Multiple sequence alignment - TraesCS7B01G239000

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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 TraesCS7B01G239000 chr7B 100.000 4419 0 0 1 4419 444474139 444478557 0.000000e+00 8161.0
1 TraesCS7B01G239000 chr7B 89.583 96 5 5 3523 3616 119045784 119045692 2.790000e-22 117.0
2 TraesCS7B01G239000 chr7B 90.217 92 5 4 3519 3608 661996482 661996393 2.790000e-22 117.0
3 TraesCS7B01G239000 chr7D 97.016 2681 60 10 892 3564 426847053 426849721 0.000000e+00 4490.0
4 TraesCS7B01G239000 chr7D 93.971 481 25 2 3941 4419 426850225 426850703 0.000000e+00 725.0
5 TraesCS7B01G239000 chr7D 87.129 606 39 20 6 588 426846295 426846884 0.000000e+00 651.0
6 TraesCS7B01G239000 chr7D 94.340 159 7 2 3602 3759 426849724 426849881 4.420000e-60 243.0
7 TraesCS7B01G239000 chr7D 95.082 122 3 2 3757 3877 426849958 426850077 5.830000e-44 189.0
8 TraesCS7B01G239000 chr7D 94.872 117 6 0 675 791 426846886 426847002 2.710000e-42 183.0
9 TraesCS7B01G239000 chr7D 90.076 131 5 3 3881 4011 426850113 426850235 3.540000e-36 163.0
10 TraesCS7B01G239000 chr7D 87.719 57 4 3 631 687 176171760 176171813 3.690000e-06 63.9
11 TraesCS7B01G239000 chr7A 96.135 2717 78 11 868 3564 506132258 506129549 0.000000e+00 4410.0
12 TraesCS7B01G239000 chr7A 91.763 607 26 6 6 588 506133009 506132403 0.000000e+00 822.0
13 TraesCS7B01G239000 chr7A 92.857 546 35 2 3876 4419 506129265 506128722 0.000000e+00 789.0
14 TraesCS7B01G239000 chr7A 89.057 265 5 5 3614 3877 506129537 506129296 1.540000e-79 307.0
15 TraesCS7B01G239000 chr7A 96.694 121 3 1 672 791 506132399 506132279 2.700000e-47 200.0
16 TraesCS7B01G239000 chr7A 95.000 80 4 0 3130 3209 506130064 506129985 4.640000e-25 126.0
17 TraesCS7B01G239000 chr6B 84.319 1218 159 13 1318 2524 688780999 688779803 0.000000e+00 1162.0
18 TraesCS7B01G239000 chr6A 89.211 621 67 0 1904 2524 599165860 599166480 0.000000e+00 776.0
19 TraesCS7B01G239000 chr6A 83.629 507 60 10 1329 1828 599165336 599165826 5.210000e-124 455.0
20 TraesCS7B01G239000 chr6D 89.796 588 57 2 1940 2524 453170711 453171298 0.000000e+00 750.0
21 TraesCS7B01G239000 chr6D 82.137 627 78 12 1327 1942 453170016 453170619 1.420000e-139 507.0
22 TraesCS7B01G239000 chr6D 78.313 415 48 18 3883 4291 472100195 472099817 3.440000e-56 230.0
23 TraesCS7B01G239000 chr6D 93.617 47 2 1 621 667 49869750 49869795 7.930000e-08 69.4
24 TraesCS7B01G239000 chr4B 82.776 389 51 5 1931 2317 140892722 140893096 2.550000e-87 333.0
25 TraesCS7B01G239000 chr4B 89.583 96 5 5 3523 3616 74721775 74721867 2.790000e-22 117.0
26 TraesCS7B01G239000 chr4B 100.000 39 0 0 629 667 628556416 628556454 6.130000e-09 73.1
27 TraesCS7B01G239000 chr2B 90.625 96 4 5 3523 3616 654124283 654124191 6.000000e-24 122.0
28 TraesCS7B01G239000 chr2B 89.583 96 5 5 3523 3616 386561712 386561620 2.790000e-22 117.0
29 TraesCS7B01G239000 chr2B 87.931 58 6 1 629 685 167084570 167084627 2.850000e-07 67.6
30 TraesCS7B01G239000 chr3B 89.583 96 5 5 3523 3616 479463277 479463369 2.790000e-22 117.0
31 TraesCS7B01G239000 chr1B 89.583 96 5 5 3523 3616 579758508 579758600 2.790000e-22 117.0
