Multiple sequence alignment - TraesCS6A01G221600

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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 TraesCS6A01G221600 chr6A 100.000 5584 0 0 1 5584 411941451 411935868 0.000000e+00 10312.0
1 TraesCS6A01G221600 chr6B 94.572 5158 150 42 7 5092 469078162 469073063 0.000000e+00 7854.0
2 TraesCS6A01G221600 chr6B 89.623 106 10 1 5091 5196 469073025 469072921 3.510000e-27 134.0
3 TraesCS6A01G221600 chr6B 100.000 35 0 0 5199 5233 469072892 469072858 1.300000e-06 65.8
4 TraesCS6A01G221600 chr6D 92.580 3706 128 51 1 3646 303467283 303463665 0.000000e+00 5184.0
5 TraesCS6A01G221600 chr6D 97.132 1604 23 11 3631 5233 303463646 303462065 0.000000e+00 2686.0
6 TraesCS6A01G221600 chr6D 94.118 272 10 2 5234 5505 303462025 303461760 5.210000e-110 409.0
7 TraesCS6A01G221600 chr6D 88.820 161 9 3 593 747 42400048 42399891 7.380000e-44 189.0
8 TraesCS6A01G221600 chr1D 91.603 917 63 5 663 1575 23445104 23446010 0.000000e+00 1254.0
9 TraesCS6A01G221600 chr1A 92.547 161 9 2 1416 1575 354536882 354536724 1.560000e-55 228.0
10 TraesCS6A01G221600 chr1A 85.366 82 4 2 1572 1646 354536709 354536629 1.670000e-10 78.7
11 TraesCS6A01G221600 chr5A 91.925 161 10 2 1416 1575 565721037 565720879 7.280000e-54 222.0
12 TraesCS6A01G221600 chr5A 85.366 82 4 2 1572 1646 565720864 565720784 1.670000e-10 78.7
13 TraesCS6A01G221600 chr7D 88.889 162 7 4 593 747 313316170 313316327 7.380000e-44 189.0
14 TraesCS6A01G221600 chr7B 88.125 160 11 3 593 747 276793876 276794032 3.440000e-42 183.0
15 TraesCS6A01G221600 chr3B 87.975 158 10 3 593 745 41969294 41969447 1.600000e-40 178.0
16 TraesCS6A01G221600 chr4A 87.342 158 12 2 593 745 672204925 672205079 2.070000e-39 174.0
17 TraesCS6A01G221600 chr3D 87.821 156 9 4 598 747 467996167 467996318 2.070000e-39 174.0


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 TraesCS6A01G221600 chr6A 411935868 411941451 5583 True 10312.000000 10312 100.000000 1 5584 1 chr6A.!!$R1 5583
1 TraesCS6A01G221600 chr6B 469072858 469078162 5304 True 2684.600000 7854 94.731667 7 5233 3 chr6B.!!$R1 5226
2 TraesCS6A01G221600 chr6D 303461760 303467283 5523 True 2759.666667 5184 94.610000 1 5505 3 chr6D.!!$R2 5504
3 TraesCS6A01G221600 chr1D 23445104 23446010 906 False 1254.000000 1254 91.603000 663 1575 1 chr1D.!!$F1 912

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
366 375 0.039437 GCAGAAACGAGACGACCTCA 60.039 55.000 9.47 0.00 42.06 3.86 F
368 377 0.237761 AGAAACGAGACGACCTCACG 59.762 55.000 9.47 0.00 42.06 4.35 F
1106 1132 1.286305 ATTACCAATGGGCCGGGAGT 61.286 55.000 14.74 5.14 37.90 3.85 F
1448 1475 0.802494 GGCAATTGACACCAGGTACG 59.198 55.000 10.34 0.00 0.00 3.67 F
1451 1478 2.550606 GCAATTGACACCAGGTACGAAA 59.449 45.455 10.34 0.00 0.00 3.46 F
1642 1696 2.602211 TGCAATGAGTTGTGTTTTTGCG 59.398 40.909 0.00 0.00 41.67 4.85 F
1824 1878 2.838202 CAGTGGATGGTGGTTAGTACCT 59.162 50.000 0.00 0.00 45.27 3.08 F
2889 2959 3.312828 CAACTTCTGTTCTGACTCCTCG 58.687 50.000 0.00 0.00 33.52 4.63 F
3100 3178 3.833070 ACCAGAGGTTCTTCTGTTACGAT 59.167 43.478 10.22 0.00 42.41 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1271 0.254178 ATGACCACTCCACAGCCATC 59.746 55.000 0.00 0.00 0.00 3.51 R
1418 1444 3.088532 TGTCAATTGCCAGGTGTATTCC 58.911 45.455 0.00 0.00 0.00 3.01 R
2494 2563 2.877097 TAGGAAATGACAAGCCAGCA 57.123 45.000 0.00 0.00 0.00 4.41 R
