Multiple sequence alignment - TraesCS1D01G006200

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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 TraesCS1D01G006200 chr1D 100.000 2672 0 0 1 2672 2883279 2880608 0.000000e+00 4935
1 TraesCS1D01G006200 chr1D 89.185 675 71 2 6 678 24766757 24767431 0.000000e+00 841
2 TraesCS1D01G006200 chr1D 92.308 143 10 1 2530 2672 397090064 397090205 4.510000e-48 202
3 TraesCS1D01G006200 chr2D 92.686 1422 88 12 697 2111 192292767 192294179 0.000000e+00 2036
4 TraesCS1D01G006200 chr2D 94.412 680 36 2 1 678 192292034 192292713 0.000000e+00 1044
5 TraesCS1D01G006200 chr2D 90.698 430 25 11 2128 2549 192294271 192294693 2.320000e-155 558
6 TraesCS1D01G006200 chr5A 93.114 1365 75 12 705 2052 604809181 604810543 0.000000e+00 1982
7 TraesCS1D01G006200 chr5A 92.192 1396 91 10 697 2079 555379926 555378536 0.000000e+00 1958
8 TraesCS1D01G006200 chr5A 95.852 675 26 2 6 678 604808445 604809119 0.000000e+00 1090
9 TraesCS1D01G006200 chr5A 93.088 680 45 2 1 678 555380659 555379980 0.000000e+00 994
10 TraesCS1D01G006200 chr5A 92.239 451 23 8 2103 2548 604810535 604810978 1.750000e-176 628
11 TraesCS1D01G006200 chr5A 91.266 458 28 7 2094 2546 555378557 555378107 4.890000e-172 614
12 TraesCS1D01G006200 chr5A 96.094 128 4 1 2546 2672 345316231 345316358 9.690000e-50 207
13 TraesCS1D01G006200 chr4A 92.935 1373 78 14 697 2052 215133242 215131872 0.000000e+00 1980
14 TraesCS1D01G006200 chr4A 91.335 1004 79 5 697 1694 694891694 694890693 0.000000e+00 1365
15 TraesCS1D01G006200 chr4A 95.704 675 27 2 6 678 215133970 215133296 0.000000e+00 1085
16 TraesCS1D01G006200 chr4A 93.667 679 40 3 2 678 694892425 694891748 0.000000e+00 1013
17 TraesCS1D01G006200 chr4A 92.239 451 24 7 2103 2548 215131880 215131436 1.750000e-176 628
18 TraesCS1D01G006200 chr6B 92.790 1373 81 11 697 2052 683636315 683637686 0.000000e+00 1971
19 TraesCS1D01G006200 chr6B 95.111 675 31 2 6 678 683635587 683636261 0.000000e+00 1062
20 TraesCS1D01G006200 chr6B 92.461 451 23 7 2103 2548 683637678 683638122 3.750000e-178 634
21 TraesCS1D01G006200 chr1A 90.040 1004 82 9 697 1694 496064505 496063514 0.000000e+00 1284
22 TraesCS1D01G006200 chr1A 93.842 682 40 2 1 680 496065238 496064557 0.000000e+00 1026
23 TraesCS1D01G006200 chr1A 91.608 143 10 1 2530 2672 299505082 299505222 2.100000e-46 196
24 TraesCS1D01G006200 chr6D 90.491 978 84 7 697 1672 439545426 439544456 0.000000e+00 1282
25 TraesCS1D01G006200 chr6D 92.941 680 46 2 1 678 439546159 439545480 0.000000e+00 989
26 TraesCS1D01G006200 chr6D 81.969 904 69 40 1655 2548 439544318 439543499 0.000000e+00 680
27 TraesCS1D01G006200 chr6D 93.478 138 6 3 2536 2672 218077939 218078074 4.510000e-48 202
28 TraesCS1D01G006200 chr3B 82.480 976 163 6 697 1669 69635045 69636015 0.000000e+00 848
29 TraesCS1D01G006200 chr3D 83.863 818 123 8 697 1512 44225722 44226532 0.000000e+00 771
30 TraesCS1D01G006200 chr3D 84.444 405 50 10 1410 1808 397181668 397182065 1.160000e-103 387
31 TraesCS1D01G006200 chr3D 97.581 124 3 0 2549 2672 272298002 272297879 2.080000e-51 213
32 TraesCS1D01G006200 chr3D 97.561 123 3 0 2550 2672 297207374 297207252 7.490000e-51 211
33 TraesCS1D01G006200 chr7D 96.923 130 2 2 2543 2672 157852786 157852913 1.610000e-52 217
34 TraesCS1D01G006200 chr4D 91.275 149 11 2 2525 2672 472869167 472869314 4.510000e-48 202
35 TraesCS1D01G006200 chr6A 92.308 143 7 4 2532 2672 509299361 509299501 1.620000e-47 200


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 TraesCS1D01G006200 chr1D 2880608 2883279 2671 True 4935.000000 4935 100.000000 1 2672 1 chr1D.!!$R1 2671
