Multiple sequence alignment - TraesCS1D01G216700

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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 TraesCS1D01G216700 chr1D 100.000 5434 0 0 966 6399 302386013 302391446 0.000000e+00 10035.0
1 TraesCS1D01G216700 chr1D 100.000 649 0 0 1 649 302385048 302385696 0.000000e+00 1199.0
2 TraesCS1D01G216700 chr1D 88.636 132 14 1 3248 3379 419481557 419481687 6.640000e-35 159.0
3 TraesCS1D01G216700 chr1B 96.105 4929 110 32 966 5850 409272479 409277369 0.000000e+00 7963.0
4 TraesCS1D01G216700 chr1B 90.033 602 32 11 5748 6346 409279094 409279670 0.000000e+00 754.0
5 TraesCS1D01G216700 chr1B 90.722 194 16 2 4398 4591 28515882 28516073 2.290000e-64 257.0
6 TraesCS1D01G216700 chr1B 84.186 215 29 1 4381 4590 28509105 28509319 3.020000e-48 204.0
7 TraesCS1D01G216700 chr1B 96.341 82 2 1 568 649 409272344 409272424 4.020000e-27 134.0
8 TraesCS1D01G216700 chr1B 84.615 78 6 3 461 538 409272275 409272346 8.900000e-09 73.1
9 TraesCS1D01G216700 chr1A 96.406 4313 89 25 1585 5850 377024190 377028483 0.000000e+00 7046.0
10 TraesCS1D01G216700 chr1A 93.314 688 25 9 966 1652 377023478 377024145 0.000000e+00 996.0
11 TraesCS1D01G216700 chr1A 93.939 264 12 2 6136 6399 377029668 377029927 4.650000e-106 396.0
12 TraesCS1D01G216700 chr1A 86.471 340 31 9 5763 6096 377029334 377029664 6.100000e-95 359.0
13 TraesCS1D01G216700 chr1A 84.456 386 34 12 1 381 377022340 377022704 2.190000e-94 357.0
14 TraesCS1D01G216700 chr1A 82.097 391 36 22 6023 6399 377028688 377029058 2.900000e-78 303.0
15 TraesCS1D01G216700 chr1A 97.701 87 1 1 563 649 377023338 377023423 1.440000e-31 148.0
16 TraesCS1D01G216700 chr1A 88.136 118 8 4 461 578 377022700 377022811 1.120000e-27 135.0
17 TraesCS1D01G216700 chr3A 82.779 691 82 18 2536 3214 547203838 547203173 3.330000e-162 582.0
18 TraesCS1D01G216700 chr3A 85.119 504 61 11 2001 2500 547184811 547185304 2.660000e-138 503.0
19 TraesCS1D01G216700 chr3A 82.947 475 51 12 2001 2472 547204305 547203858 9.990000e-108 401.0
20 TraesCS1D01G216700 chr3A 87.967 241 20 7 3548 3781 547202950 547202712 6.320000e-70 276.0
21 TraesCS1D01G216700 chr3A 81.308 107 15 4 375 480 587969407 587969305 1.480000e-11 82.4
22 TraesCS1D01G216700 chr3B 90.909 88 8 0 376 463 547120695 547120782 1.130000e-22 119.0
23 TraesCS1D01G216700 chr5A 90.000 90 7 2 375 463 691676214 691676126 1.460000e-21 115.0
24 TraesCS1D01G216700 chr4A 89.655 87 8 1 377 463 19508089 19508004 6.780000e-20 110.0
25 TraesCS1D01G216700 chr4A 87.500 88 10 1 377 464 83770823 83770909 4.080000e-17 100.0
26 TraesCS1D01G216700 chr6A 88.372 86 9 1 374 459 324283087 324283171 1.140000e-17 102.0
27 TraesCS1D01G216700 chr3D 86.022 93 9 4 373 463 159576477 159576567 5.280000e-16 97.1
28 TraesCS1D01G216700 chr6D 95.082 61 2 1 2788 2848 464734914 464734973 1.900000e-15 95.3
29 TraesCS1D01G216700 chr7A 85.227 88 12 1 376 463 509167326 509167412 8.840000e-14 89.8
30 TraesCS1D01G216700 chr4D 84.783 92 10 4 373 462 484395497 484395408 8.840000e-14 89.8


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 TraesCS1D01G216700 chr1D 302385048 302391446 6398 False 5617.000000 10035 100.000000 1 6399 2 chr1D.!!$F2 6398
1 TraesCS1D01G216700 chr1B 409272275 409279670 7395 False 2231.025000 7963 91.773500 461 6346 4 chr1B.!!$F3 5885
2 TraesCS1D01G216700 chr1A 377022340 377029927 7587 False 1217.500000 7046 90.315000 1 6399 8 chr1A.!!$F1 6398
3 TraesCS1D01G216700 chr3A 547202712 547204305 1593 True 419.666667 582 84.564333 2001 3781 3 chr3A.!!$R2 1780

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
