Multiple sequence alignment - TraesCS6D01G194700

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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 TraesCS6D01G194700 chr6D 100.000 5600 0 0 1 5600 270146462 270140863 0.000000e+00 10342.0
1 TraesCS6D01G194700 chr6A 95.027 4142 163 19 810 4931 387224450 387228568 0.000000e+00 6468.0
2 TraesCS6D01G194700 chr6A 87.278 731 27 25 5 700 387223749 387224448 0.000000e+00 774.0
3 TraesCS6D01G194700 chr6A 82.616 627 44 25 4929 5537 387228600 387229179 1.400000e-135 494.0
4 TraesCS6D01G194700 chr6A 92.593 108 8 0 700 807 545831472 545831579 7.510000e-34 156.0
5 TraesCS6D01G194700 chr6B 93.564 3123 148 13 870 3964 422708531 422705434 0.000000e+00 4604.0
6 TraesCS6D01G194700 chr6B 93.395 1181 47 9 3961 5121 422705322 422704153 0.000000e+00 1720.0
7 TraesCS6D01G194700 chr6B 88.889 441 18 14 5117 5545 422703913 422703492 1.080000e-141 514.0
8 TraesCS6D01G194700 chr6B 88.194 288 22 9 107 388 422709092 422708811 3.230000e-87 333.0
9 TraesCS6D01G194700 chr6B 97.037 135 3 1 569 702 422708713 422708579 5.640000e-55 226.0
10 TraesCS6D01G194700 chr6B 85.417 96 4 2 458 553 422708794 422708709 2.150000e-14 91.6
11 TraesCS6D01G194700 chr6B 91.525 59 2 3 5543 5599 422693477 422693420 1.670000e-10 78.7
12 TraesCS6D01G194700 chr3D 95.413 109 5 0 699 807 326124510 326124618 2.070000e-39 174.0
13 TraesCS6D01G194700 chr3D 91.964 112 9 0 701 812 565536785 565536674 2.090000e-34 158.0
14 TraesCS6D01G194700 chr1D 93.103 116 8 0 696 811 237161025 237161140 2.680000e-38 171.0
15 TraesCS6D01G194700 chr7B 93.578 109 7 0 701 809 693255225 693255333 4.490000e-36 163.0
16 TraesCS6D01G194700 chr7D 93.519 108 7 0 700 807 13294332 13294225 1.610000e-35 161.0
17 TraesCS6D01G194700 chr2B 93.519 108 7 0 700 807 629126743 629126636 1.610000e-35 161.0
18 TraesCS6D01G194700 chr5B 91.304 115 9 1 698 811 134582450 134582564 7.510000e-34 156.0
19 TraesCS6D01G194700 chr5A 89.516 124 12 1 691 814 177605081 177605203 7.510000e-34 156.0
20 TraesCS6D01G194700 chr2A 94.667 75 3 1 2513 2586 19302023 19302097 1.270000e-21 115.0


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 TraesCS6D01G194700 chr6D 270140863 270146462 5599 True 10342.000000 10342 100.000000 1 5600 1 chr6D.!!$R1 5599
1 TraesCS6D01G194700 chr6A 387223749 387229179 5430 False 2578.666667 6468 88.307000 5 5537 3 chr6A.!!$F2 5532
2 TraesCS6D01G194700 chr6B 422703492 422709092 5600 True 1248.100000 4604 91.082667 107 5545 6 chr6B.!!$R2 5438

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
212 219 1.065551 GCGTTTCATTCATGGGGTAGC 59.934 52.381 0.0 0.0 0.00 3.58 F
1076 1116 0.757188 GAATGCGAGGAGGAGGAGGA 60.757 60.000 0.0 0.0 0.00 3.71 F
1830 1885 0.679505 TAGGCTATAACGCAGGGCAG 59.320 55.000 0.0 0.0 0.00 4.85 F
1902 1960 1.039856 AGGTTGCAGGCGAACATTTT 58.960 45.000 0.0 0.0 0.00 1.82 F
2579 2651 1.355381 TGAATGCAGTTCCAGGGACAT 59.645 47.619 0.0 0.0 35.91 3.06 F
3208 3280 1.453928 GGAGAAATGGAAGGGGGCG 60.454 63.158 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1255 0.025898 CGTCGTCGCTCAGTTCGATA 59.974 55.000 0.00 0.0 38.29 2.92 R
2684 2756 0.316204 GCATTTGCTGTGTGCTTCCT 59.684 50.000 0.00 0.0 43.37 3.36 R
3208 3280 0.523966 CCTCTCGACCACTCACAGTC 59.476 60.000 0.00 0.0 0.00 3.51 R
3562 3634 1.176527 CATCCAATGCTTTCCACGGT 58.823 50.000 0.00 0.0 0.00 4.83 R
4286 4482 1.076777 TGAGGGGCAGCTAAATGGC 60.077 57.895 0.00 0.0 44.61 4.40 R
5062 5310 0.036388 TCTGGGCCGAGACATGAAAC 60.036 55.000 14.28 0.0 0.00 2.78 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
42 43 6.566197 AAATCGAGCTCTTCACTTTTTCAT 57.434 33.333 12.85 0.00 0.00 2.57
45 46 3.126000 CGAGCTCTTCACTTTTTCATCCC 59.874 47.826 12.85 0.00 0.00 3.85
61 62 1.801242 TCCCGATCATCCTGGCTTTA 58.199 50.000 0.00 0.00 0.00 1.85
147 154 2.893682 GATTTGGCGGGGGACTCAGG 62.894 65.000 0.00 0.00 0.00 3.86
212 219 1.065551 GCGTTTCATTCATGGGGTAGC 59.934 52.381 0.00 0.00 0.00 3.58
258 265 1.351017 TCGAGTTCCTGGAGCCAAAAT 59.649 47.619 6.95 0.00 0.00 1.82
267 274 3.308402 CCTGGAGCCAAAATAAGGAGTGA 60.308 47.826 0.00 0.00 0.00 3.41
269 276 4.934356 TGGAGCCAAAATAAGGAGTGATT 58.066 39.130 0.00 0.00 0.00 2.57
270 277 5.332743 TGGAGCCAAAATAAGGAGTGATTT 58.667 37.500 0.00 0.00 0.00 2.17
278 302 6.394345 AAATAAGGAGTGATTTCTGGGAGT 57.606 37.500 0.00 0.00 0.00 3.85
314 339 2.825861 TCGGTCTAGTGTTGGGTTTC 57.174 50.000 0.00 0.00 0.00 2.78
317 342 2.806244 CGGTCTAGTGTTGGGTTTCTTG 59.194 50.000 0.00 0.00 0.00 3.02
398 433 1.979155 TCTCTGTCTCGCACCCAGG 60.979 63.158 0.00 0.00 0.00 4.45
446 481 3.451894 GCAAATGCCCCAGTCCCG 61.452 66.667 0.00 0.00 34.31 5.14
448 483 1.750399 CAAATGCCCCAGTCCCGAG 60.750 63.158 0.00 0.00 0.00 4.63
449 484 1.923395 AAATGCCCCAGTCCCGAGA 60.923 57.895 0.00 0.00 0.00 4.04
450 485 2.198304 AAATGCCCCAGTCCCGAGAC 62.198 60.000 0.00 0.00 43.89 3.36
451 486 3.924013 ATGCCCCAGTCCCGAGACA 62.924 63.158 0.00 0.00 46.15 3.41
