Multiple sequence alignment - TraesCS2D01G518800

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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 TraesCS2D01G518800 chr2D 100.000 6426 0 0 1 6426 608777570 608771145 0 11867
1 TraesCS2D01G518800 chr2B 94.470 4195 108 52 791 4919 742529075 742524939 0 6348
2 TraesCS2D01G518800 chr2B 86.883 1418 71 56 41 1419 742529800 742528459 0 1482
3 TraesCS2D01G518800 chr2B 91.226 889 47 18 4916 5789 742524816 742523944 0 1181
4 TraesCS2D01G518800 chr2A 87.117 3361 202 96 55 3279 740385108 740381843 0 3594
5 TraesCS2D01G518800 chr2A 94.308 1757 66 21 3247 4976 740381843 740380094 0 2660
6 TraesCS2D01G518800 chr2A 87.835 822 61 19 4975 5789 740379833 740379044 0 928
7 TraesCS2D01G518800 chr2A 94.577 461 16 5 5975 6426 740378626 740378166 0 704


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 TraesCS2D01G518800 chr2D 608771145 608777570 6425 True 11867.000000 11867 100.000000 1 6426 1 chr2D.!!$R1 6425
1 TraesCS2D01G518800 chr2B 742523944 742529800 5856 True 3003.666667 6348 90.859667 41 5789 3 chr2B.!!$R1 5748
2 TraesCS2D01G518800 chr2A 740378166 740385108 6942 True 1971.500000 3594 90.959250 55 6426 4 chr2A.!!$R1 6371

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
403 431 0.105039 GGAATGAGAACCGATCCGCT 59.895 55.000 0.00 0.00 0.00 5.52 F
1199 1333 0.102481 AGGAATACAGCGTGGCGTAG 59.898 55.000 0.00 0.00 0.00 3.51 F
2509 2708 0.035630 CCCTTAAGTCTGCTGCTGCT 60.036 55.000 17.00 0.00 40.48 4.24 F
2709 2917 1.136828 TTAAGGTGCACCACTCCACT 58.863 50.000 36.39 12.43 38.89 4.00 F
4320 4595 2.344950 CTGTGCTCAAGTTAGCCTGAG 58.655 52.381 1.04 1.04 42.05 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1697 0.036388 GGCCAGCACTGCAACTACTA 60.036 55.000 0.0 0.0 0.00 1.82 R
2782 2991 2.128771 AAGCACCACACAACTGAACT 57.871 45.000 0.0 0.0 0.00 3.01 R
4320 4595 1.821136 CTTTGCCAGGTTGAAGATCCC 59.179 52.381 0.0 0.0 0.00 3.85 R
4556 4835 2.435418 GGGGTCATGCCACAACAAA 58.565 52.632 8.2 0.0 41.46 2.83 R
5968 6654 0.250209 CTGCACAACTGCTGACCTCT 60.250 55.000 0.0 0.0 44.57 3.69 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
21 22 4.760047 CCGGCGGACCTGGTTGAG 62.760 72.222 24.41 0.00 0.00 3.02
24 25 4.021925 GCGGACCTGGTTGAGCCT 62.022 66.667 0.00 0.00 38.35 4.58
25 26 2.656069 GCGGACCTGGTTGAGCCTA 61.656 63.158 0.00 0.00 38.35 3.93
26 27 1.980052 CGGACCTGGTTGAGCCTAA 59.020 57.895 0.00 0.00 38.35 2.69
27 28 0.391263 CGGACCTGGTTGAGCCTAAC 60.391 60.000 0.00 0.00 38.35 2.34
28 29 0.391263 GGACCTGGTTGAGCCTAACG 60.391 60.000 0.00 0.00 38.35 3.18
29 30 1.003718 ACCTGGTTGAGCCTAACGC 60.004 57.895 0.00 0.00 38.35 4.84
30 31 1.003839 CCTGGTTGAGCCTAACGCA 60.004 57.895 0.00 0.00 41.38 5.24
31 32 1.021390 CCTGGTTGAGCCTAACGCAG 61.021 60.000 9.91 9.91 41.38 5.18
50 51 1.170290 GGAAACCCAACACGTCCTGG 61.170 60.000 5.58 5.58 0.00 4.45
73 74 0.747255 CTCCATCGGGAACACTCGAT 59.253 55.000 0.00 0.00 44.38 3.59
76 77 2.202866 ATCGGGAACACTCGATGCT 58.797 52.632 4.20 0.00 43.37 3.79
77 78 1.399714 ATCGGGAACACTCGATGCTA 58.600 50.000 4.20 0.00 43.37 3.49
171 176 0.179137 CAATCGAGCGACAGGTGCTA 60.179 55.000 0.00 0.00 44.18 3.49
226 234 2.418628 CCCGTGTTTGATCATACACCAC 59.581 50.000 31.10 15.83 39.18 4.16
227 235 3.334691 CCGTGTTTGATCATACACCACT 58.665 45.455 31.10 0.00 39.18 4.00
228 236 3.370978 CCGTGTTTGATCATACACCACTC 59.629 47.826 31.10 15.26 39.18 3.51
229 237 3.370978 CGTGTTTGATCATACACCACTCC 59.629 47.826 31.10 14.71 39.18 3.85
230 238 4.323417 GTGTTTGATCATACACCACTCCA 58.677 43.478 28.84 2.28 37.32 3.86
289 316 3.781307 CGGGATCAGCACGGGGAA 61.781 66.667 0.00 0.00 40.53 3.97
356 384 5.951747 CAGACCAATCCTCCTCCAAAAATAA 59.048 40.000 0.00 0.00 0.00 1.40
359 387 7.679881 AGACCAATCCTCCTCCAAAAATAATTT 59.320 33.333 0.00 0.00 0.00 1.82
368 396 7.912719 TCCTCCAAAAATAATTTAAACCCCAG 58.087 34.615 0.00 0.00 0.00 4.45
388 416 2.148768 GGAAACTTCGAACCACGGAAT 58.851 47.619 0.00 0.00 42.82 3.01
402 430 2.606275 GGAATGAGAACCGATCCGC 58.394 57.895 0.00 0.00 0.00 5.54
403 431 0.105039 GGAATGAGAACCGATCCGCT 59.895 55.000 0.00 0.00 0.00 5.52
426 454 1.619432 CCCCCAAAATAGCAAGAGCCA 60.619 52.381 0.00 0.00 43.56 4.75
432 460 2.566833 AATAGCAAGAGCCACACACA 57.433 45.000 0.00 0.00 43.56 3.72
437 465 1.382522 CAAGAGCCACACACAACACT 58.617 50.000 0.00 0.00 0.00 3.55
439 467 2.240493 AGAGCCACACACAACACTAC 57.760 50.000 0.00 0.00 0.00 2.73
556 611 2.359107 CGCCATCCCATCCCATCG 60.359 66.667 0.00 0.00 0.00 3.84
