Multiple sequence alignment - TraesCS5D01G108700

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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 TraesCS5D01G108700 chr5D 100.000 4557 0 0 1 4557 122615046 122619602 0.000000e+00 8416.0
1 TraesCS5D01G108700 chr5B 93.554 2994 147 20 1348 4310 136006702 136009680 0.000000e+00 4418.0
2 TraesCS5D01G108700 chr5B 95.079 630 19 6 697 1320 136006081 136006704 0.000000e+00 981.0
3 TraesCS5D01G108700 chr5B 100.000 31 0 0 274 304 455202138 455202108 1.770000e-04 58.4
4 TraesCS5D01G108700 chr5A 93.211 2077 98 21 2356 4408 135059010 135061067 0.000000e+00 3014.0
5 TraesCS5D01G108700 chr5A 95.806 1693 47 11 668 2349 135056900 135058579 0.000000e+00 2712.0
6 TraesCS5D01G108700 chr5A 90.204 490 36 6 3 483 135055724 135056210 2.990000e-176 628.0
7 TraesCS5D01G108700 chr6A 100.000 31 0 0 274 304 280996437 280996467 1.770000e-04 58.4
8 TraesCS5D01G108700 chr7B 100.000 30 0 0 275 304 354979057 354979086 6.370000e-04 56.5
9 TraesCS5D01G108700 chr6D 100.000 30 0 0 275 304 101912807 101912778 6.370000e-04 56.5
10 TraesCS5D01G108700 chr4D 100.000 30 0 0 274 303 141086588 141086559 6.370000e-04 56.5
11 TraesCS5D01G108700 chr1B 100.000 30 0 0 274 303 434570134 434570105 6.370000e-04 56.5


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 TraesCS5D01G108700 chr5D 122615046 122619602 4556 False 8416.0 8416 100.000000 1 4557 1 chr5D.!!$F1 4556
1 TraesCS5D01G108700 chr5B 136006081 136009680 3599 False 2699.5 4418 94.316500 697 4310 2 chr5B.!!$F1 3613
2 TraesCS5D01G108700 chr5A 135055724 135061067 5343 False 2118.0 3014 93.073667 3 4408 3 chr5A.!!$F1 4405

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
189 191 0.178861 ATGTCCTCCAGTGGTTCCCT 60.179 55.0 9.54 0.00 0.0 4.20 F
753 1270 0.179048 TTGCATATCCACGGCTGAGG 60.179 55.0 1.96 1.96 0.0 3.86 F
1631 2156 0.394762 GCAACTGGATCTGGATGGCA 60.395 55.0 0.00 0.00 0.0 4.92 F
2089 2623 1.239968 GCCAGGAAGCAGGACACTTG 61.240 60.0 0.00 0.00 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 2122 0.041926 GTTGCAACACCGGTTACGTC 60.042 55.0 24.52 0.00 38.78 4.34 R
2735 3697 0.251297 TGGGTGAATCACTTGGCCAG 60.251 55.0 13.53 2.72 34.40 4.85 R
3149 4114 1.651240 ATCAGCACATTGAGCGTGGC 61.651 55.0 0.30 0.00 37.01 5.01 R
3958 4927 0.466124 CCAAGAATCGGAGACCCTCC 59.534 60.0 2.97 2.97 46.44 4.30 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
19 20 2.808906 AACCATTGGCTTCTACCTCC 57.191 50.000 1.54 0.00 0.00 4.30
74 76 1.304381 TGCTTGTTCTGGGATGCCC 60.304 57.895 0.00 0.00 45.71 5.36
83 85 3.530260 GGGATGCCCAATGGTGCG 61.530 66.667 0.00 0.00 44.65 5.34
104 106 2.405143 GCAATCCGGCCTTTAGGTC 58.595 57.895 0.00 0.00 37.57 3.85
111 113 1.205417 CCGGCCTTTAGGTCTAAACGA 59.795 52.381 0.00 0.00 37.76 3.85
140 142 5.305644 CCTACAGAGAGCAGTTATATGGGTT 59.694 44.000 0.00 0.00 0.00 4.11
161 163 6.037726 GGTTCTTAACACAACCGATGTTTTT 58.962 36.000 0.00 0.00 41.46 1.94
189 191 0.178861 ATGTCCTCCAGTGGTTCCCT 60.179 55.000 9.54 0.00 0.00 4.20
197 199 0.602905 CAGTGGTTCCCTTGTCCGAC 60.603 60.000 0.00 0.00 0.00 4.79
223 225 4.901881 GTCGTGTTGTTACAACTATGTTGC 59.098 41.667 25.61 8.69 41.05 4.17
225 227 4.215965 GTGTTGTTACAACTATGTTGCCG 58.784 43.478 25.61 0.00 41.05 5.69
