Multiple sequence alignment - TraesCS2A01G148300

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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 TraesCS2A01G148300 chr2A 100.000 2639 0 0 1 2639 94316649 94319287 0.000000e+00 4874.0
1 TraesCS2A01G148300 chr2A 89.256 847 69 4 1387 2214 94447034 94447877 0.000000e+00 1040.0
2 TraesCS2A01G148300 chr2A 91.554 663 49 5 1782 2440 94324405 94325064 0.000000e+00 907.0
3 TraesCS2A01G148300 chr2A 93.639 393 25 0 2247 2639 94447880 94448272 2.930000e-164 588.0
4 TraesCS2A01G148300 chr2A 85.263 570 60 10 1 559 94418961 94419517 1.370000e-157 566.0
5 TraesCS2A01G148300 chr2A 80.612 686 89 22 219 886 94323531 94324190 8.490000e-135 490.0
6 TraesCS2A01G148300 chr2A 90.476 105 4 4 67 166 94323403 94323506 1.650000e-27 134.0
7 TraesCS2A01G148300 chr2A 92.593 54 4 0 1250 1303 90030216 90030163 7.830000e-11 78.7
8 TraesCS2A01G148300 chr2A 88.710 62 4 3 1250 1311 94291106 94291164 3.640000e-09 73.1
9 TraesCS2A01G148300 chr2D 87.592 2039 164 35 487 2474 96083192 96085192 0.000000e+00 2281.0
10 TraesCS2A01G148300 chr2D 87.353 2040 171 34 487 2474 96292645 96294649 0.000000e+00 2257.0
11 TraesCS2A01G148300 chr2D 86.905 2039 154 44 483 2474 95786396 95788368 0.000000e+00 2182.0
12 TraesCS2A01G148300 chr2D 88.667 1500 123 20 1012 2474 95917196 95918685 0.000000e+00 1784.0
13 TraesCS2A01G148300 chr2D 81.238 533 66 16 487 1005 95914899 95915411 1.470000e-107 399.0
14 TraesCS2A01G148300 chr2D 78.676 136 16 9 893 1026 95786900 95787024 7.830000e-11 78.7
15 TraesCS2A01G148300 chrUn 84.610 1345 146 28 90 1387 17381958 17383288 0.000000e+00 1280.0
16 TraesCS2A01G148300 chrUn 88.845 1013 78 14 1385 2374 17383315 17384315 0.000000e+00 1212.0
17 TraesCS2A01G148300 chrUn 90.954 409 29 7 1937 2339 477994025 477993619 6.420000e-151 544.0
18 TraesCS2A01G148300 chr2B 86.784 227 20 7 1 219 147495764 147495988 7.300000e-61 244.0
19 TraesCS2A01G148300 chr2B 90.323 62 3 3 1250 1311 147491598 147491656 7.830000e-11 78.7
20 TraesCS2A01G148300 chr7A 77.778 162 30 5 1469 1627 574754198 574754356 7.780000e-16 95.3
21 TraesCS2A01G148300 chr7B 77.439 164 27 8 1469 1627 535614669 535614827 3.620000e-14 89.8
22 TraesCS2A01G148300 chr3A 87.013 77 6 2 1911 1985 628219365 628219291 1.680000e-12 84.2
23 TraesCS2A01G148300 chr3A 92.593 54 4 0 1523 1576 628219772 628219719 7.830000e-11 78.7
24 TraesCS2A01G148300 chr6D 77.953 127 23 4 1168 1292 448595461 448595584 1.010000e-09 75.0
