Multiple sequence alignment - TraesCS2B01G290900

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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 TraesCS2B01G290900 chr2B 100.000 9258 0 0 1 9258 404105413 404114670 0.000000e+00 17097.0
1 TraesCS2B01G290900 chr2B 79.503 322 41 9 6608 6904 45691917 45691596 1.220000e-48 206.0
2 TraesCS2B01G290900 chr2D 94.667 4125 147 24 1663 5760 336469820 336473898 0.000000e+00 6331.0
3 TraesCS2B01G290900 chr2D 96.572 2771 69 9 6216 8985 336474480 336477225 0.000000e+00 4567.0
4 TraesCS2B01G290900 chr2D 97.836 1063 23 0 636 1698 336468762 336469824 0.000000e+00 1836.0
5 TraesCS2B01G290900 chr2D 96.383 470 6 2 5759 6217 336473970 336474439 0.000000e+00 763.0
6 TraesCS2B01G290900 chr2D 84.444 585 57 21 1 558 336468051 336468628 6.320000e-151 545.0
7 TraesCS2B01G290900 chr2D 94.834 271 14 0 8987 9257 336477264 336477534 3.090000e-114 424.0
8 TraesCS2B01G290900 chr2A 96.914 3338 86 12 626 3955 446519167 446522495 0.000000e+00 5578.0
9 TraesCS2B01G290900 chr2A 96.964 1976 38 4 6533 8507 446525578 446527532 0.000000e+00 3297.0
10 TraesCS2B01G290900 chr2A 92.245 1341 82 9 3993 5331 446522503 446523823 0.000000e+00 1881.0
11 TraesCS2B01G290900 chr2A 95.795 761 32 0 5000 5760 446523822 446524582 0.000000e+00 1229.0
12 TraesCS2B01G290900 chr2A 96.288 431 10 4 5759 6187 446524654 446525080 0.000000e+00 702.0
13 TraesCS2B01G290900 chr2A 96.845 317 9 1 6216 6531 446525139 446525455 6.370000e-146 529.0
14 TraesCS2B01G290900 chr2A 87.626 396 31 7 183 575 446516306 446516686 2.370000e-120 444.0
15 TraesCS2B01G290900 chr2A 95.279 233 11 0 8648 8880 446528076 446528308 4.080000e-98 370.0
16 TraesCS2B01G290900 chr2A 84.906 212 20 7 1 200 446515923 446516134 4.380000e-48 204.0
17 TraesCS2B01G290900 chr2A 90.845 142 10 3 8507 8646 446527810 446527950 4.410000e-43 187.0
18 TraesCS2B01G290900 chr5B 80.472 466 50 24 6473 6904 185723993 185723535 1.500000e-82 318.0
19 TraesCS2B01G290900 chr5B 84.247 146 23 0 6216 6361 535562695 535562840 9.690000e-30 143.0
20 TraesCS2B01G290900 chr5B 88.136 59 5 2 4398 4456 55629114 55629058 1.670000e-07 69.4
21 TraesCS2B01G290900 chr5D 86.522 230 29 2 6216 6443 461542041 461541812 1.540000e-62 252.0
22 TraesCS2B01G290900 chr6B 85.088 228 33 1 6216 6442 133751218 133750991 2.010000e-56 231.0
23 TraesCS2B01G290900 chr6B 79.503 322 41 9 6608 6904 270873483 270873804 1.220000e-48 206.0
24 TraesCS2B01G290900 chr6B 79.503 322 41 9 6608 6904 416889949 416889628 1.220000e-48 206.0
25 TraesCS2B01G290900 chrUn 84.753 223 33 1 6216 6437 158035861 158035639 1.210000e-53 222.0
26 TraesCS2B01G290900 chrUn 87.050 139 17 1 6300 6437 480086872 480086734 1.240000e-33 156.0
27 TraesCS2B01G290900 chr1B 84.211 228 35 1 6216 6442 576757126 576756899 4.350000e-53 220.0
28 TraesCS2B01G290900 chr3B 84.305 223 34 1 6216 6437 824979653 824979431 5.630000e-52 217.0
29 TraesCS2B01G290900 chr3B 79.503 322 41 9 6608 6904 126480761 126481082 1.220000e-48 206.0
30 TraesCS2B01G290900 chr3B 79.503 322 41 9 6608 6904 341961391 341961070 1.220000e-48 206.0
31 TraesCS2B01G290900 chr3B 91.304 138 12 0 6521 6658 355428250 355428113 1.230000e-43 189.0
32 TraesCS2B01G290900 chr7B 79.503 322 41 9 6608 6904 399781465 399781786 1.220000e-48 206.0
33 TraesCS2B01G290900 chr1A 79.503 322 41 9 6608 6904 162990832 162990511 1.220000e-48 206.0
34 TraesCS2B01G290900 chr6A 78.313 332 50 9 6482 6794 315604038 315604366 2.640000e-45 195.0
35 TraesCS2B01G290900 chr6A 84.375 128 15 1 6216 6343 418095387 418095509 4.540000e-23 121.0
