Multiple sequence alignment - TraesCS3B01G133100

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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 TraesCS3B01G133100 chr3B 100.000 4450 0 0 1 4450 115545208 115549657 0.000000e+00 8218.0
1 TraesCS3B01G133100 chr3B 91.558 154 8 4 4283 4435 530239392 530239541 1.620000e-49 207.0
2 TraesCS3B01G133100 chr3D 91.010 3793 245 42 481 4219 69669958 69673708 0.000000e+00 5027.0
3 TraesCS3B01G133100 chr3D 86.652 457 61 0 2021 2477 69671651 69672107 1.430000e-139 507.0
4 TraesCS3B01G133100 chr3D 83.794 543 73 11 2107 2640 69671467 69672003 6.650000e-138 501.0
5 TraesCS3B01G133100 chr3D 85.622 466 32 16 1 446 69669256 69669706 1.460000e-124 457.0
6 TraesCS3B01G133100 chr3D 84.483 464 43 16 1 449 69657087 69657536 8.840000e-117 431.0
7 TraesCS3B01G133100 chr3D 83.973 443 68 1 2201 2640 69671471 69671913 5.320000e-114 422.0
8 TraesCS3B01G133100 chr3A 91.095 3369 209 45 376 3714 81085871 81089178 0.000000e+00 4475.0
9 TraesCS3B01G133100 chr3A 86.863 373 23 6 3719 4076 81089400 81089761 1.160000e-105 394.0
10 TraesCS3B01G133100 chr3A 80.261 537 82 16 2107 2640 81087506 81088021 2.510000e-102 383.0
11 TraesCS3B01G133100 chr3A 82.353 442 60 9 2199 2640 81087508 81087931 7.030000e-98 368.0
12 TraesCS3B01G133100 chr3A 85.083 181 20 5 90 264 709159770 709159591 1.270000e-40 178.0
13 TraesCS3B01G133100 chr3A 87.619 105 10 3 1 103 81085766 81085869 7.820000e-23 119.0
14 TraesCS3B01G133100 chr3A 94.231 52 2 1 4169 4219 81089772 81089823 1.330000e-10 78.7
15 TraesCS3B01G133100 chr7B 98.485 132 2 0 4305 4436 89765908 89765777 2.680000e-57 233.0
16 TraesCS3B01G133100 chr7A 98.450 129 2 0 4309 4437 83728728 83728600 1.250000e-55 228.0
17 TraesCS3B01G133100 chr6B 95.683 139 4 2 4300 4437 112908786 112908649 5.790000e-54 222.0
18 TraesCS3B01G133100 chr6B 89.634 164 9 6 4280 4441 187841692 187841849 7.550000e-48 202.0
19 TraesCS3B01G133100 chr6B 85.946 185 22 4 87 268 21447909 21448092 1.260000e-45 195.0
20 TraesCS3B01G133100 chr6B 84.530 181 26 1 90 268 10293597 10293417 1.270000e-40 178.0
21 TraesCS3B01G133100 chr5B 95.035 141 4 2 4303 4441 123712303 123712164 7.490000e-53 219.0
22 TraesCS3B01G133100 chr5B 85.083 181 25 1 90 268 56851267 56851087 2.730000e-42 183.0
23 TraesCS3B01G133100 chr5B 85.165 182 23 4 90 268 420005098 420004918 2.730000e-42 183.0
24 TraesCS3B01G133100 chr5A 95.620 137 4 2 4300 4436 395389880 395389746 7.490000e-53 219.0
25 TraesCS3B01G133100 chr2B 95.620 137 5 1 4309 4444 367825727 367825591 7.490000e-53 219.0
26 TraesCS3B01G133100 chr2B 84.530 181 26 1 90 268 18103263 18103083 1.270000e-40 178.0
27 TraesCS3B01G133100 chr4A 91.558 154 10 2 4291 4442 722866755 722866907 4.510000e-50 209.0
28 TraesCS3B01G133100 chr1B 84.699 183 23 3 91 268 550706656 550706838 1.270000e-40 178.0
29 TraesCS3B01G133100 chr1D 83.770 191 26 3 87 272 418404835 418405025 4.570000e-40 176.0
30 TraesCS3B01G133100 chr5D 88.421 95 11 0 4212 4306 230163540 230163446 1.010000e-21 115.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G133100 chr3B 115545208 115549657 4449 False 8218.000000 8218 100.000000 1 4450 1 chr3B.!!$F1 4449
1 TraesCS3B01G133100 chr3D 69669256 69673708 4452 False 1382.800000 5027 86.210200 1 4219 5 chr3D.!!$F2 4218
2 TraesCS3B01G133100 chr3A 81085766 81089823 4057 False 969.616667 4475 87.070333 1 4219 6 chr3A.!!$F1 4218

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
220 229 0.105964 CCGTCATCGCCCCTTATTCA 59.894 55.0 0.0 0.0 35.54 2.57 F
581 822 0.178984 ACCCGGTCCCAAAACGAAAT 60.179 50.0 0.0 0.0 0.00 2.17 F
2240 2504 0.103026 CTCTCCGATGCCGTCAATGA 59.897 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2289 0.605860 AGAGCTTCTTGCAGTGCAGG 60.606 55.0 20.52 20.52 45.94 4.85 R
2557 2824 0.594602 TTCTTGCAGTGCACATCAGC 59.405 50.0 19.58 16.95 38.71 4.26 R
3849 4357 0.039798 AATGCTTGCTCGCAACACTG 60.040 50.0 0.00 0.00 44.06 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 74 4.440839 AAGGAATGACATTCGCCTTTTC 57.559 40.909 19.43 6.24 40.17 2.29
74 77 1.474330 ATGACATTCGCCTTTTCCCC 58.526 50.000 0.00 0.00 0.00 4.81
77 80 1.405463 GACATTCGCCTTTTCCCCATC 59.595 52.381 0.00 0.00 0.00 3.51
80 83 3.287222 CATTCGCCTTTTCCCCATCTTA 58.713 45.455 0.00 0.00 0.00 2.10
85 88 3.447229 CGCCTTTTCCCCATCTTATTTGT 59.553 43.478 0.00 0.00 0.00 2.83
154 163 5.533482 AGTATTGCATCCAGATTCGTAGAC 58.467 41.667 0.00 0.00 34.32 2.59
160 169 2.100197 TCCAGATTCGTAGACCACCTG 58.900 52.381 0.00 0.00 34.32 4.00
171 180 0.669625 GACCACCTGGCGACAAGTAC 60.670 60.000 0.00 0.00 42.06 2.73
173 182 0.949105 CCACCTGGCGACAAGTACAC 60.949 60.000 0.00 0.00 42.06 2.90
180 189 3.173247 CGACAAGTACACGCACTGA 57.827 52.632 0.00 0.00 0.00 3.41
181 190 1.483316 CGACAAGTACACGCACTGAA 58.517 50.000 0.00 0.00 0.00 3.02
