Multiple sequence alignment - TraesCS5D01G408100

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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 TraesCS5D01G408100 chr5D 100.000 2739 0 0 1 2739 472769936 472767198 0.000000e+00 5059.0
1 TraesCS5D01G408100 chr5D 85.300 517 44 20 1328 1819 472745824 472745315 3.150000e-139 505.0
2 TraesCS5D01G408100 chr5D 76.940 464 82 20 2092 2543 545512352 545511902 9.800000e-60 241.0
3 TraesCS5D01G408100 chr5D 89.773 176 18 0 363 538 472750154 472749979 2.740000e-55 226.0
4 TraesCS5D01G408100 chr5D 89.655 87 4 4 239 325 472751816 472751735 3.730000e-19 106.0
5 TraesCS5D01G408100 chr5B 85.948 1587 115 54 867 2394 580125321 580123784 0.000000e+00 1596.0
6 TraesCS5D01G408100 chr5B 89.044 1287 103 22 1328 2593 580115552 580114283 0.000000e+00 1561.0
7 TraesCS5D01G408100 chr5B 90.402 646 32 11 158 782 580127364 580126728 0.000000e+00 822.0
8 TraesCS5D01G408100 chr5B 83.135 925 61 50 962 1822 580111710 580110817 0.000000e+00 756.0
9 TraesCS5D01G408100 chr5B 81.089 349 49 10 2201 2546 587115970 587116304 2.090000e-66 263.0
10 TraesCS5D01G408100 chr5B 89.503 181 14 1 363 538 580120192 580120012 9.870000e-55 224.0
11 TraesCS5D01G408100 chr5B 91.824 159 11 2 1 159 580127564 580127408 1.280000e-53 220.0
12 TraesCS5D01G408100 chr5B 90.110 91 4 4 235 325 580120555 580120470 2.230000e-21 113.0
13 TraesCS5D01G408100 chr5A 83.658 1744 181 61 887 2593 592520523 592518847 0.000000e+00 1546.0
14 TraesCS5D01G408100 chr5A 83.725 639 82 15 1760 2391 592425183 592424560 3.930000e-163 584.0
15 TraesCS5D01G408100 chr5A 85.434 611 27 14 235 817 592521140 592520564 1.830000e-161 579.0
16 TraesCS5D01G408100 chr5A 84.926 544 49 19 1308 1826 592302727 592302192 1.120000e-143 520.0
17 TraesCS5D01G408100 chr5A 84.234 444 36 20 1328 1761 592474457 592474038 4.250000e-108 401.0
18 TraesCS5D01G408100 chr5A 80.676 414 60 13 2134 2546 598053020 598053414 1.230000e-78 303.0
19 TraesCS5D01G408100 chr5A 96.341 82 3 0 2598 2679 426702247 426702166 4.760000e-28 135.0
20 TraesCS5D01G408100 chr4A 75.356 702 127 30 1873 2543 623953505 623954191 2.060000e-76 296.0
21 TraesCS5D01G408100 chr1D 97.590 83 2 0 2597 2679 183009614 183009532 2.840000e-30 143.0
22 TraesCS5D01G408100 chr4B 82.500 160 25 3 1 159 657976537 657976380 1.320000e-28 137.0
23 TraesCS5D01G408100 chr3A 96.341 82 3 0 2598 2679 8553092 8553011 4.760000e-28 135.0
24 TraesCS5D01G408100 chr3A 89.320 103 8 2 2579 2679 8558854 8558753 2.860000e-25 126.0
25 TraesCS5D01G408100 chr2D 96.341 82 3 0 2598 2679 88153835 88153754 4.760000e-28 135.0
26 TraesCS5D01G408100 chr3B 97.436 78 2 0 2598 2675 449992502 449992579 1.710000e-27 134.0
27 TraesCS5D01G408100 chr7B 93.333 90 5 1 2594 2683 178126529 178126617 6.150000e-27 132.0
28 TraesCS5D01G408100 chrUn 95.122 82 4 0 2598 2679 45191889 45191808 2.210000e-26 130.0
29 TraesCS5D01G408100 chr6D 81.250 160 25 4 3 159 25534451 25534294 1.030000e-24 124.0
30 TraesCS5D01G408100 chr7A 91.111 90 8 0 2590 2679 712407509 712407598 3.700000e-24 122.0
31 TraesCS5D01G408100 chr1A 98.039 51 1 0 2369 2419 569951565 569951615 3.760000e-14 89.8
32 TraesCS5D01G408100 chr2A 82.927 82 14 0 2330 2411 120105541 120105460 1.050000e-09 75.0
33 TraesCS5D01G408100 chr2A 82.759 87 12 1 2463 2549 425889428 425889511 1.050000e-09 75.0


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 TraesCS5D01G408100 chr5D 472767198 472769936 2738 True 5059.0 5059 100.0000 1 2739 1 chr5D.!!$R2 2738
