Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020403.1 Corchorus olitorius cultivar O-4 contig20436, 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: 55014
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:1905 original size:31 final size:31
Alignment explanation
Indices: 1864--2322 Score: 551
Period size: 31 Copynumber: 14.8 Consensus size: 31
1854 CAAGGCATGC
* * * *
1864 CACGTGTCACTTTTTGGTACACATGGCGTGA
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * * *
1895 CACGTATCAC-TTTTGATACATGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * * * *
1925 CACATGTCGCTTTTTGGTACATGTGACGTGC
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
*
1956 CATGTGTCGCTTTTTGCTACACGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * * * *
1987 CACATGTCACTTTTTGGTACATGTGGCGTGC
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
*
2018 CATGTGTCGCTTTTTGCTACACGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * *
2049 CACATGTCGCTTTTTGGTACATGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
*
2080 CATGTGTCGCTTTTTGCTACACGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * *
2111 CACATGTCGCTTTTTGGTACATGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* *
2142 CATGTGTTGCTTTTTGCTACACGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * *
2173 CACATGTCGCTTTTTGCTACACATGGCATGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* * * *
2204 CACATGTCGCTTTTTGGTACATGTGGCGTGC
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
*
2235 CATGTGTCGCTTTTTGCTACACGTGGCGTGT
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
* *
2266 CACATGTCGCTTTTTGCTACACGTGGCGTGG
1 CACGTGTCGCTTTTTGCTACACGTGGCGTGT
*
2297 CACGTGTCGCTTTTTGGTACACGTGG
1 CACGTGTCGCTTTTTGCTACACGTGG
2323 TGTGCTACGT
Statistics
Matches: 361, Mismatches: 66, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
30 23 0.06
31 338 0.94
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (31 bp):
CACGTGTCGCTTTTTGCTACACGTGGCGTGT
Found at i:1989 original size:62 final size:62
Alignment explanation
Indices: 1868--2322 Score: 615
Period size: 62 Copynumber: 7.4 Consensus size: 62
1858 GCATGCCACG
* ** * * * * * *
1868 TGTCACTTTTTGGTACACATGGCGTGACACGTATCAC-TTTTGATACATGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
* *
1929 TGTCGCTTTTTGGTACATGTGACGTGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
* *
1991 TGTCACTTTTTGGTACATGTGGCGTGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
2053 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
*
2115 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTTGCTTTTTGCTACACGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
* ** * ** * * * **
2177 TGTCGCTTTTTGCTACACATGGCATGTCACATGTCGCTTTTTGGTACATGTGGCGTGCCATG
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
* * ** * *
2239 TGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGGCACG
1 TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
*
2301 TGTCGCTTTTTGGTACACGTGG
1 TGTCGCTTTTTGGTACATGTGG
2323 TGTGCTACGT
Statistics
Matches: 359, Mismatches: 34, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
61 29 0.08
62 330 0.92
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.37
Consensus pattern (62 bp):
TGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACA
Found at i:2057 original size:93 final size:93
Alignment explanation
Indices: 1861--2327 Score: 621
Period size: 93 Copynumber: 5.0 Consensus size: 93
1851 TTACAAGGCA
* * * * * * * * * *
1861 TGCCACGTGTCACTTTTTGGTACACATGGCGTGACACGTATCAC-TTTTGATACATGTGGCGTGT
1 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
*
1925 CACATGTCGCTTTTTGGTACATGTGACG
66 CACATGTCGCTTTTTGGTACATGTGGCG
* * * *
1953 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCACTTTTTGGTACATGTGGCGTGC
1 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
** * *
2018 CATGTGTCGCTTTTTGCTACACGTGGCG
66 CACATGTCGCTTTTTGGTACATGTGGCG
* ** * * **
2046 TGTCACATGTCGCTTTTTGGTACATGTGGCGTGTCATGTGTCGCTTTTTGCTACACGTGGCGTGT
