Multiple sequence alignment - TraesCS6A01G007400

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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 TraesCS6A01G007400 chr6A 100.000 7892 0 0 1 7892 2951127 2959018 0.000000e+00 14574
1 TraesCS6A01G007400 chr6A 78.419 797 121 27 7124 7885 32663360 32664140 9.270000e-129 472
2 TraesCS6A01G007400 chr6D 89.289 3968 234 89 3792 7618 4632466 4636383 0.000000e+00 4796
3 TraesCS6A01G007400 chr6D 93.147 1649 58 19 718 2330 4629120 4630749 0.000000e+00 2368
4 TraesCS6A01G007400 chr6D 90.840 1452 75 20 2408 3829 4630926 4632349 0.000000e+00 1892
5 TraesCS6A01G007400 chr6D 87.857 560 53 10 45 591 4628562 4629119 1.860000e-180 643
6 TraesCS6A01G007400 chr6D 85.833 120 6 5 2292 2411 4630747 4630855 5.000000e-22 117
7 TraesCS6A01G007400 chr6B 90.114 2276 144 39 44 2272 7944888 7942647 0.000000e+00 2881
8 TraesCS6A01G007400 chr6B 91.061 1074 56 17 5542 6575 7938957 7937884 0.000000e+00 1415
9 TraesCS6A01G007400 chr6B 89.532 1089 86 6 2404 3476 7942475 7941399 0.000000e+00 1354
10 TraesCS6A01G007400 chr6B 94.342 760 32 8 3776 4532 7941126 7940375 0.000000e+00 1155
11 TraesCS6A01G007400 chr6B 93.780 418 26 0 5564 5981 7842649 7842232 5.200000e-176 628
12 TraesCS6A01G007400 chr6B 86.689 586 43 13 4978 5537 7939584 7939008 1.130000e-172 617
13 TraesCS6A01G007400 chr6B 93.333 390 24 1 4605 4994 7939985 7939598 6.870000e-160 575
14 TraesCS6A01G007400 chr6B 85.821 536 16 24 6600 7089 7937801 7937280 1.520000e-141 514
15 TraesCS6A01G007400 chr6B 80.463 691 107 27 7153 7831 130297676 130298350 3.290000e-138 503
16 TraesCS6A01G007400 chr6B 94.690 226 11 1 3618 3842 7941351 7941126 4.530000e-92 350
17 TraesCS6A01G007400 chr6B 83.155 374 47 12 2404 2770 7941984 7941620 2.120000e-85 327
18 TraesCS6A01G007400 chr6B 83.730 252 29 7 123 371 7956865 7956623 2.220000e-55 228
19 TraesCS6A01G007400 chr6B 85.047 107 5 4 2305 2411 7942639 7942544 1.810000e-16 99
20 TraesCS6A01G007400 chr1D 87.050 556 68 3 3973 4526 46313146 46312593 6.720000e-175 625
21 TraesCS6A01G007400 chr1D 81.795 780 109 27 7125 7882 445363978 445363210 2.420000e-174 623
22 TraesCS6A01G007400 chr1D 84.259 324 44 6 2511 2830 46319263 46318943 7.690000e-80 309
23 TraesCS6A01G007400 chr1D 78.539 219 37 4 2498 2706 473749258 473749476 1.380000e-27 135
24 TraesCS6A01G007400 chr1A 82.157 751 103 24 7154 7884 531655611 531654872 4.050000e-172 616
25 TraesCS6A01G007400 chr3D 81.345 788 103 33 7124 7883 4008390 4009161 1.130000e-167 601
26 TraesCS6A01G007400 chr5D 80.880 727 115 22 7166 7883 404763142 404763853 1.160000e-152 551
27 TraesCS6A01G007400 chr5D 80.713 617 95 20 7124 7729 371059689 371060292 7.220000e-125 459
28 TraesCS6A01G007400 chr3B 79.873 790 112 28 7126 7885 433686991 433686219 1.170000e-147 534
29 TraesCS6A01G007400 chr3B 81.356 354 45 10 3943 4286 20435418 20435760 1.310000e-67 268
30 TraesCS6A01G007400 chr3B 85.350 157 17 5 3948 4099 20437217 20437372 2.950000e-34 158
31 TraesCS6A01G007400 chr5A 82.669 577 74 22 7124 7691 635944958 635944399 9.200000e-134 488
32 TraesCS6A01G007400 chr4A 79.457 516 92 12 4755 5261 719166499 719165989 3.500000e-93 353
33 TraesCS6A01G007400 chr4A 83.582 134 22 0 5607 5740 719165733 719165600 8.310000e-25 126
34 TraesCS6A01G007400 chr7A 79.256 511 100 6 4755 5261 5182152 5181644 1.260000e-92 351
35 TraesCS6A01G007400 chr7A 79.029 515 95 12 4755 5261 14732732 14733241 2.730000e-89 340
36 TraesCS6A01G007400 chr7A 84.328 134 21 0 5607 5740 5181327 5181194 1.790000e-26 132
37 TraesCS6A01G007400 chr7A 82.857 140 24 0 5601 5740 14733491 14733630 8.310000e-25 126
38 TraesCS6A01G007400 chr7D 79.029 515 97 9 4755 5261 15831709 15832220 7.580000e-90 342
39 TraesCS6A01G007400 chr7D 82.857 140 24 0 5601 5740 15832526 15832665 8.310000e-25 126


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 TraesCS6A01G007400 chr6A 2951127 2959018 7891 False 14574.0 14574 100.0000 1 7892 1 chr6A.!!$F1 7891
1 TraesCS6A01G007400 chr6A 32663360 32664140 780 False 472.0 472 78.4190 7124 7885 1 chr6A.!!$F2 761
2 TraesCS6A01G007400 chr6D 4628562 4636383 7821 False 1963.2 4796 89.3932 45 7618 5 chr6D.!!$F1 7573
3 TraesCS6A01G007400 chr6B 7937280 7944888 7608 True 928.7 2881 89.3784 44 7089 10 chr6B.!!$R3 7045
4 TraesCS6A01G007400 chr6B 130297676 130298350 674 False 503.0 503 80.4630 7153 7831 1 chr6B.!!$F1 678
5 TraesCS6A01G007400 chr1D 46312593 46313146 553 True 625.0 625 87.0500 3973 4526 1 chr1D.!!$R1 553
6 TraesCS6A01G007400 chr1D 445363210 445363978 768 True 623.0 623 81.7950 7125 7882 1 chr1D.!!$R3 757
7 TraesCS6A01G007400 chr1A 531654872 531655611 739 True 616.0 616 82.1570 7154 7884 1 chr1A.!!$R1 730
8 TraesCS6A01G007400 chr3D 4008390 4009161 771 False 601.0 601 81.3450 7124 7883 1 chr3D.!!$F1 759
9 TraesCS6A01G007400 chr5D 404763142 404763853 711 False 551.0 551 80.8800 7166 7883 1 chr5D.!!$F2 717
10 TraesCS6A01G007400 chr5D 371059689 371060292 603 False 459.0 459 80.7130 7124 7729 1 chr5D.!!$F1 605
11 TraesCS6A01G007400 chr3B 433686219 433686991 772 True 534.0 534 79.8730 7126 7885 1 chr3B.!!$R1 759
12 TraesCS6A01G007400 chr3B 20435418 20437372 1954 False 213.0 268 83.3530 3943 4286 2 chr3B.!!$F1 343
