Multiple sequence alignment - TraesCS7D01G444500

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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 TraesCS7D01G444500 chr7D 100.000 4448 0 0 1 4448 565642644 565647091 0.000000e+00 8215.0
1 TraesCS7D01G444500 chr7D 84.181 2497 346 29 971 3439 566013940 566016415 0.000000e+00 2377.0
2 TraesCS7D01G444500 chr7D 82.857 2625 396 35 885 3477 565617261 565619863 0.000000e+00 2305.0
3 TraesCS7D01G444500 chr7D 83.367 2495 368 32 975 3449 566037434 566039901 0.000000e+00 2265.0
4 TraesCS7D01G444500 chr7D 89.691 291 22 8 3 290 562409022 562409307 9.090000e-97 364.0
5 TraesCS7D01G444500 chr7B 94.286 2975 142 11 752 3715 617485579 617488536 0.000000e+00 4527.0
6 TraesCS7D01G444500 chr7B 85.617 2503 315 24 996 3479 616903086 616905562 0.000000e+00 2586.0
7 TraesCS7D01G444500 chr7B 83.535 2563 366 34 912 3451 616750004 616747475 0.000000e+00 2344.0
8 TraesCS7D01G444500 chr7B 83.073 2623 361 50 885 3480 616823384 616820818 0.000000e+00 2307.0
9 TraesCS7D01G444500 chr7B 83.500 2497 366 28 971 3439 617557980 617555502 0.000000e+00 2287.0
10 TraesCS7D01G444500 chr7B 82.803 2483 393 19 1011 3477 616836254 616838718 0.000000e+00 2189.0
11 TraesCS7D01G444500 chr7B 81.887 1971 319 26 1498 3449 617578218 617580169 0.000000e+00 1628.0
12 TraesCS7D01G444500 chr7B 89.541 392 32 8 3 390 146051118 146051504 5.170000e-134 488.0
13 TraesCS7D01G444500 chr7B 95.050 202 9 1 387 587 617485375 617485576 2.580000e-82 316.0
14 TraesCS7D01G444500 chr7A 84.739 2490 315 25 1008 3482 652195204 652197643 0.000000e+00 2433.0
15 TraesCS7D01G444500 chr7A 83.240 2494 371 35 971 3437 652286409 652288882 0.000000e+00 2246.0
16 TraesCS7D01G444500 chr7A 94.796 1422 64 5 1451 2868 652232233 652233648 0.000000e+00 2207.0
17 TraesCS7D01G444500 chr7A 81.170 2581 401 58 904 3438 652337871 652340412 0.000000e+00 1995.0
18 TraesCS7D01G444500 chr7A 83.251 2030 309 20 1423 3438 652163852 652165864 0.000000e+00 1836.0
19 TraesCS7D01G444500 chr7A 88.525 793 60 13 1 781 652231311 652232084 0.000000e+00 931.0
20 TraesCS7D01G444500 chr7A 93.125 640 32 4 3630 4257 652234157 652234796 0.000000e+00 928.0
21 TraesCS7D01G444500 chr7A 76.851 743 121 23 3483 4203 652197672 652198385 5.430000e-99 372.0
22 TraesCS7D01G444500 chr7A 92.105 152 5 1 4252 4403 652234833 652234977 1.620000e-49 207.0
23 TraesCS7D01G444500 chr7A 96.000 50 2 0 4399 4448 652248176 652248225 1.030000e-11 82.4
24 TraesCS7D01G444500 chr4A 92.092 392 28 3 1 390 410049141 410049531 2.340000e-152 549.0
25 TraesCS7D01G444500 chr2B 89.504 343 31 5 43 382 27941425 27941765 3.180000e-116 429.0
26 TraesCS7D01G444500 chr2A 90.514 253 19 5 143 390 404683473 404683221 3.320000e-86 329.0
27 TraesCS7D01G444500 chr2A 90.119 253 20 5 143 390 396399053 396399305 1.540000e-84 324.0
28 TraesCS7D01G444500 chr2A 85.484 124 17 1 268 390 255912290 255912413 1.300000e-25 128.0
