Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005329.1 Hibiscus syriacus cultivar Beakdansim tig00012066_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: 44541
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4443 original size:26 final size:24
Alignment explanation
Indices: 4406--4462 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 24
4396 AATATTTCGA
4406 ATTTAAAAATAACATCTATAGTGAT
1 ATTTAAAAATAACATCTATAG-GAT
4431 ATTTAATAAATAACATCTATAGGAT
1 ATTTAA-AAATAACATCTATAGGAT
4456 ATTTAAA
1 ATTTAAA
4463 CATCATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 1 0.03
25 15 0.48
26 15 0.48
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (24 bp):
ATTTAAAAATAACATCTATAGGAT
Found at i:4677 original size:76 final size:75
Alignment explanation
Indices: 4584--4730 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 75
4574 CATTCTTTCA
* *
4584 AAACTCGAAAATTAGAGACACTTGCACTTAAATACATTCGAATTCACAATTTTTAGCAAATGTCA
1 AAACTCGAAAATTAGAGACACTTGCACTTAAACACATT-GAATTCACAATTTTCAGCAAATGTCA
4649 ATCAATCCTCC
65 ATCAATCCTCC
* * * * *
4660 AAACTCGTAAATTAGAGACGCTTGCACTTGAACACATTGAATTCACAATTTTCATCAAATGTTAA
1 AAACTCGAAAATTAGAGACACTTGCACTTAAACACATTGAATTCACAATTTTCAGCAAATGTCAA
4725 TCAATC
66 TCAATC
4731 TAAACTCTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 30 0.47
76 34 0.53
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (75 bp):
AAACTCGAAAATTAGAGACACTTGCACTTAAACACATTGAATTCACAATTTTCAGCAAATGTCAA
TCAATCCTCC
Found at i:7619 original size:17 final size:18
Alignment explanation
Indices: 7578--7617 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
7568 ATACGTCTTT
7578 ATAAAATATGTCATTTAA
1 ATAAAATATGTCATTTAA
*
7596 ATAAAATAT-T-ATTTTA
1 ATAAAATATGTCATTTAA
7612 ATAAAA
1 ATAAAA
7618 ATTTGAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAAAATATGTCATTTAA
Found at i:7621 original size:28 final size:28
Alignment explanation
Indices: 7590--7644 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
7580 AAAATATGTC
7590 ATTT-AAATAAAATATTATTTTAATAAAA
1 ATTTGAAA-AAAATATTATTTTAATAAAA
* **
7618 ATTTGAAACATTTATTATTTTAATAAA
1 ATTTGAAAAAAATATTATTTTAATAAA
7645 TTACCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTGAAAAAAATATTATTTTAATAAAA
Found at i:7912 original size:2 final size:2
Alignment explanation
Indices: 7901--7992 Score: 81
Period size: 2 Copynumber: 49.5 Consensus size: 2
7891 AATCCGAAAA
* *
7901 AT AT -T AT AT AT AT AT AT A- AA AT AT -T AT AT AT AC A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
7938 AT AA AA AT AT AA AA AT AT A- AT AT AT AT A- 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
7978 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
7993 ATCGGGGCGG
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
1 7 0.09
2 70 0.91
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:10116 original size:14 final size:15
Alignment explanation
Indices: 10087--10116 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10077 TATTTATATA
10087 TAAAAAATTAATTTT
1 TAAAAAATTAATTTT
*
10102 TAAAACATTAATTTT
1 TAAAAAATTAATTTT
10117 CTTAAATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAAAATTAATTTT
Found at i:11605 original size:180 final size:180
Alignment explanation
