Multiple sequence alignment - TraesCS7D01G203900

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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 TraesCS7D01G203900 chr7D 100.000 5744 0 0 1 5744 161838672 161844415 0.000000 10608.0
1 TraesCS7D01G203900 chr7D 94.737 38 0 1 5709 5744 171071784 171071747 0.000224 58.4
2 TraesCS7D01G203900 chr7B 91.360 3889 221 68 1885 5720 123858864 123862690 0.000000 5214.0
3 TraesCS7D01G203900 chr7B 88.738 1918 126 43 1 1878 123856867 123858734 0.000000 2263.0
4 TraesCS7D01G203900 chr7A 93.420 2082 93 29 3672 5720 162924733 162926803 0.000000 3046.0
5 TraesCS7D01G203900 chr7A 89.137 2550 131 55 307 2799 162920408 162922868 0.000000 3040.0
6 TraesCS7D01G203900 chr7A 94.040 755 33 4 2784 3534 162923934 162924680 0.000000 1134.0
7 TraesCS7D01G203900 chr7A 92.105 38 3 0 3606 3643 82192160 82192123 0.003000 54.7
8 TraesCS7D01G203900 chr5A 94.872 39 2 0 3605 3643 248531276 248531314 0.000017 62.1
9 TraesCS7D01G203900 chr5A 94.595 37 2 0 3607 3643 681242173 681242137 0.000224 58.4
10 TraesCS7D01G203900 chr2D 97.297 37 0 1 5708 5744 518035195 518035160 0.000017 62.1
11 TraesCS7D01G203900 chr2D 92.857 42 2 1 5704 5744 620316598 620316639 0.000062 60.2
12 TraesCS7D01G203900 chr2D 92.683 41 2 1 5704 5744 516411011 516410972 0.000224 58.4
13 TraesCS7D01G203900 chr1B 100.000 33 0 0 5712 5744 386038534 386038566 0.000017 62.1
14 TraesCS7D01G203900 chr1A 94.872 39 2 0 3605 3643 164468750 164468788 0.000017 62.1
15 TraesCS7D01G203900 chr1D 100.000 32 0 0 5713 5744 320215307 320215338 0.000062 60.2
16 TraesCS7D01G203900 chr6B 94.595 37 2 0 3607 3643 421000496 421000532 0.000224 58.4
17 TraesCS7D01G203900 chr5B 100.000 31 0 0 5714 5744 567777376 567777406 0.000224 58.4
18 TraesCS7D01G203900 chr3D 100.000 31 0 0 5714 5744 591718938 591718908 0.000224 58.4
19 TraesCS7D01G203900 chr3D 94.444 36 2 0 3606 3641 185065231 185065266 0.000804 56.5
20 TraesCS7D01G203900 chr4D 97.059 34 0 1 5711 5744 218123035 218123003 0.000804 56.5
21 TraesCS7D01G203900 chr4B 92.500 40 2 1 3604 3643 17843944 17843982 0.000804 56.5
22 TraesCS7D01G203900 chr2B 92.308 39 3 0 3605 3643 754761257 754761219 0.000804 56.5
23 TraesCS7D01G203900 chr2B 92.308 39 3 0 3605 3643 754775523 754775485 0.000804 56.5


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 TraesCS7D01G203900 chr7D 161838672 161844415 5743 False 10608.000000 10608 100.000 1 5744 1 chr7D.!!$F1 5743
1 TraesCS7D01G203900 chr7B 123856867 123862690 5823 False 3738.500000 5214 90.049 1 5720 2 chr7B.!!$F1 5719
2 TraesCS7D01G203900 chr7A 162920408 162926803 6395 False 2406.666667 3046 92.199 307 5720 3 chr7A.!!$F1 5413

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
119 120 0.251297 CTTTGACAGTGATGGGGCCA 60.251 55.0 4.39 0.00 0.00 5.36 F
1118 1176 0.512952 CTTGACGCCTTGAGAAACCG 59.487 55.0 0.00 0.00 0.00 4.44 F
1845 1926 0.997932 CAGAGCAGCATGACGAGTTC 59.002 55.0 0.00 0.00 39.69 3.01 F
3193 4504 0.405585 ATGCCCAGTTAACACAGCCT 59.594 50.0 8.61 0.00 0.00 4.58 F
4044 5398 0.025513 CTACGTTCGCTGCAGCATTC 59.974 55.0 36.03 23.01 42.21 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2323 0.927537 CGCGCGGTCAAGATTCAATA 59.072 50.000 24.84 0.00 0.00 1.90 R
2745 2965 0.610687 CTTGGGTCCTGAGTCCTGAC 59.389 60.000 1.49 1.49 0.00 3.51 R
3461 4772 0.179051 GCATGAGAGAGGAAGCCCAG 60.179 60.000 0.00 0.00 33.88 4.45 R
4093 5468 0.039527 CTGGTCACGACACGACATGA 60.040 55.000 0.00 0.00 34.97 3.07 R
5720 7106 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95 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
78 79 4.641396 TGGTCTGTGTCAAAACCATCTAG 58.359 43.478 0.00 0.00 36.88 2.43
82 83 5.239525 GTCTGTGTCAAAACCATCTAGCTTT 59.760 40.000 0.00 0.00 0.00 3.51
87 88 5.222048 TGTCAAAACCATCTAGCTTTACCCT 60.222 40.000 0.00 0.00 0.00 4.34
90 91 5.717119 AAACCATCTAGCTTTACCCTGAT 57.283 39.130 0.00 0.00 0.00 2.90
91 92 4.965200 ACCATCTAGCTTTACCCTGATC 57.035 45.455 0.00 0.00 0.00 2.92
92 93 3.322254 ACCATCTAGCTTTACCCTGATCG 59.678 47.826 0.00 0.00 0.00 3.69
93 94 3.574396 CCATCTAGCTTTACCCTGATCGA 59.426 47.826 0.00 0.00 0.00 3.59
94 95 4.039245 CCATCTAGCTTTACCCTGATCGAA 59.961 45.833 0.00 0.00 0.00 3.71
95 96 5.453339 CCATCTAGCTTTACCCTGATCGAAA 60.453 44.000 0.00 0.00 0.00 3.46
96 97 5.670792 TCTAGCTTTACCCTGATCGAAAA 57.329 39.130 0.00 0.00 0.00 2.29
97 98 5.416947 TCTAGCTTTACCCTGATCGAAAAC 58.583 41.667 0.00 0.00 0.00 2.43
98 99 4.015872 AGCTTTACCCTGATCGAAAACA 57.984 40.909 0.00 0.00 0.00 2.83
99 100 4.394729 AGCTTTACCCTGATCGAAAACAA 58.605 39.130 0.00 0.00 0.00 2.83
100 101 4.215613 AGCTTTACCCTGATCGAAAACAAC 59.784 41.667 0.00 0.00 0.00 3.32
101 102 4.215613 GCTTTACCCTGATCGAAAACAACT 59.784 41.667 0.00 0.00 0.00 3.16
102 103 5.278315 GCTTTACCCTGATCGAAAACAACTT 60.278 40.000 0.00 0.00 0.00 2.66