453 488 3.077556 CCCCAGTCCCGAGACAGG 61.078 72.222 1.17 1.17 46.58 4.00
454 489 3.775654 CCCAGTCCCGAGACAGGC 61.776 72.222 2.73 0.00 45.87 4.85
495 530 3.334054 ACCTGGAAGAGCAGCCCC 61.334 66.667 0.00 0.00 34.07 5.80
496 531 4.479993 CCTGGAAGAGCAGCCCCG 62.480 72.222 0.00 0.00 34.07 5.73
497 532 4.479993 CTGGAAGAGCAGCCCCGG 62.480 72.222 0.00 0.00 34.07 5.73
655 691 3.368323 GGGCACATCGGTCATTTCAAATT 60.368 43.478 0.00 0.00 0.00 1.82
700 736 9.950496 ATAGTCTCTGTAAGTCAAATGTCAAAT 57.050 29.630 0.00 0.00 33.76 2.32
702 738 9.209175 AGTCTCTGTAAGTCAAATGTCAAATAC 57.791 33.333 0.00 0.00 33.76 1.89
703 739 9.209175 GTCTCTGTAAGTCAAATGTCAAATACT 57.791 33.333 0.00 0.00 33.76 2.12
704 740 9.424319 TCTCTGTAAGTCAAATGTCAAATACTC 57.576 33.333 0.00 0.00 33.76 2.59
705 741 9.429359 CTCTGTAAGTCAAATGTCAAATACTCT 57.571 33.333 0.00 0.00 33.76 3.24
706 742 9.424319 TCTGTAAGTCAAATGTCAAATACTCTC 57.576 33.333 0.00 0.00 33.76 3.20
707 743 9.429359 CTGTAAGTCAAATGTCAAATACTCTCT 57.571 33.333 0.00 0.00 0.00 3.10
708 744 9.424319 TGTAAGTCAAATGTCAAATACTCTCTC 57.576 33.333 0.00 0.00 0.00 3.20
709 745 7.913674 AAGTCAAATGTCAAATACTCTCTCC 57.086 36.000 0.00 0.00 0.00 3.71
710 746 6.102663 AGTCAAATGTCAAATACTCTCTCCG 58.897 40.000 0.00 0.00 0.00 4.63
711 747 5.869888 GTCAAATGTCAAATACTCTCTCCGT 59.130 40.000 0.00 0.00 0.00 4.69
712 748 6.369065 GTCAAATGTCAAATACTCTCTCCGTT 59.631 38.462 0.00 0.00 0.00 4.44
713 749 6.590292 TCAAATGTCAAATACTCTCTCCGTTC 59.410 38.462 0.00 0.00 0.00 3.95
714 750 4.092771 TGTCAAATACTCTCTCCGTTCG 57.907 45.455 0.00 0.00 0.00 3.95
715 751 3.119602 TGTCAAATACTCTCTCCGTTCGG 60.120 47.826 4.74 4.74 0.00 4.30
716 752 3.128242 GTCAAATACTCTCTCCGTTCGGA 59.872 47.826 13.34 13.34 0.00 4.55
717 753 3.760151 TCAAATACTCTCTCCGTTCGGAA 59.240 43.478 14.79 5.84 33.41 4.30
718 754 4.401519 TCAAATACTCTCTCCGTTCGGAAT 59.598 41.667 14.79 2.14 33.41 3.01
719 755 5.105473 TCAAATACTCTCTCCGTTCGGAATT 60.105 40.000 14.79 7.85 33.41 2.17
720 756 6.095860 TCAAATACTCTCTCCGTTCGGAATTA 59.904 38.462 14.79 3.46 33.41 1.40
721 757 5.692613 ATACTCTCTCCGTTCGGAATTAG 57.307 43.478 14.79 13.09 33.41 1.73
722 758 3.354467 ACTCTCTCCGTTCGGAATTAGT 58.646 45.455 14.79 13.63 33.41 2.24
723 759 3.762823 ACTCTCTCCGTTCGGAATTAGTT 59.237 43.478 14.79 3.35 33.41 2.24
724 760 4.106029 TCTCTCCGTTCGGAATTAGTTG 57.894 45.455 14.79 2.23 33.41 3.16
725 761 3.508793 TCTCTCCGTTCGGAATTAGTTGT 59.491 43.478 14.79 0.00 33.41 3.32
726 762 3.841643 TCTCCGTTCGGAATTAGTTGTC 58.158 45.455 14.79 0.00 33.41 3.18
727 763 2.597305 CTCCGTTCGGAATTAGTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
728 764 2.228582 TCCGTTCGGAATTAGTTGTCGA 59.771 45.455 11.66 0.00 0.00 4.20
729 765 2.988493 CCGTTCGGAATTAGTTGTCGAA 59.012 45.455 5.19 0.00 37.48 3.71
730 766 3.429543 CCGTTCGGAATTAGTTGTCGAAA 59.570 43.478 5.19 0.00 40.67 3.46
731 767 4.084433 CCGTTCGGAATTAGTTGTCGAAAA 60.084 41.667 5.19 0.00 40.67 2.29
732 768 5.433855 CGTTCGGAATTAGTTGTCGAAAAA 58.566 37.500 0.00 0.00 40.67 1.94
782 818 9.005777 AGTTCTAGATACATCTATTTCCGAGAC 57.994 37.037 0.00 0.00 38.60 3.36
783 819 8.784994 GTTCTAGATACATCTATTTCCGAGACA 58.215 37.037 0.00 0.00 38.60 3.41
784 820 8.919777 TCTAGATACATCTATTTCCGAGACAA 57.080 34.615 0.00 0.00 38.60 3.18
785 821 9.004717 TCTAGATACATCTATTTCCGAGACAAG 57.995 37.037 0.00 0.00 38.60 3.16
786 822 7.589958 AGATACATCTATTTCCGAGACAAGT 57.410 36.000 0.00 0.00 34.85 3.16
787 823 8.693120 AGATACATCTATTTCCGAGACAAGTA 57.307 34.615 0.00 0.00 34.85 2.24
788 824 9.132923 AGATACATCTATTTCCGAGACAAGTAA 57.867 33.333 0.00 0.00 34.85 2.24
789 825 9.915629 GATACATCTATTTCCGAGACAAGTAAT 57.084 33.333 0.00 0.00 0.00 1.89
791 827 8.649973 ACATCTATTTCCGAGACAAGTAATTC 57.350 34.615 0.00 0.00 0.00 2.17
792 828 7.711339 ACATCTATTTCCGAGACAAGTAATTCC 59.289 37.037 0.00 0.00 0.00 3.01
793 829 6.270815 TCTATTTCCGAGACAAGTAATTCCG 58.729 40.000 0.00 0.00 0.00 4.30
794 830 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
795 831 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
796 832 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
797 833 3.508793 TCCGAGACAAGTAATTCCGAACT 59.491 43.478 0.00 0.00 0.00 3.01
798 834 3.612860 CCGAGACAAGTAATTCCGAACTG 59.387 47.826 0.00 0.00 0.00 3.16
799 835 4.482386 CGAGACAAGTAATTCCGAACTGA 58.518 43.478 0.00 0.00 0.00 3.41
800 836 5.103000 CGAGACAAGTAATTCCGAACTGAT 58.897 41.667 0.00 0.00 0.00 2.90
801 837 5.004821 CGAGACAAGTAATTCCGAACTGATG 59.995 44.000 0.00 0.00 0.00 3.07
802 838 5.178797 AGACAAGTAATTCCGAACTGATGG 58.821 41.667 0.00 0.00 0.00 3.51
803 839 5.046591 AGACAAGTAATTCCGAACTGATGGA 60.047 40.000 0.00 0.00 0.00 3.41
804 840 5.178797 ACAAGTAATTCCGAACTGATGGAG 58.821 41.667 0.00 0.00 35.26 3.86
970 1007 6.434028 AGATGATTAAGTGGCTTTTTGTGCTA 59.566 34.615 0.00 0.00 0.00 3.49
1074 1114 1.045350 TGGAATGCGAGGAGGAGGAG 61.045 60.000 0.00 0.00 0.00 3.69
1075 1115 1.745264 GAATGCGAGGAGGAGGAGG 59.255 63.158 0.00 0.00 0.00 4.30
