Multiple sequence alignment - TraesCS2B01G404500

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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 TraesCS2B01G404500 chr2B 100.000 2288 0 0 1 2288 572585531 572587818 0.000000e+00 4226.0
1 TraesCS2B01G404500 chr2B 80.403 1041 105 52 830 1808 701491119 701490116 0.000000e+00 701.0
2 TraesCS2B01G404500 chr2B 84.302 172 17 6 243 408 701492968 701492801 2.350000e-35 159.0
3 TraesCS2B01G404500 chr2B 85.135 148 10 5 603 740 701492397 701492252 8.520000e-30 141.0
4 TraesCS2B01G404500 chr2B 85.135 148 10 5 603 740 701492769 701492624 8.520000e-30 141.0
5 TraesCS2B01G404500 chr2B 80.838 167 21 8 433 599 5602503 5602348 1.110000e-23 121.0
6 TraesCS2B01G404500 chr2A 88.025 977 53 29 810 1732 632622358 632623324 0.000000e+00 1098.0
7 TraesCS2B01G404500 chr2A 96.000 200 8 0 597 796 632613443 632613642 2.190000e-85 326.0
8 TraesCS2B01G404500 chr2A 83.041 342 44 11 3 335 632612677 632613013 4.780000e-77 298.0
9 TraesCS2B01G404500 chr2A 85.542 166 13 8 435 599 573944246 573944401 1.820000e-36 163.0
10 TraesCS2B01G404500 chr5A 84.957 1057 71 34 835 1857 456485753 456484751 0.000000e+00 990.0
11 TraesCS2B01G404500 chr5A 83.116 995 71 42 835 1786 474537711 474536771 0.000000e+00 817.0
12 TraesCS2B01G404500 chr5A 90.625 96 8 1 329 423 474537999 474537904 2.390000e-25 126.0
13 TraesCS2B01G404500 chr2D 83.621 1044 87 43 830 1816 582495030 582494014 0.000000e+00 904.0
14 TraesCS2B01G404500 chr2D 89.564 527 32 12 1339 1851 488229819 488230336 0.000000e+00 647.0
15 TraesCS2B01G404500 chr2D 92.140 458 18 6 861 1310 488229081 488229528 4.150000e-177 630.0
16 TraesCS2B01G404500 chr2D 83.503 588 63 20 67 642 488228297 488228862 3.370000e-143 518.0
17 TraesCS2B01G404500 chr2D 94.828 232 12 0 597 828 488228855 488229086 1.670000e-96 363.0
18 TraesCS2B01G404500 chr2D 85.492 193 11 4 603 780 582495220 582495030 3.880000e-43 185.0
19 TraesCS2B01G404500 chr2D 86.364 154 2 5 2135 2288 488230907 488231041 1.420000e-32 150.0
20 TraesCS2B01G404500 chr2D 82.659 173 19 7 243 408 582495426 582495258 2.370000e-30 143.0
21 TraesCS2B01G404500 chr2D 81.034 174 18 9 427 599 487492203 487492044 8.580000e-25 124.0
22 TraesCS2B01G404500 chr5D 84.081 936 61 30 835 1732 371441019 371440134 0.000000e+00 822.0
23 TraesCS2B01G404500 chr5B 83.313 809 74 30 895 1675 448804033 448803258 0.000000e+00 689.0
24 TraesCS2B01G404500 chr5B 85.769 520 35 16 1349 1854 441442350 441441856 4.360000e-142 514.0
25 TraesCS2B01G404500 chr5B 82.895 532 44 27 828 1336 441446526 441446019 3.490000e-118 435.0
26 TraesCS2B01G404500 chr5B 91.837 98 6 2 1826 1921 441441813 441441716 3.960000e-28 135.0
27 TraesCS2B01G404500 chr5B 91.954 87 7 0 296 382 441446906 441446820 3.090000e-24 122.0
28 TraesCS2B01G404500 chr5B 76.400 250 18 17 679 895 448806394 448806153 1.870000e-16 97.1
29 TraesCS2B01G404500 chr6B 84.524 504 43 20 833 1324 674935328 674935808 1.240000e-127 466.0
30 TraesCS2B01G404500 chr6B 87.850 107 2 6 615 710 674935158 674935264 5.170000e-22 115.0
31 TraesCS2B01G404500 chr6D 82.936 545 46 17 802 1325 446489070 446489588 4.480000e-122 448.0
32 TraesCS2B01G404500 chr6D 92.222 90 1 5 629 713 446488952 446489040 3.090000e-24 122.0
