Multiple sequence alignment - TraesCS4D01G101900

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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 TraesCS4D01G101900 chr4D 100.000 3466 0 0 1 3466 80147784 80144319 0.000000e+00 6401
1 TraesCS4D01G101900 chr4D 98.810 84 1 0 1 84 39617389 39617306 2.150000e-32 150
2 TraesCS4D01G101900 chr4A 96.369 2561 58 13 928 3465 505788833 505791381 0.000000e+00 4181
3 TraesCS4D01G101900 chr4A 86.474 658 49 19 300 943 139995507 139994876 0.000000e+00 686
4 TraesCS4D01G101900 chr4A 86.818 220 21 6 81 294 505788623 505788840 4.470000e-59 239
5 TraesCS4D01G101900 chr4B 96.024 2540 92 6 928 3465 112357311 112354779 0.000000e+00 4122
6 TraesCS4D01G101900 chr4B 86.551 632 57 14 300 927 628035021 628034414 0.000000e+00 671
7 TraesCS4D01G101900 chr4B 85.581 645 74 11 298 927 416118667 416119307 0.000000e+00 658
8 TraesCS4D01G101900 chr6B 88.025 643 39 17 300 927 664720250 664720869 0.000000e+00 726
9 TraesCS4D01G101900 chr6B 84.664 639 55 22 298 927 702381145 702380541 6.400000e-167 597
10 TraesCS4D01G101900 chr3A 87.618 638 55 10 300 923 609257796 609257169 0.000000e+00 719
11 TraesCS4D01G101900 chr3A 87.383 642 44 16 300 927 13156316 13156934 0.000000e+00 702
12 TraesCS4D01G101900 chr2B 87.816 632 50 7 300 927 217413987 217414595 0.000000e+00 715
13 TraesCS4D01G101900 chr7A 87.307 646 44 19 298 929 644460270 644459649 0.000000e+00 704
14 TraesCS4D01G101900 chr7A 86.781 643 48 17 300 928 81564809 81565428 0.000000e+00 682
15 TraesCS4D01G101900 chr2A 87.247 643 42 19 301 927 84609972 84610590 0.000000e+00 697
16 TraesCS4D01G101900 chr2A 81.250 160 11 3 2976 3129 779202844 779202990 1.020000e-20 111
17 TraesCS4D01G101900 chr6A 86.730 633 53 12 300 928 517998493 517997888 0.000000e+00 675
18 TraesCS4D01G101900 chr6A 86.688 631 55 9 302 928 19414840 19414235 0.000000e+00 673
19 TraesCS4D01G101900 chr2D 86.217 653 54 20 298 935 638418913 638418282 0.000000e+00 675
20 TraesCS4D01G101900 chr7B 86.371 631 57 14 300 927 115255585 115254981 0.000000e+00 662
21 TraesCS4D01G101900 chr1B 85.354 635 63 10 298 927 453515952 453516561 6.310000e-177 630
22 TraesCS4D01G101900 chr3B 80.913 241 34 6 299 536 391478991 391479222 2.750000e-41 180
23 TraesCS4D01G101900 chr3B 98.824 85 1 0 1 85 216063798 216063714 5.990000e-33 152
24 TraesCS4D01G101900 chrUn 100.000 83 0 0 2 84 69975597 69975515 1.670000e-33 154
25 TraesCS4D01G101900 chrUn 100.000 83 0 0 2 84 284702093 284702011 1.670000e-33 154
26 TraesCS4D01G101900 chr6D 100.000 83 0 0 2 84 85400256 85400338 1.670000e-33 154
27 TraesCS4D01G101900 chr6D 98.810 84 1 0 1 84 125501777 125501860 2.150000e-32 150
28 TraesCS4D01G101900 chr1D 98.810 84 1 0 1 84 119336836 119336919 2.150000e-32 150
29 TraesCS4D01G101900 chr1D 98.810 84 1 0 1 84 261020040 261020123 2.150000e-32 150
30 TraesCS4D01G101900 chr1D 98.810 84 1 0 1 84 483341813 483341730 2.150000e-32 150


