Multiple sequence alignment - TraesCS6D01G100700

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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 TraesCS6D01G100700 chr6D 100.000 4535 0 0 1 4535 63725135 63729669 0.000000e+00 8375.0
1 TraesCS6D01G100700 chr6D 87.819 509 41 7 4044 4535 69946011 69946515 1.090000e-160 577.0
2 TraesCS6D01G100700 chr6D 83.088 408 41 17 4143 4534 48857176 48857571 3.360000e-91 346.0
3 TraesCS6D01G100700 chr6D 96.429 56 2 0 432 487 63725510 63725565 4.830000e-15 93.5
4 TraesCS6D01G100700 chr6D 96.429 56 2 0 376 431 63725566 63725621 4.830000e-15 93.5
5 TraesCS6D01G100700 chr6B 95.406 3875 103 38 691 4535 137380345 137384174 0.000000e+00 6100.0
6 TraesCS6D01G100700 chr6B 87.726 497 46 12 4044 4535 144964198 144964684 2.370000e-157 566.0
7 TraesCS6D01G100700 chr6B 81.607 473 52 23 4081 4534 122296235 122295779 4.310000e-95 359.0
8 TraesCS6D01G100700 chr6B 86.397 272 32 3 30 299 137372634 137372902 4.440000e-75 292.0
9 TraesCS6D01G100700 chr6B 90.000 130 11 1 507 636 137378971 137379098 2.810000e-37 167.0
10 TraesCS6D01G100700 chr6B 94.253 87 5 0 322 408 137378768 137378854 2.850000e-27 134.0
11 TraesCS6D01G100700 chr6A 94.749 3447 133 28 647 4074 80875470 80878887 0.000000e+00 5319.0
12 TraesCS6D01G100700 chr6A 87.154 506 45 6 4046 4535 87759469 87759970 1.430000e-154 556.0
13 TraesCS6D01G100700 chr6A 86.070 402 46 4 30 431 80874823 80875214 1.510000e-114 424.0
14 TraesCS6D01G100700 chr6A 79.061 511 63 28 4044 4534 65803625 65803139 1.230000e-80 311.0
15 TraesCS6D01G100700 chr6A 87.451 255 20 7 4062 4309 80879067 80879316 2.670000e-72 283.0
16 TraesCS6D01G100700 chr6A 87.255 204 15 6 432 635 80875159 80875351 5.900000e-54 222.0
17 TraesCS6D01G100700 chr5D 92.835 2638 143 13 996 3593 344546417 344543786 0.000000e+00 3783.0
18 TraesCS6D01G100700 chr5D 91.463 82 6 1 4044 4124 23824852 23824933 1.330000e-20 111.0
19 TraesCS6D01G100700 chr5B 92.827 2635 144 13 996 3590 407215316 407217945 0.000000e+00 3777.0
20 TraesCS6D01G100700 chr5B 94.444 54 3 0 1150 1203 311207773 311207720 2.910000e-12 84.2
21 TraesCS6D01G100700 chr5A 92.921 2557 153 6 1056 3590 447535248 447537798 0.000000e+00 3694.0
22 TraesCS6D01G100700 chr1A 89.873 474 23 4 3497 3970 278128856 278129304 1.820000e-163 586.0
23 TraesCS6D01G100700 chr2B 80.786 229 33 7 894 1111 324624149 324623921 7.800000e-38 169.0
24 TraesCS6D01G100700 chr2A 92.174 115 5 3 3655 3769 5609454 5609564 4.700000e-35 159.0
25 TraesCS6D01G100700 chr2A 94.286 70 4 0 1150 1219 704626368 704626299 1.730000e-19 108.0
26 TraesCS6D01G100700 chr2A 90.000 70 7 0 1150 1219 769384828 769384759 1.740000e-14 91.6
27 TraesCS6D01G100700 chr3A 90.588 85 7 1 4044 4127 723439304 723439220 1.330000e-20 111.0
28 TraesCS6D01G100700 chr1D 89.855 69 7 0 1151 1219 4079963 4079895 6.250000e-14 89.8


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 TraesCS6D01G100700 chr6D 63725135 63729669 4534 False 8375.000000 8375 100.000000 1 4535 1 chr6D.!!$F2 4534
1 TraesCS6D01G100700 chr6D 69946011 69946515 504 False 577.000000 577 87.819000 4044 4535 1 chr6D.!!$F3 491
2 TraesCS6D01G100700 chr6B 137378768 137384174 5406 False 2133.666667 6100 93.219667 322 4535 3 chr6B.!!$F3 4213
3 TraesCS6D01G100700 chr6A 80874823 80879316 4493 False 1562.000000 5319 88.881250 30 4309 4 chr6A.!!$F2 4279
4 TraesCS6D01G100700 chr6A 87759469 87759970 501 False 556.000000 556 87.154000 4046 4535 1 chr6A.!!$F1 489
5 TraesCS6D01G100700 chr5D 344543786 344546417 2631 True 3783.000000 3783 92.835000 996 3593 1 chr5D.!!$R1 2597
