Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013884.1 Corchorus olitorius cultivar O-4 contig13917, 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: 26452
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2065 original size:2 final size:2
Alignment explanation
Indices: 2058--2128 Score: 54
Period size: 2 Copynumber: 40.5 Consensus size: 2
2048 ATTTAATAAT
*
2058 TA TA TA TA T- TA T- TA TA TA TA TA -A T- TA TA TA TA TC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2095 TA T- TA T- TA TA TA TA -A TA TA TT TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2129 TAATAAACGG
Statistics
Matches: 55, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
1 10 0.18
2 45 0.82
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2073 original size:12 final size:12
Alignment explanation
Indices: 2056--2130 Score: 75
Period size: 12 Copynumber: 6.1 Consensus size: 12
2046 CCATTTAATA
2056 ATTATATATATT
1 ATTATATATATT
*
2068 ATTATATATATA
1 ATTATATATATT
2080 ATTATATATATCT
1 ATTATATATAT-T
2093 A--ATAT-TATT
1 ATTATATATATT
2102 ATATATAATATATTT
1 AT-TAT-ATATA-TT
2117 AATTATATATATT
1 -ATTATATATATT
2130 A
1 A
2131 ATAAACGGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
9 2 0.04
10 3 0.06
11 4 0.08
12 25 0.47
13 5 0.09
14 7 0.13
15 5 0.09
16 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATATATATT
Found at i:2102 original size:19 final size:18
Alignment explanation
Indices: 2050--2133 Score: 73
Period size: 19 Copynumber: 4.3 Consensus size: 18
2040 TTTAAACCAT
2050 TTAATAATTA-TATATATTA
1 TTAAT-ATTATTATATA-TA
2069 TTATATATATAATTATATATA
1 TTA-ATAT-T-ATTATATATA
2090 TCTAATATTATTATATATA
1 T-TAATATTATTATATATA
*
2109 AT-ATATTTAATTATATATA
1 TTAATA-TT-ATTATATATA
2128 TTAATA
1 TTAATA
2134 AACGGTCGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.05
18 3 0.05
19 26 0.47
20 7 0.13
21 8 0.15
22 8 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAATATTATTATATATA
Found at i:2121 original size:38 final size:39
Alignment explanation
Indices: 2050--2133 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 39
2040 TTTAAACCAT
*
2050 TTAATAATTATATATATTATTATATATATAATTATATATA
1 TTAAT-ATTATATATATTATAATATATATAATTATATATA
*
2090 TCTAATATTAT-TATA-TATAATATATTTAATTATATATA
1 T-TAATATTATATATATTATAATATATATAATTATATATA
2128 TTAATA
1 TTAATA
2134 AACGGTCGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
37 5 0.12
38 22 0.54
39 4 0.10
40 6 0.15
41 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
TTAATATTATATATATTATAATATATATAATTATATATA
Found at i:6823 original size:21 final size:21
Alignment explanation
Indices: 6797--6861 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
6787 TTGGTTTCAC
6797 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
6818 TTGTTTGATGAAATTGTGTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
6844 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
6862 TATCATCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:9970 original size:22 final size:22
Alignment explanation
Indices: 9945--9986 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9935 TTGTAAAAAT
9945 AATAT-TATCATTGAATTATTAC
1 AATATATATC-TTGAATTATTAC
*
9967 AATATATATCTTGATTTATT
1 AATATATATCTTGAATTATT
9987 CTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AATATATATCTTGAATTATTAC
Found at i:20586 original size:15 final size:15
Alignment explanation
Indices: 20566--20614 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
20556 GGCACCATCA
20566 TGCCGCTGATGGCGT
1 TGCCGCTGATGGCGT
20581 TGCCGCTGATGGCGT
1 TGCCGCTGATGGCGT
20596 TGCCGCTGATGGCGT
1 TGCCGCTGATGGCGT
20611 TGCC
1 TGCC
20615 ATGTGGCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.06, C:0.29, G:0.39, T:0.27
Consensus pattern (15 bp):
TGCCGCTGATGGCGT
Found at i:22396 original size:22 final size:22
Alignment explanation