1 TraesCS5D01G408100 chr5D 472745315 472745824 509 True 505.0 505 85.3000 1328 1819 1 chr5D.!!$R1 491
2 TraesCS5D01G408100 chr5B 580110817 580115552 4735 True 1158.5 1561 86.0895 962 2593 2 chr5B.!!$R1 1631
3 TraesCS5D01G408100 chr5B 580120012 580127564 7552 True 595.0 1596 89.5574 1 2394 5 chr5B.!!$R2 2393
4 TraesCS5D01G408100 chr5A 592518847 592521140 2293 True 1062.5 1546 84.5460 235 2593 2 chr5A.!!$R5 2358
5 TraesCS5D01G408100 chr5A 592424560 592425183 623 True 584.0 584 83.7250 1760 2391 1 chr5A.!!$R3 631
6 TraesCS5D01G408100 chr5A 592302192 592302727 535 True 520.0 520 84.9260 1308 1826 1 chr5A.!!$R2 518
7 TraesCS5D01G408100 chr4A 623953505 623954191 686 False 296.0 296 75.3560 1873 2543 1 chr4A.!!$F1 670

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
398 445 0.106918 TGGTGGACTGGTGGTTGTTC 60.107 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 3516 0.109597 GTCTTTGACGCCAATGCCAG 60.11 55.0 0.0 0.0 31.46 4.85 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
28 29 0.818296 AAGCTTCGCCGTAGTCAGAT 59.182 50.000 0.00 0.00 0.00 2.90
58 59 3.242543 GCAGATTGTTTGGCGAGATACAG 60.243 47.826 0.00 0.00 0.00 2.74
74 75 2.139323 ACAGCCATACAGACCGTAGA 57.861 50.000 0.00 0.00 32.28 2.59
75 76 2.453521 ACAGCCATACAGACCGTAGAA 58.546 47.619 0.00 0.00 32.28 2.10
80 81 3.368116 GCCATACAGACCGTAGAAACAGT 60.368 47.826 0.00 0.00 32.28 3.55
111 112 2.373169 ACATAGATGGCCCCATGTACTG 59.627 50.000 4.19 8.02 35.48 2.74
113 114 2.190398 AGATGGCCCCATGTACTGTA 57.810 50.000 4.19 0.00 36.70 2.74
116 117 1.200519 TGGCCCCATGTACTGTAGAC 58.799 55.000 0.00 0.00 0.00 2.59
120 121 2.766828 GCCCCATGTACTGTAGACTTCT 59.233 50.000 0.00 0.00 0.00 2.85
135 136 3.506844 AGACTTCTTACCTCTTGACCGTC 59.493 47.826 0.00 0.00 0.00 4.79
137 138 0.524862 TCTTACCTCTTGACCGTCGC 59.475 55.000 0.00 0.00 0.00 5.19
146 147 4.468643 CTCTTGACCGTCGCTCTATAATC 58.531 47.826 0.00 0.00 0.00 1.75
186 232 4.330074 CGTCCATTCTGTAAGATTGTCACC 59.670 45.833 0.00 0.00 46.36 4.02
198 244 0.840617 TTGTCACCAGCCAACAGGTA 59.159 50.000 0.00 0.00 33.11 3.08
206 252 4.462483 CACCAGCCAACAGGTAACAAATAT 59.538 41.667 0.00 0.00 33.11 1.28
210 256 5.182950 CAGCCAACAGGTAACAAATATGTGA 59.817 40.000 0.00 0.00 40.46 3.58
313 359 3.730761 GCCGGCGCCATCATCATC 61.731 66.667 28.98 1.25 0.00 2.92
317 363 1.864862 GGCGCCATCATCATCTTCG 59.135 57.895 24.80 0.00 0.00 3.79
360 407 2.167219 CGCGGTGTGCATCTACCTG 61.167 63.158 13.61 9.37 46.97 4.00
398 445 0.106918 TGGTGGACTGGTGGTTGTTC 60.107 55.000 0.00 0.00 0.00 3.18
617 686 6.420306 CGATAGATGGAGTTGTTGATCTCTTG 59.580 42.308 0.00 0.00 39.76 3.02
662 734 2.359900 AGCAAAGTAAATCTCGCTGGG 58.640 47.619 0.00 0.00 0.00 4.45
663 735 2.027192 AGCAAAGTAAATCTCGCTGGGA 60.027 45.455 0.00 0.00 0.00 4.37
754 828 2.510238 GCTAGCTCACAGCCCGTG 60.510 66.667 7.70 0.00 43.77 4.94
786 861 2.423185 CACATCACCAATACGCCATGTT 59.577 45.455 0.00 0.00 0.00 2.71
837 912 4.019321 GCATAGGCCATAGATAAAGGGACA 60.019 45.833 5.01 0.00 0.00 4.02
850 2304 2.292828 AGGGACAAGAACACAATGGG 57.707 50.000 0.00 0.00 0.00 4.00
851 2305 1.499007 AGGGACAAGAACACAATGGGT 59.501 47.619 0.00 0.00 0.00 4.51
852 2306 2.091333 AGGGACAAGAACACAATGGGTT 60.091 45.455 0.00 0.00 0.00 4.11
853 2307 2.698274 GGGACAAGAACACAATGGGTTT 59.302 45.455 1.09 0.00 0.00 3.27
854 2308 3.133901 GGGACAAGAACACAATGGGTTTT 59.866 43.478 1.09 0.00 0.00 2.43
855 2309 4.383661 GGGACAAGAACACAATGGGTTTTT 60.384 41.667 1.09 0.00 0.00 1.94
