Multiple sequence alignment - TraesCS5B01G487100

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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 TraesCS5B01G487100 chr5B 100.000 3293 0 0 1 3293 658171157 658174449 0.000000e+00 6082
1 TraesCS5B01G487100 chr5B 86.355 2030 219 26 719 2718 658368497 658370498 0.000000e+00 2161
2 TraesCS5B01G487100 chr5B 83.623 1844 250 31 600 2418 658152354 658154170 0.000000e+00 1685
3 TraesCS5B01G487100 chr5B 81.729 1943 257 53 600 2512 658157657 658159531 0.000000e+00 1531
4 TraesCS5B01G487100 chr5B 83.051 1711 242 29 960 2638 658460346 658458652 0.000000e+00 1509
5 TraesCS5B01G487100 chr5B 84.272 1367 155 38 414 1757 658371813 658373142 0.000000e+00 1279
6 TraesCS5B01G487100 chr5B 77.895 380 33 24 232 593 658151818 658152164 4.340000e-44 189
7 TraesCS5B01G487100 chr5D 94.208 3073 129 13 160 3226 521864955 521867984 0.000000e+00 4643
8 TraesCS5B01G487100 chr5D 83.290 1939 258 38 600 2512 521843730 521845628 0.000000e+00 1725
9 TraesCS5B01G487100 chr5D 83.343 1711 234 28 960 2638 522156210 522154519 0.000000e+00 1533
10 TraesCS5B01G487100 chr5D 84.019 1483 209 12 951 2418 521836824 521838293 0.000000e+00 1400
11 TraesCS5B01G487100 chr5D 78.533 368 37 24 232 593 521828214 521828545 1.550000e-48 204
12 TraesCS5B01G487100 chr5A 90.090 1665 151 9 786 2445 650159681 650161336 0.000000e+00 2148
13 TraesCS5B01G487100 chr5A 81.988 2082 293 46 600 2638 650141536 650143578 0.000000e+00 1692
14 TraesCS5B01G487100 chr5A 94.205 604 30 2 2435 3037 650161583 650162182 0.000000e+00 917
15 TraesCS5B01G487100 chr5A 85.190 817 96 17 759 1562 650147081 650147885 0.000000e+00 815
16 TraesCS5B01G487100 chr5A 85.833 720 66 18 2178 2882 650245042 650245740 0.000000e+00 732
17 TraesCS5B01G487100 chr5A 85.043 702 69 18 2255 2941 650245764 650246444 0.000000e+00 682
18 TraesCS5B01G487100 chr5A 93.103 261 9 5 3041 3293 650171859 650172118 1.120000e-99 374
19 TraesCS5B01G487100 chr5A 93.103 261 9 5 3041 3293 650176962 650177221 1.120000e-99 374
20 TraesCS5B01G487100 chr5A 93.103 261 9 5 3041 3293 650178893 650179152 1.120000e-99 374
21 TraesCS5B01G487100 chr5A 87.255 102 12 1 475 575 650146679 650146780 7.470000e-22 115
22 TraesCS5B01G487100 chr5A 82.468 154 6 11 171 304 650159122 650159274 7.470000e-22 115
23 TraesCS5B01G487100 chr2B 96.273 161 6 0 1 161 382993474 382993314 7.010000e-67 265
24 TraesCS5B01G487100 chr6B 94.410 161 9 0 1 161 57422846 57422686 7.060000e-62 248
25 TraesCS5B01G487100 chr1B 94.410 161 9 0 1 161 7058657 7058497 7.060000e-62 248
26 TraesCS5B01G487100 chr1B 94.375 160 8 1 1 159 637325910 637326069 9.130000e-61 244
27 TraesCS5B01G487100 chr1B 93.827 162 9 1 1 162 664337128 664336968 3.280000e-60 243