636 709 3.037549 GAGATCTCCATCCCACTCAACT 58.962 50.000 12.00 0.00 0.00 3.16
711 784 3.134458 CTCCACATTTCTCCGCCTATTC 58.866 50.000 0.00 0.00 0.00 1.75
956 1049 3.474570 CTGCGGAAGGGGAGGAGG 61.475 72.222 0.00 0.00 0.00 4.30
957 1050 3.984186 CTGCGGAAGGGGAGGAGGA 62.984 68.421 0.00 0.00 0.00 3.71
958 1051 2.446802 GCGGAAGGGGAGGAGGAT 60.447 66.667 0.00 0.00 0.00 3.24
959 1052 1.152312 GCGGAAGGGGAGGAGGATA 60.152 63.158 0.00 0.00 0.00 2.59
960 1053 1.188871 GCGGAAGGGGAGGAGGATAG 61.189 65.000 0.00 0.00 0.00 2.08
961 1054 1.188871 CGGAAGGGGAGGAGGATAGC 61.189 65.000 0.00 0.00 0.00 2.97
962 1055 1.188871 GGAAGGGGAGGAGGATAGCG 61.189 65.000 0.00 0.00 0.00 4.26
963 1056 1.822114 GAAGGGGAGGAGGATAGCGC 61.822 65.000 0.00 0.00 0.00 5.92
964 1057 3.686045 GGGGAGGAGGATAGCGCG 61.686 72.222 0.00 0.00 0.00 6.86
981 1074 2.040544 CGGTGGTGGTGATTGGAGC 61.041 63.158 0.00 0.00 0.00 4.70
993 1098 2.243774 ATTGGAGCCGAGGAGGAGGA 62.244 60.000 0.00 0.00 45.00 3.71
1149 1254 0.938945 TCCCTCTCCCCCGAATCTTA 59.061 55.000 0.00 0.00 0.00 2.10
1150 1255 1.049402 CCCTCTCCCCCGAATCTTAC 58.951 60.000 0.00 0.00 0.00 2.34
1199 1333 0.102481 AGGAATACAGCGTGGCGTAG 59.898 55.000 0.00 0.00 0.00 3.51
1283 1425 1.065436 GTTAGGTAGACGGCGCTCC 59.935 63.158 6.90 8.90 0.00 4.70
1327 1479 2.074230 TTAACTGCGTCGGTGTCGGT 62.074 55.000 0.00 0.00 36.95 4.69
1328 1480 2.736343 TAACTGCGTCGGTGTCGGTG 62.736 60.000 0.00 0.00 36.95 4.94
1329 1481 4.640855 CTGCGTCGGTGTCGGTGT 62.641 66.667 0.00 0.00 36.95 4.16
1330 1482 4.634133 TGCGTCGGTGTCGGTGTC 62.634 66.667 0.00 0.00 36.95 3.67
1398 1550 0.521291 TCGCAGCTTGTTACAATGGC 59.479 50.000 0.00 0.00 0.00 4.40
1423 1597 9.626045 GCACAGTAGAATTTTATTTTGTAGCTT 57.374 29.630 0.00 0.00 0.00 3.74
1432 1606 6.902771 TTTATTTTGTAGCTTGTAGGGCAA 57.097 33.333 0.00 0.00 35.50 4.52
1444 1618 5.237344 GCTTGTAGGGCAATAGTACTCATTG 59.763 44.000 0.00 9.32 36.36 2.82
1450 1624 3.371595 GGCAATAGTACTCATTGTGGGGT 60.372 47.826 18.26 0.00 36.08 4.95
1452 1626 4.384208 GCAATAGTACTCATTGTGGGGTCT 60.384 45.833 18.26 0.00 36.08 3.85
1454 1628 6.180472 CAATAGTACTCATTGTGGGGTCTTT 58.820 40.000 0.00 0.00 0.00 2.52
1490 1672 1.908344 TAAGCTCAATGGCAAGTGCA 58.092 45.000 16.14 0.00 44.36 4.57
1498 1680 1.945387 ATGGCAAGTGCATCTAGTCG 58.055 50.000 5.52 0.00 44.36 4.18
1512 1694 3.296854 TCTAGTCGTGCCATATGGTTCT 58.703 45.455 22.79 14.92 37.57 3.01
1514 1696 2.632377 AGTCGTGCCATATGGTTCTTG 58.368 47.619 22.79 9.04 37.57 3.02
1515 1697 2.027192 AGTCGTGCCATATGGTTCTTGT 60.027 45.455 22.79 2.04 37.57 3.16
1516 1698 3.196901 AGTCGTGCCATATGGTTCTTGTA 59.803 43.478 22.79 0.41 37.57 2.41
1566 1748 4.081917 TCACCGTGCATATGACAGTTTAGA 60.082 41.667 6.97 0.00 0.00 2.10
1578 1763 4.022935 TGACAGTTTAGAGCAGGCAAATTG 60.023 41.667 0.00 0.00 0.00 2.32
1613 1798 7.661847 GGGGTCACTTCTATATCACCTTTTATG 59.338 40.741 0.00 0.00 0.00 1.90
1751 1942 2.641815 AGATAGGCCTTCATGTCCATCC 59.358 50.000 12.58 0.00 0.00 3.51
1764 1955 3.670625 TGTCCATCCTAAACTTGGAACG 58.329 45.455 0.00 0.00 41.05 3.95
1766 1957 1.743394 CCATCCTAAACTTGGAACGCC 59.257 52.381 0.00 0.00 37.13 5.68
1990 2181 1.623811 TGGTTAGCTCTCCTTCACACC 59.376 52.381 0.00 0.00 0.00 4.16
2100 2291 3.262660 TGAGGTATGCATCTCATCCCATC 59.737 47.826 12.75 2.22 33.91 3.51
2272 2463 0.823356 GTGGTCTTTGCTGCCCTCAA 60.823 55.000 0.00 0.00 0.00 3.02
2342 2533 9.091220 GGTAGGTATATTCAAACTACCTCTCAT 57.909 37.037 10.00 0.00 46.35 2.90
2473 2672 7.124573 AGCAATAGTATGAGTATGACACCAA 57.875 36.000 0.00 0.00 0.00 3.67
2504 2703 4.589908 ACATTAACCCCTTAAGTCTGCTG 58.410 43.478 0.97 0.00 0.00 4.41
2505 2704 2.781681 TAACCCCTTAAGTCTGCTGC 57.218 50.000 0.97 0.00 0.00 5.25
2506 2705 1.068121 AACCCCTTAAGTCTGCTGCT 58.932 50.000 0.00 0.00 0.00 4.24
2507 2706 0.326264 ACCCCTTAAGTCTGCTGCTG 59.674 55.000 0.00 0.00 0.00 4.41
2508 2707 1.028868 CCCCTTAAGTCTGCTGCTGC 61.029 60.000 8.89 8.89 40.20 5.25
2509 2708 0.035630 CCCTTAAGTCTGCTGCTGCT 60.036 55.000 17.00 0.00 40.48 4.24
2562 2769 4.380867 GGTGTTTGCCCATACTTCAGAATG 60.381 45.833 0.00 0.00 37.54 2.67
2590 2797 1.260544 ATGGTTTTGAGGCCTTGAGC 58.739 50.000 6.77 3.72 42.60 4.26
2709 2917 1.136828 TTAAGGTGCACCACTCCACT 58.863 50.000 36.39 12.43 38.89 4.00
2710 2918 1.136828 TAAGGTGCACCACTCCACTT 58.863 50.000 36.39 21.94 38.89 3.16
2776 2985 6.097915 TCTGACGAATTTGAAGTAGTTCCT 57.902 37.500 7.84 0.00 0.00 3.36
2777 2986 6.522054 TCTGACGAATTTGAAGTAGTTCCTT 58.478 36.000 7.84 0.00 0.00 3.36
2778 2987 6.645415 TCTGACGAATTTGAAGTAGTTCCTTC 59.355 38.462 7.84 7.36 41.01 3.46
