Multiple sequence alignment - TraesCS1A01G404700

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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 TraesCS1A01G404700 chr1A 100.000 6436 0 0 1 6436 568107589 568114024 0.000000e+00 11886.0
1 TraesCS1A01G404700 chr1A 91.617 501 41 1 976 1476 545896727 545896228 0.000000e+00 691.0
2 TraesCS1A01G404700 chr1A 79.927 274 28 9 5824 6076 568127312 568127579 6.630000e-40 176.0
3 TraesCS1A01G404700 chr1A 89.720 107 9 2 3963 4067 11576111 11576217 1.130000e-27 135.0
4 TraesCS1A01G404700 chr1A 74.224 322 51 22 6129 6428 568385507 568385818 8.830000e-19 106.0
5 TraesCS1A01G404700 chr1D 91.799 5036 210 60 1512 6430 473863289 473868238 0.000000e+00 6824.0
6 TraesCS1A01G404700 chr1D 89.782 1145 62 34 371 1476 473862077 473863205 0.000000e+00 1415.0
7 TraesCS1A01G404700 chr1D 91.617 501 41 1 976 1476 451140730 451140231 0.000000e+00 691.0
8 TraesCS1A01G404700 chr1D 87.425 334 36 4 1 332 473861740 473862069 4.710000e-101 379.0
9 TraesCS1A01G404700 chr1D 85.714 231 23 6 5847 6076 473875892 473876113 1.080000e-57 235.0
10 TraesCS1A01G404700 chr1D 92.908 141 10 0 1332 1472 451243881 451243741 8.460000e-49 206.0
11 TraesCS1A01G404700 chr1D 88.889 45 5 0 6148 6192 473968164 473968208 1.000000e-03 56.5
12 TraesCS1A01G404700 chr1B 93.187 4550 184 49 1510 5976 658915708 658920214 0.000000e+00 6569.0
13 TraesCS1A01G404700 chr1B 88.642 1303 79 34 210 1476 658914360 658915629 0.000000e+00 1522.0
14 TraesCS1A01G404700 chr1B 86.767 733 72 15 1 718 637285593 637286315 0.000000e+00 793.0
15 TraesCS1A01G404700 chr1B 87.747 506 49 4 980 1476 619529331 619528830 4.330000e-161 579.0
16 TraesCS1A01G404700 chr1B 89.169 397 39 4 1078 1472 619430534 619430140 5.800000e-135 492.0
17 TraesCS1A01G404700 chr1B 88.804 393 22 8 6061 6432 658920527 658920918 4.550000e-126 462.0
18 TraesCS1A01G404700 chr1B 84.954 432 65 0 1027 1458 619535631 619535200 7.660000e-119 438.0
19 TraesCS1A01G404700 chr1B 89.349 169 18 0 1 169 658914185 658914353 5.050000e-51 213.0
20 TraesCS1A01G404700 chr1B 79.343 213 32 11 5539 5746 659049191 659049396 8.700000e-29 139.0
21 TraesCS1A01G404700 chr1B 83.696 92 2 7 987 1078 619544345 619544267 2.490000e-09 75.0
22 TraesCS1A01G404700 chr4B 87.004 731 74 12 1 718 11349139 11349861 0.000000e+00 804.0
23 TraesCS1A01G404700 chr4B 82.031 384 56 11 2562 2938 80005806 80006183 1.350000e-81 315.0
24 TraesCS1A01G404700 chr4B 80.695 259 40 9 2545 2797 37563543 37563797 6.590000e-45 193.0
25 TraesCS1A01G404700 chr3A 81.752 411 60 13 2545 2946 743488919 743488515 4.810000e-86 329.0
26 TraesCS1A01G404700 chr5B 89.015 264 28 1 1121 1384 710757632 710757894 6.220000e-85 326.0
27 TraesCS1A01G404700 chr5D 81.407 398 64 9 2545 2936 385111294 385110901 3.750000e-82 316.0
28 TraesCS1A01G404700 chr6B 80.905 398 58 10 2545 2938 151810382 151810765 1.360000e-76 298.0
29 TraesCS1A01G404700 chr7A 82.635 334 53 4 1027 1356 625381958 625381626 2.270000e-74 291.0
30 TraesCS1A01G404700 chr3D 90.000 110 8 3 3955 4062 578617988 578617880 8.700000e-29 139.0
31 TraesCS1A01G404700 chr4A 91.262 103 6 3 3963 4063 576605174 576605073 3.130000e-28 137.0
32 TraesCS1A01G404700 chr4A 89.157 83 8 1 3508 3590 274860056 274860137 1.140000e-17 102.0
33 TraesCS1A01G404700 chr7B 89.189 111 9 3 3957 4064 143336318 143336208 1.130000e-27 135.0
34 TraesCS1A01G404700 chr7B 89.720 107 9 2 3963 4067 357651590 357651484 1.130000e-27 135.0
35 TraesCS1A01G404700 chr6D 88.288 111 11 2 3960 4068 115787616 115787726 1.460000e-26 132.0
36 TraesCS1A01G404700 chr3B 85.833 120 13 3 3952 4067 581965974 581966093 2.440000e-24 124.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G404700 chr1A 568107589 568114024 6435 False 11886.000000 11886 100.000000 1 6436 1 chr1A.!!$F2 6435
1 TraesCS1A01G404700 chr1D 473861740 473868238 6498 False 2872.666667 6824 89.668667 1 6430 3 chr1D.!!$F3 6429
2 TraesCS1A01G404700 chr1B 658914185 658920918 6733 False 2191.500000 6569 89.995500 1 6432 4 chr1B.!!$F3 6431
3 TraesCS1A01G404700 chr1B 637285593 637286315 722 False 793.000000 793 86.767000 1 718 1 chr1B.!!$F1 717
4 TraesCS1A01G404700 chr1B 619528830 619529331 501 True 579.000000 579 87.747000 980 1476 1 chr1B.!!$R2 496
5 TraesCS1A01G404700 chr4B 11349139 11349861 722 False 804.000000 804 87.004000 1 718 1 chr4B.!!$F1 717

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
378 387 0.248843 AGGAAAGCGCAGAGAGAAGG 59.751 55.000 11.47 0.0 0.00 3.46 F
825 866 0.331278 CACACCCAAAGAGGCCCATA 59.669 55.000 0.00 0.0 35.39 2.74 F
826 867 0.331616 ACACCCAAAGAGGCCCATAC 59.668 55.000 0.00 0.0 35.39 2.39 F
2110 2240 0.586319 CACTCAACAAATGCGTCGGT 59.414 50.000 0.00 0.0 0.00 4.69 F
3139 3284 1.425066 TCATGTGGAGAGGTGCCTTTT 59.575 47.619 0.00 0.0 0.00 2.27 F
4958 5136 0.609131 CCAAGTGGTTTGCCGAGGAT 60.609 55.000 0.00 0.0 37.67 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1633 0.179045 GCGCACTTCACATAGGGGAT 60.179 55.000 0.30 0.0 0.00 3.85 R
2105 2235 1.139058 AGCATGACCCTCATTACCGAC 59.861 52.381 0.00 0.0 34.28 4.79 R
2508 2653 4.273724 GGCTAGCTGCTTATTTGAACCTAC 59.726 45.833 15.72 0.0 42.39 3.18 R
3982 4153 1.204704 TCATCCGATTGAGCGACAAGT 59.795 47.619 5.72 0.0 42.02 3.16 R
5048 5226 0.035056 CCTCCGCCACCTTCTTTGAT 60.035 55.000 0.00 0.0 0.00 2.57 R
