Multiple sequence alignment - TraesCS7B01G118600

Loading Multiple Alignment...

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 TraesCS7B01G118600 chr7B 100.000 5267 0 0 1 5267 138125403 138130669 0.000000e+00 9727.0
1 TraesCS7B01G118600 chr7D 94.333 2735 132 13 44 2769 171743640 171746360 0.000000e+00 4170.0
2 TraesCS7B01G118600 chr7D 95.238 1533 56 11 2785 4309 171746345 171747868 0.000000e+00 2410.0
3 TraesCS7B01G118600 chr7D 93.467 199 13 0 4508 4706 171754092 171754290 3.990000e-76 296.0
4 TraesCS7B01G118600 chr7A 96.534 2164 68 5 606 2769 174692857 174695013 0.000000e+00 3574.0
5 TraesCS7B01G118600 chr7A 94.588 1201 52 9 2785 3974 174694998 174696196 0.000000e+00 1845.0
6 TraesCS7B01G118600 chr7A 90.672 536 42 6 3811 4342 174696195 174696726 0.000000e+00 706.0
7 TraesCS7B01G118600 chr7A 82.793 709 66 20 4610 5264 174710400 174711106 2.730000e-162 582.0
8 TraesCS7B01G118600 chr7A 82.808 634 73 13 1 608 174687757 174688380 7.760000e-148 534.0
9 TraesCS7B01G118600 chr7A 91.941 273 16 2 4347 4613 174707406 174707678 1.380000e-100 377.0
10 TraesCS7B01G118600 chr7A 96.970 33 0 1 3717 3748 174696308 174696340 3.000000e-03 54.7
11 TraesCS7B01G118600 chr5A 86.121 281 39 0 1284 1564 605321659 605321379 2.380000e-78 303.0
12 TraesCS7B01G118600 chr5A 94.286 35 0 2 4743 4777 569465510 569465542 1.000000e-02 52.8
13 TraesCS7B01G118600 chr1B 84.646 254 37 2 1210 1462 62077014 62076762 8.760000e-63 252.0
14 TraesCS7B01G118600 chr1B 85.526 152 22 0 1632 1783 62076767 62076616 5.460000e-35 159.0
15 TraesCS7B01G118600 chr5D 72.961 233 48 13 3256 3482 30954318 30954095 3.400000e-07 67.6
16 TraesCS7B01G118600 chr5B 87.719 57 7 0 3426 3482 23425348 23425292 3.400000e-07 67.6
17 TraesCS7B01G118600 chr5B 96.970 33 1 0 4745 4777 550195939 550195971 7.370000e-04 56.5
18 TraesCS7B01G118600 chr6D 87.037 54 7 0 1 54 133288740 133288793 1.580000e-05 62.1
19 TraesCS7B01G118600 chr6D 92.105 38 3 0 37 74 453658077 453658114 3.000000e-03 54.7
20 TraesCS7B01G118600 chr6D 100.000 28 0 0 4748 4775 53583453 53583426 1.000000e-02 52.8
21 TraesCS7B01G118600 chr6B 100.000 28 0 0 4750 4777 9081736 9081763 1.000000e-02 52.8
22 TraesCS7B01G118600 chr6A 100.000 28 0 0 4750 4777 3745589 3745562 1.000000e-02 52.8


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 TraesCS7B01G118600 chr7B 138125403 138130669 5266 False 9727.000 9727 100.0000 1 5267 1 chr7B.!!$F1 5266
1 TraesCS7B01G118600 chr7D 171743640 171747868 4228 False 3290.000 4170 94.7855 44 4309 2 chr7D.!!$F2 4265
2 TraesCS7B01G118600 chr7A 174692857 174696726 3869 False 1544.925 3574 94.6910 606 4342 4 chr7A.!!$F2 3736
3 TraesCS7B01G118600 chr7A 174687757 174688380 623 False 534.000 534 82.8080 1 608 1 chr7A.!!$F1 607
4 TraesCS7B01G118600 chr7A 174707406 174711106 3700 False 479.500 582 87.3670 4347 5264 2 chr7A.!!$F3 917

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
493 518 0.035152 TCGGGCGTCTAACTAGGACA 60.035 55.0 0.0 0.0 33.73 4.02 F
517 544 0.037975 GAGTCTGTTTTCGCCCGGTA 60.038 55.0 0.0 0.0 0.00 4.02 F
1070 1103 0.251832 TCCCACTCTCCACTCTCCAC 60.252 60.0 0.0 0.0 0.00 4.02 F
1071 1104 0.252012 CCCACTCTCCACTCTCCACT 60.252 60.0 0.0 0.0 0.00 4.00 F
1317 1350 0.829333 TCTACTCCTACTCCGTCGCT 59.171 55.0 0.0 0.0 0.00 4.93 F
3604 3643 1.149148 GTGTTCAGGAAGAAGCCGAC 58.851 55.0 0.0 0.0 36.78 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2014 2.203728 TACTGCCACGGTGTCCCT 60.204 61.111 7.45 0.0 0.00 4.20 R
