Multiple sequence alignment - TraesCS6D01G329100

Loading Multiple Alignment...

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 TraesCS6D01G329100 chr6D 100.000 5788 0 0 1 5788 433484871 433479084 0.000000e+00 10689
1 TraesCS6D01G329100 chr6D 91.667 240 16 3 3479 3715 440639732 440639494 4.320000e-86 329
2 TraesCS6D01G329100 chr6D 77.555 548 62 27 4616 5150 433479638 433479139 2.050000e-69 274
3 TraesCS6D01G329100 chr6D 77.555 548 62 27 5234 5733 433480256 433479722 2.050000e-69 274
4 TraesCS6D01G329100 chr6D 86.792 106 13 1 538 643 11335401 11335505 3.660000e-22 117
5 TraesCS6D01G329100 chr6D 86.239 109 14 1 531 639 456017540 456017433 3.660000e-22 117
6 TraesCS6D01G329100 chr6B 93.865 3374 148 28 1871 5226 654739266 654735934 0.000000e+00 5029
7 TraesCS6D01G329100 chr6B 94.844 1280 44 13 606 1870 654740575 654739303 0.000000e+00 1978
8 TraesCS6D01G329100 chr6B 93.669 616 29 3 7 618 654742225 654741616 0.000000e+00 913
9 TraesCS6D01G329100 chr6B 78.692 535 75 24 5223 5733 654736526 654736007 2.600000e-83 320
10 TraesCS6D01G329100 chr6A 92.410 3307 161 34 1871 5151 579443668 579440426 0.000000e+00 4634
11 TraesCS6D01G329100 chr6A 93.602 1141 56 6 747 1870 579444845 579443705 0.000000e+00 1687
12 TraesCS6D01G329100 chr6A 81.132 530 61 16 6 518 579447118 579446611 7.030000e-104 388
13 TraesCS6D01G329100 chr6A 78.505 535 75 28 5223 5730 579440950 579440429 1.210000e-81 315
14 TraesCS6D01G329100 chr6A 88.991 109 12 0 531 639 602783537 602783429 1.010000e-27 135
15 TraesCS6D01G329100 chr2D 90.496 242 19 4 3474 3713 645896534 645896773 3.370000e-82 316
16 TraesCS6D01G329100 chr2A 89.540 239 23 2 3474 3711 771620173 771620410 9.430000e-78 302
17 TraesCS6D01G329100 chr1A 89.256 242 23 3 3474 3713 14115611 14115851 3.390000e-77 300
18 TraesCS6D01G329100 chr1D 88.430 242 25 3 3474 3713 12174442 12174682 7.340000e-74 289
19 TraesCS6D01G329100 chr1D 87.209 258 25 7 3466 3718 217297429 217297683 2.640000e-73 287
20 TraesCS6D01G329100 chr1D 88.017 242 26 3 3474 3713 12232123 12232363 3.410000e-72 283
21 TraesCS6D01G329100 chr2B 89.091 110 10 2 531 640 800972468 800972361 1.010000e-27 135
22 TraesCS6D01G329100 chr2B 85.088 114 14 3 531 644 777071574 777071464 4.740000e-21 113
23 TraesCS6D01G329100 chr7A 86.087 115 15 1 525 639 243856059 243856172 7.880000e-24 122
24 TraesCS6D01G329100 chrUn 88.235 102 10 2 544 643 62690430 62690329 2.830000e-23 121
25 TraesCS6D01G329100 chr5B 85.965 114 13 3 525 637 543928084 543927973 1.020000e-22 119


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 TraesCS6D01G329100 chr6D 433479084 433484871 5787 True 10689 10689 100.00000 1 5788 1 chr6D.!!$R1 5787
1 TraesCS6D01G329100 chr6D 433479139 433480256 1117 True 274 274 77.55500 4616 5733 2 chr6D.!!$R4 1117
2 TraesCS6D01G329100 chr6B 654735934 654742225 6291 True 2060 5029 90.26750 7 5733 4 chr6B.!!$R1 5726