192 194 0.036010 ATTGGAAGGAGACTGGCGTG 60.036 55.000 0.00 0.00 42.68 5.34 F
562 567 0.178955 TGGGAATATCGCGAGGGGTA 60.179 55.000 16.66 1.56 31.21 3.69 F
1549 2101 0.105778 GGTGAGCTATCTCTGTGCCC 59.894 60.000 0.00 0.00 40.03 5.36 F
1550 2102 0.249238 GTGAGCTATCTCTGTGCCCG 60.249 60.000 0.00 0.00 40.03 6.13 F
1551 2103 1.300542 GAGCTATCTCTGTGCCCGC 60.301 63.158 0.00 0.00 36.42 6.13 F
1583 2135 1.605232 TGCAGTTTCAGTCATGTGCAG 59.395 47.619 0.00 0.00 36.05 4.41 F
4989 5725 1.573108 ACTGGATACCCTGTGGACAG 58.427 55.000 0.00 0.00 42.18 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1913 0.814457 ACAAACGGCACAAAAGCTCA 59.186 45.000 0.00 0.00 34.17 4.26 R
1554 2106 2.099062 GAAACTGCATGAGCGCGG 59.901 61.111 8.83 0.00 46.23 6.46 R
3465 4190 5.089970 CAGATAATTCTGTCACTGTGGGA 57.910 43.478 8.11 1.81 43.73 4.37 R
3478 4203 6.511767 CGGTAGGTGCATCAAACAGATAATTC 60.512 42.308 0.00 0.00 34.43 2.17 R
4989 5725 0.606673 GGAAGGTCCAGTTCCAGCAC 60.607 60.000 5.24 0.00 42.79 4.40 R
5380 6116 2.356913 CACCGCGACCATGACACA 60.357 61.111 8.23 0.00 0.00 3.72 R
6353 9089 0.526662 CTAGAAAGCGTGGAGTCCGT 59.473 55.000 4.30 0.00 0.00 4.69 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
39 40 2.668632 GTGGCCGTGGAGGATTCA 59.331 61.111 0.00 0.00 45.00 2.57
47 48 1.131126 CGTGGAGGATTCATGTGTTGC 59.869 52.381 0.00 0.00 0.00 4.17
56 58 4.320494 GGATTCATGTGTTGCGAAAGAAGT 60.320 41.667 0.00 0.00 0.00 3.01
64 66 1.028905 TGCGAAAGAAGTTTGGGTGG 58.971 50.000 0.00 0.00 0.00 4.61
68 70 2.425668 CGAAAGAAGTTTGGGTGGTGTT 59.574 45.455 0.00 0.00 0.00 3.32
84 86 4.016444 TGGTGTTGGGAGAAGAATAATGC 58.984 43.478 0.00 0.00 0.00 3.56
87 89 4.576463 GTGTTGGGAGAAGAATAATGCGAT 59.424 41.667 0.00 0.00 0.00 4.58
91 93 5.541845 TGGGAGAAGAATAATGCGATACAG 58.458 41.667 0.00 0.00 0.00 2.74
93 95 5.635700 GGGAGAAGAATAATGCGATACAGAC 59.364 44.000 0.00 0.00 0.00 3.51
97 99 2.743636 ATAATGCGATACAGACGGGG 57.256 50.000 0.00 0.00 0.00 5.73
115 117 3.755483 CGGGGATGAGAAGAAGATAGGGA 60.755 52.174 0.00 0.00 0.00 4.20
121 123 6.183361 GGATGAGAAGAAGATAGGGACACAAT 60.183 42.308 0.00 0.00 0.00 2.71
125 127 3.464828 AGAAGATAGGGACACAATGGGT 58.535 45.455 0.00 0.00 0.00 4.51
136 138 0.961019 ACAATGGGTGACATGTGTGC 59.039 50.000 1.15 0.00 40.44 4.57
138 140 0.537143 AATGGGTGACATGTGTGCGT 60.537 50.000 1.15 0.00 40.44 5.24
139 141 1.236616 ATGGGTGACATGTGTGCGTG 61.237 55.000 1.15 0.00 38.70 5.34
142 144 1.163420 GGTGACATGTGTGCGTGGAA 61.163 55.000 1.15 0.00 35.99 3.53
143 145 0.660488 GTGACATGTGTGCGTGGAAA 59.340 50.000 1.15 0.00 35.99 3.13
145 147 0.238289 GACATGTGTGCGTGGAAAGG 59.762 55.000 1.15 0.00 35.99 3.11
146 148 0.179032 ACATGTGTGCGTGGAAAGGA 60.179 50.000 0.00 0.00 35.99 3.36
156 158 3.066203 TGCGTGGAAAGGAAGAGAAAAAC 59.934 43.478 0.00 0.00 0.00 2.43
160 162 3.558418 TGGAAAGGAAGAGAAAAACGACG 59.442 43.478 0.00 0.00 0.00 5.12
162 164 2.234300 AGGAAGAGAAAAACGACGCA 57.766 45.000 0.00 0.00 0.00 5.24
167 169 4.084223 GGAAGAGAAAAACGACGCATGTAA 60.084 41.667 0.00 0.00 0.00 2.41
169 171 4.304110 AGAGAAAAACGACGCATGTAAGA 58.696 39.130 0.00 0.00 0.00 2.10
178 180 3.124466 CGACGCATGTAAGAACAATTGGA 59.876 43.478 10.83 0.00 39.58 3.53
189 191 2.206576 ACAATTGGAAGGAGACTGGC 57.793 50.000 10.83 0.00 42.68 4.85
190 192 1.089920 CAATTGGAAGGAGACTGGCG 58.910 55.000 0.00 0.00 42.68 5.69
191 193 0.693049 AATTGGAAGGAGACTGGCGT 59.307 50.000 0.00 0.00 42.68 5.68
192 194 0.036010 ATTGGAAGGAGACTGGCGTG 60.036 55.000 0.00 0.00 42.68 5.34
193 195 1.118965 TTGGAAGGAGACTGGCGTGA 61.119 55.000 0.00 0.00 42.68 4.35
194 196 1.216710 GGAAGGAGACTGGCGTGAG 59.783 63.158 0.00 0.00 42.68 3.51
