Multiple sequence alignment - TraesCS5D01G153500

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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 TraesCS5D01G153500 chr5D 100.000 3035 0 0 1 3035 242015488 242012454 0.000000e+00 5605.0
1 TraesCS5D01G153500 chr5B 93.699 1825 98 10 621 2439 257003183 257001370 0.000000e+00 2717.0
2 TraesCS5D01G153500 chr5B 86.789 598 56 15 2443 3035 257001435 257000856 0.000000e+00 645.0
3 TraesCS5D01G153500 chr5B 85.069 576 33 13 99 631 257003770 257003205 3.440000e-149 538.0
4 TraesCS5D01G153500 chr5B 79.231 130 23 4 2280 2408 489236199 489236073 1.500000e-13 87.9
5 TraesCS5D01G153500 chr5A 94.722 1724 58 13 580 2279 312233763 312232049 0.000000e+00 2649.0
6 TraesCS5D01G153500 chr5A 88.354 395 37 6 2642 3035 312231780 312231394 1.650000e-127 466.0
7 TraesCS5D01G153500 chr5A 86.641 262 19 8 114 361 312234050 312233791 2.980000e-70 276.0
8 TraesCS5D01G153500 chr2D 96.471 85 3 0 4 88 646042721 646042637 1.130000e-29 141.0
9 TraesCS5D01G153500 chr2D 95.402 87 4 0 4 90 106145568 106145482 4.080000e-29 139.0
10 TraesCS5D01G153500 chr2A 95.455 88 4 0 1 88 459017220 459017307 1.130000e-29 141.0
11 TraesCS5D01G153500 chr7B 95.402 87 3 1 1 87 162843855 162843940 1.470000e-28 137.0
12 TraesCS5D01G153500 chr6D 95.349 86 4 0 1 86 18495513 18495598 1.470000e-28 137.0
13 TraesCS5D01G153500 chr6D 93.548 93 3 3 5 95 336996832 336996741 5.280000e-28 135.0
14 TraesCS5D01G153500 chr3A 94.382 89 4 1 1 89 682358902 682358989 5.280000e-28 135.0
15 TraesCS5D01G153500 chr3A 73.333 255 50 15 1111 1353 574255401 574255649 9.020000e-11 78.7
16 TraesCS5D01G153500 chr1B 93.407 91 5 1 1 90 107070033 107070123 1.900000e-27 134.0
17 TraesCS5D01G153500 chr1B 75.540 278 52 14 1033 1302 551230600 551230331 4.110000e-24 122.0
18 TraesCS5D01G153500 chr1B 74.493 345 58 23 1033 1353 551233744 551233406 4.110000e-24 122.0
19 TraesCS5D01G153500 chr1B 80.000 120 19 5 1183 1300 39565043 39565159 1.940000e-12 84.2
20 TraesCS5D01G153500 chr4B 89.320 103 10 1 1 103 582223560 582223661 8.830000e-26 128.0
21 TraesCS5D01G153500 chr1A 75.714 280 50 14 1033 1300 505483968 505483695 1.140000e-24 124.0
22 TraesCS5D01G153500 chr1D 74.269 342 61 22 1033 1353 409529037 409528702 5.320000e-23 119.0
23 TraesCS5D01G153500 chr3D 72.656 256 50 17 1111 1353 435444104 435444352 1.950000e-07 67.6
24 TraesCS5D01G153500 chr3B 74.286 175 35 8 1111 1280 571602178 571602347 7.020000e-07 65.8


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 TraesCS5D01G153500 chr5D 242012454 242015488 3034 True 5605.000000 5605 100.000000 1 3035 1 chr5D.!!$R1 3034
1 TraesCS5D01G153500 chr5B 257000856 257003770 2914 True 1300.000000 2717 88.519000 99 3035 3 chr5B.!!$R2 2936
2 TraesCS5D01G153500 chr5A 312231394 312234050 2656 True 1130.333333 2649 89.905667 114 3035 3 chr5A.!!$R1 2921

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
287 310 0.462759 GAGAGCTCCCGTGGAATTGG 60.463 60.0 10.93 0.0 0.0 3.16 F
1016 1118 0.042731 AAGATGGAGGGGGAGACGAA 59.957 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1556 1.045350 CCCGATCTGCTCCTTCTCCA 61.045 60.0 0.00 0.0 0.00 3.86 R
