Multiple sequence alignment - TraesCS5D01G455600

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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 TraesCS5D01G455600 chr5D 100.000 3202 0 0 1 3202 502730855 502734056 0.000000e+00 5914.0
1 TraesCS5D01G455600 chr5D 85.714 476 54 6 2442 2909 423327603 423328072 1.030000e-134 490.0
2 TraesCS5D01G455600 chr5D 87.889 289 35 0 976 1264 502711128 502711416 1.100000e-89 340.0
3 TraesCS5D01G455600 chr5D 94.118 136 8 0 1 136 473036994 473037129 1.160000e-49 207.0
4 TraesCS5D01G455600 chr5D 85.263 190 26 2 2441 2628 301101173 301100984 9.060000e-46 195.0
5 TraesCS5D01G455600 chr5B 90.860 2801 174 47 148 2909 631547806 631550563 0.000000e+00 3679.0
6 TraesCS5D01G455600 chr5B 75.960 1094 189 42 1061 2115 531696803 531695745 2.220000e-136 496.0
7 TraesCS5D01G455600 chr5B 95.000 300 11 4 2905 3202 631550621 631550918 4.840000e-128 468.0
8 TraesCS5D01G455600 chr2D 82.051 1131 149 29 1076 2188 569679880 569678786 0.000000e+00 915.0
9 TraesCS5D01G455600 chr2D 82.972 922 120 22 1234 2129 569808377 569807467 0.000000e+00 798.0
10 TraesCS5D01G455600 chr2D 85.115 477 56 10 2441 2909 24865118 24864649 1.040000e-129 473.0
11 TraesCS5D01G455600 chr2D 92.958 142 10 0 1 142 71645260 71645119 1.160000e-49 207.0
12 TraesCS5D01G455600 chr2D 80.851 235 32 10 2677 2909 24864742 24864519 4.250000e-39 172.0
13 TraesCS5D01G455600 chr2B 81.671 1113 150 29 1094 2188 682192058 682190982 0.000000e+00 876.0
14 TraesCS5D01G455600 chr2B 92.647 136 10 0 1 136 536475461 536475326 2.520000e-46 196.0
15 TraesCS5D01G455600 chr2B 91.912 136 11 0 1 136 536271661 536271526 1.170000e-44 191.0
16 TraesCS5D01G455600 chr2B 83.425 181 24 6 2911 3088 97416154 97415977 2.560000e-36 163.0
17 TraesCS5D01G455600 chr7A 84.366 710 94 8 1522 2223 436170353 436169653 0.000000e+00 680.0
18 TraesCS5D01G455600 chr7A 83.075 709 100 9 1523 2223 634326547 634327243 7.540000e-176 627.0
19 TraesCS5D01G455600 chr7A 84.746 118 17 1 2778 2895 543810105 543809989 2.020000e-22 117.0
20 TraesCS5D01G455600 chr3A 83.011 465 61 10 2455 2909 130831047 130831503 3.850000e-109 405.0
21 TraesCS5D01G455600 chr3A 80.488 205 30 9 2707 2909 130831441 130831637 7.160000e-32 148.0
22 TraesCS5D01G455600 chr3A 86.290 124 16 1 2772 2895 174295452 174295330 2.000000e-27 134.0
23 TraesCS5D01G455600 chr1D 83.758 314 39 6 2497 2804 461385683 461385990 1.450000e-73 287.0
24 TraesCS5D01G455600 chr1D 93.431 137 9 0 1 137 35858091 35858227 1.510000e-48 204.0
25 TraesCS5D01G455600 chr5A 87.379 206 24 2 2441 2644 44969728 44969933 5.340000e-58 235.0
26 TraesCS5D01G455600 chr7D 92.308 143 8 3 1 142 440162878 440162738 1.950000e-47 200.0
27 TraesCS5D01G455600 chr7D 91.912 136 11 0 1 136 403424473 403424338 1.170000e-44 191.0
28 TraesCS5D01G455600 chr7D 84.459 148 18 3 2772 2915 388967750 388967604 1.200000e-29 141.0
29 TraesCS5D01G455600 chr7D 75.758 297 59 11 1541 1829 613231938 613231647 1.550000e-28 137.0
30 TraesCS5D01G455600 chr6D 93.333 135 9 0 1 135 470463852 470463986 1.950000e-47 200.0
31 TraesCS5D01G455600 chr6D 91.429 140 8 4 1 138 449232876 449232739 4.220000e-44 189.0
32 TraesCS5D01G455600 chr7B 73.890 563 116 25 1526 2069 683107185 683107735 2.520000e-46 196.0
33 TraesCS5D01G455600 chr7B 81.295 139 20 5 2926 3060 85832704 85832840 1.210000e-19 108.0
34 TraesCS5D01G455600 chr4B 76.433 314 64 10 1526 1834 55704959 55705267 9.190000e-36 161.0
35 TraesCS5D01G455600 chr4D 75.641 312 70 6 1526 1834 38304741 38305049 1.990000e-32 150.0
