Multiple sequence alignment - TraesCS5D01G144100

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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 TraesCS5D01G144100 chr5D 100.000 2481 0 0 1 2481 230395130 230392650 0.000000e+00 4582.0
1 TraesCS5D01G144100 chr5A 95.274 1587 43 15 909 2480 326432981 326434550 0.000000e+00 2486.0
2 TraesCS5D01G144100 chr5A 90.428 397 37 1 395 790 326432323 326432719 2.830000e-144 521.0
3 TraesCS5D01G144100 chr5A 89.960 249 21 3 112 360 326431123 326431367 3.980000e-83 318.0
4 TraesCS5D01G144100 chr5A 100.000 40 0 0 829 868 326432931 326432970 9.520000e-10 75.0
5 TraesCS5D01G144100 chr5B 92.390 1117 52 22 892 1980 275368502 275369613 0.000000e+00 1561.0
6 TraesCS5D01G144100 chr5B 97.436 234 5 1 1979 2211 275369694 275369927 4.970000e-107 398.0
7 TraesCS5D01G144100 chr5B 85.117 383 47 4 275 654 275367152 275367527 1.390000e-102 383.0
8 TraesCS5D01G144100 chr5B 95.376 173 5 3 2311 2480 275370132 275370304 3.140000e-69 272.0
9 TraesCS5D01G144100 chr5B 92.000 100 7 1 778 877 275368427 275368525 3.330000e-29 139.0
10 TraesCS5D01G144100 chr5B 97.826 46 1 0 2264 2309 275369922 275369967 2.050000e-11 80.5
11 TraesCS5D01G144100 chr7D 97.297 37 1 0 672 708 358722560 358722524 2.060000e-06 63.9
12 TraesCS5D01G144100 chr7B 97.143 35 1 0 674 708 242718370 242718336 2.660000e-05 60.2
13 TraesCS5D01G144100 chr7A 97.059 34 1 0 675 708 262465909 262465942 9.580000e-05 58.4
14 TraesCS5D01G144100 chr6D 97.059 34 1 0 674 707 14291348 14291381 9.580000e-05 58.4


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 TraesCS5D01G144100 chr5D 230392650 230395130 2480 True 4582.00 4582 100.0000 1 2481 1 chr5D.!!$R1 2480
1 TraesCS5D01G144100 chr5A 326431123 326434550 3427 False 850.00 2486 93.9155 112 2480 4 chr5A.!!$F1 2368
2 TraesCS5D01G144100 chr5B 275367152 275370304 3152 False 472.25 1561 93.3575 275 2480 6 chr5B.!!$F1 2205

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
95 96 0.034089 GCAACCCCTCATAGCACCTT 60.034 55.0 0.0 0.0 0.0 3.50 F
105 106 0.044855 ATAGCACCTTCTCCACCCCT 59.955 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 3135 2.355363 CGAGTTGACCGCGTTGGA 60.355 61.111 4.92 0.0 42.0 3.53 R
1816 3575 3.758554 CTGCAGGCAAAGGTTATGTAAGT 59.241 43.478 5.57 0.0 0.0 2.24 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
17 18 2.804167 CAGCCGCCACAACACAAA 59.196 55.556 0.00 0.00 0.00 2.83
18 19 1.299316 CAGCCGCCACAACACAAAG 60.299 57.895 0.00 0.00 0.00 2.77
19 20 2.027460 GCCGCCACAACACAAAGG 59.973 61.111 0.00 0.00 0.00 3.11
20 21 2.027460 CCGCCACAACACAAAGGC 59.973 61.111 0.00 0.00 43.61 4.35
21 22 2.027460 CGCCACAACACAAAGGCC 59.973 61.111 0.00 0.00 44.18 5.19
22 23 2.027460 GCCACAACACAAAGGCCG 59.973 61.111 0.00 0.00 41.25 6.13