954 2408 4.248859 GCAAGCTCACTGAATTCTGAGTA 58.751 43.478 20.05 6.33 36.94 2.59
996 2450 2.767644 ATAAATAACCCCACAGGCCC 57.232 50.000 0.00 0.00 40.58 5.80
997 2451 1.383963 TAAATAACCCCACAGGCCCA 58.616 50.000 0.00 0.00 40.58 5.36
999 2453 0.041090 AATAACCCCACAGGCCCAAG 59.959 55.000 0.00 0.00 40.58 3.61
1101 2584 2.224281 ACACCACGATGAAGAAGCTTCA 60.224 45.455 27.57 9.25 0.00 3.02
1220 2703 5.450453 TCAAGTCACAACCATTTCCCTTTA 58.550 37.500 0.00 0.00 0.00 1.85
1222 2705 6.040391 TCAAGTCACAACCATTTCCCTTTAAG 59.960 38.462 0.00 0.00 0.00 1.85
1247 2731 4.403752 TCCTTCTGATATGTGTCTGTCTGG 59.596 45.833 0.00 0.00 0.00 3.86
1260 2744 2.234661 TCTGTCTGGCTGTCAGTAATGG 59.765 50.000 9.38 0.00 43.76 3.16
1294 2778 1.127225 GTTCGTTCGCTGTACGTGC 59.873 57.895 0.00 0.00 44.19 5.34
1325 2813 0.611200 TATGCTAACTGTGGCGGTGT 59.389 50.000 0.00 0.00 32.95 4.16
1338 2826 1.934463 CGGTGTGTGTGCTCTTGAC 59.066 57.895 0.00 0.00 0.00 3.18
1346 2834 0.463654 TGTGCTCTTGACCAGCGTTT 60.464 50.000 0.00 0.00 40.01 3.60
1478 2966 2.030562 AACAAGGACGAGTGCCCG 59.969 61.111 0.00 0.00 0.00 6.13
1540 3028 0.105862 CCCAAGTGCCCATGATCCAT 60.106 55.000 0.00 0.00 0.00 3.41
1541 3029 1.037493 CCAAGTGCCCATGATCCATG 58.963 55.000 0.00 0.00 41.10 3.66
1567 3102 1.893808 CATGGCGTCTACATGGGGC 60.894 63.158 0.00 0.00 41.46 5.80
1569 3104 1.708993 ATGGCGTCTACATGGGGCAT 61.709 55.000 0.00 2.15 40.35 4.40
1591 3132 6.014156 GCATATACCTACCTGAACTGGAAGAT 60.014 42.308 4.82 0.00 37.43 2.40
1592 3133 5.878406 ATACCTACCTGAACTGGAAGATG 57.122 43.478 4.82 0.00 37.43 2.90
1666 3216 7.967890 ATATGCGTGTAATCATGATCTGAAA 57.032 32.000 9.06 0.00 37.44 2.69
1832 3411 5.715434 TCCTTTGGGAAAGTAAAATTCGG 57.285 39.130 0.00 0.00 38.93 4.30
1862 3441 3.362986 CGGACTCACGTGTCAATTCAAAG 60.363 47.826 16.51 4.47 38.61 2.77
1959 3538 1.067635 GGCATTGGCGTCAAAGACATT 60.068 47.619 6.51 0.00 42.47 2.71
2105 3700 1.340889 GCAAACCATTCACCTTGAGCA 59.659 47.619 0.00 0.00 0.00 4.26
2116 3711 2.029649 CACCTTGAGCAATTGTTGGAGG 60.030 50.000 15.02 15.02 0.00 4.30
2133 3730 3.333381 TGGAGGAAAATCCACAATCTCCA 59.667 43.478 0.00 0.00 44.56 3.86
2193 3790 1.144057 GGCCTCATTGGTCGTCGAT 59.856 57.895 0.00 0.00 38.35 3.59
2336 3936 5.047021 TGTCAAATGAGAAGACGGAAGAGAT 60.047 40.000 0.00 0.00 35.09 2.75
2424 6705 2.019984 GATGAGACCAATGCCAAGTCC 58.980 52.381 0.00 0.00 0.00 3.85
2426 6707 1.355381 TGAGACCAATGCCAAGTCCAT 59.645 47.619 0.00 0.00 0.00 3.41
2443 6724 0.471617 CATAGCCAAGGAGGTGGAGG 59.528 60.000 0.00 0.00 41.65 4.30
2444 6725 1.348775 ATAGCCAAGGAGGTGGAGGC 61.349 60.000 0.00 0.00 41.65 4.70
2445 6726 4.785453 GCCAAGGAGGTGGAGGCG 62.785 72.222 0.00 0.00 41.65 5.52
2446 6727 3.322466 CCAAGGAGGTGGAGGCGT 61.322 66.667 0.00 0.00 41.65 5.68
2447 6728 2.046892 CAAGGAGGTGGAGGCGTG 60.047 66.667 0.00 0.00 0.00 5.34
2448 6729 3.322466 AAGGAGGTGGAGGCGTGG 61.322 66.667 0.00 0.00 0.00 4.94
2449 6730 3.846405 AAGGAGGTGGAGGCGTGGA 62.846 63.158 0.00 0.00 0.00 4.02
2450 6731 3.775654 GGAGGTGGAGGCGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
2509 6790 1.535462 CGAAACGAGCAAAATGACCCT 59.465 47.619 0.00 0.00 0.00 4.34
2511 6792 1.534729 AACGAGCAAAATGACCCTCC 58.465 50.000 0.00 0.00 0.00 4.30
2551 6836 1.550524 GGGGAAGCAAAAGTTCATCCC 59.449 52.381 0.00 0.00 44.73 3.85
2556 6841 3.515602 AGCAAAAGTTCATCCCAGACT 57.484 42.857 0.00 0.00 0.00 3.24
2604 6889 9.444600 TTTTATGAACTAGGGTTGATGTTAGAC 57.555 33.333 0.00 0.00 35.58 2.59
2605 6890 6.875972 ATGAACTAGGGTTGATGTTAGACT 57.124 37.500 0.00 0.00 35.58 3.24
