Multiple sequence alignment - TraesCS1B01G366200

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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 TraesCS1B01G366200 chr1B 100.000 4467 0 0 1 4467 597454974 597450508 0.000000e+00 8250.0
1 TraesCS1B01G366200 chr1A 91.877 3053 149 54 880 3872 537969829 537972842 0.000000e+00 4172.0
2 TraesCS1B01G366200 chr1A 89.738 497 30 9 3982 4463 537972842 537973332 2.280000e-172 616.0
3 TraesCS1B01G366200 chr1A 80.000 135 10 10 706 825 537969671 537969803 2.860000e-12 84.2
4 TraesCS1B01G366200 chr1D 93.364 2366 89 20 1718 4023 439871360 439869003 0.000000e+00 3437.0
5 TraesCS1B01G366200 chr1D 85.350 1727 129 62 4 1691 439873002 439871361 0.000000e+00 1674.0
6 TraesCS1B01G366200 chr1D 93.805 113 7 0 4354 4466 439868999 439868887 2.140000e-38 171.0
7 TraesCS1B01G366200 chr6B 82.963 135 19 4 4165 4297 222680057 222680189 7.850000e-23 119.0
8 TraesCS1B01G366200 chr3A 74.917 303 55 9 9 309 652828804 652828521 7.850000e-23 119.0
9 TraesCS1B01G366200 chr6D 86.364 110 12 3 4189 4297 124941279 124941386 2.820000e-22 117.0
10 TraesCS1B01G366200 chr7B 92.683 41 3 0 4233 4273 368153768 368153728 4.830000e-05 60.2


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 TraesCS1B01G366200 chr1B 597450508 597454974 4466 True 8250.000000 8250 100.000000 1 4467 1 chr1B.!!$R1 4466
1 TraesCS1B01G366200 chr1A 537969671 537973332 3661 False 1624.066667 4172 87.205000 706 4463 3 chr1A.!!$F1 3757
2 TraesCS1B01G366200 chr1D 439868887 439873002 4115 True 1760.666667 3437 90.839667 4 4466 3 chr1D.!!$R1 4462

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
304 309 0.107703 GGATCGGTGTTGGAGATGCA 60.108 55.0 0.00 0.0 33.73 3.96 F
565 573 0.240945 AACCCAAAATCAGAAGCGCG 59.759 50.0 0.00 0.0 0.00 6.86 F
616 624 0.384669 CCCCCACGTCGAAGATCTAC 59.615 60.0 5.05 0.0 40.67 2.59 F
1550 1616 0.107116 TGGGTTTGCGTACTGGTGTT 60.107 50.0 0.00 0.0 0.00 3.32 F
1613 1684 0.110295 TGGAACCCTGTCATGGTGTG 59.890 55.0 0.00 0.0 35.88 3.82 F
1614 1685 0.110486 GGAACCCTGTCATGGTGTGT 59.890 55.0 0.00 0.0 35.88 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1591 0.107116 AGTACGCAAACCCAACCACA 60.107 50.000 0.00 0.00 0.0 4.17 R
1530 1596 0.107116 ACACCAGTACGCAAACCCAA 60.107 50.000 0.00 0.00 0.0 4.12 R
2572 2675 0.034767 TTTGCTCCAGATCAGGGCTG 60.035 55.000 15.26 4.48 0.0 4.85 R
3186 3289 0.700564 ATTGCTTTCCAGGCCTCTCA 59.299 50.000 0.00 0.00 0.0 3.27 R
3189 3292 1.751351 GGTTATTGCTTTCCAGGCCTC 59.249 52.381 0.00 0.00 0.0 4.70 R
3604 3715 1.818674 GAACCCGTTGCTGATCCATTT 59.181 47.619 0.00 0.00 0.0 2.32 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
21 22 0.955428 GCCGACTTCAATGTGGAGCA 60.955 55.000 0.00 0.00 0.00 4.26
89 90 4.235762 GCGCGGGCAAGGAGGATA 62.236 66.667 20.76 0.00 39.62 2.59
127 128 3.050275 GTCAGAAGTGGGCGTGGC 61.050 66.667 0.00 0.00 0.00 5.01
130 134 3.560251 AGAAGTGGGCGTGGCTGT 61.560 61.111 0.00 0.00 0.00 4.40
151 155 2.978010 CCGAACGCCCACAAAGCT 60.978 61.111 0.00 0.00 0.00 3.74
178 182 0.875059 CCCTCACGTTTTTCTCCAGC 59.125 55.000 0.00 0.00 0.00 4.85
184 188 1.268539 ACGTTTTTCTCCAGCTTTGCG 60.269 47.619 0.00 0.00 0.00 4.85
199 203 2.325583 TTGCGGAAGAAAGTGTGTCT 57.674 45.000 0.00 0.00 0.00 3.41
205 209 2.135933 GAAGAAAGTGTGTCTGGACCG 58.864 52.381 0.00 0.00 0.00 4.79
220 224 3.536917 CCGCCCTGCAGACCGATA 61.537 66.667 17.39 0.00 0.00 2.92
221 225 2.737180 CGCCCTGCAGACCGATAT 59.263 61.111 17.39 0.00 0.00 1.63
228 232 1.200252 CTGCAGACCGATATAGGACCG 59.800 57.143 8.42 0.00 34.73 4.79
236 240 1.670087 CGATATAGGACCGCCTTGCAG 60.670 57.143 0.00 0.00 43.90 4.41
238 242 1.407656 TATAGGACCGCCTTGCAGGG 61.408 60.000 11.24 11.24 43.90 4.45
247 251 2.332514 CTTGCAGGGCACAACACG 59.667 61.111 0.00 0.00 38.71 4.49
254 259 3.343421 GGCACAACACGTCCGACC 61.343 66.667 0.00 0.00 0.00 4.79
272 277 0.300491 CCGCGTGATCCAAACGTATG 59.700 55.000 4.92 0.00 42.93 2.39
274 279 0.315059 GCGTGATCCAAACGTATGCG 60.315 55.000 0.19 0.19 42.93 4.73
275 280 1.273688 CGTGATCCAAACGTATGCGA 58.726 50.000 11.07 0.00 42.00 5.10
276 281 1.255342 CGTGATCCAAACGTATGCGAG 59.745 52.381 11.07 0.00 42.00 5.03
277 282 1.004927 GTGATCCAAACGTATGCGAGC 60.005 52.381 11.07 0.00 42.00 5.03
278 283 0.229753 GATCCAAACGTATGCGAGCG 59.770 55.000 11.07 0.00 42.00 5.03
279 284 0.179121 ATCCAAACGTATGCGAGCGA 60.179 50.000 11.07 0.00 42.00 4.93
280 285 0.179121 TCCAAACGTATGCGAGCGAT 60.179 50.000 11.07 0.00 42.00 4.58
281 286 0.650512 CCAAACGTATGCGAGCGATT 59.349 50.000 11.07 0.00 42.00 3.34
282 287 1.062002 CCAAACGTATGCGAGCGATTT 59.938 47.619 11.07 0.00 42.00 2.17
283 288 2.093638 CAAACGTATGCGAGCGATTTG 58.906 47.619 11.07 6.03 42.00 2.32
304 309 0.107703 GGATCGGTGTTGGAGATGCA 60.108 55.000 0.00 0.00 33.73 3.96
312 317 3.933332 GGTGTTGGAGATGCACTTACTAC 59.067 47.826 0.00 0.00 33.96 2.73
319 324 4.442192 GGAGATGCACTTACTACTCCCAAG 60.442 50.000 0.00 0.00 38.23 3.61
