Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001280.1 Hibiscus syriacus cultivar Beakdansim tig00002514_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: 62352
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2009 original size:21 final size:21
Alignment explanation
Indices: 1983--2058 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 21
1973 CCGTGGGGGT
1983 ATCGATTCCCTCAAGGAGGGA
1 ATCGATTCCCTCAAGGAGGGA
2004 ATCGATTCCCATTCAAAGGA-GGA
1 ATCGATTCCC--TC-AAGGAGGGA
* * *
2027 ATCGGTTCCCTTATA-G-GGGT
1 ATCGATTCCCTCA-AGGAGGGA
2047 ATCGATTCCCTC
1 ATCGATTCCCTC
2059 TGCCAAATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 14 0.31
21 12 0.27
23 14 0.31
24 5 0.11
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (21 bp):
ATCGATTCCCTCAAGGAGGGA
Found at i:2027 original size:23 final size:22
Alignment explanation
Indices: 1983--2057 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
1973 CCGTGGGGGT
1983 ATCGATTCCC-TC-AAGGAGGGA
1 ATCGATTCCCTTCAAAGGA-GGA
2004 ATCGATTCCCATTCAAAGGAGGA
1 ATCGATTCCC-TTCAAAGGAGGA
* * *
2027 ATCGGTTCCCTT-ATAGG-GGT
1 ATCGATTCCCTTCAAAGGAGGA
2047 ATCGATTCCCT
1 ATCGATTCCCT
2058 CTGCCAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 12 0.26
21 14 0.30
22 2 0.04
23 14 0.30
24 5 0.11
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (22 bp):
ATCGATTCCCTTCAAAGGAGGA
Found at i:5129 original size:19 final size:18
Alignment explanation
Indices: 5105--5148 Score: 65
Period size: 16 Copynumber: 2.5 Consensus size: 18
5095 AATAGATGCA
5105 ATGTTTTTATCAAAAGATT
1 ATGTTTTTAT-AAAAGATT
5124 ATG-TTTT-TAAAAGATT
1 ATGTTTTTATAAAAGATT
5140 ATGTTTTTA
1 ATGTTTTTA
5149 ACCCATTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 4 0.17
19 3 0.13
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (18 bp):
ATGTTTTTATAAAAGATT
Found at i:5137 original size:16 final size:16
Alignment explanation
Indices: 5116--5149 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5106 TGTTTTTATC
5116 AAAAGATTATGTTTTT
1 AAAAGATTATGTTTTT
5132 AAAAGATTATGTTTTT
1 AAAAGATTATGTTTTT
5148 AA
1 AA
5150 CCCATTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AAAAGATTATGTTTTT
Found at i:7684 original size:13 final size:13
Alignment explanation
Indices: 7666--7690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7656 TCGAATATAC
7666 TTAGAAAATCTTT
1 TTAGAAAATCTTT
7679 TTAGAAAATCTT
1 TTAGAAAATCTT
7691 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:14631 original size:2 final size:2
Alignment explanation
Indices: 14624--14655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14614 AAGACAGAAG
14624 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
14656 AAAGAACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17535 original size:2 final size:2
Alignment explanation
Indices: 17528--17563 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17518 TAAGAAAATA
17528 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
17564 TCACATTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19695 original size:20 final size:21
Alignment explanation
Indices: 19658--19696 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
19648 ATATAATAGT
*
19658 AAGATTGTGAGAAGCATATAC
1 AAGATTGTGAGAACCATATAC
*
19679 AAGATTG-GAGATCCATAT
1 AAGATTGTGAGAACCATAT
19697 TTTTCTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (21 bp):
AAGATTGTGAGAACCATATAC
Found at i:28973 original size:21 final size:21
Alignment explanation
Indices: 28947--29029 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
28937 TTTTTGTGCA
* *
28947 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCACT
* **
28968 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCACT
*
