Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018141.1 Corchorus olitorius cultivar O-4 contig18174, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20598
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:6526 original size:44 final size:44
Alignment explanation
Indices: 6461--6599 Score: 145
Period size: 44 Copynumber: 3.0 Consensus size: 44
6451 GTATGGTTTA
*
6461 CATAGTATATATACTATATTGAAATATTTTAAAGAAGTAATATG
1 CATAGTATAAATACTATATTGAAATATTTTAAAGAAGTAATATG
* * *
6505 CATA-TATAAAATACTATATTGAAATATTTTAATAAATAGTAGTGTAGTTTA
1 CATAGTAT-AAATACTATATTGAAATATTTTAA-AGA-AGTA----A-TATG
* *
6556 CATAGTATATATACTATATTGCAATATTTTAAAGAAGTAATATG
1 CATAGTATAAATACTATATTGAAATATTTTAAAGAAGTAATATG
6600 TGCATATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
43 3 0.04
44 29 0.38
45 3 0.04
46 4 0.05
49 4 0.05
50 3 0.04
51 28 0.36
52 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (44 bp):
CATAGTATAAATACTATATTGAAATATTTTAAAGAAGTAATATG
Found at i:6607 original size:95 final size:96
Alignment explanation
Indices: 6437--6611 Score: 289
Period size: 95 Copynumber: 1.8 Consensus size: 96
6427 GAGTTCATTA
*
6437 TTAATAAAATAGTAGTATGGTTTACATAGTATATATACTATATTGAAATATTTTAAAGAAGTAAT
1 TTAATAAAATAGTAGTATAGTTTACATAGTATATATACTATATTGAAATATTTTAAAGAAGTAAT
*
6502 ATGCATATATAAAATACTATATTGAAATATT
66 ATGCACATATAAAATACTATATTGAAATATT
* *
6533 TTAAT-AAATAGTAGTGTAGTTTACATAGTATATATACTATATTGCAATATTTTAAAGAAGTAAT
1 TTAATAAAATAGTAGTATAGTTTACATAGTATATATACTATATTGAAATATTTTAAAGAAGTAAT
**
6597 ATGTGCATATAAAAT
66 ATGCACATATAAAAT
6612 TGATCATTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 68 0.93
96 5 0.07
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (96 bp):
TTAATAAAATAGTAGTATAGTTTACATAGTATATATACTATATTGAAATATTTTAAAGAAGTAAT
ATGCACATATAAAATACTATATTGAAATATT
Found at i:9237 original size:28 final size:27
Alignment explanation
Indices: 9163--9241 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 27
9153 TAGAATGTAT
9163 TGAATTTGAGAAGTTCAGGGGGAAATGTCC
1 TGAATTT--GAAGTT-AGGGGGAAATGTCC
*
9193 TGAATTTG--GATAGGGGGACGAAATGTCC
1 TGAATTTGAAGTTA-GGGG--GAAATGTCC
9221 TG-ATTTGAAGTTAGGGGGAAA
1 TGAATTTGAAGTTAGGGGGAAA
9242 AACGTTATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
25 1 0.02
26 10 0.24
27 5 0.12
28 16 0.38
29 3 0.07
30 7 0.17
ACGTcount: A:0.30, C:0.08, G:0.35, T:0.27
Consensus pattern (27 bp):
TGAATTTGAAGTTAGGGGGAAATGTCC
Found at i:14337 original size:332 final size:330
Alignment explanation
Indices: 12473--16613 Score: 3694
Period size: 333 Copynumber: 12.6 Consensus size: 330
12463 CCATGATGGT
** * * * * * * *
12473 AAAAA-TGACCC-AAAAAATTTTCCTTAATTTTTGGCAAAAATACTCATGAAATATTTATAATTC
1 AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTC
* * * ** * * ***
12536 AACTTCAAAAAAAATTGTAGGACTTTTCACGATTTTAATATCGTTTTT-CATATTTTTTTAAAAT
66 AAC-GC-CAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTTCCGAAT
* * * *
12600 TAATTTCCAATTAAATCGAAAC-AGATTCAGATGCACGT-------AATCCTTAAATTCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * ** * *
12657 GCTGAGATTTGATTAGATGAATAAAAATATTTTAAGGAGTTTTTATGCCAAAAACCATGCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAAC
* * * * * *
12722 TGAGACGAGCCCCCGAAACACGTTTTTACTTTTTAGCCAAAAATCGTGA-----CGTACACGATT
258 TGAGCCG-GGCCCCGGAACGCG-------TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATT
12782 TCGGCT---A------
315 TCGGCTAAAATTTTGC
* * * **
12789 AAAACTGGA-CCGAAAAATTTTTCCTCAATTTTTTGCCACAATACTCGGAAAAAATATATAATTC
1 AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTC
12853 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