2779 2988 6.285224 TGACGAATTTGAAGTAGTTCCTTCA 58.715 36.000 7.84 0.00 46.81 3.02
3059 3268 5.048782 TGGAATATGCGCAAGGAATCATAAC 60.049 40.000 17.11 0.00 45.01 1.89
3077 3286 8.773404 ATCATAACTAACTTACACAACTGACC 57.227 34.615 0.00 0.00 0.00 4.02
3092 3301 7.093509 ACACAACTGACCTTTTATTTTTGGACT 60.094 33.333 0.00 0.00 0.00 3.85
3728 3982 3.181526 CGCTTGTGTTTCATAGCAGAGAC 60.182 47.826 0.00 0.00 33.27 3.36
3911 4184 6.860790 TCCTGGTTACATAATAGTGTCACA 57.139 37.500 5.62 0.00 33.62 3.58
4320 4595 2.344950 CTGTGCTCAAGTTAGCCTGAG 58.655 52.381 1.04 1.04 42.05 3.35
4529 4805 3.213506 GGGGCATATTGAAAAATTGGGC 58.786 45.455 0.00 0.00 0.00 5.36
4556 4835 5.648178 AACCTTGTTTCGTTGTAACCTTT 57.352 34.783 0.00 0.00 0.00 3.11
4704 4983 6.211184 ACAAGTAATGGAAATGGATCAGCAAA 59.789 34.615 0.00 0.00 0.00 3.68
4774 5053 1.066358 CGAGGGGTTCTCCAAGTAACC 60.066 57.143 0.00 0.00 43.70 2.85
4880 5159 1.798813 CGAAGCACAAGACAAGGGTAC 59.201 52.381 0.00 0.00 0.00 3.34
5007 5674 7.865385 TGTGTTACCATTCAGAATTTGCTTTAC 59.135 33.333 0.00 0.00 0.00 2.01
5009 5676 8.296713 TGTTACCATTCAGAATTTGCTTTACTC 58.703 33.333 0.00 0.00 0.00 2.59
5037 5704 4.967084 TGCCTTAACTTCACTGTTCCTA 57.033 40.909 0.00 0.00 0.00 2.94
5049 5716 4.162888 TCACTGTTCCTATCATGTGCTGAT 59.837 41.667 0.00 0.00 46.49 2.90
5181 5848 8.421784 ACACTTTCAGTAGAGTAAGTTCAATCA 58.578 33.333 0.00 0.00 0.00 2.57
5208 5880 0.679505 TATCATAGTGCTGTCCGGGC 59.320 55.000 0.00 0.00 0.00 6.13
5214 5886 1.200519 AGTGCTGTCCGGGCTAATTA 58.799 50.000 7.97 0.00 0.00 1.40
5215 5887 1.557832 AGTGCTGTCCGGGCTAATTAA 59.442 47.619 7.97 0.00 0.00 1.40
5299 5976 1.751437 GGTGCATCCTGACCTTAACC 58.249 55.000 0.00 0.00 0.00 2.85
5317 5994 6.016610 CCTTAACCAAGGTTTTGATCGAAGAA 60.017 38.462 10.13 0.00 45.59 2.52
5400 6077 1.902938 TGGTCGCCACAATCAATCAA 58.097 45.000 0.00 0.00 0.00 2.57
5448 6125 4.762251 ACTTTCAGACCATCCTTAGTTTGC 59.238 41.667 0.00 0.00 0.00 3.68
5449 6126 4.365514 TTCAGACCATCCTTAGTTTGCA 57.634 40.909 0.00 0.00 0.00 4.08
5475 6152 3.009473 ACATATGTGTGCCTCTGGTTTCT 59.991 43.478 7.78 0.00 37.14 2.52
5485 6162 0.472471 TCTGGTTTCTGTGGGTGGAC 59.528 55.000 0.00 0.00 0.00 4.02
5544 6221 0.182775 AAGAACAAGCTGGGGTTCGT 59.817 50.000 16.05 12.25 46.09 3.85
5545 6222 0.182775 AGAACAAGCTGGGGTTCGTT 59.817 50.000 16.05 2.75 46.09 3.85
5546 6223 0.591659 GAACAAGCTGGGGTTCGTTC 59.408 55.000 9.54 0.00 34.69 3.95
5547 6224 0.106918 AACAAGCTGGGGTTCGTTCA 60.107 50.000 0.00 0.00 0.00 3.18
5559 6237 4.379499 GGGGTTCGTTCAGTCATCATTTTC 60.379 45.833 0.00 0.00 0.00 2.29
5574 6252 7.329226 GTCATCATTTTCCAGGTGTAAATTGTG 59.671 37.037 0.00 0.00 0.00 3.33
5716 6399 8.629158 TGTAAATGCAGTAGAAACAAATTCAGT 58.371 29.630 0.00 0.00 40.72 3.41
5742 6425 0.101219 GGGCAATCGTGGATGCTTTC 59.899 55.000 0.00 0.00 0.00 2.62
5750 6433 2.094494 TCGTGGATGCTTTCTCACTCTC 60.094 50.000 0.00 0.00 0.00 3.20
5759 6442 4.958581 TGCTTTCTCACTCTCATGAGGATA 59.041 41.667 22.42 2.56 45.30 2.59
5760 6443 5.068855 TGCTTTCTCACTCTCATGAGGATAG 59.931 44.000 22.42 14.69 45.30 2.08
5761 6444 5.301551 GCTTTCTCACTCTCATGAGGATAGA 59.698 44.000 22.42 15.96 45.30 1.98
5770 6455 6.897966 ACTCTCATGAGGATAGAACCTTGTTA 59.102 38.462 22.42 0.00 44.29 2.41
5800 6485 2.088950 AATCATGCAAAGCTGTTGGC 57.911 45.000 0.00 2.42 42.19 4.52
5801 6486 0.248289 ATCATGCAAAGCTGTTGGCC 59.752 50.000 0.00 0.00 43.05 5.36
5802 6487 0.828762 TCATGCAAAGCTGTTGGCCT 60.829 50.000 3.32 0.00 43.05 5.19
5803 6488 0.034337 CATGCAAAGCTGTTGGCCTT 59.966 50.000 3.32 0.00 43.05 4.35
5804 6489 0.034337 ATGCAAAGCTGTTGGCCTTG 59.966 50.000 3.32 0.00 43.20 3.61
5805 6490 4.348857 CAAAGCTGTTGGCCTTGC 57.651 55.556 3.32 2.80 43.05 4.01
5806 6491 1.662446 CAAAGCTGTTGGCCTTGCG 60.662 57.895 3.32 0.00 43.05 4.85
5807 6492 3.504524 AAAGCTGTTGGCCTTGCGC 62.505 57.895 3.32 0.00 43.05 6.09
5816 6501 2.421314 GCCTTGCGCCCTGTTTTT 59.579 55.556 4.18 0.00 0.00 1.94
5837 6522 2.884207 GGTGTCGGGTCGCGATTC 60.884 66.667 14.06 8.09 0.00 2.52
5840 6525 3.245315 GTCGGGTCGCGATTCGTG 61.245 66.667 25.19 13.26 39.67 4.35
5841 6526 3.433453 TCGGGTCGCGATTCGTGA 61.433 61.111 25.19 17.71 44.12 4.35
5847 6532 3.204505 TCGCGATTCGTGAAAAGGT 57.795 47.368 19.16 0.00 43.38 3.50
5848 6533 1.065358 TCGCGATTCGTGAAAAGGTC 58.935 50.000 19.16 0.00 43.38 3.85
5849 6534 0.246757 CGCGATTCGTGAAAAGGTCG 60.247 55.000 14.20 0.00 39.94 4.79
5853 6538 2.160013 CGATTCGTGAAAAGGTCGTGTC 60.160 50.000 0.00 0.00 0.00 3.67
5863 6548 1.810030 GGTCGTGTCGATTGGCTCC 60.810 63.158 0.00 0.00 38.42 4.70
