Multiple sequence alignment - TraesCS1B01G130300

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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 TraesCS1B01G130300 chr1B 100.000 4538 0 0 1 4538 161213537 161209000 0.000000e+00 8381.0
1 TraesCS1B01G130300 chr1B 97.143 35 0 1 3848 3882 415738302 415738335 1.760000e-04 58.4
2 TraesCS1B01G130300 chr1A 96.298 3782 105 16 1 3780 107111070 107107322 0.000000e+00 6176.0
3 TraesCS1B01G130300 chr1A 90.061 654 23 16 3898 4537 107106962 107106337 0.000000e+00 809.0
4 TraesCS1B01G130300 chr1D 95.931 3809 94 20 1 3782 106234288 106238062 0.000000e+00 6119.0
5 TraesCS1B01G130300 chr1D 91.429 770 40 13 3783 4537 106238122 106238880 0.000000e+00 1033.0
6 TraesCS1B01G130300 chr5B 92.308 52 1 3 3843 3894 569149391 569149343 2.260000e-08 71.3
7 TraesCS1B01G130300 chr5B 92.308 52 1 3 3843 3894 569250605 569250557 2.260000e-08 71.3
8 TraesCS1B01G130300 chr7A 97.143 35 1 0 3849 3883 92250232 92250198 4.900000e-05 60.2
9 TraesCS1B01G130300 chr6B 92.857 42 2 1 3842 3883 28165374 28165414 4.900000e-05 60.2
10 TraesCS1B01G130300 chr6B 97.143 35 0 1 3849 3883 400352770 400352803 1.760000e-04 58.4
11 TraesCS1B01G130300 chr2B 97.222 36 0 1 3849 3884 161464908 161464942 4.900000e-05 60.2
12 TraesCS1B01G130300 chr5D 97.143 35 0 1 3849 3883 487170901 487170868 1.760000e-04 58.4
13 TraesCS1B01G130300 chr3D 97.143 35 0 1 3849 3883 551242417 551242450 1.760000e-04 58.4


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 TraesCS1B01G130300 chr1B 161209000 161213537 4537 True 8381.0 8381 100.0000 1 4538 1 chr1B.!!$R1 4537
1 TraesCS1B01G130300 chr1A 107106337 107111070 4733 True 3492.5 6176 93.1795 1 4537 2 chr1A.!!$R1 4536
2 TraesCS1B01G130300 chr1D 106234288 106238880 4592 False 3576.0 6119 93.6800 1 4537 2 chr1D.!!$F1 4536

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
372 387 0.343372 ACCAGCCCATCCCTCTTCTA 59.657 55.0 0.0 0.0 0.0 2.10 F
2110 2141 0.108992 TGGTAAGCTAAGTGTCGGCG 60.109 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2252 0.599991 GCCAGTTTCCTTTTTGGCGG 60.600 55.0 0.0 0.0 45.68 6.13 R
4081 4370 0.172803 CCTCGTCTAAACCTGTCCGG 59.827 60.0 0.0 0.0 39.35 5.14 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
28 29 1.080772 CACGCACTCACGCCTCTTA 60.081 57.895 0.00 0.00 36.19 2.10
52 54 2.778299 TCATCTTCCCACCAACTTTCG 58.222 47.619 0.00 0.00 0.00 3.46
