Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017612.1 Corchorus olitorius cultivar O-4 contig17645, 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: 38072
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2240 original size:22 final size:24
Alignment explanation
Indices: 2192--2241 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
2182 TCAGTTTTCT
*
2192 TTTTGTTTATTTATTTAGTGTAATAA
1 TTTTGTTTATTTA-TTAATGT-ATAA
2218 TTTTGTTTATTTA-TAATGT-TAA
1 TTTTGTTTATTTATTAATGTATAA
2240 TT
1 TT
2242 AAAAGGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
24 5 0.22
26 13 0.57
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (24 bp):
TTTTGTTTATTTATTAATGTATAA
Found at i:12545 original size:28 final size:28
Alignment explanation
Indices: 12505--12560 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12495 TGTTGTGGTA
12505 TAATTGGTATGGAATTGATTATCATTTG
1 TAATTGGTATGGAATTGATTATCATTTG
* *
12533 TAATTGGTTTGGACTTGATTATCATTTG
1 TAATTGGTATGGAATTGATTATCATTTG
12561 GTGTAGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.48
Consensus pattern (28 bp):
TAATTGGTATGGAATTGATTATCATTTG
Found at i:19078 original size:37 final size:37
Alignment explanation
Indices: 18960--19078 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 37
18950 ATTAACAGTT
* *
18960 ATTATAAAATGTAACTGATGTTCCTAGAATAATACAA
1 ATTATAAAATGTAACTGATGTTCCTAAAATTATACAA
* * *
18997 ATTAT-TAATAGTAATCAATGA-ATT-CTAAACATTA-ACAGTT
1 ATTATAAAAT-GTAA-C--TGATGTTCCTAAA-ATTATACA--A
19037 ATTATAAAATGTAACTGATGTTCCTAAAATTATACAA
1 ATTATAAAATGTAACTGATGTTCCTAAAATTATACAA
19074 ATTAT
1 ATTAT
19079 TAGGAGTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
36 3 0.05
37 17 0.27
38 14 0.22
39 14 0.22
40 12 0.19
41 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (37 bp):
ATTATAAAATGTAACTGATGTTCCTAAAATTATACAA
Found at i:19079 original size:40 final size:40
Alignment explanation
Indices: 18958--19080 Score: 123
Period size: 40 Copynumber: 3.1 Consensus size: 40
18948 ACATTAACAG
* *
18958 TTATTATAAAATGTAACTGATGTTCCTAGAATAATACAAA
1 TTATTATAAAATGTAACTGATGTTCCTAAAATTATACAAA
* * * *
18998 TTATTAATAGTAAT-CAA-TGA-ATT-CTAAACATTA-AC-AG
1 TTATT-ATA-AAATGTAACTGATGTTCCTAAA-ATTATACAAA
19035 TTATTATAAAATGTAACTGATGTTCCTAAAATTATACAAA
1 TTATTATAAAATGTAACTGATGTTCCTAAAATTATACAAA
19075 TTATTA
1 TTATTA
19081 GGAGTAATAC
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
35 3 0.05
36 5 0.08
37 9 0.14
38 12 0.19
39 12 0.19
40 15 0.23
41 5 0.08
42 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (40 bp):
TTATTATAAAATGTAACTGATGTTCCTAAAATTATACAAA
Found at i:19087 original size:77 final size:77
Alignment explanation
Indices: 18939--19088 Score: 255
Period size: 77 Copynumber: 1.9 Consensus size: 77
18929 TCTTTAAAAG
*
18939 GAATTCAAAACATTAACAGTTATTATAAAATGTAACTGATGTTCCTAGAATAATACAAATTATTA
1 GAATTCAAAACATTAACAGTTATTATAAAATGTAACTGATGTTCCTAAAATAATACAAATTATTA
*
19004 ATAGTAATCAAT
66 AGAGTAATCAAT
* *
19016 GAATTCTAAACATTAACAGTTATTATAAAATGTAACTGATGTTCCTAAAATTATACAAATTATTA
1 GAATTCAAAACATTAACAGTTATTATAAAATGTAACTGATGTTCCTAAAATAATACAAATTATTA
*
19081 GGAGTAAT
66 AGAGTAAT
19089 ACTTAACAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (77 bp):
GAATTCAAAACATTAACAGTTATTATAAAATGTAACTGATGTTCCTAAAATAATACAAATTATTA
AGAGTAATCAAT
Found at i:19655 original size:25 final size:25
Alignment explanation
Indices: 19612--19662 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
19602 TGATAAATTT
19612 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
19639 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
19662 T
1 T
19663 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:20006 original size:19 final size:18
Alignment explanation
Indices: 19982--20017 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19972 TGAAGATTTA
19982 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
20001 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
20018 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:20045 original size:28 final size:28
Alignment explanation
Indices: 20010--20075 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
20000 TTTGAAGACC
20010 ATTGAAGAATTATTTCCAAGAAACAAGA
1 ATTGAAGAATTATTTCCAAGAAACAAGA
20038 ATTGAAGAATTATTTCCAAGAAACAAGA
1 ATTGAAGAATTATTTCCAAGAAACAAGA
20066 ATTGAAGAAT
1 ATTGAAGAAT
20076 GGAGCTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (28 bp):
ATTGAAGAATTATTTCCAAGAAACAAGA
Found at i:28579 original size:2 final size:2
Alignment explanation
Indices: 28572--28598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28562 ACATACATAC
28572 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28599 GATTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.