Multiple sequence alignment - TraesCS1B01G212500

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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 TraesCS1B01G212500 chr1B 100.000 3917 0 0 1 3917 386158370 386162286 0.000000e+00 7234.0
1 TraesCS1B01G212500 chr1A 95.814 2413 87 8 1335 3735 355714964 355717374 0.000000e+00 3884.0
2 TraesCS1B01G212500 chr1A 92.614 677 29 10 669 1335 355714260 355714925 0.000000e+00 953.0
3 TraesCS1B01G212500 chr1A 84.289 471 68 4 1 467 355713244 355713712 4.610000e-124 455.0
4 TraesCS1B01G212500 chr1A 90.000 80 1 2 3838 3917 355718074 355718146 3.220000e-16 97.1
5 TraesCS1B01G212500 chr1D 94.013 1854 74 21 669 2489 284239223 284241072 0.000000e+00 2774.0
6 TraesCS1B01G212500 chr1D 94.983 877 29 5 2480 3348 284241255 284242124 0.000000e+00 1362.0
7 TraesCS1B01G212500 chr1D 91.031 223 8 7 3406 3626 284242129 284242341 1.380000e-74 291.0
8 TraesCS1B01G212500 chr2B 97.619 42 1 0 3627 3668 584477787 584477828 5.430000e-09 73.1
9 TraesCS1B01G212500 chr6B 97.500 40 1 0 3629 3668 577172238 577172277 7.020000e-08 69.4
10 TraesCS1B01G212500 chr2D 100.000 30 0 0 3339 3368 181601882 181601911 5.470000e-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 TraesCS1B01G212500 chr1B 386158370 386162286 3916 False 7234.000000 7234 100.000000 1 3917 1 chr1B.!!$F1 3916
1 TraesCS1B01G212500 chr1A 355713244 355718146 4902 False 1347.275000 3884 90.679250 1 3917 4 chr1A.!!$F1 3916
2 TraesCS1B01G212500 chr1D 284239223 284242341 3118 False 1475.666667 2774 93.342333 669 3626 3 chr1D.!!$F1 2957

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
252 253 0.037790 GGTGATATCCGGCAGCTCTC 60.038 60.000 0.0 0.0 0.00 3.20 F
717 1069 0.398696 TGTAACCCGCTCACATGGTT 59.601 50.000 0.0 0.0 44.31 3.67 F
810 1163 1.202330 CTCAGCATCTCCACCTCCTT 58.798 55.000 0.0 0.0 0.00 3.36 F
908 1262 1.374252 CTTCCCCGAACCTCACACG 60.374 63.158 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2373 0.253327 AGCAGCTAAGGGCACTAACC 59.747 55.000 0.0 0.0 44.79 2.85 R
1961 2382 1.451028 GGTGGCTCAGCAGCTAAGG 60.451 63.158 0.0 0.0 46.03 2.69 R
2719 3336 1.525923 CTCCCCTCTGCATCCACAG 59.474 63.158 0.0 0.0 39.12 3.66 R
2927 3546 3.961480 AGAAACACAGACGATCCATCA 57.039 42.857 0.0 0.0 0.00 3.07 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
29 30 5.050499 GCTGGAATGATACTTTGAGATCACG 60.050 44.000 0.00 0.00 34.98 4.35
32 33 5.050499 GGAATGATACTTTGAGATCACGCAG 60.050 44.000 0.00 0.00 34.98 5.18
45 46 2.020720 TCACGCAGGTGTTGTCATTTT 58.979 42.857 0.00 0.00 44.68 1.82
67 68 4.179298 TCTCATCTTGTCGCTTCATTCAG 58.821 43.478 0.00 0.00 0.00 3.02
69 70 4.179298 TCATCTTGTCGCTTCATTCAGAG 58.821 43.478 0.00 0.00 0.00 3.35
86 87 2.297315 CAGAGATGTATGAGCGCCCTTA 59.703 50.000 2.29 0.00 0.00 2.69
88 89 3.388024 AGAGATGTATGAGCGCCCTTAAA 59.612 43.478 2.29 0.00 0.00 1.52
90 91 1.663695 TGTATGAGCGCCCTTAAAGC 58.336 50.000 2.29 0.00 0.00 3.51
99 100 0.107165 GCCCTTAAAGCGGAGATGGT 60.107 55.000 0.00 0.00 0.00 3.55
102 103 1.017387 CTTAAAGCGGAGATGGTGGC 58.983 55.000 0.00 0.00 0.00 5.01
109 110 1.224069 CGGAGATGGTGGCGCTAATG 61.224 60.000 7.64 0.00 0.00 1.90
113 114 0.106708 GATGGTGGCGCTAATGGAGA 59.893 55.000 7.64 0.00 0.00 3.71
116 117 0.178068 GGTGGCGCTAATGGAGAGAA 59.822 55.000 7.64 0.00 0.00 2.87
133 134 3.034635 GAGAATGACTCTGGCCCTAGAA 58.965 50.000 0.00 0.00 41.94 2.10
135 136 1.115467 ATGACTCTGGCCCTAGAACG 58.885 55.000 0.00 0.00 0.00 3.95
