Multiple sequence alignment - TraesCS7D01G251200

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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 TraesCS7D01G251200 chr7D 100.000 2753 0 0 1 2753 223868346 223871098 0.000000e+00 5084
1 TraesCS7D01G251200 chr7A 94.332 1923 69 12 106 2018 234538639 234540531 0.000000e+00 2911
2 TraesCS7D01G251200 chr7A 86.310 504 25 11 2250 2751 234548194 234548655 2.450000e-140 508
3 TraesCS7D01G251200 chr7A 87.437 199 7 6 2001 2181 234540834 234541032 2.150000e-51 213
4 TraesCS7D01G251200 chr7A 94.366 71 4 0 2169 2239 234548084 234548154 2.900000e-20 110
5 TraesCS7D01G251200 chr7B 93.328 1319 62 14 932 2242 176207395 176206095 0.000000e+00 1925
6 TraesCS7D01G251200 chr7B 88.867 503 35 9 2250 2751 176206057 176205575 1.410000e-167 599
7 TraesCS7D01G251200 chr7B 93.156 263 8 5 465 727 176209160 176208908 7.200000e-101 377
8 TraesCS7D01G251200 chr7B 85.629 334 30 10 106 438 176209847 176209531 4.390000e-88 335
9 TraesCS7D01G251200 chr7B 93.529 170 9 2 770 939 176207585 176207418 4.550000e-63 252
10 TraesCS7D01G251200 chr7B 94.615 130 3 1 649 778 176208908 176208783 6.010000e-47 198
11 TraesCS7D01G251200 chr5A 82.851 484 72 9 1002 1481 482621904 482622380 9.110000e-115 424
12 TraesCS7D01G251200 chr5A 81.405 484 79 9 1002 1481 482533392 482533868 4.300000e-103 385
13 TraesCS7D01G251200 chr5B 82.377 488 75 9 1002 1485 458634167 458634647 5.490000e-112 414
14 TraesCS7D01G251200 chr5D 82.340 453 75 4 1002 1450 382268210 382268661 3.320000e-104 388
15 TraesCS7D01G251200 chr5D 95.283 106 3 2 1 105 398821349 398821245 1.700000e-37 167
16 TraesCS7D01G251200 chr5D 95.050 101 4 1 4 104 49283008 49282909 1.020000e-34 158
17 TraesCS7D01G251200 chrUn 95.192 104 4 1 1 104 345777056 345777158 2.190000e-36 163
18 TraesCS7D01G251200 chr1D 92.857 112 7 1 1 111 490899277 490899388 7.890000e-36 161
19 TraesCS7D01G251200 chr1D 94.286 105 5 1 1 105 74411298 74411401 2.840000e-35 159
20 TraesCS7D01G251200 chr1D 94.118 102 5 1 1 102 490374500 490374600 1.320000e-33 154
21 TraesCS7D01G251200 chr2D 94.286 105 5 1 1 104 573488391 573488495 2.840000e-35 159
22 TraesCS7D01G251200 chr2D 93.458 107 6 1 1 106 60099551 60099657 1.020000e-34 158
23 TraesCS7D01G251200 chr4D 93.333 105 5 2 1 104 480137044 480137147 1.320000e-33 154


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 TraesCS7D01G251200 chr7D 223868346 223871098 2752 False 5084.000000 5084 100.000000 1 2753 1 chr7D.!!$F1 2752
1 TraesCS7D01G251200 chr7A 234538639 234541032 2393 False 1562.000000 2911 90.884500 106 2181 2 chr7A.!!$F1 2075
2 TraesCS7D01G251200 chr7A 234548084 234548655 571 False 309.000000 508 90.338000 2169 2751 2 chr7A.!!$F2 582
3 TraesCS7D01G251200 chr7B 176205575 176209847 4272 True 614.333333 1925 91.520667 106 2751 6 chr7B.!!$R1 2645

