Multiple sequence alignment - TraesCS1A01G414700

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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 TraesCS1A01G414700 chr1A 100.000 1739 0 0 1 1739 573945782 573944044 0.000000e+00 3212.0
1 TraesCS1A01G414700 chr1A 100.000 1292 0 0 2133 3424 573943650 573942359 0.000000e+00 2386.0
2 TraesCS1A01G414700 chr1A 88.859 1104 41 32 634 1703 573931763 573930708 0.000000e+00 1282.0
3 TraesCS1A01G414700 chr1A 80.465 430 44 20 1 391 573932590 573932162 3.340000e-75 292.0
4 TraesCS1A01G414700 chr1D 90.696 1279 46 30 484 1703 477501099 477499835 0.000000e+00 1635.0
5 TraesCS1A01G414700 chr1D 93.494 707 45 1 2719 3424 66975062 66974356 0.000000e+00 1050.0
6 TraesCS1A01G414700 chr1D 93.617 329 12 6 2401 2720 477499055 477498727 1.850000e-132 483.0
7 TraesCS1A01G414700 chr1D 92.254 284 15 2 2133 2409 477499686 477499403 2.480000e-106 396.0
8 TraesCS1A01G414700 chr1D 92.793 111 8 0 1464 1574 217006899 217006789 9.830000e-36 161.0
9 TraesCS1A01G414700 chr1D 91.892 111 9 0 1464 1574 4732012 4731902 4.580000e-34 156.0
10 TraesCS1A01G414700 chr1B 88.290 1281 78 29 484 1704 665100689 665099421 0.000000e+00 1469.0
11 TraesCS1A01G414700 chr1B 92.818 181 13 0 2134 2314 665099296 665099116 2.620000e-66 263.0
12 TraesCS1A01G414700 chr1B 97.222 36 1 0 1704 1739 665099326 665099291 1.030000e-05 62.1
13 TraesCS1A01G414700 chr7A 94.618 706 38 0 2719 3424 188535064 188534359 0.000000e+00 1094.0
14 TraesCS1A01G414700 chr3D 93.909 706 42 1 2719 3423 240552591 240553296 0.000000e+00 1064.0
15 TraesCS1A01G414700 chr3D 87.302 63 4 3 2655 2717 340437371 340437429 6.130000e-08 69.4
16 TraesCS1A01G414700 chr2B 93.777 707 41 3 2719 3424 622894769 622895473 0.000000e+00 1059.0
17 TraesCS1A01G414700 chr2B 90.145 345 25 5 1160 1504 682193753 682194088 1.130000e-119 440.0
18 TraesCS1A01G414700 chr2B 92.857 112 8 0 1463 1574 468442190 468442301 2.730000e-36 163.0
19 TraesCS1A01G414700 chr2D 93.201 706 47 1 2719 3424 216016887 216016183 0.000000e+00 1037.0
20 TraesCS1A01G414700 chr2D 94.595 111 6 0 1464 1574 469198587 469198477 4.540000e-39 172.0
21 TraesCS1A01G414700 chr2D 93.694 111 7 0 1464 1574 427532726 427532836 2.110000e-37 167.0
22 TraesCS1A01G414700 chr2D 93.694 111 7 0 1464 1574 427537281 427537171 2.110000e-37 167.0
23 TraesCS1A01G414700 chr4A 92.978 712 46 2 2713 3424 154487749 154488456 0.000000e+00 1035.0
24 TraesCS1A01G414700 chr4A 90.385 52 5 0 1259 1310 589487645 589487594 6.130000e-08 69.4
25 TraesCS1A01G414700 chr5A 92.837 712 51 0 2713 3424 86868136 86868847 0.000000e+00 1033.0
26 TraesCS1A01G414700 chr5A 93.069 707 46 2 2719 3424 103382127 103381423 0.000000e+00 1031.0
27 TraesCS1A01G414700 chr3A 92.717 714 50 2 2713 3424 103646404 103645691 0.000000e+00 1029.0
28 TraesCS1A01G414700 chr3A 87.500 64 8 0 2657 2720 654060214 654060277 1.320000e-09 75.0
29 TraesCS1A01G414700 chr3A 90.385 52 5 0 1259 1310 556991664 556991715 6.130000e-08 69.4
30 TraesCS1A01G414700 chr3B 93.750 112 7 0 1463 1574 708607153 708607042 5.880000e-38 169.0
31 TraesCS1A01G414700 chr7B 89.231 65 5 2 2654 2717 120724044 120724107 2.830000e-11 80.5
32 TraesCS1A01G414700 chr5D 86.765 68 9 0 2653 2720 141425267 141425334 3.660000e-10 76.8
33 TraesCS1A01G414700 chr5D 100.000 32 0 0 2653 2684 486452197 486452228 3.690000e-05 60.2
