Multiple sequence alignment - TraesCS7B01G072600

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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 TraesCS7B01G072600 chr7B 100.000 2859 0 0 1 2859 80515418 80512560 0.000000e+00 5280
1 TraesCS7B01G072600 chr7B 81.211 644 102 17 1926 2555 448415977 448416615 4.250000e-138 501
2 TraesCS7B01G072600 chr7D 89.125 1177 66 28 764 1912 119106271 119105129 0.000000e+00 1408
3 TraesCS7B01G072600 chr7D 91.623 764 54 7 1 761 119108341 119107585 0.000000e+00 1048
4 TraesCS7B01G072600 chr7A 87.551 731 45 24 1219 1931 123264988 123264286 0.000000e+00 804
5 TraesCS7B01G072600 chr7A 89.908 327 22 4 654 974 123270994 123270673 7.370000e-111 411
6 TraesCS7B01G072600 chr7A 94.977 219 11 0 1005 1223 123270671 123270453 7.580000e-91 344
7 TraesCS7B01G072600 chr7A 89.071 183 20 0 1 183 123271961 123271779 7.970000e-56 228
8 TraesCS7B01G072600 chr5D 81.555 656 102 13 1920 2559 382425115 382425767 9.080000e-145 523
9 TraesCS7B01G072600 chr2A 81.776 642 97 12 1930 2555 66767196 66767833 1.170000e-143 520
10 TraesCS7B01G072600 chr4B 81.550 645 97 14 1929 2555 183523391 183522751 1.960000e-141 512
11 TraesCS7B01G072600 chr4B 80.542 627 104 13 1933 2543 16800423 16799799 1.550000e-127 466
12 TraesCS7B01G072600 chr1A 81.411 581 90 13 1930 2494 536931868 536932446 2.600000e-125 459
13 TraesCS7B01G072600 chr1A 86.066 244 26 6 1032 1268 528063723 528063965 3.660000e-64 255
14 TraesCS7B01G072600 chr3D 79.937 638 105 19 1933 2555 422941933 422942562 5.620000e-122 448
15 TraesCS7B01G072600 chr3D 75.894 643 137 17 1929 2559 85222978 85223614 2.140000e-81 313
16 TraesCS7B01G072600 chr2B 81.217 575 91 10 1996 2555 126170158 126170730 5.620000e-122 448
17 TraesCS7B01G072600 chr4D 80.375 586 97 11 1930 2499 460648550 460649133 2.040000e-116 429
18 TraesCS7B01G072600 chr1B 78.497 572 108 15 1992 2555 10544281 10544845 7.530000e-96 361
19 TraesCS7B01G072600 chr1B 76.948 616 119 17 1943 2541 507385281 507384672 2.120000e-86 329
20 TraesCS7B01G072600 chr1B 85.597 243 29 5 1032 1268 581412188 581412430 1.700000e-62 250
21 TraesCS7B01G072600 chr6D 82.927 369 58 5 2201 2566 46611677 46612043 7.640000e-86 327
22 TraesCS7B01G072600 chr1D 86.066 244 26 6 1032 1268 430466519 430466761 3.660000e-64 255
23 TraesCS7B01G072600 chr4A 78.176 307 57 9 1926 2227 579074014 579073713 1.350000e-43 187


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 TraesCS7B01G072600 chr7B 80512560 80515418 2858 True 5280.000000 5280 100.000000 1 2859 1 chr7B.!!$R1 2858
1 TraesCS7B01G072600 chr7B 448415977 448416615 638 False 501.000000 501 81.211000 1926 2555 1 chr7B.!!$F1 629
2 TraesCS7B01G072600 chr7D 119105129 119108341 3212 True 1228.000000 1408 90.374000 1 1912 2 chr7D.!!$R1 1911
3 TraesCS7B01G072600 chr7A 123264286 123264988 702 True 804.000000 804 87.551000 1219 1931 1 chr7A.!!$R1 712
4 TraesCS7B01G072600 chr7A 123270453 123271961 1508 True 327.666667 411 91.318667 1 1223 3 chr7A.!!$R2 1222
5 TraesCS7B01G072600 chr5D 382425115 382425767 652 False 523.000000 523 81.555000 1920 2559 1 chr5D.!!$F1 639
6 TraesCS7B01G072600 chr2A 66767196 66767833 637 False 520.000000 520 81.776000 1930 2555 1 chr2A.!!$F1 625
7 TraesCS7B01G072600 chr4B 183522751 183523391 640 True 512.000000 512 81.550000 1929 2555 1 chr4B.!!$R2 626
8 TraesCS7B01G072600 chr4B 16799799 16800423 624 True 466.000000 466 80.542000 1933 2543 1 chr4B.!!$R1 610
9 TraesCS7B01G072600 chr1A 536931868 536932446 578 False 459.000000 459 81.411000 1930 2494 1 chr1A.!!$F2 564
10 TraesCS7B01G072600 chr3D 422941933 422942562 629 False 448.000000 448 79.937000 1933 2555 1 chr3D.!!$F2 622
11 TraesCS7B01G072600 chr3D 85222978 85223614 636 False 313.000000 313 75.894000 1929 2559 1 chr3D.!!$F1 630
12 TraesCS7B01G072600 chr2B 126170158 126170730 572 False 448.000000 448 81.217000 1996 2555 1 chr2B.!!$F1 559
13 TraesCS7B01G072600 chr4D 460648550 460649133 583 False 429.000000 429 80.375000 1930 2499 1 chr4D.!!$F1 569
14 TraesCS7B01G072600 chr1B 10544281 10544845 564 False 361.000000 361 78.497000 1992 2555 1 chr1B.!!$F1 563
15 TraesCS7B01G072600 chr1B 507384672 507385281 609 True 329.000000 329 76.948000 1943 2541 1 chr1B.!!$R1 598

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
862 2535 0.39034 CAGTCAGTGTCCCATCGGTG 60.39 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 4573 0.034186 CCCAACTAGCCATGCCTGAA 60.034 55.0 0.0 0.0 0.0 3.02 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 1.523938 GAGCCCGCTCGCCTTTTAT 60.524 57.895 0.04 0.00 33.06 1.40
22 23 1.499688 GAGCCCGCTCGCCTTTTATC 61.500 60.000 0.04 0.00 33.06 1.75
30 31 2.073816 CTCGCCTTTTATCACGGTGTT 58.926 47.619 8.17 2.24 0.00 3.32
57 58 2.283298 CTAGTACTCGTCCGTAGCCAA 58.717 52.381 0.00 0.00 0.00 4.52
58 59 0.807496 AGTACTCGTCCGTAGCCAAC 59.193 55.000 0.00 0.00 0.00 3.77
67 68 2.166664 GTCCGTAGCCAACTCTCAAGAT 59.833 50.000 0.00 0.00 0.00 2.40
167 168 3.389329 TCAGGCTTCTCACTTTTGTCTCT 59.611 43.478 0.00 0.00 0.00 3.10
207 208 8.306761 CAGGCTTTTGAGTAAATATTTGGTCTT 58.693 33.333 11.05 0.00 0.00 3.01
213 214 5.885912 TGAGTAAATATTTGGTCTTCAGGCC 59.114 40.000 11.05 0.00 0.00 5.19
230 231 0.965439 GCCAGGCTCGATCTAGACAT 59.035 55.000 3.29 0.00 0.00 3.06
235 236 4.047822 CAGGCTCGATCTAGACATTTGAC 58.952 47.826 2.48 0.00 0.00 3.18
236 237 3.957497 AGGCTCGATCTAGACATTTGACT 59.043 43.478 2.48 0.00 0.00 3.41