13 TraesCS6A01G007400 chr5A 635944399 635944958 559 True 488.0 488 82.6690 7124 7691 1 chr5A.!!$R1 567
14 TraesCS6A01G007400 chr4A 719165600 719166499 899 True 239.5 353 81.5195 4755 5740 2 chr4A.!!$R1 985
15 TraesCS6A01G007400 chr7A 5181194 5182152 958 True 241.5 351 81.7920 4755 5740 2 chr7A.!!$R1 985
16 TraesCS6A01G007400 chr7A 14732732 14733630 898 False 233.0 340 80.9430 4755 5740 2 chr7A.!!$F1 985
17 TraesCS6A01G007400 chr7D 15831709 15832665 956 False 234.0 342 80.9430 4755 5740 2 chr7D.!!$F1 985

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
19 20 0.105593 GCGATGGAGAGGAAGCATGA 59.894 55.0 0.00 0.0 0.00 3.07 F
464 476 0.163788 CGCCACTTTACGTTCTGCTG 59.836 55.0 0.00 0.0 0.00 4.41 F
880 903 0.426022 ACTTCCCCTACCCAATCCCT 59.574 55.0 0.00 0.0 0.00 4.20 F
2320 2420 0.535335 TCTCACCATTCGGCAGGTAC 59.465 55.0 0.00 0.0 36.07 3.34 F
2321 2421 0.537188 CTCACCATTCGGCAGGTACT 59.463 55.0 0.00 0.0 36.07 2.73 F
3242 3427 0.603569 CAGGAACCGACACTAGCACT 59.396 55.0 0.00 0.0 0.00 4.40 F
3897 4253 0.459759 GCTAGGACCAGTAACCGCAC 60.460 60.0 0.00 0.0 0.00 5.34 F
4507 6666 0.108138 ATGTGACGTAGCAGCCCTTC 60.108 55.0 0.00 0.0 0.00 3.46 F
5950 8777 0.869880 TGGTGATATTCTGCGTCGCG 60.870 55.0 13.38 0.0 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1934 0.739813 GGCAGCCGTTCACGATAAGT 60.740 55.000 0.00 0.00 43.02 2.24 R
2023 2069 0.461693 GCTGTGCTCCTGATGGTCTC 60.462 60.000 0.00 0.00 34.23 3.36 R
2719 2895 0.036671 GCTAGTGCCGGTTACTGGTT 60.037 55.000 19.64 1.06 0.00 3.67 R
3254 3439 1.068264 GCAAAAGGGTGCTGAGCTAAC 60.068 52.381 5.83 0.00 41.51 2.34 R
3636 3840 1.186200 GGATCTTTGACTTTGGGGGC 58.814 55.000 0.00 0.00 0.00 5.80 R
4494 6653 1.696832 GCTTTCGAAGGGCTGCTACG 61.697 60.000 9.52 1.04 0.00 3.51 R
5678 8486 0.409484 AAGACAACCCATTCCCCTGG 59.591 55.000 0.00 0.00 35.95 4.45 R
6332 9178 1.373748 CCCCGTGTGGTCGTTGTAG 60.374 63.158 0.00 0.00 0.00 2.74 R
7116 10107 0.107066 TACTGTATCTCGGGCCGTCA 60.107 55.000 27.32 14.11 0.00 4.35 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
18 19 2.614581 GCGATGGAGAGGAAGCATG 58.385 57.895 0.00 0.00 0.00 4.06
19 20 0.105593 GCGATGGAGAGGAAGCATGA 59.894 55.000 0.00 0.00 0.00 3.07
20 21 1.473965 GCGATGGAGAGGAAGCATGAA 60.474 52.381 0.00 0.00 0.00 2.57
21 22 2.208431 CGATGGAGAGGAAGCATGAAC 58.792 52.381 0.00 0.00 0.00 3.18
22 23 2.570135 GATGGAGAGGAAGCATGAACC 58.430 52.381 0.00 0.00 0.00 3.62
23 24 0.250234 TGGAGAGGAAGCATGAACCG 59.750 55.000 0.00 0.00 0.00 4.44
24 25 0.250513 GGAGAGGAAGCATGAACCGT 59.749 55.000 0.00 0.00 0.00 4.83
25 26 1.646189 GAGAGGAAGCATGAACCGTC 58.354 55.000 0.00 0.00 0.00 4.79
26 27 0.976641 AGAGGAAGCATGAACCGTCA 59.023 50.000 0.00 0.00 38.41 4.35
27 28 1.556911 AGAGGAAGCATGAACCGTCAT 59.443 47.619 0.00 0.00 45.80 3.06
28 29 2.766263 AGAGGAAGCATGAACCGTCATA 59.234 45.455 0.00 0.00 42.88 2.15
29 30 3.126831 GAGGAAGCATGAACCGTCATAG 58.873 50.000 0.00 0.00 42.88 2.23
30 31 2.766263 AGGAAGCATGAACCGTCATAGA 59.234 45.455 0.00 0.00 42.88 1.98
31 32 3.126831 GGAAGCATGAACCGTCATAGAG 58.873 50.000 0.00 0.00 42.88 2.43
32 33 2.231215 AGCATGAACCGTCATAGAGC 57.769 50.000 0.00 0.00 42.88 4.09
33 34 0.855349 GCATGAACCGTCATAGAGCG 59.145 55.000 0.00 0.00 42.88 5.03
34 35 1.536072 GCATGAACCGTCATAGAGCGA 60.536 52.381 0.00 0.00 42.88 4.93
35 36 2.809446 CATGAACCGTCATAGAGCGAA 58.191 47.619 0.00 0.00 42.88 4.70
36 37 3.186909 CATGAACCGTCATAGAGCGAAA 58.813 45.455 0.00 0.00 42.88 3.46
37 38 2.602878 TGAACCGTCATAGAGCGAAAC 58.397 47.619 0.00 0.00 0.00 2.78
38 39 1.925185 GAACCGTCATAGAGCGAAACC 59.075 52.381 0.00 0.00 0.00 3.27
39 40 0.892755 ACCGTCATAGAGCGAAACCA 59.107 50.000 0.00 0.00 0.00 3.67
40 41 1.480954 ACCGTCATAGAGCGAAACCAT 59.519 47.619 0.00 0.00 0.00 3.55
41 42 1.860950 CCGTCATAGAGCGAAACCATG 59.139 52.381 0.00 0.00 0.00 3.66
42 43 1.860950 CGTCATAGAGCGAAACCATGG 59.139 52.381 11.19 11.19 0.00 3.66
43 44 1.599542 GTCATAGAGCGAAACCATGGC 59.400 52.381 13.04 0.00 0.00 4.40
52 53 0.603065 GAAACCATGGCAACCTCACC 59.397 55.000 13.04 0.00 0.00 4.02
67 68 3.886505 ACCTCACCTTTGACGCAAAAATA 59.113 39.130 6.50 0.00 32.75 1.40
68 69 4.023193 ACCTCACCTTTGACGCAAAAATAG 60.023 41.667 6.50 3.22 32.75 1.73
69 70 3.896122 TCACCTTTGACGCAAAAATAGC 58.104 40.909 6.50 0.00 32.75 2.97
83 84 2.761786 AATAGCCAGGGCAACATCAT 57.238 45.000 13.63 0.00 44.88 2.45
141 142 5.385198 GTTGGATATCCATAACACCACCAT 58.615 41.667 25.07 0.00 46.97 3.55
158 160 2.557924 ACCATCGCAAAAGAGCATGAAA 59.442 40.909 0.00 0.00 0.00 2.69
163 165 5.125100 TCGCAAAAGAGCATGAAAAAGAT 57.875 34.783 0.00 0.00 0.00 2.40
190 196 7.674471 TCATTATATCCACACGAACACAAAA 57.326 32.000 0.00 0.00 0.00 2.44
192 198 6.862711 TTATATCCACACGAACACAAAACA 57.137 33.333 0.00 0.00 0.00 2.83
193 199 5.759506 ATATCCACACGAACACAAAACAA 57.240 34.783 0.00 0.00 0.00 2.83
233 239 0.655733 CCAAGACGACGCAAACACTT 59.344 50.000 0.00 0.00 0.00 3.16
237 243 0.935196 GACGACGCAAACACTTCCTT 59.065 50.000 0.00 0.00 0.00 3.36
239 245 1.217882 CGACGCAAACACTTCCTTCT 58.782 50.000 0.00 0.00 0.00 2.85
270 277 2.650322 TCAAAAGCCGAAAGAACCACT 58.350 42.857 0.00 0.00 0.00 4.00
278 285 1.270305 CGAAAGAACCACTGCTCCAGA 60.270 52.381 0.00 0.00 35.18 3.86
