Multiple sequence alignment - TraesCS6D01G017000

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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 TraesCS6D01G017000 chr6D 100.000 5624 0 0 1 5624 7094015 7099638 0.000000e+00 10386
1 TraesCS6D01G017000 chr6D 86.973 522 38 9 1018 1523 473225176 473225683 1.370000e-155 560
2 TraesCS6D01G017000 chr6B 89.601 3212 185 59 822 3966 12659375 12662504 0.000000e+00 3943
3 TraesCS6D01G017000 chr6B 91.061 895 63 6 4278 5162 12662740 12663627 0.000000e+00 1194
4 TraesCS6D01G017000 chr6B 88.803 518 49 6 5111 5621 12663730 12664245 1.330000e-175 627
5 TraesCS6D01G017000 chr6B 83.876 645 93 10 86 725 183376097 183375459 6.230000e-169 604
6 TraesCS6D01G017000 chr6B 86.789 545 46 7 5053 5583 12665233 12665765 8.120000e-163 584
7 TraesCS6D01G017000 chr6B 92.308 234 17 1 3993 4225 12662504 12662737 1.170000e-86 331
8 TraesCS6D01G017000 chr6B 93.103 87 6 0 5079 5165 12663645 12663731 1.640000e-25 128
9 TraesCS6D01G017000 chr6A 94.003 2418 120 21 2569 4974 6723136 6725540 0.000000e+00 3639
10 TraesCS6D01G017000 chr6A 89.036 757 50 11 791 1523 6721302 6722049 0.000000e+00 907
11 TraesCS6D01G017000 chr6A 93.182 616 35 3 1520 2128 6722252 6722867 0.000000e+00 898
12 TraesCS6D01G017000 chr6A 89.644 618 62 2 1 617 6720679 6721295 0.000000e+00 785
13 TraesCS6D01G017000 chr6A 89.113 496 40 6 1021 1512 136565131 136564646 6.230000e-169 604
14 TraesCS6D01G017000 chr6A 95.149 268 9 2 2137 2404 6722849 6723112 2.420000e-113 420
15 TraesCS6D01G017000 chr6A 87.826 345 21 12 4967 5307 6725568 6725895 8.840000e-103 385
16 TraesCS6D01G017000 chr7D 85.257 719 99 5 1 715 442765153 442765868 0.000000e+00 734
17 TraesCS6D01G017000 chr7D 92.000 75 6 0 1522 1596 518889580 518889506 7.710000e-19 106
18 TraesCS6D01G017000 chr2A 85.180 722 98 7 1 717 32938681 32939398 0.000000e+00 732
19 TraesCS6D01G017000 chr2A 84.430 456 67 3 26 479 755025543 755025090 4.000000e-121 446
20 TraesCS6D01G017000 chr2D 84.306 720 88 16 10 725 623507893 623507195 0.000000e+00 680
21 TraesCS6D01G017000 chr2D 89.147 516 36 8 1018 1523 466831367 466830862 4.780000e-175 625
22 TraesCS6D01G017000 chr4D 88.760 516 36 8 1018 1523 387808045 387807542 3.720000e-171 612
23 TraesCS6D01G017000 chr4D 94.366 71 4 0 1520 1590 115695442 115695512 5.960000e-20 110
24 TraesCS6D01G017000 chr4D 94.366 71 4 0 1520 1590 437400375 437400305 5.960000e-20 110
25 TraesCS6D01G017000 chr7B 87.921 505 38 11 1018 1512 670834717 670834226 1.760000e-159 573
26 TraesCS6D01G017000 chr7B 82.713 457 77 1 156 610 737801858 737801402 6.780000e-109 405
27 TraesCS6D01G017000 chr7B 82.533 458 76 3 156 610 737102857 737102401 3.160000e-107 399
28 TraesCS6D01G017000 chr7B 82.495 457 78 1 156 610 737403482 737403026 3.160000e-107 399
29 TraesCS6D01G017000 chr3D 86.240 516 48 11 1018 1523 182926945 182927447 6.410000e-149 538
30 TraesCS6D01G017000 chr3D 95.775 71 3 0 1520 1590 182927629 182927699 1.280000e-21 115
31 TraesCS6D01G017000 chr3B 85.350 471 43 9 1018 1478 791442926 791443380 1.100000e-126 464
32 TraesCS6D01G017000 chr5A 80.488 246 39 5 2144 2387 501496400 501496162 4.480000e-41 180
33 TraesCS6D01G017000 chr7A 95.775 71 3 0 1520 1590 114453632 114453562 1.280000e-21 115
34 TraesCS6D01G017000 chr2B 95.588 68 3 0 1520 1587 553202660 553202727 5.960000e-20 110
35 TraesCS6D01G017000 chr2B 92.208 77 6 0 1520 1596 755697163 755697087 5.960000e-20 110


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 TraesCS6D01G017000 chr6D 7094015 7099638 5623 False 10386.000000 10386 100.000000 1 5624 1 chr6D.!!$F1 5623
1 TraesCS6D01G017000 chr6D 473225176 473225683 507 False 560.000000 560 86.973000 1018 1523 1 chr6D.!!$F2 505
2 TraesCS6D01G017000 chr6B 12659375 12665765 6390 False 1134.500000 3943 90.277500 822 5621 6 chr6B.!!$F1 4799
3 TraesCS6D01G017000 chr6B 183375459 183376097 638 True 604.000000 604 83.876000 86 725 1 chr6B.!!$R1 639
4 TraesCS6D01G017000 chr6A 6720679 6725895 5216 False 1172.333333 3639 91.473333 1 5307 6 chr6A.!!$F1 5306
5 TraesCS6D01G017000 chr7D 442765153 442765868 715 False 734.000000 734 85.257000 1 715 1 chr7D.!!$F1 714
6 TraesCS6D01G017000 chr2A 32938681 32939398 717 False 732.000000 732 85.180000 1 717 1 chr2A.!!$F1 716
7 TraesCS6D01G017000 chr2D 623507195 623507893 698 True 680.000000 680 84.306000 10 725 1 chr2D.!!$R2 715
