Multiple sequence alignment - TraesCS6B01G110700

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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 TraesCS6B01G110700 chr6B 100.000 4730 0 0 1 4730 92761628 92756899 0.000000e+00 8735.0
1 TraesCS6B01G110700 chrUn 98.376 4003 51 9 731 4730 20103617 20107608 0.000000e+00 7020.0
2 TraesCS6B01G110700 chrUn 88.807 679 53 7 1 679 20102612 20103267 0.000000e+00 811.0
3 TraesCS6B01G110700 chrUn 91.582 297 25 0 1 297 19932125 19932421 1.230000e-110 411.0
4 TraesCS6B01G110700 chr6A 98.351 4003 54 7 731 4730 56255558 56251565 0.000000e+00 7016.0
5 TraesCS6B01G110700 chr6A 89.706 680 69 1 1 679 56257453 56256774 0.000000e+00 867.0
6 TraesCS6B01G110700 chr6A 89.262 298 31 1 1 297 56513297 56513000 5.780000e-99 372.0
7 TraesCS6B01G110700 chr4A 90.236 297 29 0 1 297 468361799 468362095 5.740000e-104 388.0
8 TraesCS6B01G110700 chr4A 89.899 297 29 1 1 297 468261659 468261954 9.610000e-102 381.0
9 TraesCS6B01G110700 chr4A 86.477 281 36 2 294 573 703252819 703253098 1.650000e-79 307.0
10 TraesCS6B01G110700 chr2D 90.236 297 28 1 1 297 610893420 610893125 2.060000e-103 387.0
11 TraesCS6B01G110700 chr2D 89.899 297 30 0 1 297 454698294 454698590 2.670000e-102 383.0
12 TraesCS6B01G110700 chr2D 87.132 272 34 1 294 565 605457067 605457337 1.650000e-79 307.0
13 TraesCS6B01G110700 chr2D 84.615 208 25 5 390 592 103777938 103777733 2.890000e-47 200.0
14 TraesCS6B01G110700 chr7D 89.597 298 27 4 1 297 268350144 268350438 4.470000e-100 375.0
15 TraesCS6B01G110700 chr7D 85.556 90 9 2 491 576 254780511 254780600 1.810000e-14 91.6
16 TraesCS6B01G110700 chr5A 87.814 279 31 3 294 571 647359824 647359548 1.640000e-84 324.0
17 TraesCS6B01G110700 chr5A 86.517 89 9 2 491 576 342623670 342623758 1.400000e-15 95.3
18 TraesCS6B01G110700 chr2A 87.546 273 32 2 294 565 729554973 729555244 9.880000e-82 315.0
19 TraesCS6B01G110700 chr2A 84.466 103 10 5 494 592 367832191 367832091 3.900000e-16 97.1
20 TraesCS6B01G110700 chr6D 87.778 270 30 2 297 565 69292677 69292944 3.550000e-81 313.0
21 TraesCS6B01G110700 chr6D 85.556 90 9 2 491 576 89469861 89469950 1.810000e-14 91.6
22 TraesCS6B01G110700 chr1D 87.132 272 33 2 294 565 318585895 318585626 1.650000e-79 307.0
23 TraesCS6B01G110700 chr1D 83.495 103 11 6 494 592 58338851 58338751 1.810000e-14 91.6
24 TraesCS6B01G110700 chr3A 86.909 275 29 5 294 565 623614988 623614718 7.690000e-78 302.0
25 TraesCS6B01G110700 chr7B 85.816 282 38 2 294 574 742151880 742152160 9.950000e-77 298.0
26 TraesCS6B01G110700 chr2B 84.211 209 25 6 390 592 591109768 591109974 3.730000e-46 196.0
