Multiple sequence alignment - TraesCS6D01G167700

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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 TraesCS6D01G167700 chr6D 100.000 5520 0 0 1 5520 151595161 151600680 0.000000e+00 10194.0
1 TraesCS6D01G167700 chr6D 100.000 49 0 0 2288 2336 151597400 151597448 2.120000e-14 91.6
2 TraesCS6D01G167700 chr6D 100.000 49 0 0 2240 2288 151597448 151597496 2.120000e-14 91.6
3 TraesCS6D01G167700 chr6A 97.208 2650 55 5 2288 4924 192206419 192203776 0.000000e+00 4466.0
4 TraesCS6D01G167700 chr6A 93.293 2311 96 18 1 2288 192208645 192206371 0.000000e+00 3354.0
5 TraesCS6D01G167700 chr6B 96.628 2669 69 10 2294 4947 276219781 276222443 0.000000e+00 4410.0
6 TraesCS6D01G167700 chr6B 93.516 2298 94 17 1 2288 276217572 276219824 0.000000e+00 3367.0
7 TraesCS6D01G167700 chr6B 90.522 517 37 7 4975 5480 276225965 276226480 0.000000e+00 673.0
8 TraesCS6D01G167700 chr6B 93.333 45 2 1 5137 5181 702687536 702687493 1.280000e-06 65.8
9 TraesCS6D01G167700 chr7B 88.843 242 21 3 5236 5471 59311928 59311687 5.410000e-75 292.0
10 TraesCS6D01G167700 chr7D 88.559 236 21 1 5236 5471 101807109 101806880 1.170000e-71 281.0
11 TraesCS6D01G167700 chr4D 87.209 86 11 0 4957 5042 339474167 339474252 1.270000e-16 99.0
12 TraesCS6D01G167700 chr2A 84.314 102 15 1 4985 5085 513847138 513847239 1.270000e-16 99.0
13 TraesCS6D01G167700 chr4B 88.525 61 7 0 4982 5042 427254187 427254247 2.130000e-09 75.0
14 TraesCS6D01G167700 chr4B 100.000 28 0 0 4923 4950 21314485 21314512 1.000000e-02 52.8
15 TraesCS6D01G167700 chr3B 85.135 74 9 2 4984 5056 732058067 732058139 2.130000e-09 75.0
16 TraesCS6D01G167700 chr5A 90.000 40 4 0 4911 4950 279103035 279103074 1.000000e-02 52.8
17 TraesCS6D01G167700 chr1A 100.000 28 0 0 4922 4949 95822012 95822039 1.000000e-02 52.8


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 TraesCS6D01G167700 chr6D 151595161 151600680 5519 False 3459.066667 10194 100.000000 1 5520 3 chr6D.!!$F1 5519
1 TraesCS6D01G167700 chr6A 192203776 192208645 4869 True 3910.000000 4466 95.250500 1 4924 2 chr6A.!!$R1 4923
2 TraesCS6D01G167700 chr6B 276217572 276226480 8908 False 2816.666667 4410 93.555333 1 5480 3 chr6B.!!$F1 5479

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
416 436 0.030638 CGTCCCCACAGCAGTTTTTG 59.969 55.000 0.00 0.00 0.00 2.44 F
551 574 0.107459 GAGCTCACCAACTCCATCCC 60.107 60.000 9.40 0.00 0.00 3.85 F
651 674 0.107848 CGCTCCCCACTTATCGGTTT 60.108 55.000 0.00 0.00 0.00 3.27 F
1766 1791 0.608130 TCCATGACTGTCAACGAGGG 59.392 55.000 15.31 11.14 0.00 4.30 F
1932 1957 2.158623 TGTGACAACAAGGGATGAAGCT 60.159 45.455 0.00 0.00 31.82 3.74 F
3358 3393 2.025981 TGCCAAGGTATCTGAGCATGTT 60.026 45.455 0.00 0.00 30.06 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 1422 0.997196 GCCGACGTTATCTGTCAACC 59.003 55.000 0.00 0.00 36.11 3.77 R
1839 1864 1.730487 CTCCCAGACGTCATCGAGG 59.270 63.158 19.50 10.37 40.62 4.63 R
2130 2156 5.007034 TCATGAAGGGAAGCGAACATTTTA 58.993 37.500 0.00 0.00 0.00 1.52 R
3046 3077 0.111639 GGGTGGTGCTTCCCAGTAAA 59.888 55.000 0.00 0.00 42.95 2.01 R
3386 3421 0.458669 CTGTCCATGGGAATGCTTGC 59.541 55.000 13.02 0.00 31.38 4.01 R
5146 8694 0.968393 GAAGGCAGAGGAGGTCGTCT 60.968 60.000 0.00 0.00 41.26 4.18 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
126 128 4.752879 CACGAATGGGGCCGACGT 62.753 66.667 0.00 3.69 37.68 4.34
140 142 1.500396 GACGTCGTCCAAAATGCCC 59.500 57.895 14.60 0.00 0.00 5.36
