Multiple sequence alignment - TraesCS1B01G292600

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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 TraesCS1B01G292600 chr1B 100.000 3934 0 0 1 3934 509904088 509900155 0.000000e+00 7265
1 TraesCS1B01G292600 chr1B 77.252 1121 193 44 1634 2711 510809232 510810333 5.620000e-168 601
2 TraesCS1B01G292600 chr1D 93.909 3349 131 38 1 3314 379913741 379910431 0.000000e+00 4987
3 TraesCS1B01G292600 chr1D 77.569 1119 193 41 1634 2711 381019449 381020550 1.200000e-174 623
4 TraesCS1B01G292600 chr1A 93.631 2936 114 29 412 3308 480936494 480933593 0.000000e+00 4318
5 TraesCS1B01G292600 chr1A 77.648 1114 189 45 1634 2711 481674397 481675486 1.200000e-174 623
6 TraesCS1B01G292600 chr1A 85.275 455 29 21 1 453 480936911 480936493 6.040000e-118 435
7 TraesCS1B01G292600 chr3A 82.663 969 152 10 1751 2712 608751173 608752132 0.000000e+00 845
8 TraesCS1B01G292600 chr3A 75.724 1001 188 37 1751 2714 608347365 608346383 5.990000e-123 451
9 TraesCS1B01G292600 chr3A 85.235 149 20 2 1126 1273 608750338 608750485 6.810000e-33 152
10 TraesCS1B01G292600 chr3D 81.959 970 157 13 1751 2712 465510082 465511041 0.000000e+00 806
11 TraesCS1B01G292600 chr3D 92.520 508 38 0 3313 3820 432037402 432037909 0.000000e+00 728
12 TraesCS1B01G292600 chr3D 92.039 515 40 1 3308 3821 13683108 13683622 0.000000e+00 723
13 TraesCS1B01G292600 chr3D 75.972 1003 182 44 1751 2714 465027152 465026170 2.770000e-126 462
14 TraesCS1B01G292600 chr3D 83.893 149 22 2 1126 1273 465509274 465509421 1.470000e-29 141
15 TraesCS1B01G292600 chr3B 81.340 970 163 14 1751 2712 618870681 618871640 0.000000e+00 773
16 TraesCS1B01G292600 chr3B 75.549 1002 188 42 1751 2714 618442175 618441193 1.300000e-119 440
17 TraesCS1B01G292600 chr3B 83.784 148 22 2 1127 1273 618869558 618869704 5.300000e-29 139
18 TraesCS1B01G292600 chr5D 93.137 510 34 1 3312 3820 565914881 565914372 0.000000e+00 747
19 TraesCS1B01G292600 chr7D 92.802 514 35 2 3310 3821 537337954 537338467 0.000000e+00 743
20 TraesCS1B01G292600 chr6D 92.650 517 35 3 3308 3821 446432585 446432069 0.000000e+00 741
21 TraesCS1B01G292600 chr6D 92.172 511 38 2 3313 3821 132308174 132307664 0.000000e+00 721
22 TraesCS1B01G292600 chr2D 92.383 512 39 0 3310 3821 18175978 18176489 0.000000e+00 730
23 TraesCS1B01G292600 chr2D 92.353 510 37 2 3312 3821 25922954 25922447 0.000000e+00 725
24 TraesCS1B01G292600 chr2B 92.203 513 36 2 3313 3821 651612039 651612551 0.000000e+00 723
25 TraesCS1B01G292600 chr4A 75.474 1003 188 46 1751 2720 104410506 104409529 1.680000e-118 436


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 TraesCS1B01G292600 chr1B 509900155 509904088 3933 True 7265.0 7265 100.000 1 3934 1 chr1B.!!$R1 3933
1 TraesCS1B01G292600 chr1B 510809232 510810333 1101 False 601.0 601 77.252 1634 2711 1 chr1B.!!$F1 1077
2 TraesCS1B01G292600 chr1D 379910431 379913741 3310 True 4987.0 4987 93.909 1 3314 1 chr1D.!!$R1 3313
3 TraesCS1B01G292600 chr1D 381019449 381020550 1101 False 623.0 623 77.569 1634 2711 1 chr1D.!!$F1 1077
4 TraesCS1B01G292600 chr1A 480933593 480936911 3318 True 2376.5 4318 89.453 1 3308 2 chr1A.!!$R1 3307
5 TraesCS1B01G292600 chr1A 481674397 481675486 1089 False 623.0 623 77.648 1634 2711 1 chr1A.!!$F1 1077
6 TraesCS1B01G292600 chr3A 608750338 608752132 1794 False 498.5 845 83.949 1126 2712 2 chr3A.!!$F1 1586
7 TraesCS1B01G292600 chr3A 608346383 608347365 982 True 451.0 451 75.724 1751 2714 1 chr3A.!!$R1 963