36 TraesCS5D01G455600 chr6B 87.097 124 15 1 2772 2895 411238463 411238341 4.310000e-29 139.0
37 TraesCS5D01G455600 chr6B 82.955 88 14 1 2926 3013 600288283 600288197 9.520000e-11 78.7
38 TraesCS5D01G455600 chrUn 73.663 243 45 16 1600 1833 266534683 266534451 3.430000e-10 76.8


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 TraesCS5D01G455600 chr5D 502730855 502734056 3201 False 5914.0 5914 100.0000 1 3202 1 chr5D.!!$F4 3201
1 TraesCS5D01G455600 chr5B 631547806 631550918 3112 False 2073.5 3679 92.9300 148 3202 2 chr5B.!!$F1 3054
2 TraesCS5D01G455600 chr5B 531695745 531696803 1058 True 496.0 496 75.9600 1061 2115 1 chr5B.!!$R1 1054
3 TraesCS5D01G455600 chr2D 569678786 569679880 1094 True 915.0 915 82.0510 1076 2188 1 chr2D.!!$R2 1112
4 TraesCS5D01G455600 chr2D 569807467 569808377 910 True 798.0 798 82.9720 1234 2129 1 chr2D.!!$R3 895
5 TraesCS5D01G455600 chr2D 24864519 24865118 599 True 322.5 473 82.9830 2441 2909 2 chr2D.!!$R4 468
6 TraesCS5D01G455600 chr2B 682190982 682192058 1076 True 876.0 876 81.6710 1094 2188 1 chr2B.!!$R4 1094
7 TraesCS5D01G455600 chr7A 436169653 436170353 700 True 680.0 680 84.3660 1522 2223 1 chr7A.!!$R1 701
8 TraesCS5D01G455600 chr7A 634326547 634327243 696 False 627.0 627 83.0750 1523 2223 1 chr7A.!!$F1 700
9 TraesCS5D01G455600 chr3A 130831047 130831637 590 False 276.5 405 81.7495 2455 2909 2 chr3A.!!$F1 454

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
580 581 0.033601 GCATGTAATCCCCACCACCA 60.034 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2556 0.394352 AATCTGATCCAACGGCCACC 60.394 55.0 2.24 0.0 0.0 4.61 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
18 19 2.921374 TGGATTGGTCGGTTTCACG 58.079 52.632 0.00 0.00 0.00 4.35
19 20 0.107081 TGGATTGGTCGGTTTCACGT 59.893 50.000 0.00 0.00 34.94 4.49
20 21 0.515564 GGATTGGTCGGTTTCACGTG 59.484 55.000 9.94 9.94 34.94 4.49
21 22 0.110373 GATTGGTCGGTTTCACGTGC 60.110 55.000 11.67 0.00 34.94 5.34
22 23 1.837538 ATTGGTCGGTTTCACGTGCG 61.838 55.000 11.67 8.92 34.94 5.34
23 24 4.364409 GGTCGGTTTCACGTGCGC 62.364 66.667 11.67 0.00 34.94 6.09
24 25 4.696172 GTCGGTTTCACGTGCGCG 62.696 66.667 19.78 19.78 44.93 6.86
27 28 4.659874 GGTTTCACGTGCGCGGTG 62.660 66.667 25.20 21.36 43.45 4.94
39 40 3.660111 GCGGTGCTGCTTTCCGTT 61.660 61.111 23.23 0.00 45.11 4.44
40 41 3.030652 CGGTGCTGCTTTCCGTTT 58.969 55.556 17.82 0.00 39.51 3.60
41 42 1.082104 CGGTGCTGCTTTCCGTTTC 60.082 57.895 17.82 0.00 39.51 2.78
42 43 1.507141 CGGTGCTGCTTTCCGTTTCT 61.507 55.000 17.82 0.00 39.51 2.52
43 44 0.040067 GGTGCTGCTTTCCGTTTCTG 60.040 55.000 0.00 0.00 0.00 3.02
44 45 0.040067 GTGCTGCTTTCCGTTTCTGG 60.040 55.000 0.00 0.00 0.00 3.86
45 46 1.081175 GCTGCTTTCCGTTTCTGGC 60.081 57.895 0.00 0.00 0.00 4.85
46 47 1.518903 GCTGCTTTCCGTTTCTGGCT 61.519 55.000 0.00 0.00 0.00 4.75
47 48 0.239347 CTGCTTTCCGTTTCTGGCTG 59.761 55.000 0.00 0.00 0.00 4.85
48 49 0.465460 TGCTTTCCGTTTCTGGCTGT 60.465 50.000 0.00 0.00 0.00 4.40
49 50 0.238553 GCTTTCCGTTTCTGGCTGTC 59.761 55.000 0.00 0.00 0.00 3.51
50 51 1.884235 CTTTCCGTTTCTGGCTGTCT 58.116 50.000 0.00 0.00 0.00 3.41
51 52 1.532868 CTTTCCGTTTCTGGCTGTCTG 59.467 52.381 0.00 0.00 0.00 3.51
52 53 0.250295 TTCCGTTTCTGGCTGTCTGG 60.250 55.000 0.00 0.00 0.00 3.86
53 54 1.071471 CCGTTTCTGGCTGTCTGGT 59.929 57.895 0.00 0.00 0.00 4.00
54 55 0.951040 CCGTTTCTGGCTGTCTGGTC 60.951 60.000 0.00 0.00 0.00 4.02
55 56 1.284982 CGTTTCTGGCTGTCTGGTCG 61.285 60.000 0.00 0.00 0.00 4.79
56 57 1.301716 TTTCTGGCTGTCTGGTCGC 60.302 57.895 0.00 0.00 0.00 5.19
