Multiple sequence alignment - TraesCS1D01G197400

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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 TraesCS1D01G197400 chr1D 100.000 4221 0 0 1 4221 278511183 278515403 0.000000e+00 7795.0
1 TraesCS1D01G197400 chr1D 85.424 295 39 3 1719 2010 397213159 397212866 1.910000e-78 303.0
2 TraesCS1D01G197400 chr1B 93.896 2736 112 15 16 2699 378396066 378398798 0.000000e+00 4076.0
3 TraesCS1D01G197400 chr1B 92.438 1005 40 13 2743 3743 378398897 378399869 0.000000e+00 1402.0
4 TraesCS1D01G197400 chr1B 94.309 369 13 4 3738 4103 378399911 378400274 3.690000e-155 558.0
5 TraesCS1D01G197400 chr1B 83.392 283 32 10 1 273 432827627 432827350 9.060000e-62 248.0
6 TraesCS1D01G197400 chr1B 100.000 38 0 0 4184 4221 378400277 378400314 2.110000e-08 71.3
7 TraesCS1D01G197400 chr1A 92.565 1735 97 8 331 2036 350748775 350750506 0.000000e+00 2460.0
8 TraesCS1D01G197400 chr1A 94.036 1006 34 10 2743 3748 350751496 350752475 0.000000e+00 1502.0
9 TraesCS1D01G197400 chr1A 94.194 620 22 2 2080 2699 350750800 350751405 0.000000e+00 933.0
10 TraesCS1D01G197400 chr1A 95.405 370 13 4 3738 4103 350752500 350752869 1.690000e-163 586.0
11 TraesCS1D01G197400 chr1A 85.235 298 34 8 1719 2010 510700403 510700696 8.870000e-77 298.0
12 TraesCS1D01G197400 chr1A 86.022 279 29 8 4 273 403018305 403018582 1.480000e-74 291.0
13 TraesCS1D01G197400 chr1A 94.872 39 1 1 4184 4221 350752872 350752910 4.560000e-05 60.2
14 TraesCS1D01G197400 chr2B 86.622 299 34 5 1716 2010 494402008 494401712 4.070000e-85 326.0
15 TraesCS1D01G197400 chr7A 85.382 301 37 6 1715 2010 645255949 645255651 5.300000e-79 305.0
16 TraesCS1D01G197400 chr7A 82.143 112 18 2 358 468 360617657 360617547 1.250000e-15 95.3
17 TraesCS1D01G197400 chr3B 85.284 299 40 3 1716 2010 44638867 44639165 5.300000e-79 305.0
18 TraesCS1D01G197400 chr3D 84.950 299 41 3 1716 2010 469481226 469481524 2.470000e-77 300.0
19 TraesCS1D01G197400 chr3D 84.672 274 33 6 1 266 501747298 501747570 9.000000e-67 265.0
20 TraesCS1D01G197400 chr3D 82.374 278 35 8 4 273 439843054 439842783 3.280000e-56 230.0
21 TraesCS1D01G197400 chr6D 85.135 296 39 4 1719 2010 452576720 452576426 8.870000e-77 298.0
22 TraesCS1D01G197400 chr6D 100.000 86 0 0 4102 4187 79649841 79649926 4.370000e-35 159.0
23 TraesCS1D01G197400 chr5B 83.624 287 34 10 1 279 590584425 590584706 1.510000e-64 257.0
24 TraesCS1D01G197400 chr7D 83.871 279 34 5 4 273 614109038 614108762 5.420000e-64 255.0
25 TraesCS1D01G197400 chr7D 100.000 86 0 0 4102 4187 530797522 530797437 4.370000e-35 159.0
26 TraesCS1D01G197400 chr7D 81.905 105 15 3 358 460 311276542 311276440 7.520000e-13 86.1
27 TraesCS1D01G197400 chr5D 83.746 283 33 9 3 273 265522677 265522396 5.420000e-64 255.0
28 TraesCS1D01G197400 chr5D 100.000 86 0 0 4102 4187 6163847 6163762 4.370000e-35 159.0
29 TraesCS1D01G197400 chr5D 100.000 86 0 0 4102 4187 6261839 6261754 4.370000e-35 159.0
30 TraesCS1D01G197400 chr3A 82.734 278 39 6 4 273 736473866 736473590 5.450000e-59 239.0
31 TraesCS1D01G197400 chrUn 100.000 86 0 0 4102 4187 414537975 414537890 4.370000e-35 159.0
32 TraesCS1D01G197400 chr7B 100.000 86 0 0 4102 4187 137677930 137678015 4.370000e-35 159.0
