Multiple sequence alignment - TraesCS3A01G277000

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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 TraesCS3A01G277000 chr3A 100.000 2595 0 0 1 2595 507121903 507119309 0.000000e+00 4793.0
1 TraesCS3A01G277000 chr3A 96.446 619 20 1 34 652 454209948 454209332 0.000000e+00 1020.0
2 TraesCS3A01G277000 chr3D 91.603 1560 54 36 652 2162 384568143 384566612 0.000000e+00 2084.0
3 TraesCS3A01G277000 chr3D 93.506 77 4 1 2520 2595 384566545 384566469 2.110000e-21 113.0
4 TraesCS3A01G277000 chr3B 88.889 1584 65 43 652 2161 499806479 499804933 0.000000e+00 1847.0
5 TraesCS3A01G277000 chr3B 87.500 384 33 10 2216 2595 499804867 499804495 1.850000e-116 429.0
6 TraesCS3A01G277000 chr6A 97.236 615 15 1 38 652 428064103 428064715 0.000000e+00 1040.0
7 TraesCS3A01G277000 chr6A 96.446 619 20 1 34 652 384583919 384584535 0.000000e+00 1020.0
8 TraesCS3A01G277000 chr7A 96.635 624 17 2 34 655 213819102 213819723 0.000000e+00 1033.0
9 TraesCS3A01G277000 chr7A 88.710 124 11 3 981 1102 65005993 65006115 5.790000e-32 148.0
10 TraesCS3A01G277000 chr7A 77.241 145 31 2 1209 1352 65006924 65007067 1.650000e-12 84.2
11 TraesCS3A01G277000 chr5A 96.618 621 19 1 34 654 439106194 439106812 0.000000e+00 1029.0
12 TraesCS3A01G277000 chr5A 96.607 619 19 1 34 652 162405751 162405135 0.000000e+00 1026.0
13 TraesCS3A01G277000 chr5A 96.141 622 22 1 33 654 439108535 439109154 0.000000e+00 1014.0
14 TraesCS3A01G277000 chr5A 96.290 620 19 2 34 653 463485924 463485309 0.000000e+00 1014.0
15 TraesCS3A01G277000 chr1A 96.457 621 18 2 34 652 372284426 372283808 0.000000e+00 1022.0
16 TraesCS3A01G277000 chr1A 96.032 126 5 0 994 1119 531986748 531986623 3.380000e-49 206.0
17 TraesCS3A01G277000 chr1A 89.928 139 14 0 1457 1595 531986238 531986100 2.050000e-41 180.0
18 TraesCS3A01G277000 chr1A 82.911 158 27 0 1207 1364 531986507 531986350 2.690000e-30 143.0
19 TraesCS3A01G277000 chr1B 97.541 122 3 0 998 1119 585680431 585680310 2.620000e-50 209.0
20 TraesCS3A01G277000 chr1B 83.544 158 26 0 1207 1364 585680201 585680044 5.790000e-32 148.0
21 TraesCS3A01G277000 chr1D 96.032 126 5 0 994 1119 433464228 433464103 3.380000e-49 206.0
22 TraesCS3A01G277000 chr1D 83.544 158 26 0 1207 1364 433463990 433463833 5.790000e-32 148.0
23 TraesCS3A01G277000 chr7D 88.189 127 12 3 981 1105 60700006 60700131 5.790000e-32 148.0