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 TraesCS4D01G101900 chr4D 80144319 80147784 3465 True 6401 6401 100.0000 1 3466 1 chr4D.!!$R2 3465
1 TraesCS4D01G101900 chr4A 505788623 505791381 2758 False 2210 4181 91.5935 81 3465 2 chr4A.!!$F1 3384
2 TraesCS4D01G101900 chr4A 139994876 139995507 631 True 686 686 86.4740 300 943 1 chr4A.!!$R1 643
3 TraesCS4D01G101900 chr4B 112354779 112357311 2532 True 4122 4122 96.0240 928 3465 1 chr4B.!!$R1 2537
4 TraesCS4D01G101900 chr4B 628034414 628035021 607 True 671 671 86.5510 300 927 1 chr4B.!!$R2 627
5 TraesCS4D01G101900 chr4B 416118667 416119307 640 False 658 658 85.5810 298 927 1 chr4B.!!$F1 629
6 TraesCS4D01G101900 chr6B 664720250 664720869 619 False 726 726 88.0250 300 927 1 chr6B.!!$F1 627
7 TraesCS4D01G101900 chr6B 702380541 702381145 604 True 597 597 84.6640 298 927 1 chr6B.!!$R1 629
8 TraesCS4D01G101900 chr3A 609257169 609257796 627 True 719 719 87.6180 300 923 1 chr3A.!!$R1 623
9 TraesCS4D01G101900 chr3A 13156316 13156934 618 False 702 702 87.3830 300 927 1 chr3A.!!$F1 627
10 TraesCS4D01G101900 chr2B 217413987 217414595 608 False 715 715 87.8160 300 927 1 chr2B.!!$F1 627
11 TraesCS4D01G101900 chr7A 644459649 644460270 621 True 704 704 87.3070 298 929 1 chr7A.!!$R1 631
12 TraesCS4D01G101900 chr7A 81564809 81565428 619 False 682 682 86.7810 300 928 1 chr7A.!!$F1 628
13 TraesCS4D01G101900 chr2A 84609972 84610590 618 False 697 697 87.2470 301 927 1 chr2A.!!$F1 626
14 TraesCS4D01G101900 chr6A 517997888 517998493 605 True 675 675 86.7300 300 928 1 chr6A.!!$R2 628
15 TraesCS4D01G101900 chr6A 19414235 19414840 605 True 673 673 86.6880 302 928 1 chr6A.!!$R1 626
16 TraesCS4D01G101900 chr2D 638418282 638418913 631 True 675 675 86.2170 298 935 1 chr2D.!!$R1 637
17 TraesCS4D01G101900 chr7B 115254981 115255585 604 True 662 662 86.3710 300 927 1 chr7B.!!$R1 627
18 TraesCS4D01G101900 chr1B 453515952 453516561 609 False 630 630 85.3540 298 927 1 chr1B.!!$F1 629

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
49 50 0.108377 TGACGTGGCATCATTAGCGT 60.108 50.0 0.0 0.0 35.20 5.07 F
50 51 0.301687 GACGTGGCATCATTAGCGTG 59.698 55.0 0.0 0.0 32.56 5.34 F
169 170 0.464373 CGCAGGGCTAACATCATGGT 60.464 55.0 0.0 0.0 0.00 3.55 F
254 260 0.903454 GGGGAAGAAGACGACCCTCA 60.903 60.0 0.0 0.0 41.79 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1435 0.833287 CATCGGTGACAAGGGATCCT 59.167 55.000 12.58 0.0 33.87 3.24 R
1988 2079 2.262915 GCAGCAGCGTGTAGAGGT 59.737 61.111 0.00 0.0 0.00 3.85 R
2374 2465 7.172868 TCGGTGATTTACAGATAAGGTGTTA 57.827 36.000 0.00 0.0 0.00 2.41 R
2614 2705 4.886496 ACTTAGGAGGACAAAGGTGTAC 57.114 45.455 0.00 0.0 38.41 2.90 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
25 26 3.922240 TCGCGAGATTAACAACAGTAACC 59.078 43.478 3.71 0.00 33.31 2.85
26 27 3.241552 CGCGAGATTAACAACAGTAACCG 60.242 47.826 0.00 0.00 0.00 4.44
