Multiple sequence alignment - TraesCS2D01G530100

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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 TraesCS2D01G530100 chr2D 100.000 2658 0 0 2651 5308 616939833 616942490 0.000000e+00 4909.0
1 TraesCS2D01G530100 chr2D 100.000 2049 0 0 1 2049 616937183 616939231 0.000000e+00 3784.0
2 TraesCS2D01G530100 chr2B 84.335 1698 152 63 443 2038 752404839 752406524 0.000000e+00 1557.0
3 TraesCS2D01G530100 chr2B 91.676 853 55 11 2653 3495 752406619 752407465 0.000000e+00 1168.0
4 TraesCS2D01G530100 chr2B 86.814 857 83 24 2651 3495 752477056 752477894 0.000000e+00 929.0
5 TraesCS2D01G530100 chr2B 87.644 696 65 15 3675 4355 752478023 752478712 0.000000e+00 789.0
6 TraesCS2D01G530100 chr2B 84.300 707 60 25 3646 4347 752407564 752408224 1.250000e-180 643.0
7 TraesCS2D01G530100 chr2B 84.339 696 67 24 1349 2009 752476068 752476756 1.250000e-180 643.0
8 TraesCS2D01G530100 chr2B 87.361 451 23 15 1 446 752404312 752404733 2.220000e-133 486.0
9 TraesCS2D01G530100 chr2B 84.199 462 36 22 948 1373 752475417 752475877 1.060000e-111 414.0
10 TraesCS2D01G530100 chr2B 81.461 356 36 9 2676 3022 752485457 752485791 1.130000e-66 265.0
11 TraesCS2D01G530100 chr2B 81.188 202 25 8 1395 1584 752475865 752476065 3.310000e-32 150.0
12 TraesCS2D01G530100 chr2A 93.087 839 48 7 2652 3486 746936516 746937348 0.000000e+00 1219.0
13 TraesCS2D01G530100 chr2A 83.649 1266 109 45 851 2049 746935192 746936426 0.000000e+00 1101.0
14 TraesCS2D01G530100 chr2A 84.862 1123 90 35 3675 4781 746937485 746938543 0.000000e+00 1059.0
15 TraesCS2D01G530100 chr2A 95.909 440 11 6 9 446 746933819 746934253 0.000000e+00 706.0
16 TraesCS2D01G530100 chr2A 83.188 690 63 25 3675 4355 746952848 746953493 2.760000e-162 582.0
17 TraesCS2D01G530100 chr2A 89.398 415 18 13 443 836 746934337 746934746 2.850000e-137 499.0
18 TraesCS2D01G530100 chr2A 98.947 190 1 1 5119 5308 746938949 746939137 6.580000e-89 339.0
19 TraesCS2D01G530100 chr2A 83.146 178 20 7 4177 4351 746945023 746945193 2.560000e-33 154.0
20 TraesCS2D01G530100 chr2A 82.517 143 19 4 1833 1975 746944008 746944144 2.600000e-23 121.0
21 TraesCS2D01G530100 chr2A 87.273 55 7 0 819 873 746935134 746935188 4.440000e-06 63.9
22 TraesCS2D01G530100 chrUn 90.636 865 55 17 2651 3495 9575055 9575913 0.000000e+00 1125.0
23 TraesCS2D01G530100 chrUn 85.098 765 66 25 1320 2046 9574210 9574964 0.000000e+00 737.0
24 TraesCS2D01G530100 chrUn 82.695 705 69 25 3661 4354 9576016 9576678 1.280000e-160 577.0
25 TraesCS2D01G530100 chrUn 93.056 72 3 2 5177 5246 9577458 9577529 2.610000e-18 104.0
26 TraesCS2D01G530100 chrUn 90.769 65 6 0 5057 5121 9577248 9577312 2.630000e-13 87.9
27 TraesCS2D01G530100 chr5B 90.068 876 55 15 2651 3495 61390440 61391314 0.000000e+00 1107.0
28 TraesCS2D01G530100 chr5B 85.631 689 62 25 3646 4324 61391413 61392074 0.000000e+00 689.0
29 TraesCS2D01G530100 chr5B 88.462 208 24 0 1833 2040 61390138 61390345 8.820000e-63 252.0
30 TraesCS2D01G530100 chr6B 82.482 685 97 18 2819 3495 710289728 710289059 3.560000e-161 579.0
31 TraesCS2D01G530100 chr6B 86.920 474 53 6 2819 3288 42368332 42368800 1.690000e-144 523.0
32 TraesCS2D01G530100 chr7B 83.824 612 79 15 2819 3423 532036030 532036628 9.980000e-157 564.0
33 TraesCS2D01G530100 chr7B 88.000 100 12 0 268 367 740313405 740313306 9.340000e-23 119.0
34 TraesCS2D01G530100 chr3B 86.920 474 53 6 2819 3288 773725719 773725251 1.690000e-144 523.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G530100 chr2D 616937183 616942490 5307 False 4346.500000 4909 100.000000 1 5308 2 chr2D.!!$F1 5307
1 TraesCS2D01G530100 chr2B 752404312 752408224 3912 False 963.500000 1557 86.918000 1 4347 4 chr2B.!!$F2 4346
2 TraesCS2D01G530100 chr2B 752475417 752478712 3295 False 585.000000 929 84.836800 948 4355 5 chr2B.!!$F3 3407
3 TraesCS2D01G530100 chr2A 746933819 746939137 5318 False 712.414286 1219 90.446429 9 5308 7 chr2A.!!$F2 5299
4 TraesCS2D01G530100 chr2A 746952848 746953493 645 False 582.000000 582 83.188000 3675 4355 1 chr2A.!!$F1 680
5 TraesCS2D01G530100 chrUn 9574210 9577529 3319 False 526.180000 1125 88.450800 1320 5246 5 chrUn.!!$F1 3926
6 TraesCS2D01G530100 chr5B 61390138 61392074 1936 False 682.666667 1107 88.053667 1833 4324 3 chr5B.!!$F1 2491
7 TraesCS2D01G530100 chr6B 710289059 710289728 669 True 579.000000 579 82.482000 2819 3495 1 chr6B.!!$R1 676
8 TraesCS2D01G530100 chr7B 532036030 532036628 598 False 564.000000 564 83.824000 2819 3423 1 chr7B.!!$F1 604

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
695 833 0.116940 ATGGCATTGGTGGGTTCCTT 59.883 50.0 0.0 0.0 0.00 3.36 F
