Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015585.1 Corchorus olitorius cultivar O-4 contig15618, 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: 31353
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3917 original size:60 final size:60
Alignment explanation
Indices: 3819--3939 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
3809 ACCATACAAG
* *
3819 TCCGTAGGGTTACTAGGGTGATTTGGTCGGTAGAGGAGGAAGTGATTTTGTTGGAGTCCA
1 TCCGCAGGGTTACTAGGGTGATTTGGTCGGTAGAGGAGGAAATGATTTTGTTGGAGTCCA
3879 TCCGCAGGGTTACTAGGGTGATTTGGTCGGTAGAGGAGGAAATGATTTTGTTGGAGTCCA
1 TCCGCAGGGTTACTAGGGTGATTTGGTCGGTAGAGGAGGAAATGATTTTGTTGGAGTCCA
3939 T
1 T
3940 GCAAACCCTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.31
Consensus pattern (60 bp):
TCCGCAGGGTTACTAGGGTGATTTGGTCGGTAGAGGAGGAAATGATTTTGTTGGAGTCCA
Found at i:6323 original size:40 final size:40
Alignment explanation
Indices: 6279--6377 Score: 189
Period size: 40 Copynumber: 2.5 Consensus size: 40
6269 GTTGTTTTGG
6279 TAATAGGAATATTGCATACTTGGTTTTGCTTGCTGGTAGT
1 TAATAGGAATATTGCATACTTGGTTTTGCTTGCTGGTAGT
*
6319 TAATAGGAGTATTGCATACTTGGTTTTGCTTGCTGGTAGT
1 TAATAGGAATATTGCATACTTGGTTTTGCTTGCTGGTAGT
6359 TAATAGGAATATTGCATAC
1 TAATAGGAATATTGCATAC
6378 CTGTTCTGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.40
Consensus pattern (40 bp):
TAATAGGAATATTGCATACTTGGTTTTGCTTGCTGGTAGT
Found at i:9353 original size:19 final size:19
Alignment explanation
Indices: 9329--9366 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9319 GTTGCTAATT
9329 TTGGTACATTTTGATTGAA
1 TTGGTACATTTTGATTGAA
9348 TTGGTACATTTTGATTGAA
1 TTGGTACATTTTGATTGAA
9367 CTATTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (19 bp):
TTGGTACATTTTGATTGAA
Found at i:9948 original size:22 final size:22
Alignment explanation
Indices: 9923--10020 Score: 108
Period size: 22 Copynumber: 4.4 Consensus size: 22
9913 GTAACTTAGT
*
9923 TATGAAGTTCTAGTAACCTCCC
1 TATGAAATTCTAGTAACCTCCC
* *
9945 TATGAAATTTTAGTAACCTTCAC
1 TATGAAATTCTAGTAACC-TCCC
* * **
9968 TATGAAATGT-TGGTAACTTAGC
1 TATGAAAT-TCTAGTAACCTCCC
9990 TATGAAATTCTAGTAACCTCCC
1 TATGAAATTCTAGTAACCTCCC
10012 TATGAAATT
1 TATGAAATT
10021 TTCGTGACTA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.02
22 43 0.69
23 17 0.27
24 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
TATGAAATTCTAGTAACCTCCC
Found at i:9972 original size:45 final size:45
Alignment explanation
Indices: 9888--10019 Score: 119
Period size: 45 Copynumber: 3.0 Consensus size: 45
9878 CATTCACTCA
* * * *
9888 TAGTAACCTTCCTATGAAATTTTGGGTAA-CTT-AGTTATGAAGT-T
1 TAGTAACCTACCTATGAAATTTT-AGTAACCTTCA-CTATGAAATGT
*
9932 CTAGTAACCTCCCTATGAAATTTTAGTAACCTTCACTATGAAATGT
1 -TAGTAACCTACCTATGAAATTTTAGTAACCTTCACTATGAAATGT
* * * * *
9978 TGGTAACTTAGCTATGAAATTCTAGTAACC-TCCCTATGAAAT
1 TAGTAACCTACCTATGAAATTTTAGTAACCTTCACTATGAAAT
10020 TTTCGTGACT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 15 0.20
45 57 0.77
46 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (45 bp):
TAGTAACCTACCTATGAAATTTTAGTAACCTTCACTATGAAATGT
Found at i:9983 original size:67 final size:67
Alignment explanation
Indices: 9888--10022 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
9878 CATTCACTCA
* * *
9888 TAGTAACCTTCCTATGAAATTTTGGGTAACTTAGTTATGAAGTTCTAGTAACCTCCCTATGAAAT
1 TAGTAACCTTCCTATGAAATGTTGGGTAACTTAGCTATGAAATTCTAGTAACCTCCCTATGAAAT
9953 TT
66 TT
9955 TAGTAACCTTCACTATGAAATGTT-GGTAACTTAGCTATGAAATTCTAGTAACCTCCCTATGAAA
1 TAGTAACCTTC-CTATGAAATGTTGGGTAACTTAGCTATGAAATTCTAGTAACCTCCCTATGAAA
10019 TTT
65 TTT
10022 T
1 T
10023 CGTGACTAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 53 0.83
68 11 0.17
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (67 bp):
TAGTAACCTTCCTATGAAATGTTGGGTAACTTAGCTATGAAATTCTAGTAACCTCCCTATGAAAT
