Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007262.1 Corchorus capsularis cultivar CVL-1 contig07283, 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: 11922
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Found at i:5151 original size:11 final size:11
Alignment explanation
Indices: 5137--5174 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5127 ATTCATAACA
5137 AATTTATAATT
1 AATTTATAATT
5148 AATTTATAATT
1 AATTTATAATT
5159 -ATTTGATAATT
1 AATTT-ATAATT
*
5170 TATTT
1 AATTT
5175 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:5495 original size:2 final size:2
Alignment explanation
Indices: 5488--5519 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5478 GCCGCATTAG
5488 AT AT AT AT AT AT AT AT 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
5520 TTTGAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6904 original size:16 final size:15
Alignment explanation
Indices: 6876--6958 Score: 71
Period size: 16 Copynumber: 5.3 Consensus size: 15
6866 AAATAAATAA
*
6876 AAAAATCCGAACCCG
1 AAAAATCAGAACCCG
6891 AAAAAGTTCA-AACCCG
1 AAAAA--TCAGAACCCG
6907 AATAAATCAGAACCCG
1 AA-AAATCAGAACCCG
* *
6923 AAAAATCTAAAACCCC
1 AAAAATC-AGAACCCG
*
6939 ATAAAATCCGAACCC-
1 A-AAAATCAGAACCCG
6954 AAAAA
1 AAAAA
6959 AACCCTGAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.07
15 14 0.25
16 28 0.49
17 11 0.19
ACGTcount: A:0.53, C:0.28, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAATCAGAACCCG
Found at i:6936 original size:32 final size:32
Alignment explanation
Indices: 6877--6959 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
6867 AATAAATAAA
*
6877 AAAATCCGAACCCGAAAAAGTTCAAACCCGAAT
1 AAAATCCGAACCCGAAAAAGTTAAAACCC-AAT
* *
6910 -AAATCAGAACCCGAAAAA-TCTAAAACCCCAT
1 AAAATCCGAACCCGAAAAAGT-TAAAACCCAAT
*
6941 AAAATCCGAACCCAAAAAA
1 AAAATCCGAACCCGAAAAA
6960 ACCCTGAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
31 3 0.07
32 40 0.93
ACGTcount: A:0.53, C:0.28, G:0.08, T:0.11
Consensus pattern (32 bp):
AAAATCCGAACCCGAAAAAGTTAAAACCCAAT
Found at i:6960 original size:16 final size:16
Alignment explanation
Indices: 6874--6970 Score: 52
Period size: 16 Copynumber: 6.0 Consensus size: 16
6864 AAAAATAAAT
6874 AAAAAAATCCGAACCC
1 AAAAAAATCCGAACCC
* * * *
6890 GAAAAAGTTCAAACCC
1 AAAAAAATCCGAACCC
* * *
6906 GAATAAATCAGAACCC
1 AAAAAAATCCGAACCC
* **
6922 -GAAAAATCTAAAACCC
1 AAAAAAATC-CGAACCC
* *
6938 CATAAAATCCGAACCC
1 AAAAAAATCCGAACCC
*
6954 AAAAAAACCCTGAACCC
1 AAAAAAATCC-GAACCC
6971 GAACCTGAAA
Statistics
Matches: 59, Mismatches: 19, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
15 6 0.10
16 41 0.69
17 12 0.20
ACGTcount: A:0.52, C:0.30, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAAAAATCCGAACCC
Found at i:7194 original size:32 final size:32
Alignment explanation
Indices: 7153--7224 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
7143 CCCAAAATTG
*
7153 ACCCAAACCCGAATAAACCTGATCAAATTTTA
1 ACCCGAACCCGAATAAACCTGATCAAATTTTA
* *
7185 ACCCGAACCCGAATCAATCTGATCAAATTTTA
1 ACCCGAACCCGAATAAACCTGATCAAATTTTA
7217 ACCCGAAC
1 ACCCGAAC
7225 TGATTCAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.31, G:0.08, T:0.21
Consensus pattern (32 bp):
ACCCGAACCCGAATAAACCTGATCAAATTTTA
Found at i:7704 original size:2 final size:2
Alignment explanation
Indices: 7697--7729 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7687 TCACGGTCTC
7697 AT AT AT AT A- AT AT AT AT 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
7730 TATCTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7944 original size:16 final size:16
Alignment explanation
Indices: 7923--7967 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
7913 AACGTCCCGA
*
7923 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
7939 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
7955 ACCCGAACCCGAA
1 ACCCGAACCCGAA