5923 6191 0.170339 GCCGGGGATTCAAAGTTTCG 59.830 55.000 2.18 0.0 0.00 3.46 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
89 90 1.066215 ACACACAGCACAGACTCACAA 60.066 47.619 0.00 0.00 0.00 3.33
112 113 9.748708 ACAATATTATAACATGGCAATTGTCAC 57.251 29.630 16.33 2.39 32.43 3.67
123 124 8.028938 ACATGGCAATTGTCACTTAGAAATTAC 58.971 33.333 16.33 0.00 29.57 1.89
127 128 8.699749 GGCAATTGTCACTTAGAAATTACAAAC 58.300 33.333 4.85 0.00 31.33 2.93
236 237 7.815398 TTTATTTATGCTGCACAATGACAAG 57.185 32.000 3.57 0.00 0.00 3.16
253 254 8.352201 CAATGACAAGTTCCTGAATTTTACTGA 58.648 33.333 0.00 0.00 0.00 3.41
269 270 8.601845 ATTTTACTGAAACCAAAAATGCTACC 57.398 30.769 0.00 0.00 31.99 3.18
272 273 2.297597 TGAAACCAAAAATGCTACCGGG 59.702 45.455 6.32 0.00 0.00 5.73
297 298 4.263677 GCATTTGACGCATCATAAACACTG 59.736 41.667 0.00 0.00 33.85 3.66
320 321 8.157476 ACTGAACACTGAAATAATCTACTTGGT 58.843 33.333 0.00 0.00 0.00 3.67
348 349 4.592942 AGTGCTGAATGAAATCCAGCTAA 58.407 39.130 13.64 0.00 39.41 3.09
353 354 5.586243 GCTGAATGAAATCCAGCTAAGTACA 59.414 40.000 0.00 0.00 36.12 2.90
354 355 6.094048 GCTGAATGAAATCCAGCTAAGTACAA 59.906 38.462 0.00 0.00 36.12 2.41
357 358 7.446931 TGAATGAAATCCAGCTAAGTACAAACA 59.553 33.333 0.00 0.00 0.00 2.83
359 360 7.575414 TGAAATCCAGCTAAGTACAAACAAA 57.425 32.000 0.00 0.00 0.00 2.83
360 361 7.648142 TGAAATCCAGCTAAGTACAAACAAAG 58.352 34.615 0.00 0.00 0.00 2.77
361 362 6.575162 AATCCAGCTAAGTACAAACAAAGG 57.425 37.500 0.00 0.00 0.00 3.11
363 364 5.686753 TCCAGCTAAGTACAAACAAAGGAA 58.313 37.500 0.00 0.00 0.00 3.36
366 372 5.915196 CAGCTAAGTACAAACAAAGGAAAGC 59.085 40.000 0.00 0.00 0.00 3.51
378 387 0.248843 AGGAAAGCGCAGAGAGAAGG 59.751 55.000 11.47 0.00 0.00 3.46
509 524 2.841988 GCCTCGCCATCTCCTCCT 60.842 66.667 0.00 0.00 0.00 3.69
515 530 1.841103 GCCATCTCCTCCTCCTCCC 60.841 68.421 0.00 0.00 0.00 4.30
571 589 4.436998 CTCGTCGACACAGCCCCC 62.437 72.222 17.16 0.00 0.00 5.40
641 659 1.791662 CACGGCGGTGTTGAATACC 59.208 57.895 13.24 0.45 39.38 2.73
722 743 1.405256 CGCAGAGCAGAGGAAGTGAAT 60.405 52.381 0.00 0.00 0.00 2.57
726 747 2.909006 AGAGCAGAGGAAGTGAATTGGA 59.091 45.455 0.00 0.00 0.00 3.53
727 748 3.328931 AGAGCAGAGGAAGTGAATTGGAA 59.671 43.478 0.00 0.00 0.00 3.53
728 749 3.683802 AGCAGAGGAAGTGAATTGGAAG 58.316 45.455 0.00 0.00 0.00 3.46
729 750 3.073650 AGCAGAGGAAGTGAATTGGAAGT 59.926 43.478 0.00 0.00 0.00 3.01
730 751 3.190118 GCAGAGGAAGTGAATTGGAAGTG 59.810 47.826 0.00 0.00 0.00 3.16
732 753 4.453819 CAGAGGAAGTGAATTGGAAGTGAC 59.546 45.833 0.00 0.00 0.00 3.67
733 754 4.103153 AGAGGAAGTGAATTGGAAGTGACA 59.897 41.667 0.00 0.00 0.00 3.58
734 755 4.137543 AGGAAGTGAATTGGAAGTGACAC 58.862 43.478 0.00 0.00 0.00 3.67
735 756 3.253432 GGAAGTGAATTGGAAGTGACACC 59.747 47.826 0.84 0.00 0.00 4.16
736 757 2.494059 AGTGAATTGGAAGTGACACCG 58.506 47.619 0.84 0.00 0.00 4.94
737 758 1.535462 GTGAATTGGAAGTGACACCGG 59.465 52.381 0.00 0.00 0.00 5.28
739 760 2.076863 GAATTGGAAGTGACACCGGAG 58.923 52.381 9.46 1.26 0.00 4.63
755 776 1.623163 GGAGGACGAGGGGATAAGAG 58.377 60.000 0.00 0.00 0.00 2.85
756 777 1.145325 GGAGGACGAGGGGATAAGAGA 59.855 57.143 0.00 0.00 0.00 3.10
759 780 2.158579 AGGACGAGGGGATAAGAGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
760 781 1.874872 GACGAGGGGATAAGAGAGACG 59.125 57.143 0.00 0.00 0.00 4.18
762 783 1.693627 GAGGGGATAAGAGAGACGCA 58.306 55.000 0.00 0.00 0.00 5.24
763 784 1.611491 GAGGGGATAAGAGAGACGCAG 59.389 57.143 0.00 0.00 0.00 5.18
764 785 1.215673 AGGGGATAAGAGAGACGCAGA 59.784 52.381 0.00 0.00 0.00 4.26
768 792 2.287547 GGATAAGAGAGACGCAGAGCAG 60.288 54.545 0.00 0.00 0.00 4.24
770 794 0.810648 AAGAGAGACGCAGAGCAGAG 59.189 55.000 0.00 0.00 0.00 3.35
777 801 4.834828 GCAGAGCAGAGCGTTTTG 57.165 55.556 0.00 0.00 0.00 2.44
787 811 2.162408 CAGAGCGTTTTGATTTCCCCTC 59.838 50.000 0.00 0.00 0.00 4.30
790 825 0.878416 CGTTTTGATTTCCCCTCGCA 59.122 50.000 0.00 0.00 0.00 5.10
825 866 0.331278 CACACCCAAAGAGGCCCATA 59.669 55.000 0.00 0.00 35.39 2.74
826 867 0.331616 ACACCCAAAGAGGCCCATAC 59.668 55.000 0.00 0.00 35.39 2.39
867 908 2.355363 CTCAACCGTCGCCGTGAA 60.355 61.111 0.00 0.00 0.00 3.18
886 927 3.419759 CCGACAAAACGGCCGAGG 61.420 66.667 35.90 19.55 46.20 4.63
887 928 4.084888 CGACAAAACGGCCGAGGC 62.085 66.667 35.90 19.32 41.06 4.70
888 929 2.975799 GACAAAACGGCCGAGGCA 60.976 61.111 35.90 0.00 44.11 4.75
889 930 2.966309 GACAAAACGGCCGAGGCAG 61.966 63.158 35.90 19.11 44.11 4.85
890 931 4.404654 CAAAACGGCCGAGGCAGC 62.405 66.667 35.90 0.00 44.11 5.25
933 981 2.348104 CCCCGCAAAAACCCTAGCC 61.348 63.158 0.00 0.00 0.00 3.93
949 999 4.928520 CCCCATCCCCTCCCTCCC 62.929 77.778 0.00 0.00 0.00 4.30
950 1000 3.795924 CCCATCCCCTCCCTCCCT 61.796 72.222 0.00 0.00 0.00 4.20
951 1001 2.122189 CCATCCCCTCCCTCCCTC 60.122 72.222 0.00 0.00 0.00 4.30
957 1007 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
966 1016 3.039526 CTCCCTCCCCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1476 1545 1.244019 GCGCCTTCATCACCAAGGTT 61.244 55.000 0.00 0.00 42.35 3.50
1478 1547 1.068333 CGCCTTCATCACCAAGGTTTG 60.068 52.381 0.61 0.00 42.35 2.93
1480 1549 2.029918 GCCTTCATCACCAAGGTTTGAC 60.030 50.000 0.61 0.00 42.35 3.18
1481 1550 3.221771 CCTTCATCACCAAGGTTTGACA 58.778 45.455 2.07 0.00 36.40 3.58
1483 1552 3.855255 TCATCACCAAGGTTTGACAGA 57.145 42.857 0.00 0.00 0.00 3.41
