Multiple sequence alignment - TraesCS7D01G401900

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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 TraesCS7D01G401900 chr7D 100.000 5169 0 0 1 5169 518798414 518793246 0.000000e+00 9546.0
1 TraesCS7D01G401900 chr7D 78.883 412 64 16 3308 3711 215152825 215152429 1.850000e-64 257.0
2 TraesCS7D01G401900 chr7B 95.564 4531 123 36 1 4504 552130996 552126517 0.000000e+00 7182.0
3 TraesCS7D01G401900 chr7B 93.884 327 10 5 4658 4978 552126526 552126204 7.780000e-133 484.0
4 TraesCS7D01G401900 chr7B 90.598 234 18 2 4879 5108 552126195 552125962 1.810000e-79 307.0
5 TraesCS7D01G401900 chr7B 81.013 79 10 4 3876 3952 522138160 522138235 2.010000e-04 58.4
6 TraesCS7D01G401900 chr7A 96.861 1370 40 2 1975 3341 594557050 594555681 0.000000e+00 2289.0
7 TraesCS7D01G401900 chr7A 94.863 1129 34 6 3390 4504 594555685 594554567 0.000000e+00 1742.0
8 TraesCS7D01G401900 chr7A 97.277 955 22 2 906 1860 594557996 594557046 0.000000e+00 1616.0
9 TraesCS7D01G401900 chr7A 88.178 516 33 13 4658 5169 594554576 594554085 1.600000e-164 590.0
10 TraesCS7D01G401900 chr7A 96.821 346 6 3 575 920 594558709 594558369 1.610000e-159 573.0
11 TraesCS7D01G401900 chr7A 91.421 373 25 6 211 578 594578336 594577966 5.970000e-139 505.0
12 TraesCS7D01G401900 chr7A 95.349 172 6 2 4500 4669 156115836 156116007 6.600000e-69 272.0
13 TraesCS7D01G401900 chr7A 97.059 34 0 1 3923 3956 299414791 299414823 7.230000e-04 56.5
14 TraesCS7D01G401900 chr4B 91.509 212 17 1 4959 5169 634724831 634725042 1.820000e-74 291.0
15 TraesCS7D01G401900 chr2D 97.605 167 4 0 4501 4667 376861290 376861456 2.360000e-73 287.0
16 TraesCS7D01G401900 chr2D 95.930 172 6 1 4503 4673 593801760 593801589 1.420000e-70 278.0
17 TraesCS7D01G401900 chr2D 94.318 176 8 2 4500 4674 609886788 609886962 8.530000e-68 268.0
18 TraesCS7D01G401900 chr6D 94.444 180 8 2 4503 4680 104041326 104041147 5.100000e-70 276.0
19 TraesCS7D01G401900 chr5D 96.429 168 5 1 4501 4667 42949726 42949559 5.100000e-70 276.0
20 TraesCS7D01G401900 chr3D 94.382 178 8 2 4491 4666 105119483 105119306 6.600000e-69 272.0
21 TraesCS7D01G401900 chr3D 92.063 63 2 3 3889 3949 475441994 475441933 9.220000e-13 86.1
22 TraesCS7D01G401900 chr2B 92.632 190 8 4 4503 4686 341731565 341731754 8.530000e-68 268.0
23 TraesCS7D01G401900 chr2B 93.407 182 8 4 4503 4681 519599025 519598845 3.070000e-67 267.0
24 TraesCS7D01G401900 chr5A 94.828 58 1 2 3897 3953 29677646 29677702 7.130000e-14 89.8
25 TraesCS7D01G401900 chr4A 96.364 55 1 1 3895 3948 387126062 387126116 7.130000e-14 89.8
26 TraesCS7D01G401900 chr4A 96.970 33 0 1 3924 3956 420017619 420017650 3.000000e-03 54.7
27 TraesCS7D01G401900 chr2A 91.228 57 4 1 3896 3951 699875898 699875954 5.550000e-10 76.8
28 TraesCS7D01G401900 chr3B 88.889 63 4 3 3889 3949 632119055 632118994 2.000000e-09 75.0
29 TraesCS7D01G401900 chr3A 89.286 56 4 2 3892 3947 7308280 7308333 9.290000e-08 69.4
30 TraesCS7D01G401900 chr1B 95.000 40 1 1 3924 3962 662552720 662552681 1.550000e-05 62.1
31 TraesCS7D01G401900 chr1A 83.784 74 2 5 3897 3962 550888529 550888600 1.550000e-05 62.1
32 TraesCS7D01G401900 chr1A 92.857 42 2 1 3916 3957 132413990 132414030 5.590000e-05 60.2
33 TraesCS7D01G401900 chr1A 94.444 36 1 1 3924 3958 572016761 572016726 3.000000e-03 54.7


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 TraesCS7D01G401900 chr7D 518793246 518798414 5168 True 9546.000000 9546 100.000000 1 5169 1 chr7D.!!$R2 5168
