Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008450.1 Corchorus capsularis cultivar CVL-1 contig08471, 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: 43480
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:54 original size:19 final size:20
Alignment explanation
Indices: 14--55 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4 AAAGAAGGTC
*
14 AAAAAATGGATGTAGAGATA
1 AAAAAATGGATGTAAAGATA
34 AAAAAATGGTAT-TAAAG-TA
1 AAAAAATGG-ATGTAAAGATA
53 AAA
1 AAA
56 GAGTAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAAAATGGATGTAAAGATA
Found at i:185 original size:15 final size:15
Alignment explanation
Indices: 165--195 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
155 AAAGAGTAAG
*
165 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
180 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
195 A
1 A
196 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:822 original size:19 final size:18
Alignment explanation
Indices: 789--824 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
779 TTGAAATAAT
789 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
807 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
825 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:2454 original size:21 final size:20
Alignment explanation
Indices: 2414--2456 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2404 ACAATTAATC
*
2414 TAAATTAAAGCAAACTAAAT
1 TAAATTAAAGCAAACGAAAT
2434 TAAATCTAAAGCTAAA-GAAAT
1 TAAAT-TAAAGC-AAACGAAAT
2455 TA
1 TA
2457 CTTAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAATTAAAGCAAACGAAAT
Found at i:5109 original size:20 final size:20
Alignment explanation
Indices: 5071--5110 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5061 ATCACACATA
5071 AAAATACCAAAAAGCATAGG
1 AAAATACCAAAAAGCATAGG
*
5091 AAAATGACCATAAAG-ATAGG
1 AAAAT-ACCAAAAAGCATAGG
5111 GTTAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATACCAAAAAGCATAGG
Found at i:5412 original size:17 final size:16
Alignment explanation
Indices: 5390--5434 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5380 ACTGTGTTAG
*
5390 ATTTTAAAACAAAACTA
1 ATTTT-AAACAAAACAA
*
5407 ATTTTAGACAAAACAA
1 ATTTTAAACAAAACAA
*
5423 ATTTTGAACAAA
1 ATTTTAAACAAA
5435 TCTAGGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (16 bp):
ATTTTAAACAAAACAA
Found at i:9080 original size:5 final size:5
Alignment explanation
Indices: 9070--9102 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
9060 AATAGGCAAT
*
9070 CAAAG CAAAG CAAAG CAAAG CAAAG CAATG CAA
1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAA
9103 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.58, C:0.21, G:0.18, T:0.03
Consensus pattern (5 bp):
CAAAG
Found at i:9655 original size:12 final size:11
Alignment explanation
Indices: 9632--9662 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
9622 TCAGAAAATT
9632 AAAAAATTAAA
1 AAAAAATTAAA
9643 AAAAAATTAAA
1 AAAAAATTAAA
9654 AAATAAATT
1 AAA-AAATT
9663 TATGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:9796 original size:14 final size:14
Alignment explanation
Indices: 9777--9805 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9767 CCACTTGTAA
9777 TCATCAAATTGATG
1 TCATCAAATTGATG
9791 TCATCAAATTGATG
1 TCATCAAATTGATG
9805 T
1 T
9806 AATCTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (14 bp):
TCATCAAATTGATG
Found at i:19990 original size:13 final size:13
Alignment explanation
Indices: 19972--19997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19962 CAACGATACC
19972 TCGATATATCCAT
1 TCGATATATCCAT
19985 TCGATATATCCAT
1 TCGATATATCCAT
19998 GGACACATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
TCGATATATCCAT
Found at i:20285 original size:46 final size:44
Alignment explanation
Indices: 20211--20302 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 44
20201 ATCCATATTA
*
20211 AATTAAATATTTTTTTTCATTTTCACATCTAGGAATAAAAATAT
1 AATTAAATATTCTTTTTCATTTTCACATCTAGGAATAAAAATAT
* * *
20255 AATTAAATACGTTCTTTTTCATTTTTACATCTATGATTAAAAATAT
1 AATTAAATA--TTCTTTTTCATTTTCACATCTAGGAATAAAAATAT
20301 AA
1 AA
20303 GCGACATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 9 0.21
