Multiple sequence alignment - TraesCS1D01G061900

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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 TraesCS1D01G061900 chr1D 100.000 2549 0 0 1 2549 41822032 41824580 0.000000e+00 4708.0
1 TraesCS1D01G061900 chr1D 84.219 640 67 10 867 1495 41868242 41868858 2.180000e-165 592.0
2 TraesCS1D01G061900 chr1D 84.762 105 13 2 1594 1695 41868900 41869004 4.490000e-18 102.0
3 TraesCS1D01G061900 chr1D 98.182 55 1 0 1495 1549 41868837 41868891 2.090000e-16 97.1
4 TraesCS1D01G061900 chr1D 87.500 80 7 3 251 328 452744525 452744447 3.490000e-14 89.8
5 TraesCS1D01G061900 chr1B 85.543 1169 67 31 840 1971 61966361 61967464 0.000000e+00 1129.0
6 TraesCS1D01G061900 chr1B 84.923 650 55 15 876 1495 62061175 62061811 3.600000e-173 617.0
7 TraesCS1D01G061900 chr1B 81.111 540 28 22 339 824 61965539 61966058 5.180000e-97 364.0
8 TraesCS1D01G061900 chr1B 84.277 318 32 8 868 1167 62004395 62004712 6.900000e-76 294.0
9 TraesCS1D01G061900 chr1B 88.934 244 16 4 2305 2537 61992053 61992296 8.920000e-75 291.0
10 TraesCS1D01G061900 chr1B 82.533 229 29 5 871 1095 62080147 62080368 9.310000e-45 191.0
11 TraesCS1D01G061900 chr1B 93.548 124 8 0 1372 1495 62018701 62018824 4.330000e-43 185.0
12 TraesCS1D01G061900 chr1B 83.415 205 21 6 1148 1344 62004721 62004920 7.250000e-41 178.0
13 TraesCS1D01G061900 chr1B 98.413 63 1 0 6 68 61963287 61963349 7.450000e-21 111.0
14 TraesCS1D01G061900 chr1B 90.541 74 7 0 2235 2308 61990135 61990208 5.800000e-17 99.0
15 TraesCS1D01G061900 chr1B 98.182 55 1 0 1495 1549 62018803 62018857 2.090000e-16 97.1
16 TraesCS1D01G061900 chr1B 96.364 55 2 0 1495 1549 62061790 62061844 9.710000e-15 91.6
17 TraesCS1D01G061900 chr1A 87.200 1000 57 26 308 1251 41874777 41875761 0.000000e+00 1072.0
18 TraesCS1D01G061900 chr1A 84.903 828 87 18 1757 2548 41876320 41877145 0.000000e+00 802.0
19 TraesCS1D01G061900 chr1A 89.642 531 32 3 1237 1767 41875785 41876292 0.000000e+00 654.0
20 TraesCS1D01G061900 chr1A 88.361 421 42 5 867 1280 41906029 41906449 1.360000e-137 499.0
21 TraesCS1D01G061900 chr1A 80.655 336 45 13 926 1247 41894757 41895086 2.530000e-60 243.0
22 TraesCS1D01G061900 chr1A 91.096 146 13 0 1350 1495 41906484 41906629 5.560000e-47 198.0
23 TraesCS1D01G061900 chr1A 98.182 55 1 0 1495 1549 41906608 41906662 2.090000e-16 97.1
24 TraesCS1D01G061900 chr7A 81.699 153 21 6 2033 2183 557561612 557561759 1.240000e-23 121.0
25 TraesCS1D01G061900 chr2B 84.375 96 15 0 254 349 361444737 361444642 7.510000e-16 95.3
26 TraesCS1D01G061900 chr5A 84.375 96 14 1 236 330 547158969 547158874 2.700000e-15 93.5


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 TraesCS1D01G061900 chr1D 41822032 41824580 2548 False 4708.000000 4708 100.000000 1 2549 1 chr1D.!!$F1 2548
1 TraesCS1D01G061900 chr1D 41868242 41869004 762 False 263.700000 592 89.054333 867 1695 3 chr1D.!!$F2 828
2 TraesCS1D01G061900 chr1B 61963287 61967464 4177 False 534.666667 1129 88.355667 6 1971 3 chr1B.!!$F2 1965
3 TraesCS1D01G061900 chr1B 62061175 62061844 669 False 354.300000 617 90.643500 876 1549 2 chr1B.!!$F6 673
4 TraesCS1D01G061900 chr1B 62004395 62004920 525 False 236.000000 294 83.846000 868 1344 2 chr1B.!!$F4 476
5 TraesCS1D01G061900 chr1A 41874777 41877145 2368 False 842.666667 1072 87.248333 308 2548 3 chr1A.!!$F2 2240
