Multiple sequence alignment - TraesCS6A01G286700

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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 TraesCS6A01G286700 chr6A 100.000 6831 0 0 1 6831 518794057 518787227 0.000000e+00 12615.0
1 TraesCS6A01G286700 chr6A 90.887 406 37 0 1 406 497458836 497459241 4.660000e-151 545.0
2 TraesCS6A01G286700 chr6A 78.165 632 102 27 3412 4030 578564984 578564376 3.010000e-98 370.0
3 TraesCS6A01G286700 chr6A 88.591 149 15 2 1353 1500 578565900 578565753 5.440000e-41 180.0
4 TraesCS6A01G286700 chr6D 94.625 3684 109 28 3182 6831 377346949 377343321 0.000000e+00 5624.0
5 TraesCS6A01G286700 chr6D 94.048 1529 42 17 614 2112 377349513 377348004 0.000000e+00 2274.0
6 TraesCS6A01G286700 chr6D 91.702 711 29 12 2396 3092 377348005 377347311 0.000000e+00 959.0
7 TraesCS6A01G286700 chr6D 95.043 464 20 2 4423 4885 24859155 24858694 0.000000e+00 726.0
8 TraesCS6A01G286700 chr6D 94.612 464 22 2 4423 4885 68064643 68065104 0.000000e+00 715.0
9 TraesCS6A01G286700 chr6D 94.915 118 4 1 3099 3214 377347073 377346956 4.210000e-42 183.0
10 TraesCS6A01G286700 chr6B 92.024 1843 72 26 880 2671 563492522 563490704 0.000000e+00 2519.0
11 TraesCS6A01G286700 chr6B 90.924 1840 123 17 4022 5834 563489164 563487342 0.000000e+00 2433.0
12 TraesCS6A01G286700 chr6B 95.277 847 26 8 3182 4024 563490237 563489401 0.000000e+00 1330.0
13 TraesCS6A01G286700 chr6B 90.278 432 31 6 6409 6831 563486051 563485622 7.740000e-154 555.0
14 TraesCS6A01G286700 chr6B 92.532 308 17 2 2797 3098 563490707 563490400 2.930000e-118 436.0
15 TraesCS6A01G286700 chr6B 96.610 118 1 2 3099 3214 563490360 563490244 6.990000e-45 193.0
16 TraesCS6A01G286700 chr6B 89.691 97 6 4 755 847 563492858 563492762 3.350000e-23 121.0
17 TraesCS6A01G286700 chr1D 81.124 2670 326 95 3189 5746 298647780 298645177 0.000000e+00 1975.0
18 TraesCS6A01G286700 chr1D 78.711 1691 187 69 883 2516 298649889 298648315 0.000000e+00 968.0
19 TraesCS6A01G286700 chr1D 95.690 464 17 2 4423 4885 83711844 83712305 0.000000e+00 743.0
20 TraesCS6A01G286700 chr1B 83.079 1442 162 53 3358 4769 402109682 402108293 0.000000e+00 1236.0
21 TraesCS6A01G286700 chr1B 82.445 1088 117 36 883 1949 402113878 402112844 0.000000e+00 883.0
22 TraesCS6A01G286700 chr1B 83.402 729 83 14 4755 5463 402104995 402104285 5.780000e-180 641.0
23 TraesCS6A01G286700 chr1B 88.816 152 14 3 2931 3080 632021068 632020918 4.210000e-42 183.0
24 TraesCS6A01G286700 chr1B 85.484 62 8 1 1438 1499 35183041 35183101 5.720000e-06 63.9
25 TraesCS6A01G286700 chr1A 82.725 1314 158 45 3189 4464 372552707 372551425 0.000000e+00 1105.0
26 TraesCS6A01G286700 chr1A 82.621 1030 134 19 4473 5463 372551236 372550213 0.000000e+00 869.0
27 TraesCS6A01G286700 chr1A 80.672 1071 114 54 883 1942 372554931 372553943 0.000000e+00 745.0
28 TraesCS6A01G286700 chr1A 83.110 598 78 14 3 596 432517225 432517803 2.180000e-144 523.0
29 TraesCS6A01G286700 chr1A 75.403 248 37 14 5503 5746 372550040 372549813 1.570000e-16 99.0
30 TraesCS6A01G286700 chr3A 89.000 600 64 2 1 598 76202582 76203181 0.000000e+00 741.0
31 TraesCS6A01G286700 chr3A 80.467 599 97 8 1 598 623992265 623991686 2.260000e-119 440.0
32 TraesCS6A01G286700 chr7D 95.474 464 18 2 4423 4885 562979124 562979585 0.000000e+00 737.0
33 TraesCS6A01G286700 chr7D 83.028 601 79 10 1 598 83852456 83853036 2.180000e-144 523.0
34 TraesCS6A01G286700 chr7D 88.667 150 16 1 2924 3072 34373321 34373470 1.510000e-41 182.0
35 TraesCS6A01G286700 chr3D 95.474 464 18 2 4423 4885 594563834 594564295 0.000000e+00 737.0
