Multiple sequence alignment - TraesCS1D01G381200

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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 TraesCS1D01G381200 chr1D 100.000 2297 0 0 1 2297 456202134 456204430 0.000000e+00 4242.0
1 TraesCS1D01G381200 chr1D 86.364 616 43 22 750 1328 456251442 456252053 3.220000e-178 634.0
2 TraesCS1D01G381200 chr1D 90.596 436 25 8 866 1297 457033236 457033659 4.280000e-157 564.0
3 TraesCS1D01G381200 chr1D 94.035 285 17 0 1013 1297 457044149 457044433 1.260000e-117 433.0
4 TraesCS1D01G381200 chr1D 85.637 369 35 8 223 585 457022344 457022700 2.790000e-99 372.0
5 TraesCS1D01G381200 chr1D 84.712 399 25 11 102 474 456223821 456224209 1.300000e-97 366.0
6 TraesCS1D01G381200 chr1D 82.500 240 23 11 576 809 457022719 457022945 2.330000e-45 193.0
7 TraesCS1D01G381200 chr1D 92.857 112 8 0 14 125 457022175 457022286 1.830000e-36 163.0
8 TraesCS1D01G381200 chr1B 83.921 1362 101 47 14 1312 626609305 626610611 0.000000e+00 1194.0
9 TraesCS1D01G381200 chr1B 84.877 853 71 20 1491 2295 626611926 626612768 0.000000e+00 808.0
10 TraesCS1D01G381200 chr1B 95.088 285 14 0 1013 1297 626649127 626649411 1.250000e-122 449.0
11 TraesCS1D01G381200 chr1B 77.966 236 47 5 1054 1288 626601063 626601294 2.380000e-30 143.0
12 TraesCS1D01G381200 chr1A 86.008 779 59 19 589 1328 549670214 549670981 0.000000e+00 789.0
13 TraesCS1D01G381200 chr1A 94.386 285 16 0 1013 1297 549695451 549695735 2.710000e-119 438.0
14 TraesCS1D01G381200 chr1A 83.297 461 60 14 88 545 549669769 549670215 2.120000e-110 409.0
15 TraesCS1D01G381200 chr1A 77.872 235 49 3 1054 1288 549666545 549666776 2.380000e-30 143.0
16 TraesCS1D01G381200 chr7B 100.000 33 0 0 2217 2249 389005717 389005749 6.850000e-06 62.1
17 TraesCS1D01G381200 chr7B 83.051 59 10 0 49 107 641070729 641070671 1.000000e-03 54.7
18 TraesCS1D01G381200 chr3D 100.000 31 0 0 187 217 15964527 15964557 8.860000e-05 58.4


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 TraesCS1D01G381200 chr1D 456202134 456204430 2296 False 4242.000000 4242 100.000000 1 2297 1 chr1D.!!$F1 2296
1 TraesCS1D01G381200 chr1D 456251442 456252053 611 False 634.000000 634 86.364000 750 1328 1 chr1D.!!$F3 578
2 TraesCS1D01G381200 chr1D 457022175 457022945 770 False 242.666667 372 86.998000 14 809 3 chr1D.!!$F6 795
3 TraesCS1D01G381200 chr1B 626609305 626612768 3463 False 1001.000000 1194 84.399000 14 2295 2 chr1B.!!$F3 2281
4 TraesCS1D01G381200 chr1A 549666545 549670981 4436 False 447.000000 789 82.392333 88 1328 3 chr1A.!!$F2 1240

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
740 3952 0.107993 CGTCACATCAGTCTGGCCAT 60.108 55.0 5.51 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 6618 0.108992 ACAAGCGCTTCGTCGGATAA 60.109 50.0 22.21 0.0 0.0 1.75 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
27 28 8.887264 TGATAGTTGGTAATTGGTTATTTGGT 57.113 30.769 0.00 0.00 0.00 3.67
28 29 9.315363 TGATAGTTGGTAATTGGTTATTTGGTT 57.685 29.630 0.00 0.00 0.00 3.67
31 32 8.715190 AGTTGGTAATTGGTTATTTGGTTACT 57.285 30.769 0.00 0.00 0.00 2.24
32 33 9.810870 AGTTGGTAATTGGTTATTTGGTTACTA 57.189 29.630 0.00 0.00 0.00 1.82