53 55 2.105821 TCATCTTCCCACCAACTTTCGT 59.894 45.455 0.00 0.00 0.00 3.85
175 182 1.198759 TTCCTCCCGGACCCAAGAAG 61.199 60.000 0.73 0.00 39.60 2.85
227 239 0.464193 CACCATCGCCATCACCATCA 60.464 55.000 0.00 0.00 0.00 3.07
372 387 0.343372 ACCAGCCCATCCCTCTTCTA 59.657 55.000 0.00 0.00 0.00 2.10
374 389 1.413662 CCAGCCCATCCCTCTTCTAGA 60.414 57.143 0.00 0.00 0.00 2.43
376 391 1.052617 GCCCATCCCTCTTCTAGACC 58.947 60.000 0.00 0.00 0.00 3.85
414 429 2.964310 TTCTGGCTCTGGCTCTGGC 61.964 63.158 0.00 0.00 38.73 4.85
444 459 3.365265 CCAACCGCCTGGCTGAAC 61.365 66.667 17.38 0.00 39.70 3.18
449 464 1.743252 CCGCCTGGCTGAACTTCTC 60.743 63.158 17.92 0.00 0.00 2.87
457 472 4.388499 TGAACTTCTCGCGGGGGC 62.388 66.667 5.94 0.00 0.00 5.80
458 473 4.083862 GAACTTCTCGCGGGGGCT 62.084 66.667 5.94 0.00 0.00 5.19
459 474 4.083862 AACTTCTCGCGGGGGCTC 62.084 66.667 5.94 0.00 0.00 4.70
469 484 3.090532 GGGGGCTCCGGTGAGAAT 61.091 66.667 7.92 0.00 41.42 2.40
470 485 2.506472 GGGGCTCCGGTGAGAATC 59.494 66.667 7.92 0.00 41.42 2.52
471 486 2.107141 GGGCTCCGGTGAGAATCG 59.893 66.667 7.92 0.00 41.42 3.34
512 527 2.188994 GCCAGAGGCGATTCAGCT 59.811 61.111 0.00 0.00 39.62 4.24
530 559 3.402681 GCTGGGAGGCCTGCACTA 61.403 66.667 26.95 10.61 35.28 2.74
532 561 3.376935 CTGGGAGGCCTGCACTACG 62.377 68.421 26.95 4.90 0.00 3.51
542 571 1.274167 CCTGCACTACGAAGGTAACCA 59.726 52.381 0.00 0.00 37.17 3.67
590 619 4.095036 GGTTGATTTCACTCGAGGGATTTC 59.905 45.833 20.08 17.91 0.00 2.17
591 620 3.521560 TGATTTCACTCGAGGGATTTCG 58.478 45.455 20.08 0.00 41.79 3.46
608 637 1.167781 TCGTTCTGTTTTTCCGGGCC 61.168 55.000 0.00 0.00 0.00 5.80
625 654 0.685458 GCCCCTGCATGTTGGAGATT 60.685 55.000 7.54 0.00 38.14 2.40
635 664 7.308408 CCTGCATGTTGGAGATTATACTGATTG 60.308 40.741 0.00 0.00 38.14 2.67
640 669 6.756542 TGTTGGAGATTATACTGATTGTGTCG 59.243 38.462 0.00 0.00 0.00 4.35
654 683 1.076332 GTGTCGTGTGGGACTATTGC 58.924 55.000 0.00 0.00 37.81 3.56
681 710 2.264794 GTTCGCGGTGGATGGAGT 59.735 61.111 6.13 0.00 0.00 3.85
699 728 3.503363 GATGCTGCGGGTGTGCTC 61.503 66.667 0.00 0.00 35.36 4.26
738 767 4.588528 TGCCTGATAAGCAAGGTTTCTTTT 59.411 37.500 0.00 0.00 37.28 2.27
770 800 1.961277 CCTGCCGACCAAGACACAC 60.961 63.158 0.00 0.00 0.00 3.82
925 955 3.502051 TCTAGCTCCCCCTTTTTCCTA 57.498 47.619 0.00 0.00 0.00 2.94
934 964 1.272147 CCCTTTTTCCTAGCTGGCTGT 60.272 52.381 5.25 0.00 35.26 4.40
942 972 0.464870 CTAGCTGGCTGTCTGCATCT 59.535 55.000 13.58 0.00 45.15 2.90