6 TraesCS6D01G100700 chr5B 407215316 407217945 2629 False 3777.000000 3777 92.827000 996 3590 1 chr5B.!!$F1 2594
7 TraesCS6D01G100700 chr5A 447535248 447537798 2550 False 3694.000000 3694 92.921000 1056 3590 1 chr5A.!!$F1 2534

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
773 2025 0.029567 CACCGATACCTCTCACGCTC 59.970 60.0 0.00 0.00 0.0 5.03 F
778 2030 1.102222 ATACCTCTCACGCTCGTCCC 61.102 60.0 0.00 0.00 0.0 4.46 F
1275 2570 1.169661 CGCTCCTCTACCTGCTCGAT 61.170 60.0 0.00 0.00 0.0 3.59 F
1959 3278 1.718757 GAATGGCTGGTGCGATCCAC 61.719 60.0 5.94 5.94 43.9 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 3113 2.272146 CCAGGTGTTGGGATCGGG 59.728 66.667 0.0 0.0 43.75 5.14 R
2643 3962 2.284625 TCCCAGCCACGATCACCT 60.285 61.111 0.0 0.0 0.00 4.00 R
2973 4292 4.622740 GCATCCATTTCTTCTGAAAAACGG 59.377 41.667 0.0 0.0 44.22 4.44 R
3853 5180 3.008923 TGTGTGAAGCATGATCTGGGTAA 59.991 43.478 0.0 0.0 0.00 2.85 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
26 27 7.872163 TTTGAGTTGATTTTGATATGTGTGC 57.128 32.000 0.00 0.00 0.00 4.57
27 28 6.572167 TGAGTTGATTTTGATATGTGTGCA 57.428 33.333 0.00 0.00 0.00 4.57
28 29 6.979465 TGAGTTGATTTTGATATGTGTGCAA 58.021 32.000 0.00 0.00 0.00 4.08
29 30 7.604549 TGAGTTGATTTTGATATGTGTGCAAT 58.395 30.769 0.00 0.00 0.00 3.56
30 31 7.756272 TGAGTTGATTTTGATATGTGTGCAATC 59.244 33.333 0.00 0.00 0.00 2.67
31 32 7.604549 AGTTGATTTTGATATGTGTGCAATCA 58.395 30.769 0.00 0.00 0.00 2.57
32 33 8.255206 AGTTGATTTTGATATGTGTGCAATCAT 58.745 29.630 9.32 9.32 31.14 2.45
33 34 8.875803 GTTGATTTTGATATGTGTGCAATCATT 58.124 29.630 9.59 0.45 31.14 2.57
34 35 9.438228 TTGATTTTGATATGTGTGCAATCATTT 57.562 25.926 9.59 3.34 31.14 2.32
38 39 7.509050 TTGATATGTGTGCAATCATTTTTCG 57.491 32.000 9.59 0.00 30.17 3.46
49 50 9.356929 GTGCAATCATTTTTCGAAAGTTAAAAG 57.643 29.630 10.98 0.13 32.52 2.27
97 98 6.993786 TCAAAACATACGCAATTATGGAGA 57.006 33.333 2.92 0.00 34.25 3.71
98 99 7.384439 TCAAAACATACGCAATTATGGAGAA 57.616 32.000 2.92 0.00 34.25 2.87
112 113 6.618287 TTATGGAGAAGAAATTATGGTGCG 57.382 37.500 0.00 0.00 0.00 5.34
113 114 3.278574 TGGAGAAGAAATTATGGTGCGG 58.721 45.455 0.00 0.00 0.00 5.69
119 120 3.067106 AGAAATTATGGTGCGGCTATCG 58.933 45.455 0.00 0.00 42.76 2.92
128 129 2.735134 GGTGCGGCTATCGTATTTTAGG 59.265 50.000 0.00 0.00 41.72 2.69
129 130 3.553508 GGTGCGGCTATCGTATTTTAGGA 60.554 47.826 0.00 0.00 41.72 2.94
134 135 4.558898 CGGCTATCGTATTTTAGGACAGCT 60.559 45.833 7.25 0.00 41.42 4.24
136 137 4.150804 GCTATCGTATTTTAGGACAGCTGC 59.849 45.833 15.27 6.61 39.33 5.25
195 196 2.673775 TGACCATCTTTTCTTGCCCA 57.326 45.000 0.00 0.00 0.00 5.36
196 197 2.956132 TGACCATCTTTTCTTGCCCAA 58.044 42.857 0.00 0.00 0.00 4.12
197 198 3.303938 TGACCATCTTTTCTTGCCCAAA 58.696 40.909 0.00 0.00 0.00 3.28
198 199 3.708631 TGACCATCTTTTCTTGCCCAAAA 59.291 39.130 0.00 0.00 0.00 2.44
199 200 4.347583 TGACCATCTTTTCTTGCCCAAAAT 59.652 37.500 0.00 0.00 0.00 1.82
200 201 5.163216 TGACCATCTTTTCTTGCCCAAAATT 60.163 36.000 0.00 0.00 0.00 1.82
204 205 4.702831 TCTTTTCTTGCCCAAAATTCACC 58.297 39.130 0.00 0.00 0.00 4.02
223 224 2.844946 CCTTTTGGTGCCCGAAATTTT 58.155 42.857 6.99 0.00 36.44 1.82
247 248 6.679327 ACTCACTTTTTGGTGTTCTAGAAC 57.321 37.500 25.73 25.73 41.50 3.01
269 270 1.963515 GGGTTGTTGTTGGAGATGCTT 59.036 47.619 0.00 0.00 0.00 3.91
273 274 5.279456 GGGTTGTTGTTGGAGATGCTTTAAT 60.279 40.000 0.00 0.00 0.00 1.40
281 282 3.873361 TGGAGATGCTTTAATTGAGCTCG 59.127 43.478 9.64 0.00 40.75 5.03
287 288 3.310774 TGCTTTAATTGAGCTCGCATCTC 59.689 43.478 9.64 0.00 40.75 2.75
299 300 3.785486 CTCGCATCTCTGTGGTTTATGA 58.215 45.455 0.00 0.00 33.56 2.15
