Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024057.1 Corchorus olitorius cultivar O-4 contig24090, 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: 36851
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:672 original size:29 final size:29
Alignment explanation
Indices: 623--915 Score: 320
Period size: 29 Copynumber: 10.0 Consensus size: 29
613 CCAAAGAGAA
* *
623 CCTAGAGTATGCAAAAATGACCAAACTGCC
1 CCTAGA-TGTGCAAAAATGACCAAAATGCC
* *
653 CC-AGAATGTGTAAAAATGACCATAATGCC
1 CCTAG-ATGTGCAAAAATGACCAAAATGCC
* *
682 CCTGGATGGGCAAAAATGACCAAAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* * * *
711 CCTAGATGCGCAAAAATGACCATAGTACC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* * *
740 CCTAGATGTGCAAAAATAAACAAACTGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
*
769 CC-AGAATATGCAAAAATGACCAAAATGCC
1 CCTAG-ATGTGCAAAAATGACCAAAATGCC
** * *
798 CCTAGATACGCAAAAATGACCATAATACC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* * *
827 CCTAAATGTGCAAAAATAACCAAACTGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
* * *
856 CCAAAATATGCAAAAATGACCAAAATGCCC
1 CCTAGATGTGCAAAAATGACCAAAATG-CC
886 CCTAGATGTGCAAAAATGACCAAAATGCC
1 CCTAGATGTGCAAAAATGACCAAAATGCC
915 C
1 C
916 TTAAGCGTGC
Statistics
Matches: 218, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
28 2 0.01
29 184 0.84
30 32 0.15
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (29 bp):
CCTAGATGTGCAAAAATGACCAAAATGCC
Found at i:756 original size:87 final size:87
Alignment explanation
Indices: 633--907 Score: 376
Period size: 87 Copynumber: 3.1 Consensus size: 87
623 CCTAGAGTAT
* * * * * **
633 GCAAAAATGACCA-AACTGCCCC-AGAATGTGTAAAAATGACCATAA-TGCCCCTGGATGGGCAA
1 GCAAAAATGACCATAA-TACCCCTAG-ATGTGCAAAAATAACCA-AACTGCCCCAGAATATGCAA
695 AAATGACCAAAATGCCCCTAGATGC
63 AAATGACCAAAATGCCCCTAGATGC
* *
720 GCAAAAATGACCATAGTACCCCTAGATGTGCAAAAATAAACAAACTGCCCCAGAATATGCAAAAA
1 GCAAAAATGACCATAATACCCCTAGATGTGCAAAAATAACCAAACTGCCCCAGAATATGCAAAAA
*
785 TGACCAAAATGCCCCTAGATAC
66 TGACCAAAATGCCCCTAGATGC
* *
807 GCAAAAATGACCATAATACCCCTAAATGTGCAAAAATAACCAAACTGCCCCAAAATATGCAAAAA
1 GCAAAAATGACCATAATACCCCTAGATGTGCAAAAATAACCAAACTGCCCCAGAATATGCAAAAA
*
872 TGACCAAAATGCCCCCTAGATGT
66 TGACCAAAATG-CCCCTAGATGC
895 GCAAAAATGACCA
1 GCAAAAATGACCA
908 AAATGCCCTT
Statistics
Matches: 168, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
86 2 0.01
87 141 0.84
88 25 0.15
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.16
Consensus pattern (87 bp):
GCAAAAATGACCATAATACCCCTAGATGTGCAAAAATAACCAAACTGCCCCAGAATATGCAAAAA
TGACCAAAATGCCCCTAGATGC
Found at i:6277 original size:20 final size:20
Alignment explanation
Indices: 6238--6276 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
6228 CCCTTGCCTA
6238 AAAAACTAAAACTAGAAGAG
1 AAAAACTAAAACTAGAAGAG
*
6258 AAAAA-TAAATCTAG-AGAG
1 AAAAACTAAAACTAGAAGAG
6276 A
1 A
6277 GTCATGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.64, C:0.08, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAAACTAAAACTAGAAGAG
