Multiple sequence alignment - TraesCS5B01G368500

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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 TraesCS5B01G368500 chr5B 100.000 7543 0 0 1 7543 546833029 546825487 0.000000e+00 13930.0
1 TraesCS5B01G368500 chr5B 87.363 728 86 6 6818 7543 533932483 533931760 0.000000e+00 830.0
2 TraesCS5B01G368500 chr5A 94.460 5217 194 42 1570 6734 565757942 565752769 0.000000e+00 7945.0
3 TraesCS5B01G368500 chr5A 87.953 1461 124 30 94 1518 565759386 565757942 0.000000e+00 1676.0
4 TraesCS5B01G368500 chr5A 94.062 741 43 1 6803 7543 35042436 35041697 0.000000e+00 1123.0
5 TraesCS5B01G368500 chr5D 94.497 2544 128 8 4195 6729 447882985 447880445 0.000000e+00 3912.0
6 TraesCS5B01G368500 chr5D 88.377 1497 121 29 62 1518 447887049 447885566 0.000000e+00 1751.0
7 TraesCS5B01G368500 chr5D 90.625 800 52 10 2875 3665 447884364 447883579 0.000000e+00 1040.0
8 TraesCS5B01G368500 chr5D 89.176 813 61 15 1978 2776 447885161 447884362 0.000000e+00 989.0
9 TraesCS5B01G368500 chr5D 94.286 280 10 5 1570 1845 447885566 447885289 2.520000e-114 424.0
10 TraesCS5B01G368500 chr5D 83.476 466 40 13 3744 4202 447883446 447883011 4.240000e-107 399.0
11 TraesCS5B01G368500 chr5D 97.872 47 1 0 3695 3741 447883587 447883541 1.740000e-11 82.4
12 TraesCS5B01G368500 chr3B 96.242 745 21 2 6799 7543 684511240 684510503 0.000000e+00 1214.0
13 TraesCS5B01G368500 chr3B 92.044 641 34 16 6911 7543 17990515 17991146 0.000000e+00 885.0
14 TraesCS5B01G368500 chr3B 97.942 243 5 0 6805 7047 684506327 684506085 9.050000e-114 422.0
15 TraesCS5B01G368500 chr7A 93.640 739 47 0 6805 7543 685854950 685855688 0.000000e+00 1105.0
16 TraesCS5B01G368500 chr7A 91.709 398 19 4 1449 1846 96203654 96204037 2.390000e-149 540.0
17 TraesCS5B01G368500 chr7A 94.841 252 10 3 1975 2224 96204159 96204409 2.550000e-104 390.0
18 TraesCS5B01G368500 chr7D 93.649 740 39 3 6805 7543 632053179 632053911 0.000000e+00 1099.0
19 TraesCS5B01G368500 chr7D 100.000 29 0 0 6730 6758 554535127 554535155 4.000000e-03 54.7
20 TraesCS5B01G368500 chr2B 92.737 716 47 2 6833 7543 771858647 771859362 0.000000e+00 1029.0
21 TraesCS5B01G368500 chr1D 91.031 747 64 2 6800 7543 395889217 395889963 0.000000e+00 1005.0
22 TraesCS5B01G368500 chrUn 96.935 522 15 1 7022 7543 224666031 224665511 0.000000e+00 874.0
23 TraesCS5B01G368500 chr2A 91.457 398 20 4 1449 1846 622753211 622753594 1.110000e-147 534.0
24 TraesCS5B01G368500 chr2A 90.704 398 23 5 1449 1846 108513373 108512990 1.120000e-142 518.0
25 TraesCS5B01G368500 chr2A 94.841 252 10 3 1975 2224 622753716 622753966 2.550000e-104 390.0
26 TraesCS5B01G368500 chr2A 93.651 252 12 4 1975 2224 108512868 108512619 2.570000e-99 374.0


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 TraesCS5B01G368500 chr5B 546825487 546833029 7542 True 13930.0 13930 100.0000 1 7543 1 chr5B.!!$R2 7542
1 TraesCS5B01G368500 chr5B 533931760 533932483 723 True 830.0 830 87.3630 6818 7543 1 chr5B.!!$R1 725
2 TraesCS5B01G368500 chr5A 565752769 565759386 6617 True 4810.5 7945 91.2065 94 6734 2 chr5A.!!$R2 6640
3 TraesCS5B01G368500 chr5A 35041697 35042436 739 True 1123.0 1123 94.0620 6803 7543 1 chr5A.!!$R1 740
4 TraesCS5B01G368500 chr5D 447880445 447887049 6604 True 1228.2 3912 91.1870 62 6729 7 chr5D.!!$R1 6667
5 TraesCS5B01G368500 chr3B 684510503 684511240 737 True 1214.0 1214 96.2420 6799 7543 1 chr3B.!!$R2 744
6 TraesCS5B01G368500 chr3B 17990515 17991146 631 False 885.0 885 92.0440 6911 7543 1 chr3B.!!$F1 632
7 TraesCS5B01G368500 chr7A 685854950 685855688 738 False 1105.0 1105 93.6400 6805 7543 1 chr7A.!!$F1 738
8 TraesCS5B01G368500 chr7A 96203654 96204409 755 False 465.0 540 93.2750 1449 2224 2 chr7A.!!$F2 775
9 TraesCS5B01G368500 chr7D 632053179 632053911 732 False 1099.0 1099 93.6490 6805 7543 1 chr7D.!!$F2 738
10 TraesCS5B01G368500 chr2B 771858647 771859362 715 False 1029.0 1029 92.7370 6833 7543 1 chr2B.!!$F1 710
11 TraesCS5B01G368500 chr1D 395889217 395889963 746 False 1005.0 1005 91.0310 6800 7543 1 chr1D.!!$F1 743
12 TraesCS5B01G368500 chrUn 224665511 224666031 520 True 874.0 874 96.9350 7022 7543 1 chrUn.!!$R1 521
13 TraesCS5B01G368500 chr2A 622753211 622753966 755 False 462.0 534 93.1490 1449 2224 2 chr2A.!!$F1 775
14 TraesCS5B01G368500 chr2A 108512619 108513373 754 True 446.0 518 92.1775 1449 2224 2 chr2A.!!$R1 775

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
656 680 0.539986 ATGCCGAGGTAAACCGTCAT 59.460 50.000 0.00 0.0 42.08 3.06 F
859 887 0.887387 CCTGCCGGTTCCTCGAAAAA 60.887 55.000 1.90 0.0 0.00 1.94 F
1001 1029 1.039785 CCTCTCTGCTCCACATCCGA 61.040 60.000 0.00 0.0 0.00 4.55 F
2812 2940 0.661187 CATTGCGTTGCACAGACACC 60.661 55.000 0.00 0.0 38.71 4.16 F
3741 3884 1.786937 CCTGTAGAGTGCTCCTCCAT 58.213 55.000 0.00 0.0 41.47 3.41 F