33 TraesCS1D01G197400 chr4A 100.000 86 0 0 4102 4187 309455116 309455031 4.370000e-35 159.0
34 TraesCS1D01G197400 chr2D 100.000 86 0 0 4102 4187 135988594 135988679 4.370000e-35 159.0
35 TraesCS1D01G197400 chr2D 100.000 86 0 0 4102 4187 299147852 299147937 4.370000e-35 159.0


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 TraesCS1D01G197400 chr1D 278511183 278515403 4220 False 7795.000 7795 100.00000 1 4221 1 chr1D.!!$F1 4220
1 TraesCS1D01G197400 chr1B 378396066 378400314 4248 False 1526.825 4076 95.16075 16 4221 4 chr1B.!!$F1 4205
2 TraesCS1D01G197400 chr1A 350748775 350752910 4135 False 1108.240 2460 94.21440 331 4221 5 chr1A.!!$F3 3890

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
143 145 0.034767 CCTCAGAATTCCAGCTGCCA 60.035 55.0 8.66 0.00 32.27 4.92 F
389 392 0.038744 TCGACCCTCTAACCGGTTCT 59.961 55.0 26.16 2.77 30.56 3.01 F
1061 1088 0.187361 CTCCTACTCCTCTCCCCCAG 59.813 65.0 0.00 0.00 0.00 4.45 F
1579 1606 0.755686 CTGGATACTCCTGTGAGCCC 59.244 60.0 0.00 0.00 42.74 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2086 2.502633 TGCTTTGGCAGAGCAACAA 58.497 47.368 28.10 6.96 46.35 2.83 R
2357 2658 2.166459 CCATTGACGAGAAGCAGGTCTA 59.834 50.000 0.00 0.00 0.00 2.59 R
2559 2862 0.035739 TTTGACGAAGGGGGCTACAC 59.964 55.000 0.00 0.00 0.00 2.90 R
3529 3891 0.253894 CCATGTCATGGTGCTCAGGA 59.746 55.000 21.98 0.00 45.54 3.86 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
39 40 7.841956 TCTTCTCTGGTACTTATTTCTTCCAG 58.158 38.462 0.00 0.00 42.36 3.86
100 101 0.462759 GGTCATTTGGAGCTCCGGAG 60.463 60.000 27.83 27.83 40.87 4.63
141 143 0.394080 AGCCTCAGAATTCCAGCTGC 60.394 55.000 8.66 0.00 32.27 5.25
143 145 0.034767 CCTCAGAATTCCAGCTGCCA 60.035 55.000 8.66 0.00 32.27 4.92
185 187 7.254252 CGGTGTATCTTGCATTTTAAGAGAGAG 60.254 40.741 0.00 0.00 37.56 3.20
203 205 9.598517 AAGAGAGAGAAAGTATTAGAATTGCAG 57.401 33.333 0.00 0.00 0.00 4.41
326 329 2.746277 GTGCCACCCGTCATGGAC 60.746 66.667 0.00 0.00 42.00 4.02
329 332 2.747022 CCACCCGTCATGGACACA 59.253 61.111 0.00 0.00 42.00 3.72
376 379 3.072468 TCCACCCGTCATCGACCC 61.072 66.667 0.00 0.00 39.71 4.46
389 392 0.038744 TCGACCCTCTAACCGGTTCT 59.961 55.000 26.16 2.77 30.56 3.01
426 429 0.742990 TGGGCAAATCTTACGGCTCG 60.743 55.000 0.00 0.00 0.00 5.03
537 540 2.285824 TCCACTCATCATGGACGCA 58.714 52.632 0.00 0.00 41.47 5.24
590 593 2.885644 CCGTCATTCAGCCGTCCG 60.886 66.667 0.00 0.00 0.00 4.79
627 631 3.393970 CTCGCCCCAAGAGCCTCA 61.394 66.667 0.00 0.00 0.00 3.86
663 667 1.972660 GCAATGGACGGCTAGGAGGT 61.973 60.000 0.00 0.00 0.00 3.85
671 675 0.382515 CGGCTAGGAGGTTCTCTTCG 59.617 60.000 0.00 0.00 0.00 3.79
717 721 1.383799 CTCCACCATCCTTTGCCCA 59.616 57.895 0.00 0.00 0.00 5.36
719 723 1.077265 CCACCATCCTTTGCCCAGT 59.923 57.895 0.00 0.00 0.00 4.00
759 763 1.078708 CCAACGGGCAATAGACGGT 60.079 57.895 0.00 0.00 38.04 4.83
769 773 2.158943 GCAATAGACGGTTAGGAGGCTT 60.159 50.000 0.00 0.00 0.00 4.35
820 824 6.332504 CGGATATCACGCCATTCTTTATAC 57.667 41.667 4.83 0.00 0.00 1.47
827 831 4.876107 CACGCCATTCTTTATACAGGAGTT 59.124 41.667 0.00 0.00 0.00 3.01
834 861 8.979574 CCATTCTTTATACAGGAGTTCGTATTC 58.020 37.037 0.00 0.00 31.02 1.75