25 TraesCS2A01G148300 chr1D 93.333 45 3 0 1732 1776 62890537 62890581 1.700000e-07 67.6
26 TraesCS2A01G148300 chr1B 93.333 45 3 0 1732 1776 100422987 100423031 1.700000e-07 67.6


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 TraesCS2A01G148300 chr2A 94316649 94319287 2638 False 4874.000000 4874 100.000000 1 2639 1 chr2A.!!$F2 2638
1 TraesCS2A01G148300 chr2A 94447034 94448272 1238 False 814.000000 1040 91.447500 1387 2639 2 chr2A.!!$F5 1252
2 TraesCS2A01G148300 chr2A 94418961 94419517 556 False 566.000000 566 85.263000 1 559 1 chr2A.!!$F3 558
3 TraesCS2A01G148300 chr2A 94323403 94325064 1661 False 510.333333 907 87.547333 67 2440 3 chr2A.!!$F4 2373
4 TraesCS2A01G148300 chr2D 96083192 96085192 2000 False 2281.000000 2281 87.592000 487 2474 1 chr2D.!!$F1 1987
5 TraesCS2A01G148300 chr2D 96292645 96294649 2004 False 2257.000000 2257 87.353000 487 2474 1 chr2D.!!$F2 1987
6 TraesCS2A01G148300 chr2D 95786396 95788368 1972 False 1130.350000 2182 82.790500 483 2474 2 chr2D.!!$F3 1991
7 TraesCS2A01G148300 chr2D 95914899 95918685 3786 False 1091.500000 1784 84.952500 487 2474 2 chr2D.!!$F4 1987
8 TraesCS2A01G148300 chrUn 17381958 17384315 2357 False 1246.000000 1280 86.727500 90 2374 2 chrUn.!!$F1 2284

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
867 929 0.031917 TACACCTATCCCAAGCCCGA 60.032 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 3623 0.98423 TGAGTCCCTTCTTGGCGAAT 59.016 50.0 0.0 0.0 0.0 3.34 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
20 21 0.242825 ACACGGTCCACATACAGACG 59.757 55.000 0.00 0.00 33.66 4.18
26 27 1.214325 CCACATACAGACGCACCGA 59.786 57.895 0.00 0.00 0.00 4.69
27 28 1.076533 CCACATACAGACGCACCGAC 61.077 60.000 0.00 0.00 0.00 4.79
32 33 0.604511 TACAGACGCACCGACAGAGA 60.605 55.000 0.00 0.00 0.00 3.10
84 85 3.141398 CTGTTGTATGTCAGCCTGTGTT 58.859 45.455 0.00 0.00 0.00 3.32
85 86 4.314961 CTGTTGTATGTCAGCCTGTGTTA 58.685 43.478 0.00 0.00 0.00 2.41
86 87 4.905429 TGTTGTATGTCAGCCTGTGTTAT 58.095 39.130 0.00 0.00 0.00 1.89
116 123 4.703575 AGCTAGCTTGCAAATGAAATCAGA 59.296 37.500 22.05 0.00 34.99 3.27
118 125 3.846360 AGCTTGCAAATGAAATCAGAGC 58.154 40.909 0.00 0.00 0.00 4.09
132 139 8.349568 TGAAATCAGAGCTCTACTTGTAGTAA 57.650 34.615 17.75 0.00 29.00 2.24
169 179 6.969993 ACAGGGATATCTCAACTTCTACTC 57.030 41.667 5.15 0.00 0.00 2.59
174 184 6.348704 GGGATATCTCAACTTCTACTCTACGC 60.349 46.154 2.05 0.00 0.00 4.42