1486 1555 2.123589 TCACCAAGGTTTGACAGAGGA 58.876 47.619 0.00 0.00 0.00 3.71
1489 1558 2.509964 ACCAAGGTTTGACAGAGGACTT 59.490 45.455 0.00 0.00 0.00 3.01
1490 1559 2.880890 CCAAGGTTTGACAGAGGACTTG 59.119 50.000 0.00 0.00 35.02 3.16
1491 1560 2.262423 AGGTTTGACAGAGGACTTGC 57.738 50.000 0.00 0.00 0.00 4.01
1492 1561 1.490490 AGGTTTGACAGAGGACTTGCA 59.510 47.619 0.00 0.00 0.00 4.08
1499 1569 2.125512 GAGGACTTGCACCGCGAT 60.126 61.111 8.23 0.00 0.00 4.58
1502 1572 2.325082 GGACTTGCACCGCGATTGT 61.325 57.895 8.23 0.00 0.00 2.71
1503 1573 1.132640 GACTTGCACCGCGATTGTC 59.867 57.895 8.23 3.27 0.00 3.18
1513 1633 2.433491 CGATTGTCGGCCCGTTGA 60.433 61.111 1.63 0.00 36.00 3.18
1520 1640 3.158648 CGGCCCGTTGATCCCCTA 61.159 66.667 0.00 0.00 0.00 3.53
1531 1651 1.138859 TGATCCCCTATGTGAAGTGCG 59.861 52.381 0.00 0.00 0.00 5.34
1541 1661 3.469899 TGTGAAGTGCGCATATCAAAC 57.530 42.857 23.99 15.66 30.65 2.93
1545 1665 3.125146 TGAAGTGCGCATATCAAACTCAC 59.875 43.478 21.25 8.28 0.00 3.51
1551 1671 3.001330 GCGCATATCAAACTCACCTGTAC 59.999 47.826 0.30 0.00 0.00 2.90
1556 1676 7.244192 GCATATCAAACTCACCTGTACTTTTC 58.756 38.462 0.00 0.00 0.00 2.29
1647 1769 2.550830 ACGCAGGTTCTTCATGTTCT 57.449 45.000 0.00 0.00 0.00 3.01
1648 1770 2.146342 ACGCAGGTTCTTCATGTTCTG 58.854 47.619 0.00 0.00 0.00 3.02
1650 1772 2.158449 CGCAGGTTCTTCATGTTCTGTC 59.842 50.000 0.00 0.00 0.00 3.51
1651 1773 3.406764 GCAGGTTCTTCATGTTCTGTCT 58.593 45.455 0.00 0.00 0.00 3.41
1652 1774 3.817647 GCAGGTTCTTCATGTTCTGTCTT 59.182 43.478 0.00 0.00 0.00 3.01
1653 1775 4.997395 GCAGGTTCTTCATGTTCTGTCTTA 59.003 41.667 0.00 0.00 0.00 2.10
1654 1776 5.470098 GCAGGTTCTTCATGTTCTGTCTTAA 59.530 40.000 0.00 0.00 0.00 1.85
1655 1777 6.348050 GCAGGTTCTTCATGTTCTGTCTTAAG 60.348 42.308 0.00 0.00 0.00 1.85
1656 1778 5.703130 AGGTTCTTCATGTTCTGTCTTAAGC 59.297 40.000 0.00 0.00 0.00 3.09
1657 1779 5.470098 GGTTCTTCATGTTCTGTCTTAAGCA 59.530 40.000 0.00 0.00 0.00 3.91
1658 1780 6.348050 GGTTCTTCATGTTCTGTCTTAAGCAG 60.348 42.308 16.28 16.28 35.43 4.24
1659 1781 5.240891 TCTTCATGTTCTGTCTTAAGCAGG 58.759 41.667 19.91 5.73 34.89 4.85
1675 1797 5.689383 AAGCAGGTGTGTTGTTACTTATG 57.311 39.130 0.00 0.00 0.00 1.90
1682 1804 7.955324 CAGGTGTGTTGTTACTTATGTATTTCG 59.045 37.037 0.00 0.00 0.00 3.46
1685 1812 9.731519 GTGTGTTGTTACTTATGTATTTCGTAC 57.268 33.333 0.00 0.00 0.00 3.67
1698 1825 6.737118 TGTATTTCGTACTAGTGTGTTGACA 58.263 36.000 5.39 0.00 34.27 3.58
1815 1942 5.023533 TCTGTCTCAAATATAAAGCGCCT 57.976 39.130 2.29 0.00 0.00 5.52
1885 2012 4.399618 TCGAACCTGAGAAGAAGATGGTAG 59.600 45.833 0.00 0.00 0.00 3.18
1914 2041 8.344831 TGAAACATTTGTCAGAGTTACTCAATG 58.655 33.333 15.23 15.68 32.06 2.82
1915 2042 8.450578 AAACATTTGTCAGAGTTACTCAATGA 57.549 30.769 21.28 12.73 32.06 2.57
1916 2043 8.627208 AACATTTGTCAGAGTTACTCAATGAT 57.373 30.769 21.28 11.87 32.06 2.45
1919 2046 9.552114 CATTTGTCAGAGTTACTCAATGATTTC 57.448 33.333 15.23 0.45 32.06 2.17
1923 2050 8.370940 TGTCAGAGTTACTCAATGATTTCTCTT 58.629 33.333 15.23 0.00 32.06 2.85
2036 2166 3.195661 GTGAAGGGTAAGTATGCCTTCG 58.804 50.000 0.00 0.00 34.46 3.79
2047 2177 4.195308 GCCTTCGTATGTCGGCAA 57.805 55.556 0.00 0.00 42.06 4.52
2049 2179 1.014352 GCCTTCGTATGTCGGCAAAT 58.986 50.000 0.00 0.00 42.06 2.32
2105 2235 4.481930 TTTCTACCACTCAACAAATGCG 57.518 40.909 0.00 0.00 0.00 4.73
2110 2240 0.586319 CACTCAACAAATGCGTCGGT 59.414 50.000 0.00 0.00 0.00 4.69
2173 2315 4.130118 CCTCATAGAATGGCTGGTGTAAC 58.870 47.826 0.00 0.00 0.00 2.50
2208 2350 5.095145 AGAGAACATCATGCTTTGCTAGA 57.905 39.130 0.00 0.00 0.00 2.43
2209 2351 5.494724 AGAGAACATCATGCTTTGCTAGAA 58.505 37.500 0.00 0.00 0.00 2.10
2212 2354 6.409704 AGAACATCATGCTTTGCTAGAACTA 58.590 36.000 0.00 0.00 0.00 2.24
2470 2614 3.324846 AGTCAGCCACAGTGTGATTTCTA 59.675 43.478 24.99 2.12 35.23 2.10
2555 2700 7.385267 CCATTTGAAATTTGACCCTGATAACA 58.615 34.615 0.00 0.00 0.00 2.41
2693 2838 6.830324 TGGGAGATCCACATTTCTAATTTCTG 59.170 38.462 0.47 0.00 41.46 3.02
3139 3284 1.425066 TCATGTGGAGAGGTGCCTTTT 59.575 47.619 0.00 0.00 0.00 2.27
3140 3285 1.815003 CATGTGGAGAGGTGCCTTTTC 59.185 52.381 0.00 0.00 0.00 2.29
3562 3714 5.649782 ATCCTGCTGTTTTTGTATTCCTG 57.350 39.130 0.00 0.00 0.00 3.86
3691 3843 5.420421 TGTGGAAAAGTGATTTTGGTTCTGA 59.580 36.000 0.00 0.00 0.00 3.27
3720 3872 6.989155 TTTCTCTAAAGTTACTGTCCCAGA 57.011 37.500 0.00 0.00 35.18 3.86
3752 3904 9.654417 GTCTTATTTTAGCTTTTACGTGTTCAA 57.346 29.630 0.00 0.00 0.00 2.69
3788 3940 7.169982 GCTTGCGAACTCAGTGATATATACTTT 59.830 37.037 0.00 0.00 0.00 2.66
3789 3941 7.930513 TGCGAACTCAGTGATATATACTTTG 57.069 36.000 0.00 0.00 0.00 2.77
3802 3954 9.488762 TGATATATACTTTGTCTATAGGGTGGG 57.511 37.037 0.00 0.00 0.00 4.61
3898 4050 5.537188 ACTCAAACTCATGAAGACTCTGAC 58.463 41.667 0.00 0.00 0.00 3.51
3961 4132 6.968263 TTCAGACATCCACACCAAAAATAA 57.032 33.333 0.00 0.00 0.00 1.40
3966 4137 8.184192 CAGACATCCACACCAAAAATAATACTC 58.816 37.037 0.00 0.00 0.00 2.59
3967 4138 7.339466 AGACATCCACACCAAAAATAATACTCC 59.661 37.037 0.00 0.00 0.00 3.85
3968 4139 6.379988 ACATCCACACCAAAAATAATACTCCC 59.620 38.462 0.00 0.00 0.00 4.30
3969 4140 6.147437 TCCACACCAAAAATAATACTCCCT 57.853 37.500 0.00 0.00 0.00 4.20
3970 4141 7.273457 TCCACACCAAAAATAATACTCCCTA 57.727 36.000 0.00 0.00 0.00 3.53
3971 4142 7.878495 TCCACACCAAAAATAATACTCCCTAT 58.122 34.615 0.00 0.00 0.00 2.57
