Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014069.1 Corchorus olitorius cultivar O-4 contig14102, 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: 60471
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2284 original size:23 final size:23
Alignment explanation
Indices: 2258--2306 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2248 AGAAATTTAG
* * *
2258 CTTTATAGAGTTGATTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
2281 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
2304 CTT
1 CTT
2307 AGAAATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:3754 original size:16 final size:17
Alignment explanation
Indices: 3728--3764 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
3718 TTTGGAAGGA
3728 TAAAAATGAAA-AAT-G
1 TAAAAATGAAATAATAG
3743 TAAAAGATGAAATAATAG
1 TAAAA-ATGAAATAATAG
3761 TAAA
1 TAAA
3765 TGCAGGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 3 0.16
18 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.22
Consensus pattern (17 bp):
TAAAAATGAAATAATAG
Found at i:5996 original size:23 final size:23
Alignment explanation
Indices: 5970--6014 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5960 ACTCAATTAG
* * *
5970 TGTTCATGAACACGTCCGTTTAT
1 TGTTCACGAACAAGTCCATTTAT
5993 TGTTCACGAACAAGTCCATTTA
1 TGTTCACGAACAAGTCCATTTA
6015 AACGAGCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (23 bp):
TGTTCACGAACAAGTCCATTTAT
Found at i:16933 original size:28 final size:30
Alignment explanation
Indices: 16893--16971 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 30
16883 CTTTGTAGAT
*
16893 AGCATATAACAACCCTTTAG-C-CATAGGA
1 AGCAAATAACAACCCTTTAGCCACATAGGA
*
16921 AGCAAATAACAACCCTTTGTTGGCCACATAGGA
1 AGCAAATAACAACCC--T-TTAGCCACATAGGA
16954 AGCAAATAACAACCCTTT
1 AGCAAATAACAACCCTTT
16972 GTAGATAGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 14 0.32
30 3 0.07
31 4 0.09
32 1 0.02
33 22 0.50
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (30 bp):
AGCAAATAACAACCCTTTAGCCACATAGGA
Found at i:33629 original size:13 final size:13
Alignment explanation
Indices: 33611--33646 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
33601 AGATATCCAT
33611 GGATATATCGAAC
1 GGATATATCGAAC
33624 GGATATATCG-AC
1 GGATATATCGAAC
33636 GGATATATCGA
1 GGATATATCGA
33647 GGTATCGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
GGATATATCGAAC
Found at i:44558 original size:24 final size:25
Alignment explanation
Indices: 44509--44561 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
44499 TTCCAAATTT
*
44509 ATATTGAAATGGATTTTTTGGCCAAA
1 ATATTGAAATGGATTTTTT-GACAAA
*
44535 ATATTGAGATGGATTTTTT-ACAAA
1 ATATTGAAATGGATTTTTTGACAAA
44559 ATA
1 ATA
44562 AAAAAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
26 18 0.72
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (25 bp):
ATATTGAAATGGATTTTTTGACAAA
Found at i:46421 original size:18 final size:17
Alignment explanation
Indices: 46395--46428 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46385 TAGTACCTCC
46395 AGCAACCTCATCGAATAT
1 AGCAACCTCATC-AATAT
*
46413 AGCATCCTCATCAATA
1 AGCAACCTCATCAATA
46429 GCTCGTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (17 bp):
AGCAACCTCATCAATAT
Found at i:51337 original size:31 final size:31
Alignment explanation
Indices: 51267--51337 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
51257 TCTATCAGCA
* *
51267 TTTAATTTGTTTAATTTAAGGCTTTCATTTT
1 TTTAATTTATTTAATTTAAGGCTTTAATTTT
** * *
51298 AATGATTTATTTAATTTAATGC-TTAATTTGT
1 TTTAATTTATTTAATTTAAGGCTTTAATTT-T
51329 TTTAATTTA
1 TTTAATTTA
51338 CAATAATTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.59
Consensus pattern (31 bp):
TTTAATTTATTTAATTTAAGGCTTTAATTTT
Found at i:52078 original size:12 final size:12
Alignment explanation
Indices: 52051--52084 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52041 GAAGTTCGTG
*
52051 TTTGAAGAC-CA
1 TTTGAAGACTTA
52062 TTTGAAGACTTA
1 TTTGAAGACTTA
52074 TTTGAAGACTT
1 TTTGAAGACTT
52085 GAAGACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:52098 original size:29 final size:31
Alignment explanation
Indices: 52052--52110 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
52042 AAGTTCGTGT
*
52052 TTGAAGACCATTTGAAGACTTATTTGAAGAC
1 TTGAAGACCATTTGAAGACTTATTTCAAGAC
*
52083 TTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTGAAGACCATTTGAAGACTTATTTCAAGA
52111 GGAAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
30 1 0.04
31 7 0.27
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
TTGAAGACCATTTGAAGACTTATTTCAAGAC
Found at i:53501 original size:15 final size:16
Alignment explanation
Indices: 53471--53510 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
53461 TTACTCTGCT
53471 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
53487 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
53502 TTGCTTTCT
1 TTGTTTTCT
53511 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:57202 original size:21 final size:21
Alignment explanation
Indices: 57176--57222 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
57166 CCCAAAGTCT
**
57176 TGCCACCACCGGTTAAGCCCG
1 TGCCACCACCGGCCAAGCCCG
*
57197 TGCCACCACCGGCCATGCCCG
1 TGCCACCACCGGCCAAGCCCG
57218 TGCCA
1 TGCCA
57223 TCGCCATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (21 bp):
TGCCACCACCGGCCAAGCCCG
Found at i:58966 original size:8 final size:8
Alignment explanation
Indices: 58953--58979 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
58943 CTTTAAGTGA
58953 TGTGAAAT
1 TGTGAAAT
58961 TGTGAAAT
1 TGTGAAAT
58969 TGTGAAAT
1 TGTGAAAT
58977 TGT
1 TGT
58980 TATTTTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (8 bp):
TGTGAAAT
Found at i:59101 original size:12 final size:12
Alignment explanation
Indices: 59074--59107 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
59064 GAAGTTCGTG
*
59074 TTTGAAGAC-CA
1 TTTGAAGACTTA
59085 TTTGAAGACTTA
1 TTTGAAGACTTA
59097 TTTGAAGACTT
1 TTTGAAGACTT
59108 GAAGACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:59121 original size:29 final size:31
Alignment explanation
Indices: 59075--59133 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
59065 AAGTTCGTGT
*
59075 TTGAAGACCATTTGAAGACTTATTTGAAGAC
1 TTGAAGACCATTTGAAGACTTATTTCAAGAC
*
59106 TTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTGAAGACCATTTGAAGACTTATTTCAAGA
59134 GGAAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
30 1 0.04
31 7 0.27
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
TTGAAGACCATTTGAAGACTTATTTCAAGAC
Done.