34 TraesCS1A01G414700 chrUn 84.848 66 10 0 2653 2718 129566893 129566828 2.210000e-07 67.6
35 TraesCS1A01G414700 chr5B 85.938 64 5 4 2656 2717 573432281 573432342 7.930000e-07 65.8
36 TraesCS1A01G414700 chr6B 84.127 63 10 0 2654 2716 512252966 512253028 1.030000e-05 62.1
37 TraesCS1A01G414700 chr6B 81.818 66 10 2 2653 2717 574427906 574427970 2.000000e-03 54.7
38 TraesCS1A01G414700 chr7D 100.000 30 0 0 2612 2641 567516648 567516619 4.770000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G414700 chr1A 573942359 573945782 3423 True 2799.000000 3212 100.000000 1 3424 2 chr1A.!!$R2 3423
1 TraesCS1A01G414700 chr1A 573930708 573932590 1882 True 787.000000 1282 84.662000 1 1703 2 chr1A.!!$R1 1702
2 TraesCS1A01G414700 chr1D 66974356 66975062 706 True 1050.000000 1050 93.494000 2719 3424 1 chr1D.!!$R2 705
3 TraesCS1A01G414700 chr1D 477498727 477501099 2372 True 838.000000 1635 92.189000 484 2720 3 chr1D.!!$R4 2236
4 TraesCS1A01G414700 chr1B 665099116 665100689 1573 True 598.033333 1469 92.776667 484 2314 3 chr1B.!!$R1 1830
5 TraesCS1A01G414700 chr7A 188534359 188535064 705 True 1094.000000 1094 94.618000 2719 3424 1 chr7A.!!$R1 705
6 TraesCS1A01G414700 chr3D 240552591 240553296 705 False 1064.000000 1064 93.909000 2719 3423 1 chr3D.!!$F1 704
7 TraesCS1A01G414700 chr2B 622894769 622895473 704 False 1059.000000 1059 93.777000 2719 3424 1 chr2B.!!$F2 705
8 TraesCS1A01G414700 chr2D 216016183 216016887 704 True 1037.000000 1037 93.201000 2719 3424 1 chr2D.!!$R1 705
9 TraesCS1A01G414700 chr4A 154487749 154488456 707 False 1035.000000 1035 92.978000 2713 3424 1 chr4A.!!$F1 711
10 TraesCS1A01G414700 chr5A 86868136 86868847 711 False 1033.000000 1033 92.837000 2713 3424 1 chr5A.!!$F1 711
11 TraesCS1A01G414700 chr5A 103381423 103382127 704 True 1031.000000 1031 93.069000 2719 3424 1 chr5A.!!$R1 705
12 TraesCS1A01G414700 chr3A 103645691 103646404 713 True 1029.000000 1029 92.717000 2713 3424 1 chr3A.!!$R1 711

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
442 481 0.031178 CAGGAGTGCAAACAACAGCC 59.969 55.0 0.00 0.0 0.0 4.85 F
468 513 0.320508 GACTCCGACACCTCAAACCC 60.321 60.0 0.00 0.0 0.0 4.11 F
747 978 0.588252 GACGTTCAACACTGCTGCAT 59.412 50.0 1.31 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2763 2.345641 CGAGCTTTTCCAGTCATACACG 59.654 50.000 0.00 0.00 0.00 4.49 R
2364 2768 3.914426 ATACCGAGCTTTTCCAGTCAT 57.086 42.857 0.00 0.00 0.00 3.06 R
2660 3431 0.038526 AATCGTGACCGGTCAGTGAC 60.039 55.000 37.04 23.44 40.75 3.67 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
25 26 3.148026 GTACCTACGAGCAAGTTCCTC 57.852 52.381 0.00 0.00 0.00 3.71
26 27 0.896226 ACCTACGAGCAAGTTCCTCC 59.104 55.000 0.00 0.00 0.00 4.30
46 54 4.641396 TCCAACTTTCATCGTCAATGACT 58.359 39.130 11.92 0.00 44.14 3.41
68 76 2.193517 CACCCACCGACCACCAAA 59.806 61.111 0.00 0.00 0.00 3.28
69 77 1.896660 CACCCACCGACCACCAAAG 60.897 63.158 0.00 0.00 0.00 2.77
70 78 2.380285 ACCCACCGACCACCAAAGT 61.380 57.895 0.00 0.00 0.00 2.66
77 85 1.270625 CCGACCACCAAAGTAAGCTCA 60.271 52.381 0.00 0.00 0.00 4.26
81 89 1.798813 CCACCAAAGTAAGCTCACGTC 59.201 52.381 0.00 0.00 0.00 4.34
86 94 0.388649 AAGTAAGCTCACGTCTGCGG 60.389 55.000 4.00 0.00 43.45 5.69
87 95 1.805945 GTAAGCTCACGTCTGCGGG 60.806 63.158 0.00 0.00 44.11 6.13