3972 4143 7.996644 TCCACACCAAAAATAATACTCCCTATC 59.003 37.037 0.00 0.00 0.00 2.08
3973 4144 7.777910 CCACACCAAAAATAATACTCCCTATCA 59.222 37.037 0.00 0.00 0.00 2.15
3974 4145 9.354673 CACACCAAAAATAATACTCCCTATCAT 57.645 33.333 0.00 0.00 0.00 2.45
3975 4146 9.574516 ACACCAAAAATAATACTCCCTATCATC 57.425 33.333 0.00 0.00 0.00 2.92
3976 4147 9.014297 CACCAAAAATAATACTCCCTATCATCC 57.986 37.037 0.00 0.00 0.00 3.51
3977 4148 8.732854 ACCAAAAATAATACTCCCTATCATCCA 58.267 33.333 0.00 0.00 0.00 3.41
3978 4149 9.759473 CCAAAAATAATACTCCCTATCATCCAT 57.241 33.333 0.00 0.00 0.00 3.41
3988 4159 8.140112 ACTCCCTATCATCCATATTACTTGTC 57.860 38.462 0.00 0.00 0.00 3.18
3994 4165 5.912892 TCATCCATATTACTTGTCGCTCAA 58.087 37.500 0.00 0.00 34.61 3.02
4015 4186 7.095607 GCTCAATCGGATGATTTAGACGTATTT 60.096 37.037 0.00 0.00 42.14 1.40
4033 4204 6.040504 ACGTATTTCAGTGCTAGATACATCCA 59.959 38.462 0.00 0.00 0.00 3.41
4040 4211 6.098838 TCAGTGCTAGATACATCCATTTGAGT 59.901 38.462 0.00 0.00 0.00 3.41
4141 4313 5.545063 TTCCAGAGACTCATAACACAACA 57.455 39.130 5.02 0.00 0.00 3.33
4147 4319 7.148507 CCAGAGACTCATAACACAACATCTTTC 60.149 40.741 5.02 0.00 0.00 2.62
4338 4510 1.302192 TCCTCGCCTTTGAAACCCG 60.302 57.895 0.00 0.00 0.00 5.28
4409 4582 8.271458 TGCTATTATGTTTCAACTTGATAGGGA 58.729 33.333 14.25 1.55 35.26 4.20
4475 4650 2.503356 GGAAGAGGAAGATCAAGAGGCA 59.497 50.000 0.00 0.00 0.00 4.75
4488 4663 2.299013 CAAGAGGCAAACCCCCTTTTAC 59.701 50.000 0.00 0.00 36.11 2.01
4579 4754 3.639094 GCAGAATTAGGAGCTGACCTAGA 59.361 47.826 0.00 0.00 42.47 2.43
4625 4800 1.135344 AGAGAGAAGCCGCGTAAGAAC 60.135 52.381 4.92 0.00 43.02 3.01
4811 4989 3.395639 GGACGAGTCAGACGATCTAGAT 58.604 50.000 4.47 4.47 34.70 1.98
4823 5001 3.823873 ACGATCTAGATGAGGACATGGAC 59.176 47.826 10.74 0.00 36.82 4.02
4853 5031 2.190578 GCCGAAGTGCTGGCCTAT 59.809 61.111 3.32 0.00 45.73 2.57
4859 5037 2.898920 AAGTGCTGGCCTATGCGCAT 62.899 55.000 28.23 28.23 41.57 4.73
4958 5136 0.609131 CCAAGTGGTTTGCCGAGGAT 60.609 55.000 0.00 0.00 37.67 3.24
4991 5169 2.537560 CGTGCCCATGAAGCCGATC 61.538 63.158 0.00 0.00 0.00 3.69
5231 5409 0.983378 AGCGGCCCAAGAAGGAGTAT 60.983 55.000 0.00 0.00 41.22 2.12
5345 5544 3.580319 AAGAAGGGCGGCAAGGGT 61.580 61.111 12.47 0.00 0.00 4.34
5357 5556 1.299976 CAAGGGTAAGAAGGGCGCT 59.700 57.895 7.64 0.00 0.00 5.92
5378 5589 1.004918 CGGCGGTCAGAAGAAAGGT 60.005 57.895 0.00 0.00 0.00 3.50
5473 5687 1.347243 TATGGATGAGCAGCTGGGCA 61.347 55.000 17.12 0.00 35.83 5.36
5489 5703 3.120385 CATGTCGCGCCTGCTGAA 61.120 61.111 0.00 0.00 39.65 3.02
5490 5704 2.358615 ATGTCGCGCCTGCTGAAA 60.359 55.556 0.00 0.00 39.65 2.69
5498 5720 1.737838 CGCCTGCTGAAAGTTGGATA 58.262 50.000 0.00 0.00 35.30 2.59
5553 5775 1.472878 GGGTAGCTAAGCTGGTTTTGC 59.527 52.381 0.00 3.44 40.10 3.68
5633 5862 2.162208 AGTTACGCTTGTATCGGACGAA 59.838 45.455 0.00 0.00 0.00 3.85
5634 5863 3.111098 GTTACGCTTGTATCGGACGAAT 58.889 45.455 0.00 0.00 0.00 3.34
5637 5866 2.997986 ACGCTTGTATCGGACGAATTTT 59.002 40.909 0.00 0.00 0.00 1.82
5638 5867 3.061697 ACGCTTGTATCGGACGAATTTTC 59.938 43.478 0.00 0.00 0.00 2.29
5643 5872 5.018539 TGTATCGGACGAATTTTCTGGAT 57.981 39.130 0.00 0.00 0.00 3.41
5678 5907 4.425180 TGTGGTTAAAGCCTGACAGTAA 57.575 40.909 0.93 0.00 0.00 2.24
5693 5922 6.419116 CCTGACAGTAACATAATCATGACGAG 59.581 42.308 0.00 0.00 35.96 4.18
5706 5935 5.142061 TCATGACGAGCTTACCTTAAACA 57.858 39.130 0.00 0.00 0.00 2.83
5713 5942 4.025647 CGAGCTTACCTTAAACATGCTAGC 60.026 45.833 8.10 8.10 0.00 3.42
5766 5996 1.208052 TGAAGCTAGGACACATGGAGC 59.792 52.381 0.00 0.00 0.00 4.70
5767 5997 1.484240 GAAGCTAGGACACATGGAGCT 59.516 52.381 0.00 0.00 45.23 4.09
5780 6039 5.819379 ACACATGGAGCTCTACATATTTGTG 59.181 40.000 20.96 20.96 36.97 3.33
5781 6040 5.819379 CACATGGAGCTCTACATATTTGTGT 59.181 40.000 14.64 3.21 36.53 3.72
5786 6045 5.468072 GGAGCTCTACATATTTGTGTCATGG 59.532 44.000 14.64 0.00 36.53 3.66
5795 6054 7.332557 ACATATTTGTGTCATGGATGCAATTT 58.667 30.769 0.00 0.00 33.85 1.82
5805 6064 6.971184 GTCATGGATGCAATTTTCTCAGTTAG 59.029 38.462 0.00 0.00 0.00 2.34
5893 6158 3.053896 GGGGTCGCCGTTTCCTTG 61.054 66.667 0.00 0.00 0.00 3.61
5922 6190 7.822334 GGGTGAAAAGAAAGAAAGAAAAAGGAA 59.178 33.333 0.00 0.00 0.00 3.36
5923 6191 8.656849 GGTGAAAAGAAAGAAAGAAAAAGGAAC 58.343 33.333 0.00 0.00 0.00 3.62
5927 6195 9.483916 AAAAGAAAGAAAGAAAAAGGAACGAAA 57.516 25.926 0.00 0.00 0.00 3.46
5978 6246 1.041437 GGATTCCGATTCCCGTCTCT 58.959 55.000 0.00 0.00 36.31 3.10
5980 6248 1.000052 GATTCCGATTCCCGTCTCTCC 60.000 57.143 0.00 0.00 36.31 3.71
5981 6249 0.033405 TTCCGATTCCCGTCTCTCCT 60.033 55.000 0.00 0.00 36.31 3.69
5982 6250 0.752009 TCCGATTCCCGTCTCTCCTG 60.752 60.000 0.00 0.00 36.31 3.86
5993 6261 1.876156 GTCTCTCCTGGCAACTTGTTG 59.124 52.381 8.95 8.95 37.61 3.33
5994 6262 1.768275 TCTCTCCTGGCAACTTGTTGA 59.232 47.619 16.57 0.00 37.61 3.18
5996 6264 1.768275 TCTCCTGGCAACTTGTTGAGA 59.232 47.619 16.57 7.52 37.61 3.27
6011 6279 0.456221 TGAGAGAAGCGAATCCGGAC 59.544 55.000 6.12 0.00 36.06 4.79
6022 6290 1.789576 AATCCGGACCCCACAGCTTT 61.790 55.000 6.12 0.00 0.00 3.51
6023 6291 2.198304 ATCCGGACCCCACAGCTTTC 62.198 60.000 6.12 0.00 0.00 2.62
6026 6294 2.359975 GACCCCACAGCTTTCGGG 60.360 66.667 0.29 0.29 41.71 5.14
6033 6301 1.302832 ACAGCTTTCGGGCTCCAAG 60.303 57.895 0.00 0.00 41.00 3.61
6034 6302 1.003355 CAGCTTTCGGGCTCCAAGA 60.003 57.895 0.00 0.00 41.00 3.02