6 TraesCS1D01G061900 chr1A 41906029 41906662 633 False 264.700000 499 92.546333 867 1549 3 chr1A.!!$F3 682

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
781 2812 0.038166 CCCAGCAACAAGAGCCCTAA 59.962 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 4755 0.976641 ACGAGGTCATCTTTCAGGCA 59.023 50.0 0.0 0.0 0.0 4.75 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
68 69 2.567615 AGGTGGTGGTACTTCTCATGAC 59.432 50.000 0.00 0.00 0.00 3.06
70 107 3.055094 GGTGGTGGTACTTCTCATGACAT 60.055 47.826 0.00 0.00 0.00 3.06
72 109 3.837731 TGGTGGTACTTCTCATGACATCA 59.162 43.478 0.00 0.00 0.00 3.07
76 113 4.285775 TGGTACTTCTCATGACATCACCAA 59.714 41.667 8.32 0.00 30.90 3.67
77 114 5.045651 TGGTACTTCTCATGACATCACCAAT 60.046 40.000 8.32 0.00 30.90 3.16
89 126 5.703130 TGACATCACCAATGATTCGTAAACA 59.297 36.000 0.00 0.00 43.40 2.83
93 130 6.567687 TCACCAATGATTCGTAAACAATGT 57.432 33.333 0.00 0.00 0.00 2.71
94 131 6.377780 TCACCAATGATTCGTAAACAATGTG 58.622 36.000 0.00 0.00 0.00 3.21
95 132 5.060816 CACCAATGATTCGTAAACAATGTGC 59.939 40.000 0.00 0.00 0.00 4.57
96 133 5.159925 CCAATGATTCGTAAACAATGTGCA 58.840 37.500 0.00 0.00 0.00 4.57
97 134 5.286797 CCAATGATTCGTAAACAATGTGCAG 59.713 40.000 0.00 0.00 0.00 4.41
105 144 8.487313 TTCGTAAACAATGTGCAGATTACTAT 57.513 30.769 9.00 0.00 0.00 2.12
115 154 7.320443 TGTGCAGATTACTATGGAAATTCAC 57.680 36.000 0.00 0.00 0.00 3.18
139 178 2.033602 AAGTAAGTGCGGGGGCAC 59.966 61.111 11.03 11.03 40.64 5.01
156 195 4.020617 CTCCTCTGCCACGCCCAA 62.021 66.667 0.00 0.00 0.00 4.12
158 197 4.641645 CCTCTGCCACGCCCAACA 62.642 66.667 0.00 0.00 0.00 3.33
171 215 1.515521 CCCAACACTCGGTTTGCCTC 61.516 60.000 0.00 0.00 37.72 4.70
173 217 2.251642 AACACTCGGTTTGCCTCGC 61.252 57.895 0.00 0.00 35.82 5.03
174 218 2.664851 CACTCGGTTTGCCTCGCA 60.665 61.111 0.00 0.00 36.47 5.10
187 231 1.324736 GCCTCGCAATTCACGAAGTAG 59.675 52.381 0.00 0.00 41.61 2.57
196 240 5.673818 GCAATTCACGAAGTAGTTGAATCCC 60.674 44.000 0.00 0.00 41.61 3.85
198 242 1.659098 CACGAAGTAGTTGAATCCCGC 59.341 52.381 0.00 0.00 41.61 6.13
199 243 0.921347 CGAAGTAGTTGAATCCCGCG 59.079 55.000 0.00 0.00 0.00 6.46
204 2146 2.691526 AGTAGTTGAATCCCGCGTCATA 59.308 45.455 4.92 0.00 0.00 2.15
219 2161 3.575630 CGTCATATTGGTACTCCATCCG 58.424 50.000 0.00 0.00 43.91 4.18
224 2166 1.646912 TTGGTACTCCATCCGTTCCA 58.353 50.000 0.00 0.00 43.91 3.53
231 2173 5.826208 GGTACTCCATCCGTTCCAAATTATT 59.174 40.000 0.00 0.00 0.00 1.40
232 2174 6.320418 GGTACTCCATCCGTTCCAAATTATTT 59.680 38.462 0.00 0.00 0.00 1.40
233 2175 7.499895 GGTACTCCATCCGTTCCAAATTATTTA 59.500 37.037 0.00 0.00 0.00 1.40
234 2176 9.063615 GTACTCCATCCGTTCCAAATTATTTAT 57.936 33.333 0.00 0.00 0.00 1.40
295 2249 9.297037 ACTGTATTTGTTTACTTATTTCAGCCT 57.703 29.630 0.00 0.00 0.00 4.58
297 2251 8.026607 TGTATTTGTTTACTTATTTCAGCCTGC 58.973 33.333 0.00 0.00 0.00 4.85
298 2252 6.398234 TTTGTTTACTTATTTCAGCCTGCA 57.602 33.333 0.00 0.00 0.00 4.41
303 2257 6.925610 TTACTTATTTCAGCCTGCATGTAG 57.074 37.500 3.45 3.45 0.00 2.74
304 2258 3.629398 ACTTATTTCAGCCTGCATGTAGC 59.371 43.478 5.11 0.31 45.96 3.58
305 2259 1.396653 ATTTCAGCCTGCATGTAGCC 58.603 50.000 5.11 0.00 44.83 3.93
306 2260 0.680921 TTTCAGCCTGCATGTAGCCC 60.681 55.000 5.11 0.00 44.83 5.19
359 2313 0.251341 AGCGGAGGGAGTGCAAATTT 60.251 50.000 0.00 0.00 0.00 1.82
