Multiple sequence alignment - TraesCS2D01G051000

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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 TraesCS2D01G051000 chr2D 100.000 3172 0 0 1 3172 19242048 19238877 0.000000e+00 5858.0
1 TraesCS2D01G051000 chr2D 90.116 2590 153 33 649 3172 19534596 19532044 0.000000e+00 3269.0
2 TraesCS2D01G051000 chr2D 83.067 939 122 25 2199 3133 19561555 19560650 0.000000e+00 819.0
3 TraesCS2D01G051000 chr2D 83.934 722 99 9 2278 2995 19529253 19528545 0.000000e+00 675.0
4 TraesCS2D01G051000 chr2D 100.000 231 0 0 3549 3779 19238500 19238270 9.700000e-116 427.0
5 TraesCS2D01G051000 chr2D 83.607 427 38 12 1043 1445 19563425 19563007 4.610000e-99 372.0
6 TraesCS2D01G051000 chr2D 92.760 221 12 3 3561 3779 19531971 19531753 2.190000e-82 316.0
7 TraesCS2D01G051000 chr2D 86.800 250 25 3 1548 1791 19562987 19562740 4.810000e-69 272.0
8 TraesCS2D01G051000 chr2D 87.879 165 18 2 1789 1951 572684769 572684605 3.850000e-45 193.0
9 TraesCS2D01G051000 chr2D 86.747 166 19 3 1788 1951 22450793 22450957 8.340000e-42 182.0
10 TraesCS2D01G051000 chr2D 86.466 133 8 5 509 640 19534662 19534539 1.830000e-28 137.0
11 TraesCS2D01G051000 chr2A 90.453 2472 117 41 642 3062 20592161 20594564 0.000000e+00 3147.0
12 TraesCS2D01G051000 chr2A 91.950 646 38 7 1 642 20591592 20592227 0.000000e+00 893.0
13 TraesCS2D01G051000 chr2A 84.101 868 114 18 2128 2994 20604487 20605331 0.000000e+00 817.0
14 TraesCS2D01G051000 chr2A 83.563 870 118 19 2128 2994 20385380 20384533 0.000000e+00 791.0
15 TraesCS2D01G051000 chr2A 80.697 746 76 34 1006 1727 20386643 20385942 5.600000e-143 518.0
16 TraesCS2D01G051000 chr2A 80.915 503 49 18 1243 1721 20603318 20603797 1.670000e-93 353.0
17 TraesCS2D01G051000 chr2A 94.017 234 8 3 3552 3779 20600682 20600915 2.160000e-92 350.0
18 TraesCS2D01G051000 chr2A 98.039 102 1 1 3064 3164 20600263 20600364 3.880000e-40 176.0
19 TraesCS2D01G051000 chr2A 84.940 166 18 4 1085 1249 20602980 20603139 1.090000e-35 161.0
20 TraesCS2D01G051000 chr2A 100.000 28 0 0 300 327 589003757 589003730 7.000000e-03 52.8
21 TraesCS2D01G051000 chr2B 87.625 1099 72 18 787 1857 32125683 32124621 0.000000e+00 1218.0
22 TraesCS2D01G051000 chr2B 89.724 652 46 10 1 640 32126333 32125691 0.000000e+00 813.0
23 TraesCS2D01G051000 chr2B 90.395 583 52 4 2146 2726 32124367 32123787 0.000000e+00 763.0
24 TraesCS2D01G051000 chr2B 96.471 85 3 0 642 726 32125755 32125671 1.420000e-29 141.0
25 TraesCS2D01G051000 chr2B 100.000 28 0 0 300 327 525077132 525077105 7.000000e-03 52.8
26 TraesCS2D01G051000 chr3D 83.600 939 119 23 2199 3133 589667440 589668347 0.000000e+00 848.0
27 TraesCS2D01G051000 chr3D 85.480 427 34 11 649 1047 589706367 589706793 1.620000e-113 420.0
28 TraesCS2D01G051000 chr3D 89.231 195 17 2 1599 1791 589666566 589666758 1.360000e-59 241.0
29 TraesCS2D01G051000 chr3D 89.231 195 17 2 1599 1791 589710243 589710435 1.360000e-59 241.0
30 TraesCS2D01G051000 chr3D 86.466 133 8 5 509 640 589706301 589706424 1.830000e-28 137.0
31 TraesCS2D01G051000 chr3D 87.255 102 13 0 946 1047 589663393 589663494 2.380000e-22 117.0
32 TraesCS2D01G051000 chr1D 88.511 235 24 2 1554 1788 392563560 392563791 7.990000e-72 281.0
33 TraesCS2D01G051000 chr6A 87.879 165 18 1 1789 1951 108947864 108947700 3.850000e-45 193.0
34 TraesCS2D01G051000 chr5B 87.273 165 19 1 1789 1951 472754843 472754679 1.790000e-43 187.0
35 TraesCS2D01G051000 chr5A 86.747 166 20 1 1788 1951 529307306 529307141 2.320000e-42 183.0
36 TraesCS2D01G051000 chr6D 86.667 165 20 1 1789 1951 90112238 90112402 8.340000e-42 182.0
37 TraesCS2D01G051000 chr5D 86.667 165 20 1 1789 1951 391992735 391992571 8.340000e-42 182.0


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 TraesCS2D01G051000 chr2D 19238270 19242048 3778 True 3142.500000 5858 100.000000 1 3779 2 chr2D.!!$R2 3778
1 TraesCS2D01G051000 chr2D 19528545 19534662 6117 True 1099.250000 3269 88.319000 509 3779 4 chr2D.!!$R3 3270
2 TraesCS2D01G051000 chr2D 19560650 19563425 2775 True 487.666667 819 84.491333 1043 3133 3 chr2D.!!$R4 2090
3 TraesCS2D01G051000 chr2A 20591592 20594564 2972 False 2020.000000 3147 91.201500 1 3062 2 chr2A.!!$F1 3061
4 TraesCS2D01G051000 chr2A 20384533 20386643 2110 True 654.500000 791 82.130000 1006 2994 2 chr2A.!!$R2 1988
5 TraesCS2D01G051000 chr2A 20600263 20605331 5068 False 371.400000 817 88.402400 1085 3779 5 chr2A.!!$F2 2694
6 TraesCS2D01G051000 chr2B 32123787 32126333 2546 True 733.750000 1218 91.053750 1 2726 4 chr2B.!!$R2 2725
7 TraesCS2D01G051000 chr3D 589663393 589668347 4954 False 402.000000 848 86.695333 946 3133 3 chr3D.!!$F1 2187
8 TraesCS2D01G051000 chr3D 589706301 589710435 4134 False 266.000000 420 87.059000 509 1791 3 chr3D.!!$F2 1282

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
607 619 0.173708 TGCGTGCCACGTATATGTCA 59.826 50.0 19.57 3.14 44.73 3.58 F
621 633 0.321653 ATGTCACTTTCCCGGTCAGC 60.322 55.0 0.00 0.00 0.00 4.26 F
623 635 0.321653 GTCACTTTCCCGGTCAGCAT 60.322 55.0 0.00 0.00 0.00 3.79 F