27 TraesCS6B01G110700 chr1B 86.667 90 8 2 491 576 175515996 175516085 3.900000e-16 97.1


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 TraesCS6B01G110700 chr6B 92756899 92761628 4729 True 8735.0 8735 100.0000 1 4730 1 chr6B.!!$R1 4729
1 TraesCS6B01G110700 chrUn 20102612 20107608 4996 False 3915.5 7020 93.5915 1 4730 2 chrUn.!!$F2 4729
2 TraesCS6B01G110700 chr6A 56251565 56257453 5888 True 3941.5 7016 94.0285 1 4730 2 chr6A.!!$R2 4729

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
316 317 0.400093 AGTGGTATCCCCAGCCTACC 60.400 60.0 0.00 0.0 46.45 3.18 F
683 707 0.463833 GAGGATCGGCGTTGGGATTT 60.464 55.0 6.85 0.0 0.00 2.17 F
1185 2400 0.553819 AGTCCTACGCCTCCATCTCT 59.446 55.0 0.00 0.0 0.00 3.10 F
1881 3096 0.811616 CCGCTGGCTCTATTGTCACC 60.812 60.0 0.00 0.0 0.00 4.02 F
2706 3921 0.970937 CCCGAAGCCTCTACCAGTCA 60.971 60.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 3264 1.000163 AGCTTATCATACCGCTGACCG 60.000 52.381 0.00 0.00 0.00 4.79 R
2073 3288 1.738099 CTTGCGGAGAAGACGGTGG 60.738 63.158 0.00 0.00 0.00 4.61 R
2079 3294 1.964223 AGTCTGTTCTTGCGGAGAAGA 59.036 47.619 2.87 1.68 44.78 2.87 R
3312 4527 1.480137 CGACCTTTGATCTCTCCAGCT 59.520 52.381 0.00 0.00 0.00 4.24 R
4541 5759 0.854705 AACCGCAAAACTACGTCGAC 59.145 50.000 5.18 5.18 0.00 4.20 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
54 55 3.689649 GTCTCATTGAACCCTTGCGTAAT 59.310 43.478 0.00 0.00 0.00 1.89
60 61 0.679960 AACCCTTGCGTAATGGAGGC 60.680 55.000 14.10 0.00 39.49 4.70
61 62 1.823899 CCCTTGCGTAATGGAGGCC 60.824 63.158 1.27 0.00 38.20 5.19
77 78 3.112205 GCCGATGAGGGGTCAGCAT 62.112 63.158 0.00 0.00 41.48 3.79
81 82 1.000283 CGATGAGGGGTCAGCATACTC 60.000 57.143 0.00 0.00 0.00 2.59
116 117 2.328099 CCGCTCTTGCACAAGGGTC 61.328 63.158 11.72 3.86 40.95 4.46
149 150 4.986034 TGTAACTCAACACTCCATACAACG 59.014 41.667 0.00 0.00 0.00 4.10
214 215 1.633945 AGGGGCCTGAACTCGTAAATT 59.366 47.619 0.84 0.00 0.00 1.82
231 232 3.655276 AATTCGAGTGTACAACCTCGT 57.345 42.857 25.97 12.28 39.89 4.18
274 275 3.983410 TCCTACGTACCCCTAACCTCTAT 59.017 47.826 0.00 0.00 0.00 1.98
276 277 4.522022 CCTACGTACCCCTAACCTCTATTG 59.478 50.000 0.00 0.00 0.00 1.90
284 285 4.284746 CCCCTAACCTCTATTGTCAGATCC 59.715 50.000 0.00 0.00 0.00 3.36
313 314 0.550147 ACAAGTGGTATCCCCAGCCT 60.550 55.000 0.00 0.00 46.45 4.58
316 317 0.400093 AGTGGTATCCCCAGCCTACC 60.400 60.000 0.00 0.00 46.45 3.18
329 330 0.984995 GCCTACCAGGGTTCAAGTCT 59.015 55.000 0.00 0.00 35.37 3.24
337 338 1.215423 AGGGTTCAAGTCTTGGTGCTT 59.785 47.619 12.66 0.00 0.00 3.91
346 347 5.010922 TCAAGTCTTGGTGCTTGCATTATTT 59.989 36.000 12.66 0.00 41.15 1.40