300 301 4.183865 CTCGCATCTCTGTGGTTTATGAA 58.816 43.478 0.00 0.00 33.56 2.57
303 304 5.088739 CGCATCTCTGTGGTTTATGAAAAC 58.911 41.667 0.00 0.00 43.58 2.43
304 305 5.334802 CGCATCTCTGTGGTTTATGAAAACA 60.335 40.000 3.66 0.00 45.68 2.83
310 311 3.992260 TGGTTTATGAAAACACCACGG 57.008 42.857 3.66 0.00 45.68 4.94
311 312 2.034812 TGGTTTATGAAAACACCACGGC 59.965 45.455 3.66 0.00 45.68 5.68
312 313 2.295070 GGTTTATGAAAACACCACGGCT 59.705 45.455 3.66 0.00 45.68 5.52
313 314 3.502979 GGTTTATGAAAACACCACGGCTA 59.497 43.478 3.66 0.00 45.68 3.93
315 316 1.530323 ATGAAAACACCACGGCTACC 58.470 50.000 0.00 0.00 0.00 3.18
316 317 0.470766 TGAAAACACCACGGCTACCT 59.529 50.000 0.00 0.00 0.00 3.08
317 318 0.872388 GAAAACACCACGGCTACCTG 59.128 55.000 0.00 0.00 0.00 4.00
318 319 1.170290 AAAACACCACGGCTACCTGC 61.170 55.000 0.00 0.00 41.94 4.85
319 320 2.332312 AAACACCACGGCTACCTGCA 62.332 55.000 0.00 0.00 45.15 4.41
320 321 2.124507 AACACCACGGCTACCTGCAT 62.125 55.000 0.00 0.00 45.15 3.96
335 336 3.181452 ACCTGCATTGTTTTTGAGCCATT 60.181 39.130 0.00 0.00 0.00 3.16
336 337 4.040217 ACCTGCATTGTTTTTGAGCCATTA 59.960 37.500 0.00 0.00 0.00 1.90
364 365 3.639162 GCTCGACTGAGACTGGATG 57.361 57.895 0.00 0.00 45.57 3.51
415 416 9.448438 TTTTGCACATAGTTTGATAGACTGTAT 57.552 29.630 0.00 0.00 0.00 2.29
416 417 9.448438 TTTGCACATAGTTTGATAGACTGTATT 57.552 29.630 0.00 0.00 0.00 1.89
418 419 9.750125 TGCACATAGTTTGATAGACTGTATTAG 57.250 33.333 0.00 0.00 0.00 1.73
419 420 9.197694 GCACATAGTTTGATAGACTGTATTAGG 57.802 37.037 0.00 0.00 0.00 2.69
423 424 9.765795 ATAGTTTGATAGACTGTATTAGGTTGC 57.234 33.333 0.00 0.00 0.00 4.17
424 425 7.048512 AGTTTGATAGACTGTATTAGGTTGCC 58.951 38.462 0.00 0.00 0.00 4.52
427 428 3.268023 AGACTGTATTAGGTTGCCTGC 57.732 47.619 0.00 0.00 34.61 4.85
429 430 3.200825 AGACTGTATTAGGTTGCCTGCAT 59.799 43.478 0.00 0.00 34.61 3.96
430 431 3.947834 GACTGTATTAGGTTGCCTGCATT 59.052 43.478 0.00 0.00 34.61 3.56
431 432 4.344104 ACTGTATTAGGTTGCCTGCATTT 58.656 39.130 0.00 0.00 34.61 2.32
432 433 5.505780 ACTGTATTAGGTTGCCTGCATTTA 58.494 37.500 0.00 0.00 34.61 1.40
433 434 5.357032 ACTGTATTAGGTTGCCTGCATTTAC 59.643 40.000 0.00 0.00 34.61 2.01
434 435 4.642885 TGTATTAGGTTGCCTGCATTTACC 59.357 41.667 3.75 3.75 34.61 2.85
435 436 2.889170 TAGGTTGCCTGCATTTACCA 57.111 45.000 12.60 0.00 34.61 3.25
436 437 1.549203 AGGTTGCCTGCATTTACCAG 58.451 50.000 12.60 0.00 29.57 4.00
437 438 1.075374 AGGTTGCCTGCATTTACCAGA 59.925 47.619 12.60 0.00 29.57 3.86
438 439 1.892474 GGTTGCCTGCATTTACCAGAA 59.108 47.619 6.60 0.00 32.03 3.02
439 440 2.298729 GGTTGCCTGCATTTACCAGAAA 59.701 45.455 6.60 0.00 32.03 2.52
440 441 3.055891 GGTTGCCTGCATTTACCAGAAAT 60.056 43.478 6.60 0.00 32.03 2.17
441 442 4.176271 GTTGCCTGCATTTACCAGAAATC 58.824 43.478 0.00 0.00 32.03 2.17
442 443 3.429492 TGCCTGCATTTACCAGAAATCA 58.571 40.909 0.00 0.00 32.03 2.57
443 444 4.025360 TGCCTGCATTTACCAGAAATCAT 58.975 39.130 0.00 0.00 32.03 2.45
444 445 5.199723 TGCCTGCATTTACCAGAAATCATA 58.800 37.500 0.00 0.00 32.03 2.15
446 447 6.324512 TGCCTGCATTTACCAGAAATCATATT 59.675 34.615 0.00 0.00 32.03 1.28
447 448 7.147689 TGCCTGCATTTACCAGAAATCATATTT 60.148 33.333 0.00 0.00 32.03 1.40
448 449 7.712205 GCCTGCATTTACCAGAAATCATATTTT 59.288 33.333 0.00 0.00 32.03 1.82
449 450 9.037737 CCTGCATTTACCAGAAATCATATTTTG 57.962 33.333 0.00 0.00 32.03 2.44
450 451 8.422973 TGCATTTACCAGAAATCATATTTTGC 57.577 30.769 0.00 0.00 0.00 3.68
452 453 8.330302 GCATTTACCAGAAATCATATTTTGCAC 58.670 33.333 0.00 0.00 0.00 4.57
453 454 9.368674 CATTTACCAGAAATCATATTTTGCACA 57.631 29.630 0.00 0.00 0.00 4.57
