Multiple sequence alignment - TraesCS2A01G539500

Loading Multiple Alignment...

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 TraesCS2A01G539500 chr2A 100.000 3224 0 0 1 3224 751894598 751891375 0.000000e+00 5954.0
1 TraesCS2A01G539500 chr2A 87.215 1228 88 29 967 2147 751844671 751845876 0.000000e+00 1334.0
2 TraesCS2A01G539500 chr2A 79.798 1485 130 74 829 2231 752030939 752032335 0.000000e+00 924.0
3 TraesCS2A01G539500 chr2A 90.413 678 31 23 1463 2117 751757305 751757971 0.000000e+00 861.0
4 TraesCS2A01G539500 chr2A 90.476 105 5 3 1325 1428 751757281 751757181 2.020000e-27 134.0
5 TraesCS2A01G539500 chr2A 80.882 136 17 7 2019 2147 751776172 751776305 7.360000e-17 99.0
6 TraesCS2A01G539500 chr2A 89.041 73 6 2 891 962 751844615 751844686 4.430000e-14 89.8
7 TraesCS2A01G539500 chr2D 86.039 2242 156 71 924 3110 620269952 620272091 0.000000e+00 2261.0
8 TraesCS2A01G539500 chr2D 88.100 916 66 17 896 1784 620223680 620224579 0.000000e+00 1048.0
9 TraesCS2A01G539500 chr2D 81.715 1236 117 52 829 2018 620281034 620282206 0.000000e+00 929.0
10 TraesCS2A01G539500 chr2D 87.801 705 78 4 1 701 592124763 592124063 0.000000e+00 819.0
11 TraesCS2A01G539500 chr2D 86.047 215 20 2 1806 2016 620224568 620224776 4.190000e-54 222.0
12 TraesCS2A01G539500 chr2D 80.124 161 19 12 2407 2559 620282606 620282761 1.220000e-19 108.0
13 TraesCS2A01G539500 chr2B 86.084 1818 121 51 816 2559 760118275 760120034 0.000000e+00 1834.0
14 TraesCS2A01G539500 chr2B 85.221 1245 88 44 829 2018 760015324 760016527 0.000000e+00 1192.0
15 TraesCS2A01G539500 chr2B 81.404 1382 118 64 829 2156 760152824 760154120 0.000000e+00 1000.0
16 TraesCS2A01G539500 chr2B 92.135 89 6 1 749 837 760118252 760118339 1.210000e-24 124.0
17 TraesCS2A01G539500 chr2B 81.955 133 16 8 2426 2551 760154404 760154535 4.400000e-19 106.0
18 TraesCS2A01G539500 chr1B 87.604 718 84 5 1 715 117462358 117461643 0.000000e+00 828.0
19 TraesCS2A01G539500 chr5D 87.430 716 85 2 1 712 465968641 465969355 0.000000e+00 819.0
20 TraesCS2A01G539500 chr6A 88.133 691 76 5 28 715 539857534 539856847 0.000000e+00 817.0
21 TraesCS2A01G539500 chr4D 87.308 717 83 5 4 715 16451972 16451259 0.000000e+00 813.0
22 TraesCS2A01G539500 chr3D 87.101 721 87 3 1 717 284992388 284991670 0.000000e+00 811.0
23 TraesCS2A01G539500 chr6D 86.557 729 90 5 1 722 314083748 314084475 0.000000e+00 797.0
24 TraesCS2A01G539500 chr6D 86.787 719 86 4 1 715 68153506 68152793 0.000000e+00 793.0
25 TraesCS2A01G539500 chr1D 86.464 724 90 4 2 720 146496450 146495730 0.000000e+00 787.0


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 TraesCS2A01G539500 chr2A 751891375 751894598 3223 True 5954.0 5954 100.0000 1 3224 1 chr2A.!!$R2 3223
1 TraesCS2A01G539500 chr2A 752030939 752032335 1396 False 924.0 924 79.7980 829 2231 1 chr2A.!!$F3 1402
2 TraesCS2A01G539500 chr2A 751757305 751757971 666 False 861.0 861 90.4130 1463 2117 1 chr2A.!!$F1 654
3 TraesCS2A01G539500 chr2A 751844615 751845876 1261 False 711.9 1334 88.1280 891 2147 2 chr2A.!!$F4 1256
4 TraesCS2A01G539500 chr2D 620269952 620272091 2139 False 2261.0 2261 86.0390 924 3110 1 chr2D.!!$F1 2186
5 TraesCS2A01G539500 chr2D 592124063 592124763 700 True 819.0 819 87.8010 1 701 1 chr2D.!!$R1 700
6 TraesCS2A01G539500 chr2D 620223680 620224776 1096 False 635.0 1048 87.0735 896 2016 2 chr2D.!!$F2 1120
7 TraesCS2A01G539500 chr2D 620281034 620282761 1727 False 518.5 929 80.9195 829 2559 2 chr2D.!!$F3 1730
8 TraesCS2A01G539500 chr2B 760015324 760016527 1203 False 1192.0 1192 85.2210 829 2018 1 chr2B.!!$F1 1189
9 TraesCS2A01G539500 chr2B 760118252 760120034 1782 False 979.0 1834 89.1095 749 2559 2 chr2B.!!$F2 1810
10 TraesCS2A01G539500 chr2B 760152824 760154535 1711 False 553.0 1000 81.6795 829 2551 2 chr2B.!!$F3 1722
11 TraesCS2A01G539500 chr1B 117461643 117462358 715 True 828.0 828 87.6040 1 715 1 chr1B.!!$R1 714
12 TraesCS2A01G539500 chr5D 465968641 465969355 714 False 819.0 819 87.4300 1 712 1 chr5D.!!$F1 711
13 TraesCS2A01G539500 chr6A 539856847 539857534 687 True 817.0 817 88.1330 28 715 1 chr6A.!!$R1 687
14 TraesCS2A01G539500 chr4D 16451259 16451972 713 True 813.0 813 87.3080 4 715 1 chr4D.!!$R1 711
15 TraesCS2A01G539500 chr3D 284991670 284992388 718 True 811.0 811 87.1010 1 717 1 chr3D.!!$R1 716
16 TraesCS2A01G539500 chr6D 314083748 314084475 727 False 797.0 797 86.5570 1 722 1 chr6D.!!$F1 721
17 TraesCS2A01G539500 chr6D 68152793 68153506 713 True 793.0 793 86.7870 1 715 1 chr6D.!!$R1 714
18 TraesCS2A01G539500 chr1D 146495730 146496450 720 True 787.0 787 86.4640 2 720 1 chr1D.!!$R1 718

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
755 766 0.035739 GTCTTGCCGTACCCCTCAAA 59.964 55.0 0.0 0.0 0.00 2.69 F
822 833 0.253610 TTTCGGCATAATCCACCGGT 59.746 50.0 0.0 0.0 46.87 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2300 0.107456 AGCGGGTAGGCTGATGATTG 59.893 55.0 0.0 0.0 42.86 2.67 R
2819 3220 0.834687 TCCTACTTCCCAAGGCGTGT 60.835 55.0 0.0 0.0 32.55 4.49 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