2448 2603 0.034756 AGTGCAACCGTACATGCTCA 59.965 50.0 14.15 0.0 42.97 4.26 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
20 21 2.292267 AGAAATAATGCGAGCACCAGG 58.708 47.619 0.00 0.00 0.00 4.45
21 22 2.092968 AGAAATAATGCGAGCACCAGGA 60.093 45.455 0.00 0.00 0.00 3.86
22 23 1.668419 AATAATGCGAGCACCAGGAC 58.332 50.000 0.00 0.00 0.00 3.85
23 24 0.833287 ATAATGCGAGCACCAGGACT 59.167 50.000 0.00 0.00 0.00 3.85
24 25 0.613260 TAATGCGAGCACCAGGACTT 59.387 50.000 0.00 0.00 0.00 3.01
25 26 0.957395 AATGCGAGCACCAGGACTTG 60.957 55.000 0.00 0.00 0.00 3.16
26 27 1.830587 ATGCGAGCACCAGGACTTGA 61.831 55.000 0.00 0.00 0.00 3.02
27 28 1.301716 GCGAGCACCAGGACTTGAA 60.302 57.895 0.00 0.00 0.00 2.69
28 29 1.569479 GCGAGCACCAGGACTTGAAC 61.569 60.000 0.00 0.00 0.00 3.18
29 30 0.951040 CGAGCACCAGGACTTGAACC 60.951 60.000 0.00 0.00 0.00 3.62
30 31 0.606673 GAGCACCAGGACTTGAACCC 60.607 60.000 0.00 0.00 0.00 4.11
31 32 1.062488 AGCACCAGGACTTGAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
32 33 0.690762 GCACCAGGACTTGAACCCTA 59.309 55.000 0.00 0.00 0.00 3.53
33 34 1.339151 GCACCAGGACTTGAACCCTAG 60.339 57.143 0.00 0.00 0.00 3.02
34 35 1.978580 CACCAGGACTTGAACCCTAGT 59.021 52.381 0.00 0.00 0.00 2.57
35 36 1.978580 ACCAGGACTTGAACCCTAGTG 59.021 52.381 0.00 0.00 0.00 2.74
36 37 1.279271 CCAGGACTTGAACCCTAGTGG 59.721 57.143 0.00 0.00 41.37 4.00
47 48 2.453242 CCTAGTGGGCTGGGGATAC 58.547 63.158 0.00 0.00 39.43 2.24
63 64 4.388378 GGATACCACTGTCACTCTAACC 57.612 50.000 0.00 0.00 0.00 2.85
64 65 3.767673 GGATACCACTGTCACTCTAACCA 59.232 47.826 0.00 0.00 0.00 3.67
65 66 4.406003 GGATACCACTGTCACTCTAACCAT 59.594 45.833 0.00 0.00 0.00 3.55
66 67 3.963428 ACCACTGTCACTCTAACCATC 57.037 47.619 0.00 0.00 0.00 3.51
67 68 2.567615 ACCACTGTCACTCTAACCATCC 59.432 50.000 0.00 0.00 0.00 3.51
68 69 2.567169 CCACTGTCACTCTAACCATCCA 59.433 50.000 0.00 0.00 0.00 3.41
69 70 3.007940 CCACTGTCACTCTAACCATCCAA 59.992 47.826 0.00 0.00 0.00 3.53
70 71 3.997021 CACTGTCACTCTAACCATCCAAC 59.003 47.826 0.00 0.00 0.00 3.77
71 72 3.008049 ACTGTCACTCTAACCATCCAACC 59.992 47.826 0.00 0.00 0.00 3.77
72 73 2.976185 TGTCACTCTAACCATCCAACCA 59.024 45.455 0.00 0.00 0.00 3.67
73 74 3.244422 TGTCACTCTAACCATCCAACCAC 60.244 47.826 0.00 0.00 0.00 4.16
74 75 2.976185 TCACTCTAACCATCCAACCACA 59.024 45.455 0.00 0.00 0.00 4.17
75 76 3.587061 TCACTCTAACCATCCAACCACAT 59.413 43.478 0.00 0.00 0.00 3.21
76 77 3.691118 CACTCTAACCATCCAACCACATG 59.309 47.826 0.00 0.00 0.00 3.21
77 78 3.330701 ACTCTAACCATCCAACCACATGT 59.669 43.478 0.00 0.00 0.00 3.21
78 79 4.202567 ACTCTAACCATCCAACCACATGTT 60.203 41.667 0.00 0.00 37.80 2.71
88 89 3.955291 CCACATGTTGGTTCGCAAA 57.045 47.368 0.00 0.00 41.10 3.68
89 90 2.215907 CCACATGTTGGTTCGCAAAA 57.784 45.000 0.00 0.00 41.10 2.44
90 91 2.544685 CCACATGTTGGTTCGCAAAAA 58.455 42.857 0.00 0.00 41.10 1.94
212 214 9.696917 ATAGTGAAATCTTGTTCATGGAAAAAC 57.303 29.630 0.00 0.00 39.61 2.43
259 266 2.130272 TGGGTGTGCACTGTGTTAAA 57.870 45.000 19.41 0.00 0.00 1.52
287 310 0.462759 GAGAGCTCCCGTGGAATTGG 60.463 60.000 10.93 0.00 0.00 3.16
299 322 2.088423 TGGAATTGGTTACACGCCATC 58.912 47.619 0.00 0.00 35.71 3.51
325 348 6.407299 GCCACCAGAAATTCATGTCCATATTT 60.407 38.462 0.00 0.00 0.00 1.40
