Multiple sequence alignment - TraesCS5B01G193300

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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 TraesCS5B01G193300 chr5B 100.000 5967 0 0 1 5967 349186816 349180850 0.000000e+00 11020.0
1 TraesCS5B01G193300 chr5B 100.000 2598 0 0 6179 8776 349180638 349178041 0.000000e+00 4798.0
2 TraesCS5B01G193300 chr5B 84.934 916 117 16 3883 4787 349181755 349180850 0.000000e+00 907.0
3 TraesCS5B01G193300 chr5B 84.934 916 117 16 5062 5967 349182934 349182030 0.000000e+00 907.0
4 TraesCS5B01G193300 chr5B 85.849 106 8 4 6351 6449 137736139 137736034 1.200000e-18 106.0
5 TraesCS5B01G193300 chr5D 97.304 2782 69 6 3188 5966 304495962 304493184 0.000000e+00 4717.0
6 TraesCS5B01G193300 chr5D 93.825 3093 108 29 151 3198 304498978 304495924 0.000000e+00 4577.0
7 TraesCS5B01G193300 chr5D 96.135 2303 60 9 6179 8453 304492749 304490448 0.000000e+00 3733.0
8 TraesCS5B01G193300 chr5D 85.456 942 116 16 3883 4813 304494088 304493157 0.000000e+00 961.0
9 TraesCS5B01G193300 chr5D 85.496 917 109 18 5062 5967 304495268 304494365 0.000000e+00 935.0
10 TraesCS5B01G193300 chr5D 90.850 153 8 1 1 147 304499183 304499031 5.370000e-47 200.0
11 TraesCS5B01G193300 chr5D 83.060 183 16 6 6179 6361 304494251 304494084 1.530000e-32 152.0
12 TraesCS5B01G193300 chr5D 92.941 85 5 1 8549 8633 304490018 304489935 1.200000e-23 122.0
13 TraesCS5B01G193300 chr5D 93.333 75 3 2 8449 8521 304490085 304490011 9.310000e-20 110.0
14 TraesCS5B01G193300 chr5D 82.178 101 11 5 648 746 304498661 304498566 7.300000e-11 80.5
15 TraesCS5B01G193300 chr5A 94.038 2449 83 24 6230 8633 393476213 393478643 0.000000e+00 3655.0
16 TraesCS5B01G193300 chr5A 92.817 2520 94 27 149 2619 393469700 393472181 0.000000e+00 3570.0
17 TraesCS5B01G193300 chr5A 95.395 1368 42 7 3343 4704 393473031 393474383 0.000000e+00 2158.0
18 TraesCS5B01G193300 chr5A 94.650 1271 51 6 4703 5967 393474465 393475724 0.000000e+00 1954.0
19 TraesCS5B01G193300 chr5A 85.760 941 113 16 3885 4814 393474821 393475751 0.000000e+00 976.0
20 TraesCS5B01G193300 chr5A 96.118 541 16 4 2661 3198 393472181 393472719 0.000000e+00 878.0
21 TraesCS5B01G193300 chr5A 84.260 845 108 15 5052 5883 393473551 393474383 0.000000e+00 800.0
22 TraesCS5B01G193300 chr5A 95.506 178 8 0 3183 3360 393472675 393472852 1.440000e-72 285.0
23 TraesCS5B01G193300 chr5A 90.909 154 7 2 1 147 393469500 393469653 5.370000e-47 200.0
24 TraesCS5B01G193300 chr5A 82.857 175 15 6 6179 6351 393474663 393474824 9.180000e-30 143.0
25 TraesCS5B01G193300 chr5A 96.875 64 2 0 6179 6242 393476034 393476097 3.350000e-19 108.0
26 TraesCS5B01G193300 chr5A 81.818 99 11 3 649 746 393470026 393470118 9.450000e-10 76.8
27 TraesCS5B01G193300 chr7D 90.909 88 2 5 6367 6448 498229922 498229835 7.200000e-21 113.0
28 TraesCS5B01G193300 chr7B 90.217 92 2 5 6363 6447 26883101 26883010 7.200000e-21 113.0
29 TraesCS5B01G193300 chr4A 90.805 87 4 4 6366 6449 670947500 670947415 7.200000e-21 113.0
30 TraesCS5B01G193300 chr3B 90.000 90 4 4 6367 6451 55740976 55741065 2.590000e-20 111.0
31 TraesCS5B01G193300 chr3D 88.542 96 4 5 6366 6454 434025881 434025786 9.310000e-20 110.0
32 TraesCS5B01G193300 chr4B 87.500 96 5 4 6362 6450 659147069 659147164 4.330000e-18 104.0


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 TraesCS5B01G193300 chr5B 349178041 349186816 8775 True 7909.00 11020 100.000000 1 8776 2 chr5B.!!$R2 8775
1 TraesCS5B01G193300 chr5B 349180850 349182934 2084 True 907.00 907 84.934000 3883 5967 2 chr5B.!!$R3 2084
2 TraesCS5B01G193300 chr5D 304489935 304499183 9248 True 1558.75 4717 90.057800 1 8633 10 chr5D.!!$R1 8632
3 TraesCS5B01G193300 chr5A 393469500 393478643 9143 False 1233.65 3655 90.916917 1 8633 12 chr5A.!!$F1 8632

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
282 340 0.530650 TCCATGGAGCTCGATTTCGC 60.531 55.000 11.44 0.0 39.60 4.70 F
1027 1143 0.538287 AACTGCCTCCAAGCAAGACC 60.538 55.000 0.00 0.0 43.52 3.85 F
1538 1654 1.134753 TGCCGATGATTTTGGTCATGC 59.865 47.619 0.00 0.0 38.88 4.06 F
1567 1683 1.414181 GGGATCAAGCTTCCTCGATCA 59.586 52.381 20.15 0.0 36.75 2.92 F
3170 3290 0.254747 TAGTTGGAAATCAGGGGGCG 59.745 55.000 0.00 0.0 0.00 6.13 F
3189 3309 0.476771 GGGAGGGTCCACAGTGAAAA 59.523 55.000 0.62 0.0 38.64 2.29 F
3197 3317 1.075374 TCCACAGTGAAAATCAGGGGG 59.925 52.381 0.62 0.0 29.27 5.40 F
3576 3893 1.791785 GCAGACTTAGATCGCTCATGC 59.208 52.381 0.00 0.0 0.00 4.06 F
6765 7564 1.066605 CAGCTAAGCCATCAATGTGCC 59.933 52.381 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1649 0.397941 GATCCCTTCCATCGGCATGA 59.602 55.000 0.00 0.00 30.57 3.07 R