906 1509 0.323542 AGGTGGGAGACGAGACGAAT 60.324 55.0 0.0 0.0 0.00 3.34 F
1715 2633 0.046242 ATTGGGATCAGGGGGTCAGA 59.954 55.0 0.0 0.0 0.00 3.27 F
1847 2804 0.887933 CTGGTGTGTTACATTGCCCC 59.112 55.0 0.0 0.0 0.00 5.80 F
3479 4496 1.191489 TTCGTGGAGACCTCATGGCA 61.191 55.0 0.0 0.0 36.63 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 2473 1.877637 TTGGTTCAGTCATGTCCGTG 58.122 50.000 0.00 0.00 0.0 4.94 R
2800 3786 1.942776 TCAGATCTGCTCCCTGTCAA 58.057 50.000 18.36 0.00 0.0 3.18 R
3499 4516 0.392998 ATGGACCGATTGACCTGTGC 60.393 55.000 0.00 0.00 0.0 4.57 R
3673 4732 1.066143 GTTGCCAAGCTCTACTGCCTA 60.066 52.381 0.00 0.00 0.0 3.93 R
4458 5603 0.244721 TCAGCACCGTGTCAGATCTG 59.755 55.000 17.07 17.07 0.0 2.90 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
36 38 3.735237 ACGCTGGGTACAAGATATCAG 57.265 47.619 5.32 0.00 0.00 2.90
191 195 2.473457 TCGGACACGACGATCATCA 58.527 52.632 0.00 0.00 45.59 3.07
193 197 1.002792 TCGGACACGACGATCATCATC 60.003 52.381 0.00 0.00 45.59 2.92
195 199 2.656085 GGACACGACGATCATCATCTC 58.344 52.381 0.00 0.00 0.00 2.75
199 203 5.438761 ACACGACGATCATCATCTCAATA 57.561 39.130 0.00 0.00 0.00 1.90
241 245 4.498520 TACGCTGCTGCTCGCTCC 62.499 66.667 14.03 0.00 40.11 4.70
546 659 2.813179 GCCGCTACCATGAACGCTG 61.813 63.158 0.00 0.00 0.00 5.18
551 664 1.945387 CTACCATGAACGCTGCTGAT 58.055 50.000 0.00 0.00 0.00 2.90
569 682 0.457035 ATGACGCCATTGCCAATGTC 59.543 50.000 15.83 7.92 37.18 3.06
576 693 1.679944 CCATTGCCAATGTCGGTCTCT 60.680 52.381 15.83 0.00 37.18 3.10
577 694 1.399440 CATTGCCAATGTCGGTCTCTG 59.601 52.381 9.30 0.00 34.18 3.35
579 696 1.262417 TGCCAATGTCGGTCTCTGTA 58.738 50.000 0.00 0.00 0.00 2.74
581 698 1.739371 GCCAATGTCGGTCTCTGTACC 60.739 57.143 0.00 0.00 36.08 3.34
582 699 1.825474 CCAATGTCGGTCTCTGTACCT 59.175 52.381 0.00 0.00 37.39 3.08
583 700 2.417379 CCAATGTCGGTCTCTGTACCTG 60.417 54.545 0.00 0.00 37.39 4.00
585 702 2.509166 TGTCGGTCTCTGTACCTGAT 57.491 50.000 0.00 0.00 37.39 2.90
587 704 1.405821 GTCGGTCTCTGTACCTGATGG 59.594 57.143 0.00 0.00 37.39 3.51
590 707 1.405821 GGTCTCTGTACCTGATGGACG 59.594 57.143 0.00 0.00 36.53 4.79
591 708 1.405821 GTCTCTGTACCTGATGGACGG 59.594 57.143 0.00 0.00 37.04 4.79
615 753 1.760029 GGGAGATTCAGAGGACAGGAC 59.240 57.143 0.00 0.00 0.00 3.85
642 780 2.116869 TATATGCAGGGGAGCTGGAA 57.883 50.000 0.00 0.00 34.99 3.53
689 827 3.069946 ACGCATGGCATTGGTGGG 61.070 61.111 0.00 0.00 0.00 4.61
691 829 2.648143 CGCATGGCATTGGTGGGTT 61.648 57.895 0.00 0.00 0.00 4.11
692 830 1.218854 GCATGGCATTGGTGGGTTC 59.781 57.895 0.00 0.00 0.00 3.62
693 831 1.899617 CATGGCATTGGTGGGTTCC 59.100 57.895 0.00 0.00 0.00 3.62
694 832 0.615544 CATGGCATTGGTGGGTTCCT 60.616 55.000 0.00 0.00 0.00 3.36
695 833 0.116940 ATGGCATTGGTGGGTTCCTT 59.883 50.000 0.00 0.00 0.00 3.36
696 834 0.831288 TGGCATTGGTGGGTTCCTTG 60.831 55.000 0.00 0.00 0.00 3.61
697 835 1.293179 GCATTGGTGGGTTCCTTGC 59.707 57.895 0.00 0.00 33.17 4.01
698 836 1.187567 GCATTGGTGGGTTCCTTGCT 61.188 55.000 0.00 0.00 35.79 3.91
699 837 0.890683 CATTGGTGGGTTCCTTGCTC 59.109 55.000 0.00 0.00 0.00 4.26
700 838 0.609131 ATTGGTGGGTTCCTTGCTCG 60.609 55.000 0.00 0.00 0.00 5.03
701 839 1.990160 TTGGTGGGTTCCTTGCTCGT 61.990 55.000 0.00 0.00 0.00 4.18
702 840 1.966451 GGTGGGTTCCTTGCTCGTG 60.966 63.158 0.00 0.00 0.00 4.35
703 841 1.070786 GTGGGTTCCTTGCTCGTGA 59.929 57.895 0.00 0.00 0.00 4.35
704 842 0.951040 GTGGGTTCCTTGCTCGTGAG 60.951 60.000 0.00 0.00 0.00 3.51
849 1426 2.760092 GCATCACCCTAAATGCCAGAAA 59.240 45.455 0.00 0.00 41.92 2.52
897 1500 3.155167 CGGGCCTAGGTGGGAGAC 61.155 72.222 11.31 0.00 36.00 3.36
898 1501 3.155167 GGGCCTAGGTGGGAGACG 61.155 72.222 11.31 0.00 36.00 4.18
905 1508 0.325933 TAGGTGGGAGACGAGACGAA 59.674 55.000 0.00 0.00 0.00 3.85
906 1509 0.323542 AGGTGGGAGACGAGACGAAT 60.324 55.000 0.00 0.00 0.00 3.34
943 1546 0.529992 GCCGAGGACCGTGGATAAAG 60.530 60.000 9.05 0.00 36.31 1.85
965 1568 1.808411 TCAGTTTGACATCCGAAGCC 58.192 50.000 0.00 0.00 0.00 4.35
978 1581 4.643387 AAGCCGGTGGGAGTGTGC 62.643 66.667 1.90 0.00 34.06 4.57
1027 1641 2.671070 CTACAGCCACCACCCTGG 59.329 66.667 0.00 0.00 45.02 4.45
1034 1648 2.285368 CACCACCCTGGCCTCCTA 60.285 66.667 3.32 0.00 42.67 2.94
1169 1804 1.381327 CCCTCGCCCTCAACTCCTA 60.381 63.158 0.00 0.00 0.00 2.94
1176 1811 1.590147 CCTCAACTCCTACCGCGTT 59.410 57.895 4.92 0.00 0.00 4.84
1231 1866 0.324460 CGTAACCCCTCAGACCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
1240 1875 4.824515 AGACCTCCTCCCCGCTCG 62.825 72.222 0.00 0.00 0.00 5.03
1254 1898 1.445716 CGCTCGTTCTCTATCCCCGT 61.446 60.000 0.00 0.00 0.00 5.28
1260 1916 2.117051 GTTCTCTATCCCCGTTCCCTT 58.883 52.381 0.00 0.00 0.00 3.95
1267 1923 2.125512 CCCGTTCCCTTCTGCTCG 60.126 66.667 0.00 0.00 0.00 5.03