415 452 5.505173 AGCACAATCCAAATTAATCGGAG 57.495 39.130 11.17 3.34 30.84 4.63
441 478 8.182227 GGATACTTAACTTGACATTTAGGCAAC 58.818 37.037 0.00 0.00 41.37 4.17
470 517 1.755179 TATGGAAGCCAAGCTGAAGC 58.245 50.000 0.00 0.00 39.62 3.86
518 565 1.871039 GTTTACACGCTTGAAGGCAGA 59.129 47.619 0.00 0.00 0.00 4.26
521 568 2.357517 ACGCTTGAAGGCAGACCG 60.358 61.111 0.00 0.00 42.76 4.79
531 578 4.703897 TGAAGGCAGACCGGATTATTTAG 58.296 43.478 9.46 0.00 42.76 1.85
540 587 6.700520 CAGACCGGATTATTTAGGTGTAAGAC 59.299 42.308 9.46 0.00 37.07 3.01
588 635 3.948702 GAGCTCTCTCCCCCACTC 58.051 66.667 6.43 0.00 33.19 3.51
681 768 3.262142 ATTCGCAAAACCGCCCACG 62.262 57.895 0.00 0.00 39.67 4.94
721 808 0.747255 TCCTTGATGAGGCGTCTAGC 59.253 55.000 8.06 0.00 45.87 3.42
737 829 5.862860 GCGTCTAGCCTAAGTATTTCCATAC 59.137 44.000 0.00 0.00 40.81 2.39
750 842 7.897864 AGTATTTCCATACTAGTGTAGGATGC 58.102 38.462 5.39 0.53 44.24 3.91
764 856 0.528684 GGATGCACTACCAGACGAGC 60.529 60.000 0.00 0.00 0.00 5.03
774 866 4.935808 ACTACCAGACGAGCTTAAAATTGG 59.064 41.667 0.00 0.00 0.00 3.16
775 867 3.081804 ACCAGACGAGCTTAAAATTGGG 58.918 45.455 0.00 0.00 0.00 4.12
816 912 8.818141 TCAGAAACGATATACAGAAATGGATC 57.182 34.615 0.00 0.00 0.00 3.36
882 978 3.118811 AGCAACAGAGAGGAAGCATCTAC 60.119 47.826 0.00 0.00 0.00 2.59
907 1003 2.884207 GTTCACGATCGTCGGGGC 60.884 66.667 19.84 3.48 44.75 5.80
953 1049 2.485124 CCTGCTGGTCTCTTCATCCATC 60.485 54.545 0.51 0.00 0.00 3.51
975 1071 0.811915 TGAGGTGACGAAGCTAGCTC 59.188 55.000 19.65 10.69 40.21 4.09
1016 1118 0.042731 AAGATGGAGGGGGAGACGAA 59.957 55.000 0.00 0.00 0.00 3.85
1541 1649 2.653087 GGTTCCTTCCCTACGGCGT 61.653 63.158 19.64 19.64 0.00 5.68
1560 1668 2.766400 GCTCCTCGACCACCTCTCG 61.766 68.421 0.00 0.00 0.00 4.04
1761 1869 1.507174 CCAGACGAACGAGACCTCC 59.493 63.158 0.14 0.00 0.00 4.30
1877 1985 3.691342 CAACCGGGAGCTCGTGGA 61.691 66.667 24.87 0.00 0.00 4.02
2142 2250 0.447801 GGCCAAACTCACGTGCTATG 59.552 55.000 11.67 7.05 0.00 2.23
2238 2346 9.893305 CATATACTCACGTGTCATTATTGTAGA 57.107 33.333 16.51 5.31 0.00 2.59
2298 2452 4.100529 CGCCAATTTCAAGATGTGATGTC 58.899 43.478 0.00 0.00 35.70 3.06
2300 2454 4.142622 GCCAATTTCAAGATGTGATGTCGA 60.143 41.667 0.00 0.00 35.70 4.20
2311 2465 7.575414 AGATGTGATGTCGACTTAGTATCTT 57.425 36.000 17.92 0.99 0.00 2.40
2332 2486 6.991938 TCTTGAAGGTGTTCATAAATTTGGG 58.008 36.000 0.00 0.00 42.41 4.12
2350 2504 1.892474 GGGGTGTGCATGTGTACATTT 59.108 47.619 7.18 0.00 42.31 2.32
2354 2508 5.160641 GGGTGTGCATGTGTACATTTAAAG 58.839 41.667 7.18 0.00 42.31 1.85
2358 2512 6.359617 GTGTGCATGTGTACATTTAAAGTGAC 59.640 38.462 7.18 0.00 42.31 3.67
2389 2543 1.262417 GCATGTATGTGAGCATCCACG 59.738 52.381 0.00 0.00 39.80 4.94
2395 2549 1.965930 GTGAGCATCCACGGTTGCA 60.966 57.895 18.77 0.00 41.70 4.08
2436 2591 2.238521 ACCATGTGGACGCAAAAGAAT 58.761 42.857 5.96 0.00 38.94 2.40
2437 2592 3.417101 ACCATGTGGACGCAAAAGAATA 58.583 40.909 5.96 0.00 38.94 1.75
2438 2593 3.823873 ACCATGTGGACGCAAAAGAATAA 59.176 39.130 5.96 0.00 38.94 1.40
2439 2594 4.462483 ACCATGTGGACGCAAAAGAATAAT 59.538 37.500 5.96 0.00 38.94 1.28
