Multiple sequence alignment - TraesCS5D01G467400

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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 TraesCS5D01G467400 chr5D 100.000 3209 0 0 1 3209 509506168 509509376 0.000000e+00 5927.0
1 TraesCS5D01G467400 chr5B 92.725 2103 96 20 113 2211 640131301 640133350 0.000000e+00 2983.0
2 TraesCS5D01G467400 chr5B 90.000 450 14 7 2762 3209 640133606 640134026 1.300000e-153 553.0
3 TraesCS5D01G467400 chr5B 82.048 713 63 29 5 675 640130305 640130994 6.050000e-152 547.0
4 TraesCS5D01G467400 chr5B 90.406 271 15 5 407 675 640128226 640128487 2.370000e-91 346.0
5 TraesCS5D01G467400 chr5B 84.384 365 32 16 49 398 640127835 640128189 5.130000e-88 335.0
6 TraesCS5D01G467400 chr5B 92.553 94 3 3 2870 2963 652879651 652879562 7.220000e-27 132.0
7 TraesCS5D01G467400 chr5B 93.827 81 5 0 2655 2735 640133528 640133608 4.350000e-24 122.0
8 TraesCS5D01G467400 chr5A 90.869 2245 125 36 1 2211 636643233 636645431 0.000000e+00 2937.0
9 TraesCS5D01G467400 chr5A 85.106 235 19 2 2385 2603 636646180 636646414 3.220000e-55 226.0
10 TraesCS5D01G467400 chr5A 86.127 173 16 5 3038 3209 636646954 636647119 2.540000e-41 180.0
11 TraesCS5D01G467400 chr5A 80.645 155 11 5 2762 2916 636646823 636646958 5.660000e-18 102.0
12 TraesCS5D01G467400 chr5A 97.561 41 1 0 2358 2398 626226081 626226121 1.600000e-08 71.3


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 TraesCS5D01G467400 chr5D 509506168 509509376 3208 False 5927.000000 5927 100.000000 1 3209 1 chr5D.!!$F1 3208
1 TraesCS5D01G467400 chr5B 640127835 640134026 6191 False 814.333333 2983 88.898333 5 3209 6 chr5B.!!$F1 3204
2 TraesCS5D01G467400 chr5A 636643233 636647119 3886 False 861.250000 2937 85.686750 1 3209 4 chr5A.!!$F2 3208

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
218 3574 1.215647 CTGGACTCGTACAGCCCAC 59.784 63.158 0.0 0.0 34.31 4.61 F
1650 5049 0.521735 GATCAAACGCACTGGGGAAC 59.478 55.000 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 5361 0.165944 CGGCGACATCCTTCACAAAC 59.834 55.0 0.00 0.0 0.0 2.93 R
2749 7037 0.107410 AGAACAACGTGTGGCCAGAA 60.107 50.0 5.11 0.0 0.0 3.02 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
26 2493 6.531021 TGTAGCTTACTTCTAGTTGCCTTTT 58.469 36.000 0.00 0.00 30.45 2.27
37 2504 8.880878 TTCTAGTTGCCTTTTTACCAATTTTC 57.119 30.769 0.00 0.00 0.00 2.29
39 2506 8.357402 TCTAGTTGCCTTTTTACCAATTTTCTC 58.643 33.333 0.00 0.00 0.00 2.87
41 2508 7.210174 AGTTGCCTTTTTACCAATTTTCTCTC 58.790 34.615 0.00 0.00 0.00 3.20
43 2510 6.981722 TGCCTTTTTACCAATTTTCTCTCTC 58.018 36.000 0.00 0.00 0.00 3.20
45 2512 7.040409 TGCCTTTTTACCAATTTTCTCTCTCTC 60.040 37.037 0.00 0.00 0.00 3.20
48 2515 9.500785 CTTTTTACCAATTTTCTCTCTCTCTCT 57.499 33.333 0.00 0.00 0.00 3.10
53 2520 5.978919 CCAATTTTCTCTCTCTCTCTCGATG 59.021 44.000 0.00 0.00 0.00 3.84
88 2555 2.354403 CCCCCGGCTCCGTTTTATATAG 60.354 54.545 7.59 0.00 37.81 1.31
98 2565 7.444487 GGCTCCGTTTTATATAGAATGAAACCT 59.556 37.037 6.77 0.00 0.00 3.50
101 2568 9.893634 TCCGTTTTATATAGAATGAAACCTCAA 57.106 29.630 6.77 0.00 34.49 3.02
218 3574 1.215647 CTGGACTCGTACAGCCCAC 59.784 63.158 0.00 0.00 34.31 4.61
290 3646 4.099573 ACGGAGGGAACAGATTACATACAG 59.900 45.833 0.00 0.00 0.00 2.74
324 3681 6.090493 CCTGATCACATGAATGCTACTTATCG 59.910 42.308 0.00 0.00 0.00 2.92