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
314 320 0.030773 GATCCGCGAGTGAGCACATA 59.969 55.0 8.23 0.0 36.85 2.29 F
829 2465 0.534427 ATCATCGTCGTCTCCGGCTA 60.534 55.0 0.00 0.0 36.28 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 3223 0.321671 CGAAGAAGAGCCTGTTCCCA 59.678 55.0 0.00 0.00 0.00 4.37 R
1763 3432 0.433492 CGTGTCACCAACGATCGAAC 59.567 55.0 24.34 9.85 43.68 3.95 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
21 22 4.391405 ACTTGTTTTCTGCTTTTCTGGG 57.609 40.909 0.00 0.00 0.00 4.45
22 23 3.769300 ACTTGTTTTCTGCTTTTCTGGGT 59.231 39.130 0.00 0.00 0.00 4.51
23 24 4.222810 ACTTGTTTTCTGCTTTTCTGGGTT 59.777 37.500 0.00 0.00 0.00 4.11
24 25 4.122143 TGTTTTCTGCTTTTCTGGGTTG 57.878 40.909 0.00 0.00 0.00 3.77
25 26 3.513515 TGTTTTCTGCTTTTCTGGGTTGT 59.486 39.130 0.00 0.00 0.00 3.32
26 27 4.707448 TGTTTTCTGCTTTTCTGGGTTGTA 59.293 37.500 0.00 0.00 0.00 2.41
27 28 5.362430 TGTTTTCTGCTTTTCTGGGTTGTAT 59.638 36.000 0.00 0.00 0.00 2.29
28 29 5.705609 TTTCTGCTTTTCTGGGTTGTATC 57.294 39.130 0.00 0.00 0.00 2.24
29 30 3.686016 TCTGCTTTTCTGGGTTGTATCC 58.314 45.455 0.00 0.00 0.00 2.59
30 31 3.330701 TCTGCTTTTCTGGGTTGTATCCT 59.669 43.478 0.00 0.00 0.00 3.24
31 32 3.420893 TGCTTTTCTGGGTTGTATCCTG 58.579 45.455 0.00 0.00 0.00 3.86
32 33 3.181434 TGCTTTTCTGGGTTGTATCCTGT 60.181 43.478 0.00 0.00 0.00 4.00
33 34 3.826729 GCTTTTCTGGGTTGTATCCTGTT 59.173 43.478 0.00 0.00 0.00 3.16
34 35 5.007682 GCTTTTCTGGGTTGTATCCTGTTA 58.992 41.667 0.00 0.00 0.00 2.41
35 36 5.475564 GCTTTTCTGGGTTGTATCCTGTTAA 59.524 40.000 0.00 0.00 0.00 2.01
36 37 6.015772 GCTTTTCTGGGTTGTATCCTGTTAAA 60.016 38.462 0.00 0.00 0.00 1.52
37 38 6.887626 TTTCTGGGTTGTATCCTGTTAAAC 57.112 37.500 0.00 0.00 0.00 2.01
38 39 5.836024 TCTGGGTTGTATCCTGTTAAACT 57.164 39.130 0.00 0.00 0.00 2.66
39 40 6.195600 TCTGGGTTGTATCCTGTTAAACTT 57.804 37.500 0.00 0.00 0.00 2.66
40 41 6.001460 TCTGGGTTGTATCCTGTTAAACTTG 58.999 40.000 0.00 0.00 0.00 3.16
41 42 5.074115 TGGGTTGTATCCTGTTAAACTTGG 58.926 41.667 0.00 0.00 0.00 3.61
42 43 5.074804 GGGTTGTATCCTGTTAAACTTGGT 58.925 41.667 0.00 0.00 0.00 3.67
43 44 5.048294 GGGTTGTATCCTGTTAAACTTGGTG 60.048 44.000 0.00 0.00 0.00 4.17
44 45 5.458015 GTTGTATCCTGTTAAACTTGGTGC 58.542 41.667 0.00 0.00 0.00 5.01
45 46 4.076394 TGTATCCTGTTAAACTTGGTGCC 58.924 43.478 0.00 0.00 0.00 5.01
46 47 3.525800 ATCCTGTTAAACTTGGTGCCT 57.474 42.857 0.00 0.00 0.00 4.75
47 48 2.582052 TCCTGTTAAACTTGGTGCCTG 58.418 47.619 0.00 0.00 0.00 4.85
48 49 2.173782 TCCTGTTAAACTTGGTGCCTGA 59.826 45.455 0.00 0.00 0.00 3.86
49 50 2.554032 CCTGTTAAACTTGGTGCCTGAG 59.446 50.000 0.00 0.00 0.00 3.35
50 51 2.554032 CTGTTAAACTTGGTGCCTGAGG 59.446 50.000 0.00 0.00 0.00 3.86
