Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013652.1 Corchorus capsularis cultivar CVL-1 contig13673, 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: 106556
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:281 original size:99 final size:99
Alignment explanation
Indices: 141--340 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 99
131 TCCATAACCC
141 GGTTGTGGAGTTCAAAATTTACACCGTCGGTGTATCAAATAATTACTCATTGTTATTATTATAAG
1 GGTTGTGGAGTTCAAAATTTACACCGTCGGTGTATCAAATAATTACTCATTGTTATTATTATAAG
*
206 CCTAAAAAGTGAAAAATTGTTGGAACTAGGACGG
66 CCTAAAAAGTGAAAAATTGTTGGAACTACGACGG
240 GGTTGTGGAGTTCAAAATTTACACCGTCGGTGTATCAAATAATTACTCATTGTTATTATTATAAG
1 GGTTGTGGAGTTCAAAATTTACACCGTCGGTGTATCAAATAATTACTCATTGTTATTATTATAAG
*
305 CCTAAAAAGTGAAAAATTGTTGGAGCTACGACGG
66 CCTAAAAAGTGAAAAATTGTTGGAACTACGACGG
339 GG
1 GG
341 GATGGCAAGA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (99 bp):
GGTTGTGGAGTTCAAAATTTACACCGTCGGTGTATCAAATAATTACTCATTGTTATTATTATAAG
CCTAAAAAGTGAAAAATTGTTGGAACTACGACGG
Found at i:994 original size:125 final size:125
Alignment explanation
Indices: 692--995 Score: 369
Period size: 125 Copynumber: 2.4 Consensus size: 125
682 TATTGTAACG
* * ** *
692 ACGTTTGTAAATGTCGGAACAAGTTCTTCATATCATTTGATTTTGACATATTCCGACATTTGTAA
1 ACGTTTGTAAATGTCGGAACAAGTTATTCACATCATTTGATTTCAACATATTTCGACATTTGTAA
* * * * * *
757 GCGTTAGTATATATATTATATCGTGACATTTATTAAACGTTGCTAAAAAATACTATACCA
66 ACGTTAGTATAGATATTATATCATGACATTTATCAAACGTCGCTAAAAAATAATATACCA
* * ** *
817 ACGTTTGTAAATGTCGGAACAAGTTTTTCACATAATTTGATTTCAATGTATTTTGACATTTGTAA
1 ACGTTTGTAAATGTCGGAACAAGTTATTCACATCATTTGATTTCAACATATTTCGACATTTGTAA
* * *
882 ACGTT-GATATAGATATTATATCATGACATTTATCAAATGTCGCTATAAAATAATATACCG
66 ACGTTAG-TATAGATATTATATCATGACATTTATCAAACGTCGCTAAAAAATAATATACCA
* * * *
942 ATGTTT-TCAAATGTCAGCACAAGTTATTCACATCATTTGACTTCAACATATTTC
1 ACGTTTGT-AAATGTCGGAACAAGTTATTCACATCATTTGATTTCAACATATTTC
996 TAGCAATTAT
Statistics
Matches: 150, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
124 2 0.01
125 148 0.99
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (125 bp):
ACGTTTGTAAATGTCGGAACAAGTTATTCACATCATTTGATTTCAACATATTTCGACATTTGTAA
ACGTTAGTATAGATATTATATCATGACATTTATCAAACGTCGCTAAAAAATAATATACCA
Found at i:24363 original size:24 final size:24
Alignment explanation
Indices: 24331--24386 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
24321 GGTAGAGCGC
24331 CTTATGCTAAAGTGACAAAACTTG
1 CTTATGCTAAAGTGACAAAACTTG
*
24355 CTTATGCTAAAGTGACAAATCTTG
1 CTTATGCTAAAGTGACAAAACTTG
*
24379 TTTATGCT
1 CTTATGCT
24387 TTTGCTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (24 bp):
CTTATGCTAAAGTGACAAAACTTG
Found at i:24730 original size:66 final size:66
Alignment explanation
Indices: 24619--24751 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
24609 AACAGCAATA
* *
24619 CATCAACTTGTTTTGAAGTGAAGCCTCAGAAAGACATTGAATCTGAAGAATGGTTGCAGAAATCG
1 CATCAACTTGTTTCGAAGTGAAGCCTCAGAAAGACATTGAATCTGAAGAATGGTTGCAGAAACCG
24684 T
66 T
*
24685 CATCGACTTGTTTCGAAGTGAAGCCTCAGAAAGACATTGAATCTGAAGAATGGTTGCAGAAACCG
