Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009626.1 Hibiscus syriacus cultivar Beakdansim tig00117018_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: 478969
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:450943 original size:22 final size:22
Alignment explanation
Indices: 450900--450947 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
450890 CATATAATTA
* *
450900 TAAATTAGTTGAAAATGTAAAGG
1 TAAATTAGTTGAAAAT-AAAAAG
*
450923 TAAATTA-TTTAAAATAAAAAG
1 TAAATTAGTTGAAAATAAAAAG
450944 TAAA
1 TAAA
450948 CTATATCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (22 bp):
TAAATTAGTTGAAAATAAAAAG
Found at i:451882 original size:31 final size:31
Alignment explanation
Indices: 451840--451901 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
451830 ATCAAATATT
* *
451840 TTAACTATCACGTTAATTTTTCCATTAAATA
1 TTAACTATCACGTCAACTTTTCCATTAAATA
*
451871 TTAATTATCACGTCAACTTTTCCATTAAATA
1 TTAACTATCACGTCAACTTTTCCATTAAATA
451902 GTCCACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (31 bp):
TTAACTATCACGTCAACTTTTCCATTAAATA
Found at i:452294 original size:3 final size:3
Alignment explanation
Indices: 452286--452318 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
452276 TTTAATTAAA
452286 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
452319 TGAAAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:453213 original size:23 final size:23
Alignment explanation
Indices: 453187--453233 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
453177 AGTCTTTAAA
453187 AACCCAACAAATAGCTTTGCCCC
1 AACCCAACAAATAGCTTTGCCCC
453210 AACCCAACAAATAGCTTTGCCCC
1 AACCCAACAAATAGCTTTGCCCC
453233 A
1 A
453234 TATTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.38, G:0.09, T:0.17
Consensus pattern (23 bp):
AACCCAACAAATAGCTTTGCCCC
Found at i:461654 original size:2 final size:2
Alignment explanation
Indices: 461649--461673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
461639 ACACACACAC
461649 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
461674 AAAGATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:463679 original size:31 final size:31
Alignment explanation
Indices: 463622--463680 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
463612 TTCAAGTTTT
*
463622 TTTGAGTTTAAGTCGAGCTTCAAATTTTGAC
1 TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
* *
463653 TTTGAGTTTGAGTTGA-CTTAACAATTTT
1 TTTGAGTTTAAGTCGAGCTTAA-AATTTT
463681 AAGTTTGCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
Found at i:473559 original size:3 final size:3
Alignment explanation
Indices: 473551--473577 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
473541 CTTTTATTTT
473551 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
473578 CTAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:475697 original size:45 final size:45
Alignment explanation
Indices: 475638--475725 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
475628 TGTGATCCTA
* *
475638 CACTTGCCACGGCAACATCATTAACTCTACTTGCC-TCGACAACTT
1 CACTTGACACGGCAACACCATTAACTCTACTTGCCAT-GACAACTT
* *
475683 CACTTGACAGGGCAACGCCATTAACTCTACTTGCCATGACAAC
1 CACTTGACACGGCAACACCATTAACTCTACTTGCCATGACAAC
475726 GTCATTCACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (45 bp):
CACTTGACACGGCAACACCATTAACTCTACTTGCCATGACAACTT
Found at i:475934 original size:35 final size:35
Alignment explanation
Indices: 475833--475971 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 35
475823 ACTAATCTTC
475833 AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
*
475868 AATAAGAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAG-AAAATACCCAAATTTCTTATGAAACCTTT
*
475904 AATAAGAAAAATACTCAAA-TTCTTATGAAACCTTT
1 AATAAG-AAAATACCCAAATTTCTTATGAAACCTTT
475939 AATAAGAAAATACCCAAATTTCTTATGAAACCT
1 AATAAGAAAATACCCAAATTTCTTATGAAACCT
475972 AAATTGGTGA
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
34 11 0.11
35 42 0.42
36 47 0.47
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (35 bp):
AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
Found at i:478162 original size:20 final size:22
Alignment explanation
Indices: 478134--478191 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
478124 TTCCCCTTGA
*
478134 AGTGAATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
478154 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
478177 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
478192 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:478254 original size:64 final size:63
Alignment explanation
Indices: 478179--478319 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
478169 TCTTTAACAT
* * *
478179 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTCCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGTTT-CATCTTTAAAGA
* * * ** *
478242 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
478306 GTGCATCGATGCAC
1 GTGCATCGATGCAC
478320 ATTAAATATG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Done.