51 52 1.886542 GTTAAACTTGGTGCCTGAGGG 59.113 52.381 0.00 0.00 0.00 4.30
75 76 6.727569 CTTTATTAATTTAAAGCCGGACGC 57.272 37.500 5.05 0.00 33.69 5.19
76 77 2.810028 TTAATTTAAAGCCGGACGCG 57.190 45.000 5.05 3.53 44.76 6.01
77 78 1.724429 TAATTTAAAGCCGGACGCGT 58.276 45.000 13.85 13.85 44.76 6.01
78 79 0.876399 AATTTAAAGCCGGACGCGTT 59.124 45.000 15.53 0.00 44.76 4.84
79 80 0.876399 ATTTAAAGCCGGACGCGTTT 59.124 45.000 15.53 4.79 44.76 3.60
80 81 1.506493 TTTAAAGCCGGACGCGTTTA 58.494 45.000 15.53 3.60 44.76 2.01
81 82 1.070038 TTAAAGCCGGACGCGTTTAG 58.930 50.000 15.53 7.96 44.76 1.85
82 83 1.353609 TAAAGCCGGACGCGTTTAGC 61.354 55.000 15.53 16.65 44.76 3.09
92 93 3.540083 GCGTTTAGCGTCTTCGTTC 57.460 52.632 0.00 0.00 43.66 3.95
93 94 0.092519 GCGTTTAGCGTCTTCGTTCC 59.907 55.000 0.00 0.00 43.66 3.62
94 95 1.411394 CGTTTAGCGTCTTCGTTCCA 58.589 50.000 0.00 0.00 39.49 3.53
95 96 1.788308 CGTTTAGCGTCTTCGTTCCAA 59.212 47.619 0.00 0.00 39.49 3.53
96 97 2.219216 CGTTTAGCGTCTTCGTTCCAAA 59.781 45.455 0.00 0.00 39.49 3.28
97 98 3.302610 CGTTTAGCGTCTTCGTTCCAAAA 60.303 43.478 0.00 0.00 39.49 2.44
98 99 4.590226 GTTTAGCGTCTTCGTTCCAAAAA 58.410 39.130 0.00 0.00 39.49 1.94
139 140 5.489792 AGAAAGATCTGAAGTTAGCACCA 57.510 39.130 0.00 0.00 33.59 4.17
185 186 2.304761 ACCATGTCACCGAGGTTGTATT 59.695 45.455 0.00 0.00 0.00 1.89
186 187 3.516300 ACCATGTCACCGAGGTTGTATTA 59.484 43.478 0.00 0.00 0.00 0.98
187 188 4.119862 CCATGTCACCGAGGTTGTATTAG 58.880 47.826 0.00 0.00 0.00 1.73
188 189 3.241067 TGTCACCGAGGTTGTATTAGC 57.759 47.619 0.00 0.00 0.00 3.09
189 190 2.563620 TGTCACCGAGGTTGTATTAGCA 59.436 45.455 0.00 0.00 0.00 3.49
190 191 3.187700 GTCACCGAGGTTGTATTAGCAG 58.812 50.000 0.00 0.00 0.00 4.24
192 193 1.485066 ACCGAGGTTGTATTAGCAGGG 59.515 52.381 0.00 0.00 0.00 4.45
193 194 1.583054 CGAGGTTGTATTAGCAGGGC 58.417 55.000 0.00 0.00 0.00 5.19
194 195 1.810412 CGAGGTTGTATTAGCAGGGCC 60.810 57.143 0.00 0.00 0.00 5.80
226 231 8.579863 CCATTTCTGAGGAATAAAACCCATATC 58.420 37.037 0.00 0.00 0.00 1.63
255 261 9.739276 AAATAATGTCAAATGAGGTCTAGAACA 57.261 29.630 11.14 4.35 0.00 3.18
314 320 0.030773 GATCCGCGAGTGAGCACATA 59.969 55.000 8.23 0.00 36.85 2.29
315 321 0.676184 ATCCGCGAGTGAGCACATAT 59.324 50.000 8.23 0.00 36.85 1.78
426 432 7.831691 TGGTTTTCAGAAATCAGACCAATAA 57.168 32.000 12.88 0.00 31.09 1.40
427 433 8.421249 TGGTTTTCAGAAATCAGACCAATAAT 57.579 30.769 12.88 0.00 31.09 1.28
428 434 9.527157 TGGTTTTCAGAAATCAGACCAATAATA 57.473 29.630 12.88 0.00 31.09 0.98
442 448 6.810182 AGACCAATAATACGTGTGTGAGTAAC 59.190 38.462 0.00 0.00 0.00 2.50
460 816 6.039493 TGAGTAACTTACTAGCAGCTGGATAC 59.961 42.308 17.12 6.07 39.59 2.24
461 817 4.674281 AACTTACTAGCAGCTGGATACC 57.326 45.455 17.12 0.00 0.00 2.73
462 818 3.643237 ACTTACTAGCAGCTGGATACCA 58.357 45.455 17.12 0.00 0.00 3.25
