Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017027.1 Corchorus olitorius cultivar O-4 contig17060, 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: 10877
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:3196 original size:26 final size:27
Alignment explanation
Indices: 3167--3217 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3157 AAATTATAAG
*
3167 TGAACATA-AAGTGACCAAAATGCCTC
1 TGAACATACAAATGACCAAAATGCCTC
**
3193 TGAATGTACAAATGACCAAAATGCC
1 TGAACATACAAATGACCAAAATGCC
3218 CCTGGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (27 bp):
TGAACATACAAATGACCAAAATGCCTC
Found at i:3545 original size:50 final size:50
Alignment explanation
Indices: 3483--3663 Score: 292
Period size: 50 Copynumber: 3.6 Consensus size: 50
3473 CGATCAACTT
* * * *
3483 CTTTGAATTGTCTTCCAA-TCTAATATTAAAAGGGCCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC
3533 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
3583 CTTTGAACTGTCTACAAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
3633 CTTTGAATTGTCTACCAATTCAATCTTAAAA
1 CTTTGAACTGTCTACCAATTCAATCTTAAAA
3664 AGGTAATGCA
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 121 0.98
51 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:3783 original size:50 final size:50
Alignment explanation
Indices: 3718--4053 Score: 557
Period size: 50 Copynumber: 6.7 Consensus size: 50
3708 AGGTTTGAAA
3718 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
* *
3768 TGACTCGTATTGAAACGAGTTGGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
* **
3818 TGACTCGTATGGAAACGAGCTTGGCTTGT-GAGAAAGCCTACGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGA-AAAGCCTGTGTTGATAAT
*
3868 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATGAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
*
3918 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATGAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
* *
3968 TGACTCGTATGGAAATGAGTTCGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
* *
4018 TGACTCGTATGGAAACGAGTTTGACTTATGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
4054 TCAAAGCATT
Statistics
Matches: 266, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
49 2 0.01
50 262 0.98
51 2 0.01
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.31
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
Found at i:4339 original size:88 final size:88
Alignment explanation
Indices: 4140--4341 Score: 271
Period size: 91 Copynumber: 2.3 Consensus size: 88
4130 ATACCTTTGG
* ** * *
4140 AAAATAACTCTGAATCTGAAATTGTAACTGAAAACTTCTTGATTGGTGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGCAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
4205 TGCGGTCAACTTGAAAAACAACTTGA
66 TGCGGTCAACTTG---AACAACTTGA
* *
4231 AAAATAACTCTGAGTCTGATGTTGCAACTGAAAACTTCTTGATTGATGATGAAAAAGGAGCAATT
1 AAAATAACTCTGAGTCTGATGTTGCAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
* *
4296 TGCGGTCAATTTTG-ATAACTTGA
66 TGCGGTCAA-CTTGAACAACTTGA
*
4319 AGAATAACTCTGAGTCTGATGTT
1 AAAATAACTCTGAGTCTGATGTT
4342 ATGATTAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
88 30 0.30
91 67 0.67
92 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (88 bp):
AAAATAACTCTGAGTCTGATGTTGCAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
TGCGGTCAACTTGAACAACTTGA
Found at i:4810 original size:50 final size:50
Alignment explanation
Indices: 4756--4899 Score: 202
Period size: 50 Copynumber: 2.9 Consensus size: 50
4746 CTTCAATGTC
* *
4756 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * *
4806 CTTTGAAAAGCAAATTTTGATATTGAACTCACGAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
4856 --TTGAAAAGCGAATTTTGACCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAAT
4900 TTTATTGTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
48 39 0.47
50 44 0.53
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:4880 original size:48 final size:48
Alignment explanation
Indices: 4758--4911 Score: 209
Period size: 48 Copynumber: 3.1 Consensus size: 48
4748 TCAATGTCCT
* * *
4758 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * *
4806 CTTTGAAAAGCAAATTTTGATATTGAACTCACGAATGGAAAGCAATTTTA
1 --TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
4856 TTGAAAAGCGAATTTTGACCTTGAACTCATAAATGGAAAGCAATTTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