34 35 9.810870 TTGGTAATTGGTTATTTGGTTACTAGT 57.189 29.630 0.00 0.00 0.00 2.57
41 42 9.723601 TTGGTTATTTGGTTACTAGTATTTCGT 57.276 29.630 2.79 0.00 0.00 3.85
42 43 9.153721 TGGTTATTTGGTTACTAGTATTTCGTG 57.846 33.333 2.79 0.00 0.00 4.35
43 44 8.118607 GGTTATTTGGTTACTAGTATTTCGTGC 58.881 37.037 2.79 0.00 0.00 5.34
44 45 8.876790 GTTATTTGGTTACTAGTATTTCGTGCT 58.123 33.333 2.79 0.00 0.00 4.40
45 46 6.715344 TTTGGTTACTAGTATTTCGTGCTG 57.285 37.500 2.79 0.00 0.00 4.41
46 47 5.648178 TGGTTACTAGTATTTCGTGCTGA 57.352 39.130 2.79 0.00 0.00 4.26
47 48 6.028146 TGGTTACTAGTATTTCGTGCTGAA 57.972 37.500 2.79 0.00 33.85 3.02
48 49 6.636705 TGGTTACTAGTATTTCGTGCTGAAT 58.363 36.000 2.79 0.00 36.22 2.57
49 50 6.533723 TGGTTACTAGTATTTCGTGCTGAATG 59.466 38.462 2.79 0.00 36.22 2.67
52 53 5.479306 ACTAGTATTTCGTGCTGAATGTGT 58.521 37.500 0.00 0.00 36.22 3.72
53 54 5.932303 ACTAGTATTTCGTGCTGAATGTGTT 59.068 36.000 0.00 0.00 36.22 3.32
55 56 4.754618 AGTATTTCGTGCTGAATGTGTTGA 59.245 37.500 0.00 0.00 36.22 3.18
56 57 3.607422 TTTCGTGCTGAATGTGTTGAG 57.393 42.857 0.00 0.00 36.22 3.02
57 58 2.238942 TCGTGCTGAATGTGTTGAGT 57.761 45.000 0.00 0.00 0.00 3.41
58 59 2.560504 TCGTGCTGAATGTGTTGAGTT 58.439 42.857 0.00 0.00 0.00 3.01
59 60 2.942376 TCGTGCTGAATGTGTTGAGTTT 59.058 40.909 0.00 0.00 0.00 2.66
60 61 3.376859 TCGTGCTGAATGTGTTGAGTTTT 59.623 39.130 0.00 0.00 0.00 2.43
61 62 4.572795 TCGTGCTGAATGTGTTGAGTTTTA 59.427 37.500 0.00 0.00 0.00 1.52
62 63 5.238432 TCGTGCTGAATGTGTTGAGTTTTAT 59.762 36.000 0.00 0.00 0.00 1.40
63 64 5.914635 CGTGCTGAATGTGTTGAGTTTTATT 59.085 36.000 0.00 0.00 0.00 1.40
66 67 7.434897 GTGCTGAATGTGTTGAGTTTTATTTGA 59.565 33.333 0.00 0.00 0.00 2.69
67 68 8.143193 TGCTGAATGTGTTGAGTTTTATTTGAT 58.857 29.630 0.00 0.00 0.00 2.57
68 69 8.430063 GCTGAATGTGTTGAGTTTTATTTGATG 58.570 33.333 0.00 0.00 0.00 3.07
69 70 8.296799 TGAATGTGTTGAGTTTTATTTGATGC 57.703 30.769 0.00 0.00 0.00 3.91
70 71 8.143193 TGAATGTGTTGAGTTTTATTTGATGCT 58.857 29.630 0.00 0.00 0.00 3.79
71 72 8.524870 AATGTGTTGAGTTTTATTTGATGCTC 57.475 30.769 0.00 0.00 0.00 4.26
72 73 7.275888 TGTGTTGAGTTTTATTTGATGCTCT 57.724 32.000 0.00 0.00 0.00 4.09
73 74 7.715657 TGTGTTGAGTTTTATTTGATGCTCTT 58.284 30.769 0.00 0.00 0.00 2.85
74 75 8.845227 TGTGTTGAGTTTTATTTGATGCTCTTA 58.155 29.630 0.00 0.00 0.00 2.10
76 77 9.066892 TGTTGAGTTTTATTTGATGCTCTTAGT 57.933 29.630 0.00 0.00 0.00 2.24
79 80 9.944376 TGAGTTTTATTTGATGCTCTTAGTACT 57.056 29.630 0.00 0.00 0.00 2.73
83 84 5.599999 ATTTGATGCTCTTAGTACTCCGT 57.400 39.130 0.00 0.00 0.00 4.69
84 85 6.710597 ATTTGATGCTCTTAGTACTCCGTA 57.289 37.500 0.00 0.00 0.00 4.02
85 86 5.496133 TTGATGCTCTTAGTACTCCGTAC 57.504 43.478 0.00 0.00 39.10 3.67
87 88 5.922053 TGATGCTCTTAGTACTCCGTACTA 58.078 41.667 0.00 9.22 45.99 1.82
176 3315 5.306937 TGGTATGTACTGATGTGGGGATTAG 59.693 44.000 0.00 0.00 0.00 1.73
220 3359 8.616076 ACTTGAGCTTAAGTGCAATCATATTAC 58.384 33.333 21.91 0.00 39.33 1.89
221 3360 7.496529 TGAGCTTAAGTGCAATCATATTACC 57.503 36.000 4.02 0.00 34.99 2.85
222 3361 7.053498 TGAGCTTAAGTGCAATCATATTACCA 58.947 34.615 4.02 0.00 34.99 3.25
223 3362 7.227314 TGAGCTTAAGTGCAATCATATTACCAG 59.773 37.037 4.02 0.00 34.99 4.00
