Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012622.1 Corchorus olitorius cultivar O-4 contig12655, 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: 31180
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4110 original size:3 final size:3
Alignment explanation
Indices: 4102--4141 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4092 TCCTGCCTGA
4102 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4142 AATTAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:14681 original size:8 final size:8
Alignment explanation
Indices: 14661--14696 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
14651 TCATTTAAGA
14661 GCCCAAG-
1 GCCCAAGT
14668 GCCCAAGT
1 GCCCAAGT
14676 GCCCAAGT
1 GCCCAAGT
14684 GCCCAAGT
1 GCCCAAGT
14692 GCCCA
1 GCCCA
14697 TCTTTTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.25, C:0.42, G:0.25, T:0.08
Consensus pattern (8 bp):
GCCCAAGT
Found at i:17579 original size:15 final size:15
Alignment explanation
Indices: 17561--17610 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
17551 GGTTTCTTTA
17561 TTTTCCAAAATCTTC
1 TTTTCCAAAATCTTC
** * *
17576 TTTTGGAATTACCTTC
1 TTTTCCAA-AATCTTC
17592 TTTTCCAAAATCTTC
1 TTTTCCAAAATCTTC
17607 TTTT
1 TTTT
17611 GGATTTGCTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (15 bp):
TTTTCCAAAATCTTC
Found at i:17599 original size:31 final size:31
Alignment explanation
Indices: 17532--17613 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
17522 ATTTTATTAA
* * *
17532 TTTCCAAAATCTTCTTTTGG-GTTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGAATTACCTTAT
*
17562 TTTCCAAAATCTTCTTTTGGAATTACCTTCT
1 TTTCCAAAATCTTCTTTTGGAATTACCTTAT
17593 TTTCCAAAATCTTCTTTTGGA
1 TTTCCAAAATCTTCTTTTGGA
17614 TTTGCTTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 20 0.43
31 27 0.57
ACGTcount: A:0.21, C:0.20, G:0.09, T:0.51
Consensus pattern (31 bp):
TTTCCAAAATCTTCTTTTGGAATTACCTTAT
Found at i:22297 original size:27 final size:27
Alignment explanation
Indices: 22230--22291 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
22220 AGTGTACTTG
* **
22230 AAATGACTAAAATAACCCTGGACGTGC
1 AAATGACCAAAATGGCCCTGGACGTGC
22257 AAATGACCAAAATGGCCCTGGACGTGC
1 AAATGACCAAAATGGCCCTGGACGTGC
22284 AAATGACC
1 AAATGACC
22292 CCAATGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGGCCCTGGACGTGC
Found at i:27525 original size:74 final size:74
Alignment explanation
Indices: 27404--27566 Score: 326
Period size: 74 Copynumber: 2.2 Consensus size: 74
27394 AAATTAACAG
27404 AAATATCTGAATTTTACAGAAAAATGTTTTGATAAATTAACAGAAATAGAAATACACAACACAGC
1 AAATATCTGAATTTTACAGAAAAATGTTTTGATAAATTAACAGAAATAGAAATACACAACACAGC
27469 TAGGACGTA
66 TAGGACGTA
27478 AAATATCTGAATTTTACAGAAAAATGTTTTGATAAATTAACAGAAATAGAAATACACAACACAGC
1 AAATATCTGAATTTTACAGAAAAATGTTTTGATAAATTAACAGAAATAGAAATACACAACACAGC
27543 TAGGACGTA
66 TAGGACGTA
27552 AAATATCTGAATTTT
1 AAATATCTGAATTTT
27567 GGATGAACCT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 89 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (74 bp):
AAATATCTGAATTTTACAGAAAAATGTTTTGATAAATTAACAGAAATAGAAATACACAACACAGC
TAGGACGTA
Found at i:29530 original size:19 final size:18
Alignment explanation
Indices: 29506--29544 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29496 AAATATCTCC
*
29506 AATTAGGGCTAATTGCACA
1 AATTAGAGC-AATTGCACA
*
29525 AATTAGATCAATTGCACA
1 AATTAGAGCAATTGCACA
29543 AA
1 AA
29545 AAACAAGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (18 bp):
AATTAGAGCAATTGCACA
Done.