Multiple sequence alignment - TraesCS7D01G404700

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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 TraesCS7D01G404700 chr7D 100.000 3086 0 0 1 3086 521969916 521966831 0.000000e+00 5699.0
1 TraesCS7D01G404700 chr7D 76.605 483 84 21 1613 2087 65630740 65631201 3.980000e-59 239.0
2 TraesCS7D01G404700 chr7D 94.000 50 3 0 491 540 521969386 521969337 3.300000e-10 76.8
3 TraesCS7D01G404700 chr7D 94.000 50 3 0 531 580 521969426 521969377 3.300000e-10 76.8
4 TraesCS7D01G404700 chr4B 92.542 2105 126 26 1 2095 625335066 625337149 0.000000e+00 2988.0
5 TraesCS7D01G404700 chr4B 91.499 1294 79 21 1 1279 625332988 625331711 0.000000e+00 1751.0
6 TraesCS7D01G404700 chr4B 92.441 807 52 9 1296 2095 625331633 625330829 0.000000e+00 1144.0
7 TraesCS7D01G404700 chr4B 85.604 389 35 18 2136 2520 625337152 625337523 3.730000e-104 388.0
8 TraesCS7D01G404700 chr4B 85.242 393 31 19 2136 2520 625330826 625330453 2.250000e-101 379.0
9 TraesCS7D01G404700 chr4B 85.098 255 28 10 2820 3071 625329351 625329104 5.110000e-63 252.0
10 TraesCS7D01G404700 chr4B 86.222 225 27 4 2794 3016 625316751 625316529 1.110000e-59 241.0
11 TraesCS7D01G404700 chr4B 82.374 278 31 15 2794 3064 625316376 625316110 3.100000e-55 226.0
12 TraesCS7D01G404700 chr4B 81.560 282 41 11 2794 3071 625326776 625326502 4.010000e-54 222.0
13 TraesCS7D01G404700 chr5D 91.029 1817 98 44 854 2645 499709548 499711324 0.000000e+00 2392.0
14 TraesCS7D01G404700 chr5D 92.000 125 7 3 2673 2795 499744648 499744771 4.090000e-39 172.0
15 TraesCS7D01G404700 chr1B 88.189 254 30 0 1800 2053 557101935 557102188 1.390000e-78 303.0
16 TraesCS7D01G404700 chr1B 88.435 147 11 5 92 238 57102123 57101983 4.090000e-39 172.0
17 TraesCS7D01G404700 chr1B 79.221 231 38 10 2860 3086 57088672 57088448 5.330000e-33 152.0
18 TraesCS7D01G404700 chr1B 91.111 90 6 1 2996 3083 57089195 57089106 1.500000e-23 121.0
19 TraesCS7D01G404700 chr2B 74.897 486 86 24 1613 2087 795823799 795824259 4.060000e-44 189.0
20 TraesCS7D01G404700 chr2B 80.000 235 44 3 1785 2016 158871548 158871782 1.470000e-38 171.0
21 TraesCS7D01G404700 chr1A 76.250 400 67 19 1613 2001 97254588 97254970 1.460000e-43 187.0
22 TraesCS7D01G404700 chr1A 90.351 114 7 4 2675 2787 485233917 485234027 2.480000e-31 147.0
23 TraesCS7D01G404700 chr4D 80.769 234 42 2 1786 2016 2997585 2997352 2.440000e-41 180.0
24 TraesCS7D01G404700 chr1D 79.372 223 37 9 2856 3074 385179878 385180095 6.890000e-32 148.0
25 TraesCS7D01G404700 chr1D 91.429 105 5 4 2685 2787 385134101 385134203 1.150000e-29 141.0
26 TraesCS7D01G404700 chr1D 80.423 189 26 11 2880 3064 143323521 143323702 1.930000e-27 134.0
27 TraesCS7D01G404700 chr3A 83.537 164 19 7 2361 2520 735477686 735477527 2.480000e-31 147.0
28 TraesCS7D01G404700 chr3A 82.927 164 20 7 2361 2520 735480022 735479863 1.150000e-29 141.0
29 TraesCS7D01G404700 chr5B 81.006 179 27 7 2908 3083 492042821 492042995 5.370000e-28 135.0
30 TraesCS7D01G404700 chr3D 79.365 189 29 10 2880 3064 121706621 121706803 1.160000e-24 124.0


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 TraesCS7D01G404700 chr7D 521966831 521969916 3085 True 1950.866667 5699 96.000 1 3086 3 chr7D.!!$R1 3085
1 TraesCS7D01G404700 chr4B 625335066 625337523 2457 False 1688.000000 2988 89.073 1 2520 2 chr4B.!!$F1 2519