1 CATCAACTTGTTTCGAAGTGAAGCCTCAGAAAGACATTGAATCTGAAGAATGGTTGCAGAAACCG
24750 T
66 T
24751 C
1 C
24752 GTTTTATGTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (66 bp):
CATCAACTTGTTTCGAAGTGAAGCCTCAGAAAGACATTGAATCTGAAGAATGGTTGCAGAAACCG
T
Found at i:28595 original size:71 final size:71
Alignment explanation
Indices: 28508--28708 Score: 393
Period size: 71 Copynumber: 2.8 Consensus size: 71
28498 ATGAGAAATC
*
28508 AATACATAATAAATAAACAAATTACAAACTAAACTCACATTCCGTGAGACTTGAACCCATGACCT
1 AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCATGACCT
28573 ACCTAT
66 ACCTAT
28579 AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCATGACCT
1 AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCATGACCT
28644 ACCTAT
66 ACCTAT
28650 AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCA
1 AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCA
28709 GAACCTCACA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 129 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (71 bp):
AATACATAATAAATAAACAAATTACAAATTAAACTCACATTCCGTGAGACTTGAACCCATGACCT
ACCTAT
Found at i:36365 original size:13 final size:13
Alignment explanation
Indices: 36347--36381 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
36337 TCAAGATTAT
36347 GAGAAAATGAAAA
1 GAGAAAATGAAAA
36360 GAGAAAATGAAAA
1 GAGAAAATGAAAA
36373 GAGAAAATG
1 GAGAAAATG
36382 GTGACTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (13 bp):
GAGAAAATGAAAA
Found at i:43094 original size:72 final size:72
Alignment explanation
Indices: 42947--43099 Score: 168
Period size: 72 Copynumber: 2.1 Consensus size: 72
42937 AGAAACAATC
* * *
42947 TGGGTTCTTTTCAGTCATCAGAGGTAAATATGGAAGCCCAAAGTTCTAGTGAGAATAAGAAAGTA
1 TGGGTTCTTTTCAGTCATCAGAGGGAAAGATGGAAGCCCAAAGTTCTAGTGAGAATAAGAAAATA
*****
43012 GTTGCTA
66 GAAAAGA
* *
43019 TGGGTTCTTTTGA-TGCATCAGAGGGAAAGATGGGAGCCCAAAGTTCTA-TGGAGAAT-AGAACA
1 TGGGTTCTTTTCAGT-CATCAGAGGGAAAGATGGAAGCCCAAAGTTCTAGT-GAGAATAAGAA-A
43081 ATAGAAAAGA
63 ATAGAAAAGA
43091 TGGGTTCTT
1 TGGGTTCTT
43100 CTTCTTCTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
71 6 0.09
72 62 0.91
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (72 bp):
TGGGTTCTTTTCAGTCATCAGAGGGAAAGATGGAAGCCCAAAGTTCTAGTGAGAATAAGAAAATA
GAAAAGA
Found at i:52033 original size:87 final size:87
Alignment explanation
Indices: 51860--52022 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
51850 TCAGAAAGTA
* *
51860 ATGTTCTGAAACTGCAGGTGAAATTTATTTGGAAAGATGTGGGGAAACTCATCTAGAGAAAGCAG
1 ATGTTCTGAAACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAG
51925 CAGAATGTTTTATTCTAGCTGG
66 CAGAATGTTTTATTCTAGCTGG
* * * * * *
51947 ATGTTTTGAAGCTGCAGGTCAAATTTATTTGGAAAAATGTGGGGGATCTCATCTGGAGAAAGCTG
1 ATGTTCTGAAACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAG
52012 CAGAATGTTTT
66 CAGAATGTTTT
52023 TTCCGTGCTG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (87 bp):
ATGTTCTGAAACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAG
CAGAATGTTTTATTCTAGCTGG
Found at i:52049 original size:87 final size:88