8 TraesCS1B01G292600 chr3D 432037402 432037909 507 False 728.0 728 92.520 3313 3820 1 chr3D.!!$F2 507
9 TraesCS1B01G292600 chr3D 13683108 13683622 514 False 723.0 723 92.039 3308 3821 1 chr3D.!!$F1 513
10 TraesCS1B01G292600 chr3D 465509274 465511041 1767 False 473.5 806 82.926 1126 2712 2 chr3D.!!$F3 1586
11 TraesCS1B01G292600 chr3D 465026170 465027152 982 True 462.0 462 75.972 1751 2714 1 chr3D.!!$R1 963
12 TraesCS1B01G292600 chr3B 618869558 618871640 2082 False 456.0 773 82.562 1127 2712 2 chr3B.!!$F1 1585
13 TraesCS1B01G292600 chr3B 618441193 618442175 982 True 440.0 440 75.549 1751 2714 1 chr3B.!!$R1 963
14 TraesCS1B01G292600 chr5D 565914372 565914881 509 True 747.0 747 93.137 3312 3820 1 chr5D.!!$R1 508
15 TraesCS1B01G292600 chr7D 537337954 537338467 513 False 743.0 743 92.802 3310 3821 1 chr7D.!!$F1 511
16 TraesCS1B01G292600 chr6D 446432069 446432585 516 True 741.0 741 92.650 3308 3821 1 chr6D.!!$R2 513
17 TraesCS1B01G292600 chr6D 132307664 132308174 510 True 721.0 721 92.172 3313 3821 1 chr6D.!!$R1 508
18 TraesCS1B01G292600 chr2D 18175978 18176489 511 False 730.0 730 92.383 3310 3821 1 chr2D.!!$F1 511
19 TraesCS1B01G292600 chr2D 25922447 25922954 507 True 725.0 725 92.353 3312 3821 1 chr2D.!!$R1 509
20 TraesCS1B01G292600 chr2B 651612039 651612551 512 False 723.0 723 92.203 3313 3821 1 chr2B.!!$F1 508
21 TraesCS1B01G292600 chr4A 104409529 104410506 977 True 436.0 436 75.474 1751 2720 1 chr4A.!!$R1 969

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
243 245 0.320683 CAACACTCCTGCATCGTCCA 60.321 55.0 0.0 0.0 0.00 4.02 F
1606 1777 0.319813 GTGTAACTAACGTGCCCGGT 60.320 55.0 0.0 0.0 38.78 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1779 0.109412 GAACCACTCACCTACCGACG 60.109 60.0 0.0 0.0 0.0 5.12 R
3012 3690 0.036164 TCCTCGACCACCACCAAATG 59.964 55.0 0.0 0.0 0.0 2.32 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
49 50 0.798776 GGTCACATGAGGCTTTCACG 59.201 55.000 0.00 0.00 38.99 4.35
92 93 8.408601 GTGATATGCCACCATATTGAATTATCC 58.591 37.037 0.00 0.00 43.07 2.59
99 100 6.262049 CCACCATATTGAATTATCCGTGTGAA 59.738 38.462 0.00 0.00 0.00 3.18
100 101 7.132213 CACCATATTGAATTATCCGTGTGAAC 58.868 38.462 0.00 0.00 0.00 3.18
101 102 7.012327 CACCATATTGAATTATCCGTGTGAACT 59.988 37.037 0.00 0.00 0.00 3.01
104 106 9.261180 CATATTGAATTATCCGTGTGAACTAGT 57.739 33.333 0.00 0.00 0.00 2.57
197 199 3.023119 TCTGCAACAGTTTGTCCACATT 58.977 40.909 0.00 0.00 34.90 2.71
205 207 5.057149 ACAGTTTGTCCACATTCAGACTAC 58.943 41.667 0.00 0.00 34.02 2.73
207 209 5.406780 CAGTTTGTCCACATTCAGACTACTC 59.593 44.000 0.00 0.00 34.02 2.59
215 217 4.072839 ACATTCAGACTACTCAGACGACA 58.927 43.478 0.00 0.00 0.00 4.35
217 219 5.880887 ACATTCAGACTACTCAGACGACATA 59.119 40.000 0.00 0.00 0.00 2.29
218 220 6.544197 ACATTCAGACTACTCAGACGACATAT 59.456 38.462 0.00 0.00 0.00 1.78
220 222 7.479897 TTCAGACTACTCAGACGACATATAC 57.520 40.000 0.00 0.00 0.00 1.47
221 223 6.579865 TCAGACTACTCAGACGACATATACA 58.420 40.000 0.00 0.00 0.00 2.29
222 224 6.479331 TCAGACTACTCAGACGACATATACAC 59.521 42.308 0.00 0.00 0.00 2.90
223 225 6.480651 CAGACTACTCAGACGACATATACACT 59.519 42.308 0.00 0.00 0.00 3.55
224 226 6.702723 AGACTACTCAGACGACATATACACTC 59.297 42.308 0.00 0.00 0.00 3.51
225 227 6.346896 ACTACTCAGACGACATATACACTCA 58.653 40.000 0.00 0.00 0.00 3.41
226 228 6.822170 ACTACTCAGACGACATATACACTCAA 59.178 38.462 0.00 0.00 0.00 3.02
227 229 5.881447 ACTCAGACGACATATACACTCAAC 58.119 41.667 0.00 0.00 0.00 3.18
243 245 0.320683 CAACACTCCTGCATCGTCCA 60.321 55.000 0.00 0.00 0.00 4.02