7968 CCCGACCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.40, C:0.40, G:0.13, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:8691 original size:17 final size:18
Alignment explanation
Indices: 8669--8711 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
8659 TATCGAAAGT
*
8669 GAACCCGAACCCGA-CCC
1 GAACCCGAACCCGAGCCA
*
8686 GAACCCG-ATCCGAGCCA
1 GAACCCGAACCCGAGCCA
8703 GAACCCGAA
1 GAACCCGAA
8712 ATACCCGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 16 0.73
18 1 0.05
ACGTcount: A:0.33, C:0.44, G:0.21, T:0.02
Consensus pattern (18 bp):
GAACCCGAACCCGAGCCA
Found at i:8723 original size:15 final size:16
Alignment explanation
Indices: 8703--8771 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
8693 ATCCGAGCCA
8703 GAACCCG-AAATACCC
1 GAACCCGAAAATACCC
*
8718 GAACCCGAAAAAACCC
1 GAACCCGAAAATACCC
8734 GAACCCGAAAATACCC
1 GAACCCGAAAATACCC
*
8750 GAACCCG-AAGTACCC
1 GAACCCGAAAATACCC
8765 GAACCCG
1 GAACCCG
8772 CCCAATTGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
15 21 0.42
16 29 0.58
ACGTcount: A:0.41, C:0.39, G:0.16, T:0.04
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:8741 original size:31 final size:31
Alignment explanation
Indices: 8703--8771 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
8693 ATCCGAGCCA
8703 GAACCCG-AAATACCCGAACCCGAAAAAACCC
1 GAACCCGAAAATACCCGAACCCG-AAAAACCC
**
8734 GAACCCGAAAATACCCGAACCCGAAGTACCC
1 GAACCCGAAAATACCCGAACCCGAAAAACCC
8765 GAACCCG
1 GAACCCG
8772 CCCAATTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 20 0.57
32 15 0.43
ACGTcount: A:0.41, C:0.39, G:0.16, T:0.04
Consensus pattern (31 bp):
GAACCCGAAAATACCCGAACCCGAAAAACCC
Found at i:8873 original size:2 final size:2
Alignment explanation
Indices: 8866--8900 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8856 CTCCTATTAT
*
8866 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8901 GTGGTGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:9401 original size:143 final size:143
Alignment explanation
Indices: 9163--9449 Score: 565
Period size: 143 Copynumber: 2.0 Consensus size: 143
9153 TTTATCCATA
9163 TATATAAGCTAGAAGAAGAGAGATTGCGAAACCAAACGAATTGTAGGGTTCGATGAGGATTTTGT
1 TATATAAGCTAGAAGAAGAGAGATTGCGAAACCAAACGAATTGTAGGGTTCGATGAGGATTTTGT
9228 TATATATAGTTTCTGTGTTTATGCAAGGACTTAAACAACTTTGACTTTAAACCCTATTATATTTC
66 TATATATAGTTTCTGTGTTTATGCAAGGACTTAAACAACTTTGACTTTAAACCCTATTATATTTC
9293 AACCGACCTTCTT
131 AACCGACCTTCTT
9306 TATATAAGCTAGAAGAAGAGAGATTGCGAAACCAAACGAATTGTAGGGTTCGATGAGGATTTTGT
1 TATATAAGCTAGAAGAAGAGAGATTGCGAAACCAAACGAATTGTAGGGTTCGATGAGGATTTTGT
*
9371 TATATATAGTTTCTGTGTTTATGTAAGGACTTAAACAACTTTGACTTTAAACCCTATTATATTTC
66 TATATATAGTTTCTGTGTTTATGCAAGGACTTAAACAACTTTGACTTTAAACCCTATTATATTTC
9436 AACCGACCTTCTT
131 AACCGACCTTCTT
9449 T
1 T
9450 TTTGCTCTTT
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (143 bp):
TATATAAGCTAGAAGAAGAGAGATTGCGAAACCAAACGAATTGTAGGGTTCGATGAGGATTTTGT
TATATATAGTTTCTGTGTTTATGCAAGGACTTAAACAACTTTGACTTTAAACCCTATTATATTTC
AACCGACCTTCTT
Found at i:10350 original size:13 final size:13
Alignment explanation
Indices: 10329--10365 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10319 GATAATTGTT
10329 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
10342 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
10355 CTTGACCCTCC
1 TTTGACCCTCC
10366 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:10427 original size:41 final size:40
Alignment explanation
Indices: 10364--10440 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
10354 ACTTGACCCT
* *
10364 CCTAATAATTAAGGAAATAAATTAAATACAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATACAGATTTAGCCC
* *
10404 CCTAATAAATTAAGGTAAGAAATTAAATCCAGATTTA
1 CCTAAT-AATTAAGGAAAGAAATTAAATACAGATTTA
10441 ATCCCTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 6 0.19
41 26 0.81
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATACAGATTTAGCCC
Done.