968 998 1.615392 GCAATTCAGGGCTCTTGTGTT 59.385 47.619 0.00 0.00 0.00 3.32
997 1028 2.228822 CCCCAGTTTCTGTTTGGATTCG 59.771 50.000 0.00 0.00 33.76 3.34
1044 1075 2.238084 TAGCTCTGCTCCTTCTTGGA 57.762 50.000 0.00 0.00 43.86 3.53
1178 1209 1.270550 CAAAGCAGACAATTCCGGCTT 59.729 47.619 0.00 8.31 41.99 4.35
1267 1298 5.072741 ACAATCCTGTGCTGTATCAAACTT 58.927 37.500 0.00 0.00 33.30 2.66
1305 1336 1.132643 CCGTCGTCCTACTCCTTCAAG 59.867 57.143 0.00 0.00 0.00 3.02
1348 1379 1.334160 TGTCCGGCTACACTTCTTCA 58.666 50.000 0.00 0.00 0.00 3.02
1401 1432 2.450160 GCAAAGTTCAAAGTGTCCACG 58.550 47.619 0.00 0.00 36.20 4.94
1452 1483 1.377202 GCCGAGCAATTCCTCACCA 60.377 57.895 0.00 0.00 0.00 4.17
1514 1545 4.259356 CTGATTCTCTCATTTGTGCCTCA 58.741 43.478 0.00 0.00 32.10 3.86
1538 1569 4.380233 GGGAAACAGCACATCTTTCATCAG 60.380 45.833 0.00 0.00 0.00 2.90
1732 1763 4.383226 GGGATACTGACCAGAACTTCTTCC 60.383 50.000 3.76 0.00 0.00 3.46
1755 1786 6.727231 TCCTAAATTCCACTACCACTGAACTA 59.273 38.462 0.00 0.00 0.00 2.24
2110 2141 0.108992 TGGTAAGCTAAGTGTCGGCG 60.109 55.000 0.00 0.00 0.00 6.46
2139 2170 0.387622 CCAGCTTGAACAATGTGGCG 60.388 55.000 0.00 0.00 0.00 5.69
2221 2252 2.832661 TTGTGTGGCCACCAGCAC 60.833 61.111 32.62 23.40 46.50 4.40
2254 2285 4.401925 GAAACTGGCTATCATATTGGGCT 58.598 43.478 0.00 0.00 0.00 5.19
2408 2439 3.879892 CTCAATGGCCTTAGCTTCCTTAC 59.120 47.826 3.32 0.00 39.73 2.34
2410 2441 0.539986 TGGCCTTAGCTTCCTTACCG 59.460 55.000 3.32 0.00 39.73 4.02
3057 3088 0.884704 GGCAGAAGCTGACCGACAAA 60.885 55.000 0.00 0.00 41.70 2.83
3075 3106 5.063438 CGACAAATCGGATGTGTACTCATTT 59.937 40.000 13.65 0.54 44.99 2.32
3198 3229 0.915364 GGGGAGAGCTTGGTCAGATT 59.085 55.000 2.64 0.00 0.00 2.40
3277 3308 0.039437 GGTCGAGAAGTGTCTTGCGA 60.039 55.000 0.00 0.00 35.46 5.10
3436 3467 0.975887 GATGGGCTCTCTGGAGATCC 59.024 60.000 10.92 10.92 41.70 3.36
3438 3469 2.733945 GGCTCTCTGGAGATCCGC 59.266 66.667 4.97 3.86 41.86 5.54
3460 3491 1.275471 CGCAGACGAAGCAGACGAAA 61.275 55.000 0.00 0.00 43.93 3.46
3468 3499 3.345808 GCAGACGAAAGCCGCACA 61.346 61.111 0.00 0.00 43.32 4.57
3519 3550 0.107312 ATGCCTTCTCGCAGCTGATT 60.107 50.000 20.43 0.00 43.26 2.57
3570 3601 5.182001 GCATTGTTTCTGTGTCACTAAGGAT 59.818 40.000 4.27 0.00 0.00 3.24
3865 3957 1.400530 GGTACTCCCTCCGTCCCATG 61.401 65.000 0.00 0.00 0.00 3.66
3866 3958 0.396695 GTACTCCCTCCGTCCCATGA 60.397 60.000 0.00 0.00 0.00 3.07