455 456 9.770097 TTTACCAGAAATCATATTTTGCACAAA 57.230 25.926 0.00 0.00 0.00 2.83
456 457 7.894376 ACCAGAAATCATATTTTGCACAAAG 57.106 32.000 0.00 0.00 0.00 2.77
457 458 7.444299 ACCAGAAATCATATTTTGCACAAAGT 58.556 30.769 0.00 0.00 0.00 2.66
458 459 7.933033 ACCAGAAATCATATTTTGCACAAAGTT 59.067 29.630 0.00 0.00 0.00 2.66
459 460 8.776470 CCAGAAATCATATTTTGCACAAAGTTT 58.224 29.630 0.00 0.00 0.00 2.66
460 461 9.588774 CAGAAATCATATTTTGCACAAAGTTTG 57.411 29.630 14.13 14.13 0.00 2.93
479 507 8.494016 AAGTTTGATAGACTGTATTAGGTTGC 57.506 34.615 0.00 0.00 0.00 4.17
501 529 4.050852 CTGCATTAGGAGGCAAATTTCC 57.949 45.455 0.00 0.00 42.67 3.13
502 530 2.765699 TGCATTAGGAGGCAAATTTCCC 59.234 45.455 0.00 0.00 40.00 3.97
503 531 2.103094 GCATTAGGAGGCAAATTTCCCC 59.897 50.000 0.00 0.00 33.83 4.81
504 532 2.137810 TTAGGAGGCAAATTTCCCCG 57.862 50.000 0.00 0.00 33.83 5.73
505 533 0.257616 TAGGAGGCAAATTTCCCCGG 59.742 55.000 0.00 0.00 33.83 5.73
506 534 1.304962 GGAGGCAAATTTCCCCGGT 60.305 57.895 0.00 0.00 0.00 5.28
507 535 0.902984 GGAGGCAAATTTCCCCGGTT 60.903 55.000 0.00 0.00 0.00 4.44
508 536 0.246360 GAGGCAAATTTCCCCGGTTG 59.754 55.000 0.00 0.00 0.00 3.77
522 550 1.605500 CGGTTGATTGCACACATTCG 58.394 50.000 0.00 0.00 0.00 3.34
572 600 5.061853 ACACTACATCGGTCGAGTACATAT 58.938 41.667 0.00 0.00 0.00 1.78
586 614 9.938670 GTCGAGTACATATGTATAGATCCATTC 57.061 37.037 18.27 2.26 32.54 2.67
685 1921 2.063979 ATCCAGATCGACGGCCCAA 61.064 57.895 0.00 0.00 0.00 4.12
712 1963 3.537874 GGGCCTCCGCACTATCGT 61.538 66.667 0.84 0.00 34.62 3.73
713 1964 2.279517 GGCCTCCGCACTATCGTG 60.280 66.667 0.00 0.00 44.07 4.35
722 1973 2.124293 CACTATCGTGCCTAGCCCA 58.876 57.895 0.00 0.00 33.82 5.36
723 1974 0.249489 CACTATCGTGCCTAGCCCAC 60.249 60.000 2.61 2.61 33.82 4.61
728 1979 2.584608 GTGCCTAGCCCACGACAT 59.415 61.111 0.00 0.00 0.00 3.06
742 1994 1.455786 ACGACATGAAAACTCGCTTCG 59.544 47.619 0.00 0.00 0.00 3.79
761 2013 1.152984 CCAGCCCAATGCACCGATA 60.153 57.895 0.00 0.00 44.83 2.92
766 2018 0.469917 CCCAATGCACCGATACCTCT 59.530 55.000 0.00 0.00 0.00 3.69
768 2020 1.138859 CCAATGCACCGATACCTCTCA 59.861 52.381 0.00 0.00 0.00 3.27
769 2021 2.205074 CAATGCACCGATACCTCTCAC 58.795 52.381 0.00 0.00 0.00 3.51
770 2022 0.385751 ATGCACCGATACCTCTCACG 59.614 55.000 0.00 0.00 0.00 4.35
771 2023 1.589196 GCACCGATACCTCTCACGC 60.589 63.158 0.00 0.00 0.00 5.34
772 2024 2.005960 GCACCGATACCTCTCACGCT 62.006 60.000 0.00 0.00 0.00 5.07
773 2025 0.029567 CACCGATACCTCTCACGCTC 59.970 60.000 0.00 0.00 0.00 5.03
774 2026 1.280142 CCGATACCTCTCACGCTCG 59.720 63.158 0.00 0.00 0.00 5.03
778 2030 1.102222 ATACCTCTCACGCTCGTCCC 61.102 60.000 0.00 0.00 0.00 4.46
807 2061 6.524545 TCTCCTTTCTTTTCCCTCCTAAAA 57.475 37.500 0.00 0.00 0.00 1.52
849 2103 2.785868 GCCATGGCGATTCAGTTCT 58.214 52.632 23.48 0.00 0.00 3.01
850 2104 1.953559 GCCATGGCGATTCAGTTCTA 58.046 50.000 23.48 0.00 0.00 2.10
851 2105 1.869767 GCCATGGCGATTCAGTTCTAG 59.130 52.381 23.48 0.00 0.00 2.43
864 2118 5.118729 TCAGTTCTAGCTAGCTAGGTCTT 57.881 43.478 38.82 24.40 44.45 3.01
883 2137 2.452937 CCTCCCGATTCCCCTTCCC 61.453 68.421 0.00 0.00 0.00 3.97
1275 2570 1.169661 CGCTCCTCTACCTGCTCGAT 61.170 60.000 0.00 0.00 0.00 3.59
1470 2789 2.322830 CGACGAGACGGAGGTGTCA 61.323 63.158 0.00 0.00 41.41 3.58
1959 3278 1.718757 GAATGGCTGGTGCGATCCAC 61.719 60.000 5.94 5.94 43.90 4.02
1998 3317 3.282885 GGATCCCATGGTTCAAGACTTC 58.717 50.000 11.73 0.00 0.00 3.01
2322 3641 3.553095 AAGTCGAGGTGGGCTTGGC 62.553 63.158 0.00 0.00 0.00 4.52
2643 3962 4.760530 AAAGATGATGGATCACGGAGAA 57.239 40.909 0.00 0.00 40.03 2.87
2907 4226 6.587608 GGAAATGCCAAGTTCTGTTTAATGAG 59.412 38.462 0.00 0.00 36.34 2.90