8 TraesCS6D01G017000 chr2D 466830862 466831367 505 True 625.000000 625 89.147000 1018 1523 1 chr2D.!!$R1 505
9 TraesCS6D01G017000 chr4D 387807542 387808045 503 True 612.000000 612 88.760000 1018 1523 1 chr4D.!!$R1 505
10 TraesCS6D01G017000 chr3D 182926945 182927699 754 False 326.500000 538 91.007500 1018 1590 2 chr3D.!!$F1 572

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
537 541 0.030504 TGTCGTAGAACGCCGTCAAA 59.969 50.0 0.00 0.00 42.21 2.69 F
853 859 0.107848 AAAATACCGGGCTCAGGTCG 60.108 55.0 6.32 0.00 42.81 4.79 F
1438 1498 0.179145 CACCTACGACCTGGTAAGCG 60.179 60.0 0.00 1.49 34.79 4.68 F
2426 2730 0.031994 GCCGTCCTGTTTTGCACATT 59.968 50.0 0.00 0.00 33.76 2.71 F
3381 3711 0.040958 CTCTTGCACCACAAAGTCGC 60.041 55.0 0.00 0.00 37.96 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2446 0.901124 ACCCACACAAAGCAAAGCAA 59.099 45.000 0.0 0.0 0.00 3.91 R
2386 2679 1.066430 ACAATGCCTCGGTCGTAATGT 60.066 47.619 0.0 0.0 0.00 2.71 R
3235 3564 0.759346 AACTGGACACCACAGGAGAC 59.241 55.000 0.0 0.0 40.23 3.36 R
3943 4276 0.171007 AAATCAAAGATGGCACGGCG 59.829 50.000 4.8 4.8 0.00 6.46 R
5099 5586 0.101759 GCAGTATCTTCCGCCACGTA 59.898 55.000 0.0 0.0 0.00 3.57 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
45 47 2.364970 TCCTTGCATCCACCAACAAAAG 59.635 45.455 0.00 0.00 0.00 2.27
72 74 4.680237 CTTCAGCCACCGCCGTCA 62.680 66.667 0.00 0.00 34.57 4.35
138 140 3.380637 CCAAGATCCAAGAGAAAGCCATG 59.619 47.826 0.00 0.00 0.00 3.66
218 221 1.003839 GATGTGGGTTGTCGGCTGA 60.004 57.895 0.00 0.00 0.00 4.26
220 223 0.179004 ATGTGGGTTGTCGGCTGAAA 60.179 50.000 0.00 0.00 0.00 2.69
228 231 1.511850 TGTCGGCTGAAACACATCTG 58.488 50.000 0.00 0.00 0.00 2.90
243 246 4.008330 CACATCTGCACTTCTCTTGGATT 58.992 43.478 0.00 0.00 0.00 3.01
477 481 2.753043 GACCTCCACCGCCGTCTA 60.753 66.667 0.00 0.00 0.00 2.59
537 541 0.030504 TGTCGTAGAACGCCGTCAAA 59.969 50.000 0.00 0.00 42.21 2.69
558 562 1.304134 GGTGGCCCGGAAACATCTT 60.304 57.895 0.73 0.00 0.00 2.40
562 566 1.203001 TGGCCCGGAAACATCTTTTCT 60.203 47.619 0.73 0.00 0.00 2.52
640 646 2.650322 AGAAACGAGCCAAAAGGAACA 58.350 42.857 0.00 0.00 0.00 3.18
641 647 2.618709 AGAAACGAGCCAAAAGGAACAG 59.381 45.455 0.00 0.00 0.00 3.16
659 665 2.597903 GGGCTCCCCAATCCTGTC 59.402 66.667 0.00 0.00 44.65 3.51
660 666 2.190578 GGCTCCCCAATCCTGTCG 59.809 66.667 0.00 0.00 0.00 4.35
661 667 2.514824 GCTCCCCAATCCTGTCGC 60.515 66.667 0.00 0.00 0.00 5.19
662 668 2.190578 CTCCCCAATCCTGTCGCC 59.809 66.667 0.00 0.00 0.00 5.54
663 669 3.740128 CTCCCCAATCCTGTCGCCG 62.740 68.421 0.00 0.00 0.00 6.46
718 724 3.484547 CGTGCCGGCGTAGGAAAC 61.485 66.667 23.90 11.56 0.00 2.78
730 736 3.142404 GTAGGAAACGGAACTACCTCG 57.858 52.381 0.00 0.00 36.31 4.63
731 737 0.245813 AGGAAACGGAACTACCTCGC 59.754 55.000 0.00 0.00 36.31 5.03
732 738 1.074872 GGAAACGGAACTACCTCGCG 61.075 60.000 0.00 0.00 36.31 5.87
733 739 0.387750 GAAACGGAACTACCTCGCGT 60.388 55.000 5.77 0.00 36.31 6.01
734 740 0.665369 AAACGGAACTACCTCGCGTG 60.665 55.000 5.77 2.75 36.31 5.34
735 741 1.799258 AACGGAACTACCTCGCGTGT 61.799 55.000 5.77 7.69 36.31 4.49
736 742 1.513586 CGGAACTACCTCGCGTGTC 60.514 63.158 5.77 0.00 36.31 3.67
737 743 1.513586 GGAACTACCTCGCGTGTCG 60.514 63.158 5.77 3.73 40.15 4.35
748 754 2.401592 CGTGTCGCCGAGAGAGAG 59.598 66.667 0.00 0.00 0.00 3.20
749 755 2.795297 GTGTCGCCGAGAGAGAGG 59.205 66.667 0.00 0.00 0.00 3.69
750 756 2.438614 TGTCGCCGAGAGAGAGGG 60.439 66.667 0.00 0.00 0.00 4.30
751 757 3.213402 GTCGCCGAGAGAGAGGGG 61.213 72.222 0.00 0.00 41.23 4.79
752 758 4.507916 TCGCCGAGAGAGAGGGGG 62.508 72.222 0.00 0.00 40.40 5.40
755 761 2.364317 CCGAGAGAGAGGGGGCAA 60.364 66.667 0.00 0.00 0.00 4.52
756 762 2.430610 CCGAGAGAGAGGGGGCAAG 61.431 68.421 0.00 0.00 0.00 4.01
757 763 2.907236 GAGAGAGAGGGGGCAAGC 59.093 66.667 0.00 0.00 0.00 4.01
758 764 1.992277 GAGAGAGAGGGGGCAAGCA 60.992 63.158 0.00 0.00 0.00 3.91
759 765 1.970352 GAGAGAGAGGGGGCAAGCAG 61.970 65.000 0.00 0.00 0.00 4.24
760 766 1.992277 GAGAGAGGGGGCAAGCAGA 60.992 63.158 0.00 0.00 0.00 4.26
761 767 1.539869 AGAGAGGGGGCAAGCAGAA 60.540 57.895 0.00 0.00 0.00 3.02
762 768 1.377856 GAGAGGGGGCAAGCAGAAC 60.378 63.158 0.00 0.00 0.00 3.01
763 769 1.846712 GAGAGGGGGCAAGCAGAACT 61.847 60.000 0.00 0.00 0.00 3.01
764 770 1.676967 GAGGGGGCAAGCAGAACTG 60.677 63.158 0.00 0.00 0.00 3.16
776 782 2.376808 CAGAACTGCTCGACAATCCT 57.623 50.000 0.00 0.00 0.00 3.24