24 TraesCS3A01G277000 chr7D 77.241 145 31 2 1209 1352 60700886 60701029 1.650000e-12 84.2
25 TraesCS3A01G277000 chr7B 88.189 127 12 3 981 1105 3336847 3336972 5.790000e-32 148.0
26 TraesCS3A01G277000 chr7B 78.621 145 29 2 1209 1352 3337802 3337945 7.640000e-16 95.3


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 TraesCS3A01G277000 chr3A 507119309 507121903 2594 True 4793.0 4793 100.0000 1 2595 1 chr3A.!!$R2 2594
1 TraesCS3A01G277000 chr3A 454209332 454209948 616 True 1020.0 1020 96.4460 34 652 1 chr3A.!!$R1 618
2 TraesCS3A01G277000 chr3D 384566469 384568143 1674 True 1098.5 2084 92.5545 652 2595 2 chr3D.!!$R1 1943
3 TraesCS3A01G277000 chr3B 499804495 499806479 1984 True 1138.0 1847 88.1945 652 2595 2 chr3B.!!$R1 1943
4 TraesCS3A01G277000 chr6A 428064103 428064715 612 False 1040.0 1040 97.2360 38 652 1 chr6A.!!$F2 614
5 TraesCS3A01G277000 chr6A 384583919 384584535 616 False 1020.0 1020 96.4460 34 652 1 chr6A.!!$F1 618
6 TraesCS3A01G277000 chr7A 213819102 213819723 621 False 1033.0 1033 96.6350 34 655 1 chr7A.!!$F1 621
7 TraesCS3A01G277000 chr5A 162405135 162405751 616 True 1026.0 1026 96.6070 34 652 1 chr5A.!!$R1 618
8 TraesCS3A01G277000 chr5A 439106194 439109154 2960 False 1021.5 1029 96.3795 33 654 2 chr5A.!!$F1 621
9 TraesCS3A01G277000 chr5A 463485309 463485924 615 True 1014.0 1014 96.2900 34 653 1 chr5A.!!$R2 619
10 TraesCS3A01G277000 chr1A 372283808 372284426 618 True 1022.0 1022 96.4570 34 652 1 chr1A.!!$R1 618

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
685 692 0.525455 GAAATTGCGGCCGAATCCAC 60.525 55.0 33.48 10.79 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 3617 0.03659 GGGCCCACAACATTGCAATT 59.963 50.0 19.95 0.0 0.0 2.32 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
29 30 2.474816 GGGACGACTATCTGTTGATGC 58.525 52.381 0.00 0.00 34.32 3.91
30 31 2.101582 GGGACGACTATCTGTTGATGCT 59.898 50.000 0.00 0.00 34.32 3.79
31 32 3.318275 GGGACGACTATCTGTTGATGCTA 59.682 47.826 0.00 0.00 34.32 3.49
32 33 4.202121 GGGACGACTATCTGTTGATGCTAA 60.202 45.833 0.00 0.00 34.32 3.09
62 63 4.630940 TCGGTTTATTCGGTTTACATGGTC 59.369 41.667 0.00 0.00 0.00 4.02
64 65 4.701171 GGTTTATTCGGTTTACATGGTCCA 59.299 41.667 0.00 0.00 0.00 4.02
177 178 8.347035 CAAATTATTTCGGTATGGTTTCGGTAT 58.653 33.333 0.00 0.00 0.00 2.73
178 179 9.558396 AAATTATTTCGGTATGGTTTCGGTATA 57.442 29.630 0.00 0.00 0.00 1.47
219 220 4.082787 AGTTGACGCGAATTTGGAAATGAT 60.083 37.500 15.93 0.00 0.00 2.45