463 819 4.227197 ACTTACTAGCAGCTGGATACCAT 58.773 43.478 17.12 0.00 30.82 3.55
464 820 4.656112 ACTTACTAGCAGCTGGATACCATT 59.344 41.667 17.12 0.00 30.82 3.16
465 821 5.839063 ACTTACTAGCAGCTGGATACCATTA 59.161 40.000 17.12 0.00 30.82 1.90
507 863 6.255020 CGTCGTTTAATATTACCACAAGAGCT 59.745 38.462 0.00 0.00 0.00 4.09
538 894 3.238788 TCCCTCCGAATATGCTACTCA 57.761 47.619 0.00 0.00 0.00 3.41
699 1129 8.241497 TGACTACTTTTTAGGTCACTAGTTCA 57.759 34.615 0.00 0.00 34.38 3.18
700 1130 8.867097 TGACTACTTTTTAGGTCACTAGTTCAT 58.133 33.333 0.00 0.00 34.38 2.57
701 1131 9.141400 GACTACTTTTTAGGTCACTAGTTCATG 57.859 37.037 0.00 0.00 0.00 3.07
702 1132 6.803154 ACTTTTTAGGTCACTAGTTCATGC 57.197 37.500 0.00 0.00 0.00 4.06
811 2447 3.933332 GTCGTTTTTGTCCAGCTAGCTAT 59.067 43.478 18.86 0.00 0.00 2.97
829 2465 0.534427 ATCATCGTCGTCTCCGGCTA 60.534 55.000 0.00 0.00 36.28 3.93
846 2482 7.295196 TCTCCGGCTAGTCTCCCTATATATATT 59.705 40.741 0.00 0.00 0.00 1.28
936 2575 6.696583 TCACACAAAGAAAATTGCATACACAG 59.303 34.615 0.00 0.00 33.52 3.66
1554 3223 1.594331 GGTTCCTGCTCAACTTCGTT 58.406 50.000 0.00 0.00 0.00 3.85
1698 3367 2.359975 GGAAAGGGTGGCGAGGTG 60.360 66.667 0.00 0.00 0.00 4.00
1763 3432 1.089920 CAAGTCTGATCGGCCTTTGG 58.910 55.000 0.00 0.00 0.00 3.28
2045 4039 4.771590 AGTGTATGTGTGCAATTCTTGG 57.228 40.909 0.00 0.00 0.00 3.61
2048 4042 3.255395 TGTATGTGTGCAATTCTTGGTGG 59.745 43.478 0.00 0.00 0.00 4.61
2050 4044 2.937519 TGTGTGCAATTCTTGGTGGTA 58.062 42.857 0.00 0.00 0.00 3.25
2051 4045 2.621055 TGTGTGCAATTCTTGGTGGTAC 59.379 45.455 0.00 0.00 0.00 3.34
2052 4046 2.884639 GTGTGCAATTCTTGGTGGTACT 59.115 45.455 0.00 0.00 0.00 2.73
2053 4047 4.069304 GTGTGCAATTCTTGGTGGTACTA 58.931 43.478 0.00 0.00 0.00 1.82
2056 4050 5.012251 TGTGCAATTCTTGGTGGTACTAGTA 59.988 40.000 0.00 0.00 0.00 1.82
2057 4051 5.581085 GTGCAATTCTTGGTGGTACTAGTAG 59.419 44.000 1.87 0.00 0.00 2.57
2062 4057 8.475639 CAATTCTTGGTGGTACTAGTAGTGTAT 58.524 37.037 13.29 0.00 0.00 2.29
2063 4058 9.705103 AATTCTTGGTGGTACTAGTAGTGTATA 57.295 33.333 13.29 0.00 0.00 1.47
2064 4059 8.511604 TTCTTGGTGGTACTAGTAGTGTATAC 57.488 38.462 13.29 2.84 0.00 1.47
2112 4124 6.409524 AACTTGATGACAATTTCACATGGT 57.590 33.333 0.00 0.00 36.92 3.55
2223 4235 3.063452 TCGAGAAGCACACAACTTTTCAC 59.937 43.478 0.00 0.00 29.87 3.18
2325 4366 3.624326 TCAGGAAATTGTCAAAGTGCG 57.376 42.857 0.00 0.00 0.00 5.34
2360 4401 2.600420 CACGAGCTATATTGCTATGGCG 59.400 50.000 11.76 12.82 44.22 5.69
2363 4404 3.673323 CGAGCTATATTGCTATGGCGACA 60.673 47.826 11.76 0.00 44.22 4.35
2369 4410 8.901016 AGCTATATTGCTATGGCGACAAAAGAC 61.901 40.741 10.06 0.85 44.22 3.01
2407 4448 8.951243 GGCTATCATTTCCCTCTAATACAATTC 58.049 37.037 0.00 0.00 0.00 2.17
2456 4497 0.031043 TGAAACCGACGACGTGTGAT 59.969 50.000 4.58 0.00 37.88 3.06