777 783 2.266554 CAGAACTGCTCGACAATCCTC 58.733 52.381 0.00 0.00 0.00 3.71
778 784 1.135257 AGAACTGCTCGACAATCCTCG 60.135 52.381 0.00 0.00 34.83 4.63
779 785 0.108615 AACTGCTCGACAATCCTCGG 60.109 55.000 0.00 0.00 34.27 4.63
780 786 1.227089 CTGCTCGACAATCCTCGGG 60.227 63.158 0.00 0.00 37.20 5.14
782 788 2.107141 CTCGACAATCCTCGGGCC 59.893 66.667 0.00 0.00 34.27 5.80
783 789 3.774959 CTCGACAATCCTCGGGCCG 62.775 68.421 22.51 22.51 34.27 6.13
820 826 0.684153 CCATTTCGGCCCCAGAACAT 60.684 55.000 0.00 0.00 0.00 2.71
839 845 6.601613 AGAACATGTTTATCAGGCCGAAAATA 59.398 34.615 13.36 0.00 0.00 1.40
853 859 0.107848 AAAATACCGGGCTCAGGTCG 60.108 55.000 6.32 0.00 42.81 4.79
857 863 1.913951 TACCGGGCTCAGGTCGAGTA 61.914 60.000 6.32 0.00 44.33 2.59
901 911 3.190738 TTACAACAGCCCGGCAGCT 62.191 57.895 13.15 0.00 46.45 4.24
956 966 2.960359 GAAGCGGATAAGGCCACCCC 62.960 65.000 5.01 0.00 0.00 4.95
994 1004 1.790387 CCAAAGCTTCGCTCTTCCG 59.210 57.895 0.00 0.00 38.25 4.30
1086 1117 3.579302 CCCTCCAAGCACCACCCA 61.579 66.667 0.00 0.00 0.00 4.51
1438 1498 0.179145 CACCTACGACCTGGTAAGCG 60.179 60.000 0.00 1.49 34.79 4.68
1440 1500 1.226888 CTACGACCTGGTAAGCGGC 60.227 63.158 0.00 0.00 0.00 6.53
1523 1591 2.352715 GGACTGACATGACACGATGTGA 60.353 50.000 0.00 0.00 36.67 3.58
1542 1826 2.039480 TGAGCAGAAGAAGAGGCACAAT 59.961 45.455 0.00 0.00 0.00 2.71
1653 1937 0.527385 GCAAGCAGTTTGTTTCGGCA 60.527 50.000 0.00 0.00 39.08 5.69
1710 1994 5.220548 CCACGAGAAAGCATTGATAGTGAAG 60.221 44.000 0.00 0.00 0.00 3.02
1713 1997 5.502058 CGAGAAAGCATTGATAGTGAAGCTG 60.502 44.000 0.00 0.00 31.88 4.24
1769 2053 6.509418 TTGATGCATAGTACTTGGTTTTCC 57.491 37.500 0.00 0.00 41.14 3.13
1773 2057 4.010349 GCATAGTACTTGGTTTTCCTGCT 58.990 43.478 0.00 0.00 41.38 4.24
1930 2214 8.492748 GTGAATTTCGTACATTGTCAAGTTCTA 58.507 33.333 0.00 0.00 0.00 2.10
1931 2215 9.214957 TGAATTTCGTACATTGTCAAGTTCTAT 57.785 29.630 0.00 0.00 0.00 1.98
2066 2352 7.888250 AGGAAGAAACTCAAGTGAGATTTTT 57.112 32.000 15.15 10.44 44.74 1.94
2095 2388 5.181245 CCGCTGAGTTTTCCTTTCTATTTCA 59.819 40.000 0.00 0.00 0.00 2.69
2170 2463 5.927954 ATTATTTGCTTTGCTTTGTGTGG 57.072 34.783 0.00 0.00 0.00 4.17
2300 2593 5.165961 TGTCTAGCTATTCTTGTTGGCTT 57.834 39.130 0.00 0.00 34.88 4.35
2420 2724 1.769733 CATTGTGCCGTCCTGTTTTG 58.230 50.000 0.00 0.00 0.00 2.44
2423 2727 1.299089 GTGCCGTCCTGTTTTGCAC 60.299 57.895 0.00 0.00 44.53 4.57
2424 2728 1.750780 TGCCGTCCTGTTTTGCACA 60.751 52.632 0.00 0.00 0.00 4.57
2425 2729 1.106351 TGCCGTCCTGTTTTGCACAT 61.106 50.000 0.00 0.00 33.76 3.21
2426 2730 0.031994 GCCGTCCTGTTTTGCACATT 59.968 50.000 0.00 0.00 33.76 2.71
2427 2731 1.769733 CCGTCCTGTTTTGCACATTG 58.230 50.000 0.00 0.00 33.76 2.82
2428 2732 1.066908 CCGTCCTGTTTTGCACATTGT 59.933 47.619 0.00 0.00 33.76 2.71
2429 2733 2.118683 CGTCCTGTTTTGCACATTGTG 58.881 47.619 12.54 12.54 33.76 3.33
2430 2734 2.479389 CGTCCTGTTTTGCACATTGTGT 60.479 45.455 17.64 0.00 35.75 3.72
2431 2735 3.520569 GTCCTGTTTTGCACATTGTGTT 58.479 40.909 17.64 0.00 35.75 3.32
2432 2736 3.932089 GTCCTGTTTTGCACATTGTGTTT 59.068 39.130 17.64 0.00 35.75 2.83
2433 2737 4.032786 GTCCTGTTTTGCACATTGTGTTTC 59.967 41.667 17.64 2.63 35.75 2.78
2434 2738 3.931468 CCTGTTTTGCACATTGTGTTTCA 59.069 39.130 17.64 5.21 35.75 2.69
2435 2739 4.391216 CCTGTTTTGCACATTGTGTTTCAA 59.609 37.500 17.64 10.67 40.53 2.69
2438 2742 6.906659 TGTTTTGCACATTGTGTTTCAAAAT 58.093 28.000 23.98 0.00 39.79 1.82
2462 2766 4.178540 CAATTCATGCCTGTCATTTGTCC 58.821 43.478 0.00 0.00 31.79 4.02
2474 2778 7.492344 GCCTGTCATTTGTCCAAAATAATAAGG 59.508 37.037 0.00 2.07 33.56 2.69
2475 2779 7.981225 CCTGTCATTTGTCCAAAATAATAAGGG 59.019 37.037 0.00 0.00 33.56 3.95
2477 2781 9.535170 TGTCATTTGTCCAAAATAATAAGGGTA 57.465 29.630 0.00 0.00 33.56 3.69
2524 2828 2.289010 GGTCCTTTGCATGTTTGAAGGG 60.289 50.000 11.72 0.00 39.27 3.95
2530 2834 4.454728 TTGCATGTTTGAAGGGCTTATC 57.545 40.909 0.00 0.00 0.00 1.75
2531 2835 3.429492 TGCATGTTTGAAGGGCTTATCA 58.571 40.909 0.00 0.00 0.00 2.15
2537 2841 4.018506 TGTTTGAAGGGCTTATCATCCTCA 60.019 41.667 0.00 0.00 0.00 3.86
2543 2847 3.269381 AGGGCTTATCATCCTCACCAAAA 59.731 43.478 0.00 0.00 0.00 2.44
2605 2909 6.954616 TGCTTTTTCATTATGCACATTGAG 57.045 33.333 0.00 0.00 0.00 3.02
2751 3055 5.068987 TGGGAAATCTGCATTTATTAGTGCC 59.931 40.000 0.00 0.00 40.56 5.01