3868 3960 1.050988 ACTCCCTCCGTCCCATGATG 61.051 60.000 0.00 0.00 0.00 3.07
3869 3961 1.002921 TCCCTCCGTCCCATGATGT 59.997 57.895 0.00 0.00 0.00 3.06
3871 3963 1.128200 CCCTCCGTCCCATGATGTAA 58.872 55.000 0.00 0.00 0.00 2.41
3872 3964 1.070758 CCCTCCGTCCCATGATGTAAG 59.929 57.143 0.00 0.00 0.00 2.34
3873 3965 2.039418 CCTCCGTCCCATGATGTAAGA 58.961 52.381 0.00 0.00 0.00 2.10
3874 3966 2.224066 CCTCCGTCCCATGATGTAAGAC 60.224 54.545 0.00 0.00 0.00 3.01
3876 3968 1.852942 CGTCCCATGATGTAAGACGG 58.147 55.000 16.98 0.55 44.86 4.79
3879 3971 3.606687 GTCCCATGATGTAAGACGGTTT 58.393 45.455 0.00 0.00 0.00 3.27
3881 3973 4.457949 GTCCCATGATGTAAGACGGTTTTT 59.542 41.667 0.00 0.00 0.00 1.94
3917 4205 2.682352 GACGGAGGGAGTAGAACAGTAC 59.318 54.545 0.00 0.00 0.00 2.73
3925 4213 5.414144 AGGGAGTAGAACAGTACTTTACGAC 59.586 44.000 0.00 0.00 33.18 4.34
3926 4214 5.392487 GGGAGTAGAACAGTACTTTACGACC 60.392 48.000 0.00 4.16 33.18 4.79
3937 4225 0.885596 TTTACGACCAAGGGGCAACG 60.886 55.000 0.00 0.00 37.90 4.10
3948 4236 3.290948 AGGGGCAACGATTATTTAGCA 57.709 42.857 0.00 0.00 37.60 3.49
4014 4302 1.189884 CATTGTCGCAACCGCAAAAAG 59.810 47.619 0.00 0.00 38.40 2.27
4015 4303 0.452184 TTGTCGCAACCGCAAAAAGA 59.548 45.000 0.00 0.00 38.40 2.52
4016 4304 0.248296 TGTCGCAACCGCAAAAAGAC 60.248 50.000 0.00 0.00 38.40 3.01
4063 4352 4.630894 ACACACGTCAACATTTGTCAAT 57.369 36.364 0.00 0.00 0.00 2.57
4189 4487 5.220548 CCAAGAGACGATGCAACAAGATTAG 60.221 44.000 0.00 0.00 0.00 1.73
4232 4530 0.816825 CATTCGCCATCACTCCCAGG 60.817 60.000 0.00 0.00 0.00 4.45
4233 4531 1.987807 ATTCGCCATCACTCCCAGGG 61.988 60.000 0.00 0.00 0.00 4.45
4234 4532 4.181010 CGCCATCACTCCCAGGGG 62.181 72.222 5.33 0.92 0.00 4.79
4235 4533 4.512914 GCCATCACTCCCAGGGGC 62.513 72.222 5.33 0.00 34.68 5.80
4236 4534 2.693864 CCATCACTCCCAGGGGCT 60.694 66.667 5.33 0.00 34.68 5.19
4237 4535 1.384502 CCATCACTCCCAGGGGCTA 60.385 63.158 5.33 0.00 34.68 3.93
4238 4536 1.414061 CCATCACTCCCAGGGGCTAG 61.414 65.000 5.33 0.00 34.68 3.42
4239 4537 1.074167 ATCACTCCCAGGGGCTAGG 60.074 63.158 5.33 0.00 34.68 3.02
4240 4538 2.628187 ATCACTCCCAGGGGCTAGGG 62.628 65.000 5.33 0.00 46.90 3.53
4241 4539 4.825679 ACTCCCAGGGGCTAGGGC 62.826 72.222 5.33 0.00 45.07 5.19
4242 4540 4.505970 CTCCCAGGGGCTAGGGCT 62.506 72.222 5.33 0.00 45.07 5.19
4243 4541 4.499116 TCCCAGGGGCTAGGGCTC 62.499 72.222 5.33 0.00 45.07 4.70
4244 4542 4.823732 CCCAGGGGCTAGGGCTCA 62.824 72.222 0.00 0.00 41.58 4.26
