Multiple sequence alignment - TraesCS7B01G029000

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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 TraesCS7B01G029000 chr7B 100.000 3019 0 0 1 3019 27488114 27485096 0.000000e+00 5535.0
1 TraesCS7B01G029000 chr7B 95.872 533 13 5 2007 2537 584259499 584258974 0.000000e+00 854.0
2 TraesCS7B01G029000 chr7B 100.000 292 0 0 1 292 57200143 57200434 9.520000e-150 540.0
3 TraesCS7B01G029000 chr7B 100.000 292 0 0 1 292 218559584 218559875 9.520000e-150 540.0
4 TraesCS7B01G029000 chr7B 83.299 479 41 14 1106 1578 27595191 27594746 3.620000e-109 405.0
5 TraesCS7B01G029000 chr7D 88.801 1143 87 21 760 1883 80199159 80198039 0.000000e+00 1363.0
6 TraesCS7B01G029000 chr7D 84.444 1170 108 44 815 1927 80463048 80461896 0.000000e+00 1085.0
7 TraesCS7B01G029000 chr7D 90.436 826 42 17 1196 1989 80298631 80297811 0.000000e+00 1053.0
8 TraesCS7B01G029000 chr7D 95.238 483 22 1 2538 3019 80297819 80297337 0.000000e+00 763.0
9 TraesCS7B01G029000 chr7D 80.471 891 105 33 1106 1967 80417575 80416725 4.280000e-173 617.0
10 TraesCS7B01G029000 chr7D 88.912 487 47 6 2538 3019 80382640 80382156 7.210000e-166 593.0
11 TraesCS7B01G029000 chr7D 87.373 491 51 9 2535 3019 80384029 80383544 1.220000e-153 553.0
12 TraesCS7B01G029000 chr7D 87.389 452 32 9 1555 1989 80383075 80382632 2.090000e-136 496.0
13 TraesCS7B01G029000 chr7D 88.088 319 33 3 1667 1985 80384335 80384022 1.020000e-99 374.0
14 TraesCS7B01G029000 chr7D 84.688 320 30 10 701 1005 80299052 80298737 4.890000e-78 302.0
15 TraesCS7B01G029000 chr7D 78.851 435 40 13 883 1295 112411240 112411644 2.320000e-61 246.0
16 TraesCS7B01G029000 chr7D 92.437 119 9 0 1867 1985 80198022 80197904 1.440000e-38 171.0
17 TraesCS7B01G029000 chr7D 91.765 85 7 0 1571 1655 80470379 80470295 5.290000e-23 119.0
18 TraesCS7B01G029000 chr7D 94.231 52 1 2 1079 1129 80298679 80298629 8.970000e-11 78.7
19 TraesCS7B01G029000 chr4B 97.575 536 11 2 2007 2541 376256612 376257146 0.000000e+00 917.0
20 TraesCS7B01G029000 chr4B 96.792 530 16 1 2007 2536 479402648 479402120 0.000000e+00 883.0
21 TraesCS7B01G029000 chr1B 97.180 532 15 0 2007 2538 668914890 668914359 0.000000e+00 900.0
22 TraesCS7B01G029000 chr1B 96.811 533 17 0 2007 2539 256208752 256208220 0.000000e+00 891.0
23 TraesCS7B01G029000 chr1B 100.000 292 0 0 1 292 632429206 632428915 9.520000e-150 540.0
24 TraesCS7B01G029000 chr1B 88.889 99 10 1 319 416 549731287 549731385 1.470000e-23 121.0
25 TraesCS7B01G029000 chr7A 82.565 1107 108 32 818 1883 83107008 83105946 0.000000e+00 896.0
26 TraesCS7B01G029000 chr7A 82.627 967 108 33 396 1332 83170623 83169687 0.000000e+00 800.0
27 TraesCS7B01G029000 chr7A 84.254 851 75 27 1099 1919 83142422 83141601 0.000000e+00 774.0
28 TraesCS7B01G029000 chr7A 86.094 640 59 14 1365 1983 83157748 83157118 0.000000e+00 662.0
29 TraesCS7B01G029000 chr7A 100.000 292 0 0 1 292 49916714 49916423 9.520000e-150 540.0
30 TraesCS7B01G029000 chr7A 86.415 265 28 6 404 665 83172796 83172537 1.770000e-72 283.0
31 TraesCS7B01G029000 chr7A 85.660 265 30 5 404 665 83175734 83175475 3.840000e-69 272.0
32 TraesCS7B01G029000 chr7A 92.683 82 6 0 920 1001 83142587 83142506 5.290000e-23 119.0
33 TraesCS7B01G029000 chr6B 96.774 527 14 3 2007 2533 626885048 626885571 0.000000e+00 876.0
34 TraesCS7B01G029000 chr6B 90.217 92 8 1 325 415 424080593 424080502 5.290000e-23 119.0
35 TraesCS7B01G029000 chr6B 90.217 92 8 1 325 415 424303306 424303215 5.290000e-23 119.0
36 TraesCS7B01G029000 chr6B 90.217 92 8 1 325 415 654640655 654640746 5.290000e-23 119.0
37 TraesCS7B01G029000 chr2B 96.248 533 17 3 2007 2537 429165559 429165028 0.000000e+00 870.0