2776 3080 5.681639 TGCTAAGTAGGCCCTTAAATTCTC 58.318 41.667 0.00 0.00 0.00 2.87
2799 3103 6.184789 TCCTACCACCCTTTTTGTGATTATC 58.815 40.000 0.00 0.00 35.74 1.75
2894 3201 3.200593 GATCCAGTGGCAGCTGCG 61.201 66.667 31.19 17.72 43.26 5.18
2998 3305 5.641155 AGGGGTATGCTTCTACTTGTTTTT 58.359 37.500 0.00 0.00 0.00 1.94
3039 3346 6.765403 TGCTACTTTACATGTGAACCTAGTT 58.235 36.000 9.11 0.00 0.00 2.24
3048 3355 9.599866 TTACATGTGAACCTAGTTTATCATCAG 57.400 33.333 9.11 0.00 0.00 2.90
3114 3421 1.672881 GCACCCTGCTTACATGCTAAG 59.327 52.381 0.00 1.81 40.96 2.18
3135 3442 2.159462 GCAAAATGCTGCTCACCTAGAC 60.159 50.000 0.00 0.00 40.96 2.59
3167 3474 9.871238 GATAATTAGATGCCTTAAATCTCCGTA 57.129 33.333 0.00 0.00 35.92 4.02
3235 3564 6.260050 ACACGGATAAGTGCCTATATTTTGTG 59.740 38.462 0.00 0.00 45.45 3.33
3381 3711 0.040958 CTCTTGCACCACAAAGTCGC 60.041 55.000 0.00 0.00 37.96 5.19
3414 3744 5.989777 GCGATGTTTTCCTGTATGTATACCT 59.010 40.000 0.00 0.00 32.33 3.08
3452 3782 8.243961 TCCATGTTACTTTCTCAAAATTTCCA 57.756 30.769 0.00 0.00 0.00 3.53
3473 3803 7.303182 TCCACACTAATCTCTTTCTTCAGAA 57.697 36.000 0.00 0.00 0.00 3.02
3594 3924 8.515414 ACCTAAATGCTCTCAAAATTTCAGTAC 58.485 33.333 0.00 0.00 0.00 2.73
3596 3926 9.552114 CTAAATGCTCTCAAAATTTCAGTACTG 57.448 33.333 17.17 17.17 0.00 2.74
3617 3948 6.909909 ACTGATATTTTCCCGTCTTTTCAAC 58.090 36.000 0.00 0.00 0.00 3.18
3621 3952 1.210870 TTCCCGTCTTTTCAACGTCG 58.789 50.000 0.00 0.00 38.44 5.12
3653 3985 4.667519 AGTAGCCACTAAAGGATAACCG 57.332 45.455 0.00 0.00 35.58 4.44
3654 3986 3.387050 AGTAGCCACTAAAGGATAACCGG 59.613 47.826 0.00 0.00 35.58 5.28
3660 3992 5.591472 GCCACTAAAGGATAACCGGTAAATT 59.409 40.000 8.00 0.00 41.83 1.82
3853 4185 3.618150 ACAAAACTTCATTGCACTTGTGC 59.382 39.130 17.73 17.73 0.00 4.57
3861 4193 1.661480 TGCACTTGTGCAATGGAGC 59.339 52.632 23.78 0.00 42.40 4.70
3927 4260 1.863454 CGCATGTAACCTCATCTGCTC 59.137 52.381 0.00 0.00 0.00 4.26
3943 4276 3.004734 TCTGCTCAAAACTAGCTTTTGGC 59.995 43.478 20.57 20.67 46.17 4.52
3946 4279 1.000717 TCAAAACTAGCTTTTGGCGCC 60.001 47.619 22.73 22.73 46.17 6.53
3959 4292 3.430862 GCGCCGTGCCATCTTTGA 61.431 61.111 0.00 0.00 37.76 2.69
3990 4323 3.496870 GCGGAGGTATTTTGGATGAGGAT 60.497 47.826 0.00 0.00 0.00 3.24
4018 4351 4.560819 TGTGTGCTTTCATTTCGAACAAAC 59.439 37.500 0.00 0.00 31.73 2.93
4020 4353 4.797868 TGTGCTTTCATTTCGAACAAACTG 59.202 37.500 0.00 0.00 31.73 3.16
4021 4354 5.034152 GTGCTTTCATTTCGAACAAACTGA 58.966 37.500 0.00 0.00 31.73 3.41
4023 4356 6.198966 GTGCTTTCATTTCGAACAAACTGAAT 59.801 34.615 0.00 0.00 31.73 2.57
4039 4373 5.223449 ACTGAATCCGTTGTCCTTTTCTA 57.777 39.130 0.00 0.00 0.00 2.10
4047 4381 5.699458 TCCGTTGTCCTTTTCTATTCACTTC 59.301 40.000 0.00 0.00 0.00 3.01
4068 4402 3.053544 TCCCAGAGAGAAGTCGGAGTTAT 60.054 47.826 0.00 0.00 0.00 1.89
4069 4403 3.067461 CCCAGAGAGAAGTCGGAGTTATG 59.933 52.174 0.00 0.00 0.00 1.90
4114 4448 0.326264 GAGCTGAAGGATGGTGTGGT 59.674 55.000 0.00 0.00 0.00 4.16
4129 4463 2.342648 GGTCTTCAGGGCGTTCGT 59.657 61.111 0.00 0.00 0.00 3.85
4211 4545 0.788391 GCTTTGCAGCAGTCATTTGC 59.212 50.000 0.00 0.00 46.49 3.68
4246 4582 5.473504 CAGAGTTACTGCTTTGGTATTTGGT 59.526 40.000 0.00 0.00 39.86 3.67
4248 4584 7.174253 CAGAGTTACTGCTTTGGTATTTGGTAA 59.826 37.037 0.00 0.00 39.86 2.85
4249 4585 7.888546 AGAGTTACTGCTTTGGTATTTGGTAAT 59.111 33.333 0.00 0.00 0.00 1.89
4469 4806 0.879765 GTCGAGGAAGAAGACGGTGA 59.120 55.000 0.00 0.00 0.00 4.02
4512 4849 1.960689 GTGCATGTACCCAAACCAGTT 59.039 47.619 1.96 0.00 0.00 3.16
4514 4851 1.336795 GCATGTACCCAAACCAGTTGC 60.337 52.381 0.00 0.00 35.74 4.17
4617 4954 1.968540 GCTGAGACCCAAGTGGCAC 60.969 63.158 10.29 10.29 37.83 5.01
4941 5288 7.671495 ACATGCCAATTTTGAAGGAATTAAC 57.329 32.000 0.00 0.00 0.00 2.01
5047 5433 9.764870 CCATATTTGATCAATTTATACAGCTCG 57.235 33.333 9.40 0.00 0.00 5.03
5149 5689 0.101040 CAATAGCGCCAACCACCATG 59.899 55.000 2.29 0.00 0.00 3.66
5188 5728 2.579201 CCGCCGATGACCAAGACT 59.421 61.111 0.00 0.00 0.00 3.24
5242 5782 4.037446 TGCCACTATTGTGAAAAGTTGGAC 59.963 41.667 8.98 0.00 46.55 4.02
5272 5812 6.646240 GCAATTCTTAAGAGGCATCACAAAAA 59.354 34.615 16.39 0.00 0.00 1.94
5326 5866 9.173939 GATTCTTAACTTGTGCACATAATATGC 57.826 33.333 22.39 3.73 43.68 3.14
5327 5867 7.864108 TCTTAACTTGTGCACATAATATGCT 57.136 32.000 22.39 2.41 43.77 3.79
5334 5874 5.679601 TGTGCACATAATATGCTTGGACTA 58.320 37.500 17.42 0.00 43.77 2.59
