Multiple sequence alignment - TraesCS6B01G331900

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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 TraesCS6B01G331900 chr6B 100.000 3517 0 0 1 3517 583337091 583333575 0.000000e+00 6495.0
1 TraesCS6B01G331900 chr6B 76.450 845 117 41 1693 2483 575315408 575316224 1.980000e-102 383.0
2 TraesCS6B01G331900 chr6B 76.736 821 105 49 1620 2382 575321856 575322648 2.560000e-101 379.0
3 TraesCS6B01G331900 chr6B 85.990 207 22 5 45 249 575313681 575313882 7.650000e-52 215.0
4 TraesCS6B01G331900 chr6B 86.503 163 15 4 45 202 575320488 575320648 4.670000e-39 172.0
5 TraesCS6B01G331900 chr6D 89.536 2886 136 64 737 3517 389653357 389650533 0.000000e+00 3504.0
6 TraesCS6B01G331900 chr6D 75.309 1863 255 95 634 2389 385222406 385224170 0.000000e+00 702.0
7 TraesCS6B01G331900 chr6D 76.960 842 112 48 1693 2483 385166006 385166816 4.230000e-109 405.0
8 TraesCS6B01G331900 chr6D 85.646 209 21 6 44 249 385221717 385221919 9.890000e-51 211.0
9 TraesCS6B01G331900 chr6D 84.135 208 25 5 45 249 385163932 385164134 9.960000e-46 195.0
10 TraesCS6B01G331900 chr6D 83.243 185 18 7 570 741 389653734 389653550 1.310000e-34 158.0
11 TraesCS6B01G331900 chr6A 88.554 1293 60 29 1608 2848 536024064 536022808 0.000000e+00 1487.0
12 TraesCS6B01G331900 chr6A 90.527 929 34 27 706 1582 536024991 536024065 0.000000e+00 1179.0
13 TraesCS6B01G331900 chr6A 87.784 573 33 9 706 1242 536031713 536031142 1.380000e-178 636.0
14 TraesCS6B01G331900 chr6A 84.981 526 67 8 3 526 536032324 536031809 1.120000e-144 523.0
15 TraesCS6B01G331900 chr6A 84.791 526 68 8 3 526 536025602 536025087 5.200000e-143 518.0
16 TraesCS6B01G331900 chr6A 82.560 539 45 24 3011 3517 536022738 536022217 2.510000e-116 429.0
17 TraesCS6B01G331900 chr6A 76.659 844 118 42 1693 2484 529287927 529288743 9.150000e-106 394.0
18 TraesCS6B01G331900 chr6A 76.711 833 95 52 1620 2388 529485955 529486752 4.290000e-99 372.0
19 TraesCS6B01G331900 chr6A 75.467 750 89 46 1620 2312 529560062 529560773 9.620000e-71 278.0
20 TraesCS6B01G331900 chr6A 86.875 160 16 3 46 202 529374830 529374987 1.300000e-39 174.0
21 TraesCS6B01G331900 chr3B 94.444 36 2 0 525 560 76111976 76112011 4.900000e-04 56.5
22 TraesCS6B01G331900 chr4D 94.118 34 2 0 519 552 304885622 304885655 6.000000e-03 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 TraesCS6B01G331900 chr6B 583333575 583337091 3516 True 6495.00 6495 100.0000 1 3517 1 chr6B.!!$R1 3516
1 TraesCS6B01G331900 chr6B 575313681 575316224 2543 False 299.00 383 81.2200 45 2483 2 chr6B.!!$F1 2438
2 TraesCS6B01G331900 chr6B 575320488 575322648 2160 False 275.50 379 81.6195 45 2382 2 chr6B.!!$F2 2337
3 TraesCS6B01G331900 chr6D 389650533 389653734 3201 True 1831.00 3504 86.3895 570 3517 2 chr6D.!!$R1 2947
4 TraesCS6B01G331900 chr6D 385221717 385224170 2453 False 456.50 702 80.4775 44 2389 2 chr6D.!!$F2 2345
5 TraesCS6B01G331900 chr6D 385163932 385166816 2884 False 300.00 405 80.5475 45 2483 2 chr6D.!!$F1 2438
6 TraesCS6B01G331900 chr6A 536022217 536025602 3385 True 903.25 1487 86.6080 3 3517 4 chr6A.!!$R1 3514