365 2319 4.881850 CGGAGGGAGTGCAAATTTAACTAT 59.118 41.667 5.85 0.00 0.00 2.12
401 2359 4.546829 ATCTACGGACAGCCTTTTACAA 57.453 40.909 0.00 0.00 0.00 2.41
410 2368 3.769300 ACAGCCTTTTACAATGATTCCCC 59.231 43.478 0.00 0.00 0.00 4.81
444 2402 5.634859 GCTTTGTATTGTGATGAAACAAGGG 59.365 40.000 0.00 0.00 42.99 3.95
450 2411 6.723298 ATTGTGATGAAACAAGGGTACAAA 57.277 33.333 0.00 0.00 42.99 2.83
498 2460 3.134458 ACTACTGACTGAGCAAGCAAAC 58.866 45.455 0.00 0.00 0.00 2.93
499 2461 1.312815 ACTGACTGAGCAAGCAAACC 58.687 50.000 0.00 0.00 0.00 3.27
530 2492 3.967401 TGCATTGATTCAACACACACTG 58.033 40.909 0.15 0.00 0.00 3.66
539 2504 3.006940 TCAACACACACTGGAGTCAAAC 58.993 45.455 0.00 0.00 0.00 2.93
546 2512 1.869767 CACTGGAGTCAAACTGTCAGC 59.130 52.381 0.00 0.00 32.65 4.26
572 2538 1.807755 CGAACGGCTCCATGACATGAT 60.808 52.381 17.24 0.00 0.00 2.45
666 2641 0.246635 CTACGGCCTGCAACACTACT 59.753 55.000 0.00 0.00 0.00 2.57
699 2712 2.083167 AATCTTTTTGGGCACATGCG 57.917 45.000 0.00 0.00 43.26 4.73
763 2786 3.439129 GGCTGGTCATACAAAGTTACACC 59.561 47.826 0.00 0.00 0.00 4.16
778 2809 2.116125 ACCCAGCAACAAGAGCCC 59.884 61.111 0.00 0.00 0.00 5.19
779 2810 2.437897 CCCAGCAACAAGAGCCCT 59.562 61.111 0.00 0.00 0.00 5.19
780 2811 1.133809 ACCCAGCAACAAGAGCCCTA 61.134 55.000 0.00 0.00 0.00 3.53
781 2812 0.038166 CCCAGCAACAAGAGCCCTAA 59.962 55.000 0.00 0.00 0.00 2.69
782 2813 1.547675 CCCAGCAACAAGAGCCCTAAA 60.548 52.381 0.00 0.00 0.00 1.85
783 2814 2.238521 CCAGCAACAAGAGCCCTAAAA 58.761 47.619 0.00 0.00 0.00 1.52
784 2815 2.827921 CCAGCAACAAGAGCCCTAAAAT 59.172 45.455 0.00 0.00 0.00 1.82
785 2816 3.119352 CCAGCAACAAGAGCCCTAAAATC 60.119 47.826 0.00 0.00 0.00 2.17
833 3157 1.379146 GTCCCTCCCTGAAACCCAC 59.621 63.158 0.00 0.00 0.00 4.61
835 3159 0.699577 TCCCTCCCTGAAACCCACAA 60.700 55.000 0.00 0.00 0.00 3.33
967 3299 1.063912 CACGCAGTTGAAGTTGCAAGA 59.936 47.619 0.00 0.00 41.61 3.02
970 3302 2.122564 GCAGTTGAAGTTGCAAGAAGC 58.877 47.619 0.00 0.00 45.96 3.86
989 3321 1.531423 CAGCTTGTGTGCATTCCTCT 58.469 50.000 0.00 0.00 34.99 3.69
1017 3362 1.068753 CATGGCTCGGCTCTACCAG 59.931 63.158 0.00 0.00 39.03 4.00
1125 3482 0.750249 TGATCATGACGGTGCGGTAT 59.250 50.000 0.00 0.00 0.00 2.73
1150 3507 3.148279 CCGACTCGGGGGAGAAGG 61.148 72.222 9.85 0.00 44.15 3.46
1299 3741 1.298859 GAGCCAGCCGTGTGGTTTAG 61.299 60.000 2.50 0.00 40.09 1.85
1312 3754 5.173131 CGTGTGGTTTAGTTTGCTTGATTTC 59.827 40.000 0.00 0.00 0.00 2.17
1316 3758 8.584157 TGTGGTTTAGTTTGCTTGATTTCATAT 58.416 29.630 0.00 0.00 0.00 1.78
1383 3826 0.378962 TCGCCACGAAAAACCTTGTG 59.621 50.000 0.00 0.00 31.06 3.33
1435 3881 3.123157 CCTCTCTATCCGAGGTAACGA 57.877 52.381 0.00 0.00 42.47 3.85
1494 3941 4.829064 TTTCAGAACGCAAATGTAAGCT 57.171 36.364 0.00 0.00 0.00 3.74
1495 3942 4.829064 TTCAGAACGCAAATGTAAGCTT 57.171 36.364 3.48 3.48 0.00 3.74
1496 3943 4.829064 TCAGAACGCAAATGTAAGCTTT 57.171 36.364 3.20 0.00 0.00 3.51
1497 3944 4.783242 TCAGAACGCAAATGTAAGCTTTC 58.217 39.130 3.20 0.00 38.74 2.62
1498 3945 4.274705 TCAGAACGCAAATGTAAGCTTTCA 59.725 37.500 3.20 6.18 40.29 2.69
1499 3946 4.614284 CAGAACGCAAATGTAAGCTTTCAG 59.386 41.667 3.20 0.00 40.29 3.02
1500 3947 4.515191 AGAACGCAAATGTAAGCTTTCAGA 59.485 37.500 3.20 0.00 40.29 3.27
1501 3948 4.829064 ACGCAAATGTAAGCTTTCAGAA 57.171 36.364 3.20 0.00 0.00 3.02
