Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009215.1 Hibiscus syriacus cultivar Beakdansim tig00112802_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: 57397
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1806 original size:35 final size:36
Alignment explanation
Indices: 1766--1836 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
1756 AAAATAGTCA
* * *
1766 TCAATTTCATTTTAAACCTCAAATTCC-AAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATAAT
*
1801 TCAATTACATTCTAAACCCCACATTCCAAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATAAT
1837 CAAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATAAT
Found at i:2368 original size:35 final size:35
Alignment explanation
Indices: 2329--2402 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
2319 CAATATTATT
* * *
2329 TTGAAGTATTTTAGAATTTGGGGTTTAGAATATAA
1 TTGAAGTATTCTAGAATTTGGGGTTTAAAATAAAA
* *
2364 TTGAATTATTCTGGAATTTGGGGTTTAAAATAAAA
1 TTGAAGTATTCTAGAATTTGGGGTTTAAAATAAAA
2399 TTGA
1 TTGA
2403 GGATTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
TTGAAGTATTCTAGAATTTGGGGTTTAAAATAAAA
Found at i:4247 original size:12 final size:12
Alignment explanation
Indices: 4230--4254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4220 AGGTAAATAA
4230 ATTTTTTATTTT
1 ATTTTTTATTTT
4242 ATTTTTTATTTT
1 ATTTTTTATTTT
4254 A
1 A
4255 ATTTCATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:8263 original size:3 final size:3
Alignment explanation
Indices: 8255--8280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8245 ATATTAAGAA
8255 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
8281 AAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:8838 original size:2 final size:2
Alignment explanation
Indices: 8831--8886 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
8821 CTTTAATCTC
8831 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
8873 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
8887 TTCTTATCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9038 original size:2 final size:2
Alignment explanation
Indices: 9031--9060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9021 CTGAAACCTT
9031 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9061 ATTCTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15196 original size:22 final size:23
Alignment explanation
Indices: 15160--15202 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
15150 GCAAATTTTA
*
15160 AAAAAATTCTTATTAAACCTCTC
1 AAAAAATTCTAATTAAACCTCTC
*
15183 AAAAAATT-TAATTAGACCTC
1 AAAAAATTCTAATTAAACCTC
15203 ATTCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAATTCTAATTAAACCTCTC
Found at i:20804 original size:13 final size:13
Alignment explanation
Indices: 20786--20811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20776 CAGAATAAAC
20786 ACCAGTCGCGAAT
1 ACCAGTCGCGAAT
20799 ACCAGTCGCGAAT
1 ACCAGTCGCGAAT
20812 CTTGCAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
ACCAGTCGCGAAT
Found at i:29665 original size:8 final size:8
Alignment explanation
Indices: 29651--29680 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
29641 TTTCTTCACC
29651 CATATATA
1 CATATATA
*
29659 TATATATA
1 CATATATA
29667 CATATATA
1 CATATATA
29675 CATATA
1 CATATA
29681 CATACATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
CATATATA
Found at i:29673 original size:14 final size:14
Alignment explanation
Indices: 29654--29684 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29644 CTTCACCCAT
*
29654 ATATATATATATAC
1 ATATATACATATAC
29668 ATATATACATATAC
1 ATATATACATATAC
29682 ATA
1 ATA
29685 CATGTGTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATACATATAC
Found at i:30666 original size:14 final size:14
Alignment explanation
Indices: 30649--30678 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30639 TGTTTATAAA
30649 TTTTAATAAAATAT
1 TTTTAATAAAATAT
30663 TTTTAATAAAATAT
1 TTTTAATAAAATAT
30677 TT
1 TT
30679 AAATTACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAATAAAATAT
Found at i:34434 original size:16 final size:17
Alignment explanation
Indices: 34413--34444 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34403 TTACTATTCA