249 250 7.169158 AGACATTTGACTTTTGGACTTTTGA 57.831 32.000 0.00 0.00 0.00 2.69
308 309 8.515414 GCTAGACACTTGATTTAAAAAGGTGAT 58.485 33.333 17.79 11.01 0.00 3.06
380 381 9.654417 TTTTTGTTTAGCTCGATGTTAACTTAC 57.346 29.630 7.22 0.00 0.00 2.34
502 507 9.677567 GTGAACTATTTGAAATAAAGTGCTCAA 57.322 29.630 0.00 0.00 0.00 3.02
506 696 6.973229 ATTTGAAATAAAGTGCTCAATGGC 57.027 33.333 0.00 0.00 0.00 4.40
591 781 4.163458 AGGACACGTACCATGACCAATATT 59.837 41.667 13.30 0.00 34.75 1.28
647 964 5.248640 ACACTTCCACTGAATATTCCACAG 58.751 41.667 12.90 7.00 37.62 3.66
658 1020 5.936372 TGAATATTCCACAGCATGCTAGATC 59.064 40.000 22.19 11.83 42.53 2.75
755 1117 4.965814 TGAGCTTTTGACTTGACTCTGAT 58.034 39.130 0.00 0.00 0.00 2.90
788 2461 4.844998 TCCAAGTTTGCATTCGATTTCA 57.155 36.364 0.00 0.00 0.00 2.69
792 2465 6.150976 TCCAAGTTTGCATTCGATTTCACTAT 59.849 34.615 0.00 0.00 0.00 2.12
803 2476 5.604565 TCGATTTCACTATGCATGTCATCT 58.395 37.500 10.16 0.00 36.63 2.90
804 2477 6.051074 TCGATTTCACTATGCATGTCATCTT 58.949 36.000 10.16 0.00 36.63 2.40
807 2480 7.383300 CGATTTCACTATGCATGTCATCTTAGA 59.617 37.037 10.16 0.00 36.63 2.10
813 2486 7.169476 CACTATGCATGTCATCTTAGAACTCTG 59.831 40.741 10.16 0.00 36.63 3.35
862 2535 0.390340 CAGTCAGTGTCCCATCGGTG 60.390 60.000 0.00 0.00 0.00 4.94
863 2536 1.079127 GTCAGTGTCCCATCGGTGG 60.079 63.158 8.08 8.08 45.61 4.61
884 2557 1.743252 GGAAGGCTCCGTGAAGCTG 60.743 63.158 0.00 0.00 42.13 4.24
900 2573 0.654683 GCTGCAGCATACGGAAGAAG 59.345 55.000 33.36 0.00 41.59 2.85
901 2574 1.293924 CTGCAGCATACGGAAGAAGG 58.706 55.000 0.00 0.00 0.00 3.46
904 2577 1.521681 AGCATACGGAAGAAGGCGC 60.522 57.895 0.00 0.00 0.00 6.53
954 2640 0.737367 TTGCCATGAGCTTCTCGTCG 60.737 55.000 0.00 0.00 44.23 5.12
955 2641 1.880340 GCCATGAGCTTCTCGTCGG 60.880 63.158 0.00 0.00 38.99 4.79
956 2642 1.880340 CCATGAGCTTCTCGTCGGC 60.880 63.158 0.00 0.00 32.35 5.54
961 2647 2.433318 GCTTCTCGTCGGCAAGCT 60.433 61.111 17.07 0.00 39.61 3.74
963 2649 1.960994 GCTTCTCGTCGGCAAGCTTC 61.961 60.000 17.07 0.00 39.61 3.86
975 2661 1.478631 CAAGCTTCCTCCCATTTCCC 58.521 55.000 0.00 0.00 0.00 3.97
978 2664 1.609783 CTTCCTCCCATTTCCCGCT 59.390 57.895 0.00 0.00 0.00 5.52
979 2665 0.464554 CTTCCTCCCATTTCCCGCTC 60.465 60.000 0.00 0.00 0.00 5.03
980 2666 1.921869 TTCCTCCCATTTCCCGCTCC 61.922 60.000 0.00 0.00 0.00 4.70
1359 3048 3.536917 CACCCCTATCTGCGCCGA 61.537 66.667 4.18 3.73 0.00 5.54
1370 3059 3.181290 GCGCCGATTTGCTTTGCC 61.181 61.111 0.00 0.00 0.00 4.52
1474 3163 1.895798 TCGTGAGTCTTCTGCCTGAAT 59.104 47.619 0.00 0.00 33.71 2.57
1475 3164 2.300152 TCGTGAGTCTTCTGCCTGAATT 59.700 45.455 0.00 0.00 33.71 2.17
1476 3165 3.070018 CGTGAGTCTTCTGCCTGAATTT 58.930 45.455 0.00 0.00 33.71 1.82
1477 3166 3.499918 CGTGAGTCTTCTGCCTGAATTTT 59.500 43.478 0.00 0.00 33.71 1.82
1478 3167 4.612259 CGTGAGTCTTCTGCCTGAATTTTG 60.612 45.833 0.00 0.00 33.71 2.44
1479 3168 4.276926 GTGAGTCTTCTGCCTGAATTTTGT 59.723 41.667 0.00 0.00 33.71 2.83
1480 3169 4.889409 TGAGTCTTCTGCCTGAATTTTGTT 59.111 37.500 0.00 0.00 33.71 2.83
1481 3170 5.360714 TGAGTCTTCTGCCTGAATTTTGTTT 59.639 36.000 0.00 0.00 33.71 2.83
1482 3171 6.545666 TGAGTCTTCTGCCTGAATTTTGTTTA 59.454 34.615 0.00 0.00 33.71 2.01
1483 3172 7.231317 TGAGTCTTCTGCCTGAATTTTGTTTAT 59.769 33.333 0.00 0.00 33.71 1.40
1484 3173 7.373493 AGTCTTCTGCCTGAATTTTGTTTATG 58.627 34.615 0.00 0.00 33.71 1.90
1485 3174 6.089954 GTCTTCTGCCTGAATTTTGTTTATGC 59.910 38.462 0.00 0.00 33.71 3.14
1486 3175 4.484236 TCTGCCTGAATTTTGTTTATGCG 58.516 39.130 0.00 0.00 0.00 4.73
1487 3176 4.217334 TCTGCCTGAATTTTGTTTATGCGA 59.783 37.500 0.00 0.00 0.00 5.10
1488 3177 5.070770 TGCCTGAATTTTGTTTATGCGAT 57.929 34.783 0.00 0.00 0.00 4.58
1489 3178 6.094742 TCTGCCTGAATTTTGTTTATGCGATA 59.905 34.615 0.00 0.00 0.00 2.92
1490 3179 6.804677 TGCCTGAATTTTGTTTATGCGATAT 58.195 32.000 0.00 0.00 0.00 1.63
1491 3180 6.917477 TGCCTGAATTTTGTTTATGCGATATC 59.083 34.615 0.00 0.00 0.00 1.63
1492 3181 7.141363 GCCTGAATTTTGTTTATGCGATATCT 58.859 34.615 0.34 0.00 0.00 1.98
1493 3182 7.113965 GCCTGAATTTTGTTTATGCGATATCTG 59.886 37.037 0.34 0.00 0.00 2.90
1494 3183 7.113965 CCTGAATTTTGTTTATGCGATATCTGC 59.886 37.037 11.16 11.16 0.00 4.26
1495 3184 6.917477 TGAATTTTGTTTATGCGATATCTGCC 59.083 34.615 14.20 2.91 0.00 4.85
1496 3185 6.639632 ATTTTGTTTATGCGATATCTGCCT 57.360 33.333 14.20 8.92 0.00 4.75
1497 3186 5.422666 TTTGTTTATGCGATATCTGCCTG 57.577 39.130 14.20 0.00 0.00 4.85
1498 3187 4.335400 TGTTTATGCGATATCTGCCTGA 57.665 40.909 14.20 2.54 0.00 3.86
1499 3188 4.702831 TGTTTATGCGATATCTGCCTGAA 58.297 39.130 14.20 7.24 0.00 3.02
1507 3196 5.221521 TGCGATATCTGCCTGAATTAACTCT 60.222 40.000 14.20 0.00 0.00 3.24
1580 3269 4.166888 TGCCGCATCTGAGCCTCC 62.167 66.667 0.00 0.00 0.00 4.30
1726 3415 1.722034 AGGACAAGAGCTTGGAGTCA 58.278 50.000 14.14 0.00 44.45 3.41
1803 3512 3.794737 CATGCTGCCATGTACTCCT 57.205 52.632 0.00 0.00 43.07 3.69
1804 3513 2.916702 CATGCTGCCATGTACTCCTA 57.083 50.000 0.00 0.00 43.07 2.94
1805 3514 2.487934 CATGCTGCCATGTACTCCTAC 58.512 52.381 0.00 0.00 43.07 3.18
1806 3515 1.866015 TGCTGCCATGTACTCCTACT 58.134 50.000 0.00 0.00 0.00 2.57
1807 3516 1.757118 TGCTGCCATGTACTCCTACTC 59.243 52.381 0.00 0.00 0.00 2.59
1813 3522 5.706447 TGCCATGTACTCCTACTCTCTATT 58.294 41.667 0.00 0.00 0.00 1.73
1821 3530 6.472686 ACTCCTACTCTCTATTTTTGCGAT 57.527 37.500 0.00 0.00 0.00 4.58