327 332 5.597182 CACTTACTACTCCCAAGTATGCCTA 59.403 44.000 0.00 0.00 37.36 3.93
338 343 3.910627 CAAGTATGCCTAGGGGGTCTAAT 59.089 47.826 11.72 0.00 37.43 1.73
361 366 8.409358 AATGAGTAAAATATGCTAATGACCCC 57.591 34.615 0.00 0.00 0.00 4.95
391 396 2.511373 TAATGCTGCCTGGACGCG 60.511 61.111 3.53 3.53 0.00 6.01
392 397 2.906182 CTAATGCTGCCTGGACGCGA 62.906 60.000 15.93 0.00 0.00 5.87
407 412 2.656069 GCGACCCTAAGACAGCCCA 61.656 63.158 0.00 0.00 0.00 5.36
453 458 4.080526 GGATGAACAGTATAAGGGGTGTGT 60.081 45.833 0.00 0.00 0.00 3.72
454 459 5.129815 GGATGAACAGTATAAGGGGTGTGTA 59.870 44.000 0.00 0.00 0.00 2.90
471 478 1.272807 GTACACCCAGGAGTAGCCAA 58.727 55.000 0.00 0.00 40.02 4.52
472 479 1.626825 GTACACCCAGGAGTAGCCAAA 59.373 52.381 0.00 0.00 40.02 3.28
479 486 2.437413 CAGGAGTAGCCAAACCTTTCC 58.563 52.381 0.00 0.00 40.02 3.13
485 492 2.943036 AGCCAAACCTTTCCGTTAGA 57.057 45.000 0.00 0.00 0.00 2.10
487 494 3.146847 AGCCAAACCTTTCCGTTAGAAG 58.853 45.455 0.00 0.00 35.40 2.85
493 500 4.287766 ACCTTTCCGTTAGAAGAAGCAT 57.712 40.909 0.00 0.00 35.40 3.79
494 501 4.652822 ACCTTTCCGTTAGAAGAAGCATT 58.347 39.130 0.00 0.00 35.40 3.56
501 508 3.062639 CGTTAGAAGAAGCATTGCATCGT 59.937 43.478 11.91 6.72 31.18 3.73
505 512 1.297893 GAAGCATTGCATCGTCGGC 60.298 57.895 11.91 0.00 0.00 5.54
516 524 3.508840 CGTCGGCAATGGCTTCCC 61.509 66.667 5.02 0.00 40.87 3.97
517 525 2.044946 GTCGGCAATGGCTTCCCT 60.045 61.111 5.02 0.00 40.87 4.20
527 535 2.366972 GCTTCCCTGCCCTCCCTA 60.367 66.667 0.00 0.00 0.00 3.53
533 541 2.066999 CCTGCCCTCCCTACACCTC 61.067 68.421 0.00 0.00 0.00 3.85
535 543 2.040606 GCCCTCCCTACACCTCCA 59.959 66.667 0.00 0.00 0.00 3.86
537 545 1.689582 CCCTCCCTACACCTCCACC 60.690 68.421 0.00 0.00 0.00 4.61
565 573 0.240945 AACCCAAAATCAGAAGCGCG 59.759 50.000 0.00 0.00 0.00 6.86
614 622 1.305046 ACCCCCACGTCGAAGATCT 60.305 57.895 5.05 0.00 40.67 2.75
616 624 0.384669 CCCCCACGTCGAAGATCTAC 59.615 60.000 5.05 0.00 40.67 2.59
617 625 1.390565 CCCCACGTCGAAGATCTACT 58.609 55.000 5.05 0.00 40.67 2.57
619 627 2.014857 CCCACGTCGAAGATCTACTCA 58.985 52.381 5.05 0.00 40.67 3.41
622 630 3.102276 CACGTCGAAGATCTACTCAAGC 58.898 50.000 5.05 0.00 40.67 4.01
653 661 1.650528 GGATAGATGAGTGGGAGGGG 58.349 60.000 0.00 0.00 0.00 4.79
668 676 3.982891 GGGGGAAGGGGCTACTAC 58.017 66.667 0.00 0.00 0.00 2.73
669 677 1.003835 GGGGGAAGGGGCTACTACA 59.996 63.158 0.00 0.00 0.00 2.74
670 678 0.622446 GGGGGAAGGGGCTACTACAA 60.622 60.000 0.00 0.00 0.00 2.41
695 703 4.900635 AAAATGGCATAGTTGGTCGATC 57.099 40.909 0.00 0.00 0.00 3.69
696 704 3.558931 AATGGCATAGTTGGTCGATCA 57.441 42.857 0.00 0.00 0.00 2.92
698 706 1.552792 TGGCATAGTTGGTCGATCACA 59.447 47.619 0.00 0.00 0.00 3.58
699 707 1.933853 GGCATAGTTGGTCGATCACAC 59.066 52.381 0.00 0.01 0.00 3.82
701 709 3.000041 GCATAGTTGGTCGATCACACAA 59.000 45.455 0.00 0.00 0.00 3.33
706 714 2.448926 TGGTCGATCACACAATTCGT 57.551 45.000 0.00 0.00 34.60 3.85
744 761 1.590238 CACAAAGTCCGCATCGAGATC 59.410 52.381 0.00 0.00 0.00 2.75
755 772 2.943680 ATCGAGATCCGTGCACGCAG 62.944 60.000 33.17 20.66 39.75 5.18
772 789 0.597568 CAGAATGGACGGCAAGCAAA 59.402 50.000 0.00 0.00 0.00 3.68
779 796 2.887783 TGGACGGCAAGCAAATTTTAGA 59.112 40.909 0.00 0.00 0.00 2.10
782 799 3.900941 ACGGCAAGCAAATTTTAGACTG 58.099 40.909 0.00 0.00 0.00 3.51
783 800 3.568007 ACGGCAAGCAAATTTTAGACTGA 59.432 39.130 0.00 0.00 0.00 3.41
784 801 4.037446 ACGGCAAGCAAATTTTAGACTGAA 59.963 37.500 0.00 0.00 0.00 3.02
785 802 4.618489 CGGCAAGCAAATTTTAGACTGAAG 59.382 41.667 0.00 0.00 0.00 3.02
820 851 1.060713 CACGAATCTCAAAGCGACGT 58.939 50.000 0.00 0.00 0.00 4.34
825 856 2.558554 ATCTCAAAGCGACGTCCCCG 62.559 60.000 10.58 0.00 40.83 5.73
842 875 2.436646 GTGCCCTCATGTCCCGTG 60.437 66.667 0.00 0.00 0.00 4.94
850 883 1.446099 CATGTCCCGTGTCCACTCG 60.446 63.158 0.00 0.00 0.00 4.18
851 884 3.296709 ATGTCCCGTGTCCACTCGC 62.297 63.158 0.00 0.00 0.00 5.03
852 885 3.681835 GTCCCGTGTCCACTCGCT 61.682 66.667 0.00 0.00 0.00 4.93
853 886 2.915659 TCCCGTGTCCACTCGCTT 60.916 61.111 0.00 0.00 0.00 4.68
854 887 2.030562 CCCGTGTCCACTCGCTTT 59.969 61.111 0.00 0.00 0.00 3.51
855 888 2.317609 CCCGTGTCCACTCGCTTTG 61.318 63.158 0.00 0.00 0.00 2.77
856 889 1.300620 CCGTGTCCACTCGCTTTGA 60.301 57.895 0.00 0.00 0.00 2.69
866 899 2.070049 TCGCTTTGAGATTCGTGCG 58.930 52.632 0.00 0.00 43.95 5.34
867 900 1.059369 CGCTTTGAGATTCGTGCGG 59.941 57.895 0.00 0.00 39.76 5.69
868 901 1.425428 GCTTTGAGATTCGTGCGGG 59.575 57.895 0.00 0.00 0.00 6.13
869 902 1.298859 GCTTTGAGATTCGTGCGGGT 61.299 55.000 0.00 0.00 0.00 5.28
870 903 2.004583 CTTTGAGATTCGTGCGGGTA 57.995 50.000 0.00 0.00 0.00 3.69
871 904 2.550978 CTTTGAGATTCGTGCGGGTAT 58.449 47.619 0.00 0.00 0.00 2.73
872 905 2.684001 TTGAGATTCGTGCGGGTATT 57.316 45.000 0.00 0.00 0.00 1.89
873 906 2.684001 TGAGATTCGTGCGGGTATTT 57.316 45.000 0.00 0.00 0.00 1.40