2440 2595 5.036737 CCATGTGGACGCAAAAGAATAATC 58.963 41.667 0.00 0.00 37.39 1.75
2441 2596 4.335082 TGTGGACGCAAAAGAATAATCG 57.665 40.909 0.00 0.00 0.00 3.34
2442 2597 3.749088 TGTGGACGCAAAAGAATAATCGT 59.251 39.130 0.00 0.00 0.00 3.73
2443 2598 4.088648 GTGGACGCAAAAGAATAATCGTG 58.911 43.478 0.00 0.00 0.00 4.35
2444 2599 3.749088 TGGACGCAAAAGAATAATCGTGT 59.251 39.130 0.00 0.00 0.00 4.49
2445 2600 4.930405 TGGACGCAAAAGAATAATCGTGTA 59.070 37.500 0.00 0.00 0.00 2.90
2446 2601 5.583061 TGGACGCAAAAGAATAATCGTGTAT 59.417 36.000 0.00 0.00 0.00 2.29
2447 2602 5.901884 GGACGCAAAAGAATAATCGTGTATG 59.098 40.000 0.00 0.00 0.00 2.39
2448 2603 6.417191 ACGCAAAAGAATAATCGTGTATGT 57.583 33.333 0.00 0.00 0.00 2.29
2449 2604 6.247903 ACGCAAAAGAATAATCGTGTATGTG 58.752 36.000 0.00 0.00 0.00 3.21
2450 2605 6.091577 ACGCAAAAGAATAATCGTGTATGTGA 59.908 34.615 0.00 0.00 0.00 3.58
2451 2606 6.624917 CGCAAAAGAATAATCGTGTATGTGAG 59.375 38.462 0.00 0.00 0.00 3.51
2452 2607 6.412072 GCAAAAGAATAATCGTGTATGTGAGC 59.588 38.462 0.00 0.00 0.00 4.26
2453 2608 7.463544 CAAAAGAATAATCGTGTATGTGAGCA 58.536 34.615 0.00 0.00 0.00 4.26
2454 2609 7.792374 AAAGAATAATCGTGTATGTGAGCAT 57.208 32.000 0.00 0.00 39.03 3.79
2455 2610 6.775939 AGAATAATCGTGTATGTGAGCATG 57.224 37.500 0.00 0.00 36.58 4.06
2456 2611 6.283694 AGAATAATCGTGTATGTGAGCATGT 58.716 36.000 0.00 0.00 36.58 3.21
2457 2612 7.433680 AGAATAATCGTGTATGTGAGCATGTA 58.566 34.615 0.00 0.00 36.58 2.29
2458 2613 7.382488 AGAATAATCGTGTATGTGAGCATGTAC 59.618 37.037 0.00 0.00 36.58 2.90
2459 2614 2.792749 TCGTGTATGTGAGCATGTACG 58.207 47.619 0.00 10.12 42.05 3.67
2460 2615 1.852280 CGTGTATGTGAGCATGTACGG 59.148 52.381 0.00 0.00 39.63 4.02
2461 2616 2.734175 CGTGTATGTGAGCATGTACGGT 60.734 50.000 0.00 0.00 39.63 4.83
2462 2617 3.259064 GTGTATGTGAGCATGTACGGTT 58.741 45.455 0.00 0.00 36.58 4.44
2463 2618 3.062099 GTGTATGTGAGCATGTACGGTTG 59.938 47.826 0.00 0.00 36.58 3.77
2464 2619 1.086696 ATGTGAGCATGTACGGTTGC 58.913 50.000 7.05 7.05 39.17 4.17
2465 2620 0.250081 TGTGAGCATGTACGGTTGCA 60.250 50.000 15.05 0.00 41.35 4.08
2466 2621 0.165944 GTGAGCATGTACGGTTGCAC 59.834 55.000 15.05 10.48 41.35 4.57
2467 2622 0.034756 TGAGCATGTACGGTTGCACT 59.965 50.000 15.05 0.00 41.35 4.40
2468 2623 0.443869 GAGCATGTACGGTTGCACTG 59.556 55.000 15.05 0.00 41.35 3.66
2469 2624 0.250295 AGCATGTACGGTTGCACTGT 60.250 50.000 15.05 6.12 41.35 3.55
2470 2625 0.110238 GCATGTACGGTTGCACTGTG 60.110 55.000 2.76 2.76 38.36 3.66
2471 2626 1.225855 CATGTACGGTTGCACTGTGT 58.774 50.000 9.86 0.00 38.36 3.72
2472 2627 1.601903 CATGTACGGTTGCACTGTGTT 59.398 47.619 9.86 0.00 38.36 3.32
2473 2628 2.598686 TGTACGGTTGCACTGTGTTA 57.401 45.000 9.86 0.00 38.36 2.41
2474 2629 2.902523 TGTACGGTTGCACTGTGTTAA 58.097 42.857 9.86 2.80 38.36 2.01
2475 2630 3.268330 TGTACGGTTGCACTGTGTTAAA 58.732 40.909 9.86 0.00 38.36 1.52
2476 2631 3.688185 TGTACGGTTGCACTGTGTTAAAA 59.312 39.130 9.86 0.00 38.36 1.52
2477 2632 3.414549 ACGGTTGCACTGTGTTAAAAG 57.585 42.857 9.86 5.75 36.13 2.27
2478 2633 3.011119 ACGGTTGCACTGTGTTAAAAGA 58.989 40.909 9.86 0.00 36.13 2.52
2479 2634 3.630312 ACGGTTGCACTGTGTTAAAAGAT 59.370 39.130 9.86 0.00 36.13 2.40
2480 2635 4.817464 ACGGTTGCACTGTGTTAAAAGATA 59.183 37.500 9.86 0.00 36.13 1.98