2403 2436 4.742649 TCCGCCACGAGCTCCTCT 62.743 66.667 8.47 0.0 40.39 3.69 R
2894 2929 4.984161 CAGCGAAAGTTGAAATGAAATGGT 59.016 37.500 0.00 0.0 46.01 3.55 R
3401 3440 2.432628 GCCTTCTGTGGGTCGACG 60.433 66.667 9.92 0.0 0.00 5.12 R
3610 3649 1.000019 TCCCTCCTGTACCTCACGG 60.000 63.158 0.00 0.0 0.00 4.94 R
4664 7606 0.330604 AGCTCATGAATGCACCACCT 59.669 50.000 9.38 0.0 0.00 4.00 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
38 39 5.924475 ACATACAATACGCTTATCCTTGC 57.076 39.130 0.00 0.00 0.00 4.01
41 42 6.486657 ACATACAATACGCTTATCCTTGCAAT 59.513 34.615 0.00 0.00 0.00 3.56
139 140 3.532155 GCACCGCCCAACAACCAA 61.532 61.111 0.00 0.00 0.00 3.67
148 149 0.601057 CCAACAACCAAATCCCCGAC 59.399 55.000 0.00 0.00 0.00 4.79
179 180 2.107141 CAGAGGTCGGGCCGATTC 59.893 66.667 33.54 29.19 43.70 2.52
190 191 2.203056 CCGATTCGGCAGCATGGA 60.203 61.111 12.95 0.00 41.17 3.41
200 201 4.796231 AGCATGGACGACGACGCC 62.796 66.667 7.30 10.20 43.96 5.68
202 203 2.431771 CATGGACGACGACGCCAA 60.432 61.111 21.42 0.34 43.95 4.52
208 209 2.660552 CGACGACGCCAAGTTGGT 60.661 61.111 22.85 4.08 40.46 3.67
320 344 0.596083 CTCTGCACTATCCGCCTTCG 60.596 60.000 0.00 0.00 0.00 3.79
377 401 2.825836 GGAACGATGCCCTGCAGG 60.826 66.667 26.87 26.87 43.65 4.85
415 439 3.497884 GAGCCCAGTGGTGCCAACT 62.498 63.158 16.33 1.43 0.00 3.16
416 440 3.297620 GCCCAGTGGTGCCAACTG 61.298 66.667 8.74 11.33 0.00 3.16
419 443 2.253758 CCAGTGGTGCCAACTGACG 61.254 63.158 16.69 0.00 33.65 4.35
421 445 0.603707 CAGTGGTGCCAACTGACGAT 60.604 55.000 12.34 0.00 33.65 3.73
422 446 0.603707 AGTGGTGCCAACTGACGATG 60.604 55.000 0.00 0.00 0.00 3.84
423 447 0.602638 GTGGTGCCAACTGACGATGA 60.603 55.000 0.00 0.00 0.00 2.92
424 448 0.602638 TGGTGCCAACTGACGATGAC 60.603 55.000 0.00 0.00 0.00 3.06
425 449 0.602638 GGTGCCAACTGACGATGACA 60.603 55.000 0.00 0.00 0.00 3.58
426 450 1.225855 GTGCCAACTGACGATGACAA 58.774 50.000 0.00 0.00 0.00 3.18
427 451 1.069906 GTGCCAACTGACGATGACAAC 60.070 52.381 0.00 0.00 0.00 3.32
428 452 1.202639 TGCCAACTGACGATGACAACT 60.203 47.619 0.00 0.00 0.00 3.16
431 455 1.800586 CAACTGACGATGACAACTGGG 59.199 52.381 0.00 0.00 0.00 4.45
463 488 0.111639 TTACACCACAAAGGCTCCCC 59.888 55.000 0.00 0.00 43.14 4.81
477 502 1.202348 GCTCCCCAAAAAGTTGATCGG 59.798 52.381 0.00 0.00 36.83 4.18
480 505 0.109319 CCCAAAAAGTTGATCGGGCG 60.109 55.000 0.00 0.00 36.83 6.13
482 507 1.401018 CCAAAAAGTTGATCGGGCGTC 60.401 52.381 0.00 0.00 36.83 5.19
483 508 1.535462 CAAAAAGTTGATCGGGCGTCT 59.465 47.619 0.00 0.00 36.83 4.18
484 509 2.739913 CAAAAAGTTGATCGGGCGTCTA 59.260 45.455 0.00 0.00 36.83 2.59
493 518 0.035152 TCGGGCGTCTAACTAGGACA 60.035 55.000 0.00 0.00 33.73 4.02
494 519 0.381089 CGGGCGTCTAACTAGGACAG 59.619 60.000 0.00 0.00 33.73 3.51
495 520 1.472188 GGGCGTCTAACTAGGACAGT 58.528 55.000 0.00 0.00 40.05 3.55
511 538 0.868406 CAGTGGGAGTCTGTTTTCGC 59.132 55.000 0.00 0.00 0.00 4.70
513 540 1.072505 TGGGAGTCTGTTTTCGCCC 59.927 57.895 0.00 0.00 42.62 6.13
517 544 0.037975 GAGTCTGTTTTCGCCCGGTA 60.038 55.000 0.00 0.00 0.00 4.02
559 586 7.327975 AGGCAAACTTATATTTAGGCCAAAAC 58.672 34.615 5.01 0.00 42.49 2.43
618 645 6.530019 AGAACCACAAGTGTTTTGAAGAAT 57.470 33.333 0.00 0.00 0.00 2.40
626 653 7.373441 CACAAGTGTTTTGAAGAATAGTTCGAC 59.627 37.037 0.00 0.00 34.02 4.20
639 666 3.662247 AGTTCGACAGGGTTCTACTTG 57.338 47.619 0.00 0.00 0.00 3.16