36 TraesCS6A01G286700 chr3D 82.947 604 76 16 1 598 352946045 352945463 2.820000e-143 520.0
37 TraesCS6A01G286700 chr5D 95.043 464 20 2 4423 4885 501366640 501366179 0.000000e+00 726.0
38 TraesCS6A01G286700 chr4D 94.181 464 24 2 4423 4885 500241530 500241991 0.000000e+00 704.0
39 TraesCS6A01G286700 chr5A 86.184 608 72 5 1 598 603780796 603780191 0.000000e+00 647.0
40 TraesCS6A01G286700 chr5A 82.130 554 77 11 3 553 557070793 557071327 8.080000e-124 455.0
41 TraesCS6A01G286700 chr5A 80.952 189 32 4 1244 1431 602478142 602478327 5.520000e-31 147.0
42 TraesCS6A01G286700 chr7A 83.195 601 79 10 1 598 83718712 83719293 1.300000e-146 531.0
43 TraesCS6A01G286700 chr7A 81.636 599 88 11 3 598 711960048 711960627 1.720000e-130 477.0
44 TraesCS6A01G286700 chr4A 80.131 609 89 13 3 598 606406775 606406186 6.330000e-115 425.0
45 TraesCS6A01G286700 chr3B 76.294 831 141 38 3412 4231 463470238 463469453 6.420000e-105 392.0
46 TraesCS6A01G286700 chr2B 91.946 149 12 0 2924 3072 288939774 288939922 6.940000e-50 209.0
47 TraesCS6A01G286700 chr4B 89.333 150 15 1 2924 3072 438375184 438375333 3.250000e-43 187.0
48 TraesCS6A01G286700 chr2D 87.898 157 16 2 2919 3072 79056163 79056319 1.510000e-41 182.0
49 TraesCS6A01G286700 chr2D 88.667 150 16 1 2924 3072 617101064 617101213 1.510000e-41 182.0
50 TraesCS6A01G286700 chr2D 85.000 80 10 2 1423 1501 18621862 18621784 5.680000e-11 80.5
51 TraesCS6A01G286700 chr7B 87.342 158 18 2 2924 3080 505937317 505937473 5.440000e-41 180.0


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 TraesCS6A01G286700 chr6A 518787227 518794057 6830 True 12615.000000 12615 100.000000 1 6831 1 chr6A.!!$R1 6830
1 TraesCS6A01G286700 chr6A 578564376 578565900 1524 True 275.000000 370 83.378000 1353 4030 2 chr6A.!!$R2 2677
2 TraesCS6A01G286700 chr6D 377343321 377349513 6192 True 2260.000000 5624 93.822500 614 6831 4 chr6D.!!$R2 6217
3 TraesCS6A01G286700 chr6B 563485622 563492858 7236 True 1083.857143 2519 92.476571 755 6831 7 chr6B.!!$R1 6076
4 TraesCS6A01G286700 chr1D 298645177 298649889 4712 True 1471.500000 1975 79.917500 883 5746 2 chr1D.!!$R1 4863
5 TraesCS6A01G286700 chr1B 402104285 402113878 9593 True 920.000000 1236 82.975333 883 5463 3 chr1B.!!$R2 4580
6 TraesCS6A01G286700 chr1A 372549813 372554931 5118 True 704.500000 1105 80.355250 883 5746 4 chr1A.!!$R1 4863
7 TraesCS6A01G286700 chr1A 432517225 432517803 578 False 523.000000 523 83.110000 3 596 1 chr1A.!!$F1 593
8 TraesCS6A01G286700 chr3A 76202582 76203181 599 False 741.000000 741 89.000000 1 598 1 chr3A.!!$F1 597
9 TraesCS6A01G286700 chr3A 623991686 623992265 579 True 440.000000 440 80.467000 1 598 1 chr3A.!!$R1 597
10 TraesCS6A01G286700 chr7D 83852456 83853036 580 False 523.000000 523 83.028000 1 598 1 chr7D.!!$F2 597
11 TraesCS6A01G286700 chr3D 352945463 352946045 582 True 520.000000 520 82.947000 1 598 1 chr3D.!!$R1 597
12 TraesCS6A01G286700 chr5A 603780191 603780796 605 True 647.000000 647 86.184000 1 598 1 chr5A.!!$R1 597
13 TraesCS6A01G286700 chr5A 557070793 557071327 534 False 455.000000 455 82.130000 3 553 1 chr5A.!!$F1 550
14 TraesCS6A01G286700 chr7A 83718712 83719293 581 False 531.000000 531 83.195000 1 598 1 chr7A.!!$F1 597
15 TraesCS6A01G286700 chr7A 711960048 711960627 579 False 477.000000 477 81.636000 3 598 1 chr7A.!!$F2 595
16 TraesCS6A01G286700 chr4A 606406186 606406775 589 True 425.000000 425 80.131000 3 598 1 chr4A.!!$R1 595
17 TraesCS6A01G286700 chr3B 463469453 463470238 785 True 392.000000 392 76.294000 3412 4231 1 chr3B.!!$R1 819