237 3400 6.547880 TCATATTACCAGGACACTTCTCTCTC 59.452 42.308 0.00 0.00 0.00 3.20
366 3529 2.204463 TGGATCCCATGCTACAAAGGA 58.796 47.619 9.90 0.00 0.00 3.36
480 3645 4.513442 TGATGACCCATGCTTACACTTAC 58.487 43.478 0.00 0.00 0.00 2.34
500 3666 0.465097 CCATACTGCCTCAAGCCCTG 60.465 60.000 0.00 0.00 42.71 4.45
548 3714 6.431234 TCGATCGATCTCTTCCTTAATCATCA 59.569 38.462 22.43 0.00 0.00 3.07
550 3716 6.715347 TCGATCTCTTCCTTAATCATCACA 57.285 37.500 0.00 0.00 0.00 3.58
555 3721 5.721480 TCTCTTCCTTAATCATCACAGTCCA 59.279 40.000 0.00 0.00 0.00 4.02
560 3726 7.214467 TCCTTAATCATCACAGTCCAAAAAC 57.786 36.000 0.00 0.00 0.00 2.43
561 3727 6.775142 TCCTTAATCATCACAGTCCAAAAACA 59.225 34.615 0.00 0.00 0.00 2.83
570 3740 5.830457 TCACAGTCCAAAAACAATATGACCA 59.170 36.000 0.00 0.00 0.00 4.02
657 3857 3.839654 GGCACGCTCATGAATCATG 57.160 52.632 16.63 16.63 42.60 3.07
658 3858 1.302366 GGCACGCTCATGAATCATGA 58.698 50.000 22.84 22.84 46.84 3.07
727 3939 0.169230 AAAAAGCGCAACACGTCACA 59.831 45.000 11.47 0.00 46.11 3.58
728 3940 0.380378 AAAAGCGCAACACGTCACAT 59.620 45.000 11.47 0.00 46.11 3.21
730 3942 1.157257 AAGCGCAACACGTCACATCA 61.157 50.000 11.47 0.00 46.11 3.07
731 3943 1.154599 GCGCAACACGTCACATCAG 60.155 57.895 0.30 0.00 46.11 2.90
732 3944 1.831389 GCGCAACACGTCACATCAGT 61.831 55.000 0.30 0.00 46.11 3.41
733 3945 0.161658 CGCAACACGTCACATCAGTC 59.838 55.000 0.00 0.00 36.87 3.51
734 3946 1.502231 GCAACACGTCACATCAGTCT 58.498 50.000 0.00 0.00 0.00 3.24
735 3947 1.193203 GCAACACGTCACATCAGTCTG 59.807 52.381 0.00 0.00 0.00 3.51
736 3948 1.794701 CAACACGTCACATCAGTCTGG 59.205 52.381 0.00 0.00 0.00 3.86
737 3949 0.319900 ACACGTCACATCAGTCTGGC 60.320 55.000 0.00 0.00 0.00 4.85
738 3950 1.016130 CACGTCACATCAGTCTGGCC 61.016 60.000 0.00 0.00 0.00 5.36
739 3951 1.293179 CGTCACATCAGTCTGGCCA 59.707 57.895 4.71 4.71 0.00 5.36
740 3952 0.107993 CGTCACATCAGTCTGGCCAT 60.108 55.000 5.51 0.00 0.00 4.40
838 4069 4.683334 GCTTCCGCGTTGCACACC 62.683 66.667 4.92 0.00 0.00 4.16
839 4070 2.972505 CTTCCGCGTTGCACACCT 60.973 61.111 4.92 0.00 0.00 4.00
840 4071 1.666553 CTTCCGCGTTGCACACCTA 60.667 57.895 4.92 0.00 0.00 3.08
855 4102 3.064545 CACACCTACTACTACTACGTGCC 59.935 52.174 0.00 0.00 0.00 5.01
859 4106 0.731417 ACTACTACTACGTGCCGCAG 59.269 55.000 0.00 0.00 0.00 5.18
860 4107 1.012086 CTACTACTACGTGCCGCAGA 58.988 55.000 0.00 0.00 0.00 4.26
910 4166 0.251341 ATTCTCCACAACCCAGGCAC 60.251 55.000 0.00 0.00 0.00 5.01
938 4196 0.251209 TCCTCACCTACGCACAGTCT 60.251 55.000 0.00 0.00 0.00 3.24
1004 4269 0.681175 GCCCAAGAAGCAACAATGGT 59.319 50.000 0.00 0.00 39.43 3.55
1042 4307 0.388520 CGTCTGCTTCATGGTCGTGA 60.389 55.000 0.00 0.00 0.00 4.35
1269 4534 1.667830 CAAGAAGGTCTTCGCCGCA 60.668 57.895 5.22 0.00 43.97 5.69
1276 4541 3.126879 TCTTCGCCGCATGCAAGG 61.127 61.111 19.57 12.97 41.33 3.61
1278 4543 3.386867 CTTCGCCGCATGCAAGGTC 62.387 63.158 19.57 7.16 41.33 3.85
1320 5124 1.432270 GCTATTGGTGCCACGAGCTC 61.432 60.000 2.73 2.73 44.23 4.09
1337 5141 1.344114 GCTCCATCCATCTCTGTCTCC 59.656 57.143 0.00 0.00 0.00 3.71
1341 5145 0.397675 ATCCATCTCTGTCTCCCGCA 60.398 55.000 0.00 0.00 0.00 5.69