Indices: 11300--11661 Score: 512
Period size: 180 Copynumber: 2.0 Consensus size: 180
11290 TTGCTTGCCC
* *
11300 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTGCACTTGCTTTCAAGGTAAATTTGAGTTTTCAT
1 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
* *
11365 ATGATACACACGAATTCGATCATCTGAGCTATGTTTTTAGACTCAAGTGAGCGTCAGATACAAGT
66 ATGATACACACGAATTCGATCATCTAAGCTATGTTTTTAGACTCAAGTGAGCGCCAGATACAAGT
* * * * * *
11430 TTTTGATGAATCAAATTGATTCGGAATGTCTTTTTTTTTGACAATGTGCA
131 TTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
*
11480 TTGTTTCTGCTTCTGTTTTCTTGGTAGATCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
1 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
* ** * *
11545 ATGATACACACGAATT-GATCATTTAAGCTATG-TTTTAGACTCGGGTGTGAGTGCCAGATACGA
66 ATGATACACACGAATTCGATCATCTAAGCTATGTTTTTAGACTC--AAGTGAGCGCCAGATACAA
* * * *
11608 GTTTCTGACGATTTAAATCGGTTATGAATGTCTTTTGTTCTGACAATGTGCA
129 GTTTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
11660 TT
1 TT
11662 ATTAAAAAGG
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
178 10 0.06
179 14 0.09
180 136 0.85
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (180 bp):
TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
ATGATACACACGAATTCGATCATCTAAGCTATGTTTTTAGACTCAAGTGAGCGCCAGATACAAGT
TTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
Found at i:15170 original size:21 final size:24
Alignment explanation
Indices: 15137--15182 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
15127 TAAATTAAGG
15137 TTTATATTAATTAAAA-ATTATTT
1 TTTATATTAATTAAAATATTATTT
15160 TTTATA-T-ATTAAAATATTATTT
1 TTTATATTAATTAAAATATTATTT
15182 T
1 T
15183 ATGAGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATATTAATTAAAATATTATTT
Found at i:22614 original size:28 final size:29
Alignment explanation
Indices: 22570--22643 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 29
22560 GTGACAATAT
22570 AGAATTAGATCGGTTTGCTTTT-AAAAAA
1 AGAATTAGATCGGTTTGCTTTTAAAAAAA
*
22598 AGAATTAGATCGATTTGCTTTTAAAAAAA
1 AGAATTAGATCGGTTTGCTTTTAAAAAAA
*
22627 AAAATTAGATCGGTTTG
1 AGAATTAGATCGGTTTG
22644 TAAGTCGGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.35
Consensus pattern (29 bp):
AGAATTAGATCGGTTTGCTTTTAAAAAAA
Found at i:22634 original size:29 final size:28
Alignment explanation
Indices: 22572--22643 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 28
22562 GACAATATAG
*
22572 AATTAGATCGGTTTGCTTTTAAAAAAAG
1 AATTAGATCGGTTTGCTTTTAAAAAAAA
*
22600 AATTAGATCGATTTGCTTTTAAAAAAAAA
1 AATTAGATCGGTTTGCTTTT-AAAAAAAA
22629 AATTAGATCGGTTTG
1 AATTAGATCGGTTTG
22644 TAAGTCGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (28 bp):
AATTAGATCGGTTTGCTTTTAAAAAAAA
Found at i:22953 original size:22 final size:20
Alignment explanation
Indices: 22928--22967 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22918 TCTTTAAACT
22928 TTAAAATATTATACATTCATAC
1 TTAAAATA-TA-ACATTCATAC
*
22950 TTAAATTATAACATTCAT
1 TTAAAATATAACATTCAT
22968 TTTAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATATAACATTCATAC
Found at i:23139 original size:186 final size:186
Alignment explanation
Indices: 22825--23194 Score: 634
Period size: 186 Copynumber: 2.0 Consensus size: 186
22815 AAGCTATTAC
* *
