Multiple sequence alignment - TraesCS1D01G272100

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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 TraesCS1D01G272100 chr1D 100.000 3132 0 0 892 4023 366223279 366226410 0.000000e+00 5784
1 TraesCS1D01G272100 chr1D 100.000 666 0 0 1 666 366222388 366223053 0.000000e+00 1230
2 TraesCS1D01G272100 chr1D 91.667 156 5 2 5 153 366208024 366208178 4.070000e-50 209
3 TraesCS1D01G272100 chr1B 88.193 1931 114 42 1826 3701 491265091 491263220 0.000000e+00 2198
4 TraesCS1D01G272100 chr1B 89.425 539 22 18 1097 1610 491266356 491265828 0.000000e+00 647
5 TraesCS1D01G272100 chr1B 94.902 255 6 2 3776 4023 491263118 491262864 3.770000e-105 392
6 TraesCS1D01G272100 chr1B 85.422 391 25 11 173 561 491392439 491392079 1.060000e-100 377
7 TraesCS1D01G272100 chr1B 97.059 204 5 1 1632 1835 491265701 491265499 3.850000e-90 342
8 TraesCS1D01G272100 chr1B 97.248 109 3 0 558 666 491266652 491266544 6.870000e-43 185
9 TraesCS1D01G272100 chr1A 88.924 1264 71 21 2023 3272 465523765 465522557 0.000000e+00 1495
10 TraesCS1D01G272100 chr1A 90.921 749 31 18 895 1610 465524913 465524169 0.000000e+00 972
11 TraesCS1D01G272100 chr1A 94.030 268 9 1 4 264 465529268 465529001 2.250000e-107 399
12 TraesCS1D01G272100 chr1A 91.051 257 16 4 1632 1882 465524031 465523776 1.380000e-89 340
13 TraesCS1D01G272100 chr1A 85.813 289 22 7 3340 3611 465522543 465522257 5.090000e-74 289
14 TraesCS1D01G272100 chr1A 87.045 247 14 7 264 494 465525298 465525054 3.080000e-66 263
15 TraesCS1D01G272100 chr1A 91.720 157 5 2 4 153 465531713 465531558 1.130000e-50 211
16 TraesCS1D01G272100 chr1A 87.640 178 9 4 3776 3944 465522060 465521887 1.140000e-45 195
17 TraesCS1D01G272100 chr1A 89.796 147 13 2 521 666 465525055 465524910 1.910000e-43 187
18 TraesCS1D01G272100 chr3A 84.298 484 58 14 1021 1494 628302159 628302634 1.320000e-124 457
19 TraesCS1D01G272100 chr3A 76.169 449 95 11 2575 3017 628304294 628304736 4.050000e-55 226
20 TraesCS1D01G272100 chr3B 84.091 484 59 14 1021 1494 648103071 648103546 6.130000e-123 451
21 TraesCS1D01G272100 chr3B 76.180 445 90 14 2582 3017 648105003 648105440 1.880000e-53 220
22 TraesCS1D01G272100 chr3B 85.606 132 11 7 29 153 75342332 75342202 9.070000e-27 132
23 TraesCS1D01G272100 chr3D 83.884 484 60 14 1021 1494 485357871 485358346 2.850000e-121 446
24 TraesCS1D01G272100 chr3D 76.000 450 92 13 2575 3017 485359810 485360250 6.770000e-53 219
25 TraesCS1D01G272100 chr4B 88.112 143 8 3 1 135 626909951 626909810 1.160000e-35 161
26 TraesCS1D01G272100 chr2B 87.302 126 8 3 28 145 84550107 84549982 1.950000e-28 137
27 TraesCS1D01G272100 chr5B 85.714 126 11 2 29 147 470720563 470720688 4.220000e-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 TraesCS1D01G272100 chr1D 366222388 366226410 4022 False 3507.000000 5784 100.0000 1 4023 2 chr1D.!!$F2 4022
1 TraesCS1D01G272100 chr1B 491262864 491266652 3788 True 752.800000 2198 93.3654 558 4023 5 chr1B.!!$R2 3465
2 TraesCS1D01G272100 chr1A 465521887 465531713 9826 True 483.444444 1495 89.6600 4 3944 9 chr1A.!!$R1 3940
3 TraesCS1D01G272100 chr3A 628302159 628304736 2577 False 341.500000 457 80.2335 1021 3017 2 chr3A.!!$F1 1996
4 TraesCS1D01G272100 chr3B 648103071 648105440 2369 False 335.500000 451 80.1355 1021 3017 2 chr3B.!!$F1 1996
5 TraesCS1D01G272100 chr3D 485357871 485360250 2379 False 332.500000 446 79.9420 1021 3017 2 chr3D.!!$F1 1996

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
526 6698 0.180171 CACCTCCATATCCGCACCAA 59.820 55.0 0.00 0.0 0.00 3.67 F
1538 7798 0.472044 TCAGTTAGCTGGGTGCAACA 59.528 50.0 3.06 0.0 45.94 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 8956 0.036306 CAAGGCCACCTAGACGGTTT 59.964 55.0 5.01 0.0 46.37 3.27 R
3501 11572 0.036010 CCAAGCAGTCAATCTCCGGT 60.036 55.0 0.00 0.0 0.00 5.28 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
49 50 3.549873 GCAGCGAGTAATTGAACTCTCTC 59.450 47.826 6.77 0.00 39.04 3.20
50 51 4.738124 CAGCGAGTAATTGAACTCTCTCA 58.262 43.478 6.77 0.00 39.04 3.27
64 65 5.499139 ACTCTCTCATTCTGAATCTCGAC 57.501 43.478 0.00 0.00 0.00 4.20
93 94 0.529337 CTACCTCGCCTCGTCGTCTA 60.529 60.000 0.00 0.00 0.00 2.59
104 105 3.199677 CTCGTCGTCTACTCTCCTCATT 58.800 50.000 0.00 0.00 0.00 2.57
154 2607 2.754002 TCGGTCGTCACAATGTGGTATA 59.246 45.455 13.95 0.00 33.87 1.47
170 2623 2.676342 GGTATAAGTTGCTCGTTGGTGG 59.324 50.000 0.00 0.00 0.00 4.61
