Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021054.1 Corchorus olitorius cultivar O-4 contig21087, 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: 94621
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:192 original size:57 final size:58
Alignment explanation
Indices: 89--205 Score: 209
Period size: 57 Copynumber: 2.0 Consensus size: 58
79 TTTATTTTGT
* *
89 AGAATAATTAAGTAGAGATATGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
147 AGAATAATTAAGTAGAGATA-AGGGGGATAGGATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
204 AG
1 AG
206 GAAACGGATA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 37 0.65
58 20 0.35
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (58 bp):
AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
Found at i:2419 original size:18 final size:18
Alignment explanation
Indices: 2398--2434 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2388 ATTCAACGCT
2398 AAAAAGCCAAC-TGGTTAA
1 AAAAAGCC-ACGTGGTTAA
2416 AAAAAGCCACGTGGTTAA
1 AAAAAGCCACGTGGTTAA
2434 A
1 A
2435 GCTTAACGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (18 bp):
AAAAAGCCACGTGGTTAA
Found at i:2556 original size:30 final size:29
Alignment explanation
Indices: 2530--2586 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2520 TCACATTTTT
*
2530 GAAACGTTGCATCCTGAATTGAACATTTGG
1 GAAA-GTTACATCCTGAATTGAACATTTGG
* *
2560 GCAAGTTATATCCTGAATTGAACATTT
1 GAAAGTTACATCCTGAATTGAACATTT
2587 AGCCCCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (29 bp):
GAAAGTTACATCCTGAATTGAACATTTGG
Found at i:13625 original size:8 final size:8
Alignment explanation
Indices: 13612--13638 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
13602 ATCTATTTCA
13612 TAACTAAT
1 TAACTAAT
13620 TAACTAAT
1 TAACTAAT
13628 TAACTAAT
1 TAACTAAT
13636 TAA
1 TAA
13639 AATTTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
TAACTAAT
Found at i:13675 original size:40 final size:40
Alignment explanation
Indices: 13620--13731 Score: 224
Period size: 40 Copynumber: 2.8 Consensus size: 40
13610 CATAACTAAT
13620 TAACTAATTAACTAATTAAAATTTACTACTACCTATTTCA
1 TAACTAATTAACTAATTAAAATTTACTACTACCTATTTCA
13660 TAACTAATTAACTAATTAAAATTTACTACTACCTATTTCA
1 TAACTAATTAACTAATTAAAATTTACTACTACCTATTTCA
13700 TAACTAATTAACTAATTAAAATTTACTACTAC
1 TAACTAATTAACTAATTAAAATTTACTACTAC
13732 AATTCTCTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (40 bp):
TAACTAATTAACTAATTAAAATTTACTACTACCTATTTCA
Found at i:13675 original size:48 final size:48
Alignment explanation
Indices: 13604--13718 Score: 174
Period size: 40 Copynumber: 2.6 Consensus size: 48
13594 TGACACGTAT
13604 CTATTTCATAACTAATTAACTAATTAACTAATTAAAATTTACTACTAC
1 CTATTTCATAACTAATTAACTAATTAACTAATTAAAATTTACTACTAC
13652 CTA-TT--T--C--A-TAACTAATTAACTAATTAAAATTTACTACTAC
1 CTATTTCATAACTAATTAACTAATTAACTAATTAAAATTTACTACTAC
13692 CTATTTCATAACTAATTAACTAATTAA
1 CTATTTCATAACTAATTAACTAATTAA