141 142 0.684805 CTGGCCCTAGAACGGAGTCT 60.685 60.000 0.00 0.00 45.00 3.24
158 159 2.159366 AGTCTAAACAGACTCATCGCGG 60.159 50.000 6.13 0.00 45.09 6.46
163 164 0.960861 ACAGACTCATCGCGGAGACA 60.961 55.000 17.62 0.00 38.30 3.41
164 165 0.383590 CAGACTCATCGCGGAGACAT 59.616 55.000 17.62 0.00 38.30 3.06
173 174 1.439228 GCGGAGACATGCTGCTCTA 59.561 57.895 0.00 0.00 34.83 2.43
175 176 0.457443 CGGAGACATGCTGCTCTACA 59.543 55.000 0.00 0.00 31.91 2.74
190 191 3.448686 CTCTACAGTAACCCGCATGAAG 58.551 50.000 0.00 0.00 0.00 3.02
197 198 1.463674 AACCCGCATGAAGAATGACC 58.536 50.000 0.00 0.00 38.72 4.02
200 201 1.439353 CCGCATGAAGAATGACCCCG 61.439 60.000 0.00 0.00 38.72 5.73
201 202 1.439353 CGCATGAAGAATGACCCCGG 61.439 60.000 0.00 0.00 38.72 5.73
215 216 2.819284 CCCGGGGCCAATAGGTCTC 61.819 68.421 14.71 0.00 40.27 3.36
216 217 2.819284 CCGGGGCCAATAGGTCTCC 61.819 68.421 4.39 0.00 36.28 3.71
221 222 1.623542 GGCCAATAGGTCTCCGGTGT 61.624 60.000 0.00 0.00 36.28 4.16
230 231 1.234821 GTCTCCGGTGTTTGCAATGA 58.765 50.000 0.00 0.00 0.00 2.57
235 236 1.000731 CCGGTGTTTGCAATGATTGGT 59.999 47.619 7.35 0.00 0.00 3.67
251 252 0.760567 TGGTGATATCCGGCAGCTCT 60.761 55.000 0.00 0.00 33.90 4.09
252 253 0.037790 GGTGATATCCGGCAGCTCTC 60.038 60.000 0.00 0.00 0.00 3.20
258 259 1.980784 ATCCGGCAGCTCTCATTGCT 61.981 55.000 0.00 0.00 42.06 3.91
263 264 2.124819 AGCTCTCATTGCTGGCCG 60.125 61.111 0.00 0.00 39.56 6.13
264 265 3.207669 GCTCTCATTGCTGGCCGG 61.208 66.667 7.41 7.41 0.00 6.13
273 274 2.124736 GCTGGCCGGTAGCATGAA 60.125 61.111 22.64 0.00 46.50 2.57
278 279 3.149196 CTGGCCGGTAGCATGAAATAAT 58.851 45.455 2.29 0.00 46.50 1.28
279 280 3.561143 TGGCCGGTAGCATGAAATAATT 58.439 40.909 1.90 0.00 46.50 1.40
285 286 6.363357 GCCGGTAGCATGAAATAATTTTGATC 59.637 38.462 1.90 0.00 42.97 2.92
296 297 8.542080 TGAAATAATTTTGATCAAATGGGAGCT 58.458 29.630 21.10 4.55 35.09 4.09
297 298 8.726870 AAATAATTTTGATCAAATGGGAGCTG 57.273 30.769 21.10 0.00 35.09 4.24
319 320 3.290308 ACAAAGCTAGACACTCACTCG 57.710 47.619 0.00 0.00 0.00 4.18
324 325 0.888619 CTAGACACTCACTCGCCCAA 59.111 55.000 0.00 0.00 0.00 4.12
328 329 1.166531 ACACTCACTCGCCCAAAAGC 61.167 55.000 0.00 0.00 0.00 3.51
346 351 2.456577 AGCGGAGTTTATTGCCCAAAT 58.543 42.857 0.00 0.00 0.00 2.32
349 354 2.680841 CGGAGTTTATTGCCCAAATCGA 59.319 45.455 0.00 0.00 0.00 3.59
361 366 3.480470 CCCAAATCGATGTATGGCTTCT 58.520 45.455 16.02 0.00 0.00 2.85
367 372 5.537300 ATCGATGTATGGCTTCTTAGTGT 57.463 39.130 0.00 0.00 0.00 3.55
400 405 2.743636 GACATCCTTTGTCGACAGGA 57.256 50.000 24.06 24.06 45.00 3.86
402 407 1.971357 ACATCCTTTGTCGACAGGACT 59.029 47.619 24.26 12.56 46.24 3.85
411 416 2.888414 TGTCGACAGGACTGTAATGACA 59.112 45.455 15.76 20.97 46.24 3.58
412 417 3.509967 TGTCGACAGGACTGTAATGACAT 59.490 43.478 15.76 0.00 46.24 3.06
478 656 7.575414 TTGCTGTAAATTAGGAAACTGTGAA 57.425 32.000 0.00 0.00 43.88 3.18
482 660 7.468084 GCTGTAAATTAGGAAACTGTGAACACA 60.468 37.037 7.42 7.42 43.88 3.72
489 667 3.689649 GGAAACTGTGAACACAAGTGTCT 59.310 43.478 6.28 0.00 44.13 3.41
516 703 3.312736 AACTTGGTGGACTGGTTTCAT 57.687 42.857 0.00 0.00 0.00 2.57
517 704 3.312736 ACTTGGTGGACTGGTTTCATT 57.687 42.857 0.00 0.00 0.00 2.57
520 707 2.305928 TGGTGGACTGGTTTCATTGTG 58.694 47.619 0.00 0.00 0.00 3.33
534 721 4.927267 TCATTGTGAGGAACCTAACCAT 57.073 40.909 5.95 0.00 0.00 3.55
548 735 3.252215 CCTAACCATCTGAGCTACTCTCG 59.748 52.174 0.00 0.00 44.86 4.04
