Multiple sequence alignment - TraesCS7A01G245800

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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 TraesCS7A01G245800 chr7A 100.000 3934 0 0 1 3934 224035060 224038993 0.000000e+00 7265
1 TraesCS7A01G245800 chr7D 87.982 3528 173 110 506 3907 212205027 212208429 0.000000e+00 3934
2 TraesCS7A01G245800 chr7D 88.267 3375 157 110 1 3243 212204482 212207749 0.000000e+00 3818
3 TraesCS7A01G245800 chr7B 88.277 3122 150 84 506 3521 189498999 189495988 0.000000e+00 3539
4 TraesCS7A01G245800 chr7B 83.333 480 29 19 1 443 189499569 189499104 2.850000e-106 396
5 TraesCS7A01G245800 chr7B 90.960 177 6 5 3670 3846 189494745 189494579 3.060000e-56 230
6 TraesCS7A01G245800 chr5D 92.035 113 9 0 2090 2202 375678426 375678538 4.070000e-35 159
7 TraesCS7A01G245800 chr5A 91.150 113 10 0 2090 2202 476837049 476837161 1.890000e-33 154
8 TraesCS7A01G245800 chr5A 82.836 134 20 2 1364 1497 476836327 476836457 2.480000e-22 117
9 TraesCS7A01G245800 chr5B 83.942 137 19 3 1364 1497 448465851 448465987 1.150000e-25 128
10 TraesCS7A01G245800 chr5B 93.750 80 5 0 2524 2603 448467080 448467159 1.920000e-23 121


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 TraesCS7A01G245800 chr7A 224035060 224038993 3933 False 7265.000000 7265 100.000000 1 3934 1 chr7A.!!$F1 3933
1 TraesCS7A01G245800 chr7D 212204482 212208429 3947 False 3876.000000 3934 88.124500 1 3907 2 chr7D.!!$F1 3906
2 TraesCS7A01G245800 chr7B 189494579 189499569 4990 True 1388.333333 3539 87.523333 1 3846 3 chr7B.!!$R1 3845


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
342 381 0.250640 CACCCAAGCTCAGCTCAGTT 60.251 55.0 0.0 0.0 38.25 3.16 F
984 1131 0.252742 GTTTGGGAGGAGGGAGAGGA 60.253 60.0 0.0 0.0 0.00 3.71 F
1507 1669 0.623911 TCGGTACCTCTCCTCCTCCT 60.624 60.0 10.9 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1658 0.047176 AGGAGGAGAGGAGGAGGAGA 59.953 60.0 0.0 0.0 0.0 3.71 R
2241 2443 0.370273 GTAGCAATGGTGTTCTCGCG 59.630 55.0 0.0 0.0 0.0 5.87 R
3144 3360 0.031111 TCCGATCTCCCATCCCTTGT 60.031 55.0 0.0 0.0 0.0 3.16 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
17 18 4.607024 CGGTGGCTGTTTTGTTCG 57.393 55.556 0.00 0.00 0.00 3.95
19 20 0.316689 CGGTGGCTGTTTTGTTCGTC 60.317 55.000 0.00 0.00 0.00 4.20
20 21 0.316689 GGTGGCTGTTTTGTTCGTCG 60.317 55.000 0.00 0.00 0.00 5.12
21 22 0.928451 GTGGCTGTTTTGTTCGTCGC 60.928 55.000 0.00 0.00 0.00 5.19
73 76 7.215381 CCAAATTTAAATTTAAAATGACCGCGC 59.785 33.333 25.95 0.00 36.52 6.86
105 108 3.616219 TCATTGCCAGTGTAATACCACC 58.384 45.455 0.00 0.00 35.93 4.61
108 111 1.982226 TGCCAGTGTAATACCACCACT 59.018 47.619 0.00 0.00 39.93 4.00
115 118 4.890581 AGTGTAATACCACCACTGCAAAAA 59.109 37.500 0.00 0.00 38.00 1.94
147 159 1.526686 CACACAAGTGGGAGCTGCA 60.527 57.895 7.79 0.00 42.13 4.41
157 169 1.536073 GGGAGCTGCAAGGGAAAACC 61.536 60.000 7.79 0.00 40.67 3.27
172 184 3.933332 GGAAAACCGATCGAGAATTCAGT 59.067 43.478 18.66 0.00 0.00 3.41
251 276 3.119424 TGGTTTTTCTTTCGCTCCGTTTT 60.119 39.130 0.00 0.00 0.00 2.43
267 292 6.344572 TCCGTTTTATGATGATTCAGTTCG 57.655 37.500 0.00 0.00 34.73 3.95
286 311 3.976169 TCGGTCAATCAAAAGCAAAAGG 58.024 40.909 0.00 0.00 0.00 3.11
287 312 3.634448 TCGGTCAATCAAAAGCAAAAGGA 59.366 39.130 0.00 0.00 0.00 3.36
288 313 4.280677 TCGGTCAATCAAAAGCAAAAGGAT 59.719 37.500 0.00 0.00 0.00 3.24
297 322 5.541868 TCAAAAGCAAAAGGATGATAACCCA 59.458 36.000 0.00 0.00 0.00 4.51
338 377 0.536006 AACACACCCAAGCTCAGCTC 60.536 55.000 0.00 0.00 38.25 4.09
339 378 1.071987 CACACCCAAGCTCAGCTCA 59.928 57.895 0.00 0.00 38.25 4.26
340 379 0.954449 CACACCCAAGCTCAGCTCAG 60.954 60.000 0.00 0.00 38.25 3.35
341 380 1.374190 CACCCAAGCTCAGCTCAGT 59.626 57.895 0.00 0.00 38.25 3.41
342 381 0.250640 CACCCAAGCTCAGCTCAGTT 60.251 55.000 0.00 0.00 38.25 3.16
451 503 2.183046 GCACGCACCTCTCTCTCC 59.817 66.667 0.00 0.00 0.00 3.71
457 509 1.454847 CACCTCTCTCTCCCCCTCG 60.455 68.421 0.00 0.00 0.00 4.63
461 513 2.904866 CTCTCTCCCCCTCGCTCG 60.905 72.222 0.00 0.00 0.00 5.03
510 611 2.113139 CACTCCCACACCCACACC 59.887 66.667 0.00 0.00 0.00 4.16
511 612 3.175710 ACTCCCACACCCACACCC 61.176 66.667 0.00 0.00 0.00 4.61
512 613 3.174987 CTCCCACACCCACACCCA 61.175 66.667 0.00 0.00 0.00 4.51
513 614 3.491598 CTCCCACACCCACACCCAC 62.492 68.421 0.00 0.00 0.00 4.61
514 615 3.814906 CCCACACCCACACCCACA 61.815 66.667 0.00 0.00 0.00 4.17
515 616 2.518349 CCACACCCACACCCACAC 60.518 66.667 0.00 0.00 0.00 3.82
516 617 2.518349 CACACCCACACCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
517 618 3.816090 ACACCCACACCCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
518 619 3.814906 CACCCACACCCACACCCA 61.815 66.667 0.00 0.00 0.00 4.51