118 119 1.501169 GGACAACAAATGCCAAGCAC 58.499 50.000 0.00 0.00 43.04 4.40
126 127 1.841302 AATGCCAAGCACGAGGAGGA 61.841 55.000 0.00 0.00 43.04 3.71
137 138 1.668151 GAGGAGGACGTGCGCTTTT 60.668 57.895 9.73 0.00 0.00 2.27
282 283 2.433491 CCGATTCCGCGTCCAACA 60.433 61.111 4.92 0.00 0.00 3.33
448 454 3.253838 CGTGGGAGGGTTTGGGGA 61.254 66.667 0.00 0.00 0.00 4.81
475 484 4.694987 CAAATGGGGCGTGGGGGT 62.695 66.667 0.00 0.00 0.00 4.95
482 493 2.376987 GGGCGTGGGGGTGGTTATA 61.377 63.158 0.00 0.00 0.00 0.98
494 505 2.160813 GGTGGTTATACTTTGTGCCACG 59.839 50.000 0.00 0.00 45.11 4.94
555 566 2.176546 CCGTGCGCTGTCCATTTG 59.823 61.111 9.73 0.00 0.00 2.32
575 586 1.445926 CCCCAAAATCGGCGCAAAG 60.446 57.895 10.83 0.00 0.00 2.77
599 610 1.991230 CCTGGGATGGGTCGAAAGT 59.009 57.895 0.00 0.00 0.00 2.66
605 616 1.065418 GGATGGGTCGAAAGTGGACAT 60.065 52.381 0.00 0.00 36.12 3.06
654 665 1.215382 CGCTGGATCGTCTGGTTCA 59.785 57.895 0.00 0.00 0.00 3.18
660 671 3.534554 TGGATCGTCTGGTTCATTCATG 58.465 45.455 0.00 0.00 0.00 3.07
665 676 6.260936 GGATCGTCTGGTTCATTCATGTTATT 59.739 38.462 0.00 0.00 0.00 1.40
720 731 3.403936 GCGGAGTTGGCCTTATGAT 57.596 52.632 3.32 0.00 0.00 2.45
722 733 2.846193 GCGGAGTTGGCCTTATGATTA 58.154 47.619 3.32 0.00 0.00 1.75
723 734 3.412386 GCGGAGTTGGCCTTATGATTAT 58.588 45.455 3.32 0.00 0.00 1.28
724 735 3.189287 GCGGAGTTGGCCTTATGATTATG 59.811 47.826 3.32 0.00 0.00 1.90
725 736 4.389374 CGGAGTTGGCCTTATGATTATGT 58.611 43.478 3.32 0.00 0.00 2.29
726 737 5.547465 CGGAGTTGGCCTTATGATTATGTA 58.453 41.667 3.32 0.00 0.00 2.29
727 738 5.408604 CGGAGTTGGCCTTATGATTATGTAC 59.591 44.000 3.32 0.00 0.00 2.90
728 739 6.534634 GGAGTTGGCCTTATGATTATGTACT 58.465 40.000 3.32 0.00 0.00 2.73
729 740 7.524863 CGGAGTTGGCCTTATGATTATGTACTA 60.525 40.741 3.32 0.00 0.00 1.82
730 741 7.819900 GGAGTTGGCCTTATGATTATGTACTAG 59.180 40.741 3.32 0.00 0.00 2.57
731 742 8.263854 AGTTGGCCTTATGATTATGTACTAGT 57.736 34.615 3.32 0.00 0.00 2.57
732 743 9.375974 AGTTGGCCTTATGATTATGTACTAGTA 57.624 33.333 3.32 0.00 0.00 1.82
733 744 9.640963 GTTGGCCTTATGATTATGTACTAGTAG 57.359 37.037 3.32 0.00 0.00 2.57
734 745 8.951614 TGGCCTTATGATTATGTACTAGTAGT 57.048 34.615 8.14 8.14 0.00 2.73
735 746 9.021807 TGGCCTTATGATTATGTACTAGTAGTC 57.978 37.037 5.96 0.00 0.00 2.59
736 747 8.182881 GGCCTTATGATTATGTACTAGTAGTCG 58.817 40.741 5.96 0.00 0.00 4.18
737 748 8.728833 GCCTTATGATTATGTACTAGTAGTCGT 58.271 37.037 5.96 3.27 0.00 4.34
742 753 7.637229 TGATTATGTACTAGTAGTCGTCTTGC 58.363 38.462 5.96 0.00 0.00 4.01
743 754 4.897025 ATGTACTAGTAGTCGTCTTGCC 57.103 45.455 5.96 0.00 0.00 4.52
744 755 2.674852 TGTACTAGTAGTCGTCTTGCCG 59.325 50.000 5.96 0.00 0.00 5.69
745 756 1.818642 ACTAGTAGTCGTCTTGCCGT 58.181 50.000 0.00 0.00 0.00 5.68
746 757 2.977914 ACTAGTAGTCGTCTTGCCGTA 58.022 47.619 0.00 0.00 0.00 4.02
747 758 2.675348 ACTAGTAGTCGTCTTGCCGTAC 59.325 50.000 0.00 0.00 0.00 3.67
748 759 0.807496 AGTAGTCGTCTTGCCGTACC 59.193 55.000 0.00 0.00 0.00 3.34
749 760 0.179153 GTAGTCGTCTTGCCGTACCC 60.179 60.000 0.00 0.00 0.00 3.69
750 761 1.315257 TAGTCGTCTTGCCGTACCCC 61.315 60.000 0.00 0.00 0.00 4.95
751 762 2.283388 TCGTCTTGCCGTACCCCT 60.283 61.111 0.00 0.00 0.00 4.79
752 763 2.183555 CGTCTTGCCGTACCCCTC 59.816 66.667 0.00 0.00 0.00 4.30
753 764 2.642254 CGTCTTGCCGTACCCCTCA 61.642 63.158 0.00 0.00 0.00 3.86
754 765 1.675219 GTCTTGCCGTACCCCTCAA 59.325 57.895 0.00 0.00 0.00 3.02
755 766 0.035739 GTCTTGCCGTACCCCTCAAA 59.964 55.000 0.00 0.00 0.00 2.69
778 789 2.424705 AAAGTACGTCTTGCCGCCGA 62.425 55.000 0.00 0.00 36.40 5.54
780 791 4.789075 TACGTCTTGCCGCCGAGC 62.789 66.667 0.00 0.00 0.00 5.03
791 802 3.406559 GCCGAGCGGTTATCCAAC 58.593 61.111 10.94 0.00 37.65 3.77
799 810 1.711500 GGTTATCCAACCGCGTTCG 59.289 57.895 4.92 0.00 44.74 3.95
800 811 1.015607 GGTTATCCAACCGCGTTCGT 61.016 55.000 4.92 0.00 44.74 3.85
801 812 0.792031 GTTATCCAACCGCGTTCGTT 59.208 50.000 4.92 0.00 0.00 3.85
802 813 1.195222 GTTATCCAACCGCGTTCGTTT 59.805 47.619 4.92 0.00 0.00 3.60
803 814 1.510776 TATCCAACCGCGTTCGTTTT 58.489 45.000 4.92 0.00 0.00 2.43
804 815 0.664224 ATCCAACCGCGTTCGTTTTT 59.336 45.000 4.92 0.00 0.00 1.94
821 832 1.384525 TTTTCGGCATAATCCACCGG 58.615 50.000 0.00 0.00 46.87 5.28
822 833 0.253610 TTTCGGCATAATCCACCGGT 59.746 50.000 0.00 0.00 46.87 5.28
823 834 0.462937 TTCGGCATAATCCACCGGTG 60.463 55.000 28.26 28.26 46.87 4.94
824 835 1.153249 CGGCATAATCCACCGGTGT 60.153 57.895 31.80 17.17 43.23 4.16
825 836 0.746563 CGGCATAATCCACCGGTGTT 60.747 55.000 31.80 22.56 43.23 3.32
826 837 1.470051 GGCATAATCCACCGGTGTTT 58.530 50.000 31.80 25.17 0.00 2.83
827 838 1.134175 GGCATAATCCACCGGTGTTTG 59.866 52.381 31.80 19.26 0.00 2.93
883 897 0.935196 GTGTTTGATACCGCGGGATC 59.065 55.000 38.45 38.45 0.00 3.36
1107 1192 3.078097 GAGAGAGACAGAGTACTGCACA 58.922 50.000 0.00 0.00 46.95 4.57
1108 1193 3.081061 AGAGAGACAGAGTACTGCACAG 58.919 50.000 0.00 0.00 46.95 3.66
1282 1388 2.279517 ATCGATCGAACTGCGGGC 60.280 61.111 23.50 0.00 41.33 6.13
1360 1476 2.957402 TTTGGCTCTTGTCTCATGGT 57.043 45.000 0.00 0.00 0.00 3.55
