Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001722.1 Hibiscus syriacus cultivar Beakdansim tig00003482_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: 98622
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2173 original size:14 final size:15
Alignment explanation
Indices: 2139--2176 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2129 TGTGAATGAT
2139 AAAAAAATGCAAAAG
1 AAAAAAATGCAAAAG
2154 AAAAAAATG-AAAGGAG
1 AAAAAAATGCAAA--AG
2170 AAAAAAA
1 AAAAAAA
2177 GTTAGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAAAATGCAAAAG
Found at i:3284 original size:2 final size:2
Alignment explanation
Indices: 3268--3329 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
3258 TTTCAAAACC
3268 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3310 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3330 ATTCTGGACA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6217 original size:19 final size:19
Alignment explanation
Indices: 6193--6230 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6183 GTTCAAAATG
6193 GGGACCAAAATTTGGTCTC
1 GGGACCAAAATTTGGTCTC
6212 GGGACCAAAATTTGGTCTC
1 GGGACCAAAATTTGGTCTC
6231 CAACTGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
GGGACCAAAATTTGGTCTC
Found at i:6721 original size:42 final size:43
Alignment explanation
Indices: 6661--6746 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
6651 GGTGAAGAGA
* *
6661 TATAATAAATGCCGCAATAGGTGTTGAGATTTAACGGCGTTTG
1 TATAATAAACGCCGCAATAGGTGTTCAGATTTAACGGCGTTTG
* *
6704 TATAA-AAACGCCGCAATAGGTGTTCATATTTAGCGGCGTTTG
1 TATAATAAACGCCGCAATAGGTGTTCAGATTTAACGGCGTTTG
6746 T
1 T
6747 TCCAAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 34 0.87
43 5 0.13
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (43 bp):
TATAATAAACGCCGCAATAGGTGTTCAGATTTAACGGCGTTTG
Found at i:8377 original size:21 final size:21
Alignment explanation
Indices: 8353--8392 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
8343 CTCATTTTCA
8353 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
8374 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
8393 CTATCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:9228 original size:6 final size:7
Alignment explanation
Indices: 9211--9244 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
9201 TAAAACTTTT
9211 TTTTTGA
1 TTTTTGA
9218 TTTTTGA
1 TTTTTGA
9225 TTTTTGA
1 TTTTTGA
9232 TTTTTGA
1 TTTTTGA
9239 TCTTTT
1 T-TTTT
9245 TTTACTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.12, C:0.03, G:0.12, T:0.74
Consensus pattern (7 bp):
TTTTTGA
Found at i:16834 original size:30 final size:30
Alignment explanation
Indices: 16792--16853 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
16782 GTAAACATTT
16792 ACACAACAATCCTCTCAACCCGAAAACATC
1 ACACAACAATCCTCTCAACCCGAAAACATC
* *
16822 ACACAA-AGATCCTCTCAACCCGTAAATATC
1 ACACAACA-ATCCTCTCAACCCGAAAACATC
16852 AC
1 AC
16854 TTGACAATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.16
Consensus pattern (30 bp):
ACACAACAATCCTCTCAACCCGAAAACATC
Found at i:22568 original size:27 final size:28
Alignment explanation
Indices: 22497--22575 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 28
22487 CTAAAAATAT
*
22497 TAATAATTACAAAAATT-AATT-TATAAAC
1 TAATAA-TA-AAAAATTAAATTAAATAAAC
22525 TAATAATAAAAAATTAAA-TAAATAAAC
1 TAATAATAAAAAATTAAATTAAATAAAC
* * * *
22552 TATTACTAATAATTTAAATTAAAT
1 TAATAATAAAAAATTAAATTAAAT
22576 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.19
27 24 0.56
28 11 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATAATAAAAAATTAAATTAAATAAAC
Found at i:22711 original size:8 final size:8
Alignment explanation
Indices: 22700--22746 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
22690 CTAAACCAAT
22700 TTAAATAA
1 TTAAATAA
22708 TTAAATAA
1 TTAAATAA
22716 TTAAATAA
1 TTAAATAA
*
22724 -AATAATAA
1 TTA-AATAA
*
22732 TAAAAT-A
1 TTAAATAA
22739 TTAAATAA
1 TTAAATAA
22747 AATAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.21
8 25 0.74
9 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TTAAATAA