3 TraesCS6D01G329100 chr6A 579440426 579447118 6692 True 1756 4634 86.41225 6 5730 4 chr6A.!!$R2 5724

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
511 529 0.116342 TGAGAAGGTGGAGGTGGCTA 59.884 55.000 0.00 0.0 0.00 3.93 F
800 3505 0.251165 CCCCAATGGTCGTGGTTCTT 60.251 55.000 0.00 0.0 34.01 2.52 F
1419 4127 0.834612 TGGTTAACGGCCTCTATGGG 59.165 55.000 0.00 0.0 36.00 4.00 F
1434 4142 1.208165 ATGGGAGGTGGGTGGAAGAC 61.208 60.000 0.00 0.0 0.00 3.01 F
3238 6007 1.283321 GATGGGAAGCCTCCACTTCTT 59.717 52.381 3.19 0.0 44.51 2.52 F
3770 6543 1.340017 TGATGCCAGTGCCCTTAACTC 60.340 52.381 0.00 0.0 36.33 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 4951 0.167470 CACGATTGTGCAGCTCCTTG 59.833 55.000 0.00 0.00 39.67 3.61 R
2409 5173 1.838077 AGCTATTTTACCACCTCCGCT 59.162 47.619 0.00 0.00 0.00 5.52 R
3238 6007 0.396435 AGTCTTCAACCATCCGCACA 59.604 50.000 0.00 0.00 0.00 4.57 R
3320 6089 1.142474 GACATTGCAGCAAAACAGGC 58.858 50.000 12.97 0.95 0.00 4.85 R
4690 7488 0.541764 GGGGTTGCAGGGTTCATTCA 60.542 55.000 0.00 0.00 0.00 2.57 R
5762 8566 0.039437 CTGTTTGCCAAGCTCTGCAG 60.039 55.000 7.63 7.63 38.95 4.41 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
66 68 0.547471 TCAGGCTTCTGACCCCATCA 60.547 55.000 0.00 0.00 42.13 3.07
138 141 2.522923 ATCGAGGCGGGCTCTCAT 60.523 61.111 26.29 16.26 0.00 2.90
218 221 6.386050 CCTACGATAATCCATTATAACCCCCT 59.614 42.308 0.00 0.00 33.37 4.79
222 225 7.626084 ACGATAATCCATTATAACCCCCTCATA 59.374 37.037 0.00 0.00 33.37 2.15
266 270 7.901804 ACCAATCTAGTAGGAGTAGGGTATA 57.098 40.000 0.00 0.00 0.00 1.47
368 372 2.223735 CGGGACTACTGCACGTATCATT 60.224 50.000 0.00 0.00 0.00 2.57
370 374 3.043586 GGACTACTGCACGTATCATTCG 58.956 50.000 0.00 0.00 0.00 3.34
378 382 1.858458 CACGTATCATTCGCCGACATT 59.142 47.619 0.00 0.00 0.00 2.71
427 441 2.123854 CGAGGAGGTCGGATGGGA 60.124 66.667 0.00 0.00 45.58 4.37
471 489 0.600557 CTAGGCATAGGAGTGAGCGG 59.399 60.000 0.00 0.00 0.00 5.52
473 491 2.134287 GGCATAGGAGTGAGCGGGA 61.134 63.158 0.00 0.00 0.00 5.14
511 529 0.116342 TGAGAAGGTGGAGGTGGCTA 59.884 55.000 0.00 0.00 0.00 3.93
536 558 4.337264 AAAAGCCAGAGGGGTAATGATT 57.663 40.909 0.00 0.00 46.38 2.57
548 570 2.681344 GGTAATGATTGTTCGGTGGTCC 59.319 50.000 0.00 0.00 0.00 4.46
551 573 1.819928 TGATTGTTCGGTGGTCCATG 58.180 50.000 0.00 0.00 0.00 3.66
607 629 7.114388 GGTGTTTTGTATTTTCGGTGAATCTTC 59.886 37.037 0.00 0.00 0.00 2.87
800 3505 0.251165 CCCCAATGGTCGTGGTTCTT 60.251 55.000 0.00 0.00 34.01 2.52
805 3510 1.508632 ATGGTCGTGGTTCTTTGTCG 58.491 50.000 0.00 0.00 0.00 4.35
807 3512 1.200839 GTCGTGGTTCTTTGTCGCG 59.799 57.895 0.00 0.00 35.98 5.87
887 3593 0.951040 GACCACTCAAGCGTCCTTGG 60.951 60.000 3.86 0.00 46.69 3.61
1326 4034 0.909610 AGGTGGAGATTGAGGCCGAA 60.910 55.000 0.00 0.00 0.00 4.30
1416 4124 2.223971 CGTCATGGTTAACGGCCTCTAT 60.224 50.000 0.00 0.00 35.32 1.98