2 TraesCS7D01G404700 chr4B 625326502 625332988 6486 True 749.600000 1751 87.168 1 3071 5 chr4B.!!$R2 3070
3 TraesCS7D01G404700 chr4B 625316110 625316751 641 True 233.500000 241 84.298 2794 3064 2 chr4B.!!$R1 270
4 TraesCS7D01G404700 chr5D 499709548 499711324 1776 False 2392.000000 2392 91.029 854 2645 1 chr5D.!!$F1 1791

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
978 995 1.133945 TGTGCCAGCTTGTGTTCCTTA 60.134 47.619 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 3638 0.034896 TCCTGCCGTCCTTTCTCAAC 59.965 55.0 0.0 0.0 0.0 3.18 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
131 132 7.546667 CCATTTAGTACAAGGAAAAGCGTAGTA 59.453 37.037 0.00 0.00 0.00 1.82
136 137 4.251268 ACAAGGAAAAGCGTAGTATCCAC 58.749 43.478 0.00 0.00 32.47 4.02
273 274 1.202359 GCCCGTTGTTGCTTTTCTTGA 60.202 47.619 0.00 0.00 0.00 3.02
446 456 4.099881 AGGATTTTGCTGCTTCAGTTTCAA 59.900 37.500 0.00 0.00 33.43 2.69
523 533 5.961395 TTCAGTTTCGTCAGTAGTTTCAC 57.039 39.130 0.00 0.00 0.00 3.18
536 546 6.041637 TCAGTAGTTTCACTGTTAGGTGTCAT 59.958 38.462 3.41 0.00 45.11 3.06
579 589 7.773690 AGTAGTTTCACTGTTAGGTGTCATTTT 59.226 33.333 0.00 0.00 38.28 1.82
592 602 3.976942 GTGTCATTTTCAGTCATGTGCAC 59.023 43.478 10.75 10.75 0.00 4.57
593 603 3.631227 TGTCATTTTCAGTCATGTGCACA 59.369 39.130 24.08 24.08 0.00 4.57
634 644 7.605410 TCTTCGTAGTTTTGTGAGAGTTTTT 57.395 32.000 0.00 0.00 0.00 1.94
680 691 5.689383 TTTGTGTTTTGGCAGATAGTCTC 57.311 39.130 0.00 0.00 0.00 3.36
697 708 8.637986 AGATAGTCTCCAGTATTGAGTTTGATC 58.362 37.037 0.00 0.00 0.00 2.92
835 847 9.614792 TCTTTAGGACTTCTATATTTTGCCTTC 57.385 33.333 0.00 0.00 0.00 3.46
857 869 9.549078 CCTTCTCTAAGTTTTCAGTTTTCTACT 57.451 33.333 0.00 0.00 37.68 2.57
906 922 7.093354 TGTGATGTTTTTCTTTTGTTGTGCTA 58.907 30.769 0.00 0.00 0.00 3.49
913 929 6.509418 TTTCTTTTGTTGTGCTACTTCAGT 57.491 33.333 0.00 0.00 0.00 3.41
934 950 7.417612 TCAGTTTTGCTTACTCTGAAAACATC 58.582 34.615 0.00 0.00 39.63 3.06
938 954 5.489792 TGCTTACTCTGAAAACATCTCCT 57.510 39.130 0.00 0.00 0.00 3.69
949 966 8.542926 TCTGAAAACATCTCCTTCTGATGATTA 58.457 33.333 10.21 0.00 42.68 1.75
978 995 1.133945 TGTGCCAGCTTGTGTTCCTTA 60.134 47.619 0.00 0.00 0.00 2.69
982 999 3.640967 TGCCAGCTTGTGTTCCTTATTTT 59.359 39.130 0.00 0.00 0.00 1.82
1040 1057 2.749280 TCGCATTGTGAGAGTGACAT 57.251 45.000 0.00 0.00 0.00 3.06
1112 1131 8.414003 AGCGGTATTCTCTTTTTCTTTCTTTTT 58.586 29.630 0.00 0.00 0.00 1.94
1252 1274 6.252995 TGCAAGGAATAGGTTTAACCAGATT 58.747 36.000 17.10 14.31 41.95 2.40
1279 1301 0.393820 TGAACTTTAAGGCGGACGGT 59.606 50.000 0.00 0.00 0.00 4.83
1327 1410 2.293399 GGGACACAAAACCACACTGATC 59.707 50.000 0.00 0.00 0.00 2.92
1343 1426 1.417517 TGATCGGAGGTGATGATTGGG 59.582 52.381 0.00 0.00 0.00 4.12
1356 1439 0.968405 GATTGGGCCAAGTTCAAGCA 59.032 50.000 25.16 0.00 0.00 3.91
1357 1440 1.551883 GATTGGGCCAAGTTCAAGCAT 59.448 47.619 25.16 3.78 0.00 3.79
1419 1502 1.166531 ACTGGACGAACAGCAAAGGC 61.167 55.000 10.25 0.00 42.21 4.35
1435 1518 3.012560 GGCATATGTGGCTGGAGTC 57.987 57.895 8.86 0.00 46.64 3.36
1448 1531 0.603569 TGGAGTCGAGGCTGAAGAAC 59.396 55.000 0.00 0.00 0.00 3.01
1498 1581 4.252073 CAGTTGATGAAGAGGAAGAGGTG 58.748 47.826 0.00 0.00 0.00 4.00
1594 1677 2.916702 ACGCAATGATGGAGCTCATA 57.083 45.000 17.19 3.99 34.79 2.15
1627 1710 4.264373 ACATTTATACATTGGCCCACCT 57.736 40.909 0.00 0.00 36.63 4.00
