Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009575.1 Corchorus olitorius cultivar O-4 contig09607, 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: 7927
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--45 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 T
2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44 TA
1 TA
46 CGCCCAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:133 original size:22 final size:21
Alignment explanation
Indices: 108--206 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 21
98 TATTTTTATG
*
108 AAATTTTGATAATCACCCTATT
1 AAATTTTGATAATCA-CCTATA
* * *
130 AAATTTT-AGTAACCATCATATG
1 AAATTTTGA-TAATCA-CCTATA
*
152 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATCACCTATA
* * *
173 AAATTATGATAAACTCCATAATA
1 AAATTTTGATAATCACC-T-ATA
196 AAA-TTTGATAA
1 AAATTTTGATAA
207 CCTAACTATG
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 18 0.30
22 35 0.58
23 7 0.12
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAATCACCTATA
Found at i:3025 original size:22 final size:21
Alignment explanation
Indices: 2970--3095 Score: 90
Period size: 22 Copynumber: 5.8 Consensus size: 21
2960 TGAATATTTT
* *
2970 TATGAAATTTTGATGACTATCC
1 TATGAAATTTTGATAACCA-CC
* * *
2992 AATTAAAATTTGATAACCACGC
1 TATGAAATTTTGATAACCAC-C
**
3014 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-CCACC
* * *
3036 TATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATAACCACC
* *
3057 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACC-ACC
*
3080 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
3096 ACCTTCTATG
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
21 3 0.04
22 73 0.92
23 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:3050 original size:44 final size:43
Alignment explanation
Indices: 2997--3089 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
2987 TATCCAATTA
* * ** *
2997 AAATTTGATAACCACGC-TATGAAATTTTGATAATTTACCTATG
1 AAATTTGATAAACAC-CATATGAAACTTTGATAACCTAACTATG
*
3040 AAATTGTGATAAACTCCATATGAAACTTTGATAACCTAACTATG
1 AAATT-TGATAAACACCATATGAAACTTTGATAACCTAACTATG
3084 AAATTT
1 AAATTT
3090 TAATAAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
43 7 0.17
44 35 0.83
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (43 bp):
AAATTTGATAAACACCATATGAAACTTTGATAACCTAACTATG
Found at i:3096 original size:44 final size:44
Alignment explanation
Indices: 3014--3097 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
3004 ATAACCACGC
* ** * *
3014 TATGAAATTTTGATAATTTACCTATGAAATTGTGATAAACTCCA
1 TATGAAACTTTGATAACCTAACTATGAAATTGTAATAAACTCCA
*
3058 TATGAAACTTTGATAACCTAACTATGAAATTTTAATAAAC
1 TATGAAACTTTGATAACCTAACTATGAAATTGTAATAAAC
3098 CTTCTATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAACTTTGATAACCTAACTATGAAATTGTAATAAACTCCA
Found at i:3104 original size:22 final size:22
Alignment explanation
Indices: 3013--3106 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
3003 GATAACCACG
**
3013 CTATGAAATTTTGAT-AATTTA
1 CTATGAAATTTTGATAAACCTA
* *
3034 CCTATGAAATTGTGATAAA-CTC
1 -CTATGAAATTTTGATAAACCTA
*
3056 CATATGAAACTTTGAT-AACCTAA
1 C-TATGAAATTTTGATAAACCT-A
* *
3079 CTATGAAATTTTAATAAACCTT
1 CTATGAAATTTTGATAAACCTA
3101 CTATGA
1 CTATGA
3107 TTGTAAACTT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
21 3 0.05
22 47 0.81
23 8 0.14
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAAACCTA
Found at i:3106 original size:44 final size:43
Alignment explanation
Indices: 3013--3106 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
3003 GATAACCACG
* ** * *
3013 CTATGAAATTTTGATAATTTACCTATGAAATTGTGATAAACTC
1 CTATGAAACTTTGATAACCTAACTATGAAATTGTAATAAACTC
* *
3056 CATATGAAACTTTGATAACCTAACTATGAAATTTTAATAAACCTT
1 C-TATGAAACTTTGATAACCTAACTATGAAATTGTAATAAA-CTC
3101 CTATGA
1 CTATGA
3107 TTGTAAACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.02
44 38 0.90
45 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (43 bp):
CTATGAAACTTTGATAACCTAACTATGAAATTGTAATAAACTC