23 24 2.485795 GCCACAACACAAAGGCCGA 61.486 57.895 0.00 0.00 41.25 5.54
24 25 1.358759 CCACAACACAAAGGCCGAC 59.641 57.895 0.00 0.00 0.00 4.79
25 26 1.010125 CACAACACAAAGGCCGACG 60.010 57.895 0.00 0.00 0.00 5.12
26 27 2.051345 CAACACAAAGGCCGACGC 60.051 61.111 0.00 0.00 0.00 5.19
27 28 2.515057 AACACAAAGGCCGACGCA 60.515 55.556 0.00 0.00 36.38 5.24
28 29 2.115911 AACACAAAGGCCGACGCAA 61.116 52.632 0.00 0.00 36.38 4.85
29 30 2.051345 CACAAAGGCCGACGCAAC 60.051 61.111 0.00 0.00 36.38 4.17
30 31 3.284449 ACAAAGGCCGACGCAACC 61.284 61.111 0.00 0.00 36.38 3.77
31 32 4.038080 CAAAGGCCGACGCAACCC 62.038 66.667 0.00 0.00 36.38 4.11
36 37 4.084888 GCCGACGCAACCCGAAAG 62.085 66.667 0.00 0.00 41.02 2.62
37 38 2.356553 CCGACGCAACCCGAAAGA 60.357 61.111 0.00 0.00 41.02 2.52
38 39 2.664436 CCGACGCAACCCGAAAGAC 61.664 63.158 0.00 0.00 41.02 3.01
39 40 2.664436 CGACGCAACCCGAAAGACC 61.664 63.158 0.00 0.00 41.02 3.85
40 41 1.595929 GACGCAACCCGAAAGACCA 60.596 57.895 0.00 0.00 41.02 4.02
41 42 0.953960 GACGCAACCCGAAAGACCAT 60.954 55.000 0.00 0.00 41.02 3.55
42 43 0.953960 ACGCAACCCGAAAGACCATC 60.954 55.000 0.00 0.00 41.02 3.51
43 44 1.794222 GCAACCCGAAAGACCATCG 59.206 57.895 0.00 0.00 39.92 3.84
67 68 2.286121 CCCCCTGCTCAACCCCTA 60.286 66.667 0.00 0.00 0.00 3.53
68 69 2.680370 CCCCCTGCTCAACCCCTAC 61.680 68.421 0.00 0.00 0.00 3.18
69 70 2.680370 CCCCTGCTCAACCCCTACC 61.680 68.421 0.00 0.00 0.00 3.18
70 71 2.680370 CCCTGCTCAACCCCTACCC 61.680 68.421 0.00 0.00 0.00 3.69
71 72 1.616628 CCTGCTCAACCCCTACCCT 60.617 63.158 0.00 0.00 0.00 4.34
72 73 1.604378 CTGCTCAACCCCTACCCTG 59.396 63.158 0.00 0.00 0.00 4.45
73 74 0.909610 CTGCTCAACCCCTACCCTGA 60.910 60.000 0.00 0.00 0.00 3.86
74 75 1.198759 TGCTCAACCCCTACCCTGAC 61.199 60.000 0.00 0.00 0.00 3.51
75 76 1.198759 GCTCAACCCCTACCCTGACA 61.199 60.000 0.00 0.00 0.00 3.58
76 77 0.905357 CTCAACCCCTACCCTGACAG 59.095 60.000 0.00 0.00 0.00 3.51
77 78 1.198759 TCAACCCCTACCCTGACAGC 61.199 60.000 0.00 0.00 0.00 4.40
78 79 1.151899 AACCCCTACCCTGACAGCA 60.152 57.895 0.00 0.00 0.00 4.41
79 80 0.770557 AACCCCTACCCTGACAGCAA 60.771 55.000 0.00 0.00 0.00 3.91
80 81 1.299976 CCCCTACCCTGACAGCAAC 59.700 63.158 0.00 0.00 0.00 4.17
81 82 1.299976 CCCTACCCTGACAGCAACC 59.700 63.158 0.00 0.00 0.00 3.77
82 83 1.299976 CCTACCCTGACAGCAACCC 59.700 63.158 0.00 0.00 0.00 4.11
83 84 1.299976 CTACCCTGACAGCAACCCC 59.700 63.158 0.00 0.00 0.00 4.95
84 85 1.151899 TACCCTGACAGCAACCCCT 60.152 57.895 0.00 0.00 0.00 4.79
85 86 1.198759 TACCCTGACAGCAACCCCTC 61.199 60.000 0.00 0.00 0.00 4.30
86 87 2.528818 CCCTGACAGCAACCCCTCA 61.529 63.158 0.00 0.00 0.00 3.86
87 88 1.687612 CCTGACAGCAACCCCTCAT 59.312 57.895 0.00 0.00 0.00 2.90
88 89 0.911769 CCTGACAGCAACCCCTCATA 59.088 55.000 0.00 0.00 0.00 2.15
