Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006393.1 Hibiscus syriacus cultivar Beakdansim tig00015402_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: 57464
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:14063 original size:31 final size:31
Alignment explanation
Indices: 14036--14141 Score: 203
Period size: 31 Copynumber: 3.4 Consensus size: 31
14026 TATTGATTTA
*
14036 TGCATGCATACATTTCAATGTGATTGATGGT
1 TGCATGCATACATGTCAATGTGATTGATGGT
14067 TGCATGCATACATGTCAATGTGATTGATGGT
1 TGCATGCATACATGTCAATGTGATTGATGGT
14098 TGCATGCATACATGTCAATGTGATTGATGGT
1 TGCATGCATACATGTCAATGTGATTGATGGT
14129 TGCATGCATACAT
1 TGCATGCATACAT
14142 AGGATAGATG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (31 bp):
TGCATGCATACATGTCAATGTGATTGATGGT
Found at i:20887 original size:23 final size:23
Alignment explanation
Indices: 20857--20904 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
20847 ACAAAAATGA
20857 TAATTGGGATACTAAAGGTGTAG
1 TAATTGGGATACTAAAGGTGTAG
20880 TAATTGGGATACTAAAGGTGTAG
1 TAATTGGGATACTAAAGGTGTAG
20903 TA
1 TA
20905 TACCCTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.31
Consensus pattern (23 bp):
TAATTGGGATACTAAAGGTGTAG
Found at i:21673 original size:2 final size:2
Alignment explanation
Indices: 21666--21693 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21656 GATTGATCAT
21666 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
21694 CTCATCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21938 original size:29 final size:30
Alignment explanation
Indices: 21892--21954 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
21882 AATTTGACCA
* *
21892 TAATGTTTAGATGAAATATCATTTTAAACCC
1 TAATCTTTAGAT-AAATATCAATTTAAACCC
*
21923 TAATCTTTAGAT-AATATCAATTTAACCCC
1 TAATCTTTAGATAAATATCAATTTAAACCC
21952 TAA
1 TAA
21955 ATTCGATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.62
31 11 0.38
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (30 bp):
TAATCTTTAGATAAATATCAATTTAAACCC
Found at i:23072 original size:30 final size:31
Alignment explanation
Indices: 23004--23072 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
22994 AATGGCTAAC
* *
23004 TTAATATTTTATCTAAAATTTAAGTGTCAAA
1 TTAATATTTCATCTAAAATTTAAGAGTCAAA
* * *
23035 ATGATATTTCATCTAAAGTTT-AGAGTCAAA
1 TTAATATTTCATCTAAAATTTAAGAGTCAAA
23065 TTAATATT
1 TTAATATT
23073 ATACCTTAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (31 bp):
TTAATATTTCATCTAAAATTTAAGAGTCAAA
Found at i:24068 original size:122 final size:122
Alignment explanation
Indices: 23847--24091 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 122
23837 TATTGATGGC
* *
23847 CCTGCTGTGGACAGTATCAACAATTCTCTAATTGAACCAGAGATTAAAAGTGTTGATTGTTCGTC
1 CCTGCTGTGGACAGTATCAACAATTCTCTAATTGAACCAGAGATTAAAAGTATTGATTGTTCATC
23912 CGACATCGTCTTGGCCTTCGATTTCTCTTATTTTGCTTTTTAAGTAGTTCATCGTTG
66 CGACATCGTCTTGGCCTTCGATTTCTCTTATTTTGCTTTTTAAGTAGTTCATCGTTG
23969 CCTGCTGTGGACAGTATCAACAATTCTCTAATTGAACCAGAGATTAAAAGTATTGATTGTTCATC
1 CCTGCTGTGGACAGTATCAACAATTCTCTAATTGAACCAGAGATTAAAAGTATTGATTGTTCATC
*
24034 CGACATCGTCTTGGCCTTCGATTTCTCTTCTTTTGCTTTTTAAGTAGTTCATCGTTG
66 CGACATCGTCTTGGCCTTCGATTTCTCTTATTTTGCTTTTTAAGTAGTTCATCGTTG
24091 C
1 C
24092 TTCCATCCAT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (122 bp):
CCTGCTGTGGACAGTATCAACAATTCTCTAATTGAACCAGAGATTAAAAGTATTGATTGTTCATC
CGACATCGTCTTGGCCTTCGATTTCTCTTATTTTGCTTTTTAAGTAGTTCATCGTTG
Found at i:24241 original size:3 final size:3
Alignment explanation
Indices: 24233--24311 Score: 63
Period size: 3 Copynumber: 25.0 Consensus size: 3
24223 ACTAATCGAA
* *
24233 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATT ATAT AAT CGAAC AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A-AT AAT --AAT AAT
*
24281 AAT AA- AAT AAT TAT AAAT AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AA-T AAT AAT AAT
24312 TGATATCATT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