182 191 1.452025 CGACAAGTACACGCACTGAAG 59.548 52.381 0.00 0.00 0.00 3.02
183 192 1.192534 GACAAGTACACGCACTGAAGC 59.807 52.381 0.00 0.00 0.00 3.86
216 225 4.215742 CGCCGTCATCGCCCCTTA 62.216 66.667 0.00 0.00 35.54 2.69
217 226 2.426023 GCCGTCATCGCCCCTTAT 59.574 61.111 0.00 0.00 35.54 1.73
220 229 0.105964 CCGTCATCGCCCCTTATTCA 59.894 55.000 0.00 0.00 35.54 2.57
247 258 3.132925 GCCGGACAACTTGTTGTAGTAA 58.867 45.455 17.62 0.00 34.90 2.24
261 272 6.804677 TGTTGTAGTAAACAGTCGGAAAGTA 58.195 36.000 0.00 0.00 39.87 2.24
264 275 7.042797 TGTAGTAAACAGTCGGAAAGTAGTT 57.957 36.000 0.00 0.00 33.01 2.24
274 285 5.820947 AGTCGGAAAGTAGTTGTGAAAACAT 59.179 36.000 0.00 0.00 0.00 2.71
276 287 6.970613 GTCGGAAAGTAGTTGTGAAAACATTT 59.029 34.615 0.00 0.00 0.00 2.32
277 288 7.486870 GTCGGAAAGTAGTTGTGAAAACATTTT 59.513 33.333 0.00 0.00 0.00 1.82
278 289 8.675504 TCGGAAAGTAGTTGTGAAAACATTTTA 58.324 29.630 0.00 0.00 0.00 1.52
308 319 7.954835 TGGTCAAGAATTTGATGAACTTCATT 58.045 30.769 5.73 0.00 44.62 2.57
393 415 4.800993 TGTTGTTTTTGTTTATCTGCACCG 59.199 37.500 0.00 0.00 0.00 4.94
479 718 9.627395 TTTGAGAAACAAAACTATTTTTCGTCA 57.373 25.926 0.00 0.00 44.16 4.35
494 733 6.497785 TTTTCGTCAAGACACCAAAACTAA 57.502 33.333 0.72 0.00 0.00 2.24
505 744 5.407502 ACACCAAAACTAACTTGAAAGTGC 58.592 37.500 0.00 0.00 39.66 4.40
512 751 5.847670 ACTAACTTGAAAGTGCGAATCTC 57.152 39.130 0.00 0.00 39.66 2.75
523 762 1.517913 CGAATCTCGAGCTGCAGCA 60.518 57.895 38.24 19.65 43.74 4.41
537 776 1.275856 TGCAGCATTAAAAAGGGCCAG 59.724 47.619 6.18 0.00 0.00 4.85
547 786 3.806949 AAAAGGGCCAGTTCACATCTA 57.193 42.857 6.18 0.00 0.00 1.98
558 797 0.824109 TCACATCTAAGCCCACGAGG 59.176 55.000 0.00 0.00 39.47 4.63
567 807 4.157120 CCCACGAGGCTAACCCGG 62.157 72.222 0.00 0.00 39.21 5.73
581 822 0.178984 ACCCGGTCCCAAAACGAAAT 60.179 50.000 0.00 0.00 0.00 2.17
582 823 0.524414 CCCGGTCCCAAAACGAAATC 59.476 55.000 0.00 0.00 0.00 2.17
616 857 4.520846 CGCCCGCGCAACTGATTC 62.521 66.667 8.75 0.00 34.03 2.52
617 858 4.520846 GCCCGCGCAACTGATTCG 62.521 66.667 8.75 0.00 34.03 3.34
618 859 3.118454 CCCGCGCAACTGATTCGT 61.118 61.111 8.75 0.00 0.00 3.85
619 860 2.395690 CCGCGCAACTGATTCGTC 59.604 61.111 8.75 0.00 0.00 4.20
620 861 2.379634 CCGCGCAACTGATTCGTCA 61.380 57.895 8.75 0.00 0.00 4.35
712 958 1.594836 CCCCCGAACGAACGAAACA 60.595 57.895 0.14 0.00 35.09 2.83
732 978 1.081774 CAAATTTCCGCGCGAACCA 60.082 52.632 34.63 12.69 0.00 3.67
735 981 2.182614 AATTTCCGCGCGAACCACAG 62.183 55.000 34.63 13.06 0.00 3.66
769 1015 2.440501 CGGATTCGAAATTTCAAGCCG 58.559 47.619 28.39 28.39 39.16 5.52
821 1076 2.648059 CATTTCGGCAATCTTCCTCCT 58.352 47.619 0.00 0.00 0.00 3.69
1098 1362 3.319198 GGCTCCAACCTCGGGTCA 61.319 66.667 0.00 0.00 33.12 4.02
1304 1568 3.016971 TCCTCCCTCCGTCCCGTA 61.017 66.667 0.00 0.00 0.00 4.02
1385 1649 0.802494 GTCGTCAACGCCAATCCATT 59.198 50.000 0.00 0.00 39.60 3.16
1443 1707 2.580867 GAGTACGCTGCTGCTCCG 60.581 66.667 14.03 6.09 36.97 4.63
1533 1797 4.736896 GTCCCGGCGAAGAAGCGT 62.737 66.667 9.30 0.00 38.18 5.07
1596 1860 3.431725 GTTCCGGCCAAGAAGCGG 61.432 66.667 2.24 0.00 0.00 5.52
1602 1866 2.747855 GCCAAGAAGCGGGTCCAG 60.748 66.667 0.00 0.00 0.00 3.86
1636 1900 4.959596 GGATCGCCGCTGCTCCTC 62.960 72.222 0.00 0.00 30.93 3.71
1819 2083 1.144936 CAGTTCATCCCGCCCTCTC 59.855 63.158 0.00 0.00 0.00 3.20
1825 2089 1.074167 ATCCCGCCCTCTCCATCTT 60.074 57.895 0.00 0.00 0.00 2.40
1919 2183 1.371558 CCGCCACCTATCCTAAGGC 59.628 63.158 0.00 0.00 40.62 4.35
1949 2213 0.723981 GCTGAAGCGTCCAAGATGAC 59.276 55.000 0.00 0.00 0.00 3.06
2007 2271 0.958822 AATCCCGCAGAACAAACACC 59.041 50.000 0.00 0.00 0.00 4.16
2025 2289 4.541020 GCAAAAAGAGCGAGTGGC 57.459 55.556 0.00 0.00 44.05 5.01
2057 2321 2.762887 AGAAGCTCTCCGATGTCATCAA 59.237 45.455 13.22 0.00 0.00 2.57
2080 2344 2.490903 GGCATGCAATCTGAAGTTCAGT 59.509 45.455 27.83 15.26 44.58 3.41
2157 2421 0.458543 AAGTCGTCGGTAGCATGCAG 60.459 55.000 21.98 8.28 0.00 4.41
2187 2451 0.393537 ATGCCGAAGAGCCCAAGAAG 60.394 55.000 0.00 0.00 0.00 2.85
2240 2504 0.103026 CTCTCCGATGCCGTCAATGA 59.897 55.000 0.00 0.00 0.00 2.57
2263 2527 2.158623 ACACAATCTGAAGTTCAGGCCA 60.159 45.455 28.33 13.19 44.39 5.36
2267 2531 1.609208 TCTGAAGTTCAGGCCAAAGC 58.391 50.000 28.33 0.00 44.39 3.51
2276 2540 1.968540 AGGCCAAAGCGCTCAAGAC 60.969 57.895 12.06 3.90 41.24 3.01
2385 2649 5.847670 AGAAATTCGAGCAAACTAGTGAC 57.152 39.130 0.00 0.00 0.00 3.67
2390 2654 1.605457 CGAGCAAACTAGTGACCTGCA 60.605 52.381 17.01 0.00 35.44 4.41
2404 2668 1.584380 CCTGCACTGCAAGAAGCTCC 61.584 60.000 4.99 0.00 45.94 4.70
2447 2711 2.103263 AGTCTGAAGTTCAAGCCGAAGT 59.897 45.455 7.06 0.00 39.04 3.01
2451 2715 0.947244 AAGTTCAAGCCGAAGTGCTG 59.053 50.000 0.00 0.00 41.80 4.41
2498 2765 1.922570 CATTGCAAGCTCTCCAATGC 58.077 50.000 16.15 9.28 39.29 3.56