89 90 1.134280 CCTGACAGCAACCCCTCATAG 60.134 57.143 0.00 0.00 0.00 2.23
90 91 0.253044 TGACAGCAACCCCTCATAGC 59.747 55.000 0.00 0.00 0.00 2.97
91 92 0.253044 GACAGCAACCCCTCATAGCA 59.747 55.000 0.00 0.00 0.00 3.49
92 93 0.035056 ACAGCAACCCCTCATAGCAC 60.035 55.000 0.00 0.00 0.00 4.40
93 94 0.749454 CAGCAACCCCTCATAGCACC 60.749 60.000 0.00 0.00 0.00 5.01
94 95 0.916358 AGCAACCCCTCATAGCACCT 60.916 55.000 0.00 0.00 0.00 4.00
95 96 0.034089 GCAACCCCTCATAGCACCTT 60.034 55.000 0.00 0.00 0.00 3.50
96 97 2.019156 GCAACCCCTCATAGCACCTTC 61.019 57.143 0.00 0.00 0.00 3.46
97 98 1.561542 CAACCCCTCATAGCACCTTCT 59.438 52.381 0.00 0.00 0.00 2.85
98 99 1.501582 ACCCCTCATAGCACCTTCTC 58.498 55.000 0.00 0.00 0.00 2.87
99 100 0.761802 CCCCTCATAGCACCTTCTCC 59.238 60.000 0.00 0.00 0.00 3.71
100 101 1.500474 CCCTCATAGCACCTTCTCCA 58.500 55.000 0.00 0.00 0.00 3.86
101 102 1.139853 CCCTCATAGCACCTTCTCCAC 59.860 57.143 0.00 0.00 0.00 4.02
102 103 1.139853 CCTCATAGCACCTTCTCCACC 59.860 57.143 0.00 0.00 0.00 4.61
103 104 1.139853 CTCATAGCACCTTCTCCACCC 59.860 57.143 0.00 0.00 0.00 4.61
104 105 0.181350 CATAGCACCTTCTCCACCCC 59.819 60.000 0.00 0.00 0.00 4.95
105 106 0.044855 ATAGCACCTTCTCCACCCCT 59.955 55.000 0.00 0.00 0.00 4.79
106 107 0.178873 TAGCACCTTCTCCACCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
107 108 1.002011 GCACCTTCTCCACCCCTTC 60.002 63.158 0.00 0.00 0.00 3.46
108 109 1.685820 CACCTTCTCCACCCCTTCC 59.314 63.158 0.00 0.00 0.00 3.46
109 110 1.918800 ACCTTCTCCACCCCTTCCG 60.919 63.158 0.00 0.00 0.00 4.30
110 111 2.269241 CTTCTCCACCCCTTCCGC 59.731 66.667 0.00 0.00 0.00 5.54
150 151 4.884668 TTACCCAACAAAAACACCACAA 57.115 36.364 0.00 0.00 0.00 3.33
167 168 4.578516 ACCACAATGAACGAAAATCAGTCA 59.421 37.500 0.00 0.00 0.00 3.41
176 177 3.876589 AAATCAGTCACGCGCGGGT 62.877 57.895 33.41 24.30 0.00 5.28
192 193 1.750399 GGTACCTCGGCGACCTACA 60.750 63.158 4.99 0.00 0.00 2.74
193 194 1.315257 GGTACCTCGGCGACCTACAA 61.315 60.000 4.99 0.00 0.00 2.41
208 209 1.535028 CTACAAACGCACCTCAATGCA 59.465 47.619 0.00 0.00 46.47 3.96
211 212 1.032014 AAACGCACCTCAATGCAAGT 58.968 45.000 0.00 0.00 46.47 3.16
214 215 0.097674 CGCACCTCAATGCAAGTAGC 59.902 55.000 0.00 0.00 46.47 3.58
241 242 4.496670 CGTGGTGGACGGAATCTC 57.503 61.111 0.00 0.00 44.85 2.75
242 243 1.516386 CGTGGTGGACGGAATCTCG 60.516 63.158 0.00 0.00 44.85 4.04
244 245 0.458025 GTGGTGGACGGAATCTCGAC 60.458 60.000 0.00 0.00 0.00 4.20
245 246 1.226603 GGTGGACGGAATCTCGACG 60.227 63.158 0.00 0.00 0.00 5.12
254 255 1.140407 GAATCTCGACGCCGACAAGG 61.140 60.000 0.00 0.00 40.30 3.61
320 322 1.945776 GCGTCCGAGAGAGCAAAACG 61.946 60.000 0.00 0.00 0.00 3.60
373 763 2.045045 TGGCGCCTGAAATGGAGG 60.045 61.111 29.70 0.00 0.00 4.30
