Multiple sequence alignment - TraesCS7B01G169700

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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 TraesCS7B01G169700 chr7B 100.000 5878 0 0 1 5878 240641117 240635240 0.000000e+00 10855.0
1 TraesCS7B01G169700 chr7B 96.809 94 0 2 4927 5020 17611701 17611611 2.840000e-33 154.0
2 TraesCS7B01G169700 chr7B 96.667 90 1 2 4931 5020 17517327 17517240 1.320000e-31 148.0
3 TraesCS7B01G169700 chr7B 92.381 105 3 3 4926 5028 17534352 17534251 1.710000e-30 145.0
4 TraesCS7B01G169700 chr7A 95.085 2116 75 18 3072 5187 285695010 285697096 0.000000e+00 3304.0
5 TraesCS7B01G169700 chr7A 94.651 1776 61 14 1 1764 285691788 285693541 0.000000e+00 2723.0
6 TraesCS7B01G169700 chr7A 95.923 1251 28 9 1802 3031 285693764 285695012 0.000000e+00 2006.0
7 TraesCS7B01G169700 chr7A 87.787 696 44 13 5192 5867 285697132 285697806 0.000000e+00 776.0
8 TraesCS7B01G169700 chr7A 85.646 627 84 5 1 627 691517335 691516715 0.000000e+00 654.0
9 TraesCS7B01G169700 chr7A 84.848 627 89 5 1 627 514689151 514688531 1.390000e-175 627.0
10 TraesCS7B01G169700 chr7A 89.172 157 16 1 5696 5852 15123303 15123458 1.670000e-45 195.0
11 TraesCS7B01G169700 chr7D 94.690 2128 66 21 3072 5187 263036190 263038282 0.000000e+00 3260.0
12 TraesCS7B01G169700 chr7D 92.180 1803 65 30 55 1817 263033148 263034914 0.000000e+00 2479.0
13 TraesCS7B01G169700 chr7D 95.790 1259 22 10 1801 3031 263034937 263036192 0.000000e+00 2002.0
14 TraesCS7B01G169700 chr7D 91.872 689 33 8 5192 5859 263038318 263039004 0.000000e+00 941.0
15 TraesCS7B01G169700 chr7D 96.667 90 2 1 4931 5020 74395372 74395284 1.320000e-31 148.0
16 TraesCS7B01G169700 chr7D 91.089 101 5 3 4926 5025 74399242 74399145 3.700000e-27 134.0
17 TraesCS7B01G169700 chr2A 85.008 627 88 5 1 627 445577735 445577115 2.990000e-177 632.0
18 TraesCS7B01G169700 chr5A 83.614 653 62 21 1230 1857 533480443 533479811 6.610000e-159 571.0
19 TraesCS7B01G169700 chr5A 89.796 98 10 0 990 1087 533480563 533480466 6.180000e-25 126.0
20 TraesCS7B01G169700 chr5A 97.059 34 1 0 5451 5484 526891445 526891478 2.290000e-04 58.4
21 TraesCS7B01G169700 chr6B 86.705 173 21 2 5696 5867 182340743 182340572 2.160000e-44 191.0
22 TraesCS7B01G169700 chr6D 86.127 173 19 5 5696 5866 259286060 259285891 1.300000e-41 182.0
23 TraesCS7B01G169700 chr2B 85.965 171 23 1 5696 5866 64336445 64336614 1.300000e-41 182.0
24 TraesCS7B01G169700 chr2B 85.799 169 23 1 5697 5865 5724128 5724295 1.680000e-40 178.0
25 TraesCS7B01G169700 chrUn 86.047 172 16 6 5696 5866 297038232 297038396 1.680000e-40 178.0
26 TraesCS7B01G169700 chrUn 86.047 172 16 6 5696 5866 301355837 301356001 1.680000e-40 178.0
27 TraesCS7B01G169700 chr2D 85.882 170 21 3 5697 5865 8621403 8621570 1.680000e-40 178.0
28 TraesCS7B01G169700 chr5D 93.548 93 5 1 4927 5018 403077602 403077510 2.860000e-28 137.0
29 TraesCS7B01G169700 chr5D 92.708 96 4 3 4940 5034 404192167 404192260 1.030000e-27 135.0
30 TraesCS7B01G169700 chr5D 85.950 121 10 2 1319 1432 418868763 418868643 8.000000e-24 122.0


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 TraesCS7B01G169700 chr7B 240635240 240641117 5877 True 10855.00 10855 100.0000 1 5878 1 chr7B.!!$R4 5877
1 TraesCS7B01G169700 chr7A 285691788 285697806 6018 False 2202.25 3304 93.3615 1 5867 4 chr7A.!!$F2 5866
2 TraesCS7B01G169700 chr7A 691516715 691517335 620 True 654.00 654 85.6460 1 627 1 chr7A.!!$R2 626
3 TraesCS7B01G169700 chr7A 514688531 514689151 620 True 627.00 627 84.8480 1 627 1 chr7A.!!$R1 626
4 TraesCS7B01G169700 chr7D 263033148 263039004 5856 False 2170.50 3260 93.6330 55 5859 4 chr7D.!!$F1 5804