28989 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGA-TCCCCCCACT
* *
29013 G-GGGAATCGATACCCCC
1 GAGGGAACCGATCCCCCC
29030 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.12
21 26 0.53
22 1 0.02
23 9 0.18
24 7 0.14
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.14
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCACT
Found at i:37324 original size:11 final size:11
Alignment explanation
Indices: 37310--37341 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
37300 AAAATTAATT
*
37310 AAATAAAAATC
1 AAATGAAAATC
37321 AAATGAAAATC
1 AAATGAAAATC
37332 AAATGAAAAT
1 AAATGAAAAT
37342 TAGGGTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (11 bp):
AAATGAAAATC
Found at i:41898 original size:69 final size:69
Alignment explanation
Indices: 41787--41925 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
41777 GGTTGTCCTT
*
41787 AAGCAATGGATAGTTGTTAGCAAAAGAAAAATGTCATGGTAAAGTTTATAATCAAGAAAATCATG
1 AAGCAATGGATAGTTGTTAGCAAAAGAAAAATGTCATGGTAAAGTTTAGAATCAAGAAAATCATG
41852 TGGG
66 TGGG
41856 AAGCAATGGATAGTTGTTAGCAAAAGAAAAATGTCATGGTAAAGTTTAGAATCAAGAAAATCATG
1 AAGCAATGGATAGTTGTTAGCAAAAGAAAAATGTCATGGTAAAGTTTAGAATCAAGAAAATCATG
41921 TGGG
66 TGGG
41925 A
1 A
41926 TAGAGTTTCA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.25
Consensus pattern (69 bp):
AAGCAATGGATAGTTGTTAGCAAAAGAAAAATGTCATGGTAAAGTTTAGAATCAAGAAAATCATG
TGGG
Found at i:44810 original size:5 final size:5
Alignment explanation
Indices: 44800--44824 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44790 AAAACTAGAG
44800 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
44825 TCCTAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:47530 original size:6 final size:6
Alignment explanation
Indices: 47499--47523 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47489 CAATCAAAAT
47499 AACAAA AACAAA AACAAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA A
47524 TAAAAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:52065 original size:18 final size:18
Alignment explanation
Indices: 52038--52143 Score: 95
Period size: 18 Copynumber: 5.6 Consensus size: 18
52028 CATAAATACC
52038 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
* ** **
52056 ATCGTTATCATGATCTCT
1 ATCATTATCAACATCAAT
52074 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
*
52092 ATCATTATCATGATCTCTATCATT
1 ATCATTATCA--A---C-ATCAAT
*
52116 ATCATTATCAACGTCAAT
1 ATCATTATCAACATCAAT
52134 ATCATTATCA
1 ATCATTATCA
52144 TGTAATACAT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
18 50 0.72
19 1 0.01
20 1 0.01
22 1 0.01
23 1 0.01
24 15 0.22
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.39
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:52082 original size:6 final size:6
Alignment explanation
Indices: 52038--52144 Score: 65
Period size: 6 Copynumber: 17.8 Consensus size: 6
52028 CATAAATACC
** * * * **
52038 ATCATT ATCAAC ATCAAT ATCGTT ATCATG ATC-TCT ATCATT ATCAAC
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCAT-T ATCATT ATCATT
* * ** * *
52086 ATCAAT ATCATT ATCATG ATC-TCT ATCATT ATCATT ATCAAC GTCAAT
1 ATCATT ATCATT ATCATT ATCAT-T ATCATT ATCATT ATCATT ATCATT
52134 ATCATT ATCAT
1 ATCATT ATCAT
52145 GTAATACATT
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
5 2 0.03
6 73 0.95
7 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (6 bp):
ATCATT
Found at i:52100 original size:24 final size:23
Alignment explanation
Indices: 52073--52144 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 23
52063 TCATGATCTC
52073 TATCATTATCAACATCAATATCAT
1 TATCATTATCAAC-TCAATATCAT
*
52097 TATCATGAT---CTC--TATCAT
1 TATCATTATCAACTCAATATCAT
52115 TATCATTATCAACGTCAATATCAT
1 TATCATTATCAAC-TCAATATCAT
