Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017085.1 Corchorus olitorius cultivar O-4 contig17118, 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: 19625
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2035 original size:74 final size:74
Alignment explanation
Indices: 1914--2061 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
1904 TTACCTATTG
*
1914 AAGAATGCTACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
1979 GCTCAATTC
66 GCTCAATTC
*
1988 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
2053 GCTCAATTC
66 GCTCAATTC
2062 TTTCCCTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (74 bp):
AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
GCTCAATTC
Found at i:7996 original size:68 final size:68
Alignment explanation
Indices: 7885--8024 Score: 271
Period size: 68 Copynumber: 2.1 Consensus size: 68
7875 ATGAGGAAAC
7885 ATGTTACAAAATGTTACTGATGCACAATATACTCTTAAGTTGATGATGCAAAAGAACAGGCAGTA
1 ATGTTACAAAATGTTACTGATGCACAATATACTCTTAAGTTGATGATGCAAAAGAACAGGCAGTA
7950 AAT
66 AAT
*
7953 ATGTTACAAAATGTTACTGATGCACAATATACTCTTAATTTGATGATGCAAAAGAACAGGCAGTA
1 ATGTTACAAAATGTTACTGATGCACAATATACTCTTAAGTTGATGATGCAAAAGAACAGGCAGTA
8018 AAT
66 AAT
8021 ATGT
1 ATGT
8025 ATACCAATCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (68 bp):
ATGTTACAAAATGTTACTGATGCACAATATACTCTTAAGTTGATGATGCAAAAGAACAGGCAGTA
AAT
Found at i:12326 original size:25 final size:25
Alignment explanation
Indices: 12292--12342 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12282 GTACAACAAC
*
12292 TGACCAGGCAAGATAATTTTTAATG
1 TGACCAGGCAAGATAAGTTTTAATG
12317 TGACCAGGCAAGATAAGTTTTAATG
1 TGACCAGGCAAGATAAGTTTTAATG
12342 T
1 T
12343 TATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (25 bp):
TGACCAGGCAAGATAAGTTTTAATG
Found at i:14660 original size:16 final size:16
Alignment explanation
Indices: 14639--14669 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
14629 CTCCGAATCC
14639 CACTCAATATCAAACT
1 CACTCAATATCAAACT
14655 CACTCAATATCAAAC
1 CACTCAATATCAAAC
14670 ACGGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (16 bp):
CACTCAATATCAAACT
Found at i:14981 original size:16 final size:17
Alignment explanation
Indices: 14956--14988 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14946 GCTGAGAAAC
*
14956 GAAACGGCGA-ATCAGA
1 GAAACCGCGAGATCAGA
14972 GAAACCGCGAGATCAGA
1 GAAACCGCGAGATCAGA
14989 AATCTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.21, G:0.30, T:0.06
Consensus pattern (17 bp):
GAAACCGCGAGATCAGA
Found at i:16591 original size:3 final size:3
Alignment explanation
Indices: 16583--16630 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
16573 TACTATTAAT
* *
16583 TTA TTA TTA -TG TTG TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16629 TT
1 TT
16631 GTATATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16600 original size:11 final size:11
Alignment explanation
Indices: 16583--16626 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
16573 TACTATTAAT
*
16583 TTATTATTATG
1 TTATTATTATA
*
16594 TTGTTATTATA
1 TTATTATTATA
16605 TTATTATTATTA
1 TTATTATTA-TA
16617 TTATTATTAT
1 TTATTATTAT
16627 TATTGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TTATTATTATA
Found at i:18472 original size:12 final size:11
Alignment explanation
Indices: 18445--18477 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
18435 AACCGTTTAA
18445 TAATTATATAT
1 TAATTATATAT
18456 T-ATTATATAT
1 TAATTATATAT
18466 GTAATTATATAT
1 -TAATTATATAT
18478 ATCTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATTATATAT
Found at i:18506 original size:21 final size:22
Alignment explanation
Indices: 18473--18513 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18463 TATGTAATTA
**
18473 TATATATCTAATAT-TATTTTT
1 TATATATAAAATATATATTTTT
18494 TATATATAAAATATATATTT
1 TATATATAAAATATATATTT
18514 AATTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATAAAATATATATTTTT
Found at i:18519 original size:23 final size:23
Alignment explanation
Indices: 18445--18525 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
18435 AACCGTTTAA
* *
18445 TAATTATATAT-TATTATATATG
1 TAATTATATATATAATATATATT
18467 TAATTATATATATCTAATAT-TATT
1 TAATTATATATA--TAATATATATT
* *
18491 T-TTTATATATAAAATATATATT
1 TAATTATATATATAATATATATT
*
18513 TAATTATAAATAT
1 TAATTATATATAT
18526 TACTAAACGG
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.11
22 16 0.34
23 17 0.36
24 4 0.09
25 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TAATTATATATATAATATATATT
Found at i:19281 original size:2 final size:2
Alignment explanation
Indices: 19268--19304 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
19258 ACTAAGAATA
19268 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19305 GTGTGTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.