Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023551.1 Corchorus olitorius cultivar O-4 contig23584, 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: 9803
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:4702 original size:14 final size:15
Alignment explanation
Indices: 4675--4707 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4665 TTTCAAAAAA
*
4675 AAAAAATGGTTTTTT
1 AAAAAATGGTTTTTC
4690 AAAAAATGG-TTTTC
1 AAAAAATGGTTTTTC
4704 AAAA
1 AAAA
4708 TTTGTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (15 bp):
AAAAAATGGTTTTTC
Found at i:6283 original size:36 final size:35
Alignment explanation
Indices: 6213--6683 Score: 362
Period size: 36 Copynumber: 13.3 Consensus size: 35
6203 ATTTCAGATG
* * * *
6213 CTTCAGTTTATTTCAATCGA-CACAGGGCGGTCTTT
1 CTTCAATTTATTTCAGTTGATC-CAGGGCGATCTTT
* *
6248 CTTCAATTCATTTCAGTTTGATCCAGGGTGATCTTTT
1 CTTCAATTTATTTCAG-TTGATCCAGGGCGATC-TTT
* **
6285 CTTCATTTTACCTCAGTTGATCCAGGGCGATCCTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGAT-CTTT
* * *
6321 CTTCAGTTTATTTTAGTTGATCCAGGGCGATCCGTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGAT-CTTT
* * * *
6357 CTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTT
1 CTTCAATTTATTTC-AGTTGATCCAGGGCGATC-TTT
* * * *
6394 CATTCAGTTTATGTCAGTTGATCCAGGGTGATCTCT
1 C-TTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
* *
6430 CCTCAATTTA-CTCTAGTTGATCCAGGGCGATCTTTT
1 CTTCAATTTATTTC-AGTTGATCCAGGGCGATC-TTT
* * *
6466 ATTCAATTTATTTCAGTCGATCCAGGGTGATCTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
* * * * * * * * *
6501 CCTTCAACTAATTTTAGCTAACCCAGAGCGGTCATT
1 -CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
* * *
6537 CTTCAAGTTATTTCAGTTGACCCAGGGCGGTCTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
* * * *
6572 CTTCAATTCATTTCAATTGAACCAGGGCGATCTTA
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
* * *
6607 CTTCAAGTTATTTTAGTTGATCCAGGGCTATCTTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATC-TTT
*
6643 CTTCAGTTTA---C--TTGATCCAGGGCGATCTTTT
1 CTTCAATTTATTTCAGTTGATCCAGGGCGATC-TTT
*
6674 CTTCAGTTTA
1 CTTCAATTTA
6684 CTTGACCGAG
Statistics
Matches: 353, Mismatches: 71, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
31 29 0.08
34 2 0.01
35 123 0.35
36 135 0.38
37 52 0.15
38 12 0.03
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (35 bp):
CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT
Found at i:6440 original size:145 final size:142
Alignment explanation
Indices: 6213--6652 Score: 442
Period size: 145 Copynumber: 3.1 Consensus size: 142
6203 ATTTCAGATG
* * * *
6213 CTTCAGTTTATTTCAA-TCGACACAGGGCGGTCTTTCTTCAATTCATTTCAGTTTGATCCAGGGT
1 CTTCAGTTTATTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG-TTGATCCAGGGT
*
6277 GATCTTTTCTTCATTTTACCTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGAT
65 GATC-TTTCTTCAATTTA-CTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGAT
*
6342 CCAGGGCGATCCGTT
128 CCAGGGCGATCCTTT
* *
6357 CTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTTCATTCAGTTTATGTCAGTTGATCCAGGG
1 CTTCAGTTTATTTCAAGTTGACCCAGGGCGGTC-TTTC-TTCAGTTTATTTCAGTTGATCCAGGG
* * * * * * *