Found at i:22747 original size:12 final size:12
Alignment explanation
Indices: 22710--22750 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
22700 TTAAATAATT
22710 AAATAATTAAATA
1 AAAT-ATTAAATA
*
22723 AAATAAT-AATA
1 AAATATTAAATA
22734 AAATATTAAATA
1 AAATATTAAATA
22746 AAATA
1 AAATA
22751 AAATATACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.40
12 11 0.44
13 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATATTAAATA
Found at i:22752 original size:17 final size:18
Alignment explanation
Indices: 22711--22756 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
22701 TAAATAATTA
*
22711 AATAATTAAATA--AAAT
1 AATAATAAAATATTAAAT
22727 AATAATAAAATATTAAAT
1 AATAATAAAATATTAAAT
22745 AA-AATAAAATAT
1 AATAATAAAATAT
22757 ACCTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.41
17 10 0.37
18 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATAAAATATTAAAT
Found at i:26598 original size:2 final size:2
Alignment explanation
Indices: 26591--26670 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
26581 TTAAAACATA
26591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26671 CTCATTCATA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35274 original size:15 final size:15
Alignment explanation
Indices: 35256--35295 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
35246 CAATGTTTTT
35256 AAAATCGTAAACATA
1 AAAATCGTAAACATA
* *
35271 AAAATTCATAATCATA
1 AAAA-TCGTAAACATA
35287 AAAATCGTA
1 AAAATCGTA
35296 TTTGCGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAATCGTAAACATA
Found at i:44708 original size:34 final size:31
Alignment explanation
Indices: 44659--44725 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 31
44649 CACTTTTAAG
*
44659 TATTTTATTATTATTTACATATGATGTGGCATT
1 TATTTTATTAGTATTTACATATG--GTGGCATT
*
44692 TATTATTATTAGTATTTTCATATGGTGGCATT
1 TATT-TTATTAGTATTTACATATGGTGGCATT
44724 TA
1 TA
44726 ATATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 10 0.32
33 4 0.13
34 17 0.55
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (31 bp):
TATTTTATTAGTATTTACATATGGTGGCATT
Found at i:57477 original size:32 final size:30
Alignment explanation
Indices: 57404--57524 Score: 161
Period size: 32 Copynumber: 3.9 Consensus size: 30
57394 AGAGTCGAGG
* * *
57404 GTTACCTATGTCTTTCGAGACATATGGATA
1 GTTACCTATGTCCTTCGGGACATATGGACA
57434 GTTTACCTATGTCCTTCGGGACATATGGACA
1 G-TTACCTATGTCCTTCGGGACATATGGACA
*
57465 TGATTACCTATGTCCTTAGGGACATATGGACA
1 -G-TTACCTATGTCCTTCGGGACATATGGACA
* *
57497 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
57525 TAGGTTCTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.31
31 27 0.33
32 29 0.36
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGGACATATGGACA
Found at i:65090 original size:2 final size:2
Alignment explanation
Indices: 65083--65124 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
65073 ACCCATAATA
65083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65125 TTCTGAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77494 original size:16 final size:17
Alignment explanation
Indices: 77473--77506 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
77463 ATATGGTGGC
*
77473 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
77489 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
77506 A
1 A
77507 AAATAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:79879 original size:3 final size:3
Alignment explanation
Indices: 79871--79945 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
79861 TATAATCAAT
79871 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
79918 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
79946 CATTGCTCAT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:96350 original size:3 final size:3
Alignment explanation
Indices: 96342--96377 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
96332 GCTCATATTG
96342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
96378 GTTTGTGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.