4904 TTGTAAAA
1 TTG-AAAA
4912 CTTCTTGTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 46 0.50
49 4 0.04
50 42 0.46
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (48 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:5184 original size:1 final size:1
Alignment explanation
Indices: 5178--5208 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
5168 ACCCTTAGAG
*
5178 TTTTTTTTTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5209 GCACTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:5507 original size:5 final size:5
Alignment explanation
Indices: 5491--5556 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
5481 TCCATTCTCT
*
5491 TTTGA TTTTGA TTTGA TTTGA TTT-- TTTGA TTTTTA TTTGA TTT-- TTTGA
1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA -TTTGA TTTGA TTTGA TTTGA
5539 -TTGA CTTTGA TTTGA TTT
1 TTTGA -TTTGA TTTGA TTT
5557 TGGATTGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
3 6 0.12
4 4 0.08
5 28 0.55
6 13 0.25
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.67
Consensus pattern (5 bp):
TTTGA
Found at i:5507 original size:11 final size:11
Alignment explanation
Indices: 5491--5568 Score: 63
Period size: 11 Copynumber: 6.8 Consensus size: 11
5481 TCCATTCTCT
5491 TTTGATTTTGA
1 TTTGATTTTGA
5502 TTTGA-TTTGA
1 TTTGATTTTGA
*
5512 TTTTTTGATTTTTA
1 ---TTTGATTTTGA
5526 TTTGATTTTTTGA
1 TTTGA--TTTTGA
*
5539 -TTGACTTTGA
1 TTTGATTTTGA
5549 TTTGATTTTGGA
1 TTTGATTTT-GA
5561 -TTGATTTT
1 TTTGATTTT
5569 TTTTTTGATG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
10 10 0.18
11 25 0.45
12 6 0.11
13 10 0.18
14 4 0.07
ACGTcount: A:0.17, C:0.01, G:0.17, T:0.65
Consensus pattern (11 bp):
TTTGATTTTGA
Found at i:5519 original size:18 final size:18
Alignment explanation
Indices: 5496--5551 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 18
5486 TCTCTTTTGA
5496 TTTTGATTTGATTTGATT
1 TTTTGATTTGATTTGATT
*
5514 TTTTGATTTTTATTTGATT
1 TTTTGA-TTTGATTTGATT
5533 TTTTGA-TTGACTTTGATT
1 TTTTGATTTGA-TTTGATT
5551 T
1 T
5552 GATTTTGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 14 0.41
19 17 0.50
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (18 bp):
TTTTGATTTGATTTGATT
Found at i:5520 original size:24 final size:22
Alignment explanation
Indices: 5490--5557 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 22
5480 ATCCATTCTC
5490 TTTTGATTTTGATTTGATTTGATT
1 TTTTGATTTTGATTTGATTT--TT
*
5514 TTTTGATTTTTATTTGATTTTT
1 TTTTGATTTTGATTTGATTTTT
* *
5536 TGATTGACTTTGATTTGATTTT
1 T-TTTGATTTTGATTTGATTTT
5558 GGATTGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
22 3 0.08
23 17 0.44
24 19 0.49
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTTGATTTTGATTTGATTTTT
Found at i:5988 original size:20 final size:20
Alignment explanation
Indices: 5941--5991 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
5931 TTCCAAGTGC
5941 TTTTTTTCATTTTCTTTTTCA
1 TTTTTTTCATTTTCTTTTT-A
*
5962 TTTTTTTCTTTTCTTCTTTTTTA
1 TTTTTTTC-ATT-TTC-TTTTTA
5985 TTTTTTT
1 TTTTTTT
5992 ATTATTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 11 0.42
24 5 0.19
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTCATTTTCTTTTTA
Found at i:6502 original size:76 final size:76
Alignment explanation
Indices: 6361--6508 Score: 181
Period size: 76 Copynumber: 1.9 Consensus size: 76
6351 ACTCACCTTG
* * * * *
6361 AAATCATCGCTTTGACCAAAACTGATTTTGAAACATCTTTTGATTAAAACACCGTCATTCTTTTG
1 AAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTTG
*
6426 CTTACAGCTCA
66 CTCACAGCTCA
* * * * *
6437 AAATCATAGTTTTGACTAAAACTGATTTTGAAAAATCTTTTTGTTTGAAAC-TCATCATCCCTTT
1 AAATCATAGCTTTGACCAAAACTGATTTTGAAAAATC-TTTTGATTAAAACACCATCATCCCTTT
6501 GCTCACAG
65 GCTCACAG
6509 TCCAGATAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
76 49 0.82
77 11 0.18
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (76 bp):
AAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTTG
CTCACAGCTCA
Found at i:7869 original size:21 final size:22
Alignment explanation
Indices: 7834--7875 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
7824 GAAGGTTTTA
7834 ATGGAATGCATGAATGAATGCC
1 ATGGAATGCATGAATGAATGCC
*
7856 ATGGCATG-ATGAATGAATGC
1 ATGGAATGCATGAATGAATGC
7876 ATGAGGCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGGAATGCATGAATGAATGCC
Done.