2557 2824 3.482786 CTTGAGAAATTCGAGCAAACGG 58.517 45.455 0.00 0.00 30.63 4.44
2619 2886 2.597505 CGAACAGTGTCAAGTTCAAGCG 60.598 50.000 15.68 3.39 43.20 4.68
2622 2889 1.528586 CAGTGTCAAGTTCAAGCGGAG 59.471 52.381 0.00 0.00 0.00 4.63
2630 2897 4.742201 TCAAGCGGAGGCGCTCAC 62.742 66.667 7.64 0.00 45.26 3.51
2651 2918 1.127951 GAAATTCGACCACGCGATTGT 59.872 47.619 15.93 6.34 40.35 2.71
2685 2952 4.069232 CCAGCACGCGAGGAGGAA 62.069 66.667 15.93 0.00 0.00 3.36
2692 2959 3.112709 GCGAGGAGGAACACACGC 61.113 66.667 0.00 0.00 38.50 5.34
2912 3179 4.127040 CTGCTCGCTCTGCTCCGT 62.127 66.667 0.00 0.00 0.00 4.69
3276 3546 4.719369 GTCGTCGCCGGCTTCTGT 62.719 66.667 26.68 0.00 35.32 3.41
3316 3586 4.019321 TCTGGGAGAAGGTAAAATCCTGTG 60.019 45.833 0.00 0.00 37.93 3.66
3342 3612 8.638685 ATTTTCTTGTCATTGTCTTGTTTGAG 57.361 30.769 0.00 0.00 0.00 3.02
3493 3765 2.880268 CTGGCGATCAATTGCTATGGAA 59.120 45.455 0.00 0.00 37.35 3.53
3516 3792 6.879276 ATGGTGAAGAATTGCATCTCATAG 57.121 37.500 0.00 0.00 0.00 2.23
3550 3830 7.920682 GGATTGTGTCATTGTTCTAGTGTTTTT 59.079 33.333 0.00 0.00 0.00 1.94
3551 3831 9.944663 GATTGTGTCATTGTTCTAGTGTTTTTA 57.055 29.630 0.00 0.00 0.00 1.52
3578 3858 0.318107 CTTTTGGTGTGCCTTCTGCG 60.318 55.000 0.00 0.00 45.60 5.18
3610 3890 8.519526 CAGATATGGTAGAAGATTAGAGGTGTC 58.480 40.741 0.00 0.00 0.00 3.67
3637 3922 5.001232 TGGCATGTAGTTACTTTGGAGTTC 58.999 41.667 0.00 0.00 37.33 3.01
3643 3928 8.883731 CATGTAGTTACTTTGGAGTTCTATTGG 58.116 37.037 0.00 0.00 37.33 3.16
3646 3931 5.705905 AGTTACTTTGGAGTTCTATTGGCAC 59.294 40.000 0.00 0.00 37.33 5.01
3784 4292 3.326836 AGCAGAGTTTGAAGTCTAGGC 57.673 47.619 1.00 2.61 36.59 3.93
3849 4357 9.807649 ATTGAAATAAGAGCATGTATTTTCCAC 57.192 29.630 0.00 0.00 31.60 4.02
3851 4359 8.461222 TGAAATAAGAGCATGTATTTTCCACAG 58.539 33.333 0.00 0.00 31.60 3.66
3950 4471 2.094659 CCGTGCGAAGTAGTGCAGG 61.095 63.158 0.00 0.33 42.68 4.85
3975 4496 3.528594 GCATCTTCGCTGCTTGATG 57.471 52.632 16.42 16.42 39.24 3.07
4024 4545 4.256110 TCAGATCGCTGACAATCACAAAT 58.744 39.130 0.00 0.00 45.88 2.32
4036 4557 7.420002 TGACAATCACAAATTTTCACTCTCAG 58.580 34.615 0.00 0.00 0.00 3.35
4058 4579 4.702131 AGCAACTTGGTCCAAGATGATAAC 59.298 41.667 34.30 21.20 43.67 1.89
4091 4620 4.686091 TGCAGATAGAAACAAGTTCTGACG 59.314 41.667 2.60 0.00 46.48 4.35
4128 4657 6.314400 GGTAAAAAGAAACAAAACAAGGGGAC 59.686 38.462 0.00 0.00 0.00 4.46
4134 4663 2.397597 ACAAAACAAGGGGACAATGCT 58.602 42.857 0.00 0.00 0.00 3.79
4213 4742 4.742201 CGGTCAGGTGCTCCCACG 62.742 72.222 0.00 0.00 43.00 4.94
4214 4743 4.394712 GGTCAGGTGCTCCCACGG 62.395 72.222 0.00 0.00 43.00 4.94
4215 4744 3.311110 GTCAGGTGCTCCCACGGA 61.311 66.667 0.00 0.00 43.00 4.69
4217 4746 2.358737 CAGGTGCTCCCACGGAAC 60.359 66.667 0.00 0.00 43.00 3.62
4222 4751 3.782443 GCTCCCACGGAACCGGAT 61.782 66.667 9.46 0.00 44.69 4.18
4223 4752 2.499685 CTCCCACGGAACCGGATC 59.500 66.667 9.46 5.54 44.69 3.36
4224 4753 3.078836 TCCCACGGAACCGGATCC 61.079 66.667 20.51 20.51 44.69 3.36
4225 4754 3.081409 CCCACGGAACCGGATCCT 61.081 66.667 26.42 12.24 44.69 3.24
4226 4755 2.499685 CCACGGAACCGGATCCTC 59.500 66.667 26.42 8.84 44.69 3.71
4227 4756 2.058595 CCACGGAACCGGATCCTCT 61.059 63.158 26.42 10.25 44.69 3.69
4228 4757 0.754217 CCACGGAACCGGATCCTCTA 60.754 60.000 26.42 0.00 44.69 2.43
4229 4758 1.108776 CACGGAACCGGATCCTCTAA 58.891 55.000 26.42 0.00 44.69 2.10
4230 4759 1.067212 CACGGAACCGGATCCTCTAAG 59.933 57.143 26.42 14.03 44.69 2.18
4231 4760 1.064166 ACGGAACCGGATCCTCTAAGA 60.064 52.381 26.42 0.00 44.69 2.10
4232 4761 2.240279 CGGAACCGGATCCTCTAAGAT 58.760 52.381 26.42 0.00 37.34 2.40
4233 4762 2.029828 CGGAACCGGATCCTCTAAGATG 60.030 54.545 26.42 6.42 37.34 2.90
4234 4763 2.300437 GGAACCGGATCCTCTAAGATGG 59.700 54.545 22.87 3.22 36.50 3.51
4235 4764 3.231818 GAACCGGATCCTCTAAGATGGA 58.768 50.000 9.46 0.00 36.72 3.41
4236 4765 2.883026 ACCGGATCCTCTAAGATGGAG 58.117 52.381 9.46 0.00 35.63 3.86
4237 4766 2.447429 ACCGGATCCTCTAAGATGGAGA 59.553 50.000 9.46 0.00 35.63 3.71
4238 4767 3.117093 ACCGGATCCTCTAAGATGGAGAA 60.117 47.826 9.46 0.00 35.63 2.87
4239 4768 3.509575 CCGGATCCTCTAAGATGGAGAAG 59.490 52.174 10.75 0.00 35.63 2.85
4240 4769 4.148838 CGGATCCTCTAAGATGGAGAAGT 58.851 47.826 10.75 0.00 35.63 3.01
4241 4770 5.317808 CGGATCCTCTAAGATGGAGAAGTA 58.682 45.833 10.75 0.00 35.63 2.24
4242 4771 5.770663 CGGATCCTCTAAGATGGAGAAGTAA 59.229 44.000 10.75 0.00 35.63 2.24
4243 4772 6.265649 CGGATCCTCTAAGATGGAGAAGTAAA 59.734 42.308 10.75 0.00 35.63 2.01
4244 4773 7.523052 CGGATCCTCTAAGATGGAGAAGTAAAG 60.523 44.444 10.75 0.00 35.63 1.85
4245 4774 7.289084 GGATCCTCTAAGATGGAGAAGTAAAGT 59.711 40.741 3.84 0.00 35.63 2.66
4246 4775 7.648039 TCCTCTAAGATGGAGAAGTAAAGTC 57.352 40.000 0.00 0.00 33.03 3.01
