Multiple sequence alignment - TraesCS7A01G028100

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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 TraesCS7A01G028100 chr7A 100.000 2612 0 0 1 2612 11264568 11267179 0.000000e+00 4824
1 TraesCS7A01G028100 chr7A 97.451 667 17 0 1 667 3997367 3996701 0.000000e+00 1138
2 TraesCS7A01G028100 chr4A 90.723 1175 67 22 667 1803 726089720 726088550 0.000000e+00 1528
3 TraesCS7A01G028100 chr4A 91.121 473 32 7 1946 2415 726088183 726087718 1.320000e-177 632
4 TraesCS7A01G028100 chr4A 97.980 198 4 0 2415 2612 159059824 159059627 6.920000e-91 344
5 TraesCS7A01G028100 chr4A 91.597 119 6 2 1787 1903 726088538 726088422 7.480000e-36 161
6 TraesCS7A01G028100 chr2D 98.505 669 9 1 1 668 383550402 383551070 0.000000e+00 1179
7 TraesCS7A01G028100 chr7B 97.297 666 18 0 1 666 304088216 304087551 0.000000e+00 1131
8 TraesCS7A01G028100 chr7B 97.006 668 19 1 1 668 483806140 483806806 0.000000e+00 1122
9 TraesCS7A01G028100 chr2B 97.147 666 18 1 1 666 370340996 370341660 0.000000e+00 1123
10 TraesCS7A01G028100 chr1D 97.001 667 20 0 1 667 301219002 301218336 0.000000e+00 1122
11 TraesCS7A01G028100 chr4B 96.856 668 20 1 1 668 47022713 47022047 0.000000e+00 1116
12 TraesCS7A01G028100 chrUn 96.852 667 20 1 1 667 401124516 401125181 0.000000e+00 1114
13 TraesCS7A01G028100 chr5B 96.707 668 21 1 1 668 9839756 9839090 0.000000e+00 1110
14 TraesCS7A01G028100 chr5B 94.382 178 8 2 2239 2415 672836933 672836757 3.310000e-69 272
15 TraesCS7A01G028100 chr5A 97.525 202 5 0 2411 2612 32542505 32542706 1.920000e-91 346
16 TraesCS7A01G028100 chr6D 97.980 198 4 0 2415 2612 259329045 259329242 6.920000e-91 344
17 TraesCS7A01G028100 chr6D 97.970 197 4 0 2416 2612 259294770 259294966 2.490000e-90 342
18 TraesCS7A01G028100 chr6A 97.980 198 4 0 2415 2612 612817652 612817849 6.920000e-91 344
19 TraesCS7A01G028100 chr3B 97.030 202 5 1 2411 2612 297459245 297459045 3.220000e-89 339
20 TraesCS7A01G028100 chr3B 95.261 211 10 0 2402 2612 127400378 127400168 4.170000e-88 335
21 TraesCS7A01G028100 chr1A 96.569 204 7 0 2409 2612 169994662 169994459 3.220000e-89 339
22 TraesCS7A01G028100 chr2A 95.673 208 7 2 2405 2612 650856493 650856698 1.500000e-87 333


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 TraesCS7A01G028100 chr7A 11264568 11267179 2611 False 4824.000000 4824 100.000 1 2612 1 chr7A.!!$F1 2611
1 TraesCS7A01G028100 chr7A 3996701 3997367 666 True 1138.000000 1138 97.451 1 667 1 chr7A.!!$R1 666
2 TraesCS7A01G028100 chr4A 726087718 726089720 2002 True 773.666667 1528 91.147 667 2415 3 chr4A.!!$R2 1748
3 TraesCS7A01G028100 chr2D 383550402 383551070 668 False 1179.000000 1179 98.505 1 668 1 chr2D.!!$F1 667
4 TraesCS7A01G028100 chr7B 304087551 304088216 665 True 1131.000000 1131 97.297 1 666 1 chr7B.!!$R1 665
5 TraesCS7A01G028100 chr7B 483806140 483806806 666 False 1122.000000 1122 97.006 1 668 1 chr7B.!!$F1 667
6 TraesCS7A01G028100 chr2B 370340996 370341660 664 False 1123.000000 1123 97.147 1 666 1 chr2B.!!$F1 665
7 TraesCS7A01G028100 chr1D 301218336 301219002 666 True 1122.000000 1122 97.001 1 667 1 chr1D.!!$R1 666
8 TraesCS7A01G028100 chr4B 47022047 47022713 666 True 1116.000000 1116 96.856 1 668 1 chr4B.!!$R1 667
9 TraesCS7A01G028100 chrUn 401124516 401125181 665 False 1114.000000 1114 96.852 1 667 1 chrUn.!!$F1 666
10 TraesCS7A01G028100 chr5B 9839090 9839756 666 True 1110.000000 1110 96.707 1 668 1 chr5B.!!$R1 667

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
687 688 2.450476 ACACCGTAATACCTCGTTCCT 58.55 47.619 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 2840 0.032515 TCAGCCCGGGTTCTCTATCA 60.033 55.0 24.63 0.0 0.0 2.15 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 2.849943 ACAGCCTGGTATTTATGGTGGA 59.150 45.455 0.00 0.00 0.00 4.02
685 686 5.596268 AAAAACACCGTAATACCTCGTTC 57.404 39.130 0.00 0.00 0.00 3.95
686 687 2.947448 ACACCGTAATACCTCGTTCC 57.053 50.000 0.00 0.00 0.00 3.62
687 688 2.450476 ACACCGTAATACCTCGTTCCT 58.550 47.619 0.00 0.00 0.00 3.36
703 704 4.189639 GTTCCTACCAGATGAACGACTT 57.810 45.455 0.00 0.00 30.26 3.01
857 897 9.597170 CATGATCTAGCTACATACTGCATTTAT 57.403 33.333 0.00 0.00 0.00 1.40
899 939 8.276252 TGTTATAAATAAAGCTCAACCTCCAC 57.724 34.615 0.00 0.00 0.00 4.02
927 967 4.403752 CCATCCATCTCTACTCTCACACAA 59.596 45.833 0.00 0.00 0.00 3.33
953 993 7.964293 ACCTTCCATATCCATTTATCTCTACCT 59.036 37.037 0.00 0.00 0.00 3.08
955 995 7.979786 TCCATATCCATTTATCTCTACCTCC 57.020 40.000 0.00 0.00 0.00 4.30
973 1013 4.018050 ACCTCCCTCTGCTTCATTACAATT 60.018 41.667 0.00 0.00 0.00 2.32
979 1019 5.416952 CCTCTGCTTCATTACAATTCAAGGT 59.583 40.000 0.00 0.00 0.00 3.50
998 1038 3.707102 AGGTTTCTAGCTAGCCTTGTAGG 59.293 47.826 16.35 0.00 38.80 3.18
1103 1143 1.518903 GGCTCTGTCAGTGGCAAACC 61.519 60.000 20.12 0.00 34.84 3.27
1114 1154 4.662961 GCAAACCCAAGGCGGCAC 62.663 66.667 13.08 0.00 0.00 5.01
1146 1186 1.589716 AAGCATGCAAGAACGCCTCC 61.590 55.000 21.98 0.00 0.00 4.30
1157 1197 3.449227 CGCCTCCGACTACTGGCA 61.449 66.667 0.00 0.00 45.13 4.92
1198 1238 0.107831 TTTGTCAACCCTCCAGTCCG 59.892 55.000 0.00 0.00 0.00 4.79
