Multiple sequence alignment - TraesCS7D01G060500

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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 TraesCS7D01G060500 chr7D 100.000 6470 0 0 1 6470 32960011 32953542 0.000000e+00 11948.0
1 TraesCS7D01G060500 chr7D 100.000 45 0 0 6426 6470 588171035 588170991 4.160000e-12 84.2
2 TraesCS7D01G060500 chr7A 96.815 3768 91 10 12 3762 33201589 33197834 0.000000e+00 6266.0
3 TraesCS7D01G060500 chr7A 95.550 2000 73 6 3778 5764 33197774 33195778 0.000000e+00 3186.0
4 TraesCS7D01G060500 chr7A 87.018 570 58 9 5858 6412 33195781 33195213 4.260000e-176 628.0
5 TraesCS7D01G060500 chr4A 90.417 2713 157 41 3771 6426 692964894 692962228 0.000000e+00 3474.0
6 TraesCS7D01G060500 chr4A 95.774 1964 63 10 1309 3260 692967538 692965583 0.000000e+00 3149.0
7 TraesCS7D01G060500 chr4A 91.742 1332 67 16 12 1323 692968874 692967566 0.000000e+00 1810.0
8 TraesCS7D01G060500 chr4A 95.260 443 12 4 3263 3704 692965465 692965031 0.000000e+00 693.0
9 TraesCS7D01G060500 chr7B 86.420 486 47 7 1815 2285 685038632 685038151 1.240000e-141 514.0
10 TraesCS7D01G060500 chr7B 100.000 44 0 0 6427 6470 292637708 292637751 1.500000e-11 82.4
11 TraesCS7D01G060500 chr7B 100.000 44 0 0 6427 6470 716036677 716036634 1.500000e-11 82.4
12 TraesCS7D01G060500 chr6B 86.797 462 40 9 1 450 402447090 402447542 4.510000e-136 496.0
13 TraesCS7D01G060500 chr2B 85.622 466 47 13 1830 2285 152709860 152710315 7.590000e-129 472.0
14 TraesCS7D01G060500 chr5B 85.043 468 52 8 1815 2268 547361123 547360660 1.640000e-125 460.0
15 TraesCS7D01G060500 chr5B 100.000 44 0 0 6427 6470 369598591 369598548 1.500000e-11 82.4
16 TraesCS7D01G060500 chr5A 83.529 510 64 9 2443 2950 548797309 548796818 5.910000e-125 459.0
17 TraesCS7D01G060500 chr6A 83.903 497 61 8 2443 2937 454707873 454708352 2.130000e-124 457.0
18 TraesCS7D01G060500 chr3A 84.188 468 56 8 1815 2268 425584632 425584169 7.700000e-119 438.0
19 TraesCS7D01G060500 chr3A 83.441 465 59 8 1818 2268 91448700 91448240 3.610000e-112 416.0
20 TraesCS7D01G060500 chr3A 100.000 44 0 0 6427 6470 638999521 638999564 1.500000e-11 82.4
21 TraesCS7D01G060500 chr3A 100.000 44 0 0 6427 6470 639014158 639014201 1.500000e-11 82.4
22 TraesCS7D01G060500 chr3A 100.000 44 0 0 6427 6470 693631288 693631245 1.500000e-11 82.4
23 TraesCS7D01G060500 chr3A 88.679 53 2 2 5771 5823 552633525 552633477 1.950000e-05 62.1
24 TraesCS7D01G060500 chr5D 86.650 397 44 5 1868 2258 433926699 433926306 1.290000e-116 431.0
25 TraesCS7D01G060500 chr4B 84.211 456 54 8 1815 2256 471267375 471266924 1.670000e-115 427.0
26 TraesCS7D01G060500 chr1A 83.271 269 39 5 2682 2950 573212000 573211738 6.480000e-60 243.0
27 TraesCS7D01G060500 chr3D 100.000 44 0 0 6427 6470 101559455 101559412 1.500000e-11 82.4
28 TraesCS7D01G060500 chr3D 100.000 44 0 0 6427 6470 566882761 566882804 1.500000e-11 82.4
29 TraesCS7D01G060500 chr3D 90.385 52 5 0 3477 3528 2381013 2380962 1.160000e-07 69.4


