Multiple sequence alignment - TraesCS3D01G408700

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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 TraesCS3D01G408700 chr3D 100.000 6040 0 0 1 6040 523160492 523166531 0.000000e+00 11154
1 TraesCS3D01G408700 chr3D 84.291 261 40 1 1740 1999 597748980 597748720 2.790000e-63 254
2 TraesCS3D01G408700 chr3D 83.268 257 40 3 1759 2014 58438300 58438046 3.640000e-57 233
3 TraesCS3D01G408700 chr3D 80.608 263 45 3 1754 2015 250915860 250916117 1.330000e-46 198
4 TraesCS3D01G408700 chr3B 93.050 4403 218 35 1536 5906 689518251 689522597 0.000000e+00 6355
5 TraesCS3D01G408700 chr3B 94.860 1537 71 6 1 1536 689516673 689518202 0.000000e+00 2394
6 TraesCS3D01G408700 chr3B 86.111 144 15 3 5897 6036 689554865 689555007 3.770000e-32 150
7 TraesCS3D01G408700 chr3A 93.324 2831 116 23 3241 6040 657933202 657935990 0.000000e+00 4113
8 TraesCS3D01G408700 chr3A 93.945 1536 86 5 1 1536 657929679 657931207 0.000000e+00 2314
9 TraesCS3D01G408700 chr3A 92.431 1308 89 8 1644 2944 657931848 657933152 0.000000e+00 1858
10 TraesCS3D01G408700 chr3A 95.536 112 5 0 1536 1647 657931256 657931367 4.810000e-41 180
11 TraesCS3D01G408700 chr6B 82.061 262 44 3 1740 2000 163976922 163976663 2.830000e-53 220
12 TraesCS3D01G408700 chr1D 81.481 270 46 4 1740 2008 221873996 221874262 1.020000e-52 219
13 TraesCS3D01G408700 chr2A 80.451 266 52 0 1743 2008 759818613 759818348 2.850000e-48 204
14 TraesCS3D01G408700 chr4B 80.843 261 44 4 1740 2000 228423398 228423144 3.690000e-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 TraesCS3D01G408700 chr3D 523160492 523166531 6039 False 11154.00 11154 100.000 1 6040 1 chr3D.!!$F2 6039
1 TraesCS3D01G408700 chr3B 689516673 689522597 5924 False 4374.50 6355 93.955 1 5906 2 chr3B.!!$F2 5905
2 TraesCS3D01G408700 chr3A 657929679 657935990 6311 False 2116.25 4113 93.809 1 6040 4 chr3A.!!$F1 6039

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
689 691 0.179936 GAGCTTGAGCCCACTAGCAT 59.820 55.000 0.00 0.0 43.38 3.79 F
1670 2207 0.548510 GCTAGGGAGGGAATGCAAGT 59.451 55.000 0.00 0.0 0.00 3.16 F
2366 2908 0.249155 TATAAGGGTGTGCTACGCGC 60.249 55.000 5.73 0.0 46.08 6.86 F
2945 3493 0.036306 GGGATCACGGGTTTGACTGT 59.964 55.000 0.00 0.0 0.00 3.55 F
3004 3552 1.273327 GCCTATGTTGCAAAACCAGCT 59.727 47.619 0.00 0.0 0.00 4.24 F
3030 3578 1.932011 TTTGTGTTGTGCTGTGCGCT 61.932 50.000 9.73 0.0 40.03 5.92 F
4375 4929 1.005805 TGGCATCCAAGTGCAGGTATT 59.994 47.619 1.06 0.0 46.81 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2648 0.540597 GAAAACTGGAGCCCAAGCCT 60.541 55.000 0.00 0.00 41.25 4.58 R
2693 3239 0.108520 GACTATGTTTCCCGACGGCA 60.109 55.000 8.86 0.63 0.00 5.69 R
3821 4371 2.002505 AGGTCGATAGGATGAGGGTG 57.997 55.000 0.00 0.00 0.00 4.61 R
3921 4474 2.017049 GGCTATTGCAAGTGGGTACAG 58.983 52.381 4.94 0.00 41.91 2.74 R
4177 4731 2.679837 CAACCCATCGGAGAACATCTTG 59.320 50.000 0.00 0.00 43.58 3.02 R
4618 5176 4.496360 GTTGAGTACCAGTCTTCCTAAGC 58.504 47.826 0.00 0.00 0.00 3.09 R
5360 5931 0.253044 TGAGAAGGCGGAATCCCTTG 59.747 55.000 0.00 0.00 42.56 3.61 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
127 128 6.887376 TGTTATGATAGTCTCGTTCTTTGC 57.113 37.500 0.00 0.00 0.00 3.68
129 130 6.871492 TGTTATGATAGTCTCGTTCTTTGCAA 59.129 34.615 0.00 0.00 0.00 4.08
209 210 8.860088 AGTTACAAATTTGGATTTTGCTCTAGT 58.140 29.630 21.74 0.00 33.25 2.57
218 219 4.400567 GGATTTTGCTCTAGTTTGCCTCAT 59.599 41.667 0.00 0.00 0.00 2.90