108 109 5.207768 CCTGATCGAAAACAACTTTGACAG 58.792 41.667 0.00 0.00 0.00 3.51
114 115 4.734854 CGAAAACAACTTTGACAGTGATGG 59.265 41.667 0.00 0.00 35.12 3.51
118 119 0.251341 ACTTTGACAGTGATGGGGCC 60.251 55.000 0.00 0.00 32.83 5.80
119 120 0.251297 CTTTGACAGTGATGGGGCCA 60.251 55.000 4.39 0.00 0.00 5.36
145 154 2.889170 TGCATACCTAGCAAACCCAA 57.111 45.000 0.00 0.00 39.39 4.12
151 160 1.679153 ACCTAGCAAACCCAAACAACG 59.321 47.619 0.00 0.00 0.00 4.10
160 169 3.636282 ACCCAAACAACGCAATACTTC 57.364 42.857 0.00 0.00 0.00 3.01
173 182 5.123227 CGCAATACTTCAAAGATAAGGGGA 58.877 41.667 0.00 0.00 0.00 4.81
177 186 8.311109 GCAATACTTCAAAGATAAGGGGAAAAA 58.689 33.333 0.00 0.00 0.00 1.94
261 271 9.503427 GTCCTAATATTCTACAAAAACACATGC 57.497 33.333 0.00 0.00 0.00 4.06
263 273 8.394877 CCTAATATTCTACAAAAACACATGCGA 58.605 33.333 0.00 0.00 0.00 5.10
279 289 9.507280 AACACATGCGATTCAATTAATTTCTAG 57.493 29.630 0.00 0.00 0.00 2.43
287 297 9.922305 CGATTCAATTAATTTCTAGAGGTTGTC 57.078 33.333 0.00 0.00 0.00 3.18
415 429 7.193595 ACTTCCAACTAAAATGAACACTTTCG 58.806 34.615 0.00 0.00 34.04 3.46
425 439 8.782533 AAAATGAACACTTTCGAACAATCTAC 57.217 30.769 0.00 0.00 34.04 2.59
426 440 7.490962 AATGAACACTTTCGAACAATCTACA 57.509 32.000 0.00 0.00 34.04 2.74
436 450 7.490962 TTCGAACAATCTACACACAAAAGAT 57.509 32.000 0.00 0.00 0.00 2.40
446 460 5.518848 ACACACAAAAGATTCATGAAGCA 57.481 34.783 24.50 0.00 0.00 3.91
449 463 4.036734 ACACAAAAGATTCATGAAGCACGT 59.963 37.500 24.50 12.72 0.00 4.49
454 468 5.980698 AAGATTCATGAAGCACGTGATAG 57.019 39.130 24.50 4.37 43.00 2.08
479 494 0.618458 TTCAGGGAAACGATGAGGGG 59.382 55.000 0.00 0.00 0.00 4.79
482 497 2.674754 GGAAACGATGAGGGGGCA 59.325 61.111 0.00 0.00 0.00 5.36
502 517 4.439289 GGCAGAATCAATAGAGGTGCAAAC 60.439 45.833 0.00 0.00 32.27 2.93
507 522 8.514594 CAGAATCAATAGAGGTGCAAACTTTAA 58.485 33.333 0.00 0.00 0.00 1.52
539 554 5.413309 AAACAGGTCAACCAAAATGTCAA 57.587 34.783 1.33 0.00 38.89 3.18
541 556 5.009854 ACAGGTCAACCAAAATGTCAAAG 57.990 39.130 1.33 0.00 38.89 2.77
543 558 5.186797 ACAGGTCAACCAAAATGTCAAAGAA 59.813 36.000 1.33 0.00 38.89 2.52
556 571 4.707105 TGTCAAAGAATTCAGAGACTGCA 58.293 39.130 18.60 0.00 0.00 4.41
599 614 7.265915 CGGAAATTTGAAAACACGCATAATTTG 59.734 33.333 0.00 0.00 0.00 2.32
684 699 1.629043 TGTCCACCACTAGTCACTCC 58.371 55.000 0.00 0.00 0.00 3.85
705 720 3.445096 CCAGGGAATTGAAACAGTCATCC 59.555 47.826 0.00 0.00 35.43 3.51
718 733 5.779241 ACAGTCATCCTAGGGAATTTCAA 57.221 39.130 9.46 0.00 34.34 2.69
744 760 2.262915 CGGGTCTCTGTCACCAGC 59.737 66.667 0.00 0.00 38.66 4.85
974 1019 9.944663 CTTCGTCCTCTCTCTTTATATATATGC 57.055 37.037 5.44 0.00 0.00 3.14
979 1037 7.561722 TCCTCTCTCTTTATATATATGCGCCTT 59.438 37.037 4.18 0.00 0.00 4.35
990 1048 0.877071 ATGCGCCTTTGAGACAACAG 59.123 50.000 4.18 0.00 0.00 3.16
1034 1092 2.173669 AAATCGGCCATCGCAGTCG 61.174 57.895 2.24 0.00 39.05 4.18
1090 1148 1.398390 GAGACGGACAATTGGATGCAC 59.602 52.381 10.83 0.00 0.00 4.57
1118 1176 0.512952 CTTGACGCCTTGAGAAACCG 59.487 55.000 0.00 0.00 0.00 4.44
1119 1177 1.503818 TTGACGCCTTGAGAAACCGC 61.504 55.000 0.00 0.00 0.00 5.68
1124 1182 2.033194 CCTTGAGAAACCGCCGTCC 61.033 63.158 0.00 0.00 0.00 4.79
1148 1206 2.426738 TGATCCGGTCCATTTTCATTGC 59.573 45.455 0.00 0.00 0.00 3.56
1151 1209 1.133363 CGGTCCATTTTCATTGCGCG 61.133 55.000 0.00 0.00 0.00 6.86
1167 1236 3.987404 CGCCTAGCAGCAAGGTTT 58.013 55.556 0.00 0.00 36.43 3.27
1174 1243 3.256631 CCTAGCAGCAAGGTTTGTTGATT 59.743 43.478 9.39 0.69 43.54 2.57
1505 1577 1.544314 GCTCAACTGCACCTTCCTCTT 60.544 52.381 0.00 0.00 0.00 2.85
1508 1580 2.439507 TCAACTGCACCTTCCTCTTCTT 59.560 45.455 0.00 0.00 0.00 2.52
1511 1583 2.301583 ACTGCACCTTCCTCTTCTTCTC 59.698 50.000 0.00 0.00 0.00 2.87
1512 1584 2.566724 CTGCACCTTCCTCTTCTTCTCT 59.433 50.000 0.00 0.00 0.00 3.10
1513 1585 2.975489 TGCACCTTCCTCTTCTTCTCTT 59.025 45.455 0.00 0.00 0.00 2.85
1514 1586 3.392616 TGCACCTTCCTCTTCTTCTCTTT 59.607 43.478 0.00 0.00 0.00 2.52
1515 1587 4.000325 GCACCTTCCTCTTCTTCTCTTTC 59.000 47.826 0.00 0.00 0.00 2.62
1516 1588 4.503991 GCACCTTCCTCTTCTTCTCTTTCA 60.504 45.833 0.00 0.00 0.00 2.69
1527 1599 9.662545 CTCTTCTTCTCTTTCATTTTTCTTGAC 57.337 33.333 0.00 0.00 0.00 3.18
1587 1659 5.897250 GGGGAGAAGGATTTTGGCTAAAATA 59.103 40.000 19.33 0.00 44.35 1.40
1604 1676 9.185192 GGCTAAAATAATTTAGTATGCAAGCAG 57.815 33.333 11.11 0.00 46.42 4.24
1688 1764 9.087871 TGATAAATCAGAGATTCTAAGAGGAGG 57.912 37.037 0.00 0.00 32.11 4.30
1689 1765 9.308000 GATAAATCAGAGATTCTAAGAGGAGGA 57.692 37.037 0.00 0.00 0.00 3.71
1690 1766 7.986553 AAATCAGAGATTCTAAGAGGAGGAA 57.013 36.000 0.00 0.00 0.00 3.36
1691 1767 7.986553 AATCAGAGATTCTAAGAGGAGGAAA 57.013 36.000 0.00 0.00 0.00 3.13