5 TraesCS7B01G169700 chr2A 445577115 445577735 620 True 632.00 632 85.0080 1 627 1 chr2A.!!$R1 626
6 TraesCS7B01G169700 chr5A 533479811 533480563 752 True 348.50 571 86.7050 990 1857 2 chr5A.!!$R1 867

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
332 334 1.472728 GGGCGTCAGTGGTATCGAATT 60.473 52.381 0.0 0.0 0.0 2.17 F
1062 1102 0.105039 CCTAGCTTCCACCCACGATC 59.895 60.000 0.0 0.0 0.0 3.69 F
2891 3207 0.251165 ACGGTTTGATTGGTCCAGGG 60.251 55.000 0.0 0.0 0.0 4.45 F
4711 5036 0.400213 ATCACCTTCACCTTTGCCGA 59.600 50.000 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2508 0.669318 CACGTCCGCTGGAGCTTTAA 60.669 55.000 0.00 0.0 39.32 1.52 R
3044 3363 1.138859 CAGGTCAATCGCCTGTATCCA 59.861 52.381 3.37 0.0 46.22 3.41 R
4732 5057 0.244450 ATGCACGCATCCCAAACAAG 59.756 50.000 0.00 0.0 29.42 3.16 R
5840 6222 3.243975 CCCTTCCGTTGTAGGCGTTATAT 60.244 47.826 0.00 0.0 0.00 0.86 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
26 27 3.762407 TTCATTGTTTCGGTCCTCAGA 57.238 42.857 0.00 0.00 0.00 3.27
107 108 3.459232 TGAGTGTTCAGACCTTCAGTG 57.541 47.619 0.00 0.00 0.00 3.66
205 207 8.730680 CAGGTAGTTTAGCAAGTTTGTTCATAT 58.269 33.333 0.00 0.00 0.00 1.78
213 215 9.820229 TTAGCAAGTTTGTTCATATAGTTTTCG 57.180 29.630 0.00 0.00 0.00 3.46
307 309 3.979347 AGATAGATGCTGGAAATGGACCT 59.021 43.478 0.00 0.00 0.00 3.85
310 312 3.891049 AGATGCTGGAAATGGACCTAAC 58.109 45.455 0.00 0.00 0.00 2.34
311 313 3.266772 AGATGCTGGAAATGGACCTAACA 59.733 43.478 0.00 0.00 0.00 2.41
332 334 1.472728 GGGCGTCAGTGGTATCGAATT 60.473 52.381 0.00 0.00 0.00 2.17
395 397 7.375106 ACAACTCTCAGAGCAAGATAATTTG 57.625 36.000 0.00 0.00 32.04 2.32
606 609 7.437862 GGTTTTGCATTTGTTTTCATCAGTCTA 59.562 33.333 0.00 0.00 0.00 2.59
607 610 8.816144 GTTTTGCATTTGTTTTCATCAGTCTAA 58.184 29.630 0.00 0.00 0.00 2.10
608 611 8.939201 TTTGCATTTGTTTTCATCAGTCTAAA 57.061 26.923 0.00 0.00 0.00 1.85
612 615 7.359514 GCATTTGTTTTCATCAGTCTAAAAGCC 60.360 37.037 0.00 0.00 0.00 4.35
642 645 2.663188 GTGATCGGAGGCGATGGC 60.663 66.667 0.00 0.00 38.90 4.40
730 760 2.282674 ACCGGCGTAGGTGACTGA 60.283 61.111 6.01 0.00 44.07 3.41
731 761 2.181021 CCGGCGTAGGTGACTGAC 59.819 66.667 6.01 0.00 43.88 3.51
732 762 2.202440 CGGCGTAGGTGACTGACG 60.202 66.667 0.00 5.64 43.88 4.35
733 763 2.181021 GGCGTAGGTGACTGACGG 59.819 66.667 10.74 0.00 43.88 4.79
734 764 2.506438 GCGTAGGTGACTGACGGC 60.506 66.667 10.74 0.00 43.88 5.68
735 765 2.202440 CGTAGGTGACTGACGGCG 60.202 66.667 4.80 4.80 43.88 6.46
736 766 2.506438 GTAGGTGACTGACGGCGC 60.506 66.667 6.90 0.00 43.88 6.53
737 767 2.986979 TAGGTGACTGACGGCGCA 60.987 61.111 10.83 5.20 43.88 6.09
738 768 2.989881 TAGGTGACTGACGGCGCAG 61.990 63.158 23.18 23.18 43.88 5.18
1055 1095 3.015145 TGGCCCCTAGCTTCCACC 61.015 66.667 0.00 0.00 43.05 4.61
1056 1096 3.810188 GGCCCCTAGCTTCCACCC 61.810 72.222 0.00 0.00 43.05 4.61
1057 1097 3.015145 GCCCCTAGCTTCCACCCA 61.015 66.667 0.00 0.00 38.99 4.51
1058 1098 2.998949 CCCCTAGCTTCCACCCAC 59.001 66.667 0.00 0.00 0.00 4.61
1059 1099 2.584608 CCCTAGCTTCCACCCACG 59.415 66.667 0.00 0.00 0.00 4.94
1060 1100 1.987855 CCCTAGCTTCCACCCACGA 60.988 63.158 0.00 0.00 0.00 4.35
1061 1101 1.338136 CCCTAGCTTCCACCCACGAT 61.338 60.000 0.00 0.00 0.00 3.73
1062 1102 0.105039 CCTAGCTTCCACCCACGATC 59.895 60.000 0.00 0.00 0.00 3.69
1063 1103 0.105039 CTAGCTTCCACCCACGATCC 59.895 60.000 0.00 0.00 0.00 3.36
1064 1104 0.616395 TAGCTTCCACCCACGATCCA 60.616 55.000 0.00 0.00 0.00 3.41
1065 1105 1.745489 GCTTCCACCCACGATCCAC 60.745 63.158 0.00 0.00 0.00 4.02
