Multiple sequence alignment - TraesCS6A01G044700

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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 TraesCS6A01G044700 chr6A 100.000 5240 0 0 1 5240 23367397 23362158 0.000000e+00 9677.0
1 TraesCS6A01G044700 chr6B 93.816 3978 177 30 397 4354 40449296 40453224 0.000000e+00 5919.0
2 TraesCS6A01G044700 chr6B 85.831 854 89 13 4391 5240 40453222 40454047 0.000000e+00 878.0
3 TraesCS6A01G044700 chr6B 88.559 472 40 10 402 866 689827974 689827510 1.270000e-155 560.0
4 TraesCS6A01G044700 chr6B 88.372 344 26 8 63 397 40448923 40449261 8.170000e-108 401.0
5 TraesCS6A01G044700 chr6B 84.722 72 11 0 4729 4800 279099068 279099139 7.280000e-09 73.1
6 TraesCS6A01G044700 chr6D 94.019 3695 153 38 978 4644 24832300 24828646 0.000000e+00 5537.0
7 TraesCS6A01G044700 chr6D 85.012 407 25 12 22 399 24833259 24832860 1.060000e-101 381.0
8 TraesCS6A01G044700 chr6D 87.805 246 20 5 4626 4871 24827987 24827752 4.000000e-71 279.0
9 TraesCS6A01G044700 chr2A 89.095 807 72 5 3567 4373 331189181 331189971 0.000000e+00 989.0
10 TraesCS6A01G044700 chr3A 88.366 808 78 4 3566 4373 198238235 198239026 0.000000e+00 957.0
11 TraesCS6A01G044700 chr7A 87.995 808 78 6 3566 4373 271498720 271497932 0.000000e+00 937.0
12 TraesCS6A01G044700 chr7A 76.117 649 116 34 3388 4016 628663878 628664507 2.370000e-78 303.0
13 TraesCS6A01G044700 chr7A 97.436 39 1 0 1334 1372 103399775 103399737 3.390000e-07 67.6
14 TraesCS6A01G044700 chr7A 88.136 59 4 3 4757 4814 641054916 641054860 3.390000e-07 67.6
15 TraesCS6A01G044700 chr7A 100.000 30 0 0 4365 4394 126755024 126754995 7.330000e-04 56.5
16 TraesCS6A01G044700 chr4B 85.887 829 80 14 3566 4373 476635019 476634207 0.000000e+00 848.0
17 TraesCS6A01G044700 chr4B 84.680 829 89 22 63 866 350107774 350106959 0.000000e+00 793.0
18 TraesCS6A01G044700 chrUn 85.839 805 74 23 63 838 96632861 96632068 0.000000e+00 819.0
19 TraesCS6A01G044700 chr5B 89.621 501 38 4 1027 1526 51976840 51977327 4.460000e-175 625.0
20 TraesCS6A01G044700 chr3D 89.744 468 32 10 402 866 31598039 31597585 7.560000e-163 584.0
21 TraesCS6A01G044700 chr2D 84.491 619 60 22 275 866 582683100 582682491 3.520000e-161 579.0
22 TraesCS6A01G044700 chr4A 85.185 594 50 15 1027 1617 727710194 727710752 4.550000e-160 575.0
23 TraesCS6A01G044700 chr4A 100.000 28 0 0 4367 4394 732283383 732283410 9.000000e-03 52.8
24 TraesCS6A01G044700 chr1B 88.795 473 43 7 397 866 563376014 563376479 5.890000e-159 571.0
25 TraesCS6A01G044700 chr3B 90.389 437 33 6 402 836 13892099 13891670 2.740000e-157 566.0
26 TraesCS6A01G044700 chr3B 91.379 58 3 2 4757 4814 763610741 763610686 1.560000e-10 78.7
27 TraesCS6A01G044700 chr7B 88.223 467 47 5 402 866 558938446 558937986 7.670000e-153 551.0
28 TraesCS6A01G044700 chr7B 93.038 316 20 2 1304 1617 724347954 724347639 1.330000e-125 460.0
29 TraesCS6A01G044700 chr7B 77.403 593 102 27 3440 4016 589961184 589961760 1.820000e-84 324.0
30 TraesCS6A01G044700 chr7B 96.000 50 2 0 4757 4806 648363875 648363826 1.210000e-11 82.4
31 TraesCS6A01G044700 chr7B 94.872 39 2 0 1334 1372 57679981 57679943 1.580000e-05 62.1
32 TraesCS6A01G044700 chr7B 100.000 28 0 0 2919 2946 588893052 588893025 9.000000e-03 52.8
33 TraesCS6A01G044700 chr7D 88.616 448 39 10 424 866 8119844 8119404 7.720000e-148 534.0
34 TraesCS6A01G044700 chr7D 76.391 593 108 27 3440 4016 545696532 545697108 1.850000e-74 291.0