226 228 3.878103 TGTTGTTACAACTATGTTGCCGT 59.122 39.130 25.61 0.00 41.05 5.68
250 252 2.747686 GCCGTTGTCCAAGGAGGA 59.252 61.111 1.51 0.00 46.75 3.71
263 265 1.112315 AGGAGGACTGGCGAGCTATG 61.112 60.000 0.00 0.00 0.00 2.23
282 284 5.819901 GCTATGTGAAGCTCTAAAACCATCT 59.180 40.000 0.00 0.00 39.50 2.90
283 285 6.238320 GCTATGTGAAGCTCTAAAACCATCTG 60.238 42.308 0.00 0.00 39.50 2.90
285 287 3.691609 GTGAAGCTCTAAAACCATCTGGG 59.308 47.826 0.54 0.00 44.81 4.45
288 290 3.126453 AGCTCTAAAACCATCTGGGGAT 58.874 45.455 0.54 0.00 42.91 3.85
316 318 0.527565 CTTTCAAGTTGGATGCCGGG 59.472 55.000 2.18 0.00 0.00 5.73
317 319 1.531739 TTTCAAGTTGGATGCCGGGC 61.532 55.000 13.32 13.32 0.00 6.13
361 363 5.470098 TGACAAGAGAGGCTCAATGTTAAAC 59.530 40.000 18.26 6.97 34.58 2.01
369 371 2.807676 CTCAATGTTAAACCAGGGGCT 58.192 47.619 0.00 0.00 0.00 5.19
413 423 6.785633 CACGAATGCTTAATCTCACATTTG 57.214 37.500 0.00 0.00 39.03 2.32
427 437 4.558178 TCACATTTGCATCATTGGTTCAC 58.442 39.130 0.00 0.00 0.00 3.18
435 445 2.198827 TCATTGGTTCACGGCTGATT 57.801 45.000 0.00 0.00 0.00 2.57
448 458 2.361104 TGATTTGGTGGCTCGGGC 60.361 61.111 0.00 0.00 37.82 6.13
449 459 2.361104 GATTTGGTGGCTCGGGCA 60.361 61.111 10.74 2.21 40.87 5.36
453 463 3.673956 TTGGTGGCTCGGGCATACG 62.674 63.158 10.74 0.00 40.92 3.06
478 488 6.230472 GGAAGACAAAGCAAATTATGGGTTT 58.770 36.000 0.00 0.00 35.30 3.27
484 494 6.371595 AAAGCAAATTATGGGTTTGATCCA 57.628 33.333 3.03 0.00 38.51 3.41
485 495 5.603170 AGCAAATTATGGGTTTGATCCAG 57.397 39.130 3.03 0.00 38.51 3.86
486 496 5.271598 AGCAAATTATGGGTTTGATCCAGA 58.728 37.500 3.03 0.00 38.51 3.86
487 497 5.901276 AGCAAATTATGGGTTTGATCCAGAT 59.099 36.000 3.03 0.00 38.51 2.90
489 499 6.441274 CAAATTATGGGTTTGATCCAGATCG 58.559 40.000 3.33 0.00 40.63 3.69
491 501 2.401583 TGGGTTTGATCCAGATCGTG 57.598 50.000 3.33 0.00 40.63 4.35
492 502 1.017387 GGGTTTGATCCAGATCGTGC 58.983 55.000 3.33 0.00 40.63 5.34
502 913 1.592669 AGATCGTGCGCCATGTAGC 60.593 57.895 4.18 3.04 0.00 3.58
541 952 8.650714 CAGCATTCTTTTTAAAACTGCTATTCC 58.349 33.333 18.50 0.00 36.41 3.01
543 954 7.602265 GCATTCTTTTTAAAACTGCTATTCCCA 59.398 33.333 0.00 0.00 0.00 4.37
563 974 4.296621 CATGATCTGGATCCAATGGCTA 57.703 45.455 17.00 0.75 37.02 3.93
578 990 0.394352 GGCTATGGGGTGTTCTGTGG 60.394 60.000 0.00 0.00 0.00 4.17
583 995 2.154074 GGGGTGTTCTGTGGGACCT 61.154 63.158 0.00 0.00 0.00 3.85
585 997 0.250770 GGGTGTTCTGTGGGACCTTC 60.251 60.000 0.00 0.00 0.00 3.46
605 1017 7.302948 ACCTTCCCTAGTTAACATTTCCTTTT 58.697 34.615 8.61 0.00 0.00 2.27
606 1018 7.787904 ACCTTCCCTAGTTAACATTTCCTTTTT 59.212 33.333 8.61 0.00 0.00 1.94
659 1071 5.668558 AGATACCACGACACAAAGAAAAC 57.331 39.130 0.00 0.00 0.00 2.43
661 1073 5.587043 AGATACCACGACACAAAGAAAACAA 59.413 36.000 0.00 0.00 0.00 2.83
662 1074 4.091453 ACCACGACACAAAGAAAACAAG 57.909 40.909 0.00 0.00 0.00 3.16
663 1075 3.504520 ACCACGACACAAAGAAAACAAGT 59.495 39.130 0.00 0.00 0.00 3.16
664 1076 3.851403 CCACGACACAAAGAAAACAAGTG 59.149 43.478 0.00 0.00 36.34 3.16
665 1077 4.378978 CCACGACACAAAGAAAACAAGTGA 60.379 41.667 0.00 0.00 34.47 3.41
666 1078 5.331902 CACGACACAAAGAAAACAAGTGAT 58.668 37.500 0.00 0.00 34.47 3.06
667 1079 5.227805 CACGACACAAAGAAAACAAGTGATG 59.772 40.000 0.00 0.00 34.47 3.07