244 246 0.320771 AACACTCCTGCATCGTCCAC 60.321 55.000 0.00 0.00 0.00 4.02
245 247 1.188219 ACACTCCTGCATCGTCCACT 61.188 55.000 0.00 0.00 0.00 4.00
276 285 6.816640 GTGTTCTGCATGGAGTTAATACAGTA 59.183 38.462 14.43 0.00 0.00 2.74
277 286 6.816640 TGTTCTGCATGGAGTTAATACAGTAC 59.183 38.462 14.43 4.42 0.00 2.73
281 290 5.126545 TGCATGGAGTTAATACAGTACGAGT 59.873 40.000 0.00 0.00 0.00 4.18
307 316 2.877300 GCATACATCATACTGCCTGGGG 60.877 54.545 0.00 0.00 0.00 4.96
309 318 2.190398 ACATCATACTGCCTGGGGTA 57.810 50.000 0.00 0.00 0.00 3.69
347 356 3.112263 TCTACCCCATCGACAATTTCCT 58.888 45.455 0.00 0.00 0.00 3.36
348 357 2.420058 ACCCCATCGACAATTTCCTC 57.580 50.000 0.00 0.00 0.00 3.71
480 529 5.121380 ACTGATATTCCAAGACATGCCTT 57.879 39.130 0.00 0.00 0.00 4.35
512 562 1.015109 CCATCATGTCAGCACAGCTC 58.985 55.000 0.00 0.00 36.40 4.09
513 563 1.677820 CCATCATGTCAGCACAGCTCA 60.678 52.381 0.00 0.00 36.40 4.26
553 603 5.880341 AGCGTGCTTAAATTAACATTCCTC 58.120 37.500 0.00 0.00 0.00 3.71
561 611 7.581213 TTAAATTAACATTCCTCGCCATCAT 57.419 32.000 0.00 0.00 0.00 2.45
615 665 4.595762 AAAGTAGTCTGCCGTCAACTTA 57.404 40.909 0.00 0.00 0.00 2.24
653 703 2.338984 GTCGGACGCAACCACTCT 59.661 61.111 0.00 0.00 0.00 3.24
748 798 6.942576 GGCCCTATGTGACAATATTTCTATGT 59.057 38.462 0.00 0.00 0.00 2.29
896 961 3.300388 CACCTCCATCCACTCTAGCTAA 58.700 50.000 0.00 0.00 0.00 3.09
904 969 2.950309 TCCACTCTAGCTAACCATCGAC 59.050 50.000 0.00 0.00 0.00 4.20
1011 1076 1.219664 CTGCACAATGGCAATGGGG 59.780 57.895 6.97 0.00 44.40 4.96
1023 1097 3.060614 AATGGGGATGGGTGCTCGG 62.061 63.158 0.00 0.00 0.00 4.63
1057 1131 3.095163 CCCCTGCATGCCTCCTCT 61.095 66.667 16.68 0.00 0.00 3.69
1326 1492 2.504519 GGACCGGCCTACATCACC 59.495 66.667 0.00 0.00 0.00 4.02
1497 1663 0.914417 CCTTCCCCAAGCCCTACAGA 60.914 60.000 0.00 0.00 0.00 3.41
1550 1717 0.896940 TCCTACGTCACACCTCCACC 60.897 60.000 0.00 0.00 0.00 4.61
1595 1766 5.957761 CACTGTGTGTGTTCGAGTGTAACTA 60.958 44.000 0.00 0.00 44.60 2.24
1605 1776 2.448477 GTGTAACTAACGTGCCCGG 58.552 57.895 0.00 0.00 38.78 5.73
1606 1777 0.319813 GTGTAACTAACGTGCCCGGT 60.320 55.000 0.00 0.00 38.78 5.28
1607 1778 0.038343 TGTAACTAACGTGCCCGGTC 60.038 55.000 0.00 0.00 38.78 4.79
1608 1779 0.737367 GTAACTAACGTGCCCGGTCC 60.737 60.000 0.00 0.00 38.78 4.46
1609 1780 2.211619 TAACTAACGTGCCCGGTCCG 62.212 60.000 3.60 3.60 38.78 4.79
1611 1782 3.976902 CTAACGTGCCCGGTCCGTC 62.977 68.421 11.06 2.04 38.78 4.79
2037 2672 2.668185 TTCGACAACACCACCGCCAT 62.668 55.000 0.00 0.00 0.00 4.40
2494 3172 2.027625 CGCCTTCAACACCTCCGTC 61.028 63.158 0.00 0.00 0.00 4.79
2572 3250 0.955428 ACGGCTACGACTTCCACGTA 60.955 55.000 0.00 0.00 44.60 3.57
2730 3408 3.072038 GGTAGGTCAAACTAACCACCACT 59.928 47.826 0.00 0.00 39.39 4.00
2799 3477 4.639755 TGATTGAGCTGTTGACTTTTGTGA 59.360 37.500 0.00 0.00 0.00 3.58
2834 3512 3.056458 CACTGCCACCTGGACGTA 58.944 61.111 0.00 0.00 37.39 3.57
2909 3587 4.399395 CAGAAGCTGCCGCCTCCA 62.399 66.667 0.00 0.00 36.60 3.86
2966 3644 1.106285 AGATCCTTGGCGATTTTGGC 58.894 50.000 0.00 0.00 0.00 4.52
3065 3755 2.230992 CGGTTTGGCCTGAATGAATGAA 59.769 45.455 3.32 0.00 34.25 2.57
3066 3756 3.119029 CGGTTTGGCCTGAATGAATGAAT 60.119 43.478 3.32 0.00 34.25 2.57
3067 3757 4.186159 GGTTTGGCCTGAATGAATGAATG 58.814 43.478 3.32 0.00 0.00 2.67
3068 3758 4.186159 GTTTGGCCTGAATGAATGAATGG 58.814 43.478 3.32 0.00 0.00 3.16
3084 3774 1.693627 ATGGTGTGCCCGTTTTTGTA 58.306 45.000 0.00 0.00 35.15 2.41
3099 3789 7.491696 CCCGTTTTTGTAATGTTTGGTTTTCTA 59.508 33.333 0.00 0.00 0.00 2.10