519 620 3.816090 ACCCACACCCACACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
520 621 3.814906 CCCACACCCACACCCACA 61.815 66.667 0.00 0.00 0.00 4.17
521 622 2.518349 CCACACCCACACCCACAC 60.518 66.667 0.00 0.00 0.00 3.82
522 623 2.273776 CACACCCACACCCACACA 59.726 61.111 0.00 0.00 0.00 3.72
523 624 2.118404 CACACCCACACCCACACAC 61.118 63.158 0.00 0.00 0.00 3.82
524 625 2.899838 CACCCACACCCACACACG 60.900 66.667 0.00 0.00 0.00 4.49
560 661 1.492873 CTCCACGCACACACAATCG 59.507 57.895 0.00 0.00 0.00 3.34
658 771 1.202758 TGCTCGATCTCCTCTCTCTCC 60.203 57.143 0.00 0.00 0.00 3.71
663 776 4.204012 TCGATCTCCTCTCTCTCCTTTTC 58.796 47.826 0.00 0.00 0.00 2.29
664 777 4.080015 TCGATCTCCTCTCTCTCCTTTTCT 60.080 45.833 0.00 0.00 0.00 2.52
665 778 4.275936 CGATCTCCTCTCTCTCCTTTTCTC 59.724 50.000 0.00 0.00 0.00 2.87
673 786 6.139679 TCTCTCTCCTTTTCTCTCTCTCTT 57.860 41.667 0.00 0.00 0.00 2.85
674 787 6.552008 TCTCTCTCCTTTTCTCTCTCTCTTT 58.448 40.000 0.00 0.00 0.00 2.52
678 791 3.841255 TCCTTTTCTCTCTCTCTTTCCCC 59.159 47.826 0.00 0.00 0.00 4.81
680 793 3.569135 TTTCTCTCTCTCTTTCCCCCT 57.431 47.619 0.00 0.00 0.00 4.79
711 827 0.582005 CGCCGTAAAGAAGCCATAGC 59.418 55.000 0.00 0.00 40.32 2.97
792 927 1.731720 AGAAAGGAGCAATCGAGTGC 58.268 50.000 29.09 29.09 45.28 4.40
816 951 3.665675 CTCCCCGGCTGGAAAGTCG 62.666 68.421 15.09 0.00 37.49 4.18
828 963 1.509703 GAAAGTCGCCCGTCTTTTCT 58.490 50.000 12.58 0.00 34.63 2.52
832 967 1.871676 AGTCGCCCGTCTTTTCTTTTC 59.128 47.619 0.00 0.00 0.00 2.29
854 990 1.180029 CTGGGGAAGCTGAATTGGTG 58.820 55.000 0.00 0.00 0.00 4.17
915 1060 2.010582 GCTAGCCAGTGGAGGAGTCG 62.011 65.000 15.20 0.00 0.00 4.18
926 1071 0.524604 GAGGAGTCGCGCTTCTTCTC 60.525 60.000 17.03 17.03 31.80 2.87
934 1081 1.656095 CGCGCTTCTTCTCGATTTCTT 59.344 47.619 5.56 0.00 0.00 2.52
935 1082 2.284741 CGCGCTTCTTCTCGATTTCTTC 60.285 50.000 5.56 0.00 0.00 2.87
976 1123 5.264395 AGAATTATTGGTGTTTGGGAGGAG 58.736 41.667 0.00 0.00 0.00 3.69
981 1128 0.840722 GGTGTTTGGGAGGAGGGAGA 60.841 60.000 0.00 0.00 0.00 3.71
984 1131 0.252742 GTTTGGGAGGAGGGAGAGGA 60.253 60.000 0.00 0.00 0.00 3.71
989 1139 1.541672 GAGGAGGGAGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
990 1140 2.018086 AGGAGGGAGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1332 1482 2.113774 CACTCCCAGCACCAGCAA 59.886 61.111 0.00 0.00 45.49 3.91
1335 1485 1.970114 CTCCCAGCACCAGCAACAG 60.970 63.158 0.00 0.00 45.49 3.16
1496 1658 0.901580 ATGGACAACGGTCGGTACCT 60.902 55.000 10.90 0.00 45.28 3.08
1507 1669 0.623911 TCGGTACCTCTCCTCCTCCT 60.624 60.000 10.90 0.00 0.00 3.69
1540 1707 3.604875 TCGGCCTTCTTTTGGTACTAG 57.395 47.619 0.00 0.00 0.00 2.57
1548 1715 0.671163 TTTTGGTACTAGCCGCGGTG 60.671 55.000 28.70 19.18 0.00 4.94
1562 1729 0.874607 GCGGTGCCATAGTTCCTACG 60.875 60.000 0.00 0.00 0.00 3.51
1610 1777 0.954452 CCAGTTCTTGTTGGGAGCAC 59.046 55.000 0.00 0.00 0.00 4.40
1641 1808 1.212195 GGAACTAAATCCCGCCTCCTT 59.788 52.381 0.00 0.00 33.05 3.36
1675 1842 1.884926 GGGTACGAGAGCATGCTGC 60.885 63.158 28.27 15.89 45.46 5.25
1965 2147 2.730524 GGACTCCTCAGAGCCTGCC 61.731 68.421 0.00 0.00 44.65 4.85
2003 2185 6.149308 CCACAGTTACACTAGCATTTCATTCA 59.851 38.462 0.00 0.00 0.00 2.57
2006 2188 8.454106 ACAGTTACACTAGCATTTCATTCATTC 58.546 33.333 0.00 0.00 0.00 2.67
2007 2189 7.637519 CAGTTACACTAGCATTTCATTCATTCG 59.362 37.037 0.00 0.00 0.00 3.34
2008 2190 7.334421 AGTTACACTAGCATTTCATTCATTCGT 59.666 33.333 0.00 0.00 0.00 3.85
2009 2191 6.500684 ACACTAGCATTTCATTCATTCGTT 57.499 33.333 0.00 0.00 0.00 3.85
2010 2192 6.317088 ACACTAGCATTTCATTCATTCGTTG 58.683 36.000 0.00 0.00 0.00 4.10
2011 2193 5.228635 CACTAGCATTTCATTCATTCGTTGC 59.771 40.000 0.00 0.00 0.00 4.17
2031 2213 1.007734 GTGAGCACCGAACTGACGA 60.008 57.895 0.00 0.00 35.09 4.20
2036 2218 1.282930 GCACCGAACTGACGAGGTTC 61.283 60.000 0.00 0.00 39.49 3.62
2043 2225 1.242665 ACTGACGAGGTTCGGTCTCC 61.243 60.000 3.37 0.00 45.59 3.71
2079 2261 3.730761 GCGCACCAGTTCAGCCTG 61.731 66.667 0.30 0.00 0.00 4.85
2219 2401 1.402325 GGTAAACAAATCCACGCTGCC 60.402 52.381 0.00 0.00 0.00 4.85
2221 2403 2.141122 AAACAAATCCACGCTGCCCG 62.141 55.000 0.00 0.00 44.21 6.13
2231 2433 2.762360 CGCTGCCCGTTTAGATTGA 58.238 52.632 0.00 0.00 0.00 2.57
2252 2459 1.654105 CAGTATTGTCGCGAGAACACC 59.346 52.381 21.95 12.40 45.01 4.16
2259 2466 0.245266 TCGCGAGAACACCATTGCTA 59.755 50.000 3.71 0.00 37.03 3.49
2261 2468 0.727398 GCGAGAACACCATTGCTACC 59.273 55.000 0.00 0.00 0.00 3.18
2263 2470 2.632377 CGAGAACACCATTGCTACCAT 58.368 47.619 0.00 0.00 0.00 3.55
2271 2478 5.186198 ACACCATTGCTACCATTAGTCTTC 58.814 41.667 0.00 0.00 0.00 2.87
2355 2571 1.664659 CGAATCAGGAAGCTGCAAGAG 59.335 52.381 1.02 0.00 34.07 2.85