1293 1955 2.908073 GCGGGTGCCTGTTTGTGAG 61.908 63.158 0.00 0.00 33.98 3.51
1308 1970 2.257676 GAGCTGCAGCACTTTGGC 59.742 61.111 38.24 12.01 45.16 4.52
1447 2325 2.176546 CATTCCGTTGCCGCACTG 59.823 61.111 0.00 0.00 0.00 3.66
1475 2370 1.444553 GAGCTCCCAGTGACGAACG 60.445 63.158 0.87 0.00 0.00 3.95
1477 2372 2.432628 CTCCCAGTGACGAACGCC 60.433 66.667 0.00 0.00 0.00 5.68
1486 2393 0.671796 TGACGAACGCCTCTTCTTGA 59.328 50.000 0.00 0.00 0.00 3.02
1490 2397 3.139077 ACGAACGCCTCTTCTTGATTTT 58.861 40.909 0.00 0.00 0.00 1.82
1566 2473 3.391049 GCCTGGACACGAGGTAATTATC 58.609 50.000 0.00 0.00 32.60 1.75
1568 2475 4.369182 CCTGGACACGAGGTAATTATCAC 58.631 47.826 0.00 0.00 0.00 3.06
1617 2533 3.006752 AGTTTCTGCTGGACTGAGAGAAG 59.993 47.826 0.00 0.00 0.00 2.85
1619 2535 2.603021 TCTGCTGGACTGAGAGAAGTT 58.397 47.619 0.00 0.00 0.00 2.66
1713 2631 0.253583 TCATTGGGATCAGGGGGTCA 60.254 55.000 0.00 0.00 0.00 4.02
1715 2633 0.046242 ATTGGGATCAGGGGGTCAGA 59.954 55.000 0.00 0.00 0.00 3.27
1728 2646 2.771943 GGGGTCAGACAATGTAGGATCA 59.228 50.000 2.17 0.00 0.00 2.92
1734 2652 6.166279 GTCAGACAATGTAGGATCACTCAAA 58.834 40.000 0.00 0.00 0.00 2.69
1740 2658 6.876257 ACAATGTAGGATCACTCAAAGACTTC 59.124 38.462 0.00 0.00 0.00 3.01
1744 2662 3.578716 AGGATCACTCAAAGACTTCGGAA 59.421 43.478 0.00 0.00 0.00 4.30
1785 2703 2.439507 GGTGAGCTGATTATTCCCCTCA 59.560 50.000 0.00 0.00 0.00 3.86
1786 2704 3.495806 GGTGAGCTGATTATTCCCCTCAG 60.496 52.174 0.00 0.00 39.50 3.35
1787 2705 3.389329 GTGAGCTGATTATTCCCCTCAGA 59.611 47.826 0.00 0.00 38.96 3.27
1788 2706 3.645212 TGAGCTGATTATTCCCCTCAGAG 59.355 47.826 0.00 0.00 38.96 3.35
1789 2707 3.645687 GAGCTGATTATTCCCCTCAGAGT 59.354 47.826 0.00 0.00 38.96 3.24
1790 2708 3.645687 AGCTGATTATTCCCCTCAGAGTC 59.354 47.826 3.11 0.00 38.96 3.36
1794 2712 3.491766 TTATTCCCCTCAGAGTCCAGT 57.508 47.619 0.00 0.00 0.00 4.00
1810 2728 3.948473 GTCCAGTCATCTGCTACTCTGTA 59.052 47.826 0.00 0.00 40.09 2.74
1817 2768 6.831353 AGTCATCTGCTACTCTGTATTACTGT 59.169 38.462 0.00 0.00 0.00 3.55
1844 2801 3.125316 GCTACTCTGGTGTGTTACATTGC 59.875 47.826 0.00 0.00 0.00 3.56
1845 2802 2.504367 ACTCTGGTGTGTTACATTGCC 58.496 47.619 0.00 0.00 0.00 4.52
1847 2804 0.887933 CTGGTGTGTTACATTGCCCC 59.112 55.000 0.00 0.00 0.00 5.80
1854 2812 3.010696 TGTGTTACATTGCCCCTTGGATA 59.989 43.478 0.00 0.00 0.00 2.59
1867 2825 3.136443 CCCTTGGATAGGTTGCTGATGTA 59.864 47.826 0.00 0.00 43.07 2.29
1868 2826 4.385199 CCCTTGGATAGGTTGCTGATGTAA 60.385 45.833 0.00 0.00 43.07 2.41
1883 2841 7.102993 TGCTGATGTAAATTCAGTTGTAGCTA 58.897 34.615 0.00 0.00 42.12 3.32
1901 2859 1.976132 TAGCAGCAGATGGTGGCCTC 61.976 60.000 13.41 0.00 43.24 4.70
1976 2934 2.248248 CAGAGGTCCTGTGGTTACTCA 58.752 52.381 8.20 0.00 38.10 3.41
2013 2971 6.183360 CCTCGGCATAGATGATATTCGTAGAA 60.183 42.308 0.00 0.00 45.90 2.10
2025 2983 6.645003 TGATATTCGTAGAACCATCGATTTGG 59.355 38.462 3.43 3.43 45.90 3.28
2752 3716 1.732941 TGGTGGTATGTTCACGATGC 58.267 50.000 0.00 0.00 36.09 3.91
2755 3719 1.588404 GTGGTATGTTCACGATGCTCG 59.412 52.381 0.00 4.36 46.93 5.03
3049 4035 2.028930 AGTAGGTTGCTTCTCAGTTCCG 60.029 50.000 0.00 0.00 0.00 4.30
3307 4317 5.528690 ACAGTATCCATGCATGATACAACAC 59.471 40.000 29.97 18.95 35.05 3.32
3315 4325 5.861222 TGCATGATACAACACTACAACTG 57.139 39.130 0.00 0.00 0.00 3.16
3317 4327 5.408299 TGCATGATACAACACTACAACTGAC 59.592 40.000 0.00 0.00 0.00 3.51
3322 4335 7.915508 TGATACAACACTACAACTGACTTTTG 58.084 34.615 0.00 0.00 0.00 2.44
3324 4337 5.250200 ACAACACTACAACTGACTTTTGGA 58.750 37.500 0.00 0.00 0.00 3.53
3325 4338 5.885912 ACAACACTACAACTGACTTTTGGAT 59.114 36.000 0.00 0.00 0.00 3.41
3326 4339 7.051623 ACAACACTACAACTGACTTTTGGATA 58.948 34.615 0.00 0.00 0.00 2.59
3339 4352 7.999679 TGACTTTTGGATAAAATCAGCATAGG 58.000 34.615 0.00 0.00 35.39 2.57
3365 4378 3.058983 TGTGATGTGTCGCAAATTCAGAC 60.059 43.478 0.00 2.19 41.62 3.51
3470 4487 9.974750 CTTCTAAGATTTAAATTTCGTGGAGAC 57.025 33.333 1.43 0.00 0.00 3.36
3479 4496 1.191489 TTCGTGGAGACCTCATGGCA 61.191 55.000 0.00 0.00 36.63 4.92
3495 4512 2.436417 TGGCAGCAGAAACCATCTAAC 58.564 47.619 0.00 0.00 36.32 2.34
3497 4514 3.084786 GGCAGCAGAAACCATCTAACTT 58.915 45.455 0.00 0.00 36.32 2.66
3498 4515 3.119708 GGCAGCAGAAACCATCTAACTTG 60.120 47.826 0.00 0.00 36.32 3.16
3499 4516 3.119708 GCAGCAGAAACCATCTAACTTGG 60.120 47.826 0.00 0.00 36.32 3.61
3500 4517 3.084786 AGCAGAAACCATCTAACTTGGC 58.915 45.455 0.00 0.00 37.81 4.52
3501 4518 2.819608 GCAGAAACCATCTAACTTGGCA 59.180 45.455 0.00 0.00 37.81 4.92
3502 4519 3.366374 GCAGAAACCATCTAACTTGGCAC 60.366 47.826 0.00 0.00 37.81 5.01
3516 4551 1.745489 GGCACAGGTCAATCGGTCC 60.745 63.158 0.00 0.00 0.00 4.46