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
637 673 0.100682 TCTCTCAACGCTACGCATCC 59.899 55.000 0.00 0.0 0.0 3.51 F
1058 1309 1.470051 CCCAACCATAAAACCCGAGG 58.530 55.000 0.00 0.0 0.0 4.63 F
2112 2410 1.062525 GGCCATGCGTGTCGAATTC 59.937 57.895 4.96 0.0 0.0 2.17 F
2206 2505 0.687920 TATTTGGCTCACACCGTCCA 59.312 50.000 0.00 0.0 0.0 4.02 F
2536 2929 1.276705 TGCCGTCTGTATTGGTTAGCA 59.723 47.619 0.00 0.0 0.0 3.49 F
2819 5057 4.378774 TGATTTGTTTGGTGCATTTGAGG 58.621 39.130 0.00 0.0 0.0 3.86 F
4455 7441 0.175531 AAAAACTGCCTGGTGTGTGC 59.824 50.000 0.00 0.0 0.0 4.57 F
5212 11734 0.990374 ATTCCAGCTGAGCAGAACCT 59.010 50.000 17.39 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1860 0.179234 TTCCACTGCGAAGAACCACA 59.821 50.000 0.00 0.0 0.00 4.17 R
2206 2505 1.065199 TGGAGCGAGAATCCAGCAATT 60.065 47.619 0.00 0.0 41.96 2.32 R
3294 5985 1.615392 AGGCAGGAAAGCAACATGAAC 59.385 47.619 0.00 0.0 35.83 3.18 R
3416 6131 5.940470 ACACATGGGAAAGTCTTGTCTATTC 59.060 40.000 0.00 0.0 0.00 1.75 R
4379 7359 2.928801 ATGATGTATAAGCACGGCCA 57.071 45.000 2.24 0.0 0.00 5.36 R
4535 7701 2.977808 TCCATCCCAGTATCTTCCCTC 58.022 52.381 0.00 0.0 0.00 4.30 R
5506 12167 0.749649 GTCGCCATCTCCAGATCAGT 59.250 55.000 0.00 0.0 31.21 3.41 R
6790 14204 0.875059 GGGAGGCAAAACAGAAGTCG 59.125 55.000 0.00 0.0 0.00 4.18 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
81 82 2.046009 TACCTCAACCACTGGCGCAA 62.046 55.000 10.83 0.00 0.00 4.85
216 217 3.592814 CGACATCGCCGCCCTCTA 61.593 66.667 0.00 0.00 0.00 2.43
237 238 3.622826 CACGACGTTCCCCTGGGT 61.623 66.667 12.71 0.00 36.47 4.51
305 318 4.796231 CCGCCGACGAGGACAAGG 62.796 72.222 0.00 0.23 45.00 3.61
306 319 3.744719 CGCCGACGAGGACAAGGA 61.745 66.667 0.00 0.00 45.00 3.36
307 320 2.126031 GCCGACGAGGACAAGGAC 60.126 66.667 0.00 0.00 45.00 3.85
308 321 2.178521 CCGACGAGGACAAGGACG 59.821 66.667 0.00 0.00 45.00 4.79
471 495 5.943706 TTTTCCACGTCGATAAAAATGGA 57.056 34.783 0.00 0.00 34.44 3.41
478 513 3.558418 CGTCGATAAAAATGGATCGGGTT 59.442 43.478 4.62 0.00 44.01 4.11
485 520 5.456548 AAAAATGGATCGGGTTAACGTTT 57.543 34.783 5.91 0.00 34.94 3.60
493 528 2.297033 TCGGGTTAACGTTTAGCACTCT 59.703 45.455 17.07 0.00 34.94 3.24
528 563 3.928992 CACGATAGCAGATGTTTGTGTCT 59.071 43.478 0.00 0.00 42.67 3.41
544 580 0.462047 GTCTGCCGATCGACCCAAAT 60.462 55.000 18.66 0.00 0.00 2.32
546 582 0.461870 CTGCCGATCGACCCAAATGA 60.462 55.000 18.66 0.00 0.00 2.57
573 609 0.652071 ACGAACAAAAACGTCGTCCC 59.348 50.000 0.00 0.00 38.34 4.46
586 622 3.647771 GTCCCTTTGGGTCGCCCT 61.648 66.667 14.76 0.00 45.70 5.19
598 634 2.179018 CGCCCTGTTGGATTTGCG 59.821 61.111 0.00 0.00 34.92 4.85
599 635 2.625823 CGCCCTGTTGGATTTGCGT 61.626 57.895 0.00 0.00 36.19 5.24
600 636 1.302383 CGCCCTGTTGGATTTGCGTA 61.302 55.000 0.00 0.00 36.19 4.42
601 637 0.170339 GCCCTGTTGGATTTGCGTAC 59.830 55.000 0.00 0.00 35.39 3.67
602 638 1.821216 CCCTGTTGGATTTGCGTACT 58.179 50.000 0.00 0.00 35.39 2.73
603 639 2.937873 GCCCTGTTGGATTTGCGTACTA 60.938 50.000 0.00 0.00 35.39 1.82
604 640 3.541632 CCCTGTTGGATTTGCGTACTAT 58.458 45.455 0.00 0.00 35.39 2.12
605 641 3.312421 CCCTGTTGGATTTGCGTACTATG 59.688 47.826 0.00 0.00 35.39 2.23
606 642 3.312421 CCTGTTGGATTTGCGTACTATGG 59.688 47.826 0.00 0.00 34.57 2.74
607 643 3.275143 TGTTGGATTTGCGTACTATGGG 58.725 45.455 0.00 0.00 0.00 4.00
608 644 3.275999 GTTGGATTTGCGTACTATGGGT 58.724 45.455 0.00 0.00 0.00 4.51
609 645 2.912771 TGGATTTGCGTACTATGGGTG 58.087 47.619 0.00 0.00 0.00 4.61