1369 5173 2.406616 GGCATGGCCGTTGGTGTAG 61.407 63.158 8.35 0.00 39.62 2.74
1372 5176 0.608035 CATGGCCGTTGGTGTAGGTT 60.608 55.000 0.00 0.00 0.00 3.50
1377 5181 1.067915 GCCGTTGGTGTAGGTTACGTA 60.068 52.381 0.00 0.00 0.00 3.57
1404 5558 3.583966 TGAGGTAATAAAACGAGGGGTGT 59.416 43.478 0.00 0.00 0.00 4.16
1455 5649 8.732746 AAAGTAATAAATGCGGACTTATGTCT 57.267 30.769 8.51 0.00 42.54 3.41
1459 5653 9.204570 GTAATAAATGCGGACTTATGTCTATGT 57.795 33.333 8.51 0.74 42.54 2.29
1460 5654 5.991328 AAATGCGGACTTATGTCTATGTG 57.009 39.130 8.51 0.00 42.54 3.21
1461 5655 4.672587 ATGCGGACTTATGTCTATGTGT 57.327 40.909 8.51 0.00 42.54 3.72
1462 5656 4.041740 TGCGGACTTATGTCTATGTGTC 57.958 45.455 8.51 0.00 42.54 3.67
1463 5657 3.445805 TGCGGACTTATGTCTATGTGTCA 59.554 43.478 8.51 0.00 42.54 3.58
1464 5658 4.099419 TGCGGACTTATGTCTATGTGTCAT 59.901 41.667 8.51 0.00 42.54 3.06
1467 5830 6.734871 GCGGACTTATGTCTATGTGTCATGTA 60.735 42.308 8.51 0.00 42.54 2.29
1488 5851 6.946340 TGTACTCATGTCCTGTGTATTGAAT 58.054 36.000 0.00 0.00 36.51 2.57
1544 5947 4.638304 TGTTCTACTCCCGAAAAGAAAGG 58.362 43.478 0.00 0.00 30.24 3.11
1546 5949 5.012768 TGTTCTACTCCCGAAAAGAAAGGAT 59.987 40.000 0.00 0.00 30.24 3.24
1581 5985 5.446260 ACGGGGAAGAAAATACCAGTAAT 57.554 39.130 0.00 0.00 29.63 1.89
1582 5986 6.564557 ACGGGGAAGAAAATACCAGTAATA 57.435 37.500 0.00 0.00 29.63 0.98
1584 5988 7.404481 ACGGGGAAGAAAATACCAGTAATAAA 58.596 34.615 0.00 0.00 29.63 1.40
1585 5989 7.337689 ACGGGGAAGAAAATACCAGTAATAAAC 59.662 37.037 0.00 0.00 29.63 2.01
1586 5990 7.555195 CGGGGAAGAAAATACCAGTAATAAACT 59.445 37.037 0.00 0.00 39.81 2.66
1587 5991 9.910267 GGGGAAGAAAATACCAGTAATAAACTA 57.090 33.333 0.00 0.00 35.76 2.24
1599 6003 9.392259 ACCAGTAATAAACTAGATAAAACAGCC 57.608 33.333 0.00 0.00 35.76 4.85
1605 6009 3.858247 ACTAGATAAAACAGCCCGTGTC 58.142 45.455 0.00 0.00 39.03 3.67
1606 6010 2.851263 AGATAAAACAGCCCGTGTCA 57.149 45.000 0.00 0.00 39.03 3.58
1610 6014 0.031994 AAAACAGCCCGTGTCATTGC 59.968 50.000 0.00 0.00 39.03 3.56
1611 6015 2.128853 AAACAGCCCGTGTCATTGCG 62.129 55.000 0.00 0.00 39.03 4.85
1633 6037 8.715191 TGCGGAAATTCATAGCAATAAATTTT 57.285 26.923 0.00 0.00 32.90 1.82
1686 6106 4.696479 ACCTCATATCAAAGGTAGCAGG 57.304 45.455 0.00 0.00 44.12 4.85
1724 6144 2.000447 CTAGCCTTCTTGGTGCGTTAC 59.000 52.381 0.00 0.00 38.35 2.50
1734 6154 1.876799 TGGTGCGTTACAATGACTTGG 59.123 47.619 0.00 0.00 36.64 3.61
1736 6156 0.878416 TGCGTTACAATGACTTGGGC 59.122 50.000 0.00 0.00 36.64 5.36
1738 6158 1.529226 CGTTACAATGACTTGGGCCA 58.471 50.000 0.00 0.00 36.64 5.36
1784 6204 1.338973 AGAGGTTGCATGTGCTTGTTG 59.661 47.619 6.55 0.00 42.66 3.33
1785 6205 1.337703 GAGGTTGCATGTGCTTGTTGA 59.662 47.619 6.55 0.00 42.66 3.18
1789 6209 0.674534 TGCATGTGCTTGTTGATGCA 59.325 45.000 6.55 0.00 46.80 3.96
1832 6253 8.389603 TGAAAAATGAAAATGAAAGTGAAGTGC 58.610 29.630 0.00 0.00 0.00 4.40
1855 6276 5.431420 TTGTATGTGCTTAATAATGCGGG 57.569 39.130 0.00 0.00 0.00 6.13
1862 6283 3.625764 TGCTTAATAATGCGGGTGACTTC 59.374 43.478 0.00 0.00 0.00 3.01
1887 6308 6.018669 CACAAATCCTTAAGAATAGAGGACGC 60.019 42.308 3.36 0.00 42.04 5.19
1903 6324 1.246056 ACGCCATGCTTGCTTCATGT 61.246 50.000 10.76 0.00 39.60 3.21
