Multiple sequence alignment - TraesCS1A01G084000

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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 TraesCS1A01G084000 chr1A 100.000 3394 0 0 1 3394 69189206 69185813 0.000000e+00 6268.0
1 TraesCS1A01G084000 chr1A 97.619 42 1 0 570 611 69188597 69188556 4.700000e-09 73.1
2 TraesCS1A01G084000 chr1A 97.619 42 1 0 610 651 69188637 69188596 4.700000e-09 73.1
3 TraesCS1A01G084000 chr1D 94.492 1852 97 4 610 2459 69527231 69525383 0.000000e+00 2850.0
4 TraesCS1A01G084000 chr1D 94.479 815 42 2 2460 3271 350656164 350656978 0.000000e+00 1253.0
5 TraesCS1A01G084000 chr1D 90.856 514 27 6 1 500 69615017 69614510 0.000000e+00 671.0
6 TraesCS1A01G084000 chr1D 95.652 115 5 0 497 611 69527304 69527190 5.780000e-43 185.0
7 TraesCS1A01G084000 chr1B 92.492 1958 119 13 451 2399 111260294 111258356 0.000000e+00 2776.0
8 TraesCS1A01G084000 chr1B 94.828 812 39 1 2460 3268 194530491 194529680 0.000000e+00 1264.0
9 TraesCS1A01G084000 chr1B 87.640 178 9 7 1 165 111260842 111260665 9.610000e-46 195.0
10 TraesCS1A01G084000 chr6A 97.033 809 24 0 2460 3268 601958608 601957800 0.000000e+00 1362.0
11 TraesCS1A01G084000 chr6A 95.918 49 1 1 2461 2508 447575828 447575780 1.010000e-10 78.7
12 TraesCS1A01G084000 chr2A 96.420 810 28 1 2460 3268 565326125 565325316 0.000000e+00 1334.0
13 TraesCS1A01G084000 chr2A 71.488 1196 284 42 1223 2379 713531418 713532595 2.010000e-67 267.0
14 TraesCS1A01G084000 chr2D 95.104 817 36 4 2460 3276 136476326 136477138 0.000000e+00 1284.0
15 TraesCS1A01G084000 chr2D 71.864 885 215 28 1525 2389 575239415 575240285 1.230000e-54 224.0
16 TraesCS1A01G084000 chr6B 93.268 817 54 1 2460 3275 620706337 620705521 0.000000e+00 1203.0
17 TraesCS1A01G084000 chr6B 88.038 836 74 18 2460 3270 422356642 422357476 0.000000e+00 966.0
18 TraesCS1A01G084000 chr6B 93.559 295 17 2 2975 3268 647837930 647837637 4.020000e-119 438.0
19 TraesCS1A01G084000 chr6B 78.400 125 23 3 1223 1345 46421591 46421713 1.010000e-10 78.7
20 TraesCS1A01G084000 chr4D 94.102 763 42 3 2512 3272 373827466 373828227 0.000000e+00 1157.0
21 TraesCS1A01G084000 chr3D 93.868 636 37 1 2633 3268 352615761 352616394 0.000000e+00 957.0
22 TraesCS1A01G084000 chr2B 79.412 204 39 3 2051 2252 691271662 691271864 1.270000e-29 141.0


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 TraesCS1A01G084000 chr1A 69185813 69189206 3393 True 2138.066667 6268 98.412667 1 3394 3 chr1A.!!$R1 3393
1 TraesCS1A01G084000 chr1D 69525383 69527304 1921 True 1517.500000 2850 95.072000 497 2459 2 chr1D.!!$R2 1962
2 TraesCS1A01G084000 chr1D 350656164 350656978 814 False 1253.000000 1253 94.479000 2460 3271 1 chr1D.!!$F1 811
3 TraesCS1A01G084000 chr1D 69614510 69615017 507 True 671.000000 671 90.856000 1 500 1 chr1D.!!$R1 499
4 TraesCS1A01G084000 chr1B 111258356 111260842 2486 True 1485.500000 2776 90.066000 1 2399 2 chr1B.!!$R2 2398
5 TraesCS1A01G084000 chr1B 194529680 194530491 811 True 1264.000000 1264 94.828000 2460 3268 1 chr1B.!!$R1 808
6 TraesCS1A01G084000 chr6A 601957800 601958608 808 True 1362.000000 1362 97.033000 2460 3268 1 chr6A.!!$R2 808