1852 3564 7.329226 GTGTACGTGTAGTAATAACCACATGTT 59.671 37.037 0.00 0.00 42.47 2.71
1856 3568 8.711457 ACGTGTAGTAATAACCACATGTTTAAC 58.289 33.333 0.00 0.00 42.47 2.01
1881 3597 1.077858 CCTGGAGCCCTTCTGCTTC 60.078 63.158 0.00 0.00 42.95 3.86
1897 3613 8.624776 CCTTCTGCTTCGAATAAGGAAATAATT 58.375 33.333 17.36 0.00 39.26 1.40
1931 3650 5.340803 GGTTGGAACTGTTTTGTCTTCTTC 58.659 41.667 0.00 0.00 0.00 2.87
1949 3668 7.426743 GTCTTCTTCTTTGTCGAGAAAACTTTG 59.573 37.037 9.21 0.00 35.38 2.77
1982 3701 9.878667 TTCATTTTCAATTATGGTAGTACGAGA 57.121 29.630 0.00 0.00 0.00 4.04
2027 3748 2.619177 CACCCAGATCGTAGACCACTAG 59.381 54.545 0.00 0.00 42.51 2.57
2035 3756 1.089920 GTAGACCACTAGGCGACGAA 58.910 55.000 0.00 0.00 39.06 3.85
2049 3770 2.472397 GCGACGAATACAAGCACTGAAC 60.472 50.000 0.00 0.00 0.00 3.18
2053 3774 2.734606 CGAATACAAGCACTGAACCGAA 59.265 45.455 0.00 0.00 0.00 4.30
2106 3828 4.517285 CTCATGGAGCCTAGCAAAACTTA 58.483 43.478 0.00 0.00 0.00 2.24
2123 3848 7.115947 GCAAAACTTATTGTAGTAGACAGTCGT 59.884 37.037 0.00 0.00 39.88 4.34
2135 3861 4.848562 AGACAGTCGTGAAGTTGTCATA 57.151 40.909 6.29 0.00 41.74 2.15
2142 3868 4.863131 GTCGTGAAGTTGTCATACTAAGGG 59.137 45.833 0.00 0.00 38.90 3.95
2143 3869 4.768448 TCGTGAAGTTGTCATACTAAGGGA 59.232 41.667 0.00 0.00 38.90 4.20
2147 3874 4.820894 AGTTGTCATACTAAGGGACCAC 57.179 45.455 0.00 0.00 0.00 4.16
2153 3880 3.012502 TCATACTAAGGGACCACAGGACT 59.987 47.826 0.00 0.00 0.00 3.85
2198 3925 2.602694 GCCGATGAAGAGTAGCGTAGAC 60.603 54.545 0.00 0.00 0.00 2.59
2288 4026 3.916392 GAGACACGCCTCCACACGG 62.916 68.421 0.00 0.00 0.00 4.94
2314 4052 2.735444 CGACGATGCTAGACACACCATT 60.735 50.000 0.00 0.00 0.00 3.16
2329 4067 4.385358 CACCATTAAAACTGGGGTATGC 57.615 45.455 0.00 0.00 38.14 3.14
2359 4099 4.978388 ACCTTATTCCATCTTTAGGGAGCT 59.022 41.667 0.00 0.00 36.79 4.09
2365 4105 2.093447 CCATCTTTAGGGAGCTGTCGTT 60.093 50.000 0.00 0.00 0.00 3.85
2373 4113 0.318784 GGAGCTGTCGTTGTCTCGTT 60.319 55.000 0.00 0.00 0.00 3.85
2380 4120 3.635331 TGTCGTTGTCTCGTTTTCCTAG 58.365 45.455 0.00 0.00 0.00 3.02
2417 4157 7.064229 ACCCTAACAAAACTTGAAGGAACATA 58.936 34.615 0.00 0.00 38.65 2.29
2434 4174 4.574674 ACATATGAAAACAGAGCCCTCA 57.425 40.909 10.38 0.00 0.00 3.86
2489 4230 2.053618 CCCTAAGGCCATCGGAGAG 58.946 63.158 5.01 0.00 43.63 3.20
2494 4235 2.123251 GGCCATCGGAGAGGAGGA 60.123 66.667 0.00 0.00 43.16 3.71
2548 4289 2.206223 ACCCTAGGCTTTTCTAAGGGG 58.794 52.381 19.47 9.03 36.04 4.79
2551 4292 2.439880 CCTAGGCTTTTCTAAGGGGAGG 59.560 54.545 0.00 0.00 31.76 4.30
2552 4293 2.361085 AGGCTTTTCTAAGGGGAGGA 57.639 50.000 0.00 0.00 31.76 3.71
2556 4297 1.213182 CTTTTCTAAGGGGAGGAGGGC 59.787 57.143 0.00 0.00 0.00 5.19
2558 4299 2.844839 CTAAGGGGAGGAGGGCGG 60.845 72.222 0.00 0.00 0.00 6.13
2559 4300 3.691326 TAAGGGGAGGAGGGCGGT 61.691 66.667 0.00 0.00 0.00 5.68
2560 4301 3.262778 TAAGGGGAGGAGGGCGGTT 62.263 63.158 0.00 0.00 0.00 4.44
2563 4304 4.410400 GGGAGGAGGGCGGTTGTG 62.410 72.222 0.00 0.00 0.00 3.33
2564 4305 3.637273 GGAGGAGGGCGGTTGTGT 61.637 66.667 0.00 0.00 0.00 3.72
2565 4306 2.358737 GAGGAGGGCGGTTGTGTG 60.359 66.667 0.00 0.00 0.00 3.82
2566 4307 3.901797 GAGGAGGGCGGTTGTGTGG 62.902 68.421 0.00 0.00 0.00 4.17
2567 4308 4.265056 GGAGGGCGGTTGTGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
2568 4309 2.745037 GAGGGCGGTTGTGTGGTA 59.255 61.111 0.00 0.00 0.00 3.25
2569 4310 1.071814 GAGGGCGGTTGTGTGGTAA 59.928 57.895 0.00 0.00 0.00 2.85
2570 4311 1.228033 AGGGCGGTTGTGTGGTAAC 60.228 57.895 0.00 0.00 0.00 2.50
2571 4312 1.228033 GGGCGGTTGTGTGGTAACT 60.228 57.895 0.00 0.00 37.61 2.24
2572 4313 0.035176 GGGCGGTTGTGTGGTAACTA 59.965 55.000 0.00 0.00 37.61 2.24
2573 4314 1.339342 GGGCGGTTGTGTGGTAACTAT 60.339 52.381 0.00 0.00 37.61 2.12
2574 4315 2.429478 GGCGGTTGTGTGGTAACTATT 58.571 47.619 0.00 0.00 37.61 1.73
2575 4316 2.815503 GGCGGTTGTGTGGTAACTATTT 59.184 45.455 0.00 0.00 37.61 1.40
2576 4317 3.253921 GGCGGTTGTGTGGTAACTATTTT 59.746 43.478 0.00 0.00 37.61 1.82
2577 4318 4.223659 GCGGTTGTGTGGTAACTATTTTG 58.776 43.478 0.00 0.00 37.61 2.44
2578 4319 4.261280 GCGGTTGTGTGGTAACTATTTTGT 60.261 41.667 0.00 0.00 37.61 2.83
2579 4320 5.445845 CGGTTGTGTGGTAACTATTTTGTC 58.554 41.667 0.00 0.00 37.61 3.18
2580 4321 5.237779 CGGTTGTGTGGTAACTATTTTGTCT 59.762 40.000 0.00 0.00 37.61 3.41
2581 4322 6.238538 CGGTTGTGTGGTAACTATTTTGTCTT 60.239 38.462 0.00 0.00 37.61 3.01
2582 4323 7.136772 GGTTGTGTGGTAACTATTTTGTCTTC 58.863 38.462 0.00 0.00 37.61 2.87
2583 4324 7.012989 GGTTGTGTGGTAACTATTTTGTCTTCT 59.987 37.037 0.00 0.00 37.61 2.85
2584 4325 8.403236 GTTGTGTGGTAACTATTTTGTCTTCTT 58.597 33.333 0.00 0.00 37.61 2.52
2585 4326 9.616156 TTGTGTGGTAACTATTTTGTCTTCTTA 57.384 29.630 0.00 0.00 37.61 2.10
2586 4327 9.616156 TGTGTGGTAACTATTTTGTCTTCTTAA 57.384 29.630 0.00 0.00 37.61 1.85
2599 4340 8.715191 TTTGTCTTCTTAAATGTGCAAAATGT 57.285 26.923 0.00 0.00 0.00 2.71
2600 4341 8.715191 TTGTCTTCTTAAATGTGCAAAATGTT 57.285 26.923 0.00 0.00 0.00 2.71
2601 4342 8.715191 TGTCTTCTTAAATGTGCAAAATGTTT 57.285 26.923 0.00 0.00 0.00 2.83
2602 4343 9.160496 TGTCTTCTTAAATGTGCAAAATGTTTT 57.840 25.926 0.00 0.00 0.00 2.43
2603 4344 9.636965 GTCTTCTTAAATGTGCAAAATGTTTTC 57.363 29.630 0.00 0.00 0.00 2.29
2604 4345 9.376075 TCTTCTTAAATGTGCAAAATGTTTTCA 57.624 25.926 0.00 0.00 0.00 2.69
2605 4346 9.985318 CTTCTTAAATGTGCAAAATGTTTTCAA 57.015 25.926 0.00 0.00 0.00 2.69
