Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022052.1 Corchorus olitorius cultivar O-4 contig22085, 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: 16264
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Found at i:2288 original size:2 final size:2
Alignment explanation
Indices: 2276--2309 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2266 CCTTTGTCAC
*
2276 AT AT AT GT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2310 GGAATTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2557 original size:43 final size:43
Alignment explanation
Indices: 2418--2747 Score: 440
Period size: 43 Copynumber: 7.8 Consensus size: 43
2408 ATAAGGAGAA
* *
2418 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAA
1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
*
2462 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
2503 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
2546 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG--ATACAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
2587 ATGTCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
2630 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG--ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
2671 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
2714 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
2748 TTGGCTATTG
Statistics
Matches: 251, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
41 108 0.43
42 4 0.02
43 110 0.44
44 29 0.12
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.43
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:2571 original size:84 final size:84
Alignment explanation
Indices: 2416--2747 Score: 574
Period size: 84 Copynumber: 3.9 Consensus size: 84
2406 CCATAAGGAG
**
2416 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAAATGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCTGTGTTATATAT
2481 GTGTTTGGGGACTTTGATAT
65 GTGTTTGGGGACTTTGATAT
2501 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
*
2566 TGTTTGGGGACTTTGATAC
66 TGTTTGGGGACTTTGATAT
* * *
2585 AGATGTCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
2650 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * *
2669 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
2734 TGTTTGGGGACTTT
66 TGTTTGGGGACTTT
2748 TTGGCTATTG
Statistics
Matches: 236, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
84 203 0.86
85 33 0.14
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:14762 original size:27 final size:27
Alignment explanation
Indices: 14727--14827 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
14717 TCAAAAATTT
*
14727 AGGGGCATTTTAGTCATTTGCACGTCC
1 AGGGGCATTTTGGTCATTTGCACGTCC
* ** *
14754 AGGGGCATTTGGGTCATTTTTAC-ACC
1 AGGGGCATTTTGGTCATTTGCACGTCC
* *
14780 TAGGGGGCATTTTGGTCATTTGCATGTTC
1 -A-GGGGCATTTTGGTCATTTGCACGTCC
*
14809 AGGGGTATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
14828 TAGGGTCACT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
26 2 0.03
27 37 0.63
28 19 0.32
29 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.29, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACGTCC
Found at i:15106 original size:17 final size:17
Alignment explanation
Indices: 15084--15118 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15074 ATATGCATGC
15084 TTTCACATTAGTTTAAT
1 TTTCACATTAGTTTAAT
15101 TTTCACATTAGTTTAAT
1 TTTCACATTAGTTTAAT
15118 T
1 T
15119 AATTATAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTCACATTAGTTTAAT
Done.