88 96 3.001902 TAAGCTCACGTCTGCGGGG 62.002 63.158 0.00 0.00 42.74 5.73
115 140 2.360600 GCATGTACAACCCGGGCA 60.361 61.111 24.08 10.87 0.00 5.36
137 162 0.032267 GAGCATGGTACGCTAGGGAC 59.968 60.000 14.59 7.25 40.63 4.46
139 164 0.249489 GCATGGTACGCTAGGGACTG 60.249 60.000 14.59 4.49 41.52 3.51
150 175 2.392662 CTAGGGACTGGAGAGCAATGA 58.607 52.381 0.00 0.00 40.33 2.57
156 181 3.119291 GACTGGAGAGCAATGATACACG 58.881 50.000 0.00 0.00 0.00 4.49
170 195 6.570672 ATGATACACGTACGGATGAGTTAT 57.429 37.500 21.06 3.99 0.00 1.89
178 203 6.474427 CACGTACGGATGAGTTATGTATGTTT 59.526 38.462 21.06 0.00 34.09 2.83
193 218 2.177394 TGTTTTATGCAGGCAGTCGA 57.823 45.000 0.00 0.00 0.00 4.20
203 228 1.939934 CAGGCAGTCGACAACTTTTGA 59.060 47.619 19.50 0.00 35.45 2.69
214 239 7.444183 AGTCGACAACTTTTGATTGGAAATAGA 59.556 33.333 19.50 0.00 33.03 1.98
249 277 1.132453 GCCCCACTCGTAAAATTCAGC 59.868 52.381 0.00 0.00 0.00 4.26
250 278 1.743394 CCCCACTCGTAAAATTCAGCC 59.257 52.381 0.00 0.00 0.00 4.85
252 280 2.343101 CCACTCGTAAAATTCAGCCGA 58.657 47.619 0.00 0.00 0.00 5.54
253 281 2.739913 CCACTCGTAAAATTCAGCCGAA 59.260 45.455 0.00 0.00 35.05 4.30
254 282 3.374058 CCACTCGTAAAATTCAGCCGAAT 59.626 43.478 0.00 0.00 43.94 3.34
267 295 5.991328 TCAGCCGAATGAGATAATTTGTC 57.009 39.130 0.00 0.00 0.00 3.18
273 301 6.238103 GCCGAATGAGATAATTTGTCGAAAGA 60.238 38.462 0.00 0.00 38.16 2.52
291 319 6.042093 TCGAAAGATTATGTAAGGGCATCTCT 59.958 38.462 0.00 0.00 33.31 3.10
294 322 9.561069 GAAAGATTATGTAAGGGCATCTCTAAA 57.439 33.333 0.00 0.00 0.00 1.85
297 325 8.037758 AGATTATGTAAGGGCATCTCTAAATCG 58.962 37.037 0.00 0.00 30.33 3.34
306 334 4.545610 GCATCTCTAAATCGGACTCTCAG 58.454 47.826 0.00 0.00 0.00 3.35
309 337 5.105567 TCTCTAAATCGGACTCTCAGACT 57.894 43.478 0.00 0.00 0.00 3.24
311 339 2.663826 AAATCGGACTCTCAGACTGC 57.336 50.000 0.00 0.00 0.00 4.40
314 342 0.962855 TCGGACTCTCAGACTGCCTG 60.963 60.000 0.00 0.00 44.27 4.85
320 348 0.457443 TCTCAGACTGCCTGCATACG 59.543 55.000 0.00 0.00 42.62 3.06
328 356 0.174845 TGCCTGCATACGTACAGACC 59.825 55.000 13.27 6.03 35.90 3.85
329 357 0.174845 GCCTGCATACGTACAGACCA 59.825 55.000 13.27 0.00 35.90 4.02
350 389 2.037053 CGGTTTGCCATCCAACACA 58.963 52.632 0.00 0.00 31.97 3.72
352 391 0.318120 GGTTTGCCATCCAACACAGG 59.682 55.000 0.00 0.00 31.97 4.00
360 399 3.258123 GCCATCCAACACAGGTTTGTATT 59.742 43.478 0.00 0.00 35.25 1.89
364 403 6.128007 CCATCCAACACAGGTTTGTATTAGTC 60.128 42.308 0.00 0.00 35.25 2.59
367 406 5.334879 CCAACACAGGTTTGTATTAGTCTGC 60.335 44.000 0.00 0.00 35.25 4.26
369 408 4.202419 ACACAGGTTTGTATTAGTCTGCCA 60.202 41.667 0.00 0.00 35.25 4.92
373 412 3.756434 GGTTTGTATTAGTCTGCCAAGCA 59.244 43.478 0.00 0.00 36.92 3.91
385 424 1.090052 GCCAAGCAGTCCGGATGTAC 61.090 60.000 7.81 0.00 0.00 2.90
391 430 3.335579 AGCAGTCCGGATGTACTTTTTC 58.664 45.455 7.81 0.00 0.00 2.29
392 431 2.418976 GCAGTCCGGATGTACTTTTTCC 59.581 50.000 7.81 0.00 0.00 3.13
404 443 9.556030 GGATGTACTTTTTCCGAAAAATAAGAG 57.444 33.333 17.30 9.37 39.43 2.85
408 447 9.940166 GTACTTTTTCCGAAAAATAAGAGTCAA 57.060 29.630 17.30 0.00 39.43 3.18
410 449 9.297586 ACTTTTTCCGAAAAATAAGAGTCAAAC 57.702 29.630 17.30 0.00 39.43 2.93
411 450 9.296400 CTTTTTCCGAAAAATAAGAGTCAAACA 57.704 29.630 17.30 0.00 39.43 2.83
414 453 5.472137 TCCGAAAAATAAGAGTCAAACAGGG 59.528 40.000 0.00 0.00 0.00 4.45