902 929 0.655733 CCTGCGGCGATTTCGTAAAT 59.344 50.000 12.98 0.00 42.22 1.40
1061 1088 0.187361 CTCCTACTCCTCTCCCCCAG 59.813 65.000 0.00 0.00 0.00 4.45
1434 1461 1.822186 GTGCTTGGTGGACACGGTT 60.822 57.895 0.00 0.00 36.96 4.44
1579 1606 0.755686 CTGGATACTCCTGTGAGCCC 59.244 60.000 0.00 0.00 42.74 5.19
1646 1686 2.222886 CGATCGTCAGTGGAATGCTTTG 60.223 50.000 7.03 0.00 0.00 2.77
1749 1791 8.787818 TCCTTTGGTTAATAGGATAGGAATGTT 58.212 33.333 0.00 0.00 33.23 2.71
2041 2086 8.936864 GTGTAAGCAGTCAACTTCTTATAATGT 58.063 33.333 5.72 0.00 35.00 2.71
2043 2088 9.760660 GTAAGCAGTCAACTTCTTATAATGTTG 57.239 33.333 14.64 14.64 35.00 3.33
2143 2444 5.811399 TGTACCTACTTAATTGTGCATGC 57.189 39.130 11.82 11.82 0.00 4.06
2148 2449 4.094887 CCTACTTAATTGTGCATGCTCGTT 59.905 41.667 20.33 15.66 0.00 3.85
2149 2450 3.825308 ACTTAATTGTGCATGCTCGTTG 58.175 40.909 20.33 6.41 0.00 4.10
2253 2554 5.165961 TCCCAAGAAATTGACTCGAGAAT 57.834 39.130 21.68 6.48 0.00 2.40
2378 2679 1.066573 AGACCTGCTTCTCGTCAATGG 60.067 52.381 0.00 0.00 0.00 3.16
2398 2699 7.928167 TCAATGGTATGCTAGTCTCAGTTTATG 59.072 37.037 0.00 0.00 0.00 1.90
2437 2738 2.415090 GCTTTCCAGACATGTCATGTGC 60.415 50.000 27.02 17.74 45.03 4.57
2567 2870 4.141711 TGAAATCCAGATAGTGTGTAGCCC 60.142 45.833 0.00 0.00 0.00 5.19
2663 2966 1.143073 GGAGAGACCCCTTTGTGTTGT 59.857 52.381 0.00 0.00 0.00 3.32
2672 2975 3.244422 CCCCTTTGTGTTGTGCTAGACTA 60.244 47.826 0.00 0.00 0.00 2.59
2754 3112 5.423290 TGTCATTCTCCTAGCAAATCTCTCA 59.577 40.000 0.00 0.00 0.00 3.27
2817 3175 9.300681 AGATTTCTTGGATGTTTCATCAGTTAA 57.699 29.630 11.08 1.78 0.00 2.01
2853 3211 3.250040 GCCCTTTACCATGTATGTAAGCG 59.750 47.826 0.00 0.00 0.00 4.68
3005 3363 2.069776 CAGAAGTTCAGCCTGGGGA 58.930 57.895 5.50 0.00 0.00 4.81
3100 3458 1.139058 CTCAAGGTACCGATTCCTGGG 59.861 57.143 6.18 0.00 33.97 4.45
3292 3650 0.249398 AGCTACAAGCCTACAACGGG 59.751 55.000 0.00 0.00 43.77 5.28
3415 3777 5.198965 TCTCCCTGGTAACTAGTGTACATC 58.801 45.833 0.00 0.00 37.61 3.06
3422 3784 8.308931 CCTGGTAACTAGTGTACATCTTTTGTA 58.691 37.037 0.00 0.00 37.33 2.41
3476 3838 5.050490 TCATAAGAGTATTTTCAGCTCCGC 58.950 41.667 0.00 0.00 0.00 5.54
3506 3868 6.091718 GGCAACTAAACCAAAATTACCTGA 57.908 37.500 0.00 0.00 0.00 3.86
3507 3869 6.156519 GGCAACTAAACCAAAATTACCTGAG 58.843 40.000 0.00 0.00 0.00 3.35
3508 3870 6.015772 GGCAACTAAACCAAAATTACCTGAGA 60.016 38.462 0.00 0.00 0.00 3.27
3509 3871 7.430441 GCAACTAAACCAAAATTACCTGAGAA 58.570 34.615 0.00 0.00 0.00 2.87
3510 3872 7.381408 GCAACTAAACCAAAATTACCTGAGAAC 59.619 37.037 0.00 0.00 0.00 3.01
3511 3873 7.520451 ACTAAACCAAAATTACCTGAGAACC 57.480 36.000 0.00 0.00 0.00 3.62
3512 3874 5.447624 AAACCAAAATTACCTGAGAACCG 57.552 39.130 0.00 0.00 0.00 4.44
3513 3875 4.094830 ACCAAAATTACCTGAGAACCGT 57.905 40.909 0.00 0.00 0.00 4.83
3514 3876 3.818773 ACCAAAATTACCTGAGAACCGTG 59.181 43.478 0.00 0.00 0.00 4.94
3515 3877 4.069304 CCAAAATTACCTGAGAACCGTGA 58.931 43.478 0.00 0.00 0.00 4.35
3516 3878 4.083484 CCAAAATTACCTGAGAACCGTGAC 60.083 45.833 0.00 0.00 0.00 3.67
3517 3879 4.345859 AAATTACCTGAGAACCGTGACA 57.654 40.909 0.00 0.00 0.00 3.58
3518 3880 4.553330 AATTACCTGAGAACCGTGACAT 57.447 40.909 0.00 0.00 0.00 3.06
