Multiple sequence alignment - TraesCS5D01G131600

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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 TraesCS5D01G131600 chr5D 100.000 6798 0 0 1 6798 209310800 209304003 0.000000e+00 12554.0
1 TraesCS5D01G131600 chr5D 94.231 104 6 0 3342 3445 209307348 209307245 7.060000e-35 159.0
2 TraesCS5D01G131600 chr5D 94.231 104 6 0 3453 3556 209307459 209307356 7.060000e-35 159.0
3 TraesCS5D01G131600 chr5A 95.951 5607 149 19 817 6379 270177962 270172390 0.000000e+00 9025.0
4 TraesCS5D01G131600 chr5A 95.349 258 12 0 14 271 270178910 270178653 1.760000e-110 411.0
5 TraesCS5D01G131600 chr5A 83.777 413 33 18 427 828 270178375 270177986 1.800000e-95 361.0
6 TraesCS5D01G131600 chr5A 93.939 231 10 2 6547 6773 270156009 270155779 5.050000e-91 346.0
7 TraesCS5D01G131600 chr5A 96.000 150 5 1 6372 6521 270156306 270156158 6.810000e-60 243.0
8 TraesCS5D01G131600 chr5A 90.385 104 10 0 3453 3556 270175459 270175356 3.310000e-28 137.0
9 TraesCS5D01G131600 chr5A 100.000 40 0 0 6759 6798 270155777 270155738 2.630000e-09 75.0
10 TraesCS5D01G131600 chr5B 97.565 3820 81 5 2310 6127 222365209 222361400 0.000000e+00 6529.0
11 TraesCS5D01G131600 chr5B 95.017 883 40 2 817 1697 222367575 222366695 0.000000e+00 1384.0
12 TraesCS5D01G131600 chr5B 96.719 640 17 4 1674 2311 222366670 222366033 0.000000e+00 1062.0
13 TraesCS5D01G131600 chr5B 96.512 258 9 0 14 271 222368535 222368278 1.750000e-115 427.0
14 TraesCS5D01G131600 chr5B 90.734 259 16 3 6547 6798 222356926 222356669 8.450000e-89 339.0
15 TraesCS5D01G131600 chr5B 91.139 237 17 4 6145 6378 222361238 222361003 1.100000e-82 318.0
16 TraesCS5D01G131600 chr5B 94.175 103 6 0 3453 3555 222364180 222364078 2.540000e-34 158.0
17 TraesCS5D01G131600 chr5B 93.443 61 4 0 6381 6441 222357093 222357033 2.610000e-14 91.6
18 TraesCS5D01G131600 chr3D 75.987 1266 139 83 14 1225 442504118 442505272 1.020000e-137 501.0
19 TraesCS5D01G131600 chr3D 78.981 314 34 22 1309 1614 442505301 442505590 1.160000e-42 185.0
20 TraesCS5D01G131600 chr3A 77.593 723 82 46 50 734 583707306 583707986 1.390000e-96 364.0
21 TraesCS5D01G131600 chr3B 85.757 337 38 7 14 349 580038386 580038713 1.400000e-91 348.0
22 TraesCS5D01G131600 chr4A 81.746 252 44 2 1129 1379 501966750 501966500 6.910000e-50 209.0
23 TraesCS5D01G131600 chr4D 81.275 251 45 2 1130 1379 89427164 89426915 1.160000e-47 202.0
24 TraesCS5D01G131600 chr4B 80.556 252 47 2 1129 1379 126327774 126327524 6.960000e-45 193.0


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 TraesCS5D01G131600 chr5D 209304003 209310800 6797 True 4290.666667 12554 96.154000 1 6798 3 chr5D.!!$R1 6797
1 TraesCS5D01G131600 chr5A 270172390 270178910 6520 True 2483.500000 9025 91.365500 14 6379 4 chr5A.!!$R2 6365
2 TraesCS5D01G131600 chr5A 270155738 270156306 568 True 221.333333 346 96.646333 6372 6798 3 chr5A.!!$R1 426
3 TraesCS5D01G131600 chr5B 222356669 222368535 11866 True 1288.575000 6529 94.413000 14 6798 8 chr5B.!!$R1 6784
4 TraesCS5D01G131600 chr3D 442504118 442505590 1472 False 343.000000 501 77.484000 14 1614 2 chr3D.!!$F1 1600
5 TraesCS5D01G131600 chr3A 583707306 583707986 680 False 364.000000 364 77.593000 50 734 1 chr3A.!!$F1 684