416 455 5.240844 CGAAAAATAAGAGTCAAACAGGGGT 59.759 40.000 0.00 0.00 0.00 4.95
421 460 2.054799 AGAGTCAAACAGGGGTGCTTA 58.945 47.619 0.00 0.00 0.00 3.09
422 461 2.039084 AGAGTCAAACAGGGGTGCTTAG 59.961 50.000 0.00 0.00 0.00 2.18
424 463 0.476338 TCAAACAGGGGTGCTTAGCA 59.524 50.000 1.39 1.39 35.60 3.49
425 464 0.883833 CAAACAGGGGTGCTTAGCAG 59.116 55.000 7.34 0.00 40.08 4.24
430 469 1.078143 GGGGTGCTTAGCAGGAGTG 60.078 63.158 7.34 0.00 40.08 3.51
442 481 0.031178 CAGGAGTGCAAACAACAGCC 59.969 55.000 0.00 0.00 0.00 4.85
444 483 0.675633 GGAGTGCAAACAACAGCCAT 59.324 50.000 0.00 0.00 0.00 4.40
445 484 1.885887 GGAGTGCAAACAACAGCCATA 59.114 47.619 0.00 0.00 0.00 2.74
448 487 4.201950 GGAGTGCAAACAACAGCCATATAG 60.202 45.833 0.00 0.00 0.00 1.31
454 499 4.423625 AACAACAGCCATATAGGACTCC 57.576 45.455 0.00 0.00 41.22 3.85
461 506 2.877866 CCATATAGGACTCCGACACCT 58.122 52.381 0.00 0.00 41.22 4.00
462 507 2.820787 CCATATAGGACTCCGACACCTC 59.179 54.545 0.00 0.00 41.22 3.85
463 508 3.487372 CATATAGGACTCCGACACCTCA 58.513 50.000 0.00 0.00 35.52 3.86
464 509 2.526888 ATAGGACTCCGACACCTCAA 57.473 50.000 0.00 0.00 35.52 3.02
465 510 2.297698 TAGGACTCCGACACCTCAAA 57.702 50.000 0.00 0.00 35.52 2.69
468 513 0.320508 GACTCCGACACCTCAAACCC 60.321 60.000 0.00 0.00 0.00 4.11
478 523 1.007842 ACCTCAAACCCACCCAAAACT 59.992 47.619 0.00 0.00 0.00 2.66
479 524 1.686587 CCTCAAACCCACCCAAAACTC 59.313 52.381 0.00 0.00 0.00 3.01
480 525 2.383855 CTCAAACCCACCCAAAACTCA 58.616 47.619 0.00 0.00 0.00 3.41
481 526 2.362077 CTCAAACCCACCCAAAACTCAG 59.638 50.000 0.00 0.00 0.00 3.35
482 527 1.412343 CAAACCCACCCAAAACTCAGG 59.588 52.381 0.00 0.00 0.00 3.86
556 632 1.280457 GGCTGGAGGAAGAGGAAGAA 58.720 55.000 0.00 0.00 0.00 2.52
558 635 2.355615 GGCTGGAGGAAGAGGAAGAAAG 60.356 54.545 0.00 0.00 0.00 2.62
636 842 1.518903 GCAAACTCCACTGGTCAGCC 61.519 60.000 0.00 0.00 0.00 4.85
641 847 1.892819 CTCCACTGGTCAGCCGTCAT 61.893 60.000 0.00 0.00 37.67 3.06
691 901 6.876760 GTGAAGCAACGGAATCTTCAACCG 62.877 50.000 11.37 0.00 45.09 4.44
740 971 4.810790 CCATCTTCTAGACGTTCAACACT 58.189 43.478 0.00 0.00 0.00 3.55
741 972 4.623167 CCATCTTCTAGACGTTCAACACTG 59.377 45.833 0.00 0.00 0.00 3.66
742 973 3.639538 TCTTCTAGACGTTCAACACTGC 58.360 45.455 0.00 0.00 0.00 4.40
743 974 3.318275 TCTTCTAGACGTTCAACACTGCT 59.682 43.478 0.00 0.00 0.00 4.24
744 975 3.013276 TCTAGACGTTCAACACTGCTG 57.987 47.619 0.00 0.00 0.00 4.41
745 976 1.457303 CTAGACGTTCAACACTGCTGC 59.543 52.381 0.00 0.00 0.00 5.25
747 978 0.588252 GACGTTCAACACTGCTGCAT 59.412 50.000 1.31 0.00 0.00 3.96
754 993 4.916983 TCAACACTGCTGCATTTTACTT 57.083 36.364 1.31 0.00 0.00 2.24
841 1104 1.302949 TGGGCTATCCACAGCAACC 59.697 57.895 0.00 0.00 43.67 3.77
844 1107 1.032114 GGCTATCCACAGCAACCCAC 61.032 60.000 0.00 0.00 43.67 4.61
845 1108 1.369091 GCTATCCACAGCAACCCACG 61.369 60.000 0.00 0.00 41.40 4.94
846 1109 1.369091 CTATCCACAGCAACCCACGC 61.369 60.000 0.00 0.00 0.00 5.34
847 1110 2.813226 TATCCACAGCAACCCACGCC 62.813 60.000 0.00 0.00 0.00 5.68
902 1165 0.665835 GTGAATTCAACGTGGCCACA 59.334 50.000 34.16 16.07 0.00 4.17
1005 1286 3.252284 CTCCCCGCCCCTGCATAT 61.252 66.667 0.00 0.00 37.32 1.78
1034 1315 2.562912 CGGCATCGCACTTTGCTT 59.437 55.556 0.00 0.00 42.25 3.91
1078 1359 2.358615 CCAGCACCTACGCAAGCA 60.359 61.111 0.00 0.00 45.62 3.91
