Multiple sequence alignment - TraesCS2A01G464000

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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 TraesCS2A01G464000 chr2A 100.000 5039 0 0 1 5039 709771723 709776761 0.000000e+00 9306.0
1 TraesCS2A01G464000 chr2A 91.304 46 4 0 4965 5010 709776642 709776687 4.210000e-06 63.9
2 TraesCS2A01G464000 chr2A 91.304 46 4 0 4920 4965 709776687 709776732 4.210000e-06 63.9
3 TraesCS2A01G464000 chr2D 90.182 4288 246 79 657 4834 571055817 571060039 0.000000e+00 5424.0
4 TraesCS2A01G464000 chr2D 84.058 621 40 28 1 586 571055122 571055718 1.230000e-150 544.0
5 TraesCS2A01G464000 chr2D 80.303 396 47 18 4258 4637 571061945 571062325 2.310000e-68 270.0
6 TraesCS2A01G464000 chr2D 82.576 132 17 5 4835 4965 425567713 425567587 1.480000e-20 111.0
7 TraesCS2A01G464000 chr2B 87.118 3602 294 94 587 4070 683001587 683005136 0.000000e+00 3925.0
8 TraesCS2A01G464000 chr2B 85.965 570 30 11 4101 4646 683005201 683005744 9.470000e-157 564.0
9 TraesCS2A01G464000 chr2B 91.718 326 17 5 272 587 683001227 683001552 1.290000e-120 444.0
10 TraesCS2A01G464000 chr2B 86.772 189 20 4 1 189 682992710 682992893 6.610000e-49 206.0
11 TraesCS2A01G464000 chr2B 94.393 107 6 0 4632 4738 683006028 683006134 1.120000e-36 165.0
12 TraesCS2A01G464000 chr2B 100.000 69 0 0 202 270 683001132 683001200 1.470000e-25 128.0
13 TraesCS2A01G464000 chr3B 81.884 138 17 6 4830 4964 416564154 416564286 5.330000e-20 110.0
14 TraesCS2A01G464000 chr1D 88.506 87 9 1 4880 4965 397983364 397983278 2.480000e-18 104.0
15 TraesCS2A01G464000 chr5A 80.672 119 18 4 4845 4962 496527967 496528081 2.500000e-13 87.9
16 TraesCS2A01G464000 chr3A 79.688 128 17 5 4839 4965 711580905 711581024 3.230000e-12 84.2
17 TraesCS2A01G464000 chr4D 83.721 86 13 1 4881 4965 483590319 483590404 4.180000e-11 80.5


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 TraesCS2A01G464000 chr2A 709771723 709776761 5038 False 3144.600000 9306 94.202667 1 5039 3 chr2A.!!$F1 5038
1 TraesCS2A01G464000 chr2D 571055122 571062325 7203 False 2079.333333 5424 84.847667 1 4834 3 chr2D.!!$F1 4833
2 TraesCS2A01G464000 chr2B 683001132 683006134 5002 False 1045.200000 3925 91.838800 202 4738 5 chr2B.!!$F2 4536

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
95 96 0.109086 CACAAGATCACGGCGAGAGT 60.109 55.0 16.62 1.98 0.00 3.24 F
1625 1805 0.096454 GAATTTGGCGTCGGCACTAC 59.904 55.0 22.33 9.53 42.47 2.73 F
1626 1806 0.321298 AATTTGGCGTCGGCACTACT 60.321 50.0 22.33 3.52 42.47 2.57 F
2422 2634 0.608640 CAACGGCTGGGTACTTCTCT 59.391 55.0 0.00 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1849 0.178973 TTCCTGACTGGGACACGAGA 60.179 55.000 0.00 0.0 34.78 4.04 R
3148 3363 0.323629 GTTGTACACCTAGGGCAGCA 59.676 55.000 14.81 4.0 0.00 4.41 R
3184 3399 0.379669 CTTTGCTAGCCCATGAAGCG 59.620 55.000 13.29 0.0 39.14 4.68 R
4099 4347 1.080298 GCTCACATTGCAAGGCCAC 60.080 57.895 11.69 0.0 0.00 5.01 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
30 31 1.289109 GCGAACGGCAAGCAGAGTAA 61.289 55.000 0.00 0.00 42.87 2.24
31 32 0.716108 CGAACGGCAAGCAGAGTAAG 59.284 55.000 0.00 0.00 0.00 2.34
32 33 1.797025 GAACGGCAAGCAGAGTAAGT 58.203 50.000 0.00 0.00 0.00 2.24
33 34 2.670229 CGAACGGCAAGCAGAGTAAGTA 60.670 50.000 0.00 0.00 0.00 2.24
34 35 2.365408 ACGGCAAGCAGAGTAAGTAC 57.635 50.000 0.00 0.00 0.00 2.73
35 36 1.269166 CGGCAAGCAGAGTAAGTACG 58.731 55.000 0.00 0.00 0.00 3.67
66 67 0.179121 TATCCATGCGTGACGACACC 60.179 55.000 10.10 6.07 43.34 4.16
68 69 2.430075 CATGCGTGACGACACCGA 60.430 61.111 10.10 0.00 43.34 4.69
69 70 2.126463 ATGCGTGACGACACCGAG 60.126 61.111 10.10 0.04 43.34 4.63
80 81 4.641645 CACCGAGGGCAGCCACAA 62.642 66.667 15.19 0.00 0.00 3.33
93 94 1.215382 CCACAAGATCACGGCGAGA 59.785 57.895 16.62 12.96 0.00 4.04
95 96 0.109086 CACAAGATCACGGCGAGAGT 60.109 55.000 16.62 1.98 0.00 3.24
96 97 0.171455 ACAAGATCACGGCGAGAGTC 59.829 55.000 16.62 10.93 0.00 3.36
106 107 3.827898 CGAGAGTCGGGTCTGGGC 61.828 72.222 0.00 0.00 36.00 5.36
107 108 2.363147 GAGAGTCGGGTCTGGGCT 60.363 66.667 0.00 0.00 0.00 5.19
108 109 2.363147 AGAGTCGGGTCTGGGCTC 60.363 66.667 0.00 0.00 0.00 4.70
109 110 2.363147 GAGTCGGGTCTGGGCTCT 60.363 66.667 0.00 0.00 0.00 4.09
110 111 2.681778 AGTCGGGTCTGGGCTCTG 60.682 66.667 0.00 0.00 0.00 3.35
111 112 3.775654 GTCGGGTCTGGGCTCTGG 61.776 72.222 0.00 0.00 0.00 3.86
112 113 3.992641 TCGGGTCTGGGCTCTGGA 61.993 66.667 0.00 0.00 0.00 3.86
139 140 1.299014 CGAGGCGAGTGAGCTCATC 60.299 63.158 21.47 16.33 41.71 2.92
150 151 1.142262 TGAGCTCATCATGACATGGGG 59.858 52.381 13.74 8.05 31.12 4.96
169 170 1.228124 CTGGACGGTGAAAAGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
171 172 1.072505 GGACGGTGAAAAGGGCAGA 59.927 57.895 0.00 0.00 0.00 4.26
184 185 0.759436 GGGCAGAGAGATCGGGGTAA 60.759 60.000 0.00 0.00 0.00 2.85
189 190 4.020128 GGCAGAGAGATCGGGGTAAATAAT 60.020 45.833 0.00 0.00 0.00 1.28
192 193 6.071278 GCAGAGAGATCGGGGTAAATAATACT 60.071 42.308 0.00 0.00 0.00 2.12
193 194 7.540299 CAGAGAGATCGGGGTAAATAATACTC 58.460 42.308 0.00 0.00 0.00 2.59
194 195 7.394923 CAGAGAGATCGGGGTAAATAATACTCT 59.605 40.741 0.00 0.00 34.43 3.24
195 196 8.613034 AGAGAGATCGGGGTAAATAATACTCTA 58.387 37.037 0.00 0.00 32.39 2.43