2952 3026 3.254166 TCTCAACTTCATTCTTGCAAGGC 59.746 43.478 25.73 0.00 0.00 4.35 R
3077 3155 4.401022 TCGTAACAGAAGAACCTCTGGTA 58.599 43.478 5.65 0.19 46.02 3.25 R
3120 3198 5.255397 ACCAACCTCCAGATACAAATCAA 57.745 39.130 0.00 0.00 34.28 2.57 R
3488 3569 5.467063 CAGGGAAAACAAGTACTTGAGTCTC 59.533 44.000 36.14 27.17 42.93 3.36 R
4165 4295 2.768253 TGGTTGTACATCAGAGGCTG 57.232 50.000 0.00 0.00 0.00 4.85 R
4983 5118 2.615447 CAGTGAAGTGAGAGCTTTGCAA 59.385 45.455 0.00 0.00 0.00 4.08 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
96 100 5.739935 GCTTGATTTGCTTTCTTCCTTTCCA 60.740 40.000 0.00 0.00 0.00 3.53
112 116 6.805713 TCCTTTCCATTCAAACAAGTCTTTC 58.194 36.000 0.00 0.00 0.00 2.62
113 117 6.607198 TCCTTTCCATTCAAACAAGTCTTTCT 59.393 34.615 0.00 0.00 0.00 2.52
162 166 7.607991 TCTTCTCTTCTCTTCTCTTCTCTTCTC 59.392 40.741 0.00 0.00 0.00 2.87
169 173 2.881734 TCTCTTCTCTTCTCCACTGCA 58.118 47.619 0.00 0.00 0.00 4.41
213 219 4.626942 TCTATCCTTCCTCTTCCTCCAA 57.373 45.455 0.00 0.00 0.00 3.53
278 284 1.535437 CCCTGTTATCGCTGTACGGAC 60.535 57.143 5.68 0.00 43.89 4.79
331 340 6.097696 AGTTAGTAAATTGCCCACTTGTTTGT 59.902 34.615 0.00 0.00 0.00 2.83
357 366 1.743252 GAGCCCTGGCAGAAACGAG 60.743 63.158 17.94 0.00 44.88 4.18
358 367 2.172483 GAGCCCTGGCAGAAACGAGA 62.172 60.000 17.94 0.00 44.88 4.04
359 368 2.035442 GCCCTGGCAGAAACGAGAC 61.035 63.158 17.94 0.00 41.49 3.36
360 369 1.738099 CCCTGGCAGAAACGAGACG 60.738 63.158 17.94 0.00 0.00 4.18
363 372 1.006571 TGGCAGAAACGAGACGACC 60.007 57.895 0.00 0.00 0.00 4.79
364 373 1.289380 GGCAGAAACGAGACGACCT 59.711 57.895 0.00 0.00 0.00 3.85
365 374 0.733223 GGCAGAAACGAGACGACCTC 60.733 60.000 0.00 0.00 38.55 3.85
366 375 0.039437 GCAGAAACGAGACGACCTCA 60.039 55.000 9.47 0.00 42.06 3.86
367 376 1.687628 CAGAAACGAGACGACCTCAC 58.312 55.000 9.47 0.00 42.06 3.51
368 377 0.237761 AGAAACGAGACGACCTCACG 59.762 55.000 9.47 0.00 42.06 4.35
369 378 1.335697 GAAACGAGACGACCTCACGC 61.336 60.000 9.47 0.00 42.06 5.34
370 379 1.793134 AAACGAGACGACCTCACGCT 61.793 55.000 9.47 0.00 42.06 5.07
536 553 1.566298 CCCCAGGCTGTTAGCTTCCT 61.566 60.000 14.43 0.00 41.99 3.36
565 584 2.618709 GTGTGGTTAGCAGCTGAAAGTT 59.381 45.455 20.43 0.00 35.30 2.66
710 730 6.060028 TCATGTTTTCTGCAGAAAGTGTAC 57.940 37.500 33.76 29.01 43.90 2.90
789 815 8.947115 AGTAAAGCTTTGGACATTATCTTGTAC 58.053 33.333 22.02 5.78 0.00 2.90
790 816 8.947115 GTAAAGCTTTGGACATTATCTTGTACT 58.053 33.333 22.02 0.00 31.30 2.73
853 879 2.685017 TGGATGCCGAGCTCACCT 60.685 61.111 15.40 0.00 0.00 4.00
889 915 3.612860 GTGGAGATGTAACTTGTGCTACG 59.387 47.826 0.00 0.00 0.00 3.51
975 1001 2.682856 TCAAGTGTTTGTGAGGCTCAAC 59.317 45.455 20.62 14.65 35.73 3.18
1026 1052 5.491070 CAGATGTCAACAGATCCTAACCAA 58.509 41.667 0.00 0.00 0.00 3.67
1106 1132 1.286305 ATTACCAATGGGCCGGGAGT 61.286 55.000 14.74 5.14 37.90 3.85
1245 1271 2.036089 GAGCCTAAAGTATGGAGGTCCG 59.964 54.545 0.00 0.00 39.43 4.79
1326 1352 9.547753 AAGTATGTTTTCTGCCACTATGTATAG 57.452 33.333 0.00 0.00 36.46 1.31
1327 1353 8.705594 AGTATGTTTTCTGCCACTATGTATAGT 58.294 33.333 0.00 0.00 44.03 2.12
1328 1354 9.976511 GTATGTTTTCTGCCACTATGTATAGTA 57.023 33.333 4.35 0.00 41.44 1.82
1448 1475 0.802494 GGCAATTGACACCAGGTACG 59.198 55.000 10.34 0.00 0.00 3.67
1451 1478 2.550606 GCAATTGACACCAGGTACGAAA 59.449 45.455 10.34 0.00 0.00 3.46