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 TraesCS7D01G060500 chr7D 32953542 32960011 6469 True 11948.0 11948 100.000000 1 6470 1 chr7D.!!$R1 6469
1 TraesCS7D01G060500 chr7A 33195213 33201589 6376 True 3360.0 6266 93.127667 12 6412 3 chr7A.!!$R1 6400
2 TraesCS7D01G060500 chr4A 692962228 692968874 6646 True 2281.5 3474 93.298250 12 6426 4 chr4A.!!$R1 6414

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
20 21 0.380733 ACATACAGCGCTCGATCGAA 59.619 50.000 19.92 2.21 0.00 3.71 F
72 76 0.960364 TTGACGCCTCATGCCTTTCC 60.960 55.000 0.00 0.00 36.24 3.13 F
550 561 1.069906 CAGACAAACAAGCCACTACGC 60.070 52.381 0.00 0.00 0.00 4.42 F
1472 1550 0.249911 AACCTGTCACTCGAAGTGCC 60.250 55.000 9.34 0.85 45.54 5.01 F
1749 1828 1.356398 TGGTTTATTCACCTGTCCCCC 59.644 52.381 0.00 0.00 37.75 5.40 F
2160 2241 5.104652 GGTATGCTAGTACTTCCTTTTGGGA 60.105 44.000 0.00 0.00 43.41 4.37 F
2604 2690 5.977129 CCAGCGAAAACTGACATTTAAGTTT 59.023 36.000 0.00 0.00 46.03 2.66 F
3507 3712 6.299805 TGCCTGAACATAAGATACTTCTGT 57.700 37.500 0.00 0.00 30.72 3.41 F
5192 5484 0.536006 GCAAGCCGCCTCCATTATCT 60.536 55.000 0.00 0.00 32.94 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1006 1019 1.676967 GCCCAAGGTCTTCAGCCAG 60.677 63.158 0.00 0.0 0.00 4.85 R
1472 1550 1.904287 TGGACAAATTCCCCTTCACG 58.096 50.000 0.00 0.0 45.17 4.35 R
1568 1646 2.414161 GCAAAAGGAGTCAACATACGGC 60.414 50.000 0.00 0.0 0.00 5.68 R
3282 3487 3.993920 TCAAGCAAAATTTGAGGCCTTC 58.006 40.909 6.77 0.1 31.35 3.46 R
3507 3712 5.710099 GGTAAAGGTGTGAAAAGGATCATCA 59.290 40.000 0.00 0.0 0.00 3.07 R
3763 3994 0.883153 TGCATGCGCACAAGAGAAAT 59.117 45.000 14.90 0.0 45.36 2.17 R
3764 3995 2.329244 TGCATGCGCACAAGAGAAA 58.671 47.368 14.90 0.0 45.36 2.52 R
5325 5624 0.887387 TAGTTTGGGCGTTCACTGGC 60.887 55.000 0.00 0.0 0.00 4.85 R
6346 6685 0.105862 ACTGGGGGATGAATGCCATG 60.106 55.000 3.08 0.0 40.49 3.66 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 0.380733 ACATACAGCGCTCGATCGAA 59.619 50.000 19.92 2.21 0.00 3.71
72 76 0.960364 TTGACGCCTCATGCCTTTCC 60.960 55.000 0.00 0.00 36.24 3.13
104 108 3.704231 CTGGAGATTGGGTGGGGCG 62.704 68.421 0.00 0.00 0.00 6.13
108 112 4.404098 GATTGGGTGGGGCGACGT 62.404 66.667 0.00 0.00 0.00 4.34
181 188 5.627503 GCGTATTCCCCTTTCCAAGTAGTAA 60.628 44.000 0.00 0.00 0.00 2.24
274 281 6.662616 CGGCCATTTATTGTAATTCTCTGAG 58.337 40.000 2.24 0.00 0.00 3.35
470 481 4.368391 CTGCGAGCAGTGGTTTCT 57.632 55.556 16.29 0.00 39.10 2.52
550 561 1.069906 CAGACAAACAAGCCACTACGC 60.070 52.381 0.00 0.00 0.00 4.42
667 678 8.370182 AGAAATGTGTTAATTTCCAGCAGATTT 58.630 29.630 6.14 0.00 44.29 2.17
798 809 7.115520 CCGAGTTTACATATCATCTACTGCAAG 59.884 40.741 0.00 0.00 42.29 4.01
955 968 6.693315 TGTATTGCCTTTAATTGCCTAGTC 57.307 37.500 0.00 0.00 0.00 2.59
1229 1264 5.872070 GCTATATGTTTAGGATGGAGTGCTC 59.128 44.000 0.00 0.00 0.00 4.26
1325 1402 8.806429 TGATCACTAATGTTGTTTATCATGGT 57.194 30.769 0.00 0.00 0.00 3.55