1 TraesCS7D01G401900 chr7B 552125962 552130996 5034 True 2657.666667 7182 93.348667 1 5108 3 chr7B.!!$R1 5107
2 TraesCS7D01G401900 chr7A 594554085 594558709 4624 True 1362.000000 2289 94.800000 575 5169 5 chr7A.!!$R2 4594

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
152 157 0.110419 TGCAAGAAAAATCGCGTCCG 60.110 50.0 5.77 0.00 0.00 4.79 F
1311 1723 0.107606 CGAGGAGGAGAAGGAGACGA 60.108 60.0 0.00 0.00 0.00 4.20 F
1901 2313 1.178534 GCCTCCTAGCGAGCTCATCT 61.179 60.0 15.40 12.28 37.27 2.90 F
2556 2969 0.112995 TTCTTGAGTGGGCTGGCAAT 59.887 50.0 2.88 0.00 0.00 3.56 F
3182 3597 1.251251 ATCTGGGCACTGTTTTGAGC 58.749 50.0 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 2235 1.902938 TTTGATCGTCAATGCCCACA 58.097 45.000 2.09 0.0 36.11 4.17 R
2549 2962 0.106335 TGGTTGTGCCAAATTGCCAG 59.894 50.000 0.00 0.0 45.94 4.85 R
3817 4235 2.449450 GGCCGGCCTACTTGGGTAT 61.449 63.158 38.76 0.0 36.00 2.73 R
3970 4388 1.204941 CCACACTACCAGAGTACCAGC 59.795 57.143 0.00 0.0 35.64 4.85 R
4655 5084 0.105039 GCAACCTCATACTCCCTCCG 59.895 60.000 0.00 0.0 0.00 4.63 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
122 127 9.476202 GAAAAATTACTGCAACCTCTTACATTT 57.524 29.630 0.00 0.00 0.00 2.32
128 133 6.476378 ACTGCAACCTCTTACATTTGTCTAT 58.524 36.000 0.00 0.00 0.00 1.98
135 140 6.151144 ACCTCTTACATTTGTCTATGGTTTGC 59.849 38.462 0.00 0.00 0.00 3.68
136 141 6.150976 CCTCTTACATTTGTCTATGGTTTGCA 59.849 38.462 0.00 0.00 0.00 4.08
149 154 2.124122 GGTTTGCAAGAAAAATCGCGT 58.876 42.857 5.77 0.00 0.00 6.01
152 157 0.110419 TGCAAGAAAAATCGCGTCCG 60.110 50.000 5.77 0.00 0.00 4.79
215 220 2.433664 ATTCCGGACAACGCGGTC 60.434 61.111 12.47 9.21 42.52 4.79
216 221 2.939261 ATTCCGGACAACGCGGTCT 61.939 57.895 12.47 0.00 42.52 3.85
221 226 1.582968 GGACAACGCGGTCTAGACA 59.417 57.895 23.91 0.00 37.91 3.41
244 249 1.322538 GCGGGAGGTTTACGGGTCTA 61.323 60.000 0.00 0.00 0.00 2.59
285 290 2.088674 CTTAGATGAGACCCGGGCGG 62.089 65.000 24.08 0.00 37.81 6.13
298 303 2.112297 GGCGGTGTTCCACTGGAA 59.888 61.111 6.39 6.39 40.72 3.53
506 516 9.955102 AGTAAAATATAAAGTCCTTTTCTCCGT 57.045 29.630 0.00 0.00 34.23 4.69
513 523 6.803154 AAAGTCCTTTTCTCCGTGAATTAG 57.197 37.500 0.00 0.00 34.24 1.73
516 526 6.109359 AGTCCTTTTCTCCGTGAATTAGATG 58.891 40.000 0.00 0.00 34.24 2.90
536 546 2.881513 TGGTGCACACGTTTGATGTATT 59.118 40.909 20.43 0.00 0.00 1.89
635 652 2.028567 CCACCAATGTTACCGGCAAAAT 60.029 45.455 0.00 0.00 0.00 1.82
724 742 1.013596 CCAACGTCACTCTTGTTGCA 58.986 50.000 0.00 0.00 41.17 4.08
785 805 1.823899 GTGACCATCGGCCCCAATC 60.824 63.158 0.00 0.00 0.00 2.67
786 806 2.304831 TGACCATCGGCCCCAATCA 61.305 57.895 0.00 0.00 0.00 2.57
891 913 2.068277 GATTCAGCCCATCAAGCCGC 62.068 60.000 0.00 0.00 0.00 6.53
1311 1723 0.107606 CGAGGAGGAGAAGGAGACGA 60.108 60.000 0.00 0.00 0.00 4.20
1370 1782 2.267681 ATTCGCTGTCGGACGGAGAC 62.268 60.000 20.81 3.30 33.04 3.36
1823 2235 5.392767 TCTAGTTTGATCTCGTTGAAGCT 57.607 39.130 0.00 0.00 0.00 3.74
1862 2274 6.734137 TCAAATCGCACAAATTAGTCTTGTT 58.266 32.000 0.00 0.00 34.80 2.83
1867 2279 8.718102 ATCGCACAAATTAGTCTTGTTATAGT 57.282 30.769 0.00 0.00 34.80 2.12
1868 2280 8.542497 TCGCACAAATTAGTCTTGTTATAGTT 57.458 30.769 0.00 0.00 34.80 2.24
1869 2281 8.995220 TCGCACAAATTAGTCTTGTTATAGTTT 58.005 29.630 0.00 0.00 34.80 2.66
1901 2313 1.178534 GCCTCCTAGCGAGCTCATCT 61.179 60.000 15.40 12.28 37.27 2.90
1907 2319 2.493035 CTAGCGAGCTCATCTCTCTCA 58.507 52.381 15.40 0.00 37.91 3.27