668 1080 5.106317 ACGACACAAAGAAAACAAGTGATGT 60.106 36.000 0.00 0.00 46.82 3.06
688 1205 5.132897 TGTTGAAGAAACACTGCAAACTT 57.867 34.783 0.00 0.00 44.73 2.66
691 1208 5.888691 TGAAGAAACACTGCAAACTTACA 57.111 34.783 0.00 0.00 29.99 2.41
719 1236 2.231964 ACAAATGTGGCATGACATGTCC 59.768 45.455 22.85 17.17 36.66 4.02
739 1256 6.076653 TGTCCCATGTATATCCATTTTGCAT 58.923 36.000 0.00 0.00 0.00 3.96
753 1270 0.179048 TTGCATATCCACGGCTGAGG 60.179 55.000 1.96 1.96 0.00 3.86
754 1271 1.963338 GCATATCCACGGCTGAGGC 60.963 63.158 3.76 0.00 37.82 4.70
759 1276 4.864334 CCACGGCTGAGGCATCCC 62.864 72.222 6.86 0.00 40.87 3.85
762 1279 1.460305 ACGGCTGAGGCATCCCTAT 60.460 57.895 6.86 0.00 43.12 2.57
1107 1630 1.728971 CCGCTGTCTTGTCACAGATTC 59.271 52.381 4.77 0.00 45.92 2.52
1124 1647 5.065218 ACAGATTCGGTCATTTGCATAGTTC 59.935 40.000 0.00 0.00 0.00 3.01
1133 1656 5.734498 GTCATTTGCATAGTTCTAGTTTGCG 59.266 40.000 0.00 0.00 36.11 4.85
1134 1657 5.641636 TCATTTGCATAGTTCTAGTTTGCGA 59.358 36.000 0.00 0.00 36.11 5.10
1316 1839 8.800370 TCATATGCCTGTAATTTTCACACTTA 57.200 30.769 0.00 0.00 0.00 2.24
1470 1993 6.471233 AGAAAGGCAGAAAAGCTTTAACTT 57.529 33.333 13.10 9.55 32.18 2.66
1511 2036 3.895041 ACCTTACACTGGTGGGAAAATTG 59.105 43.478 5.70 0.00 36.30 2.32
1597 2122 1.863267 TTCCAAAATGGCTGCGTTTG 58.137 45.000 12.44 12.44 37.47 2.93
1608 2133 1.216941 CTGCGTTTGACGTAACCGGT 61.217 55.000 0.00 0.00 44.73 5.28
1631 2156 0.394762 GCAACTGGATCTGGATGGCA 60.395 55.000 0.00 0.00 0.00 4.92
1854 2380 2.862541 TGTATATTGCCATGTGCCTCC 58.137 47.619 4.07 0.00 40.16 4.30
1874 2400 2.283676 TCTGACCCGGAGTGTCCC 60.284 66.667 0.73 0.00 31.13 4.46
1989 2523 1.600957 CATGGTTGCATCGTGATCCTC 59.399 52.381 4.34 0.00 0.00 3.71
2034 2568 8.716674 TGGGTTAAATATCGAATACCTAGACT 57.283 34.615 0.00 0.00 0.00 3.24
2089 2623 1.239968 GCCAGGAAGCAGGACACTTG 61.240 60.000 0.00 0.00 0.00 3.16
2342 2878 1.649664 CACTCTGGCTCGAAATCTGG 58.350 55.000 0.00 0.00 0.00 3.86
2389 3349 7.485913 CGTGTTGCTTGCTTTATCTATTTTCAT 59.514 33.333 0.00 0.00 0.00 2.57
2414 3374 7.173722 TGGGATTAATTTGCATTTGGTTGATT 58.826 30.769 0.00 0.00 0.00 2.57
2505 3466 6.038161 TGTGTTTGAACAGTTCAGTTATGGAG 59.962 38.462 15.61 0.00 41.38 3.86
2688 3649 6.454795 CAATAGTAAAAGTTTGCCACCATGT 58.545 36.000 0.00 0.00 0.00 3.21
2735 3697 5.899299 TCCGAACCTTTGTACTTCTATAGC 58.101 41.667 0.00 0.00 0.00 2.97
3163 4128 1.155889 TTACAGCCACGCTCAATGTG 58.844 50.000 0.00 0.00 36.40 3.21
3211 4176 1.418097 TTCTTGAGCAGGCCACAGGA 61.418 55.000 5.01 2.67 0.00 3.86
3235 4200 1.528129 CACAGGCCAAGAAAGAGACC 58.472 55.000 5.01 0.00 0.00 3.85
3304 4269 2.847234 ACCCCTGTCACAGCGGAA 60.847 61.111 15.86 0.00 33.49 4.30
3313 4278 4.159377 TGTCACAGCGGAATCAAAATTC 57.841 40.909 0.00 0.00 40.56 2.17
3376 4341 1.565759 CTCCCCATCCCACAGAAATGA 59.434 52.381 0.00 0.00 0.00 2.57
3385 4350 2.290260 CCCACAGAAATGACAGTAGCCA 60.290 50.000 0.00 0.00 0.00 4.75
3389 4354 5.455392 CACAGAAATGACAGTAGCCAAAAG 58.545 41.667 0.00 0.00 0.00 2.27
3390 4355 5.239306 CACAGAAATGACAGTAGCCAAAAGA 59.761 40.000 0.00 0.00 0.00 2.52
3391 4356 5.827797 ACAGAAATGACAGTAGCCAAAAGAA 59.172 36.000 0.00 0.00 0.00 2.52
3392 4357 6.016777 ACAGAAATGACAGTAGCCAAAAGAAG 60.017 38.462 0.00 0.00 0.00 2.85
