Multiple sequence alignment - TraesCS6B01G412100

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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 TraesCS6B01G412100 chr6B 100.000 2888 0 0 1 2888 685635044 685637931 0.000000e+00 5334
1 TraesCS6B01G412100 chr6D 88.351 1631 122 44 100 1701 451665609 451664018 0.000000e+00 1897
2 TraesCS6B01G412100 chr6D 88.684 433 25 8 1757 2175 451664016 451663594 9.230000e-140 507
3 TraesCS6B01G412100 chr6D 91.304 92 8 0 1 92 451668591 451668500 3.020000e-25 126
4 TraesCS6B01G412100 chr6A 88.671 1121 69 32 106 1188 597284036 597285136 0.000000e+00 1314
5 TraesCS6B01G412100 chr6A 84.975 1198 134 27 1708 2886 597285889 597287059 0.000000e+00 1173
6 TraesCS6B01G412100 chr6A 86.481 466 38 15 1199 1663 597285451 597285892 3.340000e-134 488
7 TraesCS6B01G412100 chr2B 80.544 699 89 31 643 1314 374242715 374242037 7.190000e-136 494
8 TraesCS6B01G412100 chr2B 90.909 88 8 0 1381 1468 374242010 374241923 5.060000e-23 119
9 TraesCS6B01G412100 chr2D 95.817 263 11 0 1398 1660 325807956 325808218 2.660000e-115 425
10 TraesCS6B01G412100 chr2D 79.149 705 77 33 627 1314 306257908 306257257 9.570000e-115 424
11 TraesCS6B01G412100 chr2D 81.780 472 43 25 1710 2157 306256953 306256501 3.540000e-94 355
12 TraesCS6B01G412100 chr2D 84.247 292 26 12 1381 1670 306257230 306256957 1.710000e-67 267
13 TraesCS6B01G412100 chr2A 84.797 296 33 6 1576 1864 385299151 385298861 1.310000e-73 287


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 TraesCS6B01G412100 chr6B 685635044 685637931 2887 False 5334.000000 5334 100.000000 1 2888 1 chr6B.!!$F1 2887
1 TraesCS6B01G412100 chr6D 451663594 451668591 4997 True 843.333333 1897 89.446333 1 2175 3 chr6D.!!$R1 2174
2 TraesCS6B01G412100 chr6A 597284036 597287059 3023 False 991.666667 1314 86.709000 106 2886 3 chr6A.!!$F1 2780
3 TraesCS6B01G412100 chr2B 374241923 374242715 792 True 306.500000 494 85.726500 643 1468 2 chr2B.!!$R1 825
4 TraesCS6B01G412100 chr2D 306256501 306257908 1407 True 348.666667 424 81.725333 627 2157 3 chr2D.!!$R1 1530

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
28 29 0.448990 CCATGTGACTGGCGACAATG 59.551 55.0 0.0 0.0 42.06 2.82 F
1033 3963 0.109597 CATGGCGTCTTTGGTTCTGC 60.110 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 4575 0.179073 CCATAGACTGACCTTGGCCG 60.179 60.0 0.0 0.0 0.00 6.13 R
2611 5929 0.307760 GGCACAAAGTGTCCGAACAG 59.692 55.0 0.0 0.0 35.64 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.448990 CCATGTGACTGGCGACAATG 59.551 55.000 0.00 0.00 42.06 2.82
29 30 1.441738 CATGTGACTGGCGACAATGA 58.558 50.000 0.00 0.00 42.06 2.57
41 42 0.685458 GACAATGATGGGCTTGGGCT 60.685 55.000 0.00 0.00 38.73 5.19
47 48 3.426309 ATGGGCTTGGGCTGATCCG 62.426 63.158 0.00 0.00 38.73 4.18
52 53 1.904771 CTTGGGCTGATCCGGTGTA 59.095 57.895 0.00 0.00 34.94 2.90
89 90 8.723942 GTGAGTAACCATCTATCTGACAAAAT 57.276 34.615 0.00 0.00 0.00 1.82
92 93 9.553064 GAGTAACCATCTATCTGACAAAATGAT 57.447 33.333 0.00 0.00 0.00 2.45
94 95 9.113838 GTAACCATCTATCTGACAAAATGATGT 57.886 33.333 0.00 0.00 35.90 3.06
96 97 8.668510 ACCATCTATCTGACAAAATGATGTAC 57.331 34.615 0.00 0.00 32.57 2.90
97 98 8.489489 ACCATCTATCTGACAAAATGATGTACT 58.511 33.333 0.00 0.00 32.57 2.73
100 101 8.948631 TCTATCTGACAAAATGATGTACTTCC 57.051 34.615 6.32 0.00 32.57 3.46
