Multiple sequence alignment - TraesCS1B01G282600

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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 TraesCS1B01G282600 chr1B 100.000 2654 0 0 1 2654 491263691 491261038 0.000000e+00 4902.0
1 TraesCS1B01G282600 chr1B 93.576 467 24 2 1972 2438 602238461 602238001 0.000000e+00 691.0
2 TraesCS1B01G282600 chr4A 95.530 604 22 1 1972 2575 624929699 624930297 0.000000e+00 961.0
3 TraesCS1B01G282600 chr6A 95.122 574 28 0 2002 2575 11847373 11847946 0.000000e+00 905.0
4 TraesCS1B01G282600 chr6A 89.676 494 38 8 1974 2467 2983910 2984390 3.750000e-173 617.0
5 TraesCS1B01G282600 chr6A 92.941 170 10 2 2477 2646 2984738 2984905 2.040000e-61 246.0
6 TraesCS1B01G282600 chr6A 82.609 92 9 5 1974 2065 17046588 17046504 1.020000e-09 75.0
7 TraesCS1B01G282600 chr1D 89.804 716 29 17 571 1273 366226160 366226844 0.000000e+00 878.0
8 TraesCS1B01G282600 chr1D 88.180 643 51 18 1117 1748 366226733 366227361 0.000000e+00 743.0
9 TraesCS1B01G282600 chr1D 83.032 442 27 19 36 472 366225690 366226088 9.030000e-95 357.0
10 TraesCS1B01G282600 chr1D 92.958 213 11 3 1748 1956 366227409 366227621 9.230000e-80 307.0
11 TraesCS1B01G282600 chr1D 87.121 132 8 6 1178 1306 366226701 366226826 9.900000e-30 141.0
12 TraesCS1B01G282600 chr3D 92.986 499 28 3 1968 2466 655234 655725 0.000000e+00 721.0
13 TraesCS1B01G282600 chr3D 92.073 164 11 2 2477 2640 656095 656256 2.050000e-56 230.0
14 TraesCS1B01G282600 chr4D 92.757 497 28 4 1970 2466 481612578 481613066 0.000000e+00 712.0
15 TraesCS1B01G282600 chr4D 95.294 170 6 2 2477 2646 481613414 481613581 4.350000e-68 268.0
16 TraesCS1B01G282600 chr5B 94.773 440 21 2 2000 2438 707143869 707144307 0.000000e+00 684.0
17 TraesCS1B01G282600 chr1A 84.135 769 48 27 528 1262 465522102 465521374 0.000000e+00 676.0
18 TraesCS1B01G282600 chr1A 87.919 596 41 18 1178 1748 465521510 465520921 0.000000e+00 673.0
19 TraesCS1B01G282600 chr1A 88.945 398 22 9 83 464 465522535 465522144 3.090000e-129 472.0
20 TraesCS1B01G282600 chr1A 92.576 229 11 2 1752 1974 465520873 465520645 9.160000e-85 324.0
21 TraesCS1B01G282600 chr3B 91.278 493 33 3 1974 2466 777195124 777194642 0.000000e+00 664.0
22 TraesCS1B01G282600 chr3B 87.500 168 20 1 2487 2654 749039062 749038896 2.700000e-45 193.0
23 TraesCS1B01G282600 chr3B 86.250 160 7 3 2487 2646 777194291 777194147 2.730000e-35 159.0
24 TraesCS1B01G282600 chr7A 90.669 493 39 3 1974 2466 729511717 729512202 0.000000e+00 649.0
25 TraesCS1B01G282600 chr7A 90.000 170 15 2 2477 2646 729512538 729512705 4.450000e-53 219.0
26 TraesCS1B01G282600 chr7A 89.441 161 15 2 2480 2640 23748457 23748615 4.480000e-48 202.0
27 TraesCS1B01G282600 chr2B 85.897 78 11 0 2563 2640 273753695 273753618 1.690000e-12 84.2
