Multiple sequence alignment - TraesCS1B01G049100

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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 TraesCS1B01G049100 chr1B 100.000 2557 0 0 1 2557 28761877 28764433 0.000000e+00 4723.0
1 TraesCS1B01G049100 chr1B 86.457 827 64 33 753 1559 28625931 28626729 0.000000e+00 863.0
2 TraesCS1B01G049100 chr1D 91.278 1135 54 22 711 1826 19184753 19185861 0.000000e+00 1506.0
3 TraesCS1B01G049100 chr1D 84.746 826 77 21 756 1560 19150802 19151599 0.000000e+00 782.0
4 TraesCS1B01G049100 chr1D 82.374 556 77 12 58 595 19183955 19184507 4.980000e-127 464.0
5 TraesCS1B01G049100 chr1D 81.888 519 49 27 2056 2557 19186070 19186560 1.840000e-106 396.0
6 TraesCS1B01G049100 chr1A 90.507 1085 56 28 736 1809 21022557 21023605 0.000000e+00 1389.0
7 TraesCS1B01G049100 chr1A 85.731 834 81 31 742 1560 20997888 20998698 0.000000e+00 846.0
8 TraesCS1B01G049100 chr1A 84.990 513 41 15 2060 2557 21023744 21024235 2.960000e-134 488.0
9 TraesCS1B01G049100 chr1A 85.864 191 21 2 385 574 480593954 480593769 5.580000e-47 198.0
10 TraesCS1B01G049100 chr6D 85.388 438 41 21 1052 1474 16523150 16522721 1.410000e-117 433.0
11 TraesCS1B01G049100 chr6D 84.021 194 24 3 382 574 114764166 114763979 2.020000e-41 180.0
12 TraesCS1B01G049100 chr3B 82.688 491 53 24 1051 1521 829113027 829113505 8.520000e-110 407.0
13 TraesCS1B01G049100 chr3B 83.938 193 25 2 383 574 153663963 153664150 2.020000e-41 180.0
14 TraesCS1B01G049100 chr3B 85.475 179 19 3 397 574 663554220 663554048 2.020000e-41 180.0
15 TraesCS1B01G049100 chr6B 82.716 486 53 24 1004 1474 29060610 29060141 1.100000e-108 403.0
16 TraesCS1B01G049100 chr6B 93.846 65 4 0 1 65 615828225 615828161 5.820000e-17 99.0
17 TraesCS1B01G049100 chr6B 82.432 74 13 0 2164 2237 694181275 694181202 5.910000e-07 65.8
18 TraesCS1B01G049100 chr4D 86.517 267 24 8 1292 1558 352580202 352580456 1.500000e-72 283.0
19 TraesCS1B01G049100 chr7A 87.029 239 25 4 1295 1530 632581491 632581256 5.420000e-67 265.0
20 TraesCS1B01G049100 chr7A 86.864 236 25 3 1292 1524 632526856 632527088 2.520000e-65 259.0
21 TraesCS1B01G049100 chr7D 86.498 237 30 2 1295 1530 548781810 548781575 2.520000e-65 259.0
22 TraesCS1B01G049100 chr4A 90.099 202 14 6 1008 1204 112847017 112846817 9.080000e-65 257.0
23 TraesCS1B01G049100 chr4B 89.552 201 17 4 1008 1204 436102578 436102778 4.220000e-63 252.0
24 TraesCS1B01G049100 chr4B 95.161 62 3 0 1 62 90826472 90826533 5.820000e-17 99.0
25 TraesCS1B01G049100 chr4B 95.161 62 3 0 1 62 127429146 127429085 5.820000e-17 99.0
26 TraesCS1B01G049100 chr7B 82.328 232 31 6 383 613 410487590 410487368 2.600000e-45 193.0
27 TraesCS1B01G049100 chr7B 81.735 219 29 6 398 615 96526980 96526772 3.380000e-39 172.0
28 TraesCS1B01G049100 chr7B 95.161 62 3 0 1 62 193220515 193220576 5.820000e-17 99.0
29 TraesCS1B01G049100 chr2B 84.127 189 23 3 382 568 668421 668238 2.610000e-40 176.0
30 TraesCS1B01G049100 chr2B 95.238 63 3 0 1 63 749824258 749824320 1.620000e-17 100.0
31 TraesCS1B01G049100 chr6A 82.759 203 28 3 382 582 579055184 579055381 9.400000e-40 174.0
32 TraesCS1B01G049100 chr6A 79.798 99 15 5 103 199 215527030 215527125 1.640000e-07 67.6
33 TraesCS1B01G049100 chrUn 96.774 62 2 0 1 62 361476964 361477025 1.250000e-18 104.0
34 TraesCS1B01G049100 chrUn 95.161 62 3 0 1 62 344837105 344837166 5.820000e-17 99.0
35 TraesCS1B01G049100 chr5B 95.161 62 3 0 1 62 115612866 115612805 5.820000e-17 99.0
36 TraesCS1B01G049100 chr5B 95.161 62 3 0 1 62 681552508 681552447 5.820000e-17 99.0


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 TraesCS1B01G049100 chr1B 28761877 28764433 2556 False 4723.000000 4723 100.0000 1 2557 1 chr1B.!!$F2 2556
1 TraesCS1B01G049100 chr1B 28625931 28626729 798 False 863.000000 863 86.4570 753 1559 1 chr1B.!!$F1 806
2 TraesCS1B01G049100 chr1D 19183955 19186560 2605 False 788.666667 1506 85.1800 58 2557 3 chr1D.!!$F2 2499
3 TraesCS1B01G049100 chr1D 19150802 19151599 797 False 782.000000 782 84.7460 756 1560 1 chr1D.!!$F1 804
4 TraesCS1B01G049100 chr1A 21022557 21024235 1678 False 938.500000 1389 87.7485 736 2557 2 chr1A.!!$F2 1821
5 TraesCS1B01G049100 chr1A 20997888 20998698 810 False 846.000000 846 85.7310 742 1560 1 chr1A.!!$F1 818

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
205 207 0.035458 CATTCCCCTCCCTACATCGC 59.965 60.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2407 0.033781 TTTGGGACGGTTGGAGTACG 59.966 55.0 0.0 0.0 0.0 3.67 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
37 38 4.748798 CAGGGGGCCCAGGAGACT 62.749 72.222 26.86 8.08 46.44 3.24
77 78 1.524482 GGGGTGAGATGAGGCTGAC 59.476 63.158 0.00 0.00 0.00 3.51