297 308 7.118496 TCCAGATGAAGATCTAGAGAAAACC 57.882 40.000 0.00 0.00 36.75 3.27
298 309 6.098982 TCCAGATGAAGATCTAGAGAAAACCC 59.901 42.308 0.00 0.00 36.75 4.11
304 315 6.375455 TGAAGATCTAGAGAAAACCCATTTGC 59.625 38.462 0.00 0.00 0.00 3.68
315 326 2.397597 ACCCATTTGCCAGTCTTGTTT 58.602 42.857 0.00 0.00 0.00 2.83
318 329 4.407296 ACCCATTTGCCAGTCTTGTTTAAA 59.593 37.500 0.00 0.00 0.00 1.52
319 330 4.749598 CCCATTTGCCAGTCTTGTTTAAAC 59.250 41.667 11.54 11.54 0.00 2.01
351 362 2.452491 AGCCCCAAGGTCAAGGGT 60.452 61.111 0.00 0.00 43.89 4.34
398 410 0.749091 CCATGAGCTCGGCCATGAAA 60.749 55.000 13.26 0.00 38.51 2.69
421 433 3.802948 AACGAAGAGTATGGATCGCTT 57.197 42.857 0.00 0.00 38.80 4.68
454 466 2.998480 TCCCCTCGCGCCACTTTA 60.998 61.111 0.00 0.00 0.00 1.85
455 467 2.818274 CCCCTCGCGCCACTTTAC 60.818 66.667 0.00 0.00 0.00 2.01
456 468 3.186047 CCCTCGCGCCACTTTACG 61.186 66.667 0.00 0.00 0.00 3.18
457 469 2.431942 CCTCGCGCCACTTTACGT 60.432 61.111 0.00 0.00 0.00 3.57
459 471 1.414897 CTCGCGCCACTTTACGTTC 59.585 57.895 0.00 0.00 0.00 3.95
461 473 1.129809 CGCGCCACTTTACGTTCTG 59.870 57.895 0.00 0.00 0.00 3.02
462 474 1.154469 GCGCCACTTTACGTTCTGC 60.154 57.895 0.00 0.00 0.00 4.26
463 475 1.566018 GCGCCACTTTACGTTCTGCT 61.566 55.000 0.00 0.00 0.00 4.24
464 476 0.163788 CGCCACTTTACGTTCTGCTG 59.836 55.000 0.00 0.00 0.00 4.41
527 541 3.942539 TTGTCGACAACAGTGACAATG 57.057 42.857 26.53 0.41 44.97 2.82
529 543 1.867233 GTCGACAACAGTGACAATGCT 59.133 47.619 11.55 0.00 32.91 3.79
622 642 8.462811 ACTACTCTCTGTGTGTCATAATGTAAG 58.537 37.037 0.00 0.00 0.00 2.34
624 644 8.072321 ACTCTCTGTGTGTCATAATGTAAGAT 57.928 34.615 0.00 0.00 0.00 2.40
625 645 9.190317 ACTCTCTGTGTGTCATAATGTAAGATA 57.810 33.333 0.00 0.00 0.00 1.98
749 770 7.285172 TGGGGTTATTCACATAATCACATTCAG 59.715 37.037 0.00 0.00 34.88 3.02
766 787 9.682465 TCACATTCAGAAGTAGTAGTACTATGT 57.318 33.333 13.09 12.51 38.66 2.29
874 897 1.540367 CCACCACTTCCCCTACCCA 60.540 63.158 0.00 0.00 0.00 4.51
876 899 0.999712 CACCACTTCCCCTACCCAAT 59.000 55.000 0.00 0.00 0.00 3.16
880 903 0.426022 ACTTCCCCTACCCAATCCCT 59.574 55.000 0.00 0.00 0.00 4.20
1133 1175 1.369448 CTACTCCATCGCGCTCGTC 60.369 63.158 5.56 0.00 36.96 4.20
1167 1209 4.000620 TGCCCTACGACCTCCCCA 62.001 66.667 0.00 0.00 0.00 4.96
1402 1447 2.049156 CTCGGTGCTGCAGAACGA 60.049 61.111 20.43 20.22 0.00 3.85
1601 1646 3.764466 CAGGAGAAGAGGCGGCGT 61.764 66.667 9.37 0.00 0.00 5.68
1943 1988 0.969894 AGCTGACCGACTTGCTTAGT 59.030 50.000 0.00 0.00 40.71 2.24
2023 2069 4.962362 AGGCTTATGGGGAAAGGTAAATTG 59.038 41.667 0.00 0.00 0.00 2.32
2071 2133 7.083858 TGTATAAGTTGAGCTGAATTTTGTGC 58.916 34.615 0.00 0.00 0.00 4.57
2072 2134 4.660789 AAGTTGAGCTGAATTTTGTGCT 57.339 36.364 0.00 0.00 38.59 4.40
2073 2135 5.772825 AAGTTGAGCTGAATTTTGTGCTA 57.227 34.783 0.00 0.00 35.76 3.49
2074 2136 5.772825 AGTTGAGCTGAATTTTGTGCTAA 57.227 34.783 0.00 0.00 35.76 3.09
2075 2137 6.147864 AGTTGAGCTGAATTTTGTGCTAAA 57.852 33.333 0.00 0.00 35.76 1.85
2076 2138 6.752168 AGTTGAGCTGAATTTTGTGCTAAAT 58.248 32.000 0.00 0.00 35.76 1.40
2217 2284 6.948309 CCCAGGTTTATATAAATGGAAGGGAG 59.052 42.308 21.79 7.06 30.52 4.30
2251 2318 6.299141 AGTGAGCTCAAAATTCTCAAGGTAA 58.701 36.000 20.19 0.00 38.42 2.85
2316 2416 1.205655 TCTTCTCTCACCATTCGGCAG 59.794 52.381 0.00 0.00 34.57 4.85
2318 2418 0.904865 TCTCTCACCATTCGGCAGGT 60.905 55.000 0.00 0.00 39.10 4.00
2319 2419 0.824109 CTCTCACCATTCGGCAGGTA 59.176 55.000 0.00 0.00 36.07 3.08
2320 2420 0.535335 TCTCACCATTCGGCAGGTAC 59.465 55.000 0.00 0.00 36.07 3.34
2321 2421 0.537188 CTCACCATTCGGCAGGTACT 59.463 55.000 0.00 0.00 36.07 2.73
2447 2623 4.993905 AGCATTTATTTTCCGTTACAGCC 58.006 39.130 0.00 0.00 0.00 4.85
2567 2743 7.486870 ACCAGTTTGTTCGTTAAATTTTCAGTC 59.513 33.333 0.00 0.00 0.00 3.51
2569 2745 9.710979 CAGTTTGTTCGTTAAATTTTCAGTCTA 57.289 29.630 0.00 0.00 0.00 2.59
2660 2836 3.594885 CGTAAATGTAACGGTTTTGTCGC 59.405 43.478 0.00 0.00 36.71 5.19
2711 2887 3.523157 TCATGAATGGAAGTTCCCTGCTA 59.477 43.478 19.42 0.00 35.03 3.49
2719 2895 4.153411 GGAAGTTCCCTGCTATAGCTAGA 58.847 47.826 24.61 15.34 42.66 2.43
2722 2898 3.898741 AGTTCCCTGCTATAGCTAGAACC 59.101 47.826 30.27 20.86 41.43 3.62
2790 2974 4.157849 TGGATACGTGGCCATGATTTAA 57.842 40.909 31.74 10.80 42.51 1.52
2841 3025 4.210307 GCCTTCGAAGGGCTCTTC 57.790 61.111 38.28 21.05 46.56 2.87
2883 3067 1.200948 GAACCCACTGCATTCAGAAGC 59.799 52.381 0.00 0.00 42.95 3.86
2917 3101 7.488322 AGTGTCTGAACTCTTATCTATGCTTC 58.512 38.462 0.00 0.00 0.00 3.86
2993 3178 8.613060 TTCAAGTCTAATAATGAGATCCATGC 57.387 34.615 0.00 0.00 35.24 4.06
3060 3245 7.540299 TCAACCAGTTTGTTTCGTTAAATCTT 58.460 30.769 0.00 0.00 36.49 2.40
3083 3268 2.634815 ATGAGATCCATGTGACAGGC 57.365 50.000 0.00 0.00 33.39 4.85
3115 3300 7.778382 GCCATATCCCTTTTTAAGACTTCCTAA 59.222 37.037 0.00 0.00 0.00 2.69
3122 3307 7.361799 CCCTTTTTAAGACTTCCTAATTCACGG 60.362 40.741 0.00 0.00 0.00 4.94
3226 3411 1.137872 CCTGCTGTAGCTAGAACCAGG 59.862 57.143 17.52 17.52 42.66 4.45
3232 3417 2.097825 GTAGCTAGAACCAGGAACCGA 58.902 52.381 0.00 0.00 0.00 4.69
3242 3427 0.603569 CAGGAACCGACACTAGCACT 59.396 55.000 0.00 0.00 0.00 4.40