46 33 0.79
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (44 bp):
AATTAAATATTCTTTTTCATTTTCACATCTAGGAATAAAAATAT
Found at i:21535 original size:5 final size:5
Alignment explanation
Indices: 21525--21580 Score: 60
Period size: 5 Copynumber: 10.4 Consensus size: 5
21515 TATATGTAGT
21525 ATATA ATATA ATATA ATATAAA ATATA ATAT- ATATA ATAATA GTATATA
1 ATATA ATATA ATATA ATAT--A ATATA ATATA ATATA AT-ATA --ATATA
21574 ATATA AT
1 ATATA AT
21581 GTAGTATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.09
5 28 0.62
6 3 0.07
7 8 0.18
8 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:21553 original size:22 final size:23
Alignment explanation
Indices: 21525--21580 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
21515 TATATGTAGT
21525 ATATAATATAATATAAT-ATAAA
1 ATATAATATAATATAATAATAAA
**
21547 ATATAATAT-ATATAATAATAGT
1 ATATAATATAATATAATAATAAA
21569 ATATAATATAAT
1 ATATAATATAAT
21581 GTAGTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 7 0.23
22 21 0.70
23 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAATATAATATAATAATAAA
Found at i:21585 original size:17 final size:16
Alignment explanation
Indices: 21521--21587 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 16
21511 TGAATATATG
21521 TAGTATATAATATAAT
1 TAGTATATAATATAAT
* *
21537 ATAATATAAAATATAA-
1 -TAGTATATAATATAAT
21553 TA-TATAT-A-ATAA-
1 TAGTATATAATATAAT
21565 TAGTATATAATATAAT
1 TAGTATATAATATAAT
21581 GTAGTAT
1 -TAGTAT
21588 TTGGTATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 6 0.14
13 6 0.14
14 5 0.12
15 6 0.14
17 19 0.45
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (16 bp):
TAGTATATAATATAAT
Found at i:30929 original size:6 final size:6
Alignment explanation
Indices: 30918--31023 Score: 54
Period size: 6 Copynumber: 16.2 Consensus size: 6
30908 TATCGAAAAT
** * * *
30918 GAACCC GAACCC G-ACCC GGGCCC AAACCC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
30964 GAAAATACCC GAACCC GAAATACCC GAACCC GAAAATACCC GAACCC GAACCC
1 G---A-ACCC GAACCC G--A-ACCC GAACCC G---A-ACCC GAACCC GAACCC
31017 GAACCC G
1 GAACCC G
31024 TCCAATTGCC
Statistics
Matches: 78, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
5 9 0.12
6 49 0.63
7 3 0.04
8 1 0.01
9 7 0.09
10 9 0.12
ACGTcount: A:0.34, C:0.44, G:0.18, T:0.04
Consensus pattern (6 bp):
GAACCC
Found at i:30949 original size:23 final size:24
Alignment explanation
Indices: 30919--30981 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
30909 ATCGAAAATG
*
30919 AACCCGAACCCGACCCGGGCCC-A
1 AACCCGAACCCGACCCGAGCCCAA
*
30942 AACCCGAACCCGATCCGAGCCCGAAA
1 AACCCGAACCCGACCCGAGCCC--AA
30968 ATACCCGAACCCGA
1 A-ACCCGAACCCGA
30982 AATACCCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 20 0.59
26 2 0.06
27 12 0.35
ACGTcount: A:0.32, C:0.46, G:0.19, T:0.03
Consensus pattern (24 bp):
AACCCGAACCCGACCCGAGCCCAA
Found at i:30986 original size:15 final size:16
Alignment explanation
Indices: 30956--31013 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
30946 CGAACCCGAT
*
30956 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
30972 CCGAACCCG-AAATAC
1 CCGAACCCGAAAATAC
30987 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
31003 CCGAACCCGAA
1 CCGAACCCGAA
31014 CCCGAACCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 15 0.38
16 25 0.62
ACGTcount: A:0.40, C:0.40, G:0.16, T:0.05
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:32109 original size:18 final size:19
Alignment explanation
Indices: 32077--32116 Score: 64
Period size: 18 Copynumber: 2.1 Consensus size: 19
32067 GAGTGTCTAA
32077 TTAAAAAAATTTCAATTAAT
1 TTAAAAAAA-TTCAATTAAT
32097 TTAAAAAAA-TCAATTAAT
1 TTAAAAAAATTCAATTAAT
32115 TT
1 TT
32117 GAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAAAATTCAATTAAT
Found at i:41363 original size:16 final size:16
Alignment explanation
Indices: 41344--41453 Score: 84
Period size: 16 Copynumber: 6.9 Consensus size: 16
41334 GACCTGACAA
*
41344 ACCCGTGACCCGAATG
1 ACCCGAGACCCGAATG
*
41360 ACCCGACACCC-AGATG
1 ACCCGAGACCCGA-ATG
41376 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* * *
41392 ACCTGTA-ACTC-AGATA
1 ACCCG-AGACCCGA-ATG
*