1653 1736 2.415608 ATCGTCTGACGCCCACGAT 61.416 57.895 24.37 9.44 45.66 3.73
1989 2083 0.474854 TAGCCCAGAACCACCTCCAA 60.475 55.000 0.00 0.00 0.00 3.53
2010 2104 4.924305 AGTGAATGATGCTGTTGTGTTT 57.076 36.364 0.00 0.00 0.00 2.83
2016 2110 7.222611 GTGAATGATGCTGTTGTGTTTAACTTT 59.777 33.333 0.00 0.00 0.00 2.66
2073 2167 0.465460 TTGTCAACGCTTTGAGGCCT 60.465 50.000 3.86 3.86 42.60 5.19
2080 2174 1.583477 GCTTTGAGGCCTGCAGAAC 59.417 57.895 12.00 7.45 0.00 3.01
2108 2203 3.140144 GGATGGGGGTGATGGAGATTTTA 59.860 47.826 0.00 0.00 0.00 1.52
2119 2214 3.700538 TGGAGATTTTAGTGCCAGCATT 58.299 40.909 0.00 0.00 0.00 3.56
2180 2276 3.197265 GTGTGGCAGAAGCAAAATGTTT 58.803 40.909 0.00 0.00 44.61 2.83
2181 2277 3.622612 GTGTGGCAGAAGCAAAATGTTTT 59.377 39.130 0.00 0.00 44.61 2.43
2182 2278 4.094739 GTGTGGCAGAAGCAAAATGTTTTT 59.905 37.500 0.00 0.00 44.61 1.94
2184 2280 5.293079 TGTGGCAGAAGCAAAATGTTTTTAC 59.707 36.000 0.00 0.00 44.61 2.01
2185 2281 4.813697 TGGCAGAAGCAAAATGTTTTTACC 59.186 37.500 0.00 0.00 44.61 2.85
2187 2283 4.084589 GCAGAAGCAAAATGTTTTTACCGG 60.085 41.667 0.00 0.00 41.58 5.28
2189 2285 5.047188 AGAAGCAAAATGTTTTTACCGGTG 58.953 37.500 19.93 0.00 0.00 4.94
2287 2385 1.735926 TGTTGTCCCACCATGACCTA 58.264 50.000 0.00 0.00 31.60 3.08
2288 2386 2.274542 TGTTGTCCCACCATGACCTAT 58.725 47.619 0.00 0.00 31.60 2.57
2291 2389 1.837439 TGTCCCACCATGACCTATGAC 59.163 52.381 0.00 0.00 39.21 3.06
2292 2390 1.141053 GTCCCACCATGACCTATGACC 59.859 57.143 0.00 0.00 39.21 4.02
2293 2391 1.009552 TCCCACCATGACCTATGACCT 59.990 52.381 0.00 0.00 39.21 3.85
2294 2392 1.141657 CCCACCATGACCTATGACCTG 59.858 57.143 0.00 0.00 39.21 4.00
2295 2393 1.141657 CCACCATGACCTATGACCTGG 59.858 57.143 0.00 0.00 39.21 4.45
2345 2445 5.179555 CCTAATGTTTTCCCTATAAGCGCTC 59.820 44.000 12.06 0.00 0.00 5.03
2381 2481 5.006649 GTGGGAACAGCTTTTGATTTTTGAC 59.993 40.000 0.00 0.00 44.46 3.18
2423 2523 6.811253 TTTTTAACTGTCCATAGCACGATT 57.189 33.333 0.00 0.00 0.00 3.34
2530 2634 6.789959 AGTATCTCCTAATAATGAGGCAGGTT 59.210 38.462 0.00 0.00 33.73 3.50
2671 3501 2.521958 ATCGGCCCAGTTCCAAGTCG 62.522 60.000 0.00 0.00 0.00 4.18
2673 3503 1.299976 GGCCCAGTTCCAAGTCGAT 59.700 57.895 0.00 0.00 0.00 3.59
2675 3505 0.744771 GCCCAGTTCCAAGTCGATCC 60.745 60.000 0.00 0.00 0.00 3.36
2676 3506 0.107654 CCCAGTTCCAAGTCGATCCC 60.108 60.000 0.00 0.00 0.00 3.85
2677 3507 0.905357 CCAGTTCCAAGTCGATCCCT 59.095 55.000 0.00 0.00 0.00 4.20
2678 3508 2.108168 CCAGTTCCAAGTCGATCCCTA 58.892 52.381 0.00 0.00 0.00 3.53
2681 3605 1.108776 TTCCAAGTCGATCCCTACGG 58.891 55.000 0.00 0.00 0.00 4.02
2682 3606 0.033796 TCCAAGTCGATCCCTACGGT 60.034 55.000 0.00 0.00 0.00 4.83
2686 3610 2.947652 CAAGTCGATCCCTACGGTCTTA 59.052 50.000 0.00 0.00 0.00 2.10
2693 3617 1.134280 TCCCTACGGTCTTAGACTCGG 60.134 57.143 20.77 12.61 33.16 4.63
2694 3618 0.662085 CCTACGGTCTTAGACTCGGC 59.338 60.000 20.77 3.09 33.16 5.54
2699 3623 0.889306 GGTCTTAGACTCGGCAGTGT 59.111 55.000 12.41 0.00 30.63 3.55
2702 3626 2.731976 GTCTTAGACTCGGCAGTGTTTG 59.268 50.000 4.94 0.00 30.63 2.93
2703 3627 2.364324 TCTTAGACTCGGCAGTGTTTGT 59.636 45.455 0.00 0.00 30.63 2.83
2704 3628 2.902705 TAGACTCGGCAGTGTTTGTT 57.097 45.000 0.00 0.00 30.63 2.83
2707 3631 2.097466 AGACTCGGCAGTGTTTGTTTTG 59.903 45.455 0.00 0.00 30.63 2.44
2708 3632 1.134175 ACTCGGCAGTGTTTGTTTTGG 59.866 47.619 0.00 0.00 0.00 3.28