1940 2352 3.684305 TGTGATGCTGGTTGAATCGTAAG 59.316 43.478 0.00 0.00 33.26 2.34
1944 2356 5.580691 TGATGCTGGTTGAATCGTAAGTAAG 59.419 40.000 0.00 0.00 33.26 2.34
1945 2357 4.890088 TGCTGGTTGAATCGTAAGTAAGT 58.110 39.130 0.00 0.00 39.48 2.24
1946 2358 6.028146 TGCTGGTTGAATCGTAAGTAAGTA 57.972 37.500 0.00 0.00 39.48 2.24
1947 2359 6.636705 TGCTGGTTGAATCGTAAGTAAGTAT 58.363 36.000 0.00 0.00 39.48 2.12
1951 2363 9.666626 CTGGTTGAATCGTAAGTAAGTATAGAG 57.333 37.037 0.00 0.00 39.48 2.43
2002 2414 6.240894 TCCAAGTTCATAAGCCATATCCATC 58.759 40.000 0.00 0.00 0.00 3.51
2026 2438 9.823647 ATCTAGTTTAATGTGAACAGTCCATAG 57.176 33.333 0.00 0.00 0.00 2.23
2187 2600 3.806949 TGTTCTTAACCCCAGCAAGAT 57.193 42.857 0.00 0.00 0.00 2.40
2403 2816 8.803235 AGGAACGATTTCACTATGCTACATATA 58.197 33.333 0.00 0.00 32.80 0.86
2549 2962 3.823304 AGTTCTCATTTTCTTGAGTGGGC 59.177 43.478 1.76 0.00 43.02 5.36
2556 2969 0.112995 TTCTTGAGTGGGCTGGCAAT 59.887 50.000 2.88 0.00 0.00 3.56
2589 3002 5.600484 ACCATTTTGATGTGGGTACAAGAAA 59.400 36.000 0.00 0.00 40.84 2.52
2614 3027 1.616865 GTTAGGCCCCAAAAACCTGTC 59.383 52.381 0.00 0.00 34.92 3.51
2768 3183 6.797033 AGTTTTGCGAAATTTACTCTTCATCG 59.203 34.615 1.61 0.00 0.00 3.84
2955 3370 2.108952 AGTCAAGGGGCATTCTTGTTCT 59.891 45.455 12.04 9.78 41.52 3.01
3081 3496 2.839975 TGTTCATGCCTGACAACGTTA 58.160 42.857 0.00 0.00 0.00 3.18
3182 3597 1.251251 ATCTGGGCACTGTTTTGAGC 58.749 50.000 0.00 0.00 0.00 4.26
3373 3788 9.158233 CTTAATTGATGATGCCAAAAGTTCATT 57.842 29.630 0.00 0.00 0.00 2.57
3621 4039 7.710907 TCAGATTATGAACGAAGTAGATTTGGG 59.289 37.037 0.00 0.00 45.00 4.12
3748 4166 2.224843 TGATCATGTTGCAGAAGGTGGT 60.225 45.455 0.00 0.00 0.00 4.16
3779 4197 2.143231 TTTTAGGGGGAGAAGGTGGT 57.857 50.000 0.00 0.00 0.00 4.16
3827 4245 9.116067 GTTATCTAAAATGTGCATACCCAAGTA 57.884 33.333 0.00 0.00 0.00 2.24
4051 4469 6.434596 TGTGTTTGATAAGGTTGTTGATTCG 58.565 36.000 0.00 0.00 0.00 3.34
4117 4535 1.009829 CACGAGCTTATCAGTTGGGC 58.990 55.000 0.00 0.00 0.00 5.36
4301 4719 2.414994 TACTTGATCTCGACCTCCGT 57.585 50.000 0.00 0.00 39.75 4.69
4306 4724 1.142262 TGATCTCGACCTCCGTGGATA 59.858 52.381 0.00 0.00 39.71 2.59
4504 4933 1.067142 TGAAGTGGTCGAGGCATGTAC 60.067 52.381 0.00 0.00 0.00 2.90
4505 4934 1.204941 GAAGTGGTCGAGGCATGTACT 59.795 52.381 0.00 0.00 0.00 2.73
4506 4935 1.267121 AGTGGTCGAGGCATGTACTT 58.733 50.000 0.00 0.00 0.00 2.24
4507 4936 1.204941 AGTGGTCGAGGCATGTACTTC 59.795 52.381 0.00 0.00 0.00 3.01
4508 4937 0.535335 TGGTCGAGGCATGTACTTCC 59.465 55.000 0.00 0.00 0.00 3.46
4509 4938 0.824759 GGTCGAGGCATGTACTTCCT 59.175 55.000 0.00 0.00 0.00 3.36
4510 4939 1.202428 GGTCGAGGCATGTACTTCCTC 60.202 57.143 14.58 14.58 42.19 3.71
4511 4940 1.112113 TCGAGGCATGTACTTCCTCC 58.888 55.000 17.14 4.06 42.54 4.30
4512 4941 0.249073 CGAGGCATGTACTTCCTCCG 60.249 60.000 17.14 11.43 42.54 4.63
4513 4942 0.824759 GAGGCATGTACTTCCTCCGT 59.175 55.000 13.97 0.00 40.29 4.69
4514 4943 1.207329 GAGGCATGTACTTCCTCCGTT 59.793 52.381 13.97 0.00 40.29 4.44
4515 4944 1.207329 AGGCATGTACTTCCTCCGTTC 59.793 52.381 0.00 0.00 0.00 3.95
4516 4945 1.653151 GCATGTACTTCCTCCGTTCC 58.347 55.000 0.00 0.00 0.00 3.62
4517 4946 1.742750 GCATGTACTTCCTCCGTTCCC 60.743 57.143 0.00 0.00 0.00 3.97
4518 4947 1.553248 CATGTACTTCCTCCGTTCCCA 59.447 52.381 0.00 0.00 0.00 4.37
4519 4948 1.719529 TGTACTTCCTCCGTTCCCAA 58.280 50.000 0.00 0.00 0.00 4.12