2606 6891 6.681729 TGAACTAGGGTTGATGTTAGACTT 57.318 37.500 0.00 0.00 35.58 3.01
2608 6893 5.326200 ACTAGGGTTGATGTTAGACTTCG 57.674 43.478 0.00 0.00 0.00 3.79
2609 6894 4.771054 ACTAGGGTTGATGTTAGACTTCGT 59.229 41.667 0.00 0.00 0.00 3.85
2610 6895 5.948162 ACTAGGGTTGATGTTAGACTTCGTA 59.052 40.000 0.00 0.00 0.00 3.43
2611 6896 5.934402 AGGGTTGATGTTAGACTTCGTAT 57.066 39.130 0.00 0.00 0.00 3.06
2612 6897 6.295719 AGGGTTGATGTTAGACTTCGTATT 57.704 37.500 0.00 0.00 0.00 1.89
2613 6898 6.106673 AGGGTTGATGTTAGACTTCGTATTG 58.893 40.000 0.00 0.00 0.00 1.90
2615 6900 7.037438 GGGTTGATGTTAGACTTCGTATTGTA 58.963 38.462 0.00 0.00 0.00 2.41
2616 6901 7.222224 GGGTTGATGTTAGACTTCGTATTGTAG 59.778 40.741 0.00 0.00 0.00 2.74
2618 6903 6.270815 TGATGTTAGACTTCGTATTGTAGCC 58.729 40.000 0.00 0.00 0.00 3.93
2619 6904 5.002464 TGTTAGACTTCGTATTGTAGCCC 57.998 43.478 0.00 0.00 0.00 5.19
2620 6905 4.142093 TGTTAGACTTCGTATTGTAGCCCC 60.142 45.833 0.00 0.00 0.00 5.80
2621 6906 2.463752 AGACTTCGTATTGTAGCCCCA 58.536 47.619 0.00 0.00 0.00 4.96
2623 6908 2.167900 GACTTCGTATTGTAGCCCCACT 59.832 50.000 0.00 0.00 0.00 4.00
2624 6909 3.368248 ACTTCGTATTGTAGCCCCACTA 58.632 45.455 0.00 0.00 0.00 2.74
2625 6910 3.965347 ACTTCGTATTGTAGCCCCACTAT 59.035 43.478 0.00 0.00 32.15 2.12
2627 6912 3.302161 TCGTATTGTAGCCCCACTATGT 58.698 45.455 0.00 0.00 32.15 2.29
2628 6913 4.472496 TCGTATTGTAGCCCCACTATGTA 58.528 43.478 0.00 0.00 32.15 2.29
2630 6915 5.541101 TCGTATTGTAGCCCCACTATGTAAT 59.459 40.000 0.00 0.00 32.15 1.89
2631 6916 5.867716 CGTATTGTAGCCCCACTATGTAATC 59.132 44.000 0.00 0.00 32.15 1.75
2632 6917 4.699925 TTGTAGCCCCACTATGTAATCC 57.300 45.455 0.00 0.00 32.15 3.01
2633 6918 3.659841 TGTAGCCCCACTATGTAATCCA 58.340 45.455 0.00 0.00 32.15 3.41
2635 6920 5.407936 TGTAGCCCCACTATGTAATCCATA 58.592 41.667 0.00 0.00 34.86 2.74
2636 6921 4.910458 AGCCCCACTATGTAATCCATAC 57.090 45.455 0.00 0.00 34.86 2.39
2637 6922 3.587506 AGCCCCACTATGTAATCCATACC 59.412 47.826 0.00 0.00 34.86 2.73
2638 6923 3.618997 GCCCCACTATGTAATCCATACCG 60.619 52.174 0.00 0.00 34.86 4.02
2640 6925 4.773674 CCCCACTATGTAATCCATACCGTA 59.226 45.833 0.00 0.00 34.86 4.02
2643 6928 6.816640 CCCACTATGTAATCCATACCGTATTG 59.183 42.308 0.00 0.00 34.86 1.90
2662 6947 6.238456 CGTATTGGTATAGGACTTGTACGTCA 60.238 42.308 0.00 0.00 35.63 4.35
2663 6948 4.970662 TGGTATAGGACTTGTACGTCAC 57.029 45.455 0.00 0.00 35.63 3.67
2667 6952 5.163478 GGTATAGGACTTGTACGTCACCATT 60.163 44.000 0.00 0.00 35.63 3.16
2669 6954 6.726490 ATAGGACTTGTACGTCACCATTAT 57.274 37.500 0.00 0.00 35.63 1.28
2674 6959 9.524496 AGGACTTGTACGTCACCATTATATATA 57.476 33.333 0.00 0.00 35.63 0.86
2680 6965 9.849166 TGTACGTCACCATTATATATATGTGTG 57.151 33.333 5.44 7.27 0.00 3.82
2683 6968 8.364894 ACGTCACCATTATATATATGTGTGTGT 58.635 33.333 5.44 7.57 0.00 3.72
2685 6970 9.489084 GTCACCATTATATATATGTGTGTGTGT 57.511 33.333 5.44 0.00 0.00 3.72
2686 6971 9.487790 TCACCATTATATATATGTGTGTGTGTG 57.512 33.333 5.44 7.39 0.00 3.82
2687 6972 9.271828 CACCATTATATATATGTGTGTGTGTGT 57.728 33.333 5.44 0.00 0.00 3.72
2688 6973 9.271828 ACCATTATATATATGTGTGTGTGTGTG 57.728 33.333 5.44 0.00 0.00 3.82
2691 6976 9.830975 ATTATATATATGTGTGTGTGTGTGTGT 57.169 29.630 5.44 0.00 0.00 3.72
2692 6977 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