81 82 2.036992 GGGTGAGATGAGGCTGACTATG 59.963 54.545 0.00 0.00 0.00 2.23
86 87 3.505386 AGATGAGGCTGACTATGTAGGG 58.495 50.000 0.00 0.00 0.00 3.53
87 88 1.414158 TGAGGCTGACTATGTAGGGC 58.586 55.000 0.00 0.00 0.00 5.19
90 91 0.969894 GGCTGACTATGTAGGGCGAT 59.030 55.000 0.00 0.00 0.00 4.58
92 93 1.889829 GCTGACTATGTAGGGCGATCT 59.110 52.381 0.00 0.00 0.00 2.75
113 114 0.561184 ATCGATAGGAGGTGACCCCA 59.439 55.000 11.02 0.00 34.66 4.96
121 122 1.354368 GGAGGTGACCCCAATTTCTCA 59.646 52.381 0.00 0.00 34.66 3.27
122 123 2.024941 GGAGGTGACCCCAATTTCTCAT 60.025 50.000 0.00 0.00 34.66 2.90
123 124 3.019564 GAGGTGACCCCAATTTCTCATG 58.980 50.000 0.00 0.00 34.66 3.07
134 135 2.330231 TTTCTCATGCCGCTTTTTCG 57.670 45.000 0.00 0.00 0.00 3.46
140 141 1.069296 CATGCCGCTTTTTCGAAGACA 60.069 47.619 0.00 0.00 34.32 3.41
144 145 1.329292 CCGCTTTTTCGAAGACACACA 59.671 47.619 0.00 0.00 34.32 3.72
153 154 1.609840 GAAGACACACACGAGCTCGC 61.610 60.000 34.83 17.10 44.43 5.03
178 179 0.102120 CTCCGTGGTCTCATGAGCTC 59.898 60.000 18.36 6.82 40.98 4.09
182 183 2.279120 GGTCTCATGAGCTCGGCG 60.279 66.667 18.36 0.00 37.68 6.46
198 199 3.801997 CGCTGCATTCCCCTCCCT 61.802 66.667 0.00 0.00 0.00 4.20
199 200 2.443394 CGCTGCATTCCCCTCCCTA 61.443 63.158 0.00 0.00 0.00 3.53
205 207 0.035458 CATTCCCCTCCCTACATCGC 59.965 60.000 0.00 0.00 0.00 4.58
224 226 2.363018 CGAGTCTGGCTGAGGGGA 60.363 66.667 0.00 0.00 0.00 4.81
239 241 0.107361 GGGGAAATGGTCGAATCGGT 60.107 55.000 1.76 0.00 0.00 4.69
240 242 1.296727 GGGAAATGGTCGAATCGGTC 58.703 55.000 1.76 0.00 0.00 4.79
254 256 0.959372 TCGGTCGTTCCTGAGAGGAC 60.959 60.000 0.00 0.00 45.78 3.85
256 258 0.528470 GGTCGTTCCTGAGAGGACTG 59.472 60.000 0.00 0.00 45.78 3.51
258 260 0.112606 TCGTTCCTGAGAGGACTGGT 59.887 55.000 0.00 0.00 45.78 4.00
259 261 0.244994 CGTTCCTGAGAGGACTGGTG 59.755 60.000 0.00 0.00 45.78 4.17
260 262 1.633774 GTTCCTGAGAGGACTGGTGA 58.366 55.000 0.00 0.00 45.78 4.02
286 292 2.177394 TAAGGTTCGTGCAATGCAGA 57.823 45.000 8.73 5.69 40.08 4.26
293 299 0.311790 CGTGCAATGCAGACCAAACT 59.688 50.000 8.73 0.00 40.08 2.66
342 348 0.745128 TTTGTCCCACGCGAACTTGT 60.745 50.000 15.93 0.00 0.00 3.16
347 353 1.008995 CCACGCGAACTTGTTTGGG 60.009 57.895 15.93 13.89 0.00 4.12
353 359 2.031508 CGCGAACTTGTTTGGGTTGTAT 60.032 45.455 0.00 0.00 0.00 2.29
367 373 2.403259 GTTGTATGCAGGCAACCAAAC 58.597 47.619 19.47 0.00 39.07 2.93
368 374 0.595588 TGTATGCAGGCAACCAAACG 59.404 50.000 0.00 0.00 37.17 3.60
369 375 0.732538 GTATGCAGGCAACCAAACGC 60.733 55.000 0.00 0.00 37.17 4.84
370 376 1.175347 TATGCAGGCAACCAAACGCA 61.175 50.000 0.00 0.00 37.17 5.24
374 380 3.532155 GGCAACCAAACGCACCCA 61.532 61.111 0.00 0.00 0.00 4.51
377 383 0.531753 GCAACCAAACGCACCCAAAT 60.532 50.000 0.00 0.00 0.00 2.32
378 384 1.216122 CAACCAAACGCACCCAAATG 58.784 50.000 0.00 0.00 0.00 2.32
379 385 1.115467 AACCAAACGCACCCAAATGA 58.885 45.000 0.00 0.00 0.00 2.57
383 389 2.230025 CCAAACGCACCCAAATGATGTA 59.770 45.455 0.00 0.00 0.00 2.29
384 390 3.241701 CAAACGCACCCAAATGATGTAC 58.758 45.455 0.00 0.00 0.00 2.90
385 391 2.489938 ACGCACCCAAATGATGTACT 57.510 45.000 0.00 0.00 0.00 2.73
386 392 2.356135 ACGCACCCAAATGATGTACTC 58.644 47.619 0.00 0.00 0.00 2.59
387 393 1.670811 CGCACCCAAATGATGTACTCC 59.329 52.381 0.00 0.00 0.00 3.85
388 394 2.024414 GCACCCAAATGATGTACTCCC 58.976 52.381 0.00 0.00 0.00 4.30
389 395 2.357154 GCACCCAAATGATGTACTCCCT 60.357 50.000 0.00 0.00 0.00 4.20
391 397 4.344104 CACCCAAATGATGTACTCCCTTT 58.656 43.478 0.00 0.00 0.00 3.11
392 398 4.158394 CACCCAAATGATGTACTCCCTTTG 59.842 45.833 0.00 2.34 0.00 2.77
393 399 3.701040 CCCAAATGATGTACTCCCTTTGG 59.299 47.826 18.47 18.47 41.20 3.28
394 400 4.344104 CCAAATGATGTACTCCCTTTGGT 58.656 43.478 17.79 0.00 39.03 3.67
395 401 4.158394 CCAAATGATGTACTCCCTTTGGTG 59.842 45.833 17.79 0.00 39.03 4.17
396 402 4.657814 AATGATGTACTCCCTTTGGTGT 57.342 40.909 0.00 0.00 41.19 4.16
437 451 5.036737 AGATTTGCGTCAAGTCAAACTTTG 58.963 37.500 14.13 0.00 36.03 2.77
442 456 5.328691 TGCGTCAAGTCAAACTTTGTAAAG 58.671 37.500 2.94 2.94 36.03 1.85
556 574 6.106648 TGACAAAATTTGGCATTGTGGATA 57.893 33.333 10.66 0.00 45.57 2.59
562 580 9.327628 CAAAATTTGGCATTGTGGATATTGATA 57.672 29.630 0.00 0.00 0.00 2.15
564 582 7.844493 ATTTGGCATTGTGGATATTGATACT 57.156 32.000 0.00 0.00 0.00 2.12
609 627 9.961264 ACAGTAGAGATATACTATGATTTCGGA 57.039 33.333 0.00 0.00 34.21 4.55
666 684 4.616181 AAAGACAGAAGAAAACACACGG 57.384 40.909 0.00 0.00 0.00 4.94
667 685 1.940613 AGACAGAAGAAAACACACGGC 59.059 47.619 0.00 0.00 0.00 5.68
668 686 1.002792 GACAGAAGAAAACACACGGCC 60.003 52.381 0.00 0.00 0.00 6.13
669 687 1.308998 CAGAAGAAAACACACGGCCT 58.691 50.000 0.00 0.00 0.00 5.19