1 TraesCS1D01G006200 chr1D 24766757 24767431 674 False 841.000000 841 89.185000 6 678 1 chr1D.!!$F1 672
2 TraesCS1D01G006200 chr2D 192292034 192294693 2659 False 1212.666667 2036 92.598667 1 2549 3 chr2D.!!$F1 2548
3 TraesCS1D01G006200 chr5A 604808445 604810978 2533 False 1233.333333 1982 93.735000 6 2548 3 chr5A.!!$F2 2542
4 TraesCS1D01G006200 chr5A 555378107 555380659 2552 True 1188.666667 1958 92.182000 1 2546 3 chr5A.!!$R1 2545
5 TraesCS1D01G006200 chr4A 215131436 215133970 2534 True 1231.000000 1980 93.626000 6 2548 3 chr4A.!!$R1 2542
6 TraesCS1D01G006200 chr4A 694890693 694892425 1732 True 1189.000000 1365 92.501000 2 1694 2 chr4A.!!$R2 1692
7 TraesCS1D01G006200 chr6B 683635587 683638122 2535 False 1222.333333 1971 93.454000 6 2548 3 chr6B.!!$F1 2542
8 TraesCS1D01G006200 chr1A 496063514 496065238 1724 True 1155.000000 1284 91.941000 1 1694 2 chr1A.!!$R1 1693
9 TraesCS1D01G006200 chr6D 439543499 439546159 2660 True 983.666667 1282 88.467000 1 2548 3 chr6D.!!$R1 2547
10 TraesCS1D01G006200 chr3B 69635045 69636015 970 False 848.000000 848 82.480000 697 1669 1 chr3B.!!$F1 972
11 TraesCS1D01G006200 chr3D 44225722 44226532 810 False 771.000000 771 83.863000 697 1512 1 chr3D.!!$F1 815

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
537 540 1.066430 TCACAAGCATAACCGGGAGAC 60.066 52.381 6.32 0.00 0.00 3.36 F
1212 1251 0.682209 GGGAAGATGTGGTGCAGCAT 60.682 55.000 23.18 6.82 35.63 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1599 0.035439 ATTGCCTTGTACCCACGGAG 60.035 55.0 0.00 0.0 31.71 4.63 R
2586 2911 0.106819 GTGCTGCATCATCCCTTCCT 60.107 55.0 5.27 0.0 0.00 3.36 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
200 202 4.566004 TCGAAGAACAATGAGTACCCAAG 58.434 43.478 0.00 0.00 0.00 3.61
213 215 5.546499 TGAGTACCCAAGAAACCTTATGACT 59.454 40.000 0.00 0.00 0.00 3.41
217 219 4.351111 ACCCAAGAAACCTTATGACTGACT 59.649 41.667 0.00 0.00 0.00 3.41
252 255 3.676646 GGAAACTGCAATTTCTGATGTGC 59.323 43.478 19.04 0.00 38.43 4.57
265 268 4.876701 TGTGCTCCCTCACACAAC 57.123 55.556 0.00 0.00 43.48 3.32
504 507 4.081476 GGGCTCCTGCATACTTCAAAAATT 60.081 41.667 0.00 0.00 41.91 1.82
526 529 6.916360 TTATTTCTTCCCTTTCACAAGCAT 57.084 33.333 0.00 0.00 0.00 3.79
537 540 1.066430 TCACAAGCATAACCGGGAGAC 60.066 52.381 6.32 0.00 0.00 3.36
577 580 2.254546 TTCAAGACGTTGGTGCATCT 57.745 45.000 0.00 0.00 34.09 2.90
615 618 7.701539 TTCACATTTGTAAGGCAGTATGAAT 57.298 32.000 0.00 0.00 39.69 2.57
694 697 6.589830 GACAACATCGACAGCTTATAATGT 57.410 37.500 0.00 0.00 0.00 2.71
756 794 8.077991 GCAGCATCAACAGCTTATATAATCAAA 58.922 33.333 0.00 0.00 41.14 2.69
793 831 5.692115 TGAGCAGGAAGGTATCATGTTTA 57.308 39.130 0.00 0.00 41.83 2.01
840 878 3.291584 TCCAAAGTTGTACCATGTGCAA 58.708 40.909 0.00 0.00 35.94 4.08
867 905 3.952323 TGATAGAAGAGGGGTTGTACTCG 59.048 47.826 0.00 0.00 38.72 4.18
1031 1069 1.850345 TGGGAGGTTCCTTGAGTTTGT 59.150 47.619 0.00 0.00 36.57 2.83
1032 1070 2.158667 TGGGAGGTTCCTTGAGTTTGTC 60.159 50.000 0.00 0.00 36.57 3.18
1041 1079 3.578716 TCCTTGAGTTTGTCCTACCAGAG 59.421 47.826 0.00 0.00 0.00 3.35
1212 1251 0.682209 GGGAAGATGTGGTGCAGCAT 60.682 55.000 23.18 6.82 35.63 3.79
1213 1252 0.737219 GGAAGATGTGGTGCAGCATC 59.263 55.000 23.18 16.31 41.13 3.91
1214 1253 1.456296 GAAGATGTGGTGCAGCATCA 58.544 50.000 23.18 20.47 42.72 3.07
1271 1314 1.047801 GGAGCAAACCCACAACCATT 58.952 50.000 0.00 0.00 0.00 3.16
1300 1346 2.254546 ACAAAATCCTGCTCGTGTGA 57.745 45.000 0.00 0.00 0.00 3.58