2 4 0.06
3 47 0.75
4 10 0.16
5 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35678 original size:5 final size:5
Alignment explanation
Indices: 35670--35700 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
35660 TCTGCTCTTA
35670 TGCTG TGCTG TGCTG TGCTG TGCTG TGCTG T
1 TGCTG TGCTG TGCTG TGCTG TGCTG TGCTG T
35701 AATATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.39, T:0.42
Consensus pattern (5 bp):
TGCTG
Found at i:39891 original size:31 final size:28
Alignment explanation
Indices: 39833--39927 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
39823 TTATTCAATC
*
39833 ACTTAAAATATTTTTTGTTAAAGTAAAT
1 ACTTAAAATATTTTTTGTTAAACTAAAT
39861 ACTTAAAATTATTATTTTGGTTAAACTAAAT
1 ACTTAAAA-TATT-TTTT-GTTAAACTAAAT
* * * *
39892 ACCTAAAGTACTTTTTGATTAAAATAAAT
1 ACTTAAAATATTTTTTG-TTAAACTAAAT
*
39921 ACATAAA
1 ACTTAAA
39928 GTACTCTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 9 0.16
29 24 0.42
30 7 0.12
31 17 0.30
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (28 bp):
ACTTAAAATATTTTTTGTTAAACTAAAT
Found at i:43693 original size:16 final size:16
Alignment explanation
Indices: 43660--43693 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43650 ATATATATAT
* *
43660 ATAGATAGATAAATAG
1 ATAGATAGAAAAAGAG
43676 ATAGATAGAAAAAGAG
1 ATAGATAGAAAAAGAG
43692 AT
1 AT
43694 TAGGAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (16 bp):
ATAGATAGAAAAAGAG
Found at i:43847 original size:29 final size:29
Alignment explanation
Indices: 43781--43837 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
43771 TGTTAAGTTT
43781 ATCGATTATTAAAAGTTATAAAATAGTCA
1 ATCGATTATTAAAAGTTATAAAATAGTCA
43810 ATCGATTATTAAAAGTTATAAAATAGTC
1 ATCGATTATTAAAAGTTATAAAATAGTC
43838 CTTTGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (29 bp):
ATCGATTATTAAAAGTTATAAAATAGTCA
Found at i:43893 original size:60 final size:60
Alignment explanation
Indices: 43811--43943 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
43801 AAATAGTCAA
* * * * * *
43811 TCGATTATTAAAAGTTATAAAATAGTCCTTTGATTATAGGGTATTATTTTGTTGAATCTT
1 TCGACTATTAAAAATTACAAAATAGTCCTTTGACTATAGAGTATTATTTTGTTGAATCTC
* * * *
43871 TCGACTATTAAAAATTACAAAATGGTTCTTTGACTATAGAGTGTTATTTTGTTGAGTCTC
1 TCGACTATTAAAAATTACAAAATAGTCCTTTGACTATAGAGTATTATTTTGTTGAATCTC
* *
43931 CCGACTAGTAAAA
1 TCGACTATTAAAA
43944 TTTATATAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (60 bp):
TCGACTATTAAAAATTACAAAATAGTCCTTTGACTATAGAGTATTATTTTGTTGAATCTC
Found at i:48068 original size:22 final size:22
Alignment explanation
Indices: 48040--48083 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48030 AAAATATAAA
48040 CTAGAGCACTACTTTCATCATT
1 CTAGAGCACTACTTTCATCATT
48062 CTAGAGCACTACTTTCATCATT
1 CTAGAGCACTACTTTCATCATT
48084 TCTATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (22 bp):
CTAGAGCACTACTTTCATCATT
Found at i:51550 original size:2 final size:2
Alignment explanation
Indices: 51545--51579 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51535 TTGTGTGTGT
51545 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
51580 CGTATTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54166 original size:10 final size:11
Alignment explanation
Indices: 54139--54169 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
54129 GGGATGGCAA
54139 CGGGCCGGGTT
1 CGGGCCGGGTT
54150 CGGGCCGGGTT
1 CGGGCCGGGTT
54161 -GGGCCGGGT
1 CGGGCCGGGT
54170 ATTGGTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.26, G:0.58, T:0.16
Consensus pattern (11 bp):
CGGGCCGGGTT
Found at i:54428 original size:24 final size:23
Alignment explanation
Indices: 54397--54442 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
54387 TATATATATA
54397 TATTTAAATTAAATATATATTTTC
1 TATTTAAATTAAATATAT-TTTTC
*
54421 TATTTAAATTAAATTTATTTTT
1 TATTTAAATTAAATATATTTTT
54443 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTAAATTAAATATATTTTTC
Done.