6038 6306 1.135286 GCTTTCGGGCTCCAAGATTTG 60.135 52.381 0.00 0.00 0.00 2.32
6052 6320 1.738346 GATTTGGAATCCGGCCAGCC 61.738 60.000 2.24 0.00 36.64 4.85
6054 6322 3.643595 TTGGAATCCGGCCAGCCAG 62.644 63.158 9.78 0.00 36.64 4.85
6077 6576 2.543653 CGATGATGATGTAGTGACGGCA 60.544 50.000 0.00 0.00 0.00 5.69
6079 6578 2.892374 TGATGATGTAGTGACGGCAAG 58.108 47.619 0.00 0.00 0.00 4.01
6082 6591 1.204704 TGATGTAGTGACGGCAAGAGG 59.795 52.381 0.00 0.00 0.00 3.69
6083 6592 0.537188 ATGTAGTGACGGCAAGAGGG 59.463 55.000 0.00 0.00 0.00 4.30
6084 6593 0.830444 TGTAGTGACGGCAAGAGGGT 60.830 55.000 0.00 0.00 0.00 4.34
6085 6594 1.180029 GTAGTGACGGCAAGAGGGTA 58.820 55.000 0.00 0.00 0.00 3.69
6086 6595 1.134560 GTAGTGACGGCAAGAGGGTAG 59.865 57.143 0.00 0.00 0.00 3.18
6087 6596 1.218316 GTGACGGCAAGAGGGTAGG 59.782 63.158 0.00 0.00 0.00 3.18
6088 6597 1.987855 TGACGGCAAGAGGGTAGGG 60.988 63.158 0.00 0.00 0.00 3.53
6089 6598 3.387225 GACGGCAAGAGGGTAGGGC 62.387 68.421 0.00 0.00 0.00 5.19
6090 6599 3.399181 CGGCAAGAGGGTAGGGCA 61.399 66.667 0.00 0.00 0.00 5.36
6091 6600 2.746375 CGGCAAGAGGGTAGGGCAT 61.746 63.158 0.00 0.00 0.00 4.40
6150 6663 1.831106 ACCGACTAATGATGGCTCACA 59.169 47.619 0.00 0.00 33.22 3.58
6153 6666 3.461061 CGACTAATGATGGCTCACACAT 58.539 45.455 0.00 0.00 33.22 3.21
6166 6679 3.629398 GCTCACACATAGCCTAAAAGCAT 59.371 43.478 0.00 0.00 33.73 3.79
6203 6719 9.238368 CTCTGCTTACCTTAGCTTATATACTCT 57.762 37.037 0.00 0.00 41.76 3.24
6359 6886 7.253422 GTGCAAGATAACTTATTCTGCACAAT 58.747 34.615 26.03 0.00 45.94 2.71
6409 6936 3.817647 CCCTTTTCACTTGAAGGAGACAG 59.182 47.826 3.79 0.00 44.15 3.51
6410 6937 3.817647 CCTTTTCACTTGAAGGAGACAGG 59.182 47.826 0.00 0.00 44.15 4.00
6432 6961 3.519913 GACTCCCTGGTCAAACTAAGGAT 59.480 47.826 0.00 0.00 36.35 3.24
6433 6962 3.519913 ACTCCCTGGTCAAACTAAGGATC 59.480 47.826 0.00 0.00 30.92 3.36
6434 6963 3.777522 CTCCCTGGTCAAACTAAGGATCT 59.222 47.826 0.00 0.00 30.92 2.75
6435 6964 3.519510 TCCCTGGTCAAACTAAGGATCTG 59.480 47.826 0.00 0.00 30.92 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.677182 AGAGCACCCTGATAAACCAAATT 58.323 39.130 0.00 0.00 0.00 1.82
123 124 5.922544 CAGAGGAAACAGCTTATTTGGTTTG 59.077 40.000 2.64 0.00 33.92 2.93
127 128 5.964958 TTCAGAGGAAACAGCTTATTTGG 57.035 39.130 0.00 0.00 0.00 3.28
136 137 3.265791 CGGGAGAATTCAGAGGAAACAG 58.734 50.000 8.44 0.00 36.43 3.16
200 201 8.190122 TGCAGCATAAATAAATGAGTTAAGTGG 58.810 33.333 0.00 0.00 0.00 4.00
205 206 9.518906 CATTGTGCAGCATAAATAAATGAGTTA 57.481 29.630 8.83 0.00 0.00 2.24
206 207 8.252417 TCATTGTGCAGCATAAATAAATGAGTT 58.748 29.630 8.83 0.00 31.23 3.01
207 208 7.703621 GTCATTGTGCAGCATAAATAAATGAGT 59.296 33.333 8.83 0.00 34.46 3.41
208 209 7.703197 TGTCATTGTGCAGCATAAATAAATGAG 59.297 33.333 8.83 0.00 34.46 2.90
236 237 8.710835 TTTTGGTTTCAGTAAAATTCAGGAAC 57.289 30.769 0.00 0.00 0.00 3.62
253 254 1.001520 GCCCGGTAGCATTTTTGGTTT 59.998 47.619 0.00 0.00 0.00 3.27
297 298 8.547967 TGACCAAGTAGATTATTTCAGTGTTC 57.452 34.615 0.00 0.00 0.00 3.18
320 321 3.614092 GATTTCATTCAGCACTCCCTGA 58.386 45.455 0.00 0.00 39.94 3.86
348 349 2.685897 TGCGCTTTCCTTTGTTTGTACT 59.314 40.909 9.73 0.00 0.00 2.73
353 354 2.291741 CTCTCTGCGCTTTCCTTTGTTT 59.708 45.455 9.73 0.00 0.00 2.83
354 355 1.876156 CTCTCTGCGCTTTCCTTTGTT 59.124 47.619 9.73 0.00 0.00 2.83
357 358 2.421619 CTTCTCTCTGCGCTTTCCTTT 58.578 47.619 9.73 0.00 0.00 3.11
359 360 0.248843 CCTTCTCTCTGCGCTTTCCT 59.751 55.000 9.73 0.00 0.00 3.36
360 361 0.247736 TCCTTCTCTCTGCGCTTTCC 59.752 55.000 9.73 0.00 0.00 3.13
361 362 1.203523 TCTCCTTCTCTCTGCGCTTTC 59.796 52.381 9.73 0.00 0.00 2.62
363 364 1.204467 CTTCTCCTTCTCTCTGCGCTT 59.796 52.381 9.73 0.00 0.00 4.68
366 372 0.179113 GCCTTCTCCTTCTCTCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
509 524 0.266152 GAAGATGAGGAGGGGGAGGA 59.734 60.000 0.00 0.00 0.00 3.71
515 530 1.065126 GGTGGTTGAAGATGAGGAGGG 60.065 57.143 0.00 0.00 0.00 4.30
576 594 3.597728 GGAGGCGCGAGAGTAGGG 61.598 72.222 12.10 0.00 0.00 3.53
600 618 1.828660 CCAGGACGGAGCGGTATCT 60.829 63.158 0.00 0.00 36.56 1.98
718 739 1.418264 TCCGGTGTCACTTCCAATTCA 59.582 47.619 0.00 0.00 0.00 2.57
722 743 0.761323 TCCTCCGGTGTCACTTCCAA 60.761 55.000 0.00 0.00 0.00 3.53
726 747 1.524863 CTCGTCCTCCGGTGTCACTT 61.525 60.000 0.00 0.00 37.11 3.16
727 748 1.972223 CTCGTCCTCCGGTGTCACT 60.972 63.158 0.00 0.00 37.11 3.41
728 749 2.567049 CTCGTCCTCCGGTGTCAC 59.433 66.667 0.00 0.00 37.11 3.67
729 750 2.675423 CCTCGTCCTCCGGTGTCA 60.675 66.667 0.00 0.00 37.11 3.58
730 751 3.450115 CCCTCGTCCTCCGGTGTC 61.450 72.222 0.00 0.00 37.11 3.67
732 753 2.635787 TATCCCCTCGTCCTCCGGTG 62.636 65.000 0.00 0.00 37.11 4.94
733 754 1.941403 TTATCCCCTCGTCCTCCGGT 61.941 60.000 0.00 0.00 37.11 5.28
734 755 1.152610 TTATCCCCTCGTCCTCCGG 60.153 63.158 0.00 0.00 37.11 5.14
735 756 0.178998 TCTTATCCCCTCGTCCTCCG 60.179 60.000 0.00 0.00 38.13 4.63
736 757 1.145325 TCTCTTATCCCCTCGTCCTCC 59.855 57.143 0.00 0.00 0.00 4.30
737 758 2.106857 TCTCTCTTATCCCCTCGTCCTC 59.893 54.545 0.00 0.00 0.00 3.71
739 760 2.232399 GTCTCTCTTATCCCCTCGTCC 58.768 57.143 0.00 0.00 0.00 4.79
740 761 1.874872 CGTCTCTCTTATCCCCTCGTC 59.125 57.143 0.00 0.00 0.00 4.20
741 762 1.970092 CGTCTCTCTTATCCCCTCGT 58.030 55.000 0.00 0.00 0.00 4.18
742 763 0.594110 GCGTCTCTCTTATCCCCTCG 59.406 60.000 0.00 0.00 0.00 4.63