184 194 9.517609 CAACTTCTACTCTACGCAGTTTATTAT 57.482 33.333 0.00 0.00 37.78 1.28
234 253 8.037758 CACAAGTAGGAGGGATACATAATGATC 58.962 40.741 0.00 0.00 39.74 2.92
262 281 1.727467 GCAGTTGCACCACTCGTTT 59.273 52.632 0.00 0.00 41.59 3.60
268 287 1.279840 GCACCACTCGTTTGTCAGC 59.720 57.895 0.00 0.00 0.00 4.26
287 306 3.488678 CAGCTACGAGCACATGATAACTG 59.511 47.826 0.00 0.00 45.56 3.16
327 346 6.018994 GTCAAATTTAGTTACGCGAGGATGAT 60.019 38.462 15.93 0.00 0.00 2.45
343 362 6.093495 CGAGGATGATAACTTTAGTTGGCAAA 59.907 38.462 0.00 0.00 38.90 3.68
344 363 7.201732 CGAGGATGATAACTTTAGTTGGCAAAT 60.202 37.037 5.23 5.23 38.90 2.32
395 421 3.399330 ACCAGAAACTTACCATGTGTCG 58.601 45.455 0.00 0.00 0.00 4.35
398 424 4.242475 CAGAAACTTACCATGTGTCGCTA 58.758 43.478 0.00 0.00 0.00 4.26
433 459 0.318869 TAGAAAAACGTCAGCGCCGA 60.319 50.000 11.49 0.00 42.83 5.54
481 514 8.215050 TGGACTTATCATTTGGGTCGTAATATT 58.785 33.333 0.00 0.00 0.00 1.28
513 547 0.250295 TTTGCTTAGCTGCCAGACGT 60.250 50.000 5.60 0.00 0.00 4.34
525 559 4.201753 GCTGCCAGACGTATATATGCAATG 60.202 45.833 0.00 0.00 0.00 2.82
541 576 2.296792 CAATGGATCATGGCCACGTAA 58.703 47.619 8.16 0.00 38.44 3.18
593 628 2.344441 CGTCACGCGTATCATCAACTTT 59.656 45.455 13.44 0.00 35.54 2.66
603 638 1.337703 TCATCAACTTTGCAGTGTGGC 59.662 47.619 0.00 0.00 31.60 5.01
679 731 1.605710 GCTACCATGCATGCGATTTCT 59.394 47.619 21.69 1.47 0.00 2.52
682 734 1.315690 CCATGCATGCGATTTCTCCT 58.684 50.000 21.69 0.00 0.00 3.69
685 741 2.689553 TGCATGCGATTTCTCCTGTA 57.310 45.000 14.09 0.00 0.00 2.74
686 742 2.279741 TGCATGCGATTTCTCCTGTAC 58.720 47.619 14.09 0.00 0.00 2.90
687 743 1.258982 GCATGCGATTTCTCCTGTACG 59.741 52.381 0.00 0.00 0.00 3.67
688 744 2.540515 CATGCGATTTCTCCTGTACGT 58.459 47.619 0.00 0.00 0.00 3.57
701 757 8.510243 TTCTCCTGTACGTGACTATAAATACA 57.490 34.615 0.00 0.00 0.00 2.29
702 758 8.151141 TCTCCTGTACGTGACTATAAATACAG 57.849 38.462 0.00 0.00 39.36 2.74
708 764 6.068473 ACGTGACTATAAATACAGATGCGA 57.932 37.500 0.00 0.00 0.00 5.10
713 769 8.600625 GTGACTATAAATACAGATGCGAAACAA 58.399 33.333 0.00 0.00 0.00 2.83
716 772 8.604035 ACTATAAATACAGATGCGAAACAACAG 58.396 33.333 0.00 0.00 0.00 3.16
762 824 1.534729 TCGAGCAAGAGTAGCTGACA 58.465 50.000 0.00 0.00 43.58 3.58
826 888 2.968206 GTACTCGGTTCCGTGGCT 59.032 61.111 15.78 1.15 0.00 4.75
834 896 2.597217 TTCCGTGGCTTGCCAAGG 60.597 61.111 31.35 31.35 39.96 3.61