1419 4127 0.834612 TGGTTAACGGCCTCTATGGG 59.165 55.000 0.00 0.00 36.00 4.00
1434 4142 1.208165 ATGGGAGGTGGGTGGAAGAC 61.208 60.000 0.00 0.00 0.00 3.01
1642 4357 6.747125 TGCATATAAGCATTACCACAATTGG 58.253 36.000 10.83 0.00 43.81 3.16
1704 4425 7.425224 TGAATTGGACCTTTTTAGTTTGGAA 57.575 32.000 0.00 0.00 0.00 3.53
2180 4942 5.179045 AGTCACTGCTAAAATATGCATGC 57.821 39.130 11.82 11.82 38.59 4.06
2185 4947 6.318396 TCACTGCTAAAATATGCATGCTGTAA 59.682 34.615 20.33 0.00 38.59 2.41
2189 4951 9.121517 CTGCTAAAATATGCATGCTGTAATTAC 57.878 33.333 20.33 8.75 38.59 1.89
2196 4958 3.378112 TGCATGCTGTAATTACAAGGAGC 59.622 43.478 20.33 17.45 35.50 4.70
2197 4959 3.629398 GCATGCTGTAATTACAAGGAGCT 59.371 43.478 18.55 6.70 35.50 4.09
2201 4963 3.181506 GCTGTAATTACAAGGAGCTGCAC 60.182 47.826 18.55 0.00 35.50 4.57
2210 4972 1.375908 GGAGCTGCACAATCGTGGA 60.376 57.895 0.00 0.00 43.81 4.02
2217 4979 4.158394 AGCTGCACAATCGTGGAAAATAAT 59.842 37.500 1.02 0.00 43.53 1.28
2219 4981 6.039717 AGCTGCACAATCGTGGAAAATAATAT 59.960 34.615 1.02 0.00 43.53 1.28
2289 5053 6.834168 AAGGAAATTTGCGGAAAATCTCTA 57.166 33.333 6.08 0.00 37.51 2.43
2360 5124 7.821846 GGAAGACTCTATGAAGAATCAACAAGT 59.178 37.037 0.00 0.00 39.49 3.16
2480 5244 1.460497 TACACCACACCTGGGCTCA 60.460 57.895 0.00 0.00 42.74 4.26
2520 5284 2.507058 AGATTCAGGGCTATCTTGTGCA 59.493 45.455 0.00 0.00 0.00 4.57
2523 5287 4.502105 TTCAGGGCTATCTTGTGCATAA 57.498 40.909 0.00 0.00 0.00 1.90
2526 5290 5.798132 TCAGGGCTATCTTGTGCATAATAG 58.202 41.667 0.00 0.00 0.00 1.73
2528 5292 6.000219 CAGGGCTATCTTGTGCATAATAGTT 59.000 40.000 0.00 0.00 0.00 2.24
2534 5299 6.844696 ATCTTGTGCATAATAGTTGGTACG 57.155 37.500 0.00 0.00 0.00 3.67
2606 5371 8.552296 ACTTATCAATCACCATACCTTCTTTCT 58.448 33.333 0.00 0.00 0.00 2.52
2668 5433 9.950496 TTTCTATGGGCTCTTCTGATATTATTC 57.050 33.333 0.00 0.00 0.00 1.75
2669 5434 8.907829 TCTATGGGCTCTTCTGATATTATTCT 57.092 34.615 0.00 0.00 0.00 2.40
2671 5436 9.598517 CTATGGGCTCTTCTGATATTATTCTTC 57.401 37.037 0.00 0.00 0.00 2.87
2701 5466 6.660521 TCCAAGACTCTTGCATTTGTCATATT 59.339 34.615 12.69 0.74 32.41 1.28
2814 5579 2.567169 TGAGTGTGGATCCACTTGGTAG 59.433 50.000 37.92 0.00 45.46 3.18
2839 5604 9.448587 AGGGAGCTAGAAGTATTATTTTCCTTA 57.551 33.333 0.00 0.00 0.00 2.69
2852 5617 5.892160 ATTTTCCTTAAACGAAGTAGCCC 57.108 39.130 0.00 0.00 45.00 5.19
2904 5669 9.490379 CTCACTTATAATTCCTACAATACCCAC 57.510 37.037 0.00 0.00 0.00 4.61
2905 5670 9.220906 TCACTTATAATTCCTACAATACCCACT 57.779 33.333 0.00 0.00 0.00 4.00
2906 5671 9.847224 CACTTATAATTCCTACAATACCCACTT 57.153 33.333 0.00 0.00 0.00 3.16
2964 5732 6.127507 TGCCATAGACTGATGCTACATATCTC 60.128 42.308 0.00 0.00 0.00 2.75
3015 5783 3.244422 TGCCACTCCGAGTTTAATGTTCT 60.244 43.478 0.00 0.00 0.00 3.01
3054 5822 3.893753 TCCCTGAACTCAATTGGGAAA 57.106 42.857 13.56 0.00 43.27 3.13