4644 4923 1.143684 ACCTGACTGTTTGGCTCATGT 59.856 47.619 0.00 0.0 0.00 3.21 F
5427 5713 1.864176 GCATGCTGCAAAAACAGGC 59.136 52.632 11.37 0.0 44.26 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2157 1.074566 AGAGGGAGAAACAGGGCAAAG 59.925 52.381 0.00 0.00 0.00 2.77 R
2686 2812 0.038166 TGGCAACTTAGCAGAAGGGG 59.962 55.000 3.72 0.00 35.83 4.79 R
2856 2984 0.178992 TGCAGAGAAACACAAGGGGG 60.179 55.000 0.00 0.00 0.00 5.40 R
4041 4282 0.179702 TCCTCTGAGATGCACATGGC 59.820 55.000 6.17 0.00 45.13 4.40 R
5367 5653 1.002468 GCAGAAACACACATCGCAACT 60.002 47.619 0.00 0.00 0.00 3.16 R
5865 6151 0.106708 CCAGTGGCACTGTGTACACT 59.893 55.000 37.43 24.46 44.50 3.55 R
6740 7029 0.322008 TGCACGTGTGGGCATTATCA 60.322 50.000 18.38 0.00 34.58 2.15 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
71 72 9.981460 ATGCCAAATTTAAAAACCCCATTTATA 57.019 25.926 0.00 0.00 0.00 0.98
114 124 1.599542 CTAAAGCGGCACATAAGAGCC 59.400 52.381 1.45 0.00 46.60 4.70
122 132 1.952296 GCACATAAGAGCCCAATCCAG 59.048 52.381 0.00 0.00 0.00 3.86
202 214 3.502211 CGTTGGCATAAGTCTCCTGTTTT 59.498 43.478 0.00 0.00 0.00 2.43
204 216 5.390567 CGTTGGCATAAGTCTCCTGTTTTAC 60.391 44.000 0.00 0.00 0.00 2.01
205 217 5.499004 TGGCATAAGTCTCCTGTTTTACT 57.501 39.130 0.00 0.00 0.00 2.24
223 235 1.608590 ACTTCGTGGGCATGTCTTTTG 59.391 47.619 0.00 0.00 0.00 2.44
225 237 1.442520 CGTGGGCATGTCTTTTGCG 60.443 57.895 0.00 0.00 41.07 4.85
265 278 2.575735 TGCCATGTGGATCCACTTAGAA 59.424 45.455 37.92 21.82 46.30 2.10
266 279 2.945668 GCCATGTGGATCCACTTAGAAC 59.054 50.000 37.92 21.90 46.30 3.01
267 280 3.370953 GCCATGTGGATCCACTTAGAACT 60.371 47.826 37.92 15.85 46.30 3.01
268 281 4.848357 CCATGTGGATCCACTTAGAACTT 58.152 43.478 37.92 14.79 46.30 2.66
269 282 4.878397 CCATGTGGATCCACTTAGAACTTC 59.122 45.833 37.92 14.46 46.30 3.01
356 374 2.997980 TCCTGTTGTTGTCTTCTTGCA 58.002 42.857 0.00 0.00 0.00 4.08
357 375 2.682856 TCCTGTTGTTGTCTTCTTGCAC 59.317 45.455 0.00 0.00 0.00 4.57
360 378 1.067060 GTTGTTGTCTTCTTGCACCCC 59.933 52.381 0.00 0.00 0.00 4.95
389 408 9.280174 ACAATTTTGATTAGGTTTCTCTCGTAA 57.720 29.630 0.00 0.00 0.00 3.18
468 487 7.094805 GGCTTAATTATTTGGATCACGATGCTA 60.095 37.037 0.00 0.00 0.00 3.49
510 529 1.270893 GGGATCCTATTCTGAACGCCC 60.271 57.143 12.58 0.00 0.00 6.13
530 549 3.432252 CCCGTTGTCTTGTCTTACATGAC 59.568 47.826 15.40 15.40 46.95 3.06
543 562 5.287752 GTCTTACATGACGAACAAGCGAATA 59.712 40.000 0.00 0.00 34.83 1.75
547 566 2.396601 TGACGAACAAGCGAATAACGT 58.603 42.857 0.00 0.00 44.60 3.99
592 615 6.207417 CGGGGAAAATAGCATCATCACTTAAT 59.793 38.462 0.00 0.00 0.00 1.40
621 644 7.883311 ACAATCTAAGTAGCCATACACAAGTTT 59.117 33.333 0.00 0.00 34.07 2.66
656 680 0.539986 ATGCCGAGGTAAACCGTCAT 59.460 50.000 0.00 0.00 42.08 3.06
660 684 2.470821 CCGAGGTAAACCGTCATCATC 58.529 52.381 0.00 0.00 42.08 2.92
661 687 2.470821 CGAGGTAAACCGTCATCATCC 58.529 52.381 0.00 0.00 42.08 3.51
662 688 2.470821 GAGGTAAACCGTCATCATCCG 58.529 52.381 0.00 0.00 42.08 4.18
671 697 1.524355 CGTCATCATCCGCAATGACTC 59.476 52.381 12.19 0.00 47.00 3.36
711 737 8.704668 ACTTCTCAAAAATAACAAAACTCCCAT 58.295 29.630 0.00 0.00 0.00 4.00
712 738 8.885494 TTCTCAAAAATAACAAAACTCCCATG 57.115 30.769 0.00 0.00 0.00 3.66
732 758 1.993370 GCTCACTAACACCGATGACAC 59.007 52.381 0.00 0.00 0.00 3.67
806 833 4.393680 TGGATTAACAAACACTCATACGCC 59.606 41.667 0.00 0.00 0.00 5.68
829 857 3.825308 ACGTTGACATTGTGCATGATTC 58.175 40.909 0.00 0.00 36.24 2.52
859 887 0.887387 CCTGCCGGTTCCTCGAAAAA 60.887 55.000 1.90 0.00 0.00 1.94
898 926 3.341857 AAACGACAGCGCAATAACAAA 57.658 38.095 11.47 0.00 42.48 2.83
941 969 6.430925 CCCATTTATGCTCCTCGAATAATTGA 59.569 38.462 8.96 0.00 0.00 2.57
942 970 7.361542 CCCATTTATGCTCCTCGAATAATTGAG 60.362 40.741 8.96 0.00 36.90 3.02
953 981 1.321474 ATAATTGAGGGCATGCCGTG 58.679 50.000 35.16 0.00 36.85 4.94
1001 1029 1.039785 CCTCTCTGCTCCACATCCGA 61.040 60.000 0.00 0.00 0.00 4.55
1037 1065 1.444119 AAGAAAGACTGCGCCGCAAA 61.444 50.000 14.77 0.00 38.41 3.68
1299 1346 1.271054 TGACTGCCTCTGAGCCTTTTC 60.271 52.381 0.00 0.00 0.00 2.29
1329 1377 4.966787 TTCGCCCCGGCTTTGCTT 62.967 61.111 3.84 0.00 39.32 3.91
1336 1384 1.286880 CCGGCTTTGCTTTCCTGTG 59.713 57.895 0.00 0.00 0.00 3.66
1343 1399 3.004734 GCTTTGCTTTCCTGTGTGTATGT 59.995 43.478 0.00 0.00 0.00 2.29
1345 1401 5.682943 TTTGCTTTCCTGTGTGTATGTAC 57.317 39.130 0.00 0.00 0.00 2.90
1349 1405 3.328382 TTCCTGTGTGTATGTACCTGC 57.672 47.619 0.00 0.00 0.00 4.85
1351 1407 2.635427 TCCTGTGTGTATGTACCTGCAA 59.365 45.455 0.00 0.00 0.00 4.08
1360 1416 1.533625 TGTACCTGCAATCTTGTGCC 58.466 50.000 0.00 0.00 44.26 5.01
1382 1438 2.353889 CGGATTCAAATCTGGAGCACTG 59.646 50.000 3.98 0.00 37.99 3.66
1403 1459 7.201758 GCACTGATTTGATTGAACATCTGGATA 60.202 37.037 0.00 0.00 0.00 2.59
1413 1469 6.513806 TGAACATCTGGATATTTGTGGTTG 57.486 37.500 0.00 0.00 0.00 3.77