5361 5902 2.556782 CCTAACCAGGGTCCCCTTTTTC 60.557 54.545 3.51 0.00 45.70 2.29
5382 5923 8.943909 TTTTCGTATAAATTTCTCCTCTCCTC 57.056 34.615 0.00 0.00 0.00 3.71
5389 5930 5.529581 AATTTCTCCTCTCCTCGAGAATC 57.470 43.478 15.71 0.00 42.96 2.52
5416 5962 0.650512 CTTGGCCTATGTTACGTGCG 59.349 55.000 3.32 0.00 0.00 5.34
5427 5973 3.968837 TACGTGCGACCTCCCCCAT 62.969 63.158 0.00 0.00 0.00 4.00
5443 5989 2.365635 ATCCCTCACCCACCCTCG 60.366 66.667 0.00 0.00 0.00 4.63
5495 6042 1.005690 GACCCCCTACCTCCCCATT 59.994 63.158 0.00 0.00 0.00 3.16
5497 6044 2.768022 CCCCCTACCTCCCCATTGC 61.768 68.421 0.00 0.00 0.00 3.56
5506 6053 1.228706 TCCCCATTGCCGCTCAAAA 60.229 52.632 0.00 0.00 38.34 2.44
5519 6066 8.840833 TTGCCGCTCAAAACATTATATATAGA 57.159 30.769 0.00 0.00 0.00 1.98
5520 6067 9.448438 TTGCCGCTCAAAACATTATATATAGAT 57.552 29.630 0.00 0.00 0.00 1.98
5535 6082 9.857656 TTATATATAGATACCTTACCTCACGGG 57.142 37.037 0.00 0.00 41.89 5.28
5538 6085 1.052694 ATACCTTACCTCACGGGCCC 61.053 60.000 13.57 13.57 39.10 5.80
5542 6089 2.608970 CTTACCTCACGGGCCCCATG 62.609 65.000 18.66 15.76 39.10 3.66
5546 6093 3.012119 TCACGGGCCCCATGCTAA 61.012 61.111 18.66 0.00 40.92 3.09
5547 6094 2.828549 CACGGGCCCCATGCTAAC 60.829 66.667 18.66 0.00 40.92 2.34
5550 6097 2.828549 GGGCCCCATGCTAACACG 60.829 66.667 12.23 0.00 40.92 4.49
5560 6107 1.006086 TGCTAACACGCATGAATCCG 58.994 50.000 0.00 0.00 34.44 4.18
5562 6109 0.304705 CTAACACGCATGAATCCGCC 59.695 55.000 0.00 0.00 0.00 6.13
5569 6116 1.102809 GCATGAATCCGCCATCACCA 61.103 55.000 0.00 0.00 0.00 4.17
5572 6119 1.077787 GAATCCGCCATCACCACCA 60.078 57.895 0.00 0.00 0.00 4.17
5573 6120 0.679640 GAATCCGCCATCACCACCAA 60.680 55.000 0.00 0.00 0.00 3.67
5580 6127 1.606313 CATCACCACCAACCCCCAC 60.606 63.158 0.00 0.00 0.00 4.61
5584 6131 3.182263 CCACCAACCCCCACCTCA 61.182 66.667 0.00 0.00 0.00 3.86
5587 6134 0.701731 CACCAACCCCCACCTCATAA 59.298 55.000 0.00 0.00 0.00 1.90
5596 6143 3.244911 CCCCCACCTCATAACCATATCAC 60.245 52.174 0.00 0.00 0.00 3.06
5612 6159 5.071519 CCATATCACTCCACTCATCCTTCTT 59.928 44.000 0.00 0.00 0.00 2.52
5621 6168 0.546747 TCATCCTTCTTCGGGGTGGT 60.547 55.000 0.00 0.00 35.77 4.16
5622 6169 0.392998 CATCCTTCTTCGGGGTGGTG 60.393 60.000 0.00 0.00 31.72 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 1.168714 GTGGCTGAAGATTGTGGTCC 58.831 55.000 0.00 0.00 0.00 4.46
115 117 2.376518 TGGCTTTCTCTTGGATCTTGGT 59.623 45.455 0.00 0.00 0.00 3.67
201 204 0.179004 TTTCAGCCGACAACCCACAT 60.179 50.000 0.00 0.00 0.00 3.21
218 221 3.567164 CCAAGAGAAGTGCAGATGTGTTT 59.433 43.478 0.00 0.00 0.00 2.83
220 223 2.369860 TCCAAGAGAAGTGCAGATGTGT 59.630 45.455 0.00 0.00 0.00 3.72
228 231 1.442769 TCGCAATCCAAGAGAAGTGC 58.557 50.000 0.00 0.00 36.63 4.40
243 246 3.796717 CGCATGAGTACTTTAGAATCGCA 59.203 43.478 0.00 0.00 0.00 5.10
275 278 1.056700 CCGGTTCTGGATCCCCTCAT 61.057 60.000 9.90 0.00 0.00 2.90
283 286 0.394352 GATGGTTGCCGGTTCTGGAT 60.394 55.000 1.90 0.00 0.00 3.41
431 434 0.790814 GTCCTGTTTCTTCGGCTTCG 59.209 55.000 0.00 0.00 0.00 3.79
554 558 5.333875 GCCGACGTCTTTGTTAAGAAAAGAT 60.334 40.000 14.70 2.85 43.52 2.40
558 562 3.001533 GTGCCGACGTCTTTGTTAAGAAA 59.998 43.478 14.70 0.00 41.86 2.52
562 566 1.219646 GGTGCCGACGTCTTTGTTAA 58.780 50.000 14.70 0.00 0.00 2.01
702 708 3.484547 CGTTTCCTACGCCGGCAC 61.485 66.667 28.98 14.19 44.26 5.01
710 716 2.733542 GCGAGGTAGTTCCGTTTCCTAC 60.734 54.545 0.00 0.00 41.99 3.18
711 717 1.474077 GCGAGGTAGTTCCGTTTCCTA 59.526 52.381 0.00 0.00 41.99 2.94
712 718 0.245813 GCGAGGTAGTTCCGTTTCCT 59.754 55.000 0.00 0.00 41.99 3.36
713 719 1.074872 CGCGAGGTAGTTCCGTTTCC 61.075 60.000 0.00 0.00 41.99 3.13
714 720 0.387750 ACGCGAGGTAGTTCCGTTTC 60.388 55.000 15.93 0.00 41.99 2.78
715 721 0.665369 CACGCGAGGTAGTTCCGTTT 60.665 55.000 15.93 0.00 41.99 3.60
716 722 1.080974 CACGCGAGGTAGTTCCGTT 60.081 57.895 15.93 0.00 41.99 4.44
717 723 2.192608 GACACGCGAGGTAGTTCCGT 62.193 60.000 15.93 0.00 41.99 4.69
718 724 1.513586 GACACGCGAGGTAGTTCCG 60.514 63.158 15.93 0.00 41.99 4.30
719 725 1.513586 CGACACGCGAGGTAGTTCC 60.514 63.158 15.93 0.00 44.57 3.62
720 726 2.150837 GCGACACGCGAGGTAGTTC 61.151 63.158 15.93 0.00 44.55 3.01
721 727 2.126580 GCGACACGCGAGGTAGTT 60.127 61.111 15.93 0.00 44.55 2.24
731 737 2.401592 CTCTCTCTCGGCGACACG 59.598 66.667 4.99 0.00 0.00 4.49
732 738 2.766400 CCCTCTCTCTCGGCGACAC 61.766 68.421 4.99 0.00 0.00 3.67