2973 4292 2.356667 CTGGAGGTTTCCTGGGCC 59.643 66.667 0.00 0.00 44.36 5.80
3102 4421 6.187682 GTCCCTGGGAATTTTGAGAAATCTA 58.812 40.000 19.06 0.00 34.44 1.98
3369 4689 1.344065 TTCAACTCGCAGGGGAACTA 58.656 50.000 0.00 0.00 0.00 2.24
3556 4876 4.691860 AATGAGTGTGTGCTTCTAATGC 57.308 40.909 0.00 0.00 0.00 3.56
3614 4934 4.147321 GGTGGGTGCTTATCATTGATCAT 58.853 43.478 1.55 0.00 0.00 2.45
3653 4973 5.064325 CGCCCACATTAGTTAGTACCTTTTC 59.936 44.000 0.00 0.00 0.00 2.29
4032 5360 4.618912 CACGACTGATTTCAGACTACTGTG 59.381 45.833 14.29 7.69 46.59 3.66
4033 5361 4.278669 ACGACTGATTTCAGACTACTGTGT 59.721 41.667 14.29 0.00 46.59 3.72
4034 5362 5.472478 ACGACTGATTTCAGACTACTGTGTA 59.528 40.000 14.29 0.00 46.59 2.90
4332 5857 2.494471 CCATCTTGCAGGCTCATGAAAA 59.506 45.455 0.00 0.00 0.00 2.29
4395 5920 1.168714 GGTAAGAACAGCTGCAAGGG 58.831 55.000 15.27 0.00 0.00 3.95
4409 5934 4.736759 GCTGCAAGGGATGATTGAATTCTG 60.737 45.833 7.05 0.00 0.00 3.02
4437 5962 6.042777 GTGGATTGATTGAACGATGAGACTA 58.957 40.000 0.00 0.00 0.00 2.59
4489 6028 8.691797 TGCTAAAACAGTTGAAAAGGAAGTTAT 58.308 29.630 0.00 0.00 0.00 1.89
4490 6029 8.968242 GCTAAAACAGTTGAAAAGGAAGTTATG 58.032 33.333 0.00 0.00 0.00 1.90
4506 6046 6.017523 GGAAGTTATGATCTCAAAGCTAAGCC 60.018 42.308 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.589629 GCACACATATCAAAATCAACTCAAATC 58.410 33.333 0.00 0.00 0.00 2.17
1 2 8.089597 TGCACACATATCAAAATCAACTCAAAT 58.910 29.630 0.00 0.00 0.00 2.32
2 3 7.432059 TGCACACATATCAAAATCAACTCAAA 58.568 30.769 0.00 0.00 0.00 2.69
5 6 7.756272 TGATTGCACACATATCAAAATCAACTC 59.244 33.333 0.00 0.00 31.55 3.01
6 7 7.604549 TGATTGCACACATATCAAAATCAACT 58.395 30.769 0.00 0.00 31.55 3.16
7 8 7.815398 TGATTGCACACATATCAAAATCAAC 57.185 32.000 0.00 0.00 31.55 3.18
8 9 9.438228 AAATGATTGCACACATATCAAAATCAA 57.562 25.926 2.30 0.00 36.48 2.57
9 10 9.438228 AAAATGATTGCACACATATCAAAATCA 57.562 25.926 2.30 0.00 37.08 2.57
12 13 8.433893 CGAAAAATGATTGCACACATATCAAAA 58.566 29.630 2.30 0.00 31.59 2.44
13 14 7.811713 TCGAAAAATGATTGCACACATATCAAA 59.188 29.630 2.30 0.00 31.59 2.69
14 15 7.311408 TCGAAAAATGATTGCACACATATCAA 58.689 30.769 2.30 0.00 31.59 2.57
15 16 6.850555 TCGAAAAATGATTGCACACATATCA 58.149 32.000 0.69 0.69 32.03 2.15
16 17 7.739022 TTCGAAAAATGATTGCACACATATC 57.261 32.000 0.00 0.00 0.00 1.63
17 18 7.814107 ACTTTCGAAAAATGATTGCACACATAT 59.186 29.630 12.41 0.00 0.00 1.78
18 19 7.144661 ACTTTCGAAAAATGATTGCACACATA 58.855 30.769 12.41 0.00 0.00 2.29
19 20 5.984926 ACTTTCGAAAAATGATTGCACACAT 59.015 32.000 12.41 0.00 0.00 3.21
20 21 5.347342 ACTTTCGAAAAATGATTGCACACA 58.653 33.333 12.41 0.00 0.00 3.72
21 22 5.888412 ACTTTCGAAAAATGATTGCACAC 57.112 34.783 12.41 0.00 0.00 3.82
22 23 7.993821 TTAACTTTCGAAAAATGATTGCACA 57.006 28.000 12.41 0.00 0.00 4.57
23 24 9.356929 CTTTTAACTTTCGAAAAATGATTGCAC 57.643 29.630 12.41 0.00 0.00 4.57
24 25 9.092876 ACTTTTAACTTTCGAAAAATGATTGCA 57.907 25.926 12.41 0.00 0.00 4.08
25 26 9.914923 AACTTTTAACTTTCGAAAAATGATTGC 57.085 25.926 12.41 0.00 0.00 3.56
85 86 7.383300 GCACCATAATTTCTTCTCCATAATTGC 59.617 37.037 0.00 0.00 0.00 3.56
97 98 3.498397 CGATAGCCGCACCATAATTTCTT 59.502 43.478 0.00 0.00 0.00 2.52
98 99 3.067106 CGATAGCCGCACCATAATTTCT 58.933 45.455 0.00 0.00 0.00 2.52
112 113 4.686554 CAGCTGTCCTAAAATACGATAGCC 59.313 45.833 5.25 0.00 40.46 3.93
113 114 4.150804 GCAGCTGTCCTAAAATACGATAGC 59.849 45.833 16.64 0.00 40.05 2.97
119 120 4.747605 GCTCTAGCAGCTGTCCTAAAATAC 59.252 45.833 16.64 0.00 45.83 1.89
179 180 5.179929 GTGAATTTTGGGCAAGAAAAGATGG 59.820 40.000 0.00 0.00 0.00 3.51
