Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011421.1 Corchorus olitorius cultivar O-4 contig11454, 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: 10247
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:265 original size:33 final size:32
Alignment explanation
Indices: 157--304 Score: 138
Period size: 33 Copynumber: 4.5 Consensus size: 32
147 AAGAGTAATT
* * *
157 CTAAATCTGTTTTAGATGTTGTTTGCGATGATA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* ** *
190 CTAAACCTAATTTGAGTGTTGTTTGTGATGACA
1 CTAAATCTGTTTTG-GTGTTGTTTGTGATGAAA
223 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* **
256 C-AAATTCTGTTTTGGATGCTAATTGTGATGAAAA
1 CTAAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAA
290 C-AAATCTGTTTTGGT
1 CTAAATCTGTTTTGGT
305 TGATCATAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
32 7 0.07
33 82 0.85
34 8 0.08
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (32 bp):
CTAAATCTGTTTTGGTGTTGTTTGTGATGAAA
Found at i:1269 original size:21 final size:21
Alignment explanation
Indices: 1243--1284 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233 GCATCTTAGG
1243 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
1264 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
1285 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:5996 original size:33 final size:33
Alignment explanation
Indices: 5943--6023 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
5933 CTGTTTTAGA
* * * *
5943 TGTTGTTTGCGATAATACTAAACCTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAACC-AATTTCAGG
* **
5976 TGTTGTTTGTGATGACACTAAATCGGTTTCAGG
1 TGTTGTTTGTGATGACACTAAACCAATTTCAGG
6009 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
6024 AACAAATTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 4 0.10
33 36 0.90
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCAATTTCAGG
Found at i:7078 original size:33 final size:33
Alignment explanation
Indices: 6934--7083 Score: 119
Period size: 33 Copynumber: 4.5 Consensus size: 33
6924 ATGATCAACC
* ** * *
6934 AAAACAGATTT-GTTTTCATCACAATTAGCATCC
1 AAAACAGATTTAGTATT-ATCACAAACAACATCT
* *
6967 AAAACAGAATTT-GT-TTCATCACAAAAAACACCT
1 AAAACAG-ATTTAGTATT-ATCACAAACAACATCT
* *
7000 AAAACAGATTTAGTGTCATCACAAACAACA-CTT
1 AAAACAGATTTAGTATTATCACAAACAACATC-T
** *
7033 AAATTAGGTTTAGTATTATCACAAACAACATCT
1 AAAACAGATTTAGTATTATCACAAACAACATCT
*
7066 AAAACAGATTTAGAATTA
1 AAAACAGATTTAGTATTA
7084 CTCTTTGAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
32 5 0.05
33 83 0.86
34 8 0.08
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (33 bp):
AAAACAGATTTAGTATTATCACAAACAACATCT
Found at i:8659 original size:25 final size:24
Alignment explanation
Indices: 8622--8668 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
8612 CTAGAAAATT
8622 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
8648 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
8669 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:9991 original size:155 final size:154
Alignment explanation
Indices: 9455--10247 Score: 1049
Period size: 156 Copynumber: 5.1 Consensus size: 154
9445 ATTCGTATCA
* *
9455 ATTTTGGTAAGACTAGTCCATTGTGAAGTTCTTAGCTCATTTTGAACACTTGTTATTTTGGGCC-
1 ATTTTGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * * **
9519 ATTCGAGGCCCATTAGTTAGGTTTTAAAAATCGTCTTCGATTTGGCAAACAACAATGCTTTTCTT
66 A-TCGGGGCCCATTAGATACGTTTT--GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
*
9584 TCCATTGTTTATCGCCTAACTATAATC
128 TCCATTGTTTATGGCCTAACTATAATC
* * *
9611 ATTTTGGTAAGACTAGTCCATTGTGAAGTTCTTAGCTCATTTTGAACACTTGTTATTTTGGACC-
1 ATTTTGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
9675 ATTCAGGGCCCATTAG-TTCGGTTTTAAAAATCGTCTTCGATTTGGCAAACCGAT-AATGCTTTT
66 A-TCGGGGCCCATTAGATAC-GTTTT--GAATCGTCTTCGATTTGGCAAACC--TCAATGCTTTT
9738 CTTTCCATTGTTTATGGCCTAACTATAATC
125 CTTTCCATTGTTTATGGCCTAACTATAATC
* *
9768 ATTTTCGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTAATTTGGAACACTTGATATTTTGGGCC
1 ATTTT-GGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* ** *