389 779 4.462280 GGGGGTGCGGGAGTTACG 62.462 72.222 0.00 0.00 0.00 3.18
390 780 3.384532 GGGGTGCGGGAGTTACGA 61.385 66.667 0.00 0.00 0.00 3.43
442 1365 0.400213 TCGCTCCAAACCATGTTCCT 59.600 50.000 0.00 0.00 0.00 3.36
452 1375 2.162681 ACCATGTTCCTAGCAAACTGC 58.837 47.619 7.49 0.00 45.46 4.40
471 1394 2.224426 TGCTCGGACAAACTAACATGGT 60.224 45.455 0.00 0.00 0.00 3.55
477 1400 3.439129 GGACAAACTAACATGGTACCTGC 59.561 47.826 14.36 0.00 0.00 4.85
480 1403 3.350219 AACTAACATGGTACCTGCCAG 57.650 47.619 14.36 11.10 42.47 4.85
494 1417 3.009473 ACCTGCCAGAGCTTTAAGATTCA 59.991 43.478 0.00 0.00 40.80 2.57
498 1421 3.547613 GCCAGAGCTTTAAGATTCATGCG 60.548 47.826 0.00 0.00 35.50 4.73
510 1433 2.401583 TTCATGCGCAAGTGACCTAT 57.598 45.000 17.11 0.00 41.68 2.57
523 1446 1.202371 TGACCTATGGTTCGATCGTGC 60.202 52.381 15.94 8.94 35.25 5.34
542 1465 0.676151 CTTCACTGGCTCTTGGCTCC 60.676 60.000 0.00 0.00 41.46 4.70
567 1490 2.159627 GGAACGTTCACCAGCTAACATG 59.840 50.000 28.24 0.00 0.00 3.21
569 1492 3.671008 ACGTTCACCAGCTAACATGTA 57.329 42.857 0.00 0.00 0.00 2.29
617 1542 6.338146 TCCGAATTAACTGATACAACCTCTG 58.662 40.000 0.00 0.00 0.00 3.35
662 1587 8.373048 TGTATAAAGGATGCGTCGATTAATTT 57.627 30.769 0.00 0.00 0.00 1.82
702 1627 9.791801 TTGTATAGAGGCTGCATCAATTAATTA 57.208 29.630 17.19 0.00 0.00 1.40
709 1634 6.208204 AGGCTGCATCAATTAATTAGGATCAC 59.792 38.462 0.50 0.00 0.00 3.06
742 1700 5.464965 ACCGCTTTTATTTCGTCAGTATG 57.535 39.130 0.00 0.00 37.54 2.39
774 1732 7.631822 CATTCAGACAATGATTTCTCTGCTAG 58.368 38.462 5.20 0.00 37.89 3.42
797 2525 4.309950 ACCGACGGGCCAAGTCAC 62.310 66.667 24.30 5.57 38.46 3.67
868 2596 2.032799 CGTAGCAAAGAACAAACTGGCA 59.967 45.455 0.00 0.00 0.00 4.92
869 2597 3.488384 CGTAGCAAAGAACAAACTGGCAA 60.488 43.478 0.00 0.00 0.00 4.52
872 2600 3.055891 AGCAAAGAACAAACTGGCAAAGT 60.056 39.130 0.00 0.00 42.60 2.66
874 2602 4.244862 CAAAGAACAAACTGGCAAAGTGT 58.755 39.130 0.00 0.00 39.81 3.55
875 2603 5.406649 CAAAGAACAAACTGGCAAAGTGTA 58.593 37.500 0.00 0.00 39.81 2.90
876 2604 5.852282 AAGAACAAACTGGCAAAGTGTAT 57.148 34.783 0.00 0.00 39.81 2.29
877 2605 5.438761 AGAACAAACTGGCAAAGTGTATC 57.561 39.130 0.00 0.00 39.81 2.24
878 2606 3.896648 ACAAACTGGCAAAGTGTATCG 57.103 42.857 0.00 0.00 39.81 2.92
879 2607 2.031157 ACAAACTGGCAAAGTGTATCGC 60.031 45.455 0.00 0.00 39.81 4.58
880 2608 2.185004 AACTGGCAAAGTGTATCGCT 57.815 45.000 0.00 0.00 39.81 4.93
881 2609 1.726853 ACTGGCAAAGTGTATCGCTC 58.273 50.000 0.00 0.00 37.88 5.03
882 2610 1.009829 CTGGCAAAGTGTATCGCTCC 58.990 55.000 0.00 0.00 0.00 4.70
883 2611 0.613260 TGGCAAAGTGTATCGCTCCT 59.387 50.000 0.00 0.00 0.00 3.69
884 2612 1.828595 TGGCAAAGTGTATCGCTCCTA 59.171 47.619 0.00 0.00 0.00 2.94
885 2613 2.235155 TGGCAAAGTGTATCGCTCCTAA 59.765 45.455 0.00 0.00 0.00 2.69