1404 1454 6.572167 CTTCAGAAAGAAGCCAAGAAAGAT 57.428 37.500 0.00 0.00 46.54 2.40
1412 1462 6.264841 AGAAGCCAAGAAAGATAGCAAAAG 57.735 37.500 0.00 0.00 0.00 2.27
1450 1512 2.032178 AGCAAGAAAGAAGACAACGTGC 59.968 45.455 0.00 0.00 36.55 5.34
1489 1551 6.521255 GCCAAAACCTAGGAGGAAAGTTACTA 60.521 42.308 17.98 0.00 37.67 1.82
1527 1589 7.552687 AGTGAAGAAGAACACACTATCAAAACA 59.447 33.333 0.00 0.00 40.96 2.83
1537 1599 6.017934 ACACACTATCAAAACATGTGAGTCAC 60.018 38.462 16.68 16.68 42.63 3.67
1544 1606 0.318441 ACATGTGAGTCACTCCGTGG 59.682 55.000 23.29 9.22 35.11 4.94
1828 2061 1.330521 GTTGCTCGTGTTTCTGCTCAA 59.669 47.619 0.00 0.00 0.00 3.02
1876 2111 8.140628 TGTTCAAAAAGTTCATATTGCTGCTAA 58.859 29.630 0.00 0.00 0.00 3.09
1898 2134 6.451064 AAAAATAAGGTGAGGGCGAAATAG 57.549 37.500 0.00 0.00 0.00 1.73
2028 2265 9.635520 GTGTTGATTCTCTCAAATGAATTTCAT 57.364 29.630 6.06 6.06 45.27 2.57
2169 2482 5.338365 GCTTCTTCCAGCAACATTTATCAG 58.662 41.667 0.00 0.00 39.83 2.90
2185 2498 9.034544 ACATTTATCAGAAAAAGTTGTTGCTTC 57.965 29.630 0.00 0.00 0.00 3.86
2186 2499 9.033481 CATTTATCAGAAAAAGTTGTTGCTTCA 57.967 29.630 0.00 0.00 0.00 3.02
2187 2500 8.994429 TTTATCAGAAAAAGTTGTTGCTTCAA 57.006 26.923 0.00 0.00 0.00 2.69
2274 2587 4.247267 ACATTGTGGCTGATTTTGTGAG 57.753 40.909 0.00 0.00 0.00 3.51
2374 2694 4.744631 AGCACCAAACAGCGAAATTTTTAG 59.255 37.500 0.00 0.00 35.48 1.85
2497 2822 4.272489 CATCCAAAAGAGCCCAACATCTA 58.728 43.478 0.00 0.00 0.00 1.98
2523 2848 8.360390 AGTTTCCTTTACATGGAGTTTCATTTC 58.640 33.333 0.00 0.00 34.76 2.17
2549 2874 6.432162 ACACACAAAGATAACAGAGATGCATT 59.568 34.615 0.00 0.00 0.00 3.56
2550 2875 6.745907 CACACAAAGATAACAGAGATGCATTG 59.254 38.462 0.00 0.00 0.00 2.82
2551 2876 6.656270 ACACAAAGATAACAGAGATGCATTGA 59.344 34.615 0.00 0.00 0.00 2.57
2552 2877 7.338703 ACACAAAGATAACAGAGATGCATTGAT 59.661 33.333 0.00 0.00 0.00 2.57
2553 2878 7.644157 CACAAAGATAACAGAGATGCATTGATG 59.356 37.037 0.00 2.42 0.00 3.07
2563 2888 2.953669 GCATTGATGCGGCTTGAAG 58.046 52.632 0.00 0.00 44.67 3.02
2564 2889 1.143969 GCATTGATGCGGCTTGAAGC 61.144 55.000 9.04 9.04 44.67 3.86
2565 2890 0.454600 CATTGATGCGGCTTGAAGCT 59.545 50.000 17.59 0.00 41.99 3.74
2566 2891 1.672363 CATTGATGCGGCTTGAAGCTA 59.328 47.619 17.59 4.53 41.99 3.32
2567 2892 1.086696 TTGATGCGGCTTGAAGCTAC 58.913 50.000 17.59 9.86 41.99 3.58
2568 2893 1.083806 TGATGCGGCTTGAAGCTACG 61.084 55.000 17.59 13.81 41.99 3.51
2569 2894 1.079127 ATGCGGCTTGAAGCTACGT 60.079 52.632 17.59 7.92 41.99 3.57
2570 2895 1.084370 ATGCGGCTTGAAGCTACGTC 61.084 55.000 17.59 9.55 41.99 4.34
2571 2896 2.789203 GCGGCTTGAAGCTACGTCG 61.789 63.158 17.59 12.35 41.99 5.12
2572 2897 2.158959 CGGCTTGAAGCTACGTCGG 61.159 63.158 17.59 0.00 41.99 4.79
2573 2898 1.080025 GGCTTGAAGCTACGTCGGT 60.080 57.895 17.59 0.00 41.99 4.69
2574 2899 0.171903 GGCTTGAAGCTACGTCGGTA 59.828 55.000 17.59 0.00 41.99 4.02
2575 2900 1.202382 GGCTTGAAGCTACGTCGGTAT 60.202 52.381 17.59 0.00 41.99 2.73
2576 2901 2.537401 GCTTGAAGCTACGTCGGTATT 58.463 47.619 10.44 0.00 38.45 1.89
2577 2902 2.928116 GCTTGAAGCTACGTCGGTATTT 59.072 45.455 10.44 0.00 38.45 1.40
2578 2903 3.000022 GCTTGAAGCTACGTCGGTATTTC 60.000 47.826 10.44 0.00 38.45 2.17
2579 2904 3.155093 TGAAGCTACGTCGGTATTTCC 57.845 47.619 0.00 0.00 0.00 3.13
2580 2905 2.159198 TGAAGCTACGTCGGTATTTCCC 60.159 50.000 0.00 0.00 0.00 3.97
2581 2906 0.749049 AGCTACGTCGGTATTTCCCC 59.251 55.000 0.00 0.00 0.00 4.81
2582 2907 0.461135 GCTACGTCGGTATTTCCCCA 59.539 55.000 0.00 0.00 0.00 4.96
2583 2908 1.134729 GCTACGTCGGTATTTCCCCAA 60.135 52.381 0.00 0.00 0.00 4.12