4520 4949 2.048601 TGTACTTCCTCCGTTCCCAAA 58.951 47.619 0.00 0.00 0.00 3.28
4521 4950 2.640826 TGTACTTCCTCCGTTCCCAAAT 59.359 45.455 0.00 0.00 0.00 2.32
4522 4951 3.839490 TGTACTTCCTCCGTTCCCAAATA 59.161 43.478 0.00 0.00 0.00 1.40
4523 4952 4.472108 TGTACTTCCTCCGTTCCCAAATAT 59.528 41.667 0.00 0.00 0.00 1.28
4524 4953 5.662208 TGTACTTCCTCCGTTCCCAAATATA 59.338 40.000 0.00 0.00 0.00 0.86
4525 4954 5.703730 ACTTCCTCCGTTCCCAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
4526 4955 5.681639 ACTTCCTCCGTTCCCAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
4527 4956 5.191124 ACTTCCTCCGTTCCCAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
4528 4957 5.286267 TCCTCCGTTCCCAAATATAAGTC 57.714 43.478 0.00 0.00 0.00 3.01
4529 4958 4.966805 TCCTCCGTTCCCAAATATAAGTCT 59.033 41.667 0.00 0.00 0.00 3.24
4530 4959 5.427481 TCCTCCGTTCCCAAATATAAGTCTT 59.573 40.000 0.00 0.00 0.00 3.01
4531 4960 6.069847 TCCTCCGTTCCCAAATATAAGTCTTT 60.070 38.462 0.00 0.00 0.00 2.52
4532 4961 6.260271 CCTCCGTTCCCAAATATAAGTCTTTC 59.740 42.308 0.00 0.00 0.00 2.62
4533 4962 6.954232 TCCGTTCCCAAATATAAGTCTTTCT 58.046 36.000 0.00 0.00 0.00 2.52
4534 4963 8.081517 TCCGTTCCCAAATATAAGTCTTTCTA 57.918 34.615 0.00 0.00 0.00 2.10
4535 4964 8.202137 TCCGTTCCCAAATATAAGTCTTTCTAG 58.798 37.037 0.00 0.00 0.00 2.43
4536 4965 8.202137 CCGTTCCCAAATATAAGTCTTTCTAGA 58.798 37.037 0.00 0.00 0.00 2.43
4537 4966 9.250624 CGTTCCCAAATATAAGTCTTTCTAGAG 57.749 37.037 0.00 0.00 0.00 2.43
4549 4978 8.600449 AAGTCTTTCTAGAGATTCAACAAGTG 57.400 34.615 0.00 0.00 0.00 3.16
4550 4979 7.957002 AGTCTTTCTAGAGATTCAACAAGTGA 58.043 34.615 0.00 0.00 0.00 3.41
4551 4980 7.870445 AGTCTTTCTAGAGATTCAACAAGTGAC 59.130 37.037 0.00 0.00 35.39 3.67
4552 4981 7.870445 GTCTTTCTAGAGATTCAACAAGTGACT 59.130 37.037 0.00 0.00 35.39 3.41
4553 4982 9.078990 TCTTTCTAGAGATTCAACAAGTGACTA 57.921 33.333 0.00 0.00 35.39 2.59
4554 4983 9.134734 CTTTCTAGAGATTCAACAAGTGACTAC 57.865 37.037 0.00 0.00 35.39 2.73
4555 4984 7.761038 TCTAGAGATTCAACAAGTGACTACA 57.239 36.000 0.00 0.00 35.39 2.74
4556 4985 8.354711 TCTAGAGATTCAACAAGTGACTACAT 57.645 34.615 0.00 0.00 35.39 2.29
4557 4986 9.462606 TCTAGAGATTCAACAAGTGACTACATA 57.537 33.333 0.00 0.00 35.39 2.29
4558 4987 9.509855 CTAGAGATTCAACAAGTGACTACATAC 57.490 37.037 0.00 0.00 35.39 2.39
4559 4988 7.030165 AGAGATTCAACAAGTGACTACATACG 58.970 38.462 0.00 0.00 35.39 3.06
4560 4989 6.920817 AGATTCAACAAGTGACTACATACGA 58.079 36.000 0.00 0.00 35.39 3.43
4561 4990 7.375834 AGATTCAACAAGTGACTACATACGAA 58.624 34.615 0.00 0.00 35.39 3.85
4562 4991 7.542477 AGATTCAACAAGTGACTACATACGAAG 59.458 37.037 0.00 0.00 35.39 3.79
4563 4992 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
4564 4993 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
4565 4994 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
4566 4995 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
4567 4996 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
4568 4997 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
4569 4998 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
4570 4999 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
4571 5000 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
4572 5001 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
4573 5002 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4574 5003 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4575 5004 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4576 5005 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