3109 3799 6.633500 TGTTTGGTTTTCTATTGGACAGAG 57.367 37.500 0.00 0.00 0.00 3.35
3112 3804 7.013274 TGTTTGGTTTTCTATTGGACAGAGAAG 59.987 37.037 0.00 0.00 31.16 2.85
3129 3821 7.054124 ACAGAGAAGAAAAGATTGGTGTAACA 58.946 34.615 0.00 0.00 39.98 2.41
3145 3837 7.976826 TGGTGTAACAGTAAACTTGTAAACAG 58.023 34.615 0.00 0.00 39.98 3.16
3212 3913 3.570975 TGCTGTCATTCTTTCATTGCACT 59.429 39.130 0.00 0.00 0.00 4.40
3229 3930 2.239400 CACTTTTTCCTTCTCACCCCC 58.761 52.381 0.00 0.00 0.00 5.40
3246 3947 2.092646 CCCCCGGAACATCTGTTGATTA 60.093 50.000 0.73 0.00 38.56 1.75
3249 3950 5.373222 CCCCGGAACATCTGTTGATTATTA 58.627 41.667 0.73 0.00 38.56 0.98
3275 3976 3.137176 TGAAGATTGCTAGCCAGGCTATT 59.863 43.478 22.14 11.85 40.54 1.73
3354 4055 2.176045 TGTGAAGCTCATTAGTCCCGA 58.824 47.619 0.00 0.00 0.00 5.14
3369 4070 4.658063 AGTCCCGATTTGTAATTGAACCA 58.342 39.130 0.00 0.00 0.00 3.67
3383 4084 6.594788 AATTGAACCAGCACTAATGTGATT 57.405 33.333 0.00 0.00 46.55 2.57
3397 4098 5.499139 AATGTGATTATTAGTGCCGGTTG 57.501 39.130 1.90 0.00 0.00 3.77
3522 4223 2.148052 TGGTGGCTCCAACCGGTAA 61.148 57.895 8.00 0.00 44.12 2.85
3524 4225 0.323087 GGTGGCTCCAACCGGTAATT 60.323 55.000 8.00 0.00 35.97 1.40
3530 4231 3.370209 GGCTCCAACCGGTAATTAAGACT 60.370 47.826 8.00 0.00 0.00 3.24
3571 4280 1.271001 GCCACCAACCGGTACTAAAGT 60.271 52.381 8.00 0.00 46.94 2.66
3581 4291 1.607251 GGTACTAAAGTGGTGCGCTGT 60.607 52.381 9.73 0.00 0.00 4.40
3585 4295 0.105964 TAAAGTGGTGCGCTGTCACT 59.894 50.000 19.52 19.52 42.77 3.41
3710 4420 0.403655 TGTGGGCCTATTGCAAGTCA 59.596 50.000 4.94 0.00 43.89 3.41
3715 4425 2.648059 GGCCTATTGCAAGTCATCTGT 58.352 47.619 4.94 0.00 43.89 3.41
3724 4434 0.326264 AAGTCATCTGTCCTGTGGGC 59.674 55.000 0.00 0.00 0.00 5.36
3729 4439 0.253160 ATCTGTCCTGTGGGCCCTAA 60.253 55.000 25.70 10.34 0.00 2.69
3806 4516 2.887360 GTCGTGCCGGCCTAGTAA 59.113 61.111 26.77 0.00 0.00 2.24
3821 4531 4.340097 GCCTAGTAAGTGGGTTGTTTTTGT 59.660 41.667 0.00 0.00 0.00 2.83
3822 4532 5.506815 GCCTAGTAAGTGGGTTGTTTTTGTC 60.507 44.000 0.00 0.00 0.00 3.18
3823 4533 4.625972 AGTAAGTGGGTTGTTTTTGTCG 57.374 40.909 0.00 0.00 0.00 4.35
3824 4534 4.011698 AGTAAGTGGGTTGTTTTTGTCGT 58.988 39.130 0.00 0.00 0.00 4.34
3825 4535 2.931512 AGTGGGTTGTTTTTGTCGTG 57.068 45.000 0.00 0.00 0.00 4.35
3826 4536 1.135228 AGTGGGTTGTTTTTGTCGTGC 60.135 47.619 0.00 0.00 0.00 5.34
3827 4537 0.173708 TGGGTTGTTTTTGTCGTGCC 59.826 50.000 0.00 0.00 0.00 5.01
3828 4538 0.458260 GGGTTGTTTTTGTCGTGCCT 59.542 50.000 0.00 0.00 0.00 4.75
3829 4539 1.535226 GGGTTGTTTTTGTCGTGCCTC 60.535 52.381 0.00 0.00 0.00 4.70
3830 4540 1.462791 GTTGTTTTTGTCGTGCCTCG 58.537 50.000 0.00 0.00 41.41 4.63
3831 4541 1.088306 TTGTTTTTGTCGTGCCTCGT 58.912 45.000 0.00 0.00 40.80 4.18
3832 4542 0.375454 TGTTTTTGTCGTGCCTCGTG 59.625 50.000 0.00 0.00 40.80 4.35
3833 4543 0.316689 GTTTTTGTCGTGCCTCGTGG 60.317 55.000 0.00 0.00 40.80 4.94
3846 4556 2.632377 CCTCGTGGCAATCTATGTTGT 58.368 47.619 0.00 0.00 0.00 3.32
3847 4557 3.009723 CCTCGTGGCAATCTATGTTGTT 58.990 45.455 0.00 0.00 0.00 2.83
3848 4558 3.181507 CCTCGTGGCAATCTATGTTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
3849 4559 3.407698 TCGTGGCAATCTATGTTGTTGT 58.592 40.909 0.00 0.00 0.00 3.32
3850 4560 3.188254 TCGTGGCAATCTATGTTGTTGTG 59.812 43.478 0.00 0.00 0.00 3.33
3851 4561 3.188254 CGTGGCAATCTATGTTGTTGTGA 59.812 43.478 0.00 0.00 0.00 3.58
3852 4562 4.669965 CGTGGCAATCTATGTTGTTGTGAG 60.670 45.833 0.00 0.00 0.00 3.51