36 TraesCS2B01G290900 chr3D 91.304 138 12 0 6521 6658 263327722 263327585 1.230000e-43 189.0


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 TraesCS2B01G290900 chr2B 404105413 404114670 9257 False 17097.0 17097 100.000000 1 9258 1 chr2B.!!$F1 9257
1 TraesCS2B01G290900 chr2D 336468051 336477534 9483 False 2411.0 6331 94.122667 1 9257 6 chr2D.!!$F1 9256
2 TraesCS2B01G290900 chr2A 446515923 446528308 12385 False 1442.1 5578 93.370700 1 8880 10 chr2A.!!$F1 8879

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
287 499 0.178947 GAGAGGGGATGACGAGGGAT 60.179 60.000 0.00 0.00 0.00 3.85 F
332 545 0.320771 GGTCGCTAATCCATCCGCAT 60.321 55.000 0.00 0.00 0.00 4.73 F
372 585 1.133976 CCTCATTCCCTCGAGGCAATT 60.134 52.381 26.87 9.54 42.30 2.32 F
856 3534 1.227089 CCAGATCTTCGGAGCACGG 60.227 63.158 0.00 0.00 44.45 4.94 F
2296 5016 0.836400 CCCCAGAGGCCCATACGTAT 60.836 60.000 1.14 1.14 0.00 3.06 F
2926 5647 2.587956 CTGTCAATGTCAAATGTGCGG 58.412 47.619 0.00 0.00 0.00 5.69 F
4388 7129 0.034896 GTTCTTGGCCGGAGAACTCA 59.965 55.000 30.16 8.63 45.94 3.41 F
4935 7678 0.263172 TGTCTCCTCTCCCCATCTCC 59.737 60.000 0.00 0.00 0.00 3.71 F
5365 8438 0.442310 CGTCTGGTTACATTGGCACG 59.558 55.000 0.00 0.00 0.00 5.34 F
5377 8450 1.199615 TTGGCACGATATGACTCCCA 58.800 50.000 0.00 0.00 37.17 4.37 F
6891 10214 1.210478 GCCTACTTTGGAGCTGGATCA 59.790 52.381 0.00 0.00 0.00 2.92 F
6967 10290 3.165875 TGAGACACCTTCTGGTCTTAGG 58.834 50.000 0.00 0.00 46.60 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 4524 1.065401 CTTCGCAACAAGGTTTCTGCA 59.935 47.619 0.00 0.00 34.39 4.41 R
1911 4626 4.455877 ACAAAGATGAACAATCGGGACTTC 59.544 41.667 0.00 0.00 40.54 3.01 R
2296 5016 5.123820 CGCCTTGGAGATAGATTCAACAAAA 59.876 40.000 0.00 0.00 0.00 2.44 R
2557 5277 6.064060 CACAATTCCTAGAAGCATTATCCCA 58.936 40.000 0.00 0.00 0.00 4.37 R
3968 6709 0.605589 GGTTTGTAAGCCGGAGCACT 60.606 55.000 5.05 0.00 43.56 4.40 R
4767 7508 0.175760 GCTTCAGCGTGGATCCTGTA 59.824 55.000 14.23 0.00 0.00 2.74 R
6327 9526 2.115266 ACCCTTCCCAAGTTGCGG 59.885 61.111 0.00 0.58 0.00 5.69 R
6881 10204 3.072944 GCTACATCCAATGATCCAGCTC 58.927 50.000 0.00 0.00 34.31 4.09 R
7042 10365 4.329462 TGAACTACAACCCAATTTTGCC 57.671 40.909 0.00 0.00 0.00 4.52 R
7141 10464 6.602410 TTCAACTATTTCCATTGCCATCAA 57.398 33.333 0.00 0.00 36.51 2.57 R
7954 11282 0.393077 AGAAGGACGTCAGGTTGTGG 59.607 55.000 18.91 0.00 0.00 4.17 R
8957 12689 0.543749 AAGGGAAGAAGCATCCTCCG 59.456 55.000 0.65 0.00 37.09 4.63 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 2.885554 GCCACCATGAAAGGAGAACCAT 60.886 50.000 0.00 0.00 38.94 3.55
44 45 3.434309 CCACCATGAAAGGAGAACCATT 58.566 45.455 0.00 0.00 38.94 3.16
101 102 1.951209 TATCACCTCCCAAGCTGTCA 58.049 50.000 0.00 0.00 0.00 3.58
115 116 1.468985 CTGTCACATCCTCCTCGTCT 58.531 55.000 0.00 0.00 0.00 4.18
130 131 4.705023 TCCTCGTCTAGAACATGTGATCAA 59.295 41.667 0.00 0.00 0.00 2.57
154 170 1.687493 GCTAGGCAGTGGAGGAGGT 60.687 63.158 0.00 0.00 0.00 3.85
165 181 1.997874 GAGGAGGTGGTGGAGGCAT 60.998 63.158 0.00 0.00 0.00 4.40
176 192 2.672098 GTGGAGGCATAGGAGAAGAGA 58.328 52.381 0.00 0.00 0.00 3.10
203 219 3.412408 GGAGGGGGAAGTGGAGGC 61.412 72.222 0.00 0.00 0.00 4.70
224 428 1.677966 CGACACGGGGAAGAGGAGA 60.678 63.158 0.00 0.00 0.00 3.71
246 450 1.410882 GGATGGAAAGAGACGAGGGAG 59.589 57.143 0.00 0.00 0.00 4.30
250 454 2.021457 GGAAAGAGACGAGGGAGAGAG 58.979 57.143 0.00 0.00 0.00 3.20
251 455 2.356330 GGAAAGAGACGAGGGAGAGAGA 60.356 54.545 0.00 0.00 0.00 3.10
287 499 0.178947 GAGAGGGGATGACGAGGGAT 60.179 60.000 0.00 0.00 0.00 3.85
299 511 7.331026 GGATGACGAGGGATATATTTTCATCA 58.669 38.462 9.71 7.09 39.82 3.07