874 907 2.980568 TGAGATTCGTGCGGGTATTTT 58.019 42.857 0.00 0.00 0.00 1.82
875 908 4.126208 TGAGATTCGTGCGGGTATTTTA 57.874 40.909 0.00 0.00 0.00 1.52
876 909 4.116961 TGAGATTCGTGCGGGTATTTTAG 58.883 43.478 0.00 0.00 0.00 1.85
953 989 4.572571 GACCGTTGGCCACCACCA 62.573 66.667 3.88 0.00 38.16 4.17
961 997 3.017581 GCCACCACCATCCTCCCT 61.018 66.667 0.00 0.00 0.00 4.20
962 998 3.049080 GCCACCACCATCCTCCCTC 62.049 68.421 0.00 0.00 0.00 4.30
963 999 2.735772 CCACCACCATCCTCCCTCG 61.736 68.421 0.00 0.00 0.00 4.63
967 1003 4.095400 ACCATCCTCCCTCGCCCT 62.095 66.667 0.00 0.00 0.00 5.19
968 1004 3.237741 CCATCCTCCCTCGCCCTC 61.238 72.222 0.00 0.00 0.00 4.30
969 1005 2.123077 CATCCTCCCTCGCCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
1265 1314 2.126228 CGAAACCCTCGTAGCGCA 60.126 61.111 11.47 0.00 42.89 6.09
1266 1315 1.518572 CGAAACCCTCGTAGCGCAT 60.519 57.895 11.47 0.00 42.89 4.73
1267 1316 1.082117 CGAAACCCTCGTAGCGCATT 61.082 55.000 11.47 0.00 42.89 3.56
1268 1317 1.084289 GAAACCCTCGTAGCGCATTT 58.916 50.000 11.47 0.00 0.00 2.32
1305 1360 1.000618 GGGTAGGTAGGTTAGCGATGC 59.999 57.143 0.00 0.00 0.00 3.91
1329 1384 1.414897 GCCGTGTGATTCGTTCGAC 59.585 57.895 0.00 0.00 0.00 4.20
1331 1386 0.388134 CCGTGTGATTCGTTCGACCT 60.388 55.000 0.00 0.00 0.00 3.85
1357 1412 0.466189 GGTGGTGCCATGGATCGATT 60.466 55.000 18.40 0.00 37.17 3.34
1440 1496 3.827302 GCTAGGATCTCGTATTCCTGGAA 59.173 47.826 12.26 12.26 41.72 3.53
1441 1497 4.464597 GCTAGGATCTCGTATTCCTGGAAT 59.535 45.833 24.25 24.25 41.72 3.01
1442 1498 4.881019 AGGATCTCGTATTCCTGGAATG 57.119 45.455 28.00 14.79 40.88 2.67
1443 1499 3.580458 AGGATCTCGTATTCCTGGAATGG 59.420 47.826 28.00 19.98 40.88 3.16
1445 1501 4.223923 GGATCTCGTATTCCTGGAATGGAT 59.776 45.833 28.00 22.70 35.83 3.41
1446 1502 5.422331 GGATCTCGTATTCCTGGAATGGATA 59.578 44.000 28.00 18.08 35.83 2.59
1447 1503 6.070767 GGATCTCGTATTCCTGGAATGGATAA 60.071 42.308 28.00 16.48 35.83 1.75
1456 1517 6.340962 TCCTGGAATGGATAATACTGTACG 57.659 41.667 0.00 0.00 0.00 3.67
1492 1554 0.817013 GATTTGGGGCAGCGAATTCA 59.183 50.000 6.22 0.00 0.00 2.57
1520 1586 1.068434 TGATGTCTGCAGTCACGACAA 59.932 47.619 15.94 0.00 40.61 3.18
1521 1587 1.457303 GATGTCTGCAGTCACGACAAC 59.543 52.381 15.94 6.67 40.61 3.32
1522 1588 0.869880 TGTCTGCAGTCACGACAACG 60.870 55.000 14.67 0.00 45.75 4.10
1535 1601 1.874739 CGACAACGTATGTGGTTGGGT 60.875 52.381 9.20 0.00 46.89 4.51
1550 1616 0.107116 TGGGTTTGCGTACTGGTGTT 60.107 50.000 0.00 0.00 0.00 3.32
1559 1630 3.995705 TGCGTACTGGTGTTTGTATAACC 59.004 43.478 0.00 0.00 34.38 2.85
1575 1646 3.895025 CCGAAGGCAGTGGATGTG 58.105 61.111 0.00 0.00 46.14 3.21
1577 1648 1.746615 CGAAGGCAGTGGATGTGGG 60.747 63.158 0.00 0.00 0.00 4.61
1605 1676 2.696864 TCCCATCTGGAACCCTGTC 58.303 57.895 0.00 0.00 41.40 3.51
1611 1682 0.692476 TCTGGAACCCTGTCATGGTG 59.308 55.000 0.00 0.00 35.88 4.17
1612 1683 0.401738 CTGGAACCCTGTCATGGTGT 59.598 55.000 0.00 0.00 35.88 4.16
1613 1684 0.110295 TGGAACCCTGTCATGGTGTG 59.890 55.000 0.00 0.00 35.88 3.82
1614 1685 0.110486 GGAACCCTGTCATGGTGTGT 59.890 55.000 0.00 0.00 35.88 3.72
1615 1686 1.238439 GAACCCTGTCATGGTGTGTG 58.762 55.000 0.00 0.00 35.88 3.82
1616 1687 0.550914 AACCCTGTCATGGTGTGTGT 59.449 50.000 0.00 0.00 35.88 3.72
1626 1697 1.068417 GGTGTGTGTGTGCCTCGTA 59.932 57.895 0.00 0.00 0.00 3.43
1627 1698 0.944311 GGTGTGTGTGTGCCTCGTAG 60.944 60.000 0.00 0.00 0.00 3.51
1656 1727 7.039882 GTCCTTCCTACGATTCTGAATTGTTA 58.960 38.462 24.22 10.90 36.84 2.41
1691 1762 5.306419 TCTGGACTGATATTGGATGGAAGAG 59.694 44.000 0.00 0.00 0.00 2.85
1743 1814 9.809096 AGAGATTGTATATATTTATGTCTGCCG 57.191 33.333 0.00 0.00 0.00 5.69
1825 1897 7.388776 TGTGGATTGAATCTTAGTCTCTTGTTG 59.611 37.037 5.03 0.00 0.00 3.33
1826 1898 7.389053 GTGGATTGAATCTTAGTCTCTTGTTGT 59.611 37.037 5.03 0.00 0.00 3.32
1829 1901 9.604626 GATTGAATCTTAGTCTCTTGTTGTTTG 57.395 33.333 0.00 0.00 0.00 2.93
1831 1903 8.142994 TGAATCTTAGTCTCTTGTTGTTTGTC 57.857 34.615 0.00 0.00 0.00 3.18
1880 1983 7.145932 TCTTTACTTTTAGAGCTTGCCAATC 57.854 36.000 0.00 0.00 0.00 2.67
1903 2006 6.042777 TCTGCTGGTTCTTATAATGTTCTCG 58.957 40.000 0.00 0.00 0.00 4.04
2039 2142 6.365520 ACACTAATTCTTCTTTGAAGGTGGT 58.634 36.000 7.37 0.49 33.55 4.16
2052 2155 1.153823 GGTGGTCACCGTCATCGAG 60.154 63.158 4.22 0.00 42.29 4.04
2073 2176 5.407995 CGAGTCTTTCATTCTTTCTGAAGCT 59.592 40.000 0.00 0.00 38.18 3.74
2076 2179 8.860780 AGTCTTTCATTCTTTCTGAAGCTAAT 57.139 30.769 0.00 0.00 38.18 1.73
2142 2245 5.474532 TCACTCATTTTGTTCTTATGCAGCT 59.525 36.000 0.00 0.00 0.00 4.24
2218 2321 1.171308 CCTCAAAGCACACCATGGAG 58.829 55.000 21.47 14.24 0.00 3.86
2235 2338 3.149196 TGGAGACCTGTTCAAAATCTGC 58.851 45.455 0.00 0.00 0.00 4.26
2239 2342 2.294233 GACCTGTTCAAAATCTGCTGCA 59.706 45.455 0.88 0.88 0.00 4.41
2247 2350 3.062042 CAAAATCTGCTGCAAAAGGGAC 58.938 45.455 3.02 0.00 0.00 4.46