610 646 2.218603 GGATTTGCGTACTATGGGTGG 58.781 52.381 0.00 0.00 0.00 4.61
611 647 2.218603 GATTTGCGTACTATGGGTGGG 58.781 52.381 0.00 0.00 0.00 4.61
612 648 0.985760 TTTGCGTACTATGGGTGGGT 59.014 50.000 0.00 0.00 0.00 4.51
625 661 2.225522 TGGGTGGGTGTAGATCTCTCAA 60.226 50.000 0.00 0.00 0.00 3.02
630 666 2.950309 GGGTGTAGATCTCTCAACGCTA 59.050 50.000 0.00 0.00 0.00 4.26
631 667 3.243134 GGGTGTAGATCTCTCAACGCTAC 60.243 52.174 0.00 0.00 33.76 3.58
637 673 0.100682 TCTCTCAACGCTACGCATCC 59.899 55.000 0.00 0.00 0.00 3.51
674 710 7.492352 ACGAGCATAGGAAAATATTGGTAAC 57.508 36.000 0.00 0.00 0.00 2.50
678 714 6.017109 AGCATAGGAAAATATTGGTAACTGCG 60.017 38.462 0.00 0.00 37.61 5.18
1034 1285 2.747855 CCTCCCGCAAGAACAGCC 60.748 66.667 0.00 0.00 43.02 4.85
1035 1286 2.747855 CTCCCGCAAGAACAGCCC 60.748 66.667 0.00 0.00 43.02 5.19
1036 1287 4.697756 TCCCGCAAGAACAGCCCG 62.698 66.667 0.00 0.00 43.02 6.13
1058 1309 1.470051 CCCAACCATAAAACCCGAGG 58.530 55.000 0.00 0.00 0.00 4.63
1590 1860 8.537016 TCTGGTATGCTAGTGTTGTTTTAGTAT 58.463 33.333 0.00 0.00 0.00 2.12
1591 1861 8.487313 TGGTATGCTAGTGTTGTTTTAGTATG 57.513 34.615 0.00 0.00 0.00 2.39
1597 1867 7.041644 TGCTAGTGTTGTTTTAGTATGTGGTTC 60.042 37.037 0.00 0.00 0.00 3.62
1636 1906 1.362406 GCTGGTTGCTCCGAGCTTAC 61.362 60.000 20.87 17.11 42.97 2.34
1684 1959 5.881447 ACTTGCTCGAGTTACTGTACTATG 58.119 41.667 15.13 0.00 0.00 2.23
1755 2042 3.005472 CAGGAGATCGCGACCCTTAAATA 59.995 47.826 12.93 0.00 0.00 1.40
1756 2043 3.833070 AGGAGATCGCGACCCTTAAATAT 59.167 43.478 12.93 0.00 0.00 1.28
1757 2044 4.283722 AGGAGATCGCGACCCTTAAATATT 59.716 41.667 12.93 0.00 0.00 1.28
1758 2045 5.479375 AGGAGATCGCGACCCTTAAATATTA 59.521 40.000 12.93 0.00 0.00 0.98
1917 2206 5.822519 TGCCAATTATGTCTGTAGATTGGTC 59.177 40.000 13.18 7.64 45.32 4.02
1918 2207 5.050091 GCCAATTATGTCTGTAGATTGGTCG 60.050 44.000 13.18 0.00 45.32 4.79
1919 2208 5.466728 CCAATTATGTCTGTAGATTGGTCGG 59.533 44.000 5.48 0.00 41.00 4.79
1920 2209 5.871396 ATTATGTCTGTAGATTGGTCGGT 57.129 39.130 0.00 0.00 0.00 4.69
2093 2391 5.297547 CCCACATTCTAGCGTGTGTATATT 58.702 41.667 19.40 0.00 43.14 1.28
2112 2410 1.062525 GGCCATGCGTGTCGAATTC 59.937 57.895 4.96 0.00 0.00 2.17
2206 2505 0.687920 TATTTGGCTCACACCGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
2224 2523 2.752144 CAATTGCTGGATTCTCGCTC 57.248 50.000 0.00 0.00 0.00 5.03
2359 2717 5.046014 GTCCATCTGGCTCTGATAATATGGT 60.046 44.000 0.00 0.00 35.29 3.55
2380 2738 7.406031 TGGTTTTGTTTAAATCCACACACTA 57.594 32.000 0.00 0.00 39.53 2.74
2535 2928 2.018542 TGCCGTCTGTATTGGTTAGC 57.981 50.000 0.00 0.00 0.00 3.09
2536 2929 1.276705 TGCCGTCTGTATTGGTTAGCA 59.723 47.619 0.00 0.00 0.00 3.49
2584 2983 6.069994 TGAAATCATATGGTGGTATGTGCAT 58.930 36.000 2.13 0.00 34.44 3.96
2591 2990 5.772825 ATGGTGGTATGTGCATTAATGTC 57.227 39.130 16.61 9.60 0.00 3.06
2595 2994 5.008019 GGTGGTATGTGCATTAATGTCTCTG 59.992 44.000 16.61 0.00 0.00 3.35
2729 4870 8.218423 AGGGGACATTGATTGTGTGATATATA 57.782 34.615 0.00 0.00 39.18 0.86
2819 5057 4.378774 TGATTTGTTTGGTGCATTTGAGG 58.621 39.130 0.00 0.00 0.00 3.86
2938 5182 6.070656 CCCATATGTTCCCTATGTTCACAAT 58.929 40.000 1.24 0.00 0.00 2.71
2982 5226 9.996554 TTTTGTGAATCGGATGTATATAGACAT 57.003 29.630 12.70 12.70 42.82 3.06
3384 6089 6.579666 ATGTGATTTGTGCTTACAGACAAT 57.420 33.333 0.00 0.00 32.27 2.71
3395 6110 6.480320 GTGCTTACAGACAATCCACCTTATAG 59.520 42.308 0.00 0.00 0.00 1.31
3398 6113 7.490657 TTACAGACAATCCACCTTATAGTGT 57.509 36.000 0.00 0.00 35.93 3.55
3399 6114 5.978814 ACAGACAATCCACCTTATAGTGTC 58.021 41.667 0.00 0.00 38.22 3.67