104 105 8.722480 TCTGACAAAATGATGTACTTCCTATG 57.278 34.615 6.32 3.69 32.57 2.23
176 3059 5.484173 TTTTTAGCATGCAAGATACTCGG 57.516 39.130 21.98 0.00 0.00 4.63
267 3152 5.717119 AGCTCCTCAAATGTTTTATGCAAG 58.283 37.500 0.00 0.00 0.00 4.01
282 3167 2.056094 GCAAGAGGTGTGCAAATCAC 57.944 50.000 0.00 0.00 45.82 3.06
442 3341 8.232913 TGCCCTTAATTCATCCTATGTAAAAC 57.767 34.615 0.00 0.00 0.00 2.43
525 3428 2.351706 AAAAAGTGACTGGCCGGTTA 57.648 45.000 20.79 12.87 0.00 2.85
549 3452 3.559238 AATTTCAGTCGCATGTCCAAC 57.441 42.857 0.00 0.00 0.00 3.77
567 3470 3.696548 CCAACTGAGGCTCCCTAATTTTC 59.303 47.826 12.86 0.00 31.76 2.29
605 3509 3.243035 TGCGTACAAATAGCATTGCCATC 60.243 43.478 4.70 0.00 35.81 3.51
617 3521 4.400567 AGCATTGCCATCTTCTTTCCTTAC 59.599 41.667 4.70 0.00 0.00 2.34
621 3525 7.201857 GCATTGCCATCTTCTTTCCTTACTAAT 60.202 37.037 0.00 0.00 0.00 1.73
622 3526 9.342308 CATTGCCATCTTCTTTCCTTACTAATA 57.658 33.333 0.00 0.00 0.00 0.98
623 3527 9.920946 ATTGCCATCTTCTTTCCTTACTAATAA 57.079 29.630 0.00 0.00 0.00 1.40
624 3528 9.920946 TTGCCATCTTCTTTCCTTACTAATAAT 57.079 29.630 0.00 0.00 0.00 1.28
625 3529 9.342308 TGCCATCTTCTTTCCTTACTAATAATG 57.658 33.333 0.00 0.00 0.00 1.90
680 3584 4.597404 AAGATAAGATCATCTGCAGCGA 57.403 40.909 9.47 8.57 35.42 4.93
681 3585 4.597404 AGATAAGATCATCTGCAGCGAA 57.403 40.909 9.47 0.00 33.93 4.70
693 3597 1.269448 TGCAGCGAAACTCCCAAAATC 59.731 47.619 0.00 0.00 0.00 2.17
702 3606 1.003233 ACTCCCAAAATCGACCTGTCC 59.997 52.381 0.00 0.00 0.00 4.02
813 3719 3.093278 GGCGTTTCTGATCAGCCG 58.907 61.111 18.36 18.64 38.28 5.52
829 3735 1.743252 CCGAGCAAGAGACAAGGGC 60.743 63.158 0.00 0.00 0.00 5.19
882 3789 4.339247 CCATTATAGCAACCTTCCAACCTG 59.661 45.833 0.00 0.00 0.00 4.00
887 3794 2.430694 AGCAACCTTCCAACCTGAAAAC 59.569 45.455 0.00 0.00 0.00 2.43
892 3799 2.290641 CCTTCCAACCTGAAAACAGACG 59.709 50.000 0.00 0.00 0.00 4.18
957 3879 1.927174 CATTAGCCGTGAGAGAAACCG 59.073 52.381 0.00 0.00 0.00 4.44
982 3904 2.968574 TGAACTGAAAGAGAGTGAGCCT 59.031 45.455 0.00 0.00 37.43 4.58
983 3905 4.152647 TGAACTGAAAGAGAGTGAGCCTA 58.847 43.478 0.00 0.00 37.43 3.93
984 3906 4.219507 TGAACTGAAAGAGAGTGAGCCTAG 59.780 45.833 0.00 0.00 37.43 3.02
985 3907 3.773560 ACTGAAAGAGAGTGAGCCTAGT 58.226 45.455 0.00 0.00 37.43 2.57
986 3908 3.509575 ACTGAAAGAGAGTGAGCCTAGTG 59.490 47.826 0.00 0.00 37.43 2.74
1033 3963 0.109597 CATGGCGTCTTTGGTTCTGC 60.110 55.000 0.00 0.00 0.00 4.26
1034 3964 0.250901 ATGGCGTCTTTGGTTCTGCT 60.251 50.000 0.00 0.00 0.00 4.24
1035 3965 1.165907 TGGCGTCTTTGGTTCTGCTG 61.166 55.000 0.00 0.00 0.00 4.41
1061 3994 2.534042 TCTCCCTCTCCACTGTTAGG 57.466 55.000 0.00 0.00 0.00 2.69
1163 4102 3.622060 CTGCCCAACCCTACGGTGG 62.622 68.421 0.00 0.00 43.71 4.61
1182 4121 4.873827 GGTGGGTATATACATGCCGTAATG 59.126 45.833 14.70 0.00 37.78 1.90
1196 4448 3.614616 GCCGTAATGTTCAGAGTTGAGAG 59.385 47.826 0.00 0.00 34.15 3.20
1227 4485 6.751888 AGCATAAATTTTACCTTCGCATGAAC 59.248 34.615 0.00 0.00 0.00 3.18
1230 4488 9.781834 CATAAATTTTACCTTCGCATGAACTTA 57.218 29.630 0.00 0.00 0.00 2.24
1334 4610 4.019591 GTCTATGGACCTGGGTGTACTTTT 60.020 45.833 0.00 0.00 36.53 2.27
1345 4621 6.238648 CCTGGGTGTACTTTTTGTTACTTCTG 60.239 42.308 0.00 0.00 0.00 3.02
1412 4688 6.195244 CACTGTTGTGCATCGCTTAATAATTC 59.805 38.462 0.00 0.00 37.38 2.17
1421 4697 8.196771 TGCATCGCTTAATAATTCTCCAATTTT 58.803 29.630 0.00 0.00 33.95 1.82