Found at i:8176 original size:28 final size:28
Alignment explanation
Indices: 8136--8191 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
8126 TGGCATTGAT
*
8136 TAAGATTATGATCAAATTAATGCATGCA
1 TAAGATTAGGATCAAATTAATGCATGCA
8164 TAAGATTAGGATCAAATTAATGCATGCA
1 TAAGATTAGGATCAAATTAATGCATGCA
8192 GACTCCCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (28 bp):
TAAGATTAGGATCAAATTAATGCATGCA
Found at i:9020 original size:42 final size:42
Alignment explanation
Indices: 8974--9056 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
8964 GACCGGGCTG
8974 GTGGCACGGATGGCCGGGCCATGGCAGGGCAAGTGACTTGGC
1 GTGGCACGGATGGCCGGGCCATGGCAGGGCAAGTGACTTGGC
* * * *
9016 GTGGCTCGGTTGGCCGGGCCATGGCCGGGCATGTGACTTGG
1 GTGGCACGGATGGCCGGGCCATGGCAGGGCAAGTGACTTGG
9057 TGCGGCTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (42 bp):
GTGGCACGGATGGCCGGGCCATGGCAGGGCAAGTGACTTGGC
Found at i:9064 original size:42 final size:42
Alignment explanation
Indices: 8984--9065 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
8974 GTGGCACGGA
*
8984 TGGCCGGGCCATGGCAGGGCAAGTGACTTGGCGTGGCTCGGT
1 TGGCCGGGCCATGGCAGGGCAAGTGACTTGGCGCGGCTCGGT
* * *
9026 TGGCCGGGCCATGGCCGGGCATGTGACTTGGTGCGGCTCG
1 TGGCCGGGCCATGGCAGGGCAAGTGACTTGGCGCGGCTCG
9066 ATTATGGCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.10, C:0.26, G:0.45, T:0.20
Consensus pattern (42 bp):
TGGCCGGGCCATGGCAGGGCAAGTGACTTGGCGCGGCTCGGT
Found at i:11911 original size:27 final size:27
Alignment explanation
Indices: 11881--11953 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
11871 TAGAAAATAA
11881 AGAAAAACATTTTTTTTCTA-AAAACGC
1 AGAAAAAC-TTTTTTTTCTAGAAAACGC
* * *
11908 AGAAACAATTTTTTTTTTTAGAAAACGG
1 AGAAA-AACTTTTTTTTCTAGAAAACGC
11936 A-AAAAATCTTTTTTTTCT
1 AGAAAAA-CTTTTTTTTCT
11954 TTTAAAAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 27 0.71
28 9 0.24
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (27 bp):
AGAAAAACTTTTTTTTCTAGAAAACGC
Found at i:11932 original size:29 final size:30
Alignment explanation
Indices: 11890--11970 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
11880 AAGAAAAACA
*
11890 TTTTTTTTCTAAAAACGCAGAAACAAT-TT
1 TTTTTTTTATAAAAACGCAGAAACAATCTT
* *
11919 TTTTTTTTA-GAAAACG--GAAAAAATCTT
1 TTTTTTTTATAAAAACGCAGAAACAATCTT
*
11946 TTTTTTCTTTTAAAAACGCA-AAACA
1 TTTTTT-TTATAAAAACGCAGAAACA
11971 CAAAACAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
26 7 0.17
27 8 0.20
28 8 0.20
29 14 0.34
30 4 0.10
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (30 bp):
TTTTTTTTATAAAAACGCAGAAACAATCTT
Found at i:11938 original size:26 final size:26
Alignment explanation
Indices: 11881--11951 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
11871 TAGAAAATAA
*
11881 AGAAAAACA-TTTTTTTTCTAAAAACG
1 AGAAAAA-ATTTTTTTTTTTAAAAACG
*
11907 CAGAAACAATTTTTTTTTTTAGAAAACG
1 -AGAAAAAATTTTTTTTTTTA-AAAACG
*
11935 -GAAAAAATCTTTTTTTT
1 AGAAAAAATTTTTTTTTT
11952 CTTTTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 16 0.42
