Multiple sequence alignment - TraesCS1D01G146700

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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 TraesCS1D01G146700 chr1D 100.000 5334 0 0 1 5334 202949603 202944270 0.000000e+00 9851.0
1 TraesCS1D01G146700 chr1D 80.988 3298 530 65 1057 4315 202983116 202986355 0.000000e+00 2527.0
2 TraesCS1D01G146700 chr1D 100.000 29 0 0 3978 4006 30653333 30653361 3.000000e-03 54.7
3 TraesCS1D01G146700 chr1B 95.915 3966 151 4 537 4500 296658228 296654272 0.000000e+00 6416.0
4 TraesCS1D01G146700 chr1B 80.242 1655 273 34 2684 4315 296755572 296757195 0.000000e+00 1195.0
5 TraesCS1D01G146700 chr1B 78.794 962 193 8 1741 2692 296753697 296754657 2.100000e-178 636.0
6 TraesCS1D01G146700 chr1B 88.028 426 48 2 70 494 296673125 296672702 7.980000e-138 501.0
7 TraesCS1D01G146700 chr1B 91.250 80 5 1 4672 4751 296653712 296653635 2.030000e-19 108.0
8 TraesCS1D01G146700 chr1B 97.917 48 1 0 4744 4791 296652824 296652777 3.420000e-12 84.2
9 TraesCS1D01G146700 chr1B 86.792 53 6 1 1 53 296673162 296673111 2.070000e-04 58.4
10 TraesCS1D01G146700 chr1A 94.087 2469 130 5 1993 4447 256922549 256920083 0.000000e+00 3736.0
11 TraesCS1D01G146700 chr1A 81.116 3315 537 58 1057 4316 256964579 256967859 0.000000e+00 2571.0
12 TraesCS1D01G146700 chr1A 95.574 1220 46 2 778 1997 256929020 256927809 0.000000e+00 1947.0
13 TraesCS1D01G146700 chr1A 83.793 580 57 14 203 777 256929817 256929270 2.850000e-142 516.0
14 TraesCS1D01G146700 chr1A 88.770 187 16 3 4607 4792 256920004 256919822 1.930000e-54 224.0
15 TraesCS1D01G146700 chr1A 90.511 137 12 1 70 206 256931785 256931650 4.240000e-41 180.0
16 TraesCS1D01G146700 chr1A 89.209 139 15 0 4651 4789 590922486 590922624 1.970000e-39 174.0
17 TraesCS1D01G146700 chr1A 94.737 38 2 0 3978 4015 30335553 30335590 5.770000e-05 60.2
18 TraesCS1D01G146700 chr1A 100.000 29 0 0 3978 4006 30390252 30390280 3.000000e-03 54.7
19 TraesCS1D01G146700 chr7B 83.618 586 46 25 4791 5334 705330959 705331536 6.170000e-139 505.0
20 TraesCS1D01G146700 chr7B 83.509 570 44 14 4804 5334 707609439 707608881 2.230000e-133 486.0
21 TraesCS1D01G146700 chr7B 79.287 589 56 36 4798 5334 626039769 626039195 8.500000e-93 351.0
22 TraesCS1D01G146700 chr7B 86.441 59 8 0 3970 4028 711061465 711061407 1.240000e-06 65.8
23 TraesCS1D01G146700 chr2B 83.390 584 44 25 4797 5334 728927523 728928099 4.800000e-135 492.0
24 TraesCS1D01G146700 chr2B 87.943 141 17 0 4652 4792 74728725 74728865 3.300000e-37 167.0
25 TraesCS1D01G146700 chr2B 87.943 141 17 0 4652 4792 770754127 770754267 3.300000e-37 167.0
26 TraesCS1D01G146700 chr6D 83.595 573 43 25 4801 5334 409868777 409869337 1.730000e-134 490.0
27 TraesCS1D01G146700 chr6B 83.016 577 48 22 4801 5334 616327215 616327784 1.340000e-130 477.0
28 TraesCS1D01G146700 chr6B 79.212 457 43 28 4906 5334 719332822 719333254 2.450000e-68 270.0
29 TraesCS1D01G146700 chr4A 82.404 574 44 28 4797 5334 492385425 492384873 1.050000e-121 448.0
30 TraesCS1D01G146700 chr4A 76.190 189 34 8 3691 3869 54107605 54107418 7.360000e-14 89.8
31 TraesCS1D01G146700 chr7D 81.879 596 45 20 4797 5334 33422258 33422848 1.360000e-120 444.0
32 TraesCS1D01G146700 chr7D 88.028 142 15 2 4651 4792 561554756 561554617 3.300000e-37 167.0
33 TraesCS1D01G146700 chr4B 81.911 586 47 23 4801 5334 671651742 671651164 1.760000e-119 440.0
34 TraesCS1D01G146700 chr4B 75.648 193 36 8 3691 3873 489088556 489088365 9.520000e-13 86.1
35 TraesCS1D01G146700 chr6A 81.882 574 55 24 4801 5334 555319636 555320200 6.340000e-119 438.0