670 688 1.264288 CAGAAGAAAACACACGGCCTC 59.736 52.381 0.00 0.00 0.00 4.70
671 689 1.134220 AGAAGAAAACACACGGCCTCA 60.134 47.619 0.00 0.00 0.00 3.86
672 690 1.673920 GAAGAAAACACACGGCCTCAA 59.326 47.619 0.00 0.00 0.00 3.02
673 691 1.757682 AGAAAACACACGGCCTCAAA 58.242 45.000 0.00 0.00 0.00 2.69
676 811 4.079253 AGAAAACACACGGCCTCAAATAT 58.921 39.130 0.00 0.00 0.00 1.28
683 818 4.024556 CACACGGCCTCAAATATCTCAATC 60.025 45.833 0.00 0.00 0.00 2.67
693 828 3.591196 ATATCTCAATCTGCTCGCTCC 57.409 47.619 0.00 0.00 0.00 4.70
707 842 1.509004 GCTCCTGGTCACGAGAGAC 59.491 63.158 0.00 0.00 37.80 3.36
733 881 1.748493 GATCTCACGTGCTCTCTCCTT 59.252 52.381 11.67 0.00 0.00 3.36
898 1058 1.557832 GCGGGTATATAATCCCAGCCA 59.442 52.381 13.65 0.00 43.57 4.75
1228 1429 1.605451 ACCACCGTCATCCTCGTCA 60.605 57.895 0.00 0.00 0.00 4.35
1229 1430 0.970937 ACCACCGTCATCCTCGTCAT 60.971 55.000 0.00 0.00 0.00 3.06
1262 1474 1.621822 ACCTACCTCTCTCCCCGGA 60.622 63.158 0.73 0.00 0.00 5.14
1495 1708 2.982130 GGCTGAGAAGGCCGAGAA 59.018 61.111 0.00 0.00 40.19 2.87
1496 1709 1.153469 GGCTGAGAAGGCCGAGAAG 60.153 63.158 0.00 0.00 40.19 2.85
1561 1774 3.369381 CCACCAAGGCGTAGATCTG 57.631 57.895 5.18 0.00 0.00 2.90
1562 1775 0.179073 CCACCAAGGCGTAGATCTGG 60.179 60.000 5.18 0.00 0.00 3.86
1563 1776 0.811616 CACCAAGGCGTAGATCTGGC 60.812 60.000 5.18 8.76 0.00 4.85
1564 1777 0.978146 ACCAAGGCGTAGATCTGGCT 60.978 55.000 16.96 11.01 43.62 4.75
1565 1778 0.249657 CCAAGGCGTAGATCTGGCTC 60.250 60.000 16.96 9.53 40.50 4.70
1566 1779 0.249657 CAAGGCGTAGATCTGGCTCC 60.250 60.000 16.96 9.45 40.50 4.70
1567 1780 1.739338 AAGGCGTAGATCTGGCTCCG 61.739 60.000 16.96 7.94 40.50 4.63
1568 1781 2.194212 GGCGTAGATCTGGCTCCGA 61.194 63.158 16.96 0.00 0.00 4.55
1569 1782 1.284408 GCGTAGATCTGGCTCCGAG 59.716 63.158 5.18 0.00 0.00 4.63
1572 1785 2.556459 TAGATCTGGCTCCGAGCGC 61.556 63.158 14.21 0.00 43.62 5.92
1605 1829 1.892819 CTGGACTGATGGTGCTCCGT 61.893 60.000 0.00 0.00 37.18 4.69
1661 1887 0.179045 GCTGTGGTGTGTTCCAGAGT 60.179 55.000 10.65 0.00 46.42 3.24
1676 1902 2.684881 CCAGAGTGTGTTGAAGCTTGTT 59.315 45.455 2.10 0.00 0.00 2.83
1739 1965 2.064762 CGTCTTGCTTCCTCTGTTCTG 58.935 52.381 0.00 0.00 0.00 3.02
1742 1968 2.899900 TCTTGCTTCCTCTGTTCTGCTA 59.100 45.455 0.00 0.00 0.00 3.49
1743 1969 3.517100 TCTTGCTTCCTCTGTTCTGCTAT 59.483 43.478 0.00 0.00 0.00 2.97
1755 1981 7.129457 TCTGTTCTGCTATATCAATCTGGTT 57.871 36.000 0.00 0.00 0.00 3.67
1778 2004 8.325282 GGTTTCTAATGCAGTGTTTGTTAAAAC 58.675 33.333 0.00 1.37 45.00 2.43
1788 2014 4.748503 GTTTGTTAAAACGCCACTGAAC 57.251 40.909 0.00 0.00 36.60 3.18
1795 2021 0.878961 AACGCCACTGAACTTCCGTC 60.879 55.000 0.00 0.00 0.00 4.79
1798 2024 0.951040 GCCACTGAACTTCCGTCCTG 60.951 60.000 0.00 0.00 0.00 3.86
1812 2038 6.204108 ACTTCCGTCCTGTTTTAACTGTATTG 59.796 38.462 0.00 0.00 0.00 1.90
1813 2039 4.453136 TCCGTCCTGTTTTAACTGTATTGC 59.547 41.667 0.00 0.00 0.00 3.56
1814 2040 4.214545 CCGTCCTGTTTTAACTGTATTGCA 59.785 41.667 0.00 0.00 0.00 4.08
1815 2041 5.106317 CCGTCCTGTTTTAACTGTATTGCAT 60.106 40.000 0.00 0.00 0.00 3.96
1817 2043 6.861055 CGTCCTGTTTTAACTGTATTGCATTT 59.139 34.615 0.00 0.00 0.00 2.32
1818 2044 7.148983 CGTCCTGTTTTAACTGTATTGCATTTG 60.149 37.037 0.00 0.00 0.00 2.32
1819 2045 7.651704 GTCCTGTTTTAACTGTATTGCATTTGT 59.348 33.333 0.00 0.00 0.00 2.83
1821 2047 8.274939 CCTGTTTTAACTGTATTGCATTTGTTG 58.725 33.333 0.00 0.00 0.00 3.33
1822 2048 8.709386 TGTTTTAACTGTATTGCATTTGTTGT 57.291 26.923 0.00 0.00 0.00 3.32
1823 2049 9.803315 TGTTTTAACTGTATTGCATTTGTTGTA 57.197 25.926 0.00 0.00 0.00 2.41
1825 2051 8.495554 TTTAACTGTATTGCATTTGTTGTACG 57.504 30.769 0.00 0.00 0.00 3.67
1826 2052 5.933187 ACTGTATTGCATTTGTTGTACGA 57.067 34.783 0.00 0.00 0.00 3.43
1827 2053 5.927030 ACTGTATTGCATTTGTTGTACGAG 58.073 37.500 0.00 0.00 0.00 4.18
1828 2054 4.717991 TGTATTGCATTTGTTGTACGAGC 58.282 39.130 0.00 0.00 0.00 5.03
1829 2055 3.913548 ATTGCATTTGTTGTACGAGCA 57.086 38.095 0.00 0.00 0.00 4.26
1830 2056 2.679355 TGCATTTGTTGTACGAGCAC 57.321 45.000 0.00 0.00 0.00 4.40
1831 2057 1.070242 TGCATTTGTTGTACGAGCACG 60.070 47.619 0.76 0.76 45.75 5.34
1832 2058 1.591248 CATTTGTTGTACGAGCACGC 58.409 50.000 2.62 0.00 43.96 5.34
1833 2059 1.194547 CATTTGTTGTACGAGCACGCT 59.805 47.619 2.62 0.00 43.96 5.07
1834 2060 0.579630 TTTGTTGTACGAGCACGCTG 59.420 50.000 2.62 0.00 43.96 5.18
1835 2061 0.249114 TTGTTGTACGAGCACGCTGA 60.249 50.000 2.62 0.00 43.96 4.26
1839 2065 2.155194 GTACGAGCACGCTGAGCAG 61.155 63.158 4.88 0.00 43.96 4.24
1840 2066 2.626780 TACGAGCACGCTGAGCAGT 61.627 57.895 4.88 0.07 43.96 4.40
1841 2067 2.802740 TACGAGCACGCTGAGCAGTG 62.803 60.000 19.76 19.76 43.96 3.66