2693 6978 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2695 6980 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2696 6981 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2698 6983 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2699 6984 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2700 6985 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2702 6987 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2705 6990 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2706 6991 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2707 6992 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2708 6993 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2709 6994 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2710 6995 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2711 6996 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2712 6997 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2714 6999 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2715 7000 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2716 7001 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2718 7003 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2722 7007 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2725 7010 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2726 7011 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2727 7012 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2728 7013 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2731 7016 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2732 7017 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2733 7018 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2734 7019 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.057819 TCTGCTACTCTAATCTGACTACGG 58.942 45.833 0.00 0.00 0.00 4.02
28 29 3.932710 CGCCAAACAATCTGCTACTCTAA 59.067 43.478 0.00 0.00 0.00 2.10
58 59 3.187700 CTGTTTCTACGGTCTGTATGGC 58.812 50.000 0.00 0.00 31.20 4.40
74 75 4.968259 TCTATGTAGCCACACAACTGTTT 58.032 39.130 0.00 0.00 37.54 2.83
75 76 4.617253 TCTATGTAGCCACACAACTGTT 57.383 40.909 0.00 0.00 37.54 3.16
80 81 2.421388 GGCCATCTATGTAGCCACACAA 60.421 50.000 0.00 0.00 45.07 3.33
111 112 4.458642 ACGGTCAAGAGGTAAGAAGTCTAC 59.541 45.833 0.00 0.00 0.00 2.59
113 114 3.498334 ACGGTCAAGAGGTAAGAAGTCT 58.502 45.455 0.00 0.00 0.00 3.24
116 117 2.864968 CGACGGTCAAGAGGTAAGAAG 58.135 52.381 9.10 0.00 0.00 2.85
120 121 0.524862 GAGCGACGGTCAAGAGGTAA 59.475 55.000 21.39 0.00 0.00 2.85
135 136 6.090898 CGGTTTTATTCCAGGATTATAGAGCG 59.909 42.308 0.00 0.00 0.00 5.03
137 138 7.603024 GGTCGGTTTTATTCCAGGATTATAGAG 59.397 40.741 0.00 0.00 0.00 2.43
146 147 2.004733 GACGGTCGGTTTTATTCCAGG 58.995 52.381 0.00 0.00 0.00 4.45
186 232 5.182950 TCACATATTTGTTACCTGTTGGCTG 59.817 40.000 0.00 0.00 32.67 4.85
198 244 4.752101 GCTAGCCTCGATCACATATTTGTT 59.248 41.667 2.29 0.00 32.34 2.83
206 252 0.741326 GTCAGCTAGCCTCGATCACA 59.259 55.000 12.13 0.00 0.00 3.58
210 256 2.226330 CAGTAGTCAGCTAGCCTCGAT 58.774 52.381 12.13 0.00 0.00 3.59
311 357 1.009829 GGCACGAATGAAGCGAAGAT 58.990 50.000 0.00 0.00 0.00 2.40
312 358 1.019278 GGGCACGAATGAAGCGAAGA 61.019 55.000 0.00 0.00 0.00 2.87
313 359 1.425428 GGGCACGAATGAAGCGAAG 59.575 57.895 0.00 0.00 0.00 3.79
317 363 2.785258 GACGGGCACGAATGAAGC 59.215 61.111 19.19 0.00 44.60 3.86
339 385 2.202743 TAGATGCACACCGCGAGC 60.203 61.111 8.23 6.78 46.97 5.03
340 386 1.878522 GGTAGATGCACACCGCGAG 60.879 63.158 8.23 1.37 46.97 5.03
341 387 2.183300 GGTAGATGCACACCGCGA 59.817 61.111 8.23 0.00 46.97 5.87
342 388 2.167219 CAGGTAGATGCACACCGCG 61.167 63.158 0.00 0.00 46.97 6.46
