Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1854721 original size:18 final size:19
Alignment explanation
Indices: 1854686--1854767 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
1854676 TTTTAATTAC
1854686 TATATTTAT-A-TA-TTAT
1 TATATTTATAATTATTTAT
1854702 TATATTT-TAATTATTTAT
1 TATATTTATAATTATTTAT
1854720 TATATTTAATAATTA-TTAT
1 TATATTT-ATAATTATTTAT
* * *
1854739 GAATAATAATAATTATTATAT
1 -TATATTTATAATTATT-TAT
1854760 T-TATTTAT
1 TATATTTAT
1854768 TATATTCATT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
15 1 0.02
16 8 0.15
17 2 0.04
18 11 0.21
19 16 0.31
20 11 0.21
21 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TATATTTATAATTATTTAT
Found at i:1858575 original size:39 final size:39
Alignment explanation
Indices: 1858497--1858596 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 39
1858487 TATGAAACTT
*
1858497 CACGACTGCATGGCGTCTTCAGGCAAATGAAGAAGACCC
1 CACGACTGCATGGCGTCTTCAGGCAAATGAAGAAAACCC
** **
1858536 CACGACTGTGTGGCGTCTTCAGGCAAATGGGGAAAACCC
1 CACGACTGCATGGCGTCTTCAGGCAAATGAAGAAAACCC
* * * *
1858575 CAAGAGTGCACGGCATCTTCAG
1 CACGACTGCATGGCGTCTTCAG
1858597 ACCAATAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (39 bp):
CACGACTGCATGGCGTCTTCAGGCAAATGAAGAAAACCC
Found at i:1867277 original size:2 final size:2
Alignment explanation
Indices: 1867270--1867294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1867260 TAGTTTACCC
1867270 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1867295 TTGAAAATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1869005 original size:20 final size:20
Alignment explanation
Indices: 1868954--1869009 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1868944 ATTATGAAAT
1868954 CTCAGTCTCGATACCAAGCC
1 CTCAGTCTCGATACCAAGCC
1868974 CTTCAGTCTCGATACCGAA-CC
1 C-TCAGTCTCGATACC-AAGCC
*
1868995 CTCAGTATCGATACC
1 CTCAGTCTCGATACC
1869010 CCTTAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 17 0.52
22 2 0.06
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (20 bp):
CTCAGTCTCGATACCAAGCC
Found at i:1870754 original size:25 final size:24
Alignment explanation
Indices: 1870737--1870796 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1870727 TAATAAATTA
1870737 AAATTTAAAAAATGATAAAAAAAAT
1 AAATTTAAAAAAT-ATAAAAAAAAT
* *
1870762 AAATTTAAAAAGT-TAGTAAAAAAT
1 AAATTTAAAAAATATA-AAAAAAAT
*
1870786 AAAGTTAAAAA
1 AAATTTAAAAA
1870797 TTTAATTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 17 0.55
25 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (24 bp):
AAATTTAAAAAATATAAAAAAAAT
Found at i:1872401 original size:21 final size:21
Alignment explanation
Indices: 1872377--1872459 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
1872367 TCTTTTCATG
*
1872377 TTAACATTATATTTCTTCGTC
1 TTAACATTATATTTCTTCGTA
* * * **
1872398 TTAACATAATATCTATTTATA
1 TTAACATTATATTTCTTCGTA
* *
1872419 TTAATATTATATTTCTTTGTA
1 TTAACATTATATTTCTTCGTA
* *
1872440 TTAACATCACATTTCTTCGT
1 TTAACATTATATTTCTTCGT
1872460 TAAGTGAAAA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (21 bp):
TTAACATTATATTTCTTCGTA
Found at i:1872965 original size:13 final size:13
Alignment explanation
Indices: 1872949--1873001 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1872939 TGTTCGGGTC
*
1872949 TTTTATATT-TTA
1 TTTTTTATTATTA
1872961 TTTTTTATTATTA
1 TTTTTTATTATTA
**
1872974 TTAATTATTATTA
1 TTTTTTATTATTA
* *
1872987 ATTATTATTATTA
1 TTTTTTATTATTA
1873000 TT
1 TT
1873002 ATTAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
12 8 0.24
13 26 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTATTATTA
Found at i:1872973 original size:3 final size:3
Alignment explanation
Indices: 1872954--1873005 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
1872944 GGGTCTTTTA
1872954 TAT T-T TAT T-T T-T TAT TAT TAT TAAT TAT TAT TAAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT
1872998 TAT TAT TA
1 TAT TAT TA
1873006 ATTTTACATA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 33 0.73
4 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1872980 original size:10 final size:10
Alignment explanation
Indices: 1872967--1873008 Score: 77
Period size: 10 Copynumber: 4.3 Consensus size: 10
1872957 TTTATTTTTT
1872967 ATTATTATTA
1 ATTATTATTA
1872977 ATTATTATTA
1 ATTATTATTA
1872987 ATTATTATT-
1 ATTATTATTA
1872996 ATTATTATTA
1 ATTATTATTA
1873006 ATT
1 ATT
1873009 TTACATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.29
10 22 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATTATTA
Found at i:1873017 original size:19 final size:19
Alignment explanation
Indices: 1872965--1873018 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
1872955 ATTTTATTTT
1872965 TTATT-ATTATT-A-ATTA
1 TTATTAATTATTAATATTA
*
1872981 TTATTAATTATTATTATTA
1 TTATTAATTATTAATATTA
1873000 TTATTAATT-TTACATATTA
1 TTATTAATTATTA-ATATTA
1873019 CATTTTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 3 0.09
19 18 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTAATTATTAATATTA
Found at i:1886473 original size:15 final size:15
Alignment explanation
Indices: 1886453--1886495 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1886443 ACACTTAAAA
*
1886453 AAAAAAAAGGAAATG
1 AAAAAAAAGAAAATG
*
1886468 AAAAAAATGAAAATG
1 AAAAAAAAGAAAATG
*
1886483 AAAAAGAAGAAAA
1 AAAAAAAAGAAAA
1886496 AATAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
AAAAAAAAGAAAATG
Found at i:1887744 original size:131 final size:134
Alignment explanation
Indices: 1887435--1887734 Score: 346
Period size: 140 Copynumber: 2.2 Consensus size: 134
1887425 AACATCAACT
*
1887435 GACCAGA--TCCTCATCACGTAGGAGA--GTGTCAACATTAGGATAACCAGCCGTCCATCACGTA
1 GACCAGACTTCCTCATCACGTAGGA-ACCGTGTCAACCTTA-GATAACCAGCCGTCCATCACGTA
* ** *
1887496 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
64 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA-C
1887561 TACCCTTAGA
128 TA-CCTT--A
* *
1887571 CGACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCTCATCACGTA
1 -GACCAGACTTCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGCCGTC-CATCACGTA
* * * *
1887636 GGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACT-TTCATCGCGTATGAGCCGTGTCA-T
64 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCACT
1887699 -CCTT-
129 ACCTTA
* * *
1887703 GACCAGATTTCTTCATCACGTAGGAATCGTGT
1 GACCAGACTTCCTCATCACGTAGGAACCGTGT
1887735 TTCCCTTAGA
Statistics
Matches: 143, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
131 28 0.20
135 4 0.03
137 8 0.06
139 48 0.34
140 55 0.38
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (134 bp):
GACCAGACTTCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGCCGTCCATCACGTAGG
AACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCACTAC
CTTA
Done.