28 TraesCS1B01G282600 chr5A 83.516 91 9 4 1975 2065 328994219 328994135 2.190000e-11 80.5
29 TraesCS1B01G282600 chr7B 100.000 30 0 0 2582 2611 452299564 452299535 3.690000e-04 56.5
30 TraesCS1B01G282600 chr2A 100.000 28 0 0 2582 2609 232405307 232405280 5.000000e-03 52.8


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 TraesCS1B01G282600 chr1B 491261038 491263691 2653 True 4902.00 4902 100.00000 1 2654 1 chr1B.!!$R1 2653
1 TraesCS1B01G282600 chr4A 624929699 624930297 598 False 961.00 961 95.53000 1972 2575 1 chr4A.!!$F1 603
2 TraesCS1B01G282600 chr6A 11847373 11847946 573 False 905.00 905 95.12200 2002 2575 1 chr6A.!!$F1 573
3 TraesCS1B01G282600 chr6A 2983910 2984905 995 False 431.50 617 91.30850 1974 2646 2 chr6A.!!$F2 672
4 TraesCS1B01G282600 chr1D 366225690 366227621 1931 False 485.20 878 88.21900 36 1956 5 chr1D.!!$F1 1920
5 TraesCS1B01G282600 chr3D 655234 656256 1022 False 475.50 721 92.52950 1968 2640 2 chr3D.!!$F1 672
6 TraesCS1B01G282600 chr4D 481612578 481613581 1003 False 490.00 712 94.02550 1970 2646 2 chr4D.!!$F1 676
7 TraesCS1B01G282600 chr1A 465520645 465522535 1890 True 536.25 676 88.39375 83 1974 4 chr1A.!!$R1 1891
8 TraesCS1B01G282600 chr3B 777194147 777195124 977 True 411.50 664 88.76400 1974 2646 2 chr3B.!!$R2 672
9 TraesCS1B01G282600 chr7A 729511717 729512705 988 False 434.00 649 90.33450 1974 2646 2 chr7A.!!$F2 672

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
117 120 0.036765 ATCTGCGTGCCGGTTTCTAA 60.037 50.0 1.9 0.0 0.0 2.10 F
806 865 0.108567 GGCACGAGTCTCCTTCCTTC 60.109 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1674 0.401738 TGGCCCTCTTCCTCTTGTTG 59.598 55.0 0.00 0.00 0.0 3.33 R
1844 2050 1.298602 TGAACGATCGATTGCCATGG 58.701 50.0 24.34 7.63 0.0 3.66 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
18 19 3.708195 GTTTGTATGCTGCTGCCTG 57.292 52.632 13.47 0.00 38.71 4.85
19 20 0.457337 GTTTGTATGCTGCTGCCTGC 60.457 55.000 13.47 7.53 43.25 4.85
20 21 0.609957 TTTGTATGCTGCTGCCTGCT 60.610 50.000 13.47 0.00 43.37 4.24
21 22 1.310216 TTGTATGCTGCTGCCTGCTG 61.310 55.000 13.47 0.00 43.37 4.41
22 23 2.124445 TATGCTGCTGCCTGCTGG 60.124 61.111 13.47 5.03 43.37 4.85
23 24 2.672181 TATGCTGCTGCCTGCTGGA 61.672 57.895 14.77 0.04 43.92 3.86
24 25 2.604299 TATGCTGCTGCCTGCTGGAG 62.604 60.000 14.77 12.11 43.17 3.86
26 27 4.798344 CTGCTGCCTGCTGGAGGG 62.798 72.222 17.41 2.18 43.07 4.30
29 30 3.655211 CTGCCTGCTGGAGGGGTT 61.655 66.667 17.41 0.00 43.07 4.11
30 31 3.185203 TGCCTGCTGGAGGGGTTT 61.185 61.111 17.41 0.00 43.07 3.27
31 32 2.677875 GCCTGCTGGAGGGGTTTG 60.678 66.667 17.41 0.00 43.07 2.93
32 33 2.677875 CCTGCTGGAGGGGTTTGC 60.678 66.667 7.42 0.00 38.36 3.68
33 34 2.437897 CTGCTGGAGGGGTTTGCT 59.562 61.111 0.00 0.00 0.00 3.91
