Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013863.1 Corchorus capsularis cultivar CVL-1 contig13884, 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: 21823
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:597 original size:20 final size:19
Alignment explanation
Indices: 565--612 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
555 TGTTTTTTTG
565 CTTTTGTTTCTTCTTACTCC
1 CTTTTG-TTCTTCTTACTCC
**
585 CATTTTGTTCTTCTTTTTCC
1 C-TTTTGTTCTTCTTACTCC
605 CTTTTGTT
1 CTTTTGTT
613 TCCTTTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 13 0.52
21 5 0.20
ACGTcount: A:0.04, C:0.25, G:0.06, T:0.65
Consensus pattern (19 bp):
CTTTTGTTCTTCTTACTCC
Found at i:1033 original size:2 final size:2
Alignment explanation
Indices: 1021--1064 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1011 TAATCTTTAC
1021 TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1059 TC TA TA
1 TA TA TA
1065 CCTCGTATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1189 original size:13 final size:13
Alignment explanation
Indices: 1171--1195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161 TTAACATTTC
1171 AAATAATATTTAT
1 AAATAATATTTAT
1184 AAATAATATTTA
1 AAATAATATTTA
1196 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:2239 original size:19 final size:19
Alignment explanation
Indices: 2201--2240 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2191 CGCTTTTTTC
* **
2201 TTTTTTGCGTTTTCTTTTT
1 TTTTTTGCGTTGTCAATTT
2220 TTTTTTGCGTTGTCAATTT
1 TTTTTTGCGTTGTCAATTT
2239 TT
1 TT
2241 GGAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.72
Consensus pattern (19 bp):
TTTTTTGCGTTGTCAATTT
Found at i:3213 original size:20 final size:19
Alignment explanation
Indices: 3180--3217 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3170 ATTTAGGGGT
3180 GATCATCGGATCGGTTTCG
1 GATCATCGGATCGGTTTCG
*
3199 GATCAGTCGGGTCGGTTTC
1 GATCA-TCGGATCGGTTTC
3218 AATCAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.32
Consensus pattern (19 bp):
GATCATCGGATCGGTTTCG
Found at i:3526 original size:20 final size:20
Alignment explanation
Indices: 3489--3526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3479 TATATATAAT
*
3489 ATATATAATAAAATTAAAAA
1 ATATATAATAAAACTAAAAA
*
3509 ATATATAATACAACTAAA
1 ATATATAATAAAACTAAA
3527 CTTTATGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
ATATATAATAAAACTAAAAA
Found at i:4628 original size:2 final size:2
Alignment explanation
Indices: 4621--4668 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
4611 TAATAAATTA
4621 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
4663 GT AT AT
1 AT AT AT
4669 GTATTAGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6833 original size:23 final size:23
Alignment explanation
Indices: 6798--6849 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
6788 TCTTTGTTTC
*
6798 TTTTATGGGACTCC-TTAGTGAGAG
1 TTTT-TGGAACTCCTTTA-TGAGAG
6822 TTTTTGGAACTCCTTTATGAGAG
1 TTTTTGGAACTCCTTTATGAGAG
6845 TTTTT
1 TTTTT
6850 TCTATTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (23 bp):
TTTTTGGAACTCCTTTATGAGAG
Found at i:6881 original size:59 final size:59
Alignment explanation
Indices: 6807--6918 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
6797 CTTTTATGGG
*
6807 ACTCCTTAGTGAGAGTTTTTGGA-ACTCCTTTATGAGAGTTTTTTCTATTGTCTTTTGGA
1 ACTCCTTAGTGAGAGTTTTT-GATACTCCTTTATGAGAGCTTTTTCTATTGTCTTTTGGA
* *
6866 ACTCCTTTGTGAGAGTTTTTGATACTCCTTTGTGAGAGCTTTTTCTATTGTCT
1 ACTCCTTAGTGAGAGTTTTTGATACTCCTTTATGAGAGCTTTTTCTATTGTCT
6919 CCTACAAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 2 0.04
59 47 0.96
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (59 bp):
ACTCCTTAGTGAGAGTTTTTGATACTCCTTTATGAGAGCTTTTTCTATTGTCTTTTGGA
Found at i:18855 original size:31 final size:31
Alignment explanation
Indices: 18817--18878 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
18807 TATTGATGAA
* *
18817 AATTTTCTGATAAAAAACTACATAAATTTCG
1 AATTTTCTAATAAAAAACTACATAAAATTCG
**
18848 AATTTTCTAATGCAAAACTACATAAAATTCG
1 AATTTTCTAATAAAAAACTACATAAAATTCG
18879 CGAGAGGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (31 bp):
AATTTTCTAATAAAAAACTACATAAAATTCG
Found at i:19102 original size:6 final size:7
Alignment explanation
Indices: 19087--19116 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
19077 TTAGGAAAAT
19087 AAAAGAA
1 AAAAGAA
19094 AAAAG-A
1 AAAAGAA
19100 AAAAGAA
1 AAAAGAA
19107 AAAAGAA
1 AAAAGAA
19114 AAA
1 AAA
19117 CTGAACTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:19105 original size:13 final size:13
Alignment explanation
Indices: 19087--19116 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19077 TTAGGAAAAT
19087 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
19100 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
19113 AAAA
1 AAAA
19117 CTGAACTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Done.