38 TraesCS7B01G029000 chr2B 86.667 105 13 1 313 416 113599104 113599208 6.840000e-22 115.0
39 TraesCS7B01G029000 chr2B 94.643 56 3 0 2487 2542 733091822 733091767 1.490000e-13 87.9
40 TraesCS7B01G029000 chr1A 96.205 527 19 1 2007 2533 280490518 280491043 0.000000e+00 861.0
41 TraesCS7B01G029000 chr5B 97.228 505 14 0 2007 2511 368696156 368695652 0.000000e+00 856.0
42 TraesCS7B01G029000 chrUn 100.000 292 0 0 1 292 414744274 414744565 9.520000e-150 540.0
43 TraesCS7B01G029000 chr3A 100.000 292 0 0 1 292 88202028 88201737 9.520000e-150 540.0
44 TraesCS7B01G029000 chr2A 100.000 292 0 0 1 292 532083752 532083461 9.520000e-150 540.0
45 TraesCS7B01G029000 chr2A 100.000 292 0 0 1 292 533912027 533912318 9.520000e-150 540.0
46 TraesCS7B01G029000 chr2A 100.000 292 0 0 1 292 736253531 736253822 9.520000e-150 540.0
47 TraesCS7B01G029000 chr2A 100.000 292 0 0 1 292 762149938 762149647 9.520000e-150 540.0
48 TraesCS7B01G029000 chr4A 87.156 109 11 3 310 416 665186514 665186407 1.470000e-23 121.0
49 TraesCS7B01G029000 chr3B 88.889 99 10 1 325 422 684643163 684643261 1.470000e-23 121.0
50 TraesCS7B01G029000 chr1D 90.217 92 9 0 325 416 490934648 490934739 1.470000e-23 121.0
51 TraesCS7B01G029000 chr1D 87.500 104 12 1 312 414 298620959 298620856 5.290000e-23 119.0


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 TraesCS7B01G029000 chr7B 27485096 27488114 3018 True 5535.000000 5535 100.000000 1 3019 1 chr7B.!!$R1 3018
1 TraesCS7B01G029000 chr7B 584258974 584259499 525 True 854.000000 854 95.872000 2007 2537 1 chr7B.!!$R3 530
2 TraesCS7B01G029000 chr7D 80461896 80463048 1152 True 1085.000000 1085 84.444000 815 1927 1 chr7D.!!$R2 1112
3 TraesCS7B01G029000 chr7D 80197904 80199159 1255 True 767.000000 1363 90.619000 760 1985 2 chr7D.!!$R4 1225
4 TraesCS7B01G029000 chr7D 80416725 80417575 850 True 617.000000 617 80.471000 1106 1967 1 chr7D.!!$R1 861
5 TraesCS7B01G029000 chr7D 80297337 80299052 1715 True 549.175000 1053 91.148250 701 3019 4 chr7D.!!$R5 2318
6 TraesCS7B01G029000 chr7D 80382156 80384335 2179 True 504.000000 593 87.940500 1555 3019 4 chr7D.!!$R6 1464
7 TraesCS7B01G029000 chr4B 376256612 376257146 534 False 917.000000 917 97.575000 2007 2541 1 chr4B.!!$F1 534
8 TraesCS7B01G029000 chr4B 479402120 479402648 528 True 883.000000 883 96.792000 2007 2536 1 chr4B.!!$R1 529
9 TraesCS7B01G029000 chr1B 668914359 668914890 531 True 900.000000 900 97.180000 2007 2538 1 chr1B.!!$R3 531
10 TraesCS7B01G029000 chr1B 256208220 256208752 532 True 891.000000 891 96.811000 2007 2539 1 chr1B.!!$R1 532
11 TraesCS7B01G029000 chr7A 83105946 83107008 1062 True 896.000000 896 82.565000 818 1883 1 chr7A.!!$R2 1065
12 TraesCS7B01G029000 chr7A 83157118 83157748 630 True 662.000000 662 86.094000 1365 1983 1 chr7A.!!$R3 618
13 TraesCS7B01G029000 chr7A 83169687 83175734 6047 True 451.666667 800 84.900667 396 1332 3 chr7A.!!$R5 936
14 TraesCS7B01G029000 chr7A 83141601 83142587 986 True 446.500000 774 88.468500 920 1919 2 chr7A.!!$R4 999
15 TraesCS7B01G029000 chr6B 626885048 626885571 523 False 876.000000 876 96.774000 2007 2533 1 chr6B.!!$F1 526
16 TraesCS7B01G029000 chr2B 429165028 429165559 531 True 870.000000 870 96.248000 2007 2537 1 chr2B.!!$R1 530
17 TraesCS7B01G029000 chr1A 280490518 280491043 525 False 861.000000 861 96.205000 2007 2533 1 chr1A.!!$F1 526
18 TraesCS7B01G029000 chr5B 368695652 368696156 504 True 856.000000 856 97.228000 2007 2511 1 chr5B.!!$R1 504

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
525 3460 0.173935 TGCATCCACCGTAACCGTAG 59.826 55.0 0.00 0.0 0.00 3.51 F
