Multiple sequence alignment - TraesCS2B01G629100

Loading Multiple Alignment...

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 TraesCS2B01G629100 chr2B 100.000 5014 0 0 1 5014 800191520 800186507 0.000000e+00 9260.0
1 TraesCS2B01G629100 chr2B 85.714 630 63 11 1 609 800232643 800232020 1.520000e-179 640.0
2 TraesCS2B01G629100 chr2B 75.573 262 60 4 12 271 326295771 326295512 5.270000e-25 126.0
3 TraesCS2B01G629100 chr2A 93.403 5063 249 36 1 5009 766324498 766329529 0.000000e+00 7420.0
4 TraesCS2B01G629100 chr2A 74.436 266 64 4 8 271 613336989 613336726 1.480000e-20 111.0
5 TraesCS2B01G629100 chr2D 94.030 4355 201 23 1 4325 641063954 641068279 0.000000e+00 6547.0
6 TraesCS2B01G629100 chr2D 89.548 641 47 7 4382 5009 641068700 641069333 0.000000e+00 795.0
7 TraesCS2B01G629100 chr1D 81.444 997 154 20 2007 2991 470229 471206 0.000000e+00 787.0
8 TraesCS2B01G629100 chr1D 81.024 996 161 17 2007 2991 627239 626261 0.000000e+00 767.0
9 TraesCS2B01G629100 chr1D 76.488 1361 261 43 626 1967 801102 799782 0.000000e+00 686.0
10 TraesCS2B01G629100 chr1D 81.152 573 80 17 3506 4055 798210 797643 7.710000e-118 435.0
11 TraesCS2B01G629100 chr1B 81.062 998 154 19 2007 2991 4522982 4522007 0.000000e+00 763.0
12 TraesCS2B01G629100 chr1B 80.584 994 162 17 2007 2991 4813572 4812601 0.000000e+00 737.0
13 TraesCS2B01G629100 chr1B 80.619 743 115 15 2007 2741 4205958 4206679 9.490000e-152 547.0
14 TraesCS2B01G629100 chr1B 82.111 559 86 11 3506 4055 4207768 4208321 2.730000e-127 466.0
15 TraesCS2B01G629100 chr1B 81.675 573 76 19 3506 4055 3574561 3573995 2.750000e-122 449.0
16 TraesCS2B01G629100 chr1A 80.862 998 159 20 2007 2991 3464639 3463661 0.000000e+00 756.0
17 TraesCS2B01G629100 chr1A 80.485 989 167 20 2007 2987 2550269 2551239 0.000000e+00 734.0
18 TraesCS2B01G629100 chr1A 76.672 1256 235 46 732 1967 2549052 2550269 1.180000e-180 643.0
19 TraesCS2B01G629100 chr1A 81.469 572 95 8 3498 4061 3463075 3462507 4.570000e-125 459.0
20 TraesCS2B01G629100 chr5D 83.784 777 109 12 2279 3044 368366471 368365701 0.000000e+00 721.0
21 TraesCS2B01G629100 chr5D 87.230 509 59 3 3554 4057 368365098 368364591 4.350000e-160 575.0
22 TraesCS2B01G629100 chr5A 85.689 566 72 8 3498 4057 470226884 470226322 5.590000e-164 588.0
23 TraesCS2B01G629100 chr5A 85.336 566 74 6 3498 4057 470242015 470241453 1.210000e-160 577.0
24 TraesCS2B01G629100 chr5B 85.512 566 72 7 3498 4057 436282397 436281836 2.600000e-162 582.0
25 TraesCS2B01G629100 chr5B 76.680 253 55 4 12 262 271179164 271179414 2.430000e-28 137.0
26 TraesCS2B01G629100 chr6A 75.564 266 61 4 8 271 85760954 85760691 1.470000e-25 128.0
27 TraesCS2B01G629100 chr4B 75.188 266 62 4 8 271 629778692 629778429 6.820000e-24 122.0
28 TraesCS2B01G629100 chr6D 78.616 159 32 2 114 271 458351327 458351170 2.470000e-18 104.0
29 TraesCS2B01G629100 chr7D 93.478 46 1 2 4753 4797 92301968 92301924 3.240000e-07 67.6


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 TraesCS2B01G629100 chr2B 800186507 800191520 5013 True 9260.0 9260 100.0000 1 5014 1 chr2B.!!$R2 5013