1943 2059 0.967380 CCTTGAGACCCCATGGCAAC 60.967 60.000 6.09 0.00 33.59 4.17 R
3170 3290 0.476771 TTTTCACTGTGGACCCTCCC 59.523 55.000 8.11 0.00 35.03 4.30 R
3180 3300 0.609131 CGCCCCCTGATTTTCACTGT 60.609 55.000 0.00 0.00 0.00 3.55 R
6718 7517 6.122782 CACATTTTTCGTCGTATATCTGCTG 58.877 40.000 0.00 0.00 0.00 4.41 R
6733 7532 3.057315 TGGCTTAGCTGAGCACATTTTTC 60.057 43.478 29.20 11.69 44.49 2.29 R
6765 7564 1.528542 CCTGGCATCTGCATCCCTG 60.529 63.158 4.33 0.00 44.36 4.45 R
7142 7943 3.640407 AGCACCCTCCACATGCGT 61.640 61.111 0.00 0.00 44.25 5.24 R
8684 9884 0.174162 GGATTTTTCGCTGCAGCCAT 59.826 50.000 32.07 16.14 37.91 4.40 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
87 94 1.153745 GCGAAGGTGCGATCTCTGT 60.154 57.895 0.00 0.00 0.00 3.41
105 112 2.264794 CCTCGGTTCTTGGTCCGG 59.735 66.667 0.00 0.00 45.79 5.14
140 147 2.678934 TCTCCGGGGGTTCGAGTG 60.679 66.667 0.00 0.00 0.00 3.51
198 255 3.621805 TTGCCAGGACGAAGCGGA 61.622 61.111 0.00 0.00 0.00 5.54
200 257 4.070552 GCCAGGACGAAGCGGACT 62.071 66.667 0.00 0.00 0.00 3.85
216 273 2.125350 CTGCTCTGGTTCCGAGGC 60.125 66.667 10.71 3.89 0.00 4.70
227 284 2.358737 CCGAGGCGAAGTTTGGCT 60.359 61.111 18.70 18.70 45.97 4.75
229 286 1.667830 CGAGGCGAAGTTTGGCTGA 60.668 57.895 23.14 0.00 42.99 4.26
230 287 1.869690 GAGGCGAAGTTTGGCTGAC 59.130 57.895 23.14 6.76 42.99 3.51
236 293 0.668535 GAAGTTTGGCTGACACCCAC 59.331 55.000 0.00 0.00 30.65 4.61
282 340 0.530650 TCCATGGAGCTCGATTTCGC 60.531 55.000 11.44 0.00 39.60 4.70
311 369 3.057174 CGCCTCTCTCTGTACTTTTGTCT 60.057 47.826 0.00 0.00 0.00 3.41
341 399 4.462483 TGTTTTCTGTGGCTTTGAAGTTCT 59.538 37.500 4.17 0.00 0.00 3.01
352 410 4.154195 GCTTTGAAGTTCTCTTTGCCGATA 59.846 41.667 4.17 0.00 33.64 2.92
460 522 5.288472 CCAAAATAGGCGACTTTTTATGTGC 59.712 40.000 7.15 0.00 40.14 4.57
530 599 6.797995 TGTGTTCTTGTAAACGTGTTCTTTTC 59.202 34.615 0.00 0.00 31.58 2.29
548 617 8.722394 GTTCTTTTCTCCATCGATTAGAGTTTT 58.278 33.333 17.59 0.00 0.00 2.43
554 623 6.813649 TCTCCATCGATTAGAGTTTTCTGTTG 59.186 38.462 17.59 0.00 34.79 3.33
566 635 5.291971 AGTTTTCTGTTGCATGGTGAATTC 58.708 37.500 0.00 0.00 0.00 2.17
612 700 1.529226 TTACTTGGTGGGCACAATCG 58.471 50.000 0.00 0.00 0.00 3.34
670 758 9.612620 GTCATTTATTTTCTACCTCACAAAGTG 57.387 33.333 0.00 0.00 34.45 3.16
671 759 8.296713 TCATTTATTTTCTACCTCACAAAGTGC 58.703 33.333 0.00 0.00 32.98 4.40
672 760 7.817418 TTTATTTTCTACCTCACAAAGTGCT 57.183 32.000 0.00 0.00 32.98 4.40
685 773 5.050499 TCACAAAGTGCTGTTGTTGTTTTTG 60.050 36.000 0.00 0.00 37.09 2.44
775 874 9.659830 GAGTATTGTTTTCATTTCGTTACTTGT 57.340 29.630 0.00 0.00 0.00 3.16
776 875 9.445786 AGTATTGTTTTCATTTCGTTACTTGTG 57.554 29.630 0.00 0.00 0.00 3.33
779 878 3.907894 TTCATTTCGTTACTTGTGGGC 57.092 42.857 0.00 0.00 0.00 5.36
780 879 2.852449 TCATTTCGTTACTTGTGGGCA 58.148 42.857 0.00 0.00 0.00 5.36
781 880 2.550606 TCATTTCGTTACTTGTGGGCAC 59.449 45.455 0.00 0.00 0.00 5.01
782 881 0.938713 TTTCGTTACTTGTGGGCACG 59.061 50.000 0.00 0.00 0.00 5.34
819 919 4.261155 CGTGCCTTGAAACTCTGATTTTCA 60.261 41.667 16.32 16.32 40.42 2.69
834 934 4.719273 TGATTTTCAAACCTCCCCTGTTTT 59.281 37.500 0.00 0.00 33.82 2.43
872 972 9.118236 GAATGCAGTAAAATTCTACAACTTCAC 57.882 33.333 0.00 0.00 31.41 3.18
892 994 4.019771 TCACTCAACATGCATAGGTGGTAA 60.020 41.667 0.00 0.00 0.00 2.85
898 1000 6.435591 TCAACATGCATAGGTGGTAATTTTCA 59.564 34.615 0.00 0.00 0.00 2.69
916 1021 1.876799 TCAACCAACATGCCTTGTACG 59.123 47.619 0.00 0.00 37.68 3.67
937 1042 6.124088 ACGAATGCAAATGATTAGTTCCTC 57.876 37.500 0.00 0.00 0.00 3.71
961 1074 1.272490 CAGCCATGATGGATTCCATGC 59.728 52.381 22.89 18.24 45.26 4.06
1027 1143 0.538287 AACTGCCTCCAAGCAAGACC 60.538 55.000 0.00 0.00 43.52 3.85
1262 1378 7.014615 ACCTGCAGACAATTCTAAAATTTCACT 59.985 33.333 17.39 0.00 32.69 3.41
1336 1452 2.037641 CCATCCTTGACAGTGACAGTCA 59.962 50.000 6.73 6.73 43.72 3.41
1367 1483 7.112122 AGTGATGGTGATGCTAGTTTTATCAA 58.888 34.615 0.00 0.00 33.10 2.57
1470 1586 5.717078 ATGATGTGAGTGAAAATGTTGCT 57.283 34.783 0.00 0.00 0.00 3.91
1515 1631 4.006780 GGCAACTTTGGATGATTTTGGT 57.993 40.909 0.00 0.00 0.00 3.67
1516 1632 3.996363 GGCAACTTTGGATGATTTTGGTC 59.004 43.478 0.00 0.00 0.00 4.02
1517 1633 4.502950 GGCAACTTTGGATGATTTTGGTCA 60.503 41.667 0.00 0.00 0.00 4.02
1518 1634 5.240121 GCAACTTTGGATGATTTTGGTCAT 58.760 37.500 0.00 0.00 41.36 3.06
1519 1635 5.121142 GCAACTTTGGATGATTTTGGTCATG 59.879 40.000 0.00 0.00 38.88 3.07
1520 1636 4.824289 ACTTTGGATGATTTTGGTCATGC 58.176 39.130 2.02 2.02 44.36 4.06
1521 1637 3.891422 TTGGATGATTTTGGTCATGCC 57.109 42.857 6.04 0.00 43.73 4.40
1522 1638 1.750206 TGGATGATTTTGGTCATGCCG 59.250 47.619 6.04 0.00 43.73 5.69