1692 1768 8.565780 AATCAGAGATTCTAAGAGGAGGAAAT 57.434 34.615 0.00 0.00 0.00 2.17
1693 1769 9.667607 AATCAGAGATTCTAAGAGGAGGAAATA 57.332 33.333 0.00 0.00 0.00 1.40
1694 1770 8.472007 TCAGAGATTCTAAGAGGAGGAAATAC 57.528 38.462 0.00 0.00 0.00 1.89
1695 1771 8.285891 TCAGAGATTCTAAGAGGAGGAAATACT 58.714 37.037 0.00 0.00 0.00 2.12
1696 1772 9.581289 CAGAGATTCTAAGAGGAGGAAATACTA 57.419 37.037 0.00 0.00 0.00 1.82
1792 1870 3.877735 GCAATCCCACCCAAGTACTCAAT 60.878 47.826 0.00 0.00 0.00 2.57
1842 1923 1.937278 AATCAGAGCAGCATGACGAG 58.063 50.000 0.00 0.00 39.69 4.18
1845 1926 0.997932 CAGAGCAGCATGACGAGTTC 59.002 55.000 0.00 0.00 39.69 3.01
1994 2200 8.776376 AGTTTAAAAATAATGGACAATGGCAG 57.224 30.769 0.00 0.00 0.00 4.85
2023 2229 3.003378 GCGGCCTCGAAATAAGCTAAAAT 59.997 43.478 0.00 0.00 39.00 1.82
2025 2231 5.614887 GCGGCCTCGAAATAAGCTAAAATAG 60.615 44.000 0.00 0.00 39.00 1.73
2115 2323 1.211969 CGTTCGTGACCGTGGATCT 59.788 57.895 0.00 0.00 35.01 2.75
2117 2325 1.065102 CGTTCGTGACCGTGGATCTAT 59.935 52.381 0.00 0.00 35.01 1.98
2119 2327 2.858344 GTTCGTGACCGTGGATCTATTG 59.142 50.000 0.00 0.00 35.01 1.90
2120 2328 2.371306 TCGTGACCGTGGATCTATTGA 58.629 47.619 0.00 0.00 35.01 2.57
2121 2329 2.756207 TCGTGACCGTGGATCTATTGAA 59.244 45.455 0.00 0.00 35.01 2.69
2497 2713 2.143122 GCAAGTTGACGAGGTGATCAA 58.857 47.619 7.16 0.00 32.44 2.57
2679 2899 4.102681 GTGGGGCCTAATAGTATGTGAACT 59.897 45.833 0.84 0.00 0.00 3.01
2745 2965 5.121925 CAGATGATGTTTTGTCAGTCAGGAG 59.878 44.000 0.00 0.00 0.00 3.69
2747 2967 4.380531 TGATGTTTTGTCAGTCAGGAGTC 58.619 43.478 0.00 0.00 0.00 3.36
2799 3025 2.450476 TCTCAGCTGATCTGCACACTA 58.550 47.619 24.33 5.20 42.56 2.74
2821 4128 9.051027 CACTAATAAACTGCATGAAAACTAACG 57.949 33.333 0.00 0.00 0.00 3.18
2854 4165 4.612932 GAATCTGTGAGCAGTTTCATCC 57.387 45.455 11.36 0.00 44.63 3.51
3003 4314 1.194781 AGCTCTTCACCGGGACATGT 61.195 55.000 6.32 0.00 0.00 3.21
3193 4504 0.405585 ATGCCCAGTTAACACAGCCT 59.594 50.000 8.61 0.00 0.00 4.58
3199 4510 2.354805 CCAGTTAACACAGCCTAGGGTC 60.355 54.545 11.47 0.00 0.00 4.46
3273 4584 6.016777 ACTCTTCCAAGTTGCAACTTATCAAG 60.017 38.462 37.19 32.73 46.89 3.02
3430 4741 2.554636 CGGCTTCAAGCTTGTGCCA 61.555 57.895 38.25 19.47 43.44 4.92
3457 4768 3.822607 CCTTCTCAAGGGAGTGTCG 57.177 57.895 0.00 0.00 45.27 4.35
3461 4772 3.316573 CTCAAGGGAGTGTCGGGCC 62.317 68.421 0.00 0.00 36.36 5.80
3514 4830 8.507582 TCTACCTGAGATGTAAGACCTCTATA 57.492 38.462 0.00 0.00 0.00 1.31
3584 4905 6.985117 TCATGAAAAATCAACAAAGGAGAGG 58.015 36.000 0.00 0.00 0.00 3.69
3586 4907 4.895297 TGAAAAATCAACAAAGGAGAGGCT 59.105 37.500 0.00 0.00 0.00 4.58
3588 4909 1.831580 ATCAACAAAGGAGAGGCTGC 58.168 50.000 0.00 0.00 0.00 5.25
3607 4947 3.820467 CTGCCTTCCACAAACTTCATGTA 59.180 43.478 0.00 0.00 0.00 2.29
3609 4949 3.821033 GCCTTCCACAAACTTCATGTACT 59.179 43.478 0.00 0.00 0.00 2.73
3611 4951 5.472137 GCCTTCCACAAACTTCATGTACTAA 59.528 40.000 0.00 0.00 0.00 2.24
3612 4952 6.016610 GCCTTCCACAAACTTCATGTACTAAA 60.017 38.462 0.00 0.00 0.00 1.85
3613 4953 7.309194 GCCTTCCACAAACTTCATGTACTAAAT 60.309 37.037 0.00 0.00 0.00 1.40
3614 4954 8.237267 CCTTCCACAAACTTCATGTACTAAATC 58.763 37.037 0.00 0.00 0.00 2.17
3615 4955 8.684386 TTCCACAAACTTCATGTACTAAATCA 57.316 30.769 0.00 0.00 0.00 2.57
3616 4956 8.322906 TCCACAAACTTCATGTACTAAATCAG 57.677 34.615 0.00 0.00 0.00 2.90
3617 4957 7.023575 CCACAAACTTCATGTACTAAATCAGC 58.976 38.462 0.00 0.00 0.00 4.26
3618 4958 6.738200 CACAAACTTCATGTACTAAATCAGCG 59.262 38.462 0.00 0.00 0.00 5.18
3619 4959 6.649141 ACAAACTTCATGTACTAAATCAGCGA 59.351 34.615 0.00 0.00 0.00 4.93
3620 4960 6.648725 AACTTCATGTACTAAATCAGCGAC 57.351 37.500 0.00 0.00 0.00 5.19
3621 4961 5.720202 ACTTCATGTACTAAATCAGCGACA 58.280 37.500 0.00 0.00 0.00 4.35
3622 4962 6.163476 ACTTCATGTACTAAATCAGCGACAA 58.837 36.000 0.00 0.00 29.74 3.18
3623 4963 6.090898 ACTTCATGTACTAAATCAGCGACAAC 59.909 38.462 0.00 0.00 29.74 3.32
3624 4964 5.720202 TCATGTACTAAATCAGCGACAACT 58.280 37.500 0.00 0.00 29.74 3.16
3625 4965 6.859017 TCATGTACTAAATCAGCGACAACTA 58.141 36.000 0.00 0.00 29.74 2.24
3626 4966 7.317390 TCATGTACTAAATCAGCGACAACTAA 58.683 34.615 0.00 0.00 29.74 2.24
3627 4967 7.979537 TCATGTACTAAATCAGCGACAACTAAT 59.020 33.333 0.00 0.00 29.74 1.73
3628 4968 9.244799 CATGTACTAAATCAGCGACAACTAATA 57.755 33.333 0.00 0.00 29.74 0.98
3629 4969 9.982651 ATGTACTAAATCAGCGACAACTAATAT 57.017 29.630 0.00 0.00 29.74 1.28
3630 4970 9.244799 TGTACTAAATCAGCGACAACTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
3631 4971 7.715265 ACTAAATCAGCGACAACTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
3632 4972 7.497595 ACTAAATCAGCGACAACTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
3633 4973 8.150945 ACTAAATCAGCGACAACTAATATGGAT 58.849 33.333 0.00 0.00 0.00 3.41