329 541 1.068588 TCTTGGTCGCTAATCCATCCG 59.931 52.381 0.00 0.00 33.50 4.18
332 545 0.320771 GGTCGCTAATCCATCCGCAT 60.321 55.000 0.00 0.00 0.00 4.73
360 573 2.519013 AGGCAAAACTCACCTCATTCC 58.481 47.619 0.00 0.00 0.00 3.01
372 585 1.133976 CCTCATTCCCTCGAGGCAATT 60.134 52.381 26.87 9.54 42.30 2.32
378 591 1.843851 TCCCTCGAGGCAATTGGTAAT 59.156 47.619 26.87 0.00 34.51 1.89
396 609 2.537633 ATGAGGCCCAATTGTCATGT 57.462 45.000 0.00 0.00 0.00 3.21
411 624 9.467258 CAATTGTCATGTACAGAAAAGTGAAAT 57.533 29.630 14.97 7.56 39.87 2.17
468 683 4.775664 ACAACGCCGTAAAAAGTATGAAC 58.224 39.130 0.00 0.00 0.00 3.18
471 686 2.777494 GCCGTAAAAAGTATGAACGCC 58.223 47.619 0.00 0.00 32.43 5.68
486 701 2.654404 GCCGGTAGATCGTGCGAC 60.654 66.667 1.90 0.00 0.00 5.19
517 732 1.941734 GCCGACGAAGATCGCTCAG 60.942 63.158 0.00 0.00 45.12 3.35
607 3254 1.358759 GTGCCAAGAAACCACCGTG 59.641 57.895 0.00 0.00 0.00 4.94
695 3373 6.316890 GGTCACAAGTCAAAACCAGTTACTTA 59.683 38.462 0.00 0.00 0.00 2.24
735 3413 1.679305 ATCTCGCTCCGTGTCCTGT 60.679 57.895 0.00 0.00 0.00 4.00
738 3416 3.414700 CGCTCCGTGTCCTGTTGC 61.415 66.667 0.00 0.00 0.00 4.17
856 3534 1.227089 CCAGATCTTCGGAGCACGG 60.227 63.158 0.00 0.00 44.45 4.94
1471 4149 5.524281 TCTCTGCTGTGAACTAGTAGATACG 59.476 44.000 3.59 0.00 36.53 3.06
1535 4213 7.786030 TCCTTCACCTAGAATAGTCTTGATTG 58.214 38.462 0.00 0.00 36.82 2.67
1717 4431 7.574607 AGTTTGTTGGGATATACTAGAAAGGG 58.425 38.462 0.00 0.00 0.00 3.95
1731 4445 6.292150 ACTAGAAAGGGTAGCATATCTTTGC 58.708 40.000 0.00 0.00 43.09 3.68
1784 4499 3.935828 GCCTCACTAATGTTTCACTCTCC 59.064 47.826 0.00 0.00 0.00 3.71
1809 4524 8.030692 CCTGAACATTGTCAAACAATCACATAT 58.969 33.333 2.42 0.00 44.91 1.78
1825 4540 3.922240 CACATATGCAGAAACCTTGTTGC 59.078 43.478 1.58 0.00 37.09 4.17
1832 4547 3.363178 CAGAAACCTTGTTGCGAAGTTC 58.637 45.455 0.00 0.00 0.00 3.01
1839 4554 3.058501 CCTTGTTGCGAAGTTCGGTATTT 60.059 43.478 25.55 0.00 40.84 1.40
1840 4555 4.533222 CTTGTTGCGAAGTTCGGTATTTT 58.467 39.130 25.55 0.00 40.84 1.82
1882 4597 5.323371 TGTTTTTGTATCCAAGCATAGGC 57.677 39.130 0.00 0.00 41.61 3.93
2208 4927 4.436852 CCGATCCTGGTAAAATGTGTTTCG 60.437 45.833 0.00 0.00 0.00 3.46
2296 5016 0.836400 CCCCAGAGGCCCATACGTAT 60.836 60.000 1.14 1.14 0.00 3.06
2455 5175 7.295911 AGTGGAAAGCTAATCCCTTCCTATAAT 59.704 37.037 14.22 0.00 36.04 1.28
2557 5277 3.138839 TGAATATGGATGGTGCATCTGGT 59.861 43.478 0.00 0.00 40.39 4.00
2731 5452 7.158099 AGCTCCAAGGTATGAAAATACAAAC 57.842 36.000 0.00 0.00 0.00 2.93
2732 5453 6.719370 AGCTCCAAGGTATGAAAATACAAACA 59.281 34.615 0.00 0.00 0.00 2.83
2734 5455 7.702348 GCTCCAAGGTATGAAAATACAAACATC 59.298 37.037 0.00 0.00 0.00 3.06
2765 5486 6.777782 TGATATTTGGGCATTTGTTTTTCCT 58.222 32.000 0.00 0.00 0.00 3.36
2811 5532 4.219944 GGCTTCATGATATGGCATGTTCAT 59.780 41.667 10.98 14.92 44.59 2.57
2881 5602 8.743085 AATAACTAGACATGAGACATTGCAAT 57.257 30.769 5.99 5.99 0.00 3.56
2926 5647 2.587956 CTGTCAATGTCAAATGTGCGG 58.412 47.619 0.00 0.00 0.00 5.69
3219 5943 7.644986 ACTTTCGCTGATCAATATTAGTAGC 57.355 36.000 0.00 0.00 0.00 3.58
3301 6025 4.701651 TCCTCGTCGGTTTACAATCTTCTA 59.298 41.667 0.00 0.00 0.00 2.10
3850 6574 7.736447 AAATATAGAAGAAGAGAATTGGCCG 57.264 36.000 0.00 0.00 0.00 6.13
3876 6600 7.410120 CTAATAAGGAAAACTGGCCTGAAAT 57.590 36.000 17.64 1.01 34.00 2.17
3902 6626 3.753797 TGCAACTTAACTTCACACACACA 59.246 39.130 0.00 0.00 0.00 3.72
4216 6957 4.729918 CCTGGAGGCCGCTGCTTT 62.730 66.667 6.40 0.00 37.74 3.51
4224 6965 4.107051 CCGCTGCTTTGGCTTCCG 62.107 66.667 0.00 0.00 39.59 4.30
4264 7005 1.448540 CCTGCCTAGCCAACGACAG 60.449 63.158 0.00 0.00 0.00 3.51