886 2614 3.267483 GGCAAAGTGTATCGCTCCTAAA 58.733 45.455 0.00 0.00 0.00 1.85
887 2615 3.687698 GGCAAAGTGTATCGCTCCTAAAA 59.312 43.478 0.00 0.00 0.00 1.52
888 2616 4.155280 GGCAAAGTGTATCGCTCCTAAAAA 59.845 41.667 0.00 0.00 0.00 1.94
1171 2918 0.179103 CCGCCAAGCAAATCCAATCC 60.179 55.000 0.00 0.00 0.00 3.01
1186 2933 6.956202 ATCCAATCCTCTCTTGCTAAATTG 57.044 37.500 0.00 0.00 0.00 2.32
1188 2935 4.400251 CCAATCCTCTCTTGCTAAATTGCA 59.600 41.667 0.00 0.00 41.65 4.08
1425 3172 1.227527 TCCTCAAGGTGTGTGTGCG 60.228 57.895 0.00 0.00 36.34 5.34
1545 3295 9.378551 TGCCTAATTCACATGTTTTAGTAGTAG 57.621 33.333 0.00 0.00 0.00 2.57
1643 3394 4.391155 TGCCGTGGTATGTTTATAATCCC 58.609 43.478 0.00 0.00 0.00 3.85
1723 3482 1.272781 CGACAGTTCTTCAGCGGATC 58.727 55.000 0.00 0.00 0.00 3.36
1816 3575 7.558807 TCAGAGGGAGTATCTCGTAATGTTTTA 59.441 37.037 0.00 0.00 43.84 1.52
1849 3608 3.658757 TTGCCTGCAGTAAATCCAAAC 57.341 42.857 13.81 0.00 0.00 2.93
1925 3685 4.479158 AGGTTCTTTTTATCTGGTTGGCA 58.521 39.130 0.00 0.00 0.00 4.92
1959 3719 8.863086 CCCAAAATTATCATCAGTGGATAACAT 58.137 33.333 4.54 0.00 39.34 2.71
2069 3912 9.104965 CACTCGGTATTTCTAAAACATCCATTA 57.895 33.333 0.00 0.00 0.00 1.90
2353 4361 3.739300 GCTACAAAGTGTTCGCTCTGTTA 59.261 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.299316 CTTTGTGTTGTGGCGGCTG 60.299 57.895 11.43 0.00 0.00 4.85
1 2 2.489275 CCTTTGTGTTGTGGCGGCT 61.489 57.895 11.43 0.00 0.00 5.52
2 3 2.027460 CCTTTGTGTTGTGGCGGC 59.973 61.111 0.00 0.00 0.00 6.53
3 4 2.027460 GCCTTTGTGTTGTGGCGG 59.973 61.111 0.00 0.00 35.79 6.13
4 5 2.027460 GGCCTTTGTGTTGTGGCG 59.973 61.111 0.00 0.00 45.75 5.69
5 6 2.027460 CGGCCTTTGTGTTGTGGC 59.973 61.111 0.00 0.00 44.22 5.01
6 7 1.358759 GTCGGCCTTTGTGTTGTGG 59.641 57.895 0.00 0.00 0.00 4.17
7 8 1.010125 CGTCGGCCTTTGTGTTGTG 60.010 57.895 0.00 0.00 0.00 3.33
8 9 2.830285 GCGTCGGCCTTTGTGTTGT 61.830 57.895 0.00 0.00 0.00 3.32
9 10 2.051345 GCGTCGGCCTTTGTGTTG 60.051 61.111 0.00 0.00 0.00 3.33
10 11 2.115911 TTGCGTCGGCCTTTGTGTT 61.116 52.632 0.00 0.00 38.85 3.32
11 12 2.515057 TTGCGTCGGCCTTTGTGT 60.515 55.556 0.00 0.00 38.85 3.72
12 13 2.051345 GTTGCGTCGGCCTTTGTG 60.051 61.111 0.00 0.00 38.85 3.33
13 14 3.284449 GGTTGCGTCGGCCTTTGT 61.284 61.111 0.00 0.00 38.85 2.83
14 15 4.038080 GGGTTGCGTCGGCCTTTG 62.038 66.667 0.00 0.00 38.85 2.77
19 20 4.084888 CTTTCGGGTTGCGTCGGC 62.085 66.667 0.00 0.00 40.52 5.54
20 21 2.356553 TCTTTCGGGTTGCGTCGG 60.357 61.111 0.00 0.00 0.00 4.79
21 22 2.664436 GGTCTTTCGGGTTGCGTCG 61.664 63.158 0.00 0.00 0.00 5.12
22 23 0.953960 ATGGTCTTTCGGGTTGCGTC 60.954 55.000 0.00 0.00 0.00 5.19
23 24 0.953960 GATGGTCTTTCGGGTTGCGT 60.954 55.000 0.00 0.00 0.00 5.24
24 25 1.794222 GATGGTCTTTCGGGTTGCG 59.206 57.895 0.00 0.00 0.00 4.85