1077 6250 0.241481 AGTCGACGAAGACAAGGAGC 59.759 55.0 10.46 0.0 43.24 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 6798 0.178767 TGGATCGCCATGGTGAGAAG 59.821 55.0 30.38 8.35 39.92 2.85 R
2928 8269 0.029035 GCTGCATCTGCCTTGAATCG 59.971 55.0 0.00 0.00 41.18 3.34 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
46 47 4.179579 GCGGATCCGGCAAACTGC 62.180 66.667 33.98 12.14 44.08 4.40
48 49 3.508840 GGATCCGGCAAACTGCGG 61.509 66.667 0.00 0.00 46.21 5.69
56 57 3.673484 CAAACTGCGGCCCACCAG 61.673 66.667 10.29 10.29 34.57 4.00
66 67 4.864334 CCCACCAGCCGCCAGATC 62.864 72.222 0.00 0.00 0.00 2.75
68 69 4.147449 CACCAGCCGCCAGATCGA 62.147 66.667 0.00 0.00 0.00 3.59
69 70 3.842923 ACCAGCCGCCAGATCGAG 61.843 66.667 0.00 0.00 0.00 4.04
71 72 4.519437 CAGCCGCCAGATCGAGCA 62.519 66.667 2.38 0.00 0.00 4.26
72 73 3.774528 AGCCGCCAGATCGAGCAA 61.775 61.111 2.38 0.00 0.00 3.91
73 74 3.267860 GCCGCCAGATCGAGCAAG 61.268 66.667 2.38 0.00 0.00 4.01
74 75 2.587194 CCGCCAGATCGAGCAAGG 60.587 66.667 2.38 5.55 0.00 3.61
75 76 3.267860 CGCCAGATCGAGCAAGGC 61.268 66.667 22.45 22.45 41.86 4.35
76 77 3.267860 GCCAGATCGAGCAAGGCG 61.268 66.667 19.02 0.00 35.42 5.52
78 79 1.880340 CCAGATCGAGCAAGGCGAC 60.880 63.158 2.38 0.00 40.94 5.19
79 80 1.880340 CAGATCGAGCAAGGCGACC 60.880 63.158 2.38 0.00 40.94 4.79
80 81 2.956964 GATCGAGCAAGGCGACCG 60.957 66.667 0.00 0.00 40.94 4.79
81 82 4.514577 ATCGAGCAAGGCGACCGG 62.515 66.667 0.00 0.00 40.94 5.28
83 84 4.514577 CGAGCAAGGCGACCGGAT 62.515 66.667 9.46 0.00 0.00 4.18
85 86 3.077556 AGCAAGGCGACCGGATCT 61.078 61.111 9.46 0.00 0.00 2.75
86 87 2.892425 GCAAGGCGACCGGATCTG 60.892 66.667 9.46 0.00 0.00 2.90
88 89 1.443407 CAAGGCGACCGGATCTGAT 59.557 57.895 9.46 0.00 0.00 2.90
89 90 0.877649 CAAGGCGACCGGATCTGATG 60.878 60.000 9.46 0.00 0.00 3.07
93 94 2.796193 CGACCGGATCTGATGGGCA 61.796 63.158 9.46 0.00 0.00 5.36
94 95 1.070445 GACCGGATCTGATGGGCAG 59.930 63.158 9.46 0.00 46.31 4.85
226 227 3.522731 CGGGCTCTCCAGAGGTCG 61.523 72.222 5.74 0.00 42.29 4.79
229 230 2.124693 GGCTCTCCAGAGGTCGAGG 61.125 68.421 5.74 0.00 42.29 4.63
230 231 2.781158 GCTCTCCAGAGGTCGAGGC 61.781 68.421 5.74 0.00 42.29 4.70
231 232 1.379176 CTCTCCAGAGGTCGAGGCA 60.379 63.158 0.00 0.00 38.48 4.75
233 234 2.363018 TCCAGAGGTCGAGGCAGG 60.363 66.667 0.00 0.00 0.00 4.85
234 235 2.681778 CCAGAGGTCGAGGCAGGT 60.682 66.667 0.00 0.00 0.00 4.00
235 236 2.575993 CAGAGGTCGAGGCAGGTG 59.424 66.667 0.00 0.00 0.00 4.00
237 238 4.803426 GAGGTCGAGGCAGGTGCG 62.803 72.222 0.00 0.00 43.26 5.34
328 329 8.827177 TGCCTTGTTAAATACTATTATCTCCG 57.173 34.615 0.00 0.00 0.00 4.63
330 331 9.918630 GCCTTGTTAAATACTATTATCTCCGTA 57.081 33.333 0.00 0.00 0.00 4.02
349 350 7.225931 TCTCCGTACCAAATAAATGTATTGAGC 59.774 37.037 0.00 0.00 30.04 4.26
380 381 8.927675 ACAAATTTGTATTGGAGGTAGTACAA 57.072 30.769 22.10 0.00 40.16 2.41
382 383 9.840427 CAAATTTGTATTGGAGGTAGTACAAAG 57.160 33.333 10.15 0.34 45.00 2.77
385 386 7.972832 TTGTATTGGAGGTAGTACAAAGTTG 57.027 36.000 2.06 0.00 34.98 3.16
386 387 7.305813 TGTATTGGAGGTAGTACAAAGTTGA 57.694 36.000 2.06 0.00 0.00 3.18
387 388 7.383687 TGTATTGGAGGTAGTACAAAGTTGAG 58.616 38.462 2.06 0.00 0.00 3.02
388 389 6.681729 ATTGGAGGTAGTACAAAGTTGAGA 57.318 37.500 2.06 0.00 0.00 3.27
389 390 5.464030 TGGAGGTAGTACAAAGTTGAGAC 57.536 43.478 2.06 0.00 0.00 3.36
391 392 5.221382 TGGAGGTAGTACAAAGTTGAGACAC 60.221 44.000 2.06 0.00 0.00 3.67
392 393 5.010820 GGAGGTAGTACAAAGTTGAGACACT 59.989 44.000 2.06 0.00 0.00 3.55
394 395 7.255730 GGAGGTAGTACAAAGTTGAGACACTTA 60.256 40.741 2.06 0.00 35.87 2.24
395 396 8.191534 AGGTAGTACAAAGTTGAGACACTTAT 57.808 34.615 2.06 0.00 35.87 1.73
397 398 9.269453 GGTAGTACAAAGTTGAGACACTTATTT 57.731 33.333 2.06 0.00 35.87 1.40
401 402 9.651718 GTACAAAGTTGAGACACTTATTTTGAG 57.348 33.333 0.00 0.00 35.87 3.02