1076 1116 0.757188 GAATGCGAGGAGGAGGAGGA 60.757 60.000 0.00 0.00 0.00 3.71
1077 1117 0.758685 AATGCGAGGAGGAGGAGGAG 60.759 60.000 0.00 0.00 0.00 3.69
1078 1118 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
1079 1119 3.063197 GCGAGGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
1080 1120 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1081 1121 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1082 1122 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1083 1123 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1084 1124 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1085 1125 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1120 1160 2.441164 TCAGCGAGGAGGAGGAGC 60.441 66.667 0.00 0.00 0.00 4.70
1206 1255 1.506025 GGAGGAGAATGGAAGAGCCT 58.494 55.000 0.00 0.00 37.63 4.58
1272 1321 2.047274 TCGAAGAAGGCGGCCAAG 60.047 61.111 23.09 5.48 0.00 3.61
1327 1379 6.627087 ATGGTGACCATAAGAAGAAGAAGA 57.373 37.500 16.93 0.00 43.19 2.87
1328 1380 6.433847 TGGTGACCATAAGAAGAAGAAGAA 57.566 37.500 0.00 0.00 0.00 2.52
1329 1381 6.467677 TGGTGACCATAAGAAGAAGAAGAAG 58.532 40.000 0.00 0.00 0.00 2.85
1391 1443 1.686587 TGCCGATCGTGACAAGGATAT 59.313 47.619 15.09 0.00 31.12 1.63
1430 1482 0.821711 TCGCCCAACAAGAACAAGGG 60.822 55.000 0.00 0.00 42.55 3.95
1456 1508 2.555664 TCCATTCCAAGGAGAAGAGCT 58.444 47.619 0.00 0.00 0.00 4.09
1505 1557 2.040544 GGAAGATGCACCGTGGTGG 61.041 63.158 20.00 2.98 45.49 4.61
1545 1597 1.765314 AGCAGTATGATGTGGAGGTCC 59.235 52.381 0.00 0.00 39.69 4.46
1570 1622 5.030147 AGTATGACAAGTACAAGGGGATGA 58.970 41.667 0.00 0.00 0.00 2.92
1575 1627 5.534654 TGACAAGTACAAGGGGATGAAAAAG 59.465 40.000 0.00 0.00 0.00 2.27
1587 1639 6.014242 AGGGGATGAAAAAGAAGGAAATGAAC 60.014 38.462 0.00 0.00 0.00 3.18
1632 1684 1.847798 ATAACGGTGGCAGCAGGGAA 61.848 55.000 17.80 0.00 0.00 3.97
1636 1688 2.596851 GGTGGCAGCAGGGAAGAGA 61.597 63.158 12.58 0.00 0.00 3.10
1654 1709 1.892474 AGAAGAAGAAGACAGCGCTCT 59.108 47.619 7.13 0.00 0.00 4.09
1659 1714 2.077413 AGAAGACAGCGCTCTTTCTG 57.923 50.000 20.60 8.36 30.28 3.02
1671 1726 2.260822 CTCTTTCTGTCCAAGGAGGGA 58.739 52.381 0.00 0.00 38.24 4.20
1724 1779 5.163045 ACAAGGGAAACAAGAGGAAGAAGAT 60.163 40.000 0.00 0.00 0.00 2.40
1752 1807 9.123902 CCAATGATGTATGATAAGGTGAAGAAA 57.876 33.333 0.00 0.00 0.00 2.52
1755 1810 7.629157 TGATGTATGATAAGGTGAAGAAACCA 58.371 34.615 0.00 0.00 43.20 3.67
1811 1866 7.225538 CAGTTATGACAGAAAGAAGACAACACT 59.774 37.037 0.00 0.00 0.00 3.55
1812 1867 8.421784 AGTTATGACAGAAAGAAGACAACACTA 58.578 33.333 0.00 0.00 0.00 2.74
1830 1885 0.679505 TAGGCTATAACGCAGGGCAG 59.320 55.000 0.00 0.00 0.00 4.85
1855 1910 1.738099 CAAAGCGGTCACGGAGAGG 60.738 63.158 0.00 0.00 41.36 3.69
1902 1960 1.039856 AGGTTGCAGGCGAACATTTT 58.960 45.000 0.00 0.00 0.00 1.82
1947 2005 7.692460 AATGTCATCAGTTTTGCTCTTCATA 57.308 32.000 0.00 0.00 0.00 2.15
2083 2143 2.509569 TGGTGTTTAATCGGTGTGCAT 58.490 42.857 0.00 0.00 0.00 3.96
2455 2527 7.015974 TGCTCTAGAGACATAAATGGTCATCAT 59.984 37.037 24.24 0.00 37.74 2.45
2489 2561 5.376625 GTGAATATATTGGGAGCAACAGGA 58.623 41.667 1.78 0.00 0.00 3.86
2579 2651 1.355381 TGAATGCAGTTCCAGGGACAT 59.645 47.619 0.00 0.00 35.91 3.06
2636 2708 2.617532 GGAGTAGTAGGCGGGATCGTAT 60.618 54.545 0.00 0.00 38.89 3.06
2684 2756 3.576078 AGGATGGACATTTGGCGAATA 57.424 42.857 0.00 0.00 0.00 1.75
2818 2890 5.916883 CACAGTGGCTCTTGATAACAAAAAG 59.083 40.000 0.00 0.00 35.49 2.27
2820 2892 5.241506 CAGTGGCTCTTGATAACAAAAAGGA 59.758 40.000 0.00 0.00 35.49 3.36
2827 2899 9.481340 GCTCTTGATAACAAAAAGGAAAATCTT 57.519 29.630 0.00 0.00 35.49 2.40
3176 3248 6.069994 TGCAGCAAATATGAATATCCAGGAA 58.930 36.000 0.00 0.00 0.00 3.36
3204 3276 1.821136 GTGCTTGGAGAAATGGAAGGG 59.179 52.381 0.00 0.00 0.00 3.95
3208 3280 1.453928 GGAGAAATGGAAGGGGGCG 60.454 63.158 0.00 0.00 0.00 6.13
3416 3488 5.514274 TTCTGTCAATGGAAAAGGTGAAC 57.486 39.130 0.00 0.00 0.00 3.18
3562 3634 6.097554 TGAAACAAAAATAGAGCAAGTGGGAA 59.902 34.615 0.00 0.00 0.00 3.97
3754 3826 4.071423 TGCAGAACATCATTTCTTCCGAA 58.929 39.130 0.00 0.00 33.31 4.30
3912 3984 5.133221 ACAAGGCTTGTGAGTTGTTTAGAT 58.867 37.500 30.71 1.65 43.48 1.98
3953 4025 7.934665 TCTTTTGCAGTTTCACCATTACTACTA 59.065 33.333 0.00 0.00 0.00 1.82
4057 4253 4.749245 AGTGCTTTCGAAGGTTGTTATG 57.251 40.909 9.20 0.00 0.00 1.90
4202 4398 5.425630 CACCACATCAGATCTCATTTCTCA 58.574 41.667 0.00 0.00 0.00 3.27
4203 4399 5.524281 CACCACATCAGATCTCATTTCTCAG 59.476 44.000 0.00 0.00 0.00 3.35
4240 4436 6.354938 AGTACATCTTCATCCTCGTGTAGTA 58.645 40.000 0.00 0.00 0.00 1.82
4241 4437 5.759506 ACATCTTCATCCTCGTGTAGTAG 57.240 43.478 0.00 0.00 0.00 2.57
4242 4438 5.194432 ACATCTTCATCCTCGTGTAGTAGT 58.806 41.667 0.00 0.00 0.00 2.73
4243 4439 5.297278 ACATCTTCATCCTCGTGTAGTAGTC 59.703 44.000 0.00 0.00 0.00 2.59
4286 4482 1.002468 CTTGTGGTTTCAGTCTTGGCG 60.002 52.381 0.00 0.00 0.00 5.69
4328 4524 8.544622 TCACCAACCATTTACTATCTATCAACA 58.455 33.333 0.00 0.00 0.00 3.33