293 294 3.777106 ATGGACACATATCGAGCCAAT 57.223 42.857 0.00 0.00 34.99 3.16
294 295 3.558931 TGGACACATATCGAGCCAATT 57.441 42.857 0.00 0.00 0.00 2.32
298 299 5.883115 TGGACACATATCGAGCCAATTTTTA 59.117 36.000 0.00 0.00 0.00 1.52
320 321 0.332293 ATGTGACACATCCATGGGCA 59.668 50.000 15.48 0.00 32.38 5.36
323 324 1.078497 GACACATCCATGGGCACGA 60.078 57.895 13.02 0.00 33.50 4.35
389 390 3.772025 TCCTCCAACATCTCTCTTTCTCC 59.228 47.826 0.00 0.00 0.00 3.71
391 392 3.774216 CTCCAACATCTCTCTTTCTCCCT 59.226 47.826 0.00 0.00 0.00 4.20
483 484 5.846203 TCGATGTTGATTCTCTGCATGATA 58.154 37.500 0.00 0.00 0.00 2.15
509 510 1.410153 CCAACCTCTTGCAGCAACTTT 59.590 47.619 2.83 0.00 0.00 2.66
528 529 7.468631 GCAACTTTCTTGGTCTTCTCAACAATA 60.469 37.037 0.00 0.00 0.00 1.90
647 649 5.068198 ACATGTTTGTGTCTCATTTTGAGCT 59.932 36.000 0.00 0.00 38.34 4.09
682 684 0.615331 CTAAGGTGAGCTTGAGCCCA 59.385 55.000 7.22 0.00 43.38 5.36
689 691 0.179936 GAGCTTGAGCCCACTAGCAT 59.820 55.000 0.00 0.00 43.38 3.79
750 752 3.659786 TGAGTTGACCTACCAATTGTCG 58.340 45.455 4.43 0.00 0.00 4.35
768 770 1.134220 TCGGAGCTCTGTTTGTTGGTT 60.134 47.619 21.88 0.00 0.00 3.67
859 861 7.896383 AGCTATCTAAGGATGAGATGTATCC 57.104 40.000 0.00 0.00 36.79 2.59
906 908 8.453238 TCTACATGAAGAGTATTCCACTAGAC 57.547 38.462 0.00 0.00 37.72 2.59
925 927 4.551671 AGACATGTACCATCTTCTAGCCT 58.448 43.478 0.00 0.00 0.00 4.58
994 996 6.599356 TCTACTACTTGCAGTACCAAATCA 57.401 37.500 0.00 0.00 0.00 2.57
1040 1042 7.326454 TCTGAGAGAAATGTGTCTAGAATTGG 58.674 38.462 0.00 0.00 0.00 3.16
1106 1108 4.331168 CGGAAAAGAAGGCACATTCTCTAG 59.669 45.833 0.00 0.00 38.59 2.43
1157 1159 2.303175 GGCCCAATATAACCGCAAAGA 58.697 47.619 0.00 0.00 0.00 2.52
1227 1229 6.505044 TCAAAATGTGACATGGAGAGATTG 57.495 37.500 0.00 0.00 0.00 2.67
1265 1267 6.633500 TGAAGTTTTTACAATCCTCAGTGG 57.367 37.500 0.00 0.00 37.10 4.00
1324 1326 4.999950 GCTTCTATCCACTATGTTCCATGG 59.000 45.833 4.97 4.97 0.00 3.66
1356 1358 7.367285 TCAAAATGAGGTTTTTACAATCCTCG 58.633 34.615 12.11 1.26 46.24 4.63
1407 1409 9.490379 CCCTGATACTACATTAAGTTCCATTAC 57.510 37.037 0.00 0.00 0.00 1.89
1439 1441 1.543802 TCCAAACACCCGATGAATTGC 59.456 47.619 0.00 0.00 31.50 3.56
1446 1448 2.096496 CACCCGATGAATTGCTCAACTC 59.904 50.000 0.00 0.00 37.67 3.01
1448 1450 1.328680 CCGATGAATTGCTCAACTCGG 59.671 52.381 3.08 3.08 45.52 4.63
1457 1459 1.201647 TGCTCAACTCGGTGCTACTAC 59.798 52.381 0.00 0.00 0.00 2.73
1546 1597 3.858135 ACCTCTAGGAAAGGTTGTGAGA 58.142 45.455 2.23 0.00 44.93 3.27
1555 1606 6.234177 AGGAAAGGTTGTGAGAGTCTTATTG 58.766 40.000 0.00 0.00 0.00 1.90
1629 1682 8.492673 TCATAGGCTCTAACAAACAATTACAG 57.507 34.615 0.00 0.00 0.00 2.74
1641 1694 5.669164 AACAATTACAGTGTGTTTGGGTT 57.331 34.783 18.58 8.64 31.52 4.11
1666 2203 2.016905 TAGAGCTAGGGAGGGAATGC 57.983 55.000 0.00 0.00 0.00 3.56
1670 2207 0.548510 GCTAGGGAGGGAATGCAAGT 59.451 55.000 0.00 0.00 0.00 3.16
1705 2242 9.233649 ACTTGAAATATATTGTTTGGTTACGGA 57.766 29.630 0.00 0.00 0.00 4.69
1757 2294 2.667108 GGGGAGGGGTTCGGAGTTC 61.667 68.421 0.00 0.00 0.00 3.01
1962 2504 7.921786 TTTCTATTCTCAATACAACACCCTG 57.078 36.000 0.00 0.00 0.00 4.45
2041 2583 6.479884 ACAATCTCTTTCCTTGCTCTTGTAT 58.520 36.000 0.00 0.00 0.00 2.29
2103 2645 5.115480 CAGCCTAAAAACACAATTGTTGGT 58.885 37.500 8.77 1.60 45.69 3.67
2106 2648 6.322712 AGCCTAAAAACACAATTGTTGGTCTA 59.677 34.615 8.77 0.00 45.69 2.59
2132 2674 0.600057 GGCTCCAGTTTTCTGCTTGG 59.400 55.000 0.00 0.00 45.76 3.61