1234 1274 2.909217 AGGCTAAGAACCTCCTTGACT 58.091 47.619 0.00 0.00 28.76 3.41
1296 1336 1.909700 AGGTTGGCGTTGATGTCAAT 58.090 45.000 0.00 0.00 35.65 2.57
1353 1393 1.317613 TGCATGCTCTCCGTTTTTGT 58.682 45.000 20.33 0.00 0.00 2.83
1375 1415 1.183549 GGTGGACTATGAGACCGTGT 58.816 55.000 0.00 0.00 32.61 4.49
1429 1469 3.092301 AGGGAATACCAAGCTGAAAAGC 58.908 45.455 0.00 0.00 43.89 3.51
1431 1471 2.488153 GGAATACCAAGCTGAAAAGCGT 59.512 45.455 0.00 0.00 36.63 5.07
1475 1515 2.118313 CAATGTGTGGATCTGGCAGA 57.882 50.000 21.19 21.19 0.00 4.26
1477 1517 0.107312 ATGTGTGGATCTGGCAGAGC 60.107 55.000 23.95 23.95 0.00 4.09
1482 1522 1.415659 GTGGATCTGGCAGAGCATACT 59.584 52.381 31.27 10.45 30.96 2.12
1483 1523 1.690893 TGGATCTGGCAGAGCATACTC 59.309 52.381 31.27 18.21 43.82 2.59
1555 1595 5.319453 TGATCAAAGAAAATGAGGAGCTGT 58.681 37.500 0.00 0.00 0.00 4.40
1567 1607 1.376942 GAGCTGTGCATGCTGGTCT 60.377 57.895 20.33 10.76 41.30 3.85
1604 1644 5.418524 ACTTGCTTGCACCATATAATGTTCA 59.581 36.000 0.00 0.00 0.00 3.18
1654 1694 6.821160 TGCAATAAAGAGATGTAATTCCGTGA 59.179 34.615 0.00 0.00 0.00 4.35
1657 1697 8.543774 CAATAAAGAGATGTAATTCCGTGACTC 58.456 37.037 0.00 0.00 0.00 3.36
1684 1724 7.877612 GTGGGTTCTTTTCATGTAATTCCATTT 59.122 33.333 0.00 0.00 0.00 2.32
1686 1726 9.366216 GGGTTCTTTTCATGTAATTCCATTTAC 57.634 33.333 0.00 0.00 33.56 2.01
1691 1731 9.573133 CTTTTCATGTAATTCCATTTACTGTCC 57.427 33.333 0.00 0.00 33.99 4.02
1692 1732 8.642935 TTTCATGTAATTCCATTTACTGTCCA 57.357 30.769 0.00 0.00 33.99 4.02
1693 1733 8.642935 TTCATGTAATTCCATTTACTGTCCAA 57.357 30.769 0.00 0.00 33.99 3.53
1694 1734 8.821686 TCATGTAATTCCATTTACTGTCCAAT 57.178 30.769 0.00 0.00 33.99 3.16
1695 1735 9.253832 TCATGTAATTCCATTTACTGTCCAATT 57.746 29.630 0.00 0.00 33.99 2.32
1696 1736 9.520204 CATGTAATTCCATTTACTGTCCAATTC 57.480 33.333 0.00 0.00 33.99 2.17
1698 1738 7.893302 TGTAATTCCATTTACTGTCCAATTCCT 59.107 33.333 0.00 0.00 33.99 3.36
1700 1740 4.855340 TCCATTTACTGTCCAATTCCTCC 58.145 43.478 0.00 0.00 0.00 4.30
1701 1741 4.290985 TCCATTTACTGTCCAATTCCTCCA 59.709 41.667 0.00 0.00 0.00 3.86
1702 1742 4.399303 CCATTTACTGTCCAATTCCTCCAC 59.601 45.833 0.00 0.00 0.00 4.02
1703 1743 4.993705 TTTACTGTCCAATTCCTCCACT 57.006 40.909 0.00 0.00 0.00 4.00
1704 1744 2.867109 ACTGTCCAATTCCTCCACTG 57.133 50.000 0.00 0.00 0.00 3.66
1705 1745 1.271597 ACTGTCCAATTCCTCCACTGC 60.272 52.381 0.00 0.00 0.00 4.40
1706 1746 1.004044 CTGTCCAATTCCTCCACTGCT 59.996 52.381 0.00 0.00 0.00 4.24
1707 1747 1.271543 TGTCCAATTCCTCCACTGCTG 60.272 52.381 0.00 0.00 0.00 4.41
1708 1748 0.322816 TCCAATTCCTCCACTGCTGC 60.323 55.000 0.00 0.00 0.00 5.25
1709 1749 0.609957 CCAATTCCTCCACTGCTGCA 60.610 55.000 0.88 0.88 0.00 4.41
1770 1811 9.862371 CAATCTATATACTTGGTAGCCTTGTAG 57.138 37.037 0.00 0.00 0.00 2.74
1790 1831 1.737793 GTCCTATTGGTGCCTTGTTCG 59.262 52.381 0.00 0.00 34.23 3.95
1808 1877 2.276201 TCGTATGGAAAGTTCATGCCG 58.724 47.619 0.00 0.00 0.00 5.69
1818 1887 4.946784 AAGTTCATGCCGTTTGATCTAC 57.053 40.909 0.00 0.00 0.00 2.59
1824 1893 1.072489 TGCCGTTTGATCTACCCACAA 59.928 47.619 0.00 0.00 0.00 3.33
1825 1894 1.737793 GCCGTTTGATCTACCCACAAG 59.262 52.381 0.00 0.00 0.00 3.16
1859 1928 4.880759 TGATGCCATGTTAAAACACTTGG 58.119 39.130 10.00 10.00 42.51 3.61
1875 1944 1.074775 TGGTTCCTCCAAGCGCATT 59.925 52.632 11.47 0.00 44.12 3.56
1899 2006 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
1902 2009 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
1915 2022 2.292292 GAGAGAGAGGCGTGGATTAGAC 59.708 54.545 0.00 0.00 0.00 2.59
1928 2125 4.567159 GTGGATTAGACGTAGAGCCAAAAG 59.433 45.833 4.15 0.00 0.00 2.27
1931 2128 5.873164 GGATTAGACGTAGAGCCAAAAGAAA 59.127 40.000 0.00 0.00 0.00 2.52
1932 2129 6.370718 GGATTAGACGTAGAGCCAAAAGAAAA 59.629 38.462 0.00 0.00 0.00 2.29
1959 2226 5.865085 TCTTTATCGGATATTCACAAGGGG 58.135 41.667 0.00 0.00 0.00 4.79
1974 2241 2.828549 GGGGGCATACGGCTGTTG 60.829 66.667 1.99 3.40 44.01 3.33
2078 2345 5.796502 TTTATGGTTCTCCCTTGAGGAAT 57.203 39.130 0.00 0.00 46.94 3.01
2084 2351 7.278724 TGGTTCTCCCTTGAGGAATTATTTA 57.721 36.000 0.00 0.00 46.94 1.40
2173 2440 2.231478 TGAGGGTCAACTTGATCGACTC 59.769 50.000 0.00 0.00 0.00 3.36
2253 2520 9.472361 TCTACGCAAATTAGAAGTATTGATACC 57.528 33.333 0.00 0.00 33.79 2.73
2262 2529 9.836179 ATTAGAAGTATTGATACCAGGAGATCT 57.164 33.333 0.00 0.00 33.79 2.75
2274 2541 6.380079 ACCAGGAGATCTAAAATCAACACT 57.620 37.500 0.00 0.00 0.00 3.55
2406 2673 9.593134 CATATACCTATTTGTGAATAGAGAGGC 57.407 37.037 7.54 0.00 44.95 4.70
2416 2683 8.893219 TTGTGAATAGAGAGGCATTAATACTG 57.107 34.615 0.00 0.00 0.00 2.74
2417 2684 8.023021 TGTGAATAGAGAGGCATTAATACTGT 57.977 34.615 0.00 0.00 0.00 3.55
2418 2685 8.144478 TGTGAATAGAGAGGCATTAATACTGTC 58.856 37.037 7.86 7.86 0.00 3.51
2419 2686 8.144478 GTGAATAGAGAGGCATTAATACTGTCA 58.856 37.037 14.78 5.70 0.00 3.58
2420 2687 8.363390 TGAATAGAGAGGCATTAATACTGTCAG 58.637 37.037 14.78 0.00 0.00 3.51
2421 2688 5.543507 AGAGAGGCATTAATACTGTCAGG 57.456 43.478 14.78 0.00 0.00 3.86
2422 2689 5.211973 AGAGAGGCATTAATACTGTCAGGA 58.788 41.667 14.78 0.00 0.00 3.86