1414 1470 6.009589 TGAACATCTGGATATTTGTGGTTGT 58.990 36.000 0.00 0.00 0.00 3.32
1415 1471 6.493115 TGAACATCTGGATATTTGTGGTTGTT 59.507 34.615 0.00 0.00 0.00 2.83
1440 1496 2.037772 GACTGTTTCTGAGCCTCTTGGA 59.962 50.000 0.00 0.00 34.57 3.53
1441 1497 2.439507 ACTGTTTCTGAGCCTCTTGGAA 59.560 45.455 0.00 0.00 34.57 3.53
1442 1498 2.810852 CTGTTTCTGAGCCTCTTGGAAC 59.189 50.000 0.00 0.00 34.57 3.62
1443 1499 2.172505 TGTTTCTGAGCCTCTTGGAACA 59.827 45.455 7.67 7.67 34.57 3.18
1491 1553 8.506140 AATCAAAATAAGATGTGTTGTCGTTG 57.494 30.769 0.00 0.00 0.00 4.10
1540 1602 4.081752 TCAGCATGTGTTTTGTTGGAGTTT 60.082 37.500 0.00 0.00 37.40 2.66
1541 1603 4.033129 CAGCATGTGTTTTGTTGGAGTTTG 59.967 41.667 0.00 0.00 0.00 2.93
1542 1604 3.932089 GCATGTGTTTTGTTGGAGTTTGT 59.068 39.130 0.00 0.00 0.00 2.83
1543 1605 5.105554 AGCATGTGTTTTGTTGGAGTTTGTA 60.106 36.000 0.00 0.00 0.00 2.41
1567 1629 9.099454 GTATGTAAGAGGGAAAGACAAATACAG 57.901 37.037 0.00 0.00 0.00 2.74
1590 1652 2.324541 AGACTGAGCTGGTTCTTGACT 58.675 47.619 0.00 0.00 0.00 3.41
1798 1860 5.072736 AGGTGATTGCTATCATCATCCAAGA 59.927 40.000 21.02 0.00 43.15 3.02
1803 1865 8.920174 TGATTGCTATCATCATCCAAGAATTTT 58.080 29.630 6.75 0.00 35.87 1.82
1804 1866 9.408069 GATTGCTATCATCATCCAAGAATTTTC 57.592 33.333 3.09 0.00 0.00 2.29
1861 1929 6.567959 TGCAGTATTTTGTTTGACACAATCA 58.432 32.000 0.00 0.00 45.17 2.57
1876 1944 6.891361 TGACACAATCAATAAAGGTCATGGAT 59.109 34.615 0.00 0.00 33.02 3.41
1879 1947 7.562454 ACACAATCAATAAAGGTCATGGATCAT 59.438 33.333 0.00 0.00 0.00 2.45
1913 1983 6.500041 TGTGTTAACAACATGGCTTTAGTTC 58.500 36.000 10.51 0.00 44.35 3.01
1973 2043 2.492012 CAGTGCATTCTCCCTGATAGC 58.508 52.381 0.00 0.00 0.00 2.97
2019 2116 5.362717 TGGTGTCTTTACTCTGAACTTCTGA 59.637 40.000 0.00 0.00 0.00 3.27
2020 2117 5.692654 GGTGTCTTTACTCTGAACTTCTGAC 59.307 44.000 0.00 0.00 0.00 3.51
2057 2157 6.967199 GCCACAGTATGCTAAGTAATTTTGTC 59.033 38.462 0.00 0.00 42.53 3.18
2333 2435 4.280677 CCAAGGTAAGAATTTGTGCCTCAA 59.719 41.667 0.45 0.00 0.00 3.02
2463 2571 6.777091 TGAAAAGCTAATGTGTATGGCCATAT 59.223 34.615 27.84 14.30 0.00 1.78
2482 2590 6.205658 GCCATATAGAGGAAATTCTGGTCAAC 59.794 42.308 0.00 0.00 0.00 3.18
2507 2615 2.436417 TCCTAAAGTCCATGCAACAGC 58.564 47.619 0.00 0.00 0.00 4.40
2516 2624 3.689161 GTCCATGCAACAGCACAGTTATA 59.311 43.478 0.00 0.00 41.80 0.98
2521 2629 4.450976 TGCAACAGCACAGTTATATAGGG 58.549 43.478 0.00 0.00 32.31 3.53
2533 2641 8.784043 CACAGTTATATAGGGCTTTTATTGGTC 58.216 37.037 0.00 0.00 0.00 4.02
2556 2682 7.229907 GGTCCGGCCAATATAAAGAGATTTTTA 59.770 37.037 2.24 0.00 37.17 1.52
2557 2683 8.626526 GTCCGGCCAATATAAAGAGATTTTTAA 58.373 33.333 2.24 0.00 0.00 1.52
2558 2684 8.626526 TCCGGCCAATATAAAGAGATTTTTAAC 58.373 33.333 2.24 0.00 0.00 2.01
2560 2686 9.965824 CGGCCAATATAAAGAGATTTTTAACAT 57.034 29.630 2.24 0.00 0.00 2.71
2605 2731 8.762481 ACTAATTATCCTCCCCATGTAAAAAC 57.238 34.615 0.00 0.00 0.00 2.43
2670 2796 7.713073 GGCTGATAATAGACTATAAAGCCATCC 59.287 40.741 21.42 8.72 39.20 3.51
2677 2803 8.974292 ATAGACTATAAAGCCATCCCTCTAAA 57.026 34.615 0.00 0.00 0.00 1.85
2678 2804 7.309770 AGACTATAAAGCCATCCCTCTAAAG 57.690 40.000 0.00 0.00 0.00 1.85
2680 2806 7.015779 AGACTATAAAGCCATCCCTCTAAAGTC 59.984 40.741 0.00 0.00 0.00 3.01
2681 2807 6.847036 ACTATAAAGCCATCCCTCTAAAGTCT 59.153 38.462 0.00 0.00 0.00 3.24
2683 2809 7.691993 ATAAAGCCATCCCTCTAAAGTCTAA 57.308 36.000 0.00 0.00 0.00 2.10
2684 2810 6.388619 AAAGCCATCCCTCTAAAGTCTAAA 57.611 37.500 0.00 0.00 0.00 1.85
2686 2812 4.164413 AGCCATCCCTCTAAAGTCTAAACC 59.836 45.833 0.00 0.00 0.00 3.27
2709 2837 2.821969 CCTTCTGCTAAGTTGCCACAAT 59.178 45.455 0.00 0.00 0.00 2.71
2724 2852 3.737663 GCCACAATTTTTGTCTGTGCAGA 60.738 43.478 0.00 0.00 43.23 4.26
2746 2874 2.375174 TGCCTCAAGTAGGGACACAAAT 59.625 45.455 0.00 0.00 46.65 2.32
2751 2879 6.015772 GCCTCAAGTAGGGACACAAATTTTAA 60.016 38.462 0.00 0.00 46.65 1.52
2812 2940 0.661187 CATTGCGTTGCACAGACACC 60.661 55.000 0.00 0.00 38.71 4.16
2851 2979 7.095017 GGGATGCTTATGAGTTTACTGCTATTC 60.095 40.741 0.00 0.00 0.00 1.75
2971 3099 7.945134 AGATAAGCATTATTCCCAATCAACAC 58.055 34.615 0.00 0.00 42.35 3.32
2974 3102 5.969423 AGCATTATTCCCAATCAACACAAG 58.031 37.500 0.00 0.00 0.00 3.16
3172 3300 4.380761 GGTGAGTGCATGCATGTTTTATCA 60.381 41.667 25.64 19.38 0.00 2.15
3174 3302 5.457799 GTGAGTGCATGCATGTTTTATCATC 59.542 40.000 25.64 13.90 0.00 2.92
3175 3303 5.358725 TGAGTGCATGCATGTTTTATCATCT 59.641 36.000 25.64 11.25 0.00 2.90
3177 3305 6.636705 AGTGCATGCATGTTTTATCATCTTT 58.363 32.000 25.64 1.98 0.00 2.52
3178 3306 7.774134 AGTGCATGCATGTTTTATCATCTTTA 58.226 30.769 25.64 0.00 0.00 1.85
3179 3307 7.703621 AGTGCATGCATGTTTTATCATCTTTAC 59.296 33.333 25.64 3.82 0.00 2.01
3248 3376 3.334583 TTCAGCCTGACATGAACCTAC 57.665 47.619 0.00 0.00 30.67 3.18
