Multiple sequence alignment - TraesCS5A01G197400

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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 TraesCS5A01G197400 chr5A 100.000 3460 0 0 1 3460 401318653 401315194 0.000000e+00 6390
1 TraesCS5A01G197400 chr5D 95.353 2496 66 14 1 2472 297735876 297738345 0.000000e+00 3921
2 TraesCS5A01G197400 chr5D 94.400 625 18 6 2468 3088 297738424 297739035 0.000000e+00 944
3 TraesCS5A01G197400 chr5D 96.053 380 10 4 3082 3460 297749299 297749674 6.350000e-172 614
4 TraesCS5A01G197400 chr5B 94.472 1429 37 9 177 1580 338480436 338481847 0.000000e+00 2163
5 TraesCS5A01G197400 chr5B 96.717 1066 28 3 1623 2682 338481845 338482909 0.000000e+00 1768
6 TraesCS5A01G197400 chr5B 94.436 665 27 4 2680 3335 338483021 338483684 0.000000e+00 1014
7 TraesCS5A01G197400 chr5B 88.701 177 6 5 1 177 338475879 338476041 1.630000e-48 204
8 TraesCS5A01G197400 chrUn 81.274 1554 244 26 945 2471 250030275 250031808 0.000000e+00 1214
9 TraesCS5A01G197400 chrUn 83.392 1132 161 17 1358 2466 282477066 282475939 0.000000e+00 1024
10 TraesCS5A01G197400 chrUn 82.964 1127 165 17 1358 2461 267761120 267762242 0.000000e+00 992
11 TraesCS5A01G197400 chrUn 82.920 1130 166 17 1358 2464 334501261 334500136 0.000000e+00 992
12 TraesCS5A01G197400 chrUn 79.801 703 127 12 1199 1893 311734916 311735611 6.670000e-137 497
13 TraesCS5A01G197400 chrUn 79.801 703 127 12 1199 1893 311738790 311739485 6.670000e-137 497
14 TraesCS5A01G197400 chr3D 78.356 1460 261 36 982 2409 520319268 520317832 0.000000e+00 894
15 TraesCS5A01G197400 chr3D 83.668 398 46 11 966 1345 520153028 520153424 1.180000e-94 357
16 TraesCS5A01G197400 chr3A 80.529 1171 192 29 1261 2409 655886387 655885231 0.000000e+00 867
17 TraesCS5A01G197400 chr3A 76.438 1600 301 50 988 2549 636541481 636539920 0.000000e+00 797
18 TraesCS5A01G197400 chr3A 77.618 1318 253 30 1260 2551 655896922 655895621 0.000000e+00 761
19 TraesCS5A01G197400 chr3A 83.417 398 47 11 966 1345 655572389 655572785 5.490000e-93 351
20 TraesCS5A01G197400 chr3A 88.793 116 9 1 961 1072 702556043 702556158 4.660000e-29 139
21 TraesCS5A01G197400 chr3A 85.484 124 16 1 982 1103 655886632 655886509 1.010000e-25 128
22 TraesCS5A01G197400 chr3A 84.677 124 17 1 982 1103 655631694 655631817 4.690000e-24 122
23 TraesCS5A01G197400 chr3B 80.207 1157 194 28 1267 2402 684767588 684768730 0.000000e+00 835
24 TraesCS5A01G197400 chr3B 77.962 1148 220 24 1251 2387 756613663 756614788 0.000000e+00 688
25 TraesCS5A01G197400 chr3B 73.284 1617 343 56 874 2460 658489808 658491365 8.570000e-141 510
26 TraesCS5A01G197400 chr3B 84.140 372 57 2 2102 2472 756656509 756656879 3.280000e-95 359
27 TraesCS5A01G197400 chr3B 77.007 461 82 15 1962 2403 756682901 756682446 3.450000e-60 243


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 TraesCS5A01G197400 chr5A 401315194 401318653 3459 True 6390.000000 6390 100.000000 1 3460 1 chr5A.!!$R1 3459
1 TraesCS5A01G197400 chr5D 297735876 297739035 3159 False 2432.500000 3921 94.876500 1 3088 2 chr5D.!!$F2 3087
2 TraesCS5A01G197400 chr5B 338480436 338483684 3248 False 1648.333333 2163 95.208333 177 3335 3 chr5B.!!$F2 3158
3 TraesCS5A01G197400 chrUn 250030275 250031808 1533 False 1214.000000 1214 81.274000 945 2471 1 chrUn.!!$F1 1526