745 766 1.611491 CTCTGCGTCTCTCTTATCCCC 59.389 57.143 0.00 0.00 0.00 4.81
746 767 1.000717 GCTCTGCGTCTCTCTTATCCC 60.001 57.143 0.00 0.00 0.00 3.85
747 768 1.678627 TGCTCTGCGTCTCTCTTATCC 59.321 52.381 0.00 0.00 0.00 2.59
750 771 2.013400 CTCTGCTCTGCGTCTCTCTTA 58.987 52.381 0.00 0.00 0.00 2.10
751 772 0.810648 CTCTGCTCTGCGTCTCTCTT 59.189 55.000 0.00 0.00 0.00 2.85
752 773 1.656818 GCTCTGCTCTGCGTCTCTCT 61.657 60.000 0.00 0.00 0.00 3.10
755 776 2.579249 CGCTCTGCTCTGCGTCTC 60.579 66.667 9.01 0.00 46.09 3.36
760 781 0.801251 ATCAAAACGCTCTGCTCTGC 59.199 50.000 0.00 0.00 0.00 4.26
762 783 2.485814 GGAAATCAAAACGCTCTGCTCT 59.514 45.455 0.00 0.00 0.00 4.09
763 784 2.414691 GGGAAATCAAAACGCTCTGCTC 60.415 50.000 0.00 0.00 0.00 4.26
764 785 1.541588 GGGAAATCAAAACGCTCTGCT 59.458 47.619 0.00 0.00 0.00 4.24
768 792 1.130561 CGAGGGGAAATCAAAACGCTC 59.869 52.381 0.00 0.00 38.91 5.03
770 794 0.456142 GCGAGGGGAAATCAAAACGC 60.456 55.000 0.00 0.00 38.23 4.84
773 797 0.887933 GCTGCGAGGGGAAATCAAAA 59.112 50.000 0.00 0.00 0.00 2.44
777 801 2.517166 GGGCTGCGAGGGGAAATC 60.517 66.667 0.00 0.00 0.00 2.17
798 833 4.904590 TTTGGGTGTGGGCGTGGG 62.905 66.667 0.00 0.00 0.00 4.61
801 836 2.113139 CTCTTTGGGTGTGGGCGT 59.887 61.111 0.00 0.00 0.00 5.68
802 837 2.672996 CCTCTTTGGGTGTGGGCG 60.673 66.667 0.00 0.00 0.00 6.13
812 853 1.755179 CCTGTGTATGGGCCTCTTTG 58.245 55.000 4.53 0.00 0.00 2.77
860 901 1.009335 GTTTTGTCGGGTTCACGGC 60.009 57.895 0.00 0.00 39.28 5.68
862 903 1.277440 CCGTTTTGTCGGGTTCACG 59.723 57.895 0.00 0.00 45.88 4.35
918 961 0.970427 ATGGGGCTAGGGTTTTTGCG 60.970 55.000 0.00 0.00 0.00 4.85
922 965 1.590339 GGGGATGGGGCTAGGGTTTT 61.590 60.000 0.00 0.00 0.00 2.43
933 981 3.795924 AGGGAGGGAGGGGATGGG 61.796 72.222 0.00 0.00 0.00 4.00
949 999 3.039526 AGGAGGAGGGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
950 1000 3.036959 GAGGAGGAGGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
951 1001 3.368501 TGAGGAGGAGGGGGAGGG 61.369 72.222 0.00 0.00 0.00 4.30
957 1007 2.837291 CGAGCCTGAGGAGGAGGG 60.837 72.222 0.65 0.00 42.93 4.30
1476 1545 0.249868 CGGTGCAAGTCCTCTGTCAA 60.250 55.000 0.00 0.00 0.00 3.18
1478 1547 2.029844 GCGGTGCAAGTCCTCTGTC 61.030 63.158 0.00 0.00 0.00 3.51
1480 1549 2.842394 ATCGCGGTGCAAGTCCTCTG 62.842 60.000 6.13 0.00 0.00 3.35
1481 1550 2.172483 AATCGCGGTGCAAGTCCTCT 62.172 55.000 6.13 0.00 0.00 3.69
1483 1552 2.034879 CAATCGCGGTGCAAGTCCT 61.035 57.895 6.13 0.00 0.00 3.85
1486 1555 2.667318 CGACAATCGCGGTGCAAGT 61.667 57.895 6.13 0.00 31.14 3.16
1499 1569 2.046700 GGATCAACGGGCCGACAA 60.047 61.111 35.78 17.10 0.00 3.18
1502 1572 2.957902 ATAGGGGATCAACGGGCCGA 62.958 60.000 35.78 11.41 0.00 5.54
1503 1573 2.516888 ATAGGGGATCAACGGGCCG 61.517 63.158 27.06 27.06 0.00 6.13
1510 1580 2.419990 CGCACTTCACATAGGGGATCAA 60.420 50.000 0.00 0.00 0.00 2.57
1513 1633 0.179045 GCGCACTTCACATAGGGGAT 60.179 55.000 0.30 0.00 0.00 3.85
1520 1640 3.691118 AGTTTGATATGCGCACTTCACAT 59.309 39.130 14.90 4.41 0.00 3.21
1531 1651 6.743575 AAAGTACAGGTGAGTTTGATATGC 57.256 37.500 0.00 0.00 0.00 3.14
1541 1661 5.611374 TGAAGAAGGAAAAGTACAGGTGAG 58.389 41.667 0.00 0.00 0.00 3.51
1545 1665 5.239525 CCTGTTGAAGAAGGAAAAGTACAGG 59.760 44.000 0.00 0.00 42.68 4.00
1551 1671 5.590259 TGAAGACCTGTTGAAGAAGGAAAAG 59.410 40.000 1.11 0.00 37.01 2.27
1556 1676 3.181450 ACCTGAAGACCTGTTGAAGAAGG 60.181 47.826 0.00 0.00 39.65 3.46
1637 1759 4.999950 ACCTGCTTAAGACAGAACATGAAG 59.000 41.667 21.28 9.60 37.32 3.02
1639 1761 4.202357 ACACCTGCTTAAGACAGAACATGA 60.202 41.667 21.28 0.00 37.32 3.07
1640 1762 4.067896 ACACCTGCTTAAGACAGAACATG 58.932 43.478 21.28 16.44 37.32 3.21
1641 1763 4.067896 CACACCTGCTTAAGACAGAACAT 58.932 43.478 21.28 7.38 37.32 2.71
1642 1764 3.118408 ACACACCTGCTTAAGACAGAACA 60.118 43.478 21.28 3.92 37.32 3.18
1643 1765 3.467803 ACACACCTGCTTAAGACAGAAC 58.532 45.455 21.28 0.00 37.32 3.01
1644 1766 3.838244 ACACACCTGCTTAAGACAGAA 57.162 42.857 21.28 0.00 37.32 3.02
1645 1767 3.118408 ACAACACACCTGCTTAAGACAGA 60.118 43.478 21.28 0.00 37.32 3.41
1646 1768 3.206150 ACAACACACCTGCTTAAGACAG 58.794 45.455 6.67 12.53 34.82 3.51
1647 1769 3.275617 ACAACACACCTGCTTAAGACA 57.724 42.857 6.67 3.07 0.00 3.41
1648 1770 4.814771 AGTAACAACACACCTGCTTAAGAC 59.185 41.667 6.67 0.00 0.00 3.01
1650 1772 5.751243 AAGTAACAACACACCTGCTTAAG 57.249 39.130 0.00 0.00 0.00 1.85
1651 1773 6.768861 ACATAAGTAACAACACACCTGCTTAA 59.231 34.615 0.00 0.00 0.00 1.85
1652 1774 6.292923 ACATAAGTAACAACACACCTGCTTA 58.707 36.000 0.00 0.00 0.00 3.09
1653 1775 5.130350 ACATAAGTAACAACACACCTGCTT 58.870 37.500 0.00 0.00 0.00 3.91
1654 1776 4.714632 ACATAAGTAACAACACACCTGCT 58.285 39.130 0.00 0.00 0.00 4.24
1655 1777 6.737254 ATACATAAGTAACAACACACCTGC 57.263 37.500 0.00 0.00 33.13 4.85
1656 1778 7.955324 CGAAATACATAAGTAACAACACACCTG 59.045 37.037 0.00 0.00 33.13 4.00
1657 1779 7.658575 ACGAAATACATAAGTAACAACACACCT 59.341 33.333 0.00 0.00 33.13 4.00
1658 1780 7.799784 ACGAAATACATAAGTAACAACACACC 58.200 34.615 0.00 0.00 33.13 4.16
1659 1781 9.731519 GTACGAAATACATAAGTAACAACACAC 57.268 33.333 0.00 0.00 33.13 3.82
1698 1825 4.148128 TGCAAATGGGTTTGTTTCATGT 57.852 36.364 0.00 0.00 45.14 3.21
1773 1900 7.011482 AGACAGATAATGTAAATTTCAGCGGAC 59.989 37.037 0.00 0.00 44.17 4.79
1885 2012 4.574599 AACTCTGACAAATGTTTCAGCC 57.425 40.909 0.00 0.00 39.36 4.85