1506 4782 2.007113 AAACACGCGAACCCAAACCC 62.007 55.000 15.93 0.00 0.00 4.11
1670 4946 3.291101 TTGGAGGTACGCGCAGACC 62.291 63.158 17.85 17.85 35.83 3.85
1697 4973 6.016276 ACTGGCATCTCGAAACAAATAAGTTT 60.016 34.615 0.00 0.00 43.90 2.66
1701 4977 7.270579 GGCATCTCGAAACAAATAAGTTTACAC 59.729 37.037 0.00 0.00 41.48 2.90
1702 4978 8.015658 GCATCTCGAAACAAATAAGTTTACACT 58.984 33.333 0.00 0.00 41.48 3.55
1703 4979 9.318041 CATCTCGAAACAAATAAGTTTACACTG 57.682 33.333 0.00 0.00 41.48 3.66
1704 4980 7.349711 TCTCGAAACAAATAAGTTTACACTGC 58.650 34.615 0.00 0.00 41.48 4.40
1705 4981 7.011576 TCTCGAAACAAATAAGTTTACACTGCA 59.988 33.333 0.00 0.00 41.48 4.41
1706 4982 6.908284 TCGAAACAAATAAGTTTACACTGCAC 59.092 34.615 0.00 0.00 41.48 4.57
1720 4996 3.371591 ACACTGCACGACGTTTCTTTAAA 59.628 39.130 0.00 0.00 0.00 1.52
1755 5031 9.927668 AAAATGTTTACTGTATCCCAAATTCAG 57.072 29.630 0.00 0.00 0.00 3.02
1780 5056 9.981114 AGTAAATTTGACATTTTAGTTTCCTGG 57.019 29.630 0.00 0.00 0.00 4.45
1784 5064 6.385649 TTGACATTTTAGTTTCCTGGTGAC 57.614 37.500 0.00 0.00 0.00 3.67
1828 5108 1.722034 TCTCTGGGCAGTCACTCTTT 58.278 50.000 0.00 0.00 0.00 2.52
1840 5120 5.303971 CAGTCACTCTTTCTGGAATTCTGT 58.696 41.667 5.23 0.00 0.00 3.41
1845 5125 4.141158 ACTCTTTCTGGAATTCTGTTGGGT 60.141 41.667 5.23 0.00 0.00 4.51
1964 5251 5.565592 ACCGTAACGACATATGTAACTGA 57.434 39.130 8.71 0.00 0.00 3.41
2021 5317 9.106070 ACCGACAATTAATTACTAATGTTCTCC 57.894 33.333 0.00 0.00 30.24 3.71
2022 5318 9.326413 CCGACAATTAATTACTAATGTTCTCCT 57.674 33.333 0.00 0.00 30.24 3.69
2088 5384 2.001812 TGAGCTCTCTCGCAAATGTC 57.998 50.000 16.19 0.00 42.26 3.06
2164 5475 9.994432 GTAAAGATGAAGATAAAGAACATGGTG 57.006 33.333 0.00 0.00 0.00 4.17
2194 5506 6.016108 CACCTAAGTTACTAGGGCATCTCTAC 60.016 46.154 10.86 0.00 42.57 2.59
2200 5512 1.796190 TAGGGCATCTCTACGCAGCG 61.796 60.000 14.82 14.82 0.00 5.18
2210 5522 3.768185 TACGCAGCGATTCGGCTCC 62.768 63.158 24.65 0.00 42.53 4.70
2211 5523 4.880537 CGCAGCGATTCGGCTCCT 62.881 66.667 9.98 0.00 42.53 3.69
2213 5525 2.496341 CAGCGATTCGGCTCCTGA 59.504 61.111 8.34 0.00 42.53 3.86
2214 5526 1.591059 CAGCGATTCGGCTCCTGAG 60.591 63.158 8.34 0.00 42.53 3.35
2228 5540 1.007600 TCCTGAGCTCATCTTCTCCCA 59.992 52.381 18.63 0.00 0.00 4.37
2234 5546 4.226846 TGAGCTCATCTTCTCCCAAGAATT 59.773 41.667 13.74 0.00 40.68 2.17
2289 5604 3.049227 TGGAACATGATCGAGTGCG 57.951 52.632 0.00 0.00 39.35 5.34
2297 5612 0.523335 TGATCGAGTGCGTGATGTCG 60.523 55.000 0.00 0.00 38.98 4.35
2308 5623 2.724839 GCGTGATGTCGGTGTCAAATTC 60.725 50.000 0.00 0.00 0.00 2.17
2313 5628 0.515564 GTCGGTGTCAAATTCGGTGG 59.484 55.000 0.00 0.00 0.00 4.61
2317 5632 2.496111 GGTGTCAAATTCGGTGGTGTA 58.504 47.619 0.00 0.00 0.00 2.90
2323 5638 2.413310 AATTCGGTGGTGTATGGACC 57.587 50.000 0.00 0.00 36.43 4.46
2341 5656 0.895530 CCTTTGAGTAGGTCTCGGCA 59.104 55.000 0.00 0.00 45.46 5.69
2342 5657 1.134965 CCTTTGAGTAGGTCTCGGCAG 60.135 57.143 0.00 0.00 45.46 4.85
2343 5658 1.819288 CTTTGAGTAGGTCTCGGCAGA 59.181 52.381 0.00 0.00 45.46 4.26
2370 5685 2.661718 TGGGGGTTTGTGAGAAAGTTC 58.338 47.619 0.00 0.00 0.00 3.01
2372 5687 3.230976 GGGGGTTTGTGAGAAAGTTCAT 58.769 45.455 0.00 0.00 0.00 2.57
2374 5689 4.501400 GGGGGTTTGTGAGAAAGTTCATTG 60.501 45.833 0.00 0.00 0.00 2.82
2379 5694 6.473455 GGTTTGTGAGAAAGTTCATTGTTCAG 59.527 38.462 0.00 0.00 0.00 3.02