36 TraesCS1D01G146700 chr2D 81.533 574 57 21 4802 5334 642368182 642368747 1.370000e-115 427.0
37 TraesCS1D01G146700 chr5D 81.043 575 64 31 4791 5334 390548432 390547872 2.970000e-112 416.0
38 TraesCS1D01G146700 chr5D 93.333 45 3 0 3972 4016 10776063 10776107 3.450000e-07 67.6
39 TraesCS1D01G146700 chr2A 79.110 584 61 29 4800 5334 767022135 767021564 3.950000e-91 346.0
40 TraesCS1D01G146700 chr7A 84.585 253 19 7 5101 5334 670905569 670905820 3.210000e-57 233.0
41 TraesCS1D01G146700 chr3A 82.427 239 18 7 5098 5334 39730391 39730607 2.540000e-43 187.0
42 TraesCS1D01G146700 chr3A 89.437 142 14 1 4651 4792 721446550 721446410 1.530000e-40 178.0
43 TraesCS1D01G146700 chr3D 89.362 141 15 0 4652 4792 475296919 475296779 1.530000e-40 178.0
44 TraesCS1D01G146700 chr4D 76.166 193 35 8 3691 3873 397094731 397094540 2.050000e-14 91.6
45 TraesCS1D01G146700 chr5A 93.478 46 3 0 3971 4016 8904500 8904455 9.590000e-08 69.4
46 TraesCS1D01G146700 chr5B 93.333 45 3 0 3972 4016 11306261 11306217 3.450000e-07 67.6


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 TraesCS1D01G146700 chr1D 202944270 202949603 5333 True 9851.000000 9851 100.000000 1 5334 1 chr1D.!!$R1 5333
1 TraesCS1D01G146700 chr1D 202983116 202986355 3239 False 2527.000000 2527 80.988000 1057 4315 1 chr1D.!!$F2 3258
2 TraesCS1D01G146700 chr1B 296652777 296658228 5451 True 2202.733333 6416 95.027333 537 4791 3 chr1B.!!$R1 4254
3 TraesCS1D01G146700 chr1B 296753697 296757195 3498 False 915.500000 1195 79.518000 1741 4315 2 chr1B.!!$F1 2574
4 TraesCS1D01G146700 chr1A 256964579 256967859 3280 False 2571.000000 2571 81.116000 1057 4316 1 chr1A.!!$F3 3259
5 TraesCS1D01G146700 chr1A 256919822 256922549 2727 True 1980.000000 3736 91.428500 1993 4792 2 chr1A.!!$R1 2799
6 TraesCS1D01G146700 chr1A 256927809 256931785 3976 True 881.000000 1947 89.959333 70 1997 3 chr1A.!!$R2 1927
7 TraesCS1D01G146700 chr7B 705330959 705331536 577 False 505.000000 505 83.618000 4791 5334 1 chr7B.!!$F1 543
8 TraesCS1D01G146700 chr7B 707608881 707609439 558 True 486.000000 486 83.509000 4804 5334 1 chr7B.!!$R2 530
9 TraesCS1D01G146700 chr7B 626039195 626039769 574 True 351.000000 351 79.287000 4798 5334 1 chr7B.!!$R1 536
10 TraesCS1D01G146700 chr2B 728927523 728928099 576 False 492.000000 492 83.390000 4797 5334 1 chr2B.!!$F2 537
11 TraesCS1D01G146700 chr6D 409868777 409869337 560 False 490.000000 490 83.595000 4801 5334 1 chr6D.!!$F1 533
12 TraesCS1D01G146700 chr6B 616327215 616327784 569 False 477.000000 477 83.016000 4801 5334 1 chr6B.!!$F1 533
13 TraesCS1D01G146700 chr4A 492384873 492385425 552 True 448.000000 448 82.404000 4797 5334 1 chr4A.!!$R2 537
14 TraesCS1D01G146700 chr7D 33422258 33422848 590 False 444.000000 444 81.879000 4797 5334 1 chr7D.!!$F1 537
15 TraesCS1D01G146700 chr4B 671651164 671651742 578 True 440.000000 440 81.911000 4801 5334 1 chr4B.!!$R2 533
16 TraesCS1D01G146700 chr6A 555319636 555320200 564 False 438.000000 438 81.882000 4801 5334 1 chr6A.!!$F1 533
17 TraesCS1D01G146700 chr2D 642368182 642368747 565 False 427.000000 427 81.533000 4802 5334 1 chr2D.!!$F1 532
18 TraesCS1D01G146700 chr5D 390547872 390548432 560 True 416.000000 416 81.043000 4791 5334 1 chr5D.!!$R1 543
19 TraesCS1D01G146700 chr2A 767021564 767022135 571 True 346.000000 346 79.110000 4800 5334 1 chr2A.!!$R1 534

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
465 2302 0.036010 CGTGTGCATCTTTCCCCTCT 60.036 55.0 0.00 0.0 0.00 3.69 F