1921 6343 3.678056 TGTCTGTACTTAGCACAAGGG 57.322 47.619 0.00 0.00 0.00 3.95
1969 6391 8.750515 AAATTGTTTGGAAGAAATGTTGGATT 57.249 26.923 0.00 0.00 0.00 3.01
1974 6396 7.279758 TGTTTGGAAGAAATGTTGGATTGAAAC 59.720 33.333 0.00 0.00 0.00 2.78
1976 6398 6.882656 TGGAAGAAATGTTGGATTGAAACAA 58.117 32.000 0.00 0.00 40.69 2.83
2003 6425 3.491104 CGATACCAAGTGCTAGGAACCTC 60.491 52.174 0.00 0.00 0.00 3.85
2018 6440 3.181448 GGAACCTCCTCTAGTCTCTCGAT 60.181 52.174 0.00 0.00 32.53 3.59
2055 6477 5.700373 ACAAATTACATGGGAAATGTGCAAC 59.300 36.000 0.00 0.00 33.76 4.17
2056 6478 3.567576 TTACATGGGAAATGTGCAACG 57.432 42.857 0.00 0.00 42.39 4.10
2084 6528 1.934220 TAGACTCGTGCGGCTTCCTG 61.934 60.000 0.00 0.00 0.00 3.86
2085 6529 3.282745 GACTCGTGCGGCTTCCTGA 62.283 63.158 0.00 0.00 0.00 3.86
2126 6570 8.561212 GCCCAAATTGAACATATTACACGTATA 58.439 33.333 0.00 0.00 0.00 1.47
2171 6618 8.204836 AGTGTTGTGTTTTACTAGACTCAATCT 58.795 33.333 0.00 0.00 34.48 2.40
2176 6623 9.871238 TGTGTTTTACTAGACTCAATCTTATCC 57.129 33.333 0.00 0.00 39.04 2.59
2195 6642 1.626388 GACGAAGCGCTTGTCGATC 59.374 57.895 31.78 21.89 39.64 3.69
2263 6710 2.193536 GGTGTGGCAAAGGCGAGTT 61.194 57.895 0.00 0.00 42.47 3.01
2276 6723 1.657751 GCGAGTTGGGCCAGGATTTC 61.658 60.000 6.23 0.62 0.00 2.17
2278 6725 1.756430 GAGTTGGGCCAGGATTTCTC 58.244 55.000 6.23 5.84 0.00 2.87
2281 6728 2.919602 AGTTGGGCCAGGATTTCTCTAA 59.080 45.455 6.23 0.00 0.00 2.10
2283 6730 4.017130 AGTTGGGCCAGGATTTCTCTAATT 60.017 41.667 6.23 0.00 0.00 1.40
2284 6731 5.193728 AGTTGGGCCAGGATTTCTCTAATTA 59.806 40.000 6.23 0.00 0.00 1.40
2287 6734 6.682537 TGGGCCAGGATTTCTCTAATTATTT 58.317 36.000 0.00 0.00 0.00 1.40
2289 6736 6.209589 GGGCCAGGATTTCTCTAATTATTTCC 59.790 42.308 4.39 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.715190 AGTAACCAAATAACCAATTACCAACT 57.285 30.769 0.00 0.00 0.00 3.16
15 16 9.723601 ACGAAATACTAGTAACCAAATAACCAA 57.276 29.630 6.70 0.00 0.00 3.67
16 17 9.153721 CACGAAATACTAGTAACCAAATAACCA 57.846 33.333 6.70 0.00 0.00 3.67
17 18 8.118607 GCACGAAATACTAGTAACCAAATAACC 58.881 37.037 6.70 0.00 0.00 2.85
19 20 8.875803 CAGCACGAAATACTAGTAACCAAATAA 58.124 33.333 6.70 0.00 0.00 1.40
20 21 8.252417 TCAGCACGAAATACTAGTAACCAAATA 58.748 33.333 6.70 0.00 0.00 1.40
21 22 7.101054 TCAGCACGAAATACTAGTAACCAAAT 58.899 34.615 6.70 0.00 0.00 2.32
22 23 6.457355 TCAGCACGAAATACTAGTAACCAAA 58.543 36.000 6.70 0.00 0.00 3.28
23 24 6.028146 TCAGCACGAAATACTAGTAACCAA 57.972 37.500 6.70 0.00 0.00 3.67
24 25 5.648178 TCAGCACGAAATACTAGTAACCA 57.352 39.130 6.70 0.00 0.00 3.67
26 27 7.063074 ACACATTCAGCACGAAATACTAGTAAC 59.937 37.037 6.70 1.30 37.12 2.50
27 28 7.094631 ACACATTCAGCACGAAATACTAGTAA 58.905 34.615 6.70 0.00 37.12 2.24
28 29 6.627243 ACACATTCAGCACGAAATACTAGTA 58.373 36.000 4.77 4.77 37.12 1.82
31 32 5.929415 TCAACACATTCAGCACGAAATACTA 59.071 36.000 0.00 0.00 37.12 1.82
32 33 4.754618 TCAACACATTCAGCACGAAATACT 59.245 37.500 0.00 0.00 37.12 2.12
34 35 4.754618 ACTCAACACATTCAGCACGAAATA 59.245 37.500 0.00 0.00 37.12 1.40
35 36 3.565482 ACTCAACACATTCAGCACGAAAT 59.435 39.130 0.00 0.00 37.12 2.17
36 37 2.942376 ACTCAACACATTCAGCACGAAA 59.058 40.909 0.00 0.00 37.12 3.46