32 TraesCS7B01G239000 chr1B 92.308 52 3 1 628 678 603937308 603937359 6.130000e-09 73.1
33 TraesCS7B01G239000 chrUn 89.474 95 4 6 3520 3611 84435377 84435468 1.000000e-21 115.0
34 TraesCS7B01G239000 chr4D 89.362 94 6 4 3520 3611 213708416 213708325 1.000000e-21 115.0
35 TraesCS7B01G239000 chr1A 87.179 78 6 3 3921 3996 104826772 104826697 7.870000e-13 86.1
36 TraesCS7B01G239000 chr1A 85.075 67 6 4 631 694 564088422 564088357 1.030000e-06 65.8
37 TraesCS7B01G239000 chr3A 94.000 50 2 1 629 677 642160701 642160750 1.700000e-09 75.0
38 TraesCS7B01G239000 chr3D 100.000 39 0 0 629 667 595760595 595760633 6.130000e-09 73.1
39 TraesCS7B01G239000 chr4A 89.091 55 4 1 628 682 214314463 214314411 2.850000e-07 67.6


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 TraesCS7B01G239000 chr7B 444474139 444478557 4418 False 8161.000000 8161 100.000000 1 4419 1 chr7B.!!$F1 4418
1 TraesCS7B01G239000 chr7D 426846295 426850703 4408 False 949.142857 4490 93.212286 6 4419 7 chr7D.!!$F2 4413
2 TraesCS7B01G239000 chr7A 506128722 506133009 4287 True 1109.000000 4410 93.584333 6 4419 6 chr7A.!!$R1 4413
3 TraesCS7B01G239000 chr6B 688779803 688780999 1196 True 1162.000000 1162 84.319000 1318 2524 1 chr6B.!!$R1 1206
4 TraesCS7B01G239000 chr6A 599165336 599166480 1144 False 615.500000 776 86.420000 1329 2524 2 chr6A.!!$F1 1195
5 TraesCS7B01G239000 chr6D 453170016 453171298 1282 False 628.500000 750 85.966500 1327 2524 2 chr6D.!!$F2 1197

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
862 919 0.476771 AGGTTCCCCGCAAAAAGAGA 59.523 50.000 0.0 0.0 35.12 3.10 F
863 920 1.133606 AGGTTCCCCGCAAAAAGAGAA 60.134 47.619 0.0 0.0 35.12 2.87 F
1841 1925 0.827507 AAATGGTGGTGGTGCTGGTC 60.828 55.000 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1780 0.036010 CCATGTTGCCTCGGAGAACT 60.036 55.000 6.58 0.0 34.09 3.01 R
2227 2411 1.202177 CGCACCAAATCAGCATACACC 60.202 52.381 0.00 0.0 0.00 4.16 R
3593 3781 0.033306 AGAGTTACTCCCTCCGTCCC 60.033 60.000 8.96 0.0 0.00 4.46 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
24 25 1.472552 CCGTCGCTGGACCATGAAATA 60.473 52.381 0.00 0.00 40.17 1.40
111 112 3.086600 AGGCTAGAGGGGCAGCAC 61.087 66.667 0.00 0.00 39.63 4.40
161 162 3.102204 TGATCAGCACAAGGAGATGAGA 58.898 45.455 0.00 0.00 0.00 3.27
172 173 3.772387 AGGAGATGAGAACACTGACTGA 58.228 45.455 0.00 0.00 0.00 3.41
247 255 8.413229 AGTTGCATTGTAAGTTAATGTGACTTT 58.587 29.630 0.00 0.00 38.28 2.66
305 319 0.981183 AGGCGGGATATGCGGAATTA 59.019 50.000 5.95 0.00 0.00 1.40
380 401 2.476619 CGTCCGGCTATGATTGAATGAC 59.523 50.000 0.00 0.00 0.00 3.06
555 606 2.589014 CGTCTGCTTGAATTTTCAGCC 58.411 47.619 10.26 1.05 38.61 4.85
588 645 8.190784 TGCAACGATCGTCTGATTATATGATAT 58.809 33.333 22.98 0.00 34.09 1.63
589 646 9.025020 GCAACGATCGTCTGATTATATGATATT 57.975 33.333 22.98 0.00 34.09 1.28
591 648 9.737427 AACGATCGTCTGATTATATGATATTCC 57.263 33.333 22.98 0.00 34.09 3.01
592 649 8.353684 ACGATCGTCTGATTATATGATATTCCC 58.646 37.037 16.60 0.00 34.09 3.97
593 650 8.572185 CGATCGTCTGATTATATGATATTCCCT 58.428 37.037 7.03 0.00 34.09 4.20
594 651 9.906660 GATCGTCTGATTATATGATATTCCCTC 57.093 37.037 0.00 0.00 34.09 4.30