7 TraesCS1A01G084000 chr2A 565325316 565326125 809 True 1334.000000 1334 96.420000 2460 3268 1 chr2A.!!$R1 808
8 TraesCS1A01G084000 chr2A 713531418 713532595 1177 False 267.000000 267 71.488000 1223 2379 1 chr2A.!!$F1 1156
9 TraesCS1A01G084000 chr2D 136476326 136477138 812 False 1284.000000 1284 95.104000 2460 3276 1 chr2D.!!$F1 816
10 TraesCS1A01G084000 chr2D 575239415 575240285 870 False 224.000000 224 71.864000 1525 2389 1 chr2D.!!$F2 864
11 TraesCS1A01G084000 chr6B 620705521 620706337 816 True 1203.000000 1203 93.268000 2460 3275 1 chr6B.!!$R1 815
12 TraesCS1A01G084000 chr6B 422356642 422357476 834 False 966.000000 966 88.038000 2460 3270 1 chr6B.!!$F2 810
13 TraesCS1A01G084000 chr4D 373827466 373828227 761 False 1157.000000 1157 94.102000 2512 3272 1 chr4D.!!$F1 760
14 TraesCS1A01G084000 chr3D 352615761 352616394 633 False 957.000000 957 93.868000 2633 3268 1 chr3D.!!$F1 635

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
597 772 0.179936 GCAGATCCTGGGAGGTTGAG 59.820 60.0 0.0 0.0 36.53 3.02 F
599 774 0.252881 AGATCCTGGGAGGTTGAGCA 60.253 55.0 0.0 0.0 36.53 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2183 0.782384 CGCGTTTCCATAGTATCCGC 59.218 55.0 0.0 0.0 36.57 5.54 R
2452 2654 1.413118 AAACTTTCAACCCAGCCCTG 58.587 50.0 0.0 0.0 0.00 4.45 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
115 129 2.026262 TCTAAACAAGCCCCTGGATGAC 60.026 50.000 0.00 0.00 0.00 3.06
139 153 4.613437 AGGGCTTGATATGGTGAATTTGT 58.387 39.130 0.00 0.00 0.00 2.83
169 183 1.470098 GACATGATGTGGCACTGGTTC 59.530 52.381 19.83 10.71 35.22 3.62
171 185 2.305635 ACATGATGTGGCACTGGTTCTA 59.694 45.455 19.83 0.00 0.00 2.10
172 186 3.054139 ACATGATGTGGCACTGGTTCTAT 60.054 43.478 19.83 1.20 0.00 1.98
174 188 4.032960 TGATGTGGCACTGGTTCTATTT 57.967 40.909 19.83 0.00 0.00 1.40
185 212 4.105697 ACTGGTTCTATTTTCACCAAGGGA 59.894 41.667 0.00 0.00 40.15 4.20
322 352 0.689080 TGCCTTCAAACTTGGGCCAA 60.689 50.000 19.68 19.68 43.50 4.52
447 477 7.571080 TTTTGTATGTAAACTTCGAAGGGTT 57.429 32.000 27.86 21.93 0.00 4.11
509 660 0.728129 GCGCGGCTAAAGGTCAAAAC 60.728 55.000 8.83 0.00 0.00 2.43
591 766 1.030457 GCATTTGCAGATCCTGGGAG 58.970 55.000 0.00 0.00 41.59 4.30
592 767 1.688772 CATTTGCAGATCCTGGGAGG 58.311 55.000 0.00 0.00 36.46 4.30
593 768 1.064166 CATTTGCAGATCCTGGGAGGT 60.064 52.381 0.00 0.00 36.53 3.85
594 769 1.075601 TTTGCAGATCCTGGGAGGTT 58.924 50.000 0.00 0.00 36.53 3.50
595 770 0.329261 TTGCAGATCCTGGGAGGTTG 59.671 55.000 0.00 0.00 36.53 3.77
596 771 0.547471 TGCAGATCCTGGGAGGTTGA 60.547 55.000 0.00 0.00 36.53 3.18
597 772 0.179936 GCAGATCCTGGGAGGTTGAG 59.820 60.000 0.00 0.00 36.53 3.02
598 773 0.179936 CAGATCCTGGGAGGTTGAGC 59.820 60.000 0.00 0.00 36.53 4.26
599 774 0.252881 AGATCCTGGGAGGTTGAGCA 60.253 55.000 0.00 0.00 36.53 4.26
600 775 0.842635 GATCCTGGGAGGTTGAGCAT 59.157 55.000 0.00 0.00 36.53 3.79
601 776 0.549950 ATCCTGGGAGGTTGAGCATG 59.450 55.000 0.00 0.00 36.53 4.06
602 777 1.751927 CCTGGGAGGTTGAGCATGC 60.752 63.158 10.51 10.51 0.00 4.06
603 778 2.046023 TGGGAGGTTGAGCATGCG 60.046 61.111 13.01 0.00 0.00 4.73
604 779 2.825836 GGGAGGTTGAGCATGCGG 60.826 66.667 13.01 0.00 0.00 5.69