2381 5696 4.036734 TGTGAGAAAGTTCATTGTTCAGGC 59.963 41.667 0.00 0.00 0.00 4.85
2382 5697 4.036734 GTGAGAAAGTTCATTGTTCAGGCA 59.963 41.667 0.00 0.00 0.00 4.75
2383 5698 4.828939 TGAGAAAGTTCATTGTTCAGGCAT 59.171 37.500 0.00 0.00 0.00 4.40
2384 5699 5.302568 TGAGAAAGTTCATTGTTCAGGCATT 59.697 36.000 0.00 0.00 0.00 3.56
2385 5700 5.535333 AGAAAGTTCATTGTTCAGGCATTG 58.465 37.500 0.00 0.00 0.00 2.82
2386 5701 4.942761 AAGTTCATTGTTCAGGCATTGT 57.057 36.364 0.00 0.00 0.00 2.71
2387 5702 4.942761 AGTTCATTGTTCAGGCATTGTT 57.057 36.364 0.00 0.00 0.00 2.83
2388 5703 5.280654 AGTTCATTGTTCAGGCATTGTTT 57.719 34.783 0.00 0.00 0.00 2.83
2389 5704 5.051816 AGTTCATTGTTCAGGCATTGTTTG 58.948 37.500 0.00 0.00 0.00 2.93
2390 5705 3.992643 TCATTGTTCAGGCATTGTTTGG 58.007 40.909 0.00 0.00 0.00 3.28
2391 5706 3.640498 TCATTGTTCAGGCATTGTTTGGA 59.360 39.130 0.00 0.00 0.00 3.53
2440 5755 1.049289 ACGGGCTCCTTAGATGTCCC 61.049 60.000 0.00 0.00 0.00 4.46
2443 5758 1.777272 GGGCTCCTTAGATGTCCCAAT 59.223 52.381 0.00 0.00 34.01 3.16
2446 5761 3.391296 GGCTCCTTAGATGTCCCAATACA 59.609 47.826 0.00 0.00 0.00 2.29
2448 5763 5.059833 GCTCCTTAGATGTCCCAATACAAG 58.940 45.833 0.00 0.00 32.02 3.16
2466 5781 4.337145 ACAAGTAAATTTGCCCGGACATA 58.663 39.130 0.73 0.00 0.00 2.29
2551 5869 9.504708 TTTTTAATTTACTGTTCATACTCGGGA 57.495 29.630 0.00 0.00 0.00 5.14
2584 5902 5.135383 CCTGGGCTCAAATGAATATTCTCA 58.865 41.667 16.24 0.00 0.00 3.27
2589 5907 6.127366 GGGCTCAAATGAATATTCTCAAACCA 60.127 38.462 16.24 0.00 0.00 3.67
2590 5908 7.418254 GGGCTCAAATGAATATTCTCAAACCAT 60.418 37.037 16.24 0.00 0.00 3.55
2592 5910 7.650903 GCTCAAATGAATATTCTCAAACCATCC 59.349 37.037 16.24 0.00 0.00 3.51
2593 5911 7.706159 TCAAATGAATATTCTCAAACCATCCG 58.294 34.615 16.24 0.00 0.00 4.18
2602 5920 5.075858 TCTCAAACCATCCGTAAACGTAT 57.924 39.130 1.41 0.00 37.74 3.06
2603 5921 4.865925 TCTCAAACCATCCGTAAACGTATG 59.134 41.667 1.41 1.47 35.79 2.39
2604 5922 4.818642 TCAAACCATCCGTAAACGTATGA 58.181 39.130 9.33 0.00 37.81 2.15
2608 5926 5.581126 ACCATCCGTAAACGTATGAACTA 57.419 39.130 9.33 0.00 37.81 2.24
2611 5929 5.230726 CCATCCGTAAACGTATGAACTACAC 59.769 44.000 9.33 0.00 37.81 2.90
2612 5930 5.627499 TCCGTAAACGTATGAACTACACT 57.373 39.130 1.41 0.00 37.74 3.55
2621 5939 4.614306 CGTATGAACTACACTGTTCGGACA 60.614 45.833 0.00 0.00 46.59 4.02
2622 5940 3.088194 TGAACTACACTGTTCGGACAC 57.912 47.619 0.00 0.00 46.59 3.67
2626 5944 3.454375 ACTACACTGTTCGGACACTTTG 58.546 45.455 0.00 0.00 0.00 2.77
2629 5947 1.014352 ACTGTTCGGACACTTTGTGC 58.986 50.000 0.00 0.00 36.98 4.57
2634 5952 1.966451 CGGACACTTTGTGCCCTCC 60.966 63.158 1.93 0.00 33.89 4.30
2637 5955 1.620822 GACACTTTGTGCCCTCCAAT 58.379 50.000 0.00 0.00 36.98 3.16
2655 5973 3.489059 CCAATACCATGCATCAAACGTCC 60.489 47.826 0.00 0.00 0.00 4.79
2656 5974 2.481289 TACCATGCATCAAACGTCCA 57.519 45.000 0.00 0.00 0.00 4.02
2657 5975 0.881118 ACCATGCATCAAACGTCCAC 59.119 50.000 0.00 0.00 0.00 4.02
2662 5980 1.908066 GCATCAAACGTCCACGGACC 61.908 60.000 10.61 0.00 44.95 4.46
2663 5981 1.373748 ATCAAACGTCCACGGACCG 60.374 57.895 13.61 13.61 44.95 4.79
2668 5986 4.415332 CGTCCACGGACCGGTCTG 62.415 72.222 36.59 36.59 41.76 3.51
2675 5993 4.736896 GGACCGGTCTGCACGTCC 62.737 72.222 32.52 11.82 0.00 4.79
2706 6024 1.112916 AACGGGAAGCAAAGTTGGGG 61.113 55.000 0.00 0.00 0.00 4.96