733 739 2.438614 CCCTCTCTCTCGGCGACA 60.439 66.667 4.99 0.00 0.00 4.35
734 740 3.213402 CCCCTCTCTCTCGGCGAC 61.213 72.222 4.99 0.00 0.00 5.19
735 741 4.507916 CCCCCTCTCTCTCGGCGA 62.508 72.222 10.14 10.14 0.00 5.54
738 744 2.364317 TTGCCCCCTCTCTCTCGG 60.364 66.667 0.00 0.00 0.00 4.63
739 745 3.087666 GCTTGCCCCCTCTCTCTCG 62.088 68.421 0.00 0.00 0.00 4.04
740 746 1.970352 CTGCTTGCCCCCTCTCTCTC 61.970 65.000 0.00 0.00 0.00 3.20
741 747 1.994507 CTGCTTGCCCCCTCTCTCT 60.995 63.158 0.00 0.00 0.00 3.10
742 748 1.557269 TTCTGCTTGCCCCCTCTCTC 61.557 60.000 0.00 0.00 0.00 3.20
743 749 1.539869 TTCTGCTTGCCCCCTCTCT 60.540 57.895 0.00 0.00 0.00 3.10
744 750 1.377856 GTTCTGCTTGCCCCCTCTC 60.378 63.158 0.00 0.00 0.00 3.20
745 751 1.849823 AGTTCTGCTTGCCCCCTCT 60.850 57.895 0.00 0.00 0.00 3.69
746 752 1.676967 CAGTTCTGCTTGCCCCCTC 60.677 63.158 0.00 0.00 0.00 4.30
747 753 2.437897 CAGTTCTGCTTGCCCCCT 59.562 61.111 0.00 0.00 0.00 4.79
748 754 3.376918 GCAGTTCTGCTTGCCCCC 61.377 66.667 16.29 0.00 0.00 5.40
749 755 2.282745 AGCAGTTCTGCTTGCCCC 60.283 61.111 19.80 0.00 43.52 5.80
750 756 2.684843 CGAGCAGTTCTGCTTGCCC 61.685 63.158 24.91 13.21 46.36 5.36
751 757 1.669115 TCGAGCAGTTCTGCTTGCC 60.669 57.895 27.68 15.95 46.36 4.52
752 758 1.224069 TGTCGAGCAGTTCTGCTTGC 61.224 55.000 27.68 23.19 46.36 4.01
753 759 1.220529 TTGTCGAGCAGTTCTGCTTG 58.779 50.000 26.98 26.98 46.36 4.01
754 760 2.072298 GATTGTCGAGCAGTTCTGCTT 58.928 47.619 24.91 10.75 46.36 3.91
756 762 0.723981 GGATTGTCGAGCAGTTCTGC 59.276 55.000 15.88 15.88 0.00 4.26
757 763 2.266554 GAGGATTGTCGAGCAGTTCTG 58.733 52.381 0.00 0.00 0.00 3.02
758 764 1.135257 CGAGGATTGTCGAGCAGTTCT 60.135 52.381 0.00 0.00 42.85 3.01
759 765 1.272781 CGAGGATTGTCGAGCAGTTC 58.727 55.000 0.00 0.00 42.85 3.01
760 766 0.108615 CCGAGGATTGTCGAGCAGTT 60.109 55.000 0.00 0.00 42.85 3.16
761 767 1.513158 CCGAGGATTGTCGAGCAGT 59.487 57.895 0.00 0.00 42.85 4.40
762 768 1.227089 CCCGAGGATTGTCGAGCAG 60.227 63.158 0.00 0.00 42.85 4.24
763 769 2.892640 CCCGAGGATTGTCGAGCA 59.107 61.111 0.00 0.00 42.85 4.26
764 770 2.586357 GCCCGAGGATTGTCGAGC 60.586 66.667 0.00 0.00 42.85 5.03
765 771 2.107141 GGCCCGAGGATTGTCGAG 59.893 66.667 0.00 0.00 42.85 4.04
766 772 3.833645 CGGCCCGAGGATTGTCGA 61.834 66.667 0.00 0.00 42.85 4.20
783 789 4.084888 CGAAAACGCTGGACCGGC 62.085 66.667 15.94 15.94 0.00 6.13
784 790 4.084888 GCGAAAACGCTGGACCGG 62.085 66.667 0.00 0.00 0.00 5.28
785 791 4.084888 GGCGAAAACGCTGGACCG 62.085 66.667 13.81 0.00 34.92 4.79
786 792 1.862602 AATGGCGAAAACGCTGGACC 61.863 55.000 13.81 0.00 34.92 4.46
787 793 0.039527 AAATGGCGAAAACGCTGGAC 60.040 50.000 13.81 0.00 34.92 4.02
788 794 0.239879 GAAATGGCGAAAACGCTGGA 59.760 50.000 13.81 0.22 34.92 3.86
789 795 1.065031 CGAAATGGCGAAAACGCTGG 61.065 55.000 13.81 0.00 34.92 4.85
790 796 1.065031 CCGAAATGGCGAAAACGCTG 61.065 55.000 13.81 0.00 34.92 5.18
791 797 1.209127 CCGAAATGGCGAAAACGCT 59.791 52.632 13.81 0.00 34.92 5.07
792 798 3.748856 CCGAAATGGCGAAAACGC 58.251 55.556 6.05 6.05 0.00 4.84
810 816 2.689983 GCCTGATAAACATGTTCTGGGG 59.310 50.000 12.39 11.48 0.00 4.96
811 817 2.689983 GGCCTGATAAACATGTTCTGGG 59.310 50.000 12.39 10.82 0.00 4.45
812 818 2.355756 CGGCCTGATAAACATGTTCTGG 59.644 50.000 12.39 13.69 0.00 3.86
820 826 3.623960 CGGTATTTTCGGCCTGATAAACA 59.376 43.478 0.00 0.00 0.00 2.83
853 859 0.105039 CGGCCCATTGGAGAGTACTC 59.895 60.000 15.41 15.41 41.94 2.59
857 863 0.107017 CATTCGGCCCATTGGAGAGT 60.107 55.000 3.62 0.00 0.00 3.24
985 995 2.176273 CCATTGGAGCGGAAGAGCG 61.176 63.158 0.00 0.00 43.00 5.03
986 996 2.476320 GCCATTGGAGCGGAAGAGC 61.476 63.158 6.95 0.00 37.41 4.09
987 997 3.819188 GCCATTGGAGCGGAAGAG 58.181 61.111 6.95 0.00 0.00 2.85
1072 1103 2.763215 GGATGGGTGGTGCTTGGA 59.237 61.111 0.00 0.00 0.00 3.53
1440 1500 2.887568 GACTGAGCGCGTGGATGG 60.888 66.667 8.43 0.00 0.00 3.51
1478 1546 3.379650 CCGATAAGCCGGTGAACAT 57.620 52.632 1.90 0.00 44.23 2.71
1523 1591 2.039480 TGATTGTGCCTCTTCTTCTGCT 59.961 45.455 0.00 0.00 0.00 4.24
1542 1826 3.120477 CGCATAGCACGGTTTTTAGTTGA 60.120 43.478 0.00 0.00 0.00 3.18
1653 1937 2.765699 CAGCTTCTCCCTTAGCTCTTCT 59.234 50.000 0.00 0.00 45.54 2.85
1713 1997 1.073284 TGAGAGCCAGGGTTGTTTACC 59.927 52.381 0.00 0.00 46.99 2.85
1930 2214 5.667539 ATCTGACAGCAGTAACAGTACAT 57.332 39.130 0.00 0.00 42.84 2.29
1931 2215 6.208797 AGTTATCTGACAGCAGTAACAGTACA 59.791 38.462 18.77 0.00 42.84 2.90