142 144 1.209127 CGTCGTCCAAAATGCCCAC 59.791 57.895 0.00 0.00 0.00 4.61
153 155 1.801309 AATGCCCACCCAAACGAACG 61.801 55.000 0.00 0.00 0.00 3.95
211 213 3.242543 GCGTTGGAGTTGCTCTAATCATG 60.243 47.826 0.00 0.00 33.81 3.07
253 255 5.158494 CGCTTGGTGCTACGTTGATATATA 58.842 41.667 0.00 0.00 40.11 0.86
259 261 7.094631 TGGTGCTACGTTGATATATATTGACC 58.905 38.462 0.00 0.00 0.00 4.02
310 313 8.110860 ACAAATTCCACCTACATTCTTGTTAG 57.889 34.615 0.00 0.00 37.28 2.34
311 314 7.724061 ACAAATTCCACCTACATTCTTGTTAGT 59.276 33.333 0.00 0.00 37.28 2.24
416 436 0.030638 CGTCCCCACAGCAGTTTTTG 59.969 55.000 0.00 0.00 0.00 2.44
417 437 1.111277 GTCCCCACAGCAGTTTTTGT 58.889 50.000 0.00 0.00 0.00 2.83
418 438 1.480545 GTCCCCACAGCAGTTTTTGTT 59.519 47.619 0.00 0.00 0.00 2.83
419 439 1.480137 TCCCCACAGCAGTTTTTGTTG 59.520 47.619 0.00 0.00 43.01 3.33
420 440 1.289276 CCCACAGCAGTTTTTGTTGC 58.711 50.000 0.00 0.00 41.27 4.17
464 487 3.604582 CTCAGAAGAAGAACCCATCCAC 58.395 50.000 0.00 0.00 0.00 4.02
491 514 3.425404 CCATTGTTGACTTATTTCGGCG 58.575 45.455 0.00 0.00 0.00 6.46
546 569 2.435059 GCCGAGCTCACCAACTCC 60.435 66.667 15.40 0.00 0.00 3.85
547 570 3.059982 CCGAGCTCACCAACTCCA 58.940 61.111 15.40 0.00 0.00 3.86
548 571 1.599047 CCGAGCTCACCAACTCCAT 59.401 57.895 15.40 0.00 0.00 3.41
549 572 0.460987 CCGAGCTCACCAACTCCATC 60.461 60.000 15.40 0.00 0.00 3.51
550 573 0.460987 CGAGCTCACCAACTCCATCC 60.461 60.000 15.40 0.00 0.00 3.51
551 574 0.107459 GAGCTCACCAACTCCATCCC 60.107 60.000 9.40 0.00 0.00 3.85
552 575 0.842030 AGCTCACCAACTCCATCCCA 60.842 55.000 0.00 0.00 0.00 4.37
553 576 0.257039 GCTCACCAACTCCATCCCAT 59.743 55.000 0.00 0.00 0.00 4.00
554 577 1.748591 GCTCACCAACTCCATCCCATC 60.749 57.143 0.00 0.00 0.00 3.51
555 578 1.561076 CTCACCAACTCCATCCCATCA 59.439 52.381 0.00 0.00 0.00 3.07
556 579 2.174210 CTCACCAACTCCATCCCATCAT 59.826 50.000 0.00 0.00 0.00 2.45
557 580 2.173356 TCACCAACTCCATCCCATCATC 59.827 50.000 0.00 0.00 0.00 2.92
558 581 2.092267 CACCAACTCCATCCCATCATCA 60.092 50.000 0.00 0.00 0.00 3.07
559 582 2.582172 ACCAACTCCATCCCATCATCAA 59.418 45.455 0.00 0.00 0.00 2.57
560 583 3.205959 ACCAACTCCATCCCATCATCAAT 59.794 43.478 0.00 0.00 0.00 2.57
561 584 4.220724 CCAACTCCATCCCATCATCAATT 58.779 43.478 0.00 0.00 0.00 2.32
562 585 4.280174 CCAACTCCATCCCATCATCAATTC 59.720 45.833 0.00 0.00 0.00 2.17
563 586 4.801521 ACTCCATCCCATCATCAATTCA 57.198 40.909 0.00 0.00 0.00 2.57
564 587 5.335028 ACTCCATCCCATCATCAATTCAT 57.665 39.130 0.00 0.00 0.00 2.57
603 626 4.079253 TCTGAAACCCTTTGCCTCATAAC 58.921 43.478 0.00 0.00 0.00 1.89
617 640 1.400846 TCATAACTCTGTCGACGCTCC 59.599 52.381 11.62 0.00 0.00 4.70
645 668 2.432300 CGGACCGCTCCCCACTTAT 61.432 63.158 0.00 0.00 31.93 1.73
646 669 1.446366 GGACCGCTCCCCACTTATC 59.554 63.158 0.00 0.00 0.00 1.75
648 671 2.365095 GACCGCTCCCCACTTATCGG 62.365 65.000 0.00 0.00 42.24 4.18
650 673 1.520666 CGCTCCCCACTTATCGGTT 59.479 57.895 0.00 0.00 0.00 4.44
651 674 0.107848 CGCTCCCCACTTATCGGTTT 60.108 55.000 0.00 0.00 0.00 3.27
653 676 1.379527 CTCCCCACTTATCGGTTTGC 58.620 55.000 0.00 0.00 0.00 3.68
708 733 1.009675 GGTTGCTGCACTTCACACG 60.010 57.895 0.00 0.00 0.00 4.49
720 745 2.160813 ACTTCACACGTGTTTTGTCACC 59.839 45.455 20.79 0.00 35.18 4.02
721 746 1.809684 TCACACGTGTTTTGTCACCA 58.190 45.000 20.79 0.00 35.18 4.17
722 747 1.465387 TCACACGTGTTTTGTCACCAC 59.535 47.619 20.79 0.00 35.18 4.16
723 748 1.466950 CACACGTGTTTTGTCACCACT 59.533 47.619 20.79 0.00 35.18 4.00