2423 2690 5.069781 AGAGAGGCATTAATACTGTCAGGAC 59.930 44.000 14.78 0.00 0.00 3.85
2424 2691 4.101741 AGAGGCATTAATACTGTCAGGACC 59.898 45.833 4.53 0.00 0.00 4.46
2425 2692 3.136626 AGGCATTAATACTGTCAGGACCC 59.863 47.826 4.53 0.00 0.00 4.46
2426 2693 3.477530 GCATTAATACTGTCAGGACCCC 58.522 50.000 4.53 0.00 0.00 4.95
2427 2694 3.728845 CATTAATACTGTCAGGACCCCG 58.271 50.000 4.53 0.00 0.00 5.73
2428 2695 2.832643 TAATACTGTCAGGACCCCGA 57.167 50.000 4.53 0.00 0.00 5.14
2429 2696 2.176247 AATACTGTCAGGACCCCGAT 57.824 50.000 4.53 0.00 0.00 4.18
2430 2697 1.705873 ATACTGTCAGGACCCCGATC 58.294 55.000 4.53 0.00 0.00 3.69
2431 2698 0.396695 TACTGTCAGGACCCCGATCC 60.397 60.000 4.53 0.00 39.28 3.36
2437 2704 3.149038 GGACCCCGATCCTAAGCC 58.851 66.667 0.00 0.00 35.68 4.35
2438 2705 1.764854 GGACCCCGATCCTAAGCCA 60.765 63.158 0.00 0.00 35.68 4.75
2439 2706 1.446366 GACCCCGATCCTAAGCCAC 59.554 63.158 0.00 0.00 0.00 5.01
2440 2707 1.306654 ACCCCGATCCTAAGCCACA 60.307 57.895 0.00 0.00 0.00 4.17
2441 2708 0.694444 ACCCCGATCCTAAGCCACAT 60.694 55.000 0.00 0.00 0.00 3.21
2442 2709 0.035458 CCCCGATCCTAAGCCACATC 59.965 60.000 0.00 0.00 0.00 3.06
2443 2710 0.319900 CCCGATCCTAAGCCACATCG 60.320 60.000 0.00 0.00 38.28 3.84
2444 2711 0.673985 CCGATCCTAAGCCACATCGA 59.326 55.000 1.83 0.00 40.48 3.59
2445 2712 1.273606 CCGATCCTAAGCCACATCGAT 59.726 52.381 0.00 0.00 40.48 3.59
2446 2713 2.600731 CGATCCTAAGCCACATCGATC 58.399 52.381 0.00 0.00 40.48 3.69
2447 2714 2.230025 CGATCCTAAGCCACATCGATCT 59.770 50.000 0.00 0.00 40.48 2.75
2448 2715 3.440522 CGATCCTAAGCCACATCGATCTA 59.559 47.826 0.00 0.00 40.48 1.98
2449 2716 4.438065 CGATCCTAAGCCACATCGATCTAG 60.438 50.000 0.00 0.00 40.48 2.43
2450 2717 2.558795 TCCTAAGCCACATCGATCTAGC 59.441 50.000 0.00 0.00 0.00 3.42
2451 2718 2.297315 CCTAAGCCACATCGATCTAGCA 59.703 50.000 11.43 0.00 0.00 3.49
2452 2719 3.056250 CCTAAGCCACATCGATCTAGCAT 60.056 47.826 11.43 3.67 0.00 3.79
2453 2720 2.452295 AGCCACATCGATCTAGCATG 57.548 50.000 11.43 0.00 0.00 4.06
2454 2721 1.690893 AGCCACATCGATCTAGCATGT 59.309 47.619 11.43 0.00 0.00 3.21
2455 2722 2.893489 AGCCACATCGATCTAGCATGTA 59.107 45.455 11.43 0.00 0.00 2.29
2456 2723 3.321968 AGCCACATCGATCTAGCATGTAA 59.678 43.478 11.43 0.00 0.00 2.41
2457 2724 3.430218 GCCACATCGATCTAGCATGTAAC 59.570 47.826 0.00 0.00 0.00 2.50
2458 2725 4.620982 CCACATCGATCTAGCATGTAACA 58.379 43.478 0.00 0.00 0.00 2.41
2459 2726 4.445718 CCACATCGATCTAGCATGTAACAC 59.554 45.833 0.00 0.00 0.00 3.32
2460 2727 5.043248 CACATCGATCTAGCATGTAACACA 58.957 41.667 0.00 0.00 0.00 3.72
2461 2728 5.693555 CACATCGATCTAGCATGTAACACAT 59.306 40.000 0.00 0.00 39.91 3.21
2462 2729 5.923114 ACATCGATCTAGCATGTAACACATC 59.077 40.000 0.00 0.00 36.53 3.06
2463 2730 5.514274 TCGATCTAGCATGTAACACATCA 57.486 39.130 0.00 0.00 36.53 3.07
2464 2731 6.089249 TCGATCTAGCATGTAACACATCAT 57.911 37.500 0.00 0.00 36.53 2.45
2465 2732 7.214467 TCGATCTAGCATGTAACACATCATA 57.786 36.000 0.00 0.00 36.53 2.15
2466 2733 7.830739 TCGATCTAGCATGTAACACATCATAT 58.169 34.615 0.00 0.00 36.53 1.78
2467 2734 7.970614 TCGATCTAGCATGTAACACATCATATC 59.029 37.037 0.00 0.00 36.53 1.63
2468 2735 7.756722 CGATCTAGCATGTAACACATCATATCA 59.243 37.037 0.00 0.00 36.53 2.15
2469 2736 8.768957 ATCTAGCATGTAACACATCATATCAC 57.231 34.615 0.00 0.00 36.53 3.06
2470 2737 7.955918 TCTAGCATGTAACACATCATATCACT 58.044 34.615 0.00 0.00 36.53 3.41
2471 2738 8.424133 TCTAGCATGTAACACATCATATCACTT 58.576 33.333 0.00 0.00 36.53 3.16
2472 2739 7.870509 AGCATGTAACACATCATATCACTTT 57.129 32.000 0.00 0.00 36.53 2.66
2473 2740 7.700505 AGCATGTAACACATCATATCACTTTG 58.299 34.615 0.00 0.00 36.53 2.77
2474 2741 6.415867 GCATGTAACACATCATATCACTTTGC 59.584 38.462 0.00 0.00 36.53 3.68
2475 2742 6.105657 TGTAACACATCATATCACTTTGCG 57.894 37.500 0.00 0.00 0.00 4.85
2476 2743 4.621068 AACACATCATATCACTTTGCGG 57.379 40.909 0.00 0.00 0.00 5.69
2477 2744 2.355756 ACACATCATATCACTTTGCGGC 59.644 45.455 0.00 0.00 0.00 6.53
2478 2745 1.949525 ACATCATATCACTTTGCGGCC 59.050 47.619 0.00 0.00 0.00 6.13
2479 2746 2.224606 CATCATATCACTTTGCGGCCT 58.775 47.619 0.00 0.00 0.00 5.19
2480 2747 1.953559 TCATATCACTTTGCGGCCTC 58.046 50.000 0.00 0.00 0.00 4.70
2481 2748 1.209261 TCATATCACTTTGCGGCCTCA 59.791 47.619 0.00 0.00 0.00 3.86
2482 2749 1.331756 CATATCACTTTGCGGCCTCAC 59.668 52.381 0.00 0.00 0.00 3.51
2483 2750 0.739462 TATCACTTTGCGGCCTCACG 60.739 55.000 0.00 0.00 0.00 4.35
2491 2758 4.508128 CGGCCTCACGCACGGTAT 62.508 66.667 0.00 0.00 40.31 2.73
2492 2759 2.125269 GGCCTCACGCACGGTATT 60.125 61.111 0.00 0.00 40.31 1.89
2493 2760 2.171725 GGCCTCACGCACGGTATTC 61.172 63.158 0.00 0.00 40.31 1.75
2494 2761 2.171725 GCCTCACGCACGGTATTCC 61.172 63.158 0.00 0.00 37.47 3.01
2495 2762 1.520787 CCTCACGCACGGTATTCCC 60.521 63.158 0.00 0.00 0.00 3.97
2496 2763 1.216977 CTCACGCACGGTATTCCCA 59.783 57.895 0.00 0.00 0.00 4.37
2497 2764 1.079681 TCACGCACGGTATTCCCAC 60.080 57.895 0.00 0.00 0.00 4.61
2498 2765 2.125832 ACGCACGGTATTCCCACG 60.126 61.111 0.00 0.00 0.00 4.94
2499 2766 2.888534 CGCACGGTATTCCCACGG 60.889 66.667 0.00 0.00 0.00 4.94