57 58 3.573772 TTCTGGCTGTCTGGTCGCG 62.574 63.158 0.00 0.00 0.00 5.87
79 80 4.410400 CGGGCGGCTCCTTCCTTT 62.410 66.667 9.56 0.00 34.39 3.11
80 81 2.035783 GGGCGGCTCCTTCCTTTT 59.964 61.111 9.56 0.00 34.39 2.27
81 82 1.606601 GGGCGGCTCCTTCCTTTTT 60.607 57.895 9.56 0.00 34.39 1.94
95 96 3.966215 TTTTTGGGAGAGCGCTCG 58.034 55.556 30.39 0.00 42.25 5.03
96 97 1.671054 TTTTTGGGAGAGCGCTCGG 60.671 57.895 30.39 0.00 42.25 4.63
97 98 3.605749 TTTTGGGAGAGCGCTCGGG 62.606 63.158 30.39 0.00 42.25 5.14
155 156 7.408132 CGTCCATCGTTAATTGATGATTACT 57.592 36.000 17.52 0.00 44.76 2.24
178 179 5.713025 TCTATAAAACTGACCGCGTAAACT 58.287 37.500 4.92 0.00 0.00 2.66
224 225 2.187163 GTCCTGGGCTCCGCTTAC 59.813 66.667 0.00 0.00 0.00 2.34
228 229 0.105039 CCTGGGCTCCGCTTACTAAG 59.895 60.000 0.00 0.00 0.00 2.18
327 328 4.607955 CAAGAATCCGTATCTTGCTCGTA 58.392 43.478 8.53 0.00 45.02 3.43
470 471 1.639298 GGCATGTTCAGTGTCCTCGC 61.639 60.000 0.00 0.00 0.00 5.03
471 472 0.950555 GCATGTTCAGTGTCCTCGCA 60.951 55.000 0.00 0.00 0.00 5.10
517 518 2.911143 CGCTGCCTTACATCCCCT 59.089 61.111 0.00 0.00 0.00 4.79
518 519 1.227674 CGCTGCCTTACATCCCCTC 60.228 63.158 0.00 0.00 0.00 4.30
524 525 0.754217 CCTTACATCCCCTCCGTCGA 60.754 60.000 0.00 0.00 0.00 4.20
534 535 2.915659 TCCGTCGACCCAGCAGTT 60.916 61.111 10.58 0.00 0.00 3.16
537 538 1.445582 CGTCGACCCAGCAGTTACC 60.446 63.158 10.58 0.00 0.00 2.85
538 539 1.079336 GTCGACCCAGCAGTTACCC 60.079 63.158 3.51 0.00 0.00 3.69
539 540 1.229082 TCGACCCAGCAGTTACCCT 60.229 57.895 0.00 0.00 0.00 4.34
540 541 1.218316 CGACCCAGCAGTTACCCTC 59.782 63.158 0.00 0.00 0.00 4.30
543 544 2.125106 CCAGCAGTTACCCTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
544 545 2.509336 CAGCAGTTACCCTCCGCG 60.509 66.667 0.00 0.00 0.00 6.46
545 546 3.771160 AGCAGTTACCCTCCGCGG 61.771 66.667 22.12 22.12 0.00 6.46
546 547 4.078516 GCAGTTACCCTCCGCGGT 62.079 66.667 27.15 8.36 40.13 5.68
547 548 2.660802 CAGTTACCCTCCGCGGTT 59.339 61.111 27.15 10.72 37.34 4.44
548 549 1.447314 CAGTTACCCTCCGCGGTTC 60.447 63.158 27.15 8.70 37.34 3.62
549 550 1.909781 AGTTACCCTCCGCGGTTCA 60.910 57.895 27.15 4.62 37.34 3.18
550 551 1.004679 GTTACCCTCCGCGGTTCAA 60.005 57.895 27.15 10.47 37.34 2.69
551 552 1.004679 TTACCCTCCGCGGTTCAAC 60.005 57.895 27.15 0.00 37.34 3.18
552 553 2.453379 TTACCCTCCGCGGTTCAACC 62.453 60.000 27.15 0.00 37.34 3.77
561 562 4.058797 GGTTCAACCGTCACCAGG 57.941 61.111 0.00 0.00 0.00 4.45
562 563 2.258726 GGTTCAACCGTCACCAGGC 61.259 63.158 0.00 0.00 0.00 4.85
563 564 1.525077 GTTCAACCGTCACCAGGCA 60.525 57.895 0.00 0.00 0.00 4.75
573 574 0.550914 TCACCAGGCATGTAATCCCC 59.449 55.000 0.00 0.00 0.00 4.81
574 575 0.258484 CACCAGGCATGTAATCCCCA 59.742 55.000 0.00 0.00 0.00 4.96
580 581 0.033601 GCATGTAATCCCCACCACCA 60.034 55.000 0.00 0.00 0.00 4.17
588 589 1.065410 TCCCCACCACCACTGATGTT 61.065 55.000 0.00 0.00 0.00 2.71
594 595 3.148412 CACCACCACTGATGTTGATTCA 58.852 45.455 0.00 0.00 0.00 2.57
598 599 4.279169 CCACCACTGATGTTGATTCAAGTT 59.721 41.667 0.00 0.00 0.00 2.66
607 608 3.049912 GTTGATTCAAGTTTTGACGGCC 58.950 45.455 0.00 0.00 39.87 6.13
609 610 0.966179 ATTCAAGTTTTGACGGCCCC 59.034 50.000 0.00 0.00 39.87 5.80
610 611 1.448922 TTCAAGTTTTGACGGCCCCG 61.449 55.000 4.96 4.96 39.87 5.73
622 623 2.828549 GCCCCGTGATGGCGAAAT 60.829 61.111 0.00 0.00 39.48 2.17
623 624 3.110139 CCCCGTGATGGCGAAATG 58.890 61.111 0.00 0.00 35.87 2.32
624 625 2.480610 CCCCGTGATGGCGAAATGG 61.481 63.158 0.00 0.00 35.87 3.16
625 626 2.480610 CCCGTGATGGCGAAATGGG 61.481 63.158 0.00 0.00 35.87 4.00
