Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016641.1 Corchorus olitorius cultivar O-4 contig16674, 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: 20139
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Found at i:6490 original size:16 final size:16
Alignment explanation
Indices: 6466--6498 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6456 AACAATTATA
*
6466 GGAGTCACAAGTATCT
1 GGAGACACAAGTATCT
6482 GGAGACACAAGTATCT
1 GGAGACACAAGTATCT
6498 G
1 G
6499 AATGGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.21
Consensus pattern (16 bp):
GGAGACACAAGTATCT
Found at i:8235 original size:16 final size:16
Alignment explanation
Indices: 8200--8255 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
8190 AGAGATTGAC
*
8200 AGAAAGCAATTAAA-T
1 AGAAAACAATTAAACT
8215 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
8231 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
8247 AGAAAACAA
1 AGAAAACAA
8256 AGCAAAGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
15 13 0.33
16 26 0.67
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12280 original size:14 final size:14
Alignment explanation
Indices: 12261--12295 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
12251 AGGAAATAGG
12261 AAAGAAA-GGAAGAA
1 AAAGAAAGGGAA-AA
12275 AAAGAAAGGGAAAA
1 AAAGAAAGGGAAAA
12289 AAAGAAA
1 AAAGAAA
12296 TTAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGGGAAAA
Found at i:16729 original size:30 final size:30
Alignment explanation
Indices: 16693--16771 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
16683 CTAGGGTCCC
* *
16693 GCTGTAAACACATTGTTGACTTTGAATCCT
1 GCTGTAAACACACTGTTGACTTTGAATCAT
***
16723 GCTGTAAATGTACTGTTGACTTTGAATCAT
1 GCTGTAAACACACTGTTGACTTTGAATCAT
**
16753 GCTGTAAATGCACTGTTGA
1 GCTGTAAACACACTGTTGA
16772 TTGATTCCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (30 bp):
GCTGTAAACACACTGTTGACTTTGAATCAT
Found at i:16961 original size:79 final size:79
Alignment explanation
Indices: 16825--17141 Score: 555
Period size: 79 Copynumber: 4.0 Consensus size: 79
16815 CTTCTTCACT
*
16825 ATTGA-CTGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGATTCGTAACGCCCAACTTGAA
1 ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
16889 CACTAATGATTCAA
66 CACTAATGATTCAA
16903 ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
1 ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
16968 CACTAATGATTCAA
66 CACTAATGATTCAA
* *
16982 ATTGATCTGATTTCATCATTCCTTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
1 ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
17047 CACTAATGATTCAA
66 CACTAATGATTCAA
* * * *
17061 ATTGATCTGATTTCATCATTCCCTCCTCAAGTTGGCGCGTGAAGATTCGCAACGCCTAACTTGAA
1 ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
*
17126 CAGTAATGATTCAA
66 CACTAATGATTCAA
17140 AT
1 AT
17142 CGATTCTTGT
Statistics
Matches: 230, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
78 5 0.02
79 225 0.98
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (79 bp):
ATTGATCTGATTTCATCACTCCCTCCTCAAGTTGGAGCGTGAAGATTCGTAACGCCCAACTTGAA
CACTAATGATTCAA
Found at i:18529 original size:30 final size:29
Alignment explanation
Indices: 18488--18571 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
18478 TCAATCTAGG
*
18488 ATCCCGCTGTAAA-CACATTGTTGACTTTGA
1 ATCCTGCTGTAAAGCACA--GTTGACTTTGA
*
18518 ATCCTGCTGTAAATGTACAGTTGACTTTGA
1 ATCCTGCTGTAAA-GCACAGTTGACTTTGA
* *
18548 ATCCTACTGTAAATGCACTGTTGA
1 ATCCTGCTGTAAA-GCACAGTTGA
18572 TTGATTCCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 44 0.94
32 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (29 bp):
ATCCTGCTGTAAAGCACAGTTGACTTTGA
Found at i:19304 original size:41 final size:42
Alignment explanation
Indices: 19205--19528 Score: 414
Period size: 43 Copynumber: 7.7 Consensus size: 42
19195 CCAATAACCA
* *
19205 AAAGTCCCCAAACAC--ATATAACACATG-GGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GAGGCATCTATA-TAC
*
19246 AAAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
*
19288 AAAGTCCCCAAACACATATATAACACAGGGGCACTTCTA-ATAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA--TCTATATAC
*
19331 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
19372 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC
* *
19415 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
* *
19456 AAAGTCTCCAAACACATATATAACACAGGGGCATTTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA--TCTATATAC
*
19499 AAAGTCCTCAAACACATATATAACACAGAG
1 AAAGTCCCCAAACACATATATAACACAGAG
19529 ACTTTTTTCC
Statistics
Matches: 252, Mismatches: 16, Indels: 27
0.85 0.05 0.09
Matches are distributed among these distances:
41 102 0.40
42 24 0.10
43 107 0.42
44 19 0.08
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
Found at i:19561 original size:84 final size:84
Alignment explanation
Indices: 19205--19528 Score: 537
Period size: 84 Copynumber: 3.9 Consensus size: 84
19195 CCAATAACCA
* *
19205 AAAGTCCCCAAACAC--ATATAACACATGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
19268 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
*
19288 AAAGTCCCCAAACACATATATAACACAGGGGCA-CTTCTAATACAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATC-TCTATTACAAAGTCCTCAAACACATATAT
19352 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
* *
19372 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
*
19437 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
* *
19456 AAAGTCTCCAAACACATATATAACACAGGGGCATTTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
19521 ACACAGAG
66 ACACAGAG
19529 ACTTTTTTCC
Statistics
Matches: 227, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
83 15 0.07
84 190 0.84
85 22 0.10
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.