4245 4543 2.449322 CCAGGGGCTAGGGCTCAT 60.449 66.667 0.00 0.00 41.58 2.90
4246 4544 2.081161 CCAGGGGCTAGGGCTCATT 61.081 63.158 0.00 0.00 41.58 2.57
4247 4545 1.453669 CAGGGGCTAGGGCTCATTC 59.546 63.158 0.00 0.00 41.58 2.67
4248 4546 1.059006 CAGGGGCTAGGGCTCATTCT 61.059 60.000 0.00 0.00 41.58 2.40
4249 4547 1.059006 AGGGGCTAGGGCTCATTCTG 61.059 60.000 0.00 0.00 41.58 3.02
4250 4548 1.348775 GGGGCTAGGGCTCATTCTGT 61.349 60.000 0.00 0.00 41.58 3.41
4251 4549 0.548510 GGGCTAGGGCTCATTCTGTT 59.451 55.000 0.00 0.00 39.12 3.16
4252 4550 1.673168 GGCTAGGGCTCATTCTGTTG 58.327 55.000 0.00 0.00 38.73 3.33
4253 4551 1.673168 GCTAGGGCTCATTCTGTTGG 58.327 55.000 0.00 0.00 35.22 3.77
4254 4552 1.065126 GCTAGGGCTCATTCTGTTGGT 60.065 52.381 0.00 0.00 35.22 3.67
4255 4553 2.636830 CTAGGGCTCATTCTGTTGGTG 58.363 52.381 0.00 0.00 0.00 4.17
4256 4554 0.038744 AGGGCTCATTCTGTTGGTGG 59.961 55.000 0.00 0.00 0.00 4.61
4257 4555 1.598701 GGGCTCATTCTGTTGGTGGC 61.599 60.000 0.00 0.00 0.00 5.01
4258 4556 0.610232 GGCTCATTCTGTTGGTGGCT 60.610 55.000 0.00 0.00 0.00 4.75
4270 4595 4.175337 GTGGCTGGGCGGCTATCA 62.175 66.667 9.56 1.34 39.32 2.15
4334 4659 2.434428 CATTGACTTCAGCTTGCTCCT 58.566 47.619 0.00 0.00 0.00 3.69
4438 4763 0.762418 TTCTTGGTCGCCTTTCCTCA 59.238 50.000 0.00 0.00 0.00 3.86
4450 4775 0.112995 TTTCCTCATGGCCAACAGCT 59.887 50.000 10.96 0.00 43.05 4.24
4521 4849 6.545504 ACATTGATGATTAACGATACTGCC 57.454 37.500 0.00 0.00 0.00 4.85
4537 4865 0.183492 TGCCAGGAAAGCAACTCAGT 59.817 50.000 0.00 0.00 37.28 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.278957 CGAAAGTTGGTGGGAAGATGAATTT 60.279 40.000 0.00 0.0 0.00 1.82
175 182 1.663135 GCGAGATTTTGAGCAGAGTCC 59.337 52.381 0.00 0.0 0.00 3.85
227 239 2.023984 GGATGGGGATTTTGGAAGGAGT 60.024 50.000 0.00 0.0 0.00 3.85
372 387 2.104963 AGTCTTTTCTTGAAGCCGGTCT 59.895 45.455 1.90 0.0 0.00 3.85
374 389 2.222027 CAGTCTTTTCTTGAAGCCGGT 58.778 47.619 1.90 0.0 0.00 5.28
376 391 2.222027 ACCAGTCTTTTCTTGAAGCCG 58.778 47.619 0.00 0.0 0.00 5.52
414 429 1.377333 GGTTGGGAAAGCGGAGGAG 60.377 63.158 0.00 0.0 0.00 3.69
457 472 2.278857 CCGCGATTCTCACCGGAG 60.279 66.667 9.46 0.0 43.20 4.63
458 473 3.833645 CCCGCGATTCTCACCGGA 61.834 66.667 9.46 0.0 43.20 5.14
459 474 4.891727 CCCCGCGATTCTCACCGG 62.892 72.222 8.23 0.0 40.39 5.28
461 476 4.162690 AGCCCCGCGATTCTCACC 62.163 66.667 8.23 0.0 0.00 4.02
462 477 2.892425 CAGCCCCGCGATTCTCAC 60.892 66.667 8.23 0.0 0.00 3.51