273 6429 6.717084 GGAACCCTGAAGATTATAAGGATTGG 59.283 42.308 0.00 0.00 30.92 3.16
290 6446 5.243730 AGGATTGGTGAAACGAAATTGACAT 59.756 36.000 0.00 0.00 38.28 3.06
333 6489 4.491101 GGAAACCCTAGACGTCGC 57.509 61.111 10.46 0.00 0.00 5.19
383 6539 3.668656 GCCACTCAAATTCGTTTAGCAAC 59.331 43.478 0.00 0.00 0.00 4.17
389 6545 6.420604 ACTCAAATTCGTTTAGCAACAAATGG 59.579 34.615 0.00 0.00 32.54 3.16
391 6547 3.717400 TTCGTTTAGCAACAAATGGCA 57.283 38.095 0.00 0.00 32.54 4.92
409 6565 1.350193 CATCAAACCAGACCGAGTCG 58.650 55.000 5.29 5.29 37.67 4.18
410 6566 0.966920 ATCAAACCAGACCGAGTCGT 59.033 50.000 12.31 0.00 37.67 4.34
412 6568 0.249322 CAAACCAGACCGAGTCGTGT 60.249 55.000 12.31 9.04 37.67 4.49
413 6569 0.462789 AAACCAGACCGAGTCGTGTT 59.537 50.000 12.31 4.08 37.67 3.32
414 6570 0.249322 AACCAGACCGAGTCGTGTTG 60.249 55.000 12.31 6.14 37.67 3.33
415 6571 2.022129 CCAGACCGAGTCGTGTTGC 61.022 63.158 12.31 0.00 37.67 4.17
430 6602 3.605922 CGTGTTGCGAATTGTTAGCTGAA 60.606 43.478 0.00 0.00 44.77 3.02
476 6648 3.692406 GACTTCAGTCCGGGCCGT 61.692 66.667 26.32 2.75 39.07 5.68
482 6654 2.036890 AGTCCGGGCCGTACTTCT 59.963 61.111 26.32 11.95 0.00 2.85
483 6655 2.050934 AGTCCGGGCCGTACTTCTC 61.051 63.158 26.32 6.64 0.00 2.87
501 6673 3.634397 CTCCTGTGGAGGCTTGATAAA 57.366 47.619 5.75 0.00 45.43 1.40
502 6674 3.274288 CTCCTGTGGAGGCTTGATAAAC 58.726 50.000 5.75 0.00 45.43 2.01
503 6675 2.009774 CCTGTGGAGGCTTGATAAACG 58.990 52.381 0.00 0.00 30.52 3.60
504 6676 2.354704 CCTGTGGAGGCTTGATAAACGA 60.355 50.000 0.00 0.00 30.52 3.85
505 6677 3.334691 CTGTGGAGGCTTGATAAACGAA 58.665 45.455 0.00 0.00 0.00 3.85
506 6678 3.071479 TGTGGAGGCTTGATAAACGAAC 58.929 45.455 0.00 0.00 0.00 3.95
507 6679 2.418976 GTGGAGGCTTGATAAACGAACC 59.581 50.000 0.00 0.00 0.00 3.62
508 6680 2.039216 TGGAGGCTTGATAAACGAACCA 59.961 45.455 0.00 0.00 0.00 3.67
509 6681 2.418976 GGAGGCTTGATAAACGAACCAC 59.581 50.000 0.00 0.00 0.00 4.16
510 6682 2.418976 GAGGCTTGATAAACGAACCACC 59.581 50.000 0.00 0.00 0.00 4.61
511 6683 2.039879 AGGCTTGATAAACGAACCACCT 59.960 45.455 0.00 0.00 0.00 4.00
512 6684 2.418976 GGCTTGATAAACGAACCACCTC 59.581 50.000 0.00 0.00 0.00 3.85
513 6685 2.418976 GCTTGATAAACGAACCACCTCC 59.581 50.000 0.00 0.00 0.00 4.30
514 6686 3.670625 CTTGATAAACGAACCACCTCCA 58.329 45.455 0.00 0.00 0.00 3.86
515 6687 3.992943 TGATAAACGAACCACCTCCAT 57.007 42.857 0.00 0.00 0.00 3.41
516 6688 5.423704 TTGATAAACGAACCACCTCCATA 57.576 39.130 0.00 0.00 0.00 2.74
517 6689 5.623956 TGATAAACGAACCACCTCCATAT 57.376 39.130 0.00 0.00 0.00 1.78
518 6690 5.607477 TGATAAACGAACCACCTCCATATC 58.393 41.667 0.00 0.00 0.00 1.63
519 6691 3.277142 AAACGAACCACCTCCATATCC 57.723 47.619 0.00 0.00 0.00 2.59
520 6692 0.750850 ACGAACCACCTCCATATCCG 59.249 55.000 0.00 0.00 0.00 4.18
521 6693 0.600255 CGAACCACCTCCATATCCGC 60.600 60.000 0.00 0.00 0.00 5.54
522 6694 0.468226 GAACCACCTCCATATCCGCA 59.532 55.000 0.00 0.00 0.00 5.69
523 6695 0.180406 AACCACCTCCATATCCGCAC 59.820 55.000 0.00 0.00 0.00 5.34
524 6696 1.071471 CCACCTCCATATCCGCACC 59.929 63.158 0.00 0.00 0.00 5.01
525 6697 1.695114 CCACCTCCATATCCGCACCA 61.695 60.000 0.00 0.00 0.00 4.17
526 6698 0.180171 CACCTCCATATCCGCACCAA 59.820 55.000 0.00 0.00 0.00 3.67
527 6699 0.916086 ACCTCCATATCCGCACCAAA 59.084 50.000 0.00 0.00 0.00 3.28
530 6702 2.958355 CCTCCATATCCGCACCAAAAAT 59.042 45.455 0.00 0.00 0.00 1.82
534 6706 6.142818 TCCATATCCGCACCAAAAATAAAG 57.857 37.500 0.00 0.00 0.00 1.85
549 6721 7.041440 CCAAAAATAAAGGGAAAAGTTGCGAAT 60.041 33.333 0.00 0.00 0.00 3.34
551 6723 5.975693 ATAAAGGGAAAAGTTGCGAATCA 57.024 34.783 0.00 0.00 0.00 2.57
661 6834 1.394151 CTCCTTCCTCCCCTGGTCT 59.606 63.158 0.00 0.00 0.00 3.85
662 6835 0.980231 CTCCTTCCTCCCCTGGTCTG 60.980 65.000 0.00 0.00 0.00 3.51
663 6836 1.997874 CCTTCCTCCCCTGGTCTGG 60.998 68.421 0.00 0.00 0.00 3.86
664 6837 1.229658 CTTCCTCCCCTGGTCTGGT 60.230 63.158 0.00 0.00 0.00 4.00
665 6838 1.229529 TTCCTCCCCTGGTCTGGTC 60.230 63.158 0.00 0.00 0.00 4.02
1091 7266 0.753479 ATCGAGAGCCTCATCCACGT 60.753 55.000 0.00 0.00 0.00 4.49
1464 7699 2.344203 CGTCTTCCTCGGCCTCACT 61.344 63.158 0.00 0.00 0.00 3.41
1470 7705 2.477176 CCTCGGCCTCACTCTCTCG 61.477 68.421 0.00 0.00 0.00 4.04
1508 7767 7.508977 AGTCAGGAAGGTTATTTCAAATCCAAA 59.491 33.333 0.00 0.00 0.00 3.28
1509 7768 7.598869 GTCAGGAAGGTTATTTCAAATCCAAAC 59.401 37.037 0.00 0.00 0.00 2.93