2263 2366 2.509964 AGGGACTGACAAGTTGTTTCCT 59.490 45.455 22.09 13.62 37.18 3.36
2302 2405 4.175337 GCAGGCCCGGCAGTATCA 62.175 66.667 12.58 0.00 0.00 2.15
2392 2495 1.737793 CCTCTTGTTTCATGGCGTACC 59.262 52.381 0.00 0.00 0.00 3.34
2478 2581 1.314534 CGCTCATCCATGTGCCCAAA 61.315 55.000 7.78 0.00 42.51 3.28
2499 2602 6.292488 CCAAAATCATCAAAAGCACAGTTGAC 60.292 38.462 0.00 0.00 36.62 3.18
2534 2637 2.199208 TGGATGAGCTGAATCTTCCCA 58.801 47.619 0.00 0.00 40.93 4.37
2571 2674 6.430925 TGGAAACTAACCATTTCTGATGACAG 59.569 38.462 0.00 0.00 37.69 3.51
2572 2675 5.886960 AACTAACCATTTCTGATGACAGC 57.113 39.130 0.00 0.00 43.17 4.40
2575 2678 2.089980 ACCATTTCTGATGACAGCAGC 58.910 47.619 15.92 0.00 43.17 5.25
2823 2926 1.194781 ATTCTCAGTGCTGGACCGGT 61.195 55.000 6.92 6.92 0.00 5.28
2860 2963 1.345089 CCATCTGGAGGCTCTGATGAG 59.655 57.143 32.11 23.81 42.16 2.90
2893 2996 3.109928 TGAGAAGGATCTGGCATCAAGA 58.890 45.455 0.00 0.00 35.54 3.02
2920 3023 5.251932 TCCAGACCTGTATGGGTTTAATCAA 59.748 40.000 10.81 0.00 42.01 2.57
3050 3153 1.866853 CGTTCCCCTTCCAGCAAAGC 61.867 60.000 0.00 0.00 0.00 3.51
3092 3195 3.051617 CCTTGGGAAGGTTGGGAAC 57.948 57.895 0.00 0.00 43.95 3.62
3136 3239 3.964909 ACGGAAACTTTCAGATTGCAAC 58.035 40.909 0.00 0.00 0.00 4.17
3151 3254 3.071874 TGCAACCCTATCCAAACTCTG 57.928 47.619 0.00 0.00 0.00 3.35
3186 3289 1.498176 GCCTTGGTTGGTACTCCCCT 61.498 60.000 0.00 0.00 0.00 4.79
3189 3292 1.279271 CTTGGTTGGTACTCCCCTGAG 59.721 57.143 0.00 0.00 44.62 3.35
3483 3586 2.975732 TGATTCAGAGTAGCAGCAGG 57.024 50.000 0.00 0.00 0.00 4.85
3602 3713 0.313043 CAGAGCCAAAACTGCAGTGG 59.687 55.000 22.49 18.57 35.39 4.00
3604 3715 1.142870 AGAGCCAAAACTGCAGTGGTA 59.857 47.619 22.49 0.00 34.71 3.25
3671 3782 3.417101 TGTGTTCAATAAGATTGGCCGT 58.583 40.909 0.00 0.00 0.00 5.68
3834 3951 6.259167 CGGTGGCTAATAAAACATACTGCTAA 59.741 38.462 0.00 0.00 0.00 3.09
3879 3996 6.500041 TGGGTGATTTATTTATGCGCTTTAC 58.500 36.000 9.73 0.00 0.00 2.01
3891 4008 0.453282 CGCTTTACGTCGTTCCGAGA 60.453 55.000 1.78 0.00 36.23 4.04
3900 4017 1.374125 CGTTCCGAGATGTGCCACA 60.374 57.895 0.00 0.00 0.00 4.17
3904 4021 0.107643 TCCGAGATGTGCCACAACAA 59.892 50.000 0.00 0.00 32.81 2.83
3905 4022 0.518636 CCGAGATGTGCCACAACAAG 59.481 55.000 0.00 0.00 32.81 3.16
3906 4023 0.110056 CGAGATGTGCCACAACAAGC 60.110 55.000 0.00 0.00 32.81 4.01
3907 4024 0.953727 GAGATGTGCCACAACAAGCA 59.046 50.000 0.00 0.00 36.44 3.91
3908 4025 1.542915 GAGATGTGCCACAACAAGCAT 59.457 47.619 0.00 0.00 41.86 3.79
3909 4026 1.271379 AGATGTGCCACAACAAGCATG 59.729 47.619 0.00 0.00 41.86 4.06
3911 4028 1.042003 TGTGCCACAACAAGCATGGT 61.042 50.000 0.00 0.00 41.86 3.55
3912 4029 0.104671 GTGCCACAACAAGCATGGTT 59.895 50.000 3.82 3.82 41.86 3.67
3913 4030 0.104487 TGCCACAACAAGCATGGTTG 59.896 50.000 30.75 30.75 35.79 3.77
3914 4031 0.388659 GCCACAACAAGCATGGTTGA 59.611 50.000 36.93 0.00 35.79 3.18
3918 4051 4.426416 CCACAACAAGCATGGTTGATATG 58.574 43.478 36.93 30.45 32.90 1.78
3934 4067 9.764363 TGGTTGATATGCAGTTAATCTTACTAG 57.236 33.333 0.00 0.00 0.00 2.57
3955 4088 1.919240 TTCCCGTCTAGCTCAGTTGA 58.081 50.000 0.00 0.00 0.00 3.18
4052 4185 9.604626 GCTTAGCATCAGTTAACATGATTTATC 57.395 33.333 8.61 4.22 35.20 1.75
4080 4213 1.871039 CAATCGAAGGTCACGTTGGTT 59.129 47.619 0.00 0.00 0.00 3.67
4083 4216 2.472816 TCGAAGGTCACGTTGGTTAAC 58.527 47.619 0.00 0.00 0.00 2.01
4089 4222 2.540157 GGTCACGTTGGTTAACTGCAAC 60.540 50.000 14.33 14.33 34.60 4.17
4090 4223 2.096174 GTCACGTTGGTTAACTGCAACA 59.904 45.455 20.56 3.66 34.60 3.33
4091 4224 2.946329 TCACGTTGGTTAACTGCAACAT 59.054 40.909 20.56 8.76 34.60 2.71
4092 4225 4.024725 GTCACGTTGGTTAACTGCAACATA 60.025 41.667 20.56 8.20 34.60 2.29
4093 4226 4.212425 TCACGTTGGTTAACTGCAACATAG 59.788 41.667 20.56 12.76 34.60 2.23
4098 4231 7.603404 ACGTTGGTTAACTGCAACATAGTATAA 59.397 33.333 20.56 0.00 34.60 0.98
4151 4289 5.981088 TTCTAGAAAAGCCATGCAAATGA 57.019 34.783 1.68 0.00 0.00 2.57
4192 4330 3.305335 CCCCCGTTCTGAAATGTTTGAAG 60.305 47.826 0.00 0.00 0.00 3.02
4214 4352 6.860790 AGTTTTAACTTTTTCCTGGGTCAA 57.139 33.333 0.00 0.00 35.21 3.18
4231 4369 8.150296 CCTGGGTCAAACTTTTTAAGATTTGAT 58.850 33.333 14.31 0.00 38.95 2.57
4289 4427 7.961351 ACACCAAATTAGTTTCATTGGATTCA 58.039 30.769 10.14 0.00 44.01 2.57
4349 4489 2.768253 TCGAATCTGTGGCTGATGTT 57.232 45.000 0.00 0.00 0.00 2.71
4350 4490 2.621338 TCGAATCTGTGGCTGATGTTC 58.379 47.619 0.00 0.00 0.00 3.18
4352 4492 2.743664 CGAATCTGTGGCTGATGTTCAA 59.256 45.455 0.00 0.00 0.00 2.69
4439 4586 1.880027 CTGGCAAACGACCTAAAAGCT 59.120 47.619 0.00 0.00 0.00 3.74
4448 4596 3.244422 ACGACCTAAAAGCTGTTGGATCA 60.244 43.478 0.68 0.00 0.00 2.92
4463 4611 2.033675 TGGATCATGATCAAACGCATGC 59.966 45.455 31.49 7.91 41.18 4.06
4466 4614 1.817447 TCATGATCAAACGCATGCCAA 59.183 42.857 13.15 0.00 41.18 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.648467 GCTCCACATTGAAGTCGGCC 61.648 60.000 0.00 0.00 0.00 6.13