4334 4530 8.840321 ACCATTTACTATCTATCAACATGTTGC 58.160 33.333 29.84 0.00 40.24 4.17
4377 4573 2.559440 GATCCACTCTCCAATGCTGTC 58.441 52.381 0.00 0.00 0.00 3.51
4400 4596 3.170362 CAAAGGGAGGCTGGACCA 58.830 61.111 0.00 0.00 43.14 4.02
4524 4720 0.386476 CAGCAAACAAGCTTGAGGCA 59.614 50.000 32.50 0.00 43.70 4.75
4591 4787 3.119101 AGTGTACGATGTTGAGATCACCC 60.119 47.826 0.00 0.00 0.00 4.61
4627 4823 4.568152 TGCTCTTTGGTAAAGCTTTCAC 57.432 40.909 16.57 10.41 38.39 3.18
4644 4840 3.247006 TCACCCTAACGCTTTCAGATC 57.753 47.619 0.00 0.00 0.00 2.75
4958 5202 4.276460 GTCGTTTCGCTTTTGCTCTTTTA 58.724 39.130 0.00 0.00 44.80 1.52
5006 5250 1.706305 ACCTTGGATCGGTTTGGGTAA 59.294 47.619 0.00 0.00 0.00 2.85
5036 5284 1.315257 ATGTGTTTCGGCCCATCAGC 61.315 55.000 0.00 0.00 0.00 4.26
5056 5304 1.800805 GAGTGATGTGGTGACAGGTG 58.199 55.000 0.00 0.00 44.46 4.00
5059 5307 0.843309 TGATGTGGTGACAGGTGGTT 59.157 50.000 0.00 0.00 44.46 3.67
5061 5309 0.823356 ATGTGGTGACAGGTGGTTGC 60.823 55.000 0.00 0.00 44.46 4.17
5062 5310 2.203139 TGGTGACAGGTGGTTGCG 60.203 61.111 0.00 0.00 35.01 4.85
5063 5311 2.203153 GGTGACAGGTGGTTGCGT 60.203 61.111 0.00 0.00 0.00 5.24
5095 5346 0.396695 CCCAGATGGCAAGCCTCATT 60.397 55.000 12.96 0.00 36.94 2.57
5107 5358 4.836825 CAAGCCTCATTAGACAGAAAGGA 58.163 43.478 0.00 0.00 0.00 3.36
5108 5359 5.248640 CAAGCCTCATTAGACAGAAAGGAA 58.751 41.667 0.00 0.00 0.00 3.36
5110 5361 4.080638 AGCCTCATTAGACAGAAAGGAAGG 60.081 45.833 0.00 0.00 0.00 3.46
5111 5362 4.775236 CCTCATTAGACAGAAAGGAAGGG 58.225 47.826 0.00 0.00 0.00 3.95
5114 5365 3.418684 TTAGACAGAAAGGAAGGGTGC 57.581 47.619 0.00 0.00 0.00 5.01
5115 5366 1.439543 AGACAGAAAGGAAGGGTGCT 58.560 50.000 0.00 0.00 0.00 4.40
5116 5367 2.621070 AGACAGAAAGGAAGGGTGCTA 58.379 47.619 0.00 0.00 0.00 3.49
5117 5368 2.569404 AGACAGAAAGGAAGGGTGCTAG 59.431 50.000 0.00 0.00 0.00 3.42
5118 5369 2.303311 GACAGAAAGGAAGGGTGCTAGT 59.697 50.000 0.00 0.00 0.00 2.57
5121 5372 3.769844 CAGAAAGGAAGGGTGCTAGTAGA 59.230 47.826 0.00 0.00 0.00 2.59
5122 5373 4.407296 CAGAAAGGAAGGGTGCTAGTAGAT 59.593 45.833 0.00 0.00 0.00 1.98
5123 5374 5.033522 AGAAAGGAAGGGTGCTAGTAGATT 58.966 41.667 0.00 0.00 0.00 2.40
5125 5376 5.360649 AAGGAAGGGTGCTAGTAGATTTC 57.639 43.478 0.00 0.00 0.00 2.17
5126 5377 3.385111 AGGAAGGGTGCTAGTAGATTTCG 59.615 47.826 0.00 0.00 0.00 3.46
5127 5378 3.383825 GGAAGGGTGCTAGTAGATTTCGA 59.616 47.826 0.00 0.00 0.00 3.71
5133 5624 5.335819 GGGTGCTAGTAGATTTCGATAGTCC 60.336 48.000 0.00 0.00 37.40 3.85
5173 5664 3.355378 TGGTTGGTTGCCATCAGATTAG 58.645 45.455 0.00 0.00 31.53 1.73
5174 5665 3.245229 TGGTTGGTTGCCATCAGATTAGT 60.245 43.478 0.00 0.00 31.53 2.24
5175 5666 3.378427 GGTTGGTTGCCATCAGATTAGTC 59.622 47.826 0.00 0.00 31.53 2.59
5251 5748 2.125326 CGGCGTCACCCTCCATCTA 61.125 63.158 0.00 0.00 33.26 1.98
5352 5854 4.337836 GGAATCATTTTCAAGAGGAGGAGC 59.662 45.833 0.00 0.00 0.00 4.70
5356 5858 0.326264 TTTCAAGAGGAGGAGCTGGC 59.674 55.000 0.00 0.00 0.00 4.85
5357 5859 0.837691 TTCAAGAGGAGGAGCTGGCA 60.838 55.000 0.00 0.00 0.00 4.92
5458 5970 1.049289 CCCCCGACCCAAACCAAAAA 61.049 55.000 0.00 0.00 0.00 1.94
5465 5977 0.762418 CCCAAACCAAAAACCCCTCC 59.238 55.000 0.00 0.00 0.00 4.30
5493 6009 1.715585 CCATCGCATTCACACGGAC 59.284 57.895 0.00 0.00 0.00 4.79
5522 6039 2.224185 ACACATGTTCTCCAACGCTACA 60.224 45.455 0.00 0.00 34.95 2.74
5527 6044 2.037902 TGTTCTCCAACGCTACATTCCA 59.962 45.455 0.00 0.00 34.95 3.53
5533 6050 2.355756 CCAACGCTACATTCCATGGAAG 59.644 50.000 29.98 22.91 37.56 3.46
5537 6054 1.959042 CTACATTCCATGGAAGCGCT 58.041 50.000 29.98 12.65 37.56 5.92
5539 6056 1.098050 ACATTCCATGGAAGCGCTTC 58.902 50.000 36.49 36.49 37.56 3.86
5540 6057 1.340405 ACATTCCATGGAAGCGCTTCT 60.340 47.619 40.11 24.93 39.45 2.85
5551 6068 4.001017 GAAGCGCTTCTTCTTCTTCATG 57.999 45.455 36.70 0.00 45.99 3.07
5552 6069 3.051081 AGCGCTTCTTCTTCTTCATGT 57.949 42.857 2.64 0.00 0.00 3.21
5553 6070 2.999355 AGCGCTTCTTCTTCTTCATGTC 59.001 45.455 2.64 0.00 0.00 3.06
5554 6071 2.999355 GCGCTTCTTCTTCTTCATGTCT 59.001 45.455 0.00 0.00 0.00 3.41
5555 6072 4.081972 AGCGCTTCTTCTTCTTCATGTCTA 60.082 41.667 2.64 0.00 0.00 2.59
5556 6073 4.808364 GCGCTTCTTCTTCTTCATGTCTAT 59.192 41.667 0.00 0.00 0.00 1.98
5557 6074 5.980116 GCGCTTCTTCTTCTTCATGTCTATA 59.020 40.000 0.00 0.00 0.00 1.31
5558 6075 6.074569 GCGCTTCTTCTTCTTCATGTCTATAC 60.075 42.308 0.00 0.00 0.00 1.47
5559 6076 7.199766 CGCTTCTTCTTCTTCATGTCTATACT 58.800 38.462 0.00 0.00 0.00 2.12
5560 6077 7.704472 CGCTTCTTCTTCTTCATGTCTATACTT 59.296 37.037 0.00 0.00 0.00 2.24
5567 6084 8.861086 TCTTCTTCATGTCTATACTTATGGACC 58.139 37.037 9.52 0.00 41.71 4.46
5568 6085 8.547481 TTCTTCATGTCTATACTTATGGACCA 57.453 34.615 0.00 0.00 41.71 4.02
5569 6086 8.547481 TCTTCATGTCTATACTTATGGACCAA 57.453 34.615 0.00 1.52 41.71 3.67
5570 6087 8.421784 TCTTCATGTCTATACTTATGGACCAAC 58.578 37.037 0.00 0.00 41.71 3.77