3634 4974 7.807977 AAATCAGCGACAACTAATATGGATT 57.192 32.000 0.00 0.00 0.00 3.01
3635 4975 6.791887 ATCAGCGACAACTAATATGGATTG 57.208 37.500 0.00 0.00 0.00 2.67
3636 4976 5.912892 TCAGCGACAACTAATATGGATTGA 58.087 37.500 0.00 0.00 0.00 2.57
3637 4977 6.345298 TCAGCGACAACTAATATGGATTGAA 58.655 36.000 0.00 0.00 0.00 2.69
3638 4978 6.479990 TCAGCGACAACTAATATGGATTGAAG 59.520 38.462 0.00 0.00 0.00 3.02
3639 4979 5.760253 AGCGACAACTAATATGGATTGAAGG 59.240 40.000 0.00 0.00 0.00 3.46
3640 4980 5.049405 GCGACAACTAATATGGATTGAAGGG 60.049 44.000 0.00 0.00 0.00 3.95
3644 4984 4.899502 ACTAATATGGATTGAAGGGAGCG 58.100 43.478 0.00 0.00 0.00 5.03
3645 4985 2.867109 ATATGGATTGAAGGGAGCGG 57.133 50.000 0.00 0.00 0.00 5.52
3667 5007 2.009051 TGCTTTGGTGTATGATCTGCG 58.991 47.619 0.00 0.00 0.00 5.18
3668 5008 2.279741 GCTTTGGTGTATGATCTGCGA 58.720 47.619 0.00 0.00 0.00 5.10
3669 5009 2.030946 GCTTTGGTGTATGATCTGCGAC 59.969 50.000 0.00 0.00 0.00 5.19
3670 5010 1.921243 TTGGTGTATGATCTGCGACG 58.079 50.000 0.00 0.00 0.00 5.12
3680 5021 3.258228 TGATCTGCGACGAAAAATGCTA 58.742 40.909 0.00 0.00 0.00 3.49
3757 5099 0.179020 TTGACTTCCAGCACCACAGG 60.179 55.000 0.00 0.00 0.00 4.00
3787 5129 0.969149 CTGTGCTCAGTGACCTACCA 59.031 55.000 7.63 0.00 36.97 3.25
3796 5138 1.281287 AGTGACCTACCACTCGCTCTA 59.719 52.381 0.00 0.00 43.34 2.43
3808 5150 0.806868 TCGCTCTATGTTCGAACCGT 59.193 50.000 24.78 15.82 0.00 4.83
3880 5222 1.032014 TCAACTCAAACCAGGCAAGC 58.968 50.000 0.00 0.00 0.00 4.01
3883 5225 1.708341 ACTCAAACCAGGCAAGCAAT 58.292 45.000 0.00 0.00 0.00 3.56
3884 5226 1.342174 ACTCAAACCAGGCAAGCAATG 59.658 47.619 0.00 0.00 0.00 2.82
3887 5229 2.231964 TCAAACCAGGCAAGCAATGATC 59.768 45.455 0.00 0.00 0.00 2.92
3891 5233 0.685131 CAGGCAAGCAATGATCCCCA 60.685 55.000 0.00 0.00 0.00 4.96
4013 5367 2.430694 GGGCAAGAAGAACAACAGGTTT 59.569 45.455 0.00 0.00 40.63 3.27
4016 5370 3.447742 CAAGAAGAACAACAGGTTTGCC 58.552 45.455 0.00 0.00 40.63 4.52
4026 5380 1.299541 CAGGTTTGCCGCGATTATCT 58.700 50.000 8.23 0.00 40.50 1.98
4042 5396 0.179100 ATCTACGTTCGCTGCAGCAT 60.179 50.000 36.03 17.84 42.21 3.79
4044 5398 0.025513 CTACGTTCGCTGCAGCATTC 59.974 55.000 36.03 23.01 42.21 2.67
4049 5403 0.953727 TTCGCTGCAGCATTCTGTTT 59.046 45.000 36.03 0.00 42.29 2.83
4050 5404 0.953727 TCGCTGCAGCATTCTGTTTT 59.046 45.000 36.03 0.00 42.29 2.43
4052 5406 0.788391 GCTGCAGCATTCTGTTTTGC 59.212 50.000 33.36 1.32 42.29 3.68
4053 5407 1.870580 GCTGCAGCATTCTGTTTTGCA 60.871 47.619 33.36 0.00 42.29 4.08
4054 5408 2.143008 TGCAGCATTCTGTTTTGCAG 57.857 45.000 0.00 0.00 46.34 4.41
4056 5410 1.870580 GCAGCATTCTGTTTTGCAGCA 60.871 47.619 7.30 0.00 46.72 4.41
4058 5412 2.411748 CAGCATTCTGTTTTGCAGCATG 59.588 45.455 0.00 3.22 46.75 4.06
4059 5413 2.036733 AGCATTCTGTTTTGCAGCATGT 59.963 40.909 0.00 0.00 46.08 3.21
4060 5414 2.410730 GCATTCTGTTTTGCAGCATGTC 59.589 45.455 0.00 0.00 46.08 3.06
4061 5415 2.798976 TTCTGTTTTGCAGCATGTCC 57.201 45.000 0.00 0.00 44.66 4.02
4062 5416 1.689984 TCTGTTTTGCAGCATGTCCA 58.310 45.000 0.00 0.00 44.66 4.02
4063 5417 1.610038 TCTGTTTTGCAGCATGTCCAG 59.390 47.619 0.00 0.68 44.66 3.86
4064 5418 0.032403 TGTTTTGCAGCATGTCCAGC 59.968 50.000 0.00 0.00 39.31 4.85
4065 5419 0.032403 GTTTTGCAGCATGTCCAGCA 59.968 50.000 0.00 0.00 39.31 4.41
4079 5454 3.808726 TGTCCAGCATGACAAAATTTTGC 59.191 39.130 26.94 20.07 42.06 3.68
4089 5464 6.732531 TGACAAAATTTTGCAATGTTGACA 57.267 29.167 26.94 6.91 39.26 3.58
4090 5465 6.541086 TGACAAAATTTTGCAATGTTGACAC 58.459 32.000 26.94 7.82 39.26 3.67
4091 5466 5.878133 ACAAAATTTTGCAATGTTGACACC 58.122 33.333 26.94 0.00 39.26 4.16
4092 5467 5.647225 ACAAAATTTTGCAATGTTGACACCT 59.353 32.000 26.94 3.36 39.26 4.00
4093 5468 6.150809 ACAAAATTTTGCAATGTTGACACCTT 59.849 30.769 26.94 2.76 39.26 3.50
4094 5469 5.989551 AATTTTGCAATGTTGACACCTTC 57.010 34.783 0.00 0.00 0.00 3.46
4095 5470 4.462508 TTTTGCAATGTTGACACCTTCA 57.537 36.364 0.00 0.00 0.00 3.02
4096 5471 4.669206 TTTGCAATGTTGACACCTTCAT 57.331 36.364 0.00 0.00 32.84 2.57
4097 5472 3.646611 TGCAATGTTGACACCTTCATG 57.353 42.857 0.00 0.00 32.84 3.07
4105 5480 1.060713 GACACCTTCATGTCGTGTCG 58.939 55.000 19.38 0.00 44.81 4.35
4108 5483 0.671796 ACCTTCATGTCGTGTCGTGA 59.328 50.000 0.00 0.00 0.00 4.35
4137 5512 1.976132 GCCTCCACCTGCAGCATCTA 61.976 60.000 8.66 0.00 0.00 1.98
4152 5527 0.981183 ATCTAGCGAACACCCCAACA 59.019 50.000 0.00 0.00 0.00 3.33
4167 5542 2.436417 CCAACATTCATCAAGGGACGT 58.564 47.619 0.00 0.00 0.00 4.34
4170 5545 1.548719 ACATTCATCAAGGGACGTCGA 59.451 47.619 9.92 0.96 0.00 4.20
4449 5824 2.113139 CACAACACGGGGAGGCTT 59.887 61.111 0.00 0.00 0.00 4.35
4462 5837 0.393944 GAGGCTTTCGGGTAAAGGGG 60.394 60.000 0.00 0.00 44.13 4.79
4473 5848 0.392595 GTAAAGGGGGCTTCCTGTCG 60.393 60.000 1.02 0.00 37.20 4.35
4487 5862 0.886563 CTGTCGAAGTCGTTAGGGGT 59.113 55.000 0.00 0.00 40.80 4.95