35 TraesCS6A01G044700 chr7D 89.247 93 8 1 275 367 8124124 8124034 1.190000e-21 115.0
36 TraesCS6A01G044700 chr7D 100.000 39 0 0 1334 1372 101138561 101138523 7.280000e-09 73.1
37 TraesCS6A01G044700 chr7D 82.258 62 10 1 4366 4426 10928096 10928035 9.000000e-03 52.8
38 TraesCS6A01G044700 chr7D 100.000 28 0 0 2919 2946 545301872 545301845 9.000000e-03 52.8
39 TraesCS6A01G044700 chr1A 93.421 76 5 0 1342 1417 14524292 14524217 4.290000e-21 113.0
40 TraesCS6A01G044700 chr1A 95.652 46 1 1 4758 4803 394238532 394238488 7.280000e-09 73.1
41 TraesCS6A01G044700 chr5D 90.164 61 4 2 4755 4814 549200230 549200289 1.560000e-10 78.7
42 TraesCS6A01G044700 chr1D 89.655 58 3 2 4757 4814 208513798 208513744 2.620000e-08 71.3
43 TraesCS6A01G044700 chr5A 100.000 31 0 0 2575 2605 57664318 57664348 2.040000e-04 58.4


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 TraesCS6A01G044700 chr6A 23362158 23367397 5239 True 9677.000000 9677 100.000000 1 5240 1 chr6A.!!$R1 5239
1 TraesCS6A01G044700 chr6B 40448923 40454047 5124 False 2399.333333 5919 89.339667 63 5240 3 chr6B.!!$F2 5177
2 TraesCS6A01G044700 chr6D 24827752 24833259 5507 True 2065.666667 5537 88.945333 22 4871 3 chr6D.!!$R1 4849
3 TraesCS6A01G044700 chr2A 331189181 331189971 790 False 989.000000 989 89.095000 3567 4373 1 chr2A.!!$F1 806
4 TraesCS6A01G044700 chr3A 198238235 198239026 791 False 957.000000 957 88.366000 3566 4373 1 chr3A.!!$F1 807
5 TraesCS6A01G044700 chr7A 271497932 271498720 788 True 937.000000 937 87.995000 3566 4373 1 chr7A.!!$R3 807
6 TraesCS6A01G044700 chr7A 628663878 628664507 629 False 303.000000 303 76.117000 3388 4016 1 chr7A.!!$F1 628
7 TraesCS6A01G044700 chr4B 476634207 476635019 812 True 848.000000 848 85.887000 3566 4373 1 chr4B.!!$R2 807
8 TraesCS6A01G044700 chr4B 350106959 350107774 815 True 793.000000 793 84.680000 63 866 1 chr4B.!!$R1 803
9 TraesCS6A01G044700 chrUn 96632068 96632861 793 True 819.000000 819 85.839000 63 838 1 chrUn.!!$R1 775
10 TraesCS6A01G044700 chr2D 582682491 582683100 609 True 579.000000 579 84.491000 275 866 1 chr2D.!!$R1 591
11 TraesCS6A01G044700 chr4A 727710194 727710752 558 False 575.000000 575 85.185000 1027 1617 1 chr4A.!!$F1 590
12 TraesCS6A01G044700 chr7B 589961184 589961760 576 False 324.000000 324 77.403000 3440 4016 1 chr7B.!!$F1 576
13 TraesCS6A01G044700 chr7D 545696532 545697108 576 False 291.000000 291 76.391000 3440 4016 1 chr7D.!!$F1 576

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
610 702 0.179073 CCTGACCTGACCGCCATTAG 60.179 60.0 0.0 0.0 0.00 1.73 F
931 1038 0.250234 TCAGCAACCTCCATCCTTCG 59.750 55.0 0.0 0.0 0.00 3.79 F
1743 1856 0.103937 CGCTCCCAGATGACCTCTTC 59.896 60.0 0.0 0.0 29.16 2.87 F
3050 3163 0.256177 GACAGGAAGGGGGTTGATCC 59.744 60.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1838 1.134551 GTGAAGAGGTCATCTGGGAGC 60.135 57.143 0.0 0.0 38.67 4.70 R
2334 2447 1.299648 CTCCATCTTGGCGAACCCA 59.700 57.895 0.0 0.0 43.51 4.51 R
3293 3406 0.523966 CTGCTCCTCTTCTTCGTCGT 59.476 55.000 0.0 0.0 0.00 4.34 R
4680 5512 0.037590 CCTTTGGAATCGGTGTGGGA 59.962 55.000 0.0 0.0 0.00 4.37 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
31 32 2.680312 AGTGACAGCGCTGTGATTAT 57.320 45.000 45.07 24.54 45.05 1.28
32 33 2.977914 AGTGACAGCGCTGTGATTATT 58.022 42.857 45.07 21.23 45.05 1.40
33 34 2.674852 AGTGACAGCGCTGTGATTATTG 59.325 45.455 45.07 16.97 45.05 1.90
50 51 8.879932 GTGATTATTGCTGATCACTCGACAGAG 61.880 44.444 4.30 0.00 45.40 3.35