553 740 2.491675 TCTGAGCTACTCTCGGTTCA 57.508 50.000 0.00 0.00 46.16 3.18
561 748 1.901591 ACTCTCGGTTCACGTCCTAA 58.098 50.000 0.00 0.00 44.69 2.69
581 768 1.179332 CGTGCGAAATTGGTTATGCG 58.821 50.000 0.00 0.00 0.00 4.73
582 769 0.913876 GTGCGAAATTGGTTATGCGC 59.086 50.000 0.00 0.00 39.73 6.09
585 772 1.320259 GCGAAATTGGTTATGCGCAAC 59.680 47.619 17.11 9.37 39.35 4.17
587 774 2.593775 CGAAATTGGTTATGCGCAACTG 59.406 45.455 17.11 0.00 0.00 3.16
590 777 4.775058 AATTGGTTATGCGCAACTGTAA 57.225 36.364 17.11 5.48 0.00 2.41
600 787 3.091417 GCGCAACTGTAAATAAAGCTCG 58.909 45.455 0.30 0.00 0.00 5.03
639 830 9.899661 AAAAATAGCCTTTTCTTTTAGGTTGTT 57.100 25.926 0.00 0.00 33.91 2.83
644 835 8.301252 AGCCTTTTCTTTTAGGTTGTTAAAGA 57.699 30.769 0.00 0.00 36.43 2.52
700 1052 2.315720 ACCCGACCTAACCTAACTGT 57.684 50.000 0.00 0.00 0.00 3.55
717 1069 0.398696 TGTAACCCGCTCACATGGTT 59.601 50.000 0.00 0.00 44.31 3.67
810 1163 1.202330 CTCAGCATCTCCACCTCCTT 58.798 55.000 0.00 0.00 0.00 3.36
870 1223 2.044551 GAAGGAAGGCAGGCAGGG 60.045 66.667 0.00 0.00 0.00 4.45
871 1224 3.651980 GAAGGAAGGCAGGCAGGGG 62.652 68.421 0.00 0.00 0.00 4.79
908 1262 1.374252 CTTCCCCGAACCTCACACG 60.374 63.158 0.00 0.00 0.00 4.49
938 1292 1.374947 CTTCCAGAAGCCGGTCCAA 59.625 57.895 1.90 0.00 0.00 3.53
1089 1443 7.201911 CCTCTTTTCTCCTCTCTTCTCCTAATC 60.202 44.444 0.00 0.00 0.00 1.75
1144 1498 7.138692 ACTTTAAGAATGAATCAGAGCACAC 57.861 36.000 0.00 0.00 0.00 3.82
1170 1524 3.543680 TCCGCTCCTCCTTTGATTTAG 57.456 47.619 0.00 0.00 0.00 1.85
1172 1526 3.263425 TCCGCTCCTCCTTTGATTTAGTT 59.737 43.478 0.00 0.00 0.00 2.24
1174 1528 4.095036 CCGCTCCTCCTTTGATTTAGTTTC 59.905 45.833 0.00 0.00 0.00 2.78
1176 1530 5.355350 CGCTCCTCCTTTGATTTAGTTTCAT 59.645 40.000 0.00 0.00 0.00 2.57
1242 1604 5.852827 ACTATTGAGGAGCTAGCAGATTTC 58.147 41.667 18.83 4.83 0.00 2.17
1308 1670 5.300286 AGCTGCTTTTCTGTCATGTTAGTTT 59.700 36.000 0.00 0.00 0.00 2.66
1321 1715 7.962373 TGTCATGTTAGTTTGCTATTTTCATCG 59.038 33.333 0.00 0.00 0.00 3.84
1322 1716 6.966632 TCATGTTAGTTTGCTATTTTCATCGC 59.033 34.615 0.00 0.00 0.00 4.58
1324 1718 6.083630 TGTTAGTTTGCTATTTTCATCGCAC 58.916 36.000 0.00 0.00 31.04 5.34
1325 1719 4.096732 AGTTTGCTATTTTCATCGCACC 57.903 40.909 0.00 0.00 31.04 5.01
1326 1720 3.505680 AGTTTGCTATTTTCATCGCACCA 59.494 39.130 0.00 0.00 31.04 4.17
1327 1721 4.158394 AGTTTGCTATTTTCATCGCACCAT 59.842 37.500 0.00 0.00 31.04 3.55
1328 1722 3.696281 TGCTATTTTCATCGCACCATG 57.304 42.857 0.00 0.00 0.00 3.66
1330 1724 4.195416 TGCTATTTTCATCGCACCATGTA 58.805 39.130 0.00 0.00 0.00 2.29
1331 1725 4.821260 TGCTATTTTCATCGCACCATGTAT 59.179 37.500 0.00 0.00 0.00 2.29
1333 1727 3.419264 TTTTCATCGCACCATGTATGC 57.581 42.857 8.75 8.75 39.81 3.14
1352 1761 4.355543 TGCAAGATCCAAGTTAATTCGC 57.644 40.909 0.00 0.00 0.00 4.70
1375 1784 3.068732 TGTGCTCCTCGATTCTAATGGAG 59.931 47.826 9.63 9.63 45.05 3.86
1520 1929 3.244044 CCTGCCTGCCTATCTCTTAACTC 60.244 52.174 0.00 0.00 0.00 3.01
1522 1931 3.386078 TGCCTGCCTATCTCTTAACTCAG 59.614 47.826 0.00 0.00 0.00 3.35
1553 1962 1.505353 GGCTCATGCACTGTGCTTC 59.495 57.895 30.43 14.16 45.31 3.86
1569 1978 2.007608 GCTTCCATCCGACTAAACACC 58.992 52.381 0.00 0.00 0.00 4.16
1755 2164 4.160642 ACTCTCATTCCATATGCTTGCA 57.839 40.909 0.00 0.00 0.00 4.08
1845 2258 4.969484 TCCTTTCCTCCAGTTAGTTGTTC 58.031 43.478 0.00 0.00 0.00 3.18