2584 2909 2.677613 GCTACGTCGGTATTTCCCCAAA 60.678 50.000 0.00 0.00 0.00 3.28
2585 2910 2.103537 ACGTCGGTATTTCCCCAAAG 57.896 50.000 0.00 0.00 0.00 2.77
2586 2911 1.624813 ACGTCGGTATTTCCCCAAAGA 59.375 47.619 0.00 0.00 0.00 2.52
2587 2912 2.277084 CGTCGGTATTTCCCCAAAGAG 58.723 52.381 0.00 0.00 0.00 2.85
2588 2913 2.640184 GTCGGTATTTCCCCAAAGAGG 58.360 52.381 0.00 0.00 37.03 3.69
2589 2914 2.237893 GTCGGTATTTCCCCAAAGAGGA 59.762 50.000 0.00 0.00 41.22 3.71
2590 2915 2.914278 TCGGTATTTCCCCAAAGAGGAA 59.086 45.455 0.00 0.00 41.69 3.36
2591 2916 3.054655 TCGGTATTTCCCCAAAGAGGAAG 60.055 47.826 0.00 0.00 44.07 3.46
2592 2917 3.632333 GGTATTTCCCCAAAGAGGAAGG 58.368 50.000 0.00 0.00 44.07 3.46
2593 2918 2.928036 ATTTCCCCAAAGAGGAAGGG 57.072 50.000 0.00 0.00 44.07 3.95
2595 2920 3.858475 TCCCCAAAGAGGAAGGGAT 57.142 52.632 0.00 0.00 43.81 3.85
2596 2921 1.298953 TCCCCAAAGAGGAAGGGATG 58.701 55.000 0.00 0.00 43.81 3.51
2597 2922 1.203557 TCCCCAAAGAGGAAGGGATGA 60.204 52.381 0.00 0.00 43.81 2.92
2598 2923 1.855599 CCCCAAAGAGGAAGGGATGAT 59.144 52.381 0.00 0.00 45.80 2.45
2599 2924 2.423947 CCCCAAAGAGGAAGGGATGATG 60.424 54.545 0.00 0.00 45.80 3.07
2600 2925 2.305009 CCAAAGAGGAAGGGATGATGC 58.695 52.381 0.00 0.00 41.22 3.91
2601 2926 2.357465 CCAAAGAGGAAGGGATGATGCA 60.357 50.000 0.00 0.00 41.22 3.96
2602 2927 2.950309 CAAAGAGGAAGGGATGATGCAG 59.050 50.000 0.00 0.00 0.00 4.41
2603 2928 0.473326 AGAGGAAGGGATGATGCAGC 59.527 55.000 0.00 0.00 0.00 5.25
2604 2929 0.182061 GAGGAAGGGATGATGCAGCA 59.818 55.000 7.31 7.31 0.00 4.41
2605 2930 0.106819 AGGAAGGGATGATGCAGCAC 60.107 55.000 6.89 0.81 0.00 4.40
2606 2931 0.394762 GGAAGGGATGATGCAGCACA 60.395 55.000 6.89 0.00 0.00 4.57
2607 2932 1.022735 GAAGGGATGATGCAGCACAG 58.977 55.000 6.89 0.00 0.00 3.66
2608 2933 0.330604 AAGGGATGATGCAGCACAGT 59.669 50.000 6.89 0.00 0.00 3.55
2609 2934 0.393944 AGGGATGATGCAGCACAGTG 60.394 55.000 6.89 0.00 0.00 3.66
2610 2935 1.381928 GGGATGATGCAGCACAGTGG 61.382 60.000 6.89 0.00 0.00 4.00
2611 2936 1.432251 GATGATGCAGCACAGTGGC 59.568 57.895 6.89 0.00 0.00 5.01
2612 2937 1.303806 ATGATGCAGCACAGTGGCA 60.304 52.632 6.89 6.91 42.43 4.92
2613 2938 1.313091 ATGATGCAGCACAGTGGCAG 61.313 55.000 6.89 0.07 41.40 4.85
2614 2939 1.970114 GATGCAGCACAGTGGCAGT 60.970 57.895 0.00 0.00 41.40 4.40
2615 2940 0.674581 GATGCAGCACAGTGGCAGTA 60.675 55.000 0.00 0.00 41.40 2.74
2616 2941 0.675837 ATGCAGCACAGTGGCAGTAG 60.676 55.000 0.00 0.00 41.40 2.57
2617 2942 2.037136 GCAGCACAGTGGCAGTAGG 61.037 63.158 1.84 0.00 35.83 3.18
2618 2943 1.372683 CAGCACAGTGGCAGTAGGT 59.627 57.895 1.84 0.00 35.83 3.08
2619 2944 0.608130 CAGCACAGTGGCAGTAGGTA 59.392 55.000 1.84 0.00 35.83 3.08
2620 2945 1.208052 CAGCACAGTGGCAGTAGGTAT 59.792 52.381 1.84 0.00 35.83 2.73
2621 2946 1.909302 AGCACAGTGGCAGTAGGTATT 59.091 47.619 1.84 0.00 35.83 1.89
2622 2947 2.305927 AGCACAGTGGCAGTAGGTATTT 59.694 45.455 1.84 0.00 35.83 1.40
2623 2948 2.678336 GCACAGTGGCAGTAGGTATTTC 59.322 50.000 1.84 0.00 0.00 2.17
2624 2949 3.270877 CACAGTGGCAGTAGGTATTTCC 58.729 50.000 0.00 0.00 0.00 3.13
2625 2950 2.238898 ACAGTGGCAGTAGGTATTTCCC 59.761 50.000 0.00 0.00 36.75 3.97
2626 2951 2.505819 CAGTGGCAGTAGGTATTTCCCT 59.494 50.000 0.00 0.00 38.70 4.20
2627 2952 2.772515 AGTGGCAGTAGGTATTTCCCTC 59.227 50.000 0.00 0.00 35.97 4.30
2628 2953 2.504175 GTGGCAGTAGGTATTTCCCTCA 59.496 50.000 0.00 0.00 35.97 3.86
2629 2954 2.771943 TGGCAGTAGGTATTTCCCTCAG 59.228 50.000 0.00 0.00 35.97 3.35
2630 2955 3.039011 GGCAGTAGGTATTTCCCTCAGA 58.961 50.000 0.00 0.00 35.97 3.27
2631 2956 3.648545 GGCAGTAGGTATTTCCCTCAGAT 59.351 47.826 0.00 0.00 35.97 2.90