1 TraesCS2B01G629100 chr2B 800232020 800232643 623 True 640.0 640 85.7140 1 609 1 chr2B.!!$R3 608
2 TraesCS2B01G629100 chr2A 766324498 766329529 5031 False 7420.0 7420 93.4030 1 5009 1 chr2A.!!$F1 5008
3 TraesCS2B01G629100 chr2D 641063954 641069333 5379 False 3671.0 6547 91.7890 1 5009 2 chr2D.!!$F1 5008
4 TraesCS2B01G629100 chr1D 470229 471206 977 False 787.0 787 81.4440 2007 2991 1 chr1D.!!$F1 984
5 TraesCS2B01G629100 chr1D 626261 627239 978 True 767.0 767 81.0240 2007 2991 1 chr1D.!!$R1 984
6 TraesCS2B01G629100 chr1D 797643 801102 3459 True 560.5 686 78.8200 626 4055 2 chr1D.!!$R2 3429
7 TraesCS2B01G629100 chr1B 4522007 4522982 975 True 763.0 763 81.0620 2007 2991 1 chr1B.!!$R2 984
8 TraesCS2B01G629100 chr1B 4812601 4813572 971 True 737.0 737 80.5840 2007 2991 1 chr1B.!!$R3 984
9 TraesCS2B01G629100 chr1B 4205958 4208321 2363 False 506.5 547 81.3650 2007 4055 2 chr1B.!!$F1 2048
10 TraesCS2B01G629100 chr1B 3573995 3574561 566 True 449.0 449 81.6750 3506 4055 1 chr1B.!!$R1 549
11 TraesCS2B01G629100 chr1A 2549052 2551239 2187 False 688.5 734 78.5785 732 2987 2 chr1A.!!$F1 2255
12 TraesCS2B01G629100 chr1A 3462507 3464639 2132 True 607.5 756 81.1655 2007 4061 2 chr1A.!!$R1 2054
13 TraesCS2B01G629100 chr5D 368364591 368366471 1880 True 648.0 721 85.5070 2279 4057 2 chr5D.!!$R1 1778
14 TraesCS2B01G629100 chr5A 470226322 470226884 562 True 588.0 588 85.6890 3498 4057 1 chr5A.!!$R1 559
15 TraesCS2B01G629100 chr5A 470241453 470242015 562 True 577.0 577 85.3360 3498 4057 1 chr5A.!!$R2 559
16 TraesCS2B01G629100 chr5B 436281836 436282397 561 True 582.0 582 85.5120 3498 4057 1 chr5B.!!$R1 559

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
132 133 0.110295 TCTGTTTGGCAGCTTAGGCA 59.890 50.000 0.00 0.0 44.66 4.75 F
275 277 0.381089 CCACCTAACGCCTCTAGTCG 59.619 60.000 0.00 0.0 0.00 4.18 F
383 403 1.021968 GAACCGTTTGCTGTCCAACT 58.978 50.000 0.00 0.0 31.97 3.16 F
1386 1416 1.142667 TCCAATGCAGAACACCACTCA 59.857 47.619 0.00 0.0 0.00 3.41 F
2304 2348 1.227263 CCTCGTATCACGGCCAAGG 60.227 63.158 2.24 0.0 42.81 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1432 1.740025 GCTCTCCACGGAAATTGGAAG 59.260 52.381 0.00 0.00 42.76 3.46 R
1810 1844 4.275936 CACTTTTGTGCCCTATATGTAGGC 59.724 45.833 9.98 6.52 42.51 3.93 R
2277 2321 3.147629 CCGTGATACGAGGTTCTCCTAT 58.852 50.000 2.52 0.00 46.05 2.57 R
3171 3534 3.719268 ATATGTGTTGGCCACTCTGAA 57.281 42.857 3.88 0.00 44.81 3.02 R
4163 4807 0.458716 TGTTCTCGCACACGTCACAA 60.459 50.000 0.00 0.00 41.18 3.33 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
132 133 0.110295 TCTGTTTGGCAGCTTAGGCA 59.890 50.000 0.00 0.00 44.66 4.75
139 140 1.144936 GCAGCTTAGGCAGGTCGAT 59.855 57.895 0.00 0.00 41.70 3.59
166 167 7.595819 TTCAATACCTTGAGGACAAAATTGT 57.404 32.000 3.59 0.00 42.19 2.71
204 206 1.202976 GGAGGGCATGCATATCACCTT 60.203 52.381 21.36 0.00 0.00 3.50
205 207 1.884579 GAGGGCATGCATATCACCTTG 59.115 52.381 21.36 0.00 0.00 3.61
225 227 4.947147 GGGCCACGGTGCACTTGA 62.947 66.667 17.98 0.00 0.00 3.02