66 AACGCC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
* * * * *
12918 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAGAAATCCTTAAATCCATTATGAC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
*
12983 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGC-CAAAATCATGCAAAACT
195 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCAAAAAATCATGCAAAACT
* * * * **
13046 AAGCCTGGACCCC-GACACGTGTTTTTAACTC-AAAACCGTGATAATTAGTACACGATTTCGGC-
259 GAGCC-GGGCCCCGGA-ACGCGTTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTCGGCT
13108 -------T--
321 AAAATTTTGC
* * * * * * *
13109 AAAAACTGACCCGAAAAGTTCTTACACAATTTTTTTTG-CAAAATATTCAGAAAAAATATATAAT
1 AAAAATTGACCCGAAAAGTTTTTCCTCAA--TTTTTTGCCACAATACTCATAAAAAATATATAAT
* * *
13173 TCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTCCCA--TTTTTCCGAAT
64 TCAACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAAT
* * * *
13236 TAATTTCTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
13301 GCTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAAC
* * *
13366 TGATCCGGGTCTCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
258 TGAGCCGGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
13431 AAATTTTGC
322 AAATTTTGC
* *
13440 AAAAAACTGACCCGAAAATTTTTTCCTCAA-TTTTTGCCACAATACTC--AAAAAATATATAATT
1 -AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATT
* **
13502 CAACGCCAAAAAAATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTTCTAAATT
65 CAACGCC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATT
* * * * * *
13566 TATTTTTAATTGAATCGAAACAAGATTCGGATACTCGTAAAAACAAATCTTTTAATCCAATGTGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * ** * * *
13631 CTGAGATTTTGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGC-CAAAACCATACAAAACT
194 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAACT
* * * *
13695 GAGACGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACAATTTCGGC---
259 GAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
13757 -----T--
323 AATTTTGC
* * * * * * *
13758 AAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTACCACAATACTCATAGAAAATATATAATTC
1 AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTC
* **
13823 AACGTCAAAAAGATTGAA-GGACTTTCACGCTTCTAATATCGTTTTTCCATTTTTTAT--GAA-T
66 AACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-TCCGAATT
* * * * *
13884 TATTTTCTAATTAAATCAAAAAAAGATTCAGATACTCGTAAAAACATATCCTTATATCCAATGTG
129 TA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
13949 GCTGAGATTTGGTTCGATGAATATAGACATTTCCAGAAGTCTTTGCGCATAAAATCATTG-AAAA
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCA-TGCAAAA
* * * * * * *
14013 TTGAGCCGGGACTCCGGAACGCGTTTTAAGTCAAAAACTGTGATGGTTAGTATACGATTTCAGCT
257 CTGAGCCGGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
*
14078 AAAATTTTAC
321 AAAATTTTGC
*
14088 AAAAATTTACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTC-TAAAAAAATATATAATT
1 AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAT-AAAAAATATATAATT
* * *
14152 CAACGCCAGAAAAATTGAAGGATTTTTCAC-TTTTTCAATATCGTTTTTCCATTTTTTTCCGAAT
65 CAACGCCA-AAAAATTGAAGGGTTTTTCACGCTTCT-AATATCGTTTTTCCATTTTTTTCCGAAT
* * **
14216 TTATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAACAAATCGATAAATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
** * * * *
14281 GCTTG-GATTTGGTCCGATGAATACAGATATTTCAAGGAGCCTTTACGCAAAAAATCATACAAAA
193 GC-TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAA
* *
14345 CTGAACCTGGGCCCCGGAACGCGTTTTTAGCCAAAAAAACCGTGATAGTTAGTACACGATTTTCG
257 CTGAGCC-GGGCCCCGGAACGCGTTTTTAGCC--AAAAACCGTGATGGTTAGTACACGA-TTTCG