2632 2957 4.503991 GGCAGTAGGTATTTCCCTCAGATG 60.504 50.000 0.00 0.00 35.97 2.90
2633 2958 4.101741 GCAGTAGGTATTTCCCTCAGATGT 59.898 45.833 0.00 0.00 35.97 3.06
2634 2959 5.605534 CAGTAGGTATTTCCCTCAGATGTG 58.394 45.833 0.00 0.00 35.97 3.21
2635 2960 5.363868 CAGTAGGTATTTCCCTCAGATGTGA 59.636 44.000 0.00 0.00 35.97 3.58
2636 2961 5.964477 AGTAGGTATTTCCCTCAGATGTGAA 59.036 40.000 0.00 0.00 35.97 3.18
2637 2962 5.779241 AGGTATTTCCCTCAGATGTGAAA 57.221 39.130 0.00 0.00 36.75 2.69
2638 2963 5.501156 AGGTATTTCCCTCAGATGTGAAAC 58.499 41.667 0.00 0.00 36.75 2.78
2639 2964 4.640647 GGTATTTCCCTCAGATGTGAAACC 59.359 45.833 0.00 0.00 34.36 3.27
2640 2965 3.874383 TTTCCCTCAGATGTGAAACCA 57.126 42.857 0.00 0.00 34.36 3.67
2641 2966 3.874383 TTCCCTCAGATGTGAAACCAA 57.126 42.857 0.00 0.00 34.36 3.67
2642 2967 3.423539 TCCCTCAGATGTGAAACCAAG 57.576 47.619 0.00 0.00 34.36 3.61
2643 2968 2.040278 TCCCTCAGATGTGAAACCAAGG 59.960 50.000 0.00 0.00 34.36 3.61
2644 2969 2.224867 CCCTCAGATGTGAAACCAAGGT 60.225 50.000 0.00 0.00 34.36 3.50
2645 2970 3.490348 CCTCAGATGTGAAACCAAGGTT 58.510 45.455 0.00 0.00 40.45 3.50
2646 2971 4.506625 CCCTCAGATGTGAAACCAAGGTTA 60.507 45.833 4.68 0.00 37.35 2.85
2647 2972 5.256474 CCTCAGATGTGAAACCAAGGTTAT 58.744 41.667 4.68 0.00 37.35 1.89
2648 2973 5.355350 CCTCAGATGTGAAACCAAGGTTATC 59.645 44.000 4.68 4.81 37.35 1.75
2649 2974 4.935205 TCAGATGTGAAACCAAGGTTATCG 59.065 41.667 4.68 2.55 37.35 2.92
2650 2975 4.935205 CAGATGTGAAACCAAGGTTATCGA 59.065 41.667 4.68 0.00 37.35 3.59
2651 2976 5.411361 CAGATGTGAAACCAAGGTTATCGAA 59.589 40.000 4.68 0.00 37.35 3.71
2652 2977 5.411669 AGATGTGAAACCAAGGTTATCGAAC 59.588 40.000 4.68 1.11 37.35 3.95
2653 2978 3.816523 TGTGAAACCAAGGTTATCGAACC 59.183 43.478 4.68 0.00 46.57 3.62
2665 2990 4.179298 GTTATCGAACCAGTAGGACAACC 58.821 47.826 0.00 0.00 38.69 3.77
2666 2991 1.707106 TCGAACCAGTAGGACAACCA 58.293 50.000 0.00 0.00 38.69 3.67
2667 2992 2.040939 TCGAACCAGTAGGACAACCAA 58.959 47.619 0.00 0.00 38.69 3.67
2668 2993 2.036733 TCGAACCAGTAGGACAACCAAG 59.963 50.000 0.00 0.00 38.69 3.61
2669 2994 2.152016 GAACCAGTAGGACAACCAAGC 58.848 52.381 0.00 0.00 38.69 4.01
2670 2995 1.136828 ACCAGTAGGACAACCAAGCA 58.863 50.000 0.00 0.00 38.69 3.91
2671 2996 1.493022 ACCAGTAGGACAACCAAGCAA 59.507 47.619 0.00 0.00 38.69 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 180 4.282449 TCTTGGGTACTCATTGTTCTTCGA 59.718 41.667 0.00 0.00 0.00 3.71
182 184 5.070685 GGTTTCTTGGGTACTCATTGTTCT 58.929 41.667 0.00 0.00 0.00 3.01
200 202 7.159322 TCTCACTAGTCAGTCATAAGGTTTC 57.841 40.000 0.00 0.00 30.46 2.78
213 215 4.284490 AGTTTCCATTGCTCTCACTAGTCA 59.716 41.667 0.00 0.00 0.00 3.41
217 219 3.244526 TGCAGTTTCCATTGCTCTCACTA 60.245 43.478 0.00 0.00 40.87 2.74
252 255 1.210478 CCTATGGGTTGTGTGAGGGAG 59.790 57.143 0.00 0.00 0.00 4.30
265 268 1.176527 CCACTTGCAACACCTATGGG 58.823 55.000 0.00 0.00 38.88 4.00
504 507 7.093945 GGTTATGCTTGTGAAAGGGAAGAAATA 60.094 37.037 0.00 0.00 0.00 1.40
526 529 0.616679 CCCTTCTGGTCTCCCGGTTA 60.617 60.000 0.00 0.00 38.38 2.85
537 540 5.653769 TGAAATAAGAATTCAGCCCTTCTGG 59.346 40.000 8.44 0.00 43.06 3.86
577 580 6.622549 ACAAATGTGAAAACCGAGTTTTGTA 58.377 32.000 16.21 5.89 44.33 2.41
615 618 5.938125 GGTCTAGCATTGTTTCTTGTAGGAA 59.062 40.000 0.00 0.00 0.00 3.36
681 684 4.188462 TGCTGCGTTACATTATAAGCTGT 58.812 39.130 0.00 0.00 0.00 4.40
684 687 5.597813 AGATGCTGCGTTACATTATAAGC 57.402 39.130 0.00 0.00 0.00 3.09
685 688 6.852853 CCAAAGATGCTGCGTTACATTATAAG 59.147 38.462 0.00 0.00 0.00 1.73