3519 3881 3.313012 TTACCTGAGAACCGTGACATG 57.687 47.619 0.00 0.00 0.00 3.21
3520 3882 0.321671 ACCTGAGAACCGTGACATGG 59.678 55.000 12.41 12.41 0.00 3.66
3521 3883 0.608130 CCTGAGAACCGTGACATGGA 59.392 55.000 20.86 0.00 0.00 3.41
3522 3884 1.001974 CCTGAGAACCGTGACATGGAA 59.998 52.381 20.86 0.00 0.00 3.53
3523 3885 2.341257 CTGAGAACCGTGACATGGAAG 58.659 52.381 20.86 5.85 0.00 3.46
3524 3886 1.079503 GAGAACCGTGACATGGAAGC 58.920 55.000 20.86 8.61 0.00 3.86
3525 3887 0.396435 AGAACCGTGACATGGAAGCA 59.604 50.000 20.86 0.00 0.00 3.91
3526 3888 1.202758 AGAACCGTGACATGGAAGCAA 60.203 47.619 20.86 0.00 0.00 3.91
3527 3889 1.606668 GAACCGTGACATGGAAGCAAA 59.393 47.619 20.86 0.00 0.00 3.68
3528 3890 1.686355 ACCGTGACATGGAAGCAAAA 58.314 45.000 20.86 0.00 0.00 2.44
3529 3891 2.238521 ACCGTGACATGGAAGCAAAAT 58.761 42.857 20.86 0.00 0.00 1.82
3743 4108 6.866010 TTTGCATCGCTAGATACATTTCAT 57.134 33.333 0.00 0.00 34.85 2.57
3771 4185 3.565307 TGCAAGGGAATCAAACTCAAGT 58.435 40.909 0.00 0.00 0.00 3.16
3788 4202 5.034852 TCAAGTGATCAACTGTTCCTTCA 57.965 39.130 0.00 0.00 39.81 3.02
3931 4345 4.035324 CAGAACTGAGAATATGGCAGCAAG 59.965 45.833 0.00 0.00 33.03 4.01
4022 4437 8.650143 AAAAATAAGAAGCCTGTAATCTCCAA 57.350 30.769 0.00 0.00 0.00 3.53
4065 4480 5.303971 ACATAATTACAGAGCAGAGGCATC 58.696 41.667 0.00 0.00 44.61 3.91
4113 4529 3.759828 CGTCGCCGTCGGAACAAC 61.760 66.667 17.49 5.61 36.13 3.32
4114 4530 2.659244 GTCGCCGTCGGAACAACA 60.659 61.111 17.49 0.00 36.13 3.33
4115 4531 2.106534 TCGCCGTCGGAACAACAA 59.893 55.556 17.49 0.00 36.13 2.83
4116 4532 1.301087 TCGCCGTCGGAACAACAAT 60.301 52.632 17.49 0.00 36.13 2.71
4117 4533 1.131826 CGCCGTCGGAACAACAATC 59.868 57.895 17.49 0.00 0.00 2.67
4118 4534 1.289109 CGCCGTCGGAACAACAATCT 61.289 55.000 17.49 0.00 0.00 2.40
4119 4535 0.872388 GCCGTCGGAACAACAATCTT 59.128 50.000 17.49 0.00 0.00 2.40
4120 4536 1.399727 GCCGTCGGAACAACAATCTTG 60.400 52.381 17.49 0.00 0.00 3.02
4121 4537 1.399727 CCGTCGGAACAACAATCTTGC 60.400 52.381 4.91 0.00 0.00 4.01
4122 4538 1.399727 CGTCGGAACAACAATCTTGCC 60.400 52.381 0.00 0.00 0.00 4.52
4123 4539 1.880027 GTCGGAACAACAATCTTGCCT 59.120 47.619 0.00 0.00 0.00 4.75
4124 4540 3.071479 GTCGGAACAACAATCTTGCCTA 58.929 45.455 0.00 0.00 0.00 3.93
4125 4541 3.689649 GTCGGAACAACAATCTTGCCTAT 59.310 43.478 0.00 0.00 0.00 2.57
4126 4542 3.938963 TCGGAACAACAATCTTGCCTATC 59.061 43.478 0.00 0.00 0.00 2.08
4127 4543 3.941483 CGGAACAACAATCTTGCCTATCT 59.059 43.478 0.00 0.00 0.00 1.98
4128 4544 5.105106 TCGGAACAACAATCTTGCCTATCTA 60.105 40.000 0.00 0.00 0.00 1.98
4129 4545 5.760253 CGGAACAACAATCTTGCCTATCTAT 59.240 40.000 0.00 0.00 0.00 1.98
4130 4546 6.260936 CGGAACAACAATCTTGCCTATCTATT 59.739 38.462 0.00 0.00 0.00 1.73
4131 4547 7.441157 CGGAACAACAATCTTGCCTATCTATTA 59.559 37.037 0.00 0.00 0.00 0.98
4132 4548 9.120538 GGAACAACAATCTTGCCTATCTATTAA 57.879 33.333 0.00 0.00 0.00 1.40
4150 4566 9.937175 ATCTATTAAAAAGAAGTGAATTAGCGC 57.063 29.630 0.00 0.00 0.00 5.92
4151 4567 8.395633 TCTATTAAAAAGAAGTGAATTAGCGCC 58.604 33.333 2.29 0.00 0.00 6.53
4152 4568 4.846779 AAAAAGAAGTGAATTAGCGCCA 57.153 36.364 2.29 0.00 0.00 5.69
4153 4569 4.425577 AAAAGAAGTGAATTAGCGCCAG 57.574 40.909 2.29 0.00 0.00 4.85