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
774 1067 0.169009 GGAGCTTGGATGCGTTGTTC 59.831 55.000 0.00 0.00 38.13 3.18 F
1464 1833 0.041312 ACGTGTGCATTTCGCTTGTC 60.041 50.000 0.00 0.00 43.06 3.18 F
1699 2116 2.394563 TGCGTGTGTGTGTGTGTGG 61.395 57.895 0.00 0.00 0.00 4.17 F
1720 2137 3.305403 GGTTTCTTTAGCACCAGAAAGGC 60.305 47.826 4.87 0.00 39.22 4.35 F
3249 4493 2.479656 CAGAAGCTTCAAGCAGACTGTC 59.520 50.000 27.57 0.00 45.56 3.51 F
3726 4970 0.250513 CCTCTTCCCGGAACAGAAGG 59.749 60.000 15.49 5.92 38.45 3.46 F
5347 6618 0.550147 ATCAGGGTGGCAGTAAGGGT 60.550 55.000 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 2032 0.383590 CACGCACACATGGTTTCCAA 59.616 50.000 0.00 0.00 36.95 3.53 R
3222 4466 1.977854 TGCTTGAAGCTTCTGTCCCTA 59.022 47.619 26.09 2.03 42.97 3.53 R
3249 4493 2.104451 AGATGCAGCTGGGTTCTCATAG 59.896 50.000 17.12 0.00 0.00 2.23 R
3493 4737 3.198853 CCTAAGAAAGAGGGAGTTCCAGG 59.801 52.174 0.00 0.00 38.24 4.45 R
4119 5363 3.385577 CTTCGATAGCTGTTTCCCTAGC 58.614 50.000 0.00 0.00 40.18 3.42 R
5395 6666 1.153086 GGCAGTGGCAGATACAGGG 60.153 63.158 12.58 0.00 43.71 4.45 R
6523 11848 0.179048 TGCATTGGGGATCTGCTACG 60.179 55.000 5.60 0.00 36.84 3.51 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
47 51 7.921214 CCAGTAGCTTATCTTACATTCTCGAAA 59.079 37.037 0.00 0.00 0.00 3.46
124 129 1.271597 CCAAGCTTAAGGAGGCACTGT 60.272 52.381 0.00 0.00 41.55 3.55
240 254 5.740569 CCATTGCGTGTGAAATCTGAAATAG 59.259 40.000 0.00 0.00 0.00 1.73
264 278 6.763135 AGCATAAGCCATGTATCATATAACCG 59.237 38.462 0.00 0.00 43.56 4.44
308 322 6.218019 AGTATACACAACGCAAACTAGTGAA 58.782 36.000 5.50 0.00 34.47 3.18
310 324 2.353579 ACACAACGCAAACTAGTGAACC 59.646 45.455 0.00 0.00 34.47 3.62
344 358 6.450545 ACTCATATTGTCCATATCGACACAG 58.549 40.000 2.32 0.00 42.37 3.66
379 395 5.478233 TTCGTACAATATTGACACCATGC 57.522 39.130 22.16 1.32 0.00 4.06
380 396 4.508662 TCGTACAATATTGACACCATGCA 58.491 39.130 22.16 0.00 0.00 3.96
401 417 4.154195 GCATAATCACTAGCGTAATTGGGG 59.846 45.833 0.00 0.00 0.00 4.96
405 421 4.289238 TCACTAGCGTAATTGGGGAAAA 57.711 40.909 0.00 0.00 0.00 2.29
406 422 4.850680 TCACTAGCGTAATTGGGGAAAAT 58.149 39.130 0.00 0.00 0.00 1.82
407 423 5.258051 TCACTAGCGTAATTGGGGAAAATT 58.742 37.500 0.00 0.00 34.24 1.82
408 424 5.124776 TCACTAGCGTAATTGGGGAAAATTG 59.875 40.000 0.00 0.00 32.16 2.32
409 425 5.124776 CACTAGCGTAATTGGGGAAAATTGA 59.875 40.000 0.00 0.00 32.16 2.57
410 426 5.712917 ACTAGCGTAATTGGGGAAAATTGAA 59.287 36.000 0.00 0.00 32.16 2.69
411 427 4.816392 AGCGTAATTGGGGAAAATTGAAC 58.184 39.130 0.00 0.00 32.16 3.18
412 428 4.282195 AGCGTAATTGGGGAAAATTGAACA 59.718 37.500 0.00 0.00 32.16 3.18
414 430 4.619336 CGTAATTGGGGAAAATTGAACACG 59.381 41.667 0.00 0.00 32.16 4.49
415 431 4.946478 AATTGGGGAAAATTGAACACGA 57.054 36.364 0.00 0.00 0.00 4.35
416 432 4.946478 ATTGGGGAAAATTGAACACGAA 57.054 36.364 0.00 0.00 0.00 3.85
419 435 5.283457 TGGGGAAAATTGAACACGAAAAT 57.717 34.783 0.00 0.00 0.00 1.82
421 437 5.053811 GGGGAAAATTGAACACGAAAATGT 58.946 37.500 0.00 0.00 0.00 2.71
425 441 8.604890 GGGAAAATTGAACACGAAAATGTTTTA 58.395 29.630 0.00 0.00 42.89 1.52
456 672 6.790285 ATCATTTTGAACATGAAAAGGTGC 57.210 33.333 0.00 0.00 34.31 5.01