TT
Found at i:10044 original size:47 final size:44
Alignment explanation
Indices: 9943--10069 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 44
9933 TAGTAACCTC
* * *
9943 CCTATGAAATTTTAGTAACCTTCACTATGAAATGTTGGTAACTTA
1 CCTATGAAATTCTAGTAACC-TCCCTATGAAATTTTGGTAACTTA
*
9988 GCTATGAAATTCTAGTAACCTCCCTATGAAATTTTCGTGACTAA-TTA
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTTT-G-G--TAACTTA
** * *
10035 CCTATGAAATTCTAGTATTCTCCTTTTGAAATTTT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTTT
10070 TTTAACCTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 13 0.19
45 19 0.28
46 1 0.01
47 33 0.48
48 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (44 bp):
CCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACTTA
Found at i:10273 original size:20 final size:21
Alignment explanation
Indices: 10250--10296 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
10240 GAAAAATCTA
*
10250 GTAACCTC-CTTAAAATTTTG
1 GTAACCTCACATAAAATTTTG
*
10270 GTAACCTCAACATGAAATTTTG
1 GTAACCTC-ACATAAAATTTTG
10292 GTAAC
1 GTAAC
10297 TTGAAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
22 15 0.65
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (21 bp):
GTAACCTCACATAAAATTTTG
Found at i:14063 original size:30 final size:30
Alignment explanation
Indices: 14027--14085 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
14017 AATAAGCCAT
*
14027 TAAAATTTGAGGGTATAAGAGAAAAGTCAC
1 TAAAATTTAAGGGTATAAGAGAAAAGTCAC
*
14057 TAAAATTTAAGGGTATAAGAGGAAAGTCA
1 TAAAATTTAAGGGTATAAGAGAAAAGTCA
14086 AGATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (30 bp):
TAAAATTTAAGGGTATAAGAGAAAAGTCAC
Found at i:15511 original size:6 final size:6
Alignment explanation
Indices: 15500--15529 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
15490 TGAATTAGAA
15500 ATTGAG ATTGAGG ATTGAG ATTGAG ATTGA
1 ATTGAG ATTGA-G ATTGAG ATTGAG ATTGA
15530 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
ATTGAG
Found at i:15518 original size:13 final size:12
Alignment explanation
Indices: 15500--15529 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
15490 TGAATTAGAA
15500 ATTGAGATTGAGG
1 ATTGAGATTGA-G
15513 ATTGAGATTGAG
1 ATTGAGATTGAG
15525 ATTGA
1 ATTGA
15530 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (12 bp):
ATTGAGATTGAG
Found at i:25642 original size:14 final size:14
Alignment explanation
Indices: 25604--25642 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25594 TATCCTTTTC
*
25604 TTCTTTTTTTT-TT
1 TTCTTTTTTTTGGT
*
25617 TTTTTTTTTTTGGT
1 TTCTTTTTTTTGGT
25631 TTCTTTTTTTTG
1 TTCTTTTTTTTG
25643 AGTGCATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (14 bp):
TTCTTTTTTTTGGT
Found at i:26051 original size:44 final size:44
Alignment explanation
Indices: 26001--26136 Score: 272
Period size: 44 Copynumber: 3.1 Consensus size: 44
25991 CCGACTTCCG
26001 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
1 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
26045 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
1 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
26089 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
1 ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
26133 ATTA
1 ATTA
26137 GACGATCAGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 92 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (44 bp):
ATTAAGGTGATTCTAACGGCATTTGAAAGATCTCGACAAGAAGA
Found at i:27220 original size:13 final size:13
Alignment explanation
Indices: 27202--27231 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
27192 TTTTTCATCT
27202 TTATCTATACTAA
1 TTATCTATACTAA
27215 TTATCTATACTAA
1 TTATCTATACTAA
27228 TTAT
1 TTAT
27232 AATGTGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATCTATACTAA
Done.