605 780 2.268920 GGAGGTTGAGCATGCGGA 59.731 61.111 13.01 0.00 0.00 5.54
606 781 1.153086 GGAGGTTGAGCATGCGGAT 60.153 57.895 13.01 0.00 0.00 4.18
607 782 1.162800 GGAGGTTGAGCATGCGGATC 61.163 60.000 13.01 5.17 0.00 3.36
608 783 1.153086 AGGTTGAGCATGCGGATCC 60.153 57.895 13.01 13.66 0.00 3.36
609 784 2.537560 GGTTGAGCATGCGGATCCG 61.538 63.158 30.03 30.03 43.09 4.18
610 785 2.203056 TTGAGCATGCGGATCCGG 60.203 61.111 33.98 19.36 40.19 5.14
611 786 2.730524 TTGAGCATGCGGATCCGGA 61.731 57.895 33.98 32.64 45.02 5.14
612 787 2.356793 GAGCATGCGGATCCGGAG 60.357 66.667 33.98 24.31 44.01 4.63
613 788 4.615815 AGCATGCGGATCCGGAGC 62.616 66.667 33.98 31.12 44.01 4.70
614 789 4.916293 GCATGCGGATCCGGAGCA 62.916 66.667 33.98 23.83 44.01 4.26
615 790 2.031616 CATGCGGATCCGGAGCAT 59.968 61.111 33.98 24.92 45.18 3.79
616 791 1.598962 CATGCGGATCCGGAGCATT 60.599 57.895 33.98 15.05 45.18 3.56
617 792 1.149174 ATGCGGATCCGGAGCATTT 59.851 52.632 33.98 14.65 45.18 2.32
618 793 1.168407 ATGCGGATCCGGAGCATTTG 61.168 55.000 33.98 9.03 45.18 2.32
619 794 3.025619 CGGATCCGGAGCATTTGC 58.974 61.111 26.95 2.27 37.24 3.68
620 795 1.819208 CGGATCCGGAGCATTTGCA 60.819 57.895 26.95 0.00 38.56 4.08
621 796 1.779025 CGGATCCGGAGCATTTGCAG 61.779 60.000 26.95 0.00 38.56 4.41
622 797 0.464373 GGATCCGGAGCATTTGCAGA 60.464 55.000 23.22 0.00 45.16 4.26
623 798 1.602311 GATCCGGAGCATTTGCAGAT 58.398 50.000 16.44 1.75 45.16 2.90
624 799 1.534595 GATCCGGAGCATTTGCAGATC 59.465 52.381 16.44 7.11 45.16 2.75
633 808 1.064166 CATTTGCAGATCCTGGGAGGT 60.064 52.381 0.00 0.00 36.53 3.85
636 811 0.547471 TGCAGATCCTGGGAGGTTGA 60.547 55.000 0.00 0.00 36.53 3.18
647 822 1.442526 GGAGGTTGAGCATGCGGATG 61.443 60.000 13.21 13.21 0.00 3.51
727 902 5.118990 ACTCCATCAAGTCCATGTAAATCG 58.881 41.667 0.00 0.00 0.00 3.34
736 911 5.560966 GTCCATGTAAATCGGACAAACAT 57.439 39.130 2.98 0.00 46.98 2.71
741 916 2.723124 AAATCGGACAAACATGGCAC 57.277 45.000 0.00 0.00 0.00 5.01
861 1037 2.034053 TGCATTGTTGGACTTTTCGGAC 59.966 45.455 0.00 0.00 0.00 4.79
904 1080 1.597742 ATTCGCACTCTGCACAAGTT 58.402 45.000 0.00 0.00 45.36 2.66
941 1119 2.163815 ACTCTCGACGTATGGTTTCCAG 59.836 50.000 0.00 0.00 36.75 3.86
1138 1316 4.052229 ACGTGTCCTTCGCCCTCG 62.052 66.667 0.00 0.00 0.00 4.63
1146 1324 3.753070 CTTCGCCCTCGTCTACCGC 62.753 68.421 0.00 0.00 36.96 5.68
1257 1435 3.385384 CTGGCTGGACGGCTCAGA 61.385 66.667 10.55 0.00 39.32 3.27
1296 1474 4.664677 GTGGTCGAGTGCAGCGGT 62.665 66.667 8.80 0.00 0.00 5.68
1352 1530 3.535962 GCTGGAGGAGCTCGAGGG 61.536 72.222 15.58 0.00 45.21 4.30
1454 1638 2.216898 GTTGCTGCTCATCCAGGTATC 58.783 52.381 0.00 0.00 33.44 2.24
1456 1640 1.415289 TGCTGCTCATCCAGGTATCTG 59.585 52.381 0.00 0.00 40.59 2.90
1499 1683 6.746104 TTTGTTGAATGCATGAGTTAAACG 57.254 33.333 0.00 0.00 0.00 3.60
1504 1688 6.735678 TGAATGCATGAGTTAAACGTATGT 57.264 33.333 0.00 0.00 0.00 2.29
1510 1694 6.309494 TGCATGAGTTAAACGTATGTACTGTC 59.691 38.462 0.00 0.00 0.00 3.51
1544 1737 2.125753 GTGACTCGGCTGCTCTGG 60.126 66.667 0.00 0.00 0.00 3.86
1685 1878 1.681327 GTGGTCCCGTGAGCTCCTA 60.681 63.158 12.15 0.00 39.75 2.94
