Multiple sequence alignment - TraesCS7A01G125600

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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 TraesCS7A01G125600 chr7A 100.000 4206 0 0 1 4206 80855376 80851171 0.000000e+00 7768.0
1 TraesCS7A01G125600 chr7A 81.818 220 20 9 3910 4110 80804124 80803906 2.600000e-37 167.0
2 TraesCS7A01G125600 chr7A 81.643 207 31 6 9 212 533055746 533055948 9.360000e-37 165.0
3 TraesCS7A01G125600 chr7A 81.364 220 21 9 3910 4110 80701193 80700975 1.210000e-35 161.0
4 TraesCS7A01G125600 chr7A 81.364 220 21 9 3910 4110 80726993 80726775 1.210000e-35 161.0
5 TraesCS7A01G125600 chr7A 81.364 220 21 9 3910 4110 80749218 80749000 1.210000e-35 161.0
6 TraesCS7A01G125600 chr7D 90.979 3647 207 62 618 4199 76734340 76730751 0.000000e+00 4800.0
7 TraesCS7A01G125600 chr7D 87.112 419 48 5 6 422 76736688 76736274 1.770000e-128 470.0
8 TraesCS7A01G125600 chr7D 85.567 291 27 6 3353 3641 76613427 76613150 1.480000e-74 291.0
9 TraesCS7A01G125600 chr7D 100.000 35 0 0 3266 3300 76563377 76563343 9.760000e-07 65.8
10 TraesCS7A01G125600 chr7B 91.796 3425 182 44 615 3983 23443233 23439852 0.000000e+00 4676.0
11 TraesCS7A01G125600 chr7B 89.555 517 44 4 2891 3397 23396970 23396454 0.000000e+00 647.0
12 TraesCS7A01G125600 chr7B 97.248 109 2 1 4014 4121 23439855 23439747 2.580000e-42 183.0
13 TraesCS7A01G125600 chr7B 85.366 82 11 1 232 313 23444430 23444350 2.690000e-12 84.2
14 TraesCS7A01G125600 chr7B 100.000 35 0 0 3266 3300 23082812 23082778 9.760000e-07 65.8
15 TraesCS7A01G125600 chr1A 85.253 1519 191 19 1697 3187 308814417 308812904 0.000000e+00 1533.0
16 TraesCS7A01G125600 chr1A 84.646 1511 211 14 1694 3187 37480010 37481516 0.000000e+00 1485.0
17 TraesCS7A01G125600 chr1A 80.224 268 34 13 3944 4195 581583951 581584215 2.580000e-42 183.0
18 TraesCS7A01G125600 chr1A 82.353 204 29 6 12 212 38867721 38867522 2.010000e-38 171.0
19 TraesCS7A01G125600 chr1A 78.733 221 30 13 1042 1256 37478585 37478794 9.490000e-27 132.0
20 TraesCS7A01G125600 chr1A 83.784 148 12 6 1104 1249 308815965 308815828 3.410000e-26 130.0
21 TraesCS7A01G125600 chr1D 84.808 1514 201 22 1694 3187 38551133 38552637 0.000000e+00 1495.0
22 TraesCS7A01G125600 chr1D 85.912 1228 157 12 2062 3283 236806108 236807325 0.000000e+00 1295.0
23 TraesCS7A01G125600 chr1D 80.224 268 34 13 3944 4195 484402286 484402550 2.580000e-42 183.0
24 TraesCS7A01G125600 chr1D 83.448 145 16 4 1104 1247 38549826 38549963 1.230000e-25 128.0
25 TraesCS7A01G125600 chr1D 78.017 232 29 13 1025 1249 236803291 236803507 4.410000e-25 126.0
26 TraesCS7A01G125600 chr1B 84.519 1518 210 11 1692 3187 58323219 58324733 0.000000e+00 1478.0
27 TraesCS7A01G125600 chr1B 87.567 1126 140 0 2062 3187 342116466 342117591 0.000000e+00 1304.0
28 TraesCS7A01G125600 chr1B 86.735 294 35 4 1694 1983 342116064 342116357 1.460000e-84 324.0
29 TraesCS7A01G125600 chr1B 83.643 269 25 10 3944 4195 674631360 674631626 7.030000e-58 235.0
30 TraesCS7A01G125600 chr1B 82.759 145 17 4 1104 1247 58321867 58322004 5.710000e-24 122.0
31 TraesCS7A01G125600 chr5A 82.323 198 29 5 12 207 316447473 316447280 2.600000e-37 167.0
32 TraesCS7A01G125600 chr3B 81.281 203 34 3 12 213 225467701 225467502 1.210000e-35 161.0
33 TraesCS7A01G125600 chr3A 81.281 203 34 3 12 213 446585218 446585019 1.210000e-35 161.0
34 TraesCS7A01G125600 chr5D 81.159 207 32 6 9 212 437007467 437007669 4.350000e-35 159.0
35 TraesCS7A01G125600 chr5D 81.159 207 32 6 9 212 447325793 447325995 4.350000e-35 159.0