4247 4776 7.415086 TCCTCTAAGATGGAGAAGTAAAGTCT 58.585 38.462 0.00 0.00 33.03 3.24
4248 4777 7.558444 TCCTCTAAGATGGAGAAGTAAAGTCTC 59.442 40.741 0.00 0.00 40.75 3.36
4249 4778 7.323049 TCTAAGATGGAGAAGTAAAGTCTCG 57.677 40.000 0.00 0.00 42.13 4.04
4250 4779 7.110810 TCTAAGATGGAGAAGTAAAGTCTCGA 58.889 38.462 0.00 0.00 42.13 4.04
4251 4780 6.783708 AAGATGGAGAAGTAAAGTCTCGAT 57.216 37.500 0.00 0.00 41.56 3.59
4252 4781 6.142818 AGATGGAGAAGTAAAGTCTCGATG 57.857 41.667 4.01 0.00 39.71 3.84
4253 4782 4.111375 TGGAGAAGTAAAGTCTCGATGC 57.889 45.455 0.00 0.00 42.13 3.91
4254 4783 3.764434 TGGAGAAGTAAAGTCTCGATGCT 59.236 43.478 0.00 0.00 42.13 3.79
4255 4784 4.948004 TGGAGAAGTAAAGTCTCGATGCTA 59.052 41.667 0.00 0.00 42.13 3.49
4256 4785 5.594725 TGGAGAAGTAAAGTCTCGATGCTAT 59.405 40.000 0.00 0.00 42.13 2.97
4257 4786 6.771267 TGGAGAAGTAAAGTCTCGATGCTATA 59.229 38.462 0.00 0.00 42.13 1.31
4258 4787 7.041030 TGGAGAAGTAAAGTCTCGATGCTATAG 60.041 40.741 0.00 0.00 42.13 1.31
4259 4788 7.040961 GGAGAAGTAAAGTCTCGATGCTATAGT 60.041 40.741 0.84 0.00 42.13 2.12
4260 4789 7.644490 AGAAGTAAAGTCTCGATGCTATAGTG 58.356 38.462 0.84 0.00 0.00 2.74
4261 4790 5.764131 AGTAAAGTCTCGATGCTATAGTGC 58.236 41.667 0.84 0.00 0.00 4.40
4262 4791 4.927978 AAAGTCTCGATGCTATAGTGCT 57.072 40.909 0.84 0.00 0.00 4.40
4263 4792 6.711194 AGTAAAGTCTCGATGCTATAGTGCTA 59.289 38.462 0.84 0.00 0.00 3.49
4264 4793 5.621197 AAGTCTCGATGCTATAGTGCTAG 57.379 43.478 0.84 0.00 0.00 3.42
4265 4794 4.647611 AGTCTCGATGCTATAGTGCTAGT 58.352 43.478 0.84 0.00 0.00 2.57
4266 4795 4.693566 AGTCTCGATGCTATAGTGCTAGTC 59.306 45.833 0.84 0.00 0.00 2.59
4267 4796 4.693566 GTCTCGATGCTATAGTGCTAGTCT 59.306 45.833 0.84 0.00 0.00 3.24
4268 4797 5.870433 GTCTCGATGCTATAGTGCTAGTCTA 59.130 44.000 0.84 0.00 0.00 2.59
4269 4798 6.035650 GTCTCGATGCTATAGTGCTAGTCTAG 59.964 46.154 2.18 2.18 0.00 2.43
4270 4799 5.795972 TCGATGCTATAGTGCTAGTCTAGT 58.204 41.667 8.68 0.00 0.00 2.57
4271 4800 5.639931 TCGATGCTATAGTGCTAGTCTAGTG 59.360 44.000 8.68 0.00 0.00 2.74
4272 4801 5.410132 CGATGCTATAGTGCTAGTCTAGTGT 59.590 44.000 8.68 0.00 0.00 3.55
4273 4802 6.590677 CGATGCTATAGTGCTAGTCTAGTGTA 59.409 42.308 8.68 0.00 0.00 2.90
4274 4803 7.117956 CGATGCTATAGTGCTAGTCTAGTGTAA 59.882 40.741 8.68 0.00 0.00 2.41
4275 4804 8.693120 ATGCTATAGTGCTAGTCTAGTGTAAA 57.307 34.615 8.68 0.00 0.00 2.01
4276 4805 8.515695 TGCTATAGTGCTAGTCTAGTGTAAAA 57.484 34.615 8.68 0.00 0.00 1.52
4277 4806 9.132923 TGCTATAGTGCTAGTCTAGTGTAAAAT 57.867 33.333 8.68 0.00 0.00 1.82
4278 4807 9.400638 GCTATAGTGCTAGTCTAGTGTAAAATG 57.599 37.037 8.68 0.00 0.00 2.32
4283 4812 9.555727 AGTGCTAGTCTAGTGTAAAATGAAAAA 57.444 29.630 8.68 0.00 0.00 1.94
4284 4813 9.813080 GTGCTAGTCTAGTGTAAAATGAAAAAG 57.187 33.333 8.68 0.00 0.00 2.27
4285 4814 9.772973 TGCTAGTCTAGTGTAAAATGAAAAAGA 57.227 29.630 8.68 0.00 0.00 2.52
4317 4846 8.709272 AAGAACTGTTAGTATATACTCCCTCC 57.291 38.462 18.68 4.81 37.73 4.30
4318 4847 6.941436 AGAACTGTTAGTATATACTCCCTCCG 59.059 42.308 18.68 6.90 37.73 4.63
4319 4848 6.198237 ACTGTTAGTATATACTCCCTCCGT 57.802 41.667 18.68 7.46 37.73 4.69
4320 4849 6.237154 ACTGTTAGTATATACTCCCTCCGTC 58.763 44.000 18.68 3.49 37.73 4.79
4321 4850 5.564550 TGTTAGTATATACTCCCTCCGTCC 58.435 45.833 18.68 0.00 37.73 4.79
4322 4851 3.347077 AGTATATACTCCCTCCGTCCG 57.653 52.381 9.71 0.00 0.00 4.79
4323 4852 2.026449 AGTATATACTCCCTCCGTCCGG 60.026 54.545 9.71 0.00 0.00 5.14
4324 4853 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
4325 4854 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
4326 4855 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4327 4856 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4328 4857 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4329 4858 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4330 4859 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4331 4860 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4332 4861 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4333 4862 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4334 4863 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4335 4864 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4336 4865 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4337 4866 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4338 4867 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4339 4868 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4340 4869 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4341 4870 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4342 4871 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4343 4872 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4344 4873 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
4345 4874 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