626 627 1.451207 CCGTGATGGCGAAATGGGA 60.451 57.895 0.00 0.00 0.00 4.37
627 628 1.029408 CCGTGATGGCGAAATGGGAA 61.029 55.000 0.00 0.00 0.00 3.97
635 636 1.613255 GGCGAAATGGGAAGGAGAACA 60.613 52.381 0.00 0.00 0.00 3.18
636 637 2.369394 GCGAAATGGGAAGGAGAACAT 58.631 47.619 0.00 0.00 0.00 2.71
639 640 4.321974 GCGAAATGGGAAGGAGAACATTTT 60.322 41.667 0.00 0.00 41.90 1.82
649 650 3.189287 AGGAGAACATTTTAACTGCAGCG 59.811 43.478 15.27 0.00 0.00 5.18
664 665 1.234821 CAGCGGCAGGTTTTTGTCTA 58.765 50.000 1.45 0.00 0.00 2.59
668 669 2.767505 CGGCAGGTTTTTGTCTAGTCT 58.232 47.619 0.00 0.00 0.00 3.24
671 672 3.244596 GGCAGGTTTTTGTCTAGTCTCCT 60.245 47.826 0.00 0.00 0.00 3.69
672 673 4.390264 GCAGGTTTTTGTCTAGTCTCCTT 58.610 43.478 0.00 0.00 0.00 3.36
681 682 2.916089 GTCTAGTCTCCTTTTCGCGTTC 59.084 50.000 5.77 0.00 0.00 3.95
682 683 1.912110 CTAGTCTCCTTTTCGCGTTCG 59.088 52.381 5.77 0.00 0.00 3.95
694 695 1.659601 TCGCGTTCGAAGAACAACAAA 59.340 42.857 5.77 0.00 45.90 2.83
703 704 4.797868 TCGAAGAACAACAAATTGCAACTG 59.202 37.500 0.00 4.91 39.66 3.16
708 709 2.277969 CAACAAATTGCAACTGTGGCA 58.722 42.857 14.89 5.58 40.00 4.92
738 739 0.109342 CTGGTGGTTCTGCTGGAAGT 59.891 55.000 0.00 0.00 35.30 3.01
741 742 1.338020 GGTGGTTCTGCTGGAAGTTTG 59.662 52.381 0.00 0.00 35.30 2.93
745 746 1.609072 GTTCTGCTGGAAGTTTGGGAC 59.391 52.381 0.00 0.00 35.30 4.46
761 762 6.852664 GTTTGGGACTTCCTAACATTACATG 58.147 40.000 0.00 0.00 46.06 3.21
778 779 8.609176 ACATTACATGTTACACATATTTCGTCC 58.391 33.333 2.30 0.00 41.63 4.79
779 780 8.608317 CATTACATGTTACACATATTTCGTCCA 58.392 33.333 2.30 0.00 36.53 4.02
781 782 5.353123 ACATGTTACACATATTTCGTCCACC 59.647 40.000 0.00 0.00 36.53 4.61
782 783 3.927758 TGTTACACATATTTCGTCCACCG 59.072 43.478 0.00 0.00 38.13 4.94
793 794 5.918375 ATTTCGTCCACCGGAATTTAACCG 61.918 45.833 9.46 0.00 42.17 4.44
798 799 3.493213 CGGAATTTAACCGCGCCT 58.507 55.556 0.00 0.00 43.74 5.52
799 800 1.350665 CGGAATTTAACCGCGCCTC 59.649 57.895 0.00 0.00 43.74 4.70
801 802 0.377203 GGAATTTAACCGCGCCTCAG 59.623 55.000 0.00 0.00 0.00 3.35
803 804 1.654023 AATTTAACCGCGCCTCAGCC 61.654 55.000 0.00 0.00 34.57 4.85
816 817 4.404098 CAGCCGCCGTACCCCTTT 62.404 66.667 0.00 0.00 0.00 3.11
817 818 4.404098 AGCCGCCGTACCCCTTTG 62.404 66.667 0.00 0.00 0.00 2.77
822 823 2.271173 CCGTACCCCTTTGGCCTC 59.729 66.667 3.32 0.00 37.83 4.70
823 824 2.598787 CCGTACCCCTTTGGCCTCA 61.599 63.158 3.32 0.00 37.83 3.86
825 826 1.838073 CGTACCCCTTTGGCCTCACT 61.838 60.000 3.32 0.00 37.83 3.41
835 836 0.898326 TGGCCTCACTGACGAAGCTA 60.898 55.000 3.32 0.00 0.00 3.32
836 837 0.461961 GGCCTCACTGACGAAGCTAT 59.538 55.000 0.00 0.00 0.00 2.97
863 864 3.395639 GAAGATTGTTGTCCGGTACACA 58.604 45.455 0.00 0.00 38.00 3.72
869 870 2.510691 GTCCGGTACACATGGCCG 60.511 66.667 0.00 11.55 44.55 6.13
894 895 1.301716 GACGAGGAAACAGCAGGCA 60.302 57.895 0.00 0.00 0.00 4.75
912 913 3.050275 GCAGCACACGGGAAGGTC 61.050 66.667 0.00 0.00 0.00 3.85
933 934 3.932580 ATCGTCGCGGCTGAAGCAA 62.933 57.895 9.90 0.00 44.36 3.91
937 938 4.456253 CGCGGCTGAAGCAAGCAG 62.456 66.667 17.85 5.35 45.43 4.24
974 975 1.508808 TTAGTCGGGTTGGTTTGCGC 61.509 55.000 0.00 0.00 0.00 6.09
1002 1003 2.100410 CTTCTGCGCTGCTGCATG 59.900 61.111 16.29 12.04 45.26 4.06
1009 1010 2.512286 GCTGCTGCATGCGTAGGA 60.512 61.111 21.61 12.63 46.63 2.94
1047 1051 0.389817 CAGCGTCCATCGAACTGGAA 60.390 55.000 9.32 0.00 46.66 3.53
1073 1077 2.094182 ACGAGCACATCATAACCGAACT 60.094 45.455 0.00 0.00 0.00 3.01
1081 1085 4.081420 ACATCATAACCGAACTTGAGCTCT 60.081 41.667 16.19 0.00 0.00 4.09