2709 3633 1.134175 CTCGGCAGTGTTTGTTTTGGT 59.866 47.619 0.00 0.00 0.00 3.67
2710 3634 1.133407 TCGGCAGTGTTTGTTTTGGTC 59.867 47.619 0.00 0.00 0.00 4.02
2711 3635 1.135257 CGGCAGTGTTTGTTTTGGTCA 60.135 47.619 0.00 0.00 0.00 4.02
2712 3636 2.672478 CGGCAGTGTTTGTTTTGGTCAA 60.672 45.455 0.00 0.00 0.00 3.18
2713 3637 3.330267 GGCAGTGTTTGTTTTGGTCAAA 58.670 40.909 0.00 0.00 33.28 2.69
2714 3638 3.370672 GGCAGTGTTTGTTTTGGTCAAAG 59.629 43.478 0.00 0.00 35.83 2.77
2717 3641 5.614449 GCAGTGTTTGTTTTGGTCAAAGTTG 60.614 40.000 0.00 0.00 35.83 3.16
2718 3642 5.694006 CAGTGTTTGTTTTGGTCAAAGTTGA 59.306 36.000 0.00 0.00 35.83 3.18
2719 3643 5.925969 AGTGTTTGTTTTGGTCAAAGTTGAG 59.074 36.000 0.00 0.00 37.98 3.02
2720 3644 5.923684 GTGTTTGTTTTGGTCAAAGTTGAGA 59.076 36.000 0.00 0.00 37.98 3.27
2721 3645 6.422400 GTGTTTGTTTTGGTCAAAGTTGAGAA 59.578 34.615 0.00 0.00 37.98 2.87
2722 3646 6.986817 TGTTTGTTTTGGTCAAAGTTGAGAAA 59.013 30.769 0.00 0.00 37.98 2.52
2723 3647 7.170658 TGTTTGTTTTGGTCAAAGTTGAGAAAG 59.829 33.333 0.00 0.00 37.98 2.62
2724 3648 5.719173 TGTTTTGGTCAAAGTTGAGAAAGG 58.281 37.500 0.00 0.00 37.98 3.11
2725 3649 5.478679 TGTTTTGGTCAAAGTTGAGAAAGGA 59.521 36.000 0.00 0.00 37.98 3.36
2726 3650 5.576447 TTTGGTCAAAGTTGAGAAAGGAC 57.424 39.130 0.00 0.00 37.98 3.85
2727 3651 3.202906 TGGTCAAAGTTGAGAAAGGACG 58.797 45.455 0.00 0.00 37.98 4.79
2728 3652 2.548480 GGTCAAAGTTGAGAAAGGACGG 59.452 50.000 0.00 0.00 37.98 4.79
2729 3653 2.031944 GTCAAAGTTGAGAAAGGACGGC 60.032 50.000 0.00 0.00 37.98 5.68
2730 3654 1.946768 CAAAGTTGAGAAAGGACGGCA 59.053 47.619 0.00 0.00 0.00 5.69
2731 3655 1.884235 AAGTTGAGAAAGGACGGCAG 58.116 50.000 0.00 0.00 0.00 4.85
2732 3656 0.035458 AGTTGAGAAAGGACGGCAGG 59.965 55.000 0.00 0.00 0.00 4.85
2734 3658 0.984230 TTGAGAAAGGACGGCAGGAT 59.016 50.000 0.00 0.00 0.00 3.24
2735 3659 0.250234 TGAGAAAGGACGGCAGGATG 59.750 55.000 0.00 0.00 40.87 3.51
2736 3660 0.537188 GAGAAAGGACGGCAGGATGA 59.463 55.000 0.00 0.00 39.69 2.92
2737 3661 0.250513 AGAAAGGACGGCAGGATGAC 59.749 55.000 0.00 0.00 44.64 3.06
2753 3677 8.261492 GCAGGATGACAATATGTTCCTAATAG 57.739 38.462 3.97 0.00 35.90 1.73
2754 3678 7.880195 GCAGGATGACAATATGTTCCTAATAGT 59.120 37.037 3.97 0.00 35.90 2.12
2755 3679 9.784531 CAGGATGACAATATGTTCCTAATAGTT 57.215 33.333 3.97 0.00 35.90 2.24
2756 3680 9.784531 AGGATGACAATATGTTCCTAATAGTTG 57.215 33.333 2.62 0.00 36.21 3.16
2757 3681 9.778741 GGATGACAATATGTTCCTAATAGTTGA 57.221 33.333 0.00 0.00 27.44 3.18
2779 3703 9.249457 GTTGATATCATCGAAAAGTGATAGACA 57.751 33.333 6.17 10.46 39.79 3.41
2780 3704 9.816354 TTGATATCATCGAAAAGTGATAGACAA 57.184 29.630 6.17 16.34 39.79 3.18
2781 3705 9.987272 TGATATCATCGAAAAGTGATAGACAAT 57.013 29.630 0.00 0.00 39.79 2.71
2811 3735 8.602472 TTAAAATAATTAGGCCCTTCACATGT 57.398 30.769 0.00 0.00 0.00 3.21
2817 3741 1.282157 AGGCCCTTCACATGTTACTCC 59.718 52.381 0.00 0.00 0.00 3.85
2895 3832 3.518552 AACTCCACCCCCGAGTCGA 62.519 63.158 15.64 0.00 39.69 4.20
2900 3837 1.370064 CACCCCCGAGTCGAAACTT 59.630 57.895 15.64 0.00 35.28 2.66
2935 3872 0.034337 TCACCGTAGTTGCAACTCCC 59.966 55.000 34.29 23.70 40.37 4.30
2936 3873 0.250124 CACCGTAGTTGCAACTCCCA 60.250 55.000 34.29 15.87 40.37 4.37
2955 3893 0.896940 ACCCCGACTCGCTACTCAAA 60.897 55.000 0.00 0.00 0.00 2.69
2967 3905 6.642131 ACTCGCTACTCAAAACGTTTTGTATA 59.358 34.615 38.54 30.87 45.77 1.47
