Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021256.1 Corchorus olitorius cultivar O-4 contig21289, 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: 13891
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:363 original size:4 final size:4
Alignment explanation
Indices: 354--406 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
344 ATTAAGTGTG
* * * * *
354 TATA TATA TATA CATA TATA TATA TATA TATA CATA TACA TACA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
402 TATA T
1 TATA T
407 GTGAACATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:365 original size:6 final size:6
Alignment explanation
Indices: 354--406 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
344 ATTAAGTGTG
* * * * *
354 TATATA TATATA CATATA TATATA TATATA TACATA TACATA CATACA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
402 TATAT
1 TATAT
407 GTGAACATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:372 original size:10 final size:10
Alignment explanation
Indices: 357--405 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
347 AAGTGTGTAT
357 ATATATATAC
1 ATATATATAC
*
367 ATATATATAT
1 ATATATATAC
377 ATATATATAC
1 ATATATATAC
*
387 ATATACATAC
1 ATATATATAC
*
397 ATACATATA
1 ATATATATA
406 TGTGAACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATATAC
Found at i:373 original size:14 final size:14
Alignment explanation
Indices: 354--405 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
344 ATTAAGTGTG
*
354 TATATATATATACA
1 TATATACATATACA
*
368 TATAT--ATATATA
1 TATATACATATACA
380 TATATACATATACA
1 TATATACATATACA
*
394 TACATACATATA
1 TATATACATATA
406 TGTGAACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 11 0.33
14 22 0.67
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATACATATACA
Found at i:1365 original size:178 final size:178
Alignment explanation
Indices: 1040--1417 Score: 532
Period size: 178 Copynumber: 2.1 Consensus size: 178
1030 TCATAAGCTC
* * *
1040 AAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAAATAAATTCTTTGGAAGC
1 AAATTATATAATGTTAAGTAGACCGTCTATTTCCGTTAACCGAAACAAACAAATTCTTTGGAAGC
1105 ATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTATGAAAGTTGTAGATCATGGAAC
66 ATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTATGAAAGTTGTAGATCATGGAAC
* * * *
1170 AACCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTGAAGCA-A
131 AACCTTTCAAGAGACACTTAAATCACCTCAATTAGACAACCGAAG-AGA
* *
1218 AAGTTATATAATGTTAAGTGGACCGTCTA-TTCCTGTTAACCGAAAC-AACAAATT-TTCTGGAA
1 AAATTATATAATGTTAAGTAGACCGTCTATTTCC-GTTAACCGAAACAAACAAATTCTT-TGGAA
1280 GCATTTTTTATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
64 GCATTTTTTATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTT-ATGAAAGTTGTAGATCATG
* * * * * *
1344 GAACAATCTTTTAATAGACACTTAAATCACCTTAATTGGATAACCGAAGAGA
127 GAACAACCTTTCAAGAGACACTTAAATCACCTCAATTAGACAACCGAAGAGA
*
1396 AAATTATATAATGTTAAATAGA
1 AAATTATATAATGTTAAGTAGA
1418 TCGTTTAACC
Statistics
Matches: 177, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
176 6 0.03
177 56 0.32
178 115 0.65
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (178 bp):
AAATTATATAATGTTAAGTAGACCGTCTATTTCCGTTAACCGAAACAAACAAATTCTTTGGAAGC
ATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTATGAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATTAGACAACCGAAGAGA
Found at i:3805 original size:3 final size:3
Alignment explanation
Indices: 3797--3887 Score: 164
Period size: 3 Copynumber: 30.3 Consensus size: 3
3787 GAAATACAAT
*
3797 ATA ATA ATA ACA 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
*
3845 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3888 GAACAGTAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:8665 original size:15 final size:15
Alignment explanation
Indices: 8645--8683 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
8635 GTTTTTAGCC
8645 AAAAAAGAAAGAAAGA
1 AAAAAAGAAAGAAA-A
8661 AAAAAA-AAAGAAAA
1 AAAAAAGAAAGAAAA
8675 AAGAAAAGA
1 AA-AAAAGA
8684 CTACTGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAAAA
Found at i:8672 original size:11 final size:12
Alignment explanation
Indices: 8652--8683 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
8642 GCCAAAAAAG
8652 AAAG-AAAGAAA
1 AAAGAAAAGAAA
8663 AAA-AAAAGAAA
1 AAAGAAAAGAAA
8674 AAAGAAAAGA
1 AAAGAAAAGA
8684 CTACTGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:12271 original size:48 final size:48
Alignment explanation
Indices: 12200--12299 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
12190 CTTGACTCCG
* *
12200 AACTTGGAGCTTAAACTTGGCTTGACCATGGTCGAGTTTTGCTTTTGA
1 AACTTGGAGCTTAAACTCGGCTTGACCATGGTCGAGTTTTGCTTTCGA
* *
12248 AACTTGGAGCTTTAACTCGGCTTGACCGTGGTCGAGTTTTGCTTTCGA
1 AACTTGGAGCTTAAACTCGGCTTGACCATGGTCGAGTTTTGCTTTCGA
12296 AACT
1 AACT
12300 CGAACTTGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (48 bp):
AACTTGGAGCTTAAACTCGGCTTGACCATGGTCGAGTTTTGCTTTCGA
Done.