3393 4358 4.773323 AATGACAGTAGCCAAAAGAAGC 57.227 40.909 0.00 0.00 0.00 3.86
3394 4359 2.143122 TGACAGTAGCCAAAAGAAGCG 58.857 47.619 0.00 0.00 0.00 4.68
3395 4360 2.143925 GACAGTAGCCAAAAGAAGCGT 58.856 47.619 0.00 0.00 0.00 5.07
3397 4362 2.143122 CAGTAGCCAAAAGAAGCGTCA 58.857 47.619 1.61 0.00 0.00 4.35
3405 4371 4.379394 GCCAAAAGAAGCGTCATTCATACA 60.379 41.667 1.61 0.00 0.00 2.29
3597 4563 3.566351 AGCTTTAGAAGGCAAAGGTGTT 58.434 40.909 0.00 0.00 41.00 3.32
3854 4820 7.387397 GCTAATGGACCTATGAAGATTGAAGAG 59.613 40.741 0.00 0.00 0.00 2.85
3867 4833 6.251655 AGATTGAAGAGTCACTGCATTTTC 57.748 37.500 0.00 0.00 33.64 2.29
3874 4840 5.825507 AGAGTCACTGCATTTTCTGTTTTC 58.174 37.500 0.00 0.00 0.00 2.29
3885 4854 6.642131 GCATTTTCTGTTTTCTTGCATGTCTA 59.358 34.615 0.00 0.00 0.00 2.59
3942 4911 5.939764 TCTTTCATACCACAGCTATGACT 57.060 39.130 0.00 0.00 31.63 3.41
3948 4917 6.283694 TCATACCACAGCTATGACTCATTTC 58.716 40.000 0.00 0.00 0.00 2.17
3951 4920 3.801050 CCACAGCTATGACTCATTTCTCG 59.199 47.826 0.00 0.00 0.00 4.04
3953 4922 5.450550 CCACAGCTATGACTCATTTCTCGTA 60.451 44.000 0.00 0.00 0.00 3.43
3954 4923 6.036470 CACAGCTATGACTCATTTCTCGTAA 58.964 40.000 0.00 0.00 0.00 3.18
3955 4924 6.531594 CACAGCTATGACTCATTTCTCGTAAA 59.468 38.462 0.00 0.00 0.00 2.01
3958 4927 8.113062 CAGCTATGACTCATTTCTCGTAAAAAG 58.887 37.037 0.00 0.00 0.00 2.27
3981 4950 1.555533 GGGTCTCCGATTCTTGGTTCT 59.444 52.381 0.00 0.00 0.00 3.01
4056 5026 3.055591 AGATAATGTCTCGCTTGCATCG 58.944 45.455 2.85 2.85 28.45 3.84
4069 5039 3.747193 CTTGCATCGTTATGGTGTTGTC 58.253 45.455 0.00 0.00 33.38 3.18
4081 5051 4.695217 TGGTGTTGTCTTGTTGAACTTC 57.305 40.909 0.00 0.00 0.00 3.01
4082 5052 4.075682 TGGTGTTGTCTTGTTGAACTTCA 58.924 39.130 0.00 0.00 0.00 3.02
4089 5059 7.754924 TGTTGTCTTGTTGAACTTCAAAGAATC 59.245 33.333 5.76 2.70 38.22 2.52
4116 5086 8.021898 AGCACATTATAGCACCCAAAATAAAT 57.978 30.769 0.00 0.00 0.00 1.40
4149 5129 0.541863 AGCACATCTACTTTCCCCCG 59.458 55.000 0.00 0.00 0.00 5.73
4151 5131 1.339727 GCACATCTACTTTCCCCCGTT 60.340 52.381 0.00 0.00 0.00 4.44
4176 5156 4.341487 ACTAATTTGGGCTCACTTAACCC 58.659 43.478 0.00 0.00 44.52 4.11
4190 5170 3.244457 ACTTAACCCTAAGTCAGCCACAC 60.244 47.826 0.00 0.00 43.55 3.82
4217 5204 5.859205 CCCTTATCTGATTTTTGGAAGGG 57.141 43.478 15.68 15.68 44.18 3.95
4233 5222 3.195610 GGAAGGGCAGGATTAACCAAAAG 59.804 47.826 0.00 0.00 42.04 2.27
4252 5241 7.603784 ACCAAAAGAATCTGCAAAATTCCATAC 59.396 33.333 14.71 0.00 34.34 2.39
4258 5247 4.484236 TCTGCAAAATTCCATACGCTTTG 58.516 39.130 0.00 0.00 0.00 2.77
4259 5248 3.639759 GCAAAATTCCATACGCTTTGC 57.360 42.857 2.46 2.46 43.38 3.68
4261 5250 3.061161 GCAAAATTCCATACGCTTTGCTG 59.939 43.478 9.86 0.00 45.26 4.41
4397 5387 9.887629 TTCAAATCAACATTAATATGCACCATT 57.112 25.926 0.00 0.00 35.03 3.16
4425 5415 9.585099 TTTTGAACTAACATTCAATATGCATCC 57.415 29.630 0.19 0.00 45.55 3.51
4426 5416 8.523915 TTGAACTAACATTCAATATGCATCCT 57.476 30.769 0.19 0.00 42.32 3.24
4427 5417 8.523915 TGAACTAACATTCAATATGCATCCTT 57.476 30.769 0.19 0.00 35.65 3.36
4428 5418 9.625747 TGAACTAACATTCAATATGCATCCTTA 57.374 29.630 0.19 0.00 35.65 2.69
4433 5423 8.597662 AACATTCAATATGCATCCTTAATTGC 57.402 30.769 0.19 0.00 39.33 3.56
4440 5430 2.354510 TGCATCCTTAATTGCACGTAGC 59.645 45.455 0.00 0.00 43.54 3.58