805 4182 1.275657 CAACGGTGAACTGACACGC 59.724 57.895 0.00 0.00 41.12 5.34
807 4184 3.403057 CGGTGAACTGACACGCGG 61.403 66.667 12.47 1.27 41.12 6.46
810 4187 2.661537 TGAACTGACACGCGGCTG 60.662 61.111 12.47 2.37 0.00 4.85
823 4200 2.592861 GGCTGCCTCCGCATAAGG 60.593 66.667 12.43 0.00 46.11 2.69
904 4287 1.522355 CGAAGCCCACATGAGCGAT 60.522 57.895 0.00 0.00 0.00 4.58
1098 4497 4.496336 GCTGCAGCCTCCCGGATT 62.496 66.667 28.76 0.00 34.31 3.01
1177 4576 3.246112 CCCCGTCCCACACCTTCA 61.246 66.667 0.00 0.00 0.00 3.02
1239 4638 2.716017 CGAGCTCCCCAGAGACACC 61.716 68.421 8.47 0.00 43.39 4.16
1451 4850 0.543749 ATACTCTGCACCTCCAAGCC 59.456 55.000 0.00 0.00 0.00 4.35
1579 4978 0.673022 GGCTCTGACTGAACTGCTGG 60.673 60.000 0.00 0.00 0.00 4.85
1650 5049 0.521735 GATCAAACGCACTGGGGAAC 59.478 55.000 0.00 0.00 0.00 3.62
1674 5073 2.362397 GGGATACATCGAAGCAGTCAGA 59.638 50.000 0.00 0.00 39.74 3.27
1689 5088 4.746729 CAGTCAGAGAGATTGAGGAACAG 58.253 47.826 0.00 0.00 36.14 3.16
1779 5178 2.517166 GGCCTCGCTTTGGGATCC 60.517 66.667 1.92 1.92 0.00 3.36
1845 5244 6.014499 TCTGCTATGGCCCTAAATACTTCTAC 60.014 42.308 0.00 0.00 37.74 2.59
1887 5286 2.479389 CGATGAGCTTCAGTCTGGTCTC 60.479 54.545 0.00 5.21 0.00 3.36
1940 5339 2.750237 GGGCTTGGGTTACGCCAG 60.750 66.667 0.00 0.00 45.53 4.85
1949 5348 4.752879 TTACGCCAGGAGCACGGC 62.753 66.667 0.00 0.00 44.04 5.68
1962 5361 3.148279 ACGGCCGAGGAGCTTAGG 61.148 66.667 35.90 0.00 0.00 2.69
1980 5379 0.521735 GGTTTGTGAAGGATGTCGCC 59.478 55.000 0.00 0.00 0.00 5.54
2028 5427 4.745751 TACACCGGAAAGGCGGCG 62.746 66.667 9.46 0.51 46.52 6.46
2067 5466 2.627515 TGTCAGATAATCCAGGCAGC 57.372 50.000 0.00 0.00 0.00 5.25
2115 5514 2.203182 ACCGGTGGTCTCCTTGGA 59.797 61.111 6.12 0.00 0.00 3.53
2116 5515 2.214920 ACCGGTGGTCTCCTTGGAC 61.215 63.158 6.12 0.00 35.66 4.02
2187 5586 4.597507 AGAATGGACCTTGAAGAACCTGTA 59.402 41.667 0.00 0.00 0.00 2.74
2211 5610 4.774124 TCCATGCAAATCTCAACTAGGAG 58.226 43.478 0.00 0.00 36.21 3.69
2212 5611 3.881688 CCATGCAAATCTCAACTAGGAGG 59.118 47.826 0.00 0.00 35.58 4.30
2213 5612 4.384537 CCATGCAAATCTCAACTAGGAGGA 60.385 45.833 0.00 0.00 35.58 3.71
2214 5613 4.908601 TGCAAATCTCAACTAGGAGGAA 57.091 40.909 0.00 0.00 35.58 3.36
2215 5614 5.241403 TGCAAATCTCAACTAGGAGGAAA 57.759 39.130 0.00 0.00 35.58 3.13
2216 5615 5.630121 TGCAAATCTCAACTAGGAGGAAAA 58.370 37.500 0.00 0.00 35.58 2.29
2218 5617 5.392487 GCAAATCTCAACTAGGAGGAAAAGC 60.392 44.000 0.00 0.00 35.58 3.51
2221 5620 4.899502 TCTCAACTAGGAGGAAAAGCTTG 58.100 43.478 0.00 0.00 35.58 4.01
2222 5621 4.593206 TCTCAACTAGGAGGAAAAGCTTGA 59.407 41.667 0.00 0.00 35.58 3.02
2223 5622 5.071788 TCTCAACTAGGAGGAAAAGCTTGAA 59.928 40.000 0.00 0.00 35.58 2.69
2225 5624 5.940470 TCAACTAGGAGGAAAAGCTTGAATC 59.060 40.000 0.00 0.00 0.00 2.52
2226 5625 5.505181 ACTAGGAGGAAAAGCTTGAATCA 57.495 39.130 0.00 0.00 0.00 2.57
2230 5629 6.278172 AGGAGGAAAAGCTTGAATCATTTC 57.722 37.500 0.00 0.00 0.00 2.17
2231 5630 5.186603 AGGAGGAAAAGCTTGAATCATTTCC 59.813 40.000 14.88 14.88 45.96 3.13
2278 5847 4.283212 TGCAGGGCTAGCTTTTAACAAATT 59.717 37.500 15.72 0.00 0.00 1.82
2306 5875 6.924111 ACTGAGGTTGAATTTTGCGAATATT 58.076 32.000 0.00 0.00 0.00 1.28
2377 6371 3.986277 CAAATCTTTGGCTGTTGCTTCT 58.014 40.909 0.00 0.00 39.59 2.85