5571 6088 6.745116 TCATGTCTATACTTATGGACCAACG 58.255 40.000 0.00 0.00 41.71 4.10
5572 6089 5.524971 TGTCTATACTTATGGACCAACGG 57.475 43.478 0.00 0.00 41.71 4.44
5573 6090 4.957954 TGTCTATACTTATGGACCAACGGT 59.042 41.667 0.00 0.00 41.71 4.83
5574 6091 5.422970 TGTCTATACTTATGGACCAACGGTT 59.577 40.000 0.00 0.00 41.71 4.44
5575 6092 5.981915 GTCTATACTTATGGACCAACGGTTC 59.018 44.000 0.00 0.00 37.98 3.62
5576 6093 2.088950 ACTTATGGACCAACGGTTCG 57.911 50.000 0.00 0.00 35.25 3.95
5577 6094 1.338389 ACTTATGGACCAACGGTTCGG 60.338 52.381 0.00 7.51 35.25 4.30
5578 6095 0.975135 TTATGGACCAACGGTTCGGA 59.025 50.000 13.78 0.00 35.25 4.55
5579 6096 1.196911 TATGGACCAACGGTTCGGAT 58.803 50.000 13.78 3.25 35.25 4.18
5580 6097 1.196911 ATGGACCAACGGTTCGGATA 58.803 50.000 13.78 3.40 35.25 2.59
5581 6098 0.975135 TGGACCAACGGTTCGGATAA 59.025 50.000 13.78 0.16 35.25 1.75
5582 6099 1.066716 TGGACCAACGGTTCGGATAAG 60.067 52.381 13.78 0.00 35.25 1.73
5583 6100 1.205417 GGACCAACGGTTCGGATAAGA 59.795 52.381 13.78 0.00 35.25 2.10
5584 6101 2.265683 GACCAACGGTTCGGATAAGAC 58.734 52.381 13.78 0.00 35.25 3.01
5585 6102 1.897802 ACCAACGGTTCGGATAAGACT 59.102 47.619 13.78 0.00 27.29 3.24
5586 6103 2.301009 ACCAACGGTTCGGATAAGACTT 59.699 45.455 13.78 0.00 27.29 3.01
5587 6104 2.928116 CCAACGGTTCGGATAAGACTTC 59.072 50.000 0.00 0.00 0.00 3.01
5588 6105 2.928116 CAACGGTTCGGATAAGACTTCC 59.072 50.000 0.00 0.00 0.00 3.46
5589 6106 2.454538 ACGGTTCGGATAAGACTTCCT 58.545 47.619 0.00 0.00 0.00 3.36
5590 6107 2.426381 ACGGTTCGGATAAGACTTCCTC 59.574 50.000 0.00 0.00 0.00 3.71
5591 6108 2.688958 CGGTTCGGATAAGACTTCCTCT 59.311 50.000 0.00 0.00 0.00 3.69
5592 6109 3.130693 CGGTTCGGATAAGACTTCCTCTT 59.869 47.826 0.00 0.00 42.33 2.85
5593 6110 4.381718 CGGTTCGGATAAGACTTCCTCTTT 60.382 45.833 0.00 0.00 40.04 2.52
5594 6111 5.489249 GGTTCGGATAAGACTTCCTCTTTT 58.511 41.667 0.00 0.00 40.04 2.27
5595 6112 5.351740 GGTTCGGATAAGACTTCCTCTTTTG 59.648 44.000 0.00 0.00 40.04 2.44
5596 6113 5.740290 TCGGATAAGACTTCCTCTTTTGT 57.260 39.130 0.00 0.00 40.04 2.83
5597 6114 5.479306 TCGGATAAGACTTCCTCTTTTGTG 58.521 41.667 0.00 0.00 40.04 3.33
5598 6115 5.245301 TCGGATAAGACTTCCTCTTTTGTGA 59.755 40.000 0.00 0.00 40.04 3.58
5599 6116 5.348997 CGGATAAGACTTCCTCTTTTGTGAC 59.651 44.000 0.00 0.00 40.04 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.694150 CTAAAGCCAGGATGATCGGGA 59.306 52.381 6.02 0.00 39.69 5.14
45 46 2.141517 CTGCTAAAGCCAGGATGATCG 58.858 52.381 0.00 0.00 41.18 3.69
61 62 2.095059 CAGTAAAATGCGCCTTTCTGCT 60.095 45.455 11.16 7.80 0.00 4.24
97 104 1.141053 CAGGGGGTATCTGGCAACTAC 59.859 57.143 0.00 0.00 37.61 2.73
212 219 2.094762 AAGAAACCCCGACGATTGAG 57.905 50.000 0.00 0.00 0.00 3.02
258 265 4.425772 TCACTCCCAGAAATCACTCCTTA 58.574 43.478 0.00 0.00 0.00 2.69
267 274 4.768968 CCACAAGAAATCACTCCCAGAAAT 59.231 41.667 0.00 0.00 0.00 2.17
269 276 3.394274 TCCACAAGAAATCACTCCCAGAA 59.606 43.478 0.00 0.00 0.00 3.02
270 277 2.978978 TCCACAAGAAATCACTCCCAGA 59.021 45.455 0.00 0.00 0.00 3.86
278 302 5.070001 AGACCGAAAATCCACAAGAAATCA 58.930 37.500 0.00 0.00 0.00 2.57
314 339 3.243839 CCCCTTTCAACACATCCAACAAG 60.244 47.826 0.00 0.00 0.00 3.16
317 342 1.000843 GCCCCTTTCAACACATCCAAC 59.999 52.381 0.00 0.00 0.00 3.77
453 488 0.533085 GAAATAGGTGGAGGCCTCGC 60.533 60.000 26.36 20.26 39.94 5.03
454 489 1.069358 GAGAAATAGGTGGAGGCCTCG 59.931 57.143 26.36 0.00 39.94 4.63
496 531 2.994671 GCGAAAAGAAGGGCTGCCC 61.995 63.158 30.57 30.57 45.90 5.36
497 532 2.568612 GCGAAAAGAAGGGCTGCC 59.431 61.111 11.05 11.05 0.00 4.85
498 533 2.176792 CGCGAAAAGAAGGGCTGC 59.823 61.111 0.00 0.00 0.00 5.25
499 534 2.870372 CCGCGAAAAGAAGGGCTG 59.130 61.111 8.23 0.00 0.00 4.85
500 535 3.056328 GCCGCGAAAAGAAGGGCT 61.056 61.111 8.23 0.00 40.59 5.19
501 536 4.460873 CGCCGCGAAAAGAAGGGC 62.461 66.667 8.23 0.00 40.36 5.19
502 537 2.740714 CTCGCCGCGAAAAGAAGGG 61.741 63.158 17.53 0.00 34.74 3.95
503 538 2.740714 CCTCGCCGCGAAAAGAAGG 61.741 63.158 17.53 9.45 34.74 3.46
504 539 2.740714 CCCTCGCCGCGAAAAGAAG 61.741 63.158 17.53 3.67 34.74 2.85
505 540 2.740826 CCCTCGCCGCGAAAAGAA 60.741 61.111 17.53 0.00 34.74 2.52
655 691 8.840200 AGACTATAATCCCTCTCTAAACACAA 57.160 34.615 0.00 0.00 0.00 3.33
700 736 4.521146 ACTAATTCCGAACGGAGAGAGTA 58.479 43.478 15.34 5.02 46.06 2.59
701 737 3.354467 ACTAATTCCGAACGGAGAGAGT 58.646 45.455 15.34 15.25 46.06 3.24
702 738 4.106197 CAACTAATTCCGAACGGAGAGAG 58.894 47.826 15.34 14.71 46.06 3.20
703 739 3.508793 ACAACTAATTCCGAACGGAGAGA 59.491 43.478 15.34 2.49 46.06 3.10
704 740 3.846360 ACAACTAATTCCGAACGGAGAG 58.154 45.455 15.34 15.30 46.06 3.20
705 741 3.671433 CGACAACTAATTCCGAACGGAGA 60.671 47.826 15.34 8.02 46.06 3.71
706 742 2.597305 CGACAACTAATTCCGAACGGAG 59.403 50.000 15.34 7.27 46.06 4.63
707 743 2.228582 TCGACAACTAATTCCGAACGGA 59.771 45.455 12.04 12.04 43.52 4.69
708 744 2.598589 TCGACAACTAATTCCGAACGG 58.401 47.619 6.94 6.94 0.00 4.44
709 745 4.634349 TTTCGACAACTAATTCCGAACG 57.366 40.909 0.00 0.00 38.69 3.95