2296 2838 9.742144 ACTGCTATATACTAGTACTATGTGCTT 57.258 33.333 4.31 0.00 30.04 3.91
2366 2908 0.249155 TATAAGGGTGTGCTACGCGC 60.249 55.000 5.73 0.00 46.08 6.86
2381 2923 2.279120 CGCCCGCTCACTGATCTC 60.279 66.667 0.00 0.00 0.00 2.75
2407 2950 1.224592 GATGGCCGGGTCATGAGTT 59.775 57.895 20.72 0.00 0.00 3.01
2475 3018 1.039856 ACATGACCCCTTGTTGCAAC 58.960 50.000 22.83 22.83 0.00 4.17
2524 3070 3.678056 ACATGACTTCTTGCGAGGTTA 57.322 42.857 0.00 0.00 28.51 2.85
2584 3130 1.685355 AACAGGGCCCTTGTTGCAAC 61.685 55.000 28.31 22.83 0.00 4.17
2693 3239 1.666872 CTTTCCCGCGGTCGTTTCT 60.667 57.895 26.12 0.00 0.00 2.52
2713 3259 0.108520 GCCGTCGGGAAACATAGTCA 60.109 55.000 14.38 0.00 34.06 3.41
2718 3264 1.135603 TCGGGAAACATAGTCACGTCG 60.136 52.381 0.00 0.00 42.57 5.12
2725 3271 1.000607 ACATAGTCACGTCGCACAGTT 60.001 47.619 0.00 0.00 0.00 3.16
2728 3274 0.459585 AGTCACGTCGCACAGTTGTT 60.460 50.000 0.00 0.00 0.00 2.83
2729 3275 1.202203 GTCACGTCGCACAGTTGTTA 58.798 50.000 0.00 0.00 0.00 2.41
2758 3304 2.543653 CCGTTGTTGCAAAGAAGGAAGG 60.544 50.000 0.00 0.00 37.16 3.46
2810 3356 1.445582 CTTGGCTCGTCGGTGTACC 60.446 63.158 0.00 0.00 0.00 3.34
2865 3411 1.659098 CACGTACGATTTGGGAAGAGC 59.341 52.381 24.41 0.00 0.00 4.09
2929 3476 1.735376 GCTCGTGCGAGGATAAGGGA 61.735 60.000 20.97 0.00 42.19 4.20
2945 3493 0.036306 GGGATCACGGGTTTGACTGT 59.964 55.000 0.00 0.00 0.00 3.55
2954 3502 2.882137 CGGGTTTGACTGTAACAACCAT 59.118 45.455 14.04 0.00 0.00 3.55
3001 3549 2.008242 AGGCCTATGTTGCAAAACCA 57.992 45.000 1.29 0.00 0.00 3.67
3004 3552 1.273327 GCCTATGTTGCAAAACCAGCT 59.727 47.619 0.00 0.00 0.00 4.24
3008 3556 4.941263 CCTATGTTGCAAAACCAGCTAGTA 59.059 41.667 0.00 0.00 0.00 1.82
3017 3565 5.449999 GCAAAACCAGCTAGTAAGTTTGTGT 60.450 40.000 8.89 0.00 32.97 3.72
3020 3568 4.777463 ACCAGCTAGTAAGTTTGTGTTGT 58.223 39.130 0.00 0.00 0.00 3.32
3022 3570 4.527564 CAGCTAGTAAGTTTGTGTTGTGC 58.472 43.478 0.00 0.00 0.00 4.57
3030 3578 1.932011 TTTGTGTTGTGCTGTGCGCT 61.932 50.000 9.73 0.00 40.03 5.92
3087 3635 4.814294 GACGCACGCGGGGAGATT 62.814 66.667 11.92 0.00 44.69 2.40
3209 3758 3.997021 TCGAGACTTGAGAAAATTCTGGC 59.003 43.478 0.00 0.00 37.73 4.85
3393 3942 8.362639 TGTCGAACCTAGTAGTTTGTTATTTCT 58.637 33.333 0.00 0.00 33.54 2.52
3525 4075 7.783090 ACTGCTGTGATTTGTCTAATATCTG 57.217 36.000 0.00 0.00 0.00 2.90
3549 4099 3.872511 TTGGCTGCAGATATTTGGTTG 57.127 42.857 20.43 0.00 0.00 3.77
3703 4253 7.601073 TTATGAAGAATCGCATGGTCATATC 57.399 36.000 0.00 0.00 30.37 1.63
3734 4284 6.888632 AGATATCTTTGCACAGGTGAAGAATT 59.111 34.615 0.00 0.00 30.55 2.17
3800 4350 6.071728 AGCCAATCCAACAGTAAATCTTTGAG 60.072 38.462 0.00 0.00 0.00 3.02
3821 4371 8.567285 TTGAGAAATGGAAGATTAAGGAGAAC 57.433 34.615 0.00 0.00 0.00 3.01
3832 4382 2.350863 AAGGAGAACACCCTCATCCT 57.649 50.000 0.00 0.00 42.21 3.24
3834 4384 3.715648 AGGAGAACACCCTCATCCTAT 57.284 47.619 0.00 0.00 38.62 2.57
3836 4386 2.297597 GGAGAACACCCTCATCCTATCG 59.702 54.545 0.00 0.00 34.94 2.92
3921 4474 8.625786 TTGTGAGGGGAAACTTAAATACTTAC 57.374 34.615 0.00 0.00 0.00 2.34
4044 4598 2.420058 AGGCTATGTACCAAACCAGC 57.580 50.000 0.00 0.00 35.45 4.85
4064 4618 5.995282 CCAGCGGTTCCATTATAAGAACATA 59.005 40.000 15.56 0.00 43.37 2.29
4177 4731 1.166531 AAACACGTCAAGAGGCTGCC 61.167 55.000 11.65 11.65 0.00 4.85
4375 4929 1.005805 TGGCATCCAAGTGCAGGTATT 59.994 47.619 1.06 0.00 46.81 1.89
