Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020399.1 Corchorus olitorius cultivar O-4 contig20432, 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: 49236
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5943 original size:17 final size:17
Alignment explanation
Indices: 5923--5956 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5913 TTTCAATTTG
5923 TAATTTGTTTGTTTGTT
1 TAATTTGTTTGTTTGTT
5940 TAATTTGTTTGTTTGTT
1 TAATTTGTTTGTTTGTT
5957 ATGAGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (17 bp):
TAATTTGTTTGTTTGTT
Found at i:7192 original size:30 final size:29
Alignment explanation
Indices: 7157--7228 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
7147 CGTCTGAAAA
* *
7157 GGGCTTATTTGGTCTTTTTAA-AGAGTTTAG
1 GGGCTTATTTGGTC--TTCAACAGAGTTCAG
7187 GGGCTTATTTGG-CTTCAATCAGAGTTCAG
1 GGGCTTATTTGGTCTTCAA-CAGAGTTCAG
7216 GGGCTTATTTGGT
1 GGGCTTATTTGGT
7229 TGTTTTGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 4 0.11
29 21 0.57
30 12 0.32
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (29 bp):
GGGCTTATTTGGTCTTCAACAGAGTTCAG
Found at i:15141 original size:45 final size:45
Alignment explanation
Indices: 15073--15252 Score: 315
Period size: 45 Copynumber: 4.0 Consensus size: 45
15063 GGGAAACCAC
*
15073 CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
1 CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
* *
15118 CTTTGCCTGCCCCTTCACCTAGGCCGCAGATTAATTCACCCTCCT
1 CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
* *
15163 CCTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCAT
1 CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
15208 CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
1 CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
15253 TGCAGCAAAG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 126 1.00
ACGTcount: A:0.18, C:0.41, G:0.11, T:0.30
Consensus pattern (45 bp):
CTTTGCCTGCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
Found at i:15601 original size:30 final size:30
Alignment explanation
Indices: 15333--15599 Score: 347
Period size: 30 Copynumber: 8.9 Consensus size: 30
15323 GCAACAACAG
15333 CATGTATCATCTCCACAGGTGCCACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* *
15363 CATATATCATCTCCTCAGGTGCCACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* **
15393 CATGTGTCATCTCCACAGGTGCCACAGTCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
**
15423 CATGTATCATCTCCACAGGTGCCACAGTCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
*
15453 CATGTATCATCTCCACAGGTGACACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* * *
15483 CATGAATCGTCTGCAC-GTGTGCCACAACCT
1 CATGTATCATCTCCACAG-GTGCCACAACCT
* * * *
15513 CGTGTATCGTCTCCACATGTGCCACAACCC
1 CATGTATCATCTCCACAGGTGCCACAACCT
* *
15543 CATGTATCATCTCCACATGTGCCACAATCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* *
15573 CATGTATCATCTCCACATGTGTCACAA
1 CATGTATCATCTCCACAGGTGCCACAA
15600 TCATCGCCTC
Statistics
Matches: 210, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
29 1 0.00
30 209 1.00
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (30 bp):
CATGTATCATCTCCACAGGTGCCACAACCT
Found at i:37773 original size:2 final size:2
Alignment explanation
Indices: 37766--37808 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
37756 ATTTTCTTAT
*
37766 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TGA AA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
37807 TA
1 TA
37809 GGATAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38180 original size:18 final size:18
Alignment explanation
Indices: 38159--38212 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
38149 TAAATTATAT