6422 TGATCTCTCCTCAATTTACTCTAGTTGATCCAGGGCGATCTTTTATTCAATTTATTTCAGTCGAT
64 TGATCTTTCTTCAATTTACTC-AGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGAT
*
6487 CCAGGGTGAT-CTTT
128 CCAGGGCGATCCTTT
** * * * * * * *
6501 CCTTCAACTAATTT-TAGCTAACCCAGAGCGGTCATTCTTCAAG-TTATTTCAGTTGACCCAGGG
1 -CTTCAGTTTATTTCAAGTTGACCCAGGGCGGTCTTTCTTC-AGTTTATTTCAGTTGATCCAGGG
* * * * * * *
6564 CGGTCTTTCTTCAATTCATTTCAATTGAACCAGGGCGAT-CTTACTTCAAG-TTATTTTAGTTGA
64 TGATCTTTCTTCAATTTA-CTCAGTTGATCCAGGGCGATCCTTTCTTC-AGTTTATTTTAGTTGA
* *
6627 TCCAGGGCTATCTTTT
127 TCCAGGGCGATCCTTT
6643 CTTCAGTTTA
1 CTTCAGTTTA
6653 CTTGATCCAG
Statistics
Matches: 240, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
141 32 0.13
142 53 0.22
143 7 0.03
144 36 0.15
145 80 0.33
146 20 0.08
147 12 0.05
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (142 bp):
CTTCAGTTTATTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
ATCTTTCTTCAATTTACTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGATCCA
GGGCGATCCTTT
Found at i:6447 original size:109 final size:108
Alignment explanation
Indices: 6246--6506 Score: 326
Period size: 109 Copynumber: 2.4 Consensus size: 108
6236 AGGGCGGTCT
* *
6246 TTCTTCAATTCATTTCAGTTTGATCCAGGGTGATCTTTTCTTCATTTTACCTCAGTTGATCCAGG
1 TTCTTCAATTTATTTCAG-TTGATCCAGGGTGATCTTTTCTTCAGTTTACCTCAGTTGATCCAGG
* * * * *
6311 GCGATCCTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCCG
65 GCGATCCTCTCCTCAATTTACTCTAGTTGATCCAGGGCGATCCG
* * * **
6355 TTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTTCATTCAGTTTATGTCAGTTGATCCAG
1 TTCTTCAATTTATTTC-AGTTGATCCAGGGTGATCTTTTC-TTCAGTTTACCTCAGTTGATCCAG
* **
6420 GGTGAT-CTCTCCTCAATTTACTCTAGTTGATCCAGGGCGATCTT
64 GGCGATCCTCTCCTCAATTTACTCTAGTTGATCCAGGGCGATCCG
* * *
6464 TTATTCAATTTATTTCAGTCGATCCAGGGTGATCTTTCCTTCA
1 TTCTTCAATTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCA
6507 ACTAATTTTA
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
107 4 0.03
108 19 0.15
109 78 0.60
110 28 0.22
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (108 bp):
TTCTTCAATTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTACCTCAGTTGATCCAGGG
CGATCCTCTCCTCAATTTACTCTAGTTGATCCAGGGCGATCCG
Found at i:6661 original size:31 final size:31
Alignment explanation
Indices: 6618--6688 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
6608 TTCAAGTTAT
* *
6618 TTTAGTTGATCCAGGGCTATCTTTTCTTCAG
1 TTTACTTGATCCAGGGCGATCTTTTCTTCAG
6649 TTTACTTGATCCAGGGCGATCTTTTCTTCAG
1 TTTACTTGATCCAGGGCGATCTTTTCTTCAG
6680 TTTACTTGA
1 TTTACTTGA
6689 CCGAGGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTACTTGATCCAGGGCGATCTTTTCTTCAG
Found at i:6953 original size:30 final size:30
Alignment explanation
Indices: 6918--7114 Score: 254
Period size: 30 Copynumber: 6.6 Consensus size: 30
6908 AATATTCTAC
* * * *
6918 ATCATTGTTTTATTTTAATCCTGTTTGAGA
1 ATCATTGCTTCATTTTAATCCTGGTTGAGG
6948 ATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTCATTTTAATCCTGGTTGAGG
* *
6978 ATCATTGCTTCATTTTAATCCTAGTTAAGG
1 ATCATTGCTTCATTTTAATCCTGGTTGAGG
7008 ATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTCATTTTAATCCTGGTTGAGG
* *
7038 AT-ATTTGCTCCATTTTAATCCTGATTGAGG