4577 5006 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
4578 5007 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
4579 5008 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
4580 5009 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
4581 5010 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
4582 5011 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
4626 5055 8.317891 ACATTCGTATGTTGTAGTTCATTTGA 57.682 30.769 1.31 0.00 42.29 2.69
4627 5056 8.779303 ACATTCGTATGTTGTAGTTCATTTGAA 58.221 29.630 1.31 0.00 42.29 2.69
4628 5057 9.605955 CATTCGTATGTTGTAGTTCATTTGAAA 57.394 29.630 0.00 0.00 35.58 2.69
4630 5059 9.605955 TTCGTATGTTGTAGTTCATTTGAAATG 57.394 29.630 11.54 11.54 35.58 2.32
4631 5060 8.779303 TCGTATGTTGTAGTTCATTTGAAATGT 58.221 29.630 16.62 1.69 35.58 2.71
4632 5061 9.051027 CGTATGTTGTAGTTCATTTGAAATGTC 57.949 33.333 16.62 11.39 35.58 3.06
4660 5089 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4661 5090 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4662 5091 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4663 5092 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4664 5093 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4665 5094 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4843 5274 2.307098 AGCTAAGCTCCATCCAAAGTGT 59.693 45.455 0.00 0.00 30.62 3.55
4844 5275 3.084786 GCTAAGCTCCATCCAAAGTGTT 58.915 45.455 0.00 0.00 0.00 3.32
4978 5524 0.325272 GGAAAAGCTTCCCCTCGTCT 59.675 55.000 0.00 0.00 44.91 4.18
5015 5561 1.805428 GCATCAACCGTTTGGGCTGT 61.805 55.000 0.00 0.00 40.62 4.40
5030 5576 2.589442 TGTTTGACGCGTGTCCCC 60.589 61.111 25.28 13.55 44.86 4.81
5056 5603 1.200716 CCACGCATCTTGTTGCTGAAT 59.799 47.619 2.79 0.00 40.54 2.57
5079 5626 4.913355 TCTTATCCCCTCATGCCTTCATTA 59.087 41.667 0.00 0.00 0.00 1.90
5080 5627 3.515602 ATCCCCTCATGCCTTCATTAC 57.484 47.619 0.00 0.00 0.00 1.89
5109 5656 2.034687 AGCAAGCGCCATCAACCT 59.965 55.556 2.29 0.00 39.83 3.50
5127 5674 2.559231 ACCTTTCGTCCTTCACTCTCTC 59.441 50.000 0.00 0.00 0.00 3.20
5146 5693 1.062121 TCCCTCCCAACTCCCATCTAG 60.062 57.143 0.00 0.00 0.00 2.43
5158 5705 1.101635 CCATCTAGCACCGTCGGAGA 61.102 60.000 20.51 10.74 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 127 6.148948 CGATTTTTCTTGCAAACCATAGACA 58.851 36.000 0.00 0.00 0.00 3.41
128 133 2.123342 CGCGATTTTTCTTGCAAACCA 58.877 42.857 0.00 0.00 0.00 3.67
135 140 0.793104 GCCGGACGCGATTTTTCTTG 60.793 55.000 15.93 0.00 0.00 3.02
136 141 0.953960 AGCCGGACGCGATTTTTCTT 60.954 50.000 15.93 0.00 44.76 2.52
215 220 0.608640 AACCTCCCGCAACTGTCTAG 59.391 55.000 0.00 0.00 0.00 2.43
216 221 1.053424 AAACCTCCCGCAACTGTCTA 58.947 50.000 0.00 0.00 0.00 2.59
221 226 1.004200 CCGTAAACCTCCCGCAACT 60.004 57.895 0.00 0.00 0.00 3.16
244 249 2.403561 GAGTAAGGGCCTCTCCAAGAT 58.596 52.381 6.46 0.00 36.21 2.40
330 336 8.034215 CCAATGCCATTGTTCTAAATAAAGTCA 58.966 33.333 15.83 0.00 38.59 3.41
333 339 8.253113 AGTCCAATGCCATTGTTCTAAATAAAG 58.747 33.333 15.83 0.00 38.59 1.85
345 354 1.402968 CCGAGAAGTCCAATGCCATTG 59.597 52.381 10.52 10.52 39.94 2.82
407 417 8.365210 GTCAATTTGTTACTTAACGCATGATTG 58.635 33.333 0.00 0.00 39.00 2.67
414 424 7.130269 AGAACAGTCAATTTGTTACTTAACGC 58.870 34.615 0.00 0.00 38.78 4.84
506 516 3.052455 ACGTGTGCACCATCTAATTCA 57.948 42.857 15.69 0.00 0.00 2.57
513 523 1.266718 ACATCAAACGTGTGCACCATC 59.733 47.619 15.69 4.05 0.00 3.51