1149 3238 0.471617 CGCTCCTGGAATGGAAGGAT 59.528 55.0 0.00 0.0 41.74 3.24 F
1737 3826 0.317603 GCATCAATGTCAGCATCGCC 60.318 55.0 0.00 0.0 33.50 5.54 F
2679 4777 0.110486 ACCTGGACCGCAACAAGATT 59.890 50.0 0.00 0.0 0.00 2.40 F
3076 6106 0.815734 CCTGAAATCCTGCAGCTTGG 59.184 55.0 8.66 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 3580 0.670854 GGTTGAGGTGCTCGAGGTTC 60.671 60.000 15.58 0.00 32.35 3.62 R
2069 4158 1.339438 GGTCCAGCAGCTTCAGATTCA 60.339 52.381 0.00 0.00 0.00 2.57 R
3160 6190 0.319900 ACTGCAGCGACGAAGAACAT 60.320 50.000 15.27 0.00 0.00 2.71 R
4296 7370 0.389166 GAGGTCGCCGATCATGATCC 60.389 60.000 26.30 14.17 34.40 3.36 R
4490 7564 0.895530 ATCACCACCTACCAGACACG 59.104 55.000 0.00 0.00 0.00 4.49 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
43 44 6.976934 ACCAAAAGTTTCATTGTCATACCT 57.023 33.333 0.00 0.00 0.00 3.08
44 45 6.981722 ACCAAAAGTTTCATTGTCATACCTC 58.018 36.000 0.00 0.00 0.00 3.85
45 46 6.086222 CCAAAAGTTTCATTGTCATACCTCG 58.914 40.000 0.00 0.00 0.00 4.63
46 47 6.072728 CCAAAAGTTTCATTGTCATACCTCGA 60.073 38.462 0.00 0.00 0.00 4.04
47 48 7.359595 CAAAAGTTTCATTGTCATACCTCGAA 58.640 34.615 0.00 0.00 0.00 3.71
48 49 7.687941 AAAGTTTCATTGTCATACCTCGAAT 57.312 32.000 0.00 0.00 0.00 3.34
49 50 7.687941 AAGTTTCATTGTCATACCTCGAATT 57.312 32.000 0.00 0.00 0.00 2.17
50 51 7.076842 AGTTTCATTGTCATACCTCGAATTG 57.923 36.000 0.00 0.00 0.00 2.32
51 52 6.878923 AGTTTCATTGTCATACCTCGAATTGA 59.121 34.615 0.00 0.00 0.00 2.57
52 53 6.662414 TTCATTGTCATACCTCGAATTGAC 57.338 37.500 8.81 8.81 39.11 3.18
53 54 5.116180 TCATTGTCATACCTCGAATTGACC 58.884 41.667 11.74 0.06 38.12 4.02
54 55 3.536956 TGTCATACCTCGAATTGACCC 57.463 47.619 11.74 0.00 38.12 4.46
55 56 2.169769 TGTCATACCTCGAATTGACCCC 59.830 50.000 11.74 0.00 38.12 4.95
56 57 2.434702 GTCATACCTCGAATTGACCCCT 59.565 50.000 5.75 0.00 33.91 4.79
57 58 3.112263 TCATACCTCGAATTGACCCCTT 58.888 45.455 0.00 0.00 0.00 3.95
58 59 3.521937 TCATACCTCGAATTGACCCCTTT 59.478 43.478 0.00 0.00 0.00 3.11
59 60 4.717778 TCATACCTCGAATTGACCCCTTTA 59.282 41.667 0.00 0.00 0.00 1.85
60 61 5.368523 TCATACCTCGAATTGACCCCTTTAT 59.631 40.000 0.00 0.00 0.00 1.40
61 62 4.152284 ACCTCGAATTGACCCCTTTATC 57.848 45.455 0.00 0.00 0.00 1.75
62 63 3.131396 CCTCGAATTGACCCCTTTATCG 58.869 50.000 0.00 0.00 0.00 2.92
63 64 3.131396 CTCGAATTGACCCCTTTATCGG 58.869 50.000 0.00 0.00 0.00 4.18
64 65 2.767394 TCGAATTGACCCCTTTATCGGA 59.233 45.455 0.00 0.00 0.00 4.55
65 66 3.198200 TCGAATTGACCCCTTTATCGGAA 59.802 43.478 0.00 0.00 0.00 4.30
66 67 3.942748 CGAATTGACCCCTTTATCGGAAA 59.057 43.478 0.00 0.00 0.00 3.13
67 68 4.396790 CGAATTGACCCCTTTATCGGAAAA 59.603 41.667 0.00 0.00 0.00 2.29
68 69 5.106078 CGAATTGACCCCTTTATCGGAAAAA 60.106 40.000 0.00 0.00 0.00 1.94
93 94 8.889849 AATACCTCGAATTGACAAAAATTACG 57.110 30.769 0.00 0.00 29.89 3.18
126 127 9.125026 AGCATCTATCAAATTAACCCTAACAAG 57.875 33.333 0.00 0.00 0.00 3.16
150 151 7.168219 AGTATGTTTGTCTTTCTTATGGCTGA 58.832 34.615 0.00 0.00 0.00 4.26
151 152 5.947228 TGTTTGTCTTTCTTATGGCTGAG 57.053 39.130 0.00 0.00 0.00 3.35
154 155 6.321181 TGTTTGTCTTTCTTATGGCTGAGTTT 59.679 34.615 0.00 0.00 0.00 2.66
155 156 7.500892 TGTTTGTCTTTCTTATGGCTGAGTTTA 59.499 33.333 0.00 0.00 0.00 2.01
156 157 7.435068 TTGTCTTTCTTATGGCTGAGTTTAC 57.565 36.000 0.00 0.00 0.00 2.01
157 158 6.530120 TGTCTTTCTTATGGCTGAGTTTACA 58.470 36.000 0.00 0.00 0.00 2.41
159 160 8.318412 TGTCTTTCTTATGGCTGAGTTTACATA 58.682 33.333 0.00 0.00 0.00 2.29
201 202 6.223138 TCGTTTGATAGTTTGCTACAACTG 57.777 37.500 6.74 0.00 0.00 3.16