402 403 8.506168 ACAAAGTTGAGACACTTATTTTGAGA 57.494 30.769 0.00 0.00 35.87 3.27
403 404 8.398665 ACAAAGTTGAGACACTTATTTTGAGAC 58.601 33.333 0.00 0.00 35.87 3.36
404 405 6.771188 AGTTGAGACACTTATTTTGAGACG 57.229 37.500 0.00 0.00 0.00 4.18
408 409 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
409 410 4.527038 AGACACTTATTTTGAGACGGAGGA 59.473 41.667 0.00 0.00 0.00 3.71
410 411 5.011738 AGACACTTATTTTGAGACGGAGGAA 59.988 40.000 0.00 0.00 0.00 3.36
411 412 5.238583 ACACTTATTTTGAGACGGAGGAAG 58.761 41.667 0.00 0.00 0.00 3.46
414 415 7.042335 CACTTATTTTGAGACGGAGGAAGTAT 58.958 38.462 0.00 0.00 0.00 2.12
418 419 4.985538 TTGAGACGGAGGAAGTATTCTC 57.014 45.455 0.00 0.00 46.56 2.87
421 422 4.399618 TGAGACGGAGGAAGTATTCTCTTG 59.600 45.833 0.00 0.00 46.56 3.02
442 443 2.613725 GGTCCGGAATTAGTTGACGGTT 60.614 50.000 5.23 0.00 44.54 4.44
443 444 2.414138 GTCCGGAATTAGTTGACGGTTG 59.586 50.000 5.23 0.00 44.54 3.77
450 451 6.314784 GGAATTAGTTGACGGTTGAATGAAG 58.685 40.000 0.00 0.00 0.00 3.02
467 468 6.317140 TGAATGAAGGTATCTGCATGAAGAAC 59.683 38.462 7.69 7.40 38.30 3.01
474 475 7.148641 AGGTATCTGCATGAAGAACGTATTAG 58.851 38.462 7.69 0.00 0.00 1.73
497 3432 2.160219 CACAGGAGCAGTACGTACGTTA 59.840 50.000 27.92 9.76 0.00 3.18
522 3457 1.436195 CCATGCATCCACCGTAACCG 61.436 60.000 0.00 0.00 0.00 4.44
525 3460 0.173935 TGCATCCACCGTAACCGTAG 59.826 55.000 0.00 0.00 0.00 3.51
532 5652 0.895100 ACCGTAACCGTAGTGGCAGA 60.895 55.000 0.00 0.00 43.94 4.26
610 5730 2.288666 ACGTCACTGAGCAAAACACAT 58.711 42.857 0.00 0.00 0.00 3.21
615 5735 3.187022 TCACTGAGCAAAACACATGATCG 59.813 43.478 0.00 0.00 36.02 3.69
647 5767 1.669115 CCTGGTCCACGCTCAGTTG 60.669 63.158 0.00 0.00 0.00 3.16
670 5790 2.358247 CCACGCACACCCTACACC 60.358 66.667 0.00 0.00 0.00 4.16
673 5793 0.389426 CACGCACACCCTACACCTAC 60.389 60.000 0.00 0.00 0.00 3.18
678 5798 2.757099 ACCCTACACCTACGGCCG 60.757 66.667 26.86 26.86 0.00 6.13
695 5815 1.737363 GCCGAGAGACAGAACCACATC 60.737 57.143 0.00 0.00 0.00 3.06
731 5851 2.680913 CCGTTCTTTCGCAGGCAGG 61.681 63.158 0.00 0.00 0.00 4.85
733 5853 2.034066 TTCTTTCGCAGGCAGGGG 59.966 61.111 0.00 0.00 0.00 4.79
734 5854 2.829384 TTCTTTCGCAGGCAGGGGT 61.829 57.895 0.00 0.00 0.00 4.95
735 5855 2.282462 CTTTCGCAGGCAGGGGTT 60.282 61.111 0.00 0.00 0.00 4.11
737 5857 3.429372 TTTCGCAGGCAGGGGTTGT 62.429 57.895 0.00 0.00 0.00 3.32
744 5867 4.338710 GCAGGGGTTGTGGGCGTA 62.339 66.667 0.00 0.00 0.00 4.42
766 5889 4.834534 AGATGACTCGATATACTACCGCT 58.165 43.478 0.00 0.00 0.00 5.52
770 5893 2.484651 ACTCGATATACTACCGCTGCAG 59.515 50.000 10.11 10.11 0.00 4.41
910 6039 5.299531 TCGAGTTCACTATTTCCAGATCGAT 59.700 40.000 0.00 0.00 31.28 3.59
926 6071 1.751351 TCGATCTCCACTGTCACCATC 59.249 52.381 0.00 0.00 0.00 3.51
927 6072 1.478105 CGATCTCCACTGTCACCATCA 59.522 52.381 0.00 0.00 0.00 3.07
974 6119 0.666913 CCCGCGCGCCTATATATACT 59.333 55.000 27.36 0.00 0.00 2.12
998 6143 2.104331 ATCGATCGCACGGTGTCC 59.896 61.111 11.09 0.00 0.00 4.02
1009 6179 3.075186 GGTGTCCCCGGCTACTTT 58.925 61.111 0.00 0.00 0.00 2.66
1013 6183 0.906775 TGTCCCCGGCTACTTTTAGG 59.093 55.000 0.00 0.00 0.00 2.69
1021 6191 4.322953 CCCGGCTACTTTTAGGACAAGTTA 60.323 45.833 0.00 0.00 35.95 2.24
1026 6196 6.037281 GGCTACTTTTAGGACAAGTTATCAGC 59.963 42.308 0.00 0.00 35.95 4.26
1027 6197 6.819146 GCTACTTTTAGGACAAGTTATCAGCT 59.181 38.462 0.00 0.00 35.95 4.24
1028 6198 7.201565 GCTACTTTTAGGACAAGTTATCAGCTG 60.202 40.741 7.63 7.63 35.95 4.24
1029 6199 6.534634 ACTTTTAGGACAAGTTATCAGCTGT 58.465 36.000 14.67 3.75 29.75 4.40
1030 6200 6.428159 ACTTTTAGGACAAGTTATCAGCTGTG 59.572 38.462 14.67 5.88 29.75 3.66
1031 6201 5.738619 TTAGGACAAGTTATCAGCTGTGA 57.261 39.130 14.67 0.00 37.02 3.58