82 83 3.607741 TCACGGTTGGAGTAGAGTAGAG 58.392 50.000 0.00 0.00 0.00 2.43
89 90 5.105675 GGTTGGAGTAGAGTAGAGAACTTGG 60.106 48.000 0.00 0.00 39.07 3.61
118 119 2.604046 ACATTACGGCTGATCTGACC 57.396 50.000 0.00 3.70 0.00 4.02
159 181 1.063183 ACAGAAAGAGGAAGCTGCCT 58.937 50.000 15.29 15.29 42.17 4.75
328 364 9.073475 ACATTTTCTACTGCCACTTGTAAATAA 57.927 29.630 0.00 0.00 0.00 1.40
338 374 7.382898 TGCCACTTGTAAATAATTTTTCCTCC 58.617 34.615 0.00 0.00 0.00 4.30
391 431 0.395311 AGATAGACCCGCGACTTGGA 60.395 55.000 8.23 0.00 0.00 3.53
399 439 1.631072 CGCGACTTGGATTGCGTAG 59.369 57.895 0.00 0.00 45.62 3.51
490 570 5.086104 TCACTTAGGTAAATCCTCTGTGC 57.914 43.478 11.44 0.00 44.42 4.57
492 572 5.105310 TCACTTAGGTAAATCCTCTGTGCTC 60.105 44.000 11.44 0.00 44.42 4.26
505 585 1.443194 GTGCTCATTTGCCTGCGTG 60.443 57.895 0.00 0.00 0.00 5.34
546 627 4.008933 GCCACGTGTCAGCCTCCT 62.009 66.667 15.65 0.00 0.00 3.69
547 628 2.047844 CCACGTGTCAGCCTCCTG 60.048 66.667 15.65 0.00 40.54 3.86
568 650 2.707849 GCCGTTGACCTCGCTCCTA 61.708 63.158 0.00 0.00 0.00 2.94
610 702 0.179073 CCTGACCTGACCGCCATTAG 60.179 60.000 0.00 0.00 0.00 1.73
616 708 2.431057 ACCTGACCGCCATTAGAGTAAG 59.569 50.000 0.00 0.00 0.00 2.34
694 786 1.213296 AACAATGCCCCCGATCTAGT 58.787 50.000 0.00 0.00 0.00 2.57
794 898 6.639632 ACATCCAGGAATTCCATTTAATCG 57.360 37.500 26.22 9.01 38.89 3.34
833 940 0.933700 AAGAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
834 941 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
835 942 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
866 973 2.160205 GTTAGCCAAGAGTCAAACCCC 58.840 52.381 0.00 0.00 0.00 4.95
885 992 1.153862 GCCGCTGAGTCTGACAGAG 60.154 63.158 5.10 6.18 37.54 3.35
891 998 2.415893 GCTGAGTCTGACAGAGAAGCTC 60.416 54.545 19.56 15.98 37.54 4.09
892 999 1.809547 TGAGTCTGACAGAGAAGCTCG 59.190 52.381 5.10 0.00 35.36 5.03
931 1038 0.250234 TCAGCAACCTCCATCCTTCG 59.750 55.000 0.00 0.00 0.00 3.79
932 1039 0.250234 CAGCAACCTCCATCCTTCGA 59.750 55.000 0.00 0.00 0.00 3.71
945 1052 0.317479 CCTTCGACGACAAGGAGGTT 59.683 55.000 9.59 0.00 42.94 3.50
946 1053 1.270147 CCTTCGACGACAAGGAGGTTT 60.270 52.381 9.59 0.00 42.94 3.27
947 1054 1.792949 CTTCGACGACAAGGAGGTTTG 59.207 52.381 0.00 0.00 0.00 2.93
949 1056 0.600255 CGACGACAAGGAGGTTTGCT 60.600 55.000 0.00 0.00 0.00 3.91
950 1057 1.594331 GACGACAAGGAGGTTTGCTT 58.406 50.000 0.00 0.00 35.07 3.91
951 1058 1.531578 GACGACAAGGAGGTTTGCTTC 59.468 52.381 0.00 0.00 32.01 3.86
952 1059 0.512952 CGACAAGGAGGTTTGCTTCG 59.487 55.000 0.00 0.00 32.01 3.79
953 1060 1.872237 CGACAAGGAGGTTTGCTTCGA 60.872 52.381 0.00 0.00 32.01 3.71
954 1061 2.427506 GACAAGGAGGTTTGCTTCGAT 58.572 47.619 0.00 0.00 32.01 3.59
955 1062 2.416893 GACAAGGAGGTTTGCTTCGATC 59.583 50.000 0.00 0.00 32.01 3.69
956 1063 1.394917 CAAGGAGGTTTGCTTCGATCG 59.605 52.381 9.36 9.36 32.01 3.69
957 1064 0.895530 AGGAGGTTTGCTTCGATCGA 59.104 50.000 15.15 15.15 0.00 3.59
958 1065 1.482593 AGGAGGTTTGCTTCGATCGAT 59.517 47.619 20.18 0.00 0.00 3.59
959 1066 1.861575 GGAGGTTTGCTTCGATCGATC 59.138 52.381 20.18 15.68 0.00 3.69
960 1067 1.861575 GAGGTTTGCTTCGATCGATCC 59.138 52.381 20.18 13.14 0.00 3.36
961 1068 1.207089 AGGTTTGCTTCGATCGATCCA 59.793 47.619 20.18 15.64 0.00 3.41
962 1069 1.327764 GGTTTGCTTCGATCGATCCAC 59.672 52.381 20.18 11.12 0.00 4.02
963 1070 1.327764 GTTTGCTTCGATCGATCCACC 59.672 52.381 20.18 8.29 0.00 4.61
964 1071 0.534873 TTGCTTCGATCGATCCACCA 59.465 50.000 20.18 8.87 0.00 4.17
