Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004985.1 Hibiscus syriacus cultivar Beakdansim tig00011185_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: 383687
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:351577 original size:9 final size:9
Alignment explanation
Indices: 351467--351580 Score: 111
Period size: 9 Copynumber: 12.0 Consensus size: 9
351457 GTTTTCAAAT
351467 GGTTCTGACC
1 GGTT-TGACC
351477 GGTTTGACC
1 GGTTTGACC
*
351486 GGTTTCAACC
1 GGTTT-GACC
*
351496 GGTTCGAACC
1 GGTTTG-ACC
351506 GGTTTGACC
1 GGTTTGACC
* *
351515 GGTCTGAATC
1 GGTTTG-ACC
351525 GGTTTGACC
1 GGTTTGACC
* *
351534 GGTCTGAATC
1 GGTTTG-ACC
351544 GGTTTGACC
1 GGTTTGACC
*
351553 GGTCTGAGCC
1 GGTTTGA-CC
351563 GGTTTGACC
1 GGTTTGACC
351572 GGTTTGACC
1 GGTTTGACC
351581 CGACCCGACC
Statistics
Matches: 85, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
9 44 0.52
10 41 0.48
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (9 bp):
GGTTTGACC
Found at i:351597 original size:17 final size:17
Alignment explanation
Indices: 351575--351607 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
351565 TTTGACCGGT
351575 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
351592 TTGACCCGACCCGACC
1 TTGACCCGACCCGACC
351608 CGACCGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.48, G:0.21, T:0.12
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:352605 original size:63 final size:63
Alignment explanation
Indices: 352503--352626 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
352493 CTAATGTGAC
* ** * *
352503 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGC-CTTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCTC-T-CAGGCCCTAAGATGTGT
*
352566 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCTCTCAGGCCCTAAGATGT
352627 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCTCTCAGGCCCTAAGATGTGT
Found at i:358839 original size:19 final size:18
Alignment explanation
Indices: 358815--358912 Score: 108
Period size: 19 Copynumber: 5.2 Consensus size: 18
358805 CCGGTTTTCA
*
358815 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
358834 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
358853 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
*
358872 AATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
358891 AGCCGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
358910 ACC
1 ACC
358913 CGACCCGACC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.07
19 56 0.80
20 9 0.13
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:358847 original size:29 final size:29
Alignment explanation
Indices: 358804--358912 Score: 118
Period size: 29 Copynumber: 3.8 Consensus size: 29
358794 GCTGCTGGAA
358804 ACCGGTTTTCAACCGGTTCTGACCGGTTTG
1 ACCGG-TTTCAACCGGTTCTGACCGGTTTG
358834 ACCGGTTTCAACCGGTTC-GAACCGGTTTG
1 ACCGGTTTCAACCGGTTCTG-ACCGGTTTG
* * * *
358863 ACCGGTCTGAATCGGTT-TGACCGGTCTG
1 ACCGGTTTCAACCGGTTCTGACCGGTTTG
*
358891 AGCCGGTTT-GACCGG-TCTGACC
1 A-CCGGTTTCAACCGGTTCTGACC
358913 CGACCCGACC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.01
28 19 0.28
29 43 0.63
30 5 0.07
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.28
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCTGACCGGTTTG
Found at i:358868 original size:38 final size:37
Alignment explanation
Indices: 358814--358912 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 37
358804 ACCGGTTTTC
*
358814 AACCGGTTCTGACCGGTTTGACCGGTTTCAACCGGT-TCG
1 AACCGGTT-TGACCGGTCTGACCGGTTT-AACCGGTCT-G
* *
358853 AACCGGTTTGACCGGTCTGAATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG-ACCGGTTTAACCGGTCTG
*
358891 AGCCGGTTTGACCGGTCTGACC
1 AACCGGTTTGACCGGTCTGACC
358913 CGACCCGACC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.04
38 35 0.66
39 16 0.30
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (37 bp):
AACCGGTTTGACCGGTCTGACCGGTTTAACCGGTCTG
Found at i:358935 original size:22 final size:22
Alignment explanation
Indices: 358909--358951 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
358899 TGACCGGTCT
358909 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
358931 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
358952 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:358953 original size:7 final size:7
Alignment explanation
Indices: 358941--358971 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
358931 GACCCGACCC
358941 GACCGTT
1 GACCGTT
358948 GACCGTT
1 GACCGTT
358955 GACCGTT
1 GACCGTT
358962 GACCGTT