1 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
2111 CACATGTCGCTTTTTGGTACATGTGGCG
66 CACATGTCGCTTTTTGGTACATGTGGCG
* * * *
2139 TGTCATGTGTTGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACATGGCATGT
1 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
2204 CACATGTCGCTTTTTGGTACATGTGGCG
66 CACATGTCGCTTTTTGGTACATGTGGCG
*
2232 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGG
1 TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
* * *
2297 CACGTGTCGCTTTTTGGTACACGTGGTG
66 CACATGTCGCTTTTTGGTACATGTGGCG
2325 TGC
1 TGC
2328 TACGTCGAAC
Statistics
Matches: 328, Mismatches: 46, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
92 37 0.11
93 291 0.89
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (93 bp):
TGCCATGTGTCGCTTTTTGCTACACGTGGCGTGTCACATGTCGCTTTTTGCTACACGTGGCGTGT
CACATGTCGCTTTTTGGTACATGTGGCG
Found at i:3258 original size:14 final size:14
Alignment explanation
Indices: 3239--3271 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3229 TGAAAATTTC
3239 TTTTTT-TTTTTGGG
1 TTTTTTCTTTTT-GG
3253 TTTTTTCTTTTTGG
1 TTTTTTCTTTTTGG
3267 TTTTT
1 TTTTT
3272 AGATTAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTTTGG
Found at i:17822 original size:1 final size:1
Alignment explanation
Indices: 17787--17815 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
17777 GAGTTTTTTG
17787 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17816 CTAAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17971 original size:21 final size:21
Alignment explanation
Indices: 17945--17987 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17935 GCTGAAGTTG
17945 TGGCGTATATAAGCTGACCAC
1 TGGCGTATATAAGCTGACCAC
17966 TGGCGTATATAAGCTGACCAC
1 TGGCGTATATAAGCTGACCAC
17987 T
1 T
17988 TCAACTGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TGGCGTATATAAGCTGACCAC
Found at i:26228 original size:12 final size:12
Alignment explanation
Indices: 26211--26237 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
26201 GTATCATATA
26211 ATTTTATTTGAG
1 ATTTTATTTGAG
26223 ATTTTATTTGAG
1 ATTTTATTTGAG
26235 ATT
1 ATT
26238 GCTTGTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (12 bp):
ATTTTATTTGAG
Found at i:26904 original size:3 final size:3
Alignment explanation
Indices: 26896--26994 Score: 110
Period size: 3 Copynumber: 30.7 Consensus size: 3
26886 CCATCCCACG
*
26896 TAA TAA TAA TATA TATA TTA TAA TATA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TA-A TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
26943 TAA TAA TAA TAA TAA TATA TAA TATA TAA TATA TAA TATA TAA TATA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TA-A TAA TA-A TAA TA-A
26990 TAA TA
1 TAA TA
26995 TCGTGAGATT
Statistics
Matches: 86, Mismatches: 2, Indels: 16
0.83 0.02 0.15
Matches are distributed among these distances:
2 2 0.02
3 60 0.70
4 24 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:26924 original size:7 final size:7
Alignment explanation
Indices: 26896--26995 Score: 131
Period size: 7 Copynumber: 14.9 Consensus size: 7
26886 CCATCCCACG
26896 TAATA-A
1 TAATATA
26902 TAATATA
1 TAATATA
26909 T-ATATTA
1 TAATA-TA
26916 TAATATA
1 TAATATA
26923 TAATA-A
1 TAATATA
26929 TAATA-A
1 TAATATA
*
26935 TAAAATAA
1 TAATAT-A
26943 TAATA-A
1 TAATATA
26949 TAATA-A
1 TAATATA
26955 TAATATA
1 TAATATA
26962 TAATATA
1 TAATATA
26969 TAATATA
1 TAATATA
26976 TAATATA
1 TAATATA
26983 TAATATA
1 TAATATA
26990 TAATAT
1 TAATAT
26996 CGTGAGATTA
Statistics
Matches: 86, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
6 31 0.36
7 47 0.55
8 8 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATATA
Found at i:30225 original size:32 final size:32
Alignment explanation
Indices: 30184--30247 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
30174 TCTAAGATCT
30184 AAGATTGTATTT-AGATTACCTCAAAAAAAAAA
1 AAGATTGTATTTAAGATTACCT-AAAAAAAAAA
*
30216 AAGATTGTATTTAGAGATTCCCTAAAAAAAAA
1 AAGATTGTATTTA-AGATTACCTAAAAAAAAA
