Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014007.1 Corchorus olitorius cultivar O-4 contig14040, 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: 34527
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:1152 original size:6 final size:6
Alignment explanation
Indices: 1138--1216 Score: 56
Period size: 6 Copynumber: 13.5 Consensus size: 6
1128 ATTTATTTTA
* * * * * * *
1138 TTTTAT TTTTCT TTTTAT TTTTCT TCTTCC TTTTCC TTTTCC TTTTCC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
1186 TTTT-T TTTTC- TTTCCT TTTT-T TTCTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT TTT
1217 CCTGGCTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
5 11 0.18
6 46 0.77
7 3 0.05
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:1155 original size:12 final size:12
Alignment explanation
Indices: 1107--1198 Score: 55
Period size: 12 Copynumber: 7.7 Consensus size: 12
1097 AAAAATTTCC
1107 TTTT-TTTTTA-
1 TTTTCTTTTTAT
*
1117 TTTCCTTATTTAT
1 TTTTCTT-TTTAT
*
1130 TTATTTTATTTTAT
1 TT-TTCT-TTTTAT
1144 TTTTCTTTTTAT
1 TTTTCTTTTTAT
* **
1156 TTTTCTTCTTCC
1 TTTTCTTTTTAT
* **
1168 TTTTCCTTTTCC
1 TTTTCTTTTTAT
*
1180 TTTTCCTTTT-T
1 TTTTCTTTTTAT
1191 TTTTCTTT
1 TTTTCTTT
1199 CCTTTTTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
10 3 0.05
11 9 0.14
12 39 0.59
13 5 0.08
14 9 0.14
15 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTAT
Found at i:1211 original size:14 final size:15
Alignment explanation
Indices: 1102--1208 Score: 76
Period size: 15 Copynumber: 6.9 Consensus size: 15
1092 ATTTTAAAAA
*
1102 TTTCCTTTTTTTTTA
1 TTTCCTTTTTTTTTC
* *
1117 TTTCCTTATTTATTTA
1 TTTCCTT-TTTTTTTC
**
1133 TTTTATTTTATTTTTC
1 TTTCCTTTT-TTTTTC
1149 TTT--TTATTTTTCTTC
1 TTTCCTT-TTTTT-TTC
*
1164 -TTCCTTTTCCTTTTCC
1 TTTCCTTTT--TTTTTC
1180 TTTTCCTTTTTTTTTC
1 -TTTCCTTTTTTTTTC
1196 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
1209 CTTCTTTTCC
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
14 7 0.09
15 29 0.39
16 28 0.37
17 3 0.04
18 8 0.11
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCCTTTTTTTTTC
Found at i:1217 original size:18 final size:17
Alignment explanation
Indices: 1133--1219 Score: 79
Period size: 18 Copynumber: 5.0 Consensus size: 17
1123 TATTTATTTA
* * *
1133 TTTTATTTTATTTTTCT
1 TTTTTTTTTCTTTTCCT
1150 TTTTATTTTTCTTCTTCCT
1 TTTT-TTTTTCTT-TTCCT
* *
1169 TTTCCTTTTCCTTTTCC-
1 TTT-TTTTTTCTTTTCCT
1186 TTTTTTTTTC-TTTCCT
1 TTTTTTTTTCTTTTCCT
1202 TTTTTTTCTTCTTTTCCT
1 TTTTTTT-TTCTTTTCCT
1220 GGCTTGGGCC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
15 5 0.09
16 12 0.21
17 10 0.18
18 16 0.28
19 14 0.25
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTTCTTTTCCT
Found at i:8136 original size:13 final size:13
Alignment explanation
Indices: 8118--8145 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8108 ATAATATGAT
8118 AGATATTATAGGA
1 AGATATTATAGGA
8131 AGATATTATAGGA
1 AGATATTATAGGA
8144 AG
1 AG
8146 CATAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (13 bp):
AGATATTATAGGA
Found at i:10492 original size:35 final size:35
Alignment explanation
Indices: 10422--10492 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
10412 ATCGTATTTG
* * * *
10422 TTGGTAAGGTTCTAACTGGATAATTTGTCAAGATT
1 TTGGTAAGGCTCAAACTGGACAATTGGTCAAGATT
* *
10457 TTGGTAAGGCTCAAATTGGACAATTGGTCACGATT
1 TTGGTAAGGCTCAAACTGGACAATTGGTCAAGATT
10492 T
1 T
10493 AGGAGGAGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (35 bp):
TTGGTAAGGCTCAAACTGGACAATTGGTCAAGATT
Found at i:23708 original size:73 final size:73
Alignment explanation
Indices: 23589--23772 Score: 368
Period size: 73 Copynumber: 2.5 Consensus size: 73
23579 ACCTTAGACA
23589 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGAAATTTTTTATGAGAAAAGATATTAATA
1 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGAAATTTTTTATGAGAAAAGATATTAATA
23654 AATAGTAC
66 AATAGTAC
23662 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGAAATTTTTTATGAGAAAAGATATTAATA
1 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGAAATTTTTTATGAGAAAAGATATTAATA
23727 AATAGTAC
66 AATAGTAC
23735 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGA
1 ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGA
23773 GATTGATTGA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.26
Consensus pattern (73 bp):
ATAAGAAAAGAGACTGATAAGTAGTATATAACCAAAGAAATTTTTTATGAGAAAAGATATTAATA
AATAGTAC
Found at i:23754 original size:27 final size:27
Alignment explanation
Indices: 23724--23779 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
23714 AAAGATATTA
*
23724 ATAAATAGTACATAAGAAAAGAGACTG
1 ATAAATAGTACATAACAAAAGAGACTG
* * * *
23751 ATAAGTAGTATATAACCAAAGAGATTG
1 ATAAATAGTACATAACAAAAGAGACTG
23778 AT
1 AT
23780 TGATCAACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (27 bp):
ATAAATAGTACATAACAAAAGAGACTG
Found at i:25750 original size:20 final size:21
Alignment explanation
Indices: 25725--25764 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
25715 GACTAAGGGC
*
25725 ATAACA-GTAATTTCCCAAGG
1 ATAACAGGTAATTACCCAAGG
25745 ATAACATGGTAATTACCCAA
1 ATAACA-GGTAATTACCCAA
25765 AAGGGTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
ATAACAGGTAATTACCCAAGG
Found at i:31337 original size:18 final size:18
Alignment explanation
Indices: 31316--31371 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
31306 TCTCCATCAA
31316 CAAAGCAAAGTTCTTCTC
1 CAAAGCAAAGTTCTTCTC
31334 CAAAGCAAAGTTCTTCTC
1 CAAAGCAAAGTTCTTCTC
31352 CAAAGCAAAGTTCTTCTC
1 CAAAGCAAAGTTCTTCTC
31370 CA
1 CA
31372 TCAACAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.27
Consensus pattern (18 bp):
CAAAGCAAAGTTCTTCTC
Found at i:31599 original size:42 final size:42
Alignment explanation
Indices: 31538--31630 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
31528 TCAAATCTAG
* ** *
31538 CAAATCCGACAATGAGGAATAACAAGCCTTTGGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTCCGGCCATTCCTCT
31581 CAAATCCACAACGAGGAATAACAAGCCTCCGGCCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTCCGGCCATTCCTCT
31623 CAAATCCA
1 CAAATCCA
31631 TTTCATCGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (42 bp):
CAAATCCACAACGAGGAATAACAAGCCTCCGGCCATTCCTCT
Done.