2468 4509 1.636340 GTGTGATGTATGTCGCGGC 59.364 57.895 2.29 2.29 0.00 6.53
2486 4527 0.442310 GCTGCACGCGACAAAAGATA 59.558 50.000 15.93 0.00 0.00 1.98
2540 4581 1.362717 CTGGTGAACCACGACGTCT 59.637 57.895 14.70 0.00 42.01 4.18
2571 4612 0.826715 CCATGGTGGTGATCTCGTCT 59.173 55.000 2.57 0.00 31.35 4.18
2597 4638 1.354101 TTGGTGGGTGTGGTAGGTAG 58.646 55.000 0.00 0.00 0.00 3.18
2598 4639 0.545787 TGGTGGGTGTGGTAGGTAGG 60.546 60.000 0.00 0.00 0.00 3.18
2599 4640 0.546027 GGTGGGTGTGGTAGGTAGGT 60.546 60.000 0.00 0.00 0.00 3.08
2600 4641 1.273211 GGTGGGTGTGGTAGGTAGGTA 60.273 57.143 0.00 0.00 0.00 3.08
2606 4647 2.121129 TGTGGTAGGTAGGTAATGCCC 58.879 52.381 0.00 0.00 38.26 5.36
2607 4648 1.419012 GTGGTAGGTAGGTAATGCCCC 59.581 57.143 0.00 0.00 38.26 5.80
2609 4650 1.697982 GGTAGGTAGGTAATGCCCCAG 59.302 57.143 0.00 0.00 38.26 4.45
2615 4656 3.393278 GGTAGGTAATGCCCCAGATGTTA 59.607 47.826 0.00 0.00 38.26 2.41
2649 4690 1.177668 CGTACGTCTTCGGATGAACG 58.822 55.000 7.22 11.39 39.06 3.95
2661 4704 0.572590 GATGAACGATGGCGAAGTCG 59.427 55.000 0.00 0.00 43.13 4.18
2736 4780 7.484641 GCGTTGCAATGAGAGAAAATTTACATA 59.515 33.333 22.81 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.769300 ACCCAGAAAAGCAGAAAACAAGT 59.231 39.130 0.00 0.00 0.00 3.16
1 2 4.391405 ACCCAGAAAAGCAGAAAACAAG 57.609 40.909 0.00 0.00 0.00 3.16
2 3 4.020662 ACAACCCAGAAAAGCAGAAAACAA 60.021 37.500 0.00 0.00 0.00 2.83
3 4 3.513515 ACAACCCAGAAAAGCAGAAAACA 59.486 39.130 0.00 0.00 0.00 2.83
4 5 4.123497 ACAACCCAGAAAAGCAGAAAAC 57.877 40.909 0.00 0.00 0.00 2.43
5 6 5.010617 GGATACAACCCAGAAAAGCAGAAAA 59.989 40.000 0.00 0.00 0.00 2.29
6 7 4.522789 GGATACAACCCAGAAAAGCAGAAA 59.477 41.667 0.00 0.00 0.00 2.52
7 8 4.079253 GGATACAACCCAGAAAAGCAGAA 58.921 43.478 0.00 0.00 0.00 3.02
8 9 3.330701 AGGATACAACCCAGAAAAGCAGA 59.669 43.478 0.00 0.00 41.41 4.26
9 10 3.441572 CAGGATACAACCCAGAAAAGCAG 59.558 47.826 0.00 0.00 41.41 4.24
10 11 3.181434 ACAGGATACAACCCAGAAAAGCA 60.181 43.478 0.00 0.00 41.41 3.91
11 12 3.421844 ACAGGATACAACCCAGAAAAGC 58.578 45.455 0.00 0.00 41.41 3.51
12 13 7.230712 AGTTTAACAGGATACAACCCAGAAAAG 59.769 37.037 0.00 0.00 41.41 2.27
13 14 7.064229 AGTTTAACAGGATACAACCCAGAAAA 58.936 34.615 0.00 0.00 41.41 2.29
14 15 6.607019 AGTTTAACAGGATACAACCCAGAAA 58.393 36.000 0.00 0.00 41.41 2.52
15 16 6.195600 AGTTTAACAGGATACAACCCAGAA 57.804 37.500 0.00 0.00 41.41 3.02
16 17 5.836024 AGTTTAACAGGATACAACCCAGA 57.164 39.130 0.00 0.00 41.41 3.86
17 18 5.183140 CCAAGTTTAACAGGATACAACCCAG 59.817 44.000 0.00 0.00 41.41 4.45
18 19 5.074115 CCAAGTTTAACAGGATACAACCCA 58.926 41.667 0.00 0.00 41.41 4.51
19 20 5.048294 CACCAAGTTTAACAGGATACAACCC 60.048 44.000 12.36 0.00 41.41 4.11
20 21 5.564063 GCACCAAGTTTAACAGGATACAACC 60.564 44.000 12.36 0.00 41.41 3.77