840 902 2.272146 GGCTTGCCAAGGATCCGA 59.728 61.111 5.98 0.00 0.00 4.55
862 924 1.120530 ACGGCTACACCTATCCCAAG 58.879 55.000 0.00 0.00 35.61 3.61
863 925 0.249911 CGGCTACACCTATCCCAAGC 60.250 60.000 0.00 0.00 35.61 4.01
864 926 0.108774 GGCTACACCTATCCCAAGCC 59.891 60.000 0.00 0.00 42.40 4.35
865 927 0.108774 GCTACACCTATCCCAAGCCC 59.891 60.000 0.00 0.00 0.00 5.19
866 928 0.393077 CTACACCTATCCCAAGCCCG 59.607 60.000 0.00 0.00 0.00 6.13
867 929 0.031917 TACACCTATCCCAAGCCCGA 60.032 55.000 0.00 0.00 0.00 5.14
886 948 0.697854 ACCCCACTCCCATCATACCC 60.698 60.000 0.00 0.00 0.00 3.69
887 949 0.401979 CCCCACTCCCATCATACCCT 60.402 60.000 0.00 0.00 0.00 4.34
898 960 4.424867 ATACCCTCGCCCCCACCA 62.425 66.667 0.00 0.00 0.00 4.17
911 973 4.003788 CACCACCGGCGACTCCTT 62.004 66.667 9.30 0.00 0.00 3.36
928 991 1.961180 CTTCGTCGAGCCTTCCCCAT 61.961 60.000 0.00 0.00 0.00 4.00
936 999 2.308722 GCCTTCCCCATCTCCACCA 61.309 63.158 0.00 0.00 0.00 4.17
938 1001 0.916358 CCTTCCCCATCTCCACCAGT 60.916 60.000 0.00 0.00 0.00 4.00
947 1010 3.370104 CATCTCCACCAGTTACTCCTCT 58.630 50.000 0.00 0.00 0.00 3.69
1038 2888 2.265096 GGTTTCTCCTCCGACGAGT 58.735 57.895 0.00 0.00 33.93 4.18
1060 2922 2.781174 CCTACTCCACCTCCTACTCTCT 59.219 54.545 0.00 0.00 0.00 3.10
1062 2924 1.567175 ACTCCACCTCCTACTCTCTCC 59.433 57.143 0.00 0.00 0.00 3.71
1072 2934 1.581923 TACTCTCTCCCCGAGCCCTT 61.582 60.000 0.00 0.00 39.70 3.95
1094 2956 0.542232 CCTACCCCGGTCTATCCCAG 60.542 65.000 0.00 0.00 0.00 4.45
1110 2978 4.918360 AGCCCCACTCCCACCACA 62.918 66.667 0.00 0.00 0.00 4.17
1135 3009 2.687566 CCCCACCGGCTTCTACCT 60.688 66.667 0.00 0.00 0.00 3.08
1142 3016 0.396695 CCGGCTTCTACCTCTACCCA 60.397 60.000 0.00 0.00 0.00 4.51
1303 3184 4.700213 GCTTTGTCCAGGTACACATACATT 59.300 41.667 0.00 0.00 32.40 2.71
1306 3187 5.084818 TGTCCAGGTACACATACATTCAG 57.915 43.478 0.00 0.00 32.40 3.02
1329 3212 4.739046 CGCAAGTGAAGTTTGAGAGATT 57.261 40.909 0.00 0.00 0.00 2.40
1330 3213 4.461405 CGCAAGTGAAGTTTGAGAGATTG 58.539 43.478 0.00 0.00 0.00 2.67
1334 3217 7.201591 CGCAAGTGAAGTTTGAGAGATTGATAT 60.202 37.037 0.00 0.00 0.00 1.63
1335 3218 9.102757 GCAAGTGAAGTTTGAGAGATTGATATA 57.897 33.333 0.00 0.00 0.00 0.86
1337 3220 8.864069 AGTGAAGTTTGAGAGATTGATATACG 57.136 34.615 0.00 0.00 0.00 3.06
1338 3221 7.436673 AGTGAAGTTTGAGAGATTGATATACGC 59.563 37.037 0.00 0.00 0.00 4.42
1339 3222 6.701841 TGAAGTTTGAGAGATTGATATACGCC 59.298 38.462 0.00 0.00 0.00 5.68