1326 1403 9.241919 TGATCACTAATGTTGTTTATCATGGTT 57.758 29.630 0.00 0.00 0.00 3.67
1472 1550 0.249911 AACCTGTCACTCGAAGTGCC 60.250 55.000 9.34 0.85 45.54 5.01
1568 1646 4.825546 ACTTGAAGTGAAGAATGCTGTG 57.174 40.909 0.00 0.00 0.00 3.66
1577 1655 2.113860 AGAATGCTGTGCCGTATGTT 57.886 45.000 0.00 0.00 0.00 2.71
1586 1664 2.224426 TGTGCCGTATGTTGACTCCTTT 60.224 45.455 0.00 0.00 0.00 3.11
1679 1757 5.106908 GGTAGTCTGCTGTTTCTTTTAGCTG 60.107 44.000 0.00 0.00 38.25 4.24
1749 1828 1.356398 TGGTTTATTCACCTGTCCCCC 59.644 52.381 0.00 0.00 37.75 5.40
2160 2241 5.104652 GGTATGCTAGTACTTCCTTTTGGGA 60.105 44.000 0.00 0.00 43.41 4.37
2236 2322 5.998363 ACTTTGTCTCATTTCTTAGACCACC 59.002 40.000 0.00 0.00 41.19 4.61
2604 2690 5.977129 CCAGCGAAAACTGACATTTAAGTTT 59.023 36.000 0.00 0.00 46.03 2.66
3507 3712 6.299805 TGCCTGAACATAAGATACTTCTGT 57.700 37.500 0.00 0.00 30.72 3.41
3758 3989 9.693739 AATCCCACAATTAACATGTACTGATAA 57.306 29.630 0.00 0.00 0.00 1.75
3759 3990 8.500753 TCCCACAATTAACATGTACTGATAAC 57.499 34.615 0.00 0.00 0.00 1.89
3760 3991 8.103935 TCCCACAATTAACATGTACTGATAACA 58.896 33.333 0.00 0.00 0.00 2.41
3805 4080 7.552687 TGCAATTTCTTATATCGAGGAACAAGT 59.447 33.333 0.00 0.00 0.00 3.16
4241 4522 4.816385 ACACGATCTTGTGAGTCAACATTT 59.184 37.500 3.70 0.00 42.55 2.32
4301 4582 5.624344 GCTCATCAGCATGCAAATATACT 57.376 39.130 21.98 0.00 46.06 2.12
4414 4695 5.622180 TGGTTGCAGTTACATTACCAGTTA 58.378 37.500 0.00 0.00 32.30 2.24
4434 4715 9.945904 CCAGTTACCTAAATTCTAATCTATCCC 57.054 37.037 0.00 0.00 0.00 3.85
4475 4756 9.554395 TTGGAAGAATATATTGCTTACGATGAA 57.446 29.630 1.78 0.00 0.00 2.57
4766 5056 8.056407 AGTTTTCAGTCAAAGCTTCTAGTTTT 57.944 30.769 0.00 0.00 31.83 2.43
4856 5146 7.865385 TCTTGGTGTTAATTGCTTTACATTGAC 59.135 33.333 0.00 0.00 0.00 3.18
4893 5183 4.771590 GGAACAGAAGTTGCATGATGAA 57.228 40.909 0.00 0.00 44.50 2.57
4895 5185 3.818961 ACAGAAGTTGCATGATGAACG 57.181 42.857 0.00 0.00 0.00 3.95
5019 5309 1.202313 GCAGAGGAGACATCGGTGTAC 60.202 57.143 0.00 0.00 39.09 2.90
5192 5484 0.536006 GCAAGCCGCCTCCATTATCT 60.536 55.000 0.00 0.00 32.94 1.98
5223 5515 8.258007 TCTTTAACAAGGTACATACTGATGGAG 58.742 37.037 0.00 0.00 37.39 3.86
5242 5534 4.462483 TGGAGCAAAAATGGATCACCTTAC 59.538 41.667 0.00 0.00 37.04 2.34
5342 5641 2.335011 GCCAGTGAACGCCCAAAC 59.665 61.111 0.00 0.00 0.00 2.93
5367 5666 8.358148 ACTATATCACTACCAAGGTTATTCACG 58.642 37.037 0.00 0.00 0.00 4.35
5373 5672 3.219281 ACCAAGGTTATTCACGTGCTTT 58.781 40.909 11.67 0.00 0.00 3.51
5386 5685 2.616842 ACGTGCTTTCCTTTCATTTCGT 59.383 40.909 0.00 0.00 0.00 3.85
5387 5686 3.066203 ACGTGCTTTCCTTTCATTTCGTT 59.934 39.130 0.00 0.00 0.00 3.85
5399 5698 2.094957 TCATTTCGTTTTTGCGATCCCC 60.095 45.455 0.00 0.00 40.76 4.81
5402 5701 0.878416 TCGTTTTTGCGATCCCCTTG 59.122 50.000 0.00 0.00 35.83 3.61
5403 5702 0.596082 CGTTTTTGCGATCCCCTTGT 59.404 50.000 0.00 0.00 0.00 3.16
5409 5712 3.644966 TTGCGATCCCCTTGTATCTTT 57.355 42.857 0.00 0.00 0.00 2.52