232 234 1.390123 CACGGTGCACTTGATAAGTCG 59.610 52.381 17.98 10.66 40.46 4.18
254 256 0.463295 CATCACCTCGCAAGCCATCT 60.463 55.000 0.00 0.00 37.18 2.90
275 277 0.381089 CCACCTAACGCCTCTAGTCG 59.619 60.000 0.00 0.00 0.00 4.18
364 384 4.261572 CGATAAGTGCATGGTAAATTGGGG 60.262 45.833 0.00 0.00 0.00 4.96
383 403 1.021968 GAACCGTTTGCTGTCCAACT 58.978 50.000 0.00 0.00 31.97 3.16
405 425 1.527034 GGTCTTGAAGTGCTGCATCA 58.473 50.000 5.27 3.36 0.00 3.07
507 527 4.403432 AGGCAACCCTTGTGATGAATATTG 59.597 41.667 0.00 0.00 38.74 1.90
513 533 6.672593 ACCCTTGTGATGAATATTGTATGGT 58.327 36.000 0.00 0.00 0.00 3.55
538 558 2.642171 TCTATTCCCTCACCACCACT 57.358 50.000 0.00 0.00 0.00 4.00
559 579 5.122396 CACTACTGTTGGTAATGGAGAAAGC 59.878 44.000 0.00 0.00 0.00 3.51
565 585 3.278574 TGGTAATGGAGAAAGCAATCCG 58.721 45.455 0.00 0.00 38.52 4.18
589 609 1.379843 GGATGCCCCGTGGTTGAAT 60.380 57.895 0.00 0.00 0.00 2.57
747 768 8.766994 ATAGGTACCAAGCAATCATTAATTGT 57.233 30.769 15.94 0.00 45.55 2.71
903 924 2.163613 CCAAAATAAGAACGGGGCTCAC 59.836 50.000 0.00 0.00 0.00 3.51
929 950 9.099454 CCTCTATATAAGTTGTGTTCTCCAAAC 57.901 37.037 0.00 0.00 0.00 2.93
941 962 8.458573 TGTGTTCTCCAAACAATATACAAGTT 57.541 30.769 0.00 0.00 31.20 2.66
942 963 8.564574 TGTGTTCTCCAAACAATATACAAGTTC 58.435 33.333 0.00 0.00 31.20 3.01
943 964 8.564574 GTGTTCTCCAAACAATATACAAGTTCA 58.435 33.333 0.00 0.00 31.20 3.18
974 995 3.242944 CACATAGTTACGTGCTTCATCGG 59.757 47.826 0.00 0.00 0.00 4.18
986 1007 3.813529 CTTCATCGGAAGGAACACAAC 57.186 47.619 0.00 0.00 45.52 3.32
994 1015 4.960469 TCGGAAGGAACACAACTCCTATAT 59.040 41.667 0.00 0.00 42.77 0.86
1065 1086 2.305052 GTTTAGACCTTGCTACCCCACT 59.695 50.000 0.00 0.00 0.00 4.00
1081 1102 5.151454 ACCCCACTTTGGTTGAATCAATAA 58.849 37.500 0.00 0.00 35.17 1.40
1161 1186 3.389925 ACACATGCAATTCTTTGTGGG 57.610 42.857 17.56 0.92 42.86 4.61
1275 1300 7.378181 ACATTGCTTATGTTCCCAACTAAAAG 58.622 34.615 0.00 0.00 45.19 2.27
1357 1386 8.400947 CAATTATATATGCTGACTAACCATGCC 58.599 37.037 0.00 0.00 0.00 4.40
1386 1416 1.142667 TCCAATGCAGAACACCACTCA 59.857 47.619 0.00 0.00 0.00 3.41
1401 1431 6.597562 ACACCACTCATTTAAGTCCTAAACA 58.402 36.000 0.00 0.00 32.26 2.83
1402 1432 6.485648 ACACCACTCATTTAAGTCCTAAACAC 59.514 38.462 0.00 0.00 32.26 3.32
1502 1532 6.150332 TCTTTTCCCCTCTATGGACATATCA 58.850 40.000 0.00 0.00 38.35 2.15
1577 1610 8.308851 TGACCATTGACCATCATAAAAATCAT 57.691 30.769 0.00 0.00 0.00 2.45
1667 1700 9.453572 AGCATCACAACTTTAAATCATAGAGAA 57.546 29.630 0.00 0.00 0.00 2.87
1708 1741 8.355169 CCACATTCATTAATGATCCACCTAAAG 58.645 37.037 18.61 1.66 44.50 1.85
1716 1749 9.646522 ATTAATGATCCACCTAAAGCATAGTTT 57.353 29.630 0.00 0.00 0.00 2.66
1810 1844 5.355350 CACCTAAATGAACTAGGCTTGAAGG 59.645 44.000 2.20 0.00 39.78 3.46
1873 1907 4.037923 AGACATGCTACCAAAACACCAAAG 59.962 41.667 0.00 0.00 0.00 2.77
1969 2004 6.540189 AGAAATATGCTTCACACCTATCACAC 59.460 38.462 0.00 0.00 0.00 3.82
1971 2006 3.483808 TGCTTCACACCTATCACACAA 57.516 42.857 0.00 0.00 0.00 3.33
2003 2038 5.110935 AGATAGAGAGAGAGGGAGATGGAT 58.889 45.833 0.00 0.00 0.00 3.41