33 TraesCS2B01G404500 chr4D 82.745 510 62 16 839 1336 479962523 479962028 4.520000e-117 431.0
34 TraesCS2B01G404500 chr4D 87.786 131 13 3 295 423 479961482 479961353 1.420000e-32 150.0
35 TraesCS2B01G404500 chr4D 85.593 118 7 6 1920 2037 479961350 479961243 5.170000e-22 115.0
36 TraesCS2B01G404500 chr4D 92.308 65 4 1 2067 2131 479960761 479960698 8.700000e-15 91.6
37 TraesCS2B01G404500 chr4A 78.807 637 57 41 726 1325 686385836 686385241 7.770000e-95 357.0
38 TraesCS2B01G404500 chr4A 77.730 467 52 29 852 1295 641610544 641610981 2.940000e-59 239.0
39 TraesCS2B01G404500 chr4A 94.068 118 6 1 1920 2037 686384262 686384146 6.500000e-41 178.0
40 TraesCS2B01G404500 chr4A 83.663 202 8 11 604 786 641610311 641610506 1.410000e-37 167.0
41 TraesCS2B01G404500 chr6A 83.041 342 25 17 984 1325 593353796 593354104 1.730000e-71 279.0
42 TraesCS2B01G404500 chr4B 89.147 129 13 1 295 423 607287072 607286945 2.350000e-35 159.0
43 TraesCS2B01G404500 chr4B 87.288 118 5 5 1920 2037 607286942 607286835 2.390000e-25 126.0
44 TraesCS2B01G404500 chr4B 82.796 93 10 4 629 716 658585545 658585454 6.780000e-11 78.7
45 TraesCS2B01G404500 chr1B 83.951 162 15 7 438 599 151116953 151116803 6.590000e-31 145.0
46 TraesCS2B01G404500 chr7D 82.424 165 19 4 435 599 199349006 199348852 3.960000e-28 135.0
47 TraesCS2B01G404500 chr7B 82.036 167 22 3 434 600 518918123 518918281 3.960000e-28 135.0
48 TraesCS2B01G404500 chrUn 81.765 170 19 8 435 600 28586435 28586596 5.130000e-27 132.0
49 TraesCS2B01G404500 chr1D 81.707 164 19 9 435 598 8836877 8836725 2.390000e-25 126.0


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 TraesCS2B01G404500 chr2B 572585531 572587818 2287 False 4226.000000 4226 100.00000 1 2288 1 chr2B.!!$F1 2287
1 TraesCS2B01G404500 chr2B 701490116 701492968 2852 True 285.500000 701 83.74375 243 1808 4 chr2B.!!$R2 1565
2 TraesCS2B01G404500 chr2A 632622358 632623324 966 False 1098.000000 1098 88.02500 810 1732 1 chr2A.!!$F2 922
3 TraesCS2B01G404500 chr2A 632612677 632613642 965 False 312.000000 326 89.52050 3 796 2 chr2A.!!$F3 793
4 TraesCS2B01G404500 chr5A 456484751 456485753 1002 True 990.000000 990 84.95700 835 1857 1 chr5A.!!$R1 1022
5 TraesCS2B01G404500 chr5A 474536771 474537999 1228 True 471.500000 817 86.87050 329 1786 2 chr5A.!!$R2 1457
6 TraesCS2B01G404500 chr2D 488228297 488231041 2744 False 461.600000 647 89.27980 67 2288 5 chr2D.!!$F1 2221
7 TraesCS2B01G404500 chr2D 582494014 582495426 1412 True 410.666667 904 83.92400 243 1816 3 chr2D.!!$R2 1573
8 TraesCS2B01G404500 chr5D 371440134 371441019 885 True 822.000000 822 84.08100 835 1732 1 chr5D.!!$R1 897
9 TraesCS2B01G404500 chr5B 448803258 448806394 3136 True 393.050000 689 79.85650 679 1675 2 chr5B.!!$R2 996
10 TraesCS2B01G404500 chr5B 441441716 441446906 5190 True 301.500000 514 88.11375 296 1921 4 chr5B.!!$R1 1625
11 TraesCS2B01G404500 chr6B 674935158 674935808 650 False 290.500000 466 86.18700 615 1324 2 chr6B.!!$F1 709
12 TraesCS2B01G404500 chr6D 446488952 446489588 636 False 285.000000 448 87.57900 629 1325 2 chr6D.!!$F1 696
13 TraesCS2B01G404500 chr4A 686384146 686385836 1690 True 267.500000 357 86.43750 726 2037 2 chr4A.!!$R1 1311
14 TraesCS2B01G404500 chr4A 641610311 641610981 670 False 203.000000 239 80.69650 604 1295 2 chr4A.!!$F1 691