724 749 2.095466 CACACGTGTTTTGTCACCACTT 60.095 45.455 20.79 0.00 35.18 3.16
747 772 1.169661 TCGTGCTGCGGTTTTGGAAT 61.170 50.000 0.00 0.00 41.72 3.01
751 776 1.270041 TGCTGCGGTTTTGGAATTTCC 60.270 47.619 8.59 8.59 36.96 3.13
773 798 0.761802 TTGATGTTTGGGGTTTGGCC 59.238 50.000 0.00 0.00 0.00 5.36
1051 1076 2.637521 CAGCTGGTGTCTGCAATGT 58.362 52.632 5.57 0.00 39.84 2.71
1128 1153 2.430610 GCTCCAGGTGCTCGAGGAT 61.431 63.158 15.58 0.00 0.00 3.24
1245 1270 1.167155 GCAGGCTCATGGATCAGCTG 61.167 60.000 7.63 7.63 35.82 4.24
1397 1422 0.609957 TGGTGGCTGGAATTGCAGAG 60.610 55.000 28.86 6.49 0.00 3.35
1407 1432 3.245016 TGGAATTGCAGAGGTTGACAGAT 60.245 43.478 0.00 0.00 0.00 2.90
1419 1444 2.665649 TGACAGATAACGTCGGCAAT 57.334 45.000 0.00 0.00 36.11 3.56
1443 1468 2.431954 TAGCGTCTACTGCTAAGGGT 57.568 50.000 4.83 0.00 41.70 4.34
1502 1527 2.666317 TCCAGTGTCAGAGAAGTGTGA 58.334 47.619 0.00 0.00 0.00 3.58
1575 1600 6.265196 TGATTGTTGGATTATCTGGTATTGGC 59.735 38.462 0.00 0.00 0.00 4.52
1599 1624 1.626654 CGTGCCTCGCTCGACAAATT 61.627 55.000 2.14 0.00 46.28 1.82
1691 1716 3.671702 GCAGCTTGTAATGGAAGCAGAAC 60.672 47.826 7.20 0.00 46.93 3.01
1766 1791 0.608130 TCCATGACTGTCAACGAGGG 59.392 55.000 15.31 11.14 0.00 4.30
1932 1957 2.158623 TGTGACAACAAGGGATGAAGCT 60.159 45.455 0.00 0.00 31.82 3.74
1950 1975 6.279123 TGAAGCTGTTTATGAGATAGCAGAG 58.721 40.000 0.00 0.00 36.87 3.35
2194 2223 5.240403 GGTCTCATCCCTTTCTTTCATATGC 59.760 44.000 0.00 0.00 0.00 3.14
2218 2247 7.902387 CTCATCTTCTGAGTTTCAAGATTGA 57.098 36.000 0.00 0.00 45.42 2.57
2234 2264 8.996024 TCAAGATTGACTTATTGTATCAACGA 57.004 30.769 0.00 0.00 37.03 3.85
2237 2267 7.327975 AGATTGACTTATTGTATCAACGACCA 58.672 34.615 0.00 0.00 35.28 4.02
2282 2312 7.921041 ATTCATGTGAATCTACTTAGAGGGA 57.079 36.000 2.48 0.00 40.49 4.20
2283 2313 7.921041 TTCATGTGAATCTACTTAGAGGGAT 57.079 36.000 0.00 0.00 35.50 3.85
2284 2314 7.921041 TCATGTGAATCTACTTAGAGGGATT 57.079 36.000 0.00 0.00 35.50 3.01
2285 2315 9.434275 TTCATGTGAATCTACTTAGAGGGATTA 57.566 33.333 0.00 0.00 35.50 1.75
2286 2316 9.434275 TCATGTGAATCTACTTAGAGGGATTAA 57.566 33.333 0.00 0.00 35.50 1.40
2289 2319 9.434275 TGTGAATCTACTTAGAGGGATTAATCA 57.566 33.333 17.07 0.00 35.50 2.57
2295 2325 9.886132 TCTACTTAGAGGGATTAATCAAACAAC 57.114 33.333 17.07 0.00 0.00 3.32
2296 2326 9.667107 CTACTTAGAGGGATTAATCAAACAACA 57.333 33.333 17.07 0.00 0.00 3.33
2297 2327 8.934023 ACTTAGAGGGATTAATCAAACAACAA 57.066 30.769 17.07 1.93 0.00 2.83
2298 2328 9.362151 ACTTAGAGGGATTAATCAAACAACAAA 57.638 29.630 17.07 0.95 0.00 2.83
2302 2332 9.533831 AGAGGGATTAATCAAACAACAAATACT 57.466 29.630 17.07 0.00 0.00 2.12
2679 2710 4.309099 GAAGCAATGCCTGAAAATTCACA 58.691 39.130 0.00 0.00 32.90 3.58
2816 2847 6.223852 TCAAAACTAGTAGAAGGCTCACTTG 58.776 40.000 3.59 3.54 40.21 3.16
3046 3077 7.114754 TGCTAGAGTTCATGGAGATTGAAATT 58.885 34.615 0.00 0.00 35.03 1.82
3358 3393 2.025981 TGCCAAGGTATCTGAGCATGTT 60.026 45.455 0.00 0.00 30.06 2.71
3386 3421 2.415697 AACTGCCGACGAAATTTTGG 57.584 45.000 10.22 3.33 0.00 3.28
3405 3440 0.458669 GCAAGCATTCCCATGGACAG 59.541 55.000 15.22 0.86 0.00 3.51
3577 3612 2.615869 GGTTCTGAGATCTCACAGCAC 58.384 52.381 21.67 12.88 35.07 4.40
3619 3654 1.509644 CTTTCTGCGAGCTTGGTGCA 61.510 55.000 2.37 3.49 45.94 4.57
3783 3818 3.667497 TCTACAGACAGACAGCAAAGG 57.333 47.619 0.00 0.00 0.00 3.11
4087 4122 4.907809 CATACCATGCTCTCCATCAGATT 58.092 43.478 0.00 0.00 29.71 2.40
4491 4526 2.119457 CGTTTCTGAAGGCACAAAAGC 58.881 47.619 0.00 0.00 0.00 3.51