4346 4875 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
4354 4883 9.918630 ACTTGTCATCAAAATGAATAAAAGAGG 57.081 29.630 0.00 0.00 43.42 3.69
4410 4939 9.252962 ACATCTCTTTTTGTTCATTTTGATGAC 57.747 29.630 0.00 0.00 33.85 3.06
4411 4940 9.251792 CATCTCTTTTTGTTCATTTTGATGACA 57.748 29.630 0.00 0.00 32.05 3.58
4412 4941 9.820725 ATCTCTTTTTGTTCATTTTGATGACAA 57.179 25.926 0.00 0.00 0.00 3.18
4413 4942 9.304731 TCTCTTTTTGTTCATTTTGATGACAAG 57.695 29.630 0.00 0.00 37.32 3.16
4414 4943 9.090692 CTCTTTTTGTTCATTTTGATGACAAGT 57.909 29.630 0.00 0.00 37.32 3.16
4421 4950 9.179552 TGTTCATTTTGATGACAAGTATTTTCG 57.820 29.630 0.00 0.00 37.32 3.46
4422 4951 8.638565 GTTCATTTTGATGACAAGTATTTTCGG 58.361 33.333 0.00 0.00 37.32 4.30
4423 4952 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
4424 4953 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
4425 4954 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
4426 4955 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
4427 4956 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
4428 4957 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
4429 4958 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
4430 4959 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4431 4960 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
4432 4961 4.184629 CAAGTATTTTCGGACAGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
4433 4962 3.442076 AGTATTTTCGGACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
4434 4963 4.607239 AGTATTTTCGGACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
4435 4964 5.209659 AGTATTTTCGGACAGAGGGAGTAT 58.790 41.667 0.00 0.00 0.00 2.12
4436 4965 5.661759 AGTATTTTCGGACAGAGGGAGTATT 59.338 40.000 0.00 0.00 0.00 1.89
4437 4966 6.837568 AGTATTTTCGGACAGAGGGAGTATTA 59.162 38.462 0.00 0.00 0.00 0.98
4438 4967 5.593679 TTTTCGGACAGAGGGAGTATTAG 57.406 43.478 0.00 0.00 0.00 1.73
4439 4968 3.947612 TCGGACAGAGGGAGTATTAGT 57.052 47.619 0.00 0.00 0.00 2.24
4440 4969 5.378230 TTCGGACAGAGGGAGTATTAGTA 57.622 43.478 0.00 0.00 0.00 1.82
4441 4970 4.970711 TCGGACAGAGGGAGTATTAGTAG 58.029 47.826 0.00 0.00 0.00 2.57
4442 4971 4.073549 CGGACAGAGGGAGTATTAGTAGG 58.926 52.174 0.00 0.00 0.00 3.18
4443 4972 3.827876 GGACAGAGGGAGTATTAGTAGGC 59.172 52.174 0.00 0.00 0.00 3.93
4444 4973 3.827876 GACAGAGGGAGTATTAGTAGGCC 59.172 52.174 0.00 0.00 0.00 5.19
4445 4974 3.467863 ACAGAGGGAGTATTAGTAGGCCT 59.532 47.826 11.78 11.78 0.00 5.19
4446 4975 4.078513 ACAGAGGGAGTATTAGTAGGCCTT 60.079 45.833 12.58 0.00 0.00 4.35
4447 4976 4.902448 CAGAGGGAGTATTAGTAGGCCTTT 59.098 45.833 12.58 1.84 0.00 3.11
4448 4977 5.367060 CAGAGGGAGTATTAGTAGGCCTTTT 59.633 44.000 12.58 1.39 0.00 2.27
4449 4978 5.367060 AGAGGGAGTATTAGTAGGCCTTTTG 59.633 44.000 12.58 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.070770 ACTTTGCATGTGAGTTTGAACAA 57.929 34.783 0.00 0.00 0.00 2.83
27 28 5.581126 TGAGAAACTTTGCATGTGAGTTT 57.419 34.783 17.29 17.29 43.95 2.66
28 29 5.581126 TTGAGAAACTTTGCATGTGAGTT 57.419 34.783 0.00 0.00 35.27 3.01
131 134 5.509840 GGTCTACGAATCTGGATGCAATACT 60.510 44.000 0.00 0.00 0.00 2.12
132 135 4.686554 GGTCTACGAATCTGGATGCAATAC 59.313 45.833 0.00 0.00 0.00 1.89
136 139 2.107366 TGGTCTACGAATCTGGATGCA 58.893 47.619 0.00 0.00 0.00 3.96
137 140 2.474816 GTGGTCTACGAATCTGGATGC 58.525 52.381 0.00 0.00 0.00 3.91
154 163 0.949105 GTGTACTTGTCGCCAGGTGG 60.949 60.000 0.00 0.00 32.49 4.61
178 187 2.398554 GCGCCTTTGGATCGCTTCA 61.399 57.895 0.00 0.00 44.79 3.02
180 189 3.499737 CGCGCCTTTGGATCGCTT 61.500 61.111 0.00 0.00 45.87 4.68
206 215 1.052124 TCCGGTGAATAAGGGGCGAT 61.052 55.000 0.00 0.00 0.00 4.58
247 258 4.395959 TCACAACTACTTTCCGACTGTT 57.604 40.909 0.00 0.00 0.00 3.16
278 289 9.617523 AAGTTCATCAAATTCTTGACCAAAAAT 57.382 25.926 0.00 0.00 44.28 1.82
284 295 8.822652 AAATGAAGTTCATCAAATTCTTGACC 57.177 30.769 18.52 0.00 44.28 4.02
365 376 6.252441 TGCAGATAAACAAAAACAACAACTCG 59.748 34.615 0.00 0.00 0.00 4.18
374 385 4.226761 CCTCGGTGCAGATAAACAAAAAC 58.773 43.478 0.00 0.00 0.00 2.43
375 386 3.886505 ACCTCGGTGCAGATAAACAAAAA 59.113 39.130 0.00 0.00 0.00 1.94
393 415 4.089361 AGGACATGGATTTTTGGAACCTC 58.911 43.478 0.00 0.00 0.00 3.85
475 714 5.064198 TCAAGTTAGTTTTGGTGTCTTGACG 59.936 40.000 0.00 0.00 36.16 4.35
479 718 7.312899 CACTTTCAAGTTAGTTTTGGTGTCTT 58.687 34.615 0.00 0.00 37.08 3.01
494 733 2.989840 CTCGAGATTCGCACTTTCAAGT 59.010 45.455 6.58 0.00 40.21 3.16
505 744 0.875040 ATGCTGCAGCTCGAGATTCG 60.875 55.000 36.61 0.00 42.66 3.34
512 751 2.523015 CCTTTTTAATGCTGCAGCTCG 58.477 47.619 36.61 16.17 42.66 5.03
523 762 5.086621 AGATGTGAACTGGCCCTTTTTAAT 58.913 37.500 0.00 0.00 0.00 1.40
537 776 2.271800 CTCGTGGGCTTAGATGTGAAC 58.728 52.381 0.00 0.00 0.00 3.18