*
14410 ACTAAAATTTTGC
318 GCTAAAATTTTGC
* ** * * *
14423 AAAAAAGCTGACCCGAAAAG-TTTTCCTCAATTTTTCACCACAATAGT-A-AAAATATATACAAT
1 -AAAAA-TTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAAT
* *
14485 TCAATGCCTAAAAAATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAA
64 TCAACGCC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAA
* * * *
14550 TCTATTTCTAATAAAATCGAAACGAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAATGT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
14615 GGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGGAGTCTTGGCACTAAAAATCATGCAAAA
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAA
* * * * * *
14680 CTGAGTCGAGGCCCCAGAACGCGTGTTTAGCCGAAAACTGTAAT-G--AGTACACGATTTCGGCT
257 CTGAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
14742 AAAATTTTGC
321 AAAATTTTGC
* * ** * *
14752 AAAAATTGACCC-AAAAGATTTTTCCTCAATTTCTAGTGAAAATACTCATGAAAAATATATAATT
1 AAAAATTGACCCGAAAAG-TTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATT
** * *
14816 CAACGCCAAAAAAATTGAAAGTCTTTTTCACGCTTCTAATATCGTTTTTCCTACTTTATTTCCAA
65 CAACGCC-AAAAAATTG-AAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-A-TTTTTTTCCGA
* * * * * *
14881 ATTAATTTATGACTAAATCGAAACAAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
126 ATTTATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
** * * *
14946 GTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGACTCTTAGCGCCAAAAATCATGCAA
190 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAA
* * *
15011 AACTGA-CTCGGGGCCCCGGAACGCGTTTTTGGCCAAAAAACTGTGAT-G---GTACATGATTTC
255 AACTGAGC-C-GGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTC
* *
15071 GGCTGATATTTTGC
317 GGCTAAAATTTTGC
* * * *
15085 AAAAATTGATCCGAAATA-TTTTTCCTCAATTTTTAGCCACAGTACCCATAAAAAATATATAATT
1 AAAAATTGACCCGAAA-AGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATT
* ** * * *
15149 CAACGCCAAAAAGTTTGAAGGGCCTCTCACGCTTCTAATATCGTTTTTCC-TATCTTTTCTGAAT
65 CAACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTTCCGAAT
* * * *
15213 TAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTAAAAAC-AA----T---GCC----T-
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
15265 G--G-GATTTAGTTAGATGAATATAGATATTTCAAGGAGT-TTCAGCACCAAAAATCATGGAAAA
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-TGCGCAAAAAATCATGCAAAA
* * * * ** * * * **
15326 TTGAACCGGGCCCTGAAACGCGTTTTTAGCTGAACACCGTGATGATTATTACAAAATTTCGGCTA
257 CTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
*
15391 AAATTTTGT
322 AAATTTTGC
*
15400 AAAAATTGACCCG-AAAGATATTTT-CTC-ATTTTTTAGCCGCAATACTCATAAAAAATATATAA
1 AAAAATTGACCCGAAAAG-T-TTTTCCTCAATTTTTT-GCCACAATACTCATAAAAAATATATAA
* * * * * * * *
15462 TTCAACACCGAAAAGATTGAAGGG-CTTTCATGTTTTTAATATCGTTTTT-CATATTTTTCCTTA
63 TTCAACGCC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCC-GA
** * * * *
15525 ATGAATTTCTAATTAAATCAAAACAAGATTCAGATGCTTGTAAAAGCAAATCCTTAAATGCAATG
126 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * ** *
15590 TGGCTAAGATTAT-ATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
191 TGGCTGAGATT-TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAA
* * * * *
15654 AACTAAGCCGAGGCCCC-GACACACGTTTTTAGCCTAAAACTGTGATGGTTAGTACACGATTTTG
255 AACTGAGCCG-GGCCCCGGA-ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
*
15718 GCTAAAATTTCGC
318 GCTAAAATTTTGC
* * ** * * * *
15731 AAAAAGTT-ACCCGAAAAAATTTTTCCTCAATTTTTGGATAAAATATTCATAAAATATAAATAAT
1 AAAAA-TTGACCCG-AAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAAT
* * * * ** * * * *