1696 1889 4.514577 GCTCCTAGAGGCGCGCAA 62.515 66.667 34.42 13.88 36.09 4.85
1742 1938 1.468565 CGCGAGTTCGACCTTATTCCA 60.469 52.381 0.00 0.00 43.02 3.53
1823 2019 0.460811 TCGCAGCGATCAAGAAGCAT 60.461 50.000 15.11 0.00 0.00 3.79
1868 2064 4.379243 ACCACCTTCGAGGCGCTG 62.379 66.667 7.64 0.00 39.63 5.18
1884 2080 2.687200 TGGCGGCATACCTCTGGT 60.687 61.111 7.97 0.00 40.16 4.00
1991 2193 2.283529 CCTGCCGGGCGGATACTAT 61.284 63.158 29.22 0.00 37.02 2.12
2280 2482 1.737008 GTCTTCGGCGTGACCTTCC 60.737 63.158 19.18 1.20 35.61 3.46
2334 2536 0.526954 GATTACCGTGCCGATCGTGT 60.527 55.000 15.09 5.64 0.00 4.49
2430 2632 4.274214 CGTCCCTGTATGTATTACGACTCA 59.726 45.833 0.00 0.00 33.15 3.41
2503 2705 1.336632 GGAGGCTGCTCTGAGTGGAT 61.337 60.000 6.53 0.00 0.00 3.41
2507 2709 1.065564 GGCTGCTCTGAGTGGATTCTT 60.066 52.381 6.53 0.00 0.00 2.52
2552 2754 0.822811 ACTCTGATGTCGCATGCTCT 59.177 50.000 17.13 0.00 0.00 4.09
2578 2780 2.611518 CAAACGGTGTTTGCTTTGGAA 58.388 42.857 9.22 0.00 0.00 3.53
2717 2921 1.808411 GTGGCTCCGATGTTGAAGAA 58.192 50.000 0.00 0.00 0.00 2.52
2774 2979 7.232330 TCTGTCAGTGGAGAATATGAAGATAGG 59.768 40.741 0.00 0.00 0.00 2.57
2929 3139 0.976641 AGATGGTTGCCTCGTGAAGA 59.023 50.000 0.00 0.00 0.00 2.87
2999 3210 3.610114 GCATACGTGATTTCATGATGGGC 60.610 47.826 0.00 1.93 36.72 5.36
3003 3214 3.205338 CGTGATTTCATGATGGGCAGTA 58.795 45.455 0.00 0.00 34.90 2.74
3009 3220 2.470990 TCATGATGGGCAGTACTCACT 58.529 47.619 0.00 0.00 34.42 3.41
3105 3349 3.403038 AGTGTTGTGTGTTAGGAGCATC 58.597 45.455 0.00 0.00 0.00 3.91
3123 3367 0.615261 TCGGGTGGGCAGTGTATGTA 60.615 55.000 0.00 0.00 0.00 2.29
3175 3419 4.586841 CCCTCTTTTGGGTTGTTTGTATCA 59.413 41.667 0.00 0.00 42.25 2.15
3293 3538 6.560253 AAAAAGGATCGCATATGGTATGTC 57.440 37.500 4.56 0.00 0.00 3.06
3294 3539 4.890158 AAGGATCGCATATGGTATGTCA 57.110 40.909 4.56 0.00 0.00 3.58
3295 3540 4.462508 AGGATCGCATATGGTATGTCAG 57.537 45.455 4.56 0.00 0.00 3.51
3296 3541 3.834813 AGGATCGCATATGGTATGTCAGT 59.165 43.478 4.56 0.00 0.00 3.41
3297 3542 4.284490 AGGATCGCATATGGTATGTCAGTT 59.716 41.667 4.56 0.00 0.00 3.16
3298 3543 5.480422 AGGATCGCATATGGTATGTCAGTTA 59.520 40.000 4.56 0.00 0.00 2.24
3299 3544 6.155221 AGGATCGCATATGGTATGTCAGTTAT 59.845 38.462 4.56 0.00 0.00 1.89
3300 3545 6.256539 GGATCGCATATGGTATGTCAGTTATG 59.743 42.308 4.56 0.00 0.00 1.90
3301 3546 6.096673 TCGCATATGGTATGTCAGTTATGT 57.903 37.500 4.56 0.00 0.00 2.29
3302 3547 6.156519 TCGCATATGGTATGTCAGTTATGTC 58.843 40.000 4.56 0.00 0.00 3.06
3303 3548 5.925969 CGCATATGGTATGTCAGTTATGTCA 59.074 40.000 4.56 0.00 0.00 3.58
3304 3549 6.591448 CGCATATGGTATGTCAGTTATGTCAT 59.409 38.462 4.56 0.00 38.49 3.06
3305 3550 7.412237 CGCATATGGTATGTCAGTTATGTCATG 60.412 40.741 4.56 0.00 36.16 3.07
3306 3551 7.603784 GCATATGGTATGTCAGTTATGTCATGA 59.396 37.037 4.56 0.00 36.16 3.07
3307 3552 8.929746 CATATGGTATGTCAGTTATGTCATGAC 58.070 37.037 19.27 19.27 42.90 3.06
3316 3561 2.271821 TGTCATGACATGGCCCGG 59.728 61.111 24.56 0.00 36.21 5.73
3317 3562 3.211963 GTCATGACATGGCCCGGC 61.212 66.667 21.07 0.00 0.00 6.13
3335 3580 4.760047 CCAGGACGACGGCCCAAG 62.760 72.222 18.37 6.80 0.00 3.61
3336 3581 4.760047 CAGGACGACGGCCCAAGG 62.760 72.222 18.37 0.00 0.00 3.61