463 478 4.838152 GCAGCCCCGCGATTCTCA 62.838 66.667 8.23 0.0 0.00 3.27
464 479 4.537433 AGCAGCCCCGCGATTCTC 62.537 66.667 8.23 0.0 36.85 2.87
465 480 4.101448 AAGCAGCCCCGCGATTCT 62.101 61.111 8.23 0.0 36.85 2.40
466 481 3.880846 CAAGCAGCCCCGCGATTC 61.881 66.667 8.23 0.0 36.85 2.52
467 482 4.722700 ACAAGCAGCCCCGCGATT 62.723 61.111 8.23 0.0 36.85 3.34
468 483 4.722700 AACAAGCAGCCCCGCGAT 62.723 61.111 8.23 0.0 36.85 4.58
469 484 4.947147 AAACAAGCAGCCCCGCGA 62.947 61.111 8.23 0.0 36.85 5.87
470 485 4.705519 CAAACAAGCAGCCCCGCG 62.706 66.667 0.00 0.0 36.85 6.46
471 486 4.362476 CCAAACAAGCAGCCCCGC 62.362 66.667 0.00 0.0 0.00 6.13
474 489 4.362476 CGCCCAAACAAGCAGCCC 62.362 66.667 0.00 0.0 0.00 5.19
497 512 1.153409 AGCAGCTGAATCGCCTCTG 60.153 57.895 20.43 0.0 0.00 3.35
530 559 1.538687 CGAGGGGTGGTTACCTTCGT 61.539 60.000 2.07 0.0 46.66 3.85
532 561 0.248565 GACGAGGGGTGGTTACCTTC 59.751 60.000 2.07 0.0 46.66 3.46
542 571 2.681778 CCAGCTGAGACGAGGGGT 60.682 66.667 17.39 0.0 0.00 4.95
590 619 1.284715 GGCCCGGAAAAACAGAACG 59.715 57.895 0.73 0.0 0.00 3.95
591 620 1.663739 GGGCCCGGAAAAACAGAAC 59.336 57.895 5.69 0.0 0.00 3.01
608 637 4.758674 CAGTATAATCTCCAACATGCAGGG 59.241 45.833 2.31 0.0 0.00 4.45
625 654 3.764972 TCCCACACGACACAATCAGTATA 59.235 43.478 0.00 0.0 0.00 1.47
635 664 1.076332 GCAATAGTCCCACACGACAC 58.924 55.000 0.00 0.0 35.07 3.67
640 669 0.391130 TCTGCGCAATAGTCCCACAC 60.391 55.000 13.05 0.0 0.00 3.82
681 710 4.334118 AGCACACCCGCAGCATCA 62.334 61.111 0.00 0.0 0.00 3.07
699 728 2.096496 CAGGCAAGCAAGAACCTTATCG 59.904 50.000 0.00 0.0 0.00 2.92
770 800 4.520492 AGGTGTGAACAGGCTTAGATTTTG 59.480 41.667 0.00 0.0 0.00 2.44
925 955 0.037877 AAAGATGCAGACAGCCAGCT 59.962 50.000 0.00 0.0 44.83 4.24
942 972 2.318908 AGAGCCCTGAATTGCACAAAA 58.681 42.857 0.00 0.0 0.00 2.44
968 998 0.984230 CAGAAACTGGGGCTACAGGA 59.016 55.000 12.87 0.0 42.75 3.86
997 1028 1.449601 CGGTAGTGGTGCCCATGAC 60.450 63.158 0.00 0.0 35.28 3.06
1178 1209 6.703165 GCTGTGATGTGATGTCAATATAGTCA 59.297 38.462 0.00 0.0 0.00 3.41
1267 1298 3.876914 GACGGCACAATGAATATCCTTGA 59.123 43.478 2.98 0.0 0.00 3.02
1305 1336 2.892425 CGGCCACGGCTCTTCATC 60.892 66.667 8.20 0.0 41.60 2.92
1348 1379 6.782000 AGATCATAGCTCTGGTATCTGAAACT 59.218 38.462 0.00 0.0 0.00 2.66
1401 1432 3.243035 TGTCAAGTAACACAACATGCTGC 60.243 43.478 0.00 0.0 0.00 5.25
1452 1483 2.119495 AGCGAATACTCCCTGACCAAT 58.881 47.619 0.00 0.0 0.00 3.16