28 TraesCS5B01G487100 chr3B 93.789 161 10 0 1 161 591477896 591478056 3.280000e-60 243
29 TraesCS5B01G487100 chrUn 93.168 161 11 0 1 161 260673432 260673272 1.530000e-58 237
30 TraesCS5B01G487100 chr7B 93.168 161 11 0 1 161 739399825 739399665 1.530000e-58 237
31 TraesCS5B01G487100 chr4A 93.168 161 11 0 1 161 731448285 731448445 1.530000e-58 237


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 TraesCS5B01G487100 chr5B 658171157 658174449 3292 False 6082 6082 100.000000 1 3293 1 chr5B.!!$F1 3292
1 TraesCS5B01G487100 chr5B 658368497 658373142 4645 False 1720 2161 85.313500 414 2718 2 chr5B.!!$F3 2304
2 TraesCS5B01G487100 chr5B 658458652 658460346 1694 True 1509 1509 83.051000 960 2638 1 chr5B.!!$R1 1678
3 TraesCS5B01G487100 chr5B 658151818 658159531 7713 False 1135 1685 81.082333 232 2512 3 chr5B.!!$F2 2280
4 TraesCS5B01G487100 chr5D 521864955 521867984 3029 False 4643 4643 94.208000 160 3226 1 chr5D.!!$F4 3066
5 TraesCS5B01G487100 chr5D 521843730 521845628 1898 False 1725 1725 83.290000 600 2512 1 chr5D.!!$F3 1912
6 TraesCS5B01G487100 chr5D 522154519 522156210 1691 True 1533 1533 83.343000 960 2638 1 chr5D.!!$R1 1678
7 TraesCS5B01G487100 chr5D 521836824 521838293 1469 False 1400 1400 84.019000 951 2418 1 chr5D.!!$F2 1467
8 TraesCS5B01G487100 chr5A 650159122 650162182 3060 False 1060 2148 88.921000 171 3037 3 chr5A.!!$F3 2866
9 TraesCS5B01G487100 chr5A 650141536 650147885 6349 False 874 1692 84.811000 475 2638 3 chr5A.!!$F2 2163
10 TraesCS5B01G487100 chr5A 650245042 650246444 1402 False 707 732 85.438000 2178 2941 2 chr5A.!!$F5 763
11 TraesCS5B01G487100 chr5A 650176962 650179152 2190 False 374 374 93.103000 3041 3293 2 chr5A.!!$F4 252

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
404 428 0.105453 TATCCTCTGTCTGCTCCCCC 60.105 60.0 0.0 0.0 0.00 5.40 F
712 959 0.546122 TTGGCATCTTCCATAGCGGT 59.454 50.0 0.0 0.0 35.77 5.68 F
1791 2058 0.599204 CGGTTACTCACGTTGCCACT 60.599 55.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2348 0.318529 CTCATCGATCCAGAGCACCG 60.319 60.000 0.00 0.0 0.0 4.94 R
2244 2514 2.024273 TCCCCTTTCTACGTCCAGAGAT 60.024 50.000 0.00 0.0 0.0 2.75 R
3181 11230 1.476488 ACAATGCATTAGTTTCCCGGC 59.524 47.619 12.53 0.0 0.0 6.13 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 4.390048 GCCTAGTTGTGGCCGAAA 57.610 55.556 0.00 0.00 44.32 3.46
18 19 2.868253 GCCTAGTTGTGGCCGAAAT 58.132 52.632 0.00 0.00 44.32 2.17
19 20 0.451783 GCCTAGTTGTGGCCGAAATG 59.548 55.000 0.00 0.00 44.32 2.32
20 21 1.821216 CCTAGTTGTGGCCGAAATGT 58.179 50.000 0.00 0.00 0.00 2.71
21 22 1.468520 CCTAGTTGTGGCCGAAATGTG 59.531 52.381 0.00 0.00 0.00 3.21
22 23 2.151202 CTAGTTGTGGCCGAAATGTGT 58.849 47.619 0.00 0.00 0.00 3.72