558 797 1.579964 CGTTTTGGGACCGGGTTAGC 61.580 60.000 6.32 0.00 0.00 3.09
560 799 0.471617 TTCGTTTTGGGACCGGGTTA 59.528 50.000 6.32 0.00 0.00 2.85
563 802 0.524414 GATTTCGTTTTGGGACCGGG 59.476 55.000 6.32 0.00 0.00 5.73
567 807 1.544246 CTGGGGATTTCGTTTTGGGAC 59.456 52.381 0.00 0.00 0.00 4.46
613 854 1.498865 GGATGGCGCGAATGACGAAT 61.499 55.000 12.10 0.00 45.77 3.34
614 855 2.171079 GGATGGCGCGAATGACGAA 61.171 57.895 12.10 0.00 45.77 3.85
615 856 2.584970 GGATGGCGCGAATGACGA 60.585 61.111 12.10 0.00 45.77 4.20
616 857 3.640000 GGGATGGCGCGAATGACG 61.640 66.667 12.10 0.00 45.66 4.35
617 858 2.203070 AGGGATGGCGCGAATGAC 60.203 61.111 12.10 0.00 0.00 3.06
618 859 2.108976 GAGGGATGGCGCGAATGA 59.891 61.111 12.10 0.00 0.00 2.57
619 860 1.375853 TTTGAGGGATGGCGCGAATG 61.376 55.000 12.10 0.00 0.00 2.67
620 861 0.679640 TTTTGAGGGATGGCGCGAAT 60.680 50.000 12.10 1.20 0.00 3.34
676 920 2.095718 GGGGCGATTTAGCGATGAAATC 60.096 50.000 0.00 0.00 40.89 2.17
702 947 3.360289 GCGGAAATTTGTTGTTTCGTTCG 60.360 43.478 0.00 0.00 36.64 3.95
712 958 0.662077 GGTTCGCGCGGAAATTTGTT 60.662 50.000 31.69 0.00 36.14 2.83
769 1015 0.463833 ATGGCGTCTCGGGGATTTTC 60.464 55.000 0.00 0.00 0.00 2.29
821 1076 1.222387 CGAATTTGAGGGGGCGGTA 59.778 57.895 0.00 0.00 0.00 4.02
915 1177 0.974383 TTTGACCGAGGAGGGAAGAC 59.026 55.000 0.00 0.00 46.96 3.01
998 1262 3.550431 CCCCGGCGATCTCCATGT 61.550 66.667 9.30 0.00 0.00 3.21
1304 1568 1.128188 AACGAGGGGAGGCTTCTTGT 61.128 55.000 0.00 0.00 0.00 3.16
1626 1890 3.119709 GACGGAGAGAGGAGCAGCG 62.120 68.421 0.00 0.00 0.00 5.18
1825 2089 2.366590 CCCCATCTGACTTCATCGATGA 59.633 50.000 23.99 23.99 39.06 2.92
1861 2125 2.847327 TGAGGACAGGCTTCTTTGAG 57.153 50.000 0.00 0.00 0.00 3.02
1919 2183 2.787249 CTTCAGCACCATTCGCCG 59.213 61.111 0.00 0.00 0.00 6.46
1949 2213 1.566018 GACTTCGTCGGGCTTGTTGG 61.566 60.000 0.00 0.00 0.00 3.77
2024 2288 2.197643 GAGCTTCTTGCAGTGCAGGC 62.198 60.000 21.62 20.32 45.94 4.85
2025 2289 0.605860 AGAGCTTCTTGCAGTGCAGG 60.606 55.000 20.52 20.52 45.94 4.85
2057 2321 3.093814 TGAACTTCAGATTGCATGCCAT 58.906 40.909 16.68 10.12 0.00 4.40
2080 2344 3.056821 TCGAATTTCTTGAGCTCTTCGGA 60.057 43.478 24.49 13.76 36.90 4.55
2157 2421 2.670414 CTCTTCGGCATGAACTTCAGAC 59.330 50.000 0.00 0.00 31.87 3.51
2187 2451 3.061429 GCAGATCACTAGTTTGCTCGAAC 59.939 47.826 0.00 0.00 0.00 3.95
2263 2527 1.728971 CTCGAATGTCTTGAGCGCTTT 59.271 47.619 13.26 0.00 0.00 3.51
2276 2540 4.260132 GCAGATCACTAGTTTGCTCGAATG 60.260 45.833 0.00 0.00 0.00 2.67
2304 2568 3.064134 CGACGACATCAGAGAGCTTCTTA 59.936 47.826 0.00 0.00 32.41 2.10
2385 2649 1.584380 GGAGCTTCTTGCAGTGCAGG 61.584 60.000 20.52 20.52 45.94 4.85
2390 2654 1.557269 ATCGGGGAGCTTCTTGCAGT 61.557 55.000 0.00 0.00 45.94 4.40
2404 2668 3.409856 GTCATTGACGGCATCGGG 58.590 61.111 0.00 0.00 41.39 5.14
2422 2686 1.265365 GGCTTGAACTTCAGACTGTGC 59.735 52.381 1.59 0.00 0.00 4.57
2447 2711 3.606846 CGTTTGCTCGAATTTCTTCAGCA 60.607 43.478 9.33 9.33 40.51 4.41
2451 2715 4.084537 TCACTCGTTTGCTCGAATTTCTTC 60.085 41.667 0.00 0.00 39.34 2.87
2514 2781 1.277557 ACTTCGGCTTGAGCTTCAGAT 59.722 47.619 2.66 0.00 41.70 2.90
2538 2805 1.196808 GCCGTTTGCTCGAATTTCTCA 59.803 47.619 0.00 0.00 36.87 3.27
2557 2824 0.594602 TTCTTGCAGTGCACATCAGC 59.405 50.000 19.58 16.95 38.71 4.26
2563 2830 1.578423 GGAGCTTCTTGCAGTGCAC 59.422 57.895 19.58 9.40 45.94 4.57
2619 2886 1.716172 GAATTTCGTGAGCGCCTCC 59.284 57.895 2.29 0.00 38.14 4.30
2622 2889 1.058903 GTCGAATTTCGTGAGCGCC 59.941 57.895 17.61 0.00 41.35 6.53
2630 2897 0.368907 AATCGCGTGGTCGAATTTCG 59.631 50.000 12.54 12.54 42.15 3.46
2651 2918 2.669569 GCGCTGCCACTTCAGGAA 60.670 61.111 0.00 0.00 34.74 3.36
2670 2937 3.303135 TGTTCCTCCTCGCGTGCT 61.303 61.111 5.77 0.00 0.00 4.40
2685 2952 0.597637 CTTCGTCTTCCTGCGTGTGT 60.598 55.000 0.00 0.00 0.00 3.72
2692 2959 1.433534 GCCACTTCTTCGTCTTCCTG 58.566 55.000 0.00 0.00 0.00 3.86
2795 3062 1.885163 GAACACGATGGGGTCCGACT 61.885 60.000 0.00 0.00 0.00 4.18
3125 3395 0.102120 GCTCTCGCAGATGTAGCAGT 59.898 55.000 0.00 0.00 33.89 4.40
3276 3546 4.232905 AGCTTGGTGTGCTCCCTA 57.767 55.556 0.00 0.00 35.67 3.53
3316 3586 8.633075 TCAAACAAGACAATGACAAGAAAATC 57.367 30.769 0.00 0.00 0.00 2.17
3368 3638 6.760770 ACACATACACAAATCCAACCAAAAAG 59.239 34.615 0.00 0.00 0.00 2.27
3493 3765 6.363065 ACTATGAGATGCAATTCTTCACCAT 58.637 36.000 0.00 0.00 0.00 3.55
3516 3792 6.428159 AGAACAATGACACAATCCTAGACAAC 59.572 38.462 0.00 0.00 0.00 3.32
3550 3830 4.479158 AGGCACACCAAAAGGAGAAAATA 58.521 39.130 0.00 0.00 39.06 1.40
3551 3831 3.308401 AGGCACACCAAAAGGAGAAAAT 58.692 40.909 0.00 0.00 39.06 1.82
3605 3885 2.698855 ACTACATGCCATGAGACACC 57.301 50.000 12.53 0.00 0.00 4.16
3610 3890 5.185454 TCCAAAGTAACTACATGCCATGAG 58.815 41.667 12.53 7.10 0.00 2.90
3637 3922 5.643379 ACACCATAAAACTGTGCCAATAG 57.357 39.130 0.00 0.00 33.30 1.73