36 TraesCS7A01G125600 chr4D 81.373 204 31 6 12 212 504049590 504049391 4.350000e-35 159.0


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 TraesCS7A01G125600 chr7A 80851171 80855376 4205 True 7768.000000 7768 100.0000 1 4206 1 chr7A.!!$R5 4205
1 TraesCS7A01G125600 chr7D 76730751 76736688 5937 True 2635.000000 4800 89.0455 6 4199 2 chr7D.!!$R3 4193
2 TraesCS7A01G125600 chr7B 23439747 23444430 4683 True 1647.733333 4676 91.4700 232 4121 3 chr7B.!!$R3 3889
3 TraesCS7A01G125600 chr7B 23396454 23396970 516 True 647.000000 647 89.5550 2891 3397 1 chr7B.!!$R2 506
4 TraesCS7A01G125600 chr1A 308812904 308815965 3061 True 831.500000 1533 84.5185 1104 3187 2 chr1A.!!$R2 2083
5 TraesCS7A01G125600 chr1A 37478585 37481516 2931 False 808.500000 1485 81.6895 1042 3187 2 chr1A.!!$F2 2145
6 TraesCS7A01G125600 chr1D 38549826 38552637 2811 False 811.500000 1495 84.1280 1104 3187 2 chr1D.!!$F2 2083
7 TraesCS7A01G125600 chr1D 236803291 236807325 4034 False 710.500000 1295 81.9645 1025 3283 2 chr1D.!!$F3 2258
8 TraesCS7A01G125600 chr1B 342116064 342117591 1527 False 814.000000 1304 87.1510 1694 3187 2 chr1B.!!$F3 1493
9 TraesCS7A01G125600 chr1B 58321867 58324733 2866 False 800.000000 1478 83.6390 1104 3187 2 chr1B.!!$F2 2083

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
229 230 0.036388 GGGTCCGAGAGTGATTTGCA 60.036 55.0 0.0 0.0 0.00 4.08 F
1353 3989 0.248621 CGAATTGCGGGATCTTTGCC 60.249 55.0 0.0 0.0 36.03 4.52 F
1805 6623 0.110238 GATGCGTGAAAAGCTTGCGA 60.110 50.0 0.0 0.0 43.59 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 6623 0.034616 GGCCATAGCTCTTCTGCGAT 59.965 55.000 0.00 0.0 39.73 4.58 R
2232 7092 1.428912 TGTTCTTTCCCAAGCCTCCAT 59.571 47.619 0.00 0.0 0.00 3.41 R
3331 8204 2.051334 ACAATGGCAGGCGCTAATTA 57.949 45.000 7.64 0.0 38.60 1.40 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
24 25 3.004752 AGTGGTGGGTTATTCAGATGC 57.995 47.619 0.00 0.00 0.00 3.91
36 37 1.097232 TCAGATGCTGATTTTGCGGG 58.903 50.000 0.00 0.00 35.39 6.13
43 44 0.039256 CTGATTTTGCGGGGTGTGTG 60.039 55.000 0.00 0.00 0.00 3.82
44 45 0.753479 TGATTTTGCGGGGTGTGTGT 60.753 50.000 0.00 0.00 0.00 3.72
45 46 0.387565 GATTTTGCGGGGTGTGTGTT 59.612 50.000 0.00 0.00 0.00 3.32
46 47 1.609555 GATTTTGCGGGGTGTGTGTTA 59.390 47.619 0.00 0.00 0.00 2.41
59 60 7.201582 CGGGGTGTGTGTTAATACTAAGAAATC 60.202 40.741 3.89 0.00 0.00 2.17
62 63 8.448615 GGTGTGTGTTAATACTAAGAAATCCAC 58.551 37.037 3.89 0.00 0.00 4.02
67 68 8.592998 GTGTTAATACTAAGAAATCCACGTCAG 58.407 37.037 0.00 0.00 0.00 3.51
70 71 4.189639 ACTAAGAAATCCACGTCAGGTC 57.810 45.455 0.00 0.00 0.00 3.85
82 83 1.535462 CGTCAGGTCATGTTTTCACCC 59.465 52.381 0.00 0.00 0.00 4.61
91 92 4.270808 GTCATGTTTTCACCCTTGCAAAAG 59.729 41.667 0.00 0.00 0.00 2.27
124 125 2.469826 GGAAAAGCTCCAAACAAACCG 58.530 47.619 0.00 0.00 44.67 4.44
130 131 1.268539 GCTCCAAACAAACCGTCACTG 60.269 52.381 0.00 0.00 0.00 3.66
134 135 2.481104 CCAAACAAACCGTCACTGCATT 60.481 45.455 0.00 0.00 0.00 3.56
138 139 0.586319 AAACCGTCACTGCATTGTCG 59.414 50.000 14.85 14.85 0.00 4.35
140 141 0.037326 ACCGTCACTGCATTGTCGAT 60.037 50.000 21.42 5.07 30.79 3.59
167 168 4.128643 CTGGTCAAATTTGTGGCATGTTT 58.871 39.130 17.47 0.00 0.00 2.83
173 174 4.686191 AATTTGTGGCATGTTTTGAGGA 57.314 36.364 0.00 0.00 0.00 3.71
183 184 1.339631 TGTTTTGAGGATACCGGGCAG 60.340 52.381 6.32 0.00 37.17 4.85
187 188 2.690881 AGGATACCGGGCAGGCAA 60.691 61.111 6.32 0.00 46.52 4.52
193 194 2.690653 TACCGGGCAGGCAATATGGC 62.691 60.000 6.32 0.00 46.52 4.40
