Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003625.1 Hibiscus syriacus cultivar Beakdansim tig00007671_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: 89504
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:100 original size:23 final size:23
Alignment explanation
Indices: 74--126 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
64 GTCAACATTC
* *
74 GAAAATGTACCATAAAATCAAAG
1 GAAAATGTACCATAAAAGCAAAA
* **
97 GAAAATTTGTCATAAAAGCAAAA
1 GAAAATGTACCATAAAAGCAAAA
120 GAAAATG
1 GAAAATG
127 CTATACAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (23 bp):
GAAAATGTACCATAAAAGCAAAA
Found at i:4267 original size:34 final size:34
Alignment explanation
Indices: 4229--4313 Score: 170
Period size: 34 Copynumber: 2.5 Consensus size: 34
4219 TAAATATTAC
4229 GGAGTTACCATAATGGTAAAACATGACCAGGTAT
1 GGAGTTACCATAATGGTAAAACATGACCAGGTAT
4263 GGAGTTACCATAATGGTAAAACATGACCAGGTAT
1 GGAGTTACCATAATGGTAAAACATGACCAGGTAT
4297 GGAGTTACCATAATGGT
1 GGAGTTACCATAATGGT
4314 GTTTATTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (34 bp):
GGAGTTACCATAATGGTAAAACATGACCAGGTAT
Found at i:5681 original size:8 final size:8
Alignment explanation
Indices: 5663--5693 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
5653 CTTAATTGAT
5663 ATAATTTAA
1 ATAA-TTAA
5672 ATAATTAA
1 ATAATTAA
5680 ATAATTAA
1 ATAATTAA
5688 ATAATT
1 ATAATT
5694 TAATTGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAATTAA
Found at i:9985 original size:36 final size:38
Alignment explanation
Indices: 9940--10012 Score: 114
Period size: 36 Copynumber: 1.9 Consensus size: 38
9930 TGAATATCTC
9940 TCTCTCGTCTGAA-TTCTCCTAATT-CTTCTTCTCCTA
1 TCTCTCGTCTGAATTTCTCCTAATTCCTTCTTCTCCTA
9976 TCTCTCGTCTGAATTCTTCTCCTAATTCCTTCTTCTC
1 TCTCTCGTCTGAA-T-TTCTCCTAATTCCTTCTTCTC
10013 TCAAAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 13 0.39
39 11 0.33
40 9 0.27
ACGTcount: A:0.12, C:0.34, G:0.05, T:0.48
Consensus pattern (38 bp):
TCTCTCGTCTGAATTTCTCCTAATTCCTTCTTCTCCTA
Found at i:10327 original size:21 final size:21
Alignment explanation
Indices: 10303--10349 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
10293 GAGCATTCTA
10303 CTGATGAGCAGGTACAATCTC
1 CTGATGAGCAGGTACAATCTC
10324 CTGATGAGCAGGTACAATCTC
1 CTGATGAGCAGGTACAATCTC
10345 CTGAT
1 CTGAT
10350 ACTTCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
CTGATGAGCAGGTACAATCTC
Found at i:26083 original size:3 final size:3
Alignment explanation
Indices: 26075--26108 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
26065 TGAATATTTA
26075 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
26109 GAGAATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:26562 original size:16 final size:16
Alignment explanation
Indices: 26521--26563 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
26511 ATTTCGCCGT
26521 TAAAATTTAAAAAGTA
1 TAAAATTTAAAAAGTA
*
26537 TAAAAATTAAAAA-TAA
1 TAAAATTTAAAAAGT-A
*
26553 TCAAATTTAAA
1 TAAAATTTAAA
26564 TAGATAGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAAATTTAAAAAGTA
Found at i:49395 original size:12 final size:12
Alignment explanation
Indices: 49379--49422 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
49369 ATTATTTAAT
49379 TTTTTATCTATCC
1 TTTTTATCTAT-C
*
49392 TTTTATAT-TATA
1 TTTT-TATCTATC
49404 TTTTTATCTATC
1 TTTTTATCTATC
49416 TTTTTAT
1 TTTTTAT
49423 ATTTATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
13 7 0.26
14 3 0.11
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATCTATC
Found at i:49428 original size:26 final size:27
Alignment explanation
Indices: 49371--49428 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
49361 TTGTCGGTAT
49371 TATTTA-ATTTTTTATCTATCCTTTTA