3360 3605 3.775654 GGCGGAGACTGGACAGGG 61.776 72.222 4.14 0.00 0.00 4.45
3361 3606 4.459089 GCGGAGACTGGACAGGGC 62.459 72.222 4.14 0.00 0.00 5.19
3362 3607 4.135153 CGGAGACTGGACAGGGCG 62.135 72.222 4.14 0.00 0.00 6.13
3363 3608 2.997897 GGAGACTGGACAGGGCGT 60.998 66.667 4.14 0.00 0.00 5.68
3364 3609 2.584391 GGAGACTGGACAGGGCGTT 61.584 63.158 4.14 0.00 0.00 4.84
3365 3610 1.079750 GAGACTGGACAGGGCGTTC 60.080 63.158 4.14 0.00 0.00 3.95
3366 3611 2.047179 GACTGGACAGGGCGTTCC 60.047 66.667 4.14 2.70 0.00 3.62
3367 3612 3.934391 GACTGGACAGGGCGTTCCG 62.934 68.421 4.14 0.00 41.52 4.30
3368 3613 3.691342 CTGGACAGGGCGTTCCGA 61.691 66.667 0.00 0.00 41.52 4.55
3369 3614 3.649277 CTGGACAGGGCGTTCCGAG 62.649 68.421 0.00 0.00 41.52 4.63
3370 3615 3.692406 GGACAGGGCGTTCCGAGT 61.692 66.667 0.00 0.00 41.52 4.18
3371 3616 2.126031 GACAGGGCGTTCCGAGTC 60.126 66.667 8.68 8.68 41.52 3.36
3372 3617 3.644399 GACAGGGCGTTCCGAGTCC 62.644 68.421 11.37 0.00 41.52 3.85
3373 3618 3.691342 CAGGGCGTTCCGAGTCCA 61.691 66.667 0.00 0.00 41.52 4.02
3374 3619 3.382832 AGGGCGTTCCGAGTCCAG 61.383 66.667 0.00 0.00 41.52 3.86
3375 3620 4.452733 GGGCGTTCCGAGTCCAGG 62.453 72.222 0.00 0.00 0.00 4.45
3376 3621 3.379445 GGCGTTCCGAGTCCAGGA 61.379 66.667 0.00 0.00 35.69 3.86
3377 3622 2.722201 GGCGTTCCGAGTCCAGGAT 61.722 63.158 0.00 0.00 37.65 3.24
3378 3623 1.389609 GGCGTTCCGAGTCCAGGATA 61.390 60.000 0.00 0.00 37.65 2.59
3379 3624 0.458669 GCGTTCCGAGTCCAGGATAA 59.541 55.000 0.00 0.00 37.65 1.75
3380 3625 1.134907 GCGTTCCGAGTCCAGGATAAA 60.135 52.381 0.00 0.00 37.65 1.40
3381 3626 2.483188 GCGTTCCGAGTCCAGGATAAAT 60.483 50.000 0.00 0.00 37.65 1.40
3382 3627 3.243636 GCGTTCCGAGTCCAGGATAAATA 60.244 47.826 0.00 0.00 37.65 1.40
3383 3628 4.547532 CGTTCCGAGTCCAGGATAAATAG 58.452 47.826 0.00 0.00 37.65 1.73
3384 3629 4.558898 CGTTCCGAGTCCAGGATAAATAGG 60.559 50.000 0.00 0.00 37.65 2.57
3385 3630 3.507411 TCCGAGTCCAGGATAAATAGGG 58.493 50.000 0.00 0.00 31.86 3.53
3386 3631 3.141460 TCCGAGTCCAGGATAAATAGGGA 59.859 47.826 0.00 0.00 31.86 4.20
3387 3632 3.511934 CCGAGTCCAGGATAAATAGGGAG 59.488 52.174 0.00 0.00 0.00 4.30
3388 3633 4.408276 CGAGTCCAGGATAAATAGGGAGA 58.592 47.826 0.00 0.00 0.00 3.71
3389 3634 4.833380 CGAGTCCAGGATAAATAGGGAGAA 59.167 45.833 0.00 0.00 0.00 2.87
3390 3635 5.047660 CGAGTCCAGGATAAATAGGGAGAAG 60.048 48.000 0.00 0.00 0.00 2.85
3391 3636 5.793967 AGTCCAGGATAAATAGGGAGAAGT 58.206 41.667 0.00 0.00 0.00 3.01
3392 3637 5.604650 AGTCCAGGATAAATAGGGAGAAGTG 59.395 44.000 0.00 0.00 0.00 3.16
3393 3638 4.348168 TCCAGGATAAATAGGGAGAAGTGC 59.652 45.833 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 129 5.105228 ACAAATTCACCATATCAAGCCCTTG 60.105 40.000 1.62 1.62 41.71 3.61
139 153 7.442062 CAGTGCCACATCATGTCTTATGTATTA 59.558 37.037 0.00 0.00 34.61 0.98
169 183 2.291540 TGCCCTCCCTTGGTGAAAATAG 60.292 50.000 0.00 0.00 0.00 1.73
171 185 0.486879 TGCCCTCCCTTGGTGAAAAT 59.513 50.000 0.00 0.00 0.00 1.82
172 186 0.178964 CTGCCCTCCCTTGGTGAAAA 60.179 55.000 0.00 0.00 0.00 2.29
174 188 1.065410 TTCTGCCCTCCCTTGGTGAA 61.065 55.000 0.00 0.00 0.00 3.18