1030 1070 0.321671 ACTAGCAAGTGCATCCGTGT 59.678 50.0 6.00 0.00 45.16 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 9116 1.013596 TTTGGTCATCAATAGGCGCG 58.986 50.000 0.00 0.0 34.98 6.86 R
2186 10142 5.873179 TCAATAGTCACGGATTCAAAACC 57.127 39.130 0.00 0.0 0.00 3.27 R
2212 10168 8.019656 ACCTGTAAATAGAACTACCACTATGG 57.980 38.462 0.00 0.0 45.02 2.74 R
2938 14616 2.747446 AGACCAACGTCATACAATTGCC 59.253 45.455 5.05 0.0 41.87 4.52 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
62 67 7.420800 CAGTAGATTCTTGTTTTGCTGTTCTT 58.579 34.615 0.00 0.00 0.00 2.52
97 102 7.102847 ACTATTTCTGGTTTTGTTTTTCCGA 57.897 32.000 0.00 0.00 0.00 4.55
98 103 7.548967 ACTATTTCTGGTTTTGTTTTTCCGAA 58.451 30.769 0.00 0.00 0.00 4.30
99 104 6.656314 ATTTCTGGTTTTGTTTTTCCGAAC 57.344 33.333 0.00 0.00 0.00 3.95
100 105 4.112716 TCTGGTTTTGTTTTTCCGAACC 57.887 40.909 0.00 0.00 40.06 3.62
101 106 3.764972 TCTGGTTTTGTTTTTCCGAACCT 59.235 39.130 5.32 0.00 40.25 3.50
102 107 4.221041 TCTGGTTTTGTTTTTCCGAACCTT 59.779 37.500 5.32 0.00 40.25 3.50
251 259 7.316640 TGATCTAGTTCTCAACTAACTGAAGC 58.683 38.462 2.61 0.00 42.99 3.86
255 263 8.150945 TCTAGTTCTCAACTAACTGAAGCATTT 58.849 33.333 0.00 0.00 42.99 2.32
256 264 7.195839 AGTTCTCAACTAACTGAAGCATTTC 57.804 36.000 0.00 0.00 40.69 2.17
268 277 2.997485 AGCATTTCTTTCGGAGCAAC 57.003 45.000 0.00 0.00 0.00 4.17
273 282 4.148871 GCATTTCTTTCGGAGCAACTTTTC 59.851 41.667 0.00 0.00 0.00 2.29
294 303 4.151121 TCAATTTTCATGTGCTCCCTTCA 58.849 39.130 0.00 0.00 0.00 3.02
489 500 6.933521 CCAAACATATGAGGAGGTCTGATAAG 59.066 42.308 10.38 0.00 0.00 1.73
499 510 1.068194 GGTCTGATAAGCCCGATCGAG 60.068 57.143 18.66 3.84 0.00 4.04
500 511 1.880675 GTCTGATAAGCCCGATCGAGA 59.119 52.381 18.66 5.69 0.00 4.04
519 530 5.029014 CGAGACGTCCTCATACAGTAAAAG 58.971 45.833 13.01 0.00 42.06 2.27
531 543 9.462174 CTCATACAGTAAAAGATCATCTCACTC 57.538 37.037 0.00 0.00 0.00 3.51
580 592 2.555220 CGAACCGCGTATATCTTTGC 57.445 50.000 4.92 0.00 34.64 3.68
581 593 2.124903 CGAACCGCGTATATCTTTGCT 58.875 47.619 4.92 0.00 34.64 3.91
583 595 1.217882 ACCGCGTATATCTTTGCTGC 58.782 50.000 4.92 0.00 0.00 5.25
584 596 1.202533 ACCGCGTATATCTTTGCTGCT 60.203 47.619 4.92 0.00 0.00 4.24
585 597 1.867233 CCGCGTATATCTTTGCTGCTT 59.133 47.619 4.92 0.00 0.00 3.91
586 598 2.096713 CCGCGTATATCTTTGCTGCTTC 60.097 50.000 4.92 0.00 0.00 3.86
587 599 2.408991 CGCGTATATCTTTGCTGCTTCG 60.409 50.000 0.00 0.00 0.00 3.79
588 600 2.540101 GCGTATATCTTTGCTGCTTCGT 59.460 45.455 0.00 0.00 0.00 3.85
589 601 3.602491 GCGTATATCTTTGCTGCTTCGTG 60.602 47.826 0.00 0.00 0.00 4.35
591 603 0.721154 TATCTTTGCTGCTTCGTGCG 59.279 50.000 0.00 0.00 46.63 5.34
593 605 1.723542 CTTTGCTGCTTCGTGCGTG 60.724 57.895 0.00 0.00 46.63 5.34
594 606 3.805385 TTTGCTGCTTCGTGCGTGC 62.805 57.895 0.00 11.29 46.63 5.34
597 609 4.374702 CTGCTTCGTGCGTGCCAC 62.375 66.667 8.91 0.00 46.63 5.01
605 617 2.673074 GTGCGTGCCACGTATATGT 58.327 52.632 19.57 0.00 44.73 2.29
606 618 0.575390 GTGCGTGCCACGTATATGTC 59.425 55.000 19.57 0.21 44.73 3.06
607 619 0.173708 TGCGTGCCACGTATATGTCA 59.826 50.000 19.57 3.14 44.73 3.58
608 620 0.575390 GCGTGCCACGTATATGTCAC 59.425 55.000 19.57 6.79 44.73 3.67
609 621 1.801395 GCGTGCCACGTATATGTCACT 60.801 52.381 19.57 0.00 44.73 3.41
611 623 2.927477 CGTGCCACGTATATGTCACTTT 59.073 45.455 9.53 0.00 36.74 2.66
614 626 2.870411 GCCACGTATATGTCACTTTCCC 59.130 50.000 0.00 0.00 0.00 3.97
615 627 3.120792 CCACGTATATGTCACTTTCCCG 58.879 50.000 0.00 0.00 0.00 5.14
616 628 3.120792 CACGTATATGTCACTTTCCCGG 58.879 50.000 0.00 0.00 0.00 5.73
618 630 3.181483 ACGTATATGTCACTTTCCCGGTC 60.181 47.826 0.00 0.00 0.00 4.79
620 632 3.543680 ATATGTCACTTTCCCGGTCAG 57.456 47.619 0.00 0.00 0.00 3.51
621 633 0.321653 ATGTCACTTTCCCGGTCAGC 60.322 55.000 0.00 0.00 0.00 4.26
622 634 1.070786 GTCACTTTCCCGGTCAGCA 59.929 57.895 0.00 0.00 0.00 4.41
623 635 0.321653 GTCACTTTCCCGGTCAGCAT 60.322 55.000 0.00 0.00 0.00 3.79
624 636 1.066430 GTCACTTTCCCGGTCAGCATA 60.066 52.381 0.00 0.00 0.00 3.14
626 638 3.035363 TCACTTTCCCGGTCAGCATATA 58.965 45.455 0.00 0.00 0.00 0.86
629 641 3.391296 ACTTTCCCGGTCAGCATATATGT 59.609 43.478 14.14 0.00 0.00 2.29
631 643 2.604139 TCCCGGTCAGCATATATGTCA 58.396 47.619 14.14 0.00 0.00 3.58
632 644 3.173151 TCCCGGTCAGCATATATGTCAT 58.827 45.455 14.14 0.00 0.00 3.06
634 646 3.935203 CCCGGTCAGCATATATGTCATTC 59.065 47.826 14.14 0.00 0.00 2.67
638 650 5.064325 CGGTCAGCATATATGTCATTCCATG 59.936 44.000 14.14 0.00 0.00 3.66
640 652 4.945543 TCAGCATATATGTCATTCCATGGC 59.054 41.667 14.14 0.00 34.88 4.40
641 653 4.097437 CAGCATATATGTCATTCCATGGCC 59.903 45.833 14.14 0.00 32.84 5.36
643 655 4.708421 GCATATATGTCATTCCATGGCCTT 59.292 41.667 14.14 0.00 32.84 4.35
644 656 5.186409 GCATATATGTCATTCCATGGCCTTT 59.814 40.000 14.14 0.00 32.84 3.11
645 657 6.627243 CATATATGTCATTCCATGGCCTTTG 58.373 40.000 6.96 1.15 32.84 2.77
766 786 3.377172 AGTTGCACAGTTGTTGTTACTCC 59.623 43.478 0.00 0.00 38.16 3.85
920 959 1.537638 GCTCTCTCAGTCGTCTCACAA 59.462 52.381 0.00 0.00 0.00 3.33
