTCTCAACCT 57.736 36.000 0.00 0.00 0.00 3.50
4678 6103 7.066404 GGAAGGAAAATCAATCTAGTCTCAACC 59.934 40.741 0.00 0.00 0.00 3.77
4680 6105 7.922382 AGGAAGGAAAATCAATCTAGTCTCAA 58.078 34.615 0.00 0.00 0.00 3.02
4681 6106 7.502060 AGGAAGGAAAATCAATCTAGTCTCA 57.498 36.000 0.00 0.00 0.00 3.27
4707 6132 3.688694 ACGTAAACATCCAAGTAGCCA 57.311 42.857 0.00 0.00 0.00 4.75
4724 6149 6.159988 TGGATTTTTCAAACTTTGTGAACGT 58.840 32.000 1.44 0.00 34.78 3.99
4730 6155 9.154847 CTCTCTTTTGGATTTTTCAAACTTTGT 57.845 29.630 1.44 0.00 34.34 2.83
4744 6169 2.848694 TCCAGCATCCTCTCTTTTGGAT 59.151 45.455 0.00 0.00 43.23 3.41
4759 6184 1.191489 TCCGAGTTCCATGTCCAGCA 61.191 55.000 0.00 0.00 0.00 4.41
4763 6188 2.431057 ACTGTATCCGAGTTCCATGTCC 59.569 50.000 0.00 0.00 0.00 4.02
4768 6193 3.581755 CGAAAACTGTATCCGAGTTCCA 58.418 45.455 0.00 0.00 32.33 3.53
4775 6200 0.391927 TGGCCCGAAAACTGTATCCG 60.392 55.000 0.00 0.00 0.00 4.18
4823 6248 2.113986 ACTGTCCAGCAAGGCCAC 59.886 61.111 5.01 0.00 37.29 5.01
4865 6290 5.829391 CACATCACAATTCAGGGGAATGATA 59.171 40.000 0.00 0.00 42.87 2.15
4896 6322 8.615878 AGTTTATGCTGTATTTGTCAAGTGTA 57.384 30.769 0.00 0.00 0.00 2.90
4904 6330 9.938280 TGTAAGTAGAGTTTATGCTGTATTTGT 57.062 29.630 0.00 0.00 0.00 2.83
4938 6367 7.119116 TGCAAGTCTGTAACTATGGTAATTGTG 59.881 37.037 0.00 0.00 37.17 3.33
4966 6397 6.183360 CGTTGTAATTTCCATGCCTCATAACT 60.183 38.462 0.00 0.00 0.00 2.24
4980 6411 7.527084 AGCATAGTTCTCTCGTTGTAATTTC 57.473 36.000 0.00 0.00 0.00 2.17
4991 6422 8.859517 AATAAACGTCTTAGCATAGTTCTCTC 57.140 34.615 0.00 0.00 0.00 3.20
5052 6486 7.659390 TGTGTGTTAGACATTACATCATGTTCA 59.341 33.333 0.00 0.00 37.52 3.18
5070 6504 7.149973 GGAAGTGTTATCTGTAGTGTGTGTTA 58.850 38.462 0.00 0.00 0.00 2.41
5229 6673 9.418839 TGGAAATTAAACATGTCATGATATCCA 57.581 29.630 19.77 16.64 0.00 3.41
5271 6715 6.890293 TGCCTTTGGGTTTTGTAAAGTTAAT 58.110 32.000 0.00 0.00 34.45 1.40
5291 6735 1.076192 ATTGTGCTGCTCCTTGCCT 59.924 52.632 0.00 0.00 42.00 4.75
5292 6736 1.214589 CATTGTGCTGCTCCTTGCC 59.785 57.895 0.00 0.00 42.00 4.52
5348 6793 3.088532 TCTTGTGTTGCCAGTCTTGTTT 58.911 40.909 0.00 0.00 0.00 2.83
5352 6797 2.092968 TCAGTCTTGTGTTGCCAGTCTT 60.093 45.455 0.00 0.00 0.00 3.01
5354 6799 1.953559 TCAGTCTTGTGTTGCCAGTC 58.046 50.000 0.00 0.00 0.00 3.51
5355 6800 2.017049 GTTCAGTCTTGTGTTGCCAGT 58.983 47.619 0.00 0.00 0.00 4.00
5356 6801 1.003545 CGTTCAGTCTTGTGTTGCCAG 60.004 52.381 0.00 0.00 0.00 4.85
5357 6802 1.013596 CGTTCAGTCTTGTGTTGCCA 58.986 50.000 0.00 0.00 0.00 4.92
5358 6803 1.295792 TCGTTCAGTCTTGTGTTGCC 58.704 50.000 0.00 0.00 0.00 4.52
5359 6804 2.349817 CCATCGTTCAGTCTTGTGTTGC 60.350 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.