23 24 1.398692 AGTTGTGGCCGAAATGTGTT 58.601 45.000 0.00 0.00 0.00 3.32
24 25 2.577700 AGTTGTGGCCGAAATGTGTTA 58.422 42.857 0.00 0.00 0.00 2.41
25 26 2.292292 AGTTGTGGCCGAAATGTGTTAC 59.708 45.455 0.00 0.00 0.00 2.50
26 27 2.264005 TGTGGCCGAAATGTGTTACT 57.736 45.000 0.00 0.00 0.00 2.24
27 28 2.577700 TGTGGCCGAAATGTGTTACTT 58.422 42.857 0.00 0.00 0.00 2.24
28 29 2.550606 TGTGGCCGAAATGTGTTACTTC 59.449 45.455 0.00 0.00 0.00 3.01
29 30 1.801771 TGGCCGAAATGTGTTACTTCG 59.198 47.619 0.00 0.00 41.18 3.79
32 33 2.520686 CGAAATGTGTTACTTCGGCC 57.479 50.000 0.00 0.00 38.57 6.13
33 34 1.801771 CGAAATGTGTTACTTCGGCCA 59.198 47.619 2.24 0.00 38.57 5.36
34 35 2.224549 CGAAATGTGTTACTTCGGCCAA 59.775 45.455 2.24 0.00 38.57 4.52
35 36 3.304123 CGAAATGTGTTACTTCGGCCAAA 60.304 43.478 2.24 0.00 38.57 3.28
36 37 4.614993 CGAAATGTGTTACTTCGGCCAAAT 60.615 41.667 2.24 0.00 38.57 2.32
37 38 3.848272 ATGTGTTACTTCGGCCAAATG 57.152 42.857 2.24 0.00 0.00 2.32
38 39 2.852449 TGTGTTACTTCGGCCAAATGA 58.148 42.857 2.24 0.00 0.00 2.57
39 40 3.417101 TGTGTTACTTCGGCCAAATGAT 58.583 40.909 2.24 0.00 0.00 2.45
40 41 3.190327 TGTGTTACTTCGGCCAAATGATG 59.810 43.478 2.24 0.00 0.00 3.07
52 53 3.769536 CCAAATGATGGCCGAAAACTAC 58.230 45.455 0.00 0.00 43.80 2.73
53 54 3.443681 CCAAATGATGGCCGAAAACTACT 59.556 43.478 0.00 0.00 43.80 2.57
54 55 4.638421 CCAAATGATGGCCGAAAACTACTA 59.362 41.667 0.00 0.00 43.80 1.82
55 56 5.448632 CCAAATGATGGCCGAAAACTACTAC 60.449 44.000 0.00 0.00 43.80 2.73
56 57 4.755266 ATGATGGCCGAAAACTACTACT 57.245 40.909 0.00 0.00 0.00 2.57
57 58 4.546829 TGATGGCCGAAAACTACTACTT 57.453 40.909 0.00 0.00 0.00 2.24
58 59 4.501071 TGATGGCCGAAAACTACTACTTC 58.499 43.478 0.00 0.00 0.00 3.01
59 60 2.950433 TGGCCGAAAACTACTACTTCG 58.050 47.619 0.00 0.00 41.18 3.79
63 64 2.950433 CGAAAACTACTACTTCGGCCA 58.050 47.619 2.24 0.00 38.57 5.36
64 65 3.319755 CGAAAACTACTACTTCGGCCAA 58.680 45.455 2.24 0.00 38.57 4.52
65 66 3.742369 CGAAAACTACTACTTCGGCCAAA 59.258 43.478 2.24 0.00 38.57 3.28
66 67 4.211794 CGAAAACTACTACTTCGGCCAAAA 59.788 41.667 2.24 0.00 38.57 2.44
67 68 5.614013 CGAAAACTACTACTTCGGCCAAAAG 60.614 44.000 12.25 12.25 38.57 2.27
68 69 4.612264 AACTACTACTTCGGCCAAAAGA 57.388 40.909 19.09 0.00 0.00 2.52
69 70 4.820894 ACTACTACTTCGGCCAAAAGAT 57.179 40.909 19.09 8.04 0.00 2.40
70 71 4.504858 ACTACTACTTCGGCCAAAAGATG 58.495 43.478 19.09 13.27 0.00 2.90
78 79 3.187058 CCAAAAGATGGCCGACGG 58.813 61.111 10.29 10.29 43.80 4.79
79 80 2.406616 CCAAAAGATGGCCGACGGG 61.407 63.158 17.22 0.00 43.80 5.28
91 92 1.636988 CCGACGGGCTACTAGTTTTG 58.363 55.000 5.81 0.00 0.00 2.44
92 93 1.636988 CGACGGGCTACTAGTTTTGG 58.363 55.000 0.00 0.00 0.00 3.28
93 94 1.067354 CGACGGGCTACTAGTTTTGGT 60.067 52.381 0.00 0.00 0.00 3.67