13719 AATTTACTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
40 35 0.59
41 3 0.05
43 2 0.03
45 2 0.03
47 3 0.05
48 14 0.24
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (48 bp):
CTATTTCATAACTAATTAACTAATTAACTAATTAAAATTTACTACTAC
Found at i:18882 original size:3 final size:3
Alignment explanation
Indices: 18783--18872 Score: 54
Period size: 3 Copynumber: 29.7 Consensus size: 3
18773 GGACTTGAGG
* * * * *
18783 AGA AAA AGA AGGA TGA AGG AGA AGG AGA AGA AGA AGA AGA GGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * * *
18829 GGA AGA TGA GGA GGA GGA AGA AGA TGA AGA AGG TGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
18873 GGAAAGAAGA
Statistics
Matches: 65, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
3 63 0.97
4 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:41033 original size:17 final size:17
Alignment explanation
Indices: 41003--41035 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40993 GTTTTATGCC
41003 AATTTATTTACTAAATT
1 AATTTATTTACTAAATT
41020 AATTTGATTT-CTAAAT
1 AATTT-ATTTACTAAAT
41036 CAAAATAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTATTTACTAAATT
Found at i:50073 original size:31 final size:31
Alignment explanation
Indices: 50038--50099 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
50028 TACTGGGACT
50038 CGAACCTTGTTCTTAAGGATGGATGGAAGAA
1 CGAACCTTGTTCTTAAGGATGGATGGAAGAA
50069 CGAACCTTGTTCTTAAGGATGGATGGAAGAA
1 CGAACCTTGTTCTTAAGGATGGATGGAAGAA
50100 TAAATATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
CGAACCTTGTTCTTAAGGATGGATGGAAGAA
Found at i:53064 original size:24 final size:24
Alignment explanation
Indices: 53031--53087 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
53021 CACCTGCACT
* *
53031 TCCTCAACCTCAGAATCGGAACGC
1 TCCTCCACCTCAGAATCGGAACAC
*
53055 TCCTCCACCTCAGAATCGGAACAT
1 TCCTCCACCTCAGAATCGGAACAC
53079 TCCTCCACC
1 TCCTCCACC
53088 ACTTCCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.42, G:0.12, T:0.19
Consensus pattern (24 bp):
TCCTCCACCTCAGAATCGGAACAC
Found at i:54177 original size:21 final size:22
Alignment explanation
Indices: 54152--54220 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
54142 ACTGAAAGTC
54152 TGTTGAAAAC-TGACGAGAATA
1 TGTTGAAAACATGACGAGAATA
* *
54173 TGTTG-AGACATGAGGAGAATA
1 TGTTGAAAACATGACGAGAATA
* **
54194 TGTTG-AGACATGAAAAGAATA
1 TGTTGAAAACATGACGAGAATA
54215 TGTTGA
1 TGTTGA
54221 GACATGAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.93
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.26
Consensus pattern (22 bp):
TGTTGAAAACATGACGAGAATA
Found at i:54221 original size:21 final size:21
Alignment explanation
Indices: 54167--54228 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
54157 AAAACTGACG
**
54167 AGAATATGTTGAGACATGAGG
1 AGAATATGTTGAGACATGAAA
54188 AGAATATGTTGAGACATGAAA
1 AGAATATGTTGAGACATGAAA
54209 AGAATATGTTGAGACATGAA
1 AGAATATGTTGAGACATGAA
54229 GGAGAGCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (21 bp):