2500 2767 2.512974 GCACGGTATTCCCACGGG 60.513 66.667 0.00 0.00 0.00 5.28
2501 2768 2.983791 CACGGTATTCCCACGGGT 59.016 61.111 1.07 0.00 36.47 5.28
2502 2769 1.448893 CACGGTATTCCCACGGGTG 60.449 63.158 1.07 0.00 36.47 4.61
2503 2770 2.512974 CGGTATTCCCACGGGTGC 60.513 66.667 1.07 0.00 36.47 5.01
2504 2771 2.124445 GGTATTCCCACGGGTGCC 60.124 66.667 1.07 0.00 36.47 5.01
2505 2772 2.672295 GTATTCCCACGGGTGCCA 59.328 61.111 1.07 0.00 36.47 4.92
2506 2773 1.747745 GTATTCCCACGGGTGCCAC 60.748 63.158 1.07 0.00 36.47 5.01
2507 2774 2.974041 TATTCCCACGGGTGCCACC 61.974 63.158 4.93 4.93 37.60 4.61
2510 2777 3.642503 CCCACGGGTGCCACCTTA 61.643 66.667 14.71 0.00 38.64 2.69
2511 2778 2.359478 CCACGGGTGCCACCTTAC 60.359 66.667 14.71 0.00 38.64 2.34
2512 2779 2.359478 CACGGGTGCCACCTTACC 60.359 66.667 14.71 0.00 38.64 2.85
2513 2780 2.528378 ACGGGTGCCACCTTACCT 60.528 61.111 14.71 0.00 38.64 3.08
2514 2781 2.046314 CGGGTGCCACCTTACCTG 60.046 66.667 14.71 0.00 38.64 4.00
2515 2782 2.355115 GGGTGCCACCTTACCTGG 59.645 66.667 14.71 0.00 38.64 4.45
2520 2787 4.109675 CCACCTTACCTGGCCCGG 62.110 72.222 12.40 12.40 0.00 5.73
2521 2788 4.109675 CACCTTACCTGGCCCGGG 62.110 72.222 19.09 19.09 35.68 5.73
2522 2789 4.342086 ACCTTACCTGGCCCGGGA 62.342 66.667 29.31 5.96 33.36 5.14
2523 2790 3.793888 CCTTACCTGGCCCGGGAC 61.794 72.222 29.31 26.59 33.36 4.46
2524 2791 3.793888 CTTACCTGGCCCGGGACC 61.794 72.222 27.91 24.83 33.36 4.46
2534 2801 4.675029 CCGGGACCGTTTGCGTCT 62.675 66.667 10.17 0.00 37.81 4.18
2535 2802 2.663852 CGGGACCGTTTGCGTCTT 60.664 61.111 1.86 0.00 36.15 3.01
2536 2803 2.664436 CGGGACCGTTTGCGTCTTC 61.664 63.158 1.86 0.00 36.15 2.87
2537 2804 1.301479 GGGACCGTTTGCGTCTTCT 60.301 57.895 0.00 0.00 36.15 2.85
2538 2805 1.566018 GGGACCGTTTGCGTCTTCTG 61.566 60.000 0.00 0.00 36.15 3.02
2539 2806 1.566018 GGACCGTTTGCGTCTTCTGG 61.566 60.000 0.00 0.00 36.15 3.86
2540 2807 2.171489 GACCGTTTGCGTCTTCTGGC 62.171 60.000 0.00 0.00 36.15 4.85
2541 2808 1.961277 CCGTTTGCGTCTTCTGGCT 60.961 57.895 0.00 0.00 36.15 4.75
2542 2809 1.493311 CGTTTGCGTCTTCTGGCTC 59.507 57.895 0.00 0.00 0.00 4.70
2543 2810 1.221466 CGTTTGCGTCTTCTGGCTCA 61.221 55.000 0.00 0.00 0.00 4.26
2544 2811 0.235926 GTTTGCGTCTTCTGGCTCAC 59.764 55.000 0.00 0.00 0.00 3.51
2545 2812 1.221466 TTTGCGTCTTCTGGCTCACG 61.221 55.000 0.00 0.00 35.32 4.35
2546 2813 2.049063 GCGTCTTCTGGCTCACGT 60.049 61.111 0.00 0.00 34.69 4.49
2547 2814 1.211969 GCGTCTTCTGGCTCACGTA 59.788 57.895 0.00 0.00 34.69 3.57
2548 2815 0.179134 GCGTCTTCTGGCTCACGTAT 60.179 55.000 0.00 0.00 34.69 3.06
2549 2816 1.065102 GCGTCTTCTGGCTCACGTATA 59.935 52.381 0.00 0.00 34.69 1.47
2550 2817 2.287668 GCGTCTTCTGGCTCACGTATAT 60.288 50.000 0.00 0.00 34.69 0.86
2551 2818 3.300857 CGTCTTCTGGCTCACGTATATG 58.699 50.000 0.00 0.00 0.00 1.78
2552 2819 3.003378 CGTCTTCTGGCTCACGTATATGA 59.997 47.826 0.00 0.00 0.00 2.15
2553 2820 4.320567 CGTCTTCTGGCTCACGTATATGAT 60.321 45.833 0.00 0.00 0.00 2.45
2554 2821 5.106673 CGTCTTCTGGCTCACGTATATGATA 60.107 44.000 0.00 0.00 0.00 2.15
2555 2822 6.318628 GTCTTCTGGCTCACGTATATGATAG 58.681 44.000 0.00 0.00 0.00 2.08
2556 2823 6.004574 TCTTCTGGCTCACGTATATGATAGT 58.995 40.000 0.00 0.00 0.00 2.12
2557 2824 5.629079 TCTGGCTCACGTATATGATAGTG 57.371 43.478 0.00 0.00 36.06 2.74
2558 2825 5.070685 TCTGGCTCACGTATATGATAGTGT 58.929 41.667 0.00 0.00 36.16 3.55
2559 2826 5.181433 TCTGGCTCACGTATATGATAGTGTC 59.819 44.000 0.00 0.00 36.16 3.67
2560 2827 4.083484 TGGCTCACGTATATGATAGTGTCG 60.083 45.833 0.00 0.00 36.16 4.35
2561 2828 3.846896 GCTCACGTATATGATAGTGTCGC 59.153 47.826 0.00 0.00 36.16 5.19
2562 2829 4.378563 GCTCACGTATATGATAGTGTCGCT 60.379 45.833 0.00 0.00 36.16 4.93
2563 2830 5.163884 GCTCACGTATATGATAGTGTCGCTA 60.164 44.000 0.00 0.00 36.16 4.26
2564 2831 6.404712 TCACGTATATGATAGTGTCGCTAG 57.595 41.667 0.00 0.00 36.16 3.42
2565 2832 5.022653 CACGTATATGATAGTGTCGCTAGC 58.977 45.833 4.06 4.06 36.67 3.42
2570 2837 2.306847 TGATAGTGTCGCTAGCATCCA 58.693 47.619 16.45 4.65 40.72 3.41
2571 2838 2.893489 TGATAGTGTCGCTAGCATCCAT 59.107 45.455 16.45 0.00 40.72 3.41
2572 2839 4.079253 TGATAGTGTCGCTAGCATCCATA 58.921 43.478 16.45 1.98 40.72 2.74
2573 2840 4.706962 TGATAGTGTCGCTAGCATCCATAT 59.293 41.667 16.45 6.97 40.72 1.78
2574 2841 3.309961 AGTGTCGCTAGCATCCATATG 57.690 47.619 16.45 0.00 36.09 1.78
2575 2842 2.893489 AGTGTCGCTAGCATCCATATGA 59.107 45.455 16.45 0.00 34.84 2.15
2576 2843 3.513119 AGTGTCGCTAGCATCCATATGAT 59.487 43.478 16.45 0.00 34.84 2.45
2577 2844 4.706962 AGTGTCGCTAGCATCCATATGATA 59.293 41.667 16.45 0.00 34.84 2.15
2585 2852 5.690464 AGCATCCATATGATAGAGAACCC 57.310 43.478 3.65 0.00 34.84 4.11
2586 2853 4.161189 AGCATCCATATGATAGAGAACCCG 59.839 45.833 3.65 0.00 34.84 5.28
2587 2854 4.681781 GCATCCATATGATAGAGAACCCGG 60.682 50.000 3.65 0.00 34.84 5.73
2588 2855 3.441101 TCCATATGATAGAGAACCCGGG 58.559 50.000 22.25 22.25 0.00 5.73
2589 2856 2.093447 CCATATGATAGAGAACCCGGGC 60.093 54.545 24.08 4.85 0.00 6.13
2590 2857 2.696526 TATGATAGAGAACCCGGGCT 57.303 50.000 24.08 8.98 0.00 5.19
2591 2858 1.051812 ATGATAGAGAACCCGGGCTG 58.948 55.000 24.08 0.00 0.00 4.85