1642 1696 2.602211 TGCAATGAGTTGTGTTTTTGCG 59.398 40.909 0.00 0.00 41.67 4.85
1655 1709 4.728131 GTGTTTTTGCGCTTCAATTTTTCC 59.272 37.500 9.73 0.00 34.12 3.13
1824 1878 2.838202 CAGTGGATGGTGGTTAGTACCT 59.162 50.000 0.00 0.00 45.27 3.08
1861 1915 8.419922 TCTATTCTGAAGCATCTAGATCACAT 57.580 34.615 1.03 0.00 0.00 3.21
1892 1946 3.635373 TCAGATCCACCTAATGTCGGTAC 59.365 47.826 0.00 0.00 32.37 3.34
1893 1947 3.637229 CAGATCCACCTAATGTCGGTACT 59.363 47.826 0.00 0.00 32.37 2.73
1961 2020 9.424319 TCCATTCTCTACATTATATTTTCGAGC 57.576 33.333 0.00 0.00 0.00 5.03
2135 2194 8.010540 CGACATCGATATACATACTATAGTGGC 58.989 40.741 15.90 0.00 43.02 5.01
2138 2197 7.803279 TCGATATACATACTATAGTGGCCTG 57.197 40.000 15.90 9.68 0.00 4.85
2353 2412 6.128200 CCAATGAAAAGTTGATCATCTCGTGA 60.128 38.462 6.75 0.00 42.06 4.35
2562 2632 6.074005 CACTCAAGAAATCGTTTCAAGTAGC 58.926 40.000 11.33 0.00 42.10 3.58
2700 2770 5.682234 ATGATGTTTCCCTTTTCCATTCC 57.318 39.130 0.00 0.00 0.00 3.01
2889 2959 3.312828 CAACTTCTGTTCTGACTCCTCG 58.687 50.000 0.00 0.00 33.52 4.63
2908 2978 4.335315 CCTCGGAAGCATGCACTAAATTTA 59.665 41.667 21.98 0.00 0.00 1.40
2933 3007 8.735692 AGAATTGTTTGTGAAAATCATGGTTT 57.264 26.923 0.00 0.00 0.00 3.27
2942 3016 6.035435 TGTGAAAATCATGGTTTTGTTTGTCG 59.965 34.615 21.13 0.00 31.80 4.35
3100 3178 3.833070 ACCAGAGGTTCTTCTGTTACGAT 59.167 43.478 10.22 0.00 42.41 3.73
3120 3198 7.627298 ACGATAGGTAATAGCAGTCGATAAT 57.373 36.000 18.24 0.00 43.77 1.28
3218 3296 9.594478 TTTTCTAGCGATTATCATGTTTCACTA 57.406 29.630 0.00 0.00 0.00 2.74
3231 3309 7.394016 TCATGTTTCACTACCTGTGTGATAAT 58.606 34.615 0.00 0.00 46.27 1.28
3232 3310 7.882791 TCATGTTTCACTACCTGTGTGATAATT 59.117 33.333 0.00 0.00 46.27 1.40
3233 3311 8.514594 CATGTTTCACTACCTGTGTGATAATTT 58.485 33.333 0.00 0.00 46.27 1.82
3234 3312 8.458573 TGTTTCACTACCTGTGTGATAATTTT 57.541 30.769 0.00 0.00 46.27 1.82
3262 3340 4.844884 AGCATTCCAAGTAACTTAGGGAC 58.155 43.478 0.00 0.00 0.00 4.46
3288 3366 7.707624 TGGGAGAAATAATCCATGCATATTC 57.292 36.000 0.00 0.00 38.70 1.75
3360 3438 4.893424 TGCTTTGTGAGTTAAGGTGTTC 57.107 40.909 0.00 0.00 0.00 3.18
3369 3447 5.046807 GTGAGTTAAGGTGTTCCCTAGCTTA 60.047 44.000 0.00 0.00 45.47 3.09
3488 3569 9.661563 TGGAACTACTTAATACCATTAACACAG 57.338 33.333 0.00 0.00 0.00 3.66
3573 3654 6.726490 AACTTACCAGTTCTCAGTACAAGA 57.274 37.500 0.00 0.00 39.15 3.02
3696 3826 5.350914 AGAAAATGCTCGACTTCTCAATCAG 59.649 40.000 0.00 0.00 0.00 2.90
3941 4071 7.119846 GGTACAGATTTAGGGATATGTCATTGC 59.880 40.741 0.00 0.00 33.81 3.56
4182 4312 3.876274 TCTCAGCCTCTGATGTACAAC 57.124 47.619 0.00 0.00 39.92 3.32
4274 4405 4.359434 TGACACTGGCCTTTAATACACA 57.641 40.909 3.32 0.00 0.00 3.72
4520 4651 5.707298 CCACTCTTGATGTCCTTATTGTGTT 59.293 40.000 0.00 0.00 0.00 3.32
4615 4746 2.108952 AGGTGGCTCCTCATTTTTCAGT 59.891 45.455 1.37 0.00 44.42 3.41
4754 4885 1.402259 TCAAACACGGCGTCAAATGTT 59.598 42.857 10.85 8.46 36.86 2.71
5081 5216 4.563184 CAGATACTCAAGAACGTTGGTAGC 59.437 45.833 5.00 4.07 0.00 3.58
5082 5217 4.463186 AGATACTCAAGAACGTTGGTAGCT 59.537 41.667 5.00 6.26 0.00 3.32
5083 5218 5.651139 AGATACTCAAGAACGTTGGTAGCTA 59.349 40.000 5.00 0.00 0.00 3.32
5084 5219 4.175787 ACTCAAGAACGTTGGTAGCTAG 57.824 45.455 5.00 0.00 0.00 3.42
5108 5282 7.568349 AGATAAAGCTCATTGAGTGACCATTA 58.432 34.615 14.90 3.10 32.22 1.90
5146 5320 3.562108 AGAGGACTCAAACCCCTTAGA 57.438 47.619 1.75 0.00 0.00 2.10