4451 5441 2.309898 GCACGTAGCACAATCGTTTT 57.690 45.000 5.30 0.00 44.79 2.43
4452 5442 2.646250 GCACGTAGCACAATCGTTTTT 58.354 42.857 5.30 0.00 44.79 1.94
4502 5492 2.826674 TTTCAATAAGCAGGGGAGGG 57.173 50.000 0.00 0.00 0.00 4.30
4503 5493 1.979809 TTCAATAAGCAGGGGAGGGA 58.020 50.000 0.00 0.00 0.00 4.20
4504 5494 1.213296 TCAATAAGCAGGGGAGGGAC 58.787 55.000 0.00 0.00 0.00 4.46
4505 5495 0.918983 CAATAAGCAGGGGAGGGACA 59.081 55.000 0.00 0.00 0.00 4.02
4506 5496 0.919710 AATAAGCAGGGGAGGGACAC 59.080 55.000 0.00 0.00 0.00 3.67
4507 5497 0.044855 ATAAGCAGGGGAGGGACACT 59.955 55.000 0.00 0.00 0.00 3.55
4508 5498 0.714180 TAAGCAGGGGAGGGACACTA 59.286 55.000 0.00 0.00 0.00 2.74
4509 5499 0.178873 AAGCAGGGGAGGGACACTAA 60.179 55.000 0.00 0.00 0.00 2.24
4510 5500 0.178873 AGCAGGGGAGGGACACTAAA 60.179 55.000 0.00 0.00 0.00 1.85
4511 5501 0.696501 GCAGGGGAGGGACACTAAAA 59.303 55.000 0.00 0.00 0.00 1.52
4512 5502 1.074889 GCAGGGGAGGGACACTAAAAA 59.925 52.381 0.00 0.00 0.00 1.94
4533 5523 5.462034 AAAGCGAAGAAAAGATCAGATCG 57.538 39.130 4.67 0.00 35.39 3.69
4534 5524 4.377839 AGCGAAGAAAAGATCAGATCGA 57.622 40.909 4.67 0.00 34.69 3.59
4535 5525 4.942852 AGCGAAGAAAAGATCAGATCGAT 58.057 39.130 0.00 0.00 34.69 3.59
4536 5526 4.744137 AGCGAAGAAAAGATCAGATCGATG 59.256 41.667 0.54 0.00 34.69 3.84
4537 5527 4.505922 GCGAAGAAAAGATCAGATCGATGT 59.494 41.667 0.54 0.00 34.69 3.06
4538 5528 5.687730 GCGAAGAAAAGATCAGATCGATGTA 59.312 40.000 0.54 0.00 34.69 2.29
4539 5529 6.199154 GCGAAGAAAAGATCAGATCGATGTAA 59.801 38.462 0.54 0.00 34.69 2.41
4540 5530 7.095857 GCGAAGAAAAGATCAGATCGATGTAAT 60.096 37.037 0.54 0.00 34.69 1.89
4541 5531 8.759641 CGAAGAAAAGATCAGATCGATGTAATT 58.240 33.333 0.54 0.00 34.69 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.285078 GGGAGGTAGAAGCCAATGGTT 59.715 52.381 0.00 0.00 34.19 3.67
1 2 0.919710 GGGAGGTAGAAGCCAATGGT 59.080 55.000 0.00 0.00 0.00 3.55
8 9 1.497161 TTGGCTAGGGAGGTAGAAGC 58.503 55.000 0.00 0.00 0.00 3.86
74 76 1.434696 GGATTGCCTCGCACCATTG 59.565 57.895 0.00 0.00 38.71 2.82
76 78 2.514592 CGGATTGCCTCGCACCAT 60.515 61.111 0.00 0.00 38.71 3.55
104 106 4.425520 CTCTCTGTAGGGCTTTCGTTTAG 58.574 47.826 0.00 0.00 0.00 1.85
140 142 5.038033 GCAAAAACATCGGTTGTGTTAAGA 58.962 37.500 0.00 0.00 38.76 2.10
197 199 4.207635 ACATAGTTGTAACAACACGACACG 59.792 41.667 5.53 0.00 35.57 4.49
233 235 2.747686 TCCTCCTTGGACAACGGC 59.252 61.111 0.00 0.00 40.56 5.68
243 245 0.397816 ATAGCTCGCCAGTCCTCCTT 60.398 55.000 0.00 0.00 0.00 3.36
250 252 0.460987 GCTTCACATAGCTCGCCAGT 60.461 55.000 0.00 0.00 38.15 4.00
263 265 3.691609 CCCAGATGGTTTTAGAGCTTCAC 59.308 47.826 0.00 0.00 33.65 3.18
316 318 7.154656 TGTCATCTATGTATACAACATCCAGC 58.845 38.462 10.14 0.00 46.15 4.85
317 319 9.201127 CTTGTCATCTATGTATACAACATCCAG 57.799 37.037 10.14 0.07 46.15 3.86
333 335 4.713814 ACATTGAGCCTCTCTTGTCATCTA 59.286 41.667 0.00 0.00 0.00 1.98
341 343 4.985538 TGGTTTAACATTGAGCCTCTCTT 58.014 39.130 0.00 0.00 0.00 2.85
346 348 2.557452 CCCCTGGTTTAACATTGAGCCT 60.557 50.000 0.00 0.00 0.00 4.58
347 349 1.824852 CCCCTGGTTTAACATTGAGCC 59.175 52.381 0.00 0.00 0.00 4.70
361 363 0.749454 GCAAGTCACATAGCCCCTGG 60.749 60.000 0.00 0.00 0.00 4.45
393 395 6.976349 TGATGCAAATGTGAGATTAAGCATTC 59.024 34.615 13.57 9.23 41.07 2.67