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
968 4881 0.179161 CGGCGACATCGTCTTCTTCT 60.179 55.0 0.0 0.0 42.59 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 10403 0.102481 GTAATCGAAGAGGCGGCAGA 59.898 55.0 13.08 2.54 43.63 4.26 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
40 41 4.344474 CCGACGCCGCCTCCTATC 62.344 72.222 0.00 0.00 0.00 2.08
41 42 3.288290 CGACGCCGCCTCCTATCT 61.288 66.667 0.00 0.00 0.00 1.98
42 43 2.846652 CGACGCCGCCTCCTATCTT 61.847 63.158 0.00 0.00 0.00 2.40
43 44 1.300233 GACGCCGCCTCCTATCTTG 60.300 63.158 0.00 0.00 0.00 3.02
44 45 2.029666 CGCCGCCTCCTATCTTGG 59.970 66.667 0.00 0.00 0.00 3.61
48 49 2.281139 GCCTCCTATCTTGGCGCC 60.281 66.667 22.73 22.73 37.11 6.53
49 50 2.812619 GCCTCCTATCTTGGCGCCT 61.813 63.158 29.70 9.99 37.11 5.52
50 51 1.832912 CCTCCTATCTTGGCGCCTT 59.167 57.895 29.70 12.33 0.00 4.35
51 52 0.533755 CCTCCTATCTTGGCGCCTTG 60.534 60.000 29.70 19.85 0.00 3.61
52 53 0.533755 CTCCTATCTTGGCGCCTTGG 60.534 60.000 29.70 17.44 0.00 3.61
53 54 2.189499 CCTATCTTGGCGCCTTGGC 61.189 63.158 29.70 0.00 45.12 4.52
112 122 2.912542 CGGCAGGATCCTCCGCTA 60.913 66.667 28.21 0.00 42.75 4.26
117 127 0.833834 CAGGATCCTCCGCTATGGGT 60.834 60.000 12.69 0.00 42.75 4.51
156 166 2.692368 ATGTGATCCCCCTGGCGT 60.692 61.111 0.00 0.00 0.00 5.68
205 216 5.021458 GTCGGGAGGGGATTGTCTATATTA 58.979 45.833 0.00 0.00 0.00 0.98
209 220 5.045797 GGGAGGGGATTGTCTATATTACCAC 60.046 48.000 0.00 0.00 0.00 4.16
213 224 6.792473 AGGGGATTGTCTATATTACCACATGA 59.208 38.462 0.00 0.00 0.00 3.07
214 225 7.462328 AGGGGATTGTCTATATTACCACATGAT 59.538 37.037 0.00 0.00 0.00 2.45
236 247 1.406539 TCCGATGCCTTCGTAACTACC 59.593 52.381 5.57 0.00 46.65 3.18
278 289 0.843872 GCAAACGAAACGAACCAAGC 59.156 50.000 0.00 0.00 0.00 4.01
301 317 5.420725 TGAGCTTCAACTAAGGAGCATAA 57.579 39.130 0.00 0.00 35.58 1.90
331 725 7.397476 AGTTTAGATACATCACTCAACTGAGGA 59.603 37.037 11.31 6.12 46.13 3.71
382 776 8.438676 AGCTTTATCAAGGTGATTACATACAC 57.561 34.615 0.00 0.00 39.36 2.90
392 786 6.648725 GTGATTACATACACCACTGAACTC 57.351 41.667 0.00 0.00 0.00 3.01
398 793 1.961277 CACCACTGAACTCACGGGC 60.961 63.158 0.00 0.00 0.00 6.13
443 838 5.193679 GGCACATTGTTAAATACTCCCTCT 58.806 41.667 0.00 0.00 0.00 3.69
444 839 5.066505 GGCACATTGTTAAATACTCCCTCTG 59.933 44.000 0.00 0.00 0.00 3.35
505 900 8.315482 TGGACTACATACAGCACAAAATAAGTA 58.685 33.333 0.00 0.00 0.00 2.24
617 1164 6.613755 ACGGAATATTAACGAAAGGGATTG 57.386 37.500 16.20 0.00 0.00 2.67
737 1343 4.222145 AGTCCAAAGCTAAGAATCCGTGTA 59.778 41.667 0.00 0.00 0.00 2.90
837 2535 6.428295 TCTTTGTTTCTTTCTGTTCCCCTAA 58.572 36.000 0.00 0.00 0.00 2.69
968 4881 0.179161 CGGCGACATCGTCTTCTTCT 60.179 55.000 0.00 0.00 42.59 2.85
969 4882 1.551145 GGCGACATCGTCTTCTTCTC 58.449 55.000 2.85 0.00 41.36 2.87
970 4883 1.133407 GGCGACATCGTCTTCTTCTCT 59.867 52.381 2.85 0.00 41.36 3.10
971 4884 2.416162 GGCGACATCGTCTTCTTCTCTT 60.416 50.000 2.85 0.00 41.36 2.85
972 4885 2.596419 GCGACATCGTCTTCTTCTCTTG 59.404 50.000 2.85 0.00 42.22 3.02
973 4886 3.175152 CGACATCGTCTTCTTCTCTTGG 58.825 50.000 0.00 0.00 34.11 3.61
974 4887 3.516615 GACATCGTCTTCTTCTCTTGGG 58.483 50.000 0.00 0.00 0.00 4.12