3853 4563 3.758023 TGGCAATCTATGTTGTTGTGAGG 59.242 43.478 0.00 0.00 0.00 3.86
3854 4564 4.009675 GGCAATCTATGTTGTTGTGAGGA 58.990 43.478 0.00 0.00 0.00 3.71
3855 4565 4.641989 GGCAATCTATGTTGTTGTGAGGAT 59.358 41.667 0.00 0.00 0.00 3.24
3856 4566 5.449588 GGCAATCTATGTTGTTGTGAGGATG 60.450 44.000 0.00 0.00 0.00 3.51
3857 4567 5.449588 GCAATCTATGTTGTTGTGAGGATGG 60.450 44.000 0.00 0.00 0.00 3.51
3858 4568 3.609853 TCTATGTTGTTGTGAGGATGGC 58.390 45.455 0.00 0.00 0.00 4.40
3859 4569 2.291209 ATGTTGTTGTGAGGATGGCA 57.709 45.000 0.00 0.00 0.00 4.92
3860 4570 2.064434 TGTTGTTGTGAGGATGGCAA 57.936 45.000 0.00 0.00 0.00 4.52
3861 4571 2.596346 TGTTGTTGTGAGGATGGCAAT 58.404 42.857 0.00 0.00 0.00 3.56
3862 4572 2.964464 TGTTGTTGTGAGGATGGCAATT 59.036 40.909 0.00 0.00 0.00 2.32
3863 4573 3.387374 TGTTGTTGTGAGGATGGCAATTT 59.613 39.130 0.00 0.00 0.00 1.82
3864 4574 4.141756 TGTTGTTGTGAGGATGGCAATTTT 60.142 37.500 0.00 0.00 0.00 1.82
3865 4575 4.686191 TGTTGTGAGGATGGCAATTTTT 57.314 36.364 0.00 0.00 0.00 1.94
3886 4596 5.726980 TTTTAGCAAGCATGACAAATCCT 57.273 34.783 0.00 0.00 0.00 3.24
3887 4597 4.707030 TTAGCAAGCATGACAAATCCTG 57.293 40.909 0.00 0.00 0.00 3.86
3888 4598 2.522185 AGCAAGCATGACAAATCCTGT 58.478 42.857 0.00 0.00 42.61 4.00
3903 4613 8.597662 ACAAATCCTGTCAAAAATCTGAATTG 57.402 30.769 0.00 0.00 29.87 2.32
3904 4614 7.658575 ACAAATCCTGTCAAAAATCTGAATTGG 59.341 33.333 0.00 0.00 29.87 3.16
3905 4615 5.726980 TCCTGTCAAAAATCTGAATTGGG 57.273 39.130 0.00 0.00 0.00 4.12
3906 4616 5.392995 TCCTGTCAAAAATCTGAATTGGGA 58.607 37.500 0.00 0.00 0.00 4.37
3907 4617 5.243730 TCCTGTCAAAAATCTGAATTGGGAC 59.756 40.000 0.00 3.93 0.00 4.46
3908 4618 5.119931 TGTCAAAAATCTGAATTGGGACG 57.880 39.130 0.00 0.00 0.00 4.79
3909 4619 4.022416 TGTCAAAAATCTGAATTGGGACGG 60.022 41.667 0.00 0.00 0.00 4.79
3910 4620 3.056891 TCAAAAATCTGAATTGGGACGGC 60.057 43.478 0.00 0.00 0.00 5.68
3911 4621 1.094785 AAATCTGAATTGGGACGGCG 58.905 50.000 4.80 4.80 0.00 6.46
3912 4622 0.035439 AATCTGAATTGGGACGGCGT 60.035 50.000 14.65 14.65 0.00 5.68
3913 4623 0.744414 ATCTGAATTGGGACGGCGTG 60.744 55.000 21.19 0.00 0.00 5.34
3914 4624 1.375396 CTGAATTGGGACGGCGTGA 60.375 57.895 21.19 0.00 0.00 4.35
3915 4625 0.744414 CTGAATTGGGACGGCGTGAT 60.744 55.000 21.19 2.82 0.00 3.06
3916 4626 0.322098 TGAATTGGGACGGCGTGATT 60.322 50.000 21.19 12.12 0.00 2.57
3917 4627 0.808755 GAATTGGGACGGCGTGATTT 59.191 50.000 21.19 3.40 0.00 2.17
3918 4628 0.525761 AATTGGGACGGCGTGATTTG 59.474 50.000 21.19 0.00 0.00 2.32
3919 4629 1.933115 ATTGGGACGGCGTGATTTGC 61.933 55.000 21.19 0.19 0.00 3.68
3926 4636 4.895854 GCGTGATTTGCCATGCTT 57.104 50.000 0.00 0.00 43.67 3.91
3927 4637 3.126729 GCGTGATTTGCCATGCTTT 57.873 47.368 0.00 0.00 43.67 3.51
3928 4638 0.994263 GCGTGATTTGCCATGCTTTC 59.006 50.000 0.00 0.00 43.67 2.62
3929 4639 1.403249 GCGTGATTTGCCATGCTTTCT 60.403 47.619 0.00 0.00 43.67 2.52
3930 4640 2.159393 GCGTGATTTGCCATGCTTTCTA 60.159 45.455 0.00 0.00 43.67 2.10
3931 4641 3.688272 CGTGATTTGCCATGCTTTCTAG 58.312 45.455 0.00 0.00 0.00 2.43
3932 4642 3.374988 CGTGATTTGCCATGCTTTCTAGA 59.625 43.478 0.00 0.00 0.00 2.43
3933 4643 4.142622 CGTGATTTGCCATGCTTTCTAGAA 60.143 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.838736 TCACTTCTGAACTGAAGGCAC 58.161 47.619 19.76 0.00 45.49 5.01
92 93 3.909776 TCTGTACCACTAGTTCACACG 57.090 47.619 0.00 0.00 0.00 4.49
99 100 8.362464 TCTCATAATTGTTCTGTACCACTAGT 57.638 34.615 0.00 0.00 0.00 2.57
100 101 9.823647 AATCTCATAATTGTTCTGTACCACTAG 57.176 33.333 0.00 0.00 0.00 2.57