4540 4575 4.100707 GCATTATGCTGCAAACTTCAGA 57.899 40.909 10.27 0.00 40.96 3.27
4651 4699 3.060070 CGTTCCTTTTTCCAGTACACGAC 60.060 47.826 0.00 0.00 0.00 4.34
4663 4711 4.446719 CCAGTACACGACTTGTTTTCCTAC 59.553 45.833 0.00 0.00 39.91 3.18
4708 4756 1.067846 TCATACTGTCGCACTGTCCAC 60.068 52.381 2.96 0.00 32.45 4.02
4711 4759 3.207547 CTGTCGCACTGTCCACGGA 62.208 63.158 0.00 0.00 0.00 4.69
4721 4769 1.478510 CTGTCCACGGATAGTTCTGCT 59.521 52.381 1.83 0.00 0.00 4.24
4725 4773 4.020928 TGTCCACGGATAGTTCTGCTTAAA 60.021 41.667 0.00 0.00 0.00 1.52
4765 4813 4.100084 CCACATCAGCCCCAGCGA 62.100 66.667 0.00 0.00 46.67 4.93
4815 4863 2.969262 TCAGTACATGTCCACAGTCCAA 59.031 45.455 0.00 0.00 0.00 3.53
4876 4924 5.595257 GGTCTTCTACCGAAGTTCCTTAT 57.405 43.478 0.00 0.00 45.47 1.73
4877 4925 6.705863 GGTCTTCTACCGAAGTTCCTTATA 57.294 41.667 0.00 0.00 45.47 0.98
4878 4926 7.105241 GGTCTTCTACCGAAGTTCCTTATAA 57.895 40.000 0.00 0.00 45.47 0.98
4879 4927 7.724287 GGTCTTCTACCGAAGTTCCTTATAAT 58.276 38.462 0.00 0.00 45.47 1.28
4901 4949 5.420725 TCTTGTAAGAGAAGCATTGCCTA 57.579 39.130 4.70 0.00 0.00 3.93
4943 4991 1.977129 GAGCATCTCTAGCCAATCCCT 59.023 52.381 0.00 0.00 0.00 4.20
4947 4995 4.413520 AGCATCTCTAGCCAATCCCTTAAA 59.586 41.667 0.00 0.00 0.00 1.52
4948 4996 5.103940 AGCATCTCTAGCCAATCCCTTAAAA 60.104 40.000 0.00 0.00 0.00 1.52
4949 4997 5.594317 GCATCTCTAGCCAATCCCTTAAAAA 59.406 40.000 0.00 0.00 0.00 1.94
4968 5016 3.881937 AAATAGAGTAAACGGCGGAGT 57.118 42.857 13.24 0.00 0.00 3.85
4969 5017 4.989279 AAATAGAGTAAACGGCGGAGTA 57.011 40.909 13.24 0.00 0.00 2.59
4971 5019 4.989279 ATAGAGTAAACGGCGGAGTAAA 57.011 40.909 13.24 0.00 0.00 2.01
4972 5020 2.951726 AGAGTAAACGGCGGAGTAAAC 58.048 47.619 13.24 0.20 0.00 2.01
4973 5021 2.560105 AGAGTAAACGGCGGAGTAAACT 59.440 45.455 13.24 5.57 0.00 2.66
4979 8521 7.096551 AGTAAACGGCGGAGTAAACTTTAATA 58.903 34.615 13.24 0.00 0.00 0.98
4980 8522 6.799926 AAACGGCGGAGTAAACTTTAATAA 57.200 33.333 13.24 0.00 0.00 1.40
5014 8556 1.135517 CACTAAATTTTGGCCGGACCG 60.136 52.381 3.83 6.99 43.94 4.79
5016 8558 1.400494 CTAAATTTTGGCCGGACCGAG 59.600 52.381 17.49 6.74 43.94 4.63
5018 8560 2.764637 AATTTTGGCCGGACCGAGCT 62.765 55.000 17.49 0.00 43.94 4.09
5022 8564 4.162690 GGCCGGACCGAGCTGATT 62.163 66.667 17.49 0.00 0.00 2.57
5029 8571 1.001406 GGACCGAGCTGATTCCCTATG 59.999 57.143 0.00 0.00 0.00 2.23
5030 8572 1.689273 GACCGAGCTGATTCCCTATGT 59.311 52.381 0.00 0.00 0.00 2.29
5031 8573 2.891580 GACCGAGCTGATTCCCTATGTA 59.108 50.000 0.00 0.00 0.00 2.29
5034 8576 5.084519 ACCGAGCTGATTCCCTATGTATAA 58.915 41.667 0.00 0.00 0.00 0.98
5035 8577 5.721960 ACCGAGCTGATTCCCTATGTATAAT 59.278 40.000 0.00 0.00 0.00 1.28
5036 8578 6.045318 CCGAGCTGATTCCCTATGTATAATG 58.955 44.000 0.00 0.00 0.00 1.90
5066 8614 7.770801 AAACTTACTTTTGGTTTCTGCATTC 57.229 32.000 0.00 0.00 0.00 2.67
5090 8638 0.955428 AACACTTGTCATGCGGCGAT 60.955 50.000 12.98 0.00 0.00 4.58
5131 8679 0.872021 CGTCTATGCACCGGAGCTTC 60.872 60.000 24.52 6.19 34.99 3.86
5148 8696 3.703001 CTTCCCAAGCTTCACCTTAGA 57.297 47.619 0.00 0.00 0.00 2.10
5149 8697 3.339141 CTTCCCAAGCTTCACCTTAGAC 58.661 50.000 0.00 0.00 0.00 2.59
5150 8698 1.275291 TCCCAAGCTTCACCTTAGACG 59.725 52.381 0.00 0.00 0.00 4.18
5151 8699 1.275291 CCCAAGCTTCACCTTAGACGA 59.725 52.381 0.00 0.00 0.00 4.20
5153 8701 2.338500 CAAGCTTCACCTTAGACGACC 58.662 52.381 0.00 0.00 0.00 4.79
5154 8702 1.926108 AGCTTCACCTTAGACGACCT 58.074 50.000 0.00 0.00 0.00 3.85
5155 8703 1.819903 AGCTTCACCTTAGACGACCTC 59.180 52.381 0.00 0.00 0.00 3.85