196 197 8.810990 AGAGATCGGGGTAAATAATACTCTAG 57.189 38.462 0.00 0.00 30.83 2.43
197 198 7.339976 AGAGATCGGGGTAAATAATACTCTAGC 59.660 40.741 0.00 0.00 30.83 3.42
198 199 6.952358 AGATCGGGGTAAATAATACTCTAGCA 59.048 38.462 0.00 0.00 0.00 3.49
199 200 6.336842 TCGGGGTAAATAATACTCTAGCAC 57.663 41.667 0.00 0.00 0.00 4.40
200 201 5.048504 TCGGGGTAAATAATACTCTAGCACG 60.049 44.000 0.00 0.00 39.39 5.34
270 271 2.237143 GTGTGATTCATCAGAGGTGGGA 59.763 50.000 0.00 0.00 37.51 4.37
307 334 2.675423 TCCCGTCCAGTCCAGTCG 60.675 66.667 0.00 0.00 0.00 4.18
313 345 4.135153 CCAGTCCAGTCGAGGCCG 62.135 72.222 0.00 0.00 37.07 6.13
350 382 1.785041 CTGTTTGACCACCACCAGCG 61.785 60.000 0.00 0.00 0.00 5.18
396 429 9.785982 ATGCTAGAGGAGGAATAATAAAAGTTC 57.214 33.333 0.00 0.00 0.00 3.01
481 515 1.455248 TATGCCCGCCAGTTGTTAAC 58.545 50.000 0.00 0.00 0.00 2.01
521 555 8.138712 AGTGAGAGATAATCAGACGGTAATTTC 58.861 37.037 0.00 0.00 0.00 2.17
533 567 2.558378 GGTAATTTCCCTACTCCGTGC 58.442 52.381 0.00 0.00 0.00 5.34
595 667 4.906618 TGTGTAATGGGAGAAAAGAGGAC 58.093 43.478 0.00 0.00 0.00 3.85
598 670 0.912486 ATGGGAGAAAAGAGGACGGG 59.088 55.000 0.00 0.00 0.00 5.28
615 687 1.202268 CGGGCACTTTCCGTCTAGTAG 60.202 57.143 0.00 0.00 42.33 2.57
617 689 2.694109 GGGCACTTTCCGTCTAGTAGAT 59.306 50.000 2.51 0.00 0.00 1.98
618 690 3.132467 GGGCACTTTCCGTCTAGTAGATT 59.868 47.826 2.51 0.00 0.00 2.40
619 691 4.340381 GGGCACTTTCCGTCTAGTAGATTA 59.660 45.833 2.51 0.00 0.00 1.75
621 693 6.335777 GGCACTTTCCGTCTAGTAGATTAAA 58.664 40.000 2.51 4.19 0.00 1.52
622 694 6.815142 GGCACTTTCCGTCTAGTAGATTAAAA 59.185 38.462 2.51 3.90 0.00 1.52
623 695 7.010275 GGCACTTTCCGTCTAGTAGATTAAAAG 59.990 40.741 19.33 19.33 31.14 2.27
647 721 3.107642 ACTCGTCTAAGGTTGTTGGTG 57.892 47.619 0.00 0.00 0.00 4.17
650 724 2.964464 TCGTCTAAGGTTGTTGGTGGTA 59.036 45.455 0.00 0.00 0.00 3.25
651 725 3.387374 TCGTCTAAGGTTGTTGGTGGTAA 59.613 43.478 0.00 0.00 0.00 2.85
652 726 3.495753 CGTCTAAGGTTGTTGGTGGTAAC 59.504 47.826 0.00 0.00 0.00 2.50
714 799 2.071540 GGGTTTCTACGGTGCTTGTAC 58.928 52.381 0.00 0.00 0.00 2.90
715 800 2.548493 GGGTTTCTACGGTGCTTGTACA 60.548 50.000 0.00 0.00 0.00 2.90
729 814 6.534079 GGTGCTTGTACAGTAGTAATTGTAGG 59.466 42.308 0.00 0.00 29.40 3.18
789 874 1.129437 GATGAGACCTTTCGTTGCAGC 59.871 52.381 0.00 0.00 0.00 5.25
797 882 0.248296 TTTCGTTGCAGCGGAAACAC 60.248 50.000 22.99 0.00 31.43 3.32
810 895 2.159627 CGGAAACACGGAGATTTTGAGG 59.840 50.000 0.00 0.00 0.00 3.86
828 922 2.188161 GGTTCGGAAACACGGCCAA 61.188 57.895 2.24 0.00 37.10 4.52
836 930 2.543031 GGAAACACGGCCAAAGAAACTC 60.543 50.000 2.24 0.00 0.00 3.01
895 1023 2.559440 GGCAAGACATCACAGATCTCC 58.441 52.381 0.00 0.00 0.00 3.71
903 1031 2.941453 TCACAGATCTCCGCTTACAC 57.059 50.000 0.00 0.00 0.00 2.90
909 1037 1.681793 GATCTCCGCTTACACTAGCCA 59.318 52.381 0.00 0.00 37.90 4.75
910 1038 1.552578 TCTCCGCTTACACTAGCCAA 58.447 50.000 0.00 0.00 37.90 4.52
920 1048 0.322546 CACTAGCCAAAGTCCCCACC 60.323 60.000 0.00 0.00 0.00 4.61
933 1061 1.031571 CCCCACCGTGTAGCGTAGTA 61.032 60.000 0.00 0.00 39.32 1.82
934 1062 1.027357 CCCACCGTGTAGCGTAGTAT 58.973 55.000 0.00 0.00 39.32 2.12
935 1063 1.406539 CCCACCGTGTAGCGTAGTATT 59.593 52.381 0.00 0.00 39.32 1.89
936 1064 2.618241 CCCACCGTGTAGCGTAGTATTA 59.382 50.000 0.00 0.00 39.32 0.98
937 1065 3.548818 CCCACCGTGTAGCGTAGTATTAC 60.549 52.174 0.00 0.00 39.32 1.89
938 1066 3.313526 CCACCGTGTAGCGTAGTATTACT 59.686 47.826 1.30 1.30 39.32 2.24
952 1080 7.188157 CGTAGTATTACTGTGTTCTCTTCTCC 58.812 42.308 6.60 0.00 0.00 3.71
955 1083 5.669164 ATTACTGTGTTCTCTTCTCCTCC 57.331 43.478 0.00 0.00 0.00 4.30
958 1086 1.132849 TGTGTTCTCTTCTCCTCCCCA 60.133 52.381 0.00 0.00 0.00 4.96
971 1110 2.204306 CCCCACCCCCTTCTTCCT 60.204 66.667 0.00 0.00 0.00 3.36
973 1112 1.229984 CCCACCCCCTTCTTCCTCT 60.230 63.158 0.00 0.00 0.00 3.69
1040 1180 3.357079 GGGGCACACACAGAAGCG 61.357 66.667 0.00 0.00 0.00 4.68
1044 1184 4.707840 CACACACAGAAGCGCGCG 62.708 66.667 28.44 28.44 0.00 6.86
1165 1305 1.375326 GATCCCCACCCGCCTAATC 59.625 63.158 0.00 0.00 0.00 1.75
1199 1351 7.516943 GCTCCGTTATGCTTCATTTTACTACTC 60.517 40.741 0.00 0.00 0.00 2.59
1200 1352 6.759827 TCCGTTATGCTTCATTTTACTACTCC 59.240 38.462 0.00 0.00 0.00 3.85
1202 1354 6.292168 CGTTATGCTTCATTTTACTACTCCGG 60.292 42.308 0.00 0.00 0.00 5.14
1286 1447 2.226437 AGTCTAGCATGTTTTGTTGCGG 59.774 45.455 0.00 0.00 43.61 5.69
1289 1450 1.851658 AGCATGTTTTGTTGCGGTTC 58.148 45.000 0.00 0.00 43.61 3.62
1297 1458 6.470557 TGTTTTGTTGCGGTTCTATACTAC 57.529 37.500 0.00 0.00 0.00 2.73
1524 1699 6.758886 CAGTCAAAGGGAAGCTAACTATACTG 59.241 42.308 0.00 0.00 0.00 2.74
1621 1801 0.886938 TGAAGAATTTGGCGTCGGCA 60.887 50.000 18.58 18.58 42.47 5.69
1625 1805 0.096454 GAATTTGGCGTCGGCACTAC 59.904 55.000 22.33 9.53 42.47 2.73
1626 1806 0.321298 AATTTGGCGTCGGCACTACT 60.321 50.000 22.33 3.52 42.47 2.57
1627 1807 1.019278 ATTTGGCGTCGGCACTACTG 61.019 55.000 22.33 0.00 42.47 2.74
1628 1808 2.372040 TTTGGCGTCGGCACTACTGT 62.372 55.000 22.33 0.00 42.47 3.55
1629 1809 1.525718 TTGGCGTCGGCACTACTGTA 61.526 55.000 22.33 1.49 42.47 2.74
1642 1822 6.914757 CGGCACTACTGTATTTTAGTACTACC 59.085 42.308 0.91 0.00 0.00 3.18
1656 1836 5.012328 AGTACTACCTGCTAAAGTGATGC 57.988 43.478 0.00 0.00 0.00 3.91