3285 3470 3.477530 CACCCTTTTGCCCTAGCTATAC 58.522 50.000 0.00 0.00 40.80 1.47
3297 3482 6.610020 TGCCCTAGCTATACTTTAGTCTTTGA 59.390 38.462 0.00 0.00 40.80 2.69
3408 3612 4.636249 AGGAAGTCACAAGATCAGTCAAC 58.364 43.478 0.00 0.00 0.00 3.18
3472 3676 4.872691 CAGTGTGATTTGATACCCTGAGAC 59.127 45.833 0.00 0.00 0.00 3.36
3473 3677 4.080863 AGTGTGATTTGATACCCTGAGACC 60.081 45.833 0.00 0.00 0.00 3.85
3474 3678 3.843619 TGTGATTTGATACCCTGAGACCA 59.156 43.478 0.00 0.00 0.00 4.02
3475 3679 4.474651 TGTGATTTGATACCCTGAGACCAT 59.525 41.667 0.00 0.00 0.00 3.55
3478 3682 4.689612 TTTGATACCCTGAGACCATAGC 57.310 45.455 0.00 0.00 0.00 2.97
3484 3688 6.558775 TGATACCCTGAGACCATAGCTATTTT 59.441 38.462 2.64 0.00 0.00 1.82
3522 3726 3.270877 ACAATTTGATACCCTGAGACGC 58.729 45.455 2.79 0.00 0.00 5.19
3541 3745 3.093574 CGCGAGCACATTAGTTTGAATG 58.906 45.455 0.00 0.00 41.69 2.67
3596 3800 7.860584 ACCATATATTTTGCCATTTGTTTCCT 58.139 30.769 0.00 0.00 0.00 3.36
3767 3971 4.196971 ACTGCCATATCCGTTTTAAGACC 58.803 43.478 0.00 0.00 0.00 3.85
3835 4191 4.713553 TGGTTTTGTCATTCTGTAGAGCA 58.286 39.130 0.00 0.00 0.00 4.26
3873 4229 4.656100 TTGATGAATGGAAGTTCCCTGA 57.344 40.909 19.42 0.76 35.03 3.86
3895 4251 1.066757 GTAGCTAGGACCAGTAACCGC 59.933 57.143 0.00 0.00 0.00 5.68
3896 4252 0.613853 AGCTAGGACCAGTAACCGCA 60.614 55.000 0.00 0.00 0.00 5.69
3897 4253 0.459759 GCTAGGACCAGTAACCGCAC 60.460 60.000 0.00 0.00 0.00 5.34
3898 4254 1.183549 CTAGGACCAGTAACCGCACT 58.816 55.000 0.00 0.00 0.00 4.40
3903 4261 1.000060 GACCAGTAACCGCACTACACA 60.000 52.381 0.00 0.00 0.00 3.72
3906 4264 3.071479 CCAGTAACCGCACTACACATTT 58.929 45.455 0.00 0.00 0.00 2.32
3956 4314 6.828273 TGGATACACACCCATGATTTAAAGAG 59.172 38.462 0.00 0.00 46.17 2.85
3969 4327 5.546499 TGATTTAAAGAGTCCCTGTACCTGT 59.454 40.000 0.00 0.00 0.00 4.00
3970 4328 4.884668 TTAAAGAGTCCCTGTACCTGTG 57.115 45.455 0.00 0.00 0.00 3.66
4004 4362 3.931578 TGTGCCTTAGAAGAGCTCTTTC 58.068 45.455 29.02 20.68 36.11 2.62
4344 6503 5.633655 TTCCCTTTGTACCAAGAACTGTA 57.366 39.130 8.23 0.00 0.00 2.74
4392 6551 3.118811 TCCAAAAACTGTTGCTTCTTGGG 60.119 43.478 13.77 4.66 34.03 4.12
4437 6596 7.016072 AGCACTATATTTAAGCAGGTCTGATCT 59.984 37.037 1.65 0.00 0.00 2.75
4448 6607 4.829968 CAGGTCTGATCTGATTTCACACT 58.170 43.478 12.63 0.00 34.36 3.55
4475 6634 3.684408 ACCTAGAATTACTCCCGGTCT 57.316 47.619 0.00 0.00 0.00 3.85
4479 6638 0.539986 GAATTACTCCCGGTCTGGCA 59.460 55.000 0.00 0.00 35.87 4.92
4494 6653 4.332819 GGTCTGGCACTGTAATTATGTGAC 59.667 45.833 19.24 17.67 39.94 3.67
4507 6666 0.108138 ATGTGACGTAGCAGCCCTTC 60.108 55.000 0.00 0.00 0.00 3.46
4526 6685 5.360591 CCTTCGAAAGCCAGTAGTGATTAT 58.639 41.667 0.00 0.00 0.00 1.28
4527 6686 5.463724 CCTTCGAAAGCCAGTAGTGATTATC 59.536 44.000 0.00 0.00 0.00 1.75
4570 6764 3.274288 CAAACCTGAAGAGATGGGCTAC 58.726 50.000 0.00 0.00 0.00 3.58
4596 6790 6.656314 TGTTCGTATAGCACAATAACAAGG 57.344 37.500 0.00 0.00 0.00 3.61
4638 6832 6.491062 TGAGTTTTCATGAGTCATGGTTCATT 59.509 34.615 28.54 13.14 41.66 2.57
4639 6833 7.014518 TGAGTTTTCATGAGTCATGGTTCATTT 59.985 33.333 28.54 11.75 41.66 2.32
4640 6834 7.149973 AGTTTTCATGAGTCATGGTTCATTTG 58.850 34.615 28.54 5.82 41.66 2.32
4662 6856 3.181469 GGTGGAGTTGTGTTGTCTCTACA 60.181 47.826 9.33 0.00 40.00 2.74
4740 7225 7.628769 ACATGTTTCATGCTGATATGTGTTA 57.371 32.000 9.27 0.00 30.26 2.41
4752 7237 7.147742 TGCTGATATGTGTTATCCTTCTGTGTA 60.148 37.037 0.00 0.00 36.61 2.90
4775 7260 5.340891 TCAGGCTAAGTACCTCTATGGAT 57.659 43.478 0.00 0.00 39.71 3.41
4970 7455 5.783111 AGCCATTTACTCATGTTTGTTTCC 58.217 37.500 0.00 0.00 0.00 3.13
4972 7457 6.041979 AGCCATTTACTCATGTTTGTTTCCTT 59.958 34.615 0.00 0.00 0.00 3.36
5032 7551 7.259882 TGCAGATGAAAATAAAGCTAATGGTG 58.740 34.615 0.00 0.00 0.00 4.17
5052 7571 4.852104 GGTGCAGATTCGTGTATATACTCG 59.148 45.833 24.42 24.42 42.51 4.18
5079 7598 3.759581 TGCAAGGCTGAAGAAATTCTCT 58.240 40.909 0.00 0.00 35.13 3.10
5264 7783 2.237392 ACTTCTTGAGCAGGGTATGGAC 59.763 50.000 0.00 0.00 0.00 4.02
5275 7794 3.706594 CAGGGTATGGACTCAGAGCTTTA 59.293 47.826 0.00 0.00 33.59 1.85
5281 7800 7.122799 GGGTATGGACTCAGAGCTTTAAAATTT 59.877 37.037 0.00 0.00 33.59 1.82
5355 7874 9.653287 AACTGAGTTTCATTAGATTATCGTTGA 57.347 29.630 0.00 0.00 0.00 3.18
5356 7875 9.307121 ACTGAGTTTCATTAGATTATCGTTGAG 57.693 33.333 0.00 0.00 0.00 3.02
5357 7876 9.307121 CTGAGTTTCATTAGATTATCGTTGAGT 57.693 33.333 0.00 0.00 0.00 3.41
5358 7877 9.653287 TGAGTTTCATTAGATTATCGTTGAGTT 57.347 29.630 0.00 0.00 0.00 3.01
5360 7879 9.653287 AGTTTCATTAGATTATCGTTGAGTTCA 57.347 29.630 0.00 0.00 0.00 3.18
5361 7880 9.690434 GTTTCATTAGATTATCGTTGAGTTCAC 57.310 33.333 0.00 0.00 0.00 3.18
5362 7881 8.420374 TTCATTAGATTATCGTTGAGTTCACC 57.580 34.615 0.00 0.00 0.00 4.02
5364 7883 6.540438 TTAGATTATCGTTGAGTTCACCCT 57.460 37.500 0.00 0.00 0.00 4.34
5424 7972 9.102757 TGAAATATTCAGCAGTGTCTATTCTTC 57.897 33.333 0.00 0.00 34.08 2.87
5430 7978 7.175347 TCAGCAGTGTCTATTCTTCTGTTAT 57.825 36.000 0.00 0.00 0.00 1.89
5494 8042 7.816995 TGCTTGATTTTGTATTTATGTTGGACC 59.183 33.333 0.00 0.00 0.00 4.46
5496 8044 6.326375 TGATTTTGTATTTATGTTGGACCGC 58.674 36.000 0.00 0.00 0.00 5.68
5502 8050 6.818233 TGTATTTATGTTGGACCGCTACATA 58.182 36.000 8.88 8.88 34.55 2.29