1502 3949 4.537015 ACGCAAATGTAAGCTTTCAGAAC 58.463 39.130 3.20 0.00 0.00 3.01
1503 3950 3.599514 CGCAAATGTAAGCTTTCAGAACG 59.400 43.478 3.20 5.31 0.00 3.95
1504 3951 3.361940 GCAAATGTAAGCTTTCAGAACGC 59.638 43.478 3.20 3.38 0.00 4.84
1505 3952 4.536065 CAAATGTAAGCTTTCAGAACGCA 58.464 39.130 13.72 0.00 0.00 5.24
1506 3953 4.829064 AATGTAAGCTTTCAGAACGCAA 57.171 36.364 13.72 0.00 0.00 4.85
1507 3954 4.829064 ATGTAAGCTTTCAGAACGCAAA 57.171 36.364 13.72 0.00 0.00 3.68
1508 3955 4.829064 TGTAAGCTTTCAGAACGCAAAT 57.171 36.364 13.72 2.80 0.00 2.32
1643 4108 1.767681 GGAGATTGGTGATGGAGCTCT 59.232 52.381 14.64 0.00 0.00 4.09
1660 4125 5.208463 AGCTCTTCTTTTCTTTCGTCTCT 57.792 39.130 0.00 0.00 0.00 3.10
1662 4127 4.985409 GCTCTTCTTTTCTTTCGTCTCTGA 59.015 41.667 0.00 0.00 0.00 3.27
1665 4130 6.987386 TCTTCTTTTCTTTCGTCTCTGAGAT 58.013 36.000 11.07 0.00 0.00 2.75
1678 4145 6.715264 TCGTCTCTGAGATAATACATTAGGCA 59.285 38.462 11.07 0.00 0.00 4.75
1700 4167 6.403092 GGCACTTTTTATTTTGTTGTTGTGCT 60.403 34.615 0.00 0.00 44.14 4.40
1718 4185 0.387367 CTCATTCGGGGAGCGTATCG 60.387 60.000 0.00 0.00 0.00 2.92
1754 4221 3.567478 AGGCTGTGTATCTTGGATTCC 57.433 47.619 0.00 0.00 0.00 3.01
1757 4224 2.866762 GCTGTGTATCTTGGATTCCGTC 59.133 50.000 0.00 0.00 0.00 4.79
1790 4294 6.472163 TGTTTTTCTTCTGCTCAATTTTCGTC 59.528 34.615 0.00 0.00 0.00 4.20
1801 4305 4.566004 TCAATTTTCGTCAAGTCGAGGAT 58.434 39.130 0.00 0.00 40.86 3.24
1806 4310 3.538634 TCGTCAAGTCGAGGATCTCTA 57.461 47.619 0.00 0.00 33.64 2.43
1911 4417 7.514721 TGTAAGAAACAAAGAGGGATACAAGT 58.485 34.615 0.00 0.00 34.29 3.16
1919 4425 4.067944 AGAGGGATACAAGTGAGGAACT 57.932 45.455 0.00 0.00 42.60 3.01
1954 4460 3.864789 ACAGGGGGATACATTAGCTTG 57.135 47.619 0.00 0.00 39.74 4.01
1999 4525 4.271533 TGAACAAAGTAGCACCAAAGTACG 59.728 41.667 0.00 0.00 0.00 3.67
2009 4535 4.689345 AGCACCAAAGTACGTAGTTCAATC 59.311 41.667 15.77 5.47 37.78 2.67
2013 4539 5.699458 ACCAAAGTACGTAGTTCAATCCAAG 59.301 40.000 15.77 2.65 37.78 3.61
2041 4567 8.143193 TCTCAAGCAAAGCTGAATAAAATGAAA 58.857 29.630 0.00 0.00 39.62 2.69
2069 4596 0.102120 CTGCCACAACCAGCGAAAAA 59.898 50.000 0.00 0.00 0.00 1.94
2097 4624 9.523168 GGACTAGATAACAATAGACACCTATCT 57.477 37.037 0.00 0.00 34.63 1.98
2108 4635 9.613428 CAATAGACACCTATCTTATTGTTGGAA 57.387 33.333 0.00 0.00 34.63 3.53
2115 4642 6.761714 ACCTATCTTATTGTTGGAACGTCATC 59.238 38.462 0.00 0.00 0.00 2.92
2123 4650 2.753055 TGGAACGTCATCCAAATCGA 57.247 45.000 6.50 0.00 46.36 3.59
2126 4653 3.373748 TGGAACGTCATCCAAATCGATTG 59.626 43.478 12.25 6.05 46.36 2.67
2127 4654 3.374058 GGAACGTCATCCAAATCGATTGT 59.626 43.478 12.25 0.00 39.42 2.71
2147 4674 2.057137 AAGTATCCCGTGCTACCGTA 57.943 50.000 0.00 0.00 0.00 4.02
2163 4690 0.719465 CGTATCTCAACGGTTGCACC 59.281 55.000 15.89 1.72 39.19 5.01
2164 4691 1.084289 GTATCTCAACGGTTGCACCC 58.916 55.000 15.89 0.00 33.75 4.61
2176 4703 0.812014 TTGCACCCGTACGCCATATG 60.812 55.000 10.49 4.05 0.00 1.78
2181 4708 1.374252 CCGTACGCCATATGCTCCC 60.374 63.158 10.49 0.00 38.05 4.30
2183 4710 0.033504 CGTACGCCATATGCTCCCTT 59.966 55.000 0.52 0.00 38.05 3.95
2189 4716 2.224281 CGCCATATGCTCCCTTACTTCA 60.224 50.000 0.00 0.00 38.05 3.02
2195 4722 1.065199 TGCTCCCTTACTTCAGCATGG 60.065 52.381 0.00 0.00 36.96 3.66
2205 4732 3.067106 ACTTCAGCATGGTTGAGTAACG 58.933 45.455 7.87 0.00 37.69 3.18