34 35 1.685224 CTGCTGGAGGGGTTTGCTA 59.315 57.895 0.00 0.00 0.00 3.49
42 43 3.850173 TGGAGGGGTTTGCTAGAATAACT 59.150 43.478 0.00 0.00 0.00 2.24
66 69 1.662044 CCTGCTCTTGTGGTTTGGC 59.338 57.895 0.00 0.00 0.00 4.52
76 79 4.133796 GGTTTGGCTCGCCATGGC 62.134 66.667 27.67 27.67 46.64 4.40
103 106 9.185192 GTTAATTAGCATGTTCCATTTATCTGC 57.815 33.333 0.00 0.00 0.00 4.26
117 120 0.036765 ATCTGCGTGCCGGTTTCTAA 60.037 50.000 1.90 0.00 0.00 2.10
142 145 3.491447 GCTTGCCTGGTTATTATTGCCTG 60.491 47.826 0.00 0.00 0.00 4.85
143 146 3.660970 TGCCTGGTTATTATTGCCTGA 57.339 42.857 0.00 0.00 0.00 3.86
144 147 3.287222 TGCCTGGTTATTATTGCCTGAC 58.713 45.455 0.00 0.00 0.00 3.51
145 148 2.623416 GCCTGGTTATTATTGCCTGACC 59.377 50.000 0.00 0.00 0.00 4.02
146 149 3.897239 CCTGGTTATTATTGCCTGACCA 58.103 45.455 0.00 0.00 35.95 4.02
189 202 8.154203 TGGAAGTTCTCATTGATGTTAACTACA 58.846 33.333 7.22 4.34 41.97 2.74
190 203 8.660373 GGAAGTTCTCATTGATGTTAACTACAG 58.340 37.037 7.22 0.00 40.83 2.74
191 204 9.209175 GAAGTTCTCATTGATGTTAACTACAGT 57.791 33.333 7.22 1.51 40.83 3.55
193 206 9.640963 AGTTCTCATTGATGTTAACTACAGTAC 57.359 33.333 7.22 0.00 40.83 2.73
194 207 8.584600 GTTCTCATTGATGTTAACTACAGTACG 58.415 37.037 7.22 0.00 40.83 3.67
195 208 7.823665 TCTCATTGATGTTAACTACAGTACGT 58.176 34.615 7.22 0.00 40.83 3.57
196 209 8.949177 TCTCATTGATGTTAACTACAGTACGTA 58.051 33.333 7.22 0.00 40.83 3.57
199 212 7.745022 TTGATGTTAACTACAGTACGTATGC 57.255 36.000 7.22 0.00 40.83 3.14
207 220 4.760715 ACTACAGTACGTATGCTGGGATAG 59.239 45.833 15.32 10.91 42.48 2.08
369 384 2.989840 CGTCACTGAATTCTGACTGACC 59.010 50.000 19.75 9.23 35.58 4.02
374 389 5.245977 TCACTGAATTCTGACTGACCACATA 59.754 40.000 18.13 0.00 0.00 2.29
401 417 0.533308 TCAAAACCCGTTGTCCTCCG 60.533 55.000 0.00 0.00 0.00 4.63
418 434 3.492137 CCTCCGGTCCTAACCTAAAATCG 60.492 52.174 0.00 0.00 44.04 3.34
424 450 4.874396 GGTCCTAACCTAAAATCGTTCCTG 59.126 45.833 0.00 0.00 42.80 3.86
425 451 5.485620 GTCCTAACCTAAAATCGTTCCTGT 58.514 41.667 0.00 0.00 0.00 4.00
438 464 2.996621 CGTTCCTGTTCTCCTTCACATC 59.003 50.000 0.00 0.00 0.00 3.06
467 493 8.863049 CAAAGTATACAAACATCCATTTCAAGC 58.137 33.333 5.50 0.00 0.00 4.01
468 494 6.785191 AGTATACAAACATCCATTTCAAGCG 58.215 36.000 5.50 0.00 0.00 4.68
469 495 3.302365 ACAAACATCCATTTCAAGCGG 57.698 42.857 0.00 0.00 0.00 5.52
470 496 2.890311 ACAAACATCCATTTCAAGCGGA 59.110 40.909 0.00 0.00 0.00 5.54
471 497 3.320541 ACAAACATCCATTTCAAGCGGAA 59.679 39.130 0.00 0.00 31.18 4.30
509 535 3.330267 AGAGCGTTTCAAGTGGAAGATC 58.670 45.455 0.00 0.00 36.72 2.75
512 538 2.808543 GCGTTTCAAGTGGAAGATCAGT 59.191 45.455 0.00 0.00 36.72 3.41
514 540 3.364366 CGTTTCAAGTGGAAGATCAGTGC 60.364 47.826 0.00 0.00 36.72 4.40
515 541 3.490439 TTCAAGTGGAAGATCAGTGCA 57.510 42.857 0.00 0.00 0.00 4.57