3096 5865 9.553064 GACAGAAAATGGTATTCATATCTGACT 57.447 33.333 19.37 6.62 44.36 3.41
3136 5905 1.339929 CCCTTCCTTTTTGGTGTTCCG 59.660 52.381 0.00 0.00 37.07 4.30
3238 6007 1.283321 GATGGGAAGCCTCCACTTCTT 59.717 52.381 3.19 0.00 44.51 2.52
3244 6013 2.328099 GCCTCCACTTCTTGTGCGG 61.328 63.158 0.00 0.00 44.92 5.69
3293 6062 7.917505 GGAAATTCATGTACCAACTCATGATTC 59.082 37.037 0.00 9.55 46.03 2.52
3301 6070 3.820467 ACCAACTCATGATTCGCAGAAAA 59.180 39.130 0.00 0.00 45.90 2.29
3311 6080 8.071967 TCATGATTCGCAGAAAATGATATTGAC 58.928 33.333 0.00 0.00 45.90 3.18
3314 6083 5.484173 TCGCAGAAAATGATATTGACACC 57.516 39.130 0.00 0.00 0.00 4.16
3318 6087 5.967674 GCAGAAAATGATATTGACACCTTCG 59.032 40.000 0.00 0.00 0.00 3.79
3320 6089 4.536364 AAATGATATTGACACCTTCGCG 57.464 40.909 0.00 0.00 0.00 5.87
3343 6112 3.004629 CCTGTTTTGCTGCAATGTCACTA 59.995 43.478 16.77 0.00 0.00 2.74
3344 6113 4.321452 CCTGTTTTGCTGCAATGTCACTAT 60.321 41.667 16.77 0.00 0.00 2.12
3497 6266 8.598916 TGTACTTCCTCCATTTCTGTATACAAA 58.401 33.333 7.06 0.00 0.00 2.83
3498 6267 9.444600 GTACTTCCTCCATTTCTGTATACAAAA 57.555 33.333 7.06 10.48 0.00 2.44
3581 6350 9.800433 TTATATGCCACAAAAAGTATGTCATTG 57.200 29.630 0.00 0.00 0.00 2.82
3593 6362 6.140303 AGTATGTCATTGGATGCACATTTC 57.860 37.500 0.00 0.00 34.86 2.17
3598 6370 5.466058 TGTCATTGGATGCACATTTCAAAAC 59.534 36.000 0.00 0.00 0.00 2.43
3709 6482 4.507335 GCCTTGCATATAGAAATGGAGGGA 60.507 45.833 10.06 0.00 44.18 4.20
3715 6488 6.174049 GCATATAGAAATGGAGGGAGTAACC 58.826 44.000 0.00 0.00 38.08 2.85
3770 6543 1.340017 TGATGCCAGTGCCCTTAACTC 60.340 52.381 0.00 0.00 36.33 3.01
3772 6545 1.378762 GCCAGTGCCCTTAACTCCA 59.621 57.895 0.00 0.00 0.00 3.86
3801 6574 3.719268 ATAGTTGGTTGGAGCACATCA 57.281 42.857 0.00 0.00 0.00 3.07
3852 6625 2.231721 AGTAAGCGAGAACTTCACCTCC 59.768 50.000 0.00 0.00 0.00 4.30
3860 6633 5.163844 GCGAGAACTTCACCTCCTTAATTTC 60.164 44.000 0.00 0.00 0.00 2.17
3861 6634 5.932303 CGAGAACTTCACCTCCTTAATTTCA 59.068 40.000 0.00 0.00 0.00 2.69
3863 6636 7.360438 CGAGAACTTCACCTCCTTAATTTCAAG 60.360 40.741 0.00 0.00 0.00 3.02
3919 6702 2.417719 CCCTGACTGTTGTTGTAGCTC 58.582 52.381 0.00 0.00 0.00 4.09
3940 6723 6.818644 AGCTCGAGTTAGAAGCAAATAATGAA 59.181 34.615 15.13 0.00 0.00 2.57
3986 6769 2.534042 TACTGCTAACTCAGAGGGCT 57.466 50.000 1.53 0.00 37.51 5.19
4029 6812 1.478510 CACTTCACTCACGGATAGCCT 59.521 52.381 0.00 0.00 0.00 4.58
4210 7003 4.169508 CTGTCATCAGTAGGTTCAGAACG 58.830 47.826 7.22 0.00 36.97 3.95
4242 7035 6.759497 TCGAAAATACTGATCAGAGACTCA 57.241 37.500 29.27 6.99 0.00 3.41
4321 7117 5.356882 TTTCCACTTTGACATTCGACATC 57.643 39.130 0.00 0.00 0.00 3.06
4353 7149 1.625818 GGAGATGATCCGTGGCCTTAT 59.374 52.381 3.32 0.00 38.67 1.73
4357 7153 3.259374 AGATGATCCGTGGCCTTATACAG 59.741 47.826 3.32 0.00 0.00 2.74
4515 7311 5.106078 GCTCGGGTTGATGGTTTAATTAACA 60.106 40.000 0.00 0.00 38.55 2.41