3299 3427 8.698973 TGTTACCAGAAACCAGAAATATTTGA 57.301 30.769 5.17 0.00 0.00 2.69
3425 3561 1.945354 ATCCAGTACACGACCTGGCG 61.945 60.000 8.60 8.60 36.94 5.69
3473 3610 4.335647 CGTGGCCCCAAGAGCTGT 62.336 66.667 0.00 0.00 0.00 4.40
3504 3641 2.269241 CTCAGGGGCGGAAAGGAC 59.731 66.667 0.00 0.00 0.00 3.85
3606 3743 6.659668 GCCCCTAACTCAAGAAACTAATCTTT 59.340 38.462 0.00 0.00 37.56 2.52
3660 3797 9.638176 TCTTAAGTCCTTAACTACCATACTAGG 57.362 37.037 1.63 0.00 37.17 3.02
3741 3884 1.786937 CCTGTAGAGTGCTCCTCCAT 58.213 55.000 0.00 0.00 41.47 3.41
3776 4011 6.832384 TCTGAGATTACCAACTACTCCGTATT 59.168 38.462 0.00 0.00 0.00 1.89
3818 4058 5.161358 CGAGTGTTGCTGTACTGATTTCTA 58.839 41.667 3.61 0.00 0.00 2.10
3875 4116 9.884465 GTGATGCTTGTAATTCATAATTCTACC 57.116 33.333 0.00 0.00 32.38 3.18
3925 4166 7.017645 GTGACTTGATATTAACAACTGCTGTG 58.982 38.462 0.00 0.00 38.67 3.66
3964 4205 3.571590 TGCAACTGGTGGAATAAAGGTT 58.428 40.909 0.00 0.00 0.00 3.50
3980 4221 1.988107 AGGTTGAAGAGCCCAGAATGA 59.012 47.619 0.00 0.00 39.69 2.57
4007 4248 5.480642 TGGTACATGTGCAATTTGGAATT 57.519 34.783 16.11 0.00 0.00 2.17
4008 4249 6.596309 TGGTACATGTGCAATTTGGAATTA 57.404 33.333 16.11 0.00 0.00 1.40
4009 4250 7.180322 TGGTACATGTGCAATTTGGAATTAT 57.820 32.000 16.11 0.00 0.00 1.28
4066 4307 1.761784 GTGCATCTCAGAGGAGGATGT 59.238 52.381 0.00 0.00 41.69 3.06
4159 4400 5.885230 TTGTCTGTGGAATGATAAGCTTG 57.115 39.130 9.86 0.00 0.00 4.01
4161 4402 5.559770 TGTCTGTGGAATGATAAGCTTGAA 58.440 37.500 9.86 0.00 0.00 2.69
4578 4857 6.599244 CAGCATAACAGGTCTGGAATTCTTAA 59.401 38.462 5.23 0.00 34.19 1.85
4644 4923 1.143684 ACCTGACTGTTTGGCTCATGT 59.856 47.619 0.00 0.00 0.00 3.21
4790 5069 7.699566 ACGCACTCAGTTTTATTTTGTTAGAA 58.300 30.769 0.00 0.00 0.00 2.10
4869 5148 7.975616 GCTTGCTAACATCCTTTTATCATTTCA 59.024 33.333 0.00 0.00 0.00 2.69
4906 5185 2.073816 CACTACGGTTGTGTTCCCATC 58.926 52.381 13.45 0.00 0.00 3.51
5044 5323 7.415765 CCAATTAAGTGATTGCCGTATTGGTTA 60.416 37.037 4.10 0.00 41.21 2.85
5149 5428 2.274645 CCAGGCAACCATTTCCGCA 61.275 57.895 0.00 0.00 37.17 5.69
5242 5521 7.397476 TCGAAGAAGTATCTTGGCCAGATATAT 59.603 37.037 20.73 15.06 45.91 0.86
5367 5653 7.662897 ACTTGTATTTTCCTAAAATTTCCGCA 58.337 30.769 3.19 0.00 41.16 5.69
5427 5713 1.864176 GCATGCTGCAAAAACAGGC 59.136 52.632 11.37 0.00 44.26 4.85
5715 6001 4.554036 GCGTGGATCCTGGGCCTC 62.554 72.222 14.23 0.00 0.00 4.70
5865 6151 1.005037 CTGCGTCAAGTACCTGCCA 60.005 57.895 0.00 0.00 0.00 4.92
5880 6166 1.227823 GCCAGTGTACACAGTGCCA 60.228 57.895 27.06 0.00 43.97 4.92
6081 6367 1.765314 GATGAGTACAGTGCCCTGGAT 59.235 52.381 0.05 0.00 43.36 3.41
6111 6397 4.560856 ATCGACGAGGCGAGCAGC 62.561 66.667 7.26 0.00 44.26 5.25
6141 6427 3.917760 GCCGCCGACCTCAGCTAT 61.918 66.667 0.00 0.00 0.00 2.97
6477 6763 8.807948 ATGTGTAGCTAAAGTGGATGTAAATT 57.192 30.769 0.00 0.00 0.00 1.82
6621 6910 8.096414 AGTAATAAAATGGCAAATTTCAGTGCT 58.904 29.630 5.08 0.38 40.70 4.40
6734 7023 6.987404 TGCACCAAGGTTTAGGTTTAAAATTC 59.013 34.615 0.00 0.00 35.52 2.17
6735 7024 6.425721 GCACCAAGGTTTAGGTTTAAAATTCC 59.574 38.462 0.00 0.00 35.52 3.01
6736 7025 6.932400 CACCAAGGTTTAGGTTTAAAATTCCC 59.068 38.462 0.00 0.00 35.52 3.97
6737 7026 6.616137 ACCAAGGTTTAGGTTTAAAATTCCCA 59.384 34.615 0.00 0.00 33.39 4.37
6738 7027 7.127493 ACCAAGGTTTAGGTTTAAAATTCCCAA 59.873 33.333 0.00 0.00 33.39 4.12
6739 7028 7.993758 CCAAGGTTTAGGTTTAAAATTCCCAAA 59.006 33.333 0.00 0.00 30.92 3.28
6740 7029 9.567776 CAAGGTTTAGGTTTAAAATTCCCAAAT 57.432 29.630 0.00 0.00 30.92 2.32
6741 7030 9.567776 AAGGTTTAGGTTTAAAATTCCCAAATG 57.432 29.630 0.00 0.00 30.92 2.32
6742 7031 8.939932 AGGTTTAGGTTTAAAATTCCCAAATGA 58.060 29.630 0.00 0.00 30.92 2.57
6743 7032 9.733556 GGTTTAGGTTTAAAATTCCCAAATGAT 57.266 29.630 0.00 0.00 30.92 2.45
6748 7037 9.394767 AGGTTTAAAATTCCCAAATGATAATGC 57.605 29.630 0.00 0.00 0.00 3.56
6749 7038 8.620416 GGTTTAAAATTCCCAAATGATAATGCC 58.380 33.333 0.00 0.00 0.00 4.40
6750 7039 8.620416 GTTTAAAATTCCCAAATGATAATGCCC 58.380 33.333 0.00 0.00 0.00 5.36
6751 7040 5.972327 AAATTCCCAAATGATAATGCCCA 57.028 34.783 0.00 0.00 0.00 5.36
6752 7041 4.961438 ATTCCCAAATGATAATGCCCAC 57.039 40.909 0.00 0.00 0.00 4.61
6753 7042 3.395054 TCCCAAATGATAATGCCCACA 57.605 42.857 0.00 0.00 0.00 4.17
6754 7043 3.030291 TCCCAAATGATAATGCCCACAC 58.970 45.455 0.00 0.00 0.00 3.82
6755 7044 2.223782 CCCAAATGATAATGCCCACACG 60.224 50.000 0.00 0.00 0.00 4.49
6756 7045 2.426738 CCAAATGATAATGCCCACACGT 59.573 45.455 0.00 0.00 0.00 4.49
6757 7046 3.437428 CAAATGATAATGCCCACACGTG 58.563 45.455 15.48 15.48 0.00 4.49
6758 7047 1.024271 ATGATAATGCCCACACGTGC 58.976 50.000 17.22 1.22 0.00 5.34
6759 7048 0.322008 TGATAATGCCCACACGTGCA 60.322 50.000 17.22 8.30 42.52 4.57
6761 7050 0.740149 ATAATGCCCACACGTGCATG 59.260 50.000 17.22 7.38 46.97 4.06