1340 3223 6.412362 AGTTTGAGAGATTGATATACGCCT 57.588 37.500 0.00 0.00 0.00 5.52
1341 3224 7.526142 AGTTTGAGAGATTGATATACGCCTA 57.474 36.000 0.00 0.00 0.00 3.93
1398 3311 1.981256 ATCGTTGCTTTCAGGGTTGT 58.019 45.000 0.00 0.00 0.00 3.32
1413 3326 1.677217 GGTTGTGATGCCTCTGTCCTC 60.677 57.143 0.00 0.00 0.00 3.71
1452 3365 1.078143 GCCTGAACCGGAGATGCTT 60.078 57.895 9.46 0.00 0.00 3.91
1648 3578 2.442272 ACGGATGAGACCCTCCCG 60.442 66.667 9.16 9.16 39.80 5.14
1654 3584 0.252742 ATGAGACCCTCCCGAACCTT 60.253 55.000 0.00 0.00 0.00 3.50
1663 3593 2.933834 CCGAACCTTCCCCCACCT 60.934 66.667 0.00 0.00 0.00 4.00
1675 3605 2.268076 CCCACCTTTCGCCAACCTG 61.268 63.158 0.00 0.00 0.00 4.00
1680 3610 1.628846 ACCTTTCGCCAACCTGACTAT 59.371 47.619 0.00 0.00 0.00 2.12
1693 3623 6.406370 CAACCTGACTATCCTCACACAAATA 58.594 40.000 0.00 0.00 0.00 1.40
1719 3649 2.586425 CAAGAAGGGACTCAGCCAAAA 58.414 47.619 0.00 0.00 38.49 2.44
1720 3650 3.160269 CAAGAAGGGACTCAGCCAAAAT 58.840 45.455 0.00 0.00 38.49 1.82
1722 3652 2.108952 AGAAGGGACTCAGCCAAAATGT 59.891 45.455 0.00 0.00 38.49 2.71
1730 3662 0.031857 CAGCCAAAATGTCGGTTGCA 59.968 50.000 0.00 0.00 0.00 4.08
1817 3749 0.462937 CCAACGACAACTCCACCACA 60.463 55.000 0.00 0.00 0.00 4.17
1832 3764 2.173669 CACATCGATGGACGCCACC 61.174 63.158 28.09 0.00 42.26 4.61
1850 3782 1.608717 CCTACGCTGGGAAGCTGACT 61.609 60.000 0.00 0.00 0.00 3.41
1877 3809 2.063979 CCCTGCCGGTAGTGATCCA 61.064 63.158 18.86 0.00 0.00 3.41
2075 4007 0.617935 TCGAGGATGCCATGGTGAAA 59.382 50.000 14.67 0.00 0.00 2.69
2087 4019 4.686670 GCCATGGTGAAAATGGGCAATATT 60.687 41.667 14.67 0.00 44.13 1.28
2192 4125 6.211584 TCAAGGGTGGAGACTATATATTCAGC 59.788 42.308 3.24 0.00 0.00 4.26
2197 4130 4.462834 TGGAGACTATATATTCAGCCGTGG 59.537 45.833 3.24 0.00 0.00 4.94
2204 4137 2.715737 TATTCAGCCGTGGTTTTTGC 57.284 45.000 0.00 0.00 0.00 3.68
2224 4161 1.338105 CGTGTGCCTTCTGATCTTCCA 60.338 52.381 0.00 0.00 0.00 3.53
2269 4211 1.504359 TTCGCTCGTCGGTTCATTTT 58.496 45.000 0.00 0.00 39.05 1.82
2336 4278 0.388907 CGGGCAATGCTTTTCACTGG 60.389 55.000 4.82 0.00 0.00 4.00
2474 4423 3.118738 CCTAGAGTGTGTATGGTCAACCC 60.119 52.174 0.00 0.00 34.29 4.11
2520 4469 4.523173 CCTTTTCTTTTGAGGGAGGGTAAC 59.477 45.833 0.00 0.00 0.00 2.50
2522 4471 4.799715 TTCTTTTGAGGGAGGGTAACAA 57.200 40.909 0.00 0.00 39.74 2.83
2555 4504 8.485976 ACTAAGTGCTCTATCAAAATCAGTTC 57.514 34.615 0.00 0.00 0.00 3.01
2565 4514 8.474831 TCTATCAAAATCAGTTCGTATGAAGGA 58.525 33.333 0.00 0.00 33.98 3.36