2226 4753 3.058432 CGACCACGTATAGACCCATACAG 60.058 52.174 0.00 0.00 31.96 2.74
2228 4755 4.737578 ACCACGTATAGACCCATACAGAT 58.262 43.478 0.00 0.00 31.96 2.90
2232 4759 3.764434 CGTATAGACCCATACAGATGCCT 59.236 47.826 0.00 0.00 31.96 4.75
2233 4760 4.380973 CGTATAGACCCATACAGATGCCTG 60.381 50.000 0.00 0.00 45.76 4.85
2235 4762 2.481441 AGACCCATACAGATGCCTGAA 58.519 47.619 0.00 0.00 43.02 3.02
2268 4795 5.240183 TCGTACATTAGCTAATAACGCCTCT 59.760 40.000 30.28 6.63 35.74 3.69
2273 4800 5.756195 TTAGCTAATAACGCCTCTTACGA 57.244 39.130 0.86 0.00 0.00 3.43
2275 4802 4.796369 AGCTAATAACGCCTCTTACGATC 58.204 43.478 0.00 0.00 0.00 3.69
2279 4806 0.525668 AACGCCTCTTACGATCGCTG 60.526 55.000 16.60 5.62 0.00 5.18
2289 4820 4.217767 TCTTACGATCGCTGGTAATGCTAT 59.782 41.667 16.60 0.00 0.00 2.97
2292 4823 3.243737 ACGATCGCTGGTAATGCTATCAA 60.244 43.478 16.60 0.00 33.84 2.57
2297 4828 3.871006 CGCTGGTAATGCTATCAAGACAA 59.129 43.478 0.00 0.00 0.00 3.18
2309 4840 9.890629 ATGCTATCAAGACAAAGTCAACTTATA 57.109 29.630 0.00 0.00 34.61 0.98
2310 4841 9.890629 TGCTATCAAGACAAAGTCAACTTATAT 57.109 29.630 0.00 0.00 34.61 0.86
2313 4844 7.977789 TCAAGACAAAGTCAACTTATATGCA 57.022 32.000 0.00 0.00 34.61 3.96
2314 4845 7.806690 TCAAGACAAAGTCAACTTATATGCAC 58.193 34.615 0.00 0.00 34.61 4.57
2315 4846 7.443879 TCAAGACAAAGTCAACTTATATGCACA 59.556 33.333 0.00 0.00 34.61 4.57
2319 4854 9.869844 GACAAAGTCAACTTATATGCACATATC 57.130 33.333 6.42 0.00 34.61 1.63
2395 4930 7.433680 AGATGTCTGGTTAATTTGTGGAAAAC 58.566 34.615 0.00 0.00 0.00 2.43
2397 4932 5.422331 TGTCTGGTTAATTTGTGGAAAACCA 59.578 36.000 6.57 6.57 45.47 3.67
2406 4941 5.585820 TTTGTGGAAAACCAGGTAGAAAC 57.414 39.130 0.00 0.00 0.00 2.78
2408 4943 5.633655 TGTGGAAAACCAGGTAGAAACTA 57.366 39.130 0.00 0.00 0.00 2.24
2412 4947 7.662669 TGTGGAAAACCAGGTAGAAACTATTAC 59.337 37.037 0.00 0.00 0.00 1.89
2417 4952 7.974482 AACCAGGTAGAAACTATTACAACAC 57.026 36.000 0.00 0.00 0.00 3.32
2420 4955 7.822822 ACCAGGTAGAAACTATTACAACACATC 59.177 37.037 0.00 0.00 0.00 3.06
2421 4956 7.822334 CCAGGTAGAAACTATTACAACACATCA 59.178 37.037 0.00 0.00 0.00 3.07
2432 4967 1.536766 CAACACATCAACGTGGCATCT 59.463 47.619 0.00 0.00 41.38 2.90
2481 5016 1.702886 CTTCTATACATGCCTCGCCG 58.297 55.000 0.00 0.00 0.00 6.46
2499 5034 2.121832 TGGTGTCCCCGTCTCCAT 59.878 61.111 0.00 0.00 35.15 3.41
2525 5065 2.629051 GGTCCGTTTAATCCAGTCAGG 58.371 52.381 0.00 0.00 39.47 3.86
2548 5088 0.103937 CAAAACGAAAAGGCTGCCCA 59.896 50.000 16.57 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.826236 TGTAGTTGCTCGTCAGAGTAC 57.174 47.619 0.00 0.00 46.03 2.73
1 2 3.366070 GCTTGTAGTTGCTCGTCAGAGTA 60.366 47.826 0.00 0.00 46.03 2.59
2 3 2.608261 GCTTGTAGTTGCTCGTCAGAGT 60.608 50.000 0.00 0.00 46.03 3.24
4 5 1.336887 GGCTTGTAGTTGCTCGTCAGA 60.337 52.381 0.00 0.00 0.00 3.27
19 20 2.063266 GTGTTGAATGCATGTGGCTTG 58.937 47.619 0.00 0.00 45.15 4.01
68 69 7.008538 CACATTGTTTACGAATCATTGGTGATG 59.991 37.037 0.00 0.00 44.20 3.07
70 107 6.377780 CACATTGTTTACGAATCATTGGTGA 58.622 36.000 0.00 0.00 39.04 4.02
72 109 5.160641 GCACATTGTTTACGAATCATTGGT 58.839 37.500 0.00 0.00 0.00 3.67
76 113 5.878332 TCTGCACATTGTTTACGAATCAT 57.122 34.783 0.00 0.00 0.00 2.45
77 114 5.878332 ATCTGCACATTGTTTACGAATCA 57.122 34.783 0.00 0.00 0.00 2.57
89 126 8.408601 GTGAATTTCCATAGTAATCTGCACATT 58.591 33.333 0.00 0.00 0.00 2.71