208 209 6.870439 GGCAATATGGCTGAAGAATTTTATCC 59.130 38.462 1.19 0.00 40.14 2.59
215 216 3.883489 CTGAAGAATTTTATCCCGGGTCC 59.117 47.826 22.86 1.88 0.00 4.46
219 220 1.797320 ATTTTATCCCGGGTCCGAGA 58.203 50.000 22.86 3.14 42.83 4.04
227 228 0.460284 CCGGGTCCGAGAGTGATTTG 60.460 60.000 11.39 0.00 42.83 2.32
228 229 1.084370 CGGGTCCGAGAGTGATTTGC 61.084 60.000 2.83 0.00 42.83 3.68
229 230 0.036388 GGGTCCGAGAGTGATTTGCA 60.036 55.000 0.00 0.00 0.00 4.08
258 259 9.524106 AATGTAGTTTTATGATGCATGTGATTG 57.476 29.630 2.46 0.00 0.00 2.67
270 271 7.703197 TGATGCATGTGATTGTATTGATTTGAC 59.297 33.333 2.46 0.00 0.00 3.18
303 304 5.836024 TGAGGTACCTGGTTGTAGAAAAT 57.164 39.130 22.10 0.00 0.00 1.82
304 305 6.195600 TGAGGTACCTGGTTGTAGAAAATT 57.804 37.500 22.10 0.00 0.00 1.82
313 314 7.507616 ACCTGGTTGTAGAAAATTGGACATTTA 59.492 33.333 0.00 0.00 0.00 1.40
324 325 6.983906 AATTGGACATTTAAGGGATGATCC 57.016 37.500 1.94 1.94 35.23 3.36
335 336 3.576861 AGGGATGATCCGTCATTGTCTA 58.423 45.455 5.22 0.00 44.96 2.59
349 350 1.226128 GTCTACGGACGCGTACACC 60.226 63.158 23.49 14.02 32.47 4.16
357 358 1.665735 GGACGCGTACACCGACTTTTA 60.666 52.381 18.68 0.00 39.56 1.52
426 1073 7.866393 CGTGAGAACTTCTATAATATTTCCCGT 59.134 37.037 0.00 0.00 0.00 5.28
544 1365 7.680442 TCATGAAGATTCGTGTGGATTTTTA 57.320 32.000 13.10 0.00 43.12 1.52
545 1366 8.105097 TCATGAAGATTCGTGTGGATTTTTAA 57.895 30.769 13.10 0.00 43.12 1.52
573 1394 8.547894 TGTTTATTCAAATGTATAGCAGCTACG 58.452 33.333 3.59 0.00 0.00 3.51
574 1395 7.652300 TTATTCAAATGTATAGCAGCTACGG 57.348 36.000 3.59 0.00 0.00 4.02
575 1396 4.929819 TCAAATGTATAGCAGCTACGGA 57.070 40.909 3.59 0.00 0.00 4.69
576 1397 4.871513 TCAAATGTATAGCAGCTACGGAG 58.128 43.478 3.59 0.00 0.00 4.63
597 1418 9.939802 ACGGAGTAGATAAGACTTTGTTATTTT 57.060 29.630 0.00 0.00 41.94 1.82
646 3227 0.533085 GAAATAGAGCACGAGGGCCC 60.533 60.000 16.46 16.46 0.00 5.80
647 3228 0.983378 AAATAGAGCACGAGGGCCCT 60.983 55.000 29.18 29.18 0.00 5.19
648 3229 1.403687 AATAGAGCACGAGGGCCCTC 61.404 60.000 38.24 38.24 39.55 4.30
691 3275 1.004918 AAAACGGGGAGAGCTGACG 60.005 57.895 0.00 0.00 0.00 4.35
692 3276 2.450479 AAAACGGGGAGAGCTGACGG 62.450 60.000 0.00 0.00 0.00 4.79
693 3277 3.881019 AACGGGGAGAGCTGACGGA 62.881 63.158 0.00 0.00 0.00 4.69
694 3278 3.827898 CGGGGAGAGCTGACGGAC 61.828 72.222 0.00 0.00 0.00 4.79
780 3371 2.598467 GGTCACCACCAACCACCA 59.402 61.111 0.00 0.00 43.17 4.17
781 3372 1.826487 GGTCACCACCAACCACCAC 60.826 63.158 0.00 0.00 43.17 4.16
782 3373 1.826487 GTCACCACCAACCACCACC 60.826 63.158 0.00 0.00 0.00 4.61
783 3374 2.904866 CACCACCAACCACCACCG 60.905 66.667 0.00 0.00 0.00 4.94
784 3375 3.413300 ACCACCAACCACCACCGT 61.413 61.111 0.00 0.00 0.00 4.83
785 3376 2.593436 CCACCAACCACCACCGTC 60.593 66.667 0.00 0.00 0.00 4.79
977 3569 2.710440 GGTCCGTAGAGAGAGGAGC 58.290 63.158 0.00 0.00 43.87 4.70
1305 3919 2.203800 TCCTGTAATCACGCGATGTC 57.796 50.000 15.93 0.00 30.13 3.06
1325 3961 6.097156 TGTCGCGATGTATAATTTCGTTTT 57.903 33.333 14.06 0.00 35.40 2.43
1353 3989 0.248621 CGAATTGCGGGATCTTTGCC 60.249 55.000 0.00 0.00 36.03 4.52
1391 4036 0.606401 CGCTGGGAGTTGGTCAACAT 60.606 55.000 15.12 1.93 43.47 2.71
1411 4056 0.753867 TTTTTCCGAAAGTTGGGGGC 59.246 50.000 0.00 0.00 0.00 5.80
1489 5204 1.312815 ACAGCACAGGAAAGCTTGTC 58.687 50.000 0.00 0.00 39.50 3.18
1572 6378 8.970691 AACATGCTTCATTTCTGTATTACAAC 57.029 30.769 0.00 0.00 0.00 3.32
1573 6379 8.340618 ACATGCTTCATTTCTGTATTACAACT 57.659 30.769 0.00 0.00 0.00 3.16
1574 6380 8.796475 ACATGCTTCATTTCTGTATTACAACTT 58.204 29.630 0.00 0.00 0.00 2.66