2566 4515 6.721571 TCAAAATCAGTTCGTATGAAGGAC 57.278 37.500 0.00 0.00 33.98 3.85
2590 4539 4.342665 CCCTACTTCTTACTCCTAAGCCAG 59.657 50.000 0.00 0.00 30.85 4.85
2618 4567 2.783510 TCTGGTTCCTCCCTTTTCAGTT 59.216 45.455 0.00 0.00 34.77 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.739813 GGTGCGTCTGTATGTGGACC 60.740 60.000 0.00 0.00 0.00 4.46
13 14 0.604511 TCTCTGTCGGTGCGTCTGTA 60.605 55.000 0.00 0.00 0.00 2.74
20 21 1.865865 TTCAGTTTCTCTGTCGGTGC 58.134 50.000 0.00 0.00 43.97 5.01
56 57 2.153645 CTGACATACAACAGCTTGCCA 58.846 47.619 0.00 0.00 0.00 4.92
84 85 7.726216 TCATTTGCAAGCTAGCTAGTAGAATA 58.274 34.615 19.70 0.00 34.99 1.75
85 86 6.586344 TCATTTGCAAGCTAGCTAGTAGAAT 58.414 36.000 19.70 11.80 34.99 2.40
86 87 5.977635 TCATTTGCAAGCTAGCTAGTAGAA 58.022 37.500 19.70 10.00 34.99 2.10
262 281 0.887933 TCATGTGCTCGTAGCTGACA 59.112 50.000 0.00 5.74 42.97 3.58
268 287 2.469147 CGCAGTTATCATGTGCTCGTAG 59.531 50.000 4.04 0.00 34.92 3.51
374 400 3.399330 CGACACATGGTAAGTTTCTGGT 58.601 45.455 0.00 0.00 0.00 4.00
375 401 2.159627 GCGACACATGGTAAGTTTCTGG 59.840 50.000 0.00 0.00 0.00 3.86
433 459 2.831685 TGATCAGGTGCGTGTTACTT 57.168 45.000 0.00 0.00 0.00 2.24
481 514 0.539438 AAGCAAATCAACCCGGCTGA 60.539 50.000 6.90 6.90 34.56 4.26
513 547 5.829391 GTGGCCATGATCCATTGCATATATA 59.171 40.000 9.72 0.00 34.73 0.86
525 559 1.148310 CGATTACGTGGCCATGATCC 58.852 55.000 31.74 15.01 34.56 3.36
549 584 2.754995 GGCAGCGGCAGTAAGCTTC 61.755 63.158 11.88 0.00 42.52 3.86
661 700 2.158769 AGGAGAAATCGCATGCATGGTA 60.159 45.455 27.34 8.74 0.00 3.25
662 701 1.027357 GGAGAAATCGCATGCATGGT 58.973 50.000 27.34 0.00 0.00 3.55
663 702 1.001706 CAGGAGAAATCGCATGCATGG 60.002 52.381 27.34 17.21 0.00 3.66
679 731 8.565416 CATCTGTATTTATAGTCACGTACAGGA 58.435 37.037 7.67 0.00 39.44 3.86
682 734 6.854381 CGCATCTGTATTTATAGTCACGTACA 59.146 38.462 0.00 0.00 0.00 2.90
685 741 6.068473 TCGCATCTGTATTTATAGTCACGT 57.932 37.500 0.00 0.00 0.00 4.49
686 742 6.986424 TTCGCATCTGTATTTATAGTCACG 57.014 37.500 0.00 0.00 0.00 4.35
687 743 8.126871 TGTTTCGCATCTGTATTTATAGTCAC 57.873 34.615 0.00 0.00 0.00 3.67
688 744 8.600625 GTTGTTTCGCATCTGTATTTATAGTCA 58.399 33.333 0.00 0.00 0.00 3.41
701 757 3.632145 AGAAAACCTGTTGTTTCGCATCT 59.368 39.130 0.00 0.00 46.39 2.90
702 758 3.964909 AGAAAACCTGTTGTTTCGCATC 58.035 40.909 0.00 0.00 46.39 3.91
713 769 6.887002 GGGAAGATAGAATGAAGAAAACCTGT 59.113 38.462 0.00 0.00 0.00 4.00