21 22 5.458015 GCACCAAGTTTAACAGGATACAAC 58.542 41.667 12.36 0.00 41.41 3.32
22 23 4.521256 GGCACCAAGTTTAACAGGATACAA 59.479 41.667 12.36 0.00 41.41 2.41
23 24 4.076394 GGCACCAAGTTTAACAGGATACA 58.924 43.478 12.36 0.00 41.41 2.29
24 25 4.156008 CAGGCACCAAGTTTAACAGGATAC 59.844 45.833 12.36 3.51 0.00 2.24
25 26 4.042311 TCAGGCACCAAGTTTAACAGGATA 59.958 41.667 12.36 0.00 0.00 2.59
26 27 3.157087 CAGGCACCAAGTTTAACAGGAT 58.843 45.455 12.36 0.00 0.00 3.24
27 28 2.173782 TCAGGCACCAAGTTTAACAGGA 59.826 45.455 12.36 0.00 0.00 3.86
28 29 2.554032 CTCAGGCACCAAGTTTAACAGG 59.446 50.000 0.00 1.44 0.00 4.00
29 30 2.554032 CCTCAGGCACCAAGTTTAACAG 59.446 50.000 0.00 0.00 0.00 3.16
30 31 2.582052 CCTCAGGCACCAAGTTTAACA 58.418 47.619 0.00 0.00 0.00 2.41
31 32 1.886542 CCCTCAGGCACCAAGTTTAAC 59.113 52.381 0.00 0.00 0.00 2.01
32 33 2.286365 CCCTCAGGCACCAAGTTTAA 57.714 50.000 0.00 0.00 0.00 1.52
34 35 4.929807 CCCTCAGGCACCAAGTTT 57.070 55.556 0.00 0.00 0.00 2.66
52 53 5.394322 CGCGTCCGGCTTTAAATTAATAAAG 59.606 40.000 0.00 6.41 42.93 1.85
53 54 5.163774 ACGCGTCCGGCTTTAAATTAATAAA 60.164 36.000 5.58 0.00 40.44 1.40
54 55 4.332268 ACGCGTCCGGCTTTAAATTAATAA 59.668 37.500 5.58 0.00 40.44 1.40
55 56 3.870419 ACGCGTCCGGCTTTAAATTAATA 59.130 39.130 5.58 0.00 40.44 0.98
56 57 2.679336 ACGCGTCCGGCTTTAAATTAAT 59.321 40.909 5.58 0.00 40.44 1.40
57 58 2.075338 ACGCGTCCGGCTTTAAATTAA 58.925 42.857 5.58 0.00 40.44 1.40
58 59 1.724429 ACGCGTCCGGCTTTAAATTA 58.276 45.000 5.58 0.00 40.44 1.40
59 60 0.876399 AACGCGTCCGGCTTTAAATT 59.124 45.000 14.44 0.00 40.44 1.82
60 61 0.876399 AAACGCGTCCGGCTTTAAAT 59.124 45.000 14.44 0.00 40.44 1.40
61 62 1.460359 CTAAACGCGTCCGGCTTTAAA 59.540 47.619 14.44 0.00 40.44 1.52
62 63 1.070038 CTAAACGCGTCCGGCTTTAA 58.930 50.000 14.44 0.00 40.44 1.52
63 64 1.353609 GCTAAACGCGTCCGGCTTTA 61.354 55.000 14.44 5.33 40.44 1.85
64 65 2.674084 GCTAAACGCGTCCGGCTTT 61.674 57.895 14.44 4.19 40.44 3.51
65 66 3.116531 GCTAAACGCGTCCGGCTT 61.117 61.111 14.44 5.06 40.44 4.35
76 77 3.865224 TTTGGAACGAAGACGCTAAAC 57.135 42.857 0.00 0.00 43.96 2.01
77 78 4.879104 TTTTTGGAACGAAGACGCTAAA 57.121 36.364 0.00 0.00 43.96 1.85
139 140 1.327303 ACCCGATGCAACAAACATGT 58.673 45.000 0.00 0.00 0.00 3.21
167 168 3.196901 TGCTAATACAACCTCGGTGACAT 59.803 43.478 0.00 0.00 0.00 3.06
169 170 3.187700 CTGCTAATACAACCTCGGTGAC 58.812 50.000 0.00 0.00 0.00 3.67
185 186 1.295020 AATGGTGTTAGGCCCTGCTA 58.705 50.000 0.00 0.00 0.00 3.49
186 187 0.409484 AAATGGTGTTAGGCCCTGCT 59.591 50.000 0.00 0.00 0.00 4.24
187 188 0.817654 GAAATGGTGTTAGGCCCTGC 59.182 55.000 0.00 0.00 0.00 4.85
188 189 2.094675 CAGAAATGGTGTTAGGCCCTG 58.905 52.381 0.00 0.00 0.00 4.45
189 190 1.992557 TCAGAAATGGTGTTAGGCCCT 59.007 47.619 0.00 0.00 0.00 5.19
190 191 2.369394 CTCAGAAATGGTGTTAGGCCC 58.631 52.381 0.00 0.00 0.00 5.80