427 432 8.918658 CATTTGACTCATGTACAAGAAAAATGG 58.081 33.333 21.53 7.82 32.08 3.16
528 533 9.471702 TTTCCGGTATATACCATAAAAACCAAA 57.528 29.630 27.58 11.39 46.80 3.28
565 570 7.931578 TGAAAAGTTCATACCATACCGAAAT 57.068 32.000 0.00 0.00 34.08 2.17
625 632 7.040548 TCGGTTTATTTTCGGTATGGTTTTTCT 60.041 33.333 0.00 0.00 0.00 2.52
685 692 0.525455 GAAATTGCGGCCGAATCCAC 60.525 55.000 33.48 10.79 0.00 4.02
697 704 3.171828 AATCCACGGGTGTGTGCGA 62.172 57.895 0.00 0.00 44.92 5.10
698 705 3.876589 ATCCACGGGTGTGTGCGAC 62.877 63.158 0.00 0.00 44.92 5.19
727 734 2.858476 TGTGGGTGGGGCTCATGT 60.858 61.111 0.00 0.00 0.00 3.21
728 735 2.430704 CTGTGGGTGGGGCTCATGTT 62.431 60.000 0.00 0.00 0.00 2.71
729 736 1.978617 GTGGGTGGGGCTCATGTTG 60.979 63.158 0.00 0.00 0.00 3.33
743 757 4.465512 GTTGATGGCAGCGCACCG 62.466 66.667 11.47 0.00 0.00 4.94
774 788 1.801178 GAAGTTGAAGGGCGAACTCAG 59.199 52.381 0.00 0.00 31.02 3.35
781 795 0.692419 AGGGCGAACTCAGGATGGAT 60.692 55.000 0.00 0.00 36.16 3.41
822 913 2.424956 GCAGTTGGGATCCAGACATTTC 59.575 50.000 15.23 0.00 33.81 2.17
823 914 3.019564 CAGTTGGGATCCAGACATTTCC 58.980 50.000 15.23 0.00 33.81 3.13
1139 1350 4.876652 GGTACGTCGAACCCACTC 57.123 61.111 0.00 0.00 0.00 3.51
1175 1386 2.354656 CATGAGCCATGCATGCGC 60.355 61.111 21.69 23.24 37.00 6.09
1371 2111 2.400798 CATGCATGCACGTCGGAC 59.599 61.111 25.37 0.00 0.00 4.79
1606 2346 1.186339 GCATGTAGACGACGACGACG 61.186 60.000 17.60 17.60 42.66 5.12
1608 2348 0.368227 ATGTAGACGACGACGACGAC 59.632 55.000 25.15 18.88 42.66 4.34
1762 2533 4.470304 ACTACTTACCACCCCTCTTGATTC 59.530 45.833 0.00 0.00 0.00 2.52
1777 2548 6.228273 TCTTGATTCATCCGCGATATTTTC 57.772 37.500 8.23 0.00 0.00 2.29
1778 2549 5.179368 TCTTGATTCATCCGCGATATTTTCC 59.821 40.000 8.23 0.00 0.00 3.13
1832 2605 9.670180 CGTTTCGGCTAATAATTTTGATTTTTC 57.330 29.630 0.00 0.00 0.00 2.29
1869 2643 0.761802 TTTGGTCATTTGGGTTGCCC 59.238 50.000 0.00 0.00 45.71 5.36
2003 2790 6.283694 TGTCTGCTTCAACTCCATATACATC 58.716 40.000 0.00 0.00 0.00 3.06
2122 3438 4.039703 CCACTCAAATTTGATGCGCATAG 58.960 43.478 25.40 16.57 36.46 2.23
2133 3449 5.912360 TGATGCGCATAGACTCTTTATTG 57.088 39.130 25.40 0.00 0.00 1.90
2137 3455 3.733337 CGCATAGACTCTTTATTGGGCT 58.267 45.455 0.00 0.00 0.00 5.19
2138 3456 4.130118 CGCATAGACTCTTTATTGGGCTT 58.870 43.478 0.00 0.00 0.00 4.35
2139 3457 5.297547 CGCATAGACTCTTTATTGGGCTTA 58.702 41.667 0.00 0.00 0.00 3.09
2186 3504 1.379527 GGGGACGAGCCACATAAAAG 58.620 55.000 0.00 0.00 41.00 2.27