52139 TATCAT
1 TATCAT
52145 GTAATACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 14 0.35
20 2 0.05
21 2 0.05
22 2 0.05
24 20 0.50
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (23 bp):
TATCATTATCAACTCAATATCAT
Found at i:52126 original size:36 final size:36
Alignment explanation
Indices: 52038--52119 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
52028 CATAAATACC
*
52038 ATCATTATCAACATCAATATCGTTATCATGATCTCT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
52074 ATCATTATCAACATCAATATCATTATCATGATCTCT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
52110 ATCATTATCA
1 ATCATTATCA
52120 TTATCAACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (36 bp):
ATCATTATCAACATCAATATCATTATCATGATCTCT
Found at i:52137 original size:36 final size:36
Alignment explanation
Indices: 52038--52138 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
52028 CATAAATACC
* **
52038 ATCATTATCAACATCAATATCGTTATCATGATCTCT
1 ATCATTATCAACATCAACATCAATATCATGATCTCT
* *
52074 ATCATTATCAACATCAATATCATTATCATGATCTCT
1 ATCATTATCAACATCAACATCAATATCATGATCTCT
** *
52110 ATCATTATCATTATCAACGTCAATATCAT
1 ATCATTATCAACATCAACATCAATATCAT
52139 TATCATGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.39
Consensus pattern (36 bp):
ATCATTATCAACATCAACATCAATATCATGATCTCT
Found at i:52335 original size:30 final size:30
Alignment explanation
Indices: 52285--52349 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
52275 TGTATATTTT
* *
52285 TGATATCTTTTTTAGACCCATATATAGTAC
1 TGATATCTTTTTAAGACCCATATACAGTAC
* *
52315 TGATATCTTTTATAAG-CCCATGTACATTAC
1 TGATATCTTTT-TAAGACCCATATACAGTAC
52345 TGATA
1 TGATA
52350 ACTTAAGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (30 bp):
TGATATCTTTTTAAGACCCATATACAGTAC
Found at i:52664 original size:31 final size:31
Alignment explanation
Indices: 52412--52662 Score: 385
Period size: 31 Copynumber: 8.1 Consensus size: 31
52402 ACTCCTATAA
*
52412 TAATTTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
52443 TAATCTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
52474 TAATCTGTCCATATGTCCCGAAGAACACAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
52505 TAATATGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
52536 TAATCTGTCCATATGTCCCAAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* * * *
52567 TAATCTATCCATATGGCCCGAAGAGCTTAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* **
52598 TAAACTGTCCATATGTCATGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* *
52629 TAACCTGTCCATATATCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
52660 TAA
1 TAA
52663 CCCTCGACTC
Statistics
Matches: 198, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 198 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:55152 original size:64 final size:63
Alignment explanation
Indices: 55038--55230 Score: 189
Period size: 64 Copynumber: 3.0 Consensus size: 63
55028 CGGTGCACTA
* * *
55038 AGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAA--AATAGCCCGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCA-CAAATGCATTCGATGTTTCAATTAA-A-TCAGAGTGCATCGATGCATG
55101 G
63 G
* * *
55102 CTG-GTGTATCGATGCACCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGG
1 -AGAGTGCATCGATGCA-CAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGG
* * *
55166 AGAGTGCATCGGTGCATAGAATGCATTCGATGTTTCAATT-TATCCATTGA-TGCATCGATGCAT
1 AGAGTGCATCGATGCACA-AATGCATTCGATGTTTCAATTAAAT-CA--GAGTGCATCGATGCAT
55229 GG
62 GG
55231 TATTTATGCA
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
63 4 0.04
64 83 0.77
65 17 0.16
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (63 bp):
AGAGTGCATCGATGCACAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGG
Done.