992 4936 0.668535 GGTCTTGGCGTCAGCTTTTT 59.331 50.000 0.00 0.00 44.37 1.94
995 4939 0.667993 CTTGGCGTCAGCTTTTTGGA 59.332 50.000 0.00 0.00 44.37 3.53
1083 5066 0.597637 CGACGTGCTTCAAGTGGACT 60.598 55.000 0.00 0.00 0.00 3.85
1194 5177 3.582647 TCAAGAACAAGGTCAGCTCCATA 59.417 43.478 0.00 0.00 0.00 2.74
1208 5191 1.003355 CCATATTCGCCGAGCCCAT 60.003 57.895 0.00 0.00 0.00 4.00
1209 5192 1.021390 CCATATTCGCCGAGCCCATC 61.021 60.000 0.00 0.00 0.00 3.51
1210 5193 1.021390 CATATTCGCCGAGCCCATCC 61.021 60.000 0.00 0.00 0.00 3.51
1211 5194 2.185310 ATATTCGCCGAGCCCATCCC 62.185 60.000 0.00 0.00 0.00 3.85
1224 5216 3.480133 ATCCCCTTCTTCGGCGGG 61.480 66.667 7.21 0.00 37.73 6.13
1381 9124 4.928661 CAAGTTCAGGTCTTGGATTACG 57.071 45.455 0.00 0.00 38.70 3.18
1405 9193 5.047660 GCTCGAGGAACTGTATATTGAGGAT 60.048 44.000 15.58 0.00 41.55 3.24
1562 9612 3.190874 GTTCACTTCTTCATAGGGCTCG 58.809 50.000 0.00 0.00 0.00 5.03
1581 9632 4.387862 GCTCGGTTCGAAGAAATTTACAGA 59.612 41.667 0.00 0.00 45.90 3.41
1675 9901 7.384932 CCACCCAAATCTCTTTACAAATCAAAC 59.615 37.037 0.00 0.00 0.00 2.93
1733 9959 9.561069 GTGGTTTTGTAATCCTAGTGATATCAT 57.439 33.333 9.02 1.07 31.83 2.45
1765 9997 6.257994 AGAGGACATATGTCATTCCAATGT 57.742 37.500 31.51 12.99 46.47 2.71
1911 10230 1.133790 GCCATCTGCACCTTGATTGAC 59.866 52.381 0.00 0.00 40.77 3.18
1915 10234 0.592637 CTGCACCTTGATTGACGCAA 59.407 50.000 0.00 0.00 0.00 4.85
1917 10236 1.001487 TGCACCTTGATTGACGCAAAG 60.001 47.619 0.00 0.00 0.00 2.77
1922 10241 3.886505 ACCTTGATTGACGCAAAGGTTTA 59.113 39.130 0.11 0.00 0.00 2.01
1923 10242 4.023193 ACCTTGATTGACGCAAAGGTTTAG 60.023 41.667 0.11 0.00 0.00 1.85
1954 10273 9.629878 CCAAACTATCTCTACTTCCTAGACTAA 57.370 37.037 0.00 0.00 0.00 2.24
1973 10292 3.636282 AAACTCGGCACATTGTTAACC 57.364 42.857 2.48 0.00 0.00 2.85
1979 10298 2.243810 GGCACATTGTTAACCAAGGGA 58.756 47.619 2.48 0.00 39.13 4.20
2037 10356 0.249073 AATACGTGAGCTGCTAGCCG 60.249 55.000 13.29 7.09 43.77 5.52
2038 10357 2.685387 ATACGTGAGCTGCTAGCCGC 62.685 60.000 22.11 22.11 43.77 6.53
2040 10359 4.154347 GTGAGCTGCTAGCCGCCT 62.154 66.667 25.24 13.90 43.77 5.52
2041 10360 3.842923 TGAGCTGCTAGCCGCCTC 61.843 66.667 25.24 20.66 43.77 4.70
2042 10361 3.535962 GAGCTGCTAGCCGCCTCT 61.536 66.667 25.24 9.18 43.77 3.69
2043 10362 3.080121 AGCTGCTAGCCGCCTCTT 61.080 61.111 25.24 6.16 43.77 2.85
2044 10363 2.587473 GCTGCTAGCCGCCTCTTC 60.587 66.667 19.39 0.00 38.05 2.87
2045 10364 2.279120 CTGCTAGCCGCCTCTTCG 60.279 66.667 13.29 0.00 38.05 3.79
2046 10365 2.754254 TGCTAGCCGCCTCTTCGA 60.754 61.111 13.29 0.00 38.05 3.71
2047 10366 2.081425 CTGCTAGCCGCCTCTTCGAT 62.081 60.000 13.29 0.00 38.05 3.59
2048 10367 1.068250 GCTAGCCGCCTCTTCGATT 59.932 57.895 2.29 0.00 0.00 3.34
2049 10368 0.314302 GCTAGCCGCCTCTTCGATTA 59.686 55.000 2.29 0.00 0.00 1.75
2050 10369 1.931263 GCTAGCCGCCTCTTCGATTAC 60.931 57.143 2.29 0.00 0.00 1.89
2051 10370 1.337071 CTAGCCGCCTCTTCGATTACA 59.663 52.381 0.00 0.00 0.00 2.41
2052 10371 0.179108 AGCCGCCTCTTCGATTACAC 60.179 55.000 0.00 0.00 0.00 2.90
2053 10372 0.459585 GCCGCCTCTTCGATTACACA 60.460 55.000 0.00 0.00 0.00 3.72
2054 10373 2.004583 CCGCCTCTTCGATTACACAA 57.995 50.000 0.00 0.00 0.00 3.33
2055 10374 1.927174 CCGCCTCTTCGATTACACAAG 59.073 52.381 0.00 0.00 0.00 3.16