4313 7054 2.555199 CTTGATAGAGGACAAAGCCGG 58.445 52.381 0.00 0.00 0.00 6.13
4370 7111 3.130160 GTACGACGCCTCTCCGGT 61.130 66.667 0.00 0.00 34.25 5.28
4371 7112 2.360350 TACGACGCCTCTCCGGTT 60.360 61.111 0.00 0.00 34.25 4.44
4388 7129 0.034896 GTTCTTGGCCGGAGAACTCA 59.965 55.000 30.16 8.63 45.94 3.41
4396 7137 1.740718 GCCGGAGAACTCAAGATCCAC 60.741 57.143 5.05 0.00 0.00 4.02
4402 7143 3.854666 AGAACTCAAGATCCACATGACG 58.145 45.455 0.00 0.00 0.00 4.35
4465 7206 3.680786 CACCGTCCGAGTCTGCCA 61.681 66.667 0.00 0.00 0.00 4.92
4473 7214 1.278985 TCCGAGTCTGCCATCAACATT 59.721 47.619 0.00 0.00 0.00 2.71
4488 7229 0.965363 ACATTGATCGGGTTGGTGCC 60.965 55.000 0.00 0.00 0.00 5.01
4549 7290 2.995077 AAGCCCCGCCATCCATCAA 61.995 57.895 0.00 0.00 0.00 2.57
4565 7306 0.676466 TCAAAGCACGGGTAGCCATG 60.676 55.000 12.31 7.31 0.00 3.66
4610 7351 2.571216 CCGTCGTCTCACCACCCTT 61.571 63.158 0.00 0.00 0.00 3.95
4680 7421 0.681887 TGCATCACTTCCTGCCATGG 60.682 55.000 7.63 7.63 37.59 3.66
4681 7422 0.394762 GCATCACTTCCTGCCATGGA 60.395 55.000 18.40 0.00 32.15 3.41
4689 7430 2.338015 CCTGCCATGGAGTGTGTGC 61.338 63.158 18.40 0.00 0.00 4.57
4714 7455 1.077930 GCAAGAGGCCAGATCTGCA 60.078 57.895 17.76 0.00 36.11 4.41
4725 7466 0.674895 AGATCTGCACAAAGGACGCC 60.675 55.000 0.00 0.00 0.00 5.68
4760 7501 4.344865 GCCGCCCCAGTTTCCTCA 62.345 66.667 0.00 0.00 0.00 3.86
4862 7605 2.356313 AGGAGCAGCAACGTCACG 60.356 61.111 0.00 0.00 0.00 4.35
4891 7634 1.812686 AACTCGCACCGGCTTGTCTA 61.813 55.000 0.00 0.00 38.10 2.59
4932 7675 0.689080 TGCTGTCTCCTCTCCCCATC 60.689 60.000 0.00 0.00 0.00 3.51
4933 7676 0.398381 GCTGTCTCCTCTCCCCATCT 60.398 60.000 0.00 0.00 0.00 2.90
4934 7677 1.703411 CTGTCTCCTCTCCCCATCTC 58.297 60.000 0.00 0.00 0.00 2.75
4935 7678 0.263172 TGTCTCCTCTCCCCATCTCC 59.737 60.000 0.00 0.00 0.00 3.71
4936 7679 0.471022 GTCTCCTCTCCCCATCTCCC 60.471 65.000 0.00 0.00 0.00 4.30
4937 7680 1.152139 CTCCTCTCCCCATCTCCCC 60.152 68.421 0.00 0.00 0.00 4.81
4938 7681 1.946707 TCCTCTCCCCATCTCCCCA 60.947 63.158 0.00 0.00 0.00 4.96
4939 7682 1.241327 CCTCTCCCCATCTCCCCAT 59.759 63.158 0.00 0.00 0.00 4.00
5064 7807 3.077359 AGCTTTAGGTCAGTTGATGTGC 58.923 45.455 0.00 0.00 0.00 4.57
5089 7832 2.159761 TCGCGTTGCTACAATTAACTGC 60.160 45.455 5.77 0.00 0.00 4.40
5093 7836 4.142988 GCGTTGCTACAATTAACTGCTGTA 60.143 41.667 0.00 0.00 0.00 2.74
5123 8196 5.013913 AGCTGATGTTTAGGATGGCTATCAT 59.986 40.000 12.54 7.48 39.13 2.45
5306 8379 6.951198 ACTTGGTTTTGATTATATGGTGGTCA 59.049 34.615 0.00 0.00 0.00 4.02
5365 8438 0.442310 CGTCTGGTTACATTGGCACG 59.558 55.000 0.00 0.00 0.00 5.34
5375 8448 2.838736 ACATTGGCACGATATGACTCC 58.161 47.619 4.00 0.00 37.17 3.85
5377 8450 1.199615 TTGGCACGATATGACTCCCA 58.800 50.000 0.00 0.00 37.17 4.37
5694 8767 6.588756 TGGTGTCGAGACATTTAAGTATGAAC 59.411 38.462 15.28 0.00 43.97 3.18
5715 8788 5.255710 ACCAGTCATTAGTCTTGAGATCG 57.744 43.478 0.00 0.00 0.00 3.69
5985 9141 2.996249 TGAATCTCTCCATGTGCCTC 57.004 50.000 0.00 0.00 0.00 4.70
6021 9177 6.970484 ACTTGTGGTGAATAACTTCATGTTC 58.030 36.000 0.00 0.00 43.08 3.18
6277 9476 5.473504 GGCCGAATCATATGGTTCACTAAAT 59.526 40.000 24.75 0.00 0.00 1.40
6603 9924 2.223688 TGCACCACAAGTTGCATAACAC 60.224 45.455 1.81 0.00 39.30 3.32
6605 9926 1.606668 ACCACAAGTTGCATAACACGG 59.393 47.619 1.81 0.00 39.30 4.94
6685 10007 5.171476 TGAACTAAAGCTTCATTCTCCTCG 58.829 41.667 0.00 0.00 0.00 4.63
6800 10122 4.827284 CCACAACACTGAAACCCTAGAAAT 59.173 41.667 0.00 0.00 0.00 2.17
6881 10204 1.305930 GGCCAGAACGCCTACTTTGG 61.306 60.000 0.00 0.00 46.10 3.28