1577 6383 9.278978 TGCTTCATTTCTGTATTACAACTTACA 57.721 29.630 0.00 0.00 0.00 2.41
1599 6407 4.348863 AGCATGTACATCAGGATCTTCC 57.651 45.455 5.07 0.00 36.58 3.46
1603 6411 5.357878 GCATGTACATCAGGATCTTCCAAAA 59.642 40.000 5.07 0.00 39.61 2.44
1611 6422 8.599792 ACATCAGGATCTTCCAAAATTTTCAAT 58.400 29.630 0.00 0.00 39.61 2.57
1634 6446 9.630098 CAATAGTTTATGATGACTTGCAGTTTT 57.370 29.630 0.00 0.00 0.00 2.43
1647 6463 8.128582 TGACTTGCAGTTTTAATTCAGTTGTAG 58.871 33.333 0.00 0.00 0.00 2.74
1687 6503 0.695347 ACTTCTGGGCCTCTTTCAGG 59.305 55.000 4.53 0.00 46.82 3.86
1759 6577 4.399219 AGAGTAGCATCGCTGTAATAGGA 58.601 43.478 0.00 0.00 40.10 2.94
1805 6623 0.110238 GATGCGTGAAAAGCTTGCGA 60.110 50.000 0.00 0.00 43.59 5.10
1846 6664 3.131396 CCGTGCTGTTTCAGAACTAACT 58.869 45.455 6.36 0.00 37.86 2.24
1930 6748 0.177141 TCGCTTTATCCTGGAACCGG 59.823 55.000 0.00 0.00 0.00 5.28
1986 6806 6.246163 AGGTAAGGGTTCTTTTATCAACTGG 58.754 40.000 0.00 0.00 34.59 4.00
2000 6845 3.554934 TCAACTGGTCATTTGCTTGTCT 58.445 40.909 0.00 0.00 0.00 3.41
2040 6888 2.438021 ACACAGTTTGGGTAGAAGCTCA 59.562 45.455 0.00 0.00 28.13 4.26
2043 6891 4.023707 CACAGTTTGGGTAGAAGCTCAAAG 60.024 45.833 0.00 0.00 30.97 2.77
2232 7092 2.451490 TGTCAGAAGTGGGCAAAACAA 58.549 42.857 0.00 0.00 0.00 2.83
2464 7324 2.872842 GCATTTGGCTGCAAAAGGATGT 60.873 45.455 17.55 0.00 41.87 3.06
2494 7354 1.918609 GTTATCGTGAACCGCTCAGTC 59.081 52.381 0.00 0.00 33.60 3.51
3172 8041 3.614092 GGTCATGGAGCAGAAGATCAAA 58.386 45.455 0.00 0.00 0.00 2.69
3199 8068 2.100749 GGTGGAGAAACAACAAACCCAG 59.899 50.000 0.00 0.00 0.00 4.45
3232 8101 2.877335 CGGTCTAGTTTCTGCCTGTAC 58.123 52.381 0.00 0.00 0.00 2.90
3301 8173 2.942604 TAACCCTCTCTTACTGGGCT 57.057 50.000 0.00 0.00 44.56 5.19
3308 8180 2.430332 CTCTCTTACTGGGCTCTCCTTG 59.570 54.545 0.00 0.00 36.20 3.61
3310 8182 1.203313 TCTTACTGGGCTCTCCTTGGT 60.203 52.381 0.00 0.00 36.20 3.67
3316 8189 2.040412 CTGGGCTCTCCTTGGTTAGTTT 59.960 50.000 0.00 0.00 36.20 2.66
3320 8193 3.496160 GGCTCTCCTTGGTTAGTTTGTCA 60.496 47.826 0.00 0.00 0.00 3.58
3350 8223 2.051334 TAATTAGCGCCTGCCATTGT 57.949 45.000 2.29 0.00 44.31 2.71
3397 8270 5.231991 GCAAAATGTTTGTACTCCACAACAG 59.768 40.000 2.92 0.00 46.80 3.16
3398 8271 6.559810 CAAAATGTTTGTACTCCACAACAGA 58.440 36.000 0.00 0.00 46.80 3.41
3399 8272 5.751243 AATGTTTGTACTCCACAACAGAC 57.249 39.130 0.00 0.00 46.80 3.51
3400 8273 4.209307 TGTTTGTACTCCACAACAGACA 57.791 40.909 0.00 0.00 46.80 3.41
3401 8274 4.580868 TGTTTGTACTCCACAACAGACAA 58.419 39.130 0.00 0.00 46.80 3.18
3460 8333 5.185828 GGCCTATTTGATTCACAGGAAAAGT 59.814 40.000 10.82 0.00 36.43 2.66
3462 8335 6.071952 GCCTATTTGATTCACAGGAAAAGTGA 60.072 38.462 10.82 0.00 43.72 3.41
3519 8392 9.066892 TCTTTAGTGGCAATATTTATCCATGTC 57.933 33.333 0.00 0.00 0.00 3.06
3568 8443 5.482163 TGGATGGATTTTTCCTTTGGTTC 57.518 39.130 0.00 0.00 32.95 3.62
3596 8471 8.567104 AGTTTCAAAGAAACAACAAAGCATTTT 58.433 25.926 20.71 0.00 31.88 1.82
3608 8483 6.655078 ACAAAGCATTTTCTACAATCCACT 57.345 33.333 0.00 0.00 35.03 4.00
3616 8493 8.897752 GCATTTTCTACAATCCACTCTAATCTT 58.102 33.333 0.00 0.00 0.00 2.40
3662 8547 4.764679 TGCCCTAAATTGCATAATAGCG 57.235 40.909 0.00 0.00 37.31 4.26
3668 8553 6.183360 CCCTAAATTGCATAATAGCGATCCAG 60.183 42.308 0.00 0.00 37.64 3.86
3685 8570 8.260818 AGCGATCCAGTATTATATTAGCATGTT 58.739 33.333 0.00 0.00 0.00 2.71
3738 8623 5.475564 GGTGCTTGTGTTTTTCCTATTCCTA 59.524 40.000 0.00 0.00 0.00 2.94
3759 8644 4.220693 ACGAATCAATCACTCAATCCCA 57.779 40.909 0.00 0.00 0.00 4.37