2056 10375 2.607187 CGCCTCTTCGATTACACAAGT 58.393 47.619 0.00 0.00 0.00 3.16
2057 10376 2.599082 CGCCTCTTCGATTACACAAGTC 59.401 50.000 0.00 0.00 0.00 3.01
2058 10377 3.673594 CGCCTCTTCGATTACACAAGTCT 60.674 47.826 0.00 0.00 0.00 3.24
2059 10378 4.246458 GCCTCTTCGATTACACAAGTCTT 58.754 43.478 0.00 0.00 0.00 3.01
2060 10379 4.092091 GCCTCTTCGATTACACAAGTCTTG 59.908 45.833 11.17 11.17 0.00 3.02
2061 10380 4.627467 CCTCTTCGATTACACAAGTCTTGG 59.373 45.833 16.85 8.26 34.12 3.61
2062 10381 4.566004 TCTTCGATTACACAAGTCTTGGG 58.434 43.478 13.50 13.50 40.79 4.12
2063 10382 4.282449 TCTTCGATTACACAAGTCTTGGGA 59.718 41.667 21.80 0.00 37.55 4.37
2064 10383 4.188247 TCGATTACACAAGTCTTGGGAG 57.812 45.455 21.80 10.56 37.55 4.30
2065 10384 2.673368 CGATTACACAAGTCTTGGGAGC 59.327 50.000 21.80 1.75 37.55 4.70
2066 10385 3.617531 CGATTACACAAGTCTTGGGAGCT 60.618 47.826 21.80 4.80 37.55 4.09
2067 10386 3.857157 TTACACAAGTCTTGGGAGCTT 57.143 42.857 21.80 1.30 37.55 3.74
2068 10387 2.736670 ACACAAGTCTTGGGAGCTTT 57.263 45.000 21.80 0.00 37.55 3.51
2069 10388 2.301346 ACACAAGTCTTGGGAGCTTTG 58.699 47.619 21.80 8.49 37.55 2.77
2070 10389 1.000938 CACAAGTCTTGGGAGCTTTGC 60.001 52.381 16.85 0.00 35.62 3.68
2071 10390 1.321474 CAAGTCTTGGGAGCTTTGCA 58.679 50.000 4.52 0.00 0.00 4.08
2072 10391 1.268899 CAAGTCTTGGGAGCTTTGCAG 59.731 52.381 4.52 0.00 0.00 4.41
2073 10392 0.475906 AGTCTTGGGAGCTTTGCAGT 59.524 50.000 0.00 0.00 0.00 4.40
2074 10393 1.133668 AGTCTTGGGAGCTTTGCAGTT 60.134 47.619 0.00 0.00 0.00 3.16
2075 10394 1.683385 GTCTTGGGAGCTTTGCAGTTT 59.317 47.619 0.00 0.00 0.00 2.66
2076 10395 1.956477 TCTTGGGAGCTTTGCAGTTTC 59.044 47.619 0.00 0.00 0.00 2.78
2077 10396 1.682854 CTTGGGAGCTTTGCAGTTTCA 59.317 47.619 0.00 0.00 0.00 2.69
2078 10397 1.321474 TGGGAGCTTTGCAGTTTCAG 58.679 50.000 0.00 0.00 0.00 3.02
2079 10398 1.322442 GGGAGCTTTGCAGTTTCAGT 58.678 50.000 0.00 0.00 0.00 3.41
2080 10399 1.268079 GGGAGCTTTGCAGTTTCAGTC 59.732 52.381 0.00 0.00 0.00 3.51
2081 10400 2.225467 GGAGCTTTGCAGTTTCAGTCT 58.775 47.619 0.00 0.00 0.00 3.24
2082 10401 2.031333 GGAGCTTTGCAGTTTCAGTCTG 60.031 50.000 0.00 0.00 36.18 3.51
2089 10408 1.155042 CAGTTTCAGTCTGCTCTGCC 58.845 55.000 0.00 0.00 35.63 4.85
2090 10409 0.320247 AGTTTCAGTCTGCTCTGCCG 60.320 55.000 0.00 0.00 35.63 5.69
2091 10410 1.669115 TTTCAGTCTGCTCTGCCGC 60.669 57.895 0.00 0.00 35.63 6.53
2092 10411 3.596066 TTCAGTCTGCTCTGCCGCC 62.596 63.158 0.00 0.00 35.63 6.13
2093 10412 4.079850 CAGTCTGCTCTGCCGCCT 62.080 66.667 0.00 0.00 0.00 5.52
2104 10423 0.103208 CTGCCGCCTCTTCGATTACT 59.897 55.000 0.00 0.00 0.00 2.24
2105 10424 0.179111 TGCCGCCTCTTCGATTACTG 60.179 55.000 0.00 0.00 0.00 2.74
2127 10446 0.395312 GGTTTCGTCCTGGGTCTCAA 59.605 55.000 0.00 0.00 0.00 3.02
2130 10449 1.827399 TTCGTCCTGGGTCTCAAGCC 61.827 60.000 0.00 0.00 43.74 4.35
2140 10918 1.001706 GGTCTCAAGCCCGAAAAACAC 60.002 52.381 0.00 0.00 0.00 3.32
2143 10921 1.266989 CTCAAGCCCGAAAAACACTCC 59.733 52.381 0.00 0.00 0.00 3.85
2212 10990 5.279106 CCAAGAATTTTTCAGCTCATGTGGA 60.279 40.000 0.00 0.00 0.00 4.02
2213 10991 6.218019 CAAGAATTTTTCAGCTCATGTGGAA 58.782 36.000 0.00 0.00 0.00 3.53
2214 10992 5.776744 AGAATTTTTCAGCTCATGTGGAAC 58.223 37.500 0.00 0.00 37.35 3.62