360 407 2.280457 GCGGATAGACAGGCAGGC 60.280 66.667 0.00 0.00 0.00 4.85
443 490 4.770874 CCGTTGTACTGGCCCGGG 62.771 72.222 19.09 19.09 35.11 5.73
448 495 2.388232 CGCCTTCCGTTGTACTGGC 61.388 63.158 0.00 0.00 37.24 4.85
485 532 4.899239 GGAGCACGCTAGCCGCAT 62.899 66.667 21.98 9.96 41.76 4.73
617 686 3.002965 ACTGCTAACAAACACGTAAAGGC 59.997 43.478 0.00 0.00 0.00 4.35
662 734 2.645730 AGATCGAGCAGTGAACTGTC 57.354 50.000 11.87 7.42 45.45 3.51
663 735 4.158579 TGATTAGATCGAGCAGTGAACTGT 59.841 41.667 11.87 0.00 45.45 3.55
754 828 1.160137 GGTGATGTGCTGGTCAGTTC 58.840 55.000 0.00 0.00 0.00 3.01
761 835 0.378257 GCGTATTGGTGATGTGCTGG 59.622 55.000 0.00 0.00 0.00 4.85
856 2310 3.039252 ACCCATTGTGTCCCTCAAAAA 57.961 42.857 0.00 0.00 0.00 1.94
857 2311 2.765689 ACCCATTGTGTCCCTCAAAA 57.234 45.000 0.00 0.00 0.00 2.44
858 2312 2.765689 AACCCATTGTGTCCCTCAAA 57.234 45.000 0.00 0.00 0.00 2.69
859 2313 2.765689 AAACCCATTGTGTCCCTCAA 57.234 45.000 0.00 0.00 0.00 3.02
860 2314 2.765689 AAAACCCATTGTGTCCCTCA 57.234 45.000 0.00 0.00 0.00 3.86
861 2315 3.005791 CAGAAAAACCCATTGTGTCCCTC 59.994 47.826 0.00 0.00 0.00 4.30
862 2316 2.965147 CAGAAAAACCCATTGTGTCCCT 59.035 45.455 0.00 0.00 0.00 4.20
863 2317 2.547855 GCAGAAAAACCCATTGTGTCCC 60.548 50.000 0.00 0.00 0.00 4.46
864 2318 2.547855 GGCAGAAAAACCCATTGTGTCC 60.548 50.000 0.00 0.00 0.00 4.02
865 2319 2.365293 AGGCAGAAAAACCCATTGTGTC 59.635 45.455 0.00 0.00 0.00 3.67
866 2320 2.397597 AGGCAGAAAAACCCATTGTGT 58.602 42.857 0.00 0.00 0.00 3.72
867 2321 3.473923 AAGGCAGAAAAACCCATTGTG 57.526 42.857 0.00 0.00 0.00 3.33
868 2322 3.454082 TCAAAGGCAGAAAAACCCATTGT 59.546 39.130 0.00 0.00 0.00 2.71
869 2323 4.060205 CTCAAAGGCAGAAAAACCCATTG 58.940 43.478 0.00 0.00 0.00 2.82
870 2324 3.494924 GCTCAAAGGCAGAAAAACCCATT 60.495 43.478 0.00 0.00 0.00 3.16
871 2325 2.037641 GCTCAAAGGCAGAAAAACCCAT 59.962 45.455 0.00 0.00 0.00 4.00
872 2326 1.412343 GCTCAAAGGCAGAAAAACCCA 59.588 47.619 0.00 0.00 0.00 4.51
873 2327 1.602920 CGCTCAAAGGCAGAAAAACCC 60.603 52.381 0.00 0.00 0.00 4.11
954 2408 1.328279 GCCCAAAAGCTTGTGGTACT 58.672 50.000 29.94 0.00 32.60 2.73
996 2450 1.622811 AGCTGGAGGAGTGAGTTCTTG 59.377 52.381 0.00 0.00 0.00 3.02
997 2451 1.899142 GAGCTGGAGGAGTGAGTTCTT 59.101 52.381 0.00 0.00 0.00 2.52
999 2453 0.534873 GGAGCTGGAGGAGTGAGTTC 59.465 60.000 0.00 0.00 0.00 3.01
1055 2529 1.601759 GTTGCTTGGCTCTGGCAGA 60.602 57.895 17.68 17.68 39.75 4.26
1222 2705 5.809562 CAGACAGACACATATCAGAAGGAAC 59.190 44.000 0.00 0.00 0.00 3.62
1247 2731 2.680312 TGAGCTCCATTACTGACAGC 57.320 50.000 12.15 0.00 0.00 4.40
1294 2778 2.064762 GTTAGCATAGATGGCAGCGAG 58.935 52.381 0.00 0.00 0.00 5.03
1325 2813 1.595109 CGCTGGTCAAGAGCACACA 60.595 57.895 0.00 0.00 36.12 3.72
1338 2826 2.427410 GCTGTCGCAAAACGCTGG 60.427 61.111 0.00 0.00 43.23 4.85
1478 2966 2.092882 GGTCTTGTCGCGGTAGCAC 61.093 63.158 6.13 0.00 45.49 4.40
1565 3100 3.901844 TCCAGTTCAGGTAGGTATATGCC 59.098 47.826 0.75 0.75 0.00 4.40
1567 3102 6.978674 TCTTCCAGTTCAGGTAGGTATATG 57.021 41.667 0.00 0.00 0.00 1.78
1569 3104 5.304614 GCATCTTCCAGTTCAGGTAGGTATA 59.695 44.000 0.00 0.00 0.00 1.47
1591 3132 6.134055 ACTAAGTACAGTACATGATAGGGCA 58.866 40.000 13.37 0.00 0.00 5.36
1592 3133 6.651975 ACTAAGTACAGTACATGATAGGGC 57.348 41.667 13.37 0.00 0.00 5.19
1666 3216 1.153369 CGGATCATGAACCAGGCGT 60.153 57.895 20.74 0.00 0.00 5.68
1770 3348 5.125739 AGGAAATTACTGGACAGACTCTACG 59.874 44.000 6.29 0.00 0.00 3.51
1832 3411 2.266627 ACGTGAGTCCGGTCACTCC 61.267 63.158 19.59 11.00 44.19 3.85