395 397 6.459670 TGATGCAAATGTGAGATTAAGCAT 57.540 33.333 12.65 12.65 43.38 3.79
396 398 5.900865 TGATGCAAATGTGAGATTAAGCA 57.099 34.783 5.17 5.17 35.03 3.91
413 423 0.179156 CAGCCGTGAACCAATGATGC 60.179 55.000 0.00 0.00 0.00 3.91
427 437 2.753966 CGAGCCACCAAATCAGCCG 61.754 63.158 0.00 0.00 0.00 5.52
435 445 2.270850 GTATGCCCGAGCCACCAA 59.729 61.111 0.00 0.00 38.69 3.67
448 458 4.701956 ATTTGCTTTGTCTTCCCGTATG 57.298 40.909 0.00 0.00 0.00 2.39
449 459 6.183360 CCATAATTTGCTTTGTCTTCCCGTAT 60.183 38.462 0.00 0.00 0.00 3.06
453 463 4.222810 ACCCATAATTTGCTTTGTCTTCCC 59.777 41.667 0.00 0.00 0.00 3.97
478 488 2.031674 ATGGCGCACGATCTGGATCA 62.032 55.000 10.83 0.00 37.69 2.92
483 493 1.825285 GCTACATGGCGCACGATCTG 61.825 60.000 10.83 0.00 0.00 2.90
484 494 1.592669 GCTACATGGCGCACGATCT 60.593 57.895 10.83 0.00 0.00 2.75
485 495 2.931386 GCTACATGGCGCACGATC 59.069 61.111 10.83 0.00 0.00 3.69
516 927 7.819415 GGGAATAGCAGTTTTAAAAAGAATGCT 59.181 33.333 23.34 23.34 44.20 3.79
522 933 9.305925 GATCATGGGAATAGCAGTTTTAAAAAG 57.694 33.333 1.31 0.00 0.00 2.27
530 941 4.096190 CCAGATCATGGGAATAGCAGTT 57.904 45.455 0.00 0.00 46.36 3.16
543 954 4.325109 CCATAGCCATTGGATCCAGATCAT 60.325 45.833 15.53 2.29 39.54 2.45
563 974 1.767692 GTCCCACAGAACACCCCAT 59.232 57.895 0.00 0.00 0.00 4.00
578 990 5.045066 AGGAAATGTTAACTAGGGAAGGTCC 60.045 44.000 7.22 1.59 35.23 4.46
626 1038 5.298777 GTGTCGTGGTATCTACTCCTTGTAT 59.701 44.000 0.00 0.00 0.00 2.29
639 1051 5.355910 ACTTGTTTTCTTTGTGTCGTGGTAT 59.644 36.000 0.00 0.00 0.00 2.73
666 1078 4.782019 AGTTTGCAGTGTTTCTTCAACA 57.218 36.364 0.00 0.00 43.55 3.33
667 1079 6.090129 TGTAAGTTTGCAGTGTTTCTTCAAC 58.910 36.000 0.00 0.00 29.87 3.18
668 1080 6.260870 TGTAAGTTTGCAGTGTTTCTTCAA 57.739 33.333 0.00 0.00 0.00 2.69
669 1081 5.888691 TGTAAGTTTGCAGTGTTTCTTCA 57.111 34.783 0.00 0.00 0.00 3.02
678 1195 8.868916 CATTTGTAAAGTTTGTAAGTTTGCAGT 58.131 29.630 0.00 3.09 43.77 4.40
688 1205 6.920758 GTCATGCCACATTTGTAAAGTTTGTA 59.079 34.615 0.00 0.00 0.00 2.41
691 1208 5.911752 TGTCATGCCACATTTGTAAAGTTT 58.088 33.333 0.00 0.00 0.00 2.66
719 1236 8.296211 TGGATATGCAAAATGGATATACATGG 57.704 34.615 11.39 0.00 43.96 3.66
739 1256 1.748403 GATGCCTCAGCCGTGGATA 59.252 57.895 0.00 0.00 38.69 2.59
909 1432 4.154347 GCTGCTCGGGAGGTCCTG 62.154 72.222 0.00 0.00 43.86 3.86
1107 1630 6.250819 CAAACTAGAACTATGCAAATGACCG 58.749 40.000 0.00 0.00 0.00 4.79
1124 1647 6.073873 GGAATCTCATGAATCTCGCAAACTAG 60.074 42.308 0.00 0.00 0.00 2.57
1133 1656 4.515944 CAGCCTTGGAATCTCATGAATCTC 59.484 45.833 0.00 0.00 0.00 2.75
1134 1657 4.079901 ACAGCCTTGGAATCTCATGAATCT 60.080 41.667 0.00 0.00 0.00 2.40
1374 1897 2.359850 GGACTGAACGCATGGGCA 60.360 61.111 10.10 0.00 41.24 5.36
1597 2122 0.041926 GTTGCAACACCGGTTACGTC 60.042 55.000 24.52 0.00 38.78 4.34
1608 2133 2.439409 CATCCAGATCCAGTTGCAACA 58.561 47.619 30.11 11.44 0.00 3.33
1874 2400 5.541845 TGGATTCTGGAATCTAATAGTGCG 58.458 41.667 18.80 0.00 44.90 5.34
1939 2465 3.087370 AGTTTCTCAAATACCAGGCCC 57.913 47.619 0.00 0.00 0.00 5.80
2019 2553 8.651589 TGAATTATCCAGTCTAGGTATTCGAT 57.348 34.615 0.00 0.00 31.26 3.59
2034 2568 7.064847 GCACTGCAAATTTTCATGAATTATCCA 59.935 33.333 9.40 2.51 0.00 3.41