272 2109 1.128200 AGCTGTAAGTGTGTGACCCA 58.872 50.000 0.00 0.00 35.30 4.51
279 2116 1.172180 AGTGTGTGACCCATTTGCGG 61.172 55.000 0.00 0.00 0.00 5.69
282 2119 1.303236 TGTGACCCATTTGCGGAGG 60.303 57.895 0.00 0.00 0.00 4.30
291 2128 0.962356 ATTTGCGGAGGGCTGTTGAG 60.962 55.000 0.00 0.00 44.05 3.02
310 2147 1.739466 AGCTCAACCGCAATGTATGTG 59.261 47.619 0.00 0.00 39.33 3.21
325 2162 5.731957 TGTATGTGTGGTGTGTGTATAGT 57.268 39.130 0.00 0.00 0.00 2.12
331 2168 4.684703 GTGTGGTGTGTGTATAGTCTTGTC 59.315 45.833 0.00 0.00 0.00 3.18
339 2176 6.700081 TGTGTGTATAGTCTTGTCTGTTTGAC 59.300 38.462 0.00 0.00 45.54 3.18
348 2185 0.575390 GTCTGTTTGACGTGTCGGTG 59.425 55.000 0.00 0.00 35.81 4.94
354 2191 3.054878 GTTTGACGTGTCGGTGTTCTAT 58.945 45.455 0.00 0.00 0.00 1.98
358 2195 5.816449 TGACGTGTCGGTGTTCTATATTA 57.184 39.130 0.00 0.00 0.00 0.98
369 2206 7.338703 TCGGTGTTCTATATTATGGGCTACTAG 59.661 40.741 0.00 0.00 0.00 2.57
370 2207 7.416438 CGGTGTTCTATATTATGGGCTACTAGG 60.416 44.444 0.00 0.00 0.00 3.02
395 2232 6.509677 GCGTAGTCAATTGCCTCTGTAATTAC 60.510 42.308 8.75 8.75 34.99 1.89
396 2233 6.291637 CGTAGTCAATTGCCTCTGTAATTACG 60.292 42.308 10.92 6.19 34.99 3.18
398 2235 6.636705 AGTCAATTGCCTCTGTAATTACGTA 58.363 36.000 10.92 0.00 34.99 3.57
399 2236 7.101054 AGTCAATTGCCTCTGTAATTACGTAA 58.899 34.615 11.02 11.02 34.99 3.18
400 2237 7.604927 AGTCAATTGCCTCTGTAATTACGTAAA 59.395 33.333 12.81 0.00 34.99 2.01
401 2238 8.231837 GTCAATTGCCTCTGTAATTACGTAAAA 58.768 33.333 12.81 0.62 34.99 1.52
402 2239 8.231837 TCAATTGCCTCTGTAATTACGTAAAAC 58.768 33.333 12.81 13.64 34.99 2.43
403 2240 7.916914 ATTGCCTCTGTAATTACGTAAAACT 57.083 32.000 12.81 2.80 0.00 2.66
405 2242 6.225318 TGCCTCTGTAATTACGTAAAACTGT 58.775 36.000 12.81 0.00 0.00 3.55
406 2243 6.366877 TGCCTCTGTAATTACGTAAAACTGTC 59.633 38.462 12.81 10.86 0.00 3.51
409 2246 9.630098 CCTCTGTAATTACGTAAAACTGTCTAA 57.370 33.333 12.81 2.22 0.00 2.10
429 2266 6.150809 GTCTAAGTAGGTGTAGCACTACTGTT 59.849 42.308 9.12 0.00 37.00 3.16
440 2277 3.003689 AGCACTACTGTTCATGTTTGTGC 59.996 43.478 0.00 0.00 41.82 4.57
442 2279 2.032030 ACTACTGTTCATGTTTGTGCGC 60.032 45.455 0.00 0.00 0.00 6.09
443 2280 1.024271 ACTGTTCATGTTTGTGCGCT 58.976 45.000 9.73 0.00 0.00 5.92
446 2283 1.082169 TTCATGTTTGTGCGCTCGC 60.082 52.632 9.73 7.38 42.35 5.03
465 2302 0.036010 CGTGTGCATCTTTCCCCTCT 60.036 55.000 0.00 0.00 0.00 3.69
481 2318 5.394738 TCCCCTCTCGTCTAAATCATGTAT 58.605 41.667 0.00 0.00 0.00 2.29
483 2320 6.326583 TCCCCTCTCGTCTAAATCATGTATTT 59.673 38.462 0.00 0.80 40.87 1.40
521 2361 8.372521 CAATTGCACCATCGTAAAGAAAAATAC 58.627 33.333 0.00 0.00 0.00 1.89
522 2362 5.945155 TGCACCATCGTAAAGAAAAATACC 58.055 37.500 0.00 0.00 0.00 2.73
525 2365 6.621164 GCACCATCGTAAAGAAAAATACCGAA 60.621 38.462 0.00 0.00 0.00 4.30
528 2368 5.861222 TCGTAAAGAAAAATACCGAACCC 57.139 39.130 0.00 0.00 0.00 4.11
541 2381 4.976224 ACCGAACCCAGCATAATTAAAC 57.024 40.909 0.00 0.00 0.00 2.01
543 2383 3.951680 CCGAACCCAGCATAATTAAACCT 59.048 43.478 0.00 0.00 0.00 3.50
585 2425 7.869800 ACAATGACACAACAACAAAACAAAAT 58.130 26.923 0.00 0.00 0.00 1.82
586 2426 8.014517 ACAATGACACAACAACAAAACAAAATC 58.985 29.630 0.00 0.00 0.00 2.17
589 2429 8.763049 TGACACAACAACAAAACAAAATCATA 57.237 26.923 0.00 0.00 0.00 2.15
592 2432 9.818796 ACACAACAACAAAACAAAATCATAAAC 57.181 25.926 0.00 0.00 0.00 2.01
644 2484 9.442047 AGACCTTCTAGTCAATGTTCTAAAATG 57.558 33.333 0.00 0.00 39.34 2.32
680 2520 1.349357 AGAACTCCTTCAACCTGCTCC 59.651 52.381 0.00 0.00 0.00 4.70
697 2537 5.304686 TGCTCCTTCTCAACCTCTTTTTA 57.695 39.130 0.00 0.00 0.00 1.52