7 TraesCS6B01G331900 chr6A 536031142 536032324 1182 True 579.50 636 86.3825 3 1242 2 chr6A.!!$R2 1239
8 TraesCS6B01G331900 chr6A 529287927 529288743 816 False 394.00 394 76.6590 1693 2484 1 chr6A.!!$F1 791
9 TraesCS6B01G331900 chr6A 529485955 529486752 797 False 372.00 372 76.7110 1620 2388 1 chr6A.!!$F3 768
10 TraesCS6B01G331900 chr6A 529560062 529560773 711 False 278.00 278 75.4670 1620 2312 1 chr6A.!!$F4 692

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
375 935 0.108804 CTCCCATCGTAAGTGTGCGT 60.109 55.0 0.0 0.0 39.48 5.24 F
672 1292 0.178068 TAGAGCAGCCATTTCCCGTC 59.822 55.0 0.0 0.0 0.00 4.79 F
1600 2520 0.685660 GGTCTCGGTTCTCCTGGTTT 59.314 55.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 2310 0.680618 TGGCCAAAAATCACCAGCAG 59.319 50.000 0.61 0.0 0.00 4.24 R
2170 3174 1.062886 TGCAGGAGCTAGATGGTACCT 60.063 52.381 14.36 0.0 42.74 3.08 R
3377 4458 0.249531 TCGCCGTTTGTTCTGCAGTA 60.250 50.000 14.67 0.0 0.00 2.74 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
157 163 1.675714 CGTGCCAGATAAGTGCTCCAA 60.676 52.381 0.00 0.00 0.00 3.53
204 210 4.504461 CGTCAGTCTATCAAGCCACATAAC 59.496 45.833 0.00 0.00 0.00 1.89
205 211 4.504461 GTCAGTCTATCAAGCCACATAACG 59.496 45.833 0.00 0.00 0.00 3.18
206 212 3.246226 CAGTCTATCAAGCCACATAACGC 59.754 47.826 0.00 0.00 0.00 4.84
225 231 3.784338 CGCCACCCGTCTATTAAAAGTA 58.216 45.455 0.00 0.00 0.00 2.24
231 609 4.406972 ACCCGTCTATTAAAAGTACTCCCC 59.593 45.833 0.00 0.00 0.00 4.81
236 614 7.148356 CCGTCTATTAAAAGTACTCCCCAAAAC 60.148 40.741 0.00 0.00 0.00 2.43
241 619 3.782656 AAGTACTCCCCAAAACGATGT 57.217 42.857 0.00 0.00 0.00 3.06
249 627 2.819608 CCCCAAAACGATGTGAGTGAAT 59.180 45.455 0.00 0.00 0.00 2.57
259 637 4.034858 CGATGTGAGTGAATCCAAATCTGG 59.965 45.833 0.00 0.00 45.08 3.86
264 642 0.810648 TGAATCCAAATCTGGCGTGC 59.189 50.000 0.00 0.00 43.17 5.34
266 644 1.656818 AATCCAAATCTGGCGTGCCG 61.657 55.000 6.37 1.46 43.17 5.69
301 787 2.897969 ACACGACCTGAACTCCACTATT 59.102 45.455 0.00 0.00 0.00 1.73
359 919 4.368391 CGCAGCCCACATATCTCC 57.632 61.111 0.00 0.00 0.00 3.71
364 924 0.979665 AGCCCACATATCTCCCATCG 59.020 55.000 0.00 0.00 0.00 3.84
368 928 3.617531 GCCCACATATCTCCCATCGTAAG 60.618 52.174 0.00 0.00 0.00 2.34
375 935 0.108804 CTCCCATCGTAAGTGTGCGT 60.109 55.000 0.00 0.00 39.48 5.24
401 977 4.441495 CGAAACTCTCATGCCACCAGTATA 60.441 45.833 0.00 0.00 0.00 1.47
404 980 5.991933 ACTCTCATGCCACCAGTATATAG 57.008 43.478 0.00 0.00 0.00 1.31
406 982 6.259893 ACTCTCATGCCACCAGTATATAGAT 58.740 40.000 0.00 0.00 0.00 1.98
407 983 6.379703 ACTCTCATGCCACCAGTATATAGATC 59.620 42.308 0.00 0.00 0.00 2.75
409 985 6.725834 TCTCATGCCACCAGTATATAGATCAA 59.274 38.462 0.00 0.00 0.00 2.57
472 1049 6.798476 GCAACATGGATCATAATAACGTGATG 59.202 38.462 0.00 0.00 35.33 3.07
485 1062 7.603963 AATAACGTGATGCTGTGTTATGTTA 57.396 32.000 0.00 0.00 37.52 2.41
486 1063 5.933187 AACGTGATGCTGTGTTATGTTAA 57.067 34.783 0.00 0.00 0.00 2.01
487 1064 5.277601 ACGTGATGCTGTGTTATGTTAAC 57.722 39.130 0.00 0.00 0.00 2.01
488 1065 4.752604 ACGTGATGCTGTGTTATGTTAACA 59.247 37.500 11.41 11.41 0.00 2.41
489 1066 5.411361 ACGTGATGCTGTGTTATGTTAACAT 59.589 36.000 23.80 23.80 40.22 2.71