1846 3425 2.878406 ACCTCCTTTGAATTGACACGTG 59.122 45.455 15.48 15.48 0.00 4.49
1862 3441 4.949856 TCAATTGGATAAAGCTTCACCTCC 59.050 41.667 5.42 4.58 0.00 4.30
1937 3516 0.109597 GTCTTTGACGCCAATGCCAG 60.110 55.000 0.00 0.00 31.46 4.85
1959 3538 8.877864 ATGAACAAGGAAAGGAAATGTATACA 57.122 30.769 8.27 8.27 0.00 2.29
2105 3700 5.885449 TTGTGGATTTTCCTCCAACAATT 57.115 34.783 0.00 0.00 46.66 2.32
2116 3711 9.541143 TTAAACTTTTGGAGATTGTGGATTTTC 57.459 29.630 0.00 0.00 0.00 2.29
2129 3726 6.753744 GCATATTGCTCCTTAAACTTTTGGAG 59.246 38.462 14.31 14.31 46.38 3.86
2130 3727 6.210385 TGCATATTGCTCCTTAAACTTTTGGA 59.790 34.615 0.75 0.00 45.31 3.53
2133 3730 6.101997 GCTGCATATTGCTCCTTAAACTTTT 58.898 36.000 0.00 0.00 45.31 2.27
2155 3752 1.074566 CCTCTCACCTCTTTTTGGGCT 59.925 52.381 0.00 0.00 0.00 5.19
2193 3790 3.711704 ACCTCTTCTCACTTTCACTTGGA 59.288 43.478 0.00 0.00 0.00 3.53
2262 3861 3.270877 AGTTTCTTGCAAGACGAGTGTT 58.729 40.909 28.46 7.67 34.13 3.32
2302 3902 7.080724 GTCTTCTCATTTGACACCTCATTTTC 58.919 38.462 0.00 0.00 0.00 2.29
2336 3936 2.106338 TCCTCATTGTCTTGGTGCTTCA 59.894 45.455 0.00 0.00 0.00 3.02
2424 6705 0.471617 CCTCCACCTCCTTGGCTATG 59.528 60.000 0.00 0.00 40.22 2.23
2426 6707 1.995626 GCCTCCACCTCCTTGGCTA 60.996 63.158 0.00 0.00 40.36 3.93
2443 6724 2.533391 GATTGGTGCAAGCTCCACGC 62.533 60.000 14.76 6.94 39.03 5.34
2444 6725 0.957395 AGATTGGTGCAAGCTCCACG 60.957 55.000 14.76 0.00 34.96 4.94
2445 6726 0.807496 GAGATTGGTGCAAGCTCCAC 59.193 55.000 14.76 8.53 46.93 4.02
2446 6727 3.254629 GAGATTGGTGCAAGCTCCA 57.745 52.632 11.47 11.47 46.93 3.86
2449 6730 1.542492 CTTGGAGATTGGTGCAAGCT 58.458 50.000 0.00 0.00 43.01 3.74
2450 6731 0.529378 CCTTGGAGATTGGTGCAAGC 59.471 55.000 0.00 0.00 42.78 4.01
2458 6739 5.494724 TGATCTTCACTTCCTTGGAGATTG 58.505 41.667 0.00 0.00 41.29 2.67
2551 6836 6.378710 AAAATGATCATGCATCTCAGTCTG 57.621 37.500 9.46 0.00 31.92 3.51
2593 6878 6.755141 GGCTACAATACGAAGTCTAACATCAA 59.245 38.462 0.00 0.00 43.93 2.57
2594 6879 6.270815 GGCTACAATACGAAGTCTAACATCA 58.729 40.000 0.00 0.00 43.93 3.07
2597 6882 4.142093 GGGGCTACAATACGAAGTCTAACA 60.142 45.833 0.00 0.00 43.93 2.41
2598 6883 4.142093 TGGGGCTACAATACGAAGTCTAAC 60.142 45.833 0.00 0.00 43.93 2.34
2600 6885 3.382546 GTGGGGCTACAATACGAAGTCTA 59.617 47.826 0.00 0.00 43.93 2.59
2601 6886 2.167900 GTGGGGCTACAATACGAAGTCT 59.832 50.000 0.00 0.00 43.93 3.24
2602 6887 2.167900 AGTGGGGCTACAATACGAAGTC 59.832 50.000 0.00 0.00 43.93 3.01
2603 6888 3.965347 ATAGTGGGGCTACAATACGAAGT 59.035 43.478 0.00 0.00 37.18 3.01
2604 6889 2.981859 AGTGGGGCTACAATACGAAG 57.018 50.000 0.00 0.00 0.00 3.79
2605 6890 3.707611 ACATAGTGGGGCTACAATACGAA 59.292 43.478 0.00 0.00 31.59 3.85
2606 6891 3.302161 ACATAGTGGGGCTACAATACGA 58.698 45.455 0.00 0.00 31.59 3.43
2608 6893 6.171213 GGATTACATAGTGGGGCTACAATAC 58.829 44.000 0.00 0.00 31.59 1.89
2609 6894 5.847265 TGGATTACATAGTGGGGCTACAATA 59.153 40.000 0.00 0.00 31.59 1.90
2610 6895 4.663120 TGGATTACATAGTGGGGCTACAAT 59.337 41.667 0.00 0.00 31.59 2.71
2611 6896 4.041464 TGGATTACATAGTGGGGCTACAA 58.959 43.478 0.00 0.00 31.59 2.41
2612 6897 3.659841 TGGATTACATAGTGGGGCTACA 58.340 45.455 0.00 0.00 31.59 2.74
2613 6898 4.910458 ATGGATTACATAGTGGGGCTAC 57.090 45.455 0.00 0.00 38.26 3.58
2615 6900 3.587506 GGTATGGATTACATAGTGGGGCT 59.412 47.826 0.00 0.00 42.50 5.19
2616 6901 3.618997 CGGTATGGATTACATAGTGGGGC 60.619 52.174 0.00 0.00 42.50 5.80
2618 6903 4.884668 ACGGTATGGATTACATAGTGGG 57.115 45.455 0.00 0.00 42.50 4.61