3400 6115 5.721960 ACAGACAATCCACCTTATAGTGTCT 59.278 40.000 0.00 0.00 46.17 3.41
3401 6116 6.895756 ACAGACAATCCACCTTATAGTGTCTA 59.104 38.462 4.58 0.00 44.18 2.59
3402 6117 7.147880 ACAGACAATCCACCTTATAGTGTCTAC 60.148 40.741 4.58 0.00 44.18 2.59
3403 6118 7.068839 CAGACAATCCACCTTATAGTGTCTACT 59.931 40.741 4.58 0.00 44.18 2.57
3404 6119 7.068839 AGACAATCCACCTTATAGTGTCTACTG 59.931 40.741 3.14 0.00 44.17 2.74
3405 6120 6.668283 ACAATCCACCTTATAGTGTCTACTGT 59.332 38.462 0.00 0.00 37.78 3.55
3406 6121 6.963083 ATCCACCTTATAGTGTCTACTGTC 57.037 41.667 0.00 0.00 37.78 3.51
3605 6332 8.801715 TGCAAAGAAATAAACATTCAGTCTTC 57.198 30.769 0.00 0.00 0.00 2.87
3612 6339 9.358872 GAAATAAACATTCAGTCTTCCCATTTC 57.641 33.333 0.00 0.00 0.00 2.17
3613 6340 8.655935 AATAAACATTCAGTCTTCCCATTTCT 57.344 30.769 0.00 0.00 0.00 2.52
3614 6341 9.753674 AATAAACATTCAGTCTTCCCATTTCTA 57.246 29.630 0.00 0.00 0.00 2.10
4255 7232 8.774890 TTAATCCATTCCATGTGTTGATTTTG 57.225 30.769 0.00 0.00 0.00 2.44
4259 7236 6.718912 TCCATTCCATGTGTTGATTTTGACTA 59.281 34.615 0.00 0.00 0.00 2.59
4348 7328 9.757227 GAGTACTATTAGCATTTTCAGATCTGT 57.243 33.333 21.92 3.86 0.00 3.41
4379 7359 4.774726 TCTCTTGCTGTTCTATCTGGACTT 59.225 41.667 0.00 0.00 0.00 3.01
4382 7362 2.284190 GCTGTTCTATCTGGACTTGGC 58.716 52.381 0.00 0.00 0.00 4.52
4455 7441 0.175531 AAAAACTGCCTGGTGTGTGC 59.824 50.000 0.00 0.00 0.00 4.57
4496 7662 7.063544 GCCTATAGCACTGGTTAATCTATTTCG 59.936 40.741 0.00 0.00 42.97 3.46
4578 7744 5.474578 AGTCTGTCACTGATGCTTCTTTA 57.525 39.130 0.88 0.00 32.26 1.85
4593 7763 7.251704 TGCTTCTTTACTTGAGCATTATAGC 57.748 36.000 0.00 0.00 0.00 2.97
4842 11333 8.830915 TGCAAGGAAACCAATAATAAAGGATA 57.169 30.769 0.00 0.00 0.00 2.59
4843 11334 9.432982 TGCAAGGAAACCAATAATAAAGGATAT 57.567 29.630 0.00 0.00 0.00 1.63
4951 11453 3.193479 CCAAATACCCCTCTTTCAAGTGC 59.807 47.826 0.00 0.00 0.00 4.40
4963 11465 5.053811 TCTTTCAAGTGCGATTCTTACACA 58.946 37.500 0.00 0.00 36.76 3.72
5048 11555 2.632377 CTTAGGCACATGACGAATGGT 58.368 47.619 0.00 0.00 40.94 3.55
5103 11610 2.886523 CCTGAAGCAAATGGAACTGACA 59.113 45.455 0.00 0.00 0.00 3.58
5187 11709 2.490903 CTGCCAGAAGGAAAACAGGATG 59.509 50.000 0.00 0.00 39.04 3.51
5212 11734 0.990374 ATTCCAGCTGAGCAGAACCT 59.010 50.000 17.39 0.00 0.00 3.50
5344 11869 1.066002 CACCACTCTTGCTGTTGTTGG 59.934 52.381 0.00 0.00 0.00 3.77
5572 12238 6.271391 TCCTCATGTGAAACTCCTAGGTTTTA 59.729 38.462 9.08 0.00 39.20 1.52
5754 12424 5.695851 TTTGGAAGCACAAAATCTCTCTC 57.304 39.130 0.00 0.00 37.40 3.20
5789 12459 2.257286 CTTGCGGAATCAACTGCCCG 62.257 60.000 0.00 0.00 44.34 6.13
5835 12519 5.100751 GCATTTAGCAGCTCGATGTTATT 57.899 39.130 15.65 0.00 44.79 1.40
5920 12846 4.003648 GGCAAACACTAACATGACTAGCT 58.996 43.478 0.00 0.00 0.00 3.32
6020 13006 3.853671 GGAAGCTGTTTGATTATGTTGCG 59.146 43.478 0.00 0.00 0.00 4.85
6091 13083 0.950555 TTCTGGATCGTGTGTGCAGC 60.951 55.000 0.00 0.00 35.32 5.25
6149 13144 7.518689 GCATAGTGAGAAATGAGCAATCTCTTC 60.519 40.741 14.00 9.34 40.18 2.87
6175 13170 2.218953 TCAGACCAGACGTTGTTGTC 57.781 50.000 0.00 0.00 39.21 3.18
6176 13171 1.202486 TCAGACCAGACGTTGTTGTCC 60.202 52.381 0.00 0.00 39.77 4.02
6177 13172 0.106149 AGACCAGACGTTGTTGTCCC 59.894 55.000 0.00 0.00 39.77 4.46
6195 13194 9.521841 TGTTGTCCCAAAGTATATGATTACAAA 57.478 29.630 0.00 0.00 0.00 2.83
6236 13238 9.859427 ATGTATCACAGTTAAATTCATGTTTGG 57.141 29.630 0.00 0.00 0.00 3.28
6253 13255 2.605837 TGGTACGTGCAAAAGAGACA 57.394 45.000 5.86 0.00 0.00 3.41
6504 13910 7.012421 GCCCAGAACAACATTTAGTAATAGGAG 59.988 40.741 0.00 0.00 0.00 3.69
