Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014963.1 Corchorus olitorius cultivar O-4 contig14996, 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: 28543
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3881 original size:21 final size:21
Alignment explanation
Indices: 3848--3901 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3838 CTCCACCTAG
*
3848 GCACCCACATGG-TTGCCTTGA
1 GCACCCACGTGGTTTG-CTTGA
*
3869 GCACCCATGTGGTTTGCTTGA
1 GCACCCACGTGGTTTGCTTGA
* *
3890 GAACCCAGGTGG
1 GCACCCACGTGG
3902 GCAGTGTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.24
Consensus pattern (21 bp):
GCACCCACGTGGTTTGCTTGA
Found at i:5032 original size:3 final size:3
Alignment explanation
Indices: 5024--5072 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5014 GTTACTAACC
5024 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5072 T
1 T
5073 AATATATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9989 original size:21 final size:21
Alignment explanation
Indices: 9956--10004 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
9946 AAGAATTTTA
**
9956 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
9976 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
9997 GCATTCCT
1 GC-TTCCT
10005 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:13851 original size:27 final size:27
Alignment explanation
Indices: 13821--13873 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
13811 GTCTCTGTAC
13821 AACCACCGGT-AAGTTCATCTCAAGTTT
1 AACCACCGGTGAA-TTCATCTCAAGTTT
** *
13848 AACCTGCGGTGAATTCATCTCCAGTT
1 AACCACCGGTGAATTCATCTCAAGTT
13874 ATTTCCTGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (27 bp):
AACCACCGGTGAATTCATCTCAAGTTT
Found at i:16374 original size:2 final size:2
Alignment explanation
Indices: 16367--16408 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
16357 TAACATGAGA
16367 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16408 A
1 A
16409 ACACGAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20622 original size:32 final size:32
Alignment explanation
Indices: 20576--20637 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
20566 CTGGATAACT
20576 ATGGTGGGAATTGATGGTCT-AACGGAATGATA
1 ATGGTGGGAATTGATGGTCTGAA-GGAATGATA
* *
20608 ATGGTTGGAGTTGATGGTCTGAAGGAATGA
1 ATGGTGGGAATTGATGGTCTGAAGGAATGA
20638 AATTATACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (32 bp):
ATGGTGGGAATTGATGGTCTGAAGGAATGATA
Found at i:21836 original size:111 final size:111
Alignment explanation
Indices: 21612--21829 Score: 364
Period size: 111 Copynumber: 2.0 Consensus size: 111
21602 TTAGTCATTC
* *
21612 AACGAAGCAAATTTCTGGCCCTATTGAGAAGCTTATTTCAAGGTAACCAACCAGTTTAAATATCC
1 AACGAAGCAAATCTCTGGCCCTATTGAGAAGCTTATTTCAAGCTAACCAACCAGTTTAAATATCC
21677 ACCCCTCACCAGCCATGTCATCAGCATTGTTTCCTTCTCTTCAAAG
66 ACCCCTCACCAGCCATGTCATCAGCATTGTTTCCTTCTCTTCAAAG
* * *
21723 AACGAAGCGAATCTCTGGCCCTATTGAGAAGCTTATTTCAATCTAACCAAGCAGTTTAAATATCC
1 AACGAAGCAAATCTCTGGCCCTATTGAGAAGCTTATTTCAAGCTAACCAACCAGTTTAAATATCC
* * *
21788 ACTCTTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTTC
66 ACCCCTCACCAGCCATGTCATCAGCATTGTTTCCTTCTCTTC
21830 TTAGAACTTG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (111 bp):
AACGAAGCAAATCTCTGGCCCTATTGAGAAGCTTATTTCAAGCTAACCAACCAGTTTAAATATCC
ACCCCTCACCAGCCATGTCATCAGCATTGTTTCCTTCTCTTCAAAG
Found at i:23945 original size:22 final size:20
Alignment explanation
Indices: 23916--23996 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 20
23906 TGAATATTTT
23916 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAA-TA-CC
*
23938 TATTAAATTTTGATAATCACGC
1 TATGAAATTTTGATAAT-AC-C
*
23960 TATGAAATTCTGATAATTACC
1 TATGAAATTTTGATAA-TACC
*
23981 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
23997 ACTCCATGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 18 0.35
22 33 0.63
23 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (20 bp):
TATGAAATTTTGATAATACC
Found at i:23995 original size:43 final size:44
Alignment explanation
Indices: 23916--24033 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 44
23906 TGAATATTTT
* * * *
23916 TATGAAATTTTGATAACTATCCTATTAAATTTTGATAATCACGC-
1 TATGAAATTCTGATAACTATCCTATGAAATTGTGATAAACAC-CA
* *
23960 TATGAAATTCTGATAATTA-CCTATGAAATTGTGATAAACTCCA
1 TATGAAATTCTGATAACTATCCTATGAAATTGTGATAAACACCA
* * **
24003 TGTGAAATTCTGATAACCAAACTATGAAATT
1 TATGAAATTCTGATAACTATCCTATGAAATT
24034 TAAATAAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 34 0.55
44 27 0.44
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