2592 2859 0.032515 TGATAGAGAACCCGGGCTGA 60.033 55.000 24.08 0.00 0.00 4.26
2593 2860 0.389757 GATAGAGAACCCGGGCTGAC 59.610 60.000 24.08 10.50 0.00 3.51
2594 2861 0.325296 ATAGAGAACCCGGGCTGACA 60.325 55.000 24.08 1.28 0.00 3.58
2595 2862 0.325296 TAGAGAACCCGGGCTGACAT 60.325 55.000 24.08 5.01 0.00 3.06
2596 2863 1.450312 GAGAACCCGGGCTGACATG 60.450 63.158 24.08 0.00 0.00 3.21
2597 2864 2.438434 GAACCCGGGCTGACATGG 60.438 66.667 24.08 0.00 0.00 3.66
2598 2865 4.740822 AACCCGGGCTGACATGGC 62.741 66.667 24.08 0.00 0.00 4.40
2600 2867 3.479203 CCCGGGCTGACATGGCTA 61.479 66.667 8.08 0.00 0.00 3.93
2601 2868 2.109799 CCGGGCTGACATGGCTAG 59.890 66.667 0.00 0.00 0.00 3.42
2602 2869 2.735772 CCGGGCTGACATGGCTAGT 61.736 63.158 0.00 0.00 0.00 2.57
2603 2870 1.227380 CGGGCTGACATGGCTAGTC 60.227 63.158 0.00 0.00 36.55 2.59
2604 2871 1.227380 GGGCTGACATGGCTAGTCG 60.227 63.158 0.00 2.82 38.83 4.18
2605 2872 1.517832 GGCTGACATGGCTAGTCGT 59.482 57.895 0.00 0.00 38.83 4.34
2606 2873 0.807667 GGCTGACATGGCTAGTCGTG 60.808 60.000 15.06 15.06 38.83 4.35
2607 2874 0.173481 GCTGACATGGCTAGTCGTGA 59.827 55.000 23.11 0.52 38.83 4.35
2608 2875 1.404181 GCTGACATGGCTAGTCGTGAA 60.404 52.381 23.11 9.63 38.83 3.18
2609 2876 2.263077 CTGACATGGCTAGTCGTGAAC 58.737 52.381 23.11 15.45 38.83 3.18
2610 2877 1.067142 TGACATGGCTAGTCGTGAACC 60.067 52.381 23.11 11.46 38.83 3.62
2611 2878 0.249398 ACATGGCTAGTCGTGAACCC 59.751 55.000 23.11 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.806608 TGGACTAGCGAACGTCTTTT 57.193 45.000 0.00 0.00 0.00 2.27
366 367 6.882140 TCCATATTGTCGGAGTTAACAACAAT 59.118 34.615 21.56 21.56 41.83 2.71
678 679 3.166489 GTTCATCTGGTAGGAACGAGG 57.834 52.381 0.00 0.00 38.93 4.63
682 683 3.870633 AGTCGTTCATCTGGTAGGAAC 57.129 47.619 0.00 0.00 43.76 3.62
685 686 8.888579 AAAATATAAGTCGTTCATCTGGTAGG 57.111 34.615 0.00 0.00 0.00 3.18
686 687 9.751542 AGAAAATATAAGTCGTTCATCTGGTAG 57.248 33.333 0.00 0.00 0.00 3.18
687 688 9.529325 CAGAAAATATAAGTCGTTCATCTGGTA 57.471 33.333 0.00 0.00 0.00 3.25
857 897 7.920160 TTATAACATGTGCAGTGAGATTTCA 57.080 32.000 0.00 0.00 0.00 2.69
899 939 3.768757 GAGAGTAGAGATGGATGGATGGG 59.231 52.174 0.00 0.00 0.00 4.00
927 967 7.964293 AGGTAGAGATAAATGGATATGGAAGGT 59.036 37.037 0.00 0.00 0.00 3.50
953 993 5.178096 TGAATTGTAATGAAGCAGAGGGA 57.822 39.130 0.00 0.00 0.00 4.20
955 995 5.416952 ACCTTGAATTGTAATGAAGCAGAGG 59.583 40.000 0.00 0.00 0.00 3.69
979 1019 3.990369 TCCCTACAAGGCTAGCTAGAAA 58.010 45.455 25.15 1.45 32.73 2.52
1103 1143 2.535485 TATGAGGTGTGCCGCCTTGG 62.535 60.000 8.45 0.00 45.19 3.61
1107 1147 1.815421 CACTATGAGGTGTGCCGCC 60.815 63.158 0.00 0.00 40.50 6.13
1111 1151 1.339055 TGCTTCCACTATGAGGTGTGC 60.339 52.381 0.00 0.00 35.63 4.57
1114 1154 1.945394 GCATGCTTCCACTATGAGGTG 59.055 52.381 11.37 0.00 37.00 4.00
1146 1186 1.726791 GTGATGTTGTGCCAGTAGTCG 59.273 52.381 0.00 0.00 0.00 4.18
1157 1197 3.079578 CAGAATGCCTCTGTGATGTTGT 58.920 45.455 5.02 0.00 45.76 3.32
1180 1220 0.761323 TCGGACTGGAGGGTTGACAA 60.761 55.000 0.00 0.00 0.00 3.18
1198 1238 1.648467 GCCTTGGCACTCCGATTGTC 61.648 60.000 6.79 0.00 34.14 3.18
1209 1249 0.328258 GGAGGTTCTTAGCCTTGGCA 59.672 55.000 14.54 0.00 36.29 4.92
1213 1253 3.252351 AGTCAAGGAGGTTCTTAGCCTT 58.748 45.455 0.00 0.00 41.22 4.35
1353 1393 1.182667 CGGTCTCATAGTCCACCACA 58.817 55.000 0.00 0.00 0.00 4.17
1375 1415 3.072330 TCACAGATGTTAAGGGTGCTCAA 59.928 43.478 0.00 0.00 0.00 3.02
1482 1522 4.020751 AGCTCAGACAAGCACTCATTAAGA 60.021 41.667 0.00 0.00 45.00 2.10
1483 1523 4.252073 AGCTCAGACAAGCACTCATTAAG 58.748 43.478 0.00 0.00 45.00 1.85
1487 1527 2.424557 CAAGCTCAGACAAGCACTCAT 58.575 47.619 0.00 0.00 45.00 2.90
1500 1540 2.227194 CATGGCATATCAGCAAGCTCA 58.773 47.619 0.00 0.00 35.83 4.26
1525 1565 3.507233 TCATTTTCTTTGATCAGCGCCTT 59.493 39.130 2.29 0.00 0.00 4.35
1528 1568 3.127548 TCCTCATTTTCTTTGATCAGCGC 59.872 43.478 0.00 0.00 0.00 5.92
1530 1570 4.398673 AGCTCCTCATTTTCTTTGATCAGC 59.601 41.667 0.00 0.00 32.05 4.26
1531 1571 5.415077 ACAGCTCCTCATTTTCTTTGATCAG 59.585 40.000 0.00 0.00 0.00 2.90
1555 1595 0.983467 TTGAGGTAGACCAGCATGCA 59.017 50.000 21.98 0.00 38.89 3.96
1567 1607 3.813166 GCAAGCAAGTTAGTGTTGAGGTA 59.187 43.478 0.00 0.00 0.00 3.08
1637 1677 4.294416 CGAGTCACGGAATTACATCTCT 57.706 45.455 0.00 0.00 38.46 3.10
1654 1694 3.208747 ACATGAAAAGAACCCACGAGT 57.791 42.857 0.00 0.00 0.00 4.18
1657 1697 5.048364 TGGAATTACATGAAAAGAACCCACG 60.048 40.000 0.00 0.00 0.00 4.94
1684 1724 2.027192 GCAGTGGAGGAATTGGACAGTA 60.027 50.000 0.00 0.00 0.00 2.74
1686 1726 1.004044 AGCAGTGGAGGAATTGGACAG 59.996 52.381 0.00 0.00 0.00 3.51
1687 1727 1.067295 AGCAGTGGAGGAATTGGACA 58.933 50.000 0.00 0.00 0.00 4.02
1688 1728 1.457346 CAGCAGTGGAGGAATTGGAC 58.543 55.000 0.00 0.00 0.00 4.02
1691 1731 1.250328 TTGCAGCAGTGGAGGAATTG 58.750 50.000 0.00 0.00 0.00 2.32
1692 1732 1.999648 TTTGCAGCAGTGGAGGAATT 58.000 45.000 0.00 0.00 0.00 2.17
1693 1733 2.226962 ATTTGCAGCAGTGGAGGAAT 57.773 45.000 0.00 0.00 0.00 3.01
1694 1734 2.877097 TATTTGCAGCAGTGGAGGAA 57.123 45.000 0.00 0.00 0.00 3.36