6762 7051 1.311651 TAATGCCCACACGTGCATGG 61.312 55.000 17.22 16.70 46.97 3.66
6767 7056 3.293714 CACACGTGCATGGCCCAA 61.294 61.111 17.22 0.00 0.00 4.12
6768 7057 2.520500 ACACGTGCATGGCCCAAA 60.521 55.556 17.22 0.00 0.00 3.28
6769 7058 2.049248 CACGTGCATGGCCCAAAC 60.049 61.111 11.36 0.00 0.00 2.93
6770 7059 3.669344 ACGTGCATGGCCCAAACG 61.669 61.111 11.36 13.45 40.00 3.60
6778 7067 2.679996 GGCCCAAACGCCTCCATT 60.680 61.111 0.00 0.00 46.10 3.16
6779 7068 1.379309 GGCCCAAACGCCTCCATTA 60.379 57.895 0.00 0.00 46.10 1.90
6780 7069 0.755327 GGCCCAAACGCCTCCATTAT 60.755 55.000 0.00 0.00 46.10 1.28
6781 7070 1.111277 GCCCAAACGCCTCCATTATT 58.889 50.000 0.00 0.00 0.00 1.40
6782 7071 2.303175 GCCCAAACGCCTCCATTATTA 58.697 47.619 0.00 0.00 0.00 0.98
6783 7072 2.890945 GCCCAAACGCCTCCATTATTAT 59.109 45.455 0.00 0.00 0.00 1.28
6784 7073 3.320826 GCCCAAACGCCTCCATTATTATT 59.679 43.478 0.00 0.00 0.00 1.40
6785 7074 4.558697 GCCCAAACGCCTCCATTATTATTC 60.559 45.833 0.00 0.00 0.00 1.75
6786 7075 4.582656 CCCAAACGCCTCCATTATTATTCA 59.417 41.667 0.00 0.00 0.00 2.57
6787 7076 5.243730 CCCAAACGCCTCCATTATTATTCAT 59.756 40.000 0.00 0.00 0.00 2.57
6788 7077 6.239289 CCCAAACGCCTCCATTATTATTCATT 60.239 38.462 0.00 0.00 0.00 2.57
6789 7078 7.209475 CCAAACGCCTCCATTATTATTCATTT 58.791 34.615 0.00 0.00 0.00 2.32
6790 7079 7.710475 CCAAACGCCTCCATTATTATTCATTTT 59.290 33.333 0.00 0.00 0.00 1.82
6791 7080 8.542132 CAAACGCCTCCATTATTATTCATTTTG 58.458 33.333 0.00 0.00 0.00 2.44
6792 7081 6.215845 ACGCCTCCATTATTATTCATTTTGC 58.784 36.000 0.00 0.00 0.00 3.68
6793 7082 5.634859 CGCCTCCATTATTATTCATTTTGCC 59.365 40.000 0.00 0.00 0.00 4.52
6794 7083 6.523840 GCCTCCATTATTATTCATTTTGCCA 58.476 36.000 0.00 0.00 0.00 4.92
6795 7084 7.163441 GCCTCCATTATTATTCATTTTGCCAT 58.837 34.615 0.00 0.00 0.00 4.40
6796 7085 7.118680 GCCTCCATTATTATTCATTTTGCCATG 59.881 37.037 0.00 0.00 0.00 3.66
6797 7086 8.152246 CCTCCATTATTATTCATTTTGCCATGT 58.848 33.333 0.00 0.00 0.00 3.21
6798 7087 9.199982 CTCCATTATTATTCATTTTGCCATGTC 57.800 33.333 0.00 0.00 0.00 3.06
6888 7178 8.584157 AGATAGACCTGATAGTTAGCTTTCATG 58.416 37.037 0.00 1.40 33.42 3.07
6941 7231 6.683537 TCCTCTCCAAGATTGTAATCTCCTA 58.316 40.000 7.52 0.00 44.67 2.94
7039 7341 1.826720 AGGGTAAGACGTTTCCGCATA 59.173 47.619 0.00 0.00 37.70 3.14
7089 7395 0.676736 CCCATCTAGCTTCTCCCGAC 59.323 60.000 0.00 0.00 0.00 4.79
7218 7524 2.029288 CAGATCACGCCGCAGTTGT 61.029 57.895 0.00 0.00 0.00 3.32
7245 7551 3.592059 GCCGGTGTCTTCAACTATGTTA 58.408 45.455 1.90 0.00 0.00 2.41
7384 7690 3.181456 GGATATCTGCTGAGCAACCTCTT 60.181 47.826 9.07 0.00 38.41 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.147732 TGGGGTTTTTAAATTTGGCATATTTTT 57.852 25.926 18.68 5.68 0.00 1.94
40 41 8.712228 TGGGGTTTTTAAATTTGGCATATTTT 57.288 26.923 18.68 7.85 0.00 1.82
41 42 8.891985 ATGGGGTTTTTAAATTTGGCATATTT 57.108 26.923 17.80 17.80 0.00 1.40
42 43 8.891985 AATGGGGTTTTTAAATTTGGCATATT 57.108 26.923 0.00 0.00 0.00 1.28
43 44 8.891985 AAATGGGGTTTTTAAATTTGGCATAT 57.108 26.923 0.00 0.00 0.00 1.78
44 45 9.981460 ATAAATGGGGTTTTTAAATTTGGCATA 57.019 25.926 0.00 0.00 0.00 3.14
45 46 8.891985 ATAAATGGGGTTTTTAAATTTGGCAT 57.108 26.923 0.00 0.00 0.00 4.40
46 47 9.981460 ATATAAATGGGGTTTTTAAATTTGGCA 57.019 25.926 0.00 0.00 0.00 4.92
60 61 8.686334 GCGATTCATGATTAATATAAATGGGGT 58.314 33.333 0.00 0.00 0.00 4.95
71 72 4.261741 GGGCAGTTGCGATTCATGATTAAT 60.262 41.667 0.00 0.00 43.26 1.40
78 79 2.418368 TTAGGGCAGTTGCGATTCAT 57.582 45.000 0.00 0.00 43.26 2.57
83 84 2.032634 CGCTTTAGGGCAGTTGCGA 61.033 57.895 0.00 0.00 45.15 5.10
85 86 2.877691 CCGCTTTAGGGCAGTTGC 59.122 61.111 0.00 0.00 41.14 4.17
114 124 5.824904 CCAAACTAGAATGTCTGGATTGG 57.175 43.478 13.59 13.59 45.84 3.16
122 132 2.092323 GGCCCACCAAACTAGAATGTC 58.908 52.381 0.00 0.00 35.26 3.06
194 205 1.141254 TGCCCACGAAGTAAAACAGGA 59.859 47.619 0.00 0.00 41.61 3.86
202 214 2.811431 CAAAAGACATGCCCACGAAGTA 59.189 45.455 0.00 0.00 41.61 2.24
204 216 1.666888 GCAAAAGACATGCCCACGAAG 60.667 52.381 0.00 0.00 37.85 3.79
205 217 0.313672 GCAAAAGACATGCCCACGAA 59.686 50.000 0.00 0.00 37.85 3.85
223 235 1.663135 GCATGTCTCTTCTTTCCTCGC 59.337 52.381 0.00 0.00 0.00 5.03
225 237 2.677337 GCAGCATGTCTCTTCTTTCCTC 59.323 50.000 0.00 0.00 39.31 3.71
315 333 7.093509 ACAGGAACCTAATGACAACTTGTTTTT 60.094 33.333 0.00 0.00 0.00 1.94
320 338 5.299279 ACAACAGGAACCTAATGACAACTTG 59.701 40.000 10.58 0.00 0.00 3.16
356 374 6.508030 AACCTAATCAAAATTGTTTGGGGT 57.492 33.333 18.01 12.02 43.70 4.95
357 375 7.223584 AGAAACCTAATCAAAATTGTTTGGGG 58.776 34.615 18.01 12.83 43.70 4.96
360 378 8.905702 CGAGAGAAACCTAATCAAAATTGTTTG 58.094 33.333 0.00 0.00 44.71 2.93
389 408 0.991146 TCATGCCACCACATACCACT 59.009 50.000 0.00 0.00 0.00 4.00
444 463 9.599322 GTTAGCATCGTGATCCAAATAATTAAG 57.401 33.333 0.00 0.00 0.00 1.85