25 26 1.794222 CGATGGTCTTTCGGGTTGC 59.206 57.895 0.00 0.00 33.05 4.17
50 51 2.286121 TAGGGGTTGAGCAGGGGG 60.286 66.667 0.00 0.00 0.00 5.40
51 52 2.680370 GGTAGGGGTTGAGCAGGGG 61.680 68.421 0.00 0.00 0.00 4.79
52 53 2.680370 GGGTAGGGGTTGAGCAGGG 61.680 68.421 0.00 0.00 0.00 4.45
53 54 1.616628 AGGGTAGGGGTTGAGCAGG 60.617 63.158 0.00 0.00 0.00 4.85
54 55 0.909610 TCAGGGTAGGGGTTGAGCAG 60.910 60.000 0.00 0.00 0.00 4.24
55 56 1.159905 TCAGGGTAGGGGTTGAGCA 59.840 57.895 0.00 0.00 0.00 4.26
56 57 1.198759 TGTCAGGGTAGGGGTTGAGC 61.199 60.000 0.00 0.00 0.00 4.26
57 58 0.905357 CTGTCAGGGTAGGGGTTGAG 59.095 60.000 0.00 0.00 0.00 3.02
58 59 1.198759 GCTGTCAGGGTAGGGGTTGA 61.199 60.000 1.14 0.00 0.00 3.18
59 60 1.299976 GCTGTCAGGGTAGGGGTTG 59.700 63.158 1.14 0.00 0.00 3.77
60 61 0.770557 TTGCTGTCAGGGTAGGGGTT 60.771 55.000 1.14 0.00 0.00 4.11
61 62 1.151899 TTGCTGTCAGGGTAGGGGT 60.152 57.895 1.14 0.00 0.00 4.95
62 63 1.299976 GTTGCTGTCAGGGTAGGGG 59.700 63.158 1.14 0.00 0.00 4.79
63 64 1.299976 GGTTGCTGTCAGGGTAGGG 59.700 63.158 1.14 0.00 0.00 3.53
64 65 1.299976 GGGTTGCTGTCAGGGTAGG 59.700 63.158 1.14 0.00 0.00 3.18
65 66 1.201429 AGGGGTTGCTGTCAGGGTAG 61.201 60.000 1.14 0.00 0.00 3.18
66 67 1.151899 AGGGGTTGCTGTCAGGGTA 60.152 57.895 1.14 0.00 0.00 3.69
67 68 2.450502 AGGGGTTGCTGTCAGGGT 60.451 61.111 1.14 0.00 0.00 4.34
68 69 1.856539 ATGAGGGGTTGCTGTCAGGG 61.857 60.000 1.14 0.00 0.00 4.45
69 70 0.911769 TATGAGGGGTTGCTGTCAGG 59.088 55.000 1.14 0.00 0.00 3.86
70 71 1.745141 GCTATGAGGGGTTGCTGTCAG 60.745 57.143 0.00 0.00 0.00 3.51
71 72 0.253044 GCTATGAGGGGTTGCTGTCA 59.747 55.000 0.00 0.00 0.00 3.58
72 73 0.253044 TGCTATGAGGGGTTGCTGTC 59.747 55.000 0.00 0.00 0.00 3.51
73 74 0.035056 GTGCTATGAGGGGTTGCTGT 60.035 55.000 0.00 0.00 0.00 4.40
74 75 0.749454 GGTGCTATGAGGGGTTGCTG 60.749 60.000 0.00 0.00 0.00 4.41
75 76 0.916358 AGGTGCTATGAGGGGTTGCT 60.916 55.000 0.00 0.00 0.00 3.91
76 77 0.034089 AAGGTGCTATGAGGGGTTGC 60.034 55.000 0.00 0.00 0.00 4.17
77 78 1.561542 AGAAGGTGCTATGAGGGGTTG 59.438 52.381 0.00 0.00 0.00 3.77
78 79 1.840635 GAGAAGGTGCTATGAGGGGTT 59.159 52.381 0.00 0.00 0.00 4.11
79 80 1.501582 GAGAAGGTGCTATGAGGGGT 58.498 55.000 0.00 0.00 0.00 4.95
80 81 0.761802 GGAGAAGGTGCTATGAGGGG 59.238 60.000 0.00 0.00 0.00 4.79
81 82 1.139853 GTGGAGAAGGTGCTATGAGGG 59.860 57.143 0.00 0.00 0.00 4.30
82 83 1.139853 GGTGGAGAAGGTGCTATGAGG 59.860 57.143 0.00 0.00 0.00 3.86
83 84 1.139853 GGGTGGAGAAGGTGCTATGAG 59.860 57.143 0.00 0.00 0.00 2.90
84 85 1.204146 GGGTGGAGAAGGTGCTATGA 58.796 55.000 0.00 0.00 0.00 2.15
85 86 0.181350 GGGGTGGAGAAGGTGCTATG 59.819 60.000 0.00 0.00 0.00 2.23
86 87 0.044855 AGGGGTGGAGAAGGTGCTAT 59.955 55.000 0.00 0.00 0.00 2.97
