Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001406.1 Hibiscus syriacus cultivar Beakdansim tig00002743_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: 78592
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:2182 original size:30 final size:30
Alignment explanation
Indices: 2140--2208 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2130 AGATACTGAT
* *
2140 GTGGCATGTCCATATATATTATATGAAGAC
1 GTGGCATGTCCATATATACTAAATGAAGAC
* **
2170 GTGGCA-GATCCATGTATACTAAATGCTGAC
1 GTGGCATG-TCCATATATACTAAATGAAGAC
2200 GTGGCATGT
1 GTGGCATGT
2209 ACACGTGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 30 0.94
31 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (30 bp):
GTGGCATGTCCATATATACTAAATGAAGAC
Found at i:3311 original size:31 final size:31
Alignment explanation
Indices: 3273--3395 Score: 201
Period size: 31 Copynumber: 4.0 Consensus size: 31
3263 CCCGAAGGAC
*
3273 CAGTCCATATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
3304 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
3335 CAGTCCATATGTCCCGACGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
3366 CAGCCCATATGTTCCGAAAAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
3396 CCCTCGACTC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:7036 original size:20 final size:20
Alignment explanation
Indices: 7010--7056 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
7000 AGGGATGTTT
7010 CGATACCCTATAGAGGGTAC
1 CGATACCCTATAGAGGGTAC
*
7030 TGATACCCTATAGAGGGTAC
1 CGATACCCTATAGAGGGTAC
7050 CGATACC
1 CGATACC
7057 TATCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (20 bp):
CGATACCCTATAGAGGGTAC
Found at i:7717 original size:30 final size:31
Alignment explanation
Indices: 7681--7739 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
7671 GAGTCGAGGG
*
7681 TTACCTATGTTTTTC-GAACATATAGACTCA
1 TTACCTATGTTCTTCAGAACATATAGACTCA
* *
7711 TTACCTATGTTCTTCAGAATATATGGACT
1 TTACCTATGTTCTTCAGAACATATAGACT
7740 AGTTTTTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCAGAACATATAGACTCA
Found at i:8086 original size:28 final size:28
Alignment explanation
Indices: 8046--8101 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
8036 TAAAGCTAAG
8046 TTCAAAGGAACAACATATCTCTACTCAA
1 TTCAAAGGAACAACATATCTCTACTCAA
*
8074 TTCAAAGGAACAACATATCTCTGCTCAA
1 TTCAAAGGAACAACATATCTCTACTCAA
8102 AGATCAGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (28 bp):
TTCAAAGGAACAACATATCTCTACTCAA
Found at i:8377 original size:35 final size:35
Alignment explanation
Indices: 8331--8401 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
8321 TCGGGTTGAA
8331 TACGGGTTGGGGTGTTACATTTAATCACCCGGTAT
1 TACGGGTTGGGGTGTTACATTTAATCACCCGGTAT
8366 TACGGGTTGGGGTGTTACATTTAATCACCCGGTAT
1 TACGGGTTGGGGTGTTACATTTAATCACCCGGTAT
8401 T
1 T
8402 GAGGATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (35 bp):
TACGGGTTGGGGTGTTACATTTAATCACCCGGTAT
Found at i:12125 original size:21 final size:21
Alignment explanation
Indices: 12094--12144 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12084 TTTACATCCG
12094 AAAATTTATATTATCAAAT-AAT
1 AAAA-TTATATT-TCAAATCAAT
* *
12116 AAAATTATATTTTATATCAAT
1 AAAATTATATTTCAAATCAAT
12137 AAAATTAT
1 AAAATTAT
12145 TTTTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTATATTTCAAATCAAT
Found at i:12202 original size:19 final size:19
Alignment explanation
Indices: 12169--12207 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12159 TGATTTAAGC
* *
12169 ATTTAAATTTTATTTAAAA
1 ATTTAAATATAATTTAAAA
12188 ATTTAAATATAATTTAAAA
1 ATTTAAATATAATTTAAAA
12207 A
1 A
12208 CCATACATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAAATATAATTTAAAA
Found at i:13700 original size:62 final size:62
Alignment explanation
Indices: 13602--13723 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
13592 GTGTGCATTG
*
13602 AAACATATAATGCACTCCAAGTGAAATCATAACATGAGCACCAACGGTGCGGATCATAATTA
1 AAACATATAATGCACTCCAAATGAAATCATAACATGAGCACCAACGGTGCGGATCATAATTA
*
13664 AAACATATAATGCACTCCAAATGTAATCA-AAGCATGAGCACCAACGGTGCGGATCATAAT
1 AAACATATAATGCACTCCAAATGAAATCATAA-CATGAGCACCAACGGTGCGGATCATAAT
13724 GTACACAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 2 0.04
62 55 0.96
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (62 bp):
AAACATATAATGCACTCCAAATGAAATCATAACATGAGCACCAACGGTGCGGATCATAATTA
Found at i:24565 original size:2 final size:2
Alignment explanation
Indices: 24558--24620 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
24548 TTCCACAAGT
24558 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
24600 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
24621 TAGCATTTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25768 original size:59 final size:60
Alignment explanation
Indices: 25699--25816 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
25689 ATTTAGATTG
* ** * *
25699 AGAATTATAATTTGGGGATGAAATTAAAATATGT-AAAAGTTT-AAGATTAATTTAAAATA
1 AGAATCATAATTTGAAGATGAAATTAAAATAT-TAAAAAGTTTAAAAATCAATTTAAAATA
*
25758 AGAATCATAATTTGAAGATGAAATTAGAATATTCAAAAAGTTTAAAAATCAATTTAAAA
1 AGAATCATAATTTGAAGATGAAATTAAAATATT-AAAAAGTTTAAAAATCAATTTAAAA
25817 AAGTGAGTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 1 0.02
59 28 0.56
60 8 0.16
61 13 0.26
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.33
Consensus pattern (60 bp):
AGAATCATAATTTGAAGATGAAATTAAAATATTAAAAAGTTTAAAAATCAATTTAAAATA
Found at i:28627 original size:42 final size:42
Alignment explanation