2481 2636 5.297278 ACGGTTGCACTGTGTTAAAAGATAA 59.703 36.000 9.86 0.00 36.13 1.75
2482 2637 6.183360 ACGGTTGCACTGTGTTAAAAGATAAA 60.183 34.615 9.86 0.00 36.13 1.40
2483 2638 6.861055 CGGTTGCACTGTGTTAAAAGATAAAT 59.139 34.615 9.86 0.00 0.00 1.40
2484 2639 8.018520 CGGTTGCACTGTGTTAAAAGATAAATA 58.981 33.333 9.86 0.00 0.00 1.40
2485 2640 9.685828 GGTTGCACTGTGTTAAAAGATAAATAA 57.314 29.630 9.86 0.00 0.00 1.40
2488 2643 9.388346 TGCACTGTGTTAAAAGATAAATAAACG 57.612 29.630 9.86 0.00 0.00 3.60
2489 2644 9.389570 GCACTGTGTTAAAAGATAAATAAACGT 57.610 29.630 9.86 0.00 0.00 3.99
2491 2646 9.389570 ACTGTGTTAAAAGATAAATAAACGTGC 57.610 29.630 0.00 0.00 0.00 5.34
2492 2647 8.424628 TGTGTTAAAAGATAAATAAACGTGCG 57.575 30.769 0.00 0.00 0.00 5.34
2493 2648 7.534578 TGTGTTAAAAGATAAATAAACGTGCGG 59.465 33.333 0.00 0.00 0.00 5.69
2494 2649 7.745594 GTGTTAAAAGATAAATAAACGTGCGGA 59.254 33.333 0.00 0.00 0.00 5.54
2495 2650 7.745594 TGTTAAAAGATAAATAAACGTGCGGAC 59.254 33.333 0.00 0.00 0.00 4.79
2535 2690 8.828688 AAACTCTGTCTACGCTTTTTATACTT 57.171 30.769 0.00 0.00 0.00 2.24
2558 2713 2.335316 TTGGCTTCTTACACGGTTGT 57.665 45.000 0.00 0.00 40.02 3.32
2588 2743 6.173339 TCTTCATCCTTGTTCATACTTCACC 58.827 40.000 0.00 0.00 0.00 4.02
2590 2745 4.221924 TCATCCTTGTTCATACTTCACCGA 59.778 41.667 0.00 0.00 0.00 4.69
2599 2754 6.152154 TGTTCATACTTCACCGAATGTCTCTA 59.848 38.462 0.00 0.00 0.00 2.43
2610 2765 4.212847 CCGAATGTCTCTATCATTGCAAGG 59.787 45.833 4.34 4.34 35.94 3.61
2614 2769 6.690194 ATGTCTCTATCATTGCAAGGTTTC 57.310 37.500 11.36 0.00 0.00 2.78
2615 2770 5.809001 TGTCTCTATCATTGCAAGGTTTCT 58.191 37.500 11.36 0.00 0.00 2.52
2616 2771 5.645067 TGTCTCTATCATTGCAAGGTTTCTG 59.355 40.000 11.36 0.00 0.00 3.02
2617 2772 5.877012 GTCTCTATCATTGCAAGGTTTCTGA 59.123 40.000 11.36 5.80 0.00 3.27
2618 2773 6.372659 GTCTCTATCATTGCAAGGTTTCTGAA 59.627 38.462 11.36 0.00 0.00 3.02
2665 2821 7.641020 TGAACTCTTTTAATCGTTTTCGGTTTC 59.359 33.333 0.00 0.00 44.79 2.78
2667 2823 7.645402 ACTCTTTTAATCGTTTTCGGTTTCAT 58.355 30.769 0.00 0.00 44.79 2.57
2673 2829 4.118023 TCGTTTTCGGTTTCATTGTACG 57.882 40.909 0.00 0.00 44.25 3.67
2970 3126 8.964420 TCTGTTTTTAAATGCATACTAACAGC 57.036 30.769 22.27 11.66 40.40 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.092968 TCCTGGTGCTCGCATTATTTCT 60.093 45.455 0.00 0.00 0.00 2.52
1 2 2.032178 GTCCTGGTGCTCGCATTATTTC 59.968 50.000 0.00 0.00 0.00 2.17
2 3 2.017049 GTCCTGGTGCTCGCATTATTT 58.983 47.619 0.00 0.00 0.00 1.40
3 4 1.210478 AGTCCTGGTGCTCGCATTATT 59.790 47.619 0.00 0.00 0.00 1.40
4 5 0.833287 AGTCCTGGTGCTCGCATTAT 59.167 50.000 0.00 0.00 0.00 1.28
5 6 0.613260 AAGTCCTGGTGCTCGCATTA 59.387 50.000 0.00 0.00 0.00 1.90
6 7 0.957395 CAAGTCCTGGTGCTCGCATT 60.957 55.000 0.00 0.00 0.00 3.56
7 8 1.376424 CAAGTCCTGGTGCTCGCAT 60.376 57.895 0.00 0.00 0.00 4.73
8 9 2.031012 CAAGTCCTGGTGCTCGCA 59.969 61.111 0.00 0.00 0.00 5.10
9 10 1.301716 TTCAAGTCCTGGTGCTCGC 60.302 57.895 0.00 0.00 0.00 5.03
10 11 0.951040 GGTTCAAGTCCTGGTGCTCG 60.951 60.000 0.00 0.00 0.00 5.03
11 12 0.606673 GGGTTCAAGTCCTGGTGCTC 60.607 60.000 0.00 0.00 0.00 4.26
12 13 1.062488 AGGGTTCAAGTCCTGGTGCT 61.062 55.000 0.00 0.00 31.11 4.40