1523 1639 2.023673 GGATGATTTTGGTCATGCCGA 58.976 47.619 0.00 0.00 40.00 5.54
1533 1649 1.750778 GGTCATGCCGATGATTTTGGT 59.249 47.619 0.00 0.00 40.78 3.67
1538 1654 1.134753 TGCCGATGATTTTGGTCATGC 59.865 47.619 0.00 0.00 38.88 4.06
1562 1678 1.561542 TGGAAGGGATCAAGCTTCCTC 59.438 52.381 3.20 1.04 44.04 3.71
1563 1679 1.474143 GGAAGGGATCAAGCTTCCTCG 60.474 57.143 4.98 0.00 41.39 4.63
1564 1680 1.482593 GAAGGGATCAAGCTTCCTCGA 59.517 52.381 4.98 0.00 33.53 4.04
1565 1681 1.799933 AGGGATCAAGCTTCCTCGAT 58.200 50.000 0.00 0.00 33.53 3.59
1566 1682 1.691434 AGGGATCAAGCTTCCTCGATC 59.309 52.381 13.52 13.52 34.74 3.69
1567 1683 1.414181 GGGATCAAGCTTCCTCGATCA 59.586 52.381 20.15 0.00 36.75 2.92
1568 1684 2.158900 GGGATCAAGCTTCCTCGATCAA 60.159 50.000 20.15 0.00 36.75 2.57
1569 1685 3.535561 GGATCAAGCTTCCTCGATCAAA 58.464 45.455 20.15 0.00 36.75 2.69
1570 1686 3.941483 GGATCAAGCTTCCTCGATCAAAA 59.059 43.478 20.15 0.00 36.75 2.44
1571 1687 4.396166 GGATCAAGCTTCCTCGATCAAAAA 59.604 41.667 20.15 0.00 36.75 1.94
1572 1688 4.749245 TCAAGCTTCCTCGATCAAAAAC 57.251 40.909 0.00 0.00 0.00 2.43
1573 1689 4.133820 TCAAGCTTCCTCGATCAAAAACA 58.866 39.130 0.00 0.00 0.00 2.83
1629 1745 4.636206 GGAACACATGGATGTAAAGACCTC 59.364 45.833 0.00 0.00 39.39 3.85
1644 1760 6.633500 AAAGACCTCGATGACAATTTTGAA 57.367 33.333 0.00 0.00 0.00 2.69
1655 1771 9.055248 CGATGACAATTTTGAACATCTTAAGTC 57.945 33.333 20.44 0.00 39.99 3.01
1656 1772 9.897744 GATGACAATTTTGAACATCTTAAGTCA 57.102 29.630 18.13 0.00 39.57 3.41
1688 1804 8.804743 CAATGACTGTAATGAAATTGAGATTGC 58.195 33.333 0.00 0.00 36.99 3.56
1727 1843 6.238731 CCAAATGACTCAAGCTTACACAAAGA 60.239 38.462 0.00 0.00 37.38 2.52
1778 1894 2.011947 GGGGCAAAATCCTACACGTAC 58.988 52.381 0.00 0.00 0.00 3.67
1788 1904 6.579666 AATCCTACACGTACTACTGACAAA 57.420 37.500 0.00 0.00 0.00 2.83
1796 1912 8.205131 ACACGTACTACTGACAAAAGAAAAAT 57.795 30.769 0.00 0.00 0.00 1.82
1797 1913 8.671028 ACACGTACTACTGACAAAAGAAAAATT 58.329 29.630 0.00 0.00 0.00 1.82
1859 1975 9.898152 AATATCTACTGAAAGGGAAGAAGAAAG 57.102 33.333 0.00 0.00 39.30 2.62
2039 2155 9.739276 TGAGGAATACATTTTTCACAGTTAGAT 57.261 29.630 0.00 0.00 0.00 1.98
2103 2219 8.724436 TCAATGCTAATTATTGCAGGGAAACCA 61.724 37.037 5.72 0.00 45.45 3.67
2173 2289 6.126332 TGGAAATGTAGCTTCCCATGGTATAA 60.126 38.462 11.73 1.07 41.54 0.98
2338 2455 7.491682 TCACTTTCATCACGATCTTCATCATA 58.508 34.615 0.00 0.00 0.00 2.15
2674 2791 3.719268 ATCCAGTTGTGCATTGACCTA 57.281 42.857 0.00 0.00 0.00 3.08
3130 3250 6.090223 GGCAATTTTGTACGGGATTAAAGTTG 59.910 38.462 0.00 0.00 34.73 3.16
3168 3288 5.850046 AGATATAGTTGGAAATCAGGGGG 57.150 43.478 0.00 0.00 0.00 5.40
3169 3289 2.755952 ATAGTTGGAAATCAGGGGGC 57.244 50.000 0.00 0.00 0.00 5.80
3170 3290 0.254747 TAGTTGGAAATCAGGGGGCG 59.745 55.000 0.00 0.00 0.00 6.13
3171 3291 2.052104 GTTGGAAATCAGGGGGCGG 61.052 63.158 0.00 0.00 0.00 6.13
3172 3292 3.295386 TTGGAAATCAGGGGGCGGG 62.295 63.158 0.00 0.00 0.00 6.13
3173 3293 3.416880 GGAAATCAGGGGGCGGGA 61.417 66.667 0.00 0.00 0.00 5.14
3174 3294 2.193248 GAAATCAGGGGGCGGGAG 59.807 66.667 0.00 0.00 0.00 4.30
3175 3295 3.420482 AAATCAGGGGGCGGGAGG 61.420 66.667 0.00 0.00 0.00 4.30
3185 3305 4.394712 GCGGGAGGGTCCACAGTG 62.395 72.222 0.00 0.00 38.64 3.66
3186 3306 2.603473 CGGGAGGGTCCACAGTGA 60.603 66.667 0.62 0.00 38.64 3.41
3187 3307 2.214216 CGGGAGGGTCCACAGTGAA 61.214 63.158 0.62 0.00 38.64 3.18
3188 3308 1.764571 CGGGAGGGTCCACAGTGAAA 61.765 60.000 0.62 0.00 38.64 2.69
3189 3309 0.476771 GGGAGGGTCCACAGTGAAAA 59.523 55.000 0.62 0.00 38.64 2.29
3190 3310 1.075536 GGGAGGGTCCACAGTGAAAAT 59.924 52.381 0.62 0.00 38.64 1.82
3191 3311 2.437413 GGAGGGTCCACAGTGAAAATC 58.563 52.381 0.62 0.00 36.28 2.17
3192 3312 2.224769 GGAGGGTCCACAGTGAAAATCA 60.225 50.000 0.62 0.00 36.28 2.57
3193 3313 3.077359 GAGGGTCCACAGTGAAAATCAG 58.923 50.000 0.62 0.00 0.00 2.90
3194 3314 2.162681 GGGTCCACAGTGAAAATCAGG 58.837 52.381 0.62 0.00 0.00 3.86
3195 3315 2.162681 GGTCCACAGTGAAAATCAGGG 58.837 52.381 0.62 0.00 0.00 4.45
3196 3316 2.162681 GTCCACAGTGAAAATCAGGGG 58.837 52.381 0.62 0.00 0.00 4.79
3197 3317 1.075374 TCCACAGTGAAAATCAGGGGG 59.925 52.381 0.62 0.00 29.27 5.40
3290 3410 3.676093 AGGTGTTTTAGCCAACTCTAGC 58.324 45.455 0.00 0.00 0.00 3.42
3331 3451 7.174107 AGGGGATATTTGTGTCTCAAAAATG 57.826 36.000 4.30 0.00 46.97 2.32
3576 3893 1.791785 GCAGACTTAGATCGCTCATGC 59.208 52.381 0.00 0.00 0.00 4.06
3640 3957 6.222389 TCCAAATGAATAGTTGCCTTTTGTG 58.778 36.000 0.00 0.00 30.87 3.33
3663 3980 3.928727 TGAGTCGAAGTTAACGTCCAT 57.071 42.857 14.71 2.40 0.00 3.41
3806 4123 8.396272 ACAATTAAAGTTGCACTCTGAGTATT 57.604 30.769 10.47 0.66 32.32 1.89