1080 1361 1.499056 CAGCACCTACGCAAGCAAG 59.501 57.895 0.00 0.00 45.62 4.01
1082 1363 0.671781 AGCACCTACGCAAGCAAGAG 60.672 55.000 0.00 0.00 45.62 2.85
1094 1386 3.736126 GCAAGCAAGAGACAAGCAAACTT 60.736 43.478 0.00 0.00 36.19 2.66
1204 1505 2.267961 GTGGAGGCGTTCCCGATT 59.732 61.111 5.77 0.00 46.19 3.34
1732 2132 5.120830 CGAGGTTTTTCAAGATGATCGTCTT 59.879 40.000 22.07 22.07 38.95 3.01
2187 2587 3.737172 GCGGCGGCACTGTTCATT 61.737 61.111 9.78 0.00 39.62 2.57
2193 2593 1.535462 GCGGCACTGTTCATTAGTTGT 59.465 47.619 0.00 0.00 0.00 3.32
2208 2608 8.752766 TCATTAGTTGTACTGTAGTAACTTGC 57.247 34.615 17.35 0.00 31.52 4.01
2228 2628 7.743104 ACTTGCTGTAAGAATTGTAGAAATCG 58.257 34.615 12.54 0.00 39.76 3.34
2343 2743 2.233922 AGTCGAATGGTCCAACTACAGG 59.766 50.000 0.00 0.00 0.00 4.00
2344 2744 2.232941 GTCGAATGGTCCAACTACAGGA 59.767 50.000 0.00 0.00 0.00 3.86
2356 2760 7.365295 GGTCCAACTACAGGATAATAACAGGAA 60.365 40.741 0.00 0.00 37.52 3.36
2359 2763 6.176014 ACTACAGGATAATAACAGGAAGGC 57.824 41.667 0.00 0.00 0.00 4.35
2364 2768 4.652421 AGGATAATAACAGGAAGGCGTGTA 59.348 41.667 0.00 0.00 41.86 2.90
2392 2799 3.606687 GAAAAGCTCGGTATTCTTCCCA 58.393 45.455 0.00 0.00 0.00 4.37
2481 3244 0.036164 CGTGGTCCCTTCCATGTCAA 59.964 55.000 0.00 0.00 39.81 3.18
2484 3247 1.305930 GGTCCCTTCCATGTCAACGC 61.306 60.000 0.00 0.00 0.00 4.84
2486 3249 0.327924 TCCCTTCCATGTCAACGCAT 59.672 50.000 0.00 0.00 0.00 4.73
2651 3414 3.287222 CGCCCCAAATCCTTCTCAAATA 58.713 45.455 0.00 0.00 0.00 1.40
2660 3431 0.814010 CTTCTCAAATACCCGCCCGG 60.814 60.000 0.00 0.00 37.81 5.73
2664 3435 2.110352 CAAATACCCGCCCGGTCAC 61.110 63.158 0.00 0.00 43.58 3.67
2667 3438 3.968837 ATACCCGCCCGGTCACTGA 62.969 63.158 0.00 0.00 43.58 3.41
2683 3454 2.096417 CACTGACCGGTCACGATTTTTC 60.096 50.000 33.23 4.24 44.60 2.29
2688 3459 2.224209 ACCGGTCACGATTTTTCTGTCT 60.224 45.455 0.00 0.00 44.60 3.41
2689 3460 3.006110 ACCGGTCACGATTTTTCTGTCTA 59.994 43.478 0.00 0.00 44.60 2.59
2693 3464 5.227908 GGTCACGATTTTTCTGTCTAGACA 58.772 41.667 23.80 23.80 39.32 3.41
2822 3593 2.621338 GAGATCATGACGGTGCTTTGA 58.379 47.619 0.00 0.00 0.00 2.69
2844 3615 4.038271 AGATGGAGATCAAAGGCACAAA 57.962 40.909 0.00 0.00 0.00 2.83
2861 3632 5.047164 GGCACAAAATGATGATGGCCATATA 60.047 40.000 20.84 11.71 36.38 0.86
2866 3637 8.092068 ACAAAATGATGATGGCCATATAATGTG 58.908 33.333 20.84 12.51 35.17 3.21
2967 3739 9.823647 TGATCTCTCACTAAATTTCAAGGTATC 57.176 33.333 0.00 0.00 0.00 2.24
3045 3817 3.134623 TGATGATCGGGTGTGATAAGCTT 59.865 43.478 3.48 3.48 0.00 3.74
3243 4016 1.748493 TCACGTGATGATCGGACATGA 59.252 47.619 15.76 0.00 29.99 3.07
3251 4024 6.346120 CGTGATGATCGGACATGATTTAGTTC 60.346 42.308 0.00 0.00 0.00 3.01
3268 4041 8.908786 ATTTAGTTCATATGGATCACGTGATT 57.091 30.769 30.46 18.14 34.37 2.57
3285 4058 9.338622 TCACGTGATTATTTAGATGACTAGAGA 57.661 33.333 15.76 0.00 0.00 3.10
3370 4145 6.963049 ACTTAGTACCTGATAGTTTTTGCG 57.037 37.500 0.00 0.00 0.00 4.85
3397 4172 6.413892 TCTATGTTGTTGTAGATCAATGGCA 58.586 36.000 0.00 0.00 38.38 4.92
3398 4173 7.056006 TCTATGTTGTTGTAGATCAATGGCAT 58.944 34.615 0.00 0.00 38.38 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.869344 TCTAGTCATTGACGATGAAAGTTGG 59.131 40.000 11.01 0.00 45.96 3.77
26 27 6.454848 GCTCTAGTCATTGACGATGAAAGTTG 60.455 42.308 11.01 7.11 45.96 3.16