1850 2076 1.661341 GCTGAGCAGTGTTGGGATAG 58.339 55.000 0.00 0.00 0.00 2.08
1855 2081 0.811281 GCAGTGTTGGGATAGTTGCC 59.189 55.000 0.00 0.00 0.00 4.52
1856 2082 1.086696 CAGTGTTGGGATAGTTGCCG 58.913 55.000 0.00 0.00 35.76 5.69
1862 2088 0.037590 TGGGATAGTTGCCGTTGCTT 59.962 50.000 0.00 0.00 35.76 3.91
1863 2089 1.279558 TGGGATAGTTGCCGTTGCTTA 59.720 47.619 0.00 0.00 35.76 3.09
1867 2093 3.181510 GGATAGTTGCCGTTGCTTACAAG 60.182 47.826 0.00 0.00 36.16 3.16
1879 2105 5.164158 CGTTGCTTACAAGTTTCATGATTGC 60.164 40.000 7.32 0.00 36.16 3.56
1882 2108 6.514947 TGCTTACAAGTTTCATGATTGCTTT 58.485 32.000 7.32 2.71 0.00 3.51
1883 2109 7.656412 TGCTTACAAGTTTCATGATTGCTTTA 58.344 30.769 7.32 2.02 0.00 1.85
1885 2111 7.594758 GCTTACAAGTTTCATGATTGCTTTACA 59.405 33.333 7.32 0.00 0.00 2.41
1898 2124 7.715657 TGATTGCTTTACAACTGATTTTCTGT 58.284 30.769 0.00 0.00 42.27 3.41
1900 2126 9.677567 GATTGCTTTACAACTGATTTTCTGTAA 57.322 29.630 0.00 0.00 42.27 2.41
1901 2127 9.683069 ATTGCTTTACAACTGATTTTCTGTAAG 57.317 29.630 0.00 0.00 42.27 2.34
1902 2128 7.648142 TGCTTTACAACTGATTTTCTGTAAGG 58.352 34.615 0.00 0.00 36.08 2.69
1907 2133 7.454260 ACAACTGATTTTCTGTAAGGGATTC 57.546 36.000 0.00 0.00 0.00 2.52
1908 2134 7.234355 ACAACTGATTTTCTGTAAGGGATTCT 58.766 34.615 0.00 0.00 0.00 2.40
1911 2137 8.152023 ACTGATTTTCTGTAAGGGATTCTACT 57.848 34.615 0.00 0.00 0.00 2.57
1912 2138 8.606830 ACTGATTTTCTGTAAGGGATTCTACTT 58.393 33.333 0.00 0.00 0.00 2.24
1913 2139 9.454859 CTGATTTTCTGTAAGGGATTCTACTTT 57.545 33.333 0.00 0.00 0.00 2.66
1918 2144 9.498176 TTTCTGTAAGGGATTCTACTTTACAAC 57.502 33.333 0.00 0.00 0.00 3.32
1920 2146 9.537852 TCTGTAAGGGATTCTACTTTACAACTA 57.462 33.333 0.00 0.00 0.00 2.24
1921 2147 9.804758 CTGTAAGGGATTCTACTTTACAACTAG 57.195 37.037 0.00 0.00 0.00 2.57
1926 2152 9.722184 AGGGATTCTACTTTACAACTAGTTTTC 57.278 33.333 5.07 0.00 0.00 2.29
1927 2153 8.944029 GGGATTCTACTTTACAACTAGTTTTCC 58.056 37.037 5.07 0.00 0.00 3.13
1946 2172 9.433153 AGTTTTCCTTAAGGTATTCTACGAAAG 57.567 33.333 21.04 0.00 36.34 2.62
1973 2199 6.680810 TGTATTTGGAACAGCTTCTGATTTG 58.319 36.000 0.29 0.00 42.39 2.32
1977 2203 3.318839 TGGAACAGCTTCTGATTTGGTTG 59.681 43.478 0.29 0.00 35.18 3.77
1986 2212 8.680903 CAGCTTCTGATTTGGTTGATTAGTTAT 58.319 33.333 0.00 0.00 32.44 1.89
1987 2213 8.680903 AGCTTCTGATTTGGTTGATTAGTTATG 58.319 33.333 0.00 0.00 0.00 1.90
2048 2274 5.760253 AGACTGAATCTTTGAAACGTGACAT 59.240 36.000 0.00 0.00 31.62 3.06
2049 2275 5.990408 ACTGAATCTTTGAAACGTGACATC 58.010 37.500 0.00 0.00 0.00 3.06
2136 2390 2.414481 GTGCATGCTCAAGTCACACTAG 59.586 50.000 20.33 0.00 0.00 2.57
2145 2399 5.814705 GCTCAAGTCACACTAGCAAATCTAT 59.185 40.000 0.00 0.00 31.76 1.98
2153 2407 9.453325 GTCACACTAGCAAATCTATAGTAGTTC 57.547 37.037 0.00 0.00 0.00 3.01
2178 2432 2.025898 TCCAACCGTCCCAAAAAGTTC 58.974 47.619 0.00 0.00 0.00 3.01
2180 2434 0.382873 AACCGTCCCAAAAAGTTCGC 59.617 50.000 0.00 0.00 0.00 4.70
2224 2478 7.604549 TGGATGAATGTAGACACGTTTTAGTA 58.395 34.615 0.00 0.00 33.95 1.82
2266 2525 5.842907 AGACAAATACAAGCTTTTTGGGAC 58.157 37.500 20.61 13.52 35.23 4.46
2303 2568 4.156008 GCAAGGTAACAGTGTCTAAATGGG 59.844 45.833 0.00 0.00 41.41 4.00
2322 2587 4.521146 TGGGCATTGTGTTTGTTGATTTT 58.479 34.783 0.00 0.00 0.00 1.82
2323 2588 4.574013 TGGGCATTGTGTTTGTTGATTTTC 59.426 37.500 0.00 0.00 0.00 2.29
2326 2594 6.481644 GGGCATTGTGTTTGTTGATTTTCTAA 59.518 34.615 0.00 0.00 0.00 2.10
2361 2655 8.557864 CATGGTTCTTGTTTTGCAAATGAATAA 58.442 29.630 13.65 5.26 36.53 1.40
2362 2656 8.140677 TGGTTCTTGTTTTGCAAATGAATAAG 57.859 30.769 13.65 11.90 36.53 1.73
2363 2657 7.226325 TGGTTCTTGTTTTGCAAATGAATAAGG 59.774 33.333 13.65 0.00 36.53 2.69
2364 2658 7.307930 GGTTCTTGTTTTGCAAATGAATAAGGG 60.308 37.037 13.65 0.00 36.53 3.95
2365 2659 6.229733 TCTTGTTTTGCAAATGAATAAGGGG 58.770 36.000 13.65 0.00 36.53 4.79
2366 2660 4.904241 TGTTTTGCAAATGAATAAGGGGG 58.096 39.130 13.65 0.00 0.00 5.40
2367 2661 4.349342 TGTTTTGCAAATGAATAAGGGGGT 59.651 37.500 13.65 0.00 0.00 4.95
2368 2662 5.544176 TGTTTTGCAAATGAATAAGGGGGTA 59.456 36.000 13.65 0.00 0.00 3.69
2369 2663 5.669164 TTTGCAAATGAATAAGGGGGTAC 57.331 39.130 8.05 0.00 0.00 3.34
2370 2664 4.601406 TGCAAATGAATAAGGGGGTACT 57.399 40.909 0.00 0.00 0.00 2.73
2371 2665 5.718801 TGCAAATGAATAAGGGGGTACTA 57.281 39.130 0.00 0.00 0.00 1.82
2372 2666 5.442391 TGCAAATGAATAAGGGGGTACTAC 58.558 41.667 0.00 0.00 0.00 2.73
2373 2667 5.192923 TGCAAATGAATAAGGGGGTACTACT 59.807 40.000 0.00 0.00 0.00 2.57
2374 2668 6.387513 TGCAAATGAATAAGGGGGTACTACTA 59.612 38.462 0.00 0.00 0.00 1.82
2375 2669 7.092354 TGCAAATGAATAAGGGGGTACTACTAA 60.092 37.037 0.00 0.00 0.00 2.24
2376 2670 7.444487 GCAAATGAATAAGGGGGTACTACTAAG 59.556 40.741 0.00 0.00 0.00 2.18