29 TraesCS7D01G444500 chr3B 87.544 281 23 10 134 408 186531593 186531319 9.290000e-82 315.0
30 TraesCS7D01G444500 chr3B 87.544 281 23 10 134 408 186540227 186539953 9.290000e-82 315.0
31 TraesCS7D01G444500 chr3B 89.873 79 5 1 3 78 186531697 186531619 1.020000e-16 99.0
32 TraesCS7D01G444500 chr3B 89.873 79 5 1 3 78 186540331 186540253 1.020000e-16 99.0
33 TraesCS7D01G444500 chr6B 94.737 76 4 0 3 78 70268585 70268660 7.820000e-23 119.0


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 TraesCS7D01G444500 chr7D 565642644 565647091 4447 False 8215.00 8215 100.00000 1 4448 1 chr7D.!!$F3 4447
1 TraesCS7D01G444500 chr7D 566013940 566016415 2475 False 2377.00 2377 84.18100 971 3439 1 chr7D.!!$F4 2468
2 TraesCS7D01G444500 chr7D 565617261 565619863 2602 False 2305.00 2305 82.85700 885 3477 1 chr7D.!!$F2 2592
3 TraesCS7D01G444500 chr7D 566037434 566039901 2467 False 2265.00 2265 83.36700 975 3449 1 chr7D.!!$F5 2474
4 TraesCS7D01G444500 chr7B 616903086 616905562 2476 False 2586.00 2586 85.61700 996 3479 1 chr7B.!!$F3 2483
5 TraesCS7D01G444500 chr7B 617485375 617488536 3161 False 2421.50 4527 94.66800 387 3715 2 chr7B.!!$F5 3328
6 TraesCS7D01G444500 chr7B 616747475 616750004 2529 True 2344.00 2344 83.53500 912 3451 1 chr7B.!!$R1 2539
7 TraesCS7D01G444500 chr7B 616820818 616823384 2566 True 2307.00 2307 83.07300 885 3480 1 chr7B.!!$R2 2595
8 TraesCS7D01G444500 chr7B 617555502 617557980 2478 True 2287.00 2287 83.50000 971 3439 1 chr7B.!!$R3 2468
9 TraesCS7D01G444500 chr7B 616836254 616838718 2464 False 2189.00 2189 82.80300 1011 3477 1 chr7B.!!$F2 2466
10 TraesCS7D01G444500 chr7B 617578218 617580169 1951 False 1628.00 1628 81.88700 1498 3449 1 chr7B.!!$F4 1951
11 TraesCS7D01G444500 chr7A 652286409 652288882 2473 False 2246.00 2246 83.24000 971 3437 1 chr7A.!!$F3 2466
12 TraesCS7D01G444500 chr7A 652337871 652340412 2541 False 1995.00 1995 81.17000 904 3438 1 chr7A.!!$F4 2534
13 TraesCS7D01G444500 chr7A 652163852 652165864 2012 False 1836.00 1836 83.25100 1423 3438 1 chr7A.!!$F1 2015
14 TraesCS7D01G444500 chr7A 652195204 652198385 3181 False 1402.50 2433 80.79500 1008 4203 2 chr7A.!!$F5 3195
15 TraesCS7D01G444500 chr7A 652231311 652234977 3666 False 1068.25 2207 92.13775 1 4403 4 chr7A.!!$F6 4402

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
182 183 0.412244 ACAGGTCCTAGTACAGGCCA 59.588 55.0 5.01 0.0 45.10 5.36 F
1483 1549 0.809241 GCAGAGCTTCGACCATCCAG 60.809 60.0 0.00 0.0 0.00 3.86 F
2596 2717 0.037882 CGTCCTGAAGCAGCAGAAGA 60.038 55.0 7.34 0.0 38.14 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2158 0.170561 CTAGGAACCCGTCTGTCGTG 59.829 60.0 0.00 0.0 37.94 4.35 R
3441 3698 0.527817 CTCGCCTGGTGGATTACGTC 60.528 60.0 7.51 0.0 34.57 4.34 R
3966 4278 0.744874 ACGATAGATGTGACGTGGGG 59.255 55.0 0.00 0.0 37.58 4.96 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
40 41 1.305219 CCGTGTCGGTGCAAATCCAT 61.305 55.000 0.00 0.00 42.73 3.41
