Multiple sequence alignment - TraesCS4A01G402000

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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 TraesCS4A01G402000 chr4A 100.000 2648 0 0 1 2648 675853865 675856512 0.000000e+00 4891
1 TraesCS4A01G402000 chr4A 96.235 425 16 0 1066 1490 48275440 48275864 0.000000e+00 697
2 TraesCS4A01G402000 chr7D 89.286 980 72 15 795 1756 58768126 58769090 0.000000e+00 1197
3 TraesCS4A01G402000 chr7D 87.650 915 45 28 1768 2645 58769064 58769947 0.000000e+00 1002
4 TraesCS4A01G402000 chr7D 87.328 726 44 34 803 1493 58863931 58863219 0.000000e+00 787
5 TraesCS4A01G402000 chr7D 96.009 426 17 0 1065 1490 70905324 70904899 0.000000e+00 693
6 TraesCS4A01G402000 chr7D 78.895 507 56 22 237 716 58767554 58768036 1.990000e-76 296
7 TraesCS4A01G402000 chr7D 86.631 187 21 4 16 201 58767372 58767555 1.240000e-48 204
8 TraesCS4A01G402000 chr7A 94.247 591 23 5 983 1566 63117624 63118210 0.000000e+00 893
9 TraesCS4A01G402000 chr7A 87.933 721 49 20 803 1493 63427883 63427171 0.000000e+00 815
10 TraesCS4A01G402000 chr7A 90.576 573 34 16 934 1493 63398899 63398334 0.000000e+00 741
11 TraesCS4A01G402000 chr7A 86.982 169 19 3 765 931 63117020 63117187 1.250000e-43 187
12 TraesCS4A01G402000 chrUn 86.216 740 71 19 466 1180 468331060 468331793 0.000000e+00 773
13 TraesCS4A01G402000 chrUn 96.495 428 14 1 1065 1492 84317805 84317379 0.000000e+00 706
14 TraesCS4A01G402000 chrUn 94.432 449 21 4 1045 1492 82565912 82566357 0.000000e+00 688
15 TraesCS4A01G402000 chrUn 84.507 213 16 4 214 417 294071627 294071423 7.480000e-46 195


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 TraesCS4A01G402000 chr4A 675853865 675856512 2647 False 4891.00 4891 100.0000 1 2648 1 chr4A.!!$F2 2647
1 TraesCS4A01G402000 chr7D 58863219 58863931 712 True 787.00 787 87.3280 803 1493 1 chr7D.!!$R1 690
2 TraesCS4A01G402000 chr7D 58767372 58769947 2575 False 674.75 1197 85.6155 16 2645 4 chr7D.!!$F1 2629
3 TraesCS4A01G402000 chr7A 63427171 63427883 712 True 815.00 815 87.9330 803 1493 1 chr7A.!!$R2 690
4 TraesCS4A01G402000 chr7A 63398334 63398899 565 True 741.00 741 90.5760 934 1493 1 chr7A.!!$R1 559
5 TraesCS4A01G402000 chr7A 63117020 63118210 1190 False 540.00 893 90.6145 765 1566 2 chr7A.!!$F1 801
6 TraesCS4A01G402000 chrUn 468331060 468331793 733 False 773.00 773 86.2160 466 1180 1 chrUn.!!$F2 714

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
544 556 0.324738 CCAGACTAGTGAGCCCCAGA 60.325 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2438 0.401738 CTCCTTCTCAACCTGCCCAA 59.598 55.0 0.0 0.0 0.0 4.12 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
25 26 0.741221 GGAGTTGCTCTTAGGCCGTG 60.741 60.000 0.00 0.00 0.00 4.94
54 55 9.634163 ACTTTATTCATAAAACGGGATGAAAAC 57.366 29.630 1.76 0.00 43.39 2.43
64 65 7.883229 AAACGGGATGAAAACATATTTTGAC 57.117 32.000 0.00 0.00 38.17 3.18
67 68 7.090173 ACGGGATGAAAACATATTTTGACAAG 58.910 34.615 0.00 0.00 38.17 3.16
69 70 7.812191 CGGGATGAAAACATATTTTGACAAGAA 59.188 33.333 0.00 0.00 38.17 2.52
87 88 9.868160 TGACAAGAATATCTACTATCTCTTCCA 57.132 33.333 0.00 0.00 0.00 3.53
93 94 9.693739 GAATATCTACTATCTCTTCCATCTCCA 57.306 37.037 0.00 0.00 0.00 3.86
94 95 9.474313 AATATCTACTATCTCTTCCATCTCCAC 57.526 37.037 0.00 0.00 0.00 4.02
104 105 5.026121 TCTTCCATCTCCACTAGAACATGT 58.974 41.667 0.00 0.00 37.89 3.21
111 112 8.370940 CCATCTCCACTAGAACATGTAACATAT 58.629 37.037 0.00 0.00 37.89 1.78
124 125 7.414436 ACATGTAACATATGGTTTGCGATTAC 58.586 34.615 7.80 4.89 40.96 1.89
137 138 3.462982 TGCGATTACCACATGTATGACC 58.537 45.455 0.00 0.00 0.00 4.02
156 157 4.098044 TGACCGGACATGACTATCTTCTTC 59.902 45.833 9.46 0.00 0.00 2.87
157 158 4.282496 ACCGGACATGACTATCTTCTTCT 58.718 43.478 9.46 0.00 0.00 2.85
158 159 4.339814 ACCGGACATGACTATCTTCTTCTC 59.660 45.833 9.46 0.00 0.00 2.87
160 161 5.507149 CCGGACATGACTATCTTCTTCTCAG 60.507 48.000 0.00 0.00 0.00 3.35
166 168 7.543868 ACATGACTATCTTCTTCTCAGTTTTCG 59.456 37.037 0.00 0.00 0.00 3.46
168 170 7.085116 TGACTATCTTCTTCTCAGTTTTCGAC 58.915 38.462 0.00 0.00 0.00 4.20
189 191 6.035650 TCGACACTTCTCAACAACTAACAAAG 59.964 38.462 0.00 0.00 0.00 2.77
245 247 5.991328 ATAAAGTGATGCGTGTTATCCTG 57.009 39.130 0.00 0.00 0.00 3.86
262 264 1.078891 TGGAACAGGGCATGCCATT 59.921 52.632 36.56 26.32 37.98 3.16
271 273 2.446666 AGGGCATGCCATTCCTATACAA 59.553 45.455 36.56 0.00 37.98 2.41
272 274 2.821969 GGGCATGCCATTCCTATACAAG 59.178 50.000 36.56 0.00 37.98 3.16
273 275 3.490348 GGCATGCCATTCCTATACAAGT 58.510 45.455 32.08 0.00 35.81 3.16
274 276 4.506625 GGGCATGCCATTCCTATACAAGTA 60.507 45.833 36.56 0.00 37.98 2.24
275 277 5.256474 GGCATGCCATTCCTATACAAGTAT 58.744 41.667 32.08 0.00 35.81 2.12
276 278 6.414732 GGCATGCCATTCCTATACAAGTATA 58.585 40.000 32.08 0.49 35.81 1.47
277 279 6.316390 GGCATGCCATTCCTATACAAGTATAC 59.684 42.308 32.08 0.00 35.81 1.47