4685 6060 0.316204 ACAGGTGCAAAGCTTGATGC 59.684 50.000 14.88 14.88 42.86 3.91
4790 6165 7.655328 ACAGTATCAGACTTGCTATATCTTTGC 59.345 37.037 0.00 0.00 35.64 3.68
4794 6169 7.066307 TCAGACTTGCTATATCTTTGCCATA 57.934 36.000 0.00 0.00 0.00 2.74
4842 6223 1.354368 TCAGACCCAGGGAAATCCAAC 59.646 52.381 14.54 0.00 38.24 3.77
5207 6589 1.926426 CTTTCCCCGGCTCCCAAGAT 61.926 60.000 0.00 0.00 0.00 2.40
5465 6849 5.823045 GGGTGGTAAAAGATAATGTCTCCTG 59.177 44.000 0.00 0.00 35.67 3.86
5500 6884 3.503827 TCACCACATAGTAGTTGAGCG 57.496 47.619 0.00 0.00 0.00 5.03
5510 6894 6.994496 ACATAGTAGTTGAGCGTATAGGTACA 59.006 38.462 0.00 0.00 0.00 2.90
5526 6910 3.257127 AGGTACAACAGACTTGAGAGCTC 59.743 47.826 5.27 5.27 0.00 4.09
5547 6931 7.271511 AGCTCTCTCCAGTATCAAAATTACTG 58.728 38.462 4.29 4.29 40.47 2.74
5559 6943 9.076596 GTATCAAAATTACTGAGTGGCAAAATC 57.923 33.333 0.00 0.00 0.00 2.17
5619 7004 7.009815 CACCTGAATAATCACAATTTCACATGC 59.990 37.037 0.00 0.00 0.00 4.06
5620 7005 6.477688 CCTGAATAATCACAATTTCACATGCC 59.522 38.462 0.00 0.00 0.00 4.40
5621 7006 7.172868 TGAATAATCACAATTTCACATGCCT 57.827 32.000 0.00 0.00 0.00 4.75
5632 7017 4.746535 TTCACATGCCTTCCTCGTATAA 57.253 40.909 0.00 0.00 0.00 0.98
5639 7025 8.402472 CACATGCCTTCCTCGTATAATTTTTAA 58.598 33.333 0.00 0.00 0.00 1.52
5689 7075 8.757982 ATCACTAAAGAGCAAATATGGACATT 57.242 30.769 0.00 0.00 0.00 2.71
5720 7106 4.522789 AGGTGCACCATAACAAAACTAAGG 59.477 41.667 36.39 0.00 38.89 2.69
5721 7107 4.321675 GGTGCACCATAACAAAACTAAGGG 60.322 45.833 31.23 0.00 35.64 3.95
5722 7108 3.829601 TGCACCATAACAAAACTAAGGGG 59.170 43.478 0.00 0.00 0.00 4.79
5723 7109 3.194755 GCACCATAACAAAACTAAGGGGG 59.805 47.826 0.00 0.00 0.00 5.40
5724 7110 4.412843 CACCATAACAAAACTAAGGGGGT 58.587 43.478 0.00 0.00 0.00 4.95
5725 7111 4.219725 CACCATAACAAAACTAAGGGGGTG 59.780 45.833 0.00 0.00 36.49 4.61
5726 7112 4.140876 ACCATAACAAAACTAAGGGGGTGT 60.141 41.667 0.00 0.00 0.00 4.16
5727 7113 4.836175 CCATAACAAAACTAAGGGGGTGTT 59.164 41.667 0.00 0.00 33.94 3.32
5728 7114 5.305902 CCATAACAAAACTAAGGGGGTGTTT 59.694 40.000 0.00 0.00 35.71 2.83
5729 7115 4.746535 AACAAAACTAAGGGGGTGTTTG 57.253 40.909 0.00 0.00 34.63 2.93
5730 7116 3.035363 ACAAAACTAAGGGGGTGTTTGG 58.965 45.455 0.00 0.00 34.63 3.28
5731 7117 3.035363 CAAAACTAAGGGGGTGTTTGGT 58.965 45.455 0.00 0.00 34.63 3.67
5732 7118 3.408157 AAACTAAGGGGGTGTTTGGTT 57.592 42.857 0.00 0.00 33.36 3.67
5733 7119 2.670019 ACTAAGGGGGTGTTTGGTTC 57.330 50.000 0.00 0.00 0.00 3.62
5734 7120 1.854280 ACTAAGGGGGTGTTTGGTTCA 59.146 47.619 0.00 0.00 0.00 3.18
5735 7121 2.158519 ACTAAGGGGGTGTTTGGTTCAG 60.159 50.000 0.00 0.00 0.00 3.02
5736 7122 0.930726 AAGGGGGTGTTTGGTTCAGA 59.069 50.000 0.00 0.00 0.00 3.27
5737 7123 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
5738 7124 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
5739 7125 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
5740 7126 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
5741 7127 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
5742 7128 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
5743 7129 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 4.215613 AGTTGTTTTCGATCAGGGTAAAGC 59.784 41.667 0.00 0.00 0.00 3.51
82 83 5.237779 GTCAAAGTTGTTTTCGATCAGGGTA 59.762 40.000 0.00 0.00 0.00 3.69
87 88 5.352846 TCACTGTCAAAGTTGTTTTCGATCA 59.647 36.000 0.00 0.00 36.83 2.92
90 91 5.448496 CCATCACTGTCAAAGTTGTTTTCGA 60.448 40.000 0.00 0.00 36.83 3.71
91 92 4.734854 CCATCACTGTCAAAGTTGTTTTCG 59.265 41.667 0.00 0.00 36.83 3.46
92 93 5.043248 CCCATCACTGTCAAAGTTGTTTTC 58.957 41.667 0.00 0.00 36.83 2.29
93 94 4.141959 CCCCATCACTGTCAAAGTTGTTTT 60.142 41.667 0.00 0.00 36.83 2.43
94 95 3.384467 CCCCATCACTGTCAAAGTTGTTT 59.616 43.478 0.00 0.00 36.83 2.83
95 96 2.958355 CCCCATCACTGTCAAAGTTGTT 59.042 45.455 0.00 0.00 36.83 2.83
96 97 2.586425 CCCCATCACTGTCAAAGTTGT 58.414 47.619 0.00 0.00 36.83 3.32
97 98 1.270550 GCCCCATCACTGTCAAAGTTG 59.729 52.381 0.00 0.00 36.83 3.16
98 99 1.620822 GCCCCATCACTGTCAAAGTT 58.379 50.000 0.00 0.00 36.83 2.66
99 100 0.251341 GGCCCCATCACTGTCAAAGT 60.251 55.000 0.00 0.00 40.93 2.66
100 101 0.251297 TGGCCCCATCACTGTCAAAG 60.251 55.000 0.00 0.00 0.00 2.77
101 102 0.539438 GTGGCCCCATCACTGTCAAA 60.539 55.000 0.00 0.00 32.78 2.69
102 103 1.074775 GTGGCCCCATCACTGTCAA 59.925 57.895 0.00 0.00 32.78 3.18
108 109 1.945355 GCAAAATTGTGGCCCCATCAC 60.945 52.381 0.00 0.00 35.82 3.06
114 115 1.554617 AGGTATGCAAAATTGTGGCCC 59.445 47.619 0.00 0.00 0.00 5.80
145 154 7.305474 CCTTATCTTTGAAGTATTGCGTTGTT 58.695 34.615 0.00 0.00 0.00 2.83
151 160 7.404671 TTTCCCCTTATCTTTGAAGTATTGC 57.595 36.000 0.00 0.00 0.00 3.56
177 186 9.883142 TGTTTTTCTTCCATACATTTTCTTGTT 57.117 25.926 0.00 0.00 0.00 2.83
