Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009871.1 Corchorus olitorius cultivar O-4 contig09903, 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: 7011
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:2917 original size:56 final size:56
Alignment explanation
Indices: 2850--2986 Score: 179
Period size: 56 Copynumber: 2.4 Consensus size: 56
2840 GCAATGGAGT
* *
2850 AGAAATGACCAAAATGCCCCTGGACGTGC-AAATGA-CTTAAATACCCCTGAATGTG
1 AGAAATGACCAAAATGCCCCTGGACGTGCAAAATGACCAT-AATACCACTGAATGTG
* * *
2905 CAGAAATGACCAAAATGCCCCTGAAGGTGCAAAAATGACCATAATGCCACTGAATGTG
1 -AGAAATGACCAAAATGCCCCTGGACGTGC-AAAATGACCATAATACCACTGAATGTG
*
2963 AAAAATGACCAAAATGCCCCTGGA
1 AGAAATGACCAAAATGCCCCTGGA
2987 TTTTTGAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
56 27 0.38
57 22 0.31
58 20 0.28
59 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (56 bp):
AGAAATGACCAAAATGCCCCTGGACGTGCAAAATGACCATAATACCACTGAATGTG
Found at i:2978 original size:28 final size:29
Alignment explanation
Indices: 2852--3011 Score: 164
Period size: 29 Copynumber: 5.6 Consensus size: 29
2842 AATGGAGTAG
* *
2852 AAATGACCAAAATGCCCCTGGACGTGC--
1 AAATGACCAAAATGCCCCTGAATGTGCAA
** * *
2879 AAATGACTTAAATACCCCTGAATGTGCAG
1 AAATGACCAAAATGCCCCTGAATGTGCAA
*
2908 AAATGACCAAAATGCCCCTGAAGGTGCAA
1 AAATGACCAAAATGCCCCTGAATGTGCAA
* *
2937 AAATGACCATAATGCCACTGAATGTG-AA
1 AAATGACCAAAATGCCCCTGAATGTGCAA
* * ***
2965 AAATGACCAAAATGCCCCTGGATTTTTGA
1 AAATGACCAAAATGCCCCTGAATGTGCAA
*
2994 AAATGACCAAAACGCCCC
1 AAATGACCAAAATGCCCC
3012 CTAGGTGATC
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 22 0.20
28 23 0.21
29 65 0.59
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCTGAATGTGCAA
Found at i:2997 original size:57 final size:57
Alignment explanation
Indices: 2852--3002 Score: 164
Period size: 57 Copynumber: 2.6 Consensus size: 57
2842 AATGGAGTAG
* * * * *
2852 AAATGACCAAAATGCCCCTGGACGTGCAAATGA-CTTAAATACCCCTGAATGTGCAG
1 AAATGACCAAAATGCCCCTGGATGTGAAAATGACCATAAATACCACTGAATGTGCAA
* * *
2908 AAATGACCAAAATGCCCCTGAAGGTGCAAAAATGACCAT-AATGCCACTGAATGTG-AA
1 AAATGACCAAAATGCCCCTGGATGTG--AAAATGACCATAAATACCACTGAATGTGCAA
*
2965 AAATGACCAAAATGCCCCTGGATTTTTGAAAATGACCA
1 AAATGACCAAAATGCCCCTGGA--TGTGAAAATGACCA
3003 AAACGCCCCC
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
56 24 0.30
57 32 0.40
58 20 0.25
59 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (57 bp):
AAATGACCAAAATGCCCCTGGATGTGAAAATGACCATAAATACCACTGAATGTGCAA
Found at i:3351 original size:50 final size:50
Alignment explanation
Indices: 3287--3389 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
3277 AAGAGATCCT
* *
3287 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAA
1 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTACGGAAA
*
3337 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAA
1 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTACGGAAA
3387 CGA
1 CGA
3390 ATAATTGACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (50 bp):
CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTACGGAAA
Found at i:3397 original size:23 final size:23
Alignment explanation
Indices: 3367--3412 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3357 GCCTATGTTG
*
3367 ATAATTGACTCGTACGGAAACGA
1 ATAATTGACTCATACGGAAACGA
*
3390 ATAATTGACTCATATGGAAACGA
1 ATAATTGACTCATACGGAAACGA
3413 GTTTGGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (23 bp):
ATAATTGACTCATACGGAAACGA
Found at i:3436 original size:73 final size:73
Alignment explanation
Indices: 3317--3462 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
3307 GCCTATGTTG
* *
3317 ATAATTGACCCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTAC
1 ATAATTGACCCATATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTAC
3382 GGAAACGA
66 GGAAACGA
* * *
3390 ATAATTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTAT
1 ATAATTGACCCATATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTAC
3455 GGAAACGA
66 GGAAACGA
3463 GTTTGGCTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (73 bp):
ATAATTGACCCATATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTAC
GGAAACGA
Found at i:3448 original size:50 final size:50
Alignment explanation
Indices: 3390--3935 Score: 923
Period size: 50 Copynumber: 10.9 Consensus size: 50
3380 ACGGAAACGA
*
3390 ATAATTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* *
3440 ATAATTGACCCGTATGGAAACGAGTTTGGCTTGTGGAAGAGCCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
3490 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* *
3540 ATAATTGACGCGTATGGAAACGAGTTTGGCTTGTGGAAAAGGCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
3590 ATAATTGAC-CGATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