278 280 6.878923 GCATGCCATTCCTATACAAGTATACA 59.121 38.462 6.36 0.00 0.00 2.29
279 281 7.554118 GCATGCCATTCCTATACAAGTATACAT 59.446 37.037 6.36 0.00 0.00 2.29
394 404 2.163818 TACAACTGCGTCCAAAGAGG 57.836 50.000 0.00 0.00 39.47 3.69
414 424 5.723887 AGAGGAAATGTATCTCTGGACACTT 59.276 40.000 0.00 0.00 36.61 3.16
415 425 6.897966 AGAGGAAATGTATCTCTGGACACTTA 59.102 38.462 0.00 0.00 36.61 2.24
416 426 7.400339 AGAGGAAATGTATCTCTGGACACTTAA 59.600 37.037 0.00 0.00 36.61 1.85
417 427 7.918076 AGGAAATGTATCTCTGGACACTTAAA 58.082 34.615 0.00 0.00 0.00 1.52
418 428 7.824779 AGGAAATGTATCTCTGGACACTTAAAC 59.175 37.037 0.00 0.00 0.00 2.01
419 429 7.606456 GGAAATGTATCTCTGGACACTTAAACA 59.394 37.037 0.00 0.00 0.00 2.83
420 430 7.907214 AATGTATCTCTGGACACTTAAACAC 57.093 36.000 0.00 0.00 0.00 3.32
421 431 6.665992 TGTATCTCTGGACACTTAAACACT 57.334 37.500 0.00 0.00 0.00 3.55
422 432 7.062749 TGTATCTCTGGACACTTAAACACTT 57.937 36.000 0.00 0.00 0.00 3.16
437 447 9.328845 ACTTAAACACTTAAGGACGAACAATTA 57.671 29.630 7.53 0.00 45.70 1.40
448 459 3.682696 ACGAACAATTAAGGGTCCCTTC 58.317 45.455 27.22 9.89 43.57 3.46
451 462 4.329392 GAACAATTAAGGGTCCCTTCGAA 58.671 43.478 27.22 16.83 43.57 3.71
455 466 4.586306 ATTAAGGGTCCCTTCGAATTGT 57.414 40.909 27.22 2.79 43.57 2.71
457 468 5.703730 TTAAGGGTCCCTTCGAATTGTAT 57.296 39.130 27.22 1.17 43.57 2.29
458 469 4.586306 AAGGGTCCCTTCGAATTGTATT 57.414 40.909 18.29 0.00 40.17 1.89
520 532 3.648339 AAGTGCCATGTCATGTTGAAC 57.352 42.857 11.84 2.46 0.00 3.18
528 540 3.417069 TGTCATGTTGAACCCTACCAG 57.583 47.619 0.00 0.00 0.00 4.00
543 555 0.616111 ACCAGACTAGTGAGCCCCAG 60.616 60.000 0.00 0.00 0.00 4.45
544 556 0.324738 CCAGACTAGTGAGCCCCAGA 60.325 60.000 0.00 0.00 0.00 3.86
554 566 1.895131 TGAGCCCCAGAAATTTTGAGC 59.105 47.619 0.00 0.84 0.00 4.26
562 574 4.168760 CCAGAAATTTTGAGCATTCGACC 58.831 43.478 0.00 0.00 0.00 4.79
564 576 5.464168 CAGAAATTTTGAGCATTCGACCTT 58.536 37.500 0.00 0.00 0.00 3.50
566 578 7.253422 CAGAAATTTTGAGCATTCGACCTTAT 58.747 34.615 0.00 0.00 0.00 1.73
571 583 6.903883 TTTGAGCATTCGACCTTATAGAAC 57.096 37.500 0.00 0.00 0.00 3.01
572 584 5.854010 TGAGCATTCGACCTTATAGAACT 57.146 39.130 0.00 0.00 0.00 3.01
573 585 5.592054 TGAGCATTCGACCTTATAGAACTG 58.408 41.667 0.00 0.00 0.00 3.16
634 680 8.753133 CCCTGAAATAGAAAAATCCTAAAGCTT 58.247 33.333 0.00 0.00 0.00 3.74
716 769 8.477419 TTTTCCCACAGAACTGAATTTTCTAT 57.523 30.769 8.87 0.00 32.95 1.98
718 771 5.415701 TCCCACAGAACTGAATTTTCTATGC 59.584 40.000 8.87 0.00 31.86 3.14
721 774 6.373779 CACAGAACTGAATTTTCTATGCGTT 58.626 36.000 8.87 0.00 31.86 4.84
723 776 6.024049 CAGAACTGAATTTTCTATGCGTTCC 58.976 40.000 0.00 0.00 31.86 3.62
724 777 4.965119 ACTGAATTTTCTATGCGTTCCC 57.035 40.909 0.00 0.00 0.00 3.97
754 849 1.739929 TGCACCGAAACGCGATGAT 60.740 52.632 15.93 0.00 44.57 2.45
767 862 1.548973 CGATGATAGCGCGGGAACAC 61.549 60.000 8.83 0.00 0.00 3.32
800 895 1.069765 AGCTTCACACCACACCTCG 59.930 57.895 0.00 0.00 0.00 4.63
826 922 1.595328 CCAATCACGTCACACGAAACA 59.405 47.619 2.48 0.00 46.05 2.83
829 925 0.806884 TCACGTCACACGAAACACCC 60.807 55.000 2.48 0.00 46.05 4.61
896 994 2.801631 CCCAGCCGTCCATCTCCTC 61.802 68.421 0.00 0.00 0.00 3.71
966 1088 1.600511 CCCAAAATTTCCCCGACCCG 61.601 60.000 0.00 0.00 0.00 5.28
1327 1837 0.246910 GGACTTCAAGACCGACCTCC 59.753 60.000 0.00 0.00 0.00 4.30
1329 1839 1.446272 CTTCAAGACCGACCTCCGC 60.446 63.158 0.00 0.00 36.84 5.54
1532 2042 3.007506 TCTTGCGATCTGGTTGTAAGGAA 59.992 43.478 6.21 0.00 35.35 3.36
1533 2043 3.410631 TGCGATCTGGTTGTAAGGAAA 57.589 42.857 0.00 0.00 0.00 3.13
1537 2047 4.437390 GCGATCTGGTTGTAAGGAAATGTG 60.437 45.833 0.00 0.00 0.00 3.21
1538 2048 4.437390 CGATCTGGTTGTAAGGAAATGTGC 60.437 45.833 0.00 0.00 0.00 4.57
1539 2049 4.098914 TCTGGTTGTAAGGAAATGTGCT 57.901 40.909 0.00 0.00 0.00 4.40
1540 2050 3.820467 TCTGGTTGTAAGGAAATGTGCTG 59.180 43.478 0.00 0.00 0.00 4.41
1543 2053 2.558359 GTTGTAAGGAAATGTGCTGGCT 59.442 45.455 0.00 0.00 0.00 4.75
1549 2059 0.244721 GAAATGTGCTGGCTGGGTTC 59.755 55.000 0.00 0.00 0.00 3.62
1551 2061 3.590466 ATGTGCTGGCTGGGTTCCC 62.590 63.158 0.12 0.12 0.00 3.97
1552 2062 4.284550 GTGCTGGCTGGGTTCCCA 62.285 66.667 10.37 10.37 34.56 4.37
1570 2080 6.428159 GGTTCCCATGTAGTGTTGATATGATC 59.572 42.308 0.00 0.00 0.00 2.92
1574 2084 7.933577 TCCCATGTAGTGTTGATATGATCTTTC 59.066 37.037 0.00 0.00 0.00 2.62
1575 2085 7.935755 CCCATGTAGTGTTGATATGATCTTTCT 59.064 37.037 0.00 0.00 0.00 2.52
1579 2089 9.809096 TGTAGTGTTGATATGATCTTTCTTCTC 57.191 33.333 0.00 0.00 0.00 2.87
1582 2092 7.704472 AGTGTTGATATGATCTTTCTTCTCGTC 59.296 37.037 0.00 0.00 0.00 4.20
1583 2093 7.704472 GTGTTGATATGATCTTTCTTCTCGTCT 59.296 37.037 0.00 0.00 0.00 4.18
1584 2094 7.918033 TGTTGATATGATCTTTCTTCTCGTCTC 59.082 37.037 0.00 0.00 0.00 3.36
1585 2095 7.815840 TGATATGATCTTTCTTCTCGTCTCT 57.184 36.000 0.00 0.00 0.00 3.10
1586 2096 7.647228 TGATATGATCTTTCTTCTCGTCTCTG 58.353 38.462 0.00 0.00 0.00 3.35