1671 1851 3.008330 GTGATGCTGATTTCACTGCTCT 58.992 45.455 0.00 0.00 39.30 4.09
1672 1852 3.063725 GTGATGCTGATTTCACTGCTCTC 59.936 47.826 0.00 0.00 39.30 3.20
1706 1886 5.415701 TCAGGAAATAGAAGTGTCAAATGGC 59.584 40.000 0.00 0.00 0.00 4.40
1717 1897 4.009675 GTGTCAAATGGCCATTCTACTGA 58.990 43.478 30.74 25.50 0.00 3.41
1723 1903 1.204704 TGGCCATTCTACTGACTGTCG 59.795 52.381 0.00 0.99 0.00 4.35
1733 1914 0.861837 CTGACTGTCGCTGTCCAAAC 59.138 55.000 2.98 0.00 32.56 2.93
1763 1946 6.974932 AATCTTGCATGACACTAGTACTTG 57.025 37.500 0.00 0.59 0.00 3.16
1781 1964 7.425606 AGTACTTGTAATTTCTTGGCACTTTG 58.574 34.615 0.00 0.00 0.00 2.77
1816 2003 6.426587 AGCTTCCTGCCTAGAAATATTTTGA 58.573 36.000 1.43 0.00 44.23 2.69
1818 2005 6.319911 GCTTCCTGCCTAGAAATATTTTGAGT 59.680 38.462 1.43 0.00 35.15 3.41
1821 2008 7.175104 TCCTGCCTAGAAATATTTTGAGTTGT 58.825 34.615 1.43 0.00 0.00 3.32
1836 2023 7.490962 TTTGAGTTGTAATGAATGAAGACGT 57.509 32.000 0.00 0.00 0.00 4.34
1845 2057 9.917129 TGTAATGAATGAAGACGTTCTAAGTTA 57.083 29.630 0.00 0.00 41.17 2.24
1856 2068 6.696148 AGACGTTCTAAGTTATAATGCTTCCG 59.304 38.462 0.00 0.00 0.00 4.30
1862 2074 9.692749 TTCTAAGTTATAATGCTTCCGTAGATG 57.307 33.333 0.00 0.00 0.00 2.90
1869 2081 4.744795 ATGCTTCCGTAGATGAAGACTT 57.255 40.909 4.30 0.00 41.38 3.01
1874 2086 5.733937 GCTTCCGTAGATGAAGACTTACCTC 60.734 48.000 4.30 0.00 41.38 3.85
1948 2160 2.671070 CTGGGAGCCCACAATCGT 59.329 61.111 3.58 0.00 41.89 3.73
2058 2270 4.265556 CGATGTTCTTGACGAAGGTACATC 59.734 45.833 15.32 15.32 41.81 3.06
2069 2281 3.979495 CGAAGGTACATCCATAACGCTAC 59.021 47.826 0.00 0.00 39.02 3.58
2084 2296 7.254658 CCATAACGCTACCCTATTTGTGTTTAG 60.255 40.741 0.00 0.00 35.27 1.85
2140 2352 2.178890 CCATCTCGCTCTGCTTGCC 61.179 63.158 0.00 0.00 0.00 4.52
2162 2374 4.007644 CAGACAGCTCCGGTGCCA 62.008 66.667 24.18 0.00 34.04 4.92
2266 2478 2.618709 CAAGAGTTCAGTTCACCAACCC 59.381 50.000 0.00 0.00 32.22 4.11
2296 2508 3.881688 GCAACTCAAGCATGATACATCCT 59.118 43.478 0.00 0.00 34.37 3.24
2305 2517 1.921243 TGATACATCCTGTGCGAACG 58.079 50.000 0.00 0.00 0.00 3.95
2345 2557 0.667487 ATGCGACAGTGGTCTTGACG 60.667 55.000 0.00 0.00 42.05 4.35
2353 2565 1.375908 TGGTCTTGACGATGCCAGC 60.376 57.895 0.00 0.00 0.00 4.85
2389 2601 1.144936 CCATGGAGGCGAGAAGACC 59.855 63.158 5.56 0.00 0.00 3.85
2422 2634 0.608640 CAACGGCTGGGTACTTCTCT 59.391 55.000 0.00 0.00 0.00 3.10
2488 2700 2.042686 ACAAGCAGACTGTTCAGCAA 57.957 45.000 3.99 0.00 36.73 3.91
2495 2707 1.670811 AGACTGTTCAGCAAAACACCG 59.329 47.619 0.00 0.00 35.39 4.94
2535 2750 2.280797 GAGTGCGCACCAGGTGAA 60.281 61.111 35.51 4.80 35.23 3.18
2680 2895 1.638388 CTTTCGCTTCGCATCAGCCA 61.638 55.000 0.00 0.00 37.52 4.75
2698 2913 1.453015 AAAGTTGGTCAGGCACGCA 60.453 52.632 0.00 0.00 0.00 5.24
2737 2952 1.634702 GTTCTAGCGCCAACTCAGAG 58.365 55.000 2.29 0.00 0.00 3.35
2767 2982 2.351738 GGGTCAAGCTGAAACCAATTCG 60.352 50.000 12.87 0.00 41.18 3.34
2829 3044 9.869844 CTTTCTCATTGTTACTTTACAGTTCAG 57.130 33.333 0.00 0.00 34.06 3.02
2837 3052 9.834628 TTGTTACTTTACAGTTCAGTTTTCTTG 57.165 29.630 0.00 0.00 34.06 3.02
3061 3276 4.141620 ACGGCATCAATAGGAGAAGACAAT 60.142 41.667 0.00 0.00 0.00 2.71
3107 3322 4.529377 ACAGAAAAGGTGGCATGAATGAAT 59.471 37.500 0.00 0.00 0.00 2.57
3148 3363 3.007290 GGCTCAAGGCAAGGAAAGAAATT 59.993 43.478 0.00 0.00 44.01 1.82
3184 3399 7.064728 GGTGTACAACTAGGAAAGATGAACATC 59.935 40.741 2.87 6.68 38.09 3.06
3199 3414 0.533755 ACATCGCTTCATGGGCTAGC 60.534 55.000 6.04 6.04 0.00 3.42
3251 3466 0.672889 GAGCATCGCTGATCTGGAGA 59.327 55.000 0.00 0.00 39.88 3.71
3298 3513 3.567797 GCAGCATTCGAGGACGCC 61.568 66.667 0.00 0.00 39.58 5.68
3313 3528 4.007659 AGGACGCCGAAAATTCTAAACAT 58.992 39.130 0.00 0.00 0.00 2.71
3326 3541 8.951787 AAATTCTAAACATACAGCACGGTATA 57.048 30.769 0.00 0.00 32.83 1.47
3327 3542 9.555727 AAATTCTAAACATACAGCACGGTATAT 57.444 29.630 0.00 0.00 32.83 0.86
3329 3544 8.583810 TTCTAAACATACAGCACGGTATATTC 57.416 34.615 0.00 0.00 32.83 1.75
3331 3546 4.948341 ACATACAGCACGGTATATTCCA 57.052 40.909 0.00 0.00 32.83 3.53
3332 3547 5.483685 ACATACAGCACGGTATATTCCAT 57.516 39.130 0.00 0.00 32.83 3.41
3333 3548 5.479306 ACATACAGCACGGTATATTCCATC 58.521 41.667 0.00 0.00 32.83 3.51
3334 3549 5.011635 ACATACAGCACGGTATATTCCATCA 59.988 40.000 0.00 0.00 32.83 3.07
3344 3563 6.127591 ACGGTATATTCCATCAGACTATCTGC 60.128 42.308 0.74 0.00 43.95 4.26
3388 3607 9.290988 TCTACTAGTGAGCTATAAAAGGAGATG 57.709 37.037 5.39 0.00 0.00 2.90
3440 3659 8.134895 GTGGTTTTCTTCATGTTGTCTGAAATA 58.865 33.333 0.00 0.00 32.53 1.40
3531 3750 7.488322 ACAAAAGTTGAATCCGAAATGAAGAA 58.512 30.769 0.00 0.00 0.00 2.52
3532 3751 7.649306 ACAAAAGTTGAATCCGAAATGAAGAAG 59.351 33.333 0.00 0.00 0.00 2.85
3553 3772 3.519510 AGCTAGAGGTGCATTTCCACTAA 59.480 43.478 0.00 0.00 36.03 2.24
3558 3777 6.670695 AGAGGTGCATTTCCACTAAATTTT 57.329 33.333 0.00 0.00 35.54 1.82
3560 3779 8.366359 AGAGGTGCATTTCCACTAAATTTTAT 57.634 30.769 0.00 0.00 35.54 1.40
3618 3845 8.209584 ACATACTCTGAATGCATCATACTCTTT 58.790 33.333 0.00 0.00 37.44 2.52
3655 3891 6.980978 GCTAGTAATGACAAGCTGTTCTATGA 59.019 38.462 0.00 0.00 0.00 2.15
3742 3978 4.735132 CGCGTGGCCGAGGAGAAA 62.735 66.667 0.00 0.00 35.63 2.52
3821 4057 1.266178 TCTGATTCGCCAGACAGGAA 58.734 50.000 0.00 0.00 41.22 3.36