5345 5584 9.120538 TGATATAAGGCAAAATCTTCAAGTACC 57.879 33.333 0.00 0.00 0.00 3.34
5383 5622 9.823647 ATCATATCGTTCATAGTGAGACTTTTT 57.176 29.630 0.00 0.00 0.00 1.94
5428 5667 8.273780 GGAAAAGCATCTCATATCCGATATTT 57.726 34.615 0.00 0.00 0.00 1.40
5481 5720 8.143193 AGCAAAGACAATATGACACAAAAATCA 58.857 29.630 0.00 0.00 0.00 2.57
5482 5721 8.928733 GCAAAGACAATATGACACAAAAATCAT 58.071 29.630 0.00 0.00 38.99 2.45
5490 5729 8.806429 ATATGACACAAAAATCATACTGGTCA 57.194 30.769 0.00 0.00 39.88 4.02
5505 5744 7.942341 TCATACTGGTCAACTTCTTTTGGTTAT 59.058 33.333 0.00 0.00 0.00 1.89
5506 5745 9.226606 CATACTGGTCAACTTCTTTTGGTTATA 57.773 33.333 0.00 0.00 0.00 0.98
5507 5746 7.506328 ACTGGTCAACTTCTTTTGGTTATAC 57.494 36.000 0.00 0.00 0.00 1.47
5508 5747 7.057894 ACTGGTCAACTTCTTTTGGTTATACA 58.942 34.615 0.00 0.00 0.00 2.29
5509 5748 7.012989 ACTGGTCAACTTCTTTTGGTTATACAC 59.987 37.037 0.00 0.00 0.00 2.90
5519 5758 2.199291 GGTTATACACCGTCCGACAG 57.801 55.000 0.00 0.00 35.12 3.51
5520 5759 1.745087 GGTTATACACCGTCCGACAGA 59.255 52.381 0.00 0.00 35.12 3.41
5521 5760 2.223433 GGTTATACACCGTCCGACAGAG 60.223 54.545 0.00 0.00 35.12 3.35
5522 5761 2.408271 TATACACCGTCCGACAGAGT 57.592 50.000 0.00 0.00 0.00 3.24
5523 5762 1.542492 ATACACCGTCCGACAGAGTT 58.458 50.000 0.00 0.00 0.00 3.01
5524 5763 1.321474 TACACCGTCCGACAGAGTTT 58.679 50.000 0.00 0.00 0.00 2.66
5525 5764 0.249322 ACACCGTCCGACAGAGTTTG 60.249 55.000 0.00 0.00 0.00 2.93
5526 5765 0.031585 CACCGTCCGACAGAGTTTGA 59.968 55.000 0.00 0.00 0.00 2.69
5527 5766 0.748450 ACCGTCCGACAGAGTTTGAA 59.252 50.000 0.00 0.00 0.00 2.69
5528 5767 1.137479 ACCGTCCGACAGAGTTTGAAA 59.863 47.619 0.00 0.00 0.00 2.69
5529 5768 2.206750 CCGTCCGACAGAGTTTGAAAA 58.793 47.619 0.00 0.00 0.00 2.29
5530 5769 2.610374 CCGTCCGACAGAGTTTGAAAAA 59.390 45.455 0.00 0.00 0.00 1.94
5531 5770 3.545426 CCGTCCGACAGAGTTTGAAAAAC 60.545 47.826 0.00 0.00 0.00 2.43
5532 5771 3.062909 CGTCCGACAGAGTTTGAAAAACA 59.937 43.478 5.72 0.00 0.00 2.83
5533 5772 4.340263 GTCCGACAGAGTTTGAAAAACAC 58.660 43.478 5.72 0.00 0.00 3.32
5534 5773 4.004314 TCCGACAGAGTTTGAAAAACACA 58.996 39.130 5.72 0.00 0.00 3.72
5535 5774 4.095610 CCGACAGAGTTTGAAAAACACAC 58.904 43.478 5.72 0.00 0.00 3.82
5536 5775 4.142687 CCGACAGAGTTTGAAAAACACACT 60.143 41.667 5.72 0.00 41.46 3.55
5543 5782 6.084326 AGTTTGAAAAACACACTCAACAGT 57.916 33.333 5.72 0.00 34.92 3.55
5544 5783 7.209471 AGTTTGAAAAACACACTCAACAGTA 57.791 32.000 5.72 0.00 34.92 2.74
5545 5784 7.653647 AGTTTGAAAAACACACTCAACAGTAA 58.346 30.769 5.72 0.00 34.92 2.24
5546 5785 8.303876 AGTTTGAAAAACACACTCAACAGTAAT 58.696 29.630 5.72 0.00 34.92 1.89
5547 5786 8.372521 GTTTGAAAAACACACTCAACAGTAATG 58.627 33.333 0.00 0.00 0.00 1.90
5548 5787 7.384439 TGAAAAACACACTCAACAGTAATGA 57.616 32.000 0.00 0.00 0.00 2.57
5549 5788 7.821652 TGAAAAACACACTCAACAGTAATGAA 58.178 30.769 0.00 0.00 0.00 2.57
5550 5789 8.300286 TGAAAAACACACTCAACAGTAATGAAA 58.700 29.630 0.00 0.00 0.00 2.69
5551 5790 9.134734 GAAAAACACACTCAACAGTAATGAAAA 57.865 29.630 0.00 0.00 0.00 2.29
5552 5791 8.687824 AAAACACACTCAACAGTAATGAAAAG 57.312 30.769 0.00 0.00 0.00 2.27
5553 5792 6.377327 ACACACTCAACAGTAATGAAAAGG 57.623 37.500 0.00 0.00 0.00 3.11
5554 5793 5.299279 ACACACTCAACAGTAATGAAAAGGG 59.701 40.000 0.00 0.00 0.00 3.95
5555 5794 5.530915 CACACTCAACAGTAATGAAAAGGGA 59.469 40.000 0.00 0.00 0.00 4.20