2004 2039 6.279405 AGATAGAGAGAGAGGGAGATGGATA 58.721 44.000 0.00 0.00 0.00 2.59
2096 2133 2.884012 TGAGCAACACCATCGACAAAAT 59.116 40.909 0.00 0.00 0.00 1.82
2224 2265 6.755141 CACAAGGCCAATGAAAATCTAGATTG 59.245 38.462 18.61 6.63 0.00 2.67
2229 2270 6.545298 GGCCAATGAAAATCTAGATTGTCTCT 59.455 38.462 28.15 17.00 36.29 3.10
2242 2283 9.426534 TCTAGATTGTCTCTAAAGGATCATGAA 57.573 33.333 0.00 0.00 36.02 2.57
2304 2348 1.227263 CCTCGTATCACGGCCAAGG 60.227 63.158 2.24 0.00 42.81 3.61
2345 2389 6.700081 TGTTTATTATGTCGTGCTCCATAGTC 59.300 38.462 0.00 0.00 0.00 2.59
2463 2510 4.523083 TGAGTATATGGGCTTCACCAAAC 58.477 43.478 0.00 0.00 45.13 2.93
2681 2729 8.553459 AGATATTCGCTTCTTTACATATTGGG 57.447 34.615 0.00 0.00 0.00 4.12
2705 2753 5.965334 GCCGTAAGTGTAATCAATGTCATTG 59.035 40.000 17.95 17.95 41.57 2.82
2821 3133 6.835488 ACATAGACAATAATGCATGTTCCCTT 59.165 34.615 0.00 0.00 0.00 3.95
2874 3190 2.817258 GGGTGCTACAACTTACAATGCA 59.183 45.455 0.00 0.00 0.00 3.96
3203 3566 5.878116 GGCCAACACATATAACACTAGTGAA 59.122 40.000 29.30 16.41 34.47 3.18
3392 3779 8.033626 AGTAGCGCAAATAAACTTAGAACTACT 58.966 33.333 11.47 0.00 32.71 2.57
3394 3781 8.182658 AGCGCAAATAAACTTAGAACTACTAC 57.817 34.615 11.47 0.00 0.00 2.73
3572 4014 5.195001 TGTCACCCAAGATTTTTGCTAAC 57.805 39.130 0.00 0.00 0.00 2.34
3606 4051 6.963805 GCTTATACTCTTCTTGTGCATGAAAC 59.036 38.462 0.00 0.00 0.00 2.78
3851 4351 7.344913 AGAAGAAATCTGCCTACTTCAATCAT 58.655 34.615 0.00 0.00 39.22 2.45
4014 4653 1.821753 CAGGTGGTTGTGTTGGTTGAA 59.178 47.619 0.00 0.00 0.00 2.69
4040 4680 8.587952 AGCAAAAGTTGTATTGTAATTTGGAC 57.412 30.769 0.00 0.00 0.00 4.02
4086 4726 9.180678 GAATTTGTCAAACTGTAACATGGTAAG 57.819 33.333 0.00 0.00 0.00 2.34
4093 4733 6.630203 AACTGTAACATGGTAAGGATGGTA 57.370 37.500 0.00 0.00 0.00 3.25
4095 4735 6.412214 ACTGTAACATGGTAAGGATGGTAAC 58.588 40.000 0.00 0.00 0.00 2.50
4115 4759 8.768397 TGGTAACCATCATGTCTCTAGTTTATT 58.232 33.333 0.00 0.00 0.00 1.40
4162 4806 2.402564 AGTCATTCCCATCACGAGGAT 58.597 47.619 0.00 0.00 36.39 3.24
4163 4807 2.774234 AGTCATTCCCATCACGAGGATT 59.226 45.455 0.00 0.00 32.57 3.01
4200 4844 8.653338 GCGAGAACACAATAGTAAGTTAAATCA 58.347 33.333 0.00 0.00 0.00 2.57
4257 4901 4.601406 ATGGGCAATGGAACCTAAGTAA 57.399 40.909 0.00 0.00 0.00 2.24
4261 4905 5.011227 TGGGCAATGGAACCTAAGTAAAAAC 59.989 40.000 0.00 0.00 0.00 2.43
4265 4909 6.463190 GCAATGGAACCTAAGTAAAAACCCAA 60.463 38.462 0.00 0.00 0.00 4.12
4269 4913 6.896307 TGGAACCTAAGTAAAAACCCAAAGAA 59.104 34.615 0.00 0.00 0.00 2.52
4288 4932 9.345517 CCAAAGAATAAATGTGCATATTATCCG 57.654 33.333 9.27 1.75 0.00 4.18
4325 4969 5.251700 GGAATCTACATGGGATAAGTGGGAT 59.748 44.000 0.00 0.00 0.00 3.85
4328 4972 2.138542 ACATGGGATAAGTGGGATGCT 58.861 47.619 0.00 0.00 0.00 3.79
4404 5412 2.559698 TACCAATATGGATGCCACCG 57.440 50.000 2.85 0.00 40.96 4.94
4406 5414 0.953727 CCAATATGGATGCCACCGTG 59.046 55.000 0.00 0.00 40.96 4.94
4407 5415 1.679139 CAATATGGATGCCACCGTGT 58.321 50.000 0.00 0.00 35.80 4.49
4418 5426 0.460311 CCACCGTGTCAGGGAGATAC 59.540 60.000 18.37 0.00 35.25 2.24