480 739 8.143193 TGCCAAATATCTAATGTTTATTGCCAG 58.857 33.333 0.00 0.00 0.00 4.85
486 745 6.543430 TCTAATGTTTATTGCCAGCCAAAT 57.457 33.333 0.00 0.00 36.92 2.32
487 746 7.652524 TCTAATGTTTATTGCCAGCCAAATA 57.347 32.000 0.00 0.00 36.92 1.40
490 749 9.328845 CTAATGTTTATTGCCAGCCAAATAAAT 57.671 29.630 9.67 1.00 36.92 1.40
492 751 9.678260 AATGTTTATTGCCAGCCAAATAAATTA 57.322 25.926 9.67 5.22 36.92 1.40
493 752 8.715191 TGTTTATTGCCAGCCAAATAAATTAG 57.285 30.769 9.67 0.00 36.92 1.73
498 758 7.710676 TTGCCAGCCAAATAAATTAGTAGAA 57.289 32.000 0.00 0.00 0.00 2.10
509 769 8.895932 AATAAATTAGTAGAAGTTTGCTTGCG 57.104 30.769 0.00 0.00 34.61 4.85
516 776 2.740981 AGAAGTTTGCTTGCGAGATCTG 59.259 45.455 4.70 0.00 34.61 2.90
555 824 1.289066 CTCACCGGTGATGTGACGT 59.711 57.895 36.21 0.00 37.80 4.34
556 825 0.524414 CTCACCGGTGATGTGACGTA 59.476 55.000 36.21 12.13 37.80 3.57
557 826 0.524414 TCACCGGTGATGTGACGTAG 59.476 55.000 33.23 3.20 37.80 3.51
558 827 1.076533 CACCGGTGATGTGACGTAGC 61.077 60.000 31.31 0.00 35.74 3.58
559 828 1.248785 ACCGGTGATGTGACGTAGCT 61.249 55.000 6.12 0.00 0.00 3.32
560 829 0.802222 CCGGTGATGTGACGTAGCTG 60.802 60.000 0.00 0.00 0.00 4.24
561 830 0.170339 CGGTGATGTGACGTAGCTGA 59.830 55.000 0.00 0.00 0.00 4.26
564 838 3.262420 GGTGATGTGACGTAGCTGAAAT 58.738 45.455 0.00 0.00 0.00 2.17
566 840 4.868171 GGTGATGTGACGTAGCTGAAATAA 59.132 41.667 0.00 0.00 0.00 1.40
580 854 0.462047 AAATAAGAGGAGCCGGTGCG 60.462 55.000 1.90 0.00 44.33 5.34
617 898 1.423056 GCAACGAGCTCATCAGTGC 59.577 57.895 15.40 10.96 41.15 4.40
623 904 4.479993 GCTCATCAGTGCGGGGCT 62.480 66.667 0.00 0.00 0.00 5.19
630 911 3.157252 AGTGCGGGGCTCGATGAT 61.157 61.111 12.93 0.00 42.43 2.45
672 953 0.338120 AGGAGGTGGAAGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
673 954 0.336737 GGAGGTGGAAGAGGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
674 955 1.687996 GGAGGTGGAAGAGGAGGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
675 956 0.338120 AGGTGGAAGAGGAGGAGAGG 59.662 60.000 0.00 0.00 0.00 3.69
676 957 0.336737 GGTGGAAGAGGAGGAGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
677 958 1.687996 GGTGGAAGAGGAGGAGAGGAG 60.688 61.905 0.00 0.00 0.00 3.69
678 959 1.286553 GTGGAAGAGGAGGAGAGGAGA 59.713 57.143 0.00 0.00 0.00 3.71
714 1001 1.000612 GACGGAGGAGGAGGAAGGT 59.999 63.158 0.00 0.00 0.00 3.50
721 1013 1.521141 GAGGAGGAAGGTAACCGCC 59.479 63.158 0.00 0.00 45.48 6.13
722 1014 2.186125 GGAGGAAGGTAACCGCCG 59.814 66.667 0.00 0.00 37.59 6.46
723 1015 2.186125 GAGGAAGGTAACCGCCGG 59.814 66.667 0.00 0.00 37.17 6.13
724 1016 4.091939 AGGAAGGTAACCGCCGGC 62.092 66.667 19.07 19.07 37.17 6.13
725 1017 4.397832 GGAAGGTAACCGCCGGCA 62.398 66.667 28.98 2.89 37.17 5.69
765 1058 1.382420 AGCGGAGAGGAGCTTGGAT 60.382 57.895 0.00 0.00 41.52 3.41
767 1060 1.227497 CGGAGAGGAGCTTGGATGC 60.227 63.158 0.00 0.00 0.00 3.91
774 1067 0.169009 GGAGCTTGGATGCGTTGTTC 59.831 55.000 0.00 0.00 38.13 3.18
777 1082 1.501741 CTTGGATGCGTTGTTCCGG 59.498 57.895 0.00 0.00 34.58 5.14
780 1085 4.160635 GATGCGTTGTTCCGGCCG 62.161 66.667 21.04 21.04 0.00 6.13
798 1103 1.481056 CGGGGAATAAGCGGGGATCT 61.481 60.000 0.00 0.00 0.00 2.75
810 1124 2.210711 GGGATCTCGGGCTACCTGG 61.211 68.421 0.00 0.00 33.28 4.45
812 1126 2.844839 ATCTCGGGCTACCTGGGC 60.845 66.667 0.00 0.00 28.52 5.36