94 95 2.611224 CGACGGGCTACTAGTTTTGGTT 60.611 50.000 0.00 0.00 0.00 3.67
95 96 3.405831 GACGGGCTACTAGTTTTGGTTT 58.594 45.455 0.00 0.00 0.00 3.27
96 97 3.817084 GACGGGCTACTAGTTTTGGTTTT 59.183 43.478 0.00 0.00 0.00 2.43
97 98 4.209538 ACGGGCTACTAGTTTTGGTTTTT 58.790 39.130 0.00 0.00 0.00 1.94
121 122 7.548196 TTTGCATTAAGTCCTATAGTTTCCG 57.452 36.000 0.00 0.00 0.00 4.30
122 123 6.474140 TGCATTAAGTCCTATAGTTTCCGA 57.526 37.500 0.00 0.00 0.00 4.55
123 124 6.880484 TGCATTAAGTCCTATAGTTTCCGAA 58.120 36.000 0.00 0.00 0.00 4.30
124 125 7.332557 TGCATTAAGTCCTATAGTTTCCGAAA 58.667 34.615 0.00 0.00 0.00 3.46
125 126 7.825270 TGCATTAAGTCCTATAGTTTCCGAAAA 59.175 33.333 0.00 0.00 0.00 2.29
126 127 8.837389 GCATTAAGTCCTATAGTTTCCGAAAAT 58.163 33.333 0.00 0.00 0.00 1.82
128 129 6.679327 AAGTCCTATAGTTTCCGAAAATGC 57.321 37.500 4.10 0.00 0.00 3.56
129 130 5.990668 AGTCCTATAGTTTCCGAAAATGCT 58.009 37.500 4.10 0.00 0.00 3.79
130 131 7.120923 AGTCCTATAGTTTCCGAAAATGCTA 57.879 36.000 4.10 0.00 0.00 3.49
131 132 7.736893 AGTCCTATAGTTTCCGAAAATGCTAT 58.263 34.615 4.10 6.05 0.00 2.97
132 133 8.867097 AGTCCTATAGTTTCCGAAAATGCTATA 58.133 33.333 4.10 6.76 0.00 1.31
133 134 9.485206 GTCCTATAGTTTCCGAAAATGCTATAA 57.515 33.333 4.10 0.00 0.00 0.98
175 176 4.695217 AAAAATCATGTATTGACGGCGT 57.305 36.364 14.65 14.65 37.11 5.68
312 333 6.205853 CCACTTCGAAGCTAGACTACTATCAT 59.794 42.308 24.86 0.00 0.00 2.45
313 334 7.388224 CCACTTCGAAGCTAGACTACTATCATA 59.612 40.741 24.86 0.00 0.00 2.15
314 335 8.941977 CACTTCGAAGCTAGACTACTATCATAT 58.058 37.037 24.86 0.00 0.00 1.78
315 336 9.158233 ACTTCGAAGCTAGACTACTATCATATC 57.842 37.037 24.86 0.00 0.00 1.63
316 337 9.157104 CTTCGAAGCTAGACTACTATCATATCA 57.843 37.037 13.09 0.00 0.00 2.15
383 404 6.862090 GCTCTTAGAGTCTTTGTTCGTCTTAA 59.138 38.462 11.18 0.00 31.39 1.85
404 428 0.105453 TATCCTCTGTCTGCTCCCCC 60.105 60.000 0.00 0.00 0.00 5.40
451 481 1.140407 CTCGACCCAGCGAAATCGAC 61.140 60.000 7.06 0.00 43.02 4.20
516 555 2.086849 CGCGCAGTGTTTTATTTTGACG 59.913 45.455 8.75 0.00 0.00 4.35
707 954 0.813610 CCGCGTTGGCATCTTCCATA 60.814 55.000 4.92 0.00 39.92 2.74
712 959 0.546122 TTGGCATCTTCCATAGCGGT 59.454 50.000 0.00 0.00 35.77 5.68
713 960 0.546122 TGGCATCTTCCATAGCGGTT 59.454 50.000 0.00 0.00 35.57 4.44
714 961 1.230324 GGCATCTTCCATAGCGGTTC 58.770 55.000 0.00 0.00 35.57 3.62
715 962 1.202698 GGCATCTTCCATAGCGGTTCT 60.203 52.381 0.00 0.00 35.57 3.01
749 996 7.703621 CCAAAATAACCATAGCTCTGTTGAATG 59.296 37.037 0.00 0.00 0.00 2.67
779 1026 3.470709 TCTGTCTTGCTATTATGCTGGC 58.529 45.455 0.00 0.00 0.00 4.85
1342 1603 3.341823 CTTGAGACCTTCATTCCAGGTG 58.658 50.000 0.00 0.00 45.30 4.00
1366 1627 2.012673 GTGCCAGCCTCAACTTCTATG 58.987 52.381 0.00 0.00 0.00 2.23