1873 2287 2.659428 ACTTGCTTCTCTTTTGTGCCT 58.341 42.857 0.00 0.00 0.00 4.75
1936 2357 8.910351 AAAGATGGTCAATTAGCTTATCTACC 57.090 34.615 0.00 0.09 0.00 3.18
1952 2373 8.834465 GCTTATCTACCATGGATATTTGCATAG 58.166 37.037 21.47 6.32 31.94 2.23
1961 2382 5.070001 TGGATATTTGCATAGGTTAGTGCC 58.930 41.667 0.00 0.00 40.56 5.01
2104 2525 6.374333 TGCTAGAACTCGCCTTTGATTTATTT 59.626 34.615 0.00 0.00 0.00 1.40
2113 2534 5.056480 GCCTTTGATTTATTTATGGGGCAC 58.944 41.667 0.00 0.00 36.31 5.01
2164 2585 7.220030 TCTTGAGATGTAAGCTTTCTCTGTTT 58.780 34.615 21.50 0.00 37.40 2.83
2193 2614 6.237901 TGTTAACTTGCAGATCTATGTGGTT 58.762 36.000 7.22 0.61 0.00 3.67
2246 2667 2.634453 CCAGGGCTGAATTTCAGGTTTT 59.366 45.455 24.09 0.00 44.43 2.43
2411 2832 2.094675 ACAAGCAAGACATGGTATGCC 58.905 47.619 13.20 0.00 39.29 4.40
2611 3228 9.996317 CTGCATTTATGTAGGGCTGAAGTAGCT 62.996 44.444 0.00 0.00 41.38 3.32
2687 3304 8.968242 GCTTAGAAAACAGGTTTATTTTCACTG 58.032 33.333 10.96 0.00 43.99 3.66
2690 3307 7.203218 AGAAAACAGGTTTATTTTCACTGCTC 58.797 34.615 10.96 0.00 43.99 4.26
2718 3335 5.869344 TGCTTAATCATGTAGTGTCTGTGTC 59.131 40.000 0.00 0.00 0.00 3.67
2719 3336 5.292101 GCTTAATCATGTAGTGTCTGTGTCC 59.708 44.000 0.00 0.00 0.00 4.02
2927 3546 3.057033 ACATCGGCGTAAAGAGTAACAGT 60.057 43.478 6.85 0.00 0.00 3.55
2951 3570 2.367241 TGGATCGTCTGTGTTTCTTGGA 59.633 45.455 0.00 0.00 0.00 3.53
2963 3582 7.340743 TCTGTGTTTCTTGGAACCTCATTTTTA 59.659 33.333 0.00 0.00 0.00 1.52
3039 3659 7.275183 TGTAGTATGAATGATTCACAAGAGGG 58.725 38.462 10.45 0.00 43.48 4.30
3075 3695 1.908483 GGGGTGCTCCTCCTAGTTG 59.092 63.158 4.53 0.00 35.33 3.16
3254 3875 6.365970 TGCCAAGGCTAAAAATGGAAAATA 57.634 33.333 12.96 0.00 42.51 1.40
3255 3876 6.956497 TGCCAAGGCTAAAAATGGAAAATAT 58.044 32.000 12.96 0.00 42.51 1.28
3340 3961 2.545946 GTCGAAGAAGCTGAAGCAAAGT 59.454 45.455 4.90 0.00 45.16 2.66
3368 3989 2.117779 GTACTCCCTCCGTCCCGAC 61.118 68.421 0.00 0.00 0.00 4.79
3375 3996 0.102481 CCTCCGTCCCGACATAAGTG 59.898 60.000 0.00 0.00 0.00 3.16
3394 4015 0.875059 GTCTCAAGCTTTTGGGACGG 59.125 55.000 2.69 0.00 41.90 4.79
3421 4042 6.766467 GGGAGTACTAGGTATGAAAATTGTGG 59.234 42.308 0.00 0.00 0.00 4.17
3456 4078 4.038633 GGACCCCTACTATTCTGGAGTTT 58.961 47.826 0.00 0.00 0.00 2.66
3459 4081 3.136626 CCCCTACTATTCTGGAGTTTGGG 59.863 52.174 0.00 0.00 38.33 4.12
3460 4082 3.433740 CCCTACTATTCTGGAGTTTGGGC 60.434 52.174 0.00 0.00 34.71 5.36
3481 4106 4.435386 GGCAATGTTGTTGTTGTTGTTGTC 60.435 41.667 0.00 0.00 0.00 3.18
3689 4317 9.809096 GAGTAGAAATCAGAGTGTGAATATTGA 57.191 33.333 0.00 0.00 39.19 2.57
3691 4319 7.856145 AGAAATCAGAGTGTGAATATTGACC 57.144 36.000 2.44 0.00 39.19 4.02
3695 4323 4.707934 TCAGAGTGTGAATATTGACCGGTA 59.292 41.667 7.34 0.00 29.64 4.02
3696 4324 5.186215 TCAGAGTGTGAATATTGACCGGTAA 59.814 40.000 7.34 0.00 29.64 2.85
3700 4328 5.046159 AGTGTGAATATTGACCGGTAAGGAA 60.046 40.000 7.34 0.00 45.00 3.36
3720 4348 1.305219 TTGTGCCTGAACCTATGCGC 61.305 55.000 0.00 0.00 34.92 6.09
3721 4349 1.745115 GTGCCTGAACCTATGCGCA 60.745 57.895 14.96 14.96 34.50 6.09
3796 5061 3.704800 AACTAAGAAGGAACTCCCAGC 57.295 47.619 0.00 0.00 38.49 4.85
3797 5062 1.550976 ACTAAGAAGGAACTCCCAGCG 59.449 52.381 0.00 0.00 38.49 5.18
3798 5063 1.825474 CTAAGAAGGAACTCCCAGCGA 59.175 52.381 0.00 0.00 38.49 4.93
3799 5064 1.056660 AAGAAGGAACTCCCAGCGAA 58.943 50.000 0.00 0.00 38.49 4.70
3800 5065 1.280457 AGAAGGAACTCCCAGCGAAT 58.720 50.000 0.00 0.00 38.49 3.34
