Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021608.1 Corchorus olitorius cultivar O-4 contig21641, 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: 19849
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:812 original size:21 final size:21
Alignment explanation
Indices: 786--840 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
776 CGCCCATTCA
*
786 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
* *
807 CCGTGCCACAACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
828 CCGTGCCATCACC
1 CCGTGCCACCACC
841 ATTCAGTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.45, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:4152 original size:15 final size:16
Alignment explanation
Indices: 4122--4155 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
4112 TTACTTTGCT
4122 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
4138 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
4153 TTG
1 TTG
4156 CTTTATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:5548 original size:90 final size:90
Alignment explanation
Indices: 5395--5670 Score: 405
Period size: 90 Copynumber: 3.1 Consensus size: 90
5385 CACCAGATTA
* * * *
5395 AACTTTGAAGAAATACTACACCG-AGTTAACTTGATTCACCGAATCATCCTGGACTGTTTGAAAA
1 AACTTTAAAGAAATAATGCACCGCA-TTAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAA
5459 TGTACTTCACCTAGCTCACCGAATCC
65 TGTACTTCACCTAGCTCACCGAATCC
5485 AACTTTAAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAAT
1 AACTTTAAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAAT
* * *
5550 GTAC-TAAACTGAGCTCACCCAATCC
66 GTACTTCACCT-AGCTCACCGAATCC
* *
5575 AACTTTAAAGAAATAATGCATCGCATTAACTTGATTCACCGAATCATCCCGAACTGTTTGAAAAT
1 AACTTTAAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAAT
* *
5640 GT-GTTGCACCGAGCTCACCGAATCC
66 GTACTT-CACCTAGCTCACCGAATCC
5665 AACTTT
1 AACTTT
5671 GAACTGCTCA
Statistics
Matches: 168, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
89 4 0.02
90 161 0.96
91 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (90 bp):
AACTTTAAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAAT
GTACTTCACCTAGCTCACCGAATCC
Found at i:6302 original size:2 final size:2
Alignment explanation
Indices: 6295--6323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6285 ACATACATAC
6295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6324 AGACGTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8147 original size:30 final size:30
Alignment explanation
Indices: 8111--8171 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
8101 GAAGTTCGTG
*
8111 ATTGAAGATTTATTGAAG-ATAATTTTAAGA
1 ATTGAAGA-TCATTGAAGAATAATTTTAAGA
*
8141 ATTGAAGATCATTGAAGAATTATTTTAAGA
1 ATTGAAGATCATTGAAGAATAATTTTAAGA
8171 A
1 A
8172 GCAAGAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (30 bp):
ATTGAAGATCATTGAAGAATAATTTTAAGA
Found at i:8707 original size:11 final size:12
Alignment explanation
Indices: 8691--8726 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
8681 TCTCAATTTC
8691 TTTTCTTCTA-T
1 TTTTCTTCTAGT
8702 TTTTC-TCTAGT
1 TTTTCTTCTAGT
8713 TTTTCTT-TAGT
1 TTTTCTTCTAGT
8724 TTT
1 TTT
8727 AGTTAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 18 0.78
12 1 0.04
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:9227 original size:26 final size:27
Alignment explanation
Indices: 9198--9259 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
9188 AGGGGTATTT
**
9198 TGGTCATTTTTACACT-AAAGGCATTC
1 TGGTCATTTGCACACTCAAAGGCATTC
** *
9224 TGGTCATTTGCACACTCAGGGGCATTT
1 TGGTCATTTGCACACTCAAAGGCATTC
9251 TGGTCATTT
1 TGGTCATTT
9260 CAAGCCCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (27 bp):
TGGTCATTTGCACACTCAAAGGCATTC
Found at i:9255 original size:27 final size:26
Alignment explanation
Indices: 9186--9259 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
9176 TTAGGGTCAC
* **
9186 CTAGGGGTATTTTGGTCATTTTTACA
1 CTAGGGGCATTTTGGTCATTTGCACA
** *
9212 CTAAAGGCATTCTGGTCATTTGCACA
1 CTAGGGGCATTTTGGTCATTTGCACA
9238 CTCAGGGGCATTTTGGTCATTT
1 CT-AGGGGCATTTTGGTCATTT
9260 CAAGCCCAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (26 bp):
CTAGGGGCATTTTGGTCATTTGCACA
Found at i:9774 original size:20 final size:20
Alignment explanation
Indices: 9749--9788 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9739 AAAATACAAA
*
9749 GCATTTGATTTACAAATTGG
1 GCATTTAATTTACAAATTGG
*
9769 GCATTTAATTTGCAAATTGG
1 GCATTTAATTTACAAATTGG
9789 TGCCCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
GCATTTAATTTACAAATTGG
Found at i:15407 original size:62 final size:62
Alignment explanation
Indices: 15281--15468 Score: 322
Period size: 62 Copynumber: 3.0 Consensus size: 62
15271 CATCCTTTAA
* *
15281 GTAATTTCATTTGGGTTGGGTTTTTAACTTTTTAACTCATTCCTTTGGGCTTTTTCCTATTTG
1 GTAATTTCATTTGGGTTGGGTTCTTAACTTTTAAACTCATTCCTTTGGGC-TTTTCCTATTTG
* *
15344 GTAATTCCATTTGGGTTGGGTTCTTAAATTTTAAACTCATTCCTTTGGGCTTTTCCTATTTG
1 GTAATTTCATTTGGGTTGGGTTCTTAACTTTTAAACTCATTCCTTTGGGCTTTTCCTATTTG
*
15406 GTAATTTCATTTGGGTTGGGTTCTTAACTTTTAAACTCATTCCTTTGGGCCTTTCCTATTTG
1 GTAATTTCATTTGGGTTGGGTTCTTAACTTTTAAACTCATTCCTTTGGGCTTTTCCTATTTG
15468 G
1 G
15469 CCCATTTTCT
Statistics
Matches: 118, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
62 72 0.61
63 46 0.39
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (62 bp):
GTAATTTCATTTGGGTTGGGTTCTTAACTTTTAAACTCATTCCTTTGGGCTTTTCCTATTTG
Found at i:17255 original size:11 final size:11
Alignment explanation
Indices: 17239--17282 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
17229 CAAGGCAGTA
*
17239 AAAAAAAATTC
1 AAAAAAAATAC
17250 AAAAAAAATAC
1 AAAAAAAATAC
*
17261 AAACAGAAAACAC
1 AAA-A-AAAATAC
17274 AAAAAAAAT
1 AAAAAAAAT
17283 GGAGCTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 17 0.61
12 2 0.07
13 9 0.32
ACGTcount: A:0.77, C:0.11, G:0.02, T:0.09
Consensus pattern (11 bp):
AAAAAAAATAC
Found at i:18166 original size:29 final size:29
Alignment explanation
Indices: 18106--18181 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
18096 GAAGTTCGTG
* **
18106 TTTGAAGACCATTTGAAGACTTATTTGGAGA
1 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
18137 TTTGAAGACTTTGAAGATTTATTTCAAGA
1 TTTGAAGACTTTGAAGATTTATTTCAAGA
*
18166 --TGAAGA-ATTGAAGATT
1 TTTGAAGACTTTGAAGATT
18182 GGAGCTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.22
27 6 0.15
29 17 0.41
30 1 0.02
31 8 0.20
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (29 bp):
TTTGAAGACTTTGAAGATTTATTTCAAGA
Found at i:19550 original size:15 final size:16
Alignment explanation
Indices: 19520--19559 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
19510 TTACTTTGCT
19520 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
19536 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
19551 TTGCTTTCT
1 TTGTTTTCT
19560 TTCATCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Done.