192 193 3.350219 TCCTCAGAAATGGTGTTAGGC 57.650 47.619 0.00 0.00 0.00 3.93
193 194 7.938140 TTTATTCCTCAGAAATGGTGTTAGG 57.062 36.000 0.00 0.00 35.09 2.69
194 195 8.244113 GGTTTTATTCCTCAGAAATGGTGTTAG 58.756 37.037 0.00 0.00 35.09 2.34
226 231 9.098355 TCTAGACCTCATTTGACATTATTTTCG 57.902 33.333 0.00 0.00 0.00 3.46
255 261 4.905429 TGGCATATACTTAACCGATGCAT 58.095 39.130 0.00 0.00 43.74 3.96
373 379 7.837689 AGGATGAAGAATGATGGATGAAAAGAA 59.162 33.333 0.00 0.00 0.00 2.52
397 403 6.434028 TGGTCTGATTTCTGAAAACCAATAGG 59.566 38.462 17.64 4.97 42.21 2.57
426 432 6.149973 TGCTAGTAAGTTACTCACACACGTAT 59.850 38.462 18.77 0.00 40.14 3.06
427 433 5.469760 TGCTAGTAAGTTACTCACACACGTA 59.530 40.000 18.77 0.00 40.14 3.57
428 434 4.276678 TGCTAGTAAGTTACTCACACACGT 59.723 41.667 18.77 0.00 40.14 4.49
442 448 4.881019 ATGGTATCCAGCTGCTAGTAAG 57.119 45.455 8.66 0.00 36.75 2.34
460 816 4.635765 CGATATGCCCAGTAATGGTAATGG 59.364 45.833 8.66 0.00 43.73 3.16
461 817 5.245531 ACGATATGCCCAGTAATGGTAATG 58.754 41.667 8.66 0.00 0.00 1.90
462 818 5.488341 GACGATATGCCCAGTAATGGTAAT 58.512 41.667 8.66 3.92 0.00 1.89
463 819 4.559906 CGACGATATGCCCAGTAATGGTAA 60.560 45.833 8.66 0.00 0.00 2.85
464 820 3.057104 CGACGATATGCCCAGTAATGGTA 60.057 47.826 8.66 0.00 0.00 3.25
465 821 2.288825 CGACGATATGCCCAGTAATGGT 60.289 50.000 8.66 0.00 0.00 3.55
484 840 6.759827 GGAGCTCTTGTGGTAATATTAAACGA 59.240 38.462 14.64 0.00 0.00 3.85
507 863 1.227102 CGGAGGGATGCCAATTGGA 59.773 57.895 29.02 13.44 37.39 3.53
699 1129 1.575419 ATTCAAAGGCCACCATGCAT 58.425 45.000 5.01 0.00 0.00 3.96
700 1130 2.101783 CTATTCAAAGGCCACCATGCA 58.898 47.619 5.01 0.00 0.00 3.96
701 1131 2.360165 CTCTATTCAAAGGCCACCATGC 59.640 50.000 5.01 0.00 0.00 4.06
702 1132 3.624777 ACTCTATTCAAAGGCCACCATG 58.375 45.455 5.01 0.00 0.00 3.66
936 2575 0.681733 TCTCACTCCACCTTGCAGTC 59.318 55.000 0.00 0.00 0.00 3.51
1518 3187 2.760385 CCCCTGTCGAGGACCTCC 60.760 72.222 16.13 3.36 42.93 4.30
1554 3223 0.321671 CGAAGAAGAGCCTGTTCCCA 59.678 55.000 0.00 0.00 0.00 4.37
1698 3367 3.372206 CGGTCATCTCCATTTTGTCACTC 59.628 47.826 0.00 0.00 0.00 3.51
1735 3404 1.802508 CGATCAGACTTGCATGCCGTA 60.803 52.381 16.68 0.00 0.00 4.02
1763 3432 0.433492 CGTGTCACCAACGATCGAAC 59.567 55.000 24.34 9.85 43.68 3.95
1931 3600 1.251251 CAGGGCCTCTTTGGAAACAG 58.749 55.000 0.95 0.00 44.54 3.16
1964 3635 2.422479 GACTTGTCTCACATGCATGCAT 59.578 45.455 27.46 27.46 37.08 3.96
1965 3636 1.808343 GACTTGTCTCACATGCATGCA 59.192 47.619 26.53 25.04 0.00 3.96
1966 3637 1.808343 TGACTTGTCTCACATGCATGC 59.192 47.619 26.53 11.82 0.00 4.06
1967 3638 3.242316 CGATGACTTGTCTCACATGCATG 60.242 47.826 25.09 25.09 0.00 4.06
1968 3639 2.934553 CGATGACTTGTCTCACATGCAT 59.065 45.455 0.00 0.00 0.00 3.96
1969 3640 2.340337 CGATGACTTGTCTCACATGCA 58.660 47.619 0.00 0.00 0.00 3.96