27 28 3.922240 GCGAGATTAACAACAGTAACCGA 59.078 43.478 0.00 0.00 0.00 4.69
28 29 4.031426 GCGAGATTAACAACAGTAACCGAG 59.969 45.833 0.00 0.00 0.00 4.63
29 30 4.561606 CGAGATTAACAACAGTAACCGAGG 59.438 45.833 0.00 0.00 0.00 4.63
30 31 5.476614 GAGATTAACAACAGTAACCGAGGT 58.523 41.667 0.00 0.00 0.00 3.85
31 32 5.235516 AGATTAACAACAGTAACCGAGGTG 58.764 41.667 0.00 0.00 0.00 4.00
32 33 4.669206 TTAACAACAGTAACCGAGGTGA 57.331 40.909 0.00 0.00 0.00 4.02
33 34 2.521105 ACAACAGTAACCGAGGTGAC 57.479 50.000 1.38 1.38 0.00 3.67
34 35 1.269413 ACAACAGTAACCGAGGTGACG 60.269 52.381 4.20 2.83 34.72 4.35
35 36 1.035139 AACAGTAACCGAGGTGACGT 58.965 50.000 4.20 0.00 34.72 4.34
36 37 0.313043 ACAGTAACCGAGGTGACGTG 59.687 55.000 0.00 6.04 34.72 4.49
37 38 0.388134 CAGTAACCGAGGTGACGTGG 60.388 60.000 0.00 0.00 34.72 4.94
38 39 1.735559 GTAACCGAGGTGACGTGGC 60.736 63.158 0.00 0.00 33.35 5.01
39 40 2.201708 TAACCGAGGTGACGTGGCA 61.202 57.895 0.00 0.00 33.35 4.92
40 41 1.537814 TAACCGAGGTGACGTGGCAT 61.538 55.000 0.00 0.00 33.35 4.40
41 42 2.509336 CCGAGGTGACGTGGCATC 60.509 66.667 0.00 0.00 0.00 3.91
42 43 2.261361 CGAGGTGACGTGGCATCA 59.739 61.111 0.00 0.00 0.00 3.07
43 44 1.153568 CGAGGTGACGTGGCATCAT 60.154 57.895 0.00 0.00 0.00 2.45
44 45 0.740868 CGAGGTGACGTGGCATCATT 60.741 55.000 0.00 0.00 0.00 2.57
45 46 1.470805 CGAGGTGACGTGGCATCATTA 60.471 52.381 0.00 0.00 0.00 1.90
46 47 2.205074 GAGGTGACGTGGCATCATTAG 58.795 52.381 0.00 0.00 0.00 1.73
47 48 0.657840 GGTGACGTGGCATCATTAGC 59.342 55.000 0.00 0.00 0.00 3.09
48 49 0.301687 GTGACGTGGCATCATTAGCG 59.698 55.000 0.00 0.00 0.00 4.26
49 50 0.108377 TGACGTGGCATCATTAGCGT 60.108 50.000 0.00 0.00 35.20 5.07
50 51 0.301687 GACGTGGCATCATTAGCGTG 59.698 55.000 0.00 0.00 32.56 5.34
51 52 1.089481 ACGTGGCATCATTAGCGTGG 61.089 55.000 0.00 0.00 0.00 4.94
52 53 0.809636 CGTGGCATCATTAGCGTGGA 60.810 55.000 0.00 0.00 0.00 4.02
53 54 1.378531 GTGGCATCATTAGCGTGGAA 58.621 50.000 0.00 0.00 0.00 3.53
54 55 1.949525 GTGGCATCATTAGCGTGGAAT 59.050 47.619 0.00 0.00 0.00 3.01
55 56 2.358898 GTGGCATCATTAGCGTGGAATT 59.641 45.455 0.00 0.00 0.00 2.17
56 57 3.563808 GTGGCATCATTAGCGTGGAATTA 59.436 43.478 0.00 0.00 0.00 1.40
57 58 3.563808 TGGCATCATTAGCGTGGAATTAC 59.436 43.478 0.00 0.00 0.00 1.89
58 59 3.815401 GGCATCATTAGCGTGGAATTACT 59.185 43.478 0.00 0.00 0.00 2.24
59 60 4.319766 GGCATCATTAGCGTGGAATTACTG 60.320 45.833 0.00 0.00 0.00 2.74
60 61 4.273480 GCATCATTAGCGTGGAATTACTGT 59.727 41.667 0.00 0.00 0.00 3.55
61 62 5.465390 GCATCATTAGCGTGGAATTACTGTA 59.535 40.000 0.00 0.00 0.00 2.74
62 63 6.346919 GCATCATTAGCGTGGAATTACTGTAG 60.347 42.308 0.00 0.00 0.00 2.74
63 64 5.047847 TCATTAGCGTGGAATTACTGTAGC 58.952 41.667 0.00 0.00 0.00 3.58
64 65 4.730949 TTAGCGTGGAATTACTGTAGCT 57.269 40.909 0.00 0.00 37.48 3.32
65 66 3.611766 AGCGTGGAATTACTGTAGCTT 57.388 42.857 0.00 0.00 0.00 3.74
66 67 4.730949 AGCGTGGAATTACTGTAGCTTA 57.269 40.909 0.00 0.00 0.00 3.09