813 1127 3.396822 ATCTCGGGCTACCTGGGCT 62.397 63.158 0.00 0.00 28.52 5.19
814 1128 3.854669 CTCGGGCTACCTGGGCTG 61.855 72.222 0.00 0.00 39.17 4.85
828 1172 1.657751 GGGCTGGGAGAAATGCGTTC 61.658 60.000 0.00 0.00 36.38 3.95
867 1211 0.178767 TGACCATTCCGCCAGATCAG 59.821 55.000 0.00 0.00 0.00 2.90
951 1303 3.055719 CCTGGCACGAACCGCAAT 61.056 61.111 0.00 0.00 0.00 3.56
1103 1455 1.378646 TCAGCTCGTCATCGGAGGT 60.379 57.895 0.00 0.00 37.69 3.85
1416 1779 3.265221 TCCGTTACACTCCCTTCTCTCTA 59.735 47.826 0.00 0.00 0.00 2.43
1464 1833 0.041312 ACGTGTGCATTTCGCTTGTC 60.041 50.000 0.00 0.00 43.06 3.18
1663 2032 5.065218 GGTTGCATAGAGTCGAATTGAACAT 59.935 40.000 0.00 0.00 0.00 2.71
1699 2116 2.394563 TGCGTGTGTGTGTGTGTGG 61.395 57.895 0.00 0.00 0.00 4.17
1720 2137 3.305403 GGTTTCTTTAGCACCAGAAAGGC 60.305 47.826 4.87 0.00 39.22 4.35
1835 2253 4.735985 TGATTTGCAATCACTCGATTTGG 58.264 39.130 0.00 0.00 39.96 3.28
1928 2346 9.965902 AGTAATCTGTAAGTCATTCCTTCAAAT 57.034 29.630 0.00 0.00 33.76 2.32
1938 2356 8.434589 AGTCATTCCTTCAAATTTTTATGGGA 57.565 30.769 0.00 0.00 0.00 4.37
2188 2607 9.464714 GATATTGTTGTCGTATCAGTCTGTTAT 57.535 33.333 0.00 0.00 0.00 1.89
2786 4030 3.619733 GCAACACCAGTACCATCTGATGA 60.620 47.826 18.92 0.00 37.61 2.92
2876 4120 4.649674 AGAGGCACTGAATTCGTATCCTAA 59.350 41.667 15.94 0.00 41.55 2.69
2913 4157 8.915871 TTTCAATTCTTCTTCAACAACTCAAG 57.084 30.769 0.00 0.00 0.00 3.02
3004 4248 5.771469 TGCCAGATATTGTGAAGTTTGTTG 58.229 37.500 0.00 0.00 0.00 3.33
3205 4449 6.544564 TCCTGAACAAAACTGTAAAACCCTAG 59.455 38.462 0.00 0.00 0.00 3.02
3221 4465 5.678955 ACCCTAGGTTCTCAAAGTATCAC 57.321 43.478 8.29 0.00 27.29 3.06
3222 4466 5.342866 ACCCTAGGTTCTCAAAGTATCACT 58.657 41.667 8.29 0.00 27.29 3.41
3249 4493 2.479656 CAGAAGCTTCAAGCAGACTGTC 59.520 50.000 27.57 0.00 45.56 3.51
3322 4566 2.957402 TGAGGATCAAAAGGTGTGCT 57.043 45.000 0.00 0.00 45.97 4.40
3493 4737 0.890683 CCACAAGGAAGTTGATGCCC 59.109 55.000 0.00 0.00 38.60 5.36
3716 4960 2.300437 GGATCCATAAGACCTCTTCCCG 59.700 54.545 6.95 0.00 37.40 5.14
3726 4970 0.250513 CCTCTTCCCGGAACAGAAGG 59.749 60.000 15.49 5.92 38.45 3.46
3737 4981 4.177026 CGGAACAGAAGGTCAGATGTAAG 58.823 47.826 0.00 0.00 0.00 2.34
3767 5011 2.337583 TGCAGCGATGACTGTTAACTC 58.662 47.619 4.02 0.00 39.96 3.01
3836 5080 7.236640 AGAGACAGAAAAGTTAAAGAGGGATCT 59.763 37.037 0.00 0.00 0.00 2.75
3864 5108 1.734465 CTCCAGAACTCGAAACCATGC 59.266 52.381 0.00 0.00 0.00 4.06
3921 5165 3.118905 GGTGATACCTCCAAGATGAGC 57.881 52.381 0.00 0.00 34.73 4.26
4119 5363 7.432869 TCACAAGATTTTACTTTTGGGATGTG 58.567 34.615 0.00 0.00 28.63 3.21
4281 5525 8.406297 GTTGAAGATTTTACCAGTGAAGTCTTT 58.594 33.333 12.26 0.80 36.05 2.52
4292 5536 8.498054 ACCAGTGAAGTCTTTCATGTAATATG 57.502 34.615 0.00 0.00 44.62 1.78
4511 5755 2.726241 GCCTTGCTGCTTTAAAACTTCG 59.274 45.455 0.00 0.00 0.00 3.79
4595 5839 4.338682 AGTTTAGTAGTCGGAGCACCTATG 59.661 45.833 0.00 0.00 0.00 2.23
4711 5955 5.245531 TGTTTGGCTCGATCACTTTAAGAT 58.754 37.500 0.00 0.00 0.00 2.40
5291 6562 6.644347 CAGATTATGCCTGGTATAAGGGTAG 58.356 44.000 19.63 6.98 37.84 3.18
5299 6570 5.748139 GCCTGGTATAAGGGTAGAATTTCCC 60.748 48.000 0.00 6.29 43.71 3.97
5347 6618 0.550147 ATCAGGGTGGCAGTAAGGGT 60.550 55.000 0.00 0.00 0.00 4.34