1066 1106 1.078426 CTTCCACCCACGATCCACC 60.078 63.158 0.00 0.00 0.00 4.61
1175 1229 2.185310 AACCAGGCACCGTCATCTCC 62.185 60.000 0.00 0.00 0.00 3.71
1202 1256 2.107750 CGCTCGCTCATGGTGGAT 59.892 61.111 0.00 0.00 0.00 3.41
1247 1301 0.753262 GCTCCATCCACTATCCACGT 59.247 55.000 0.00 0.00 0.00 4.49
1401 1457 5.243730 TCATTCATCTCATCGTATGCCTACA 59.756 40.000 0.00 0.00 0.00 2.74
1764 1845 2.556189 CAATCGGACCATCAAACCACAA 59.444 45.455 0.00 0.00 0.00 3.33
1765 1846 2.577606 TCGGACCATCAAACCACAAT 57.422 45.000 0.00 0.00 0.00 2.71
1766 1847 2.870175 TCGGACCATCAAACCACAATT 58.130 42.857 0.00 0.00 0.00 2.32
1768 1849 4.594970 TCGGACCATCAAACCACAATTAT 58.405 39.130 0.00 0.00 0.00 1.28
1769 1850 5.746284 TCGGACCATCAAACCACAATTATA 58.254 37.500 0.00 0.00 0.00 0.98
1770 1851 6.361433 TCGGACCATCAAACCACAATTATAT 58.639 36.000 0.00 0.00 0.00 0.86
1771 1852 7.510407 TCGGACCATCAAACCACAATTATATA 58.490 34.615 0.00 0.00 0.00 0.86
1772 1853 7.442969 TCGGACCATCAAACCACAATTATATAC 59.557 37.037 0.00 0.00 0.00 1.47
1773 1854 7.444183 CGGACCATCAAACCACAATTATATACT 59.556 37.037 0.00 0.00 0.00 2.12
1774 1855 8.567948 GGACCATCAAACCACAATTATATACTG 58.432 37.037 0.00 0.00 0.00 2.74
1775 1856 9.120538 GACCATCAAACCACAATTATATACTGT 57.879 33.333 0.00 0.00 0.00 3.55
1798 1879 8.083462 TGTAATTATTATCAGTTGCGGACATC 57.917 34.615 0.00 0.00 0.00 3.06
1820 2063 4.081142 TCCCAAACTAGATGCATTTCGAGA 60.081 41.667 0.00 0.00 0.00 4.04
1823 2104 6.253746 CCAAACTAGATGCATTTCGAGAAAG 58.746 40.000 0.00 0.00 33.32 2.62
1931 2212 2.351157 GCTCATGCAGAAGTTTGTGACC 60.351 50.000 0.00 0.00 39.41 4.02
1955 2236 3.258372 TCGTAGTGAACAAGCTCAAGGAT 59.742 43.478 0.00 0.00 0.00 3.24
2025 2306 2.953648 CTGCATGCAATATCTTGACCCA 59.046 45.455 22.88 0.00 34.04 4.51
2037 2318 3.766545 TCTTGACCCATTTTCTTCCTGG 58.233 45.455 0.00 0.00 0.00 4.45
2059 2340 7.766278 CCTGGTGAATACTTATACCTATCATGC 59.234 40.741 0.00 0.00 34.32 4.06
2185 2467 3.122369 GGCAGCTAAGATGGCCATT 57.878 52.632 21.84 8.45 45.70 3.16
2226 2508 2.430248 TGGATCATGTGCAAGCAGAT 57.570 45.000 0.00 0.00 0.00 2.90
2709 3020 1.202639 TGACAGAATCACACGGTTGCT 60.203 47.619 0.00 0.00 29.99 3.91
2738 3054 2.370849 ACAGTACCACGGAGGAACAAAT 59.629 45.455 2.94 0.00 41.22 2.32
2795 3111 3.456431 CTACGACGAGGCGCCTCTG 62.456 68.421 44.11 37.77 40.69 3.35
2831 3147 1.202359 GCAGAGACAGACGAATCCTCC 60.202 57.143 0.00 0.00 0.00 4.30
2880 3196 6.207614 TGTTGATTTATGGATGAACGGTTTGA 59.792 34.615 0.00 0.00 0.00 2.69
2891 3207 0.251165 ACGGTTTGATTGGTCCAGGG 60.251 55.000 0.00 0.00 0.00 4.45
2923 3239 1.077212 CCAAGTGGGGCCATCTGAG 60.077 63.158 4.39 0.00 0.00 3.35
3031 3350 4.513318 GGTTCTCTTCAGTTCTCTTGTTGG 59.487 45.833 0.00 0.00 0.00 3.77
3032 3351 5.360591 GTTCTCTTCAGTTCTCTTGTTGGA 58.639 41.667 0.00 0.00 0.00 3.53
3033 3352 5.614324 TCTCTTCAGTTCTCTTGTTGGAA 57.386 39.130 0.00 0.00 0.00 3.53
3034 3353 6.179906 TCTCTTCAGTTCTCTTGTTGGAAT 57.820 37.500 0.00 0.00 0.00 3.01
3035 3354 5.994054 TCTCTTCAGTTCTCTTGTTGGAATG 59.006 40.000 0.00 0.00 0.00 2.67
3036 3355 5.065914 TCTTCAGTTCTCTTGTTGGAATGG 58.934 41.667 0.00 0.00 0.00 3.16
3037 3356 4.705110 TCAGTTCTCTTGTTGGAATGGA 57.295 40.909 0.00 0.00 0.00 3.41
3038 3357 5.047566 TCAGTTCTCTTGTTGGAATGGAA 57.952 39.130 0.00 0.00 0.00 3.53
3039 3358 5.634118 TCAGTTCTCTTGTTGGAATGGAAT 58.366 37.500 0.00 0.00 0.00 3.01
3040 3359 5.474532 TCAGTTCTCTTGTTGGAATGGAATG 59.525 40.000 0.00 0.00 0.00 2.67
3041 3360 4.768968 AGTTCTCTTGTTGGAATGGAATGG 59.231 41.667 0.00 0.00 0.00 3.16
3042 3361 4.656100 TCTCTTGTTGGAATGGAATGGA 57.344 40.909 0.00 0.00 0.00 3.41
3043 3362 4.996793 TCTCTTGTTGGAATGGAATGGAA 58.003 39.130 0.00 0.00 0.00 3.53