5413 5716 5.305585 TGCGATCCCCTTGTATCTTTAATC 58.694 41.667 0.00 0.00 0.00 1.75
5621 5925 5.728351 TGTTTTCAGACCGACTTTAGTTG 57.272 39.130 0.00 0.00 0.00 3.16
5666 5972 1.537202 GACAGCCTGCACAAAGGTAAG 59.463 52.381 0.00 0.00 39.75 2.34
5675 5981 3.183754 GCACAAAGGTAAGCACGTTTTT 58.816 40.909 0.00 0.00 39.96 1.94
5771 6079 1.286248 ATTTAACCGAGCCACTCCCT 58.714 50.000 0.00 0.00 0.00 4.20
5837 6145 3.775661 AAGTTGTGCTAAAACTGCGTT 57.224 38.095 0.93 0.00 37.90 4.84
5838 6146 3.065019 AGTTGTGCTAAAACTGCGTTG 57.935 42.857 0.00 0.00 36.52 4.10
5855 6163 4.035091 TGCGTTGATTAATTTGGATCGGAG 59.965 41.667 0.00 0.00 0.00 4.63
5913 6221 9.994432 GTATGATTTCTTGTTGAGATCGAAAAT 57.006 29.630 0.00 0.00 38.65 1.82
5919 6227 3.809234 TGTTGAGATCGAAAATGTTGCG 58.191 40.909 0.00 0.00 0.00 4.85
5927 6235 1.971962 CGAAAATGTTGCGACTTGAGC 59.028 47.619 5.50 0.00 0.00 4.26
6030 6340 6.870965 GTCTAACAAGATGGATGAAGCGATAT 59.129 38.462 0.00 0.00 0.00 1.63
6089 6402 0.883833 CATCGGCCAGTTTTCTGCTT 59.116 50.000 2.24 0.00 45.76 3.91
6106 6419 0.617249 CTTCTCCCAGAGACCAGCCT 60.617 60.000 0.00 0.00 38.51 4.58
6115 6428 0.462759 GAGACCAGCCTGATTTCCCG 60.463 60.000 0.00 0.00 0.00 5.14
6117 6430 2.045045 CCAGCCTGATTTCCCGCA 60.045 61.111 0.00 0.00 0.00 5.69
6270 6606 2.203640 TCGCCTGACCTGACCTGT 60.204 61.111 0.00 0.00 0.00 4.00
6285 6621 4.497984 TGTTGCGCCTGGTGGTGT 62.498 61.111 4.18 0.00 45.25 4.16
6305 6641 3.120792 GTGCTCTGAAGTTGTAACGACA 58.879 45.455 0.00 0.00 0.00 4.35
6306 6642 3.060473 GTGCTCTGAAGTTGTAACGACAC 60.060 47.826 0.00 0.00 34.48 3.67
6311 6647 1.523934 GAAGTTGTAACGACACCACCG 59.476 52.381 0.00 0.00 34.48 4.94
6337 6676 4.084223 GCAAATCATCTGGCAAAGTTGTTG 60.084 41.667 0.00 0.00 0.00 3.33
6338 6677 2.798976 TCATCTGGCAAAGTTGTTGC 57.201 45.000 2.43 2.43 44.22 4.17
6346 6685 0.932399 CAAAGTTGTTGCCTTGCTGC 59.068 50.000 0.00 0.00 0.00 5.25
6355 6694 4.827481 CCTTGCTGCATGGCATTC 57.173 55.556 19.90 0.00 42.09 2.67
6368 6707 1.643286 TGGCATTCATCCCCCAGTTTA 59.357 47.619 0.00 0.00 0.00 2.01
6412 6751 7.710907 GCAAAATGTTTCTCCTTAGTTTTTCCT 59.289 33.333 0.00 0.00 0.00 3.36
6423 6762 5.338137 CCTTAGTTTTTCCTGGGTCGTATCT 60.338 44.000 0.00 0.00 0.00 1.98
6426 6765 4.070009 GTTTTTCCTGGGTCGTATCTTGT 58.930 43.478 0.00 0.00 0.00 3.16
6427 6766 3.328382 TTTCCTGGGTCGTATCTTGTG 57.672 47.619 0.00 0.00 0.00 3.33
6428 6767 1.933021 TCCTGGGTCGTATCTTGTGT 58.067 50.000 0.00 0.00 0.00 3.72
6429 6768 3.090210 TCCTGGGTCGTATCTTGTGTA 57.910 47.619 0.00 0.00 0.00 2.90
6430 6769 3.021695 TCCTGGGTCGTATCTTGTGTAG 58.978 50.000 0.00 0.00 0.00 2.74
6431 6770 3.021695 CCTGGGTCGTATCTTGTGTAGA 58.978 50.000 0.00 0.00 37.28 2.59
6432 6771 3.066900 CCTGGGTCGTATCTTGTGTAGAG 59.933 52.174 0.00 0.00 36.02 2.43
6433 6772 3.945921 CTGGGTCGTATCTTGTGTAGAGA 59.054 47.826 0.00 0.00 36.02 3.10
6434 6773 3.945921 TGGGTCGTATCTTGTGTAGAGAG 59.054 47.826 0.00 0.00 36.02 3.20
6435 6774 3.315749 GGGTCGTATCTTGTGTAGAGAGG 59.684 52.174 0.00 0.00 36.02 3.69