3850 4086 1.687123 GGGTCACGTATCCTATGCTGT 59.313 52.381 7.87 0.00 0.00 4.40
3856 4092 1.069204 CGTATCCTATGCTGTGGCTGT 59.931 52.381 0.00 0.00 39.59 4.40
3884 4125 5.648526 TGTGAACCTTAGCACTTGTTTAACA 59.351 36.000 0.00 0.00 36.05 2.41
3912 4157 7.814264 AGCCTGTTAAAATATGATTGAGGAG 57.186 36.000 0.00 0.00 0.00 3.69
3976 4221 4.922206 AGTATGCAAAAGGGAATGTCTGA 58.078 39.130 0.00 0.00 0.00 3.27
3991 4236 6.041409 GGAATGTCTGATCTAGGTGATTCAGA 59.959 42.308 0.00 0.00 37.19 3.27
4000 4247 6.208988 TCTAGGTGATTCAGATGTACACAC 57.791 41.667 0.00 0.00 33.82 3.82
4001 4248 4.890158 AGGTGATTCAGATGTACACACA 57.110 40.909 0.00 0.00 39.52 3.72
4008 4255 6.311200 TGATTCAGATGTACACACATTCTTCG 59.689 38.462 0.00 0.00 45.58 3.79
4098 4346 4.951715 TCCTACCTATAAGCTGTTCGTTCA 59.048 41.667 0.00 0.00 0.00 3.18
4099 4347 5.067413 TCCTACCTATAAGCTGTTCGTTCAG 59.933 44.000 0.00 5.52 38.35 3.02
4100 4348 4.803098 ACCTATAAGCTGTTCGTTCAGT 57.197 40.909 10.16 0.00 37.70 3.41
4104 4352 1.166531 AAGCTGTTCGTTCAGTGGCC 61.167 55.000 0.00 0.00 37.70 5.36
4105 4353 1.598130 GCTGTTCGTTCAGTGGCCT 60.598 57.895 3.32 0.00 37.70 5.19
4106 4354 1.166531 GCTGTTCGTTCAGTGGCCTT 61.167 55.000 3.32 0.00 37.70 4.35
4107 4355 0.588252 CTGTTCGTTCAGTGGCCTTG 59.412 55.000 3.32 2.41 0.00 3.61
4108 4356 1.282875 GTTCGTTCAGTGGCCTTGC 59.717 57.895 3.32 0.00 0.00 4.01
4116 4408 0.242825 CAGTGGCCTTGCAATGTGAG 59.757 55.000 3.32 0.00 0.00 3.51
4199 4492 6.863126 CCAAGTTACAGGTCAAATTCATGTTC 59.137 38.462 0.00 0.00 32.26 3.18
4219 4512 6.650120 TGTTCCTGGGATCTTACATAAAGTC 58.350 40.000 0.00 0.00 36.51 3.01
4220 4513 6.214615 TGTTCCTGGGATCTTACATAAAGTCA 59.785 38.462 0.00 0.00 36.51 3.41
4289 4603 1.292541 GAGGTGTTCACGGGTCTCC 59.707 63.158 0.00 0.00 0.00 3.71
4420 4740 2.437359 GAACGGGCAGCAGCTGAT 60.437 61.111 27.39 8.90 41.70 2.90
4421 4741 2.749044 AACGGGCAGCAGCTGATG 60.749 61.111 27.28 27.28 41.70 3.07
4422 4742 3.258228 AACGGGCAGCAGCTGATGA 62.258 57.895 34.79 0.00 41.70 2.92
4423 4743 2.895865 CGGGCAGCAGCTGATGAG 60.896 66.667 34.79 20.17 41.70 2.90
4424 4744 2.271497 GGGCAGCAGCTGATGAGT 59.729 61.111 34.79 1.45 41.70 3.41
4425 4745 1.524002 GGGCAGCAGCTGATGAGTA 59.476 57.895 34.79 0.00 41.70 2.59
4426 4746 0.813210 GGGCAGCAGCTGATGAGTAC 60.813 60.000 34.79 19.61 41.70 2.73
4430 4750 2.725490 CAGCAGCTGATGAGTACTACG 58.275 52.381 27.60 0.00 32.44 3.51
4469 4789 4.587262 ACTTCCATCAGTTGGTAAAAACCC 59.413 41.667 0.00 0.00 46.52 4.11
4489 4809 1.662629 CTGCAAACTATGGACTCGCTG 59.337 52.381 0.00 0.00 0.00 5.18
4493 4813 2.659897 CTATGGACTCGCTGCGGC 60.660 66.667 23.03 7.70 0.00 6.53
4548 4868 2.266055 CTTCAGTCAGTCCGCCCC 59.734 66.667 0.00 0.00 0.00 5.80
4592 4912 8.948631 ATCTACAGTTGACATTTCATATCGTT 57.051 30.769 0.00 0.00 0.00 3.85
4595 4915 7.295952 ACAGTTGACATTTCATATCGTTCTC 57.704 36.000 0.00 0.00 0.00 2.87
4598 4918 3.802139 TGACATTTCATATCGTTCTCCGC 59.198 43.478 0.00 0.00 36.19 5.54
4602 4922 0.469331 TCATATCGTTCTCCGCCCCT 60.469 55.000 0.00 0.00 36.19 4.79
4639 4959 8.888716 ACCAAAATCATTGTTTTGACCTTTTAC 58.111 29.630 18.07 0.00 46.78 2.01
4690 5308 8.773645 GCTTTAAAATTTTAACACAATCTGGCT 58.226 29.630 20.35 0.00 32.77 4.75
4783 5401 0.320697 AAAGTGACAGGCGGTAGGAC 59.679 55.000 0.00 0.00 0.00 3.85
4784 5402 1.874345 AAGTGACAGGCGGTAGGACG 61.874 60.000 0.00 0.00 0.00 4.79
4799 5417 1.678101 AGGACGTGTATACCTTACCGC 59.322 52.381 0.00 0.00 0.00 5.68
4814 5432 1.047801 ACCGCCAAAGCCATTCTTTT 58.952 45.000 0.00 0.00 42.82 2.27
4815 5433 1.416030 ACCGCCAAAGCCATTCTTTTT 59.584 42.857 0.00 0.00 42.82 1.94
4844 5984 7.922837 TCGAGAACGAACAGACATATATAACA 58.077 34.615 0.00 0.00 45.74 2.41
4872 6012 0.833287 AGGGACATAGCTGCGTGAAT 59.167 50.000 13.58 0.00 0.00 2.57
4874 6014 1.473257 GGGACATAGCTGCGTGAATGA 60.473 52.381 13.58 0.00 0.00 2.57
4877 6017 3.126858 GGACATAGCTGCGTGAATGAAAA 59.873 43.478 13.58 0.00 0.00 2.29
4878 6018 4.379394 GGACATAGCTGCGTGAATGAAAAA 60.379 41.667 13.58 0.00 0.00 1.94
4902 6042 7.754851 AAAAATAGGGAGTCAAAACGTACAT 57.245 32.000 0.00 0.00 0.00 2.29
4903 6043 6.737254 AAATAGGGAGTCAAAACGTACATG 57.263 37.500 0.00 0.00 0.00 3.21
4942 6083 3.142838 CAGCGGGCATTTGAGGGG 61.143 66.667 0.00 0.00 0.00 4.79
4959 6100 1.001974 GGGGCCAAATTTGTTCAGTCC 59.998 52.381 16.73 11.59 0.00 3.85
4960 6101 1.336795 GGGCCAAATTTGTTCAGTCCG 60.337 52.381 16.73 0.41 0.00 4.79
4961 6102 1.336795 GGCCAAATTTGTTCAGTCCGG 60.337 52.381 16.73 0.00 0.00 5.14
4962 6103 1.934849 GCCAAATTTGTTCAGTCCGGC 60.935 52.381 16.73 6.08 0.00 6.13
4963 6104 1.613437 CCAAATTTGTTCAGTCCGGCT 59.387 47.619 16.73 0.00 0.00 5.52
4964 6105 2.607771 CCAAATTTGTTCAGTCCGGCTG 60.608 50.000 16.73 16.84 46.34 4.85
4965 6106 1.247567 AATTTGTTCAGTCCGGCTGG 58.752 50.000 20.90 4.71 45.08 4.85
4966 6107 0.110486 ATTTGTTCAGTCCGGCTGGT 59.890 50.000 20.90 0.00 45.08 4.00
4967 6108 0.817634 TTTGTTCAGTCCGGCTGGTG 60.818 55.000 20.90 3.29 45.08 4.17
4968 6109 3.050275 GTTCAGTCCGGCTGGTGC 61.050 66.667 20.90 6.12 45.08 5.01
4969 6110 4.680237 TTCAGTCCGGCTGGTGCG 62.680 66.667 20.90 0.74 45.08 5.34
4984 6125 4.520846 GCGTCGCGGGCATTTGAG 62.521 66.667 16.36 0.00 0.00 3.02
4985 6126 3.864686 CGTCGCGGGCATTTGAGG 61.865 66.667 6.13 0.00 0.00 3.86