1069 6240 3.508793 ACAGGGAAAATAGTCGACGAAGA 59.491 43.478 10.46 0.00 0.00 2.87
1070 6241 3.858238 CAGGGAAAATAGTCGACGAAGAC 59.142 47.826 10.46 6.87 41.23 3.01
1077 6250 0.241481 AGTCGACGAAGACAAGGAGC 59.759 55.000 10.46 0.00 43.24 4.70
1078 6251 0.241481 GTCGACGAAGACAAGGAGCT 59.759 55.000 0.00 0.00 40.65 4.09
1079 6252 1.467734 GTCGACGAAGACAAGGAGCTA 59.532 52.381 0.00 0.00 40.65 3.32
1080 6253 1.738350 TCGACGAAGACAAGGAGCTAG 59.262 52.381 0.00 0.00 0.00 3.42
1081 6254 1.795889 CGACGAAGACAAGGAGCTAGC 60.796 57.143 6.62 6.62 0.00 3.42
1082 6255 1.474879 GACGAAGACAAGGAGCTAGCT 59.525 52.381 19.45 19.45 0.00 3.32
1083 6256 2.683867 GACGAAGACAAGGAGCTAGCTA 59.316 50.000 19.38 0.00 0.00 3.32
1087 6260 4.083003 CGAAGACAAGGAGCTAGCTATAGG 60.083 50.000 19.38 10.64 0.00 2.57
1212 6413 2.435586 CGCTGCCACTCTTCCTGG 60.436 66.667 0.00 0.00 0.00 4.45
1390 6621 2.093973 AGTGTAATTCGTGCAGGAGGAG 60.094 50.000 9.34 0.00 0.00 3.69
1550 6790 2.989639 CTCCGCCTCATGTTCCCA 59.010 61.111 0.00 0.00 0.00 4.37
1558 6798 1.133976 CCTCATGTTCCCATCCTCCAC 60.134 57.143 0.00 0.00 0.00 4.02
1559 6799 1.842562 CTCATGTTCCCATCCTCCACT 59.157 52.381 0.00 0.00 0.00 4.00
1560 6800 2.240667 CTCATGTTCCCATCCTCCACTT 59.759 50.000 0.00 0.00 0.00 3.16
1571 6817 0.393537 CCTCCACTTCTCACCATGGC 60.394 60.000 13.04 0.00 31.87 4.40
1753 7017 2.541556 GGAGTTTAGCAAGTCGGCTAG 58.458 52.381 0.00 0.00 46.25 3.42
1784 7064 0.524414 TACTCATGTCACCACCGACG 59.476 55.000 0.00 0.00 38.84 5.12
1785 7065 1.176619 ACTCATGTCACCACCGACGA 61.177 55.000 0.00 0.00 38.84 4.20
1786 7066 0.732880 CTCATGTCACCACCGACGAC 60.733 60.000 0.00 0.00 38.84 4.34
1820 7103 1.442769 CTGGTTGAATGTGGGAGTCG 58.557 55.000 0.00 0.00 0.00 4.18
1824 7107 0.605319 TTGAATGTGGGAGTCGTGGC 60.605 55.000 0.00 0.00 0.00 5.01
1864 7163 9.291664 GTGTGTCTAGTTAATTAGCTTACTGAG 57.708 37.037 7.17 0.00 0.00 3.35
1937 7271 8.146053 TGAGTTTATTTCTCTTGTCCAGGATA 57.854 34.615 0.00 0.00 33.59 2.59
1989 7323 7.539366 CGGTGAAATGTTGAAAATTATTACGGT 59.461 33.333 0.00 0.00 0.00 4.83
1990 7324 9.198837 GGTGAAATGTTGAAAATTATTACGGTT 57.801 29.630 0.00 0.00 0.00 4.44
2106 7440 1.174712 TTGCAAGCAGGTTCAGGAGC 61.175 55.000 0.00 0.00 0.00 4.70
2344 7681 1.574428 CGAGGGTTTTCCGCAACAG 59.426 57.895 0.00 0.00 41.82 3.16
2604 7942 7.429636 AATTTTCACTGGATTTGCATTTGAG 57.570 32.000 0.00 0.00 0.00 3.02
2676 8014 5.105752 GCACCATACAAAATTGCCGAAATA 58.894 37.500 0.00 0.00 0.00 1.40
2712 8050 4.202202 TGAAATTTTGAACCCGCTCATGTT 60.202 37.500 0.00 0.00 0.00 2.71
2775 8113 2.046023 TCTCCCGACCTCGCGTTA 60.046 61.111 5.77 0.00 38.18 3.18
2786 8124 0.736325 CTCGCGTTACTCCCACAAGG 60.736 60.000 5.77 0.00 0.00 3.61
2833 8174 1.929088 GTAGCCACCCCTCCCCTTT 60.929 63.158 0.00 0.00 0.00 3.11
2884 8225 4.715523 GGCTAAGCCCGTGCCACA 62.716 66.667 0.00 0.00 44.06 4.17
2885 8226 2.671619 GCTAAGCCCGTGCCACAA 60.672 61.111 0.00 0.00 38.69 3.33
2964 8305 3.961197 CGATCGTCCCGGCATCGA 61.961 66.667 7.03 14.38 41.61 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.042733 TTTGCCGGATCCGCCAGAT 62.043 57.895 29.12 0.00 38.17 2.90
25 26 3.711814 TTTGCCGGATCCGCCAGA 61.712 61.111 29.12 17.03 38.24 3.86
26 27 3.508840 GTTTGCCGGATCCGCCAG 61.509 66.667 29.12 16.30 38.24 4.85
27 28 4.028490 AGTTTGCCGGATCCGCCA 62.028 61.111 29.12 22.41 38.24 5.69
28 29 3.508840 CAGTTTGCCGGATCCGCC 61.509 66.667 29.12 19.56 38.24 6.13
29 30 4.179579 GCAGTTTGCCGGATCCGC 62.180 66.667 29.12 22.80 37.42 5.54
30 31 3.864686 CGCAGTTTGCCGGATCCG 61.865 66.667 27.65 27.65 41.12 4.18
32 33 4.179579 GCCGCAGTTTGCCGGATC 62.180 66.667 5.05 0.00 41.12 3.36
39 40 3.673484 CTGGTGGGCCGCAGTTTG 61.673 66.667 20.39 0.00 37.67 2.93