2606 4347 9.985318 TTCTTAAATGTGCAAAATGTTTTCAAG 57.015 25.926 0.00 0.00 0.00 3.02
2607 4348 9.160496 TCTTAAATGTGCAAAATGTTTTCAAGT 57.840 25.926 0.00 0.00 0.00 3.16
2613 4354 9.719279 ATGTGCAAAATGTTTTCAAGTATTTTG 57.281 25.926 13.83 13.83 45.92 2.44
2614 4355 8.725148 TGTGCAAAATGTTTTCAAGTATTTTGT 58.275 25.926 17.36 0.00 45.38 2.83
2615 4356 8.997960 GTGCAAAATGTTTTCAAGTATTTTGTG 58.002 29.630 17.36 1.42 45.38 3.33
2616 4357 8.939929 TGCAAAATGTTTTCAAGTATTTTGTGA 58.060 25.926 17.36 6.92 45.38 3.58
2617 4358 9.424659 GCAAAATGTTTTCAAGTATTTTGTGAG 57.575 29.630 17.36 0.14 45.38 3.51
2622 4363 9.736023 ATGTTTTCAAGTATTTTGTGAGAACTC 57.264 29.630 7.52 0.00 37.31 3.01
2623 4364 7.908082 TGTTTTCAAGTATTTTGTGAGAACTCG 59.092 33.333 7.52 0.00 37.31 4.18
2624 4365 5.591643 TCAAGTATTTTGTGAGAACTCGC 57.408 39.130 8.23 8.23 40.32 5.03
2625 4366 5.053811 TCAAGTATTTTGTGAGAACTCGCA 58.946 37.500 13.04 13.04 46.99 5.10
2632 4373 3.607422 TGTGAGAACTCGCAAAACATG 57.393 42.857 14.39 0.00 45.85 3.21
2633 4374 2.942376 TGTGAGAACTCGCAAAACATGT 59.058 40.909 14.39 0.00 45.85 3.21
2634 4375 3.376859 TGTGAGAACTCGCAAAACATGTT 59.623 39.130 14.39 4.92 45.85 2.71
2635 4376 4.142491 TGTGAGAACTCGCAAAACATGTTT 60.142 37.500 18.13 18.13 45.85 2.83
2636 4377 5.065346 TGTGAGAACTCGCAAAACATGTTTA 59.935 36.000 23.53 7.73 45.85 2.01
2637 4378 6.142817 GTGAGAACTCGCAAAACATGTTTAT 58.857 36.000 23.53 11.41 39.72 1.40
2638 4379 6.086765 GTGAGAACTCGCAAAACATGTTTATG 59.913 38.462 23.53 21.43 39.72 1.90
2639 4380 6.017523 TGAGAACTCGCAAAACATGTTTATGA 60.018 34.615 23.53 18.56 37.73 2.15
2640 4381 6.913170 AGAACTCGCAAAACATGTTTATGAT 58.087 32.000 23.53 5.84 37.73 2.45
2641 4382 7.370383 AGAACTCGCAAAACATGTTTATGATT 58.630 30.769 23.53 13.14 37.73 2.57
2642 4383 7.538678 AGAACTCGCAAAACATGTTTATGATTC 59.461 33.333 23.53 19.41 37.73 2.52
2643 4384 6.676950 ACTCGCAAAACATGTTTATGATTCA 58.323 32.000 23.53 4.53 37.73 2.57
2644 4385 6.803320 ACTCGCAAAACATGTTTATGATTCAG 59.197 34.615 23.53 14.53 37.73 3.02
2645 4386 6.092092 TCGCAAAACATGTTTATGATTCAGG 58.908 36.000 23.53 6.70 37.73 3.86
2646 4387 5.863397 CGCAAAACATGTTTATGATTCAGGT 59.137 36.000 23.53 1.72 37.73 4.00
2647 4388 6.033831 CGCAAAACATGTTTATGATTCAGGTC 59.966 38.462 23.53 8.20 37.73 3.85
2648 4389 6.867816 GCAAAACATGTTTATGATTCAGGTCA 59.132 34.615 23.53 0.00 37.73 4.02
2649 4390 7.546667 GCAAAACATGTTTATGATTCAGGTCAT 59.453 33.333 23.53 0.55 41.49 3.06
2731 4472 9.902196 AAAACTATTACCTAATGTTTTGTTCCG 57.098 29.630 0.00 0.00 36.60 4.30
2732 4473 7.080353 ACTATTACCTAATGTTTTGTTCCGC 57.920 36.000 0.00 0.00 0.00 5.54
2733 4474 5.968528 ATTACCTAATGTTTTGTTCCGCA 57.031 34.783 0.00 0.00 0.00 5.69
2734 4475 5.769484 TTACCTAATGTTTTGTTCCGCAA 57.231 34.783 0.00 0.00 34.87 4.85
2735 4476 4.657436 ACCTAATGTTTTGTTCCGCAAA 57.343 36.364 0.00 0.00 44.52 3.68
2756 4497 3.011885 AGGAGCTCCTAGTCCGCT 58.988 61.111 34.40 7.35 46.48 5.52
2757 4498 1.152839 AGGAGCTCCTAGTCCGCTC 60.153 63.158 34.40 13.68 46.48 5.03
2758 4499 3.027292 GAGCTCCTAGTCCGCTCG 58.973 66.667 0.87 0.00 40.48 5.03
2759 4500 1.820481 GAGCTCCTAGTCCGCTCGT 60.820 63.158 0.87 0.00 40.48 4.18
2760 4501 0.532417 GAGCTCCTAGTCCGCTCGTA 60.532 60.000 0.87 0.00 40.48 3.43
2761 4502 0.533308 AGCTCCTAGTCCGCTCGTAG 60.533 60.000 0.00 0.00 0.00 3.51
2762 4503 1.508808 GCTCCTAGTCCGCTCGTAGG 61.509 65.000 0.00 0.00 35.53 3.18
2763 4504 0.885596 CTCCTAGTCCGCTCGTAGGG 60.886 65.000 5.11 0.00 35.03 3.53
2764 4505 1.153005 CCTAGTCCGCTCGTAGGGT 60.153 63.158 0.00 0.00 31.21 4.34
2765 4506 1.445716 CCTAGTCCGCTCGTAGGGTG 61.446 65.000 0.00 0.00 31.21 4.61
2766 4507 0.463295 CTAGTCCGCTCGTAGGGTGA 60.463 60.000 0.00 0.00 0.00 4.02
2767 4508 0.182061 TAGTCCGCTCGTAGGGTGAT 59.818 55.000 0.00 0.00 0.00 3.06
2768 4509 1.065928 GTCCGCTCGTAGGGTGATG 59.934 63.158 0.00 0.00 0.00 3.07
2769 4510 2.125326 TCCGCTCGTAGGGTGATGG 61.125 63.158 0.00 0.00 0.00 3.51
2770 4511 2.417516 CGCTCGTAGGGTGATGGG 59.582 66.667 0.00 0.00 0.00 4.00
2771 4512 2.822399 GCTCGTAGGGTGATGGGG 59.178 66.667 0.00 0.00 0.00 4.96
2772 4513 1.760875 GCTCGTAGGGTGATGGGGA 60.761 63.158 0.00 0.00 0.00 4.81
2773 4514 1.749334 GCTCGTAGGGTGATGGGGAG 61.749 65.000 0.00 0.00 0.00 4.30
2774 4515 1.749334 CTCGTAGGGTGATGGGGAGC 61.749 65.000 0.00 0.00 0.00 4.70
2775 4516 2.808206 CGTAGGGTGATGGGGAGCC 61.808 68.421 0.00 0.00 0.00 4.70
2776 4517 1.692749 GTAGGGTGATGGGGAGCCA 60.693 63.158 0.00 0.00 33.09 4.75
2777 4518 1.384502 TAGGGTGATGGGGAGCCAG 60.385 63.158 0.00 0.00 33.09 4.85
2778 4519 1.897037 TAGGGTGATGGGGAGCCAGA 61.897 60.000 0.00 0.00 33.09 3.86
2779 4520 2.308722 GGGTGATGGGGAGCCAGAA 61.309 63.158 0.00 0.00 0.00 3.02
2780 4521 1.225704 GGTGATGGGGAGCCAGAAG 59.774 63.158 0.00 0.00 0.00 2.85
2781 4522 1.274703 GGTGATGGGGAGCCAGAAGA 61.275 60.000 0.00 0.00 0.00 2.87
2782 4523 0.842635 GTGATGGGGAGCCAGAAGAT 59.157 55.000 0.00 0.00 0.00 2.40
2783 4524 0.841961 TGATGGGGAGCCAGAAGATG 59.158 55.000 0.00 0.00 0.00 2.90
2784 4525 0.536915 GATGGGGAGCCAGAAGATGC 60.537 60.000 0.00 0.00 0.00 3.91
2785 4526 1.284111 ATGGGGAGCCAGAAGATGCA 61.284 55.000 0.00 0.00 0.00 3.96
2786 4527 1.153005 GGGGAGCCAGAAGATGCAG 60.153 63.158 0.00 0.00 0.00 4.41
2787 4528 1.153005 GGGAGCCAGAAGATGCAGG 60.153 63.158 0.00 0.00 0.00 4.85
2788 4529 1.630126 GGGAGCCAGAAGATGCAGGA 61.630 60.000 0.00 0.00 0.00 3.86
2789 4530 0.179051 GGAGCCAGAAGATGCAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2790 4531 0.179051 GAGCCAGAAGATGCAGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