643 670 2.561419 TCGACAGGGTTCTACTTGGAAG 59.439 50.000 0.00 0.00 0.00 3.46
651 678 4.202430 GGGTTCTACTTGGAAGTTGAGGAA 60.202 45.833 0.00 0.00 40.74 3.36
692 719 3.191162 TGGAAAGGCGAATGATGAACAAG 59.809 43.478 0.00 0.00 0.00 3.16
700 727 5.106791 GGCGAATGATGAACAAGAGGATATG 60.107 44.000 0.00 0.00 0.00 1.78
766 793 7.201679 CCAACACATTCTTATTCTCTCATCACC 60.202 40.741 0.00 0.00 0.00 4.02
1045 1078 0.984995 TCTCGTCCTCTCCTCACTCA 59.015 55.000 0.00 0.00 0.00 3.41
1051 1084 0.969894 CCTCTCCTCACTCACCGTTT 59.030 55.000 0.00 0.00 0.00 3.60
1066 1099 0.969894 CGTTTCCCACTCTCCACTCT 59.030 55.000 0.00 0.00 0.00 3.24
1067 1100 1.067495 CGTTTCCCACTCTCCACTCTC 60.067 57.143 0.00 0.00 0.00 3.20
1068 1101 1.276705 GTTTCCCACTCTCCACTCTCC 59.723 57.143 0.00 0.00 0.00 3.71
1069 1102 0.487325 TTCCCACTCTCCACTCTCCA 59.513 55.000 0.00 0.00 0.00 3.86
1070 1103 0.251832 TCCCACTCTCCACTCTCCAC 60.252 60.000 0.00 0.00 0.00 4.02
1071 1104 0.252012 CCCACTCTCCACTCTCCACT 60.252 60.000 0.00 0.00 0.00 4.00
1072 1105 1.181786 CCACTCTCCACTCTCCACTC 58.818 60.000 0.00 0.00 0.00 3.51
1114 1147 1.427419 CTGCTCTCTGTCCTCGTCG 59.573 63.158 0.00 0.00 0.00 5.12
1164 1197 3.759828 GGCGACACCGACGTTTCG 61.760 66.667 0.00 5.82 43.47 3.46
1317 1350 0.829333 TCTACTCCTACTCCGTCGCT 59.171 55.000 0.00 0.00 0.00 4.93
1950 1983 2.109181 GTGGGCGTGCTATCCCTC 59.891 66.667 8.74 2.63 43.04 4.30
2304 2337 2.202349 GTGCGCGGCAAGATTGTC 60.202 61.111 8.83 0.00 41.47 3.18
2391 2424 1.672356 GATGGTGCTGGCGAACACT 60.672 57.895 2.21 0.00 36.99 3.55
2481 2514 2.621998 CGGTGACAAGATACGGGACTAT 59.378 50.000 0.00 0.00 0.00 2.12
2484 2517 2.034179 TGACAAGATACGGGACTATGCG 59.966 50.000 0.00 0.00 0.00 4.73
2727 2760 1.561643 ACATCATCTCCGGTGAGTGT 58.438 50.000 12.42 12.86 39.75 3.55
2746 2779 7.011482 GTGAGTGTACTGTTCAGATTCAGTTTT 59.989 37.037 12.17 0.46 43.39 2.43
2768 2801 8.928733 GTTTTTGCTGATATTGTCATCATGTTT 58.071 29.630 0.00 0.00 33.35 2.83
2769 2802 9.491675 TTTTTGCTGATATTGTCATCATGTTTT 57.508 25.926 0.00 0.00 33.35 2.43
2770 2803 9.491675 TTTTGCTGATATTGTCATCATGTTTTT 57.508 25.926 0.00 0.00 33.35 1.94
2814 2847 9.113838 GTCATCATGTTTGGAATTACTACTCAT 57.886 33.333 0.00 0.00 0.00 2.90
2877 2912 4.587262 ACCCACAAACAAATCCTTTAGACC 59.413 41.667 0.00 0.00 0.00 3.85
3245 3284 1.448540 CCCACACATCAGCGGACTC 60.449 63.158 0.00 0.00 0.00 3.36
3581 3620 2.101582 CCTCAACTACCCATCCTTCTCG 59.898 54.545 0.00 0.00 0.00 4.04
3604 3643 1.149148 GTGTTCAGGAAGAAGCCGAC 58.851 55.000 0.00 0.00 36.78 4.79
3610 3649 4.135493 GAAGAAGCCGACGCACGC 62.135 66.667 0.00 0.00 41.07 5.34
3683 3722 4.021925 GTGAAGGTGAGCGGCCCT 62.022 66.667 0.00 0.00 0.00 5.19
3776 3815 0.690192 TCACCTTCGAATCCAAGGCA 59.310 50.000 6.56 0.00 43.96 4.75
3777 3816 1.281867 TCACCTTCGAATCCAAGGCAT 59.718 47.619 6.56 0.00 43.96 4.40
3885 3924 1.198713 GAAGATGTGAGGAGCAGGGA 58.801 55.000 0.00 0.00 0.00 4.20
3916 3959 1.472552 GGCCCTGTTGGTGTTTGTTTC 60.473 52.381 0.00 0.00 36.04 2.78
3920 3963 3.056179 CCCTGTTGGTGTTTGTTTCAGTT 60.056 43.478 0.00 0.00 0.00 3.16
3921 3964 4.158764 CCCTGTTGGTGTTTGTTTCAGTTA 59.841 41.667 0.00 0.00 0.00 2.24
4021 4233 2.659428 AGCTCTCAACTGCAAAACCTT 58.341 42.857 0.00 0.00 0.00 3.50
4025 4237 2.358898 TCTCAACTGCAAAACCTTGAGC 59.641 45.455 10.62 0.00 39.58 4.26
4120 4332 2.017783 GCGCCGTTAACGTGTGAGA 61.018 57.895 25.15 0.00 37.74 3.27
4132 4344 7.689400 CGTTAACGTGTGAGAGTTTAAGTTTTT 59.311 33.333 19.75 0.00 34.11 1.94
