Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022550.1 Corchorus olitorius cultivar O-4 contig22583, 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: 29924
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:362 original size:139 final size:140
Alignment explanation
Indices: 195--457 Score: 329
Period size: 139 Copynumber: 1.9 Consensus size: 140
185 TTTTTTACTT
* *
195 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATTTGCAACTATTTCATTTAACT-T
1 TTAACAATAATTTAAAATTTCTTAAAATAAAGGAGGAGTAATGTGCAAC--TTTCA-TT-ACTAT
259 ATAA-T-CCTCTAGGGACAAAATTAA-A-AGTTTAAGATTTTAATTTTCAATTAATTTAATCATG
62 ATAATTACCTCTAGGGACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAATCATG
320 TTGGGTCACGTGTG
127 TTGGGTCACGTGTG
* * * * *
334 TTAATAATAATTTAAATTTTCTTTAAATAAAGGAGGGGTAATGTGCAACTTTCATTATTATATAA
1 TTAACAATAATTTAAAATTTCTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTACTATATAA
* * **
399 TTAACCTTTAGGGACAAAATTAATAGTTTGTTTAAGATTTTAATTTTCCTTTAATTTAA
66 TT-ACCTCTAGGGACAAAATTAATA--TAGTTTAAGATTTTAATTTTCAATTAATTTAA
458 ACACGTTAAG
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
135 2 0.02
136 7 0.07
137 6 0.06
139 61 0.58
140 1 0.01
143 28 0.27
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (140 bp):
TTAACAATAATTTAAAATTTCTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTACTATATAA
TTACCTCTAGGGACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAATCATGTTGG
GTCACGTGTG
Found at i:3309 original size:139 final size:141
Alignment explanation
Indices: 3135--3400 Score: 355
Period size: 139 Copynumber: 1.9 Consensus size: 141
3125 TTTTTTACTT
*
3135 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATTTGCAACTATTTCATTTAACT-T
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAAC--TTTCA-TT-ACTAT
3199 ATAA-T-CCTCTAGGGACAAAATT-A-AG-AGTTTAAGATTTTAATTTTCAGTTAATTTAAACAT
62 ATAATTACCTCTAGGGACAAAATTAATAGTAGTTTAAGATTTTAATTTTCAGTTAATTTAAACAT
3259 GTTGGGTCACGTGTG
127 GTTGGGTCACGTGTG
* * * * *
3274 TTAACAGTAATTTAAATTTTGTTTAAATAAAGGAGGGGTAATGTGCAACTTTCATTATTATATAA
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTACTATATAA
* * *
3339 TTAACCTTTAGGGACAAAATTAATAGTTTGTTTAAGATTTTAATTTTCATTTAATTTAAACA
66 TT-ACCTCTAGGGACAAAATTAATAG-TAGTTTAAGATTTTAATTTTCAGTTAATTTAAACA
3401 CGTTAAGTCA
Statistics
Matches: 110, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
135 2 0.02
136 7 0.06
137 6 0.05
139 60 0.55
140 1 0.01
141 2 0.02
143 32 0.29
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (141 bp):
TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTACTATATAA
TTACCTCTAGGGACAAAATTAATAGTAGTTTAAGATTTTAATTTTCAGTTAATTTAAACATGTTG
GGTCACGTGTG
Found at i:6220 original size:139 final size:141
Alignment explanation
Indices: 6067--6332 Score: 362
Period size: 139 Copynumber: 1.9 Consensus size: 141
6057 GTTTTTACTT
*
6067 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATTTGCAACTATTTCATT-TAAC-T
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAAC--TTTCATTATAACAT
*
6130 TA-TAATCCTCTAGGGACAAAATTAA-A-AGTTTAAGATTATAATTTTCAATTAATTTAAACATG
64 AATTAA-CCTCTAGGGACAAAATTAATATAGTTTAAGATTATAATTTTCAATTAATTTAAACATG
6192 TTGGGTCACGTGTG
128 TTGGGTCACGTGTG
* * * *
6206 TTAACAATAATTTAAATTTTGTTTAAATAAAGGAGGGGTAATGTGCAACTTTCATTATTACATAA
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTATAACATAA
* * * *
6271 TTAACCTTTAGGGACAAAATTAATAGTTTGTTTAAGATTTTAATTTTCATTTAATTTAAACA
66 TTAACCTCTAGGGACAAAATTAATA--TAGTTTAAGATTATAATTTTCAATTAATTTAAACA
6333 CCTTAAGTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
137 7 0.06
138 3 0.03
139 65 0.59
140 4 0.04
143 31 0.28
