Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016535.1 Corchorus olitorius cultivar O-4 contig16568, 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: 73375
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:223 original size:36 final size:36
Alignment explanation
Indices: 176--245 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
166 TTCAATAACC
* *
176 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
212 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
246 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1321 original size:42 final size:40
Alignment explanation
Indices: 1262--1345 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
1252 AAACCTAAGA
*
1262 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAC
1 ATTTAATTAATGTAAGTATTTCAATTATTATA-TA-TATTAC
*
1304 ATTTAATTAATGTAAGTATTTTAATTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAATTATTATATATATTAC
1344 AT
1 AT
1346 CGGAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 8 0.20
41 2 0.05
42 30 0.75
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAATTATTATATATATTAC
Found at i:2337 original size:32 final size:32
Alignment explanation
Indices: 2281--2362 Score: 157
Period size: 32 Copynumber: 2.6 Consensus size: 32
2271 TAGACTATTA
2281 AAATAGATAATCTTG-TTTTTTTTTGGCAATC
1 AAATAGATAATCTTGTTTTTTTTTTGGCAATC
2312 AAATAGATAATCTTGTTTTTTTTTTGGCAATC
1 AAATAGATAATCTTGTTTTTTTTTTGGCAATC
2344 AAATAGATAATCTTGTTTT
1 AAATAGATAATCTTGTTTT
2363 ATGAAGCAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 15 0.30
32 35 0.70
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (32 bp):
AAATAGATAATCTTGTTTTTTTTTTGGCAATC
Found at i:4922 original size:90 final size:89
Alignment explanation
Indices: 4769--5035 Score: 372
Period size: 92 Copynumber: 2.9 Consensus size: 89
4759 TTGGACCCTA
* * * * *
4769 TAAGCTCGTGTTCTTTGGACTCTGTTTTGTTTTCTTTTCTTATCAATAATACTCCCTGTTTCGCC
1 TAAGCTCGTGTTCTTTGGACTCT-ATTTCTTTCCTTTTCTTATCAATAATATTCTCTGTTTCGCC
4834 TTTCAAAAAAATTGAATATGAACCC
65 TTTCAAAAAAATTGAATATGAACCC
*
4859 TAAGCTCGTGTTCTTTGGACTCTATTTCTTTCCATTTTTTTATCAATAATATTCTCTGTTTCGCC
1 TAAGCTCGTGTTCTTTGGACTCTATTTCTTTCC-TTTTCTTATCAATAATATTCTCTGTTTCGCC
* *
4924 TTTCAAAAAAAAATTAAATATGGACCC
65 TTTC--AAAAAAATTGAATATGAACCC
* * * *
4951 TAAGCTCATGTTCTTTGGACTCTGTTTCTTTCTCTTTTCTTATCAATAATATTCTCTATTTCGTC
1 TAAGCTCGTGTTCTTTGGACTCTATTTCTTTC-CTTTTCTTATCAATAATATTCTCTGTTTCGCC
5016 TTTCAAAAAAATTTGAATAT
65 TTTCAAAAAAA-TTGAATAT
5036 TTTTACAAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
89 7 0.04
90 62 0.39
91 7 0.04
92 81 0.51
93 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.45
Consensus pattern (89 bp):
TAAGCTCGTGTTCTTTGGACTCTATTTCTTTCCTTTTCTTATCAATAATATTCTCTGTTTCGCCT
TTCAAAAAAATTGAATATGAACCC
Found at i:28707 original size:11 final size:11
Alignment explanation
Indices: 28691--28716 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28681 GTAATTCTCA
28691 TAACATCTATT
1 TAACATCTATT
28702 TAACATCTATT
1 TAACATCTATT
28713 TAAC
1 TAAC
28717 GATCCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (11 bp):
TAACATCTATT
Found at i:56185 original size:21 final size:21
Alignment explanation
Indices: 56161--56207 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
56151 ATTGAAATGG
*
56161 TGAGATTAAATATTGTACAGA
1 TGAGATTAAATACTGTACAGA
* *
56182 TGAGATTAGATACTGTATAGA
1 TGAGATTAAATACTGTACAGA
56203 TGAGA
1 TGAGA
56208 ATATAATTAT
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:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (21 bp):
TGAGATTAAATACTGTACAGA
Found at i:59452 original size:53 final size:53
Alignment explanation
Indices: 59394--59576 Score: 177
Period size: 53 Copynumber: 3.5 Consensus size: 53
59384 CATATTCCGT
* * *
59394 GTTTTGCTCTGACTAATCCGAATTTGACCCGCATCATGCATTTGGGTTTGACA
1 GTTTTACTCTGACTAATCCGAATTTGACCCGCGTCATGCACTTGGGTTTGACA
* * * * * ** * *
59447 GTTTTGCTCTGATTAATCCGGATTTGACCTGTGTCGCGCAGTTCGGTTTGACA
1 GTTTTACTCTGACTAATCCGAATTTGACCCGCGTCATGCACTTGGGTTTGACA
* * * * * *
59500 TTTTTACTCTGATTAATCTGAATTCGACCCGCGTCATGCACCTGGATTTGACA
1 GTTTTACTCTGACTAATCCGAATTTGACCCGCGTCATGCACTTGGGTTTGACA
* **
59553 ATTTTACTCACACTAATCCGAATT
1 GTTTTACTCTGACTAATCCGAATT
59577 CGATTTCGAT
Statistics
Matches: 103, Mismatches: 27, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (53 bp):
GTTTTACTCTGACTAATCCGAATTTGACCCGCGTCATGCACTTGGGTTTGACA
Found at i:60881 original size:1 final size:1
Alignment explanation
Indices: 60870--60902 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
60860 TTCGAAATTT
*
60870 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60903 CCTCCAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:71106 original size:10 final size:10
Alignment explanation
Indices: 71091--71122 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
71081 GATTTGAAAA
71091 ATAAACAAAT
1 ATAAACAAAT
71101 ATAAACAAAT
1 ATAAACAAAT
71111 AT--ACAAAT
1 ATAAACAAAT
71119 ATAA
1 ATAA
71123 GTAAAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (10 bp):
ATAAACAAAT
Found at i:73372 original size:25 final size:24
Alignment explanation
Indices: 73321--73375 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
73311 GTCAGCCTTG
*
73321 AATTT-TTTAATGTTTTATTCTTA
1 AATTTATTTAATGTTTTATTATTA
*
73344 AATTTATTTAATGTCTTTATTATTC
1 AATTTATTTAATGT-TTTATTATTA
73369 AATTTAT
1 AATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.18
24 8 0.29
25 15 0.54
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (24 bp):
AATTTATTTAATGTTTTATTATTA
Done.