Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012267.1 Corchorus olitorius cultivar O-4 contig12300, 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: 26530
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:144 original size:29 final size:30
Alignment explanation
Indices: 102--175 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
92 CTCATTTTTG
* *
102 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
131 AAACATAAGGGATTACTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
162 AAACATAAGGGATT
1 AAACATAAGGGATT
176 TTTTTGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:2181 original size:6 final size:6
Alignment explanation
Indices: 2167--2205 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2157 TATGGGCCAA
* *
2167 TAAAAT TACAAT TACAAT TAAAAT TAAAAT TAAAAT TAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAA
2206 TCCAACCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAAAT
Found at i:3162 original size:6 final size:6
Alignment explanation
Indices: 3151--3213 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
3141 TTGACAGCTT
* * *
3151 AACAAA AAC-AA AACGAA AAC-GA AACAAAA AACAAAA AACAAA AATAAA
1 AACAAA AACAAA AACAAA AACAAA AAC-AAA AAC-AAA AACAAA AACAAA
3199 AACAAAA AACAAA AA
1 AAC-AAA AACAAA AA
3214 AACAGACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
5 9 0.18
6 23 0.47
7 17 0.35
ACGTcount: A:0.81, C:0.14, G:0.03, T:0.02
Consensus pattern (6 bp):
AACAAA
Found at i:3184 original size:7 final size:7
Alignment explanation
Indices: 3172--3214 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
3162 AACGAAAACG
3172 AAACAAA
1 AAACAAA
3179 AAACAAA
1 AAACAAA
3186 AAAC-AA
1 AAACAAA
*
3192 AAA-TAA
1 AAACAAA
3198 AAACAAA
1 AAACAAA
3205 AAACAAA
1 AAACAAA
3212 AAA
1 AAA
3215 ACAGACCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (7 bp):
AAACAAA
Found at i:3199 original size:19 final size:19
Alignment explanation
Indices: 3177--3213 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3167 AAACGAAACA
3177 AAAAACAAAAAACAAAAAT
1 AAAAACAAAAAACAAAAAT
3196 AAAAACAAAAAACAAAAA
1 AAAAACAAAAAACAAAAA
3214 AACAGACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (19 bp):
AAAAACAAAAAACAAAAAT
Found at i:21542 original size:3 final size:3
Alignment explanation
Indices: 21534--21563 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21524 CACAATTGAT
21534 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21564 AAAGAAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24933 original size:46 final size:46
Alignment explanation
Indices: 24880--25009 Score: 260
Period size: 46 Copynumber: 2.8 Consensus size: 46
24870 CTTATATTTA
24880 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATTATTCTAGC
1 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATTATTCTAGC
24926 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATTATTCTAGC
1 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATTATTCTAGC
24972 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATT
1 ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATT
25010 TTCCTTCCTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (46 bp):
ATTGTTTATAATTTAGATTTGATTGATAACTCTTGATTATTCTAGC
Found at i:26130 original size:6 final size:6
Alignment explanation
Indices: 26119--26154 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
26109 TGCCTTCTTT
*
26119 TATATC TATATC TATATT TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATAT-C TATAT
26155 AAATCTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (6 bp):
TATATC
Found at i:26140 original size:18 final size:19
Alignment explanation
Indices: 26117--26154 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
26107 TTTGCCTTCT
26117 TTTATATCTATAT-CTATA
1 TTTATATCTATATACTATA
26135 TTTATATCTATATACTATA
1 TTTATATCTATATACTATA
26154 T
1 T
26155 AAATCTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATATCTATATACTATA
Done.