Alignment explanation
Indices: 51870--52050 Score: 228
Period size: 87 Copynumber: 2.1 Consensus size: 88
51860 ATGTTCTGAA
* *
51870 ACTGCAGGTGAAATTTATTTGGAAAGATGTGGGGAAACTCATCTAGAGAAAGCAGCAGAATGTTT
1 ACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAGCAGAATGTTT
**
51935 TATTCTAGCTGGATGTTTTGAAG
66 TATTCTAGCTGGATGTTTACAAG
* * * *
51958 -CTGCAGGTCAAATTTATTTGGAAAAATGTGGGGGATCTCATCTGGAGAAAGCTGCAGAATGTTT
1 ACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAGCAGAATGTTT
52022 T-TTCCGT-GCTGGGA-G-TTACAAG
66 TATT-C-TAGCT-GGATGTTTACAAG
52044 ACTGCAG
1 ACTGCAG
52051 CAGAAGTGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
86 7 0.09
87 70 0.86
88 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (88 bp):
ACTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAAACTCATCTAGAGAAAGCAGCAGAATGTTT
TATTCTAGCTGGATGTTTACAAG
Found at i:56065 original size:22 final size:22
Alignment explanation
Indices: 56037--56082 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
56027 AGAAATATAA
56037 GAGAAGTAAAAAGAAGAAATCT
1 GAGAAGTAAAAAGAAGAAATCT
56059 GAGAAGTAAAAAGAAGAAATCT
1 GAGAAGTAAAAAGAAGAAATCT
56081 GA
1 GA
56083 TGAATCAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.24, T:0.13
Consensus pattern (22 bp):
GAGAAGTAAAAAGAAGAAATCT
Found at i:71991 original size:16 final size:16
Alignment explanation
Indices: 71958--71989 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
71948 ACGGCTGCAC
71958 TTCTTTCTTTTTTCTT
1 TTCTTTCTTTTTTCTT
71974 TTCTTT-TTTTTT-TT
1 TTCTTTCTTTTTTCTT
71988 TT
1 TT
71990 TTAATTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTCTTTCTTTTTTCTT
Found at i:72829 original size:31 final size:32
Alignment explanation
Indices: 72775--72835 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
72765 ATCGAAGTCC
*
72775 TTTCACTCTATTCAAATGGTTGGTGTATTAGA
1 TTTCAATCTATTCAAATGGTTGGTGTATTAGA
*
72807 TTTCAATCTA-TCAAA-GGATTGGTTTATTA
1 TTTCAATCTATTCAAATGG-TTGGTGTATTA
72836 TAATTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 15 0.58
32 9 0.35
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (32 bp):
TTTCAATCTATTCAAATGGTTGGTGTATTAGA
Found at i:77905 original size:87 final size:87
Alignment explanation
Indices: 77756--77916 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
77746 TTAATGGTAA
** * * * *
77756 GTTTTGAAATTGCAGGTCAAATTTATTTGGAAAAATGTGGGGAATCTGCTGTAAAGAGAGCTGCT
1 GTTTTGAAAAGGCAGGTCAAATATATTTGGAAAAATGTGGGGAATCTGATGTAAAGAAAGCTGCA
*
77821 GAATGTTTTGTTCTTGCGGGAC
66 AAATGTTTTGTTCTTGCGGGAC
* **
77843 GTTTTGAAAAGGCAGGTCAAATATATTTGGAAAAATGTGGGGAATCTTATGTGGAGAAAGCTGCA
1 GTTTTGAAAAGGCAGGTCAAATATATTTGGAAAAATGTGGGGAATCTGATGTAAAGAAAGCTGCA
77908 AAATGTTTT
66 AAATGTTTT
77917 TTCCAAGCTG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (87 bp):
GTTTTGAAAAGGCAGGTCAAATATATTTGGAAAAATGTGGGGAATCTGATGTAAAGAAAGCTGCA
AAATGTTTTGTTCTTGCGGGAC
Found at i:92139 original size:2 final size:2
Alignment explanation
Indices: 92132--92158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92122 CGTCGTTTTA