3525 4560 6.317642 CACAGGTCAATCGGTCCATTTAAATA 59.682 38.462 0.00 0.00 0.00 1.40
3526 4561 6.542370 ACAGGTCAATCGGTCCATTTAAATAG 59.458 38.462 0.00 0.00 0.00 1.73
3530 4565 8.248253 GGTCAATCGGTCCATTTAAATAGTTTT 58.752 33.333 0.00 0.00 0.00 2.43
3531 4566 9.634163 GTCAATCGGTCCATTTAAATAGTTTTT 57.366 29.630 0.00 0.00 0.00 1.94
3574 4609 5.497464 TGGATTGTGTTCCACTATCAAGA 57.503 39.130 16.58 2.47 44.17 3.02
3575 4610 5.491070 TGGATTGTGTTCCACTATCAAGAG 58.509 41.667 16.58 0.00 44.17 2.85
3576 4611 5.248248 TGGATTGTGTTCCACTATCAAGAGA 59.752 40.000 16.58 0.00 44.17 3.10
3577 4612 6.070021 TGGATTGTGTTCCACTATCAAGAGAT 60.070 38.462 16.58 0.00 44.17 2.75
3578 4613 7.125659 TGGATTGTGTTCCACTATCAAGAGATA 59.874 37.037 16.58 0.00 44.17 1.98
3579 4614 7.987458 GGATTGTGTTCCACTATCAAGAGATAA 59.013 37.037 16.58 0.00 44.17 1.75
3580 4615 9.383519 GATTGTGTTCCACTATCAAGAGATAAA 57.616 33.333 11.97 0.00 42.77 1.40
3581 4616 8.777865 TTGTGTTCCACTATCAAGAGATAAAG 57.222 34.615 0.00 0.00 36.35 1.85
3582 4617 7.331026 TGTGTTCCACTATCAAGAGATAAAGG 58.669 38.462 0.00 0.00 36.35 3.11
3583 4618 7.180229 TGTGTTCCACTATCAAGAGATAAAGGA 59.820 37.037 0.00 0.00 37.68 3.36
3584 4619 8.041323 GTGTTCCACTATCAAGAGATAAAGGAA 58.959 37.037 11.29 11.29 41.99 3.36
3585 4620 8.260818 TGTTCCACTATCAAGAGATAAAGGAAG 58.739 37.037 13.88 0.00 43.28 3.46
3586 4621 8.478877 GTTCCACTATCAAGAGATAAAGGAAGA 58.521 37.037 13.88 0.00 43.28 2.87
3587 4622 8.609617 TCCACTATCAAGAGATAAAGGAAGAA 57.390 34.615 0.00 0.00 37.07 2.52
3588 4623 9.046846 TCCACTATCAAGAGATAAAGGAAGAAA 57.953 33.333 0.00 0.00 37.07 2.52
3589 4624 9.672673 CCACTATCAAGAGATAAAGGAAGAAAA 57.327 33.333 0.00 0.00 36.35 2.29
3595 4630 9.184523 TCAAGAGATAAAGGAAGAAAAACAACA 57.815 29.630 0.00 0.00 0.00 3.33
3596 4631 9.801873 CAAGAGATAAAGGAAGAAAAACAACAA 57.198 29.630 0.00 0.00 0.00 2.83
3632 4667 5.337571 CCTGAAATAGTTAGACTGTGCCTGA 60.338 44.000 0.00 0.00 0.00 3.86
3765 4824 6.761714 CAGTAGGATCGTTTATTAAGCCAACT 59.238 38.462 0.00 0.00 0.00 3.16
3898 4962 6.539649 TCCATGTATTTACTATTTCGCTGC 57.460 37.500 0.00 0.00 0.00 5.25
3900 4964 6.202762 TCCATGTATTTACTATTTCGCTGCAG 59.797 38.462 10.11 10.11 0.00 4.41
3911 4975 0.036483 TCGCTGCAGCTGGATTGTAA 60.036 50.000 34.22 9.05 39.32 2.41
3913 4977 2.158971 TCGCTGCAGCTGGATTGTAATA 60.159 45.455 34.22 7.73 39.32 0.98
3916 4981 4.070716 GCTGCAGCTGGATTGTAATATCT 58.929 43.478 31.33 0.00 38.21 1.98
3918 4983 4.309933 TGCAGCTGGATTGTAATATCTCG 58.690 43.478 17.12 0.00 0.00 4.04
3920 4985 4.564041 CAGCTGGATTGTAATATCTCGCT 58.436 43.478 5.57 0.00 33.52 4.93
4023 5100 1.656652 CTGACGGGACATTCATGGAC 58.343 55.000 0.00 0.00 0.00 4.02
4077 5154 4.523173 CCCTTAAGAGATCCATACGCTGTA 59.477 45.833 3.36 0.00 0.00 2.74
4086 5163 4.729227 TCCATACGCTGTATTCTGTCAA 57.271 40.909 0.00 0.00 0.00 3.18
4113 5190 6.317140 TCAGTATGAGAATTTGACATCCTTGC 59.683 38.462 0.00 0.00 42.56 4.01
4114 5191 6.094464 CAGTATGAGAATTTGACATCCTTGCA 59.906 38.462 0.00 0.00 39.69 4.08
4183 5280 3.646534 AGATTAAATTTGGGGAGCCTGG 58.353 45.455 0.00 0.00 0.00 4.45
4195 5292 2.276309 GAGCCTGGGCCAGCAAGTAT 62.276 60.000 28.51 8.92 43.17 2.12
4230 5327 0.540923 GCACTGATGGCTCTTCTCCT 59.459 55.000 0.00 0.00 0.00 3.69
4232 5329 2.630158 CACTGATGGCTCTTCTCCTTG 58.370 52.381 0.00 0.00 0.00 3.61
4233 5330 2.235650 CACTGATGGCTCTTCTCCTTGA 59.764 50.000 0.00 0.00 0.00 3.02
4236 5333 4.018597 ACTGATGGCTCTTCTCCTTGAAAT 60.019 41.667 0.00 0.00 33.79 2.17
4238 5335 6.065976 TGATGGCTCTTCTCCTTGAAATTA 57.934 37.500 0.00 0.00 33.79 1.40
4239 5336 5.882557 TGATGGCTCTTCTCCTTGAAATTAC 59.117 40.000 0.00 0.00 33.79 1.89
4290 5389 0.110486 GGCTCTTGTCCTGGGTGAAA 59.890 55.000 0.00 0.00 0.00 2.69
4339 5438 5.520748 ACCAGAACTATGTCCCATTTCTT 57.479 39.130 0.00 0.00 0.00 2.52
4360 5459 9.959721 TTTCTTGAATGGAGGTTATATATAGCC 57.040 33.333 15.87 15.87 34.24 3.93
4361 5460 8.679344 TCTTGAATGGAGGTTATATATAGCCA 57.321 34.615 23.14 14.89 36.24 4.75
4363 5462 9.911788 CTTGAATGGAGGTTATATATAGCCATT 57.088 33.333 23.14 21.29 44.67 3.16
4369 5468 9.739276 TGGAGGTTATATATAGCCATTTTCTTG 57.261 33.333 23.14 0.00 36.24 3.02
4370 5469 9.959721 GGAGGTTATATATAGCCATTTTCTTGA 57.040 33.333 23.14 0.00 36.24 3.02
4458 5603 1.100510 TGCTTCTCATTGATGCTGCC 58.899 50.000 0.00 0.00 43.64 4.85
4478 5624 1.134877 CAGATCTGACACGGTGCTGAT 60.135 52.381 18.34 14.48 0.00 2.90
4490 5636 4.079253 ACGGTGCTGATTAACAAAAGGAT 58.921 39.130 0.00 0.00 0.00 3.24
4494 5640 5.869344 GGTGCTGATTAACAAAAGGATTTCC 59.131 40.000 0.00 0.00 37.28 3.13
4512 5665 4.640771 TTCCTCACTTAATGCAGGAACT 57.359 40.909 0.00 0.00 38.57 3.01
4611 5765 4.831155 AGCAGGCTGTATTATGCATCAATT 59.169 37.500 17.16 0.00 41.14 2.32
4660 5814 4.760715 AGCATCATTGACATTGGATAGCTC 59.239 41.667 0.00 0.00 0.00 4.09