4411 4969 8.201554 TGTCTCAATTTGAGTGATATGCTTAC 57.798 34.615 22.44 11.75 44.58 2.34
4412 4970 8.043113 TGTCTCAATTTGAGTGATATGCTTACT 58.957 33.333 22.44 0.00 44.58 2.24
4413 4971 8.887717 GTCTCAATTTGAGTGATATGCTTACTT 58.112 33.333 22.44 0.00 44.58 2.24
4420 4978 6.820335 TGAGTGATATGCTTACTTATGCTGT 58.180 36.000 0.00 0.00 0.00 4.40
4436 4994 7.279536 ACTTATGCTGTCTGTCAAGATTGTATG 59.720 37.037 0.00 0.00 34.13 2.39
4445 5003 9.803315 GTCTGTCAAGATTGTATGTACATCTAA 57.197 33.333 12.68 9.24 35.89 2.10
4594 5152 8.166726 AGTTAAAATGAGGAGACCTGAAATCTT 58.833 33.333 0.00 0.00 31.76 2.40
4948 5512 4.885907 ACAATATCCTCACTTGCTTCCATG 59.114 41.667 0.00 0.00 0.00 3.66
5061 5625 3.207265 TGTTCCATGCACAGTAACTGT 57.793 42.857 0.00 0.00 46.51 3.55
5063 5627 3.138304 GTTCCATGCACAGTAACTGTCA 58.862 45.455 0.00 0.00 43.43 3.58
5064 5628 3.483808 TCCATGCACAGTAACTGTCAA 57.516 42.857 0.00 0.00 43.43 3.18
5097 5668 7.013655 TCGTCCAGGTTATACTATGGTTAGTTC 59.986 40.741 0.00 0.00 39.42 3.01
5124 5695 3.876309 AATTCAGTGTAGGTGGTGGTT 57.124 42.857 0.00 0.00 0.00 3.67
5130 5701 0.107831 TGTAGGTGGTGGTTGTGCTC 59.892 55.000 0.00 0.00 0.00 4.26
5170 5741 1.815003 GCTTCAGCTAGTTGCCAATGT 59.185 47.619 0.97 0.00 44.23 2.71
5360 5931 2.693069 CAGATGTTCCACTCCACTGTC 58.307 52.381 0.00 0.00 0.00 3.51
5362 5933 2.705658 AGATGTTCCACTCCACTGTCAA 59.294 45.455 0.00 0.00 0.00 3.18
5484 6055 0.460459 TTCGCGACACTGGTGACAAA 60.460 50.000 9.15 0.00 42.06 2.83
5487 6071 0.163788 GCGACACTGGTGACAAATCG 59.836 55.000 7.78 6.97 42.06 3.34
5504 6088 3.834489 ATCGTTCTCTGCCAGATGATT 57.166 42.857 0.00 0.00 0.00 2.57
5506 6090 3.942829 TCGTTCTCTGCCAGATGATTTT 58.057 40.909 0.00 0.00 0.00 1.82
5518 6102 2.025887 AGATGATTTTGAAGGCTCGGGT 60.026 45.455 0.00 0.00 0.00 5.28
5528 6112 5.367945 TGAAGGCTCGGGTATAAAGAATT 57.632 39.130 0.00 0.00 0.00 2.17
5531 6115 5.568620 AGGCTCGGGTATAAAGAATTGAT 57.431 39.130 0.00 0.00 0.00 2.57
5535 6119 5.744887 GCTCGGGTATAAAGAATTGATGGGA 60.745 44.000 0.00 0.00 0.00 4.37
5563 6147 1.278985 CCTAGATTGTGTGAGTGGCCA 59.721 52.381 0.00 0.00 0.00 5.36
5569 6153 1.598130 GTGTGAGTGGCCAGTGGTC 60.598 63.158 20.47 6.88 0.00 4.02
5617 6201 5.740406 TCTCGTTCGGTTTGTGTTTAAATC 58.260 37.500 0.00 0.00 0.00 2.17
5619 6203 5.877031 TCGTTCGGTTTGTGTTTAAATCAA 58.123 33.333 0.00 0.00 0.00 2.57
5641 6225 6.922957 TCAAAACATTAAAGTTCTCACCATGC 59.077 34.615 0.00 0.00 0.00 4.06
5659 6243 5.543790 ACCATGCTGTTCCTTTATTTTCCTT 59.456 36.000 0.00 0.00 0.00 3.36
5687 6271 8.729805 TTTTATGTTCTTTCAAAAAGGCATGT 57.270 26.923 14.59 0.00 0.00 3.21
5689 6273 5.336150 TGTTCTTTCAAAAAGGCATGTGA 57.664 34.783 0.00 0.00 0.00 3.58
5690 6274 5.108517 TGTTCTTTCAAAAAGGCATGTGAC 58.891 37.500 0.00 0.00 0.00 3.67
5709 6293 3.250762 TGACATGTGCTTTGCTGTAAGAC 59.749 43.478 1.15 0.00 34.07 3.01
5714 6298 3.882288 TGTGCTTTGCTGTAAGACAATCA 59.118 39.130 0.00 0.00 34.07 2.57
5716 6300 5.009911 TGTGCTTTGCTGTAAGACAATCAAT 59.990 36.000 0.00 0.00 34.07 2.57
5717 6301 6.206438 TGTGCTTTGCTGTAAGACAATCAATA 59.794 34.615 0.00 0.00 34.07 1.90
5719 6303 7.594758 GTGCTTTGCTGTAAGACAATCAATAAA 59.405 33.333 0.00 0.00 34.07 1.40
5858 6442 1.935199 GCGGATGGGCAATGAAATTTG 59.065 47.619 0.00 0.00 31.22 2.32
5860 6444 3.430098 GCGGATGGGCAATGAAATTTGTA 60.430 43.478 0.00 0.00 31.22 2.41
5861 6445 4.362279 CGGATGGGCAATGAAATTTGTAG 58.638 43.478 0.00 0.00 31.22 2.74
5913 6504 2.437281 TCCAGCAAAAAGAATGCCCAAA 59.563 40.909 0.00 0.00 44.91 3.28
5916 6507 2.880268 AGCAAAAAGAATGCCCAAAAGC 59.120 40.909 0.00 0.00 44.91 3.51