4569 7365 3.241067 TGAACTAATCGGTACCTGTGC 57.759 47.619 10.90 0.61 0.00 4.57
4690 7488 4.277423 CCTTAAAATGTTCAACCGTGGACT 59.723 41.667 0.00 0.00 33.92 3.85
4691 7489 3.708563 AAAATGTTCAACCGTGGACTG 57.291 42.857 0.00 0.00 33.92 3.51
4692 7490 2.631160 AATGTTCAACCGTGGACTGA 57.369 45.000 0.00 0.00 33.92 3.41
4693 7491 2.631160 ATGTTCAACCGTGGACTGAA 57.369 45.000 0.00 0.00 33.92 3.02
5733 8537 7.125053 TCTGATATGTTGTGTTACTGGGTGATA 59.875 37.037 0.00 0.00 0.00 2.15
5734 8538 7.625469 TGATATGTTGTGTTACTGGGTGATAA 58.375 34.615 0.00 0.00 0.00 1.75
5735 8539 8.271458 TGATATGTTGTGTTACTGGGTGATAAT 58.729 33.333 0.00 0.00 0.00 1.28
5736 8540 8.677148 ATATGTTGTGTTACTGGGTGATAATC 57.323 34.615 0.00 0.00 0.00 1.75
5737 8541 5.870706 TGTTGTGTTACTGGGTGATAATCA 58.129 37.500 0.00 0.00 0.00 2.57
5738 8542 6.480763 TGTTGTGTTACTGGGTGATAATCAT 58.519 36.000 0.00 0.00 0.00 2.45
5739 8543 6.374053 TGTTGTGTTACTGGGTGATAATCATG 59.626 38.462 0.00 0.00 0.00 3.07
5740 8544 5.436175 TGTGTTACTGGGTGATAATCATGG 58.564 41.667 0.00 0.00 0.00 3.66
5741 8545 5.190726 TGTGTTACTGGGTGATAATCATGGA 59.809 40.000 0.00 0.00 0.00 3.41
5742 8546 6.119536 GTGTTACTGGGTGATAATCATGGAA 58.880 40.000 0.00 0.00 0.00 3.53
5743 8547 6.260936 GTGTTACTGGGTGATAATCATGGAAG 59.739 42.308 0.00 0.00 0.00 3.46
5744 8548 6.069673 TGTTACTGGGTGATAATCATGGAAGT 60.070 38.462 0.00 0.00 0.00 3.01
5745 8549 5.456921 ACTGGGTGATAATCATGGAAGTT 57.543 39.130 0.00 0.00 0.00 2.66
5746 8550 6.575244 ACTGGGTGATAATCATGGAAGTTA 57.425 37.500 0.00 0.00 0.00 2.24
5747 8551 7.154191 ACTGGGTGATAATCATGGAAGTTAT 57.846 36.000 0.00 0.00 0.00 1.89
5748 8552 7.586349 ACTGGGTGATAATCATGGAAGTTATT 58.414 34.615 0.00 0.00 0.00 1.40
5749 8553 8.723365 ACTGGGTGATAATCATGGAAGTTATTA 58.277 33.333 0.00 0.00 0.00 0.98
5750 8554 9.573166 CTGGGTGATAATCATGGAAGTTATTAA 57.427 33.333 0.00 0.00 0.00 1.40
5751 8555 9.928618 TGGGTGATAATCATGGAAGTTATTAAA 57.071 29.630 0.00 0.00 0.00 1.52
5764 8568 9.421806 TGGAAGTTATTAAAAATGATGCAACTG 57.578 29.630 0.00 0.00 0.00 3.16
5765 8569 8.382875 GGAAGTTATTAAAAATGATGCAACTGC 58.617 33.333 0.00 0.00 42.50 4.40
5775 8579 2.257676 GCAACTGCAGAGCTTGGC 59.742 61.111 23.35 2.63 41.59 4.52
5776 8580 2.558286 GCAACTGCAGAGCTTGGCA 61.558 57.895 23.35 12.01 41.59 4.92
5777 8581 2.035421 CAACTGCAGAGCTTGGCAA 58.965 52.632 23.35 0.00 39.93 4.52
5778 8582 0.386476 CAACTGCAGAGCTTGGCAAA 59.614 50.000 23.35 0.00 39.93 3.68
5779 8583 0.386838 AACTGCAGAGCTTGGCAAAC 59.613 50.000 23.35 0.00 39.93 2.93
5780 8584 0.752743 ACTGCAGAGCTTGGCAAACA 60.753 50.000 23.35 0.00 39.93 2.83
5781 8585 0.039437 CTGCAGAGCTTGGCAAACAG 60.039 55.000 8.42 0.00 39.93 3.16
5782 8586 0.752743 TGCAGAGCTTGGCAAACAGT 60.753 50.000 10.41 0.00 37.03 3.55
5783 8587 0.318445 GCAGAGCTTGGCAAACAGTG 60.318 55.000 0.00 0.00 0.00 3.66
5784 8588 1.027357 CAGAGCTTGGCAAACAGTGT 58.973 50.000 0.00 0.00 0.00 3.55