4986 6127 3.508840 GTCGCGGGCATTTGAGGG 61.509 66.667 6.13 0.00 0.00 4.30
4987 6128 4.794648 TCGCGGGCATTTGAGGGG 62.795 66.667 6.13 0.00 0.00 4.79
4992 6133 3.804490 GGCATTTGAGGGGCCAAA 58.196 55.556 4.39 0.00 46.92 3.28
4993 6134 2.299975 GGCATTTGAGGGGCCAAAT 58.700 52.632 4.39 0.00 46.92 2.32
4994 6135 0.620030 GGCATTTGAGGGGCCAAATT 59.380 50.000 4.39 0.00 46.92 1.82
4995 6136 1.004628 GGCATTTGAGGGGCCAAATTT 59.995 47.619 4.39 0.00 46.92 1.82
4996 6137 2.086094 GCATTTGAGGGGCCAAATTTG 58.914 47.619 11.40 11.40 42.26 2.32
4997 6138 2.552809 GCATTTGAGGGGCCAAATTTGT 60.553 45.455 16.73 0.00 42.26 2.83
4998 6139 3.753815 CATTTGAGGGGCCAAATTTGTT 58.246 40.909 16.73 0.00 42.26 2.83
4999 6140 3.483808 TTTGAGGGGCCAAATTTGTTC 57.516 42.857 16.73 8.07 31.73 3.18
5000 6141 2.094100 TGAGGGGCCAAATTTGTTCA 57.906 45.000 16.73 9.23 0.00 3.18
5001 6142 2.402564 TGAGGGGCCAAATTTGTTCAA 58.597 42.857 16.73 0.00 0.00 2.69
5002 6143 2.978278 TGAGGGGCCAAATTTGTTCAAT 59.022 40.909 16.73 0.22 0.00 2.57
5003 6144 4.163427 TGAGGGGCCAAATTTGTTCAATA 58.837 39.130 16.73 0.00 0.00 1.90
5004 6145 4.020662 TGAGGGGCCAAATTTGTTCAATAC 60.021 41.667 16.73 4.03 0.00 1.89
5023 6164 2.656002 ACGGCTGTAGATGCTCTTAGA 58.344 47.619 0.00 0.00 0.00 2.10
5026 6167 3.613671 CGGCTGTAGATGCTCTTAGATGG 60.614 52.174 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.924060 GCATGGATATACTTTTGTCTCGTACT 59.076 38.462 0.00 0.00 0.00 2.73
31 32 6.129168 CGCATGGATATACTTTTGTCTCGTAC 60.129 42.308 0.00 0.00 0.00 3.67
32 33 5.918576 CGCATGGATATACTTTTGTCTCGTA 59.081 40.000 0.00 0.00 0.00 3.43
33 34 4.745125 CGCATGGATATACTTTTGTCTCGT 59.255 41.667 0.00 0.00 0.00 4.18
34 35 4.745125 ACGCATGGATATACTTTTGTCTCG 59.255 41.667 0.00 0.00 0.00 4.04
35 36 5.753438 TCACGCATGGATATACTTTTGTCTC 59.247 40.000 0.00 0.00 0.00 3.36
50 51 3.478394 CGGTGTCGTCACGCATGG 61.478 66.667 6.71 0.00 44.68 3.66
66 67 1.817099 GATCTTGTGGCTGCCCTCG 60.817 63.158 17.53 2.06 0.00 4.63
68 69 1.001641 GTGATCTTGTGGCTGCCCT 60.002 57.895 17.53 0.00 0.00 5.19
69 70 2.401766 CGTGATCTTGTGGCTGCCC 61.402 63.158 17.53 8.23 0.00 5.36
71 72 3.044059 GCCGTGATCTTGTGGCTGC 62.044 63.158 9.77 0.00 44.16 5.25
77 78 0.171455 GACTCTCGCCGTGATCTTGT 59.829 55.000 0.00 0.00 0.00 3.16
78 79 0.863538 CGACTCTCGCCGTGATCTTG 60.864 60.000 0.00 0.00 31.14 3.02
79 80 1.429825 CGACTCTCGCCGTGATCTT 59.570 57.895 0.00 0.00 31.14 2.40
80 81 2.473760 CCGACTCTCGCCGTGATCT 61.474 63.158 0.00 0.00 38.82 2.75
93 94 2.681778 CAGAGCCCAGACCCGACT 60.682 66.667 0.00 0.00 0.00 4.18
95 96 3.965026 CTCCAGAGCCCAGACCCGA 62.965 68.421 0.00 0.00 0.00 5.14
96 97 3.465403 CTCCAGAGCCCAGACCCG 61.465 72.222 0.00 0.00 0.00 5.28
135 136 0.184211 CCAGCCCCATGTCATGATGA 59.816 55.000 14.67 0.00 0.00 2.92
139 140 1.820906 CGTCCAGCCCCATGTCATG 60.821 63.158 5.79 5.79 0.00 3.07
150 151 2.626780 GCCCTTTTCACCGTCCAGC 61.627 63.158 0.00 0.00 0.00 4.85
169 170 7.471890 AGAGTATTATTTACCCCGATCTCTCT 58.528 38.462 0.00 0.00 0.00 3.10
171 172 7.339976 GCTAGAGTATTATTTACCCCGATCTCT 59.660 40.741 0.00 0.00 33.92 3.10
184 185 7.648510 GCTCTGTTTACGTGCTAGAGTATTATT 59.351 37.037 16.74 0.00 37.71 1.40
189 190 4.008330 AGCTCTGTTTACGTGCTAGAGTA 58.992 43.478 16.74 0.00 37.71 2.59
192 193 3.005472 ACAAGCTCTGTTTACGTGCTAGA 59.995 43.478 0.00 0.00 32.99 2.43
193 194 3.318017 ACAAGCTCTGTTTACGTGCTAG 58.682 45.455 0.00 0.00 32.99 3.42
194 195 3.380479 ACAAGCTCTGTTTACGTGCTA 57.620 42.857 0.00 0.00 32.99 3.49
195 196 2.240493 ACAAGCTCTGTTTACGTGCT 57.760 45.000 0.00 0.00 32.99 4.40
196 197 3.057734 ACTACAAGCTCTGTTTACGTGC 58.942 45.455 0.00 0.00 39.64 5.34
197 198 4.148348 GTGACTACAAGCTCTGTTTACGTG 59.852 45.833 0.00 0.00 39.64 4.49
198 199 4.037684 AGTGACTACAAGCTCTGTTTACGT 59.962 41.667 6.82 0.00 39.64 3.57
199 200 4.383052 CAGTGACTACAAGCTCTGTTTACG 59.617 45.833 6.82 0.00 39.64 3.18
200 201 5.402867 GTCAGTGACTACAAGCTCTGTTTAC 59.597 44.000 16.26 0.00 39.64 2.01
270 271 1.203661 AGCCCTATCCCATCCATCCAT 60.204 52.381 0.00 0.00 0.00 3.41
350 382 3.965539 ATCTCAGCAGCACGGTGGC 62.966 63.158 10.60 5.77 43.59 5.01
354 386 0.585357 GCATAATCTCAGCAGCACGG 59.415 55.000 0.00 0.00 0.00 4.94
396 429 1.228429 TCCAAACTCCAAAGCCCCG 60.228 57.895 0.00 0.00 0.00 5.73
467 501 2.224784 GGTTAGTGTTAACAACTGGCGG 59.775 50.000 10.51 0.00 40.77 6.13
521 555 4.143333 CACGGGCACGGAGTAGGG 62.143 72.222 15.46 0.00 41.61 3.53
533 567 0.459237 GCATCTCTCACTGACACGGG 60.459 60.000 0.00 0.00 0.00 5.28
598 670 7.758528 TCTTTTAATCTACTAGACGGAAAGTGC 59.241 37.037 0.00 0.00 0.00 4.40
615 687 9.595357 CAACCTTAGACGAGTTTTCTTTTAATC 57.405 33.333 0.00 0.00 0.00 1.75
617 689 8.496707 ACAACCTTAGACGAGTTTTCTTTTAA 57.503 30.769 0.00 0.00 0.00 1.52
618 690 8.392612 CAACAACCTTAGACGAGTTTTCTTTTA 58.607 33.333 0.00 0.00 0.00 1.52
619 691 6.997239 ACAACCTTAGACGAGTTTTCTTTT 57.003 33.333 0.00 0.00 0.00 2.27
621 693 5.296035 CCAACAACCTTAGACGAGTTTTCTT 59.704 40.000 0.00 0.00 0.00 2.52
622 694 4.814771 CCAACAACCTTAGACGAGTTTTCT 59.185 41.667 0.00 0.00 0.00 2.52
623 695 4.573607 ACCAACAACCTTAGACGAGTTTTC 59.426 41.667 0.00 0.00 0.00 2.29
627 699 2.224209 CCACCAACAACCTTAGACGAGT 60.224 50.000 0.00 0.00 0.00 4.18
628 700 2.224209 ACCACCAACAACCTTAGACGAG 60.224 50.000 0.00 0.00 0.00 4.18
629 701 1.764134 ACCACCAACAACCTTAGACGA 59.236 47.619 0.00 0.00 0.00 4.20