1587 2097 4.710423 TGATCTTTCTTCTCGTCTCTGG 57.290 45.455 0.00 0.00 0.00 3.86
1588 2098 4.082845 TGATCTTTCTTCTCGTCTCTGGT 58.917 43.478 0.00 0.00 0.00 4.00
1595 2105 4.082845 TCTTCTCGTCTCTGGTGATCTTT 58.917 43.478 0.00 0.00 0.00 2.52
1603 2113 4.081198 GTCTCTGGTGATCTTTCCTGATGT 60.081 45.833 0.00 0.00 32.78 3.06
1604 2114 5.127845 GTCTCTGGTGATCTTTCCTGATGTA 59.872 44.000 0.00 0.00 32.78 2.29
1605 2115 5.362143 TCTCTGGTGATCTTTCCTGATGTAG 59.638 44.000 0.00 0.00 32.78 2.74
1611 2121 6.344500 GTGATCTTTCCTGATGTAGTGTGAT 58.656 40.000 0.00 0.00 0.00 3.06
1612 2122 6.257411 GTGATCTTTCCTGATGTAGTGTGATG 59.743 42.308 0.00 0.00 0.00 3.07
1619 2129 4.093998 CCTGATGTAGTGTGATGCTGAAAC 59.906 45.833 0.00 0.00 0.00 2.78
1621 2131 3.378911 TGTAGTGTGATGCTGAAACGA 57.621 42.857 0.00 0.00 0.00 3.85
1625 2135 4.151258 AGTGTGATGCTGAAACGAAATG 57.849 40.909 0.00 0.00 0.00 2.32
1638 2149 5.233902 TGAAACGAAATGGCAATGAAAAGTG 59.766 36.000 0.00 0.00 0.00 3.16
1649 2160 5.574443 GGCAATGAAAAGTGCAGTTATCTTC 59.426 40.000 7.33 8.57 42.74 2.87
1650 2161 5.284660 GCAATGAAAAGTGCAGTTATCTTCG 59.715 40.000 7.33 0.00 40.58 3.79
1652 2163 4.637276 TGAAAAGTGCAGTTATCTTCGGA 58.363 39.130 7.33 0.00 0.00 4.55
1653 2164 5.245531 TGAAAAGTGCAGTTATCTTCGGAT 58.754 37.500 7.33 0.00 38.39 4.18
1654 2165 5.122239 TGAAAAGTGCAGTTATCTTCGGATG 59.878 40.000 7.33 0.00 36.01 3.51
1655 2166 2.555199 AGTGCAGTTATCTTCGGATGC 58.445 47.619 0.00 0.00 36.01 3.91
1656 2167 2.093500 AGTGCAGTTATCTTCGGATGCA 60.093 45.455 0.00 0.00 36.01 3.96
1657 2168 2.677836 GTGCAGTTATCTTCGGATGCAA 59.322 45.455 2.12 0.00 33.50 4.08
1658 2169 3.126858 GTGCAGTTATCTTCGGATGCAAA 59.873 43.478 2.12 0.00 33.50 3.68
1659 2170 3.947196 TGCAGTTATCTTCGGATGCAAAT 59.053 39.130 0.00 0.00 36.01 2.32
1660 2171 4.398988 TGCAGTTATCTTCGGATGCAAATT 59.601 37.500 0.00 0.00 36.01 1.82
1665 2176 3.848272 TCTTCGGATGCAAATTTGTCC 57.152 42.857 19.03 16.73 0.00 4.02
1679 2190 4.853924 ATTTGTCCTGTGGTGTCATTTC 57.146 40.909 0.00 0.00 0.00 2.17
1683 2194 3.631686 TGTCCTGTGGTGTCATTTCTTTG 59.368 43.478 0.00 0.00 0.00 2.77
1688 2199 2.035066 GTGGTGTCATTTCTTTGCTGCT 59.965 45.455 0.00 0.00 0.00 4.24
1697 2208 7.495279 TGTCATTTCTTTGCTGCTTAATTGTTT 59.505 29.630 0.00 0.00 0.00 2.83
1698 2209 8.337532 GTCATTTCTTTGCTGCTTAATTGTTTT 58.662 29.630 0.00 0.00 0.00 2.43
1699 2210 9.539825 TCATTTCTTTGCTGCTTAATTGTTTTA 57.460 25.926 0.00 0.00 0.00 1.52
1705 2216 9.749490 CTTTGCTGCTTAATTGTTTTAATCATG 57.251 29.630 0.00 0.00 0.00 3.07
1708 2219 8.306038 TGCTGCTTAATTGTTTTAATCATGTCT 58.694 29.630 0.00 0.00 0.00 3.41
1711 2222 8.924691 TGCTTAATTGTTTTAATCATGTCTTGC 58.075 29.630 0.00 0.00 0.00 4.01
1722 2233 6.879276 AATCATGTCTTGCTGATTAGATGG 57.121 37.500 0.00 0.00 39.64 3.51
1723 2234 5.363562 TCATGTCTTGCTGATTAGATGGT 57.636 39.130 0.00 0.00 0.00 3.55
1728 2239 5.645067 TGTCTTGCTGATTAGATGGTTGAAG 59.355 40.000 0.00 0.00 0.00 3.02
1737 2248 6.942005 TGATTAGATGGTTGAAGAACACATGT 59.058 34.615 0.00 0.00 33.27 3.21
1744 2255 4.520492 GGTTGAAGAACACATGTCCTGAAT 59.480 41.667 0.00 0.00 33.27 2.57
1747 2258 7.301054 GTTGAAGAACACATGTCCTGAATTAG 58.699 38.462 0.00 0.00 31.78 1.73
1754 2265 4.216042 CACATGTCCTGAATTAGTGTTGCA 59.784 41.667 0.00 0.00 0.00 4.08
1755 2266 4.216257 ACATGTCCTGAATTAGTGTTGCAC 59.784 41.667 0.00 0.00 34.10 4.57
1757 2268 3.814842 TGTCCTGAATTAGTGTTGCACTG 59.185 43.478 11.57 0.00 45.01 3.66
1758 2269 4.065088 GTCCTGAATTAGTGTTGCACTGA 58.935 43.478 11.57 4.26 45.01 3.41
1759 2270 4.697352 GTCCTGAATTAGTGTTGCACTGAT 59.303 41.667 11.57 6.41 45.01 2.90
1760 2271 4.696877 TCCTGAATTAGTGTTGCACTGATG 59.303 41.667 11.57 0.00 45.01 3.07
1761 2272 4.142534 CCTGAATTAGTGTTGCACTGATGG 60.143 45.833 11.57 3.94 45.01 3.51
1762 2273 3.758023 TGAATTAGTGTTGCACTGATGGG 59.242 43.478 11.57 0.00 45.01 4.00
1763 2274 3.719268 ATTAGTGTTGCACTGATGGGA 57.281 42.857 11.57 0.00 45.01 4.37
1764 2275 3.719268 TTAGTGTTGCACTGATGGGAT 57.281 42.857 11.57 0.00 45.01 3.85
1765 2276 2.592102 AGTGTTGCACTGATGGGATT 57.408 45.000 0.53 0.00 43.63 3.01
1766 2277 2.165167 AGTGTTGCACTGATGGGATTG 58.835 47.619 0.53 0.00 43.63 2.67
1767 2278 2.161855 GTGTTGCACTGATGGGATTGA 58.838 47.619 0.00 0.00 0.00 2.57
1768 2279 2.557924 GTGTTGCACTGATGGGATTGAA 59.442 45.455 0.00 0.00 0.00 2.69
1769 2280 2.557924 TGTTGCACTGATGGGATTGAAC 59.442 45.455 0.00 0.00 0.00 3.18
1770 2281 2.557924 GTTGCACTGATGGGATTGAACA 59.442 45.455 0.00 0.00 0.00 3.18
1771 2282 2.874014 TGCACTGATGGGATTGAACAA 58.126 42.857 0.00 0.00 0.00 2.83
1772 2283 3.433343 TGCACTGATGGGATTGAACAAT 58.567 40.909 0.00 0.00 0.00 2.71
1773 2284 3.193903 TGCACTGATGGGATTGAACAATG 59.806 43.478 4.72 0.00 0.00 2.82
1774 2285 3.777478 CACTGATGGGATTGAACAATGC 58.223 45.455 9.87 9.87 38.25 3.56
1775 2286 3.193903 CACTGATGGGATTGAACAATGCA 59.806 43.478 17.70 0.00 40.36 3.96
1776 2287 4.028131 ACTGATGGGATTGAACAATGCAT 58.972 39.130 17.70 0.00 40.36 3.96