226 256 2.273776 GCTTCTGCTCCTTCCCCC 59.726 66.667 0.00 0.00 36.03 5.40
230 260 1.656652 TATTGCGCTTCTGCTCCTTC 58.343 50.000 9.73 0.00 36.97 3.46
273 303 2.398754 ATCCCGTCCCTGATATCACA 57.601 50.000 0.00 0.00 0.00 3.58
322 352 2.956333 AGCAAAAAGGAGCGGTAGTTTT 59.044 40.909 0.00 0.00 35.48 2.43
378 408 2.813754 ACGCAACAATCTTGTACTGCAT 59.186 40.909 15.97 2.58 42.23 3.96
380 410 2.574322 CACGCAACAATCTTGTACTGC 58.426 47.619 8.87 8.87 41.31 4.40
381 411 2.224079 AGCACGCAACAATCTTGTACTG 59.776 45.455 0.00 0.00 41.31 2.74
382 412 2.224079 CAGCACGCAACAATCTTGTACT 59.776 45.455 0.00 0.00 41.31 2.73
434 464 6.895782 TGGATGAATATAACCCTTCGAAGTT 58.104 36.000 23.03 14.99 0.00 2.66
441 471 9.284968 CGTAAAAGATGGATGAATATAACCCTT 57.715 33.333 0.00 0.00 0.00 3.95
509 660 3.916172 CACACAATTTCATCCTCGCAAAG 59.084 43.478 0.00 0.00 0.00 2.77
591 766 2.537560 CGGATCCGCATGCTCAACC 61.538 63.158 23.37 12.63 0.00 3.77
592 767 2.537560 CCGGATCCGCATGCTCAAC 61.538 63.158 29.12 4.78 38.24 3.18
593 768 2.203056 CCGGATCCGCATGCTCAA 60.203 61.111 29.12 0.64 38.24 3.02
594 769 3.153781 TCCGGATCCGCATGCTCA 61.154 61.111 29.12 1.48 38.24 4.26
595 770 2.356793 CTCCGGATCCGCATGCTC 60.357 66.667 29.12 6.50 38.24 4.26
596 771 4.615815 GCTCCGGATCCGCATGCT 62.616 66.667 29.12 0.00 38.24 3.79
597 772 4.916293 TGCTCCGGATCCGCATGC 62.916 66.667 29.12 27.41 38.24 4.06
598 773 1.168407 AAATGCTCCGGATCCGCATG 61.168 55.000 29.12 19.65 43.02 4.06
599 774 1.149174 AAATGCTCCGGATCCGCAT 59.851 52.632 29.12 22.36 45.50 4.73
600 775 1.819208 CAAATGCTCCGGATCCGCA 60.819 57.895 29.12 21.08 38.24 5.69
601 776 3.025619 CAAATGCTCCGGATCCGC 58.974 61.111 29.12 15.75 38.24 5.54
602 777 1.779025 CTGCAAATGCTCCGGATCCG 61.779 60.000 27.65 27.65 42.66 4.18
603 778 0.464373 TCTGCAAATGCTCCGGATCC 60.464 55.000 3.57 0.00 42.66 3.36
604 779 1.534595 GATCTGCAAATGCTCCGGATC 59.465 52.381 3.57 0.00 42.66 3.36
605 780 1.602311 GATCTGCAAATGCTCCGGAT 58.398 50.000 3.57 5.44 42.66 4.18
606 781 0.464373 GGATCTGCAAATGCTCCGGA 60.464 55.000 2.93 2.93 42.66 5.14
607 782 0.465097 AGGATCTGCAAATGCTCCGG 60.465 55.000 6.97 0.00 42.66 5.14
608 783 0.661552 CAGGATCTGCAAATGCTCCG 59.338 55.000 6.97 0.00 42.66 4.63
609 784 1.030457 CCAGGATCTGCAAATGCTCC 58.970 55.000 6.97 5.58 42.66 4.70
610 785 1.030457 CCCAGGATCTGCAAATGCTC 58.970 55.000 6.97 0.00 42.66 4.26
611 786 0.627451 TCCCAGGATCTGCAAATGCT 59.373 50.000 6.97 0.00 42.66 3.79
612 787 1.030457 CTCCCAGGATCTGCAAATGC 58.970 55.000 0.00 0.00 42.50 3.56
613 788 1.064166 ACCTCCCAGGATCTGCAAATG 60.064 52.381 0.00 0.00 37.67 2.32
614 789 1.302907 ACCTCCCAGGATCTGCAAAT 58.697 50.000 0.00 0.00 37.67 2.32
615 790 1.075601 AACCTCCCAGGATCTGCAAA 58.924 50.000 0.00 0.00 37.67 3.68
616 791 0.329261 CAACCTCCCAGGATCTGCAA 59.671 55.000 0.00 0.00 37.67 4.08
617 792 0.547471 TCAACCTCCCAGGATCTGCA 60.547 55.000 0.00 0.00 37.67 4.41
618 793 0.179936 CTCAACCTCCCAGGATCTGC 59.820 60.000 0.00 0.00 37.67 4.26
619 794 0.179936 GCTCAACCTCCCAGGATCTG 59.820 60.000 0.00 0.00 37.67 2.90
620 795 0.252881 TGCTCAACCTCCCAGGATCT 60.253 55.000 0.00 0.00 37.67 2.75
621 796 0.842635 ATGCTCAACCTCCCAGGATC 59.157 55.000 0.00 0.00 37.67 3.36