5156 8704 1.135053 GCTTCACCTTAGACGACCTCC 60.135 57.143 0.00 0.00 0.00 4.30
5187 8735 1.407437 GGGACGCCTCATTCTCATTGT 60.407 52.381 0.00 0.00 0.00 2.71
5196 8744 5.688500 GCCTCATTCTCATTGTCATCCCTTA 60.689 44.000 0.00 0.00 0.00 2.69
5208 8756 1.125711 ATCCCTTATACCGGGCGCTT 61.126 55.000 7.64 0.00 41.69 4.68
5273 8821 2.350895 CATGGAAGGTGTGGCCGA 59.649 61.111 0.00 0.00 43.70 5.54
5346 8894 1.444553 CGCAGTCGAAGGAGTCACC 60.445 63.158 0.00 0.00 38.10 4.02
5350 8898 2.981909 TCGAAGGAGTCACCGCGT 60.982 61.111 4.92 0.00 44.74 6.01
5352 8900 2.649034 GAAGGAGTCACCGCGTCA 59.351 61.111 4.92 0.00 44.74 4.35
5415 8968 2.224885 GGAGCGCGTCGATGAAGAC 61.225 63.158 9.31 0.00 37.76 3.01
5416 8969 1.226435 GAGCGCGTCGATGAAGACT 60.226 57.895 9.31 0.00 38.90 3.24
5428 8981 1.737008 GAAGACTTGGTCGACGCCC 60.737 63.158 9.92 0.00 37.67 6.13
5486 9039 0.467804 GAGCTCTGGTCCATTCCTCC 59.532 60.000 6.43 0.00 0.00 4.30
5487 9040 0.252881 AGCTCTGGTCCATTCCTCCA 60.253 55.000 0.00 0.00 0.00 3.86
5488 9041 0.107459 GCTCTGGTCCATTCCTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
5489 9042 0.543749 CTCTGGTCCATTCCTCCACC 59.456 60.000 0.00 0.00 0.00 4.61
5490 9043 0.178876 TCTGGTCCATTCCTCCACCA 60.179 55.000 0.00 0.00 37.37 4.17
5491 9044 0.035056 CTGGTCCATTCCTCCACCAC 60.035 60.000 0.00 0.00 35.05 4.16
5492 9045 1.078426 GGTCCATTCCTCCACCACG 60.078 63.158 0.00 0.00 0.00 4.94
5493 9046 1.677552 GTCCATTCCTCCACCACGT 59.322 57.895 0.00 0.00 0.00 4.49
5494 9047 0.391263 GTCCATTCCTCCACCACGTC 60.391 60.000 0.00 0.00 0.00 4.34
5495 9048 1.078426 CCATTCCTCCACCACGTCC 60.078 63.158 0.00 0.00 0.00 4.79
5496 9049 1.553690 CCATTCCTCCACCACGTCCT 61.554 60.000 0.00 0.00 0.00 3.85
5497 9050 0.108138 CATTCCTCCACCACGTCCTC 60.108 60.000 0.00 0.00 0.00 3.71
5498 9051 1.605058 ATTCCTCCACCACGTCCTCG 61.605 60.000 0.00 0.00 43.34 4.63
5499 9052 2.675423 CCTCCACCACGTCCTCGA 60.675 66.667 0.00 0.00 40.62 4.04
5500 9053 2.567049 CTCCACCACGTCCTCGAC 59.433 66.667 0.00 0.00 40.62 4.20
5501 9054 1.972223 CTCCACCACGTCCTCGACT 60.972 63.158 0.00 0.00 40.62 4.18
5502 9055 1.924320 CTCCACCACGTCCTCGACTC 61.924 65.000 0.00 0.00 40.62 3.36
5503 9056 2.176055 CACCACGTCCTCGACTCG 59.824 66.667 0.00 0.00 40.62 4.18
5504 9057 2.281345 ACCACGTCCTCGACTCGT 60.281 61.111 0.00 0.07 40.62 4.18
5505 9058 2.323580 ACCACGTCCTCGACTCGTC 61.324 63.158 0.00 0.00 40.62 4.20
5514 9067 3.438088 CGACTCGTCGTTGTCTGC 58.562 61.111 11.05 0.00 46.99 4.26
5515 9068 2.081212 CGACTCGTCGTTGTCTGCC 61.081 63.158 11.05 0.00 46.99 4.85
5516 9069 2.050351 ACTCGTCGTTGTCTGCCG 60.050 61.111 0.00 0.00 0.00 5.69
5517 9070 3.470567 CTCGTCGTTGTCTGCCGC 61.471 66.667 0.00 0.00 0.00 6.53
5518 9071 4.273257 TCGTCGTTGTCTGCCGCA 62.273 61.111 0.00 0.00 0.00 5.69
5519 9072 3.112075 CGTCGTTGTCTGCCGCAT 61.112 61.111 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 2.438975 CATGGTCGGCATGTGGCT 60.439 61.111 5.01 0.00 44.01 4.75
126 128 1.605165 GGGTGGGCATTTTGGACGA 60.605 57.895 0.00 0.00 0.00 4.20
131 133 0.390860 TCGTTTGGGTGGGCATTTTG 59.609 50.000 0.00 0.00 0.00 2.44
159 161 3.518634 AACAAATGCACGTTTTGTCCT 57.481 38.095 15.31 1.12 44.32 3.85
160 162 4.316792 CGTAAACAAATGCACGTTTTGTCC 60.317 41.667 15.31 7.59 44.32 4.02
173 175 1.131016 CGCGCCGACGTAAACAAAT 59.869 52.632 0.00 0.00 42.83 2.32
175 177 2.657944 ACGCGCCGACGTAAACAA 60.658 55.556 5.73 0.00 46.19 2.83
253 255 2.092429 AGACAACCATATGCGGGTCAAT 60.092 45.455 16.26 0.74 37.77 2.57