634 708 4.857679 ACTTGTTACCACCAACAACCTTA 58.142 39.130 0.00 0.00 42.08 2.69
647 721 4.261578 TGCTGTACCTGTACTTGTTACC 57.738 45.455 8.75 0.00 37.00 2.85
650 724 3.558418 CGTTTGCTGTACCTGTACTTGTT 59.442 43.478 8.75 0.00 37.00 2.83
651 725 3.128349 CGTTTGCTGTACCTGTACTTGT 58.872 45.455 8.75 0.00 37.00 3.16
652 726 2.478894 CCGTTTGCTGTACCTGTACTTG 59.521 50.000 8.75 3.59 37.00 3.16
654 728 1.607251 GCCGTTTGCTGTACCTGTACT 60.607 52.381 8.75 0.00 37.00 2.73
655 729 0.794473 GCCGTTTGCTGTACCTGTAC 59.206 55.000 0.45 0.45 36.87 2.90
656 730 3.220447 GCCGTTTGCTGTACCTGTA 57.780 52.632 0.00 0.00 36.87 2.74
657 731 4.058797 GCCGTTTGCTGTACCTGT 57.941 55.556 0.00 0.00 36.87 4.00
714 799 5.011090 TGCTGCTCCTACAATTACTACTG 57.989 43.478 0.00 0.00 0.00 2.74
715 800 4.442192 GCTGCTGCTCCTACAATTACTACT 60.442 45.833 8.53 0.00 36.03 2.57
743 828 2.526958 TGGAAGCACAGACCACAGA 58.473 52.632 0.00 0.00 0.00 3.41
747 832 1.227943 GCAGTGGAAGCACAGACCA 60.228 57.895 0.00 0.00 0.00 4.02
748 833 2.320587 CGCAGTGGAAGCACAGACC 61.321 63.158 0.00 0.00 0.00 3.85
749 834 1.595382 ACGCAGTGGAAGCACAGAC 60.595 57.895 0.00 0.00 42.51 3.51
789 874 2.159627 CCTCAAAATCTCCGTGTTTCCG 59.840 50.000 0.00 0.00 0.00 4.30
797 882 1.066430 TCCGAACCCTCAAAATCTCCG 60.066 52.381 0.00 0.00 0.00 4.63
810 895 1.726533 TTTGGCCGTGTTTCCGAACC 61.727 55.000 0.00 0.00 34.80 3.62
828 922 2.843701 CAGTCCACAGCTGAGTTTCTT 58.156 47.619 23.35 0.00 36.12 2.52
895 1023 2.000447 GGACTTTGGCTAGTGTAAGCG 59.000 52.381 0.00 0.00 43.74 4.68
903 1031 1.078426 CGGTGGGGACTTTGGCTAG 60.078 63.158 0.00 0.00 0.00 3.42
909 1037 1.373812 GCTACACGGTGGGGACTTT 59.626 57.895 13.48 0.00 0.00 2.66
910 1038 2.939261 CGCTACACGGTGGGGACTT 61.939 63.158 13.48 0.00 38.44 3.01
933 1061 4.468153 GGGAGGAGAAGAGAACACAGTAAT 59.532 45.833 0.00 0.00 0.00 1.89
934 1062 3.833070 GGGAGGAGAAGAGAACACAGTAA 59.167 47.826 0.00 0.00 0.00 2.24
935 1063 3.432378 GGGAGGAGAAGAGAACACAGTA 58.568 50.000 0.00 0.00 0.00 2.74
936 1064 2.252714 GGGAGGAGAAGAGAACACAGT 58.747 52.381 0.00 0.00 0.00 3.55
937 1065 1.552792 GGGGAGGAGAAGAGAACACAG 59.447 57.143 0.00 0.00 0.00 3.66
938 1066 1.132849 TGGGGAGGAGAAGAGAACACA 60.133 52.381 0.00 0.00 0.00 3.72
952 1080 2.309504 GGAAGAAGGGGGTGGGGAG 61.310 68.421 0.00 0.00 0.00 4.30
955 1083 1.229984 AGAGGAAGAAGGGGGTGGG 60.230 63.158 0.00 0.00 0.00 4.61
958 1086 0.793617 TGAGAGAGGAAGAAGGGGGT 59.206 55.000 0.00 0.00 0.00 4.95
971 1110 0.851332 TGGGGAGGGAGAGTGAGAGA 60.851 60.000 0.00 0.00 0.00 3.10
973 1112 1.149782 AGTGGGGAGGGAGAGTGAGA 61.150 60.000 0.00 0.00 0.00 3.27
1044 1184 4.767255 CTGGTCTGCTGGCCGGAC 62.767 72.222 18.31 0.56 46.98 4.79
1217 1378 7.800380 GCACATCTATATCCAGAAAACGAAATG 59.200 37.037 0.00 0.00 0.00 2.32
1297 1458 8.340618 TGATCTTGTGATAAGAAAAGGGAAAG 57.659 34.615 0.00 0.00 32.19 2.62
1433 1608 5.704053 ACAGTTTATAAACAAGCCGCTAACT 59.296 36.000 26.06 2.19 41.30 2.24
1621 1801 8.820153 AGCAGGTAGTACTAAAATACAGTAGT 57.180 34.615 3.61 0.00 36.40 2.73
1626 1806 9.865321 CACTTTAGCAGGTAGTACTAAAATACA 57.135 33.333 3.61 0.00 35.93 2.29
1629 1809 9.601217 CATCACTTTAGCAGGTAGTACTAAAAT 57.399 33.333 3.61 0.00 35.93 1.82
1642 1822 5.330295 GTGAAATCAGCATCACTTTAGCAG 58.670 41.667 0.00 0.00 42.07 4.24
1656 1836 2.665537 GACACGAGAGCAGTGAAATCAG 59.334 50.000 3.20 0.00 41.83 2.90
1667 1847 1.214062 CTGACTGGGACACGAGAGC 59.786 63.158 0.00 0.00 0.00 4.09
1669 1849 0.178973 TTCCTGACTGGGACACGAGA 60.179 55.000 0.00 0.00 34.78 4.04
1671 1851 1.348064 ATTTCCTGACTGGGACACGA 58.652 50.000 0.00 0.00 34.78 4.35
1672 1852 2.496070 TCTATTTCCTGACTGGGACACG 59.504 50.000 0.00 0.00 34.78 4.49
1706 1886 2.094494 ACAGCGACAGTCAGTAGAATGG 60.094 50.000 0.41 0.00 43.78 3.16
1717 1897 0.874607 GACGTTTGGACAGCGACAGT 60.875 55.000 0.00 0.00 0.00 3.55
1723 1903 5.147162 CAAGATTTTAGACGTTTGGACAGC 58.853 41.667 0.00 0.00 0.00 4.40
1733 1914 5.536554 AGTGTCATGCAAGATTTTAGACG 57.463 39.130 0.00 0.00 0.00 4.18
1763 1946 6.072452 AGCTCTACAAAGTGCCAAGAAATTAC 60.072 38.462 0.00 0.00 42.05 1.89
1816 2003 8.827177 TTAGAACGTCTTCATTCATTACAACT 57.173 30.769 0.00 0.00 0.00 3.16
1818 2005 8.827177 ACTTAGAACGTCTTCATTCATTACAA 57.173 30.769 0.00 0.00 0.00 2.41
1825 2012 9.851043 GCATTATAACTTAGAACGTCTTCATTC 57.149 33.333 0.00 0.00 0.00 2.67
1829 2016 8.541312 GGAAGCATTATAACTTAGAACGTCTTC 58.459 37.037 0.00 0.00 0.00 2.87
1830 2017 7.222224 CGGAAGCATTATAACTTAGAACGTCTT 59.778 37.037 0.00 0.00 0.00 3.01
1831 2018 6.696148 CGGAAGCATTATAACTTAGAACGTCT 59.304 38.462 0.00 0.00 0.00 4.18
1832 2019 6.474751 ACGGAAGCATTATAACTTAGAACGTC 59.525 38.462 0.00 0.00 0.00 4.34
1833 2020 6.335777 ACGGAAGCATTATAACTTAGAACGT 58.664 36.000 0.00 0.00 0.00 3.99
1834 2021 6.823678 ACGGAAGCATTATAACTTAGAACG 57.176 37.500 0.00 0.00 0.00 3.95
1836 2023 9.692749 CATCTACGGAAGCATTATAACTTAGAA 57.307 33.333 0.00 0.00 0.00 2.10
1845 2057 6.412362 AGTCTTCATCTACGGAAGCATTAT 57.588 37.500 0.00 0.00 41.16 1.28
1856 2068 6.070710 ACCAAAGGAGGTAAGTCTTCATCTAC 60.071 42.308 0.00 0.00 40.98 2.59
1862 2074 4.353383 ACACCAAAGGAGGTAAGTCTTC 57.647 45.455 0.00 0.00 40.77 2.87
1869 2081 4.019681 CCTACATGAACACCAAAGGAGGTA 60.020 45.833 0.00 0.00 40.77 3.08
1874 2086 2.489329 CTGCCTACATGAACACCAAAGG 59.511 50.000 0.00 0.00 0.00 3.11