5919 6510 3.793819 AAAAGAATGCCCAAAAGCCAT 57.206 38.095 0.00 0.00 0.00 4.40
5967 6558 5.414454 GTGAATCAAACACCTAGGTATGCAA 59.586 40.000 15.80 0.70 32.84 4.08
5970 6561 7.178274 TGAATCAAACACCTAGGTATGCAAAAT 59.822 33.333 15.80 0.00 0.00 1.82
5979 6570 8.686334 CACCTAGGTATGCAAAATTTCTATGTT 58.314 33.333 15.80 0.00 0.00 2.71
6014 6605 6.926280 TGTTTTACGCATGCATTCTTTAAG 57.074 33.333 19.57 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 4.217118 ACAGAGAGAATGTCCATGCAAAAC 59.783 41.667 0.00 0.00 0.00 2.43
119 120 5.678132 AAGCATTGGATTTTGCAAAGAAC 57.322 34.783 12.41 7.01 41.35 3.01
182 183 9.346725 CTAGAGCAAAATCCAAATTTGTAACTC 57.653 33.333 16.73 12.09 39.42 3.01
194 195 3.758554 GAGGCAAACTAGAGCAAAATCCA 59.241 43.478 0.00 0.00 0.00 3.41
195 196 3.758554 TGAGGCAAACTAGAGCAAAATCC 59.241 43.478 0.00 0.00 0.00 3.01
209 210 5.815581 AGAATGTTGGTACTATGAGGCAAA 58.184 37.500 0.00 0.00 0.00 3.68
218 219 7.103641 GGTTCAGATTGAGAATGTTGGTACTA 58.896 38.462 0.00 0.00 0.00 1.82
293 294 7.632462 GCCCATGGATGTGTCACATTATAAAAA 60.632 37.037 19.33 2.12 39.27 1.94
294 295 6.183360 GCCCATGGATGTGTCACATTATAAAA 60.183 38.462 19.33 3.38 39.27 1.52
298 299 3.225104 GCCCATGGATGTGTCACATTAT 58.775 45.455 19.33 13.73 39.27 1.28
320 321 2.439960 TTGTGTGCCTCCCTGTCGT 61.440 57.895 0.00 0.00 0.00 4.34
323 324 1.645402 AAGGTTGTGTGCCTCCCTGT 61.645 55.000 0.00 0.00 34.81 4.00
389 390 1.280133 TGGGAATCAAGAGTGCTGAGG 59.720 52.381 0.00 0.00 0.00 3.86
391 392 2.942752 GCATGGGAATCAAGAGTGCTGA 60.943 50.000 0.00 0.00 0.00 4.26
439 440 4.589908 GATGGTGTGGTTCCTCATAAGTT 58.410 43.478 0.00 0.00 0.00 2.66
483 484 0.971386 CTGCAAGAGGTTGGCCAAAT 59.029 50.000 22.47 12.48 34.07 2.32
509 510 7.963532 AGTAGTTATTGTTGAGAAGACCAAGA 58.036 34.615 0.00 0.00 0.00 3.02
528 529 9.573133 CATTGACAAGACAAAAGAAAAGTAGTT 57.427 29.630 0.00 0.00 33.44 2.24
541 542 4.082300 ACAAAGTGCACATTGACAAGACAA 60.082 37.500 34.25 0.00 0.00 3.18
647 649 7.303182 TCACCTTAGAGAAATCTCAAACTCA 57.697 36.000 12.65 0.00 45.21 3.41
682 684 8.970859 ATAAGTTTGAATTAGAGCATGCTAGT 57.029 30.769 22.74 13.84 0.00 2.57
750 752 2.297701 TCAACCAACAAACAGAGCTCC 58.702 47.619 10.93 0.00 0.00 4.70
768 770 5.610982 ACCAAAGGGCCTATACAATAGATCA 59.389 40.000 6.41 0.00 37.90 2.92
859 861 7.096402 AGATATAGAAAAGGAATCAAGGGGG 57.904 40.000 0.00 0.00 0.00 5.40
925 927 5.476599 AGCTATTGTGGCAATTCAACAAGTA 59.523 36.000 0.00 0.00 0.00 2.24
994 996 4.782156 AGAAGAGTCTCTTGACATCCCAAT 59.218 41.667 19.95 0.00 45.20 3.16
1033 1035 3.034635 AGTGCTCGATAGGACCAATTCT 58.965 45.455 0.00 0.00 44.67 2.40
1040 1042 7.948278 ATATTTTTGTAGTGCTCGATAGGAC 57.052 36.000 0.00 0.00 43.97 3.85
1106 1108 6.617879 ACTTCAGTTTGTTTTGTAACTCCAC 58.382 36.000 0.00 0.00 32.50 4.02
1227 1229 2.641305 ACTTCATGGAGAGCATGCTTC 58.359 47.619 23.61 19.36 0.00 3.86
1245 1247 5.690865 TCACCACTGAGGATTGTAAAAACT 58.309 37.500 0.00 0.00 41.22 2.66
1265 1267 7.907214 AGTATTTGTACCTCATCAACTTCAC 57.093 36.000 0.00 0.00 0.00 3.18
1356 1358 7.041508 GGTTAAGAGGTCATCAACATCATCATC 60.042 40.741 0.00 0.00 41.17 2.92
1407 1409 3.081804 GGTGTTTGGATGGACTAGTTGG 58.918 50.000 0.00 0.00 0.00 3.77
1439 1441 3.570926 TTGTAGTAGCACCGAGTTGAG 57.429 47.619 0.00 0.00 0.00 3.02
1446 1448 0.107897 TGCCCATTGTAGTAGCACCG 60.108 55.000 0.00 0.00 0.00 4.94
1448 1450 3.071023 TCCTATGCCCATTGTAGTAGCAC 59.929 47.826 0.00 0.00 36.06 4.40
1457 1459 1.538512 CATCGCTTCCTATGCCCATTG 59.461 52.381 0.00 0.00 0.00 2.82