6891 10214 1.210478 GCCTACTTTGGAGCTGGATCA 59.790 52.381 0.00 0.00 0.00 2.92
6964 10287 3.392616 ACAATGAGACACCTTCTGGTCTT 59.607 43.478 0.00 0.00 46.60 3.01
6967 10290 3.165875 TGAGACACCTTCTGGTCTTAGG 58.834 50.000 0.00 0.00 46.60 2.69
7042 10365 3.775661 TGCATTCATCTGCATCTGTTG 57.224 42.857 0.00 0.00 46.76 3.33
7141 10464 4.406456 TCCATAAGCTTGTTTGTCACCAT 58.594 39.130 9.86 0.00 0.00 3.55
7353 10681 6.291955 CGTACGAAAAGCAGAGTGAACTTTTA 60.292 38.462 10.44 0.00 42.16 1.52
7354 10682 6.619801 ACGAAAAGCAGAGTGAACTTTTAT 57.380 33.333 0.00 0.00 42.16 1.40
7355 10683 7.027778 ACGAAAAGCAGAGTGAACTTTTATT 57.972 32.000 0.00 0.00 42.16 1.40
7356 10684 7.480810 ACGAAAAGCAGAGTGAACTTTTATTT 58.519 30.769 0.00 0.00 42.16 1.40
7357 10685 7.973944 ACGAAAAGCAGAGTGAACTTTTATTTT 59.026 29.630 0.00 0.00 42.16 1.82
7401 10729 6.825721 TCCTTCAGAGAAATGCTTTATCCTTC 59.174 38.462 0.00 0.00 31.44 3.46
8203 11531 2.903784 GGGAAAGGGTAAGGTTGCAAAT 59.096 45.455 0.00 0.00 0.00 2.32
8497 11825 5.069318 TCTCAACATACCTTGAAATGCACA 58.931 37.500 0.00 0.00 29.66 4.57
8570 12176 3.849911 GGCTAACCTTCAAAATTCTGGC 58.150 45.455 0.00 0.00 0.00 4.85
8627 12235 6.518493 AGCCTTGAACGGTAAATCGATTATA 58.482 36.000 11.83 3.73 0.00 0.98
8628 12236 6.645415 AGCCTTGAACGGTAAATCGATTATAG 59.355 38.462 11.83 6.22 0.00 1.31
8630 12238 7.042254 GCCTTGAACGGTAAATCGATTATAGTT 60.042 37.037 11.83 14.48 32.40 2.24
8631 12239 8.823818 CCTTGAACGGTAAATCGATTATAGTTT 58.176 33.333 11.83 2.65 30.96 2.66
8680 12412 3.198872 GCTTTTCCCTCTTCCGTATCAG 58.801 50.000 0.00 0.00 0.00 2.90
8687 12419 3.322254 CCCTCTTCCGTATCAGCATAGTT 59.678 47.826 0.00 0.00 0.00 2.24
8694 12426 5.680619 TCCGTATCAGCATAGTTCCATTTT 58.319 37.500 0.00 0.00 0.00 1.82
8739 12471 5.828328 AGAGTACTTTTTAAGCAGCTTTGGT 59.172 36.000 14.29 7.96 0.00 3.67
8779 12511 0.106769 TTTTCCACTGAGCACTGGCA 60.107 50.000 0.00 0.00 44.61 4.92
8895 12627 8.739039 ACTCTAATATCATCACTGATCAGCTAC 58.261 37.037 22.83 0.00 41.29 3.58
8900 12632 6.922247 ATCATCACTGATCAGCTACAAAAG 57.078 37.500 22.83 5.13 37.58 2.27
8935 12667 3.113477 TTCCCTTGGCCCAACCCA 61.113 61.111 0.00 0.00 37.83 4.51
8957 12689 2.282040 AAGCTCTGCCAGTGCCAC 60.282 61.111 14.68 0.00 35.47 5.01
8966 12698 2.821366 CAGTGCCACGGAGGATGC 60.821 66.667 0.00 0.00 41.22 3.91
8978 12710 1.283321 GGAGGATGCTTCTTCCCTTGT 59.717 52.381 17.30 0.00 41.23 3.16
8985 12717 1.613925 GCTTCTTCCCTTGTTCCCAAC 59.386 52.381 0.00 0.00 0.00 3.77
8993 12762 1.142474 CTTGTTCCCAACGTACGACC 58.858 55.000 24.41 1.76 0.00 4.79
9078 12847 3.575630 TGTTGAGTCTAATCGTGCAGTC 58.424 45.455 0.00 0.00 0.00 3.51
9080 12849 4.177026 GTTGAGTCTAATCGTGCAGTCAT 58.823 43.478 0.00 0.00 0.00 3.06
9087 12856 0.746659 ATCGTGCAGTCATCGGATGA 59.253 50.000 16.44 16.44 36.84 2.92
9201 12970 9.394477 GTAAAGTTGACTGGAACATTACAATTC 57.606 33.333 11.69 0.00 38.75 2.17
9239 13008 7.262048 ACAAAGTGTAAACTACCCAACATTTG 58.738 34.615 0.00 0.00 32.65 2.32
9257 13026 7.900782 ACATTTGGTGTACTATATATTCGCC 57.099 36.000 0.00 0.00 39.91 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.568612 CGCGAGCAAGAGGAAGCAAA 61.569 55.000 0.00 0.00 0.00 3.68
44 45 2.029288 CGCGAGCAAGAGGAAGCAA 61.029 57.895 0.00 0.00 0.00 3.91
101 102 3.367646 TGTTCTAGACGAGGAGGATGT 57.632 47.619 0.00 0.00 0.00 3.06
115 116 3.628942 GCATGGCTTGATCACATGTTCTA 59.371 43.478 20.02 0.00 42.89 2.10
154 170 1.008327 TCTTCTCCTATGCCTCCACCA 59.992 52.381 0.00 0.00 0.00 4.17
165 181 0.540454 TCTCGCCGTCTCTTCTCCTA 59.460 55.000 0.00 0.00 0.00 2.94
203 219 4.796231 CTCTTCCCCGTGTCGCCG 62.796 72.222 0.00 0.00 0.00 6.46
224 428 1.490574 CCTCGTCTCTTTCCATCCCT 58.509 55.000 0.00 0.00 0.00 4.20