1695 1735 2.646930 CATATTTGCAGCAGTGGAGGA 58.353 47.619 0.00 0.00 0.00 3.71
1707 1747 8.404137 GCATGAAGTTGATGCTGCATATTTGC 62.404 42.308 18.66 11.82 42.52 3.68
1708 1748 5.051039 GCATGAAGTTGATGCTGCATATTTG 60.051 40.000 18.66 6.32 42.52 2.32
1709 1749 5.047847 GCATGAAGTTGATGCTGCATATTT 58.952 37.500 18.66 3.95 42.52 1.40
1737 1778 7.981789 GCTACCAAGTATATAGATTGCTGCATA 59.018 37.037 1.84 0.00 0.00 3.14
1749 1790 7.533083 AGGACTACAAGGCTACCAAGTATATA 58.467 38.462 0.00 0.00 0.00 0.86
1770 1811 1.737793 CGAACAAGGCACCAATAGGAC 59.262 52.381 0.00 0.00 38.69 3.85
1790 1831 4.083003 TCAAACGGCATGAACTTTCCATAC 60.083 41.667 0.00 0.00 0.00 2.39
1808 1877 2.092323 GGCCTTGTGGGTAGATCAAAC 58.908 52.381 0.00 0.00 37.43 2.93
1818 1887 0.758123 AACATTTGTGGCCTTGTGGG 59.242 50.000 3.32 0.00 38.36 4.61
1824 1893 0.609662 GGCATCAACATTTGTGGCCT 59.390 50.000 3.32 0.00 42.98 5.19
1825 1894 0.321021 TGGCATCAACATTTGTGGCC 59.679 50.000 0.00 0.00 44.92 5.36
1859 1928 0.109597 CACAATGCGCTTGGAGGAAC 60.110 55.000 19.13 0.00 39.30 3.62
1875 1944 2.505407 CTCTCTCTCTCTCTCTCCCACA 59.495 54.545 0.00 0.00 0.00 4.17
1899 2006 1.948145 CTACGTCTAATCCACGCCTCT 59.052 52.381 0.00 0.00 41.10 3.69
1902 2009 1.599916 GCTCTACGTCTAATCCACGCC 60.600 57.143 0.00 0.00 41.10 5.68
1932 2129 8.850156 CCCTTGTGAATATCCGATAAAGAAAAT 58.150 33.333 0.00 0.00 0.00 1.82
1939 2136 4.634012 CCCCCTTGTGAATATCCGATAA 57.366 45.455 0.00 0.00 0.00 1.75
1959 2226 0.177141 TCTACAACAGCCGTATGCCC 59.823 55.000 0.00 0.00 42.71 5.36
1961 2228 1.134788 ACCTCTACAACAGCCGTATGC 60.135 52.381 0.00 0.00 41.71 3.14
1962 2229 2.540515 CACCTCTACAACAGCCGTATG 58.459 52.381 0.00 0.00 0.00 2.39
1963 2230 1.480954 CCACCTCTACAACAGCCGTAT 59.519 52.381 0.00 0.00 0.00 3.06
1971 2238 5.655532 TGTAAGATAGGTCCACCTCTACAAC 59.344 44.000 0.09 0.00 44.77 3.32
1974 2241 6.980416 ATTGTAAGATAGGTCCACCTCTAC 57.020 41.667 0.09 1.65 44.77 2.59
2045 2312 7.246027 AGGGAGAACCATAAATTAACTTTGGT 58.754 34.615 0.00 0.00 43.89 3.67
2047 2314 8.802267 TCAAGGGAGAACCATAAATTAACTTTG 58.198 33.333 0.00 0.00 43.89 2.77
2059 2326 6.347061 AATAATTCCTCAAGGGAGAACCAT 57.653 37.500 0.00 0.00 46.01 3.55
2084 2351 6.997655 TGCTCATCTCTTGACCGATATTTAT 58.002 36.000 0.00 0.00 0.00 1.40
2092 2359 2.376808 AGTTGCTCATCTCTTGACCG 57.623 50.000 0.00 0.00 0.00 4.79
2096 2363 5.686159 ACTTTGAAGTTGCTCATCTCTTG 57.314 39.130 0.00 0.00 35.21 3.02
2132 2399 7.125507 ACCCTCATCAATTTAATGGTTGCATAA 59.874 33.333 0.00 0.00 0.00 1.90
2133 2400 6.610830 ACCCTCATCAATTTAATGGTTGCATA 59.389 34.615 0.00 0.00 0.00 3.14
2134 2401 5.426185 ACCCTCATCAATTTAATGGTTGCAT 59.574 36.000 0.00 0.00 0.00 3.96
2217 2484 7.609760 TCTAATTTGCGTAGATGTGTTCAAT 57.390 32.000 0.00 0.00 0.00 2.57
2232 2499 8.677148 TCCTGGTATCAATACTTCTAATTTGC 57.323 34.615 0.00 0.00 33.81 3.68
2251 2518 6.013379 TGAGTGTTGATTTTAGATCTCCTGGT 60.013 38.462 0.00 0.00 0.00 4.00
2253 2520 6.875726 TGTGAGTGTTGATTTTAGATCTCCTG 59.124 38.462 0.00 0.00 0.00 3.86
2399 2666 5.069781 GTCCTGACAGTATTAATGCCTCTCT 59.930 44.000 0.93 0.00 0.00 3.10
2400 2667 5.293560 GTCCTGACAGTATTAATGCCTCTC 58.706 45.833 0.93 0.00 0.00 3.20
2401 2668 4.101741 GGTCCTGACAGTATTAATGCCTCT 59.898 45.833 0.93 0.00 0.00 3.69
2402 2669 4.381411 GGTCCTGACAGTATTAATGCCTC 58.619 47.826 0.93 0.00 0.00 4.70
2403 2670 3.136626 GGGTCCTGACAGTATTAATGCCT 59.863 47.826 0.93 0.00 0.00 4.75
2406 2673 3.386726 TCGGGGTCCTGACAGTATTAATG 59.613 47.826 0.93 0.00 0.00 1.90
2415 2682 2.777853 AGGATCGGGGTCCTGACA 59.222 61.111 0.00 0.00 46.76 3.58
2420 2687 1.764854 TGGCTTAGGATCGGGGTCC 60.765 63.158 0.00 0.00 38.62 4.46
2421 2688 1.335132 TGTGGCTTAGGATCGGGGTC 61.335 60.000 0.00 0.00 0.00 4.46
2422 2689 0.694444 ATGTGGCTTAGGATCGGGGT 60.694 55.000 0.00 0.00 0.00 4.95
2423 2690 0.035458 GATGTGGCTTAGGATCGGGG 59.965 60.000 0.00 0.00 0.00 5.73
2424 2691 0.319900 CGATGTGGCTTAGGATCGGG 60.320 60.000 0.00 0.00 35.22 5.14
2425 2692 0.673985 TCGATGTGGCTTAGGATCGG 59.326 55.000 0.00 0.00 38.56 4.18
2426 2693 2.230025 AGATCGATGTGGCTTAGGATCG 59.770 50.000 0.54 0.00 39.22 3.69
2427 2694 3.951775 AGATCGATGTGGCTTAGGATC 57.048 47.619 0.54 0.00 0.00 3.36
2428 2695 3.194542 GCTAGATCGATGTGGCTTAGGAT 59.805 47.826 21.42 0.00 0.00 3.24
2429 2696 2.558795 GCTAGATCGATGTGGCTTAGGA 59.441 50.000 21.42 0.00 0.00 2.94
2430 2697 2.297315 TGCTAGATCGATGTGGCTTAGG 59.703 50.000 27.00 4.33 0.00 2.69
2431 2698 3.650070 TGCTAGATCGATGTGGCTTAG 57.350 47.619 27.00 8.44 0.00 2.18
2432 2699 3.321968 ACATGCTAGATCGATGTGGCTTA 59.678 43.478 27.00 12.04 0.00 3.09
2433 2700 2.103771 ACATGCTAGATCGATGTGGCTT 59.896 45.455 27.00 19.89 0.00 4.35
2434 2701 1.690893 ACATGCTAGATCGATGTGGCT 59.309 47.619 27.00 13.05 0.00 4.75
2435 2702 2.160822 ACATGCTAGATCGATGTGGC 57.839 50.000 21.82 21.82 0.00 5.01
2436 2703 4.445718 GTGTTACATGCTAGATCGATGTGG 59.554 45.833 0.54 0.91 32.59 4.17
2437 2704 5.043248 TGTGTTACATGCTAGATCGATGTG 58.957 41.667 0.54 0.00 32.59 3.21
2438 2705 5.262588 TGTGTTACATGCTAGATCGATGT 57.737 39.130 0.54 0.00 34.68 3.06
2439 2706 5.922544 TGATGTGTTACATGCTAGATCGATG 59.077 40.000 0.54 0.00 39.27 3.84
2440 2707 6.089249 TGATGTGTTACATGCTAGATCGAT 57.911 37.500 0.00 0.00 39.27 3.59