1 ATCA-TTGCTTCATTTTAATCCTGGTTGAGG
*
7068 AT-ATTTGCTCCATTTTAATCCTGGTTGAGG
1 ATCA-TTGCTTCATTTTAATCCTGGTTGAGG
** *
7098 ATTGTTGCTTTATTTTA
1 ATCATTGCTTCATTTTA
7115 GGATTGTTGC
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
29 1 0.01
30 150 0.99
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.47
Consensus pattern (30 bp):
ATCATTGCTTCATTTTAATCCTGGTTGAGG
Found at i:6993 original size:60 final size:60
Alignment explanation
Indices: 6918--7401 Score: 503
Period size: 60 Copynumber: 8.2 Consensus size: 60
6908 AATATTCTAC
* *
6918 ATCATTGTTTTATTTTAATCCTGTTTGAGAATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
* *
6978 ATCATTGCTTCATTTTAATCCTAG-TTAAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
** * *
7038 AT-ATTTGCTCCATTTTAATCCTGATTGAGGAT-ATTTGCTCCATTTTAATCCTGGTTGAGG
1 ATCA-TTGCTTTATTTTAATCCTGTTTGAGGATCA-TTGCTTCATTTTAATCCTGGTTGAGG
** ** * *
7098 ---ATTG--TTGCTTT-A---T-TTT-AGGATTGTTGCTTTATTTTAATCCTGATTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
* * * *
7147 AT-ATTTGCTTTATTTTGATCCTGGTTGAGGATCATTGCATCATTTTAATCCTGATTGAGG
1 ATCA-TTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
* * * * *
7207 ATCATTGCTTTGTTTTAATTCTGTTTGAGGATCGTTGCTTTATATTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
* * * * **
7267 ATCATTGCTTTGTTTTAGTCCTGGTTGAGGATCTTTGCTTTGTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
* * * * * * *
7327 ATCATTGATTTGTTTTAATCCTGTTTGAGGATCGTTGTTTTATTCTAATCCTGATTGAGG
1 ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
7387 ATCATTGCTTTATTT
1 ATCATTGCTTTATTT
7402 CAGTTATTGC
Statistics
Matches: 359, Mismatches: 48, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
49 28 0.08
50 2 0.01
51 2 0.01
52 3 0.01
54 6 0.02
55 4 0.01
57 3 0.01
58 2 0.01
59 5 0.01
60 302 0.84
61 2 0.01
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (60 bp):
ATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGG
Found at i:7076 original size:90 final size:89
Alignment explanation
Indices: 6918--7401 Score: 451
Period size: 90 Copynumber: 5.5 Consensus size: 89
6908 AATATTCTAC
* * * * * *
6918 ATCATTGTTTTATTTTAATCCTGTTTGAGAATCA-TTGCTTCATTTTAATCCTGGTTGAGGATCA
1 ATCATTGCTTCATTTTAATCCTGATTGAGGAT-ATTTGCTTTATTTTAATCCTGATTGAGGAT-A
* * *
6982 TTGCTTCATTTTAATCCTAGTTAAGG
64 TTGCTTTATTTTAATCCTGGTTGAGG
* **
7008 ATCATTGCTTCATTTTAATCCTGGTTGAGGATATTTGCTCCATTTTAATCCTGATTGAGGATATT
1 ATCATTGCTTCATTTTAATCCTGATTGAGGATATTTGCTTTATTTTAATCCTGATTGAGGATA-T
**
7073 TGCTCCATTTTAATCCTGGTTGAGG
65 TGCTTTATTTTAATCCTGGTTGAGG
7098 ---ATTG-TTGC--TTT-AT--T--TT-AGGAT-TGTTGCTTTATTTTAATCCTGATTGAGGATA
1 ATCATTGCTT-CATTTTAATCCTGATTGAGGATAT-TTGCTTTATTTTAATCCTGATTGAGGATA
*
7150 TTTGCTTTATTTTGATCCTGGTTGAGG
64 -TTGCTTTATTTTAATCCTGGTTGAGG
* * * * *
7177 ATCATTGCATCATTTTAATCCTGATTGAGGATCA-TTGCTTTGTTTTAATTCTGTTTGAGGATCG
1 ATCATTGCTTCATTTTAATCCTGATTGAGGAT-ATTTGCTTTATTTTAATCCTGATTGAGGAT-A
*
7241 TTGCTTTATATTAATCCTGGTTGAGG
64 TTGCTTTATTTTAATCCTGGTTGAGG
** * * * * *
7267 ATCATTGCTTTGTTTTAGTCCTGGTTGAGGATCTTTGCTTTGTTTTAATCCTGGTTGAGGATCAT
1 ATCATTGCTTCATTTTAATCCTGATTGAGGATATTTGCTTTATTTTAATCCTGATTGAGGAT-AT
* * *
7332 TGATTTGTTTTAATCCTGTTTGAGG