1970 3641 1.662629 CCGATGACTTGTCTCACATGC 59.337 52.381 0.00 0.00 0.00 4.06
1971 3642 2.926200 GTCCGATGACTTGTCTCACATG 59.074 50.000 2.35 0.00 38.53 3.21
1972 3643 2.562738 TGTCCGATGACTTGTCTCACAT 59.437 45.455 2.35 0.00 42.28 3.21
1973 3644 1.960689 TGTCCGATGACTTGTCTCACA 59.039 47.619 2.35 0.00 42.28 3.58
1974 3645 2.600731 CTGTCCGATGACTTGTCTCAC 58.399 52.381 2.35 0.00 42.28 3.51
2056 4050 6.720288 ACAGGTGAAGAACAGTAGTATACACT 59.280 38.462 5.50 4.08 46.26 3.55
2057 4051 6.921914 ACAGGTGAAGAACAGTAGTATACAC 58.078 40.000 5.50 1.76 46.26 2.90
2062 4057 6.513884 CGTTGTACAGGTGAAGAACAGTAGTA 60.514 42.308 0.00 0.00 0.00 1.82
2063 4058 5.598769 GTTGTACAGGTGAAGAACAGTAGT 58.401 41.667 0.00 0.00 0.00 2.73
2064 4059 4.680110 CGTTGTACAGGTGAAGAACAGTAG 59.320 45.833 0.00 0.00 0.00 2.57
2077 4089 4.509970 TGTCATCAAGTTTCGTTGTACAGG 59.490 41.667 0.00 0.00 0.00 4.00
2112 4124 3.621268 GCAAATTCGTGCACTACTCCATA 59.379 43.478 16.19 0.00 44.29 2.74
2241 4253 0.685097 TGCACTTTCGGGAGTAGCTT 59.315 50.000 0.00 0.00 0.00 3.74
2242 4254 0.905357 ATGCACTTTCGGGAGTAGCT 59.095 50.000 0.00 0.00 0.00 3.32
2243 4255 1.739067 AATGCACTTTCGGGAGTAGC 58.261 50.000 0.00 0.00 0.00 3.58
2244 4256 2.159517 GCAAATGCACTTTCGGGAGTAG 60.160 50.000 0.00 0.00 41.59 2.57
2245 4257 1.810151 GCAAATGCACTTTCGGGAGTA 59.190 47.619 0.00 0.00 41.59 2.59
2246 4258 0.598065 GCAAATGCACTTTCGGGAGT 59.402 50.000 0.00 0.00 41.59 3.85
2360 4401 1.197721 CACTGATGGCCGTCTTTTGTC 59.802 52.381 25.20 0.00 0.00 3.18
2363 4404 0.609131 CCCACTGATGGCCGTCTTTT 60.609 55.000 25.20 7.09 45.76 2.27
2407 4448 2.202570 CCGCACCTAGACGAACCG 60.203 66.667 0.00 0.00 0.00 4.44
2456 4497 2.813474 GTGCAGCCGCGACATACA 60.813 61.111 8.23 0.00 42.97 2.29
2468 4509 1.527793 GCTATCTTTTGTCGCGTGCAG 60.528 52.381 5.77 0.00 0.00 4.41
2486 4527 3.753434 CCGAGACACTCAGCCGCT 61.753 66.667 0.00 0.00 0.00 5.52
2571 4612 3.575247 ACACCCACCAATGCCCGA 61.575 61.111 0.00 0.00 0.00 5.14
2597 4638 2.230660 GCTAACATCTGGGGCATTACC 58.769 52.381 0.00 0.00 37.93 2.85
2598 4639 1.873591 CGCTAACATCTGGGGCATTAC 59.126 52.381 0.00 0.00 0.00 1.89
2599 4640 1.813862 GCGCTAACATCTGGGGCATTA 60.814 52.381 0.00 0.00 38.50 1.90
2600 4641 1.103398 GCGCTAACATCTGGGGCATT 61.103 55.000 0.00 0.00 38.50 3.56
2606 4647 4.285149 GCGCGCGCTAACATCTGG 62.285 66.667 44.38 11.16 38.26 3.86
2607 4648 4.617454 CGCGCGCGCTAACATCTG 62.617 66.667 45.97 27.76 39.32 2.90
2637 4678 0.527600 TCGCCATCGTTCATCCGAAG 60.528 55.000 0.00 0.00 40.73 3.79
2661 4704 4.794248 AAAAAGAAATTCAAGTTGCCGC 57.206 36.364 0.00 0.00 0.00 6.53
2689 4732 4.584029 CACGAGTATTTGTGCTAGTTGG 57.416 45.455 0.00 0.00 32.16 3.77
2711 4754 7.801547 ATGTAAATTTTCTCTCATTGCAACG 57.198 32.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.