1777 2288 4.142026 ACTGATGGGATTGAACAATGCATG 60.142 41.667 17.70 0.00 40.36 4.06
1778 2289 4.024670 TGATGGGATTGAACAATGCATGA 58.975 39.130 17.70 4.83 40.36 3.07
1779 2290 4.651962 TGATGGGATTGAACAATGCATGAT 59.348 37.500 17.70 8.51 40.36 2.45
1780 2291 4.659111 TGGGATTGAACAATGCATGATC 57.341 40.909 17.70 0.00 40.36 2.92
1781 2292 4.283337 TGGGATTGAACAATGCATGATCT 58.717 39.130 17.70 0.00 40.36 2.75
1782 2293 5.447757 TGGGATTGAACAATGCATGATCTA 58.552 37.500 17.70 0.00 40.36 1.98
1783 2294 5.892686 TGGGATTGAACAATGCATGATCTAA 59.107 36.000 17.70 0.00 40.36 2.10
1784 2295 6.551975 TGGGATTGAACAATGCATGATCTAAT 59.448 34.615 17.70 0.00 40.36 1.73
1785 2296 7.070198 TGGGATTGAACAATGCATGATCTAATT 59.930 33.333 17.70 0.00 40.36 1.40
1786 2297 7.384115 GGGATTGAACAATGCATGATCTAATTG 59.616 37.037 17.70 0.00 40.36 2.32
1787 2298 8.139350 GGATTGAACAATGCATGATCTAATTGA 58.861 33.333 0.00 0.00 38.74 2.57
1788 2299 9.692749 GATTGAACAATGCATGATCTAATTGAT 57.307 29.630 0.00 0.00 38.27 2.57
1790 2301 9.878667 TTGAACAATGCATGATCTAATTGATTT 57.121 25.926 0.00 0.00 35.14 2.17
1799 2310 9.443283 GCATGATCTAATTGATTTAACACTGTC 57.557 33.333 0.00 0.00 35.14 3.51
1813 2324 1.069022 CACTGTCGCTTGGATTTGGTG 60.069 52.381 0.00 0.00 0.00 4.17
1823 2334 5.335583 CGCTTGGATTTGGTGATTCTGTTAA 60.336 40.000 0.00 0.00 0.00 2.01
1829 2340 6.096001 GGATTTGGTGATTCTGTTAATCTGCT 59.904 38.462 0.00 0.00 0.00 4.24
1834 2345 5.645497 GGTGATTCTGTTAATCTGCTCTGTT 59.355 40.000 0.00 0.00 0.00 3.16
1864 2375 3.213206 TGGTTGCTGTGAGATTCAGTT 57.787 42.857 0.00 0.00 35.60 3.16
1867 2378 3.058639 GGTTGCTGTGAGATTCAGTTGTC 60.059 47.826 0.00 0.00 35.60 3.18
1880 2391 8.558973 AGATTCAGTTGTCTTTTTCCTATCAG 57.441 34.615 0.00 0.00 0.00 2.90
1899 2410 8.774586 CCTATCAGGTAATTTTGTACACTATGC 58.225 37.037 0.00 0.00 0.00 3.14
1913 2424 3.276857 CACTATGCAAGGCAGATTGTCT 58.723 45.455 0.00 0.00 43.65 3.41
1924 2435 4.834496 AGGCAGATTGTCTTTCCATTTTCA 59.166 37.500 0.00 0.00 0.00 2.69
1925 2436 4.925646 GGCAGATTGTCTTTCCATTTTCAC 59.074 41.667 0.00 0.00 0.00 3.18
1927 2438 5.279156 GCAGATTGTCTTTCCATTTTCACCT 60.279 40.000 0.00 0.00 0.00 4.00
1950 2491 1.407989 GGCAGGTTGAGAAGGAGATGG 60.408 57.143 0.00 0.00 0.00 3.51
1952 2493 2.679349 GCAGGTTGAGAAGGAGATGGAC 60.679 54.545 0.00 0.00 0.00 4.02
1956 2497 2.834549 GTTGAGAAGGAGATGGACTGGA 59.165 50.000 0.00 0.00 0.00 3.86
1982 2523 3.229293 TGATCTGTTGAAACCATTGCCA 58.771 40.909 0.00 0.00 0.00 4.92
2011 2552 1.542472 TGGCAATGAACATGAGCACAG 59.458 47.619 0.00 0.00 0.00 3.66
2012 2553 1.542915 GGCAATGAACATGAGCACAGT 59.457 47.619 0.00 0.00 0.00 3.55
2013 2554 2.592194 GCAATGAACATGAGCACAGTG 58.408 47.619 0.00 0.00 0.00 3.66
2024 2565 4.115401 TGAGCACAGTGTGTCTGATATC 57.885 45.455 23.73 11.15 46.27 1.63
2085 2626 7.069950 TCCTTGCTTTGCAGTTCTATAGAGATA 59.930 37.037 2.02 0.00 40.61 1.98
2122 2663 6.155910 TCAGATCTCTTTCAGTTTAGGCATCT 59.844 38.462 0.00 0.00 0.00 2.90
2124 2665 7.437862 CAGATCTCTTTCAGTTTAGGCATCTAC 59.562 40.741 0.00 0.00 0.00 2.59
2130 2671 3.118884 TCAGTTTAGGCATCTACGGGAAC 60.119 47.826 0.00 0.00 0.00 3.62
2149 2690 3.626028 ACGTTCAGAAACAATTGCCTC 57.374 42.857 5.05 2.17 34.93 4.70
2164 2705 9.515226 AACAATTGCCTCTTCATAACTTTACTA 57.485 29.630 5.05 0.00 0.00 1.82
2176 2717 2.991250 ACTTTACTAGCAGTGCATGGG 58.009 47.619 19.20 6.50 0.00 4.00
2191 2732 4.671590 GGGTTTGGGTCCCGGGTG 62.672 72.222 22.86 0.00 35.27 4.61
2196 2737 4.667935 TGGGTCCCGGGTGTGGAT 62.668 66.667 22.86 0.00 33.65 3.41
2291 2834 3.473625 TGATATGATGCTTGCTGTCTGG 58.526 45.455 0.00 0.00 0.00 3.86
2296 2839 1.669779 GATGCTTGCTGTCTGGTGATC 59.330 52.381 0.00 0.00 0.00 2.92
2297 2840 0.689055 TGCTTGCTGTCTGGTGATCT 59.311 50.000 0.00 0.00 0.00 2.75
2298 2841 1.072806 TGCTTGCTGTCTGGTGATCTT 59.927 47.619 0.00 0.00 0.00 2.40
2299 2842 2.157738 GCTTGCTGTCTGGTGATCTTT 58.842 47.619 0.00 0.00 0.00 2.52
2300 2843 2.161211 GCTTGCTGTCTGGTGATCTTTC 59.839 50.000 0.00 0.00 0.00 2.62
2301 2844 3.672808 CTTGCTGTCTGGTGATCTTTCT 58.327 45.455 0.00 0.00 0.00 2.52
2335 2878 1.001378 ACGCTGAAATGAAGTGGCAAC 60.001 47.619 0.00 0.00 0.00 4.17
2341 2884 4.109050 TGAAATGAAGTGGCAACGAAAAC 58.891 39.130 0.00 0.00 42.51 2.43
2365 2909 7.889469 ACTTCAGTTCTATGATGCAAATTTGT 58.111 30.769 19.03 0.26 0.00 2.83
2366 2910 8.025445 ACTTCAGTTCTATGATGCAAATTTGTC 58.975 33.333 19.03 10.43 0.00 3.18
2371 2915 6.441093 TCTATGATGCAAATTTGTCCTGTC 57.559 37.500 19.03 10.54 0.00 3.51
2387 2931 2.290367 CCTGTCGTCTCATTTGTTTGCA 59.710 45.455 0.00 0.00 0.00 4.08
2393 2937 4.274705 TCGTCTCATTTGTTTGCAGCTTAA 59.725 37.500 0.00 0.00 0.00 1.85
2478 3022 7.672240 TGTTGTACAGATGGTATTGAACACTA 58.328 34.615 0.00 0.00 33.76 2.74
2505 3049 9.915629 TTATATTTTGGTTTAACATTGTCGCTT 57.084 25.926 0.00 0.00 0.00 4.68
2506 3050 8.825667 ATATTTTGGTTTAACATTGTCGCTTT 57.174 26.923 0.00 0.00 0.00 3.51
2507 3051 5.957910 TTTGGTTTAACATTGTCGCTTTG 57.042 34.783 0.00 0.00 0.00 2.77
2508 3052 4.902443 TGGTTTAACATTGTCGCTTTGA 57.098 36.364 0.00 0.00 0.00 2.69