2377 2671 8.491958 CAAATGAATAAGGGGGTACTACTAAGT 58.508 37.037 0.00 0.00 39.91 2.24
2378 2672 7.613551 ATGAATAAGGGGGTACTACTAAGTG 57.386 40.000 0.00 0.00 36.36 3.16
2403 2697 9.072375 TGACCATTCTGTGTGTTGATTTATAAA 57.928 29.630 0.00 0.00 0.00 1.40
2440 2735 7.173907 CCAGATATGCCAACTATTTTCTGTAGG 59.826 40.741 0.00 0.00 0.00 3.18
2473 2768 6.899393 TGTCATTTAGGTTGAAATTCTGCT 57.101 33.333 0.00 0.00 0.00 4.24
2478 2773 8.896744 TCATTTAGGTTGAAATTCTGCTATCAG 58.103 33.333 0.00 0.00 41.67 2.90
2492 2787 4.546674 TGCTATCAGGAACCATCTCTGTA 58.453 43.478 0.00 0.00 0.00 2.74
2495 2790 6.162777 GCTATCAGGAACCATCTCTGTATTC 58.837 44.000 0.00 0.00 0.00 1.75
2496 2791 6.014669 GCTATCAGGAACCATCTCTGTATTCT 60.015 42.308 0.00 0.00 0.00 2.40
2497 2792 6.821616 ATCAGGAACCATCTCTGTATTCTT 57.178 37.500 0.00 0.00 0.00 2.52
2499 2794 6.409704 TCAGGAACCATCTCTGTATTCTTTG 58.590 40.000 0.00 0.00 0.00 2.77
2506 2801 6.013725 ACCATCTCTGTATTCTTTGTGGTGTA 60.014 38.462 0.00 0.00 36.20 2.90
2537 2832 4.818005 CAGCAGCCATGACATACTTGATTA 59.182 41.667 0.00 0.00 0.00 1.75
2545 2840 6.367149 CCATGACATACTTGATTATCTGACCG 59.633 42.308 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.748798 AGTCTCCTGGGCCCCCTG 62.749 72.222 22.27 9.62 36.94 4.45
21 22 4.748798 CAGTCTCCTGGGCCCCCT 62.749 72.222 22.27 2.06 34.90 4.79
29 30 4.087892 CGCACCCCCAGTCTCCTG 62.088 72.222 0.00 0.00 38.50 3.86
67 68 1.974236 GCCCTACATAGTCAGCCTCAT 59.026 52.381 0.00 0.00 0.00 2.90
73 74 5.447954 CGATTAGATCGCCCTACATAGTCAG 60.448 48.000 0.00 0.00 46.55 3.51
74 75 4.395231 CGATTAGATCGCCCTACATAGTCA 59.605 45.833 0.00 0.00 46.55 3.41
90 91 3.499926 GGGGTCACCTCCTATCGATTAGA 60.500 52.174 1.71 0.00 36.80 2.10
92 93 2.178325 TGGGGTCACCTCCTATCGATTA 59.822 50.000 1.71 0.00 41.11 1.75
98 99 3.459969 GAGAAATTGGGGTCACCTCCTAT 59.540 47.826 0.00 0.00 41.11 2.57
99 100 2.844348 GAGAAATTGGGGTCACCTCCTA 59.156 50.000 0.00 0.00 41.11 2.94
100 101 1.636003 GAGAAATTGGGGTCACCTCCT 59.364 52.381 0.00 0.00 41.11 3.69
113 114 3.057596 TCGAAAAAGCGGCATGAGAAATT 60.058 39.130 1.45 0.00 0.00 1.82
121 122 1.069227 GTGTCTTCGAAAAAGCGGCAT 60.069 47.619 1.45 0.00 0.00 4.40
122 123 0.306533 GTGTCTTCGAAAAAGCGGCA 59.693 50.000 1.45 0.00 0.00 5.69
123 124 0.306533 TGTGTCTTCGAAAAAGCGGC 59.693 50.000 0.00 0.00 0.00 6.53
134 135 1.609840 GCGAGCTCGTGTGTGTCTTC 61.610 60.000 34.46 12.23 42.22 2.87
153 154 2.021068 ATGAGACCACGGAGATGGCG 62.021 60.000 0.00 0.00 44.33 5.69
162 163 1.226802 CCGAGCTCATGAGACCACG 60.227 63.158 27.04 21.19 0.00 4.94
163 164 1.520342 GCCGAGCTCATGAGACCAC 60.520 63.158 27.04 8.42 0.00 4.16
182 183 1.149401 GTAGGGAGGGGAATGCAGC 59.851 63.158 0.00 0.00 0.00 5.25
184 185 1.140312 GATGTAGGGAGGGGAATGCA 58.860 55.000 0.00 0.00 0.00 3.96
185 186 0.035458 CGATGTAGGGAGGGGAATGC 59.965 60.000 0.00 0.00 0.00 3.56
198 199 2.782222 GCCAGACTCGGGCGATGTA 61.782 63.158 4.30 0.00 42.39 2.29
199 200 4.148825 GCCAGACTCGGGCGATGT 62.149 66.667 4.30 0.00 42.39 3.06
205 207 3.465403 CCCTCAGCCAGACTCGGG 61.465 72.222 0.00 0.00 31.53 5.14
218 220 1.583054 CGATTCGACCATTTCCCCTC 58.417 55.000 0.00 0.00 0.00 4.30
247 249 0.972883 AAGCACTCACCAGTCCTCTC 59.027 55.000 0.00 0.00 0.00 3.20
254 256 2.480419 CGAACCTTAAAGCACTCACCAG 59.520 50.000 0.00 0.00 0.00 4.00
256 258 2.223377 CACGAACCTTAAAGCACTCACC 59.777 50.000 0.00 0.00 0.00 4.02
258 260 1.871039 GCACGAACCTTAAAGCACTCA 59.129 47.619 0.00 0.00 0.00 3.41
259 261 1.871039 TGCACGAACCTTAAAGCACTC 59.129 47.619 0.00 0.00 0.00 3.51
260 262 1.961793 TGCACGAACCTTAAAGCACT 58.038 45.000 0.00 0.00 0.00 4.40
293 299 4.443621 TCGTTTGGTTGACTGTATTCACA 58.556 39.130 0.00 0.00 0.00 3.58
325 331 0.745128 AAACAAGTTCGCGTGGGACA 60.745 50.000 5.77 0.00 0.00 4.02
326 332 0.316689 CAAACAAGTTCGCGTGGGAC 60.317 55.000 5.77 1.08 0.00 4.46
332 338 0.099791 ACAACCCAAACAAGTTCGCG 59.900 50.000 0.00 0.00 0.00 5.87
333 339 3.305110 CATACAACCCAAACAAGTTCGC 58.695 45.455 0.00 0.00 0.00 4.70
335 341 4.298332 CTGCATACAACCCAAACAAGTTC 58.702 43.478 0.00 0.00 0.00 3.01
342 348 1.342819 GTTGCCTGCATACAACCCAAA 59.657 47.619 17.07 0.00 40.19 3.28
347 353 2.403259 GTTTGGTTGCCTGCATACAAC 58.597 47.619 18.81 18.81 44.29 3.32
353 359 3.143515 TGCGTTTGGTTGCCTGCA 61.144 55.556 0.00 0.00 0.00 4.41
364 370 3.153919 AGTACATCATTTGGGTGCGTTT 58.846 40.909 0.00 0.00 0.00 3.60
367 373 1.670811 GGAGTACATCATTTGGGTGCG 59.329 52.381 0.00 0.00 0.00 5.34
368 374 2.024414 GGGAGTACATCATTTGGGTGC 58.976 52.381 0.00 0.00 0.00 5.01
369 375 3.652057 AGGGAGTACATCATTTGGGTG 57.348 47.619 0.00 0.00 0.00 4.61
370 376 4.344104 CAAAGGGAGTACATCATTTGGGT 58.656 43.478 13.91 0.00 34.71 4.51
374 380 4.998051 ACACCAAAGGGAGTACATCATTT 58.002 39.130 0.00 0.00 36.11 2.32