416 436 2.947109 AACGCAACGCAACGCAAC 60.947 55.556 0.00 0.00 0.00 4.17
417 437 2.946597 CAACGCAACGCAACGCAA 60.947 55.556 0.00 0.00 0.00 4.85
418 438 4.896028 CCAACGCAACGCAACGCA 62.896 61.111 0.00 0.00 0.00 5.24
420 440 4.896028 TGCCAACGCAACGCAACG 62.896 61.111 0.00 0.00 43.74 4.10
453 476 1.678970 GGCAGGTGTGGATGGGTTC 60.679 63.158 0.00 0.00 0.00 3.62
454 477 1.803453 ATGGCAGGTGTGGATGGGTT 61.803 55.000 0.00 0.00 0.00 4.11
455 478 1.803453 AATGGCAGGTGTGGATGGGT 61.803 55.000 0.00 0.00 0.00 4.51
464 487 4.789012 AATAAGTCAACAATGGCAGGTG 57.211 40.909 0.00 0.00 31.99 4.00
491 514 2.358247 TTCTTCCGGTGCGCCTTC 60.358 61.111 15.69 0.00 0.00 3.46
546 569 6.834168 TGATGATGAATTGATGATGGGATG 57.166 37.500 0.00 0.00 0.00 3.51
547 570 7.579531 GCAATGATGATGAATTGATGATGGGAT 60.580 37.037 0.00 0.00 36.13 3.85
548 571 6.295067 GCAATGATGATGAATTGATGATGGGA 60.295 38.462 0.00 0.00 36.13 4.37
549 572 5.869344 GCAATGATGATGAATTGATGATGGG 59.131 40.000 0.00 0.00 36.13 4.00
550 573 6.691508 AGCAATGATGATGAATTGATGATGG 58.308 36.000 0.00 0.00 36.13 3.51
554 577 4.686091 GGCAGCAATGATGATGAATTGATG 59.314 41.667 1.35 8.78 45.81 3.07
555 578 4.343814 TGGCAGCAATGATGATGAATTGAT 59.656 37.500 1.35 0.00 45.81 2.57
556 579 3.702045 TGGCAGCAATGATGATGAATTGA 59.298 39.130 1.35 0.00 45.81 2.57
557 580 4.053469 TGGCAGCAATGATGATGAATTG 57.947 40.909 1.35 0.00 45.81 2.32
558 581 4.161565 ACTTGGCAGCAATGATGATGAATT 59.838 37.500 1.35 0.00 45.81 2.17
559 582 3.704566 ACTTGGCAGCAATGATGATGAAT 59.295 39.130 1.35 0.00 45.81 2.57
560 583 3.093814 ACTTGGCAGCAATGATGATGAA 58.906 40.909 1.35 0.00 45.81 2.57
561 584 2.686405 GACTTGGCAGCAATGATGATGA 59.314 45.455 1.35 0.00 45.81 2.92
562 585 2.688446 AGACTTGGCAGCAATGATGATG 59.312 45.455 1.35 0.00 45.70 3.07
563 586 2.688446 CAGACTTGGCAGCAATGATGAT 59.312 45.455 1.35 0.00 0.00 2.45
564 587 2.089201 CAGACTTGGCAGCAATGATGA 58.911 47.619 1.35 0.00 0.00 2.92
603 626 4.180946 CCGGGAGCGTCGACAGAG 62.181 72.222 17.16 0.00 0.00 3.35
645 668 2.851263 ACTTATCAGTGGCAAACCGA 57.149 45.000 0.00 0.00 39.70 4.69
646 669 4.000988 ACTTACTTATCAGTGGCAAACCG 58.999 43.478 0.00 0.00 39.70 4.44
648 671 5.178809 ACGAACTTACTTATCAGTGGCAAAC 59.821 40.000 0.00 0.00 34.06 2.93
650 673 4.890088 ACGAACTTACTTATCAGTGGCAA 58.110 39.130 0.00 0.00 34.06 4.52
651 674 4.530710 ACGAACTTACTTATCAGTGGCA 57.469 40.909 0.00 0.00 34.06 4.92
708 733 4.035017 CGAATCAAGTGGTGACAAAACAC 58.965 43.478 0.00 0.00 46.06 3.32
747 772 2.883026 ACCCCAAACATCAATCGGAAA 58.117 42.857 0.00 0.00 0.00 3.13
751 776 2.930455 GCCAAACCCCAAACATCAATCG 60.930 50.000 0.00 0.00 0.00 3.34
773 798 0.392998 CCAGAAATCACCCGTCCCAG 60.393 60.000 0.00 0.00 0.00 4.45
782 807 1.200020 CCGCTTCAACCCAGAAATCAC 59.800 52.381 0.00 0.00 0.00 3.06
1128 1153 0.032952 CCTCAAGGTCCGACACGAAA 59.967 55.000 0.00 0.00 0.00 3.46
1245 1270 1.335324 GCCTTGATGATATTGGCACGC 60.335 52.381 0.00 0.00 42.79 5.34
1397 1422 0.997196 GCCGACGTTATCTGTCAACC 59.003 55.000 0.00 0.00 36.11 3.77
1407 1432 2.400399 GCTATAGCATTGCCGACGTTA 58.600 47.619 20.01 0.00 41.59 3.18
1419 1444 3.502595 CCTTAGCAGTAGACGCTATAGCA 59.497 47.826 23.99 1.75 41.43 3.49
1575 1600 3.175240 CGAGCGAGGCACGACTTG 61.175 66.667 8.92 5.18 44.57 3.16
1599 1624 4.399395 CCAGGCGGCTGAGAAGCA 62.399 66.667 37.74 0.00 36.33 3.91
1691 1716 6.530534 CCTAACAAGACGTTTATGGTACTCAG 59.469 42.308 0.00 0.00 39.14 3.35
1741 1766 2.032030 CGTTGACAGTCATGGAACCAAC 60.032 50.000 3.45 0.00 0.00 3.77
1766 1791 2.738846 TCTTCAAGATCTTTGCTCGTGC 59.261 45.455 4.86 1.71 40.20 5.34