3044 3363 5.582953 TCTCTTGTTGGAATGGAATGGAAT 58.417 37.500 0.00 0.00 0.00 3.01
3045 3364 5.419788 TCTCTTGTTGGAATGGAATGGAATG 59.580 40.000 0.00 0.00 0.00 2.67
3046 3365 4.467082 TCTTGTTGGAATGGAATGGAATGG 59.533 41.667 0.00 0.00 0.00 3.16
3047 3366 4.058417 TGTTGGAATGGAATGGAATGGA 57.942 40.909 0.00 0.00 0.00 3.41
3048 3367 4.622815 TGTTGGAATGGAATGGAATGGAT 58.377 39.130 0.00 0.00 0.00 3.41
3049 3368 5.775268 TGTTGGAATGGAATGGAATGGATA 58.225 37.500 0.00 0.00 0.00 2.59
3050 3369 5.598005 TGTTGGAATGGAATGGAATGGATAC 59.402 40.000 0.00 0.00 0.00 2.24
3063 3382 1.496060 TGGATACAGGCGATTGACCT 58.504 50.000 0.00 0.00 46.17 3.85
3070 3389 1.270907 AGGCGATTGACCTGAGAAGT 58.729 50.000 0.00 0.00 35.72 3.01
3071 3390 1.625818 AGGCGATTGACCTGAGAAGTT 59.374 47.619 0.00 0.00 35.72 2.66
3072 3391 2.039084 AGGCGATTGACCTGAGAAGTTT 59.961 45.455 0.00 0.00 35.72 2.66
3073 3392 2.160417 GGCGATTGACCTGAGAAGTTTG 59.840 50.000 0.00 0.00 0.00 2.93
3081 3400 5.482908 TGACCTGAGAAGTTTGCTATCTTC 58.517 41.667 9.99 9.99 39.93 2.87
3170 3495 2.743718 CCGGAGCAGAAGGTGTGT 59.256 61.111 0.00 0.00 0.00 3.72
3266 3591 1.520342 GCGGTCTGTCAGCATCCTC 60.520 63.158 0.00 0.00 37.22 3.71
3352 3677 2.432628 CTTCACGGACCAGACGGC 60.433 66.667 0.00 0.00 34.57 5.68
3392 3717 0.763604 TGTACACGGAGGGGGACAAA 60.764 55.000 0.00 0.00 27.02 2.83
3398 3723 2.359975 GAGGGGGACAAAGTGCCG 60.360 66.667 1.56 0.00 45.19 5.69
3461 3786 2.357154 GGCCTACAACATGACCAAGGAT 60.357 50.000 0.00 0.00 0.00 3.24
3503 3828 2.425143 CCACCAGGTACGTACTAGGA 57.575 55.000 30.30 0.00 0.00 2.94
3504 3829 2.295885 CCACCAGGTACGTACTAGGAG 58.704 57.143 30.30 24.75 0.00 3.69
3505 3830 2.356535 CCACCAGGTACGTACTAGGAGT 60.357 54.545 30.30 17.58 0.00 3.85
3506 3831 3.118261 CCACCAGGTACGTACTAGGAGTA 60.118 52.174 30.30 0.00 0.00 2.59
3507 3832 4.125703 CACCAGGTACGTACTAGGAGTAG 58.874 52.174 30.30 18.34 30.12 2.57
3508 3833 3.777522 ACCAGGTACGTACTAGGAGTAGT 59.222 47.826 30.30 14.05 42.49 2.73
3509 3834 4.962995 ACCAGGTACGTACTAGGAGTAGTA 59.037 45.833 30.30 0.00 40.23 1.82
3519 3844 5.181690 ACTAGGAGTAGTACGTCTCTACG 57.818 47.826 18.50 10.71 42.36 3.51
3549 3874 8.407064 ACTAGTATTATATATCTTGCGAGTGGC 58.593 37.037 0.00 0.00 43.96 5.01
3599 3924 4.284550 GGTGGGTGGCAGCTTCCA 62.285 66.667 17.16 0.00 0.00 3.53
3987 4312 2.317609 CGAGGTGCAGTGGAAACCG 61.318 63.158 0.00 0.00 39.07 4.44
4000 4325 4.974989 AACCGGCGGTGTTCGACC 62.975 66.667 34.87 0.00 45.97 4.79
4405 4730 2.156051 GACGTGCCCGGAGAAGAAGT 62.156 60.000 0.73 0.00 38.78 3.01
4468 4793 1.421410 GATCTGCGGCAACTACACGG 61.421 60.000 3.44 0.00 0.00 4.94
4470 4795 2.663520 TGCGGCAACTACACGGTG 60.664 61.111 6.58 6.58 0.00 4.94
4476 4801 1.448922 GCAACTACACGGTGGGCAAA 61.449 55.000 13.48 0.00 0.00 3.68
4655 4980 1.859080 GACCGCCGAGCAATAAGTAAG 59.141 52.381 0.00 0.00 0.00 2.34
4665 4990 5.174761 CGAGCAATAAGTAAGCTAAGCTCAG 59.825 44.000 11.06 0.00 45.45 3.35
4686 5011 8.128582 GCTCAGATATGTACTGCTATGTAGATC 58.871 40.741 0.00 0.00 35.61 2.75
4700 5025 7.035004 GCTATGTAGATCATCTCATCACCTTC 58.965 42.308 0.00 0.00 37.91 3.46
4707 5032 4.582869 TCATCTCATCACCTTCACCTTTG 58.417 43.478 0.00 0.00 0.00 2.77
4708 5033 2.783135 TCTCATCACCTTCACCTTTGC 58.217 47.619 0.00 0.00 0.00 3.68
4709 5034 1.815003 CTCATCACCTTCACCTTTGCC 59.185 52.381 0.00 0.00 0.00 4.52
4710 5035 0.523072 CATCACCTTCACCTTTGCCG 59.477 55.000 0.00 0.00 0.00 5.69
4711 5036 0.400213 ATCACCTTCACCTTTGCCGA 59.600 50.000 0.00 0.00 0.00 5.54
4712 5037 0.534203 TCACCTTCACCTTTGCCGAC 60.534 55.000 0.00 0.00 0.00 4.79
4713 5038 1.228154 ACCTTCACCTTTGCCGACC 60.228 57.895 0.00 0.00 0.00 4.79