41 42 0.521291 CGTGTCGGTGCAAATCCATT 59.479 50.000 0.00 0.00 0.00 3.16
70 71 1.002624 TTGCAATCCGAGACCCCAC 60.003 57.895 0.00 0.00 0.00 4.61
85 86 1.072332 CCACGGTGGTCAACCATGA 59.928 57.895 19.15 0.00 45.35 3.07
92 93 0.697658 TGGTCAACCATGATGAGGCA 59.302 50.000 0.00 0.00 42.01 4.75
97 98 2.515290 CCATGATGAGGCAGCGCA 60.515 61.111 11.47 0.00 0.00 6.09
123 124 3.016474 GCTGCGAGCGAAACAGACC 62.016 63.158 0.00 0.00 33.10 3.85
124 125 2.357034 TGCGAGCGAAACAGACCC 60.357 61.111 0.00 0.00 0.00 4.46
125 126 2.357034 GCGAGCGAAACAGACCCA 60.357 61.111 0.00 0.00 0.00 4.51
126 127 2.383527 GCGAGCGAAACAGACCCAG 61.384 63.158 0.00 0.00 0.00 4.45
127 128 1.738099 CGAGCGAAACAGACCCAGG 60.738 63.158 0.00 0.00 0.00 4.45
156 157 2.224784 CCGTCCTTGTTTTAGGGTTTCG 59.775 50.000 0.00 0.00 35.90 3.46
168 169 1.952635 GGTTTCGCGTTCGACAGGT 60.953 57.895 5.77 0.00 45.43 4.00
173 174 1.226323 CGCGTTCGACAGGTCCTAG 60.226 63.158 0.00 0.00 38.10 3.02
174 175 1.881602 GCGTTCGACAGGTCCTAGT 59.118 57.895 0.00 0.00 0.00 2.57
175 176 1.089920 GCGTTCGACAGGTCCTAGTA 58.910 55.000 0.00 0.00 0.00 1.82
176 177 1.202121 GCGTTCGACAGGTCCTAGTAC 60.202 57.143 0.00 0.00 0.00 2.73
177 178 2.079158 CGTTCGACAGGTCCTAGTACA 58.921 52.381 0.00 0.00 0.00 2.90
178 179 2.095532 CGTTCGACAGGTCCTAGTACAG 59.904 54.545 0.00 0.00 0.00 2.74
180 181 0.739561 CGACAGGTCCTAGTACAGGC 59.260 60.000 0.00 0.00 45.10 4.85
181 182 1.112950 GACAGGTCCTAGTACAGGCC 58.887 60.000 0.00 0.00 45.10 5.19
182 183 0.412244 ACAGGTCCTAGTACAGGCCA 59.588 55.000 5.01 0.00 45.10 5.36
183 184 1.008449 ACAGGTCCTAGTACAGGCCAT 59.992 52.381 5.01 0.00 45.10 4.40
184 185 2.119495 CAGGTCCTAGTACAGGCCATT 58.881 52.381 5.01 0.00 45.10 3.16
185 186 3.305720 CAGGTCCTAGTACAGGCCATTA 58.694 50.000 5.01 0.00 45.10 1.90
186 187 3.709653 CAGGTCCTAGTACAGGCCATTAA 59.290 47.826 5.01 0.00 45.10 1.40
187 188 3.967987 AGGTCCTAGTACAGGCCATTAAG 59.032 47.826 5.01 0.00 45.10 1.85
188 189 3.494573 GGTCCTAGTACAGGCCATTAAGC 60.495 52.174 5.01 0.00 45.10 3.09
208 209 2.738743 CCAGTAGGCCCAATTGAATGT 58.261 47.619 7.12 0.00 0.00 2.71
284 285 0.944386 CCGCGATTTAGGTGGGATTG 59.056 55.000 8.23 0.00 0.00 2.67
286 287 1.867233 CGCGATTTAGGTGGGATTGAG 59.133 52.381 0.00 0.00 0.00 3.02
335 336 7.042950 TCTAAAAATGACGATCCAACGGATAA 58.957 34.615 0.00 0.00 43.27 1.75
348 349 7.581213 TCCAACGGATAAAAATGCTAATGAT 57.419 32.000 0.00 0.00 0.00 2.45
357 358 9.499479 GATAAAAATGCTAATGATCTGAGAGGA 57.501 33.333 0.00 0.00 0.00 3.71
360 361 4.933505 TGCTAATGATCTGAGAGGACAG 57.066 45.455 0.00 0.00 39.02 3.51
383 385 9.672673 ACAGAAAAGTGCTCAGTTATAATGTAT 57.327 29.630 0.00 0.00 0.00 2.29
421 423 8.851541 AAATTCATTGACTATTGGTGCATTTT 57.148 26.923 0.00 0.00 0.00 1.82
465 467 6.422776 TTCAAACAACTTCTCAGAAGACAC 57.577 37.500 21.82 0.00 0.00 3.67
591 598 2.997986 CCGCCACAGAAAACTACGTTAT 59.002 45.455 0.00 0.00 0.00 1.89
648 655 8.526147 CCTTTTCCTAAGTGTCATCAAATCAAT 58.474 33.333 0.00 0.00 0.00 2.57