4178 4390 4.021981 GCAAGCAAGAAATAACCCTGAACT 60.022 41.667 0.00 0.00 0.00 3.01
4191 4403 2.039084 CCCTGAACTAAAGTGGCTCAGT 59.961 50.000 8.67 0.00 33.21 3.41
4206 4418 3.531538 GCTCAGTCGTTTGATCCCAATA 58.468 45.455 0.00 0.00 31.46 1.90
4244 4456 0.695462 TATGCCCATCCTGGTGCTCT 60.695 55.000 0.00 0.72 35.17 4.09
4312 4524 3.056607 GCAATATGGTTGCTTGGAACTGT 60.057 43.478 9.60 0.00 41.87 3.55
4313 4525 4.487948 CAATATGGTTGCTTGGAACTGTG 58.512 43.478 5.10 0.00 0.00 3.66
4314 4526 2.071778 ATGGTTGCTTGGAACTGTGT 57.928 45.000 5.10 0.00 0.00 3.72
4338 4550 4.108699 TGTTTGAACCAGCTTGTTCTTG 57.891 40.909 25.85 0.00 43.96 3.02
4342 4554 4.108699 TGAACCAGCTTGTTCTTGTTTG 57.891 40.909 25.85 0.00 43.96 2.93
4343 4555 2.584492 ACCAGCTTGTTCTTGTTTGC 57.416 45.000 0.00 0.00 0.00 3.68
4344 4556 1.824230 ACCAGCTTGTTCTTGTTTGCA 59.176 42.857 0.00 0.00 0.00 4.08
4345 4557 2.159198 ACCAGCTTGTTCTTGTTTGCAG 60.159 45.455 0.00 0.00 0.00 4.41
4346 4558 2.159198 CCAGCTTGTTCTTGTTTGCAGT 60.159 45.455 0.00 0.00 0.00 4.40
4347 4559 3.111098 CAGCTTGTTCTTGTTTGCAGTC 58.889 45.455 0.00 0.00 0.00 3.51
4348 4560 3.019564 AGCTTGTTCTTGTTTGCAGTCT 58.980 40.909 0.00 0.00 0.00 3.24
4349 4561 3.445096 AGCTTGTTCTTGTTTGCAGTCTT 59.555 39.130 0.00 0.00 0.00 3.01
4350 4562 4.082026 AGCTTGTTCTTGTTTGCAGTCTTT 60.082 37.500 0.00 0.00 0.00 2.52
4351 4563 4.032104 GCTTGTTCTTGTTTGCAGTCTTTG 59.968 41.667 0.00 0.00 0.00 2.77
4374 4586 3.504863 CTTTTCGTCAGAATGGGCATTG 58.495 45.455 0.00 0.00 36.09 2.82
4435 4647 2.282040 AGCAGCTGGTCCAAGCAC 60.282 61.111 13.85 0.00 46.08 4.40
4439 4651 0.820891 CAGCTGGTCCAAGCACAAGT 60.821 55.000 5.57 0.00 46.08 3.16
4468 4680 5.528043 TCTGGAATGAGATCAAGTAGAGC 57.472 43.478 0.00 0.00 0.00 4.09
4469 4681 4.343526 TCTGGAATGAGATCAAGTAGAGCC 59.656 45.833 0.00 0.00 31.44 4.70
4475 4687 3.449018 TGAGATCAAGTAGAGCCTTCCAC 59.551 47.826 0.00 0.00 31.44 4.02
4487 4699 1.745653 GCCTTCCACAAATCTGGTAGC 59.254 52.381 0.00 0.00 32.50 3.58
4518 4735 4.946157 ACATCATTGCGGAAGATTCTTCTT 59.054 37.500 22.34 1.71 44.99 2.52
4536 4753 5.827267 TCTTCTTGGAATTTGATGTGTGTCA 59.173 36.000 0.00 0.00 0.00 3.58
4645 7587 2.355444 TGCGGACATGCATATGAACTTG 59.645 45.455 6.97 0.00 40.62 3.16
4659 7601 2.104792 TGAACTTGACTAGTGGCTGCTT 59.895 45.455 0.00 0.00 37.12 3.91
4661 7603 4.202315 TGAACTTGACTAGTGGCTGCTTAA 60.202 41.667 0.00 0.00 37.12 1.85
4664 7606 1.974957 TGACTAGTGGCTGCTTAACCA 59.025 47.619 0.00 0.00 0.00 3.67
4698 7640 2.833794 TGAGCTGTGAAACACTACACC 58.166 47.619 0.00 0.00 45.67 4.16
4721 7675 4.323028 CCTTATCAGGACTGAAGAGTGCAA 60.323 45.833 6.06 0.00 44.19 4.08
4724 7678 2.170397 TCAGGACTGAAGAGTGCAAACA 59.830 45.455 0.00 0.00 42.86 2.83
4739 7693 2.434428 CAAACAGCAGAAGCAGAGGAT 58.566 47.619 0.00 0.00 45.49 3.24
4740 7694 2.110901 AACAGCAGAAGCAGAGGATG 57.889 50.000 0.00 0.00 45.49 3.51
4747 7701 0.742281 GAAGCAGAGGATGAAGCGCA 60.742 55.000 11.47 0.00 0.00 6.09
4766 7720 3.066064 CGCAGGAGCTATATCTCGCTTAT 59.934 47.826 0.00 0.00 36.45 1.73
4769 7723 5.298276 GCAGGAGCTATATCTCGCTTATAGT 59.702 44.000 0.00 0.00 36.45 2.12
4781 7735 2.353208 CGCTTATAGTGAGATGGCTCCC 60.353 54.545 0.00 0.00 40.55 4.30
4804 7758 1.017387 GCCTGAAGCATTTCCCTACG 58.983 55.000 0.00 0.00 42.97 3.51
4815 7769 1.683943 TTCCCTACGCGCTACAGTAT 58.316 50.000 5.73 0.00 0.00 2.12
4820 7774 1.066605 CTACGCGCTACAGTATTGGGT 59.933 52.381 5.73 6.98 0.00 4.51
4822 7776 0.650512 CGCGCTACAGTATTGGGTTG 59.349 55.000 5.56 0.00 0.00 3.77