AGAATATGTTGAGACATGAAA
Found at i:62657 original size:20 final size:20
Alignment explanation
Indices: 62620--62657 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62610 TCACAAATAC
*
62620 GGTTTTGTGACAGTTTTTAG
1 GGTTTTGTGACAGATTTTAG
*
62640 GGTTTTGTGACGGATTTT
1 GGTTTTGTGACAGATTTT
62658 GGCTGTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.05, G:0.32, T:0.50
Consensus pattern (20 bp):
GGTTTTGTGACAGATTTTAG
Found at i:63732 original size:179 final size:177
Alignment explanation
Indices: 63419--63802 Score: 457
Period size: 179 Copynumber: 2.1 Consensus size: 177
63409 TTCCACCATA
* * * * *
63419 AGCACAAATTATTTAATATTAAGTAGACCGTCTATTTCCTTTAACCGAAACAACTAATTCTTTGA
1 AGCA-AAATTATATAATATTAAGTAGACCGTCTACTCCCGTTAACCGAAACAACAAATTCTTTGA
63484 AAGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCAAGCCCTTCATGAAAGTTGTAGATCAT
65 AAGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCAAGCCCTTCATGAAAGTTGTAGATCAT
* * * * *
63549 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTGG
130 GGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* * *
63597 AGCAAAAGTTATATAATATTAAGTGGACTGTGTACTCCCGTTAACCGAAACAACAAATT-TTTCG
1 AGCAAAA-TTATATAATATTAAGTAGACCGTCTACTCCCGTTAACCGAAACAACAAATTCTTT-G
* * * * *
63661 GAAGCATTTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
64 AAAGCAATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCAAGCCCTTCATGAAAGTTGTAGAT
* * * * * *
63725 GATGGAACAATCTTTTAATAGACACTTAAATTACCTCAATCAGATAACCGG
127 CATGGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* * *
63776 AGAAAAAATTATATAATGTTAAATAGA
1 AG-CAAAATTATATAATATTAAGTAGA
63803 TCGTTTAGCC
Statistics
Matches: 173, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
177 6 0.03
178 61 0.35
179 102 0.59
180 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
AGCAAAATTATATAATATTAAGTAGACCGTCTACTCCCGTTAACCGAAACAACAAATTCTTTGAA
AGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCAAGCCCTTCATGAAAGTTGTAGATCATG
GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
Found at i:70665 original size:436 final size:438
Alignment explanation
Indices: 69813--70723 Score: 1077
Period size: 439 Copynumber: 2.1 Consensus size: 438
69803 AGATAAAAAA
* * * * * *
69813 AATCCAGC-AAAAAATATTAGTTTATGGAGACGAAACATAAAAATTTCCTTTTGAACCCTTAATG
1 AATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTTCCTCTCGAACCATTAACG
*
69877 AAACTAATGAATCAAATTCAACTTTCAGGCCCTTAATGAAAATCGTAGATCACAAATAACCTTTT
66 AAACTAATGAATCAAATTCAACTTTCAGGCCCTTAACGAAAATCGTAGATCACAAATAACCTTTT
* * *
69942 AACCGACACTTGAACAACTTCGATTGGACAAGTGGACCAAAAATTACACAACATTAAATAGACCG
131 AACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTACACAACATTAAATAGACCG
* * * * *
70007 ACAATTGAAACCACAAGATTGAGAAGCATTTTTAGAATTAAAACATTAAAATTGACTTCTGAGTT
196 ACAATCGAAACCACAAAATTCAGAAGCATTTTTAGAATCAAAACATTAAAATTGACTTCTGAGTC
* * **
70072 CTTCATGGAAGTTGTAGATCATGAAATCACCTTTTTATAGACACTTGAATCAACTTGATCGGCCA