140 142 4.141869 GGCCTGCCATTAATCATTGAAACT 60.142 41.667 2.58 0.00 35.81 2.66
197 199 6.479331 GTGTATATGTCGTCTGAGTAGTCTGA 59.521 42.308 3.19 3.19 0.00 3.27
205 207 5.739630 GTGTTGAGTGTATATGTCGTCTGAG 59.260 44.000 0.00 0.00 0.00 3.35
207 209 5.641709 AGTGTTGAGTGTATATGTCGTCTG 58.358 41.667 0.00 0.00 0.00 3.51
215 217 5.605534 GATGCAGGAGTGTTGAGTGTATAT 58.394 41.667 0.00 0.00 0.00 0.86
217 219 3.677148 CGATGCAGGAGTGTTGAGTGTAT 60.677 47.826 0.00 0.00 0.00 2.29
218 220 2.352715 CGATGCAGGAGTGTTGAGTGTA 60.353 50.000 0.00 0.00 0.00 2.90
220 222 1.073964 CGATGCAGGAGTGTTGAGTG 58.926 55.000 0.00 0.00 0.00 3.51
221 223 0.681733 ACGATGCAGGAGTGTTGAGT 59.318 50.000 0.00 0.00 0.00 3.41
222 224 1.354040 GACGATGCAGGAGTGTTGAG 58.646 55.000 0.00 0.00 0.00 3.02
223 225 0.037326 GGACGATGCAGGAGTGTTGA 60.037 55.000 0.00 0.00 0.00 3.18
224 226 0.320683 TGGACGATGCAGGAGTGTTG 60.321 55.000 0.00 0.00 0.00 3.33
225 227 0.320771 GTGGACGATGCAGGAGTGTT 60.321 55.000 0.00 0.00 0.00 3.32
226 228 1.188219 AGTGGACGATGCAGGAGTGT 61.188 55.000 0.00 0.00 0.00 3.55
227 229 0.036952 AAGTGGACGATGCAGGAGTG 60.037 55.000 0.00 0.00 0.00 3.51
243 245 3.030291 TCCATGCAGAACACCAAAAAGT 58.970 40.909 0.00 0.00 0.00 2.66
244 246 3.068590 ACTCCATGCAGAACACCAAAAAG 59.931 43.478 0.00 0.00 0.00 2.27
245 247 3.030291 ACTCCATGCAGAACACCAAAAA 58.970 40.909 0.00 0.00 0.00 1.94
307 316 8.406297 GGGGTAGAAGATGATCAACATTTTTAC 58.594 37.037 0.00 0.00 39.56 2.01
309 318 6.953520 TGGGGTAGAAGATGATCAACATTTTT 59.046 34.615 0.00 0.00 39.56 1.94
451 500 7.254727 GCATGTCTTGGAATATCAGTTTCTCTC 60.255 40.741 0.00 0.00 0.00 3.20
512 562 2.476686 CGCTACTTCATGTGCACCATTG 60.477 50.000 15.69 9.69 0.00 2.82
513 563 1.739466 CGCTACTTCATGTGCACCATT 59.261 47.619 15.69 0.00 0.00 3.16
561 611 4.877378 TTCTGAAACCTAGGAAACGCTA 57.123 40.909 17.98 0.00 0.00 4.26
653 703 1.061905 ATCGGATCCATTGGCCCTGA 61.062 55.000 13.41 3.17 0.00 3.86
748 798 2.432563 CTGGGTTTGGTGGGCGTA 59.567 61.111 0.00 0.00 0.00 4.42
896 961 1.903877 CTGCAAGGGAGGTCGATGGT 61.904 60.000 0.00 0.00 0.00 3.55
904 969 2.271497 CAGGAGCTGCAAGGGAGG 59.729 66.667 8.35 0.00 0.00 4.30
1225 1299 1.595794 GTTGTTGTGGACGTTGACGAT 59.404 47.619 10.87 0.00 43.02 3.73
1311 1477 2.285069 TGGGTGATGTAGGCCGGT 60.285 61.111 1.90 0.00 0.00 5.28
1497 1663 1.333636 CGAGCATGAGGGGGACTTCT 61.334 60.000 0.00 0.00 37.34 2.85
1530 1697 0.243095 GTGGAGGTGTGACGTAGGAC 59.757 60.000 0.00 0.00 0.00 3.85
1531 1698 0.896940 GGTGGAGGTGTGACGTAGGA 60.897 60.000 0.00 0.00 0.00 2.94
1532 1699 1.590147 GGTGGAGGTGTGACGTAGG 59.410 63.158 0.00 0.00 0.00 3.18
1533 1700 1.590147 GGGTGGAGGTGTGACGTAG 59.410 63.158 0.00 0.00 0.00 3.51
1534 1701 1.909781 GGGGTGGAGGTGTGACGTA 60.910 63.158 0.00 0.00 0.00 3.57
1535 1702 3.239253 GGGGTGGAGGTGTGACGT 61.239 66.667 0.00 0.00 0.00 4.34
1536 1703 2.124507 AATGGGGTGGAGGTGTGACG 62.125 60.000 0.00 0.00 0.00 4.35
1538 1705 0.404040 GAAATGGGGTGGAGGTGTGA 59.596 55.000 0.00 0.00 0.00 3.58
1539 1706 0.611896 GGAAATGGGGTGGAGGTGTG 60.612 60.000 0.00 0.00 0.00 3.82
1540 1707 1.774300 GGAAATGGGGTGGAGGTGT 59.226 57.895 0.00 0.00 0.00 4.16
1541 1708 1.000359 GGGAAATGGGGTGGAGGTG 60.000 63.158 0.00 0.00 0.00 4.00
1542 1709 2.612493 CGGGAAATGGGGTGGAGGT 61.612 63.158 0.00 0.00 0.00 3.85
1543 1710 2.275418 CGGGAAATGGGGTGGAGG 59.725 66.667 0.00 0.00 0.00 4.30
1550 1717 1.003003 ACAAAAATGGCGGGAAATGGG 59.997 47.619 0.00 0.00 0.00 4.00
1605 1776 1.505353 CACTCACCTACCGACGGAC 59.495 63.158 23.38 0.00 0.00 4.79
1606 1777 1.676635 CCACTCACCTACCGACGGA 60.677 63.158 23.38 3.17 0.00 4.69