490 1067 5.959527 CGTGATGCTGTGTTATGTTAACATC 59.040 40.000 24.00 11.83 37.76 3.06
491 1068 6.402011 CGTGATGCTGTGTTATGTTAACATCA 60.402 38.462 24.00 14.27 40.06 3.07
492 1069 7.304735 GTGATGCTGTGTTATGTTAACATCAA 58.695 34.615 24.00 13.66 42.87 2.57
493 1070 7.807433 GTGATGCTGTGTTATGTTAACATCAAA 59.193 33.333 24.00 11.63 42.87 2.69
494 1071 8.522003 TGATGCTGTGTTATGTTAACATCAAAT 58.478 29.630 24.00 11.87 39.57 2.32
529 1106 8.776376 TTATTCGGTTTTATTACTTTCTCCGT 57.224 30.769 0.00 0.00 38.21 4.69
530 1107 7.677454 ATTCGGTTTTATTACTTTCTCCGTT 57.323 32.000 0.00 0.00 38.21 4.44
531 1108 6.470557 TCGGTTTTATTACTTTCTCCGTTG 57.529 37.500 0.00 0.00 38.21 4.10
532 1109 5.084055 CGGTTTTATTACTTTCTCCGTTGC 58.916 41.667 0.00 0.00 33.39 4.17
533 1110 5.334260 CGGTTTTATTACTTTCTCCGTTGCA 60.334 40.000 0.00 0.00 33.39 4.08
534 1111 6.617879 GGTTTTATTACTTTCTCCGTTGCAT 58.382 36.000 0.00 0.00 0.00 3.96
535 1112 7.413219 CGGTTTTATTACTTTCTCCGTTGCATA 60.413 37.037 0.00 0.00 33.39 3.14
536 1113 8.238631 GGTTTTATTACTTTCTCCGTTGCATAA 58.761 33.333 0.00 0.00 0.00 1.90
537 1114 9.783256 GTTTTATTACTTTCTCCGTTGCATAAT 57.217 29.630 0.00 0.00 0.00 1.28
544 1121 8.958119 ACTTTCTCCGTTGCATAATATAAGAA 57.042 30.769 0.00 0.00 0.00 2.52
545 1122 8.827677 ACTTTCTCCGTTGCATAATATAAGAAC 58.172 33.333 0.00 0.00 0.00 3.01
546 1123 7.402811 TTCTCCGTTGCATAATATAAGAACG 57.597 36.000 0.00 0.00 36.75 3.95
547 1124 6.509656 TCTCCGTTGCATAATATAAGAACGT 58.490 36.000 0.00 0.00 35.56 3.99
548 1125 6.982141 TCTCCGTTGCATAATATAAGAACGTT 59.018 34.615 0.00 0.00 35.56 3.99
549 1126 7.493320 TCTCCGTTGCATAATATAAGAACGTTT 59.507 33.333 0.46 0.00 35.56 3.60
550 1127 7.976826 TCCGTTGCATAATATAAGAACGTTTT 58.023 30.769 0.46 0.00 35.56 2.43
551 1128 8.452534 TCCGTTGCATAATATAAGAACGTTTTT 58.547 29.630 9.22 9.22 35.56 1.94
552 1129 8.730427 CCGTTGCATAATATAAGAACGTTTTTC 58.270 33.333 7.42 0.00 35.56 2.29
553 1130 9.268255 CGTTGCATAATATAAGAACGTTTTTCA 57.732 29.630 7.42 0.00 33.33 2.69
556 1133 9.284594 TGCATAATATAAGAACGTTTTTCAAGC 57.715 29.630 7.42 5.08 0.00 4.01
557 1134 9.284594 GCATAATATAAGAACGTTTTTCAAGCA 57.715 29.630 7.42 0.00 0.00 3.91
561 1138 9.959749 AATATAAGAACGTTTTTCAAGCAAAGA 57.040 25.926 7.42 0.00 0.00 2.52
562 1139 7.914537 ATAAGAACGTTTTTCAAGCAAAGAG 57.085 32.000 7.42 0.00 0.00 2.85
563 1140 4.105486 AGAACGTTTTTCAAGCAAAGAGC 58.895 39.130 0.46 0.00 46.19 4.09
599 1176 9.877178 CTAACACCAAATATCATACTAGGATCC 57.123 37.037 2.48 2.48 0.00 3.36
600 1177 8.511748 AACACCAAATATCATACTAGGATCCT 57.488 34.615 20.48 20.48 0.00 3.24
603 1180 6.045318 CCAAATATCATACTAGGATCCTGCG 58.955 44.000 25.28 16.89 0.00 5.18
632 1248 1.691196 TTTTTCCTCCACCACAGCAG 58.309 50.000 0.00 0.00 0.00 4.24
641 1261 0.518636 CACCACAGCAGAAACCATCG 59.481 55.000 0.00 0.00 0.00 3.84
672 1292 0.178068 TAGAGCAGCCATTTCCCGTC 59.822 55.000 0.00 0.00 0.00 4.79
673 1293 2.044946 AGCAGCCATTTCCCGTCC 60.045 61.111 0.00 0.00 0.00 4.79
678 1298 1.227383 GCCATTTCCCGTCCTGGAT 59.773 57.895 0.00 0.00 42.00 3.41
835 1664 2.038813 TGGACGGCCCAGATCTGA 59.961 61.111 24.62 0.00 40.82 3.27
1344 2249 4.256920 CCATTCTCTGTTCGGAAATGTCT 58.743 43.478 0.00 0.00 0.00 3.41