2378 6372 5.125100 CAAATCTTTGGCTGTTGCTTCTA 57.875 39.130 0.00 0.00 39.59 2.10
2379 6373 5.159209 CAAATCTTTGGCTGTTGCTTCTAG 58.841 41.667 0.00 0.00 39.59 2.43
2380 6374 3.769739 TCTTTGGCTGTTGCTTCTAGA 57.230 42.857 0.00 0.00 39.59 2.43
2381 6375 3.668447 TCTTTGGCTGTTGCTTCTAGAG 58.332 45.455 0.00 0.00 39.59 2.43
2382 6376 3.071602 TCTTTGGCTGTTGCTTCTAGAGT 59.928 43.478 0.00 0.00 39.59 3.24
2383 6377 2.751166 TGGCTGTTGCTTCTAGAGTC 57.249 50.000 0.00 0.00 39.59 3.36
2384 6378 1.276421 TGGCTGTTGCTTCTAGAGTCC 59.724 52.381 0.00 0.00 39.59 3.85
2385 6379 1.276421 GGCTGTTGCTTCTAGAGTCCA 59.724 52.381 0.00 0.00 39.59 4.02
2386 6380 2.093235 GGCTGTTGCTTCTAGAGTCCAT 60.093 50.000 0.00 0.00 39.59 3.41
2387 6381 3.604582 GCTGTTGCTTCTAGAGTCCATT 58.395 45.455 0.00 0.00 36.03 3.16
2388 6382 3.373439 GCTGTTGCTTCTAGAGTCCATTG 59.627 47.826 0.00 0.00 36.03 2.82
2389 6383 3.937706 CTGTTGCTTCTAGAGTCCATTGG 59.062 47.826 0.00 0.00 0.00 3.16
2390 6384 3.582647 TGTTGCTTCTAGAGTCCATTGGA 59.417 43.478 0.00 0.00 0.00 3.53
2391 6385 4.187694 GTTGCTTCTAGAGTCCATTGGAG 58.812 47.826 5.39 0.00 29.39 3.86
2392 6386 3.713003 TGCTTCTAGAGTCCATTGGAGA 58.287 45.455 5.39 0.00 29.39 3.71
2393 6387 4.096681 TGCTTCTAGAGTCCATTGGAGAA 58.903 43.478 5.39 4.99 29.39 2.87
2424 6418 3.459232 TTCTCCCAACTGCGATAGATG 57.541 47.619 0.00 0.00 39.76 2.90
2440 6434 6.511416 CGATAGATGTGGAGATCTTGAAACT 58.489 40.000 0.00 0.00 34.42 2.66
2451 6445 5.360591 AGATCTTGAAACTGACGAACACTT 58.639 37.500 0.00 0.00 0.00 3.16
2452 6446 4.857871 TCTTGAAACTGACGAACACTTG 57.142 40.909 0.00 0.00 0.00 3.16
2467 6461 3.279434 ACACTTGTTCTTCAACTGTCCC 58.721 45.455 0.00 0.00 31.04 4.46
2481 6475 2.303175 CTGTCCCTACTCCAGAGCTAC 58.697 57.143 0.00 0.00 0.00 3.58
2498 6492 5.955355 AGAGCTACTTGGTTTCACTCTATCT 59.045 40.000 0.00 0.00 31.52 1.98
2500 6494 7.284489 AGAGCTACTTGGTTTCACTCTATCTAG 59.716 40.741 0.00 0.00 31.52 2.43
2515 6509 6.665680 ACTCTATCTAGCCTTTTGAACTGAGA 59.334 38.462 0.00 0.00 0.00 3.27
2516 6510 7.344352 ACTCTATCTAGCCTTTTGAACTGAGAT 59.656 37.037 0.00 0.00 0.00 2.75
2580 6589 4.390297 GCACCTGAGTCTTCTGTAATTGAC 59.610 45.833 0.00 0.00 0.00 3.18
2581 6590 4.932200 CACCTGAGTCTTCTGTAATTGACC 59.068 45.833 0.00 0.00 0.00 4.02
2584 6593 6.176183 CCTGAGTCTTCTGTAATTGACCATT 58.824 40.000 0.00 0.00 0.00 3.16
2585 6594 6.314896 CCTGAGTCTTCTGTAATTGACCATTC 59.685 42.308 0.00 0.00 0.00 2.67
2598 6607 5.620738 TTGACCATTCCCTCTATCTTCTG 57.379 43.478 0.00 0.00 0.00 3.02
2603 6612 2.856760 TCCCTCTATCTTCTGTGGCT 57.143 50.000 0.00 0.00 0.00 4.75
2604 6613 2.392662 TCCCTCTATCTTCTGTGGCTG 58.607 52.381 0.00 0.00 0.00 4.85
2607 6616 3.244146 CCCTCTATCTTCTGTGGCTGATG 60.244 52.174 0.00 0.00 0.00 3.07
2608 6617 3.391965 CTCTATCTTCTGTGGCTGATGC 58.608 50.000 0.00 0.00 38.76 3.91
2609 6618 2.767960 TCTATCTTCTGTGGCTGATGCA 59.232 45.455 0.00 0.00 41.91 3.96
2612 6621 1.066358 TCTTCTGTGGCTGATGCAGAG 60.066 52.381 0.00 0.00 39.92 3.35
2613 6622 0.689055 TTCTGTGGCTGATGCAGAGT 59.311 50.000 0.00 0.00 39.92 3.24
2614 6623 0.248565 TCTGTGGCTGATGCAGAGTC 59.751 55.000 0.00 0.00 41.91 3.36
2615 6624 0.249676 CTGTGGCTGATGCAGAGTCT 59.750 55.000 0.00 0.00 41.91 3.24
2616 6625 0.036671 TGTGGCTGATGCAGAGTCTG 60.037 55.000 16.21 16.21 41.91 3.51
2633 6911 6.148315 CAGAGTCTGATGTATCAAAGTGCAAA 59.852 38.462 15.46 0.00 36.18 3.68