1839 1864 1.730487 CTCCCAGACGTCATCGAGG 59.270 63.158 19.50 10.37 40.62 4.63
1950 1975 7.339466 TCTTTGGATATTTCTACCTTTTCAGCC 59.661 37.037 0.00 0.00 0.00 4.85
2130 2156 5.007034 TCATGAAGGGAAGCGAACATTTTA 58.993 37.500 0.00 0.00 0.00 1.52
2194 2223 7.902387 TCAATCTTGAAACTCAGAAGATGAG 57.098 36.000 3.39 3.39 46.49 2.90
2218 2247 6.032956 TGACTGGTCGTTGATACAATAAGT 57.967 37.500 0.00 0.00 0.00 2.24
2260 2290 7.921041 AATCCCTCTAAGTAGATTCACATGA 57.079 36.000 0.00 0.00 0.00 3.07
2263 2293 9.434275 TGATTAATCCCTCTAAGTAGATTCACA 57.566 33.333 12.90 0.00 31.63 3.58
2269 2299 9.886132 GTTGTTTGATTAATCCCTCTAAGTAGA 57.114 33.333 12.90 0.00 0.00 2.59
2270 2300 9.667107 TGTTGTTTGATTAATCCCTCTAAGTAG 57.333 33.333 12.90 0.00 0.00 2.57
2272 2302 8.934023 TTGTTGTTTGATTAATCCCTCTAAGT 57.066 30.769 12.90 0.00 0.00 2.24
2276 2306 9.533831 AGTATTTGTTGTTTGATTAATCCCTCT 57.466 29.630 12.90 0.00 0.00 3.69
2304 2334 9.607333 TCCCTCTAAGTAGATTCACATGAATAT 57.393 33.333 7.09 7.00 44.14 1.28
2305 2335 9.607333 ATCCCTCTAAGTAGATTCACATGAATA 57.393 33.333 7.09 0.00 44.14 1.75
2306 2336 7.921041 TCCCTCTAAGTAGATTCACATGAAT 57.079 36.000 6.82 6.82 46.54 2.57
2307 2337 7.921041 ATCCCTCTAAGTAGATTCACATGAA 57.079 36.000 0.00 0.00 38.56 2.57
2308 2338 7.921041 AATCCCTCTAAGTAGATTCACATGA 57.079 36.000 0.00 0.00 0.00 3.07
2679 2710 3.383185 TGCGAGAACCATGAAAAACCTTT 59.617 39.130 0.00 0.00 0.00 3.11
2836 2867 6.238022 CCATGTCATGCATATGATACATCGAC 60.238 42.308 6.97 10.69 44.62 4.20
3046 3077 0.111639 GGGTGGTGCTTCCCAGTAAA 59.888 55.000 0.00 0.00 42.95 2.01
3163 3194 1.899814 ACGATAAGAGCTTGTGACCCA 59.100 47.619 0.00 0.00 0.00 4.51
3164 3195 2.673368 CAACGATAAGAGCTTGTGACCC 59.327 50.000 0.00 0.00 0.00 4.46
3165 3196 2.094417 GCAACGATAAGAGCTTGTGACC 59.906 50.000 0.00 0.00 0.00 4.02
3166 3197 2.996621 AGCAACGATAAGAGCTTGTGAC 59.003 45.455 0.00 0.00 32.67 3.67
3386 3421 0.458669 CTGTCCATGGGAATGCTTGC 59.541 55.000 13.02 0.00 31.38 4.01
3783 3818 7.573968 AAACCTTGGATAGCTTCAATGATAC 57.426 36.000 0.00 0.00 0.00 2.24
4087 4122 2.575735 TGATCCTCCCTTTGCATACACA 59.424 45.455 0.00 0.00 0.00 3.72
4588 4623 6.042777 TGAATAAGCTCTTATCTGAACGTGG 58.957 40.000 2.92 0.00 34.90 4.94
4651 4699 7.928706 TCTTCTCTCTTTCTGTAGGAAAACAAG 59.071 37.037 0.00 0.00 42.52 3.16
4663 4711 6.819649 AGCTTTCATGATCTTCTCTCTTTCTG 59.180 38.462 0.00 0.00 0.00 3.02
4708 4756 7.426410 TCAGACTATTTAAGCAGAACTATCCG 58.574 38.462 0.00 0.00 0.00 4.18
4711 4759 7.786030 TGCTCAGACTATTTAAGCAGAACTAT 58.214 34.615 0.00 0.00 38.01 2.12
4725 4773 8.263640 GTGGATATGGATAATTGCTCAGACTAT 58.736 37.037 0.00 0.00 0.00 2.12
4765 4813 7.704899 GTGGCAACTTACTTCTGTTAATTTGTT 59.295 33.333 0.00 0.00 37.61 2.83
4815 4863 3.567478 AGACTTGACTGCTTTGGTCTT 57.433 42.857 0.00 0.00 35.04 3.01
4876 4924 6.418101 AGGCAATGCTTCTCTTACAAGATTA 58.582 36.000 4.82 0.00 33.93 1.75
4877 4925 5.259632 AGGCAATGCTTCTCTTACAAGATT 58.740 37.500 4.82 0.00 33.93 2.40
4878 4926 4.853007 AGGCAATGCTTCTCTTACAAGAT 58.147 39.130 4.82 0.00 33.93 2.40
4879 4927 4.292186 AGGCAATGCTTCTCTTACAAGA 57.708 40.909 4.82 0.00 0.00 3.02
4901 4949 8.585881 TGCTCTAATAGACTCAAAAACTGTACT 58.414 33.333 0.00 0.00 0.00 2.73
4947 4995 4.198028 ACTCCGCCGTTTACTCTATTTT 57.802 40.909 0.00 0.00 0.00 1.82
4948 4996 3.881937 ACTCCGCCGTTTACTCTATTT 57.118 42.857 0.00 0.00 0.00 1.40
4949 4997 4.989279 TTACTCCGCCGTTTACTCTATT 57.011 40.909 0.00 0.00 0.00 1.73
4950 4998 4.400567 AGTTTACTCCGCCGTTTACTCTAT 59.599 41.667 0.00 0.00 0.00 1.98