5866 6552 1.079819 CGTGTCGATTGGCTCCAGT 60.080 57.895 0.00 0.00 0.00 4.00
5871 6557 0.036732 TCGATTGGCTCCAGTTGCTT 59.963 50.000 0.00 0.00 0.00 3.91
5873 6559 1.270550 CGATTGGCTCCAGTTGCTTTT 59.729 47.619 0.00 0.00 0.00 2.27
5875 6561 0.752054 TTGGCTCCAGTTGCTTTTGG 59.248 50.000 0.00 0.00 35.74 3.28
5883 6569 2.033801 CCAGTTGCTTTTGGTGTCTGAG 59.966 50.000 0.00 0.00 0.00 3.35
5891 6577 4.497507 GCTTTTGGTGTCTGAGGTTAACAC 60.498 45.833 8.10 1.61 41.97 3.32
5892 6578 4.497291 TTTGGTGTCTGAGGTTAACACT 57.503 40.909 8.10 2.06 42.26 3.55
5894 6580 3.035363 TGGTGTCTGAGGTTAACACTCA 58.965 45.455 19.35 19.35 42.26 3.41
5900 6586 3.838244 TGAGGTTAACACTCAGCAACT 57.162 42.857 17.63 0.05 39.87 3.16
5901 6587 3.466836 TGAGGTTAACACTCAGCAACTG 58.533 45.455 17.63 0.00 39.87 3.16
5903 6589 3.206150 AGGTTAACACTCAGCAACTGTG 58.794 45.455 8.10 0.00 37.67 3.66
5904 6590 2.290641 GGTTAACACTCAGCAACTGTGG 59.709 50.000 8.10 0.00 36.16 4.17
5905 6591 2.943033 GTTAACACTCAGCAACTGTGGT 59.057 45.455 0.00 0.00 36.16 4.16
5906 6592 2.128771 AACACTCAGCAACTGTGGTT 57.871 45.000 0.00 1.34 36.16 3.67
5907 6593 3.275617 AACACTCAGCAACTGTGGTTA 57.724 42.857 0.00 0.00 36.16 2.85
5908 6594 2.838736 ACACTCAGCAACTGTGGTTAG 58.161 47.619 0.00 0.00 36.16 2.34
5909 6595 2.170607 ACACTCAGCAACTGTGGTTAGT 59.829 45.455 0.00 0.00 39.66 2.24
5910 6596 2.545526 CACTCAGCAACTGTGGTTAGTG 59.454 50.000 6.01 6.01 45.74 2.74
5911 6597 2.170607 ACTCAGCAACTGTGGTTAGTGT 59.829 45.455 2.19 0.00 38.08 3.55
5912 6598 3.386726 ACTCAGCAACTGTGGTTAGTGTA 59.613 43.478 2.19 0.00 38.08 2.90
5913 6599 3.724374 TCAGCAACTGTGGTTAGTGTAC 58.276 45.455 0.00 0.00 33.88 2.90
5914 6600 3.133183 TCAGCAACTGTGGTTAGTGTACA 59.867 43.478 0.00 0.00 33.88 2.90
5915 6601 3.494626 CAGCAACTGTGGTTAGTGTACAG 59.505 47.826 0.00 0.00 45.48 2.74
5916 6602 2.223377 GCAACTGTGGTTAGTGTACAGC 59.777 50.000 0.00 0.00 44.22 4.40
5917 6603 3.462982 CAACTGTGGTTAGTGTACAGCA 58.537 45.455 0.00 0.00 44.22 4.41
5918 6604 3.107642 ACTGTGGTTAGTGTACAGCAC 57.892 47.619 0.00 0.62 44.22 4.40
5919 6605 6.067834 CAACTGTGGTTAGTGTACAGCACG 62.068 50.000 0.00 0.39 44.22 5.34
5936 6622 3.956199 AGCACGCTGTAAGGTTATAGGTA 59.044 43.478 0.00 0.00 0.00 3.08
5940 6626 6.567050 CACGCTGTAAGGTTATAGGTAAAGA 58.433 40.000 0.00 0.00 0.00 2.52
5942 6628 6.379417 ACGCTGTAAGGTTATAGGTAAAGACT 59.621 38.462 0.00 0.00 0.00 3.24
5944 6630 8.074972 CGCTGTAAGGTTATAGGTAAAGACTAG 58.925 40.741 0.00 0.00 0.00 2.57
5962 6648 6.971340 AGACTAGTGTCATTCCTAGAGGTAA 58.029 40.000 0.00 0.00 45.20 2.85
5963 6649 6.829811 AGACTAGTGTCATTCCTAGAGGTAAC 59.170 42.308 0.00 0.00 45.20 2.50
5964 6650 4.985538 AGTGTCATTCCTAGAGGTAACG 57.014 45.455 0.00 0.00 46.39 3.18
5965 6651 4.597004 AGTGTCATTCCTAGAGGTAACGA 58.403 43.478 0.00 0.00 46.39 3.85
5966 6652 5.014858 AGTGTCATTCCTAGAGGTAACGAA 58.985 41.667 0.00 0.00 46.39 3.85
5968 6654 6.832384 AGTGTCATTCCTAGAGGTAACGAATA 59.168 38.462 0.00 0.00 46.39 1.75
5969 6655 7.013464 AGTGTCATTCCTAGAGGTAACGAATAG 59.987 40.741 0.00 0.00 46.39 1.73
5973 6940 5.643421 TCCTAGAGGTAACGAATAGAGGT 57.357 43.478 0.00 0.00 46.39 3.85
5981 6948 3.963428 AACGAATAGAGGTCAGCAGTT 57.037 42.857 0.00 0.00 0.00 3.16
5984 6951 2.926200 CGAATAGAGGTCAGCAGTTGTG 59.074 50.000 0.00 0.00 0.00 3.33
5997 6964 0.898320 AGTTGTGCAGCGGATACTCT 59.102 50.000 0.00 0.00 0.00 3.24
5998 6965 2.100197 AGTTGTGCAGCGGATACTCTA 58.900 47.619 0.00 0.00 0.00 2.43
5999 6966 2.695666 AGTTGTGCAGCGGATACTCTAT 59.304 45.455 0.00 0.00 0.00 1.98
6000 6967 2.797156 GTTGTGCAGCGGATACTCTATG 59.203 50.000 0.00 0.00 0.00 2.23
6001 6968 2.306847 TGTGCAGCGGATACTCTATGA 58.693 47.619 0.00 0.00 0.00 2.15
6002 6969 2.893489 TGTGCAGCGGATACTCTATGAT 59.107 45.455 0.00 0.00 0.00 2.45
6003 6970 3.057245 TGTGCAGCGGATACTCTATGATC 60.057 47.826 0.00 0.00 0.00 2.92
6008 6980 3.761218 AGCGGATACTCTATGATCCAGTG 59.239 47.826 2.10 0.00 41.61 3.66
6051 7023 4.568152 AAAGACAAACCAACGGAATCTG 57.432 40.909 0.00 0.00 0.00 2.90
6064 7036 3.129871 CGGAATCTGAAGGAGAATCTGC 58.870 50.000 0.00 0.00 31.52 4.26
6075 7047 2.935201 GGAGAATCTGCACTAGCTTGTG 59.065 50.000 21.92 21.92 42.74 3.33
6120 7095 0.036875 CCTCCCGCTCCTTTCAGTTT 59.963 55.000 0.00 0.00 0.00 2.66
6168 7143 4.904253 AACGCAGTAGAGTAATCTCTCC 57.096 45.455 0.00 0.00 44.32 3.71
6192 7167 0.600255 AGCTTTGGTCAACGGACTCG 60.600 55.000 0.00 0.00 43.77 4.18
6258 7233 1.821332 CAAGGCGGCAGAAGGGATC 60.821 63.158 13.08 0.00 0.00 3.36
6380 7355 1.471676 CCTCGTTCCTTCCTTCCATCG 60.472 57.143 0.00 0.00 0.00 3.84