4690 5844 3.126831 GACTCGGCAGTTGATTAGGATG 58.873 50.000 0.00 0.00 30.63 3.51
4701 5855 2.705658 TGATTAGGATGCCACACCCTAG 59.294 50.000 0.00 0.00 34.39 3.02
4783 5970 5.075858 TGAGTTTGCCCATTCATTCATTC 57.924 39.130 0.00 0.00 0.00 2.67
4790 5977 3.689280 GCCCATTCATTCATTCTGGAGGA 60.689 47.826 0.00 0.00 0.00 3.71
4793 5980 5.243283 CCCATTCATTCATTCTGGAGGATTC 59.757 44.000 0.00 0.00 0.00 2.52
4836 6023 1.448985 TGCTGAATTGTTAGGGCGAC 58.551 50.000 0.00 0.00 0.00 5.19
4880 6068 8.770438 TTTCAAACTTTGTTGCTTGATAGTTT 57.230 26.923 1.44 0.00 36.55 2.66
4903 6091 5.966742 AGATATTGATAGTGCAGAGCGTA 57.033 39.130 0.00 0.00 0.00 4.42
4960 6148 6.402983 CCTGAACATCTGCTCTATGAACAAAC 60.403 42.308 0.00 0.00 0.00 2.93
4971 6159 7.443879 TGCTCTATGAACAAACTTGTGATGTAA 59.556 33.333 0.00 0.00 41.31 2.41
4972 6160 8.454106 GCTCTATGAACAAACTTGTGATGTAAT 58.546 33.333 0.00 0.00 41.31 1.89
4975 6163 9.897744 CTATGAACAAACTTGTGATGTAATTGT 57.102 29.630 0.00 0.00 41.31 2.71
4977 6165 8.404889 TGAACAAACTTGTGATGTAATTGTTG 57.595 30.769 5.79 0.00 41.31 3.33
4978 6166 6.826893 ACAAACTTGTGATGTAATTGTTGC 57.173 33.333 0.00 0.00 40.49 4.17
4985 6173 6.682423 TGTGATGTAATTGTTGCTCATAGG 57.318 37.500 0.00 0.00 0.00 2.57
4987 6175 5.590259 GTGATGTAATTGTTGCTCATAGGGT 59.410 40.000 0.00 0.00 0.00 4.34
4988 6176 5.822519 TGATGTAATTGTTGCTCATAGGGTC 59.177 40.000 0.00 0.00 0.00 4.46
4989 6177 4.523083 TGTAATTGTTGCTCATAGGGTCC 58.477 43.478 0.00 0.00 0.00 4.46
4991 6179 5.427157 TGTAATTGTTGCTCATAGGGTCCTA 59.573 40.000 0.00 0.00 0.00 2.94
4992 6180 4.696479 ATTGTTGCTCATAGGGTCCTAG 57.304 45.455 2.97 0.00 31.45 3.02
5011 6199 2.235016 AGCTAGCTAGGATTCCTCGTG 58.765 52.381 17.69 2.35 34.61 4.35
5012 6200 1.271102 GCTAGCTAGGATTCCTCGTGG 59.729 57.143 22.10 0.00 34.61 4.94
5014 6202 0.760945 AGCTAGGATTCCTCGTGGGG 60.761 60.000 8.94 0.00 34.61 4.96
5015 6203 1.759459 GCTAGGATTCCTCGTGGGGG 61.759 65.000 8.94 0.00 34.61 5.40
5017 6205 2.252012 TAGGATTCCTCGTGGGGGCT 62.252 60.000 8.94 0.00 34.61 5.19
5019 6207 1.342672 GGATTCCTCGTGGGGGCTAA 61.343 60.000 3.23 0.00 35.33 3.09
5021 6227 1.975680 GATTCCTCGTGGGGGCTAATA 59.024 52.381 3.23 0.00 35.33 0.98
5035 6241 2.356741 GGCTAATAACCTCTTGCCACCA 60.357 50.000 0.00 0.00 40.04 4.17
5037 6243 1.821216 AATAACCTCTTGCCACCACG 58.179 50.000 0.00 0.00 0.00 4.94
5040 6246 1.978455 AACCTCTTGCCACCACGTCA 61.978 55.000 0.00 0.00 0.00 4.35
5085 6291 3.016031 TGTTGTTCTTGCACACAGTCAT 58.984 40.909 0.00 0.00 0.00 3.06
5087 6293 1.948834 TGTTCTTGCACACAGTCATGG 59.051 47.619 0.00 0.00 0.00 3.66
5089 6295 1.596603 TCTTGCACACAGTCATGGTG 58.403 50.000 0.00 0.00 41.95 4.17
5121 6327 1.294041 TCCTGACATGGGTGCCATTA 58.706 50.000 0.00 0.00 42.23 1.90
5122 6328 1.064758 TCCTGACATGGGTGCCATTAC 60.065 52.381 0.00 0.00 42.23 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.517316 CTTGTACCCAGCGTTTCTGC 59.483 55.000 0.00 0.00 41.50 4.26
36 38 2.907897 AAGCGTCTATGCGAGGGTGC 62.908 60.000 0.00 0.00 38.17 5.01
191 195 9.512588 ACTCTGTTTGAATTTCTGTATTGAGAT 57.487 29.630 0.00 0.00 0.00 2.75
193 197 9.956720 AAACTCTGTTTGAATTTCTGTATTGAG 57.043 29.630 0.00 0.00 0.00 3.02
210 214 4.152402 CAGCAGCGTACATAAAACTCTGTT 59.848 41.667 0.00 0.00 33.29 3.16
212 216 3.484229 GCAGCAGCGTACATAAAACTCTG 60.484 47.826 0.00 0.00 33.76 3.35
241 245 1.123756 GTACGTTTCTTTCCTCACGCG 59.876 52.381 3.53 3.53 36.05 6.01
242 246 2.155155 CAGTACGTTTCTTTCCTCACGC 59.845 50.000 0.00 0.00 36.05 5.34
243 247 2.729882 CCAGTACGTTTCTTTCCTCACG 59.270 50.000 0.00 0.00 38.62 4.35
246 250 1.725164 CGCCAGTACGTTTCTTTCCTC 59.275 52.381 0.00 0.00 0.00 3.71
546 659 1.936436 TTGGCAATGGCGTCATCAGC 61.936 55.000 16.40 16.40 42.47 4.26
551 664 1.882311 GACATTGGCAATGGCGTCA 59.118 52.632 35.77 0.00 43.21 4.35
569 682 1.405821 GTCCATCAGGTACAGAGACCG 59.594 57.143 0.00 0.00 44.88 4.79
576 693 1.119684 CATCCCGTCCATCAGGTACA 58.880 55.000 0.00 0.00 35.89 2.90
577 694 0.393077 CCATCCCGTCCATCAGGTAC 59.607 60.000 0.00 0.00 35.89 3.34
579 696 2.072487 CCCATCCCGTCCATCAGGT 61.072 63.158 0.00 0.00 35.89 4.00
581 698 0.760567 TCTCCCATCCCGTCCATCAG 60.761 60.000 0.00 0.00 0.00 2.90
582 699 0.104986 ATCTCCCATCCCGTCCATCA 60.105 55.000 0.00 0.00 0.00 3.07
583 700 1.002544 GAATCTCCCATCCCGTCCATC 59.997 57.143 0.00 0.00 0.00 3.51
585 702 0.326143 TGAATCTCCCATCCCGTCCA 60.326 55.000 0.00 0.00 0.00 4.02
587 704 1.342819 CTCTGAATCTCCCATCCCGTC 59.657 57.143 0.00 0.00 0.00 4.79
590 707 1.696884 GTCCTCTGAATCTCCCATCCC 59.303 57.143 0.00 0.00 0.00 3.85
591 708 2.368221 CTGTCCTCTGAATCTCCCATCC 59.632 54.545 0.00 0.00 0.00 3.51
615 753 1.086696 CCCCTGCATATAAATCGCCG 58.913 55.000 0.00 0.00 0.00 6.46
