Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011319.1 Corchorus capsularis cultivar CVL-1 contig11340, 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: 50771
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:972 original size:16 final size:16
Alignment explanation
Indices: 951--1016 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
941 ATCGGGTTCA
*
951 GGTCATTTTGGATTTG
1 GGTCATTTTGGATTCG
* *
967 GGTCATTTCGGGTTCG
1 GGTCATTTTGGATTCG
*
983 GGTC-GTTTGGATTCG
1 GGTCATTTTGGATTCG
* *
998 GGTCATTTCGGGTTCG
1 GGTCATTTTGGATTCG
1014 GGT
1 GGT
1017 ACCCAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 12 0.30
16 28 0.70
ACGTcount: A:0.08, C:0.14, G:0.38, T:0.41
Consensus pattern (16 bp):
GGTCATTTTGGATTCG
Found at i:995 original size:31 final size:32
Alignment explanation
Indices: 942--1016 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
932 GTCGGGTTGA
* * *
942 TCGGGTTCAGGTCATTTTGGATTTGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
974 TCGGGTTCGGGTC-GTTTGGATTCGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
1005 TCGGGTTCGGGT
1 TCGGGTTCGGGT
1017 ACCCAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 28 0.70
32 12 0.30
ACGTcount: A:0.08, C:0.15, G:0.37, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
Found at i:1925 original size:22 final size:22
Alignment explanation
Indices: 1900--2065 Score: 100
Period size: 22 Copynumber: 7.5 Consensus size: 22
1890 GGAGATTAAT
*
1900 AAAATTTCATAGAGAGGTTATAA
1 AAAATTTCATAGAGAGGTTAT-C
** **
1923 AAAAAATCATATTGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* * *
1945 AAAATTTCATTGAAAGGTTATT
1 AAAATTTCATAGAGAGGTTATC
**
1967 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
** * *
1989 AGTATTTCATTGAGAGTTTATC
1 AAAATTTCATAGAGAGGTTATC
* * * * *
2011 ACAATTTCACAGGGTA-ATTATA
1 AAAATTTCATAGAG-AGGTTATC
* * * *
2033 AAAATTTCATTGGGTGGTTCTC
1 AAAATTTCATAGAGAGGTTATC
2055 AAAATTTCATA
1 AAAATTTCATA
2066 AAAATATTTA
Statistics
Matches: 104, Mismatches: 37, Indels: 5
0.71 0.25 0.03
Matches are distributed among these distances:
22 86 0.83
23 18 0.17
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTATC
Found at i:1950 original size:45 final size:44
Alignment explanation
Indices: 1900--2009 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
1890 GGAGATTAAT
*
1900 AAAATTTCATAGAGAGGTTATAAAAAAAATCATA-TTGAGGTTATC
1 AAAATTTCATTGAGAGGTTAT-AAAAAAATCATAGTT-AGGTTATC
* * **
1945 AAAATTTCATTGAAAGGTTATTAAAATTTCATAGTTAGGTTATC
1 AAAATTTCATTGAGAGGTTATAAAAAAATCATAGTTAGGTTATC
** *
1989 AGTATTTCATTGAGAGTTTAT
1 AAAATTTCATTGAGAGGTTAT
2010 CACAATTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 34 0.62
45 21 0.38
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (44 bp):
AAAATTTCATTGAGAGGTTATAAAAAAATCATAGTTAGGTTATC
Found at i:6035 original size:44 final size:44
Alignment explanation
Indices: 6010--6137 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 44
6000 TCATAGGAAG
*
6010 GTTTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGA
1 GTTTATCAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGA
* * * * * * *
6054 GTTTATCACAATTTCATAGTTA-ATTATCAAAATTTTAAAGGGT
1 GTTTATCAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGA
* * *
6097 GGTTATCAAAATTT-ACTAGAGTAGGTTATCAAAATTTCATA
1 GTTTATCAAAATTTCA-TAG-TTAGGTTATCAAAGTTTCATA
6138 AAAATATTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
43 30 0.45
44 22 0.33
45 14 0.21
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (44 bp):
GTTTATCAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGA
Found at i:6046 original size:22 final size:22
Alignment explanation
Indices: 5967--6137 Score: 129
Period size: 22 Copynumber: 7.8 Consensus size: 22
5957 TTCACAAGAT
* *
5967 GGTTATCAAAA-ATCATAGGAA
1 GGTTATCAAAATTTCATAGGTA
** *
5988 GGTTA-CACTATTTCATAGGAA
1 GGTTATCAAAATTTCATAGGTA
* *
6009 GGTTTATTAAAATTTCATAGTTA
1 GG-TTATCAAAATTTCATAGGTA
*
6032 GGTTATCAAAGTTTCATATGG-A
1 GGTTATCAAAATTTCATA-GGTA
* * *
6054 GTTTATCACAATTTCATAGTTA
1 GGTTATCAAAATTTCATAGGTA
* * *
6076 -ATTATCAAAATTTTAAAGGGT-
1 GGTTATCAAAATTTCATA-GGTA
6097 GGTTATCAAAATTT-ACTAGAGTA
1 GGTTATCAAAATTTCA-TAG-GTA
6120 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
6138 AAAATATTCA
Statistics
Matches: 117, Mismatches: 22, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
20 3 0.03
21 32 0.27
22 51 0.44
23 30 0.26