6436 6775 4.197750 GGTCGTATCTTGTGTAGAGAGGA 58.802 47.826 0.00 0.00 36.83 3.71
6437 6776 4.822896 GGTCGTATCTTGTGTAGAGAGGAT 59.177 45.833 0.00 0.00 40.07 3.24
6438 6777 5.996513 GGTCGTATCTTGTGTAGAGAGGATA 59.003 44.000 0.00 0.00 40.07 2.59
6439 6778 6.655848 GGTCGTATCTTGTGTAGAGAGGATAT 59.344 42.308 0.00 0.00 40.07 1.63
6440 6779 7.175293 GGTCGTATCTTGTGTAGAGAGGATATT 59.825 40.741 0.00 0.00 40.07 1.28
6441 6780 8.569641 GTCGTATCTTGTGTAGAGAGGATATTT 58.430 37.037 0.00 0.00 40.07 1.40
6442 6781 8.568794 TCGTATCTTGTGTAGAGAGGATATTTG 58.431 37.037 0.00 0.00 34.92 2.32
6443 6782 7.810282 CGTATCTTGTGTAGAGAGGATATTTGG 59.190 40.741 0.00 0.00 36.02 3.28
6444 6783 7.682787 ATCTTGTGTAGAGAGGATATTTGGT 57.317 36.000 0.00 0.00 36.02 3.67
6445 6784 6.878317 TCTTGTGTAGAGAGGATATTTGGTG 58.122 40.000 0.00 0.00 0.00 4.17
6446 6785 5.023533 TGTGTAGAGAGGATATTTGGTGC 57.976 43.478 0.00 0.00 0.00 5.01
6447 6786 4.469586 TGTGTAGAGAGGATATTTGGTGCA 59.530 41.667 0.00 0.00 0.00 4.57
6448 6787 5.045942 TGTGTAGAGAGGATATTTGGTGCAA 60.046 40.000 0.00 0.00 0.00 4.08
6449 6788 5.294552 GTGTAGAGAGGATATTTGGTGCAAC 59.705 44.000 0.00 0.00 0.00 4.17
6450 6789 4.851639 AGAGAGGATATTTGGTGCAACT 57.148 40.909 2.04 0.00 36.74 3.16
6451 6790 4.775236 AGAGAGGATATTTGGTGCAACTC 58.225 43.478 2.04 0.00 36.74 3.01
6452 6791 4.225942 AGAGAGGATATTTGGTGCAACTCA 59.774 41.667 2.04 0.00 36.74 3.41
6453 6792 5.104193 AGAGAGGATATTTGGTGCAACTCAT 60.104 40.000 2.04 0.00 36.74 2.90
6454 6793 5.513233 AGAGGATATTTGGTGCAACTCATT 58.487 37.500 2.04 0.00 36.74 2.57
6455 6794 5.359009 AGAGGATATTTGGTGCAACTCATTG 59.641 40.000 2.04 0.00 38.99 2.82
6456 6795 5.018809 AGGATATTTGGTGCAACTCATTGT 58.981 37.500 2.04 0.00 38.17 2.71
6457 6796 6.186957 AGGATATTTGGTGCAACTCATTGTA 58.813 36.000 2.04 0.00 38.17 2.41
6458 6797 6.835488 AGGATATTTGGTGCAACTCATTGTAT 59.165 34.615 2.04 0.00 38.17 2.29
6459 6798 7.342799 AGGATATTTGGTGCAACTCATTGTATT 59.657 33.333 2.04 0.00 38.17 1.89
6460 6799 7.649306 GGATATTTGGTGCAACTCATTGTATTC 59.351 37.037 2.04 0.00 38.17 1.75
6461 6800 4.782019 TTGGTGCAACTCATTGTATTCC 57.218 40.909 2.04 0.00 38.17 3.01
6462 6801 3.760738 TGGTGCAACTCATTGTATTCCA 58.239 40.909 2.04 0.00 38.17 3.53
6463 6802 4.343231 TGGTGCAACTCATTGTATTCCAT 58.657 39.130 2.04 0.00 38.17 3.41
6464 6803 4.158209 TGGTGCAACTCATTGTATTCCATG 59.842 41.667 2.04 0.00 38.17 3.66
6465 6804 4.440525 GGTGCAACTCATTGTATTCCATGG 60.441 45.833 4.97 4.97 38.17 3.66
6466 6805 4.398988 GTGCAACTCATTGTATTCCATGGA 59.601 41.667 11.44 11.44 38.17 3.41
6467 6806 4.641541 TGCAACTCATTGTATTCCATGGAG 59.358 41.667 15.53 1.18 38.17 3.86
6468 6807 4.641989 GCAACTCATTGTATTCCATGGAGT 59.358 41.667 15.53 15.19 38.02 3.85
6469 6808 5.822519 GCAACTCATTGTATTCCATGGAGTA 59.177 40.000 15.53 14.01 36.41 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.223187 TCGATCGAGCGCTGTATGTA 58.777 50.000 18.48 0.00 0.00 2.29
1 2 0.380733 TTCGATCGAGCGCTGTATGT 59.619 50.000 18.48 0.00 0.00 2.29