3801 5066 1.065854 AGAAGGAACTCCCAGCGAATG 60.066 52.381 0.00 0.00 38.49 2.67
3802 5067 0.678048 AAGGAACTCCCAGCGAATGC 60.678 55.000 0.00 0.00 38.49 3.56
3803 5068 1.377202 GGAACTCCCAGCGAATGCA 60.377 57.895 0.00 0.00 46.23 3.96
3817 5082 2.254951 TGCAATCGCAGCCGTTTG 59.745 55.556 0.00 2.86 45.36 2.93
3818 5083 2.257302 TGCAATCGCAGCCGTTTGA 61.257 52.632 9.45 0.00 45.36 2.69
3819 5084 1.137404 GCAATCGCAGCCGTTTGAT 59.863 52.632 9.45 0.00 43.36 2.57
3820 5085 0.863119 GCAATCGCAGCCGTTTGATC 60.863 55.000 9.45 0.00 43.36 2.92
3821 5086 0.447406 CAATCGCAGCCGTTTGATCA 59.553 50.000 0.00 0.00 43.36 2.92
3822 5087 1.135717 CAATCGCAGCCGTTTGATCAA 60.136 47.619 3.38 3.38 43.36 2.57
3823 5088 0.729116 ATCGCAGCCGTTTGATCAAG 59.271 50.000 8.41 0.00 35.54 3.02
3824 5089 0.320334 TCGCAGCCGTTTGATCAAGA 60.320 50.000 8.41 0.00 35.54 3.02
3825 5090 0.729116 CGCAGCCGTTTGATCAAGAT 59.271 50.000 8.41 0.00 0.00 2.40
3826 5091 1.267732 CGCAGCCGTTTGATCAAGATC 60.268 52.381 8.41 3.12 38.29 2.75
3827 5092 1.739466 GCAGCCGTTTGATCAAGATCA 59.261 47.619 8.41 8.61 45.30 2.92
3912 5177 3.009033 CCAGAAATTGTCACCCTCCTACA 59.991 47.826 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.050499 GCGTGATCTCAAAGTATCATTCCAG 60.050 44.000 0.00 0.00 34.77 3.86
19 20 1.202639 ACAACACCTGCGTGATCTCAA 60.203 47.619 0.00 0.00 43.14 3.02
20 21 0.392706 ACAACACCTGCGTGATCTCA 59.607 50.000 0.00 0.00 43.14 3.27
29 30 3.988379 TGAGAAAATGACAACACCTGC 57.012 42.857 0.00 0.00 0.00 4.85
32 33 6.076981 ACAAGATGAGAAAATGACAACACC 57.923 37.500 0.00 0.00 0.00 4.16
45 46 4.082026 TCTGAATGAAGCGACAAGATGAGA 60.082 41.667 0.00 0.00 0.00 3.27
67 68 3.386768 TTAAGGGCGCTCATACATCTC 57.613 47.619 11.40 0.00 0.00 2.75
69 70 2.224314 GCTTTAAGGGCGCTCATACATC 59.776 50.000 11.40 0.00 0.00 3.06
86 87 2.436646 CGCCACCATCTCCGCTTT 60.437 61.111 0.00 0.00 0.00 3.51
90 91 1.069765 ATTAGCGCCACCATCTCCG 59.930 57.895 2.29 0.00 0.00 4.63
99 100 1.762370 TCATTCTCTCCATTAGCGCCA 59.238 47.619 2.29 0.00 0.00 5.69
113 114 2.769095 GTTCTAGGGCCAGAGTCATTCT 59.231 50.000 6.18 0.00 36.25 2.40
116 117 1.115467 CGTTCTAGGGCCAGAGTCAT 58.885 55.000 6.18 0.00 0.00 3.06
141 142 2.089201 TCTCCGCGATGAGTCTGTTTA 58.911 47.619 8.23 0.00 33.93 2.01
156 157 0.457443 TGTAGAGCAGCATGTCTCCG 59.543 55.000 0.00 0.00 39.15 4.63
173 174 2.851263 TTCTTCATGCGGGTTACTGT 57.149 45.000 0.00 0.00 0.00 3.55
175 176 3.270877 GTCATTCTTCATGCGGGTTACT 58.729 45.455 0.00 0.00 32.13 2.24
178 179 1.463674 GGTCATTCTTCATGCGGGTT 58.536 50.000 0.00 0.00 32.13 4.11
179 180 0.394352 GGGTCATTCTTCATGCGGGT 60.394 55.000 0.00 0.00 32.13 5.28
183 184 1.103398 CCCGGGGTCATTCTTCATGC 61.103 60.000 14.71 0.00 32.13 4.06
197 198 2.772622 AGACCTATTGGCCCCGGG 60.773 66.667 15.80 15.80 36.63 5.73
200 201 2.819284 CCGGAGACCTATTGGCCCC 61.819 68.421 0.00 0.00 36.63 5.80
201 202 2.070650 ACCGGAGACCTATTGGCCC 61.071 63.158 9.46 0.00 36.63 5.80
215 216 1.000731 ACCAATCATTGCAAACACCGG 59.999 47.619 1.71 0.00 0.00 5.28
216 217 2.060284 CACCAATCATTGCAAACACCG 58.940 47.619 1.71 0.00 0.00 4.94
221 222 4.037803 CCGGATATCACCAATCATTGCAAA 59.962 41.667 1.71 0.00 0.00 3.68
230 231 0.767375 AGCTGCCGGATATCACCAAT 59.233 50.000 5.05 0.00 0.00 3.16
235 236 1.637338 ATGAGAGCTGCCGGATATCA 58.363 50.000 5.05 0.25 36.00 2.15
251 252 2.124736 GCTACCGGCCAGCAATGA 60.125 61.111 20.71 0.00 38.93 2.57
252 253 2.438254 TGCTACCGGCCAGCAATG 60.438 61.111 24.77 0.00 45.71 2.82