1514 1516 8.080363 ACCTTTCCTAGAGGTAGATTTTGTAG 57.920 38.462 0.00 0.00 45.50 2.74
1546 1597 8.971073 CCCTAAATGAACCAAATCAATAAGACT 58.029 33.333 0.00 0.00 32.06 3.24
1555 1606 9.936759 TTATTTTCACCCTAAATGAACCAAATC 57.063 29.630 0.00 0.00 35.82 2.17
1629 1682 5.240844 AGCTCTAATTACAACCCAAACACAC 59.759 40.000 0.00 0.00 0.00 3.82
1641 1694 4.827036 TCCCTCCCTAGCTCTAATTACA 57.173 45.455 0.00 0.00 0.00 2.41
1705 2242 6.067350 GCCTAATCTCTTCTCAATTCCCAAT 58.933 40.000 0.00 0.00 0.00 3.16
1757 2294 6.014669 TGGAATCACTAAACCAATTCCCTTTG 60.015 38.462 9.76 0.00 44.28 2.77
1902 2440 9.213799 TCCATTTATTTACAATCCTTTGTTTGC 57.786 29.630 0.00 0.00 43.57 3.68
1907 2449 8.945481 TGCATCCATTTATTTACAATCCTTTG 57.055 30.769 0.00 0.00 38.86 2.77
1908 2450 9.768662 GATGCATCCATTTATTTACAATCCTTT 57.231 29.630 16.23 0.00 0.00 3.11
1909 2451 8.370182 GGATGCATCCATTTATTTACAATCCTT 58.630 33.333 35.93 0.00 46.38 3.36
1962 2504 1.847088 AGGGGAATGGGAGTTTAGAGC 59.153 52.381 0.00 0.00 0.00 4.09
2041 2583 4.136796 CTGCCTATGCCTATGTTTAAGCA 58.863 43.478 0.00 0.00 40.00 3.91
2103 2645 0.547712 AACTGGAGCCCAAGCCTAGA 60.548 55.000 0.00 0.00 41.25 2.43
2106 2648 0.540597 GAAAACTGGAGCCCAAGCCT 60.541 55.000 0.00 0.00 41.25 4.58
2132 2674 5.376854 TGCTTGTGCTTTTTCTAGGATTC 57.623 39.130 0.00 0.00 40.48 2.52
2183 2725 8.671921 GGAATATACATGAACTATTGCATCTGG 58.328 37.037 0.00 0.00 0.00 3.86
2366 2908 3.526931 TTAAAGAGATCAGTGAGCGGG 57.473 47.619 2.10 0.00 0.00 6.13
2371 2913 5.882557 GGCCATCTTTTAAAGAGATCAGTGA 59.117 40.000 13.07 0.00 41.61 3.41
2374 2916 4.274459 CCGGCCATCTTTTAAAGAGATCAG 59.726 45.833 13.07 4.83 41.61 2.90
2381 2923 2.442413 TGACCCGGCCATCTTTTAAAG 58.558 47.619 2.24 0.00 0.00 1.85
2407 2950 3.756434 TCATACGCATCATAGATCGGACA 59.244 43.478 0.00 0.00 0.00 4.02
2475 3018 1.398390 GCAACGAGAACCCTATTGCAG 59.602 52.381 2.54 0.00 41.07 4.41
2513 3056 4.341520 AGGGTCTAGTTATAACCTCGCAAG 59.658 45.833 12.05 1.63 33.42 4.01
2524 3070 6.303839 TCTTGTTGCAAAAGGGTCTAGTTAT 58.696 36.000 0.00 0.00 0.00 1.89
2618 3164 1.279271 AGGGTCATGTTACAGCCTCAC 59.721 52.381 0.00 0.00 35.51 3.51
2686 3232 2.366480 TTTCCCGACGGCAGAAACGA 62.366 55.000 8.86 0.00 34.93 3.85
2693 3239 0.108520 GACTATGTTTCCCGACGGCA 60.109 55.000 8.86 0.63 0.00 5.69
2713 3259 1.454276 CGAATAACAACTGTGCGACGT 59.546 47.619 0.00 0.00 0.00 4.34
2718 3264 0.793104 GCGGCGAATAACAACTGTGC 60.793 55.000 12.98 0.00 0.00 4.57
2725 3271 1.229315 AACAACGGCGGCGAATAACA 61.229 50.000 38.93 0.00 0.00 2.41
2728 3274 3.029564 GCAACAACGGCGGCGAATA 62.030 57.895 38.93 0.00 0.00 1.75
2729 3275 4.398598 GCAACAACGGCGGCGAAT 62.399 61.111 38.93 22.79 0.00 3.34
2758 3304 0.868186 TCCCTCCTATTCTCCTCCCC 59.132 60.000 0.00 0.00 0.00 4.81
2843 3389 0.368907 CTTCCCAAATCGTACGTGCG 59.631 55.000 20.49 20.49 0.00 5.34
2849 3395 1.187974 TCGGCTCTTCCCAAATCGTA 58.812 50.000 0.00 0.00 0.00 3.43
2865 3411 5.244851 TCCTCTATTTCTTCTCCATCATCGG 59.755 44.000 0.00 0.00 0.00 4.18
2929 3476 3.478857 TGTTACAGTCAAACCCGTGAT 57.521 42.857 0.00 0.00 0.00 3.06
2945 3493 2.289565 TGTGCAACACGATGGTTGTTA 58.710 42.857 16.33 7.39 45.67 2.41
2962 3510 4.864247 GCCTTATTGCAAACATAGGTTGTG 59.136 41.667 1.71 0.00 38.99 3.33
3001 3549 4.273480 CAGCACAACACAAACTTACTAGCT 59.727 41.667 0.00 0.00 0.00 3.32
3004 3552 4.201871 GCACAGCACAACACAAACTTACTA 60.202 41.667 0.00 0.00 0.00 1.82
3008 3556 1.732077 CGCACAGCACAACACAAACTT 60.732 47.619 0.00 0.00 0.00 2.66