206 208 2.434884 CGTGAGCGGCAGATTGGT 60.435 61.111 1.45 0.00 0.00 3.67
212 214 2.514592 CGGCAGATTGGTCGCCAT 60.515 61.111 0.00 0.00 41.21 4.40
233 235 7.361201 CGCCATATCGAGATCATTTACCAAAAT 60.361 37.037 0.00 0.00 35.65 1.82
284 286 5.069318 TGACACATGCAGAGTTTTCCATTA 58.931 37.500 0.00 0.00 0.00 1.90
285 287 5.534278 TGACACATGCAGAGTTTTCCATTAA 59.466 36.000 0.00 0.00 0.00 1.40
286 288 6.040278 TGACACATGCAGAGTTTTCCATTAAA 59.960 34.615 0.00 0.00 0.00 1.52
382 387 9.722184 AACTATTCAGTTTTAGAAACTACTCCC 57.278 33.333 5.81 0.00 42.51 4.30
383 388 9.102453 ACTATTCAGTTTTAGAAACTACTCCCT 57.898 33.333 5.81 0.00 0.00 4.20
384 389 9.589111 CTATTCAGTTTTAGAAACTACTCCCTC 57.411 37.037 5.81 0.00 0.00 4.30
385 390 6.356186 TCAGTTTTAGAAACTACTCCCTCC 57.644 41.667 5.81 0.00 0.00 4.30
386 391 5.047519 TCAGTTTTAGAAACTACTCCCTCCG 60.048 44.000 5.81 0.00 0.00 4.63
387 392 4.837298 AGTTTTAGAAACTACTCCCTCCGT 59.163 41.667 4.36 0.00 0.00 4.69
388 393 5.047448 AGTTTTAGAAACTACTCCCTCCGTC 60.047 44.000 4.36 0.00 0.00 4.79
389 394 1.849977 AGAAACTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
390 395 1.358445 AGAAACTACTCCCTCCGTCCT 59.642 52.381 0.00 0.00 0.00 3.85
391 396 2.579860 AGAAACTACTCCCTCCGTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
392 397 3.204831 AGAAACTACTCCCTCCGTCCTAT 59.795 47.826 0.00 0.00 0.00 2.57
393 398 4.414846 AGAAACTACTCCCTCCGTCCTATA 59.585 45.833 0.00 0.00 0.00 1.31
394 399 4.803329 AACTACTCCCTCCGTCCTATAA 57.197 45.455 0.00 0.00 0.00 0.98
395 400 5.336491 AACTACTCCCTCCGTCCTATAAT 57.664 43.478 0.00 0.00 0.00 1.28
396 401 6.460103 AACTACTCCCTCCGTCCTATAATA 57.540 41.667 0.00 0.00 0.00 0.98
397 402 6.655376 ACTACTCCCTCCGTCCTATAATAT 57.345 41.667 0.00 0.00 0.00 1.28
398 403 7.761981 ACTACTCCCTCCGTCCTATAATATA 57.238 40.000 0.00 0.00 0.00 0.86
399 404 8.167691 ACTACTCCCTCCGTCCTATAATATAA 57.832 38.462 0.00 0.00 0.00 0.98
400 405 8.273605 ACTACTCCCTCCGTCCTATAATATAAG 58.726 40.741 0.00 0.00 0.00 1.73
401 406 7.281366 ACTCCCTCCGTCCTATAATATAAGA 57.719 40.000 0.00 0.00 0.00 2.10
402 407 7.706674 ACTCCCTCCGTCCTATAATATAAGAA 58.293 38.462 0.00 0.00 0.00 2.52
403 408 8.345306 ACTCCCTCCGTCCTATAATATAAGAAT 58.655 37.037 0.00 0.00 0.00 2.40
404 409 9.203163 CTCCCTCCGTCCTATAATATAAGAATT 57.797 37.037 0.00 0.00 0.00 2.17
405 410 9.556772 TCCCTCCGTCCTATAATATAAGAATTT 57.443 33.333 0.00 0.00 0.00 1.82
457 462 8.848474 ACATTCTTATATTATGAAACGGAGGG 57.152 34.615 0.00 0.00 0.00 4.30
458 463 8.656806 ACATTCTTATATTATGAAACGGAGGGA 58.343 33.333 0.00 0.00 0.00 4.20
459 464 9.155975 CATTCTTATATTATGAAACGGAGGGAG 57.844 37.037 0.00 0.00 0.00 4.30
499 504 4.289238 TGGTTACCAAAGCCGATTCTTA 57.711 40.909 0.00 0.00 31.91 2.10
500 505 4.850680 TGGTTACCAAAGCCGATTCTTAT 58.149 39.130 0.00 0.00 31.91 1.73
501 506 5.991861 TGGTTACCAAAGCCGATTCTTATA 58.008 37.500 0.00 0.00 31.91 0.98
502 507 6.597562 TGGTTACCAAAGCCGATTCTTATAT 58.402 36.000 0.00 0.00 31.91 0.86
503 508 7.057894 TGGTTACCAAAGCCGATTCTTATATT 58.942 34.615 0.00 0.00 31.91 1.28
504 509 8.212312 TGGTTACCAAAGCCGATTCTTATATTA 58.788 33.333 0.00 0.00 31.91 0.98
505 510 9.227777 GGTTACCAAAGCCGATTCTTATATTAT 57.772 33.333 0.00 0.00 0.00 1.28
554 559 4.292977 CTTGGAAAGTTGGGAATATCGC 57.707 45.455 0.00 0.00 39.70 4.58
562 567 0.178955 TGGGAATATCGCGAGGGGTA 60.179 55.000 16.66 1.56 31.21 3.69
1219 1765 1.996898 TGGCTTAATTACTGTGACGCG 59.003 47.619 3.53 3.53 0.00 6.01
1241 1792 1.059942 GGTTTGATTTTTCTGCGCCG 58.940 50.000 4.18 0.00 0.00 6.46
1333 1884 2.028190 CGAGGCTCTGGTATGGCG 59.972 66.667 13.50 0.00 0.00 5.69