651 658 9.912634 TTTCCTAAGTGTCATCAAATCAATTTC 57.087 29.630 0.00 0.00 0.00 2.17
653 660 7.606073 TCCTAAGTGTCATCAAATCAATTTCGA 59.394 33.333 0.00 0.00 0.00 3.71
717 730 2.609459 CTGCTGTTACTATTTCCTGGCG 59.391 50.000 0.00 0.00 0.00 5.69
732 745 3.615709 GCGGGGGTTGCTGCTTTT 61.616 61.111 0.00 0.00 0.00 2.27
760 773 1.072331 ACCTGCTTTGTAGGTCACAGG 59.928 52.381 5.34 5.34 45.10 4.00
776 789 2.501610 GGCCATGTCGGACTCTCC 59.498 66.667 9.88 2.10 41.26 3.71
783 796 1.979693 GTCGGACTCTCCAGCCACT 60.980 63.158 0.00 0.00 35.91 4.00
789 802 2.487265 GGACTCTCCAGCCACTGAAAAA 60.487 50.000 0.00 0.00 36.28 1.94
791 804 4.565652 GGACTCTCCAGCCACTGAAAAATA 60.566 45.833 0.00 0.00 36.28 1.40
792 805 4.985538 ACTCTCCAGCCACTGAAAAATAA 58.014 39.130 0.00 0.00 32.44 1.40
817 830 0.889186 ACGGCACAGACCAAACCATC 60.889 55.000 0.00 0.00 0.00 3.51
818 831 1.875963 GGCACAGACCAAACCATCG 59.124 57.895 0.00 0.00 0.00 3.84
820 833 1.234821 GCACAGACCAAACCATCGAA 58.765 50.000 0.00 0.00 0.00 3.71
874 892 4.025401 CACCGTGGCCGCTTTGAC 62.025 66.667 15.69 0.00 0.00 3.18
878 896 2.671177 CGTGGCCGCTTTGACTGAG 61.671 63.158 15.69 0.00 0.00 3.35
968 998 1.379044 CTGCGCCCCCTGAGAATTT 60.379 57.895 4.18 0.00 0.00 1.82
1004 1043 2.282110 TCCGCCAACCACCATGTG 60.282 61.111 0.00 0.00 0.00 3.21
1483 1549 0.809241 GCAGAGCTTCGACCATCCAG 60.809 60.000 0.00 0.00 0.00 3.86
2064 2158 3.422303 TGCGCGCACAACAGATCC 61.422 61.111 33.09 0.00 0.00 3.36
2089 2183 2.678934 ACGGGTTCCTAGCGCTGA 60.679 61.111 22.90 6.79 0.00 4.26
2146 2240 3.741476 CCGCCCAGAGCAAAGCAC 61.741 66.667 0.00 0.00 44.04 4.40
2333 2433 1.896220 TTGCAAGATCTTGGCGTCTT 58.104 45.000 31.41 0.00 40.74 3.01
2463 2584 3.054582 TCCTTGCTAGGAGAAGACGACTA 60.055 47.826 13.28 0.00 45.82 2.59
2596 2717 0.037882 CGTCCTGAAGCAGCAGAAGA 60.038 55.000 7.34 0.00 38.14 2.87
2727 2854 2.603776 AACCTCGTCCGGCTCCTT 60.604 61.111 0.00 0.00 0.00 3.36
3441 3698 3.108289 CAGCACCTCGTCACGCTG 61.108 66.667 0.00 0.00 45.17 5.18
3454 3711 4.902308 CGCTGACGTAATCCACCA 57.098 55.556 0.00 0.00 33.53 4.17
3461 3718 1.883084 CGTAATCCACCAGGCGAGC 60.883 63.158 0.00 0.00 33.74 5.03
3559 3848 0.102300 AAAGCACGTGTGGCCTTTTC 59.898 50.000 18.38 0.00 0.00 2.29
3572 3861 4.156739 GTGGCCTTTTCTTCTTCGAATCAT 59.843 41.667 3.32 0.00 0.00 2.45
3584 3873 4.161189 TCTTCGAATCATTCAGGAGAGCTT 59.839 41.667 0.00 0.00 0.00 3.74
3705 4001 6.267471 ACACAAAAGGTTAACATGATGACCAT 59.733 34.615 17.53 4.42 34.60 3.55
3832 4135 3.880846 CCTCTCGCGCCAAATGCC 61.881 66.667 0.00 0.00 36.24 4.40
3850 4153 1.616725 GCCCCAACTGATCAACATGGA 60.617 52.381 18.12 0.00 32.16 3.41
3861 4164 9.520515 AACTGATCAACATGGAAAAGTAGTATT 57.479 29.630 0.00 0.00 0.00 1.89
3877 4183 4.939509 AGTATTGTGTGGCACGTATTTC 57.060 40.909 13.77 2.56 37.14 2.17
3889 4195 6.961554 GTGGCACGTATTTCTTTTCTTCTATG 59.038 38.462 0.00 0.00 0.00 2.23
3987 4299 2.460918 CCCACGTCACATCTATCGTTC 58.539 52.381 0.00 0.00 34.30 3.95
4058 4375 8.157476 AGTGAATATAATGGACCAATAGTCACC 58.843 37.037 27.52 17.35 45.42 4.02