4154 4570 1.373570 AGAAGTGAATTAGCGCCAGC 58.626 50.000 2.29 0.00 45.58 4.85
4167 4583 3.259207 GCGCCAGCAGATTTAGTAATG 57.741 47.619 0.00 0.00 44.35 1.90
4168 4584 2.614057 GCGCCAGCAGATTTAGTAATGT 59.386 45.455 0.00 0.00 44.35 2.71
4169 4585 3.546815 GCGCCAGCAGATTTAGTAATGTG 60.547 47.826 0.00 0.00 44.35 3.21
4177 4593 6.757897 CAGATTTAGTAATGTGCCAGGAAA 57.242 37.500 0.00 0.00 29.58 3.13
4178 4594 7.156876 CAGATTTAGTAATGTGCCAGGAAAA 57.843 36.000 0.00 0.00 29.58 2.29
4179 4595 7.601856 CAGATTTAGTAATGTGCCAGGAAAAA 58.398 34.615 0.00 0.00 29.58 1.94
4180 4596 8.253113 CAGATTTAGTAATGTGCCAGGAAAAAT 58.747 33.333 0.00 0.00 29.58 1.82
4181 4597 8.815912 AGATTTAGTAATGTGCCAGGAAAAATT 58.184 29.630 0.00 0.00 0.00 1.82
4182 4598 8.776376 ATTTAGTAATGTGCCAGGAAAAATTG 57.224 30.769 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.684049 AGAGAAGAGCCTCGGTGGG 60.684 63.158 0.00 0.00 38.19 4.61
4 5 1.515020 CAGAGAAGAGCCTCGGTGG 59.485 63.158 0.00 0.00 38.19 4.61
5 6 1.254284 ACCAGAGAAGAGCCTCGGTG 61.254 60.000 0.00 0.00 38.06 4.94
6 7 0.331954 TACCAGAGAAGAGCCTCGGT 59.668 55.000 0.00 0.00 40.46 4.69
7 8 0.741915 GTACCAGAGAAGAGCCTCGG 59.258 60.000 0.00 0.00 38.19 4.63
8 9 1.757682 AGTACCAGAGAAGAGCCTCG 58.242 55.000 0.00 0.00 38.19 4.63
9 10 5.862678 AATAAGTACCAGAGAAGAGCCTC 57.137 43.478 0.00 0.00 0.00 4.70
10 11 5.961421 AGAAATAAGTACCAGAGAAGAGCCT 59.039 40.000 0.00 0.00 0.00 4.58
11 12 6.228616 AGAAATAAGTACCAGAGAAGAGCC 57.771 41.667 0.00 0.00 0.00 4.70
12 13 6.759356 GGAAGAAATAAGTACCAGAGAAGAGC 59.241 42.308 0.00 0.00 0.00 4.09
13 14 7.841956 TGGAAGAAATAAGTACCAGAGAAGAG 58.158 38.462 0.00 0.00 0.00 2.85
14 15 7.455008 ACTGGAAGAAATAAGTACCAGAGAAGA 59.545 37.037 16.21 0.00 45.02 2.87
82 83 0.537188 TCTCCGGAGCTCCAAATGAC 59.463 55.000 31.67 3.61 35.14 3.06
124 126 0.034767 TGGCAGCTGGAATTCTGAGG 60.035 55.000 17.12 0.00 32.26 3.86
128 130 0.251474 TTGCTGGCAGCTGGAATTCT 60.251 50.000 36.50 0.00 42.97 2.40
141 143 1.089920 CGAAAGAGGGACATTGCTGG 58.910 55.000 0.00 0.00 0.00 4.85
143 145 0.693049 ACCGAAAGAGGGACATTGCT 59.307 50.000 0.00 0.00 35.02 3.91
189 191 9.787532 TTTCACTTTATGCTGCAATTCTAATAC 57.212 29.630 6.36 0.00 0.00 1.89
238 240 9.729023 CCATTTTGATCGTGTTTGCTATTATTA 57.271 29.630 0.00 0.00 0.00 0.98
247 249 7.218773 GTGATACATCCATTTTGATCGTGTTTG 59.781 37.037 0.00 0.00 0.00 2.93
262 265 2.837498 CAGCGGATTGTGATACATCCA 58.163 47.619 0.00 0.00 30.93 3.41
263 266 1.532868 GCAGCGGATTGTGATACATCC 59.467 52.381 0.00 0.00 0.00 3.51
326 329 3.172575 CGCTACAGTCGGCGTGTG 61.173 66.667 12.72 10.90 45.34 3.82
389 392 4.508128 GACGGCTCATTCGCGGGA 62.508 66.667 6.13 0.00 34.89 5.14
413 416 1.065928 CGAGGCGAGCCGTAAGATT 59.934 57.895 8.63 0.00 41.95 2.40
537 540 0.169672 CGAATCGGTACAGTCGGTGT 59.830 55.000 0.00 0.00 43.86 4.16
581 584 2.511600 GATCAACCCGGACGGCTG 60.512 66.667 0.73 5.06 33.26 4.85
590 593 2.202892 GAGCCGTCCGATCAACCC 60.203 66.667 0.00 0.00 0.00 4.11
717 721 4.347865 GAGAAGGCTCTCGGGACT 57.652 61.111 0.00 0.00 38.91 3.85
752 756 3.097342 AGAAAGCCTCCTAACCGTCTA 57.903 47.619 0.00 0.00 0.00 2.59
797 801 5.867174 TGTATAAAGAATGGCGTGATATCCG 59.133 40.000 0.00 4.84 0.00 4.18
803 807 4.161565 ACTCCTGTATAAAGAATGGCGTGA 59.838 41.667 0.00 0.00 0.00 4.35