1349 2254 4.282449 TCTCTGTTCGGAAATGTCTGGTAA 59.718 41.667 0.00 0.00 0.00 2.85
1352 2257 6.001460 TCTGTTCGGAAATGTCTGGTAAAAT 58.999 36.000 0.00 0.00 0.00 1.82
1400 2310 1.110518 TTTGTCCCTTTTCGGTGGCC 61.111 55.000 0.00 0.00 0.00 5.36
1436 2346 4.256180 AGGCGCCGATCAATCCCC 62.256 66.667 23.20 0.00 0.00 4.81
1600 2520 0.685660 GGTCTCGGTTCTCCTGGTTT 59.314 55.000 0.00 0.00 0.00 3.27
1601 2521 1.897802 GGTCTCGGTTCTCCTGGTTTA 59.102 52.381 0.00 0.00 0.00 2.01
1602 2522 2.500504 GGTCTCGGTTCTCCTGGTTTAT 59.499 50.000 0.00 0.00 0.00 1.40
1603 2523 3.703052 GGTCTCGGTTCTCCTGGTTTATA 59.297 47.826 0.00 0.00 0.00 0.98
1604 2524 4.344390 GGTCTCGGTTCTCCTGGTTTATAT 59.656 45.833 0.00 0.00 0.00 0.86
1605 2525 5.537674 GGTCTCGGTTCTCCTGGTTTATATA 59.462 44.000 0.00 0.00 0.00 0.86
1614 2534 9.726438 GTTCTCCTGGTTTATATATATGCAAGT 57.274 33.333 5.44 0.00 0.00 3.16
1638 2558 5.356751 TGGGTTATTCATGATCCGTTTTCAG 59.643 40.000 0.00 0.00 0.00 3.02
1674 2594 9.693739 TCCAGTGCTAATTATTTGGAATTCTAA 57.306 29.630 5.23 2.23 32.15 2.10
1897 2855 6.860023 GCTTGCTCTGCCATGTTAATTAATAG 59.140 38.462 0.31 0.00 0.00 1.73
1899 2857 8.972458 TTGCTCTGCCATGTTAATTAATAGTA 57.028 30.769 0.31 0.00 0.00 1.82
1903 2861 9.507329 CTCTGCCATGTTAATTAATAGTACCAT 57.493 33.333 0.31 0.00 0.00 3.55
2074 3073 8.701540 GTTTAGTTTACTAGTCAAGAGTCAAGC 58.298 37.037 0.00 0.00 0.00 4.01
2075 3074 6.658188 AGTTTACTAGTCAAGAGTCAAGCT 57.342 37.500 0.00 0.00 0.00 3.74
2182 3186 5.202004 ACTTGGTCACTAGGTACCATCTAG 58.798 45.833 15.94 9.82 44.98 2.43
2187 3191 3.722627 TCACTAGGTACCATCTAGCTCCT 59.277 47.826 15.94 0.00 38.13 3.69
2189 3193 1.710816 AGGTACCATCTAGCTCCTGC 58.289 55.000 15.94 0.00 40.05 4.85
2231 3236 4.869861 CACAATCTGTCATCGACCACATAA 59.130 41.667 0.00 0.00 0.00 1.90
2235 3240 4.242475 TCTGTCATCGACCACATAAACAC 58.758 43.478 0.00 0.00 0.00 3.32
2237 3242 4.574892 TGTCATCGACCACATAAACACAT 58.425 39.130 0.00 0.00 0.00 3.21
2238 3243 4.391523 TGTCATCGACCACATAAACACATG 59.608 41.667 0.00 0.00 0.00 3.21
2239 3244 4.629634 GTCATCGACCACATAAACACATGA 59.370 41.667 0.00 0.00 0.00 3.07
2240 3245 4.869861 TCATCGACCACATAAACACATGAG 59.130 41.667 0.00 0.00 0.00 2.90
2323 3335 6.874288 TGTTTGTGACATTGTGACATGATA 57.126 33.333 9.92 0.00 28.84 2.15
2382 3408 2.833604 ATTCTGCAGCCAGGAGTGCC 62.834 60.000 9.47 0.00 39.04 5.01
2444 3470 0.179048 GCACCATCACATCCATCCGA 60.179 55.000 0.00 0.00 0.00 4.55
2607 3633 0.109504 CCATGTTTAAACCGCCCGTG 60.110 55.000 15.59 2.38 0.00 4.94
2833 3868 0.668706 TCTCTTGCTGCTCTTGACGC 60.669 55.000 0.00 0.00 0.00 5.19
2849 3884 2.726832 ACGCAGTTCTCTGGTAAGTC 57.273 50.000 0.00 0.00 37.78 3.01
2850 3885 1.961394 ACGCAGTTCTCTGGTAAGTCA 59.039 47.619 0.00 0.00 37.78 3.41
2851 3886 2.288273 ACGCAGTTCTCTGGTAAGTCAC 60.288 50.000 0.00 0.00 37.78 3.67
2852 3887 5.414862 ACGCAGTTCTCTGGTAAGTCACC 62.415 52.174 0.00 0.00 44.37 4.02
2892 3949 4.394300 CAGGTCATGGTGTTCAGAAGAATC 59.606 45.833 0.00 0.00 35.92 2.52
2979 4036 1.193665 GCAAGCGTGTGTGTCGTTTG 61.194 55.000 0.59 9.67 46.43 2.93
2980 4037 0.096281 CAAGCGTGTGTGTCGTTTGT 59.904 50.000 6.71 0.00 41.77 2.83