1493 1648 3.782244 CTCTGCTTCGCCGCACAC 61.782 66.667 0.00 0.00 35.74 3.82
1496 1651 2.432456 TGCTTCGCCGCACACTAG 60.432 61.111 0.00 0.00 34.44 2.57
1497 1652 2.432628 GCTTCGCCGCACACTAGT 60.433 61.111 0.00 0.00 0.00 2.57
1498 1653 1.153901 GCTTCGCCGCACACTAGTA 60.154 57.895 0.00 0.00 0.00 1.82
2030 2295 4.885270 TGCCGGTGGTTGGTGGTG 62.885 66.667 1.90 0.00 0.00 4.17
2035 2300 3.605664 GTGGTTGGTGGTGGCTGC 61.606 66.667 0.00 0.00 0.00 5.25
2037 2302 2.837291 GGTTGGTGGTGGCTGCAA 60.837 61.111 0.50 0.00 0.00 4.08
2209 2532 1.990563 GTTTGTAGAGCGCATACACGT 59.009 47.619 20.91 0.00 33.01 4.49
2256 2589 7.236474 TGTACTACGTACGTATCACTTTTGAG 58.764 38.462 26.98 15.83 41.41 3.02
2293 2638 0.543749 ATTACTGCCCAGCTGGTCTC 59.456 55.000 30.63 19.03 36.04 3.36
2301 2646 2.619074 GCCCAGCTGGTCTCAAAAGTAT 60.619 50.000 30.63 0.00 36.04 2.12
2303 2648 3.441572 CCCAGCTGGTCTCAAAAGTATTG 59.558 47.826 30.63 6.74 0.00 1.90
2305 2650 3.441572 CAGCTGGTCTCAAAAGTATTGGG 59.558 47.826 5.57 0.00 0.00 4.12
2306 2651 3.330701 AGCTGGTCTCAAAAGTATTGGGA 59.669 43.478 0.00 0.00 0.00 4.37
2307 2652 4.079253 GCTGGTCTCAAAAGTATTGGGAA 58.921 43.478 0.00 0.00 29.59 3.97
2308 2653 4.522789 GCTGGTCTCAAAAGTATTGGGAAA 59.477 41.667 0.00 0.00 29.59 3.13
2309 2654 5.335976 GCTGGTCTCAAAAGTATTGGGAAAG 60.336 44.000 0.00 0.00 29.59 2.62
2311 2656 4.379499 GGTCTCAAAAGTATTGGGAAAGCG 60.379 45.833 0.00 0.00 29.59 4.68
2313 2658 4.825085 TCTCAAAAGTATTGGGAAAGCGTT 59.175 37.500 0.00 0.00 0.00 4.84
2314 2659 5.998981 TCTCAAAAGTATTGGGAAAGCGTTA 59.001 36.000 0.00 0.00 0.00 3.18
2315 2660 6.657541 TCTCAAAAGTATTGGGAAAGCGTTAT 59.342 34.615 0.00 0.00 0.00 1.89
2316 2661 7.825270 TCTCAAAAGTATTGGGAAAGCGTTATA 59.175 33.333 0.00 0.00 0.00 0.98
2318 2663 5.978934 AAGTATTGGGAAAGCGTTATACG 57.021 39.130 0.00 0.00 45.88 3.06
2319 2664 5.266733 AGTATTGGGAAAGCGTTATACGA 57.733 39.130 3.04 0.00 46.05 3.43
2321 2666 1.930567 TGGGAAAGCGTTATACGAGC 58.069 50.000 3.04 0.00 46.05 5.03
2329 2687 4.148563 AGCGTTATACGAGCATCACTAG 57.851 45.455 3.04 0.00 46.05 2.57
2337 2695 8.679100 GTTATACGAGCATCACTAGAATATCCT 58.321 37.037 0.00 0.00 33.17 3.24
2361 2719 5.474532 TGCTGTGCTAAAACTCATGAGATTT 59.525 36.000 29.27 28.26 37.26 2.17
2399 2758 5.290493 TCGCAATTGATTCCAGTACCTAT 57.710 39.130 10.34 0.00 0.00 2.57
2466 2862 4.030913 TGAGATTCTCCCTGTTATTCGGT 58.969 43.478 11.12 0.00 0.00 4.69
2473 2869 4.159135 TCTCCCTGTTATTCGGTCTTGTAC 59.841 45.833 0.00 0.00 0.00 2.90
2507 2908 3.762288 TGTAGGCCTAATATAGTGCCTCG 59.238 47.826 15.83 0.00 44.09 4.63
2537 2938 8.757164 AATTTCGGAAACATAAACTCCATTTC 57.243 30.769 5.12 0.00 0.00 2.17
2582 2983 3.185797 GTCGTTGTTGCTCTTAACGGATT 59.814 43.478 8.58 0.00 45.08 3.01
2583 2984 3.185594 TCGTTGTTGCTCTTAACGGATTG 59.814 43.478 8.58 0.00 45.08 2.67
2584 2985 3.185594 CGTTGTTGCTCTTAACGGATTGA 59.814 43.478 0.00 0.00 42.31 2.57
2665 3066 1.834263 GGGTGTCTCCATACAAGCTCT 59.166 52.381 0.00 0.00 38.11 4.09
2666 3067 2.419297 GGGTGTCTCCATACAAGCTCTG 60.419 54.545 0.00 0.00 38.11 3.35
2686 3087 1.296392 GGATGCTGTTTTTGCCCCC 59.704 57.895 0.00 0.00 0.00 5.40
2690 3091 1.071299 GCTGTTTTTGCCCCCTTGG 59.929 57.895 0.00 0.00 37.09 3.61
2692 3093 1.351076 CTGTTTTTGCCCCCTTGGAT 58.649 50.000 0.00 0.00 35.39 3.41
2698 3099 2.440980 GCCCCCTTGGATGTCTGC 60.441 66.667 0.00 0.00 35.39 4.26
2708 3109 0.889994 GGATGTCTGCATTGCACCAA 59.110 50.000 7.38 0.00 35.07 3.67
2715 3116 4.280425 TGTCTGCATTGCACCAAAATTCTA 59.720 37.500 7.38 0.00 33.79 2.10
2719 3120 3.368739 GCATTGCACCAAAATTCTAGCCT 60.369 43.478 3.15 0.00 0.00 4.58
2722 3123 1.468054 GCACCAAAATTCTAGCCTGCG 60.468 52.381 0.00 0.00 0.00 5.18
2725 3126 1.133025 CCAAAATTCTAGCCTGCGTGG 59.867 52.381 0.00 0.00 39.35 4.94
2727 3128 2.487762 CAAAATTCTAGCCTGCGTGGAA 59.512 45.455 0.00 0.00 38.35 3.53
2737 3138 1.812571 CCTGCGTGGAACTTAAAGCAT 59.187 47.619 0.00 0.00 38.35 3.79
2742 3143 3.119990 GCGTGGAACTTAAAGCATTGCTA 60.120 43.478 12.39 0.00 33.06 3.49
2743 3144 4.651994 CGTGGAACTTAAAGCATTGCTAG 58.348 43.478 12.39 8.45 33.06 3.42
2746 3147 3.696548 GGAACTTAAAGCATTGCTAGGCT 59.303 43.478 12.39 0.35 44.61 4.58
2762 3163 5.845391 CTAGGCTTAGCTGAGTAGAAACT 57.155 43.478 7.41 0.00 39.21 2.66
2764 3165 5.079689 AGGCTTAGCTGAGTAGAAACTTC 57.920 43.478 7.41 0.00 35.56 3.01
2765 3166 4.775253 AGGCTTAGCTGAGTAGAAACTTCT 59.225 41.667 7.41 0.00 41.24 2.85
2770 3171 7.010091 GCTTAGCTGAGTAGAAACTTCTGAATC 59.990 40.741 7.41 0.00 38.19 2.52
2772 3173 6.397272 AGCTGAGTAGAAACTTCTGAATCAG 58.603 40.000 17.46 17.46 40.96 2.90
2787 3188 7.962964 TCTGAATCAGTCGTTTTCATTTAGT 57.037 32.000 10.36 0.00 32.61 2.24
2817 3218 4.864334 CCATCTGCGGCCCTCACC 62.864 72.222 0.00 0.00 0.00 4.02
2819 3220 2.041922 ATCTGCGGCCCTCACCTA 60.042 61.111 0.00 0.00 0.00 3.08
2843 3244 1.483004 GCCTTGGGAAGTAGGAGAGAC 59.517 57.143 0.00 0.00 0.00 3.36
2846 3247 3.292460 CTTGGGAAGTAGGAGAGACGAT 58.708 50.000 0.00 0.00 0.00 3.73
2849 3250 3.148412 GGGAAGTAGGAGAGACGATACC 58.852 54.545 0.00 0.00 0.00 2.73
2862 3263 5.598830 AGAGACGATACCAGACAACCATTAT 59.401 40.000 0.00 0.00 0.00 1.28