3855 4172 5.333299 ACATATACGCTTGGTACTTCACA 57.667 39.130 0.00 0.00 32.95 3.58
6718 7517 7.148853 GCGATTTGCAGAATATTGAATCAATCC 60.149 37.037 12.23 3.62 45.45 3.01
6733 7532 4.160736 TCAATCCAGCAGATATACGACG 57.839 45.455 0.00 0.00 33.66 5.12
6765 7564 1.066605 CAGCTAAGCCATCAATGTGCC 59.933 52.381 0.00 0.00 0.00 5.01
6903 7702 1.405256 CGAGATGAAGAGTTGCAGCCT 60.405 52.381 0.00 0.00 0.00 4.58
7338 8139 7.281098 TGGTTACAAAAACTATGTGAGTGGTA 58.719 34.615 0.00 0.00 38.87 3.25
7499 8300 2.477825 CCGTCTGAAGAATCATGCGAT 58.522 47.619 0.00 0.00 35.79 4.58
7679 8480 1.514811 GCAATGTTCGATCGACTCTCG 59.485 52.381 19.26 7.95 42.10 4.04
7734 8535 3.702048 TGAAACGGGAGGCGGAGG 61.702 66.667 0.00 0.00 0.00 4.30
8009 8810 4.601084 TCTGGGGTAAAGTTTGTTTGTCA 58.399 39.130 0.00 0.00 0.00 3.58
8080 8882 0.686789 TGTGCTTCTCTGCCTGCTTA 59.313 50.000 0.00 0.00 0.00 3.09
8199 9006 7.286316 AGGTGTTTTTGAGTTCTCAATCTCATT 59.714 33.333 14.67 6.09 39.85 2.57
8234 9047 1.199789 GCAGATGATTCCGTGCAACAA 59.800 47.619 0.00 0.00 35.74 2.83
8262 9078 6.590234 TTCTTCTGTATGTGCTCAGAGTTA 57.410 37.500 0.00 0.00 40.91 2.24
8282 9098 0.832135 AGAGTTCTGACCCTCGGCAA 60.832 55.000 0.00 0.00 32.88 4.52
8293 9117 1.247567 CCTCGGCAACATGGAGTTTT 58.752 50.000 0.00 0.00 38.74 2.43
8294 9118 1.068333 CCTCGGCAACATGGAGTTTTG 60.068 52.381 0.00 0.00 38.74 2.44
8382 9208 4.096003 CACCTCAATCGCCCCCGT 62.096 66.667 0.00 0.00 35.54 5.28
8394 9220 2.738480 CCCCGTTTCGTCTGGACA 59.262 61.111 1.63 0.00 0.00 4.02
8399 9225 0.249322 CGTTTCGTCTGGACAGGTGT 60.249 55.000 0.00 0.00 0.00 4.16
8622 9822 3.110178 GGCGACGGACTTCAACGG 61.110 66.667 0.00 0.00 0.00 4.44
8651 9851 4.873129 TCGAGCGCGCAATCCCTC 62.873 66.667 35.10 19.61 37.46 4.30
8658 9858 4.918201 CGCAATCCCTCGGCTCCC 62.918 72.222 0.00 0.00 0.00 4.30
8659 9859 3.797353 GCAATCCCTCGGCTCCCA 61.797 66.667 0.00 0.00 0.00 4.37
8660 9860 2.507944 CAATCCCTCGGCTCCCAG 59.492 66.667 0.00 0.00 0.00 4.45
8661 9861 2.770048 AATCCCTCGGCTCCCAGG 60.770 66.667 0.00 0.00 0.00 4.45
8681 9881 4.170062 CCGCGAGCACAATGGCAG 62.170 66.667 8.23 0.00 35.83 4.85
8682 9882 3.425713 CGCGAGCACAATGGCAGT 61.426 61.111 0.00 0.00 35.83 4.40
8683 9883 2.956987 GCGAGCACAATGGCAGTT 59.043 55.556 0.00 0.00 35.83 3.16
8684 9884 1.634757 CGCGAGCACAATGGCAGTTA 61.635 55.000 0.00 0.00 35.83 2.24
8685 9885 0.734889 GCGAGCACAATGGCAGTTAT 59.265 50.000 0.00 0.00 35.83 1.89
8686 9886 1.532505 GCGAGCACAATGGCAGTTATG 60.533 52.381 0.00 0.00 35.83 1.90
8687 9887 1.064505 CGAGCACAATGGCAGTTATGG 59.935 52.381 0.00 0.00 35.83 2.74
8696 9896 4.206958 CAGTTATGGCTGCAGCGA 57.793 55.556 31.19 28.73 43.26 4.93
8697 9897 2.470156 CAGTTATGGCTGCAGCGAA 58.530 52.632 31.19 22.52 43.26 4.70
8698 9898 0.804364 CAGTTATGGCTGCAGCGAAA 59.196 50.000 31.19 21.34 43.26 3.46
8699 9899 1.199789 CAGTTATGGCTGCAGCGAAAA 59.800 47.619 31.19 21.00 43.26 2.29
8700 9900 1.885887 AGTTATGGCTGCAGCGAAAAA 59.114 42.857 31.19 22.12 43.26 1.94
8701 9901 2.493278 AGTTATGGCTGCAGCGAAAAAT 59.507 40.909 31.19 20.11 43.26 1.82
8702 9902 2.849880 TATGGCTGCAGCGAAAAATC 57.150 45.000 31.19 16.48 43.26 2.17
8703 9903 0.174162 ATGGCTGCAGCGAAAAATCC 59.826 50.000 31.19 15.74 43.26 3.01
8704 9904 0.895100 TGGCTGCAGCGAAAAATCCT 60.895 50.000 31.19 0.00 43.26 3.24
8705 9905 1.094785 GGCTGCAGCGAAAAATCCTA 58.905 50.000 31.19 0.00 43.26 2.94
8706 9906 1.678101 GGCTGCAGCGAAAAATCCTAT 59.322 47.619 31.19 0.00 43.26 2.57
8707 9907 2.099756 GGCTGCAGCGAAAAATCCTATT 59.900 45.455 31.19 0.00 43.26 1.73
8708 9908 3.429410 GGCTGCAGCGAAAAATCCTATTT 60.429 43.478 31.19 0.00 43.26 1.40
8709 9909 3.549070 GCTGCAGCGAAAAATCCTATTTG 59.451 43.478 25.23 0.00 0.00 2.32
8710 9910 4.675146 GCTGCAGCGAAAAATCCTATTTGA 60.675 41.667 25.23 0.00 0.00 2.69
8711 9911 5.384063 TGCAGCGAAAAATCCTATTTGAA 57.616 34.783 0.00 0.00 0.00 2.69
8712 9912 5.401550 TGCAGCGAAAAATCCTATTTGAAG 58.598 37.500 0.00 0.00 0.00 3.02
8713 9913 4.266265 GCAGCGAAAAATCCTATTTGAAGC 59.734 41.667 0.00 0.00 0.00 3.86
8714 9914 5.644644 CAGCGAAAAATCCTATTTGAAGCT 58.355 37.500 0.00 0.00 31.68 3.74
8715 9915 5.741040 CAGCGAAAAATCCTATTTGAAGCTC 59.259 40.000 0.00 0.00 30.22 4.09
8716 9916 5.649831 AGCGAAAAATCCTATTTGAAGCTCT 59.350 36.000 0.00 0.00 0.00 4.09
8717 9917 5.968261 GCGAAAAATCCTATTTGAAGCTCTC 59.032 40.000 0.00 0.00 0.00 3.20
8718 9918 6.183360 GCGAAAAATCCTATTTGAAGCTCTCT 60.183 38.462 0.00 0.00 0.00 3.10
8719 9919 7.185453 CGAAAAATCCTATTTGAAGCTCTCTG 58.815 38.462 0.00 0.00 0.00 3.35
8720 9920 6.448207 AAAATCCTATTTGAAGCTCTCTGC 57.552 37.500 0.00 0.00 43.29 4.26
8728 9928 1.789506 GAAGCTCTCTGCGTCAAACT 58.210 50.000 0.00 0.00 46.81 2.66