2707 6025 2.275380 CGGGAAGCAAAGTTGGGGG 61.275 63.158 0.00 0.00 0.00 5.40
2709 6027 0.471022 GGGAAGCAAAGTTGGGGGAA 60.471 55.000 0.00 0.00 0.00 3.97
2710 6028 0.969149 GGAAGCAAAGTTGGGGGAAG 59.031 55.000 0.00 0.00 0.00 3.46
2719 6037 0.539669 GTTGGGGGAAGTTGTGGGAG 60.540 60.000 0.00 0.00 0.00 4.30
2722 6040 1.423794 GGGGGAAGTTGTGGGAGTCA 61.424 60.000 0.00 0.00 0.00 3.41
2723 6041 0.036875 GGGGAAGTTGTGGGAGTCAG 59.963 60.000 0.00 0.00 0.00 3.51
2724 6042 0.036875 GGGAAGTTGTGGGAGTCAGG 59.963 60.000 0.00 0.00 0.00 3.86
2753 6071 4.509737 GTAGGCGCTCGACACCCC 62.510 72.222 7.64 0.00 0.00 4.95
2761 6079 0.672711 GCTCGACACCCCAAACCTAC 60.673 60.000 0.00 0.00 0.00 3.18
2764 6082 1.381463 GACACCCCAAACCTACCCC 59.619 63.158 0.00 0.00 0.00 4.95
2772 6090 1.272258 CCAAACCTACCCCAAACCGAT 60.272 52.381 0.00 0.00 0.00 4.18
2774 6092 0.323087 AACCTACCCCAAACCGATGC 60.323 55.000 0.00 0.00 0.00 3.91
2799 6117 2.612721 GCCCACATGTTTGGACAATTCC 60.613 50.000 14.11 0.00 43.19 3.01
2811 6129 3.638484 GGACAATTCCACACTTTTTCCG 58.362 45.455 0.00 0.00 42.30 4.30
2812 6130 3.067601 GGACAATTCCACACTTTTTCCGT 59.932 43.478 0.00 0.00 42.30 4.69
2813 6131 4.040445 ACAATTCCACACTTTTTCCGTG 57.960 40.909 0.00 0.00 38.32 4.94
2822 6141 2.096248 ACTTTTTCCGTGTGAAAGCCA 58.904 42.857 0.00 0.00 43.57 4.75
2827 6146 1.528309 CCGTGTGAAAGCCACCCTT 60.528 57.895 0.00 0.00 45.09 3.95
2841 6160 2.558359 CCACCCTTTCCATGTTGTCTTC 59.442 50.000 0.00 0.00 0.00 2.87
2842 6161 3.221771 CACCCTTTCCATGTTGTCTTCA 58.778 45.455 0.00 0.00 0.00 3.02
2851 6170 2.347697 TGTTGTCTTCACTCCGATCG 57.652 50.000 8.51 8.51 0.00 3.69
2853 6172 0.108804 TTGTCTTCACTCCGATCGCC 60.109 55.000 10.32 0.00 0.00 5.54
2872 6191 4.489771 CCGCCACCCATCCCAGTC 62.490 72.222 0.00 0.00 0.00 3.51
2886 6205 4.324991 AGTCCCCACCCGTTTCGC 62.325 66.667 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.441738 CATCATTGTCGCCAGTCACA 58.558 50.000 0.00 0.00 0.00 3.58
13 14 0.729116 CCATCATTGTCGCCAGTCAC 59.271 55.000 0.00 0.00 0.00 3.67
28 29 1.530183 GGATCAGCCCAAGCCCATC 60.530 63.158 0.00 0.00 41.25 3.51
29 30 2.605299 GGATCAGCCCAAGCCCAT 59.395 61.111 0.00 0.00 41.25 4.00
95 96 9.793259 TTCTTGACTTTATTGTTCATAGGAAGT 57.207 29.630 0.00 0.00 32.62 3.01
176 3059 3.423154 GCACACACCTAGCGCACC 61.423 66.667 11.47 0.00 0.00 5.01
205 3089 6.533730 ACAGGTCTTCAAATGTCTTATCACA 58.466 36.000 0.00 0.00 0.00 3.58
236 3121 4.537135 ACATTTGAGGAGCTCGTAGAAA 57.463 40.909 9.29 11.51 34.09 2.52
237 3122 4.537135 AACATTTGAGGAGCTCGTAGAA 57.463 40.909 9.29 7.58 34.09 2.10
252 3137 4.990426 GCACACCTCTTGCATAAAACATTT 59.010 37.500 0.00 0.00 39.93 2.32
541 3444 0.548682 AGGGAGCCTCAGTTGGACAT 60.549 55.000 0.00 0.00 0.00 3.06
549 3452 6.659242 TGTAAAAGAAAATTAGGGAGCCTCAG 59.341 38.462 0.00 0.00 34.61 3.35
586 3490 6.382869 AGAAGATGGCAATGCTATTTGTAC 57.617 37.500 5.37 0.00 27.76 2.90
623 3527 9.529325 CATCAGAATATGACAATGCTTTTTCAT 57.471 29.630 15.69 15.69 41.91 2.57
624 3528 8.525316 ACATCAGAATATGACAATGCTTTTTCA 58.475 29.630 3.92 3.92 41.91 2.69
625 3529 8.922058 ACATCAGAATATGACAATGCTTTTTC 57.078 30.769 0.00 0.00 41.91 2.29
675 3579 1.804151 TCGATTTTGGGAGTTTCGCTG 59.196 47.619 0.00 0.00 0.00 5.18
680 3584 3.146847 GACAGGTCGATTTTGGGAGTTT 58.853 45.455 0.00 0.00 0.00 2.66
681 3585 2.552373 GGACAGGTCGATTTTGGGAGTT 60.552 50.000 0.00 0.00 0.00 3.01