862 1465 3.070576 GCCCAATGCACTCCACCC 61.071 66.667 0.00 0.00 40.77 4.61
887 1490 0.323542 ATTCGTCTCGTCTCCCACCT 60.324 55.000 0.00 0.00 0.00 4.00
892 1495 1.400846 TGCAGTATTCGTCTCGTCTCC 59.599 52.381 0.00 0.00 0.00 3.71
897 1500 1.202973 CCGCTGCAGTATTCGTCTCG 61.203 60.000 16.64 6.59 0.00 4.04
898 1501 1.483424 GCCGCTGCAGTATTCGTCTC 61.483 60.000 16.64 0.00 37.47 3.36
905 1508 2.892425 GCTTCGCCGCTGCAGTAT 60.892 61.111 16.64 0.00 37.32 2.12
929 1532 3.671716 ACTGAAACTTTATCCACGGTCC 58.328 45.455 0.00 0.00 0.00 4.46
943 1546 3.555518 GCTTCGGATGTCAAACTGAAAC 58.444 45.455 0.00 0.00 32.20 2.78
1231 1866 0.822532 GGATAGAGAACGAGCGGGGA 60.823 60.000 0.00 0.00 0.00 4.81
1240 1875 1.790818 AGGGAACGGGGATAGAGAAC 58.209 55.000 0.00 0.00 0.00 3.01
1254 1898 1.293498 GTCAGCGAGCAGAAGGGAA 59.707 57.895 0.00 0.00 0.00 3.97
1287 1949 0.382873 CAAAGTGCTGCAGCTCACAA 59.617 50.000 36.61 16.02 42.66 3.33
1293 1955 4.712425 CCGCCAAAGTGCTGCAGC 62.712 66.667 31.89 31.89 42.50 5.25
1475 2370 3.930634 ACTGCAAAATCAAGAAGAGGC 57.069 42.857 0.00 0.00 0.00 4.70
1477 2372 7.168804 GGAAAAGAACTGCAAAATCAAGAAGAG 59.831 37.037 0.00 0.00 0.00 2.85
1486 2393 2.102252 TGCCGGAAAAGAACTGCAAAAT 59.898 40.909 5.05 0.00 0.00 1.82
1490 2397 1.781025 CGTGCCGGAAAAGAACTGCA 61.781 55.000 5.05 0.00 0.00 4.41
1539 2446 3.958147 CTCGTGTCCAGGCCGCAAT 62.958 63.158 0.00 0.00 0.00 3.56
1540 2447 4.680237 CTCGTGTCCAGGCCGCAA 62.680 66.667 0.00 0.00 0.00 4.85
1566 2473 1.877637 TTGGTTCAGTCATGTCCGTG 58.122 50.000 0.00 0.00 0.00 4.94
1568 2475 4.475944 GAATTTTGGTTCAGTCATGTCCG 58.524 43.478 0.00 0.00 0.00 4.79
1617 2533 5.053145 AGTTGTCTGTCATCAGTTCTCAAC 58.947 41.667 0.00 0.00 41.91 3.18
1619 2535 4.262207 GGAGTTGTCTGTCATCAGTTCTCA 60.262 45.833 0.00 0.00 41.91 3.27
1713 2631 6.212388 AGTCTTTGAGTGATCCTACATTGTCT 59.788 38.462 0.00 0.00 0.00 3.41
1715 2633 6.365970 AGTCTTTGAGTGATCCTACATTGT 57.634 37.500 0.00 0.00 0.00 2.71
1728 2646 5.485209 AGGTAATTCCGAAGTCTTTGAGT 57.515 39.130 0.93 0.00 41.99 3.41
1740 2658 4.357996 GAACTTCTCGGTAGGTAATTCCG 58.642 47.826 0.00 0.00 44.76 4.30
1744 2662 2.692041 CCGGAACTTCTCGGTAGGTAAT 59.308 50.000 0.00 0.00 41.23 1.89
1785 2703 3.053693 AGAGTAGCAGATGACTGGACTCT 60.054 47.826 0.00 0.00 43.62 3.24
1786 2704 3.066621 CAGAGTAGCAGATGACTGGACTC 59.933 52.174 0.00 0.00 43.62 3.36
1787 2705 3.023119 CAGAGTAGCAGATGACTGGACT 58.977 50.000 0.00 0.00 43.62 3.85
1788 2706 2.757868 ACAGAGTAGCAGATGACTGGAC 59.242 50.000 0.00 0.00 43.62 4.02
1789 2707 3.093057 ACAGAGTAGCAGATGACTGGA 57.907 47.619 0.00 0.00 43.62 3.86
1790 2708 5.528043 AATACAGAGTAGCAGATGACTGG 57.472 43.478 0.00 0.00 43.62 4.00
1794 2712 7.057264 AGACAGTAATACAGAGTAGCAGATGA 58.943 38.462 0.00 0.00 0.00 2.92
1810 2728 4.400884 CACCAGAGTAGCAGAGACAGTAAT 59.599 45.833 0.00 0.00 0.00 1.89
1817 2768 2.294449 ACACACCAGAGTAGCAGAGA 57.706 50.000 0.00 0.00 0.00 3.10
1847 2804 6.949352 ATTTACATCAGCAACCTATCCAAG 57.051 37.500 0.00 0.00 0.00 3.61
1854 2812 5.536161 ACAACTGAATTTACATCAGCAACCT 59.464 36.000 3.57 0.00 46.56 3.50
1867 2825 4.326826 TGCTGCTAGCTACAACTGAATTT 58.673 39.130 17.23 0.00 42.97 1.82
1868 2826 3.937706 CTGCTGCTAGCTACAACTGAATT 59.062 43.478 17.23 0.00 42.97 2.17
1883 2841 3.336568 AGGCCACCATCTGCTGCT 61.337 61.111 5.01 0.00 0.00 4.24
1901 2859 3.869272 GCAAGCGCATCCCAGTCG 61.869 66.667 11.47 0.00 38.36 4.18
1940 2898 3.723235 CTGTATGAGCGCGCACCCT 62.723 63.158 35.10 18.99 0.00 4.34
2752 3716 6.036408 TGCTCTGTTATTCAAATGATGACGAG 59.964 38.462 0.00 0.00 37.92 4.18
2755 3719 7.065563 AGACTGCTCTGTTATTCAAATGATGAC 59.934 37.037 0.00 0.00 37.92 3.06
2800 3786 1.942776 TCAGATCTGCTCCCTGTCAA 58.057 50.000 18.36 0.00 0.00 3.18
3307 4317 9.831737 CTGATTTTATCCAAAAGTCAGTTGTAG 57.168 33.333 12.31 0.00 37.08 2.74
3315 4325 8.000780 ACCTATGCTGATTTTATCCAAAAGTC 57.999 34.615 0.00 0.00 37.08 3.01
3317 4327 9.125026 AGTACCTATGCTGATTTTATCCAAAAG 57.875 33.333 0.00 0.00 37.08 2.27
3322 4335 7.217200 TCACAGTACCTATGCTGATTTTATCC 58.783 38.462 0.00 0.00 40.79 2.59
3324 4337 8.213679 ACATCACAGTACCTATGCTGATTTTAT 58.786 33.333 0.00 0.00 40.79 1.40
3325 4338 7.495606 CACATCACAGTACCTATGCTGATTTTA 59.504 37.037 0.00 0.00 40.79 1.52
3326 4339 6.317140 CACATCACAGTACCTATGCTGATTTT 59.683 38.462 0.00 0.00 40.79 1.82
3339 4352 4.084066 TGAATTTGCGACACATCACAGTAC 60.084 41.667 0.00 0.00 0.00 2.73
3365 4378 6.252869 GCAATCTGTTTTCATTACATCAGCTG 59.747 38.462 7.63 7.63 0.00 4.24
3448 4465 8.098286 TGAGGTCTCCACGAAATTTAAATCTTA 58.902 33.333 0.10 0.00 0.00 2.10
3451 4468 6.737254 TGAGGTCTCCACGAAATTTAAATC 57.263 37.500 0.10 0.00 0.00 2.17
3452 4469 6.095440 CCATGAGGTCTCCACGAAATTTAAAT 59.905 38.462 0.00 0.00 0.00 1.40
3470 4487 0.609957 TGGTTTCTGCTGCCATGAGG 60.610 55.000 0.00 0.00 38.23 3.86