67 68 5.080969 AGCGTGGAATTACTGTAGCTTAA 57.919 39.130 0.00 0.00 0.00 1.85
68 69 5.671493 AGCGTGGAATTACTGTAGCTTAAT 58.329 37.500 0.00 0.00 0.00 1.40
69 70 6.113411 AGCGTGGAATTACTGTAGCTTAATT 58.887 36.000 0.00 0.00 31.86 1.40
70 71 7.270047 AGCGTGGAATTACTGTAGCTTAATTA 58.730 34.615 0.00 0.00 29.81 1.40
71 72 7.931948 AGCGTGGAATTACTGTAGCTTAATTAT 59.068 33.333 0.00 0.00 29.81 1.28
72 73 8.221766 GCGTGGAATTACTGTAGCTTAATTATC 58.778 37.037 0.00 0.00 29.81 1.75
73 74 8.709646 CGTGGAATTACTGTAGCTTAATTATCC 58.290 37.037 0.00 0.00 29.81 2.59
74 75 8.709646 GTGGAATTACTGTAGCTTAATTATCCG 58.290 37.037 0.00 0.00 29.81 4.18
75 76 7.876068 TGGAATTACTGTAGCTTAATTATCCGG 59.124 37.037 0.00 0.00 29.81 5.14
76 77 7.333672 GGAATTACTGTAGCTTAATTATCCGGG 59.666 40.741 0.00 0.00 29.81 5.73
77 78 4.004196 ACTGTAGCTTAATTATCCGGGC 57.996 45.455 0.00 0.00 0.00 6.13
78 79 2.993899 CTGTAGCTTAATTATCCGGGCG 59.006 50.000 0.00 0.00 0.00 6.13
79 80 2.366266 TGTAGCTTAATTATCCGGGCGT 59.634 45.455 0.00 0.00 0.00 5.68
86 87 0.884704 ATTATCCGGGCGTCACATGC 60.885 55.000 0.00 0.00 0.00 4.06
92 93 4.830765 GGCGTCACATGCGGCCTA 62.831 66.667 0.00 0.00 46.90 3.93
116 117 3.200593 GAGCGACGAGTAGGCCGA 61.201 66.667 0.00 0.00 0.00 5.54
126 127 3.592814 TAGGCCGACGATGGAGCG 61.593 66.667 0.00 0.00 37.29 5.03
143 144 4.326766 GGCAAAAGCGAGCGTGCA 62.327 61.111 18.02 0.00 38.78 4.57
169 170 0.464373 CGCAGGGCTAACATCATGGT 60.464 55.000 0.00 0.00 0.00 3.55
177 178 1.935873 CTAACATCATGGTGTGAGGCG 59.064 52.381 13.50 0.00 42.22 5.52
194 196 2.436646 GGGGCACGTGTGAGATGG 60.437 66.667 18.38 0.00 0.00 3.51
202 204 2.029918 CACGTGTGAGATGGAAGACAGA 60.030 50.000 7.58 0.00 0.00 3.41
205 207 2.828520 GTGTGAGATGGAAGACAGAGGA 59.171 50.000 0.00 0.00 0.00 3.71
206 208 3.095332 TGTGAGATGGAAGACAGAGGAG 58.905 50.000 0.00 0.00 0.00 3.69
214 216 2.654863 GAAGACAGAGGAGAGAGAGGG 58.345 57.143 0.00 0.00 0.00 4.30
215 217 1.681229 AGACAGAGGAGAGAGAGGGT 58.319 55.000 0.00 0.00 0.00 4.34
254 260 0.903454 GGGGAAGAAGACGACCCTCA 60.903 60.000 0.00 0.00 41.79 3.86
277 283 1.779157 CTGATCGTACGGCATACAACG 59.221 52.381 16.52 0.00 36.71 4.10
285 291 2.878580 ACGGCATACAACGAACGAATA 58.121 42.857 0.14 0.00 0.00 1.75
286 292 2.855963 ACGGCATACAACGAACGAATAG 59.144 45.455 0.14 0.00 0.00 1.73
287 293 2.855963 CGGCATACAACGAACGAATAGT 59.144 45.455 0.14 0.00 0.00 2.12
288 294 3.301579 CGGCATACAACGAACGAATAGTG 60.302 47.826 0.14 0.00 0.00 2.74
289 295 3.615496 GGCATACAACGAACGAATAGTGT 59.385 43.478 0.14 0.00 0.00 3.55
290 296 4.491924 GGCATACAACGAACGAATAGTGTG 60.492 45.833 0.14 4.01 0.00 3.82
291 297 4.491924 GCATACAACGAACGAATAGTGTGG 60.492 45.833 0.14 0.00 0.00 4.17
292 298 1.796459 ACAACGAACGAATAGTGTGGC 59.204 47.619 0.14 0.00 0.00 5.01
293 299 2.066262 CAACGAACGAATAGTGTGGCT 58.934 47.619 0.14 0.00 0.00 4.75
294 300 2.450609 ACGAACGAATAGTGTGGCTT 57.549 45.000 0.14 0.00 0.00 4.35
295 301 2.762745 ACGAACGAATAGTGTGGCTTT 58.237 42.857 0.14 0.00 0.00 3.51