2981 4038 0.800012 AAGCGTGTGTGTCGTTTGTT 59.200 45.000 0.00 0.00 31.40 2.83
2982 4039 0.800012 AGCGTGTGTGTCGTTTGTTT 59.200 45.000 0.00 0.00 0.00 2.83
2990 4047 4.093703 TGTGTGTCGTTTGTTTGTTCTAGG 59.906 41.667 0.00 0.00 0.00 3.02
2994 4051 1.662026 CGTTTGTTTGTTCTAGGCGGC 60.662 52.381 0.00 0.00 0.00 6.53
3052 4109 1.595993 CCGTGACCTGATCTCACCGT 61.596 60.000 7.73 0.00 35.54 4.83
3107 4164 2.327343 GCCGCTGCAGATCACAACA 61.327 57.895 20.43 0.00 37.47 3.33
3132 4197 2.186903 CCATGGCCTACGCGAGTT 59.813 61.111 15.93 0.00 46.40 3.01
3166 4231 4.660938 GGGCCGGGTTTCTGTGCT 62.661 66.667 2.18 0.00 0.00 4.40
3190 4255 7.337480 TGCTCATTGTATATTGCTGTTCATT 57.663 32.000 0.00 0.00 0.00 2.57
3193 4258 6.506147 TCATTGTATATTGCTGTTCATTGCC 58.494 36.000 0.00 0.00 0.00 4.52
3221 4286 0.799917 CACTCGATGTGTGCTCTCCG 60.800 60.000 6.79 0.00 41.53 4.63
3227 4292 0.603707 ATGTGTGCTCTCCGGTGTTG 60.604 55.000 0.00 0.00 0.00 3.33
3231 4296 1.597854 TGCTCTCCGGTGTTGCAAG 60.598 57.895 18.81 5.03 0.00 4.01
3284 4349 0.108615 AACGAAGCGATCTGTCCAGG 60.109 55.000 0.00 0.00 0.00 4.45
3288 4353 1.617947 AAGCGATCTGTCCAGGGTCC 61.618 60.000 0.00 0.00 0.00 4.46
3291 4356 0.684479 CGATCTGTCCAGGGTCCTGA 60.684 60.000 17.91 2.30 46.30 3.86
3293 4358 0.972983 ATCTGTCCAGGGTCCTGACG 60.973 60.000 17.91 3.04 46.30 4.35
3335 4401 1.940613 GCAGGTTCGTTGTCAGAAGTT 59.059 47.619 0.00 0.00 0.00 2.66
3338 4404 1.668751 GGTTCGTTGTCAGAAGTTGCA 59.331 47.619 0.00 0.00 0.00 4.08
3339 4405 2.286418 GGTTCGTTGTCAGAAGTTGCAG 60.286 50.000 0.00 0.00 0.00 4.41
3340 4406 2.309528 TCGTTGTCAGAAGTTGCAGT 57.690 45.000 0.00 0.00 0.00 4.40
3341 4407 1.933181 TCGTTGTCAGAAGTTGCAGTG 59.067 47.619 0.00 0.00 0.00 3.66
3342 4408 1.003545 CGTTGTCAGAAGTTGCAGTGG 60.004 52.381 0.00 0.00 0.00 4.00
3343 4409 2.017049 GTTGTCAGAAGTTGCAGTGGT 58.983 47.619 0.00 0.00 0.00 4.16
3344 4410 3.202906 GTTGTCAGAAGTTGCAGTGGTA 58.797 45.455 0.00 0.00 0.00 3.25
3345 4411 2.833794 TGTCAGAAGTTGCAGTGGTAC 58.166 47.619 0.00 0.00 0.00 3.34
3350 4431 2.969950 AGAAGTTGCAGTGGTACTGGTA 59.030 45.455 10.62 0.00 46.01 3.25
3377 4458 3.571401 CCAGCAATGGTCTGTCTTCTTTT 59.429 43.478 0.00 0.00 0.00 2.27
3395 4476 0.584396 TTACTGCAGAACAAACGGCG 59.416 50.000 23.35 4.80 34.02 6.46
3398 4479 0.179215 CTGCAGAACAAACGGCGATC 60.179 55.000 16.62 3.55 34.02 3.69
3459 4541 4.113354 GAGCCGATGAAAGGTACTAACAG 58.887 47.826 0.00 0.00 38.49 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.707599 TTTGTGTGTTTTTAACTTTTCCCG 57.292 33.333 0.00 0.00 0.00 5.14
32 33 7.324354 AGATTTACGTTACACCACTTTGTTT 57.676 32.000 0.00 0.00 0.00 2.83
33 34 6.930667 AGATTTACGTTACACCACTTTGTT 57.069 33.333 0.00 0.00 0.00 2.83
34 35 6.316890 ACAAGATTTACGTTACACCACTTTGT 59.683 34.615 0.00 0.00 0.00 2.83
77 83 6.312426 TGTTTTTGTCCTTTTGCATGTGTTAG 59.688 34.615 0.00 0.00 0.00 2.34
157 163 4.693566 TCAACTTGTGTCTCACTTTTTCGT 59.306 37.500 1.72 0.00 35.11 3.85
204 210 2.624636 ACTTTTAATAGACGGGTGGCG 58.375 47.619 0.00 0.00 0.00 5.69
205 211 4.763073 AGTACTTTTAATAGACGGGTGGC 58.237 43.478 0.00 0.00 0.00 5.01
206 212 5.354767 GGAGTACTTTTAATAGACGGGTGG 58.645 45.833 0.00 0.00 0.00 4.61