24 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGTA
Found at i:21179 original size:2 final size:2
Alignment explanation
Indices: 21172--21207 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
21162 TCTTTGATAA
21172 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21208 TGATTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23877 original size:20 final size:20
Alignment explanation
Indices: 23852--23889 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23842 GGAACAAGTT
23852 TGTAGCTGTAGAAGCGTGCG
1 TGTAGCTGTAGAAGCGTGCG
*
23872 TGTAGCTGTCGAAGCGTG
1 TGTAGCTGTAGAAGCGTG
23890 TTTGAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.26
Consensus pattern (20 bp):
TGTAGCTGTAGAAGCGTGCG
Found at i:28221 original size:30 final size:28
Alignment explanation
Indices: 28185--28287 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 28
28175 CTGTGTTATA
*
28185 TGTGTTTGGGGACTTTAGTATATATGTCTC
1 TGTGTTTAGGGACTTTAGTATA-ATG-CTC
* *
28215 TGTGTTTAGGGACTTTAATATAGATGCCC
1 TGTGTTTAGGGACTTTAGTATA-ATGCTC
*
28244 TTGTGCTT-GAGGACTTTGATGTA-AATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTATAATG-CTC
28275 TGTGTTTAGGGAC
1 TGTGTTTAGGGAC
28288 GAATACCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
29 3 0.05
30 49 0.83
31 5 0.08
32 2 0.03
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.41
Consensus pattern (28 bp):
TGTGTTTAGGGACTTTAGTATAATGCTC
Found at i:28335 original size:53 final size:53
Alignment explanation
Indices: 28241--28418 Score: 272
Period size: 53 Copynumber: 3.4 Consensus size: 53
28231 AATATAGATG
* *
28241 CCCTTGTGCTTGAGGAC-TTTGATGTA-A-ATGCCTCTGTGTTTAGGGACGAATA
1 CCCTTGTGTTTGAGGACTTTTGA-G-ACAGATGCCTCTGTGTTTAGGGATGAATA
* *
28293 CCCTTGTGTTTGAGGACTTTTGAGAGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTTGAGACAGATGCCTCTGTGTTTAGGGATGAATA
*
28346 CCCTTGTGTTTGAGGACTTTTGATACAGATGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTTGAGACAGATGCCTCTGTGTTTAGGGATGAATA
28399 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGTTTGAGGACTTT
28419 AATTATTGGG
Statistics
Matches: 117, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
51 1 0.01
52 18 0.15
53 98 0.84
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (53 bp):
CCCTTGTGTTTGAGGACTTTTGAGACAGATGCCTCTGTGTTTAGGGATGAATA
Found at i:39650 original size:6 final size:6
Alignment explanation
Indices: 39639--39665 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39629 AAAGCAAAGC
39639 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
39666 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:40608 original size:10 final size:10
Alignment explanation
Indices: 40593--40617 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40583 AAGGACTCTA
40593 GAATTTTCTG
1 GAATTTTCTG
40603 GAATTTTCTG
1 GAATTTTCTG
40613 GAATT
1 GAATT
40618 AAGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:49776 original size:30 final size:29
Alignment explanation
Indices: 49740--49841 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 29
49730 CTGTGTTATA
*
49740 TGTGTTTGGGGACTTTATTATAGATGCCTC
1 TGTGTTTAGGGACTTTA-TATAGATGCCTC
*
49770 TGTGTTTAGGGACTTTAATATGGATGCC-C
1 TGTGTTTAGGGACTTT-ATATAGATGCCTC
* *
49799 TTGTGCTT-GAGGACTTTGATGTAGATGCCTC
1 -TGTGTTTAG-GGACTTT-ATATAGATGCCTC
49830 TGTGTTTAGGGA
1 TGTGTTTAGGGA
49842 TGAATACCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.03
30 55 0.92
31 3 0.05
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (29 bp):
TGTGTTTAGGGACTTTATATAGATGCCTC
Found at i:49865 original size:52 final size:53
Alignment explanation
Indices: 49796--49978 Score: 237
Period size: 53 Copynumber: 3.4 Consensus size: 53
49786 AATATGGATG
*
49796 CCCTTGTGCTTGAGGACTTTGATGTAGA-TGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
49848 CCCTTGTGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGAC-TTTGATGTAGA-GTGCCTCTGTGTTTAGGGATGAATA
* * * *
49901 CCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATG
1 CCCTTGTGTTTGAGGACTTTGATGTAG-AGTGCCTCTGTGTTTAGGG----ATGAATA
49959 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGTTTGAGGACTTT
49979 AATTATTGGG
Statistics
Matches: 116, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
51 3 0.03
52 22 0.19
53 46 0.40
54 19 0.16
55 1 0.01
58 25 0.22
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (53 bp):
CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
Done.