686 689 6.724263 CCAAAGATGCTGCGTTACATTATAA 58.276 36.000 0.00 0.00 0.00 0.98
688 691 4.498009 GCCAAAGATGCTGCGTTACATTAT 60.498 41.667 0.00 0.00 0.00 1.28
689 692 3.181501 GCCAAAGATGCTGCGTTACATTA 60.182 43.478 0.00 0.00 0.00 1.90
690 693 2.415893 GCCAAAGATGCTGCGTTACATT 60.416 45.455 0.00 0.00 0.00 2.71
691 694 1.133025 GCCAAAGATGCTGCGTTACAT 59.867 47.619 0.00 0.00 0.00 2.29
693 696 0.521291 TGCCAAAGATGCTGCGTTAC 59.479 50.000 0.00 0.00 0.00 2.50
694 697 1.199789 CTTGCCAAAGATGCTGCGTTA 59.800 47.619 0.00 0.00 35.19 3.18
756 794 3.341823 CTGCTCAAGATTAGGCACTTGT 58.658 45.455 0.00 0.00 42.50 3.16
840 878 2.503356 CAACCCCTCTTCTATCACAGCT 59.497 50.000 0.00 0.00 0.00 4.24
867 905 4.253685 TCTCAAAGTAATGGCAGCTACAC 58.746 43.478 10.98 0.00 0.00 2.90
915 953 7.880195 ACATTAAGCTGTATCATCACCCTTATC 59.120 37.037 0.00 0.00 0.00 1.75
982 1020 3.000041 CCATGTTTGTCGTAGCTGCTTA 59.000 45.455 7.79 0.00 0.00 3.09
1031 1069 3.827302 GAGAGTGTTTGTCTCTGGTAGGA 59.173 47.826 0.05 0.00 41.58 2.94
1032 1070 3.574396 TGAGAGTGTTTGTCTCTGGTAGG 59.426 47.826 0.05 0.00 41.58 3.18
1041 1079 5.051641 CGAGTTGTACTTGAGAGTGTTTGTC 60.052 44.000 0.00 0.00 36.60 3.18
1145 1184 2.280660 CTATGGGCCAGAGCTGCG 60.281 66.667 16.30 0.00 39.73 5.18
1212 1251 2.416107 CTGCTTGAGGGGGTTGCTGA 62.416 60.000 0.00 0.00 0.00 4.26
1213 1252 1.975407 CTGCTTGAGGGGGTTGCTG 60.975 63.158 0.00 0.00 0.00 4.41
1214 1253 2.437897 CTGCTTGAGGGGGTTGCT 59.562 61.111 0.00 0.00 0.00 3.91
1271 1314 2.627945 CAGGATTTTGTAGCGGTGCTA 58.372 47.619 3.95 0.00 40.44 3.49
1300 1346 0.878961 GTTGGTCGACCTTGCTTCGT 60.879 55.000 33.39 0.00 37.73 3.85
1404 1454 4.887071 TCTTTCTTGGCTGTTCTTTTGCTA 59.113 37.500 0.00 0.00 0.00 3.49
1412 1462 3.715628 TGCTTTCTTTCTTGGCTGTTC 57.284 42.857 0.00 0.00 0.00 3.18
1450 1512 1.221466 TTTGGCTTGCTCGACGACTG 61.221 55.000 0.00 0.00 0.00 3.51
1489 1551 6.127647 TGTTCTTCTTCACTGCAAAATGAACT 60.128 34.615 4.10 0.00 33.51 3.01
1537 1599 0.035439 ATTGCCTTGTACCCACGGAG 60.035 55.000 0.00 0.00 31.71 4.63
1544 1606 0.381801 CGCCATCATTGCCTTGTACC 59.618 55.000 0.00 0.00 0.00 3.34
1563 1625 7.593825 ACTGACATTTTGTTGTAAGATTAGCC 58.406 34.615 0.00 0.00 33.03 3.93
1745 1966 8.654215 GGACTTAAATTTTCAGTACTTCTACCG 58.346 37.037 0.00 0.00 0.00 4.02
1767 1988 3.933861 AAACCTCTGACAAAGTGGACT 57.066 42.857 0.71 0.00 41.36 3.85
1828 2061 2.830104 ACGCGGTTTTGAGAAGTAACT 58.170 42.857 12.47 0.00 0.00 2.24
1876 2111 5.506708 ACTATTTCGCCCTCACCTTATTTT 58.493 37.500 0.00 0.00 0.00 1.82
1880 2115 5.364446 TCATAACTATTTCGCCCTCACCTTA 59.636 40.000 0.00 0.00 0.00 2.69
1898 2134 8.905702 CAAAACACAGTAAGAATGCTTCATAAC 58.094 33.333 0.00 0.00 35.56 1.89
2019 2256 9.703892 ATTGTCGGAAAATTTACATGAAATTCA 57.296 25.926 0.00 0.00 45.21 2.57
2028 2265 6.325919 AGAAGCATTGTCGGAAAATTTACA 57.674 33.333 0.00 0.00 0.00 2.41
2038 2275 2.253392 GCTGAAAGAAGCATTGTCGG 57.747 50.000 0.00 0.00 43.01 4.79
2229 2542 7.068593 TGTTAAGGAATTGGAATTGCTAGATGG 59.931 37.037 6.56 0.00 44.79 3.51
2231 2544 8.773033 ATGTTAAGGAATTGGAATTGCTAGAT 57.227 30.769 6.56 0.00 44.79 1.98
2274 2587 5.428253 TCTACCATGTGCTTCCTTATGTTC 58.572 41.667 0.00 0.00 0.00 3.18
2374 2694 8.082242 ACTATGTGGTGAATTTTAAGCAAGTTC 58.918 33.333 0.00 0.00 0.00 3.01
2466 2791 2.800250 CTCTTTTGGATGGCTGGAACT 58.200 47.619 0.00 0.00 0.00 3.01
2467 2792 1.203287 GCTCTTTTGGATGGCTGGAAC 59.797 52.381 0.00 0.00 0.00 3.62
2523 2848 5.179929 TGCATCTCTGTTATCTTTGTGTGTG 59.820 40.000 0.00 0.00 0.00 3.82
2549 2874 1.083806 CGTAGCTTCAAGCCGCATCA 61.084 55.000 5.53 0.00 43.77 3.07
2550 2875 1.084370 ACGTAGCTTCAAGCCGCATC 61.084 55.000 5.53 0.00 43.77 3.91