2867 3268 3.382083 ACCAGACAACCATTATTCCCC 57.618 47.619 0.00 0.00 0.00 4.81
2879 3280 0.267960 TATTCCCCACTCCTCTCCCC 59.732 60.000 0.00 0.00 0.00 4.81
2880 3281 1.837533 ATTCCCCACTCCTCTCCCCA 61.838 60.000 0.00 0.00 0.00 4.96
2885 3286 4.316823 ACTCCTCTCCCCACGCCA 62.317 66.667 0.00 0.00 0.00 5.69
2892 3293 2.517402 TCCCCACGCCACACAAAC 60.517 61.111 0.00 0.00 0.00 2.93
2897 3298 4.130554 ACGCCACACAAACCCCCA 62.131 61.111 0.00 0.00 0.00 4.96
2898 3299 2.600173 CGCCACACAAACCCCCAT 60.600 61.111 0.00 0.00 0.00 4.00
2907 3308 1.256812 CAAACCCCCATTCACACTCC 58.743 55.000 0.00 0.00 0.00 3.85
2918 3319 2.363147 ACACTCCTCTCCCCTCGC 60.363 66.667 0.00 0.00 0.00 5.03
2949 3350 1.484240 CCCCATTGACACTCCTCTCTC 59.516 57.143 0.00 0.00 0.00 3.20
2954 3355 1.252175 TGACACTCCTCTCTCACTGC 58.748 55.000 0.00 0.00 0.00 4.40
2956 3357 1.892474 GACACTCCTCTCTCACTGCTT 59.108 52.381 0.00 0.00 0.00 3.91
2967 3368 3.515630 TCTCACTGCTTCTTCATTAGCG 58.484 45.455 0.00 0.00 40.26 4.26
2976 3377 1.134521 TCTTCATTAGCGCCGATGGTT 60.135 47.619 17.41 0.00 0.00 3.67
2978 3379 1.860676 TCATTAGCGCCGATGGTTAC 58.139 50.000 17.41 0.00 0.00 2.50
2992 3393 0.618458 GGTTACTGATGCTCACCCCA 59.382 55.000 0.00 0.00 0.00 4.96
2994 3395 1.279271 GTTACTGATGCTCACCCCACT 59.721 52.381 0.00 0.00 0.00 4.00
2996 3397 1.748122 CTGATGCTCACCCCACTGC 60.748 63.158 0.00 0.00 0.00 4.40
2997 3398 2.194388 CTGATGCTCACCCCACTGCT 62.194 60.000 0.00 0.00 0.00 4.24
2998 3399 1.451028 GATGCTCACCCCACTGCTC 60.451 63.158 0.00 0.00 0.00 4.26
3007 3408 1.734477 CCCACTGCTCGACTCGTTG 60.734 63.158 0.00 0.00 0.00 4.10
3052 3453 2.091775 AGTAGTAGGTTGCCTCCTCGAT 60.092 50.000 0.00 0.00 38.86 3.59
3053 3454 1.115467 AGTAGGTTGCCTCCTCGATG 58.885 55.000 0.00 0.00 38.86 3.84
3067 3468 0.965866 TCGATGAAGGTGGAGCTCGT 60.966 55.000 7.83 0.00 0.00 4.18
3070 3471 1.617947 ATGAAGGTGGAGCTCGTCCC 61.618 60.000 18.18 12.84 46.31 4.46
3071 3472 1.985116 GAAGGTGGAGCTCGTCCCT 60.985 63.158 18.18 14.61 46.31 4.20
3078 3479 1.446966 GAGCTCGTCCCTGCTGAAC 60.447 63.158 0.00 0.00 39.91 3.18
3088 3489 1.739562 CTGCTGAACTGGCGAGGAC 60.740 63.158 0.00 0.00 0.00 3.85
3110 3511 1.075970 GAAGGCCCTTTCCCCCATC 60.076 63.158 0.00 0.00 0.00 3.51
3111 3512 2.589610 GAAGGCCCTTTCCCCCATCC 62.590 65.000 0.00 0.00 0.00 3.51
3112 3513 4.157660 GGCCCTTTCCCCCATCCC 62.158 72.222 0.00 0.00 0.00 3.85
3113 3514 3.355344 GCCCTTTCCCCCATCCCA 61.355 66.667 0.00 0.00 0.00 4.37
3114 3515 2.715125 GCCCTTTCCCCCATCCCAT 61.715 63.158 0.00 0.00 0.00 4.00
3115 3516 1.233949 CCCTTTCCCCCATCCCATG 59.766 63.158 0.00 0.00 0.00 3.66
3116 3517 1.295915 CCCTTTCCCCCATCCCATGA 61.296 60.000 0.00 0.00 0.00 3.07
3117 3518 0.186873 CCTTTCCCCCATCCCATGAG 59.813 60.000 0.00 0.00 0.00 2.90
3118 3519 0.186873 CTTTCCCCCATCCCATGAGG 59.813 60.000 0.00 0.00 0.00 3.86
3119 3520 1.948403 TTTCCCCCATCCCATGAGGC 61.948 60.000 0.00 0.00 34.51 4.70
3120 3521 3.105248 CCCCCATCCCATGAGGCA 61.105 66.667 0.00 0.00 34.51 4.75
3121 3522 2.703362 CCCCCATCCCATGAGGCAA 61.703 63.158 0.00 0.00 34.51 4.52
3122 3523 1.456331 CCCCATCCCATGAGGCAAC 60.456 63.158 0.00 0.00 34.51 4.17
3123 3524 1.456331 CCCATCCCATGAGGCAACC 60.456 63.158 0.00 0.00 34.51 3.77
3124 3525 1.307309 CCATCCCATGAGGCAACCA 59.693 57.895 0.00 0.00 34.51 3.67
3125 3526 1.039233 CCATCCCATGAGGCAACCAC 61.039 60.000 0.00 0.00 34.51 4.16
3126 3527 0.033796 CATCCCATGAGGCAACCACT 60.034 55.000 0.00 0.00 34.51 4.00
3127 3528 0.033796 ATCCCATGAGGCAACCACTG 60.034 55.000 0.00 0.00 34.51 3.66
3128 3529 1.075482 CCCATGAGGCAACCACTGT 59.925 57.895 0.00 0.00 37.17 3.55
3129 3530 1.246056 CCCATGAGGCAACCACTGTG 61.246 60.000 0.00 0.00 37.17 3.66
3130 3531 1.246056 CCATGAGGCAACCACTGTGG 61.246 60.000 24.80 24.80 45.02 4.17
3131 3532 1.604593 ATGAGGCAACCACTGTGGC 60.605 57.895 26.20 12.48 42.67 5.01
3132 3533 3.357079 GAGGCAACCACTGTGGCG 61.357 66.667 26.20 18.22 42.81 5.69
3133 3534 4.954970 AGGCAACCACTGTGGCGG 62.955 66.667 26.20 18.70 42.81 6.13
3135 3536 2.281208 GCAACCACTGTGGCGGTA 60.281 61.111 26.20 0.00 42.67 4.02
3136 3537 1.894756 GCAACCACTGTGGCGGTAA 60.895 57.895 26.20 0.00 42.67 2.85
3137 3538 1.852067 GCAACCACTGTGGCGGTAAG 61.852 60.000 26.20 10.84 42.67 2.34
3138 3539 1.072505 AACCACTGTGGCGGTAAGG 59.927 57.895 26.20 0.60 42.67 2.69
3139 3540 1.702022 AACCACTGTGGCGGTAAGGT 61.702 55.000 26.20 1.37 42.67 3.50
3140 3541 0.832983 ACCACTGTGGCGGTAAGGTA 60.833 55.000 26.20 0.00 42.67 3.08
3141 3542 0.108329 CCACTGTGGCGGTAAGGTAG 60.108 60.000 14.87 0.00 0.00 3.18
3142 3543 0.606604 CACTGTGGCGGTAAGGTAGT 59.393 55.000 0.00 0.00 0.00 2.73
3143 3544 1.001633 CACTGTGGCGGTAAGGTAGTT 59.998 52.381 0.00 0.00 0.00 2.24
3144 3545 1.274447 ACTGTGGCGGTAAGGTAGTTC 59.726 52.381 0.00 0.00 0.00 3.01
3145 3546 0.244450 TGTGGCGGTAAGGTAGTTCG 59.756 55.000 0.00 0.00 0.00 3.95
3146 3547 0.244721 GTGGCGGTAAGGTAGTTCGT 59.755 55.000 0.00 0.00 0.00 3.85
3147 3548 0.968405 TGGCGGTAAGGTAGTTCGTT 59.032 50.000 0.00 0.00 0.00 3.85
3148 3549 1.344114 TGGCGGTAAGGTAGTTCGTTT 59.656 47.619 0.00 0.00 0.00 3.60