2791 4532 1.153005 GCCAGAAGATGCAGGAGGG 60.153 63.158 0.00 0.00 0.00 4.30
2792 4533 1.530771 CCAGAAGATGCAGGAGGGG 59.469 63.158 0.00 0.00 0.00 4.79
2793 4534 1.153005 CAGAAGATGCAGGAGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
2794 4535 2.194326 GAAGATGCAGGAGGGGCC 59.806 66.667 0.00 0.00 0.00 5.80
2843 4584 3.455469 GGCACCTTCAGGCATGGC 61.455 66.667 12.14 12.14 39.32 4.40
2844 4585 2.362120 GCACCTTCAGGCATGGCT 60.362 61.111 17.44 17.44 39.32 4.75
2845 4586 1.077501 GCACCTTCAGGCATGGCTA 60.078 57.895 22.88 6.51 39.32 3.93
2846 4587 1.099879 GCACCTTCAGGCATGGCTAG 61.100 60.000 22.88 16.32 39.32 3.42
2847 4588 0.254178 CACCTTCAGGCATGGCTAGT 59.746 55.000 22.88 13.77 39.32 2.57
2848 4589 0.995024 ACCTTCAGGCATGGCTAGTT 59.005 50.000 22.88 1.95 39.32 2.24
2849 4590 1.340405 ACCTTCAGGCATGGCTAGTTG 60.340 52.381 22.88 10.73 39.32 3.16
2850 4591 1.386533 CTTCAGGCATGGCTAGTTGG 58.613 55.000 22.88 9.39 0.00 3.77
2851 4592 0.034186 TTCAGGCATGGCTAGTTGGG 60.034 55.000 22.88 8.61 0.00 4.12
2852 4593 2.123428 CAGGCATGGCTAGTTGGGC 61.123 63.158 22.88 0.00 0.00 5.36
2853 4594 2.276740 GGCATGGCTAGTTGGGCT 59.723 61.111 12.86 0.00 0.00 5.19
2854 4595 1.825622 GGCATGGCTAGTTGGGCTC 60.826 63.158 12.86 0.00 0.00 4.70
2855 4596 2.182842 GCATGGCTAGTTGGGCTCG 61.183 63.158 0.00 0.00 0.00 5.03
2856 4597 1.524621 CATGGCTAGTTGGGCTCGG 60.525 63.158 0.00 0.00 0.00 4.63
2857 4598 3.406595 ATGGCTAGTTGGGCTCGGC 62.407 63.158 0.00 0.00 36.25 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.676916 CGGACGAGTACTAGGTGGACA 60.677 57.143 7.94 0.00 0.00 4.02
38 39 2.009774 GTTGGCTACGGACGAGTACTA 58.990 52.381 0.00 0.00 0.00 1.82
44 45 0.607217 TGAGAGTTGGCTACGGACGA 60.607 55.000 0.00 0.00 0.00 4.20
135 136 2.266554 GAGAAGCCTGACGAACATGAG 58.733 52.381 0.00 0.00 0.00 2.90
167 168 4.020617 CCTGCCCGAGCTTGGTCA 62.021 66.667 19.14 11.67 40.80 4.02
183 184 8.303876 TGAAGACCAAATATTTACTCAAAAGCC 58.696 33.333 0.00 0.00 0.00 4.35
207 208 0.825425 CTAGATCGAGCCTGGCCTGA 60.825 60.000 16.57 14.07 0.00 3.86
213 214 4.047822 GTCAAATGTCTAGATCGAGCCTG 58.952 47.826 0.00 0.00 0.00 4.85
230 231 5.641636 GGCTTTCAAAAGTCCAAAAGTCAAA 59.358 36.000 4.54 0.00 38.28 2.69
249 250 2.754254 GATTTCGGGCGGGGCTTT 60.754 61.111 0.00 0.00 0.00 3.51
308 309 4.902443 TTAGCGGTGAACAACAAATGAA 57.098 36.364 0.00 0.00 0.00 2.57
380 381 9.333497 CACATGTGTATAGTTTTGATGACAAAG 57.667 33.333 18.03 0.00 44.97 2.77
476 481 9.677567 TTGAGCACTTTATTTCAAATAGTTCAC 57.322 29.630 0.00 0.00 0.00 3.18
502 507 2.203153 GTGGAATACGGGCGCCAT 60.203 61.111 30.85 18.69 32.26 4.40
511 701 5.622770 ATCAAAAAGTCACCGTGGAATAC 57.377 39.130 0.00 0.00 0.00 1.89
647 964 2.686915 ACAAGGCAAAGATCTAGCATGC 59.313 45.455 10.51 10.51 36.31 4.06
734 1096 4.754114 ACATCAGAGTCAAGTCAAAAGCTC 59.246 41.667 0.00 0.00 0.00 4.09
755 1117 4.072131 GCAAACTTGGATTGGACTAGACA 58.928 43.478 0.00 0.00 0.00 3.41
788 2461 7.208777 CAGAGTTCTAAGATGACATGCATAGT 58.791 38.462 0.00 0.00 37.34 2.12
792 2465 4.467438 TCCAGAGTTCTAAGATGACATGCA 59.533 41.667 0.00 0.00 0.00 3.96
803 2476 8.548025 TGGAAATATGATGTTCCAGAGTTCTAA 58.452 33.333 7.97 0.00 46.58 2.10
804 2477 8.089625 TGGAAATATGATGTTCCAGAGTTCTA 57.910 34.615 7.97 0.00 46.58 2.10
862 2535 0.391793 CTTCACGGAGCCTTCCTTCC 60.392 60.000 0.00 0.00 41.67 3.46
863 2536 1.021920 GCTTCACGGAGCCTTCCTTC 61.022 60.000 0.00 0.00 41.67 3.46
864 2537 1.003233 GCTTCACGGAGCCTTCCTT 60.003 57.895 0.00 0.00 41.67 3.36
865 2538 1.915769 AGCTTCACGGAGCCTTCCT 60.916 57.895 0.00 0.00 43.74 3.36
884 2557 1.766143 CGCCTTCTTCCGTATGCTGC 61.766 60.000 0.00 0.00 0.00 5.25
900 2573 3.098555 CCTGAAATACACGGCGCC 58.901 61.111 19.07 19.07 0.00 6.53
901 2574 2.309764 CTGCCTGAAATACACGGCGC 62.310 60.000 6.90 0.00 41.90 6.53
904 2577 1.009829 GAGCTGCCTGAAATACACGG 58.990 55.000 0.00 0.00 0.00 4.94
906 2579 1.929836 CGAGAGCTGCCTGAAATACAC 59.070 52.381 0.00 0.00 0.00 2.90
907 2580 2.299993 CGAGAGCTGCCTGAAATACA 57.700 50.000 0.00 0.00 0.00 2.29
954 2640 0.820226 GAAATGGGAGGAAGCTTGCC 59.180 55.000 15.04 10.33 0.00 4.52
955 2641 0.820226 GGAAATGGGAGGAAGCTTGC 59.180 55.000 10.41 10.41 0.00 4.01
956 2642 1.478631 GGGAAATGGGAGGAAGCTTG 58.521 55.000 2.10 0.00 0.00 4.01
961 2647 1.607612 GAGCGGGAAATGGGAGGAA 59.392 57.895 0.00 0.00 0.00 3.36
963 2649 2.193248 GGAGCGGGAAATGGGAGG 59.807 66.667 0.00 0.00 0.00 4.30
975 2661 2.202797 CGGATGTCAGGTGGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
978 2664 2.348104 CGGTCGGATGTCAGGTGGA 61.348 63.158 0.00 0.00 0.00 4.02
979 2665 2.184322 CGGTCGGATGTCAGGTGG 59.816 66.667 0.00 0.00 0.00 4.61
980 2666 2.509336 GCGGTCGGATGTCAGGTG 60.509 66.667 0.00 0.00 0.00 4.00
1295 2983 1.614241 CGGGTTGGTTCGAGGAGGAT 61.614 60.000 0.00 0.00 0.00 3.24
1359 3048 1.360185 TTGATGGGGGCAAAGCAAAT 58.640 45.000 0.00 0.00 0.00 2.32
1370 3059 7.277396 AGCAAAATCAAGATAATTTGATGGGG 58.723 34.615 10.04 0.00 44.74 4.96
1438 3127 0.676151 ACGAGTCGGTCTCTGGTACC 60.676 60.000 18.30 4.43 40.75 3.34
1439 3128 0.447011 CACGAGTCGGTCTCTGGTAC 59.553 60.000 18.30 0.00 40.75 3.34
1452 3141 0.600557 CAGGCAGAAGACTCACGAGT 59.399 55.000 0.00 0.00 45.84 4.18
1474 3163 5.588246 TCAGGCAGATATCGCATAAACAAAA 59.412 36.000 17.27 0.00 0.00 2.44
1475 3164 5.122519 TCAGGCAGATATCGCATAAACAAA 58.877 37.500 17.27 0.00 0.00 2.83