225 231 1.420138 ACTCACATCGTTTTGGGGAGT 59.580 47.619 0.00 0.00 33.34 3.85
231 609 4.747540 TGGATTCACTCACATCGTTTTG 57.252 40.909 0.00 0.00 0.00 2.44
236 614 5.152923 CAGATTTGGATTCACTCACATCG 57.847 43.478 0.00 0.00 0.00 3.84
266 644 2.601763 GGTCGTGTTCATCCGTAATGAC 59.398 50.000 0.00 0.00 44.14 3.06
301 787 5.023452 TGACTAGCCTAGATCAAGGAAACA 58.977 41.667 5.58 0.00 39.15 2.83
339 899 3.349006 GATATGTGGGCTGCGCGG 61.349 66.667 13.18 13.18 0.00 6.46
340 900 2.280389 AGATATGTGGGCTGCGCG 60.280 61.111 12.21 0.00 0.00 6.86
342 902 1.302033 GGGAGATATGTGGGCTGCG 60.302 63.158 0.00 0.00 0.00 5.18
359 919 1.988409 CGACGCACACTTACGATGG 59.012 57.895 0.00 0.00 0.00 3.51
364 924 0.448379 GTTTCGCGACGCACACTTAC 60.448 55.000 21.35 4.83 0.00 2.34
368 928 2.167918 GAGTTTCGCGACGCACAC 59.832 61.111 21.35 12.42 0.00 3.82
375 935 1.014044 GTGGCATGAGAGTTTCGCGA 61.014 55.000 3.71 3.71 0.00 5.87
446 1023 6.054941 TCACGTTATTATGATCCATGTTGCT 58.945 36.000 0.00 0.00 0.00 3.91
452 1029 6.148315 CACAGCATCACGTTATTATGATCCAT 59.852 38.462 0.00 0.00 33.18 3.41
503 1080 9.218440 ACGGAGAAAGTAATAAAACCGAATAAA 57.782 29.630 0.00 0.00 41.30 1.40
504 1081 8.776376 ACGGAGAAAGTAATAAAACCGAATAA 57.224 30.769 0.00 0.00 41.30 1.40
505 1082 8.658609 CAACGGAGAAAGTAATAAAACCGAATA 58.341 33.333 0.00 0.00 41.30 1.75
506 1083 7.524065 CAACGGAGAAAGTAATAAAACCGAAT 58.476 34.615 0.00 0.00 41.30 3.34
507 1084 6.566376 GCAACGGAGAAAGTAATAAAACCGAA 60.566 38.462 0.00 0.00 41.30 4.30
508 1085 5.106987 GCAACGGAGAAAGTAATAAAACCGA 60.107 40.000 0.00 0.00 41.30 4.69
509 1086 5.084055 GCAACGGAGAAAGTAATAAAACCG 58.916 41.667 0.00 0.00 43.79 4.44
510 1087 6.004408 TGCAACGGAGAAAGTAATAAAACC 57.996 37.500 0.00 0.00 0.00 3.27
511 1088 9.783256 ATTATGCAACGGAGAAAGTAATAAAAC 57.217 29.630 0.00 0.00 0.00 2.43
519 1096 8.827677 GTTCTTATATTATGCAACGGAGAAAGT 58.172 33.333 0.00 0.00 0.00 2.66
520 1097 8.004344 CGTTCTTATATTATGCAACGGAGAAAG 58.996 37.037 0.00 0.00 34.42 2.62
521 1098 7.493320 ACGTTCTTATATTATGCAACGGAGAAA 59.507 33.333 15.28 0.00 40.64 2.52
522 1099 6.982141 ACGTTCTTATATTATGCAACGGAGAA 59.018 34.615 15.28 0.00 40.64 2.87
523 1100 6.509656 ACGTTCTTATATTATGCAACGGAGA 58.490 36.000 15.28 0.00 40.64 3.71
524 1101 6.764877 ACGTTCTTATATTATGCAACGGAG 57.235 37.500 15.28 0.00 40.64 4.63
525 1102 7.542534 AAACGTTCTTATATTATGCAACGGA 57.457 32.000 0.00 0.00 40.64 4.69
526 1103 8.609478 AAAAACGTTCTTATATTATGCAACGG 57.391 30.769 0.00 4.55 40.64 4.44
527 1104 9.268255 TGAAAAACGTTCTTATATTATGCAACG 57.732 29.630 0.00 11.80 41.76 4.10
530 1107 9.284594 GCTTGAAAAACGTTCTTATATTATGCA 57.715 29.630 0.00 0.00 0.00 3.96
531 1108 9.284594 TGCTTGAAAAACGTTCTTATATTATGC 57.715 29.630 0.00 0.00 0.00 3.14
535 1112 9.959749 TCTTTGCTTGAAAAACGTTCTTATATT 57.040 25.926 0.00 0.00 0.00 1.28
536 1113 9.612620 CTCTTTGCTTGAAAAACGTTCTTATAT 57.387 29.630 0.00 0.00 0.00 0.86
537 1114 7.589954 GCTCTTTGCTTGAAAAACGTTCTTATA 59.410 33.333 0.00 0.00 38.95 0.98
538 1115 6.417930 GCTCTTTGCTTGAAAAACGTTCTTAT 59.582 34.615 0.00 0.00 38.95 1.73
539 1116 5.741982 GCTCTTTGCTTGAAAAACGTTCTTA 59.258 36.000 0.00 0.00 38.95 2.10
540 1117 4.562789 GCTCTTTGCTTGAAAAACGTTCTT 59.437 37.500 0.00 0.00 38.95 2.52