3643 3928 4.755123 ACAGACTACACCATAAAACTGTGC 59.245 41.667 0.00 0.00 36.29 4.57
3646 3931 8.827177 TTTCTACAGACTACACCATAAAACTG 57.173 34.615 0.00 0.00 0.00 3.16
3704 3992 4.792068 ACCCAACTTCTTGACATCAGAAA 58.208 39.130 0.00 0.00 0.00 2.52
3784 4292 9.877178 AATTACAACTAGAGACTGTTAATCCAG 57.123 33.333 0.00 0.00 38.45 3.86
3849 4357 0.039798 AATGCTTGCTCGCAACACTG 60.040 50.000 0.00 0.00 44.06 3.66
3851 4359 1.466360 CCTAATGCTTGCTCGCAACAC 60.466 52.381 0.00 0.00 44.06 3.32
3871 4389 6.136541 ACTGAATAAATTCCGAGGCAAATC 57.863 37.500 0.41 0.00 35.97 2.17
3950 4471 3.528594 CAGCGAAGATGCTCATTGC 57.471 52.632 0.00 0.00 45.23 3.56
3975 4496 5.516090 TGCGGTTTTGAATTCTTTAGTCAC 58.484 37.500 7.05 0.00 29.11 3.67
4024 4545 3.620488 ACCAAGTTGCTGAGAGTGAAAA 58.380 40.909 0.00 0.00 0.00 2.29
4036 4557 4.458989 TGTTATCATCTTGGACCAAGTTGC 59.541 41.667 29.25 19.88 41.66 4.17
4058 4579 2.620251 TCTATCTGCACCGGGAAATG 57.380 50.000 6.32 0.00 0.00 2.32
4128 4657 5.660629 TCAACATTTTGAAAGCAGCATTG 57.339 34.783 0.00 0.00 38.87 2.82
4213 4742 2.300437 CCATCTTAGAGGATCCGGTTCC 59.700 54.545 22.05 22.05 33.66 3.62
4214 4743 3.231818 TCCATCTTAGAGGATCCGGTTC 58.768 50.000 5.98 1.67 33.66 3.62
4215 4744 3.117093 TCTCCATCTTAGAGGATCCGGTT 60.117 47.826 5.98 0.00 33.66 4.44
4217 4746 3.162147 TCTCCATCTTAGAGGATCCGG 57.838 52.381 5.98 0.00 33.66 5.14
4219 4748 7.289084 ACTTTACTTCTCCATCTTAGAGGATCC 59.711 40.741 2.48 2.48 33.66 3.36
4220 4749 8.245195 ACTTTACTTCTCCATCTTAGAGGATC 57.755 38.462 0.00 0.00 32.53 3.36
4221 4750 8.065007 AGACTTTACTTCTCCATCTTAGAGGAT 58.935 37.037 0.00 0.00 32.53 3.24
4222 4751 7.415086 AGACTTTACTTCTCCATCTTAGAGGA 58.585 38.462 0.00 0.00 31.96 3.71
4223 4752 7.468084 CGAGACTTTACTTCTCCATCTTAGAGG 60.468 44.444 0.00 0.00 36.87 3.69
4224 4753 7.281324 TCGAGACTTTACTTCTCCATCTTAGAG 59.719 40.741 0.00 0.00 36.87 2.43
4225 4754 7.110810 TCGAGACTTTACTTCTCCATCTTAGA 58.889 38.462 0.00 0.00 36.87 2.10
4226 4755 7.323049 TCGAGACTTTACTTCTCCATCTTAG 57.677 40.000 0.00 0.00 36.87 2.18
4227 4756 7.682261 GCATCGAGACTTTACTTCTCCATCTTA 60.682 40.741 0.00 0.00 36.87 2.10
4228 4757 6.568869 CATCGAGACTTTACTTCTCCATCTT 58.431 40.000 0.00 0.00 36.87 2.40
4229 4758 5.451242 GCATCGAGACTTTACTTCTCCATCT 60.451 44.000 0.00 0.00 36.87 2.90
4230 4759 4.742659 GCATCGAGACTTTACTTCTCCATC 59.257 45.833 0.00 0.00 36.87 3.51
4231 4760 4.404073 AGCATCGAGACTTTACTTCTCCAT 59.596 41.667 0.00 0.00 36.87 3.41
4232 4761 3.764434 AGCATCGAGACTTTACTTCTCCA 59.236 43.478 0.00 0.00 36.87 3.86
4233 4762 4.379339 AGCATCGAGACTTTACTTCTCC 57.621 45.455 0.00 0.00 36.87 3.71
4234 4763 7.801315 CACTATAGCATCGAGACTTTACTTCTC 59.199 40.741 0.00 0.00 36.85 2.87
4235 4764 7.644490 CACTATAGCATCGAGACTTTACTTCT 58.356 38.462 0.00 0.00 0.00 2.85
4236 4765 6.361214 GCACTATAGCATCGAGACTTTACTTC 59.639 42.308 0.00 0.00 0.00 3.01
4237 4766 6.039941 AGCACTATAGCATCGAGACTTTACTT 59.960 38.462 0.00 0.00 36.85 2.24
4238 4767 5.533154 AGCACTATAGCATCGAGACTTTACT 59.467 40.000 0.00 0.00 36.85 2.24
4239 4768 5.764131 AGCACTATAGCATCGAGACTTTAC 58.236 41.667 0.00 0.00 36.85 2.01
4240 4769 6.711194 ACTAGCACTATAGCATCGAGACTTTA 59.289 38.462 0.00 0.00 36.85 1.85
4241 4770 4.927978 AGCACTATAGCATCGAGACTTT 57.072 40.909 0.00 0.00 36.85 2.66
4242 4771 5.067273 ACTAGCACTATAGCATCGAGACTT 58.933 41.667 0.00 0.00 36.85 3.01
4243 4772 4.647611 ACTAGCACTATAGCATCGAGACT 58.352 43.478 0.00 0.00 36.85 3.24
4244 4773 4.693566 AGACTAGCACTATAGCATCGAGAC 59.306 45.833 0.00 0.00 36.85 3.36
4245 4774 4.900684 AGACTAGCACTATAGCATCGAGA 58.099 43.478 0.00 0.00 36.85 4.04
4246 4775 5.872617 ACTAGACTAGCACTATAGCATCGAG 59.127 44.000 9.52 0.00 36.85 4.04
4247 4776 5.639931 CACTAGACTAGCACTATAGCATCGA 59.360 44.000 9.52 0.00 36.85 3.59
4248 4777 5.410132 ACACTAGACTAGCACTATAGCATCG 59.590 44.000 9.52 0.00 36.85 3.84
4249 4778 6.811253 ACACTAGACTAGCACTATAGCATC 57.189 41.667 9.52 0.00 36.85 3.91
4250 4779 8.693120 TTTACACTAGACTAGCACTATAGCAT 57.307 34.615 9.52 0.00 36.85 3.79
4251 4780 8.515695 TTTTACACTAGACTAGCACTATAGCA 57.484 34.615 9.52 0.00 36.85 3.49
4252 4781 9.400638 CATTTTACACTAGACTAGCACTATAGC 57.599 37.037 9.52 0.00 0.00 2.97
4257 4786 9.555727 TTTTTCATTTTACACTAGACTAGCACT 57.444 29.630 9.52 0.00 0.00 4.40
4258 4787 9.813080 CTTTTTCATTTTACACTAGACTAGCAC 57.187 33.333 9.52 0.00 0.00 4.40
4259 4788 9.772973 TCTTTTTCATTTTACACTAGACTAGCA 57.227 29.630 9.52 0.00 0.00 3.49
4291 4820 9.804977 GGAGGGAGTATATACTAACAGTTCTTA 57.195 37.037 15.42 0.00 36.50 2.10
4292 4821 7.447853 CGGAGGGAGTATATACTAACAGTTCTT 59.552 40.741 15.42 0.00 36.50 2.52
4293 4822 6.941436 CGGAGGGAGTATATACTAACAGTTCT 59.059 42.308 15.42 5.78 36.50 3.01
4294 4823 6.714356 ACGGAGGGAGTATATACTAACAGTTC 59.286 42.308 15.42 9.84 36.50 3.01
4295 4824 6.608922 ACGGAGGGAGTATATACTAACAGTT 58.391 40.000 15.42 0.00 36.50 3.16