2441 2708 5.514274 TGATGTGTTACATGCTAGATCGA 57.486 39.130 0.00 0.00 39.27 3.59
2442 2709 7.756722 TGATATGATGTGTTACATGCTAGATCG 59.243 37.037 0.00 0.00 39.27 3.69
2443 2710 8.867935 GTGATATGATGTGTTACATGCTAGATC 58.132 37.037 0.00 0.00 39.27 2.75
2444 2711 8.591940 AGTGATATGATGTGTTACATGCTAGAT 58.408 33.333 0.00 0.00 39.27 1.98
2445 2712 7.955918 AGTGATATGATGTGTTACATGCTAGA 58.044 34.615 0.00 0.00 39.27 2.43
2446 2713 8.599055 AAGTGATATGATGTGTTACATGCTAG 57.401 34.615 0.00 0.00 39.27 3.42
2447 2714 8.829612 CAAAGTGATATGATGTGTTACATGCTA 58.170 33.333 0.00 0.00 39.27 3.49
2448 2715 7.680350 GCAAAGTGATATGATGTGTTACATGCT 60.680 37.037 0.00 0.00 39.27 3.79
2449 2716 6.415867 GCAAAGTGATATGATGTGTTACATGC 59.584 38.462 0.00 0.00 39.27 4.06
2450 2717 6.630045 CGCAAAGTGATATGATGTGTTACATG 59.370 38.462 0.00 0.00 39.27 3.21
2451 2718 6.238456 CCGCAAAGTGATATGATGTGTTACAT 60.238 38.462 0.00 0.00 42.43 2.29
2452 2719 5.064579 CCGCAAAGTGATATGATGTGTTACA 59.935 40.000 0.00 0.00 0.00 2.41
2453 2720 5.501715 CCGCAAAGTGATATGATGTGTTAC 58.498 41.667 0.00 0.00 0.00 2.50
2454 2721 4.035091 GCCGCAAAGTGATATGATGTGTTA 59.965 41.667 0.00 0.00 0.00 2.41
2455 2722 3.181497 GCCGCAAAGTGATATGATGTGTT 60.181 43.478 0.00 0.00 0.00 3.32
2456 2723 2.355756 GCCGCAAAGTGATATGATGTGT 59.644 45.455 0.00 0.00 0.00 3.72
2457 2724 2.287188 GGCCGCAAAGTGATATGATGTG 60.287 50.000 0.00 0.00 0.00 3.21
2458 2725 1.949525 GGCCGCAAAGTGATATGATGT 59.050 47.619 0.00 0.00 0.00 3.06
2459 2726 2.224606 AGGCCGCAAAGTGATATGATG 58.775 47.619 0.00 0.00 0.00 3.07
2460 2727 2.158769 TGAGGCCGCAAAGTGATATGAT 60.159 45.455 6.75 0.00 0.00 2.45
2461 2728 1.209261 TGAGGCCGCAAAGTGATATGA 59.791 47.619 6.75 0.00 0.00 2.15
2462 2729 1.331756 GTGAGGCCGCAAAGTGATATG 59.668 52.381 12.05 0.00 0.00 1.78
2463 2730 1.668419 GTGAGGCCGCAAAGTGATAT 58.332 50.000 12.05 0.00 0.00 1.63
2464 2731 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.00 0.00 2.15
2465 2732 2.034879 CGTGAGGCCGCAAAGTGAT 61.035 57.895 12.05 0.00 0.00 3.06
2466 2733 2.664851 CGTGAGGCCGCAAAGTGA 60.665 61.111 12.05 0.00 0.00 3.41
2474 2741 4.508128 ATACCGTGCGTGAGGCCG 62.508 66.667 0.00 0.00 42.61 6.13
2475 2742 2.125269 AATACCGTGCGTGAGGCC 60.125 61.111 0.00 0.00 42.61 5.19
2476 2743 2.171725 GGAATACCGTGCGTGAGGC 61.172 63.158 0.00 0.00 43.96 4.70
2477 2744 1.520787 GGGAATACCGTGCGTGAGG 60.521 63.158 0.00 0.00 36.97 3.86
2478 2745 1.082117 GTGGGAATACCGTGCGTGAG 61.082 60.000 0.00 0.00 44.64 3.51
2479 2746 1.079681 GTGGGAATACCGTGCGTGA 60.080 57.895 0.00 0.00 44.64 4.35
2480 2747 2.449525 CGTGGGAATACCGTGCGTG 61.450 63.158 0.00 0.00 44.64 5.34
2481 2748 2.125832 CGTGGGAATACCGTGCGT 60.126 61.111 0.00 0.00 44.64 5.24
2482 2749 2.888534 CCGTGGGAATACCGTGCG 60.889 66.667 0.00 0.00 44.64 5.34
2483 2750 2.512974 CCCGTGGGAATACCGTGC 60.513 66.667 0.00 0.00 44.64 5.34
2484 2751 1.448893 CACCCGTGGGAATACCGTG 60.449 63.158 13.01 0.00 44.64 4.94
2485 2752 2.983791 CACCCGTGGGAATACCGT 59.016 61.111 13.01 0.00 44.64 4.83
2486 2753 2.512974 GCACCCGTGGGAATACCG 60.513 66.667 13.01 0.00 44.64 4.02
2487 2754 2.124445 GGCACCCGTGGGAATACC 60.124 66.667 13.01 3.33 38.96 2.73
2488 2755 1.747745 GTGGCACCCGTGGGAATAC 60.748 63.158 13.01 1.54 38.96 1.89
2489 2756 2.672295 GTGGCACCCGTGGGAATA 59.328 61.111 13.01 0.00 38.96 1.75
2490 2757 4.360405 GGTGGCACCCGTGGGAAT 62.360 66.667 26.51 0.00 38.96 3.01
2493 2760 3.642503 TAAGGTGGCACCCGTGGG 61.643 66.667 32.30 2.58 39.75 4.61
2494 2761 2.359478 GTAAGGTGGCACCCGTGG 60.359 66.667 32.30 0.00 39.75 4.94
2495 2762 2.359478 GGTAAGGTGGCACCCGTG 60.359 66.667 32.30 0.00 39.75 4.94
2496 2763 2.528378 AGGTAAGGTGGCACCCGT 60.528 61.111 32.30 22.68 39.75 5.28
2497 2764 2.046314 CAGGTAAGGTGGCACCCG 60.046 66.667 32.30 10.84 39.75 5.28
2498 2765 2.355115 CCAGGTAAGGTGGCACCC 59.645 66.667 32.30 17.45 39.75 4.61
2503 2770 4.109675 CCGGGCCAGGTAAGGTGG 62.110 72.222 14.74 0.00 38.21 4.61
2504 2771 4.109675 CCCGGGCCAGGTAAGGTG 62.110 72.222 21.37 0.00 0.00 4.00
2505 2772 4.342086 TCCCGGGCCAGGTAAGGT 62.342 66.667 21.37 0.00 0.00 3.50
2506 2773 3.793888 GTCCCGGGCCAGGTAAGG 61.794 72.222 21.37 5.33 0.00 2.69
2507 2774 3.793888 GGTCCCGGGCCAGGTAAG 61.794 72.222 24.17 5.72 0.00 2.34
2517 2784 4.675029 AGACGCAAACGGTCCCGG 62.675 66.667 10.91 0.00 46.04 5.73
2518 2785 2.663852 AAGACGCAAACGGTCCCG 60.664 61.111 3.76 3.76 46.04 5.14
2519 2786 1.301479 AGAAGACGCAAACGGTCCC 60.301 57.895 0.00 0.00 46.04 4.46
2520 2787 1.566018 CCAGAAGACGCAAACGGTCC 61.566 60.000 0.00 0.00 46.04 4.46
2521 2788 1.860078 CCAGAAGACGCAAACGGTC 59.140 57.895 0.00 0.00 46.04 4.79
2522 2789 2.251642 GCCAGAAGACGCAAACGGT 61.252 57.895 0.00 0.00 46.04 4.83
2523 2790 1.901650 GAGCCAGAAGACGCAAACGG 61.902 60.000 0.00 0.00 46.04 4.44
2525 2792 0.235926 GTGAGCCAGAAGACGCAAAC 59.764 55.000 0.00 0.00 0.00 2.93
2526 2793 1.221466 CGTGAGCCAGAAGACGCAAA 61.221 55.000 0.00 0.00 0.00 3.68
2527 2794 1.664649 CGTGAGCCAGAAGACGCAA 60.665 57.895 0.00 0.00 0.00 4.85
2528 2795 1.520600 TACGTGAGCCAGAAGACGCA 61.521 55.000 0.00 0.00 35.21 5.24
2529 2796 0.179134 ATACGTGAGCCAGAAGACGC 60.179 55.000 0.00 0.00 35.21 5.19