2385 2601 2.561478 ACATGGACAAGGTACACACC 57.439 50.000 0.00 0.00 46.19 4.16
2396 2612 1.476477 GTACACACCCTCTCTCTCCC 58.524 60.000 0.00 0.00 0.00 4.30
2397 2613 1.081481 TACACACCCTCTCTCTCCCA 58.919 55.000 0.00 0.00 0.00 4.37
2398 2614 0.252012 ACACACCCTCTCTCTCCCAG 60.252 60.000 0.00 0.00 0.00 4.45
2399 2615 1.305718 ACACCCTCTCTCTCCCAGC 60.306 63.158 0.00 0.00 0.00 4.85
2400 2616 1.001503 CACCCTCTCTCTCCCAGCT 59.998 63.158 0.00 0.00 0.00 4.24
2460 2676 5.183140 AGAACAGTGTATGGTTACCAAATGC 59.817 40.000 8.63 0.00 36.95 3.56
2463 2679 1.746220 TGTATGGTTACCAAATGCGCC 59.254 47.619 8.63 0.00 36.95 6.53
2512 2728 1.374758 CCGAGACCTGCAACTCCAC 60.375 63.158 8.83 0.00 0.00 4.02
2517 2733 2.485814 GAGACCTGCAACTCCACATTTC 59.514 50.000 0.00 0.00 0.00 2.17
2518 2734 2.107204 AGACCTGCAACTCCACATTTCT 59.893 45.455 0.00 0.00 0.00 2.52
2519 2735 2.485814 GACCTGCAACTCCACATTTCTC 59.514 50.000 0.00 0.00 0.00 2.87
2520 2736 2.107204 ACCTGCAACTCCACATTTCTCT 59.893 45.455 0.00 0.00 0.00 3.10
2601 2817 0.250513 CCAGGAGCAGGTCAAGGTAC 59.749 60.000 1.20 0.00 0.00 3.34
2608 2824 1.130561 GCAGGTCAAGGTACGCAAATC 59.869 52.381 0.00 0.00 0.00 2.17
2633 2849 7.559897 TCATCCTCCCAATTACCATAAACTTTC 59.440 37.037 0.00 0.00 0.00 2.62
2635 2851 7.116736 TCCTCCCAATTACCATAAACTTTCTC 58.883 38.462 0.00 0.00 0.00 2.87
2636 2852 6.889722 CCTCCCAATTACCATAAACTTTCTCA 59.110 38.462 0.00 0.00 0.00 3.27
2638 2854 6.661805 TCCCAATTACCATAAACTTTCTCACC 59.338 38.462 0.00 0.00 0.00 4.02
2639 2855 6.435904 CCCAATTACCATAAACTTTCTCACCA 59.564 38.462 0.00 0.00 0.00 4.17
2661 2877 5.221048 CCAAGAGAGGCATAAAATAAACCGG 60.221 44.000 0.00 0.00 0.00 5.28
2662 2878 5.112129 AGAGAGGCATAAAATAAACCGGT 57.888 39.130 0.00 0.00 0.00 5.28
2663 2879 5.506708 AGAGAGGCATAAAATAAACCGGTT 58.493 37.500 15.86 15.86 0.00 4.44
2667 2883 6.436218 AGAGGCATAAAATAAACCGGTTTCTT 59.564 34.615 34.79 27.46 34.23 2.52
2669 2885 6.209788 AGGCATAAAATAAACCGGTTTCTTGA 59.790 34.615 34.79 21.91 34.23 3.02
2678 2894 6.779115 AAACCGGTTTCTTGATTAATTTGC 57.221 33.333 26.87 0.00 0.00 3.68
2721 2937 3.431486 GCCAGTGAGGTCTAAATCAGGAG 60.431 52.174 0.00 0.00 40.61 3.69
2803 3019 8.879342 ATCTGAATTACTACTACTACGTACGT 57.121 34.615 25.98 25.98 0.00 3.57
2804 3020 9.967346 ATCTGAATTACTACTACTACGTACGTA 57.033 33.333 25.41 25.41 0.00 3.57
2805 3021 9.234384 TCTGAATTACTACTACTACGTACGTAC 57.766 37.037 23.60 15.90 0.00 3.67
2806 3022 9.239002 CTGAATTACTACTACTACGTACGTACT 57.761 37.037 23.60 16.88 0.00 2.73
2824 3040 4.980434 CGTACTACATAATCCAGAAACCGG 59.020 45.833 0.00 0.00 0.00 5.28
2918 3134 2.693762 GGCGAGCAAGCATCAGCAA 61.694 57.895 5.80 0.00 45.49 3.91
2919 3135 1.513586 GCGAGCAAGCATCAGCAAC 60.514 57.895 0.00 0.00 45.49 4.17
2920 3136 1.871077 CGAGCAAGCATCAGCAACA 59.129 52.632 0.00 0.00 45.49 3.33
2927 3143 2.393271 AGCATCAGCAACAGTACTCC 57.607 50.000 0.00 0.00 45.49 3.85
2944 3160 1.748493 CTCCGGTTGAGAGAAGAGAGG 59.252 57.143 0.00 0.00 44.42 3.69
2983 3199 4.133820 TCTCATCTCTAGAAGAAGCTCCG 58.866 47.826 0.00 0.00 37.61 4.63
3018 3234 8.115490 ACCTGGAGAATTTAGAAACAAGATTG 57.885 34.615 0.00 0.00 0.00 2.67
3035 3251 4.149598 AGATTGTTTGGGGAAGGTGTAAC 58.850 43.478 0.00 0.00 0.00 2.50
3081 3297 1.745232 TGCGGTTTGGGTATAAGCAG 58.255 50.000 0.00 0.00 0.00 4.24
3085 3301 2.452505 GGTTTGGGTATAAGCAGGCAA 58.547 47.619 0.00 0.00 0.00 4.52
3086 3302 2.427095 GGTTTGGGTATAAGCAGGCAAG 59.573 50.000 0.00 0.00 0.00 4.01
3087 3303 1.762708 TTGGGTATAAGCAGGCAAGC 58.237 50.000 0.00 0.00 0.00 4.01
3090 3306 1.221414 GGTATAAGCAGGCAAGCGAG 58.779 55.000 0.00 0.00 40.15 5.03
3091 3307 0.583917 GTATAAGCAGGCAAGCGAGC 59.416 55.000 0.00 0.00 40.15 5.03
3092 3308 0.177836 TATAAGCAGGCAAGCGAGCA 59.822 50.000 9.43 0.00 40.15 4.26
3093 3309 0.677731 ATAAGCAGGCAAGCGAGCAA 60.678 50.000 9.43 0.00 40.15 3.91
3094 3310 1.300971 TAAGCAGGCAAGCGAGCAAG 61.301 55.000 9.43 0.00 40.15 4.01
3095 3311 4.773117 GCAGGCAAGCGAGCAAGC 62.773 66.667 5.80 0.41 35.83 4.01
3096 3312 3.359523 CAGGCAAGCGAGCAAGCA 61.360 61.111 12.36 0.00 40.15 3.91
3097 3313 3.054503 AGGCAAGCGAGCAAGCAG 61.055 61.111 12.36 0.00 40.15 4.24
3105 3321 2.124778 GAGCAAGCAGAGGAGGGC 60.125 66.667 0.00 0.00 0.00 5.19
3141 3357 2.691526 TGGCATCATCAAGGATTCAAGC 59.308 45.455 0.00 0.00 0.00 4.01
3144 3360 4.382254 GGCATCATCAAGGATTCAAGCAAA 60.382 41.667 0.00 0.00 0.00 3.68
3148 3364 5.775686 TCATCAAGGATTCAAGCAAACAAG 58.224 37.500 0.00 0.00 0.00 3.16
3151 3367 3.243359 AGGATTCAAGCAAACAAGGGA 57.757 42.857 0.00 0.00 0.00 4.20
3153 3369 3.512724 AGGATTCAAGCAAACAAGGGATG 59.487 43.478 0.00 0.00 0.00 3.51
3154 3370 3.368739 GGATTCAAGCAAACAAGGGATGG 60.369 47.826 0.00 0.00 0.00 3.51
3155 3371 1.631405 TCAAGCAAACAAGGGATGGG 58.369 50.000 0.00 0.00 0.00 4.00