1538 7798 0.472044 TCAGTTAGCTGGGTGCAACA 59.528 50.000 3.06 0.00 45.94 3.33
1556 7816 4.606961 CAACACCTGCGTTTGAAATACTT 58.393 39.130 0.00 0.00 0.00 2.24
1557 7817 4.911514 ACACCTGCGTTTGAAATACTTT 57.088 36.364 0.00 0.00 0.00 2.66
1558 7818 4.855531 ACACCTGCGTTTGAAATACTTTC 58.144 39.130 0.00 0.00 40.08 2.62
1559 7819 3.906008 CACCTGCGTTTGAAATACTTTCG 59.094 43.478 0.00 0.00 42.55 3.46
1562 7822 5.236911 ACCTGCGTTTGAAATACTTTCGTTA 59.763 36.000 0.00 0.00 42.55 3.18
1563 7823 5.788531 CCTGCGTTTGAAATACTTTCGTTAG 59.211 40.000 0.00 0.00 42.55 2.34
1565 7825 6.946165 TGCGTTTGAAATACTTTCGTTAGAA 58.054 32.000 0.00 0.00 42.55 2.10
1610 7873 7.905604 TTGAAGTATATAATTCATGAGGCCG 57.094 36.000 22.33 0.00 39.59 6.13
1611 7874 7.239763 TGAAGTATATAATTCATGAGGCCGA 57.760 36.000 18.97 0.00 35.64 5.54
1612 7875 7.851228 TGAAGTATATAATTCATGAGGCCGAT 58.149 34.615 18.97 0.00 35.64 4.18
1613 7876 8.977412 TGAAGTATATAATTCATGAGGCCGATA 58.023 33.333 18.97 0.00 35.64 2.92
1615 7878 9.601217 AAGTATATAATTCATGAGGCCGATAAC 57.399 33.333 0.00 0.00 0.00 1.89
1618 7881 1.953559 TTCATGAGGCCGATAACTGC 58.046 50.000 0.00 0.00 0.00 4.40
1620 7883 1.202568 TCATGAGGCCGATAACTGCTG 60.203 52.381 0.00 0.00 0.00 4.41
1621 7884 0.833287 ATGAGGCCGATAACTGCTGT 59.167 50.000 0.00 0.00 0.00 4.40
1622 7885 0.613260 TGAGGCCGATAACTGCTGTT 59.387 50.000 13.80 13.80 39.98 3.16
1624 7887 0.613260 AGGCCGATAACTGCTGTTGA 59.387 50.000 18.22 4.09 37.59 3.18
1625 7888 1.210478 AGGCCGATAACTGCTGTTGAT 59.790 47.619 18.22 8.29 37.59 2.57
1628 7891 3.002348 GGCCGATAACTGCTGTTGATAAC 59.998 47.826 18.22 5.82 37.59 1.89
1629 7892 3.871594 GCCGATAACTGCTGTTGATAACT 59.128 43.478 18.22 0.00 37.59 2.24
1630 7893 4.260375 GCCGATAACTGCTGTTGATAACTG 60.260 45.833 18.22 2.89 37.59 3.16
1655 8034 4.711846 TGTAGATGACCTGATAACTGCTGT 59.288 41.667 0.00 0.00 0.00 4.40
1667 8046 7.495606 CCTGATAACTGCTGTTGTATGTATTGA 59.504 37.037 18.22 0.00 37.59 2.57
1721 8100 3.430333 AACCAAAACAGTGTTAAGGCG 57.570 42.857 20.70 6.71 0.00 5.52
1744 8126 4.019501 GGGATGATTAGACATCTCCAGCAT 60.020 45.833 0.00 0.00 44.02 3.79
1908 8710 9.359653 TGTATAATTTCTACTACCCTACTGGAC 57.640 37.037 0.00 0.00 38.00 4.02
1911 8713 3.834489 TCTACTACCCTACTGGACTCG 57.166 52.381 0.00 0.00 38.00 4.18
1912 8714 2.437281 TCTACTACCCTACTGGACTCGG 59.563 54.545 0.00 0.00 38.00 4.63
1922 8724 1.081892 CTGGACTCGGACTTGCAATG 58.918 55.000 0.00 0.00 0.00 2.82
1928 8730 2.480555 GGACTTGCAATGCCGTCG 59.519 61.111 15.20 0.00 31.79 5.12
1969 8771 3.052036 GAGCTCGAGCATTCTCAAGATC 58.948 50.000 36.87 18.67 45.16 2.75
1971 8773 2.224018 GCTCGAGCATTCTCAAGATCCT 60.224 50.000 31.91 0.00 39.30 3.24
1972 8774 3.740764 GCTCGAGCATTCTCAAGATCCTT 60.741 47.826 31.91 0.00 39.30 3.36
1973 8775 4.500545 GCTCGAGCATTCTCAAGATCCTTA 60.501 45.833 31.91 0.00 39.30 2.69
1974 8776 5.595885 CTCGAGCATTCTCAAGATCCTTAA 58.404 41.667 0.00 0.00 39.30 1.85
1975 8777 5.977635 TCGAGCATTCTCAAGATCCTTAAA 58.022 37.500 0.00 0.00 39.30 1.52
1976 8778 6.406370 TCGAGCATTCTCAAGATCCTTAAAA 58.594 36.000 0.00 0.00 39.30 1.52
1977 8779 6.878923 TCGAGCATTCTCAAGATCCTTAAAAA 59.121 34.615 0.00 0.00 39.30 1.94
1978 8780 7.065085 TCGAGCATTCTCAAGATCCTTAAAAAG 59.935 37.037 0.00 0.00 39.30 2.27
2051 8853 1.880027 GTGAAATTTGGCGGAGAGTGT 59.120 47.619 0.00 0.00 0.00 3.55
2093 8895 5.898397 AGTGTATTCTTAGAAGGGGGACTAC 59.102 44.000 0.03 0.00 0.00 2.73
2094 8896 5.659971 GTGTATTCTTAGAAGGGGGACTACA 59.340 44.000 0.03 0.04 0.00 2.74
2107 8909 3.146847 GGGACTACACTTTTCCTTGTGG 58.853 50.000 0.00 0.00 38.39 4.17
2152 8954 8.138712 TGCTTATAAATATTTTAGTTTGCCCGG 58.861 33.333 5.91 0.00 0.00 5.73
2154 8956 4.810191 AAATATTTTAGTTTGCCCGGCA 57.190 36.364 8.43 8.43 36.47 5.69
2188 8990 1.683385 GCCTTGGCCATTCCACTAATC 59.317 52.381 6.09 0.00 46.55 1.75
2193 8995 4.640771 TGGCCATTCCACTAATCTATCC 57.359 45.455 0.00 0.00 40.72 2.59
2407 9209 4.614535 GCAGCAAACAGAATTCACACCTAG 60.615 45.833 8.44 0.00 0.00 3.02
2408 9210 4.516698 CAGCAAACAGAATTCACACCTAGT 59.483 41.667 8.44 0.00 0.00 2.57
2409 9211 5.700832 CAGCAAACAGAATTCACACCTAGTA 59.299 40.000 8.44 0.00 0.00 1.82
2414 9216 6.665992 ACAGAATTCACACCTAGTAGAACA 57.334 37.500 8.44 0.00 0.00 3.18
2534 10419 7.715657 TGATTGCAGTTCACTTGTTAATTCTT 58.284 30.769 0.00 0.00 0.00 2.52
2557 10442 8.861086 TCTTATTTGATCTATCACCTAGTCACC 58.139 37.037 0.00 0.00 36.36 4.02
2575 10460 6.715280 AGTCACCTACTGATTTTGATGACAT 58.285 36.000 0.00 0.00 38.11 3.06