595 652 9.653516 ATCGTCTGATTATATGATATTCCCTCT 57.346 33.333 0.00 0.00 0.00 3.69
596 653 9.480861 TCGTCTGATTATATGATATTCCCTCTT 57.519 33.333 0.00 0.00 0.00 2.85
597 654 9.526713 CGTCTGATTATATGATATTCCCTCTTG 57.473 37.037 0.00 0.00 0.00 3.02
604 661 9.788815 TTATATGATATTCCCTCTTGAGATGGA 57.211 33.333 1.42 1.42 37.13 3.41
605 662 5.815233 TGATATTCCCTCTTGAGATGGAC 57.185 43.478 4.73 0.00 38.34 4.02
606 663 5.218959 TGATATTCCCTCTTGAGATGGACA 58.781 41.667 4.73 0.00 38.34 4.02
607 664 5.306419 TGATATTCCCTCTTGAGATGGACAG 59.694 44.000 4.73 0.00 38.34 3.51
608 665 1.198713 TCCCTCTTGAGATGGACAGC 58.801 55.000 1.42 0.00 34.57 4.40
609 666 0.907486 CCCTCTTGAGATGGACAGCA 59.093 55.000 0.00 0.00 32.39 4.41
610 667 1.280133 CCCTCTTGAGATGGACAGCAA 59.720 52.381 0.00 0.00 32.39 3.91
611 668 2.290514 CCCTCTTGAGATGGACAGCAAA 60.291 50.000 0.00 0.00 32.39 3.68
612 669 2.746362 CCTCTTGAGATGGACAGCAAAC 59.254 50.000 0.00 0.00 0.00 2.93
613 670 2.746362 CTCTTGAGATGGACAGCAAACC 59.254 50.000 0.00 0.00 0.00 3.27
614 671 2.106338 TCTTGAGATGGACAGCAAACCA 59.894 45.455 0.00 0.00 40.57 3.67
616 673 2.439409 TGAGATGGACAGCAAACCATG 58.561 47.619 12.06 0.00 45.41 3.66
617 674 2.040145 TGAGATGGACAGCAAACCATGA 59.960 45.455 12.06 0.00 45.41 3.07
618 675 3.285484 GAGATGGACAGCAAACCATGAT 58.715 45.455 12.06 2.82 45.41 2.45
619 676 3.698040 GAGATGGACAGCAAACCATGATT 59.302 43.478 12.06 0.00 45.41 2.57
620 677 4.858850 AGATGGACAGCAAACCATGATTA 58.141 39.130 12.06 0.00 45.41 1.75
621 678 5.452255 AGATGGACAGCAAACCATGATTAT 58.548 37.500 12.06 0.00 45.41 1.28
622 679 6.604171 AGATGGACAGCAAACCATGATTATA 58.396 36.000 12.06 0.00 45.41 0.98
623 680 7.236529 AGATGGACAGCAAACCATGATTATAT 58.763 34.615 12.06 0.00 45.41 0.86
624 681 8.385491 AGATGGACAGCAAACCATGATTATATA 58.615 33.333 12.06 0.00 45.41 0.86
625 682 8.938801 ATGGACAGCAAACCATGATTATATAA 57.061 30.769 7.56 0.00 44.01 0.98
626 683 8.394971 TGGACAGCAAACCATGATTATATAAG 57.605 34.615 1.02 0.00 0.00 1.73
627 684 7.998383 TGGACAGCAAACCATGATTATATAAGT 59.002 33.333 1.02 0.00 0.00 2.24
628 685 8.850156 GGACAGCAAACCATGATTATATAAGTT 58.150 33.333 1.02 0.00 0.00 2.66
666 723 8.608844 ATGCTCTTATATTTCTTTACGAAGGG 57.391 34.615 0.00 0.00 33.56 3.95
667 724 6.990349 TGCTCTTATATTTCTTTACGAAGGGG 59.010 38.462 0.00 0.00 33.56 4.79
668 725 6.427242 GCTCTTATATTTCTTTACGAAGGGGG 59.573 42.308 0.00 0.00 33.56 5.40
669 726 7.441903 TCTTATATTTCTTTACGAAGGGGGT 57.558 36.000 0.00 0.00 33.56 4.95
670 727 7.277396 TCTTATATTTCTTTACGAAGGGGGTG 58.723 38.462 0.00 0.00 33.56 4.61
671 728 1.900245 TTTCTTTACGAAGGGGGTGC 58.100 50.000 0.00 0.00 33.56 5.01
672 729 1.061546 TTCTTTACGAAGGGGGTGCT 58.938 50.000 0.00 0.00 33.56 4.40
673 730 1.941377 TCTTTACGAAGGGGGTGCTA 58.059 50.000 0.00 0.00 33.56 3.49
741 798 1.033574 TTACGTGCCCAAACCAAAGG 58.966 50.000 0.00 0.00 0.00 3.11
782 839 1.680735 CAGCAGTACACCAGCCAAAAA 59.319 47.619 0.00 0.00 0.00 1.94
784 841 2.965147 AGCAGTACACCAGCCAAAAATT 59.035 40.909 0.00 0.00 0.00 1.82
791 848 3.938334 ACACCAGCCAAAAATTTGTGTTC 59.062 39.130 7.58 0.00 36.45 3.18
792 849 3.312146 CACCAGCCAAAAATTTGTGTTCC 59.688 43.478 7.58 0.00 36.45 3.62
793 850 2.877786 CCAGCCAAAAATTTGTGTTCCC 59.122 45.455 7.58 0.00 36.45 3.97