2969 3907 6.011277 CGCTACTCAAAACGTTTTGTATACC 58.989 40.000 38.54 27.16 45.77 2.73
2991 5266 3.670377 GGTTGCAACTCCACCCGC 61.670 66.667 27.64 6.02 0.00 6.13
2992 5267 2.594592 GTTGCAACTCCACCCGCT 60.595 61.111 22.36 0.00 0.00 5.52
2993 5268 2.281484 TTGCAACTCCACCCGCTC 60.281 61.111 0.00 0.00 0.00 5.03
2994 5269 3.113514 TTGCAACTCCACCCGCTCA 62.114 57.895 0.00 0.00 0.00 4.26
3006 5319 2.720758 CCGCTCAAGTCGCAACTCG 61.721 63.158 0.00 0.00 33.48 4.18
3015 5328 2.029073 CGCAACTCGAGTGGGTGT 59.971 61.111 20.85 0.00 41.67 4.16
3016 5329 1.174078 TCGCAACTCGAGTGGGTGTA 61.174 55.000 20.85 8.56 43.16 2.90
3047 5907 2.510613 TGCCCTAGTTGCAAGTTAACC 58.489 47.619 12.95 0.31 35.40 2.85
3054 5914 2.623416 AGTTGCAAGTTAACCCTCAAGC 59.377 45.455 0.00 0.00 0.00 4.01
3063 5923 3.121030 CCCTCAAGCCGCAACTCG 61.121 66.667 0.00 0.00 38.08 4.18
3082 5942 3.182996 GGGGTGGGGAGTGGTTGT 61.183 66.667 0.00 0.00 0.00 3.32
3085 5945 1.073199 GGTGGGGAGTGGTTGTCTG 59.927 63.158 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.046708 ACCATAGTGCTTACTTCATGATTTACA 58.953 33.333 0.00 0.00 0.00 2.41
45 46 8.438676 ACCATAGTGCTTACTTCATGATTTAC 57.561 34.615 0.00 0.00 0.00 2.01
114 115 4.020485 AGTGGATACTACGCTTTTCCTTGT 60.020 41.667 0.00 0.00 34.74 3.16
131 132 4.711846 TGTAGTAGATGCAGACAAGTGGAT 59.288 41.667 0.00 0.00 0.00 3.41
136 137 5.330455 TCCTTGTAGTAGATGCAGACAAG 57.670 43.478 13.27 13.27 44.21 3.16
244 245 1.737363 GCAACAACGGGCAGACAAAAA 60.737 47.619 0.00 0.00 0.00 1.94
248 249 1.034838 AAAGCAACAACGGGCAGACA 61.035 50.000 0.00 0.00 0.00 3.41
253 254 1.202359 TCAAGAAAAGCAACAACGGGC 60.202 47.619 0.00 0.00 0.00 6.13
273 274 2.327325 TTCAGGAAGCTACTCACCCT 57.673 50.000 0.00 0.00 0.00 4.34
414 424 2.734492 GCAGCAAAATCCTCATGTGAGC 60.734 50.000 4.48 0.00 40.75 4.26
480 490 7.552330 ACTGAATAAAATGGCACTTTGTTTTGT 59.448 29.630 3.86 4.45 0.00 2.83
579 589 3.884693 ACTGAAAATGTGCACATGACTGA 59.115 39.130 31.98 13.10 36.56 3.41
592 602 4.666176 CGAAGAAACGACACACTGAAAATG 59.334 41.667 0.00 0.00 35.09 2.32
593 603 4.331717 ACGAAGAAACGACACACTGAAAAT 59.668 37.500 0.00 0.00 37.03 1.82
634 644 5.456548 TGAGTAAATCAACTACACGACCA 57.543 39.130 0.00 0.00 34.02 4.02
680 691 9.551734 TGAATATCTGATCAAACTCAATACTGG 57.448 33.333 0.00 0.00 0.00 4.00
744 756 7.060421 TCAGGGTTTTCAGTTCAAAACTAGAT 58.940 34.615 0.00 0.00 43.18 1.98
897 913 3.694072 AGCAAAACTGAAGTAGCACAACA 59.306 39.130 0.00 0.00 0.00 3.33
906 922 7.094377 TGTTTTCAGAGTAAGCAAAACTGAAGT 60.094 33.333 0.00 0.00 44.45 3.01
913 929 6.772716 AGGAGATGTTTTCAGAGTAAGCAAAA 59.227 34.615 0.00 0.00 0.00 2.44
934 950 5.486735 AGCAGGATAATCATCAGAAGGAG 57.513 43.478 0.00 0.00 32.32 3.69
938 954 5.066893 GCACAAAGCAGGATAATCATCAGAA 59.933 40.000 0.00 0.00 44.79 3.02
982 999 7.576666 GCACACCATCCTACACATCAAATAAAA 60.577 37.037 0.00 0.00 0.00 1.52
1040 1057 2.618241 ACAATGCGAAAAGTCTGCTCAA 59.382 40.909 0.00 0.00 0.00 3.02
1201 1223 5.599732 CATGGGATGTTCTGTTGACAAAAA 58.400 37.500 0.00 0.00 0.00 1.94
1202 1224 4.501229 GCATGGGATGTTCTGTTGACAAAA 60.501 41.667 0.00 0.00 0.00 2.44
1204 1226 2.557924 GCATGGGATGTTCTGTTGACAA 59.442 45.455 0.00 0.00 0.00 3.18
1205 1227 2.161855 GCATGGGATGTTCTGTTGACA 58.838 47.619 0.00 0.00 0.00 3.58
1206 1228 2.095059 GTGCATGGGATGTTCTGTTGAC 60.095 50.000 0.00 0.00 0.00 3.18
1207 1229 2.161855 GTGCATGGGATGTTCTGTTGA 58.838 47.619 0.00 0.00 0.00 3.18