3149 3550 1.728425 GGCGGTAAGGTAGTTCGTTTG 59.272 52.381 0.00 0.00 0.00 2.93
3150 3551 1.127397 GCGGTAAGGTAGTTCGTTTGC 59.873 52.381 0.00 0.00 0.00 3.68
3151 3552 2.680577 CGGTAAGGTAGTTCGTTTGCT 58.319 47.619 0.00 0.00 0.00 3.91
3152 3553 2.410730 CGGTAAGGTAGTTCGTTTGCTG 59.589 50.000 0.00 0.00 0.00 4.41
3153 3554 2.159037 GGTAAGGTAGTTCGTTTGCTGC 59.841 50.000 0.00 0.00 0.00 5.25
3154 3555 0.865769 AAGGTAGTTCGTTTGCTGCG 59.134 50.000 0.00 0.00 0.00 5.18
3155 3556 0.949105 AGGTAGTTCGTTTGCTGCGG 60.949 55.000 0.00 0.00 0.00 5.69
3156 3557 0.947180 GGTAGTTCGTTTGCTGCGGA 60.947 55.000 0.00 0.00 0.00 5.54
3157 3558 0.438830 GTAGTTCGTTTGCTGCGGAG 59.561 55.000 0.00 0.00 0.00 4.63
3158 3559 0.669318 TAGTTCGTTTGCTGCGGAGG 60.669 55.000 5.93 0.00 0.00 4.30
3159 3560 2.668212 TTCGTTTGCTGCGGAGGG 60.668 61.111 5.93 0.00 0.00 4.30
3160 3561 4.697756 TCGTTTGCTGCGGAGGGG 62.698 66.667 5.93 0.00 0.00 4.79
3170 3571 3.330720 CGGAGGGGGCAAGGAGTT 61.331 66.667 0.00 0.00 0.00 3.01
3171 3572 2.677848 GGAGGGGGCAAGGAGTTC 59.322 66.667 0.00 0.00 0.00 3.01
3172 3573 2.231380 GGAGGGGGCAAGGAGTTCA 61.231 63.158 0.00 0.00 0.00 3.18
3173 3574 1.575447 GGAGGGGGCAAGGAGTTCAT 61.575 60.000 0.00 0.00 0.00 2.57
3174 3575 0.394899 GAGGGGGCAAGGAGTTCATG 60.395 60.000 0.00 0.00 0.00 3.07
3175 3576 1.142688 AGGGGGCAAGGAGTTCATGT 61.143 55.000 0.00 0.00 0.00 3.21
3176 3577 0.967380 GGGGGCAAGGAGTTCATGTG 60.967 60.000 0.00 0.00 0.00 3.21
3177 3578 0.251341 GGGGCAAGGAGTTCATGTGT 60.251 55.000 0.00 0.00 0.00 3.72
3178 3579 0.883833 GGGCAAGGAGTTCATGTGTG 59.116 55.000 0.00 0.00 0.00 3.82
3179 3580 0.883833 GGCAAGGAGTTCATGTGTGG 59.116 55.000 0.00 0.00 0.00 4.17
3180 3581 1.609208 GCAAGGAGTTCATGTGTGGT 58.391 50.000 0.00 0.00 0.00 4.16
3181 3582 1.956477 GCAAGGAGTTCATGTGTGGTT 59.044 47.619 0.00 0.00 0.00 3.67
3182 3583 2.030805 GCAAGGAGTTCATGTGTGGTTC 60.031 50.000 0.00 0.00 0.00 3.62
3183 3584 2.554032 CAAGGAGTTCATGTGTGGTTCC 59.446 50.000 0.00 0.00 0.00 3.62
3184 3585 1.073923 AGGAGTTCATGTGTGGTTCCC 59.926 52.381 0.00 0.00 0.00 3.97
3185 3586 1.156736 GAGTTCATGTGTGGTTCCCG 58.843 55.000 0.00 0.00 0.00 5.14
3186 3587 0.472471 AGTTCATGTGTGGTTCCCGT 59.528 50.000 0.00 0.00 0.00 5.28
3187 3588 0.591170 GTTCATGTGTGGTTCCCGTG 59.409 55.000 0.00 0.00 0.00 4.94
3188 3589 0.470341 TTCATGTGTGGTTCCCGTGA 59.530 50.000 0.00 0.00 0.00 4.35
3189 3590 0.250124 TCATGTGTGGTTCCCGTGAC 60.250 55.000 0.00 0.00 0.00 3.67
3190 3591 0.533978 CATGTGTGGTTCCCGTGACA 60.534 55.000 0.00 0.00 0.00 3.58
3191 3592 0.250295 ATGTGTGGTTCCCGTGACAG 60.250 55.000 0.00 0.00 0.00 3.51
3192 3593 2.110213 TGTGGTTCCCGTGACAGC 59.890 61.111 0.00 0.00 0.00 4.40
3193 3594 2.668550 GTGGTTCCCGTGACAGCC 60.669 66.667 0.00 0.00 0.00 4.85
3194 3595 4.308458 TGGTTCCCGTGACAGCCG 62.308 66.667 0.00 0.00 0.00 5.52
3214 3615 4.832608 GCGGTAGGGGCGAGGTTG 62.833 72.222 0.00 0.00 0.00 3.77
3215 3616 3.387947 CGGTAGGGGCGAGGTTGT 61.388 66.667 0.00 0.00 0.00 3.32
3216 3617 2.951101 CGGTAGGGGCGAGGTTGTT 61.951 63.158 0.00 0.00 0.00 2.83
3217 3618 1.376812 GGTAGGGGCGAGGTTGTTG 60.377 63.158 0.00 0.00 0.00 3.33
3218 3619 2.038837 GTAGGGGCGAGGTTGTTGC 61.039 63.158 0.00 0.00 34.28 4.17
3223 3624 2.954611 GCGAGGTTGTTGCCCTTC 59.045 61.111 0.00 0.00 30.60 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 3.916392 AAAGCGCACGTCCTCCTCG 62.916 63.158 11.47 0.00 0.00 4.63
137 138 2.092212 GGAGAAGGAGGCCATCATCAAA 60.092 50.000 5.01 0.00 0.00 2.69
233 234 4.367023 CGGAGGGCGGTCGTCAAA 62.367 66.667 4.58 0.00 32.28 2.69
254 255 1.725557 CGGAATCGGCGAAGAGGAGA 61.726 60.000 15.93 0.00 0.00 3.71
402 403 2.609610 CCTTCCTCCCCCGTCCAA 60.610 66.667 0.00 0.00 0.00 3.53
448 454 1.299321 CCCCATTTGGCGCCATTTT 59.701 52.632 33.25 15.52 0.00 1.82
471 480 2.097036 GGCACAAAGTATAACCACCCC 58.903 52.381 0.00 0.00 0.00 4.95
475 484 2.038689 TCCGTGGCACAAAGTATAACCA 59.961 45.455 19.09 0.00 44.16 3.67
480 491 1.610624 CCTGTCCGTGGCACAAAGTAT 60.611 52.381 19.09 0.00 44.16 2.12
482 493 1.525995 CCTGTCCGTGGCACAAAGT 60.526 57.895 19.09 0.00 44.16 2.66
555 566 2.148558 TTTGCGCCGATTTTGGGGTC 62.149 55.000 4.18 0.00 43.50 4.46
575 586 3.662117 GACCCATCCCAGGCCCAAC 62.662 68.421 0.00 0.00 0.00 3.77
599 610 5.504337 CGAACTTTTGTCCGTTTTATGTCCA 60.504 40.000 0.00 0.00 0.00 4.02
643 654 6.406370 AGAATAACATGAATGAACCAGACGA 58.594 36.000 0.00 0.00 0.00 4.20
654 665 7.566760 TGCATCCGTTTAGAATAACATGAAT 57.433 32.000 0.00 0.00 0.00 2.57
703 714 4.389374 ACATAATCATAAGGCCAACTCCG 58.611 43.478 5.01 0.00 0.00 4.63
720 731 5.007039 CGGCAAGACGACTACTAGTACATAA 59.993 44.000 0.00 0.00 35.47 1.90
722 733 3.311871 CGGCAAGACGACTACTAGTACAT 59.688 47.826 0.00 0.00 35.47 2.29
723 734 2.674852 CGGCAAGACGACTACTAGTACA 59.325 50.000 0.00 0.00 35.47 2.90
724 735 2.675348 ACGGCAAGACGACTACTAGTAC 59.325 50.000 0.66 0.00 37.61 2.73
725 736 2.977914 ACGGCAAGACGACTACTAGTA 58.022 47.619 0.66 1.89 37.61 1.82
726 737 1.818642 ACGGCAAGACGACTACTAGT 58.181 50.000 0.66 0.00 37.61 2.57
727 738 2.031437 GGTACGGCAAGACGACTACTAG 59.969 54.545 0.66 0.00 37.61 2.57
728 739 2.009774 GGTACGGCAAGACGACTACTA 58.990 52.381 0.66 0.00 37.61 1.82