258 259 2.719531 TTATTTCATGCTACCGGCCA 57.280 45.000 0.00 0.00 40.92 5.36
269 270 9.333724 GCTCCCATTTGATCAAAATTATTTCAT 57.666 29.630 23.91 2.25 36.28 2.57
273 274 8.081517 TCAGCTCCCATTTGATCAAAATTATT 57.918 30.769 23.91 5.21 36.28 1.40
278 279 4.588106 TGTTCAGCTCCCATTTGATCAAAA 59.412 37.500 23.91 7.48 33.56 2.44
279 280 4.151121 TGTTCAGCTCCCATTTGATCAAA 58.849 39.130 22.52 22.52 34.46 2.69
285 286 2.680577 GCTTTGTTCAGCTCCCATTTG 58.319 47.619 0.00 0.00 36.79 2.32
296 297 4.621991 GAGTGAGTGTCTAGCTTTGTTCA 58.378 43.478 0.00 0.00 0.00 3.18
297 298 3.670991 CGAGTGAGTGTCTAGCTTTGTTC 59.329 47.826 0.00 0.00 0.00 3.18
309 310 1.166531 GCTTTTGGGCGAGTGAGTGT 61.167 55.000 0.00 0.00 0.00 3.55
319 320 2.606108 CAATAAACTCCGCTTTTGGGC 58.394 47.619 0.00 0.00 0.00 5.36
324 325 1.917872 TGGGCAATAAACTCCGCTTT 58.082 45.000 0.00 0.00 0.00 3.51
328 329 2.680841 TCGATTTGGGCAATAAACTCCG 59.319 45.455 0.00 0.00 0.00 4.63
331 336 6.239008 CCATACATCGATTTGGGCAATAAACT 60.239 38.462 0.00 0.00 0.00 2.66
333 338 5.508825 GCCATACATCGATTTGGGCAATAAA 60.509 40.000 18.63 0.00 39.66 1.40
346 351 5.339008 AACACTAAGAAGCCATACATCGA 57.661 39.130 0.00 0.00 0.00 3.59
349 354 5.189736 TCAGGAACACTAAGAAGCCATACAT 59.810 40.000 0.00 0.00 0.00 2.29
361 366 3.323979 GTCAACCTCCTCAGGAACACTAA 59.676 47.826 0.00 0.00 43.65 2.24
367 372 1.909302 GGATGTCAACCTCCTCAGGAA 59.091 52.381 0.00 0.00 43.65 3.36
449 454 8.565416 ACAGTTTCCTAATTTACAGCAAACTAC 58.435 33.333 0.00 0.00 32.64 2.73
452 457 7.422399 TCACAGTTTCCTAATTTACAGCAAAC 58.578 34.615 0.00 0.00 0.00 2.93
457 462 7.925993 TGTGTTCACAGTTTCCTAATTTACAG 58.074 34.615 1.23 0.00 0.00 2.74
467 472 3.689649 AGACACTTGTGTTCACAGTTTCC 59.310 43.478 7.87 0.00 0.00 3.13
482 660 4.881850 CCACCAAGTTTCAAGTAGACACTT 59.118 41.667 0.00 0.00 45.61 3.16
489 667 3.201266 ACCAGTCCACCAAGTTTCAAGTA 59.799 43.478 0.00 0.00 0.00 2.24
494 681 3.020984 TGAAACCAGTCCACCAAGTTTC 58.979 45.455 6.92 6.92 44.09 2.78
516 703 3.907474 TCAGATGGTTAGGTTCCTCACAA 59.093 43.478 5.68 0.00 0.00 3.33
517 704 3.515502 CTCAGATGGTTAGGTTCCTCACA 59.484 47.826 5.68 0.36 0.00 3.58
520 707 2.769095 AGCTCAGATGGTTAGGTTCCTC 59.231 50.000 0.00 0.00 0.00 3.71
534 721 2.085320 GTGAACCGAGAGTAGCTCAGA 58.915 52.381 0.00 0.00 44.15 3.27
561 748 1.465020 CGCATAACCAATTTCGCACGT 60.465 47.619 0.00 0.00 0.00 4.49
563 750 0.913876 GCGCATAACCAATTTCGCAC 59.086 50.000 0.30 0.00 41.84 5.34
564 751 3.320884 GCGCATAACCAATTTCGCA 57.679 47.368 0.30 0.00 41.84 5.10
565 752 1.320259 GTTGCGCATAACCAATTTCGC 59.680 47.619 12.75 0.00 42.47 4.70
566 753 2.593775 CAGTTGCGCATAACCAATTTCG 59.406 45.455 12.75 0.00 0.00 3.46
568 755 3.658757 ACAGTTGCGCATAACCAATTT 57.341 38.095 12.75 0.00 0.00 1.82
581 768 5.928153 AGAACGAGCTTTATTTACAGTTGC 58.072 37.500 0.00 0.00 0.00 4.17
585 772 9.907576 CTGAAATAGAACGAGCTTTATTTACAG 57.092 33.333 0.00 0.00 0.00 2.74
619 810 8.301252 TCTTTAACAACCTAAAAGAAAAGGCT 57.699 30.769 0.00 0.00 36.55 4.58
700 1052 0.398696 ACAACCATGTGAGCGGGTTA 59.601 50.000 0.00 0.00 42.78 2.85
717 1069 0.824182 CTTTTACGTGGGCCCCAACA 60.824 55.000 22.27 0.00 34.18 3.33
810 1163 4.753662 CGACGGGGGAGGAGGACA 62.754 72.222 0.00 0.00 0.00 4.02
908 1262 3.314388 CTGGAAGTTTCTGCGGCGC 62.314 63.158 27.44 27.44 0.00 6.53
938 1292 2.511452 CCGCCGAAGAGGATGGGAT 61.511 63.158 0.00 0.00 45.00 3.85
967 1321 2.187239 TGGATCAGGAGAATCTGGCT 57.813 50.000 0.00 0.00 35.58 4.75