8729 9929 1.458827 GAAGCTCTCTGCGTCAAACTG 59.541 52.381 0.00 0.00 46.81 3.16
8730 9930 2.906047 GCTCTCTGCGTCAAACTGT 58.094 52.632 0.00 0.00 0.00 3.55
8731 9931 0.787183 GCTCTCTGCGTCAAACTGTC 59.213 55.000 0.00 0.00 0.00 3.51
8732 9932 1.423395 CTCTCTGCGTCAAACTGTCC 58.577 55.000 0.00 0.00 0.00 4.02
8733 9933 0.318699 TCTCTGCGTCAAACTGTCCG 60.319 55.000 0.00 0.00 0.00 4.79
8734 9934 1.284982 CTCTGCGTCAAACTGTCCGG 61.285 60.000 0.00 0.00 0.00 5.14
8735 9935 2.954753 CTGCGTCAAACTGTCCGGC 61.955 63.158 0.00 0.00 0.00 6.13
8736 9936 4.072088 GCGTCAAACTGTCCGGCG 62.072 66.667 0.00 0.00 0.00 6.46
8737 9937 2.355363 CGTCAAACTGTCCGGCGA 60.355 61.111 9.30 0.00 0.00 5.54
8738 9938 1.952133 CGTCAAACTGTCCGGCGAA 60.952 57.895 9.30 0.00 0.00 4.70
8739 9939 1.860078 GTCAAACTGTCCGGCGAAG 59.140 57.895 9.30 5.48 0.00 3.79
8753 9953 3.296516 CGAAGCAAAACCATCGAGC 57.703 52.632 0.00 0.00 37.48 5.03
8754 9954 0.519175 CGAAGCAAAACCATCGAGCG 60.519 55.000 0.00 0.00 37.48 5.03
8755 9955 0.517316 GAAGCAAAACCATCGAGCGT 59.483 50.000 0.00 0.00 0.00 5.07
8756 9956 0.238289 AAGCAAAACCATCGAGCGTG 59.762 50.000 0.00 0.00 0.00 5.34
8757 9957 0.602638 AGCAAAACCATCGAGCGTGA 60.603 50.000 0.00 0.00 0.00 4.35
8758 9958 0.179215 GCAAAACCATCGAGCGTGAG 60.179 55.000 0.00 0.00 0.00 3.51
8773 9973 3.296322 CGTGAGCAATGCCCTTAAAAA 57.704 42.857 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.907042 ACCAAGAACAGGAGAGGGTAAG 59.093 50.000 0.00 0.00 0.00 2.34
105 112 2.279784 CGAGGAGGAGGCAATCGC 60.280 66.667 0.00 0.00 37.44 4.58
140 147 1.455248 AGAGTCAGTCAGTACGCCTC 58.545 55.000 0.00 0.00 0.00 4.70
198 255 2.948720 GCCTCGGAACCAGAGCAGT 61.949 63.158 0.00 0.00 34.56 4.40
200 257 4.069232 CGCCTCGGAACCAGAGCA 62.069 66.667 0.00 0.00 34.56 4.26
216 273 0.817634 TGGGTGTCAGCCAAACTTCG 60.818 55.000 21.40 0.00 43.74 3.79
246 303 0.106149 GGACGAACACTCACCTTGGT 59.894 55.000 0.00 0.00 0.00 3.67
352 410 5.004630 CACGCGCACAATGATTGATTAATTT 59.995 36.000 12.80 0.00 0.00 1.82
378 440 3.336122 ACCTACACGGTTCGAGACT 57.664 52.632 0.00 0.00 46.37 3.24
530 599 6.456181 GCAACAGAAAACTCTAATCGATGGAG 60.456 42.308 20.29 20.29 0.00 3.86
548 617 2.821378 CAGGAATTCACCATGCAACAGA 59.179 45.455 7.93 0.00 0.00 3.41
554 623 2.166870 TGCATTCAGGAATTCACCATGC 59.833 45.455 17.65 17.65 37.37 4.06
566 635 6.183360 GCAATTCAGATTTTTCTGCATTCAGG 60.183 38.462 0.00 0.00 40.69 3.86
612 700 6.114221 TCGCCTATTTTACATGTAAGCAAC 57.886 37.500 17.36 6.82 0.00 4.17
670 758 6.645700 TTCAAGATCAAAAACAACAACAGC 57.354 33.333 0.00 0.00 0.00 4.40
717 816 7.169982 CCATGTAACAGGAAACTCTAATCGATC 59.830 40.741 0.00 0.00 40.21 3.69
775 874 0.392461 GTAAGCAAGGATCGTGCCCA 60.392 55.000 14.51 2.65 43.27 5.36
776 875 1.095807 GGTAAGCAAGGATCGTGCCC 61.096 60.000 14.51 7.07 43.27 5.36
779 878 0.108329 ACGGGTAAGCAAGGATCGTG 60.108 55.000 0.00 0.00 0.00 4.35
780 879 0.108329 CACGGGTAAGCAAGGATCGT 60.108 55.000 0.00 0.00 0.00 3.73
781 880 1.429148 GCACGGGTAAGCAAGGATCG 61.429 60.000 0.00 0.00 0.00 3.69
782 881 1.095807 GGCACGGGTAAGCAAGGATC 61.096 60.000 0.00 0.00 0.00 3.36
864 964 4.456911 ACCTATGCATGTTGAGTGAAGTTG 59.543 41.667 10.16 0.00 0.00 3.16
872 972 6.455360 AAATTACCACCTATGCATGTTGAG 57.545 37.500 10.16 0.00 0.00 3.02
892 994 4.420522 ACAAGGCATGTTGGTTGAAAAT 57.579 36.364 0.00 0.00 40.06 1.82
898 1000 2.264005 TCGTACAAGGCATGTTGGTT 57.736 45.000 0.00 0.00 43.63 3.67
916 1021 7.093322 ACAGAGGAACTAATCATTTGCATTC 57.907 36.000 0.00 0.00 41.55 2.67
937 1042 2.228059 GGAATCCATCATGGCTGACAG 58.772 52.381 0.00 0.00 37.47 3.51
961 1074 6.241207 ACAACGAAGACAAGTTATGATTGG 57.759 37.500 0.00 0.00 31.76 3.16
1262 1378 1.847798 ATGGCGGGGCACTTTCAGTA 61.848 55.000 0.00 0.00 0.00 2.74
1367 1483 0.978907 CAGAATGGGCTGCCCTTTTT 59.021 50.000 35.80 27.25 45.70 1.94
1470 1586 2.497675 GCAGTTCTCTGAGACATGGGTA 59.502 50.000 6.92 0.00 43.76 3.69
1506 1622 2.720915 TCATCGGCATGACCAAAATCA 58.279 42.857 0.00 0.00 39.03 2.57
1507 1623 3.996150 ATCATCGGCATGACCAAAATC 57.004 42.857 0.00 0.00 42.05 2.17
1508 1624 4.741321 AAATCATCGGCATGACCAAAAT 57.259 36.364 0.00 0.00 42.05 1.82
1509 1625 4.244066 CAAAATCATCGGCATGACCAAAA 58.756 39.130 0.00 0.00 42.05 2.44
1510 1626 3.368220 CCAAAATCATCGGCATGACCAAA 60.368 43.478 0.00 0.00 42.05 3.28
1511 1627 2.166050 CCAAAATCATCGGCATGACCAA 59.834 45.455 0.00 0.00 42.05 3.67
1512 1628 1.750206 CCAAAATCATCGGCATGACCA 59.250 47.619 0.00 0.00 42.05 4.02
1513 1629 1.750778 ACCAAAATCATCGGCATGACC 59.249 47.619 0.00 0.00 42.05 4.02
1514 1630 2.423185 TGACCAAAATCATCGGCATGAC 59.577 45.455 0.00 0.00 42.05 3.06
1515 1631 2.720915 TGACCAAAATCATCGGCATGA 58.279 42.857 0.00 2.83 43.45 3.07
1516 1632 3.377439 CATGACCAAAATCATCGGCATG 58.623 45.455 0.00 0.00 37.20 4.06