795 852 1.870402 GCCAAAAATTTGTGTTCCCCG 59.130 47.619 7.58 0.00 36.45 5.73
796 853 1.870402 CCAAAAATTTGTGTTCCCCGC 59.130 47.619 7.58 0.00 36.45 6.13
797 854 2.555199 CAAAAATTTGTGTTCCCCGCA 58.445 42.857 0.00 0.00 33.59 5.69
798 855 2.939103 CAAAAATTTGTGTTCCCCGCAA 59.061 40.909 0.00 0.00 41.66 4.85
802 859 2.990066 TTTGTGTTCCCCGCAAATTT 57.010 40.000 0.00 0.00 45.93 1.82
803 860 2.990066 TTGTGTTCCCCGCAAATTTT 57.010 40.000 0.00 0.00 40.48 1.82
804 861 2.990066 TGTGTTCCCCGCAAATTTTT 57.010 40.000 0.00 0.00 0.00 1.94
859 916 2.606065 CGTAAAGGTTCCCCGCAAAAAG 60.606 50.000 0.00 0.00 35.12 2.27
861 918 1.328279 AAGGTTCCCCGCAAAAAGAG 58.672 50.000 0.00 0.00 35.12 2.85
862 919 0.476771 AGGTTCCCCGCAAAAAGAGA 59.523 50.000 0.00 0.00 35.12 3.10
863 920 1.133606 AGGTTCCCCGCAAAAAGAGAA 60.134 47.619 0.00 0.00 35.12 2.87
864 921 1.684450 GGTTCCCCGCAAAAAGAGAAA 59.316 47.619 0.00 0.00 0.00 2.52
865 922 2.101750 GGTTCCCCGCAAAAAGAGAAAA 59.898 45.455 0.00 0.00 0.00 2.29
866 923 3.431068 GGTTCCCCGCAAAAAGAGAAAAA 60.431 43.478 0.00 0.00 0.00 1.94
911 968 1.166531 GGGAGTTGTTCAGCGTTGCT 61.167 55.000 0.00 0.00 40.77 3.91
1261 1324 1.659794 CAAGCCCAAGGACAAACCG 59.340 57.895 0.00 0.00 44.74 4.44
1262 1325 1.530655 AAGCCCAAGGACAAACCGG 60.531 57.895 0.00 0.00 44.74 5.28
1263 1326 2.002018 AAGCCCAAGGACAAACCGGA 62.002 55.000 9.46 0.00 44.74 5.14
1264 1327 1.971695 GCCCAAGGACAAACCGGAG 60.972 63.158 9.46 0.00 44.74 4.63
1265 1328 1.971695 CCCAAGGACAAACCGGAGC 60.972 63.158 9.46 0.00 44.74 4.70
1266 1329 1.971695 CCAAGGACAAACCGGAGCC 60.972 63.158 9.46 1.08 44.74 4.70
1267 1330 2.032071 AAGGACAAACCGGAGCCG 59.968 61.111 9.46 1.06 44.74 5.52
1699 1780 1.067142 GTGTCTGACTATGCCGTTGGA 60.067 52.381 9.51 0.00 0.00 3.53
1841 1925 0.827507 AAATGGTGGTGGTGCTGGTC 60.828 55.000 0.00 0.00 0.00 4.02
1858 1942 3.197790 CGCCAGGCTGTTCCATCG 61.198 66.667 14.43 3.27 37.29 3.84
1869 1953 3.270877 CTGTTCCATCGGTTAAGGGAAG 58.729 50.000 0.00 0.00 39.91 3.46
1901 1988 1.133809 TGGTTCCAAGGTCTCCCCTG 61.134 60.000 0.00 0.00 45.47 4.45
2105 2289 1.666234 GCGATCCGGGAGATGCTTC 60.666 63.158 0.00 0.00 34.42 3.86
2110 2294 0.909610 TCCGGGAGATGCTTCCACTT 60.910 55.000 0.00 0.00 39.09 3.16
2160 2344 2.898729 ACTGAGGTGTCACAAGTGAG 57.101 50.000 5.12 0.00 40.75 3.51
2482 2666 7.640240 GCAGATTCATCCTTCATAAAACGTTAC 59.360 37.037 0.00 0.00 0.00 2.50
2560 2744 3.387962 TGATCCCCTAGAGAAATGCAGT 58.612 45.455 0.00 0.00 0.00 4.40
2812 2996 4.791974 CAAGATTCCAAGCTCTGTCAAAC 58.208 43.478 0.00 0.00 0.00 2.93
3056 3240 2.238084 AGAGTACCATCAGGCTGTGA 57.762 50.000 15.27 0.00 40.38 3.58
3095 3279 5.705441 TCAAATGAAGATGGACACTTGGTAC 59.295 40.000 0.00 0.00 0.00 3.34
3115 3299 3.771216 ACTGAAGAATGGTGAAATGCCT 58.229 40.909 0.00 0.00 0.00 4.75
3123 3307 3.574284 TGGTGAAATGCCTTGAATTCG 57.426 42.857 0.04 0.00 0.00 3.34
3124 3308 3.153130 TGGTGAAATGCCTTGAATTCGA 58.847 40.909 0.04 0.00 0.00 3.71
3125 3309 3.763360 TGGTGAAATGCCTTGAATTCGAT 59.237 39.130 0.04 0.00 0.00 3.59
3126 3310 4.946772 TGGTGAAATGCCTTGAATTCGATA 59.053 37.500 0.04 0.00 0.00 2.92
3127 3311 5.593909 TGGTGAAATGCCTTGAATTCGATAT 59.406 36.000 0.04 0.00 0.00 1.63