716 772 6.258947 CGAGGGAAGATAGAATGAAGAAAACC 59.741 42.308 0.00 0.00 0.00 3.27
728 784 2.224548 TGCTCGATCGAGGGAAGATAGA 60.225 50.000 38.18 5.94 42.19 1.98
730 786 2.271944 TGCTCGATCGAGGGAAGATA 57.728 50.000 38.18 10.15 42.19 1.98
762 824 1.519719 GCCATCTTCCTCTGCTCGT 59.480 57.895 0.00 0.00 0.00 4.18
811 873 2.030562 CAAGCCACGGAACCGAGT 59.969 61.111 20.14 0.00 42.83 4.18
826 888 0.174845 CGTAGTCGGATCCTTGGCAA 59.825 55.000 10.75 0.00 0.00 4.52
840 902 1.216175 TGGGATAGGTGTAGCCGTAGT 59.784 52.381 0.00 0.00 43.70 2.73
863 925 3.480133 GATGGGAGTGGGGTCGGG 61.480 72.222 0.00 0.00 0.00 5.14
864 926 0.762842 TATGATGGGAGTGGGGTCGG 60.763 60.000 0.00 0.00 0.00 4.79
865 927 0.393077 GTATGATGGGAGTGGGGTCG 59.607 60.000 0.00 0.00 0.00 4.79
866 928 0.765510 GGTATGATGGGAGTGGGGTC 59.234 60.000 0.00 0.00 0.00 4.46
867 929 0.697854 GGGTATGATGGGAGTGGGGT 60.698 60.000 0.00 0.00 0.00 4.95
904 966 0.179158 GAAGGCTCGACGAAGGAGTC 60.179 60.000 0.00 0.00 36.40 3.36
911 973 2.363795 ATGGGGAAGGCTCGACGA 60.364 61.111 0.00 0.00 0.00 4.20
914 976 1.762460 GGAGATGGGGAAGGCTCGA 60.762 63.158 0.00 0.00 0.00 4.04
928 991 2.808919 CAGAGGAGTAACTGGTGGAGA 58.191 52.381 0.00 0.00 0.00 3.71
936 999 1.268283 GGCTGGGCAGAGGAGTAACT 61.268 60.000 0.00 0.00 0.00 2.24
938 1001 1.995626 GGGCTGGGCAGAGGAGTAA 60.996 63.158 0.00 0.00 0.00 2.24
967 1030 2.529753 GGGATAGCCCGGGGTAGA 59.470 66.667 33.98 18.06 46.48 2.59
1038 2888 2.778850 GAGAGTAGGAGGTGGAGTAGGA 59.221 54.545 0.00 0.00 0.00 2.94
1060 2922 2.322156 TAGGAGAAGGGCTCGGGGA 61.322 63.158 0.00 0.00 44.91 4.81
1062 2924 2.134933 GGTAGGAGAAGGGCTCGGG 61.135 68.421 0.00 0.00 44.91 5.14
1072 2934 0.776176 GGATAGACCGGGGTAGGAGA 59.224 60.000 6.32 0.00 34.73 3.71
1094 2956 4.660938 GTGTGGTGGGAGTGGGGC 62.661 72.222 0.00 0.00 0.00 5.80
1135 3009 1.306141 CAGGTGGAGGCTGGGTAGA 60.306 63.158 0.00 0.00 0.00 2.59
1142 3016 3.644606 CAGTGGCAGGTGGAGGCT 61.645 66.667 0.00 0.00 0.00 4.58
1263 3144 1.621992 AGCAGTCGTGGAAGAAGAGA 58.378 50.000 0.00 0.00 0.00 3.10
1303 3184 2.866156 CTCAAACTTCACTTGCGTCTGA 59.134 45.455 0.00 0.00 0.00 3.27
1306 3187 3.123804 TCTCTCAAACTTCACTTGCGTC 58.876 45.455 0.00 0.00 0.00 5.19
1329 3212 5.243060 AGTGCACAACTATAGGCGTATATCA 59.757 40.000 21.04 0.00 37.36 2.15
1330 3213 5.573282 CAGTGCACAACTATAGGCGTATATC 59.427 44.000 21.04 0.00 36.83 1.63
1334 3217 2.737359 GCAGTGCACAACTATAGGCGTA 60.737 50.000 21.04 0.00 36.83 4.42