729 740 0.807496 GGTACGGCAAGACGACTACT 59.193 55.000 0.66 0.00 37.61 2.57
730 741 0.179153 GGGTACGGCAAGACGACTAC 60.179 60.000 0.66 0.00 37.61 2.73
731 742 1.315257 GGGGTACGGCAAGACGACTA 61.315 60.000 0.66 0.00 37.61 2.59
732 743 2.643232 GGGGTACGGCAAGACGACT 61.643 63.158 0.66 0.00 37.61 4.18
733 744 2.125793 GGGGTACGGCAAGACGAC 60.126 66.667 0.66 0.00 37.61 4.34
734 745 2.283388 AGGGGTACGGCAAGACGA 60.283 61.111 0.66 0.00 37.61 4.20
735 746 2.162338 TTGAGGGGTACGGCAAGACG 62.162 60.000 0.00 0.00 40.31 4.18
736 747 0.035739 TTTGAGGGGTACGGCAAGAC 59.964 55.000 0.00 0.00 0.00 3.01
737 748 0.766131 TTTTGAGGGGTACGGCAAGA 59.234 50.000 0.00 0.00 0.00 3.02
738 749 1.539827 CTTTTTGAGGGGTACGGCAAG 59.460 52.381 0.00 0.00 0.00 4.01
739 750 1.143277 TCTTTTTGAGGGGTACGGCAA 59.857 47.619 0.00 0.00 0.00 4.52
740 751 0.766131 TCTTTTTGAGGGGTACGGCA 59.234 50.000 0.00 0.00 0.00 5.69
741 752 1.900245 TTCTTTTTGAGGGGTACGGC 58.100 50.000 0.00 0.00 0.00 5.68
742 753 3.483421 ACTTTCTTTTTGAGGGGTACGG 58.517 45.455 0.00 0.00 0.00 4.02
743 754 4.151157 CGTACTTTCTTTTTGAGGGGTACG 59.849 45.833 0.00 0.00 39.71 3.67
744 755 5.059161 ACGTACTTTCTTTTTGAGGGGTAC 58.941 41.667 0.00 0.00 0.00 3.34
745 756 5.070847 AGACGTACTTTCTTTTTGAGGGGTA 59.929 40.000 0.00 0.00 0.00 3.69
746 757 4.132336 GACGTACTTTCTTTTTGAGGGGT 58.868 43.478 0.00 0.00 0.00 4.95
747 758 4.386711 AGACGTACTTTCTTTTTGAGGGG 58.613 43.478 0.00 0.00 0.00 4.79
748 759 5.748592 CAAGACGTACTTTCTTTTTGAGGG 58.251 41.667 4.31 0.00 36.61 4.30
749 760 5.205565 GCAAGACGTACTTTCTTTTTGAGG 58.794 41.667 4.31 0.00 36.61 3.86
750 761 5.205565 GGCAAGACGTACTTTCTTTTTGAG 58.794 41.667 4.31 0.00 36.61 3.02
751 762 4.260456 CGGCAAGACGTACTTTCTTTTTGA 60.260 41.667 4.31 0.00 36.61 2.69
752 763 3.966218 CGGCAAGACGTACTTTCTTTTTG 59.034 43.478 4.31 0.00 36.61 2.44
753 764 3.547413 GCGGCAAGACGTACTTTCTTTTT 60.547 43.478 0.00 0.00 36.61 1.94
754 765 2.032290 GCGGCAAGACGTACTTTCTTTT 60.032 45.455 0.00 0.00 36.61 2.27
755 766 1.529865 GCGGCAAGACGTACTTTCTTT 59.470 47.619 0.00 0.00 36.61 2.52
806 817 0.746563 AACACCGGTGGATTATGCCG 60.747 55.000 36.47 9.65 44.55 5.69
807 818 1.134175 CAAACACCGGTGGATTATGCC 59.866 52.381 36.47 0.00 34.19 4.40
808 819 2.088423 TCAAACACCGGTGGATTATGC 58.912 47.619 36.47 0.00 34.19 3.14
809 820 3.315191 GGATCAAACACCGGTGGATTATG 59.685 47.826 36.47 24.99 34.19 1.90
810 821 3.053991 TGGATCAAACACCGGTGGATTAT 60.054 43.478 36.47 23.70 34.19 1.28
811 822 2.306219 TGGATCAAACACCGGTGGATTA 59.694 45.455 36.47 20.22 34.19 1.75
812 823 1.074727 TGGATCAAACACCGGTGGATT 59.925 47.619 36.47 27.07 34.19 3.01
813 824 0.695924 TGGATCAAACACCGGTGGAT 59.304 50.000 36.47 27.94 34.19 3.41
814 825 0.474614 TTGGATCAAACACCGGTGGA 59.525 50.000 36.47 24.70 34.19 4.02
815 826 0.596082 GTTGGATCAAACACCGGTGG 59.404 55.000 36.47 20.25 34.19 4.61
816 827 0.237235 CGTTGGATCAAACACCGGTG 59.763 55.000 32.83 32.83 0.00 4.94
817 828 0.887387 CCGTTGGATCAAACACCGGT 60.887 55.000 13.42 0.00 29.00 5.28
818 829 0.887387 ACCGTTGGATCAAACACCGG 60.887 55.000 13.42 10.77 36.06 5.28
819 830 0.237235 CACCGTTGGATCAAACACCG 59.763 55.000 13.42 2.43 0.00 4.94
820 831 1.314730 ACACCGTTGGATCAAACACC 58.685 50.000 13.42 0.00 0.00 4.16
821 832 3.112580 CAAACACCGTTGGATCAAACAC 58.887 45.455 13.42 0.00 0.00 3.32
822 833 2.755655 ACAAACACCGTTGGATCAAACA 59.244 40.909 13.42 0.00 32.50 2.83
823 834 3.430333 ACAAACACCGTTGGATCAAAC 57.570 42.857 2.55 2.55 32.50 2.93
824 835 4.457834 AAACAAACACCGTTGGATCAAA 57.542 36.364 0.00 0.00 32.50 2.69
825 836 4.457834 AAAACAAACACCGTTGGATCAA 57.542 36.364 0.00 0.00 32.50 2.57
826 837 4.457834 AAAAACAAACACCGTTGGATCA 57.542 36.364 0.00 0.00 32.50 2.92
850 861 3.149981 TCAAACACCGGTTGATTATGCA 58.850 40.909 2.97 0.00 37.30 3.96
1150 1240 2.359975 GGGAACTCAGCAACGGGG 60.360 66.667 0.00 0.00 0.00 5.73
1274 1373 1.544246 GGAACAAAATTAGCCCGCAGT 59.456 47.619 0.00 0.00 0.00 4.40
1282 1388 4.627058 ACCGCAAAAGGGAACAAAATTAG 58.373 39.130 0.00 0.00 35.02 1.73
1360 1476 1.677576 CTTGAGCACAACCTTCTGCAA 59.322 47.619 0.00 0.00 35.73 4.08
1440 1556 5.103473 AGGGATGAGTCAAGAGATAGTACCA 60.103 44.000 0.00 0.00 0.00 3.25
1493 1648 7.293745 CCTTCAATTGAGCGCATAATTACTAG 58.706 38.462 11.47 12.14 0.00 2.57
1496 1651 4.676924 GCCTTCAATTGAGCGCATAATTAC 59.323 41.667 11.47 0.98 0.00 1.89
1497 1652 4.261572 GGCCTTCAATTGAGCGCATAATTA 60.262 41.667 22.79 1.22 0.00 1.40
1498 1653 3.491447 GGCCTTCAATTGAGCGCATAATT 60.491 43.478 22.79 13.02 0.00 1.40
2035 2300 0.107456 AGCGGGTAGGCTGATGATTG 59.893 55.000 0.00 0.00 42.86 2.67
2037 2302 4.302622 AGCGGGTAGGCTGATGAT 57.697 55.556 0.00 0.00 42.86 2.45
2236 2559 6.486253 ACTCTCAAAAGTGATACGTACGTA 57.514 37.500 28.62 28.62 31.85 3.57
2268 2613 3.181450 ACCAGCTGGGCAGTAATATTCTC 60.181 47.826 35.42 0.00 42.05 2.87
2293 2638 6.685403 CGTATAACGCTTTCCCAATACTTTTG 59.315 38.462 0.00 0.00 33.65 2.44
2301 2646 2.273557 GCTCGTATAACGCTTTCCCAA 58.726 47.619 0.00 0.00 42.21 4.12
2303 2648 1.930567 TGCTCGTATAACGCTTTCCC 58.069 50.000 0.00 0.00 42.21 3.97
