Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012415.1 Corchorus olitorius cultivar O-4 contig12448, 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: 34618
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:6572 original size:6 final size:6
Alignment explanation
Indices: 6563--6595 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
6553 GAATGAGAAA
6563 AAGATG AAGATG AAGATG AAGATG AAGATG AAG
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAG
6596 CTTAGGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (6 bp):
AAGATG
Found at i:19273 original size:21 final size:21
Alignment explanation
Indices: 19248--19328 Score: 135
Period size: 21 Copynumber: 3.9 Consensus size: 21
19238 GCTGCTCTAA
19248 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
*
19269 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGTACC
19290 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* *
19311 TAATCTAATCTATACAGT
1 TAATCTCATCTGTACAGT
19329 TGCCAAACAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:24120 original size:14 final size:15
Alignment explanation
Indices: 24101--24149 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
24091 TGTTAAGAAT
24101 TTTCTTTCTTC-TTC
1 TTTCTTTCTTCTTTC
24115 TTTCTTT-TTCTTTC
1 TTTCTTTCTTCTTTC
* *
24129 TTTTTTTCTTTTTTC
1 TTTCTTTCTTCTTTC
*
24144 CTTCTT
1 TTTCTT
24150 CTTAAGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 10 0.34
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTCTTCTTTC
Found at i:24142 original size:10 final size:10
Alignment explanation
Indices: 24100--24141 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
24090 TTGTTAAGAA
24100 TTTTCTTTCT
1 TTTTCTTTCT
*
24110 TCTTCTTTCT
1 TTTTCTTTCT
24120 TTTTCTTTC-
1 TTTTCTTTCT
24129 TTTT-TTTCT
1 TTTTCTTTCT
24138 TTTT
1 TTTT
24142 TCCTTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 8 0.28
10 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:25899 original size:133 final size:133
Alignment explanation
Indices: 25661--25926 Score: 514
Period size: 133 Copynumber: 2.0 Consensus size: 133
25651 GAGCTCTCTT
25661 CTTCTCTTTTATATATGTTACTAATGAAGCCTTGTTGAATTTGTTATTTCTGTAGTAAACTTTGA
1 CTTCTCTTTTATATATGTTACTAATGAAGCCTTGTTGAATTTGTTATTTCTGTAGTAAACTTTGA
*
25726 GAATAAGAGTAAGGGTATTAGTAAGGGCATCTTCATAGCCGCTGTGGTTTGCAGTATTTCCTGTG
66 GAATAAGAGTAAGGGTATTAGTAAGGGCATCTTCATAGCCGCTGTGGTTGGCAGTATTTCCTGTG
25791 CAG
131 CAG
*
25794 CTTCTCTTTTATATATGTTACTAATGAAGCCTTGTTGAATTTGTTATTTCTGTAGTGAACTTTGA
1 CTTCTCTTTTATATATGTTACTAATGAAGCCTTGTTGAATTTGTTATTTCTGTAGTAAACTTTGA
25859 GAATAAGAGTAAGGGTATTAGTAAGGGCATCTTCATAGCCGCTGTGGTTGGCAGTATTTCCTGTG
66 GAATAAGAGTAAGGGTATTAGTAAGGGCATCTTCATAGCCGCTGTGGTTGGCAGTATTTCCTGTG
25924 CAG
131 CAG
25927 TTGCATTGTC
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (133 bp):
CTTCTCTTTTATATATGTTACTAATGAAGCCTTGTTGAATTTGTTATTTCTGTAGTAAACTTTGA
GAATAAGAGTAAGGGTATTAGTAAGGGCATCTTCATAGCCGCTGTGGTTGGCAGTATTTCCTGTG
CAG
Found at i:31642 original size:13 final size:12
Alignment explanation
Indices: 31621--31655 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
31611 AATAAAGTAA
31621 TAATACTATTAT
1 TAATACTATTAT
31633 TAATTACTATTAT
1 TAA-TACTATTAT
31646 TAATACTATT
1 TAATACTATT
31656 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:33663 original size:3 final size:3
Alignment explanation
Indices: 33655--33757 Score: 125
Period size: 3 Copynumber: 33.7 Consensus size: 3
33645 TTGTTTAGAT
* * * * **
33655 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATTT TTG GCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
*
33701 TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33749 ATAA ATA AT
1 AT-A ATA AT
33758 GTAATAACTA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 83 0.95
4 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Done.