41408 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
41424 ACCCAAGACCC-ATATG
1 ACCCGAGACCCGA-ATG
*
41440 ACCCGAAACCCGAA
1 ACCCGAGACCCGAA
41454 AAACCCAAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
15 4 0.05
16 65 0.89
17 4 0.05
ACGTcount: A:0.35, C:0.37, G:0.18, T:0.10
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:41380 original size:32 final size:31
Alignment explanation
Indices: 41351--41453 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 31
41341 CAAACCCGTG
*
41351 ACCCGAATGACCCGACACCCAGATGACCCGAG
1 ACCCGAATGACCCGA-ACCCAGATGACCCGAA
* * *
41383 ACCCGAATGACCTGTAACTCAGATAACCCGAA
1 ACCCGAATGACCCG-AACCCAGATGACCCGAA
* *
41415 ACCCGAATGACCCAAGACCCATATGACCCGAA
1 ACCCGAATGACCCGA-ACCCAGATGACCCGAA
41447 ACCCGAA
1 ACCCGAA
41454 AAACCCAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
31 1 0.02
32 58 0.97
33 1 0.02
ACGTcount: A:0.36, C:0.37, G:0.17, T:0.10
Consensus pattern (31 bp):
ACCCGAATGACCCGAACCCAGATGACCCGAA
Found at i:42782 original size:42 final size:42
Alignment explanation
Indices: 42723--42803 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
42713 GTTGAGACAG
42723 ACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACTT
1 ACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACTT
*
42765 ACCCCACCTGATAATTAATTTTGTATTTAATATTCAAAA
1 ACCCCACCTGATAATTAATTATGTATTTAATATTCAAAA
42804 TTAATATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (42 bp):
ACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACTT
Found at i:42994 original size:16 final size:15
Alignment explanation
Indices: 42975--43144 Score: 123
Period size: 16 Copynumber: 10.9 Consensus size: 15
42965 TTCAATGCTG
42975 ACCCAATTGACCCGAA
1 ACCCAA-TGACCCGAA
*
42991 ACCCGAGTGACCCG-A
1 ACCC-AATGACCCGAA
*
43006 AGCCAA-GACCC-AA
1 ACCCAATGACCCGAA
*** *
43019 ACCCACCCAACCCGAG
1 ACCCA-ATGACCCGAA
*
43035 ACCCGAATGACCCGGA
1 ACCC-AATGACCCGAA
*
43051 ACCCGAATGACCCGAG
1 ACCC-AATGACCCGAA
43067 ACCCGAATGACCCGAA
1 ACCC-AATGACCCGAA
* *
43083 ACCCGTATGACCCGAG
1 ACCC-AATGACCCGAA
*
43099 ACCCGAATAACCC-AA
1 ACCC-AATGACCCGAA
43114 ACCCAGATGACCCGAA
1 ACCCA-ATGACCCGAA
43130 ACCCGAATGACCCGA
1 ACCC-AATGACCCGA
43145 GAAAACTACC
Statistics
Matches: 124, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
13 10 0.08
14 2 0.02
15 19 0.15
16 90 0.73
17 3 0.02
ACGTcount: A:0.35, C:0.40, G:0.19, T:0.06
Consensus pattern (15 bp):
ACCCAATGACCCGAA
Found at i:43064 original size:32 final size:32
Alignment explanation
Indices: 42974--43144 Score: 178
Period size: 32 Copynumber: 5.5 Consensus size: 32
42964 ATTCAATGCT
*
42974 GACCC-AATTGACCCGAAACCCGAGTGACCCGA
1 GACCCGAA-TGACCCGAAACCCGAATGACCCGA
* ***
43006 -AGCC-AA-GACCC-AAACCC-ACCCAACCCGA
1 GACCCGAATGACCCGAAACCCGA-ATGACCCGA
*
43034 GACCCGAATGACCCGGAACCCGAATGACCCGA
1 GACCCGAATGACCCGAAACCCGAATGACCCGA
*
43066 GACCCGAATGACCCGAAACCCGTATGACCCGA
1 GACCCGAATGACCCGAAACCCGAATGACCCGA
*
43098 GACCCGAATAACCC-AAACCC-AGATGACCCGA
1 GACCCGAATGACCCGAAACCCGA-ATGACCCGA
*
43129 AACCCGAATGACCCGA
1 GACCCGAATGACCCGA
43145 GAAAACTACC
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.01
28 12 0.10
29 8 0.07
30 2 0.02
31 37 0.32
32 55 0.47
33 1 0.01
ACGTcount: A:0.35, C:0.40, G:0.19, T:0.06
Consensus pattern (32 bp):
GACCCGAATGACCCGAAACCCGAATGACCCGA
Found at i:43140 original size:47 final size:47
Alignment explanation
Indices: 42982--43146 Score: 178
Period size: 48 Copynumber: 3.6 Consensus size: 47
42972 CTGACCCAAT
* * **
42982 TGACCCGAAACCCGAGTGACCCGA-AGCC-AA-GACCCAAACCCACC
1 TGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCAAACCCAGA
** * *
43026 CAACCCGAGACCCGAATGACCCG-GAACCCGAATGACCCGAGACCC-GAA
1 TGACCCGAAACCCGAATGACCCGAG-ACCCGAATGACCC-AAACCCAG-A
* *
43074 TGACCCGAAACCCGTATGACCCGAGACCCGAATAACCCAAACCCAGA
1 TGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCAAACCCAGA
43121 TGACCCGAAACCCGAATGACCCGAGA
1 TGACCCGAAACCCGAATGACCCGAGA
43147 AAACTACCTG
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
44 19 0.19
45 3 0.03
46 2 0.02
47 36 0.37
48 37 0.38
49 1 0.01
ACGTcount: A:0.35, C:0.39, G:0.20, T:0.06
Consensus pattern (47 bp):
TGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCAAACCCAGA
Done.