2305 2650 3.797256 AGTGATGCTCGTATAACGCTTTC 59.203 43.478 0.00 0.00 42.21 2.62
2306 2651 3.782046 AGTGATGCTCGTATAACGCTTT 58.218 40.909 0.00 0.00 42.21 3.51
2307 2652 3.438297 AGTGATGCTCGTATAACGCTT 57.562 42.857 0.00 0.00 42.21 4.68
2308 2653 3.813724 TCTAGTGATGCTCGTATAACGCT 59.186 43.478 0.00 0.00 42.21 5.07
2309 2654 4.143194 TCTAGTGATGCTCGTATAACGC 57.857 45.455 0.00 0.00 42.21 4.84
2311 2656 8.679100 AGGATATTCTAGTGATGCTCGTATAAC 58.321 37.037 0.00 0.00 0.00 1.89
2313 2658 7.201741 GCAGGATATTCTAGTGATGCTCGTATA 60.202 40.741 0.00 0.00 0.00 1.47
2314 2659 6.405286 GCAGGATATTCTAGTGATGCTCGTAT 60.405 42.308 0.00 0.00 0.00 3.06
2315 2660 5.106118 GCAGGATATTCTAGTGATGCTCGTA 60.106 44.000 0.00 0.00 0.00 3.43
2316 2661 4.321601 GCAGGATATTCTAGTGATGCTCGT 60.322 45.833 0.00 0.00 0.00 4.18
2318 2663 5.170021 CAGCAGGATATTCTAGTGATGCTC 58.830 45.833 0.00 0.00 40.58 4.26
2319 2664 4.592351 ACAGCAGGATATTCTAGTGATGCT 59.408 41.667 0.00 0.00 43.14 3.79
2321 2666 4.689812 GCACAGCAGGATATTCTAGTGATG 59.310 45.833 12.32 1.16 0.00 3.07
2329 2687 5.586243 TGAGTTTTAGCACAGCAGGATATTC 59.414 40.000 0.00 0.00 0.00 1.75
2337 2695 4.006780 TCTCATGAGTTTTAGCACAGCA 57.993 40.909 21.92 0.00 0.00 4.41
2361 2719 7.760437 TCAATTGCGATTTGATGAGAAATACA 58.240 30.769 0.00 0.00 0.00 2.29
2373 2732 5.036737 GGTACTGGAATCAATTGCGATTTG 58.963 41.667 0.00 0.00 35.74 2.32
2419 2815 2.224843 ACCCACAATCATCACAAGAGCA 60.225 45.455 0.00 0.00 0.00 4.26
2420 2816 2.163010 CACCCACAATCATCACAAGAGC 59.837 50.000 0.00 0.00 0.00 4.09
2421 2817 2.751259 CCACCCACAATCATCACAAGAG 59.249 50.000 0.00 0.00 0.00 2.85
2422 2818 2.794103 CCACCCACAATCATCACAAGA 58.206 47.619 0.00 0.00 0.00 3.02
2423 2819 1.203052 GCCACCCACAATCATCACAAG 59.797 52.381 0.00 0.00 0.00 3.16
2466 2862 7.040961 GGCCTACAACAGTTTAAATGTACAAGA 60.041 37.037 0.00 0.00 0.00 3.02
2507 2908 8.077386 TGGAGTTTATGTTTCCGAAATTACAAC 58.923 33.333 0.00 0.04 33.60 3.32
2537 2938 2.232696 CCCACCCCAAAATAGAAAACCG 59.767 50.000 0.00 0.00 0.00 4.44
2582 2983 5.104817 TGAGCATCTGTCTGGTGAATAATCA 60.105 40.000 0.00 0.00 34.92 2.57
2583 2984 5.363101 TGAGCATCTGTCTGGTGAATAATC 58.637 41.667 0.00 0.00 34.92 1.75
2584 2985 5.363562 TGAGCATCTGTCTGGTGAATAAT 57.636 39.130 0.00 0.00 34.92 1.28
2665 3066 1.479368 GGGCAAAAACAGCATCCCCA 61.479 55.000 0.00 0.00 0.00 4.96
2666 3067 1.296392 GGGCAAAAACAGCATCCCC 59.704 57.895 0.00 0.00 0.00 4.81
2686 3087 1.135199 GGTGCAATGCAGACATCCAAG 60.135 52.381 8.73 0.00 40.08 3.61
2690 3091 2.728690 TTTGGTGCAATGCAGACATC 57.271 45.000 8.73 0.00 40.08 3.06
2692 3093 3.069872 AGAATTTTGGTGCAATGCAGACA 59.930 39.130 8.73 8.43 40.08 3.41
2698 3099 4.178540 CAGGCTAGAATTTTGGTGCAATG 58.821 43.478 0.00 0.00 0.00 2.82
2708 3109 2.084546 GTTCCACGCAGGCTAGAATTT 58.915 47.619 0.00 0.00 37.29 1.82
2715 3116 1.523758 CTTTAAGTTCCACGCAGGCT 58.476 50.000 0.00 0.00 37.29 4.58
2719 3120 2.606795 GCAATGCTTTAAGTTCCACGCA 60.607 45.455 0.00 0.00 0.00 5.24
2722 3123 4.675408 GCCTAGCAATGCTTTAAGTTCCAC 60.675 45.833 14.85 0.00 40.44 4.02
2725 3126 4.972514 AGCCTAGCAATGCTTTAAGTTC 57.027 40.909 14.85 0.00 40.44 3.01
2737 3138 9.150424 AAGTTTCTACTCAGCTAAGCCTAGCAA 62.150 40.741 16.49 3.50 42.63 3.91
2742 3143 4.775253 AGAAGTTTCTACTCAGCTAAGCCT 59.225 41.667 0.00 0.00 35.34 4.58
2743 3144 4.867608 CAGAAGTTTCTACTCAGCTAAGCC 59.132 45.833 0.00 0.00 35.34 4.35
2746 3147 7.896811 TGATTCAGAAGTTTCTACTCAGCTAA 58.103 34.615 0.00 0.00 35.34 3.09
2748 3149 6.014669 ACTGATTCAGAAGTTTCTACTCAGCT 60.015 38.462 20.33 0.00 38.49 4.24
2749 3150 6.162777 ACTGATTCAGAAGTTTCTACTCAGC 58.837 40.000 20.33 0.00 38.49 4.26
2750 3151 6.526325 CGACTGATTCAGAAGTTTCTACTCAG 59.474 42.308 20.33 17.24 39.55 3.35
2758 3159 6.677781 TGAAAACGACTGATTCAGAAGTTT 57.322 33.333 24.32 24.32 41.64 2.66
2762 3163 8.378172 ACTAAATGAAAACGACTGATTCAGAA 57.622 30.769 20.33 0.00 36.59 3.02
2764 3165 7.954248 CAGACTAAATGAAAACGACTGATTCAG 59.046 37.037 12.17 12.17 36.59 3.02
2765 3166 7.095229 CCAGACTAAATGAAAACGACTGATTCA 60.095 37.037 0.00 0.00 37.47 2.57
2770 3171 4.452455 AGCCAGACTAAATGAAAACGACTG 59.548 41.667 0.00 0.00 0.00 3.51
2772 3173 4.142881 GGAGCCAGACTAAATGAAAACGAC 60.143 45.833 0.00 0.00 0.00 4.34
2805 3206 3.702048 GTGTAGGTGAGGGCCGCA 61.702 66.667 5.62 5.62 0.00 5.69
2807 3208 4.814294 GCGTGTAGGTGAGGGCCG 62.814 72.222 0.00 0.00 0.00 6.13
2817 3218 1.134788 CCTACTTCCCAAGGCGTGTAG 60.135 57.143 0.00 0.00 0.00 2.74
2819 3220 0.834687 TCCTACTTCCCAAGGCGTGT 60.835 55.000 0.00 0.00 32.55 4.49
2843 3244 4.755123 GGGAATAATGGTTGTCTGGTATCG 59.245 45.833 0.00 0.00 0.00 2.92
2846 3247 3.853181 TGGGGAATAATGGTTGTCTGGTA 59.147 43.478 0.00 0.00 0.00 3.25
2849 3250 3.947834 GAGTGGGGAATAATGGTTGTCTG 59.052 47.826 0.00 0.00 0.00 3.51
2862 3263 2.454941 GGGGAGAGGAGTGGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
2867 3268 3.775654 GGCGTGGGGAGAGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
2879 3280 3.601685 GGGGGTTTGTGTGGCGTG 61.602 66.667 0.00 0.00 0.00 5.34
2880 3281 2.937959 AATGGGGGTTTGTGTGGCGT 62.938 55.000 0.00 0.00 0.00 5.68
2885 3286 1.063266 AGTGTGAATGGGGGTTTGTGT 60.063 47.619 0.00 0.00 0.00 3.72
