Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007079.1 Corchorus capsularis cultivar CVL-1 contig07100, 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: 39957
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:335 original size:6 final size:6
Alignment explanation
Indices: 324--351 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
314 ACACCAAAGT
324 AATTGA AATTGA AATTGA AATTGA AATT
1 AATTGA AATTGA AATTGA AATTGA AATT
352 TTAGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
AATTGA
Found at i:616 original size:6 final size:6
Alignment explanation
Indices: 605--634 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
595 CAACACCTAT
605 ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA
635 CAATGTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:1669 original size:2 final size:2
Alignment explanation
Indices: 1664--1698 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1654 AAAAGTGGAG
1664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1699 TATCCACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5432 original size:6 final size:6
Alignment explanation
Indices: 5421--5451 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
5411 AAATAGTGGA
5421 TGGCAT TGGCAT TGGCAT TGGCATT TGGCAT
1 TGGCAT TGGCAT TGGCAT TGGCA-T TGGCAT
5452 AATATGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGCAT
Found at i:11474 original size:5 final size:5
Alignment explanation
Indices: 11464--11488 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11454 TACCAAACAC
11464 GGAAA GGAAA GGAAA GGAAA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA
11489 CAGGAAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:11652 original size:3 final size:3
Alignment explanation
Indices: 11644--11674 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11634 CACCTATCAA
11644 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
11675 TACATCTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:18335 original size:7 final size:7
Alignment explanation
Indices: 18323--18349 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
18313 AAATATATAC
18323 TGCAGGG
1 TGCAGGG
18330 TGCAGGG
1 TGCAGGG
18337 TGCAGGG
1 TGCAGGG
18344 TGCAGG
1 TGCAGG
18350 CACATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (7 bp):
TGCAGGG
Found at i:23115 original size:7 final size:7
Alignment explanation
Indices: 23103--23127 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23093 AAGTTGCGCC
23103 ACTCAGG
1 ACTCAGG
23110 ACTCAGG
1 ACTCAGG
23117 ACTCAGG
1 ACTCAGG
23124 ACTC
1 ACTC
23128 GGGAGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (7 bp):
ACTCAGG
Found at i:25467 original size:4 final size:4
Alignment explanation
Indices: 25458--25484 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25448 AACTCCCTAT
25458 ATCC ATCC ATCC ATCC ATCC ATCC ATC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATC
25485 ATCAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:27690 original size:19 final size:19
Alignment explanation
Indices: 27664--27722 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
27654 CTGTTTAGTA
27664 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
* * *
27683 ATTGTACAGATTAGATTAGGT
1 ACTGTACAAATGAGATTA--T
*
27704 ACTGTATAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
27723 TAGAGCAGCG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAT
Found at i:30024 original size:12 final size:12
Alignment explanation
Indices: 30004--30035 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
29994 GAAGAACAAC
30004 CTTTCTTTTTTT
1 CTTTCTTTTTTT
30016 CTTT-TTTTTTT
1 CTTTCTTTTTTT
30027 -TTTCTTTTT
1 CTTTCTTTTT
30036 GGGGTGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 12 0.63
12 4 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
CTTTCTTTTTTT
Found at i:30028 original size:14 final size:14
Alignment explanation
Indices: 30009--30035 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29999 ACAACCTTTC
30009 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
30023 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
30036 GGGGTGTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:34830 original size:6 final size:6
Alignment explanation
Indices: 34819--34843 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34809 GAACTTGTAG
34819 ACTAGT ACTAGT ACTAGT ACTAGT A
1 ACTAGT ACTAGT ACTAGT ACTAGT A
34844 GTTGCATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ACTAGT
Found at i:35890 original size:28 final size:29
Alignment explanation
Indices: 35846--35903 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
35836 ATGACGTTCG
* *
35846 TCATATTAGTTTTTACTCAATCGCAGAGT
1 TCATATTAGTTTATACTCAATCACAGAGT
*
35875 TCAT-TTAGTTTATACTCGATCACAGAGT
1 TCATATTAGTTTATACTCAATCACAGAGT
35903 T
1 T
35904 ATGCTCGACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
TCATATTAGTTTATACTCAATCACAGAGT
Found at i:39955 original size:2 final size:2
Alignment explanation
Indices: 39907--39936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39897 AACTTGAAGA
39907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39937 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.