2187 3505 1.065709 GGGGACGAGCCACATAAAAGA 60.066 52.381 0.00 0.00 41.00 2.52
2188 3506 2.421529 GGGGACGAGCCACATAAAAGAT 60.422 50.000 0.00 0.00 41.00 2.40
2189 3507 3.279434 GGGACGAGCCACATAAAAGATT 58.721 45.455 0.00 0.00 38.95 2.40
2190 3508 3.312697 GGGACGAGCCACATAAAAGATTC 59.687 47.826 0.00 0.00 38.95 2.52
2191 3509 3.001330 GGACGAGCCACATAAAAGATTCG 59.999 47.826 0.00 0.00 36.34 3.34
2192 3510 3.596214 ACGAGCCACATAAAAGATTCGT 58.404 40.909 0.00 0.00 35.48 3.85
2194 3512 4.092968 ACGAGCCACATAAAAGATTCGTTC 59.907 41.667 0.00 0.00 36.76 3.95
2197 3515 4.876107 AGCCACATAAAAGATTCGTTCGAT 59.124 37.500 0.00 0.00 0.00 3.59
2198 3516 5.006746 AGCCACATAAAAGATTCGTTCGATC 59.993 40.000 0.00 0.00 0.00 3.69
2199 3517 5.220586 GCCACATAAAAGATTCGTTCGATCA 60.221 40.000 0.00 0.00 0.00 2.92
2200 3518 6.674519 GCCACATAAAAGATTCGTTCGATCAA 60.675 38.462 0.00 0.00 0.00 2.57
2203 3521 7.744276 CACATAAAAGATTCGTTCGATCAAACA 59.256 33.333 0.00 0.00 0.00 2.83
2204 3522 8.286800 ACATAAAAGATTCGTTCGATCAAACAA 58.713 29.630 0.00 0.00 0.00 2.83
2206 3524 9.840427 ATAAAAGATTCGTTCGATCAAACAATT 57.160 25.926 0.00 0.00 0.00 2.32
2207 3525 8.574196 AAAAGATTCGTTCGATCAAACAATTT 57.426 26.923 0.00 0.00 0.00 1.82
2210 3528 8.029642 AGATTCGTTCGATCAAACAATTTAGT 57.970 30.769 0.00 0.00 0.00 2.24
2212 3530 6.160664 TCGTTCGATCAAACAATTTAGTCC 57.839 37.500 0.00 0.00 0.00 3.85
2213 3531 5.697178 TCGTTCGATCAAACAATTTAGTCCA 59.303 36.000 0.00 0.00 0.00 4.02
2214 3532 5.788531 CGTTCGATCAAACAATTTAGTCCAC 59.211 40.000 0.00 0.00 0.00 4.02
2218 3547 5.512788 CGATCAAACAATTTAGTCCACATGC 59.487 40.000 0.00 0.00 0.00 4.06
2222 3551 2.493278 ACAATTTAGTCCACATGCTGCC 59.507 45.455 0.00 0.00 0.00 4.85
2251 3580 2.197324 AGCGGACCAGCCCAAAAA 59.803 55.556 4.93 0.00 38.01 1.94
2263 3592 1.939381 GCCCAAAAACGCAATTCCCTC 60.939 52.381 0.00 0.00 0.00 4.30
2273 3602 3.194861 CGCAATTCCCTCGAAGAATGTA 58.805 45.455 10.27 0.00 34.23 2.29
2276 3605 5.391523 CGCAATTCCCTCGAAGAATGTAAAA 60.392 40.000 10.27 0.00 34.23 1.52
2311 3642 1.946081 CAATGTTGTGGGCCCAAAAAC 59.054 47.619 31.57 31.57 0.00 2.43
2318 3649 2.583441 GGGCCCAAAAACTGCTCCC 61.583 63.158 19.95 0.00 0.00 4.30
2324 3655 0.890996 CAAAAACTGCTCCCGCCTCT 60.891 55.000 0.00 0.00 34.43 3.69
2325 3656 0.606673 AAAAACTGCTCCCGCCTCTC 60.607 55.000 0.00 0.00 34.43 3.20
2338 3669 2.280628 CGCCTCTCCCAACAAATAGAC 58.719 52.381 0.00 0.00 0.00 2.59