3156 3372 1.146774 TCAAGCAAACAAGGGATGGGA 59.853 47.619 0.00 0.00 0.00 4.37
3157 3373 1.547372 CAAGCAAACAAGGGATGGGAG 59.453 52.381 0.00 0.00 0.00 4.30
3158 3374 1.075601 AGCAAACAAGGGATGGGAGA 58.924 50.000 0.00 0.00 0.00 3.71
3159 3375 1.642762 AGCAAACAAGGGATGGGAGAT 59.357 47.619 0.00 0.00 0.00 2.75
3160 3376 2.027385 GCAAACAAGGGATGGGAGATC 58.973 52.381 0.00 0.00 0.00 2.75
3172 3388 0.830023 GGGAGATCGGAGAAGGGAGG 60.830 65.000 0.00 0.00 43.58 4.30
3174 3390 1.616159 GAGATCGGAGAAGGGAGGAG 58.384 60.000 0.00 0.00 43.58 3.69
3176 3392 0.186386 GATCGGAGAAGGGAGGAGGA 59.814 60.000 0.00 0.00 43.58 3.71
3177 3393 0.637195 ATCGGAGAAGGGAGGAGGAA 59.363 55.000 0.00 0.00 43.58 3.36
3181 3397 0.692756 GAGAAGGGAGGAGGAAGGGG 60.693 65.000 0.00 0.00 0.00 4.79
3183 3399 0.253207 GAAGGGAGGAGGAAGGGGAA 60.253 60.000 0.00 0.00 0.00 3.97
3292 3508 6.354130 GGTGCATTCCCATAGAAAGTTACTA 58.646 40.000 0.00 0.00 38.21 1.82
3293 3509 6.260271 GGTGCATTCCCATAGAAAGTTACTAC 59.740 42.308 0.00 0.00 38.21 2.73
3294 3510 7.048512 GTGCATTCCCATAGAAAGTTACTACT 58.951 38.462 0.00 0.00 38.21 2.57
3310 3526 1.129251 CTACTGCCATTGTTGTCAGCG 59.871 52.381 0.00 0.00 0.00 5.18
3348 3581 0.802607 GGCTCTCTCGCTTAACACCG 60.803 60.000 0.00 0.00 0.00 4.94
3386 3620 2.224549 CACACTCCGTCGCCAATAAAAA 59.775 45.455 0.00 0.00 0.00 1.94
3406 3640 3.317603 AATATTGCACCGCTTTGCTTT 57.682 38.095 7.79 0.00 43.41 3.51
3412 3646 1.639280 CACCGCTTTGCTTTTGTGTT 58.361 45.000 0.00 0.00 0.00 3.32
3454 3688 0.952010 CCTGGCAGCAATTTTGTGCC 60.952 55.000 20.48 20.48 46.14 5.01
3463 3712 0.446222 AATTTTGTGCCGGACGATCG 59.554 50.000 14.88 14.88 0.00 3.69
3473 3722 1.300233 GGACGATCGGGTCAGATGC 60.300 63.158 20.98 0.00 38.70 3.91
3501 3750 3.492102 TCTGCTTGCCCAATATAGTCC 57.508 47.619 0.00 0.00 0.00 3.85
3542 3842 3.014856 GCGAGTCGGCATAAAGGC 58.985 61.111 15.52 0.00 39.93 4.35
3587 3899 1.464997 GTCCAATGAACGGCTGAGAAC 59.535 52.381 0.00 0.00 0.00 3.01
3607 3919 1.818221 GCGTGGCTACTTTATCGCCG 61.818 60.000 0.00 0.00 46.67 6.46
3641 3974 4.833380 TCTCTCCTCCAAAATATAGTCCCG 59.167 45.833 0.00 0.00 0.00 5.14
3657 3990 2.093447 GTCCCGTGTCCATCTCAATTCT 60.093 50.000 0.00 0.00 0.00 2.40
3658 3991 2.571653 TCCCGTGTCCATCTCAATTCTT 59.428 45.455 0.00 0.00 0.00 2.52
3659 3992 3.009033 TCCCGTGTCCATCTCAATTCTTT 59.991 43.478 0.00 0.00 0.00 2.52
3660 3993 3.375299 CCCGTGTCCATCTCAATTCTTTC 59.625 47.826 0.00 0.00 0.00 2.62
3661 3994 4.256920 CCGTGTCCATCTCAATTCTTTCT 58.743 43.478 0.00 0.00 0.00 2.52
3684 5038 3.802139 CGGCCAGAAAAGAAAAGAAAACC 59.198 43.478 2.24 0.00 0.00 3.27
3719 5073 3.490759 CGCGCAAACTCCGAGCAT 61.491 61.111 8.75 0.00 0.00 3.79
3741 5095 1.333636 TGGGGCTGTGGTTGGTTTTG 61.334 55.000 0.00 0.00 0.00 2.44
3784 5138 3.698289 TCTTCGATCCTTCTGGTAGTGT 58.302 45.455 0.00 0.00 34.23 3.55
3785 5139 4.087182 TCTTCGATCCTTCTGGTAGTGTT 58.913 43.478 0.00 0.00 34.23 3.32
3786 5140 3.868757 TCGATCCTTCTGGTAGTGTTG 57.131 47.619 0.00 0.00 34.23 3.33
3787 5141 2.496070 TCGATCCTTCTGGTAGTGTTGG 59.504 50.000 0.00 0.00 34.23 3.77
3788 5142 2.418746 CGATCCTTCTGGTAGTGTTGGG 60.419 54.545 0.00 0.00 34.23 4.12
3806 5162 0.466739 GGTTGGTTATTAGGGGCGGG 60.467 60.000 0.00 0.00 0.00 6.13
3807 5163 0.466739 GTTGGTTATTAGGGGCGGGG 60.467 60.000 0.00 0.00 0.00 5.73
3810 5166 0.552363 GGTTATTAGGGGCGGGGAAA 59.448 55.000 0.00 0.00 0.00 3.13
3811 5167 1.063792 GGTTATTAGGGGCGGGGAAAA 60.064 52.381 0.00 0.00 0.00 2.29
3812 5168 2.304092 GTTATTAGGGGCGGGGAAAAG 58.696 52.381 0.00 0.00 0.00 2.27
3813 5169 1.598869 TATTAGGGGCGGGGAAAAGT 58.401 50.000 0.00 0.00 0.00 2.66
3843 5199 1.429148 GGGTGCCTATCGTGAAAGCG 61.429 60.000 0.00 0.00 0.00 4.68
3871 5227 8.905702 CACGAAATCTTTGTTTTATCTGAAAGG 58.094 33.333 0.00 0.00 0.00 3.11
3891 5247 4.434483 AAAAAGACGGGGATGGCC 57.566 55.556 0.00 0.00 0.00 5.36
3893 5249 2.132089 AAAAAGACGGGGATGGCCGA 62.132 55.000 0.00 0.00 33.83 5.54
3907 5263 1.657751 GGCCGAGGAAAAGATGTGGC 61.658 60.000 0.00 0.00 40.25 5.01
3908 5264 1.657751 GCCGAGGAAAAGATGTGGCC 61.658 60.000 0.00 0.00 35.01 5.36
3909 5265 1.032114 CCGAGGAAAAGATGTGGCCC 61.032 60.000 0.00 0.00 0.00 5.80
3910 5266 1.369091 CGAGGAAAAGATGTGGCCCG 61.369 60.000 0.00 0.00 0.00 6.13
3911 5267 1.657751 GAGGAAAAGATGTGGCCCGC 61.658 60.000 0.00 0.00 0.00 6.13
3912 5268 2.485122 GAAAAGATGTGGCCCGCG 59.515 61.111 0.00 0.00 0.00 6.46
3913 5269 3.683587 GAAAAGATGTGGCCCGCGC 62.684 63.158 0.00 0.00 0.00 6.86
3927 5283 2.474266 GCGCGCTCGTGAATGAAA 59.526 55.556 26.67 0.00 38.14 2.69
3928 5284 1.859135 GCGCGCTCGTGAATGAAAC 60.859 57.895 26.67 0.00 38.14 2.78
3929 5285 1.225745 CGCGCTCGTGAATGAAACC 60.226 57.895 5.56 0.00 0.00 3.27
3930 5286 1.866237 GCGCTCGTGAATGAAACCA 59.134 52.632 0.00 0.00 0.00 3.67