4834 7788 5.181245 CAGTATTGGGTTGTCTCATTTTCGT 59.819 40.000 0.00 0.00 0.00 3.85
4845 7799 1.593469 TCATTTTCGTGCGTTCGTTCA 59.407 42.857 1.99 0.00 0.00 3.18
4847 7801 0.026544 TTTTCGTGCGTTCGTTCACC 59.973 50.000 1.99 0.00 0.00 4.02
4849 7803 1.484227 TTCGTGCGTTCGTTCACCAG 61.484 55.000 1.99 0.00 0.00 4.00
4856 7810 0.040958 GTTCGTTCACCAGCTTGCTG 60.041 55.000 15.02 15.02 0.00 4.41
4857 7811 0.463654 TTCGTTCACCAGCTTGCTGT 60.464 50.000 19.49 6.83 0.00 4.40
4876 7830 1.785041 TTGCTGGCTGCGTTCACTTC 61.785 55.000 11.85 0.00 46.63 3.01
4922 7879 9.603298 GTTCTTTTGTTTTATAGGTTTACCTCG 57.397 33.333 4.35 0.00 44.77 4.63
4927 7884 7.671495 TGTTTTATAGGTTTACCTCGGTTTC 57.329 36.000 4.35 0.00 44.77 2.78
4929 7886 7.884354 TGTTTTATAGGTTTACCTCGGTTTCAT 59.116 33.333 4.35 0.00 44.77 2.57
4935 7892 4.979815 GGTTTACCTCGGTTTCATTTGTTG 59.020 41.667 0.00 0.00 0.00 3.33
4944 7901 4.559300 CGGTTTCATTTGTTGCTTCCTCAT 60.559 41.667 0.00 0.00 0.00 2.90
4950 7907 8.954950 TTCATTTGTTGCTTCCTCATTTTTAA 57.045 26.923 0.00 0.00 0.00 1.52
4957 7914 7.772757 TGTTGCTTCCTCATTTTTAATGGTTTT 59.227 29.630 0.00 0.00 0.00 2.43
5021 7992 4.725556 TGTTTCTTTCTCGGTTTCATCG 57.274 40.909 0.00 0.00 0.00 3.84
5080 8054 9.624697 TCTTCATTAATTTCTCGGTTTTCATTG 57.375 29.630 0.00 0.00 0.00 2.82
5081 8055 8.755696 TTCATTAATTTCTCGGTTTTCATTGG 57.244 30.769 0.00 0.00 0.00 3.16
5085 8078 8.582433 TTAATTTCTCGGTTTTCATTGGTTTC 57.418 30.769 0.00 0.00 0.00 2.78
5146 8142 9.936759 TTTTTCACTGGTTTTCTTTGTTTCTAT 57.063 25.926 0.00 0.00 0.00 1.98
5162 8158 7.938563 TGTTTCTATTTTTGGTTTTCATCGG 57.061 32.000 0.00 0.00 0.00 4.18
5170 8166 4.473477 TTGGTTTTCATCGGGTTTTTGT 57.527 36.364 0.00 0.00 0.00 2.83
5174 8170 5.113383 GGTTTTCATCGGGTTTTTGTTTCT 58.887 37.500 0.00 0.00 0.00 2.52
5185 8181 8.347035 TCGGGTTTTTGTTTCTCTTTTAGTATG 58.653 33.333 0.00 0.00 0.00 2.39
5260 8256 4.455917 TTTTCCGTACACGTTGAACATC 57.544 40.909 0.58 0.00 37.74 3.06
5263 8259 3.719924 TCCGTACACGTTGAACATCTTT 58.280 40.909 0.58 0.00 37.74 2.52
5264 8260 4.121317 TCCGTACACGTTGAACATCTTTT 58.879 39.130 0.58 0.00 37.74 2.27
5265 8261 4.209703 TCCGTACACGTTGAACATCTTTTC 59.790 41.667 0.58 0.00 37.74 2.29
5266 8262 4.025563 CCGTACACGTTGAACATCTTTTCA 60.026 41.667 0.58 0.00 37.74 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.356751 TGTTGATTGCAAGGATAAGCGTATT 59.643 36.000 4.94 0.00 34.01 1.89
27 28 5.928264 AGTTTTGTTGATTGCAAGGATAAGC 59.072 36.000 4.94 0.00 34.01 3.09
38 39 6.583806 GCCAATCTCACTAGTTTTGTTGATTG 59.416 38.462 15.11 15.11 36.69 2.67
41 42 5.129634 TGCCAATCTCACTAGTTTTGTTGA 58.870 37.500 0.00 0.00 0.00 3.18
139 140 4.208686 GCTCGAGCGTCGGGGATT 62.209 66.667 23.61 0.00 41.50 3.01
179 180 4.794439 TCGTCGTCCATGCTGCCG 62.794 66.667 0.00 0.00 0.00 5.69
183 184 4.796231 GGCGTCGTCGTCCATGCT 62.796 66.667 3.66 0.00 39.49 3.79
185 186 2.431771 TTGGCGTCGTCGTCCATG 60.432 61.111 15.69 0.00 41.33 3.66
186 187 2.126071 CTTGGCGTCGTCGTCCAT 60.126 61.111 15.69 0.00 41.33 3.41
190 191 2.660552 CCAACTTGGCGTCGTCGT 60.661 61.111 3.66 0.00 39.49 4.34
200 201 0.896940 AGCTGCCATGGACCAACTTG 60.897 55.000 18.40 0.00 0.00 3.16
202 203 1.001641 GAGCTGCCATGGACCAACT 60.002 57.895 18.40 5.36 0.00 3.16
300 324 0.747255 GAAGGCGGATAGTGCAGAGA 59.253 55.000 0.00 0.00 0.00 3.10
393 417 4.008933 GCACCACTGGGCTCGTCT 62.009 66.667 0.00 0.00 37.90 4.18
412 436 1.270839 CCCCAGTTGTCATCGTCAGTT 60.271 52.381 0.00 0.00 0.00 3.16