3174 3358 9.922477 ATCTGCATATCAAATGAAGATGGATAT 57.078 29.630 7.53 0.00 41.60 1.63
3227 3411 8.091385 TGAATTCGATATGATGATGAACCTTG 57.909 34.615 0.04 0.00 0.00 3.61
3319 3503 7.148474 GCATGTCGTTCTCTAAAAATAGTTGGA 60.148 37.037 0.00 0.00 0.00 3.53
3585 3773 7.807977 ACTATGACAGTGTCAAAAATGTCTT 57.192 32.000 28.70 12.15 45.96 3.01
3586 3774 8.902540 ACTATGACAGTGTCAAAAATGTCTTA 57.097 30.769 28.70 12.62 45.96 2.10
3587 3775 9.507329 ACTATGACAGTGTCAAAAATGTCTTAT 57.493 29.630 28.70 10.95 45.96 1.73
3605 3793 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
3606 3794 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3607 3795 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3608 3796 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
3609 3797 2.077687 TATGGGACGGAGGGAGTAAC 57.922 55.000 0.00 0.00 0.00 2.50
3610 3798 0.338814 ATGGGACGGAGGGAGTAACT 59.661 55.000 0.00 0.00 0.00 2.24
3611 3799 0.324091 TGGGACGGAGGGAGTAACTC 60.324 60.000 0.00 0.00 0.00 3.01
3612 3800 0.033306 GGGACGGAGGGAGTAACTCT 60.033 60.000 0.00 0.00 35.34 3.24
3766 4034 8.170061 CCATTTACCTCTATTATGGATTTGGGA 58.830 37.037 0.00 0.00 38.39 4.37
3767 4035 9.014297 CATTTACCTCTATTATGGATTTGGGAC 57.986 37.037 0.00 0.00 0.00 4.46
3792 4060 0.178990 GGGAGTGGAACAGCAAACCT 60.179 55.000 0.00 0.00 41.80 3.50
3874 4142 8.357402 GTGTGGTGTTCTTTAATTTTGTAGGAT 58.643 33.333 0.00 0.00 0.00 3.24
3878 4179 9.406828 GGTGTTCTTTAATTTTGTAGGATTGTC 57.593 33.333 0.00 0.00 0.00 3.18
3947 4248 8.595533 CATGAAAGAATTGATCTGATTTTGCTG 58.404 33.333 0.00 0.00 38.79 4.41
3949 4250 8.145767 TGAAAGAATTGATCTGATTTTGCTGTT 58.854 29.630 0.00 0.00 38.79 3.16
3960 4261 6.542005 TCTGATTTTGCTGTTGTTTGTCTCTA 59.458 34.615 0.00 0.00 0.00 2.43
4013 4366 8.668353 TCTATCTGTAGATTTTTGTTCATGTGC 58.332 33.333 0.00 0.00 36.05 4.57
4057 4410 8.659925 ATGTACAATTTTGTTCATGCAAGAAA 57.340 26.923 5.85 0.00 44.16 2.52
4116 4469 3.018856 TGTAGCTCAATCATTTGCCCAG 58.981 45.455 0.00 0.00 32.61 4.45
4117 4470 1.481871 AGCTCAATCATTTGCCCAGG 58.518 50.000 0.00 0.00 32.61 4.45
4118 4471 0.179092 GCTCAATCATTTGCCCAGGC 60.179 55.000 0.38 0.38 42.35 4.85
4147 4500 5.393068 TCTTCCATCTGGGCAATCTTTAT 57.607 39.130 0.00 0.00 36.21 1.40
4279 4632 1.618343 TCGATGACACTCTGCTCCAAA 59.382 47.619 0.00 0.00 0.00 3.28
4291 4644 0.318762 GCTCCAAACCGTCTCTGTCT 59.681 55.000 0.00 0.00 0.00 3.41
4295 4648 3.228453 TCCAAACCGTCTCTGTCTAAGT 58.772 45.455 0.00 0.00 0.00 2.24
4296 4649 4.401022 TCCAAACCGTCTCTGTCTAAGTA 58.599 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.744414 ATTTCATGGTCCAGCGACGG 60.744 55.000 0.00 0.00 40.17 4.79
42 43 1.964223 TCTTTTGAGCCGAGAGACTGT 59.036 47.619 0.00 0.00 0.00 3.55
44 45 1.964223 TGTCTTTTGAGCCGAGAGACT 59.036 47.619 11.72 0.00 38.02 3.24
117 118 1.144496 GTAGCCCGACGCCCAAATA 59.856 57.895 0.00 0.00 38.78 1.40
161 162 0.179045 GGTGCCAGTCAGTCAGTGTT 60.179 55.000 0.00 0.00 0.00 3.32
172 173 4.290622 CAGCCCAAGGGTGCCAGT 62.291 66.667 7.05 0.00 44.28 4.00
247 255 5.262422 CGCGCATGAAATTCTAAACACATA 58.738 37.500 8.75 0.00 0.00 2.29
283 297 4.624364 CCGCATATCCCGCCTGCA 62.624 66.667 0.00 0.00 35.64 4.41