3931 5287 0.237235 GCGCTCGTGAATGAAACCAA 59.763 50.000 0.00 0.00 0.00 3.67
3932 5288 1.334599 GCGCTCGTGAATGAAACCAAA 60.335 47.619 0.00 0.00 0.00 3.28
3933 5289 2.307049 CGCTCGTGAATGAAACCAAAC 58.693 47.619 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.718220 CAGCGAGCGACGAACAAAAC 60.718 55.000 0.00 0.00 45.77 2.43
20 21 0.926846 GAGTAACATCAGCAGCGAGC 59.073 55.000 0.00 0.00 46.19 5.03
21 22 2.159324 TCTGAGTAACATCAGCAGCGAG 60.159 50.000 0.00 0.00 45.25 5.03
58 61 0.952280 TGTGGCGCGGTCATTTTAAA 59.048 45.000 8.83 0.00 0.00 1.52
59 62 1.131504 GATGTGGCGCGGTCATTTTAA 59.868 47.619 8.83 0.00 0.00 1.52
60 63 0.730265 GATGTGGCGCGGTCATTTTA 59.270 50.000 8.83 0.00 0.00 1.52
61 64 1.506262 GATGTGGCGCGGTCATTTT 59.494 52.632 8.83 0.00 0.00 1.82
62 65 2.406616 GGATGTGGCGCGGTCATTT 61.407 57.895 8.83 0.00 0.00 2.32
63 66 2.824041 GGATGTGGCGCGGTCATT 60.824 61.111 8.83 0.00 0.00 2.57
73 76 0.323633 TGGCAATGAGTGGGATGTGG 60.324 55.000 0.00 0.00 0.00 4.17
115 118 6.655003 CCCACTTGTGTGTATGTAGAGAATTT 59.345 38.462 0.00 0.00 42.34 1.82
128 131 1.526917 GCAGCTCCCACTTGTGTGT 60.527 57.895 0.00 0.00 42.34 3.72
147 159 3.629142 ATTCTCGATCGGTTTTCCCTT 57.371 42.857 16.41 0.00 36.42 3.95
157 169 1.590238 GTGGCACTGAATTCTCGATCG 59.410 52.381 11.13 9.36 0.00 3.69
208 220 4.235762 CGGTGGCGGGTGATAGGG 62.236 72.222 0.00 0.00 0.00 3.53
231 256 5.910723 TCATAAAACGGAGCGAAAGAAAAAC 59.089 36.000 0.00 0.00 0.00 2.43
235 260 4.932799 TCATCATAAAACGGAGCGAAAGAA 59.067 37.500 0.00 0.00 0.00 2.52
237 262 4.857871 TCATCATAAAACGGAGCGAAAG 57.142 40.909 0.00 0.00 0.00 2.62
241 266 4.271049 ACTGAATCATCATAAAACGGAGCG 59.729 41.667 0.00 0.00 34.37 5.03
251 276 6.581712 TGATTGACCGAACTGAATCATCATA 58.418 36.000 0.00 0.00 34.37 2.15
267 292 5.540911 TCATCCTTTTGCTTTTGATTGACC 58.459 37.500 0.00 0.00 0.00 4.02
286 311 7.425606 GTGGAATTACAACATGGGTTATCATC 58.574 38.462 0.00 0.00 34.87 2.92
287 312 6.323739 GGTGGAATTACAACATGGGTTATCAT 59.676 38.462 0.00 0.00 34.87 2.45
288 313 5.654650 GGTGGAATTACAACATGGGTTATCA 59.345 40.000 0.00 0.00 34.87 2.15
297 322 7.440856 GTGTTTTGATTGGTGGAATTACAACAT 59.559 33.333 9.79 0.00 37.99 2.71
338 377 1.528586 CGGCTCAACTGAACTGAACTG 59.471 52.381 0.00 0.00 0.00 3.16
339 378 1.412710 TCGGCTCAACTGAACTGAACT 59.587 47.619 0.00 0.00 0.00 3.01
340 379 1.527311 GTCGGCTCAACTGAACTGAAC 59.473 52.381 0.00 0.00 34.69 3.18
341 380 1.138069 TGTCGGCTCAACTGAACTGAA 59.862 47.619 0.00 0.00 34.69 3.02
342 381 0.750249 TGTCGGCTCAACTGAACTGA 59.250 50.000 0.00 0.00 34.69 3.41
438 477 1.760480 GAGGGGGAGAGAGAGGTGC 60.760 68.421 0.00 0.00 0.00 5.01
439 491 1.454847 CGAGGGGGAGAGAGAGGTG 60.455 68.421 0.00 0.00 0.00 4.00
440 492 3.011885 CGAGGGGGAGAGAGAGGT 58.988 66.667 0.00 0.00 0.00 3.85
441 493 2.520741 GCGAGGGGGAGAGAGAGG 60.521 72.222 0.00 0.00 0.00 3.69
510 611 3.582120 GTGCGTGTGTGGGTGTGG 61.582 66.667 0.00 0.00 0.00 4.17
511 612 3.935872 CGTGCGTGTGTGGGTGTG 61.936 66.667 0.00 0.00 0.00 3.82
514 615 2.796483 ATATGCGTGCGTGTGTGGGT 62.796 55.000 0.00 0.00 0.00 4.51
515 616 0.808060 TATATGCGTGCGTGTGTGGG 60.808 55.000 0.00 0.00 0.00 4.61
516 617 1.003108 TTATATGCGTGCGTGTGTGG 58.997 50.000 0.00 0.00 0.00 4.17
517 618 2.796976 TTTATATGCGTGCGTGTGTG 57.203 45.000 0.00 0.00 0.00 3.82
518 619 4.349663 AATTTTATATGCGTGCGTGTGT 57.650 36.364 0.00 0.00 0.00 3.72
519 620 4.546081 GCAAATTTTATATGCGTGCGTGTG 60.546 41.667 0.00 0.00 0.00 3.82
520 621 3.545873 GCAAATTTTATATGCGTGCGTGT 59.454 39.130 0.00 0.00 0.00 4.49
521 622 3.790820 AGCAAATTTTATATGCGTGCGTG 59.209 39.130 0.00 0.00 44.60 5.34
522 623 4.027572 AGCAAATTTTATATGCGTGCGT 57.972 36.364 0.00 0.00 44.60 5.24
523 624 3.421888 GGAGCAAATTTTATATGCGTGCG 59.578 43.478 0.00 0.00 44.60 5.34
524 625 4.207019 GTGGAGCAAATTTTATATGCGTGC 59.793 41.667 0.00 0.00 44.60 5.34
560 661 3.424105 AGGGATTGGGGGCTCTGC 61.424 66.667 0.00 0.00 0.00 4.26
658 771 3.843619 AGGGGGAAAGAGAGAGAGAAAAG 59.156 47.826 0.00 0.00 0.00 2.27
663 776 1.290732 AGGAGGGGGAAAGAGAGAGAG 59.709 57.143 0.00 0.00 0.00 3.20
664 777 1.289530 GAGGAGGGGGAAAGAGAGAGA 59.710 57.143 0.00 0.00 0.00 3.10
665 778 1.691163 GGAGGAGGGGGAAAGAGAGAG 60.691 61.905 0.00 0.00 0.00 3.20
673 786 2.768344 GCGATGGAGGAGGGGGAA 60.768 66.667 0.00 0.00 0.00 3.97
674 787 3.758133 GAGCGATGGAGGAGGGGGA 62.758 68.421 0.00 0.00 0.00 4.81
678 791 4.292178 GGCGAGCGATGGAGGAGG 62.292 72.222 0.00 0.00 0.00 4.30
711 827 0.584396 CTACGCTACTCGCTCCTCTG 59.416 60.000 0.00 0.00 43.23 3.35
732 860 2.682494 TCCCCCACACCGAGCTAC 60.682 66.667 0.00 0.00 0.00 3.58
733 861 2.238319 ATCTCCCCCACACCGAGCTA 62.238 60.000 0.00 0.00 0.00 3.32
734 862 3.625632 ATCTCCCCCACACCGAGCT 62.626 63.158 0.00 0.00 0.00 4.09