51 52 4.147449 TCGATCTGGCGGCTGGTG 62.147 66.667 15.75 6.33 0.00 4.17
55 56 3.729965 CTTGCTCGATCTGGCGGCT 62.730 63.158 11.43 0.00 0.00 5.52
56 57 3.267860 CTTGCTCGATCTGGCGGC 61.268 66.667 0.00 0.00 0.00 6.53
57 58 2.587194 CCTTGCTCGATCTGGCGG 60.587 66.667 0.00 0.00 0.00 6.13
59 60 3.267860 CGCCTTGCTCGATCTGGC 61.268 66.667 11.83 11.83 40.14 4.85
61 62 1.880340 GGTCGCCTTGCTCGATCTG 60.880 63.158 0.00 0.00 38.29 2.90
62 63 2.496817 GGTCGCCTTGCTCGATCT 59.503 61.111 0.00 0.00 38.29 2.75
64 65 4.514577 CCGGTCGCCTTGCTCGAT 62.515 66.667 0.00 0.00 38.29 3.59
66 67 4.514577 ATCCGGTCGCCTTGCTCG 62.515 66.667 0.00 0.00 0.00 5.03
68 69 3.077556 AGATCCGGTCGCCTTGCT 61.078 61.111 0.00 0.00 0.00 3.91
69 70 2.650813 ATCAGATCCGGTCGCCTTGC 62.651 60.000 0.00 0.00 0.00 4.01
70 71 0.877649 CATCAGATCCGGTCGCCTTG 60.878 60.000 0.00 0.00 0.00 3.61
71 72 1.443407 CATCAGATCCGGTCGCCTT 59.557 57.895 0.00 0.00 0.00 4.35
72 73 2.502492 CCATCAGATCCGGTCGCCT 61.502 63.158 0.00 0.00 0.00 5.52
73 74 2.029666 CCATCAGATCCGGTCGCC 59.970 66.667 0.00 0.00 0.00 5.54
74 75 2.029666 CCCATCAGATCCGGTCGC 59.970 66.667 0.00 0.00 0.00 5.19
75 76 2.029666 GCCCATCAGATCCGGTCG 59.970 66.667 0.00 0.00 0.00 4.79
76 77 1.070445 CTGCCCATCAGATCCGGTC 59.930 63.158 0.00 0.00 45.72 4.79
78 79 3.554716 TCTGCCCATCAGATCCGG 58.445 61.111 0.00 0.00 46.34 5.14
208 209 3.844090 GACCTCTGGAGAGCCCGC 61.844 72.222 0.00 0.00 40.75 6.13
209 210 3.522731 CGACCTCTGGAGAGCCCG 61.523 72.222 0.00 0.67 40.75 6.13
210 211 2.043852 TCGACCTCTGGAGAGCCC 60.044 66.667 0.00 0.00 40.75 5.19
211 212 2.124693 CCTCGACCTCTGGAGAGCC 61.125 68.421 0.00 0.00 40.75 4.70
213 214 1.379176 TGCCTCGACCTCTGGAGAG 60.379 63.158 0.00 0.00 41.71 3.20
214 215 1.379176 CTGCCTCGACCTCTGGAGA 60.379 63.158 0.00 0.00 31.90 3.71
215 216 2.422231 CCTGCCTCGACCTCTGGAG 61.422 68.421 0.00 0.00 0.00 3.86
218 219 2.575993 CACCTGCCTCGACCTCTG 59.424 66.667 0.00 0.00 0.00 3.35
219 220 3.386237 GCACCTGCCTCGACCTCT 61.386 66.667 0.00 0.00 34.31 3.69
303 304 8.426489 ACGGAGATAATAGTATTTAACAAGGCA 58.574 33.333 0.00 0.00 0.00 4.75
322 323 9.273016 CTCAATACATTTATTTGGTACGGAGAT 57.727 33.333 0.00 0.00 0.00 2.75
323 324 7.225931 GCTCAATACATTTATTTGGTACGGAGA 59.774 37.037 0.00 0.00 0.00 3.71
324 325 7.226720 AGCTCAATACATTTATTTGGTACGGAG 59.773 37.037 0.00 0.00 0.00 4.63
355 356 8.927675 TTGTACTACCTCCAATACAAATTTGT 57.072 30.769 25.99 25.99 44.86 2.83
356 357 9.840427 CTTTGTACTACCTCCAATACAAATTTG 57.160 33.333 16.67 16.67 43.14 2.32
357 358 9.582648 ACTTTGTACTACCTCCAATACAAATTT 57.417 29.630 8.41 0.00 43.14 1.82
360 361 8.212312 TCAACTTTGTACTACCTCCAATACAAA 58.788 33.333 7.85 7.85 42.36 2.83
362 363 7.233962 TCTCAACTTTGTACTACCTCCAATACA 59.766 37.037 0.00 0.00 0.00 2.29
363 364 7.544915 GTCTCAACTTTGTACTACCTCCAATAC 59.455 40.741 0.00 0.00 0.00 1.89
364 365 7.233962 TGTCTCAACTTTGTACTACCTCCAATA 59.766 37.037 0.00 0.00 0.00 1.90
365 366 6.042781 TGTCTCAACTTTGTACTACCTCCAAT 59.957 38.462 0.00 0.00 0.00 3.16
369 370 6.086785 AGTGTCTCAACTTTGTACTACCTC 57.913 41.667 0.00 0.00 0.00 3.85
371 372 8.828688 AATAAGTGTCTCAACTTTGTACTACC 57.171 34.615 0.00 0.00 40.77 3.18
374 375 9.391006 TCAAAATAAGTGTCTCAACTTTGTACT 57.609 29.630 0.00 0.00 40.77 2.73
376 377 9.607988 TCTCAAAATAAGTGTCTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
377 378 8.398665 GTCTCAAAATAAGTGTCTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
378 379 7.584123 CGTCTCAAAATAAGTGTCTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
379 380 7.254795 CCGTCTCAAAATAAGTGTCTCAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
380 381 6.202954 CCGTCTCAAAATAAGTGTCTCAACTT 59.797 38.462 0.00 0.00 42.89 2.66
382 383 5.694910 TCCGTCTCAAAATAAGTGTCTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