415 439 1.676968 CCCCCAGTTGTCATCGTCA 59.323 57.895 0.00 0.00 0.00 4.35
416 440 4.617875 CCCCCAGTTGTCATCGTC 57.382 61.111 0.00 0.00 0.00 4.20
441 465 1.607148 GGAGCCTTTGTGGTGTAACAC 59.393 52.381 0.00 0.00 39.98 3.32
442 466 1.477923 GGGAGCCTTTGTGGTGTAACA 60.478 52.381 0.00 0.00 39.98 2.41
444 468 0.111639 GGGGAGCCTTTGTGGTGTAA 59.888 55.000 0.00 0.00 38.35 2.41
450 474 1.762370 ACTTTTTGGGGAGCCTTTGTG 59.238 47.619 0.00 0.00 0.00 3.33
463 488 1.535462 AGACGCCCGATCAACTTTTTG 59.465 47.619 0.00 0.00 0.00 2.44
477 502 1.134560 CCACTGTCCTAGTTAGACGCC 59.865 57.143 0.00 0.00 37.60 5.68
480 505 3.695556 GACTCCCACTGTCCTAGTTAGAC 59.304 52.174 0.00 0.00 37.60 2.59
482 507 3.697045 CAGACTCCCACTGTCCTAGTTAG 59.303 52.174 0.00 0.00 37.60 2.34
483 508 3.075582 ACAGACTCCCACTGTCCTAGTTA 59.924 47.826 0.00 0.00 43.84 2.24
484 509 2.158295 ACAGACTCCCACTGTCCTAGTT 60.158 50.000 0.00 0.00 43.84 2.24
493 518 0.250338 GGCGAAAACAGACTCCCACT 60.250 55.000 0.00 0.00 0.00 4.00
494 519 1.235281 GGGCGAAAACAGACTCCCAC 61.235 60.000 0.00 0.00 34.01 4.61
495 520 1.072505 GGGCGAAAACAGACTCCCA 59.927 57.895 0.00 0.00 34.01 4.37
511 538 0.616371 TGTGTGGGAATCTTACCGGG 59.384 55.000 6.32 0.00 32.07 5.73
513 540 4.574828 CCTAAATGTGTGGGAATCTTACCG 59.425 45.833 0.00 0.00 32.07 4.02
517 544 4.046286 TGCCTAAATGTGTGGGAATCTT 57.954 40.909 0.00 0.00 0.00 2.40
585 612 7.875327 AACACTTGTGGTTCTACACTTTAAT 57.125 32.000 5.72 0.00 41.84 1.40
618 645 3.508793 CCAAGTAGAACCCTGTCGAACTA 59.491 47.826 0.00 0.00 0.00 2.24
626 653 4.319177 CTCAACTTCCAAGTAGAACCCTG 58.681 47.826 0.00 0.00 38.57 4.45
639 666 2.028385 TCGGCTTACTTCCTCAACTTCC 60.028 50.000 0.00 0.00 0.00 3.46
643 670 5.416947 TCTATTTCGGCTTACTTCCTCAAC 58.583 41.667 0.00 0.00 0.00 3.18
651 678 3.709653 TCCACCATCTATTTCGGCTTACT 59.290 43.478 0.00 0.00 0.00 2.24
692 719 6.551385 AATTCGTTGATCAAGCATATCCTC 57.449 37.500 8.80 0.00 0.00 3.71
700 727 5.909610 GTGCCTAATAATTCGTTGATCAAGC 59.090 40.000 8.80 4.73 0.00 4.01
986 1013 3.467803 GTGGTGATAATGGCTAGTGTCC 58.532 50.000 0.00 0.00 0.00 4.02
1045 1078 0.763223 AGTGGAGAGTGGGAAACGGT 60.763 55.000 0.00 0.00 0.00 4.83
1051 1084 0.251832 GTGGAGAGTGGAGAGTGGGA 60.252 60.000 0.00 0.00 0.00 4.37
1114 1147 2.970974 GCGAGTGGCTTGCAAGGAC 61.971 63.158 27.10 11.78 40.38 3.85
1188 1221 2.277084 GGGTCCATGAACACGATGTAC 58.723 52.381 0.00 0.00 0.00 2.90
1503 1536 2.304761 GTCAAGAACCCCTATGACCACA 59.695 50.000 0.00 0.00 36.94 4.17
1630 1663 3.760035 GAGCTTCCTCCCGCACGA 61.760 66.667 0.00 0.00 31.68 4.35
1981 2014 2.203728 TACTGCCACGGTGTCCCT 60.204 61.111 7.45 0.00 0.00 4.20
2403 2436 4.742649 TCCGCCACGAGCTCCTCT 62.743 66.667 8.47 0.00 40.39 3.69
2727 2760 6.542005 TCAGCAAAAACTGAATCTGAACAGTA 59.458 34.615 16.83 2.06 44.94 2.74
2775 2808 9.258826 CCAAACATGATGACAATAACTTTTTCA 57.741 29.630 0.00 0.00 0.00 2.69
2776 2809 9.474920 TCCAAACATGATGACAATAACTTTTTC 57.525 29.630 0.00 0.00 0.00 2.29
2777 2810 9.829507 TTCCAAACATGATGACAATAACTTTTT 57.170 25.926 0.00 0.00 0.00 1.94
2785 2818 9.466497 AGTAGTAATTCCAAACATGATGACAAT 57.534 29.630 0.00 0.00 0.00 2.71
2786 2819 8.862325 AGTAGTAATTCCAAACATGATGACAA 57.138 30.769 0.00 0.00 0.00 3.18
2787 2820 8.100164 TGAGTAGTAATTCCAAACATGATGACA 58.900 33.333 0.00 0.00 0.00 3.58
2788 2821 8.492673 TGAGTAGTAATTCCAAACATGATGAC 57.507 34.615 0.00 0.00 0.00 3.06
2789 2822 9.685276 AATGAGTAGTAATTCCAAACATGATGA 57.315 29.630 0.00 0.00 0.00 2.92