693 3597 2.675423 TCCCTCACGGACAGGTCG 60.675 66.667 0.00 0.00 34.86 4.79
744 3650 2.956333 CGAGGGTTTCACCTTCCTTTTT 59.044 45.455 0.00 0.00 40.91 1.94
813 3719 0.036022 ACAGCCCTTGTCTCTTGCTC 59.964 55.000 0.00 0.00 33.87 4.26
829 3735 2.002586 GGTCCATGATCACGTGAACAG 58.997 52.381 28.66 20.67 35.25 3.16
892 3799 0.107945 GGGAGTGGCAGACAGTGATC 60.108 60.000 0.00 0.00 31.34 2.92
920 3842 6.516527 CGGCTAATGCATGGGTTTAAATACAT 60.517 38.462 0.00 0.00 41.91 2.29
957 3879 5.106752 GGCTCACTCTCTTTCAGTTCAATTC 60.107 44.000 0.00 0.00 0.00 2.17
982 3904 4.058124 GACATGTTTGTGCTCACTCACTA 58.942 43.478 0.00 0.00 35.79 2.74
983 3905 2.874701 GACATGTTTGTGCTCACTCACT 59.125 45.455 0.00 0.00 35.79 3.41
984 3906 2.874701 AGACATGTTTGTGCTCACTCAC 59.125 45.455 0.00 0.00 35.79 3.51
985 3907 2.874086 CAGACATGTTTGTGCTCACTCA 59.126 45.455 8.19 0.00 35.79 3.41
986 3908 2.350197 GCAGACATGTTTGTGCTCACTC 60.350 50.000 16.90 0.00 35.79 3.51
1033 3963 2.093235 GTGGAGAGGGAGATGGTTTCAG 60.093 54.545 0.00 0.00 0.00 3.02
1034 3964 1.909302 GTGGAGAGGGAGATGGTTTCA 59.091 52.381 0.00 0.00 0.00 2.69
1035 3965 2.093235 CAGTGGAGAGGGAGATGGTTTC 60.093 54.545 0.00 0.00 0.00 2.78
1163 4102 7.094631 TCTGAACATTACGGCATGTATATACC 58.905 38.462 10.38 0.00 36.30 2.73
1182 4121 3.677596 GCTTGTAGCTCTCAACTCTGAAC 59.322 47.826 0.00 0.00 38.45 3.18
1196 4448 6.196538 GCGAAGGTAAAATTTATGCTTGTAGC 59.803 38.462 0.00 0.00 42.82 3.58
1227 4485 4.154195 GCCCTACAAGTTGACACACATAAG 59.846 45.833 10.54 0.00 0.00 1.73
1230 4488 2.504367 GCCCTACAAGTTGACACACAT 58.496 47.619 10.54 0.00 0.00 3.21
1299 4575 0.179073 CCATAGACTGACCTTGGCCG 60.179 60.000 0.00 0.00 0.00 6.13
1300 4576 1.134371 GTCCATAGACTGACCTTGGCC 60.134 57.143 0.00 0.00 40.10 5.36
1368 4644 9.681692 CAACAGTGAAAATTTCATCAACTATCA 57.318 29.630 11.87 0.00 42.47 2.15
1369 4645 9.683069 ACAACAGTGAAAATTTCATCAACTATC 57.317 29.630 11.87 0.00 42.47 2.08
1370 4646 9.467258 CACAACAGTGAAAATTTCATCAACTAT 57.533 29.630 11.87 0.00 42.47 2.12
1371 4647 7.434897 GCACAACAGTGAAAATTTCATCAACTA 59.565 33.333 11.87 0.00 42.47 2.24
1412 4688 3.365472 CCTTCCCCTGGTAAAATTGGAG 58.635 50.000 0.00 0.00 0.00 3.86
1421 4697 1.987368 GTAAACACCCTTCCCCTGGTA 59.013 52.381 0.00 0.00 32.32 3.25
1506 4782 8.586273 CATTTGTTTTTACTGACAGAAACTGTG 58.414 33.333 10.08 6.59 45.44 3.66
1670 4946 1.428448 TTGTTTCGAGATGCCAGTCG 58.572 50.000 0.00 0.00 37.54 4.18
1697 4973 2.212869 AAGAAACGTCGTGCAGTGTA 57.787 45.000 0.00 0.00 0.00 2.90
1755 5031 9.758651 ACCAGGAAACTAAAATGTCAAATTTAC 57.241 29.630 0.00 0.00 40.21 2.01
1780 5056 5.420409 CCCTGTCTTTCCTGTATAAGTCAC 58.580 45.833 0.00 0.00 0.00 3.67
1784 5064 4.080863 ACAGCCCTGTCTTTCCTGTATAAG 60.081 45.833 0.00 0.00 40.24 1.73
1828 5108 1.780309 ACCACCCAACAGAATTCCAGA 59.220 47.619 0.65 0.00 0.00 3.86
1840 5120 0.550914 ACAAGAAGAGCACCACCCAA 59.449 50.000 0.00 0.00 0.00 4.12
1845 5125 4.623932 ATTGTAGACAAGAAGAGCACCA 57.376 40.909 1.09 0.00 39.47 4.17
1901 5183 2.992593 TCGCTGGTGCATATTTTGGTA 58.007 42.857 0.00 0.00 39.64 3.25
1918 5200 1.930567 ACCCGTACAATACACATCGC 58.069 50.000 0.00 0.00 0.00 4.58
1964 5251 4.080751 ACTGCGGGTACTGGTATTTACATT 60.081 41.667 0.00 0.00 33.56 2.71
1974 5261 2.684001 TTATTGACTGCGGGTACTGG 57.316 50.000 0.00 0.00 33.56 4.00
2020 5316 0.961857 TGCACCATGCTGCTTACAGG 60.962 55.000 13.92 0.00 45.31 4.00