756 792 9.005777 GTCTCGGAAATAGATGTATCTAGAACT 57.994 37.037 0.00 0.00 42.20 3.01
757 793 8.784994 TGTCTCGGAAATAGATGTATCTAGAAC 58.215 37.037 0.00 0.00 42.20 3.01
758 794 8.919777 TGTCTCGGAAATAGATGTATCTAGAA 57.080 34.615 0.00 0.00 42.20 2.10
759 795 8.919777 TTGTCTCGGAAATAGATGTATCTAGA 57.080 34.615 7.57 0.00 42.20 2.43
760 796 8.788806 ACTTGTCTCGGAAATAGATGTATCTAG 58.211 37.037 7.57 0.00 42.20 2.43
761 797 8.693120 ACTTGTCTCGGAAATAGATGTATCTA 57.307 34.615 4.22 4.22 43.00 1.98
762 798 7.589958 ACTTGTCTCGGAAATAGATGTATCT 57.410 36.000 0.00 0.00 40.86 1.98
763 799 9.915629 ATTACTTGTCTCGGAAATAGATGTATC 57.084 33.333 0.00 0.00 0.00 2.24
765 801 9.745880 GAATTACTTGTCTCGGAAATAGATGTA 57.254 33.333 0.00 0.00 0.00 2.29
766 802 7.711339 GGAATTACTTGTCTCGGAAATAGATGT 59.289 37.037 0.00 0.00 0.00 3.06
767 803 7.096023 CGGAATTACTTGTCTCGGAAATAGATG 60.096 40.741 0.00 0.00 0.00 2.90
768 804 6.924060 CGGAATTACTTGTCTCGGAAATAGAT 59.076 38.462 0.00 0.00 0.00 1.98
769 805 6.095860 TCGGAATTACTTGTCTCGGAAATAGA 59.904 38.462 0.00 0.00 0.00 1.98
770 806 6.270815 TCGGAATTACTTGTCTCGGAAATAG 58.729 40.000 0.00 0.00 0.00 1.73
771 807 6.211587 TCGGAATTACTTGTCTCGGAAATA 57.788 37.500 0.00 0.00 0.00 1.40
772 808 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
773 809 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
774 810 4.021719 AGTTCGGAATTACTTGTCTCGGAA 60.022 41.667 0.00 0.00 0.00 4.30
775 811 3.508793 AGTTCGGAATTACTTGTCTCGGA 59.491 43.478 0.00 0.00 0.00 4.55
776 812 3.612860 CAGTTCGGAATTACTTGTCTCGG 59.387 47.826 0.00 0.00 0.00 4.63
777 813 4.482386 TCAGTTCGGAATTACTTGTCTCG 58.518 43.478 0.00 0.00 0.00 4.04
778 814 5.292101 CCATCAGTTCGGAATTACTTGTCTC 59.708 44.000 0.00 0.00 0.00 3.36
779 815 5.046591 TCCATCAGTTCGGAATTACTTGTCT 60.047 40.000 0.00 0.00 0.00 3.41
780 816 5.175859 TCCATCAGTTCGGAATTACTTGTC 58.824 41.667 0.00 0.00 0.00 3.18
781 817 5.160607 TCCATCAGTTCGGAATTACTTGT 57.839 39.130 0.00 0.00 0.00 3.16
782 818 5.178797 ACTCCATCAGTTCGGAATTACTTG 58.821 41.667 0.00 0.00 26.56 3.16
783 819 5.422214 ACTCCATCAGTTCGGAATTACTT 57.578 39.130 0.00 0.00 26.56 2.24
784 820 5.657302 ACTACTCCATCAGTTCGGAATTACT 59.343 40.000 0.00 0.00 36.43 2.24
785 821 5.903810 ACTACTCCATCAGTTCGGAATTAC 58.096 41.667 0.00 0.00 36.43 1.89
786 822 7.834881 ATACTACTCCATCAGTTCGGAATTA 57.165 36.000 0.00 0.00 36.43 1.40
787 823 6.732896 ATACTACTCCATCAGTTCGGAATT 57.267 37.500 0.00 0.00 36.43 2.17
788 824 6.732896 AATACTACTCCATCAGTTCGGAAT 57.267 37.500 0.00 0.00 36.43 3.01
789 825 6.540438 AAATACTACTCCATCAGTTCGGAA 57.460 37.500 0.00 0.00 36.43 4.30
790 826 6.153851 TGAAAATACTACTCCATCAGTTCGGA 59.846 38.462 0.00 0.00 36.43 4.55
791 827 6.338146 TGAAAATACTACTCCATCAGTTCGG 58.662 40.000 0.00 0.00 36.43 4.30
792 828 7.827819 TTGAAAATACTACTCCATCAGTTCG 57.172 36.000 0.00 0.00 36.43 3.95
793 829 8.169268 CGTTTGAAAATACTACTCCATCAGTTC 58.831 37.037 0.00 0.00 36.43 3.01
794 830 7.119262 CCGTTTGAAAATACTACTCCATCAGTT 59.881 37.037 0.00 0.00 36.43 3.16
795 831 6.594159 CCGTTTGAAAATACTACTCCATCAGT 59.406 38.462 0.00 0.00 39.41 3.41
796 832 6.037172 CCCGTTTGAAAATACTACTCCATCAG 59.963 42.308 0.00 0.00 0.00 2.90
797 833 5.878116 CCCGTTTGAAAATACTACTCCATCA 59.122 40.000 0.00 0.00 0.00 3.07
798 834 5.220796 GCCCGTTTGAAAATACTACTCCATC 60.221 44.000 0.00 0.00 0.00 3.51
799 835 4.638865 GCCCGTTTGAAAATACTACTCCAT 59.361 41.667 0.00 0.00 0.00 3.41
800 836 4.004982 GCCCGTTTGAAAATACTACTCCA 58.995 43.478 0.00 0.00 0.00 3.86
801 837 4.004982 TGCCCGTTTGAAAATACTACTCC 58.995 43.478 0.00 0.00 0.00 3.85
802 838 4.453136 TGTGCCCGTTTGAAAATACTACTC 59.547 41.667 0.00 0.00 0.00 2.59
803 839 4.391155 TGTGCCCGTTTGAAAATACTACT 58.609 39.130 0.00 0.00 0.00 2.57
804 840 4.752661 TGTGCCCGTTTGAAAATACTAC 57.247 40.909 0.00 0.00 0.00 2.73
970 1007 3.173953 TCTCCTGCCCAAACAATTGAT 57.826 42.857 13.59 0.00 38.94 2.57
1033 1070 3.680786 CGTGTCACGGCTCCTGGA 61.681 66.667 17.75 0.00 38.08 3.86
1074 1114 0.106419 ACGTCTCATCCTCCTCCTCC 60.106 60.000 0.00 0.00 0.00 4.30
1075 1115 1.028905 CACGTCTCATCCTCCTCCTC 58.971 60.000 0.00 0.00 0.00 3.71
1076 1116 1.040339 GCACGTCTCATCCTCCTCCT 61.040 60.000 0.00 0.00 0.00 3.69
1077 1117 1.323271 TGCACGTCTCATCCTCCTCC 61.323 60.000 0.00 0.00 0.00 4.30
1078 1118 0.532573 TTGCACGTCTCATCCTCCTC 59.467 55.000 0.00 0.00 0.00 3.71
1079 1119 0.976641 TTTGCACGTCTCATCCTCCT 59.023 50.000 0.00 0.00 0.00 3.69
1080 1120 1.808411 TTTTGCACGTCTCATCCTCC 58.192 50.000 0.00 0.00 0.00 4.30
1081 1121 2.476854 GCATTTTGCACGTCTCATCCTC 60.477 50.000 0.00 0.00 44.26 3.71
1082 1122 1.470098 GCATTTTGCACGTCTCATCCT 59.530 47.619 0.00 0.00 44.26 3.24
1083 1123 1.900237 GCATTTTGCACGTCTCATCC 58.100 50.000 0.00 0.00 44.26 3.51
1120 1160 0.618680 TCCCACATCTCCACCTCCTG 60.619 60.000 0.00 0.00 0.00 3.86
1206 1255 0.025898 CGTCGTCGCTCAGTTCGATA 59.974 55.000 0.00 0.00 38.29 2.92
1272 1321 2.354604 CCTCCTCTTCTTCTCCTTGTGC 60.355 54.545 0.00 0.00 0.00 4.57
