Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008575.1 Hibiscus syriacus cultivar Beakdansim tig00111504_pilon, 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: 896659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:869063 original size:23 final size:24
Alignment explanation
Indices: 869030--869081 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
869020 ACTATGATAT
* ** *
869030 ATAAAATATATCACTTAAATTATA
1 ATAAAATATATAAAATAAATTAAA
869054 ATAAAA-ATATAAAATAAATTAAA
1 ATAAAATATATAAAATAAATTAAA
869077 ATAAA
1 ATAAA
869082 TCATTAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
ATAAAATATATAAAATAAATTAAA
Found at i:869111 original size:24 final size:23
Alignment explanation
Indices: 869079--869128 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
869069 AAATTAAAAT
869079 AAATCATTAAGTAAT-AAATAATTA
1 AAATCATTAA--AATAAAATAATTA
* *
869103 AAATTATTAAAATAAAATTATTA
1 AAATCATTAAAATAAAATAATTA
869126 AAA
1 AAA
869129 AATAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 11 0.48
24 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATCATTAAAATAAAATAATTA
Found at i:869133 original size:38 final size:38
Alignment explanation
Indices: 869053--869133 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
869043 CTTAAATTAT
**
869053 AATAAAAATATAAAATAAATTAAAATAAATCATTAAGT
1 AATAAAAATATAAAATAAATTAAAATAAATCATTAAAA
* *
869091 AATAAATAAT-TAAAAT-TATTAAAATAAAATTATTAAAA
1 AATAAA-AATATAAAATAAATTAAAAT-AAATCATTAAAA
869129 AATAA
1 AATAA
869134 TTTTGATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 8 0.22
38 26 0.70
39 3 0.08
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (38 bp):
AATAAAAATATAAAATAAATTAAAATAAATCATTAAAA
Found at i:869135 original size:14 final size:14
Alignment explanation
Indices: 869101--869128 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
869091 AATAAATAAT
869101 TAAAATTATTAAAA
1 TAAAATTATTAAAA
869115 TAAAATTATTAAAA
1 TAAAATTATTAAAA
869129 AATAATTTTG
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAATTATTAAAA
Found at i:869159 original size:27 final size:25
Alignment explanation
Indices: 869117--869172 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
869107 TATTAAAATA
*
869117 AAATTATTAAAAAATAATTTTGATATT
1 AAATTATTAAAAAATAA-ATT-ATATT
**
869144 AAATTATTAAGTAATAAATTATATT
1 AAATTATTAAAAAATAAATTATATT
869169 AAAT
1 AAAT
869173 ATAGAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 2 0.08
27 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATTATTAAAAAATAAATTATATT
Found at i:869223 original size:25 final size:28
Alignment explanation
Indices: 869195--869247 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
869185 TTATATTTAC
869195 TTTTAAATA-GTTAA-AATAAATTATTT
1 TTTTAAATATGTTAATAATAAATTATTT
* *
869221 TTTTAAGTATGTTAATATTAAATTATT
1 TTTTAAATATGTTAATAATAAATTATT
869248 AAAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 5 0.22
28 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (28 bp):
TTTTAAATATGTTAATAATAAATTATTT
Found at i:881761 original size:15 final size:15
Alignment explanation
Indices: 881741--881769 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
881731 GAGTCATTAC
881741 CCGCCCCGCATCCGT
1 CCGCCCCGCATCCGT
881756 CCGCCCCGCATCCG
1 CCGCCCCGCATCCG
881770 CCCATCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.62, G:0.21, T:0.10
Consensus pattern (15 bp):
CCGCCCCGCATCCGT
Found at i:882595 original size:2 final size:2
Alignment explanation
Indices: 882588--882620 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
882578 AATGTTTCTA
882588 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
882621 ACCAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:884675 original size:23 final size:23
Alignment explanation
Indices: 884626--884695 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
884616 GTTCGTGAAT
* * * *
884626 ATGTTCGTTTAGTGTTTACTAAT
1 ATGTTCGTTTAGTATTCACAAAC
884649 ATGTTCGTTTAGTATTCACAAAC
1 ATGTTCGTTTAGTATTCACAAAC
* *
884672 ATGTT-TTTTATATATTCACAAAC
1 ATGTTCGTTTA-GTATTCACAAAC
884695 A
1 A
884696 ACGAAATAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (23 bp):
ATGTTCGTTTAGTATTCACAAAC
Done.