1089 1443 0.958091 TCCATTCGCCCAACAAACTG 59.042 50.000 0.00 0.00 0.00 3.16
1112 1466 6.338146 TGATTCATTCTTAAAGTCGGTCGAT 58.662 36.000 0.00 0.00 0.00 3.59
1144 1498 0.390860 AAAGGAGGAGCGGATCGATG 59.609 55.000 0.54 0.00 0.00 3.84
1221 1583 5.129320 TGTGAAATCTGCTAGCTCCTCAATA 59.871 40.000 17.23 2.57 0.00 1.90
1223 1585 3.261643 TGTGAAATCTGCTAGCTCCTCAA 59.738 43.478 17.23 0.00 0.00 3.02
1308 1670 3.016031 ACATGGTGCGATGAAAATAGCA 58.984 40.909 0.00 0.00 37.26 3.49
1321 1715 2.300433 TGGATCTTGCATACATGGTGC 58.700 47.619 15.89 15.89 42.81 5.01
1322 1716 3.949754 ACTTGGATCTTGCATACATGGTG 59.050 43.478 0.00 0.00 0.00 4.17
1324 1718 6.698008 TTAACTTGGATCTTGCATACATGG 57.302 37.500 0.00 0.00 0.00 3.66
1325 1719 7.588854 CGAATTAACTTGGATCTTGCATACATG 59.411 37.037 0.00 0.00 0.00 3.21
1326 1720 7.642669 CGAATTAACTTGGATCTTGCATACAT 58.357 34.615 0.00 0.00 0.00 2.29
1327 1721 6.458206 GCGAATTAACTTGGATCTTGCATACA 60.458 38.462 0.00 0.00 0.00 2.29
1328 1722 5.909610 GCGAATTAACTTGGATCTTGCATAC 59.090 40.000 0.00 0.00 0.00 2.39
1330 1724 4.641989 AGCGAATTAACTTGGATCTTGCAT 59.358 37.500 0.00 0.00 0.00 3.96
1331 1725 4.009675 AGCGAATTAACTTGGATCTTGCA 58.990 39.130 0.00 0.00 0.00 4.08
1333 1727 5.327091 CACAGCGAATTAACTTGGATCTTG 58.673 41.667 0.00 0.00 0.00 3.02
1352 1761 3.068732 TCCATTAGAATCGAGGAGCACAG 59.931 47.826 0.00 0.00 0.00 3.66
1520 1929 5.105797 TGCATGAGCCCAAAATTAGTTACTG 60.106 40.000 0.00 0.00 41.13 2.74
1522 1931 5.102313 GTGCATGAGCCCAAAATTAGTTAC 58.898 41.667 0.00 0.00 41.13 2.50
1553 1962 1.737793 GCTTGGTGTTTAGTCGGATGG 59.262 52.381 0.00 0.00 0.00 3.51
1569 1978 2.887152 AGCAAAGTAGTTCAAGGGCTTG 59.113 45.455 0.00 0.00 41.71 4.01
1755 2164 9.389570 GCTACTTAAAATACAACGAAACAACAT 57.610 29.630 0.00 0.00 0.00 2.71
1845 2258 7.517259 GCACAAAAGAGAAGCAAGTAAAAATGG 60.517 37.037 0.00 0.00 0.00 3.16
1885 2299 3.877508 GGTGACTGCTACTGAACTTGTTT 59.122 43.478 0.00 0.00 0.00 2.83
1936 2357 6.349611 GGCACTAACCTATGCAAATATCCATG 60.350 42.308 0.00 0.00 43.93 3.66
1952 2373 0.253327 AGCAGCTAAGGGCACTAACC 59.747 55.000 0.00 0.00 44.79 2.85
1961 2382 1.451028 GGTGGCTCAGCAGCTAAGG 60.451 63.158 0.00 0.00 46.03 2.69
2104 2525 2.040947 TCACAAATCACTGTGCCCCATA 59.959 45.455 2.12 0.00 45.25 2.74
2164 2585 8.506437 CACATAGATCTGCAAGTTAACAAAAGA 58.494 33.333 5.18 5.67 33.76 2.52
2246 2667 4.635765 CAGGTTCTCGATAAGAAATGCCAA 59.364 41.667 0.00 0.00 45.50 4.52
2411 2832 6.381801 GTGATACCAAAAGAAACCATGACAG 58.618 40.000 0.00 0.00 0.00 3.51
2638 3255 6.950619 AGCCAGAATAAACTCTTCCTTTTCAT 59.049 34.615 0.00 0.00 0.00 2.57
2661 3278 8.968242 CAGTGAAAATAAACCTGTTTTCTAAGC 58.032 33.333 0.00 0.00 41.05 3.09
2687 3304 5.692204 ACACTACATGATTAAGCATACGAGC 59.308 40.000 5.78 0.00 0.00 5.03
2690 3307 6.697455 ACAGACACTACATGATTAAGCATACG 59.303 38.462 5.78 0.00 0.00 3.06
2718 3335 1.980784 CTCCCCTCTGCATCCACAGG 61.981 65.000 0.00 0.00 38.26 4.00
2719 3336 1.525923 CTCCCCTCTGCATCCACAG 59.474 63.158 0.00 0.00 39.12 3.66
2927 3546 3.961480 AGAAACACAGACGATCCATCA 57.039 42.857 0.00 0.00 0.00 3.07
2951 3570 7.277760 GCAGACACAAAAAGTAAAAATGAGGTT 59.722 33.333 0.00 0.00 0.00 3.50
2963 3582 1.750778 CACAGGGCAGACACAAAAAGT 59.249 47.619 0.00 0.00 0.00 2.66
3031 3651 0.693049 AGAAACGCATCCCCTCTTGT 59.307 50.000 0.00 0.00 0.00 3.16
3039 3659 1.373570 CCCTCTTCAGAAACGCATCC 58.626 55.000 0.00 0.00 0.00 3.51
3075 3695 5.233988 AGAACAGAATAGATATGCGCTTCC 58.766 41.667 9.73 0.00 0.00 3.46