820 824 2.101582 CTCCCTGGAATACGAACTCCTG 59.898 54.545 0.00 0.00 32.51 3.86
862 889 4.219944 AGGAAAACCCTTAAAAATCGAGCC 59.780 41.667 0.00 0.00 44.85 4.70
890 917 7.216317 AGCGATTTTCTTTCATTTACGAAATCG 59.784 33.333 18.45 18.45 46.33 3.34
902 929 2.030007 CCCAAGCAGCGATTTTCTTTCA 60.030 45.455 0.00 0.00 0.00 2.69
1146 1173 4.704103 TCGAGTGGGCTGCCTCCT 62.704 66.667 19.68 14.16 0.00 3.69
1579 1606 2.847327 TTGAGAGCAAGAAGTGGGAG 57.153 50.000 0.00 0.00 0.00 4.30
1646 1686 8.437742 CAATCATTCAGTGGCTAAAATTCAAAC 58.562 33.333 0.00 0.00 0.00 2.93
1922 1966 4.466015 TCCTTTGGAGCTCTTTGTTTTGTT 59.534 37.500 14.64 0.00 0.00 2.83
1928 1972 5.876651 AAAATTCCTTTGGAGCTCTTTGT 57.123 34.783 14.64 0.00 31.21 2.83
1975 2020 6.615726 TGGCTTATAGGACTTCTGTAGGAATT 59.384 38.462 0.00 0.00 33.01 2.17
1985 2030 4.709250 CCTCCTTTGGCTTATAGGACTTC 58.291 47.826 0.00 0.00 34.47 3.01
2041 2086 2.502633 TGCTTTGGCAGAGCAACAA 58.497 47.368 28.10 6.96 46.35 2.83
2143 2444 4.563184 GCTGTATACCTGAAAGTCAACGAG 59.437 45.833 0.00 0.00 0.00 4.18
2148 2449 7.928167 CAGAATATGCTGTATACCTGAAAGTCA 59.072 37.037 2.05 0.00 31.80 3.41
2149 2450 8.144478 TCAGAATATGCTGTATACCTGAAAGTC 58.856 37.037 10.66 0.00 34.27 3.01
2253 2554 8.437360 AGTTGAAGCATTAATTATCGTCATGA 57.563 30.769 0.00 0.00 0.00 3.07
2357 2658 2.166459 CCATTGACGAGAAGCAGGTCTA 59.834 50.000 0.00 0.00 0.00 2.59
2378 2679 5.176590 GCAGCATAAACTGAGACTAGCATAC 59.823 44.000 0.00 0.00 40.25 2.39
2398 2699 3.515330 AGCTGAAATAACCAATGCAGC 57.485 42.857 0.00 0.00 42.68 5.25
2559 2862 0.035739 TTTGACGAAGGGGGCTACAC 59.964 55.000 0.00 0.00 0.00 2.90
2567 2870 1.401018 GCGAAATGGTTTGACGAAGGG 60.401 52.381 0.00 0.00 0.00 3.95
2623 2926 7.342799 TCTCTCCCTAATTTGCTAATTTGCATT 59.657 33.333 15.23 10.12 42.96 3.56
2754 3112 6.606796 TGATGTGCACCTCAAATATTTGGTAT 59.393 34.615 24.40 8.76 38.66 2.73
2817 3175 5.836358 TGGTAAAGGGCAACTTGTATTCTTT 59.164 36.000 0.00 0.00 39.96 2.52
2853 3211 6.711277 TGGCATATCTATGTTATCAAGGACC 58.289 40.000 0.00 0.00 36.11 4.46
3005 3363 1.277557 CTCCAGCAGCTCCTTAACAGT 59.722 52.381 0.00 0.00 0.00 3.55
3100 3458 0.818040 ACGACTTGGCCTTGTTGTCC 60.818 55.000 3.32 0.00 0.00 4.02
3292 3650 3.356529 TCAAAGAGGGAGAAGAATGCC 57.643 47.619 0.00 0.00 0.00 4.40
3392 3750 4.662966 TGTACACTAGTTACCAGGGAGA 57.337 45.455 0.00 0.00 0.00 3.71
3397 3755 9.871238 ATACAAAAGATGTACACTAGTTACCAG 57.129 33.333 0.00 0.00 46.90 4.00
3476 3838 1.896220 TGGTTTAGTTGCCTGAGCTG 58.104 50.000 0.00 0.00 40.80 4.24
3502 3864 0.608130 TCCATGTCACGGTTCTCAGG 59.392 55.000 0.00 0.00 0.00 3.86
3503 3865 2.341257 CTTCCATGTCACGGTTCTCAG 58.659 52.381 0.00 0.00 0.00 3.35
3504 3866 1.608025 GCTTCCATGTCACGGTTCTCA 60.608 52.381 0.00 0.00 0.00 3.27
3505 3867 1.079503 GCTTCCATGTCACGGTTCTC 58.920 55.000 0.00 0.00 0.00 2.87
3506 3868 0.396435 TGCTTCCATGTCACGGTTCT 59.604 50.000 0.00 0.00 0.00 3.01
3507 3869 1.234821 TTGCTTCCATGTCACGGTTC 58.765 50.000 0.00 0.00 0.00 3.62
3508 3870 1.686355 TTTGCTTCCATGTCACGGTT 58.314 45.000 0.00 0.00 0.00 4.44
3509 3871 1.686355 TTTTGCTTCCATGTCACGGT 58.314 45.000 0.00 0.00 0.00 4.83
3510 3872 2.415893 GGATTTTGCTTCCATGTCACGG 60.416 50.000 0.00 0.00 33.21 4.94
3511 3873 2.489329 AGGATTTTGCTTCCATGTCACG 59.511 45.455 0.00 0.00 35.59 4.35