355 356 5.292589 GGTGCTTGCATTATTTCTGGATTTG 59.707 40.000 0.00 0.00 0.00 2.32
361 362 8.899427 TTGCATTATTTCTGGATTTGTTTCAA 57.101 26.923 0.00 0.00 0.00 2.69
385 386 1.154225 CCGGTGATGCGTTTTCAGC 60.154 57.895 0.00 4.27 38.05 4.26
421 422 1.672030 TCGACGACGAGGTGCCTAA 60.672 57.895 5.75 0.00 43.81 2.69
481 482 0.551396 TCTCGGAGGTGCTCATAGGA 59.449 55.000 4.96 0.00 31.08 2.94
500 523 8.523658 TCATAGGAATAGAGTATGTGTGTATGC 58.476 37.037 0.00 0.00 0.00 3.14
501 524 6.731292 AGGAATAGAGTATGTGTGTATGCA 57.269 37.500 0.00 0.00 0.00 3.96
502 525 7.308450 AGGAATAGAGTATGTGTGTATGCAT 57.692 36.000 3.79 3.79 0.00 3.96
503 526 7.739825 AGGAATAGAGTATGTGTGTATGCATT 58.260 34.615 3.54 0.00 0.00 3.56
504 527 7.875041 AGGAATAGAGTATGTGTGTATGCATTC 59.125 37.037 3.54 0.00 0.00 2.67
505 528 7.657354 GGAATAGAGTATGTGTGTATGCATTCA 59.343 37.037 3.54 2.29 0.00 2.57
506 529 9.212641 GAATAGAGTATGTGTGTATGCATTCAT 57.787 33.333 3.54 5.51 36.73 2.57
508 531 9.866798 ATAGAGTATGTGTGTATGCATTCATAG 57.133 33.333 3.54 0.00 35.96 2.23
509 532 7.157347 AGAGTATGTGTGTATGCATTCATAGG 58.843 38.462 3.54 0.00 35.96 2.57
510 533 6.233434 AGTATGTGTGTATGCATTCATAGGG 58.767 40.000 3.54 0.00 35.96 3.53
511 534 3.819368 TGTGTGTATGCATTCATAGGGG 58.181 45.455 3.54 0.00 35.96 4.79
512 535 3.201930 TGTGTGTATGCATTCATAGGGGT 59.798 43.478 3.54 0.00 35.96 4.95
513 536 3.565482 GTGTGTATGCATTCATAGGGGTG 59.435 47.826 3.54 0.00 35.96 4.61
514 537 3.457749 TGTGTATGCATTCATAGGGGTGA 59.542 43.478 3.54 0.00 35.96 4.02
515 538 4.067896 GTGTATGCATTCATAGGGGTGAG 58.932 47.826 3.54 0.00 35.96 3.51
516 539 3.716353 TGTATGCATTCATAGGGGTGAGT 59.284 43.478 3.54 0.00 35.96 3.41
517 540 2.715749 TGCATTCATAGGGGTGAGTG 57.284 50.000 0.00 0.00 38.45 3.51
518 541 1.915489 TGCATTCATAGGGGTGAGTGT 59.085 47.619 0.00 0.00 37.92 3.55
519 542 3.111484 TGCATTCATAGGGGTGAGTGTA 58.889 45.455 0.00 0.00 37.92 2.90
520 543 3.716353 TGCATTCATAGGGGTGAGTGTAT 59.284 43.478 0.00 0.00 37.92 2.29
521 544 4.067896 GCATTCATAGGGGTGAGTGTATG 58.932 47.826 0.00 0.00 37.92 2.39
522 545 3.838244 TTCATAGGGGTGAGTGTATGC 57.162 47.619 0.00 0.00 0.00 3.14
532 555 2.466571 GTGAGTGTATGCGCGTATGTAC 59.533 50.000 20.45 16.94 0.00 2.90
550 573 1.874019 CGAGCGCTTGCGTCTGTAT 60.874 57.895 13.26 0.00 45.69 2.29
602 625 3.097614 ACTATTACAGTTGGAGAGCGGT 58.902 45.455 0.00 0.00 31.59 5.68
612 636 1.822990 TGGAGAGCGGTCTTTCGTATT 59.177 47.619 19.66 0.00 30.97 1.89
618 642 3.187700 AGCGGTCTTTCGTATTCATGTC 58.812 45.455 0.00 0.00 0.00 3.06
623 647 3.924686 GTCTTTCGTATTCATGTCCGTGT 59.075 43.478 0.00 0.00 0.00 4.49
648 672 1.206878 TCACCCCTGATCATGGACTG 58.793 55.000 17.83 12.07 0.00 3.51