2551 2876 1.079127 ACGTAGCTTCAAGCCGCAT 60.079 52.632 5.53 0.00 43.77 4.73
2552 2877 1.736645 GACGTAGCTTCAAGCCGCA 60.737 57.895 5.53 0.00 43.77 5.69
2553 2878 2.789203 CGACGTAGCTTCAAGCCGC 61.789 63.158 5.53 0.00 43.77 6.53
2554 2879 2.158959 CCGACGTAGCTTCAAGCCG 61.159 63.158 5.53 6.11 43.77 5.52
2555 2880 0.171903 TACCGACGTAGCTTCAAGCC 59.828 55.000 5.53 0.00 43.77 4.35
2556 2881 2.205307 ATACCGACGTAGCTTCAAGC 57.795 50.000 0.00 0.00 42.84 4.01
2557 2882 3.550678 GGAAATACCGACGTAGCTTCAAG 59.449 47.826 0.00 0.00 0.00 3.02
2558 2883 3.514645 GGAAATACCGACGTAGCTTCAA 58.485 45.455 0.00 0.00 0.00 2.69
2559 2884 2.159198 GGGAAATACCGACGTAGCTTCA 60.159 50.000 0.00 0.00 40.11 3.02
2560 2885 2.467838 GGGAAATACCGACGTAGCTTC 58.532 52.381 0.00 0.00 40.11 3.86
2561 2886 1.137675 GGGGAAATACCGACGTAGCTT 59.862 52.381 0.00 0.00 40.11 3.74
2562 2887 0.749049 GGGGAAATACCGACGTAGCT 59.251 55.000 0.00 0.00 40.11 3.32
2563 2888 0.461135 TGGGGAAATACCGACGTAGC 59.539 55.000 0.00 0.00 40.11 3.58
2564 2889 2.965572 TTGGGGAAATACCGACGTAG 57.034 50.000 0.00 0.00 40.11 3.51
2565 2890 2.830923 TCTTTGGGGAAATACCGACGTA 59.169 45.455 0.00 0.00 40.11 3.57
2566 2891 1.624813 TCTTTGGGGAAATACCGACGT 59.375 47.619 0.00 0.00 40.11 4.34
2567 2892 2.277084 CTCTTTGGGGAAATACCGACG 58.723 52.381 0.00 0.00 40.11 5.12
2568 2893 2.237893 TCCTCTTTGGGGAAATACCGAC 59.762 50.000 0.00 0.00 40.11 4.79
2569 2894 2.553464 TCCTCTTTGGGGAAATACCGA 58.447 47.619 0.00 0.00 40.11 4.69
2570 2895 3.279434 CTTCCTCTTTGGGGAAATACCG 58.721 50.000 0.32 0.00 41.58 4.02
2571 2896 3.627492 CCCTTCCTCTTTGGGGAAATACC 60.627 52.174 0.32 0.00 41.58 2.73
2572 2897 3.268595 TCCCTTCCTCTTTGGGGAAATAC 59.731 47.826 0.32 0.00 44.10 1.89
2573 2898 3.547903 TCCCTTCCTCTTTGGGGAAATA 58.452 45.455 0.32 0.00 44.10 1.40
2574 2899 2.368170 TCCCTTCCTCTTTGGGGAAAT 58.632 47.619 0.32 0.00 44.10 2.17
2575 2900 1.841334 TCCCTTCCTCTTTGGGGAAA 58.159 50.000 0.32 0.00 44.10 3.13
2576 2901 3.608912 TCCCTTCCTCTTTGGGGAA 57.391 52.632 0.00 0.00 44.10 3.97
2578 2903 1.298953 TCATCCCTTCCTCTTTGGGG 58.701 55.000 0.00 0.00 41.22 4.96
2579 2904 2.941480 CATCATCCCTTCCTCTTTGGG 58.059 52.381 0.00 0.00 42.20 4.12
2580 2905 2.305009 GCATCATCCCTTCCTCTTTGG 58.695 52.381 0.00 0.00 37.10 3.28
2581 2906 2.950309 CTGCATCATCCCTTCCTCTTTG 59.050 50.000 0.00 0.00 0.00 2.77
2582 2907 2.686118 GCTGCATCATCCCTTCCTCTTT 60.686 50.000 0.00 0.00 0.00 2.52
2583 2908 1.133853 GCTGCATCATCCCTTCCTCTT 60.134 52.381 0.00 0.00 0.00 2.85
2584 2909 0.473326 GCTGCATCATCCCTTCCTCT 59.527 55.000 0.00 0.00 0.00 3.69
2585 2910 0.182061 TGCTGCATCATCCCTTCCTC 59.818 55.000 0.00 0.00 0.00 3.71
2586 2911 0.106819 GTGCTGCATCATCCCTTCCT 60.107 55.000 5.27 0.00 0.00 3.36
2587 2912 0.394762 TGTGCTGCATCATCCCTTCC 60.395 55.000 5.27 0.00 0.00 3.46
2588 2913 1.022735 CTGTGCTGCATCATCCCTTC 58.977 55.000 5.27 0.00 0.00 3.46
2589 2914 0.330604 ACTGTGCTGCATCATCCCTT 59.669 50.000 5.27 0.00 0.00 3.95
2590 2915 0.393944 CACTGTGCTGCATCATCCCT 60.394 55.000 5.27 0.00 0.00 4.20
2591 2916 1.381928 CCACTGTGCTGCATCATCCC 61.382 60.000 5.27 0.00 0.00 3.85
2592 2917 2.001361 GCCACTGTGCTGCATCATCC 62.001 60.000 5.27 0.00 0.00 3.51
2593 2918 1.310216 TGCCACTGTGCTGCATCATC 61.310 55.000 5.27 0.00 0.00 2.92
2594 2919 1.303806 TGCCACTGTGCTGCATCAT 60.304 52.632 5.27 0.00 0.00 2.45
2595 2920 1.969589 CTGCCACTGTGCTGCATCA 60.970 57.895 5.27 5.20 33.97 3.07
2596 2921 0.674581 TACTGCCACTGTGCTGCATC 60.675 55.000 5.27 0.09 33.97 3.91
2597 2922 0.675837 CTACTGCCACTGTGCTGCAT 60.676 55.000 5.27 5.96 33.97 3.96