37 38 2.560504 ACTCAACACATTCAGCACGAA 58.439 42.857 0.00 0.00 38.22 3.85
38 39 2.238942 ACTCAACACATTCAGCACGA 57.761 45.000 0.00 0.00 0.00 4.35
39 40 3.338818 AAACTCAACACATTCAGCACG 57.661 42.857 0.00 0.00 0.00 5.34
40 41 7.434897 TCAAATAAAACTCAACACATTCAGCAC 59.565 33.333 0.00 0.00 0.00 4.40
41 42 7.487484 TCAAATAAAACTCAACACATTCAGCA 58.513 30.769 0.00 0.00 0.00 4.41
42 43 7.928908 TCAAATAAAACTCAACACATTCAGC 57.071 32.000 0.00 0.00 0.00 4.26
43 44 8.430063 GCATCAAATAAAACTCAACACATTCAG 58.570 33.333 0.00 0.00 0.00 3.02
44 45 8.143193 AGCATCAAATAAAACTCAACACATTCA 58.857 29.630 0.00 0.00 0.00 2.57
45 46 8.524870 AGCATCAAATAAAACTCAACACATTC 57.475 30.769 0.00 0.00 0.00 2.67
46 47 8.362639 AGAGCATCAAATAAAACTCAACACATT 58.637 29.630 0.00 0.00 37.82 2.71
47 48 7.889469 AGAGCATCAAATAAAACTCAACACAT 58.111 30.769 0.00 0.00 37.82 3.21
48 49 7.275888 AGAGCATCAAATAAAACTCAACACA 57.724 32.000 0.00 0.00 37.82 3.72
49 50 9.334693 CTAAGAGCATCAAATAAAACTCAACAC 57.665 33.333 0.00 0.00 37.82 3.32
53 54 9.944376 AGTACTAAGAGCATCAAATAAAACTCA 57.056 29.630 0.00 0.00 37.82 3.41
55 56 9.384764 GGAGTACTAAGAGCATCAAATAAAACT 57.615 33.333 0.00 0.00 37.82 2.66
56 57 8.328864 CGGAGTACTAAGAGCATCAAATAAAAC 58.671 37.037 0.00 0.00 37.82 2.43
57 58 8.038944 ACGGAGTACTAAGAGCATCAAATAAAA 58.961 33.333 0.00 0.00 41.94 1.52
58 59 7.553334 ACGGAGTACTAAGAGCATCAAATAAA 58.447 34.615 0.00 0.00 41.94 1.40
59 60 7.108841 ACGGAGTACTAAGAGCATCAAATAA 57.891 36.000 0.00 0.00 41.94 1.40
60 61 6.710597 ACGGAGTACTAAGAGCATCAAATA 57.289 37.500 0.00 0.00 41.94 1.40
61 62 5.599999 ACGGAGTACTAAGAGCATCAAAT 57.400 39.130 0.00 0.00 41.94 2.32
76 77 4.012374 CCAACAGAACCTAGTACGGAGTA 58.988 47.826 0.00 0.00 45.11 2.59
79 80 2.880443 ACCAACAGAACCTAGTACGGA 58.120 47.619 0.00 0.00 0.00 4.69
80 81 4.996788 ATACCAACAGAACCTAGTACGG 57.003 45.455 0.00 0.00 0.00 4.02
83 84 8.192743 TGTGTAAATACCAACAGAACCTAGTA 57.807 34.615 0.00 0.00 0.00 1.82
84 85 7.069877 TGTGTAAATACCAACAGAACCTAGT 57.930 36.000 0.00 0.00 0.00 2.57
85 86 9.095065 GTATGTGTAAATACCAACAGAACCTAG 57.905 37.037 0.00 0.00 0.00 3.02
86 87 8.595421 TGTATGTGTAAATACCAACAGAACCTA 58.405 33.333 0.00 0.00 32.93 3.08
87 88 7.455058 TGTATGTGTAAATACCAACAGAACCT 58.545 34.615 0.00 0.00 32.93 3.50
220 3359 3.260380 ACAATGAGAGAGAAGTGTCCTGG 59.740 47.826 0.00 0.00 0.00 4.45
221 3360 4.021632 TGACAATGAGAGAGAAGTGTCCTG 60.022 45.833 1.40 0.00 35.59 3.86
222 3361 4.155709 TGACAATGAGAGAGAAGTGTCCT 58.844 43.478 1.40 0.00 35.59 3.85
223 3362 4.527509 TGACAATGAGAGAGAAGTGTCC 57.472 45.455 1.40 0.00 35.59 4.02
336 3499 3.390639 AGCATGGGATCCAAAACAAACAA 59.609 39.130 15.23 0.00 36.95 2.83
338 3501 3.683365 AGCATGGGATCCAAAACAAAC 57.317 42.857 15.23 0.00 36.95 2.93
339 3502 4.155709 TGTAGCATGGGATCCAAAACAAA 58.844 39.130 15.23 0.00 36.95 2.83
340 3503 3.772387 TGTAGCATGGGATCCAAAACAA 58.228 40.909 15.23 0.00 36.95 2.83
341 3504 3.448093 TGTAGCATGGGATCCAAAACA 57.552 42.857 15.23 2.02 36.95 2.83
342 3505 4.381932 CCTTTGTAGCATGGGATCCAAAAC 60.382 45.833 15.23 0.00 36.95 2.43
480 3645 1.152881 GGGCTTGAGGCAGTATGGG 60.153 63.158 6.90 0.00 44.01 4.00
500 3666 0.984230 TCCTGGTTCATGGAGTGTCC 59.016 55.000 0.00 0.00 36.96 4.02