1030 1070 0.321671 ACTAGCAAGTGCATCCGTGT 59.678 50.000 6.00 0.00 45.16 4.49
1055 7511 4.831155 TGCATGACCCCTAGTACTACATAC 59.169 45.833 0.00 0.00 0.00 2.39
1092 7548 6.294473 CAGAATCCCATATGGCCATATACTC 58.706 44.000 32.92 23.22 33.01 2.59
1265 7908 2.490148 CGACCTCGCCATCAGCCTA 61.490 63.158 0.00 0.00 38.78 3.93
1311 7954 1.448540 GGTGTCATGTCCAGGCTCG 60.449 63.158 0.00 0.00 0.00 5.03
1445 8112 7.044798 AGAGAAGGTTCGAATTCTTCCAATAG 58.955 38.462 26.40 0.00 38.03 1.73
1573 8250 6.839124 ATGTTTGCATTTCAGGTATCTCAA 57.161 33.333 0.00 0.00 29.54 3.02
1646 8323 4.096532 ACGACAAGCGATCAAGATCTCTTA 59.903 41.667 13.22 0.00 39.91 2.10
1721 8400 2.193127 ACATCAACGGGAGGGAACATA 58.807 47.619 0.00 0.00 0.00 2.29
1850 8814 7.400599 TCCAATATGGACTACATACGGATAC 57.599 40.000 0.00 0.00 42.67 2.24
1851 8815 6.949463 TCCAATATGGACTACATACGGATACA 59.051 38.462 0.00 0.00 42.67 2.29
2088 9107 1.225991 GTGTGCGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2089 9108 1.669437 TGTGCGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2090 9109 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2092 9111 3.097672 CGTGTGTGTGTGTGTGGG 58.902 61.111 0.00 0.00 0.00 4.61
2093 9112 2.798009 GTGTGTGTGTGTGTGGGC 59.202 61.111 0.00 0.00 0.00 5.36
2094 9113 2.821810 TGTGTGTGTGTGTGGGCG 60.822 61.111 0.00 0.00 0.00 6.13
2212 10168 7.908601 GGTTTTGAATCCGTGACTATTGATAAC 59.091 37.037 0.00 0.00 0.00 1.89
2862 14539 0.931005 GGATCGTTCAGCCGTGATTC 59.069 55.000 0.00 0.00 30.85 2.52
2938 14616 0.468029 AAACAACAGTGCAGAGGGGG 60.468 55.000 0.00 0.00 0.00 5.40
3097 14776 2.425668 CTCGAAACCCAGGTGTGTTTTT 59.574 45.455 0.00 0.00 34.97 1.94
3127 14806 2.396590 TTCAGTACGAAATCAGGGGC 57.603 50.000 0.00 0.00 0.00 5.80
3133 14812 4.098960 CAGTACGAAATCAGGGGCTAGTTA 59.901 45.833 0.00 0.00 0.00 2.24
3134 14813 4.713321 AGTACGAAATCAGGGGCTAGTTAA 59.287 41.667 0.00 0.00 0.00 2.01
3135 14814 4.772886 ACGAAATCAGGGGCTAGTTAAT 57.227 40.909 0.00 0.00 0.00 1.40
3136 14815 4.451900 ACGAAATCAGGGGCTAGTTAATG 58.548 43.478 0.00 0.00 0.00 1.90
3137 14816 4.080526 ACGAAATCAGGGGCTAGTTAATGT 60.081 41.667 0.00 0.00 0.00 2.71
3138 14817 4.881850 CGAAATCAGGGGCTAGTTAATGTT 59.118 41.667 0.00 0.00 0.00 2.71
3139 14818 6.053005 CGAAATCAGGGGCTAGTTAATGTTA 58.947 40.000 0.00 0.00 0.00 2.41
3140 14819 6.540914 CGAAATCAGGGGCTAGTTAATGTTAA 59.459 38.462 0.00 0.00 0.00 2.01
3141 14820 7.066525 CGAAATCAGGGGCTAGTTAATGTTAAA 59.933 37.037 0.00 0.00 0.00 1.52
3142 14821 8.658840 AAATCAGGGGCTAGTTAATGTTAAAA 57.341 30.769 0.00 0.00 0.00 1.52
3143 14822 8.658840 AATCAGGGGCTAGTTAATGTTAAAAA 57.341 30.769 0.00 0.00 0.00 1.94
3169 14848 3.061093 GCTAGTTGCCCCTAACGTC 57.939 57.895 0.00 0.00 35.73 4.34
3170 14849 0.535797 GCTAGTTGCCCCTAACGTCT 59.464 55.000 0.00 0.00 35.73 4.18
3171 14850 1.753073 GCTAGTTGCCCCTAACGTCTA 59.247 52.381 0.00 0.00 35.73 2.59
3573 15252 8.824159 CAATCGGATACAAATGAGTAGATTCT 57.176 34.615 0.00 0.00 0.00 2.40
3574 15253 9.914131 CAATCGGATACAAATGAGTAGATTCTA 57.086 33.333 0.00 0.00 0.00 2.10
3584 15263 9.708222 CAAATGAGTAGATTCTAAATGTTTCGG 57.292 33.333 0.00 0.00 0.00 4.30
3585 15264 8.438676 AATGAGTAGATTCTAAATGTTTCGGG 57.561 34.615 0.00 0.00 0.00 5.14
3586 15265 7.177832 TGAGTAGATTCTAAATGTTTCGGGA 57.822 36.000 0.00 0.00 0.00 5.14
3587 15266 7.617225 TGAGTAGATTCTAAATGTTTCGGGAA 58.383 34.615 0.00 0.00 0.00 3.97
3588 15267 7.764443 TGAGTAGATTCTAAATGTTTCGGGAAG 59.236 37.037 0.00 0.00 0.00 3.46
3589 15268 7.048512 AGTAGATTCTAAATGTTTCGGGAAGG 58.951 38.462 0.00 0.00 0.00 3.46
3590 15269 4.640647 AGATTCTAAATGTTTCGGGAAGGC 59.359 41.667 0.00 0.00 0.00 4.35
3591 15270 3.713826 TCTAAATGTTTCGGGAAGGCT 57.286 42.857 0.00 0.00 0.00 4.58
3592 15271 4.829872 TCTAAATGTTTCGGGAAGGCTA 57.170 40.909 0.00 0.00 0.00 3.93
3593 15272 5.367945 TCTAAATGTTTCGGGAAGGCTAT 57.632 39.130 0.00 0.00 0.00 2.97
3594 15273 5.365619 TCTAAATGTTTCGGGAAGGCTATC 58.634 41.667 0.00 0.00 0.00 2.08
3595 15274 3.933861 AATGTTTCGGGAAGGCTATCT 57.066 42.857 0.00 0.00 0.00 1.98
3596 15275 3.933861 ATGTTTCGGGAAGGCTATCTT 57.066 42.857 0.00 0.00 38.65 2.40
3607 15286 3.274095 AGGCTATCTTCCTTCTGTTGC 57.726 47.619 0.00 0.00 0.00 4.17
3608 15287 2.573462 AGGCTATCTTCCTTCTGTTGCA 59.427 45.455 0.00 0.00 0.00 4.08
3609 15288 2.941720 GGCTATCTTCCTTCTGTTGCAG 59.058 50.000 0.00 0.00 0.00 4.41
3610 15289 2.941720 GCTATCTTCCTTCTGTTGCAGG 59.058 50.000 0.00 0.00 31.51 4.85
3611 15290 1.831580 ATCTTCCTTCTGTTGCAGGC 58.168 50.000 0.00 0.00 31.51 4.85
3612 15291 0.767375 TCTTCCTTCTGTTGCAGGCT 59.233 50.000 0.00 0.00 31.51 4.58
3613 15292 1.143684 TCTTCCTTCTGTTGCAGGCTT 59.856 47.619 0.00 0.00 31.51 4.35
3614 15293 1.959282 CTTCCTTCTGTTGCAGGCTTT 59.041 47.619 0.00 0.00 31.51 3.51
3615 15294 2.071778 TCCTTCTGTTGCAGGCTTTT 57.928 45.000 0.00 0.00 31.51 2.27
3616 15295 3.222173 TCCTTCTGTTGCAGGCTTTTA 57.778 42.857 0.00 0.00 31.51 1.52
3617 15296 3.766545 TCCTTCTGTTGCAGGCTTTTAT 58.233 40.909 0.00 0.00 31.51 1.40
3618 15297 4.151883 TCCTTCTGTTGCAGGCTTTTATT 58.848 39.130 0.00 0.00 31.51 1.40