9833 TATCGGGGCCCATTAGAGACGTACTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTC
65 TATCGGGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
* **
9898 CATTTTTTATGAACTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
* * * * *
9923 ATTTTGGTAAGTTTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGAGTCC
1 ATTTTGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTG-GGCC
* * * * *
9988 TATCGGGGCCCATTAGATCCGTTTTGAATCGTTTTCGAATTGGCAAACCACAATGTTTTTCTTTC
65 TATCGGGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
10053 CAATTGTTTATGGCCTAACTATAATC
130 C-ATTGTTTATGGCCTAACTATAATC
** * *
10079 ATTTT-GTGGGATTAGTCCAATGTGAAGTT-TTGAGCTCATTTGGAACACTTGTTATTTTGAGCC
1 ATTTTGGTAAGATTAGTCCATTGTGAAGTTCTT-AGCTCATTTGGAACACTTGTTATTTTGGGCC
* *
10142 TATCGGTGCCCATTAGATCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
65 TATCGGGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
*
10207 CATTGTTTATGGCCTATCTATAATC
130 CATTGTTTATGGCCTAACTATAATC
*
10232 ATTTTGGTGAGATTAG
1 ATTTTGGTAAGATTAG
Statistics
Matches: 570, Mismatches: 56, Indels: 24
0.88 0.09 0.04
Matches are distributed among these distances:
153 28 0.05
154 124 0.22
155 147 0.26
156 156 0.27
157 43 0.08
158 70 0.12
159 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (154 bp):
ATTTTGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
ATCGGGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
ATTGTTTATGGCCTAACTATAATC
Found at i:10192 original size:309 final size:308
Alignment explanation
Indices: 9455--10239 Score: 1060
Period size: 309 Copynumber: 2.5 Consensus size: 308
9445 ATTCGTATCA
* * *
9455 ATTTTGGTAAGACTAGTCCATTGTGAAGTTCTTAGCTCATTTTGAACACTTGTTATTTTGGGCC-
1 ATTTTCGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * **
9519 ATTCGAGGCCCATTAGTTAGGTTTTAAAAATCGTCTTCGATTTGGCAAACAACAATGCTTTTCTT
66 A-TCG-GGCCCATTAGATACGTTTT--GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
9584 TCCATTGTTTATCGCCTAACTATAATCATTTTGGTAAGACTAGTCCATTGTGAAGTTCTTAGCTC
127 TCCATTGTTTAT-GCCTAACTATAATCATTTTGGTAAGACTAGTCCACTGTGAAGTTCTTAACTC
* * *
9649 ATTTTGAACACTTGTTATTTTGGACCATTCAGGGCCCATTAGTTCGGTTTTAAAAATCGTCTTCG
191 ATTTGGAACACTTGTTATTTTGGACCATTCAGGGCCCATTAGATCCGTTTT-AAAATCGTCTTCG
* *
9714 ATTTGGCAAACCGATAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
255 AATTGGCAAACCGACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
* *
9768 ATTTTCGGTAAGATTAGTCCATTGTGAAGTTCTTAGCTAATTTGGAACACTTGATATTTTGGGCC
1 ATTTTC-GTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* ** *
9833 TATCGGGGCCCATTAGAGACGTACTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTC
65 TATC-GGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
* * ** *
9898 CATTTTTTATGAACTAACTATAATCATTTTGGTAAGTTTAGTCCACTGTGAAGTTTTTAACTCAT
129 CATTGTTTATG-CCTAACTATAATCATTTTGGTAAGACTAGTCCACTGTGAAGTTCTTAACTCAT
* * * *
9963 TTGGAACACTTGTTATTTTGAGTCC-TATCGGGGCCCATTAGATCCGTTTT-GAATCGTTTTCGA
193 TTGGAACACTTGTTATTTTG-GACCAT-TCAGGGCCCATTAGATCCGTTTTAAAATCGTCTTCGA
*
10026 ATTGGCAAACC-ACAATGTTTTTCTTTCCAATTGTTTATGGCCTAACTATAATC
256 ATTGGCAAACCGACAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTATAATC
** * *
10079 ATTTT-GTGGGATTAGTCCAATGTGAAGTT-TTGAGCTCATTTGGAACACTTGTTATTTTGAGCC
1 ATTTTCGTAAGATTAGTCCATTGTGAAGTTCTT-AGCTCATTTGGAACACTTGTTATTTTGGGCC
*
10142 TATCGGTGCCCATTAGATCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
65 TATCGG-GCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
*
10207 CATTGTTTATGGCCTATCTATAATCATTTTGGT
129 CATTGTTTAT-GCCTAACTATAATCATTTTGGT
10240 GAGATTAG
Statistics
Matches: 417, Mismatches: 45, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
308 4 0.01
309 134 0.32
310 16 0.04
311 51 0.12
312 112 0.27
313 28 0.07
314 70 0.17
315 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (308 bp):
ATTTTCGTAAGATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
ATCGGGCCCATTAGATACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA
TTGTTTATGCCTAACTATAATCATTTTGGTAAGACTAGTCCACTGTGAAGTTCTTAACTCATTTG
GAACACTTGTTATTTTGGACCATTCAGGGCCCATTAGATCCGTTTTAAAATCGTCTTCGAATTGG
CAAACCGACAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
Done.