3022 3570 1.067693 TTTGATCGTACAGCGCACAG 58.932 50.000 11.47 0.64 41.07 3.66
3049 3597 3.114616 CGCCTCTGCAACTGTCCG 61.115 66.667 0.00 0.00 37.32 4.79
3087 3635 1.302192 GCTTGTGTTCACCCGGCTA 60.302 57.895 0.00 0.00 0.00 3.93
3151 3699 5.473931 AGAGCTGTTATATCACTATTGGCG 58.526 41.667 0.00 0.00 0.00 5.69
3239 3788 6.200878 ACAGAAAAAGATTAGTCCTTCCCA 57.799 37.500 0.00 0.00 0.00 4.37
3287 3836 6.443849 ACCCAACTAACAGAAGAGGATTATCA 59.556 38.462 0.00 0.00 0.00 2.15
3403 3952 9.907229 AGATAGATCGAAAACCCTTAAAAGATT 57.093 29.630 0.00 0.00 0.00 2.40
3418 3968 7.987750 AGCTTATGTAGACAGATAGATCGAA 57.012 36.000 0.00 0.00 0.00 3.71
3525 4075 5.014808 ACCAAATATCTGCAGCCAATTTC 57.985 39.130 9.47 0.00 0.00 2.17
3549 4099 6.634436 CCTAAATTCAGATAGTGCGAAAATGC 59.366 38.462 0.00 0.00 0.00 3.56
3703 4253 4.813161 ACCTGTGCAAAGATATCTGAATCG 59.187 41.667 5.12 0.00 0.00 3.34
3734 4284 9.953565 AGCATAACAGTTAGGTATAGAACAAAA 57.046 29.630 6.82 0.00 0.00 2.44
3800 4350 6.095580 GGGTGTTCTCCTTAATCTTCCATTTC 59.904 42.308 0.00 0.00 0.00 2.17
3821 4371 2.002505 AGGTCGATAGGATGAGGGTG 57.997 55.000 0.00 0.00 0.00 4.61
3832 4382 6.704493 CCATCCGATTCTTTAAAAGGTCGATA 59.296 38.462 13.93 5.76 38.44 2.92
3834 4384 4.873827 CCATCCGATTCTTTAAAAGGTCGA 59.126 41.667 13.93 0.00 38.44 4.20
3836 4386 4.202020 GGCCATCCGATTCTTTAAAAGGTC 60.202 45.833 0.00 0.00 0.00 3.85
3921 4474 2.017049 GGCTATTGCAAGTGGGTACAG 58.983 52.381 4.94 0.00 41.91 2.74
4044 4598 9.489084 TCTGAATATGTTCTTATAATGGAACCG 57.511 33.333 12.55 0.00 40.50 4.44
4177 4731 2.679837 CAACCCATCGGAGAACATCTTG 59.320 50.000 0.00 0.00 43.58 3.02
4411 4969 7.279536 ACATACAATCTTGACAGACAGCATAAG 59.720 37.037 0.00 0.00 0.00 1.73
4412 4970 7.105588 ACATACAATCTTGACAGACAGCATAA 58.894 34.615 0.00 0.00 0.00 1.90
4413 4971 6.643388 ACATACAATCTTGACAGACAGCATA 58.357 36.000 0.00 0.00 0.00 3.14
4414 4972 5.494724 ACATACAATCTTGACAGACAGCAT 58.505 37.500 0.00 0.00 0.00 3.79
4453 5011 8.819974 CAGTATGCACCAATTCAATAAATTTCC 58.180 33.333 0.00 0.00 35.32 3.13
4470 5028 5.221322 TGGTCATAGATCTGACAGTATGCAC 60.221 44.000 14.90 6.32 45.95 4.57
4618 5176 4.496360 GTTGAGTACCAGTCTTCCTAAGC 58.504 47.826 0.00 0.00 0.00 3.09
4687 5245 4.655963 ACCACAAGAACAGTTAGCATGAT 58.344 39.130 0.00 0.00 0.00 2.45
4927 5491 5.121380 ACATGGAAGCAAGTGAGGATATT 57.879 39.130 0.00 0.00 0.00 1.28
4948 5512 4.510340 ACAAAGTTGTGTCATCCTAACGAC 59.490 41.667 0.00 0.00 40.49 4.34
5064 5628 9.720769 CCATAGTATAACCTGGACGATATTTTT 57.279 33.333 0.00 0.00 0.00 1.94
5097 5668 7.069578 ACCACCACCTACACTGAATTATACTAG 59.930 40.741 0.00 0.00 0.00 2.57
5107 5678 1.140052 CACAACCACCACCTACACTGA 59.860 52.381 0.00 0.00 0.00 3.41
5124 5695 4.388485 TGTATTTCTTTCTGCAGAGCACA 58.612 39.130 17.43 10.86 33.79 4.57
5130 5701 7.755591 TGAAGCTAATGTATTTCTTTCTGCAG 58.244 34.615 7.63 7.63 0.00 4.41
5170 5741 7.712204 TCATACAGGTACAACAGAGATGTTA 57.288 36.000 0.00 0.00 32.27 2.41
5360 5931 0.253044 TGAGAAGGCGGAATCCCTTG 59.747 55.000 0.00 0.00 42.56 3.61
5362 5933 1.216990 AATGAGAAGGCGGAATCCCT 58.783 50.000 0.00 0.00 0.00 4.20
5484 6055 3.834489 AATCATCTGGCAGAGAACGAT 57.166 42.857 23.24 17.15 33.12 3.73
5487 6071 5.392811 CCTTCAAAATCATCTGGCAGAGAAC 60.393 44.000 23.24 0.00 33.12 3.01
5504 6088 4.829872 TCTTTATACCCGAGCCTTCAAA 57.170 40.909 0.00 0.00 0.00 2.69
5506 6090 5.104693 TCAATTCTTTATACCCGAGCCTTCA 60.105 40.000 0.00 0.00 0.00 3.02
5518 6102 7.287696 GGAGGCTTTTCCCATCAATTCTTTATA 59.712 37.037 0.00 0.00 34.51 0.98