377 383 4.447138 AAACACCAAAGGGAGTACATCA 57.553 40.909 0.00 0.00 36.95 3.07
378 384 5.784578 AAAAACACCAAAGGGAGTACATC 57.215 39.130 0.00 0.00 36.95 3.06
527 545 8.944029 CCACAATGCCAAATTTTGTCAATATTA 58.056 29.630 8.26 0.00 31.48 0.98
530 548 6.528321 TCCACAATGCCAAATTTTGTCAATA 58.472 32.000 8.26 0.00 31.48 1.90
534 552 7.333921 TCAATATCCACAATGCCAAATTTTGTC 59.666 33.333 8.26 0.00 31.48 3.18
539 557 8.253867 AGTATCAATATCCACAATGCCAAATT 57.746 30.769 0.00 0.00 0.00 1.82
544 562 8.416329 AGAAAAAGTATCAATATCCACAATGCC 58.584 33.333 0.00 0.00 0.00 4.40
643 661 5.399013 CCGTGTGTTTTCTTCTGTCTTTTT 58.601 37.500 0.00 0.00 0.00 1.94
644 662 4.674362 GCCGTGTGTTTTCTTCTGTCTTTT 60.674 41.667 0.00 0.00 0.00 2.27
645 663 3.181500 GCCGTGTGTTTTCTTCTGTCTTT 60.181 43.478 0.00 0.00 0.00 2.52
646 664 2.354821 GCCGTGTGTTTTCTTCTGTCTT 59.645 45.455 0.00 0.00 0.00 3.01
648 666 1.002792 GGCCGTGTGTTTTCTTCTGTC 60.003 52.381 0.00 0.00 0.00 3.51
649 667 1.021968 GGCCGTGTGTTTTCTTCTGT 58.978 50.000 0.00 0.00 0.00 3.41
651 669 1.134220 TGAGGCCGTGTGTTTTCTTCT 60.134 47.619 0.00 0.00 0.00 2.85
652 670 1.305201 TGAGGCCGTGTGTTTTCTTC 58.695 50.000 0.00 0.00 0.00 2.87
653 671 1.757682 TTGAGGCCGTGTGTTTTCTT 58.242 45.000 0.00 0.00 0.00 2.52
654 672 1.757682 TTTGAGGCCGTGTGTTTTCT 58.242 45.000 0.00 0.00 0.00 2.52
655 673 2.793278 ATTTGAGGCCGTGTGTTTTC 57.207 45.000 0.00 0.00 0.00 2.29
656 674 4.079253 AGATATTTGAGGCCGTGTGTTTT 58.921 39.130 0.00 0.00 0.00 2.43
659 677 2.236146 TGAGATATTTGAGGCCGTGTGT 59.764 45.455 0.00 0.00 0.00 3.72
660 678 2.905075 TGAGATATTTGAGGCCGTGTG 58.095 47.619 0.00 0.00 0.00 3.82
661 679 3.627395 TTGAGATATTTGAGGCCGTGT 57.373 42.857 0.00 0.00 0.00 4.49
662 680 4.212847 CAGATTGAGATATTTGAGGCCGTG 59.787 45.833 0.00 0.00 0.00 4.94
663 681 4.384056 CAGATTGAGATATTTGAGGCCGT 58.616 43.478 0.00 0.00 0.00 5.68
664 682 3.188048 GCAGATTGAGATATTTGAGGCCG 59.812 47.826 0.00 0.00 0.00 6.13
665 683 4.396522 AGCAGATTGAGATATTTGAGGCC 58.603 43.478 0.00 0.00 0.00 5.19
666 684 4.152045 CGAGCAGATTGAGATATTTGAGGC 59.848 45.833 0.00 0.00 0.00 4.70
667 685 4.152045 GCGAGCAGATTGAGATATTTGAGG 59.848 45.833 0.00 0.00 0.00 3.86
668 686 4.989797 AGCGAGCAGATTGAGATATTTGAG 59.010 41.667 0.00 0.00 0.00 3.02
669 687 4.953667 AGCGAGCAGATTGAGATATTTGA 58.046 39.130 0.00 0.00 0.00 2.69
670 688 4.152045 GGAGCGAGCAGATTGAGATATTTG 59.848 45.833 0.00 0.00 0.00 2.32
671 689 4.040217 AGGAGCGAGCAGATTGAGATATTT 59.960 41.667 0.00 0.00 0.00 1.40
672 690 3.577848 AGGAGCGAGCAGATTGAGATATT 59.422 43.478 0.00 0.00 0.00 1.28
673 691 3.056678 CAGGAGCGAGCAGATTGAGATAT 60.057 47.826 0.00 0.00 0.00 1.63
676 811 0.459078 CAGGAGCGAGCAGATTGAGA 59.541 55.000 0.00 0.00 0.00 3.27
683 818 2.125753 GTGACCAGGAGCGAGCAG 60.126 66.667 0.00 0.00 0.00 4.24
707 842 0.596083 GAGCACGTGAGATCATCGGG 60.596 60.000 22.23 0.00 0.00 5.14
752 900 2.203126 GGCCAATCAGAGGAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
753 901 2.203126 GGGCCAATCAGAGGAGCG 60.203 66.667 4.39 0.00 0.00 5.03
754 902 2.203126 CGGGCCAATCAGAGGAGC 60.203 66.667 4.39 0.00 0.00 4.70
755 903 2.203126 GCGGGCCAATCAGAGGAG 60.203 66.667 4.39 0.00 0.00 3.69
756 904 4.161295 CGCGGGCCAATCAGAGGA 62.161 66.667 4.39 0.00 0.00 3.71
848 997 2.885644 GCGATCCGCGTGATGTGT 60.886 61.111 13.68 0.00 44.55 3.72
898 1058 1.000274 GTTTGAAAATGGAGGCGCTGT 60.000 47.619 7.64 0.00 0.00 4.40
984 1156 2.753043 ATCTTGCTTGCTGGCGGG 60.753 61.111 0.00 0.00 34.52 6.13
985 1157 2.488355 CATCTTGCTTGCTGGCGG 59.512 61.111 0.00 0.00 34.52 6.13
986 1158 2.042259 TCCATCTTGCTTGCTGGCG 61.042 57.895 0.00 0.00 34.52 5.69
987 1159 1.509923 GTCCATCTTGCTTGCTGGC 59.490 57.895 0.00 0.00 0.00 4.85
988 1160 1.651240 CCGTCCATCTTGCTTGCTGG 61.651 60.000 0.00 0.00 0.00 4.85
989 1161 1.798735 CCGTCCATCTTGCTTGCTG 59.201 57.895 0.00 0.00 0.00 4.41
990 1162 2.042831 GCCGTCCATCTTGCTTGCT 61.043 57.895 0.00 0.00 0.00 3.91
1216 1405 1.067821 GAGGGTGATGACGAGGATGAC 59.932 57.143 0.00 0.00 0.00 3.06
1219 1408 0.760945 GGGAGGGTGATGACGAGGAT 60.761 60.000 0.00 0.00 0.00 3.24
1228 1429 2.041819 GTCGGAGGGGAGGGTGAT 60.042 66.667 0.00 0.00 0.00 3.06
1229 1430 4.393778 GGTCGGAGGGGAGGGTGA 62.394 72.222 0.00 0.00 0.00 4.02
1262 1474 3.296709 ATCGGCGGCTCGTTTCAGT 62.297 57.895 7.21 0.00 0.00 3.41
1492 1705 1.371558 GACTTGGTGGCGGTCTTCT 59.628 57.895 0.00 0.00 0.00 2.85
1493 1706 2.027625 CGACTTGGTGGCGGTCTTC 61.028 63.158 0.00 0.00 44.96 2.87
1494 1707 2.030562 CGACTTGGTGGCGGTCTT 59.969 61.111 0.00 0.00 44.96 3.01
1503 1716 1.073199 CCTTCTTGGGCGACTTGGT 59.927 57.895 0.00 0.00 0.00 3.67
1585 1809 1.892819 CGGAGCACCATCAGTCCAGT 61.893 60.000 0.00 0.00 35.59 4.00