1335 3218 2.007049 GCAGTGCACAACTATAGGCGT 61.007 52.381 21.04 0.00 36.83 5.68
1337 3220 1.737838 TGCAGTGCACAACTATAGGC 58.262 50.000 21.04 9.34 36.83 3.93
1398 3311 0.041684 TCAGGAGGACAGAGGCATCA 59.958 55.000 0.00 0.00 0.00 3.07
1427 3340 2.597217 CCGGTTCAGGCTTGCCAA 60.597 61.111 14.54 0.00 0.00 4.52
1527 3440 4.357947 GCGCAGGAGACGACACCA 62.358 66.667 0.30 0.00 0.00 4.17
1629 3542 1.381327 GGGAGGGTCTCATCCGTCA 60.381 63.158 7.53 0.00 44.27 4.35
1648 3578 0.608308 CGAAAGGTGGGGGAAGGTTC 60.608 60.000 0.00 0.00 0.00 3.62
1654 3584 3.179339 TTGGCGAAAGGTGGGGGA 61.179 61.111 0.00 0.00 0.00 4.81
1663 3593 1.906574 AGGATAGTCAGGTTGGCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
1675 3605 5.177696 GGCGAATATTTGTGTGAGGATAGTC 59.822 44.000 4.60 0.00 0.00 2.59
1680 3610 3.342377 TGGCGAATATTTGTGTGAGGA 57.658 42.857 4.60 0.00 0.00 3.71
1693 3623 0.984230 TGAGTCCCTTCTTGGCGAAT 59.016 50.000 0.00 0.00 0.00 3.34
1760 3692 2.286523 ACGGAAGGAGGAGCAGTGG 61.287 63.158 0.00 0.00 0.00 4.00
1817 3749 1.740285 GTAGGTGGCGTCCATCGAT 59.260 57.895 0.00 0.00 40.09 3.59
1877 3809 3.307906 TAGTCCTGCGGCACCGTT 61.308 61.111 11.27 0.00 42.09 4.44
2075 4007 4.870636 TCTTCACCTCAATATTGCCCATT 58.129 39.130 10.76 0.00 0.00 3.16
2087 4019 3.706055 GGTGCTGTTCTTCACCTCA 57.294 52.632 4.31 0.00 46.90 3.86
2192 4125 2.227568 GCACACGCAAAAACCACGG 61.228 57.895 0.00 0.00 38.36 4.94
2197 4130 1.199624 CAGAAGGCACACGCAAAAAC 58.800 50.000 0.00 0.00 41.24 2.43
2204 4137 1.338105 TGGAAGATCAGAAGGCACACG 60.338 52.381 0.00 0.00 0.00 4.49
2252 4193 3.061563 TGAATAAAATGAACCGACGAGCG 59.938 43.478 0.00 0.00 40.47 5.03
2477 4426 1.808945 GAGTGTTTGCATCCAGTCAGG 59.191 52.381 13.35 0.00 39.47 3.86
2478 4427 1.808945 GGAGTGTTTGCATCCAGTCAG 59.191 52.381 17.75 0.00 33.57 3.51
2492 4441 4.464947 CTCCCTCAAAAGAAAAGGAGTGT 58.535 43.478 0.00 0.00 36.87 3.55
2493 4442 3.823304 CCTCCCTCAAAAGAAAAGGAGTG 59.177 47.826 0.00 0.00 39.43 3.51
2520 4469 8.932945 TGATAGAGCACTTAGTAGAATTGTTG 57.067 34.615 0.00 0.00 0.00 3.33
2522 4471 9.944376 TTTTGATAGAGCACTTAGTAGAATTGT 57.056 29.630 0.00 0.00 0.00 2.71
2555 4504 3.297736 AGAAGTAGGGGTCCTTCATACG 58.702 50.000 0.00 0.00 39.61 3.06
2565 4514 4.288398 GCTTAGGAGTAAGAAGTAGGGGT 58.712 47.826 0.00 0.00 38.39 4.95
2566 4515 3.642377 GGCTTAGGAGTAAGAAGTAGGGG 59.358 52.174 0.00 0.00 38.39 4.79


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

AutoCloner maintained by Alex Coulton.