653 677 0.465097 CCTGATCATGGACTGTGGGC 60.465 60.000 0.00 0.00 0.00 5.36
663 687 2.627699 TGGACTGTGGGCAAGAAAATTC 59.372 45.455 0.00 0.00 0.00 2.17
668 692 2.159382 GTGGGCAAGAAAATTCGAGGA 58.841 47.619 0.00 0.00 0.00 3.71
681 705 2.822399 GAGGATCGGCGTTGGGAT 59.178 61.111 6.85 0.00 0.00 3.85
683 707 0.463833 GAGGATCGGCGTTGGGATTT 60.464 55.000 6.85 0.00 0.00 2.17
684 708 0.748005 AGGATCGGCGTTGGGATTTG 60.748 55.000 6.85 0.00 0.00 2.32
687 1902 1.656818 ATCGGCGTTGGGATTTGCAG 61.657 55.000 6.85 0.00 0.00 4.41
702 1917 2.189594 TGCAGGAAGATGTTGGAGTG 57.810 50.000 0.00 0.00 0.00 3.51
711 1926 2.567169 AGATGTTGGAGTGGATTCGTCA 59.433 45.455 0.00 0.00 0.00 4.35
717 1932 2.083774 GGAGTGGATTCGTCATGCAAA 58.916 47.619 0.00 0.00 34.49 3.68
718 1933 2.159517 GGAGTGGATTCGTCATGCAAAC 60.160 50.000 0.00 0.00 34.49 2.93
719 1934 2.483877 GAGTGGATTCGTCATGCAAACA 59.516 45.455 0.00 0.00 34.49 2.83
720 1935 3.084039 AGTGGATTCGTCATGCAAACAT 58.916 40.909 0.00 0.00 34.49 2.71
721 1936 3.127548 AGTGGATTCGTCATGCAAACATC 59.872 43.478 0.00 0.00 34.49 3.06
722 1937 3.127548 GTGGATTCGTCATGCAAACATCT 59.872 43.478 0.00 0.00 34.49 2.90
723 1938 3.374988 TGGATTCGTCATGCAAACATCTC 59.625 43.478 0.00 0.00 32.87 2.75
724 1939 3.242870 GGATTCGTCATGCAAACATCTCC 60.243 47.826 0.00 0.00 32.87 3.71
725 1940 2.470983 TCGTCATGCAAACATCTCCA 57.529 45.000 0.00 0.00 32.87 3.86
726 1941 2.076100 TCGTCATGCAAACATCTCCAC 58.924 47.619 0.00 0.00 32.87 4.02
727 1942 1.805943 CGTCATGCAAACATCTCCACA 59.194 47.619 0.00 0.00 32.87 4.17
728 1943 2.159612 CGTCATGCAAACATCTCCACAG 60.160 50.000 0.00 0.00 32.87 3.66
729 1944 1.814394 TCATGCAAACATCTCCACAGC 59.186 47.619 0.00 0.00 32.87 4.40
1185 2400 0.553819 AGTCCTACGCCTCCATCTCT 59.446 55.000 0.00 0.00 0.00 3.10
1833 3048 1.768870 ACTGCACTACTTGACACCCTT 59.231 47.619 0.00 0.00 0.00 3.95
1881 3096 0.811616 CCGCTGGCTCTATTGTCACC 60.812 60.000 0.00 0.00 0.00 4.02
2073 3288 3.491267 GTCAGCGGTATGATAAGCTTGTC 59.509 47.826 15.70 15.70 37.94 3.18
2079 3294 3.431766 GGTATGATAAGCTTGTCCACCGT 60.432 47.826 20.77 4.57 0.00 4.83
2241 3456 8.929260 TGCATTTGTATAGATCAAGATTGGAT 57.071 30.769 0.00 0.00 0.00 3.41
2329 3544 3.055530 CACAGAAGAGGCTTGTCTGGTAT 60.056 47.826 24.00 8.13 42.54 2.73
2523 3738 1.168714 GCAAGAGTGGGAATGTGGAC 58.831 55.000 0.00 0.00 0.00 4.02
2676 3891 3.480470 ACTCGAAATGCAAGATATGGGG 58.520 45.455 0.00 0.00 0.00 4.96
2706 3921 0.970937 CCCGAAGCCTCTACCAGTCA 60.971 60.000 0.00 0.00 0.00 3.41
2867 4082 1.462432 TGGCCAGGGAGGTGTACAA 60.462 57.895 0.00 0.00 40.61 2.41
2964 4179 1.076332 GTATTGGTGACGCACTGACC 58.924 55.000 9.31 0.00 34.40 4.02
3312 4527 0.321671 CCGGGTCTCTTGAAGCAAGA 59.678 55.000 9.28 9.28 46.50 3.02