1476 3165 4.702831 TCAGGCAGATATCGCATAAACAA 58.297 39.130 17.27 0.00 0.00 2.83
1477 3166 4.335400 TCAGGCAGATATCGCATAAACA 57.665 40.909 17.27 0.00 0.00 2.83
1478 3167 5.869753 ATTCAGGCAGATATCGCATAAAC 57.130 39.130 17.27 4.23 0.00 2.01
1479 3168 7.661437 AGTTAATTCAGGCAGATATCGCATAAA 59.339 33.333 17.27 6.95 0.00 1.40
1480 3169 7.161404 AGTTAATTCAGGCAGATATCGCATAA 58.839 34.615 17.27 10.35 0.00 1.90
1481 3170 6.701340 AGTTAATTCAGGCAGATATCGCATA 58.299 36.000 17.27 2.01 0.00 3.14
1482 3171 5.555017 AGTTAATTCAGGCAGATATCGCAT 58.445 37.500 17.27 10.25 0.00 4.73
1483 3172 4.960938 AGTTAATTCAGGCAGATATCGCA 58.039 39.130 17.27 2.28 0.00 5.10
1484 3173 5.119898 CAGAGTTAATTCAGGCAGATATCGC 59.880 44.000 10.01 10.01 0.00 4.58
1485 3174 6.219473 ACAGAGTTAATTCAGGCAGATATCG 58.781 40.000 0.44 0.00 0.00 2.92
1486 3175 7.441017 AGACAGAGTTAATTCAGGCAGATATC 58.559 38.462 0.44 0.00 0.00 1.63
1487 3176 7.372260 AGACAGAGTTAATTCAGGCAGATAT 57.628 36.000 0.44 0.00 0.00 1.63
1488 3177 6.183360 GGAGACAGAGTTAATTCAGGCAGATA 60.183 42.308 0.44 0.00 0.00 1.98
1489 3178 5.396213 GGAGACAGAGTTAATTCAGGCAGAT 60.396 44.000 0.44 0.00 0.00 2.90
1490 3179 4.081420 GGAGACAGAGTTAATTCAGGCAGA 60.081 45.833 0.44 0.00 0.00 4.26
1491 3180 4.187694 GGAGACAGAGTTAATTCAGGCAG 58.812 47.826 0.44 0.00 0.00 4.85
1492 3181 3.368427 CGGAGACAGAGTTAATTCAGGCA 60.368 47.826 0.44 0.00 0.00 4.75
1493 3182 3.190874 CGGAGACAGAGTTAATTCAGGC 58.809 50.000 0.44 0.00 0.00 4.85
1494 3183 4.457834 ACGGAGACAGAGTTAATTCAGG 57.542 45.455 0.44 0.00 0.00 3.86
1495 3184 7.884816 TTTTACGGAGACAGAGTTAATTCAG 57.115 36.000 0.44 0.00 0.00 3.02
1496 3185 8.092068 TGATTTTACGGAGACAGAGTTAATTCA 58.908 33.333 0.44 0.00 0.00 2.57
1497 3186 8.381387 GTGATTTTACGGAGACAGAGTTAATTC 58.619 37.037 0.00 0.00 0.00 2.17
1498 3187 7.876068 TGTGATTTTACGGAGACAGAGTTAATT 59.124 33.333 0.00 0.00 0.00 1.40
1499 3188 7.383687 TGTGATTTTACGGAGACAGAGTTAAT 58.616 34.615 0.00 0.00 0.00 1.40
1507 3196 3.745975 CAGCTTGTGATTTTACGGAGACA 59.254 43.478 0.00 0.00 0.00 3.41
1580 3269 2.035193 CCGTCAGGTGATCTCCATACAG 59.965 54.545 15.93 9.03 0.00 2.74
1726 3415 2.173519 CACAGCTCAACCAATTCCCAT 58.826 47.619 0.00 0.00 0.00 4.00
1767 3456 0.540133 TGCATTGGGAGCAAGCTGAA 60.540 50.000 0.00 0.00 39.39 3.02
1772 3461 0.179111 CAGCATGCATTGGGAGCAAG 60.179 55.000 21.98 0.00 46.27 4.01
1799 3508 7.778470 AAATCGCAAAAATAGAGAGTAGGAG 57.222 36.000 0.00 0.00 0.00 3.69
1800 3509 8.450964 CAAAAATCGCAAAAATAGAGAGTAGGA 58.549 33.333 0.00 0.00 0.00 2.94
1801 3510 8.237267 ACAAAAATCGCAAAAATAGAGAGTAGG 58.763 33.333 0.00 0.00 0.00 3.18
1802 3511 9.055248 CACAAAAATCGCAAAAATAGAGAGTAG 57.945 33.333 0.00 0.00 0.00 2.57
1803 3512 8.564574 ACACAAAAATCGCAAAAATAGAGAGTA 58.435 29.630 0.00 0.00 0.00 2.59
1804 3513 7.425606 ACACAAAAATCGCAAAAATAGAGAGT 58.574 30.769 0.00 0.00 0.00 3.24
1805 3514 7.858052 ACACAAAAATCGCAAAAATAGAGAG 57.142 32.000 0.00 0.00 0.00 3.20
1806 3515 7.532546 CGTACACAAAAATCGCAAAAATAGAGA 59.467 33.333 0.00 0.00 0.00 3.10
1807 3516 7.322699 ACGTACACAAAAATCGCAAAAATAGAG 59.677 33.333 0.00 0.00 0.00 2.43
1813 3522 4.413087 ACACGTACACAAAAATCGCAAAA 58.587 34.783 0.00 0.00 0.00 2.44
1821 3530 8.547069 GTGGTTATTACTACACGTACACAAAAA 58.453 33.333 0.00 0.00 35.94 1.94
1852 3564 1.559682 GGGCTCCAGGAGACATGTTAA 59.440 52.381 24.89 0.00 39.95 2.01
1856 3568 0.179936 GAAGGGCTCCAGGAGACATG 59.820 60.000 24.89 0.00 39.95 3.21
1865 3577 1.480212 TTCGAAGCAGAAGGGCTCCA 61.480 55.000 0.00 0.00 45.07 3.86
1897 3613 8.808092 CAAAACAGTTCCAACCCCTTATATTTA 58.192 33.333 0.00 0.00 0.00 1.40
1913 3632 6.466097 CGACAAAGAAGAAGACAAAACAGTTC 59.534 38.462 0.00 0.00 0.00 3.01
2002 3722 2.756760 TGGTCTACGATCTGGGTGTAAC 59.243 50.000 0.00 0.00 0.00 2.50
2008 3728 2.231529 CCTAGTGGTCTACGATCTGGG 58.768 57.143 0.00 0.00 0.00 4.45
2027 3748 0.370273 CAGTGCTTGTATTCGTCGCC 59.630 55.000 0.00 0.00 0.00 5.54
2035 3756 3.067106 CAGTTCGGTTCAGTGCTTGTAT 58.933 45.455 0.00 0.00 0.00 2.29
2074 3795 2.444706 TCCATGAGGGAGAGGCGG 60.445 66.667 0.00 0.00 42.15 6.13
2095 3817 9.635520 GACTGTCTACTACAATAAGTTTTGCTA 57.364 33.333 0.00 0.00 37.74 3.49
2106 3828 5.961396 ACTTCACGACTGTCTACTACAAT 57.039 39.130 6.21 0.00 37.74 2.71
2123 3848 4.841813 TGGTCCCTTAGTATGACAACTTCA 59.158 41.667 0.00 0.00 39.11 3.02
2135 3861 2.888911 GCTAGTCCTGTGGTCCCTTAGT 60.889 54.545 0.00 0.00 0.00 2.24
2142 3868 1.070134 TGTTGTGCTAGTCCTGTGGTC 59.930 52.381 0.00 0.00 0.00 4.02
2143 3869 1.070758 CTGTTGTGCTAGTCCTGTGGT 59.929 52.381 0.00 0.00 0.00 4.16
2147 3874 3.111853 TGTTCTGTTGTGCTAGTCCTG 57.888 47.619 0.00 0.00 0.00 3.86
2153 3880 3.303725 GCGATTGTTGTTCTGTTGTGCTA 60.304 43.478 0.00 0.00 0.00 3.49
2198 3925 0.905357 AGTCAGGTTGGATCCTTCGG 59.095 55.000 14.23 3.55 35.37 4.30
2216 3944 2.481568 TCTGGTCGTAGTTCGTGTGTAG 59.518 50.000 0.00 0.00 40.80 2.74
2288 4026 1.589196 GTCTAGCATCGTCGGTGGC 60.589 63.158 7.76 1.63 0.00 5.01
2314 4052 1.210967 CTCCCGCATACCCCAGTTTTA 59.789 52.381 0.00 0.00 0.00 1.52
2327 4065 1.281419 TGGAATAAGGTTCTCCCGCA 58.719 50.000 0.00 0.00 38.74 5.69
2329 4067 4.423625 AAGATGGAATAAGGTTCTCCCG 57.576 45.455 0.00 0.00 38.74 5.14
2359 4099 2.589798 AGGAAAACGAGACAACGACA 57.410 45.000 0.00 0.00 37.03 4.35
2365 4105 2.743636 CTGCCTAGGAAAACGAGACA 57.256 50.000 14.75 0.00 0.00 3.41
2380 4120 1.073284 TGTTAGGGTTTCTGTCCTGCC 59.927 52.381 0.00 0.00 34.75 4.85
2389 4129 6.459670 TCCTTCAAGTTTTGTTAGGGTTTC 57.540 37.500 10.52 0.00 35.63 2.78