1514 1545 3.228188 TGAAAGATGTGCTGTTTCCCT 57.772 42.857 0.00 0.0 36.53 4.20
1538 1569 8.768955 CAGGAACAGATATTACTTCAATAGCAC 58.231 37.037 0.00 0.0 37.86 4.40
1732 1763 9.449719 AAATAGTTCAGTGGTAGTGGAATTTAG 57.550 33.333 0.00 0.0 0.00 1.85
2110 2141 0.827507 TTCAAGCTGGAAGGCCCAAC 60.828 55.000 0.00 0.0 46.07 3.77
2221 2252 0.599991 GCCAGTTTCCTTTTTGGCGG 60.600 55.000 0.00 0.0 45.68 6.13
2254 2285 0.679505 CCAACACCTCCGAGAACAGA 59.320 55.000 0.00 0.0 0.00 3.41
2514 2545 0.388520 CGACAACCATCTGCTCGTCA 60.389 55.000 0.00 0.0 0.00 4.35
3057 3088 3.206150 GCCAAATGAGTACACATCCGAT 58.794 45.455 6.24 0.0 0.00 4.18
3075 3106 3.535629 CTCCAGCAAGACCACGCCA 62.536 63.158 0.00 0.0 0.00 5.69
3312 3343 3.480470 CACAAACTCCAGATTCCACAGT 58.520 45.455 0.00 0.0 0.00 3.55
3438 3469 2.049156 TCTGCTTCGTCTGCGGTG 60.049 61.111 0.00 0.0 37.96 4.94
3460 3491 1.472480 GTAATCCATGTTTGTGCGGCT 59.528 47.619 0.00 0.0 0.00 5.52
3468 3499 6.045318 CGACATCTGAGAGTAATCCATGTTT 58.955 40.000 0.00 0.0 0.00 2.83
3519 3550 3.071023 CAGTTCACCTCCCTTCAGTGTTA 59.929 47.826 0.00 0.0 33.21 2.41
3570 3601 5.394663 CCAGGTCAACATGTTTTTACCAACA 60.395 40.000 25.41 0.0 40.92 3.33
3706 3737 9.234827 TGACAAACATCTAACAGATCATCATTT 57.765 29.630 0.00 0.0 31.32 2.32
3707 3738 8.797350 TGACAAACATCTAACAGATCATCATT 57.203 30.769 0.00 0.0 31.32 2.57
3763 3794 7.068103 AGTGTTCCAATTAAGTTCATGTGTTCA 59.932 33.333 0.00 0.0 0.00 3.18
3882 3974 2.029110 CCTCCGTCCCGTAGTGTAAAAA 60.029 50.000 0.00 0.0 0.00 1.94
3883 3975 1.545582 CCTCCGTCCCGTAGTGTAAAA 59.454 52.381 0.00 0.0 0.00 1.52
3885 3977 0.680921 CCCTCCGTCCCGTAGTGTAA 60.681 60.000 0.00 0.0 0.00 2.41
3886 3978 1.077501 CCCTCCGTCCCGTAGTGTA 60.078 63.158 0.00 0.0 0.00 2.90
3887 3979 2.362120 CCCTCCGTCCCGTAGTGT 60.362 66.667 0.00 0.0 0.00 3.55
3890 3982 0.534652 CTACTCCCTCCGTCCCGTAG 60.535 65.000 0.00 0.0 0.00 3.51
3891 3983 0.982852 TCTACTCCCTCCGTCCCGTA 60.983 60.000 0.00 0.0 0.00 4.02
3892 3984 1.856539 TTCTACTCCCTCCGTCCCGT 61.857 60.000 0.00 0.0 0.00 5.28
3917 4205 0.879090 GTTGCCCCTTGGTCGTAAAG 59.121 55.000 0.00 0.0 0.00 1.85
3925 4213 3.243401 GCTAAATAATCGTTGCCCCTTGG 60.243 47.826 0.00 0.0 0.00 3.61
3926 4214 3.380004 TGCTAAATAATCGTTGCCCCTTG 59.620 43.478 0.00 0.0 0.00 3.61
3937 4225 5.810587 TCCAGACGTCACTTGCTAAATAATC 59.189 40.000 19.50 0.0 0.00 1.75
3948 4236 1.480954 AGTGTTGTCCAGACGTCACTT 59.519 47.619 19.50 0.0 41.38 3.16