286 300 0.981183 TAATTCCGCATATCCCGCCT 59.019 50.000 0.00 0.00 0.00 5.52
305 319 1.073474 TCCTCCCCCATGCAGCTAT 60.073 57.895 0.00 0.00 0.00 2.97
380 401 5.759506 AGTCCATCTCTACGTACATTCAG 57.240 43.478 0.00 0.00 0.00 3.02
530 581 3.826157 TGAAAATTCAAGCAGACGGGAAT 59.174 39.130 0.00 0.00 33.55 3.01
590 647 0.907486 TGCTGTCCATCTCAAGAGGG 59.093 55.000 4.32 4.32 46.62 4.30
591 648 2.746362 GTTTGCTGTCCATCTCAAGAGG 59.254 50.000 0.00 0.00 0.00 3.69
592 649 2.746362 GGTTTGCTGTCCATCTCAAGAG 59.254 50.000 0.00 0.00 0.00 2.85
593 650 2.106338 TGGTTTGCTGTCCATCTCAAGA 59.894 45.455 0.00 0.00 0.00 3.02
594 651 2.507484 TGGTTTGCTGTCCATCTCAAG 58.493 47.619 0.00 0.00 0.00 3.02
595 652 2.655090 TGGTTTGCTGTCCATCTCAA 57.345 45.000 0.00 0.00 0.00 3.02
596 653 2.040145 TCATGGTTTGCTGTCCATCTCA 59.960 45.455 0.00 0.00 41.79 3.27
597 654 2.715046 TCATGGTTTGCTGTCCATCTC 58.285 47.619 0.00 0.00 41.79 2.75
598 655 2.885135 TCATGGTTTGCTGTCCATCT 57.115 45.000 0.00 0.00 41.79 2.90
599 656 5.779529 ATAATCATGGTTTGCTGTCCATC 57.220 39.130 0.00 0.00 41.79 3.51
600 657 8.938801 TTATATAATCATGGTTTGCTGTCCAT 57.061 30.769 0.00 0.00 44.15 3.41
601 658 7.998383 ACTTATATAATCATGGTTTGCTGTCCA 59.002 33.333 0.00 0.00 38.14 4.02
602 659 8.396272 ACTTATATAATCATGGTTTGCTGTCC 57.604 34.615 0.00 0.00 0.00 4.02
640 697 9.057089 CCCTTCGTAAAGAAATATAAGAGCATT 57.943 33.333 0.00 0.00 38.57 3.56
641 698 7.661847 CCCCTTCGTAAAGAAATATAAGAGCAT 59.338 37.037 0.00 0.00 38.57 3.79
642 699 6.990349 CCCCTTCGTAAAGAAATATAAGAGCA 59.010 38.462 0.00 0.00 38.57 4.26
643 700 6.427242 CCCCCTTCGTAAAGAAATATAAGAGC 59.573 42.308 0.00 0.00 38.57 4.09
644 701 7.441458 CACCCCCTTCGTAAAGAAATATAAGAG 59.559 40.741 0.00 0.00 38.57 2.85
645 702 7.277396 CACCCCCTTCGTAAAGAAATATAAGA 58.723 38.462 0.00 0.00 38.57 2.10
646 703 6.017357 GCACCCCCTTCGTAAAGAAATATAAG 60.017 42.308 0.00 0.00 38.57 1.73
647 704 5.824097 GCACCCCCTTCGTAAAGAAATATAA 59.176 40.000 0.00 0.00 38.57 0.98
648 705 5.131475 AGCACCCCCTTCGTAAAGAAATATA 59.869 40.000 0.00 0.00 38.57 0.86
649 706 4.079958 AGCACCCCCTTCGTAAAGAAATAT 60.080 41.667 0.00 0.00 38.57 1.28
650 707 3.264964 AGCACCCCCTTCGTAAAGAAATA 59.735 43.478 0.00 0.00 38.57 1.40
651 708 2.041216 AGCACCCCCTTCGTAAAGAAAT 59.959 45.455 0.00 0.00 38.57 2.17
652 709 1.422402 AGCACCCCCTTCGTAAAGAAA 59.578 47.619 0.00 0.00 38.57 2.52
653 710 1.061546 AGCACCCCCTTCGTAAAGAA 58.938 50.000 0.00 0.00 34.14 2.52
654 711 1.551883 GTAGCACCCCCTTCGTAAAGA 59.448 52.381 0.00 0.00 34.14 2.52
655 712 1.406477 GGTAGCACCCCCTTCGTAAAG 60.406 57.143 0.00 0.00 30.04 1.85
656 713 0.614812 GGTAGCACCCCCTTCGTAAA 59.385 55.000 0.00 0.00 30.04 2.01
657 714 0.544833 TGGTAGCACCCCCTTCGTAA 60.545 55.000 0.00 0.00 37.50 3.18
658 715 0.325860 ATGGTAGCACCCCCTTCGTA 60.326 55.000 0.00 0.00 37.50 3.43
659 716 1.615424 ATGGTAGCACCCCCTTCGT 60.615 57.895 0.00 0.00 37.50 3.85
660 717 1.153168 CATGGTAGCACCCCCTTCG 60.153 63.158 0.00 0.00 37.50 3.79
661 718 0.623723 TTCATGGTAGCACCCCCTTC 59.376 55.000 0.00 0.00 37.50 3.46
662 719 1.063717 CATTCATGGTAGCACCCCCTT 60.064 52.381 0.00 0.00 37.50 3.95
663 720 0.552848 CATTCATGGTAGCACCCCCT 59.447 55.000 0.00 0.00 37.50 4.79