93 130 6.543465 CCTGTGAATTTCCATAGTAATCTGCA 59.457 38.462 0.00 0.00 0.00 4.41
94 131 6.016777 CCCTGTGAATTTCCATAGTAATCTGC 60.017 42.308 0.00 0.00 0.00 4.26
95 132 6.488006 CCCCTGTGAATTTCCATAGTAATCTG 59.512 42.308 0.00 0.00 0.00 2.90
96 133 6.605119 CCCCTGTGAATTTCCATAGTAATCT 58.395 40.000 0.00 0.00 0.00 2.40
97 134 5.241728 GCCCCTGTGAATTTCCATAGTAATC 59.758 44.000 0.00 0.00 0.00 1.75
105 144 1.133199 ACTTGCCCCTGTGAATTTCCA 60.133 47.619 0.00 0.00 0.00 3.53
115 154 2.040544 CCGCACTTACTTGCCCCTG 61.041 63.158 0.00 0.00 39.53 4.45
139 178 4.020617 TTGGGCGTGGCAGAGGAG 62.021 66.667 0.00 0.00 0.00 3.69
142 181 3.357079 GTGTTGGGCGTGGCAGAG 61.357 66.667 0.00 0.00 0.00 3.35
143 182 3.825160 GAGTGTTGGGCGTGGCAGA 62.825 63.158 0.00 0.00 0.00 4.26
150 189 2.637025 CAAACCGAGTGTTGGGCG 59.363 61.111 0.00 0.00 37.23 6.13
155 194 2.251642 GCGAGGCAAACCGAGTGTT 61.252 57.895 0.00 0.00 42.76 3.32
156 195 2.665185 GCGAGGCAAACCGAGTGT 60.665 61.111 0.00 0.00 42.76 3.55
158 197 2.110213 TTGCGAGGCAAACCGAGT 59.890 55.556 0.00 0.00 45.96 4.18
171 215 4.383774 TTCAACTACTTCGTGAATTGCG 57.616 40.909 0.00 0.00 0.00 4.85
173 217 5.445939 CGGGATTCAACTACTTCGTGAATTG 60.446 44.000 0.00 0.00 30.44 2.32
174 218 4.630069 CGGGATTCAACTACTTCGTGAATT 59.370 41.667 0.00 0.00 30.44 2.17
187 231 2.032030 CCAATATGACGCGGGATTCAAC 60.032 50.000 12.47 0.00 0.00 3.18
196 240 2.502213 TGGAGTACCAATATGACGCG 57.498 50.000 3.53 3.53 43.91 6.01
290 2244 0.109153 TATGGGCTACATGCAGGCTG 59.891 55.000 18.17 10.94 45.15 4.85
291 2245 1.070604 ATATGGGCTACATGCAGGCT 58.929 50.000 18.17 3.21 45.15 4.58
292 2246 1.915141 AATATGGGCTACATGCAGGC 58.085 50.000 11.02 11.02 45.15 4.85
293 2247 6.594788 ATTTTAATATGGGCTACATGCAGG 57.405 37.500 0.00 0.00 45.15 4.85
295 2249 9.306777 TGAATATTTTAATATGGGCTACATGCA 57.693 29.630 0.00 0.00 40.82 3.96
434 2392 4.095185 CAGACGTTTTGTACCCTTGTTTCA 59.905 41.667 0.00 0.00 0.00 2.69
435 2393 4.095334 ACAGACGTTTTGTACCCTTGTTTC 59.905 41.667 5.01 0.00 0.00 2.78
436 2394 4.011698 ACAGACGTTTTGTACCCTTGTTT 58.988 39.130 5.01 0.00 0.00 2.83
450 2411 6.505044 AACTTGGAAGTTAAAACAGACGTT 57.495 33.333 2.86 0.00 46.75 3.99
498 2460 2.945447 ATCAATGCATGTGGTTTCGG 57.055 45.000 0.00 0.00 0.00 4.30
499 2461 3.835779 TGAATCAATGCATGTGGTTTCG 58.164 40.909 0.00 0.00 0.00 3.46
530 2492 2.411904 CTCAGCTGACAGTTTGACTCC 58.588 52.381 13.74 0.00 0.00 3.85
539 2504 2.091112 CGTTCGCCTCAGCTGACAG 61.091 63.158 13.74 8.54 36.60 3.51
546 2512 3.376935 ATGGAGCCGTTCGCCTCAG 62.377 63.158 5.63 0.00 38.78 3.35
666 2641 2.205022 AAGATTTACCAGCAGCAGCA 57.795 45.000 3.17 0.00 45.49 4.41
699 2712 1.571215 GCCAAACAAATGCCAGCAGC 61.571 55.000 0.00 0.00 44.14 5.25
707 2730 3.125316 CCACTCAACTGCCAAACAAATG 58.875 45.455 0.00 0.00 0.00 2.32
763 2786 1.909700 TTTAGGGCTCTTGTTGCTGG 58.090 50.000 0.00 0.00 0.00 4.85
778 2809 5.450412 CCGTGGATCCCAATTGTGATTTTAG 60.450 44.000 9.90 0.00 34.18 1.85
779 2810 4.400884 CCGTGGATCCCAATTGTGATTTTA 59.599 41.667 9.90 0.00 34.18 1.52
780 2811 3.195396 CCGTGGATCCCAATTGTGATTTT 59.805 43.478 9.90 0.00 34.18 1.82
781 2812 2.760092 CCGTGGATCCCAATTGTGATTT 59.240 45.455 9.90 0.00 34.18 2.17
782 2813 2.291540 ACCGTGGATCCCAATTGTGATT 60.292 45.455 9.90 0.00 34.18 2.57
783 2814 1.284785 ACCGTGGATCCCAATTGTGAT 59.715 47.619 9.90 2.80 34.18 3.06
784 2815 0.695924 ACCGTGGATCCCAATTGTGA 59.304 50.000 9.90 0.00 34.18 3.58