1517 1633 2.223876 GCATGACCAAAATCATCGGCAT 60.224 45.455 0.00 0.00 37.20 4.40
1518 1634 1.134753 GCATGACCAAAATCATCGGCA 59.865 47.619 0.00 0.00 37.20 5.69
1519 1635 1.536709 GGCATGACCAAAATCATCGGC 60.537 52.381 0.00 0.00 37.20 5.54
1520 1636 1.268692 CGGCATGACCAAAATCATCGG 60.269 52.381 0.00 0.00 37.20 4.18
1521 1637 1.670295 TCGGCATGACCAAAATCATCG 59.330 47.619 0.00 0.00 37.20 3.84
1522 1638 3.551454 CCATCGGCATGACCAAAATCATC 60.551 47.826 0.00 0.00 37.20 2.92
1523 1639 2.363038 CCATCGGCATGACCAAAATCAT 59.637 45.455 0.00 0.00 40.03 2.45
1533 1649 0.397941 GATCCCTTCCATCGGCATGA 59.602 55.000 0.00 0.00 30.57 3.07
1538 1654 0.471617 AGCTTGATCCCTTCCATCGG 59.528 55.000 0.00 0.00 0.00 4.18
1562 1678 7.689812 CAGCTATTTGACTAGTGTTTTTGATCG 59.310 37.037 0.00 0.00 0.00 3.69
1563 1679 8.721478 TCAGCTATTTGACTAGTGTTTTTGATC 58.279 33.333 0.00 0.00 0.00 2.92
1564 1680 8.621532 TCAGCTATTTGACTAGTGTTTTTGAT 57.378 30.769 0.00 0.00 0.00 2.57
1565 1681 7.173218 CCTCAGCTATTTGACTAGTGTTTTTGA 59.827 37.037 0.00 0.00 0.00 2.69
1566 1682 7.041098 ACCTCAGCTATTTGACTAGTGTTTTTG 60.041 37.037 0.00 0.00 0.00 2.44
1567 1683 6.998673 ACCTCAGCTATTTGACTAGTGTTTTT 59.001 34.615 0.00 0.00 0.00 1.94
1568 1684 6.428159 CACCTCAGCTATTTGACTAGTGTTTT 59.572 38.462 0.00 0.00 0.00 2.43
1569 1685 5.934625 CACCTCAGCTATTTGACTAGTGTTT 59.065 40.000 0.00 0.00 0.00 2.83
1570 1686 5.482908 CACCTCAGCTATTTGACTAGTGTT 58.517 41.667 0.00 0.00 0.00 3.32
1571 1687 4.621747 GCACCTCAGCTATTTGACTAGTGT 60.622 45.833 0.00 0.00 0.00 3.55
1572 1688 3.868077 GCACCTCAGCTATTTGACTAGTG 59.132 47.826 0.00 0.00 0.00 2.74
1573 1689 3.515502 TGCACCTCAGCTATTTGACTAGT 59.484 43.478 0.00 0.00 34.99 2.57
1629 1745 8.955061 ACTTAAGATGTTCAAAATTGTCATCG 57.045 30.769 10.09 11.91 40.96 3.84
1644 1760 6.546395 GTCATTGCGATTTGACTTAAGATGT 58.454 36.000 10.09 0.00 39.30 3.06
1655 1771 7.745022 ATTTCATTACAGTCATTGCGATTTG 57.255 32.000 0.00 0.00 0.00 2.32
1656 1772 8.028354 TCAATTTCATTACAGTCATTGCGATTT 58.972 29.630 0.00 0.00 0.00 2.17
1673 1789 7.774157 AGTCTGTATCAGCAATCTCAATTTCAT 59.226 33.333 0.00 0.00 0.00 2.57
1688 1804 7.323420 TGAGTCATTTGGTAAGTCTGTATCAG 58.677 38.462 0.00 0.00 0.00 2.90
1727 1843 2.158769 TGTGTCTGCACTTGATCAGGTT 60.159 45.455 7.91 0.00 45.44 3.50
1764 1880 6.579666 TTGTCAGTAGTACGTGTAGGATTT 57.420 37.500 0.00 0.00 0.00 2.17
1778 1894 7.169813 GGGCTTCAATTTTTCTTTTGTCAGTAG 59.830 37.037 0.00 0.00 0.00 2.57
1788 1904 4.651045 ACAGAGTGGGCTTCAATTTTTCTT 59.349 37.500 0.00 0.00 0.00 2.52
1796 1912 2.325484 TGTCTACAGAGTGGGCTTCAA 58.675 47.619 0.00 0.00 0.00 2.69
1797 1913 2.009681 TGTCTACAGAGTGGGCTTCA 57.990 50.000 0.00 0.00 0.00 3.02
1859 1975 1.379044 CTGGTGATGGAACTGCCCC 60.379 63.158 0.00 0.00 34.97 5.80
1943 2059 0.967380 CCTTGAGACCCCATGGCAAC 60.967 60.000 6.09 0.00 33.59 4.17
2080 2196 4.961730 TGGTTTCCCTGCAATAATTAGCAT 59.038 37.500 0.34 0.00 40.42 3.79
2103 2219 4.001652 CTGACAGAGAAAGTGCACATGAT 58.998 43.478 21.04 1.50 0.00 2.45
2106 2222 2.149578 GCTGACAGAGAAAGTGCACAT 58.850 47.619 21.04 3.48 0.00 3.21
2338 2455 9.466497 TTTGAGCTGAAAATAGTGGATTCTTAT 57.534 29.630 0.00 0.00 0.00 1.73
2701 2818 9.270640 CTGCTTAAGACAAGATAGCTTCATATT 57.729 33.333 6.67 0.00 33.15 1.28
2704 2824 6.882656 TCTGCTTAAGACAAGATAGCTTCAT 58.117 36.000 6.67 0.00 33.15 2.57
3130 3250 3.414700 CTTGACACCTCACGCCGC 61.415 66.667 0.00 0.00 0.00 6.53
3168 3288 4.394712 CACTGTGGACCCTCCCGC 62.395 72.222 0.00 0.00 35.03 6.13
3169 3289 1.764571 TTTCACTGTGGACCCTCCCG 61.765 60.000 8.11 0.00 35.03 5.14
3170 3290 0.476771 TTTTCACTGTGGACCCTCCC 59.523 55.000 8.11 0.00 35.03 4.30
3171 3291 2.224769 TGATTTTCACTGTGGACCCTCC 60.225 50.000 8.11 0.00 36.96 4.30
3172 3292 3.077359 CTGATTTTCACTGTGGACCCTC 58.923 50.000 8.11 0.00 0.00 4.30
3173 3293 2.224867 CCTGATTTTCACTGTGGACCCT 60.225 50.000 8.11 0.00 0.00 4.34
3174 3294 2.162681 CCTGATTTTCACTGTGGACCC 58.837 52.381 8.11 0.00 0.00 4.46
3175 3295 2.162681 CCCTGATTTTCACTGTGGACC 58.837 52.381 8.11 0.00 0.00 4.46
3176 3296 2.162681 CCCCTGATTTTCACTGTGGAC 58.837 52.381 8.11 0.00 0.00 4.02
3177 3297 1.075374 CCCCCTGATTTTCACTGTGGA 59.925 52.381 8.11 0.00 0.00 4.02
3178 3298 1.549203 CCCCCTGATTTTCACTGTGG 58.451 55.000 8.11 0.00 0.00 4.17
3179 3299 0.890683 GCCCCCTGATTTTCACTGTG 59.109 55.000 0.17 0.17 0.00 3.66
3180 3300 0.609131 CGCCCCCTGATTTTCACTGT 60.609 55.000 0.00 0.00 0.00 3.55
3181 3301 1.315257 CCGCCCCCTGATTTTCACTG 61.315 60.000 0.00 0.00 0.00 3.66
3182 3302 1.000896 CCGCCCCCTGATTTTCACT 60.001 57.895 0.00 0.00 0.00 3.41
3183 3303 2.052104 CCCGCCCCCTGATTTTCAC 61.052 63.158 0.00 0.00 0.00 3.18
3184 3304 2.210144 CTCCCGCCCCCTGATTTTCA 62.210 60.000 0.00 0.00 0.00 2.69