2634 6912 6.370994 AGAGTCTGATGTATCAAAGTGCAAAG 59.629 38.462 0.00 0.00 36.18 2.77
2635 6913 5.091431 GTCTGATGTATCAAAGTGCAAAGC 58.909 41.667 0.00 0.00 36.18 3.51
2706 6994 5.879777 TCGATCAGCTTCAAATCAATAACCA 59.120 36.000 0.00 0.00 0.00 3.67
2723 7011 3.634397 ACCACACCCTGTTATCTGATG 57.366 47.619 0.00 0.00 0.00 3.07
2732 7020 4.277672 CCCTGTTATCTGATGAAATGGCTG 59.722 45.833 0.00 0.00 0.00 4.85
2733 7021 4.885907 CCTGTTATCTGATGAAATGGCTGT 59.114 41.667 0.00 0.00 0.00 4.40
2734 7022 5.359009 CCTGTTATCTGATGAAATGGCTGTT 59.641 40.000 0.00 0.00 0.00 3.16
2735 7023 6.543465 CCTGTTATCTGATGAAATGGCTGTTA 59.457 38.462 0.00 0.00 0.00 2.41
2736 7024 7.067372 CCTGTTATCTGATGAAATGGCTGTTAA 59.933 37.037 0.00 0.00 0.00 2.01
2737 7025 7.761409 TGTTATCTGATGAAATGGCTGTTAAC 58.239 34.615 0.00 0.00 0.00 2.01
2738 7026 5.841957 ATCTGATGAAATGGCTGTTAACC 57.158 39.130 2.48 0.00 0.00 2.85
2739 7027 4.661222 TCTGATGAAATGGCTGTTAACCA 58.339 39.130 2.48 0.00 42.61 3.67
2740 7028 5.076182 TCTGATGAAATGGCTGTTAACCAA 58.924 37.500 2.48 0.00 41.49 3.67
2741 7029 5.716228 TCTGATGAAATGGCTGTTAACCAAT 59.284 36.000 2.48 0.00 41.49 3.16
2742 7030 5.722263 TGATGAAATGGCTGTTAACCAATG 58.278 37.500 2.48 0.00 41.49 2.82
2743 7031 3.924144 TGAAATGGCTGTTAACCAATGC 58.076 40.909 2.48 2.60 41.49 3.56
2744 7032 3.577848 TGAAATGGCTGTTAACCAATGCT 59.422 39.130 2.48 0.00 41.49 3.79
2745 7033 4.040217 TGAAATGGCTGTTAACCAATGCTT 59.960 37.500 2.48 0.00 41.49 3.91
2746 7034 3.874392 ATGGCTGTTAACCAATGCTTC 57.126 42.857 2.48 0.00 41.49 3.86
2747 7035 2.591923 TGGCTGTTAACCAATGCTTCA 58.408 42.857 2.48 0.00 33.12 3.02
2748 7036 3.164268 TGGCTGTTAACCAATGCTTCAT 58.836 40.909 2.48 0.00 33.12 2.57
2749 7037 3.577848 TGGCTGTTAACCAATGCTTCATT 59.422 39.130 2.48 0.00 33.12 2.57
2750 7038 4.040217 TGGCTGTTAACCAATGCTTCATTT 59.960 37.500 2.48 0.00 33.12 2.32
2751 7039 4.627035 GGCTGTTAACCAATGCTTCATTTC 59.373 41.667 2.48 0.00 31.05 2.17
2752 7040 5.473039 GCTGTTAACCAATGCTTCATTTCT 58.527 37.500 2.48 0.00 31.05 2.52
2753 7041 5.346822 GCTGTTAACCAATGCTTCATTTCTG 59.653 40.000 2.48 0.00 31.05 3.02
2754 7042 5.782047 TGTTAACCAATGCTTCATTTCTGG 58.218 37.500 2.48 0.00 31.05 3.86
2755 7043 3.323751 AACCAATGCTTCATTTCTGGC 57.676 42.857 0.00 0.00 31.05 4.85
2756 7044 1.551883 ACCAATGCTTCATTTCTGGCC 59.448 47.619 0.00 0.00 31.05 5.36
2757 7045 1.551430 CCAATGCTTCATTTCTGGCCA 59.449 47.619 4.71 4.71 31.05 5.36
2758 7046 2.613691 CAATGCTTCATTTCTGGCCAC 58.386 47.619 0.00 0.00 31.05 5.01
2759 7047 1.927487 ATGCTTCATTTCTGGCCACA 58.073 45.000 0.00 0.00 0.00 4.17
2760 7048 0.961019 TGCTTCATTTCTGGCCACAC 59.039 50.000 0.00 0.00 0.00 3.82
2849 7137 7.938715 ACAATCTCTTTGATCAGATAAATGGC 58.061 34.615 0.00 0.00 38.76 4.40
2850 7138 7.558807 ACAATCTCTTTGATCAGATAAATGGCA 59.441 33.333 0.00 0.00 38.76 4.92
2851 7139 8.410912 CAATCTCTTTGATCAGATAAATGGCAA 58.589 33.333 0.00 0.00 37.53 4.52
2852 7140 7.325660 TCTCTTTGATCAGATAAATGGCAAC 57.674 36.000 0.00 0.00 0.00 4.17
2853 7141 7.114754 TCTCTTTGATCAGATAAATGGCAACT 58.885 34.615 0.00 0.00 37.61 3.16
2854 7142 7.281774 TCTCTTTGATCAGATAAATGGCAACTC 59.718 37.037 0.00 0.00 37.61 3.01
2855 7143 6.885918 TCTTTGATCAGATAAATGGCAACTCA 59.114 34.615 0.00 0.00 37.61 3.41
2856 7144 6.688637 TTGATCAGATAAATGGCAACTCAG 57.311 37.500 0.00 0.00 37.61 3.35