13 14 0.690762 TAGGGTTCAAGTCCTGGTGC 59.309 55.000 0.00 0.00 34.75 5.01
14 15 1.978580 ACTAGGGTTCAAGTCCTGGTG 59.021 52.381 0.00 0.00 42.16 4.17
15 16 1.978580 CACTAGGGTTCAAGTCCTGGT 59.021 52.381 0.00 0.00 44.12 4.00
16 17 1.279271 CCACTAGGGTTCAAGTCCTGG 59.721 57.143 0.00 0.00 37.61 4.45
17 18 2.770164 CCACTAGGGTTCAAGTCCTG 57.230 55.000 0.00 0.00 34.75 3.86
29 30 1.128188 GGTATCCCCAGCCCACTAGG 61.128 65.000 0.00 0.00 39.47 3.02
30 31 0.399949 TGGTATCCCCAGCCCACTAG 60.400 60.000 0.00 0.00 38.72 2.57
31 32 0.693092 GTGGTATCCCCAGCCCACTA 60.693 60.000 0.00 0.00 46.45 2.74
32 33 2.001269 GTGGTATCCCCAGCCCACT 61.001 63.158 0.00 0.00 46.45 4.00
33 34 2.001269 AGTGGTATCCCCAGCCCAC 61.001 63.158 0.00 0.00 46.45 4.61
34 35 2.000701 CAGTGGTATCCCCAGCCCA 61.001 63.158 0.00 0.00 46.45 5.36
35 36 1.984288 GACAGTGGTATCCCCAGCCC 61.984 65.000 0.00 0.00 46.45 5.19
36 37 1.271840 TGACAGTGGTATCCCCAGCC 61.272 60.000 0.00 0.00 46.45 4.85
37 38 0.107654 GTGACAGTGGTATCCCCAGC 60.108 60.000 0.00 0.00 46.45 4.85
38 39 1.482593 GAGTGACAGTGGTATCCCCAG 59.517 57.143 0.00 0.00 46.45 4.45
39 40 1.078823 AGAGTGACAGTGGTATCCCCA 59.921 52.381 0.00 0.00 42.51 4.96
40 41 1.867363 AGAGTGACAGTGGTATCCCC 58.133 55.000 0.00 0.00 0.00 4.81
41 42 3.132467 GGTTAGAGTGACAGTGGTATCCC 59.868 52.174 0.00 0.00 0.00 3.85
42 43 3.767673 TGGTTAGAGTGACAGTGGTATCC 59.232 47.826 0.00 0.00 0.00 2.59
43 44 5.452077 GGATGGTTAGAGTGACAGTGGTATC 60.452 48.000 0.00 0.00 0.00 2.24
44 45 4.406003 GGATGGTTAGAGTGACAGTGGTAT 59.594 45.833 0.00 0.00 0.00 2.73
45 46 3.767673 GGATGGTTAGAGTGACAGTGGTA 59.232 47.826 0.00 0.00 0.00 3.25
46 47 2.567615 GGATGGTTAGAGTGACAGTGGT 59.432 50.000 0.00 0.00 0.00 4.16
47 48 2.567169 TGGATGGTTAGAGTGACAGTGG 59.433 50.000 0.00 0.00 0.00 4.00
48 49 3.961480 TGGATGGTTAGAGTGACAGTG 57.039 47.619 0.00 0.00 0.00 3.66
49 50 3.008049 GGTTGGATGGTTAGAGTGACAGT 59.992 47.826 0.00 0.00 0.00 3.55
50 51 3.007940 TGGTTGGATGGTTAGAGTGACAG 59.992 47.826 0.00 0.00 0.00 3.51
51 52 2.976185 TGGTTGGATGGTTAGAGTGACA 59.024 45.455 0.00 0.00 0.00 3.58
52 53 3.244422 TGTGGTTGGATGGTTAGAGTGAC 60.244 47.826 0.00 0.00 0.00 3.67
53 54 2.976185 TGTGGTTGGATGGTTAGAGTGA 59.024 45.455 0.00 0.00 0.00 3.41
54 55 3.417069 TGTGGTTGGATGGTTAGAGTG 57.583 47.619 0.00 0.00 0.00 3.51
55 56 3.330701 ACATGTGGTTGGATGGTTAGAGT 59.669 43.478 0.00 0.00 0.00 3.24
56 57 3.955471 ACATGTGGTTGGATGGTTAGAG 58.045 45.455 0.00 0.00 0.00 2.43
57 58 4.380843 AACATGTGGTTGGATGGTTAGA 57.619 40.909 0.00 0.00 38.60 2.10
204 206 8.084684 CCCTCAAATTTTGTTTTTGTTTTTCCA 58.915 29.630 8.89 0.00 35.90 3.53
239 242 2.130272 TTAACACAGTGCACACCCAA 57.870 45.000 21.04 2.09 0.00 4.12
265 272 0.324738 ATTCCACGGGAGCTCTCTGA 60.325 55.000 12.81 2.50 31.21 3.27
278 285 1.240256 TGGCGTGTAACCAATTCCAC 58.760 50.000 0.00 0.00 33.12 4.02
287 310 2.746803 GGTGGCGATGGCGTGTAAC 61.747 63.158 0.00 0.00 41.24 2.50
299 322 1.133025 GGACATGAATTTCTGGTGGCG 59.867 52.381 0.00 0.00 0.00 5.69
325 348 5.862678 TGATCGTGATAATTAGGACCACA 57.137 39.130 0.00 0.00 0.00 4.17
415 452 7.859325 TGCCTAAATGTCAAGTTAAGTATCC 57.141 36.000 0.00 0.00 0.00 2.59
441 478 3.644966 TGGCTTCCATAACTACCCAAG 57.355 47.619 0.00 0.00 0.00 3.61