664 721 0.550914 TCATTCATGGTAGCACCCCC 59.449 55.000 0.00 0.00 37.50 5.40
665 722 2.435372 TTCATTCATGGTAGCACCCC 57.565 50.000 0.00 0.00 37.50 4.95
666 723 2.099756 GCTTTCATTCATGGTAGCACCC 59.900 50.000 0.00 0.00 37.50 4.61
667 724 2.754552 TGCTTTCATTCATGGTAGCACC 59.245 45.455 0.00 0.00 38.62 5.01
668 725 4.142315 ACATGCTTTCATTCATGGTAGCAC 60.142 41.667 14.81 0.00 42.66 4.40
669 726 4.018490 ACATGCTTTCATTCATGGTAGCA 58.982 39.130 14.85 14.85 43.11 3.49
670 727 4.357142 CACATGCTTTCATTCATGGTAGC 58.643 43.478 7.08 6.96 43.11 3.58
671 728 4.400251 ACCACATGCTTTCATTCATGGTAG 59.600 41.667 7.08 0.00 43.11 3.18
672 729 4.343231 ACCACATGCTTTCATTCATGGTA 58.657 39.130 7.08 0.00 43.11 3.25
673 730 3.167485 ACCACATGCTTTCATTCATGGT 58.833 40.909 7.08 0.00 43.11 3.55
782 839 3.483808 AAATTTGCGGGGAACACAAAT 57.516 38.095 0.00 0.00 45.19 2.32
784 841 2.990066 AAAATTTGCGGGGAACACAA 57.010 40.000 0.00 0.00 0.00 3.33
883 940 3.632145 GCTGAACAACTCCCTCAAAGAAA 59.368 43.478 0.00 0.00 0.00 2.52
886 943 1.532868 CGCTGAACAACTCCCTCAAAG 59.467 52.381 0.00 0.00 0.00 2.77
911 968 2.203669 AAATGGCAGGCCTGTGCA 60.204 55.556 32.81 12.31 45.93 4.57
912 969 1.980772 AGAAATGGCAGGCCTGTGC 60.981 57.895 32.81 21.12 43.19 4.57
913 970 1.888018 CAGAAATGGCAGGCCTGTG 59.112 57.895 32.81 17.88 36.94 3.66
1093 1156 2.104331 ATGTCGATGTCGCCGTCC 59.896 61.111 0.00 0.00 39.60 4.79
1213 1276 3.500642 GCCTTCGGCTTCGGCTTC 61.501 66.667 0.00 0.00 46.69 3.86
1266 1329 3.431725 GTTTTGGCTCCGGCTCCG 61.432 66.667 0.00 0.48 38.73 4.63
1267 1330 3.062466 GGTTTTGGCTCCGGCTCC 61.062 66.667 0.00 0.00 38.73 4.70
1699 1780 0.036010 CCATGTTGCCTCGGAGAACT 60.036 55.000 6.58 0.00 34.09 3.01
1841 1925 3.197790 CGATGGAACAGCCTGGCG 61.198 66.667 13.96 10.87 44.85 5.69
1858 1942 1.613520 GGGTGCTGACTTCCCTTAACC 60.614 57.143 0.00 0.00 38.29 2.85
1893 1980 1.944177 CTCAGGTTCTTCAGGGGAGA 58.056 55.000 0.00 0.00 0.00 3.71
1901 1988 2.725221 ATCCATGGCTCAGGTTCTTC 57.275 50.000 6.96 0.00 0.00 2.87
2110 2294 2.604686 AGGCGCTCTTCCAGTGGA 60.605 61.111 8.12 8.12 32.64 4.02
2160 2344 4.340894 TGCATTAGAGCAACAAATCGAC 57.659 40.909 0.00 0.00 42.46 4.20
2227 2411 1.202177 CGCACCAAATCAGCATACACC 60.202 52.381 0.00 0.00 0.00 4.16
2482 2666 4.590647 TCTTGCTCCTTGACTATATGGGAG 59.409 45.833 0.00 0.00 44.41 4.30
2542 2726 1.210478 GCACTGCATTTCTCTAGGGGA 59.790 52.381 0.00 0.00 0.00 4.81
2560 2744 4.274147 TGGTTTTCCTTTGTTCAGTAGCA 58.726 39.130 0.00 0.00 41.38 3.49
3095 3279 4.219070 TCAAGGCATTTCACCATTCTTCAG 59.781 41.667 0.00 0.00 0.00 3.02
3148 3332 9.922477 ATATCCATCTTCATTTGATATGCAGAT 57.078 29.630 0.00 0.00 33.46 2.90
3174 3358 6.873076 GCATTTCACCATTCTTCAATACCAAA 59.127 34.615 0.00 0.00 0.00 3.28
3227 3411 4.757149 ACTTCAAGCACTTTGGACATCTAC 59.243 41.667 0.00 0.00 37.39 2.59
3319 3503 6.183360 GCCCATCTTTATTGCTAAGAACACAT 60.183 38.462 0.00 0.00 35.43 3.21
3561 3749 7.807977 AAGACATTTTTGACACTGTCATAGT 57.192 32.000 12.71 7.29 42.40 2.12
3572 3760 9.878599 CGTCCCATAATATAAGACATTTTTGAC 57.121 33.333 0.00 0.00 0.00 3.18
3573 3761 9.062524 CCGTCCCATAATATAAGACATTTTTGA 57.937 33.333 0.00 0.00 0.00 2.69
3574 3762 9.062524 TCCGTCCCATAATATAAGACATTTTTG 57.937 33.333 0.00 0.00 0.00 2.44