34413 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
34429 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
34445 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:35217 original size:15 final size:16
Alignment explanation
Indices: 35197--35228 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35187 TGGCAGATCC
35197 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
35212 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
35228 A
1 A
35229 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:44919 original size:31 final size:31
Alignment explanation
Indices: 44879--44937 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
44869 AATCATCTAA
*
44879 AGCAGTTTCAACTCGAAAGGAACAAATTTCT
1 AGCAATTTCAACTCGAAAGGAACAAATTTCT
*
44910 AGCAATTTCAACTTGAAAGGAACAAATT
1 AGCAATTTCAACTCGAAAGGAACAAATT
44938 CCAATACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (31 bp):
AGCAATTTCAACTCGAAAGGAACAAATTTCT
Found at i:47074 original size:29 final size:30
Alignment explanation
Indices: 47021--47082 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
47011 AGATATTCTG
*
47021 AATTAAAAATTATTTGAAAATTTAATGATTA
1 AATTAAAAA-TATTTGAAAATTTAATAATTA
47052 AATTAAAAA-ATTT-AAAATTTTAATAATTA
1 AATTAAAAATATTTGAAAA-TTTAATAATTA
47081 AA
1 AA
47083 ACAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 16 0.55
31 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (30 bp):
AATTAAAAATATTTGAAAATTTAATAATTA
Found at i:47088 original size:29 final size:29
Alignment explanation
Indices: 47032--47088 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
47022 ATTAAAAATT
* **
47032 ATTTGAAAATTTAATGATTAAATTAAAAA
1 ATTTGAAAATTTAATAATTAAAACAAAAA
47061 ATTT-AAAATTTTAATAATTAAAACAAAA
1 ATTTGAAAA-TTTAATAATTAAAACAAAA
47089 TTTTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (29 bp):
ATTTGAAAATTTAATAATTAAAACAAAAA
Found at i:48329 original size:18 final size:18
Alignment explanation
Indices: 48306--48340 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48296 AGTTTCTAAT
*
48306 TTTTTTTTGAGTTCAAGC
1 TTTTTTTTGAATTCAAGC
48324 TTTTTTTTGAATTCAAG
1 TTTTTTTTGAATTCAAG
48341 TTTCAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTTTTTTGAATTCAAGC
Found at i:48572 original size:18 final size:17
Alignment explanation
Indices: 48540--48573 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
48530 TAAGCCGGTC
48540 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
48557 CGGTTCTGATCGGTTCA
1 CGGTT-TGAACGGTTCA
48574 CTAATAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:48631 original size:28 final size:28
Alignment explanation
Indices: 48599--48663 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
48589 TCGGTTTAGA
48599 TTGAACCGGATTAAGCAACGATTCCCGG
1 TTGAACCGGATTAAGCAACGATTCCCGG
*
48627 TTGAACCGGATTAAGCAACGGTTCCCGG
1 TTGAACCGGATTAAGCAACGATTCCCGG
48655 TTGAACCGG
1 TTGAACCGG
48664 TTGAACCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (28 bp):
TTGAACCGGATTAAGCAACGATTCCCGG
Found at i:48814 original size:26 final size:26
Alignment explanation
Indices: 48752--48804 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
48742 TATCATTTTC
48752 ACCCTAAATTAATAAAATAAAAATAT
1 ACCCTAAATTAATAAAATAAAAATAT
48778 ACCCTAAATTAATAAAATAAAAATAT
1 ACCCTAAATTAATAAAATAAAAATAT
48804 A
1 A
48805 TTTGATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (26 bp):
ACCCTAAATTAATAAAATAAAAATAT
Found at i:53189 original size:33 final size:33
Alignment explanation
Indices: 53147--53210 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
53137 TGGGGTGTGA
53147 GTGGAATGAAATCTGAGCTTATTGTCATGGCAC
1 GTGGAATGAAATCTGAGCTTATTGTCATGGCAC
53180 GTGGAATGAAATCTGAGCTTATTGTCATGGC
1 GTGGAATGAAATCTGAGCTTATTGTCATGGC
53211 TCAGGGACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (33 bp):
GTGGAATGAAATCTGAGCTTATTGTCATGGCAC
Found at i:55925 original size:22 final size:22
Alignment explanation
Indices: 55884--55926 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
55874 TCATTGCATA
55884 AAAATTAAACAGTTATAACTCCT
1 AAAATTAAACAG-TATAACTCCT
55907 AAAATTAAATCA-TATAACTC
1 AAAATTAAA-CAGTATAACTC
55927 ATGTAACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTAAACAGTATAACTCCT
Done.