2066 2352 2.358322 AGGAAAACTCAGCGGGAAAA 57.642 45.000 0.00 0.00 0.00 2.29
2069 2355 1.420138 AGAAAGGAAAACTCAGCGGGA 59.580 47.619 0.00 0.00 0.00 5.14
2143 2436 9.881529 CACACAAAGCAAAGCAAATAATAAATT 57.118 25.926 0.00 0.00 0.00 1.82
2144 2437 8.505625 CCACACAAAGCAAAGCAAATAATAAAT 58.494 29.630 0.00 0.00 0.00 1.40
2145 2438 7.041508 CCCACACAAAGCAAAGCAAATAATAAA 60.042 33.333 0.00 0.00 0.00 1.40
2146 2439 6.426328 CCCACACAAAGCAAAGCAAATAATAA 59.574 34.615 0.00 0.00 0.00 1.40
2147 2440 5.931146 CCCACACAAAGCAAAGCAAATAATA 59.069 36.000 0.00 0.00 0.00 0.98
2148 2441 4.756135 CCCACACAAAGCAAAGCAAATAAT 59.244 37.500 0.00 0.00 0.00 1.28
2149 2442 4.125703 CCCACACAAAGCAAAGCAAATAA 58.874 39.130 0.00 0.00 0.00 1.40
2150 2443 3.133721 ACCCACACAAAGCAAAGCAAATA 59.866 39.130 0.00 0.00 0.00 1.40
2151 2444 2.093021 ACCCACACAAAGCAAAGCAAAT 60.093 40.909 0.00 0.00 0.00 2.32
2152 2445 1.277557 ACCCACACAAAGCAAAGCAAA 59.722 42.857 0.00 0.00 0.00 3.68
2153 2446 0.901124 ACCCACACAAAGCAAAGCAA 59.099 45.000 0.00 0.00 0.00 3.91
2154 2447 1.680735 CTACCCACACAAAGCAAAGCA 59.319 47.619 0.00 0.00 0.00 3.91
2155 2448 1.681264 ACTACCCACACAAAGCAAAGC 59.319 47.619 0.00 0.00 0.00 3.51
2156 2449 2.687935 ACACTACCCACACAAAGCAAAG 59.312 45.455 0.00 0.00 0.00 2.77
2157 2450 2.685897 GACACTACCCACACAAAGCAAA 59.314 45.455 0.00 0.00 0.00 3.68
2170 2463 1.180029 TGGACGCTAAGGACACTACC 58.820 55.000 0.00 0.00 0.00 3.18
2300 2593 4.216902 CAGGATTGTGCATGAGAAGTCAAA 59.783 41.667 0.00 0.00 35.88 2.69
2386 2679 1.066430 ACAATGCCTCGGTCGTAATGT 60.066 47.619 0.00 0.00 0.00 2.71
2387 2680 1.327460 CACAATGCCTCGGTCGTAATG 59.673 52.381 0.00 0.00 0.00 1.90
2409 2713 2.118683 CACAATGTGCAAAACAGGACG 58.881 47.619 0.00 0.00 43.64 4.79
2420 2724 4.533225 TGCATTTTGAAACACAATGTGC 57.467 36.364 14.01 0.00 43.23 4.57
2423 2727 8.210026 CATGAATTGCATTTTGAAACACAATG 57.790 30.769 0.00 0.00 35.09 2.82
2474 2778 7.234355 ACATGATTTTGGATCCTCCTTATACC 58.766 38.462 14.23 0.00 37.46 2.73
2475 2779 7.939039 TGACATGATTTTGGATCCTCCTTATAC 59.061 37.037 14.23 0.00 37.46 1.47
2477 2781 6.914665 TGACATGATTTTGGATCCTCCTTAT 58.085 36.000 14.23 0.00 37.46 1.73
2484 2788 4.038402 GGACCATGACATGATTTTGGATCC 59.962 45.833 17.24 4.20 0.00 3.36
2554 2858 9.726652 ATGAAGTAGATATGACCATCATCCTAT 57.273 33.333 0.00 0.00 38.26 2.57
2559 2863 8.162085 AGCAAATGAAGTAGATATGACCATCAT 58.838 33.333 0.00 0.00 40.72 2.45
2619 2923 9.569167 CTCGTACTGTTCAGATTGTCTTTATTA 57.431 33.333 6.83 0.00 0.00 0.98
2633 2937 3.257375 AGGCATGTTACTCGTACTGTTCA 59.743 43.478 0.00 0.00 0.00 3.18
2751 3055 6.064717 AGAATTTAAGGGCCTACTTAGCATG 58.935 40.000 6.41 0.00 34.67 4.06
2776 3080 6.095440 CAGATAATCACAAAAAGGGTGGTAGG 59.905 42.308 0.00 0.00 36.90 3.18
3048 3355 6.276091 TCTGACAGCTACATCACATCAATAC 58.724 40.000 0.00 0.00 0.00 1.89
3114 3421 2.086869 TCTAGGTGAGCAGCATTTTGC 58.913 47.619 0.00 0.00 45.46 3.68
3201 3530 4.508124 GGCACTTATCCGTGTCATCTAAAG 59.492 45.833 0.00 0.00 39.26 1.85
3206 3535 2.604046 AGGCACTTATCCGTGTCATC 57.396 50.000 0.00 0.00 41.80 2.92
3235 3564 0.759346 AACTGGACACCACAGGAGAC 59.241 55.000 0.00 0.00 40.23 3.36
3381 3711 1.749063 GGAAAACATCGCCCCTTTAGG 59.251 52.381 0.00 0.00 0.00 2.69
3414 3744 8.786826 AAAGTAACATGGATTTTACAGATCGA 57.213 30.769 0.00 0.00 31.66 3.59
3594 3924 6.021596 CGTTGAAAAGACGGGAAAATATCAG 58.978 40.000 0.00 0.00 36.90 2.90
3596 3926 5.934921 ACGTTGAAAAGACGGGAAAATATC 58.065 37.500 1.64 0.00 44.34 1.63
3607 3937 3.615763 CGAGCGACGTTGAAAAGAC 57.384 52.632 7.08 0.00 37.22 3.01
3617 3948 7.919639 AGTGGCTACTAATTTACGAGCGACG 62.920 48.000 0.00 4.95 43.88 5.12
3621 3952 6.200475 CCTTTAGTGGCTACTAATTTACGAGC 59.800 42.308 21.60 0.00 45.93 5.03
3644 3976 3.551846 CTGGCAATTTACCGGTTATCCT 58.448 45.455 15.04 0.00 0.00 3.24
3645 3977 2.621526 CCTGGCAATTTACCGGTTATCC 59.378 50.000 15.04 6.73 0.00 2.59
3653 3985 1.751351 GGAAGAGCCTGGCAATTTACC 59.249 52.381 22.65 12.03 0.00 2.85
3654 3986 2.164422 GTGGAAGAGCCTGGCAATTTAC 59.836 50.000 22.65 12.68 37.63 2.01
3660 3992 4.704833 GCGTGGAAGAGCCTGGCA 62.705 66.667 22.65 0.00 36.14 4.92
3847 4179 4.978083 AGAAATAGCTCCATTGCACAAG 57.022 40.909 0.00 0.00 34.99 3.16
3943 4276 0.171007 AAATCAAAGATGGCACGGCG 59.829 50.000 4.80 4.80 0.00 6.46
3946 4279 2.256174 CAGCAAATCAAAGATGGCACG 58.744 47.619 0.00 0.00 0.00 5.34