3619 15298 4.588528 TCCTTCTGTTGCAGGCTTTTATTT 59.411 37.500 0.00 0.00 31.51 1.40
3620 15299 5.070313 TCCTTCTGTTGCAGGCTTTTATTTT 59.930 36.000 0.00 0.00 31.51 1.82
3621 15300 5.759763 CCTTCTGTTGCAGGCTTTTATTTTT 59.240 36.000 0.00 0.00 31.51 1.94
3644 15323 7.889873 TTTTCTTGTATTTTCTTGGACCTCA 57.110 32.000 0.00 0.00 0.00 3.86
3645 15324 7.889873 TTTCTTGTATTTTCTTGGACCTCAA 57.110 32.000 0.00 0.00 0.00 3.02
3646 15325 8.477419 TTTCTTGTATTTTCTTGGACCTCAAT 57.523 30.769 0.00 0.00 34.45 2.57
3647 15326 8.477419 TTCTTGTATTTTCTTGGACCTCAATT 57.523 30.769 0.00 0.00 34.45 2.32
3648 15327 8.477419 TCTTGTATTTTCTTGGACCTCAATTT 57.523 30.769 0.00 0.00 34.45 1.82
3649 15328 8.576442 TCTTGTATTTTCTTGGACCTCAATTTC 58.424 33.333 0.00 0.00 34.45 2.17
3650 15329 7.227049 TGTATTTTCTTGGACCTCAATTTCC 57.773 36.000 0.00 0.00 34.45 3.13
3651 15330 4.846779 TTTTCTTGGACCTCAATTTCCG 57.153 40.909 0.00 0.00 34.24 4.30
3652 15331 3.502123 TTCTTGGACCTCAATTTCCGT 57.498 42.857 0.00 0.00 34.24 4.69
3653 15332 4.627284 TTCTTGGACCTCAATTTCCGTA 57.373 40.909 0.00 0.00 34.24 4.02
3654 15333 3.934068 TCTTGGACCTCAATTTCCGTAC 58.066 45.455 0.00 0.00 34.24 3.67
3655 15334 3.325425 TCTTGGACCTCAATTTCCGTACA 59.675 43.478 0.00 0.00 34.24 2.90
3656 15335 3.992943 TGGACCTCAATTTCCGTACAT 57.007 42.857 0.00 0.00 34.24 2.29
3657 15336 4.295141 TGGACCTCAATTTCCGTACATT 57.705 40.909 0.00 0.00 34.24 2.71
3658 15337 5.423704 TGGACCTCAATTTCCGTACATTA 57.576 39.130 0.00 0.00 34.24 1.90
3659 15338 5.180271 TGGACCTCAATTTCCGTACATTAC 58.820 41.667 0.00 0.00 34.24 1.89
3660 15339 4.573607 GGACCTCAATTTCCGTACATTACC 59.426 45.833 0.00 0.00 0.00 2.85
3661 15340 5.425630 GACCTCAATTTCCGTACATTACCT 58.574 41.667 0.00 0.00 0.00 3.08
3662 15341 5.812286 ACCTCAATTTCCGTACATTACCTT 58.188 37.500 0.00 0.00 0.00 3.50
3663 15342 5.646360 ACCTCAATTTCCGTACATTACCTTG 59.354 40.000 0.00 0.00 0.00 3.61
3664 15343 5.448632 CCTCAATTTCCGTACATTACCTTGC 60.449 44.000 0.00 0.00 0.00 4.01
3665 15344 4.093703 TCAATTTCCGTACATTACCTTGCG 59.906 41.667 0.00 0.00 0.00 4.85
3666 15345 2.747396 TTCCGTACATTACCTTGCGT 57.253 45.000 0.00 0.00 0.00 5.24
3667 15346 3.865011 TTCCGTACATTACCTTGCGTA 57.135 42.857 0.00 0.00 0.00 4.42
3668 15347 3.865011 TCCGTACATTACCTTGCGTAA 57.135 42.857 0.00 0.00 41.18 3.18
3669 15348 4.389890 TCCGTACATTACCTTGCGTAAT 57.610 40.909 0.00 0.00 46.55 1.89
3679 15358 6.548441 TTACCTTGCGTAATGTAATATGCC 57.452 37.500 9.39 0.00 37.06 4.40
3680 15359 4.714632 ACCTTGCGTAATGTAATATGCCT 58.285 39.130 0.00 0.00 37.06 4.75
3681 15360 4.755123 ACCTTGCGTAATGTAATATGCCTC 59.245 41.667 0.00 0.00 37.06 4.70
3682 15361 4.143115 CCTTGCGTAATGTAATATGCCTCG 60.143 45.833 0.00 0.00 37.06 4.63
3683 15362 3.985008 TGCGTAATGTAATATGCCTCGT 58.015 40.909 0.00 0.00 37.06 4.18
3684 15363 5.123805 TGCGTAATGTAATATGCCTCGTA 57.876 39.130 0.00 0.00 37.06 3.43
3685 15364 5.158494 TGCGTAATGTAATATGCCTCGTAG 58.842 41.667 0.00 0.00 37.06 3.51
3686 15365 5.048573 TGCGTAATGTAATATGCCTCGTAGA 60.049 40.000 0.00 0.00 37.06 2.59
3719 15398 8.530269 AAAATGTAATAGGTATACTGTAGCGC 57.470 34.615 0.00 0.00 0.00 5.92
3720 15399 6.829229 ATGTAATAGGTATACTGTAGCGCA 57.171 37.500 11.47 0.00 0.00 6.09
3721 15400 6.638096 TGTAATAGGTATACTGTAGCGCAA 57.362 37.500 11.47 0.00 0.00 4.85
3722 15401 6.675026 TGTAATAGGTATACTGTAGCGCAAG 58.325 40.000 11.47 6.71 43.44 4.01
3723 15402 4.785511 ATAGGTATACTGTAGCGCAAGG 57.214 45.455 11.47 0.00 38.28 3.61
3724 15403 2.662866 AGGTATACTGTAGCGCAAGGA 58.337 47.619 11.47 0.05 38.28 3.36
3725 15404 2.623889 AGGTATACTGTAGCGCAAGGAG 59.376 50.000 11.47 1.75 38.28 3.69
3726 15405 2.621998 GGTATACTGTAGCGCAAGGAGA 59.378 50.000 11.47 0.00 38.28 3.71
3727 15406 3.256136 GGTATACTGTAGCGCAAGGAGAT 59.744 47.826 11.47 0.00 38.28 2.75
3728 15407 3.651803 ATACTGTAGCGCAAGGAGATC 57.348 47.619 11.47 0.00 38.28 2.75
3729 15408 1.186200 ACTGTAGCGCAAGGAGATCA 58.814 50.000 11.47 0.00 38.28 2.92
3730 15409 1.550524 ACTGTAGCGCAAGGAGATCAA 59.449 47.619 11.47 0.00 38.28 2.57
3731 15410 1.929836 CTGTAGCGCAAGGAGATCAAC 59.070 52.381 11.47 0.00 38.28 3.18
3732 15411 1.550524 TGTAGCGCAAGGAGATCAACT 59.449 47.619 11.47 0.00 38.28 3.16
3733 15412 2.028112 TGTAGCGCAAGGAGATCAACTT 60.028 45.455 11.47 0.00 38.28 2.66
3734 15413 3.194755 TGTAGCGCAAGGAGATCAACTTA 59.805 43.478 11.47 0.00 38.28 2.24
3735 15414 3.550437 AGCGCAAGGAGATCAACTTAT 57.450 42.857 11.47 0.00 38.28 1.73
3736 15415 3.201290 AGCGCAAGGAGATCAACTTATG 58.799 45.455 11.47 0.00 38.28 1.90
3737 15416 3.118629 AGCGCAAGGAGATCAACTTATGA 60.119 43.478 11.47 0.00 39.61 2.15
3738 15417 3.623060 GCGCAAGGAGATCAACTTATGAA 59.377 43.478 0.30 0.00 38.95 2.57
3739 15418 4.274459 GCGCAAGGAGATCAACTTATGAAT 59.726 41.667 0.30 0.00 38.95 2.57
3740 15419 5.559799 GCGCAAGGAGATCAACTTATGAATC 60.560 44.000 0.30 0.00 38.95 2.52
3741 15420 5.757320 CGCAAGGAGATCAACTTATGAATCT 59.243 40.000 0.00 0.00 42.54 2.40
3742 15421 6.925718 CGCAAGGAGATCAACTTATGAATCTA 59.074 38.462 0.00 0.00 42.54 1.98
3743 15422 7.439356 CGCAAGGAGATCAACTTATGAATCTAA 59.561 37.037 0.00 0.00 42.54 2.10