3479 4496 3.084786 GCCAAGTTAGATGGTTTCTGCT 58.915 45.455 0.00 0.00 40.23 4.24
3495 4512 0.606401 ACCGATTGACCTGTGCCAAG 60.606 55.000 0.00 0.00 0.00 3.61
3497 4514 1.003839 GACCGATTGACCTGTGCCA 60.004 57.895 0.00 0.00 0.00 4.92
3498 4515 1.745489 GGACCGATTGACCTGTGCC 60.745 63.158 0.00 0.00 0.00 5.01
3499 4516 0.392998 ATGGACCGATTGACCTGTGC 60.393 55.000 0.00 0.00 0.00 4.57
3500 4517 2.113860 AATGGACCGATTGACCTGTG 57.886 50.000 0.00 0.00 0.00 3.66
3501 4518 2.879103 AAATGGACCGATTGACCTGT 57.121 45.000 0.00 0.00 0.00 4.00
3502 4519 5.835113 ATTTAAATGGACCGATTGACCTG 57.165 39.130 0.00 0.00 0.00 4.00
3558 4593 7.556844 TCCTTTATCTCTTGATAGTGGAACAC 58.443 38.462 0.00 0.00 45.97 3.32
3559 4594 7.733773 TCCTTTATCTCTTGATAGTGGAACA 57.266 36.000 0.00 0.00 36.45 3.18
3560 4595 8.478877 TCTTCCTTTATCTCTTGATAGTGGAAC 58.521 37.037 12.89 0.00 39.91 3.62
3561 4596 8.609617 TCTTCCTTTATCTCTTGATAGTGGAA 57.390 34.615 14.61 14.61 41.00 3.53
3562 4597 8.609617 TTCTTCCTTTATCTCTTGATAGTGGA 57.390 34.615 0.00 0.00 37.00 4.02
3563 4598 9.672673 TTTTCTTCCTTTATCTCTTGATAGTGG 57.327 33.333 0.00 0.00 36.62 4.00
3569 4604 9.184523 TGTTGTTTTTCTTCCTTTATCTCTTGA 57.815 29.630 0.00 0.00 0.00 3.02
3570 4605 9.801873 TTGTTGTTTTTCTTCCTTTATCTCTTG 57.198 29.630 0.00 0.00 0.00 3.02
3597 4632 9.713713 GTCTAACTATTTCAGGAGACTCTTTTT 57.286 33.333 1.74 0.00 40.21 1.94
3598 4633 9.095700 AGTCTAACTATTTCAGGAGACTCTTTT 57.904 33.333 1.74 0.00 43.20 2.27
3599 4634 8.527810 CAGTCTAACTATTTCAGGAGACTCTTT 58.472 37.037 1.74 0.00 44.10 2.52
3600 4635 7.672239 ACAGTCTAACTATTTCAGGAGACTCTT 59.328 37.037 1.74 0.00 44.10 2.85
3601 4636 7.122055 CACAGTCTAACTATTTCAGGAGACTCT 59.878 40.741 1.74 0.00 44.10 3.24
3602 4637 7.254852 CACAGTCTAACTATTTCAGGAGACTC 58.745 42.308 0.00 0.00 44.10 3.36
3603 4638 6.350612 GCACAGTCTAACTATTTCAGGAGACT 60.351 42.308 0.00 0.00 45.56 3.24
3604 4639 5.808030 GCACAGTCTAACTATTTCAGGAGAC 59.192 44.000 0.00 0.00 39.74 3.36
3605 4640 5.105310 GGCACAGTCTAACTATTTCAGGAGA 60.105 44.000 0.00 0.00 0.00 3.71
3606 4641 5.105146 AGGCACAGTCTAACTATTTCAGGAG 60.105 44.000 0.00 0.00 0.00 3.69
3607 4642 4.777896 AGGCACAGTCTAACTATTTCAGGA 59.222 41.667 0.00 0.00 0.00 3.86
3608 4643 4.872691 CAGGCACAGTCTAACTATTTCAGG 59.127 45.833 0.00 0.00 0.00 3.86
3609 4644 5.578727 GTCAGGCACAGTCTAACTATTTCAG 59.421 44.000 0.00 0.00 0.00 3.02
3610 4645 5.011635 TGTCAGGCACAGTCTAACTATTTCA 59.988 40.000 0.00 0.00 0.00 2.69
3611 4646 5.479306 TGTCAGGCACAGTCTAACTATTTC 58.521 41.667 0.00 0.00 0.00 2.17
3612 4647 5.482908 CTGTCAGGCACAGTCTAACTATTT 58.517 41.667 0.00 0.00 46.81 1.40
3613 4648 5.078411 CTGTCAGGCACAGTCTAACTATT 57.922 43.478 0.00 0.00 46.81 1.73
3614 4649 4.727507 CTGTCAGGCACAGTCTAACTAT 57.272 45.455 0.00 0.00 46.81 2.12
3655 4714 6.072112 TGCCTATCAGAAAAACAAACAGTC 57.928 37.500 0.00 0.00 0.00 3.51
3657 4716 6.076981 ACTGCCTATCAGAAAAACAAACAG 57.923 37.500 0.00 0.00 45.72 3.16
3668 4727 2.961741 CCAAGCTCTACTGCCTATCAGA 59.038 50.000 0.00 0.00 45.72 3.27
3671 4730 1.414181 TGCCAAGCTCTACTGCCTATC 59.586 52.381 0.00 0.00 0.00 2.08
3673 4732 1.066143 GTTGCCAAGCTCTACTGCCTA 60.066 52.381 0.00 0.00 0.00 3.93
3765 4824 3.646715 CCCGGAGTTTCCCCAGCA 61.647 66.667 0.73 0.00 31.13 4.41
3897 4961 3.124297 GCGAGATATTACAATCCAGCTGC 59.876 47.826 8.66 0.00 0.00 5.25
3898 4962 4.564041 AGCGAGATATTACAATCCAGCTG 58.436 43.478 6.78 6.78 37.57 4.24
3900 4964 5.062809 GCTTAGCGAGATATTACAATCCAGC 59.937 44.000 0.00 0.00 32.29 4.85
3911 4975 7.484975 AGCGAAAATATAGCTTAGCGAGATAT 58.515 34.615 0.00 1.37 40.04 1.63
3913 4977 5.715070 AGCGAAAATATAGCTTAGCGAGAT 58.285 37.500 0.00 0.00 38.13 2.75
3916 4981 6.747739 CAGATAGCGAAAATATAGCTTAGCGA 59.252 38.462 0.00 0.00 41.88 4.93
3918 4983 6.700978 GCAGATAGCGAAAATATAGCTTAGC 58.299 40.000 0.00 0.00 41.88 3.09
3933 4998 5.741388 AAAAGGAAACTATGCAGATAGCG 57.259 39.130 0.00 0.00 44.77 4.26
4023 5100 1.929836 GATAGCTCACTTGTGCTTCCG 59.070 52.381 10.81 0.00 41.50 4.30
4077 5154 8.944029 CAAATTCTCATACTGACTTGACAGAAT 58.056 33.333 7.06 0.00 40.63 2.40
4086 5163 7.192852 AGGATGTCAAATTCTCATACTGACT 57.807 36.000 5.93 0.00 37.79 3.41
4102 5179 1.629861 TCAGGATGTGCAAGGATGTCA 59.370 47.619 0.00 0.00 37.40 3.58
4113 5190 6.639686 GCATTAGCACAAATAATCAGGATGTG 59.360 38.462 0.00 0.00 43.17 3.21
4114 5191 6.742109 GCATTAGCACAAATAATCAGGATGT 58.258 36.000 0.00 0.00 41.58 3.06
4142 5227 9.587772 TTAATCTTAGTGACAATTAGAGTCTGC 57.412 33.333 1.86 0.00 36.94 4.26
4195 5292 1.850289 TGCAAGGGGGTAGAAGGCA 60.850 57.895 0.00 0.00 0.00 4.75
4203 5300 2.765969 CCATCAGTGCAAGGGGGT 59.234 61.111 0.00 0.00 0.00 4.95
4205 5302 1.751927 GAGCCATCAGTGCAAGGGG 60.752 63.158 0.00 0.00 0.00 4.79