548 3714 5.833131 ACTGGTCATATTGTTTTTGGACTGT 59.167 36.000 0.00 0.00 0.00 3.55
550 3716 5.278957 GCACTGGTCATATTGTTTTTGGACT 60.279 40.000 0.00 0.00 0.00 3.85
555 3721 4.558496 CGGTGCACTGGTCATATTGTTTTT 60.558 41.667 18.43 0.00 0.00 1.94
560 3726 1.665679 GTCGGTGCACTGGTCATATTG 59.334 52.381 25.15 0.00 0.00 1.90
561 3727 1.739035 CGTCGGTGCACTGGTCATATT 60.739 52.381 25.15 0.00 0.00 1.28
565 3735 4.961511 GCGTCGGTGCACTGGTCA 62.962 66.667 25.15 3.42 34.15 4.02
652 3852 2.092212 GGTCAGTGGAACCCATCATGAT 60.092 50.000 1.18 1.18 37.80 2.45
653 3853 1.281867 GGTCAGTGGAACCCATCATGA 59.718 52.381 0.00 0.00 37.80 3.07
654 3854 1.683011 GGGTCAGTGGAACCCATCATG 60.683 57.143 13.93 0.00 45.83 3.07
655 3855 0.625849 GGGTCAGTGGAACCCATCAT 59.374 55.000 13.93 0.00 45.83 2.45
656 3856 2.074967 GGGTCAGTGGAACCCATCA 58.925 57.895 13.93 0.00 45.83 3.07
688 3897 4.835284 TTACTATGTGAACATGGCCAGA 57.165 40.909 13.05 0.00 38.24 3.86
727 3939 1.267574 ACGGACATGGCCAGACTGAT 61.268 55.000 20.22 0.00 0.00 2.90
728 3940 0.613572 TACGGACATGGCCAGACTGA 60.614 55.000 20.22 0.00 0.00 3.41
730 3942 1.614241 GGTACGGACATGGCCAGACT 61.614 60.000 20.22 0.00 0.00 3.24
731 3943 1.153429 GGTACGGACATGGCCAGAC 60.153 63.158 20.22 14.46 0.00 3.51
732 3944 3.305314 GGTACGGACATGGCCAGA 58.695 61.111 20.22 0.16 0.00 3.86
855 4102 0.660595 CGTCTTATAGGCCGTCTGCG 60.661 60.000 0.00 0.00 42.61 5.18
859 4106 0.596859 GGTGCGTCTTATAGGCCGTC 60.597 60.000 0.00 0.00 38.23 4.79
860 4107 1.440476 GGTGCGTCTTATAGGCCGT 59.560 57.895 0.00 0.00 38.23 5.68
886 4133 1.384191 GGGTTGTGGAGAATGGGCT 59.616 57.895 0.00 0.00 0.00 5.19
910 4166 1.687146 TAGGTGAGGAGCTGGCTGG 60.687 63.158 0.00 0.00 0.00 4.85
938 4196 2.050077 CTCGCGCAGTGTCTGTGA 60.050 61.111 8.75 0.00 43.78 3.58
948 4206 4.362476 TGAAGCTGCTCTCGCGCA 62.362 61.111 8.75 0.00 39.65 6.09
967 4225 0.759436 GCTCGGATGGGAGGGAAGTA 60.759 60.000 0.00 0.00 34.56 2.24
1021 4286 0.532573 ACGACCATGAAGCAGACGAT 59.467 50.000 0.00 0.00 0.00 3.73
1320 5124 0.678395 CGGGAGACAGAGATGGATGG 59.322 60.000 0.00 0.00 0.00 3.51
1322 5126 0.397675 TGCGGGAGACAGAGATGGAT 60.398 55.000 0.00 0.00 0.00 3.41
1337 5141 0.526739 CATGCCACATTGTCATGCGG 60.527 55.000 5.77 0.00 35.88 5.69
1352 5156 2.406616 CCTACACCAACGGCCATGC 61.407 63.158 2.24 0.00 0.00 4.06
1377 5181 5.452356 CCCCTCGTTTTATTACCTCACGTAT 60.452 44.000 0.00 0.00 32.65 3.06
1431 5588 9.998106 ATAGACATAAGTCCGCATTTATTACTT 57.002 29.630 0.00 0.00 46.15 2.24
1434 5591 9.203421 CACATAGACATAAGTCCGCATTTATTA 57.797 33.333 0.00 0.00 46.15 0.98
1445 5639 8.406297 TGAGTACATGACACATAGACATAAGTC 58.594 37.037 0.00 0.00 45.31 3.01
1463 5657 6.544928 TCAATACACAGGACATGAGTACAT 57.455 37.500 0.00 0.00 37.72 2.29
1464 5658 5.993748 TCAATACACAGGACATGAGTACA 57.006 39.130 0.00 0.00 37.72 2.90
1467 5830 6.053632 TGATTCAATACACAGGACATGAGT 57.946 37.500 0.00 0.00 36.60 3.41
1521 5924 5.061179 CCTTTCTTTTCGGGAGTAGAACAA 58.939 41.667 0.00 0.00 0.00 2.83
1523 5926 4.891260 TCCTTTCTTTTCGGGAGTAGAAC 58.109 43.478 0.00 0.00 0.00 3.01
1524 5927 5.757099 ATCCTTTCTTTTCGGGAGTAGAA 57.243 39.130 0.00 0.00 0.00 2.10
1529 5932 6.819397 AAAGTAATCCTTTCTTTTCGGGAG 57.181 37.500 0.00 0.00 39.17 4.30