3744 15423 8.555361 GCAAGGAGATCAACTTATGAATCTAAC 58.445 37.037 0.00 0.00 42.54 2.34
3745 15424 9.829507 CAAGGAGATCAACTTATGAATCTAACT 57.170 33.333 0.00 0.00 42.54 2.24
3747 15426 9.206690 AGGAGATCAACTTATGAATCTAACTCA 57.793 33.333 0.00 0.00 42.54 3.41
3748 15427 9.474920 GGAGATCAACTTATGAATCTAACTCAG 57.525 37.037 0.00 0.00 42.54 3.35
3761 15440 9.438228 TGAATCTAACTCAGACTACTATATCCG 57.562 37.037 0.00 0.00 35.62 4.18
3762 15441 9.439500 GAATCTAACTCAGACTACTATATCCGT 57.561 37.037 0.00 0.00 35.62 4.69
3763 15442 9.796180 AATCTAACTCAGACTACTATATCCGTT 57.204 33.333 0.00 0.00 35.62 4.44
3764 15443 9.796180 ATCTAACTCAGACTACTATATCCGTTT 57.204 33.333 0.00 0.00 35.62 3.60
3765 15444 9.053840 TCTAACTCAGACTACTATATCCGTTTG 57.946 37.037 0.00 0.00 0.00 2.93
3766 15445 7.876936 AACTCAGACTACTATATCCGTTTGA 57.123 36.000 0.00 0.00 0.00 2.69
3767 15446 7.261829 ACTCAGACTACTATATCCGTTTGAC 57.738 40.000 0.00 0.00 0.00 3.18
3768 15447 6.018098 ACTCAGACTACTATATCCGTTTGACG 60.018 42.308 0.00 0.00 42.11 4.35
3769 15448 6.051074 TCAGACTACTATATCCGTTTGACGA 58.949 40.000 1.51 0.00 46.05 4.20
3770 15449 6.709397 TCAGACTACTATATCCGTTTGACGAT 59.291 38.462 1.51 0.00 46.05 3.73
3771 15450 7.228108 TCAGACTACTATATCCGTTTGACGATT 59.772 37.037 1.51 0.00 46.05 3.34
3772 15451 7.534578 CAGACTACTATATCCGTTTGACGATTC 59.465 40.741 1.51 0.00 46.05 2.52
3773 15452 7.228108 AGACTACTATATCCGTTTGACGATTCA 59.772 37.037 1.51 0.00 46.05 2.57
3774 15453 7.883217 ACTACTATATCCGTTTGACGATTCAT 58.117 34.615 1.51 0.00 46.05 2.57
3775 15454 9.006839 ACTACTATATCCGTTTGACGATTCATA 57.993 33.333 1.51 0.00 46.05 2.15
3776 15455 9.491934 CTACTATATCCGTTTGACGATTCATAG 57.508 37.037 1.51 6.09 46.05 2.23
3777 15456 7.883217 ACTATATCCGTTTGACGATTCATAGT 58.117 34.615 1.51 6.61 46.05 2.12
3778 15457 8.358148 ACTATATCCGTTTGACGATTCATAGTT 58.642 33.333 1.51 0.00 46.05 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 44 6.858478 GGAAGAACAGCAAAACAAGAATCTAC 59.142 38.462 0.00 0.00 0.00 2.59
62 67 3.780294 ACCAGAAATAGTATGTGCTGGGA 59.220 43.478 21.15 0.00 45.42 4.37
97 102 2.362077 GTCCACATGAAACAGCAAGGTT 59.638 45.455 0.00 0.00 0.00 3.50
98 103 1.956477 GTCCACATGAAACAGCAAGGT 59.044 47.619 0.00 0.00 0.00 3.50
99 104 1.955778 TGTCCACATGAAACAGCAAGG 59.044 47.619 0.00 0.00 0.00 3.61
100 105 3.366679 GGATGTCCACATGAAACAGCAAG 60.367 47.826 0.00 0.00 36.57 4.01
101 106 2.557924 GGATGTCCACATGAAACAGCAA 59.442 45.455 0.00 0.00 36.57 3.91
102 107 2.161855 GGATGTCCACATGAAACAGCA 58.838 47.619 0.00 0.00 36.57 4.41
199 206 3.996480 AGGCCGAAACTATCAATCTAGC 58.004 45.455 0.00 0.00 0.00 3.42
244 252 2.485814 GCTCCGAAAGAAATGCTTCAGT 59.514 45.455 0.00 0.00 35.24 3.41
245 253 2.485426 TGCTCCGAAAGAAATGCTTCAG 59.515 45.455 0.00 0.00 35.24 3.02
251 259 5.280945 TGAAAAGTTGCTCCGAAAGAAATG 58.719 37.500 0.00 0.00 0.00 2.32
255 263 5.514274 AATTGAAAAGTTGCTCCGAAAGA 57.486 34.783 0.00 0.00 0.00 2.52
256 264 6.255453 TGAAAATTGAAAAGTTGCTCCGAAAG 59.745 34.615 0.00 0.00 32.69 2.62
268 277 5.544650 AGGGAGCACATGAAAATTGAAAAG 58.455 37.500 0.00 0.00 0.00 2.27
273 282 4.524316 TGAAGGGAGCACATGAAAATTG 57.476 40.909 0.00 0.00 0.00 2.32
385 396 0.901580 AGGGCATTTGGGTGCTTCAG 60.902 55.000 0.00 0.00 44.45 3.02
390 401 0.323360 TGAGTAGGGCATTTGGGTGC 60.323 55.000 0.00 0.00 44.31 5.01
489 500 3.183776 GAGGACGTCTCGATCGGGC 62.184 68.421 16.41 7.31 32.18 6.13
499 510 6.561614 TGATCTTTTACTGTATGAGGACGTC 58.438 40.000 7.13 7.13 0.00 4.34
500 511 6.525578 TGATCTTTTACTGTATGAGGACGT 57.474 37.500 0.00 0.00 0.00 4.34
519 530 5.375417 ACTGATCGATGAGTGAGATGATC 57.625 43.478 17.11 0.00 34.32 2.92
531 543 1.403382 CGGCTGGGATACTGATCGATG 60.403 57.143 0.54 0.00 32.28 3.84
580 592 4.374702 GTGGCACGCACGAAGCAG 62.375 66.667 0.00 0.00 46.13 4.24
593 605 2.870411 GGGAAAGTGACATATACGTGGC 59.130 50.000 0.00 0.00 0.00 5.01
594 606 3.120792 CGGGAAAGTGACATATACGTGG 58.879 50.000 0.00 0.00 0.00 4.94
595 607 3.120792 CCGGGAAAGTGACATATACGTG 58.879 50.000 0.00 0.00 0.00 4.49
597 609 3.181484 TGACCGGGAAAGTGACATATACG 60.181 47.826 6.32 0.00 0.00 3.06
598 610 4.369182 CTGACCGGGAAAGTGACATATAC 58.631 47.826 6.32 0.00 0.00 1.47
599 611 3.181469 GCTGACCGGGAAAGTGACATATA 60.181 47.826 6.32 0.00 0.00 0.86
600 612 2.420129 GCTGACCGGGAAAGTGACATAT 60.420 50.000 6.32 0.00 0.00 1.78
601 613 1.066430 GCTGACCGGGAAAGTGACATA 60.066 52.381 6.32 0.00 0.00 2.29
603 615 1.070786 GCTGACCGGGAAAGTGACA 59.929 57.895 6.32 0.00 0.00 3.58
604 616 0.321653 ATGCTGACCGGGAAAGTGAC 60.322 55.000 6.32 0.00 0.00 3.67
605 617 1.271856 TATGCTGACCGGGAAAGTGA 58.728 50.000 6.32 0.00 0.00 3.41
606 618 2.332063 ATATGCTGACCGGGAAAGTG 57.668 50.000 6.32 0.00 0.00 3.16
607 619 3.391296 ACATATATGCTGACCGGGAAAGT 59.609 43.478 12.79 0.00 0.00 2.66
608 620 3.997021 GACATATATGCTGACCGGGAAAG 59.003 47.826 12.79 0.39 0.00 2.62
609 621 3.389656 TGACATATATGCTGACCGGGAAA 59.610 43.478 12.79 0.00 0.00 3.13
611 623 2.604139 TGACATATATGCTGACCGGGA 58.396 47.619 12.79 0.00 0.00 5.14
614 626 4.568956 TGGAATGACATATATGCTGACCG 58.431 43.478 12.79 0.00 0.00 4.79