3761 8646 3.001634 CGAATCAATCACTCAATCCCACG 59.998 47.826 0.00 0.00 0.00 4.94
3812 8697 7.100409 TGTTTTAAAAACCAAGTGAAGAAGGG 58.900 34.615 1.31 0.00 0.00 3.95
3824 8709 0.033699 AAGAAGGGCAAGCTCCATCC 60.034 55.000 0.00 0.00 0.00 3.51
3834 8719 2.817258 CAAGCTCCATCCGGTTTTTACA 59.183 45.455 0.00 0.00 0.00 2.41
3835 8720 2.433436 AGCTCCATCCGGTTTTTACAC 58.567 47.619 0.00 0.00 0.00 2.90
3891 8788 5.479375 TCTTAAAACCTGAGAGACATACGGT 59.521 40.000 0.00 0.00 0.00 4.83
3932 8831 9.559732 TGTACACTGAAATTATTCATGGATAGG 57.440 33.333 0.00 0.00 44.29 2.57
3955 8854 1.226491 GCTGCGCAATGTGGTCATC 60.226 57.895 13.05 0.00 32.56 2.92
3985 8885 8.956426 TCAGTCTTGTTGTTAAATCTCTTTGTT 58.044 29.630 0.00 0.00 0.00 2.83
3995 8895 9.349713 TGTTAAATCTCTTTGTTAGTGTCCAAT 57.650 29.630 0.00 0.00 0.00 3.16
4118 9036 5.577164 CCGAGGTTTGAACAACTCATAGTAG 59.423 44.000 0.00 0.00 32.78 2.57
4119 9037 6.157211 CGAGGTTTGAACAACTCATAGTAGT 58.843 40.000 0.00 0.00 32.78 2.73
4123 9045 7.549488 AGGTTTGAACAACTCATAGTAGTATGC 59.451 37.037 12.07 0.00 36.68 3.14
4141 9063 9.482627 GTAGTATGCTTAGTCTTTAATCTGCAT 57.517 33.333 0.00 0.00 41.76 3.96
4167 9091 5.836024 ATTTCCTTACCTGTCTGTGGTTA 57.164 39.130 0.00 0.00 38.88 2.85
4168 9092 5.836024 TTTCCTTACCTGTCTGTGGTTAT 57.164 39.130 0.00 0.00 38.88 1.89
4171 9095 7.504926 TTCCTTACCTGTCTGTGGTTATATT 57.495 36.000 0.00 0.00 38.88 1.28
4181 9105 4.398988 TCTGTGGTTATATTTTGCAGGCAG 59.601 41.667 0.00 0.00 0.00 4.85
4201 9125 2.921126 GCTGATGCTTACAACACACAC 58.079 47.619 0.00 0.00 36.03 3.82
4202 9126 2.290367 GCTGATGCTTACAACACACACA 59.710 45.455 0.00 0.00 36.03 3.72
4203 9127 3.243035 GCTGATGCTTACAACACACACAA 60.243 43.478 0.00 0.00 36.03 3.33
4204 9128 4.282068 CTGATGCTTACAACACACACAAC 58.718 43.478 0.00 0.00 0.00 3.32
4205 9129 3.691609 TGATGCTTACAACACACACAACA 59.308 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.715534 TCTGAATAACCCACCACTTTGA 57.284 40.909 0.00 0.00 0.00 2.69
1 2 4.380867 GCATCTGAATAACCCACCACTTTG 60.381 45.833 0.00 0.00 0.00 2.77
2 3 3.763897 GCATCTGAATAACCCACCACTTT 59.236 43.478 0.00 0.00 0.00 2.66
3 4 3.010584 AGCATCTGAATAACCCACCACTT 59.989 43.478 0.00 0.00 0.00 3.16
4 5 2.578021 AGCATCTGAATAACCCACCACT 59.422 45.455 0.00 0.00 0.00 4.00
24 25 0.039256 CACACACCCCGCAAAATCAG 60.039 55.000 0.00 0.00 0.00 2.90
36 37 8.448615 GTGGATTTCTTAGTATTAACACACACC 58.551 37.037 0.00 0.00 0.00 4.16
43 44 7.763071 ACCTGACGTGGATTTCTTAGTATTAAC 59.237 37.037 0.00 0.00 0.00 2.01
44 45 7.844009 ACCTGACGTGGATTTCTTAGTATTAA 58.156 34.615 0.00 0.00 0.00 1.40
45 46 7.123098 TGACCTGACGTGGATTTCTTAGTATTA 59.877 37.037 0.00 0.00 0.00 0.98
46 47 6.070995 TGACCTGACGTGGATTTCTTAGTATT 60.071 38.462 0.00 0.00 0.00 1.89
59 60 2.032030 GTGAAAACATGACCTGACGTGG 60.032 50.000 0.00 0.00 0.00 4.94
62 63 1.535462 GGGTGAAAACATGACCTGACG 59.465 52.381 0.00 0.00 0.00 4.35
67 68 1.686052 TGCAAGGGTGAAAACATGACC 59.314 47.619 0.00 0.00 0.00 4.02
70 71 3.560896 CCTTTTGCAAGGGTGAAAACATG 59.439 43.478 0.00 0.00 45.63 3.21
82 83 4.024556 CCACGATATAGCTCCTTTTGCAAG 60.025 45.833 0.00 0.00 0.00 4.01
91 92 3.991121 GAGCTTTTCCACGATATAGCTCC 59.009 47.826 10.04 0.00 45.41 4.70
118 119 1.660052 CGACAATGCAGTGACGGTTTG 60.660 52.381 26.59 10.52 33.89 2.93
134 135 5.182950 ACAAATTTGACCAGCATTATCGACA 59.817 36.000 24.64 0.00 0.00 4.35
138 139 4.567959 GCCACAAATTTGACCAGCATTATC 59.432 41.667 24.64 0.00 0.00 1.75
140 141 3.323115 TGCCACAAATTTGACCAGCATTA 59.677 39.130 24.64 3.70 0.00 1.90
146 147 3.834489 AACATGCCACAAATTTGACCA 57.166 38.095 24.64 16.49 0.00 4.02