5428 6699 1.321474 CTGCCAAAACTGCTGAAGGA 58.679 50.000 0.00 0.00 0.00 3.36
5518 6789 0.392729 CAGAGCAAGAGCCCAGAAGG 60.393 60.000 0.00 0.00 43.56 3.46
5695 6966 2.346847 GCAGACACAGAAGCAGTATTCG 59.653 50.000 0.00 0.00 34.27 3.34
5752 7023 1.394917 GATAAGCTTGTGGACAGCGTG 59.605 52.381 9.86 0.00 0.00 5.34
5801 7072 4.355543 GCAAAGGCGTCTAATTGATGAA 57.644 40.909 5.65 0.00 33.63 2.57
5848 7119 1.198637 CCTTTTCTCTTTGAGCGGCAG 59.801 52.381 1.45 0.00 0.00 4.85
5923 7194 4.433615 GGATTATGTTCTTCGTCAGCTCA 58.566 43.478 0.00 0.00 0.00 4.26
5934 7205 1.005242 CGTCAGCTCATCAAATCAGCG 60.005 52.381 0.00 0.00 38.26 5.18
6070 7343 1.429930 TTGCTGAGGGTTCACTGGTA 58.570 50.000 0.00 0.00 0.00 3.25
6085 7358 5.657474 TCACTGGTATCGAATAAACTGGAC 58.343 41.667 0.00 0.00 0.00 4.02
6102 7375 2.240612 GACCACTGCGATTCGTTGGC 62.241 60.000 17.88 10.53 30.51 4.52
6133 7406 2.704464 GGGCCTACCAAAACGTCTAT 57.296 50.000 0.84 0.00 39.85 1.98
6145 7429 2.361643 ACGTCTATGGAGGGAGTACC 57.638 55.000 3.73 0.00 40.67 3.34
6154 7570 8.007742 GTCTATGGAGGGAGTACCATATGATAT 58.992 40.741 3.65 0.00 44.64 1.63
6169 7585 8.244494 CCATATGATATGGTTGAGTTTCTACG 57.756 38.462 20.81 0.00 34.56 3.51
6275 7691 1.465777 GTTGGCTGCATTTGATTTGGC 59.534 47.619 0.50 0.00 0.00 4.52
6276 7692 0.685660 TGGCTGCATTTGATTTGGCA 59.314 45.000 0.50 0.00 34.66 4.92
6302 7718 1.873591 ACGCAGTTGATTGGTCTTGAC 59.126 47.619 0.00 0.00 37.78 3.18
6364 7780 4.549458 CAGTGTTGCCTTTGGTAATCAAG 58.451 43.478 0.00 0.00 36.62 3.02
6365 7781 4.037923 CAGTGTTGCCTTTGGTAATCAAGT 59.962 41.667 0.00 0.00 36.62 3.16
6449 11774 4.553323 CATCTCCAACAGCTTTCCAAAAG 58.447 43.478 0.00 0.00 0.00 2.27
6518 11843 1.944709 GTTTGAAAGGTGTGTAGCCGT 59.055 47.619 0.00 0.00 0.00 5.68
6540 11865 0.886490 GCCGTAGCAGATCCCCAATG 60.886 60.000 0.00 0.00 39.53 2.82
6556 12011 2.613691 CAATGCAACTTCTCCAATGGC 58.386 47.619 0.00 0.00 0.00 4.40
6709 12169 2.203181 GGAGCTGCTGGAGATGCC 60.203 66.667 7.01 0.00 37.10 4.40
6726 12186 6.239887 GGAGATGCCCTTAGATGGTTATACAA 60.240 42.308 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.886505 GGGTATGCATCATTTTTACGGGA 59.113 43.478 0.19 0.00 0.00 5.14
1 2 3.634448 TGGGTATGCATCATTTTTACGGG 59.366 43.478 0.19 0.00 0.00 5.28
2 3 4.338118 ACTGGGTATGCATCATTTTTACGG 59.662 41.667 0.19 0.00 0.00 4.02
3 4 5.499139 ACTGGGTATGCATCATTTTTACG 57.501 39.130 0.19 0.00 0.00 3.18
4 5 6.263168 AGCTACTGGGTATGCATCATTTTTAC 59.737 38.462 0.19 0.00 0.00 2.01
5 6 6.364701 AGCTACTGGGTATGCATCATTTTTA 58.635 36.000 0.19 0.00 0.00 1.52
6 7 5.203528 AGCTACTGGGTATGCATCATTTTT 58.796 37.500 0.19 0.00 0.00 1.94
7 8 4.796606 AGCTACTGGGTATGCATCATTTT 58.203 39.130 0.19 0.00 0.00 1.82
8 9 4.443978 AGCTACTGGGTATGCATCATTT 57.556 40.909 0.19 0.00 0.00 2.32
9 10 4.443978 AAGCTACTGGGTATGCATCATT 57.556 40.909 0.19 0.00 0.00 2.57
10 11 5.486775 AGATAAGCTACTGGGTATGCATCAT 59.513 40.000 0.19 0.00 0.00 2.45
11 12 4.840680 AGATAAGCTACTGGGTATGCATCA 59.159 41.667 0.19 0.00 0.00 3.07
12 13 5.413309 AGATAAGCTACTGGGTATGCATC 57.587 43.478 0.19 0.00 0.00 3.91
124 129 8.206126 TGGAAAGCCACATCTATTATCTATCA 57.794 34.615 0.00 0.00 39.92 2.15
240 254 6.761242 TCGGTTATATGATACATGGCTTATGC 59.239 38.462 0.00 0.00 40.59 3.14