2 3 1.646238 GATTCGATCGAGCGCTGTATG 59.354 52.381 18.48 1.10 0.00 2.39
3 4 1.401670 GGATTCGATCGAGCGCTGTAT 60.402 52.381 18.48 7.93 0.00 2.29
4 5 0.040336 GGATTCGATCGAGCGCTGTA 60.040 55.000 18.48 1.58 0.00 2.74
5 6 1.299468 GGATTCGATCGAGCGCTGT 60.299 57.895 18.48 6.28 0.00 4.40
6 7 2.360542 CGGATTCGATCGAGCGCTG 61.361 63.158 18.48 12.29 39.00 5.18
7 8 2.050895 CGGATTCGATCGAGCGCT 60.051 61.111 19.88 11.27 39.00 5.92
8 9 3.100191 CCGGATTCGATCGAGCGC 61.100 66.667 19.88 11.15 39.00 5.92
9 10 2.429236 CCCGGATTCGATCGAGCG 60.429 66.667 18.51 18.51 39.00 5.03
10 11 0.940047 GAACCCGGATTCGATCGAGC 60.940 60.000 18.54 13.98 39.00 5.03
40 41 2.379634 CGTCAATCAGTCGGCGCAA 61.380 57.895 10.83 0.00 0.00 4.85
104 108 7.312899 ACAAAATTTCCTAAATCCATCACGTC 58.687 34.615 0.00 0.00 0.00 4.34
140 147 6.752815 GGAATACGCTACTCCATAATTAGAGC 59.247 42.308 2.46 0.00 33.18 4.09
470 481 4.001652 CCAATTGCAATGCCACAAACATA 58.998 39.130 13.82 0.00 0.00 2.29
798 809 6.329838 TGCGCATTTTTAATCATTTAGTGC 57.670 33.333 5.66 0.00 0.00 4.40
1006 1019 1.676967 GCCCAAGGTCTTCAGCCAG 60.677 63.158 0.00 0.00 0.00 4.85
1099 1112 7.762159 TCGATATATACTTTGTTCAGTTGCACA 59.238 33.333 0.00 0.00 0.00 4.57
1323 1400 2.166459 GGCAGGCTAAATTCCAGAAACC 59.834 50.000 0.00 0.00 0.00 3.27
1324 1401 2.825532 TGGCAGGCTAAATTCCAGAAAC 59.174 45.455 0.00 0.00 0.00 2.78
1325 1402 3.168035 TGGCAGGCTAAATTCCAGAAA 57.832 42.857 0.00 0.00 0.00 2.52
1326 1403 2.897271 TGGCAGGCTAAATTCCAGAA 57.103 45.000 0.00 0.00 0.00 3.02
1472 1550 1.904287 TGGACAAATTCCCCTTCACG 58.096 50.000 0.00 0.00 45.17 4.35
1568 1646 2.414161 GCAAAAGGAGTCAACATACGGC 60.414 50.000 0.00 0.00 0.00 5.68
1577 1655 8.084073 CAGAAAATCAATTAGCAAAAGGAGTCA 58.916 33.333 0.00 0.00 0.00 3.41
1679 1757 4.684242 GCTAGTGTGGTTGGTAAAATTTGC 59.316 41.667 0.00 0.00 0.00 3.68
1749 1828 6.889301 AGTATGCATGGGTGATTTAATCAG 57.111 37.500 10.16 0.00 40.53 2.90
2121 2202 2.945668 GCATACCTTGTTGAGATGACCC 59.054 50.000 0.00 0.00 0.00 4.46
2160 2241 9.679661 AAAACAAAACCCAAGATAATTCAAACT 57.320 25.926 0.00 0.00 0.00 2.66
2604 2690 5.189736 ACAGTACATCCCAGATTTAGCAGAA 59.810 40.000 0.00 0.00 0.00 3.02
2939 3026 9.577222 TGTACCAAAATAAAAGGTAGCTTTAGT 57.423 29.630 19.61 8.41 38.49 2.24
2942 3029 7.726738 TCCTGTACCAAAATAAAAGGTAGCTTT 59.273 33.333 14.07 14.07 38.49 3.51
3188 3278 7.829211 ACATGAACCTATAACTAGTTGCACATT 59.171 33.333 18.56 7.11 0.00 2.71
3282 3487 3.993920 TCAAGCAAAATTTGAGGCCTTC 58.006 40.909 6.77 0.10 31.35 3.46
3507 3712 5.710099 GGTAAAGGTGTGAAAAGGATCATCA 59.290 40.000 0.00 0.00 0.00 3.07
3758 3989 4.665212 CATGCGCACAAGAGAAATTATGT 58.335 39.130 14.90 0.00 0.00 2.29
3759 3990 3.484649 GCATGCGCACAAGAGAAATTATG 59.515 43.478 14.90 2.78 38.36 1.90
3760 3991 3.129113 TGCATGCGCACAAGAGAAATTAT 59.871 39.130 14.90 0.00 45.36 1.28
3762 3993 1.270274 TGCATGCGCACAAGAGAAATT 59.730 42.857 14.90 0.00 45.36 1.82
3763 3994 0.883153 TGCATGCGCACAAGAGAAAT 59.117 45.000 14.90 0.00 45.36 2.17