735 863 3.083997 ATCTCCCCCACACCGAGC 61.084 66.667 0.00 0.00 0.00 5.03
737 865 2.758327 CGATCTCCCCCACACCGA 60.758 66.667 0.00 0.00 0.00 4.69
738 866 2.758327 TCGATCTCCCCCACACCG 60.758 66.667 0.00 0.00 0.00 4.94
743 874 4.137615 TCCGCTCGATCTCCCCCA 62.138 66.667 0.00 0.00 0.00 4.96
767 902 4.693095 ACTCGATTGCTCCTTTCTTTTCTC 59.307 41.667 0.00 0.00 0.00 2.87
769 904 4.716943 CACTCGATTGCTCCTTTCTTTTC 58.283 43.478 0.00 0.00 0.00 2.29
773 908 1.731720 GCACTCGATTGCTCCTTTCT 58.268 50.000 19.43 0.00 39.59 2.52
792 927 4.479993 CCAGCCGGGGAGCAGAAG 62.480 72.222 2.18 0.00 34.23 2.85
816 951 0.601558 GGGGAAAAGAAAAGACGGGC 59.398 55.000 0.00 0.00 0.00 6.13
832 967 0.685458 CAATTCAGCTTCCCCAGGGG 60.685 60.000 20.55 20.55 46.11 4.79
854 990 1.296867 CACGCACGCGAATCAATCC 60.297 57.895 19.66 0.00 42.83 3.01
915 1060 3.297020 GAAGAAATCGAGAAGAAGCGC 57.703 47.619 0.00 0.00 0.00 5.92
976 1123 1.365105 TAGCTCCCTCCTCCTCTCCC 61.365 65.000 0.00 0.00 0.00 4.30
981 1128 1.232792 CAGCTAGCTCCCTCCTCCT 59.767 63.158 16.15 0.00 0.00 3.69
984 1131 0.264359 ACATCAGCTAGCTCCCTCCT 59.736 55.000 16.15 0.00 0.00 3.69
989 1139 0.319125 GCCGTACATCAGCTAGCTCC 60.319 60.000 16.15 0.00 0.00 4.70
990 1140 0.671251 AGCCGTACATCAGCTAGCTC 59.329 55.000 16.15 0.95 34.38 4.09
1046 1196 4.692129 CGGAGGAGTTCATCGTCG 57.308 61.111 0.00 0.00 42.57 5.12
1169 1319 1.374252 CGGGAGAAGACGTTGTGGG 60.374 63.158 0.00 0.00 0.00 4.61
1170 1320 2.027625 GCGGGAGAAGACGTTGTGG 61.028 63.158 0.00 0.00 0.00 4.17
1171 1321 0.600255 AAGCGGGAGAAGACGTTGTG 60.600 55.000 0.00 0.00 0.00 3.33
1263 1413 4.241555 ATGGCGGCGGAGTCATCC 62.242 66.667 9.78 0.00 42.81 3.51
1496 1658 0.047176 AGGAGGAGAGGAGGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
1507 1669 2.176247 AGGCCGAATTAAGGAGGAGA 57.824 50.000 0.00 0.00 0.00 3.71
1540 1707 3.573491 GAACTATGGCACCGCGGC 61.573 66.667 28.58 12.69 41.67 6.53
1562 1729 0.660300 GGCTGTAATAATTGCGGCGC 60.660 55.000 27.44 27.44 46.89 6.53
1610 1777 4.338400 GGGATTTAGTTCCCGAAATGGAAG 59.662 45.833 0.00 0.00 45.84 3.46
1641 1808 2.125147 CCTGAATTCAGCGGCGGA 60.125 61.111 27.01 0.00 42.47 5.54
1650 1817 2.961526 TGCTCTCGTACCCTGAATTC 57.038 50.000 0.00 0.00 0.00 2.17
1944 2126 3.151022 GGCTCTGAGGAGTCCCGG 61.151 72.222 5.25 0.00 41.38 5.73
1983 2165 7.464358 ACGAATGAATGAAATGCTAGTGTAAC 58.536 34.615 0.00 0.00 0.00 2.50
2010 2192 3.414700 CAGTTCGGTGCTCACGGC 61.415 66.667 3.11 0.00 42.22 5.68
2011 2193 2.022129 GTCAGTTCGGTGCTCACGG 61.022 63.158 1.70 1.70 0.00 4.94
2079 2261 3.358076 CTCCGACGAGGTCTTGGGC 62.358 68.421 0.00 0.00 41.99 5.36
2204 2386 3.055719 CGGGCAGCGTGGATTTGT 61.056 61.111 0.00 0.00 0.00 2.83
2205 2387 2.141122 AAACGGGCAGCGTGGATTTG 62.141 55.000 0.00 0.00 0.00 2.32
2231 2433 2.325761 GTGTTCTCGCGACAATACTGT 58.674 47.619 14.89 0.00 38.98 3.55
2241 2443 0.370273 GTAGCAATGGTGTTCTCGCG 59.630 55.000 0.00 0.00 0.00 5.87
2244 2451 5.186198 ACTAATGGTAGCAATGGTGTTCTC 58.814 41.667 0.00 0.00 0.00 2.87
2245 2452 5.045578 AGACTAATGGTAGCAATGGTGTTCT 60.046 40.000 3.51 0.00 0.00 3.01
2246 2453 5.186198 AGACTAATGGTAGCAATGGTGTTC 58.814 41.667 3.51 0.00 0.00 3.18
2247 2454 5.179452 AGACTAATGGTAGCAATGGTGTT 57.821 39.130 3.51 0.00 0.00 3.32
2252 2459 7.055667 TCTAGGAAGACTAATGGTAGCAATG 57.944 40.000 0.00 0.00 0.00 2.82
2259 2466 5.221342 CGCTTGATCTAGGAAGACTAATGGT 60.221 44.000 6.30 0.00 33.57 3.55
2261 2468 5.221342 ACCGCTTGATCTAGGAAGACTAATG 60.221 44.000 6.30 0.00 33.57 1.90
2263 2470 4.279145 ACCGCTTGATCTAGGAAGACTAA 58.721 43.478 6.30 0.00 33.57 2.24
2271 2478 2.868583 CACATCAACCGCTTGATCTAGG 59.131 50.000 2.91 1.11 44.04 3.02
2355 2571 2.171635 GTCCATGTTTGGGACGAGC 58.828 57.895 0.00 0.00 44.80 5.03
2385 2601 1.457455 GGGAGCTGGGAGAGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
2389 2605 3.284251 TGGGGGAGCTGGGAGAGA 61.284 66.667 0.00 0.00 0.00 3.10
2390 2606 3.086600 GTGGGGGAGCTGGGAGAG 61.087 72.222 0.00 0.00 0.00 3.20
2391 2607 4.741239 GGTGGGGGAGCTGGGAGA 62.741 72.222 0.00 0.00 0.00 3.71
2396 2612 2.608988 AGACTGGTGGGGGAGCTG 60.609 66.667 0.00 0.00 0.00 4.24
2397 2613 2.106923 TACAGACTGGTGGGGGAGCT 62.107 60.000 7.51 0.00 0.00 4.09
2398 2614 1.612442 TACAGACTGGTGGGGGAGC 60.612 63.158 7.51 0.00 0.00 4.70
2399 2615 1.617947 GCTACAGACTGGTGGGGGAG 61.618 65.000 7.51 0.00 0.00 4.30
2400 2616 1.612442 GCTACAGACTGGTGGGGGA 60.612 63.158 7.51 0.00 0.00 4.81
2410 2626 3.958798 TCCTATTGGTACAGGCTACAGAC 59.041 47.826 0.00 0.00 42.39 3.51
2460 2676 2.672651 TGTGGTCCTTGCATGGCG 60.673 61.111 13.75 0.00 0.00 5.69
2463 2679 0.827089 TTGGGTGTGGTCCTTGCATG 60.827 55.000 0.00 0.00 0.00 4.06
2512 2728 3.119919 GGTTTGCTGCAGAGAGAGAAATG 60.120 47.826 20.43 0.00 0.00 2.32