4714 5039 1.228124 CCTTCACCTTTGCCGACCA 60.228 57.895 0.00 0.00 0.00 4.02
4715 5040 0.609131 CCTTCACCTTTGCCGACCAT 60.609 55.000 0.00 0.00 0.00 3.55
4716 5041 0.523072 CTTCACCTTTGCCGACCATG 59.477 55.000 0.00 0.00 0.00 3.66
4717 5042 0.893270 TTCACCTTTGCCGACCATGG 60.893 55.000 11.19 11.19 0.00 3.66
4718 5043 1.603455 CACCTTTGCCGACCATGGT 60.603 57.895 19.89 19.89 32.93 3.55
4731 5056 3.671433 CGACCATGGTCTTTTTCATGCTG 60.671 47.826 35.84 16.44 42.54 4.41
4732 5057 2.028748 ACCATGGTCTTTTTCATGCTGC 60.029 45.455 13.00 0.00 39.36 5.25
4780 5109 6.183360 TGTTGTACTTTGTTGATTCCTGTGAC 60.183 38.462 0.00 0.00 0.00 3.67
5013 5342 1.373435 CCACTAGACCAAACGCCCA 59.627 57.895 0.00 0.00 0.00 5.36
5024 5353 3.829601 ACCAAACGCCCAGATTGAAATTA 59.170 39.130 0.00 0.00 34.95 1.40
5025 5354 4.173256 CCAAACGCCCAGATTGAAATTAC 58.827 43.478 0.00 0.00 34.95 1.89
5026 5355 4.321601 CCAAACGCCCAGATTGAAATTACA 60.322 41.667 0.00 0.00 34.95 2.41
5037 5366 7.703621 CCAGATTGAAATTACATGTCATTGGAC 59.296 37.037 0.00 0.24 44.57 4.02
5038 5367 8.464404 CAGATTGAAATTACATGTCATTGGACT 58.536 33.333 0.00 0.00 44.61 3.85
5090 5419 4.196193 GACGAGGAGAGAAGAGATGAAGA 58.804 47.826 0.00 0.00 0.00 2.87
5101 5430 8.260114 AGAGAAGAGATGAAGAGGAATTCTTTC 58.740 37.037 5.23 7.92 46.12 2.62
5183 5512 1.165270 ACAAGGCAATGCTAACCGAC 58.835 50.000 4.82 0.00 0.00 4.79
5188 5517 1.429148 GCAATGCTAACCGACGAGGG 61.429 60.000 0.00 1.14 46.96 4.30
5190 5519 0.460311 AATGCTAACCGACGAGGGAG 59.540 55.000 0.00 3.27 46.96 4.30
5339 5706 8.794335 AAAACTTTGGGCACAAGTTATAAAAA 57.206 26.923 14.27 0.00 37.97 1.94
5445 5812 9.816787 TGAATATTTTTACCCAGGTTAACTCTT 57.183 29.630 5.42 0.00 0.00 2.85
5484 5851 6.462347 CCCTACACCTTGCTTGTGTTTTATTT 60.462 38.462 10.82 0.00 44.19 1.40
5499 5866 7.012515 TGTGTTTTATTTCGTTGGAGTGTGTAT 59.987 33.333 0.00 0.00 0.00 2.29
5575 5953 3.314693 TCCTTGGGTACATGGATCCTAC 58.685 50.000 9.19 7.20 43.67 3.18
5577 5955 4.171243 TCCTTGGGTACATGGATCCTACTA 59.829 45.833 9.19 0.00 43.67 1.82
5586 5964 1.674441 TGGATCCTACTACGCTTCGTG 59.326 52.381 14.23 0.00 41.39 4.35
5616 5994 1.279271 AGATCCTTCCACGAAACCCTG 59.721 52.381 0.00 0.00 0.00 4.45
5656 6034 4.079253 TGGGGTGATAAGCTTTTTCTCAC 58.921 43.478 3.20 12.57 36.38 3.51
5665 6043 8.177663 TGATAAGCTTTTTCTCACGAATGATTC 58.822 33.333 3.20 0.00 33.22 2.52
5685 6063 8.010733 TGATTCCATATTGAGGTGGATTTTTC 57.989 34.615 0.00 0.00 43.61 2.29
5687 6065 5.836705 TCCATATTGAGGTGGATTTTTCCA 58.163 37.500 0.00 0.00 39.51 3.53
5688 6066 6.442961 TCCATATTGAGGTGGATTTTTCCAT 58.557 36.000 0.00 0.00 42.41 3.41
5689 6067 6.324512 TCCATATTGAGGTGGATTTTTCCATG 59.675 38.462 0.00 0.00 42.41 3.66
5690 6068 6.098695 CCATATTGAGGTGGATTTTTCCATGT 59.901 38.462 0.00 0.00 42.41 3.21
5691 6069 7.287466 CCATATTGAGGTGGATTTTTCCATGTA 59.713 37.037 0.00 0.00 42.41 2.29
5692 6070 8.863086 CATATTGAGGTGGATTTTTCCATGTAT 58.137 33.333 0.00 0.00 42.41 2.29
5693 6071 6.528537 TTGAGGTGGATTTTTCCATGTATG 57.471 37.500 0.00 0.00 42.41 2.39
5780 6161 5.438761 ACTAAGATGAACACAGCCAAAAC 57.561 39.130 0.00 0.00 0.00 2.43
5782 6163 4.734398 AAGATGAACACAGCCAAAACAA 57.266 36.364 0.00 0.00 0.00 2.83
5840 6222 3.349022 ACAAAGAAACGTTTGGAGTCCA 58.651 40.909 20.10 8.12 41.03 4.02
5859 6241 3.384146 TCCATATAACGCCTACAACGGAA 59.616 43.478 0.00 0.00 34.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.396435 TTGTAGGCTGTGGTGGTCTG 59.604 55.000 0.00 0.00 0.00 3.51
26 27 1.349542 TGGTTGTAGGCTGTGGTGGT 61.350 55.000 0.00 0.00 0.00 4.16
107 108 3.944087 AGACTTAACATGGACTGAAGCC 58.056 45.455 0.00 0.00 0.00 4.35
205 207 7.653647 ACAAAATGCAGATAAACCGAAAACTA 58.346 30.769 0.00 0.00 0.00 2.24