1 TATTTATATTTTTTATCTATCCTTTTA
*
49397 TA-TTATA-TTTTTATCTATCTTTTTA
1 TATTTATATTTTTTATCTATCCTTTTA
49422 TATTTAT
1 TATTTAT
49429 GATACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTATATTTTTTATCTATCCTTTTA
Found at i:49452 original size:23 final size:23
Alignment explanation
Indices: 49416--49478 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
49406 TTTATCTATC
*
49416 TTTTTATATT-TATGATACGATTT
1 TTTTTAT-TTCTATGATACAATTT
*
49439 TTTTTATTTCTATGATATAATTT
1 TTTTTATTTCTATGATACAATTT
* *
49462 TCTATATTTCTATGATA
1 TTTTTATTTCTATGATA
49479 TGTTTTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTTTATTTCTATGATACAATTT
Found at i:49479 original size:23 final size:23
Alignment explanation
Indices: 49443--49491 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
49433 CGATTTTTTT
49443 TATTTCTATGATATAATTTTCTA
1 TATTTCTATGATATAATTTTCTA
**
49466 TATTTCTATGATATGTTTTTCTA
1 TATTTCTATGATATAATTTTCTA
49489 TAT
1 TAT
49492 ATTTTTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.59
Consensus pattern (23 bp):
TATTTCTATGATATAATTTTCTA
Found at i:65007 original size:20 final size:20
Alignment explanation
Indices: 64933--65004 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
64923 CAAAGCCGGT
*
64933 AGTATCGATACTACCTAGTG
1 AGTATCAATACTACCTAGTG
*
64953 AGTATCGATACTACCTAGTG
1 AGTATCAATACTACCTAGTG
* *
64973 AGTATCAATACTTCCTAGTA
1 AGTATCAATACTACCTAGTG
64993 AGTATCAATACT
1 AGTATCAATACT
65005 TCCCTTACCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
AGTATCAATACTACCTAGTG
Found at i:66322 original size:19 final size:20
Alignment explanation
Indices: 66280--66322 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
66270 CTAAATCATT
* * *
66280 TTTCAAAATTTCATTTTGGT
1 TTTCAAAATTCCATTTTAGC
66300 TTTCAAAA-TCCATTTTAGC
1 TTTCAAAATTCCATTTTAGC
66319 TTTC
1 TTTC
66323 CAAAGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTCAAAATTCCATTTTAGC
Found at i:69755 original size:2 final size:2
Alignment explanation
Indices: 69748--69798 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
69738 TTTTCAAAAT
69748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69790 TA TA TA TA T
1 TA TA TA TA T
69799 TTTAAGTTCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74119 original size:22 final size:21
Alignment explanation
Indices: 74077--74116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74067 AAGACTATTT
74077 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
74098 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
74117 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:76084 original size:18 final size:17
Alignment explanation
Indices: 76030--76078 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
76020 TTGGATCCTT
* *
76030 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
76048 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
76066 AGTGCATTCGATG
1 AGTGCA-TCGATG
76079 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:76129 original size:63 final size:65
Alignment explanation
Indices: 76050--76206 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 65
76040 TGCACTAAGA
*
76050 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAT-AGTGC-TCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC-TCAGTGCATCGATGCATGG-
76111 T-G
63 TAG
* * * * *
76113 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGTATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTCAGTGCATCGATGCATGGTAG
*
76178 GTGCATCGATGCATGAAATGCATTCGATG
1 GTGCATCGATGCATCAAATGCATTCGATG
76207 CTCAATTTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 28 0.35
64 14 0.17
65 39 0.48
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTCAGTGCATCGATGCATGGTAG
Done.