1208 1230 2.094906 CAGTGCATGGGATGTTCTGTTG 60.095 50.000 0.00 0.00 32.70 3.33
1252 1274 2.882137 CGCCTTAAAGTTCAACCCAGAA 59.118 45.455 0.00 0.00 0.00 3.02
1279 1301 1.269883 ACATCAACAACGTACCTGCGA 60.270 47.619 0.00 0.00 35.59 5.10
1282 1304 4.052608 TGTACACATCAACAACGTACCTG 58.947 43.478 0.00 0.00 33.16 4.00
1288 1310 1.804151 CCCCTGTACACATCAACAACG 59.196 52.381 0.00 0.00 0.00 4.10
1313 1396 1.420138 ACCTCCGATCAGTGTGGTTTT 59.580 47.619 0.00 0.00 0.00 2.43
1316 1399 0.541998 TCACCTCCGATCAGTGTGGT 60.542 55.000 0.00 0.00 33.21 4.16
1327 1410 1.526917 GGCCCAATCATCACCTCCG 60.527 63.158 0.00 0.00 0.00 4.63
1343 1426 2.666619 CGAAGTCATGCTTGAACTTGGC 60.667 50.000 16.49 7.37 37.59 4.52
1356 1439 2.264794 GCCCCACGTCGAAGTCAT 59.735 61.111 0.00 0.00 0.00 3.06
1357 1440 3.220999 CTGCCCCACGTCGAAGTCA 62.221 63.158 0.00 0.00 0.00 3.41
1419 1502 1.269988 CCTCGACTCCAGCCACATATG 60.270 57.143 0.00 0.00 0.00 1.78
1435 1518 0.108424 CTCCCTGTTCTTCAGCCTCG 60.108 60.000 0.00 0.00 42.38 4.63
1448 1531 1.221293 CTTCAGCAGCTCCTCCCTG 59.779 63.158 0.00 0.00 0.00 4.45
1498 1581 0.947244 GCCCGTGATCATCATTGACC 59.053 55.000 0.00 0.00 33.85 4.02
1594 1677 9.342308 CCAATGTATAAATGTTGGATAGTGAGT 57.658 33.333 0.00 0.00 42.88 3.41
1653 1736 0.815095 CATCAGCTTGCCTGCAATGA 59.185 50.000 4.84 7.73 41.50 2.57
1989 2083 4.924305 AAACACAACAGCATCATTCACT 57.076 36.364 0.00 0.00 0.00 3.41
2010 2104 8.602424 TGTTCTTCATTGATCTCCCTAAAGTTA 58.398 33.333 0.00 0.00 0.00 2.24
2016 2110 8.496534 TGATATGTTCTTCATTGATCTCCCTA 57.503 34.615 0.00 0.00 37.91 3.53
2125 2220 5.589050 GGGTTCTGGACATGAGGTAATAAAC 59.411 44.000 0.00 0.00 0.00 2.01
2180 2276 0.869068 CACATTGTCGCACCGGTAAA 59.131 50.000 6.87 0.00 0.00 2.01
2181 2277 1.570347 GCACATTGTCGCACCGGTAA 61.570 55.000 6.87 0.00 0.00 2.85
2182 2278 2.030401 GCACATTGTCGCACCGGTA 61.030 57.895 6.87 0.00 0.00 4.02
2184 2280 1.089481 ATAGCACATTGTCGCACCGG 61.089 55.000 0.00 0.00 0.00 5.28
2185 2281 0.301687 GATAGCACATTGTCGCACCG 59.698 55.000 11.85 0.00 0.00 4.94
2187 2283 3.680642 AATGATAGCACATTGTCGCAC 57.319 42.857 11.85 5.62 38.76 5.34
2213 2311 8.528044 ACCACCTCATAAAACAAAGAAAAGTA 57.472 30.769 0.00 0.00 0.00 2.24
2214 2312 7.418337 ACCACCTCATAAAACAAAGAAAAGT 57.582 32.000 0.00 0.00 0.00 2.66
2215 2313 9.981114 ATAACCACCTCATAAAACAAAGAAAAG 57.019 29.630 0.00 0.00 0.00 2.27
2243 2341 9.605275 CATAGGAACTTGACAAATTCATCTCTA 57.395 33.333 11.17 4.20 41.75 2.43
2244 2342 8.105829 ACATAGGAACTTGACAAATTCATCTCT 58.894 33.333 11.17 2.26 41.75 3.10
2245 2343 8.273780 ACATAGGAACTTGACAAATTCATCTC 57.726 34.615 11.17 0.00 41.75 2.75
2246 2344 8.517878 CAACATAGGAACTTGACAAATTCATCT 58.482 33.333 11.17 3.20 41.75 2.90
2247 2345 8.299570 ACAACATAGGAACTTGACAAATTCATC 58.700 33.333 11.17 0.00 41.75 2.92
2248 2346 8.181904 ACAACATAGGAACTTGACAAATTCAT 57.818 30.769 11.17 6.73 41.75 2.57
2249 2347 7.255451 GGACAACATAGGAACTTGACAAATTCA 60.255 37.037 11.17 0.00 41.75 2.57
2250 2348 7.084486 GGACAACATAGGAACTTGACAAATTC 58.916 38.462 0.70 0.70 41.75 2.17
2252 2350 5.476945 GGGACAACATAGGAACTTGACAAAT 59.523 40.000 0.00 0.00 41.75 2.32
2253 2351 4.825085 GGGACAACATAGGAACTTGACAAA 59.175 41.667 0.00 0.00 41.75 2.83
2287 2385 3.602104 CCTGCATTTCCCAGGTCAT 57.398 52.632 0.00 0.00 43.86 3.06
2292 2390 2.892852 TCAAAAGTCCTGCATTTCCCAG 59.107 45.455 0.00 0.00 0.00 4.45
2293 2391 2.956132 TCAAAAGTCCTGCATTTCCCA 58.044 42.857 0.00 0.00 0.00 4.37