965 1072 0.534873 TGCTTCGATCGATCCACCAA 59.465 50.000 20.18 0.37 0.00 3.67
966 1073 1.138859 TGCTTCGATCGATCCACCAAT 59.861 47.619 20.18 0.00 0.00 3.16
967 1074 1.528586 GCTTCGATCGATCCACCAATG 59.471 52.381 20.18 3.96 0.00 2.82
968 1075 2.826428 CTTCGATCGATCCACCAATGT 58.174 47.619 20.18 0.00 0.00 2.71
969 1076 2.223537 TCGATCGATCCACCAATGTG 57.776 50.000 19.51 2.52 42.39 3.21
1008 1115 1.752694 TTAGCTGGAAATGGCGGGC 60.753 57.895 0.00 0.00 0.00 6.13
1173 1280 1.450312 CCTTGATGCTCCGGTGGAC 60.450 63.158 0.00 0.00 0.00 4.02
1215 1322 2.437359 GATGAAGGCGGCTGCTGT 60.437 61.111 19.18 6.84 42.25 4.40
1485 1598 2.888998 GCGGGTGTTCAACGTGTCC 61.889 63.158 0.00 0.00 0.00 4.02
1743 1856 0.103937 CGCTCCCAGATGACCTCTTC 59.896 60.000 0.00 0.00 29.16 2.87
1744 1857 1.198713 GCTCCCAGATGACCTCTTCA 58.801 55.000 0.00 0.00 39.11 3.02
1845 1958 2.110967 CCTCGTCCGCCTCGACTTA 61.111 63.158 0.00 0.00 33.71 2.24
1950 2063 4.760047 CTCACCGGTGGCCTTCCG 62.760 72.222 33.40 25.45 46.49 4.30
2334 2447 3.133014 CCAGAGGACGGCATCGAT 58.867 61.111 0.00 0.00 40.11 3.59
2949 3062 2.445845 TCCGGCGAGATCCCCATT 60.446 61.111 9.30 0.00 0.00 3.16
2973 3086 1.611936 GGCCAGTTCTTCACCTTCTCC 60.612 57.143 0.00 0.00 0.00 3.71
2979 3092 2.048222 TTCACCTTCTCCAGCGCG 60.048 61.111 0.00 0.00 0.00 6.86
3042 3155 1.376037 GAAGTGCGACAGGAAGGGG 60.376 63.158 0.00 0.00 0.00 4.79
3044 3157 3.637273 GTGCGACAGGAAGGGGGT 61.637 66.667 0.00 0.00 0.00 4.95
3050 3163 0.256177 GACAGGAAGGGGGTTGATCC 59.744 60.000 0.00 0.00 0.00 3.36
3293 3406 2.683933 GGTGCTCCTCTTCCCCGA 60.684 66.667 0.00 0.00 0.00 5.14
3310 3423 0.521659 CGACGACGAAGAAGAGGAGC 60.522 60.000 0.00 0.00 42.66 4.70
3320 3433 2.875684 GAAGAGGAGCAGACGACGGC 62.876 65.000 1.39 1.39 37.48 5.68
3321 3434 4.838486 GAGGAGCAGACGACGGCG 62.838 72.222 10.39 10.39 41.73 6.46
4260 4385 6.647067 ACTGAAGCTTGTGTAGATAACTGAAC 59.353 38.462 2.10 0.00 0.00 3.18
4319 4464 7.065324 TCTCGTGTAAATTTTGACAAGAGTTGT 59.935 33.333 24.10 0.00 46.14 3.32
4320 4465 7.531716 TCGTGTAAATTTTGACAAGAGTTGTT 58.468 30.769 0.00 0.00 45.52 2.83
4321 4466 7.483375 TCGTGTAAATTTTGACAAGAGTTGTTG 59.517 33.333 0.00 0.00 45.52 3.33
4387 4532 3.808466 TGCTAAATCTCAGTCGATGCT 57.192 42.857 0.00 0.00 0.00 3.79
4393 4538 7.757173 TGCTAAATCTCAGTCGATGCTATATTC 59.243 37.037 0.00 0.00 0.00 1.75
4426 4572 9.781834 TTTACATGAAGAACTGTGTAAAGTTTG 57.218 29.630 0.00 0.00 40.48 2.93
4427 4573 6.265577 ACATGAAGAACTGTGTAAAGTTTGC 58.734 36.000 0.00 0.00 40.48 3.68
4428 4574 5.888691 TGAAGAACTGTGTAAAGTTTGCA 57.111 34.783 1.88 1.88 40.48 4.08
4430 4576 6.862209 TGAAGAACTGTGTAAAGTTTGCATT 58.138 32.000 9.69 0.46 40.48 3.56
4431 4577 6.751425 TGAAGAACTGTGTAAAGTTTGCATTG 59.249 34.615 9.69 8.17 40.48 2.82
4432 4578 6.449635 AGAACTGTGTAAAGTTTGCATTGA 57.550 33.333 9.69 0.00 40.48 2.57
4483 4640 8.265165 ACCAAGATTTAGTTAAGTTTCGATCC 57.735 34.615 0.00 0.00 0.00 3.36
4485 4642 8.893727 CCAAGATTTAGTTAAGTTTCGATCCAT 58.106 33.333 0.00 0.00 0.00 3.41
4503 4660 3.069586 TCCATTAAGATCTAGCCACACCG 59.930 47.826 0.00 0.00 0.00 4.94
4504 4661 3.069586 CCATTAAGATCTAGCCACACCGA 59.930 47.826 0.00 0.00 0.00 4.69
4541 4698 1.078918 TCTGCACCGCATCCAAGAG 60.079 57.895 0.00 0.00 38.13 2.85
4604 4761 4.792521 ACAAACCAACAAGCAACACTTA 57.207 36.364 0.00 0.00 36.04 2.24
4609 4766 6.660887 AACCAACAAGCAACACTTATTTTG 57.339 33.333 0.00 0.00 36.04 2.44
4669 5501 3.617706 CACAAGAACACAAGCAAATGCAA 59.382 39.130 8.28 0.00 45.16 4.08