210 211 4.499037 AAGTGAGTAAAATTTCGGGCAC 57.501 40.909 0.00 0.00 0.00 5.01
212 213 5.176774 CCAAAAAGTGAGTAAAATTTCGGGC 59.823 40.000 0.00 0.00 0.00 6.13
216 217 9.366216 AGAACACCAAAAAGTGAGTAAAATTTC 57.634 29.630 0.00 0.00 40.34 2.17
219 220 9.403583 TCTAGAACACCAAAAAGTGAGTAAAAT 57.596 29.630 0.00 0.00 40.34 1.82
223 224 7.332557 TGTTCTAGAACACCAAAAAGTGAGTA 58.667 34.615 30.07 5.73 45.42 2.59
243 244 2.241176 TCTCCAACAACAACCCTGTTCT 59.759 45.455 0.00 0.00 44.15 3.01
244 245 2.650322 TCTCCAACAACAACCCTGTTC 58.350 47.619 0.00 0.00 44.15 3.18
247 248 1.270550 GCATCTCCAACAACAACCCTG 59.729 52.381 0.00 0.00 0.00 4.45
250 251 3.733443 AAAGCATCTCCAACAACAACC 57.267 42.857 0.00 0.00 0.00 3.77
269 270 3.867493 CACAGAGATGCGAGCTCAATTAA 59.133 43.478 15.40 0.00 34.85 1.40
273 274 0.108472 CCACAGAGATGCGAGCTCAA 60.108 55.000 15.40 0.88 34.85 3.02
281 282 5.858581 GTGTTTTCATAAACCACAGAGATGC 59.141 40.000 0.00 0.00 42.39 3.91
299 300 1.170290 GCAGGTAGCCGTGGTGTTTT 61.170 55.000 0.00 0.00 37.23 2.43
300 301 1.599797 GCAGGTAGCCGTGGTGTTT 60.600 57.895 0.00 0.00 37.23 2.83
303 304 1.377202 AATGCAGGTAGCCGTGGTG 60.377 57.895 0.00 0.00 44.83 4.17
304 305 1.377202 CAATGCAGGTAGCCGTGGT 60.377 57.895 0.00 0.00 44.83 4.16
305 306 0.960364 AACAATGCAGGTAGCCGTGG 60.960 55.000 0.00 0.00 44.83 4.94
306 307 0.881118 AAACAATGCAGGTAGCCGTG 59.119 50.000 0.00 0.00 44.83 4.94
307 308 1.616159 AAAACAATGCAGGTAGCCGT 58.384 45.000 0.00 0.00 44.83 5.68
308 309 2.030363 TCAAAAACAATGCAGGTAGCCG 60.030 45.455 0.00 0.00 44.83 5.52
310 311 2.989166 GCTCAAAAACAATGCAGGTAGC 59.011 45.455 0.00 0.00 45.96 3.58
311 312 3.005684 TGGCTCAAAAACAATGCAGGTAG 59.994 43.478 0.00 0.00 0.00 3.18
312 313 2.961741 TGGCTCAAAAACAATGCAGGTA 59.038 40.909 0.00 0.00 0.00 3.08
313 314 1.761784 TGGCTCAAAAACAATGCAGGT 59.238 42.857 0.00 0.00 0.00 4.00
315 316 5.466058 TGTTAATGGCTCAAAAACAATGCAG 59.534 36.000 0.00 0.00 0.00 4.41
316 317 5.363101 TGTTAATGGCTCAAAAACAATGCA 58.637 33.333 0.00 0.00 0.00 3.96
317 318 5.921004 TGTTAATGGCTCAAAAACAATGC 57.079 34.783 0.00 0.00 0.00 3.56
318 319 7.894376 AGATGTTAATGGCTCAAAAACAATG 57.106 32.000 8.61 0.00 34.08 2.82
319 320 9.590451 CATAGATGTTAATGGCTCAAAAACAAT 57.410 29.630 8.61 5.44 34.08 2.71
320 321 8.034215 CCATAGATGTTAATGGCTCAAAAACAA 58.966 33.333 8.61 0.00 36.50 2.83
335 336 4.276183 GTCTCAGTCGAGCCATAGATGTTA 59.724 45.833 0.00 0.00 39.30 2.41
336 337 3.067461 GTCTCAGTCGAGCCATAGATGTT 59.933 47.826 0.00 0.00 39.30 2.71
350 351 2.451490 TCCACTCATCCAGTCTCAGTC 58.549 52.381 0.00 0.00 30.26 3.51
408 409 2.985896 TGCAGGCAACCTAATACAGTC 58.014 47.619 0.00 0.00 29.64 3.51
409 410 3.652057 ATGCAGGCAACCTAATACAGT 57.348 42.857 0.00 0.00 29.64 3.55
411 412 4.642885 GGTAAATGCAGGCAACCTAATACA 59.357 41.667 0.00 0.00 29.64 2.29
412 413 4.642885 TGGTAAATGCAGGCAACCTAATAC 59.357 41.667 13.15 4.78 29.64 1.89
415 416 3.088532 CTGGTAAATGCAGGCAACCTAA 58.911 45.455 13.15 0.00 29.64 2.69
416 417 2.307392 TCTGGTAAATGCAGGCAACCTA 59.693 45.455 13.15 1.67 29.64 3.08
417 418 1.075374 TCTGGTAAATGCAGGCAACCT 59.925 47.619 13.15 0.00 37.17 3.50
418 419 1.544724 TCTGGTAAATGCAGGCAACC 58.455 50.000 6.66 6.66 37.17 3.77
419 420 3.658757 TTTCTGGTAAATGCAGGCAAC 57.341 42.857 0.00 0.00 0.00 4.17
421 422 3.429492 TGATTTCTGGTAAATGCAGGCA 58.571 40.909 0.00 0.00 0.00 4.75
422 423 4.660789 ATGATTTCTGGTAAATGCAGGC 57.339 40.909 0.00 0.00 0.00 4.85
423 424 9.037737 CAAAATATGATTTCTGGTAAATGCAGG 57.962 33.333 0.00 0.00 0.00 4.85
424 425 8.545420 GCAAAATATGATTTCTGGTAAATGCAG 58.455 33.333 0.00 0.00 0.00 4.41
427 428 9.368674 TGTGCAAAATATGATTTCTGGTAAATG 57.631 29.630 0.00 0.00 0.00 2.32