2089 2623 5.855740 ACTACTAGTGCCTTTCTGATACC 57.144 43.478 5.39 0.00 0.00 2.73
2342 2878 4.631813 ACGACATGATGAAACTTAAGCTCC 59.368 41.667 0.00 0.00 0.00 4.70
2389 3349 6.119240 TCAACCAAATGCAAATTAATCCCA 57.881 33.333 0.00 0.00 0.00 4.37
2470 3430 4.816385 ACTGTTCAAACACACAGACCATAG 59.184 41.667 6.32 0.00 42.74 2.23
2471 3431 4.776349 ACTGTTCAAACACACAGACCATA 58.224 39.130 6.32 0.00 42.74 2.74
2472 3432 3.620488 ACTGTTCAAACACACAGACCAT 58.380 40.909 6.32 0.00 42.74 3.55
2505 3466 3.701241 TGCAACGAACCAAGAAATTGTC 58.299 40.909 0.00 0.00 0.00 3.18
2735 3697 0.251297 TGGGTGAATCACTTGGCCAG 60.251 55.000 13.53 2.72 34.40 4.85
2840 3802 8.842358 AAAAATGACGTATGTCTAGGAAGAAA 57.158 30.769 15.91 0.00 45.70 2.52
2892 3854 8.912988 ACCTATTTCAATCTCAAACTTGTTCAA 58.087 29.630 0.00 0.00 0.00 2.69
3149 4114 1.651240 ATCAGCACATTGAGCGTGGC 61.651 55.000 0.30 0.00 37.01 5.01
3158 4123 6.379133 ACATCATTACCTCAAATCAGCACATT 59.621 34.615 0.00 0.00 0.00 2.71
3163 4128 6.690194 AGAACATCATTACCTCAAATCAGC 57.310 37.500 0.00 0.00 0.00 4.26
3235 4200 5.100259 ACTATCATACAAACCTTGTCGACG 58.900 41.667 11.62 0.00 44.12 5.12
3304 4269 5.537674 AGCACCAAGTTCAGAGAATTTTGAT 59.462 36.000 0.00 0.00 0.00 2.57
3313 4278 2.224137 TGAGTCAGCACCAAGTTCAGAG 60.224 50.000 0.00 0.00 0.00 3.35
3351 4316 2.043953 GTGGGATGGGGAGTTGCC 60.044 66.667 0.00 0.00 0.00 4.52
3376 4341 2.143925 GACGCTTCTTTTGGCTACTGT 58.856 47.619 0.00 0.00 0.00 3.55
3385 4350 7.962918 GTGTTATGTATGAATGACGCTTCTTTT 59.037 33.333 0.00 0.00 0.00 2.27
3389 4354 5.556382 CGGTGTTATGTATGAATGACGCTTC 60.556 44.000 0.00 0.00 29.87 3.86
3390 4355 4.270084 CGGTGTTATGTATGAATGACGCTT 59.730 41.667 0.00 0.00 29.87 4.68
3391 4356 3.802139 CGGTGTTATGTATGAATGACGCT 59.198 43.478 0.00 0.00 29.87 5.07
3392 4357 3.799963 TCGGTGTTATGTATGAATGACGC 59.200 43.478 0.00 0.00 0.00 5.19
3393 4358 6.525121 AATCGGTGTTATGTATGAATGACG 57.475 37.500 0.00 0.00 0.00 4.35
3405 4371 5.417580 ACCTGCAAAACATAATCGGTGTTAT 59.582 36.000 0.00 0.00 38.76 1.89
3597 4563 2.564504 CAGAAGTCCACAGATCCAGACA 59.435 50.000 0.00 0.00 0.00 3.41
3854 4820 5.276536 GCAAGAAAACAGAAAATGCAGTGAC 60.277 40.000 0.00 0.00 32.80 3.67
3867 4833 6.963796 ACTTCTTAGACATGCAAGAAAACAG 58.036 36.000 14.88 8.60 39.58 3.16
3874 4840 7.493971 AGCTGTATAACTTCTTAGACATGCAAG 59.506 37.037 0.00 0.00 34.37 4.01
3942 4911 5.012768 AGACCCTCCTTTTTACGAGAAATGA 59.987 40.000 0.00 0.00 0.00 2.57
3948 4917 3.248495 GGAGACCCTCCTTTTTACGAG 57.752 52.381 5.78 0.00 46.41 4.18
3958 4927 0.466124 CCAAGAATCGGAGACCCTCC 59.534 60.000 2.97 2.97 46.44 4.30
3991 4960 7.170965 AGCGAGTGATCATATGGGAATAAAAT 58.829 34.615 0.00 0.00 0.00 1.82
3996 4966 4.321718 CAAGCGAGTGATCATATGGGAAT 58.678 43.478 0.00 0.00 0.00 3.01
4056 5026 6.131544 AGTTCAACAAGACAACACCATAAC 57.868 37.500 0.00 0.00 0.00 1.89
4069 5039 6.753279 TGCTTGATTCTTTGAAGTTCAACAAG 59.247 34.615 26.33 26.33 37.95 3.16
4081 5051 6.694411 GGTGCTATAATGTGCTTGATTCTTTG 59.306 38.462 0.00 0.00 0.00 2.77
4082 5052 6.183360 GGGTGCTATAATGTGCTTGATTCTTT 60.183 38.462 0.00 0.00 0.00 2.52
4089 5059 4.717233 TTTGGGTGCTATAATGTGCTTG 57.283 40.909 0.00 0.00 0.00 4.01
4120 5090 9.120538 GGGAAAGTAGATGTGCTTGATTATTTA 57.879 33.333 0.00 0.00 0.00 1.40
4124 5094 5.437060 GGGGAAAGTAGATGTGCTTGATTA 58.563 41.667 0.00 0.00 0.00 1.75