1361 1913 3.047877 CGCCCGGCTCGAGTTTTT 61.048 61.111 15.13 0.00 0.00 1.94
1386 1938 3.063316 GCTTTTGTGCCGTTTGTTTTGAT 59.937 39.130 0.00 0.00 0.00 2.57
1505 2057 3.869272 GCCGAGTTCCTGCATGCG 61.869 66.667 14.09 7.87 0.00 4.73
1549 2101 0.105778 GGTGAGCTATCTCTGTGCCC 59.894 60.000 0.00 0.00 40.03 5.36
1550 2102 0.249238 GTGAGCTATCTCTGTGCCCG 60.249 60.000 0.00 0.00 40.03 6.13
1551 2103 1.300542 GAGCTATCTCTGTGCCCGC 60.301 63.158 0.00 0.00 36.42 6.13
1552 2104 2.659897 GCTATCTCTGTGCCCGCG 60.660 66.667 0.00 0.00 0.00 6.46
1553 2105 2.659897 CTATCTCTGTGCCCGCGC 60.660 66.667 0.00 0.00 0.00 6.86
1554 2106 4.221422 TATCTCTGTGCCCGCGCC 62.221 66.667 0.00 0.00 0.00 6.53
1583 2135 1.605232 TGCAGTTTCAGTCATGTGCAG 59.395 47.619 0.00 0.00 36.05 4.41
1612 2276 3.564225 GGTTATTCAGGGGTTATGCTTCG 59.436 47.826 0.00 0.00 0.00 3.79
1622 2286 4.366586 GGGTTATGCTTCGAGTAACTACC 58.633 47.826 10.06 0.00 0.00 3.18
1695 2359 9.402320 TGCTATTAATAAGTGCAGTGGAATAAA 57.598 29.630 0.00 0.00 0.00 1.40
1755 2419 5.909621 ATTGCTCAATACAAGTTCTGCAT 57.090 34.783 0.00 0.00 0.00 3.96
2654 3339 9.759473 ATCTTCTTGGATCTTAATCTTTTTCCA 57.241 29.630 0.00 0.00 32.12 3.53
3008 3694 6.721668 CCTATGGACTGACACATTCCTATCTA 59.278 42.308 8.99 0.00 34.79 1.98
3375 4070 8.793592 AGTGTTTGGTTTTAACTCCAGATTATC 58.206 33.333 0.00 0.00 35.05 1.75
3376 4071 8.793592 GTGTTTGGTTTTAACTCCAGATTATCT 58.206 33.333 0.00 0.00 35.05 1.98
3377 4072 8.792633 TGTTTGGTTTTAACTCCAGATTATCTG 58.207 33.333 14.80 14.80 43.91 2.90
3378 4073 8.793592 GTTTGGTTTTAACTCCAGATTATCTGT 58.206 33.333 19.37 5.08 42.80 3.41
3379 4074 8.934023 TTGGTTTTAACTCCAGATTATCTGTT 57.066 30.769 19.37 10.71 42.80 3.16
3421 4143 6.825721 CCAATGGCTTAGACTACTGATTTTCT 59.174 38.462 0.00 0.00 0.00 2.52
3478 4203 5.089970 TGATATTCTTCCCACAGTGACAG 57.910 43.478 0.62 0.00 0.00 3.51
3503 4230 2.093306 TCTGTTTGATGCACCTACCG 57.907 50.000 0.00 0.00 0.00 4.02
3710 4443 8.660435 TGAGCTTATTAAGGACCTAATAATGCT 58.340 33.333 21.10 21.10 38.77 3.79
4749 5485 3.211045 TCAACTCCAACTTGCCACTTAC 58.789 45.455 0.00 0.00 0.00 2.34
4989 5725 1.573108 ACTGGATACCCTGTGGACAG 58.427 55.000 0.00 0.00 42.18 3.51
5200 5936 3.329520 TGGGCAGTAAAGATGTAGGTGTT 59.670 43.478 0.00 0.00 0.00 3.32
5380 6116 2.175069 AGCAAGGGATGAGATTGATGCT 59.825 45.455 0.00 0.00 38.01 3.79
5430 6166 9.273016 ACATACCATGTGCTTGTAATATACTTC 57.727 33.333 0.00 0.00 43.01 3.01
5546 6283 6.093633 CAGTTACCTTGCTGTAAATAACTCCC 59.906 42.308 10.08 0.00 32.21 4.30
5796 6554 2.361230 GCCCCGAACTCCCCTTTG 60.361 66.667 0.00 0.00 0.00 2.77
5808 6566 3.117512 ACTCCCCTTTGAAAGAAAGAGCA 60.118 43.478 6.49 0.00 0.00 4.26
5835 6593 3.917329 TCGTTTCCAGACTGTAGACTG 57.083 47.619 0.93 4.70 37.52 3.51
5838 8563 3.004419 CGTTTCCAGACTGTAGACTGTGA 59.996 47.826 0.93 5.10 36.37 3.58
5911 8638 5.840243 TCGTTACCTGCTATTGCTAACTA 57.160 39.130 0.00 0.00 40.48 2.24
5934 8661 5.422214 TCCTGGCCTTACTAAAAGAGAAG 57.578 43.478 3.32 0.00 0.00 2.85
5954 8681 2.288025 GGTAACCGTCCTGGCCTGA 61.288 63.158 11.88 0.66 43.94 3.86
5955 8682 1.623542 GGTAACCGTCCTGGCCTGAT 61.624 60.000 11.88 0.00 43.94 2.90
5956 8683 0.179081 GTAACCGTCCTGGCCTGATC 60.179 60.000 11.88 2.77 43.94 2.92
5957 8684 0.325296 TAACCGTCCTGGCCTGATCT 60.325 55.000 11.88 0.00 43.94 2.75
5958 8685 1.903877 AACCGTCCTGGCCTGATCTG 61.904 60.000 11.88 2.99 43.94 2.90
5959 8686 2.060383 CCGTCCTGGCCTGATCTGA 61.060 63.158 11.88 0.00 0.00 3.27
5960 8687 1.617018 CCGTCCTGGCCTGATCTGAA 61.617 60.000 11.88 0.00 0.00 3.02
5961 8688 0.467384 CGTCCTGGCCTGATCTGAAT 59.533 55.000 11.88 0.00 0.00 2.57
5971 8698 4.314121 GCCTGATCTGAATCCTGATACAC 58.686 47.826 0.38 0.00 32.13 2.90