2823 2856 5.710513 TTCATAGTCAATTTGTGCAAGCT 57.289 34.783 0.00 0.00 0.00 3.74
2862 2897 7.654022 TGAAACAAAGGTCTAAAGGATTTGT 57.346 32.000 0.00 0.00 43.80 2.83
2877 2912 5.816449 AATGGTGCCTTTTTGAAACAAAG 57.184 34.783 0.00 0.00 0.00 2.77
2894 2929 4.984161 CAGCGAAAGTTGAAATGAAATGGT 59.016 37.500 0.00 0.00 46.01 3.55
3401 3440 2.432628 GCCTTCTGTGGGTCGACG 60.433 66.667 9.92 0.00 0.00 5.12
3410 3449 3.394836 GGGGAGAGCGCCTTCTGT 61.395 66.667 2.29 0.00 43.42 3.41
3581 3620 1.149148 GCTTCTTCCTGAACACGACC 58.851 55.000 0.00 0.00 0.00 4.79
3604 3643 4.710695 TGTACCTCACGGCGTGCG 62.711 66.667 33.59 27.82 32.98 5.34
3610 3649 1.000019 TCCCTCCTGTACCTCACGG 60.000 63.158 0.00 0.00 0.00 4.94
3885 3924 0.106015 AACAGGGCCTGAACTTGCTT 60.106 50.000 38.99 18.41 35.18 3.91
3916 3959 5.152623 TCTCCTGAACCTGAACATAACTG 57.847 43.478 0.00 0.00 0.00 3.16
3920 3963 6.213397 TCTTTCATCTCCTGAACCTGAACATA 59.787 38.462 0.00 0.00 43.54 2.29
3921 3964 4.916041 TTCATCTCCTGAACCTGAACAT 57.084 40.909 0.00 0.00 38.97 2.71
4021 4233 2.650116 GGCACCGAGGAAGAGCTCA 61.650 63.158 17.77 0.00 0.00 4.26
4025 4237 3.358076 GACCGGCACCGAGGAAGAG 62.358 68.421 11.42 0.00 42.83 2.85
4134 4346 8.076178 GCTTGCAAACATAGAACTAGAAAGAAA 58.924 33.333 0.00 0.00 0.00 2.52
4135 4347 7.228507 TGCTTGCAAACATAGAACTAGAAAGAA 59.771 33.333 0.00 0.00 0.00 2.52
4137 4349 6.902341 TGCTTGCAAACATAGAACTAGAAAG 58.098 36.000 0.00 0.00 0.00 2.62
4149 4361 4.996758 GGGTTATTTCTTGCTTGCAAACAT 59.003 37.500 2.88 4.62 0.00 2.71
4178 4390 3.462483 TCAAACGACTGAGCCACTTTA 57.538 42.857 0.00 0.00 0.00 1.85
4191 4403 5.759763 CAGATGACATATTGGGATCAAACGA 59.240 40.000 0.00 0.00 36.36 3.85
4206 4418 6.000219 GGCATAGAAATACACCAGATGACAT 59.000 40.000 0.00 0.00 0.00 3.06
4312 4524 5.587289 GAACAAGCTGGTTCAAACATAACA 58.413 37.500 26.13 0.00 45.07 2.41
4342 4554 7.495886 ATTCTGACGAAAAGGCAAAGACTGC 62.496 44.000 0.00 0.00 37.47 4.40
4343 4555 2.872245 TCTGACGAAAAGGCAAAGACTG 59.128 45.455 0.00 0.00 37.47 3.51
4344 4556 3.194005 TCTGACGAAAAGGCAAAGACT 57.806 42.857 0.00 0.00 37.47 3.24
4345 4557 3.963383 TTCTGACGAAAAGGCAAAGAC 57.037 42.857 0.00 0.00 37.47 3.01
4346 4558 3.253188 CCATTCTGACGAAAAGGCAAAGA 59.747 43.478 0.00 0.00 37.47 2.52
4347 4559 3.568538 CCATTCTGACGAAAAGGCAAAG 58.431 45.455 0.00 0.00 37.47 2.77
4348 4560 2.295909 CCCATTCTGACGAAAAGGCAAA 59.704 45.455 0.00 0.00 37.47 3.68
4349 4561 1.885887 CCCATTCTGACGAAAAGGCAA 59.114 47.619 0.00 0.00 37.47 4.52
4350 4562 1.533625 CCCATTCTGACGAAAAGGCA 58.466 50.000 0.00 0.00 35.81 4.75
4351 4563 0.171231 GCCCATTCTGACGAAAAGGC 59.829 55.000 0.00 0.00 41.33 4.35
4352 4564 1.533625 TGCCCATTCTGACGAAAAGG 58.466 50.000 0.00 0.00 31.91 3.11
4353 4565 3.504863 CAATGCCCATTCTGACGAAAAG 58.495 45.455 0.00 0.00 31.91 2.27
4374 4586 3.364441 TGGAGTTGGCGTGCATGC 61.364 61.111 22.99 22.99 0.00 4.06
4403 4615 0.179171 CTGCTGGCTTCTGATTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
4405 4617 3.715854 GCTGCTGGCTTCTGATTTG 57.284 52.632 0.00 0.00 38.06 2.32
4432 4644 2.533266 TCCAGAACTGAGACTTGTGC 57.467 50.000 3.19 0.00 0.00 4.57
4435 4647 5.144692 TCTCATTCCAGAACTGAGACTTG 57.855 43.478 13.71 1.48 40.24 3.16
4439 4651 5.483231 ACTTGATCTCATTCCAGAACTGAGA 59.517 40.000 17.23 17.23 46.75 3.27
4468 4680 2.290896 TGGCTACCAGATTTGTGGAAGG 60.291 50.000 0.02 0.00 40.44 3.46
4469 4681 3.071874 TGGCTACCAGATTTGTGGAAG 57.928 47.619 0.02 0.00 40.44 3.46