87 88 0.178873 AAGGGGTGGAGAAGGTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
88 89 1.464198 AAGGGGTGGAGAAGGTGCT 60.464 57.895 0.00 0.00 0.00 4.40
89 90 1.002011 GAAGGGGTGGAGAAGGTGC 60.002 63.158 0.00 0.00 0.00 5.01
90 91 1.685820 GGAAGGGGTGGAGAAGGTG 59.314 63.158 0.00 0.00 0.00 4.00
91 92 1.918800 CGGAAGGGGTGGAGAAGGT 60.919 63.158 0.00 0.00 0.00 3.50
92 93 2.990479 CGGAAGGGGTGGAGAAGG 59.010 66.667 0.00 0.00 0.00 3.46
93 94 2.269241 GCGGAAGGGGTGGAGAAG 59.731 66.667 0.00 0.00 0.00 2.85
94 95 3.327404 GGCGGAAGGGGTGGAGAA 61.327 66.667 0.00 0.00 0.00 2.87
95 96 3.943137 ATGGCGGAAGGGGTGGAGA 62.943 63.158 0.00 0.00 0.00 3.71
96 97 3.411517 ATGGCGGAAGGGGTGGAG 61.412 66.667 0.00 0.00 0.00 3.86
97 98 3.727258 CATGGCGGAAGGGGTGGA 61.727 66.667 0.00 0.00 0.00 4.02
98 99 4.820744 CCATGGCGGAAGGGGTGG 62.821 72.222 0.00 0.00 36.56 4.61
99 100 3.727258 TCCATGGCGGAAGGGGTG 61.727 66.667 6.96 0.00 42.52 4.61
107 108 1.264020 CGTGATGTTTATCCATGGCGG 59.736 52.381 6.96 0.00 32.09 6.13
108 109 2.209273 TCGTGATGTTTATCCATGGCG 58.791 47.619 6.96 0.31 32.09 5.69
109 110 4.836125 AATCGTGATGTTTATCCATGGC 57.164 40.909 6.96 0.00 32.09 4.40
110 111 5.181245 GGGTAATCGTGATGTTTATCCATGG 59.819 44.000 4.97 4.97 34.43 3.66
117 118 6.879276 TTTGTTGGGTAATCGTGATGTTTA 57.121 33.333 0.00 0.00 0.00 2.01
125 126 3.700038 TGGTGTTTTTGTTGGGTAATCGT 59.300 39.130 0.00 0.00 0.00 3.73
150 151 2.159841 CGCGTGACTGATTTTCGTTCAT 60.160 45.455 0.00 0.00 0.00 2.57
176 177 0.527565 GTTTGTAGGTCGCCGAGGTA 59.472 55.000 0.00 0.00 0.00 3.08
235 236 1.140407 CCTTGTCGGCGTCGAGATTC 61.140 60.000 14.75 0.35 46.91 2.52
241 242 3.966026 GAGGTCCTTGTCGGCGTCG 62.966 68.421 1.15 1.15 37.82 5.12
242 243 2.126031 GAGGTCCTTGTCGGCGTC 60.126 66.667 6.85 0.72 0.00 5.19
244 245 2.432628 GTGAGGTCCTTGTCGGCG 60.433 66.667 0.00 0.00 0.00 6.46
245 246 0.951040 CAAGTGAGGTCCTTGTCGGC 60.951 60.000 0.00 0.00 35.63 5.54
254 255 2.198304 ATTCCCCGCCAAGTGAGGTC 62.198 60.000 0.00 0.00 0.00 3.85
320 322 2.670939 CCATTTTCCCCCTTCCTCATC 58.329 52.381 0.00 0.00 0.00 2.92
373 763 2.728435 ATCGTAACTCCCGCACCCC 61.728 63.158 0.00 0.00 0.00 4.95
452 1375 3.930848 GGTACCATGTTAGTTTGTCCGAG 59.069 47.826 7.15 0.00 0.00 4.63
471 1394 4.225042 TGAATCTTAAAGCTCTGGCAGGTA 59.775 41.667 15.73 0.00 41.70 3.08
477 1400 3.547613 GCGCATGAATCTTAAAGCTCTGG 60.548 47.826 0.30 0.00 0.00 3.86
480 1403 3.680642 TGCGCATGAATCTTAAAGCTC 57.319 42.857 5.66 0.00 0.00 4.09
494 1417 0.253044 ACCATAGGTCACTTGCGCAT 59.747 50.000 12.75 0.00 0.00 4.73
498 1421 2.380084 TCGAACCATAGGTCACTTGC 57.620 50.000 0.00 0.00 33.12 4.01
510 1433 0.317160 AGTGAAGCACGATCGAACCA 59.683 50.000 24.34 9.02 39.64 3.67
523 1446 0.676151 GGAGCCAAGAGCCAGTGAAG 60.676 60.000 0.00 0.00 45.47 3.02
542 1465 4.379174 CTGGTGAACGTTCCCCAG 57.621 61.111 35.07 35.07 44.38 4.45