3764 3995 2.329244 TGCATGCGCACAAGAGAAA 58.671 47.368 14.90 0.00 45.36 2.52
3774 4049 4.711721 TCGATATAAGAAATTGCATGCGC 58.288 39.130 14.09 0.00 39.24 6.09
3805 4080 9.330063 CTAAGAACATATTCACAGCCTCATAAA 57.670 33.333 0.00 0.00 37.29 1.40
4241 4522 5.477291 ACGACCTGATTGAAGAGAAGTTCTA 59.523 40.000 5.09 0.00 34.14 2.10
4301 4582 4.926140 TTTGGTGCAACATTGACATGTA 57.074 36.364 4.62 0.00 43.34 2.29
4502 4783 2.684881 CAACTCTGCCTTGACAAACACT 59.315 45.455 0.00 0.00 0.00 3.55
4766 5056 2.028112 GCACTCTGGAATGTACCTGTCA 60.028 50.000 0.00 0.00 0.00 3.58
4856 5146 4.023279 TCTGTTCCAAATGGATTTGTCACG 60.023 41.667 2.38 0.00 44.98 4.35
5019 5309 5.604565 AGGATTTCTTTTGGCAGTTTGAAG 58.395 37.500 0.00 0.00 0.00 3.02
5192 5484 8.644216 TCAGTATGTACCTTGTTAAAGAGTTCA 58.356 33.333 0.00 0.00 37.40 3.18
5223 5515 6.311200 GTGATTGTAAGGTGATCCATTTTTGC 59.689 38.462 0.00 0.00 35.89 3.68
5242 5534 5.277202 CGCCAATATCAGAGTGAAGTGATTG 60.277 44.000 0.00 0.00 35.08 2.67
5317 5616 4.643387 GTTCACTGGCCTGGCGGT 62.643 66.667 13.40 11.21 0.00 5.68
5325 5624 0.887387 TAGTTTGGGCGTTCACTGGC 60.887 55.000 0.00 0.00 0.00 4.85
5342 5641 8.358148 ACGTGAATAACCTTGGTAGTGATATAG 58.642 37.037 0.00 0.00 0.00 1.31
5367 5666 5.966636 AAAACGAAATGAAAGGAAAGCAC 57.033 34.783 0.00 0.00 0.00 4.40
5373 5672 4.294416 TCGCAAAAACGAAATGAAAGGA 57.706 36.364 0.00 0.00 39.54 3.36
5386 5685 3.963129 AGATACAAGGGGATCGCAAAAA 58.037 40.909 12.32 0.00 0.00 1.94
5387 5686 3.644966 AGATACAAGGGGATCGCAAAA 57.355 42.857 12.32 0.00 0.00 2.44
5409 5712 7.577303 AGGAGATATTTCAGCACTTTGGATTA 58.423 34.615 0.00 0.00 0.00 1.75
5413 5716 6.376581 AGAAAGGAGATATTTCAGCACTTTGG 59.623 38.462 0.00 0.00 38.79 3.28
5567 5870 4.616802 GTGTGAGGTTGTAAATGCAATTCG 59.383 41.667 0.00 0.00 33.67 3.34
5620 5924 8.352201 CAAAGAGAACTGTATGATGTTTTTCCA 58.648 33.333 0.00 0.00 0.00 3.53
5621 5925 8.567948 TCAAAGAGAACTGTATGATGTTTTTCC 58.432 33.333 0.00 0.00 0.00 3.13
5666 5972 3.548214 GGAGAAACAGAGGAAAAACGTGC 60.548 47.826 0.00 0.00 0.00 5.34
5675 5981 0.034896 GCGTTGGGAGAAACAGAGGA 59.965 55.000 0.00 0.00 0.00 3.71
5810 6118 6.510478 CGCAGTTTTAGCACAACTTTGTACTA 60.510 38.462 0.00 0.00 39.91 1.82
5811 6119 5.578776 GCAGTTTTAGCACAACTTTGTACT 58.421 37.500 0.65 0.65 39.91 2.73
5812 6120 4.436523 CGCAGTTTTAGCACAACTTTGTAC 59.563 41.667 0.00 0.00 39.91 2.90
5813 6121 4.095185 ACGCAGTTTTAGCACAACTTTGTA 59.905 37.500 0.00 0.00 37.78 2.41
5814 6122 3.119637 ACGCAGTTTTAGCACAACTTTGT 60.120 39.130 0.00 0.00 37.78 2.83
5837 6145 4.746702 GCTCCCTCCGATCCAAATTAATCA 60.747 45.833 0.00 0.00 0.00 2.57
5838 6146 3.753797 GCTCCCTCCGATCCAAATTAATC 59.246 47.826 0.00 0.00 0.00 1.75
5855 6163 3.995048 GTCTGTACACTTTTACTGCTCCC 59.005 47.826 0.00 0.00 0.00 4.30
5913 6221 1.094650 TGCAAGCTCAAGTCGCAACA 61.095 50.000 0.00 0.00 0.00 3.33
5919 6227 4.394300 AGTGTCAATATGCAAGCTCAAGTC 59.606 41.667 0.00 0.00 0.00 3.01
5927 6235 2.357009 GAGGGCAGTGTCAATATGCAAG 59.643 50.000 0.00 0.00 41.78 4.01