2530 2797 3.003378 TCATATACGTGAGCCAGAAGACG 59.997 47.826 0.00 0.00 37.82 4.18
2531 2798 4.569761 TCATATACGTGAGCCAGAAGAC 57.430 45.455 0.00 0.00 0.00 3.01
2532 2799 6.004574 ACTATCATATACGTGAGCCAGAAGA 58.995 40.000 0.00 0.00 0.00 2.87
2533 2800 6.089476 CACTATCATATACGTGAGCCAGAAG 58.911 44.000 0.00 0.00 0.00 2.85
2534 2801 5.535030 ACACTATCATATACGTGAGCCAGAA 59.465 40.000 0.00 0.00 0.00 3.02
2535 2802 5.070685 ACACTATCATATACGTGAGCCAGA 58.929 41.667 0.00 0.00 0.00 3.86
2536 2803 5.378292 ACACTATCATATACGTGAGCCAG 57.622 43.478 0.00 0.00 0.00 4.85
2537 2804 4.083484 CGACACTATCATATACGTGAGCCA 60.083 45.833 0.00 0.00 0.00 4.75
2538 2805 4.404324 CGACACTATCATATACGTGAGCC 58.596 47.826 0.00 0.00 0.00 4.70
2539 2806 3.846896 GCGACACTATCATATACGTGAGC 59.153 47.826 0.00 0.00 0.00 4.26
2540 2807 5.284428 AGCGACACTATCATATACGTGAG 57.716 43.478 0.00 0.00 0.00 3.51
2541 2808 5.163884 GCTAGCGACACTATCATATACGTGA 60.164 44.000 0.00 0.00 0.00 4.35
2542 2809 5.022653 GCTAGCGACACTATCATATACGTG 58.977 45.833 0.00 0.00 0.00 4.49
2543 2810 4.694037 TGCTAGCGACACTATCATATACGT 59.306 41.667 10.77 0.00 0.00 3.57
2544 2811 5.217895 TGCTAGCGACACTATCATATACG 57.782 43.478 10.77 0.00 0.00 3.06
2545 2812 6.183360 TGGATGCTAGCGACACTATCATATAC 60.183 42.308 10.77 0.00 37.73 1.47
2546 2813 5.885912 TGGATGCTAGCGACACTATCATATA 59.114 40.000 10.77 0.00 37.73 0.86
2547 2814 4.706962 TGGATGCTAGCGACACTATCATAT 59.293 41.667 10.77 0.00 37.73 1.78
2548 2815 4.079253 TGGATGCTAGCGACACTATCATA 58.921 43.478 10.77 0.00 37.73 2.15
2549 2816 2.893489 TGGATGCTAGCGACACTATCAT 59.107 45.455 10.77 0.00 39.77 2.45
2550 2817 2.306847 TGGATGCTAGCGACACTATCA 58.693 47.619 10.77 0.00 31.82 2.15
2551 2818 3.584406 ATGGATGCTAGCGACACTATC 57.416 47.619 10.77 6.09 0.00 2.08
2552 2819 4.706962 TCATATGGATGCTAGCGACACTAT 59.293 41.667 10.77 7.20 32.62 2.12
2553 2820 4.079253 TCATATGGATGCTAGCGACACTA 58.921 43.478 10.77 0.00 32.62 2.74
2554 2821 2.893489 TCATATGGATGCTAGCGACACT 59.107 45.455 10.77 0.00 32.62 3.55
2555 2822 3.303881 TCATATGGATGCTAGCGACAC 57.696 47.619 10.77 0.81 32.62 3.67
2556 2823 4.949856 TCTATCATATGGATGCTAGCGACA 59.050 41.667 10.77 9.20 36.72 4.35
2557 2824 5.298026 TCTCTATCATATGGATGCTAGCGAC 59.702 44.000 10.77 6.33 36.72 5.19
2558 2825 5.440610 TCTCTATCATATGGATGCTAGCGA 58.559 41.667 10.77 0.00 36.72 4.93
2559 2826 5.764487 TCTCTATCATATGGATGCTAGCG 57.236 43.478 10.77 0.00 36.72 4.26
2560 2827 6.279882 GGTTCTCTATCATATGGATGCTAGC 58.720 44.000 8.10 8.10 36.72 3.42
2561 2828 6.460814 CGGGTTCTCTATCATATGGATGCTAG 60.461 46.154 2.13 0.00 36.72 3.42
2562 2829 5.360999 CGGGTTCTCTATCATATGGATGCTA 59.639 44.000 2.13 0.00 36.72 3.49
2563 2830 4.161189 CGGGTTCTCTATCATATGGATGCT 59.839 45.833 2.13 0.00 36.72 3.79
2564 2831 4.437239 CGGGTTCTCTATCATATGGATGC 58.563 47.826 2.13 0.00 36.72 3.91
2565 2832 4.141846 CCCGGGTTCTCTATCATATGGATG 60.142 50.000 14.18 0.00 36.72 3.51
2566 2833 4.033709 CCCGGGTTCTCTATCATATGGAT 58.966 47.826 14.18 0.00 40.14 3.41
2567 2834 3.441101 CCCGGGTTCTCTATCATATGGA 58.559 50.000 14.18 0.00 0.00 3.41
2568 2835 2.093447 GCCCGGGTTCTCTATCATATGG 60.093 54.545 24.63 0.00 0.00 2.74
2569 2836 2.834549 AGCCCGGGTTCTCTATCATATG 59.165 50.000 24.63 0.00 0.00 1.78
2570 2837 2.834549 CAGCCCGGGTTCTCTATCATAT 59.165 50.000 24.63 0.00 0.00 1.78
2571 2838 2.158370 TCAGCCCGGGTTCTCTATCATA 60.158 50.000 24.63 0.00 0.00 2.15
2572 2839 1.051812 CAGCCCGGGTTCTCTATCAT 58.948 55.000 24.63 0.00 0.00 2.45
2573 2840 0.032515 TCAGCCCGGGTTCTCTATCA 60.033 55.000 24.63 0.00 0.00 2.15
2574 2841 0.389757 GTCAGCCCGGGTTCTCTATC 59.610 60.000 24.63 1.65 0.00 2.08
2575 2842 0.325296 TGTCAGCCCGGGTTCTCTAT 60.325 55.000 24.63 0.00 0.00 1.98
2576 2843 0.325296 ATGTCAGCCCGGGTTCTCTA 60.325 55.000 24.63 5.07 0.00 2.43
2577 2844 1.613630 ATGTCAGCCCGGGTTCTCT 60.614 57.895 24.63 7.57 0.00 3.10
2578 2845 1.450312 CATGTCAGCCCGGGTTCTC 60.450 63.158 24.63 11.76 0.00 2.87
2579 2846 2.671070 CATGTCAGCCCGGGTTCT 59.329 61.111 24.63 8.89 0.00 3.01
2580 2847 2.438434 CCATGTCAGCCCGGGTTC 60.438 66.667 24.63 6.10 0.00 3.62
2581 2848 4.740822 GCCATGTCAGCCCGGGTT 62.741 66.667 24.63 15.04 0.00 4.11
2583 2850 3.466791 CTAGCCATGTCAGCCCGGG 62.467 68.421 19.09 19.09 0.00 5.73
2584 2851 2.109799 CTAGCCATGTCAGCCCGG 59.890 66.667 0.00 0.00 0.00 5.73
2585 2852 1.227380 GACTAGCCATGTCAGCCCG 60.227 63.158 0.00 0.00 34.80 6.13
2586 2853 1.227380 CGACTAGCCATGTCAGCCC 60.227 63.158 0.00 0.00 34.37 5.19
2587 2854 0.807667 CACGACTAGCCATGTCAGCC 60.808 60.000 0.00 0.00 34.37 4.85
2588 2855 0.173481 TCACGACTAGCCATGTCAGC 59.827 55.000 0.00 0.00 34.37 4.26
2589 2856 2.263077 GTTCACGACTAGCCATGTCAG 58.737 52.381 0.00 0.00 34.37 3.51
2590 2857 1.067142 GGTTCACGACTAGCCATGTCA 60.067 52.381 0.00 0.00 34.37 3.58
2591 2858 1.641577 GGTTCACGACTAGCCATGTC 58.358 55.000 0.00 0.00 0.00 3.06
2592 2859 0.249398 GGGTTCACGACTAGCCATGT 59.751 55.000 0.00 0.00 32.24 3.21
2593 2860 3.065575 GGGTTCACGACTAGCCATG 57.934 57.895 0.00 0.00 32.24 3.66


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

AutoCloner maintained by Alex Coulton.