6383 7358 1.136305 CGTTCCTTCCTTCCATCGCTA 59.864 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.760047 CTCAACCAGGTCCGCCGG 62.760 72.222 0.00 0.00 40.50 6.13
7 8 2.180159 TTAGGCTCAACCAGGTCCGC 62.180 60.000 0.00 0.00 43.14 5.54
8 9 0.391263 GTTAGGCTCAACCAGGTCCG 60.391 60.000 0.00 0.00 43.14 4.79
9 10 0.391263 CGTTAGGCTCAACCAGGTCC 60.391 60.000 0.00 0.00 43.14 4.46
10 11 1.019805 GCGTTAGGCTCAACCAGGTC 61.020 60.000 0.00 0.00 43.14 3.85
11 12 1.003718 GCGTTAGGCTCAACCAGGT 60.004 57.895 0.00 0.00 43.14 4.00
12 13 1.003839 TGCGTTAGGCTCAACCAGG 60.004 57.895 0.00 0.00 43.14 4.45
13 14 1.021390 CCTGCGTTAGGCTCAACCAG 61.021 60.000 0.00 4.73 43.14 4.00
14 15 1.003839 CCTGCGTTAGGCTCAACCA 60.004 57.895 0.00 0.00 43.14 3.67
15 16 0.321298 TTCCTGCGTTAGGCTCAACC 60.321 55.000 0.00 0.00 46.87 3.77
16 17 1.197036 GTTTCCTGCGTTAGGCTCAAC 59.803 52.381 0.00 0.00 46.87 3.18
17 18 1.519408 GTTTCCTGCGTTAGGCTCAA 58.481 50.000 0.00 0.00 46.87 3.02
18 19 0.321298 GGTTTCCTGCGTTAGGCTCA 60.321 55.000 0.00 0.00 46.87 4.26
19 20 1.025113 GGGTTTCCTGCGTTAGGCTC 61.025 60.000 0.00 0.00 46.87 4.70
20 21 1.002502 GGGTTTCCTGCGTTAGGCT 60.003 57.895 0.00 0.00 46.87 4.58
21 22 0.891904 TTGGGTTTCCTGCGTTAGGC 60.892 55.000 3.30 0.00 46.87 3.93
23 24 1.265905 GTGTTGGGTTTCCTGCGTTAG 59.734 52.381 0.00 0.00 0.00 2.34
24 25 1.310904 GTGTTGGGTTTCCTGCGTTA 58.689 50.000 0.00 0.00 0.00 3.18
25 26 1.720694 CGTGTTGGGTTTCCTGCGTT 61.721 55.000 0.00 0.00 0.00 4.84
26 27 2.184167 CGTGTTGGGTTTCCTGCGT 61.184 57.895 0.00 0.00 0.00 5.24
27 28 2.113131 GACGTGTTGGGTTTCCTGCG 62.113 60.000 0.00 0.00 0.00 5.18
28 29 1.652563 GACGTGTTGGGTTTCCTGC 59.347 57.895 0.00 0.00 0.00 4.85
29 30 0.179029 AGGACGTGTTGGGTTTCCTG 60.179 55.000 0.00 0.00 35.28 3.86
30 31 0.179029 CAGGACGTGTTGGGTTTCCT 60.179 55.000 0.00 0.00 37.15 3.36
31 32 1.170290 CCAGGACGTGTTGGGTTTCC 61.170 60.000 0.00 0.00 0.00 3.13
32 33 0.179040 TCCAGGACGTGTTGGGTTTC 60.179 55.000 13.38 0.00 35.13 2.78
33 34 0.476771 ATCCAGGACGTGTTGGGTTT 59.523 50.000 13.38 0.00 35.13 3.27
34 35 1.002773 GTATCCAGGACGTGTTGGGTT 59.997 52.381 13.38 6.02 35.13 4.11
35 36 0.611714 GTATCCAGGACGTGTTGGGT 59.388 55.000 13.38 9.84 35.13 4.51
36 37 0.902531 AGTATCCAGGACGTGTTGGG 59.097 55.000 13.38 1.13 35.13 4.12
37 38 2.295253 GAGTATCCAGGACGTGTTGG 57.705 55.000 8.32 8.32 35.74 3.77
50 51 2.287668 CGAGTGTTCCCGATGGAGTATC 60.288 54.545 0.00 0.00 43.07 2.24
73 74 2.053277 TGCCGTGGGACGTATAGCA 61.053 57.895 0.00 0.00 40.58 3.49
76 77 0.971959 AAGGTGCCGTGGGACGTATA 60.972 55.000 6.17 0.00 40.58 1.47
77 78 1.833787 AAAGGTGCCGTGGGACGTAT 61.834 55.000 6.17 0.00 40.58 3.06
323 350 2.434884 ATTGGTCTGCGTGCTCCG 60.435 61.111 0.00 0.00 40.40 4.63
356 384 4.732065 TCGAAGTTTCCTGGGGTTTAAAT 58.268 39.130 0.00 0.00 0.00 1.40
359 387 3.479489 GTTCGAAGTTTCCTGGGGTTTA 58.521 45.455 0.00 0.00 0.00 2.01
368 396 1.585297 TTCCGTGGTTCGAAGTTTCC 58.415 50.000 0.00 0.00 42.86 3.13
388 416 2.184322 GCAGCGGATCGGTTCTCA 59.816 61.111 1.93 0.00 34.62 3.27
415 443 1.134250 TGTTGTGTGTGGCTCTTGCTA 60.134 47.619 0.00 0.00 39.59 3.49
416 444 0.394216 TGTTGTGTGTGGCTCTTGCT 60.394 50.000 0.00 0.00 39.59 3.91
418 446 1.382522 AGTGTTGTGTGTGGCTCTTG 58.617 50.000 0.00 0.00 0.00 3.02
419 447 2.093181 TGTAGTGTTGTGTGTGGCTCTT 60.093 45.455 0.00 0.00 0.00 2.85
421 449 1.597663 GTGTAGTGTTGTGTGTGGCTC 59.402 52.381 0.00 0.00 0.00 4.70
426 454 1.407712 GGTGGGTGTAGTGTTGTGTGT 60.408 52.381 0.00 0.00 0.00 3.72
432 460 2.428622 GGCGGTGGGTGTAGTGTT 59.571 61.111 0.00 0.00 0.00 3.32
556 611 2.361104 TTTCGCCAGGTGGGATGC 60.361 61.111 0.00 0.00 40.01 3.91
946 1039 2.203714 GCGCTATCCTCCTCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
948 1041 3.686045 CCGCGCTATCCTCCTCCC 61.686 72.222 5.56 0.00 0.00 4.30
949 1042 2.913060 ACCGCGCTATCCTCCTCC 60.913 66.667 5.56 0.00 0.00 4.30
950 1043 2.336809 CACCGCGCTATCCTCCTC 59.663 66.667 5.56 0.00 0.00 3.71
951 1044 3.227276 CCACCGCGCTATCCTCCT 61.227 66.667 5.56 0.00 0.00 3.69
952 1045 3.537874 ACCACCGCGCTATCCTCC 61.538 66.667 5.56 0.00 0.00 4.30
953 1046 2.279517 CACCACCGCGCTATCCTC 60.280 66.667 5.56 0.00 0.00 3.71
954 1047 3.849951 CCACCACCGCGCTATCCT 61.850 66.667 5.56 0.00 0.00 3.24
955 1048 4.157120 ACCACCACCGCGCTATCC 62.157 66.667 5.56 0.00 0.00 2.59
956 1049 2.644555 ATCACCACCACCGCGCTATC 62.645 60.000 5.56 0.00 0.00 2.08
957 1050 2.252072 AATCACCACCACCGCGCTAT 62.252 55.000 5.56 0.00 0.00 2.97
958 1051 2.949909 AATCACCACCACCGCGCTA 61.950 57.895 5.56 0.00 0.00 4.26