705 2545 9.468532 CCTTCTCAACCTCTTTTTATCTTTTTG 57.531 33.333 0.00 0.00 0.00 2.44
753 2593 0.603975 AAGGAAACGAGCAGACAGGC 60.604 55.000 0.00 0.00 0.00 4.85
862 2951 3.554934 TCCCATATCAAATGTCCACTGC 58.445 45.455 0.00 0.00 0.00 4.40
958 3047 3.010420 TGACATGGTTGACAAACGAACA 58.990 40.909 0.00 0.00 37.15 3.18
972 3061 3.594603 ACGAACAAACGATCCTCATCT 57.405 42.857 0.00 0.00 37.03 2.90
1029 3118 2.349590 CATGATCACCGTCAAGCAAGA 58.650 47.619 0.00 0.00 0.00 3.02
1052 3141 1.680651 CCAGCCGAGACACTCTCCT 60.681 63.158 0.00 0.00 40.34 3.69
1149 3238 0.471617 CGCTCCTGGAATGGAAGGAT 59.528 55.000 0.00 0.00 41.74 3.24
1275 3364 4.368543 GTCTTCGGCCGGGTCGTT 62.369 66.667 27.83 0.00 30.45 3.85
1375 3464 0.944311 CAACCTCAGCTACAACGCGT 60.944 55.000 5.58 5.58 34.40 6.01
1491 3580 3.099619 CTTGCCTGCGTACATGCCG 62.100 63.158 0.00 0.00 36.68 5.69
1737 3826 0.317603 GCATCAATGTCAGCATCGCC 60.318 55.000 0.00 0.00 33.50 5.54
1787 3876 2.263741 GCCACTGCACCAACCTCAG 61.264 63.158 0.00 0.00 37.47 3.35
1830 3919 3.080121 CTCTCCGGGAAGCTGCCT 61.080 66.667 11.64 0.00 0.00 4.75
2069 4158 1.000283 GGCGATCATCGGAAGTCTGAT 60.000 52.381 9.59 0.00 42.40 2.90
2679 4777 0.110486 ACCTGGACCGCAACAAGATT 59.890 50.000 0.00 0.00 0.00 2.40
2682 4780 2.615493 CCTGGACCGCAACAAGATTACT 60.615 50.000 0.00 0.00 0.00 2.24
2721 5742 2.672996 GGTGACATGGCCGCACTT 60.673 61.111 14.72 0.00 33.25 3.16
2838 5859 2.768344 TCAGGCCCGATCCCTTCC 60.768 66.667 0.00 0.00 0.00 3.46
2844 5865 1.221840 CCCGATCCCTTCCACACTG 59.778 63.158 0.00 0.00 0.00 3.66
2856 5877 1.954146 CACACTGGGGAACGTCACG 60.954 63.158 0.00 0.00 0.00 4.35
3076 6106 0.815734 CCTGAAATCCTGCAGCTTGG 59.184 55.000 8.66 0.00 0.00 3.61
3077 6107 1.542492 CTGAAATCCTGCAGCTTGGT 58.458 50.000 8.66 0.00 0.00 3.67
3312 6360 1.135333 GAGTTCTCCTTCGGCGAGATT 59.865 52.381 10.46 0.00 36.30 2.40
3393 6441 2.666862 TACCACGCCAAAGTGCCG 60.667 61.111 0.00 0.00 40.59 5.69
3738 6786 4.175489 ATCCACCGCGACGTCTCG 62.175 66.667 20.42 20.42 43.28 4.04
4327 7401 1.866496 CGACCTCGTTAGTTCGCGG 60.866 63.158 6.13 0.00 40.84 6.46
4375 7449 6.339587 ACCATTTGTACAGGTTTGTATTGG 57.660 37.500 0.00 1.15 41.56 3.16
4490 7564 3.126831 CTCTGCGTGATTATTCTGGGAC 58.873 50.000 0.00 0.00 0.00 4.46
4500 7574 1.933021 ATTCTGGGACGTGTCTGGTA 58.067 50.000 0.00 0.00 0.00 3.25
4502 7576 0.611062 TCTGGGACGTGTCTGGTAGG 60.611 60.000 0.00 0.00 0.00 3.18
4503 7577 0.898789 CTGGGACGTGTCTGGTAGGT 60.899 60.000 0.00 0.00 0.00 3.08
4540 8033 9.416794 TGCATTGTATTTAAATAAGGTTGTGTG 57.583 29.630 9.48 3.01 0.00 3.82
4541 8034 9.418045 GCATTGTATTTAAATAAGGTTGTGTGT 57.582 29.630 9.48 0.00 0.00 3.72
4556 8056 5.068460 GGTTGTGTGTCTAGAGCTCATCTAT 59.932 44.000 17.77 0.00 39.82 1.98
4570 8070 7.015001 AGAGCTCATCTATATGTGACATCAACA 59.985 37.037 17.77 0.00 36.10 3.33
4572 8072 8.155510 AGCTCATCTATATGTGACATCAACATT 58.844 33.333 0.00 0.00 34.50 2.71
4573 8073 8.781196 GCTCATCTATATGTGACATCAACATTT 58.219 33.333 0.00 0.00 34.50 2.32
4632 8132 5.197682 TGTCATCAATTGATTGTTGTGCA 57.802 34.783 18.41 9.60 38.19 4.57
4637 8137 8.710551 GTCATCAATTGATTGTTGTGCATTTTA 58.289 29.630 18.41 0.00 38.19 1.52
4649 8149 7.904094 TGTTGTGCATTTTATTTGTTTGTCTC 58.096 30.769 0.00 0.00 0.00 3.36
4650 8150 7.010923 TGTTGTGCATTTTATTTGTTTGTCTCC 59.989 33.333 0.00 0.00 0.00 3.71
4651 8151 6.815089 TGTGCATTTTATTTGTTTGTCTCCT 58.185 32.000 0.00 0.00 0.00 3.69
4773 9089 6.918569 CCCACTTACAAGAACTATCACTATCG 59.081 42.308 0.00 0.00 0.00 2.92
4792 9108 9.929722 CACTATCGTATGCAAATTTAGCTAAAA 57.070 29.630 22.13 6.51 0.00 1.52