2347 3678 6.831353 TCTCCCAACAAATAGACAAAAAGACA 59.169 34.615 0.00 0.00 0.00 3.41
2364 3695 9.683069 CAAAAAGACATAAAAATGCACTAGACT 57.317 29.630 0.00 0.00 0.00 3.24
2365 3696 9.683069 AAAAAGACATAAAAATGCACTAGACTG 57.317 29.630 0.00 0.00 0.00 3.51
2366 3697 8.621532 AAAGACATAAAAATGCACTAGACTGA 57.378 30.769 0.00 0.00 0.00 3.41
2398 3729 6.663734 ACTCCCCAAAAATAATCTAGGACAG 58.336 40.000 0.00 0.00 0.00 3.51
2502 3834 9.533253 AAAGATTTCTACAAAGTTTGACATTGG 57.467 29.630 22.23 1.98 31.69 3.16
2503 3835 8.237811 AGATTTCTACAAAGTTTGACATTGGT 57.762 30.769 22.23 0.33 31.69 3.67
2584 3917 8.588290 TGCCATCTTTAATACACCAATTTACT 57.412 30.769 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.985486 GATAGTCGTCCCGAGCGCAC 62.985 65.000 11.47 0.96 36.23 5.34
2 3 2.827190 ATAGTCGTCCCGAGCGCA 60.827 61.111 11.47 0.00 36.23 6.09
3 4 2.051166 GATAGTCGTCCCGAGCGC 60.051 66.667 0.00 0.00 36.23 5.92
4 5 1.280142 CAGATAGTCGTCCCGAGCG 59.720 63.158 0.00 0.00 36.23 5.03
5 6 0.739561 AACAGATAGTCGTCCCGAGC 59.260 55.000 0.00 0.00 36.23 5.03
6 7 2.014857 TCAACAGATAGTCGTCCCGAG 58.985 52.381 0.00 0.00 36.23 4.63
7 8 2.118313 TCAACAGATAGTCGTCCCGA 57.882 50.000 0.00 0.00 0.00 5.14
8 9 2.732366 CATCAACAGATAGTCGTCCCG 58.268 52.381 0.00 0.00 0.00 5.14
9 10 2.101582 AGCATCAACAGATAGTCGTCCC 59.898 50.000 0.00 0.00 0.00 4.46
10 11 3.444703 AGCATCAACAGATAGTCGTCC 57.555 47.619 0.00 0.00 0.00 4.79
11 12 5.457148 CACTTAGCATCAACAGATAGTCGTC 59.543 44.000 0.00 0.00 0.00 4.20
12 13 5.344066 CACTTAGCATCAACAGATAGTCGT 58.656 41.667 0.00 0.00 0.00 4.34
13 14 4.208047 GCACTTAGCATCAACAGATAGTCG 59.792 45.833 0.00 0.00 44.79 4.18
14 15 4.208047 CGCACTTAGCATCAACAGATAGTC 59.792 45.833 0.00 0.00 46.13 2.59
15 16 4.115516 CGCACTTAGCATCAACAGATAGT 58.884 43.478 0.00 0.00 46.13 2.12
16 17 4.115516 ACGCACTTAGCATCAACAGATAG 58.884 43.478 0.00 0.00 46.13 2.08
17 18 4.123497 ACGCACTTAGCATCAACAGATA 57.877 40.909 0.00 0.00 46.13 1.98
18 19 2.977914 ACGCACTTAGCATCAACAGAT 58.022 42.857 0.00 0.00 46.13 2.90
19 20 2.455674 ACGCACTTAGCATCAACAGA 57.544 45.000 0.00 0.00 46.13 3.41
20 21 2.472886 CGAACGCACTTAGCATCAACAG 60.473 50.000 0.00 0.00 46.13 3.16
21 22 1.459209 CGAACGCACTTAGCATCAACA 59.541 47.619 0.00 0.00 46.13 3.33
22 23 1.201921 CCGAACGCACTTAGCATCAAC 60.202 52.381 0.00 0.00 46.13 3.18
23 24 1.075542 CCGAACGCACTTAGCATCAA 58.924 50.000 0.00 0.00 46.13 2.57
24 25 0.037697 ACCGAACGCACTTAGCATCA 60.038 50.000 0.00 0.00 46.13 3.07