5556 5795 6.207417 CACACTCAACAGTAATGAAAAGGGAT 59.793 38.462 0.00 0.00 0.00 3.85
5557 5796 6.207417 ACACTCAACAGTAATGAAAAGGGATG 59.793 38.462 0.00 0.00 0.00 3.51
5558 5797 6.207417 CACTCAACAGTAATGAAAAGGGATGT 59.793 38.462 0.00 0.00 0.00 3.06
5559 5798 6.431234 ACTCAACAGTAATGAAAAGGGATGTC 59.569 38.462 0.00 0.00 0.00 3.06
5560 5799 6.542821 TCAACAGTAATGAAAAGGGATGTCT 58.457 36.000 0.00 0.00 0.00 3.41
5561 5800 6.430925 TCAACAGTAATGAAAAGGGATGTCTG 59.569 38.462 0.00 0.00 0.00 3.51
5562 5801 4.702131 ACAGTAATGAAAAGGGATGTCTGC 59.298 41.667 0.00 0.00 0.00 4.26
5563 5802 4.701651 CAGTAATGAAAAGGGATGTCTGCA 59.298 41.667 0.00 0.00 0.00 4.41
5564 5803 5.183713 CAGTAATGAAAAGGGATGTCTGCAA 59.816 40.000 0.00 0.00 0.00 4.08
5565 5804 5.774690 AGTAATGAAAAGGGATGTCTGCAAA 59.225 36.000 0.00 0.00 0.00 3.68
5566 5805 4.525912 ATGAAAAGGGATGTCTGCAAAC 57.474 40.909 0.00 0.00 0.00 2.93
5567 5806 3.295093 TGAAAAGGGATGTCTGCAAACA 58.705 40.909 0.00 0.00 0.00 2.83
5568 5807 3.068024 TGAAAAGGGATGTCTGCAAACAC 59.932 43.478 0.00 0.00 30.55 3.32
5569 5808 1.620822 AAGGGATGTCTGCAAACACC 58.379 50.000 0.00 0.00 30.55 4.16
5570 5809 0.773644 AGGGATGTCTGCAAACACCT 59.226 50.000 0.00 0.00 30.55 4.00
5571 5810 1.168714 GGGATGTCTGCAAACACCTC 58.831 55.000 0.00 0.00 30.55 3.85
5572 5811 0.798776 GGATGTCTGCAAACACCTCG 59.201 55.000 0.00 0.00 30.55 4.63
5573 5812 0.166814 GATGTCTGCAAACACCTCGC 59.833 55.000 0.00 0.00 30.55 5.03
5574 5813 1.237285 ATGTCTGCAAACACCTCGCC 61.237 55.000 0.00 0.00 30.55 5.54
5575 5814 1.891919 GTCTGCAAACACCTCGCCA 60.892 57.895 0.00 0.00 0.00 5.69
5576 5815 1.073025 TCTGCAAACACCTCGCCAT 59.927 52.632 0.00 0.00 0.00 4.40
5577 5816 0.323302 TCTGCAAACACCTCGCCATA 59.677 50.000 0.00 0.00 0.00 2.74
5578 5817 0.447801 CTGCAAACACCTCGCCATAC 59.552 55.000 0.00 0.00 0.00 2.39
5579 5818 0.250510 TGCAAACACCTCGCCATACA 60.251 50.000 0.00 0.00 0.00 2.29
5580 5819 0.878416 GCAAACACCTCGCCATACAA 59.122 50.000 0.00 0.00 0.00 2.41
5581 5820 1.472480 GCAAACACCTCGCCATACAAT 59.528 47.619 0.00 0.00 0.00 2.71
5582 5821 2.680841 GCAAACACCTCGCCATACAATA 59.319 45.455 0.00 0.00 0.00 1.90
5583 5822 3.486875 GCAAACACCTCGCCATACAATAC 60.487 47.826 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.565592 AGCAAATCAAGCAACGATGATTA 57.434 34.783 0.00 0.00 43.54 1.75
96 100 7.734942 AGAGAGAGAGAAAGACTTGTTTGAAT 58.265 34.615 0.00 0.00 0.00 2.57
112 116 2.363038 AGCAGCAGCAATAGAGAGAGAG 59.637 50.000 3.17 0.00 45.49 3.20
113 117 2.386779 AGCAGCAGCAATAGAGAGAGA 58.613 47.619 3.17 0.00 45.49 3.10
169 173 1.281899 GCGAACGCTAATCTGCTCTT 58.718 50.000 11.97 0.00 38.26 2.85
190 196 4.551671 TGGAGGAAGAGGAAGGATAGAAG 58.448 47.826 0.00 0.00 0.00 2.85
213 219 1.852157 TCCAGGTTGGTGGCAGGAT 60.852 57.895 0.00 0.00 39.03 3.24
278 284 5.807520 ACGCAGACATACTAATCAAACTGAG 59.192 40.000 0.00 0.00 0.00 3.35
331 340 1.423541 TCTGCCAGGGCTCTACAAAAA 59.576 47.619 12.19 0.00 42.51 1.94
357 366 2.342910 TAGAAAAGCGTGAGGTCGTC 57.657 50.000 0.00 0.00 43.76 4.20
358 367 2.223876 TGTTAGAAAAGCGTGAGGTCGT 60.224 45.455 0.00 0.00 43.76 4.34
359 368 2.400399 TGTTAGAAAAGCGTGAGGTCG 58.600 47.619 0.00 0.00 43.76 4.79
360 369 4.806342 TTTGTTAGAAAAGCGTGAGGTC 57.194 40.909 0.00 0.00 43.76 3.85
363 372 8.114359 TCAAATTTTTGTTAGAAAAGCGTGAG 57.886 30.769 3.18 0.00 39.18 3.51
364 373 8.376942 GTTCAAATTTTTGTTAGAAAAGCGTGA 58.623 29.630 3.18 0.00 39.18 4.35