21 22 3.557903 ATGCTGTTGTGGAGCGGCT 62.558 57.895 0.00 0.00 39.47 5.52
55 56 4.776322 CGCATTCCCGCCTGGTGA 62.776 66.667 9.25 0.00 34.77 4.02
78 79 1.285078 ACCCCAAACTATCCTCCTTGC 59.715 52.381 0.00 0.00 0.00 4.01
89 90 2.120274 CATGGCCCACCCCAAACT 59.880 61.111 0.00 0.00 38.61 2.66
127 128 2.280524 TGGGCGTTCGGACAACAG 60.281 61.111 0.00 0.00 0.00 3.16
130 134 1.440938 CTTTGTGGGCGTTCGGACAA 61.441 55.000 0.00 0.00 0.00 3.18
157 161 0.109723 TGGAGAAAAACGTGAGGGGG 59.890 55.000 0.00 0.00 0.00 5.40
158 162 1.523758 CTGGAGAAAAACGTGAGGGG 58.476 55.000 0.00 0.00 0.00 4.79
159 163 0.875059 GCTGGAGAAAAACGTGAGGG 59.125 55.000 0.00 0.00 0.00 4.30
160 164 1.884235 AGCTGGAGAAAAACGTGAGG 58.116 50.000 0.00 0.00 0.00 3.86
161 165 3.621794 CAAAGCTGGAGAAAAACGTGAG 58.378 45.455 0.00 0.00 0.00 3.51
162 166 2.223479 GCAAAGCTGGAGAAAAACGTGA 60.223 45.455 0.00 0.00 0.00 4.35
163 167 2.119457 GCAAAGCTGGAGAAAAACGTG 58.881 47.619 0.00 0.00 0.00 4.49
164 168 1.268539 CGCAAAGCTGGAGAAAAACGT 60.269 47.619 0.00 0.00 0.00 3.99
165 169 1.398595 CGCAAAGCTGGAGAAAAACG 58.601 50.000 0.00 0.00 0.00 3.60
170 174 0.396435 TCTTCCGCAAAGCTGGAGAA 59.604 50.000 0.00 0.00 34.21 2.87
178 182 2.614057 AGACACACTTTCTTCCGCAAAG 59.386 45.455 0.00 0.00 36.97 2.77
184 188 2.495084 GGTCCAGACACACTTTCTTCC 58.505 52.381 0.00 0.00 0.00 3.46
205 209 0.247736 CCTATATCGGTCTGCAGGGC 59.752 60.000 15.13 7.27 0.00 5.19
236 240 3.343421 GTCGGACGTGTTGTGCCC 61.343 66.667 0.00 0.00 35.07 5.36
238 242 3.698463 CGGTCGGACGTGTTGTGC 61.698 66.667 0.00 0.00 35.21 4.57
247 251 3.636313 TTGGATCACGCGGTCGGAC 62.636 63.158 12.47 0.00 40.69 4.79
254 259 0.315059 GCATACGTTTGGATCACGCG 60.315 55.000 3.53 3.53 41.53 6.01
272 277 1.552348 CCGATCCTCAAATCGCTCGC 61.552 60.000 0.91 0.00 45.56 5.03
274 279 1.212616 CACCGATCCTCAAATCGCTC 58.787 55.000 0.91 0.00 45.56 5.03
275 280 0.537188 ACACCGATCCTCAAATCGCT 59.463 50.000 0.91 0.00 45.56 4.93
276 281 1.062587 CAACACCGATCCTCAAATCGC 59.937 52.381 0.91 0.00 45.56 4.58
277 282 1.665679 CCAACACCGATCCTCAAATCG 59.334 52.381 0.00 0.00 46.28 3.34
278 283 2.939103 CTCCAACACCGATCCTCAAATC 59.061 50.000 0.00 0.00 0.00 2.17
279 284 2.571653 TCTCCAACACCGATCCTCAAAT 59.428 45.455 0.00 0.00 0.00 2.32
280 285 1.974957 TCTCCAACACCGATCCTCAAA 59.025 47.619 0.00 0.00 0.00 2.69
281 286 1.639722 TCTCCAACACCGATCCTCAA 58.360 50.000 0.00 0.00 0.00 3.02
282 287 1.482182 CATCTCCAACACCGATCCTCA 59.518 52.381 0.00 0.00 0.00 3.86
283 288 1.808133 GCATCTCCAACACCGATCCTC 60.808 57.143 0.00 0.00 0.00 3.71
290 295 3.059352 AGTAAGTGCATCTCCAACACC 57.941 47.619 0.00 0.00 34.83 4.16
304 309 4.621769 AGGCATACTTGGGAGTAGTAAGT 58.378 43.478 0.00 0.00 41.45 2.24
319 324 3.515901 CTCATTAGACCCCCTAGGCATAC 59.484 52.174 2.05 0.00 40.58 2.39
327 332 6.332901 AGCATATTTTACTCATTAGACCCCCT 59.667 38.462 0.00 0.00 0.00 4.79
338 343 5.995282 CGGGGTCATTAGCATATTTTACTCA 59.005 40.000 0.00 0.00 0.00 3.41
391 396 2.019156 GCAATGGGCTGTCTTAGGGTC 61.019 57.143 0.00 0.00 40.25 4.46
392 397 0.034089 GCAATGGGCTGTCTTAGGGT 60.034 55.000 0.00 0.00 40.25 4.34
394 399 1.098050 GTGCAATGGGCTGTCTTAGG 58.902 55.000 0.00 0.00 45.15 2.69
397 402 0.537143 TTCGTGCAATGGGCTGTCTT 60.537 50.000 0.00 0.00 45.15 3.01
431 436 5.099042 ACACACCCCTTATACTGTTCATC 57.901 43.478 0.00 0.00 0.00 2.92
435 440 5.156608 GTGTACACACCCCTTATACTGTT 57.843 43.478 21.14 0.00 40.85 3.16
453 458 1.626825 GTTTGGCTACTCCTGGGTGTA 59.373 52.381 0.00 2.27 35.26 2.90
454 459 0.400594 GTTTGGCTACTCCTGGGTGT 59.599 55.000 0.00 0.09 35.26 4.16
458 463 2.437413 GAAAGGTTTGGCTACTCCTGG 58.563 52.381 0.00 0.00 35.26 4.45
460 465 1.003233 CGGAAAGGTTTGGCTACTCCT 59.997 52.381 0.00 0.00 35.26 3.69
471 478 4.081322 TGCTTCTTCTAACGGAAAGGTT 57.919 40.909 0.00 0.00 33.07 3.50
472 479 3.764237 TGCTTCTTCTAACGGAAAGGT 57.236 42.857 0.00 0.00 33.07 3.50
479 486 3.062639 ACGATGCAATGCTTCTTCTAACG 59.937 43.478 17.14 6.98 31.76 3.18
485 492 0.729116 CCGACGATGCAATGCTTCTT 59.271 50.000 17.14 9.36 31.76 2.52
487 494 1.297893 GCCGACGATGCAATGCTTC 60.298 57.895 6.82 9.01 0.00 3.86
494 501 3.507924 GCCATTGCCGACGATGCA 61.508 61.111 0.00 0.00 36.48 3.96
516 524 2.066999 GGAGGTGTAGGGAGGGCAG 61.067 68.421 0.00 0.00 0.00 4.85
517 525 2.040606 GGAGGTGTAGGGAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
527 535 4.626081 GCTGTGCGGTGGAGGTGT 62.626 66.667 0.00 0.00 0.00 4.16
547 555 1.875963 CGCGCTTCTGATTTTGGGT 59.124 52.632 5.56 0.00 0.00 4.51
550 558 0.854853 CTCGCGCGCTTCTGATTTTG 60.855 55.000 30.48 9.37 0.00 2.44
604 612 3.701241 CAGGCTTGAGTAGATCTTCGAC 58.299 50.000 0.00 0.00 0.00 4.20
606 614 2.100584 AGCAGGCTTGAGTAGATCTTCG 59.899 50.000 0.00 0.00 0.00 3.79
614 622 1.903877 GCAGGGAGCAGGCTTGAGTA 61.904 60.000 0.00 0.00 44.79 2.59
616 624 2.438075 GCAGGGAGCAGGCTTGAG 60.438 66.667 0.00 0.00 44.79 3.02