785 2816 2.093181 TCTACCGTGGATCCCAATTGTG 60.093 50.000 9.90 0.00 34.18 3.33
833 3157 3.884895 TGCATAGTTCCCACTACCATTG 58.115 45.455 0.00 0.00 38.38 2.82
835 3159 3.073062 GGATGCATAGTTCCCACTACCAT 59.927 47.826 0.00 0.00 38.38 3.55
967 3299 0.316204 GGAATGCACACAAGCTGCTT 59.684 50.000 9.53 9.53 35.53 3.91
970 3302 1.199327 CAGAGGAATGCACACAAGCTG 59.801 52.381 0.00 0.00 34.99 4.24
973 3305 3.434641 CACTACAGAGGAATGCACACAAG 59.565 47.826 0.00 0.00 0.00 3.16
1017 3362 3.053849 GACGGAGAGGACGGTGAGC 62.054 68.421 0.00 0.00 35.23 4.26
1024 3369 2.164827 GGAAGAAGAAGACGGAGAGGAC 59.835 54.545 0.00 0.00 0.00 3.85
1150 3507 1.868251 GGTGCGTCGAGATCGTGAC 60.868 63.158 9.54 9.54 40.80 3.67
1299 3741 8.758715 GCCAGAAATATATGAAATCAAGCAAAC 58.241 33.333 0.00 0.00 0.00 2.93
1312 3754 5.409520 TCGCAAGCTTAGCCAGAAATATATG 59.590 40.000 0.00 0.00 37.18 1.78
1316 3758 3.260475 TCGCAAGCTTAGCCAGAAATA 57.740 42.857 0.00 0.00 37.18 1.40
1435 3881 2.587307 AGATAGGGAGGGGCAAAATGTT 59.413 45.455 0.00 0.00 0.00 2.71
1494 3941 4.829064 AGCTTACATTTGCGTTCTGAAA 57.171 36.364 0.00 0.00 0.00 2.69
1495 3942 4.994852 AGTAGCTTACATTTGCGTTCTGAA 59.005 37.500 0.00 0.00 0.00 3.02
1496 3943 4.388773 CAGTAGCTTACATTTGCGTTCTGA 59.611 41.667 0.00 0.00 32.66 3.27
1497 3944 4.388773 TCAGTAGCTTACATTTGCGTTCTG 59.611 41.667 0.00 0.00 0.00 3.02
1498 3945 4.389077 GTCAGTAGCTTACATTTGCGTTCT 59.611 41.667 0.00 0.00 0.00 3.01
1499 3946 4.435651 GGTCAGTAGCTTACATTTGCGTTC 60.436 45.833 0.00 0.00 0.00 3.95
1500 3947 3.435671 GGTCAGTAGCTTACATTTGCGTT 59.564 43.478 0.00 0.00 0.00 4.84
1501 3948 3.000727 GGTCAGTAGCTTACATTTGCGT 58.999 45.455 0.00 0.00 0.00 5.24
1502 3949 3.262420 AGGTCAGTAGCTTACATTTGCG 58.738 45.455 0.00 0.00 0.00 4.85
1503 3950 5.393962 CAAAGGTCAGTAGCTTACATTTGC 58.606 41.667 12.23 0.00 42.53 3.68
1504 3951 5.393962 GCAAAGGTCAGTAGCTTACATTTG 58.606 41.667 16.94 16.94 42.53 2.32
1505 3952 4.459337 GGCAAAGGTCAGTAGCTTACATTT 59.541 41.667 0.00 0.00 42.53 2.32
1506 3953 4.010349 GGCAAAGGTCAGTAGCTTACATT 58.990 43.478 0.00 0.00 42.53 2.71
1507 3954 3.264450 AGGCAAAGGTCAGTAGCTTACAT 59.736 43.478 0.00 0.00 42.53 2.29
1508 3955 2.637872 AGGCAAAGGTCAGTAGCTTACA 59.362 45.455 0.00 0.00 42.53 2.41
1678 4145 7.897575 TGAGCACAACAACAAAATAAAAAGT 57.102 28.000 0.00 0.00 0.00 2.66
1700 4167 1.658114 CGATACGCTCCCCGAATGA 59.342 57.895 0.00 0.00 41.02 2.57
1754 4221 7.301054 AGCAGAAGAAAAACAAATAGATGACG 58.699 34.615 0.00 0.00 0.00 4.35
1757 4224 9.635520 ATTGAGCAGAAGAAAAACAAATAGATG 57.364 29.630 0.00 0.00 0.00 2.90
1790 4294 4.047822 GCACAATAGAGATCCTCGACTTG 58.952 47.826 0.00 0.00 35.36 3.16
1911 4417 7.679783 TGTTTTCTATCTCAATCAGTTCCTCA 58.320 34.615 0.00 0.00 0.00 3.86
1919 4425 4.788075 TCCCCCTGTTTTCTATCTCAATCA 59.212 41.667 0.00 0.00 0.00 2.57
1977 4503 4.271776 ACGTACTTTGGTGCTACTTTGTTC 59.728 41.667 0.00 0.00 0.00 3.18
1999 4525 5.470098 TGCTTGAGAACTTGGATTGAACTAC 59.530 40.000 0.00 0.00 0.00 2.73
2009 4535 2.620115 TCAGCTTTGCTTGAGAACTTGG 59.380 45.455 0.00 0.00 36.40 3.61
2013 4539 7.596248 TCATTTTATTCAGCTTTGCTTGAGAAC 59.404 33.333 0.00 0.00 36.40 3.01
2049 4575 2.348605 TTTTCGCTGGTTGTGGCAGC 62.349 55.000 0.00 0.00 38.48 5.25
2069 4596 9.884814 ATAGGTGTCTATTGTTATCTAGTCCTT 57.115 33.333 0.00 0.00 32.57 3.36
2071 4598 9.523168 AGATAGGTGTCTATTGTTATCTAGTCC 57.477 37.037 0.00 0.00 36.40 3.85