281 295 8.030692 TCACTAGTTTGCGTTGTGTATACTATT 58.969 33.333 4.17 0.00 29.40 1.73
283 297 6.912082 TCACTAGTTTGCGTTGTGTATACTA 58.088 36.000 4.17 0.00 0.00 1.82
287 301 4.212636 GGTTCACTAGTTTGCGTTGTGTAT 59.787 41.667 0.00 0.00 0.00 2.29
290 304 2.612212 AGGTTCACTAGTTTGCGTTGTG 59.388 45.455 0.00 0.00 0.00 3.33
299 313 8.974060 TGAGTTTGATTTAAGGTTCACTAGTT 57.026 30.769 0.00 0.00 0.00 2.24
308 322 8.877864 TGGACAATATGAGTTTGATTTAAGGT 57.122 30.769 0.00 0.00 0.00 3.50
359 373 4.873768 TGCATGGTGTCAATATTGTACG 57.126 40.909 14.97 5.38 0.00 3.67
379 395 5.547465 TCCCCAATTACGCTAGTGATTATG 58.453 41.667 10.99 3.89 34.82 1.90
380 396 5.818678 TCCCCAATTACGCTAGTGATTAT 57.181 39.130 10.99 0.00 34.82 1.28
435 651 4.815308 TGGCACCTTTTCATGTTCAAAATG 59.185 37.500 0.00 0.00 0.00 2.32
456 672 7.599998 GGCTGGCAATAAACATTAGATATTTGG 59.400 37.037 0.00 0.00 0.00 3.28
480 739 9.639601 AAGCAAACTTCTACTAATTTATTTGGC 57.360 29.630 0.00 0.00 0.00 4.52
486 745 7.601130 TCTCGCAAGCAAACTTCTACTAATTTA 59.399 33.333 0.00 0.00 32.29 1.40
487 746 6.426937 TCTCGCAAGCAAACTTCTACTAATTT 59.573 34.615 0.00 0.00 32.29 1.82
490 749 4.878439 TCTCGCAAGCAAACTTCTACTAA 58.122 39.130 0.00 0.00 32.29 2.24
492 751 3.386768 TCTCGCAAGCAAACTTCTACT 57.613 42.857 0.00 0.00 32.29 2.57
493 752 3.929610 AGATCTCGCAAGCAAACTTCTAC 59.070 43.478 0.00 0.00 32.29 2.59
498 758 1.446907 CCAGATCTCGCAAGCAAACT 58.553 50.000 0.00 0.00 37.18 2.66
509 769 1.719378 TCCTCCTATCCCCCAGATCTC 59.281 57.143 0.00 0.00 36.33 2.75
516 776 1.537643 CAGCCTCCTCCTATCCCCC 60.538 68.421 0.00 0.00 0.00 5.40
555 824 2.365617 CCGGCTCCTCTTATTTCAGCTA 59.634 50.000 0.00 0.00 0.00 3.32
556 825 1.139853 CCGGCTCCTCTTATTTCAGCT 59.860 52.381 0.00 0.00 0.00 4.24
557 826 1.134371 ACCGGCTCCTCTTATTTCAGC 60.134 52.381 0.00 0.00 0.00 4.26
558 827 2.555199 CACCGGCTCCTCTTATTTCAG 58.445 52.381 0.00 0.00 0.00 3.02
559 828 1.406887 GCACCGGCTCCTCTTATTTCA 60.407 52.381 0.00 0.00 36.96 2.69
560 829 1.300481 GCACCGGCTCCTCTTATTTC 58.700 55.000 0.00 0.00 36.96 2.17
561 830 0.462047 CGCACCGGCTCCTCTTATTT 60.462 55.000 0.00 0.00 38.10 1.40
564 838 4.143333 GCGCACCGGCTCCTCTTA 62.143 66.667 0.30 0.00 38.10 2.10
580 854 3.499737 CCAGATCCACCAACGCGC 61.500 66.667 5.73 0.00 0.00 6.86
617 898 2.587247 ATCCCATCATCGAGCCCCG 61.587 63.158 0.00 0.00 40.25 5.73
623 904 1.341209 CCGTCTTCATCCCATCATCGA 59.659 52.381 0.00 0.00 0.00 3.59
630 911 2.115427 TGCTTATCCGTCTTCATCCCA 58.885 47.619 0.00 0.00 0.00 4.37
672 953 0.326713 AAGGTTAGCCCCCTCTCCTC 60.327 60.000 0.00 0.00 34.57 3.71
673 954 0.621862 CAAGGTTAGCCCCCTCTCCT 60.622 60.000 0.00 0.00 34.57 3.69
674 955 1.636769 CCAAGGTTAGCCCCCTCTCC 61.637 65.000 0.00 0.00 34.57 3.71
675 956 0.914902 ACCAAGGTTAGCCCCCTCTC 60.915 60.000 0.00 0.00 34.57 3.20
676 957 0.914902 GACCAAGGTTAGCCCCCTCT 60.915 60.000 0.00 0.00 34.57 3.69
677 958 1.608154 GACCAAGGTTAGCCCCCTC 59.392 63.158 0.00 0.00 34.57 4.30
678 959 2.298661 CGACCAAGGTTAGCCCCCT 61.299 63.158 0.00 0.00 34.57 4.79
753 1045 0.674895 ACAACGCATCCAAGCTCCTC 60.675 55.000 0.00 0.00 0.00 3.71
777 1082 4.949098 CCCCGCTTATTCCCCGGC 62.949 72.222 0.00 0.00 40.65 6.13
780 1085 0.325272 GAGATCCCCGCTTATTCCCC 59.675 60.000 0.00 0.00 0.00 4.81
810 1124 1.803289 GAACGCATTTCTCCCAGCC 59.197 57.895 0.00 0.00 0.00 4.85