27 16 0.42
28 6 0.16
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (26 bp):
AGAAAAAATTTTTTTTTTTAAAAACG
Found at i:11968 original size:28 final size:27
Alignment explanation
Indices: 11883--11973 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 27
11873 GAAAATAAAG
*
11883 AAAAAC-A-TTTTTTTTCTAAAAACGC
1 AAAAACAATTTTTTTTTTTAAAAACGC
* *
11908 AGAAACAATTTTTTTTTTTAGAAAACGG
1 AAAAACAATTTTTTTTTTTA-AAAACGC
*
11936 AAAAA-ATCTTTTTTTTCTTTTAAAAACGC
1 AAAAACA--ATTTTTTT-TTTTAAAAACGC
11965 AAAACACAA
1 AAAA-ACAA
11974 AACAATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
25 5 0.10
26 1 0.02
27 11 0.22
28 10 0.20
29 17 0.33
30 6 0.12
31 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (27 bp):
AAAAACAATTTTTTTTTTTAAAAACGC
Found at i:18962 original size:18 final size:19
Alignment explanation
Indices: 18925--18963 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18915 AAAGAGAAAA
* *
18925 TTAGCGCGGAGCTTAGTTT
1 TTAGCGCAGAGCTGAGTTT
18944 TTAGCGCAGAGC-GAGTTT
1 TTAGCGCAGAGCTGAGTTT
18962 TT
1 TT
18964 TTGCACGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (19 bp):
TTAGCGCAGAGCTGAGTTT
Found at i:27488 original size:57 final size:57
Alignment explanation
Indices: 27378--27491 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
27368 CTAATCATAA
* * *
27378 CAATCTCTCTAGCAAACTCTCAATCTAATCAACCCAAAACCCATACCATCCAAAGGT
1 CAATCTCTCTAGCAAACTCTCAATATAATCAACCCAAAACCCATAACACCCAAAGGT
* * * *
27435 CAATCTCTCTAGCAAATTCTCAATATAATCAACCCGAAGCTCATAACACCCAAAGGT
1 CAATCTCTCTAGCAAACTCTCAATATAATCAACCCAAAACCCATAACACCCAAAGGT
27492 GTATCGCTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.22
Consensus pattern (57 bp):
CAATCTCTCTAGCAAACTCTCAATATAATCAACCCAAAACCCATAACACCCAAAGGT
Found at i:31077 original size:16 final size:16
Alignment explanation
Indices: 31058--31113 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
31048 GTCCGAATGT
31058 GAACCCGAAATTGCCC
1 GAACCCGAAATTGCCC
31074 GAACCCGAAATTGCCC
1 GAACCCGAAATTGCCC
* *
31090 GAACCCGAAAATACCC
1 GAACCCGAAATTGCCC
*
31106 AAACCCGA
1 GAACCCGA
31114 GGCAGCCCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.38, G:0.16, T:0.09
Consensus pattern (16 bp):
GAACCCGAAATTGCCC
Found at i:31214 original size:21 final size:20
Alignment explanation
Indices: 31173--31216 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
31163 TAATAATTTA
* **
31173 TAAAATAAAATATTTTTTTT
1 TAAAAAAAAATATTTCCTTT
31193 TAAAAAAAACATATTTCCTTT
1 TAAAAAAAA-ATATTTCCTTT
31214 TAA
1 TAA
31217 TATTAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAAAAAATATTTCCTTT
Found at i:34622 original size:16 final size:15
Alignment explanation
Indices: 34584--34625 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
34574 ACAGAGGTTG
34584 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
34599 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
34614 ACTAGAAAACAA
1 AC-AGAAAACAA
34626 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.