4 TraesCS5A01G197400 chrUn 282475939 282477066 1127 True 1024.000000 1024 83.392000 1358 2466 1 chrUn.!!$R1 1108
5 TraesCS5A01G197400 chrUn 267761120 267762242 1122 False 992.000000 992 82.964000 1358 2461 1 chrUn.!!$F2 1103
6 TraesCS5A01G197400 chrUn 334500136 334501261 1125 True 992.000000 992 82.920000 1358 2464 1 chrUn.!!$R2 1106
7 TraesCS5A01G197400 chrUn 311734916 311739485 4569 False 497.000000 497 79.801000 1199 1893 2 chrUn.!!$F3 694
8 TraesCS5A01G197400 chr3D 520317832 520319268 1436 True 894.000000 894 78.356000 982 2409 1 chr3D.!!$R1 1427
9 TraesCS5A01G197400 chr3A 636539920 636541481 1561 True 797.000000 797 76.438000 988 2549 1 chr3A.!!$R1 1561
10 TraesCS5A01G197400 chr3A 655895621 655896922 1301 True 761.000000 761 77.618000 1260 2551 1 chr3A.!!$R2 1291
11 TraesCS5A01G197400 chr3A 655885231 655886632 1401 True 497.500000 867 83.006500 982 2409 2 chr3A.!!$R3 1427
12 TraesCS5A01G197400 chr3B 684767588 684768730 1142 False 835.000000 835 80.207000 1267 2402 1 chr3B.!!$F2 1135
13 TraesCS5A01G197400 chr3B 756613663 756614788 1125 False 688.000000 688 77.962000 1251 2387 1 chr3B.!!$F3 1136
14 TraesCS5A01G197400 chr3B 658489808 658491365 1557 False 510.000000 510 73.284000 874 2460 1 chr3B.!!$F1 1586

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
144 145 0.169451 GGTATTGGGCGAACGTTTGG 59.831 55.0 17.16 6.79 0.00 3.28 F
187 188 0.251916 CGACCAAATGCCCAGGTAGA 59.748 55.0 0.00 0.00 35.36 2.59 F
385 386 6.189859 TGGATCACTATTTGAAGGCTGAATT 58.810 36.0 0.00 0.00 37.92 2.17 F
1840 5799 0.896226 AGGCGTGAAAGACTCCCTAC 59.104 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1416 0.106419 TTCGGGGAACAAGGTGCTTT 60.106 50.000 0.00 0.00 0.00 3.51 R
1840 5799 0.809636 TGCATATGCTTCACGGACCG 60.810 55.000 27.13 13.61 42.66 4.79 R
2075 6059 3.322541 TCGGGAGTTCAAATACTCACACA 59.677 43.478 6.81 0.00 46.67 3.72 R
3349 7571 0.030638 CCTCCAACTTGCAAACCACG 59.969 55.000 0.00 0.00 0.00 4.94 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
60 61 5.047377 CAGGAGAAAGTATGAGGATAGAGGC 60.047 48.000 0.00 0.00 0.00 4.70
62 63 5.083821 GAGAAAGTATGAGGATAGAGGCCT 58.916 45.833 3.86 3.86 38.81 5.19
64 65 6.252995 AGAAAGTATGAGGATAGAGGCCTAG 58.747 44.000 4.42 0.00 35.44 3.02
112 113 4.730487 GCACTCTTGCCCAGTGAT 57.270 55.556 10.20 0.00 43.54 3.06
114 115 0.321919 GCACTCTTGCCCAGTGATCA 60.322 55.000 10.20 0.00 43.54 2.92
115 116 1.735386 CACTCTTGCCCAGTGATCAG 58.265 55.000 0.00 0.00 43.54 2.90
116 117 0.617413 ACTCTTGCCCAGTGATCAGG 59.383 55.000 0.00 0.00 0.00 3.86
125 126 2.558795 CCCAGTGATCAGGGTACTATCG 59.441 54.545 11.21 0.00 40.34 2.92
126 127 2.558795 CCAGTGATCAGGGTACTATCGG 59.441 54.545 0.00 0.00 0.00 4.18
134 135 2.028385 CAGGGTACTATCGGTATTGGGC 60.028 54.545 0.00 0.00 32.56 5.36
144 145 0.169451 GGTATTGGGCGAACGTTTGG 59.831 55.000 17.16 6.79 0.00 3.28
187 188 0.251916 CGACCAAATGCCCAGGTAGA 59.748 55.000 0.00 0.00 35.36 2.59
207 208 6.812160 GGTAGAGTGTGTCGACTGAAATATTT 59.188 38.462 17.92 0.00 31.70 1.40
247 248 9.851686 TTATCTCACAATGGTATTAAGCTTGAT 57.148 29.630 9.86 9.34 0.00 2.57
263 264 6.959639 AGCTTGATGTTGAAGTTTTTAGGA 57.040 33.333 0.00 0.00 0.00 2.94
265 266 7.597386 AGCTTGATGTTGAAGTTTTTAGGATC 58.403 34.615 0.00 0.00 0.00 3.36
351 352 9.970395 TGTCATGATATTCTGCCATTTATTTTC 57.030 29.630 0.00 0.00 0.00 2.29