33 41 3.119291 GGTGCTCTAGTCATTGACGATG 58.881 50.000 11.01 5.91 37.67 3.84
46 54 2.118732 TGGTCGGTGGGTGCTCTA 59.881 61.111 0.00 0.00 0.00 2.43
68 76 1.213013 CCGCAGACGTGAGCTTACT 59.787 57.895 7.09 0.00 37.70 2.24
69 77 1.805945 CCCGCAGACGTGAGCTTAC 60.806 63.158 0.00 0.00 37.70 2.34
70 78 2.571757 CCCGCAGACGTGAGCTTA 59.428 61.111 0.00 0.00 37.70 3.09
86 94 1.093496 GTACATGCCCTAACGCACCC 61.093 60.000 0.00 0.00 42.70 4.61
87 95 0.391927 TGTACATGCCCTAACGCACC 60.392 55.000 0.00 0.00 42.70 5.01
88 96 1.129811 GTTGTACATGCCCTAACGCAC 59.870 52.381 0.00 0.00 42.70 5.34
115 140 0.747255 CCTAGCGTACCATGCTCAGT 59.253 55.000 0.00 0.00 40.15 3.41
123 148 0.395311 CTCCAGTCCCTAGCGTACCA 60.395 60.000 0.00 0.00 0.00 3.25
137 162 3.170791 ACGTGTATCATTGCTCTCCAG 57.829 47.619 0.00 0.00 0.00 3.86
139 164 3.043586 CGTACGTGTATCATTGCTCTCC 58.956 50.000 7.22 0.00 0.00 3.71
150 175 5.762825 ACATAACTCATCCGTACGTGTAT 57.237 39.130 15.21 1.81 0.00 2.29
170 195 3.373748 CGACTGCCTGCATAAAACATACA 59.626 43.478 0.00 0.00 0.00 2.29
178 203 1.001974 AGTTGTCGACTGCCTGCATAA 59.998 47.619 17.92 0.00 37.17 1.90
193 218 6.211384 CCCCTCTATTTCCAATCAAAAGTTGT 59.789 38.462 0.00 0.00 0.00 3.32
203 228 1.859574 CCCACCCCCTCTATTTCCAAT 59.140 52.381 0.00 0.00 0.00 3.16
249 277 7.234187 TCTTTCGACAAATTATCTCATTCGG 57.766 36.000 0.00 0.00 0.00 4.30
267 295 6.226787 AGAGATGCCCTTACATAATCTTTCG 58.773 40.000 0.00 0.00 0.00 3.46
273 301 7.038302 TCCGATTTAGAGATGCCCTTACATAAT 60.038 37.037 0.00 0.00 0.00 1.28
277 305 3.964688 TCCGATTTAGAGATGCCCTTACA 59.035 43.478 0.00 0.00 0.00 2.41
291 319 2.427453 GGCAGTCTGAGAGTCCGATTTA 59.573 50.000 3.32 0.00 0.00 1.40
294 322 0.033601 AGGCAGTCTGAGAGTCCGAT 60.034 55.000 3.32 0.00 0.00 4.18
295 323 0.962855 CAGGCAGTCTGAGAGTCCGA 60.963 60.000 3.32 0.00 46.18 4.55
297 325 1.217779 GCAGGCAGTCTGAGAGTCC 59.782 63.158 6.09 0.00 46.18 3.85
306 334 1.134367 TCTGTACGTATGCAGGCAGTC 59.866 52.381 11.91 0.00 38.95 3.51
309 337 0.174845 GGTCTGTACGTATGCAGGCA 59.825 55.000 16.71 0.00 44.30 4.75
311 339 1.797713 CGTGGTCTGTACGTATGCAGG 60.798 57.143 11.91 0.00 38.95 4.85
314 342 1.469126 CGCGTGGTCTGTACGTATGC 61.469 60.000 0.00 0.00 43.09 3.14
328 356 2.913765 TTGGATGGCAAACCGCGTG 61.914 57.895 4.92 0.00 43.84 5.34
329 357 2.596046 TTGGATGGCAAACCGCGT 60.596 55.556 4.92 0.00 43.84 6.01
350 389 4.010349 GCTTGGCAGACTAATACAAACCT 58.990 43.478 0.00 0.00 0.00 3.50
367 406 0.537188 AGTACATCCGGACTGCTTGG 59.463 55.000 6.12 0.00 0.00 3.61
369 408 3.418684 AAAAGTACATCCGGACTGCTT 57.581 42.857 6.12 7.44 0.00 3.91
385 424 9.296400 TGTTTGACTCTTATTTTTCGGAAAAAG 57.704 29.630 26.80 18.04 42.97 2.27
391 430 5.335661 CCCCTGTTTGACTCTTATTTTTCGG 60.336 44.000 0.00 0.00 0.00 4.30
392 431 5.240844 ACCCCTGTTTGACTCTTATTTTTCG 59.759 40.000 0.00 0.00 0.00 3.46
394 433 5.221441 GCACCCCTGTTTGACTCTTATTTTT 60.221 40.000 0.00 0.00 0.00 1.94
398 437 2.644798 AGCACCCCTGTTTGACTCTTAT 59.355 45.455 0.00 0.00 0.00 1.73
400 439 0.846693 AGCACCCCTGTTTGACTCTT 59.153 50.000 0.00 0.00 0.00 2.85
401 440 0.846693 AAGCACCCCTGTTTGACTCT 59.153 50.000 0.00 0.00 0.00 3.24
402 441 2.427506 CTAAGCACCCCTGTTTGACTC 58.572 52.381 0.00 0.00 0.00 3.36
403 442 1.545651 GCTAAGCACCCCTGTTTGACT 60.546 52.381 0.00 0.00 0.00 3.41
404 443 0.881796 GCTAAGCACCCCTGTTTGAC 59.118 55.000 0.00 0.00 0.00 3.18
