Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008662.1 Hibiscus syriacus cultivar Beakdansim tig00111662_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: 1703488
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1665704 original size:27 final size:27
Alignment explanation
Indices: 1665674--1665744 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
1665664 AAAAAAAGAG
*
1665674 AGAAAAGAGAGAAAAATCAATTC-GAAA
1 AGAAAAGAGAGAAAAATCAA-ACAGAAA
*
1665701 AGAAAAACAGAGAAAAAATCAAACAGAAA
1 AG-AAAAGAGAG-AAAAATCAAACAGAAA
*
1665730 A-AATAGAGAGAAAAA
1 AGAAAAGAGAGAAAAA
1665745 CTGTAACATC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.14
27 9 0.24
28 9 0.24
29 14 0.38
ACGTcount: A:0.69, C:0.07, G:0.17, T:0.07
Consensus pattern (27 bp):
AGAAAAGAGAGAAAAATCAAACAGAAA
Found at i:1667442 original size:31 final size:31
Alignment explanation
Indices: 1667404--1667559 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1667394 AGGGTCGAGG
1667404 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1667435 GTTTACCTATGTTCTTCGGGACATATCGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1667466 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1667497 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1667528 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1667559 G
1 G
1667560 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1671074 original size:19 final size:18
Alignment explanation
Indices: 1671039--1671073 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1671029 AGTATGTTCA
1671039 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
1671057 GGGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
1671074 CCTAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.34, T:0.26
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:1672115 original size:62 final size:62
Alignment explanation
Indices: 1671966--1672119 Score: 229
Period size: 62 Copynumber: 2.5 Consensus size: 62
1671956 GGTCGAGGGT
* * *
1671966 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATCGACTGT
1 TTACCTAGGTTCTTCGGAACATATGGACTGTTTACCTATGTTCTTCGGGACATATCGACTGA
* * *
1672028 TTACCTATGTTCTTCGGTACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTAGGTTCTTCGGAACATATGGACTGTTTACCTATGTTCTTCGGGACATATCGACTGA
*
1672090 TTACCTAGGTTCTTTGGAATC-TATGGACTG
1 TTACCTAGGTTCTTCGGAA-CATATGGACTG
1672120 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
62 84 0.99
63 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (62 bp):
TTACCTAGGTTCTTCGGAACATATGGACTGTTTACCTATGTTCTTCGGGACATATCGACTGA
Found at i:1672119 original size:31 final size:31
Alignment explanation
Indices: 1671964--1672103 Score: 244
Period size: 31 Copynumber: 4.5 Consensus size: 31
1671954 AGGGTCGAGG
1671964 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1671995 GTTTACCTATGTTCTTCGGGACATATCGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1672026 GTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1672057 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1672088 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1672104 TGGAATCTAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1680097 original size:24 final size:24
Alignment explanation
Indices: 1680065--1680120 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1680055 CAATTGAAAG
*
1680065 AATTAATATATTTCTTATAGACTA
1 AATTGATATATTTCTTATAGACTA
*
1680089 AATTGATATTTTTCTTATAGACTA
1 AATTGATATATTTCTTATAGACTA
1680113 AATTGATA
1 AATTGATA
1680121 CGTAAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (24 bp):
AATTGATATATTTCTTATAGACTA
Found at i:1694670 original size:17 final size:18
Alignment explanation
Indices: 1694648--1694683 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1694638 TTTCTTTTCA
1694648 TTTATCTTCA-CCTCATT
1 TTTATCTTCATCCTCATT
1694665 TTTATCTTCATCCTCATT
1 TTTATCTTCATCCTCATT
1694683 T
1 T
1694684 CTTTATCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATCTTCATCCTCATT
Found at i:1696275 original size:88 final size:88
Alignment explanation
Indices: 1696135--1696297 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 88
1696125 CTAAGTAGGC
** *
1696135 TAGAGGGGTATGTGTCTCTGAGATATAGTGAAACCCTCTGACCACACCATGATATATACCCTTGT
1 TAGAGGGGTATGTGTCTCTGAGATATAGCAAAACCCTCCGACCACACCATGATATATACCCTTGT
1696200 -TCGTGTGTTTGATATAAGTATAT
66 CT-GTGTGTTTGATATAAGTATAT
* * * *
1696223 TAGAGGGGTGTGTGTCTTTGAGATGTAGCAAAACCCTCCGACCACACCATGATGTATACCCTTGT
1 TAGAGGGGTATGTGTCTCTGAGATATAGCAAAACCCTCCGACCACACCATGATATATACCCTTGT
1696288 CTGTGTGTTT
66 CTGTGTGTTT
1696298 TATACTTGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
88 66 0.99
89 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (88 bp):
TAGAGGGGTATGTGTCTCTGAGATATAGCAAAACCCTCCGACCACACCATGATATATACCCTTGT
CTGTGTGTTTGATATAAGTATAT
Done.