541 1118 4.105486 GCTCTTTGCTTGAAAAACGTTCT 58.895 39.130 0.00 0.00 38.95 3.01
542 1119 3.061863 CGCTCTTTGCTTGAAAAACGTTC 60.062 43.478 0.00 0.00 40.11 3.95
543 1120 2.851824 CGCTCTTTGCTTGAAAAACGTT 59.148 40.909 0.00 0.00 40.11 3.99
544 1121 2.159435 ACGCTCTTTGCTTGAAAAACGT 60.159 40.909 0.00 0.00 40.11 3.99
545 1122 2.450160 ACGCTCTTTGCTTGAAAAACG 58.550 42.857 0.00 0.00 40.11 3.60
546 1123 4.598062 AGTACGCTCTTTGCTTGAAAAAC 58.402 39.130 0.00 0.00 40.11 2.43
547 1124 4.893424 AGTACGCTCTTTGCTTGAAAAA 57.107 36.364 0.00 0.00 40.11 1.94
548 1125 4.574828 AGAAGTACGCTCTTTGCTTGAAAA 59.425 37.500 0.00 0.00 40.11 2.29
549 1126 4.127171 AGAAGTACGCTCTTTGCTTGAAA 58.873 39.130 0.00 0.00 40.11 2.69
550 1127 3.728845 AGAAGTACGCTCTTTGCTTGAA 58.271 40.909 0.00 0.00 40.11 2.69
551 1128 3.386768 AGAAGTACGCTCTTTGCTTGA 57.613 42.857 0.00 0.00 40.11 3.02
552 1129 3.743396 AGAAGAAGTACGCTCTTTGCTTG 59.257 43.478 12.71 0.00 40.11 4.01
553 1130 3.996480 AGAAGAAGTACGCTCTTTGCTT 58.004 40.909 12.71 0.00 40.11 3.91
554 1131 3.669251 AGAAGAAGTACGCTCTTTGCT 57.331 42.857 12.71 5.76 40.11 3.91
555 1132 4.684703 TGTTAGAAGAAGTACGCTCTTTGC 59.315 41.667 12.71 4.00 38.57 3.68
556 1133 5.118817 GGTGTTAGAAGAAGTACGCTCTTTG 59.881 44.000 12.71 0.00 0.00 2.77
557 1134 5.221382 TGGTGTTAGAAGAAGTACGCTCTTT 60.221 40.000 12.71 7.32 0.00 2.52
558 1135 4.280174 TGGTGTTAGAAGAAGTACGCTCTT 59.720 41.667 11.66 11.66 0.00 2.85
559 1136 3.825014 TGGTGTTAGAAGAAGTACGCTCT 59.175 43.478 0.00 0.00 0.00 4.09
560 1137 4.170292 TGGTGTTAGAAGAAGTACGCTC 57.830 45.455 0.00 0.00 0.00 5.03
561 1138 4.595762 TTGGTGTTAGAAGAAGTACGCT 57.404 40.909 0.00 0.00 0.00 5.07
562 1139 5.857822 ATTTGGTGTTAGAAGAAGTACGC 57.142 39.130 0.00 0.00 0.00 4.42
563 1140 8.697846 TGATATTTGGTGTTAGAAGAAGTACG 57.302 34.615 0.00 0.00 0.00 3.67
600 1177 0.525761 GGAAAAATGGCTGCTACGCA 59.474 50.000 0.00 0.00 36.92 5.24
603 1180 2.164422 GTGGAGGAAAAATGGCTGCTAC 59.836 50.000 0.00 0.00 0.00 3.58
607 1184 1.273327 GTGGTGGAGGAAAAATGGCTG 59.727 52.381 0.00 0.00 0.00 4.85
608 1185 1.133199 TGTGGTGGAGGAAAAATGGCT 60.133 47.619 0.00 0.00 0.00 4.75
609 1186 1.273327 CTGTGGTGGAGGAAAAATGGC 59.727 52.381 0.00 0.00 0.00 4.40
632 1248 3.822594 TGTTATGTGCACGATGGTTTC 57.177 42.857 13.13 0.00 0.00 2.78
641 1261 2.289002 GGCTGCTCTATGTTATGTGCAC 59.711 50.000 10.75 10.75 0.00 4.57
672 1292 4.445448 CCATCCCTTCTCTGTTAATCCAGG 60.445 50.000 0.00 0.00 33.14 4.45
673 1293 4.164988 ACCATCCCTTCTCTGTTAATCCAG 59.835 45.833 0.00 0.00 0.00 3.86
678 1298 5.935789 CGTAAAACCATCCCTTCTCTGTTAA 59.064 40.000 0.00 0.00 0.00 2.01
744 1573 5.616270 TGGAATTATAGCGATTAAGGCACA 58.384 37.500 4.36 0.00 0.00 4.57
778 1607 1.667724 GGACGCTTGTTGATCTGATGG 59.332 52.381 0.00 0.00 0.00 3.51
781 1610 1.338105 CCTGGACGCTTGTTGATCTGA 60.338 52.381 0.00 0.00 0.00 3.27
1400 2310 0.680618 TGGCCAAAAATCACCAGCAG 59.319 50.000 0.61 0.00 0.00 4.24
1603 2523 9.182214 GATCATGAATAACCCACTTGCATATAT 57.818 33.333 0.00 0.00 0.00 0.86
1604 2524 7.611467 GGATCATGAATAACCCACTTGCATATA 59.389 37.037 0.00 0.00 0.00 0.86
1605 2525 6.435277 GGATCATGAATAACCCACTTGCATAT 59.565 38.462 0.00 0.00 0.00 1.78