4093 4410 7.028962 CGCATCCTTGATTTTTGTCATTCTAA 58.971 34.615 0.00 0.00 0.00 2.10
4203 4521 9.952188 GGTGATTTCAACCTTATTAGAAATAGC 57.048 33.333 0.00 0.00 39.88 2.97
4230 4548 7.014230 TCTGGAAAGAAAATCCCACTAAAACTG 59.986 37.037 0.00 0.00 36.04 3.16
4273 4633 6.072508 TCCAATGCTTGTTCTGATAACTTGAC 60.073 38.462 0.00 0.00 0.00 3.18
4281 4641 5.168569 GTTCTGATAACTTGACGGATCACA 58.831 41.667 0.00 0.00 33.38 3.58
4296 4656 3.503748 GGATCACACCTTTGAGAAGTTGG 59.496 47.826 0.00 0.00 30.25 3.77
4306 4666 5.048434 CCTTTGAGAAGTTGGATGGAGTTTC 60.048 44.000 0.00 0.00 0.00 2.78
4316 4676 2.833943 GGATGGAGTTTCATTTTGCCCT 59.166 45.455 0.00 0.00 0.00 5.19
4317 4677 3.368739 GGATGGAGTTTCATTTTGCCCTG 60.369 47.826 0.00 0.00 0.00 4.45
4318 4678 2.956132 TGGAGTTTCATTTTGCCCTGA 58.044 42.857 0.00 0.00 0.00 3.86
4319 4679 3.509442 TGGAGTTTCATTTTGCCCTGAT 58.491 40.909 0.00 0.00 0.00 2.90
4320 4680 3.511146 TGGAGTTTCATTTTGCCCTGATC 59.489 43.478 0.00 0.00 0.00 2.92
4321 4681 3.766051 GGAGTTTCATTTTGCCCTGATCT 59.234 43.478 0.00 0.00 0.00 2.75
4322 4682 4.381292 GGAGTTTCATTTTGCCCTGATCTG 60.381 45.833 0.00 0.00 0.00 2.90
4403 4763 1.201414 CCTTTATTGTTGGACACGGGC 59.799 52.381 0.00 0.00 0.00 6.13
4404 4764 2.159382 CTTTATTGTTGGACACGGGCT 58.841 47.619 0.00 0.00 0.00 5.19
4405 4765 1.816074 TTATTGTTGGACACGGGCTC 58.184 50.000 0.00 0.00 0.00 4.70
4406 4766 0.687920 TATTGTTGGACACGGGCTCA 59.312 50.000 0.00 0.00 0.00 4.26
4407 4767 0.889186 ATTGTTGGACACGGGCTCAC 60.889 55.000 0.00 0.00 0.00 3.51
4408 4768 2.110213 GTTGGACACGGGCTCACA 59.890 61.111 0.00 0.00 0.00 3.58
4409 4769 1.302511 GTTGGACACGGGCTCACAT 60.303 57.895 0.00 0.00 0.00 3.21
4410 4770 0.036765 GTTGGACACGGGCTCACATA 60.037 55.000 0.00 0.00 0.00 2.29
4411 4771 0.687920 TTGGACACGGGCTCACATAA 59.312 50.000 0.00 0.00 0.00 1.90
4412 4772 0.908910 TGGACACGGGCTCACATAAT 59.091 50.000 0.00 0.00 0.00 1.28
4413 4773 2.112190 TGGACACGGGCTCACATAATA 58.888 47.619 0.00 0.00 0.00 0.98
4414 4774 2.703536 TGGACACGGGCTCACATAATAT 59.296 45.455 0.00 0.00 0.00 1.28
4415 4775 3.898741 TGGACACGGGCTCACATAATATA 59.101 43.478 0.00 0.00 0.00 0.86
4416 4776 4.530553 TGGACACGGGCTCACATAATATAT 59.469 41.667 0.00 0.00 0.00 0.86
4417 4777 5.109903 GGACACGGGCTCACATAATATATC 58.890 45.833 0.00 0.00 0.00 1.63
4418 4778 5.105310 GGACACGGGCTCACATAATATATCT 60.105 44.000 0.00 0.00 0.00 1.98
4419 4779 5.967088 ACACGGGCTCACATAATATATCTC 58.033 41.667 0.00 0.00 0.00 2.75
4420 4780 5.480422 ACACGGGCTCACATAATATATCTCA 59.520 40.000 0.00 0.00 0.00 3.27
4421 4781 6.014584 ACACGGGCTCACATAATATATCTCAA 60.015 38.462 0.00 0.00 0.00 3.02
4422 4782 6.311445 CACGGGCTCACATAATATATCTCAAC 59.689 42.308 0.00 0.00 0.00 3.18
4423 4783 5.812642 CGGGCTCACATAATATATCTCAACC 59.187 44.000 0.00 0.00 0.00 3.77
4424 4784 6.116126 GGGCTCACATAATATATCTCAACCC 58.884 44.000 0.00 0.00 0.00 4.11
4425 4785 6.296432 GGGCTCACATAATATATCTCAACCCA 60.296 42.308 0.00 0.00 0.00 4.51