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (141 bp):
TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCATTATAACATAA
TTAACCTCTAGGGACAAAATTAATATAGTTTAAGATTATAATTTTCAATTAATTTAAACATGTTG
GGTCACGTGTG
Found at i:7693 original size:36 final size:36
Alignment explanation
Indices: 7646--7747 Score: 186
Period size: 36 Copynumber: 2.8 Consensus size: 36
7636 TGGGGCGGCG
7646 TGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCC
1 TGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCC
7682 TGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCC
1 TGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCC
* *
7718 TGGCGCGGCCAAGTGCCTAGGCCTGGCGCG
1 TGGCGCGGCCCAGCGCCTAGGCCTGGCGCG
7748 GCCCAGTGCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.07, C:0.39, G:0.42, T:0.12
Consensus pattern (36 bp):
TGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCC
Found at i:7742 original size:23 final size:23
Alignment explanation
Indices: 7716--7770 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
7706 GGCGCGCGGT
7716 CCTGGCGCGGCCAAGTGCCTAGG
1 CCTGGCGCGGCCAAGTGCCTAGG
*
7739 CCTGGCGCGGCCCAGTGCCTAGG
1 CCTGGCGCGGCCAAGTGCCTAGG
7762 CCTGGCGCG
1 CCTGGCGCG
7771 CGGGCTGGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.09, C:0.38, G:0.40, T:0.13
Consensus pattern (23 bp):
CCTGGCGCGGCCAAGTGCCTAGG
Found at i:7744 original size:59 final size:58
Alignment explanation
Indices: 7680--7805 Score: 200
Period size: 59 Copynumber: 2.2 Consensus size: 58
7670 GGCGCGCGGT
7680 CCTGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGTCCTGGCGCGG-CCAAGTGCCTAGG
1 CCTGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGG-CCTGGCGCGGTCC-AGTGCCTAGG
* *
7739 CCTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGCGGGCTGGCGCGGTCCAGTGCCTAGG
1 CCTGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGCCTGGCGCGGTCCAGTGCCTAGG
*
7797 CTTGGCGCG
1 CCTGGCGCG
7806 TGGGCCTGGT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
58 27 0.43
59 36 0.57
ACGTcount: A:0.07, C:0.37, G:0.42, T:0.13
Consensus pattern (58 bp):
CCTGGCGCGGCCCAGCGCCTAGGCCTGGCGCGCGGCCTGGCGCGGTCCAGTGCCTAGG
Found at i:7789 original size:35 final size:35
Alignment explanation
Indices: 7740--7866 Score: 166
Period size: 35 Copynumber: 3.6 Consensus size: 35
7730 GTGCCTAGGC
7740 CTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGCGGG
1 CTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGCGGG
* * *
7775 CTGGCGCGGTCCAGTGCCTAGGCTTGGCGCGTGGG
1 CTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGCGGG
* * * *
7810 CCTGGTGCGGCCCAGCGCCTAGGCCAGGCGCACGGGG
1 -CTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGC-GGG
7847 CT-GCGCGGCCCAGTGCCTAG
1 CTGGCGCGGCCCAGTGCCTAG
7867 CCAGGCTTGG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 48 0.62
36 27 0.35
37 3 0.04
ACGTcount: A:0.08, C:0.35, G:0.43, T:0.13
Consensus pattern (35 bp):
CTGGCGCGGCCCAGTGCCTAGGCCTGGCGCGCGGG
Found at i:10752 original size:139 final size:141
Alignment explanation
Indices: 10601--10863 Score: 349
Period size: 139 Copynumber: 1.9 Consensus size: 141
10591 TTTTTTACTT
*
10601 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATTTGCAACTATTTC-AT-TTA-AC
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAAC--TTTCAATATTACA-
* *
10663 TTA-TAATCCTCTAGGGACAAAATTAA-A-AGTTTAAGATTTTAATTTTCAATTAATTTAAACAT
63 TAATTAA-CCTCTAGGCACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAAACAT
10725 GTTGGGTCACGTGTG
127 GTTGGGTCACGTGTG
* * *
10740 TTAACAATAATTTAAATTTTGTTTAAATAAAGGAGGGGTAATGTGCAACTTTCAATATTACATAA
1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCAATATTACATAA
* * *
10805 TTAACCTTTAGGCACAAAATTAATAGTTTGTTTAAGATTTTAATTTTCATTTAATTTAA
66 TTAACCTCTAGGCACAAAATTAATA--TAGTTTAAGATTTTAATTTTCAATTAATTTAA
10864 GCACGTTAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
137 4 0.04
138 2 0.02
139 67 0.63
140 5 0.05
143 29 0.27
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (141 bp):
TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCAATATTACATAA
TTAACCTCTAGGCACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAAACATGTTG
GGTCACGTGTG
Found at i:21927 original size:7 final size:7
Alignment explanation
Indices: 21915--21950 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
21905 GGCAACCCAA
21915 TTTTAAT
1 TTTTAAT
21922 TTTTAATTT
1 TTTTAA--T
21931 TTTTAAT
1 TTTTAAT
21938 TTTTAAT
1 TTTTAAT
21945 TTTTAA
1 TTTTAA
21951 CTTAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 20 0.74
9 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTAAT
Found at i:21936 original size:16 final size:16
Alignment explanation
Indices: 21915--21948 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21905 GGCAACCCAA
21915 TTTTAATTTTTAATTT
1 TTTTAATTTTTAATTT
21931 TTTTAATTTTTAATTT
1 TTTTAATTTTTAATTT
21947 TT
1 TT
21949 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTAATTTTTAATTT
Found at i:21964 original size:23 final size:22
Alignment explanation
Indices: 21913--21964 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
21903 GAGGCAACCC
*
21913 AATTTTAATTTTTAATTTTTTT
1 AATTTTAATTTTTAATTATTTT
21935 AATTTTTAATTTTTAACTTAATTTT
1 AA-TTTTAATTTTTAA-TT-ATTTT
21960 -ATTTT
1 AATTTT
21965 GTTCATAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 17 0.65
24 3 0.12
25 4 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATTTTAATTTTTAATTATTTT
Found at i:22179 original size:21 final size:20
Alignment explanation
Indices: 22153--22210 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
22143 CAACAGCCAA
22153 GCCAAGGCCAGGCCAG-CGC
1 GCCAAGGCCAGGCCAGCCGC
**
22172 GCAACAAGGGTAGGCCATGCCGC
1 GC--CAAGGCCAGGCCA-GCCGC
*
22195 GCCAAGCCCAGGCCAG
1 GCCAAGGCCAGGCCAG
22211 GCCAGGCCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.07
20 1 0.03
21 21 0.70
22 1 0.03
23 5 0.17
ACGTcount: A:0.24, C:0.38, G:0.34, T:0.03
Consensus pattern (20 bp):
GCCAAGGCCAGGCCAGCCGC
Found at i:22550 original size:17 final size:16
Alignment explanation
Indices: 22505--22554 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
22495 TCAAAACGCA
22505 AGAAGCAATATTTTGG
1 AGAAGCAATATTTTGG
*
22521 AG-AGCAA-ATTTTTGAT
1 AGAAGCAATA-TTTTG-G
22537 AGAAGCAATATTTTGG
1 AGAAGCAATATTTTGG
22553 AG
1 AG
22555 GAGAATTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.04
15 10 0.36
16 6 0.21
17 10 0.36
18 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (16 bp):
AGAAGCAATATTTTGG
Found at i:24554 original size:16 final size:15
Alignment explanation
Indices: 24516--24557 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
24506 ACAGAGGTTG
24516 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
24531 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
24546 ACTAGAAAACAA
1 AC-AGAAAACAA
24558 AGCATAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:27724 original size:11 final size:11
Alignment explanation
Indices: 27690--27726 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27680 GGCTTGGAAT
27690 GGTGATGGCAC
1 GGTGATGGCAC
27701 GG-GCATGGC-C
1 GGTG-ATGGCAC
27711 GGTGATGGCAC
1 GGTGATGGCAC
27722 GGTGA
1 GGTGA
27727 ATGGGCGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16
Consensus pattern (11 bp):
GGTGATGGCAC
Done.