4475 4687 3.005684 TGTGCTTTTGGCTACCAGATTTG 59.994 43.478 0.00 0.00 42.39 2.32
4487 4699 1.067706 TCCGCAATGATGTGCTTTTGG 60.068 47.619 0.00 0.00 42.62 3.28
4496 4708 5.271625 CAAGAAGAATCTTCCGCAATGATG 58.728 41.667 18.46 3.20 44.11 3.07
4518 4735 5.359292 TCAAAGTGACACACATCAAATTCCA 59.641 36.000 8.59 0.00 36.74 3.53
4536 4753 1.680338 AGCCGAACAAAGCTCAAAGT 58.320 45.000 0.00 0.00 32.71 2.66
4645 7587 2.622436 CTGGTTAAGCAGCCACTAGTC 58.378 52.381 20.79 0.00 30.85 2.59
4664 7606 0.330604 AGCTCATGAATGCACCACCT 59.669 50.000 9.38 0.00 0.00 4.00
4698 7640 3.196469 TGCACTCTTCAGTCCTGATAAGG 59.804 47.826 0.00 0.00 39.64 2.69
4721 7675 1.627329 TCATCCTCTGCTTCTGCTGTT 59.373 47.619 0.00 0.00 40.48 3.16
4724 7678 1.407162 GCTTCATCCTCTGCTTCTGCT 60.407 52.381 0.00 0.00 40.48 4.24
4727 7681 0.461693 GCGCTTCATCCTCTGCTTCT 60.462 55.000 0.00 0.00 0.00 2.85
4734 7688 1.886777 GCTCCTGCGCTTCATCCTC 60.887 63.158 9.73 0.00 0.00 3.71
4739 7693 2.230025 GAGATATAGCTCCTGCGCTTCA 59.770 50.000 9.73 0.00 45.42 3.02
4740 7694 2.730715 CGAGATATAGCTCCTGCGCTTC 60.731 54.545 12.27 0.00 45.42 3.86
4747 7701 6.654959 TCACTATAAGCGAGATATAGCTCCT 58.345 40.000 12.27 7.64 43.78 3.69
4766 7720 1.500474 CAAGGGGAGCCATCTCACTA 58.500 55.000 0.00 0.00 42.42 2.74
4769 7723 3.001514 GCAAGGGGAGCCATCTCA 58.998 61.111 0.00 0.00 41.13 3.27
4794 7748 0.822164 ACTGTAGCGCGTAGGGAAAT 59.178 50.000 8.43 0.00 46.37 2.17
4800 7754 1.066605 ACCCAATACTGTAGCGCGTAG 59.933 52.381 8.43 4.24 0.00 3.51
4804 7758 1.664151 GACAACCCAATACTGTAGCGC 59.336 52.381 0.00 0.00 0.00 5.92
4815 7769 2.034053 GCACGAAAATGAGACAACCCAA 59.966 45.455 0.00 0.00 0.00 4.12
4820 7774 2.348125 CGAACGCACGAAAATGAGACAA 60.348 45.455 0.00 0.00 35.09 3.18
4822 7776 1.191647 ACGAACGCACGAAAATGAGAC 59.808 47.619 8.71 0.00 37.03 3.36
4834 7788 1.522806 AAGCTGGTGAACGAACGCA 60.523 52.632 0.00 0.00 0.00 5.24
4849 7803 2.049433 CAGCCAGCAACAGCAAGC 60.049 61.111 0.00 0.00 0.00 4.01
4856 7810 2.050985 GTGAACGCAGCCAGCAAC 60.051 61.111 0.00 0.00 46.13 4.17
4857 7811 1.785041 GAAGTGAACGCAGCCAGCAA 61.785 55.000 0.00 0.00 46.13 3.91
4919 7876 3.004734 AGGAAGCAACAAATGAAACCGAG 59.995 43.478 0.00 0.00 0.00 4.63
4922 7879 4.320608 TGAGGAAGCAACAAATGAAACC 57.679 40.909 0.00 0.00 0.00 3.27
4927 7884 8.231837 CCATTAAAAATGAGGAAGCAACAAATG 58.768 33.333 1.23 0.00 0.00 2.32
4929 7886 7.278875 ACCATTAAAAATGAGGAAGCAACAAA 58.721 30.769 1.23 0.00 0.00 2.83
4990 7947 4.733405 CCGAGAAAGAAACAAAGAAAACCG 59.267 41.667 0.00 0.00 0.00 4.44
5055 8027 8.863049 CCAATGAAAACCGAGAAATTAATGAAG 58.137 33.333 0.00 0.00 0.00 3.02
5057 8029 7.891561 ACCAATGAAAACCGAGAAATTAATGA 58.108 30.769 0.00 0.00 0.00 2.57
5058 8030 8.532977 AACCAATGAAAACCGAGAAATTAATG 57.467 30.769 0.00 0.00 0.00 1.90
5059 8031 9.203421 GAAACCAATGAAAACCGAGAAATTAAT 57.797 29.630 0.00 0.00 0.00 1.40
5061 8033 7.947282 AGAAACCAATGAAAACCGAGAAATTA 58.053 30.769 0.00 0.00 0.00 1.40
5062 8034 6.816136 AGAAACCAATGAAAACCGAGAAATT 58.184 32.000 0.00 0.00 0.00 1.82
5092 8085 6.811665 AGAAACAAAGGAAACGAAAGGAAAAG 59.188 34.615 0.00 0.00 0.00 2.27
5097 8090 6.961359 AAAAGAAACAAAGGAAACGAAAGG 57.039 33.333 0.00 0.00 0.00 3.11
5146 8142 5.705905 ACAAAAACCCGATGAAAACCAAAAA 59.294 32.000 0.00 0.00 0.00 1.94
5170 8166 9.567776 TGTTCATGTTCCATACTAAAAGAGAAA 57.432 29.630 0.00 0.00 0.00 2.52
5174 8170 8.918202 AAGTGTTCATGTTCCATACTAAAAGA 57.082 30.769 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.