4426 4786 7.341805 GGCTCACATAATATATCTCAACCCAT 58.658 38.462 0.00 0.00 0.00 4.00
4427 4787 7.831193 GGCTCACATAATATATCTCAACCCATT 59.169 37.037 0.00 0.00 0.00 3.16
4428 4788 9.236006 GCTCACATAATATATCTCAACCCATTT 57.764 33.333 0.00 0.00 0.00 2.32
4439 4799 9.753674 ATATCTCAACCCATTTTTAGACTTGAA 57.246 29.630 0.00 0.00 0.00 2.69
4440 4800 7.889873 TCTCAACCCATTTTTAGACTTGAAA 57.110 32.000 0.00 0.00 0.00 2.69
4441 4801 8.299990 TCTCAACCCATTTTTAGACTTGAAAA 57.700 30.769 0.64 0.64 0.00 2.29
4442 4802 8.754080 TCTCAACCCATTTTTAGACTTGAAAAA 58.246 29.630 0.00 0.00 39.42 1.94
4443 4803 9.546428 CTCAACCCATTTTTAGACTTGAAAAAT 57.454 29.630 3.74 3.74 43.77 1.82
4444 4804 9.541143 TCAACCCATTTTTAGACTTGAAAAATC 57.459 29.630 5.92 0.00 42.02 2.17
4445 4805 8.773645 CAACCCATTTTTAGACTTGAAAAATCC 58.226 33.333 5.92 0.00 42.02 3.01
4446 4806 8.262601 ACCCATTTTTAGACTTGAAAAATCCT 57.737 30.769 5.92 0.00 42.02 3.24
4447 4807 9.374711 ACCCATTTTTAGACTTGAAAAATCCTA 57.625 29.630 5.92 0.00 42.02 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.981254 CAATGGATTTGCACCGACAC 58.019 50.000 0.00 0.00 0.00 3.67
76 77 0.745486 CGCTGCCTCATCATGGTTGA 60.745 55.000 0.00 0.00 36.00 3.18
110 111 1.376037 CCCTGGGTCTGTTTCGCTC 60.376 63.158 3.97 0.00 0.00 5.03
140 141 3.294102 GAACGCGAAACCCTAAAACAAG 58.706 45.455 15.93 0.00 0.00 3.16
156 157 1.089920 TACTAGGACCTGTCGAACGC 58.910 55.000 3.53 0.00 0.00 4.84
188 189 2.689983 GACATTCAATTGGGCCTACTGG 59.310 50.000 4.53 0.00 0.00 4.00
189 190 3.355378 TGACATTCAATTGGGCCTACTG 58.645 45.455 4.53 0.00 0.00 2.74
190 191 3.266772 TCTGACATTCAATTGGGCCTACT 59.733 43.478 4.53 0.00 0.00 2.57
191 192 3.620488 TCTGACATTCAATTGGGCCTAC 58.380 45.455 4.53 0.00 0.00 3.18
192 193 4.209538 CATCTGACATTCAATTGGGCCTA 58.790 43.478 4.53 0.00 0.00 3.93
248 249 3.804193 GGTACAGGCTGCGCTTGC 61.804 66.667 15.89 13.35 39.28 4.01
250 251 4.760047 CGGGTACAGGCTGCGCTT 62.760 66.667 15.89 0.00 0.00 4.68
254 255 4.530857 ATCGCGGGTACAGGCTGC 62.531 66.667 15.89 0.00 0.00 5.25
284 285 2.026879 GCCGTCCGATCTGCTCTC 59.973 66.667 0.00 0.00 0.00 3.20
286 287 2.852495 TTTGGCCGTCCGATCTGCTC 62.852 60.000 0.00 0.00 34.14 4.26
319 320 4.035208 AGCATTTTTATCCGTTGGATCGTC 59.965 41.667 0.71 0.00 42.11 4.20
325 326 7.592533 CAGATCATTAGCATTTTTATCCGTTGG 59.407 37.037 0.00 0.00 0.00 3.77
335 336 6.656902 TGTCCTCTCAGATCATTAGCATTTT 58.343 36.000 0.00 0.00 0.00 1.82
348 349 2.968574 AGCACTTTTCTGTCCTCTCAGA 59.031 45.455 0.00 0.00 41.85 3.27
357 358 7.986085 ACATTATAACTGAGCACTTTTCTGT 57.014 32.000 0.00 0.00 0.00 3.41
465 467 0.227234 CGTTTGCGCGACAGCTATAG 59.773 55.000 12.10 0.00 42.32 1.31
591 598 3.132289 GGACAATAGGATGGAAGACGTGA 59.868 47.826 0.00 0.00 0.00 4.35
605 612 3.739401 AAGGTTTCCCTGGGACAATAG 57.261 47.619 16.85 0.00 41.56 1.73
630 637 8.322906 AGTCGAAATTGATTTGATGACACTTA 57.677 30.769 12.01 0.00 33.95 2.24
648 655 7.410800 TCGCTTAGTTTATTCAAAGTCGAAA 57.589 32.000 0.00 0.00 30.45 3.46