5785 8589 1.406539 CAGAGCTTGGCAAACAGTGTT 59.593 47.619 1.64 1.64 0.00 3.32
5786 8590 1.406539 AGAGCTTGGCAAACAGTGTTG 59.593 47.619 9.79 5.25 0.00 3.33
5787 8591 1.134946 GAGCTTGGCAAACAGTGTTGT 59.865 47.619 9.79 0.00 39.87 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.953775 CGACCTGGTGGGCCAACT 61.954 66.667 24.40 1.25 45.51 3.16
66 68 5.362430 CAGAGTCTTCTAGTGGAGGCTTATT 59.638 44.000 0.00 0.00 30.73 1.40
138 141 2.731571 GGACTAGCCATGGCCGACA 61.732 63.158 33.14 14.85 43.17 4.35
266 270 4.778143 GCCCTCGCGGTGGATGTT 62.778 66.667 17.37 0.00 0.00 2.71
368 372 1.375396 CCAACTCCAATGTCGGCGA 60.375 57.895 4.99 4.99 0.00 5.54
370 374 1.305930 GGTCCAACTCCAATGTCGGC 61.306 60.000 0.00 0.00 0.00 5.54
378 382 3.246112 CACCCCGGTCCAACTCCA 61.246 66.667 0.00 0.00 0.00 3.86
421 435 1.367840 CCTTCCCGACGATCCCATC 59.632 63.158 0.00 0.00 0.00 3.51
427 441 0.320421 CACAACACCTTCCCGACGAT 60.320 55.000 0.00 0.00 0.00 3.73
471 489 7.112779 TCTCATTAAAAGATTCCTTCCTGTCC 58.887 38.462 0.00 0.00 0.00 4.02
473 491 7.613411 CCTTCTCATTAAAAGATTCCTTCCTGT 59.387 37.037 0.00 0.00 0.00 4.00
511 529 4.291249 TCATTACCCCTCTGGCTTTTAAGT 59.709 41.667 0.00 0.00 37.83 2.24
536 558 0.251916 GATCCATGGACCACCGAACA 59.748 55.000 18.99 0.00 39.42 3.18
642 1716 9.284968 CCTAGATAACCAATCCGTTGAATAAAT 57.715 33.333 0.00 0.00 37.53 1.40
646 1720 5.063880 GCCTAGATAACCAATCCGTTGAAT 58.936 41.667 0.00 0.00 37.53 2.57
711 1937 2.552155 GGGCATATCGAATTGCACCCTA 60.552 50.000 20.37 0.00 40.66 3.53
723 1949 0.930310 CGACACACAAGGGCATATCG 59.070 55.000 0.00 0.00 0.00 2.92
728 1954 0.317160 CTAGTCGACACACAAGGGCA 59.683 55.000 19.50 0.00 0.00 5.36
800 3505 3.334751 CACGAACAGCCGCGACAA 61.335 61.111 8.23 0.00 0.00 3.18
805 3510 3.712881 GTCACCACGAACAGCCGC 61.713 66.667 0.00 0.00 0.00 6.53
807 3512 2.110213 TGGTCACCACGAACAGCC 59.890 61.111 0.00 0.00 36.00 4.85
887 3593 3.491652 GAACGGCTGAGAAGCGCC 61.492 66.667 2.29 0.00 42.86 6.53
927 3635 1.153369 AATCGCGGGGATGACTGTG 60.153 57.895 6.13 0.00 34.93 3.66
1251 3959 4.489771 AGCCGGCTCCCCAAATCG 62.490 66.667 27.08 0.00 0.00 3.34
1416 4124 1.846124 GTCTTCCACCCACCTCCCA 60.846 63.158 0.00 0.00 0.00 4.37
1434 4142 5.175856 CGAATAAAATAGAAGCGAGAGGGTG 59.824 44.000 0.00 0.00 0.00 4.61
1642 4357 5.006358 GCAAATCAACAGAATTCATGGATGC 59.994 40.000 8.44 10.52 0.00 3.91
1704 4425 5.020941 ACAGTAACCCCTACCTTTCTAGT 57.979 43.478 0.00 0.00 0.00 2.57
1716 4437 4.851843 AGCTATGGTTTTACAGTAACCCC 58.148 43.478 3.20 2.45 43.55 4.95
1828 4553 5.640218 AAACAACAATCAAACATTCAGCG 57.360 34.783 0.00 0.00 0.00 5.18
1881 4642 9.042008 GTATTAGTCGGAAAGAGATAATTGCAA 57.958 33.333 0.00 0.00 0.00 4.08
1985 4747 3.403038 ACCAGAAAGTAGTGTGCATCAC 58.597 45.455 10.33 10.33 46.46 3.06
2180 4942 4.002982 TGTGCAGCTCCTTGTAATTACAG 58.997 43.478 17.36 11.84 37.52 2.74
2185 4947 2.679837 CGATTGTGCAGCTCCTTGTAAT 59.320 45.455 0.00 0.00 0.00 1.89