617 625 4.399395 CGCAGGGAGCAGGCTTGA 62.399 66.667 0.00 0.00 46.13 3.02
653 661 3.444792 TTTTTGTAGTAGCCCCTTCCC 57.555 47.619 0.00 0.00 0.00 3.97
695 703 5.658568 TCGTACCGAATCACGAATTGTGTG 61.659 45.833 0.00 4.93 43.63 3.82
696 704 3.612241 TCGTACCGAATCACGAATTGTGT 60.612 43.478 0.00 0.00 43.63 3.72
698 706 3.176708 CTCGTACCGAATCACGAATTGT 58.823 45.455 0.00 0.00 45.63 2.71
699 707 3.001070 CACTCGTACCGAATCACGAATTG 60.001 47.826 0.00 0.00 45.63 2.32
701 709 2.479049 CCACTCGTACCGAATCACGAAT 60.479 50.000 0.00 0.00 45.63 3.34
706 714 1.200716 GTGTCCACTCGTACCGAATCA 59.799 52.381 0.00 0.00 34.74 2.57
744 761 2.741985 TCCATTCTGCGTGCACGG 60.742 61.111 37.47 23.44 40.23 4.94
755 772 2.368655 AATTTGCTTGCCGTCCATTC 57.631 45.000 0.00 0.00 0.00 2.67
779 796 3.689649 GCGGGTATTTGTGAATCTTCAGT 59.310 43.478 0.00 0.00 37.98 3.41
782 799 3.485216 CGTGCGGGTATTTGTGAATCTTC 60.485 47.826 0.00 0.00 0.00 2.87
783 800 2.418628 CGTGCGGGTATTTGTGAATCTT 59.581 45.455 0.00 0.00 0.00 2.40
784 801 2.006888 CGTGCGGGTATTTGTGAATCT 58.993 47.619 0.00 0.00 0.00 2.40
785 802 2.004017 TCGTGCGGGTATTTGTGAATC 58.996 47.619 0.00 0.00 0.00 2.52
820 851 3.399181 GACATGAGGGCACGGGGA 61.399 66.667 0.00 0.00 0.00 4.81
825 856 2.436646 CACGGGACATGAGGGCAC 60.437 66.667 0.00 0.00 0.00 5.01
826 857 2.927856 ACACGGGACATGAGGGCA 60.928 61.111 0.00 0.00 0.00 5.36
831 864 1.873270 CGAGTGGACACGGGACATGA 61.873 60.000 0.00 0.00 36.20 3.07
832 865 1.446099 CGAGTGGACACGGGACATG 60.446 63.158 0.00 0.00 36.20 3.21
842 875 1.656095 CGAATCTCAAAGCGAGTGGAC 59.344 52.381 0.00 0.00 42.88 4.02
850 883 1.298859 ACCCGCACGAATCTCAAAGC 61.299 55.000 0.00 0.00 0.00 3.51
851 884 2.004583 TACCCGCACGAATCTCAAAG 57.995 50.000 0.00 0.00 0.00 2.77
852 885 2.684001 ATACCCGCACGAATCTCAAA 57.316 45.000 0.00 0.00 0.00 2.69
853 886 2.684001 AATACCCGCACGAATCTCAA 57.316 45.000 0.00 0.00 0.00 3.02
854 887 2.684001 AAATACCCGCACGAATCTCA 57.316 45.000 0.00 0.00 0.00 3.27
855 888 4.117685 ACTAAAATACCCGCACGAATCTC 58.882 43.478 0.00 0.00 0.00 2.75
856 889 4.117685 GACTAAAATACCCGCACGAATCT 58.882 43.478 0.00 0.00 0.00 2.40
857 890 4.025979 CAGACTAAAATACCCGCACGAATC 60.026 45.833 0.00 0.00 0.00 2.52
858 891 3.869246 CAGACTAAAATACCCGCACGAAT 59.131 43.478 0.00 0.00 0.00 3.34
859 892 3.255725 CAGACTAAAATACCCGCACGAA 58.744 45.455 0.00 0.00 0.00 3.85
860 893 2.417651 CCAGACTAAAATACCCGCACGA 60.418 50.000 0.00 0.00 0.00 4.35
861 894 1.931172 CCAGACTAAAATACCCGCACG 59.069 52.381 0.00 0.00 0.00 5.34
862 895 3.255969 TCCAGACTAAAATACCCGCAC 57.744 47.619 0.00 0.00 0.00 5.34
863 896 3.985019 TTCCAGACTAAAATACCCGCA 57.015 42.857 0.00 0.00 0.00 5.69
864 897 3.376234 GGTTTCCAGACTAAAATACCCGC 59.624 47.826 0.00 0.00 0.00 6.13
865 898 3.619929 CGGTTTCCAGACTAAAATACCCG 59.380 47.826 0.00 0.00 0.00 5.28
866 899 3.376234 GCGGTTTCCAGACTAAAATACCC 59.624 47.826 0.00 0.00 0.00 3.69
867 900 3.063045 CGCGGTTTCCAGACTAAAATACC 59.937 47.826 0.00 0.00 0.00 2.73
868 901 3.928375 TCGCGGTTTCCAGACTAAAATAC 59.072 43.478 6.13 0.00 0.00 1.89
869 902 3.928375 GTCGCGGTTTCCAGACTAAAATA 59.072 43.478 6.13 0.00 31.32 1.40
870 903 2.740447 GTCGCGGTTTCCAGACTAAAAT 59.260 45.455 6.13 0.00 31.32 1.82
871 904 2.137523 GTCGCGGTTTCCAGACTAAAA 58.862 47.619 6.13 0.00 31.32 1.52
872 905 1.787012 GTCGCGGTTTCCAGACTAAA 58.213 50.000 6.13 0.00 31.32 1.85
873 906 0.387622 CGTCGCGGTTTCCAGACTAA 60.388 55.000 6.13 0.00 31.65 2.24
874 907 1.210931 CGTCGCGGTTTCCAGACTA 59.789 57.895 6.13 0.00 31.65 2.59
875 908 2.049433 CGTCGCGGTTTCCAGACT 60.049 61.111 6.13 0.00 31.65 3.24
876 909 3.774702 GCGTCGCGGTTTCCAGAC 61.775 66.667 6.13 0.00 0.00 3.51
953 989 2.200092 GAGAGGGCGAGGGAGGAT 59.800 66.667 0.00 0.00 0.00 3.24
961 997 3.024356 AGAGAGGGGAGAGGGCGA 61.024 66.667 0.00 0.00 0.00 5.54
962 998 2.520741 GAGAGAGGGGAGAGGGCG 60.521 72.222 0.00 0.00 0.00 6.13
963 999 2.123033 GGAGAGAGGGGAGAGGGC 60.123 72.222 0.00 0.00 0.00 5.19
1216 1261 2.606826 GGAGGGGTCGACCTGGTT 60.607 66.667 32.52 16.19 42.10 3.67
1217 1262 4.716977 GGGAGGGGTCGACCTGGT 62.717 72.222 32.52 17.98 42.10 4.00
1268 1317 0.535553 CCCAACGAGACGGGGAAAAA 60.536 55.000 0.00 0.00 45.08 1.94
1305 1360 2.395690 GAATCACACGGCGCTTCG 59.604 61.111 6.90 5.82 0.00 3.79
1357 1412 1.876664 GAGCATCGGATCGGATCGA 59.123 57.895 12.50 12.13 41.13 3.59
1440 1496 3.244582 TGGCCCGTACAGTATTATCCAT 58.755 45.455 0.00 0.00 0.00 3.41
1441 1497 2.680251 TGGCCCGTACAGTATTATCCA 58.320 47.619 0.00 0.00 0.00 3.41
1442 1498 3.396560 GTTGGCCCGTACAGTATTATCC 58.603 50.000 0.00 0.00 0.00 2.59
1443 1499 3.070590 AGGTTGGCCCGTACAGTATTATC 59.929 47.826 0.00 0.00 38.74 1.75
1445 1501 2.431782 GAGGTTGGCCCGTACAGTATTA 59.568 50.000 0.00 0.00 38.74 0.98
1446 1502 1.208776 GAGGTTGGCCCGTACAGTATT 59.791 52.381 0.00 0.00 38.74 1.89
1447 1503 0.828677 GAGGTTGGCCCGTACAGTAT 59.171 55.000 0.00 0.00 38.74 2.12