1391 1443 1.614525 AGCAGCATGTCCCTCCTCA 60.615 57.895 0.00 0.00 39.31 3.86
1430 1482 1.005924 TCTCCTTGGAATGGAAAGGGC 59.994 52.381 1.82 0.00 42.77 5.19
1456 1508 2.342650 GGCTGCTCGGCATTTTCCA 61.343 57.895 0.00 0.00 38.13 3.53
1505 1557 5.527951 TGCTTTTGTTATCATTGTGGTGAC 58.472 37.500 0.00 0.00 0.00 3.67
1545 1597 3.446161 TCCCCTTGTACTTGTCATACTCG 59.554 47.826 0.00 0.00 0.00 4.18
1570 1622 9.987272 CTTATCCTTGTTCATTTCCTTCTTTTT 57.013 29.630 0.00 0.00 0.00 1.94
1575 1627 8.029522 GGTTTCTTATCCTTGTTCATTTCCTTC 58.970 37.037 0.00 0.00 0.00 3.46
1587 1639 1.743394 GGCCACGGTTTCTTATCCTTG 59.257 52.381 0.00 0.00 0.00 3.61
1632 1684 1.892474 AGCGCTGTCTTCTTCTTCTCT 59.108 47.619 10.39 0.00 0.00 3.10
1636 1688 2.829741 AAGAGCGCTGTCTTCTTCTT 57.170 45.000 18.48 6.54 30.55 2.52
1654 1709 3.963476 TTTTCCCTCCTTGGACAGAAA 57.037 42.857 5.66 5.66 38.35 2.52
1659 1714 1.550524 GGCATTTTTCCCTCCTTGGAC 59.449 52.381 0.00 0.00 38.35 4.02
1671 1726 2.423538 GTCGTCCAGCATAGGCATTTTT 59.576 45.455 0.67 0.00 44.61 1.94
1724 1779 5.939447 TCACCTTATCATACATCATTGGCA 58.061 37.500 0.00 0.00 0.00 4.92
1752 1807 1.445942 CTTGTCACTGGTCCGTGGT 59.554 57.895 12.09 0.00 35.63 4.16
1755 1810 0.321671 CATCCTTGTCACTGGTCCGT 59.678 55.000 0.00 0.00 0.00 4.69
1811 1866 0.679505 CTGCCCTGCGTTATAGCCTA 59.320 55.000 0.00 0.00 36.02 3.93
1812 1867 1.048724 TCTGCCCTGCGTTATAGCCT 61.049 55.000 0.00 0.00 36.02 4.58
1830 1885 1.282875 GTGACCGCTTTGCACCTTC 59.717 57.895 0.00 0.00 0.00 3.46
1902 1960 5.645056 TTATGCATACCAGGAATTCCTCA 57.355 39.130 24.67 17.67 46.65 3.86
1947 2005 9.577110 CAAAGTCATGTAGCATAATGAAAACAT 57.423 29.630 0.00 0.00 34.70 2.71
2083 2143 2.290197 TGGTATCAACTGCACATCAGCA 60.290 45.455 0.00 0.00 46.76 4.41
2358 2418 1.329292 CTTCACCTCGCGTTTCAACAA 59.671 47.619 5.77 0.00 0.00 2.83
2455 2527 9.573166 CTCCCAATATATTCACCAGAAACATAA 57.427 33.333 0.00 0.00 37.29 1.90
2489 2561 7.822334 TGTATATCCATCAGACTTTGTTTTCGT 59.178 33.333 0.00 0.00 0.00 3.85
2579 2651 3.326836 TGAATTGGCAGACATACGACA 57.673 42.857 0.00 0.00 0.00 4.35
2636 2708 4.567195 AGCCACTGAGGATCCACA 57.433 55.556 15.82 13.57 41.22 4.17
2648 2720 3.209410 CATCCTTGTTATCTGGAGCCAC 58.791 50.000 0.00 0.00 32.95 5.01
2684 2756 0.316204 GCATTTGCTGTGTGCTTCCT 59.684 50.000 0.00 0.00 43.37 3.36
2818 2890 5.449725 GCACTCTCCAATGCTAAGATTTTCC 60.450 44.000 0.00 0.00 38.84 3.13
2820 2892 5.012239 TGCACTCTCCAATGCTAAGATTTT 58.988 37.500 0.00 0.00 42.55 1.82
2827 2899 2.483877 CGTTTTGCACTCTCCAATGCTA 59.516 45.455 0.00 0.00 42.55 3.49
3204 3276 2.048127 GACCACTCACAGTCGCCC 60.048 66.667 0.00 0.00 0.00 6.13
3208 3280 0.523966 CCTCTCGACCACTCACAGTC 59.476 60.000 0.00 0.00 0.00 3.51
3416 3488 6.149474 CCTAGAAAATTATGGTAAGGCATCCG 59.851 42.308 0.00 0.00 0.00 4.18
3562 3634 1.176527 CATCCAATGCTTTCCACGGT 58.823 50.000 0.00 0.00 0.00 4.83
3675 3747 2.079925 CTAGTTGGCAAACCTCTCTGC 58.920 52.381 0.00 0.00 36.94 4.26
3754 3826 5.916661 TTGCTAGACTTCGTATCTTCCTT 57.083 39.130 0.00 0.00 0.00 3.36
3912 3984 9.515226 AACTGCAAAAGAAGACTATTTATGGTA 57.485 29.630 0.00 0.00 0.00 3.25
4057 4253 4.310769 ACAGCGATCTTAGCATATGTTCC 58.689 43.478 4.29 0.00 37.01 3.62
4202 4398 9.896645 ATGAAGATGTACTCATAACAACATTCT 57.103 29.630 0.00 0.00 32.87 2.40
4240 4436 4.307432 CTGATAAACCTCAACACACGACT 58.693 43.478 0.00 0.00 0.00 4.18
4241 4437 3.432252 CCTGATAAACCTCAACACACGAC 59.568 47.826 0.00 0.00 0.00 4.34
4242 4438 3.070446 ACCTGATAAACCTCAACACACGA 59.930 43.478 0.00 0.00 0.00 4.35
4243 4439 3.399330 ACCTGATAAACCTCAACACACG 58.601 45.455 0.00 0.00 0.00 4.49
4286 4482 1.076777 TGAGGGGCAGCTAAATGGC 60.077 57.895 0.00 0.00 44.61 4.40
4328 4524 5.503927 ACTCCTACAATGAAGATGCAACAT 58.496 37.500 0.00 0.00 0.00 2.71
4334 4530 5.050490 CGGGTAACTCCTACAATGAAGATG 58.950 45.833 0.00 0.00 36.25 2.90
4400 4596 5.591877 GGATCCTTCAGCATTACAATGTTCT 59.408 40.000 3.84 0.00 38.65 3.01
4524 4720 1.965754 GAAGCACGCAGAGATCCCCT 61.966 60.000 0.00 0.00 0.00 4.79
4591 4787 0.383231 GAGCAATGGCCTCATTTCCG 59.617 55.000 3.32 0.00 41.29 4.30
4627 4823 5.629079 AAAAAGATCTGAAAGCGTTAGGG 57.371 39.130 0.00 0.00 0.00 3.53
4655 4851 2.341911 AAAAATGTTGCCCGGCGG 59.658 55.556 21.46 21.46 0.00 6.13
4671 4867 6.015772 GGAGATTAACAGGTGTTAGCCAAAAA 60.016 38.462 2.95 0.00 41.03 1.94
4934 5178 0.721483 GAGCAAAAGCGAAACGACCG 60.721 55.000 0.00 0.00 0.00 4.79
4958 5202 3.290710 CCACGGGATCCAATCAAGAAAT 58.709 45.455 15.23 0.00 0.00 2.17
5006 5250 2.295909 CCGAAACACATGGTCATGGTTT 59.704 45.455 20.04 20.04 42.91 3.27
5036 5284 0.318441 ACCTGTCACCACATCACTCG 59.682 55.000 0.00 0.00 0.00 4.18
5056 5304 0.165944 CCGAGACATGAAACGCAACC 59.834 55.000 0.00 0.00 0.00 3.77
5059 5307 2.032634 GGCCGAGACATGAAACGCA 61.033 57.895 0.00 0.00 0.00 5.24
5061 5309 1.361668 CTGGGCCGAGACATGAAACG 61.362 60.000 9.58 1.34 0.00 3.60
5062 5310 0.036388 TCTGGGCCGAGACATGAAAC 60.036 55.000 14.28 0.00 0.00 2.78
5063 5311 0.911769 ATCTGGGCCGAGACATGAAA 59.088 50.000 20.84 0.00 0.00 2.69