4675 5507 5.476599 AGAACACAAGCAAATGCAAGGTATA 59.523 36.000 8.28 0.00 45.16 1.47
4680 5512 5.532406 ACAAGCAAATGCAAGGTATATCGAT 59.468 36.000 8.28 2.16 45.16 3.59
4722 5554 6.723052 AGGGATCATTTGAAGTTTTGATGTCT 59.277 34.615 0.00 0.00 0.00 3.41
4750 5582 9.288576 TGAAAACATATTTGACAGACTGATCTT 57.711 29.630 10.08 0.00 30.42 2.40
4879 5711 0.036952 CACCAGCGTCTCATGGAAGT 60.037 55.000 0.00 0.00 39.02 3.01
4890 5722 3.012518 CTCATGGAAGTCCTTTGCGATT 58.987 45.455 0.00 0.00 36.82 3.34
4896 5728 3.004315 GGAAGTCCTTTGCGATTGAAACA 59.996 43.478 0.00 0.00 0.00 2.83
4897 5729 3.904136 AGTCCTTTGCGATTGAAACAG 57.096 42.857 0.00 0.00 0.00 3.16
4913 5745 9.601217 GATTGAAACAGAGGATAAGCTAAACTA 57.399 33.333 0.00 0.00 0.00 2.24
4937 5769 9.274206 CTAGTTTATGGGAAAAGGACTAATAGC 57.726 37.037 0.00 0.00 0.00 2.97
4939 5771 6.584471 TTATGGGAAAAGGACTAATAGCCA 57.416 37.500 4.15 0.00 0.00 4.75
4965 5797 3.075884 TCCAAATACTCGTTTTTCCGGG 58.924 45.455 0.00 0.00 0.00 5.73
5037 5869 5.263872 ACATGGTTTTGGGTGGTTAGATA 57.736 39.130 0.00 0.00 0.00 1.98
5059 5891 9.614792 AGATACCTAAACATGATTAGTGGAAAC 57.385 33.333 18.26 7.49 32.16 2.78
5063 5895 5.391312 AAACATGATTAGTGGAAACTGGC 57.609 39.130 0.00 0.00 0.00 4.85
5074 5906 3.442625 GTGGAAACTGGCTTGGTATAACC 59.557 47.826 0.00 0.00 39.22 2.85
5114 5946 3.496870 CCTTAGTGTTGAAAGGTGCCTCT 60.497 47.826 0.00 0.00 37.96 3.69
5115 5947 4.262894 CCTTAGTGTTGAAAGGTGCCTCTA 60.263 45.833 0.00 0.00 37.96 2.43
5123 5955 6.374333 TGTTGAAAGGTGCCTCTATGTAATTC 59.626 38.462 0.00 0.00 0.00 2.17
5136 5968 7.556275 CCTCTATGTAATTCCAAAGTTGCCTAA 59.444 37.037 0.00 0.00 0.00 2.69
5137 5969 8.871629 TCTATGTAATTCCAAAGTTGCCTAAA 57.128 30.769 0.00 0.00 0.00 1.85
5157 5989 6.712095 CCTAAATATGATGCTCAGTTGCCTAA 59.288 38.462 0.00 0.00 0.00 2.69
5158 5990 6.382869 AAATATGATGCTCAGTTGCCTAAC 57.617 37.500 0.00 0.00 37.06 2.34
5163 5996 2.426522 TGCTCAGTTGCCTAACATGAC 58.573 47.619 0.00 0.00 39.30 3.06
5187 6020 6.017933 CGAAAGTTGTGTGCTATCATTTCTC 58.982 40.000 0.00 0.00 0.00 2.87
5188 6021 5.536554 AAGTTGTGTGCTATCATTTCTCG 57.463 39.130 0.00 0.00 0.00 4.04
5190 6023 3.610040 TGTGTGCTATCATTTCTCGGT 57.390 42.857 0.00 0.00 0.00 4.69
5212 6045 7.437267 TCGGTTTTCTACAATATACTTGCTAGC 59.563 37.037 8.10 8.10 0.00 3.42
5219 6052 9.698309 TCTACAATATACTTGCTAGCTGAATTC 57.302 33.333 17.23 0.00 0.00 2.17
5220 6053 9.481340 CTACAATATACTTGCTAGCTGAATTCA 57.519 33.333 17.23 8.12 0.00 2.57
5221 6054 8.375608 ACAATATACTTGCTAGCTGAATTCAG 57.624 34.615 27.82 27.82 46.40 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.577689 ACAGCGCTGTCACTATTCAGAATGA 62.578 44.000 36.44 0.00 41.74 2.57
2 3 3.001026 CAGCGCTGTCACTATTCAGAATG 59.999 47.826 29.24 0.00 34.02 2.67
3 4 3.193263 CAGCGCTGTCACTATTCAGAAT 58.807 45.455 29.24 0.20 34.02 2.40
4 5 2.029020 ACAGCGCTGTCACTATTCAGAA 60.029 45.455 36.44 0.00 40.24 3.02
5 6 1.546029 ACAGCGCTGTCACTATTCAGA 59.454 47.619 36.44 0.00 40.24 3.27
6 7 1.657594 CACAGCGCTGTCACTATTCAG 59.342 52.381 38.87 20.91 42.83 3.02
7 8 1.272212 TCACAGCGCTGTCACTATTCA 59.728 47.619 38.87 13.06 42.83 2.57
8 9 1.996292 TCACAGCGCTGTCACTATTC 58.004 50.000 38.87 0.00 42.83 1.75
9 10 2.680312 ATCACAGCGCTGTCACTATT 57.320 45.000 38.87 14.68 42.83 1.73
10 11 2.680312 AATCACAGCGCTGTCACTAT 57.320 45.000 38.87 25.11 42.83 2.12
11 12 3.801114 ATAATCACAGCGCTGTCACTA 57.199 42.857 38.87 23.55 42.83 2.74
12 13 2.674852 CAATAATCACAGCGCTGTCACT 59.325 45.455 38.87 21.85 42.83 3.41