246 450 6.549364 TCTCCTGTGAAAATATCTCCTCTCTC 59.451 42.308 0.00 0.00 0.00 3.20
250 454 5.221621 CCCTCTCCTGTGAAAATATCTCCTC 60.222 48.000 0.00 0.00 0.00 3.71
251 455 4.657969 CCCTCTCCTGTGAAAATATCTCCT 59.342 45.833 0.00 0.00 0.00 3.69
299 511 1.098050 GCGACCAAGAAGGCAATCAT 58.902 50.000 0.00 0.00 43.14 2.45
329 541 1.541588 AGTTTTGCCTCCTTTCGATGC 59.458 47.619 0.00 0.00 33.07 3.91
332 545 2.218603 GTGAGTTTTGCCTCCTTTCGA 58.781 47.619 0.00 0.00 0.00 3.71
360 573 2.874701 CTCATTACCAATTGCCTCGAGG 59.125 50.000 27.83 27.83 38.53 4.63
372 585 2.042297 TGACAATTGGGCCTCATTACCA 59.958 45.455 10.83 2.31 0.00 3.25
378 591 2.040947 TGTACATGACAATTGGGCCTCA 59.959 45.455 10.83 4.65 34.15 3.86
396 609 9.491675 TTTACATCCGTATTTCACTTTTCTGTA 57.508 29.630 0.00 0.00 0.00 2.74
411 624 1.113788 CCCTCCGGTTTACATCCGTA 58.886 55.000 0.00 0.00 45.63 4.02
468 683 4.246206 TCGCACGATCTACCGGCG 62.246 66.667 0.00 0.00 44.36 6.46
471 686 2.025727 GGGTCGCACGATCTACCG 59.974 66.667 3.00 0.00 32.53 4.02
486 701 3.702048 TCGGCCGTTCCTTCTGGG 61.702 66.667 27.15 0.00 0.00 4.45
517 732 1.301795 GCTAGCCTACCCGCCATTC 60.302 63.158 2.29 0.00 0.00 2.67
575 819 7.496263 GGTTTCTTGGCACCAGTTTTTATTTTA 59.504 33.333 0.00 0.00 32.74 1.52
579 823 4.407296 TGGTTTCTTGGCACCAGTTTTTAT 59.593 37.500 0.00 0.00 38.20 1.40
695 3373 3.279434 GTCAGTGTGAGACAAAAAGGGT 58.721 45.455 0.00 0.00 36.06 4.34
1471 4149 9.832445 TCACATGAGTAAGTATTAAATCCTTCC 57.168 33.333 0.00 0.00 28.70 3.46
1504 4182 4.892934 ACTATTCTAGGTGAAGGAGCAGAG 59.107 45.833 0.00 0.00 38.18 3.35
1585 4263 4.113354 CTGGTAGGATAAAGCTGAACGTC 58.887 47.826 0.00 0.00 0.00 4.34
1691 4369 8.053355 CCCTTTCTAGTATATCCCAACAAACTT 58.947 37.037 0.00 0.00 0.00 2.66
1717 4431 4.739046 AATCAGCGCAAAGATATGCTAC 57.261 40.909 11.47 0.00 44.21 3.58
1731 4445 5.823045 AGAATAAAGGGGAACTAAATCAGCG 59.177 40.000 0.00 0.00 0.00 5.18
1809 4524 1.065401 CTTCGCAACAAGGTTTCTGCA 59.935 47.619 0.00 0.00 34.39 4.41
1825 4540 7.903431 CCTGAAATCTAAAAATACCGAACTTCG 59.097 37.037 4.07 4.07 40.07 3.79
1832 4547 9.379791 ACTAAGTCCTGAAATCTAAAAATACCG 57.620 33.333 0.00 0.00 0.00 4.02
1911 4626 4.455877 ACAAAGATGAACAATCGGGACTTC 59.544 41.667 0.00 0.00 40.54 3.01
2208 4927 7.487829 TCAAACAATCAACTGTAAAAGAAGTGC 59.512 33.333 0.00 0.00 0.00 4.40
2296 5016 5.123820 CGCCTTGGAGATAGATTCAACAAAA 59.876 40.000 0.00 0.00 0.00 2.44
2420 5140 6.610741 GATTAGCTTTCCACTAATCCACTG 57.389 41.667 10.91 0.00 45.33 3.66
2455 5175 9.716531 CCAGAATATTCATGTTAGCTTCAGATA 57.283 33.333 17.56 0.00 0.00 1.98
2557 5277 6.064060 CACAATTCCTAGAAGCATTATCCCA 58.936 40.000 0.00 0.00 0.00 4.37
2774 5495 6.474140 TCATGAAGCCAATCAGCAAATATT 57.526 33.333 0.00 0.00 31.76 1.28
2811 5532 6.815641 CACTTCAGCTGCTAAATCTTCTCTAA 59.184 38.462 9.47 0.00 0.00 2.10
2886 5607 4.947388 ACAGGAGTGCTTCACTTTAACAAA 59.053 37.500 0.66 0.00 45.44 2.83
2984 5705 7.541162 TCATTTTGAAGCTAGGATGACAAATG 58.459 34.615 0.00 0.00 0.00 2.32
3156 5880 7.820578 TTTATTTAAACAGGGTTTTCTCGGA 57.179 32.000 0.00 0.00 0.00 4.55
3219 5943 8.023706 GGTTGCTTAAACAAGAGATCTTTTAGG 58.976 37.037 0.00 0.00 40.86 2.69
3262 5986 2.487762 CGAGGAAGTTTGCAGGCATTTA 59.512 45.455 0.00 0.00 0.00 1.40
3796 6520 1.074405 ACTCCTGCCAGATGCTCAAAA 59.926 47.619 0.00 0.00 42.00 2.44
3850 6574 3.381590 CAGGCCAGTTTTCCTTATTAGGC 59.618 47.826 5.01 0.00 41.69 3.93
3872 6596 6.303259 GTGTGAAGTTAAGTTGCATCGATTTC 59.697 38.462 0.00 0.00 0.00 2.17
3876 6600 4.025229 GTGTGTGAAGTTAAGTTGCATCGA 60.025 41.667 0.00 0.00 0.00 3.59
3902 6626 4.400961 GGCGCAGTCTCAGGGCTT 62.401 66.667 10.83 0.00 43.57 4.35
3926 6650 2.156098 TGGATTACAAAGTTGTCGGCC 58.844 47.619 0.00 0.00 42.35 6.13