261 CTTCATGAAAGTTGTAGATCATGAAATCACCTTTTAATAGACACTTGAATCAACTTGATCGAACA
* * * * *
70137 AATAGAACAGAAAATACAAAAATAAAAACCGAAGCGTTAAATTGTCCAACCCATAATTGTAAAGG
326 AATAAAACAAAAAATACAAAAATAAAAACCGAAACGTTAAATCGTCCAACCCAGAATTGTAAAGG
* * *
70202 ATTATATAGCATAAAGTATAAAAAGTAT-G-A-GGATCATTTGATAAAT
391 ACTAAATAGCATAAAGCAT-AAAAGTATAGTAGGGATCATTTGATAAAT
*
70248 AATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAA-TTCTCTCTCGAA-CATTCCA
1 AATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTTC-CTCTCGAACCATT-AA
* * * *
70311 CGAAACTCATTAATCAAATTCAGCTTTCAGGCCCTTCACGAAAATCGTAGATCACAGAATAACCT
64 CGAAACTAATGAATCAAATTCAACTTTCAGGCCCTTAACGAAAATCGTAGATCACA-AATAACCT
* * * * *
70376 TTTAATCGACACTTGAACAACCTCAATCGGACAAGTGGACCTAAAATTATACAATATTAGATAGA
128 TTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTACACAACATTAAATAGA
* * * * * * *
70441 CCGGCAATCGAGACCATAAAATTTCAGAAGTATTTTTTAGAATCAAAATATTAAAATTGGCTTTT
193 CCGACAATCGAAACCACAAAA-TTCAGAAGCA-TTTTTAGAATCAAAACATTAAAATTGACTTCT
* * * * *
70506 GAGTCCTTCATTAAAGTTGTAGATCATGAAATTACCTTTTAATAGGCACTTGAATCACCTTGATT
256 GAGTCCTTCATGAAAGTTGTAGATCATGAAATCACCTTTTAATAGACACTTGAATCAACTTGATC
* * * * * * * *
70571 GAAGAAGTAAAACAAAAAATA-ATAGACTTAAAGCTGAAACGTTCAATCGTCCAACCCAGAATTT
321 GAACAAATAAAACAAAAAATACA-AAAATAAAAACCGAAACGTTAAATCGTCCAACCCAGAA-TT
* * *
70635 GTGAGGGACTAAATAGC-T-TAGCAT-AAAGTATAAAAGTATAGGGATCATTTGATAAAT
384 GTAAAGGACTAAATAGCATAAAGCATAAAAGTAT---AG--TAGGGATCATTTGATAAAT
*
70692 AATCCAGCAAAAAAATGATTTGTTTATTGAGA
1 AATCCAGCAAAAAAAT-ATTTGTTTATGGAGA
70724 GCGGGACCCA
Statistics
Matches: 398, Mismatches: 61, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
435 14 0.04
436 97 0.24
437 81 0.20
438 13 0.03
439 130 0.33
440 16 0.04
443 1 0.00
444 32 0.08
445 14 0.04
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (438 bp):
AATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTTCCTCTCGAACCATTAACG
AAACTAATGAATCAAATTCAACTTTCAGGCCCTTAACGAAAATCGTAGATCACAAATAACCTTTT
AACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTACACAACATTAAATAGACCG
ACAATCGAAACCACAAAATTCAGAAGCATTTTTAGAATCAAAACATTAAAATTGACTTCTGAGTC
CTTCATGAAAGTTGTAGATCATGAAATCACCTTTTAATAGACACTTGAATCAACTTGATCGAACA
AATAAAACAAAAAATACAAAAATAAAAACCGAAACGTTAAATCGTCCAACCCAGAATTGTAAAGG
ACTAAATAGCATAAAGCATAAAAGTATAGTAGGGATCATTTGATAAAT
Found at i:73917 original size:33 final size:33
Alignment explanation
Indices: 73879--73945 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
73869 TTTACATAAA
73879 GTAAGAGTATACCAACTCTTATTACATCATAGT
1 GTAAGAGTATACCAACTCTTATTACATCATAGT
73912 GTAAGAGTATACCAACTCTTATTACATCATAGT
1 GTAAGAGTATACCAACTCTTATTACATCATAGT
73945 G
1 G
73946 ATATAACTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
GTAAGAGTATACCAACTCTTATTACATCATAGT
Found at i:75211 original size:37 final size:37
Alignment explanation
Indices: 75167--75237 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
75157 CTTGATCAAC
* * * *