3959 4292 0.258774 AATACCTCCGCCCAGCAAAT 59.741 50.000 0.00 0.00 0.00 2.32
3990 4323 6.975197 TGTTCGAAATGAAAGCACACATTAAA 59.025 30.769 0.00 0.00 38.60 1.52
4018 4351 6.371548 TGAATAGAAAAGGACAACGGATTCAG 59.628 38.462 0.00 0.00 0.00 3.02
4020 4353 6.371825 AGTGAATAGAAAAGGACAACGGATTC 59.628 38.462 0.00 0.00 0.00 2.52
4021 4354 6.238648 AGTGAATAGAAAAGGACAACGGATT 58.761 36.000 0.00 0.00 0.00 3.01
4023 4356 5.223449 AGTGAATAGAAAAGGACAACGGA 57.777 39.130 0.00 0.00 0.00 4.69
4047 4381 1.551452 AACTCCGACTTCTCTCTGGG 58.449 55.000 0.00 0.00 0.00 4.45
4068 4402 0.991355 ACCAGTTGGGGGAGTCAACA 60.991 55.000 2.79 0.00 44.84 3.33
4069 4403 0.250770 GACCAGTTGGGGGAGTCAAC 60.251 60.000 2.79 0.00 43.31 3.18
4114 4448 0.320374 ATTCACGAACGCCCTGAAGA 59.680 50.000 0.00 0.00 0.00 2.87
4129 4463 7.772292 AGCTCTTCATACTTTATCTGCAATTCA 59.228 33.333 0.00 0.00 0.00 2.57
4225 4559 9.695155 ATATTACCAAATACCAAAGCAGTAACT 57.305 29.630 0.00 0.00 30.42 2.24
4248 4584 9.224267 GTTGCCTGTCATGAAGATAACATATAT 57.776 33.333 0.00 0.00 0.00 0.86
4249 4585 7.661437 GGTTGCCTGTCATGAAGATAACATATA 59.339 37.037 0.00 0.00 0.00 0.86
4334 4671 5.779771 AGGAAAGAAGGTGCCAATAAATCAA 59.220 36.000 0.00 0.00 0.00 2.57
4374 4711 2.983136 GAGTCCAGATATCGCAATGTCG 59.017 50.000 0.00 0.00 0.00 4.35
4469 4806 1.890876 TAAATGCAACTCGCCACTGT 58.109 45.000 0.00 0.00 41.33 3.55
4494 4831 1.336795 GCAACTGGTTTGGGTACATGC 60.337 52.381 0.00 0.00 35.51 4.06
4617 4954 1.709147 GGCAACCGCAGCATCAGTAG 61.709 60.000 0.00 0.00 41.24 2.57
4833 5179 0.865111 TGCAAGACGACGGTGAAATG 59.135 50.000 0.00 0.00 0.00 2.32
4941 5288 7.769272 TGTTTTCTTCTTGGCTGTATTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
4998 5380 0.248866 GGGTGAAGTGGTTTGTTGCG 60.249 55.000 0.00 0.00 0.00 4.85
5047 5433 8.409358 AGGGATCTGGTTGCAATTTATAATAC 57.591 34.615 0.59 0.00 0.00 1.89
5099 5586 0.101759 GCAGTATCTTCCGCCACGTA 59.898 55.000 0.00 0.00 0.00 3.57
5205 5745 3.189568 TGGCAACACTCACTTTGCT 57.810 47.368 6.29 0.00 46.11 3.91
5242 5782 4.707030 TGCCTCTTAAGAATTGCATGTG 57.293 40.909 16.00 0.00 0.00 3.21
5286 5826 2.362760 AATCCATGGCCGCTTGCA 60.363 55.556 6.96 0.00 43.89 4.08
5294 5834 3.193267 TGCACAAGTTAAGAATCCATGGC 59.807 43.478 6.96 0.00 0.00 4.40
5326 5866 4.384208 CCTGGTTAGGTCCAATAGTCCAAG 60.384 50.000 0.00 0.00 39.39 3.61
5327 5867 3.521937 CCTGGTTAGGTCCAATAGTCCAA 59.478 47.826 0.00 0.00 39.39 3.53
5361 5902 6.205076 TCTCGAGGAGAGGAGAAATTTATACG 59.795 42.308 13.56 0.00 46.82 3.06
5382 5923 0.933097 CCAAGGTGATGCGATTCTCG 59.067 55.000 0.00 0.00 43.89 4.04
5389 5930 0.464373 ACATAGGCCAAGGTGATGCG 60.464 55.000 5.01 0.00 0.00 4.73
5393 5934 1.903860 ACGTAACATAGGCCAAGGTGA 59.096 47.619 5.01 0.00 0.00 4.02
5394 5935 2.006888 CACGTAACATAGGCCAAGGTG 58.993 52.381 5.01 0.00 0.00 4.00
5395 5936 1.677820 GCACGTAACATAGGCCAAGGT 60.678 52.381 5.01 0.00 0.00 3.50
5416 5962 2.073101 GTGAGGGATGGGGGAGGTC 61.073 68.421 0.00 0.00 0.00 3.85
5427 5973 4.715130 CCGAGGGTGGGTGAGGGA 62.715 72.222 0.00 0.00 0.00 4.20
5430 5976 2.214216 TTGACCGAGGGTGGGTGAG 61.214 63.158 0.00 0.00 38.07 3.51
5443 5989 2.046217 GGCGGGAAGAGGTTGACC 60.046 66.667 0.00 0.00 0.00 4.02
5528 6075 3.042733 TTAGCATGGGGCCCGTGAG 62.043 63.158 42.28 22.04 42.73 3.51
5531 6078 3.334891 TGTTAGCATGGGGCCCGT 61.335 61.111 19.83 16.52 46.50 5.28
5535 6082 2.749839 TGCGTGTTAGCATGGGGC 60.750 61.111 0.68 0.00 42.92 5.80
5542 6089 0.316196 GCGGATTCATGCGTGTTAGC 60.316 55.000 5.68 2.71 43.82 3.09
5546 6093 1.439353 GATGGCGGATTCATGCGTGT 61.439 55.000 5.68 0.00 43.82 4.49
5547 6094 1.280746 GATGGCGGATTCATGCGTG 59.719 57.895 0.00 0.00 43.82 5.34
5550 6097 1.102809 TGGTGATGGCGGATTCATGC 61.103 55.000 0.00 0.00 0.00 4.06
5560 6107 2.679996 GGGGTTGGTGGTGATGGC 60.680 66.667 0.00 0.00 0.00 4.40
5562 6109 1.606313 GTGGGGGTTGGTGGTGATG 60.606 63.158 0.00 0.00 0.00 3.07
5569 6116 0.702316 GTTATGAGGTGGGGGTTGGT 59.298 55.000 0.00 0.00 0.00 3.67
5572 6119 1.693799 ATGGTTATGAGGTGGGGGTT 58.306 50.000 0.00 0.00 0.00 4.11
5573 6120 2.598288 TATGGTTATGAGGTGGGGGT 57.402 50.000 0.00 0.00 0.00 4.95
5580 6127 5.305386 TGAGTGGAGTGATATGGTTATGAGG 59.695 44.000 0.00 0.00 0.00 3.86
5584 6131 6.087456 AGGATGAGTGGAGTGATATGGTTAT 58.913 40.000 0.00 0.00 0.00 1.89
5587 6134 3.933886 AGGATGAGTGGAGTGATATGGT 58.066 45.455 0.00 0.00 0.00 3.55
5596 6143 1.137872 CCCGAAGAAGGATGAGTGGAG 59.862 57.143 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.