812 1126 1.982073 GCCGAACGCATTTCTCCCAG 61.982 60.000 0.00 0.00 37.47 4.45
813 1127 2.038269 GCCGAACGCATTTCTCCCA 61.038 57.895 0.00 0.00 37.47 4.37
814 1128 2.038269 TGCCGAACGCATTTCTCCC 61.038 57.895 0.00 0.00 44.64 4.30
815 1129 3.573558 TGCCGAACGCATTTCTCC 58.426 55.556 0.00 0.00 44.64 3.71
898 1242 4.976116 CCCTTTTTAACAGCAGTCGAAAAG 59.024 41.667 16.44 16.44 38.24 2.27
1093 1445 4.770362 TCCCGCCACCTCCGATGA 62.770 66.667 0.00 0.00 0.00 2.92
1416 1779 5.014123 TCCCCCAAATAATAGAGAATCGCAT 59.986 40.000 0.00 0.00 42.67 4.73
1505 1874 5.793457 GCATACCTACTAACAACGCAAAAAG 59.207 40.000 0.00 0.00 0.00 2.27
1663 2032 0.383590 CACGCACACATGGTTTCCAA 59.616 50.000 0.00 0.00 36.95 3.53
1699 2116 3.570125 AGCCTTTCTGGTGCTAAAGAAAC 59.430 43.478 0.00 0.00 37.46 2.78
1720 2137 9.234384 CTGAAGCAATATCAAAGCAAATTCTAG 57.766 33.333 0.00 0.00 0.00 2.43
1835 2253 6.538021 AGATCATCAAGCAGTGAAGATGTTAC 59.462 38.462 11.47 10.13 43.15 2.50
2188 2607 3.960755 AGTTCATCATATCGGTCTGGTCA 59.039 43.478 0.00 0.00 0.00 4.02
2876 4120 3.782992 AGAATTGAAAGCTTGACCCCAT 58.217 40.909 0.00 0.00 0.00 4.00
2913 4157 2.887152 ACCAAGAGGCACATTGTTCTTC 59.113 45.455 0.28 0.00 39.06 2.87
3004 4248 4.177026 TCTCTTAAAGCAGATGAACGAGC 58.823 43.478 0.00 0.00 0.00 5.03
3114 4358 2.992313 CGACCGCGGTTATTGTCG 59.008 61.111 34.65 25.55 43.64 4.35
3205 4449 5.187186 TGTCCCTAGTGATACTTTGAGAACC 59.813 44.000 0.00 0.00 0.00 3.62
3221 4465 2.027745 TGCTTGAAGCTTCTGTCCCTAG 60.028 50.000 26.09 12.59 42.97 3.02
3222 4466 1.977854 TGCTTGAAGCTTCTGTCCCTA 59.022 47.619 26.09 2.03 42.97 3.53
3249 4493 2.104451 AGATGCAGCTGGGTTCTCATAG 59.896 50.000 17.12 0.00 0.00 2.23
3322 4566 3.202829 TGCATTCATATCAGCTGCTGA 57.797 42.857 32.07 32.07 44.99 4.26
3493 4737 3.198853 CCTAAGAAAGAGGGAGTTCCAGG 59.801 52.174 0.00 0.00 38.24 4.45
3716 4960 5.186021 TCTCTTACATCTGACCTTCTGTTCC 59.814 44.000 0.00 0.00 0.00 3.62
3737 4981 1.069427 ATCGCTGCAGAGCCATCTC 59.931 57.895 20.43 0.00 42.91 2.75
3767 5011 4.023707 GGTCATGGTCAGACAAAGTTGAAG 60.024 45.833 2.17 0.00 37.74 3.02
3836 5080 2.735151 TCGAGTTCTGGAGAATAGGCA 58.265 47.619 0.00 0.00 36.33 4.75
3864 5108 1.446907 GAACAGATGCAGGTCCAGTG 58.553 55.000 0.00 0.00 0.00 3.66
4119 5363 3.385577 CTTCGATAGCTGTTTCCCTAGC 58.614 50.000 0.00 0.00 40.18 3.42
4396 5640 7.637631 TTGTTGGCAGCACAAGATATAAATA 57.362 32.000 2.60 0.00 30.49 1.40
4511 5755 9.149225 TCATAACACATCCAAACAAATTAATGC 57.851 29.630 0.00 0.00 0.00 3.56
4595 5839 4.214971 AGACAACACATGCTCATGAAAGAC 59.785 41.667 15.96 4.51 41.20 3.01
5291 6562 1.186200 GGCAGAACCCTGGGAAATTC 58.814 55.000 22.23 13.07 40.72 2.17
5347 6618 4.946772 TCGCCATTACTTTGATTTCCATCA 59.053 37.500 0.00 0.00 37.67 3.07
5395 6666 1.153086 GGCAGTGGCAGATACAGGG 60.153 63.158 12.58 0.00 43.71 4.45
5428 6699 5.411669 CCGGTAGCAAGTTTCTTTATCAACT 59.588 40.000 0.00 0.00 34.58 3.16
5695 6966 4.750098 TCTTCCGAGTCTGATGAAACAAAC 59.250 41.667 0.00 0.00 0.00 2.93
5752 7023 0.595095 CTTTCTGCAGACTGCCCAAC 59.405 55.000 24.33 0.00 44.23 3.77
5801 7072 1.635663 GCGTTGCTGCGATTACCAGT 61.636 55.000 4.77 0.00 32.93 4.00
5848 7119 2.575461 GGGTGGCTGCTGCAATTC 59.425 61.111 17.89 3.07 41.91 2.17
5861 7132 0.322098 TTCAGTATGGCAACGGGGTG 60.322 55.000 0.00 0.00 42.51 4.61