75167 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCCTTCCAAATAAACATAACTTTATGATCA
75204 ATACATGTCCTTCCAAATAAACATAACTTTATGA
1 ATACATGTCCTTCCAAATAAACATAACTTTATGA
75238 ATAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (37 bp):
ATACATGTCCTTCCAAATAAACATAACTTTATGATCA
Found at i:86254 original size:93 final size:93
Alignment explanation
Indices: 86157--86326 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
86147 TAGTAATATC
*
86157 GTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGAGT
1 GTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGACT
86222 AAAACCATAAAAGTAAAATAATAAAATG
66 AAAACCATAAAAGTAAAATAATAAAATG
* * * *
86250 GTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAGATAAAAATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGACT
*
86315 AAAACTATAAAA
66 AAAACCATAAAA
86327 ATTTAAACAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (93 bp):
GTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGACT
AAAACCATAAAAGTAAAATAATAAAATG
Found at i:87346 original size:20 final size:20
Alignment explanation
Indices: 87309--87364 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
87299 AGAAAAGAAT
87309 AAAAAATAAAAAAGTTAAAG
1 AAAAAATAAAAAAGTTAAAG
* *
87329 AAAAAGATAATAAA-TTAAGTG
1 AAAAA-ATAAAAAAGTTAA-AG
*
87350 AAAAAA-AAAGAAGTT
1 AAAAAATAAAAAAGTT
87365 GATATAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
21 13 0.45
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (20 bp):
AAAAAATAAAAAAGTTAAAG
Found at i:88161 original size:599 final size:590
Alignment explanation
Indices: 87008--88194 Score: 2060
Period size: 599 Copynumber: 2.0 Consensus size: 590
86998 GGCAACAAAT
* *
87008 TTATTTGCCCACTTGCTGTCATATTCAGAAGAATTGGCCACGTCATGAAGTCGTATTTGAATTTT
1 TTATTTGCCCACTTGCTGTCATATTCAGAAGAATTGGCCACATCATGAAGTCGTATTTGAACTTT
87073 GAGAAAGGCTTTGATTCAACAATTTTTAGTATAGTTTGGATCCCTTGGACACATCTTTGCAAATC
66 GAGAAAGGCTTTGATTCAACAATTTTTAGTATAGTTTGGATCCCTTGGACACATCTTTGCAAATC
* * *
87138 TTGAGGATCCTTGAAGTAGTTAAAGGTAACAGATGGGTTATCGTTCGGAGCTCCAAATGGCCTGT
131 TTGAGGATCCATGAACTAATTAAAGGTAACAGATGGGTTATCGTTCGGAGCTCCAAATGGCCTGT
87203 TGAAATCGGACCCATAATTTTTTCTATTATGAATCCGCCTCTCAGAAATGGCTTCAAAACGGTAC
196 TGAAATCGGACCCATAATTTTTTCTATTATGAATCCGCCTCTCAGAAATGGCTTCAAAACGGTAC
87268 AGTACCATTGTGTTTGGCTTCCTTTGAAGGAAGAAAAGAATAAAAAATAAAAAAGTTAAAGAAAA
261 AGTACCATTGTGTTTGGCTTCCTTTGAAGGAAGAAAAGAATAAAAAATAAAAAAGTTAAAGAAAA
*
87333 AGATAATAAATTAAGTGAAAAAAAAAGAAGTTGATATAAACGGTTGGAATAAAAAAGGTAGTAAA
326 AGATAATAAATCAAGTGAAAAAAAAAGAAGTTGATATAAACGGTTGGAATAAAAAAGGTAGTAAA
* *
87398 AATCTATCACGATGATTACCACATATGAATTCATTTCAAAAGGTTTTTAAAACCGGTTTAGCAGG
391 AATCTATCACGAGGATTACCACATATGAATTCATTTCAAAAGGTTTTTAAAACCAGTTTAGCAGG
*
87463 TTAAACCTTTTAGTATCCGACGGTCAGGAAAATAGATGTTGCATCCAATGGTCAGAATTGAATGG
456 TTAAACCTTTTAGTATCCGACGATCAGGAAAATAGATGTTGCATCCAATGGTCAGAATTGAATGG
87528 GTGCATCACATTGAAAAATGGGAGCATCACAACGGGAGCACCAAAGTCTACACCTAAAGTTAAAC
521 GTGCATCACATTGAAAAATGGGAGCATCACAACGGGAGCACCAAAGTCTACACCTAAAGTTAAAC