468 487 1.450312 GCTAGCGGACATGGCTGTT 60.450 57.895 9.70 5.42 41.69 3.16
510 529 3.978855 TCGTCATGTAAGACAAGACAACG 59.021 43.478 13.51 3.04 44.41 4.10
530 549 2.662637 TGGTACGTTATTCGCTTGTTCG 59.337 45.455 0.00 0.00 44.19 3.95
566 585 2.030805 GTGATGATGCTATTTTCCCCGC 60.031 50.000 0.00 0.00 0.00 6.13
592 615 9.378551 CTTGTGTATGGCTACTTAGATTGTTAA 57.621 33.333 0.00 0.00 0.00 2.01
627 650 7.498570 ACGGTTTACCTCGGCATATTTTAATAA 59.501 33.333 0.00 0.00 0.00 1.40
628 651 6.991531 ACGGTTTACCTCGGCATATTTTAATA 59.008 34.615 0.00 0.00 0.00 0.98
633 657 3.200483 GACGGTTTACCTCGGCATATTT 58.800 45.455 0.00 0.00 34.05 1.40
635 659 1.758280 TGACGGTTTACCTCGGCATAT 59.242 47.619 0.00 0.00 39.71 1.78
656 680 2.349590 CAAGTGAGTCATTGCGGATGA 58.650 47.619 0.00 0.00 42.42 2.92
671 697 1.795286 GAGAAGTTGTCTCGGCAAGTG 59.205 52.381 0.00 0.00 43.46 3.16
694 720 5.539955 AGTGAGCATGGGAGTTTTGTTATTT 59.460 36.000 0.00 0.00 0.00 1.40
695 721 5.079643 AGTGAGCATGGGAGTTTTGTTATT 58.920 37.500 0.00 0.00 0.00 1.40
711 737 1.616374 TGTCATCGGTGTTAGTGAGCA 59.384 47.619 0.00 0.00 0.00 4.26
712 738 1.993370 GTGTCATCGGTGTTAGTGAGC 59.007 52.381 0.00 0.00 0.00 4.26
732 758 2.679355 TTCTTTTTGTGCGATGTCGG 57.321 45.000 4.44 0.00 40.23 4.79
806 833 1.194322 TCATGCACAATGTCAACGTCG 59.806 47.619 0.00 0.00 37.56 5.12
863 891 7.056783 GCGCTGTCGTTTTATTTTTCATTTTTC 59.943 33.333 0.00 0.00 38.14 2.29
870 898 4.939948 TTGCGCTGTCGTTTTATTTTTC 57.060 36.364 9.73 0.00 38.14 2.29
876 904 4.469625 TTGTTATTGCGCTGTCGTTTTA 57.530 36.364 9.73 0.00 38.14 1.52
880 908 4.647964 CTTATTTGTTATTGCGCTGTCGT 58.352 39.130 9.73 0.00 38.14 4.34
881 909 3.478516 GCTTATTTGTTATTGCGCTGTCG 59.521 43.478 9.73 0.00 39.07 4.35
941 969 4.838152 CGCTACACGGCATGCCCT 62.838 66.667 30.79 17.25 38.44 5.19
942 970 4.830765 TCGCTACACGGCATGCCC 62.831 66.667 30.79 14.48 43.89 5.36
953 981 6.124088 AGATGATTTGGAAATTGTCGCTAC 57.876 37.500 0.00 0.00 0.00 3.58
1037 1065 6.283694 GGAGAAAAGTTGGAATTTTGCTTCT 58.716 36.000 0.00 0.00 30.22 2.85
1099 1128 4.821589 GAGGAGCTCGGCCGGTTG 62.822 72.222 27.83 16.86 0.00 3.77
1167 1214 1.374252 ACCTCGTCAACCATGCGTC 60.374 57.895 0.00 0.00 0.00 5.19
1299 1346 0.100861 GGGCGAAGACTAGAGGTTCG 59.899 60.000 16.37 16.37 44.63 3.95
1329 1377 2.635427 TGCAGGTACATACACACAGGAA 59.365 45.455 0.00 0.00 0.00 3.36
1336 1384 4.437390 GCACAAGATTGCAGGTACATACAC 60.437 45.833 0.00 0.00 42.49 2.90
1343 1399 0.676466 CGGGCACAAGATTGCAGGTA 60.676 55.000 0.00 0.00 44.94 3.08
1345 1401 2.703798 CCGGGCACAAGATTGCAGG 61.704 63.158 0.00 0.00 44.94 4.85
1349 1405 1.462616 TGAATCCGGGCACAAGATTG 58.537 50.000 0.00 0.00 32.88 2.67
1351 1407 2.214376 TTTGAATCCGGGCACAAGAT 57.786 45.000 0.00 0.00 0.00 2.40
1360 1416 1.672881 GTGCTCCAGATTTGAATCCGG 59.327 52.381 0.00 0.00 36.04 5.14
1378 1434 6.505044 TCCAGATGTTCAATCAAATCAGTG 57.495 37.500 0.00 0.00 0.00 3.66
1403 1459 6.934083 AGAAACAGTCAAAAACAACCACAAAT 59.066 30.769 0.00 0.00 0.00 2.32
1413 1469 4.336713 AGAGGCTCAGAAACAGTCAAAAAC 59.663 41.667 18.26 0.00 0.00 2.43
1414 1470 4.526970 AGAGGCTCAGAAACAGTCAAAAA 58.473 39.130 18.26 0.00 0.00 1.94
1415 1471 4.156455 AGAGGCTCAGAAACAGTCAAAA 57.844 40.909 18.26 0.00 0.00 2.44
1443 1499 9.269695 GATTACGAATCTAAACGAGAACGCGTT 62.270 40.741 26.97 26.97 43.76 4.84
1444 1500 7.899085 GATTACGAATCTAAACGAGAACGCGT 61.899 42.308 5.58 5.58 39.81 6.01
1445 1501 1.909532 ACGAATCTAAACGAGAACGCG 59.090 47.619 3.53 3.53 43.96 6.01
1446 1502 5.228635 TGATTACGAATCTAAACGAGAACGC 59.771 40.000 0.00 0.00 39.81 4.84
1447 1503 6.785633 TGATTACGAATCTAAACGAGAACG 57.214 37.500 0.00 0.00 41.03 3.95
1475 1537 2.341846 ACCCAACGACAACACATCTT 57.658 45.000 0.00 0.00 0.00 2.40
1480 1542 1.088306 TGACAACCCAACGACAACAC 58.912 50.000 0.00 0.00 0.00 3.32
1491 1553 2.076863 GCACAGAGTACATGACAACCC 58.923 52.381 0.00 0.00 0.00 4.11
1540 1602 8.598916 TGTATTTGTCTTTCCCTCTTACATACA 58.401 33.333 0.00 0.00 0.00 2.29
1541 1603 9.099454 CTGTATTTGTCTTTCCCTCTTACATAC 57.901 37.037 0.00 0.00 0.00 2.39
1542 1604 8.822805 ACTGTATTTGTCTTTCCCTCTTACATA 58.177 33.333 0.00 0.00 0.00 2.29
1543 1605 7.690256 ACTGTATTTGTCTTTCCCTCTTACAT 58.310 34.615 0.00 0.00 0.00 2.29
1567 1629 3.991121 GTCAAGAACCAGCTCAGTCTAAC 59.009 47.826 0.00 0.00 0.00 2.34
1578 1640 4.320788 GGCATCAAGAAAGTCAAGAACCAG 60.321 45.833 0.00 0.00 0.00 4.00
1580 1642 3.823304 AGGCATCAAGAAAGTCAAGAACC 59.177 43.478 0.00 0.00 0.00 3.62
1590 1652 2.694628 ACAAACTGCAGGCATCAAGAAA 59.305 40.909 19.93 0.00 0.00 2.52
1798 1860 9.525826 AGATTCAGATACAGAAACTGGAAAATT 57.474 29.630 0.00 0.00 35.51 1.82
1803 1865 7.268586 GCTAAGATTCAGATACAGAAACTGGA 58.731 38.462 0.00 0.00 35.51 3.86
1804 1866 6.481644 GGCTAAGATTCAGATACAGAAACTGG 59.518 42.308 0.00 0.00 35.51 4.00
1861 1929 9.293404 CACATTAGATGATCCATGACCTTTATT 57.707 33.333 8.71 0.00 0.00 1.40