5923 7194 1.372582 ACATGTCGCGCTGATTTGAT 58.627 45.000 5.56 0.00 0.00 2.57
5953 7224 4.256920 GAGATGAAATGTATATGGCCGCT 58.743 43.478 0.00 0.00 0.00 5.52
6009 7280 2.300723 TGAAGCTTGTCGGTTAGCCTTA 59.699 45.455 2.10 0.00 38.14 2.69
6010 7281 1.071699 TGAAGCTTGTCGGTTAGCCTT 59.928 47.619 2.10 0.00 38.14 4.35
6011 7282 0.685097 TGAAGCTTGTCGGTTAGCCT 59.315 50.000 2.10 0.00 38.14 4.58
6012 7283 1.739067 ATGAAGCTTGTCGGTTAGCC 58.261 50.000 2.10 0.00 38.14 3.93
6013 7284 3.831715 AAATGAAGCTTGTCGGTTAGC 57.168 42.857 2.10 0.00 37.66 3.09
6014 7285 4.391830 TGCTAAATGAAGCTTGTCGGTTAG 59.608 41.667 2.10 5.74 43.19 2.34
6015 7286 4.320023 TGCTAAATGAAGCTTGTCGGTTA 58.680 39.130 2.10 0.00 43.19 2.85
6016 7287 3.146066 TGCTAAATGAAGCTTGTCGGTT 58.854 40.909 2.10 0.00 43.19 4.44
6017 7288 2.778299 TGCTAAATGAAGCTTGTCGGT 58.222 42.857 2.10 0.00 43.19 4.69
6070 7343 3.270877 GCAGTGGTCCAGTTTATTCGAT 58.729 45.455 0.00 0.00 0.00 3.59
6085 7358 1.851021 TTGCCAACGAATCGCAGTGG 61.851 55.000 14.00 14.00 33.30 4.00
6132 7405 5.907662 CCATATCATATGGTACTCCCTCCAT 59.092 44.000 14.96 0.00 45.10 3.41
6133 7406 5.280499 CCATATCATATGGTACTCCCTCCA 58.720 45.833 14.96 0.00 38.14 3.86
6145 7429 8.818141 ACGTAGAAACTCAACCATATCATATG 57.182 34.615 0.00 0.00 0.00 1.78
6154 7570 1.000060 CCCGACGTAGAAACTCAACCA 60.000 52.381 0.00 0.00 0.00 3.67
6169 7585 2.987232 ACTATTTTTCTCTGCCCCGAC 58.013 47.619 0.00 0.00 0.00 4.79
6275 7691 4.083324 AGACCAATCAACTGCGTATGTTTG 60.083 41.667 0.00 0.00 0.00 2.93
6276 7692 4.072131 AGACCAATCAACTGCGTATGTTT 58.928 39.130 0.00 0.00 0.00 2.83
6302 7718 1.609208 ACAAAGGCAGCACTGGTAAG 58.391 50.000 0.00 0.00 0.00 2.34
6327 7743 4.765339 GCAACACTGGTACCCTAGAAAAAT 59.235 41.667 10.07 0.00 0.00 1.82
6333 7749 1.276622 AGGCAACACTGGTACCCTAG 58.723 55.000 10.07 3.26 41.41 3.02
6364 7780 3.699671 GTGCGCACCAAACCAAAC 58.300 55.556 30.12 0.00 0.00 2.93
6435 11760 2.959030 GGAAGGTCTTTTGGAAAGCTGT 59.041 45.455 0.00 0.00 0.00 4.40
6449 11774 6.434340 CCAATAAGCATTTATAGGGGAAGGTC 59.566 42.308 0.00 0.00 0.00 3.85
6518 11843 1.533273 GGGGATCTGCTACGGCCTA 60.533 63.158 0.00 0.00 37.74 3.93
6521 11846 0.886490 CATTGGGGATCTGCTACGGC 60.886 60.000 0.00 0.00 39.26 5.68
6522 11847 0.886490 GCATTGGGGATCTGCTACGG 60.886 60.000 0.00 0.00 33.15 4.02
6523 11848 0.179048 TGCATTGGGGATCTGCTACG 60.179 55.000 5.60 0.00 36.84 3.51
6524 11849 1.678101 GTTGCATTGGGGATCTGCTAC 59.322 52.381 5.60 4.51 36.84 3.58
6525 11850 1.565759 AGTTGCATTGGGGATCTGCTA 59.434 47.619 5.60 0.00 36.84 3.49
6526 11851 0.333993 AGTTGCATTGGGGATCTGCT 59.666 50.000 5.60 0.00 36.84 4.24
6527 11852 1.135721 GAAGTTGCATTGGGGATCTGC 59.864 52.381 0.00 0.00 36.45 4.26
6530 11855 2.027385 GGAGAAGTTGCATTGGGGATC 58.973 52.381 0.00 0.00 0.00 3.36
6540 11865 1.508088 CGGCCATTGGAGAAGTTGC 59.492 57.895 6.95 0.00 0.00 4.17
6624 12079 7.559897 TCTTCCCCTATAACCAAATTGACATTC 59.440 37.037 0.00 0.00 0.00 2.67
6673 12132 4.222810 GCTCCCATCTACCCAAATGTTTTT 59.777 41.667 0.00 0.00 0.00 1.94
6709 12169 8.980481 ATTTGGACTTGTATAACCATCTAAGG 57.020 34.615 0.00 0.00 32.31 2.69
6726 12186 8.260114 GTCCATTTTGAATATTGGATTTGGACT 58.740 33.333 19.54 0.00 43.72 3.85


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

AutoCloner maintained by Alex Coulton.