213 215 7.599998 AGTGAAATGACAAAATGCAGATAAACC 59.400 33.333 0.00 0.00 0.00 3.27
290 292 3.620488 TGTTAGGTCCATTTCCAGCATC 58.380 45.455 0.00 0.00 0.00 3.91
307 309 1.479323 GATACCACTGACGCCCTGTTA 59.521 52.381 0.00 0.00 0.00 2.41
310 312 1.226974 CGATACCACTGACGCCCTG 60.227 63.158 0.00 0.00 0.00 4.45
311 313 0.968901 TTCGATACCACTGACGCCCT 60.969 55.000 0.00 0.00 0.00 5.19
332 334 3.649502 AGCATGTATCTGATCATGGTGGA 59.350 43.478 22.20 0.00 46.31 4.02
395 397 1.378531 TGTTGGCGCAGATCCATAAC 58.621 50.000 10.83 1.70 32.92 1.89
606 609 2.821969 CACTGATGCTACTTGGGCTTTT 59.178 45.455 0.00 0.00 0.00 2.27
607 610 2.040278 TCACTGATGCTACTTGGGCTTT 59.960 45.455 0.00 0.00 0.00 3.51
608 611 1.630369 TCACTGATGCTACTTGGGCTT 59.370 47.619 0.00 0.00 0.00 4.35
612 615 2.101415 TCCGATCACTGATGCTACTTGG 59.899 50.000 0.00 0.00 0.00 3.61
642 645 2.230940 CGGACGTGCTTCGCTATGG 61.231 63.158 5.27 0.00 44.19 2.74
735 765 4.210304 GAATCGTCACGCCGCTGC 62.210 66.667 0.00 0.00 0.00 5.25
736 766 3.554692 GGAATCGTCACGCCGCTG 61.555 66.667 0.00 0.00 0.00 5.18
737 767 4.814294 GGGAATCGTCACGCCGCT 62.814 66.667 0.00 0.00 0.00 5.52
970 1010 2.550699 TAAAGGGATGGCGCTGTGGG 62.551 60.000 7.64 0.00 37.38 4.61
1055 1095 1.451927 CATGGTGGGTGGATCGTGG 60.452 63.158 0.00 0.00 0.00 4.94
1056 1096 0.744414 GACATGGTGGGTGGATCGTG 60.744 60.000 0.00 0.00 0.00 4.35
1057 1097 1.602237 GACATGGTGGGTGGATCGT 59.398 57.895 0.00 0.00 0.00 3.73
1058 1098 1.153168 GGACATGGTGGGTGGATCG 60.153 63.158 0.00 0.00 0.00 3.69
1059 1099 1.227383 GGGACATGGTGGGTGGATC 59.773 63.158 0.00 0.00 0.00 3.36
1060 1100 1.230281 AGGGACATGGTGGGTGGAT 60.230 57.895 0.00 0.00 0.00 3.41
1061 1101 1.923395 GAGGGACATGGTGGGTGGA 60.923 63.158 0.00 0.00 0.00 4.02
1062 1102 2.677228 GAGGGACATGGTGGGTGG 59.323 66.667 0.00 0.00 0.00 4.61
1063 1103 1.915078 GAGGAGGGACATGGTGGGTG 61.915 65.000 0.00 0.00 0.00 4.61
1064 1104 1.616628 GAGGAGGGACATGGTGGGT 60.617 63.158 0.00 0.00 0.00 4.51
1065 1105 2.378634 GGAGGAGGGACATGGTGGG 61.379 68.421 0.00 0.00 0.00 4.61
1066 1106 1.616327 TGGAGGAGGGACATGGTGG 60.616 63.158 0.00 0.00 0.00 4.61
1299 1353 2.031807 CGTAGGACTCGATGACGTTGAT 59.968 50.000 0.00 0.00 40.69 2.57
1401 1457 2.545952 GGAATGGACGATGAGCACGTAT 60.546 50.000 0.00 0.00 43.97 3.06
1769 1850 9.204570 GTCCGCAACTGATAATAATTACAGTAT 57.795 33.333 6.83 0.00 41.73 2.12
1770 1851 8.198778 TGTCCGCAACTGATAATAATTACAGTA 58.801 33.333 6.83 0.00 41.73 2.74
1771 1852 7.045416 TGTCCGCAACTGATAATAATTACAGT 58.955 34.615 0.00 0.00 43.92 3.55
1772 1853 7.477144 TGTCCGCAACTGATAATAATTACAG 57.523 36.000 0.00 0.00 36.58 2.74
1773 1854 7.172532 GGATGTCCGCAACTGATAATAATTACA 59.827 37.037 0.00 0.00 0.00 2.41
1774 1855 7.360946 GGGATGTCCGCAACTGATAATAATTAC 60.361 40.741 0.00 0.00 36.71 1.89
1775 1856 6.653320 GGGATGTCCGCAACTGATAATAATTA 59.347 38.462 0.00 0.00 36.71 1.40
1776 1857 5.473504 GGGATGTCCGCAACTGATAATAATT 59.526 40.000 0.00 0.00 36.71 1.40
1777 1858 5.003804 GGGATGTCCGCAACTGATAATAAT 58.996 41.667 0.00 0.00 36.71 1.28
1778 1859 4.141597 TGGGATGTCCGCAACTGATAATAA 60.142 41.667 0.00 0.00 38.76 1.40
1779 1860 3.389656 TGGGATGTCCGCAACTGATAATA 59.610 43.478 0.00 0.00 38.76 0.98
1798 1879 4.191544 TCTCGAAATGCATCTAGTTTGGG 58.808 43.478 0.00 0.00 0.00 4.12
1931 2212 2.724977 TGAGCTTGTTCACTACGAGG 57.275 50.000 0.00 0.00 38.51 4.63
2012 2293 6.608808 CCAGGAAGAAAATGGGTCAAGATATT 59.391 38.462 0.00 0.00 0.00 1.28
2025 2306 9.628500 GGTATAAGTATTCACCAGGAAGAAAAT 57.372 33.333 0.00 0.00 39.30 1.82
2037 2318 8.607459 GCATGCATGATAGGTATAAGTATTCAC 58.393 37.037 30.64 1.38 0.00 3.18