5605 8413 3.990092 TGTCCATACGTGGCATATTCTC 58.010 45.455 0.00 0.00 45.63 2.87
5678 8486 4.393371 GTGATCTTTGCTGAAGGAGTAACC 59.607 45.833 0.00 0.00 35.98 2.85
5768 8576 2.044946 AACCCAGAGGCGCATTCC 60.045 61.111 10.83 0.00 36.11 3.01
5822 8630 1.085091 CTTCATGCCTCTCACTGTGC 58.915 55.000 2.12 0.00 0.00 4.57
5830 8657 1.495878 CTCTCACTGTGCACACTCAC 58.504 55.000 17.42 0.00 37.48 3.51
5845 8672 5.803461 GCACACTCACGTCTAATATGTGTTA 59.197 40.000 11.31 0.00 44.23 2.41
5857 8684 9.685828 GTCTAATATGTGTTACTCCTCAGATTC 57.314 37.037 0.00 0.00 0.00 2.52
5950 8777 0.869880 TGGTGATATTCTGCGTCGCG 60.870 55.000 13.38 0.00 0.00 5.87
6037 8864 4.631813 AGCAAAGAGTTATTTGAGGCTACG 59.368 41.667 3.59 0.00 41.71 3.51
6041 8868 5.203060 AGAGTTATTTGAGGCTACGATCC 57.797 43.478 0.00 0.00 0.00 3.36
6068 8895 5.957842 TGCGAAACTTTTTCCATGACTAT 57.042 34.783 0.00 0.00 0.00 2.12
6069 8896 7.624360 ATGCGAAACTTTTTCCATGACTATA 57.376 32.000 0.00 0.00 0.00 1.31
6070 8897 6.837992 TGCGAAACTTTTTCCATGACTATAC 58.162 36.000 0.00 0.00 0.00 1.47
6071 8898 6.653320 TGCGAAACTTTTTCCATGACTATACT 59.347 34.615 0.00 0.00 0.00 2.12
6072 8899 7.820386 TGCGAAACTTTTTCCATGACTATACTA 59.180 33.333 0.00 0.00 0.00 1.82
6073 8900 8.662141 GCGAAACTTTTTCCATGACTATACTAA 58.338 33.333 0.00 0.00 0.00 2.24
6109 8950 7.267600 CAGAATGAAAATTTTGAAAATGCGAGC 59.732 33.333 8.47 0.00 39.69 5.03
6131 8977 4.171005 CCATCATCATTTGTCACTTGTGC 58.829 43.478 0.00 0.00 0.00 4.57
6146 8992 4.641645 TGCTGGACCAGGCAACCG 62.642 66.667 23.09 0.00 35.40 4.44
6215 9061 1.299773 CGAGGAGAAGATCAGCCGC 60.300 63.158 0.00 0.00 0.00 6.53
6332 9178 1.373570 CGATGAAGTTCAAGGAGGCC 58.626 55.000 10.14 0.00 0.00 5.19
6533 9379 2.490217 CGAGCCGAATGAGACCGT 59.510 61.111 0.00 0.00 0.00 4.83
6576 9468 2.484770 GCCGGTTCCTACTAATGATGCA 60.485 50.000 1.90 0.00 0.00 3.96
6579 9471 3.431626 CGGTTCCTACTAATGATGCACCA 60.432 47.826 0.00 0.00 0.00 4.17
6605 9499 2.652530 GCCAGTCGGTTCCGTACA 59.347 61.111 11.04 0.00 33.28 2.90
6684 9596 5.127519 TGATGGATGGGATGTTTTTCATGTC 59.872 40.000 0.00 0.00 36.83 3.06
6817 9743 8.434661 CACCAAAATTGATTAATTTCGTTCTGG 58.565 33.333 16.18 16.18 43.74 3.86
6818 9744 7.602265 ACCAAAATTGATTAATTTCGTTCTGGG 59.398 33.333 19.50 11.34 43.74 4.45
6831 9760 0.535780 TTCTGGGACTGCTGCTGTTG 60.536 55.000 13.49 5.39 0.00 3.33
6845 9774 4.130118 CTGCTGTTGGGAGTATGTATTCC 58.870 47.826 0.00 0.00 0.00 3.01
6879 9817 5.277047 CAGAGAAAACAAAGACTTTGCTCC 58.723 41.667 24.63 13.01 44.39 4.70
7001 9962 4.320608 TTTGCCCTTGAATTGTTCACTC 57.679 40.909 0.00 0.00 39.87 3.51
7031 9993 1.605712 CCCTCGCGTCATCTAATTCCC 60.606 57.143 5.77 0.00 0.00 3.97
7035 9997 2.093921 TCGCGTCATCTAATTCCCAACA 60.094 45.455 5.77 0.00 0.00 3.33
7036 9998 2.872245 CGCGTCATCTAATTCCCAACAT 59.128 45.455 0.00 0.00 0.00 2.71
7064 10026 9.998106 GGGAGTAATATCTTTATGTGCTTTCTA 57.002 33.333 0.00 0.00 0.00 2.10
7133 10124 1.101635 TCTGACGGCCCGAGATACAG 61.102 60.000 11.71 10.94 0.00 2.74
7148 10139 7.081349 CCGAGATACAGTATCACTCTCATTTC 58.919 42.308 20.62 6.90 37.65 2.17
7152 10143 8.762645 AGATACAGTATCACTCTCATTTCCAAA 58.237 33.333 20.62 0.00 37.65 3.28
7885 11058 1.217882 CACGTTGTGTCTTCTCCCAC 58.782 55.000 0.00 0.00 0.00 4.61
7886 11059 0.106149 ACGTTGTGTCTTCTCCCACC 59.894 55.000 0.00 0.00 0.00 4.61
7887 11060 0.393077 CGTTGTGTCTTCTCCCACCT 59.607 55.000 0.00 0.00 0.00 4.00
7888 11061 1.202651 CGTTGTGTCTTCTCCCACCTT 60.203 52.381 0.00 0.00 0.00 3.50
7889 11062 2.745152 CGTTGTGTCTTCTCCCACCTTT 60.745 50.000 0.00 0.00 0.00 3.11
7890 11063 2.879026 GTTGTGTCTTCTCCCACCTTTC 59.121 50.000 0.00 0.00 0.00 2.62
7891 11064 2.123589 TGTGTCTTCTCCCACCTTTCA 58.876 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.105593 TCATGCTTCCTCTCCATCGC 59.894 55.000 0.00 0.00 0.00 4.58
1 2 2.208431 GTTCATGCTTCCTCTCCATCG 58.792 52.381 0.00 0.00 0.00 3.84
2 3 2.570135 GGTTCATGCTTCCTCTCCATC 58.430 52.381 0.00 0.00 0.00 3.51
5 6 0.250513 ACGGTTCATGCTTCCTCTCC 59.749 55.000 0.00 0.00 0.00 3.71
6 7 1.066858 TGACGGTTCATGCTTCCTCTC 60.067 52.381 0.00 0.00 0.00 3.20
8 9 2.029838 ATGACGGTTCATGCTTCCTC 57.970 50.000 0.00 0.00 41.23 3.71
9 10 2.766263 TCTATGACGGTTCATGCTTCCT 59.234 45.455 0.00 0.00 42.79 3.36
10 11 3.126831 CTCTATGACGGTTCATGCTTCC 58.873 50.000 0.00 0.00 42.79 3.46
11 12 2.541762 GCTCTATGACGGTTCATGCTTC 59.458 50.000 0.00 0.00 42.79 3.86
12 13 2.555199 GCTCTATGACGGTTCATGCTT 58.445 47.619 0.00 0.00 42.79 3.91
13 14 1.536922 CGCTCTATGACGGTTCATGCT 60.537 52.381 0.00 0.00 42.79 3.79
14 15 0.855349 CGCTCTATGACGGTTCATGC 59.145 55.000 0.00 0.00 42.79 4.06
15 16 2.492019 TCGCTCTATGACGGTTCATG 57.508 50.000 0.00 0.00 42.79 3.07
16 17 3.187700 GTTTCGCTCTATGACGGTTCAT 58.812 45.455 0.00 0.00 45.04 2.57
17 18 2.602878 GTTTCGCTCTATGACGGTTCA 58.397 47.619 0.00 0.00 35.73 3.18
18 19 1.925185 GGTTTCGCTCTATGACGGTTC 59.075 52.381 0.00 0.00 0.00 3.62
19 20 1.274167 TGGTTTCGCTCTATGACGGTT 59.726 47.619 0.00 0.00 0.00 4.44
20 21 0.892755 TGGTTTCGCTCTATGACGGT 59.107 50.000 0.00 0.00 0.00 4.83
21 22 1.860950 CATGGTTTCGCTCTATGACGG 59.139 52.381 0.00 0.00 0.00 4.79
22 23 1.860950 CCATGGTTTCGCTCTATGACG 59.139 52.381 2.57 0.00 0.00 4.35
23 24 1.599542 GCCATGGTTTCGCTCTATGAC 59.400 52.381 14.67 0.00 0.00 3.06