622 797 0.549950 CATGCTCAACCTCCCAGGAT 59.450 55.000 0.00 0.00 37.67 3.24
623 798 1.993653 CATGCTCAACCTCCCAGGA 59.006 57.895 0.00 0.00 37.67 3.86
624 799 1.751927 GCATGCTCAACCTCCCAGG 60.752 63.158 11.37 0.00 42.49 4.45
647 822 1.005294 CAAACATTGCAGCTGACCGC 61.005 55.000 20.43 1.45 39.57 5.68
727 902 2.818130 ACATTGTGCCATGTTTGTCC 57.182 45.000 0.00 0.00 0.00 4.02
734 909 5.523552 TCTCGTCTTATAACATTGTGCCATG 59.476 40.000 0.00 0.00 0.00 3.66
736 911 5.079689 TCTCGTCTTATAACATTGTGCCA 57.920 39.130 0.00 0.00 0.00 4.92
741 916 4.985409 GGGAGCTCTCGTCTTATAACATTG 59.015 45.833 14.64 0.00 0.00 2.82
861 1037 3.121030 CAGCCGGAAAGTCCAGCG 61.121 66.667 5.05 0.00 44.50 5.18
904 1080 3.533547 GAGAGTTACTCTCGGCAGTAGA 58.466 50.000 24.12 0.00 45.76 2.59
941 1119 2.098770 GCAGGATGATCTTGGAACAAGC 59.901 50.000 6.69 0.00 42.25 4.01
1146 1324 4.889856 TCATCCATCACGCGGGCG 62.890 66.667 12.47 12.04 46.03 6.13
1215 1393 3.508793 GGTAGTAGTGCACCAGTACTTCA 59.491 47.826 23.63 6.66 45.05 3.02
1220 1398 1.466856 CGGGTAGTAGTGCACCAGTA 58.533 55.000 14.63 4.16 36.48 2.74
1221 1399 1.885163 GCGGGTAGTAGTGCACCAGT 61.885 60.000 14.63 5.36 36.48 4.00
1262 1440 3.917760 CTAGCTTCCGCCCCTCCG 61.918 72.222 0.00 0.00 36.60 4.63
1278 1456 4.363990 CCGCTGCACTCGACCACT 62.364 66.667 0.00 0.00 0.00 4.00
1296 1474 1.676968 CACGAACATCACCCCCTCA 59.323 57.895 0.00 0.00 0.00 3.86
1434 1618 2.158842 AGATACCTGGATGAGCAGCAAC 60.159 50.000 0.00 0.00 0.00 4.17
1454 1638 7.387397 ACAAATGCAAATTAACCACCATTACAG 59.613 33.333 0.00 0.00 0.00 2.74
1456 1640 7.665561 ACAAATGCAAATTAACCACCATTAC 57.334 32.000 0.00 0.00 0.00 1.89
1498 1682 5.240844 TGACCATGATAGGACAGTACATACG 59.759 44.000 0.00 0.00 0.00 3.06
1499 1683 6.448006 GTGACCATGATAGGACAGTACATAC 58.552 44.000 0.00 0.00 34.13 2.39
1504 1688 3.960755 CTGGTGACCATGATAGGACAGTA 59.039 47.826 4.03 0.00 34.13 2.74
1510 1694 2.118679 TCACCTGGTGACCATGATAGG 58.881 52.381 25.12 9.51 37.67 2.57
1544 1737 3.577313 GCGAAGATGAAGCCGCCC 61.577 66.667 0.00 0.00 41.59 6.13
1577 1770 1.520564 GATGGCGTCGCACATGGTA 60.521 57.895 20.50 0.00 0.00 3.25
1665 1858 4.436998 GAGCTCACGGGACCACGG 62.437 72.222 9.40 0.00 38.39 4.94
1808 2004 1.202627 GGGAGATGCTTCTTGATCGCT 60.203 52.381 3.29 0.00 30.30 4.93
1823 2019 1.749638 GCGAACGAGAGGAGGGAGA 60.750 63.158 0.00 0.00 0.00 3.71
1868 2064 2.203070 CACCAGAGGTATGCCGCC 60.203 66.667 0.00 0.00 40.50 6.13
1981 2183 0.782384 CGCGTTTCCATAGTATCCGC 59.218 55.000 0.00 0.00 36.57 5.54
2096 2298 2.670934 ACGTACTCGGCGGTCACT 60.671 61.111 7.21 0.00 41.85 3.41
2452 2654 1.413118 AAACTTTCAACCCAGCCCTG 58.587 50.000 0.00 0.00 0.00 4.45
2503 2705 2.228103 ACATAGTCGACACAGCGAAGAA 59.772 45.455 19.50 0.00 42.55 2.52
2507 2709 1.538075 TCAACATAGTCGACACAGCGA 59.462 47.619 19.50 3.94 38.07 4.93
2578 2780 3.330720 CTCCGCCCCCTTGTCCTT 61.331 66.667 0.00 0.00 0.00 3.36
2651 2854 2.441750 GTGGAAGACAATATAGGGGGCA 59.558 50.000 0.00 0.00 0.00 5.36
2717 2921 0.835941 CTCCCTAAGCTCAGGCATGT 59.164 55.000 0.00 0.00 41.70 3.21
2862 3069 0.890996 CCAAGCGGCTCTCAAAAGGT 60.891 55.000 1.45 0.00 0.00 3.50
2929 3139 6.272318 TGCGTTTGTTTCTCTTTGATTTCAT 58.728 32.000 0.00 0.00 0.00 2.57