621 633 8.931089 AGCAAAGGCCATGGAATGACATATATG 61.931 40.741 18.40 11.29 46.28 1.78
622 634 6.978906 AGCAAAGGCCATGGAATGACATATAT 60.979 38.462 18.40 0.00 46.28 0.86
623 635 5.693592 AGCAAAGGCCATGGAATGACATATA 60.694 40.000 18.40 0.00 46.28 0.86
624 636 4.938444 AGCAAAGGCCATGGAATGACATAT 60.938 41.667 18.40 0.00 46.28 1.78
626 638 2.891026 AGCAAAGGCCATGGAATGACAT 60.891 45.455 18.40 0.00 46.28 3.06
629 641 1.187974 CAGCAAAGGCCATGGAATGA 58.812 50.000 18.40 0.00 46.28 2.57
631 643 0.616679 AGCAGCAAAGGCCATGGAAT 60.617 50.000 18.40 0.00 42.56 3.01
632 644 0.832983 AAGCAGCAAAGGCCATGGAA 60.833 50.000 18.40 0.00 42.56 3.53
634 646 1.217244 GAAGCAGCAAAGGCCATGG 59.783 57.895 7.63 7.63 42.56 3.66
638 650 2.968206 CAGGAAGCAGCAAAGGCC 59.032 61.111 0.00 0.00 42.56 5.19
640 652 2.263741 ACGCAGGAAGCAGCAAAGG 61.264 57.895 0.00 0.00 46.13 3.11
641 653 1.081641 CACGCAGGAAGCAGCAAAG 60.082 57.895 0.00 0.00 46.13 2.77
643 655 3.663176 GCACGCAGGAAGCAGCAA 61.663 61.111 0.00 0.00 46.13 3.91
747 767 3.118408 AGAGGAGTAACAACAACTGTGCA 60.118 43.478 0.00 0.00 38.67 4.57
766 786 0.952280 GGTGCATGCATCCATCAGAG 59.048 55.000 25.64 0.00 0.00 3.35
870 909 1.058404 GTACGAGACGTTTGACTGGC 58.942 55.000 1.53 0.00 41.54 4.85
920 959 5.464030 AACAGAAAAGAAAGAGCATGCAT 57.536 34.783 21.98 4.82 0.00 3.96
1030 1070 5.069518 TGTAGTACTAGGGGTCATGCATA 57.930 43.478 1.87 0.00 0.00 3.14
1055 7511 3.335356 ATTCTGCGGGTGCCCTCAG 62.335 63.158 18.53 18.53 46.96 3.35
1072 7528 5.797305 AGAGAGTATATGGCCATATGGGAT 58.203 41.667 37.86 24.78 40.01 3.85
1260 7903 2.794981 CGATCACGTCGTCAAATAGGCT 60.795 50.000 0.00 0.00 45.19 4.58
1311 7954 0.470341 GCTTGGGTACTGATCCCCTC 59.530 60.000 6.36 0.00 44.00 4.30
1380 8047 2.690497 TCATAGGCTTCTCCTCTTGTCG 59.310 50.000 0.00 0.00 43.20 4.35
1465 8135 9.299963 CAAGAACCATATTAATCAATTCGCAAA 57.700 29.630 0.00 0.00 0.00 3.68
1485 8155 8.514594 TGATCCAATTTGAATGTAGACAAGAAC 58.485 33.333 0.00 0.00 0.00 3.01
1721 8400 7.954056 TGCTTAGTGGTAATATAGATACCTGGT 59.046 37.037 4.05 4.05 42.73 4.00
1877 8841 7.888021 ACAAACTATATGGACCAAAATGAGTGA 59.112 33.333 0.00 0.00 0.00 3.41
1962 8981 9.504710 GATGATTTCTGAGAACAATCTTGAATG 57.495 33.333 8.00 0.00 35.54 2.67
2093 9112 4.707840 CATCAATAGGCGCGCGCG 62.708 66.667 45.73 45.73 43.06 6.86
2094 9113 3.337889 TCATCAATAGGCGCGCGC 61.338 61.111 44.40 44.40 41.06 6.86
2096 9115 1.436195 TTGGTCATCAATAGGCGCGC 61.436 55.000 25.94 25.94 0.00 6.86
2097 9116 1.013596 TTTGGTCATCAATAGGCGCG 58.986 50.000 0.00 0.00 34.98 6.86
2186 10142 5.873179 TCAATAGTCACGGATTCAAAACC 57.127 39.130 0.00 0.00 0.00 3.27
2212 10168 8.019656 ACCTGTAAATAGAACTACCACTATGG 57.980 38.462 0.00 0.00 45.02 2.74
2390 10367 9.458374 GTACACAACAATATACTTTGCAGTTTT 57.542 29.630 0.00 0.00 34.06 2.43
2654 10634 5.733620 TTCCGAGACATTGGTAAACTAGT 57.266 39.130 0.00 0.00 0.00 2.57
2664 10646 3.264947 TCTGCTCATTTCCGAGACATTG 58.735 45.455 0.00 0.00 34.79 2.82
2938 14616 2.747446 AGACCAACGTCATACAATTGCC 59.253 45.455 5.05 0.00 41.87 4.52
2939 14617 5.539582 TTAGACCAACGTCATACAATTGC 57.460 39.130 5.05 0.00 41.87 3.56
3055 14734 9.912634 TTCGAGAAAATTTTGCTTATGAAAGAT 57.087 25.926 8.47 0.00 34.37 2.40
3056 14735 9.743057 TTTCGAGAAAATTTTGCTTATGAAAGA 57.257 25.926 8.47 0.00 34.37 2.52
3057 14736 9.783425 GTTTCGAGAAAATTTTGCTTATGAAAG 57.217 29.630 8.47 0.00 32.19 2.62
3058 14737 8.760569 GGTTTCGAGAAAATTTTGCTTATGAAA 58.239 29.630 8.47 12.41 31.33 2.69
3061 14740 6.644592 TGGGTTTCGAGAAAATTTTGCTTATG 59.355 34.615 8.47 1.42 31.33 1.90
3062 14741 6.754193 TGGGTTTCGAGAAAATTTTGCTTAT 58.246 32.000 8.47 0.00 31.33 1.73
3063 14742 6.150396 TGGGTTTCGAGAAAATTTTGCTTA 57.850 33.333 8.47 0.00 31.33 3.09
3064 14743 5.017294 TGGGTTTCGAGAAAATTTTGCTT 57.983 34.783 8.47 0.00 31.33 3.91
3065 14744 4.501400 CCTGGGTTTCGAGAAAATTTTGCT 60.501 41.667 8.47 5.44 31.33 3.91
3066 14745 3.740832 CCTGGGTTTCGAGAAAATTTTGC 59.259 43.478 8.47 0.00 31.33 3.68
3067 14746 4.744631 CACCTGGGTTTCGAGAAAATTTTG 59.255 41.667 8.47 0.00 31.33 2.44
3068 14747 4.404394 ACACCTGGGTTTCGAGAAAATTTT 59.596 37.500 2.28 2.28 31.33 1.82
3069 14748 3.958147 ACACCTGGGTTTCGAGAAAATTT 59.042 39.130 0.00 0.00 31.33 1.82
3070 14749 3.317993 CACACCTGGGTTTCGAGAAAATT 59.682 43.478 0.00 0.00 31.33 1.82
3071 14750 2.884639 CACACCTGGGTTTCGAGAAAAT 59.115 45.455 0.00 0.00 31.33 1.82
3115 14794 4.451900 ACATTAACTAGCCCCTGATTTCG 58.548 43.478 0.00 0.00 0.00 3.46
3151 14830 0.535797 AGACGTTAGGGGCAACTAGC 59.464 55.000 0.00 0.00 44.65 3.42
3548 15227 8.824159 AGAATCTACTCATTTGTATCCGATTG 57.176 34.615 0.00 0.00 0.00 2.67
3558 15237 9.708222 CCGAAACATTTAGAATCTACTCATTTG 57.292 33.333 0.00 0.00 0.00 2.32
3559 15238 8.893727 CCCGAAACATTTAGAATCTACTCATTT 58.106 33.333 0.00 0.00 0.00 2.32
3560 15239 8.265055 TCCCGAAACATTTAGAATCTACTCATT 58.735 33.333 0.00 0.00 0.00 2.57
3561 15240 7.792032 TCCCGAAACATTTAGAATCTACTCAT 58.208 34.615 0.00 0.00 0.00 2.90
3562 15241 7.177832 TCCCGAAACATTTAGAATCTACTCA 57.822 36.000 0.00 0.00 0.00 3.41
3563 15242 7.224949 CCTTCCCGAAACATTTAGAATCTACTC 59.775 40.741 0.00 0.00 0.00 2.59