65 TGCTTTATTTTAATCCTGGTTGAGG
* * * *
7357 ATCGTTGTTTTATTCTAATCCTGATTGAGGATCA-TTGCTTTATTT
1 ATCATTGCTTCATTTTAATCCTGATTGAGGAT-ATTTGCTTTATTT
7402 CAGTTATTGC
Statistics
Matches: 331, Mismatches: 42, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.00
79 56 0.17
80 2 0.01
82 6 0.02
83 1 0.00
84 5 0.02
85 5 0.02
86 2 0.01
87 6 0.02
89 4 0.01
90 243 0.73
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (89 bp):
ATCATTGCTTCATTTTAATCCTGATTGAGGATATTTGCTTTATTTTAATCCTGATTGAGGATATT
GCTTTATTTTAATCCTGGTTGAGG
Found at i:7143 original size:23 final size:19
Alignment explanation
Indices: 7095--7133 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7085 ATCCTGGTTG
7095 AGGATTGTTGCTTTATTTT
1 AGGATTGTTGCTTTATTTT
7114 AGGATTGTTGCTTTATTTT
1 AGGATTGTTGCTTTATTTT
7133 A
1 A
7134 ATCCTGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (19 bp):
AGGATTGTTGCTTTATTTT
Found at i:7148 original size:30 final size:30
Alignment explanation
Indices: 7121--7401 Score: 357
Period size: 30 Copynumber: 9.4 Consensus size: 30
7111 TTTAGGATTG
*
7121 TTGCTTTATTTTAATCCTGATTGAGGAT-A
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
7150 TTTGCTTTATTTTGATCCTGGTTGAGGATCA
1 -TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * *
7181 TTGCATCATTTTAATCCTGATTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * * *
7211 TTGCTTTGTTTTAATTCTGTTTGAGGATCG
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
7241 TTGCTTTATATTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * *
7271 TTGCTTTGTTTTAGTCCTGGTTGAGGATCT
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
7301 TTGCTTTGTTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * * *
7331 TTGATTTGTTTTAATCCTGTTTGAGGATCG
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * *
7361 TTGTTTTATTCTAATCCTGATTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
7391 TTGCTTTATTT
1 TTGCTTTATTT
7402 CAGTTATTGC
Statistics
Matches: 217, Mismatches: 33, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 216 1.00
31 1 0.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (30 bp):
TTGCTTTATTTTAATCCTGGTTGAGGATCA
Found at i:7956 original size:28 final size:27
Alignment explanation
Indices: 7897--7972 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
7887 AGGGTCATTT
** *
7897 AGGGGCATTTTGGGTCATTTGCATGTTC
1 AGGGGCATTTT-GGTCATTTGCACATCC
*
7925 AGGGGCATTTTAGTCATTTGCACATCC
1 AGGGGCATTTTGGTCATTTGCACATCC
7952 AAGGGGGCATTTTGGTCATTT
1 -A-GGGGCATTTTGGTCATTT
7973 TTAAGTTCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.29
28 12 0.29
29 17 0.41
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATCC
Found at i:9452 original size:15 final size:15
Alignment explanation
Indices: 9432--9483 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
9422 TCTCGGATGA
9432 TCTCTCACCTCACTC
1 TCTCTCACCTCACTC
*
9447 TCTCTCACC-AACCTCCC
1 TCTCTCACCTCA-CT--C
*
9464 TCTCTCACCTCACCC
1 TCTCTCACCTCACTC
9479 TCTCT
1 TCTCT
9484 GACCAACTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 1 0.03
15 17 0.57
17 11 0.37
18 1 0.03
ACGTcount: A:0.13, C:0.56, G:0.00, T:0.31
Consensus pattern (15 bp):
TCTCTCACCTCACTC
Done.