1085 1089 1.004560 CCGAACTTGAGCTCTGGCA 60.005 57.895 16.19 0.00 41.70 4.92
1089 1093 0.251077 AACTTGAGCTCTGGCAAGGG 60.251 55.000 16.19 0.00 44.33 3.95
1090 1094 1.130054 ACTTGAGCTCTGGCAAGGGA 61.130 55.000 16.19 0.00 44.33 4.20
1103 1107 1.766461 AAGGGATGGGACCTAGGCG 60.766 63.158 9.30 0.00 37.35 5.52
1161 1165 0.472898 TCGCCGAGGAGAGGAAGATA 59.527 55.000 0.00 0.00 0.00 1.98
1188 1193 1.598517 GGGGTTCGGTTCGGTGTAT 59.401 57.895 0.00 0.00 0.00 2.29
1191 1196 1.202452 GGGTTCGGTTCGGTGTATAGG 60.202 57.143 0.00 0.00 0.00 2.57
1433 1471 3.695830 TCCCGACAGATGCTTAACTTT 57.304 42.857 0.00 0.00 0.00 2.66
1436 1474 3.125316 CCCGACAGATGCTTAACTTTGTC 59.875 47.826 0.00 0.00 33.44 3.18
1447 1492 4.082354 GCTTAACTTTGTCGGAGAGGTAGA 60.082 45.833 0.00 0.00 36.95 2.59
1632 1700 2.839438 CGCGAACGTGATGCTCGAG 61.839 63.158 8.45 8.45 34.52 4.04
1911 1982 1.447838 CCACCGGAACCTGATCGTG 60.448 63.158 9.46 0.00 0.00 4.35
2078 2156 1.227147 GCCGGTGCTTGTAGCGATA 60.227 57.895 11.43 0.00 46.26 2.92
2079 2157 1.215655 GCCGGTGCTTGTAGCGATAG 61.216 60.000 11.43 0.00 46.26 2.08
2144 2228 0.458543 ATGGCGATGTGTCTGACGAC 60.459 55.000 2.98 3.71 40.64 4.34
2285 2375 5.055642 AGATTGTCATTGTCACTTGCATG 57.944 39.130 0.00 0.00 0.00 4.06
2447 2556 1.270839 ACCCAACAGAACACCATCTCG 60.271 52.381 0.00 0.00 0.00 4.04
2574 2684 5.122519 GGTGTGTTGTGGGATTTGAATTTT 58.877 37.500 0.00 0.00 0.00 1.82
2684 2795 4.217210 CCACCACCAAGCACCCCA 62.217 66.667 0.00 0.00 0.00 4.96
2793 2911 0.987294 CACCTTCATCCAGACCAGGT 59.013 55.000 0.00 0.00 37.86 4.00
2923 3107 3.263503 CTCCGCTCGACACCGACAA 62.264 63.158 0.00 0.00 40.30 3.18
2957 3141 2.129607 CCACTTTTGCAACATCACTGC 58.870 47.619 0.00 0.00 40.35 4.40
2993 3178 0.592247 GTGCAACAAGACCGCTGTTG 60.592 55.000 10.52 10.52 43.90 3.33
3004 3189 3.123050 GACCGCTGTTGCAAAAGAAAAT 58.877 40.909 21.21 1.85 39.64 1.82
3018 3203 6.708676 CAAAAGAAAATTGCACAAAGACCTC 58.291 36.000 0.00 0.00 0.00 3.85
3029 3214 5.184096 TGCACAAAGACCTCTGTTACAAAAA 59.816 36.000 0.00 0.00 0.00 1.94
3148 3334 0.745845 CAGTCTTGGGAATCGGCAGG 60.746 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107081 ACGTGAAACCGACCAATCCA 59.893 50.000 0.00 0.00 0.00 3.41
1 2 0.515564 CACGTGAAACCGACCAATCC 59.484 55.000 10.90 0.00 0.00 3.01
2 3 0.110373 GCACGTGAAACCGACCAATC 60.110 55.000 22.23 0.00 0.00 2.67
3 4 1.837538 CGCACGTGAAACCGACCAAT 61.838 55.000 22.23 0.00 0.00 3.16
4 5 2.526993 CGCACGTGAAACCGACCAA 61.527 57.895 22.23 0.00 0.00 3.67
5 6 2.962786 CGCACGTGAAACCGACCA 60.963 61.111 22.23 0.00 0.00 4.02
6 7 4.364409 GCGCACGTGAAACCGACC 62.364 66.667 22.23 0.00 0.00 4.79
7 8 4.696172 CGCGCACGTGAAACCGAC 62.696 66.667 22.23 8.44 33.53 4.79
10 11 4.659874 CACCGCGCACGTGAAACC 62.660 66.667 22.23 0.00 37.70 3.27
24 25 0.040067 CAGAAACGGAAAGCAGCACC 60.040 55.000 0.00 0.00 0.00 5.01
25 26 0.040067 CCAGAAACGGAAAGCAGCAC 60.040 55.000 0.00 0.00 0.00 4.40
26 27 1.795170 GCCAGAAACGGAAAGCAGCA 61.795 55.000 0.00 0.00 0.00 4.41
27 28 1.081175 GCCAGAAACGGAAAGCAGC 60.081 57.895 0.00 0.00 0.00 5.25
28 29 0.239347 CAGCCAGAAACGGAAAGCAG 59.761 55.000 0.00 0.00 0.00 4.24
29 30 0.465460 ACAGCCAGAAACGGAAAGCA 60.465 50.000 0.00 0.00 0.00 3.91
30 31 0.238553 GACAGCCAGAAACGGAAAGC 59.761 55.000 0.00 0.00 0.00 3.51
31 32 1.532868 CAGACAGCCAGAAACGGAAAG 59.467 52.381 0.00 0.00 0.00 2.62
32 33 1.593196 CAGACAGCCAGAAACGGAAA 58.407 50.000 0.00 0.00 0.00 3.13
33 34 0.250295 CCAGACAGCCAGAAACGGAA 60.250 55.000 0.00 0.00 0.00 4.30
34 35 1.371183 CCAGACAGCCAGAAACGGA 59.629 57.895 0.00 0.00 0.00 4.69