4951 4999 3.758554 AGTTTACTCCGCCGTTTACTCTA 59.241 43.478 0.00 0.00 0.00 2.43
4952 5000 2.560105 AGTTTACTCCGCCGTTTACTCT 59.440 45.455 0.00 0.00 0.00 3.24
4953 5001 2.951726 AGTTTACTCCGCCGTTTACTC 58.048 47.619 0.00 0.00 0.00 2.59
4954 5002 3.391506 AAGTTTACTCCGCCGTTTACT 57.608 42.857 0.00 0.00 0.00 2.24
4955 5003 5.590104 TTAAAGTTTACTCCGCCGTTTAC 57.410 39.130 0.00 0.00 0.00 2.01
4956 5004 7.897575 TTATTAAAGTTTACTCCGCCGTTTA 57.102 32.000 0.00 0.00 0.00 2.01
4959 5007 6.413018 CTTTATTAAAGTTTACTCCGCCGT 57.587 37.500 7.84 0.00 33.80 5.68
5000 8542 2.750237 GCTCGGTCCGGCCAAAAT 60.750 61.111 12.29 0.00 36.97 1.82
5014 8556 8.317679 ACTTCATTATACATAGGGAATCAGCTC 58.682 37.037 0.00 0.00 0.00 4.09
5016 8558 9.944376 TTACTTCATTATACATAGGGAATCAGC 57.056 33.333 0.00 0.00 0.00 4.26
5035 8577 9.849166 CAGAAACCAAAAGTAAGTTTTACTTCA 57.151 29.630 12.98 0.00 39.51 3.02
5036 8578 8.804743 GCAGAAACCAAAAGTAAGTTTTACTTC 58.195 33.333 12.98 1.98 39.51 3.01
5066 8614 1.660052 CCGCATGACAAGTGTTCAACG 60.660 52.381 0.00 0.00 0.00 4.10
5131 8679 1.275291 TCGTCTAAGGTGAAGCTTGGG 59.725 52.381 2.10 0.00 0.00 4.12
5146 8694 0.968393 GAAGGCAGAGGAGGTCGTCT 60.968 60.000 0.00 0.00 41.26 4.18
5147 8695 1.513622 GAAGGCAGAGGAGGTCGTC 59.486 63.158 0.00 0.00 0.00 4.20
5148 8696 2.344203 CGAAGGCAGAGGAGGTCGT 61.344 63.158 0.00 0.00 0.00 4.34
5149 8697 2.492090 CGAAGGCAGAGGAGGTCG 59.508 66.667 0.00 0.00 0.00 4.79
5150 8698 2.896443 CCGAAGGCAGAGGAGGTC 59.104 66.667 0.00 0.00 46.14 3.85
5172 8720 2.883386 GGGATGACAATGAGAATGAGGC 59.117 50.000 0.00 0.00 0.00 4.70
5241 8789 2.512286 ATGTGCCCTGCATCGACG 60.512 61.111 0.00 0.00 41.91 5.12
5257 8805 1.077501 CATCGGCCACACCTTCCAT 60.078 57.895 2.24 0.00 35.61 3.41
5329 8877 1.444553 CGGTGACTCCTTCGACTGC 60.445 63.158 0.00 0.00 0.00 4.40
5340 8888 2.661866 GCAAGTGACGCGGTGACT 60.662 61.111 12.47 6.04 29.99 3.41
5370 8918 1.944676 GTCTACCGCGCCATTCTCG 60.945 63.158 0.00 0.00 0.00 4.04
5372 8920 1.940883 TTCGTCTACCGCGCCATTCT 61.941 55.000 0.00 0.00 36.19 2.40
5373 8921 1.480219 CTTCGTCTACCGCGCCATTC 61.480 60.000 0.00 0.00 36.19 2.67
5374 8922 1.518572 CTTCGTCTACCGCGCCATT 60.519 57.895 0.00 0.00 36.19 3.16
5377 8930 1.944676 CATCTTCGTCTACCGCGCC 60.945 63.158 0.00 0.00 36.19 6.53
5400 8953 1.341802 CAAGTCTTCATCGACGCGC 59.658 57.895 5.73 0.00 38.90 6.86
5428 8981 2.027625 GTTCCACCTCCAAGACGCG 61.028 63.158 3.53 3.53 0.00 6.01
5480 9033 2.273179 CGAGGACGTGGTGGAGGAA 61.273 63.158 0.00 0.00 34.56 3.36
5481 9034 2.675423 CGAGGACGTGGTGGAGGA 60.675 66.667 0.00 0.00 34.56 3.71
5482 9035 2.675423 TCGAGGACGTGGTGGAGG 60.675 66.667 0.00 0.00 40.69 4.30
5483 9036 1.924320 GAGTCGAGGACGTGGTGGAG 61.924 65.000 0.00 0.00 37.67 3.86
5484 9037 1.970114 GAGTCGAGGACGTGGTGGA 60.970 63.158 0.00 0.00 37.67 4.02
5485 9038 2.567049 GAGTCGAGGACGTGGTGG 59.433 66.667 0.00 0.00 37.67 4.61
5486 9039 2.176055 CGAGTCGAGGACGTGGTG 59.824 66.667 6.73 0.00 37.67 4.17
5487 9040 2.281345 ACGAGTCGAGGACGTGGT 60.281 61.111 21.50 0.00 38.79 4.16
5488 9041 2.479650 GACGAGTCGAGGACGTGG 59.520 66.667 21.50 0.00 40.29 4.94
5498 9051 2.081212 CGGCAGACAACGACGAGTC 61.081 63.158 0.00 9.43 35.02 3.36
5499 9052 2.050351 CGGCAGACAACGACGAGT 60.050 61.111 0.00 0.00 0.00 4.18
5500 9053 3.470567 GCGGCAGACAACGACGAG 61.471 66.667 0.00 0.00 0.00 4.18
5501 9054 3.567478 ATGCGGCAGACAACGACGA 62.567 57.895 9.25 0.00 0.00 4.20
5502 9055 3.112075 ATGCGGCAGACAACGACG 61.112 61.111 9.25 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.