959 1052 4.329545 AATCACCACCACCGCGCT 62.330 61.111 5.56 0.00 0.00 5.92
960 1053 4.101790 CAATCACCACCACCGCGC 62.102 66.667 0.00 0.00 0.00 6.86
961 1054 3.430862 CCAATCACCACCACCGCG 61.431 66.667 0.00 0.00 0.00 6.46
962 1055 2.033448 TCCAATCACCACCACCGC 59.967 61.111 0.00 0.00 0.00 5.68
963 1056 2.040544 GCTCCAATCACCACCACCG 61.041 63.158 0.00 0.00 0.00 4.94
964 1057 1.678970 GGCTCCAATCACCACCACC 60.679 63.158 0.00 0.00 0.00 4.61
993 1098 2.677228 CAGAACCCCATTCCGCCT 59.323 61.111 0.00 0.00 38.16 5.52
1125 1230 4.548513 CGGGGGAGAGGGAGAGGG 62.549 77.778 0.00 0.00 0.00 4.30
1127 1232 0.830023 GATTCGGGGGAGAGGGAGAG 60.830 65.000 0.00 0.00 0.00 3.20
1128 1233 1.233369 GATTCGGGGGAGAGGGAGA 59.767 63.158 0.00 0.00 0.00 3.71
1149 1254 2.027605 CAGGTATCGCGCATCGGT 59.972 61.111 8.75 0.00 39.05 4.69
1150 1255 2.734723 CCAGGTATCGCGCATCGG 60.735 66.667 8.75 0.00 39.05 4.18
1170 1275 1.777272 GCTGTATTCCTCCAATCCCCT 59.223 52.381 0.00 0.00 0.00 4.79
1283 1425 1.563435 GCGACAGGGATGATGATGCG 61.563 60.000 0.00 0.00 0.00 4.73
1327 1479 0.037590 AGCCAAAACCTATGCCGACA 59.962 50.000 0.00 0.00 0.00 4.35
1328 1480 1.173913 AAGCCAAAACCTATGCCGAC 58.826 50.000 0.00 0.00 0.00 4.79
1329 1481 2.791347 TAAGCCAAAACCTATGCCGA 57.209 45.000 0.00 0.00 0.00 5.54
1330 1482 2.687935 ACATAAGCCAAAACCTATGCCG 59.312 45.455 0.00 0.00 0.00 5.69
1331 1483 3.181476 CCACATAAGCCAAAACCTATGCC 60.181 47.826 0.00 0.00 0.00 4.40
1332 1484 3.181476 CCCACATAAGCCAAAACCTATGC 60.181 47.826 0.00 0.00 0.00 3.14
1419 1571 4.030913 TGAGTACTATTGCCCTACAAGCT 58.969 43.478 0.00 0.00 42.87 3.74
1420 1572 4.402056 TGAGTACTATTGCCCTACAAGC 57.598 45.455 0.00 0.00 42.87 4.01
1423 1597 5.396324 CCACAATGAGTACTATTGCCCTACA 60.396 44.000 17.67 2.47 38.72 2.74
1432 1606 5.487488 TCAAAGACCCCACAATGAGTACTAT 59.513 40.000 0.00 0.00 0.00 2.12
1444 1618 2.969262 TGGGAAAAATCAAAGACCCCAC 59.031 45.455 0.00 0.00 37.44 4.61
1450 1624 6.350445 GCTTATCTGCTGGGAAAAATCAAAGA 60.350 38.462 0.00 0.00 0.00 2.52
1452 1626 5.481473 AGCTTATCTGCTGGGAAAAATCAAA 59.519 36.000 0.00 0.00 42.33 2.69
1454 1628 4.603131 AGCTTATCTGCTGGGAAAAATCA 58.397 39.130 0.00 0.00 42.33 2.57
1490 1672 3.898123 AGAACCATATGGCACGACTAGAT 59.102 43.478 22.18 0.00 39.32 1.98
1498 1680 5.671493 ACTACTACAAGAACCATATGGCAC 58.329 41.667 22.18 15.19 39.32 5.01
1512 1694 2.766313 CCAGCACTGCAACTACTACAA 58.234 47.619 3.30 0.00 0.00 2.41
1514 1696 1.079503 GCCAGCACTGCAACTACTAC 58.920 55.000 3.30 0.00 0.00 2.73
1515 1697 0.036388 GGCCAGCACTGCAACTACTA 60.036 55.000 0.00 0.00 0.00 1.82
1516 1698 1.302832 GGCCAGCACTGCAACTACT 60.303 57.895 0.00 0.00 0.00 2.57
1566 1748 2.584835 TGGACTACAATTTGCCTGCT 57.415 45.000 0.00 0.00 0.00 4.24
1578 1763 2.188817 AGAAGTGACCCCATGGACTAC 58.811 52.381 15.22 6.79 34.81 2.73
1613 1798 6.163159 TGCAATTTCTTCAACAACAACAAC 57.837 33.333 0.00 0.00 0.00 3.32
1751 1942 0.442699 GCGAGGCGTTCCAAGTTTAG 59.557 55.000 0.00 0.00 33.74 1.85
1764 1955 0.108424 ATTCAGTCACAGAGCGAGGC 60.108 55.000 0.00 0.00 0.00 4.70
1766 1957 1.470632 GGGATTCAGTCACAGAGCGAG 60.471 57.143 0.00 0.00 0.00 5.03
2100 2291 2.496070 TCTGGTGACGGTTTCAGGATAG 59.504 50.000 0.00 0.00 33.71 2.08
2150 2341 4.357325 AGAAGATGCTCAAGAAGAGGGTA 58.643 43.478 0.00 0.00 44.86 3.69
2272 2463 3.879892 GCCAAGAGTGAGTTTTGAGAACT 59.120 43.478 0.00 0.00 0.00 3.01
2473 2672 4.741928 AAGGGGTTAATGTCTCCTTTGT 57.258 40.909 0.00 0.00 34.50 2.83
2562 2769 4.770531 AGGCCTCAAAACCATTTTACTACC 59.229 41.667 0.00 0.00 0.00 3.18
2590 2797 5.101628 CCAAAATTGGTATTCATCCACACG 58.898 41.667 3.95 0.00 43.43 4.49
2776 2985 4.188462 CACCACACAACTGAACTACTGAA 58.812 43.478 0.00 0.00 0.00 3.02
2777 2986 3.792401 CACCACACAACTGAACTACTGA 58.208 45.455 0.00 0.00 0.00 3.41
2778 2987 2.287915 GCACCACACAACTGAACTACTG 59.712 50.000 0.00 0.00 0.00 2.74
2779 2988 2.170607 AGCACCACACAACTGAACTACT 59.829 45.455 0.00 0.00 0.00 2.57
2780 2989 2.561569 AGCACCACACAACTGAACTAC 58.438 47.619 0.00 0.00 0.00 2.73
2781 2990 3.275617 AAGCACCACACAACTGAACTA 57.724 42.857 0.00 0.00 0.00 2.24
2782 2991 2.128771 AAGCACCACACAACTGAACT 57.871 45.000 0.00 0.00 0.00 3.01
2783 2992 2.939460 AAAGCACCACACAACTGAAC 57.061 45.000 0.00 0.00 0.00 3.18
3092 3301 6.406370 AGACGACTGATTCATAATTCAACCA 58.594 36.000 0.00 0.00 0.00 3.67
3268 3513 3.631227 TCACAACTCACAATGTCATGCAA 59.369 39.130 0.00 0.00 0.00 4.08
3728 3982 7.603404 TCAACAATAGGATTTGCAAATTCCAAG 59.397 33.333 27.65 18.68 46.22 3.61
3911 4184 8.585471 ATCATTAGTCATTCCACTGTGATTTT 57.415 30.769 9.86 0.00 33.04 1.82