2665 10689 0.039798 CACGCTGAATGTGCTGCTTT 60.040 50.000 0.00 0.00 0.00 3.51
2680 10704 3.572682 GCTGCTTTTGGTACTTAAACCCT 59.427 43.478 0.00 0.00 38.90 4.34
2682 10706 5.452776 GCTGCTTTTGGTACTTAAACCCTTT 60.453 40.000 0.00 0.00 38.90 3.11
2683 10707 6.547930 TGCTTTTGGTACTTAAACCCTTTT 57.452 33.333 0.00 0.00 38.90 2.27
2684 10708 6.575267 TGCTTTTGGTACTTAAACCCTTTTC 58.425 36.000 0.00 0.00 38.90 2.29
2691 10715 5.868258 GGTACTTAAACCCTTTTCTCTCTCG 59.132 44.000 0.00 0.00 33.02 4.04
2725 10749 2.304470 TGCACATGTATACACACCTGGT 59.696 45.455 7.96 0.00 37.54 4.00
2800 10834 4.160329 TCTTCCAAAGCCTGAGTCTTCTA 58.840 43.478 0.00 0.00 0.00 2.10
2911 10945 4.119363 GCATGGAGCTCCTGGGCA 62.119 66.667 32.28 13.40 41.15 5.36
3034 11068 3.368739 CGATAAACTAAGGGTGGAACGGT 60.369 47.826 0.00 0.00 38.12 4.83
3039 11073 0.537828 TAAGGGTGGAACGGTTTGCC 60.538 55.000 0.00 0.00 38.12 4.52
3183 11228 7.339466 TCTTCTTCTTTACATAATCAAAGGGCC 59.661 37.037 0.00 0.00 33.48 5.80
3205 11254 8.069979 GGGCCTATAGTAGGGGTATAGAAAATA 58.930 40.741 0.84 0.00 46.32 1.40
3237 11286 9.591792 GGAAATTATACGTTCTGTAAAGTACCT 57.408 33.333 0.00 0.00 36.44 3.08
3250 11299 8.071368 TCTGTAAAGTACCTATTTTGTTTTGCG 58.929 33.333 0.00 0.00 0.00 4.85
3265 11314 1.663695 TTGCGCCTGGCTAGAATAAC 58.336 50.000 17.92 0.00 44.05 1.89
3272 11321 4.202121 CGCCTGGCTAGAATAACTTGTAGA 60.202 45.833 17.92 0.00 31.47 2.59
3279 11328 6.405953 GGCTAGAATAACTTGTAGACTGCTGA 60.406 42.308 0.00 0.00 34.22 4.26
3280 11329 7.206687 GCTAGAATAACTTGTAGACTGCTGAT 58.793 38.462 0.00 0.00 31.47 2.90
3281 11330 7.168972 GCTAGAATAACTTGTAGACTGCTGATG 59.831 40.741 0.00 0.00 31.47 3.07
3283 11332 3.340814 AACTTGTAGACTGCTGATGGG 57.659 47.619 0.00 0.00 0.00 4.00
3284 11333 1.556911 ACTTGTAGACTGCTGATGGGG 59.443 52.381 0.00 0.00 0.00 4.96
3285 11334 1.556911 CTTGTAGACTGCTGATGGGGT 59.443 52.381 0.00 0.00 0.00 4.95
3286 11335 1.656587 TGTAGACTGCTGATGGGGTT 58.343 50.000 0.00 0.00 0.00 4.11
3287 11336 1.278985 TGTAGACTGCTGATGGGGTTG 59.721 52.381 0.00 0.00 0.00 3.77
3288 11337 1.555075 GTAGACTGCTGATGGGGTTGA 59.445 52.381 0.00 0.00 0.00 3.18
3293 11342 2.048603 GCTGATGGGGTTGAGGTGC 61.049 63.158 0.00 0.00 0.00 5.01
3294 11343 1.379044 CTGATGGGGTTGAGGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
3295 11344 2.141011 CTGATGGGGTTGAGGTGCCA 62.141 60.000 0.00 0.00 0.00 4.92
3296 11345 1.307647 GATGGGGTTGAGGTGCCAT 59.692 57.895 0.00 0.00 0.00 4.40
3297 11346 1.000739 ATGGGGTTGAGGTGCCATG 59.999 57.895 0.00 0.00 0.00 3.66
3298 11347 2.362889 GGGGTTGAGGTGCCATGG 60.363 66.667 7.63 7.63 0.00 3.66
3299 11348 2.440599 GGGTTGAGGTGCCATGGT 59.559 61.111 14.67 0.00 0.00 3.55
3300 11349 1.978617 GGGTTGAGGTGCCATGGTG 60.979 63.158 14.67 0.00 0.00 4.17
3301 11350 1.228552 GGTTGAGGTGCCATGGTGT 60.229 57.895 14.67 0.00 0.00 4.16
3309 11358 1.476488 GGTGCCATGGTGTGAATAACC 59.524 52.381 14.67 5.12 38.26 2.85
3323 11372 3.118629 TGAATAACCTGTAGCCTGCTCTG 60.119 47.826 0.00 0.00 0.00 3.35
3324 11373 1.938585 TAACCTGTAGCCTGCTCTGT 58.061 50.000 0.00 0.00 0.00 3.41
3335 11384 1.392589 CTGCTCTGTTGTGGTTTGGT 58.607 50.000 0.00 0.00 0.00 3.67
3385 11438 2.829720 TCTGTGTGCCGGTTTCTACTAT 59.170 45.455 1.90 0.00 0.00 2.12
3389 11442 3.864003 GTGTGCCGGTTTCTACTATCTTC 59.136 47.826 1.90 0.00 0.00 2.87
3437 11496 3.822735 TGCTTCTTGGAAGTTCTCATTGG 59.177 43.478 2.25 0.00 0.00 3.16
3461 11530 5.642919 GTGTTAACCACGTATTGTTGGGATA 59.357 40.000 2.48 0.00 33.61 2.59
3464 11533 7.230108 TGTTAACCACGTATTGTTGGGATAAAA 59.770 33.333 2.48 0.00 0.00 1.52
3501 11572 2.340210 TCACCACAGCTAAAGTGCAA 57.660 45.000 0.00 0.00 35.69 4.08
3532 11603 2.481952 GACTGCTTGGTCACATGAGTTC 59.518 50.000 0.00 0.00 36.35 3.01
3533 11604 2.105477 ACTGCTTGGTCACATGAGTTCT 59.895 45.455 0.00 0.00 0.00 3.01
3534 11605 2.483106 CTGCTTGGTCACATGAGTTCTG 59.517 50.000 0.00 0.00 0.00 3.02
3545 11617 3.319972 ACATGAGTTCTGCATTTGCTGTT 59.680 39.130 0.00 0.00 42.66 3.16
3553 11625 5.772825 TCTGCATTTGCTGTTTTTCTAGT 57.227 34.783 3.94 0.00 42.66 2.57
3576 11648 0.776451 GTCGTGTGTACTCTGCAACG 59.224 55.000 0.00 0.00 0.00 4.10
3582 11659 1.037493 TGTACTCTGCAACGTGACCT 58.963 50.000 0.00 0.00 0.00 3.85
3611 11688 3.242518 CTCGCAAGTCGTCACTGAATTA 58.757 45.455 0.00 0.00 39.67 1.40
3614 11691 3.367932 CGCAAGTCGTCACTGAATTATGT 59.632 43.478 0.00 0.00 31.06 2.29
3615 11692 4.561213 CGCAAGTCGTCACTGAATTATGTA 59.439 41.667 0.00 0.00 31.06 2.29
3616 11693 5.498700 CGCAAGTCGTCACTGAATTATGTAC 60.499 44.000 0.00 0.00 31.06 2.90
