Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012766.1 Corchorus capsularis cultivar CVL-1 contig12787, 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: 34746
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:3255 original size:16 final size:16
Alignment explanation
Indices: 3228--3300 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
3218 GTCGGGTTGA
3228 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
3244 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
* **
3260 TCGGGTTCGGCTTGTT
1 TCGGGTTCGGGTCATT
* *
3276 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTCATT
3291 TCGGGTTCGG
1 TCGGGTTCGG
3301 TACCTAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 11 0.25
16 33 0.75
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:16162 original size:17 final size:17
Alignment explanation
Indices: 16140--16194 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
16130 ATATTGGTTT
16140 AATTAGTTTGTTACTTA
1 AATTAGTTTGTTACTTA
16157 AATTAG--T-TT-CTT-
1 AATTAGTTTGTTACTTA
16169 AATTAGTTTGTTACTTA
1 AATTAGTTTGTTACTTA
16186 AATTAGTTT
1 AATTAGTTT
16195 CTTAGTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 3 0.09
15 3 0.09
16 3 0.09
17 15 0.45
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (17 bp):
AATTAGTTTGTTACTTA
Found at i:16170 original size:29 final size:29
Alignment explanation
Indices: 16138--16204 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
16128 AGATATTGGT
16138 TTAATTAGTTTGTTACTTAAATTAGTTTC
1 TTAATTAGTTTGTTACTTAAATTAGTTTC
16167 TTAATTAGTTTGTTACTTAAATTAGTTTC
1 TTAATTAGTTTGTTACTTAAATTAGTTTC
*
16196 TTAGTTAGT
1 TTAATTAGT
16205 GGGTTAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (29 bp):
TTAATTAGTTTGTTACTTAAATTAGTTTC
Found at i:16992 original size:28 final size:28
Alignment explanation
Indices: 16952--17021 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
16942 AACCTTCTTT
16952 ATCCAATGATGTGTTTAAAAAAAAAATC
1 ATCCAATGATGTGTTTAAAAAAAAAATC
16980 ATCCAATGATGTGTTTAAAAAAAAAATC
1 ATCCAATGATGTGTTTAAAAAAAAAATC
17008 ATCCAATGATGTGT
1 ATCCAATGATGTGT
17022 CCTGGCCAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (28 bp):
ATCCAATGATGTGTTTAAAAAAAAAATC
Found at i:21072 original size:2 final size:2
Alignment explanation
Indices: 21065--21093 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21055 AAGCTGACGC
21065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21094 AATTATAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22818 original size:279 final size:279
Alignment explanation
Indices: 22318--22879 Score: 1052
Period size: 279 Copynumber: 2.0 Consensus size: 279
22308 GTGCAGATTT
22318 GTGGCATAGGTCCACAAGAAAATTTTGCTTTGTTGTTTCCGCTTTAATTATTTGTTTGATTAATT
1 GTGGCATAGGTCCACAAGAAAATTTTGCTTTGTTGTTTCCGCTTTAATTATTTGTTTGATTAATT
22383 CCTGGGATATCCGAAGTTACAACAAGTGGTATCAAGAGCCTGGTTGATTAGAGATGACAAAAAGC
66 CCTGGGATATCCGAAGTTACAACAAGTGGTATCAAGAGCCTGGTTGATTAGAGATGACAAAAAGC
*
22448 AGTGGATCAACTTTAAAGTTTGAGATCGGGCAGTTTAATGGAACGAACAGTTTTCAGATGTGGCA
131 AGTGGATCAACTTTAAAGTTTGAGATCGAGCAGTTTAATGGAACGAACAGTTTTCAGATGTGGCA
* *
22513 GAGTACGGTAACAGATGTGTTAGTACAATAAGGATTGTGAGATGCGCTTGAAGCTGATAAGCCTT
196 GAGTACGGTAACAGATATGTTAGTACAACAAGGATTGTGAGATGCGCTTGAAGCTGATAAGCCTT
22578 CAACGATGAATGACAACAA
261 CAACGATGAATGACAACAA
*
22597 GTGGCATAGGTCCACAAGAAAATTTTGCTTTGTTGTTTTCGCTTTAATTATTTGTTTGATTAATT
1 GTGGCATAGGTCCACAAGAAAATTTTGCTTTGTTGTTTCCGCTTTAATTATTTGTTTGATTAATT
*
22662 CCTGGGATATCCGAAGTTACAACAAGTGGTATCAAGAGCCTGGTTGATTAGAGATGACAAAAAGT