38159 TAATTAATTATATAAATA
1 TAATTAATTATATAAATA
* *
38177 TAATT--GTA-A-ATAT-
1 TAATTAATTATATAAATA
38190 TAATTAATTATATAAATA
1 TAATTAATTATATAAATA
38208 TAATT
1 TAATT
38213 GTAAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
13 5 0.19
14 3 0.11
15 3 0.11
16 3 0.11
17 3 0.11
18 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TAATTAATTATATAAATA
Found at i:38193 original size:31 final size:31
Alignment explanation
Indices: 38155--38220 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
38145 GAATTAAATT
38155 ATATTAATTAATTATATAAATATAATTGTAA
1 ATATTAATTAATTATATAAATATAATTGTAA
38186 ATATTAATTAATTATATAAATATAATTGTAA
1 ATATTAATTAATTATATAAATATAATTGTAA
38217 ATAT
1 ATAT
38221 ATACTACCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
ATATTAATTAATTATATAAATATAATTGTAA
Found at i:41573 original size:160 final size:158
Alignment explanation
Indices: 41309--41627 Score: 467
Period size: 160 Copynumber: 2.0 Consensus size: 158
41299 ATCTGATGCA
* * *
41309 AATCGATCCCAGATTAATTAAAATTGATTCCCGATACAACTCGATCCCCATATTAGTTTAAAATT
1 AATCGATCCCAGATTAATTAAAATTAATTCACGATACAACTCGATCCCCAGATTAGTTTAAAATT
*
41374 TATTAATGTAACTATTGGAGATGGACAACTGGAATATAAGGCATTCAGTCACATCAAACTATAGG
66 TATTAATGTAACTATTGGAGATGGACAACTGGAATATAAGGCACTCAGTCACATCAAA-T-TAGG
* * *
41439 GTGGACAAACACCTAAAACAAAATGGACTC
129 ATGAACAAACACCCAAAACAAAATGGACTC
* * * * * *
41469 AATCGATCCTAGATTAGTTAAAATTAATTCACGATGCAACTCGATCCCCAGGTTAGTTTCAATTT
1 AATCGATCCCAGATTAATTAAAATTAATTCACGATACAACTCGATCCCCAGATTAGTTTAAAATT
* * *
41534 TATTAATGTATCTATTGGAGATGGACAACTTGAATATAAGTCACTCAGTCACATCAAATTAGGAT
66 TATTAATGTAACTATTGGAGATGGACAACTGGAATATAAGGCACTCAGTCACATCAAATTAGGAT
*
41599 GAACAAACACCCAAAACAAAATGGTCTC
131 GAACAAACACCCAAAACAAAATGGACTC
41627 A
1 A
41628 CACAAGTCTG
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
158 31 0.22
159 1 0.01
160 110 0.77
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (158 bp):
AATCGATCCCAGATTAATTAAAATTAATTCACGATACAACTCGATCCCCAGATTAGTTTAAAATT
TATTAATGTAACTATTGGAGATGGACAACTGGAATATAAGGCACTCAGTCACATCAAATTAGGAT
GAACAAACACCCAAAACAAAATGGACTC
Found at i:44783 original size:29 final size:32
Alignment explanation
Indices: 44736--44810 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 32
44726 GCGCTGAGAG
44736 TCTAGGGGGCAAAACGTCCAAAAT-TA-AAGT
1 TCTAGGGGGCAAAACGTCCAAAATGTACAAGT
* *
44766 T-TAGGGGGCAAAATGTCCAAACTGTACAAGT
1 TCTAGGGGGCAAAACGTCCAAAATGTACAAGT
*
44797 TCAAGGGGGCAAAA
1 TCTAGGGGGCAAAA
44811 AGGGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 20 0.51
30 3 0.08
31 5 0.13
32 11 0.28
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (32 bp):
TCTAGGGGGCAAAACGTCCAAAATGTACAAGT
Found at i:47937 original size:21 final size:22
Alignment explanation
Indices: 47913--47953 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47903 GTGTATAATA
*
47913 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
47934 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
47954 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:48856 original size:7 final size:7
Alignment explanation
Indices: 48844--48876 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
48834 AATCATATGT
48844 ATAGGAA
1 ATAGGAA
48851 ATAGGAA
1 ATAGGAA
48858 ATAGGAA
1 ATAGGAA
*
48865 AAAGG-A
1 ATAGGAA
48871 ATAGGA
1 ATAGGA
48877 GTTTTCATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (7 bp):
ATAGGAA
Found at i:49200 original size:1 final size:1
Alignment explanation
Indices: 49196--49231 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
49186 AGAAAAAAAG
* *
49196 TTTTTTTTTTTTTTTTTTNTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49232 ACTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Done.