6016 8743 1.419381 TTTGGGGCTCTTTGTTTCCC 58.581 50.000 0.00 0.00 38.03 3.97
6036 8763 2.677508 GGTCAGACAAGAGCCTCCT 58.322 57.895 2.17 0.00 0.00 3.69
6037 8764 0.534873 GGTCAGACAAGAGCCTCCTC 59.465 60.000 2.17 0.00 38.42 3.71
6045 8772 1.001503 AGAGCCTCCTCTCCTGGTG 59.998 63.158 0.00 0.00 45.21 4.17
6311 9047 9.137459 AGTATATGCTAGTATGTTGAACTGACT 57.863 33.333 3.24 7.61 0.00 3.41
6350 9086 2.787473 TCTCCACCTGGTATTTGCTG 57.213 50.000 0.00 0.00 36.34 4.41
6352 9088 0.698238 TCCACCTGGTATTTGCTGCT 59.302 50.000 0.00 0.00 36.34 4.24
6353 9089 1.912731 TCCACCTGGTATTTGCTGCTA 59.087 47.619 0.00 0.00 36.34 3.49
6354 9090 2.017049 CCACCTGGTATTTGCTGCTAC 58.983 52.381 0.00 0.00 0.00 3.58
6355 9091 1.665679 CACCTGGTATTTGCTGCTACG 59.334 52.381 0.00 0.00 0.00 3.51
6356 9092 1.299541 CCTGGTATTTGCTGCTACGG 58.700 55.000 0.00 0.00 0.00 4.02
6357 9093 1.134521 CCTGGTATTTGCTGCTACGGA 60.135 52.381 0.00 0.00 0.00 4.69
6358 9094 1.933853 CTGGTATTTGCTGCTACGGAC 59.066 52.381 0.00 0.00 0.00 4.79
6359 9095 1.553248 TGGTATTTGCTGCTACGGACT 59.447 47.619 0.00 0.00 0.00 3.85
6360 9096 2.202566 GGTATTTGCTGCTACGGACTC 58.797 52.381 0.00 0.00 0.00 3.36
6365 9101 2.202623 CTGCTACGGACTCCACGC 60.203 66.667 0.00 0.00 34.00 5.34
6374 9110 1.467713 CGGACTCCACGCTTTCTAGAC 60.468 57.143 0.00 0.00 0.00 2.59
6388 9124 6.020520 CGCTTTCTAGACCTACGATTTTCTTC 60.021 42.308 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.735973 CAGATCCTGTCGCCGATGA 59.264 57.895 0.00 0.00 0.00 2.92
6 7 4.498520 ACGCAGATCCTGTCGCCG 62.499 66.667 0.00 0.00 35.60 6.46
15 16 4.451150 TCCACGGCCACGCAGATC 62.451 66.667 2.24 0.00 46.04 2.75
39 40 3.490761 CCCAAACTTCTTTCGCAACACAT 60.491 43.478 0.00 0.00 0.00 3.21
47 48 2.021457 ACACCACCCAAACTTCTTTCG 58.979 47.619 0.00 0.00 0.00 3.46
56 58 0.631753 TTCTCCCAACACCACCCAAA 59.368 50.000 0.00 0.00 0.00 3.28
64 66 3.938963 TCGCATTATTCTTCTCCCAACAC 59.061 43.478 0.00 0.00 0.00 3.32
68 70 5.304357 TCTGTATCGCATTATTCTTCTCCCA 59.696 40.000 0.00 0.00 0.00 4.37
84 86 1.605753 TCTCATCCCCGTCTGTATCG 58.394 55.000 0.00 0.00 0.00 2.92
87 89 2.820728 TCTTCTCATCCCCGTCTGTA 57.179 50.000 0.00 0.00 0.00 2.74
91 93 3.257127 CCTATCTTCTTCTCATCCCCGTC 59.743 52.174 0.00 0.00 0.00 4.79
93 95 2.564947 CCCTATCTTCTTCTCATCCCCG 59.435 54.545 0.00 0.00 0.00 5.73
97 99 5.860941 TGTGTCCCTATCTTCTTCTCATC 57.139 43.478 0.00 0.00 0.00 2.92
115 117 1.955778 CACACATGTCACCCATTGTGT 59.044 47.619 0.00 3.78 45.61 3.72
121 123 1.891449 CACGCACACATGTCACCCA 60.891 57.895 0.00 0.00 0.00 4.51
125 127 0.943673 CTTTCCACGCACACATGTCA 59.056 50.000 0.00 0.00 0.00 3.58
127 129 0.179032 TCCTTTCCACGCACACATGT 60.179 50.000 0.00 0.00 0.00 3.21
136 138 3.558418 TCGTTTTTCTCTTCCTTTCCACG 59.442 43.478 0.00 0.00 0.00 4.94
138 140 3.558418 CGTCGTTTTTCTCTTCCTTTCCA 59.442 43.478 0.00 0.00 0.00 3.53
139 141 3.606384 GCGTCGTTTTTCTCTTCCTTTCC 60.606 47.826 0.00 0.00 0.00 3.13
142 144 2.557317 TGCGTCGTTTTTCTCTTCCTT 58.443 42.857 0.00 0.00 0.00 3.36
143 145 2.234300 TGCGTCGTTTTTCTCTTCCT 57.766 45.000 0.00 0.00 0.00 3.36
145 147 3.521524 ACATGCGTCGTTTTTCTCTTC 57.478 42.857 0.00 0.00 0.00 2.87
146 148 4.748102 TCTTACATGCGTCGTTTTTCTCTT 59.252 37.500 0.00 0.00 0.00 2.85
156 158 3.124466 TCCAATTGTTCTTACATGCGTCG 59.876 43.478 4.43 0.00 33.44 5.12
160 162 5.415701 TCTCCTTCCAATTGTTCTTACATGC 59.584 40.000 4.43 0.00 33.44 4.06
162 164 6.656693 CAGTCTCCTTCCAATTGTTCTTACAT 59.343 38.462 4.43 0.00 33.44 2.29
167 169 3.812167 GCCAGTCTCCTTCCAATTGTTCT 60.812 47.826 4.43 0.00 0.00 3.01
169 171 2.519013 GCCAGTCTCCTTCCAATTGTT 58.481 47.619 4.43 0.00 0.00 2.83