1614 2534 5.257262 TGAAAACGGATCATGAATAACCCA 58.743 37.500 0.00 0.00 0.00 4.51
1674 2594 6.694447 TCAGTACTCGCCTAAATTAAACAGT 58.306 36.000 0.00 0.00 0.00 3.55
1897 2855 7.306983 GCAAATACATACACCGAGTAATGGTAC 60.307 40.741 0.00 0.00 37.72 3.34
1899 2857 5.526111 GCAAATACATACACCGAGTAATGGT 59.474 40.000 0.00 0.00 41.47 3.55
1903 2861 8.198778 TGATTAGCAAATACATACACCGAGTAA 58.801 33.333 0.00 0.00 36.05 2.24
2170 3174 1.062886 TGCAGGAGCTAGATGGTACCT 60.063 52.381 14.36 0.00 42.74 3.08
2182 3186 6.127619 ACAATTAAAGAAATACCTGCAGGAGC 60.128 38.462 39.19 20.68 42.57 4.70
2187 3191 7.517614 TGTGACAATTAAAGAAATACCTGCA 57.482 32.000 0.00 0.00 0.00 4.41
2323 3335 2.564947 GACACAGACAGACAAGGGATCT 59.435 50.000 0.00 0.00 0.00 2.75
2382 3408 2.481854 CTTCTTGATCTGATGCTCCCG 58.518 52.381 0.00 0.00 0.00 5.14
2607 3633 2.609737 GGCTACCCATCTGTATACACGC 60.610 54.545 0.08 0.00 0.00 5.34
2700 3735 1.492993 GGGCAGGAGAGGAAACCACT 61.493 60.000 0.00 0.00 0.00 4.00
2765 3800 8.421673 AACAGGAATTACTACGAAAAGATAGC 57.578 34.615 0.00 0.00 0.00 2.97
2843 3878 1.375523 CCACGCCCTGGTGACTTAC 60.376 63.158 3.27 0.00 40.38 2.34
2892 3949 2.721971 AAGGCGAGGCACACTGTCAG 62.722 60.000 0.00 0.00 0.00 3.51
2969 4026 3.064271 GCCTAGAACAAACAAACGACACA 59.936 43.478 0.00 0.00 0.00 3.72
2979 4036 1.632948 GACCGCCGCCTAGAACAAAC 61.633 60.000 0.00 0.00 0.00 2.93
2980 4037 1.375013 GACCGCCGCCTAGAACAAA 60.375 57.895 0.00 0.00 0.00 2.83
2981 4038 2.263540 GACCGCCGCCTAGAACAA 59.736 61.111 0.00 0.00 0.00 2.83
2982 4039 3.766691 GGACCGCCGCCTAGAACA 61.767 66.667 0.00 0.00 0.00 3.18
3052 4109 2.886913 TGGGTTTGATTGCATCAGGAA 58.113 42.857 0.00 0.00 40.94 3.36
3121 4182 1.349259 CCGGTCAAAACTCGCGTAGG 61.349 60.000 5.77 0.00 0.00 3.18
3132 4197 4.323477 CTCGGGTGGCCGGTCAAA 62.323 66.667 12.16 0.00 0.00 2.69
3166 4231 6.947644 ATGAACAGCAATATACAATGAGCA 57.052 33.333 0.00 0.00 0.00 4.26
3193 4258 1.065572 CACATCGAGTGTCGTGTCCG 61.066 60.000 6.79 0.00 43.40 4.79
3215 4280 2.671177 CGCTTGCAACACCGGAGAG 61.671 63.158 9.46 0.00 0.00 3.20
3219 4284 2.051345 GTTCGCTTGCAACACCGG 60.051 61.111 0.00 0.00 0.00 5.28
3221 4286 2.051345 CCGTTCGCTTGCAACACC 60.051 61.111 0.00 0.00 0.00 4.16
3227 4292 2.485122 CAATCCCCGTTCGCTTGC 59.515 61.111 0.00 0.00 0.00 4.01
3231 4296 1.892391 GATCCCAATCCCCGTTCGC 60.892 63.158 0.00 0.00 0.00 4.70
3288 4353 1.144936 GGATTCTGGAGGGCGTCAG 59.855 63.158 9.66 5.11 0.00 3.51
3291 4356 2.990479 GTGGATTCTGGAGGGCGT 59.010 61.111 0.00 0.00 0.00 5.68
3293 4358 1.700042 ATCCGTGGATTCTGGAGGGC 61.700 60.000 0.00 0.00 34.75 5.19
3335 4401 2.173519 GTACCTACCAGTACCACTGCA 58.826 52.381 0.64 0.00 44.63 4.41
3377 4458 0.249531 TCGCCGTTTGTTCTGCAGTA 60.250 50.000 14.67 0.00 0.00 2.74
3395 4476 3.005578 AGCTAAATTACCGTCCCGAGATC 59.994 47.826 0.00 0.00 0.00 2.75
3398 4479 2.884894 AGCTAAATTACCGTCCCGAG 57.115 50.000 0.00 0.00 0.00 4.63
3438 4520 3.514309 ACTGTTAGTACCTTTCATCGGCT 59.486 43.478 0.00 0.00 0.00 5.52
3459 4541 3.157523 CGTCACGTCGCGTCTCAC 61.158 66.667 5.77 0.00 38.32 3.51


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

AutoCloner maintained by Alex Coulton.