148 149 5.277442 CCTCAAAACATGCCACAAATTTGAC 60.277 40.000 24.64 13.21 34.27 3.18
149 150 4.815308 CCTCAAAACATGCCACAAATTTGA 59.185 37.500 24.64 2.30 35.96 2.69
150 151 4.815308 TCCTCAAAACATGCCACAAATTTG 59.185 37.500 16.67 16.67 0.00 2.32
151 152 5.033589 TCCTCAAAACATGCCACAAATTT 57.966 34.783 0.00 0.00 0.00 1.82
167 168 2.742116 GCCTGCCCGGTATCCTCAA 61.742 63.158 0.00 0.00 34.25 3.02
173 174 0.038166 CCATATTGCCTGCCCGGTAT 59.962 55.000 0.00 0.00 34.25 2.73
183 184 6.870439 GGATAAAATTCTTCAGCCATATTGCC 59.130 38.462 0.00 0.00 0.00 4.52
184 185 6.870439 GGGATAAAATTCTTCAGCCATATTGC 59.130 38.462 0.00 0.00 0.00 3.56
187 188 5.711976 CCGGGATAAAATTCTTCAGCCATAT 59.288 40.000 0.00 0.00 0.00 1.78
193 194 3.883489 GGACCCGGGATAAAATTCTTCAG 59.117 47.826 32.02 0.00 0.00 3.02
208 209 0.460284 CAAATCACTCTCGGACCCGG 60.460 60.000 8.73 0.00 40.25 5.73
215 216 4.151258 ACATTTGTGCAAATCACTCTCG 57.849 40.909 7.14 0.00 45.81 4.04
219 220 9.195411 CATAAAACTACATTTGTGCAAATCACT 57.805 29.630 7.14 0.00 45.81 3.41
227 228 7.276218 ACATGCATCATAAAACTACATTTGTGC 59.724 33.333 0.00 0.00 33.12 4.57
228 229 8.588789 CACATGCATCATAAAACTACATTTGTG 58.411 33.333 0.00 0.00 34.02 3.33
229 230 8.522003 TCACATGCATCATAAAACTACATTTGT 58.478 29.630 0.00 0.00 0.00 2.83
230 231 8.914328 TCACATGCATCATAAAACTACATTTG 57.086 30.769 0.00 0.00 0.00 2.32
262 263 9.109393 GTACCTCATTAGCTAAATGTCAAATCA 57.891 33.333 10.85 0.00 44.58 2.57
270 271 5.930135 ACCAGGTACCTCATTAGCTAAATG 58.070 41.667 12.84 9.50 45.47 2.32
303 304 4.080015 ACGGATCATCCCTTAAATGTCCAA 60.080 41.667 0.00 0.00 31.13 3.53
304 305 3.458118 ACGGATCATCCCTTAAATGTCCA 59.542 43.478 0.00 0.00 31.13 4.02
313 314 2.774234 AGACAATGACGGATCATCCCTT 59.226 45.455 0.00 0.00 45.26 3.95
349 350 2.685850 ATCCGGTCCCTTAAAAGTCG 57.314 50.000 0.00 0.00 0.00 4.18
357 358 3.197983 GCATATAGCTAATCCGGTCCCTT 59.802 47.826 0.00 0.00 41.15 3.95
490 1137 9.371136 TCAAGTGATGTAGAAATTAGATGTGAC 57.629 33.333 0.00 0.00 0.00 3.67
508 1155 7.966753 CACGAATCTTCATGAAAATCAAGTGAT 59.033 33.333 9.88 3.38 36.07 3.06
522 1169 9.357652 CAATTAAAAATCCACACGAATCTTCAT 57.642 29.630 0.00 0.00 0.00 2.57
561 1382 6.817641 GTCTTATCTACTCCGTAGCTGCTATA 59.182 42.308 13.20 0.00 36.22 1.31
562 1383 5.644636 GTCTTATCTACTCCGTAGCTGCTAT 59.355 44.000 13.20 0.00 36.22 2.97
563 1384 4.996122 GTCTTATCTACTCCGTAGCTGCTA 59.004 45.833 5.02 5.02 36.22 3.49
564 1385 3.816523 GTCTTATCTACTCCGTAGCTGCT 59.183 47.826 7.57 7.57 36.22 4.24
566 1387 6.183360 ACAAAGTCTTATCTACTCCGTAGCTG 60.183 42.308 0.00 0.00 36.22 4.24
571 1392 9.939802 AAAATAACAAAGTCTTATCTACTCCGT 57.060 29.630 0.00 0.00 0.00 4.69
646 3227 3.666902 CGGCACTGTTTTATTTCCACGAG 60.667 47.826 0.00 0.00 0.00 4.18
647 3228 2.224549 CGGCACTGTTTTATTTCCACGA 59.775 45.455 0.00 0.00 0.00 4.35
648 3229 2.224549 TCGGCACTGTTTTATTTCCACG 59.775 45.455 0.00 0.00 0.00 4.94
649 3230 3.907894 TCGGCACTGTTTTATTTCCAC 57.092 42.857 0.00 0.00 0.00 4.02
650 3231 5.492895 TCTATCGGCACTGTTTTATTTCCA 58.507 37.500 0.00 0.00 0.00 3.53
652 3233 7.007099 CGTTTTCTATCGGCACTGTTTTATTTC 59.993 37.037 0.00 0.00 0.00 2.17
691 3275 3.525545 GGGCTCGGTCTACGGTCC 61.526 72.222 0.00 0.00 44.45 4.46
692 3276 3.885521 CGGGCTCGGTCTACGGTC 61.886 72.222 0.00 0.00 44.45 4.79
693 3277 3.925630 TTCGGGCTCGGTCTACGGT 62.926 63.158 5.94 0.00 44.45 4.83
694 3278 3.122250 CTTCGGGCTCGGTCTACGG 62.122 68.421 5.94 0.00 44.45 4.02
808 3400 0.405973 AGTGGGAAGGAAGAAAGGCC 59.594 55.000 0.00 0.00 0.00 5.19
977 3569 2.470362 CGAGGAATGCAGCAGGCTG 61.470 63.158 16.68 16.68 45.15 4.85
