Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018074.1 Corchorus olitorius cultivar O-4 contig18107, 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: 34380
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:708 original size:36 final size:36
Alignment explanation
Indices: 661--730 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
651 GAGATTTTAG
* *
661 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
697 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
731 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:1485 original size:181 final size:181
Alignment explanation
Indices: 1181--1527 Score: 613
Period size: 181 Copynumber: 1.9 Consensus size: 181
1171 TTACTAATGT
*
1181 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTTTAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
*
1246 TCAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
1311 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAA
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAA
* * *
1362 TATTAAGAATGTAAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCTTTTATAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
* * *
1427 TTAAGTAATTAAATTGGCAACTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
*
1492 AAGATTATTTGAATCTAGATAGTACTATAATGTTTT
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTT
1528 CATAACTTTT
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 157 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (181 bp):
TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAA
Found at i:3251 original size:95 final size:95
Alignment explanation
Indices: 3146--3327 Score: 301
Period size: 95 Copynumber: 1.9 Consensus size: 95
3136 AAATTGATAA
*
3146 TCTTCTTGCATCAGAAATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAGTAGCC
1 TCTTCTTGCATCAGAAATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
* *
3211 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
66 CTATAGTTCTTTTAGAAAATTCTTTCTTCT
* * *
3241 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTTATTAATGTTTAACTTCGTTCTTAATAGCC
1 TCTTCTTGCATCAGAAATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
*
3306 CTATAGTTTTTTTAGAAAATTC
66 CTATAGTTCTTTTAGAAAATTC
3328 AAATAAGAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (95 bp):
TCTTCTTGCATCAGAAATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
CTATAGTTCTTTTAGAAAATTCTTTCTTCT
Found at i:11236 original size:12 final size:13
Alignment explanation
Indices: 11219--11247 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11209 GCACACAGCC
11219 AAAAAAACAAAA-
1 AAAAAAACAAAAT
11231 AAAAAAACAAAAT
1 AAAAAAACAAAAT
11244 AAAA
1 AAAA
11248 TAAAACCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAT
Found at i:21914 original size:26 final size:27
Alignment explanation
Indices: 21877--21927 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21867 TATACTCAAC
* *
21877 TTTTAT-ATTTTTTTTAGCAATAAAAA
1 TTTTATAATTTTCTTTAGAAATAAAAA
21903 TTTTATAATTTTCTTTAGAAATAAA
1 TTTTATAATTTTCTTTAGAAATAAA
21928 CTTTTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
TTTTATAATTTTCTTTAGAAATAAAAA
Found at i:21932 original size:26 final size:26
Alignment explanation
Indices: 21874--21932 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
21864 ATATATACTC
* *
21874 AACTTTTATATTTTTTTTAGCAATAA
1 AACTTTTATATTTTCTTTAGAAATAA
*
21900 AAATTTTATAATTTTCTTTAGAAAT-A
1 AACTTTTAT-ATTTTCTTTAGAAATAA
21926 AACTTTT
1 AACTTTT
21933 TGATTAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (26 bp):
AACTTTTATATTTTCTTTAGAAATAA
Found at i:22475 original size:20 final size:20
Alignment explanation
Indices: 22450--22494 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
22440 TAGATAACAG
22450 TTTATAGAATGAATAATTAA
1 TTTATAGAATGAATAATTAA
22470 TTTATAGAATGAATAATTAA
1 TTTATAGAATGAATAATTAA
22490 TTTAT
1 TTTAT
22495 CTTGCAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTATAGAATGAATAATTAA
Found at i:23335 original size:57 final size:59
Alignment explanation
Indices: 23247--23369 Score: 196
Period size: 62 Copynumber: 2.1 Consensus size: 59
23237 ACAACAAAGC
*
23247 CGTTTAAGAACAACCAGAGAGAAGTAGAA-T-TATTGGTGTGTAAAAATGGGGAAAACA
1 CGTTTAAGAACAACCAGAGAGAAGTAGAATTATATTGGTGTGTAAAAATGAGGAAAACA
23304 CGTTTAAGAACAACCAGAGAGAAGTAGAATTAGAATATTGGTGTGTAAAAATGAGGAAAACA
1 CGTTTAAGAACAACCAGAGAGAAGTAGAATT---ATATTGGTGTGTAAAAATGAGGAAAACA
23366 CGTT
1 CGTT
23370 CTTATTTATA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
57 29 0.48
58 1 0.02
62 30 0.50
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (59 bp):
CGTTTAAGAACAACCAGAGAGAAGTAGAATTATATTGGTGTGTAAAAATGAGGAAAACA
Done.