1928 2055 8.766994 AACATTAAAGGGATGCTAACACATAT 57.233 30.769 0.00 0.00 0.00 1.78
1929 2056 9.116067 GTAACATTAAAGGGATGCTAACACATA 57.884 33.333 0.00 0.00 0.00 2.29
2047 2177 6.527423 AGAAAAATGACCATGCAAACTCATT 58.473 32.000 9.26 9.26 35.34 2.57
2049 2179 5.534207 AGAAAAATGACCATGCAAACTCA 57.466 34.783 0.00 0.00 0.00 3.41
2105 2235 1.139058 AGCATGACCCTCATTACCGAC 59.861 52.381 0.00 0.00 34.28 4.79
2110 2240 6.747414 ACTATTGTAGCATGACCCTCATTA 57.253 37.500 0.00 0.00 34.28 1.90
2508 2653 4.273724 GGCTAGCTGCTTATTTGAACCTAC 59.726 45.833 15.72 0.00 42.39 3.18
2513 2658 5.653507 CAAATGGCTAGCTGCTTATTTGAA 58.346 37.500 24.88 1.99 46.32 2.69
2599 2744 7.405292 AGGACCAGATGTTCAGATAATTTCAA 58.595 34.615 0.00 0.00 0.00 2.69
2693 2838 6.533723 TCGTACCTGAATGAATCACATACAAC 59.466 38.462 0.00 0.00 38.38 3.32
3562 3714 5.050295 GTGTACAAGGCAAAGTAAGACAGAC 60.050 44.000 0.00 0.00 0.00 3.51
3691 3843 9.668497 GGGACAGTAACTTTAGAGAAATTACAT 57.332 33.333 0.00 0.00 0.00 2.29
3752 3904 1.522806 TTCGCAAGCACGGACAACT 60.523 52.632 0.00 0.00 37.18 3.16
3788 3940 5.157770 AGATCTTTCCCACCCTATAGACA 57.842 43.478 0.00 0.00 0.00 3.41
3789 3941 5.602978 TGAAGATCTTTCCCACCCTATAGAC 59.397 44.000 9.87 0.00 0.00 2.59
3802 3954 4.322567 ACTCAACAGCCTGAAGATCTTTC 58.677 43.478 9.87 3.85 0.00 2.62
3898 4050 5.363101 TCTTCATCAGAATCCATTTCCTCG 58.637 41.667 0.00 0.00 34.67 4.63
3925 4077 6.655003 GTGGATGTCTGAAAAATTACCTCAGA 59.345 38.462 9.03 9.03 42.49 3.27
3927 4079 6.206634 GTGTGGATGTCTGAAAAATTACCTCA 59.793 38.462 0.00 0.00 0.00 3.86
3946 4098 6.147437 AGGGAGTATTATTTTTGGTGTGGA 57.853 37.500 0.00 0.00 0.00 4.02
3961 4132 9.790297 ACAAGTAATATGGATGATAGGGAGTAT 57.210 33.333 0.00 0.00 0.00 2.12
3966 4137 5.812642 GCGACAAGTAATATGGATGATAGGG 59.187 44.000 0.00 0.00 0.00 3.53
3967 4138 6.634805 AGCGACAAGTAATATGGATGATAGG 58.365 40.000 0.00 0.00 0.00 2.57
3968 4139 7.315890 TGAGCGACAAGTAATATGGATGATAG 58.684 38.462 0.00 0.00 0.00 2.08
3969 4140 7.227049 TGAGCGACAAGTAATATGGATGATA 57.773 36.000 0.00 0.00 0.00 2.15
3970 4141 6.101650 TGAGCGACAAGTAATATGGATGAT 57.898 37.500 0.00 0.00 0.00 2.45
3971 4142 5.529581 TGAGCGACAAGTAATATGGATGA 57.470 39.130 0.00 0.00 0.00 2.92
3972 4143 6.400409 CGATTGAGCGACAAGTAATATGGATG 60.400 42.308 5.72 0.00 42.02 3.51
3973 4144 5.635280 CGATTGAGCGACAAGTAATATGGAT 59.365 40.000 5.72 0.00 42.02 3.41
3974 4145 4.982295 CGATTGAGCGACAAGTAATATGGA 59.018 41.667 5.72 0.00 42.02 3.41
3975 4146 4.150627 CCGATTGAGCGACAAGTAATATGG 59.849 45.833 5.72 0.00 42.02 2.74
3976 4147 4.982295 TCCGATTGAGCGACAAGTAATATG 59.018 41.667 5.72 0.00 42.02 1.78
3977 4148 5.196341 TCCGATTGAGCGACAAGTAATAT 57.804 39.130 5.72 0.00 42.02 1.28
3978 4149 4.642445 TCCGATTGAGCGACAAGTAATA 57.358 40.909 5.72 0.00 42.02 0.98
3979 4150 3.520290 TCCGATTGAGCGACAAGTAAT 57.480 42.857 5.72 0.00 42.02 1.89
3980 4151 3.119280 TCATCCGATTGAGCGACAAGTAA 60.119 43.478 5.72 0.00 42.02 2.24
3981 4152 2.425668 TCATCCGATTGAGCGACAAGTA 59.574 45.455 5.72 0.00 42.02 2.24
3982 4153 1.204704 TCATCCGATTGAGCGACAAGT 59.795 47.619 5.72 0.00 42.02 3.16
3983 4154 1.926561 TCATCCGATTGAGCGACAAG 58.073 50.000 5.72 0.00 42.02 3.16
3984 4155 2.602257 ATCATCCGATTGAGCGACAA 57.398 45.000 2.29 2.29 42.95 3.18
3988 4159 3.120286 CGTCTAAATCATCCGATTGAGCG 59.880 47.826 0.00 0.00 41.12 5.03
3994 4165 7.382488 CACTGAAATACGTCTAAATCATCCGAT 59.618 37.037 0.00 0.00 0.00 4.18
4015 4186 6.098838 ACTCAAATGGATGTATCTAGCACTGA 59.901 38.462 0.00 0.00 0.00 3.41
4040 4211 6.386927 ACCCCTCTGATTCATATTACTTGTCA 59.613 38.462 0.00 0.00 0.00 3.58
4129 4301 9.166173 CCTGATTAGAAAGATGTTGTGTTATGA 57.834 33.333 0.00 0.00 0.00 2.15
4141 4313 7.971201 TGAGCATCATACCTGATTAGAAAGAT 58.029 34.615 0.00 0.00 42.56 2.40
4351 4524 3.674997 TCAAGTTGAGTCCATTGGCTAC 58.325 45.455 0.08 0.00 0.00 3.58
4395 4568 4.425772 TCTTCACCTCCCTATCAAGTTGA 58.574 43.478 8.27 8.27 0.00 3.18
4406 4579 2.224402 GCTACCATCATCTTCACCTCCC 60.224 54.545 0.00 0.00 0.00 4.30
4407 4580 2.546795 CGCTACCATCATCTTCACCTCC 60.547 54.545 0.00 0.00 0.00 4.30
4409 4582 2.388735 TCGCTACCATCATCTTCACCT 58.611 47.619 0.00 0.00 0.00 4.00
4475 4650 5.274015 TCAAAAGACAGTAAAAGGGGGTTT 58.726 37.500 0.00 0.00 0.00 3.27
4488 4663 3.486584 GCTTCGCTGAATCAAAAGACAG 58.513 45.455 4.51 0.00 0.00 3.51
4579 4754 3.772387 TCCTCACTGTCACTCTTCTCAT 58.228 45.455 0.00 0.00 0.00 2.90
4625 4800 5.536161 TCCTGAATCCACCTTCTTTTTCAAG 59.464 40.000 0.00 0.00 0.00 3.02
4811 4989 0.891904 TGTCGTCGTCCATGTCCTCA 60.892 55.000 0.00 0.00 0.00 3.86
4823 5001 3.851845 TTCGGCCTTGGTGTCGTCG 62.852 63.158 0.00 0.00 0.00 5.12
4859 5037 3.771479 TCTGCTTCTTCCTCAGCATCTTA 59.229 43.478 0.00 0.00 44.98 2.10
4958 5136 1.367471 CACGGTGTGCCTCTTCTCA 59.633 57.895 0.00 0.00 0.00 3.27
4991 5169 2.266055 GCCACCTCCTCCTTCGTG 59.734 66.667 0.00 0.00 0.00 4.35
5012 5190 0.107703 CCCTGAACTGCGCCTTCATA 60.108 55.000 15.69 0.00 0.00 2.15
5021 5199 0.526524 CGTCGATCTCCCTGAACTGC 60.527 60.000 0.00 0.00 0.00 4.40
5048 5226 0.035056 CCTCCGCCACCTTCTTTGAT 60.035 55.000 0.00 0.00 0.00 2.57
5051 5229 2.034221 GCCTCCGCCACCTTCTTT 59.966 61.111 0.00 0.00 0.00 2.52
5210 5388 3.984193 CTCCTTCTTGGGCCGCTGG 62.984 68.421 0.00 0.00 36.20 4.85
5231 5409 2.520458 CCCTTCTTGGCCACCACA 59.480 61.111 3.88 0.00 30.78 4.17
5345 5544 4.467084 CCGCCAGCGCCCTTCTTA 62.467 66.667 2.29 0.00 38.24 2.10