178 180 2.659610 GCTCACGCCAGTCTCCTT 59.340 61.111 0.00 0.00 0.00 3.36
189 191 2.434884 ACCAATCTGCCGCTCACG 60.435 61.111 0.00 0.00 39.67 4.35
190 192 2.456119 CGACCAATCTGCCGCTCAC 61.456 63.158 0.00 0.00 0.00 3.51
191 193 2.125552 CGACCAATCTGCCGCTCA 60.126 61.111 0.00 0.00 0.00 4.26
192 194 3.567797 GCGACCAATCTGCCGCTC 61.568 66.667 0.00 0.00 43.75 5.03
195 197 0.603707 ATATGGCGACCAATCTGCCG 60.604 55.000 2.68 0.00 43.35 5.69
196 198 1.160137 GATATGGCGACCAATCTGCC 58.840 55.000 2.68 0.00 41.83 4.85
197 199 0.792640 CGATATGGCGACCAATCTGC 59.207 55.000 2.68 0.00 36.95 4.26
198 200 2.029918 TCTCGATATGGCGACCAATCTG 60.030 50.000 2.68 5.32 36.95 2.90
199 201 2.239400 TCTCGATATGGCGACCAATCT 58.761 47.619 2.68 0.00 36.95 2.40
200 202 2.724977 TCTCGATATGGCGACCAATC 57.275 50.000 2.68 6.76 36.95 2.67
201 203 2.562738 TGATCTCGATATGGCGACCAAT 59.437 45.455 2.68 0.00 36.95 3.16
202 204 1.960689 TGATCTCGATATGGCGACCAA 59.039 47.619 2.68 0.00 36.95 3.67
203 205 1.616159 TGATCTCGATATGGCGACCA 58.384 50.000 1.01 1.01 38.19 4.02
204 206 2.949451 ATGATCTCGATATGGCGACC 57.051 50.000 0.00 0.00 36.17 4.79
205 207 4.563184 GGTAAATGATCTCGATATGGCGAC 59.437 45.833 0.00 0.00 36.17 5.19
206 208 4.219725 TGGTAAATGATCTCGATATGGCGA 59.780 41.667 0.00 0.00 38.74 5.54
376 381 8.397951 TCTTATATTATAGGACGGAGGGAGTA 57.602 38.462 0.00 0.00 0.00 2.59
377 382 7.281366 TCTTATATTATAGGACGGAGGGAGT 57.719 40.000 0.00 0.00 0.00 3.85
378 383 8.770010 ATTCTTATATTATAGGACGGAGGGAG 57.230 38.462 0.00 0.00 0.00 4.30
379 384 9.556772 AAATTCTTATATTATAGGACGGAGGGA 57.443 33.333 0.00 0.00 0.00 4.20
431 436 9.284968 CCCTCCGTTTCATAATATAAGAATGTT 57.715 33.333 0.00 0.00 0.00 2.71
432 437 8.656806 TCCCTCCGTTTCATAATATAAGAATGT 58.343 33.333 0.00 0.00 0.00 2.71
433 438 9.155975 CTCCCTCCGTTTCATAATATAAGAATG 57.844 37.037 0.00 0.00 0.00 2.67
434 439 8.881262 ACTCCCTCCGTTTCATAATATAAGAAT 58.119 33.333 0.00 0.00 0.00 2.40
435 440 8.258850 ACTCCCTCCGTTTCATAATATAAGAA 57.741 34.615 0.00 0.00 0.00 2.52
436 441 7.850935 ACTCCCTCCGTTTCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
437 442 8.804204 AGTACTCCCTCCGTTTCATAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
438 443 8.716674 AGTACTCCCTCCGTTTCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
439 444 7.946219 TGAGTACTCCCTCCGTTTCATAATATA 59.054 37.037 20.11 0.00 0.00 0.86
440 445 6.781014 TGAGTACTCCCTCCGTTTCATAATAT 59.219 38.462 20.11 0.00 0.00 1.28
441 446 6.131264 TGAGTACTCCCTCCGTTTCATAATA 58.869 40.000 20.11 0.00 0.00 0.98
442 447 4.960469 TGAGTACTCCCTCCGTTTCATAAT 59.040 41.667 20.11 0.00 0.00 1.28
443 448 4.346730 TGAGTACTCCCTCCGTTTCATAA 58.653 43.478 20.11 0.00 0.00 1.90
444 449 3.972133 TGAGTACTCCCTCCGTTTCATA 58.028 45.455 20.11 0.00 0.00 2.15
445 450 2.816411 TGAGTACTCCCTCCGTTTCAT 58.184 47.619 20.11 0.00 0.00 2.57
446 451 2.297698 TGAGTACTCCCTCCGTTTCA 57.702 50.000 20.11 0.00 0.00 2.69
447 452 3.672767 TTTGAGTACTCCCTCCGTTTC 57.327 47.619 20.11 0.00 0.00 2.78
448 453 4.635699 AATTTGAGTACTCCCTCCGTTT 57.364 40.909 20.11 2.11 0.00 3.60
449 454 4.635699 AAATTTGAGTACTCCCTCCGTT 57.364 40.909 20.11 4.40 0.00 4.44
450 455 5.750352 TTAAATTTGAGTACTCCCTCCGT 57.250 39.130 20.11 4.15 0.00 4.69
451 456 7.625828 ATTTTAAATTTGAGTACTCCCTCCG 57.374 36.000 20.11 0.00 0.00 4.63
454 459 9.996554 CCAAAATTTTAAATTTGAGTACTCCCT 57.003 29.630 20.11 1.89 38.50 4.20
455 460 9.772973 ACCAAAATTTTAAATTTGAGTACTCCC 57.227 29.630 20.11 0.00 38.50 4.30
482 487 9.431887 GTCATAATATAAGAATCGGCTTTGGTA 57.568 33.333 0.00 0.00 0.00 3.25
499 504 9.167311 ACGCAAAAGAAAGAAGAGTCATAATAT 57.833 29.630 0.00 0.00 0.00 1.28