1586 1810 1.153489 CGGAGCACCATCAGTCCAG 60.153 63.158 0.00 0.00 35.59 3.86
1587 1811 1.888436 GACGGAGCACCATCAGTCCA 61.888 60.000 0.00 0.00 38.13 4.02
1588 1812 1.153549 GACGGAGCACCATCAGTCC 60.154 63.158 0.00 0.00 38.13 3.85
1589 1813 1.591703 TGACGGAGCACCATCAGTC 59.408 57.895 0.00 0.00 42.54 3.51
1605 1829 2.283604 TAGGCACACGAGGGCTGA 60.284 61.111 7.12 0.00 41.71 4.26
1661 1887 3.925913 GCAAAAGAACAAGCTTCAACACA 59.074 39.130 0.00 0.00 0.00 3.72
1676 1902 2.733945 GCGGGGCAAAGCAAAAGA 59.266 55.556 0.00 0.00 0.00 2.52
1739 1965 8.327941 TGCATTAGAAACCAGATTGATATAGC 57.672 34.615 0.00 0.00 0.00 2.97
1742 1968 7.776969 ACACTGCATTAGAAACCAGATTGATAT 59.223 33.333 0.00 0.00 0.00 1.63
1743 1969 7.112122 ACACTGCATTAGAAACCAGATTGATA 58.888 34.615 0.00 0.00 0.00 2.15
1755 1981 6.197468 GCGTTTTAACAAACACTGCATTAGAA 59.803 34.615 0.00 0.00 42.30 2.10
1788 2014 6.599437 CAATACAGTTAAAACAGGACGGAAG 58.401 40.000 0.00 0.00 0.00 3.46
1795 2021 7.945033 ACAAATGCAATACAGTTAAAACAGG 57.055 32.000 0.00 0.00 33.44 4.00
1812 2038 1.591248 CGTGCTCGTACAACAAATGC 58.409 50.000 0.00 0.00 0.00 3.56
1813 2039 1.194547 AGCGTGCTCGTACAACAAATG 59.805 47.619 10.18 0.00 39.49 2.32
1814 2040 1.194547 CAGCGTGCTCGTACAACAAAT 59.805 47.619 10.18 0.00 39.49 2.32
1815 2041 0.579630 CAGCGTGCTCGTACAACAAA 59.420 50.000 10.18 0.00 39.49 2.83
1817 2043 0.663269 CTCAGCGTGCTCGTACAACA 60.663 55.000 10.18 0.00 39.49 3.33
1818 2044 1.945776 GCTCAGCGTGCTCGTACAAC 61.946 60.000 10.18 0.00 39.49 3.32
1819 2045 1.733041 GCTCAGCGTGCTCGTACAA 60.733 57.895 10.18 0.00 39.49 2.41
1821 2047 2.126463 TGCTCAGCGTGCTCGTAC 60.126 61.111 10.18 0.00 39.49 3.67
1822 2048 2.179267 CTGCTCAGCGTGCTCGTA 59.821 61.111 10.18 0.00 39.49 3.43
1823 2049 3.983494 ACTGCTCAGCGTGCTCGT 61.983 61.111 10.18 0.00 39.49 4.18
1824 2050 3.476646 CACTGCTCAGCGTGCTCG 61.477 66.667 8.38 3.31 40.37 5.03
1825 2051 1.958205 AACACTGCTCAGCGTGCTC 60.958 57.895 17.91 0.00 36.88 4.26
1826 2052 2.109799 AACACTGCTCAGCGTGCT 59.890 55.556 17.91 6.63 36.88 4.40
1827 2053 2.250485 CAACACTGCTCAGCGTGC 59.750 61.111 17.91 0.00 36.88 5.34
1828 2054 2.610694 CCCAACACTGCTCAGCGTG 61.611 63.158 16.81 16.81 38.35 5.34
1829 2055 2.116983 ATCCCAACACTGCTCAGCGT 62.117 55.000 0.00 0.00 0.00 5.07
1830 2056 0.108186 TATCCCAACACTGCTCAGCG 60.108 55.000 0.00 0.00 0.00 5.18
1831 2057 1.065854 ACTATCCCAACACTGCTCAGC 60.066 52.381 0.00 0.00 0.00 4.26
1832 2058 3.005554 CAACTATCCCAACACTGCTCAG 58.994 50.000 0.00 0.00 0.00 3.35
1833 2059 2.875672 GCAACTATCCCAACACTGCTCA 60.876 50.000 0.00 0.00 0.00 4.26
1834 2060 1.740025 GCAACTATCCCAACACTGCTC 59.260 52.381 0.00 0.00 0.00 4.26
1835 2061 1.614317 GGCAACTATCCCAACACTGCT 60.614 52.381 0.00 0.00 0.00 4.24
1839 2065 1.199097 CAACGGCAACTATCCCAACAC 59.801 52.381 0.00 0.00 0.00 3.32
1840 2066 1.529226 CAACGGCAACTATCCCAACA 58.471 50.000 0.00 0.00 0.00 3.33
1841 2067 0.170339 GCAACGGCAACTATCCCAAC 59.830 55.000 0.00 0.00 40.72 3.77
1845 2071 2.352388 TGTAAGCAACGGCAACTATCC 58.648 47.619 0.00 0.00 44.61 2.59
1850 2076 2.485266 AACTTGTAAGCAACGGCAAC 57.515 45.000 0.00 0.00 44.61 4.17
1855 2081 5.164158 GCAATCATGAAACTTGTAAGCAACG 60.164 40.000 0.00 0.00 0.00 4.10
1856 2082 5.922544 AGCAATCATGAAACTTGTAAGCAAC 59.077 36.000 0.00 0.00 0.00 4.17
1862 2088 8.629158 AGTTGTAAAGCAATCATGAAACTTGTA 58.371 29.630 0.00 0.00 39.55 2.41
1863 2089 7.436080 CAGTTGTAAAGCAATCATGAAACTTGT 59.564 33.333 0.00 0.00 39.55 3.16
1867 2093 8.524870 AATCAGTTGTAAAGCAATCATGAAAC 57.475 30.769 0.00 0.00 39.55 2.78
1879 2105 8.391075 TCCCTTACAGAAAATCAGTTGTAAAG 57.609 34.615 0.00 0.00 36.08 1.85
1882 2108 8.383175 AGAATCCCTTACAGAAAATCAGTTGTA 58.617 33.333 0.00 0.00 0.00 2.41
1883 2109 7.234355 AGAATCCCTTACAGAAAATCAGTTGT 58.766 34.615 0.00 0.00 0.00 3.32
1885 2111 8.606830 AGTAGAATCCCTTACAGAAAATCAGTT 58.393 33.333 0.00 0.00 0.00 3.16
1916 2142 9.866798 CGTAGAATACCTTAAGGAAAACTAGTT 57.133 33.333 28.52 1.12 38.71 2.24
1917 2143 9.247861 TCGTAGAATACCTTAAGGAAAACTAGT 57.752 33.333 28.52 8.59 38.71 2.57
1920 2146 9.433153 CTTTCGTAGAATACCTTAAGGAAAACT 57.567 33.333 28.52 20.49 45.90 2.66
1921 2147 9.212641 ACTTTCGTAGAATACCTTAAGGAAAAC 57.787 33.333 28.52 15.15 45.90 2.43
1923 2149 9.783081 AAACTTTCGTAGAATACCTTAAGGAAA 57.217 29.630 28.52 15.39 45.90 3.13
1925 2151 8.370182 ACAAACTTTCGTAGAATACCTTAAGGA 58.630 33.333 28.52 11.97 45.90 3.36
1926 2152 8.543862 ACAAACTTTCGTAGAATACCTTAAGG 57.456 34.615 20.42 20.42 45.90 2.69
1931 2157 8.943002 CCAAATACAAACTTTCGTAGAATACCT 58.057 33.333 0.00 0.00 45.90 3.08
1932 2158 8.938906 TCCAAATACAAACTTTCGTAGAATACC 58.061 33.333 0.00 0.00 45.90 2.73
1937 2163 7.519328 GCTGTTCCAAATACAAACTTTCGTAGA 60.519 37.037 0.00 0.00 0.00 2.59