516 542 2.771089 TCAAGTGGAAGATCAGTGCAC 58.229 47.619 9.40 9.40 37.58 4.57
517 543 2.104622 TCAAGTGGAAGATCAGTGCACA 59.895 45.455 21.04 0.00 39.57 4.57
518 544 2.175878 AGTGGAAGATCAGTGCACAC 57.824 50.000 21.04 4.83 39.57 3.82
544 594 2.014335 TGGTCATCGTCAGAGCAATG 57.986 50.000 0.00 0.00 40.19 2.82
556 606 5.622460 CGTCAGAGCAATGGAAACTAGTAGT 60.622 44.000 0.00 0.00 0.00 2.73
564 614 7.287927 AGCAATGGAAACTAGTAGTAGCAGATA 59.712 37.037 2.50 0.00 0.00 1.98
565 615 8.091449 GCAATGGAAACTAGTAGTAGCAGATAT 58.909 37.037 2.50 0.00 0.00 1.63
579 629 7.911651 AGTAGCAGATATATAGGTTGTTGCAT 58.088 34.615 0.00 0.00 33.00 3.96
589 639 1.659954 TTGTTGCATTTGACGCGGC 60.660 52.632 12.47 8.67 0.00 6.53
656 706 1.425031 CCGTCAACATCGGTGCATG 59.575 57.895 0.00 0.00 42.62 4.06
658 708 1.226101 GTCAACATCGGTGCATGCG 60.226 57.895 14.09 0.00 0.00 4.73
659 709 1.670730 TCAACATCGGTGCATGCGT 60.671 52.632 14.09 0.00 0.00 5.24
660 710 0.390472 TCAACATCGGTGCATGCGTA 60.390 50.000 14.09 0.00 0.00 4.42
741 800 5.469760 GCATCTAAACTTGGCCAAAACAAAT 59.530 36.000 20.91 6.38 0.00 2.32
751 810 6.716934 TGGCCAAAACAAATAACAAGAGTA 57.283 33.333 0.61 0.00 0.00 2.59
806 865 0.108567 GGCACGAGTCTCCTTCCTTC 60.109 60.000 0.00 0.00 0.00 3.46
807 866 0.108567 GCACGAGTCTCCTTCCTTCC 60.109 60.000 0.00 0.00 0.00 3.46
808 867 1.551452 CACGAGTCTCCTTCCTTCCT 58.449 55.000 0.00 0.00 0.00 3.36
809 868 1.203523 CACGAGTCTCCTTCCTTCCTG 59.796 57.143 0.00 0.00 0.00 3.86
904 973 0.314302 CGTCGCTCCCCTATACTTGG 59.686 60.000 0.00 0.00 0.00 3.61
1169 1244 4.329545 GAAGGTGCTGGCCGTGGA 62.330 66.667 0.00 0.00 0.00 4.02
1173 1248 3.695606 GTGCTGGCCGTGGAGAGA 61.696 66.667 0.00 0.00 0.00 3.10
1181 1256 1.587054 CCGTGGAGAGAAAGAGCGT 59.413 57.895 0.00 0.00 0.00 5.07
1182 1257 0.456995 CCGTGGAGAGAAAGAGCGTC 60.457 60.000 0.00 0.00 0.00 5.19
1183 1258 0.241213 CGTGGAGAGAAAGAGCGTCA 59.759 55.000 0.00 0.00 0.00 4.35
1185 1260 2.333014 GTGGAGAGAAAGAGCGTCAAG 58.667 52.381 0.00 0.00 0.00 3.02
1186 1261 1.273606 TGGAGAGAAAGAGCGTCAAGG 59.726 52.381 0.00 0.00 0.00 3.61
1187 1262 1.355005 GAGAGAAAGAGCGTCAAGGC 58.645 55.000 0.00 0.00 0.00 4.35
1197 1278 2.669569 GTCAAGGCAGCTGGCGAA 60.670 61.111 31.82 19.45 46.16 4.70
1202 1283 2.983725 AAGGCAGCTGGCGAAAAGGT 62.984 55.000 31.82 12.26 46.16 3.50
1466 1589 0.664224 TCGCTGGCGTCGATATACAA 59.336 50.000 14.55 0.00 40.74 2.41
1521 1644 2.776913 CGAGGAGGCGGAAGAGGAC 61.777 68.421 0.00 0.00 0.00 3.85
1526 1649 1.720694 GAGGCGGAAGAGGACGAGAG 61.721 65.000 0.00 0.00 0.00 3.20
1528 1651 1.749638 GCGGAAGAGGACGAGAGGA 60.750 63.158 0.00 0.00 0.00 3.71
1543 1666 2.182858 GAGGAGTGAGGGGAAGGGGA 62.183 65.000 0.00 0.00 0.00 4.81
1545 1668 0.845102 GGAGTGAGGGGAAGGGGAAA 60.845 60.000 0.00 0.00 0.00 3.13