500 505 8.547967 ACGCAAAAGAAAGAAGAGTCATAATA 57.452 30.769 0.00 0.00 0.00 0.98
501 506 7.440523 ACGCAAAAGAAAGAAGAGTCATAAT 57.559 32.000 0.00 0.00 0.00 1.28
502 507 6.861065 ACGCAAAAGAAAGAAGAGTCATAA 57.139 33.333 0.00 0.00 0.00 1.90
503 508 6.861065 AACGCAAAAGAAAGAAGAGTCATA 57.139 33.333 0.00 0.00 0.00 2.15
504 509 5.757850 AACGCAAAAGAAAGAAGAGTCAT 57.242 34.783 0.00 0.00 0.00 3.06
505 510 5.331902 CAAACGCAAAAGAAAGAAGAGTCA 58.668 37.500 0.00 0.00 0.00 3.41
546 551 3.493503 CAGTTTTACCCCTCGCGATATTC 59.506 47.826 10.36 0.00 0.00 1.75
554 559 0.036306 ACTGCCAGTTTTACCCCTCG 59.964 55.000 0.00 0.00 0.00 4.63
562 567 5.989168 GCCTGTATTTTTAACTGCCAGTTTT 59.011 36.000 16.40 0.00 39.51 2.43
998 1544 3.420206 TTCTCCATGGCCGCCATCC 62.420 63.158 22.62 0.00 43.15 3.51
1006 1552 2.301505 CGATCACGTTCTCCATGGC 58.698 57.895 6.96 0.00 34.56 4.40
1219 1765 1.792367 GCGCAGAAAAATCAAACCCAC 59.208 47.619 0.30 0.00 0.00 4.61
1346 1897 2.162716 CTCAAAAACTCGAGCCGGG 58.837 57.895 13.61 0.00 0.00 5.73
1356 1908 2.267426 ACGGCACAAAAGCTCAAAAAC 58.733 42.857 0.00 0.00 34.17 2.43
1358 1910 2.663826 AACGGCACAAAAGCTCAAAA 57.336 40.000 0.00 0.00 34.17 2.44
1361 1913 0.814457 ACAAACGGCACAAAAGCTCA 59.186 45.000 0.00 0.00 34.17 4.26
1386 1938 4.120589 GCACAACCCCGAAATTAAACAAA 58.879 39.130 0.00 0.00 0.00 2.83
1505 2057 3.723348 GTGAACCGACGCCTTGGC 61.723 66.667 0.75 0.75 0.00 4.52
1553 2105 3.386867 GAAACTGCATGAGCGCGGG 62.387 63.158 8.83 0.00 46.23 6.13
1554 2106 2.099062 GAAACTGCATGAGCGCGG 59.901 61.111 8.83 0.00 46.23 6.46
1583 2135 2.211532 ACCCCTGAATAACCCCCTAAC 58.788 52.381 0.00 0.00 0.00 2.34
1612 2276 7.146648 GCATCCATTACTACTGGTAGTTACTC 58.853 42.308 16.95 0.00 43.35 2.59
1622 2286 6.949352 AAAATCAGGCATCCATTACTACTG 57.051 37.500 0.00 0.00 0.00 2.74
1695 2359 7.106239 GCAGGTGCAGGTACAAATAGATATAT 58.894 38.462 0.00 0.00 41.59 0.86
1696 2360 6.464222 GCAGGTGCAGGTACAAATAGATATA 58.536 40.000 0.00 0.00 41.59 0.86
1697 2361 5.308825 GCAGGTGCAGGTACAAATAGATAT 58.691 41.667 0.00 0.00 41.59 1.63
1699 2363 3.545703 GCAGGTGCAGGTACAAATAGAT 58.454 45.455 0.00 0.00 41.59 1.98
1700 2364 2.985896 GCAGGTGCAGGTACAAATAGA 58.014 47.619 0.00 0.00 41.59 1.98
1746 2410 5.987953 CACACATATGTAGCTATGCAGAACT 59.012 40.000 8.32 0.00 36.72 3.01
1747 2411 5.985530 TCACACATATGTAGCTATGCAGAAC 59.014 40.000 8.32 0.00 36.72 3.01
1748 2412 6.160576 TCACACATATGTAGCTATGCAGAA 57.839 37.500 8.32 0.00 36.72 3.02
1749 2413 5.789643 TCACACATATGTAGCTATGCAGA 57.210 39.130 8.32 0.00 36.72 4.26
1750 2414 8.713737 ATTATCACACATATGTAGCTATGCAG 57.286 34.615 8.32 0.00 36.72 4.41
2123 2805 3.760151 GCCATATGCAAATCAGCCTGATA 59.240 43.478 7.81 0.00 36.54 2.15
2261 2943 4.852138 CAGCATGTACACAATAAGCATCC 58.148 43.478 0.00 0.00 0.00 3.51
2654 3339 8.625467 AGAAAATGTAGAAGTAATACCCCTCT 57.375 34.615 0.00 0.00 0.00 3.69
2789 3475 6.475504 TGCCTAGATCAGAAAATGTGAAGAA 58.524 36.000 0.00 0.00 0.00 2.52
2790 3476 6.053632 TGCCTAGATCAGAAAATGTGAAGA 57.946 37.500 0.00 0.00 0.00 2.87
2791 3477 6.748333 TTGCCTAGATCAGAAAATGTGAAG 57.252 37.500 0.00 0.00 0.00 3.02
3179 3874 8.971321 ACATACGTAATTATTCAACGTCATACC 58.029 33.333 8.85 0.00 46.04 2.73
3375 4070 6.558771 TGGAGTGAAATGTACATCAAACAG 57.441 37.500 9.23 0.00 0.00 3.16
3376 4071 6.951062 TTGGAGTGAAATGTACATCAAACA 57.049 33.333 9.23 4.68 0.00 2.83
3377 4072 6.808212 CCATTGGAGTGAAATGTACATCAAAC 59.192 38.462 9.23 7.63 33.93 2.93
3378 4073 6.572119 GCCATTGGAGTGAAATGTACATCAAA 60.572 38.462 9.23 0.00 33.93 2.69
3379 4074 5.105797 GCCATTGGAGTGAAATGTACATCAA 60.106 40.000 9.23 7.52 33.93 2.57