Found at i:3119 original size:17 final size:17
Alignment explanation
Indices: 3093--3125 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3083 GAAATTTTAA
3093 TAAACCTTCTATGATTG
1 TAAACCTTCTATGATTG
*
3110 TAAACTTTCTATGATT
1 TAAACCTTCTATGATT
3126 TTTTATAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (17 bp):
TAAACCTTCTATGATTG
Found at i:3637 original size:27 final size:27
Alignment explanation
Indices: 3576--3629 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3566 AAAAATATAC
* *
3576 AAAATTATATTTTAATAGTGGCATAATT
1 AAAA-TATTTTTTAATAATGGCATAATT
3604 AAAATATTTTTTAATAATGGCA-AATT
1 AAAATATTTTTTAATAATGGCATAATT
3630 TGAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (27 bp):
AAAATATTTTTTAATAATGGCATAATT
Found at i:3642 original size:26 final size:26
Alignment explanation
Indices: 3576--3643 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
3566 AAAAATATAC
*
3576 AAAATTATATTTTAATAGTGGCATAATT
1 AAAA-TATA-TTTAATAATGGCATAATT
*
3604 AAAATATTTTTTAATAATGGCA-AATTT
1 AAAATA-TATTTAATAATGGCATAA-TT
*
3631 GAAATATATTTAA
1 AAAATATATTTAA
3644 AAAAAGGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.24
27 21 0.62
28 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (26 bp):
AAAATATATTTAATAATGGCATAATT
Found at i:6829 original size:22 final size:22
Alignment explanation
Indices: 6781--6836 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
6771 TATTTTTATT
*
6781 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* ** *
6803 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAACCACACTATA
*
6825 AAATTCTGATAA
1 AAATTTTGATAA
6837 ACTCCGAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:7145 original size:22 final size:22
Alignment explanation
Indices: 7120--7226 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
7110 TGGAACTTTA
* *
7120 ATAACTACACTATGAAATTCTG
1 ATAACCACACTATGAAATTTTG
*
7142 ATAACCATC-CTATGAAGTTTTG
1 ATAACCA-CACTATGAAATTTTG
* * *
7164 GTCACCACACTCTGAAATTTTG
1 ATAACCACACTATGAAATTTTG
*
7186 ATAACCACAGTAT-AAATTTATG
1 ATAACCACACTATGAAATTT-TG
*
7208 ATAACCTCTA-TATGAAATT
1 ATAACCAC-ACTATGAAATT
7227 AATTTTGATG
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
21 7 0.10
22 54 0.79
23 7 0.10
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:7246 original size:26 final size:27
Alignment explanation
Indices: 7200--7252 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
7190 CCACAGTATA
*
7200 AATTTATGATAACCTCTATATGAAATT
1 AATTTATGATAACCTCTATATAAAATT
*
7227 AATTT-TGATGACCT-TAATATAAAATT
1 AATTTATGATAACCTCT-ATATAAAATT
7253 TTGAATACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.74
27 5 0.22
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (27 bp):
AATTTATGATAACCTCTATATAAAATT
Found at i:7343 original size:22 final size:22
Alignment explanation
Indices: 7295--7486 Score: 93
Period size: 22 Copynumber: 8.5 Consensus size: 22
7285 AATTTGGTAG
* * **
7295 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCTC
7317 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * * * *
7339 TCTATGGAATGTTAATAACTTC
1 ACTATGAAATTTTGATAACCTC
* * * *
7361 CCTATAGAATTTAGTACTGTTAATCTC
1 ACTAT-GAAATT--T--TGATAACCTC
* *
7388 ACTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCTC
* * * *
7410 AATTTGAAACTTTGATTACCT-
1 ACTATGAAATTTTGATAACCTC
*
7431 TCTATGAAATTTTTG-TAA-CTAC
1 ACTATGAAA-TTTTGATAACCT-C
* * *
7453 ATTATGAAATTTTGATAGCCAC
1 ACTATGAAATTTTGATAACCTC
7475 ACTATGAAATTT
1 ACTATGAAATTT
7487 CAATAATCTA
Statistics
Matches: 122, Mismatches: 38, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
20 2 0.02
21 13 0.11
22 86 0.70
23 4 0.03
24 1 0.01
25 1 0.01
26 5 0.04
27 10 0.08
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:7769 original size:12 final size:12
Alignment explanation
Indices: 7752--7778 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7742 GGCCAAGACT
7752 TTAAATTTATAA
1 TTAAATTTATAA
7764 TTAAATTTATAA
1 TTAAATTTATAA
7776 TTA
1 TTA
7779 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTATAA
Done.