1 ATAATTGACTCG-TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* * *
3640 ATAATTAACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCTTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* *
3690 ATAATTGACTCGTATGGAAACAAGTTTGACTTGTGGAAAAGCCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* * *
3740 ATAATTGACTCGTATGCAAAACGAGTTTGACTTGTGGAAAAGCCTATATTG
1 ATAATTGACTCGTATG-GAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
* *
3791 ATAATTGACTCGTATGGAAACGAGTTTGGCTAGTGGAAAAGCCTATGGTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
*
3841 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTCGAAAAGCCTATGTTG
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
3891 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
3936 AACATTCGGA
Statistics
Matches: 465, Mismatches: 28, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
49 2 0.00
50 414 0.89
51 49 0.11
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (50 bp):
ATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
Found at i:3509 original size:123 final size:123
Alignment explanation
Indices: 3287--3512 Score: 425
Period size: 123 Copynumber: 1.8 Consensus size: 123
3277 AAGAGATCCT
3287 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAGCTTGGCTTGTG
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAGCTTGGCTTGTG
3352 GAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAATAATTGACTCATATGGAAA
66 GAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAATAATTGACTCATATGGAAA
*
3410 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAGTTTGGCTTGTG
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAGCTTGGCTTGTG
* *
3475 GAAGAGCCTATGTTGATAATTGACTCGTATGGAAACGA
66 GAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGA
3513 GTTTGGCTTG
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 100 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (123 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAGCTTGGCTTGTG
GAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAATAATTGACTCATATGGAAA
Found at i:4120 original size:13 final size:12
Alignment explanation
Indices: 4088--4117 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4078 AATGTGCGAT
4088 CAACTTGAAAAA
1 CAACTTGAAAAA
4100 CAACTTGAAAAA
1 CAACTTGAAAAA
*
4112 TAACTT
1 CAACTT
4118 TGAGTCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (12 bp):
CAACTTGAAAAA
Found at i:4126 original size:90 final size:91
Alignment explanation
Indices: 4018--4195 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 91
4008 ATACCTTCGG
4018 AAAATAACTCTGAATCTGATGTTGTAACTG-AAACTTCTTGATTGATGATGAAAAAGGACCAA-T
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAACT
4081 GTGC-GATCAACTTGAAAAACAACTTGA
66 -TGCTG-TCAACTTGAAAAACAACTTGA
* * * *
4108 AAAATAACTTTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGCAAGAGGACCAACT
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAACT
*
4173 TGCTGTCAACTTGAAAAATAACT
66 TGCTGTCAACTTGAAAAACAACT
4196 CTAAGTCTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
90 28 0.35
91 50 0.62
92 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (91 bp):
AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAACT
TGCTGTCAACTTGAAAAACAACTTGA
Found at i:4361 original size:26 final size:26
Alignment explanation
Indices: 4330--4391 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
4320 AAACTTTGCT
4330 TTCTTGATTTTGCTTCATTTCCGCTC
1 TTCTTGATTTTGCTTCATTTCCGCTC
4356 TTCTTGATTTTGCTTCATTTCCGCTC
1 TTCTTGATTTTGCTTCATTTCCGCTC
4382 TTCTTGATTT
1 TTCTTGATTT
4392 GTCCTTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.08, C:0.24, G:0.11, T:0.56
Consensus pattern (26 bp):
TTCTTGATTTTGCTTCATTTCCGCTC
Found at i:4877 original size:50 final size:50
Alignment explanation
Indices: 4733--4880 Score: 217
Period size: 50 Copynumber: 3.0 Consensus size: 50
4723 TCAATGTCCT
* * * * * *
4733 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCGATCTTACT
1 TTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACA
4783 TTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACA
1 TTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACA
*
4833 TTGAAAAGGC-AATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 TTGAAAA-GCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
4881 TTGTAAAACT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 88 0.98
51 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACA
Found at i:6010 original size:7 final size:8
Alignment explanation
Indices: 5993--6017 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5983 AGTGCCTTTA
5993 TTTTCATT
1 TTTTCATT
6001 TTTTCATT
1 TTTTCATT
6009 TTTTCATT
1 TTTTCATT
6017 T
1 T
6018 CATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Done.