Indices: 22371--22515 Score: 102
Period size: 22 Copynumber: 6.6 Consensus size: 22
22361 CTCCAATGTA
*
22371 GAAATATTGATAACCACATTTT
1 GAAATATTGATAACCACATTAT
*
22393 GAAA-ATTTGATAACCTCATTAT
1 GAAATA-TTGATAACCACATTAT
*
22415 GAAAT-TTCGATAA-CATCCTTAT
1 GAAATATT-GATAACCA-CATTAT
* * *
22437 GAAA-ATTTGATAACAACACTGT
1 GAAATA-TTGATAACCACATTAT
* *
22459 GAAATATTGGTAACCACACTAT
1 GAAATATTGATAACCACATTAT
* * *
22481 GAAAT-TTCGATAACCTCAGTGT
1 GAAATATT-GATAACCACATTAT
*
22503 GAAATTTTGATAA
1 GAAATATTGATAA
22516 TCTACCTATA
Statistics
Matches: 98, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
21 6 0.06
22 86 0.88
23 6 0.06
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
GAAATATTGATAACCACATTAT
Found at i:22427 original size:44 final size:44
Alignment explanation
Indices: 22371--22515 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
22361 CTCCAATGTA
* * *
22371 GAAATATTGATAACCACATTTTGAAAATTTGATAACCTCATTAT
1 GAAATATTGATAACCACATTATGAAAATTTGATAACCTCACTGT
* **
22415 GAAAT-TTCGATAA-CATCCTTATGAAAATTTGATAACAACACTGT
1 GAAATATT-GATAACCA-CATTATGAAAATTTGATAACCTCACTGT
* * *
22459 GAAATATTGGTAACCACACTATG-AAATTTCGATAACCTCAGTGT
1 GAAATATTGATAACCACATTATGAAAATTT-GATAACCTCACTGT
*
22503 GAAATTTTGATAA
1 GAAATATTGATAA
22516 TCTACCTATA
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
43 10 0.12
44 68 0.83
45 4 0.05
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (44 bp):
GAAATATTGATAACCACATTATGAAAATTTGATAACCTCACTGT
Found at i:22506 original size:66 final size:66
Alignment explanation
Indices: 22372--22515 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
22362 TCCAATGTAG
* * * * * **
22372 AAATATTGATAACCACATTTTGAAAATTTGATAACCTCATTATGAAATTTCGATAACATCCTTAT
1 AAAT-TTGATAACAACACTGTGAAAATTTGATAACCACACTATGAAATTTCGATAACATCAGTAT
22437 GA
65 GA
* * *
22439 AAATTTGATAACAACACTGTG-AAATATTGGTAACCACACTATGAAATTTCGATAACCTCAGTGT
1 AAATTTGATAACAACACTGTGAAAAT-TTGATAACCACACTATGAAATTTCGATAACATCAGTAT
22503 GA
65 GA
*
22505 AATTTTGATAA
1 AAATTTGATAA
22516 TCTACCTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 4 0.06
66 57 0.88
67 4 0.06
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (66 bp):
AAATTTGATAACAACACTGTGAAAATTTGATAACCACACTATGAAATTTCGATAACATCAGTATG
A
Found at i:22530 original size:44 final size:41
Alignment explanation
Indices: 22394--22531 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 41
22384 CCACATTTTG
* * *
22394 AAAATTTGATAACCTCATTATGAAATTTCGATAACATCCTTAT
1 AAAATTTGATAACCTCACTGTGAAATTTTGATAACA-CC-TAT
** * *
22437 GAAAATTTGATAACAACACTGTGAAATATTGGTAACCACACTAT
1 -AAAATTTGATAACCTCACTGTGAAATTTTGATAA-CAC-CTAT
* *
22481 GAAATTTCGATAACCTCAGTGTGAAATTTTGATAATCTACCTAT
1 AAAATTT-GATAACCTCACTGTGAAATTTTGATAA-C-ACCTAT
22525 AAAATTT
1 AAAATTT
22532 TAATAATCAC
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
43 6 0.08
44 64 0.85
45 5 0.07
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (41 bp):
AAAATTTGATAACCTCACTGTGAAATTTTGATAACACCTAT
Found at i:22594 original size:19 final size:21
Alignment explanation
Indices: 22570--22627 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 21
22560 TCGCATTATG
22570 AAAATTTCGATAACCTCA-C-
1 AAAATTTCGATAACCTCACCA
* *
22589 AAAATTTTGATAACCACACCA
1 AAAATTTCGATAACCTCACCA
22610 AGAAATTTCGATAACCTC
1 A-AAATTTCGATAACCTC
22628 CCTAGAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.50
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAATTTCGATAACCTCACCA
Found at i:22813 original size:22 final size:22
Alignment explanation
Indices: 22788--22930 Score: 128
Period size: 22 Copynumber: 6.5 Consensus size: 22
22778 ACATCCCTAA
* *
22788 GAAATTTTGGTAACCTTTTTAT
1 GAAATTTTGGTAACCTCTATAT
22810 GAAATTTTGGTAACCTCTATAT
1 GAAATTTTGGTAACCTCTATAT
* *
22832 GAAATTTTGATAA-CTACAATAT
1 GAAATTTTGGTAACCT-CTATAT
* *
22854 GAAGTTTTGATAACCTCTATAT