22825 TATCAAATGATTGAGAGCCTTTCGAATATATATTACACCCTGTGTTCACCCCATACAAAGAGTCC
1 TATCAAATGATTGAGAGCCTTTCGAAGATATATTACACCCTGTATTCACCCCATACAAAGAGTCC
*
22890 CTAAATTATAATTCTCATTTTAAATCAATCTTTAAACTTTAAAATATTATACATTCATACTTAAA
66 CTAAATTATAATTCTCATTCTAAATCAATCTTTAAACTTTAAAATATTATACATTCATACTTAAA
22955 TTATAACATTCATTTTAAATTGTTCACCAAATTTTAAAACATTCAATATTAATCAT
131 TTATAACATTCATTTTAAATTGTTCACCAAATTTTAAAACATTCAATATTAATCAT
* *
23011 TATCAAATGGTTGATAGCCTTTCGAAGATATATTACACCCTGTATTCACCCCATACAAAGAGTCC
1 TATCAAATGATTGAGAGCCTTTCGAAGATATATTACACCCTGTATTCACCCCATACAAAGAGTCC
* *
23076 CTAAATTATAATTCTCATTCTAAATCAGT-TTTAAAACTTTAAAATATTATATATTCATACTTAA
66 CTAAATTATAATTCTCATTCTAAATCAATCTTT-AAACTTTAAAATATTATACATTCATACTTAA
* * *
23140 ATTATGACCTTCATTTTAAATTGTTCTCCAAATTTTAAAACATTCAATATTAATC
130 ATTATAACATTCATTTTAAATTGTTCACCAAATTTTAAAACATTCAATATTAATC
23195 TTTAAATTAT
Statistics
Matches: 173, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
185 3 0.02
186 170 0.98
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (186 bp):
TATCAAATGATTGAGAGCCTTTCGAAGATATATTACACCCTGTATTCACCCCATACAAAGAGTCC
CTAAATTATAATTCTCATTCTAAATCAATCTTTAAACTTTAAAATATTATACATTCATACTTAAA
TTATAACATTCATTTTAAATTGTTCACCAAATTTTAAAACATTCAATATTAATCAT
Found at i:24402 original size:2 final size:2
Alignment explanation
Indices: 24395--24424 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
24385 TTGTGTAATA
*
24395 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24425 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29071 original size:20 final size:20
Alignment explanation
Indices: 29027--29080 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
29017 TTGAACCGAT
* *
29027 TCAACCCGACCCGAACTAAG
1 TCAATCCGACCTGAACTAAG
*
29047 TCAATCCGACCTGAACTTAG
1 TCAATCCGACCTGAACTAAG
*
29067 TCAATCGGACCTGA
1 TCAATCCGACCTGA
29081 CCCGTTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (20 bp):
TCAATCCGACCTGAACTAAG
Found at i:29110 original size:23 final size:24
Alignment explanation
Indices: 29084--29143 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
29074 GACCTGACCC
29084 GTTGACTTTGGA-CATATTTGACA
1 GTTGACTTTGGACCATATTTGACA
29107 GTTGACTTT-GACCATATTTGACA
1 GTTGACTTTGGACCATATTTGACA
29130 GTTGACTTT-GACCA
1 GTTGACTTTGGACCA
29144 AAAAGTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
GTTGACTTTGGACCATATTTGACA
Found at i:35860 original size:2 final size:2
Alignment explanation
Indices: 35812--35844 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35802 AACTTTTGTT
35812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35845 TGTTCATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43614 original size:40 final size:40
Alignment explanation
Indices: 43557--43678 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
43547 GAATAATCTT
* *
43557 TGTTTTTAATAGTAGGATTTGGGTTTTAAATTTATTAAAA
1 TGTTTATAATAGTAGGATATGGGTTTTAAATTTATTAAAA
* * * *
43597 TGTTTATAATAGGAGGATCTGGGTTTTACATTTATTCAAA
1 TGTTTATAATAGTAGGATATGGGTTTTAAATTTATTAAAA
* * *
43637 TGTTTATAATAGTAGGATATGAGTTTTTAATTTATTTAAA
1 TGTTTATAATAGTAGGATATGGGTTTTAAATTTATTAAAA
43677 TG
1 TG
43679 ATGTAGACGA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (40 bp):
TGTTTATAATAGTAGGATATGGGTTTTAAATTTATTAAAA
Done.