24 25 1.209261 TGCCATGGTTTCGCTCTATGA 59.791 47.619 14.67 0.00 0.00 2.15
25 26 1.667236 TGCCATGGTTTCGCTCTATG 58.333 50.000 14.67 0.00 0.00 2.23
26 27 2.017049 GTTGCCATGGTTTCGCTCTAT 58.983 47.619 14.67 0.00 0.00 1.98
27 28 1.448985 GTTGCCATGGTTTCGCTCTA 58.551 50.000 14.67 0.00 0.00 2.43
28 29 1.244019 GGTTGCCATGGTTTCGCTCT 61.244 55.000 14.67 0.00 0.00 4.09
29 30 1.212751 GGTTGCCATGGTTTCGCTC 59.787 57.895 14.67 0.00 0.00 5.03
30 31 1.228552 AGGTTGCCATGGTTTCGCT 60.229 52.632 14.67 1.42 0.00 4.93
31 32 1.212751 GAGGTTGCCATGGTTTCGC 59.787 57.895 14.67 0.00 0.00 4.70
32 33 0.240945 GTGAGGTTGCCATGGTTTCG 59.759 55.000 14.67 0.00 0.00 3.46
33 34 0.603065 GGTGAGGTTGCCATGGTTTC 59.397 55.000 14.67 3.69 0.00 2.78
34 35 0.188342 AGGTGAGGTTGCCATGGTTT 59.812 50.000 14.67 0.00 0.00 3.27
35 36 0.188342 AAGGTGAGGTTGCCATGGTT 59.812 50.000 14.67 0.00 0.00 3.67
36 37 0.188342 AAAGGTGAGGTTGCCATGGT 59.812 50.000 14.67 0.00 0.00 3.55
37 38 0.604578 CAAAGGTGAGGTTGCCATGG 59.395 55.000 7.63 7.63 0.00 3.66
38 39 1.270550 GTCAAAGGTGAGGTTGCCATG 59.729 52.381 0.00 0.00 33.27 3.66
39 40 1.620822 GTCAAAGGTGAGGTTGCCAT 58.379 50.000 0.00 0.00 33.27 4.40
40 41 0.817634 CGTCAAAGGTGAGGTTGCCA 60.818 55.000 0.00 0.00 35.38 4.92
41 42 1.949257 CGTCAAAGGTGAGGTTGCC 59.051 57.895 0.00 0.00 35.38 4.52
42 43 1.282875 GCGTCAAAGGTGAGGTTGC 59.717 57.895 0.00 0.00 40.93 4.17
43 44 1.021202 TTGCGTCAAAGGTGAGGTTG 58.979 50.000 0.00 0.00 40.93 3.77
52 53 3.244976 CCTGGCTATTTTTGCGTCAAAG 58.755 45.455 5.42 0.00 34.72 2.77
67 68 0.260816 ATGATGATGTTGCCCTGGCT 59.739 50.000 9.97 0.00 42.51 4.75
68 69 0.387929 CATGATGATGTTGCCCTGGC 59.612 55.000 0.00 0.00 42.35 4.85
69 70 2.061509 TCATGATGATGTTGCCCTGG 57.938 50.000 0.00 0.00 0.00 4.45
141 142 4.566545 TCTTTTTCATGCTCTTTTGCGA 57.433 36.364 0.00 0.00 35.36 5.10
158 160 8.612619 GTTCGTGTGGATATAATGAACATCTTT 58.387 33.333 0.00 0.00 38.90 2.52
163 165 6.166982 TGTGTTCGTGTGGATATAATGAACA 58.833 36.000 5.76 5.76 43.82 3.18
190 196 4.526650 GTCCTTCAAATATTGGGTGGTTGT 59.473 41.667 0.00 0.00 0.00 3.32
192 198 4.093743 GGTCCTTCAAATATTGGGTGGTT 58.906 43.478 0.00 0.00 0.00 3.67
193 199 3.565670 GGGTCCTTCAAATATTGGGTGGT 60.566 47.826 0.00 0.00 0.00 4.16
233 239 6.071391 GGCTTTTGATGTTGGATTTAGAAGGA 60.071 38.462 0.00 0.00 0.00 3.36
237 243 5.007034 TCGGCTTTTGATGTTGGATTTAGA 58.993 37.500 0.00 0.00 0.00 2.10
239 245 5.713792 TTCGGCTTTTGATGTTGGATTTA 57.286 34.783 0.00 0.00 0.00 1.40
278 285 7.067981 GCAAATGGGTTTTCTCTAGATCTTCAT 59.932 37.037 0.00 0.00 0.00 2.57
297 308 4.444056 CGTTTAAACAAGACTGGCAAATGG 59.556 41.667 18.07 0.00 0.00 3.16
298 309 5.277825 TCGTTTAAACAAGACTGGCAAATG 58.722 37.500 18.07 0.00 0.00 2.32
304 315 5.334105 CCATGTCTCGTTTAAACAAGACTGG 60.334 44.000 29.94 27.78 42.13 4.00
315 326 2.225491 GCTGCAAACCATGTCTCGTTTA 59.775 45.455 0.00 0.00 31.15 2.01
318 329 1.237285 GGCTGCAAACCATGTCTCGT 61.237 55.000 0.50 0.00 0.00 4.18
319 330 1.503542 GGCTGCAAACCATGTCTCG 59.496 57.895 0.50 0.00 0.00 4.04
398 410 4.504858 AGCGATCCATACTCTTCGTTTTT 58.495 39.130 0.00 0.00 34.24 1.94
402 414 2.799917 GCAAGCGATCCATACTCTTCGT 60.800 50.000 0.00 0.00 34.24 3.85
403 415 1.789464 GCAAGCGATCCATACTCTTCG 59.211 52.381 0.00 0.00 34.83 3.79
405 417 2.555199 GTGCAAGCGATCCATACTCTT 58.445 47.619 0.00 0.00 0.00 2.85
410 422 0.463654 GGTGGTGCAAGCGATCCATA 60.464 55.000 0.00 0.00 36.92 2.74
443 455 1.129809 CAGAACGTAAAGTGGCGCG 59.870 57.895 0.00 0.00 0.00 6.86
451 463 3.598980 TCGGCGTCAGCAGAACGTAAA 62.599 52.381 6.85 0.00 44.21 2.01
454 466 3.973516 TCGGCGTCAGCAGAACGT 61.974 61.111 6.85 0.00 44.21 3.99
461 473 0.387367 ATCGTATCATCGGCGTCAGC 60.387 55.000 6.85 0.00 44.18 4.26
462 474 1.069227 TGATCGTATCATCGGCGTCAG 60.069 52.381 6.85 0.00 33.59 3.51
463 475 0.948678 TGATCGTATCATCGGCGTCA 59.051 50.000 6.85 0.00 33.59 4.35
464 476 2.046283 TTGATCGTATCATCGGCGTC 57.954 50.000 6.85 0.00 39.39 5.19
537 551 4.478206 TCTCAATCCAACCATCTCACTC 57.522 45.455 0.00 0.00 0.00 3.51
538 552 4.916041 TTCTCAATCCAACCATCTCACT 57.084 40.909 0.00 0.00 0.00 3.41
539 553 5.335976 GGTTTTCTCAATCCAACCATCTCAC 60.336 44.000 0.00 0.00 38.89 3.51
541 555 5.012893 AGGTTTTCTCAATCCAACCATCTC 58.987 41.667 2.91 0.00 41.14 2.75
593 613 7.815068 ACATTATGACACACAGAGAGTAGTTTC 59.185 37.037 0.00 0.00 0.00 2.78
596 616 6.842437 ACATTATGACACACAGAGAGTAGT 57.158 37.500 0.00 0.00 0.00 2.73
678 699 2.224378 TGAGGTCAGCTTCAGTTTCAGG 60.224 50.000 0.00 0.00 0.00 3.86
724 745 7.502226 TCTGAATGTGATTATGTGAATAACCCC 59.498 37.037 0.00 0.00 0.00 4.95
761 782 5.339008 TGGCAACTTGGTAGAGTACATAG 57.661 43.478 0.00 0.00 37.61 2.23
762 783 5.748670 TTGGCAACTTGGTAGAGTACATA 57.251 39.130 0.00 0.00 37.61 2.29
764 785 4.425180 TTTGGCAACTTGGTAGAGTACA 57.575 40.909 0.00 0.00 37.61 2.90
765 786 5.761165 TTTTTGGCAACTTGGTAGAGTAC 57.239 39.130 0.00 0.00 37.61 2.73
936 971 1.002134 CCCAATGCTTGAGACGGGT 60.002 57.895 0.00 0.00 0.00 5.28
940 976 3.642705 GTCAAAACCCAATGCTTGAGAC 58.357 45.455 0.00 0.00 0.00 3.36
1148 1190 2.682494 GGGAGGTCGTAGGGCACA 60.682 66.667 0.00 0.00 0.00 4.57
1268 1310 4.873129 CGGATCGGCTCCACCACG 62.873 72.222 0.00 0.00 45.24 4.94