4125 5095 4.273318 GGGGAAAGTAGATGTGCTTGATT 58.727 43.478 0.00 0.00 0.00 2.57
4126 5096 3.372025 GGGGGAAAGTAGATGTGCTTGAT 60.372 47.826 0.00 0.00 0.00 2.57
4127 5097 2.026262 GGGGGAAAGTAGATGTGCTTGA 60.026 50.000 0.00 0.00 0.00 3.02
4132 5112 2.027561 TCAACGGGGGAAAGTAGATGTG 60.028 50.000 0.00 0.00 0.00 3.21
4134 5114 3.007635 GTTCAACGGGGGAAAGTAGATG 58.992 50.000 0.00 0.00 0.00 2.90
4149 5129 5.453567 AAGTGAGCCCAAATTAGTTCAAC 57.546 39.130 0.00 0.00 0.00 3.18
4151 5131 5.475564 GGTTAAGTGAGCCCAAATTAGTTCA 59.524 40.000 0.00 0.00 0.00 3.18
4176 5156 1.134670 GGCTAGGTGTGGCTGACTTAG 60.135 57.143 0.00 0.00 0.00 2.18
4190 5170 5.694995 TCCAAAAATCAGATAAGGGCTAGG 58.305 41.667 0.00 0.00 0.00 3.02
4217 5204 5.105063 GCAGATTCTTTTGGTTAATCCTGC 58.895 41.667 0.00 0.00 37.07 4.85
4233 5222 4.925068 AGCGTATGGAATTTTGCAGATTC 58.075 39.130 13.57 13.57 33.71 2.52
4252 5241 7.123830 GGTATACACTTTATAACAGCAAAGCG 58.876 38.462 5.01 0.00 35.58 4.68
4258 5247 9.590451 TTGTACTGGTATACACTTTATAACAGC 57.410 33.333 13.83 2.97 44.78 4.40
4339 5328 9.553064 AAAAATTTGTGACCTGTGCAATATTAA 57.447 25.926 0.00 0.00 0.00 1.40
4341 5330 9.723601 ATAAAAATTTGTGACCTGTGCAATATT 57.276 25.926 0.00 0.00 0.00 1.28
4407 5397 9.695526 GCAATTAAGGATGCATATTGAATGTTA 57.304 29.630 18.88 0.00 42.12 2.41
4408 5398 8.205512 TGCAATTAAGGATGCATATTGAATGTT 58.794 29.630 18.88 0.00 46.87 2.71
4409 5399 7.728148 TGCAATTAAGGATGCATATTGAATGT 58.272 30.769 18.88 0.00 46.87 2.71
4420 5410 2.987046 GCTACGTGCAATTAAGGATGC 58.013 47.619 0.00 4.26 42.86 3.91
4432 5422 2.309898 AAAACGATTGTGCTACGTGC 57.690 45.000 0.00 0.00 40.10 5.34
4481 5471 3.026694 CCCTCCCCTGCTTATTGAAAAG 58.973 50.000 0.00 0.00 0.00 2.27
4482 5472 2.652348 TCCCTCCCCTGCTTATTGAAAA 59.348 45.455 0.00 0.00 0.00 2.29
4483 5473 2.025321 GTCCCTCCCCTGCTTATTGAAA 60.025 50.000 0.00 0.00 0.00 2.69
4484 5474 1.564348 GTCCCTCCCCTGCTTATTGAA 59.436 52.381 0.00 0.00 0.00 2.69
4485 5475 1.213296 GTCCCTCCCCTGCTTATTGA 58.787 55.000 0.00 0.00 0.00 2.57
4486 5476 0.918983 TGTCCCTCCCCTGCTTATTG 59.081 55.000 0.00 0.00 0.00 1.90
4487 5477 0.919710 GTGTCCCTCCCCTGCTTATT 59.080 55.000 0.00 0.00 0.00 1.40
4488 5478 0.044855 AGTGTCCCTCCCCTGCTTAT 59.955 55.000 0.00 0.00 0.00 1.73
4489 5479 0.714180 TAGTGTCCCTCCCCTGCTTA 59.286 55.000 0.00 0.00 0.00 3.09
4490 5480 0.178873 TTAGTGTCCCTCCCCTGCTT 60.179 55.000 0.00 0.00 0.00 3.91
4491 5481 0.178873 TTTAGTGTCCCTCCCCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
4492 5482 0.696501 TTTTAGTGTCCCTCCCCTGC 59.303 55.000 0.00 0.00 0.00 4.85
4509 5499 6.147821 TCGATCTGATCTTTTCTTCGCTTTTT 59.852 34.615 15.16 0.00 0.00 1.94
4510 5500 5.639506 TCGATCTGATCTTTTCTTCGCTTTT 59.360 36.000 15.16 0.00 0.00 2.27
4511 5501 5.171476 TCGATCTGATCTTTTCTTCGCTTT 58.829 37.500 15.16 0.00 0.00 3.51
4512 5502 4.748892 TCGATCTGATCTTTTCTTCGCTT 58.251 39.130 15.16 0.00 0.00 4.68
4513 5503 4.377839 TCGATCTGATCTTTTCTTCGCT 57.622 40.909 15.16 0.00 0.00 4.93
4514 5504 4.505922 ACATCGATCTGATCTTTTCTTCGC 59.494 41.667 15.16 0.00 34.13 4.70
4515 5505 7.685532 TTACATCGATCTGATCTTTTCTTCG 57.314 36.000 15.16 1.72 34.13 3.79


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

AutoCloner maintained by Alex Coulton.