365 374 8.379902 AGTTCAAATTTTTGTTAGAAAAGCGTG 58.620 29.630 3.18 0.00 39.18 5.34
366 375 8.474006 AGTTCAAATTTTTGTTAGAAAAGCGT 57.526 26.923 3.18 0.00 39.18 5.07
367 376 9.753669 AAAGTTCAAATTTTTGTTAGAAAAGCG 57.246 25.926 3.18 0.00 39.18 4.68
370 379 9.833182 GCCAAAGTTCAAATTTTTGTTAGAAAA 57.167 25.926 3.18 0.00 39.18 2.29
452 469 8.031864 GCTCAGCTCAAGTATTATGCTCTTATA 58.968 37.037 0.00 0.00 34.41 0.98
453 470 6.873076 GCTCAGCTCAAGTATTATGCTCTTAT 59.127 38.462 0.00 0.00 34.41 1.73
710 730 3.127203 CCAGATTTGAGAAGCTTGCAGAG 59.873 47.826 2.10 0.00 26.63 3.35
853 879 1.228094 TCCACAGTGGCGCATCAAA 60.228 52.632 15.64 0.00 37.47 2.69
889 915 0.176449 GCAATGAGGGGACAAATGGC 59.824 55.000 0.00 0.00 0.00 4.40
975 1001 0.678950 ACAAAATTTGGTGCTCCGGG 59.321 50.000 10.71 0.00 36.30 5.73
1245 1271 0.254178 ATGACCACTCCACAGCCATC 59.746 55.000 0.00 0.00 0.00 3.51
1346 1372 5.929058 ATGCTCTCTTTCTCACTGATGTA 57.071 39.130 0.00 0.00 0.00 2.29
1418 1444 3.088532 TGTCAATTGCCAGGTGTATTCC 58.911 45.455 0.00 0.00 0.00 3.01
1541 1569 3.797039 TCCAGCAGAAATGAAGTATCCG 58.203 45.455 0.00 0.00 0.00 4.18
1605 1652 6.146601 TCATTGCAACAAGATCAAGTGAAA 57.853 33.333 0.00 0.00 0.00 2.69
1642 1696 9.129209 GTCACTATTTACTGGAAAAATTGAAGC 57.871 33.333 0.00 0.00 0.00 3.86
1655 1709 9.507280 CATAATTGGCAAAGTCACTATTTACTG 57.493 33.333 3.01 0.00 0.00 2.74
1813 1867 6.832384 AGATTAGACGAATCAGGTACTAACCA 59.168 38.462 10.43 0.00 45.69 3.67
1824 1878 7.716612 TGCTTCAGAATAGATTAGACGAATCA 58.283 34.615 10.43 0.00 45.69 2.57
1961 2020 7.047891 TGTTACAGGAGCACATATTCCTTTAG 58.952 38.462 0.00 0.00 41.86 1.85
2003 2062 7.981225 CAGCCATTAAAGTATAAGCCATTGTTT 59.019 33.333 0.00 0.00 0.00 2.83
2008 2067 6.364701 TGACAGCCATTAAAGTATAAGCCAT 58.635 36.000 0.00 0.00 0.00 4.40
2135 2194 7.010183 CACACTAACTTTATCGTCCATAACAGG 59.990 40.741 0.00 0.00 0.00 4.00
2138 2197 6.534079 AGCACACTAACTTTATCGTCCATAAC 59.466 38.462 0.00 0.00 0.00 1.89
2378 2437 7.042335 GTGCTAACTGACCATACACTTCTAAT 58.958 38.462 0.00 0.00 0.00 1.73
2489 2557 5.448654 AGGAAATGACAAGCCAGCAATATA 58.551 37.500 0.00 0.00 0.00 0.86
2494 2563 2.877097 TAGGAAATGACAAGCCAGCA 57.123 45.000 0.00 0.00 0.00 4.41
2562 2632 4.272504 TGCTTCTGTTACCTCTTTTCAACG 59.727 41.667 0.00 0.00 0.00 4.10
2663 2733 8.362639 GGGAAACATCATATGCTTTACATGATT 58.637 33.333 0.00 0.00 40.06 2.57
2664 2734 7.727186 AGGGAAACATCATATGCTTTACATGAT 59.273 33.333 0.00 0.00 40.06 2.45
2665 2735 7.062322 AGGGAAACATCATATGCTTTACATGA 58.938 34.615 0.00 0.00 40.06 3.07
2889 2959 7.761249 ACAATTCTAAATTTAGTGCATGCTTCC 59.239 33.333 21.69 6.86 32.61 3.46
2908 2978 8.735692 AAACCATGATTTTCACAAACAATTCT 57.264 26.923 0.00 0.00 0.00 2.40
2933 3007 6.529829 GCAAGGCAAATATATTCGACAAACAA 59.470 34.615 0.00 0.00 0.00 2.83
2952 3026 3.254166 TCTCAACTTCATTCTTGCAAGGC 59.746 43.478 25.73 0.00 0.00 4.35
3077 3155 4.401022 TCGTAACAGAAGAACCTCTGGTA 58.599 43.478 5.65 0.19 46.02 3.25
3120 3198 5.255397 ACCAACCTCCAGATACAAATCAA 57.745 39.130 0.00 0.00 34.28 2.57
3198 3276 5.755375 CAGGTAGTGAAACATGATAATCGCT 59.245 40.000 0.00 6.43 41.43 4.93
3233 3311 8.141268 CCTAAGTTACTTGGAATGCTTCAAAAA 58.859 33.333 10.06 0.00 0.00 1.94
3234 3312 7.255801 CCCTAAGTTACTTGGAATGCTTCAAAA 60.256 37.037 10.06 0.00 0.00 2.44
3262 3340 7.713734 ATATGCATGGATTATTTCTCCCAAG 57.286 36.000 10.16 0.00 31.77 3.61