2857 7145 5.128205 TGATCAGATAAATGGCAACTCAGG 58.872 41.667 0.00 0.00 37.61 3.86
2858 7146 3.282021 TCAGATAAATGGCAACTCAGGC 58.718 45.455 0.00 0.00 37.61 4.85
2865 7153 4.102113 GCAACTCAGGCCAACCAT 57.898 55.556 5.01 0.00 39.06 3.55
2866 7154 1.885871 GCAACTCAGGCCAACCATC 59.114 57.895 5.01 0.00 39.06 3.51
2867 7155 0.610232 GCAACTCAGGCCAACCATCT 60.610 55.000 5.01 0.00 39.06 2.90
2931 7219 8.829373 ATTGAAATAAAGAGGCTGGTAGATTT 57.171 30.769 0.00 0.00 0.00 2.17
2963 7251 6.015940 GGAAGCGATGATTGGAAATAGGAAAT 60.016 38.462 0.00 0.00 0.00 2.17
3011 7299 3.316308 TGCTTCCTGCTCTGTTTTCTTTC 59.684 43.478 0.00 0.00 43.37 2.62
3012 7300 3.567585 GCTTCCTGCTCTGTTTTCTTTCT 59.432 43.478 0.00 0.00 38.95 2.52
3014 7302 5.756849 CTTCCTGCTCTGTTTTCTTTCTTC 58.243 41.667 0.00 0.00 0.00 2.87
3015 7303 5.041191 TCCTGCTCTGTTTTCTTTCTTCT 57.959 39.130 0.00 0.00 0.00 2.85
3016 7304 4.818546 TCCTGCTCTGTTTTCTTTCTTCTG 59.181 41.667 0.00 0.00 0.00 3.02
3018 7306 3.885297 TGCTCTGTTTTCTTTCTTCTGGG 59.115 43.478 0.00 0.00 0.00 4.45
3026 7315 6.490040 TGTTTTCTTTCTTCTGGGTAATCAGG 59.510 38.462 0.00 0.00 35.58 3.86
3103 7392 3.421844 CCCTGAGGGTGTTTTCCTTAAG 58.578 50.000 10.09 0.00 38.25 1.85
3193 7483 0.610232 ACTGAATGCTGGGTTGAGCC 60.610 55.000 0.00 0.00 38.28 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 2485 7.287696 AGAGAGAGAAAATTGGTAAAAAGGCAA 59.712 33.333 0.00 0.00 0.00 4.52
21 2488 8.628630 AGAGAGAGAGAAAATTGGTAAAAAGG 57.371 34.615 0.00 0.00 0.00 3.11
26 2493 6.659668 TCGAGAGAGAGAGAGAAAATTGGTAA 59.340 38.462 0.00 0.00 34.84 2.85
45 2512 0.602562 GAGCCCCTGATCATCGAGAG 59.397 60.000 0.00 0.00 0.00 3.20
48 2515 0.829602 GGAGAGCCCCTGATCATCGA 60.830 60.000 0.00 0.00 0.00 3.59
88 2555 6.152661 TGGAATGTATGGTTGAGGTTTCATTC 59.847 38.462 0.00 0.00 39.09 2.67
98 2565 5.241403 ACTGAACTGGAATGTATGGTTGA 57.759 39.130 0.00 0.00 0.00 3.18
101 2568 6.976934 AAAAACTGAACTGGAATGTATGGT 57.023 33.333 0.00 0.00 0.00 3.55
127 3481 4.613850 GCTGTTTTACTTTCTGCTGCTACC 60.614 45.833 0.00 0.00 0.00 3.18
218 3574 7.325660 AGTATGGTCATAACTGCTGAAAATG 57.674 36.000 0.00 0.00 0.00 2.32
290 3646 0.107312 ATGTGATCAGGCCTGACTGC 60.107 55.000 37.39 27.22 43.11 4.40
324 3681 0.599728 GGATGCATCCAGAGCTCGAC 60.600 60.000 35.93 8.54 46.38 4.20
832 4211 4.323477 TTTCCAGGGCGTCCACCG 62.323 66.667 9.71 0.00 40.40 4.94
833 4212 2.671963 GTTTCCAGGGCGTCCACC 60.672 66.667 9.71 0.00 34.83 4.61
871 4254 1.660104 GCTTCGGGCGTCGTTTTATAA 59.340 47.619 0.00 0.00 40.32 0.98
874 4257 2.028733 GGCTTCGGGCGTCGTTTTA 61.029 57.895 0.00 0.00 42.94 1.52
904 4287 2.658422 GTTTGTCCGTCGGGCCTA 59.342 61.111 14.50 0.00 0.00 3.93
1098 4497 3.393970 CTGGAGAGGAAGCCGCCA 61.394 66.667 0.00 0.00 0.00 5.69
1224 4623 2.680352 TCGGTGTCTCTGGGGAGC 60.680 66.667 0.00 0.00 39.31 4.70
1239 4638 1.811266 CCGCTTGATCCACACCTCG 60.811 63.158 0.00 0.00 0.00 4.63
1296 4695 3.289525 AGGAACTCGAGCTTCCGG 58.710 61.111 26.78 0.00 41.97 5.14
1470 4869 2.915659 AGGTTGCCGACGAGACCA 60.916 61.111 13.96 0.00 34.60 4.02
1519 4918 0.251386 TCTCTCTGCGAGACCAGGTT 60.251 55.000 0.00 0.00 43.72 3.50
1579 4978 1.859302 TCTTCCAGGAGCCTCTTCTC 58.141 55.000 0.00 0.00 0.00 2.87
1650 5049 1.414181 ACTGCTTCGATGTATCCCCAG 59.586 52.381 0.00 0.85 0.00 4.45
1674 5073 6.371595 AACTGAATCTGTTCCTCAATCTCT 57.628 37.500 0.00 0.00 33.26 3.10