2215 10993 5.537674 AGAATTTTTCAGCTCATGTGGAACT 59.462 36.000 0.00 0.00 38.04 3.01
2216 10994 4.572985 TTTTTCAGCTCATGTGGAACTG 57.427 40.909 0.00 0.00 40.38 3.16
2217 10995 2.936919 TTCAGCTCATGTGGAACTGT 57.063 45.000 0.00 0.00 40.03 3.55
2218 10996 2.174363 TCAGCTCATGTGGAACTGTG 57.826 50.000 0.00 0.00 40.03 3.66
2219 10997 0.520404 CAGCTCATGTGGAACTGTGC 59.480 55.000 0.00 0.00 35.45 4.57
2220 10998 0.607489 AGCTCATGTGGAACTGTGCC 60.607 55.000 0.00 0.00 36.12 5.01
2221 10999 0.890542 GCTCATGTGGAACTGTGCCA 60.891 55.000 2.48 2.48 38.04 4.92
2222 11000 1.608055 CTCATGTGGAACTGTGCCAA 58.392 50.000 9.65 0.47 37.12 4.52
2223 11001 1.267806 CTCATGTGGAACTGTGCCAAC 59.732 52.381 9.65 4.82 37.12 3.77
2224 11002 1.031235 CATGTGGAACTGTGCCAACA 58.969 50.000 9.65 10.51 37.12 3.33
2235 11013 0.940126 GTGCCAACAGACTCACACAG 59.060 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.797278 CCAAGATAGGAGGCGGCGT 61.797 63.158 9.37 0.00 0.00 5.68
31 32 2.281139 GGCGCCAAGATAGGAGGC 60.281 66.667 24.80 0.00 45.76 4.70
34 35 1.526887 CCAAGGCGCCAAGATAGGA 59.473 57.895 31.54 0.00 0.00 2.94
38 39 3.064324 GTGCCAAGGCGCCAAGAT 61.064 61.111 31.54 8.92 44.94 2.40
47 48 3.305516 GGTGCCAAGGTGCCAAGG 61.306 66.667 0.00 0.00 0.00 3.61
48 49 3.673484 CGGTGCCAAGGTGCCAAG 61.673 66.667 0.00 0.00 0.00 3.61
141 151 4.530857 CGACGCCAGGGGGATCAC 62.531 72.222 8.67 0.00 35.59 3.06
193 204 7.819415 CGGACATCATGTGGTAATATAGACAAT 59.181 37.037 0.00 0.00 0.00 2.71
205 216 0.464373 GGCATCGGACATCATGTGGT 60.464 55.000 0.00 0.00 0.00 4.16
236 247 1.265905 GAAGTAGTGTTTTGGGCCACG 59.734 52.381 5.23 0.00 36.69 4.94
278 289 3.325293 TGCTCCTTAGTTGAAGCTCAG 57.675 47.619 0.00 0.00 33.36 3.35
331 725 1.667236 TGCGATGATGCGGAAATCTT 58.333 45.000 0.00 0.00 37.81 2.40
382 776 0.817634 TTTGCCCGTGAGTTCAGTGG 60.818 55.000 0.00 0.00 0.00 4.00
392 786 2.610232 CCCTTCATTCTTTTTGCCCGTG 60.610 50.000 0.00 0.00 0.00 4.94
398 793 4.501071 CAGATGGCCCTTCATTCTTTTTG 58.499 43.478 0.00 0.00 0.00 2.44
474 869 7.552458 TTTGTGCTGTATGTAGTCCATATTG 57.448 36.000 0.00 0.00 38.29 1.90
526 921 9.800572 ACAGTACATACAGATGTAGATAGACAT 57.199 33.333 0.00 0.00 46.79 3.06
599 1144 8.466798 CCTTGTTTCAATCCCTTTCGTTAATAT 58.533 33.333 0.00 0.00 0.00 1.28
610 1157 4.152647 GTTCCTTCCTTGTTTCAATCCCT 58.847 43.478 0.00 0.00 0.00 4.20
617 1164 3.149981 CTCCCTGTTCCTTCCTTGTTTC 58.850 50.000 0.00 0.00 0.00 2.78
808 2506 6.318900 GGGAACAGAAAGAAACAAAGAGAGAA 59.681 38.462 0.00 0.00 0.00 2.87
828 2526 0.465642 CGGGCTTGGATTAGGGGAAC 60.466 60.000 0.00 0.00 0.00 3.62
917 4818 0.762082 TTGCTTTGGTTGGCCATGGA 60.762 50.000 18.40 0.00 45.56 3.41
968 4881 1.371183 CTGACGCCAAGACCCAAGA 59.629 57.895 0.00 0.00 0.00 3.02
969 4882 2.328099 GCTGACGCCAAGACCCAAG 61.328 63.158 0.00 0.00 0.00 3.61
970 4883 2.281484 GCTGACGCCAAGACCCAA 60.281 61.111 0.00 0.00 0.00 4.12
971 4884 2.337879 AAAGCTGACGCCAAGACCCA 62.338 55.000 0.00 0.00 36.60 4.51
972 4885 1.172812 AAAAGCTGACGCCAAGACCC 61.173 55.000 0.00 0.00 36.60 4.46
973 4886 0.668535 AAAAAGCTGACGCCAAGACC 59.331 50.000 0.00 0.00 36.60 3.85
974 4887 1.600413 CCAAAAAGCTGACGCCAAGAC 60.600 52.381 0.00 0.00 36.60 3.01
992 4936 1.630369 CCTTGTTCTCCATCAGGTCCA 59.370 52.381 0.00 0.00 35.89 4.02
995 4939 0.995024 CCCCTTGTTCTCCATCAGGT 59.005 55.000 0.00 0.00 35.89 4.00