3336 4551 0.466124 GAGAGATCAAAGGTCGGGGG 59.534 60.000 0.00 0.00 0.00 5.40
3872 5087 6.419771 GTCTAGTTGTTTGAGAAGTTTTCGG 58.580 40.000 0.00 0.00 34.02 4.30
4292 5507 9.403583 TCTAATAGACCAAAAGTTCAAAACAGT 57.596 29.630 0.00 0.00 0.00 3.55
4541 5759 6.239345 GGTGTCCCTTGATGTATTCTACTAGG 60.239 46.154 0.00 0.00 0.00 3.02
4547 5765 5.919272 TGATGTATTCTACTAGGTCGACG 57.081 43.478 9.92 0.00 0.00 5.12
4567 5785 2.793237 CGTAGTTTTGCGGTTTGTGCTT 60.793 45.455 0.00 0.00 0.00 3.91
4651 5869 3.496130 GCAGGTTCCTTATCATGACATCG 59.504 47.826 0.00 0.00 0.00 3.84
4672 5890 5.690816 TCGTCATTATCTAGAAGCTTAGCG 58.309 41.667 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.386661 ATGAGACAGTAAAGGTGCGG 57.613 50.000 0.00 0.00 0.00 5.69
54 55 4.414956 ACCCCTCATCGGCCTCCA 62.415 66.667 0.00 0.00 0.00 3.86
60 61 0.034059 GTATGCTGACCCCTCATCGG 59.966 60.000 0.00 0.00 0.00 4.18
61 62 1.000283 GAGTATGCTGACCCCTCATCG 60.000 57.143 0.00 0.00 0.00 3.84
77 78 3.626729 GGAGGGGCGGCTTATATAGAGTA 60.627 52.174 9.56 0.00 0.00 2.59
81 82 0.460311 CGGAGGGGCGGCTTATATAG 59.540 60.000 9.56 0.00 0.00 1.31
104 105 2.904866 GTGCGGACCCTTGTGCAA 60.905 61.111 0.00 0.00 39.34 4.08
116 117 2.119484 TTGAGTTACAGGGGGTGCGG 62.119 60.000 0.00 0.00 0.00 5.69
126 127 4.986034 CGTTGTATGGAGTGTTGAGTTACA 59.014 41.667 0.00 0.00 0.00 2.41
231 232 3.843304 GGCAGAGCCTAGCTACGA 58.157 61.111 0.00 0.00 46.69 3.43
274 275 0.037697 CGTGGGAACGGATCTGACAA 60.038 55.000 9.00 0.00 0.00 3.18
276 277 0.458025 GTCGTGGGAACGGATCTGAC 60.458 60.000 9.00 1.79 0.00 3.51
313 314 2.105821 CACCAAGACTTGAACCCTGGTA 59.894 50.000 16.99 0.00 0.00 3.25
316 317 0.954452 GCACCAAGACTTGAACCCTG 59.046 55.000 16.99 1.22 0.00 4.45
329 330 3.831333 TCCAGAAATAATGCAAGCACCAA 59.169 39.130 0.00 0.00 0.00 3.67
337 338 8.366401 TCTTGAAACAAATCCAGAAATAATGCA 58.634 29.630 0.00 0.00 0.00 3.96
346 347 5.048083 CCGGAAATCTTGAAACAAATCCAGA 60.048 40.000 0.00 0.00 0.00 3.86
355 356 3.501950 GCATCACCGGAAATCTTGAAAC 58.498 45.455 9.46 0.00 0.00 2.78
361 362 1.821216 AAACGCATCACCGGAAATCT 58.179 45.000 9.46 0.00 0.00 2.40
385 386 4.767633 CGAGAACGTCTCCTTCCG 57.232 61.111 8.73 0.00 40.34 4.30
415 416 2.241160 TGTACGAAGTCACCTTAGGCA 58.759 47.619 0.00 0.00 43.93 4.75
421 422 6.565234 CATCTTTAGATGTACGAAGTCACCT 58.435 40.000 10.85 0.00 45.10 4.00
451 452 1.521010 CTCCGAGAGACTACGCCGA 60.521 63.158 0.00 0.00 0.00 5.54
454 455 1.722677 CACCTCCGAGAGACTACGC 59.277 63.158 0.00 0.00 0.00 4.42
500 523 4.067896 GCATACACTCACCCCTATGAATG 58.932 47.826 0.00 0.00 32.12 2.67
501 524 3.244215 CGCATACACTCACCCCTATGAAT 60.244 47.826 0.00 0.00 0.00 2.57