1555 5959 4.076394 CTGGTATTTTCTTCCCCGTTTCA 58.924 43.478 0.00 0.00 0.00 2.69
1559 5963 4.914177 TTACTGGTATTTTCTTCCCCGT 57.086 40.909 0.00 0.00 0.00 5.28
1560 5964 7.555195 AGTTTATTACTGGTATTTTCTTCCCCG 59.445 37.037 0.00 0.00 35.19 5.73
1581 5985 5.797051 ACACGGGCTGTTTTATCTAGTTTA 58.203 37.500 0.00 0.00 0.00 2.01
1582 5986 4.648651 ACACGGGCTGTTTTATCTAGTTT 58.351 39.130 0.00 0.00 0.00 2.66
1584 5988 3.259876 TGACACGGGCTGTTTTATCTAGT 59.740 43.478 0.00 0.00 31.03 2.57
1585 5989 3.857052 TGACACGGGCTGTTTTATCTAG 58.143 45.455 0.00 0.00 31.03 2.43
1586 5990 3.965379 TGACACGGGCTGTTTTATCTA 57.035 42.857 0.00 0.00 31.03 1.98
1587 5991 2.851263 TGACACGGGCTGTTTTATCT 57.149 45.000 0.00 0.00 31.03 1.98
1588 5992 3.758300 CAATGACACGGGCTGTTTTATC 58.242 45.455 0.00 0.00 31.03 1.75
1605 6009 7.697352 TTTATTGCTATGAATTTCCGCAATG 57.303 32.000 25.04 4.04 46.91 2.82
1751 6171 3.896888 TGCAACCTCTCCACATCATTTTT 59.103 39.130 0.00 0.00 0.00 1.94
1752 6172 3.499338 TGCAACCTCTCCACATCATTTT 58.501 40.909 0.00 0.00 0.00 1.82
1753 6173 3.159213 TGCAACCTCTCCACATCATTT 57.841 42.857 0.00 0.00 0.00 2.32
1754 6174 2.885135 TGCAACCTCTCCACATCATT 57.115 45.000 0.00 0.00 0.00 2.57
1763 6183 1.242076 ACAAGCACATGCAACCTCTC 58.758 50.000 6.64 0.00 45.16 3.20
1789 6209 8.533657 TCATTTTTCAATACATGCAAATCCTCT 58.466 29.630 0.00 0.00 0.00 3.69
1824 6244 3.904136 AAGCACATACAAGCACTTCAC 57.096 42.857 0.00 0.00 0.00 3.18
1825 6245 7.680442 TTATTAAGCACATACAAGCACTTCA 57.320 32.000 0.00 0.00 0.00 3.02
1826 6246 7.166473 GCATTATTAAGCACATACAAGCACTTC 59.834 37.037 0.00 0.00 0.00 3.01
1827 6247 6.974622 GCATTATTAAGCACATACAAGCACTT 59.025 34.615 0.00 0.00 0.00 3.16
1832 6253 5.008613 ACCCGCATTATTAAGCACATACAAG 59.991 40.000 0.00 0.00 0.00 3.16
1855 6276 9.436957 TCTATTCTTAAGGATTTGTGAAGTCAC 57.563 33.333 0.40 4.43 46.59 3.67
1862 6283 6.018669 GCGTCCTCTATTCTTAAGGATTTGTG 60.019 42.308 0.40 0.00 41.11 3.33
1867 6288 4.223953 TGGCGTCCTCTATTCTTAAGGAT 58.776 43.478 0.92 0.92 41.11 3.24
1887 6308 1.816835 ACAGACATGAAGCAAGCATGG 59.183 47.619 15.00 3.70 45.62 3.66
1903 6324 3.236047 TCACCCTTGTGCTAAGTACAGA 58.764 45.455 0.00 0.00 42.46 3.41
1952 6374 6.477053 TGTTTCAATCCAACATTTCTTCCA 57.523 33.333 0.00 0.00 0.00 3.53
1954 6376 7.442062 ACCATTGTTTCAATCCAACATTTCTTC 59.558 33.333 0.00 0.00 34.13 2.87
1993 6415 6.681816 TCGAGAGACTAGAGGAGGTTCCTAG 61.682 52.000 0.00 0.00 41.01 3.02
2018 6440 8.187480 CCCATGTAATTTGTATCAACGATTCAA 58.813 33.333 0.00 0.00 29.87 2.69
2025 6447 9.086336 CACATTTCCCATGTAATTTGTATCAAC 57.914 33.333 0.00 0.00 0.00 3.18
2126 6570 6.454223 ACACTTATTCCATGGCCTACATAT 57.546 37.500 6.96 0.00 37.84 1.78
2127 6571 5.904984 ACACTTATTCCATGGCCTACATA 57.095 39.130 6.96 0.00 37.84 2.29
2138 6582 9.048446 GTCTAGTAAAACACAACACTTATTCCA 57.952 33.333 0.00 0.00 0.00 3.53
2171 6618 0.108992 ACAAGCGCTTCGTCGGATAA 60.109 50.000 22.21 0.00 0.00 1.75
2174 6621 2.430244 GACAAGCGCTTCGTCGGA 60.430 61.111 22.21 0.00 0.00 4.55
2195 6642 0.827368 GAAGAGGGTAGCCTGACCTG 59.173 60.000 20.52 0.00 39.66 4.00
2263 6710 5.930209 ATAATTAGAGAAATCCTGGCCCA 57.070 39.130 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.