3564 15243 7.048512 CCTTCCCGAAACATTTAGAATCTACT 58.951 38.462 0.00 0.00 0.00 2.57
3565 15244 6.238402 GCCTTCCCGAAACATTTAGAATCTAC 60.238 42.308 0.00 0.00 0.00 2.59
3566 15245 5.820947 GCCTTCCCGAAACATTTAGAATCTA 59.179 40.000 0.00 0.00 0.00 1.98
3567 15246 4.640647 GCCTTCCCGAAACATTTAGAATCT 59.359 41.667 0.00 0.00 0.00 2.40
3568 15247 4.640647 AGCCTTCCCGAAACATTTAGAATC 59.359 41.667 0.00 0.00 0.00 2.52
3569 15248 4.600062 AGCCTTCCCGAAACATTTAGAAT 58.400 39.130 0.00 0.00 0.00 2.40
3570 15249 4.028993 AGCCTTCCCGAAACATTTAGAA 57.971 40.909 0.00 0.00 0.00 2.10
3571 15250 3.713826 AGCCTTCCCGAAACATTTAGA 57.286 42.857 0.00 0.00 0.00 2.10
3572 15251 5.368989 AGATAGCCTTCCCGAAACATTTAG 58.631 41.667 0.00 0.00 0.00 1.85
3573 15252 5.367945 AGATAGCCTTCCCGAAACATTTA 57.632 39.130 0.00 0.00 0.00 1.40
3574 15253 4.236527 AGATAGCCTTCCCGAAACATTT 57.763 40.909 0.00 0.00 0.00 2.32
3575 15254 3.933861 AGATAGCCTTCCCGAAACATT 57.066 42.857 0.00 0.00 0.00 2.71
3576 15255 3.809905 GAAGATAGCCTTCCCGAAACAT 58.190 45.455 0.00 0.00 44.27 2.71
3577 15256 3.261981 GAAGATAGCCTTCCCGAAACA 57.738 47.619 0.00 0.00 44.27 2.83
3587 15266 2.573462 TGCAACAGAAGGAAGATAGCCT 59.427 45.455 0.00 0.00 37.35 4.58
3588 15267 2.941720 CTGCAACAGAAGGAAGATAGCC 59.058 50.000 0.00 0.00 32.44 3.93
3589 15268 2.941720 CCTGCAACAGAAGGAAGATAGC 59.058 50.000 0.00 0.00 35.40 2.97
3590 15269 2.941720 GCCTGCAACAGAAGGAAGATAG 59.058 50.000 0.00 0.00 35.40 2.08
3591 15270 2.573462 AGCCTGCAACAGAAGGAAGATA 59.427 45.455 0.00 0.00 35.40 1.98
3592 15271 1.353694 AGCCTGCAACAGAAGGAAGAT 59.646 47.619 0.00 0.00 35.40 2.40
3593 15272 0.767375 AGCCTGCAACAGAAGGAAGA 59.233 50.000 0.00 0.00 35.40 2.87
3594 15273 1.613836 AAGCCTGCAACAGAAGGAAG 58.386 50.000 0.00 0.00 35.40 3.46
3595 15274 2.071778 AAAGCCTGCAACAGAAGGAA 57.928 45.000 0.00 0.00 35.40 3.36
3596 15275 2.071778 AAAAGCCTGCAACAGAAGGA 57.928 45.000 0.00 0.00 35.40 3.36
3597 15276 4.525912 AATAAAAGCCTGCAACAGAAGG 57.474 40.909 0.00 0.00 32.44 3.46
3598 15277 6.849588 AAAAATAAAAGCCTGCAACAGAAG 57.150 33.333 0.00 0.00 32.44 2.85
3619 15298 8.299990 TGAGGTCCAAGAAAATACAAGAAAAA 57.700 30.769 0.00 0.00 0.00 1.94
3620 15299 7.889873 TGAGGTCCAAGAAAATACAAGAAAA 57.110 32.000 0.00 0.00 0.00 2.29
3621 15300 7.889873 TTGAGGTCCAAGAAAATACAAGAAA 57.110 32.000 0.00 0.00 0.00 2.52
3622 15301 8.477419 AATTGAGGTCCAAGAAAATACAAGAA 57.523 30.769 0.00 0.00 38.31 2.52
3623 15302 8.477419 AAATTGAGGTCCAAGAAAATACAAGA 57.523 30.769 0.00 0.00 38.31 3.02
3624 15303 7.814587 GGAAATTGAGGTCCAAGAAAATACAAG 59.185 37.037 0.00 0.00 38.31 3.16
3625 15304 7.523052 CGGAAATTGAGGTCCAAGAAAATACAA 60.523 37.037 0.00 0.00 38.31 2.41
3626 15305 6.072175 CGGAAATTGAGGTCCAAGAAAATACA 60.072 38.462 0.00 0.00 38.31 2.29
3627 15306 6.072119 ACGGAAATTGAGGTCCAAGAAAATAC 60.072 38.462 0.00 0.00 38.31 1.89
3628 15307 6.007703 ACGGAAATTGAGGTCCAAGAAAATA 58.992 36.000 0.00 0.00 38.31 1.40
3629 15308 4.832823 ACGGAAATTGAGGTCCAAGAAAAT 59.167 37.500 0.00 0.00 38.31 1.82
3630 15309 4.211920 ACGGAAATTGAGGTCCAAGAAAA 58.788 39.130 0.00 0.00 38.31 2.29
3631 15310 3.827722 ACGGAAATTGAGGTCCAAGAAA 58.172 40.909 0.00 0.00 38.31 2.52
3632 15311 3.502123 ACGGAAATTGAGGTCCAAGAA 57.498 42.857 0.00 0.00 38.31 2.52
3633 15312 3.325425 TGTACGGAAATTGAGGTCCAAGA 59.675 43.478 0.00 0.00 38.31 3.02
3634 15313 3.670625 TGTACGGAAATTGAGGTCCAAG 58.329 45.455 0.00 0.00 38.31 3.61
3635 15314 3.773418 TGTACGGAAATTGAGGTCCAA 57.227 42.857 0.00 0.00 39.41 3.53
3636 15315 3.992943 ATGTACGGAAATTGAGGTCCA 57.007 42.857 0.00 0.00 33.10 4.02
3637 15316 4.573607 GGTAATGTACGGAAATTGAGGTCC 59.426 45.833 0.00 0.00 0.00 4.46
3638 15317 5.425630 AGGTAATGTACGGAAATTGAGGTC 58.574 41.667 0.00 0.00 0.00 3.85
3639 15318 5.431179 AGGTAATGTACGGAAATTGAGGT 57.569 39.130 0.00 0.00 0.00 3.85
3640 15319 5.448632 GCAAGGTAATGTACGGAAATTGAGG 60.449 44.000 0.00 0.00 0.00 3.86
3641 15320 5.569413 GCAAGGTAATGTACGGAAATTGAG 58.431 41.667 0.00 0.00 0.00 3.02
3642 15321 4.093703 CGCAAGGTAATGTACGGAAATTGA 59.906 41.667 0.00 0.00 0.00 2.57
3643 15322 4.142773 ACGCAAGGTAATGTACGGAAATTG 60.143 41.667 0.00 0.00 46.39 2.32
3644 15323 4.004982 ACGCAAGGTAATGTACGGAAATT 58.995 39.130 0.00 0.00 46.39 1.82
3645 15324 3.602483 ACGCAAGGTAATGTACGGAAAT 58.398 40.909 0.00 0.00 46.39 2.17
3646 15325 3.042871 ACGCAAGGTAATGTACGGAAA 57.957 42.857 0.00 0.00 46.39 3.13
3647 15326 2.747396 ACGCAAGGTAATGTACGGAA 57.253 45.000 0.00 0.00 46.39 4.30
3648 15327 3.865011 TTACGCAAGGTAATGTACGGA 57.135 42.857 0.00 0.00 46.39 4.69
3656 15335 6.292923 AGGCATATTACATTACGCAAGGTAA 58.707 36.000 7.97 7.97 42.99 2.85
3657 15336 5.860611 AGGCATATTACATTACGCAAGGTA 58.139 37.500 0.00 0.00 46.39 3.08
3658 15337 4.714632 AGGCATATTACATTACGCAAGGT 58.285 39.130 0.00 0.00 46.39 3.50
3659 15338 4.143115 CGAGGCATATTACATTACGCAAGG 60.143 45.833 0.00 0.00 46.39 3.61
3661 15340 4.373527 ACGAGGCATATTACATTACGCAA 58.626 39.130 0.00 0.00 0.00 4.85
3662 15341 3.985008 ACGAGGCATATTACATTACGCA 58.015 40.909 0.00 0.00 0.00 5.24
3663 15342 5.396484 TCTACGAGGCATATTACATTACGC 58.604 41.667 0.00 0.00 0.00 4.42