2294 2392 3.321968 AGTTCAAAAGTCCTGCATTTCCC 59.678 43.478 0.00 0.00 0.00 3.97
2295 2393 4.590850 AGTTCAAAAGTCCTGCATTTCC 57.409 40.909 0.00 0.00 0.00 3.13
2352 2452 2.173782 TCAAAAGCTGTTCCCACCTACA 59.826 45.455 0.00 0.00 0.00 2.74
2353 2453 2.858745 TCAAAAGCTGTTCCCACCTAC 58.141 47.619 0.00 0.00 0.00 3.18
2354 2454 3.806949 ATCAAAAGCTGTTCCCACCTA 57.193 42.857 0.00 0.00 0.00 3.08
2355 2455 2.683211 ATCAAAAGCTGTTCCCACCT 57.317 45.000 0.00 0.00 0.00 4.00
2357 2457 5.006649 GTCAAAAATCAAAAGCTGTTCCCAC 59.993 40.000 0.00 0.00 0.00 4.61
2358 2458 5.104982 AGTCAAAAATCAAAAGCTGTTCCCA 60.105 36.000 0.00 0.00 0.00 4.37
2364 2464 8.807667 ACTAATCAGTCAAAAATCAAAAGCTG 57.192 30.769 0.00 0.00 0.00 4.24
2433 2535 6.668323 ACCAACACTTAATCAACTGATTTCG 58.332 36.000 10.08 5.06 41.64 3.46
2501 2604 9.868277 CTGCCTCATTATTAGGAGATACTAAAG 57.132 37.037 0.00 0.00 36.60 1.85
2598 2753 9.781834 CAGAAGTGTTAACAAAAGAATACACAA 57.218 29.630 10.51 0.00 38.59 3.33
2648 3478 3.508840 GGAACTGGGCCGATTGCG 61.509 66.667 0.00 0.00 42.61 4.85
2654 3484 2.521958 ATCGACTTGGAACTGGGCCG 62.522 60.000 0.00 0.00 0.00 6.13
2656 3486 0.744771 GGATCGACTTGGAACTGGGC 60.745 60.000 0.00 0.00 0.00 5.36
2676 3506 1.331138 CTGCCGAGTCTAAGACCGTAG 59.669 57.143 0.00 0.00 32.18 3.51
2677 3507 1.339438 ACTGCCGAGTCTAAGACCGTA 60.339 52.381 0.00 0.00 32.18 4.02
2678 3508 0.608582 ACTGCCGAGTCTAAGACCGT 60.609 55.000 0.00 0.00 32.18 4.83
2681 3605 2.726832 AACACTGCCGAGTCTAAGAC 57.273 50.000 0.00 0.00 0.00 3.01
2682 3606 2.364324 ACAAACACTGCCGAGTCTAAGA 59.636 45.455 0.00 0.00 0.00 2.10
2686 3610 2.038387 AAACAAACACTGCCGAGTCT 57.962 45.000 0.00 0.00 0.00 3.24
2693 3617 3.993736 ACTTTGACCAAAACAAACACTGC 59.006 39.130 0.00 0.00 34.30 4.40
2694 3618 5.694006 TCAACTTTGACCAAAACAAACACTG 59.306 36.000 0.00 0.00 34.30 3.66
2699 3623 6.648725 CCTTTCTCAACTTTGACCAAAACAAA 59.351 34.615 0.00 0.00 36.15 2.83
2702 3626 5.805486 GTCCTTTCTCAACTTTGACCAAAAC 59.195 40.000 0.00 0.00 32.90 2.43
2703 3627 5.392595 CGTCCTTTCTCAACTTTGACCAAAA 60.393 40.000 0.00 0.00 32.90 2.44
2704 3628 4.095782 CGTCCTTTCTCAACTTTGACCAAA 59.904 41.667 0.00 0.00 32.90 3.28
2707 3631 2.548480 CCGTCCTTTCTCAACTTTGACC 59.452 50.000 0.00 0.00 32.90 4.02
2708 3632 2.031944 GCCGTCCTTTCTCAACTTTGAC 60.032 50.000 0.00 0.00 32.90 3.18
2709 3633 2.218603 GCCGTCCTTTCTCAACTTTGA 58.781 47.619 0.00 0.00 35.57 2.69
2710 3634 1.946768 TGCCGTCCTTTCTCAACTTTG 59.053 47.619 0.00 0.00 0.00 2.77
2711 3635 2.222027 CTGCCGTCCTTTCTCAACTTT 58.778 47.619 0.00 0.00 0.00 2.66
2712 3636 1.543429 CCTGCCGTCCTTTCTCAACTT 60.543 52.381 0.00 0.00 0.00 2.66
2713 3637 0.035458 CCTGCCGTCCTTTCTCAACT 59.965 55.000 0.00 0.00 0.00 3.16
2714 3638 0.034896 TCCTGCCGTCCTTTCTCAAC 59.965 55.000 0.00 0.00 0.00 3.18
2717 3641 0.537188 TCATCCTGCCGTCCTTTCTC 59.463 55.000 0.00 0.00 0.00 2.87
2718 3642 0.250513 GTCATCCTGCCGTCCTTTCT 59.749 55.000 0.00 0.00 0.00 2.52
2719 3643 0.036388 TGTCATCCTGCCGTCCTTTC 60.036 55.000 0.00 0.00 0.00 2.62
2720 3644 0.400213 TTGTCATCCTGCCGTCCTTT 59.600 50.000 0.00 0.00 0.00 3.11
2721 3645 0.620556 ATTGTCATCCTGCCGTCCTT 59.379 50.000 0.00 0.00 0.00 3.36
2722 3646 1.496060 TATTGTCATCCTGCCGTCCT 58.504 50.000 0.00 0.00 0.00 3.85
2723 3647 2.146342 CATATTGTCATCCTGCCGTCC 58.854 52.381 0.00 0.00 0.00 4.79
2724 3648 2.838736 ACATATTGTCATCCTGCCGTC 58.161 47.619 0.00 0.00 0.00 4.79