363 364 7.999679 TGCCATTTATTTTCTACTTCTGATGG 58.000 34.615 0.00 0.00 34.80 3.51
385 386 6.189859 TGGATCACTATTTGAAGGCTGAATT 58.810 36.000 0.00 0.00 37.92 2.17
428 429 9.710900 CTGCTTGATGTATATGGATTAGTTGTA 57.289 33.333 0.00 0.00 0.00 2.41
441 442 8.177119 TGGATTAGTTGTAAGAATTGCTTGTT 57.823 30.769 0.00 0.00 37.42 2.83
473 474 8.143193 TGGCAATTTCAAATATTGTATAGCAGG 58.857 33.333 0.00 0.00 35.82 4.85
1840 5799 0.896226 AGGCGTGAAAGACTCCCTAC 59.104 55.000 0.00 0.00 0.00 3.18
1862 5821 4.576843 CGTGAAGCATATGCACGC 57.423 55.556 28.62 23.93 46.86 5.34
2054 6038 9.331282 GAGGTACATCTTTTTCTAGTATTGCAT 57.669 33.333 0.00 0.00 0.00 3.96
2568 6661 2.991250 ACATCCTGTATGGTGTTCTGC 58.009 47.619 0.00 0.00 40.16 4.26
2736 6947 7.115805 TGTCTTGTATCTGTTTTAGTAACTGCG 59.884 37.037 0.00 0.00 0.00 5.18
2758 6969 4.735822 CGATGAGATTGAAGAAGACGGTAC 59.264 45.833 0.00 0.00 0.00 3.34
2787 6998 1.432024 ACCGATGGCCCCTACTAGTAT 59.568 52.381 2.33 0.00 0.00 2.12
2840 7051 4.156556 TGATGCTCCAACTTTAGTGAATGC 59.843 41.667 0.00 0.00 0.00 3.56
2841 7052 2.819608 TGCTCCAACTTTAGTGAATGCC 59.180 45.455 0.00 0.00 0.00 4.40
2878 7089 6.568869 AGATCTAGAAATTCACAGAAGTCGG 58.431 40.000 0.00 0.00 0.00 4.79
2958 7169 7.581213 AAATACACTCACAAGTTTGAATGGA 57.419 32.000 0.00 0.00 31.71 3.41
2984 7195 5.126396 AGCAGAACCAGATTGCTAAAAAC 57.874 39.130 0.00 0.00 45.67 2.43
3055 7266 2.095768 CGCCACAAGTTCGATGAAATGT 60.096 45.455 0.00 0.00 0.00 2.71
3058 7269 3.253188 CCACAAGTTCGATGAAATGTGGT 59.747 43.478 23.97 5.85 45.89 4.16
3065 7279 2.569853 TCGATGAAATGTGGTGTACCCT 59.430 45.455 0.00 0.00 34.29 4.34
3066 7280 2.936498 CGATGAAATGTGGTGTACCCTC 59.064 50.000 0.00 0.00 34.29 4.30
3067 7281 3.369471 CGATGAAATGTGGTGTACCCTCT 60.369 47.826 0.00 0.00 34.29 3.69
3104 7318 2.015736 GTGCAGGTCACACTGATAGG 57.984 55.000 0.00 0.00 44.98 2.57
3159 7373 2.190578 GCCTTGTGGGGATCCGAG 59.809 66.667 5.45 0.00 35.24 4.63
3174 7388 1.628340 TCCGAGTTGGATGGACATGTT 59.372 47.619 0.00 0.00 43.74 2.71
3241 7455 2.028484 GTCGAGCCGAACACACCA 59.972 61.111 0.00 0.00 37.72 4.17
3308 7530 1.995542 AGGTCTGTTGGTTCATGGGAT 59.004 47.619 0.00 0.00 0.00 3.85
3313 7535 2.493278 CTGTTGGTTCATGGGATGGTTC 59.507 50.000 0.00 0.00 0.00 3.62
3323 7545 1.296832 TGGGATGGTTCCAGGAGGATA 59.703 52.381 0.00 0.00 45.26 2.59
3328 7550 4.263243 GGATGGTTCCAGGAGGATATTCAG 60.263 50.000 0.00 0.00 45.26 3.02
3329 7551 3.736094 TGGTTCCAGGAGGATATTCAGT 58.264 45.455 0.00 0.00 45.26 3.41
3330 7552 4.890988 TGGTTCCAGGAGGATATTCAGTA 58.109 43.478 0.00 0.00 45.26 2.74
3331 7553 4.901849 TGGTTCCAGGAGGATATTCAGTAG 59.098 45.833 0.00 0.00 45.26 2.57
3333 7555 4.834406 TCCAGGAGGATATTCAGTAGGT 57.166 45.455 0.00 0.00 39.61 3.08
3334 7556 5.942977 TCCAGGAGGATATTCAGTAGGTA 57.057 43.478 0.00 0.00 39.61 3.08
3335 7557 6.485388 TCCAGGAGGATATTCAGTAGGTAT 57.515 41.667 0.00 0.00 39.61 2.73
3336 7558 7.599353 TCCAGGAGGATATTCAGTAGGTATA 57.401 40.000 0.00 0.00 39.61 1.47
3337 7559 8.008104 TCCAGGAGGATATTCAGTAGGTATAA 57.992 38.462 0.00 0.00 39.61 0.98
3338 7560 8.633724 TCCAGGAGGATATTCAGTAGGTATAAT 58.366 37.037 0.00 0.00 39.61 1.28
3339 7561 8.700051 CCAGGAGGATATTCAGTAGGTATAATG 58.300 40.741 0.00 0.00 36.89 1.90
3340 7562 8.200792 CAGGAGGATATTCAGTAGGTATAATGC 58.799 40.741 0.00 0.00 0.00 3.56
3341 7563 7.901322 AGGAGGATATTCAGTAGGTATAATGCA 59.099 37.037 0.00 0.00 0.00 3.96