1466 1727 6.420008 GCCATCAATGATTTGCTATTTGTCTC 59.580 38.462 7.12 0.00 32.61 3.36
1695 1962 2.240667 AGTTCCTCAGCTAATGCATGGT 59.759 45.455 0.00 0.00 42.74 3.55
1719 1986 1.194781 ACTTGGTGTCATCCTCGGCT 61.195 55.000 0.00 0.00 0.00 5.52
1722 1989 2.512515 GTGTCATCCTCGGCTGCC 60.513 66.667 9.11 9.11 0.00 4.85
1791 2058 0.599204 CGGTTACTCACGTTGCCACT 60.599 55.000 0.00 0.00 0.00 4.00
1854 2121 0.869454 CCGAAGCAAAGCGCAACAAA 60.869 50.000 11.47 0.00 46.13 2.83
2043 2313 1.380380 GGGGATCAGGGCAAAGGTG 60.380 63.158 0.00 0.00 0.00 4.00
2078 2348 2.597510 AGGCAAAAGTGGGACGGC 60.598 61.111 0.00 0.00 0.00 5.68
2244 2514 1.650314 TTGTCGTCGATGGCTCGCTA 61.650 55.000 11.10 0.00 44.65 4.26
2358 2643 2.091555 ACCTGGTTTGTTGGTGGTATGT 60.092 45.455 0.00 0.00 32.16 2.29
2474 3046 2.098443 TCACCGTGAAAACTTTTGCTCC 59.902 45.455 0.00 0.00 0.00 4.70
2501 3078 5.221722 TGTCCTAGTGAAATGCAAGACTTCT 60.222 40.000 0.00 0.00 0.00 2.85
2504 3081 7.550906 GTCCTAGTGAAATGCAAGACTTCTTAT 59.449 37.037 0.00 0.00 34.28 1.73
2663 8576 0.108945 GGCTGTCTGATTTTGCTGGC 60.109 55.000 0.00 0.00 0.00 4.85
2665 8578 1.402456 GCTGTCTGATTTTGCTGGCAG 60.402 52.381 10.94 10.94 40.88 4.85
2677 8590 2.486951 GCTGGCAGCATGAATTACTG 57.513 50.000 33.33 0.00 41.89 2.74
2941 8889 2.239400 AGCCTGGAACAACTTAAAGCC 58.761 47.619 0.00 0.00 38.70 4.35
2963 8911 4.378459 CCAACACTCGTTCTTTATTGAGGC 60.378 45.833 0.00 0.00 31.13 4.70
3037 9013 8.470805 GTTAGACAGAAGTGATCTATCCTTCAA 58.529 37.037 16.62 5.89 36.32 2.69
3073 11116 7.453393 AGATTTGAGTTGTGATCCTAGACAAA 58.547 34.615 0.00 0.00 33.96 2.83
3106 11149 3.964031 ACTTGGAAGACTCAGAACTGTCT 59.036 43.478 1.73 0.00 44.40 3.41
3171 11220 8.742777 TGATCCTGAAAAGGAATGAAACTAATG 58.257 33.333 0.00 0.00 41.90 1.90
3230 11304 7.649306 CCACAGTTTCTTTTTGAAGAACCTATG 59.351 37.037 1.35 0.45 38.41 2.23
3260 11334 3.737850 AGGAGAGCTTCAACTGTCAAAG 58.262 45.455 0.00 0.00 31.73 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.264005 ACACATTTCGGCCACAACTA 57.736 45.000 2.24 0.00 0.00 2.24
5 6 2.292292 AGTAACACATTTCGGCCACAAC 59.708 45.455 2.24 0.00 0.00 3.32
6 7 2.577700 AGTAACACATTTCGGCCACAA 58.422 42.857 2.24 0.00 0.00 3.33
7 8 2.264005 AGTAACACATTTCGGCCACA 57.736 45.000 2.24 0.00 0.00 4.17
8 9 2.412325 CGAAGTAACACATTTCGGCCAC 60.412 50.000 2.24 0.00 41.28 5.01
9 10 1.801771 CGAAGTAACACATTTCGGCCA 59.198 47.619 2.24 0.00 41.28 5.36
10 11 2.520686 CGAAGTAACACATTTCGGCC 57.479 50.000 0.00 0.00 41.28 6.13
13 14 1.801771 TGGCCGAAGTAACACATTTCG 59.198 47.619 0.00 0.00 43.73 3.46
14 15 3.907894 TTGGCCGAAGTAACACATTTC 57.092 42.857 0.00 0.00 0.00 2.17
15 16 4.279671 TCATTTGGCCGAAGTAACACATTT 59.720 37.500 12.01 0.00 0.00 2.32
16 17 3.823873 TCATTTGGCCGAAGTAACACATT 59.176 39.130 12.01 0.00 0.00 2.71