3968 6709 0.605589 GGTTTGTAAGCCGGAGCACT 60.606 55.000 5.05 0.00 43.56 4.40
4100 6841 2.671070 CAGGTGTGGAAGCCCGAT 59.329 61.111 0.00 0.00 34.29 4.18
4224 6965 3.423154 CGGCCTCAAGTCCGTTGC 61.423 66.667 0.00 0.00 40.72 4.17
4243 6984 2.214216 TCGTTGGCTAGGCAGGTGT 61.214 57.895 19.32 0.00 0.00 4.16
4264 7005 1.268743 GCTTGTGTTGTCCTGCAGTTC 60.269 52.381 13.81 5.71 0.00 3.01
4347 7088 4.527157 GAGGCGTCGTACCCGTCG 62.527 72.222 0.00 0.00 45.94 5.12
4348 7089 3.105852 GAGAGGCGTCGTACCCGTC 62.106 68.421 0.00 0.00 35.01 4.79
4370 7111 0.762418 TTGAGTTCTCCGGCCAAGAA 59.238 50.000 12.42 12.42 0.00 2.52
4371 7112 0.321671 CTTGAGTTCTCCGGCCAAGA 59.678 55.000 2.24 1.31 37.10 3.02
4388 7129 1.759445 CTCCCTCGTCATGTGGATCTT 59.241 52.381 0.00 0.00 32.77 2.40
4396 7137 0.176680 CCTTCACCTCCCTCGTCATG 59.823 60.000 0.00 0.00 0.00 3.07
4402 7143 2.285743 AGCCCCTTCACCTCCCTC 60.286 66.667 0.00 0.00 0.00 4.30
4473 7214 2.350895 CTGGCACCAACCCGATCA 59.649 61.111 0.00 0.00 0.00 2.92
4488 7229 1.163554 GAGCTCCAAGTGAAAGCCTG 58.836 55.000 0.87 0.00 36.69 4.85
4565 7306 1.268113 CGGCATGTTGTTTGTGACGC 61.268 55.000 0.00 0.00 37.58 5.19
4610 7351 3.244078 GGTTGACTATATGCCGTGGATGA 60.244 47.826 0.00 0.00 0.00 2.92
4680 7421 3.660111 GCGGGTTGGCACACACTC 61.660 66.667 0.00 0.00 39.29 3.51
4681 7422 4.497984 TGCGGGTTGGCACACACT 62.498 61.111 0.00 0.00 39.29 3.55
4689 7430 4.659172 TGGCCTCTTGCGGGTTGG 62.659 66.667 3.32 0.00 42.61 3.77
4714 7455 1.079127 CAGATCCGGCGTCCTTTGT 60.079 57.895 6.01 0.00 0.00 2.83
4760 7501 1.475403 CGTGGATCCTGTAGTCCAGT 58.525 55.000 14.23 0.00 44.71 4.00
4766 7507 1.804372 GCTTCAGCGTGGATCCTGTAG 60.804 57.143 14.23 7.11 31.92 2.74
4767 7508 0.175760 GCTTCAGCGTGGATCCTGTA 59.824 55.000 14.23 0.00 0.00 2.74
4835 7578 4.504916 CTGCTCCTCTGGACGGCG 62.505 72.222 4.80 4.80 0.00 6.46
4862 7605 2.412325 CCGGTGCGAGTTCACAATTAAC 60.412 50.000 0.00 0.00 38.66 2.01
4932 7675 5.584913 ACTCATAGGTCATAGTATGGGGAG 58.415 45.833 10.26 9.95 32.21 4.30
4933 7676 5.616975 ACTCATAGGTCATAGTATGGGGA 57.383 43.478 10.26 0.00 32.21 4.81
4934 7677 7.792364 TTTACTCATAGGTCATAGTATGGGG 57.208 40.000 10.26 0.00 32.21 4.96
4935 7678 7.819900 GCTTTTACTCATAGGTCATAGTATGGG 59.180 40.741 10.26 0.00 33.89 4.00
4936 7679 8.589338 AGCTTTTACTCATAGGTCATAGTATGG 58.411 37.037 10.26 0.00 0.00 2.74
4937 7680 9.416794 CAGCTTTTACTCATAGGTCATAGTATG 57.583 37.037 3.55 3.55 0.00 2.39
4938 7681 9.148879 ACAGCTTTTACTCATAGGTCATAGTAT 57.851 33.333 0.00 0.00 0.00 2.12
4939 7682 8.534954 ACAGCTTTTACTCATAGGTCATAGTA 57.465 34.615 0.00 0.00 0.00 1.82
5089 7832 6.582636 TCCTAAACATCAGCTATTGGTACAG 58.417 40.000 0.00 0.00 42.39 2.74
5093 7836 5.380043 CCATCCTAAACATCAGCTATTGGT 58.620 41.667 0.00 0.00 0.00 3.67
5123 8196 5.401531 AAGTTCGAATGGCTCACTAGTAA 57.598 39.130 0.00 0.00 0.00 2.24
5236 8309 8.732531 CATAAATCATACCATGCATGTGTCATA 58.267 33.333 24.58 9.56 0.00 2.15
5298 8371 4.986054 AAGGTGTTAACTATGACCACCA 57.014 40.909 13.59 0.00 33.99 4.17
5365 8438 3.822996 CGTCATACGTGGGAGTCATATC 58.177 50.000 0.00 0.00 36.74 1.63
5553 8626 3.408229 ACATCTGTGAGGCAGGGG 58.592 61.111 0.00 0.00 45.08 4.79
5694 8767 5.506686 TCGATCTCAAGACTAATGACTGG 57.493 43.478 0.00 0.00 0.00 4.00
5970 9126 2.836636 AGTAGAGGCACATGGAGAGA 57.163 50.000 0.00 0.00 0.00 3.10
5985 9141 4.883083 TCACCACAAGTTAGCTGAAGTAG 58.117 43.478 0.00 0.00 0.00 2.57
6190 9347 6.346096 TGGTGGCAGATCTTATAACAAGTAC 58.654 40.000 0.00 0.00 0.00 2.73
6277 9476 5.982516 CCAAACTGACAAAATTCATTCCGAA 59.017 36.000 0.00 0.00 38.22 4.30
6290 9489 7.051623 ACTGAACAAGTATACCAAACTGACAA 58.948 34.615 0.00 0.00 37.36 3.18