4903 9270 5.379732 TTTTCCGTATCATTTGGGTTGAC 57.620 39.130 0.00 0.00 0.00 3.18
4938 9305 5.131308 TGTGGAATCGATTGACCCCTATTTA 59.869 40.000 16.96 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.888716 GGTATGACAATGAAACTTTTGGTTTTT 58.111 29.630 0.00 0.00 46.77 1.94
17 18 8.264347 AGGTATGACAATGAAACTTTTGGTTTT 58.736 29.630 0.00 0.00 46.77 2.43
19 20 7.360113 AGGTATGACAATGAAACTTTTGGTT 57.640 32.000 0.00 0.00 40.28 3.67
20 21 6.293955 CGAGGTATGACAATGAAACTTTTGGT 60.294 38.462 0.00 0.00 0.00 3.67
21 22 6.072728 TCGAGGTATGACAATGAAACTTTTGG 60.073 38.462 0.00 0.00 0.00 3.28
22 23 6.898041 TCGAGGTATGACAATGAAACTTTTG 58.102 36.000 0.00 0.00 0.00 2.44
23 24 7.504924 TTCGAGGTATGACAATGAAACTTTT 57.495 32.000 0.00 0.00 0.00 2.27
24 25 7.687941 ATTCGAGGTATGACAATGAAACTTT 57.312 32.000 0.00 0.00 0.00 2.66
25 26 7.390440 TCAATTCGAGGTATGACAATGAAACTT 59.610 33.333 0.00 0.00 0.00 2.66
26 27 6.878923 TCAATTCGAGGTATGACAATGAAACT 59.121 34.615 0.00 0.00 0.00 2.66
27 28 6.961554 GTCAATTCGAGGTATGACAATGAAAC 59.038 38.462 13.60 0.00 41.35 2.78
28 29 6.093495 GGTCAATTCGAGGTATGACAATGAAA 59.907 38.462 17.73 0.00 43.02 2.69
29 30 5.584649 GGTCAATTCGAGGTATGACAATGAA 59.415 40.000 17.73 0.00 43.02 2.57
30 31 5.116180 GGTCAATTCGAGGTATGACAATGA 58.884 41.667 17.73 0.00 43.02 2.57
31 32 4.273480 GGGTCAATTCGAGGTATGACAATG 59.727 45.833 17.73 0.00 43.02 2.82
32 33 4.451900 GGGTCAATTCGAGGTATGACAAT 58.548 43.478 17.73 0.00 43.02 2.71
33 34 3.370103 GGGGTCAATTCGAGGTATGACAA 60.370 47.826 17.73 0.00 43.02 3.18
34 35 2.169769 GGGGTCAATTCGAGGTATGACA 59.830 50.000 17.73 0.00 43.02 3.58
35 36 2.434702 AGGGGTCAATTCGAGGTATGAC 59.565 50.000 11.30 11.30 41.06 3.06
36 37 2.759355 AGGGGTCAATTCGAGGTATGA 58.241 47.619 0.00 0.00 0.00 2.15
37 38 3.560636 AAGGGGTCAATTCGAGGTATG 57.439 47.619 0.00 0.00 0.00 2.39
38 39 5.510861 CGATAAAGGGGTCAATTCGAGGTAT 60.511 44.000 0.00 0.00 0.00 2.73
39 40 4.202182 CGATAAAGGGGTCAATTCGAGGTA 60.202 45.833 0.00 0.00 0.00 3.08
40 41 3.431766 CGATAAAGGGGTCAATTCGAGGT 60.432 47.826 0.00 0.00 0.00 3.85
41 42 3.131396 CGATAAAGGGGTCAATTCGAGG 58.869 50.000 0.00 0.00 0.00 4.63
42 43 3.131396 CCGATAAAGGGGTCAATTCGAG 58.869 50.000 0.00 0.00 0.00 4.04
43 44 2.767394 TCCGATAAAGGGGTCAATTCGA 59.233 45.455 0.00 0.00 0.00 3.71
44 45 3.188159 TCCGATAAAGGGGTCAATTCG 57.812 47.619 0.00 0.00 0.00 3.34
45 46 5.907866 TTTTCCGATAAAGGGGTCAATTC 57.092 39.130 0.00 0.00 0.00 2.17
67 68 9.337091 CGTAATTTTTGTCAATTCGAGGTATTT 57.663 29.630 0.00 0.00 0.00 1.40
68 69 8.723311 TCGTAATTTTTGTCAATTCGAGGTATT 58.277 29.630 0.00 0.00 29.89 1.89
109 110 9.974980 ACAAACATACTTGTTAGGGTTAATTTG 57.025 29.630 0.00 0.00 45.30 2.32
126 127 7.119846 ACTCAGCCATAAGAAAGACAAACATAC 59.880 37.037 0.00 0.00 0.00 2.39
132 133 6.995686 TGTAAACTCAGCCATAAGAAAGACAA 59.004 34.615 0.00 0.00 0.00 3.18
133 134 6.530120 TGTAAACTCAGCCATAAGAAAGACA 58.470 36.000 0.00 0.00 0.00 3.41
134 135 7.617041 ATGTAAACTCAGCCATAAGAAAGAC 57.383 36.000 0.00 0.00 0.00 3.01
154 155 9.715123 CGATGTAAACAAAGAAATGCATATGTA 57.285 29.630 0.00 0.00 0.00 2.29
155 156 8.243426 ACGATGTAAACAAAGAAATGCATATGT 58.757 29.630 0.00 0.00 0.00 2.29
156 157 8.619146 ACGATGTAAACAAAGAAATGCATATG 57.381 30.769 0.00 0.00 0.00 1.78
157 158 9.638239 AAACGATGTAAACAAAGAAATGCATAT 57.362 25.926 0.00 0.00 0.00 1.78
159 160 7.651304 TCAAACGATGTAAACAAAGAAATGCAT 59.349 29.630 0.00 0.00 0.00 3.96
201 202 4.094146 GCATCACAAGCCTCTCTTTCTAAC 59.906 45.833 0.00 0.00 31.27 2.34
249 2086 0.396435 TCACACACTTACAGCTGGGG 59.604 55.000 19.93 9.83 0.00 4.96