17 18 3.417101 TCATTTGGCCGAAGTAACACAT 58.583 40.909 12.01 0.00 0.00 3.21
18 19 2.852449 TCATTTGGCCGAAGTAACACA 58.148 42.857 12.01 0.00 0.00 3.72
19 20 3.427503 CCATCATTTGGCCGAAGTAACAC 60.428 47.826 12.01 0.00 39.09 3.32
20 21 2.752354 CCATCATTTGGCCGAAGTAACA 59.248 45.455 12.01 0.00 39.09 2.41
21 22 3.420839 CCATCATTTGGCCGAAGTAAC 57.579 47.619 12.01 0.00 39.09 2.50
32 33 4.701956 AGTAGTTTTCGGCCATCATTTG 57.298 40.909 2.24 0.00 0.00 2.32
33 34 5.497474 AGTAGTAGTTTTCGGCCATCATTT 58.503 37.500 2.24 0.00 0.00 2.32
34 35 5.099042 AGTAGTAGTTTTCGGCCATCATT 57.901 39.130 2.24 0.00 0.00 2.57
35 36 4.755266 AGTAGTAGTTTTCGGCCATCAT 57.245 40.909 2.24 0.00 0.00 2.45
36 37 4.501071 GAAGTAGTAGTTTTCGGCCATCA 58.499 43.478 2.24 0.00 0.00 3.07
37 38 3.550678 CGAAGTAGTAGTTTTCGGCCATC 59.449 47.826 2.24 0.00 39.82 3.51
38 39 3.518590 CGAAGTAGTAGTTTTCGGCCAT 58.481 45.455 2.24 0.00 39.82 4.40
39 40 2.950433 CGAAGTAGTAGTTTTCGGCCA 58.050 47.619 2.24 0.00 39.82 5.36
43 44 2.950433 TGGCCGAAGTAGTAGTTTTCG 58.050 47.619 0.00 8.95 42.31 3.46
44 45 5.467735 TCTTTTGGCCGAAGTAGTAGTTTTC 59.532 40.000 15.82 0.00 0.00 2.29
45 46 5.370679 TCTTTTGGCCGAAGTAGTAGTTTT 58.629 37.500 15.82 0.00 0.00 2.43
46 47 4.964593 TCTTTTGGCCGAAGTAGTAGTTT 58.035 39.130 15.82 0.00 0.00 2.66
47 48 4.612264 TCTTTTGGCCGAAGTAGTAGTT 57.388 40.909 15.82 0.00 0.00 2.24
48 49 4.504858 CATCTTTTGGCCGAAGTAGTAGT 58.495 43.478 15.82 0.00 0.00 2.73
49 50 3.871594 CCATCTTTTGGCCGAAGTAGTAG 59.128 47.826 15.82 6.77 39.09 2.57
50 51 3.869065 CCATCTTTTGGCCGAAGTAGTA 58.131 45.455 15.82 0.00 39.09 1.82
51 52 2.711542 CCATCTTTTGGCCGAAGTAGT 58.288 47.619 15.82 4.22 39.09 2.73
62 63 3.187058 CCCGTCGGCCATCTTTTG 58.813 61.111 5.50 0.00 0.00 2.44
72 73 1.636988 CAAAACTAGTAGCCCGTCGG 58.363 55.000 3.60 3.60 0.00 4.79
73 74 1.067354 ACCAAAACTAGTAGCCCGTCG 60.067 52.381 0.00 0.00 0.00 5.12
74 75 2.756840 ACCAAAACTAGTAGCCCGTC 57.243 50.000 0.00 0.00 0.00 4.79
75 76 3.497103 AAACCAAAACTAGTAGCCCGT 57.503 42.857 0.00 0.00 0.00 5.28
76 77 4.841443 AAAAACCAAAACTAGTAGCCCG 57.159 40.909 0.00 0.00 0.00 6.13
95 96 8.455682 CGGAAACTATAGGACTTAATGCAAAAA 58.544 33.333 4.43 0.00 0.00 1.94
96 97 7.825270 TCGGAAACTATAGGACTTAATGCAAAA 59.175 33.333 4.43 0.00 0.00 2.44
97 98 7.332557 TCGGAAACTATAGGACTTAATGCAAA 58.667 34.615 4.43 0.00 0.00 3.68
98 99 6.880484 TCGGAAACTATAGGACTTAATGCAA 58.120 36.000 4.43 0.00 0.00 4.08
99 100 6.474140 TCGGAAACTATAGGACTTAATGCA 57.526 37.500 4.43 0.00 0.00 3.96
100 101 7.781548 TTTCGGAAACTATAGGACTTAATGC 57.218 36.000 4.43 0.00 0.00 3.56
102 103 8.837389 GCATTTTCGGAAACTATAGGACTTAAT 58.163 33.333 1.96 0.00 0.00 1.40
103 104 8.044908 AGCATTTTCGGAAACTATAGGACTTAA 58.955 33.333 1.96 0.00 0.00 1.85