385 386 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
386 387 4.527038 TCCTCCGTCTCAAAATAAGTGTCT 59.473 41.667 0.00 0.00 0.00 3.41
387 388 4.817517 TCCTCCGTCTCAAAATAAGTGTC 58.182 43.478 0.00 0.00 0.00 3.67
388 389 4.884668 TCCTCCGTCTCAAAATAAGTGT 57.115 40.909 0.00 0.00 0.00 3.55
389 390 5.238583 ACTTCCTCCGTCTCAAAATAAGTG 58.761 41.667 0.00 0.00 0.00 3.16
391 392 7.982354 AGAATACTTCCTCCGTCTCAAAATAAG 59.018 37.037 0.00 0.00 0.00 1.73
392 393 7.848128 AGAATACTTCCTCCGTCTCAAAATAA 58.152 34.615 0.00 0.00 0.00 1.40
394 395 6.155393 AGAGAATACTTCCTCCGTCTCAAAAT 59.845 38.462 0.00 0.00 35.11 1.82
395 396 5.480772 AGAGAATACTTCCTCCGTCTCAAAA 59.519 40.000 0.00 0.00 35.11 2.44
397 398 4.601084 AGAGAATACTTCCTCCGTCTCAA 58.399 43.478 0.00 0.00 35.11 3.02
401 402 3.447944 ACCAAGAGAATACTTCCTCCGTC 59.552 47.826 0.00 0.00 0.00 4.79
402 403 3.442076 ACCAAGAGAATACTTCCTCCGT 58.558 45.455 0.00 0.00 0.00 4.69
403 404 3.181474 GGACCAAGAGAATACTTCCTCCG 60.181 52.174 0.00 0.00 0.00 4.63
404 405 3.181474 CGGACCAAGAGAATACTTCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
408 409 4.467198 TTCCGGACCAAGAGAATACTTC 57.533 45.455 1.83 0.00 0.00 3.01
409 410 5.437191 AATTCCGGACCAAGAGAATACTT 57.563 39.130 1.83 0.00 0.00 2.24
410 411 5.661759 ACTAATTCCGGACCAAGAGAATACT 59.338 40.000 1.83 0.00 0.00 2.12
411 412 5.915175 ACTAATTCCGGACCAAGAGAATAC 58.085 41.667 1.83 0.00 0.00 1.89
414 415 4.285003 TCAACTAATTCCGGACCAAGAGAA 59.715 41.667 1.83 0.00 0.00 2.87
418 419 2.671396 CGTCAACTAATTCCGGACCAAG 59.329 50.000 1.83 3.84 0.00 3.61
421 422 1.066645 ACCGTCAACTAATTCCGGACC 60.067 52.381 1.83 0.00 41.08 4.46
442 443 5.993055 TCTTCATGCAGATACCTTCATTCA 58.007 37.500 0.00 0.00 0.00 2.57
443 444 6.510799 CGTTCTTCATGCAGATACCTTCATTC 60.511 42.308 0.00 0.00 0.00 2.67
450 451 6.128795 GCTAATACGTTCTTCATGCAGATACC 60.129 42.308 0.00 0.00 0.00 2.73
467 468 1.137086 ACTGCTCCTGTGGCTAATACG 59.863 52.381 0.00 0.00 0.00 3.06
474 475 0.458025 GTACGTACTGCTCCTGTGGC 60.458 60.000 18.47 0.00 0.00 5.01
522 3457 0.809385 TCGCTACTGTCTGCCACTAC 59.191 55.000 0.00 0.00 0.00 2.73
525 3460 0.456995 GAGTCGCTACTGTCTGCCAC 60.457 60.000 0.00 0.00 35.56 5.01
532 5652 2.045131 GTCCCGGAGTCGCTACTGT 61.045 63.158 0.73 0.00 35.56 3.55
553 5673 2.099831 CTCGGCCTCGACACGTAC 59.900 66.667 0.00 0.00 40.88 3.67
554 5674 3.129502 CCTCGGCCTCGACACGTA 61.130 66.667 0.00 0.00 40.88 3.57
591 5711 2.287644 TCATGTGTTTTGCTCAGTGACG 59.712 45.455 0.00 0.00 0.00 4.35
610 5730 2.032634 GCCGGTTGCTTGTCGATCA 61.033 57.895 1.90 0.00 36.87 2.92
615 5735 3.365265 CAGGGCCGGTTGCTTGTC 61.365 66.667 1.90 0.00 40.92 3.18
670 5790 0.099082 GTTCTGTCTCTCGGCCGTAG 59.901 60.000 27.15 22.85 0.00 3.51
673 5793 2.182030 GGTTCTGTCTCTCGGCCG 59.818 66.667 22.12 22.12 0.00 6.13
678 5798 3.732471 GCGTAGATGTGGTTCTGTCTCTC 60.732 52.174 0.00 0.00 0.00 3.20
695 5815 2.388232 GCCGAGTTTGTGGGCGTAG 61.388 63.158 0.00 0.00 40.69 3.51
731 5851 0.743345 GTCATCTACGCCCACAACCC 60.743 60.000 0.00 0.00 0.00 4.11
733 5853 1.641577 GAGTCATCTACGCCCACAAC 58.358 55.000 0.00 0.00 0.00 3.32
734 5854 0.172578 CGAGTCATCTACGCCCACAA 59.827 55.000 0.00 0.00 0.00 3.33
735 5855 0.678684 TCGAGTCATCTACGCCCACA 60.679 55.000 0.00 0.00 0.00 4.17
737 5857 2.265589 TATCGAGTCATCTACGCCCA 57.734 50.000 0.00 0.00 0.00 5.36
740 5860 6.035070 GGTAGTATATCGAGTCATCTACGC 57.965 45.833 0.00 0.00 0.00 4.42
871 5994 4.758251 CGACGTGGGCTCATGGCA 62.758 66.667 13.33 0.00 44.01 4.92
876 5999 2.197605 TGAACTCGACGTGGGCTCA 61.198 57.895 0.00 0.00 0.00 4.26
926 6071 0.852777 CCGATGGCTACGTTCGATTG 59.147 55.000 8.10 1.40 0.00 2.67
927 6072 0.874607 GCCGATGGCTACGTTCGATT 60.875 55.000 8.10 0.00 46.69 3.34
