Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013044.1 Corchorus olitorius cultivar O-4 contig13077, 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: 21524
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3195 original size:20 final size:20
Alignment explanation
Indices: 3170--3210 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3160 TATACAAACA
3170 ATATGAAATTTAAACTTGCT
1 ATATGAAATTTAAACTTGCT
3190 ATATGAAATTTAAACTTGCT
1 ATATGAAATTTAAACTTGCT
3210 A
1 A
3211 CAATTACAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (20 bp):
ATATGAAATTTAAACTTGCT
Found at i:5557 original size:14 final size:14
Alignment explanation
Indices: 5534--5563 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5524 ATTGCTCGCA
*
5534 CCCAATTCGTTGCT
1 CCCAACTCGTTGCT
5548 CCCAACTCGTTGCT
1 CCCAACTCGTTGCT
5562 CC
1 CC
5564 TTAGCCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.43, G:0.13, T:0.30
Consensus pattern (14 bp):
CCCAACTCGTTGCT
Found at i:6278 original size:31 final size:30
Alignment explanation
Indices: 6259--6319 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
6249 AAAACAAATT
*
6259 AAGCATTAAATTAAACAAATAATTAAAATGA
1 AAGCATTAAATTAAACAAATAA-AAAAATGA
*
6290 AAGCCTTAAATTAAACAAATAAAAAAATGA
1 AAGCATTAAATTAAACAAATAAAAAAATGA
6320 TAGACACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.23
Consensus pattern (30 bp):
AAGCATTAAATTAAACAAATAAAAAAATGA
Found at i:7733 original size:116 final size:115
Alignment explanation
Indices: 7506--7739 Score: 423
Period size: 116 Copynumber: 2.0 Consensus size: 115
7496 CGCACTCCAC
7506 GGGTTAAGTCTTGGAAGGCCGCTAATTGGCTTGAGACTTGACGGGTTGGACCGCACAGGGAGAGA
1 GGGTTAAGTCTTGGAAGGCCGCTAATTGGCTTGAGACTTGACGGGTTGGACCGCACAGGGAGAGA
7571 TGAGAACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGA
66 TGAGAACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGA
* * *
7621 GGGTTAAGTCTTGGAAGGCCGGTAATTGGCTTGAGACTTGACGGGTTGGGCCGCACGGGGGAGAG
1 GGGTTAAGTCTTGGAAGGCCGCTAATTGGCTTGAGACTTGACGGGTTGGACCGCAC-AGGGAGAG
*
7686 ATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGA
65 ATGAGAACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGA
7737 GGG
1 GGG
7740 AACATCCCAC
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
115 54 0.47
116 60 0.53
ACGTcount: A:0.25, C:0.14, G:0.38, T:0.22
Consensus pattern (115 bp):
GGGTTAAGTCTTGGAAGGCCGCTAATTGGCTTGAGACTTGACGGGTTGGACCGCACAGGGAGAGA
TGAGAACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGA
Found at i:8558 original size:3 final size:3
Alignment explanation
Indices: 8550--8581 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8540 TACTCCAATT
8550 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
8582 AACCATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9552 original size:18 final size:18
Alignment explanation
Indices: 9529--9569 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
9519 TCTAGGATCC
9529 CTTAAGTTAGATCATCAT
1 CTTAAGTTAGATCATCAT
9547 CTTAAGTTAGATCATCAT
1 CTTAAGTTAGATCATCAT
9565 CTTAA
1 CTTAA
9570 TGTATAGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (18 bp):
CTTAAGTTAGATCATCAT
Found at i:10381 original size:29 final size:31
Alignment explanation
Indices: 10331--10401 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
10321 AGGCCTTTAA
* *
10331 TTGAACATTTTTTGTAACGTTAGGTCCTGAT
1 TTGAACATTTTTTGCAACGTTAGATCCTGAT
*
10362 TTGAAC-TTTTTT-CAATGTTAGATCCTGAT
1 TTGAACATTTTTTGCAACGTTAGATCCTGAT
10391 TT-AAGCATTTT
1 TTGAA-CATTTT
10402 AACAAACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
30 10 0.29
31 6 0.17
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (31 bp):
TTGAACATTTTTTGCAACGTTAGATCCTGAT
Found at i:13183 original size:14 final size:14
Alignment explanation
Indices: 13164--13191 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13154 TCTGTTATCC
13164 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
13178 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
13192 TTTGGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:13600 original size:44 final size:44
Alignment explanation
Indices: 13550--13639 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
13540 TATTTATTAA
13550 AATTCAAGATTCTAGCTTAGTATTAGTATCAACGTTACGAACGG
1 AATTCAAGATTCTAGCTTAGTATTAGTATCAACGTTACGAACGG
13594 AATTCAAGATTCTAGCTTAGTATTAGTATCAACGTTACGAACGG
1 AATTCAAGATTCTAGCTTAGTATTAGTATCAACGTTACGAACGG
13638 AA
1 AA
13640 GTGAAAATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (44 bp):
AATTCAAGATTCTAGCTTAGTATTAGTATCAACGTTACGAACGG
Found at i:17431 original size:20 final size:21
Alignment explanation
Indices: 17406--17446 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
17396 TAGCTCAAGT
*
17406 CTGAATTGGAA-TCTCAAATA
1 CTGAATTAGAACTCTCAAATA
17426 CTGAATTAGAACTCTCAAATA
1 CTGAATTAGAACTCTCAAATA
17447 AAGGAGCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (21 bp):
CTGAATTAGAACTCTCAAATA
Found at i:20987 original size:33 final size:33
Alignment explanation
Indices: 20945--21078 Score: 121
Period size: 33 Copynumber: 4.1 Consensus size: 33
20935 CTGATTTGAG
*
20945 TGTTGTTTGCAATGACA-TGAAATCTGTTTTAGA
1 TGTTGTTTGCGATGACACT-AAATCTGTTTTAGA
* * * **
20978 TGTTGTTTGCGATAATACTAAACCTAATTT-GA
1 TGTTGTTTGCGATGACACTAAATCTGTTTTAGA
* *
21010 GTGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 -TGTTGTTTGCGATGACACTAAATCTGTTTTAGA
* * *
21044 TGTTGTTTGTGATGAAAC-AAATTCTGTTTTGGA
1 TGTTGTTTGCGATGACACTAAA-TCTGTTTTAGA
21077 TG
1 TG
21079 CTAATTGTGA
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
32 5 0.06
33 74 0.91
34 2 0.02
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.43
Consensus pattern (33 bp):
TGTTGTTTGCGATGACACTAAATCTGTTTTAGA
Done.