296 302 3.135994 ACGAACGAATAGTGTGGCTTTT 58.864 40.909 0.14 0.00 0.00 2.27
328 335 4.705337 TCGGTTTATTGGTTTACATGGC 57.295 40.909 0.00 0.00 0.00 4.40
923 997 2.756829 TCGGTTTTCGTATGCACAGAA 58.243 42.857 0.00 0.00 40.32 3.02
967 1041 1.407656 ATCTCGATTTGGGCCGGCTA 61.408 55.000 28.56 13.55 0.00 3.93
1008 1084 6.351881 GGGATCATTTACTACTCAGAACACCA 60.352 42.308 0.00 0.00 0.00 4.17
1011 1087 7.724305 TCATTTACTACTCAGAACACCAAAC 57.276 36.000 0.00 0.00 0.00 2.93
1020 1096 2.349275 CAGAACACCAAACGTAACGTGT 59.651 45.455 8.24 8.24 39.99 4.49
1043 1119 3.062122 TCCCGTTACAGTGGAAATTCC 57.938 47.619 4.79 4.79 36.96 3.01
1044 1120 2.372504 TCCCGTTACAGTGGAAATTCCA 59.627 45.455 11.23 11.23 45.98 3.53
1070 1146 1.443194 CACAGGCTTGCGCAATGAC 60.443 57.895 25.26 19.30 38.10 3.06
1165 1256 3.649277 CTCTCGTTGGGCGGGACTG 62.649 68.421 0.00 0.00 46.45 3.51
1189 1280 3.834799 GCGTCGGTACCAGAGGGG 61.835 72.222 13.54 4.32 44.81 4.79
1494 1585 2.050714 GACGTTCTCGGCGTGTCA 60.051 61.111 6.85 0.00 43.04 3.58
2216 2307 4.081420 AGCAAATACTGACACTGGGACTAG 60.081 45.833 0.00 0.00 0.00 2.57
2374 2465 3.193479 GCCCTGATTTTCTCCAAATTCGT 59.807 43.478 0.00 0.00 35.02 3.85
2457 2548 2.690497 ACTGATCATACGAGGGACACAG 59.310 50.000 0.00 0.00 0.00 3.66
2460 2551 1.262417 TCATACGAGGGACACAGCAA 58.738 50.000 0.00 0.00 0.00 3.91
2614 2705 4.948847 AGGGCTAAACAGAAAGCAAAAAG 58.051 39.130 0.00 0.00 40.61 2.27
2615 2706 4.405680 AGGGCTAAACAGAAAGCAAAAAGT 59.594 37.500 0.00 0.00 40.61 2.66
2730 2826 7.587037 TCTTCTTGGAGAATCAAATGTTTGT 57.413 32.000 5.48 0.00 33.13 2.83
2907 3003 1.808390 CCGTAACGGGCTAGTGCAC 60.808 63.158 9.40 9.40 44.15 4.57
3438 3535 0.398318 ACCTGACTGAAGCTTGGTCC 59.602 55.000 19.90 2.06 0.00 4.46
3465 3562 6.321181 TCACCCAAGGATGTTCTATTAATTGC 59.679 38.462 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.930040 ACTGTTGTTAATCTCGCGATGG 59.070 45.455 10.36 0.00 0.00 3.51
1 2 5.481472 GTTACTGTTGTTAATCTCGCGATG 58.519 41.667 10.36 3.99 0.00 3.84
2 3 4.565564 GGTTACTGTTGTTAATCTCGCGAT 59.434 41.667 10.36 0.00 0.00 4.58
3 4 3.922240 GGTTACTGTTGTTAATCTCGCGA 59.078 43.478 9.26 9.26 0.00 5.87
4 5 3.241552 CGGTTACTGTTGTTAATCTCGCG 60.242 47.826 0.00 0.00 0.00 5.87
5 6 3.922240 TCGGTTACTGTTGTTAATCTCGC 59.078 43.478 0.00 0.00 0.00 5.03
6 7 4.561606 CCTCGGTTACTGTTGTTAATCTCG 59.438 45.833 0.00 0.00 0.00 4.04
7 8 5.347907 CACCTCGGTTACTGTTGTTAATCTC 59.652 44.000 0.00 0.00 0.00 2.75
8 9 5.011329 TCACCTCGGTTACTGTTGTTAATCT 59.989 40.000 0.00 0.00 0.00 2.40
9 10 5.119743 GTCACCTCGGTTACTGTTGTTAATC 59.880 44.000 0.00 0.00 0.00 1.75
10 11 4.992951 GTCACCTCGGTTACTGTTGTTAAT 59.007 41.667 0.00 0.00 0.00 1.40
11 12 4.370917 GTCACCTCGGTTACTGTTGTTAA 58.629 43.478 0.00 0.00 0.00 2.01
12 13 3.550639 CGTCACCTCGGTTACTGTTGTTA 60.551 47.826 0.00 0.00 0.00 2.41
13 14 2.800629 CGTCACCTCGGTTACTGTTGTT 60.801 50.000 0.00 0.00 0.00 2.83