261 271 9.922305 GACAACCTCTAGAAATTAATTGAATCG 57.078 33.333 0.39 0.00 0.00 3.34
315 326 8.888579 ATCGTATCACCTAACCATTTTTAGAG 57.111 34.615 0.00 0.00 31.60 2.43
415 429 9.121517 CATGAATCTTTTGTGTGTAGATTGTTC 57.878 33.333 0.00 0.00 38.40 3.18
425 439 4.380678 CGTGCTTCATGAATCTTTTGTGTG 59.619 41.667 8.96 0.00 0.00 3.82
426 440 4.036734 ACGTGCTTCATGAATCTTTTGTGT 59.963 37.500 8.96 0.00 0.00 3.72
436 450 5.478407 TCTTTCTATCACGTGCTTCATGAA 58.522 37.500 11.67 8.12 0.00 2.57
446 460 5.677319 TTCCCTGAATCTTTCTATCACGT 57.323 39.130 0.00 0.00 0.00 4.49
449 463 6.294361 TCGTTTCCCTGAATCTTTCTATCA 57.706 37.500 0.00 0.00 0.00 2.15
454 468 4.333926 CCTCATCGTTTCCCTGAATCTTTC 59.666 45.833 0.00 0.00 0.00 2.62
479 494 2.923121 TGCACCTCTATTGATTCTGCC 58.077 47.619 0.00 0.00 0.00 4.85
482 497 8.635765 TTAAAGTTTGCACCTCTATTGATTCT 57.364 30.769 0.00 0.00 0.00 2.40
539 554 2.613977 CCCGTGCAGTCTCTGAATTCTT 60.614 50.000 7.05 0.00 32.44 2.52
541 556 1.066858 TCCCGTGCAGTCTCTGAATTC 60.067 52.381 0.00 0.00 32.44 2.17
543 558 0.247736 GTCCCGTGCAGTCTCTGAAT 59.752 55.000 0.66 0.00 32.44 2.57
556 571 1.003812 TCCGATTTGGAAATGTCCCGT 59.996 47.619 0.00 0.00 46.38 5.28
599 614 0.031449 GACTAGGCATCTCGGAGTGC 59.969 60.000 18.26 18.26 40.55 4.40
684 699 4.338879 AGGATGACTGTTTCAATTCCCTG 58.661 43.478 0.00 0.00 37.92 4.45
705 720 4.017126 GGTTCCCACTTGAAATTCCCTAG 58.983 47.826 0.00 0.00 0.00 3.02
718 733 1.913762 CAGAGACCCGGTTCCCACT 60.914 63.158 0.00 0.00 0.00 4.00
744 760 1.824230 TGAATTGATTTCCGGGCCTTG 59.176 47.619 0.84 0.00 33.04 3.61
820 836 3.787001 CTTGGGGCCCTCCTCGAC 61.787 72.222 25.93 2.81 34.77 4.20
952 997 7.013846 AGGCGCATATATATAAAGAGAGAGGAC 59.986 40.741 10.83 0.00 0.00 3.85
973 1018 1.166531 ACCTGTTGTCTCAAAGGCGC 61.167 55.000 0.00 0.00 32.73 6.53
974 1019 0.588252 CACCTGTTGTCTCAAAGGCG 59.412 55.000 0.00 0.00 32.73 5.52
979 1037 2.363306 ATTGGCACCTGTTGTCTCAA 57.637 45.000 0.00 0.00 0.00 3.02
990 1048 3.871775 CCGATGCATAATTGGCACC 57.128 52.632 0.00 0.00 45.23 5.01
1124 1182 4.924305 ATGAAAATGGACCGGATCAATG 57.076 40.909 9.46 0.00 0.00 2.82
1151 1209 0.961753 AACAAACCTTGCTGCTAGGC 59.038 50.000 26.43 0.00 36.17 3.93
1159 1217 3.791245 TGAACCAATCAACAAACCTTGC 58.209 40.909 0.00 0.00 34.30 4.01
1160 1218 4.751098 CCATGAACCAATCAACAAACCTTG 59.249 41.667 0.00 0.00 42.54 3.61
1161 1219 4.408596 ACCATGAACCAATCAACAAACCTT 59.591 37.500 0.00 0.00 42.54 3.50
1167 1236 2.158400 TCCCACCATGAACCAATCAACA 60.158 45.455 0.00 0.00 42.54 3.33
1174 1243 1.676968 CTCGTCCCACCATGAACCA 59.323 57.895 0.00 0.00 0.00 3.67
1455 1524 2.943033 ACAAACCTTGTTGAACTCGAGG 59.057 45.455 18.41 10.08 42.22 4.63
1505 1577 7.469181 GCCTGTCAAGAAAAATGAAAGAGAAGA 60.469 37.037 0.00 0.00 34.62 2.87
1508 1580 5.010012 GGCCTGTCAAGAAAAATGAAAGAGA 59.990 40.000 0.00 0.00 34.62 3.10
1511 1583 4.039609 AGGGCCTGTCAAGAAAAATGAAAG 59.960 41.667 4.50 0.00 32.83 2.62
1512 1584 3.966665 AGGGCCTGTCAAGAAAAATGAAA 59.033 39.130 4.50 0.00 0.00 2.69
1513 1585 3.573967 GAGGGCCTGTCAAGAAAAATGAA 59.426 43.478 12.95 0.00 0.00 2.57
1514 1586 3.157087 GAGGGCCTGTCAAGAAAAATGA 58.843 45.455 12.95 0.00 0.00 2.57
1515 1587 3.160269 AGAGGGCCTGTCAAGAAAAATG 58.840 45.455 12.95 0.00 0.00 2.32
1516 1588 3.532641 AGAGGGCCTGTCAAGAAAAAT 57.467 42.857 12.95 0.00 0.00 1.82
1527 1599 5.359194 TCAGTAGAAAATTAGAGGGCCTG 57.641 43.478 12.95 0.00 0.00 4.85
1587 1659 7.174107 ACAAATCCTGCTTGCATACTAAATT 57.826 32.000 0.00 0.00 0.00 1.82
1700 1776 9.654663 GTTCCATGACTTGACTAGTTACTTAAT 57.345 33.333 0.00 0.00 37.17 1.40
1701 1777 8.867097 AGTTCCATGACTTGACTAGTTACTTAA 58.133 33.333 0.00 0.00 37.17 1.85
1702 1778 8.418597 AGTTCCATGACTTGACTAGTTACTTA 57.581 34.615 0.00 0.00 37.17 2.24
1705 1781 9.088512 CAATAGTTCCATGACTTGACTAGTTAC 57.911 37.037 0.00 0.00 37.17 2.50
1792 1870 1.538075 GAAAATTTGACCGGCGAGGAA 59.462 47.619 9.30 0.00 45.00 3.36
1878 1959 3.094572 CCAGGATTCAAGACAAGGCAAT 58.905 45.455 0.00 0.00 0.00 3.56
1880 1961 1.704628 TCCAGGATTCAAGACAAGGCA 59.295 47.619 0.00 0.00 0.00 4.75
1881 1962 2.290577 ACTCCAGGATTCAAGACAAGGC 60.291 50.000 0.00 0.00 0.00 4.35
1883 1964 4.904241 AGAACTCCAGGATTCAAGACAAG 58.096 43.478 11.86 0.00 0.00 3.16
1934 2140 6.258727 TCTCTGCTAGAGTGTTTTCTTTTGTG 59.741 38.462 11.37 0.00 42.83 3.33
2001 2207 1.578583 TTAGCTTATTTCGAGGCCGC 58.421 50.000 0.00 0.00 35.37 6.53
2023 2229 4.331717 GGTTTTAGTCATTTAGCAGCGCTA 59.668 41.667 10.99 0.00 40.44 4.26
2025 2231 3.426323 GGTTTTAGTCATTTAGCAGCGC 58.574 45.455 0.00 0.00 0.00 5.92
2033 2239 6.017687 GCGGGATATAACGGTTTTAGTCATTT 60.018 38.462 0.00 0.00 0.00 2.32
2081 2287 0.997196 AACGCGTTCTCTAATTCCGC 59.003 50.000 20.79 0.00 40.87 5.54
2115 2323 0.927537 CGCGCGGTCAAGATTCAATA 59.072 50.000 24.84 0.00 0.00 1.90
2117 2325 3.022401 GCGCGCGGTCAAGATTCAA 62.022 57.895 33.06 0.00 0.00 2.69