35 36 0.951040 GACCAGACAGCCAGAAACGG 60.951 60.000 0.00 0.00 0.00 4.44
36 37 1.284982 CGACCAGACAGCCAGAAACG 61.285 60.000 0.00 0.00 0.00 3.60
37 38 1.569479 GCGACCAGACAGCCAGAAAC 61.569 60.000 0.00 0.00 0.00 2.78
38 39 1.301716 GCGACCAGACAGCCAGAAA 60.302 57.895 0.00 0.00 0.00 2.52
39 40 2.343758 GCGACCAGACAGCCAGAA 59.656 61.111 0.00 0.00 0.00 3.02
40 41 4.056125 CGCGACCAGACAGCCAGA 62.056 66.667 0.00 0.00 0.00 3.86
62 63 3.920093 AAAAGGAAGGAGCCGCCCG 62.920 63.158 0.00 0.00 37.37 6.13
63 64 1.606601 AAAAAGGAAGGAGCCGCCC 60.607 57.895 0.00 0.00 37.37 6.13
64 65 4.097218 AAAAAGGAAGGAGCCGCC 57.903 55.556 0.00 0.00 0.00 6.13
78 79 1.671054 CCGAGCGCTCTCCCAAAAA 60.671 57.895 32.88 0.00 35.94 1.94
79 80 2.047274 CCGAGCGCTCTCCCAAAA 60.047 61.111 32.88 0.00 35.94 2.44
80 81 4.082523 CCCGAGCGCTCTCCCAAA 62.083 66.667 32.88 0.00 35.94 3.28
132 133 8.594881 AGAGTAATCATCAATTAACGATGGAC 57.405 34.615 13.91 10.63 40.58 4.02
144 145 9.529325 CGGTCAGTTTTATAGAGTAATCATCAA 57.471 33.333 0.00 0.00 0.00 2.57
145 146 7.652105 GCGGTCAGTTTTATAGAGTAATCATCA 59.348 37.037 0.00 0.00 0.00 3.07
146 147 7.148950 CGCGGTCAGTTTTATAGAGTAATCATC 60.149 40.741 0.00 0.00 0.00 2.92
149 150 5.975939 ACGCGGTCAGTTTTATAGAGTAATC 59.024 40.000 12.47 0.00 0.00 1.75
154 155 5.803967 AGTTTACGCGGTCAGTTTTATAGAG 59.196 40.000 12.47 0.00 0.00 2.43
155 156 5.574055 CAGTTTACGCGGTCAGTTTTATAGA 59.426 40.000 12.47 0.00 0.00 1.98
178 179 0.108207 TTCGCGGTAAACCCCTTTCA 59.892 50.000 6.13 0.00 0.00 2.69
224 225 0.809241 CAAGCAGCGAGGGAGCTTAG 60.809 60.000 0.00 0.00 46.80 2.18
296 297 1.512734 CGGATTCTTGCGTTGCAGC 60.513 57.895 0.00 0.00 40.61 5.25
327 328 0.892814 GGTAGGAGGCGCCGTATAGT 60.893 60.000 23.20 0.68 43.43 2.12
361 362 3.112709 GTTGACGGAGAGTGCGGC 61.113 66.667 0.00 0.00 40.72 6.53
470 471 1.098050 GCTAGAGCACCAACCCAATG 58.902 55.000 0.00 0.00 41.59 2.82
471 472 3.577389 GCTAGAGCACCAACCCAAT 57.423 52.632 0.00 0.00 41.59 3.16
508 509 1.454479 GGTCGACGGAGGGGATGTA 60.454 63.158 9.92 0.00 0.00 2.29
512 513 4.753662 CTGGGTCGACGGAGGGGA 62.754 72.222 9.92 0.00 0.00 4.81
517 518 1.604308 TAACTGCTGGGTCGACGGA 60.604 57.895 9.92 0.00 0.00 4.69
518 519 1.445582 GTAACTGCTGGGTCGACGG 60.446 63.158 9.92 3.50 0.00 4.79
524 525 2.291043 CGGAGGGTAACTGCTGGGT 61.291 63.158 0.00 0.00 35.02 4.51
534 535 2.658422 GTTGAACCGCGGAGGGTA 59.342 61.111 35.90 10.30 42.60 3.69
544 545 2.258726 GCCTGGTGACGGTTGAACC 61.259 63.158 3.76 3.76 33.66 3.62
545 546 0.889186 ATGCCTGGTGACGGTTGAAC 60.889 55.000 0.00 0.00 33.66 3.18
546 547 0.888736 CATGCCTGGTGACGGTTGAA 60.889 55.000 0.00 0.00 33.66 2.69
547 548 1.302431 CATGCCTGGTGACGGTTGA 60.302 57.895 0.00 0.00 33.66 3.18
548 549 0.321210 TACATGCCTGGTGACGGTTG 60.321 55.000 0.00 0.00 33.66 3.77
549 550 0.398696 TTACATGCCTGGTGACGGTT 59.601 50.000 0.00 0.00 33.66 4.44
550 551 0.618458 ATTACATGCCTGGTGACGGT 59.382 50.000 0.00 0.00 33.66 4.83
551 552 1.299541 GATTACATGCCTGGTGACGG 58.700 55.000 0.00 0.00 0.00 4.79
552 553 1.299541 GGATTACATGCCTGGTGACG 58.700 55.000 0.00 0.00 0.00 4.35
553 554 1.680338 GGGATTACATGCCTGGTGAC 58.320 55.000 0.00 0.00 37.84 3.67
554 555 0.550914 GGGGATTACATGCCTGGTGA 59.449 55.000 0.00 0.00 41.10 4.02
555 556 0.258484 TGGGGATTACATGCCTGGTG 59.742 55.000 0.00 0.00 41.10 4.17
556 557 0.258774 GTGGGGATTACATGCCTGGT 59.741 55.000 0.00 0.00 41.10 4.00
557 558 0.468029 GGTGGGGATTACATGCCTGG 60.468 60.000 0.00 0.00 41.10 4.45
558 559 0.258484 TGGTGGGGATTACATGCCTG 59.742 55.000 0.00 0.00 41.10 4.85
559 560 0.258774 GTGGTGGGGATTACATGCCT 59.741 55.000 0.00 0.00 41.10 4.75