3185 3305 1.453928 CTCCCGCCCCCTGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
3186 3306 2.683475 CTCCCGCCCCCTGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
3187 3307 3.420482 CCTCCCGCCCCCTGATTT 61.420 66.667 0.00 0.00 0.00 2.17
3197 3317 4.394712 CACTGTGGACCCTCCCGC 62.395 72.222 0.00 0.00 35.03 6.13
3240 3360 1.484653 CAACATACGGACCCATCTCCA 59.515 52.381 0.00 0.00 0.00 3.86
3290 3410 2.895404 CCCCTAGGCATGATCCAAAATG 59.105 50.000 2.05 0.00 0.00 2.32
3331 3451 6.378710 AAGGACAACAGAAGTAAAGCTTTC 57.621 37.500 16.57 7.71 37.59 2.62
3435 3751 6.435292 AACTTTACTGTCTATGGTTGAGGT 57.565 37.500 0.00 0.00 0.00 3.85
3576 3893 0.034756 TGTGTTGGACGTGAGATGGG 59.965 55.000 0.00 0.00 0.00 4.00
3640 3957 2.728318 GGACGTTAACTTCGACTCAACC 59.272 50.000 3.71 0.00 0.00 3.77
3663 3980 0.833949 TGGTGACACTTGTGTAGCCA 59.166 50.000 18.31 18.31 33.40 4.75
6718 7517 6.122782 CACATTTTTCGTCGTATATCTGCTG 58.877 40.000 0.00 0.00 0.00 4.41
6733 7532 3.057315 TGGCTTAGCTGAGCACATTTTTC 60.057 43.478 29.20 11.69 44.49 2.29
6765 7564 1.528542 CCTGGCATCTGCATCCCTG 60.529 63.158 4.33 0.00 44.36 4.45
6903 7702 7.514721 ACCCTTGTAGTAATTCAAGAAGTTGA 58.485 34.615 10.64 0.00 42.22 3.18
7142 7943 3.640407 AGCACCCTCCACATGCGT 61.640 61.111 0.00 0.00 44.25 5.24
7499 8300 1.888512 GCTGCAAGGTTCTTGATGGAA 59.111 47.619 11.35 0.00 0.00 3.53
7679 8480 0.747283 CCATGGCACCTGAGAGCTTC 60.747 60.000 0.00 0.00 0.00 3.86
7931 8732 3.443681 CCATCAACAACACCCAAGATACC 59.556 47.826 0.00 0.00 0.00 2.73
8009 8810 0.813184 CAGCCATCATCGGTGCTTTT 59.187 50.000 0.00 0.00 30.08 2.27
8144 8949 2.607750 GCCCAGGACTCAGGACCA 60.608 66.667 0.00 0.00 0.00 4.02
8182 8989 8.906867 AGAAAAACAAATGAGATTGAGAACTCA 58.093 29.630 0.00 0.00 45.19 3.41
8199 9006 8.632679 GGAATCATCTGCCATATAGAAAAACAA 58.367 33.333 0.00 0.00 0.00 2.83
8234 9047 3.008375 TGAGCACATACAGAAGAAAGCCT 59.992 43.478 0.00 0.00 0.00 4.58
8262 9078 0.832135 TGCCGAGGGTCAGAACTCTT 60.832 55.000 2.78 0.00 35.91 2.85
8282 9098 0.537143 TGAGCGCCAAAACTCCATGT 60.537 50.000 2.29 0.00 31.65 3.21
8293 9117 1.746239 CCACATGACATGAGCGCCA 60.746 57.895 22.19 1.52 0.00 5.69
8294 9118 3.104766 CCACATGACATGAGCGCC 58.895 61.111 22.19 0.00 0.00 6.53
8382 9208 1.340248 GAGACACCTGTCCAGACGAAA 59.660 52.381 1.66 0.00 45.85 3.46
8394 9220 2.584391 GGCGAACAGGGAGACACCT 61.584 63.158 0.00 0.00 43.08 4.00
8399 9225 2.683933 GGGAGGCGAACAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
8430 9256 4.219999 GAGGGCAGCGAGAGGAGC 62.220 72.222 0.00 0.00 0.00 4.70
8524 9724 4.873129 GATCGCTTCTCCGCCGCA 62.873 66.667 0.00 0.00 0.00 5.69
8634 9834 4.873129 GAGGGATTGCGCGCTCGA 62.873 66.667 33.29 18.39 37.96 4.04
8641 9841 4.918201 GGGAGCCGAGGGATTGCG 62.918 72.222 0.00 0.00 0.00 4.85
8642 9842 3.764160 CTGGGAGCCGAGGGATTGC 62.764 68.421 0.00 0.00 0.00 3.56
8643 9843 2.507944 CTGGGAGCCGAGGGATTG 59.492 66.667 0.00 0.00 0.00 2.67
8644 9844 2.770048 CCTGGGAGCCGAGGGATT 60.770 66.667 9.52 0.00 0.00 3.01
8664 9864 4.170062 CTGCCATTGTGCTCGCGG 62.170 66.667 6.13 0.00 0.00 6.46
8665 9865 1.634757 TAACTGCCATTGTGCTCGCG 61.635 55.000 0.00 0.00 0.00 5.87
8666 9866 0.734889 ATAACTGCCATTGTGCTCGC 59.265 50.000 0.00 0.00 0.00 5.03
8667 9867 1.064505 CCATAACTGCCATTGTGCTCG 59.935 52.381 0.00 0.00 0.00 5.03
8668 9868 1.202336 GCCATAACTGCCATTGTGCTC 60.202 52.381 0.00 0.00 0.00 4.26
8669 9869 0.819582 GCCATAACTGCCATTGTGCT 59.180 50.000 0.00 0.00 0.00 4.40
8670 9870 0.819582 AGCCATAACTGCCATTGTGC 59.180 50.000 0.00 0.00 0.00 4.57
8671 9871 2.572191 CAGCCATAACTGCCATTGTG 57.428 50.000 0.00 0.00 0.00 3.33
8679 9879 0.804364 TTTCGCTGCAGCCATAACTG 59.196 50.000 32.07 16.56 40.80 3.16
8680 9880 1.533625 TTTTCGCTGCAGCCATAACT 58.466 45.000 32.07 0.00 37.91 2.24
8681 9881 2.346099 TTTTTCGCTGCAGCCATAAC 57.654 45.000 32.07 4.82 37.91 1.89
8682 9882 2.159254 GGATTTTTCGCTGCAGCCATAA 60.159 45.455 32.07 18.56 37.91 1.90
8683 9883 1.405105 GGATTTTTCGCTGCAGCCATA 59.595 47.619 32.07 13.07 37.91 2.74
8684 9884 0.174162 GGATTTTTCGCTGCAGCCAT 59.826 50.000 32.07 16.14 37.91 4.40
8685 9885 0.895100 AGGATTTTTCGCTGCAGCCA 60.895 50.000 32.07 18.81 37.91 4.75
8686 9886 1.094785 TAGGATTTTTCGCTGCAGCC 58.905 50.000 32.07 16.16 37.91 4.85
8687 9887 3.427161 AATAGGATTTTTCGCTGCAGC 57.573 42.857 29.12 29.12 37.78 5.25
8688 9888 4.985413 TCAAATAGGATTTTTCGCTGCAG 58.015 39.130 10.11 10.11 0.00 4.41
8689 9889 5.384063 TTCAAATAGGATTTTTCGCTGCA 57.616 34.783 0.00 0.00 0.00 4.41
8690 9890 4.266265 GCTTCAAATAGGATTTTTCGCTGC 59.734 41.667 0.00 0.00 0.00 5.25
8691 9891 5.644644 AGCTTCAAATAGGATTTTTCGCTG 58.355 37.500 0.00 0.00 0.00 5.18