3342 7564 8.540388 GGAGGATATTCAGTAGGTATAATGCAA 58.460 37.037 0.00 0.00 0.00 4.08
3343 7565 9.944376 GAGGATATTCAGTAGGTATAATGCAAA 57.056 33.333 0.00 0.00 0.00 3.68
3350 7572 8.360325 TCAGTAGGTATAATGCAAATGTAACG 57.640 34.615 0.00 0.00 0.00 3.18
3351 7573 7.982919 TCAGTAGGTATAATGCAAATGTAACGT 59.017 33.333 0.00 0.00 0.00 3.99
3352 7574 8.061857 CAGTAGGTATAATGCAAATGTAACGTG 58.938 37.037 0.00 0.00 0.00 4.49
3353 7575 6.371809 AGGTATAATGCAAATGTAACGTGG 57.628 37.500 0.00 0.00 0.00 4.94
3354 7576 5.883673 AGGTATAATGCAAATGTAACGTGGT 59.116 36.000 0.00 0.00 0.00 4.16
3355 7577 6.376018 AGGTATAATGCAAATGTAACGTGGTT 59.624 34.615 0.00 0.00 0.00 3.67
3356 7578 7.030768 GGTATAATGCAAATGTAACGTGGTTT 58.969 34.615 0.00 0.00 0.00 3.27
3357 7579 6.942886 ATAATGCAAATGTAACGTGGTTTG 57.057 33.333 0.00 0.00 35.30 2.93
3361 7583 4.690731 CAAATGTAACGTGGTTTGCAAG 57.309 40.909 0.00 0.00 0.00 4.01
3362 7584 4.109050 CAAATGTAACGTGGTTTGCAAGT 58.891 39.130 0.00 0.00 0.00 3.16
3363 7585 4.379339 AATGTAACGTGGTTTGCAAGTT 57.621 36.364 0.00 2.63 0.00 2.66
3364 7586 3.138205 TGTAACGTGGTTTGCAAGTTG 57.862 42.857 10.36 0.00 0.00 3.16
3365 7587 2.159366 TGTAACGTGGTTTGCAAGTTGG 60.159 45.455 10.36 0.00 0.00 3.77
3366 7588 1.178276 AACGTGGTTTGCAAGTTGGA 58.822 45.000 4.75 0.00 0.00 3.53
3367 7589 0.738389 ACGTGGTTTGCAAGTTGGAG 59.262 50.000 4.75 0.00 0.00 3.86
3368 7590 0.030638 CGTGGTTTGCAAGTTGGAGG 59.969 55.000 4.75 0.00 0.00 4.30
3369 7591 1.111277 GTGGTTTGCAAGTTGGAGGT 58.889 50.000 4.75 0.00 0.00 3.85
3370 7592 1.067060 GTGGTTTGCAAGTTGGAGGTC 59.933 52.381 4.75 0.00 0.00 3.85
3371 7593 1.064017 TGGTTTGCAAGTTGGAGGTCT 60.064 47.619 4.75 0.00 0.00 3.85
3372 7594 2.031870 GGTTTGCAAGTTGGAGGTCTT 58.968 47.619 4.75 0.00 0.00 3.01
3373 7595 3.219281 GGTTTGCAAGTTGGAGGTCTTA 58.781 45.455 4.75 0.00 0.00 2.10
3374 7596 3.634910 GGTTTGCAAGTTGGAGGTCTTAA 59.365 43.478 4.75 0.00 0.00 1.85
3375 7597 4.261614 GGTTTGCAAGTTGGAGGTCTTAAG 60.262 45.833 4.75 0.00 0.00 1.85
3376 7598 3.140325 TGCAAGTTGGAGGTCTTAAGG 57.860 47.619 4.75 0.00 0.00 2.69
3377 7599 1.813178 GCAAGTTGGAGGTCTTAAGGC 59.187 52.381 4.75 0.00 0.00 4.35
3378 7600 2.814097 GCAAGTTGGAGGTCTTAAGGCA 60.814 50.000 9.72 0.00 0.00 4.75
3379 7601 3.486383 CAAGTTGGAGGTCTTAAGGCAA 58.514 45.455 9.72 0.00 0.00 4.52
3380 7602 3.141767 AGTTGGAGGTCTTAAGGCAAC 57.858 47.619 9.72 4.73 0.00 4.17
3381 7603 1.804748 GTTGGAGGTCTTAAGGCAACG 59.195 52.381 9.72 0.00 46.39 4.10
3382 7604 1.053424 TGGAGGTCTTAAGGCAACGT 58.947 50.000 9.72 0.00 46.39 3.99
3383 7605 2.250031 TGGAGGTCTTAAGGCAACGTA 58.750 47.619 9.72 0.00 46.39 3.57
3384 7606 2.028748 TGGAGGTCTTAAGGCAACGTAC 60.029 50.000 9.72 0.34 46.39 3.67
3385 7607 2.028748 GGAGGTCTTAAGGCAACGTACA 60.029 50.000 9.72 0.00 46.39 2.90
3386 7608 3.251571 GAGGTCTTAAGGCAACGTACAG 58.748 50.000 9.72 0.00 46.39 2.74
3387 7609 2.028385 AGGTCTTAAGGCAACGTACAGG 60.028 50.000 9.72 0.00 46.39 4.00
3388 7610 2.344025 GTCTTAAGGCAACGTACAGGG 58.656 52.381 1.16 0.00 46.39 4.45
3389 7611 1.276989 TCTTAAGGCAACGTACAGGGG 59.723 52.381 1.85 0.00 46.39 4.79
3390 7612 1.002773 CTTAAGGCAACGTACAGGGGT 59.997 52.381 0.00 0.00 46.39 4.95
3391 7613 0.609662 TAAGGCAACGTACAGGGGTC 59.390 55.000 0.00 0.00 46.39 4.46
3392 7614 2.046604 GGCAACGTACAGGGGTCC 60.047 66.667 0.00 0.00 0.00 4.46
3393 7615 2.046604 GCAACGTACAGGGGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