516 526 3.552604 AATACATCAAACGTGTGCACC 57.447 42.857 15.69 4.74 0.00 5.01
536 546 4.219070 CGGGTCATAATCGTGTTAGGGATA 59.781 45.833 0.00 0.00 0.00 2.59
553 563 0.601558 GCTCACTGAGTTACGGGTCA 59.398 55.000 7.89 0.00 31.39 4.02
664 682 6.019779 TGCATAAACATTGGTGGTAAGTTC 57.980 37.500 0.00 0.00 0.00 3.01
704 722 0.317020 GCAACAAGAGTGACGTTGGC 60.317 55.000 0.00 0.00 40.26 4.52
785 805 1.421410 GGGCTCGACGCTATTGTGTG 61.421 60.000 0.00 0.00 37.00 3.82
786 806 1.153628 GGGCTCGACGCTATTGTGT 60.154 57.895 6.78 0.00 39.95 3.72
891 913 2.029073 ACGTGAGCCACCAGAACG 59.971 61.111 0.00 0.00 40.00 3.95
1049 1458 4.473520 CCGGCTGCCCTTCATCGT 62.474 66.667 14.12 0.00 0.00 3.73
1217 1629 5.427157 AGGAAATTAGGAGGGAAAGAGAGAC 59.573 44.000 0.00 0.00 0.00 3.36
1311 1723 2.237143 TCTTCGCTTCATCATTCACCCT 59.763 45.455 0.00 0.00 0.00 4.34
1607 2019 9.021807 CAGTAGGGCAATATTTAGCTAGTACTA 57.978 37.037 1.89 1.89 0.00 1.82
1608 2020 7.509659 ACAGTAGGGCAATATTTAGCTAGTACT 59.490 37.037 0.00 0.00 0.00 2.73
1609 2021 7.668492 ACAGTAGGGCAATATTTAGCTAGTAC 58.332 38.462 0.00 0.00 0.00 2.73
1683 2095 3.820557 CCCCACCTCATACAATACCTTG 58.179 50.000 0.00 0.00 38.39 3.61
1823 2235 1.902938 TTTGATCGTCAATGCCCACA 58.097 45.000 2.09 0.00 36.11 4.17
1901 2313 7.871463 CAGCATCACATCACTTAATATGAGAGA 59.129 37.037 0.00 0.00 0.00 3.10
1907 2319 7.056006 TCAACCAGCATCACATCACTTAATAT 58.944 34.615 0.00 0.00 0.00 1.28
1923 2335 4.890088 ACTTACTTACGATTCAACCAGCA 58.110 39.130 0.00 0.00 0.00 4.41
1975 2387 5.048434 GGATATGGCTTATGAACTTGGAAGC 60.048 44.000 0.00 0.00 42.87 3.86
2002 2414 9.653287 TTCTATGGACTGTTCACATTAAACTAG 57.347 33.333 0.00 0.00 0.00 2.57
2165 2578 4.112634 TCTTGCTGGGGTTAAGAACAAT 57.887 40.909 0.00 0.00 0.00 2.71
2187 2600 8.007405 TCACGAATTCAACCATATCTTCTCTA 57.993 34.615 6.22 0.00 0.00 2.43
2330 2743 8.067784 ACATGTAGTTTCGTGAAATTTACACAG 58.932 33.333 17.35 15.67 36.73 3.66
2345 2758 7.690228 TGTTTGTACACTGAACATGTAGTTTC 58.310 34.615 7.38 0.00 41.51 2.78
2403 2816 7.096551 ACTTTTGCGATAAAAACAGCCATTAT 58.903 30.769 0.00 0.00 0.00 1.28
2406 2819 4.881920 ACTTTTGCGATAAAAACAGCCAT 58.118 34.783 0.00 0.00 0.00 4.40
2421 2834 6.806739 GTCCACCATAAAATCTGTACTTTTGC 59.193 38.462 0.00 0.00 0.00 3.68
2549 2962 0.106335 TGGTTGTGCCAAATTGCCAG 59.894 50.000 0.00 0.00 45.94 4.85
2589 3002 2.605257 GTTTTTGGGGCCTAACTTCCT 58.395 47.619 0.02 0.00 0.00 3.36
2614 3027 1.165907 TTCACGGCTTCTTGTGCAGG 61.166 55.000 0.00 0.00 36.06 4.85
2733 3148 9.607285 GTAAATTTCGCAAAACTAGAGATTCAA 57.393 29.630 0.00 0.00 0.00 2.69
2768 3183 5.695816 GGAATGTGAGACTGCAAGATAGATC 59.304 44.000 0.00 0.00 37.43 2.75
3081 3496 4.614946 GCAGACTGAAAACAGCAGAAAAT 58.385 39.130 6.65 0.00 36.86 1.82
3304 3719 5.500234 CTCAGGTAAGATCATTCAAACCCA 58.500 41.667 0.00 0.00 32.18 4.51
3621 4039 5.723295 ACATCCCTGTAACATGAAAAATGC 58.277 37.500 0.00 0.00 32.49 3.56
3779 4197 6.308015 ACCAAATATCACCTAGCAACTACA 57.692 37.500 0.00 0.00 0.00 2.74
3817 4235 2.449450 GGCCGGCCTACTTGGGTAT 61.449 63.158 38.76 0.00 36.00 2.73
3970 4388 1.204941 CCACACTACCAGAGTACCAGC 59.795 57.143 0.00 0.00 35.64 4.85
4040 4458 4.468095 AGCACTGTAACGAATCAACAAC 57.532 40.909 0.00 0.00 0.00 3.32
4051 4469 6.128526 GGATCAGTAACTCAAAGCACTGTAAC 60.129 42.308 0.00 0.00 39.50 2.50
4117 4535 1.515088 CTCGTCGGCACAGCTGTAG 60.515 63.158 21.20 14.91 36.18 2.74
4301 4719 6.494146 TGATTTTGCATTCATAGGCATATCCA 59.506 34.615 0.00 0.00 41.23 3.41