560 561 0.755327 GGTGGTGGGGATTACATGCC 60.755 60.000 0.00 0.00 40.52 4.40
561 562 0.033601 TGGTGGTGGGGATTACATGC 60.034 55.000 0.00 0.00 0.00 4.06
562 563 1.284785 AGTGGTGGTGGGGATTACATG 59.715 52.381 0.00 0.00 0.00 3.21
563 564 1.284785 CAGTGGTGGTGGGGATTACAT 59.715 52.381 0.00 0.00 0.00 2.29
573 574 3.148412 TGAATCAACATCAGTGGTGGTG 58.852 45.455 15.70 15.70 43.42 4.17
574 575 3.507162 TGAATCAACATCAGTGGTGGT 57.493 42.857 8.56 0.00 43.42 4.16
580 581 6.201517 CGTCAAAACTTGAATCAACATCAGT 58.798 36.000 0.00 0.00 42.15 3.41
588 589 1.611491 GGGCCGTCAAAACTTGAATCA 59.389 47.619 0.00 0.00 42.15 2.57
607 608 2.480610 CCCATTTCGCCATCACGGG 61.481 63.158 0.00 0.00 34.06 5.28
609 610 0.378257 CTTCCCATTTCGCCATCACG 59.622 55.000 0.00 0.00 0.00 4.35
610 611 0.740737 CCTTCCCATTTCGCCATCAC 59.259 55.000 0.00 0.00 0.00 3.06
612 613 1.134098 TCTCCTTCCCATTTCGCCATC 60.134 52.381 0.00 0.00 0.00 3.51
614 615 0.695924 TTCTCCTTCCCATTTCGCCA 59.304 50.000 0.00 0.00 0.00 5.69
615 616 1.095600 GTTCTCCTTCCCATTTCGCC 58.904 55.000 0.00 0.00 0.00 5.54
617 618 5.391312 AAAATGTTCTCCTTCCCATTTCG 57.609 39.130 0.00 0.00 36.72 3.46
621 622 5.185828 GCAGTTAAAATGTTCTCCTTCCCAT 59.814 40.000 0.00 0.00 0.00 4.00
622 623 4.522789 GCAGTTAAAATGTTCTCCTTCCCA 59.477 41.667 0.00 0.00 0.00 4.37
623 624 4.522789 TGCAGTTAAAATGTTCTCCTTCCC 59.477 41.667 0.00 0.00 0.00 3.97
624 625 5.703876 CTGCAGTTAAAATGTTCTCCTTCC 58.296 41.667 5.25 0.00 0.00 3.46
625 626 5.157067 GCTGCAGTTAAAATGTTCTCCTTC 58.843 41.667 16.64 0.00 0.00 3.46
626 627 4.320494 CGCTGCAGTTAAAATGTTCTCCTT 60.320 41.667 16.64 0.00 0.00 3.36
627 628 3.189287 CGCTGCAGTTAAAATGTTCTCCT 59.811 43.478 16.64 0.00 0.00 3.69
649 650 3.075148 GGAGACTAGACAAAAACCTGCC 58.925 50.000 0.00 0.00 0.00 4.85
664 665 0.313043 TCGAACGCGAAAAGGAGACT 59.687 50.000 15.93 0.00 44.78 3.24
681 682 4.562394 ACAGTTGCAATTTGTTGTTCTTCG 59.438 37.500 0.59 0.00 0.00 3.79
682 683 5.220453 CCACAGTTGCAATTTGTTGTTCTTC 60.220 40.000 14.62 0.00 0.00 2.87
694 695 3.756933 ATTTCTTGCCACAGTTGCAAT 57.243 38.095 12.24 0.00 46.68 3.56
703 704 3.191371 CCACCAGAGTAATTTCTTGCCAC 59.809 47.826 0.00 0.00 0.00 5.01
708 709 4.762251 GCAGAACCACCAGAGTAATTTCTT 59.238 41.667 0.00 0.00 0.00 2.52
776 777 1.020333 CGCGGTTAAATTCCGGTGGA 61.020 55.000 0.00 0.00 46.90 4.02
777 778 1.426223 CGCGGTTAAATTCCGGTGG 59.574 57.895 0.00 0.00 46.90 4.61
778 779 1.226184 GCGCGGTTAAATTCCGGTG 60.226 57.895 8.83 0.00 46.90 4.94
779 780 2.400962 GGCGCGGTTAAATTCCGGT 61.401 57.895 8.83 0.00 46.90 5.28
782 783 0.377203 CTGAGGCGCGGTTAAATTCC 59.623 55.000 8.83 0.00 0.00 3.01
799 800 4.404098 AAAGGGGTACGGCGGCTG 62.404 66.667 13.24 7.39 0.00 4.85
804 805 3.989838 GAGGCCAAAGGGGTACGGC 62.990 68.421 5.01 0.00 44.10 5.68
806 807 1.376812 GTGAGGCCAAAGGGGTACG 60.377 63.158 5.01 0.00 39.65 3.67
807 808 0.322546 CAGTGAGGCCAAAGGGGTAC 60.323 60.000 5.01 0.00 39.65 3.34
808 809 0.474854 TCAGTGAGGCCAAAGGGGTA 60.475 55.000 5.01 0.00 39.65 3.69
809 810 1.774217 TCAGTGAGGCCAAAGGGGT 60.774 57.895 5.01 0.00 39.65 4.95
810 811 1.303643 GTCAGTGAGGCCAAAGGGG 60.304 63.158 5.01 0.00 40.85 4.79
812 813 0.250295 TTCGTCAGTGAGGCCAAAGG 60.250 55.000 5.01 0.00 0.00 3.11
813 814 1.151668 CTTCGTCAGTGAGGCCAAAG 58.848 55.000 5.01 3.56 0.00 2.77
814 815 0.884704 GCTTCGTCAGTGAGGCCAAA 60.885 55.000 5.01 0.00 35.13 3.28
815 816 1.301716 GCTTCGTCAGTGAGGCCAA 60.302 57.895 5.01 0.00 35.13 4.52
816 817 0.898326 TAGCTTCGTCAGTGAGGCCA 60.898 55.000 5.01 0.00 41.49 5.36
817 818 0.461961 ATAGCTTCGTCAGTGAGGCC 59.538 55.000 7.98 0.00 41.49 5.19