1 GAAATTTTGGTAACCTCTATAT
* * *
22876 GGAATTTTGGTAATCAC-ACTAT
1 GAAATTTTGGTAACCTCTA-TAT
* * * *
22898 GAAATTTTGATAATCTTTCTAT
1 GAAATTTTGGTAACCTCTATAT
*
22920 GTAATTTTGGT
1 GAAATTTTGGT
22931 TTGATTGTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
21 3 0.03
22 94 0.95
23 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
GAAATTTTGGTAACCTCTATAT
Found at i:22836 original size:44 final size:44
Alignment explanation
Indices: 22807--22930 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
22797 GTAACCTTTT
* *
22807 TATGAAATTTTGGTAACCTCTATATGAAATTTTGATAACTACAA
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACTACAA
* * *
22851 TATGAAGTTTTGATAACCTCTATATGGAATTTTGGTAA-TCACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACT-ACAA
* * * *
22895 TATGAAATTTTGATAATCTTTCTATGTAATTTTGGT
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGT
22931 TTGATTGTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 1 0.01
44 68 0.99
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACTACAA
Found at i:24923 original size:5 final size:5
Alignment explanation
Indices: 24905--24947 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
24895 AATATAGTAG
24905 TAAGA T-AG- TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
24948 TATAAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 8 0.24
5 24 0.71
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:24923 original size:13 final size:13
Alignment explanation
Indices: 24893--24947 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
24883 AATAGTAATA
*
24893 ATAATATAGT-AG
1 ATAAGATAGTAAG
24905 -TAAGATAGTAAG
1 ATAAGATAGTAAG
24917 ATAAGATAGTAAG
1 ATAAGATAGTAAG
24930 ATAAGATAAGATAAG
1 ATAAGAT-AG-TAAG
24945 ATA
1 ATA
24948 TATAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
11 8 0.21
12 2 0.05
13 19 0.50
14 2 0.05
15 7 0.18
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (13 bp):
ATAAGATAGTAAG
Found at i:24956 original size:18 final size:19
Alignment explanation
Indices: 24913--24969 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
24903 AGTAAGATAG
*
24913 TAAGATAAGAT-AG-TAAGA
1 TAAGATAAGATAAGAT-ATA
24931 TAAGATAAGATAAGATATA
1 TAAGATAAGATAAGATATA
* *
24950 TAA-ATAATATAATATATA
1 TAAGATAAGATAAGATATA
24968 TA
1 TA
24970 TATATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 26 0.76
19 7 0.21
20 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (19 bp):
TAAGATAAGATAAGATATA
Found at i:24956 original size:23 final size:23
Alignment explanation
Indices: 24913--24975 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
24903 AGTAAGATAG
*
24913 TAAGATAAGATAGTA-AGATAAGA
1 TAAGATAAGATA-TATAAATAAGA
*
24936 TAAGATAAGATATATAAATAATA
1 TAAGATAAGATATATAAATAAGA
* *
24959 TAATATATATATATATA
1 TAAGATA-AGATATATA
24976 TATATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.06
23 24 0.71
24 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (23 bp):
TAAGATAAGATATATAAATAAGA
Found at i:24966 original size:2 final size:2
Alignment explanation
Indices: 24945--24986 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
24935 ATAAGATAAG
*
24945 AT AT AT AA AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24984 AT A
1 AT A
24987 CCTACTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:25239 original size:53 final size:53
Alignment explanation
Indices: 25176--25338 Score: 317
Period size: 53 Copynumber: 3.1 Consensus size: 53
25166 TGTTTATTCA
*
25176 ATTGAACCTATTAAATAAGCACACATACCAAATACTACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
25229 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
25282 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
25335 ATTG
1 ATTG
25339 GATTTAAAGA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 109 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Done.