87593 CCACG
586 CCACG
87598 TTATTTGCCCACTTGCTGTCATATTCAGAAGAATTGGCCACATCATGAAGTCGTATTTGAACTTT
1 TTATTTGCCCACTTGCTGTCATATTCAGAAGAATTGGCCACATCATGAAGTCGTATTTGAACTTT
87663 GAGAAAGGCTTTGATTCAACAATTTTCT-GTATAGTTTGGATCCCTTGGACACATCTTTGCAAAT
66 GAGAAAGGCTTTGATTCAACAATTTT-TAGTATAGTTTGGATCCCTTGGACACATCTTTGCAAAT
*
87727 CTTGAGGATCCATGAACTAATTAAAGGTAGCAGATGGGTTATCGTTCGGGTTACGGGTTCGGAGC
130 CTTGAGGATCCATGAACTAATTAAAGGTAACAGATGGGTTA----------T-C--GTTCGGAGC
87792 TCCAAATGGCCTGTTGAAATCGGACCCATAATTTTTTCTATTATGAATCCGCCTCTCAGAAATGG
182 TCCAAATGGCCTGTTGAAATCGGACCCATAATTTTTTCTATTATGAATCCGCCTCTCAGAAATGG
87857 CTTCAAAACGGTACAGTACCATTGTGTTTGGCTTCCTTTGAAGGAAGAAAAGAAT-AAAAATAAA
247 CTTCAAAACGGTACAGTACCATTGTGTTTGGCTTCCTTTGAAGGAAGAAAAGAATAAAAAATAAA
* * *
87921 AAAGTTAGAGAAAAAGATAATAAATCAAGTG-AAAAAAAAGTAGTTGATATCAACGGTTGGAAT-
312 AAAGTTAAAGAAAAAGATAATAAATCAAGTGAAAAAAAAAGAAGTTGATATAAACGGTTGGAATA
87984 AAAAAGGT-GTAAAAATCTATCACGAGGATTACCACATATGAATTCATTTCAAAAGGTTTTTAAA
377 AAAAAGGTAGTAAAAATCTATCACGAGGATTACCACATATGAATTCATTTCAAAAGGTTTTTAAA
*
88048 ACTAGTTTAGCAGGTTAAACCTTTTAGTATCCGACGATCAGGAAAATAGATGTTGCATCCAATGG
442 ACCAGTTTAGCAGGTTAAACCTTTTAGTATCCGACGATCAGGAAAATAGATGTTGCATCCAATGG
** *
88113 TCAGAATTGAATGGGTGCATCACATTGAAATGTGGGAGCATCACAACGGGAGCACCGAAGTCTAC
507 TCAGAATTGAATGGGTGCATCACATTGAAAAATGGGAGCATCACAACGGGAGCACCAAAGTCTAC
88178 ACCTAAAGTTAAACCCA
572 ACCTAAAGTTAAACCCA
88195 TTTTTGACCA
Statistics
Matches: 566, Mismatches: 17, Indels: 19
0.94 0.03 0.03
Matches are distributed among these distances:
590 162 0.29
591 1 0.00
599 196 0.35
600 9 0.02
601 31 0.05
602 38 0.07
603 129 0.23
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (590 bp):
TTATTTGCCCACTTGCTGTCATATTCAGAAGAATTGGCCACATCATGAAGTCGTATTTGAACTTT
GAGAAAGGCTTTGATTCAACAATTTTTAGTATAGTTTGGATCCCTTGGACACATCTTTGCAAATC
TTGAGGATCCATGAACTAATTAAAGGTAACAGATGGGTTATCGTTCGGAGCTCCAAATGGCCTGT
TGAAATCGGACCCATAATTTTTTCTATTATGAATCCGCCTCTCAGAAATGGCTTCAAAACGGTAC
AGTACCATTGTGTTTGGCTTCCTTTGAAGGAAGAAAAGAATAAAAAATAAAAAAGTTAAAGAAAA
AGATAATAAATCAAGTGAAAAAAAAAGAAGTTGATATAAACGGTTGGAATAAAAAAGGTAGTAAA
AATCTATCACGAGGATTACCACATATGAATTCATTTCAAAAGGTTTTTAAAACCAGTTTAGCAGG
TTAAACCTTTTAGTATCCGACGATCAGGAAAATAGATGTTGCATCCAATGGTCAGAATTGAATGG
GTGCATCACATTGAAAAATGGGAGCATCACAACGGGAGCACCAAAGTCTACACCTAAAGTTAAAC
CCACG
Found at i:89596 original size:61 final size:61
Alignment explanation
Indices: 89511--89633 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
89501 AAGGATATTA
89511 CAAAATGGCGCTTTTTGGAATATCTGTTGGGCGCAAACGGTTACATCTTCCATATGGATTT
1 CAAAATGGCGCTTTTTGGAATATCTGTTGGGCGCAAACGGTTACATCTTCCATATGGATTT
* * * *
89572 CAAAGTGGCTCTTTTTGGAATATCTGTTGGGCGCAAACGGTTGCATCTTCCCTATGGATTT
1 CAAAATGGCGCTTTTTGGAATATCTGTTGGGCGCAAACGGTTACATCTTCCATATGGATTT
89633 C
1 C
89634 TTAGAAGGGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (61 bp):
CAAAATGGCGCTTTTTGGAATATCTGTTGGGCGCAAACGGTTACATCTTCCATATGGATTT
Done.