Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022516.1 Corchorus olitorius cultivar O-4 contig22549, 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: 3997
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:1943 original size:19 final size:19
Alignment explanation
Indices: 1919--1959 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1909 ATTGTTATAT
1919 ATATATATAATTCATAAAA
1 ATATATATAATTCATAAAA
1938 ATATATATAATTCATAAAA
1 ATATATATAATTCATAAAA
1957 ATA
1 ATA
1960 ACATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATATAATTCATAAAA
Found at i:1983 original size:18 final size:17
Alignment explanation
Indices: 1962--2004 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1952 TAAAAATAAC
1962 ATATATATAT-TAAATTA
1 ATATATATATGT-AATTA
*
1979 TATATATGTATGTAATTA
1 -ATATATATATGTAATTA
1997 ATATATAT
1 ATATATAT
2005 TTCAAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
ATATATATATGTAATTA
Found at i:3315 original size:18 final size:18
Alignment explanation
Indices: 3292--3326 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3282 ACAAAAATTG
3292 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
3310 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
3327 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:3402 original size:11 final size:12
Alignment explanation
Indices: 3369--3402 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3359 AACAAAATAT
3369 TATATAATTATA
1 TATATAATTATA
3381 TATATATATTATA
1 TATATA-ATTATA
3394 TA-ATAATTA
1 TATATAATTA
3403 AATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 9 0.43
13 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATAATTATA
Found at i:3478 original size:19 final size:18
Alignment explanation
Indices: 3454--3499 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3444 TTTATAATTT
* *
3454 TTATTAATAATATATATTA
1 TTATTAAT-ATATAAATGA
3473 TTATTAATATATAAATGA
1 TTATTAATATATAAATGA
3491 TTATATAAT
1 TTAT-TAAT
3500 TAATGAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATTAATATATAAATGA
Found at i:3503 original size:23 final size:19
Alignment explanation
Indices: 3419--3494 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 19
3409 AATTTAAATA
3419 TATTAGATAATAGAATATTAT
1 TATTA-ATAATA-AATATTAT
* *
3440 TATT-TTTAT-AAT-TT-T
1 TATTAATAATAAATATTAT
*
3455 TATTAATAATATATATTAT
1 TATTAATAATAAATATTAT
3474 TATTAATATATAAATGATTAT
1 TATTAATA-ATAAAT-ATTAT
3495 ATAATTAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.12
16 5 0.12
17 5 0.12
18 2 0.05
19 12 0.28
20 5 0.12
21 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTAATAATAAATATTAT
Found at i:3717 original size:19 final size:20
Alignment explanation
Indices: 3687--3750 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
3677 TTGACACTGT
3687 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
3708 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
3727 TTAGGTACTGTACATATGAGA
1 TTA-GCACTGTACAGATGAGA
3748 TTA
1 TTA
3751 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:3738 original size:21 final size:19
Alignment explanation
Indices: 3693--3750 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
3683 CTGTTTAGCA
3693 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
3712 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
3733 ACTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
3751 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Done.