3575 3763 9.284968 CTCCGTCCCATAATATAAGACATTTTT 57.715 33.333 0.00 0.00 0.00 1.94
3576 3764 7.883311 CCTCCGTCCCATAATATAAGACATTTT 59.117 37.037 0.00 0.00 0.00 1.82
3577 3765 7.394816 CCTCCGTCCCATAATATAAGACATTT 58.605 38.462 0.00 0.00 0.00 2.32
3578 3766 6.070194 CCCTCCGTCCCATAATATAAGACATT 60.070 42.308 0.00 0.00 0.00 2.71
3579 3767 5.425539 CCCTCCGTCCCATAATATAAGACAT 59.574 44.000 0.00 0.00 0.00 3.06
3580 3768 4.775780 CCCTCCGTCCCATAATATAAGACA 59.224 45.833 0.00 0.00 0.00 3.41
3581 3769 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
3582 3770 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3583 3771 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3584 3772 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3585 3773 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3586 3774 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3587 3775 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
3588 3776 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
3589 3777 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
3590 3778 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
3591 3779 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3592 3780 0.324091 GAGTTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3593 3781 0.033306 AGAGTTACTCCCTCCGTCCC 60.033 60.000 8.96 0.00 0.00 4.46
3605 3793 8.467598 TGACCTACTCATGATGTAAAGAGTTAC 58.532 37.037 0.00 0.00 41.27 2.50
3606 3794 8.589701 TGACCTACTCATGATGTAAAGAGTTA 57.410 34.615 0.00 0.00 41.27 2.24
3607 3795 7.482169 TGACCTACTCATGATGTAAAGAGTT 57.518 36.000 0.00 0.00 41.27 3.01
3608 3796 7.039011 TGTTGACCTACTCATGATGTAAAGAGT 60.039 37.037 0.00 0.00 43.25 3.24
3609 3797 7.323420 TGTTGACCTACTCATGATGTAAAGAG 58.677 38.462 0.00 0.00 0.00 2.85
3610 3798 7.239763 TGTTGACCTACTCATGATGTAAAGA 57.760 36.000 0.00 0.00 0.00 2.52
3611 3799 7.466455 GCATGTTGACCTACTCATGATGTAAAG 60.466 40.741 0.00 0.00 39.68 1.85
3612 3800 6.316140 GCATGTTGACCTACTCATGATGTAAA 59.684 38.462 0.00 0.00 39.68 2.01
3766 4034 2.348411 CTGTTCCACTCCCAAACAGT 57.652 50.000 6.36 0.00 43.03 3.55
3792 4060 3.515502 TGAACACCAAACCAAATCACCAA 59.484 39.130 0.00 0.00 0.00 3.67
3874 4142 9.693739 AATCCACAACAATATATGGTTAGACAA 57.306 29.630 5.13 0.00 33.67 3.18
3947 4248 9.548208 GAGCAAAAATCTATAGAGACAAACAAC 57.452 33.333 8.70 0.00 33.41 3.32
3949 4250 8.846943 TGAGCAAAAATCTATAGAGACAAACA 57.153 30.769 8.70 0.00 33.41 2.83
3960 4261 3.069158 GCCCAGCATGAGCAAAAATCTAT 59.931 43.478 0.00 0.00 45.49 1.98
4013 4366 3.319405 ACATATAGACAGTCCAGCTTCCG 59.681 47.826 0.00 0.00 0.00 4.30
4078 4431 7.205992 TGAGCTACACATGAGAATAAGATGAC 58.794 38.462 0.00 0.00 0.00 3.06
4116 4469 3.217626 CCCAGATGGAAGAACAATAGCC 58.782 50.000 0.00 0.00 37.39 3.93
4117 4470 2.620585 GCCCAGATGGAAGAACAATAGC 59.379 50.000 0.00 0.00 37.39 2.97
4118 4471 3.889815 TGCCCAGATGGAAGAACAATAG 58.110 45.455 0.00 0.00 37.39 1.73
4147 4500 7.982761 AAAATTTTAAGCATGGATCTGCAAA 57.017 28.000 0.37 2.47 44.77 3.68
4279 4632 8.798859 TTTAAGTATACTTAGACAGAGACGGT 57.201 34.615 21.45 0.00 39.36 4.83


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

AutoCloner maintained by Alex Coulton.