2725 3649 3.206150 GAACATATTGTCATCCTGCCGT 58.794 45.455 0.00 0.00 0.00 5.68
2726 3650 2.549754 GGAACATATTGTCATCCTGCCG 59.450 50.000 0.00 0.00 27.44 5.69
2727 3651 3.825328 AGGAACATATTGTCATCCTGCC 58.175 45.455 1.08 0.00 36.52 4.85
2728 3652 7.880195 ACTATTAGGAACATATTGTCATCCTGC 59.120 37.037 9.97 0.00 37.94 4.85
2729 3653 9.784531 AACTATTAGGAACATATTGTCATCCTG 57.215 33.333 9.97 0.00 37.94 3.86
2730 3654 9.784531 CAACTATTAGGAACATATTGTCATCCT 57.215 33.333 6.24 6.24 39.96 3.24
2731 3655 9.778741 TCAACTATTAGGAACATATTGTCATCC 57.221 33.333 0.00 0.00 29.48 3.51
2752 3676 9.469807 GTCTATCACTTTTCGATGATATCAACT 57.530 33.333 9.99 0.00 37.23 3.16
2753 3677 9.249457 TGTCTATCACTTTTCGATGATATCAAC 57.751 33.333 9.99 6.18 37.23 3.18
2754 3678 9.816354 TTGTCTATCACTTTTCGATGATATCAA 57.184 29.630 9.99 11.15 37.23 2.57
2755 3679 9.987272 ATTGTCTATCACTTTTCGATGATATCA 57.013 29.630 8.10 8.10 37.23 2.15
2784 3708 9.883142 CATGTGAAGGGCCTAATTATTTTAAAA 57.117 29.630 6.41 2.51 0.00 1.52
2785 3709 9.041354 ACATGTGAAGGGCCTAATTATTTTAAA 57.959 29.630 6.41 0.00 0.00 1.52
2786 3710 8.602472 ACATGTGAAGGGCCTAATTATTTTAA 57.398 30.769 6.41 0.00 0.00 1.52
2787 3711 8.602472 AACATGTGAAGGGCCTAATTATTTTA 57.398 30.769 6.41 0.00 0.00 1.52
2788 3712 7.494922 AACATGTGAAGGGCCTAATTATTTT 57.505 32.000 6.41 0.00 0.00 1.82
2789 3713 7.839200 AGTAACATGTGAAGGGCCTAATTATTT 59.161 33.333 6.41 0.00 0.00 1.40
2790 3714 7.354312 AGTAACATGTGAAGGGCCTAATTATT 58.646 34.615 6.41 0.00 0.00 1.40
2791 3715 6.911308 AGTAACATGTGAAGGGCCTAATTAT 58.089 36.000 6.41 0.00 0.00 1.28
2792 3716 6.321821 AGTAACATGTGAAGGGCCTAATTA 57.678 37.500 6.41 0.00 0.00 1.40
2803 3727 0.035820 GGCGGGGAGTAACATGTGAA 60.036 55.000 0.00 0.00 0.00 3.18
2805 3729 1.451387 GGGCGGGGAGTAACATGTG 60.451 63.158 0.00 0.00 0.00 3.21
2811 3735 2.757099 GTCGAGGGCGGGGAGTAA 60.757 66.667 0.00 0.00 38.28 2.24
2817 3741 4.697756 TTGCAAGTCGAGGGCGGG 62.698 66.667 0.00 0.00 38.28 6.13
2869 3806 0.769247 GGGGGTGGAGTTGTAACTGT 59.231 55.000 1.35 0.00 39.88 3.55
2875 3812 2.122547 ACTCGGGGGTGGAGTTGT 60.123 61.111 0.00 0.00 41.83 3.32
2895 3832 6.589907 GGTGAAACACAAAACATCTCAAGTTT 59.410 34.615 0.00 0.00 38.72 2.66
2900 3837 3.692101 ACGGTGAAACACAAAACATCTCA 59.308 39.130 0.00 0.00 39.98 3.27
2935 3872 1.592400 TTGAGTAGCGAGTCGGGGTG 61.592 60.000 15.52 0.00 0.00 4.61
2936 3873 0.896940 TTTGAGTAGCGAGTCGGGGT 60.897 55.000 15.52 0.00 0.00 4.95
2969 3907 4.278513 TGGAGTTGCAACCGGGGG 62.279 66.667 25.62 0.00 0.00 5.40
2974 3912 3.670377 GCGGGTGGAGTTGCAACC 61.670 66.667 25.62 16.44 0.00 3.77
2992 5267 0.318699 CCACTCGAGTTGCGACTTGA 60.319 55.000 20.90 20.90 45.59 3.02
2993 5268 1.284982 CCCACTCGAGTTGCGACTTG 61.285 60.000 17.26 14.57 45.59 3.16
2994 5269 1.006102 CCCACTCGAGTTGCGACTT 60.006 57.895 17.26 0.00 45.59 3.01
3006 5319 4.024302 GCAACTACAAAACTACACCCACTC 60.024 45.833 0.00 0.00 0.00 3.51
3015 5328 4.758165 GCAACTAGGGCAACTACAAAACTA 59.242 41.667 4.00 0.00 0.00 2.24
3016 5329 3.568430 GCAACTAGGGCAACTACAAAACT 59.432 43.478 4.00 0.00 0.00 2.66
3041 5901 0.240145 GTTGCGGCTTGAGGGTTAAC 59.760 55.000 0.00 0.00 0.00 2.01
3043 5903 0.321298 GAGTTGCGGCTTGAGGGTTA 60.321 55.000 0.00 0.00 0.00 2.85
3046 5906 3.121030 CGAGTTGCGGCTTGAGGG 61.121 66.667 0.00 0.00 36.03 4.30
3066 5926 2.154074 AGACAACCACTCCCCACCC 61.154 63.158 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.