651 658 6.989437 TCATCGCTTAGTTTATTCAAAGTCG 58.011 36.000 0.00 0.00 0.00 4.18
653 660 7.907214 ACTCATCGCTTAGTTTATTCAAAGT 57.093 32.000 0.00 0.00 0.00 2.66
701 708 1.476291 CCCCCGCCAGGAAATAGTAAC 60.476 57.143 0.00 0.00 41.02 2.50
717 730 1.338107 AAGTAAAAGCAGCAACCCCC 58.662 50.000 0.00 0.00 0.00 5.40
730 743 5.889289 ACCTACAAAGCAGGTCAAAAGTAAA 59.111 36.000 0.00 0.00 43.04 2.01
731 744 5.442391 ACCTACAAAGCAGGTCAAAAGTAA 58.558 37.500 0.00 0.00 43.04 2.24
732 745 5.043737 ACCTACAAAGCAGGTCAAAAGTA 57.956 39.130 0.00 0.00 43.04 2.24
760 773 1.142748 CTGGAGAGTCCGACATGGC 59.857 63.158 0.40 0.00 40.17 4.40
776 789 6.128849 CCGTTGATTTTATTTTTCAGTGGCTG 60.129 38.462 0.00 0.00 0.00 4.85
783 796 6.419413 GTCTGTGCCGTTGATTTTATTTTTCA 59.581 34.615 0.00 0.00 0.00 2.69
789 802 3.417101 TGGTCTGTGCCGTTGATTTTAT 58.583 40.909 0.00 0.00 0.00 1.40
791 804 1.686355 TGGTCTGTGCCGTTGATTTT 58.314 45.000 0.00 0.00 0.00 1.82
792 805 1.686355 TTGGTCTGTGCCGTTGATTT 58.314 45.000 0.00 0.00 0.00 2.17
817 830 2.802816 GTGTATGGCTCTTATGGCTTCG 59.197 50.000 0.00 0.00 0.00 3.79
818 831 2.802816 CGTGTATGGCTCTTATGGCTTC 59.197 50.000 0.00 0.00 0.00 3.86
820 833 1.541233 GCGTGTATGGCTCTTATGGCT 60.541 52.381 0.00 0.00 0.00 4.75
874 892 0.992072 CACGTGCGTGTATTCCTCAG 59.008 55.000 15.60 0.00 40.91 3.35
899 917 3.446184 CGCAAGAAATATCATCTCGCC 57.554 47.619 0.00 0.00 43.02 5.54
954 980 1.393603 GCAGTAAATTCTCAGGGGGC 58.606 55.000 0.00 0.00 0.00 5.80
968 998 1.302993 GCCCTTCCGTTTGGCAGTA 60.303 57.895 0.00 0.00 44.70 2.74
1004 1043 1.106285 GAAGGTGGCCATGATCAACC 58.894 55.000 9.72 2.76 0.00 3.77
1113 1176 1.896660 GAACTTGCCCTGTGCCGAA 60.897 57.895 0.00 0.00 40.16 4.30
2059 2153 0.898789 AACCCGTCTGTCGTGGATCT 60.899 55.000 8.27 0.00 37.94 2.75
2064 2158 0.170561 CTAGGAACCCGTCTGTCGTG 59.829 60.000 0.00 0.00 37.94 4.35
2089 2183 2.990479 GGGGAGCTTCACATCCGT 59.010 61.111 0.00 0.00 36.38 4.69
2128 2222 4.269523 TGCTTTGCTCTGGGCGGT 62.270 61.111 0.00 0.00 45.43 5.68
2146 2240 1.291184 TGGCAAGTCGATTCGCACTG 61.291 55.000 0.00 0.00 0.00 3.66
2286 2386 0.813210 CTGAAAGCCGGAGATGGAGC 60.813 60.000 5.05 0.00 0.00 4.70
2333 2433 1.750341 TTTCTTCCCGTCTGTGCCGA 61.750 55.000 0.00 0.00 0.00 5.54
2463 2584 1.208293 GAGGATCCCTTCTCGTTTGCT 59.792 52.381 8.55 0.00 31.76 3.91
2596 2717 0.839946 AGCTGGGTTGTGTTGTCTCT 59.160 50.000 0.00 0.00 0.00 3.10
2727 2854 1.300971 CGTCCGACGAGTAGAACCCA 61.301 60.000 16.03 0.00 46.05 4.51
2825 2952 3.387947 AGTACCGTTCGGGCCAGG 61.388 66.667 15.66 3.33 40.62 4.45
2831 2958 0.930310 CATGATGCAGTACCGTTCGG 59.070 55.000 9.81 9.81 0.00 4.30
3441 3698 0.527817 CTCGCCTGGTGGATTACGTC 60.528 60.000 7.51 0.00 34.57 4.34
3461 3718 1.398390 GTGTAAGAAGATTGGCGCAGG 59.602 52.381 10.83 0.00 0.00 4.85
3559 3848 4.507388 GCTCTCCTGAATGATTCGAAGAAG 59.493 45.833 3.35 0.00 45.90 2.85
3572 3861 3.361281 AATGCATGAAGCTCTCCTGAA 57.639 42.857 0.00 0.00 45.94 3.02
3584 3873 5.111989 CGTTCCTCTCTCTTTAATGCATGA 58.888 41.667 0.00 0.00 0.00 3.07