13 14 2.789092 GCAATAATCACAGCGCTGTCAC 60.789 50.000 38.87 17.84 42.83 3.67
14 15 1.398041 GCAATAATCACAGCGCTGTCA 59.602 47.619 38.87 30.02 42.83 3.58
15 16 1.667724 AGCAATAATCACAGCGCTGTC 59.332 47.619 38.87 24.46 42.83 3.51
16 17 1.399440 CAGCAATAATCACAGCGCTGT 59.601 47.619 36.44 36.44 46.17 4.40
17 18 1.667212 TCAGCAATAATCACAGCGCTG 59.333 47.619 34.89 34.89 46.34 5.18
18 19 2.028420 TCAGCAATAATCACAGCGCT 57.972 45.000 2.64 2.64 0.00 5.92
19 20 2.288729 TGATCAGCAATAATCACAGCGC 59.711 45.455 0.00 0.00 0.00 5.92
20 21 3.558829 AGTGATCAGCAATAATCACAGCG 59.441 43.478 15.53 0.00 44.11 5.18
31 32 2.643933 CTCTGTCGAGTGATCAGCAA 57.356 50.000 0.00 0.00 32.47 3.91
44 45 4.395542 ACCGTGAGTGATTACTACTCTGTC 59.604 45.833 0.00 0.00 43.79 3.51
45 46 4.333690 ACCGTGAGTGATTACTACTCTGT 58.666 43.478 0.00 0.00 43.79 3.41
50 51 4.082354 ACTCCAACCGTGAGTGATTACTAC 60.082 45.833 0.00 0.00 41.40 2.73
56 57 2.755655 CTCTACTCCAACCGTGAGTGAT 59.244 50.000 3.30 0.00 42.80 3.06
57 58 2.160205 CTCTACTCCAACCGTGAGTGA 58.840 52.381 3.30 0.00 42.80 3.41
58 59 1.887198 ACTCTACTCCAACCGTGAGTG 59.113 52.381 3.30 0.00 42.80 3.51
59 60 2.289592 ACTCTACTCCAACCGTGAGT 57.710 50.000 0.00 0.00 44.85 3.41
61 62 3.262660 TCTCTACTCTACTCCAACCGTGA 59.737 47.826 0.00 0.00 0.00 4.35
82 83 5.912955 CGTAATGTTTCTTCAACCCAAGTTC 59.087 40.000 0.00 0.00 33.97 3.01
89 90 3.500680 TCAGCCGTAATGTTTCTTCAACC 59.499 43.478 0.00 0.00 33.97 3.77
118 119 3.019964 TGCACCTACCTGCACAAAG 57.980 52.632 0.00 0.00 42.36 2.77
367 407 4.369182 CAAGTCGCGGGTCTATCTATTTT 58.631 43.478 6.13 0.00 0.00 1.82
391 431 8.338259 GTGAATATTTCATGAGAACTACGCAAT 58.662 33.333 0.00 0.00 42.47 3.56
399 439 7.383102 ACACAGGTGAATATTTCATGAGAAC 57.617 36.000 6.40 0.00 42.47 3.01
490 570 1.063616 CAGATCACGCAGGCAAATGAG 59.936 52.381 0.00 0.00 0.00 2.90
492 572 1.089112 TCAGATCACGCAGGCAAATG 58.911 50.000 0.00 0.00 0.00 2.32
505 585 1.539929 CCCAGCTCCAATCGTCAGATC 60.540 57.143 0.00 0.00 35.74 2.75
581 663 4.798682 AGGTCAGGTAGGGGCCGG 62.799 72.222 0.00 0.00 0.00 6.13
583 665 2.040606 TCAGGTCAGGTAGGGGCC 59.959 66.667 0.00 0.00 0.00 5.80
584 666 2.368011 GGTCAGGTCAGGTAGGGGC 61.368 68.421 0.00 0.00 0.00 5.80
610 702 3.866651 TGAGGAGCTTGATTGCTTACTC 58.133 45.455 12.10 12.10 44.17 2.59
616 708 1.674962 GTGGATGAGGAGCTTGATTGC 59.325 52.381 0.00 0.00 0.00 3.56
694 786 5.297547 CAGCCAGTGTGTTTAGACTTTAGA 58.702 41.667 0.00 0.00 0.00 2.10
763 856 3.433740 GGAATTCCTGGATGTAGGTGGAC 60.434 52.174 17.73 0.00 38.99 4.02
794 898 1.811359 TCTTCTTCGTCGTCTTCCTCC 59.189 52.381 0.00 0.00 0.00 4.30
833 940 0.888619 GGCTAACCAACCTTGCTTCC 59.111 55.000 0.00 0.00 35.26 3.46
834 941 1.616159 TGGCTAACCAACCTTGCTTC 58.384 50.000 0.00 0.00 45.37 3.86
835 942 3.839979 TGGCTAACCAACCTTGCTT 57.160 47.368 0.00 0.00 45.37 3.91
866 973 2.505777 CTGTCAGACTCAGCGGCG 60.506 66.667 0.51 0.51 0.00 6.46
885 992 4.789784 CTGTAGCTAACTATCCGAGCTTC 58.210 47.826 0.00 0.00 44.08 3.86
926 1033 0.317479 AACCTCCTTGTCGTCGAAGG 59.683 55.000 6.64 6.64 41.36 3.46
931 1038 1.531578 GAAGCAAACCTCCTTGTCGTC 59.468 52.381 0.00 0.00 0.00 4.20
932 1039 1.594331 GAAGCAAACCTCCTTGTCGT 58.406 50.000 0.00 0.00 0.00 4.34
941 1048 1.207089 TGGATCGATCGAAGCAAACCT 59.793 47.619 23.50 2.02 0.00 3.50
945 1052 0.534873 TGGTGGATCGATCGAAGCAA 59.465 50.000 23.50 8.14 0.00 3.91
946 1053 0.534873 TTGGTGGATCGATCGAAGCA 59.465 50.000 23.50 18.24 0.00 3.91
947 1054 1.528586 CATTGGTGGATCGATCGAAGC 59.471 52.381 23.50 15.73 0.00 3.86