1689 5088 0.861837 CGCCGCCAGATAACTGAATC 59.138 55.000 0.79 0.00 46.03 2.52
1704 5103 0.179250 CGTCAAACTGAACATCGCCG 60.179 55.000 0.00 0.00 0.00 6.46
1845 5244 2.509052 TCAGACCTTGAACACAGTCG 57.491 50.000 0.00 0.00 34.41 4.18
1887 5286 7.440255 TCAATGCTGACTATATCATGTGAGTTG 59.560 37.037 0.00 0.00 36.48 3.16
1949 5348 1.275291 TCACAAACCTAAGCTCCTCGG 59.725 52.381 0.00 0.00 0.00 4.63
1950 5349 2.743636 TCACAAACCTAAGCTCCTCG 57.256 50.000 0.00 0.00 0.00 4.63
1953 5352 3.418684 TCCTTCACAAACCTAAGCTCC 57.581 47.619 0.00 0.00 0.00 4.70
1956 5355 3.125316 CGACATCCTTCACAAACCTAAGC 59.875 47.826 0.00 0.00 0.00 3.09
1962 5361 0.165944 CGGCGACATCCTTCACAAAC 59.834 55.000 0.00 0.00 0.00 2.93
2019 5418 1.519898 CATACCGTACGCCGCCTTT 60.520 57.895 10.49 0.00 34.38 3.11
2028 5427 3.118884 ACATGTCCTTCACCATACCGTAC 60.119 47.826 0.00 0.00 0.00 3.67
2080 5479 1.227823 TGTGCACAAAGAGGACCCG 60.228 57.895 19.28 0.00 0.00 5.28
2115 5514 6.156949 ACAACTGATCCACCTTATCATACAGT 59.843 38.462 0.00 0.00 37.62 3.55
2116 5515 6.586344 ACAACTGATCCACCTTATCATACAG 58.414 40.000 0.00 0.00 33.08 2.74
2187 5586 4.225942 TCCTAGTTGAGATTTGCATGGAGT 59.774 41.667 0.00 0.00 0.00 3.85
2211 5610 7.658982 AGAAAAGGAAATGATTCAAGCTTTTCC 59.341 33.333 20.29 20.29 43.40 3.13
2212 5611 8.493547 CAGAAAAGGAAATGATTCAAGCTTTTC 58.506 33.333 15.78 15.78 43.12 2.29
2213 5612 7.989170 ACAGAAAAGGAAATGATTCAAGCTTTT 59.011 29.630 0.00 0.00 37.31 2.27
2214 5613 7.503549 ACAGAAAAGGAAATGATTCAAGCTTT 58.496 30.769 0.00 0.00 37.29 3.51
2215 5614 7.059202 ACAGAAAAGGAAATGATTCAAGCTT 57.941 32.000 0.00 0.00 37.29 3.74
2216 5615 6.266103 TGACAGAAAAGGAAATGATTCAAGCT 59.734 34.615 0.00 0.00 37.29 3.74
2218 5617 7.040201 TCCTGACAGAAAAGGAAATGATTCAAG 60.040 37.037 3.32 0.00 39.68 3.02
2221 5620 6.824305 TCCTGACAGAAAAGGAAATGATTC 57.176 37.500 3.32 0.00 39.68 2.52
2222 5621 6.950041 TCATCCTGACAGAAAAGGAAATGATT 59.050 34.615 3.32 0.00 45.56 2.57
2223 5622 6.376581 GTCATCCTGACAGAAAAGGAAATGAT 59.623 38.462 3.32 0.00 46.22 2.45
2225 5624 5.947443 GTCATCCTGACAGAAAAGGAAATG 58.053 41.667 3.32 0.00 46.22 2.32
2260 5829 8.458843 TCAGTATCAATTTGTTAAAAGCTAGCC 58.541 33.333 12.13 0.00 0.00 3.93
2278 5847 5.000591 TCGCAAAATTCAACCTCAGTATCA 58.999 37.500 0.00 0.00 0.00 2.15
2356 6350 3.986277 AGAAGCAACAGCCAAAGATTTG 58.014 40.909 0.00 0.00 37.90 2.32
2377 6371 9.807921 ACTTTTTAAATTCTCCAATGGACTCTA 57.192 29.630 0.00 0.00 0.00 2.43
2378 6372 8.712228 ACTTTTTAAATTCTCCAATGGACTCT 57.288 30.769 0.00 0.00 0.00 3.24
2379 6373 9.764363 AAACTTTTTAAATTCTCCAATGGACTC 57.236 29.630 0.00 0.00 0.00 3.36
2380 6374 9.764363 GAAACTTTTTAAATTCTCCAATGGACT 57.236 29.630 0.00 0.00 0.00 3.85
2381 6375 9.764363 AGAAACTTTTTAAATTCTCCAATGGAC 57.236 29.630 0.00 0.00 0.00 4.02
2382 6376 9.981114 GAGAAACTTTTTAAATTCTCCAATGGA 57.019 29.630 14.41 0.48 41.08 3.41
2389 6383 9.249457 CAGTTGGGAGAAACTTTTTAAATTCTC 57.751 33.333 16.08 16.08 44.41 2.87
2390 6384 7.710907 GCAGTTGGGAGAAACTTTTTAAATTCT 59.289 33.333 2.20 2.20 38.34 2.40
2391 6385 7.306574 CGCAGTTGGGAGAAACTTTTTAAATTC 60.307 37.037 0.00 0.00 38.34 2.17
2392 6386 6.478673 CGCAGTTGGGAGAAACTTTTTAAATT 59.521 34.615 0.00 0.00 38.34 1.82
2393 6387 5.983118 CGCAGTTGGGAGAAACTTTTTAAAT 59.017 36.000 0.00 0.00 38.34 1.40
2424 6418 3.914312 TCGTCAGTTTCAAGATCTCCAC 58.086 45.455 0.00 0.00 0.00 4.02