3618 11695 4.103357 AGTCGTCACTGAATTATGTACGC 58.897 43.478 0.00 0.00 0.00 4.42
3620 11697 3.129813 TCGTCACTGAATTATGTACGCCT 59.870 43.478 0.00 0.00 0.00 5.52
3621 11698 3.242944 CGTCACTGAATTATGTACGCCTG 59.757 47.826 0.00 0.00 0.00 4.85
3624 11722 3.309682 CACTGAATTATGTACGCCTGGTG 59.690 47.826 5.54 5.54 0.00 4.17
3641 11739 0.614134 GTGGTCCTCCCGTCCTAACT 60.614 60.000 0.00 0.00 35.15 2.24
3650 11748 4.874396 CCTCCCGTCCTAACTTAAAATCAC 59.126 45.833 0.00 0.00 0.00 3.06
3653 11751 4.874396 CCCGTCCTAACTTAAAATCACTCC 59.126 45.833 0.00 0.00 0.00 3.85
3682 11790 8.777865 TCCTTCACATTCTCAAAGTATACAAG 57.222 34.615 5.50 0.00 0.00 3.16
3707 11815 4.012374 TCCATTTCAAGTGGAAGATGAGC 58.988 43.478 0.00 0.00 42.56 4.26
3708 11816 3.181503 CCATTTCAAGTGGAAGATGAGCG 60.182 47.826 0.00 0.00 39.12 5.03
3718 11865 1.028330 AAGATGAGCGCACACATGGG 61.028 55.000 10.42 0.00 41.65 4.00
3734 11881 1.220749 GGGCACCGTCAGAGCAATA 59.779 57.895 0.00 0.00 40.86 1.90
3735 11882 0.179045 GGGCACCGTCAGAGCAATAT 60.179 55.000 0.00 0.00 40.86 1.28
3736 11883 1.221414 GGCACCGTCAGAGCAATATC 58.779 55.000 0.00 0.00 0.00 1.63
3737 11884 1.202580 GGCACCGTCAGAGCAATATCT 60.203 52.381 0.00 0.00 0.00 1.98
3738 11885 2.131183 GCACCGTCAGAGCAATATCTC 58.869 52.381 0.00 0.00 0.00 2.75
3739 11886 2.748605 CACCGTCAGAGCAATATCTCC 58.251 52.381 0.00 0.00 33.66 3.71
3740 11887 1.338337 ACCGTCAGAGCAATATCTCCG 59.662 52.381 0.00 0.00 33.66 4.63
3741 11888 1.413382 CGTCAGAGCAATATCTCCGC 58.587 55.000 0.00 0.00 33.66 5.54
3742 11889 1.413382 GTCAGAGCAATATCTCCGCG 58.587 55.000 0.00 0.00 33.66 6.46
3743 11890 0.319040 TCAGAGCAATATCTCCGCGC 60.319 55.000 0.00 0.00 33.66 6.86
3744 11891 0.598419 CAGAGCAATATCTCCGCGCA 60.598 55.000 8.75 0.00 33.66 6.09
3745 11892 0.598680 AGAGCAATATCTCCGCGCAC 60.599 55.000 8.75 0.00 33.66 5.34
3746 11893 1.880601 GAGCAATATCTCCGCGCACG 61.881 60.000 8.75 0.00 39.67 5.34
3747 11894 2.546321 CAATATCTCCGCGCACGC 59.454 61.111 8.75 4.64 38.22 5.34
3767 11914 2.720067 GCGTGCGATAGTAGAAACTAGC 59.280 50.000 0.00 0.00 41.46 3.42
3773 11920 4.498345 GCGATAGTAGAAACTAGCAGCAGT 60.498 45.833 0.00 0.00 43.39 4.40
3919 12090 0.936600 AAAGCCGTTTTGCATTGCAC 59.063 45.000 11.66 0.00 38.71 4.57
3950 12121 3.370672 GGCCAAAACAAACAACAAGAGTG 59.629 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.461961 CTCGAGGACCAGGGCTTTAG 59.538 60.000 3.91 0.00 0.00 1.85
1 2 0.976073 CCTCGAGGACCAGGGCTTTA 60.976 60.000 28.21 0.00 37.39 1.85
2 3 2.294078 CCTCGAGGACCAGGGCTTT 61.294 63.158 28.21 0.00 37.39 3.51
49 50 1.765314 AGGGGGTCGAGATTCAGAATG 59.235 52.381 0.00 0.00 37.54 2.67
50 51 2.182516 AGGGGGTCGAGATTCAGAAT 57.817 50.000 0.00 0.00 0.00 2.40
64 65 2.134933 GCGAGGTAGGAGAAGGGGG 61.135 68.421 0.00 0.00 0.00 5.40
93 94 2.300152 TCGCACAAAGAATGAGGAGAGT 59.700 45.455 0.00 0.00 0.00 3.24
104 105 0.179084 GGGGATCGATCGCACAAAGA 60.179 55.000 34.64 0.00 41.06 2.52
154 2607 0.106918 TTCCCACCAACGAGCAACTT 60.107 50.000 0.00 0.00 0.00 2.66
170 2623 0.102663 GTAGCTAGCGGTGGTCTTCC 59.897 60.000 9.55 0.00 0.00 3.46
273 6429 4.398549 TCCGATGTCAATTTCGTTTCAC 57.601 40.909 0.00 0.00 33.60 3.18
333 6489 0.821711 TTTTTGCACTCCCCTCACGG 60.822 55.000 0.00 0.00 0.00 4.94
383 6539 2.671914 CGGTCTGGTTTGATGCCATTTG 60.672 50.000 0.00 0.00 35.19 2.32
389 6545 1.079503 GACTCGGTCTGGTTTGATGC 58.920 55.000 0.00 0.00 0.00 3.91
391 6547 0.966920 ACGACTCGGTCTGGTTTGAT 59.033 50.000 2.98 0.00 0.00 2.57
409 6565 3.536158 TCAGCTAACAATTCGCAACAC 57.464 42.857 0.00 0.00 0.00 3.32
410 6566 4.560136 TTTCAGCTAACAATTCGCAACA 57.440 36.364 0.00 0.00 0.00 3.33
412 6568 5.181690 AGTTTTCAGCTAACAATTCGCAA 57.818 34.783 0.93 0.00 0.00 4.85
413 6569 4.829064 AGTTTTCAGCTAACAATTCGCA 57.171 36.364 0.93 0.00 0.00 5.10
414 6570 4.143535 GCAAGTTTTCAGCTAACAATTCGC 60.144 41.667 0.93 0.00 0.00 4.70
415 6571 4.975502 TGCAAGTTTTCAGCTAACAATTCG 59.024 37.500 0.93 0.00 0.00 3.34
423 6595 3.980775 GCGAAAATGCAAGTTTTCAGCTA 59.019 39.130 20.07 0.00 44.44 3.32
430 6602 0.387565 ACGGGCGAAAATGCAAGTTT 59.612 45.000 0.00 0.00 36.50 2.66
470 6642 1.218316 CACAGGAGAAGTACGGCCC 59.782 63.158 0.00 0.00 0.00 5.80
482 6654 2.354704 CGTTTATCAAGCCTCCACAGGA 60.355 50.000 0.00 0.00 43.65 3.86
483 6655 2.009774 CGTTTATCAAGCCTCCACAGG 58.990 52.381 0.00 0.00 43.82 4.00
494 6666 3.773418 TGGAGGTGGTTCGTTTATCAA 57.227 42.857 0.00 0.00 0.00 2.57
495 6667 3.992943 ATGGAGGTGGTTCGTTTATCA 57.007 42.857 0.00 0.00 0.00 2.15