1546 1669 1.073098 GAGTGAGGGGAAGGGGAAAA 58.927 55.000 0.00 0.00 0.00 2.29
1547 1670 1.427753 GAGTGAGGGGAAGGGGAAAAA 59.572 52.381 0.00 0.00 0.00 1.94
1548 1671 1.429299 AGTGAGGGGAAGGGGAAAAAG 59.571 52.381 0.00 0.00 0.00 2.27
1549 1672 1.427753 GTGAGGGGAAGGGGAAAAAGA 59.572 52.381 0.00 0.00 0.00 2.52
1550 1673 2.148702 TGAGGGGAAGGGGAAAAAGAA 58.851 47.619 0.00 0.00 0.00 2.52
1551 1674 2.158370 TGAGGGGAAGGGGAAAAAGAAC 60.158 50.000 0.00 0.00 0.00 3.01
1554 1677 2.367567 GGGGAAGGGGAAAAAGAACAAC 59.632 50.000 0.00 0.00 0.00 3.32
1559 1682 5.451937 GGAAGGGGAAAAAGAACAACAAGAG 60.452 44.000 0.00 0.00 0.00 2.85
1562 1685 4.404394 GGGGAAAAAGAACAACAAGAGGAA 59.596 41.667 0.00 0.00 0.00 3.36
1563 1686 5.451937 GGGGAAAAAGAACAACAAGAGGAAG 60.452 44.000 0.00 0.00 0.00 3.46
1569 1692 0.402121 ACAACAAGAGGAAGAGGGCC 59.598 55.000 0.00 0.00 0.00 5.80
1571 1694 0.402121 AACAAGAGGAAGAGGGCCAC 59.598 55.000 6.18 0.00 0.00 5.01
1574 1697 2.683933 GAGGAAGAGGGCCACGGA 60.684 66.667 6.18 0.00 0.00 4.69
1748 1896 1.812235 CTAGATGGCAATGGCGCATA 58.188 50.000 10.83 0.00 42.47 3.14
1749 1897 2.362736 CTAGATGGCAATGGCGCATAT 58.637 47.619 10.83 0.00 42.47 1.78
1750 1898 2.495155 AGATGGCAATGGCGCATATA 57.505 45.000 10.83 0.00 42.47 0.86
1801 2001 5.796424 AGAAACCATCAAGCTTCACATTT 57.204 34.783 0.00 0.00 0.00 2.32
1844 2050 7.279981 TGGTGTATATACTCACTTGATGTTTGC 59.720 37.037 13.89 0.00 35.26 3.68
1869 2075 2.111756 GCAATCGATCGTTCATTTGCC 58.888 47.619 15.94 5.85 35.17 4.52
1959 2165 2.237643 ACGGCCACAAGACACCAATATA 59.762 45.455 2.24 0.00 0.00 0.86
1980 2186 0.321298 ACCCGCAACGTAAGAGCATT 60.321 50.000 0.00 0.00 40.78 3.56
2054 2260 0.392461 TGCCGGCGAGATTTTAAGCT 60.392 50.000 23.90 0.00 0.00 3.74
2264 2470 4.157120 GGGGTGTAGCGACGGCAT 62.157 66.667 0.00 0.00 43.41 4.40
2277 2483 4.148825 GGCATCGACGGGCAGAGT 62.149 66.667 13.07 0.00 0.00 3.24
2481 2729 4.021925 GGGGTGGTCAGCGAGCTT 62.022 66.667 0.00 0.00 0.00 3.74
2626 3202 4.755614 GCTCGACCGTCGACGCTT 62.756 66.667 31.73 20.47 44.82 4.68
2650 3226 4.308458 CGTGCCCCGAGTGTTCCA 62.308 66.667 0.00 0.00 39.56 3.53
2651 3227 2.358737 GTGCCCCGAGTGTTCCAG 60.359 66.667 0.00 0.00 0.00 3.86
2652 3228 2.847234 TGCCCCGAGTGTTCCAGT 60.847 61.111 0.00 0.00 0.00 4.00
2653 3229 2.047179 GCCCCGAGTGTTCCAGTC 60.047 66.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.457337 GCAGGCAGCAGCATACAAAC 60.457 55.000 2.65 0.00 44.61 2.93
1 2 1.885157 GCAGGCAGCAGCATACAAA 59.115 52.632 2.65 0.00 44.61 2.83
2 3 3.594568 GCAGGCAGCAGCATACAA 58.405 55.556 2.65 0.00 44.61 2.41
12 13 3.215587 AAACCCCTCCAGCAGGCAG 62.216 63.158 0.00 0.00 41.80 4.85
13 14 3.185203 AAACCCCTCCAGCAGGCA 61.185 61.111 0.00 0.00 41.80 4.75
14 15 2.677875 CAAACCCCTCCAGCAGGC 60.678 66.667 0.00 0.00 41.80 4.85