4426 5434 3.260884 GTGTCAGGGAGATACAAGGACAA 59.739 47.826 0.00 0.00 38.17 3.18
4428 5436 3.107601 TCAGGGAGATACAAGGACAAGG 58.892 50.000 0.00 0.00 0.00 3.61
4469 5477 3.706600 ACCACTTTCGGGTTGCTATAA 57.293 42.857 0.00 0.00 34.10 0.98
4479 5487 3.532542 GGGTTGCTATAAGGTGTGAGTC 58.467 50.000 0.00 0.00 0.00 3.36
4483 5491 5.986135 GGTTGCTATAAGGTGTGAGTCTATG 59.014 44.000 0.00 0.00 0.00 2.23
4496 5504 1.992557 AGTCTATGGAACTTTGGGCCA 59.007 47.619 0.00 0.00 35.91 5.36
4503 5511 1.337118 GAACTTTGGGCCATGGTTGA 58.663 50.000 23.11 0.00 0.00 3.18
4513 5521 1.002315 GCCATGGTTGATTGCTTGGTT 59.998 47.619 14.67 0.00 0.00 3.67
4538 5558 3.871594 CCTACTTGGGCGATTTTAGAGTG 59.128 47.826 0.00 0.00 0.00 3.51
4543 5563 1.604278 GGGCGATTTTAGAGTGATGGC 59.396 52.381 0.00 0.00 0.00 4.40
4584 5604 8.495949 GTCATTATAAAGGATGTAATGGTCGTG 58.504 37.037 0.00 0.00 0.00 4.35
4585 5605 6.854496 TTATAAAGGATGTAATGGTCGTGC 57.146 37.500 0.00 0.00 0.00 5.34
4601 5621 0.664166 GTGCCGTTTCTGCCATTGTG 60.664 55.000 0.00 0.00 0.00 3.33
4606 5626 1.788308 CGTTTCTGCCATTGTGCTTTG 59.212 47.619 0.00 0.00 0.00 2.77
4609 5629 4.367450 GTTTCTGCCATTGTGCTTTGTTA 58.633 39.130 0.00 0.00 0.00 2.41
4645 5665 5.105957 TGCCATTATAAACACATGGACACAC 60.106 40.000 6.28 0.00 40.10 3.82
4661 5681 2.501723 ACACACAGCTTACCCCTATGAG 59.498 50.000 0.00 0.00 0.00 2.90
4675 5695 3.068873 CCCTATGAGCACCACTAAGAGAC 59.931 52.174 0.00 0.00 0.00 3.36
4793 5814 8.722480 AGGCTAAAATAAATCCAGAAAAATGC 57.278 30.769 0.00 0.00 0.00 3.56
4840 5861 7.406031 ACTTAATCATCTTTGGACGACTAGA 57.594 36.000 0.00 0.00 0.00 2.43
4841 5862 7.837863 ACTTAATCATCTTTGGACGACTAGAA 58.162 34.615 0.00 0.00 0.00 2.10
4849 5870 3.462483 TGGACGACTAGAAAGCACAAA 57.538 42.857 0.00 0.00 0.00 2.83
4875 5896 3.149899 AGCATTTCACGCTCTCAGG 57.850 52.632 0.00 0.00 33.35 3.86
4879 5900 1.929836 CATTTCACGCTCTCAGGTAGC 59.070 52.381 0.00 0.00 36.60 3.58
4880 5901 1.257743 TTTCACGCTCTCAGGTAGCT 58.742 50.000 0.00 0.00 37.85 3.32
4881 5902 2.124277 TTCACGCTCTCAGGTAGCTA 57.876 50.000 0.00 0.00 37.85 3.32
4882 5903 1.669604 TCACGCTCTCAGGTAGCTAG 58.330 55.000 0.00 0.00 37.85 3.42
4883 5904 0.665835 CACGCTCTCAGGTAGCTAGG 59.334 60.000 0.00 0.00 37.85 3.02
4884 5905 1.104577 ACGCTCTCAGGTAGCTAGGC 61.105 60.000 0.00 0.00 37.85 3.93
4885 5906 0.821711 CGCTCTCAGGTAGCTAGGCT 60.822 60.000 0.00 0.00 43.41 4.58
4886 5907 1.408969 GCTCTCAGGTAGCTAGGCTT 58.591 55.000 0.00 0.00 40.44 4.35
4887 5908 2.588620 GCTCTCAGGTAGCTAGGCTTA 58.411 52.381 0.00 0.00 40.44 3.09
4896 5917 1.084370 AGCTAGGCTTAGTTTGCGCG 61.084 55.000 0.00 0.00 33.89 6.86
4910 5931 3.055719 CGCGGTGGCTTTGGTGAT 61.056 61.111 0.00 0.00 36.88 3.06
4911 5932 1.743623 CGCGGTGGCTTTGGTGATA 60.744 57.895 0.00 0.00 36.88 2.15
4964 5985 1.850377 TTGGTACGTACAACCACACG 58.150 50.000 26.02 0.00 46.56 4.49
5009 6030 9.373603 TGTGGTTTGTATACACATGATTAGTAC 57.626 33.333 4.68 0.00 39.92 2.73
5010 6031 9.373603 GTGGTTTGTATACACATGATTAGTACA 57.626 33.333 4.68 0.00 33.76 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 5.648092 CCTCAAGGTATTGAAAAATCGACCT 59.352 40.000 0.00 0.00 44.68 3.85