4296 4825 6.198237 ACGGAGGGAGTATATACTAACAGT 57.802 41.667 15.42 10.45 36.50 3.55
4297 4826 5.647225 GGACGGAGGGAGTATATACTAACAG 59.353 48.000 15.42 9.93 36.50 3.16
4298 4827 5.564550 GGACGGAGGGAGTATATACTAACA 58.435 45.833 15.42 0.00 36.50 2.41
4299 4828 4.633565 CGGACGGAGGGAGTATATACTAAC 59.366 50.000 15.42 11.17 36.50 2.34
4300 4829 4.323792 CCGGACGGAGGGAGTATATACTAA 60.324 50.000 15.42 0.00 35.25 2.24
4301 4830 3.198635 CCGGACGGAGGGAGTATATACTA 59.801 52.174 15.42 0.00 35.25 1.82
4302 4831 2.026449 CCGGACGGAGGGAGTATATACT 60.026 54.545 15.37 15.37 36.96 2.12
4303 4832 2.026822 TCCGGACGGAGGGAGTATATAC 60.027 54.545 9.76 4.60 39.76 1.47
4304 4833 2.269023 TCCGGACGGAGGGAGTATATA 58.731 52.381 9.76 0.00 39.76 0.86
4305 4834 1.070604 TCCGGACGGAGGGAGTATAT 58.929 55.000 9.76 0.00 39.76 0.86
4306 4835 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
4307 4836 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
4308 4837 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4309 4838 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4310 4839 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4311 4840 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4312 4841 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4313 4842 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4314 4843 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4315 4844 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4316 4845 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4317 4846 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4318 4847 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4319 4848 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
4320 4849 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
4321 4850 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
4328 4857 9.918630 CCTCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
4384 4913 9.252962 GTCATCAAAATGAACAAAAAGAGATGT 57.747 29.630 0.00 0.00 43.42 3.06
4385 4914 9.251792 TGTCATCAAAATGAACAAAAAGAGATG 57.748 29.630 0.00 0.00 43.42 2.90
4386 4915 9.820725 TTGTCATCAAAATGAACAAAAAGAGAT 57.179 25.926 0.00 0.00 43.42 2.75
4387 4916 9.304731 CTTGTCATCAAAATGAACAAAAAGAGA 57.695 29.630 0.87 0.00 43.42 3.10
4388 4917 9.090692 ACTTGTCATCAAAATGAACAAAAAGAG 57.909 29.630 0.00 0.00 43.42 2.85
4395 4924 9.179552 CGAAAATACTTGTCATCAAAATGAACA 57.820 29.630 0.00 0.00 43.42 3.18
4396 4925 8.638565 CCGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
4397 4926 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
4398 4927 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
4399 4928 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
4400 4929 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
4401 4930 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
4402 4931 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
4403 4932 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
4404 4933 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
4405 4934 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
4406 4935 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
4407 4936 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
4408 4937 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
4409 4938 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
4410 4939 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
4411 4940 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
4412 4941 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
4413 4942 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
4414 4943 6.837568 ACTAATACTCCCTCTGTCCGAAAATA 59.162 38.462 0.00 0.00 0.00 1.40
4415 4944 5.661759 ACTAATACTCCCTCTGTCCGAAAAT 59.338 40.000 0.00 0.00 0.00 1.82
4416 4945 5.021458 ACTAATACTCCCTCTGTCCGAAAA 58.979 41.667 0.00 0.00 0.00 2.29
4417 4946 4.607239 ACTAATACTCCCTCTGTCCGAAA 58.393 43.478 0.00 0.00 0.00 3.46
4418 4947 4.246712 ACTAATACTCCCTCTGTCCGAA 57.753 45.455 0.00 0.00 0.00 4.30
4419 4948 3.947612 ACTAATACTCCCTCTGTCCGA 57.052 47.619 0.00 0.00 0.00 4.55
4420 4949 4.073549 CCTACTAATACTCCCTCTGTCCG 58.926 52.174 0.00 0.00 0.00 4.79
4421 4950 3.827876 GCCTACTAATACTCCCTCTGTCC 59.172 52.174 0.00 0.00 0.00 4.02
4422 4951 3.827876 GGCCTACTAATACTCCCTCTGTC 59.172 52.174 0.00 0.00 0.00 3.51
4423 4952 3.467863 AGGCCTACTAATACTCCCTCTGT 59.532 47.826 1.29 0.00 0.00 3.41
4424 4953 4.120946 AGGCCTACTAATACTCCCTCTG 57.879 50.000 1.29 0.00 0.00 3.35
4425 4954 4.836255 AAGGCCTACTAATACTCCCTCT 57.164 45.455 5.16 0.00 0.00 3.69
4426 4955 5.612351 CAAAAGGCCTACTAATACTCCCTC 58.388 45.833 5.16 0.00 0.00 4.30
4427 4956 5.632034 CAAAAGGCCTACTAATACTCCCT 57.368 43.478 5.16 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.