3206 3827 6.313519 TCTAGCTAGTCATTCCCAACAAAT 57.686 37.500 20.10 0.00 0.00 2.32
3254 3875 4.080751 CCAATCCAAGAAAAGCATCCCAAT 60.081 41.667 0.00 0.00 0.00 3.16
3255 3876 3.261390 CCAATCCAAGAAAAGCATCCCAA 59.739 43.478 0.00 0.00 0.00 4.12
3340 3961 1.968493 GGAGGGAGTACAACACAGACA 59.032 52.381 0.00 0.00 0.00 3.41
3368 3989 4.761739 TCCCAAAAGCTTGAGACACTTATG 59.238 41.667 0.00 0.00 34.14 1.90
3375 3996 0.875059 CCGTCCCAAAAGCTTGAGAC 59.125 55.000 0.00 4.10 37.04 3.36
3394 4015 7.711339 CACAATTTTCATACCTAGTACTCCCTC 59.289 40.741 0.00 0.00 0.00 4.30
3421 4042 4.846940 AGTAGGGGTCCCAGAAATATCATC 59.153 45.833 10.98 0.00 38.92 2.92
3433 4055 2.090663 ACTCCAGAATAGTAGGGGTCCC 60.091 54.545 0.00 0.00 27.09 4.46
3456 4078 2.027745 ACAACAACAACAACATTGCCCA 60.028 40.909 0.00 0.00 0.00 5.36
3459 4081 4.636975 GACAACAACAACAACAACATTGC 58.363 39.130 0.00 0.00 0.00 3.56
3460 4082 4.201570 CCGACAACAACAACAACAACATTG 60.202 41.667 0.00 0.00 0.00 2.82
3481 4106 2.478134 CTCTTTGTTTCTGCTGACTCCG 59.522 50.000 0.00 0.00 0.00 4.63
3660 4288 3.769844 TCACACTCTGATTTCTACTCCCC 59.230 47.826 0.00 0.00 0.00 4.81
3689 4317 0.696501 AGGCACAATTCCTTACCGGT 59.303 50.000 13.98 13.98 0.00 5.28
3691 4319 2.107950 TCAGGCACAATTCCTTACCG 57.892 50.000 0.00 0.00 0.00 4.02
3695 4323 2.683211 AGGTTCAGGCACAATTCCTT 57.317 45.000 0.00 0.00 0.00 3.36
3696 4324 3.624777 CATAGGTTCAGGCACAATTCCT 58.375 45.455 0.00 0.00 0.00 3.36
3700 4328 1.382522 CGCATAGGTTCAGGCACAAT 58.617 50.000 0.00 0.00 0.00 2.71
3764 5029 9.628500 AGTTCCTTCTTAGTTTTCAGTTAACAT 57.372 29.630 8.61 0.00 0.00 2.71
3765 5030 9.106070 GAGTTCCTTCTTAGTTTTCAGTTAACA 57.894 33.333 8.61 0.00 0.00 2.41
3766 5031 8.557864 GGAGTTCCTTCTTAGTTTTCAGTTAAC 58.442 37.037 0.00 0.00 0.00 2.01
3767 5032 7.718314 GGGAGTTCCTTCTTAGTTTTCAGTTAA 59.282 37.037 0.00 0.00 35.95 2.01
3768 5033 7.147444 TGGGAGTTCCTTCTTAGTTTTCAGTTA 60.147 37.037 0.00 0.00 36.20 2.24
3769 5034 6.062749 GGGAGTTCCTTCTTAGTTTTCAGTT 58.937 40.000 0.00 0.00 35.95 3.16
3770 5035 5.132144 TGGGAGTTCCTTCTTAGTTTTCAGT 59.868 40.000 0.00 0.00 36.20 3.41
3771 5036 5.621193 TGGGAGTTCCTTCTTAGTTTTCAG 58.379 41.667 0.00 0.00 36.20 3.02
3772 5037 5.621193 CTGGGAGTTCCTTCTTAGTTTTCA 58.379 41.667 0.00 0.00 36.20 2.69
3773 5038 4.456222 GCTGGGAGTTCCTTCTTAGTTTTC 59.544 45.833 0.00 0.00 36.20 2.29
3774 5039 4.399219 GCTGGGAGTTCCTTCTTAGTTTT 58.601 43.478 0.00 0.00 36.20 2.43
3775 5040 3.557264 CGCTGGGAGTTCCTTCTTAGTTT 60.557 47.826 0.00 0.00 36.20 2.66
3801 5066 0.863119 GATCAAACGGCTGCGATTGC 60.863 55.000 0.00 0.00 43.20 3.56
3802 5067 0.447406 TGATCAAACGGCTGCGATTG 59.553 50.000 0.00 0.00 0.00 2.67
3803 5068 1.131126 CTTGATCAAACGGCTGCGATT 59.869 47.619 9.88 0.00 0.00 3.34
3816 5081 7.770801 AATTATCGTCGTTTGATCTTGATCA 57.229 32.000 9.02 9.02 0.00 2.92
3817 5082 9.490663 AAAAATTATCGTCGTTTGATCTTGATC 57.509 29.630 3.82 3.82 0.00 2.92
3873 5138 3.435275 TCTGGAGACTAGCATGACACTT 58.565 45.455 0.00 0.00 0.00 3.16
3874 5139 3.093057 TCTGGAGACTAGCATGACACT 57.907 47.619 0.00 0.00 0.00 3.55
3875 5140 3.876274 TTCTGGAGACTAGCATGACAC 57.124 47.619 0.00 0.00 0.00 3.67
3876 5141 5.181009 CAATTTCTGGAGACTAGCATGACA 58.819 41.667 0.00 0.00 0.00 3.58
3877 5142 5.181748 ACAATTTCTGGAGACTAGCATGAC 58.818 41.667 0.00 0.00 0.00 3.06
3878 5143 5.046376 TGACAATTTCTGGAGACTAGCATGA 60.046 40.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.