2509 3053 5.446143 TGGTTTAACATTGTCGCTTTGAT 57.554 34.783 0.00 0.00 0.00 2.57
2522 3066 4.618489 GTCGCTTTGATTTTGGTGATTCTG 59.382 41.667 0.00 0.00 0.00 3.02
2524 3068 4.618489 CGCTTTGATTTTGGTGATTCTGTC 59.382 41.667 0.00 0.00 0.00 3.51
2581 3127 8.378565 TGATATTCAGTTGTCTTTTCTCCTTCT 58.621 33.333 0.00 0.00 0.00 2.85
2596 3142 7.843490 TTCTCCTTCTGGAAAATTATGTACG 57.157 36.000 0.00 0.00 42.66 3.67
2611 3157 1.154282 TACGTGCGACTCAGAAGCG 60.154 57.895 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.546476 CCTAAGAGCAACTCCACTCGT 59.454 52.381 0.00 0.00 37.99 4.18
2 3 1.406205 GGCCTAAGAGCAACTCCACTC 60.406 57.143 0.00 0.00 0.00 3.51
3 4 0.615850 GGCCTAAGAGCAACTCCACT 59.384 55.000 0.00 0.00 0.00 4.00
4 5 0.741221 CGGCCTAAGAGCAACTCCAC 60.741 60.000 0.00 0.00 0.00 4.02
5 6 1.192146 ACGGCCTAAGAGCAACTCCA 61.192 55.000 0.00 0.00 0.00 3.86
6 7 0.741221 CACGGCCTAAGAGCAACTCC 60.741 60.000 0.00 0.00 0.00 3.85
7 8 0.037232 ACACGGCCTAAGAGCAACTC 60.037 55.000 0.00 0.00 0.00 3.01
8 9 0.320771 CACACGGCCTAAGAGCAACT 60.321 55.000 0.00 0.00 0.00 3.16
9 10 0.320421 TCACACGGCCTAAGAGCAAC 60.320 55.000 0.00 0.00 0.00 4.17
10 11 0.320421 GTCACACGGCCTAAGAGCAA 60.320 55.000 0.00 0.00 0.00 3.91
11 12 1.185618 AGTCACACGGCCTAAGAGCA 61.186 55.000 0.00 0.00 0.00 4.26
12 13 0.037232 AAGTCACACGGCCTAAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
13 14 2.457366 AAAGTCACACGGCCTAAGAG 57.543 50.000 0.00 0.00 0.00 2.85
14 15 4.020928 TGAATAAAGTCACACGGCCTAAGA 60.021 41.667 0.00 0.00 0.00 2.10
25 26 7.981142 TCATCCCGTTTTATGAATAAAGTCAC 58.019 34.615 0.00 0.00 34.13 3.67
67 68 9.693739 TGGAGATGGAAGAGATAGTAGATATTC 57.306 37.037 0.00 0.00 0.00 1.75
69 70 8.845793 AGTGGAGATGGAAGAGATAGTAGATAT 58.154 37.037 0.00 0.00 0.00 1.63
83 84 6.212589 TGTTACATGTTCTAGTGGAGATGGAA 59.787 38.462 2.30 0.00 32.88 3.53
86 87 9.201127 CATATGTTACATGTTCTAGTGGAGATG 57.799 37.037 2.30 0.00 32.88 2.90
87 88 8.370940 CCATATGTTACATGTTCTAGTGGAGAT 58.629 37.037 2.30 0.00 32.88 2.75
88 89 7.344612 ACCATATGTTACATGTTCTAGTGGAGA 59.655 37.037 2.30 0.00 0.00 3.71
93 94 7.201609 CGCAAACCATATGTTACATGTTCTAGT 60.202 37.037 2.30 0.00 35.67 2.57
94 95 7.011016 TCGCAAACCATATGTTACATGTTCTAG 59.989 37.037 2.30 0.41 35.67 2.43
104 105 5.880887 TGTGGTAATCGCAAACCATATGTTA 59.119 36.000 1.24 0.00 46.96 2.41
111 112 2.509569 ACATGTGGTAATCGCAAACCA 58.490 42.857 0.00 0.00 43.47 3.67
124 125 2.212652 CATGTCCGGTCATACATGTGG 58.787 52.381 20.49 0.00 45.08 4.17
137 138 5.067153 ACTGAGAAGAAGATAGTCATGTCCG 59.933 44.000 0.00 0.00 0.00 4.79
144 145 7.061326 GTGTCGAAAACTGAGAAGAAGATAGTC 59.939 40.741 0.00 0.00 0.00 2.59
156 157 4.566759 TGTTGAGAAGTGTCGAAAACTGAG 59.433 41.667 2.95 0.00 0.00 3.35
157 158 4.500127 TGTTGAGAAGTGTCGAAAACTGA 58.500 39.130 2.95 0.00 0.00 3.41
158 159 4.857871 TGTTGAGAAGTGTCGAAAACTG 57.142 40.909 2.95 0.00 0.00 3.16
160 161 5.217895 AGTTGTTGAGAAGTGTCGAAAAC 57.782 39.130 0.00 0.00 0.00 2.43
166 168 7.303634 TCTTTGTTAGTTGTTGAGAAGTGTC 57.696 36.000 0.00 0.00 0.00 3.67
217 219 8.774586 GGATAACACGCATCACTTTATATTCTT 58.225 33.333 0.00 0.00 0.00 2.52
218 220 8.150945 AGGATAACACGCATCACTTTATATTCT 58.849 33.333 0.00 0.00 0.00 2.40
219 221 8.223769 CAGGATAACACGCATCACTTTATATTC 58.776 37.037 0.00 0.00 0.00 1.75
220 222 7.173218 CCAGGATAACACGCATCACTTTATATT 59.827 37.037 0.00 0.00 0.00 1.28
221 223 6.650807 CCAGGATAACACGCATCACTTTATAT 59.349 38.462 0.00 0.00 0.00 0.86
222 224 5.989168 CCAGGATAACACGCATCACTTTATA 59.011 40.000 0.00 0.00 0.00 0.98
223 225 4.816385 CCAGGATAACACGCATCACTTTAT 59.184 41.667 0.00 0.00 0.00 1.40
224 226 4.081365 TCCAGGATAACACGCATCACTTTA 60.081 41.667 0.00 0.00 0.00 1.85
225 227 3.009723 CCAGGATAACACGCATCACTTT 58.990 45.455 0.00 0.00 0.00 2.66
226 228 2.236146 TCCAGGATAACACGCATCACTT 59.764 45.455 0.00 0.00 0.00 3.16
227 229 1.831106 TCCAGGATAACACGCATCACT 59.169 47.619 0.00 0.00 0.00 3.41
228 230 2.309528 TCCAGGATAACACGCATCAC 57.690 50.000 0.00 0.00 0.00 3.06
229 231 2.027653 TGTTCCAGGATAACACGCATCA 60.028 45.455 0.00 0.00 32.07 3.07
230 232 2.609459 CTGTTCCAGGATAACACGCATC 59.391 50.000 0.00 0.00 33.45 3.91
231 233 2.632377 CTGTTCCAGGATAACACGCAT 58.368 47.619 0.00 0.00 33.45 4.73
232 234 2.093306 CTGTTCCAGGATAACACGCA 57.907 50.000 0.00 0.00 33.45 5.24
245 247 1.679559 GGAATGGCATGCCCTGTTCC 61.680 60.000 32.36 32.36 39.87 3.62
273 275 9.995957 CGTCATGGAAAAACAAATGTATGTATA 57.004 29.630 0.00 0.00 32.02 1.47
274 276 8.735315 TCGTCATGGAAAAACAAATGTATGTAT 58.265 29.630 0.00 0.00 32.02 2.29
275 277 8.100508 TCGTCATGGAAAAACAAATGTATGTA 57.899 30.769 0.00 0.00 32.02 2.29
276 278 6.976088 TCGTCATGGAAAAACAAATGTATGT 58.024 32.000 0.00 0.00 34.24 2.29
277 279 7.410728 GCTTCGTCATGGAAAAACAAATGTATG 60.411 37.037 0.00 0.00 0.00 2.39
278 280 6.586082 GCTTCGTCATGGAAAAACAAATGTAT 59.414 34.615 0.00 0.00 0.00 2.29
279 281 5.918011 GCTTCGTCATGGAAAAACAAATGTA 59.082 36.000 0.00 0.00 0.00 2.29