139 140 9.323985 CAATTTTGTCCTCAAGGTATTGAAAAA 57.676 29.630 0.00 2.56 44.68 1.94
166 167 4.340617 CCTCCCAAGGCACAACTTATTTA 58.659 43.478 0.00 0.00 35.37 1.40
225 227 2.623416 TGCGAGGTGATGATCGACTTAT 59.377 45.455 0.00 0.00 41.40 1.73
232 234 0.462581 TGGCTTGCGAGGTGATGATC 60.463 55.000 2.37 0.00 0.00 2.92
254 256 2.648059 GACTAGAGGCGTTAGGTGGTA 58.352 52.381 0.00 0.00 0.00 3.25
364 384 1.021968 AGTTGGACAGCAAACGGTTC 58.978 50.000 0.00 0.00 0.00 3.62
375 395 1.142870 CTTCAAGACCCCAGTTGGACA 59.857 52.381 0.00 0.00 37.39 4.02
383 403 1.228245 GCAGCACTTCAAGACCCCA 60.228 57.895 0.00 0.00 0.00 4.96
405 425 2.040813 AGAGCTCCACCAAATGTGTCAT 59.959 45.455 10.93 0.00 43.85 3.06
428 448 5.482006 TCTGTACCAATGTCATCTCAAGTG 58.518 41.667 0.00 0.00 0.00 3.16
429 449 5.745312 TCTGTACCAATGTCATCTCAAGT 57.255 39.130 0.00 0.00 0.00 3.16
441 461 2.511218 AGGTCATGCCATCTGTACCAAT 59.489 45.455 8.58 0.00 40.61 3.16
507 527 6.542735 GGTGAGGGAATAGAAAAGAACCATAC 59.457 42.308 0.00 0.00 0.00 2.39
513 533 4.352595 TGGTGGTGAGGGAATAGAAAAGAA 59.647 41.667 0.00 0.00 0.00 2.52
538 558 5.235850 TGCTTTCTCCATTACCAACAGTA 57.764 39.130 0.00 0.00 0.00 2.74
559 579 1.815866 GGCATCCCCAAACGGATTG 59.184 57.895 0.00 0.00 40.88 2.67
589 609 6.329197 ACAAGCTATTTAGGCTTCCTATACCA 59.671 38.462 0.00 0.00 46.59 3.25
631 651 7.804712 CAAAGAATGGATGCATGACTATCTAC 58.195 38.462 2.46 0.00 0.00 2.59
808 829 1.522668 TCCAGTGCACCATTCTTTCG 58.477 50.000 14.63 0.00 0.00 3.46
830 851 8.783093 TGATTCACTCAACATTTAACAAGTAGG 58.217 33.333 0.00 0.00 0.00 3.18
903 924 9.099454 GTTTGGAGAACACAACTTATATAGAGG 57.901 37.037 0.00 0.00 0.00 3.69
941 962 6.311935 GCACGTAACTATGTGTTTCCTTATGA 59.688 38.462 10.09 0.00 43.38 2.15
942 963 6.312918 AGCACGTAACTATGTGTTTCCTTATG 59.687 38.462 10.09 0.00 43.38 1.90
943 964 6.403878 AGCACGTAACTATGTGTTTCCTTAT 58.596 36.000 10.09 0.00 43.38 1.73
974 995 9.444600 TTTGTAATATAGGAGTTGTGTTCCTTC 57.555 33.333 0.00 0.00 42.40 3.46
986 1007 6.837312 TCACCACCCATTTGTAATATAGGAG 58.163 40.000 0.00 0.00 0.00 3.69
994 1015 6.153680 GGAACATAATCACCACCCATTTGTAA 59.846 38.462 0.00 0.00 0.00 2.41
1065 1086 7.823310 CCATCCATGTTTATTGATTCAACCAAA 59.177 33.333 0.15 2.94 0.00 3.28
1081 1102 6.962182 TCTTCTGTAGATTTCCATCCATGTT 58.038 36.000 0.00 0.00 0.00 2.71
1161 1186 7.500141 AGAATTGGATAAATGCATAAACCACC 58.500 34.615 0.00 0.14 0.00 4.61
1255 1280 8.027189 CCTAAACTTTTAGTTGGGAACATAAGC 58.973 37.037 7.74 0.00 38.66 3.09
1275 1300 6.053650 AGTTTCTACTTGTGGTGTCCTAAAC 58.946 40.000 0.00 0.00 0.00 2.01
1357 1386 5.163513 GTGTTCTGCATTGGAAATGTTAGG 58.836 41.667 0.00 0.00 0.00 2.69
1401 1431 2.876079 GCTCTCCACGGAAATTGGAAGT 60.876 50.000 0.00 0.00 42.76 3.01
1402 1432 1.740025 GCTCTCCACGGAAATTGGAAG 59.260 52.381 0.00 0.00 42.76 3.46
1589 1622 6.348132 CCTTTTATATTTATCGCACGCCATCA 60.348 38.462 0.00 0.00 0.00 3.07
1632 1665 9.630098 ATTTAAAGTTGTGATGCTTATGTTGAG 57.370 29.630 0.00 0.00 0.00 3.02
1634 1667 9.409312 TGATTTAAAGTTGTGATGCTTATGTTG 57.591 29.630 0.00 0.00 0.00 3.33
1708 1741 8.466798 ACCATAATTAACCTTGACAAACTATGC 58.533 33.333 0.00 0.00 0.00 3.14