1938 2164 6.577427 GCTGTTCCAAATACAAACTTTCGTAG 59.423 38.462 0.00 0.00 0.00 3.51
1939 2165 6.261381 AGCTGTTCCAAATACAAACTTTCGTA 59.739 34.615 0.00 0.00 0.00 3.43
1940 2166 5.067283 AGCTGTTCCAAATACAAACTTTCGT 59.933 36.000 0.00 0.00 0.00 3.85
1941 2167 5.519722 AGCTGTTCCAAATACAAACTTTCG 58.480 37.500 0.00 0.00 0.00 3.46
1946 2172 6.072112 TCAGAAGCTGTTCCAAATACAAAC 57.928 37.500 0.00 0.00 32.48 2.93
1954 2180 3.565307 ACCAAATCAGAAGCTGTTCCAA 58.435 40.909 0.00 0.00 32.48 3.53
1955 2181 3.228188 ACCAAATCAGAAGCTGTTCCA 57.772 42.857 0.00 0.00 32.48 3.53
1960 2186 6.506500 ACTAATCAACCAAATCAGAAGCTG 57.493 37.500 0.00 0.00 0.00 4.24
1973 2199 7.770897 AGAGATGAACACCATAACTAATCAACC 59.229 37.037 0.00 0.00 35.17 3.77
1977 2203 6.763135 TGCAGAGATGAACACCATAACTAATC 59.237 38.462 0.00 0.00 35.17 1.75
1986 2212 3.708403 AGAATGCAGAGATGAACACCA 57.292 42.857 0.00 0.00 0.00 4.17
1987 2213 4.352600 CAAGAATGCAGAGATGAACACC 57.647 45.455 0.00 0.00 0.00 4.16
2012 2238 6.865834 AAGATTCAGTCTATTGTGACTCCT 57.134 37.500 0.00 0.00 44.56 3.69
2013 2239 7.099764 TCAAAGATTCAGTCTATTGTGACTCC 58.900 38.462 0.00 0.00 44.56 3.85
2016 2242 7.742089 CGTTTCAAAGATTCAGTCTATTGTGAC 59.258 37.037 0.00 0.00 35.67 3.67
2017 2243 7.441157 ACGTTTCAAAGATTCAGTCTATTGTGA 59.559 33.333 0.00 0.00 35.67 3.58
2020 2246 7.742089 GTCACGTTTCAAAGATTCAGTCTATTG 59.258 37.037 0.00 0.00 35.67 1.90
2048 2274 4.583907 TCAAGTCAGGCATGAAATTTGTGA 59.416 37.500 0.92 0.00 37.14 3.58
2049 2275 4.873817 TCAAGTCAGGCATGAAATTTGTG 58.126 39.130 0.92 0.00 37.14 3.33
2136 2390 7.646314 TGGAGTACGAACTACTATAGATTTGC 58.354 38.462 6.78 0.00 37.47 3.68
2145 2399 3.674997 ACGGTTGGAGTACGAACTACTA 58.325 45.455 0.00 0.00 37.47 1.82
2153 2407 0.033781 TTTGGGACGGTTGGAGTACG 59.966 55.000 0.00 0.00 0.00 3.67
2178 2432 5.700832 TCCATATCTAAGCAAATGTAAGGCG 59.299 40.000 0.00 0.00 0.00 5.52
2180 2434 8.853077 TCATCCATATCTAAGCAAATGTAAGG 57.147 34.615 0.00 0.00 0.00 2.69
2266 2525 5.640357 TGTTACCTTGCAAAATACTACTCCG 59.360 40.000 0.00 0.00 0.00 4.63
2303 2568 7.307337 CCCTTAGAAAATCAACAAACACAATGC 60.307 37.037 0.00 0.00 0.00 3.56
2322 2587 4.338795 AGAACCATGTCTCTCCCTTAGA 57.661 45.455 0.00 0.00 0.00 2.10
2323 2588 4.223923 ACAAGAACCATGTCTCTCCCTTAG 59.776 45.833 0.00 0.00 0.00 2.18
2326 2594 2.625639 ACAAGAACCATGTCTCTCCCT 58.374 47.619 0.00 0.00 0.00 4.20
2361 2655 2.656432 TGGTCACTTAGTAGTACCCCCT 59.344 50.000 0.00 0.00 32.01 4.79
2362 2656 3.105959 TGGTCACTTAGTAGTACCCCC 57.894 52.381 0.00 0.00 32.01 5.40
2363 2657 4.961099 AGAATGGTCACTTAGTAGTACCCC 59.039 45.833 0.00 0.00 32.01 4.95
2364 2658 5.421374 ACAGAATGGTCACTTAGTAGTACCC 59.579 44.000 0.00 0.00 43.62 3.69
2365 2659 6.071503 ACACAGAATGGTCACTTAGTAGTACC 60.072 42.308 0.00 4.40 43.62 3.34
2366 2660 6.807230 CACACAGAATGGTCACTTAGTAGTAC 59.193 42.308 0.00 0.00 43.62 2.73
2367 2661 6.492429 ACACACAGAATGGTCACTTAGTAGTA 59.508 38.462 0.00 0.00 43.62 1.82
2368 2662 5.304614 ACACACAGAATGGTCACTTAGTAGT 59.695 40.000 0.00 0.00 43.62 2.73
2369 2663 5.784177 ACACACAGAATGGTCACTTAGTAG 58.216 41.667 0.00 0.00 43.62 2.57
2370 2664 5.801531 ACACACAGAATGGTCACTTAGTA 57.198 39.130 0.00 0.00 43.62 1.82
2371 2665 4.689612 ACACACAGAATGGTCACTTAGT 57.310 40.909 0.00 0.00 43.62 2.24
2372 2666 5.056480 TCAACACACAGAATGGTCACTTAG 58.944 41.667 0.00 0.00 43.62 2.18
2373 2667 5.029807 TCAACACACAGAATGGTCACTTA 57.970 39.130 0.00 0.00 43.62 2.24
2374 2668 3.884895 TCAACACACAGAATGGTCACTT 58.115 40.909 0.00 0.00 43.62 3.16
2375 2669 3.558931 TCAACACACAGAATGGTCACT 57.441 42.857 0.00 0.00 43.62 3.41
2376 2670 4.836125 AATCAACACACAGAATGGTCAC 57.164 40.909 0.00 0.00 43.62 3.67
2377 2671 8.628630 TTATAAATCAACACACAGAATGGTCA 57.371 30.769 0.00 0.00 43.62 4.02
2403 2697 4.763355 TGGCATATCTGGTACTCCCTTAT 58.237 43.478 0.00 0.00 0.00 1.73
2415 2709 7.716998 ACCTACAGAAAATAGTTGGCATATCTG 59.283 37.037 0.00 0.00 39.09 2.90
2457 2752 6.560003 TCCTGATAGCAGAATTTCAACCTA 57.440 37.500 10.19 0.00 45.17 3.08
2458 2753 5.441718 TCCTGATAGCAGAATTTCAACCT 57.558 39.130 10.19 0.00 45.17 3.50
2473 2768 7.921041 AAGAATACAGAGATGGTTCCTGATA 57.079 36.000 0.00 0.00 0.00 2.15
2478 2773 5.355350 CCACAAAGAATACAGAGATGGTTCC 59.645 44.000 0.00 0.00 0.00 3.62
2492 2787 6.294731 GCTGATTCCTTTACACCACAAAGAAT 60.295 38.462 0.00 0.00 35.43 2.40
2495 2790 4.278170 TGCTGATTCCTTTACACCACAAAG 59.722 41.667 0.00 0.00 33.62 2.77
2496 2791 4.211125 TGCTGATTCCTTTACACCACAAA 58.789 39.130 0.00 0.00 0.00 2.83
2497 2792 3.820467 CTGCTGATTCCTTTACACCACAA 59.180 43.478 0.00 0.00 0.00 3.33
2499 2794 2.162408 GCTGCTGATTCCTTTACACCAC 59.838 50.000 0.00 0.00 0.00 4.16
2506 2801 2.097825 GTCATGGCTGCTGATTCCTTT 58.902 47.619 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.