14 15 1.269413 CGTCACCTCGGTTACTGTTGT 60.269 52.381 0.00 0.00 0.00 3.32
15 16 1.269413 ACGTCACCTCGGTTACTGTTG 60.269 52.381 0.00 0.00 34.94 3.33
16 17 1.035139 ACGTCACCTCGGTTACTGTT 58.965 50.000 0.00 0.00 34.94 3.16
17 18 0.313043 CACGTCACCTCGGTTACTGT 59.687 55.000 0.00 0.00 34.94 3.55
18 19 0.388134 CCACGTCACCTCGGTTACTG 60.388 60.000 0.00 0.00 34.94 2.74
19 20 1.962144 CCACGTCACCTCGGTTACT 59.038 57.895 0.00 0.00 34.94 2.24
20 21 1.735559 GCCACGTCACCTCGGTTAC 60.736 63.158 0.00 0.00 34.94 2.50
21 22 1.537814 ATGCCACGTCACCTCGGTTA 61.538 55.000 0.00 0.00 34.94 2.85
22 23 2.781595 GATGCCACGTCACCTCGGTT 62.782 60.000 0.00 0.00 34.94 4.44
23 24 3.296709 GATGCCACGTCACCTCGGT 62.297 63.158 0.00 0.00 34.94 4.69
24 25 2.509336 GATGCCACGTCACCTCGG 60.509 66.667 0.00 0.00 34.94 4.63
25 26 0.740868 AATGATGCCACGTCACCTCG 60.741 55.000 0.00 0.00 0.00 4.63
26 27 2.205074 CTAATGATGCCACGTCACCTC 58.795 52.381 0.00 0.00 0.00 3.85
27 28 1.743772 GCTAATGATGCCACGTCACCT 60.744 52.381 0.00 0.00 0.00 4.00
28 29 0.657840 GCTAATGATGCCACGTCACC 59.342 55.000 0.00 0.00 0.00 4.02
29 30 0.301687 CGCTAATGATGCCACGTCAC 59.698 55.000 0.00 0.00 0.00 3.67
30 31 0.108377 ACGCTAATGATGCCACGTCA 60.108 50.000 0.00 0.00 0.00 4.35
31 32 0.301687 CACGCTAATGATGCCACGTC 59.698 55.000 0.00 0.00 0.00 4.34
32 33 1.089481 CCACGCTAATGATGCCACGT 61.089 55.000 0.00 0.00 0.00 4.49
33 34 0.809636 TCCACGCTAATGATGCCACG 60.810 55.000 0.00 0.00 0.00 4.94
34 35 1.378531 TTCCACGCTAATGATGCCAC 58.621 50.000 0.00 0.00 0.00 5.01
35 36 2.346766 ATTCCACGCTAATGATGCCA 57.653 45.000 0.00 0.00 0.00 4.92
36 37 3.815401 AGTAATTCCACGCTAATGATGCC 59.185 43.478 0.00 0.00 0.00 4.40
37 38 4.273480 ACAGTAATTCCACGCTAATGATGC 59.727 41.667 0.00 0.00 0.00 3.91
38 39 5.991328 ACAGTAATTCCACGCTAATGATG 57.009 39.130 0.00 0.00 0.00 3.07
39 40 5.696724 GCTACAGTAATTCCACGCTAATGAT 59.303 40.000 0.00 0.00 0.00 2.45
40 41 5.047847 GCTACAGTAATTCCACGCTAATGA 58.952 41.667 0.00 0.00 0.00 2.57
41 42 5.050490 AGCTACAGTAATTCCACGCTAATG 58.950 41.667 0.00 0.00 0.00 1.90
42 43 5.277857 AGCTACAGTAATTCCACGCTAAT 57.722 39.130 0.00 0.00 0.00 1.73
43 44 4.730949 AGCTACAGTAATTCCACGCTAA 57.269 40.909 0.00 0.00 0.00 3.09
44 45 4.730949 AAGCTACAGTAATTCCACGCTA 57.269 40.909 0.00 0.00 0.00 4.26
45 46 3.611766 AAGCTACAGTAATTCCACGCT 57.388 42.857 0.00 0.00 0.00 5.07
46 47 5.986004 ATTAAGCTACAGTAATTCCACGC 57.014 39.130 0.00 0.00 0.00 5.34
47 48 8.709646 GGATAATTAAGCTACAGTAATTCCACG 58.290 37.037 4.73 0.00 33.20 4.94
48 49 8.709646 CGGATAATTAAGCTACAGTAATTCCAC 58.290 37.037 4.73 0.34 33.20 4.02
49 50 7.876068 CCGGATAATTAAGCTACAGTAATTCCA 59.124 37.037 0.00 0.00 33.20 3.53
50 51 7.333672 CCCGGATAATTAAGCTACAGTAATTCC 59.666 40.741 0.73 1.92 33.20 3.01
51 52 7.148457 GCCCGGATAATTAAGCTACAGTAATTC 60.148 40.741 0.73 0.00 33.20 2.17
52 53 6.653740 GCCCGGATAATTAAGCTACAGTAATT 59.346 38.462 0.73 6.42 34.91 1.40
53 54 6.171213 GCCCGGATAATTAAGCTACAGTAAT 58.829 40.000 0.73 0.00 0.00 1.89