1716 1749 4.938832 CACCGACCATAATTAACCTTGACA 59.061 41.667 0.00 0.00 0.00 3.58
1754 1788 9.840427 CTTTTTAGGTTGTCAATTATGTACCAG 57.160 33.333 0.00 0.00 0.00 4.00
1810 1844 4.275936 CACTTTTGTGCCCTATATGTAGGC 59.724 45.833 9.98 6.52 42.51 3.93
1827 1861 7.649306 GTCTTGTTTACAATGCTCATCACTTTT 59.351 33.333 0.00 0.00 35.02 2.27
1994 2029 6.068010 TGACTCTTTCTCTCTATCCATCTCC 58.932 44.000 0.00 0.00 0.00 3.71
1998 2033 9.393512 CAAATTTGACTCTTTCTCTCTATCCAT 57.606 33.333 13.08 0.00 0.00 3.41
1999 2034 7.826252 CCAAATTTGACTCTTTCTCTCTATCCA 59.174 37.037 19.86 0.00 0.00 3.41
2000 2035 7.826744 ACCAAATTTGACTCTTTCTCTCTATCC 59.173 37.037 19.86 0.00 0.00 2.59
2003 2038 8.980481 AAACCAAATTTGACTCTTTCTCTCTA 57.020 30.769 19.86 0.00 0.00 2.43
2004 2039 7.888250 AAACCAAATTTGACTCTTTCTCTCT 57.112 32.000 19.86 0.00 0.00 3.10
2033 2070 4.809193 TCTTCTATCCTCCACATAGCAGT 58.191 43.478 0.00 0.00 0.00 4.40
2277 2321 3.147629 CCGTGATACGAGGTTCTCCTAT 58.852 50.000 2.52 0.00 46.05 2.57
2316 2360 5.350365 TGGAGCACGACATAATAAACAAGTC 59.650 40.000 0.00 0.00 0.00 3.01
2463 2510 7.488471 GCTCCAGATTCTTGAGAATTTTCAATG 59.512 37.037 16.76 6.99 44.14 2.82
2681 2729 5.734855 ATGACATTGATTACACTTACGGC 57.265 39.130 0.00 0.00 0.00 5.68
2991 3307 7.726033 ATAGTGATCTTGTTGACTAGGAAGT 57.274 36.000 0.00 0.00 39.21 3.01
3171 3534 3.719268 ATATGTGTTGGCCACTCTGAA 57.281 42.857 3.88 0.00 44.81 3.02
3180 3543 6.978343 TTCACTAGTGTTATATGTGTTGGC 57.022 37.500 21.99 0.00 0.00 4.52
3196 3559 7.151308 TGCATAAATGTTTGGGTTTTCACTAG 58.849 34.615 0.00 0.00 0.00 2.57
3361 3734 9.815936 TTCTAAGTTTATTTGCGCTACTTTTAC 57.184 29.630 9.73 0.00 31.94 2.01
3363 3736 8.565416 AGTTCTAAGTTTATTTGCGCTACTTTT 58.435 29.630 9.73 0.00 31.94 2.27
3392 3779 3.689161 GCCACATTAGCAAGTCATGTGTA 59.311 43.478 9.91 0.00 44.26 2.90
3394 3781 2.488937 TGCCACATTAGCAAGTCATGTG 59.511 45.455 4.80 4.80 45.00 3.21
3436 3823 4.788925 AATAGTTGCAAGCCACCCTATA 57.211 40.909 0.00 0.00 0.00 1.31
3481 3870 7.150783 ACCATAGCACTGAAATCTTTCTTTC 57.849 36.000 4.46 0.00 38.02 2.62
3851 4351 7.776030 TGACCCTTTGAGTTGTATTTCTTAACA 59.224 33.333 0.00 0.00 0.00 2.41
4014 4653 9.040939 GTCCAAATTACAATACAACTTTTGCTT 57.959 29.630 0.00 0.00 0.00 3.91
4095 4735 9.784531 ACCATTAATAAACTAGAGACATGATGG 57.215 33.333 0.00 5.40 35.22 3.51
4115 4759 2.484889 GGCGGCAAAAACAAACCATTA 58.515 42.857 3.07 0.00 0.00 1.90
4119 4763 1.153349 TGGGCGGCAAAAACAAACC 60.153 52.632 12.47 0.00 0.00 3.27
4125 4769 1.338655 GACTTAAGTGGGCGGCAAAAA 59.661 47.619 14.14 0.00 0.00 1.94
4162 4806 0.648441 GTTCTCGCACACGTCACAAA 59.352 50.000 0.00 0.00 41.18 2.83
4163 4807 0.458716 TGTTCTCGCACACGTCACAA 60.459 50.000 0.00 0.00 41.18 3.33
4200 4844 8.993424 AGAGGTTCAGTCATATGGTATTTTAGT 58.007 33.333 2.13 0.00 0.00 2.24
4207 4851 4.895889 CCAGAGAGGTTCAGTCATATGGTA 59.104 45.833 2.13 0.00 0.00 3.25
4242 4886 7.565768 TCTTTGGGTTTTTACTTAGGTTCCATT 59.434 33.333 0.00 0.00 0.00 3.16
4257 4901 9.737844 AATATGCACATTTATTCTTTGGGTTTT 57.262 25.926 0.00 0.00 0.00 2.43
4261 4905 9.643693 GGATAATATGCACATTTATTCTTTGGG 57.356 33.333 0.00 0.00 0.00 4.12