25 26 1.076332 AACCGAACGCACTTAGCATC 58.924 50.000 0.00 0.00 46.13 3.91
26 27 1.519408 AAACCGAACGCACTTAGCAT 58.481 45.000 0.00 0.00 46.13 3.79
27 28 2.151881 TAAACCGAACGCACTTAGCA 57.848 45.000 0.00 0.00 46.13 3.49
28 29 3.667050 GAATAAACCGAACGCACTTAGC 58.333 45.455 0.00 0.00 40.87 3.09
29 30 3.241868 CCGAATAAACCGAACGCACTTAG 60.242 47.826 0.00 0.00 0.00 2.18
30 31 2.667481 CCGAATAAACCGAACGCACTTA 59.333 45.455 0.00 0.00 0.00 2.24
31 32 1.461897 CCGAATAAACCGAACGCACTT 59.538 47.619 0.00 0.00 0.00 3.16
32 33 1.073177 CCGAATAAACCGAACGCACT 58.927 50.000 0.00 0.00 0.00 4.40
62 63 8.582433 ACAAACTGAAAAACCGTATAAATTGG 57.418 30.769 0.00 0.00 0.00 3.16
64 65 9.384682 CGTACAAACTGAAAAACCGTATAAATT 57.615 29.630 0.00 0.00 0.00 1.82
178 179 7.971722 GCGTCAACTTTGGTTTTTATGGTATAT 59.028 33.333 0.00 0.00 32.73 0.86
384 389 4.624024 TCAAATGCACTACTAAGCACGTAC 59.376 41.667 0.00 0.00 44.49 3.67
427 432 5.048782 TGAGATGAACAACCATACAAGTTGC 60.049 40.000 1.81 0.00 46.85 4.17
592 597 3.827876 ACCGAAAATAAACCGAACCCAAT 59.172 39.130 0.00 0.00 0.00 3.16
595 600 4.201940 CCATACCGAAAATAAACCGAACCC 60.202 45.833 0.00 0.00 0.00 4.11
625 632 5.163602 ACTCTGTGCATTTAAAAACCGAACA 60.164 36.000 0.00 0.00 0.00 3.18
685 692 3.101428 GTACGTCGCACACACCCG 61.101 66.667 0.00 0.00 0.00 5.28
710 717 2.468868 AACATGAGCCCCACCCACA 61.469 57.895 0.00 0.00 0.00 4.17
727 734 4.695993 TCGGTGCGCTGCCATCAA 62.696 61.111 18.72 1.93 0.00 2.57
728 735 4.695993 TTCGGTGCGCTGCCATCA 62.696 61.111 18.72 2.57 0.00 3.07
729 736 3.869272 CTTCGGTGCGCTGCCATC 61.869 66.667 18.72 0.00 0.00 3.51
743 757 0.949105 TTCAACTTCGCGCCTCCTTC 60.949 55.000 0.00 0.00 0.00 3.46
774 788 1.076044 CCCAACCACCCATCCATCC 60.076 63.158 0.00 0.00 0.00 3.51
781 795 2.833227 CTTCGTCCCAACCACCCA 59.167 61.111 0.00 0.00 0.00 4.51
823 914 4.806339 AGGAAGAGGCCGAGGGGG 62.806 72.222 0.00 0.00 39.58 5.40
829 920 1.076339 AGAGGAGAGGAAGAGGCCG 60.076 63.158 0.00 0.00 0.00 6.13
830 921 0.759060 GGAGAGGAGAGGAAGAGGCC 60.759 65.000 0.00 0.00 0.00 5.19
831 922 0.759060 GGGAGAGGAGAGGAAGAGGC 60.759 65.000 0.00 0.00 0.00 4.70
945 1140 1.167781 GGGGTCGATCGGTCTCTCTC 61.168 65.000 16.41 0.00 0.00 3.20
946 1141 1.152922 GGGGTCGATCGGTCTCTCT 60.153 63.158 16.41 0.00 0.00 3.10
1133 1344 0.451783 GCCAAATAGCAACGAGTGGG 59.548 55.000 0.00 0.00 0.00 4.61
1139 1350 1.226379 CAGGCGCCAAATAGCAACG 60.226 57.895 31.54 0.00 34.54 4.10
1170 1381 2.026734 CAGAGATCGTCGGCGCAT 59.973 61.111 10.83 0.00 38.14 4.73