15 16 1.852157 TAGCAAACCCCTCCAGCAGG 61.852 60.000 0.00 0.00 43.01 4.85
16 17 0.393537 CTAGCAAACCCCTCCAGCAG 60.394 60.000 0.00 0.00 0.00 4.24
17 18 0.840288 TCTAGCAAACCCCTCCAGCA 60.840 55.000 0.00 0.00 0.00 4.41
18 19 0.328258 TTCTAGCAAACCCCTCCAGC 59.672 55.000 0.00 0.00 0.00 4.85
19 20 4.080299 AGTTATTCTAGCAAACCCCTCCAG 60.080 45.833 0.00 0.00 0.00 3.86
20 21 3.850173 AGTTATTCTAGCAAACCCCTCCA 59.150 43.478 0.00 0.00 0.00 3.86
21 22 4.505324 AGTTATTCTAGCAAACCCCTCC 57.495 45.455 0.00 0.00 0.00 4.30
22 23 5.254115 ACAAGTTATTCTAGCAAACCCCTC 58.746 41.667 0.00 0.00 0.00 4.30
23 24 5.256806 ACAAGTTATTCTAGCAAACCCCT 57.743 39.130 0.00 0.00 0.00 4.79
24 25 5.066117 GCTACAAGTTATTCTAGCAAACCCC 59.934 44.000 0.00 0.00 34.20 4.95
25 26 5.066117 GGCTACAAGTTATTCTAGCAAACCC 59.934 44.000 0.00 0.00 35.33 4.11
26 27 5.880887 AGGCTACAAGTTATTCTAGCAAACC 59.119 40.000 0.00 0.00 35.33 3.27
27 28 6.675728 GCAGGCTACAAGTTATTCTAGCAAAC 60.676 42.308 0.00 0.00 35.33 2.93
28 29 5.354234 GCAGGCTACAAGTTATTCTAGCAAA 59.646 40.000 0.00 0.00 35.33 3.68
29 30 4.876107 GCAGGCTACAAGTTATTCTAGCAA 59.124 41.667 0.00 0.00 35.33 3.91
30 31 4.162320 AGCAGGCTACAAGTTATTCTAGCA 59.838 41.667 0.00 0.00 35.33 3.49
31 32 4.698575 AGCAGGCTACAAGTTATTCTAGC 58.301 43.478 0.00 0.00 33.51 3.42
32 33 6.155475 AGAGCAGGCTACAAGTTATTCTAG 57.845 41.667 0.00 0.00 0.00 2.43
33 34 6.070767 ACAAGAGCAGGCTACAAGTTATTCTA 60.071 38.462 0.00 0.00 0.00 2.10
34 35 5.181748 CAAGAGCAGGCTACAAGTTATTCT 58.818 41.667 0.00 0.00 0.00 2.40
42 43 0.764890 ACCACAAGAGCAGGCTACAA 59.235 50.000 0.00 0.00 0.00 2.41
117 120 4.524328 GGCAATAATAACCAGGCAAGCTAT 59.476 41.667 0.00 0.00 0.00 2.97
142 145 0.036858 GAAGCACTCCTGGTCTGGTC 60.037 60.000 0.00 0.00 0.00 4.02
143 146 0.472734 AGAAGCACTCCTGGTCTGGT 60.473 55.000 0.00 0.00 0.00 4.00
144 147 0.689623 AAGAAGCACTCCTGGTCTGG 59.310 55.000 0.00 0.00 0.00 3.86
145 148 1.610102 CCAAGAAGCACTCCTGGTCTG 60.610 57.143 0.00 0.00 0.00 3.51
146 149 0.689623 CCAAGAAGCACTCCTGGTCT 59.310 55.000 0.00 0.00 0.00 3.85
189 202 5.864418 TTTTCTATCCCAGCATACGTACT 57.136 39.130 0.00 0.00 0.00 2.73
190 203 5.408604 CCATTTTCTATCCCAGCATACGTAC 59.591 44.000 0.00 0.00 0.00 3.67
191 204 5.071250 ACCATTTTCTATCCCAGCATACGTA 59.929 40.000 0.00 0.00 0.00 3.57
192 205 4.141482 ACCATTTTCTATCCCAGCATACGT 60.141 41.667 0.00 0.00 0.00 3.57
193 206 4.214119 CACCATTTTCTATCCCAGCATACG 59.786 45.833 0.00 0.00 0.00 3.06
194 207 5.376625 TCACCATTTTCTATCCCAGCATAC 58.623 41.667 0.00 0.00 0.00 2.39
195 208 5.645056 TCACCATTTTCTATCCCAGCATA 57.355 39.130 0.00 0.00 0.00 3.14
196 209 4.524802 TCACCATTTTCTATCCCAGCAT 57.475 40.909 0.00 0.00 0.00 3.79
199 212 5.945784 TCTGTTTCACCATTTTCTATCCCAG 59.054 40.000 0.00 0.00 0.00 4.45
401 417 4.874396 CAGGAACGATTTTAGGTTAGGACC 59.126 45.833 0.00 0.00 46.92 4.46