949 1056 2.549926 CACATTGGTGGATCGATCGAA 58.450 47.619 23.50 2.26 41.45 3.71
950 1057 2.223537 CACATTGGTGGATCGATCGA 57.776 50.000 21.86 21.86 41.45 3.59
960 1067 1.619654 TTCAAGAGCCCACATTGGTG 58.380 50.000 0.00 0.00 44.85 4.17
961 1068 2.173519 CATTCAAGAGCCCACATTGGT 58.826 47.619 0.00 0.00 35.17 3.67
962 1069 2.426024 CTCATTCAAGAGCCCACATTGG 59.574 50.000 0.00 0.00 37.25 3.16
963 1070 3.777465 CTCATTCAAGAGCCCACATTG 57.223 47.619 0.00 0.00 0.00 2.82
972 1079 4.569966 AGCTAACGATTGCTCATTCAAGAG 59.430 41.667 0.00 0.00 33.90 2.85
973 1080 4.330894 CAGCTAACGATTGCTCATTCAAGA 59.669 41.667 0.00 0.00 37.44 3.02
974 1081 4.495349 CCAGCTAACGATTGCTCATTCAAG 60.495 45.833 0.00 0.00 37.44 3.02
975 1082 3.374988 CCAGCTAACGATTGCTCATTCAA 59.625 43.478 0.00 0.00 37.44 2.69
976 1083 2.938451 CCAGCTAACGATTGCTCATTCA 59.062 45.455 0.00 0.00 37.44 2.57
985 1092 1.670811 CGCCATTTCCAGCTAACGATT 59.329 47.619 0.00 0.00 0.00 3.34
1249 1356 4.712425 CACCACCCCGACGACGAC 62.712 72.222 9.28 0.00 42.66 4.34
1624 1737 1.277557 GAGCCTGTTCATGGACAGTCT 59.722 52.381 28.53 23.61 44.34 3.24
1626 1739 1.277557 GAGAGCCTGTTCATGGACAGT 59.722 52.381 28.53 14.37 44.34 3.55
1725 1838 1.134551 GTGAAGAGGTCATCTGGGAGC 60.135 57.143 0.00 0.00 38.67 4.70
2334 2447 1.299648 CTCCATCTTGGCGAACCCA 59.700 57.895 0.00 0.00 43.51 4.51
2412 2525 2.359230 AGCACCTTGAGCTTCCGC 60.359 61.111 0.00 0.00 39.87 5.54
2594 2707 3.173240 GCACCTTCTCGTCGTCGC 61.173 66.667 0.00 0.00 36.96 5.19
2742 2855 2.032376 TGCAATCTGTCCAGCGCA 59.968 55.556 11.47 2.93 0.00 6.09
2750 2863 1.350193 GTCGACGATGTGCAATCTGT 58.650 50.000 0.00 0.00 0.00 3.41
2949 3062 2.281484 GTGAAGAACTGGCCGCCA 60.281 61.111 12.67 12.67 0.00 5.69
2979 3092 4.772687 GGGTTCCCCGCGAAGTCC 62.773 72.222 8.23 3.02 32.13 3.85
2988 3101 4.410400 CACAGGAGCGGGTTCCCC 62.410 72.222 1.93 0.00 41.09 4.81
2998 3111 2.317609 CGTGGAAACCGCACAGGAG 61.318 63.158 0.00 0.00 45.00 3.69
3034 3147 2.001269 CCGGATCAACCCCCTTCCT 61.001 63.158 0.00 0.00 34.64 3.36
3072 3185 4.473520 CGGCCGTCATTGCTCCCT 62.474 66.667 19.50 0.00 0.00 4.20
3228 3341 1.737008 GGTGCTTTCCTCGTCGTCC 60.737 63.158 0.00 0.00 0.00 4.79
3293 3406 0.523966 CTGCTCCTCTTCTTCGTCGT 59.476 55.000 0.00 0.00 0.00 4.34
3310 3423 2.579787 GATCACCGCCGTCGTCTG 60.580 66.667 0.00 0.00 0.00 3.51
3320 3433 0.802222 ATCGTCAAGCGTGATCACCG 60.802 55.000 20.03 15.58 42.13 4.94
3321 3434 0.647410 CATCGTCAAGCGTGATCACC 59.353 55.000 20.03 12.53 42.13 4.02
3322 3435 1.059692 CACATCGTCAAGCGTGATCAC 59.940 52.381 16.21 16.21 42.13 3.06
3337 3450 2.100631 CCGTCGCCTTCACCACATC 61.101 63.158 0.00 0.00 0.00 3.06
3339 3452 4.308458 CCCGTCGCCTTCACCACA 62.308 66.667 0.00 0.00 0.00 4.17
3570 3683 2.737830 GGGTAGATGAGGAGGCGC 59.262 66.667 0.00 0.00 0.00 6.53
4260 4385 4.066490 ACAGCTAGCTACTGTAGTATCGG 58.934 47.826 18.86 2.42 46.32 4.18
4319 4464 7.174080 TCCATTCAATCTTTACACACGAATCAA 59.826 33.333 0.00 0.00 0.00 2.57
4320 4465 6.652900 TCCATTCAATCTTTACACACGAATCA 59.347 34.615 0.00 0.00 0.00 2.57
4321 4466 6.961554 GTCCATTCAATCTTTACACACGAATC 59.038 38.462 0.00 0.00 0.00 2.52
4393 4538 8.099364 ACACAGTTCTTCATGTAAAATGTAGG 57.901 34.615 9.12 3.64 30.86 3.18
4412 4558 8.491331 AAAAATCAATGCAAACTTTACACAGT 57.509 26.923 0.00 0.00 0.00 3.55
4454 4611 9.280174 TCGAAACTTAACTAAATCTTGGTCAAT 57.720 29.630 0.00 0.00 0.00 2.57
4474 4631 6.146347 GTGGCTAGATCTTAATGGATCGAAAC 59.854 42.308 0.00 0.00 44.71 2.78