280 282 4.744631 GCTTCGTCATGGAAAAACAAATGT 59.255 37.500 0.00 0.00 0.00 2.71
287 289 2.214347 TCGTGCTTCGTCATGGAAAAA 58.786 42.857 0.00 0.00 40.80 1.94
358 368 6.015772 GCAGTTGTATTTCTTTCCCTGGTTTA 60.016 38.462 0.00 0.00 0.00 2.01
394 404 8.443937 GTGTTTAAGTGTCCAGAGATACATTTC 58.556 37.037 0.00 0.00 36.63 2.17
414 424 8.776470 CCTTAATTGTTCGTCCTTAAGTGTTTA 58.224 33.333 0.97 0.00 32.03 2.01
415 425 7.255346 CCCTTAATTGTTCGTCCTTAAGTGTTT 60.255 37.037 0.97 0.00 32.03 2.83
416 426 6.206048 CCCTTAATTGTTCGTCCTTAAGTGTT 59.794 38.462 0.97 0.00 32.03 3.32
417 427 5.704053 CCCTTAATTGTTCGTCCTTAAGTGT 59.296 40.000 0.97 0.00 32.03 3.55
418 428 5.704053 ACCCTTAATTGTTCGTCCTTAAGTG 59.296 40.000 0.97 0.00 32.03 3.16
419 429 5.872963 ACCCTTAATTGTTCGTCCTTAAGT 58.127 37.500 0.97 0.00 32.03 2.24
420 430 5.353400 GGACCCTTAATTGTTCGTCCTTAAG 59.647 44.000 0.00 0.00 37.41 1.85
421 431 5.247862 GGACCCTTAATTGTTCGTCCTTAA 58.752 41.667 8.54 0.00 37.41 1.85
422 432 4.323715 GGGACCCTTAATTGTTCGTCCTTA 60.324 45.833 2.09 0.00 39.77 2.69
438 448 4.586306 AAATACAATTCGAAGGGACCCT 57.414 40.909 7.44 7.44 33.87 4.34
520 532 1.404843 GGCTCACTAGTCTGGTAGGG 58.595 60.000 0.00 0.00 0.00 3.53
528 540 3.636153 AATTTCTGGGGCTCACTAGTC 57.364 47.619 0.00 0.00 0.00 2.59
543 555 8.612619 TCTATAAGGTCGAATGCTCAAAATTTC 58.387 33.333 0.00 0.00 0.00 2.17
544 556 8.506168 TCTATAAGGTCGAATGCTCAAAATTT 57.494 30.769 0.00 0.00 0.00 1.82
554 566 8.425577 ACAATTCAGTTCTATAAGGTCGAATG 57.574 34.615 0.00 0.00 0.00 2.67
680 726 8.359642 CAGTTCTGTGGGAAAATCTTGATTTTA 58.640 33.333 17.86 4.17 35.51 1.52
686 732 5.772825 TTCAGTTCTGTGGGAAAATCTTG 57.227 39.130 0.00 0.00 35.51 3.02
687 733 6.983906 AATTCAGTTCTGTGGGAAAATCTT 57.016 33.333 0.00 0.00 35.51 2.40
688 734 6.983906 AAATTCAGTTCTGTGGGAAAATCT 57.016 33.333 0.00 0.00 35.51 2.40
690 743 7.365497 AGAAAATTCAGTTCTGTGGGAAAAT 57.635 32.000 0.00 0.00 34.03 1.82
694 747 5.415701 GCATAGAAAATTCAGTTCTGTGGGA 59.584 40.000 13.67 0.00 41.77 4.37
767 862 4.489771 GCTGATCCGTGGGTGGGG 62.490 72.222 0.00 0.00 0.00 4.96
800 895 2.359850 TGACGTGATTGGCTGGCC 60.360 61.111 4.43 4.43 0.00 5.36
868 965 1.963464 GACGGCTGGGATCGGGTTTA 61.963 60.000 0.00 0.00 0.00 2.01
896 994 1.376683 TTTGGAGCGTTGGATCGGG 60.377 57.895 0.00 0.00 0.00 5.14
1327 1837 4.821589 GGCGGAGGACTGGAAGCG 62.822 72.222 0.00 0.00 37.60 4.68
1329 1839 3.358076 GACGGCGGAGGACTGGAAG 62.358 68.421 13.24 0.00 42.29 3.46
1496 2006 1.497991 GCAAGACACGAACTGCTACA 58.502 50.000 0.00 0.00 0.00 2.74
1532 2042 1.607467 GGAACCCAGCCAGCACATT 60.607 57.895 0.00 0.00 0.00 2.71
1533 2043 2.036256 GGAACCCAGCCAGCACAT 59.964 61.111 0.00 0.00 0.00 3.21
1549 2059 7.935755 AGAAAGATCATATCAACACTACATGGG 59.064 37.037 0.00 0.00 0.00 4.00
1570 2080 3.924918 TCACCAGAGACGAGAAGAAAG 57.075 47.619 0.00 0.00 0.00 2.62
1574 2084 4.420168 GAAAGATCACCAGAGACGAGAAG 58.580 47.826 0.00 0.00 0.00 2.85
1575 2085 3.193691 GGAAAGATCACCAGAGACGAGAA 59.806 47.826 0.00 0.00 0.00 2.87
1579 2089 2.493675 TCAGGAAAGATCACCAGAGACG 59.506 50.000 0.00 0.00 0.00 4.18
1582 2092 4.484537 ACATCAGGAAAGATCACCAGAG 57.515 45.455 0.00 0.00 0.00 3.35
1583 2093 5.026121 ACTACATCAGGAAAGATCACCAGA 58.974 41.667 0.00 0.00 0.00 3.86
1584 2094 5.114780 CACTACATCAGGAAAGATCACCAG 58.885 45.833 0.00 0.00 0.00 4.00
1585 2095 4.532126 ACACTACATCAGGAAAGATCACCA 59.468 41.667 0.00 0.00 0.00 4.17
1586 2096 4.872691 CACACTACATCAGGAAAGATCACC 59.127 45.833 0.00 0.00 0.00 4.02
1587 2097 5.724328 TCACACTACATCAGGAAAGATCAC 58.276 41.667 0.00 0.00 0.00 3.06
1588 2098 6.343703 CATCACACTACATCAGGAAAGATCA 58.656 40.000 0.00 0.00 0.00 2.92
1595 2105 3.099141 TCAGCATCACACTACATCAGGA 58.901 45.455 0.00 0.00 0.00 3.86
1603 2113 4.154015 CCATTTCGTTTCAGCATCACACTA 59.846 41.667 0.00 0.00 0.00 2.74
1604 2114 3.058016 CCATTTCGTTTCAGCATCACACT 60.058 43.478 0.00 0.00 0.00 3.55
1605 2115 3.236816 CCATTTCGTTTCAGCATCACAC 58.763 45.455 0.00 0.00 0.00 3.82
1611 2121 2.295629 TCATTGCCATTTCGTTTCAGCA 59.704 40.909 0.00 0.00 0.00 4.41
1612 2122 2.945278 TCATTGCCATTTCGTTTCAGC 58.055 42.857 0.00 0.00 0.00 4.26
1619 2129 3.058450 TGCACTTTTCATTGCCATTTCG 58.942 40.909 0.00 0.00 38.00 3.46
1621 2131 4.075963 ACTGCACTTTTCATTGCCATTT 57.924 36.364 0.00 0.00 38.00 2.32
1625 2135 5.064441 AGATAACTGCACTTTTCATTGCC 57.936 39.130 0.00 0.00 38.00 4.52
1638 2149 4.558538 ATTTGCATCCGAAGATAACTGC 57.441 40.909 0.00 0.00 0.00 4.40
1649 2160 2.598589 CACAGGACAAATTTGCATCCG 58.401 47.619 18.12 15.02 36.28 4.18
1650 2161 2.299867 ACCACAGGACAAATTTGCATCC 59.700 45.455 18.12 17.17 0.00 3.51
1652 2163 2.699846 ACACCACAGGACAAATTTGCAT 59.300 40.909 18.12 6.06 0.00 3.96
1653 2164 2.100584 GACACCACAGGACAAATTTGCA 59.899 45.455 18.12 0.00 0.00 4.08
1654 2165 2.100584 TGACACCACAGGACAAATTTGC 59.899 45.455 18.12 10.56 0.00 3.68
1655 2166 4.589216 ATGACACCACAGGACAAATTTG 57.411 40.909 16.67 16.67 0.00 2.32