3512 3874 3.507233 TCAGGATTTTGCTTCCATGTCAC 59.493 43.478 0.00 0.00 35.59 3.67
3513 3875 3.760151 CTCAGGATTTTGCTTCCATGTCA 59.240 43.478 0.00 0.00 35.59 3.58
3514 3876 3.428589 GCTCAGGATTTTGCTTCCATGTC 60.429 47.826 0.00 0.00 35.59 3.06
3515 3877 2.494870 GCTCAGGATTTTGCTTCCATGT 59.505 45.455 0.00 0.00 35.59 3.21
3516 3878 2.494471 TGCTCAGGATTTTGCTTCCATG 59.506 45.455 0.00 0.00 35.59 3.66
3517 3879 2.494870 GTGCTCAGGATTTTGCTTCCAT 59.505 45.455 0.00 0.00 35.59 3.41
3518 3880 1.888512 GTGCTCAGGATTTTGCTTCCA 59.111 47.619 0.00 0.00 35.59 3.53
3519 3881 1.203287 GGTGCTCAGGATTTTGCTTCC 59.797 52.381 0.00 0.00 0.00 3.46
3520 3882 1.888512 TGGTGCTCAGGATTTTGCTTC 59.111 47.619 0.00 0.00 0.00 3.86
3521 3883 1.999648 TGGTGCTCAGGATTTTGCTT 58.000 45.000 0.00 0.00 0.00 3.91
3522 3884 1.822990 CATGGTGCTCAGGATTTTGCT 59.177 47.619 0.00 0.00 0.00 3.91
3523 3885 1.820519 TCATGGTGCTCAGGATTTTGC 59.179 47.619 0.00 0.00 30.49 3.68
3524 3886 2.821378 TGTCATGGTGCTCAGGATTTTG 59.179 45.455 0.00 0.00 38.51 2.44
3525 3887 3.159213 TGTCATGGTGCTCAGGATTTT 57.841 42.857 0.00 0.00 38.51 1.82
3526 3888 2.885135 TGTCATGGTGCTCAGGATTT 57.115 45.000 0.00 0.00 38.51 2.17
3527 3889 2.651455 CATGTCATGGTGCTCAGGATT 58.349 47.619 4.78 0.00 38.51 3.01
3528 3890 1.133884 CCATGTCATGGTGCTCAGGAT 60.134 52.381 21.98 0.00 45.54 3.24
3529 3891 0.253894 CCATGTCATGGTGCTCAGGA 59.746 55.000 21.98 0.00 45.54 3.86
3743 4108 6.041409 TGAGTTTGATTCCCTTGCATTTTGTA 59.959 34.615 0.00 0.00 0.00 2.41
3788 4202 2.826725 ACCTTAAGCAAGCTCTCGTACT 59.173 45.455 0.00 0.00 0.00 2.73
3931 4345 2.977405 ATTTGCTGAGAAGCGTTGTC 57.023 45.000 0.00 0.00 37.69 3.18
4002 4416 6.374417 AAGTTGGAGATTACAGGCTTCTTA 57.626 37.500 0.00 0.00 0.00 2.10
4103 4519 1.880027 AGGCAAGATTGTTGTTCCGAC 59.120 47.619 0.00 0.00 0.00 4.79
4105 4521 3.941483 AGATAGGCAAGATTGTTGTTCCG 59.059 43.478 0.00 0.00 0.00 4.30
4106 4522 7.573968 AATAGATAGGCAAGATTGTTGTTCC 57.426 36.000 0.00 0.00 0.00 3.62
4124 4540 9.937175 GCGCTAATTCACTTCTTTTTAATAGAT 57.063 29.630 0.00 0.00 0.00 1.98
4125 4541 8.395633 GGCGCTAATTCACTTCTTTTTAATAGA 58.604 33.333 7.64 0.00 0.00 1.98
4126 4542 8.181573 TGGCGCTAATTCACTTCTTTTTAATAG 58.818 33.333 7.64 0.00 0.00 1.73
4127 4543 8.046294 TGGCGCTAATTCACTTCTTTTTAATA 57.954 30.769 7.64 0.00 0.00 0.98
4128 4544 6.919721 TGGCGCTAATTCACTTCTTTTTAAT 58.080 32.000 7.64 0.00 0.00 1.40
4129 4545 6.320494 TGGCGCTAATTCACTTCTTTTTAA 57.680 33.333 7.64 0.00 0.00 1.52
4130 4546 5.619086 GCTGGCGCTAATTCACTTCTTTTTA 60.619 40.000 7.64 0.00 0.00 1.52
4131 4547 4.798574 CTGGCGCTAATTCACTTCTTTTT 58.201 39.130 7.64 0.00 0.00 1.94
4132 4548 3.366374 GCTGGCGCTAATTCACTTCTTTT 60.366 43.478 7.64 0.00 0.00 2.27
4133 4549 2.162408 GCTGGCGCTAATTCACTTCTTT 59.838 45.455 7.64 0.00 0.00 2.52
4134 4550 1.740025 GCTGGCGCTAATTCACTTCTT 59.260 47.619 7.64 0.00 0.00 2.52
4135 4551 1.339055 TGCTGGCGCTAATTCACTTCT 60.339 47.619 7.64 0.00 36.97 2.85
4136 4552 1.063174 CTGCTGGCGCTAATTCACTTC 59.937 52.381 7.64 0.00 36.97 3.01
4137 4553 1.089920 CTGCTGGCGCTAATTCACTT 58.910 50.000 7.64 0.00 36.97 3.16
4138 4554 0.250234 TCTGCTGGCGCTAATTCACT 59.750 50.000 7.64 0.00 36.97 3.41