54 55 5.544650 GCCCGGATAATTAAGCTACAGTAA 58.455 41.667 0.73 0.00 0.00 2.24
55 56 4.321452 CGCCCGGATAATTAAGCTACAGTA 60.321 45.833 0.73 0.00 0.00 2.74
56 57 3.554337 CGCCCGGATAATTAAGCTACAGT 60.554 47.826 0.73 0.00 0.00 3.55
57 58 2.993899 CGCCCGGATAATTAAGCTACAG 59.006 50.000 0.73 0.00 0.00 2.74
58 59 2.366266 ACGCCCGGATAATTAAGCTACA 59.634 45.455 0.73 0.00 0.00 2.74
59 60 2.991866 GACGCCCGGATAATTAAGCTAC 59.008 50.000 0.73 0.00 0.00 3.58
60 61 2.629137 TGACGCCCGGATAATTAAGCTA 59.371 45.455 0.73 0.00 0.00 3.32
61 62 1.414919 TGACGCCCGGATAATTAAGCT 59.585 47.619 0.73 0.00 0.00 3.74
62 63 1.529865 GTGACGCCCGGATAATTAAGC 59.470 52.381 0.73 0.00 0.00 3.09
63 64 2.828877 TGTGACGCCCGGATAATTAAG 58.171 47.619 0.73 0.00 0.00 1.85
64 65 2.983907 TGTGACGCCCGGATAATTAA 57.016 45.000 0.73 0.00 0.00 1.40
65 66 2.761559 CATGTGACGCCCGGATAATTA 58.238 47.619 0.73 0.00 0.00 1.40
66 67 1.593196 CATGTGACGCCCGGATAATT 58.407 50.000 0.73 0.00 0.00 1.40
67 68 0.884704 GCATGTGACGCCCGGATAAT 60.885 55.000 0.73 0.00 0.00 1.28
68 69 1.522806 GCATGTGACGCCCGGATAA 60.523 57.895 0.73 0.00 0.00 1.75
69 70 2.108157 GCATGTGACGCCCGGATA 59.892 61.111 0.73 0.00 0.00 2.59
75 76 4.830765 TAGGCCGCATGTGACGCC 62.831 66.667 16.22 16.22 0.00 5.68
76 77 2.588877 ATAGGCCGCATGTGACGC 60.589 61.111 8.11 3.18 0.00 5.19
77 78 2.885676 GCATAGGCCGCATGTGACG 61.886 63.158 18.22 0.00 0.00 4.35
78 79 0.249868 TAGCATAGGCCGCATGTGAC 60.250 55.000 18.22 0.00 42.56 3.67
79 80 0.249868 GTAGCATAGGCCGCATGTGA 60.250 55.000 18.22 7.09 42.56 3.58
86 87 2.429236 CGCTCGTAGCATAGGCCG 60.429 66.667 0.00 0.00 42.58 6.13
92 93 0.582482 CTACTCGTCGCTCGTAGCAT 59.418 55.000 7.47 0.00 42.58 3.79
116 117 2.690778 GCTTTTGCCGCTCCATCGT 61.691 57.895 0.00 0.00 40.15 3.73
126 127 4.326766 TGCACGCTCGCTTTTGCC 62.327 61.111 0.00 0.00 43.93 4.52
128 129 2.127118 CCTGCACGCTCGCTTTTG 60.127 61.111 0.00 0.00 0.00 2.44
129 130 2.280797 TCCTGCACGCTCGCTTTT 60.281 55.556 0.00 0.00 0.00 2.27
150 151 0.464373 ACCATGATGTTAGCCCTGCG 60.464 55.000 0.00 0.00 0.00 5.18
151 152 1.027357 CACCATGATGTTAGCCCTGC 58.973 55.000 0.00 0.00 0.00 4.85
177 178 2.436646 CCATCTCACACGTGCCCC 60.437 66.667 17.22 0.00 0.00 5.80
181 182 2.029918 TCTGTCTTCCATCTCACACGTG 60.030 50.000 15.48 15.48 0.00 4.49
182 183 2.230025 CTCTGTCTTCCATCTCACACGT 59.770 50.000 0.00 0.00 0.00 4.49
183 184 2.416566 CCTCTGTCTTCCATCTCACACG 60.417 54.545 0.00 0.00 0.00 4.49
184 185 2.828520 TCCTCTGTCTTCCATCTCACAC 59.171 50.000 0.00 0.00 0.00 3.82
185 186 3.095332 CTCCTCTGTCTTCCATCTCACA 58.905 50.000 0.00 0.00 0.00 3.58
186 187 3.360867 TCTCCTCTGTCTTCCATCTCAC 58.639 50.000 0.00 0.00 0.00 3.51
187 188 3.268072 TCTCTCCTCTGTCTTCCATCTCA 59.732 47.826 0.00 0.00 0.00 3.27
188 189 3.885297 CTCTCTCCTCTGTCTTCCATCTC 59.115 52.174 0.00 0.00 0.00 2.75
194 196 2.025321 ACCCTCTCTCTCCTCTGTCTTC 60.025 54.545 0.00 0.00 0.00 2.87
223 225 1.604604 TCTTCCCCGTGCAAGAAAAG 58.395 50.000 0.00 2.08 0.00 2.27