1948 2160 1.297689 GCTGCTGATGACCCTCACA 59.702 57.895 0.00 0.00 0.00 3.58
2058 2270 4.448210 ACACAAATAGGGTAGCGTTATGG 58.552 43.478 0.00 0.00 26.29 2.74
2069 2281 9.406828 GAAAAAGTAAGCTAAACACAAATAGGG 57.593 33.333 0.00 0.00 0.00 3.53
2084 2296 5.010282 TCCTTGATCAGGGAAAAAGTAAGC 58.990 41.667 23.38 0.00 44.12 3.09
2108 2320 4.111198 GCGAGATGGCTATAGATGTGATG 58.889 47.826 3.21 0.00 0.00 3.07
2140 2352 1.006102 ACCGGAGCTGTCTGAAACG 60.006 57.895 9.46 0.00 0.00 3.60
2162 2374 2.203669 TGCTGCAGGGCATTTGGT 60.204 55.556 17.12 0.00 38.13 3.67
2266 2478 4.139420 CTTGAGTTGCTCGGCGCG 62.139 66.667 0.00 0.00 43.27 6.86
2296 2508 3.263503 CTCCTCGACCGTTCGCACA 62.264 63.158 0.00 0.00 45.46 4.57
2305 2517 1.079750 GTTGCTGTCCTCCTCGACC 60.080 63.158 0.00 0.00 31.35 4.79
2345 2557 3.823330 GCTGCTGGTGCTGGCATC 61.823 66.667 0.00 0.00 40.48 3.91
2353 2565 0.595095 GGAACTCAAAGCTGCTGGTG 59.405 55.000 1.35 5.00 0.00 4.17
2422 2634 1.902508 CACTTGGAGGAAGCCTGTCTA 59.097 52.381 0.00 0.00 34.68 2.59
2561 2776 1.739049 CGTGGTGTTTGGGCACAAT 59.261 52.632 0.06 0.00 40.89 2.71
2680 2895 1.447317 CTGCGTGCCTGACCAACTTT 61.447 55.000 0.00 0.00 0.00 2.66
2698 2913 2.570752 ACCTTGATCTGCACAGACATCT 59.429 45.455 1.71 0.00 40.75 2.90
2737 2952 3.895232 TCAGCTTGACCCTTCTGATAC 57.105 47.619 0.00 0.00 31.35 2.24
2767 2982 2.965572 TGCAGGGCTTAATTGCAATC 57.034 45.000 13.38 0.00 44.13 2.67
2829 3044 5.510671 TGACAGAAATCGAAGCAAGAAAAC 58.489 37.500 0.00 0.00 0.00 2.43
2836 3051 3.727726 TCAGTTGACAGAAATCGAAGCA 58.272 40.909 0.00 0.00 0.00 3.91
2837 3052 4.935885 ATCAGTTGACAGAAATCGAAGC 57.064 40.909 0.00 0.00 0.00 3.86
2998 3213 5.817816 AGGAGTTGATGGTATCGAACAATTC 59.182 40.000 0.00 0.00 0.00 2.17
3061 3276 5.114764 TGAAATAAGGACCATCATCTGCA 57.885 39.130 0.00 0.00 0.00 4.41
3107 3322 3.265221 AGCCTGATTTCATCCTCTGACAA 59.735 43.478 0.00 0.00 32.17 3.18
3148 3363 0.323629 GTTGTACACCTAGGGCAGCA 59.676 55.000 14.81 4.00 0.00 4.41
3184 3399 0.379669 CTTTGCTAGCCCATGAAGCG 59.620 55.000 13.29 0.00 39.14 4.68
3199 3414 7.202526 CAGAGACTAATTCTAGCTCCTCTTTG 58.797 42.308 0.00 0.00 33.22 2.77
3229 3444 2.028778 AGATCAGCGATGCTCGGC 59.971 61.111 0.00 0.00 40.84 5.54
3298 3513 5.732647 CCGTGCTGTATGTTTAGAATTTTCG 59.267 40.000 0.00 0.00 0.00 3.46
3313 3528 4.830600 TCTGATGGAATATACCGTGCTGTA 59.169 41.667 0.00 0.00 0.00 2.74
3333 3548 2.952978 ACGAAGGGTAGCAGATAGTCTG 59.047 50.000 2.65 2.65 46.90 3.51
3334 3549 3.300239 ACGAAGGGTAGCAGATAGTCT 57.700 47.619 0.00 0.00 0.00 3.24
3344 3563 5.295152 AGTAGAACAAACAACGAAGGGTAG 58.705 41.667 0.00 0.00 0.00 3.18
3531 3750 1.912043 AGTGGAAATGCACCTCTAGCT 59.088 47.619 1.14 0.00 30.86 3.32
3532 3751 2.409948 AGTGGAAATGCACCTCTAGC 57.590 50.000 1.14 0.00 30.86 3.42
3583 3808 4.152402 GCATTCAGAGTATGTGTTCGTGTT 59.848 41.667 0.00 0.00 0.00 3.32
3584 3809 3.679980 GCATTCAGAGTATGTGTTCGTGT 59.320 43.478 0.00 0.00 0.00 4.49
3588 3813 6.615264 ATGATGCATTCAGAGTATGTGTTC 57.385 37.500 0.00 0.00 37.89 3.18
3599 3824 7.871973 AGCTACTAAAGAGTATGATGCATTCAG 59.128 37.037 0.00 0.00 37.53 3.02
3644 3880 1.661112 GCGTTCCTGTCATAGAACAGC 59.339 52.381 13.43 12.85 44.34 4.40
3645 3881 1.920574 CGCGTTCCTGTCATAGAACAG 59.079 52.381 0.00 0.00 45.10 3.16
3655 3891 2.981977 TTTTCTCCGCGCGTTCCTGT 62.982 55.000 29.95 0.00 0.00 4.00
3781 4017 1.899437 CGGCCTTCTGAACTGCCCTA 61.899 60.000 16.44 0.00 40.87 3.53
3821 4057 2.040178 GATACGTGACCCAGGAATCCT 58.960 52.381 0.00 0.00 0.00 3.24
3829 4065 1.686587 CAGCATAGGATACGTGACCCA 59.313 52.381 0.00 0.00 46.39 4.51
3850 4086 2.435372 AAGGTTCACAGAAACAGCCA 57.565 45.000 0.00 0.00 0.00 4.75
3856 4092 4.523083 ACAAGTGCTAAGGTTCACAGAAA 58.477 39.130 0.00 0.00 35.76 2.52
3884 4125 9.125026 CCTCAATCATATTTTAACAGGCTAGTT 57.875 33.333 7.34 7.34 35.55 2.24
3912 4157 7.592164 GCTGACTATAGAACGAGGAAATTAGAC 59.408 40.741 6.78 0.00 0.00 2.59
3976 4221 6.381133 TGTGTGTACATCTGAATCACCTAGAT 59.619 38.462 0.00 0.00 39.09 1.98
4028 4275 4.752101 AGAACTTGCACATCTCACACTAAC 59.248 41.667 0.00 0.00 0.00 2.34
4039 4286 5.581126 TCAGAAAACAAGAACTTGCACAT 57.419 34.783 13.50 0.00 44.03 3.21
4073 4321 4.534797 ACGAACAGCTTATAGGTAGGAGT 58.465 43.478 0.00 0.00 0.00 3.85
4074 4322 5.067413 TGAACGAACAGCTTATAGGTAGGAG 59.933 44.000 0.00 0.00 0.00 3.69
4075 4323 4.951715 TGAACGAACAGCTTATAGGTAGGA 59.048 41.667 0.00 0.00 0.00 2.94
4076 4324 5.163540 ACTGAACGAACAGCTTATAGGTAGG 60.164 44.000 11.90 0.00 41.06 3.18
4077 4325 5.744345 CACTGAACGAACAGCTTATAGGTAG 59.256 44.000 11.90 0.00 41.06 3.18
4078 4326 5.393787 CCACTGAACGAACAGCTTATAGGTA 60.394 44.000 11.90 0.00 41.06 3.08
4079 4327 4.495422 CACTGAACGAACAGCTTATAGGT 58.505 43.478 11.90 0.00 41.06 3.08
4098 4346 1.530013 GCTCACATTGCAAGGCCACT 61.530 55.000 11.69 0.00 0.00 4.00
4099 4347 1.080298 GCTCACATTGCAAGGCCAC 60.080 57.895 11.69 0.00 0.00 5.01
4100 4348 1.114119 TTGCTCACATTGCAAGGCCA 61.114 50.000 11.69 0.67 44.24 5.36
4105 4353 3.257469 TGGTTTTTGCTCACATTGCAA 57.743 38.095 0.00 0.00 46.90 4.08
4106 4354 2.975732 TGGTTTTTGCTCACATTGCA 57.024 40.000 0.00 0.00 38.80 4.08
4107 4355 4.319694 GGAAATGGTTTTTGCTCACATTGC 60.320 41.667 0.00 0.00 32.60 3.56
4108 4356 4.815308 TGGAAATGGTTTTTGCTCACATTG 59.185 37.500 0.00 0.00 32.60 2.82