6327 9526 2.115266 ACCCTTCCCAAGTTGCGG 59.885 61.111 0.00 0.58 0.00 5.69
6470 9669 6.348540 CGCTTTAAGCACTTAAAAGGTGAGAT 60.349 38.462 17.51 0.00 42.58 2.75
6576 9897 3.949132 TGCAACTTGTGGTGCATCTATA 58.051 40.909 4.52 0.00 31.01 1.31
6580 9901 3.244976 GTTATGCAACTTGTGGTGCATC 58.755 45.455 22.33 8.13 40.41 3.91
6603 9924 4.034048 CCTATGCTTTGCTAACAGTTACCG 59.966 45.833 0.00 0.00 0.00 4.02
6605 9926 4.201920 GGCCTATGCTTTGCTAACAGTTAC 60.202 45.833 0.00 0.00 37.74 2.50
6685 10007 9.856488 TTTGAAGCTATGGAACGATATATAGAC 57.144 33.333 0.00 0.00 0.00 2.59
6730 10052 5.574443 GCAAATTAGGAAAGAGATGTGCAAC 59.426 40.000 0.00 0.00 37.35 4.17
6846 10168 4.104086 TCTGGCCAGATTTAGAGAGGAAA 58.896 43.478 32.00 3.90 31.41 3.13
6881 10204 3.072944 GCTACATCCAATGATCCAGCTC 58.927 50.000 0.00 0.00 34.31 4.09
6891 10214 5.130975 TCATGGTGAGTTAGCTACATCCAAT 59.869 40.000 0.00 0.00 30.90 3.16
7042 10365 4.329462 TGAACTACAACCCAATTTTGCC 57.671 40.909 0.00 0.00 0.00 4.52
7141 10464 6.602410 TTCAACTATTTCCATTGCCATCAA 57.398 33.333 0.00 0.00 36.51 2.57
7441 10769 2.825532 GCAAAGTTCTTGGAATGCCCTA 59.174 45.455 0.00 0.00 35.38 3.53
7675 11003 4.883354 GGAGCATGGGGAAGGGCG 62.883 72.222 0.00 0.00 0.00 6.13
7954 11282 0.393077 AGAAGGACGTCAGGTTGTGG 59.607 55.000 18.91 0.00 0.00 4.17
8203 11531 0.609957 CCCTTTGATGTGCTGCTCCA 60.610 55.000 0.00 0.00 0.00 3.86
8385 11713 6.639279 AGCGCAAGAATAATAAACAAAACGTT 59.361 30.769 11.47 0.00 38.94 3.99
8386 11714 6.087555 CAGCGCAAGAATAATAAACAAAACGT 59.912 34.615 11.47 0.00 43.02 3.99
8560 12166 3.716601 CAACCGAACTTGCCAGAATTTT 58.283 40.909 0.00 0.00 0.00 1.82
8627 12235 0.834612 TCCTCACAACGGGACAAACT 59.165 50.000 0.00 0.00 0.00 2.66
8628 12236 1.670791 TTCCTCACAACGGGACAAAC 58.329 50.000 0.00 0.00 0.00 2.93
8630 12238 2.621055 CAAATTCCTCACAACGGGACAA 59.379 45.455 0.00 0.00 0.00 3.18
8631 12239 2.226330 CAAATTCCTCACAACGGGACA 58.774 47.619 0.00 0.00 0.00 4.02
8680 12412 7.009174 CGTGAATAACCAAAAATGGAACTATGC 59.991 37.037 1.10 0.00 0.00 3.14
8687 12419 7.661968 TGAAATCGTGAATAACCAAAAATGGA 58.338 30.769 1.10 0.00 0.00 3.41
8694 12426 7.936584 ACTCTTTTGAAATCGTGAATAACCAA 58.063 30.769 0.00 0.00 0.00 3.67
8729 12461 1.599071 GAAGCCAAAAACCAAAGCTGC 59.401 47.619 0.00 0.00 33.18 5.25
8739 12471 8.079203 GGAAAAGAAAAACAAAGAAGCCAAAAA 58.921 29.630 0.00 0.00 0.00 1.94
8779 12511 2.735126 CGTCCTTGTTTGTGCAAGCTTT 60.735 45.455 0.00 0.00 43.17 3.51
8890 12622 3.526019 TGCCCCCTTATACTTTTGTAGCT 59.474 43.478 0.00 0.00 38.44 3.32
8892 12624 6.039382 GTCAATGCCCCCTTATACTTTTGTAG 59.961 42.308 0.00 0.00 38.44 2.74
8895 12627 4.956075 AGTCAATGCCCCCTTATACTTTTG 59.044 41.667 0.00 0.00 0.00 2.44
8900 12632 3.487372 GGAAGTCAATGCCCCCTTATAC 58.513 50.000 0.00 0.00 0.00 1.47
8935 12667 0.886563 GCACTGGCAGAGCTTCATTT 59.113 50.000 26.50 0.00 40.72 2.32
8957 12689 0.543749 AAGGGAAGAAGCATCCTCCG 59.456 55.000 0.65 0.00 37.09 4.63
8978 12710 3.442441 ACGGTCGTACGTTGGGAA 58.558 55.556 16.05 0.00 46.25 3.97
8993 12762 3.800506 GGTACATCCATCGTAGGAAAACG 59.199 47.826 2.88 0.00 41.92 3.60
9000 12769 2.502213 TTGCGGTACATCCATCGTAG 57.498 50.000 0.00 0.00 35.57 3.51
9078 12847 7.997107 AAAATTCATCATTTGTCATCCGATG 57.003 32.000 1.55 1.55 35.09 3.84
9140 12909 7.875327 AAAACTCTAATGTGTGTTACAGGTT 57.125 32.000 0.00 0.00 43.80 3.50
9142 12911 9.825972 CAATAAAACTCTAATGTGTGTTACAGG 57.174 33.333 0.00 0.00 43.80 4.00
9175 12944 9.394477 GAATTGTAATGTTCCAGTCAACTTTAC 57.606 33.333 12.04 12.04 42.14 2.01
9201 12970 9.931210 AGTTTACACTTTGTTCTTATTCTTTCG 57.069 29.630 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.