445 482 2.945668 CAGCTTGGCTTCCATAACTACC 59.054 50.000 0.00 0.00 36.40 3.18
447 484 4.517285 CTTCAGCTTGGCTTCCATAACTA 58.483 43.478 0.00 0.00 36.40 2.24
470 517 6.146216 CCAGTTTACGTCTCTCTAGCATATG 58.854 44.000 0.00 0.00 0.00 1.78
503 550 2.671177 CGGTCTGCCTTCAAGCGTG 61.671 63.158 0.00 0.00 34.65 5.34
504 551 2.357517 CGGTCTGCCTTCAAGCGT 60.358 61.111 0.00 0.00 34.65 5.07
506 553 0.678048 AATCCGGTCTGCCTTCAAGC 60.678 55.000 0.00 0.00 0.00 4.01
518 565 6.343703 GTGTCTTACACCTAAATAATCCGGT 58.656 40.000 0.00 0.00 43.05 5.28
540 587 5.796935 GTGCAAGAAATGTGTAAGCTATGTG 59.203 40.000 0.00 0.00 0.00 3.21
588 635 0.172803 ATCGTCCCTCGTTCCTTTCG 59.827 55.000 0.00 0.00 40.80 3.46
681 768 2.681344 ACGGTTTTTCCATATCTTCGGC 59.319 45.455 0.00 0.00 35.57 5.54
721 808 9.584008 TCCTACACTAGTATGGAAATACTTAGG 57.416 37.037 0.00 11.71 38.27 2.69
750 842 5.163854 CCAATTTTAAGCTCGTCTGGTAGTG 60.164 44.000 0.00 0.00 0.00 2.74
764 856 4.513198 TTCCAGTTCGCCCAATTTTAAG 57.487 40.909 0.00 0.00 0.00 1.85
774 866 6.564125 CGTTTCTGATATATTTCCAGTTCGCC 60.564 42.308 0.00 0.00 0.00 5.54
775 867 6.200286 TCGTTTCTGATATATTTCCAGTTCGC 59.800 38.462 0.00 0.00 0.00 4.70
816 912 2.047655 TGTGCTCGGGGTTAAGCG 60.048 61.111 0.00 0.00 41.51 4.68
907 1003 1.070376 CGTGTGCAGATATGCGAATGG 60.070 52.381 7.97 0.00 37.69 3.16
953 1049 0.524392 CTAGCTTCGTCACCTCAGCG 60.524 60.000 0.00 0.00 37.35 5.18
975 1071 0.887247 TGCGTGTTCCAATCCAATGG 59.113 50.000 0.00 0.00 42.12 3.16
1448 1556 1.045350 CCCGATCTGCTCCTTCTCCA 61.045 60.000 0.00 0.00 0.00 3.86
1541 1649 1.679305 GAGAGGTGGTCGAGGAGCA 60.679 63.158 0.00 0.00 37.74 4.26
1725 1833 3.094062 GCACCCGCTCAGCAGGATA 62.094 63.158 5.71 0.00 34.30 2.59
2142 2250 2.230266 ACTTGACCCACACACAAACAAC 59.770 45.455 0.00 0.00 0.00 3.32
2258 2366 4.170292 GGCGAAGACAGAGTTGTAAGTA 57.830 45.455 0.00 0.00 37.76 2.24
2298 2452 6.387465 TGAACACCTTCAAGATACTAAGTCG 58.613 40.000 0.00 0.00 33.20 4.18
2311 2465 5.011533 CACCCCAAATTTATGAACACCTTCA 59.988 40.000 0.00 0.00 40.77 3.02
2326 2480 1.892474 GTACACATGCACACCCCAAAT 59.108 47.619 0.00 0.00 0.00 2.32
2330 2484 1.544724 AATGTACACATGCACACCCC 58.455 50.000 0.00 0.00 36.56 4.95
2332 2486 5.629020 CACTTTAAATGTACACATGCACACC 59.371 40.000 0.00 0.00 36.56 4.16
2350 2504 6.569780 ACATGCATATACACTCGTCACTTTA 58.430 36.000 0.00 0.00 0.00 1.85
2354 2508 5.920840 ACATACATGCATATACACTCGTCAC 59.079 40.000 0.00 0.00 0.00 3.67
2358 2512 5.061435 GCTCACATACATGCATATACACTCG 59.939 44.000 0.00 0.00 0.00 4.18
2417 2572 4.433186 TTATTCTTTTGCGTCCACATGG 57.567 40.909 0.00 0.00 0.00 3.66
2436 2591 4.973663 CGTACATGCTCACATACACGATTA 59.026 41.667 0.00 0.00 41.58 1.75
2437 2592 3.796717 CGTACATGCTCACATACACGATT 59.203 43.478 0.00 0.00 41.58 3.34
2438 2593 3.372060 CGTACATGCTCACATACACGAT 58.628 45.455 0.00 0.00 41.58 3.73
2439 2594 2.478879 CCGTACATGCTCACATACACGA 60.479 50.000 11.11 0.00 41.58 4.35
2440 2595 1.852280 CCGTACATGCTCACATACACG 59.148 52.381 0.00 0.00 40.05 4.49
2441 2596 2.888594 ACCGTACATGCTCACATACAC 58.111 47.619 0.00 0.00 33.67 2.90
2442 2597 3.258228 CAACCGTACATGCTCACATACA 58.742 45.455 0.00 0.00 33.67 2.29
2443 2598 2.030457 GCAACCGTACATGCTCACATAC 59.970 50.000 7.76 0.00 39.46 2.39