2417 4157 1.813513 CGTGAGGGCTCTGTTTTCAT 58.186 50.000 0.00 0.00 0.00 2.57
2489 4230 3.597728 CGCCGCTAGTCCTCCTCC 61.598 72.222 0.00 0.00 0.00 4.30
2515 4256 1.679032 CCTAGGGTTCTTTTGCCTCCG 60.679 57.143 0.00 0.00 0.00 4.63
2548 4289 2.358737 CACACAACCGCCCTCCTC 60.359 66.667 0.00 0.00 0.00 3.71
2551 4292 1.071814 TTACCACACAACCGCCCTC 59.928 57.895 0.00 0.00 0.00 4.30
2552 4293 1.228033 GTTACCACACAACCGCCCT 60.228 57.895 0.00 0.00 0.00 5.19
2556 4297 5.237779 AGACAAAATAGTTACCACACAACCG 59.762 40.000 0.00 0.00 0.00 4.44
2558 4299 7.927048 AGAAGACAAAATAGTTACCACACAAC 58.073 34.615 0.00 0.00 0.00 3.32
2559 4300 8.514330 AAGAAGACAAAATAGTTACCACACAA 57.486 30.769 0.00 0.00 0.00 3.33
2560 4301 9.616156 TTAAGAAGACAAAATAGTTACCACACA 57.384 29.630 0.00 0.00 0.00 3.72
2573 4314 9.160496 ACATTTTGCACATTTAAGAAGACAAAA 57.840 25.926 0.00 0.00 39.30 2.44
2574 4315 8.715191 ACATTTTGCACATTTAAGAAGACAAA 57.285 26.923 0.00 0.00 0.00 2.83
2575 4316 8.715191 AACATTTTGCACATTTAAGAAGACAA 57.285 26.923 0.00 0.00 0.00 3.18
2576 4317 8.715191 AAACATTTTGCACATTTAAGAAGACA 57.285 26.923 0.00 0.00 0.00 3.41
2577 4318 9.636965 GAAAACATTTTGCACATTTAAGAAGAC 57.363 29.630 0.00 0.00 0.00 3.01
2578 4319 9.376075 TGAAAACATTTTGCACATTTAAGAAGA 57.624 25.926 0.00 0.00 0.00 2.87
2579 4320 9.985318 TTGAAAACATTTTGCACATTTAAGAAG 57.015 25.926 0.00 0.00 0.00 2.85
2580 4321 9.985318 CTTGAAAACATTTTGCACATTTAAGAA 57.015 25.926 0.00 0.00 0.00 2.52
2581 4322 9.160496 ACTTGAAAACATTTTGCACATTTAAGA 57.840 25.926 0.00 0.00 0.00 2.10
2587 4328 9.719279 CAAAATACTTGAAAACATTTTGCACAT 57.281 25.926 5.88 0.00 36.84 3.21
2588 4329 8.725148 ACAAAATACTTGAAAACATTTTGCACA 58.275 25.926 15.04 0.00 41.85 4.57
2589 4330 8.997960 CACAAAATACTTGAAAACATTTTGCAC 58.002 29.630 15.04 0.00 41.85 4.57
2590 4331 8.939929 TCACAAAATACTTGAAAACATTTTGCA 58.060 25.926 15.04 0.00 41.85 4.08
2591 4332 9.424659 CTCACAAAATACTTGAAAACATTTTGC 57.575 29.630 15.04 0.00 41.85 3.68
2596 4337 9.736023 GAGTTCTCACAAAATACTTGAAAACAT 57.264 29.630 0.00 0.00 0.00 2.71
2597 4338 7.908082 CGAGTTCTCACAAAATACTTGAAAACA 59.092 33.333 0.79 0.00 0.00 2.83
2598 4339 7.097006 GCGAGTTCTCACAAAATACTTGAAAAC 60.097 37.037 0.00 0.00 0.00 2.43
2599 4340 6.910433 GCGAGTTCTCACAAAATACTTGAAAA 59.090 34.615 0.00 0.00 0.00 2.29
2600 4341 6.037720 TGCGAGTTCTCACAAAATACTTGAAA 59.962 34.615 0.00 0.00 0.00 2.69
2601 4342 5.525745 TGCGAGTTCTCACAAAATACTTGAA 59.474 36.000 0.00 0.00 0.00 2.69
2602 4343 5.053811 TGCGAGTTCTCACAAAATACTTGA 58.946 37.500 0.00 0.00 0.00 3.02
2603 4344 5.342806 TGCGAGTTCTCACAAAATACTTG 57.657 39.130 0.00 0.00 0.00 3.16
2604 4345 6.371809 TTTGCGAGTTCTCACAAAATACTT 57.628 33.333 11.82 0.00 0.00 2.24
2605 4346 6.183360 TGTTTTGCGAGTTCTCACAAAATACT 60.183 34.615 22.56 0.00 42.16 2.12
2606 4347 5.968848 TGTTTTGCGAGTTCTCACAAAATAC 59.031 36.000 22.56 15.83 42.16 1.89
2607 4348 6.125327 TGTTTTGCGAGTTCTCACAAAATA 57.875 33.333 22.56 19.18 42.16 1.40
2608 4349 4.992688 TGTTTTGCGAGTTCTCACAAAAT 58.007 34.783 22.56 0.00 42.16 1.82
2609 4350 4.427096 TGTTTTGCGAGTTCTCACAAAA 57.573 36.364 18.52 18.52 39.09 2.44
2610 4351 4.142491 ACATGTTTTGCGAGTTCTCACAAA 60.142 37.500 10.62 10.62 0.00 2.83
2611 4352 3.376859 ACATGTTTTGCGAGTTCTCACAA 59.623 39.130 0.00 0.00 0.00 3.33
2612 4353 2.942376 ACATGTTTTGCGAGTTCTCACA 59.058 40.909 0.00 0.00 0.00 3.58
2613 4354 3.609103 ACATGTTTTGCGAGTTCTCAC 57.391 42.857 0.00 0.00 0.00 3.51
2614 4355 4.630894 AAACATGTTTTGCGAGTTCTCA 57.369 36.364 18.13 0.00 0.00 3.27
2615 4356 6.370593 TCATAAACATGTTTTGCGAGTTCTC 58.629 36.000 27.66 0.00 34.23 2.87
2616 4357 6.312399 TCATAAACATGTTTTGCGAGTTCT 57.688 33.333 27.66 3.30 34.23 3.01
2617 4358 7.325821 TGAATCATAAACATGTTTTGCGAGTTC 59.674 33.333 27.66 21.21 34.23 3.01
2618 4359 7.144661 TGAATCATAAACATGTTTTGCGAGTT 58.855 30.769 27.66 15.14 34.23 3.01
2619 4360 6.676950 TGAATCATAAACATGTTTTGCGAGT 58.323 32.000 27.66 19.46 34.23 4.18
2620 4361 6.252015 CCTGAATCATAAACATGTTTTGCGAG 59.748 38.462 27.66 13.62 34.23 5.03
2621 4362 6.092092 CCTGAATCATAAACATGTTTTGCGA 58.908 36.000 27.66 20.40 34.23 5.10
2622 4363 5.863397 ACCTGAATCATAAACATGTTTTGCG 59.137 36.000 27.66 16.33 34.23 4.85
2623 4364 6.867816 TGACCTGAATCATAAACATGTTTTGC 59.132 34.615 27.66 10.16 34.23 3.68
2624 4365 8.991243 ATGACCTGAATCATAAACATGTTTTG 57.009 30.769 27.66 22.50 37.56 2.44
2705 4446 9.902196 CGGAACAAAACATTAGGTAATAGTTTT 57.098 29.630 12.39 12.39 37.37 2.43
2706 4447 8.024865 GCGGAACAAAACATTAGGTAATAGTTT 58.975 33.333 0.00 0.00 33.05 2.66
2707 4448 7.175293 TGCGGAACAAAACATTAGGTAATAGTT 59.825 33.333 0.00 0.00 0.00 2.24
2708 4449 6.655848 TGCGGAACAAAACATTAGGTAATAGT 59.344 34.615 0.00 0.00 0.00 2.12
2709 4450 7.079182 TGCGGAACAAAACATTAGGTAATAG 57.921 36.000 0.00 0.00 0.00 1.73
2710 4451 7.450124 TTGCGGAACAAAACATTAGGTAATA 57.550 32.000 0.00 0.00 34.56 0.98
2711 4452 5.968528 TGCGGAACAAAACATTAGGTAAT 57.031 34.783 0.00 0.00 0.00 1.89
2712 4453 5.769484 TTGCGGAACAAAACATTAGGTAA 57.231 34.783 0.00 0.00 34.56 2.85
2713 4454 5.769484 TTTGCGGAACAAAACATTAGGTA 57.231 34.783 0.00 0.00 45.22 3.08
2714 4455 4.657436 TTTGCGGAACAAAACATTAGGT 57.343 36.364 0.00 0.00 45.22 3.08
2735 4476 1.066071 GCGGACTAGGAGCTCCTTTTT 60.066 52.381 39.23 23.46 46.09 1.94
2736 4477 0.537653 GCGGACTAGGAGCTCCTTTT 59.462 55.000 39.23 26.02 46.09 2.27
2737 4478 0.324830 AGCGGACTAGGAGCTCCTTT 60.325 55.000 39.23 26.39 46.09 3.11