1194 5177 4.256180 GGGATGGGCTCGGCGAAT 62.256 66.667 12.13 0.18 0.00 3.34
1380 9123 4.222886 CTCAATATACAGTTCCTCGAGCG 58.777 47.826 6.99 0.19 0.00 5.03
1381 9124 4.278669 TCCTCAATATACAGTTCCTCGAGC 59.721 45.833 6.99 0.00 0.00 5.03
1675 9901 3.781079 TTTGACAGCACAGGAAAACAG 57.219 42.857 0.00 0.00 0.00 3.16
1733 9959 7.931015 ATGACATATGTCCTCTTTAACCCTA 57.069 36.000 28.64 9.32 44.15 3.53
1873 10192 4.118168 TGGCCCTTCATTCTTTTTCTCT 57.882 40.909 0.00 0.00 0.00 3.10
1911 10230 3.284336 GGGGGCTAAACCTTTGCG 58.716 61.111 0.00 0.00 39.10 4.85
1943 10262 3.159472 TGTGCCGAGTTTAGTCTAGGAA 58.841 45.455 0.00 0.00 33.10 3.36
1954 10273 2.577700 TGGTTAACAATGTGCCGAGTT 58.422 42.857 8.10 0.00 0.00 3.01
1958 10277 1.067915 CCCTTGGTTAACAATGTGCCG 60.068 52.381 8.10 0.00 38.65 5.69
1973 10292 6.070424 TGGTAGTCCTAGTGTTAATTCCCTTG 60.070 42.308 0.00 0.00 34.23 3.61
1979 10298 4.781087 TGGCTGGTAGTCCTAGTGTTAATT 59.219 41.667 0.00 0.00 34.23 1.40
2037 10356 3.851098 AGACTTGTGTAATCGAAGAGGC 58.149 45.455 0.00 0.00 43.63 4.70
2038 10357 4.627467 CCAAGACTTGTGTAATCGAAGAGG 59.373 45.833 14.03 0.00 43.63 3.69
2039 10358 4.627467 CCCAAGACTTGTGTAATCGAAGAG 59.373 45.833 14.03 0.00 43.63 2.85
2040 10359 4.282449 TCCCAAGACTTGTGTAATCGAAGA 59.718 41.667 14.03 0.00 45.75 2.87
2041 10360 4.566004 TCCCAAGACTTGTGTAATCGAAG 58.434 43.478 14.03 0.00 0.00 3.79
2042 10361 4.566004 CTCCCAAGACTTGTGTAATCGAA 58.434 43.478 14.03 0.00 0.00 3.71
2043 10362 3.616560 GCTCCCAAGACTTGTGTAATCGA 60.617 47.826 14.03 0.00 0.00 3.59
2044 10363 2.673368 GCTCCCAAGACTTGTGTAATCG 59.327 50.000 14.03 0.00 0.00 3.34
2045 10364 3.944087 AGCTCCCAAGACTTGTGTAATC 58.056 45.455 14.03 0.00 0.00 1.75
2046 10365 4.373156 AAGCTCCCAAGACTTGTGTAAT 57.627 40.909 14.03 0.00 0.00 1.89
2047 10366 3.857157 AAGCTCCCAAGACTTGTGTAA 57.143 42.857 14.03 0.00 0.00 2.41
2048 10367 3.476552 CAAAGCTCCCAAGACTTGTGTA 58.523 45.455 14.03 0.00 0.00 2.90
2049 10368 2.301346 CAAAGCTCCCAAGACTTGTGT 58.699 47.619 14.03 0.00 0.00 3.72
2050 10369 1.000938 GCAAAGCTCCCAAGACTTGTG 60.001 52.381 14.03 2.73 0.00 3.33
2051 10370 1.322442 GCAAAGCTCCCAAGACTTGT 58.678 50.000 14.03 0.00 0.00 3.16
2052 10371 1.268899 CTGCAAAGCTCCCAAGACTTG 59.731 52.381 8.31 8.31 0.00 3.16
2053 10372 1.133668 ACTGCAAAGCTCCCAAGACTT 60.134 47.619 0.00 0.00 0.00 3.01
2054 10373 0.475906 ACTGCAAAGCTCCCAAGACT 59.524 50.000 0.00 0.00 0.00 3.24
2055 10374 1.322442 AACTGCAAAGCTCCCAAGAC 58.678 50.000 0.00 0.00 0.00 3.01
2056 10375 1.956477 GAAACTGCAAAGCTCCCAAGA 59.044 47.619 0.00 0.00 0.00 3.02
2057 10376 1.682854 TGAAACTGCAAAGCTCCCAAG 59.317 47.619 0.00 0.00 0.00 3.61
2058 10377 1.682854 CTGAAACTGCAAAGCTCCCAA 59.317 47.619 0.00 0.00 0.00 4.12
2059 10378 1.321474 CTGAAACTGCAAAGCTCCCA 58.679 50.000 0.00 0.00 0.00 4.37
2060 10379 1.268079 GACTGAAACTGCAAAGCTCCC 59.732 52.381 0.00 0.00 0.00 4.30
2061 10380 2.031333 CAGACTGAAACTGCAAAGCTCC 60.031 50.000 0.00 0.00 0.00 4.70
2062 10381 3.265070 CAGACTGAAACTGCAAAGCTC 57.735 47.619 0.00 0.00 0.00 4.09
2070 10389 1.155042 GGCAGAGCAGACTGAAACTG 58.845 55.000 6.65 12.16 39.94 3.16
2071 10390 0.320247 CGGCAGAGCAGACTGAAACT 60.320 55.000 6.65 0.00 39.94 2.66
2072 10391 1.905922 GCGGCAGAGCAGACTGAAAC 61.906 60.000 6.65 0.00 39.94 2.78