250 2087 1.512926 GTCACACACTTACAGCTGGG 58.487 55.000 19.93 10.20 0.00 4.45
272 2109 0.962356 CTCAACAGCCCTCCGCAAAT 60.962 55.000 0.00 0.00 41.38 2.32
291 2128 1.468520 ACACATACATTGCGGTTGAGC 59.531 47.619 0.00 0.00 37.71 4.26
298 2135 1.535028 ACACACCACACATACATTGCG 59.465 47.619 0.00 0.00 0.00 4.85
310 2147 4.923871 CAGACAAGACTATACACACACCAC 59.076 45.833 0.00 0.00 0.00 4.16
314 2151 6.700081 GTCAAACAGACAAGACTATACACACA 59.300 38.462 0.00 0.00 46.77 3.72
331 2168 1.003851 AACACCGACACGTCAAACAG 58.996 50.000 0.00 0.00 0.00 3.16
339 2176 4.921515 CCCATAATATAGAACACCGACACG 59.078 45.833 0.00 0.00 0.00 4.49
348 2185 6.096564 ACGCCTAGTAGCCCATAATATAGAAC 59.903 42.308 0.00 0.00 0.00 3.01
369 2206 1.009829 CAGAGGCAATTGACTACGCC 58.990 55.000 15.47 3.63 45.23 5.68
370 2207 1.726853 ACAGAGGCAATTGACTACGC 58.273 50.000 15.47 1.45 30.09 4.42
381 2218 6.225318 ACAGTTTTACGTAATTACAGAGGCA 58.775 36.000 15.67 0.00 0.00 4.75
395 2232 6.525976 GCTACACCTACTTAGACAGTTTTACG 59.474 42.308 0.00 0.00 36.88 3.18
396 2233 7.328005 GTGCTACACCTACTTAGACAGTTTTAC 59.672 40.741 0.00 0.00 36.88 2.01
398 2235 6.041751 AGTGCTACACCTACTTAGACAGTTTT 59.958 38.462 0.00 0.00 34.20 2.43
399 2236 5.539193 AGTGCTACACCTACTTAGACAGTTT 59.461 40.000 0.00 0.00 34.20 2.66
400 2237 5.078256 AGTGCTACACCTACTTAGACAGTT 58.922 41.667 0.00 0.00 34.20 3.16
401 2238 4.664392 AGTGCTACACCTACTTAGACAGT 58.336 43.478 0.00 0.00 35.74 3.55
402 2239 5.881443 AGTAGTGCTACACCTACTTAGACAG 59.119 44.000 11.39 0.00 38.48 3.51
403 2240 5.646793 CAGTAGTGCTACACCTACTTAGACA 59.353 44.000 11.39 0.00 38.48 3.41
405 2242 5.813383 ACAGTAGTGCTACACCTACTTAGA 58.187 41.667 11.39 0.00 38.48 2.10
406 2243 6.150641 TGAACAGTAGTGCTACACCTACTTAG 59.849 42.308 11.39 0.00 38.48 2.18
409 2246 4.404640 TGAACAGTAGTGCTACACCTACT 58.595 43.478 11.39 0.00 38.48 2.57
414 2251 5.236478 ACAAACATGAACAGTAGTGCTACAC 59.764 40.000 11.39 0.00 38.48 2.90
429 2266 2.555782 GCGAGCGCACAAACATGA 59.444 55.556 11.47 0.00 41.49 3.07
440 2277 2.870146 GAAAGATGCACACGCGAGCG 62.870 60.000 15.93 16.38 42.97 5.03
442 2279 1.421485 GGAAAGATGCACACGCGAG 59.579 57.895 15.93 7.88 42.97 5.03
443 2280 2.032634 GGGAAAGATGCACACGCGA 61.033 57.895 15.93 0.00 42.97 5.87
446 2283 0.036010 AGAGGGGAAAGATGCACACG 60.036 55.000 0.00 0.00 0.00 4.49
453 2290 4.962995 TGATTTAGACGAGAGGGGAAAGAT 59.037 41.667 0.00 0.00 0.00 2.40
455 2292 4.737855 TGATTTAGACGAGAGGGGAAAG 57.262 45.455 0.00 0.00 0.00 2.62
483 2320 9.862371 ACGATGGTGCAATTGTTTAATTTATTA 57.138 25.926 7.40 0.00 34.34 0.98
496 2333 7.544217 GGTATTTTTCTTTACGATGGTGCAATT 59.456 33.333 0.00 0.00 0.00 2.32
508 2345 5.048573 TGCTGGGTTCGGTATTTTTCTTTAC 60.049 40.000 0.00 0.00 0.00 2.01
521 2361 3.951680 AGGTTTAATTATGCTGGGTTCGG 59.048 43.478 0.00 0.00 0.00 4.30
522 2362 5.105917 ACAAGGTTTAATTATGCTGGGTTCG 60.106 40.000 0.00 0.00 0.00 3.95
525 2365 5.185056 GTCACAAGGTTTAATTATGCTGGGT 59.815 40.000 0.00 0.00 0.00 4.51
528 2368 7.968405 GGTAAGTCACAAGGTTTAATTATGCTG 59.032 37.037 0.00 0.00 0.00 4.41
541 2381 2.140717 GTTGGTCGGTAAGTCACAAGG 58.859 52.381 0.00 0.00 0.00 3.61
543 2383 2.983907 TGTTGGTCGGTAAGTCACAA 57.016 45.000 0.00 0.00 0.00 3.33
585 2425 4.572795 TGCTGTGTTGTTCTTCGTTTATGA 59.427 37.500 0.00 0.00 0.00 2.15
586 2426 4.843147 TGCTGTGTTGTTCTTCGTTTATG 58.157 39.130 0.00 0.00 0.00 1.90
589 2429 3.840890 TTGCTGTGTTGTTCTTCGTTT 57.159 38.095 0.00 0.00 0.00 3.60
592 2432 2.111756 GCTTTGCTGTGTTGTTCTTCG 58.888 47.619 0.00 0.00 0.00 3.79
697 2537 3.568430 GTCACCCCGAAAGACAAAAAGAT 59.432 43.478 0.00 0.00 32.68 2.40