5357 5556 3.171828 TTTCTTCTGACCGCCGCCA 62.172 57.895 0.00 0.00 0.00 5.69
5366 5577 1.073923 GCCTTCCCACCTTTCTTCTGA 59.926 52.381 0.00 0.00 0.00 3.27
5473 5687 2.358615 TTTCAGCAGGCGCGACAT 60.359 55.556 17.71 0.00 45.49 3.06
5480 5694 1.403323 GCTATCCAACTTTCAGCAGGC 59.597 52.381 0.00 0.00 32.46 4.85
5481 5695 2.941720 GAGCTATCCAACTTTCAGCAGG 59.058 50.000 0.00 0.00 34.65 4.85
5482 5696 2.606725 CGAGCTATCCAACTTTCAGCAG 59.393 50.000 0.00 0.00 34.65 4.24
5483 5697 2.621338 CGAGCTATCCAACTTTCAGCA 58.379 47.619 0.00 0.00 34.65 4.41
5484 5698 1.328986 GCGAGCTATCCAACTTTCAGC 59.671 52.381 0.00 0.00 0.00 4.26
5485 5699 2.863137 GAGCGAGCTATCCAACTTTCAG 59.137 50.000 0.00 0.00 0.00 3.02
5486 5700 2.497675 AGAGCGAGCTATCCAACTTTCA 59.502 45.455 0.00 0.00 0.00 2.69
5487 5701 3.120041 GAGAGCGAGCTATCCAACTTTC 58.880 50.000 8.40 0.00 0.00 2.62
5489 5703 2.100584 CAGAGAGCGAGCTATCCAACTT 59.899 50.000 15.11 0.00 35.09 2.66
5490 5704 1.680735 CAGAGAGCGAGCTATCCAACT 59.319 52.381 15.11 0.00 35.09 3.16
5594 5823 6.138081 GCGTAACTTACAAAACTTTTCTGACG 59.862 38.462 0.00 0.00 0.00 4.35
5637 5866 8.821686 ACCACAATCACAAATTATTATCCAGA 57.178 30.769 0.00 0.00 0.00 3.86
5643 5872 9.646427 GGCTTTAACCACAATCACAAATTATTA 57.354 29.630 0.00 0.00 0.00 0.98
5678 5907 5.537300 AGGTAAGCTCGTCATGATTATGT 57.463 39.130 0.00 0.00 35.73 2.29
5693 5922 4.200092 AGGCTAGCATGTTTAAGGTAAGC 58.800 43.478 18.24 0.00 0.00 3.09
5713 5942 4.003648 CTGTTTTCTAGTAGGCCACAAGG 58.996 47.826 5.01 0.00 38.23 3.61
5766 5996 6.484308 TGCATCCATGACACAAATATGTAGAG 59.516 38.462 0.00 0.00 37.82 2.43
5767 5997 6.355747 TGCATCCATGACACAAATATGTAGA 58.644 36.000 0.00 0.00 37.82 2.59
5780 6039 5.320549 ACTGAGAAAATTGCATCCATGAC 57.679 39.130 0.00 0.00 0.00 3.06
5781 6040 5.988310 AACTGAGAAAATTGCATCCATGA 57.012 34.783 0.00 0.00 0.00 3.07
5786 6045 5.261661 CGAGCTAACTGAGAAAATTGCATC 58.738 41.667 0.00 0.00 0.00 3.91
5795 6054 4.801330 TTCATTCCGAGCTAACTGAGAA 57.199 40.909 0.00 0.00 0.00 2.87
5805 6064 1.339151 ACCACCTCTTTCATTCCGAGC 60.339 52.381 0.00 0.00 0.00 5.03
5893 6158 5.494632 TTCTTTCTTTCTTTTCACCCGAC 57.505 39.130 0.00 0.00 0.00 4.79
5922 6190 1.530323 CCGGGGATTCAAAGTTTCGT 58.470 50.000 0.00 0.00 0.00 3.85
5923 6191 0.170339 GCCGGGGATTCAAAGTTTCG 59.830 55.000 2.18 0.00 0.00 3.46
5927 6195 1.750682 GCTATGCCGGGGATTCAAAGT 60.751 52.381 6.28 0.00 0.00 2.66
5978 6246 1.768275 TCTCTCAACAAGTTGCCAGGA 59.232 47.619 8.04 3.68 40.24 3.86
5980 6248 2.031333 GCTTCTCTCAACAAGTTGCCAG 60.031 50.000 8.04 6.39 40.24 4.85
5981 6249 1.949525 GCTTCTCTCAACAAGTTGCCA 59.050 47.619 8.04 0.00 40.24 4.92
5982 6250 1.069636 CGCTTCTCTCAACAAGTTGCC 60.070 52.381 8.04 0.00 40.24 4.52
5993 6261 0.249114 GGTCCGGATTCGCTTCTCTC 60.249 60.000 7.81 0.00 34.56 3.20
5994 6262 1.677637 GGGTCCGGATTCGCTTCTCT 61.678 60.000 7.81 0.00 34.56 3.10
5996 6264 2.732619 GGGGTCCGGATTCGCTTCT 61.733 63.158 7.81 0.00 34.56 2.85
6011 6279 4.351054 AGCCCGAAAGCTGTGGGG 62.351 66.667 19.59 19.59 42.95 4.96
6033 6301 1.735973 GCTGGCCGGATTCCAAATC 59.264 57.895 18.31 0.00 32.41 2.17
6034 6302 1.758122 GGCTGGCCGGATTCCAAAT 60.758 57.895 18.31 0.00 32.41 2.32
6046 6314 3.285215 CATCATCGGCTGGCTGGC 61.285 66.667 7.92 7.92 37.94 4.85
6052 6320 3.055591 GTCACTACATCATCATCGGCTG 58.944 50.000 0.00 0.00 0.00 4.85
6054 6322 2.054363 CGTCACTACATCATCATCGGC 58.946 52.381 0.00 0.00 0.00 5.54
6077 6576 1.619363 TGCCATGCCCTACCCTCTT 60.619 57.895 0.00 0.00 0.00 2.85
6079 6578 1.635817 TTCTGCCATGCCCTACCCTC 61.636 60.000 0.00 0.00 0.00 4.30
6082 6591 0.538287 GGATTCTGCCATGCCCTACC 60.538 60.000 0.00 0.00 0.00 3.18
6083 6592 0.183492 TGGATTCTGCCATGCCCTAC 59.817 55.000 0.00 0.00 31.66 3.18
6084 6593 0.475475 CTGGATTCTGCCATGCCCTA 59.525 55.000 0.00 0.00 37.30 3.53
6085 6594 1.229359 CTGGATTCTGCCATGCCCT 59.771 57.895 0.00 0.00 37.30 5.19
6086 6595 1.076485 ACTGGATTCTGCCATGCCC 60.076 57.895 0.00 0.00 37.30 5.36
6087 6596 1.105759 GGACTGGATTCTGCCATGCC 61.106 60.000 0.00 0.00 37.30 4.40
6088 6597 1.442526 CGGACTGGATTCTGCCATGC 61.443 60.000 0.00 0.00 37.30 4.06
6089 6598 0.178767 TCGGACTGGATTCTGCCATG 59.821 55.000 0.00 0.00 37.30 3.66
6090 6599 1.135094 ATCGGACTGGATTCTGCCAT 58.865 50.000 0.00 0.00 37.30 4.40
6091 6600 0.178767 CATCGGACTGGATTCTGCCA 59.821 55.000 0.00 0.00 36.30 4.92
6150 6663 3.954258 GTGGGAATGCTTTTAGGCTATGT 59.046 43.478 0.00 0.00 0.00 2.29
6153 6666 4.316025 AAGTGGGAATGCTTTTAGGCTA 57.684 40.909 0.00 0.00 0.00 3.93
6166 6679 2.504367 GTAAGCAGAGCAAAGTGGGAA 58.496 47.619 0.00 0.00 0.00 3.97
6203 6719 8.463930 ACTCCAAACATCTTCACAAAAGAATA 57.536 30.769 0.00 0.00 0.00 1.75
6204 6720 7.352079 ACTCCAAACATCTTCACAAAAGAAT 57.648 32.000 0.00 0.00 0.00 2.40
6285 6808 3.624861 CGTATGCTTCTGATTCTTTGGCT 59.375 43.478 0.00 0.00 0.00 4.75
6320 6847 1.068127 CTTGCACAGGAAAAGCTTGCT 59.932 47.619 0.00 0.00 32.62 3.91
6321 6848 1.067516 TCTTGCACAGGAAAAGCTTGC 59.932 47.619 0.00 0.00 0.00 4.01
6322 6849 3.655276 ATCTTGCACAGGAAAAGCTTG 57.345 42.857 0.00 0.00 0.00 4.01
6359 6886 2.803285 AAGAGAGGGGGCATCTCATA 57.197 50.000 13.79 0.00 42.78 2.15
6409 6936 2.027100 CCTTAGTTTGACCAGGGAGTCC 60.027 54.545 0.00 0.00 35.83 3.85
6410 6937 2.904434 TCCTTAGTTTGACCAGGGAGTC 59.096 50.000 0.00 0.00 37.28 3.36


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

AutoCloner maintained by Alex Coulton.