5095 5346 2.621070 AGCACCCTTCCTTTCTGTCTA 58.379 47.619 0.00 0.00 0.00 2.59
5107 5358 5.834204 ACTATCGAAATCTACTAGCACCCTT 59.166 40.000 0.00 0.00 0.00 3.95
5108 5359 5.386924 ACTATCGAAATCTACTAGCACCCT 58.613 41.667 0.00 0.00 0.00 4.34
5110 5361 5.335819 GGGACTATCGAAATCTACTAGCACC 60.336 48.000 0.00 0.00 0.00 5.01
5111 5362 5.335819 GGGGACTATCGAAATCTACTAGCAC 60.336 48.000 0.00 0.00 0.00 4.40
5114 5365 6.239396 TCAGGGGACTATCGAAATCTACTAG 58.761 44.000 0.00 0.00 40.21 2.57
5115 5366 6.196918 TCAGGGGACTATCGAAATCTACTA 57.803 41.667 0.00 0.00 40.21 1.82
5116 5367 5.063017 TCAGGGGACTATCGAAATCTACT 57.937 43.478 0.00 0.00 40.21 2.57
5117 5368 5.786264 TTCAGGGGACTATCGAAATCTAC 57.214 43.478 0.00 0.00 40.21 2.59
5118 5369 6.996180 AATTCAGGGGACTATCGAAATCTA 57.004 37.500 0.00 0.00 40.21 1.98
5121 5372 5.104109 TGGAAATTCAGGGGACTATCGAAAT 60.104 40.000 0.00 0.00 40.21 2.17
5122 5373 4.226394 TGGAAATTCAGGGGACTATCGAAA 59.774 41.667 0.00 0.00 40.21 3.46
5123 5374 3.778075 TGGAAATTCAGGGGACTATCGAA 59.222 43.478 0.00 0.00 40.21 3.71
5125 5376 3.838244 TGGAAATTCAGGGGACTATCG 57.162 47.619 0.00 0.00 40.21 2.92
5126 5377 7.020827 TCATATGGAAATTCAGGGGACTATC 57.979 40.000 2.13 0.00 40.21 2.08
5127 5378 7.594849 ATCATATGGAAATTCAGGGGACTAT 57.405 36.000 2.13 0.00 40.21 2.12
5133 5624 6.463331 CCAACCAATCATATGGAAATTCAGGG 60.463 42.308 2.13 0.00 43.54 4.45
5173 5664 4.448537 ACTTCTGAGAGCACAGTATGAC 57.551 45.455 0.00 0.00 39.69 3.06
5174 5665 4.642437 CCTACTTCTGAGAGCACAGTATGA 59.358 45.833 0.00 0.00 39.69 2.15
5175 5666 4.202101 CCCTACTTCTGAGAGCACAGTATG 60.202 50.000 0.00 0.00 46.00 2.39
5251 5748 5.299279 CCATTAAGACGCATTTAATCTGGGT 59.701 40.000 7.65 7.65 41.82 4.51
5401 5913 4.079253 TGACCTGAAATTAAGAAGGTGGC 58.921 43.478 0.00 0.00 43.12 5.01
5402 5914 5.945784 TGATGACCTGAAATTAAGAAGGTGG 59.054 40.000 0.00 0.00 43.12 4.61
5493 6009 4.058721 TGGAGAACATGTGTCATATCCG 57.941 45.455 0.00 0.00 0.00 4.18
5522 6039 2.019984 GAAGAAGCGCTTCCATGGAAT 58.980 47.619 39.16 21.12 45.90 3.01
5533 6050 2.999355 AGACATGAAGAAGAAGAAGCGC 59.001 45.455 0.00 0.00 0.00 5.92
5542 6059 8.642432 TGGTCCATAAGTATAGACATGAAGAAG 58.358 37.037 0.00 0.00 0.00 2.85
5543 6060 8.547481 TGGTCCATAAGTATAGACATGAAGAA 57.453 34.615 0.00 0.00 0.00 2.52
5545 6062 7.382488 CGTTGGTCCATAAGTATAGACATGAAG 59.618 40.741 0.00 0.00 0.00 3.02
5546 6063 7.207383 CGTTGGTCCATAAGTATAGACATGAA 58.793 38.462 0.00 0.00 0.00 2.57
5547 6064 6.239204 CCGTTGGTCCATAAGTATAGACATGA 60.239 42.308 0.00 0.00 0.00 3.07
5548 6065 5.926542 CCGTTGGTCCATAAGTATAGACATG 59.073 44.000 0.00 0.00 0.00 3.21
5549 6066 5.601313 ACCGTTGGTCCATAAGTATAGACAT 59.399 40.000 0.00 0.00 0.00 3.06
5550 6067 4.957954 ACCGTTGGTCCATAAGTATAGACA 59.042 41.667 0.00 0.00 0.00 3.41
5551 6068 5.526506 ACCGTTGGTCCATAAGTATAGAC 57.473 43.478 0.00 0.00 0.00 2.59
5552 6069 5.221106 CGAACCGTTGGTCCATAAGTATAGA 60.221 44.000 0.00 0.00 33.12 1.98
5553 6070 4.980434 CGAACCGTTGGTCCATAAGTATAG 59.020 45.833 0.00 0.00 33.12 1.31
5554 6071 4.202141 CCGAACCGTTGGTCCATAAGTATA 60.202 45.833 0.00 0.00 33.12 1.47
5555 6072 3.431207 CCGAACCGTTGGTCCATAAGTAT 60.431 47.826 0.00 0.00 33.12 2.12
5556 6073 2.094078 CCGAACCGTTGGTCCATAAGTA 60.094 50.000 0.00 0.00 33.12 2.24
5557 6074 1.338389 CCGAACCGTTGGTCCATAAGT 60.338 52.381 0.00 0.00 33.12 2.24
5558 6075 1.066716 TCCGAACCGTTGGTCCATAAG 60.067 52.381 0.00 0.00 33.12 1.73
5559 6076 0.975135 TCCGAACCGTTGGTCCATAA 59.025 50.000 0.00 0.00 33.12 1.90
5560 6077 1.196911 ATCCGAACCGTTGGTCCATA 58.803 50.000 0.00 0.00 33.12 2.74
5561 6078 1.196911 TATCCGAACCGTTGGTCCAT 58.803 50.000 0.00 0.00 33.12 3.41
5562 6079 0.975135 TTATCCGAACCGTTGGTCCA 59.025 50.000 0.00 0.00 33.12 4.02
5563 6080 1.205417 TCTTATCCGAACCGTTGGTCC 59.795 52.381 0.00 0.00 33.12 4.46
5564 6081 2.094338 AGTCTTATCCGAACCGTTGGTC 60.094 50.000 0.00 0.00 33.12 4.02
5565 6082 1.897802 AGTCTTATCCGAACCGTTGGT 59.102 47.619 0.00 0.00 37.65 3.67
5566 6083 2.667473 AGTCTTATCCGAACCGTTGG 57.333 50.000 0.00 0.00 0.00 3.77
5567 6084 2.928116 GGAAGTCTTATCCGAACCGTTG 59.072 50.000 0.00 0.00 0.00 4.10
5568 6085 2.830321 AGGAAGTCTTATCCGAACCGTT 59.170 45.455 0.00 0.00 42.03 4.44
5569 6086 2.426381 GAGGAAGTCTTATCCGAACCGT 59.574 50.000 0.00 0.00 42.03 4.83
5570 6087 2.688958 AGAGGAAGTCTTATCCGAACCG 59.311 50.000 0.00 0.00 42.03 4.44
5571 6088 4.739587 AAGAGGAAGTCTTATCCGAACC 57.260 45.455 0.00 0.00 44.26 3.62
5572 6089 5.932883 ACAAAAGAGGAAGTCTTATCCGAAC 59.067 40.000 0.00 0.00 45.44 3.95
5573 6090 5.932303 CACAAAAGAGGAAGTCTTATCCGAA 59.068 40.000 0.00 0.00 45.44 4.30
5574 6091 5.245301 TCACAAAAGAGGAAGTCTTATCCGA 59.755 40.000 0.00 0.00 45.44 4.55
5575 6092 5.348997 GTCACAAAAGAGGAAGTCTTATCCG 59.651 44.000 0.00 0.00 45.44 4.18
5576 6093 6.729391 GTCACAAAAGAGGAAGTCTTATCC 57.271 41.667 0.00 0.00 45.44 2.59


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

AutoCloner maintained by Alex Coulton.