418 434 3.008485 AGGATGTGAAGGAGAACAGGAAC 59.992 47.826 0.00 0.00 0.00 3.62
424 450 4.646572 ACTTTGAGGATGTGAAGGAGAAC 58.353 43.478 0.00 0.00 0.00 3.01
425 451 4.982241 ACTTTGAGGATGTGAAGGAGAA 57.018 40.909 0.00 0.00 0.00 2.87
438 464 8.739039 TGAAATGGATGTTTGTATACTTTGAGG 58.261 33.333 4.17 0.00 0.00 3.86
484 510 4.398044 TCTTCCACTTGAAACGCTCTTTTT 59.602 37.500 0.00 0.00 31.06 1.94
487 513 3.194005 TCTTCCACTTGAAACGCTCTT 57.806 42.857 0.00 0.00 31.06 2.85
489 515 3.067106 TGATCTTCCACTTGAAACGCTC 58.933 45.455 0.00 0.00 31.06 5.03
491 517 2.808543 ACTGATCTTCCACTTGAAACGC 59.191 45.455 0.00 0.00 31.06 4.84
492 518 3.364366 GCACTGATCTTCCACTTGAAACG 60.364 47.826 0.00 0.00 31.06 3.60
493 519 3.565482 TGCACTGATCTTCCACTTGAAAC 59.435 43.478 0.00 0.00 31.06 2.78
494 520 3.565482 GTGCACTGATCTTCCACTTGAAA 59.435 43.478 10.32 0.00 31.06 2.69
496 522 2.104622 TGTGCACTGATCTTCCACTTGA 59.895 45.455 19.41 0.00 0.00 3.02
499 525 1.271054 GGTGTGCACTGATCTTCCACT 60.271 52.381 19.41 0.00 0.00 4.00
509 535 1.655885 CCATGTGTGGTGTGCACTG 59.344 57.895 19.41 4.90 40.83 3.66
556 606 9.002600 CAAATGCAACAACCTATATATCTGCTA 57.997 33.333 0.00 0.00 0.00 3.49
564 614 4.495679 CGCGTCAAATGCAACAACCTATAT 60.496 41.667 0.00 0.00 0.00 0.86
565 615 3.181515 CGCGTCAAATGCAACAACCTATA 60.182 43.478 0.00 0.00 0.00 1.31
567 617 1.069568 CGCGTCAAATGCAACAACCTA 60.070 47.619 0.00 0.00 0.00 3.08
568 618 0.317770 CGCGTCAAATGCAACAACCT 60.318 50.000 0.00 0.00 0.00 3.50
569 619 1.274798 CCGCGTCAAATGCAACAACC 61.275 55.000 4.92 0.00 0.00 3.77
570 620 1.875419 GCCGCGTCAAATGCAACAAC 61.875 55.000 4.92 0.00 0.00 3.32
579 629 0.252479 TAATTAGGGGCCGCGTCAAA 59.748 50.000 15.00 8.16 0.00 2.69
589 639 7.067494 CAGAAAACCACAGATCTTAATTAGGGG 59.933 40.741 0.00 0.00 0.00 4.79
656 706 1.287425 GTTCCTGGCATGTACTACGC 58.713 55.000 0.00 0.00 0.00 4.42
658 708 3.939066 ACTTGTTCCTGGCATGTACTAC 58.061 45.455 0.00 0.00 0.00 2.73
659 709 5.484715 GTTACTTGTTCCTGGCATGTACTA 58.515 41.667 0.00 0.00 0.00 1.82
660 710 4.324267 GTTACTTGTTCCTGGCATGTACT 58.676 43.478 0.00 0.00 0.00 2.73
741 800 4.456535 TGCCTTTGCTTGTACTCTTGTTA 58.543 39.130 0.00 0.00 38.71 2.41
751 810 0.820871 TCGGTTTTGCCTTTGCTTGT 59.179 45.000 0.00 0.00 38.71 3.16
904 973 3.122948 CGCGCGGGATAAATATATATGCC 59.877 47.826 24.84 0.00 39.62 4.40
1032 1107 1.676678 CCATCTCCACCGTGGTCGAT 61.677 60.000 17.32 16.00 39.03 3.59
1109 1184 1.226547 CTCTTGCTCTCCGACTCGC 60.227 63.158 0.00 0.00 0.00 5.03
1160 1235 1.975327 CTCTTTCTCTCCACGGCCA 59.025 57.895 2.24 0.00 0.00 5.36
1169 1244 0.681733 TGCCTTGACGCTCTTTCTCT 59.318 50.000 0.00 0.00 0.00 3.10
1173 1248 1.072159 AGCTGCCTTGACGCTCTTT 59.928 52.632 0.00 0.00 0.00 2.52
1181 1256 1.518056 CTTTTCGCCAGCTGCCTTGA 61.518 55.000 8.66 0.00 36.24 3.02