1305 3919 5.206206 GCAAAACGAAATTATACATCGCG 57.794 39.130 0.00 0.00 40.09 5.87
1374 4010 4.670896 AAAAATGTTGACCAACTCCCAG 57.329 40.909 13.26 0.00 41.67 4.45
1411 4056 3.813166 AGTACACCGAAAATGTTGACCAG 59.187 43.478 0.00 0.00 0.00 4.00
1489 5204 3.186613 GCAGAGTAAAAACGACAAGGGAG 59.813 47.826 0.00 0.00 0.00 4.30
1572 6378 6.286758 AGATCCTGATGTACATGCTTGTAAG 58.713 40.000 14.43 7.84 39.96 2.34
1573 6379 6.239217 AGATCCTGATGTACATGCTTGTAA 57.761 37.500 14.43 5.76 39.96 2.41
1574 6380 5.876651 AGATCCTGATGTACATGCTTGTA 57.123 39.130 14.43 8.29 37.28 2.41
1575 6381 4.767578 AGATCCTGATGTACATGCTTGT 57.232 40.909 14.43 10.40 39.98 3.16
1576 6382 4.514441 GGAAGATCCTGATGTACATGCTTG 59.486 45.833 14.43 0.00 32.53 4.01
1577 6383 4.164796 TGGAAGATCCTGATGTACATGCTT 59.835 41.667 14.43 6.72 37.46 3.91
1578 6384 3.713248 TGGAAGATCCTGATGTACATGCT 59.287 43.478 14.43 0.00 37.46 3.79
1652 6468 7.503902 GGCCCAGAAGTTTCTAATTTATGAGAT 59.496 37.037 0.00 0.00 35.34 2.75
1653 6469 6.828785 GGCCCAGAAGTTTCTAATTTATGAGA 59.171 38.462 0.00 0.00 35.34 3.27
1654 6470 6.830838 AGGCCCAGAAGTTTCTAATTTATGAG 59.169 38.462 0.00 0.00 35.34 2.90
1656 6472 6.830838 AGAGGCCCAGAAGTTTCTAATTTATG 59.169 38.462 0.00 0.00 35.34 1.90
1657 6473 6.974795 AGAGGCCCAGAAGTTTCTAATTTAT 58.025 36.000 0.00 0.00 35.34 1.40
1658 6474 6.388619 AGAGGCCCAGAAGTTTCTAATTTA 57.611 37.500 0.00 0.00 35.34 1.40
1687 6503 2.991190 CAAAACATTGTCAGATGCCAGC 59.009 45.455 0.00 0.00 0.00 4.85
1688 6504 4.247267 ACAAAACATTGTCAGATGCCAG 57.753 40.909 0.00 0.00 0.00 4.85
1689 6505 4.669206 AACAAAACATTGTCAGATGCCA 57.331 36.364 0.00 0.00 33.35 4.92
1690 6506 5.523188 TGAAAACAAAACATTGTCAGATGCC 59.477 36.000 0.00 0.00 33.35 4.40
1759 6577 1.202533 GGTGCTGTGTGTACACTGAGT 60.203 52.381 25.60 0.00 46.55 3.41
1805 6623 0.034616 GGCCATAGCTCTTCTGCGAT 59.965 55.000 0.00 0.00 39.73 4.58
1846 6664 7.761704 GCAGCCTCTTCGATATGATTAAGATTA 59.238 37.037 0.00 0.00 0.00 1.75
1930 6748 6.665680 TCCAATCTACTATCTCTCTAATGCCC 59.334 42.308 0.00 0.00 0.00 5.36
1986 6806 6.407475 ACAACAAAAAGACAAGCAAATGAC 57.593 33.333 0.00 0.00 0.00 3.06
2000 6845 6.758886 ACTGTGTTCTTGAACAACAACAAAAA 59.241 30.769 16.46 0.82 35.53 1.94
2040 6888 0.826062 AAACAAGCAGTGCAGCCTTT 59.174 45.000 19.20 6.10 34.23 3.11
2043 6891 0.932399 CAAAAACAAGCAGTGCAGCC 59.068 50.000 19.20 0.00 34.23 4.85
2232 7092 1.428912 TGTTCTTTCCCAAGCCTCCAT 59.571 47.619 0.00 0.00 0.00 3.41
2464 7324 4.737054 GGTTCACGATAACGACCTTCTTA 58.263 43.478 0.00 0.00 42.66 2.10
2494 7354 2.408333 GATGGCATCCACCCTTTCG 58.592 57.895 16.75 0.00 35.80 3.46
3172 8041 5.234752 GTTTGTTGTTTCTCCACCTTTGTT 58.765 37.500 0.00 0.00 0.00 2.83
3199 8068 2.685897 ACTAGACCGCTGATCTCAGTTC 59.314 50.000 8.87 3.94 45.45 3.01
3232 8101 6.151985 GGACAGACTGGGAGTATATGTAGATG 59.848 46.154 7.51 0.00 0.00 2.90
3301 8173 6.126409 ACAATTGACAAACTAACCAAGGAGA 58.874 36.000 13.59 0.00 0.00 3.71
3316 8189 7.713507 AGGCGCTAATTAACTATACAATTGACA 59.286 33.333 13.59 0.00 0.00 3.58
3320 8193 6.072673 GGCAGGCGCTAATTAACTATACAATT 60.073 38.462 7.64 0.00 38.60 2.32
3331 8204 2.051334 ACAATGGCAGGCGCTAATTA 57.949 45.000 7.64 0.00 38.60 1.40
3350 8223 5.172687 TGTCTCAACATATTTGGCACCTA 57.827 39.130 0.00 0.00 0.00 3.08
3397 8270 5.221880 TGATAATGCACAAAAGCTGTTGTC 58.778 37.500 19.70 14.23 39.73 3.18
3398 8271 5.199024 TGATAATGCACAAAAGCTGTTGT 57.801 34.783 16.88 16.88 42.48 3.32
3399 8272 5.062934 CCATGATAATGCACAAAAGCTGTTG 59.937 40.000 15.38 15.38 35.47 3.33
3400 8273 5.047164 TCCATGATAATGCACAAAAGCTGTT 60.047 36.000 0.00 0.00 35.47 3.16