4306 4724 4.100344 TGCTGATTTTGCATTCATAGGCAT 59.900 37.500 0.00 0.00 41.23 4.40
4428 4849 2.039746 TGTGGGGATTACAAGTGGTCAG 59.960 50.000 0.00 0.00 0.00 3.51
4504 4933 5.681639 ACTTATATTTGGGAACGGAGGAAG 58.318 41.667 0.00 0.00 0.00 3.46
4505 4934 5.427481 AGACTTATATTTGGGAACGGAGGAA 59.573 40.000 0.00 0.00 0.00 3.36
4506 4935 4.966805 AGACTTATATTTGGGAACGGAGGA 59.033 41.667 0.00 0.00 0.00 3.71
4507 4936 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
4508 4937 7.048512 AGAAAGACTTATATTTGGGAACGGAG 58.951 38.462 0.00 0.00 0.00 4.63
4509 4938 6.954232 AGAAAGACTTATATTTGGGAACGGA 58.046 36.000 0.00 0.00 0.00 4.69
4510 4939 8.202137 TCTAGAAAGACTTATATTTGGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
4511 4940 9.250624 CTCTAGAAAGACTTATATTTGGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
4523 4952 9.698309 CACTTGTTGAATCTCTAGAAAGACTTA 57.302 33.333 4.05 0.00 0.00 2.24
4524 4953 8.424918 TCACTTGTTGAATCTCTAGAAAGACTT 58.575 33.333 4.05 0.00 0.00 3.01
4525 4954 7.870445 GTCACTTGTTGAATCTCTAGAAAGACT 59.130 37.037 4.05 0.00 35.39 3.24
4526 4955 7.870445 AGTCACTTGTTGAATCTCTAGAAAGAC 59.130 37.037 4.05 0.00 35.39 3.01
4527 4956 7.957002 AGTCACTTGTTGAATCTCTAGAAAGA 58.043 34.615 4.05 0.00 35.39 2.52
4528 4957 9.134734 GTAGTCACTTGTTGAATCTCTAGAAAG 57.865 37.037 0.00 0.00 35.39 2.62
4529 4958 8.638873 TGTAGTCACTTGTTGAATCTCTAGAAA 58.361 33.333 0.00 0.00 35.39 2.52
4530 4959 8.178313 TGTAGTCACTTGTTGAATCTCTAGAA 57.822 34.615 0.00 0.00 35.39 2.10
4531 4960 7.761038 TGTAGTCACTTGTTGAATCTCTAGA 57.239 36.000 0.00 0.00 35.39 2.43
4532 4961 9.509855 GTATGTAGTCACTTGTTGAATCTCTAG 57.490 37.037 0.00 0.00 35.39 2.43
4533 4962 8.182227 CGTATGTAGTCACTTGTTGAATCTCTA 58.818 37.037 0.00 0.00 35.39 2.43
4534 4963 7.030165 CGTATGTAGTCACTTGTTGAATCTCT 58.970 38.462 0.00 0.00 35.39 3.10
4535 4964 7.027760 TCGTATGTAGTCACTTGTTGAATCTC 58.972 38.462 0.00 0.00 35.39 2.75
4536 4965 6.920817 TCGTATGTAGTCACTTGTTGAATCT 58.079 36.000 0.00 0.00 35.39 2.40
4537 4966 7.576750 TTCGTATGTAGTCACTTGTTGAATC 57.423 36.000 0.00 0.00 35.39 2.52
4538 4967 6.090898 GCTTCGTATGTAGTCACTTGTTGAAT 59.909 38.462 0.00 0.00 35.39 2.57
4539 4968 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
4540 4969 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
4541 4970 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
4542 4971 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
4543 4972 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
4544 4973 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
4545 4974 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
4546 4975 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
4547 4976 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
4548 4977 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4549 4978 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4550 4979 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4551 4980 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4552 4981 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
4553 4982 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
4554 4983 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
4555 4984 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
4556 4985 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
4557 4986 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
4558 4987 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