496 6668 4.995487 GGATATGGAGGTGGTTCGTTTATC 59.005 45.833 0.00 0.00 0.00 1.75
497 6669 4.502604 CGGATATGGAGGTGGTTCGTTTAT 60.503 45.833 0.00 0.00 0.00 1.40
498 6670 3.181473 CGGATATGGAGGTGGTTCGTTTA 60.181 47.826 0.00 0.00 0.00 2.01
499 6671 2.419574 CGGATATGGAGGTGGTTCGTTT 60.420 50.000 0.00 0.00 0.00 3.60
500 6672 1.138266 CGGATATGGAGGTGGTTCGTT 59.862 52.381 0.00 0.00 0.00 3.85
501 6673 0.750850 CGGATATGGAGGTGGTTCGT 59.249 55.000 0.00 0.00 0.00 3.85
502 6674 0.600255 GCGGATATGGAGGTGGTTCG 60.600 60.000 0.00 0.00 0.00 3.95
503 6675 0.468226 TGCGGATATGGAGGTGGTTC 59.532 55.000 0.00 0.00 0.00 3.62
504 6676 0.180406 GTGCGGATATGGAGGTGGTT 59.820 55.000 0.00 0.00 0.00 3.67
505 6677 1.696097 GGTGCGGATATGGAGGTGGT 61.696 60.000 0.00 0.00 0.00 4.16
506 6678 1.071471 GGTGCGGATATGGAGGTGG 59.929 63.158 0.00 0.00 0.00 4.61
507 6679 0.180171 TTGGTGCGGATATGGAGGTG 59.820 55.000 0.00 0.00 0.00 4.00
508 6680 0.916086 TTTGGTGCGGATATGGAGGT 59.084 50.000 0.00 0.00 0.00 3.85
509 6681 2.051334 TTTTGGTGCGGATATGGAGG 57.949 50.000 0.00 0.00 0.00 4.30
510 6682 5.766150 TTATTTTTGGTGCGGATATGGAG 57.234 39.130 0.00 0.00 0.00 3.86
511 6683 5.068460 CCTTTATTTTTGGTGCGGATATGGA 59.932 40.000 0.00 0.00 0.00 3.41
512 6684 5.288804 CCTTTATTTTTGGTGCGGATATGG 58.711 41.667 0.00 0.00 0.00 2.74
513 6685 5.068460 TCCCTTTATTTTTGGTGCGGATATG 59.932 40.000 0.00 0.00 0.00 1.78
514 6686 5.205056 TCCCTTTATTTTTGGTGCGGATAT 58.795 37.500 0.00 0.00 0.00 1.63
515 6687 4.601084 TCCCTTTATTTTTGGTGCGGATA 58.399 39.130 0.00 0.00 0.00 2.59
516 6688 3.436243 TCCCTTTATTTTTGGTGCGGAT 58.564 40.909 0.00 0.00 0.00 4.18
517 6689 2.877866 TCCCTTTATTTTTGGTGCGGA 58.122 42.857 0.00 0.00 0.00 5.54
518 6690 3.669251 TTCCCTTTATTTTTGGTGCGG 57.331 42.857 0.00 0.00 0.00 5.69
519 6691 5.053811 ACTTTTCCCTTTATTTTTGGTGCG 58.946 37.500 0.00 0.00 0.00 5.34
520 6692 6.724263 CAACTTTTCCCTTTATTTTTGGTGC 58.276 36.000 0.00 0.00 0.00 5.01
521 6693 6.510960 CGCAACTTTTCCCTTTATTTTTGGTG 60.511 38.462 0.00 0.00 0.00 4.17
522 6694 5.525745 CGCAACTTTTCCCTTTATTTTTGGT 59.474 36.000 0.00 0.00 0.00 3.67
523 6695 5.755861 TCGCAACTTTTCCCTTTATTTTTGG 59.244 36.000 0.00 0.00 0.00 3.28
524 6696 6.836577 TCGCAACTTTTCCCTTTATTTTTG 57.163 33.333 0.00 0.00 0.00 2.44
525 6697 7.713073 TGATTCGCAACTTTTCCCTTTATTTTT 59.287 29.630 0.00 0.00 0.00 1.94
526 6698 7.170828 GTGATTCGCAACTTTTCCCTTTATTTT 59.829 33.333 0.00 0.00 0.00 1.82
527 6699 6.645003 GTGATTCGCAACTTTTCCCTTTATTT 59.355 34.615 0.00 0.00 0.00 1.40
530 6702 4.319911 CGTGATTCGCAACTTTTCCCTTTA 60.320 41.667 0.00 0.00 0.00 1.85
534 6706 1.533731 TCGTGATTCGCAACTTTTCCC 59.466 47.619 0.00 0.00 39.67 3.97
1464 7699 2.750637 GAGGCCGACCACGAGAGA 60.751 66.667 0.00 0.00 42.66 3.10
1470 7705 2.262915 CTGACTGAGGCCGACCAC 59.737 66.667 0.00 0.00 39.06 4.16
1494 7729 9.447157 GAATTTGATGGGTTTGGATTTGAAATA 57.553 29.630 0.00 0.00 0.00 1.40
1499 7758 6.232692 ACTGAATTTGATGGGTTTGGATTTG 58.767 36.000 0.00 0.00 0.00 2.32
1558 7818 9.916397 GGTTTGTATCAGTTCATTATTCTAACG 57.084 33.333 0.00 0.00 0.00 3.18
1588 7851 9.817809 TTATCGGCCTCATGAATTATATACTTC 57.182 33.333 0.00 6.00 0.00 3.01
1595 7858 4.697352 GCAGTTATCGGCCTCATGAATTAT 59.303 41.667 0.00 0.00 0.00 1.28
1610 7873 5.352569 ACAGCAGTTATCAACAGCAGTTATC 59.647 40.000 8.78 0.00 45.20 1.75
1611 7874 5.248640 ACAGCAGTTATCAACAGCAGTTAT 58.751 37.500 8.78 0.00 45.20 1.89
1612 7875 4.641396 ACAGCAGTTATCAACAGCAGTTA 58.359 39.130 8.78 0.00 45.20 2.24
1613 7876 3.480470 ACAGCAGTTATCAACAGCAGTT 58.520 40.909 8.78 0.00 45.20 3.16
1615 7878 4.498241 TCTACAGCAGTTATCAACAGCAG 58.502 43.478 8.78 3.78 45.20 4.24
1618 7881 5.521735 GGTCATCTACAGCAGTTATCAACAG 59.478 44.000 0.00 0.00 0.00 3.16
1620 7883 5.521735 CAGGTCATCTACAGCAGTTATCAAC 59.478 44.000 0.00 0.00 0.00 3.18
1621 7884 5.422012 TCAGGTCATCTACAGCAGTTATCAA 59.578 40.000 0.00 0.00 0.00 2.57
1622 7885 4.956075 TCAGGTCATCTACAGCAGTTATCA 59.044 41.667 0.00 0.00 0.00 2.15
1624 7887 7.288852 AGTTATCAGGTCATCTACAGCAGTTAT 59.711 37.037 0.00 0.00 0.00 1.89
1625 7888 6.607600 AGTTATCAGGTCATCTACAGCAGTTA 59.392 38.462 0.00 0.00 0.00 2.24
1628 7891 5.288015 CAGTTATCAGGTCATCTACAGCAG 58.712 45.833 0.00 0.00 0.00 4.24
1629 7892 4.442052 GCAGTTATCAGGTCATCTACAGCA 60.442 45.833 0.00 0.00 0.00 4.41
1630 7893 4.054671 GCAGTTATCAGGTCATCTACAGC 58.945 47.826 0.00 0.00 0.00 4.40
1655 8034 6.543465 CCCTGCTGAATCTTCAATACATACAA 59.457 38.462 0.00 0.00 36.64 2.41