5528 6112 2.845659 TCTAGGAGGCTTTTCCCATCA 58.154 47.619 0.00 0.00 38.02 3.07
5531 6115 2.919602 ACAATCTAGGAGGCTTTTCCCA 59.080 45.455 0.00 0.00 38.02 4.37
5535 6119 4.042187 ACTCACACAATCTAGGAGGCTTTT 59.958 41.667 0.00 0.00 0.00 2.27
5563 6147 0.952497 CAATGCAGCACTCGACCACT 60.952 55.000 0.00 0.00 0.00 4.00
5569 6153 2.097160 GACGCAATGCAGCACTCG 59.903 61.111 5.91 4.08 0.00 4.18
5617 6201 6.925165 AGCATGGTGAGAACTTTAATGTTTTG 59.075 34.615 8.03 1.32 0.00 2.44
5619 6203 6.040842 ACAGCATGGTGAGAACTTTAATGTTT 59.959 34.615 30.46 0.00 43.62 2.83
5630 6214 2.957402 AAGGAACAGCATGGTGAGAA 57.043 45.000 30.46 0.00 33.00 2.87
5635 6219 5.086621 AGGAAAATAAAGGAACAGCATGGT 58.913 37.500 0.00 0.00 42.46 3.55
5663 6247 7.984050 TCACATGCCTTTTTGAAAGAACATAAA 59.016 29.630 0.00 0.00 0.00 1.40
5664 6248 7.437862 GTCACATGCCTTTTTGAAAGAACATAA 59.562 33.333 0.00 0.00 0.00 1.90
5665 6249 6.922957 GTCACATGCCTTTTTGAAAGAACATA 59.077 34.615 0.00 0.00 0.00 2.29
5666 6250 5.754890 GTCACATGCCTTTTTGAAAGAACAT 59.245 36.000 0.00 3.38 0.00 2.71
5667 6251 5.108517 GTCACATGCCTTTTTGAAAGAACA 58.891 37.500 0.00 1.36 0.00 3.18
5668 6252 5.108517 TGTCACATGCCTTTTTGAAAGAAC 58.891 37.500 0.00 0.00 0.00 3.01
5669 6253 5.336150 TGTCACATGCCTTTTTGAAAGAA 57.664 34.783 0.00 0.00 0.00 2.52
5670 6254 4.998671 TGTCACATGCCTTTTTGAAAGA 57.001 36.364 0.00 0.00 0.00 2.52
5671 6255 5.050634 CACATGTCACATGCCTTTTTGAAAG 60.051 40.000 18.19 0.00 0.00 2.62
5672 6256 4.809958 CACATGTCACATGCCTTTTTGAAA 59.190 37.500 18.19 0.00 0.00 2.69
5673 6257 4.370049 CACATGTCACATGCCTTTTTGAA 58.630 39.130 18.19 0.00 0.00 2.69
5674 6258 3.799574 GCACATGTCACATGCCTTTTTGA 60.800 43.478 18.19 0.00 33.06 2.69
5675 6259 2.477375 GCACATGTCACATGCCTTTTTG 59.523 45.455 18.19 8.45 33.06 2.44
5676 6260 2.366266 AGCACATGTCACATGCCTTTTT 59.634 40.909 18.19 0.00 40.33 1.94
5687 6271 3.250762 GTCTTACAGCAAAGCACATGTCA 59.749 43.478 0.00 0.00 0.00 3.58
5689 6273 3.213506 TGTCTTACAGCAAAGCACATGT 58.786 40.909 0.00 0.00 0.00 3.21
5690 6274 3.902261 TGTCTTACAGCAAAGCACATG 57.098 42.857 0.00 0.00 0.00 3.21
5714 6298 9.739276 TGTTCTGTTACTCTCATCCATTTTATT 57.261 29.630 0.00 0.00 0.00 1.40
5716 6300 9.383519 GATGTTCTGTTACTCTCATCCATTTTA 57.616 33.333 0.00 0.00 0.00 1.52
5717 6301 8.105829 AGATGTTCTGTTACTCTCATCCATTTT 58.894 33.333 0.00 0.00 34.22 1.82
5719 6303 7.192852 AGATGTTCTGTTACTCTCATCCATT 57.807 36.000 0.00 0.00 34.22 3.16
5722 6306 9.039870 CATTAAGATGTTCTGTTACTCTCATCC 57.960 37.037 0.00 0.00 34.22 3.51
5736 6320 6.701400 ACAAAAGCAACACCATTAAGATGTTC 59.299 34.615 0.00 0.00 34.36 3.18
5858 6442 8.420374 TTTGCAGCTAATCACATAAGTACTAC 57.580 34.615 0.00 0.00 0.00 2.73
5860 6444 7.390440 TGTTTTGCAGCTAATCACATAAGTACT 59.610 33.333 0.00 0.00 0.00 2.73
5861 6445 7.481798 GTGTTTTGCAGCTAATCACATAAGTAC 59.518 37.037 19.69 1.34 0.00 2.73
5913 6504 0.327924 TTGATGGACGTGGATGGCTT 59.672 50.000 0.00 0.00 0.00 4.35
5916 6507 3.141398 CCTTATTGATGGACGTGGATGG 58.859 50.000 0.00 0.00 0.00 3.51
5919 6510 3.104512 AGACCTTATTGATGGACGTGGA 58.895 45.455 0.00 0.00 0.00 4.02
5979 6570 8.604035 TGCATGCGTAAAACAAAGAATTAAAAA 58.396 25.926 14.09 0.00 0.00 1.94
5983 6574 7.812191 AGAATGCATGCGTAAAACAAAGAATTA 59.188 29.630 13.96 0.00 0.00 1.40
5999 6590 4.082026 ACTCCCAACTTAAAGAATGCATGC 60.082 41.667 11.82 11.82 0.00 4.06
6014 6605 2.789409 AGCATAAGGTCACTCCCAAC 57.211 50.000 0.00 0.00 36.75 3.77


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

AutoCloner maintained by Alex Coulton.