705 2545 0.685660 AAGGAGTCACCCCGAAAGAC 59.314 55.000 0.00 0.00 40.05 3.01
711 2551 1.003718 GGTTGAAGGAGTCACCCCG 60.004 63.158 0.00 0.00 32.61 5.73
753 2593 3.266636 GTGTTGGTTTGTTTTTCCCCTG 58.733 45.455 0.00 0.00 0.00 4.45
806 2895 3.373439 GGTAGAAGAGTTGATGCTTGCAG 59.627 47.826 0.87 0.00 0.00 4.41
843 2932 3.317149 CAGGCAGTGGACATTTGATATGG 59.683 47.826 0.00 0.00 0.00 2.74
862 2951 0.741915 GGTCCGAGCTCTTCTACAGG 59.258 60.000 12.85 3.57 0.00 4.00
906 2995 4.421365 TCCAATTGGAGTGCAGCC 57.579 55.556 23.63 0.00 39.78 4.85
958 3047 3.701542 TCAGCAGTAGATGAGGATCGTTT 59.298 43.478 0.00 0.00 34.77 3.60
972 3061 3.118223 TCTCTCTCGGAGAATCAGCAGTA 60.118 47.826 9.32 0.00 46.85 2.74
1029 3118 4.057428 GTGTCTCGGCTGGACGCT 62.057 66.667 16.06 0.00 39.99 5.07
1491 3580 0.670854 GGTTGAGGTGCTCGAGGTTC 60.671 60.000 15.58 0.00 32.35 3.62
1552 3641 0.843309 TGAAGCCTGGTCAAGTTGGA 59.157 50.000 2.34 0.00 0.00 3.53
1830 3919 3.872603 AGCTTGGCCCACGACACA 61.873 61.111 0.00 0.00 0.00 3.72
1970 4059 3.147595 CGACCTCTGCGGGGATCA 61.148 66.667 0.00 0.00 36.97 2.92
2069 4158 1.339438 GGTCCAGCAGCTTCAGATTCA 60.339 52.381 0.00 0.00 0.00 2.57
2721 5742 2.009774 GCAGCGAGGCTCAAATCTTTA 58.990 47.619 15.95 0.00 36.40 1.85
2769 5790 2.744202 CAACTGTAATTTGCCGAGCTCT 59.256 45.455 12.85 0.00 0.00 4.09
2793 5814 1.896220 TGTGCCTCAGGTTCACATTC 58.104 50.000 0.17 0.00 35.99 2.67
2838 5859 1.954146 CGTGACGTTCCCCAGTGTG 60.954 63.158 0.00 0.00 0.00 3.82
2844 5865 1.740296 CATGGTCGTGACGTTCCCC 60.740 63.158 4.40 1.94 0.00 4.81
3160 6190 0.319900 ACTGCAGCGACGAAGAACAT 60.320 50.000 15.27 0.00 0.00 2.71
3738 6786 1.202604 TCCAGAAGGACGTTGTTGACC 60.203 52.381 0.00 0.00 39.61 4.02
4112 7186 0.838987 TGGTCCACCAGGTCCCTAAC 60.839 60.000 0.00 0.00 41.83 2.34
4162 7236 2.672996 ATGAACACCACCTGCGCC 60.673 61.111 4.18 0.00 0.00 6.53
4178 7252 1.067212 GGATAGTGCCACGACGAAGAT 59.933 52.381 0.00 0.00 0.00 2.40
4296 7370 0.389166 GAGGTCGCCGATCATGATCC 60.389 60.000 26.30 14.17 34.40 3.36
4327 7401 6.994221 ACTACTAACCAGCACATATCATACC 58.006 40.000 0.00 0.00 0.00 2.73
4375 7449 1.310904 TACAGAACCACCGCCAAAAC 58.689 50.000 0.00 0.00 0.00 2.43
4475 7549 3.865745 CAGACACGTCCCAGAATAATCAC 59.134 47.826 0.00 0.00 0.00 3.06
4481 7555 1.825474 CTACCAGACACGTCCCAGAAT 59.175 52.381 0.00 0.00 0.00 2.40
4490 7564 0.895530 ATCACCACCTACCAGACACG 59.104 55.000 0.00 0.00 0.00 4.49
4500 7574 1.541147 CAATGCAAACGATCACCACCT 59.459 47.619 0.00 0.00 0.00 4.00
4502 7576 2.704725 ACAATGCAAACGATCACCAC 57.295 45.000 0.00 0.00 0.00 4.16
4503 7577 5.384063 AAATACAATGCAAACGATCACCA 57.616 34.783 0.00 0.00 0.00 4.17
4540 8033 7.680442 TGTCACATATAGATGAGCTCTAGAC 57.320 40.000 16.19 8.06 39.82 2.59
4541 8034 8.105829 TGATGTCACATATAGATGAGCTCTAGA 58.894 37.037 16.19 0.00 39.82 2.43
4542 8035 8.278729 TGATGTCACATATAGATGAGCTCTAG 57.721 38.462 16.19 0.00 39.82 2.43
4546 8046 7.059202 TGTTGATGTCACATATAGATGAGCT 57.941 36.000 3.93 0.00 36.48 4.09
4664 8164 9.599866 CAACTCAATAAAGTAGTCATGATGGTA 57.400 33.333 0.00 0.00 0.00 3.25
4889 9256 2.899256 CCCAACTGTCAACCCAAATGAT 59.101 45.455 0.00 0.00 0.00 2.45
4896 9263 3.763671 CAGCCCAACTGTCAACCC 58.236 61.111 0.00 0.00 41.86 4.11
4943 9310 2.424956 GAGCCCAAGAAGCAATTCGATT 59.575 45.455 0.00 0.00 0.00 3.34
5172 9576 8.937884 GTTGGTATTTCCTTTAAGAAGAGAGAC 58.062 37.037 0.00 0.00 34.71 3.36
5247 9676 9.628500 GGAATTGGTATTAACCTCAAAGTAGAT 57.372 33.333 0.00 0.00 46.91 1.98


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

AutoCloner maintained by Alex Coulton.