1172 1383 2.652496 GTCAGAGATCGTCGGCGC 60.652 66.667 3.52 0.00 38.14 6.53
1173 1384 0.932123 CATGTCAGAGATCGTCGGCG 60.932 60.000 1.15 1.15 39.92 6.46
1174 1385 0.101399 ACATGTCAGAGATCGTCGGC 59.899 55.000 0.00 0.00 0.00 5.54
1175 1386 2.568696 AACATGTCAGAGATCGTCGG 57.431 50.000 0.00 0.00 0.00 4.79
1371 2111 0.758123 GAGGGCAGAGATGAGAAGGG 59.242 60.000 0.00 0.00 0.00 3.95
1622 2362 1.396996 GGTAGTATTGTTGGTGCTGCG 59.603 52.381 0.00 0.00 0.00 5.18
1626 2366 0.730840 GCCGGTAGTATTGTTGGTGC 59.269 55.000 1.90 0.00 0.00 5.01
1629 2369 2.116827 TTGGCCGGTAGTATTGTTGG 57.883 50.000 1.90 0.00 0.00 3.77
1630 2370 3.754323 TCTTTTGGCCGGTAGTATTGTTG 59.246 43.478 1.90 0.00 0.00 3.33
1631 2371 3.754850 GTCTTTTGGCCGGTAGTATTGTT 59.245 43.478 1.90 0.00 0.00 2.83
1762 2533 1.165270 GGGGGAAAATATCGCGGATG 58.835 55.000 6.13 0.00 41.73 3.51
1778 2549 3.634504 TCATCATCATGAAACAAGGGGG 58.365 45.455 0.00 0.00 35.99 5.40
1832 2605 6.069684 ACCAAAACGATACGTATAGGAGAG 57.930 41.667 18.23 6.95 39.99 3.20
1869 2643 0.796312 CCGGATCCACAACTCAAACG 59.204 55.000 13.41 0.00 0.00 3.60
2003 2790 1.576356 GCAGGAGCAGAATAGGAACG 58.424 55.000 0.00 0.00 41.58 3.95
2122 3438 7.921214 GCCTTTTAATAAGCCCAATAAAGAGTC 59.079 37.037 0.00 0.00 0.00 3.36
2133 3449 4.521130 GCTATGGCCTTTTAATAAGCCC 57.479 45.455 3.32 0.00 45.14 5.19
2167 3485 1.065709 TCTTTTATGTGGCTCGTCCCC 60.066 52.381 0.00 0.00 0.00 4.81
2168 3486 2.396590 TCTTTTATGTGGCTCGTCCC 57.603 50.000 0.00 0.00 0.00 4.46
2169 3487 3.001330 CGAATCTTTTATGTGGCTCGTCC 59.999 47.826 0.00 0.00 0.00 4.79
2170 3488 3.617263 ACGAATCTTTTATGTGGCTCGTC 59.383 43.478 0.00 0.00 33.32 4.20
2171 3489 3.596214 ACGAATCTTTTATGTGGCTCGT 58.404 40.909 0.00 0.00 33.76 4.18
2172 3490 4.578601 GAACGAATCTTTTATGTGGCTCG 58.421 43.478 0.00 0.00 0.00 5.03
2173 3491 4.328983 TCGAACGAATCTTTTATGTGGCTC 59.671 41.667 0.00 0.00 0.00 4.70
2174 3492 4.250464 TCGAACGAATCTTTTATGTGGCT 58.750 39.130 0.00 0.00 0.00 4.75
2175 3493 4.593597 TCGAACGAATCTTTTATGTGGC 57.406 40.909 0.00 0.00 0.00 5.01
2178 3496 7.802738 TGTTTGATCGAACGAATCTTTTATGT 58.197 30.769 18.84 0.00 32.18 2.29
2179 3497 8.653984 TTGTTTGATCGAACGAATCTTTTATG 57.346 30.769 18.84 0.00 32.18 1.90
2181 3499 9.672086 AAATTGTTTGATCGAACGAATCTTTTA 57.328 25.926 17.99 0.00 32.18 1.52
2182 3500 8.574196 AAATTGTTTGATCGAACGAATCTTTT 57.426 26.923 17.99 11.65 32.18 2.27
2186 3504 7.425595 GGACTAAATTGTTTGATCGAACGAATC 59.574 37.037 17.99 11.07 32.18 2.52