2451 6445 3.323979 GGAGTAGGGACAGTTGAAGAACA 59.676 47.826 0.00 0.00 34.17 3.18
2452 6446 3.323979 TGGAGTAGGGACAGTTGAAGAAC 59.676 47.826 0.00 0.00 0.00 3.01
2464 6458 2.358300 CCAAGTAGCTCTGGAGTAGGGA 60.358 54.545 3.80 0.00 0.00 4.20
2467 6461 4.220821 TGAAACCAAGTAGCTCTGGAGTAG 59.779 45.833 14.62 0.00 0.00 2.57
2481 6475 5.606348 AGGCTAGATAGAGTGAAACCAAG 57.394 43.478 0.00 0.00 37.80 3.61
2498 6492 4.287067 AGTGGATCTCAGTTCAAAAGGCTA 59.713 41.667 0.00 0.00 0.00 3.93
2500 6494 3.416156 AGTGGATCTCAGTTCAAAAGGC 58.584 45.455 0.00 0.00 0.00 4.35
2548 6557 5.350914 CAGAAGACTCAGGTGCTTGATAAAG 59.649 44.000 0.00 0.00 0.00 1.85
2552 6561 2.636893 ACAGAAGACTCAGGTGCTTGAT 59.363 45.455 0.00 0.00 0.00 2.57
2580 6589 3.495806 GCCACAGAAGATAGAGGGAATGG 60.496 52.174 0.00 0.00 0.00 3.16
2581 6590 3.390639 AGCCACAGAAGATAGAGGGAATG 59.609 47.826 0.00 0.00 0.00 2.67
2584 6593 2.023984 TCAGCCACAGAAGATAGAGGGA 60.024 50.000 0.00 0.00 0.00 4.20
2585 6594 2.392662 TCAGCCACAGAAGATAGAGGG 58.607 52.381 0.00 0.00 0.00 4.30
2598 6607 0.248565 TCAGACTCTGCATCAGCCAC 59.751 55.000 0.62 0.00 41.13 5.01
2603 6612 5.603170 TTGATACATCAGACTCTGCATCA 57.397 39.130 0.62 5.15 38.19 3.07
2604 6613 6.018913 CACTTTGATACATCAGACTCTGCATC 60.019 42.308 0.62 2.91 38.19 3.91
2607 6616 4.033817 GCACTTTGATACATCAGACTCTGC 59.966 45.833 0.62 0.00 38.19 4.26
2608 6617 5.173664 TGCACTTTGATACATCAGACTCTG 58.826 41.667 0.00 0.00 38.19 3.35
2609 6618 5.411831 TGCACTTTGATACATCAGACTCT 57.588 39.130 0.00 0.00 38.19 3.24
2612 6621 5.091431 GCTTTGCACTTTGATACATCAGAC 58.909 41.667 0.00 0.00 38.19 3.51
2613 6622 4.142838 CGCTTTGCACTTTGATACATCAGA 60.143 41.667 0.00 0.00 38.19 3.27
2614 6623 4.093514 CGCTTTGCACTTTGATACATCAG 58.906 43.478 0.00 0.00 38.19 2.90
2615 6624 3.501828 ACGCTTTGCACTTTGATACATCA 59.498 39.130 0.00 0.00 34.44 3.07
2616 6625 4.083581 ACGCTTTGCACTTTGATACATC 57.916 40.909 0.00 0.00 0.00 3.06
2633 6911 1.066573 AGTTTCTGCATCAGCTACGCT 60.067 47.619 0.00 0.00 42.74 5.07
2634 6912 1.325943 GAGTTTCTGCATCAGCTACGC 59.674 52.381 0.00 0.00 42.74 4.42
2635 6913 2.610433 TGAGTTTCTGCATCAGCTACG 58.390 47.619 0.00 0.00 42.74 3.51
2651 6939 3.445096 GTGGCCAGAAATAAAGCATGAGT 59.555 43.478 5.11 0.00 0.00 3.41
2706 6994 5.195940 CCATTTCATCAGATAACAGGGTGT 58.804 41.667 0.00 0.00 0.00 4.16
2723 7011 4.192429 AGCATTGGTTAACAGCCATTTC 57.808 40.909 8.10 0.00 35.71 2.17
2732 7020 4.627035 GCCAGAAATGAAGCATTGGTTAAC 59.373 41.667 0.22 0.00 34.04 2.01
2733 7021 4.322650 GGCCAGAAATGAAGCATTGGTTAA 60.323 41.667 0.00 0.00 34.04 2.01
2734 7022 3.195396 GGCCAGAAATGAAGCATTGGTTA 59.805 43.478 0.00 0.00 34.04 2.85
2735 7023 2.027837 GGCCAGAAATGAAGCATTGGTT 60.028 45.455 0.00 0.00 34.04 3.67
2736 7024 1.551883 GGCCAGAAATGAAGCATTGGT 59.448 47.619 0.00 0.00 34.04 3.67
2737 7025 1.551430 TGGCCAGAAATGAAGCATTGG 59.449 47.619 0.00 0.00 34.04 3.16
2738 7026 2.028839 TGTGGCCAGAAATGAAGCATTG 60.029 45.455 5.11 0.00 34.04 2.82
2739 7027 2.028748 GTGTGGCCAGAAATGAAGCATT 60.029 45.455 5.11 0.00 35.39 3.56
2740 7028 1.547372 GTGTGGCCAGAAATGAAGCAT 59.453 47.619 5.11 0.00 0.00 3.79
2741 7029 0.961019 GTGTGGCCAGAAATGAAGCA 59.039 50.000 5.11 0.00 0.00 3.91
2742 7030 0.109597 CGTGTGGCCAGAAATGAAGC 60.110 55.000 5.11 0.00 0.00 3.86
2743 7031 1.238439 ACGTGTGGCCAGAAATGAAG 58.762 50.000 5.11 0.00 0.00 3.02