1375 1420 2.737376 GCACCGAGTTGACCGACC 60.737 66.667 0.00 0.00 0.00 4.79
1402 1447 1.004080 TCCTCGTCGTCGAACTCCT 60.004 57.895 6.19 0.00 45.61 3.69
1601 1646 3.147595 CACGCCATCCTCCTCCGA 61.148 66.667 0.00 0.00 0.00 4.55
1679 1724 1.226974 CACGCAGTAGCCGCAGTAT 60.227 57.895 0.00 0.00 41.61 2.12
1883 1928 1.320555 CCGTTCACGATAAGTTGCTCG 59.679 52.381 0.00 7.80 43.02 5.03
1889 1934 0.739813 GGCAGCCGTTCACGATAAGT 60.740 55.000 0.00 0.00 43.02 2.24
2000 2045 4.899898 ATTTACCTTTCCCCATAAGCCT 57.100 40.909 0.00 0.00 0.00 4.58
2023 2069 0.461693 GCTGTGCTCCTGATGGTCTC 60.462 60.000 0.00 0.00 34.23 3.36
2069 2131 7.069826 AGGAGGCAAATTATTAGCAATTTAGCA 59.930 33.333 12.93 0.00 36.26 3.49
2070 2132 7.436933 AGGAGGCAAATTATTAGCAATTTAGC 58.563 34.615 0.00 0.00 36.26 3.09
2071 2133 9.822185 AAAGGAGGCAAATTATTAGCAATTTAG 57.178 29.630 0.00 0.00 36.26 1.85
2073 2135 9.166173 GAAAAGGAGGCAAATTATTAGCAATTT 57.834 29.630 0.00 0.00 38.37 1.82
2074 2136 7.770433 GGAAAAGGAGGCAAATTATTAGCAATT 59.230 33.333 0.00 0.00 0.00 2.32
2075 2137 7.092935 TGGAAAAGGAGGCAAATTATTAGCAAT 60.093 33.333 0.00 0.00 0.00 3.56
2076 2138 6.212388 TGGAAAAGGAGGCAAATTATTAGCAA 59.788 34.615 0.00 0.00 0.00 3.91
2217 2284 8.510505 AGAATTTTGAGCTCACTCTTTGTAATC 58.489 33.333 18.03 1.25 43.85 1.75
2368 2468 1.828595 TCCTCGATCGTGATTTCCCAA 59.171 47.619 18.20 0.00 0.00 4.12
2379 2479 1.056103 CGCAGCTAAATCCTCGATCG 58.944 55.000 9.36 9.36 0.00 3.69
2380 2480 1.423395 CCGCAGCTAAATCCTCGATC 58.577 55.000 0.00 0.00 0.00 3.69
2381 2481 0.601311 GCCGCAGCTAAATCCTCGAT 60.601 55.000 0.00 0.00 35.50 3.59
2382 2482 1.227263 GCCGCAGCTAAATCCTCGA 60.227 57.895 0.00 0.00 35.50 4.04
2447 2623 1.359848 AGGATGCTTAAGTGAACGCG 58.640 50.000 3.53 3.53 0.00 6.01
2567 2743 5.466393 TGGCATTTATCGTGTCACATGATAG 59.534 40.000 17.39 9.36 41.46 2.08
2569 2745 4.198530 TGGCATTTATCGTGTCACATGAT 58.801 39.130 16.79 16.79 42.04 2.45
2580 2756 9.559958 GTCTTAAAATGGATATGGCATTTATCG 57.440 33.333 4.78 0.00 0.00 2.92
2621 2797 5.907866 TTTACGGGGAAAATCCTGATTTC 57.092 39.130 5.64 0.00 39.88 2.17
2626 2802 5.448089 CGTTACATTTACGGGGAAAATCCTG 60.448 44.000 0.00 0.00 36.57 3.86
2660 2836 9.632807 AAATATTTAATAGAGCGCTCTACAGAG 57.367 33.333 41.35 1.68 44.11 3.35
2711 2887 2.364647 GCCGGTTACTGGTTCTAGCTAT 59.635 50.000 12.29 0.00 0.00 2.97
2719 2895 0.036671 GCTAGTGCCGGTTACTGGTT 60.037 55.000 19.64 1.06 0.00 3.67
2722 2898 0.739813 GGTGCTAGTGCCGGTTACTG 60.740 60.000 19.64 12.30 38.71 2.74
2742 2926 4.886971 CGCTGAACTAAAACAGAGCATAC 58.113 43.478 0.00 0.00 36.38 2.39
2790 2974 1.073897 GCAGGTGCAGGGACTCTTT 59.926 57.895 0.00 0.00 41.59 2.52
2841 3025 6.430962 TCTTAGATCCAAATGATGAGAGGG 57.569 41.667 0.00 0.00 32.41 4.30
2846 3030 6.069440 AGTGGGTTCTTAGATCCAAATGATGA 60.069 38.462 11.03 0.00 32.41 2.92
2933 3117 1.196127 GTAAACACAGCTGTAACGGGC 59.804 52.381 21.20 4.93 0.00 6.13
2934 3118 2.762745 AGTAAACACAGCTGTAACGGG 58.237 47.619 21.20 9.46 0.00 5.28
3021 3206 6.544928 AACTGGTTGATCCTTTTTCTTGTT 57.455 33.333 0.00 0.00 37.07 2.83
3060 3245 5.280164 GGCCTGTCACATGGATCTCATTATA 60.280 44.000 0.00 0.00 32.92 0.98
3083 3268 5.656416 TCTTAAAAAGGGATATGGCAGTTGG 59.344 40.000 0.00 0.00 0.00 3.77
3115 3300 3.194755 GGAAACCCTAATTTGCCGTGAAT 59.805 43.478 0.00 0.00 0.00 2.57
3203 3388 1.410882 GGTTCTAGCTACAGCAGGGAG 59.589 57.143 3.70 0.00 45.16 4.30
3226 3411 3.179830 CATACAGTGCTAGTGTCGGTTC 58.820 50.000 0.00 0.00 33.15 3.62
3242 3427 3.677148 GCTGAGCTAACACAGAGCATACA 60.677 47.826 0.00 0.00 42.69 2.29
3254 3439 1.068264 GCAAAAGGGTGCTGAGCTAAC 60.068 52.381 5.83 0.00 41.51 2.34
3315 3500 9.893305 GCTATAACGGAAAATAAATGCTATTGT 57.107 29.630 0.00 0.00 0.00 2.71
3408 3612 2.949714 ATTTGTCGTCACTTGCTTCG 57.050 45.000 0.00 0.00 0.00 3.79
3497 3701 5.181245 CGTCTCAGGGTATCAAATTGTTTGT 59.819 40.000 2.74 0.00 41.36 2.83
3503 3707 2.167693 TCGCGTCTCAGGGTATCAAATT 59.832 45.455 5.77 0.00 0.00 1.82
3610 3814 5.351233 TGCCGTTAAAACAACAGAGTATG 57.649 39.130 0.00 0.00 0.00 2.39
3636 3840 1.186200 GGATCTTTGACTTTGGGGGC 58.814 55.000 0.00 0.00 0.00 5.80
3690 3894 4.364415 TGGTTGTTCCTTTTTCTTGTCG 57.636 40.909 0.00 0.00 37.07 4.35
3740 3944 3.558931 AAACGGATATGGCAGTCATCA 57.441 42.857 0.00 0.00 37.30 3.07
3767 3971 3.684788 CCTAATTTGTCGTGAACTGGGAG 59.315 47.826 0.00 0.00 0.00 4.30
3868 4224 1.967066 CTGGTCCTAGCTACATCAGGG 59.033 57.143 0.00 0.00 0.00 4.45
3873 4229 2.957006 CGGTTACTGGTCCTAGCTACAT 59.043 50.000 0.00 0.00 0.00 2.29
3895 4251 6.360681 GCTAAAACAGAGCAAAATGTGTAGTG 59.639 38.462 0.00 0.00 39.84 2.74
3896 4252 6.263168 AGCTAAAACAGAGCAAAATGTGTAGT 59.737 34.615 0.00 0.00 42.69 2.73
3897 4253 6.672147 AGCTAAAACAGAGCAAAATGTGTAG 58.328 36.000 0.00 0.00 42.69 2.74
3898 4254 6.262049 TGAGCTAAAACAGAGCAAAATGTGTA 59.738 34.615 0.00 0.00 42.69 2.90
3903 4261 4.614535 CGCTGAGCTAAAACAGAGCAAAAT 60.615 41.667 1.78 0.00 42.69 1.82
3906 4264 1.800586 CGCTGAGCTAAAACAGAGCAA 59.199 47.619 1.78 0.00 42.69 3.91
3956 4314 1.265454 CCTCCCACAGGTACAGGGAC 61.265 65.000 9.72 0.00 46.42 4.46
3969 4327 2.046023 CACATCGCTTGCCTCCCA 60.046 61.111 0.00 0.00 0.00 4.37
3970 4328 3.512516 GCACATCGCTTGCCTCCC 61.513 66.667 0.00 0.00 37.77 4.30
4004 4362 2.286831 GCATGAAGCGAATGATGTGAGG 60.287 50.000 0.00 0.00 0.00 3.86
