Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020608.1 Corchorus olitorius cultivar O-4 contig20641, 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: 25649
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:1827 original size:20 final size:20
Alignment explanation
Indices: 1802--1839 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1792 CTAAAAATGA
1802 GATATAAATA-AATAATTAAG
1 GATATAAA-ACAATAATTAAG
1822 GATATAAAACAATAATTA
1 GATATAAAACAATAATTA
1840 GAGGGTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (20 bp):
GATATAAAACAATAATTAAG
Found at i:3710 original size:15 final size:15
Alignment explanation
Indices: 3678--3707 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3668 TAAATTTCAA
3678 TAAAATAAAATATAT
1 TAAAATAAAATATAT
3693 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
3707 T
1 T
3708 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:9326 original size:2 final size:2
Alignment explanation
Indices: 9319--9367 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
9309 TTTTTATCTT
*
9319 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9360 TA -A TA TA T
1 TA TA TA TA T
9368 TCTATAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9368 original size:8 final size:9
Alignment explanation
Indices: 9318--9373 Score: 59
Period size: 8 Copynumber: 6.8 Consensus size: 9
9308 ATTTTTATCT
9318 TTATATATA
1 TTATATATA
9327 -TATATATA
1 TTATATATA
*
9335 -TACATATA
1 TTATATATA
9343 -TATATATA
1 TTATATATA
9351 -TATATATA
1 TTATATATA
9359 TTA-ATATA
1 TTATATATA
*
9367 TTCTATA
1 TTATATA
9374 AGTTTAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 37 0.88
9 5 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (9 bp):
TTATATATA
Found at i:10899 original size:3 final size:3
Alignment explanation
Indices: 10888--10988 Score: 184
Period size: 3 Copynumber: 33.7 Consensus size: 3
10878 CAACAACAAC
* *
10888 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAG AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10936 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10984 AAT AA
1 AAT AA
10989 ATACTAAAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:15487 original size:13 final size:13
Alignment explanation
Indices: 15465--15496 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
15455 AAGACATTGA
15465 AATAGT-ATTAAT
1 AATAGTAATTAAT
15477 AATAGTAATTAAT
1 AATAGTAATTAAT
15490 AATAGTA
1 AATAGTA
15497 TTATTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (13 bp):
AATAGTAATTAAT
Found at i:17075 original size:10 final size:10
Alignment explanation
Indices: 17059--17126 Score: 86
Period size: 10 Copynumber: 7.0 Consensus size: 10
17049 ATATACATAC
17059 ATATATGTAT
1 ATATATGTAT
*
17069 ATGTATGTAT
1 ATATATGTAT
*
17079 ATATATGTAC
1 ATATATGTAT
17089 ATATATGTAT
1 ATATATGTAT
*
17099 ATACA--TAT
1 ATATATGTAT
*
17107 ATGTATGTAT
1 ATATATGTAT
17117 ATATATGTAT
1 ATATATGTAT
17127 TCTTGGCTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.12
10 42 0.88
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (10 bp):
ATATATGTAT
Found at i:17083 original size:4 final size:4
Alignment explanation
Indices: 17045--17122 Score: 57
Period size: 4 Copynumber: 19.5 Consensus size: 4
17035 CCAAGAATAC
* * * * * * *
17045 ATAT ATAT ACAT ACAT ATAT GTAT ATGT ATGT ATAT ATAT GTAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
17093 ATGT ATAT ACAT ATAT GTAT GTAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
17123 GTATTCTTGG
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:17083 original size:14 final size:14
Alignment explanation
Indices: 17042--17126 Score: 80
Period size: 14 Copynumber: 5.9 Consensus size: 14
17032 GAGCCAAGAA
* **
17042 TACATATATATACA
1 TACATATATGTATG
17056 TACATATATGTATATG
1 TACATATATG--TATG
** *
17072 TATGTATATATATG
1 TACATATATGTATG
*
17086 TACATATATGTATA
1 TACATATATGTATG
17100 TACATATATGTATG
1 TACATATATGTATG
*
17114 TATATATATGTAT
1 TACATATATGTAT
17127 TCTTGGCTCC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
14 48 0.84
16 9 0.16
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (14 bp):
TACATATATGTATG
Found at i:17276 original size:13 final size:12
Alignment explanation
Indices: 17255--17289 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
17245 AATAAAGTAA
17255 TAATACTATTAT
1 TAATACTATTAT
17267 TAATTACTATTAT
1 TAA-TACTATTAT
17280 TAATACTATT
1 TAATACTATT
17290 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:19356 original size:70 final size:71
Alignment explanation
Indices: 19278--19419 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 71
19268 ATTACTAAGC
19278 ATGTAAATTTAATAAATTAGTTGATGGTATTATACCTTTTTAGAATCATTATTTTTTT-AACCTT
1 ATGTAAATTTAATAAATTAGTTGATGGTATTATACCTTTTTAGAATCATTATTTTTTTAAACCTT
*
19342 AGTTAT
66 AGGTAT
19348 ATGTAAATTTAATAAATTAGTTGATGGTATTATACCTTTTTAGAATCATTATTTTTTTAAACCTT
1 ATGTAAATTTAATAAATTAGTTGATGGTATTATACCTTTTTAGAATCATTATTTTTTTAAACCTT
19413 AGGTAT
66 AGGTAT
19419 A
1 A
19420 AAAAAAAACT
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 58 0.83
71 12 0.17
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (71 bp):
ATGTAAATTTAATAAATTAGTTGATGGTATTATACCTTTTTAGAATCATTATTTTTTTAAACCTT
AGGTAT
Done.