3705 4001 7.921214 CGTCTTATCCTTGAAGCTTATTAGTGA 59.079 37.037 0.00 0.00 0.00 3.41
3717 4013 4.710375 AGCTTAGGACGTCTTATCCTTGAA 59.290 41.667 16.46 0.00 44.64 2.69
3718 4014 4.279145 AGCTTAGGACGTCTTATCCTTGA 58.721 43.478 16.46 0.00 44.64 3.02
3832 4135 4.281688 ACTTTTCCATGTTGATCAGTTGGG 59.718 41.667 16.27 9.14 29.76 4.12
3850 4153 4.131596 ACGTGCCACACAATACTACTTTT 58.868 39.130 0.00 0.00 33.40 2.27
3861 4164 3.880490 AGAAAAGAAATACGTGCCACACA 59.120 39.130 0.00 0.00 33.40 3.72
3889 4195 5.299279 TGATCTCCCAAAAATATCTTTCGCC 59.701 40.000 0.00 0.00 0.00 5.54
3966 4278 0.744874 ACGATAGATGTGACGTGGGG 59.255 55.000 0.00 0.00 37.58 4.96
3987 4299 2.861935 ACGTTTGAACAACTCCTACGTG 59.138 45.455 11.61 0.00 39.88 4.49
4040 4352 4.712829 TCTTCGGTGACTATTGGTCCATTA 59.287 41.667 0.00 0.00 43.89 1.90
4045 4362 4.113354 GTCATCTTCGGTGACTATTGGTC 58.887 47.826 0.21 0.00 42.04 4.02
4058 4375 0.933097 CAAGGATGCGGTCATCTTCG 59.067 55.000 10.66 0.00 46.41 3.79
4203 4521 7.231519 AGTTTTAGTGGGATTTTCTTTCCAGAG 59.768 37.037 0.00 0.00 34.77 3.35
4207 4525 7.145985 GTCAGTTTTAGTGGGATTTTCTTTCC 58.854 38.462 0.00 0.00 0.00 3.13
4255 4615 5.869344 TGATCCGTCAAGTTATCAGAACAAG 59.131 40.000 0.00 0.00 0.00 3.16
4273 4633 3.045601 ACTTCTCAAAGGTGTGATCCG 57.954 47.619 0.00 0.00 36.78 4.18
4281 4641 3.395941 ACTCCATCCAACTTCTCAAAGGT 59.604 43.478 0.00 0.00 36.78 3.50
4296 4656 3.511146 TCAGGGCAAAATGAAACTCCATC 59.489 43.478 0.00 0.00 0.00 3.51
4306 4666 2.029623 CCTCCAGATCAGGGCAAAATG 58.970 52.381 4.05 0.00 0.00 2.32
4316 4676 2.777692 GGGGTAATGTTCCTCCAGATCA 59.222 50.000 0.00 0.00 0.00 2.92
4317 4677 2.777692 TGGGGTAATGTTCCTCCAGATC 59.222 50.000 0.00 0.00 0.00 2.75
4318 4678 2.858644 TGGGGTAATGTTCCTCCAGAT 58.141 47.619 0.00 0.00 0.00 2.90
4319 4679 2.352561 TGGGGTAATGTTCCTCCAGA 57.647 50.000 0.00 0.00 0.00 3.86
4320 4680 2.423373 CCATGGGGTAATGTTCCTCCAG 60.423 54.545 2.85 0.00 32.11 3.86
4321 4681 1.568597 CCATGGGGTAATGTTCCTCCA 59.431 52.381 2.85 0.00 32.74 3.86
4322 4682 1.754201 GCCATGGGGTAATGTTCCTCC 60.754 57.143 15.13 0.00 36.17 4.30
4413 4773 9.753674 TTCAAGTCTAAAAATGGGTTGAGATAT 57.246 29.630 0.00 0.00 0.00 1.63
4414 4774 9.581289 TTTCAAGTCTAAAAATGGGTTGAGATA 57.419 29.630 0.00 0.00 0.00 1.98
4415 4775 8.477419 TTTCAAGTCTAAAAATGGGTTGAGAT 57.523 30.769 0.00 0.00 0.00 2.75
4416 4776 7.889873 TTTCAAGTCTAAAAATGGGTTGAGA 57.110 32.000 0.00 0.00 0.00 3.27
4417 4777 8.940768 TTTTTCAAGTCTAAAAATGGGTTGAG 57.059 30.769 0.00 0.00 32.40 3.02
4418 4778 9.541143 GATTTTTCAAGTCTAAAAATGGGTTGA 57.459 29.630 9.73 0.00 43.22 3.18
4419 4779 8.773645 GGATTTTTCAAGTCTAAAAATGGGTTG 58.226 33.333 9.73 0.00 43.22 3.77
4420 4780 8.713971 AGGATTTTTCAAGTCTAAAAATGGGTT 58.286 29.630 9.73 0.00 43.22 4.11
4421 4781 8.262601 AGGATTTTTCAAGTCTAAAAATGGGT 57.737 30.769 9.73 0.00 43.22 4.51


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

AutoCloner maintained by Alex Coulton.