2059 2340 5.163893 GGTGCATTTCATTTGAGAAAGCATG 60.164 40.000 12.82 0.00 40.35 4.06
2226 2508 0.669318 CACGTCCGCTGGAGCTTTAA 60.669 55.000 0.00 0.00 39.32 1.52
2576 2880 2.580601 CCCCACCGAGAAGAACCGT 61.581 63.158 0.00 0.00 0.00 4.83
2738 3054 2.557372 GGCGCCCGTTCTTCCAAAA 61.557 57.895 18.11 0.00 0.00 2.44
2795 3111 2.603560 CTCTGCTTTACCGAATTCGTCC 59.396 50.000 25.10 8.07 37.74 4.79
2831 3147 9.113838 ACATAGTTAAGCATATTCAGAGTTTGG 57.886 33.333 0.00 0.00 0.00 3.28
2880 3196 3.075882 TCTTTGAACATCCCTGGACCAAT 59.924 43.478 0.00 0.00 0.00 3.16
2891 3207 2.229784 CCACTTGGGCTCTTTGAACATC 59.770 50.000 0.00 0.00 0.00 3.06
3031 3350 4.219288 GCCTGTATCCATTCCATTCCATTC 59.781 45.833 0.00 0.00 0.00 2.67
3032 3351 4.154942 GCCTGTATCCATTCCATTCCATT 58.845 43.478 0.00 0.00 0.00 3.16
3033 3352 3.771216 GCCTGTATCCATTCCATTCCAT 58.229 45.455 0.00 0.00 0.00 3.41
3034 3353 2.487086 CGCCTGTATCCATTCCATTCCA 60.487 50.000 0.00 0.00 0.00 3.53
3035 3354 2.154462 CGCCTGTATCCATTCCATTCC 58.846 52.381 0.00 0.00 0.00 3.01
3036 3355 3.126001 TCGCCTGTATCCATTCCATTC 57.874 47.619 0.00 0.00 0.00 2.67
3037 3356 3.795688 ATCGCCTGTATCCATTCCATT 57.204 42.857 0.00 0.00 0.00 3.16
3038 3357 3.072915 TCAATCGCCTGTATCCATTCCAT 59.927 43.478 0.00 0.00 0.00 3.41
3039 3358 2.437651 TCAATCGCCTGTATCCATTCCA 59.562 45.455 0.00 0.00 0.00 3.53
3040 3359 2.808543 GTCAATCGCCTGTATCCATTCC 59.191 50.000 0.00 0.00 0.00 3.01
3041 3360 2.808543 GGTCAATCGCCTGTATCCATTC 59.191 50.000 0.00 0.00 0.00 2.67
3042 3361 2.439507 AGGTCAATCGCCTGTATCCATT 59.560 45.455 0.00 0.00 34.56 3.16
3043 3362 2.050144 AGGTCAATCGCCTGTATCCAT 58.950 47.619 0.00 0.00 34.56 3.41
3044 3363 1.138859 CAGGTCAATCGCCTGTATCCA 59.861 52.381 3.37 0.00 46.22 3.41
3045 3364 1.871080 CAGGTCAATCGCCTGTATCC 58.129 55.000 3.37 0.00 46.22 2.59
3051 3370 1.270907 ACTTCTCAGGTCAATCGCCT 58.729 50.000 0.00 0.00 36.66 5.52
3052 3371 2.100605 AACTTCTCAGGTCAATCGCC 57.899 50.000 0.00 0.00 0.00 5.54
3053 3372 2.413371 GCAAACTTCTCAGGTCAATCGC 60.413 50.000 0.00 0.00 0.00 4.58
3054 3373 3.070018 AGCAAACTTCTCAGGTCAATCG 58.930 45.455 0.00 0.00 0.00 3.34
3055 3374 6.112058 AGATAGCAAACTTCTCAGGTCAATC 58.888 40.000 0.00 0.00 0.00 2.67
3056 3375 6.059787 AGATAGCAAACTTCTCAGGTCAAT 57.940 37.500 0.00 0.00 0.00 2.57
3057 3376 5.489792 AGATAGCAAACTTCTCAGGTCAA 57.510 39.130 0.00 0.00 0.00 3.18
3058 3377 5.247110 AGAAGATAGCAAACTTCTCAGGTCA 59.753 40.000 11.57 0.00 46.28 4.02
3059 3378 5.729510 AGAAGATAGCAAACTTCTCAGGTC 58.270 41.667 11.57 0.00 46.28 3.85
3060 3379 5.753721 AGAAGATAGCAAACTTCTCAGGT 57.246 39.130 11.57 0.00 46.28 4.00
3066 3385 7.287229 GCGATCATAAGAAGATAGCAAACTTC 58.713 38.462 0.00 0.00 41.73 3.01
3067 3386 6.203723 GGCGATCATAAGAAGATAGCAAACTT 59.796 38.462 9.75 0.00 43.22 2.66
3068 3387 5.698545 GGCGATCATAAGAAGATAGCAAACT 59.301 40.000 9.75 0.00 43.22 2.66
3069 3388 5.388890 CGGCGATCATAAGAAGATAGCAAAC 60.389 44.000 0.00 0.00 43.22 2.93
3070 3389 4.686091 CGGCGATCATAAGAAGATAGCAAA 59.314 41.667 0.00 0.00 43.22 3.68
3071 3390 4.022329 TCGGCGATCATAAGAAGATAGCAA 60.022 41.667 4.99 0.00 43.22 3.91
3072 3391 3.506067 TCGGCGATCATAAGAAGATAGCA 59.494 43.478 4.99 0.00 43.22 3.49
3073 3392 4.098055 TCGGCGATCATAAGAAGATAGC 57.902 45.455 4.99 0.00 41.50 2.97
3081 3400 2.733552 CAGGTCAATCGGCGATCATAAG 59.266 50.000 24.20 10.85 0.00 1.73
3141 3466 1.066587 GCTCCGGGATCTCGAACAG 59.933 63.158 18.72 10.28 0.00 3.16
3170 3495 1.525077 GTTGGACAGGAACGCCACA 60.525 57.895 0.00 0.00 36.29 4.17
3352 3677 0.518636 CTCCCACACATTGTTCTGCG 59.481 55.000 0.00 0.00 0.00 5.18
3392 3717 1.000955 CTGAACTTGTAGGTCGGCACT 59.999 52.381 0.00 0.00 33.73 4.40