1656 2167 5.363580 AGAAATGACACCACAGGACAAATTT 59.636 36.000 0.00 0.00 0.00 1.82
1657 2168 4.895297 AGAAATGACACCACAGGACAAATT 59.105 37.500 0.00 0.00 0.00 1.82
1658 2169 4.473444 AGAAATGACACCACAGGACAAAT 58.527 39.130 0.00 0.00 0.00 2.32
1659 2170 3.897239 AGAAATGACACCACAGGACAAA 58.103 40.909 0.00 0.00 0.00 2.83
1660 2171 3.576078 AGAAATGACACCACAGGACAA 57.424 42.857 0.00 0.00 0.00 3.18
1665 2176 3.635331 CAGCAAAGAAATGACACCACAG 58.365 45.455 0.00 0.00 0.00 3.66
1679 2190 9.749490 CATGATTAAAACAATTAAGCAGCAAAG 57.251 29.630 0.00 0.00 34.38 2.77
1683 2194 8.693542 AGACATGATTAAAACAATTAAGCAGC 57.306 30.769 0.00 0.00 34.38 5.25
1697 2208 7.994911 ACCATCTAATCAGCAAGACATGATTAA 59.005 33.333 0.00 2.50 43.93 1.40
1698 2209 7.512130 ACCATCTAATCAGCAAGACATGATTA 58.488 34.615 0.00 7.26 42.77 1.75
1699 2210 6.363065 ACCATCTAATCAGCAAGACATGATT 58.637 36.000 0.00 5.80 45.59 2.57
1705 2216 5.877012 TCTTCAACCATCTAATCAGCAAGAC 59.123 40.000 0.00 0.00 0.00 3.01
1708 2219 6.003326 TGTTCTTCAACCATCTAATCAGCAA 58.997 36.000 0.00 0.00 0.00 3.91
1711 2222 7.120285 ACATGTGTTCTTCAACCATCTAATCAG 59.880 37.037 0.00 0.00 0.00 2.90
1713 2224 7.383102 ACATGTGTTCTTCAACCATCTAATC 57.617 36.000 0.00 0.00 0.00 1.75
1722 2233 5.695851 ATTCAGGACATGTGTTCTTCAAC 57.304 39.130 1.15 0.00 29.58 3.18
1723 2234 6.998074 ACTAATTCAGGACATGTGTTCTTCAA 59.002 34.615 1.15 0.00 29.58 2.69
1728 2239 6.373779 CAACACTAATTCAGGACATGTGTTC 58.626 40.000 1.15 0.00 42.70 3.18
1737 2248 4.350368 TCAGTGCAACACTAATTCAGGA 57.650 40.909 0.00 0.00 43.43 3.86
1744 2255 3.719268 ATCCCATCAGTGCAACACTAA 57.281 42.857 0.00 0.00 43.43 2.24
1747 2258 2.161855 TCAATCCCATCAGTGCAACAC 58.838 47.619 0.00 0.00 41.43 3.32
1754 2265 3.433343 TGCATTGTTCAATCCCATCAGT 58.567 40.909 0.00 0.00 0.00 3.41
1755 2266 4.098807 TCATGCATTGTTCAATCCCATCAG 59.901 41.667 0.00 0.00 0.00 2.90
1756 2267 4.024670 TCATGCATTGTTCAATCCCATCA 58.975 39.130 0.00 0.00 0.00 3.07
1757 2268 4.659111 TCATGCATTGTTCAATCCCATC 57.341 40.909 0.00 0.00 0.00 3.51
1758 2269 4.899457 AGATCATGCATTGTTCAATCCCAT 59.101 37.500 0.00 0.12 0.00 4.00
1759 2270 4.283337 AGATCATGCATTGTTCAATCCCA 58.717 39.130 0.00 0.00 0.00 4.37
1760 2271 4.931661 AGATCATGCATTGTTCAATCCC 57.068 40.909 0.00 0.00 0.00 3.85
1761 2272 8.139350 TCAATTAGATCATGCATTGTTCAATCC 58.861 33.333 0.00 0.00 0.00 3.01
1762 2273 9.692749 ATCAATTAGATCATGCATTGTTCAATC 57.307 29.630 0.00 0.00 28.20 2.67
1764 2275 9.878667 AAATCAATTAGATCATGCATTGTTCAA 57.121 25.926 0.00 0.00 35.39 2.69
1771 2282 9.961265 CAGTGTTAAATCAATTAGATCATGCAT 57.039 29.630 0.00 0.00 35.39 3.96
1772 2283 8.959548 ACAGTGTTAAATCAATTAGATCATGCA 58.040 29.630 0.00 0.00 35.39 3.96
1773 2284 9.443283 GACAGTGTTAAATCAATTAGATCATGC 57.557 33.333 0.00 0.00 35.39 4.06
1774 2285 9.642312 CGACAGTGTTAAATCAATTAGATCATG 57.358 33.333 0.00 0.00 35.39 3.07
1775 2286 8.338259 GCGACAGTGTTAAATCAATTAGATCAT 58.662 33.333 0.00 0.00 35.39 2.45
1776 2287 7.549134 AGCGACAGTGTTAAATCAATTAGATCA 59.451 33.333 0.00 0.00 35.39 2.92
1777 2288 7.910304 AGCGACAGTGTTAAATCAATTAGATC 58.090 34.615 0.00 0.00 35.39 2.75
1778 2289 7.849804 AGCGACAGTGTTAAATCAATTAGAT 57.150 32.000 0.00 0.00 39.09 1.98
1779 2290 7.360861 CCAAGCGACAGTGTTAAATCAATTAGA 60.361 37.037 0.00 0.00 0.00 2.10
1780 2291 6.742718 CCAAGCGACAGTGTTAAATCAATTAG 59.257 38.462 0.00 0.00 0.00 1.73
1781 2292 6.428465 TCCAAGCGACAGTGTTAAATCAATTA 59.572 34.615 0.00 0.00 0.00 1.40
1782 2293 5.240623 TCCAAGCGACAGTGTTAAATCAATT 59.759 36.000 0.00 0.00 0.00 2.32
1783 2294 4.759693 TCCAAGCGACAGTGTTAAATCAAT 59.240 37.500 0.00 0.00 0.00 2.57
1784 2295 4.130857 TCCAAGCGACAGTGTTAAATCAA 58.869 39.130 0.00 0.00 0.00 2.57
1785 2296 3.734463 TCCAAGCGACAGTGTTAAATCA 58.266 40.909 0.00 0.00 0.00 2.57
1786 2297 4.946784 ATCCAAGCGACAGTGTTAAATC 57.053 40.909 0.00 0.00 0.00 2.17
1787 2298 5.460646 CAAATCCAAGCGACAGTGTTAAAT 58.539 37.500 0.00 0.00 0.00 1.40
1788 2299 4.261405 CCAAATCCAAGCGACAGTGTTAAA 60.261 41.667 0.00 0.00 0.00 1.52
1789 2300 3.252215 CCAAATCCAAGCGACAGTGTTAA 59.748 43.478 0.00 0.00 0.00 2.01
1790 2301 2.811431 CCAAATCCAAGCGACAGTGTTA 59.189 45.455 0.00 0.00 0.00 2.41
1791 2302 1.608590 CCAAATCCAAGCGACAGTGTT 59.391 47.619 0.00 0.00 0.00 3.32
1799 2310 2.489329 ACAGAATCACCAAATCCAAGCG 59.511 45.455 0.00 0.00 0.00 4.68
1813 2324 9.928236 GAAATAACAGAGCAGATTAACAGAATC 57.072 33.333 0.00 0.00 0.00 2.52
1823 2334 6.479884 ACCAAGAAGAAATAACAGAGCAGAT 58.520 36.000 0.00 0.00 0.00 2.90
1829 2340 5.827797 ACAGCAACCAAGAAGAAATAACAGA 59.172 36.000 0.00 0.00 0.00 3.41
1834 2345 5.620206 TCTCACAGCAACCAAGAAGAAATA 58.380 37.500 0.00 0.00 0.00 1.40
1864 2375 9.362151 ACAAAATTACCTGATAGGAAAAAGACA 57.638 29.630 1.13 0.00 37.67 3.41
1880 2391 6.033966 GCCTTGCATAGTGTACAAAATTACC 58.966 40.000 0.00 0.00 0.00 2.85
1899 2410 4.796038 AATGGAAAGACAATCTGCCTTG 57.204 40.909 0.00 0.00 0.00 3.61
1913 2424 2.368221 CTGCCCAAGGTGAAAATGGAAA 59.632 45.455 0.00 0.00 36.27 3.13