2189 4951 0.167470 CACGATTGTGCAGCTCCTTG 59.833 55.000 0.00 0.00 39.67 3.61
2196 4958 9.546909 GATATATTATTTTCCACGATTGTGCAG 57.453 33.333 7.65 0.00 45.04 4.41
2197 4959 9.061435 TGATATATTATTTTCCACGATTGTGCA 57.939 29.630 7.65 0.00 45.04 4.57
2231 4995 8.113462 ACAACTTGGTGTACCTGGATAATAAAT 58.887 33.333 0.00 0.00 36.82 1.40
2235 4999 5.497474 GACAACTTGGTGTACCTGGATAAT 58.503 41.667 0.00 0.00 36.82 1.28
2289 5053 3.006110 CCACCAAGTGAATGAGCAACAAT 59.994 43.478 0.00 0.00 35.23 2.71
2360 5124 4.104579 TCCATATTAAGGCATGGCTCTTCA 59.895 41.667 23.56 9.03 41.33 3.02
2397 5161 5.123936 ACCACCTCCGCTTATATTTTCTTC 58.876 41.667 0.00 0.00 0.00 2.87
2404 5168 6.013639 AGCTATTTTACCACCTCCGCTTATAT 60.014 38.462 0.00 0.00 0.00 0.86
2408 5172 2.238898 AGCTATTTTACCACCTCCGCTT 59.761 45.455 0.00 0.00 0.00 4.68
2409 5173 1.838077 AGCTATTTTACCACCTCCGCT 59.162 47.619 0.00 0.00 0.00 5.52
2410 5174 1.940613 CAGCTATTTTACCACCTCCGC 59.059 52.381 0.00 0.00 0.00 5.54
2412 5176 2.092375 AGCCAGCTATTTTACCACCTCC 60.092 50.000 0.00 0.00 0.00 4.30
2480 5244 8.934023 TGAATCTTACTTGTTTATTCCACCTT 57.066 30.769 0.00 0.00 0.00 3.50
2534 5299 5.799213 CCTCCCACTGATAGAATGGTATTC 58.201 45.833 0.00 0.00 0.00 1.75
2649 5414 6.773638 TGGAAGAATAATATCAGAAGAGCCC 58.226 40.000 0.00 0.00 0.00 5.19
2668 5433 2.810852 GCAAGAGTCTTGGACTTGGAAG 59.189 50.000 29.45 5.26 43.53 3.46
2669 5434 2.172505 TGCAAGAGTCTTGGACTTGGAA 59.827 45.455 29.45 0.00 43.53 3.53
2671 5436 2.260844 TGCAAGAGTCTTGGACTTGG 57.739 50.000 29.45 7.30 43.53 3.61
2701 5466 5.991933 TGTCCATTTTAAATAGCAAGGCA 57.008 34.783 0.00 0.00 0.00 4.75
2839 5604 6.887626 TTAGAAAATTGGGCTACTTCGTTT 57.112 33.333 0.00 0.00 0.00 3.60
2920 5688 4.522789 TGGCAGGGAAATGAACTCTTTTAC 59.477 41.667 0.00 0.00 0.00 2.01
2964 5732 4.844349 TCTGGAAGGAGGAAACCATAAG 57.156 45.455 0.00 0.00 0.00 1.73
3015 5783 6.773200 TCAGGGACAAACACAAATACACAATA 59.227 34.615 0.00 0.00 0.00 1.90
3110 5879 1.146982 ACCAAAAAGGAAGGGCAGCTA 59.853 47.619 0.00 0.00 41.22 3.32
3136 5905 1.208259 CAGCGGTTTGTTCCAAAAGC 58.792 50.000 9.15 9.15 34.86 3.51
3166 5935 4.058817 CCGTTCTCCCAACTATAAGATGC 58.941 47.826 0.00 0.00 0.00 3.91
3238 6007 0.396435 AGTCTTCAACCATCCGCACA 59.604 50.000 0.00 0.00 0.00 4.57
3244 6013 2.621338 TCATCGCAGTCTTCAACCATC 58.379 47.619 0.00 0.00 0.00 3.51
3293 6062 5.490139 AGGTGTCAATATCATTTTCTGCG 57.510 39.130 0.00 0.00 0.00 5.18
3301 6070 1.867233 GCGCGAAGGTGTCAATATCAT 59.133 47.619 12.10 0.00 0.00 2.45
3311 6080 1.370414 CAAAACAGGCGCGAAGGTG 60.370 57.895 12.10 2.67 0.00 4.00
3314 6083 1.727022 CAGCAAAACAGGCGCGAAG 60.727 57.895 12.10 0.00 36.08 3.79
3318 6087 1.665599 ATTGCAGCAAAACAGGCGC 60.666 52.632 12.97 0.00 36.08 6.53
3320 6089 1.142474 GACATTGCAGCAAAACAGGC 58.858 50.000 12.97 0.95 0.00 4.85
3343 6112 8.220559 ACCTGCATAATAACAAGGTCATAAGAT 58.779 33.333 0.00 0.00 0.00 2.40