2738 4479 1.308326 AGCGGACTAGGAGCTCCTT 59.692 57.895 39.23 23.77 46.09 3.36
2742 4483 0.533308 CTACGAGCGGACTAGGAGCT 60.533 60.000 8.31 8.31 44.80 4.09
2743 4484 1.508808 CCTACGAGCGGACTAGGAGC 61.509 65.000 0.00 0.00 28.40 4.70
2744 4485 0.885596 CCCTACGAGCGGACTAGGAG 60.886 65.000 6.62 0.00 30.11 3.69
2745 4486 1.147824 CCCTACGAGCGGACTAGGA 59.852 63.158 6.62 0.00 30.11 2.94
2746 4487 1.153005 ACCCTACGAGCGGACTAGG 60.153 63.158 0.00 0.00 0.00 3.02
2747 4488 0.463295 TCACCCTACGAGCGGACTAG 60.463 60.000 0.00 0.00 0.00 2.57
2748 4489 0.182061 ATCACCCTACGAGCGGACTA 59.818 55.000 0.00 0.00 0.00 2.59
2749 4490 1.076923 ATCACCCTACGAGCGGACT 60.077 57.895 0.00 0.00 0.00 3.85
2750 4491 1.065928 CATCACCCTACGAGCGGAC 59.934 63.158 0.00 0.00 0.00 4.79
2751 4492 2.125326 CCATCACCCTACGAGCGGA 61.125 63.158 0.00 0.00 0.00 5.54
2752 4493 2.417516 CCATCACCCTACGAGCGG 59.582 66.667 0.00 0.00 0.00 5.52
2753 4494 2.417516 CCCATCACCCTACGAGCG 59.582 66.667 0.00 0.00 0.00 5.03
2754 4495 1.749334 CTCCCCATCACCCTACGAGC 61.749 65.000 0.00 0.00 0.00 5.03
2755 4496 1.749334 GCTCCCCATCACCCTACGAG 61.749 65.000 0.00 0.00 0.00 4.18
2756 4497 1.760875 GCTCCCCATCACCCTACGA 60.761 63.158 0.00 0.00 0.00 3.43
2757 4498 2.808206 GGCTCCCCATCACCCTACG 61.808 68.421 0.00 0.00 0.00 3.51
2758 4499 1.692749 TGGCTCCCCATCACCCTAC 60.693 63.158 0.00 0.00 35.79 3.18
2759 4500 1.384502 CTGGCTCCCCATCACCCTA 60.385 63.158 0.00 0.00 41.21 3.53
2760 4501 2.693864 CTGGCTCCCCATCACCCT 60.694 66.667 0.00 0.00 41.21 4.34
2761 4502 2.276309 CTTCTGGCTCCCCATCACCC 62.276 65.000 0.00 0.00 41.21 4.61
2762 4503 1.225704 CTTCTGGCTCCCCATCACC 59.774 63.158 0.00 0.00 41.21 4.02
2763 4504 0.842635 ATCTTCTGGCTCCCCATCAC 59.157 55.000 0.00 0.00 41.21 3.06
2764 4505 0.841961 CATCTTCTGGCTCCCCATCA 59.158 55.000 0.00 0.00 41.21 3.07
2765 4506 0.536915 GCATCTTCTGGCTCCCCATC 60.537 60.000 0.00 0.00 41.21 3.51
2766 4507 1.284111 TGCATCTTCTGGCTCCCCAT 61.284 55.000 0.00 0.00 41.21 4.00
2767 4508 1.918467 CTGCATCTTCTGGCTCCCCA 61.918 60.000 0.00 0.00 39.32 4.96
2768 4509 1.153005 CTGCATCTTCTGGCTCCCC 60.153 63.158 0.00 0.00 0.00 4.81
2769 4510 1.153005 CCTGCATCTTCTGGCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
2770 4511 0.179051 CTCCTGCATCTTCTGGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
2771 4512 0.179051 CCTCCTGCATCTTCTGGCTC 60.179 60.000 0.00 0.00 0.00 4.70
2772 4513 1.633915 CCCTCCTGCATCTTCTGGCT 61.634 60.000 0.00 0.00 0.00 4.75
2773 4514 1.153005 CCCTCCTGCATCTTCTGGC 60.153 63.158 0.00 0.00 0.00 4.85
2774 4515 1.530771 CCCCTCCTGCATCTTCTGG 59.469 63.158 0.00 0.00 0.00 3.86
2775 4516 1.153005 GCCCCTCCTGCATCTTCTG 60.153 63.158 0.00 0.00 0.00 3.02
2776 4517 2.381941 GGCCCCTCCTGCATCTTCT 61.382 63.158 0.00 0.00 0.00 2.85
2777 4518 1.056700 TAGGCCCCTCCTGCATCTTC 61.057 60.000 0.00 0.00 46.98 2.87
2778 4519 0.402566 ATAGGCCCCTCCTGCATCTT 60.403 55.000 0.00 0.00 46.98 2.40
2779 4520 0.402566 AATAGGCCCCTCCTGCATCT 60.403 55.000 0.00 0.00 46.98 2.90
2780 4521 0.480252 AAATAGGCCCCTCCTGCATC 59.520 55.000 0.00 0.00 46.98 3.91
2781 4522 0.186873 CAAATAGGCCCCTCCTGCAT 59.813 55.000 0.00 0.00 46.98 3.96
2782 4523 1.614711 CAAATAGGCCCCTCCTGCA 59.385 57.895 0.00 0.00 46.98 4.41
2783 4524 1.152673 CCAAATAGGCCCCTCCTGC 60.153 63.158 0.00 0.00 46.98 4.85
2815 4556 2.726850 GAAGGTGCCCGTTTGCGAAC 62.727 60.000 6.77 6.77 41.33 3.95
2816 4557 2.517402 AAGGTGCCCGTTTGCGAA 60.517 55.556 0.00 0.00 41.33 4.70
2817 4558 2.975799 GAAGGTGCCCGTTTGCGA 60.976 61.111 0.00 0.00 41.33 5.10
2818 4559 3.254014 CTGAAGGTGCCCGTTTGCG 62.254 63.158 0.00 0.00 37.95 4.85
2819 4560 2.644992 CTGAAGGTGCCCGTTTGC 59.355 61.111 0.00 0.00 0.00 3.68
2820 4561 2.919494 GCCTGAAGGTGCCCGTTTG 61.919 63.158 0.00 0.00 37.57 2.93
2821 4562 2.597510 GCCTGAAGGTGCCCGTTT 60.598 61.111 0.00 0.00 37.57 3.60
2822 4563 3.210012 ATGCCTGAAGGTGCCCGTT 62.210 57.895 0.00 0.00 37.57 4.44
2823 4564 3.650950 ATGCCTGAAGGTGCCCGT 61.651 61.111 0.00 0.00 37.57 5.28
2824 4565 3.136123 CATGCCTGAAGGTGCCCG 61.136 66.667 0.00 0.00 37.57 6.13
2825 4566 2.757099 CCATGCCTGAAGGTGCCC 60.757 66.667 0.00 0.00 37.57 5.36
2826 4567 2.556840 TAGCCATGCCTGAAGGTGCC 62.557 60.000 0.00 0.00 37.57 5.01
2827 4568 1.077501 TAGCCATGCCTGAAGGTGC 60.078 57.895 0.00 0.00 37.57 5.01
2828 4569 0.254178 ACTAGCCATGCCTGAAGGTG 59.746 55.000 0.00 0.00 37.57 4.00
2829 4570 0.995024 AACTAGCCATGCCTGAAGGT 59.005 50.000 0.00 0.00 37.57 3.50
2830 4571 1.386533 CAACTAGCCATGCCTGAAGG 58.613 55.000 0.00 0.00 38.53 3.46
2831 4572 1.386533 CCAACTAGCCATGCCTGAAG 58.613 55.000 0.00 0.00 0.00 3.02
2832 4573 0.034186 CCCAACTAGCCATGCCTGAA 60.034 55.000 0.00 0.00 0.00 3.02
2833 4574 1.609239 CCCAACTAGCCATGCCTGA 59.391 57.895 0.00 0.00 0.00 3.86
2834 4575 2.123428 GCCCAACTAGCCATGCCTG 61.123 63.158 0.00 0.00 0.00 4.85
2835 4576 2.276309 GAGCCCAACTAGCCATGCCT 62.276 60.000 0.00 0.00 0.00 4.75
2836 4577 1.825622 GAGCCCAACTAGCCATGCC 60.826 63.158 0.00 0.00 0.00 4.40
2837 4578 2.182842 CGAGCCCAACTAGCCATGC 61.183 63.158 0.00 0.00 0.00 4.06
2838 4579 1.524621 CCGAGCCCAACTAGCCATG 60.525 63.158 0.00 0.00 0.00 3.66
2839 4580 2.911143 CCGAGCCCAACTAGCCAT 59.089 61.111 0.00 0.00 0.00 4.40
2840 4581 4.096003 GCCGAGCCCAACTAGCCA 62.096 66.667 0.00 0.00 0.00 4.75
2841 4582 4.858680 GGCCGAGCCCAACTAGCC 62.859 72.222 3.73 0.00 44.06 3.93


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

AutoCloner maintained by Alex Coulton.