502 525 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
503 526 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
504 527 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
505 528 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
506 529 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
507 530 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
508 531 2.287457 TACGCGCATACACTCACCCC 62.287 60.000 5.73 0.00 0.00 4.95
509 532 0.249322 ATACGCGCATACACTCACCC 60.249 55.000 5.73 0.00 0.00 4.61
510 533 0.852777 CATACGCGCATACACTCACC 59.147 55.000 5.73 0.00 0.00 4.02
511 534 1.556564 ACATACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
512 535 2.723209 GTACATACGCGCATACACTCA 58.277 47.619 5.73 0.00 0.00 3.41
513 536 1.707117 CGTACATACGCGCATACACTC 59.293 52.381 5.73 0.00 43.14 3.51
514 537 1.750351 CGTACATACGCGCATACACT 58.250 50.000 5.73 0.00 43.14 3.55
532 555 1.413767 AATACAGACGCAAGCGCTCG 61.414 55.000 12.06 14.49 44.19 5.03
584 607 2.180276 AGACCGCTCTCCAACTGTAAT 58.820 47.619 0.00 0.00 0.00 1.89
602 625 4.182693 ACACGGACATGAATACGAAAGA 57.817 40.909 0.00 0.00 0.00 2.52
612 636 2.165641 GGTGATCAGTACACGGACATGA 59.834 50.000 0.00 0.00 38.90 3.07
618 642 0.175760 CAGGGGTGATCAGTACACGG 59.824 60.000 0.00 0.00 38.90 4.94
641 665 2.380064 TTTTCTTGCCCACAGTCCAT 57.620 45.000 0.00 0.00 0.00 3.41
648 672 2.159382 TCCTCGAATTTTCTTGCCCAC 58.841 47.619 0.00 0.00 0.00 4.61
653 677 2.285834 CGCCGATCCTCGAATTTTCTTG 60.286 50.000 0.00 0.00 43.74 3.02
663 687 2.644555 AATCCCAACGCCGATCCTCG 62.645 60.000 0.00 0.36 40.07 4.63
668 692 1.656818 CTGCAAATCCCAACGCCGAT 61.657 55.000 0.00 0.00 0.00 4.18
672 696 0.109132 CTTCCTGCAAATCCCAACGC 60.109 55.000 0.00 0.00 0.00 4.84
679 703 3.760684 ACTCCAACATCTTCCTGCAAATC 59.239 43.478 0.00 0.00 0.00 2.17
681 705 2.886523 CACTCCAACATCTTCCTGCAAA 59.113 45.455 0.00 0.00 0.00 3.68
683 707 1.271543 CCACTCCAACATCTTCCTGCA 60.272 52.381 0.00 0.00 0.00 4.41
684 708 1.003580 TCCACTCCAACATCTTCCTGC 59.996 52.381 0.00 0.00 0.00 4.85
687 1902 2.939103 CGAATCCACTCCAACATCTTCC 59.061 50.000 0.00 0.00 0.00 3.46
702 1917 3.242870 GGAGATGTTTGCATGACGAATCC 60.243 47.826 0.00 0.00 35.07 3.01
711 1926 1.542915 GTGCTGTGGAGATGTTTGCAT 59.457 47.619 0.00 0.00 38.18 3.96
717 1932 1.209019 GGAGATGTGCTGTGGAGATGT 59.791 52.381 0.00 0.00 0.00 3.06
718 1933 1.474677 GGGAGATGTGCTGTGGAGATG 60.475 57.143 0.00 0.00 0.00 2.90
719 1934 0.835941 GGGAGATGTGCTGTGGAGAT 59.164 55.000 0.00 0.00 0.00 2.75
720 1935 1.267574 GGGGAGATGTGCTGTGGAGA 61.268 60.000 0.00 0.00 0.00 3.71
721 1936 1.222936 GGGGAGATGTGCTGTGGAG 59.777 63.158 0.00 0.00 0.00 3.86