92132 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
92159 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:101309 original size:9 final size:9
Alignment explanation
Indices: 101295--101319 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
101285 TTGATTAAGT
101295 AAGAAGAGG
1 AAGAAGAGG
101304 AAGAAGAGG
1 AAGAAGAGG
101313 AAGAAGA
1 AAGAAGA
101320 AGAGGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
AAGAAGAGG
Found at i:102006 original size:56 final size:56
Alignment explanation
Indices: 101910--102246 Score: 329
Period size: 56 Copynumber: 6.0 Consensus size: 56
101900 AATTTTCGAA
* * * *
101910 CTCTATAAAT-GGAGAAATGACACATATCGTTATGTGGTTGAACCGGGTATATTTGT
1 CTCTATAAATAGGA-AGATGACACATATCGCTATATGGTTGAACCGAGTATATTTGT
* * * * *
101966 CTCTATAAATAGGAAGATAACACGTATTGCTATATGGTTGAATCGTGTATATTTTGT
1 CTCTATAAATAGGAAGATGACACATATCGCTATATGGTTGAACCGAGTATA-TTTGT
* * * * * *
102023 CTTTATAAATGGGAAGATGACACATACCGTTATATGGTTAAACCGAGTATATTTGC
1 CTCTATAAATAGGAAGATGACACATATCGCTATATGGTTGAACCGAGTATATTTGT
* * * * * *
102079 CTTTACAAATAGAAATATGACACATATCACTATATGGTTGAATCC-AGTATATCTGT
1 CTCTATAAATAGGAAGATGACACATATCGCTATATGGTTGAA-CCGAGTATATTTGT
* * * * * * *
102135 CTATTTAGATAGGAATATGACACATATCGCTATATGGTTGAATCGAGTATATCTGC
1 CTCTATAAATAGGAAGATGACACATATCGCTATATGGTTGAACCGAGTATATTTGT
* * * *
102191 CTAC-ATAAATAGGAAAATGACACATATCGTTATATGATTGAATCGAGTATATTTGT
1 CT-CTATAAATAGGAAGATGACACATATCGCTATATGGTTGAACCGAGTATATTTGT
102247 TCCTTTTTAT
Statistics
Matches: 231, Mismatches: 45, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
55 1 0.00
56 179 0.77
57 51 0.22
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (56 bp):
CTCTATAAATAGGAAGATGACACATATCGCTATATGGTTGAACCGAGTATATTTGT
Found at i:102112 original size:113 final size:112
Alignment explanation
Indices: 101913--102244 Score: 373
Period size: 112 Copynumber: 2.9 Consensus size: 112
101903 TTTCGAACTC
* * * *
101913 TATAAATGGAGAAATGACACATATCGTTATGTGGTTGAACCGGGTATATTTGTCTCTATAAATAG
1 TATAAATGG-GAAATGACACATATCGTTATATGGTTGAACCGAGTATATTTGCCTATATAAATA-
* * * * *
101978 GAAGATAACACGTATTGCTATATGGTTGAATCGTGTATATTTTGTCT-T
64 GAAAATGACACATATCGCTATATGGTTGAATCGAGTATATTTTGTCTAT
* * * *
102026 TATAAATGGGAAGATGACACATACCGTTATATGGTTAAACCGAGTATATTTGCCTTTACAAATAG
1 TATAAATGGGAA-ATGACACATATCGTTATATGGTTGAACCGAGTATATTTGCCTATATAAATAG
* * *
102091 AAATATGACACATATCACTATATGGTTGAATCCAGTATA-TCTGTCTAT
65 AAA-ATGACACATATCGCTATATGGTTGAATCGAGTATATTTTGTCTAT
* * * * * *
102139 T-TAGATAGGAATATGACACATATCGCTATATGGTTGAATCGAGTATATCTGCCTACATAAATAG
1 TATAAATGGGAA-ATGACACATATCGTTATATGGTTGAACCGAGTATATTTGCCTATATAAATA-
* *
102203 GAAAATGACACATATCGTTATATGATTGAATCGAGTATATTT
64 GAAAATGACACATATCGCTATATGGTTGAATCGAGTATATTT
102245 GTTCCTTTTT
Statistics
Matches: 183, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
112 94 0.51
113 89 0.49
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (112 bp):
TATAAATGGGAAATGACACATATCGTTATATGGTTGAACCGAGTATATTTGCCTATATAAATAGA
AAATGACACATATCGCTATATGGTTGAATCGAGTATATTTTGTCTAT
Done.