3401 8274 4.463539 TCCATGATAATGCACAAAAGCTGT 59.536 37.500 0.00 0.00 39.56 4.40
3519 8392 8.806177 TTTTTGTCTGAGTCATCATTTGAATG 57.194 30.769 0.00 0.00 35.70 2.67
3568 8443 5.344665 TGCTTTGTTGTTTCTTTGAAACTCG 59.655 36.000 19.52 6.96 0.00 4.18
3645 8530 7.369803 ACTGGATCGCTATTATGCAATTTAG 57.630 36.000 0.00 0.00 0.00 1.85
3660 8545 8.425577 AACATGCTAATATAATACTGGATCGC 57.574 34.615 0.00 0.00 0.00 4.58
3697 8582 8.669243 CACAAGCACCCTAAAAATTAAACAAAA 58.331 29.630 0.00 0.00 0.00 2.44
3702 8587 8.794335 AAAACACAAGCACCCTAAAAATTAAA 57.206 26.923 0.00 0.00 0.00 1.52
3706 8591 5.820423 GGAAAAACACAAGCACCCTAAAAAT 59.180 36.000 0.00 0.00 0.00 1.82
3715 8600 5.453567 AGGAATAGGAAAAACACAAGCAC 57.546 39.130 0.00 0.00 0.00 4.40
3717 8602 5.410439 TCGTAGGAATAGGAAAAACACAAGC 59.590 40.000 0.00 0.00 0.00 4.01
3718 8603 7.429636 TTCGTAGGAATAGGAAAAACACAAG 57.570 36.000 0.00 0.00 0.00 3.16
3738 8623 3.941483 GTGGGATTGAGTGATTGATTCGT 59.059 43.478 0.00 0.00 0.00 3.85
3759 8644 6.370718 GGATTATGTAAACACAGGAACTTCGT 59.629 38.462 0.00 0.00 34.60 3.85
3761 8646 7.824779 AGAGGATTATGTAAACACAGGAACTTC 59.175 37.037 0.00 0.00 34.60 3.01
3794 8679 2.745968 TGCCCTTCTTCACTTGGTTTT 58.254 42.857 0.00 0.00 0.00 2.43
3812 8697 0.603065 AAAAACCGGATGGAGCTTGC 59.397 50.000 9.46 0.00 39.21 4.01
3824 8709 1.865970 TGTAGTGGCGTGTAAAAACCG 59.134 47.619 0.00 0.00 0.00 4.44
3834 8719 1.094785 GGAATTGCATGTAGTGGCGT 58.905 50.000 0.00 0.00 0.00 5.68
3835 8720 1.064505 CAGGAATTGCATGTAGTGGCG 59.935 52.381 0.00 0.00 0.00 5.69
3885 8782 2.968574 AGATGCAATGAGGAGACCGTAT 59.031 45.455 0.00 0.00 0.00 3.06
3886 8783 2.101415 CAGATGCAATGAGGAGACCGTA 59.899 50.000 0.00 0.00 0.00 4.02
3887 8784 1.134580 CAGATGCAATGAGGAGACCGT 60.135 52.381 0.00 0.00 0.00 4.83
3891 8788 3.771479 AGTGTACAGATGCAATGAGGAGA 59.229 43.478 9.10 0.00 0.00 3.71
3898 8795 8.959548 TGAATAATTTCAGTGTACAGATGCAAT 58.040 29.630 0.00 0.00 36.94 3.56
3955 8854 9.956720 AAGAGATTTAACAACAAGACTGAAATG 57.043 29.630 0.00 0.00 0.00 2.32
4005 8922 1.138247 GCATGCAAAAGGAGCCTCG 59.862 57.895 14.21 0.00 0.00 4.63
4007 8924 0.893447 GAAGCATGCAAAAGGAGCCT 59.107 50.000 21.98 0.00 0.00 4.58
4008 8925 0.893447 AGAAGCATGCAAAAGGAGCC 59.107 50.000 21.98 0.00 0.00 4.70
4010 8927 2.818432 AGACAGAAGCATGCAAAAGGAG 59.182 45.455 21.98 5.24 0.00 3.69
4011 8928 2.816087 GAGACAGAAGCATGCAAAAGGA 59.184 45.455 21.98 0.00 0.00 3.36
4012 8929 2.818432 AGAGACAGAAGCATGCAAAAGG 59.182 45.455 21.98 7.63 0.00 3.11
4045 8963 3.350219 AGCAACCCGATCTACAACATT 57.650 42.857 0.00 0.00 0.00 2.71
4046 8964 3.270877 GAAGCAACCCGATCTACAACAT 58.729 45.455 0.00 0.00 0.00 2.71
4057 8975 0.036010 AGATCAGTGGAAGCAACCCG 60.036 55.000 0.00 0.00 0.00 5.28
4118 9036 8.370493 TGATGCAGATTAAAGACTAAGCATAC 57.630 34.615 0.00 0.00 41.07 2.39
4139 9061 6.484643 CCACAGACAGGTAAGGAAATATGATG 59.515 42.308 0.00 0.00 0.00 3.07
4141 9063 5.487488 ACCACAGACAGGTAAGGAAATATGA 59.513 40.000 0.00 0.00 37.67 2.15
4153 9077 5.321102 TGCAAAATATAACCACAGACAGGT 58.679 37.500 0.00 0.00 42.34 4.00
4155 9079 5.677091 GCCTGCAAAATATAACCACAGACAG 60.677 44.000 0.00 0.00 0.00 3.51
4167 9091 2.223971 GCATCAGCTGCCTGCAAAATAT 60.224 45.455 26.56 4.21 45.66 1.28
4168 9092 1.135527 GCATCAGCTGCCTGCAAAATA 59.864 47.619 26.56 2.05 45.66 1.40
4171 9095 2.967397 GCATCAGCTGCCTGCAAA 59.033 55.556 26.56 4.10 45.66 3.68
4181 9105 2.290367 TGTGTGTGTTGTAAGCATCAGC 59.710 45.455 0.00 0.00 42.56 4.26


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

AutoCloner maintained by Alex Coulton.