2080 4607 9.396022 CCAACAATAAGATAGGTGTCTATTGTT 57.604 33.333 10.99 10.99 39.53 2.83
2083 4610 9.614792 GTTCCAACAATAAGATAGGTGTCTATT 57.385 33.333 0.00 0.00 36.40 1.73
2084 4611 7.926555 CGTTCCAACAATAAGATAGGTGTCTAT 59.073 37.037 0.00 0.00 38.80 1.98
2108 4635 5.175859 ACTTACAATCGATTTGGATGACGT 58.824 37.500 8.21 3.37 39.80 4.34
2115 4642 5.050363 CACGGGATACTTACAATCGATTTGG 60.050 44.000 8.21 0.45 39.80 3.28
2123 4650 3.243636 CGGTAGCACGGGATACTTACAAT 60.244 47.826 13.54 0.00 36.19 2.71
2126 4653 1.678101 ACGGTAGCACGGGATACTTAC 59.322 52.381 13.54 0.00 36.19 2.34
2127 4654 2.057137 ACGGTAGCACGGGATACTTA 57.943 50.000 13.54 0.00 36.19 2.24
2176 4703 1.065126 ACCATGCTGAAGTAAGGGAGC 60.065 52.381 0.00 0.00 0.00 4.70
2181 4708 5.163953 CGTTACTCAACCATGCTGAAGTAAG 60.164 44.000 8.40 0.00 0.00 2.34
2183 4710 4.021807 TCGTTACTCAACCATGCTGAAGTA 60.022 41.667 0.00 0.00 0.00 2.24
2189 4716 1.346395 TGGTCGTTACTCAACCATGCT 59.654 47.619 0.00 0.00 38.14 3.79
2205 4732 4.139786 TCTGTATGGGTCTATACGTGGTC 58.860 47.826 0.00 0.00 36.54 4.02
2211 4738 4.772624 TCAGGCATCTGTATGGGTCTATAC 59.227 45.833 0.00 0.00 41.59 1.47
2215 4742 2.180946 TCAGGCATCTGTATGGGTCT 57.819 50.000 0.00 0.00 41.59 3.85
2218 4745 3.565764 TCTTTCAGGCATCTGTATGGG 57.434 47.619 0.00 0.00 41.59 4.00
2223 4750 2.575279 AGGTCATCTTTCAGGCATCTGT 59.425 45.455 0.00 0.00 41.59 3.41
2226 4753 2.208431 CGAGGTCATCTTTCAGGCATC 58.792 52.381 0.00 0.00 0.00 3.91
2228 4755 0.976641 ACGAGGTCATCTTTCAGGCA 59.023 50.000 0.00 0.00 0.00 4.75
2232 4759 5.127194 AGCTAATGTACGAGGTCATCTTTCA 59.873 40.000 0.00 0.00 0.00 2.69
2233 4760 5.593010 AGCTAATGTACGAGGTCATCTTTC 58.407 41.667 0.00 0.00 0.00 2.62
2235 4762 6.710597 TTAGCTAATGTACGAGGTCATCTT 57.289 37.500 0.86 0.00 0.00 2.40
2268 4795 2.882927 AGCATTACCAGCGATCGTAA 57.117 45.000 17.81 7.65 37.01 3.18
2273 4800 4.202253 TGTCTTGATAGCATTACCAGCGAT 60.202 41.667 0.00 0.00 37.01 4.58
2275 4802 3.457234 TGTCTTGATAGCATTACCAGCG 58.543 45.455 0.00 0.00 37.01 5.18
2279 4806 6.985188 TGACTTTGTCTTGATAGCATTACC 57.015 37.500 0.00 0.00 33.15 2.85
2289 4820 7.443879 TGTGCATATAAGTTGACTTTGTCTTGA 59.556 33.333 1.20 0.00 37.40 3.02
2292 4823 7.928307 ATGTGCATATAAGTTGACTTTGTCT 57.072 32.000 1.20 0.00 37.40 3.41
2324 4859 3.441572 CGAGTCCTAAGGTCCGACTTAAA 59.558 47.826 0.00 0.00 37.00 1.52
2333 4868 6.258507 TGTTTAACAAAACGAGTCCTAAGGTC 59.741 38.462 0.00 0.00 35.50 3.85
2367 4902 6.542821 TCCACAAATTAACCAGACATCTCTT 58.457 36.000 0.00 0.00 0.00 2.85
2377 4912 4.717280 ACCTGGTTTTCCACAAATTAACCA 59.283 37.500 6.57 6.57 46.22 3.67
2395 4930 7.822334 TGATGTGTTGTAATAGTTTCTACCTGG 59.178 37.037 0.00 0.00 0.00 4.45
2397 4932 9.216117 GTTGATGTGTTGTAATAGTTTCTACCT 57.784 33.333 0.00 0.00 0.00 3.08
2406 4941 4.153296 TGCCACGTTGATGTGTTGTAATAG 59.847 41.667 2.95 0.00 38.20 1.73
2408 4943 2.881513 TGCCACGTTGATGTGTTGTAAT 59.118 40.909 2.95 0.00 38.20 1.89
2412 4947 1.536766 AGATGCCACGTTGATGTGTTG 59.463 47.619 2.95 0.00 38.20 3.33
2417 4952 1.349627 GCGAGATGCCACGTTGATG 59.650 57.895 0.00 0.00 37.76 3.07
2481 5016 2.240162 GATGGAGACGGGGACACCAC 62.240 65.000 0.00 0.00 40.22 4.16
2491 5026 2.491022 GGACCCCGAGATGGAGACG 61.491 68.421 0.00 0.00 42.00 4.18
2525 5065 1.868109 GCAGCCTTTTCGTTTTGACCC 60.868 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.