2187 3505 7.094975 TGGACTAAATTGTTTGATCGAACGAAT 60.095 33.333 17.99 15.34 32.18 3.34
2188 3506 6.203145 TGGACTAAATTGTTTGATCGAACGAA 59.797 34.615 17.99 14.02 32.18 3.85
2189 3507 5.697178 TGGACTAAATTGTTTGATCGAACGA 59.303 36.000 16.67 16.67 32.18 3.85
2190 3508 5.788531 GTGGACTAAATTGTTTGATCGAACG 59.211 40.000 18.84 7.72 32.18 3.95
2191 3509 6.664515 TGTGGACTAAATTGTTTGATCGAAC 58.335 36.000 17.60 17.60 0.00 3.95
2192 3510 6.869315 TGTGGACTAAATTGTTTGATCGAA 57.131 33.333 0.00 0.00 0.00 3.71
2194 3512 5.512788 GCATGTGGACTAAATTGTTTGATCG 59.487 40.000 0.00 0.00 0.00 3.69
2197 3515 5.771469 CAGCATGTGGACTAAATTGTTTGA 58.229 37.500 0.00 0.00 0.00 2.69
2198 3516 4.386652 GCAGCATGTGGACTAAATTGTTTG 59.613 41.667 0.00 0.00 39.31 2.93
2199 3517 4.559153 GCAGCATGTGGACTAAATTGTTT 58.441 39.130 0.00 0.00 39.31 2.83
2200 3518 3.056607 GGCAGCATGTGGACTAAATTGTT 60.057 43.478 0.00 0.00 39.31 2.83
2203 3521 2.102578 GGGCAGCATGTGGACTAAATT 58.897 47.619 0.00 0.00 39.31 1.82
2204 3522 1.767759 GGGCAGCATGTGGACTAAAT 58.232 50.000 0.00 0.00 39.31 1.40
2206 3524 1.078497 CGGGCAGCATGTGGACTAA 60.078 57.895 0.00 0.00 39.31 2.24
2207 3525 1.337384 ATCGGGCAGCATGTGGACTA 61.337 55.000 0.00 0.00 39.31 2.59
2210 3528 2.124612 CATCGGGCAGCATGTGGA 60.125 61.111 0.00 0.00 39.31 4.02
2251 3580 2.009774 CATTCTTCGAGGGAATTGCGT 58.990 47.619 11.35 0.00 31.90 5.24
2286 3617 0.036590 GGGCCCACAACATTGCAATT 59.963 50.000 19.95 0.00 0.00 2.32
2290 3621 0.179034 TTTTGGGCCCACAACATTGC 60.179 50.000 28.70 0.00 0.00 3.56
2318 3649 2.280628 GTCTATTTGTTGGGAGAGGCG 58.719 52.381 0.00 0.00 0.00 5.52
2324 3655 7.595819 ATGTCTTTTTGTCTATTTGTTGGGA 57.404 32.000 0.00 0.00 0.00 4.37
2325 3656 9.757227 TTTATGTCTTTTTGTCTATTTGTTGGG 57.243 29.630 0.00 0.00 0.00 4.12
2338 3669 9.683069 AGTCTAGTGCATTTTTATGTCTTTTTG 57.317 29.630 0.00 0.00 0.00 2.44
2477 3809 8.695456 ACCAATGTCAAACTTTGTAGAAATCTT 58.305 29.630 1.44 0.00 33.08 2.40
2480 3812 8.006298 TCACCAATGTCAAACTTTGTAGAAAT 57.994 30.769 1.44 0.00 33.08 2.17
2481 3813 7.397892 TCACCAATGTCAAACTTTGTAGAAA 57.602 32.000 1.44 0.00 33.08 2.52
2482 3814 7.068103 ACATCACCAATGTCAAACTTTGTAGAA 59.932 33.333 1.44 0.00 45.78 2.10
2483 3815 6.545666 ACATCACCAATGTCAAACTTTGTAGA 59.454 34.615 1.44 3.70 45.78 2.59
2503 3835 8.763356 GCATTTTCAGAATTTTGTTGTACATCA 58.237 29.630 2.41 2.41 0.00 3.07


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

AutoCloner maintained by Alex Coulton.