4559 4988 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
4600 5029 9.425577 TCAAATGAACTACAACATACGAATGTA 57.574 29.630 0.00 0.00 45.79 2.29
4602 5031 9.605955 TTTCAAATGAACTACAACATACGAATG 57.394 29.630 0.00 0.00 34.97 2.67
4604 5033 9.605955 CATTTCAAATGAACTACAACATACGAA 57.394 29.630 3.82 0.00 33.13 3.85
4605 5034 8.779303 ACATTTCAAATGAACTACAACATACGA 58.221 29.630 17.30 0.00 33.13 3.43
4606 5035 8.948853 ACATTTCAAATGAACTACAACATACG 57.051 30.769 17.30 0.00 33.13 3.06
4634 5063 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4635 5064 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4636 5065 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4637 5066 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4638 5067 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4639 5068 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4640 5069 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4641 5070 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4642 5071 7.951806 TCATACTCCCTCCGTTCCTAAATATAA 59.048 37.037 0.00 0.00 0.00 0.98
4643 5072 7.472741 TCATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
4644 5073 6.320518 TCATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
4645 5074 5.708544 TCATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
4646 5075 4.553678 TCATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
4647 5076 3.958798 CTCATACTCCCTCCGTTCCTAAA 59.041 47.826 0.00 0.00 0.00 1.85
4648 5077 3.563223 CTCATACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
4649 5078 2.158505 CCTCATACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
4650 5079 1.411787 CCTCATACTCCCTCCGTTCCT 60.412 57.143 0.00 0.00 0.00 3.36
4651 5080 1.041437 CCTCATACTCCCTCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62
4652 5081 1.777941 ACCTCATACTCCCTCCGTTC 58.222 55.000 0.00 0.00 0.00 3.95
4653 5082 1.831736 CAACCTCATACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
4654 5083 1.486211 CAACCTCATACTCCCTCCGT 58.514 55.000 0.00 0.00 0.00 4.69
4655 5084 0.105039 GCAACCTCATACTCCCTCCG 59.895 60.000 0.00 0.00 0.00 4.63
4656 5085 1.139853 CAGCAACCTCATACTCCCTCC 59.860 57.143 0.00 0.00 0.00 4.30
4657 5086 1.834263 ACAGCAACCTCATACTCCCTC 59.166 52.381 0.00 0.00 0.00 4.30
4658 5087 1.958288 ACAGCAACCTCATACTCCCT 58.042 50.000 0.00 0.00 0.00 4.20
4659 5088 2.789409 AACAGCAACCTCATACTCCC 57.211 50.000 0.00 0.00 0.00 4.30
4685 5114 7.430502 GTGAAAAACTTGCTGATCTGTATATGC 59.569 37.037 1.27 0.00 0.00 3.14
4686 5115 7.912250 GGTGAAAAACTTGCTGATCTGTATATG 59.088 37.037 1.27 0.00 0.00 1.78
4687 5116 7.831193 AGGTGAAAAACTTGCTGATCTGTATAT 59.169 33.333 1.27 0.00 0.00 0.86
4688 5117 7.168219 AGGTGAAAAACTTGCTGATCTGTATA 58.832 34.615 1.27 0.00 0.00 1.47
4694 5125 5.218139 CAGAAGGTGAAAAACTTGCTGATC 58.782 41.667 0.00 0.00 30.45 2.92
4869 5300 3.277142 TCTACTCGTGTGCCTCTATGA 57.723 47.619 0.00 0.00 0.00 2.15
4899 5330 3.321968 CCTAAGCCTGCTGGTTTTCTTTT 59.678 43.478 16.54 0.00 37.87 2.27
4992 5538 0.387202 CCCAAACGGTTGATGCACAA 59.613 50.000 16.49 0.00 36.83 3.33
5056 5603 2.775418 TGAAGGCATGAGGGGATAAGA 58.225 47.619 0.00 0.00 0.00 2.10
5079 5626 1.831580 GCTTGCTGAGATTTCCTGGT 58.168 50.000 0.00 0.00 0.00 4.00
5080 5627 0.731417 CGCTTGCTGAGATTTCCTGG 59.269 55.000 0.00 0.00 0.00 4.45
5109 5656 1.893801 GGGAGAGAGTGAAGGACGAAA 59.106 52.381 0.00 0.00 0.00 3.46
5127 5674 1.428869 CTAGATGGGAGTTGGGAGGG 58.571 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.