3288 3366 7.927048 TGTCTTGAATCATTCATTCTATGCAG 58.073 34.615 0.00 0.00 41.58 4.41
3387 3465 7.611770 TGCATCAGAGCTTTAGTAAAAGACTA 58.388 34.615 2.15 0.00 44.14 2.59
3388 3466 6.467677 TGCATCAGAGCTTTAGTAAAAGACT 58.532 36.000 2.15 0.00 44.14 3.24
3488 3569 5.467063 CAGGGAAAACAAGTACTTGAGTCTC 59.533 44.000 36.14 27.17 42.93 3.36
3928 4058 3.441572 GCATGGGTAGCAATGACATATCC 59.558 47.826 13.61 0.00 0.00 2.59
3941 4071 6.675026 CATCACATTAGAATTGCATGGGTAG 58.325 40.000 0.00 0.00 0.00 3.18
4165 4295 2.768253 TGGTTGTACATCAGAGGCTG 57.232 50.000 0.00 0.00 0.00 4.85
4292 4423 3.489180 TTAGTCTCAGTAGCGAAGTGC 57.511 47.619 0.00 0.00 46.98 4.40
4293 4424 5.220303 GCAAATTAGTCTCAGTAGCGAAGTG 60.220 44.000 0.00 0.00 0.00 3.16
4294 4425 4.865365 GCAAATTAGTCTCAGTAGCGAAGT 59.135 41.667 0.00 0.00 0.00 3.01
4295 4426 5.105752 AGCAAATTAGTCTCAGTAGCGAAG 58.894 41.667 0.00 0.00 0.00 3.79
4296 4427 5.073311 AGCAAATTAGTCTCAGTAGCGAA 57.927 39.130 0.00 0.00 0.00 4.70
4309 4440 3.795623 ATCAGCAGCCAAGCAAATTAG 57.204 42.857 0.00 0.00 36.85 1.73
4520 4651 3.243359 AGAACTTGGGCCTTCAAATGA 57.757 42.857 4.53 0.00 0.00 2.57
4615 4746 7.126421 AGAGCTCTCCAAACCTTTCATCTATTA 59.874 37.037 11.45 0.00 0.00 0.98
4983 5118 2.615447 CAGTGAAGTGAGAGCTTTGCAA 59.385 45.455 0.00 0.00 0.00 4.08
5108 5282 5.364157 GTCCTCTTCTAGTCATAACATGGGT 59.636 44.000 0.00 0.00 0.00 4.51
5146 5320 3.686726 GTCAGAACTCCGAGCATGAAAAT 59.313 43.478 0.00 0.00 0.00 1.82
5252 5491 7.495934 TGAATCAGCTTAGCCAAAGAGTATAAC 59.504 37.037 0.00 0.00 37.38 1.89
5260 5499 4.456911 TGACTTGAATCAGCTTAGCCAAAG 59.543 41.667 0.00 0.00 38.32 2.77
5383 5622 3.386726 TCCGGTGTCTTTTCTCTCTCAAA 59.613 43.478 0.00 0.00 0.00 2.69
5385 5624 2.594131 TCCGGTGTCTTTTCTCTCTCA 58.406 47.619 0.00 0.00 0.00 3.27
5386 5625 3.662247 TTCCGGTGTCTTTTCTCTCTC 57.338 47.619 0.00 0.00 0.00 3.20
5400 5639 3.744660 GGATATGAGATGCTTTTCCGGT 58.255 45.455 0.00 0.00 0.00 5.28
5401 5640 2.738846 CGGATATGAGATGCTTTTCCGG 59.261 50.000 0.00 0.00 39.72 5.14
5402 5641 3.653344 TCGGATATGAGATGCTTTTCCG 58.347 45.455 2.20 2.20 42.52 4.30
5428 5667 7.372714 TGTAGCGTCTGTAGTTTTTCTTGATA 58.627 34.615 0.00 0.00 0.00 2.15
5481 5720 9.227777 GTATAACCAAAAGAAGTTGACCAGTAT 57.772 33.333 0.00 0.00 0.00 2.12
5482 5721 8.212312 TGTATAACCAAAAGAAGTTGACCAGTA 58.788 33.333 0.00 0.00 0.00 2.74
5483 5722 7.012989 GTGTATAACCAAAAGAAGTTGACCAGT 59.987 37.037 0.00 0.00 0.00 4.00
5484 5723 7.360361 GTGTATAACCAAAAGAAGTTGACCAG 58.640 38.462 0.00 0.00 0.00 4.00
5505 5744 1.001048 CAAACTCTGTCGGACGGTGTA 60.001 52.381 21.14 1.47 31.66 2.90
5506 5745 0.249322 CAAACTCTGTCGGACGGTGT 60.249 55.000 16.65 16.65 33.10 4.16
5507 5746 0.031585 TCAAACTCTGTCGGACGGTG 59.968 55.000 16.14 15.78 0.00 4.94
5508 5747 0.748450 TTCAAACTCTGTCGGACGGT 59.252 50.000 16.14 6.18 0.00 4.83
5509 5748 1.860676 TTTCAAACTCTGTCGGACGG 58.139 50.000 10.78 10.78 0.00 4.79
5510 5749 3.062909 TGTTTTTCAAACTCTGTCGGACG 59.937 43.478 3.34 0.00 0.00 4.79
5511 5750 4.142773 TGTGTTTTTCAAACTCTGTCGGAC 60.143 41.667 0.00 0.00 0.00 4.79
5512 5751 4.004314 TGTGTTTTTCAAACTCTGTCGGA 58.996 39.130 1.33 0.00 0.00 4.55
5513 5752 4.095610 GTGTGTTTTTCAAACTCTGTCGG 58.904 43.478 1.33 0.00 31.90 4.79
5514 5753 4.969816 AGTGTGTTTTTCAAACTCTGTCG 58.030 39.130 1.33 0.00 40.27 4.35
5520 5759 6.084326 ACTGTTGAGTGTGTTTTTCAAACT 57.916 33.333 1.33 0.00 46.27 2.66