1876 1944 6.484977 TGTTGTTAACACAGCACATTAGATGA 59.515 34.615 8.07 0.00 39.05 2.92
1879 1947 6.293900 CCATGTTGTTAACACAGCACATTAGA 60.294 38.462 17.14 0.00 45.78 2.10
1937 2007 2.989166 GCACTGCTAAAAAGAATGTGCC 59.011 45.455 0.00 0.00 42.09 5.01
2019 2116 5.531634 CATACTGTGGCTGTTCATTTTTGT 58.468 37.500 0.00 0.00 0.00 2.83
2020 2117 4.386652 GCATACTGTGGCTGTTCATTTTTG 59.613 41.667 0.00 0.00 0.00 2.44
2057 2157 1.074566 AGAGGGAGAAACAGGGCAAAG 59.925 52.381 0.00 0.00 0.00 2.77
2463 2571 4.287067 AGCTGTTGACCAGAATTTCCTCTA 59.713 41.667 0.00 0.00 44.49 2.43
2482 2590 2.715046 TGCATGGACTTTAGGAAGCTG 58.285 47.619 0.00 0.00 36.29 4.24
2507 2615 8.691661 ACCAATAAAAGCCCTATATAACTGTG 57.308 34.615 0.00 0.00 0.00 3.66
2516 2624 2.751816 GCCGGACCAATAAAAGCCCTAT 60.752 50.000 5.05 0.00 0.00 2.57
2533 2641 8.410141 TGTTAAAAATCTCTTTATATTGGCCGG 58.590 33.333 0.00 0.00 0.00 6.13
2584 2710 7.189087 ACTTGTTTTTACATGGGGAGGATAAT 58.811 34.615 0.00 0.00 0.00 1.28
2670 2796 4.783763 AGAAGGGGGTTTAGACTTTAGAGG 59.216 45.833 0.00 0.00 0.00 3.69
2677 2803 2.046280 AGCAGAAGGGGGTTTAGACT 57.954 50.000 0.00 0.00 0.00 3.24
2678 2804 3.263681 ACTTAGCAGAAGGGGGTTTAGAC 59.736 47.826 3.72 0.00 0.00 2.59
2680 2806 4.010349 CAACTTAGCAGAAGGGGGTTTAG 58.990 47.826 3.72 0.00 0.00 1.85
2681 2807 3.812882 GCAACTTAGCAGAAGGGGGTTTA 60.813 47.826 3.72 0.00 0.00 2.01
2683 2809 1.547901 GCAACTTAGCAGAAGGGGGTT 60.548 52.381 3.72 0.00 0.00 4.11
2684 2810 0.038310 GCAACTTAGCAGAAGGGGGT 59.962 55.000 3.72 0.00 0.00 4.95
2686 2812 0.038166 TGGCAACTTAGCAGAAGGGG 59.962 55.000 3.72 0.00 35.83 4.79
2709 2837 2.294233 GAGGCATCTGCACAGACAAAAA 59.706 45.455 1.71 0.00 44.36 1.94
2724 2852 1.656587 TGTGTCCCTACTTGAGGCAT 58.343 50.000 0.00 0.00 45.17 4.40
2746 2874 9.237187 TGACTTATTGTCTATGGCACATTAAAA 57.763 29.630 0.00 0.00 44.87 1.52
2751 2879 5.744171 TGTGACTTATTGTCTATGGCACAT 58.256 37.500 0.00 0.00 44.87 3.21
2812 2940 3.515602 AGCATCCCTATTTTAGGCAGG 57.484 47.619 0.00 0.00 44.86 4.85
2856 2984 0.178992 TGCAGAGAAACACAAGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
2971 3099 4.188247 TGTTAGGTCTTCATCGGTCTTG 57.812 45.455 0.00 0.00 0.00 3.02
2974 3102 3.921677 TGTTGTTAGGTCTTCATCGGTC 58.078 45.455 0.00 0.00 0.00 4.79
3203 3331 6.143915 AGCTCCCTGTTCTCCTAACAATATA 58.856 40.000 0.00 0.00 0.00 0.86
3248 3376 9.965902 ATAATATGATTCTTAGTAGGCCAAAGG 57.034 33.333 5.01 0.00 0.00 3.11
3275 3403 8.573035 TGTCAAATATTTCTGGTTTCTGGTAAC 58.427 33.333 0.00 0.00 0.00 2.50
3322 3450 7.493320 ACCAATTGCTGTAATATGCTTCAAATG 59.507 33.333 0.00 0.00 0.00 2.32
3356 3484 5.066375 AGTTTATGCAATTGCTTCGCATCTA 59.934 36.000 29.37 7.84 44.89 1.98
3425 3561 2.039613 AGCAAGCCCTAGAGCCATTATC 59.960 50.000 0.00 0.00 0.00 1.75
3486 3623 3.717294 TCCTTTCCGCCCCTGAGC 61.717 66.667 0.00 0.00 0.00 4.26
3606 3743 9.753674 ATTGGGATCAAGTAAGTTATGAAAGAA 57.246 29.630 0.00 0.00 36.19 2.52
3669 3806 5.888161 CAGGTTTATCATTCCCTAGCTTGTT 59.112 40.000 0.00 0.00 0.00 2.83
3741 3884 3.969312 TGGTAATCTCAGATGCTCCATCA 59.031 43.478 7.83 0.00 42.72 3.07
3776 4011 5.007234 CACTCGTCTGTTGTGGACAAAAATA 59.993 40.000 0.00 0.00 37.93 1.40
3818 4058 9.686683 AAGGTATGTAGAACAGCTAAAATTGAT 57.313 29.630 0.00 0.00 0.00 2.57
3841 4081 6.680810 TGAATTACAAGCATCACAAAGAAGG 58.319 36.000 0.00 0.00 0.00 3.46
3875 4116 6.572167 TGGGTTATTGGGTAAAACTTAACG 57.428 37.500 0.00 0.00 0.00 3.18
3964 4205 4.267536 CATTTCTCATTCTGGGCTCTTCA 58.732 43.478 0.00 0.00 0.00 3.02
3980 4221 5.245751 TCCAAATTGCACATGTACCATTTCT 59.754 36.000 0.00 0.00 0.00 2.52
4041 4282 0.179702 TCCTCTGAGATGCACATGGC 59.820 55.000 6.17 0.00 45.13 4.40
4125 4366 6.817765 TTCCACAGACAAAAGAATATGGTC 57.182 37.500 0.00 0.00 0.00 4.02
4159 4400 6.151691 TGCTTCAAATCACAGTTAGCATTTC 58.848 36.000 0.00 0.00 32.73 2.17
4161 4402 5.710513 TGCTTCAAATCACAGTTAGCATT 57.289 34.783 0.00 0.00 32.73 3.56
4236 4510 6.593807 ACCCGGTATTATTTGTATAACAGCA 58.406 36.000 0.00 0.00 0.00 4.41
4237 4511 7.500720 AACCCGGTATTATTTGTATAACAGC 57.499 36.000 0.00 0.00 0.00 4.40
4238 4512 9.985730 TCTAACCCGGTATTATTTGTATAACAG 57.014 33.333 0.00 0.00 0.00 3.16
4578 4857 5.594317 GGACAAGCCACCATATGAAATAAGT 59.406 40.000 3.65 0.00 36.34 2.24
4644 4923 2.260844 CAGTGCTTCTGTCCCTGAAA 57.739 50.000 2.20 0.00 39.17 2.69
4766 5045 7.855904 ACTTCTAACAAAATAAAACTGAGTGCG 59.144 33.333 0.00 0.00 0.00 5.34
4906 5185 7.615582 TGACCAGTATATTGCAAAAGAAGAG 57.384 36.000 1.71 0.00 0.00 2.85
5020 5299 6.524101 AACCAATACGGCAATCACTTAATT 57.476 33.333 0.00 0.00 39.03 1.40
5149 5428 5.445939 CGCTTGCTTGATAATTGAGTACGTT 60.446 40.000 0.00 0.00 0.00 3.99
5194 5473 5.185828 CGATGTATGGATGATCTTCACCCTA 59.814 44.000 10.48 0.00 28.81 3.53
5242 5521 8.972662 TGAGGATCCAATTAATATCAGGACTA 57.027 34.615 15.82 0.00 0.00 2.59
5367 5653 1.002468 GCAGAAACACACATCGCAACT 60.002 47.619 0.00 0.00 0.00 3.16