104 105 7.562135 AGCATTTTCGGAAACTATAGGACTTA 58.438 34.615 1.96 0.00 0.00 2.24
105 106 6.415573 AGCATTTTCGGAAACTATAGGACTT 58.584 36.000 1.96 0.00 0.00 3.01
106 107 5.990668 AGCATTTTCGGAAACTATAGGACT 58.009 37.500 1.96 0.00 0.00 3.85
107 108 7.964604 ATAGCATTTTCGGAAACTATAGGAC 57.035 36.000 1.96 0.00 0.00 3.85
154 155 4.155099 TGACGCCGTCAATACATGATTTTT 59.845 37.500 18.96 0.00 39.78 1.94
155 156 3.687212 TGACGCCGTCAATACATGATTTT 59.313 39.130 18.96 0.00 39.78 1.82
156 157 3.063452 GTGACGCCGTCAATACATGATTT 59.937 43.478 23.04 0.00 44.49 2.17
157 158 2.607635 GTGACGCCGTCAATACATGATT 59.392 45.455 23.04 0.00 44.49 2.57
158 159 2.201732 GTGACGCCGTCAATACATGAT 58.798 47.619 23.04 0.00 44.49 2.45
159 160 1.635844 GTGACGCCGTCAATACATGA 58.364 50.000 23.04 0.00 44.49 3.07
160 161 0.650512 GGTGACGCCGTCAATACATG 59.349 55.000 23.04 0.00 44.49 3.21
161 162 0.535335 AGGTGACGCCGTCAATACAT 59.465 50.000 23.04 4.43 44.49 2.29
175 176 2.820787 GAGAGGACGAGAGAAAAGGTGA 59.179 50.000 0.00 0.00 0.00 4.02
255 265 1.448922 GAGAGATACCTCGCCGCTGT 61.449 60.000 0.00 0.00 44.08 4.40
312 333 0.567687 TCAGCCCCTCCCTCATGATA 59.432 55.000 0.00 0.00 0.00 2.15
313 334 0.104037 ATCAGCCCCTCCCTCATGAT 60.104 55.000 0.00 0.00 0.00 2.45
314 335 0.327867 AATCAGCCCCTCCCTCATGA 60.328 55.000 0.00 0.00 0.00 3.07
315 336 0.178998 CAATCAGCCCCTCCCTCATG 60.179 60.000 0.00 0.00 0.00 3.07
316 337 0.327867 TCAATCAGCCCCTCCCTCAT 60.328 55.000 0.00 0.00 0.00 2.90
383 404 2.334023 GGGGAGCAGACAGAGGATAAT 58.666 52.381 0.00 0.00 0.00 1.28
404 428 0.171679 GTTAACGGCGGGGAATTTGG 59.828 55.000 13.24 0.00 0.00 3.28
410 434 2.162338 CTGACAGTTAACGGCGGGGA 62.162 60.000 13.24 0.00 0.00 4.81
451 481 2.481449 CCGAGGAGAAACTACCATTCGG 60.481 54.545 0.00 0.00 37.55 4.30
499 538 7.515643 CCTACTACCGTCAAAATAAAACACTG 58.484 38.462 0.00 0.00 0.00 3.66
516 555 2.563620 GAGCCTCCATTAGCCTACTACC 59.436 54.545 0.00 0.00 0.00 3.18
707 954 4.612264 TTTTGGTAGAAGTAGAACCGCT 57.388 40.909 0.00 0.00 35.98 5.52
712 959 9.609346 GCTATGGTTATTTTGGTAGAAGTAGAA 57.391 33.333 0.00 0.00 0.00 2.10
713 960 8.989131 AGCTATGGTTATTTTGGTAGAAGTAGA 58.011 33.333 0.00 0.00 0.00 2.59
714 961 9.262358 GAGCTATGGTTATTTTGGTAGAAGTAG 57.738 37.037 0.00 0.00 0.00 2.57
715 962 8.989131 AGAGCTATGGTTATTTTGGTAGAAGTA 58.011 33.333 0.00 0.00 0.00 2.24
749 996 8.801913 GCATAATAGCAAGACAGATTTGAAAAC 58.198 33.333 0.00 0.00 0.00 2.43
757 1004 4.070716 GCCAGCATAATAGCAAGACAGAT 58.929 43.478 0.00 0.00 36.85 2.90
779 1026 7.378181 ACTGCAACTCCAATTTAAACCATTAG 58.622 34.615 0.00 0.00 0.00 1.73
891 1143 7.987458 TGATTTAAACAATTGGCACAGGTAAAA 59.013 29.630 10.83 0.00 42.39 1.52
954 1209 0.257039 CCTCCATTGGTCCTTCCCTG 59.743 60.000 1.86 0.00 34.77 4.45
