Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012468.1 Corchorus olitorius cultivar O-4 contig12501, 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: 44657
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9161 original size:19 final size:19
Alignment explanation
Indices: 9137--9196 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
9127 TCTACCCATT
9137 TGAGTAACACCTGAGTTTG
1 TGAGTAACACCTGAGTTTG
* **
9156 TGAGTATA-A-AT-AAATT-
1 TGAGTA-ACACCTGAGTTTG
9172 TGAGTAACACCTGAGTTTG
1 TGAGTAACACCTGAGTTTG
9191 TGAGTA
1 TGAGTA
9197 TAAATAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
15 1 0.03
16 7 0.23
17 4 0.13
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (19 bp):
TGAGTAACACCTGAGTTTG
Found at i:9180 original size:35 final size:35
Alignment explanation
Indices: 9134--9207 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
9124 TGTTCTACCC
9134 ATTTGAGTAACACCTGAGTTTGTGAGTATAAATAA
1 ATTTGAGTAACACCTGAGTTTGTGAGTATAAATAA
9169 ATTTGAGTAACACCTGAGTTTGTGAGTATAAATAA
1 ATTTGAGTAACACCTGAGTTTGTGAGTATAAATAA
9204 ATTT
1 ATTT
9208 AAATCCTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (35 bp):
ATTTGAGTAACACCTGAGTTTGTGAGTATAAATAA
Found at i:20911 original size:14 final size:16
Alignment explanation
Indices: 20875--20912 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
20865 AAGGTTGCGG
20875 TTTGAAAAAGTTTGCT
1 TTTGAAAAAGTTTGCT
*
20891 TTGGAAAAA-TTT-CT
1 TTTGAAAAAGTTTGCT
20905 TTTGAAAA
1 TTTGAAAA
20913 GTACTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (16 bp):
TTTGAAAAAGTTTGCT
Found at i:23650 original size:2 final size:2
Alignment explanation
Indices: 23645--23691 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
23635 ACACATGATA
* * *
23645 AT AT AT AT AT AT AT AT AT AT AGG GT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
23688 AT AT
1 AT AT
23692 TAACCACAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27567 original size:39 final size:39
Alignment explanation
Indices: 27513--27668 Score: 179
Period size: 39 Copynumber: 4.0 Consensus size: 39
27503 ACTTAAACGG
* *
27513 AACAGAGACCTAAGCATGTTTGCTTAAACGGAAATTCTA
1 AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
27552 AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
1 AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
* *** * *
27591 AACAGGGACCTAAGTAGGTTCAATCAAAC-GAGATTCTA
1 AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
* * * * **
27629 AGCAGGGGCCTGAGCAGGTTTTCTTAAACAAAAATTCTA
1 AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
27668 A
1 A
27669 CGAGATTCTA
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 29 0.30
39 69 0.70
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (39 bp):
AACAGGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTA
Found at i:27800 original size:5 final size:5
Alignment explanation
Indices: 27790--27825 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
27780 TGTTTATTTG
27790 TTTTC TTTTC TTCTTC TTTTC TTCTTC TTTTC TTTT
1 TTTTC TTTTC TT-TTC TTTTC TT-TTC TTTTC TTTT
27826 ATTAAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:27806 original size:11 final size:11
Alignment explanation
Indices: 27792--27823 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
27782 TTTATTTGTT
27792 TTCTTTTCTTC
1 TTCTTTTCTTC
27803 TTCTTTTCTTC
1 TTCTTTTCTTC
27814 TTCTTTTCTT
1 TTCTTTTCTT
27824 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:28253 original size:16 final size:16
Alignment explanation
Indices: 28216--28255 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
28206 AGAGGTTGAA
*
28216 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
*
28232 -GAAAACAATTATACT
1 AGAAAACAATTAAACT
28247 AGAAAACAA
1 AGAAAACAA
28256 AGCAAAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:29662 original size:29 final size:31
Alignment explanation
Indices: 29625--29684 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
29615 AATTCTTTCC
* *
29625 TCTTGAAATAATTCTTC-AAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAAATAGTCTTCAAA
29654 TCTTCAAATAAGTCTTCAAATAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAATAGTCTTCAAA
29685 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 3 0.11
31 9 0.33
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (31 bp):
TCTTCAAATAAGTCTTCAAATAGTCTTCAAA
Found at i:29680 original size:11 final size:12
Alignment explanation
Indices: 29654--29684 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
29644 TGTCTTCAAA
29654 TCTTCAAATAAG
1 TCTTCAAATAAG
29666 TCTTCAAAT-AG
1 TCTTCAAATAAG
29677 TCTTCAAA
1 TCTTCAAA
29685 CACGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:31518 original size:20 final size:21
Alignment explanation
Indices: 31480--31518 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31470 AAATCATCAA
31480 CGGTGATGGCACGGGTATAAC
1 CGGTGATGGCACGGGTATAAC
*
31501 CGGTGGTGGCAC-GGTATA
1 CGGTGATGGCACGGGTATA
31519 TGGCCGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.18, G:0.41, T:0.21
Consensus pattern (21 bp):
CGGTGATGGCACGGGTATAAC
Done.