3465 4190 5.089970 CAGATAATTCTGTCACTGTGGGA 57.910 43.478 8.11 1.81 43.73 4.37
3478 4203 6.511767 CGGTAGGTGCATCAAACAGATAATTC 60.512 42.308 0.00 0.00 34.43 2.17
4989 5725 0.606673 GGAAGGTCCAGTTCCAGCAC 60.607 60.000 5.24 0.00 42.79 4.40
5380 6116 2.356913 CACCGCGACCATGACACA 60.357 61.111 8.23 0.00 0.00 3.72
5430 6166 5.048991 ACAAAATGCGTTGAACTAAGGTAGG 60.049 40.000 0.00 0.00 32.59 3.18
5651 6408 6.127423 TGCATCCTACTAAGAAGTACCAGAAC 60.127 42.308 0.00 0.00 37.15 3.01
5652 6409 5.955959 TGCATCCTACTAAGAAGTACCAGAA 59.044 40.000 0.00 0.00 37.15 3.02
5653 6410 5.516044 TGCATCCTACTAAGAAGTACCAGA 58.484 41.667 0.00 0.00 37.15 3.86
5796 6554 5.864628 ACGAAATAGGTGCTCTTTCTTTC 57.135 39.130 0.00 0.00 28.60 2.62
5808 6566 4.618920 ACAGTCTGGAAACGAAATAGGT 57.381 40.909 4.53 0.00 0.00 3.08
5835 6593 6.793492 AGAAGCAGAAAGTCTAAATGTCAC 57.207 37.500 0.00 0.00 0.00 3.67
5838 8563 9.343539 ACTAAAAGAAGCAGAAAGTCTAAATGT 57.656 29.630 0.00 0.00 0.00 2.71
5911 8638 5.726793 TCTTCTCTTTTAGTAAGGCCAGGAT 59.273 40.000 5.01 0.00 0.00 3.24
5934 8661 1.988406 AGGCCAGGACGGTTACCTC 60.988 63.158 5.01 0.00 35.35 3.85
5954 8681 6.126681 TGGACAATGTGTATCAGGATTCAGAT 60.127 38.462 0.00 0.00 0.00 2.90
5955 8682 5.189539 TGGACAATGTGTATCAGGATTCAGA 59.810 40.000 0.00 0.00 0.00 3.27
5956 8683 5.430886 TGGACAATGTGTATCAGGATTCAG 58.569 41.667 0.00 0.00 0.00 3.02
5957 8684 5.045651 ACTGGACAATGTGTATCAGGATTCA 60.046 40.000 0.00 0.00 36.61 2.57
5958 8685 5.295292 CACTGGACAATGTGTATCAGGATTC 59.705 44.000 0.00 0.00 36.61 2.52
5959 8686 5.188434 CACTGGACAATGTGTATCAGGATT 58.812 41.667 0.00 0.00 36.61 3.01
5960 8687 4.384537 CCACTGGACAATGTGTATCAGGAT 60.385 45.833 0.00 0.00 36.61 3.24
5961 8688 3.055167 CCACTGGACAATGTGTATCAGGA 60.055 47.826 0.00 0.00 36.61 3.86
5971 8698 1.538512 CAAGAGCACCACTGGACAATG 59.461 52.381 0.71 0.00 0.00 2.82
6016 8743 1.216710 GAGGCTCTTGTCTGACCCG 59.783 63.158 7.40 0.00 0.00 5.28
6033 8760 5.188555 GCATATATGATTCACCAGGAGAGGA 59.811 44.000 17.10 0.00 0.00 3.71
6034 8761 5.046087 TGCATATATGATTCACCAGGAGAGG 60.046 44.000 17.10 0.00 0.00 3.69
6035 8762 5.873712 GTGCATATATGATTCACCAGGAGAG 59.126 44.000 17.10 0.00 0.00 3.20
6036 8763 5.545335 AGTGCATATATGATTCACCAGGAGA 59.455 40.000 17.10 0.00 0.00 3.71
6037 8764 5.802465 AGTGCATATATGATTCACCAGGAG 58.198 41.667 17.10 0.00 0.00 3.69
6118 8854 7.438459 GCTACAGATAACAAATTATCAGACGGT 59.562 37.037 9.17 0.00 46.38 4.83
6148 8884 3.017442 TGACTCGTCTCTGGAGTATTGG 58.983 50.000 0.00 0.00 44.41 3.16
6311 9047 5.221165 GGAGAATCACCGAAGAAACCAAAAA 60.221 40.000 0.00 0.00 36.25 1.94
6350 9086 1.077089 GAAAGCGTGGAGTCCGTAGC 61.077 60.000 13.46 13.46 0.00 3.58
6352 9088 1.741706 CTAGAAAGCGTGGAGTCCGTA 59.258 52.381 4.30 0.00 0.00 4.02
6353 9089 0.526662 CTAGAAAGCGTGGAGTCCGT 59.473 55.000 4.30 0.00 0.00 4.69
6354 9090 0.809385 TCTAGAAAGCGTGGAGTCCG 59.191 55.000 4.30 0.00 0.00 4.79
6355 9091 1.135053 GGTCTAGAAAGCGTGGAGTCC 60.135 57.143 0.73 0.73 0.00 3.85
6356 9092 1.819903 AGGTCTAGAAAGCGTGGAGTC 59.180 52.381 0.00 0.00 0.00 3.36
6357 9093 1.926108 AGGTCTAGAAAGCGTGGAGT 58.074 50.000 0.00 0.00 0.00 3.85
6358 9094 2.223294 CGTAGGTCTAGAAAGCGTGGAG 60.223 54.545 0.00 0.00 0.00 3.86
6359 9095 1.741706 CGTAGGTCTAGAAAGCGTGGA 59.258 52.381 0.00 0.00 0.00 4.02
6360 9096 1.741706 TCGTAGGTCTAGAAAGCGTGG 59.258 52.381 0.00 0.00 0.00 4.94
6365 9101 6.757478 GGGAAGAAAATCGTAGGTCTAGAAAG 59.243 42.308 0.00 0.00 0.00 2.62
6374 9110 2.547826 GACGGGGAAGAAAATCGTAGG 58.452 52.381 0.00 0.00 34.06 3.18


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

AutoCloner maintained by Alex Coulton.