30248 GATTGTACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 9 0.31
34 8 0.28
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (32 bp):
AAGATTGTATTTAAGATTACCTAAAAAAAAAA
Found at i:30244 original size:34 final size:32
Alignment explanation
Indices: 30184--30247 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
30174 TCTAAGATCT
*
30184 AAGATTGTATTTAGATTACCTCAAAAAAAAAA
1 AAGATTGTATTTAGATTACCTAAAAAAAAAAA
*
30216 AAGATTGTATTTAGAGATTCCCTAAAAAAAAA
1 AAGATTGTATTT--AGATTACCTAAAAAAAAA
30248 GATTGTACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.43
34 16 0.57
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (32 bp):
AAGATTGTATTTAGATTACCTAAAAAAAAAAA
Found at i:39148 original size:21 final size:21
Alignment explanation
Indices: 39124--39164 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39114 ATTGATTGAA
39124 AATAACAAAT-GACTAAAATGC
1 AATAA-AAATCGACTAAAATGC
*
39145 AATAAAAATCTACTAAAATG
1 AATAAAAATCGACTAAAATG
39165 GTTCAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (21 bp):
AATAAAAATCGACTAAAATGC
Found at i:42899 original size:18 final size:18
Alignment explanation
Indices: 42876--42910 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42866 GGAAGCAGCC
*
42876 GTTGAACAATCCGAACCT
1 GTTGAACAATCAGAACCT
*
42894 GTTGAAGAATCAGAACC
1 GTTGAACAATCAGAACC
42911 AGGACCTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (18 bp):
GTTGAACAATCAGAACCT
Found at i:43670 original size:19 final size:19
Alignment explanation
Indices: 43627--43666 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
43617 TATTACAATC
43627 AAAG-AACTTTGATTTCAA
1 AAAGTAACTTTGATTTCAA
*
43645 GAAGTAACTTTGA-TTCAA
1 AAAGTAACTTTGATTTCAA
43663 AAAG
1 AAAG
43667 GTAAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (19 bp):
AAAGTAACTTTGATTTCAA
Found at i:49715 original size:15 final size:15
Alignment explanation
Indices: 49695--49726 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49685 ACAAACACTA
49695 TTACTATTACTTAGT
1 TTACTATTACTTAGT
49710 TTACTATTACTTAGT
1 TTACTATTACTTAGT
49725 TT
1 TT
49727 TTTCATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (15 bp):
TTACTATTACTTAGT
Found at i:51984 original size:19 final size:19
Alignment explanation
Indices: 51960--51996 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
51950 TGTACCTGTA
51960 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
*
51979 ACCGTTTCATCACCGTTT
1 ACCGTTTCACCACCGTTT
51997 TGGGTCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:52506 original size:30 final size:30
Alignment explanation
Indices: 52459--52519 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
52449 ATGACTTTTA
52459 TTTTCTTTTGCCACTAATAGATCCTAAGAC
1 TTTTCTTTTGCCACTAATAGATCCTAAGAC
* *
52489 TTTT-TTTTGGCATCTAATTGATCCTAAGAC
1 TTTTCTTTTGCCA-CTAATAGATCCTAAGAC
52519 T
1 T
52520 AGATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTTCTTTTGCCACTAATAGATCCTAAGAC
Found at i:52749 original size:3 final size:3
Alignment explanation
Indices: 52741--52789 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
52731 TTTAGTTGAT
52741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52789 T
1 T
52790 ATTCATAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53975 original size:25 final size:25
Alignment explanation
Indices: 53941--53989 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
53931 GATTGATTTG
53941 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
53966 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
53990 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:54996 original size:19 final size:19
Alignment explanation
Indices: 54972--55009 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54962 TTAATGATTA
54972 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
54991 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
55010 TAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (19 bp):
GCCAACTTATTTTAACTTT
Done.