Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019158.1 Corchorus olitorius cultivar O-4 contig19191, 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: 10562
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:6156 original size:44 final size:44
Alignment explanation
Indices: 6064--6170 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
6054 TAAATATTTT
* * ** * *
6064 TATGAAATTTTGATAAACACACTATGAAATTTTGATGATTATAT
1 TATGAAATTTTGATAAACTCACAATGAAATACTGATAATTATAC
* *
6108 TATGAAATTGTGATAAACTCCCAATGAAATACTGATAACTTA-AC
1 TATGAAATTTTGATAAACTCACAATGAAATACTGATAA-TTATAC
*
6152 TATGAAATTTTAATAAACT
1 TATGAAATTTTGATAAACT
6171 TTTCTATGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 49 0.94
45 3 0.06
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAAACTCACAATGAAATACTGATAATTATAC
Found at i:6231 original size:23 final size:22
Alignment explanation
Indices: 6064--6294 Score: 105
Period size: 22 Copynumber: 10.4 Consensus size: 22
6054 TAAATATTTT
* * *
6064 TATGAAATTTTGATAAACACAC
1 TATGAAATTTTGATAACCTCTC
* * * *
6086 TATGAAATTTTGATGA-TTATAT
1 TATGAAATTTTGATAACCTCT-C
* * *
6108 TATGAAATTGTGATAAACTCCC
1 TATGAAATTTTGATAACCTCTC
* ** * **
6130 AATGAAATACTGATAACTTAAC
1 TATGAAATTTTGATAACCTCTC
* * *
6152 TATGAAATTTTAATAAACTTTTC
1 TATGAAATTTTGAT-AACCTCTC
6175 TATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCTC
**
6196 ATATGATTTTTTTGATAACCCTCTC
1 -TATGA-AATTTTGATAA-CCTCTC
* *
6221 TATGAAATTTT-ATTAATCTCCC
1 TATGAAATTTTGA-TAACCTCTC
**
6243 TAT-AAATTTTTGAT-ACCAT-AG
1 TATGAAA-TTTTGATAACC-TCTC
* *
6264 TATGAAATTTCGATAATCTCTC
1 TATGAAATTTTGATAACCTCTC
6286 TATGAAATT
1 TATGAAATT
6295 ATATATCATT
Statistics
Matches: 154, Mismatches: 41, Indels: 28
0.69 0.18 0.13
Matches are distributed among these distances:
21 16 0.10
22 91 0.59
23 37 0.24
24 9 0.06
25 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTC
Found at i:7140 original size:43 final size:44
Alignment explanation
Indices: 7092--7177 Score: 129
Period size: 43 Copynumber: 1.9 Consensus size: 44
7082 TAATAATGGC
* *
7092 AATTTTATATATTTTAATAGTGAT-ATAATTAAAATATATTGGT
1 AATTTTATATATTTTAATAATAATGATAATTAAAATATATTGGT
7135 AATTTTATATATTTTAATAATAATGGCATAATTAAAATATATT
1 AATTTTATATATTTTAATAATAAT-G-ATAATTAAAATATATT
7178 TTAATAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 22 0.58
46 16 0.42
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (44 bp):
AATTTTATATATTTTAATAATAATGATAATTAAAATATATTGGT
Found at i:7351 original size:22 final size:22
Alignment explanation
Indices: 7326--7400 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
7316 TTGAATGTTT
7326 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* * **
7348 TTATTAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACTACC
*
7370 TTAT-AGAATTTTGATAATTTACC
1 TTATGA-AATTTTGATAA-CTACC
7393 -TATGAAAT
1 TTATGAAAT
7401 ATGAAACTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.02
22 39 0.93
23 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:7450 original size:23 final size:23
Alignment explanation
Indices: 7421--7478 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
7411 GATAACCTAA
7421 CTATGAAATTTTAATAAACATTC
1 CTATGAAATTTTAATAAACATTC
7444 CTATGAAATTTTAATAAACATTC
1 CTATGAAATTTTAATAAACATTC
7467 CTATGAAATTTT
1 CTATGAAATTTT
7479 GTAACCTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACATTC
Found at i:7490 original size:21 final size:21
Alignment explanation
Indices: 7400--7506 Score: 81
Period size: 23 Copynumber: 4.9 Consensus size: 21
7390 ACCTATGAAA
* **
7400 TATGAAACTTTGATAACCTAAC
1 TATGAAATTTTG-TAACCTTCC
* *
7422 TATGAAATTTTAATAAACATTCC
1 TATGAAATTTT-GT-AACCTTCC
* *
7445 TATGAAATTTTAATAAACATTCC
1 TATGAAATTTT-GT-AACCTTCC
7468 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
*
7489 TATG-ATTTTTGATAACCT
1 TATGAAATTTTG-TAACCT
7507 CTCTGTGAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 6 0.08
21 17 0.23
22 12 0.16
23 39 0.53
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:9124 original size:10 final size:10
Alignment explanation
Indices: 9102--9131 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
9092 ATACTTTTAT
9102 ATATAGTATAG
1 ATATAG-ATAG
9113 ATATAGATAG
1 ATATAGATAG
9123 ATATAGATA
1 ATATAGATA
9132 TTTCCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (10 bp):
ATATAGATAG
Found at i:9174 original size:12 final size:12
Alignment explanation
Indices: 9157--9183 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9147 AAACATTATA
9157 TTTATTCGTACT
1 TTTATTCGTACT
9169 TTTATTCGTACT
1 TTTATTCGTACT
9181 TTT
1 TTT
9184 GTCTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTATTCGTACT
Found at i:9283 original size:18 final size:18
Alignment explanation
Indices: 9260--9296 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9250 TTCTTCTGGG
*
9260 TCTAGTATATTTTATTTA
1 TCTAGTACATTTTATTTA
*
9278 TCTAGTCCATTTTATTTA
1 TCTAGTACATTTTATTTA
9296 T
1 T
9297 TGGTTTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.59
Consensus pattern (18 bp):
TCTAGTACATTTTATTTA
Done.