4014 4302 2.550180 GCCTTGTCTGAACCTGAAAGTC 59.450 50.000 0.00 0.0 0.00 3.01
4015 4303 2.576615 GCCTTGTCTGAACCTGAAAGT 58.423 47.619 0.00 0.0 0.00 2.66
4016 4304 1.532868 CGCCTTGTCTGAACCTGAAAG 59.467 52.381 0.00 0.0 0.00 2.62
4081 4370 0.172803 CCTCGTCTAAACCTGTCCGG 59.827 60.000 0.00 0.0 39.35 5.14
4083 4372 1.477295 CCTCCTCGTCTAAACCTGTCC 59.523 57.143 0.00 0.0 0.00 4.02
4189 4487 0.668535 GCACCACCCTCAACTTGAAC 59.331 55.000 0.00 0.0 0.00 3.18
4214 4512 1.528824 CCTGGGAGTGATGGCGAAT 59.471 57.895 0.00 0.0 0.00 3.34
4218 4516 4.512914 GCCCCTGGGAGTGATGGC 62.513 72.222 16.20 2.8 37.50 4.40
4232 4530 0.548510 AACAGAATGAGCCCTAGCCC 59.451 55.000 0.00 0.0 39.69 5.19
4233 4531 1.673168 CAACAGAATGAGCCCTAGCC 58.327 55.000 0.00 0.0 39.69 3.93
4234 4532 1.065126 ACCAACAGAATGAGCCCTAGC 60.065 52.381 0.00 0.0 39.69 3.42
4235 4533 2.636830 CACCAACAGAATGAGCCCTAG 58.363 52.381 0.00 0.0 39.69 3.02
4236 4534 1.281867 CCACCAACAGAATGAGCCCTA 59.718 52.381 0.00 0.0 39.69 3.53
4237 4535 0.038744 CCACCAACAGAATGAGCCCT 59.961 55.000 0.00 0.0 39.69 5.19
4238 4536 1.598701 GCCACCAACAGAATGAGCCC 61.599 60.000 0.00 0.0 39.69 5.19
4239 4537 0.610232 AGCCACCAACAGAATGAGCC 60.610 55.000 0.00 0.0 39.69 4.70
4240 4538 0.524862 CAGCCACCAACAGAATGAGC 59.475 55.000 0.00 0.0 39.69 4.26
4241 4539 1.171308 CCAGCCACCAACAGAATGAG 58.829 55.000 0.00 0.0 39.69 2.90
4242 4540 0.251297 CCCAGCCACCAACAGAATGA 60.251 55.000 0.00 0.0 39.69 2.57
4243 4541 1.880819 GCCCAGCCACCAACAGAATG 61.881 60.000 0.00 0.0 46.00 2.67
4244 4542 1.607467 GCCCAGCCACCAACAGAAT 60.607 57.895 0.00 0.0 0.00 2.40
4245 4543 2.203480 GCCCAGCCACCAACAGAA 60.203 61.111 0.00 0.0 0.00 3.02
4246 4544 4.641645 CGCCCAGCCACCAACAGA 62.642 66.667 0.00 0.0 0.00 3.41
4252 4550 4.937431 GATAGCCGCCCAGCCACC 62.937 72.222 0.00 0.0 0.00 4.61
4253 4551 4.175337 TGATAGCCGCCCAGCCAC 62.175 66.667 0.00 0.0 0.00 5.01
4254 4552 4.175337 GTGATAGCCGCCCAGCCA 62.175 66.667 0.00 0.0 0.00 4.75
4257 4555 4.609018 CCCGTGATAGCCGCCCAG 62.609 72.222 0.00 0.0 0.00 4.45
4334 4659 1.832167 GCAAGAGCCACCCACCAAA 60.832 57.895 0.00 0.0 33.58 3.28
4438 4763 0.182061 ATGATCGAGCTGTTGGCCAT 59.818 50.000 6.09 0.0 43.05 4.40
4450 4775 2.405618 ATCCAAGGAGGGATGATCGA 57.594 50.000 0.00 0.0 45.90 3.59
4512 4840 1.398390 GTTGCTTTCCTGGCAGTATCG 59.602 52.381 14.43 0.0 40.90 2.92


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

AutoCloner maintained by Alex Coulton.