4142 4417 6.442541 TGACAAAAGTTAGTAGGAATCCCA 57.557 37.500 0.00 0.00 33.88 4.37
4320 4595 1.821136 CTTTGCCAGGTTGAAGATCCC 59.179 52.381 0.00 0.00 0.00 3.85
4505 4781 5.455899 GCCCAATTTTTCAATATGCCCCATA 60.456 40.000 0.00 0.00 0.00 2.74
4529 4805 5.910723 GGTTACAACGAAACAAGGTTATGTG 59.089 40.000 0.00 0.00 32.81 3.21
4556 4835 2.435418 GGGGTCATGCCACAACAAA 58.565 52.632 8.20 0.00 41.46 2.83
4704 4983 4.406456 TGACAACCTGCCATAATCTTTGT 58.594 39.130 0.00 0.00 0.00 2.83
4774 5053 3.986572 GCAGATCTTCACCAGATATCACG 59.013 47.826 5.32 0.00 42.92 4.35
4861 5140 3.127425 AGTACCCTTGTCTTGTGCTTC 57.873 47.619 0.00 0.00 0.00 3.86
4928 5334 9.932699 TGCAAAATCATTGAAAAATTAACACTG 57.067 25.926 0.00 0.00 0.00 3.66
5007 5674 4.217118 AGTGAAGTTAAGGCATGCTTTGAG 59.783 41.667 23.96 0.00 0.00 3.02
5009 5676 4.232221 CAGTGAAGTTAAGGCATGCTTTG 58.768 43.478 23.96 1.68 0.00 2.77
5019 5686 7.413438 GCACATGATAGGAACAGTGAAGTTAAG 60.413 40.741 0.00 0.00 0.00 1.85
5020 5687 6.371548 GCACATGATAGGAACAGTGAAGTTAA 59.628 38.462 0.00 0.00 0.00 2.01
5021 5688 5.874810 GCACATGATAGGAACAGTGAAGTTA 59.125 40.000 0.00 0.00 0.00 2.24
5022 5689 4.697352 GCACATGATAGGAACAGTGAAGTT 59.303 41.667 0.00 0.00 0.00 2.66
5023 5690 4.019860 AGCACATGATAGGAACAGTGAAGT 60.020 41.667 0.00 0.00 0.00 3.01
5049 5716 1.266718 GCTTTCATTCACAACCTGCGA 59.733 47.619 0.00 0.00 0.00 5.10
5102 5769 3.394674 TGTAAGCCATCTTCGACAACA 57.605 42.857 0.00 0.00 33.85 3.33
5181 5848 5.065218 CGGACAGCACTATGATAAAAGCTTT 59.935 40.000 5.69 5.69 0.00 3.51
5208 5880 8.539770 AGACCATATCGCAGTTGATTAATTAG 57.460 34.615 0.00 0.00 0.00 1.73
5214 5886 4.406648 TGAGACCATATCGCAGTTGATT 57.593 40.909 0.00 0.00 31.35 2.57
5215 5887 4.202295 ACATGAGACCATATCGCAGTTGAT 60.202 41.667 0.00 0.00 40.79 2.57
5251 5923 8.840321 CCCATGTAATCCTACAGAAAAACATAG 58.160 37.037 0.00 0.00 41.33 2.23
5252 5924 8.553153 TCCCATGTAATCCTACAGAAAAACATA 58.447 33.333 0.00 0.00 41.33 2.29
5253 5925 7.339466 GTCCCATGTAATCCTACAGAAAAACAT 59.661 37.037 0.00 0.00 41.33 2.71
5255 5927 6.183360 CGTCCCATGTAATCCTACAGAAAAAC 60.183 42.308 0.00 0.00 41.33 2.43
5256 5928 5.878116 CGTCCCATGTAATCCTACAGAAAAA 59.122 40.000 0.00 0.00 41.33 1.94
5299 5976 7.746475 GTGTAATCTTCTTCGATCAAAACCTTG 59.254 37.037 0.00 0.00 0.00 3.61
5317 5994 1.207329 GGGAAGCTGTCGGTGTAATCT 59.793 52.381 0.00 0.00 0.00 2.40
5400 6077 1.153549 GCTTCTCCCGAATCACGCT 60.154 57.895 0.00 0.00 41.07 5.07
5475 6152 0.468958 CAACCCAATGTCCACCCACA 60.469 55.000 0.00 0.00 0.00 4.17
5485 6162 0.318120 GGCCAACAGTCAACCCAATG 59.682 55.000 0.00 0.00 0.00 2.82
5522 6199 2.882137 CGAACCCCAGCTTGTTCTTAAA 59.118 45.455 14.98 0.00 38.93 1.52
5524 6201 1.418637 ACGAACCCCAGCTTGTTCTTA 59.581 47.619 14.98 0.00 38.93 2.10
5527 6204 0.591659 GAACGAACCCCAGCTTGTTC 59.408 55.000 9.47 9.47 37.97 3.18
5544 6221 4.728772 ACACCTGGAAAATGATGACTGAA 58.271 39.130 0.00 0.00 0.00 3.02
5545 6222 4.371624 ACACCTGGAAAATGATGACTGA 57.628 40.909 0.00 0.00 0.00 3.41
5546 6223 6.573664 TTTACACCTGGAAAATGATGACTG 57.426 37.500 0.00 0.00 0.00 3.51
5547 6224 7.233348 ACAATTTACACCTGGAAAATGATGACT 59.767 33.333 0.00 0.00 0.00 3.41
5559 6237 2.870175 TGGGACACAATTTACACCTGG 58.130 47.619 0.00 0.00 0.00 4.45
5574 6252 2.785105 CGCGACGAAACGATGGGAC 61.785 63.158 0.00 0.00 35.09 4.46
5597 6275 4.322080 TCAATCTATCGACACCATGACC 57.678 45.455 0.00 0.00 0.00 4.02
5627 6307 1.882912 TTGATCACTGTCACTGCCAC 58.117 50.000 0.00 0.00 0.00 5.01
5716 6399 1.963855 CCACGATTGCCCACACGAA 60.964 57.895 0.00 0.00 0.00 3.85
5742 6425 5.139727 AGGTTCTATCCTCATGAGAGTGAG 58.860 45.833 24.62 14.38 44.12 3.51
5759 6442 9.023962 TGATTTTGCATCTAATAACAAGGTTCT 57.976 29.630 0.00 0.00 0.00 3.01
5760 6443 9.807649 ATGATTTTGCATCTAATAACAAGGTTC 57.192 29.630 0.00 0.00 0.00 3.62
5761 6444 9.590451 CATGATTTTGCATCTAATAACAAGGTT 57.410 29.630 0.00 0.00 0.00 3.50
5789 6474 2.730094 CGCAAGGCCAACAGCTTT 59.270 55.556 5.01 0.00 42.44 3.51
5790 6475 3.982241 GCGCAAGGCCAACAGCTT 61.982 61.111 5.01 0.00 43.05 3.74
5828 6513 0.788391 ACCTTTTCACGAATCGCGAC 59.212 50.000 12.93 0.00 44.57 5.19
5831 6516 0.788391 ACGACCTTTTCACGAATCGC 59.212 50.000 1.15 0.00 32.95 4.58
5834 6519 1.790623 CGACACGACCTTTTCACGAAT 59.209 47.619 0.00 0.00 0.00 3.34
5837 6522 1.415374 ATCGACACGACCTTTTCACG 58.585 50.000 0.00 0.00 39.18 4.35
5840 6525 1.136057 GCCAATCGACACGACCTTTTC 60.136 52.381 0.00 0.00 39.18 2.29
5841 6526 0.872388 GCCAATCGACACGACCTTTT 59.128 50.000 0.00 0.00 39.18 2.27
5846 6531 1.078759 CTGGAGCCAATCGACACGAC 61.079 60.000 0.00 0.00 39.18 4.34