2517 2733 1.534595 GTTGGTTTGCTGCAGAGAGAG 59.465 52.381 20.43 0.00 0.00 3.20
2518 2734 1.134128 TGTTGGTTTGCTGCAGAGAGA 60.134 47.619 20.43 0.00 0.00 3.10
2519 2735 1.002033 GTGTTGGTTTGCTGCAGAGAG 60.002 52.381 20.43 0.00 0.00 3.20
2520 2736 1.024271 GTGTTGGTTTGCTGCAGAGA 58.976 50.000 20.43 0.77 0.00 3.10
2601 2817 3.004734 GGTAATTGGGAGGATGATTTGCG 59.995 47.826 0.00 0.00 0.00 4.85
2608 2824 7.561356 AGAAAGTTTATGGTAATTGGGAGGATG 59.439 37.037 0.00 0.00 0.00 3.51
2633 2849 7.415653 GGTTTATTTTATGCCTCTCTTGGTGAG 60.416 40.741 0.00 0.00 43.96 3.51
2635 2851 6.564328 GGTTTATTTTATGCCTCTCTTGGTG 58.436 40.000 0.00 0.00 0.00 4.17
2636 2852 5.357032 CGGTTTATTTTATGCCTCTCTTGGT 59.643 40.000 0.00 0.00 0.00 3.67
2638 2854 5.357032 ACCGGTTTATTTTATGCCTCTCTTG 59.643 40.000 0.00 0.00 0.00 3.02
2639 2855 5.506708 ACCGGTTTATTTTATGCCTCTCTT 58.493 37.500 0.00 0.00 0.00 2.85
2661 2877 4.625311 CCACCCGCAAATTAATCAAGAAAC 59.375 41.667 0.00 0.00 0.00 2.78
2662 2878 4.322349 CCCACCCGCAAATTAATCAAGAAA 60.322 41.667 0.00 0.00 0.00 2.52
2663 2879 3.194542 CCCACCCGCAAATTAATCAAGAA 59.805 43.478 0.00 0.00 0.00 2.52
2667 2883 2.096248 GACCCACCCGCAAATTAATCA 58.904 47.619 0.00 0.00 0.00 2.57
2669 2885 2.223803 TGACCCACCCGCAAATTAAT 57.776 45.000 0.00 0.00 0.00 1.40
2678 2894 1.602605 GGAAAGGTTGACCCACCCG 60.603 63.158 0.00 0.00 37.58 5.28
2794 3010 7.643528 TCTGGATTATGTAGTACGTACGTAG 57.356 40.000 27.48 13.25 35.06 3.51
2798 3014 6.634436 CGGTTTCTGGATTATGTAGTACGTAC 59.366 42.308 18.10 18.10 0.00 3.67
2801 3017 4.980434 CCGGTTTCTGGATTATGTAGTACG 59.020 45.833 0.00 0.00 0.00 3.67
2803 3019 4.202284 GCCCGGTTTCTGGATTATGTAGTA 60.202 45.833 0.00 0.00 0.00 1.82
2804 3020 3.433173 GCCCGGTTTCTGGATTATGTAGT 60.433 47.826 0.00 0.00 0.00 2.73
2805 3021 3.139077 GCCCGGTTTCTGGATTATGTAG 58.861 50.000 0.00 0.00 0.00 2.74
2806 3022 2.775384 AGCCCGGTTTCTGGATTATGTA 59.225 45.455 0.00 0.00 0.00 2.29
2807 3023 1.564348 AGCCCGGTTTCTGGATTATGT 59.436 47.619 0.00 0.00 0.00 2.29
2808 3024 2.348411 AGCCCGGTTTCTGGATTATG 57.652 50.000 0.00 0.00 0.00 1.90
2809 3025 3.023832 CAAAGCCCGGTTTCTGGATTAT 58.976 45.455 0.00 0.00 28.35 1.28
2810 3026 2.040545 TCAAAGCCCGGTTTCTGGATTA 59.959 45.455 0.00 0.00 28.35 1.75
2811 3027 1.203001 TCAAAGCCCGGTTTCTGGATT 60.203 47.619 0.00 0.00 0.00 3.01
2824 3040 2.475487 GTGACGAGTAACTGTCAAAGCC 59.525 50.000 4.89 0.00 45.84 4.35
2918 3134 2.581216 TCTCTCAACCGGAGTACTGT 57.419 50.000 9.46 0.00 44.40 3.55
2919 3135 3.082548 TCTTCTCTCAACCGGAGTACTG 58.917 50.000 9.46 0.00 44.40 2.74
2920 3136 3.009253 TCTCTTCTCTCAACCGGAGTACT 59.991 47.826 9.46 0.00 44.40 2.73
2927 3143 0.820871 CCCCTCTCTTCTCTCAACCG 59.179 60.000 0.00 0.00 0.00 4.44
2949 3165 4.371624 AGAGATGAGATGAGACCGATCT 57.628 45.455 0.00 0.00 38.15 2.75
2950 3166 5.487433 TCTAGAGATGAGATGAGACCGATC 58.513 45.833 0.00 0.00 0.00 3.69
2951 3167 5.497464 TCTAGAGATGAGATGAGACCGAT 57.503 43.478 0.00 0.00 0.00 4.18
2952 3168 4.965200 TCTAGAGATGAGATGAGACCGA 57.035 45.455 0.00 0.00 0.00 4.69
2953 3169 5.304778 TCTTCTAGAGATGAGATGAGACCG 58.695 45.833 0.00 0.00 0.00 4.79
2955 3171 6.488006 AGCTTCTTCTAGAGATGAGATGAGAC 59.512 42.308 8.51 0.00 33.49 3.36
2956 3172 6.604171 AGCTTCTTCTAGAGATGAGATGAGA 58.396 40.000 8.51 0.00 33.49 3.27
2957 3173 6.072286 GGAGCTTCTTCTAGAGATGAGATGAG 60.072 46.154 8.51 0.03 33.49 2.90
2958 3174 5.769662 GGAGCTTCTTCTAGAGATGAGATGA 59.230 44.000 8.51 0.00 33.49 2.92
2959 3175 5.335113 CGGAGCTTCTTCTAGAGATGAGATG 60.335 48.000 0.00 0.00 33.49 2.90
2960 3176 4.761739 CGGAGCTTCTTCTAGAGATGAGAT 59.238 45.833 0.00 0.00 33.49 2.75
2961 3177 4.133820 CGGAGCTTCTTCTAGAGATGAGA 58.866 47.826 0.00 0.00 33.49 3.27
2983 3199 3.618690 ATTCTCCAGGTCTTGTACAGC 57.381 47.619 0.00 0.00 0.00 4.40
3018 3234 0.594602 GCGTTACACCTTCCCCAAAC 59.405 55.000 0.00 0.00 0.00 2.93
3026 3242 3.677976 GCTACTACCATGCGTTACACCTT 60.678 47.826 0.00 0.00 0.00 3.50
3035 3251 2.268298 ACGAAAAGCTACTACCATGCG 58.732 47.619 0.00 0.00 0.00 4.73
3081 3297 3.036783 CTCTGCTTGCTCGCTTGCC 62.037 63.158 0.00 0.00 0.00 4.52
3085 3301 2.578128 CTCCTCTGCTTGCTCGCT 59.422 61.111 0.00 0.00 0.00 4.93
3086 3302 2.511145 CCTCCTCTGCTTGCTCGC 60.511 66.667 0.00 0.00 0.00 5.03
3087 3303 2.186384 CCCTCCTCTGCTTGCTCG 59.814 66.667 0.00 0.00 0.00 5.03
3095 3311 4.845580 ATTGCGCGCCCTCCTCTG 62.846 66.667 30.77 0.00 0.00 3.35
3096 3312 4.845580 CATTGCGCGCCCTCCTCT 62.846 66.667 30.77 1.68 0.00 3.69
3105 3321 4.170062 CCACTGCTCCATTGCGCG 62.170 66.667 0.00 0.00 35.36 6.86
3141 3357 2.292267 CGATCTCCCATCCCTTGTTTG 58.708 52.381 0.00 0.00 0.00 2.93
3144 3360 0.031111 TCCGATCTCCCATCCCTTGT 60.031 55.000 0.00 0.00 0.00 3.16
3148 3364 0.972883 CTTCTCCGATCTCCCATCCC 59.027 60.000 0.00 0.00 0.00 3.85