1607 1778 1.530013 AACCACTCACCTACCGACGG 61.530 60.000 13.61 13.61 0.00 4.79
1608 1779 0.109412 GAACCACTCACCTACCGACG 60.109 60.000 0.00 0.00 0.00 5.12
1609 1780 0.963962 TGAACCACTCACCTACCGAC 59.036 55.000 0.00 0.00 0.00 4.79
1611 1782 1.792006 GTTGAACCACTCACCTACCG 58.208 55.000 0.00 0.00 32.21 4.02
2037 2672 3.190849 CGTACTCGAGGACGGCGA 61.191 66.667 37.06 2.14 39.71 5.54
2194 2857 0.832135 AGAAGAAGCTCCGGTCCACA 60.832 55.000 0.00 0.00 0.00 4.17
2494 3172 4.007644 TCCTGCAGCACCACCTCG 62.008 66.667 8.66 0.00 0.00 4.63
2799 3477 3.949754 CAGTGCATGATCCAAACACCTAT 59.050 43.478 0.00 0.00 31.58 2.57
2834 3512 2.847292 ATAGGCCCCAGCTCAGGTGT 62.847 60.000 0.00 0.00 39.73 4.16
2909 3587 1.533273 CGTGGGGATATCGGAGGGT 60.533 63.158 0.00 0.00 0.00 4.34
3012 3690 0.036164 TCCTCGACCACCACCAAATG 59.964 55.000 0.00 0.00 0.00 2.32
3065 3755 1.693627 TACAAAAACGGGCACACCAT 58.306 45.000 0.00 0.00 40.22 3.55
3066 3756 1.471119 TTACAAAAACGGGCACACCA 58.529 45.000 0.00 0.00 40.22 4.17
3067 3757 2.223852 ACATTACAAAAACGGGCACACC 60.224 45.455 0.00 0.00 0.00 4.16
3068 3758 3.086818 ACATTACAAAAACGGGCACAC 57.913 42.857 0.00 0.00 0.00 3.82
3084 3774 7.505585 TCTCTGTCCAATAGAAAACCAAACATT 59.494 33.333 0.00 0.00 0.00 2.71
3099 3789 6.208204 CACCAATCTTTTCTTCTCTGTCCAAT 59.792 38.462 0.00 0.00 0.00 3.16
3109 3799 9.447040 GTTTACTGTTACACCAATCTTTTCTTC 57.553 33.333 0.00 0.00 0.00 2.87
3112 3804 9.233232 CAAGTTTACTGTTACACCAATCTTTTC 57.767 33.333 0.00 0.00 0.00 2.29
3129 3821 6.264518 CCATGGAACCTGTTTACAAGTTTACT 59.735 38.462 5.56 0.00 31.25 2.24
3196 3897 7.440255 AGAAGGAAAAAGTGCAATGAAAGAATG 59.560 33.333 0.00 0.00 0.00 2.67
3212 3913 0.111639 CCGGGGGTGAGAAGGAAAAA 59.888 55.000 0.00 0.00 0.00 1.94
3229 3930 7.279981 TCAACCTAATAATCAACAGATGTTCCG 59.720 37.037 0.00 0.00 35.83 4.30
3246 3947 5.116084 TGGCTAGCAATCTTCAACCTAAT 57.884 39.130 18.24 0.00 0.00 1.73
3249 3950 2.356535 CCTGGCTAGCAATCTTCAACCT 60.357 50.000 18.24 0.00 0.00 3.50
3354 4055 7.814107 CACATTAGTGCTGGTTCAATTACAAAT 59.186 33.333 0.00 0.00 39.21 2.32
3443 4144 2.568062 TGGCATGAACCGGTACTAAAGA 59.432 45.455 8.00 0.00 0.00 2.52
3471 4172 1.907255 GGCCACCACCTCTTTAGTACT 59.093 52.381 0.00 0.00 0.00 2.73
3522 4223 5.866159 CCGTACTAAAGGGGAGTCTTAAT 57.134 43.478 0.00 0.00 0.00 1.40
3585 4295 2.217750 ACTAAACATTGTGCACTGCGA 58.782 42.857 19.41 1.75 0.00 5.10
3668 4378 0.829990 GCCTGCTTAGAGAGGAGCTT 59.170 55.000 2.36 0.00 42.08 3.74
3715 4425 3.754043 CCATTAGGGCCCACAGGA 58.246 61.111 27.56 4.62 33.47 3.86
3771 4481 3.181499 ACGACCTGCATACGACTAGAAAG 60.181 47.826 12.72 0.00 0.00 2.62
3801 4511 5.064962 CACGACAAAAACAACCCACTTACTA 59.935 40.000 0.00 0.00 0.00 1.82
3806 4516 1.135228 GCACGACAAAAACAACCCACT 60.135 47.619 0.00 0.00 0.00 4.00
3826 4536 2.632377 ACAACATAGATTGCCACGAGG 58.368 47.619 0.00 0.00 32.47 4.63
3827 4537 3.436704 ACAACAACATAGATTGCCACGAG 59.563 43.478 0.00 0.00 32.47 4.18
3828 4538 3.188254 CACAACAACATAGATTGCCACGA 59.812 43.478 0.00 0.00 32.47 4.35
3829 4539 3.188254 TCACAACAACATAGATTGCCACG 59.812 43.478 0.00 0.00 32.47 4.94
3830 4540 4.379813 CCTCACAACAACATAGATTGCCAC 60.380 45.833 0.00 0.00 32.47 5.01
3831 4541 3.758023 CCTCACAACAACATAGATTGCCA 59.242 43.478 0.00 0.00 32.47 4.92
3832 4542 4.009675 TCCTCACAACAACATAGATTGCC 58.990 43.478 0.00 0.00 32.47 4.52
3833 4543 5.449588 CCATCCTCACAACAACATAGATTGC 60.450 44.000 0.00 0.00 32.47 3.56
3834 4544 5.449588 GCCATCCTCACAACAACATAGATTG 60.450 44.000 0.00 0.00 35.59 2.67