3344 6113 7.573710 ACCTGCATAATAACAAGGTCATAAGA 58.426 34.615 0.00 0.00 0.00 2.10
3477 6246 8.822805 AGTAGTTTTGTATACAGAAATGGAGGA 58.177 33.333 16.65 0.00 0.00 3.71
3581 6350 5.754890 AGAAAGTGTTTTGAAATGTGCATCC 59.245 36.000 0.00 0.00 0.00 3.51
3679 6452 4.502105 TTCTATATGCAAGGCCACTTCA 57.498 40.909 5.01 0.00 33.81 3.02
3780 6553 4.835284 TGATGTGCTCCAACCAACTATA 57.165 40.909 0.00 0.00 0.00 1.31
3801 6574 0.930310 CATGTTGACGCCGAATCGAT 59.070 50.000 3.36 0.00 0.00 3.59
3860 6633 7.986085 TTTAGGGACAGAGAAAGATTTCTTG 57.014 36.000 9.11 10.96 46.84 3.02
3861 6634 9.593565 AATTTTAGGGACAGAGAAAGATTTCTT 57.406 29.630 9.11 0.00 46.84 2.52
3940 6723 3.637911 TGGATAACATGCGGGTACTTT 57.362 42.857 0.00 0.00 0.00 2.66
3986 6769 4.400884 GTCTACAGAATCCTCTTGCTGAGA 59.599 45.833 8.51 0.26 45.39 3.27
4029 6812 9.368674 CATAAATTGCAATGATGTTACCTTCAA 57.631 29.630 13.82 0.00 0.00 2.69
4242 7035 6.438741 ACAGTATATACAGCATGCCATACTCT 59.561 38.462 15.66 8.73 42.53 3.24
4321 7117 4.630505 CGGATCATCTCCTCTGCAATAATG 59.369 45.833 0.00 0.00 42.47 1.90
4357 7153 3.246880 ACCCGTTCCCAGGTCACC 61.247 66.667 0.00 0.00 0.00 4.02
4569 7365 1.535204 AAAAGGAGCCCCGCACATTG 61.535 55.000 0.00 0.00 37.58 2.82
4580 7376 6.874288 ATGATATCTAACAGCAAAAGGAGC 57.126 37.500 3.98 0.00 0.00 4.70
4608 7404 4.697352 AGTTCAGAAATCATGCACCACTAC 59.303 41.667 0.00 0.00 0.00 2.73
4690 7488 0.541764 GGGGTTGCAGGGTTCATTCA 60.542 55.000 0.00 0.00 0.00 2.57
4691 7489 1.257750 GGGGGTTGCAGGGTTCATTC 61.258 60.000 0.00 0.00 0.00 2.67
4692 7490 1.229177 GGGGGTTGCAGGGTTCATT 60.229 57.895 0.00 0.00 0.00 2.57
4693 7491 2.445155 GGGGGTTGCAGGGTTCAT 59.555 61.111 0.00 0.00 0.00 2.57
5738 8542 9.421806 CAGTTGCATCATTTTTAATAACTTCCA 57.578 29.630 0.00 0.00 0.00 3.53
5739 8543 8.382875 GCAGTTGCATCATTTTTAATAACTTCC 58.617 33.333 0.00 0.00 41.59 3.46
5758 8562 2.079020 TTGCCAAGCTCTGCAGTTGC 62.079 55.000 20.85 20.85 38.95 4.17
5759 8563 0.386476 TTTGCCAAGCTCTGCAGTTG 59.614 50.000 14.67 10.95 38.95 3.16
5760 8564 0.386838 GTTTGCCAAGCTCTGCAGTT 59.613 50.000 14.67 0.00 38.95 3.16
5761 8565 0.752743 TGTTTGCCAAGCTCTGCAGT 60.753 50.000 14.67 0.00 38.95 4.40
5762 8566 0.039437 CTGTTTGCCAAGCTCTGCAG 60.039 55.000 7.63 7.63 38.95 4.41
5763 8567 0.752743 ACTGTTTGCCAAGCTCTGCA 60.753 50.000 6.05 6.05 35.27 4.41
5764 8568 0.318445 CACTGTTTGCCAAGCTCTGC 60.318 55.000 0.64 0.64 0.00 4.26
5765 8569 1.027357 ACACTGTTTGCCAAGCTCTG 58.973 50.000 0.00 0.00 0.00 3.35
5766 8570 1.406539 CAACACTGTTTGCCAAGCTCT 59.593 47.619 0.00 0.00 0.00 4.09
5767 8571 1.134946 ACAACACTGTTTGCCAAGCTC 59.865 47.619 0.00 0.00 28.57 4.09
5768 8572 1.185315 ACAACACTGTTTGCCAAGCT 58.815 45.000 0.00 0.00 28.57 3.74
5769 8573 3.739077 ACAACACTGTTTGCCAAGC 57.261 47.368 0.00 0.00 28.57 4.01


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

AutoCloner maintained by Alex Coulton.