722 1937 0.915872 ATGGGGAGATGTGCTGTGGA 60.916 55.000 0.00 0.00 0.00 4.02
723 1938 0.033796 AATGGGGAGATGTGCTGTGG 60.034 55.000 0.00 0.00 0.00 4.17
724 1939 1.386533 GAATGGGGAGATGTGCTGTG 58.613 55.000 0.00 0.00 0.00 3.66
725 1940 0.257039 GGAATGGGGAGATGTGCTGT 59.743 55.000 0.00 0.00 0.00 4.40
726 1941 0.466922 GGGAATGGGGAGATGTGCTG 60.467 60.000 0.00 0.00 0.00 4.41
727 1942 1.649271 GGGGAATGGGGAGATGTGCT 61.649 60.000 0.00 0.00 0.00 4.40
728 1943 1.152673 GGGGAATGGGGAGATGTGC 60.153 63.158 0.00 0.00 0.00 4.57
729 1944 0.106519 GTGGGGAATGGGGAGATGTG 60.107 60.000 0.00 0.00 0.00 3.21
1833 3048 1.449601 GGATGCTTCGGCGAAAGGA 60.450 57.895 23.81 17.84 45.37 3.36
2049 3264 1.000163 AGCTTATCATACCGCTGACCG 60.000 52.381 0.00 0.00 0.00 4.79
2073 3288 1.738099 CTTGCGGAGAAGACGGTGG 60.738 63.158 0.00 0.00 0.00 4.61
2079 3294 1.964223 AGTCTGTTCTTGCGGAGAAGA 59.036 47.619 2.87 1.68 44.78 2.87
2268 3483 4.009675 GTGCCCTGATCAGATTGTTGTAA 58.990 43.478 24.62 0.00 0.00 2.41
2329 3544 5.458595 TCCATCTTCTATAGACTGCTCCAA 58.541 41.667 0.67 0.00 35.19 3.53
2676 3891 2.511600 CTTCGGGTCGGGATGTGC 60.512 66.667 0.00 0.00 0.00 4.57
2706 3921 4.158394 AGCTCACACAATTCACAAACAACT 59.842 37.500 0.00 0.00 0.00 3.16
2867 4082 2.362369 CCTGCAGACTCCATCCGGT 61.362 63.158 17.39 0.00 0.00 5.28
2964 4179 9.740239 TTCTTCTCATGAATGAAGTTGAAAAAG 57.260 29.630 18.94 0.00 40.20 2.27
3051 4266 2.159057 CCAAAATACCATTGCCTGCTCC 60.159 50.000 0.00 0.00 0.00 4.70
3213 4428 6.441274 CAACAGAAGCACATTACACAAGAAT 58.559 36.000 0.00 0.00 0.00 2.40
3312 4527 1.480137 CGACCTTTGATCTCTCCAGCT 59.520 52.381 0.00 0.00 0.00 4.24
3336 4551 1.672881 CCAATCAAGAATCGTCCTGCC 59.327 52.381 0.00 0.00 0.00 4.85
3474 4689 2.191513 CCCTGCCATGCTCAATCCG 61.192 63.158 0.00 0.00 0.00 4.18
3751 4966 2.299993 TCAGATCAACAGACGGATGC 57.700 50.000 0.00 0.00 0.00 3.91
4126 5341 9.944663 AAACGATGTAATTTATGCGAATACAAT 57.055 25.926 0.00 0.00 0.00 2.71
4128 5343 8.391859 ACAAACGATGTAATTTATGCGAATACA 58.608 29.630 0.00 0.00 41.63 2.29
4129 5344 8.669801 CACAAACGATGTAATTTATGCGAATAC 58.330 33.333 0.00 0.00 41.46 1.89
4230 5445 7.621796 ACCCAGATTAACTAGAACCACTTTAG 58.378 38.462 0.00 0.00 0.00 1.85
4541 5759 0.854705 AACCGCAAAACTACGTCGAC 59.145 50.000 5.18 5.18 0.00 4.20
4547 5765 2.485266 AGCACAAACCGCAAAACTAC 57.515 45.000 0.00 0.00 0.00 2.73
4563 5781 7.584122 TTATTGTTACACCAGGTAAAAAGCA 57.416 32.000 0.00 0.00 41.34 3.91
4611 5829 9.667107 GGAACCTGCATTGCTTATAATATACTA 57.333 33.333 10.49 0.00 0.00 1.82
4651 5869 6.525280 GCTACGCTAAGCTTCTAGATAATGAC 59.475 42.308 0.00 0.00 39.50 3.06


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

AutoCloner maintained by Alex Coulton.