4229 6388 5.010617 GTCAAGGCCTGGTCATAAAAAGAAA 59.989 40.000 5.69 0.00 0.00 2.52
4344 6503 8.884124 TTCTTTTCTGATCCAAATAATCAGGT 57.116 30.769 11.92 0.00 46.62 4.00
4448 6607 7.759607 ACCGGGAGTAATTCTAGGTATAAGTA 58.240 38.462 6.32 0.00 35.08 2.24
4455 6614 3.297736 CAGACCGGGAGTAATTCTAGGT 58.702 50.000 6.32 0.00 37.92 3.08
4469 6628 2.684001 TAATTACAGTGCCAGACCGG 57.316 50.000 0.00 0.00 38.11 5.28
4475 6634 3.932822 ACGTCACATAATTACAGTGCCA 58.067 40.909 12.71 0.00 33.44 4.92
4479 6638 4.804139 GCTGCTACGTCACATAATTACAGT 59.196 41.667 0.00 0.00 0.00 3.55
4494 6653 1.696832 GCTTTCGAAGGGCTGCTACG 61.697 60.000 9.52 1.04 0.00 3.51
4507 6666 5.352284 ACAGATAATCACTACTGGCTTTCG 58.648 41.667 0.00 0.00 35.08 3.46
4526 6685 5.366477 TGTGCAAGGGATCAGATAATACAGA 59.634 40.000 0.00 0.00 0.00 3.41
4527 6686 5.614308 TGTGCAAGGGATCAGATAATACAG 58.386 41.667 0.00 0.00 0.00 2.74
4545 6726 2.507484 CCATCTCTTCAGGTTTGTGCA 58.493 47.619 0.00 0.00 0.00 4.57
4570 6764 6.505039 TGTTATTGTGCTATACGAACATCG 57.495 37.500 0.00 0.00 46.93 3.84
4623 6817 3.156293 CCACCAAATGAACCATGACTCA 58.844 45.455 0.00 0.00 0.00 3.41
4638 6832 2.238646 AGAGACAACACAACTCCACCAA 59.761 45.455 0.00 0.00 0.00 3.67
4639 6833 1.837439 AGAGACAACACAACTCCACCA 59.163 47.619 0.00 0.00 0.00 4.17
4640 6834 2.622064 AGAGACAACACAACTCCACC 57.378 50.000 0.00 0.00 0.00 4.61
4662 6856 6.935741 TGTAAGTCTTTACACAACTGCATT 57.064 33.333 0.00 0.00 43.12 3.56
4752 7237 5.340891 TCCATAGAGGTACTTAGCCTGAT 57.659 43.478 0.00 0.00 41.55 2.90
4775 7260 3.486383 GTTCATCTTGGGTGAACCTTGA 58.514 45.455 11.32 0.00 46.03 3.02
5052 7571 7.263496 AGAATTTCTTCAGCCTTGCATTTATC 58.737 34.615 0.00 0.00 33.56 1.75
5079 7598 4.022935 GCGATGATATCCAAAAGCCAATCA 60.023 41.667 0.00 0.00 0.00 2.57
5289 7808 9.607988 TCATCTTATTATTAAAGGCGAAACTGA 57.392 29.630 0.00 0.00 0.00 3.41
5335 7854 9.690434 GTGAACTCAACGATAATCTAATGAAAC 57.310 33.333 0.00 0.00 0.00 2.78
5341 7860 6.540438 AGGGTGAACTCAACGATAATCTAA 57.460 37.500 0.00 0.00 33.46 2.10
5389 7933 7.283127 ACACTGCTGAATATTTCAAATCGGTAT 59.717 33.333 0.00 0.00 39.58 2.73
5450 7998 7.122138 TCAAGCAATCTGAGACAGAGATTAT 57.878 36.000 7.50 0.00 44.08 1.28
5539 8087 5.518848 AAACAGAAAACAGCACATGATGA 57.481 34.783 3.76 0.00 35.09 2.92
5540 8088 5.749588 TGAAAACAGAAAACAGCACATGATG 59.250 36.000 0.00 0.00 37.48 3.07
5605 8413 2.820059 TGATACCTCAATAGCCTGCG 57.180 50.000 0.00 0.00 0.00 5.18
5678 8486 0.409484 AAGACAACCCATTCCCCTGG 59.591 55.000 0.00 0.00 35.95 4.45
5768 8576 3.356529 AATTACTTGGTGAGAGGCTGG 57.643 47.619 0.00 0.00 0.00 4.85
5830 8657 7.260558 TCTGAGGAGTAACACATATTAGACG 57.739 40.000 0.00 0.00 0.00 4.18
5845 8672 2.244486 TCAGCTGGAATCTGAGGAGT 57.756 50.000 15.13 0.00 35.81 3.85
5950 8777 3.067461 CCACTAGGTCATAGTCACTGAGC 59.933 52.174 0.00 0.00 43.13 4.26
6037 8864 4.340263 GAAAAAGTTTCGCATACCGGATC 58.660 43.478 9.46 0.00 37.59 3.36
6041 8868 3.546002 TGGAAAAAGTTTCGCATACCG 57.454 42.857 0.00 0.00 38.61 4.02
6075 8902 8.876275 TTCAAAATTTTCATTCTGAAGACCAG 57.124 30.769 0.00 0.00 44.27 4.00
6090 8931 5.469421 TGATGGCTCGCATTTTCAAAATTTT 59.531 32.000 0.00 0.00 0.00 1.82
6097 8938 2.367486 TGATGATGGCTCGCATTTTCA 58.633 42.857 0.00 0.00 0.00 2.69
6109 8950 4.082408 AGCACAAGTGACAAATGATGATGG 60.082 41.667 4.04 0.00 0.00 3.51
6131 8977 2.669569 CACGGTTGCCTGGTCCAG 60.670 66.667 12.40 12.40 0.00 3.86
6243 9089 3.382832 CACCGGGGAGAAGTCGCT 61.383 66.667 6.32 0.00 35.92 4.93
6332 9178 1.373748 CCCCGTGTGGTCGTTGTAG 60.374 63.158 0.00 0.00 0.00 2.74
6684 9596 6.030548 TCTATCTCAAGAACCAAGACACAG 57.969 41.667 0.00 0.00 0.00 3.66
6817 9743 1.673665 CTCCCAACAGCAGCAGTCC 60.674 63.158 0.00 0.00 0.00 3.85
6818 9744 0.321671 TACTCCCAACAGCAGCAGTC 59.678 55.000 0.00 0.00 0.00 3.51
6831 9760 5.382664 TCCCAAAAGGAATACATACTCCC 57.617 43.478 0.00 0.00 43.78 4.30
6845 9774 4.654091 TGTTTTCTCTGCTTCCCAAAAG 57.346 40.909 0.00 0.00 0.00 2.27
6901 9842 2.888834 AACAAATGCCGCAAAGTCTT 57.111 40.000 0.00 0.00 0.00 3.01
6903 9844 3.123050 AGAAAACAAATGCCGCAAAGTC 58.877 40.909 0.00 0.00 0.00 3.01
6905 9846 4.534794 AAAGAAAACAAATGCCGCAAAG 57.465 36.364 0.00 0.00 0.00 2.77
6906 9847 4.954092 AAAAGAAAACAAATGCCGCAAA 57.046 31.818 0.00 0.00 0.00 3.68
6907 9848 4.154918 ACAAAAAGAAAACAAATGCCGCAA 59.845 33.333 0.00 0.00 0.00 4.85
6909 9850 4.271590 ACAAAAAGAAAACAAATGCCGC 57.728 36.364 0.00 0.00 0.00 6.53
6912 9853 6.742264 CACCTGAACAAAAAGAAAACAAATGC 59.258 34.615 0.00 0.00 0.00 3.56
7001 9962 0.727398 GACGCGAGGGAAGGAAAATG 59.273 55.000 15.93 0.00 0.00 2.32
7036 9998 9.998106 GAAAGCACATAAAGATATTACTCCCTA 57.002 33.333 0.00 0.00 0.00 3.53
7067 10029 9.955208 CGTTGTAACATACTGTAACTGGATATA 57.045 33.333 0.00 0.00 0.00 0.86
7107 10098 3.162666 TCTCGGGCCGTCAGATATTATT 58.837 45.455 27.32 0.00 0.00 1.40
7113 10104 0.467474 TGTATCTCGGGCCGTCAGAT 60.467 55.000 26.90 26.90 0.00 2.90
7116 10107 0.107066 TACTGTATCTCGGGCCGTCA 60.107 55.000 27.32 14.11 0.00 4.35
7347 10422 8.093659 TGTTCATCGATTCTACAAATGTTCAA 57.906 30.769 0.00 0.00 0.00 2.69
7357 10432 7.526608 TCCAACAAAATGTTCATCGATTCTAC 58.473 34.615 0.00 0.00 38.77 2.59


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

AutoCloner maintained by Alex Coulton.