5999 6307 7.766278 GCTTCATCCATCTTGTTAGACTTAGAA 59.234 37.037 0.00 0.00 31.99 2.10
6085 6395 1.548357 GCTGGTCTCTGGGAGAAGCA 61.548 60.000 13.23 7.22 40.34 3.91
6089 6402 1.305633 CAGGCTGGTCTCTGGGAGA 60.306 63.158 6.61 0.00 36.22 3.71
6115 6428 1.880340 CGACAGAGGCCGAGAATGC 60.880 63.158 0.00 0.00 0.00 3.56
6117 6430 2.351244 TGCGACAGAGGCCGAGAAT 61.351 57.895 0.00 0.00 0.00 2.40
6160 6486 0.613853 AAAGGGACCGACGATCTCCA 60.614 55.000 0.00 0.00 0.00 3.86
6226 6552 2.124693 CCCCACAACACACCACCAC 61.125 63.158 0.00 0.00 0.00 4.16
6285 6621 3.120792 GTGTCGTTACAACTTCAGAGCA 58.879 45.455 0.00 0.00 37.36 4.26
6305 6641 2.361104 ATGATTTGCGGCGGTGGT 60.361 55.556 9.78 0.00 0.00 4.16
6306 6642 2.114670 AGATGATTTGCGGCGGTGG 61.115 57.895 9.78 0.00 0.00 4.61
6311 6647 0.108709 TTTGCCAGATGATTTGCGGC 60.109 50.000 0.00 0.00 43.28 6.53
6346 6685 0.105862 ACTGGGGGATGAATGCCATG 60.106 55.000 3.08 0.00 40.49 3.66
6355 6694 1.680860 GGAACGGTAAACTGGGGGATG 60.681 57.143 0.00 0.00 0.00 3.51
6368 6707 0.679960 GCAGGGCATAAAGGAACGGT 60.680 55.000 0.00 0.00 0.00 4.83
6412 6751 3.945921 CTCTCTACACAAGATACGACCCA 59.054 47.826 0.00 0.00 32.41 4.51
6423 6762 5.045942 TGCACCAAATATCCTCTCTACACAA 60.046 40.000 0.00 0.00 0.00 3.33
6426 6765 5.189736 AGTTGCACCAAATATCCTCTCTACA 59.810 40.000 0.00 0.00 0.00 2.74
6427 6766 5.675538 AGTTGCACCAAATATCCTCTCTAC 58.324 41.667 0.00 0.00 0.00 2.59
6428 6767 5.425217 TGAGTTGCACCAAATATCCTCTCTA 59.575 40.000 0.00 0.00 0.00 2.43
6429 6768 4.225942 TGAGTTGCACCAAATATCCTCTCT 59.774 41.667 0.00 0.00 0.00 3.10
6430 6769 4.517285 TGAGTTGCACCAAATATCCTCTC 58.483 43.478 0.00 0.00 0.00 3.20
6431 6770 4.574674 TGAGTTGCACCAAATATCCTCT 57.425 40.909 0.00 0.00 0.00 3.69
6432 6771 5.126061 ACAATGAGTTGCACCAAATATCCTC 59.874 40.000 0.00 0.00 38.96 3.71
6433 6772 5.018809 ACAATGAGTTGCACCAAATATCCT 58.981 37.500 0.00 0.00 38.96 3.24
6434 6773 5.329035 ACAATGAGTTGCACCAAATATCC 57.671 39.130 0.00 0.00 38.96 2.59
6435 6774 7.649306 GGAATACAATGAGTTGCACCAAATATC 59.351 37.037 0.00 0.00 38.96 1.63
6436 6775 7.123997 TGGAATACAATGAGTTGCACCAAATAT 59.876 33.333 0.00 0.00 38.96 1.28
6437 6776 6.435591 TGGAATACAATGAGTTGCACCAAATA 59.564 34.615 0.00 0.00 38.96 1.40
6438 6777 5.245751 TGGAATACAATGAGTTGCACCAAAT 59.754 36.000 0.00 0.00 38.96 2.32
6439 6778 4.586421 TGGAATACAATGAGTTGCACCAAA 59.414 37.500 0.00 0.00 38.96 3.28
6440 6779 4.148079 TGGAATACAATGAGTTGCACCAA 58.852 39.130 0.00 0.00 38.96 3.67
6441 6780 3.760738 TGGAATACAATGAGTTGCACCA 58.239 40.909 0.00 0.00 38.96 4.17
6442 6781 4.440525 CCATGGAATACAATGAGTTGCACC 60.441 45.833 5.56 0.00 38.96 5.01
6443 6782 4.398988 TCCATGGAATACAATGAGTTGCAC 59.601 41.667 13.46 0.00 38.96 4.57
6444 6783 4.598022 TCCATGGAATACAATGAGTTGCA 58.402 39.130 13.46 0.00 38.96 4.08
6445 6784 4.641989 ACTCCATGGAATACAATGAGTTGC 59.358 41.667 17.00 0.00 39.53 4.17


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

AutoCloner maintained by Alex Coulton.