3395 7617 2.063774 CAACGTACAGGGGTCCCTT 58.936 57.895 8.15 0.00 45.70 3.95
3396 7618 0.399075 CAACGTACAGGGGTCCCTTT 59.601 55.000 8.15 2.59 45.70 3.11
3397 7619 1.624813 CAACGTACAGGGGTCCCTTTA 59.375 52.381 8.15 1.49 45.70 1.85
3398 7620 2.028561 ACGTACAGGGGTCCCTTTAA 57.971 50.000 8.15 0.00 45.70 1.52
3399 7621 2.554563 ACGTACAGGGGTCCCTTTAAT 58.445 47.619 8.15 0.00 45.70 1.40
3400 7622 2.502947 ACGTACAGGGGTCCCTTTAATC 59.497 50.000 8.15 0.00 45.70 1.75
3401 7623 2.770232 CGTACAGGGGTCCCTTTAATCT 59.230 50.000 8.15 0.00 45.70 2.40
3402 7624 3.431766 CGTACAGGGGTCCCTTTAATCTG 60.432 52.174 8.15 7.93 45.70 2.90
3403 7625 2.644151 ACAGGGGTCCCTTTAATCTGT 58.356 47.619 8.15 8.61 45.70 3.41
3404 7626 2.308866 ACAGGGGTCCCTTTAATCTGTG 59.691 50.000 12.88 0.00 45.70 3.66
3405 7627 2.576191 CAGGGGTCCCTTTAATCTGTGA 59.424 50.000 8.15 0.00 45.70 3.58
3406 7628 3.203040 CAGGGGTCCCTTTAATCTGTGAT 59.797 47.826 8.15 0.00 45.70 3.06
3407 7629 3.203040 AGGGGTCCCTTTAATCTGTGATG 59.797 47.826 8.15 0.00 45.70 3.07
3408 7630 3.053619 GGGGTCCCTTTAATCTGTGATGT 60.054 47.826 8.15 0.00 0.00 3.06
3409 7631 4.165372 GGGGTCCCTTTAATCTGTGATGTA 59.835 45.833 8.15 0.00 0.00 2.29
3410 7632 5.123936 GGGTCCCTTTAATCTGTGATGTAC 58.876 45.833 0.00 0.00 0.00 2.90
3411 7633 5.123936 GGTCCCTTTAATCTGTGATGTACC 58.876 45.833 0.00 0.00 0.00 3.34
3412 7634 5.338871 GGTCCCTTTAATCTGTGATGTACCA 60.339 44.000 0.00 0.00 0.00 3.25
3413 7635 5.817816 GTCCCTTTAATCTGTGATGTACCAG 59.182 44.000 0.00 0.00 0.00 4.00
3414 7636 4.576463 CCCTTTAATCTGTGATGTACCAGC 59.424 45.833 0.00 0.00 0.00 4.85
3415 7637 4.271049 CCTTTAATCTGTGATGTACCAGCG 59.729 45.833 0.00 0.00 0.00 5.18
3416 7638 1.656652 AATCTGTGATGTACCAGCGC 58.343 50.000 0.00 0.00 0.00 5.92
3417 7639 0.179073 ATCTGTGATGTACCAGCGCC 60.179 55.000 2.29 0.00 28.49 6.53
3418 7640 1.815421 CTGTGATGTACCAGCGCCC 60.815 63.158 2.29 0.00 28.49 6.13
3419 7641 2.513897 GTGATGTACCAGCGCCCC 60.514 66.667 2.29 0.00 0.00 5.80
3420 7642 3.792736 TGATGTACCAGCGCCCCC 61.793 66.667 2.29 0.00 0.00 5.40
3437 7659 2.260822 CCCCCTCTCTTGAGTTCTTCA 58.739 52.381 0.00 0.00 38.61 3.02
3438 7660 2.639839 CCCCCTCTCTTGAGTTCTTCAA 59.360 50.000 0.00 0.00 43.40 2.69
3447 7669 4.342862 TTGAGTTCTTCAAGTCTGGGAG 57.657 45.455 0.00 0.00 40.82 4.30
3448 7670 2.037772 TGAGTTCTTCAAGTCTGGGAGC 59.962 50.000 0.00 0.00 33.56 4.70
3449 7671 2.037772 GAGTTCTTCAAGTCTGGGAGCA 59.962 50.000 0.00 0.00 0.00 4.26
3450 7672 2.641815 AGTTCTTCAAGTCTGGGAGCAT 59.358 45.455 0.00 0.00 0.00 3.79
3451 7673 3.006247 GTTCTTCAAGTCTGGGAGCATC 58.994 50.000 0.00 0.00 0.00 3.91
3452 7674 2.544721 TCTTCAAGTCTGGGAGCATCT 58.455 47.619 0.00 0.00 33.73 2.90
3453 7675 3.713003 TCTTCAAGTCTGGGAGCATCTA 58.287 45.455 0.00 0.00 33.73 1.98
3454 7676 4.293494 TCTTCAAGTCTGGGAGCATCTAT 58.707 43.478 0.00 0.00 33.73 1.98
3455 7677 4.100653 TCTTCAAGTCTGGGAGCATCTATG 59.899 45.833 0.00 0.00 33.73 2.23
3456 7678 2.702478 TCAAGTCTGGGAGCATCTATGG 59.298 50.000 0.00 0.00 33.73 2.74
3457 7679 1.727062 AGTCTGGGAGCATCTATGGG 58.273 55.000 0.00 0.00 33.73 4.00
3458 7680 0.036022 GTCTGGGAGCATCTATGGGC 59.964 60.000 0.00 0.00 33.73 5.36
3459 7681 0.400381 TCTGGGAGCATCTATGGGCA 60.400 55.000 0.00 0.00 33.73 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.309091 TCTATCCTCATACTTTCTCCTGGAAT 58.691 38.462 0.00 0.00 33.53 3.01