4139 4555 1.303309 ATCTGCTGGCGCTAATTCAC 58.697 50.000 7.64 0.00 36.97 3.18
4140 4556 2.042686 AATCTGCTGGCGCTAATTCA 57.957 45.000 7.64 0.00 36.97 2.57
4141 4557 3.561725 ACTAAATCTGCTGGCGCTAATTC 59.438 43.478 7.64 0.00 36.97 2.17
4142 4558 3.545703 ACTAAATCTGCTGGCGCTAATT 58.454 40.909 7.64 0.00 36.97 1.40
4143 4559 3.199880 ACTAAATCTGCTGGCGCTAAT 57.800 42.857 7.64 0.00 36.97 1.73
4144 4560 2.691409 ACTAAATCTGCTGGCGCTAA 57.309 45.000 7.64 0.00 36.97 3.09
4145 4561 3.812156 TTACTAAATCTGCTGGCGCTA 57.188 42.857 7.64 0.00 36.97 4.26
4146 4562 2.691409 TTACTAAATCTGCTGGCGCT 57.309 45.000 7.64 0.00 36.97 5.92
4147 4563 2.614057 ACATTACTAAATCTGCTGGCGC 59.386 45.455 0.00 0.00 0.00 6.53
4148 4564 3.546815 GCACATTACTAAATCTGCTGGCG 60.547 47.826 0.00 0.00 35.01 5.69
4149 4565 3.243201 GGCACATTACTAAATCTGCTGGC 60.243 47.826 0.00 0.00 37.23 4.85
4150 4566 3.947196 TGGCACATTACTAAATCTGCTGG 59.053 43.478 0.00 0.00 37.23 4.85
4151 4567 4.036027 CCTGGCACATTACTAAATCTGCTG 59.964 45.833 0.00 0.00 37.23 4.41
4152 4568 4.080356 TCCTGGCACATTACTAAATCTGCT 60.080 41.667 0.00 0.00 37.23 4.24
4153 4569 4.199310 TCCTGGCACATTACTAAATCTGC 58.801 43.478 0.00 0.00 38.20 4.26
4154 4570 6.757897 TTTCCTGGCACATTACTAAATCTG 57.242 37.500 0.00 0.00 38.20 2.90
4155 4571 7.775053 TTTTTCCTGGCACATTACTAAATCT 57.225 32.000 0.00 0.00 38.20 2.40
4156 4572 8.872845 CAATTTTTCCTGGCACATTACTAAATC 58.127 33.333 0.00 0.00 38.20 2.17
4157 4573 7.823799 CCAATTTTTCCTGGCACATTACTAAAT 59.176 33.333 0.00 0.00 38.20 1.40
4158 4574 7.158021 CCAATTTTTCCTGGCACATTACTAAA 58.842 34.615 0.00 0.00 38.20 1.85
4159 4575 6.268847 ACCAATTTTTCCTGGCACATTACTAA 59.731 34.615 0.00 0.00 38.20 2.24
4160 4576 5.777732 ACCAATTTTTCCTGGCACATTACTA 59.222 36.000 0.00 0.00 38.20 1.82
4161 4577 4.592778 ACCAATTTTTCCTGGCACATTACT 59.407 37.500 0.00 0.00 38.20 2.24
4162 4578 4.893608 ACCAATTTTTCCTGGCACATTAC 58.106 39.130 0.00 0.00 38.20 1.89
4163 4579 5.777732 AGTACCAATTTTTCCTGGCACATTA 59.222 36.000 0.00 0.00 38.20 1.90
4164 4580 4.592778 AGTACCAATTTTTCCTGGCACATT 59.407 37.500 0.00 0.00 38.20 2.71
4165 4581 4.021192 CAGTACCAATTTTTCCTGGCACAT 60.021 41.667 0.00 0.00 38.20 3.21
4166 4582 3.320541 CAGTACCAATTTTTCCTGGCACA 59.679 43.478 0.00 0.00 0.00 4.57
4167 4583 3.320826 ACAGTACCAATTTTTCCTGGCAC 59.679 43.478 0.00 0.00 0.00 5.01
4168 4584 3.571590 ACAGTACCAATTTTTCCTGGCA 58.428 40.909 0.00 0.00 0.00 4.92
4169 4585 4.202212 ACAACAGTACCAATTTTTCCTGGC 60.202 41.667 0.00 0.00 0.00 4.85
4170 4586 5.529581 ACAACAGTACCAATTTTTCCTGG 57.470 39.130 0.00 0.00 0.00 4.45
4171 4587 7.598493 CCATAACAACAGTACCAATTTTTCCTG 59.402 37.037 0.00 0.00 0.00 3.86
4172 4588 7.289084 ACCATAACAACAGTACCAATTTTTCCT 59.711 33.333 0.00 0.00 0.00 3.36
4173 4589 7.438564 ACCATAACAACAGTACCAATTTTTCC 58.561 34.615 0.00 0.00 0.00 3.13
4174 4590 9.401873 GTACCATAACAACAGTACCAATTTTTC 57.598 33.333 0.00 0.00 31.02 2.29
4175 4591 8.915036 TGTACCATAACAACAGTACCAATTTTT 58.085 29.630 0.00 0.00 35.33 1.94
4176 4592 8.466617 TGTACCATAACAACAGTACCAATTTT 57.533 30.769 0.00 0.00 35.33 1.82
4177 4593 8.466617 TTGTACCATAACAACAGTACCAATTT 57.533 30.769 0.00 0.00 34.50 1.82


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

AutoCloner maintained by Alex Coulton.