2444 2599 2.276201 GCAACCGTACATGCTCACATA 58.724 47.619 7.76 0.00 39.46 2.29
2445 2600 1.086696 GCAACCGTACATGCTCACAT 58.913 50.000 7.76 0.00 39.46 3.21
2446 2601 0.250081 TGCAACCGTACATGCTCACA 60.250 50.000 14.15 0.00 42.97 3.58
2447 2602 0.165944 GTGCAACCGTACATGCTCAC 59.834 55.000 14.15 3.60 42.97 3.51
2448 2603 0.034756 AGTGCAACCGTACATGCTCA 59.965 50.000 14.15 0.00 42.97 4.26
2449 2604 0.443869 CAGTGCAACCGTACATGCTC 59.556 55.000 14.15 11.26 42.97 4.26
2450 2605 0.250295 ACAGTGCAACCGTACATGCT 60.250 50.000 14.15 0.00 42.97 3.79
2451 2606 0.110238 CACAGTGCAACCGTACATGC 60.110 55.000 8.01 8.01 42.86 4.06
2452 2607 1.225855 ACACAGTGCAACCGTACATG 58.774 50.000 0.00 0.00 37.80 3.21
2453 2608 1.961793 AACACAGTGCAACCGTACAT 58.038 45.000 0.00 0.00 37.80 2.29
2454 2609 2.598686 TAACACAGTGCAACCGTACA 57.401 45.000 0.00 0.00 37.80 2.90
2455 2610 3.948196 TTTAACACAGTGCAACCGTAC 57.052 42.857 0.00 0.00 37.80 3.67
2456 2611 4.190001 TCTTTTAACACAGTGCAACCGTA 58.810 39.130 0.00 0.00 37.80 4.02
2457 2612 3.011119 TCTTTTAACACAGTGCAACCGT 58.989 40.909 0.00 0.00 37.80 4.83
2458 2613 3.684103 TCTTTTAACACAGTGCAACCG 57.316 42.857 0.00 0.00 37.80 4.44
2459 2614 9.685828 TTATTTATCTTTTAACACAGTGCAACC 57.314 29.630 0.00 0.00 37.80 3.77
2462 2617 9.388346 CGTTTATTTATCTTTTAACACAGTGCA 57.612 29.630 0.00 0.00 0.00 4.57
2463 2618 9.389570 ACGTTTATTTATCTTTTAACACAGTGC 57.610 29.630 0.00 0.00 0.00 4.40
2465 2620 9.389570 GCACGTTTATTTATCTTTTAACACAGT 57.610 29.630 0.00 0.00 0.00 3.55
2466 2621 8.563949 CGCACGTTTATTTATCTTTTAACACAG 58.436 33.333 0.00 0.00 0.00 3.66
2467 2622 7.534578 CCGCACGTTTATTTATCTTTTAACACA 59.465 33.333 0.00 0.00 0.00 3.72
2468 2623 7.745594 TCCGCACGTTTATTTATCTTTTAACAC 59.254 33.333 0.00 0.00 0.00 3.32
2469 2624 7.745594 GTCCGCACGTTTATTTATCTTTTAACA 59.254 33.333 0.00 0.00 0.00 2.41
2470 2625 7.046060 CGTCCGCACGTTTATTTATCTTTTAAC 60.046 37.037 0.00 0.00 41.42 2.01
2471 2626 6.954852 CGTCCGCACGTTTATTTATCTTTTAA 59.045 34.615 0.00 0.00 41.42 1.52
2472 2627 6.468484 CGTCCGCACGTTTATTTATCTTTTA 58.532 36.000 0.00 0.00 41.42 1.52
2473 2628 5.318349 CGTCCGCACGTTTATTTATCTTTT 58.682 37.500 0.00 0.00 41.42 2.27
2474 2629 4.889241 CGTCCGCACGTTTATTTATCTTT 58.111 39.130 0.00 0.00 41.42 2.52
2475 2630 4.509915 CGTCCGCACGTTTATTTATCTT 57.490 40.909 0.00 0.00 41.42 2.40
2541 2696 0.788391 CGACAACCGTGTAAGAAGCC 59.212 55.000 0.00 0.00 38.41 4.35
2553 2708 4.036380 ACAAGGATGAAGAAAACGACAACC 59.964 41.667 0.00 0.00 0.00 3.77
2558 2713 6.934645 AGTATGAACAAGGATGAAGAAAACGA 59.065 34.615 0.00 0.00 0.00 3.85
2588 2743 4.813161 ACCTTGCAATGATAGAGACATTCG 59.187 41.667 8.84 0.00 36.07 3.34
2590 2745 6.888632 AGAAACCTTGCAATGATAGAGACATT 59.111 34.615 8.84 0.00 38.30 2.71
2599 2754 7.173735 GGAAAAATTCAGAAACCTTGCAATGAT 59.826 33.333 8.84 0.00 0.00 2.45
2639 2795 6.607735 ACCGAAAACGATTAAAAGAGTTCA 57.392 33.333 0.00 0.00 0.00 3.18
2893 3049 9.372541 CATGTTAAAGAAATTGTTTGTGCATTC 57.627 29.630 0.00 0.00 0.00 2.67
2997 3153 9.528018 GAGAAGTGAAAAATTGTTTGACCAATA 57.472 29.630 0.00 0.00 34.01 1.90


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

AutoCloner maintained by Alex Coulton.