8692 9892 5.649831 AGAGCTTCAAATAGGATTTTTCGCT 59.350 36.000 0.00 0.00 0.00 4.93
8693 9893 5.884771 AGAGCTTCAAATAGGATTTTTCGC 58.115 37.500 0.00 0.00 0.00 4.70
8694 9894 7.185453 CAGAGAGCTTCAAATAGGATTTTTCG 58.815 38.462 0.00 0.00 0.00 3.46
8695 9895 6.971756 GCAGAGAGCTTCAAATAGGATTTTTC 59.028 38.462 0.00 0.00 41.15 2.29
8696 9896 6.404074 CGCAGAGAGCTTCAAATAGGATTTTT 60.404 38.462 0.00 0.00 42.61 1.94
8697 9897 5.065731 CGCAGAGAGCTTCAAATAGGATTTT 59.934 40.000 0.00 0.00 42.61 1.82
8698 9898 4.574013 CGCAGAGAGCTTCAAATAGGATTT 59.426 41.667 0.00 0.00 42.61 2.17
8699 9899 4.125703 CGCAGAGAGCTTCAAATAGGATT 58.874 43.478 0.00 0.00 42.61 3.01
8700 9900 3.133721 ACGCAGAGAGCTTCAAATAGGAT 59.866 43.478 0.00 0.00 42.61 3.24
8701 9901 2.497675 ACGCAGAGAGCTTCAAATAGGA 59.502 45.455 0.00 0.00 42.61 2.94
8702 9902 2.863137 GACGCAGAGAGCTTCAAATAGG 59.137 50.000 0.00 0.00 40.92 2.57
8703 9903 3.515630 TGACGCAGAGAGCTTCAAATAG 58.484 45.455 0.00 0.00 46.97 1.73
8704 9904 3.592898 TGACGCAGAGAGCTTCAAATA 57.407 42.857 0.00 0.00 46.97 1.40
8705 9905 2.462456 TGACGCAGAGAGCTTCAAAT 57.538 45.000 0.00 0.00 46.97 2.32
8706 9906 3.986970 TGACGCAGAGAGCTTCAAA 57.013 47.368 0.00 0.00 46.97 2.69
8709 9909 1.458827 CAGTTTGACGCAGAGAGCTTC 59.541 52.381 0.00 0.00 41.56 3.86
8710 9910 1.202580 ACAGTTTGACGCAGAGAGCTT 60.203 47.619 0.00 0.00 42.61 3.74
8711 9911 0.390860 ACAGTTTGACGCAGAGAGCT 59.609 50.000 0.00 0.00 42.61 4.09
8712 9912 0.787183 GACAGTTTGACGCAGAGAGC 59.213 55.000 0.00 0.00 40.87 4.09
8713 9913 1.423395 GGACAGTTTGACGCAGAGAG 58.577 55.000 0.00 0.00 0.00 3.20
8714 9914 0.318699 CGGACAGTTTGACGCAGAGA 60.319 55.000 0.00 0.00 0.00 3.10
8715 9915 1.284982 CCGGACAGTTTGACGCAGAG 61.285 60.000 0.00 0.00 0.00 3.35
8716 9916 1.300620 CCGGACAGTTTGACGCAGA 60.301 57.895 0.00 0.00 0.00 4.26
8717 9917 2.954753 GCCGGACAGTTTGACGCAG 61.955 63.158 5.05 0.00 0.00 5.18
8718 9918 2.970324 GCCGGACAGTTTGACGCA 60.970 61.111 5.05 0.00 0.00 5.24
8719 9919 4.072088 CGCCGGACAGTTTGACGC 62.072 66.667 5.05 0.00 0.00 5.19
8720 9920 1.886861 CTTCGCCGGACAGTTTGACG 61.887 60.000 5.05 0.00 0.00 4.35
8721 9921 1.860078 CTTCGCCGGACAGTTTGAC 59.140 57.895 5.05 0.00 0.00 3.18
8722 9922 1.959226 GCTTCGCCGGACAGTTTGA 60.959 57.895 5.05 0.00 0.00 2.69
8723 9923 1.781025 TTGCTTCGCCGGACAGTTTG 61.781 55.000 5.05 0.00 0.00 2.93
8724 9924 1.098712 TTTGCTTCGCCGGACAGTTT 61.099 50.000 5.05 0.00 0.00 2.66
8725 9925 1.098712 TTTTGCTTCGCCGGACAGTT 61.099 50.000 5.05 0.00 0.00 3.16
8726 9926 1.525077 TTTTGCTTCGCCGGACAGT 60.525 52.632 5.05 0.00 0.00 3.55
8727 9927 1.082104 GTTTTGCTTCGCCGGACAG 60.082 57.895 5.05 0.00 0.00 3.51
8728 9928 2.548295 GGTTTTGCTTCGCCGGACA 61.548 57.895 5.05 0.00 0.00 4.02
8729 9929 1.862602 ATGGTTTTGCTTCGCCGGAC 61.863 55.000 5.05 0.00 0.00 4.79
8730 9930 1.582610 GATGGTTTTGCTTCGCCGGA 61.583 55.000 5.05 0.00 0.00 5.14
8731 9931 1.154035 GATGGTTTTGCTTCGCCGG 60.154 57.895 0.00 0.00 0.00 6.13
8732 9932 1.511887 CGATGGTTTTGCTTCGCCG 60.512 57.895 0.00 0.00 0.00 6.46
8733 9933 0.179189 CTCGATGGTTTTGCTTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
8734 9934 0.794605 GCTCGATGGTTTTGCTTCGC 60.795 55.000 0.00 0.00 0.00 4.70
8735 9935 0.519175 CGCTCGATGGTTTTGCTTCG 60.519 55.000 0.00 0.00 0.00 3.79
8736 9936 0.517316 ACGCTCGATGGTTTTGCTTC 59.483 50.000 0.00 0.00 0.00 3.86
8737 9937 0.238289 CACGCTCGATGGTTTTGCTT 59.762 50.000 0.00 0.00 0.00 3.91
8738 9938 0.602638 TCACGCTCGATGGTTTTGCT 60.603 50.000 0.00 0.00 0.00 3.91
8739 9939 0.179215 CTCACGCTCGATGGTTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
8740 9940 0.179215 GCTCACGCTCGATGGTTTTG 60.179 55.000 0.00 0.00 0.00 2.44
8741 9941 0.602638 TGCTCACGCTCGATGGTTTT 60.603 50.000 0.00 0.00 36.97 2.43
8742 9942 0.602638 TTGCTCACGCTCGATGGTTT 60.603 50.000 0.00 0.00 36.97 3.27
8743 9943 0.391661 ATTGCTCACGCTCGATGGTT 60.392 50.000 0.00 0.00 36.97 3.67
8744 9944 1.086067 CATTGCTCACGCTCGATGGT 61.086 55.000 0.00 0.00 36.97 3.55
8745 9945 1.640069 CATTGCTCACGCTCGATGG 59.360 57.895 0.00 0.00 36.97 3.51
8746 9946 1.011463 GCATTGCTCACGCTCGATG 60.011 57.895 0.16 0.00 36.97 3.84
8747 9947 2.176273 GGCATTGCTCACGCTCGAT 61.176 57.895 8.82 0.00 36.97 3.59
8748 9948 2.815211 GGCATTGCTCACGCTCGA 60.815 61.111 8.82 0.00 36.97 4.04
8749 9949 3.869272 GGGCATTGCTCACGCTCG 61.869 66.667 8.82 0.00 36.97 5.03
8750 9950 0.744414 TAAGGGCATTGCTCACGCTC 60.744 55.000 11.86 0.00 36.97 5.03
8751 9951 0.322456 TTAAGGGCATTGCTCACGCT 60.322 50.000 11.86 0.00 36.97 5.07
8752 9952 0.525761 TTTAAGGGCATTGCTCACGC 59.474 50.000 11.86 0.00 0.00 5.34
8753 9953 3.296322 TTTTTAAGGGCATTGCTCACG 57.704 42.857 11.86 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.