2619 6904 6.816640 CCAATACGGTATGGATTACATAGTGG 59.183 42.308 4.03 0.00 42.50 4.00
2620 6905 7.827819 CCAATACGGTATGGATTACATAGTG 57.172 40.000 4.03 0.00 42.50 2.74
2635 6920 9.067541 GACGTACAAGTCCTATACCAATACGGT 62.068 44.444 0.00 0.00 42.35 4.83
2636 6921 5.009010 ACGTACAAGTCCTATACCAATACGG 59.991 44.000 0.00 0.00 37.02 4.02
2637 6922 6.064846 ACGTACAAGTCCTATACCAATACG 57.935 41.667 0.00 0.00 37.92 3.06
2638 6923 6.914757 GTGACGTACAAGTCCTATACCAATAC 59.085 42.308 0.00 0.00 40.26 1.89
2640 6925 5.163478 GGTGACGTACAAGTCCTATACCAAT 60.163 44.000 0.00 0.00 40.26 3.16
2643 6928 3.696051 TGGTGACGTACAAGTCCTATACC 59.304 47.826 0.00 0.00 40.26 2.73
2645 6930 7.828508 ATAATGGTGACGTACAAGTCCTATA 57.171 36.000 0.00 0.00 40.26 1.31
2646 6931 6.726490 ATAATGGTGACGTACAAGTCCTAT 57.274 37.500 0.00 0.00 40.26 2.57
2647 6932 7.828508 ATATAATGGTGACGTACAAGTCCTA 57.171 36.000 0.00 0.00 40.26 2.94
2648 6933 6.726490 ATATAATGGTGACGTACAAGTCCT 57.274 37.500 0.00 0.00 40.26 3.85
2658 6943 8.647226 CACACACACATATATATAATGGTGACG 58.353 37.037 20.47 15.32 0.00 4.35
2662 6947 9.271828 CACACACACACACATATATATAATGGT 57.728 33.333 10.53 2.26 0.00 3.55
2663 6948 9.271828 ACACACACACACACATATATATAATGG 57.728 33.333 10.53 1.76 0.00 3.16
2667 6952 8.254508 ACACACACACACACACACATATATATA 58.745 33.333 0.00 0.00 0.00 0.86
2669 6954 6.367422 CACACACACACACACACACATATATA 59.633 38.462 0.00 0.00 0.00 0.86
2674 6959 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
2675 6960 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2676 6961 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2677 6962 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2678 6963 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2680 6965 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2683 6968 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2685 6970 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2686 6971 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2687 6972 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2688 6973 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2691 6976 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2692 6977 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2693 6978 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2695 6980 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2696 6981 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2698 6983 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2699 6984 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2700 6985 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2702 6987 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2705 6990 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2706 6991 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2707 6992 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2708 6993 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2709 6994 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2710 6995 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2711 6996 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2712 6997 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2714 6999 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2715 7000 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2716 7001 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2718 7003 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.