1182 1257 1.080974 CTTTTCGCCAGCTGCCTTG 60.081 57.895 8.66 0.00 36.24 3.61
1183 1258 2.270986 CCTTTTCGCCAGCTGCCTT 61.271 57.895 8.66 0.00 36.24 4.35
1185 1260 2.985847 ACCTTTTCGCCAGCTGCC 60.986 61.111 8.66 0.00 36.24 4.85
1186 1261 2.256461 CACCTTTTCGCCAGCTGC 59.744 61.111 8.66 2.87 0.00 5.25
1187 1262 2.256461 GCACCTTTTCGCCAGCTG 59.744 61.111 6.78 6.78 0.00 4.24
1379 1502 4.974721 CTTGCCCGCCACCCTTGT 62.975 66.667 0.00 0.00 0.00 3.16
1392 1515 4.070552 ACGGCCTCCTCGTCTTGC 62.071 66.667 0.00 0.00 35.87 4.01
1425 1548 2.685380 AACCTCGGCCTCCTCCTG 60.685 66.667 0.00 0.00 0.00 3.86
1456 1579 4.275196 CCTCCTCGTGTTCTTGTATATCGA 59.725 45.833 0.00 0.00 0.00 3.59
1466 1589 1.187087 GTCCATCCTCCTCGTGTTCT 58.813 55.000 0.00 0.00 0.00 3.01
1521 1644 1.040339 CCTTCCCCTCACTCCTCTCG 61.040 65.000 0.00 0.00 0.00 4.04
1526 1649 0.845102 TTTCCCCTTCCCCTCACTCC 60.845 60.000 0.00 0.00 0.00 3.85
1528 1651 1.429299 CTTTTTCCCCTTCCCCTCACT 59.571 52.381 0.00 0.00 0.00 3.41
1543 1666 5.360999 CCCTCTTCCTCTTGTTGTTCTTTTT 59.639 40.000 0.00 0.00 0.00 1.94
1545 1668 4.464947 CCCTCTTCCTCTTGTTGTTCTTT 58.535 43.478 0.00 0.00 0.00 2.52
1546 1669 3.748989 GCCCTCTTCCTCTTGTTGTTCTT 60.749 47.826 0.00 0.00 0.00 2.52
1547 1670 2.224646 GCCCTCTTCCTCTTGTTGTTCT 60.225 50.000 0.00 0.00 0.00 3.01
1548 1671 2.155279 GCCCTCTTCCTCTTGTTGTTC 58.845 52.381 0.00 0.00 0.00 3.18
1549 1672 1.202940 GGCCCTCTTCCTCTTGTTGTT 60.203 52.381 0.00 0.00 0.00 2.83
1550 1673 0.402121 GGCCCTCTTCCTCTTGTTGT 59.598 55.000 0.00 0.00 0.00 3.32
1551 1674 0.401738 TGGCCCTCTTCCTCTTGTTG 59.598 55.000 0.00 0.00 0.00 3.33
1554 1677 1.078848 CGTGGCCCTCTTCCTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
1559 1682 2.190578 CATCCGTGGCCCTCTTCC 59.809 66.667 0.00 0.00 0.00 3.46
1562 1685 2.765807 CTCCATCCGTGGCCCTCT 60.766 66.667 0.00 0.00 45.63 3.69
1563 1686 4.554036 GCTCCATCCGTGGCCCTC 62.554 72.222 0.00 0.00 45.63 4.30
1748 1896 4.540099 TGAGGGGAAACAAACCAGATCTAT 59.460 41.667 0.00 0.00 0.00 1.98
1749 1897 3.913799 TGAGGGGAAACAAACCAGATCTA 59.086 43.478 0.00 0.00 0.00 1.98
1750 1898 2.716424 TGAGGGGAAACAAACCAGATCT 59.284 45.455 0.00 0.00 0.00 2.75
1801 2001 4.658063 ACACCAATAAAATTCCCAGACGA 58.342 39.130 0.00 0.00 0.00 4.20
1844 2050 1.298602 TGAACGATCGATTGCCATGG 58.701 50.000 24.34 7.63 0.00 3.66
1959 2165 1.666872 GCTCTTACGTTGCGGGTGT 60.667 57.895 0.00 0.00 0.00 4.16
2054 2260 2.958355 CTGAAAGAAAGTTCAGCCCCAA 59.042 45.455 2.26 0.00 45.84 4.12
2065 2271 3.457234 GGGCCAAACAACTGAAAGAAAG 58.543 45.455 4.39 0.00 37.43 2.62
2222 2428 2.048597 CGGCTGCAACGACCACTA 60.049 61.111 0.50 0.00 0.00 2.74
2481 2729 4.113815 CTCATGGCCGCCTTCCCA 62.114 66.667 11.61 0.00 35.21 4.37


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

AutoCloner maintained by Alex Coulton.