3664 15343 6.609533 ACTCTACGAGGCATATTACATTACG 58.390 40.000 0.00 0.00 33.35 3.18
3665 15344 7.028361 GGACTCTACGAGGCATATTACATTAC 58.972 42.308 0.00 0.00 39.95 1.89
3666 15345 6.717997 TGGACTCTACGAGGCATATTACATTA 59.282 38.462 0.00 0.00 39.95 1.90
3667 15346 5.538813 TGGACTCTACGAGGCATATTACATT 59.461 40.000 0.00 0.00 39.95 2.71
3668 15347 5.077564 TGGACTCTACGAGGCATATTACAT 58.922 41.667 0.00 0.00 39.95 2.29
3669 15348 4.466827 TGGACTCTACGAGGCATATTACA 58.533 43.478 0.00 0.00 39.95 2.41
3670 15349 5.449107 TTGGACTCTACGAGGCATATTAC 57.551 43.478 0.00 0.00 39.95 1.89
3671 15350 6.474140 TTTTGGACTCTACGAGGCATATTA 57.526 37.500 0.00 0.00 39.95 0.98
3672 15351 5.353394 TTTTGGACTCTACGAGGCATATT 57.647 39.130 0.00 0.00 39.95 1.28
3673 15352 5.353394 TTTTTGGACTCTACGAGGCATAT 57.647 39.130 0.00 0.00 39.95 1.78
3674 15353 4.811969 TTTTTGGACTCTACGAGGCATA 57.188 40.909 0.00 0.00 39.95 3.14
3675 15354 3.695830 TTTTTGGACTCTACGAGGCAT 57.304 42.857 0.00 0.00 39.95 4.40
3693 15372 8.985805 GCGCTACAGTATACCTATTACATTTTT 58.014 33.333 0.00 0.00 0.00 1.94
3694 15373 8.145767 TGCGCTACAGTATACCTATTACATTTT 58.854 33.333 9.73 0.00 0.00 1.82
3695 15374 7.663827 TGCGCTACAGTATACCTATTACATTT 58.336 34.615 9.73 0.00 0.00 2.32
3696 15375 7.223260 TGCGCTACAGTATACCTATTACATT 57.777 36.000 9.73 0.00 0.00 2.71
3697 15376 6.829229 TGCGCTACAGTATACCTATTACAT 57.171 37.500 9.73 0.00 0.00 2.29
3698 15377 6.294342 CCTTGCGCTACAGTATACCTATTACA 60.294 42.308 9.73 0.00 0.00 2.41
3699 15378 6.072286 TCCTTGCGCTACAGTATACCTATTAC 60.072 42.308 9.73 0.00 0.00 1.89
3700 15379 6.005823 TCCTTGCGCTACAGTATACCTATTA 58.994 40.000 9.73 0.00 0.00 0.98
3701 15380 4.831155 TCCTTGCGCTACAGTATACCTATT 59.169 41.667 9.73 0.00 0.00 1.73
3702 15381 4.404640 TCCTTGCGCTACAGTATACCTAT 58.595 43.478 9.73 0.00 0.00 2.57
3703 15382 3.819337 CTCCTTGCGCTACAGTATACCTA 59.181 47.826 9.73 0.00 0.00 3.08
3704 15383 2.623889 CTCCTTGCGCTACAGTATACCT 59.376 50.000 9.73 0.00 0.00 3.08
3705 15384 2.621998 TCTCCTTGCGCTACAGTATACC 59.378 50.000 9.73 0.00 0.00 2.73
3706 15385 3.984508 TCTCCTTGCGCTACAGTATAC 57.015 47.619 9.73 0.00 0.00 1.47
3707 15386 4.142038 TGATCTCCTTGCGCTACAGTATA 58.858 43.478 9.73 0.00 0.00 1.47
3708 15387 2.959030 TGATCTCCTTGCGCTACAGTAT 59.041 45.455 9.73 0.00 0.00 2.12
3709 15388 2.375146 TGATCTCCTTGCGCTACAGTA 58.625 47.619 9.73 0.00 0.00 2.74
3710 15389 1.186200 TGATCTCCTTGCGCTACAGT 58.814 50.000 9.73 0.00 0.00 3.55
3711 15390 1.929836 GTTGATCTCCTTGCGCTACAG 59.070 52.381 9.73 1.45 0.00 2.74
3712 15391 1.550524 AGTTGATCTCCTTGCGCTACA 59.449 47.619 9.73 0.00 0.00 2.74
3713 15392 2.301577 AGTTGATCTCCTTGCGCTAC 57.698 50.000 9.73 0.00 0.00 3.58
3714 15393 4.099419 TCATAAGTTGATCTCCTTGCGCTA 59.901 41.667 9.73 0.00 0.00 4.26
3715 15394 3.118629 TCATAAGTTGATCTCCTTGCGCT 60.119 43.478 9.73 0.00 0.00 5.92
3716 15395 3.198068 TCATAAGTTGATCTCCTTGCGC 58.802 45.455 0.00 0.00 0.00 6.09
3717 15396 5.757320 AGATTCATAAGTTGATCTCCTTGCG 59.243 40.000 7.46 0.00 33.34 4.85
3718 15397 8.555361 GTTAGATTCATAAGTTGATCTCCTTGC 58.445 37.037 7.46 0.00 33.34 4.01
3719 15398 9.829507 AGTTAGATTCATAAGTTGATCTCCTTG 57.170 33.333 7.46 0.00 33.34 3.61
3721 15400 9.206690 TGAGTTAGATTCATAAGTTGATCTCCT 57.793 33.333 0.00 0.00 33.34 3.69
3722 15401 9.474920 CTGAGTTAGATTCATAAGTTGATCTCC 57.525 37.037 0.00 0.00 33.34 3.71
3735 15414 9.438228 CGGATATAGTAGTCTGAGTTAGATTCA 57.562 37.037 0.00 0.00 37.83 2.57
3736 15415 9.439500 ACGGATATAGTAGTCTGAGTTAGATTC 57.561 37.037 0.00 0.00 37.83 2.52
3737 15416 9.796180 AACGGATATAGTAGTCTGAGTTAGATT 57.204 33.333 0.00 0.00 37.83 2.40
3738 15417 9.796180 AAACGGATATAGTAGTCTGAGTTAGAT 57.204 33.333 0.00 0.00 37.83 1.98
3739 15418 9.053840 CAAACGGATATAGTAGTCTGAGTTAGA 57.946 37.037 0.00 0.00 0.00 2.10
3740 15419 9.053840 TCAAACGGATATAGTAGTCTGAGTTAG 57.946 37.037 0.00 0.00 0.00 2.34
3741 15420 8.834465 GTCAAACGGATATAGTAGTCTGAGTTA 58.166 37.037 0.00 0.00 0.00 2.24
3742 15421 7.466996 CGTCAAACGGATATAGTAGTCTGAGTT 60.467 40.741 0.00 0.00 38.08 3.01
3743 15422 6.018098 CGTCAAACGGATATAGTAGTCTGAGT 60.018 42.308 0.00 0.00 38.08 3.41
3744 15423 6.202379 TCGTCAAACGGATATAGTAGTCTGAG 59.798 42.308 0.00 0.00 42.81 3.35
3745 15424 6.051074 TCGTCAAACGGATATAGTAGTCTGA 58.949 40.000 0.00 0.00 42.81 3.27
3746 15425 6.296365 TCGTCAAACGGATATAGTAGTCTG 57.704 41.667 0.00 0.00 42.81 3.51
3747 15426 7.228108 TGAATCGTCAAACGGATATAGTAGTCT 59.772 37.037 0.00 0.00 42.81 3.24
3748 15427 7.358066 TGAATCGTCAAACGGATATAGTAGTC 58.642 38.462 0.00 0.00 42.81 2.59
3749 15428 7.268199 TGAATCGTCAAACGGATATAGTAGT 57.732 36.000 0.00 0.00 42.81 2.73
3750 15429 9.491934 CTATGAATCGTCAAACGGATATAGTAG 57.508 37.037 0.00 0.00 42.81 2.57
3751 15430 9.006839 ACTATGAATCGTCAAACGGATATAGTA 57.993 33.333 12.89 0.00 42.81 1.82
3752 15431 7.883217 ACTATGAATCGTCAAACGGATATAGT 58.117 34.615 0.00 6.69 42.81 2.12
3753 15432 8.744008 AACTATGAATCGTCAAACGGATATAG 57.256 34.615 0.00 6.18 42.81 1.31


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

AutoCloner maintained by Alex Coulton.