4116 4408 4.630111 TCAGTCATGGAAATGGTTTTTGC 58.370 39.130 0.00 0.00 0.00 3.68
4199 4492 5.368989 GGTGACTTTATGTAAGATCCCAGG 58.631 45.833 0.00 0.00 37.30 4.45
4239 4532 1.081892 CCAAGACAGATGAACAGCCG 58.918 55.000 0.00 0.00 0.00 5.52
4291 4605 2.815647 GTACTGGCGCACTGCTCC 60.816 66.667 10.83 2.83 45.43 4.70
4302 4616 1.419922 GCGTCATGCGTTGTACTGG 59.580 57.895 10.44 0.00 43.66 4.00
4373 4690 6.406849 CCTCTTCTATTCCATAGCTATGAGCC 60.407 46.154 31.14 0.00 43.77 4.70
4403 4723 2.437359 ATCAGCTGCTGCCCGTTC 60.437 61.111 24.38 0.00 40.80 3.95
4404 4724 2.749044 CATCAGCTGCTGCCCGTT 60.749 61.111 24.38 4.16 40.80 4.44
4405 4725 3.677284 CTCATCAGCTGCTGCCCGT 62.677 63.158 24.38 7.70 40.80 5.28
4420 4740 2.234661 TCCTCGAACCTCGTAGTACTCA 59.765 50.000 0.00 0.00 41.35 3.41
4421 4741 2.898705 TCCTCGAACCTCGTAGTACTC 58.101 52.381 0.00 0.00 41.35 2.59
4422 4742 3.340814 TTCCTCGAACCTCGTAGTACT 57.659 47.619 0.00 0.00 41.35 2.73
4423 4743 3.438434 ACTTTCCTCGAACCTCGTAGTAC 59.562 47.826 0.00 0.00 41.35 2.73
4424 4744 3.679389 ACTTTCCTCGAACCTCGTAGTA 58.321 45.455 0.00 0.00 41.35 1.82
4425 4745 2.512705 ACTTTCCTCGAACCTCGTAGT 58.487 47.619 0.00 0.00 41.35 2.73
4426 4746 3.688673 AGTACTTTCCTCGAACCTCGTAG 59.311 47.826 0.00 0.00 41.35 3.51
4469 4789 1.662629 CAGCGAGTCCATAGTTTGCAG 59.337 52.381 0.00 0.00 0.00 4.41
4493 4813 2.507992 CTGGAAGCCTCGCTGACG 60.508 66.667 0.00 0.00 39.62 4.35
4548 4868 1.154016 CCACCGAGCACTGACTACG 60.154 63.158 0.00 0.00 0.00 3.51
4592 4912 3.797353 GCATGGAAGGGGCGGAGA 61.797 66.667 0.00 0.00 0.00 3.71
4639 4959 6.614160 GGGATCAAATTGCCAAAATTTTGAG 58.386 36.000 28.44 19.63 40.55 3.02
4649 5267 1.265236 AAAGCGGGATCAAATTGCCA 58.735 45.000 0.00 0.00 0.00 4.92
4783 5401 2.582728 TTGGCGGTAAGGTATACACG 57.417 50.000 5.01 2.45 0.00 4.49
4784 5402 2.610833 GCTTTGGCGGTAAGGTATACAC 59.389 50.000 5.01 0.00 0.00 2.90
4814 5432 2.359848 TGTCTGTTCGTTCTCGAGGAAA 59.640 45.455 13.56 0.00 46.81 3.13
4815 5433 1.951602 TGTCTGTTCGTTCTCGAGGAA 59.048 47.619 13.56 5.52 46.81 3.36
4820 5438 8.556517 TTGTTATATATGTCTGTTCGTTCTCG 57.443 34.615 0.00 0.00 38.55 4.04
4840 5980 6.150976 CAGCTATGTCCCTCACATTTTTGTTA 59.849 38.462 0.00 0.00 43.89 2.41
4843 5983 4.676196 GCAGCTATGTCCCTCACATTTTTG 60.676 45.833 0.00 0.00 43.89 2.44
4844 5984 3.445096 GCAGCTATGTCCCTCACATTTTT 59.555 43.478 0.00 0.00 43.89 1.94
4849 5989 1.257750 ACGCAGCTATGTCCCTCACA 61.258 55.000 0.00 0.00 40.18 3.58
4878 6018 7.590279 CATGTACGTTTTGACTCCCTATTTTT 58.410 34.615 0.00 0.00 0.00 1.94
4879 6019 6.349033 GCATGTACGTTTTGACTCCCTATTTT 60.349 38.462 0.00 0.00 0.00 1.82
4898 6038 3.071837 TCAGCGTCCGGGCATGTA 61.072 61.111 6.96 0.00 34.64 2.29
4925 6065 3.142838 CCCCTCAAATGCCCGCTG 61.143 66.667 0.00 0.00 0.00 5.18
4929 6070 1.273986 ATTTGGCCCCTCAAATGCCC 61.274 55.000 0.00 0.00 43.31 5.36
4942 6083 1.934849 GCCGGACTGAACAAATTTGGC 60.935 52.381 21.74 13.53 0.00 4.52
4967 6108 4.520846 CTCAAATGCCCGCGACGC 62.521 66.667 8.23 10.49 0.00 5.19
4968 6109 3.864686 CCTCAAATGCCCGCGACG 61.865 66.667 8.23 0.00 0.00 5.12
4969 6110 3.508840 CCCTCAAATGCCCGCGAC 61.509 66.667 8.23 0.00 0.00 5.19
4970 6111 4.794648 CCCCTCAAATGCCCGCGA 62.795 66.667 8.23 0.00 0.00 5.87
4973 6114 4.757355 TGGCCCCTCAAATGCCCG 62.757 66.667 0.00 0.00 44.72 6.13
4974 6115 1.273986 ATTTGGCCCCTCAAATGCCC 61.274 55.000 0.00 0.00 43.31 5.36
4975 6116 0.620030 AATTTGGCCCCTCAAATGCC 59.380 50.000 0.00 0.00 43.93 4.40
4976 6117 2.086094 CAAATTTGGCCCCTCAAATGC 58.914 47.619 10.49 0.00 43.93 3.56
4977 6118 3.421919 ACAAATTTGGCCCCTCAAATG 57.578 42.857 21.74 0.00 43.93 2.32
4978 6119 3.393941 TGAACAAATTTGGCCCCTCAAAT 59.606 39.130 21.74 0.00 45.86 2.32
4979 6120 2.774234 TGAACAAATTTGGCCCCTCAAA 59.226 40.909 21.74 0.00 40.37 2.69
4980 6121 2.402564 TGAACAAATTTGGCCCCTCAA 58.597 42.857 21.74 0.00 0.00 3.02
4981 6122 2.094100 TGAACAAATTTGGCCCCTCA 57.906 45.000 21.74 12.45 0.00 3.86
4982 6123 3.701205 ATTGAACAAATTTGGCCCCTC 57.299 42.857 21.74 10.33 0.00 4.30
4983 6124 3.056179 CGTATTGAACAAATTTGGCCCCT 60.056 43.478 21.74 6.60 0.00 4.79
4984 6125 3.258228 CGTATTGAACAAATTTGGCCCC 58.742 45.455 21.74 8.40 0.00 5.80
4985 6126 3.258228 CCGTATTGAACAAATTTGGCCC 58.742 45.455 21.74 10.65 0.00 5.80
4986 6127 2.670905 GCCGTATTGAACAAATTTGGCC 59.329 45.455 21.74 12.93 39.59 5.36
4987 6128 3.367630 CAGCCGTATTGAACAAATTTGGC 59.632 43.478 21.74 13.53 43.00 4.52
4988 6129 4.555262 ACAGCCGTATTGAACAAATTTGG 58.445 39.130 21.74 4.79 0.00 3.28
4989 6130 6.607689 TCTACAGCCGTATTGAACAAATTTG 58.392 36.000 16.67 16.67 0.00 2.32
4990 6131 6.811253 TCTACAGCCGTATTGAACAAATTT 57.189 33.333 0.00 0.00 0.00 1.82
4991 6132 6.677920 GCATCTACAGCCGTATTGAACAAATT 60.678 38.462 0.00 0.00 0.00 1.82
4992 6133 5.220854 GCATCTACAGCCGTATTGAACAAAT 60.221 40.000 0.00 0.00 0.00 2.32
4993 6134 4.094294 GCATCTACAGCCGTATTGAACAAA 59.906 41.667 0.00 0.00 0.00 2.83
4994 6135 3.621268 GCATCTACAGCCGTATTGAACAA 59.379 43.478 0.00 0.00 0.00 2.83
4995 6136 3.118775 AGCATCTACAGCCGTATTGAACA 60.119 43.478 0.00 0.00 0.00 3.18
4996 6137 3.458189 AGCATCTACAGCCGTATTGAAC 58.542 45.455 0.00 0.00 0.00 3.18
4997 6138 3.717707 GAGCATCTACAGCCGTATTGAA 58.282 45.455 0.00 0.00 0.00 2.69
4998 6139 3.371102 GAGCATCTACAGCCGTATTGA 57.629 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.