TATGAAATTCTGATAACTATCCTATGAAATTGTGATAAACACCA
Found at i:24030 original size:22 final size:22
Alignment explanation
Indices: 23916--24033 Score: 62
Period size: 22 Copynumber: 5.4 Consensus size: 22
23906 TGAATATTTT
* * **
23916 TATGAAATTTTGATAACTATCC
1 TATGAAATTCTGATAACCAAAC
* * * **
23938 TATTAAATTTTGATAATCACGC
1 TATGAAATTCTGATAACCAAAC
** *
23960 TATGAAATTCTGATAA-TTACC
1 TATGAAATTCTGATAACCAAAC
* *
23981 TATGAAATTGTGATAAACTC-CA-
1 TATGAAATTCTGAT-AAC-CAAAC
*
24003 TGTGAAATTCTGATAACCAAAC
1 TATGAAATTCTGATAACCAAAC
24025 TATGAAATT
1 TATGAAATT
24034 TAAATAAACA
Statistics
Matches: 72, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 18 0.25
22 53 0.74
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTCTGATAACCAAAC
Found at i:26245 original size:15 final size:15
Alignment explanation
Indices: 26203--26246 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
26193 TCCCGATGGA
*
26203 AAGCGTCCTAATGAT
1 AAGCGTCCTGATGAT
26218 AAGTCGTCCTGATGAT
1 AAG-CGTCCTGATGAT
*
26234 AAGCGTCTTGATG
1 AAGCGTCCTGATG
26247 GTGAGTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (15 bp):
AAGCGTCCTGATGAT
Found at i:26257 original size:15 final size:15
Alignment explanation
Indices: 26239--26268 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26229 ATGATAAGCG
26239 TCTTGATGGTGAGTC
1 TCTTGATGGTGAGTC
26254 TCTTGATGGTGAGTC
1 TCTTGATGGTGAGTC
26269 GATTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (15 bp):
TCTTGATGGTGAGTC
Found at i:26465 original size:27 final size:27
Alignment explanation
Indices: 26435--26501 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
26425 ATCATCTCAT
26435 GACCATCGGGATCAACCTTGGCATCCC
1 GACCATCGGGATCAACCTTGGCATCCC
26462 GACCATCGGGATCAACCTTGGCATCCC
1 GACCATCGGGATCAACCTTGGCATCCC
*
26489 GACCATCAGGATC
1 GACCATCGGGATC
26502 CAATTTCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (27 bp):
GACCATCGGGATCAACCTTGGCATCCC
Found at i:27026 original size:23 final size:23
Alignment explanation
Indices: 27000--27118 Score: 79
Period size: 23 Copynumber: 5.2 Consensus size: 23
26990 GCTCTTTGTG
27000 ATTTTTCCATCCAGATGGTATAA
1 ATTTTTCCATCCAGATGGTATAA
* **
27023 ATTTCTTCACA-CCATCA-GG-ACCA
1 ATTT-TTC-CATCCA-GATGGTATAA
27046 ATTTTTCCATCCAGATGGTATAA
1 ATTTTTCCATCCAGATGGTATAA
* *
27069 ATTTCTTCACA-CCATCA-GG-ATCA
1 ATTT-TTC-CATCCA-GATGGTATAA
* *
27092 ATTTCTCCATCCTGATGGTATAA
1 ATTTTTCCATCCAGATGGTATAA
27115 ATTT
1 ATTT
27119 CCTCACACCA
Statistics
Matches: 72, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
21 6 0.08
22 14 0.19
23 30 0.42
24 16 0.22
25 6 0.08
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (23 bp):
ATTTTTCCATCCAGATGGTATAA
Found at i:27053 original size:46 final size:46
Alignment explanation
Indices: 27000--27222 Score: 374
Period size: 46 Copynumber: 4.8 Consensus size: 46
26990 GCTCTTTGTG
* *
27000 ATTTTTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGACCA
1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
*
27046 ATTTTTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
* * *
27092 ATTTCTCCATCCTGATGGTATAAATTTCCTCACACCATCAAGATCA
1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
*
27138 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA
1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
*
27184 ATTTCTCCATCCTGATGGTATAAATTTCTTCACACCATC
1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATC
27223 GAGACCAATT
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 169 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.34
Consensus pattern (46 bp):
ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGATCA
Found at i:27119 original size:23 final size:23
Alignment explanation
Indices: 27045--27212 Score: 93
Period size: 23 Copynumber: 7.3 Consensus size: 23
27035 CATCAGGACC
* *
27045 AATTTTTCCATCCAGATGGTATA
1 AATTTCTCCATCCTGATGGTATA
* *
27068 AATTTCTTCACA-CCATCA-GG-ATC
1 AATTTC-TC-CATCC-TGATGGTATA
27091 AATTTCTCCATCCTGATGGTATA
1 AATTTCTCCATCCTGATGGTATA
* * *
27114 AATTTCCTCACA-CCATCA-AG-ATC
1 AATTT-CTC-CATCC-TGATGGTATA
*
27137 AATTTCTCCATCCAGATGGTATA
1 AATTTCTCCATCCTGATGGTATA
* * *
27160 AATTTCTTCACA-CCATCA-AG-ATC
1 AATTTC-TC-CATCC-TGATGGTATA
27183 AATTTCTCCATCCTGATGGTATA
1 AATTTCTCCATCCTGATGGTATA
27206 AATTTCT
1 AATTTCT
27213 TCACACCATC
Statistics
Matches: 107, Mismatches: 20, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
21 11 0.10
22 17 0.16
23 52 0.49
24 17 0.16
25 10 0.09
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (23 bp):
AATTTCTCCATCCTGATGGTATA
Done.