3398 3723 1.000506 TCGGTGCTGAACTTGTAGGTC 59.999 52.381 0.00 0.00 31.00 3.85
3461 3786 3.264193 TGTACCAGAGGTAGTCGGTCTTA 59.736 47.826 0.00 0.00 39.02 2.10
3548 3873 1.455248 AACATTGGCATTGGCATTGC 58.545 45.000 25.89 22.57 41.12 3.56
3549 3874 3.366476 CCAAAACATTGGCATTGGCATTG 60.366 43.478 24.91 24.91 43.71 2.82
3571 3896 0.601841 CCACCCACCGTACAAGACAC 60.602 60.000 0.00 0.00 0.00 3.67
3574 3899 2.107041 CTGCCACCCACCGTACAAGA 62.107 60.000 0.00 0.00 0.00 3.02
3575 3900 1.671054 CTGCCACCCACCGTACAAG 60.671 63.158 0.00 0.00 0.00 3.16
3849 4174 1.298859 GGATGGTGACCGAGTGCAAC 61.299 60.000 0.00 0.00 0.00 4.17
3850 4175 1.003839 GGATGGTGACCGAGTGCAA 60.004 57.895 0.00 0.00 0.00 4.08
3982 4307 2.968697 GTCGAACACCGCCGGTTT 60.969 61.111 5.76 4.55 38.37 3.27
4000 4325 2.809601 GTACCACGTGAGCGGCTG 60.810 66.667 19.30 0.00 43.45 4.85
4212 4537 1.137872 CCTTCCTCCTCGAAGATGGTG 59.862 57.143 0.00 0.00 41.57 4.17
4405 4730 0.478072 AACACCACCTGCTGGATCAA 59.522 50.000 17.64 0.00 43.95 2.57
4655 4980 5.132897 AGCAGTACATATCTGAGCTTAGC 57.867 43.478 0.00 0.00 35.20 3.09
4686 5011 3.128242 GCAAAGGTGAAGGTGATGAGATG 59.872 47.826 0.00 0.00 0.00 2.90
4700 5025 1.586154 GACCATGGTCGGCAAAGGTG 61.586 60.000 28.52 0.00 35.30 4.00
4708 5033 4.677914 AGCATGAAAAAGACCATGGTCGG 61.678 47.826 33.78 19.12 45.05 4.79
4709 5034 2.489329 AGCATGAAAAAGACCATGGTCG 59.511 45.455 33.78 20.35 45.05 4.79
4710 5035 3.841643 CAGCATGAAAAAGACCATGGTC 58.158 45.455 33.72 33.72 46.03 4.02
4712 5037 2.232941 AGCAGCATGAAAAAGACCATGG 59.767 45.455 11.19 11.19 39.69 3.66
4713 5038 3.587797 AGCAGCATGAAAAAGACCATG 57.412 42.857 0.00 0.00 39.69 3.66
4714 5039 3.322828 ACAAGCAGCATGAAAAAGACCAT 59.677 39.130 4.23 0.00 39.69 3.55
4715 5040 2.694628 ACAAGCAGCATGAAAAAGACCA 59.305 40.909 4.23 0.00 39.69 4.02
4716 5041 3.375782 ACAAGCAGCATGAAAAAGACC 57.624 42.857 4.23 0.00 39.69 3.85
4717 5042 4.025480 CCAAACAAGCAGCATGAAAAAGAC 60.025 41.667 4.23 0.00 39.69 3.01
4718 5043 4.121317 CCAAACAAGCAGCATGAAAAAGA 58.879 39.130 4.23 0.00 39.69 2.52
4731 5056 1.734117 GCACGCATCCCAAACAAGC 60.734 57.895 0.00 0.00 0.00 4.01
4732 5057 0.244450 ATGCACGCATCCCAAACAAG 59.756 50.000 0.00 0.00 29.42 3.16
4780 5109 4.261405 CGCTCCATCTACTCCTAGAACAAG 60.261 50.000 0.00 0.00 32.49 3.16
4936 5265 0.321741 TTCTCGCAACGCCCCAATAA 60.322 50.000 0.00 0.00 0.00 1.40
5013 5342 8.585471 AGTCCAATGACATGTAATTTCAATCT 57.415 30.769 5.62 0.00 44.33 2.40
5024 5353 9.645059 CGAAATATATAGAGTCCAATGACATGT 57.355 33.333 0.00 0.00 44.33 3.21
5025 5354 9.645059 ACGAAATATATAGAGTCCAATGACATG 57.355 33.333 0.00 0.00 44.33 3.21
5090 5419 4.195416 GAGAATGGAGCGAAAGAATTCCT 58.805 43.478 0.65 0.00 31.52 3.36
5101 5430 1.826385 AAGTTTGGGAGAATGGAGCG 58.174 50.000 0.00 0.00 0.00 5.03
5174 5503 1.316651 ATACTCCCTCGTCGGTTAGC 58.683 55.000 0.00 0.00 0.00 3.09
5339 5706 5.499139 TTTGCTTTCGAGACAATGACTTT 57.501 34.783 0.00 0.00 0.00 2.66
5445 5812 5.098663 AGGTGTAGGGTTTTATCTCCTTGA 58.901 41.667 0.00 0.00 32.46 3.02
5484 5851 4.637534 GGTACTCTATACACACTCCAACGA 59.362 45.833 0.00 0.00 0.00 3.85
5499 5866 9.702253 ATATCTCAAAAGTCTCTTGGTACTCTA 57.298 33.333 0.00 0.00 0.00 2.43
5616 5994 6.609616 TCACCCCAGAAATATTCAATAAACCC 59.390 38.462 0.00 0.00 0.00 4.11
5656 6034 5.308014 TCCACCTCAATATGGAATCATTCG 58.692 41.667 0.00 0.00 42.14 3.34
5665 6043 6.098695 ACATGGAAAAATCCACCTCAATATGG 59.901 38.462 0.00 0.00 43.37 2.74
5829 6211 3.805207 AGGCGTTATATGGACTCCAAAC 58.195 45.455 0.66 1.57 36.95 2.93
5840 6222 3.243975 CCCTTCCGTTGTAGGCGTTATAT 60.244 47.826 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.