405 444 0.476338 TGCTAAGCACCCCTGTTTGA 59.524 50.000 0.00 0.00 31.71 2.69
406 445 0.883833 CTGCTAAGCACCCCTGTTTG 59.116 55.000 0.00 0.00 33.79 2.93
408 447 1.133809 TCCTGCTAAGCACCCCTGTT 61.134 55.000 0.00 0.00 33.79 3.16
410 449 1.222936 CTCCTGCTAAGCACCCCTG 59.777 63.158 0.00 0.00 33.79 4.45
411 450 1.229658 ACTCCTGCTAAGCACCCCT 60.230 57.895 0.00 0.00 33.79 4.79
414 453 0.606401 TTGCACTCCTGCTAAGCACC 60.606 55.000 0.00 0.00 44.57 5.01
416 455 1.238439 GTTTGCACTCCTGCTAAGCA 58.762 50.000 0.00 0.00 44.57 3.91
421 460 1.027357 CTGTTGTTTGCACTCCTGCT 58.973 50.000 0.00 0.00 44.57 4.24
422 461 0.595825 GCTGTTGTTTGCACTCCTGC 60.596 55.000 0.00 0.00 44.52 4.85
424 463 0.395586 TGGCTGTTGTTTGCACTCCT 60.396 50.000 0.00 0.00 0.00 3.69
425 464 0.675633 ATGGCTGTTGTTTGCACTCC 59.324 50.000 0.00 0.00 0.00 3.85
430 469 3.947834 AGTCCTATATGGCTGTTGTTTGC 59.052 43.478 0.00 0.00 35.26 3.68
432 471 4.683400 CGGAGTCCTATATGGCTGTTGTTT 60.683 45.833 7.77 0.00 35.26 2.83
433 472 3.181465 CGGAGTCCTATATGGCTGTTGTT 60.181 47.826 7.77 0.00 35.26 2.83
442 481 3.487372 TGAGGTGTCGGAGTCCTATATG 58.513 50.000 7.77 0.00 0.00 1.78
444 483 3.657398 TTGAGGTGTCGGAGTCCTATA 57.343 47.619 7.77 0.00 0.00 1.31
445 484 2.496470 GTTTGAGGTGTCGGAGTCCTAT 59.504 50.000 7.77 0.00 0.00 2.57
448 487 0.320508 GGTTTGAGGTGTCGGAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
454 499 1.599797 GGGTGGGTTTGAGGTGTCG 60.600 63.158 0.00 0.00 0.00 4.35
461 506 2.383855 CTGAGTTTTGGGTGGGTTTGA 58.616 47.619 0.00 0.00 0.00 2.69
462 507 1.412343 CCTGAGTTTTGGGTGGGTTTG 59.588 52.381 0.00 0.00 0.00 2.93
463 508 1.007842 ACCTGAGTTTTGGGTGGGTTT 59.992 47.619 0.00 0.00 31.48 3.27
464 509 0.634465 ACCTGAGTTTTGGGTGGGTT 59.366 50.000 0.00 0.00 31.48 4.11
465 510 0.634465 AACCTGAGTTTTGGGTGGGT 59.366 50.000 0.00 0.00 33.20 4.51
468 513 1.338020 GCTCAACCTGAGTTTTGGGTG 59.662 52.381 5.61 0.00 45.94 4.61
478 523 1.001764 CCCATGCAGCTCAACCTGA 60.002 57.895 0.00 0.00 34.77 3.86
479 524 1.001764 TCCCATGCAGCTCAACCTG 60.002 57.895 0.00 0.00 35.93 4.00
480 525 1.001641 GTCCCATGCAGCTCAACCT 60.002 57.895 0.00 0.00 0.00 3.50
481 526 0.895100 TTGTCCCATGCAGCTCAACC 60.895 55.000 0.00 0.00 0.00 3.77
482 527 0.242017 GTTGTCCCATGCAGCTCAAC 59.758 55.000 0.00 0.07 0.00 3.18
489 559 1.963855 CGAACCGTTGTCCCATGCA 60.964 57.895 0.00 0.00 0.00 3.96
531 602 1.306141 TCTTCCTCCAGCCCGTCAT 60.306 57.895 0.00 0.00 0.00 3.06
556 632 9.859152 TTTTTATTTCAATCACATTTTCCCCTT 57.141 25.926 0.00 0.00 0.00 3.95
586 665 5.064707 GCAACTATTTCTCAATCGCCTAACA 59.935 40.000 0.00 0.00 0.00 2.41
636 842 4.701361 CACTTGTGTGTGTTGATATGACG 58.299 43.478 0.00 0.00 39.24 4.35
641 847 6.625873 TTAATGCACTTGTGTGTGTTGATA 57.374 33.333 0.00 0.00 45.44 2.15
691 901 4.363999 CTGGATGGATGACTAAACTCGTC 58.636 47.826 0.00 0.00 0.00 4.20
740 971 5.125900 AGCATATCACAAGTAAAATGCAGCA 59.874 36.000 0.00 0.00 41.61 4.41
741 972 5.457799 CAGCATATCACAAGTAAAATGCAGC 59.542 40.000 7.73 0.00 41.61 5.25
742 973 5.975344 CCAGCATATCACAAGTAAAATGCAG 59.025 40.000 7.73 0.00 41.61 4.41
743 974 5.679382 GCCAGCATATCACAAGTAAAATGCA 60.679 40.000 7.73 0.00 41.61 3.96
744 975 4.741676 GCCAGCATATCACAAGTAAAATGC 59.258 41.667 0.00 0.00 39.93 3.56
745 976 5.163530 TGGCCAGCATATCACAAGTAAAATG 60.164 40.000 0.00 0.00 0.00 2.32
747 978 4.339748 TGGCCAGCATATCACAAGTAAAA 58.660 39.130 0.00 0.00 0.00 1.52
