Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019166.1 Corchorus olitorius cultivar O-4 contig19199, 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: 4705
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Found at i:2225 original size:6 final size:6
Alignment explanation
Indices: 2216--2260 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2206 ATATTACTAT
* * *
2216 TATTAC TATTAC TATTAC TATTAC TATTAT TATTAT TACTAC TAT
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TAT
2261 ATAAAATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:2225 original size:15 final size:15
Alignment explanation
Indices: 2207--2256 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
2197 CTTACTACTA
2207 TATTACTATTATTAC
1 TATTACTATTATTAC
2222 TATTAC---TATTAC
1 TATTACTATTATTAC
*
2234 TATTACTATTATTAT
1 TATTACTATTATTAC
2249 TATTACTA
1 TATTACTA
2257 CTATATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 12 0.39
15 19 0.61
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTACTATTATTAC
Found at i:2799 original size:26 final size:26
Alignment explanation
Indices: 2770--2829 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
2760 ACTTTAGTAT
2770 TATCAATATCAAGTAACAATTAACAA
1 TATCAATATCAAGTAACAATTAACAA
2796 TATCAATATCAAGTAACAATTAACAA
1 TATCAATATCAAGTAACAATTAACAA
*
2822 TATTAATA
1 TATCAATA
2830 AACACCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (26 bp):
TATCAATATCAAGTAACAATTAACAA
Found at i:3507 original size:21 final size:22
Alignment explanation
Indices: 3481--3547 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
3471 CACACTAAAT
* *
3481 AAAA-TTGGTAACCGCACTATG
1 AAAATTTGATAACCACACTATG
3502 AAAATTTTGATAACCACACTATG
1 AAAA-TTTGATAACCACACTATG
* * *
3525 AAATTTTGATAACCTCCCTATG
1 AAAATTTGATAACCACACTATG
3547 A
1 A
3548 GAATGAAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 4 0.10
22 17 0.44
23 18 0.46
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (22 bp):
AAAATTTGATAACCACACTATG
Found at i:3531 original size:22 final size:22
Alignment explanation
Indices: 3377--3547 Score: 132
Period size: 22 Copynumber: 7.7 Consensus size: 22
3367 ACAAGCATTC
*
3377 GATAACCACACTATGAAATTTG
1 GATAACCACACTATGAAATTTT
* *
3399 GGTAACCACACTATGAAATTTC
1 GATAACCACACTATGAAATTTT
* * * *
3421 GATAATCTCAATGTGAAATTTT
1 GATAACCACACTATGAAATTTT
** *
3443 GATAATCTGC-CTATAAAATTTT
1 GATAA-CCACACTATGAAATTTT
* * *
3465 AATAATCACACTAAAT-AAA-ATT
1 GATAACCACACT--ATGAAATTTT
* *
3487 GGTAACCGCACTATGAAAATTTT
1 GATAACCACACTATG-AAATTTT
3510 GATAACCACACTATGAAATTTT
1 GATAACCACACTATGAAATTTT
* *
3532 GATAACCTCCCTATGA
1 GATAACCACACTATGA
3548 GAATGAAACT
Statistics
Matches: 114, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.02
21 1 0.01
22 90 0.79
23 19 0.17
24 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
GATAACCACACTATGAAATTTT
Found at i:3610 original size:22 final size:23
Alignment explanation
Indices: 3576--3652 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 23
3566 CTCTATATGT
*
3576 ATTTTCGATAACCTTTCC-ATAAA
1 ATTTTCGATAACC-TCCCTATAAA
3599 ATTTTC-ATAACCTCCCTATAAA
1 ATTTTCGATAACCTCCCTATAAA
* * **
3621 ATTTT-GTTAACCTCTCTAGGAA
1 ATTTTCGATAACCTCCCTATAAA
3643 ATTTT-GATAA
1 ATTTTCGATAA
3653 GCACAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 3 0.07
22 37 0.80
23 6 0.13
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (23 bp):
ATTTTCGATAACCTCCCTATAAA
Found at i:3704 original size:22 final size:22
Alignment explanation
Indices: 3679--3761 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
3669 CCTCCCTCCC
* *
3679 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCTA
3701 TATGAAATTTTGATAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
* *
3722 CTATGAAGTTTTGATAATCTCTA
1 -TATGAAATTTTGATAACCTCTA
* *
3745 TATGAAAATTTGGTAAC
1 TATGAAATTTTGATAAC
3762 AACACTACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 2 0.04
22 45 0.90
23 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:3801 original size:44 final size:44
Alignment explanation
Indices: 3682--3802 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 44
3672 CCCTCCCTAT
* * * * * *
3682 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACACTAT
1 GAAATTTTGATAATCTCTATATGAAATTTTGGTAACAACACTAC
* *
3726 GAAGTTTTGATAATCTCTATATGAAAATTTGGTAACAACACTAC
1 GAAATTTTGATAATCTCTATATGAAATTTTGGTAACAACACTAC
* * *
3770 GAAATTTTGATAATCTTTCTATGTAATTTTGGT
1 GAAATTTTGATAATCTCTATATGAAATTTTGGT
3803 TTGATTGTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (44 bp):
GAAATTTTGATAATCTCTATATGAAATTTTGGTAACAACACTAC
Found at i:4577 original size:5 final size:5
Alignment explanation
Indices: 4567--4704 Score: 240
Period size: 5 Copynumber: 26.8 Consensus size: 5
4557 CAATTACGTA
4567 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
4617 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
4667 TTTTG TTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTG TTTTG -TTTTG -TTTTG -TTTTG -TTTTG TTTT
4705 A
Statistics
Matches: 132, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 109 0.83
6 23 0.17
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Done.