60 61 1.084370 CGCTTTCGCCTTGACCTAGG 61.084 60.000 7.41 7.41 38.40 3.02
62 63 4.590487 CGCTTTCGCCTTGACCTA 57.410 55.556 0.00 0.00 0.00 3.08
106 107 3.223435 ACCGATAGTACCCTGATCACTG 58.777 50.000 0.00 0.00 0.00 3.66
107 108 3.596940 ACCGATAGTACCCTGATCACT 57.403 47.619 0.00 0.00 0.00 3.41
109 110 4.770531 CCAATACCGATAGTACCCTGATCA 59.229 45.833 0.00 0.00 32.46 2.92
111 112 4.094476 CCCAATACCGATAGTACCCTGAT 58.906 47.826 0.00 0.00 32.46 2.90
112 113 3.503365 CCCAATACCGATAGTACCCTGA 58.497 50.000 0.00 0.00 32.46 3.86
114 115 2.254508 GCCCAATACCGATAGTACCCT 58.745 52.381 0.00 0.00 32.46 4.34
115 116 1.067354 CGCCCAATACCGATAGTACCC 60.067 57.143 0.00 0.00 32.46 3.69
116 117 1.888512 TCGCCCAATACCGATAGTACC 59.111 52.381 0.00 0.00 32.46 3.34
117 118 3.311966 GTTCGCCCAATACCGATAGTAC 58.688 50.000 0.00 0.00 32.46 2.73
118 119 2.030893 CGTTCGCCCAATACCGATAGTA 60.031 50.000 0.00 0.00 33.04 1.82
119 120 1.269413 CGTTCGCCCAATACCGATAGT 60.269 52.381 0.00 0.00 33.04 2.12
120 121 1.269413 ACGTTCGCCCAATACCGATAG 60.269 52.381 0.00 0.00 33.04 2.08
121 122 0.746063 ACGTTCGCCCAATACCGATA 59.254 50.000 0.00 0.00 33.04 2.92
122 123 0.108041 AACGTTCGCCCAATACCGAT 60.108 50.000 0.00 0.00 33.04 4.18
123 124 0.320596 AAACGTTCGCCCAATACCGA 60.321 50.000 0.00 0.00 0.00 4.69
124 125 0.179210 CAAACGTTCGCCCAATACCG 60.179 55.000 0.00 0.00 0.00 4.02
125 126 0.169451 CCAAACGTTCGCCCAATACC 59.831 55.000 0.00 0.00 0.00 2.73
126 127 0.876399 ACCAAACGTTCGCCCAATAC 59.124 50.000 0.00 0.00 0.00 1.89
134 135 2.051703 CGCCCAACCAAACGTTCG 60.052 61.111 0.00 0.00 29.93 3.95
351 352 9.258826 CTTCAAATAGTGATCCATCAGAAGTAG 57.741 37.037 0.00 0.00 37.51 2.57
352 353 8.206867 CCTTCAAATAGTGATCCATCAGAAGTA 58.793 37.037 10.64 0.00 37.51 2.24
363 364 7.093322 ACAATTCAGCCTTCAAATAGTGATC 57.907 36.000 0.00 0.00 35.70 2.92
385 386 6.172630 TCAAGCAGCAAGATAATGAACTACA 58.827 36.000 0.00 0.00 0.00 2.74
428 429 3.493176 GCCACTGGAAACAAGCAATTCTT 60.493 43.478 0.00 0.00 42.06 2.52
441 442 6.767456 ACAATATTTGAAATTGCCACTGGAA 58.233 32.000 0.00 0.00 37.77 3.53
689 712 4.955925 TCGGGTTACATTGTTTAGCATG 57.044 40.909 0.00 0.00 0.00 4.06
1354 1416 0.106419 TTCGGGGAACAAGGTGCTTT 60.106 50.000 0.00 0.00 0.00 3.51
1840 5799 0.809636 TGCATATGCTTCACGGACCG 60.810 55.000 27.13 13.61 42.66 4.79
1862 5821 7.693969 AAGTATGAAATCTTTCCTGAACTGG 57.306 36.000 0.48 0.00 36.36 4.00
2075 6059 3.322541 TCGGGAGTTCAAATACTCACACA 59.677 43.478 6.81 0.00 46.67 3.72
2403 6407 0.179108 GGATTCCTAGCACGCTCGTT 60.179 55.000 0.00 0.00 0.00 3.85
2736 6947 5.651530 TGTACCGTCTTCTTCAATCTCATC 58.348 41.667 0.00 0.00 0.00 2.92
2758 6969 1.308998 GGGCCATCGGTACTTTGATG 58.691 55.000 4.39 13.09 41.27 3.07
2787 6998 0.392706 ATGGATCATACGGCGAGCAA 59.607 50.000 16.62 0.00 0.00 3.91
2840 7051 9.844257 AATTTCTAGATCTTTCTGTGATAAGGG 57.156 33.333 0.00 0.00 33.17 3.95
2878 7089 2.166664 CCAAGTGCACCTAGACCTAGAC 59.833 54.545 14.63 0.00 35.21 2.59
2958 7169 5.789643 TTAGCAATCTGGTTCTGCTTTTT 57.210 34.783 0.57 0.00 43.83 1.94
2984 7195 3.384467 TCCAGTTCTCCTTTTGCTTTTGG 59.616 43.478 0.00 0.00 0.00 3.28
3040 7251 4.454504 GGTACACCACATTTCATCGAACTT 59.545 41.667 0.00 0.00 35.64 2.66
3055 7266 0.618458 GCCATGAAGAGGGTACACCA 59.382 55.000 0.00 0.00 43.89 4.17
3058 7269 0.616395 TCCGCCATGAAGAGGGTACA 60.616 55.000 0.00 0.00 0.00 2.90