819 820 1.804372 GCCATAGCTTCGTCAGTGAGG 60.804 57.143 6.49 6.49 35.50 3.86
822 823 1.756375 GCGCCATAGCTTCGTCAGTG 61.756 60.000 0.00 0.00 36.60 3.66
823 824 1.519455 GCGCCATAGCTTCGTCAGT 60.519 57.895 0.00 0.00 36.60 3.41
825 826 2.551097 TTCGCGCCATAGCTTCGTCA 62.551 55.000 0.00 0.00 36.60 4.35
835 836 0.447801 GACAACAATCTTCGCGCCAT 59.552 50.000 0.00 0.00 0.00 4.40
836 837 1.573829 GGACAACAATCTTCGCGCCA 61.574 55.000 0.00 0.00 0.00 5.69
869 870 0.456995 CTGTTTCCTCGTCGCTCTCC 60.457 60.000 0.00 0.00 0.00 3.71
894 895 3.537206 GACCTTCCCGTGTGCTGCT 62.537 63.158 0.00 0.00 0.00 4.24
898 899 4.980805 TGCGACCTTCCCGTGTGC 62.981 66.667 0.00 0.00 0.00 4.57
900 901 2.264794 GATGCGACCTTCCCGTGT 59.735 61.111 0.00 0.00 0.00 4.49
902 903 3.352338 GACGATGCGACCTTCCCGT 62.352 63.158 0.00 0.00 0.00 5.28
957 958 3.284449 GCGCAAACCAACCCGACT 61.284 61.111 0.30 0.00 0.00 4.18
1022 1026 4.862092 CGATGGACGCTGCGCTCT 62.862 66.667 23.51 1.84 34.51 4.09
1027 1031 2.456119 CCAGTTCGATGGACGCTGC 61.456 63.158 0.00 0.00 43.57 5.25
1029 1033 3.694746 TCCAGTTCGATGGACGCT 58.305 55.556 3.55 0.00 44.56 5.07
1047 1051 2.479730 GGTTATGATGTGCTCGTCGTCT 60.480 50.000 5.99 0.00 32.01 4.18
1073 1077 0.034767 CATCCCTTGCCAGAGCTCAA 60.035 55.000 17.77 0.42 40.80 3.02
1081 1085 0.988145 CTAGGTCCCATCCCTTGCCA 60.988 60.000 0.00 0.00 33.35 4.92
1085 1089 1.766461 CGCCTAGGTCCCATCCCTT 60.766 63.158 11.31 0.00 33.35 3.95
1103 1107 3.050275 GCTCGGTGTGGCAGAACC 61.050 66.667 8.87 8.87 39.84 3.62
1131 1135 1.663702 CTCGGCGAAGTTGTCCGTT 60.664 57.895 12.13 0.00 43.35 4.44
1134 1138 1.446272 CTCCTCGGCGAAGTTGTCC 60.446 63.158 12.13 0.00 0.00 4.02
1180 1185 2.091720 TCAAGTAGCCCCTATACACCGA 60.092 50.000 0.00 0.00 0.00 4.69
1188 1193 1.078159 TGGTCACTCAAGTAGCCCCTA 59.922 52.381 0.00 0.00 0.00 3.53
1191 1196 1.623811 TCTTGGTCACTCAAGTAGCCC 59.376 52.381 6.07 0.00 43.25 5.19
1447 1492 0.395311 TGGTCTACGCGGAAGGAGAT 60.395 55.000 12.47 0.00 0.00 2.75
1632 1700 2.514592 TTAGCGCTGCCTGATGCC 60.515 61.111 22.90 0.00 40.16 4.40
1770 1838 3.434319 TACACGTCGGACTCGGCC 61.434 66.667 6.57 0.00 37.80 6.13
1929 2000 0.886490 AGCTTGTCAAACTCGCCAGG 60.886 55.000 0.00 0.00 0.00 4.45
2078 2156 4.473520 CCGGAACCAGGCATCGCT 62.474 66.667 0.00 0.00 0.00 4.93
2080 2158 4.856801 CCCCGGAACCAGGCATCG 62.857 72.222 0.73 0.00 0.00 3.84
2081 2159 3.406595 CTCCCCGGAACCAGGCATC 62.407 68.421 0.73 0.00 0.00 3.91
2082 2160 3.411517 CTCCCCGGAACCAGGCAT 61.412 66.667 0.73 0.00 0.00 4.40
2083 2161 3.943137 ATCTCCCCGGAACCAGGCA 62.943 63.158 0.73 0.00 0.00 4.75
2144 2228 7.439157 TGATTCATTCAAGTAACCAGAGTTG 57.561 36.000 0.00 0.00 36.68 3.16
2152 2236 9.173939 CAGTTTCAGTTGATTCATTCAAGTAAC 57.826 33.333 0.00 0.00 44.50 2.50
2447 2556 0.394352 AATCTGATCCAACGGCCACC 60.394 55.000 2.24 0.00 0.00 4.61
2453 2562 6.427974 CATCTCATTCAAATCTGATCCAACG 58.572 40.000 0.00 0.00 0.00 4.10
2574 2684 2.130426 GCTGCTCTCGAGGGGATCA 61.130 63.158 15.59 2.41 0.00 2.92
2661 2771 4.947147 GCTTGGTGGTGGGCGACA 62.947 66.667 1.14 0.00 0.00 4.35
2662 2772 4.947147 TGCTTGGTGGTGGGCGAC 62.947 66.667 0.00 0.00 0.00 5.19
2684 2795 2.359107 CATCTGCGGTGGCACAGT 60.359 61.111 20.82 0.00 46.21 3.55
2750 2861 1.783979 GAGGAGGAGAGAGGGTGGATA 59.216 57.143 0.00 0.00 0.00 2.59
2957 3141 4.337985 TGCACATTTGTTTTTGCAACAG 57.662 36.364 0.00 0.00 41.90 3.16
3004 3189 3.879998 TGTAACAGAGGTCTTTGTGCAA 58.120 40.909 0.00 0.00 0.00 4.08
3029 3214 5.296748 ACAAAGATATTGTTGCGGCTTTTT 58.703 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.