2021 5317 0.883153 TTGCACCATGCTGCTTACAG 59.117 50.000 13.92 0.00 45.31 2.74
2022 5318 0.883153 CTTGCACCATGCTGCTTACA 59.117 50.000 13.92 0.00 45.31 2.41
2023 5319 0.457337 GCTTGCACCATGCTGCTTAC 60.457 55.000 13.92 0.10 45.31 2.34
2043 5339 5.156355 CGCTTGCACTGAAAACTTAATCAT 58.844 37.500 0.00 0.00 0.00 2.45
2088 5384 5.396484 CAAGTGCCATTGTAGAACTTGATG 58.604 41.667 5.83 0.00 46.81 3.07
2164 5475 4.587684 TGCCCTAGTAACTTAGGTGATAGC 59.412 45.833 0.00 0.00 38.86 2.97
2175 5486 2.885894 GCGTAGAGATGCCCTAGTAACT 59.114 50.000 0.00 0.00 0.00 2.24
2210 5522 2.765135 TCTTGGGAGAAGATGAGCTCAG 59.235 50.000 22.96 3.70 32.83 3.35
2211 5523 2.825223 TCTTGGGAGAAGATGAGCTCA 58.175 47.619 20.79 20.79 32.83 4.26
2213 5525 4.858965 AATTCTTGGGAGAAGATGAGCT 57.141 40.909 0.00 0.00 44.65 4.09
2214 5526 5.882557 TGTTAATTCTTGGGAGAAGATGAGC 59.117 40.000 0.00 0.00 44.65 4.26
2225 5537 8.885494 TTTTGAATTGACTGTTAATTCTTGGG 57.115 30.769 27.51 0.00 42.31 4.12
2269 5584 1.259770 CGCACTCGATCATGTTCCATG 59.740 52.381 0.00 0.00 38.10 3.66
2276 5591 1.520174 GACATCACGCACTCGATCATG 59.480 52.381 0.00 0.00 39.41 3.07
2280 5595 1.226688 CCGACATCACGCACTCGAT 60.227 57.895 0.00 0.00 39.41 3.59
2282 5597 2.126463 ACCGACATCACGCACTCG 60.126 61.111 0.00 0.00 42.43 4.18
2289 5604 2.159707 CCGAATTTGACACCGACATCAC 60.160 50.000 0.00 0.00 0.00 3.06
2297 5612 1.314730 ACACCACCGAATTTGACACC 58.685 50.000 0.00 0.00 0.00 4.16
2308 5623 1.002659 TCAAAGGTCCATACACCACCG 59.997 52.381 0.00 0.00 39.16 4.94
2323 5638 1.819288 TCTGCCGAGACCTACTCAAAG 59.181 52.381 0.00 0.00 45.14 2.77
2350 5665 2.024846 TGAACTTTCTCACAAACCCCCA 60.025 45.455 0.00 0.00 0.00 4.96
2355 5670 6.473455 CCTGAACAATGAACTTTCTCACAAAC 59.527 38.462 0.00 0.00 0.00 2.93
2356 5671 6.563422 CCTGAACAATGAACTTTCTCACAAA 58.437 36.000 0.00 0.00 0.00 2.83
2357 5672 5.450412 GCCTGAACAATGAACTTTCTCACAA 60.450 40.000 0.00 0.00 0.00 3.33
2358 5673 4.036734 GCCTGAACAATGAACTTTCTCACA 59.963 41.667 0.00 0.00 0.00 3.58
2364 5679 5.280654 ACAATGCCTGAACAATGAACTTT 57.719 34.783 0.00 0.00 0.00 2.66
2370 5685 3.742369 GTCCAAACAATGCCTGAACAATG 59.258 43.478 0.00 0.00 0.00 2.82
2372 5687 2.102252 GGTCCAAACAATGCCTGAACAA 59.898 45.455 0.00 0.00 0.00 2.83
2374 5689 1.335872 CGGTCCAAACAATGCCTGAAC 60.336 52.381 0.00 0.00 0.00 3.18
2379 5694 2.736192 CAAAATCGGTCCAAACAATGCC 59.264 45.455 0.00 0.00 0.00 4.40
2381 5696 5.982465 AAACAAAATCGGTCCAAACAATG 57.018 34.783 0.00 0.00 0.00 2.82
2382 5697 8.669946 AAATAAACAAAATCGGTCCAAACAAT 57.330 26.923 0.00 0.00 0.00 2.71
2383 5698 9.765795 ATAAATAAACAAAATCGGTCCAAACAA 57.234 25.926 0.00 0.00 0.00 2.83
2384 5699 9.765795 AATAAATAAACAAAATCGGTCCAAACA 57.234 25.926 0.00 0.00 0.00 2.83
2424 5739 3.391296 TGTATTGGGACATCTAAGGAGCC 59.609 47.826 0.00 0.00 39.30 4.70
2431 5746 8.682710 GCAAATTTACTTGTATTGGGACATCTA 58.317 33.333 0.00 0.00 39.30 1.98
2433 5748 6.756542 GGCAAATTTACTTGTATTGGGACATC 59.243 38.462 0.00 0.00 39.30 3.06
2440 5755 5.099575 GTCCGGGCAAATTTACTTGTATTG 58.900 41.667 0.00 0.00 0.00 1.90
2443 5758 3.752665 TGTCCGGGCAAATTTACTTGTA 58.247 40.909 6.10 0.00 0.00 2.41
2446 5761 4.142556 CGTTATGTCCGGGCAAATTTACTT 60.143 41.667 15.45 0.00 0.00 2.24
2448 5763 3.127376 ACGTTATGTCCGGGCAAATTTAC 59.873 43.478 15.45 6.07 0.00 2.01
2466 5781 5.007332 GTCAACCAAGACACTCAAATACGTT 59.993 40.000 0.00 0.00 38.40 3.99