3102 7316 3.004752 ACTTCTTGCACAAGACAACCT 57.995 42.857 12.50 0.00 46.13 3.50
3104 7318 4.622701 AGAACTTCTTGCACAAGACAAC 57.377 40.909 12.50 5.53 46.13 3.32
3159 7373 3.317711 TGTCAACAACATGTCCATCCAAC 59.682 43.478 0.00 0.00 31.20 3.77
3174 7388 1.557371 TCCCAGAACAGTGTGTCAACA 59.443 47.619 0.00 0.00 0.00 3.33
3308 7530 3.736094 ACTGAATATCCTCCTGGAACCA 58.264 45.455 0.00 0.00 46.80 3.67
3313 7535 8.700051 CATTATACCTACTGAATATCCTCCTGG 58.300 40.741 0.00 0.00 0.00 4.45
3328 7550 7.011669 ACCACGTTACATTTGCATTATACCTAC 59.988 37.037 0.00 0.00 0.00 3.18
3329 7551 7.049133 ACCACGTTACATTTGCATTATACCTA 58.951 34.615 0.00 0.00 0.00 3.08
3330 7552 5.883673 ACCACGTTACATTTGCATTATACCT 59.116 36.000 0.00 0.00 0.00 3.08
3331 7553 6.126568 ACCACGTTACATTTGCATTATACC 57.873 37.500 0.00 0.00 0.00 2.73
3334 7556 6.942886 CAAACCACGTTACATTTGCATTAT 57.057 33.333 0.00 0.00 0.00 1.28
3340 7562 4.109050 ACTTGCAAACCACGTTACATTTG 58.891 39.130 0.00 0.00 35.57 2.32
3341 7563 4.379339 ACTTGCAAACCACGTTACATTT 57.621 36.364 0.00 0.00 0.00 2.32
3342 7564 4.109050 CAACTTGCAAACCACGTTACATT 58.891 39.130 0.00 0.00 34.53 2.71
3343 7565 3.490078 CCAACTTGCAAACCACGTTACAT 60.490 43.478 0.00 0.00 34.53 2.29
3344 7566 2.159366 CCAACTTGCAAACCACGTTACA 60.159 45.455 0.00 0.00 34.53 2.41
3345 7567 2.097791 TCCAACTTGCAAACCACGTTAC 59.902 45.455 0.00 0.00 34.53 2.50
3346 7568 2.356382 CTCCAACTTGCAAACCACGTTA 59.644 45.455 0.00 0.00 34.53 3.18
3347 7569 1.134175 CTCCAACTTGCAAACCACGTT 59.866 47.619 0.00 0.00 36.46 3.99
3348 7570 0.738389 CTCCAACTTGCAAACCACGT 59.262 50.000 0.00 0.00 0.00 4.49
3349 7571 0.030638 CCTCCAACTTGCAAACCACG 59.969 55.000 0.00 0.00 0.00 4.94
3350 7572 1.067060 GACCTCCAACTTGCAAACCAC 59.933 52.381 0.00 0.00 0.00 4.16
3351 7573 1.064017 AGACCTCCAACTTGCAAACCA 60.064 47.619 0.00 0.00 0.00 3.67
3352 7574 1.692411 AGACCTCCAACTTGCAAACC 58.308 50.000 0.00 0.00 0.00 3.27
3353 7575 4.261614 CCTTAAGACCTCCAACTTGCAAAC 60.262 45.833 3.36 0.00 0.00 2.93
3354 7576 3.888930 CCTTAAGACCTCCAACTTGCAAA 59.111 43.478 3.36 0.00 0.00 3.68
3355 7577 3.486383 CCTTAAGACCTCCAACTTGCAA 58.514 45.455 3.36 0.00 0.00 4.08
3356 7578 2.814097 GCCTTAAGACCTCCAACTTGCA 60.814 50.000 3.36 0.00 0.00 4.08
3357 7579 1.813178 GCCTTAAGACCTCCAACTTGC 59.187 52.381 3.36 0.00 0.00 4.01
3358 7580 3.140325 TGCCTTAAGACCTCCAACTTG 57.860 47.619 3.36 0.00 0.00 3.16
3359 7581 3.487372 GTTGCCTTAAGACCTCCAACTT 58.513 45.455 3.36 0.00 32.21 2.66
3360 7582 2.550208 CGTTGCCTTAAGACCTCCAACT 60.550 50.000 3.36 0.00 32.62 3.16
3361 7583 1.804748 CGTTGCCTTAAGACCTCCAAC 59.195 52.381 3.36 8.09 0.00 3.77
3362 7584 1.418637 ACGTTGCCTTAAGACCTCCAA 59.581 47.619 3.36 0.00 0.00 3.53
3363 7585 1.053424 ACGTTGCCTTAAGACCTCCA 58.947 50.000 3.36 0.00 0.00 3.86
3364 7586 2.028748 TGTACGTTGCCTTAAGACCTCC 60.029 50.000 3.36 0.00 0.00 4.30
3365 7587 3.251571 CTGTACGTTGCCTTAAGACCTC 58.748 50.000 3.36 0.00 0.00 3.85
3366 7588 2.028385 CCTGTACGTTGCCTTAAGACCT 60.028 50.000 3.36 0.00 0.00 3.85
3367 7589 2.344025 CCTGTACGTTGCCTTAAGACC 58.656 52.381 3.36 0.00 0.00 3.85
3368 7590 2.344025 CCCTGTACGTTGCCTTAAGAC 58.656 52.381 3.36 0.00 0.00 3.01
3369 7591 1.276989 CCCCTGTACGTTGCCTTAAGA 59.723 52.381 3.36 0.00 0.00 2.10
3370 7592 1.002773 ACCCCTGTACGTTGCCTTAAG 59.997 52.381 0.00 0.00 0.00 1.85