6509 13915 6.281405 ACAACATTTAGTAATAGGAGCCTCG 58.719 40.000 0.00 0.00 0.00 4.63
6555 13961 8.088981 TGAGAAAAACTAGAATAGACTGGTCAC 58.911 37.037 0.00 0.00 42.77 3.67
6557 13963 7.873505 AGAAAAACTAGAATAGACTGGTCACAC 59.126 37.037 0.00 0.00 42.77 3.82
6627 14039 5.518487 CACTTCCAGCGTACAACAAAATTTT 59.482 36.000 0.00 0.00 0.00 1.82
6743 14155 9.838339 TTTAAATCTCCTCTTCTAAGGCTAATG 57.162 33.333 0.00 0.00 36.29 1.90
6744 14156 7.444703 AAATCTCCTCTTCTAAGGCTAATGT 57.555 36.000 0.00 0.00 36.29 2.71
6745 14157 5.860941 TCTCCTCTTCTAAGGCTAATGTG 57.139 43.478 0.00 0.00 36.29 3.21
6746 14158 4.651503 TCTCCTCTTCTAAGGCTAATGTGG 59.348 45.833 0.00 0.00 36.29 4.17
6747 14159 3.134804 TCCTCTTCTAAGGCTAATGTGGC 59.865 47.826 0.00 0.00 36.29 5.01
6762 14176 1.980765 TGTGGCTCTCTCTTGAACCAT 59.019 47.619 0.00 0.00 0.00 3.55
6768 14182 4.335037 GGCTCTCTCTTGAACCATCAATTC 59.665 45.833 0.00 0.00 44.29 2.17
6770 14184 5.647225 GCTCTCTCTTGAACCATCAATTCTT 59.353 40.000 0.00 0.00 44.29 2.52
6790 14204 5.131784 TCTTATACCTTCGTCCTCTTCTCC 58.868 45.833 0.00 0.00 0.00 3.71
6825 14239 5.826643 TGCCTCCCTGTCAATAGTAAAATT 58.173 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
458 482 5.234757 CGTTAACCCGATCCATTTTTATCGA 59.765 40.000 6.31 0.00 46.08 3.59
471 495 3.056322 AGAGTGCTAAACGTTAACCCGAT 60.056 43.478 0.00 0.00 0.00 4.18
493 528 0.880441 TATCGTGTTTGGGTCGACGA 59.120 50.000 9.92 1.42 44.27 4.20
528 563 0.035915 TTCATTTGGGTCGATCGGCA 60.036 50.000 22.85 0.03 0.00 5.69
544 580 5.213675 ACGTTTTTGTTCGTCTTTTGTTCA 58.786 33.333 0.00 0.00 35.30 3.18
583 619 1.821216 AGTACGCAAATCCAACAGGG 58.179 50.000 0.00 0.00 38.37 4.45
586 622 3.275143 CCCATAGTACGCAAATCCAACA 58.725 45.455 0.00 0.00 0.00 3.33
598 634 4.481072 AGATCTACACCCACCCATAGTAC 58.519 47.826 0.00 0.00 0.00 2.73
599 635 4.419200 AGAGATCTACACCCACCCATAGTA 59.581 45.833 0.00 0.00 0.00 1.82
600 636 3.207777 AGAGATCTACACCCACCCATAGT 59.792 47.826 0.00 0.00 0.00 2.12
601 637 3.829601 GAGAGATCTACACCCACCCATAG 59.170 52.174 0.00 0.00 0.00 2.23
602 638 3.206639 TGAGAGATCTACACCCACCCATA 59.793 47.826 0.00 0.00 0.00 2.74
603 639 2.023015 TGAGAGATCTACACCCACCCAT 60.023 50.000 0.00 0.00 0.00 4.00
604 640 1.361197 TGAGAGATCTACACCCACCCA 59.639 52.381 0.00 0.00 0.00 4.51
605 641 2.160721 TGAGAGATCTACACCCACCC 57.839 55.000 0.00 0.00 0.00 4.61
606 642 2.159226 CGTTGAGAGATCTACACCCACC 60.159 54.545 0.00 0.00 0.00 4.61
607 643 2.735762 GCGTTGAGAGATCTACACCCAC 60.736 54.545 0.00 0.00 0.00 4.61
608 644 1.476891 GCGTTGAGAGATCTACACCCA 59.523 52.381 0.00 0.00 0.00 4.51
609 645 1.751924 AGCGTTGAGAGATCTACACCC 59.248 52.381 0.00 0.00 0.00 4.61
610 646 3.546417 CGTAGCGTTGAGAGATCTACACC 60.546 52.174 0.00 0.00 32.24 4.16
611 647 3.609475 CGTAGCGTTGAGAGATCTACAC 58.391 50.000 0.00 0.00 32.24 2.90
612 648 3.946308 CGTAGCGTTGAGAGATCTACA 57.054 47.619 0.00 0.00 32.24 2.74
630 666 2.472695 TTCAACAAGCTAGGATGCGT 57.527 45.000 0.00 0.00 38.13 5.24
631 667 2.474526 CGTTTCAACAAGCTAGGATGCG 60.475 50.000 0.00 0.00 38.13 4.73
637 673 4.033358 CCTATGCTCGTTTCAACAAGCTAG 59.967 45.833 4.34 4.02 39.62 3.42
655 691 7.490962 TCGCAGTTACCAATATTTTCCTATG 57.509 36.000 0.00 0.00 0.00 2.23
659 695 6.038271 AGTGATCGCAGTTACCAATATTTTCC 59.962 38.462 9.33 0.00 0.00 3.13
660 696 7.016361 AGTGATCGCAGTTACCAATATTTTC 57.984 36.000 9.33 0.00 0.00 2.29
750 787 1.704641 TACGCTGTAGATCTGGCCAT 58.295 50.000 5.51 0.00 0.00 4.40
837 874 2.046009 TAGTGTTTGCGAGTGGGGCA 62.046 55.000 0.00 0.00 38.93 5.36
838 875 1.298859 CTAGTGTTTGCGAGTGGGGC 61.299 60.000 0.00 0.00 0.00 5.80