2119 2327 4.559386 CGCGCGCGGTCAAGATTC 62.559 66.667 43.28 10.21 35.56 2.52
2148 2360 1.306148 CTCCGTCATCTGCATGCAAT 58.694 50.000 22.88 14.74 0.00 3.56
2149 2361 1.371337 GCTCCGTCATCTGCATGCAA 61.371 55.000 22.88 13.05 0.00 4.08
2150 2362 1.816679 GCTCCGTCATCTGCATGCA 60.817 57.895 21.29 21.29 0.00 3.96
2215 2427 2.629210 CCGAAGCACGCGTTGAAA 59.371 55.556 10.22 0.00 41.07 2.69
2497 2713 3.681835 GAGGTCGCCGTCCACAGT 61.682 66.667 2.72 0.00 0.00 3.55
2679 2899 4.533707 ACTCTTGAGGGTGAAATGATCAGA 59.466 41.667 0.09 0.00 39.19 3.27
2745 2965 0.610687 CTTGGGTCCTGAGTCCTGAC 59.389 60.000 1.49 1.49 0.00 3.51
2747 2967 1.209019 CATCTTGGGTCCTGAGTCCTG 59.791 57.143 0.00 0.00 0.00 3.86
2799 3025 5.861787 GGCGTTAGTTTTCATGCAGTTTATT 59.138 36.000 0.00 0.00 0.00 1.40
2854 4165 2.662700 GATATGCGTCCCGTACTTCTG 58.337 52.381 0.00 0.00 0.00 3.02
2871 4182 2.475466 GCTCACCCCGACGACGATA 61.475 63.158 9.28 0.00 42.66 2.92
3003 4314 0.842030 AGTGTGAAGGAGGCATGGGA 60.842 55.000 0.00 0.00 0.00 4.37
3072 4383 2.504367 AGTTTCAGTTTGGGATGGTCG 58.496 47.619 0.00 0.00 0.00 4.79
3193 4504 4.205587 GACTAGTCATTCCTTCGACCCTA 58.794 47.826 18.20 0.00 32.33 3.53
3273 4584 3.540314 AGATGACCTGCTTCATGACTC 57.460 47.619 0.00 0.00 36.30 3.36
3406 4717 1.375908 AAGCTTGAAGCCGATCGCA 60.376 52.632 14.45 0.00 43.77 5.10
3409 4720 0.179179 GCACAAGCTTGAAGCCGATC 60.179 55.000 32.50 7.75 43.77 3.69
3457 4768 3.803162 GAGAGGAAGCCCAGGCCC 61.803 72.222 4.70 0.00 43.17 5.80
3461 4772 0.179051 GCATGAGAGAGGAAGCCCAG 60.179 60.000 0.00 0.00 33.88 4.45
3542 4862 4.162131 TCATGAAACTGCTAGACCTATGCA 59.838 41.667 0.00 0.00 35.30 3.96
3543 4863 4.697514 TCATGAAACTGCTAGACCTATGC 58.302 43.478 0.00 0.00 0.00 3.14
3584 4905 1.032014 TGAAGTTTGTGGAAGGCAGC 58.968 50.000 0.00 0.00 0.00 5.25
3586 4907 2.665165 ACATGAAGTTTGTGGAAGGCA 58.335 42.857 0.00 0.00 0.00 4.75
3588 4909 7.504924 TTTAGTACATGAAGTTTGTGGAAGG 57.495 36.000 0.00 0.00 0.00 3.46
3607 4947 7.497595 TCCATATTAGTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
3609 4949 8.773645 CAATCCATATTAGTTGTCGCTGATTTA 58.226 33.333 0.00 0.00 0.00 1.40
3611 4951 6.992123 TCAATCCATATTAGTTGTCGCTGATT 59.008 34.615 0.00 0.00 0.00 2.57
3612 4952 6.524734 TCAATCCATATTAGTTGTCGCTGAT 58.475 36.000 0.00 0.00 0.00 2.90
3613 4953 5.912892 TCAATCCATATTAGTTGTCGCTGA 58.087 37.500 0.00 0.00 0.00 4.26
3614 4954 6.293081 CCTTCAATCCATATTAGTTGTCGCTG 60.293 42.308 0.00 0.00 0.00 5.18
3615 4955 5.760253 CCTTCAATCCATATTAGTTGTCGCT 59.240 40.000 0.00 0.00 0.00 4.93
3616 4956 5.049405 CCCTTCAATCCATATTAGTTGTCGC 60.049 44.000 0.00 0.00 0.00 5.19
3617 4957 6.288294 TCCCTTCAATCCATATTAGTTGTCG 58.712 40.000 0.00 0.00 0.00 4.35
3618 4958 6.205658 GCTCCCTTCAATCCATATTAGTTGTC 59.794 42.308 0.00 0.00 0.00 3.18
3619 4959 6.064717 GCTCCCTTCAATCCATATTAGTTGT 58.935 40.000 0.00 0.00 0.00 3.32
3620 4960 5.180117 CGCTCCCTTCAATCCATATTAGTTG 59.820 44.000 0.00 0.00 0.00 3.16
3621 4961 5.308825 CGCTCCCTTCAATCCATATTAGTT 58.691 41.667 0.00 0.00 0.00 2.24
3622 4962 4.263068 CCGCTCCCTTCAATCCATATTAGT 60.263 45.833 0.00 0.00 0.00 2.24
3623 4963 4.256920 CCGCTCCCTTCAATCCATATTAG 58.743 47.826 0.00 0.00 0.00 1.73
3624 4964 3.650942 ACCGCTCCCTTCAATCCATATTA 59.349 43.478 0.00 0.00 0.00 0.98
3625 4965 2.443255 ACCGCTCCCTTCAATCCATATT 59.557 45.455 0.00 0.00 0.00 1.28
3626 4966 2.057922 ACCGCTCCCTTCAATCCATAT 58.942 47.619 0.00 0.00 0.00 1.78
3627 4967 1.507140 ACCGCTCCCTTCAATCCATA 58.493 50.000 0.00 0.00 0.00 2.74
3628 4968 0.625849 AACCGCTCCCTTCAATCCAT 59.374 50.000 0.00 0.00 0.00 3.41
3629 4969 0.322456 CAACCGCTCCCTTCAATCCA 60.322 55.000 0.00 0.00 0.00 3.41
3630 4970 1.657751 GCAACCGCTCCCTTCAATCC 61.658 60.000 0.00 0.00 34.30 3.01
3631 4971 1.803289 GCAACCGCTCCCTTCAATC 59.197 57.895 0.00 0.00 34.30 2.67
3632 4972 4.002797 GCAACCGCTCCCTTCAAT 57.997 55.556 0.00 0.00 34.30 2.57
3644 4984 3.428045 GCAGATCATACACCAAAGCAACC 60.428 47.826 0.00 0.00 0.00 3.77
3645 4985 3.728864 CGCAGATCATACACCAAAGCAAC 60.729 47.826 0.00 0.00 0.00 4.17
3653 4993 2.203800 TTCGTCGCAGATCATACACC 57.796 50.000 0.00 0.00 40.67 4.16
3654 4994 4.577687 TTTTTCGTCGCAGATCATACAC 57.422 40.909 0.00 0.00 40.67 2.90
3667 5007 7.478667 CAGTGACATAGTTTAGCATTTTTCGTC 59.521 37.037 0.00 0.00 0.00 4.20
3668 5008 7.298122 CAGTGACATAGTTTAGCATTTTTCGT 58.702 34.615 0.00 0.00 0.00 3.85
3669 5009 6.249260 GCAGTGACATAGTTTAGCATTTTTCG 59.751 38.462 0.00 0.00 0.00 3.46
3670 5010 7.308435 AGCAGTGACATAGTTTAGCATTTTTC 58.692 34.615 0.00 0.00 0.00 2.29
3680 5021 7.171678 GTCTGTTAAAGAGCAGTGACATAGTTT 59.828 37.037 0.00 0.00 34.84 2.66
3739 5081 1.344953 ACCTGTGGTGCTGGAAGTCA 61.345 55.000 0.00 0.00 39.25 3.41
3787 5129 1.202154 CGGTTCGAACATAGAGCGAGT 60.202 52.381 28.24 0.00 35.31 4.18