4476 4633 5.304357 TGTGGCTAGATCTTAATGGATCGAA 59.696 40.000 0.00 0.00 44.71 3.71
4483 4640 4.322080 TCGGTGTGGCTAGATCTTAATG 57.678 45.455 0.00 0.00 0.00 1.90
4485 4642 6.474140 TTAATCGGTGTGGCTAGATCTTAA 57.526 37.500 0.00 0.00 0.00 1.85
4487 4644 5.552870 ATTAATCGGTGTGGCTAGATCTT 57.447 39.130 0.00 0.00 0.00 2.40
4503 4660 9.070149 GTGCAGAGTTGAAATTCTGAATTAATC 57.930 33.333 15.45 11.03 43.16 1.75
4504 4661 8.031277 GGTGCAGAGTTGAAATTCTGAATTAAT 58.969 33.333 15.45 1.70 43.16 1.40
4556 4713 5.543507 TGTGGGAAATGTATTGCTTGTTT 57.456 34.783 0.00 0.00 0.00 2.83
4632 4789 8.832521 TGTGTTCTTGTGGTTAACTAAATACAG 58.167 33.333 5.42 0.00 0.00 2.74
4644 4801 3.951775 TTTGCTTGTGTTCTTGTGGTT 57.048 38.095 0.00 0.00 0.00 3.67
4645 4802 3.784338 CATTTGCTTGTGTTCTTGTGGT 58.216 40.909 0.00 0.00 0.00 4.16
4646 4803 2.540931 GCATTTGCTTGTGTTCTTGTGG 59.459 45.455 0.00 0.00 38.21 4.17
4647 4804 3.188492 TGCATTTGCTTGTGTTCTTGTG 58.812 40.909 3.94 0.00 42.66 3.33
4648 4805 3.523606 TGCATTTGCTTGTGTTCTTGT 57.476 38.095 3.94 0.00 42.66 3.16
4651 5483 2.431782 ACCTTGCATTTGCTTGTGTTCT 59.568 40.909 3.94 0.00 42.66 3.01
4669 5501 2.168496 CGGTGTGGGATCGATATACCT 58.832 52.381 0.00 0.00 36.96 3.08
4675 5507 0.393077 GGAATCGGTGTGGGATCGAT 59.607 55.000 0.00 0.00 44.19 3.59
4680 5512 0.037590 CCTTTGGAATCGGTGTGGGA 59.962 55.000 0.00 0.00 0.00 4.37
4722 5554 9.897744 GATCAGTCTGTCAAATATGTTTTCAAA 57.102 29.630 0.00 0.00 0.00 2.69
4751 5583 5.128992 GGGACGAAAGCCTATTTCAAAAA 57.871 39.130 0.00 0.00 0.00 1.94
4752 5584 4.776795 GGGACGAAAGCCTATTTCAAAA 57.223 40.909 0.00 0.00 0.00 2.44
4796 5628 1.080093 TGCCGTGGCTACTTCTTCG 60.080 57.895 12.84 0.00 42.51 3.79
4824 5656 2.225019 CGTCCATTATGGCAAGATCAGC 59.775 50.000 6.33 0.00 37.47 4.26
4864 5696 1.270907 AAGGACTTCCATGAGACGCT 58.729 50.000 0.00 0.00 38.89 5.07
4879 5711 2.813754 CCTCTGTTTCAATCGCAAAGGA 59.186 45.455 0.00 0.00 0.00 3.36
4890 5722 8.135382 ACTAGTTTAGCTTATCCTCTGTTTCA 57.865 34.615 0.00 0.00 0.00 2.69
4896 5728 8.652290 CCCATAAACTAGTTTAGCTTATCCTCT 58.348 37.037 27.21 8.99 38.30 3.69
4897 5729 8.648693 TCCCATAAACTAGTTTAGCTTATCCTC 58.351 37.037 27.21 0.00 38.30 3.71
4913 5745 7.061054 GGCTATTAGTCCTTTTCCCATAAACT 58.939 38.462 0.00 0.00 0.00 2.66
4937 5769 7.358848 CGGAAAAACGAGTATTTGGAAAAATGG 60.359 37.037 0.00 0.00 35.47 3.16
4939 5771 6.643360 CCGGAAAAACGAGTATTTGGAAAAAT 59.357 34.615 0.00 0.00 35.47 1.82
5037 5869 6.659242 CCAGTTTCCACTAATCATGTTTAGGT 59.341 38.462 21.85 9.42 34.19 3.08
5046 5878 3.181434 ACCAAGCCAGTTTCCACTAATCA 60.181 43.478 0.00 0.00 0.00 2.57
5053 5885 3.692690 GGTTATACCAAGCCAGTTTCCA 58.307 45.455 0.00 0.00 38.42 3.53
5063 5895 8.910094 TTGTTTGGACACGATGGTTATACCAAG 61.910 40.741 2.19 3.27 43.29 3.61
5074 5906 0.385473 GGCGTTGTTTGGACACGATG 60.385 55.000 0.00 0.00 34.98 3.84
5080 5912 1.944709 ACACTAAGGCGTTGTTTGGAC 59.055 47.619 0.97 0.00 0.00 4.02
5123 5955 6.183360 TGAGCATCATATTTAGGCAACTTTGG 60.183 38.462 0.00 0.00 44.68 3.28
5157 5989 2.288666 AGCACACAACTTTCGTCATGT 58.711 42.857 0.00 0.00 0.00 3.21
5158 5990 4.152223 TGATAGCACACAACTTTCGTCATG 59.848 41.667 0.00 0.00 0.00 3.07
5163 5996 5.931532 AGAAATGATAGCACACAACTTTCG 58.068 37.500 0.00 0.00 0.00 3.46
5187 6020 7.438459 AGCTAGCAAGTATATTGTAGAAAACCG 59.562 37.037 18.83 0.00 0.00 4.44
5188 6021 8.552034 CAGCTAGCAAGTATATTGTAGAAAACC 58.448 37.037 18.83 0.00 0.00 3.27
5190 6023 9.884636 TTCAGCTAGCAAGTATATTGTAGAAAA 57.115 29.630 18.83 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.