974 6119 3.553765 GTGCGATCGATGCGTGCA 61.554 61.111 21.57 4.80 34.24 4.57
998 6143 2.027469 ACTTGTCCTAAAAGTAGCCGGG 60.027 50.000 2.18 0.00 36.11 5.73
1009 6179 5.246203 AGTCACAGCTGATAACTTGTCCTAA 59.754 40.000 23.35 0.00 0.00 2.69
1013 6183 4.151335 CACAGTCACAGCTGATAACTTGTC 59.849 45.833 23.35 4.79 39.62 3.18
1021 6191 2.673326 CGTGATCACAGTCACAGCTGAT 60.673 50.000 24.93 0.00 46.89 2.90
1026 6196 3.560902 ACTACGTGATCACAGTCACAG 57.439 47.619 24.93 17.71 46.89 3.66
1027 6197 3.816523 TGTACTACGTGATCACAGTCACA 59.183 43.478 24.93 20.45 46.89 3.58
1028 6198 4.404324 CTGTACTACGTGATCACAGTCAC 58.596 47.826 24.93 18.72 43.90 3.67
1029 6199 3.439129 CCTGTACTACGTGATCACAGTCA 59.561 47.826 24.93 17.53 35.85 3.41
1030 6200 3.181499 CCCTGTACTACGTGATCACAGTC 60.181 52.174 24.93 14.64 35.85 3.51
1031 6201 2.753452 CCCTGTACTACGTGATCACAGT 59.247 50.000 24.93 21.83 35.85 3.55
1069 6240 2.158234 AGCCCTATAGCTAGCTCCTTGT 60.158 50.000 23.26 6.14 42.70 3.16
1070 6241 2.534990 AGCCCTATAGCTAGCTCCTTG 58.465 52.381 23.26 10.79 42.70 3.61
1078 6251 1.616187 CGGTGGCTAGCCCTATAGCTA 60.616 57.143 30.81 6.69 46.10 3.32
1079 6252 0.900647 CGGTGGCTAGCCCTATAGCT 60.901 60.000 30.81 0.00 46.10 3.32
1080 6253 1.592223 CGGTGGCTAGCCCTATAGC 59.408 63.158 30.81 19.70 46.13 2.97
1081 6254 1.889530 GCCGGTGGCTAGCCCTATAG 61.890 65.000 30.81 16.24 46.69 1.31
1082 6255 1.911766 GCCGGTGGCTAGCCCTATA 60.912 63.158 30.81 9.60 46.69 1.31
1083 6256 3.242291 GCCGGTGGCTAGCCCTAT 61.242 66.667 30.81 0.00 46.69 2.57
1181 6382 0.598065 GCAGCGTGGGTTTCTTGATT 59.402 50.000 0.00 0.00 0.00 2.57
1266 6476 2.418910 CCATCTCCCAGTCGCGAGT 61.419 63.158 10.24 10.93 0.00 4.18
1550 6790 1.842562 CCATGGTGAGAAGTGGAGGAT 59.157 52.381 2.57 0.00 33.53 3.24
1558 6798 0.178767 TGGATCGCCATGGTGAGAAG 59.821 55.000 30.38 8.35 39.92 2.85
1559 6799 2.295904 TGGATCGCCATGGTGAGAA 58.704 52.632 30.38 16.84 39.92 2.87
1560 6800 4.048696 TGGATCGCCATGGTGAGA 57.951 55.556 30.38 19.23 39.92 3.27
1571 6817 1.660575 GGTGACGGCGTATGGATCG 60.661 63.158 14.74 0.00 0.00 3.69
1751 7015 3.699538 ACATGAGTATGTTGAGCCGTCTA 59.300 43.478 0.00 0.00 45.01 2.59
1753 7017 2.893637 ACATGAGTATGTTGAGCCGTC 58.106 47.619 0.00 0.00 45.01 4.79
1784 7064 1.151668 CAGCAGTGCCAAGTGTAGTC 58.848 55.000 12.58 0.00 0.00 2.59
1785 7065 0.250467 CCAGCAGTGCCAAGTGTAGT 60.250 55.000 12.58 0.00 0.00 2.73
1786 7066 0.250467 ACCAGCAGTGCCAAGTGTAG 60.250 55.000 12.58 0.00 0.00 2.74
1989 7323 8.986929 ATCAACCAAATTTGTTGGGAAATAAA 57.013 26.923 22.19 9.65 43.71 1.40
1990 7324 8.986929 AATCAACCAAATTTGTTGGGAAATAA 57.013 26.923 22.19 10.11 43.71 1.40
1992 7326 9.585369 AATAATCAACCAAATTTGTTGGGAAAT 57.415 25.926 22.19 12.43 43.71 2.17
1993 7327 8.986929 AATAATCAACCAAATTTGTTGGGAAA 57.013 26.923 22.19 11.27 43.71 3.13
1994 7328 8.213679 TGAATAATCAACCAAATTTGTTGGGAA 58.786 29.630 22.19 13.68 43.71 3.97
1995 7329 7.739825 TGAATAATCAACCAAATTTGTTGGGA 58.260 30.769 22.19 13.76 43.71 4.37
1996 7330 7.976135 TGAATAATCAACCAAATTTGTTGGG 57.024 32.000 22.19 10.68 43.71 4.12
2604 7942 4.574013 CAGATCAGGTTCACTAATTCCAGC 59.426 45.833 0.00 0.00 0.00 4.85
2764 8102 1.153881 GTGGGAGTAACGCGAGGTC 60.154 63.158 15.93 3.30 0.00 3.85
2786 8124 0.535797 CTAAGGTTCCCCTCGTGTCC 59.464 60.000 0.00 0.00 41.56 4.02
2884 8225 0.178975 TTTCCCCATCGCCACTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
2885 8226 0.609131 CTTTCCCCATCGCCACTGTT 60.609 55.000 0.00 0.00 0.00 3.16
2928 8269 0.029035 GCTGCATCTGCCTTGAATCG 59.971 55.000 0.00 0.00 41.18 3.34
2964 8305 0.474660 ACAACTCTGAGGGAGGGCTT 60.475 55.000 9.85 0.00 45.83 4.35


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

AutoCloner maintained by Alex Coulton.