3835 4545 4.641989 GCCATCCTCACAACAACATAGATT 59.358 41.667 0.00 0.00 0.00 2.40
3836 4546 4.202441 GCCATCCTCACAACAACATAGAT 58.798 43.478 0.00 0.00 0.00 1.98
3837 4547 3.008923 TGCCATCCTCACAACAACATAGA 59.991 43.478 0.00 0.00 0.00 1.98
3838 4548 3.346315 TGCCATCCTCACAACAACATAG 58.654 45.455 0.00 0.00 0.00 2.23
3839 4549 3.431673 TGCCATCCTCACAACAACATA 57.568 42.857 0.00 0.00 0.00 2.29
3840 4550 2.291209 TGCCATCCTCACAACAACAT 57.709 45.000 0.00 0.00 0.00 2.71
3841 4551 2.064434 TTGCCATCCTCACAACAACA 57.936 45.000 0.00 0.00 0.00 3.33
3842 4552 3.665745 AATTGCCATCCTCACAACAAC 57.334 42.857 0.00 0.00 0.00 3.32
3843 4553 4.686191 AAAATTGCCATCCTCACAACAA 57.314 36.364 0.00 0.00 0.00 2.83
3844 4554 4.686191 AAAAATTGCCATCCTCACAACA 57.314 36.364 0.00 0.00 0.00 3.33
3863 4573 5.927689 CAGGATTTGTCATGCTTGCTAAAAA 59.072 36.000 0.00 0.00 0.00 1.94
3864 4574 5.010922 ACAGGATTTGTCATGCTTGCTAAAA 59.989 36.000 0.00 0.00 33.87 1.52
3865 4575 4.523943 ACAGGATTTGTCATGCTTGCTAAA 59.476 37.500 0.00 0.00 33.87 1.85
3866 4576 4.081406 ACAGGATTTGTCATGCTTGCTAA 58.919 39.130 0.00 0.00 33.87 3.09
3867 4577 3.689347 ACAGGATTTGTCATGCTTGCTA 58.311 40.909 0.00 0.00 33.87 3.49
3868 4578 2.522185 ACAGGATTTGTCATGCTTGCT 58.478 42.857 0.00 0.00 33.87 3.91
3878 4588 7.658575 CCAATTCAGATTTTTGACAGGATTTGT 59.341 33.333 0.00 0.00 44.55 2.83
3879 4589 7.118680 CCCAATTCAGATTTTTGACAGGATTTG 59.881 37.037 0.00 0.00 0.00 2.32
3880 4590 7.016465 TCCCAATTCAGATTTTTGACAGGATTT 59.984 33.333 0.00 0.00 0.00 2.17
3881 4591 6.497954 TCCCAATTCAGATTTTTGACAGGATT 59.502 34.615 0.00 0.00 0.00 3.01
3882 4592 6.018469 TCCCAATTCAGATTTTTGACAGGAT 58.982 36.000 0.00 0.00 0.00 3.24
3883 4593 5.243730 GTCCCAATTCAGATTTTTGACAGGA 59.756 40.000 0.00 0.00 0.00 3.86
3884 4594 5.473039 GTCCCAATTCAGATTTTTGACAGG 58.527 41.667 0.00 0.00 0.00 4.00
3885 4595 5.156355 CGTCCCAATTCAGATTTTTGACAG 58.844 41.667 0.00 0.00 0.00 3.51
3886 4596 4.022416 CCGTCCCAATTCAGATTTTTGACA 60.022 41.667 0.00 0.00 0.00 3.58
3887 4597 4.485163 CCGTCCCAATTCAGATTTTTGAC 58.515 43.478 0.00 0.00 0.00 3.18
3888 4598 3.056891 GCCGTCCCAATTCAGATTTTTGA 60.057 43.478 0.00 0.00 0.00 2.69
3889 4599 3.253230 GCCGTCCCAATTCAGATTTTTG 58.747 45.455 0.00 0.00 0.00 2.44
3890 4600 2.094752 CGCCGTCCCAATTCAGATTTTT 60.095 45.455 0.00 0.00 0.00 1.94
3891 4601 1.472480 CGCCGTCCCAATTCAGATTTT 59.528 47.619 0.00 0.00 0.00 1.82
3892 4602 1.094785 CGCCGTCCCAATTCAGATTT 58.905 50.000 0.00 0.00 0.00 2.17
3893 4603 0.035439 ACGCCGTCCCAATTCAGATT 60.035 50.000 0.00 0.00 0.00 2.40
3894 4604 0.744414 CACGCCGTCCCAATTCAGAT 60.744 55.000 0.00 0.00 0.00 2.90
3895 4605 1.375396 CACGCCGTCCCAATTCAGA 60.375 57.895 0.00 0.00 0.00 3.27
3896 4606 0.744414 ATCACGCCGTCCCAATTCAG 60.744 55.000 0.00 0.00 0.00 3.02
3897 4607 0.322098 AATCACGCCGTCCCAATTCA 60.322 50.000 0.00 0.00 0.00 2.57
3898 4608 0.808755 AAATCACGCCGTCCCAATTC 59.191 50.000 0.00 0.00 0.00 2.17
3899 4609 0.525761 CAAATCACGCCGTCCCAATT 59.474 50.000 0.00 0.00 0.00 2.32
3900 4610 1.933115 GCAAATCACGCCGTCCCAAT 61.933 55.000 0.00 0.00 0.00 3.16
3901 4611 2.622011 GCAAATCACGCCGTCCCAA 61.622 57.895 0.00 0.00 0.00 4.12
3902 4612 3.053291 GCAAATCACGCCGTCCCA 61.053 61.111 0.00 0.00 0.00 4.37
3903 4613 3.810896 GGCAAATCACGCCGTCCC 61.811 66.667 0.00 0.00 40.35 4.46
3909 4619 0.994263 GAAAGCATGGCAAATCACGC 59.006 50.000 0.00 0.00 0.00 5.34
3910 4620 2.642139 AGAAAGCATGGCAAATCACG 57.358 45.000 0.00 0.00 0.00 4.35
3911 4621 4.970662 TCTAGAAAGCATGGCAAATCAC 57.029 40.909 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.