1492 1554 1.632409 ACTGCAGACATCACCAGGAAT 59.368 47.619 23.35 0.00 0.00 3.01
1520 1586 0.955905 GCAAACCCAACCACATACGT 59.044 50.000 0.00 0.00 0.00 3.57
1521 1587 0.109964 CGCAAACCCAACCACATACG 60.110 55.000 0.00 0.00 0.00 3.06
1522 1588 0.955905 ACGCAAACCCAACCACATAC 59.044 50.000 0.00 0.00 0.00 2.39
1523 1589 2.152830 GTACGCAAACCCAACCACATA 58.847 47.619 0.00 0.00 0.00 2.29
1524 1590 0.955905 GTACGCAAACCCAACCACAT 59.044 50.000 0.00 0.00 0.00 3.21
1525 1591 0.107116 AGTACGCAAACCCAACCACA 60.107 50.000 0.00 0.00 0.00 4.17
1526 1592 0.309612 CAGTACGCAAACCCAACCAC 59.690 55.000 0.00 0.00 0.00 4.16
1527 1593 0.820074 CCAGTACGCAAACCCAACCA 60.820 55.000 0.00 0.00 0.00 3.67
1528 1594 0.820482 ACCAGTACGCAAACCCAACC 60.820 55.000 0.00 0.00 0.00 3.77
1529 1595 0.309612 CACCAGTACGCAAACCCAAC 59.690 55.000 0.00 0.00 0.00 3.77
1530 1596 0.107116 ACACCAGTACGCAAACCCAA 60.107 50.000 0.00 0.00 0.00 4.12
1533 1599 1.402613 ACAAACACCAGTACGCAAACC 59.597 47.619 0.00 0.00 0.00 3.27
1535 1601 5.049543 GGTTATACAAACACCAGTACGCAAA 60.050 40.000 0.00 0.00 0.00 3.68
1550 1616 2.568062 TCCACTGCCTTCGGTTATACAA 59.432 45.455 0.00 0.00 0.00 2.41
1559 1630 1.746615 CCCACATCCACTGCCTTCG 60.747 63.158 0.00 0.00 0.00 3.79
1564 1635 1.747355 CAGATTTCCCACATCCACTGC 59.253 52.381 0.00 0.00 0.00 4.40
1565 1636 1.747355 GCAGATTTCCCACATCCACTG 59.253 52.381 0.00 0.00 0.00 3.66
1566 1637 1.355381 TGCAGATTTCCCACATCCACT 59.645 47.619 0.00 0.00 0.00 4.00
1568 1639 2.658285 GATGCAGATTTCCCACATCCA 58.342 47.619 0.00 0.00 32.76 3.41
1577 1648 3.219176 TCCAGATGGGATGCAGATTTC 57.781 47.619 0.00 0.00 42.15 2.17
1590 1661 1.283029 ACCATGACAGGGTTCCAGATG 59.717 52.381 5.82 0.00 34.10 2.90
1591 1662 1.283029 CACCATGACAGGGTTCCAGAT 59.717 52.381 9.56 0.00 36.19 2.90
1592 1663 0.692476 CACCATGACAGGGTTCCAGA 59.308 55.000 9.56 0.00 36.19 3.86
1594 1665 0.110295 CACACCATGACAGGGTTCCA 59.890 55.000 9.56 0.00 36.19 3.53
1599 1670 0.179020 ACACACACACCATGACAGGG 60.179 55.000 4.17 4.17 0.00 4.45
1600 1671 0.946528 CACACACACACCATGACAGG 59.053 55.000 0.00 0.00 0.00 4.00
1603 1674 0.819259 AGGCACACACACACCATGAC 60.819 55.000 0.00 0.00 0.00 3.06
1605 1676 1.844771 CGAGGCACACACACACCATG 61.845 60.000 0.00 0.00 0.00 3.66
1611 1682 0.314302 ACTCTACGAGGCACACACAC 59.686 55.000 0.00 0.00 33.35 3.82
1612 1683 0.313987 CACTCTACGAGGCACACACA 59.686 55.000 0.00 0.00 33.35 3.72
1613 1684 0.314302 ACACTCTACGAGGCACACAC 59.686 55.000 0.00 0.00 33.35 3.82
1614 1685 0.596577 GACACTCTACGAGGCACACA 59.403 55.000 0.00 0.00 33.35 3.72
1615 1686 0.109226 GGACACTCTACGAGGCACAC 60.109 60.000 0.00 0.00 33.35 3.82
1616 1687 0.251209 AGGACACTCTACGAGGCACA 60.251 55.000 0.00 0.00 33.35 4.57
1626 1697 3.697045 CAGAATCGTAGGAAGGACACTCT 59.303 47.826 0.00 0.00 0.00 3.24
1627 1698 3.695060 TCAGAATCGTAGGAAGGACACTC 59.305 47.826 0.00 0.00 0.00 3.51
1637 1708 8.491152 GTGATGATAACAATTCAGAATCGTAGG 58.509 37.037 0.00 0.00 0.00 3.18
1641 1712 7.011763 ACCAGTGATGATAACAATTCAGAATCG 59.988 37.037 0.00 0.00 0.00 3.34
1643 1714 8.051535 AGACCAGTGATGATAACAATTCAGAAT 58.948 33.333 0.00 0.00 0.00 2.40
1644 1715 7.335171 CAGACCAGTGATGATAACAATTCAGAA 59.665 37.037 0.00 0.00 0.00 3.02
1656 1727 2.825223 TCAGTCCAGACCAGTGATGAT 58.175 47.619 0.00 0.00 0.00 2.45
1825 1897 4.095334 ACAACTTAACCGACAAGGACAAAC 59.905 41.667 0.00 0.00 45.00 2.93
1826 1898 4.263435 ACAACTTAACCGACAAGGACAAA 58.737 39.130 0.00 0.00 45.00 2.83
1829 1901 4.874970 TCTACAACTTAACCGACAAGGAC 58.125 43.478 0.00 0.00 45.00 3.85
1864 1962 2.751259 CAGCAGATTGGCAAGCTCTAAA 59.249 45.455 16.22 0.00 34.61 1.85
1868 1966 0.964358 ACCAGCAGATTGGCAAGCTC 60.964 55.000 16.22 10.56 42.18 4.09
1880 1983 5.812642 ACGAGAACATTATAAGAACCAGCAG 59.187 40.000 0.00 0.00 0.00 4.24
1903 2006 2.627699 TCTGATTGAGGGGCAAAAACAC 59.372 45.455 0.00 0.00 40.48 3.32
2039 2142 1.883926 TGAAAGACTCGATGACGGTGA 59.116 47.619 0.00 0.00 40.21 4.02
2043 2146 5.574830 AGAAAGAATGAAAGACTCGATGACG 59.425 40.000 0.00 0.00 41.26 4.35
2073 2176 4.349048 AGGGCTCATGCTCATGTCTTATTA 59.651 41.667 9.41 0.00 43.51 0.98
2076 2179 2.121948 AGGGCTCATGCTCATGTCTTA 58.878 47.619 9.41 0.00 43.51 2.10
2078 2181 0.917533 AAGGGCTCATGCTCATGTCT 59.082 50.000 9.41 2.21 43.51 3.41
2142 2245 2.843730 TGCTTAAGTCTGGAAGCCCATA 59.156 45.455 14.27 0.00 46.12 2.74
2179 2282 1.532437 GCATTTTCACTTTTGGCTGGC 59.468 47.619 0.00 0.00 0.00 4.85
2218 2321 2.294233 TGCAGCAGATTTTGAACAGGTC 59.706 45.455 0.00 0.00 0.00 3.85
2235 2338 2.301346 ACTTGTCAGTCCCTTTTGCAG 58.699 47.619 0.00 0.00 0.00 4.41
2239 2342 4.159693 GGAAACAACTTGTCAGTCCCTTTT 59.840 41.667 0.00 0.00 30.45 2.27
2247 2350 4.335315 TGTTGCTAGGAAACAACTTGTCAG 59.665 41.667 0.00 0.00 45.07 3.51
2263 2366 2.837591 TGGAGGTAAGATGCTGTTGCTA 59.162 45.455 0.00 0.00 40.48 3.49
2302 2405 2.746472 GCAGACCAAGTCTTGTGAAGGT 60.746 50.000 11.61 1.63 41.37 3.50
2392 2495 4.854924 TCGACCATGCATGCCCCG 62.855 66.667 21.69 20.80 0.00 5.73