5427 5713 3.242969 GCATGACCATTATCACAGCTGTG 60.243 47.826 36.07 36.07 46.91 3.66
5865 6151 0.106708 CCAGTGGCACTGTGTACACT 59.893 55.000 37.43 24.46 44.50 3.55
5880 6166 2.600769 AGGAACCGCTCGTCCAGT 60.601 61.111 2.51 0.00 0.00 4.00
5952 6238 1.278985 CTGTGGATGTCCTTGTAGCCA 59.721 52.381 0.09 0.00 36.82 4.75
6253 6539 0.597637 CTGCACGAGTTCAGGAACGT 60.598 55.000 6.52 0.00 45.50 3.99
6734 7023 2.223782 CGTGTGGGCATTATCATTTGGG 60.224 50.000 0.00 0.00 0.00 4.12
6735 7024 2.426738 ACGTGTGGGCATTATCATTTGG 59.573 45.455 0.00 0.00 0.00 3.28
6736 7025 3.437428 CACGTGTGGGCATTATCATTTG 58.563 45.455 7.58 0.00 0.00 2.32
6737 7026 2.159254 GCACGTGTGGGCATTATCATTT 60.159 45.455 18.38 0.00 0.00 2.32
6738 7027 1.405105 GCACGTGTGGGCATTATCATT 59.595 47.619 18.38 0.00 0.00 2.57
6739 7028 1.024271 GCACGTGTGGGCATTATCAT 58.976 50.000 18.38 0.00 0.00 2.45
6740 7029 0.322008 TGCACGTGTGGGCATTATCA 60.322 50.000 18.38 0.00 34.58 2.15
6741 7030 2.476772 TGCACGTGTGGGCATTATC 58.523 52.632 18.38 0.00 34.58 1.75
6742 7031 4.732568 TGCACGTGTGGGCATTAT 57.267 50.000 18.38 0.00 34.58 1.28
6750 7039 2.854401 TTTGGGCCATGCACGTGTG 61.854 57.895 18.38 8.35 32.76 3.82
6751 7040 2.520500 TTTGGGCCATGCACGTGT 60.521 55.556 18.38 0.00 32.76 4.49
6752 7041 2.049248 GTTTGGGCCATGCACGTG 60.049 61.111 12.28 12.28 32.76 4.49
6753 7042 3.669344 CGTTTGGGCCATGCACGT 61.669 61.111 19.79 0.00 32.76 4.49
6762 7051 1.111277 AATAATGGAGGCGTTTGGGC 58.889 50.000 0.00 0.00 42.69 5.36
6763 7052 4.582656 TGAATAATAATGGAGGCGTTTGGG 59.417 41.667 0.00 0.00 0.00 4.12
6764 7053 5.766150 TGAATAATAATGGAGGCGTTTGG 57.234 39.130 0.00 0.00 0.00 3.28
6765 7054 8.542132 CAAAATGAATAATAATGGAGGCGTTTG 58.458 33.333 0.00 0.00 0.00 2.93
6766 7055 7.224557 GCAAAATGAATAATAATGGAGGCGTTT 59.775 33.333 0.00 0.00 0.00 3.60
6767 7056 6.701400 GCAAAATGAATAATAATGGAGGCGTT 59.299 34.615 0.00 0.00 0.00 4.84
6768 7057 6.215845 GCAAAATGAATAATAATGGAGGCGT 58.784 36.000 0.00 0.00 0.00 5.68
6769 7058 5.634859 GGCAAAATGAATAATAATGGAGGCG 59.365 40.000 0.00 0.00 0.00 5.52
6770 7059 6.523840 TGGCAAAATGAATAATAATGGAGGC 58.476 36.000 0.00 0.00 0.00 4.70
6771 7060 8.152246 ACATGGCAAAATGAATAATAATGGAGG 58.848 33.333 0.00 0.00 0.00 4.30
6772 7061 9.199982 GACATGGCAAAATGAATAATAATGGAG 57.800 33.333 0.00 0.00 0.00 3.86
6773 7062 8.702819 TGACATGGCAAAATGAATAATAATGGA 58.297 29.630 0.00 0.00 0.00 3.41
6774 7063 8.890124 TGACATGGCAAAATGAATAATAATGG 57.110 30.769 0.00 0.00 0.00 3.16
6777 7066 9.585099 GTCTTGACATGGCAAAATGAATAATAA 57.415 29.630 16.38 0.00 0.00 1.40
6778 7067 8.970020 AGTCTTGACATGGCAAAATGAATAATA 58.030 29.630 16.38 0.00 0.00 0.98
6779 7068 7.762615 CAGTCTTGACATGGCAAAATGAATAAT 59.237 33.333 16.38 0.00 0.00 1.28
6780 7069 7.092079 CAGTCTTGACATGGCAAAATGAATAA 58.908 34.615 16.38 0.00 0.00 1.40
6781 7070 6.209192 ACAGTCTTGACATGGCAAAATGAATA 59.791 34.615 22.12 0.00 0.00 1.75
6782 7071 5.011329 ACAGTCTTGACATGGCAAAATGAAT 59.989 36.000 22.12 11.89 0.00 2.57
6783 7072 4.341806 ACAGTCTTGACATGGCAAAATGAA 59.658 37.500 22.12 0.34 0.00 2.57
6784 7073 3.890756 ACAGTCTTGACATGGCAAAATGA 59.109 39.130 22.12 12.55 0.00 2.57
6785 7074 4.247267 ACAGTCTTGACATGGCAAAATG 57.753 40.909 16.38 16.69 0.00 2.32
6786 7075 4.942761 AACAGTCTTGACATGGCAAAAT 57.057 36.364 16.38 3.09 0.00 1.82
6787 7076 5.843673 TTAACAGTCTTGACATGGCAAAA 57.156 34.783 16.38 0.00 0.00 2.44
6788 7077 5.126222 TGTTTAACAGTCTTGACATGGCAAA 59.874 36.000 16.38 3.74 0.00 3.68
6789 7078 4.642437 TGTTTAACAGTCTTGACATGGCAA 59.358 37.500 14.66 14.66 0.00 4.52
6790 7079 4.203226 TGTTTAACAGTCTTGACATGGCA 58.797 39.130 0.00 0.00 0.00 4.92
6791 7080 4.320494 CCTGTTTAACAGTCTTGACATGGC 60.320 45.833 21.63 0.00 44.50 4.40
6792 7081 4.821805 ACCTGTTTAACAGTCTTGACATGG 59.178 41.667 21.63 7.58 44.50 3.66
6793 7082 7.490962 TTACCTGTTTAACAGTCTTGACATG 57.509 36.000 21.63 7.36 44.50 3.21
6794 7083 8.567948 CAATTACCTGTTTAACAGTCTTGACAT 58.432 33.333 21.63 3.61 44.50 3.06
6795 7084 7.468084 GCAATTACCTGTTTAACAGTCTTGACA 60.468 37.037 21.63 1.59 44.50 3.58
6796 7085 6.856426 GCAATTACCTGTTTAACAGTCTTGAC 59.144 38.462 21.63 11.73 44.50 3.18
6797 7086 6.544197 TGCAATTACCTGTTTAACAGTCTTGA 59.456 34.615 21.63 5.23 44.50 3.02
6798 7087 6.636850 GTGCAATTACCTGTTTAACAGTCTTG 59.363 38.462 21.63 17.91 44.50 3.02
6801 7090 5.458015 GGTGCAATTACCTGTTTAACAGTC 58.542 41.667 21.63 4.74 44.50 3.51
6941 7231 7.542890 CGCATACAGAGAGGTTGAGATATTAT 58.457 38.462 0.00 0.00 0.00 1.28
7039 7341 2.358898 GGCTTTGATTACCATGTGCGAT 59.641 45.455 0.00 0.00 0.00 4.58
7089 7395 1.369625 GTGTAGGGCACGATTGGAAG 58.630 55.000 0.00 0.00 38.45 3.46
7218 7524 4.980805 GAAGACACCGGCGCCACA 62.981 66.667 28.98 0.00 0.00 4.17
7384 7690 1.666011 GTGACGAGCACCTCCTTGA 59.334 57.895 0.00 0.00 41.78 3.02


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

AutoCloner maintained by Alex Coulton.