2073 10392 1.669115 GCGGCAGAGCAGACTGAAA 60.669 57.895 6.65 0.00 39.94 2.69
2074 10393 2.047844 GCGGCAGAGCAGACTGAA 60.048 61.111 6.65 0.00 39.94 3.02
2075 10394 4.074526 GGCGGCAGAGCAGACTGA 62.075 66.667 6.65 0.00 39.94 3.41
2076 10395 4.079850 AGGCGGCAGAGCAGACTG 62.080 66.667 13.08 0.00 41.23 3.51
2077 10396 3.768922 GAGGCGGCAGAGCAGACT 61.769 66.667 13.08 0.00 46.30 3.24
2078 10397 3.308014 AAGAGGCGGCAGAGCAGAC 62.308 63.158 13.08 0.00 39.27 3.51
2079 10398 2.999648 AAGAGGCGGCAGAGCAGA 61.000 61.111 13.08 0.00 39.27 4.26
2080 10399 2.511145 GAAGAGGCGGCAGAGCAG 60.511 66.667 13.08 0.00 39.27 4.24
2081 10400 4.441695 CGAAGAGGCGGCAGAGCA 62.442 66.667 13.08 0.00 39.27 4.26
2082 10401 2.914777 AATCGAAGAGGCGGCAGAGC 62.915 60.000 13.08 0.00 43.63 4.09
2083 10402 0.385751 TAATCGAAGAGGCGGCAGAG 59.614 55.000 13.08 0.00 43.63 3.35
2084 10403 0.102481 GTAATCGAAGAGGCGGCAGA 59.898 55.000 13.08 2.54 43.63 4.26
2085 10404 0.103208 AGTAATCGAAGAGGCGGCAG 59.897 55.000 13.08 0.00 43.63 4.85
2086 10405 0.179111 CAGTAATCGAAGAGGCGGCA 60.179 55.000 13.08 0.00 43.63 5.69
2087 10406 1.491505 GCAGTAATCGAAGAGGCGGC 61.492 60.000 0.00 0.00 43.63 6.53
2088 10407 0.179111 TGCAGTAATCGAAGAGGCGG 60.179 55.000 0.00 0.00 43.63 6.13
2089 10408 1.203928 CTGCAGTAATCGAAGAGGCG 58.796 55.000 5.25 0.00 43.63 5.52
2090 10409 1.134670 ACCTGCAGTAATCGAAGAGGC 60.135 52.381 13.81 0.00 43.63 4.70
2091 10410 2.969628 ACCTGCAGTAATCGAAGAGG 57.030 50.000 13.81 0.00 43.63 3.69
2092 10411 3.304559 CGAAACCTGCAGTAATCGAAGAG 59.695 47.826 20.91 2.71 43.63 2.85
2093 10412 3.250744 CGAAACCTGCAGTAATCGAAGA 58.749 45.455 20.91 0.00 39.19 2.87
2127 10446 1.228459 GGGGAGTGTTTTTCGGGCT 60.228 57.895 0.00 0.00 0.00 5.19
2130 10449 0.109723 TGGAGGGGAGTGTTTTTCGG 59.890 55.000 0.00 0.00 0.00 4.30
2132 10451 3.496331 TGAATGGAGGGGAGTGTTTTTC 58.504 45.455 0.00 0.00 0.00 2.29
2133 10452 3.611025 TGAATGGAGGGGAGTGTTTTT 57.389 42.857 0.00 0.00 0.00 1.94
2140 10918 6.006449 CCTTATACATTTGAATGGAGGGGAG 58.994 44.000 8.44 0.00 40.70 4.30
2143 10921 5.010012 GTGCCTTATACATTTGAATGGAGGG 59.990 44.000 8.44 5.25 40.70 4.30
2215 10993 0.251634 TGTGTGAGTCTGTTGGCACA 59.748 50.000 0.00 0.00 38.78 4.57
2216 10994 0.940126 CTGTGTGAGTCTGTTGGCAC 59.060 55.000 0.00 0.00 0.00 5.01
2217 10995 0.829990 TCTGTGTGAGTCTGTTGGCA 59.170 50.000 0.00 0.00 0.00 4.92
2218 10996 1.953559 TTCTGTGTGAGTCTGTTGGC 58.046 50.000 0.00 0.00 0.00 4.52
2219 10997 4.818546 AGATTTTCTGTGTGAGTCTGTTGG 59.181 41.667 0.00 0.00 0.00 3.77
2220 10998 5.998454 AGATTTTCTGTGTGAGTCTGTTG 57.002 39.130 0.00 0.00 0.00 3.33
2221 10999 7.396540 AAAAGATTTTCTGTGTGAGTCTGTT 57.603 32.000 0.00 0.00 0.00 3.16
2222 11000 7.337942 AGAAAAAGATTTTCTGTGTGAGTCTGT 59.662 33.333 15.24 0.00 37.37 3.41
2223 11001 7.701445 AGAAAAAGATTTTCTGTGTGAGTCTG 58.299 34.615 15.24 0.00 37.37 3.51
2224 11002 7.872113 AGAAAAAGATTTTCTGTGTGAGTCT 57.128 32.000 15.24 0.00 37.37 3.24
2225 11003 8.917415 AAAGAAAAAGATTTTCTGTGTGAGTC 57.083 30.769 16.36 0.00 38.62 3.36
2226 11004 9.788960 GTAAAGAAAAAGATTTTCTGTGTGAGT 57.211 29.630 16.36 0.00 38.62 3.41
2227 11005 9.787532 TGTAAAGAAAAAGATTTTCTGTGTGAG 57.212 29.630 16.36 0.00 38.62 3.51


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

AutoCloner maintained by Alex Coulton.