429 430 9.770097 TTTGTGCAAAATATGATTTCTGGTAAA 57.230 25.926 0.00 0.00 0.00 2.01
430 431 9.421806 CTTTGTGCAAAATATGATTTCTGGTAA 57.578 29.630 0.00 0.00 0.00 2.85
431 432 8.584157 ACTTTGTGCAAAATATGATTTCTGGTA 58.416 29.630 0.00 0.00 0.00 3.25
432 433 7.444299 ACTTTGTGCAAAATATGATTTCTGGT 58.556 30.769 0.00 0.00 0.00 4.00
433 434 7.894376 ACTTTGTGCAAAATATGATTTCTGG 57.106 32.000 0.00 0.00 0.00 3.86
434 435 9.588774 CAAACTTTGTGCAAAATATGATTTCTG 57.411 29.630 0.00 0.00 0.00 3.02
435 436 9.545105 TCAAACTTTGTGCAAAATATGATTTCT 57.455 25.926 0.00 0.00 0.00 2.52
440 441 9.624697 GTCTATCAAACTTTGTGCAAAATATGA 57.375 29.630 0.00 4.28 0.00 2.15
441 442 9.630098 AGTCTATCAAACTTTGTGCAAAATATG 57.370 29.630 0.00 0.00 0.00 1.78
442 443 9.630098 CAGTCTATCAAACTTTGTGCAAAATAT 57.370 29.630 0.00 0.00 0.00 1.28
443 444 8.629158 ACAGTCTATCAAACTTTGTGCAAAATA 58.371 29.630 0.00 0.00 0.00 1.40
444 445 7.491682 ACAGTCTATCAAACTTTGTGCAAAAT 58.508 30.769 0.00 0.00 0.00 1.82
446 447 6.449635 ACAGTCTATCAAACTTTGTGCAAA 57.550 33.333 1.44 0.00 0.00 3.68
447 448 7.744087 ATACAGTCTATCAAACTTTGTGCAA 57.256 32.000 1.44 0.00 0.00 4.08
448 449 7.744087 AATACAGTCTATCAAACTTTGTGCA 57.256 32.000 1.44 0.00 0.00 4.57
449 450 8.391106 CCTAATACAGTCTATCAAACTTTGTGC 58.609 37.037 1.44 0.00 0.00 4.57
450 451 9.436957 ACCTAATACAGTCTATCAAACTTTGTG 57.563 33.333 1.44 0.00 0.00 3.33
453 454 8.947115 GCAACCTAATACAGTCTATCAAACTTT 58.053 33.333 0.00 0.00 0.00 2.66
455 456 7.048512 GGCAACCTAATACAGTCTATCAAACT 58.951 38.462 0.00 0.00 0.00 2.66
456 457 7.011482 CAGGCAACCTAATACAGTCTATCAAAC 59.989 40.741 0.00 0.00 29.64 2.93
457 458 7.047891 CAGGCAACCTAATACAGTCTATCAAA 58.952 38.462 0.00 0.00 29.64 2.69
458 459 6.582636 CAGGCAACCTAATACAGTCTATCAA 58.417 40.000 0.00 0.00 29.64 2.57
459 460 5.453339 GCAGGCAACCTAATACAGTCTATCA 60.453 44.000 0.00 0.00 29.64 2.15
460 461 4.991687 GCAGGCAACCTAATACAGTCTATC 59.008 45.833 0.00 0.00 29.64 2.08
490 518 0.178947 TCAACCGGGGAAATTTGCCT 60.179 50.000 25.69 5.94 38.90 4.75
493 521 2.289320 TGCAATCAACCGGGGAAATTTG 60.289 45.455 6.32 6.15 0.00 2.32
496 524 0.894835 GTGCAATCAACCGGGGAAAT 59.105 50.000 6.32 0.00 0.00 2.17
500 528 1.250154 ATGTGTGCAATCAACCGGGG 61.250 55.000 6.32 0.00 0.00 5.73
501 529 0.602562 AATGTGTGCAATCAACCGGG 59.397 50.000 6.32 0.00 0.00 5.73
502 530 1.728825 CGAATGTGTGCAATCAACCGG 60.729 52.381 0.00 0.00 0.00 5.28
503 531 1.605500 CGAATGTGTGCAATCAACCG 58.394 50.000 0.00 0.00 0.00 4.44
504 532 1.981254 CCGAATGTGTGCAATCAACC 58.019 50.000 0.00 0.00 0.00 3.77
505 533 1.339711 GCCGAATGTGTGCAATCAAC 58.660 50.000 0.00 0.00 0.00 3.18
506 534 0.243365 GGCCGAATGTGTGCAATCAA 59.757 50.000 0.00 0.00 0.00 2.57
507 535 0.608856 AGGCCGAATGTGTGCAATCA 60.609 50.000 0.00 0.00 0.00 2.57
508 536 1.378531 TAGGCCGAATGTGTGCAATC 58.621 50.000 0.00 0.00 0.00 2.67
522 550 7.631717 ACTCTTAATCAAGTCAAATTAGGCC 57.368 36.000 0.00 0.00 33.20 5.19
557 585 6.760298 GGATCTATACATATGTACTCGACCGA 59.240 42.308 17.69 7.20 32.72 4.69
610 666 6.817765 AAAAAGATCAAAATAGACTCGGCA 57.182 33.333 0.00 0.00 0.00 5.69
636 692 3.710044 CGTCCGTCGGTCGATCTA 58.290 61.111 23.72 0.00 42.86 1.98
645 701 0.738762 TCTACTCTGTCCGTCCGTCG 60.739 60.000 0.00 0.00 39.52 5.12
648 1884 1.025113 TGCTCTACTCTGTCCGTCCG 61.025 60.000 0.00 0.00 0.00 4.79
651 1887 1.341089 TGGATGCTCTACTCTGTCCGT 60.341 52.381 0.00 0.00 0.00 4.69
661 1897 1.239347 CCGTCGATCTGGATGCTCTA 58.761 55.000 0.00 0.00 0.00 2.43
685 1921 3.703127 GGAGGCCCGTCGTTTCCT 61.703 66.667 0.00 0.00 0.00 3.36
708 1959 2.758327 TCGTGGGCTAGGCACGAT 60.758 61.111 27.38 0.00 44.81 3.73
711 1962 1.815421 CATGTCGTGGGCTAGGCAC 60.815 63.158 19.14 12.82 0.00 5.01