5521 5760 7.861176 TTACTGTTGAGTGTGTTTTTCAAAC 57.139 32.000 0.00 0.00 33.10 2.93
5522 5761 8.300286 TCATTACTGTTGAGTGTGTTTTTCAAA 58.700 29.630 0.00 0.00 33.10 2.69
5523 5762 7.821652 TCATTACTGTTGAGTGTGTTTTTCAA 58.178 30.769 0.00 0.00 33.21 2.69
5524 5763 7.384439 TCATTACTGTTGAGTGTGTTTTTCA 57.616 32.000 0.00 0.00 33.21 2.69
5525 5764 8.682128 TTTCATTACTGTTGAGTGTGTTTTTC 57.318 30.769 0.00 0.00 33.21 2.29
5526 5765 9.139174 CTTTTCATTACTGTTGAGTGTGTTTTT 57.861 29.630 0.00 0.00 33.21 1.94
5527 5766 7.759433 CCTTTTCATTACTGTTGAGTGTGTTTT 59.241 33.333 0.00 0.00 33.21 2.43
5528 5767 7.257722 CCTTTTCATTACTGTTGAGTGTGTTT 58.742 34.615 0.00 0.00 33.21 2.83
5529 5768 6.183360 CCCTTTTCATTACTGTTGAGTGTGTT 60.183 38.462 0.00 0.00 33.21 3.32
5530 5769 5.299279 CCCTTTTCATTACTGTTGAGTGTGT 59.701 40.000 0.00 0.00 33.21 3.72
5531 5770 5.530915 TCCCTTTTCATTACTGTTGAGTGTG 59.469 40.000 0.00 0.00 33.21 3.82
5532 5771 5.690865 TCCCTTTTCATTACTGTTGAGTGT 58.309 37.500 0.00 0.00 33.21 3.55
5533 5772 6.207417 ACATCCCTTTTCATTACTGTTGAGTG 59.793 38.462 0.00 0.00 33.21 3.51
5534 5773 6.306987 ACATCCCTTTTCATTACTGTTGAGT 58.693 36.000 0.00 0.00 36.07 3.41
5535 5774 6.656693 AGACATCCCTTTTCATTACTGTTGAG 59.343 38.462 0.00 0.00 0.00 3.02
5536 5775 6.430925 CAGACATCCCTTTTCATTACTGTTGA 59.569 38.462 0.00 0.00 0.00 3.18
5537 5776 6.615088 CAGACATCCCTTTTCATTACTGTTG 58.385 40.000 0.00 0.00 0.00 3.33
5538 5777 5.183904 GCAGACATCCCTTTTCATTACTGTT 59.816 40.000 0.00 0.00 0.00 3.16
5539 5778 4.702131 GCAGACATCCCTTTTCATTACTGT 59.298 41.667 0.00 0.00 0.00 3.55
5540 5779 4.701651 TGCAGACATCCCTTTTCATTACTG 59.298 41.667 0.00 0.00 0.00 2.74
5541 5780 4.922206 TGCAGACATCCCTTTTCATTACT 58.078 39.130 0.00 0.00 0.00 2.24
5542 5781 5.643379 TTGCAGACATCCCTTTTCATTAC 57.357 39.130 0.00 0.00 0.00 1.89
5543 5782 5.538053 TGTTTGCAGACATCCCTTTTCATTA 59.462 36.000 5.87 0.00 0.00 1.90
5544 5783 4.344679 TGTTTGCAGACATCCCTTTTCATT 59.655 37.500 5.87 0.00 0.00 2.57
5545 5784 3.896888 TGTTTGCAGACATCCCTTTTCAT 59.103 39.130 5.87 0.00 0.00 2.57
5546 5785 3.068024 GTGTTTGCAGACATCCCTTTTCA 59.932 43.478 13.78 0.00 0.00 2.69
5547 5786 3.552890 GGTGTTTGCAGACATCCCTTTTC 60.553 47.826 13.78 0.00 0.00 2.29
5548 5787 2.365293 GGTGTTTGCAGACATCCCTTTT 59.635 45.455 13.78 0.00 0.00 2.27
5549 5788 1.963515 GGTGTTTGCAGACATCCCTTT 59.036 47.619 13.78 0.00 0.00 3.11
5550 5789 1.145738 AGGTGTTTGCAGACATCCCTT 59.854 47.619 16.49 0.00 30.84 3.95
5551 5790 0.773644 AGGTGTTTGCAGACATCCCT 59.226 50.000 16.49 14.23 30.84 4.20
5552 5791 1.168714 GAGGTGTTTGCAGACATCCC 58.831 55.000 16.49 12.24 30.84 3.85
5553 5792 0.798776 CGAGGTGTTTGCAGACATCC 59.201 55.000 16.49 16.35 30.84 3.51
5554 5793 0.166814 GCGAGGTGTTTGCAGACATC 59.833 55.000 13.78 13.17 36.12 3.06
5555 5794 1.237285 GGCGAGGTGTTTGCAGACAT 61.237 55.000 13.78 0.00 37.99 3.06
5556 5795 1.891919 GGCGAGGTGTTTGCAGACA 60.892 57.895 5.87 5.87 37.99 3.41
5557 5796 1.237285 ATGGCGAGGTGTTTGCAGAC 61.237 55.000 0.00 0.00 37.99 3.51
5558 5797 0.323302 TATGGCGAGGTGTTTGCAGA 59.677 50.000 0.00 0.00 37.99 4.26
5559 5798 0.447801 GTATGGCGAGGTGTTTGCAG 59.552 55.000 0.00 0.00 37.99 4.41
5560 5799 0.250510 TGTATGGCGAGGTGTTTGCA 60.251 50.000 0.00 0.00 37.99 4.08
5561 5800 0.878416 TTGTATGGCGAGGTGTTTGC 59.122 50.000 0.00 0.00 35.26 3.68
5562 5801 4.273005 GTATTGTATGGCGAGGTGTTTG 57.727 45.455 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.