839 876 0.034896 ACTAGTGTTTGCGAGTGGGG 59.965 55.000 0.00 0.00 0.00 4.96
843 880 0.944311 CGCCACTAGTGTTTGCGAGT 60.944 55.000 29.54 0.00 43.36 4.18
847 1071 1.332375 TGTTTCGCCACTAGTGTTTGC 59.668 47.619 21.18 15.86 0.00 3.68
949 1198 1.602377 CAGTGAGGTTTGGGTTTCGTC 59.398 52.381 0.00 0.00 0.00 4.20
1034 1285 1.609635 GGTTTTATGGTTGGGGGCGG 61.610 60.000 0.00 0.00 0.00 6.13
1035 1286 1.609635 GGGTTTTATGGTTGGGGGCG 61.610 60.000 0.00 0.00 0.00 6.13
1036 1287 1.609635 CGGGTTTTATGGTTGGGGGC 61.610 60.000 0.00 0.00 0.00 5.80
1037 1288 0.039911 TCGGGTTTTATGGTTGGGGG 59.960 55.000 0.00 0.00 0.00 5.40
1058 1309 1.540435 TTGGGGGAAATGGAAAGCGC 61.540 55.000 0.00 0.00 0.00 5.92
1590 1860 0.179234 TTCCACTGCGAAGAACCACA 59.821 50.000 0.00 0.00 0.00 4.17
1591 1861 1.002792 GTTTCCACTGCGAAGAACCAC 60.003 52.381 0.00 0.00 0.00 4.16
1636 1906 5.275326 CGAAAACTAGTCGTCAGCTAAATCG 60.275 44.000 0.00 0.00 33.80 3.34
1648 1918 3.955887 GAGCAAGTCGAAAACTAGTCG 57.044 47.619 0.00 0.00 37.17 4.18
1684 1959 7.234384 CAGACAACCAAATCGAACTACATAAC 58.766 38.462 0.00 0.00 0.00 1.89
1755 2042 7.094162 ACACTGATCGGATCGACTGATTATAAT 60.094 37.037 9.00 0.00 43.77 1.28
1756 2043 6.206829 ACACTGATCGGATCGACTGATTATAA 59.793 38.462 9.00 0.00 43.77 0.98
1757 2044 5.705905 ACACTGATCGGATCGACTGATTATA 59.294 40.000 9.00 0.00 43.77 0.98
1758 2045 4.520874 ACACTGATCGGATCGACTGATTAT 59.479 41.667 9.00 0.00 43.77 1.28
1776 2063 0.611200 TACATCGTCCCCCAACACTG 59.389 55.000 0.00 0.00 0.00 3.66
1777 2064 0.902531 CTACATCGTCCCCCAACACT 59.097 55.000 0.00 0.00 0.00 3.55
1917 2206 6.780706 ACAAAATTAAGTACAGAGACACCG 57.219 37.500 0.00 0.00 0.00 4.94
1918 2207 7.288672 CGAACAAAATTAAGTACAGAGACACC 58.711 38.462 0.00 0.00 0.00 4.16
1919 2208 6.790825 GCGAACAAAATTAAGTACAGAGACAC 59.209 38.462 0.00 0.00 0.00 3.67
1920 2209 6.480651 TGCGAACAAAATTAAGTACAGAGACA 59.519 34.615 0.00 0.00 0.00 3.41
2093 2391 1.643868 GAATTCGACACGCATGGCCA 61.644 55.000 8.56 8.56 0.00 5.36
2112 2410 6.152661 ACATATAAACACCAAATCACCACCAG 59.847 38.462 0.00 0.00 0.00 4.00
2206 2505 1.065199 TGGAGCGAGAATCCAGCAATT 60.065 47.619 0.00 0.00 41.96 2.32
2241 2540 6.587990 CGACTATATTAGCACTGGAAATGGAG 59.412 42.308 0.00 0.00 0.00 3.86
2535 2928 8.658609 CAAAGGTTCAAAGGTGCATTATAAATG 58.341 33.333 0.00 0.00 0.00 2.32
2536 2929 8.592809 TCAAAGGTTCAAAGGTGCATTATAAAT 58.407 29.630 0.00 0.00 0.00 1.40
2584 2983 6.271391 TCCTAAAGGGTGAACAGAGACATTAA 59.729 38.462 0.00 0.00 36.25 1.40
2591 2990 4.160626 CCTAGTCCTAAAGGGTGAACAGAG 59.839 50.000 0.00 0.00 36.25 3.35
2595 2994 3.118702 GCTCCTAGTCCTAAAGGGTGAAC 60.119 52.174 0.00 0.00 36.25 3.18
2982 5226 6.993786 TGAGTGAACAAACACATTAGAACA 57.006 33.333 0.00 0.00 42.45 3.18
2989 5233 9.897744 CATACTTAAATGAGTGAACAAACACAT 57.102 29.630 0.00 0.00 42.45 3.21
3013 5257 9.466497 GGATATTTCAATATGGTCCACATACAT 57.534 33.333 0.00 0.00 44.41 2.29
3021 5265 9.696917 GATGTTTTGGATATTTCAATATGGTCC 57.303 33.333 0.00 0.00 31.96 4.46
3056 5300 2.464796 TAATTACTCCCTCCGCTCCA 57.535 50.000 0.00 0.00 0.00 3.86
3057 5301 5.420409 CAATATAATTACTCCCTCCGCTCC 58.580 45.833 0.00 0.00 0.00 4.70
3135 5620 4.331168 CAGTAACACTAGATTGCCAGAAGC 59.669 45.833 0.00 0.00 44.14 3.86
3294 5985 1.615392 AGGCAGGAAAGCAACATGAAC 59.385 47.619 0.00 0.00 35.83 3.18
3384 6089 6.075949 AGACAGTAGACACTATAAGGTGGA 57.924 41.667 0.00 0.00 41.09 4.02
3416 6131 5.940470 ACACATGGGAAAGTCTTGTCTATTC 59.060 40.000 0.00 0.00 0.00 1.75
3453 6171 7.379750 AGAAAGTAGAACAGACCACTCATTAC 58.620 38.462 0.00 0.00 0.00 1.89
