Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018117.1 Corchorus olitorius cultivar O-4 contig18150, 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: 10354
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4158 original size:32 final size:32
Alignment explanation
Indices: 4054--4143 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
4044 TGCTGGAAAA
4054 TAGCGGCGTCTATTGAAACAAACGCCCTTATT
1 TAGCGGCGTCTATTGAAACAAACGCCCTTATT
*
4086 TAGCGGCGTCTATTCAAACAAACGCCCTTATT
1 TAGCGGCGTCTATTGAAACAAACGCCCTTATT
**
4118 TAGCGGCGTCTATTGAAGTAAACGCC
1 TAGCGGCGTCTATTGAAACAAACGCC
4144 GCTAATTAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (32 bp):
TAGCGGCGTCTATTGAAACAAACGCCCTTATT
Found at i:4622 original size:26 final size:25
Alignment explanation
Indices: 4589--4639 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4579 AAAACAATTT
*
4589 TTGTTTTCAATTTCGATTCATCCTTG
1 TTGTTTTCAATTAC-ATTCATCCTTG
**
4615 TTGTTTTCGGTTACATTCATCCTTG
1 TTGTTTTCAATTACATTCATCCTTG
4640 GGTTTTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.53
Consensus pattern (25 bp):
TTGTTTTCAATTACATTCATCCTTG
Found at i:4650 original size:24 final size:25
Alignment explanation
Indices: 4604--4650 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4594 TTCAATTTCG
*
4604 ATTCATCCTTGTTGTTTTCGGTTAC
1 ATTCATCCTTGTGGTTTTCGGTTAC
*
4629 ATTCATCCTTG-GGTTTTTGGTT
1 ATTCATCCTTGTGGTTTTCGGTT
4651 GCTTAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.53
Consensus pattern (25 bp):
ATTCATCCTTGTGGTTTTCGGTTAC
Found at i:5757 original size:21 final size:21
Alignment explanation
Indices: 5717--5757 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5707 TACCTATGGC
**
5717 TCCAAATTTTATTGGCAGTCA
1 TCCAAATTTTATTGAAAGTCA
*
5738 TCCAAATTTTCTTGAAAGTC
1 TCCAAATTTTATTGAAAGTC
5758 CTTACTGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (21 bp):
TCCAAATTTTATTGAAAGTCA
Found at i:7375 original size:27 final size:28
Alignment explanation
Indices: 7337--7521 Score: 209
Period size: 27 Copynumber: 6.6 Consensus size: 28
7327 TTGCTGGTCC
7337 GGCTCTCC-CTTCGACCCCAGCAGTGGA
1 GGCTCTCCACTTCGACCCCAGCAGTGGA
* *
7364 GGCTCTCC-CTTCGACCCCAGCAGTAGT
1 GGCTCTCCACTTCGACCCCAGCAGTGGA
*
7391 GGACCCTCCCACTTCGACCCCAGCAGTGGA
1 GG-CTCT-CCACTTCGACCCCAGCAGTGGA
* *
7421 GGCTCTCC-CTTCGACCCCAGCAGTAGT
1 GGCTCTCCACTTCGACCCCAGCAGTGGA
*
7448 GGATCCTCCCACTTCGACCCCAGCAGTGGA
1 GGCT-CT-CCACTTCGACCCCAGCAGTGGA
**
7478 TCCTC-CCACTTCGACCCCAGCAGTGGA
1 GGCTCTCCACTTCGACCCCAGCAGTGGA
**
7505 TCCTC-CCACTTCGACCC
1 GGCTCTCCACTTCGACCC
7522 GGGTCGGTTC
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
27 86 0.62
28 7 0.05
29 8 0.06
30 37 0.27
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (28 bp):
GGCTCTCCACTTCGACCCCAGCAGTGGA
Found at i:7406 original size:57 final size:57
Alignment explanation
Indices: 7345--7521 Score: 290
Period size: 57 Copynumber: 3.2 Consensus size: 57
7335 CCGGCTCTCC
*
7345 CTTCGACCCCAGCAGTGGAGGCTCTCCCTTCGACCCCAGCAGTAGTGGACCCTCCCA
1 CTTCGACCCCAGCAGTGGAGGCTCTCCCTTCGACCCCAGCAGTAGTGGATCCTCCCA
7402 CTTCGACCCCAGCAGTGGAGGCTCTCCCTTCGACCCCAGCAGTAGTGGATCCTCCCA
1 CTTCGACCCCAGCAGTGGAGGCTCTCCCTTCGACCCCAGCAGTAGTGGATCCTCCCA
**
7459 CTTCGACCCCAGCAGTGGATCCTC-CCACTTCGACCCCAGC---AGTGGATCCTCCCA
1 CTTCGACCCCAGCAGTGGAGGCTCTCC-CTTCGACCCCAGCAGTAGTGGATCCTCCCA
7513 CTTCGACCC
1 CTTCGACCC
7522 GGGTCGGTTC
Statistics
Matches: 116, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
54 23 0.20
56 2 0.02
57 91 0.78
ACGTcount: A:0.18, C:0.43, G:0.21, T:0.19
Consensus pattern (57 bp):
CTTCGACCCCAGCAGTGGAGGCTCTCCCTTCGACCCCAGCAGTAGTGGATCCTCCCA
Found at i:7443 original size:84 final size:84
Alignment explanation
Indices: 7337--7521 Score: 252
Period size: 84 Copynumber: 2.2 Consensus size: 84
7327 TTGCTGGTCC
* *
7337 GGCTCTCCCTTCGACCCCAGCAGTGGAGGCT-CT-CC-CTTCGACCCCAGCAGTAGTGGACCCTC
1 GGCTCTCCCTTCGACCCCAGCAGTAGAGGATCCTCCCACTTCGACCCCAGC---AGTGGACCCTC
7399 CCACTTCGACCCCAGCAGTGGA
63 CCACTTCGACCCCAGCAGTGGA
* *
7421 GGCTCTCCCTTCGACCCCAGCAGTAGTGGATCCTCCCACTTCGACCCCAGCAGTGGATCCTCCCA
1 GGCTCTCCCTTCGACCCCAGCAGTAGAGGATCCTCCCACTTCGACCCCAGCAGTGGACCCTCCCA
7486 CTTCGACCCCAGCAGTGGA
66 CTTCGACCCCAGCAGTGGA
**
7505 TCCTC-CCACTTCGACCC
1 GGCTCTCC-CTTCGACCC
7522 GGGTCGGTTC
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
83 2 0.02
84 72 0.79
85 2 0.02
86 2 0.02
87 13 0.14
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (84 bp):
GGCTCTCCCTTCGACCCCAGCAGTAGAGGATCCTCCCACTTCGACCCCAGCAGTGGACCCTCCCA
CTTCGACCCCAGCAGTGGA
Found at i:9934 original size:32 final size:32
Alignment explanation
Indices: 9898--10083 Score: 327
Period size: 32 Copynumber: 5.8 Consensus size: 32
9888 GTGTGAAAAG
*
9898 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
9930 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
9962 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
9994 AAAACGCCCTTATATAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
* * *
10026 AAAATGCCCTTATTTAGCAGCGTCTACAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
10058 AAAACGCCCTTATTTAGCGGCGTCTA
1 AAAACGCCCTTATTTAGCGGCGTCTA
10084 AATTATCAAG
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 146 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
Done.