Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006018.1 Corchorus capsularis cultivar CVL-1 contig06036, 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: 17452
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:116 original size:31 final size:30
Alignment explanation
Indices: 48--117 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
38 AATGTGCAAA
*
48 TGGGTCCCTGAAGTGAACTTAGTGAGCAAT
1 TGGGTCCCTGAAGTGAACTTAGTGACCAAT
* * *
78 TGAGTCCCTGAAGTTG-AGTTAATTGACCAAT
1 TGGGTCCCTGAAG-TGAACTT-AGTGACCAAT
109 TGGGTCCCT
1 TGGGTCCCT
118 CACCAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGGTCCCTGAAGTGAACTTAGTGACCAAT
Found at i:6483 original size:180 final size:180
Alignment explanation
Indices: 6136--6488 Score: 489
Period size: 180 Copynumber: 2.0 Consensus size: 180
6126 TTCCACCATA
* * * * *
6136 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTTTTTGG
1 AGCACAAATTATATAATATTAAGTAGACCATCTATTCCCATTAACCAAAACAACTAATTTTTTGG
* *
6201 AAGCATTTTTAATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCAT
66 AAGCATTTTTAATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCAT
* *
6266 GGAACAACCTTTCAAGAGACACTTGAAACATCTTAATCAGATATATCTGG
131 GGAAAAACCTTTCAAGAGACACTTGAAACACCTTAATCAGATATATCTGG
* *
6316 AGCA-AAAGTTATATAATATTATGTGGACCATCTATTCCCATTAACCAAAACAAC-AATTTTTTC
1 AGCACAAA-TTATATAATATTAAGTAGACCATCTATTCCCATTAACCAAAACAACTAATTTTTT-
*
6379 GGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGAT
64 GGAAGCATTTTTAATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGAT
* * * * *
6443 CATGGAAAAATCTTTGAATAGATACTT-AAATCACCTTAATCGGATA
128 CATGGAAAAACCTTTCAAGAGACACTTGAAA-CACCTTAATCAGATA
6489 ACCAGAGAGA
Statistics
Matches: 152, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
179 18 0.12
180 134 0.88
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (180 bp):
AGCACAAATTATATAATATTAAGTAGACCATCTATTCCCATTAACCAAAACAACTAATTTTTTGG
AAGCATTTTTAATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCAT
GGAAAAACCTTTCAAGAGACACTTGAAACACCTTAATCAGATATATCTGG
Found at i:6957 original size:2 final size:2
Alignment explanation
Indices: 6950--6992 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
6940 TTGTAGATAA
* *
6950 AT AT AT AT AT AT AT AT AT AT AT AT AC AC 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
6992 A
1 A
6993 CACACAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6981 original size:20 final size:20
Alignment explanation
Indices: 6958--6998 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6948 AAATATATAT
*
6958 ATATATATATATATATACAC
1 ATATATATATATATACACAC
6978 ATATATATATATATACACAC
1 ATATATATATATATACACAC
6998 A
1 A
6999 AATTTGACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATATATATATATACACAC
Found at i:6993 original size:18 final size:18
Alignment explanation
Indices: 6950--6996 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
6940 TTGTAGATAA
* *
6950 ATATATATATATATATAT
1 ATATATACACATATATAT
6968 ATATATACACATATATAT
1 ATATATACACATATATAT
6986 ATATATACACA
1 ATATATACACA
6997 CAAATTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATACACATATATAT
Found at i:9213 original size:11 final size:11
Alignment explanation
Indices: 9197--9222 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9187 GTTATGTTTA
9197 TTATAGTTTGT
1 TTATAGTTTGT
9208 TTATAGTTTGT
1 TTATAGTTTGT
9219 TTAT
1 TTAT
9223 TTGGTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.65
Consensus pattern (11 bp):
TTATAGTTTGT
Found at i:9770 original size:21 final size:21
Alignment explanation
Indices: 9730--9780 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
9720 AAACTAATCG
9730 AACCCACATAAAGGGACACAA
1 AACCCACATAAAGGGACACAA
*
9751 AGA-CCACATACAGTGG-CACAA
1 A-ACCCACATAAAG-GGACACAA
9772 AACCCACAT
1 AACCCACAT
9781 GTAATTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.47, C:0.31, G:0.14, T:0.08
Consensus pattern (21 bp):
AACCCACATAAAGGGACACAA
Found at i:9875 original size:3 final size:3
Alignment explanation
Indices: 9860--9903 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9850 AACTTGGGTG
*
9860 TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9904 ACCTTCAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11580 original size:8 final size:8
Alignment explanation
Indices: 11569--11594 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11559 GGCCCCTTCC
11569 TTTCCCTT
1 TTTCCCTT
11577 TTTCCCTT
1 TTTCCCTT
11585 TTTCCCTT
1 TTTCCCTT
11593 TT
1 TT
11595 GTTGTGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTCCCTT
Found at i:13697 original size:15 final size:16
Alignment explanation
Indices: 13670--13699 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13660 CACAAAGAAC
13670 AATTAATTTCTATCAT
1 AATTAATTTCTATCAT
13686 AATTAA-TTCTATCA
1 AATTAATTTCTATCA
13700 GAGAAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTTCTATCAT
Done.