66 CCTGGGATATCCGAAGTTACAACAAGTGGTATCAAGAGCCTGGTTGATTAGAGATGACAAAAAGC
* *
22727 AGTGGATCAACTTTGAAGTTTGAGATTGAGCAGTTTAATGGAACGAACAGTTTTCAGATGTGGCA
131 AGTGGATCAACTTTAAAGTTTGAGATCGAGCAGTTTAATGGAACGAACAGTTTTCAGATGTGGCA
*
22792 GAGTACGGTAACAGATATGTTAGTACAACAAGGATTGTGAGATGCGCTTGAAGTTGATAAGCCTT
196 GAGTACGGTAACAGATATGTTAGTACAACAAGGATTGTGAGATGCGCTTGAAGCTGATAAGCCTT
22857 CAACGATGAATGACAACAA
261 CAACGATGAATGACAACAA
22876 GTGG
1 GTGG
22880 AGAGATATTC
Statistics
Matches: 275, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
279 275 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (279 bp):
GTGGCATAGGTCCACAAGAAAATTTTGCTTTGTTGTTTCCGCTTTAATTATTTGTTTGATTAATT
CCTGGGATATCCGAAGTTACAACAAGTGGTATCAAGAGCCTGGTTGATTAGAGATGACAAAAAGC
AGTGGATCAACTTTAAAGTTTGAGATCGAGCAGTTTAATGGAACGAACAGTTTTCAGATGTGGCA
GAGTACGGTAACAGATATGTTAGTACAACAAGGATTGTGAGATGCGCTTGAAGCTGATAAGCCTT
CAACGATGAATGACAACAA
Found at i:29804 original size:1 final size:1
Alignment explanation
Indices: 29798--29845 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
29788 AAGTTAACAT
* * * *
29798 AAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29846 CTACTGAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29814 original size:10 final size:10
Alignment explanation
Indices: 29799--29846 Score: 73
Period size: 9 Copynumber: 5.0 Consensus size: 10
29789 AGTTAACATA
29799 AAAAAAAAAC
1 AAAAAAAAAC
29809 -AAAAAAAAC
1 AAAAAAAAAC
29818 AAAAAAAAAC
1 AAAAAAAAAC
*
29828 AAAAAACAA-
1 AAAAAAAAAC
29837 AAAAAAAAAC
1 AAAAAAAAAC
29847 TACTGAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:29823 original size:19 final size:19
Alignment explanation
Indices: 29793--29846 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
29783 TTGGCAAGTT
29793 AACATAAAAAAAAAACAAAA
1 AACA-AAAAAAAAAACAAAA
29813 AA-AACAAAAAAAAACAAAA
1 AACAA-AAAAAAAAACAAAA
29832 AACAAAAAAAAAAAC
1 AACAAAAAAAAAAAC
29847 TACTGAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.03
19 27 0.84
20 4 0.12
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (19 bp):
AACAAAAAAAAAAACAAAA
Found at i:34138 original size:6 final size:6
Alignment explanation
Indices: 34127--34197 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
34117 TATCGAAAAT
* * *
34127 GAACCC GAACCC -AACCC AAACCC GAA--A AAACCC GAACCC GAAGTACCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC G-A--ACCC
34175 GAACCC GAACCC G--CCC GAACCC G
1 GAACCC GAACCC GAACCC GAACCC G
34198 CCCAATTGCC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
4 6 0.12
5 5 0.10
6 34 0.65
7 1 0.02
8 1 0.02
9 5 0.10
ACGTcount: A:0.37, C:0.46, G:0.15, T:0.01
Consensus pattern (6 bp):
GAACCC
Found at i:34164 original size:16 final size:16
Alignment explanation
Indices: 34139--34183 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
34129 ACCCGAACCC
*
34139 AACCCAAACCCGAAAA
1 AACCCGAACCCGAAAA
*
34155 AACCCGAACCCG-AAG
1 AACCCGAACCCGAAAA
*
34170 TACCCGAACCCGAA
1 AACCCGAACCCGAA
34184 CCCGCCCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.44, C:0.40, G:0.13, T:0.02
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:34726 original size:17 final size:16
Alignment explanation
Indices: 34700--34734 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
34690 CAATCTTGAC
34700 TTACCCATCTCCAACT
1 TTACCCATCTCCAACT
34716 TTACTCCATCTCCAACT
1 TTAC-CCATCTCCAACT
34733 TT
1 TT
34735 CAAGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (16 bp):
TTACCCATCTCCAACT
Done.