567 1490 7.600065 TCGCAGGGAGTATAAGATTTACATAC 58.400 38.462 0.00 0.00 0.00 2.39
569 1492 6.665992 TCGCAGGGAGTATAAGATTTACAT 57.334 37.500 0.00 0.00 0.00 2.29
643 1568 4.196193 TCCAAATTAATCGACGCATCCTT 58.804 39.130 0.00 0.00 0.00 3.36
662 1587 6.239430 GCCTCTATACAATGTTGAGAGATCCA 60.239 42.308 19.59 0.00 36.55 3.41
702 1627 6.374417 AGCGGTATAAAATATGGTGATCCT 57.626 37.500 0.00 0.00 34.23 3.24
709 1634 9.887406 ACGAAATAAAAGCGGTATAAAATATGG 57.113 29.630 0.00 0.00 0.00 2.74
742 1700 4.882671 ATCATTGTCTGAATGCGGTTAC 57.117 40.909 0.00 0.00 37.44 2.50
781 1739 3.530910 AAGTGACTTGGCCCGTCGG 62.531 63.158 15.14 3.60 34.17 4.79
789 2517 4.816385 ACAGACATTACACAAGTGACTTGG 59.184 41.667 27.01 18.30 44.81 3.61
792 2520 8.559536 CAAATTACAGACATTACACAAGTGACT 58.440 33.333 7.28 0.00 0.00 3.41
797 2525 8.234546 GGGTACAAATTACAGACATTACACAAG 58.765 37.037 0.00 0.00 0.00 3.16
897 2625 4.381505 CCGCCTATACACTTTGCCATTTTT 60.382 41.667 0.00 0.00 0.00 1.94
898 2626 3.130340 CCGCCTATACACTTTGCCATTTT 59.870 43.478 0.00 0.00 0.00 1.82
899 2627 2.687935 CCGCCTATACACTTTGCCATTT 59.312 45.455 0.00 0.00 0.00 2.32
900 2628 2.092646 TCCGCCTATACACTTTGCCATT 60.093 45.455 0.00 0.00 0.00 3.16
901 2629 1.488812 TCCGCCTATACACTTTGCCAT 59.511 47.619 0.00 0.00 0.00 4.40
902 2630 0.906066 TCCGCCTATACACTTTGCCA 59.094 50.000 0.00 0.00 0.00 4.92
903 2631 1.873591 CATCCGCCTATACACTTTGCC 59.126 52.381 0.00 0.00 0.00 4.52
904 2632 2.544267 GTCATCCGCCTATACACTTTGC 59.456 50.000 0.00 0.00 0.00 3.68
905 2633 2.794910 CGTCATCCGCCTATACACTTTG 59.205 50.000 0.00 0.00 0.00 2.77
910 2638 0.178984 TCCCGTCATCCGCCTATACA 60.179 55.000 0.00 0.00 34.38 2.29
1035 2782 2.440980 GATTCCAGCTGCCCACCC 60.441 66.667 8.66 0.00 0.00 4.61
1125 2872 4.636206 AGGAATTTTGAGTAGATCGTTGGC 59.364 41.667 0.00 0.00 0.00 4.52
1388 3135 2.355363 CGAGTTGACCGCGTTGGA 60.355 61.111 4.92 0.00 42.00 3.53
1425 3172 4.816984 ATGGAGGGCAGCAGCAGC 62.817 66.667 2.65 0.00 44.61 5.25
1468 3217 8.682710 ACGTAATAATAATGTCAAAACCTGCAT 58.317 29.630 0.00 0.00 0.00 3.96
1469 3218 8.046294 ACGTAATAATAATGTCAAAACCTGCA 57.954 30.769 0.00 0.00 0.00 4.41
1545 3295 8.130307 AGAAACAAAACAATTGTGCATAAGAC 57.870 30.769 12.82 1.56 32.22 3.01
1625 3375 9.733556 TCATACATGGGATTATAAACATACCAC 57.266 33.333 0.00 0.00 37.47 4.16
1643 3394 8.857216 GCTCAAAACAGAAAAGAATCATACATG 58.143 33.333 0.00 0.00 0.00 3.21
1816 3575 3.758554 CTGCAGGCAAAGGTTATGTAAGT 59.241 43.478 5.57 0.00 0.00 2.24
1849 3608 5.123936 GCACTAATCAGTTTAAGGGTAGGG 58.876 45.833 0.00 0.00 30.46 3.53
1925 3685 6.013466 ACTGATGATAATTTTGGGGCAAAAGT 60.013 34.615 0.00 0.00 44.72 2.66
1959 3719 7.553402 GGTATCTAGTTATCATCTCGAGCCTAA 59.447 40.741 7.81 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.