2744 7032 1.336440 CAACGTGTGGCCAGAAATGAA 59.664 47.619 5.11 0.00 0.00 2.57
2745 7033 0.950836 CAACGTGTGGCCAGAAATGA 59.049 50.000 5.11 0.00 0.00 2.57
2746 7034 0.667993 ACAACGTGTGGCCAGAAATG 59.332 50.000 5.11 7.53 0.00 2.32
2747 7035 1.336755 GAACAACGTGTGGCCAGAAAT 59.663 47.619 5.11 0.00 0.00 2.17
2748 7036 0.736053 GAACAACGTGTGGCCAGAAA 59.264 50.000 5.11 0.00 0.00 2.52
2749 7037 0.107410 AGAACAACGTGTGGCCAGAA 60.107 50.000 5.11 0.00 0.00 3.02
2750 7038 0.753867 TAGAACAACGTGTGGCCAGA 59.246 50.000 5.11 0.00 0.00 3.86
2751 7039 1.148310 CTAGAACAACGTGTGGCCAG 58.852 55.000 5.11 0.00 0.00 4.85
2752 7040 0.882927 GCTAGAACAACGTGTGGCCA 60.883 55.000 0.00 0.00 0.00 5.36
2753 7041 0.882927 TGCTAGAACAACGTGTGGCC 60.883 55.000 0.00 0.00 0.00 5.36
2754 7042 0.941542 TTGCTAGAACAACGTGTGGC 59.058 50.000 0.00 0.00 0.00 5.01
2755 7043 2.663279 GTTGCTAGAACAACGTGTGG 57.337 50.000 0.00 0.00 40.45 4.17
2826 7114 8.411683 GTTGCCATTTATCTGATCAAAGAGATT 58.588 33.333 0.00 0.00 37.00 2.40
2849 7137 1.457346 GAGATGGTTGGCCTGAGTTG 58.543 55.000 3.32 0.00 35.27 3.16
2850 7138 0.329596 GGAGATGGTTGGCCTGAGTT 59.670 55.000 3.32 0.00 35.27 3.01
2851 7139 0.842030 TGGAGATGGTTGGCCTGAGT 60.842 55.000 3.32 0.00 35.27 3.41
2852 7140 0.549950 ATGGAGATGGTTGGCCTGAG 59.450 55.000 3.32 0.00 35.27 3.35
2853 7141 0.256752 CATGGAGATGGTTGGCCTGA 59.743 55.000 3.32 0.00 35.27 3.86
2854 7142 1.389609 GCATGGAGATGGTTGGCCTG 61.390 60.000 3.32 0.00 35.27 4.85
2855 7143 1.076485 GCATGGAGATGGTTGGCCT 60.076 57.895 3.32 0.00 35.27 5.19
2856 7144 2.129785 GGCATGGAGATGGTTGGCC 61.130 63.158 0.00 0.00 0.00 5.36
2857 7145 0.757935 ATGGCATGGAGATGGTTGGC 60.758 55.000 0.00 0.00 35.41 4.52
2858 7146 1.784358 AATGGCATGGAGATGGTTGG 58.216 50.000 0.00 0.00 0.00 3.77
2859 7147 3.317149 CACTAATGGCATGGAGATGGTTG 59.683 47.826 14.70 1.20 0.00 3.77
2860 7148 3.559069 CACTAATGGCATGGAGATGGTT 58.441 45.455 14.70 0.00 0.00 3.67
2861 7149 2.750807 GCACTAATGGCATGGAGATGGT 60.751 50.000 14.70 0.00 0.00 3.55
2862 7150 1.884579 GCACTAATGGCATGGAGATGG 59.115 52.381 14.70 0.00 0.00 3.51
2863 7151 2.552743 CTGCACTAATGGCATGGAGATG 59.447 50.000 14.70 10.47 41.06 2.90
2864 7152 2.488528 CCTGCACTAATGGCATGGAGAT 60.489 50.000 14.70 0.00 41.06 2.75
2865 7153 1.134007 CCTGCACTAATGGCATGGAGA 60.134 52.381 14.70 0.00 41.06 3.71
2866 7154 1.134007 TCCTGCACTAATGGCATGGAG 60.134 52.381 0.00 4.31 41.06 3.86
2867 7155 0.918258 TCCTGCACTAATGGCATGGA 59.082 50.000 0.00 0.00 41.06 3.41
2931 7219 2.094597 CCAATCATCGCTTCCTTTTGCA 60.095 45.455 0.00 0.00 0.00 4.08
2963 7251 9.685276 ATGACCTGAATTCATACAAATTACAGA 57.315 29.630 8.96 0.00 31.68 3.41
2973 7261 5.128919 AGGAAGCATGACCTGAATTCATAC 58.871 41.667 8.96 4.36 34.99 2.39
3011 7299 4.392940 CCATAAGCCTGATTACCCAGAAG 58.607 47.826 0.00 0.00 36.29 2.85
3012 7300 3.435026 GCCATAAGCCTGATTACCCAGAA 60.435 47.826 0.00 0.00 36.29 3.02
3014 7302 2.158623 TGCCATAAGCCTGATTACCCAG 60.159 50.000 0.00 0.00 42.71 4.45
3015 7303 1.849692 TGCCATAAGCCTGATTACCCA 59.150 47.619 0.00 0.00 42.71 4.51
3016 7304 2.656947 TGCCATAAGCCTGATTACCC 57.343 50.000 0.00 0.00 42.71 3.69
3018 7306 9.177608 TGATTATTATGCCATAAGCCTGATTAC 57.822 33.333 3.22 0.00 42.71 1.89


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

AutoCloner maintained by Alex Coulton.