754 993 0.106619 TGCATGGCCAGCATATCACA 60.107 50.000 21.35 4.63 37.02 3.58
844 1107 4.988598 ACTTGGTGGTGCTCGGCG 62.989 66.667 0.00 0.00 0.00 6.46
845 1108 3.050275 GACTTGGTGGTGCTCGGC 61.050 66.667 0.00 0.00 0.00 5.54
846 1109 1.961277 GTGACTTGGTGGTGCTCGG 60.961 63.158 0.00 0.00 0.00 4.63
847 1110 1.961277 GGTGACTTGGTGGTGCTCG 60.961 63.158 0.00 0.00 0.00 5.03
848 1111 0.465460 TTGGTGACTTGGTGGTGCTC 60.465 55.000 0.00 0.00 0.00 4.26
1005 1286 3.768185 GATGCCGGCTCGCGTCTTA 62.768 63.158 29.70 3.35 40.87 2.10
1034 1315 2.054021 TGAGAGTTTGGTGGTGGATGA 58.946 47.619 0.00 0.00 0.00 2.92
1078 1359 3.372025 AGGGTCAAGTTTGCTTGTCTCTT 60.372 43.478 7.15 0.00 44.95 2.85
1204 1505 3.494254 ACGCCCTTGGTGAACCCA 61.494 61.111 0.00 0.00 43.27 4.51
1688 1989 4.659172 TCAGCAACCGCCTTGGGG 62.659 66.667 0.00 0.00 44.64 4.96
2174 2574 3.994392 AGTACAACTAATGAACAGTGCCG 59.006 43.478 0.00 0.00 0.00 5.69
2182 2582 9.199982 GCAAGTTACTACAGTACAACTAATGAA 57.800 33.333 0.00 0.00 29.51 2.57
2187 2587 7.281040 ACAGCAAGTTACTACAGTACAACTA 57.719 36.000 0.00 0.00 29.51 2.24
2193 2593 9.419297 CAATTCTTACAGCAAGTTACTACAGTA 57.581 33.333 0.00 0.00 35.58 2.74
2208 2608 8.759641 CAGGATCGATTTCTACAATTCTTACAG 58.240 37.037 0.00 0.00 0.00 2.74
2228 2628 6.500684 TGTTTGAACAGCTTAATCAGGATC 57.499 37.500 0.00 0.00 34.30 3.36
2343 2743 6.145696 GTCATACACGCCTTCCTGTTATTATC 59.854 42.308 0.00 0.00 0.00 1.75
2344 2744 5.989777 GTCATACACGCCTTCCTGTTATTAT 59.010 40.000 0.00 0.00 0.00 1.28
2356 2760 2.699954 CTTTTCCAGTCATACACGCCT 58.300 47.619 0.00 0.00 0.00 5.52
2359 2763 2.345641 CGAGCTTTTCCAGTCATACACG 59.654 50.000 0.00 0.00 0.00 4.49
2364 2768 3.914426 ATACCGAGCTTTTCCAGTCAT 57.086 42.857 0.00 0.00 0.00 3.06
2392 2799 5.070770 TGCTCTGTTTTTGTCAAACACAT 57.929 34.783 15.72 0.00 35.45 3.21
2660 3431 0.038526 AATCGTGACCGGTCAGTGAC 60.039 55.000 37.04 23.44 40.75 3.67
2664 3435 2.157668 CAGAAAAATCGTGACCGGTCAG 59.842 50.000 37.04 27.77 40.75 3.51
2667 3438 2.140717 GACAGAAAAATCGTGACCGGT 58.859 47.619 6.92 6.92 33.95 5.28
2688 3459 3.006967 GGCCTGTTTGAGAAGTCTGTCTA 59.993 47.826 0.00 0.00 0.00 2.59
2689 3460 2.224402 GGCCTGTTTGAGAAGTCTGTCT 60.224 50.000 0.00 0.00 0.00 3.41
2693 3464 2.050144 TGAGGCCTGTTTGAGAAGTCT 58.950 47.619 12.00 0.00 0.00 3.24
2742 3513 3.441163 CACGACTATTGCTACCGCTTAA 58.559 45.455 0.00 0.00 36.97 1.85
2754 3525 4.876107 CCAACTATTGCTTCCACGACTATT 59.124 41.667 0.00 0.00 0.00 1.73
2822 3593 3.726557 TGTGCCTTTGATCTCCATCTT 57.273 42.857 0.00 0.00 0.00 2.40
2844 3615 6.949463 TGTCACATTATATGGCCATCATCATT 59.051 34.615 24.80 0.00 37.30 2.57
2861 3632 8.035984 TCACATGCAATCAAAATATGTCACATT 58.964 29.630 0.00 0.00 30.15 2.71
2866 3637 7.997107 ACATCACATGCAATCAAAATATGTC 57.003 32.000 0.00 0.00 30.15 3.06
2913 3684 1.299697 GCTACCGCCGTACTAAGCC 60.300 63.158 0.00 0.00 0.00 4.35
3045 3817 3.058450 CACCCGTTGTATGTGAACGTAA 58.942 45.455 0.00 0.00 43.70 3.18
3243 4016 8.908786 AATCACGTGATCCATATGAACTAAAT 57.091 30.769 30.06 6.94 32.75 1.40
3285 4058 8.602472 AAGAACTTCCACTTAGATAGACATCT 57.398 34.615 0.00 0.00 44.04 2.90
3370 4145 8.499162 GCCATTGATCTACAACAACATAGATAC 58.501 37.037 0.00 0.00 41.52 2.24
3397 4172 0.981183 TCAAGGGAACGGTAGCACAT 59.019 50.000 0.00 0.00 0.00 3.21
3398 4173 0.759959 TTCAAGGGAACGGTAGCACA 59.240 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.