1 GACCGTT
358969 GAC
1 GAC
358972 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:359926 original size:32 final size:31
Alignment explanation
Indices: 359842--359918 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
359832 CTAATGTGAC
* *
359842 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
359873 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
359905 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
359919 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:359944 original size:63 final size:63
Alignment explanation
Indices: 359842--359965 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
359832 CTAATGTGAC
* ** * * *
359842 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAAGCCCTAAGATGTGT
* *
359905 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAAGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAAGCCCTAAGATGT
359966 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.94
64 2 0.04
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAAGCCCTAAGATGTGT
Found at i:364346 original size:16 final size:16
Alignment explanation
Indices: 364325--364365 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
364315 AATATATGGT
364325 AATGAAATAAGAAAAA
1 AATGAAATAAGAAAAA
* * *
364341 AATGAAAGAATAAAGA
1 AATGAAATAAGAAAAA
364357 AATGAAATA
1 AATGAAATA
364366 GTAAGAAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AATGAAATAAGAAAAA
Found at i:364616 original size:18 final size:17
Alignment explanation
Indices: 364582--364620 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
364572 TAGGAGTATT
364582 TTTTCTTTTCTTTTTGC
1 TTTTCTTTTCTTTTTGC
364599 TTTTCTTCTT-TTTGTTGC
1 TTTTCTT-TTCTTT-TTGC
364617 TTTT
1 TTTT
364621 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTGC
Found at i:368907 original size:13 final size:13
Alignment explanation
Indices: 368885--368914 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
368875 ACTAAACACC
368885 TTTC-ACATACCT
1 TTTCAACATACCT
368897 TTTCAACATACCT
1 TTTCAACATACCT
368910 TTTCA
1 TTTCA
368915 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:372147 original size:8 final size:8
Alignment explanation
Indices: 372134--372178 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
372124 AAATCTTTTT
372134 TTTTCTTC
1 TTTTCTTC
372142 TTTTCTTC
1 TTTTCTTC
*
372150 TTTCCTTC
1 TTTTCTTC
372158 TTTT-TGTC
1 TTTTCT-TC
372166 TTTTCCTTC
1 TTTT-CTTC
372175 TTTT
1 TTTT
372179 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 1 0.03
8 24 0.75
9 6 0.19
10 1 0.03
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTCTTC
Found at i:372159 original size:16 final size:15
Alignment explanation
Indices: 372127--372179 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 15
372117 CTTTTTGAAA
372127 TCTTTTTT-TTT-CT
1 TCTTTTTTCTTTCCT
372140 TCTTTTCTTCTTTCCT
1 TCTTTT-TTCTTTCCT
372156 TCTTTTTGTCTTTTCCT
1 TCTTTTT-TC-TTTCCT
372173 TCTTTTT
1 TCTTTTT
372180 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.17
14 2 0.06
15 4 0.11
16 10 0.29
17 13 0.37
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (15 bp):
TCTTTTTTCTTTCCT
Found at i:372487 original size:19 final size:20
Alignment explanation
Indices: 372432--372489 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
372422 ATAATGGGTT
*
372432 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
372451 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
372471 TAAG-AAT-AAAATGAAATAA
1 TAAGTAATGAAAAT-AAATAA
372490 ATAAAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 8 0.23
19 22 0.63
20 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:376098 original size:35 final size:37
Alignment explanation
Indices: 376052--376131 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
376042 TTTGAGAATT
*
376052 TGGTGATGATATAGGCGTGAT-ATGG-TGATGAACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
* *
376087 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
376124 TGGTGATG
1 TGGTGATG
376132 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
Found at i:381705 original size:35 final size:37
Alignment explanation
Indices: 381659--381738 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
381649 TTGAGAATTT
* * *
381659 TGGTGATGATATATGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
381694 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
381731 TGGTGATG
1 TGGTGATG
381739 GAAATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.34
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Done.