2999 3210 4.491234 AGACACGAGAAAGTGAGTACTG 57.509 45.455 0.00 0.00 44.43 2.74
3003 3214 2.358267 ACGAAGACACGAGAAAGTGAGT 59.642 45.455 4.00 0.00 44.43 3.41
3009 3220 1.598676 CCACGACGAAGACACGAGAAA 60.599 52.381 0.00 0.00 37.03 2.52
3105 3349 0.468226 ATACATACACTGCCCACCCG 59.532 55.000 0.00 0.00 0.00 5.28
3123 3367 3.253955 GCACGAAGCACCACGAAT 58.746 55.556 0.00 0.00 44.79 3.34
3175 3419 1.746787 ACGAAAAACTGGGCGAAAACT 59.253 42.857 0.00 0.00 0.00 2.66
3275 3520 4.193826 ACTGACATACCATATGCGATCC 57.806 45.455 0.00 0.00 0.00 3.36
3276 3521 6.813649 ACATAACTGACATACCATATGCGATC 59.186 38.462 0.00 0.00 0.00 3.69
3277 3522 6.701340 ACATAACTGACATACCATATGCGAT 58.299 36.000 0.00 0.00 0.00 4.58
3278 3523 6.096673 ACATAACTGACATACCATATGCGA 57.903 37.500 0.00 0.00 0.00 5.10
3279 3524 5.925969 TGACATAACTGACATACCATATGCG 59.074 40.000 0.00 0.00 0.00 4.73
3280 3525 7.603784 TCATGACATAACTGACATACCATATGC 59.396 37.037 0.00 0.00 35.94 3.14
3281 3526 8.929746 GTCATGACATAACTGACATACCATATG 58.070 37.037 21.07 0.00 39.24 1.78
3282 3527 8.650490 TGTCATGACATAACTGACATACCATAT 58.350 33.333 24.56 0.00 43.10 1.78
3283 3528 8.017418 TGTCATGACATAACTGACATACCATA 57.983 34.615 24.56 0.00 43.10 2.74
3284 3529 6.888105 TGTCATGACATAACTGACATACCAT 58.112 36.000 24.56 0.00 43.10 3.55
3285 3530 6.293004 TGTCATGACATAACTGACATACCA 57.707 37.500 24.56 0.00 43.10 3.25
3299 3544 2.271821 CCGGGCCATGTCATGACA 59.728 61.111 29.67 29.67 46.44 3.58
3300 3545 3.211963 GCCGGGCCATGTCATGAC 61.212 66.667 19.27 19.27 0.00 3.06
3318 3563 4.760047 CTTGGGCCGTCGTCCTGG 62.760 72.222 0.00 0.00 0.00 4.45
3319 3564 4.760047 CCTTGGGCCGTCGTCCTG 62.760 72.222 0.00 0.00 0.00 3.86
3341 3586 2.575993 CTGTCCAGTCTCCGCCTG 59.424 66.667 0.00 0.00 0.00 4.85
3342 3587 2.681778 CCTGTCCAGTCTCCGCCT 60.682 66.667 0.00 0.00 0.00 5.52
3343 3588 3.775654 CCCTGTCCAGTCTCCGCC 61.776 72.222 0.00 0.00 0.00 6.13
3344 3589 4.459089 GCCCTGTCCAGTCTCCGC 62.459 72.222 0.00 0.00 0.00 5.54
3345 3590 4.135153 CGCCCTGTCCAGTCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
3346 3591 2.508586 GAACGCCCTGTCCAGTCTCC 62.509 65.000 0.00 0.00 0.00 3.71
3347 3592 1.079750 GAACGCCCTGTCCAGTCTC 60.080 63.158 0.00 0.00 0.00 3.36
3348 3593 2.584391 GGAACGCCCTGTCCAGTCT 61.584 63.158 0.00 0.00 0.00 3.24
3349 3594 2.047179 GGAACGCCCTGTCCAGTC 60.047 66.667 0.00 0.00 0.00 3.51
3362 3607 4.262506 CCCTATTTATCCTGGACTCGGAAC 60.263 50.000 0.00 0.00 33.55 3.62
3363 3608 3.901844 CCCTATTTATCCTGGACTCGGAA 59.098 47.826 0.00 0.00 33.55 4.30
3364 3609 3.141460 TCCCTATTTATCCTGGACTCGGA 59.859 47.826 0.00 0.00 34.52 4.55
3365 3610 3.507411 TCCCTATTTATCCTGGACTCGG 58.493 50.000 0.00 0.00 0.00 4.63
3366 3611 4.408276 TCTCCCTATTTATCCTGGACTCG 58.592 47.826 0.00 0.00 0.00 4.18
3367 3612 5.841783 ACTTCTCCCTATTTATCCTGGACTC 59.158 44.000 0.00 0.00 0.00 3.36
3368 3613 5.604650 CACTTCTCCCTATTTATCCTGGACT 59.395 44.000 0.00 0.00 0.00 3.85
3369 3614 5.743422 GCACTTCTCCCTATTTATCCTGGAC 60.743 48.000 0.00 0.00 0.00 4.02
3370 3615 4.348168 GCACTTCTCCCTATTTATCCTGGA 59.652 45.833 0.00 0.00 0.00 3.86
3371 3616 4.646572 GCACTTCTCCCTATTTATCCTGG 58.353 47.826 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.