2892 3293 0.543749 GAGAGGAGTGTGAATGGGGG 59.456 60.000 0.00 0.00 0.00 5.40
2897 3298 1.872773 GAGGGGAGAGGAGTGTGAAT 58.127 55.000 0.00 0.00 0.00 2.57
2898 3299 0.612174 CGAGGGGAGAGGAGTGTGAA 60.612 60.000 0.00 0.00 0.00 3.18
2907 3308 2.454832 TTTGTGCAGCGAGGGGAGAG 62.455 60.000 0.00 0.00 0.00 3.20
2936 3337 1.544724 AGCAGTGAGAGAGGAGTGTC 58.455 55.000 0.00 0.00 0.00 3.67
2949 3350 1.063174 GGCGCTAATGAAGAAGCAGTG 59.937 52.381 7.64 0.00 38.70 3.66
2954 3355 1.528586 CCATCGGCGCTAATGAAGAAG 59.471 52.381 19.62 3.69 0.00 2.85
2956 3357 0.464036 ACCATCGGCGCTAATGAAGA 59.536 50.000 19.62 4.94 0.00 2.87
2967 3368 1.221414 GAGCATCAGTAACCATCGGC 58.779 55.000 0.00 0.00 33.17 5.54
2992 3393 2.049063 GGCAACGAGTCGAGCAGT 60.049 61.111 26.68 2.32 34.53 4.40
2994 3395 2.355837 GTGGCAACGAGTCGAGCA 60.356 61.111 26.68 15.33 42.51 4.26
3018 3419 2.567615 CCTACTACTCCTGGTTGCTGTT 59.432 50.000 0.00 0.00 0.00 3.16
3052 3453 2.283529 GGGACGAGCTCCACCTTCA 61.284 63.158 18.95 0.00 41.63 3.02
3053 3454 1.985116 AGGGACGAGCTCCACCTTC 60.985 63.158 18.95 7.55 41.63 3.46
3067 3468 2.922503 TCGCCAGTTCAGCAGGGA 60.923 61.111 0.00 0.00 0.00 4.20
3070 3471 1.739562 GTCCTCGCCAGTTCAGCAG 60.740 63.158 0.00 0.00 0.00 4.24
3071 3472 2.343758 GTCCTCGCCAGTTCAGCA 59.656 61.111 0.00 0.00 0.00 4.41
3110 3511 1.075482 ACAGTGGTTGCCTCATGGG 59.925 57.895 0.00 0.00 38.36 4.00
3111 3512 1.246056 CCACAGTGGTTGCCTCATGG 61.246 60.000 11.99 0.00 31.35 3.66
3112 3513 1.870055 GCCACAGTGGTTGCCTCATG 61.870 60.000 21.26 0.00 40.46 3.07
3113 3514 1.604593 GCCACAGTGGTTGCCTCAT 60.605 57.895 21.26 0.00 40.46 2.90
3114 3515 2.203337 GCCACAGTGGTTGCCTCA 60.203 61.111 21.26 0.00 40.46 3.86
3115 3516 3.357079 CGCCACAGTGGTTGCCTC 61.357 66.667 21.26 2.00 40.46 4.70
3116 3517 4.954970 CCGCCACAGTGGTTGCCT 62.955 66.667 21.26 0.00 40.46 4.75
3123 3524 0.606604 ACTACCTTACCGCCACAGTG 59.393 55.000 0.00 0.00 0.00 3.66
3124 3525 1.274447 GAACTACCTTACCGCCACAGT 59.726 52.381 0.00 0.00 0.00 3.55
3125 3526 1.734707 CGAACTACCTTACCGCCACAG 60.735 57.143 0.00 0.00 0.00 3.66
3126 3527 0.244450 CGAACTACCTTACCGCCACA 59.756 55.000 0.00 0.00 0.00 4.17
3127 3528 0.244721 ACGAACTACCTTACCGCCAC 59.755 55.000 0.00 0.00 0.00 5.01
3128 3529 0.968405 AACGAACTACCTTACCGCCA 59.032 50.000 0.00 0.00 0.00 5.69
3129 3530 1.728425 CAAACGAACTACCTTACCGCC 59.272 52.381 0.00 0.00 0.00 6.13
3130 3531 1.127397 GCAAACGAACTACCTTACCGC 59.873 52.381 0.00 0.00 0.00 5.68
3131 3532 2.410730 CAGCAAACGAACTACCTTACCG 59.589 50.000 0.00 0.00 0.00 4.02
3132 3533 2.159037 GCAGCAAACGAACTACCTTACC 59.841 50.000 0.00 0.00 0.00 2.85
3133 3534 2.159881 CGCAGCAAACGAACTACCTTAC 60.160 50.000 0.00 0.00 0.00 2.34
3134 3535 2.063266 CGCAGCAAACGAACTACCTTA 58.937 47.619 0.00 0.00 0.00 2.69
3135 3536 0.865769 CGCAGCAAACGAACTACCTT 59.134 50.000 0.00 0.00 0.00 3.50
3136 3537 0.949105 CCGCAGCAAACGAACTACCT 60.949 55.000 0.00 0.00 0.00 3.08
3137 3538 0.947180 TCCGCAGCAAACGAACTACC 60.947 55.000 0.00 0.00 0.00 3.18
3138 3539 0.438830 CTCCGCAGCAAACGAACTAC 59.561 55.000 0.00 0.00 0.00 2.73
3139 3540 0.669318 CCTCCGCAGCAAACGAACTA 60.669 55.000 0.00 0.00 0.00 2.24
3140 3541 1.961277 CCTCCGCAGCAAACGAACT 60.961 57.895 0.00 0.00 0.00 3.01
3141 3542 2.556287 CCTCCGCAGCAAACGAAC 59.444 61.111 0.00 0.00 0.00 3.95
3142 3543 2.668212 CCCTCCGCAGCAAACGAA 60.668 61.111 0.00 0.00 0.00 3.85
3143 3544 4.697756 CCCCTCCGCAGCAAACGA 62.698 66.667 0.00 0.00 0.00 3.85
3153 3554 3.330720 AACTCCTTGCCCCCTCCG 61.331 66.667 0.00 0.00 0.00 4.63
3154 3555 1.575447 ATGAACTCCTTGCCCCCTCC 61.575 60.000 0.00 0.00 0.00 4.30
3155 3556 0.394899 CATGAACTCCTTGCCCCCTC 60.395 60.000 0.00 0.00 0.00 4.30
3156 3557 1.142688 ACATGAACTCCTTGCCCCCT 61.143 55.000 0.00 0.00 0.00 4.79
3157 3558 0.967380 CACATGAACTCCTTGCCCCC 60.967 60.000 0.00 0.00 0.00 5.40
3158 3559 0.251341 ACACATGAACTCCTTGCCCC 60.251 55.000 0.00 0.00 0.00 5.80
3159 3560 0.883833 CACACATGAACTCCTTGCCC 59.116 55.000 0.00 0.00 0.00 5.36
3160 3561 0.883833 CCACACATGAACTCCTTGCC 59.116 55.000 0.00 0.00 0.00 4.52
3161 3562 1.609208 ACCACACATGAACTCCTTGC 58.391 50.000 0.00 0.00 0.00 4.01
3162 3563 2.554032 GGAACCACACATGAACTCCTTG 59.446 50.000 0.00 0.00 0.00 3.61
3163 3564 2.863809 GGAACCACACATGAACTCCTT 58.136 47.619 0.00 0.00 0.00 3.36
3164 3565 2.568623 GGAACCACACATGAACTCCT 57.431 50.000 0.00 0.00 0.00 3.69
3197 3598 4.832608 CAACCTCGCCCCTACCGC 62.833 72.222 0.00 0.00 0.00 5.68
3198 3599 2.951101 AACAACCTCGCCCCTACCG 61.951 63.158 0.00 0.00 0.00 4.02
3199 3600 1.376812 CAACAACCTCGCCCCTACC 60.377 63.158 0.00 0.00 0.00 3.18
3200 3601 2.038837 GCAACAACCTCGCCCCTAC 61.039 63.158 0.00 0.00 0.00 3.18
3201 3602 2.349755 GCAACAACCTCGCCCCTA 59.650 61.111 0.00 0.00 0.00 3.53
3202 3603 4.660938 GGCAACAACCTCGCCCCT 62.661 66.667 0.00 0.00 40.07 4.79
3205 3606 2.597510 AAGGGCAACAACCTCGCC 60.598 61.111 0.00 0.00 45.47 5.54
3206 3607 2.954611 GAAGGGCAACAACCTCGC 59.045 61.111 0.00 0.00 37.35 5.03


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

AutoCloner maintained by Alex Coulton.