2401 2504 1.021390 GCTTCCCACTGTCGACCATG 61.021 60.000 14.12 11.01 0.00 3.66
2478 2581 4.275689 TCGTCAACTGTGCTTTTGATGATT 59.724 37.500 2.78 0.00 40.98 2.57
2499 2602 1.028330 ATCCATGCTGGCAGTTGTCG 61.028 55.000 17.16 3.40 37.47 4.35
2534 2637 7.663043 TGGTTAGTTTCCAAACAGGTAAATT 57.337 32.000 5.03 0.00 41.30 1.82
2571 2674 2.203181 GCTCCAGATCAGGGCTGC 60.203 66.667 4.05 3.48 32.06 5.25
2572 2675 0.034767 TTTGCTCCAGATCAGGGCTG 60.035 55.000 15.26 4.48 0.00 4.85
2575 2678 1.004044 ACACTTTGCTCCAGATCAGGG 59.996 52.381 4.05 0.39 0.00 4.45
2633 2736 4.624452 GCTTTTCTTTGCTTTGCTAGGATG 59.376 41.667 0.00 0.00 0.00 3.51
2823 2926 3.136443 AGATGGTGGTTTGTCACTCTCAA 59.864 43.478 0.00 0.00 37.75 3.02
2850 2953 2.101082 TCAGACAGCATCTCATCAGAGC 59.899 50.000 0.00 0.00 41.81 4.09
2860 2963 3.815856 TCCTTCTCATCAGACAGCATC 57.184 47.619 0.00 0.00 0.00 3.91
2893 2996 7.294720 TGATTAAACCCATACAGGTCTGGATAT 59.705 37.037 5.49 0.00 40.05 1.63
2935 3038 3.500642 GCTTCTTCCCTTCGGCGC 61.501 66.667 0.00 0.00 0.00 6.53
2943 3046 4.225497 CCACATCGGCTTCTTCCC 57.775 61.111 0.00 0.00 0.00 3.97
2962 3065 1.880027 GGCGACAAGAACCAATCAAGT 59.120 47.619 0.00 0.00 0.00 3.16
2968 3071 1.072505 GAGGGGCGACAAGAACCAA 59.927 57.895 0.00 0.00 0.00 3.67
3050 3153 9.401058 AGGACTTTCTATCAAGGATTTGTTATG 57.599 33.333 0.00 0.00 35.73 1.90
3085 3188 3.380004 CCAGCTTATTATTGCGTTCCCAA 59.620 43.478 0.00 0.00 0.00 4.12
3092 3195 3.126001 TCCCTCCAGCTTATTATTGCG 57.874 47.619 0.00 0.00 0.00 4.85
3136 3239 1.831736 ACCGACAGAGTTTGGATAGGG 59.168 52.381 0.00 0.00 0.00 3.53
3151 3254 2.472909 GGCCTTGCTATGCACCGAC 61.473 63.158 0.00 0.00 38.71 4.79
3186 3289 0.700564 ATTGCTTTCCAGGCCTCTCA 59.299 50.000 0.00 0.00 0.00 3.27
3189 3292 1.751351 GGTTATTGCTTTCCAGGCCTC 59.249 52.381 0.00 0.00 0.00 4.70
3340 3443 2.094078 CCAGAGCTCCTTCTTGAGAGTG 60.094 54.545 10.93 0.00 34.11 3.51
3483 3586 2.294512 CAGAAAGAAACAAGTGCCCTCC 59.705 50.000 0.00 0.00 0.00 4.30
3602 3713 2.365582 ACCCGTTGCTGATCCATTTAC 58.634 47.619 0.00 0.00 0.00 2.01
3604 3715 1.818674 GAACCCGTTGCTGATCCATTT 59.181 47.619 0.00 0.00 0.00 2.32
3626 3737 4.244802 CGAGAGCCCGCGAGACTC 62.245 72.222 8.23 11.43 37.82 3.36
3641 3752 0.320858 TATTGAACACAAGGCGGCGA 60.321 50.000 12.98 0.00 0.00 5.54
3718 3829 3.434637 ACACAACAACAGTTTTCGCATC 58.565 40.909 0.00 0.00 0.00 3.91
3719 3830 3.502191 ACACAACAACAGTTTTCGCAT 57.498 38.095 0.00 0.00 0.00 4.73
3720 3831 2.999507 ACACAACAACAGTTTTCGCA 57.000 40.000 0.00 0.00 0.00 5.10
3721 3832 4.026407 GTCTACACAACAACAGTTTTCGC 58.974 43.478 0.00 0.00 0.00 4.70
3722 3833 5.211266 TGTCTACACAACAACAGTTTTCG 57.789 39.130 0.00 0.00 0.00 3.46
3723 3834 5.971202 CCATGTCTACACAACAACAGTTTTC 59.029 40.000 0.00 0.00 35.64 2.29
3834 3951 4.374399 CAGAAAAGCACATCAAGCCTTTT 58.626 39.130 0.00 0.00 0.00 2.27
3891 4008 0.319083 CCATGCTTGTTGTGGCACAT 59.681 50.000 22.73 0.72 44.52 3.21
3906 4023 9.060347 AGTAAGATTAACTGCATATCAACCATG 57.940 33.333 0.00 0.00 0.00 3.66
3908 4025 9.764363 CTAGTAAGATTAACTGCATATCAACCA 57.236 33.333 0.00 0.00 0.00 3.67
3909 4026 9.982651 TCTAGTAAGATTAACTGCATATCAACC 57.017 33.333 0.00 0.00 0.00 3.77
3934 4067 2.427453 TCAACTGAGCTAGACGGGAATC 59.573 50.000 0.00 0.00 0.00 2.52
3937 4070 1.919240 TTCAACTGAGCTAGACGGGA 58.081 50.000 0.00 0.00 0.00 5.14
4029 4162 8.764287 CACGATAAATCATGTTAACTGATGCTA 58.236 33.333 16.33 12.67 33.69 3.49
4052 4185 3.481951 CGTGACCTTCGATTGATTTCACG 60.482 47.826 19.22 19.22 40.96 4.35
4062 4195 3.062042 GTTAACCAACGTGACCTTCGAT 58.938 45.455 0.00 0.00 0.00 3.59
4080 4213 9.582431 GACTTCTGTTATACTATGTTGCAGTTA 57.418 33.333 0.00 0.00 0.00 2.24
4083 4216 8.709386 AAGACTTCTGTTATACTATGTTGCAG 57.291 34.615 0.00 0.00 0.00 4.41
4174 4312 9.072294 AGTTAAAACTTCAAACATTTCAGAACG 57.928 29.630 0.00 0.00 35.21 3.95
4192 4330 7.101054 AGTTTGACCCAGGAAAAAGTTAAAAC 58.899 34.615 0.00 0.00 0.00 2.43
4203 4341 7.669089 AATCTTAAAAAGTTTGACCCAGGAA 57.331 32.000 0.00 0.00 0.00 3.36
4208 4346 9.541143 TTGATCAAATCTTAAAAAGTTTGACCC 57.459 29.630 5.45 11.37 39.23 4.46
4262 4400 9.921637 GAATCCAATGAAACTAATTTGGTGTTA 57.078 29.630 0.00 0.00 0.00 2.41
4308 4446 8.665643 TCGAAGTTATACTTTTTCTGTTCCAA 57.334 30.769 0.00 0.00 38.80 3.53
4322 4460 5.348986 TCAGCCACAGATTCGAAGTTATAC 58.651 41.667 3.35 0.00 0.00 1.47
4323 4461 5.592104 TCAGCCACAGATTCGAAGTTATA 57.408 39.130 3.35 0.00 0.00 0.98
4324 4462 4.471904 TCAGCCACAGATTCGAAGTTAT 57.528 40.909 3.35 0.00 0.00 1.89
4331 4471 2.349590 TGAACATCAGCCACAGATTCG 58.650 47.619 0.00 0.00 0.00 3.34
4420 4567 1.606668 CAGCTTTTAGGTCGTTTGCCA 59.393 47.619 0.00 0.00 0.00 4.92
4424 4571 3.547746 TCCAACAGCTTTTAGGTCGTTT 58.452 40.909 0.00 0.00 0.00 3.60
4439 4586 3.080319 TGCGTTTGATCATGATCCAACA 58.920 40.909 34.20 22.27 41.09 3.33


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

AutoCloner maintained by Alex Coulton.