3796 5138 1.375523 GCCCTGACGGTTCGAACAT 60.376 57.895 28.24 16.53 0.00 2.71
3880 5222 5.585844 GGTTTTAAGCAAATGGGGATCATTG 59.414 40.000 0.00 0.00 44.68 2.82
3883 5225 4.163427 TGGTTTTAAGCAAATGGGGATCA 58.837 39.130 0.00 0.00 32.80 2.92
3884 5226 4.817318 TGGTTTTAAGCAAATGGGGATC 57.183 40.909 0.00 0.00 32.80 3.36
3887 5229 4.506758 CAGATGGTTTTAAGCAAATGGGG 58.493 43.478 0.00 0.00 40.14 4.96
3891 5233 5.876460 GGATTGCAGATGGTTTTAAGCAAAT 59.124 36.000 0.00 0.00 43.97 2.32
4013 5367 1.762419 GAACGTAGATAATCGCGGCA 58.238 50.000 6.13 0.00 0.00 5.69
4026 5380 0.389817 AGAATGCTGCAGCGAACGTA 60.390 50.000 32.11 15.38 45.83 3.57
4049 5403 4.426971 ATGCTGGACATGCTGCAA 57.573 50.000 6.36 0.00 37.70 4.08
4054 5408 8.947587 GCAAAATTTTGTCATGCTGGACATGC 62.948 42.308 27.13 12.06 46.37 4.06
4056 5410 4.453136 GCAAAATTTTGTCATGCTGGACAT 59.547 37.500 27.13 0.00 46.37 3.06
4058 5412 3.808726 TGCAAAATTTTGTCATGCTGGAC 59.191 39.130 27.13 10.69 40.24 4.02
4059 5413 4.069300 TGCAAAATTTTGTCATGCTGGA 57.931 36.364 27.13 2.89 40.24 3.86
4060 5414 4.815040 TTGCAAAATTTTGTCATGCTGG 57.185 36.364 27.13 4.13 40.24 4.85
4061 5415 5.753744 ACATTGCAAAATTTTGTCATGCTG 58.246 33.333 27.38 22.46 40.24 4.41
4062 5416 6.038382 TCAACATTGCAAAATTTTGTCATGCT 59.962 30.769 27.38 19.93 40.24 3.79
4063 5417 6.141053 GTCAACATTGCAAAATTTTGTCATGC 59.859 34.615 27.38 18.70 40.24 4.06
4064 5418 7.164498 GTGTCAACATTGCAAAATTTTGTCATG 59.836 33.333 27.13 26.81 40.24 3.07
4065 5419 7.188157 GTGTCAACATTGCAAAATTTTGTCAT 58.812 30.769 27.13 18.02 40.24 3.06
4067 5421 5.964751 GGTGTCAACATTGCAAAATTTTGTC 59.035 36.000 27.13 20.36 40.24 3.18
4068 5422 5.647225 AGGTGTCAACATTGCAAAATTTTGT 59.353 32.000 27.13 9.37 40.24 2.83
4070 5424 6.373774 TGAAGGTGTCAACATTGCAAAATTTT 59.626 30.769 1.71 0.00 31.51 1.82
4071 5425 5.879223 TGAAGGTGTCAACATTGCAAAATTT 59.121 32.000 1.71 0.00 31.51 1.82
4074 5428 4.462508 TGAAGGTGTCAACATTGCAAAA 57.537 36.364 1.71 0.00 31.51 2.44
4075 5429 4.141981 ACATGAAGGTGTCAACATTGCAAA 60.142 37.500 1.71 0.00 40.50 3.68
4079 5454 3.250762 ACGACATGAAGGTGTCAACATTG 59.749 43.478 0.00 0.00 46.89 2.82
4089 5464 0.671796 TCACGACACGACATGAAGGT 59.328 50.000 0.00 0.00 0.00 3.50
4090 5465 1.060713 GTCACGACACGACATGAAGG 58.939 55.000 0.00 0.00 33.43 3.46
4091 5466 1.060713 GGTCACGACACGACATGAAG 58.939 55.000 0.00 0.00 34.97 3.02
4092 5467 0.386113 TGGTCACGACACGACATGAA 59.614 50.000 0.00 0.00 34.97 2.57
4093 5468 0.039527 CTGGTCACGACACGACATGA 60.040 55.000 0.00 0.00 34.97 3.07
4094 5469 1.008875 CCTGGTCACGACACGACATG 61.009 60.000 0.00 0.00 34.97 3.21
4095 5470 1.289066 CCTGGTCACGACACGACAT 59.711 57.895 0.00 0.00 34.97 3.06
4096 5471 2.725641 CCTGGTCACGACACGACA 59.274 61.111 0.00 0.00 34.97 4.35
4097 5472 1.859427 TAGCCTGGTCACGACACGAC 61.859 60.000 0.00 0.00 0.00 4.34
4100 5475 1.215647 CCTAGCCTGGTCACGACAC 59.784 63.158 0.00 0.00 0.00 3.67
4137 5512 0.179004 TGAATGTTGGGGTGTTCGCT 60.179 50.000 0.00 0.00 0.00 4.93
4142 5517 2.528564 CCTTGATGAATGTTGGGGTGT 58.471 47.619 0.00 0.00 0.00 4.16
4152 5527 2.100197 TCTCGACGTCCCTTGATGAAT 58.900 47.619 10.58 0.00 0.00 2.57
4167 5542 1.452953 ATATCGGCGGCTTGTCTCGA 61.453 55.000 7.21 0.00 0.00 4.04
4170 5545 1.069765 CCATATCGGCGGCTTGTCT 59.930 57.895 7.21 0.00 0.00 3.41
4240 5615 2.264794 GACGTGGGCGAACATCCT 59.735 61.111 0.00 0.00 42.00 3.24
4442 5817 0.393944 CCCTTTACCCGAAAGCCTCC 60.394 60.000 0.00 0.00 42.91 4.30
4449 5824 1.687014 GAAGCCCCCTTTACCCGAA 59.313 57.895 0.00 0.00 0.00 4.30
4473 5848 1.447314 CGCCACCCCTAACGACTTC 60.447 63.158 0.00 0.00 0.00 3.01
4645 6020 2.930019 CAGCCAGTGTCCAGGGGA 60.930 66.667 0.00 0.00 0.00 4.81
4654 6029 1.598962 CACCTGTGACCAGCCAGTG 60.599 63.158 0.00 0.00 37.38 3.66
4685 6060 1.410882 GTGAGATCTTCCCCTTCTCGG 59.589 57.143 0.00 0.00 38.97 4.63
4842 6223 2.293122 TCAGAAACAGAAATGTTGCCCG 59.707 45.455 0.00 0.00 31.64 6.13
5500 6884 6.095720 AGCTCTCAAGTCTGTTGTACCTATAC 59.904 42.308 0.00 0.00 0.00 1.47
5526 6910 7.493971 CCACTCAGTAATTTTGATACTGGAGAG 59.506 40.741 12.31 6.60 46.56 3.20
5547 6931 5.573337 AGCTTAGAATGATTTTGCCACTC 57.427 39.130 0.00 0.00 0.00 3.51
5619 7004 7.936584 TGCCATTAAAAATTATACGAGGAAGG 58.063 34.615 0.00 0.00 0.00 3.46
5620 7005 9.398170 CATGCCATTAAAAATTATACGAGGAAG 57.602 33.333 0.00 0.00 0.00 3.46
5621 7006 9.126151 TCATGCCATTAAAAATTATACGAGGAA 57.874 29.630 0.00 0.00 0.00 3.36
5632 7017 9.976511 CTCTTATGATGTCATGCCATTAAAAAT 57.023 29.630 5.78 0.00 37.15 1.82
5639 7025 5.938279 AGTTCTCTTATGATGTCATGCCAT 58.062 37.500 5.78 0.00 37.15 4.40
5672 7058 7.784037 TGCAATTTAATGTCCATATTTGCTCT 58.216 30.769 0.00 0.00 0.00 4.09
5720 7106 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
5721 7107 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
5722 7108 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.