5847 6532 1.215382 CTGGAGCCAATCGACACGA 59.785 57.895 0.00 0.00 41.13 4.35
5848 6533 0.670546 AACTGGAGCCAATCGACACG 60.671 55.000 0.00 0.00 0.00 4.49
5849 6534 0.798776 CAACTGGAGCCAATCGACAC 59.201 55.000 0.00 0.00 0.00 3.67
5853 6538 0.883833 AAAGCAACTGGAGCCAATCG 59.116 50.000 0.00 0.00 0.00 3.34
5863 6548 2.033801 CCTCAGACACCAAAAGCAACTG 59.966 50.000 0.00 0.00 0.00 3.16
5866 6552 2.435372 ACCTCAGACACCAAAAGCAA 57.565 45.000 0.00 0.00 0.00 3.91
5871 6557 4.080807 TGAGTGTTAACCTCAGACACCAAA 60.081 41.667 17.63 0.00 43.49 3.28
5873 6559 3.035363 TGAGTGTTAACCTCAGACACCA 58.965 45.455 17.63 4.29 43.49 4.17
5883 6569 2.290641 CCACAGTTGCTGAGTGTTAACC 59.709 50.000 2.48 0.00 39.94 2.85
5891 6577 2.838736 ACACTAACCACAGTTGCTGAG 58.161 47.619 2.91 0.00 36.68 3.35
5892 6578 3.133183 TGTACACTAACCACAGTTGCTGA 59.867 43.478 2.91 0.00 36.68 4.26
5894 6580 3.728845 CTGTACACTAACCACAGTTGCT 58.271 45.455 0.00 0.00 36.68 3.91
5896 6582 3.247648 GTGCTGTACACTAACCACAGTTG 59.752 47.826 0.00 0.00 46.41 3.16
5914 6600 2.764572 ACCTATAACCTTACAGCGTGCT 59.235 45.455 0.00 0.00 0.00 4.40
5915 6601 3.175109 ACCTATAACCTTACAGCGTGC 57.825 47.619 0.00 0.00 0.00 5.34
5916 6602 6.474751 GTCTTTACCTATAACCTTACAGCGTG 59.525 42.308 0.00 0.00 0.00 5.34
5917 6603 6.379417 AGTCTTTACCTATAACCTTACAGCGT 59.621 38.462 0.00 0.00 0.00 5.07
5918 6604 6.803642 AGTCTTTACCTATAACCTTACAGCG 58.196 40.000 0.00 0.00 0.00 5.18
5919 6605 8.911965 ACTAGTCTTTACCTATAACCTTACAGC 58.088 37.037 0.00 0.00 0.00 4.40
5921 6607 9.759473 ACACTAGTCTTTACCTATAACCTTACA 57.241 33.333 0.00 0.00 0.00 2.41
5923 6609 9.979897 TGACACTAGTCTTTACCTATAACCTTA 57.020 33.333 0.00 0.00 45.20 2.69
5924 6610 8.890410 TGACACTAGTCTTTACCTATAACCTT 57.110 34.615 0.00 0.00 45.20 3.50
5925 6611 9.490083 AATGACACTAGTCTTTACCTATAACCT 57.510 33.333 0.00 0.00 45.20 3.50
5926 6612 9.747293 GAATGACACTAGTCTTTACCTATAACC 57.253 37.037 0.00 0.00 45.20 2.85
5927 6613 9.747293 GGAATGACACTAGTCTTTACCTATAAC 57.253 37.037 0.00 0.00 45.20 1.89
5928 6614 9.710818 AGGAATGACACTAGTCTTTACCTATAA 57.289 33.333 0.00 0.00 41.40 0.98
5930 6616 9.357161 CTAGGAATGACACTAGTCTTTACCTAT 57.643 37.037 0.00 0.97 41.40 2.57
5931 6617 8.554870 TCTAGGAATGACACTAGTCTTTACCTA 58.445 37.037 0.00 2.19 41.40 3.08
5932 6618 7.411808 TCTAGGAATGACACTAGTCTTTACCT 58.588 38.462 0.00 1.05 41.40 3.08
5933 6619 7.201839 CCTCTAGGAATGACACTAGTCTTTACC 60.202 44.444 0.00 0.00 41.40 2.85
5936 6622 6.257586 ACCTCTAGGAATGACACTAGTCTTT 58.742 40.000 2.23 0.00 42.70 2.52
5940 6626 5.589452 CGTTACCTCTAGGAATGACACTAGT 59.411 44.000 2.23 0.00 38.24 2.57
5942 6628 5.748402 TCGTTACCTCTAGGAATGACACTA 58.252 41.667 2.23 0.00 38.94 2.74
5944 6630 4.978083 TCGTTACCTCTAGGAATGACAC 57.022 45.455 2.23 0.00 38.94 3.67
5962 6648 2.563179 ACAACTGCTGACCTCTATTCGT 59.437 45.455 0.00 0.00 0.00 3.85
5963 6649 2.926200 CACAACTGCTGACCTCTATTCG 59.074 50.000 0.00 0.00 0.00 3.34
5964 6650 2.675348 GCACAACTGCTGACCTCTATTC 59.325 50.000 0.00 0.00 40.63 1.75
5965 6651 2.038952 TGCACAACTGCTGACCTCTATT 59.961 45.455 0.00 0.00 44.57 1.73
5966 6652 1.625315 TGCACAACTGCTGACCTCTAT 59.375 47.619 0.00 0.00 44.57 1.98
5968 6654 0.250209 CTGCACAACTGCTGACCTCT 60.250 55.000 0.00 0.00 44.57 3.69
5969 6655 1.849976 GCTGCACAACTGCTGACCTC 61.850 60.000 0.00 0.00 44.57 3.85
5973 6940 2.736579 ATCCGCTGCACAACTGCTGA 62.737 55.000 0.00 0.00 44.57 4.26
5981 6948 2.306847 TCATAGAGTATCCGCTGCACA 58.693 47.619 0.00 0.00 33.66 4.57
5984 6951 2.493675 TGGATCATAGAGTATCCGCTGC 59.506 50.000 0.00 0.00 43.96 5.25
6001 6968 2.731572 CAAAAGATCCTGCCACTGGAT 58.268 47.619 0.00 5.77 43.28 3.41
6002 6969 1.887956 GCAAAAGATCCTGCCACTGGA 60.888 52.381 0.00 0.00 36.01 3.86
6003 6970 0.529378 GCAAAAGATCCTGCCACTGG 59.471 55.000 1.48 0.00 32.18 4.00
6051 7023 3.817709 AGCTAGTGCAGATTCTCCTTC 57.182 47.619 0.00 0.00 42.74 3.46
6075 7047 2.724839 CGGCACTTTGTTTCATCGTAGC 60.725 50.000 0.00 0.00 0.00 3.58
6120 7095 1.068417 CCGTTCGTTGGTGGTCTGA 59.932 57.895 0.00 0.00 0.00 3.27
6159 7134 2.168521 CCAAAGCTCCGTGGAGAGATTA 59.831 50.000 19.98 0.00 41.46 1.75
6168 7143 1.569493 CGTTGACCAAAGCTCCGTG 59.431 57.895 0.00 0.00 0.00 4.94
6192 7167 4.674475 ACATTTTTGGTGTTCGGTACAAC 58.326 39.130 0.00 0.00 38.80 3.32
6380 7355 3.807071 GCAGAAGCCTGTTTATCTCTAGC 59.193 47.826 0.00 0.00 42.35 3.42
6383 7358 3.988976 TGCAGAAGCCTGTTTATCTCT 57.011 42.857 0.00 0.00 42.35 3.10


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

AutoCloner maintained by Alex Coulton.