4348 7328 4.156455 AGAACAGCAAGAGAAAAGGACA 57.844 40.909 0.00 0.00 0.00 4.02
4379 7359 2.928801 ATGATGTATAAGCACGGCCA 57.071 45.000 2.24 0.00 0.00 5.36
4382 7362 7.315890 TCAGAATCTATGATGTATAAGCACGG 58.684 38.462 0.00 0.00 0.00 4.94
4521 7687 9.218525 AGTATCTTCCCTCAAATCAAGATTAGA 57.781 33.333 0.00 0.00 36.98 2.10
4522 7688 9.270640 CAGTATCTTCCCTCAAATCAAGATTAG 57.729 37.037 0.00 0.00 36.98 1.73
4532 7698 3.459598 CCATCCCAGTATCTTCCCTCAAA 59.540 47.826 0.00 0.00 0.00 2.69
4535 7701 2.977808 TCCATCCCAGTATCTTCCCTC 58.022 52.381 0.00 0.00 0.00 4.30
4578 7744 8.043710 AGTCTTACTTTGCTATAATGCTCAAGT 58.956 33.333 0.00 0.00 39.10 3.16
4593 7763 9.291664 GCTTATAGTCACAGTAGTCTTACTTTG 57.708 37.037 0.00 0.00 38.05 2.77
4750 7930 5.465056 CACCGCAAATAAACAAATCAAGGTT 59.535 36.000 0.00 0.00 0.00 3.50
4951 11453 5.292765 ACAGGATAGCATGTGTAAGAATCG 58.707 41.667 0.00 0.00 37.69 3.34
5048 11555 0.776810 TTGATTCTTCCCCAGCCACA 59.223 50.000 0.00 0.00 0.00 4.17
5187 11709 0.107800 TGCTCAGCTGGAATGCTCTC 60.108 55.000 15.13 0.00 41.98 3.20
5212 11734 3.011144 ACTCTCTGTCTTGGAGATCCTGA 59.989 47.826 0.00 0.00 38.85 3.86
5344 11869 2.449556 GAACACCGTTGCAGCAGCTC 62.450 60.000 7.73 0.00 42.74 4.09
5506 12167 0.749649 GTCGCCATCTCCAGATCAGT 59.250 55.000 0.00 0.00 31.21 3.41
5572 12238 1.934589 GCCAAGGCGTCAAAAACTTT 58.065 45.000 0.00 0.00 0.00 2.66
5754 12424 2.283617 CGCAAGTAGCAGATACAGCTTG 59.716 50.000 10.38 0.00 46.13 4.01
5789 12459 6.969473 GCAACAATTAGCAGAGGAAGTTTATC 59.031 38.462 0.00 0.00 0.00 1.75
5824 12508 9.507280 AAGCACATCAAATAAAATAACATCGAG 57.493 29.630 0.00 0.00 0.00 4.04
5828 12512 9.853555 TCGAAAGCACATCAAATAAAATAACAT 57.146 25.926 0.00 0.00 0.00 2.71
5829 12513 9.340695 CTCGAAAGCACATCAAATAAAATAACA 57.659 29.630 0.00 0.00 0.00 2.41
5830 12514 9.554724 TCTCGAAAGCACATCAAATAAAATAAC 57.445 29.630 0.00 0.00 0.00 1.89
5835 12519 7.552687 AGGTATCTCGAAAGCACATCAAATAAA 59.447 33.333 0.00 0.00 0.00 1.40
5889 12642 3.181434 TGTTAGTGTTTGCCAAGGGATCT 60.181 43.478 0.00 0.00 0.00 2.75
5894 12647 3.569701 AGTCATGTTAGTGTTTGCCAAGG 59.430 43.478 0.00 0.00 0.00 3.61
5953 12928 6.889198 TCTTTAGGATTAGACCCAATCTGTG 58.111 40.000 0.00 0.00 38.49 3.66
6020 13006 3.335579 ACGCAAATTTGGTCCTCTAGAC 58.664 45.455 19.47 0.00 45.51 2.59
6091 13083 4.970711 AGAGGCATAGATCAGGATTTGTG 58.029 43.478 0.00 0.00 0.00 3.33
6149 13144 3.243771 ACAACGTCTGGTCTGAAGGTAAG 60.244 47.826 0.00 0.00 0.00 2.34
6236 13238 4.026407 GTGTTTGTCTCTTTTGCACGTAC 58.974 43.478 0.00 0.00 0.00 3.67
6253 13255 4.712122 ACATTTGGAAACGTCTGTGTTT 57.288 36.364 0.00 1.54 44.36 2.83
6493 13899 3.484407 GACACCGAGGCTCCTATTACTA 58.516 50.000 9.32 0.00 0.00 1.82
6504 13910 2.509336 CGTCATGGACACCGAGGC 60.509 66.667 0.00 0.00 32.09 4.70
6509 13915 1.000955 AGTGAAGTCGTCATGGACACC 59.999 52.381 5.12 0.00 38.90 4.16
6606 14018 4.268884 GCAAAATTTTGTTGTACGCTGGAA 59.731 37.500 27.13 0.00 40.24 3.53
6627 14039 2.685897 GGTACAAGTTTGTGGTGAAGCA 59.314 45.455 7.73 0.00 42.31 3.91
6745 14157 3.340814 TTGATGGTTCAAGAGAGAGCC 57.659 47.619 0.00 0.00 36.94 4.70
6746 14158 5.184711 AGAATTGATGGTTCAAGAGAGAGC 58.815 41.667 0.00 0.00 44.75 4.09
6747 14159 8.961294 ATAAGAATTGATGGTTCAAGAGAGAG 57.039 34.615 0.00 0.00 44.75 3.20
6762 14176 7.342284 AGAAGAGGACGAAGGTATAAGAATTGA 59.658 37.037 0.00 0.00 0.00 2.57
6768 14182 4.023878 CGGAGAAGAGGACGAAGGTATAAG 60.024 50.000 0.00 0.00 0.00 1.73
6770 14184 3.135348 TCGGAGAAGAGGACGAAGGTATA 59.865 47.826 0.00 0.00 31.79 1.47
6790 14204 0.875059 GGGAGGCAAAACAGAAGTCG 59.125 55.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.