15795 TTAACACCATAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTT-CATACTTTTTCTGAA
64 TCAACGCCA-AAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTTCCGAA
* *
15859 TTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * * * * *
15924 AGCTGAAATTTGATTATATGAATATGGATATATCAAGGAAGCCTTGGCGCAAAAAATCATGCAAC
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG-AGTCTTTGCGCAAAAAATCATGCAAA
* * * * ** * * *
15989 ACTGAGCTGGGGCCCCGAAACGCTTTTTTAGTCAAAAATTGTTATAGTTATTACACGATTTCGGC
256 ACTGAGC-CGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
*
16054 TAAAATTTTGT
320 TAAAATTTTGC
* * * * * *
16065 AAAACTTGACCTG-AAAGATTTTTCCTCAATTTCTGGCTAAAATACTCATAAAAAATATATATAT
1 AAAAATTGACCCGAAAAG-TTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATA-AT
* * * ** *
16129 T-AACACCAAATAGATTGAAGGGCTTTGGACGTTTCTAATATCGTTTTTCC-TATTTTTT-CGAA
64 TCAACGCCAAA-AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTTCCGAA
*
16191 -TTAGTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
127 TTTA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * ** * *
16255 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTC-AGAAATCATGCAA
191 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCG-CAAAAAATCATGCAA
* *
16319 AA-TCGAGGCGGGTCCCTGGAACGCGTTTTTAG-CATAAAACCGTGATGGTTAGTTATAGTACAC
255 AACT-GAGCCGGG-CCCCGGAACGCGTTTTTAGCCA-AAAACCGTGAT-G---G-T-TAGTACAC
*
16382 GATTTCGGCTAAAATTTTGT
311 GATTTCGGCTAAAATTTTGC
* * * * *
16402 AAAAATTGACACG-AAAGATTTCTCCTCAATTTTTGGCTAAAATACTCAT-AAAAATATATAATT
1 AAAAATTGACCCGAAAAG-TTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATT
* * * * * * * * **
16465 CAACGCCAAAAAGATTGGAGAGTTTCTCACGCTTTTAATATTG-TATTAC-TTACTATTTCTAAA
65 CAACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT--TTTTTCCGAA
* * ** *
16528 TTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTTATAAAAACAAATTCTTAAATCCAATGT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* *
16593 TGCTGAGCTTTGGTTAGATGA
192 GGCTGAGATTTGGTTAGATGA
16614 TGTAAAGTAT
Statistics
Matches: 3161, Mismatches: 495, Indels: 317
0.80 0.12 0.08
Matches are distributed among these distances:
311 9 0.00
312 22 0.01
313 62 0.02
314 76 0.02
315 78 0.02
316 96 0.03
317 93 0.03
318 19 0.01
319 131 0.04
320 211 0.07
321 101 0.03
322 70 0.02
323 33 0.01
324 58 0.02
326 6 0.00
327 7 0.00
328 149 0.05
329 160 0.05
330 204 0.06
331 180 0.06
332 362 0.11
333 429 0.14
334 192 0.06
335 179 0.06
336 74 0.02
337 158 0.05
338 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (330 bp):
AAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTC
AACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAACTGA
GCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:17119 original size:12 final size:12
Alignment explanation
Indices: 17102--17126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17092 ATCTTTCCAT
17102 AATTAATAAGAA
1 AATTAATAAGAA
17114 AATTAATAAGAA
1 AATTAATAAGAA
17126 A
1 A
17127 GTTTAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AATTAATAAGAA
Found at i:19183 original size:54 final size:54
Alignment explanation
Indices: 19119--19227 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
19109 TAATGTGGTT
19119 CCATTTTGGTCCTTTATTCACATCATTACTATATTAACAATTGAAAATTTTGTC
1 CCATTTTGGTCCTTTATTCACATCATTACTATATTAACAATTGAAAATTTTGTC
19173 CCATTTTGGTCCTTTATTCACATCATTACTATATTAACAATTGAAAATTTTGTC
1 CCATTTTGGTCCTTTATTCACATCATTACTATATTAACAATTGAAAATTTTGTC
19227 C
1 C
19228 ATGTGAATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.44
Consensus pattern (54 bp):
CCATTTTGGTCCTTTATTCACATCATTACTATATTAACAATTGAAAATTTTGTC
Done.