Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012995.1 Corchorus olitorius cultivar O-4 contig13028, 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: 21591
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3451 original size:25 final size:25
Alignment explanation
Indices: 3415--3464 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3405 TTAGTCGATT
3415 AAATCAGATTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
*
3440 AAATCAGCTTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
3465 CAAAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (25 bp):
AAATCAGATTTGAGCTACATGAATG
Found at i:3698 original size:28 final size:28
Alignment explanation
Indices: 3600--3819 Score: 264
Period size: 28 Copynumber: 7.8 Consensus size: 28
3590 AAAGTGGACT
* * * *
3600 CAAAATGACCAACATGCCCCCTGAATATG
1 CAAAATGACCAAAATG-TCCCTGGATGTG
*
3629 C-AAATGACCGAAATG-CCCTTGGATGTG
1 CAAAATGACCAAAATGTCCC-TGGATGTG
*
3656 CAAAAATGTCCAAAATGTCCCTGGATGTG
1 C-AAAATGACCAAAATGTCCCTGGATGTG
*
3685 CAAAATGACCAAAATGTCCCTGGATATG
1 CAAAATGACCAAAATGTCCCTGGATGTG
* *
3713 CAAAAATAACCAAAATGTCCCCGGATGTG
1 C-AAAATGACCAAAATGTCCCTGGATGTG
* *
3742 CAAAATGACCAAAATATCCCTGAATGTG
1 CAAAATGACCAAAATGTCCCTGGATGTG
*
3770 CAAAAATGACCAAAATGTCCCCGGATGTG
1 C-AAAATGACCAAAATGTCCCTGGATGTG
*
3799 CAAAATGACCAAAATGCCCCT
1 CAAAATGACCAAAATGTCCCT
3820 CCTTAAGTGA
Statistics
Matches: 165, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.02
27 7 0.04
28 80 0.48
29 72 0.44
30 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (28 bp):
CAAAATGACCAAAATGTCCCTGGATGTG
Found at i:3700 original size:57 final size:56
Alignment explanation
Indices: 3601--3817 Score: 292
Period size: 57 Copynumber: 3.8 Consensus size: 56
3591 AAGTGGACTC
* * * * *
3601 AAAATGACCAACATGCCCCCTGAATATGC-AAATGACCGAAATGCCCTTGGATGTGCA
1 AAAATGACCAAAATGTCCCC-GGATGTGCAAAATGACCAAAATGCCC-TGGATGTGCA
* * *
3658 AAAATGTCCAAAATGTCCCTGGATGTGCAAAATGACCAAAATGTCCCTGGATATGCA
1 AAAATGACCAAAATGTCCCCGGATGTGCAAAATGACCAAAATG-CCCTGGATGTGCA
* * *
3715 AAAATAACCAAAATGTCCCCGGATGTGCAAAATGACCAAAATATCCCTGAATGTGCA
1 AAAATGACCAAAATGTCCCCGGATGTGCAAAATGACCAAAAT-GCCCTGGATGTGCA
3772 AAAATGACCAAAATGTCCCCGGATGTGCAAAATGACCAAAATGCCC
1 AAAATGACCAAAATGTCCCCGGATGTGCAAAATGACCAAAATGCCC
3818 CTCCTTAAGT
Statistics
Matches: 141, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
56 9 0.06
57 129 0.91
58 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (56 bp):
AAAATGACCAAAATGTCCCCGGATGTGCAAAATGACCAAAATGCCCTGGATGTGCA
Found at i:8135 original size:22 final size:22
Alignment explanation
Indices: 8107--8150 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
8097 GTCGCCAAGC
8107 TGTCGAAAAGTTCAGGTCCGGG
1 TGTCGAAAAGTTCAGGTCCGGG
* *
8129 TGTCGAAACGTTCGGGTCCGGG
1 TGTCGAAAAGTTCAGGTCCGGG
8151 GAACCCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.39, T:0.23
Consensus pattern (22 bp):
TGTCGAAAAGTTCAGGTCCGGG
Found at i:10888 original size:14 final size:14
Alignment explanation
Indices: 10871--10910 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
10861 TTGAGTGAGA
*
10871 GAAGATGAGGGTAG
1 GAAGATGAGAGTAG
10885 GAAGATGAGAGTAG
1 GAAGATGAGAGTAG
10899 GAAGATGAGAGT
1 GAAGATGAGAGT
10911 GTGTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (14 bp):
GAAGATGAGAGTAG
Found at i:12691 original size:27 final size:27
Alignment explanation
Indices: 12633--12722 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
12623 AAGTGAACTT
*
12633 AAAATGACCAAAATGCCCCTGAGCATG--
1 AAAATGACCAAAATGCCCCT-AG-GTGTA
*
12660 CAAATGACCAAAATGCCCCTAGGTGTA
1 AAAATGACCAAAATGCCCCTAGGTGTA
*
12687 AAAATGACCATAATGCCCCTAGGTGTA
1 AAAATGACCAAAATGCCCCTAGGTGTA
*
12714 AAAGTGACC
1 AAAATGACC
12723 CTAATGCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 52 0.93
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAGGTGTA
Found at i:12727 original size:27 final size:27
Alignment explanation
Indices: 12661--12730 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
12651 CTGAGCATGC
*
12661 AAATGACCAAAATGCCCCTAGGTGTAA
1 AAATGACCATAATGCCCCTAGGTGTAA
12688 AAATGACCATAATGCCCCTAGGTGTAA
1 AAATGACCATAATGCCCCTAGGTGTAA
* *
12715 AAGTGACCCTAATGCC
1 AAATGACCATAATGCC
12731 AATTAAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCATAATGCCCCTAGGTGTAA
Found at i:21167 original size:107 final size:107
Alignment explanation
Indices: 20981--21188 Score: 344
Period size: 107 Copynumber: 1.9 Consensus size: 107
20971 TCATTATAGA
*
20981 GTTTTAGAAATAAAATATAAAACTAATTGAACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTA
1 GTTTTAGAAATAAAATACAAAACTAATTGAACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTA
* *
21046 TTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTCTAGG
66 TCTTAAGGGTAAATTCCAAAATTAATAACTTATTGTTCTAGG
** * *
21088 GTTTTAGAAATAAAATACAAAACTAATTTCACTATGTTTAGCCCCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATACAAAACTAATTGAACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTA
*
21153 TCTTAAGGGTAAATTCCATAATTAATAACTTATTGT
66 TCTTAAGGGTAAATTCCAAAATTAATAACTTATTGT
21189 GTGAAGCCTA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (107 bp):
GTTTTAGAAATAAAATACAAAACTAATTGAACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTA
TCTTAAGGGTAAATTCCAAAATTAATAACTTATTGTTCTAGG
Done.