2528 5843 6.759827 GCTCCCGAGTATGAACAGTAAATTAA 59.240 38.462 0.00 0.00 0.00 1.40
2529 5844 6.127281 TGCTCCCGAGTATGAACAGTAAATTA 60.127 38.462 0.00 0.00 0.00 1.40
2532 5847 3.512329 TGCTCCCGAGTATGAACAGTAAA 59.488 43.478 0.00 0.00 0.00 2.01
2535 5850 1.478510 CTGCTCCCGAGTATGAACAGT 59.521 52.381 0.00 0.00 0.00 3.55
2536 5851 1.751351 TCTGCTCCCGAGTATGAACAG 59.249 52.381 0.00 0.00 0.00 3.16
2544 5862 2.430610 GGCTCATCTGCTCCCGAGT 61.431 63.158 0.00 0.00 0.00 4.18
2576 5894 6.110707 ACGTTTACGGATGGTTTGAGAATAT 58.889 36.000 7.24 0.00 44.95 1.28
2589 5907 6.032094 CAGTGTAGTTCATACGTTTACGGAT 58.968 40.000 7.24 0.06 45.12 4.18
2590 5908 5.048782 ACAGTGTAGTTCATACGTTTACGGA 60.049 40.000 7.24 0.00 44.95 4.69
2592 5910 6.450282 CGAACAGTGTAGTTCATACGTTTACG 60.450 42.308 0.00 0.00 46.32 3.18
2593 5911 6.183359 CCGAACAGTGTAGTTCATACGTTTAC 60.183 42.308 0.00 0.00 46.32 2.01
2602 5920 2.691526 AGTGTCCGAACAGTGTAGTTCA 59.308 45.455 0.00 0.00 46.32 3.18
2603 5921 3.366440 AGTGTCCGAACAGTGTAGTTC 57.634 47.619 0.00 0.00 43.39 3.01
2604 5922 3.814005 AAGTGTCCGAACAGTGTAGTT 57.186 42.857 0.00 0.00 39.06 2.24
2608 5926 2.006888 CACAAAGTGTCCGAACAGTGT 58.993 47.619 0.00 0.00 39.06 3.55
2611 5929 0.307760 GGCACAAAGTGTCCGAACAG 59.692 55.000 0.00 0.00 35.64 3.16
2612 5930 2.399856 GGCACAAAGTGTCCGAACA 58.600 52.632 0.00 0.00 35.75 3.18
2621 5939 1.427368 TGGTATTGGAGGGCACAAAGT 59.573 47.619 0.00 0.00 0.00 2.66
2622 5940 2.214376 TGGTATTGGAGGGCACAAAG 57.786 50.000 0.00 0.00 0.00 2.77
2626 5944 0.395586 TGCATGGTATTGGAGGGCAC 60.396 55.000 0.00 0.00 0.00 5.01
2629 5947 2.662535 TGATGCATGGTATTGGAGGG 57.337 50.000 2.46 0.00 0.00 4.30
2634 5952 3.128415 TGGACGTTTGATGCATGGTATTG 59.872 43.478 2.46 0.00 0.00 1.90
2637 5955 2.080693 GTGGACGTTTGATGCATGGTA 58.919 47.619 2.46 0.00 0.00 3.25
2663 5981 1.359459 GGAATTCGGACGTGCAGACC 61.359 60.000 8.11 0.00 0.00 3.85
2690 6008 0.471022 TTCCCCCAACTTTGCTTCCC 60.471 55.000 0.00 0.00 0.00 3.97
2691 6009 0.969149 CTTCCCCCAACTTTGCTTCC 59.031 55.000 0.00 0.00 0.00 3.46
2692 6010 1.704641 ACTTCCCCCAACTTTGCTTC 58.295 50.000 0.00 0.00 0.00 3.86
2706 6024 1.056660 TCCTGACTCCCACAACTTCC 58.943 55.000 0.00 0.00 0.00 3.46
2707 6025 1.416401 TGTCCTGACTCCCACAACTTC 59.584 52.381 0.00 0.00 0.00 3.01
2709 6027 1.141053 GTTGTCCTGACTCCCACAACT 59.859 52.381 6.55 0.00 43.47 3.16
2710 6028 1.594331 GTTGTCCTGACTCCCACAAC 58.406 55.000 0.00 0.00 41.24 3.32
2719 6037 2.424705 TACGTGGCGGTTGTCCTGAC 62.425 60.000 0.00 0.00 0.00 3.51
2722 6040 2.654877 CTACGTGGCGGTTGTCCT 59.345 61.111 0.00 0.00 0.00 3.85
2723 6041 2.433664 CCTACGTGGCGGTTGTCC 60.434 66.667 0.00 0.00 0.00 4.02
2744 6062 1.482748 GGGTAGGTTTGGGGTGTCGA 61.483 60.000 0.00 0.00 0.00 4.20
2753 6071 1.816224 CATCGGTTTGGGGTAGGTTTG 59.184 52.381 0.00 0.00 0.00 2.93
2754 6072 1.889262 GCATCGGTTTGGGGTAGGTTT 60.889 52.381 0.00 0.00 0.00 3.27
2755 6073 0.323087 GCATCGGTTTGGGGTAGGTT 60.323 55.000 0.00 0.00 0.00 3.50
2774 6092 1.303236 TCCAAACATGTGGGCTCCG 60.303 57.895 11.12 0.00 39.34 4.63
2803 6121 2.459934 GTGGCTTTCACACGGAAAAAG 58.540 47.619 0.00 0.00 44.52 2.27
2813 6131 1.273327 CATGGAAAGGGTGGCTTTCAC 59.727 52.381 0.00 0.00 45.34 3.18
2822 6141 3.117512 AGTGAAGACAACATGGAAAGGGT 60.118 43.478 0.00 0.00 0.00 4.34
2827 6146 2.367241 TCGGAGTGAAGACAACATGGAA 59.633 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.