2598 2923 1.301953 CTACTGCCACTGTGCTGCA 60.302 57.895 10.55 10.55 33.92 4.41
2599 2924 2.037136 CCTACTGCCACTGTGCTGC 61.037 63.158 1.29 2.04 33.92 5.25
2600 2925 0.608130 TACCTACTGCCACTGTGCTG 59.392 55.000 1.29 5.11 36.39 4.41
2601 2926 1.573108 ATACCTACTGCCACTGTGCT 58.427 50.000 1.29 0.00 0.00 4.40
2602 2927 2.403252 AATACCTACTGCCACTGTGC 57.597 50.000 1.29 0.00 0.00 4.57
2603 2928 3.270877 GGAAATACCTACTGCCACTGTG 58.729 50.000 0.00 0.00 35.41 3.66
2604 2929 2.238898 GGGAAATACCTACTGCCACTGT 59.761 50.000 0.00 0.00 38.98 3.55
2605 2930 2.505819 AGGGAAATACCTACTGCCACTG 59.494 50.000 0.00 0.00 39.65 3.66
2606 2931 2.772515 GAGGGAAATACCTACTGCCACT 59.227 50.000 0.00 0.00 42.10 4.00
2607 2932 2.504175 TGAGGGAAATACCTACTGCCAC 59.496 50.000 0.00 0.00 42.10 5.01
2608 2933 2.771943 CTGAGGGAAATACCTACTGCCA 59.228 50.000 0.00 0.00 42.10 4.92
2609 2934 3.039011 TCTGAGGGAAATACCTACTGCC 58.961 50.000 0.00 0.00 42.10 4.85
2610 2935 4.101741 ACATCTGAGGGAAATACCTACTGC 59.898 45.833 0.00 0.00 42.10 4.40
2611 2936 5.363868 TCACATCTGAGGGAAATACCTACTG 59.636 44.000 0.00 0.00 42.10 2.74
2612 2937 5.529289 TCACATCTGAGGGAAATACCTACT 58.471 41.667 0.00 0.00 42.10 2.57
2613 2938 5.871396 TCACATCTGAGGGAAATACCTAC 57.129 43.478 0.00 0.00 42.10 3.18
2614 2939 6.352737 GGTTTCACATCTGAGGGAAATACCTA 60.353 42.308 8.44 0.00 42.10 3.08
2615 2940 5.501156 GTTTCACATCTGAGGGAAATACCT 58.499 41.667 8.44 0.00 45.57 3.08
2616 2941 4.640647 GGTTTCACATCTGAGGGAAATACC 59.359 45.833 8.44 4.83 32.52 2.73
2617 2942 5.253330 TGGTTTCACATCTGAGGGAAATAC 58.747 41.667 8.44 6.61 32.52 1.89
2618 2943 5.512942 TGGTTTCACATCTGAGGGAAATA 57.487 39.130 8.44 1.76 32.52 1.40
2619 2944 4.387026 TGGTTTCACATCTGAGGGAAAT 57.613 40.909 8.44 0.00 32.52 2.17
2620 2945 3.874383 TGGTTTCACATCTGAGGGAAA 57.126 42.857 0.00 0.00 0.00 3.13
2621 2946 3.498481 CCTTGGTTTCACATCTGAGGGAA 60.498 47.826 0.00 0.00 0.00 3.97
2622 2947 2.040278 CCTTGGTTTCACATCTGAGGGA 59.960 50.000 0.00 0.00 0.00 4.20
2623 2948 2.224867 ACCTTGGTTTCACATCTGAGGG 60.225 50.000 0.00 0.00 0.00 4.30
2624 2949 3.146104 ACCTTGGTTTCACATCTGAGG 57.854 47.619 0.00 0.00 0.00 3.86
2625 2950 5.063944 CGATAACCTTGGTTTCACATCTGAG 59.936 44.000 10.52 0.00 0.00 3.35
2626 2951 4.935205 CGATAACCTTGGTTTCACATCTGA 59.065 41.667 10.52 0.00 0.00 3.27
2627 2952 4.935205 TCGATAACCTTGGTTTCACATCTG 59.065 41.667 10.52 4.99 0.00 2.90
2628 2953 5.160607 TCGATAACCTTGGTTTCACATCT 57.839 39.130 10.52 0.00 0.00 2.90
2629 2954 5.628134 GTTCGATAACCTTGGTTTCACATC 58.372 41.667 10.52 6.65 0.00 3.06
2630 2955 5.622770 GTTCGATAACCTTGGTTTCACAT 57.377 39.130 10.52 0.00 0.00 3.21
2642 2967 7.304933 TGGTTGTCCTACTGGTTCGATAACC 62.305 48.000 14.99 14.99 43.85 2.85
2643 2968 4.179298 GGTTGTCCTACTGGTTCGATAAC 58.821 47.826 0.00 0.00 34.66 1.89
2644 2969 3.833650 TGGTTGTCCTACTGGTTCGATAA 59.166 43.478 0.00 0.00 34.23 1.75
2645 2970 3.433343 TGGTTGTCCTACTGGTTCGATA 58.567 45.455 0.00 0.00 34.23 2.92
2646 2971 2.253610 TGGTTGTCCTACTGGTTCGAT 58.746 47.619 0.00 0.00 34.23 3.59
2647 2972 1.707106 TGGTTGTCCTACTGGTTCGA 58.293 50.000 0.00 0.00 34.23 3.71
2648 2973 2.413837 CTTGGTTGTCCTACTGGTTCG 58.586 52.381 0.00 0.00 34.23 3.95
2649 2974 2.152016 GCTTGGTTGTCCTACTGGTTC 58.848 52.381 0.00 0.00 34.23 3.62
2650 2975 1.493022 TGCTTGGTTGTCCTACTGGTT 59.507 47.619 0.00 0.00 34.23 3.67
2651 2976 1.136828 TGCTTGGTTGTCCTACTGGT 58.863 50.000 0.00 0.00 34.23 4.00
2652 2977 2.270352 TTGCTTGGTTGTCCTACTGG 57.730 50.000 0.00 0.00 34.23 4.00


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

AutoCloner maintained by Alex Coulton.