4230 5327 3.278574 CTCCCTGCATCGGTAATTTCAA 58.721 45.455 0.00 0.00 0.00 2.69
4232 5329 2.158813 TCCTCCCTGCATCGGTAATTTC 60.159 50.000 0.00 0.00 0.00 2.17
4233 5330 1.843851 TCCTCCCTGCATCGGTAATTT 59.156 47.619 0.00 0.00 0.00 1.82
4236 5333 0.539986 GTTCCTCCCTGCATCGGTAA 59.460 55.000 0.00 0.00 0.00 2.85
4238 5335 2.990479 GTTCCTCCCTGCATCGGT 59.010 61.111 0.00 0.00 0.00 4.69
4239 5336 2.202932 CGTTCCTCCCTGCATCGG 60.203 66.667 0.00 0.00 0.00 4.18
4290 5389 7.341805 ACAAACAGCTATATGACCTTGAGAAT 58.658 34.615 0.00 0.00 0.00 2.40
4360 5459 9.393512 AGTTCTAGATCTCCATTCAAGAAAATG 57.606 33.333 0.00 0.00 36.57 2.32
4397 5526 9.244292 TGATGATTAAGTACTCACTACTTCACT 57.756 33.333 0.00 0.00 43.52 3.41
4398 5527 9.509855 CTGATGATTAAGTACTCACTACTTCAC 57.490 37.037 0.00 0.00 43.52 3.18
4399 5528 8.687242 CCTGATGATTAAGTACTCACTACTTCA 58.313 37.037 0.00 1.58 43.52 3.02
4400 5529 8.688151 ACCTGATGATTAAGTACTCACTACTTC 58.312 37.037 0.00 0.00 43.52 3.01
4401 5530 8.596781 ACCTGATGATTAAGTACTCACTACTT 57.403 34.615 0.00 0.00 45.93 2.24
4402 5531 9.696572 TTACCTGATGATTAAGTACTCACTACT 57.303 33.333 0.00 0.00 37.28 2.57
4435 5579 3.551890 GCAGCATCAATGAGAAGCAAATG 59.448 43.478 7.63 0.21 43.20 2.32
4458 5603 0.244721 TCAGCACCGTGTCAGATCTG 59.755 55.000 17.07 17.07 0.00 2.90
4490 5636 4.985538 AGTTCCTGCATTAAGTGAGGAAA 58.014 39.130 11.54 0.00 41.51 3.13
4494 5640 6.204301 CCATGATAGTTCCTGCATTAAGTGAG 59.796 42.308 0.00 0.00 0.00 3.51
4496 5642 5.824624 ACCATGATAGTTCCTGCATTAAGTG 59.175 40.000 0.00 0.00 0.00 3.16
4597 5751 7.231925 ACTCTGGCAATCAATTGATGCATAATA 59.768 33.333 28.26 15.98 40.14 0.98
4601 5755 3.704566 ACTCTGGCAATCAATTGATGCAT 59.295 39.130 28.26 0.00 40.14 3.96
4611 5765 3.753272 GCTTCAACTTACTCTGGCAATCA 59.247 43.478 0.00 0.00 0.00 2.57
4690 5844 1.204941 CACTACAGTCTAGGGTGTGGC 59.795 57.143 7.85 0.00 0.00 5.01
4701 5855 6.313164 GCATTTCTAACTAACCCACTACAGTC 59.687 42.308 0.00 0.00 0.00 3.51
4783 5970 3.270027 TGTACGCAAATGAATCCTCCAG 58.730 45.455 0.00 0.00 0.00 3.86
4790 5977 1.732941 TCCGCTGTACGCAAATGAAT 58.267 45.000 9.69 0.00 41.76 2.57
4793 5980 1.258982 GAGATCCGCTGTACGCAAATG 59.741 52.381 9.69 0.00 41.76 2.32
4813 6000 2.480073 CGCCCTAACAATTCAGCAATGG 60.480 50.000 0.00 0.00 0.00 3.16
4880 6068 5.966742 ACGCTCTGCACTATCAATATCTA 57.033 39.130 0.00 0.00 0.00 1.98
4885 6073 4.503910 TGTTTACGCTCTGCACTATCAAT 58.496 39.130 0.00 0.00 0.00 2.57
4929 6117 1.872313 GAGCAGATGTTCAGGCATAGC 59.128 52.381 0.00 0.00 33.14 2.97
4933 6121 2.767960 TCATAGAGCAGATGTTCAGGCA 59.232 45.455 0.00 0.00 0.00 4.75
4960 6148 7.191551 CCTATGAGCAACAATTACATCACAAG 58.808 38.462 0.00 0.00 0.00 3.16
4971 6159 3.181450 GCTAGGACCCTATGAGCAACAAT 60.181 47.826 4.82 0.00 0.00 2.71
4972 6160 2.170607 GCTAGGACCCTATGAGCAACAA 59.829 50.000 4.82 0.00 0.00 2.83
4973 6161 1.762957 GCTAGGACCCTATGAGCAACA 59.237 52.381 4.82 0.00 0.00 3.33
4974 6162 2.043227 AGCTAGGACCCTATGAGCAAC 58.957 52.381 10.83 0.00 0.00 4.17
4975 6163 2.478872 AGCTAGGACCCTATGAGCAA 57.521 50.000 10.83 0.00 0.00 3.91
4976 6164 2.819726 GCTAGCTAGGACCCTATGAGCA 60.820 54.545 22.10 0.00 32.44 4.26
4977 6165 1.822371 GCTAGCTAGGACCCTATGAGC 59.178 57.143 22.10 1.73 0.00 4.26
4978 6166 3.449746 AGCTAGCTAGGACCCTATGAG 57.550 52.381 17.69 0.00 0.00 2.90
4989 6177 3.438781 CACGAGGAATCCTAGCTAGCTAG 59.561 52.174 35.39 35.39 44.07 3.42
4991 6179 2.235016 CACGAGGAATCCTAGCTAGCT 58.765 52.381 23.12 23.12 31.76 3.32
4992 6180 1.271102 CCACGAGGAATCCTAGCTAGC 59.729 57.143 15.74 6.62 36.89 3.42
5002 6190 2.105993 GTTATTAGCCCCCACGAGGAAT 59.894 50.000 0.00 0.00 38.24 3.01
5009 6197 2.932261 CAAGAGGTTATTAGCCCCCAC 58.068 52.381 0.00 0.00 0.00 4.61
5011 6199 1.478837 GGCAAGAGGTTATTAGCCCCC 60.479 57.143 0.00 0.00 36.17 5.40
5012 6200 1.214424 TGGCAAGAGGTTATTAGCCCC 59.786 52.381 0.00 0.00 41.33 5.80
5014 6202 2.298610 GGTGGCAAGAGGTTATTAGCC 58.701 52.381 0.00 0.00 42.32 3.93
5015 6203 2.683362 GTGGTGGCAAGAGGTTATTAGC 59.317 50.000 0.00 0.00 0.00 3.09
5017 6205 2.303600 ACGTGGTGGCAAGAGGTTATTA 59.696 45.455 0.00 0.00 0.00 0.98
5019 6207 0.690762 ACGTGGTGGCAAGAGGTTAT 59.309 50.000 0.00 0.00 0.00 1.89
5021 6227 1.227853 GACGTGGTGGCAAGAGGTT 60.228 57.895 0.00 0.00 0.00 3.50
5085 6291 3.396276 TCAGGAAATTTACACCTCCACCA 59.604 43.478 2.58 0.00 31.06 4.17
5087 6293 4.394729 TGTCAGGAAATTTACACCTCCAC 58.605 43.478 2.58 0.62 31.06 4.02
5089 6295 4.399303 CCATGTCAGGAAATTTACACCTCC 59.601 45.833 2.58 0.00 31.06 4.30
5121 6327 2.039879 GGGACATTAGTGTGGGTCAAGT 59.960 50.000 0.00 0.00 39.09 3.16
5122 6328 2.711542 GGGACATTAGTGTGGGTCAAG 58.288 52.381 0.00 0.00 39.09 3.02


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

AutoCloner maintained by Alex Coulton.