1342 1603 1.109323 AAGTTGAGGCTGGCACCAAC 61.109 55.000 22.41 22.41 39.17 3.77
1366 1627 1.831286 CCTGGGATGCAATGGGCTC 60.831 63.158 0.00 0.00 45.15 4.70
1466 1727 3.077359 GTTTCACCAGTGAGAGGATTGG 58.923 50.000 0.09 0.00 41.13 3.16
1578 1839 1.067295 TGGCAGTCAGTTGGAAGGAT 58.933 50.000 0.00 0.00 0.00 3.24
1695 1962 3.056107 CCGAGGATGACACCAAGTAAAGA 60.056 47.826 0.00 0.00 0.00 2.52
1719 1986 4.539083 ACACCACACGAAGCGGCA 62.539 61.111 1.45 0.00 0.00 5.69
1722 1989 1.626654 GGATGACACCACACGAAGCG 61.627 60.000 0.00 0.00 0.00 4.68
1791 2058 1.409790 GCCATATTGCCAATGTGCAGA 59.590 47.619 8.51 0.00 43.21 4.26
2043 2313 1.134670 CCTCGGAACATCTCCAACCTC 60.135 57.143 0.00 0.00 45.74 3.85
2078 2348 0.318529 CTCATCGATCCAGAGCACCG 60.319 60.000 0.00 0.00 0.00 4.94
2115 2385 2.630214 CGACCTATCGCTGAGGCTA 58.370 57.895 0.00 0.00 42.43 3.93
2244 2514 2.024273 TCCCCTTTCTACGTCCAGAGAT 60.024 50.000 0.00 0.00 0.00 2.75
2427 2998 9.618890 AATGCAATTAGACTGATGTACTAACAT 57.381 29.630 0.00 0.00 41.63 2.71
2431 3002 7.710907 GGTGAATGCAATTAGACTGATGTACTA 59.289 37.037 0.00 0.00 36.07 1.82
2432 3003 6.540189 GGTGAATGCAATTAGACTGATGTACT 59.460 38.462 0.00 0.00 36.07 2.73
2433 3004 6.510157 CGGTGAATGCAATTAGACTGATGTAC 60.510 42.308 0.00 0.00 36.07 2.90
2448 3019 3.791973 AAAGTTTTCACGGTGAATGCA 57.208 38.095 22.97 7.00 36.11 3.96
2474 3046 4.153117 GTCTTGCATTTCACTAGGACACAG 59.847 45.833 0.00 0.00 0.00 3.66
2663 8576 8.008279 CGATTCTGAATACAGTAATTCATGCTG 58.992 37.037 2.28 0.00 43.16 4.41
2665 8578 6.794158 GCGATTCTGAATACAGTAATTCATGC 59.206 38.462 2.28 0.00 43.16 4.06
2677 8590 5.536554 CCATATGGTGCGATTCTGAATAC 57.463 43.478 14.09 0.00 0.00 1.89
2714 8655 5.719173 TGAAGAAAAACAACAGGTTGAAGG 58.281 37.500 18.28 0.00 42.93 3.46
2901 8847 4.192317 GCTTGATTAGTGGACTAACCCTG 58.808 47.826 1.31 0.00 40.81 4.45
2941 8889 4.213270 TGCCTCAATAAAGAACGAGTGTTG 59.787 41.667 0.00 0.00 38.78 3.33
2963 8911 7.727181 AGTAGGTACTTAACAGATAGGCAATG 58.273 38.462 0.00 0.00 41.75 2.82
2978 8927 9.052759 CAAAATTCAGTACACAAGTAGGTACTT 57.947 33.333 0.00 0.00 45.86 2.24
2980 8929 8.280497 CACAAAATTCAGTACACAAGTAGGTAC 58.720 37.037 0.00 0.00 40.06 3.34
3037 9013 4.516698 ACAACTCAAATCTCGTTGCAGATT 59.483 37.500 0.00 0.00 43.70 2.40
3073 11116 2.106684 GTCTTCCAAGTCCTTTCCAGGT 59.893 50.000 0.00 0.00 41.69 4.00
3106 11149 4.220821 TCCGCAGCATAAATTTTACCCAAA 59.779 37.500 0.00 0.00 0.00 3.28
3181 11230 1.476488 ACAATGCATTAGTTTCCCGGC 59.524 47.619 12.53 0.00 0.00 6.13
3182 11231 3.866883 AACAATGCATTAGTTTCCCGG 57.133 42.857 12.53 0.00 0.00 5.73
3230 11304 4.161377 AGTTGAAGCTCTCCTACATTCTCC 59.839 45.833 0.00 0.00 0.00 3.71
3260 11334 4.394439 TGTTTTAAACCTTTGGCCTGAC 57.606 40.909 3.32 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.