4288 4932 8.037758 CCCATGTAGATTCCTAGTTCATCATAC 58.962 40.741 0.00 0.00 0.00 2.39
4325 4969 1.202510 GGTGTTCAACATTTGGCAGCA 60.203 47.619 0.00 0.00 35.85 4.41
4380 5028 4.588528 GGTGGCATCCATATTGGTATGTTT 59.411 41.667 0.00 0.00 39.03 2.83
4404 5412 2.832129 TGTCCTTGTATCTCCCTGACAC 59.168 50.000 0.00 0.00 0.00 3.67
4406 5414 3.118592 CCTTGTCCTTGTATCTCCCTGAC 60.119 52.174 0.00 0.00 0.00 3.51
4407 5415 3.107601 CCTTGTCCTTGTATCTCCCTGA 58.892 50.000 0.00 0.00 0.00 3.86
4418 5426 3.746492 CGACTTAAAGACCCTTGTCCTTG 59.254 47.826 0.00 0.00 42.81 3.61
4426 5434 2.242882 TAGCCCGACTTAAAGACCCT 57.757 50.000 0.00 0.00 0.00 4.34
4428 5436 3.538634 ACATAGCCCGACTTAAAGACC 57.461 47.619 0.00 0.00 0.00 3.85
4469 5477 4.263068 CCAAAGTTCCATAGACTCACACCT 60.263 45.833 0.00 0.00 0.00 4.00
4479 5487 2.034124 CCATGGCCCAAAGTTCCATAG 58.966 52.381 0.00 0.00 38.46 2.23
4483 5491 0.321346 CAACCATGGCCCAAAGTTCC 59.679 55.000 13.04 0.00 0.00 3.62
4496 5504 1.067635 GCGAACCAAGCAATCAACCAT 60.068 47.619 0.00 0.00 34.19 3.55
4503 5511 1.812571 CAAGTAGGCGAACCAAGCAAT 59.187 47.619 0.00 0.00 39.06 3.56
4538 5558 2.288152 ACATGACCAAAACAACGCCATC 60.288 45.455 0.00 0.00 0.00 3.51
4543 5563 8.735303 TTTATAATGACATGACCAAAACAACG 57.265 30.769 0.00 0.00 0.00 4.10
4584 5604 1.734117 GCACAATGGCAGAAACGGC 60.734 57.895 0.00 0.00 0.00 5.68
4585 5605 0.314935 AAGCACAATGGCAGAAACGG 59.685 50.000 0.00 0.00 35.83 4.44
4601 5621 5.154222 GGCAAGTGTTCATACTAACAAAGC 58.846 41.667 0.00 0.00 40.85 3.51
4609 5629 8.458843 GTGTTTATAATGGCAAGTGTTCATACT 58.541 33.333 0.00 0.00 0.00 2.12
4645 5665 1.202698 GGTGCTCATAGGGGTAAGCTG 60.203 57.143 0.00 0.00 35.76 4.24
4661 5681 0.391793 GCCCAGTCTCTTAGTGGTGC 60.392 60.000 0.00 0.00 46.08 5.01
4675 5695 8.469200 TCATCAATCTTAAAATTGTTAGCCCAG 58.531 33.333 1.57 0.00 37.77 4.45
4760 5780 8.311109 TCTGGATTTATTTTAGCCTTTTCCAAC 58.689 33.333 0.00 0.00 30.86 3.77
4761 5781 8.429237 TCTGGATTTATTTTAGCCTTTTCCAA 57.571 30.769 0.00 0.00 30.86 3.53
4862 5883 2.017782 CTAGCTACCTGAGAGCGTGAA 58.982 52.381 0.00 0.00 44.98 3.18
4866 5887 0.821711 AGCCTAGCTACCTGAGAGCG 60.822 60.000 0.00 0.00 44.98 5.03
4875 5896 1.593469 GCGCAAACTAAGCCTAGCTAC 59.407 52.381 0.30 0.00 38.25 3.58
4879 5900 0.739813 ACCGCGCAAACTAAGCCTAG 60.740 55.000 8.75 0.00 0.00 3.02
4880 5901 1.017177 CACCGCGCAAACTAAGCCTA 61.017 55.000 8.75 0.00 0.00 3.93
4881 5902 2.032071 ACCGCGCAAACTAAGCCT 59.968 55.556 8.75 0.00 0.00 4.58
4882 5903 2.175811 CACCGCGCAAACTAAGCC 59.824 61.111 8.75 0.00 0.00 4.35
4883 5904 2.175811 CCACCGCGCAAACTAAGC 59.824 61.111 8.75 0.00 0.00 3.09
4884 5905 1.852067 AAGCCACCGCGCAAACTAAG 61.852 55.000 8.75 0.00 41.18 2.18
4885 5906 1.448922 AAAGCCACCGCGCAAACTAA 61.449 50.000 8.75 0.00 41.18 2.24
4886 5907 1.894756 AAAGCCACCGCGCAAACTA 60.895 52.632 8.75 0.00 41.18 2.24
4887 5908 3.216292 AAAGCCACCGCGCAAACT 61.216 55.556 8.75 0.00 41.18 2.66
4896 5917 2.789409 AGTCTATCACCAAAGCCACC 57.211 50.000 0.00 0.00 0.00 4.61
4964 5985 7.026631 ACCACATACATACACAAATACATGC 57.973 36.000 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.