3371 7593 1.002315 GACCCCTGTACGTTGCCTTAA 59.998 52.381 0.00 0.00 0.00 1.85
3372 7594 0.609662 GACCCCTGTACGTTGCCTTA 59.390 55.000 0.00 0.00 0.00 2.69
3373 7595 1.373812 GACCCCTGTACGTTGCCTT 59.626 57.895 0.00 0.00 0.00 4.35
3374 7596 2.590114 GGACCCCTGTACGTTGCCT 61.590 63.158 0.00 0.00 0.00 4.75
3375 7597 2.046604 GGACCCCTGTACGTTGCC 60.047 66.667 0.00 0.00 0.00 4.52
3376 7598 2.046604 GGGACCCCTGTACGTTGC 60.047 66.667 0.00 0.00 0.00 4.17
3377 7599 3.801620 AGGGACCCCTGTACGTTG 58.198 61.111 7.00 0.00 46.22 4.10
3386 7608 3.053619 ACATCACAGATTAAAGGGACCCC 60.054 47.826 7.00 1.17 0.00 4.95
3387 7609 4.236527 ACATCACAGATTAAAGGGACCC 57.763 45.455 0.59 0.59 0.00 4.46
3388 7610 5.123936 GGTACATCACAGATTAAAGGGACC 58.876 45.833 0.00 0.00 0.00 4.46
3389 7611 5.741011 TGGTACATCACAGATTAAAGGGAC 58.259 41.667 0.00 0.00 0.00 4.46
3390 7612 5.629133 GCTGGTACATCACAGATTAAAGGGA 60.629 44.000 0.00 0.00 38.20 4.20
3391 7613 4.576463 GCTGGTACATCACAGATTAAAGGG 59.424 45.833 0.00 0.00 38.20 3.95
3392 7614 4.271049 CGCTGGTACATCACAGATTAAAGG 59.729 45.833 0.00 0.00 38.20 3.11
3393 7615 4.260375 GCGCTGGTACATCACAGATTAAAG 60.260 45.833 0.00 0.00 38.20 1.85
3394 7616 3.621268 GCGCTGGTACATCACAGATTAAA 59.379 43.478 0.00 0.00 38.20 1.52
3395 7617 3.194861 GCGCTGGTACATCACAGATTAA 58.805 45.455 0.00 0.00 38.20 1.40
3396 7618 2.483013 GGCGCTGGTACATCACAGATTA 60.483 50.000 7.64 0.00 38.20 1.75
3397 7619 1.656652 GCGCTGGTACATCACAGATT 58.343 50.000 0.00 0.00 38.20 2.40
3398 7620 0.179073 GGCGCTGGTACATCACAGAT 60.179 55.000 7.64 0.00 38.20 2.90
3399 7621 1.218047 GGCGCTGGTACATCACAGA 59.782 57.895 7.64 0.00 38.20 3.41
3400 7622 1.815421 GGGCGCTGGTACATCACAG 60.815 63.158 7.64 0.00 38.20 3.66
3401 7623 2.267642 GGGCGCTGGTACATCACA 59.732 61.111 7.64 0.00 38.20 3.58
3402 7624 2.513897 GGGGCGCTGGTACATCAC 60.514 66.667 7.64 0.00 38.20 3.06
3403 7625 3.792736 GGGGGCGCTGGTACATCA 61.793 66.667 7.64 0.00 38.20 3.07
3417 7639 2.260822 TGAAGAACTCAAGAGAGGGGG 58.739 52.381 3.73 0.00 46.44 5.40
3426 7648 3.495100 GCTCCCAGACTTGAAGAACTCAA 60.495 47.826 0.00 0.00 41.93 3.02
3427 7649 2.037772 GCTCCCAGACTTGAAGAACTCA 59.962 50.000 0.00 0.00 0.00 3.41
3428 7650 2.037772 TGCTCCCAGACTTGAAGAACTC 59.962 50.000 0.00 0.00 0.00 3.01
3429 7651 2.050144 TGCTCCCAGACTTGAAGAACT 58.950 47.619 0.00 0.00 0.00 3.01
3430 7652 2.550830 TGCTCCCAGACTTGAAGAAC 57.449 50.000 0.00 0.00 0.00 3.01
3431 7653 2.909006 AGATGCTCCCAGACTTGAAGAA 59.091 45.455 0.00 0.00 0.00 2.52
3432 7654 2.544721 AGATGCTCCCAGACTTGAAGA 58.455 47.619 0.00 0.00 0.00 2.87
3433 7655 4.378774 CATAGATGCTCCCAGACTTGAAG 58.621 47.826 0.00 0.00 0.00 3.02
3434 7656 3.135348 CCATAGATGCTCCCAGACTTGAA 59.865 47.826 0.00 0.00 0.00 2.69
3435 7657 2.702478 CCATAGATGCTCCCAGACTTGA 59.298 50.000 0.00 0.00 0.00 3.02
3436 7658 2.224475 CCCATAGATGCTCCCAGACTTG 60.224 54.545 0.00 0.00 0.00 3.16
3437 7659 2.053244 CCCATAGATGCTCCCAGACTT 58.947 52.381 0.00 0.00 0.00 3.01
3438 7660 1.727062 CCCATAGATGCTCCCAGACT 58.273 55.000 0.00 0.00 0.00 3.24
3439 7661 0.036022 GCCCATAGATGCTCCCAGAC 59.964 60.000 0.00 0.00 0.00 3.51
3440 7662 0.400381 TGCCCATAGATGCTCCCAGA 60.400 55.000 0.00 0.00 0.00 3.86
3441 7663 2.148611 TGCCCATAGATGCTCCCAG 58.851 57.895 0.00 0.00 0.00 4.45
3442 7664 4.416901 TGCCCATAGATGCTCCCA 57.583 55.556 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.