1927 2438 0.401738 CTCCTTCTCAACCTGCCCAA 59.598 55.000 0.00 0.00 0.00 4.12
1936 2477 3.190383 TCCAGTCCATCTCCTTCTCAA 57.810 47.619 0.00 0.00 0.00 3.02
1950 2491 4.478206 TCAACAGATCAGGAATCCAGTC 57.522 45.455 0.61 0.00 34.67 3.51
1952 2493 4.397417 GGTTTCAACAGATCAGGAATCCAG 59.603 45.833 0.61 0.00 34.67 3.86
1956 2497 5.337009 GCAATGGTTTCAACAGATCAGGAAT 60.337 40.000 0.00 0.00 0.00 3.01
2003 2544 3.511146 TGATATCAGACACACTGTGCTCA 59.489 43.478 9.20 0.00 45.86 4.26
2011 2552 3.935203 CACCTTGGTGATATCAGACACAC 59.065 47.826 14.15 0.00 38.57 3.82
2012 2553 3.837731 TCACCTTGGTGATATCAGACACA 59.162 43.478 17.57 0.55 38.57 3.72
2013 2554 4.471904 TCACCTTGGTGATATCAGACAC 57.528 45.455 17.57 0.00 36.44 3.67
2024 2565 4.455877 GGATACAAGAAGTTCACCTTGGTG 59.544 45.833 13.24 13.24 42.86 4.17
2085 2626 5.627182 AAGAGATCTGATTGCCACTGTAT 57.373 39.130 0.00 0.00 0.00 2.29
2124 2665 3.296628 CAATTGTTTCTGAACGTTCCCG 58.703 45.455 24.78 15.78 38.65 5.14
2130 2671 3.904136 AGAGGCAATTGTTTCTGAACG 57.096 42.857 7.40 0.00 38.65 3.95
2132 2673 7.231317 AGTTATGAAGAGGCAATTGTTTCTGAA 59.769 33.333 7.40 3.65 0.00 3.02
2149 2690 6.968131 TGCACTGCTAGTAAAGTTATGAAG 57.032 37.500 1.98 0.00 0.00 3.02
2164 2705 1.909781 CCCAAACCCATGCACTGCT 60.910 57.895 1.98 0.00 0.00 4.24
2176 2717 2.596338 CACACCCGGGACCCAAAC 60.596 66.667 32.02 0.00 0.00 2.93
2191 2732 6.877611 TCCTTTGACTAGACAAAAATCCAC 57.122 37.500 18.57 0.00 38.90 4.02
2196 2737 6.061441 TGCTGATCCTTTGACTAGACAAAAA 58.939 36.000 18.57 11.64 38.90 1.94
2244 2785 1.004560 AGACACCCAGCACACATCG 60.005 57.895 0.00 0.00 0.00 3.84
2291 2834 3.251004 ACAACGCAGGAAAGAAAGATCAC 59.749 43.478 0.00 0.00 0.00 3.06
2296 2839 2.599848 CGTCACAACGCAGGAAAGAAAG 60.600 50.000 0.00 0.00 42.82 2.62
2297 2840 1.329292 CGTCACAACGCAGGAAAGAAA 59.671 47.619 0.00 0.00 42.82 2.52
2298 2841 0.934496 CGTCACAACGCAGGAAAGAA 59.066 50.000 0.00 0.00 42.82 2.52
2299 2842 2.600388 CGTCACAACGCAGGAAAGA 58.400 52.632 0.00 0.00 42.82 2.52
2318 2861 3.624326 TTCGTTGCCACTTCATTTCAG 57.376 42.857 0.00 0.00 0.00 3.02
2335 2878 6.169419 TGCATCATAGAACTGAAGTTTTCG 57.831 37.500 0.00 0.00 38.56 3.46
2341 2884 7.487189 GGACAAATTTGCATCATAGAACTGAAG 59.513 37.037 18.12 0.00 0.00 3.02
2365 2909 2.548057 GCAAACAAATGAGACGACAGGA 59.452 45.455 0.00 0.00 0.00 3.86
2366 2910 2.290367 TGCAAACAAATGAGACGACAGG 59.710 45.455 0.00 0.00 0.00 4.00
2371 2915 2.693797 AGCTGCAAACAAATGAGACG 57.306 45.000 1.02 0.00 0.00 4.18
2401 2945 3.895232 TCTTGTTAGCAGGAGATGACC 57.105 47.619 0.00 0.00 0.00 4.02
2482 3026 7.921214 TCAAAGCGACAATGTTAAACCAAAATA 59.079 29.630 0.00 0.00 0.00 1.40
2484 3028 6.100004 TCAAAGCGACAATGTTAAACCAAAA 58.900 32.000 0.00 0.00 0.00 2.44
2485 3029 5.651530 TCAAAGCGACAATGTTAAACCAAA 58.348 33.333 0.00 0.00 0.00 3.28
2488 3032 6.763303 AAATCAAAGCGACAATGTTAAACC 57.237 33.333 0.00 0.00 0.00 3.27
2490 3034 6.758886 ACCAAAATCAAAGCGACAATGTTAAA 59.241 30.769 0.00 0.00 0.00 1.52
2491 3035 6.199908 CACCAAAATCAAAGCGACAATGTTAA 59.800 34.615 0.00 0.00 0.00 2.01
2492 3036 5.689514 CACCAAAATCAAAGCGACAATGTTA 59.310 36.000 0.00 0.00 0.00 2.41
2493 3037 4.507388 CACCAAAATCAAAGCGACAATGTT 59.493 37.500 0.00 0.00 0.00 2.71
2494 3038 4.050553 CACCAAAATCAAAGCGACAATGT 58.949 39.130 0.00 0.00 0.00 2.71
2495 3039 4.297510 TCACCAAAATCAAAGCGACAATG 58.702 39.130 0.00 0.00 0.00 2.82
2496 3040 4.582701 TCACCAAAATCAAAGCGACAAT 57.417 36.364 0.00 0.00 0.00 2.71
2497 3041 4.582701 ATCACCAAAATCAAAGCGACAA 57.417 36.364 0.00 0.00 0.00 3.18
2498 3042 4.278170 AGAATCACCAAAATCAAAGCGACA 59.722 37.500 0.00 0.00 0.00 4.35
2499 3043 4.618489 CAGAATCACCAAAATCAAAGCGAC 59.382 41.667 0.00 0.00 0.00 5.19
2500 3044 4.278170 ACAGAATCACCAAAATCAAAGCGA 59.722 37.500 0.00 0.00 0.00 4.93
2501 3045 4.549458 ACAGAATCACCAAAATCAAAGCG 58.451 39.130 0.00 0.00 0.00 4.68
2502 3046 4.618489 CGACAGAATCACCAAAATCAAAGC 59.382 41.667 0.00 0.00 0.00 3.51
2503 3047 5.156355 CCGACAGAATCACCAAAATCAAAG 58.844 41.667 0.00 0.00 0.00 2.77
2504 3048 4.582656 ACCGACAGAATCACCAAAATCAAA 59.417 37.500 0.00 0.00 0.00 2.69
2505 3049 4.141287 ACCGACAGAATCACCAAAATCAA 58.859 39.130 0.00 0.00 0.00 2.57
2506 3050 3.750371 ACCGACAGAATCACCAAAATCA 58.250 40.909 0.00 0.00 0.00 2.57
2507 3051 4.003648 AGACCGACAGAATCACCAAAATC 58.996 43.478 0.00 0.00 0.00 2.17
2508 3052 3.753272 CAGACCGACAGAATCACCAAAAT 59.247 43.478 0.00 0.00 0.00 1.82
2509 3053 3.138304 CAGACCGACAGAATCACCAAAA 58.862 45.455 0.00 0.00 0.00 2.44
2522 3066 4.683832 ACAATATAACAGAGCAGACCGAC 58.316 43.478 0.00 0.00 0.00 4.79
2524 3068 5.220662 CCAAACAATATAACAGAGCAGACCG 60.221 44.000 0.00 0.00 0.00 4.79
2581 3127 4.247258 AGTCGCACGTACATAATTTTCCA 58.753 39.130 0.00 0.00 0.00 3.53
2596 3142 1.849219 CTATTCGCTTCTGAGTCGCAC 59.151 52.381 0.00 0.00 0.00 5.34
2611 3157 0.599728 CCCGAGCTCTGCTGCTATTC 60.600 60.000 12.85 0.00 44.17 1.75


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

AutoCloner maintained by Alex Coulton.