1667 8046 1.493871 CTCCATCCCCTGCTGAATCTT 59.506 52.381 0.00 0.00 0.00 2.40
1708 8087 0.981183 TCATCCCGCCTTAACACTGT 59.019 50.000 0.00 0.00 0.00 3.55
1721 8100 3.326006 TGCTGGAGATGTCTAATCATCCC 59.674 47.826 3.52 5.54 43.46 3.85
1744 8126 8.494347 GCAAAACACATGCAACAAATAAGAATA 58.506 29.630 0.00 0.00 43.29 1.75
1875 8677 8.643324 AGGGTAGTAGAAATTATACAAGAGCAG 58.357 37.037 0.45 0.00 0.00 4.24
1908 8710 1.970917 GACGGCATTGCAAGTCCGAG 61.971 60.000 34.39 16.70 44.23 4.63
1911 8713 2.480555 CGACGGCATTGCAAGTCC 59.519 61.111 22.30 7.48 35.48 3.85
1912 8714 2.480555 CCGACGGCATTGCAAGTC 59.519 61.111 19.95 19.95 35.53 3.01
1928 8730 1.616374 CCCTAAGAAGATCGAGAGGCC 59.384 57.143 0.00 0.00 0.00 5.19
2051 8853 9.444600 GAATACACTACCTTCCAGATTTAACAA 57.555 33.333 0.00 0.00 0.00 2.83
2107 8909 5.346181 AGCATGTCTCTAGTACCCTTTTC 57.654 43.478 0.00 0.00 0.00 2.29
2152 8954 2.038837 GGCCACCTAGACGGTTTGC 61.039 63.158 0.00 0.00 46.37 3.68
2154 8956 0.036306 CAAGGCCACCTAGACGGTTT 59.964 55.000 5.01 0.00 46.37 3.27
2534 10419 9.298250 GTAGGTGACTAGGTGATAGATCAAATA 57.702 37.037 0.00 0.00 45.49 1.40
2549 10434 7.323420 TGTCATCAAAATCAGTAGGTGACTAG 58.677 38.462 0.00 0.00 45.49 2.57
2550 10435 7.239763 TGTCATCAAAATCAGTAGGTGACTA 57.760 36.000 0.00 0.00 43.67 2.59
2552 10437 6.676456 GCATGTCATCAAAATCAGTAGGTGAC 60.676 42.308 0.00 0.00 38.28 3.67
2553 10438 5.355071 GCATGTCATCAAAATCAGTAGGTGA 59.645 40.000 0.00 0.00 40.38 4.02
2554 10439 5.449588 GGCATGTCATCAAAATCAGTAGGTG 60.450 44.000 0.00 0.00 0.00 4.00
2555 10440 4.641989 GGCATGTCATCAAAATCAGTAGGT 59.358 41.667 0.00 0.00 0.00 3.08
2556 10441 4.885907 AGGCATGTCATCAAAATCAGTAGG 59.114 41.667 0.00 0.00 0.00 3.18
2557 10442 6.446781 AAGGCATGTCATCAAAATCAGTAG 57.553 37.500 0.00 0.00 0.00 2.57
2575 10460 4.265893 TCAGACTACAAACACAAAAGGCA 58.734 39.130 0.00 0.00 0.00 4.75
2665 10689 7.145474 AGAGAGAAAAGGGTTTAAGTACCAA 57.855 36.000 0.00 0.00 40.09 3.67
2680 10704 1.412710 AGGTGTGTGCGAGAGAGAAAA 59.587 47.619 0.00 0.00 0.00 2.29
2682 10706 0.315251 CAGGTGTGTGCGAGAGAGAA 59.685 55.000 0.00 0.00 0.00 2.87
2683 10707 1.959848 CAGGTGTGTGCGAGAGAGA 59.040 57.895 0.00 0.00 0.00 3.10
2684 10708 1.735920 GCAGGTGTGTGCGAGAGAG 60.736 63.158 0.00 0.00 32.74 3.20
2691 10715 2.026590 GTGCAAGCAGGTGTGTGC 59.973 61.111 0.00 0.00 44.35 4.57
2725 10749 2.034999 GTCATTGCCCCCGGAACA 59.965 61.111 0.73 0.00 0.00 3.18
2726 10750 2.754254 GGTCATTGCCCCCGGAAC 60.754 66.667 0.73 0.00 0.00 3.62
2730 10754 1.682005 AATGTGGTCATTGCCCCCG 60.682 57.895 0.00 0.00 41.95 5.73
2754 10779 2.242797 GATTTGGCCGCCCTGCAAAT 62.243 55.000 7.03 6.04 0.00 2.32
2800 10834 1.668826 TGGGGAACAAGCAGTATCCT 58.331 50.000 0.00 0.00 31.86 3.24
2911 10945 2.487934 GTGCTCATGAATGGATACGCT 58.512 47.619 0.00 0.00 42.51 5.07
2965 10999 1.946984 ACATGAGGAAGACCGGGTAA 58.053 50.000 6.32 0.00 41.83 2.85
2971 11005 3.706594 TGGAGACATACATGAGGAAGACC 59.293 47.826 0.00 0.00 33.40 3.85
3233 11282 3.057174 CCAGGCGCAAAACAAAATAGGTA 60.057 43.478 10.83 0.00 0.00 3.08
3234 11283 2.288763 CCAGGCGCAAAACAAAATAGGT 60.289 45.455 10.83 0.00 0.00 3.08
3235 11284 2.336667 CCAGGCGCAAAACAAAATAGG 58.663 47.619 10.83 0.00 0.00 2.57
3237 11286 1.342819 AGCCAGGCGCAAAACAAAATA 59.657 42.857 10.83 0.00 41.38 1.40
3239 11288 0.747255 TAGCCAGGCGCAAAACAAAA 59.253 45.000 10.83 0.00 41.38 2.44
3250 11299 5.051153 GTCTACAAGTTATTCTAGCCAGGC 58.949 45.833 1.84 1.84 0.00 4.85
3265 11314 1.556911 ACCCCATCAGCAGTCTACAAG 59.443 52.381 0.00 0.00 0.00 3.16
3272 11321 1.136329 ACCTCAACCCCATCAGCAGT 61.136 55.000 0.00 0.00 0.00 4.40
3279 11328 1.000739 CATGGCACCTCAACCCCAT 59.999 57.895 0.00 0.00 38.56 4.00
3280 11329 2.440147 CATGGCACCTCAACCCCA 59.560 61.111 0.00 0.00 0.00 4.96
3281 11330 2.362889 CCATGGCACCTCAACCCC 60.363 66.667 0.00 0.00 0.00 4.95
3283 11332 1.228552 ACACCATGGCACCTCAACC 60.229 57.895 13.04 0.00 0.00 3.77
3284 11333 0.537143 TCACACCATGGCACCTCAAC 60.537 55.000 13.04 0.00 0.00 3.18
3285 11334 0.184692 TTCACACCATGGCACCTCAA 59.815 50.000 13.04 0.00 0.00 3.02
3286 11335 0.405198 ATTCACACCATGGCACCTCA 59.595 50.000 13.04 0.00 0.00 3.86
3287 11336 2.418368 TATTCACACCATGGCACCTC 57.582 50.000 13.04 0.00 0.00 3.85
3288 11337 2.446435 GTTATTCACACCATGGCACCT 58.554 47.619 13.04 0.00 0.00 4.00
3293 11342 3.627577 GCTACAGGTTATTCACACCATGG 59.372 47.826 11.19 11.19 36.67 3.66
3294 11343 3.627577 GGCTACAGGTTATTCACACCATG 59.372 47.826 0.00 0.00 36.67 3.66