Indices: 28544--28691 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 42
28534 CATTCCCAAT
* * * * *
28544 CTTTTTACATTTTTAATTAATGATCCTAAATTTTTCAATCTCA
1 CTTTTTACATTTATAATTGA-GACCCTGATTTTTTCAATCTCA
*
28587 CTTTGTACATTTATAATTGA-ACTCCTGATTTTTTCAATCTCA
1 CTTTTTACATTTATAATTGAGAC-CCTGATTTTTTCAATCTCA
* * * *
28629 CTTTTTA-ACTTTATAATTGAGGCCCTTATTTTTTTAATCTTA
1 CTTTTTACA-TTTATAATTGAGACCCTGATTTTTTCAATCTCA
*
28671 CTTTTTACCTTTATAATTGAG
1 CTTTTTACATTTATAATTGAG
28692 GTCTCTAATT
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.02
42 69 0.78
43 18 0.20
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.51
Consensus pattern (42 bp):
CTTTTTACATTTATAATTGAGACCCTGATTTTTTCAATCTCA
Found at i:28692 original size:42 final size:42
Alignment explanation
Indices: 28568--28729 Score: 166
Period size: 42 Copynumber: 3.8 Consensus size: 42
28558 AATTAATGAT
* * * *
28568 CCTAAATTTTTCAATCTCACTTTGTACATTTATAATTGA-AC
1 CCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGC
* *
28609 TCCTGATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGC
1 -CCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGC
* * *
28652 CCTTATTTTTTTAATCTTACTTTTTACCTTTATAATTGAGGTC
1 CCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGG-C
* * *
28695 TCTAATTTTTTTCAATCAT-ACATTTTACTTTTATA
1 CCTAA-TTTTTTCAATC-TCACTTTTTACCTTTATA
28730 GTTTAAGGCC
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 71 0.70
43 5 0.05
44 24 0.24
45 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (42 bp):
CCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGC
Found at i:36063 original size:21 final size:20
Alignment explanation
Indices: 36023--36064 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36013 CCAACTTACA
*
36023 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
36043 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
36064 A
1 A
36065 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:40740 original size:21 final size:20
Alignment explanation
Indices: 40700--40741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40690 CCAACTTACA
*
40700 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
40720 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
40741 A
1 A
40742 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:45095 original size:3 final size:3
Alignment explanation
Indices: 45082--45128 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
45072 ATGAGTATTT
* * * *
45082 TAA TTA TAA TAA TAA TAA TAA TAG TAA TAG TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45129 TGGATAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58819 original size:47 final size:46
Alignment explanation
Indices: 58750--58839 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
58740 ATTATTTCGC
* * **
58750 TTAGGATGAAAACCCGAGAGGGCGTCCTATGTTTGAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTA-AATTGAAAAAAAAACGT
*
58797 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
58840 TAGAAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
46 12 0.32
47 26 0.68
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (46 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAACGT
Found at i:59800 original size:105 final size:105
Alignment explanation
Indices: 59618--60183 Score: 1033
Period size: 105 Copynumber: 5.4 Consensus size: 105
59608 AGGTTTTACC
* *
59618 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
59683 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
59723 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
59788 ACGAAGGAACCGCTGGTTGTCAACAAACATTTCTCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
59828 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
59893 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
59933 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
59998 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
60038 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
60103 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* *
60144 CAGAGCCAATTTTAACTTCACAACGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
60184 GGAACAGTAC
Statistics
Matches: 448, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
105 400 0.89
106 48 0.11
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:71054 original size:2 final size:2
Alignment explanation
Indices: 71049--71096 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
71039 TTGAAAAATG
71049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
71090 TA TA TA T
1 TA TA TA T
71097 CGTAATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71760 original size:19 final size:20
Alignment explanation
Indices: 71717--71773 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
71707 CTCCCTTCCC
* *
71717 CCACTTCCCCCTTTTATCAT
1 CCACTTCTCCCTATTATCAT
*
71737 CCACTTCTCCCTATTAT-GT
1 CCACTTCTCCCTATTATCAT
71756 CCACTTCTCCCTATTATC
1 CCACTTCTCCCTATTATC
71774 GACCGCCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.16, C:0.42, G:0.02, T:0.40
Consensus pattern (20 bp):
CCACTTCTCCCTATTATCAT
Found at i:72263 original size:30 final size:30
Alignment explanation
Indices: 72227--72298 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
72217 AACACATAAC
*
72227 GTTAAGCACCAATTTTTTAGTATAAAATTG
1 GTTAAGCACCAATTTTTTAGTAAAAAATTG
*
72257 GTTAAGCAACAATTTTTTAGTAAAAAATTG
1 GTTAAGCACCAATTTTTTAGTAAAAAATTG
72287 GTTAAGCACCAA
1 GTTAAGCACCAA
72299 ATCGTTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (30 bp):
GTTAAGCACCAATTTTTTAGTAAAAAATTG
Done.