712 1963 1.549243 TTCATGTCGTGGGCTAGGCA 61.549 55.000 19.14 1.31 0.00 4.75
713 1964 0.392461 TTTCATGTCGTGGGCTAGGC 60.392 55.000 8.00 8.00 0.00 3.93
716 1967 2.695359 GAGTTTTCATGTCGTGGGCTA 58.305 47.619 0.00 0.00 0.00 3.93
717 1968 1.523758 GAGTTTTCATGTCGTGGGCT 58.476 50.000 0.00 0.00 0.00 5.19
718 1969 0.165944 CGAGTTTTCATGTCGTGGGC 59.834 55.000 0.00 0.00 0.00 5.36
719 1970 0.165944 GCGAGTTTTCATGTCGTGGG 59.834 55.000 4.82 0.00 36.09 4.61
722 1973 1.455786 CGAAGCGAGTTTTCATGTCGT 59.544 47.619 4.82 0.00 36.09 4.34
723 1974 2.130815 CGAAGCGAGTTTTCATGTCG 57.869 50.000 0.00 0.00 36.77 4.35
761 2013 3.063084 GGGACGAGCGTGAGAGGT 61.063 66.667 0.00 0.00 0.00 3.85
766 2018 1.303398 AAGAGAGGGACGAGCGTGA 60.303 57.895 0.00 0.00 0.00 4.35
768 2020 1.001887 AGAAGAGAGGGACGAGCGT 60.002 57.895 0.00 0.00 0.00 5.07
769 2021 1.720694 GGAGAAGAGAGGGACGAGCG 61.721 65.000 0.00 0.00 0.00 5.03
770 2022 0.395173 AGGAGAAGAGAGGGACGAGC 60.395 60.000 0.00 0.00 0.00 5.03
771 2023 2.137810 AAGGAGAAGAGAGGGACGAG 57.862 55.000 0.00 0.00 0.00 4.18
772 2024 2.041891 AGAAAGGAGAAGAGAGGGACGA 59.958 50.000 0.00 0.00 0.00 4.20
773 2025 2.452505 AGAAAGGAGAAGAGAGGGACG 58.547 52.381 0.00 0.00 0.00 4.79
774 2026 4.901197 AAAGAAAGGAGAAGAGAGGGAC 57.099 45.455 0.00 0.00 0.00 4.46
778 2030 5.487433 GAGGGAAAAGAAAGGAGAAGAGAG 58.513 45.833 0.00 0.00 0.00 3.20
807 2061 4.515567 GTCTCTCTGTCGATTTGGGTTTTT 59.484 41.667 0.00 0.00 0.00 1.94
864 2118 1.384082 GGAAGGGGAATCGGGAGGA 60.384 63.158 0.00 0.00 0.00 3.71
883 2137 4.821589 GTCCAAGCCGGCCGAGAG 62.822 72.222 30.73 11.80 33.14 3.20
967 2229 3.121019 CGCTAGGGTTCTCTCGGG 58.879 66.667 0.00 0.00 0.00 5.14
1209 2504 1.254284 CGGAGAGCTTGGAGTGGAGT 61.254 60.000 0.00 0.00 0.00 3.85
1275 2570 3.068691 CGGTGGGAGGAGAGCGAA 61.069 66.667 0.00 0.00 35.10 4.70
1577 2896 4.008933 GAGTGGAGCTGGGCACGT 62.009 66.667 0.00 0.00 0.00 4.49
1585 2904 3.699894 CAGGGTGCGAGTGGAGCT 61.700 66.667 0.00 0.00 34.00 4.09
1794 3113 2.272146 CCAGGTGTTGGGATCGGG 59.728 66.667 0.00 0.00 43.75 5.14
2322 3641 3.005472 CCAAAGCATCAATCTGCCCATAG 59.995 47.826 0.00 0.00 43.33 2.23
2643 3962 2.284625 TCCCAGCCACGATCACCT 60.285 61.111 0.00 0.00 0.00 4.00
2907 4226 5.200368 AGTTGGTCACAAAATGGTTCATC 57.800 39.130 0.00 0.00 38.54 2.92
2973 4292 4.622740 GCATCCATTTCTTCTGAAAAACGG 59.377 41.667 0.00 0.00 44.22 4.44
3102 4421 9.926158 TGTAATATGATGTCAAACAAAGCAAAT 57.074 25.926 0.00 0.00 0.00 2.32
3369 4689 6.165577 CAAATCTTCACCCATTTTCCGAAAT 58.834 36.000 0.00 0.00 35.90 2.17
3614 4934 5.545063 TGTGGGCGAGAAATATCAGATAA 57.455 39.130 0.00 0.00 0.00 1.75
3667 4987 8.514594 CAGCACTTCAAATATACTCCAAAAAGA 58.485 33.333 0.00 0.00 0.00 2.52
3668 4988 7.756722 CCAGCACTTCAAATATACTCCAAAAAG 59.243 37.037 0.00 0.00 0.00 2.27
3779 5102 3.019564 AGTATTTGAGAACATGCTGGCC 58.980 45.455 0.00 0.00 0.00 5.36
3853 5180 3.008923 TGTGTGAAGCATGATCTGGGTAA 59.991 43.478 0.00 0.00 0.00 2.85
4332 5857 6.942532 TTTAGAGTGTTGCTTCATCAGTTT 57.057 33.333 0.00 0.00 0.00 2.66
4395 5920 7.500227 TCAATCCACCTACAGAATTCAATCATC 59.500 37.037 8.44 0.00 0.00 2.92
4409 5934 5.116180 TCATCGTTCAATCAATCCACCTAC 58.884 41.667 0.00 0.00 0.00 3.18
4437 5962 6.458888 GCAACAGAAAGCAAAAGAGTTAGACT 60.459 38.462 0.00 0.00 0.00 3.24
4489 6028 6.239217 TCATTAGGCTTAGCTTTGAGATCA 57.761 37.500 3.59 0.00 0.00 2.92
4490 6029 6.933521 TCATCATTAGGCTTAGCTTTGAGATC 59.066 38.462 3.59 0.00 0.00 2.75
4491 6030 6.835174 TCATCATTAGGCTTAGCTTTGAGAT 58.165 36.000 3.59 0.48 0.00 2.75


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

AutoCloner maintained by Alex Coulton.