3295 11344 3.523564 AGGCTACAGGTTATTCACACCAT 59.476 43.478 0.00 0.00 36.67 3.55
3296 11345 2.910319 AGGCTACAGGTTATTCACACCA 59.090 45.455 0.00 0.00 36.67 4.17
3297 11346 3.270877 CAGGCTACAGGTTATTCACACC 58.729 50.000 0.00 0.00 34.06 4.16
3298 11347 2.678336 GCAGGCTACAGGTTATTCACAC 59.322 50.000 0.00 0.00 0.00 3.82
3299 11348 2.571653 AGCAGGCTACAGGTTATTCACA 59.428 45.455 0.00 0.00 0.00 3.58
3300 11349 3.118592 AGAGCAGGCTACAGGTTATTCAC 60.119 47.826 0.00 0.00 0.00 3.18
3301 11350 3.107601 AGAGCAGGCTACAGGTTATTCA 58.892 45.455 0.00 0.00 0.00 2.57
3309 11358 1.436600 CACAACAGAGCAGGCTACAG 58.563 55.000 0.00 0.00 0.00 2.74
3323 11372 1.810532 TGGCGAACCAAACCACAAC 59.189 52.632 0.00 0.00 45.37 3.32
3324 11373 4.338815 TGGCGAACCAAACCACAA 57.661 50.000 0.00 0.00 45.37 3.33
3335 11384 1.093972 CATGCTAACACCATGGCGAA 58.906 50.000 13.04 0.00 37.12 4.70
3345 11394 5.647658 CACAGATAAAGGGAACATGCTAACA 59.352 40.000 0.00 0.00 0.00 2.41
3359 11412 3.074412 AGAAACCGGCACACAGATAAAG 58.926 45.455 0.00 0.00 0.00 1.85
3385 11438 4.044308 TCAGGCAATAATACCAGGGAAGA 58.956 43.478 0.00 0.00 0.00 2.87
3389 11442 2.174639 TGGTCAGGCAATAATACCAGGG 59.825 50.000 0.00 0.00 35.34 4.45
3437 11496 3.814283 TCCCAACAATACGTGGTTAACAC 59.186 43.478 8.10 3.28 46.78 3.32
3501 11572 0.036010 CCAAGCAGTCAATCTCCGGT 60.036 55.000 0.00 0.00 0.00 5.28
3532 11603 5.766222 AGACTAGAAAAACAGCAAATGCAG 58.234 37.500 8.28 1.87 45.16 4.41
3533 11604 5.560760 CGAGACTAGAAAAACAGCAAATGCA 60.561 40.000 8.28 0.00 45.16 3.96
3534 11605 4.848299 CGAGACTAGAAAAACAGCAAATGC 59.152 41.667 0.00 0.00 42.49 3.56
3545 11617 3.976793 ACACACGACGAGACTAGAAAA 57.023 42.857 0.00 0.00 0.00 2.29
3553 11625 0.516001 GCAGAGTACACACGACGAGA 59.484 55.000 0.00 0.00 0.00 4.04
3576 11648 4.683832 ACTTGCGAGTCAATATAGGTCAC 58.316 43.478 0.00 0.00 33.57 3.67
3611 11688 1.612442 AGGACCACCAGGCGTACAT 60.612 57.895 0.00 0.00 39.06 2.29
3614 11691 2.682494 GGAGGACCACCAGGCGTA 60.682 66.667 2.58 0.00 39.06 4.42
3618 11695 3.391382 GACGGGAGGACCACCAGG 61.391 72.222 12.40 5.08 40.22 4.45
3620 11697 2.096707 TTAGGACGGGAGGACCACCA 62.097 60.000 10.41 0.00 40.22 4.17
3621 11698 1.305549 TTAGGACGGGAGGACCACC 60.306 63.158 0.00 0.00 40.22 4.61
3624 11722 2.149973 TAAGTTAGGACGGGAGGACC 57.850 55.000 0.00 0.00 0.00 4.46
3641 11739 6.837312 TGTGAAGGAGAAGGAGTGATTTTAA 58.163 36.000 0.00 0.00 0.00 1.52
3650 11748 4.815533 TGAGAATGTGAAGGAGAAGGAG 57.184 45.455 0.00 0.00 0.00 3.69
3653 11751 9.092876 GTATACTTTGAGAATGTGAAGGAGAAG 57.907 37.037 0.00 0.00 0.00 2.85
3682 11790 4.400251 TCATCTTCCACTTGAAATGGATGC 59.600 41.667 0.00 0.00 45.71 3.91
3701 11809 3.104766 CCCATGTGTGCGCTCATC 58.895 61.111 16.02 9.82 0.00 2.92
3702 11810 3.136123 GCCCATGTGTGCGCTCAT 61.136 61.111 16.02 8.95 0.00 2.90
3704 11812 4.107051 GTGCCCATGTGTGCGCTC 62.107 66.667 9.73 5.51 35.20 5.03
3708 11816 3.737172 GACGGTGCCCATGTGTGC 61.737 66.667 0.00 0.00 0.00 4.57
3718 11865 2.131183 GAGATATTGCTCTGACGGTGC 58.869 52.381 1.25 1.25 35.27 5.01
3721 11868 1.932604 GCGGAGATATTGCTCTGACGG 60.933 57.143 0.00 0.00 42.63 4.79
3743 11890 1.252015 GTTTCTACTATCGCACGCGTG 59.748 52.381 34.01 34.01 40.74 5.34
3744 11891 1.131883 AGTTTCTACTATCGCACGCGT 59.868 47.619 5.58 5.58 35.21 6.01
3745 11892 1.823828 AGTTTCTACTATCGCACGCG 58.176 50.000 3.53 3.53 35.07 6.01
3746 11893 2.720067 GCTAGTTTCTACTATCGCACGC 59.280 50.000 0.00 0.00 36.32 5.34
3747 11894 3.948851 TGCTAGTTTCTACTATCGCACG 58.051 45.455 0.00 0.00 34.78 5.34
3748 11895 3.731717 GCTGCTAGTTTCTACTATCGCAC 59.268 47.826 0.00 0.00 34.78 5.34
3749 11896 3.380320 TGCTGCTAGTTTCTACTATCGCA 59.620 43.478 0.00 0.00 36.35 5.10
3750 11897 3.966154 TGCTGCTAGTTTCTACTATCGC 58.034 45.455 0.00 0.00 36.32 4.58
3751 11898 5.176407 ACTGCTGCTAGTTTCTACTATCG 57.824 43.478 0.00 0.00 36.32 2.92
3752 11899 7.266922 ACTACTGCTGCTAGTTTCTACTATC 57.733 40.000 0.00 0.00 36.32 2.08
3753 11900 7.484975 CAACTACTGCTGCTAGTTTCTACTAT 58.515 38.462 10.54 0.00 36.32 2.12
3754 11901 6.853720 CAACTACTGCTGCTAGTTTCTACTA 58.146 40.000 10.54 0.00 33.05 1.82
3755 11902 5.715070 CAACTACTGCTGCTAGTTTCTACT 58.285 41.667 10.54 0.00 33.05 2.57
3919 12090 4.508662 TGTTTGTTTTGGCCAAGTTTAGG 58.491 39.130 19.48 0.00 0.00 2.69
3950 12121 0.529555 TCGGTTTTGCCTTTGCTTGC 60.530 50.000 0.00 0.00 38.71 4.01


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

AutoCloner maintained by Alex Coulton.