224 226 1.953686 CTTCTTCCCCGTGCAAGAAAA 59.046 47.619 0.00 0.00 38.00 2.29
277 283 4.691216 AGAGAAAAGCCACACTATTCGTTC 59.309 41.667 0.00 0.00 0.00 3.95
285 291 1.312815 GCACAGAGAAAAGCCACACT 58.687 50.000 0.00 0.00 0.00 3.55
286 292 0.040958 CGCACAGAGAAAAGCCACAC 60.041 55.000 0.00 0.00 0.00 3.82
287 293 0.463654 ACGCACAGAGAAAAGCCACA 60.464 50.000 0.00 0.00 0.00 4.17
288 294 0.663153 AACGCACAGAGAAAAGCCAC 59.337 50.000 0.00 0.00 0.00 5.01
289 295 0.944386 GAACGCACAGAGAAAAGCCA 59.056 50.000 0.00 0.00 0.00 4.75
290 296 0.110644 CGAACGCACAGAGAAAAGCC 60.111 55.000 0.00 0.00 0.00 4.35
291 297 0.110644 CCGAACGCACAGAGAAAAGC 60.111 55.000 0.00 0.00 0.00 3.51
292 298 1.217882 ACCGAACGCACAGAGAAAAG 58.782 50.000 0.00 0.00 0.00 2.27
293 299 1.658994 AACCGAACGCACAGAGAAAA 58.341 45.000 0.00 0.00 0.00 2.29
294 300 1.658994 AAACCGAACGCACAGAGAAA 58.341 45.000 0.00 0.00 0.00 2.52
295 301 2.512485 TAAACCGAACGCACAGAGAA 57.488 45.000 0.00 0.00 0.00 2.87
296 302 2.734606 CAATAAACCGAACGCACAGAGA 59.265 45.455 0.00 0.00 0.00 3.10
384 392 8.308320 CCAAAACCGAATCGTATTTTAATTTCG 58.692 33.333 12.41 0.00 0.00 3.46
447 490 5.613964 TTTTCAAATTCGCGTCAACTTTC 57.386 34.783 5.77 0.00 0.00 2.62
567 612 8.671028 TGAATCAATGCATGCATATATACTCAC 58.329 33.333 32.36 17.00 35.31 3.51
569 614 9.880064 GATGAATCAATGCATGCATATATACTC 57.120 33.333 32.36 21.99 35.31 2.59
664 733 7.942341 ACATGAGTCAAATTCCCTACTAAACAA 59.058 33.333 0.00 0.00 0.00 2.83
667 736 8.598916 TGTACATGAGTCAAATTCCCTACTAAA 58.401 33.333 0.00 0.00 0.00 1.85
923 997 4.790962 CCTGCCAGCCGCACTCAT 62.791 66.667 0.00 0.00 44.64 2.90
967 1041 0.923358 TCCCTGGGTGGCGATTAAAT 59.077 50.000 13.56 0.00 0.00 1.40
1008 1084 0.929615 CGGGAACACACGTTACGTTT 59.070 50.000 7.98 0.00 38.32 3.60
1011 1087 4.324424 ACGGGAACACACGTTACG 57.676 55.556 2.19 2.19 40.99 3.18
1020 1096 3.495434 ATTTCCACTGTAACGGGAACA 57.505 42.857 0.00 0.00 40.24 3.18
1070 1146 1.571460 GAACACCTTGTGAGCAGCG 59.429 57.895 0.49 0.00 36.96 5.18
1344 1435 0.833287 CATCGGTGACAAGGGATCCT 59.167 55.000 12.58 0.00 33.87 3.24
1504 1595 3.777925 CAGCCGCACGTTCTTCCG 61.778 66.667 0.00 0.00 0.00 4.30
1702 1793 4.899239 CATCCAGGACGGCGAGGC 62.899 72.222 16.62 1.71 33.14 4.70
1988 2079 2.262915 GCAGCAGCGTGTAGAGGT 59.737 61.111 0.00 0.00 0.00 3.85
2374 2465 7.172868 TCGGTGATTTACAGATAAGGTGTTA 57.827 36.000 0.00 0.00 0.00 2.41
2614 2705 4.886496 ACTTAGGAGGACAAAGGTGTAC 57.114 45.455 0.00 0.00 38.41 2.90
2615 2706 5.152934 AGAACTTAGGAGGACAAAGGTGTA 58.847 41.667 0.00 0.00 38.41 2.90
2700 2796 9.300681 ACATTTGATTCTCCAAGAAGATTGTAA 57.699 29.630 0.00 0.00 37.69 2.41
2730 2826 0.106419 AAACCCCTCGCCAGAAAACA 60.106 50.000 0.00 0.00 0.00 2.83
3057 3154 8.465273 TCTTCTATTCCTTCGATATCAACTCA 57.535 34.615 3.12 0.00 0.00 3.41
3438 3535 8.408601 CAATTAATAGAACATCCTTGGGTGAAG 58.591 37.037 6.95 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.