3151 3367 0.563173 TCCCTTCTCCGATCTCCCAT 59.437 55.000 0.00 0.00 0.00 4.00
3153 3369 0.830023 CCTCCCTTCTCCGATCTCCC 60.830 65.000 0.00 0.00 0.00 4.30
3154 3370 0.186386 TCCTCCCTTCTCCGATCTCC 59.814 60.000 0.00 0.00 0.00 3.71
3155 3371 1.616159 CTCCTCCCTTCTCCGATCTC 58.384 60.000 0.00 0.00 0.00 2.75
3156 3372 0.187361 CCTCCTCCCTTCTCCGATCT 59.813 60.000 0.00 0.00 0.00 2.75
3157 3373 0.186386 TCCTCCTCCCTTCTCCGATC 59.814 60.000 0.00 0.00 0.00 3.69
3158 3374 0.637195 TTCCTCCTCCCTTCTCCGAT 59.363 55.000 0.00 0.00 0.00 4.18
3159 3375 0.033011 CTTCCTCCTCCCTTCTCCGA 60.033 60.000 0.00 0.00 0.00 4.55
3160 3376 1.045911 CCTTCCTCCTCCCTTCTCCG 61.046 65.000 0.00 0.00 0.00 4.63
3172 3388 2.437651 CTCCATCTTCTTCCCCTTCCTC 59.562 54.545 0.00 0.00 0.00 3.71
3174 3390 1.492599 CCTCCATCTTCTTCCCCTTCC 59.507 57.143 0.00 0.00 0.00 3.46
3176 3392 0.922626 GCCTCCATCTTCTTCCCCTT 59.077 55.000 0.00 0.00 0.00 3.95
3177 3393 0.990818 GGCCTCCATCTTCTTCCCCT 60.991 60.000 0.00 0.00 0.00 4.79
3181 3397 0.105778 CTCCGGCCTCCATCTTCTTC 59.894 60.000 0.00 0.00 0.00 2.87
3183 3399 0.325671 TTCTCCGGCCTCCATCTTCT 60.326 55.000 0.00 0.00 0.00 2.85
3262 3478 2.301870 TCTATGGGAATGCACCGGATAC 59.698 50.000 9.46 0.00 0.00 2.24
3294 3510 1.898094 AGCGCTGACAACAATGGCA 60.898 52.632 10.39 0.00 44.25 4.92
3310 3526 0.810823 CTAGAGCTCCTTGCAGCAGC 60.811 60.000 10.93 5.67 45.94 5.25
3339 3572 3.979495 GTGTGAGTAGTGACGGTGTTAAG 59.021 47.826 0.00 0.00 0.00 1.85
3348 3581 1.335810 TGTGACCGTGTGAGTAGTGAC 59.664 52.381 0.00 0.00 0.00 3.67
3394 3628 2.378445 AAACACAAAAGCAAAGCGGT 57.622 40.000 0.00 0.00 0.00 5.68
3395 3629 2.787382 GCAAAACACAAAAGCAAAGCGG 60.787 45.455 0.00 0.00 0.00 5.52
3396 3630 2.094099 AGCAAAACACAAAAGCAAAGCG 59.906 40.909 0.00 0.00 0.00 4.68
3406 3640 1.086634 GGCCGCAAAGCAAAACACAA 61.087 50.000 0.00 0.00 0.00 3.33
3454 3688 1.008424 CATCTGACCCGATCGTCCG 60.008 63.158 15.09 2.63 31.35 4.79
3463 3712 2.096496 CAGAATTGAACGCATCTGACCC 59.904 50.000 0.00 0.00 41.38 4.46
3473 3722 0.597568 TGGGCAAGCAGAATTGAACG 59.402 50.000 0.00 0.00 31.55 3.95
3501 3750 0.039165 GCCTTTCACTTTCAAGCCCG 60.039 55.000 0.00 0.00 0.00 6.13
3542 3842 2.738521 CGTGAACTCACCGGCCAG 60.739 66.667 0.00 0.00 43.66 4.85
3562 3862 4.160635 CCGTTCATTGGACGCCGC 62.161 66.667 12.12 0.00 39.09 6.53
3565 3865 1.970917 CTCAGCCGTTCATTGGACGC 61.971 60.000 12.12 7.75 39.09 5.19
3587 3899 1.558383 GCGATAAAGTAGCCACGCG 59.442 57.895 3.53 3.53 37.06 6.01
3607 3919 3.462678 GGAGAGACAGCGACCCCC 61.463 72.222 0.00 0.00 0.00 5.40
3641 3974 4.331168 CCGAGAAAGAATTGAGATGGACAC 59.669 45.833 0.00 0.00 0.00 3.67
3657 3990 4.204012 TCTTTTCTTTTCTGGCCGAGAAA 58.796 39.130 19.97 19.97 46.93 2.52
3658 3991 3.815809 TCTTTTCTTTTCTGGCCGAGAA 58.184 40.909 12.03 12.03 39.05 2.87
3659 3992 3.485463 TCTTTTCTTTTCTGGCCGAGA 57.515 42.857 0.00 0.00 0.00 4.04
3660 3993 4.568152 TTTCTTTTCTTTTCTGGCCGAG 57.432 40.909 0.00 0.00 0.00 4.63
3661 3994 4.440940 GGTTTTCTTTTCTTTTCTGGCCGA 60.441 41.667 0.00 0.00 0.00 5.54
3673 4006 1.270041 TGCGCCCATGGTTTTCTTTTC 60.270 47.619 11.73 0.00 0.00 2.29
3684 5038 4.884257 GCTGCCATTGCGCCCATG 62.884 66.667 4.18 7.37 41.78 3.66
3719 5073 0.618968 AACCAACCACAGCCCCAAAA 60.619 50.000 0.00 0.00 0.00 2.44
3784 5138 1.341187 CGCCCCTAATAACCAACCCAA 60.341 52.381 0.00 0.00 0.00 4.12
3785 5139 0.256464 CGCCCCTAATAACCAACCCA 59.744 55.000 0.00 0.00 0.00 4.51
3786 5140 0.466739 CCGCCCCTAATAACCAACCC 60.467 60.000 0.00 0.00 0.00 4.11
3787 5141 0.466739 CCCGCCCCTAATAACCAACC 60.467 60.000 0.00 0.00 0.00 3.77
3788 5142 0.466739 CCCCGCCCCTAATAACCAAC 60.467 60.000 0.00 0.00 0.00 3.77
3806 5162 1.336795 CCCCATGCGTCAAACTTTTCC 60.337 52.381 0.00 0.00 0.00 3.13
3807 5163 1.339929 ACCCCATGCGTCAAACTTTTC 59.660 47.619 0.00 0.00 0.00 2.29
3810 5166 1.805428 GCACCCCATGCGTCAAACTT 61.805 55.000 0.00 0.00 46.55 2.66
3811 5167 2.268076 GCACCCCATGCGTCAAACT 61.268 57.895 0.00 0.00 46.55 2.66
3812 5168 2.258286 GCACCCCATGCGTCAAAC 59.742 61.111 0.00 0.00 46.55 2.93
3843 5199 6.378582 TCAGATAAAACAAAGATTTCGTGCC 58.621 36.000 0.00 0.00 0.00 5.01
3891 5247 1.369091 CGGGCCACATCTTTTCCTCG 61.369 60.000 4.39 0.00 0.00 4.63
3893 5249 1.678970 GCGGGCCACATCTTTTCCT 60.679 57.895 4.39 0.00 0.00 3.36
3909 5265 3.347588 TTTCATTCACGAGCGCGCG 62.348 57.895 31.62 31.62 42.48 6.86
3910 5266 1.859135 GTTTCATTCACGAGCGCGC 60.859 57.895 26.66 26.66 42.48 6.86
3911 5267 1.225745 GGTTTCATTCACGAGCGCG 60.226 57.895 8.75 8.75 44.79 6.86
3912 5268 0.237235 TTGGTTTCATTCACGAGCGC 59.763 50.000 0.00 0.00 0.00 5.92
3913 5269 2.307049 GTTTGGTTTCATTCACGAGCG 58.693 47.619 0.00 0.00 0.00 5.03



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

AutoCloner maintained by Alex Coulton.