Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003236.1 Hibiscus syriacus cultivar Beakdansim tig00006808_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: 62219
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6165 original size:29 final size:32
Alignment explanation
Indices: 6106--6168 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
6096 GTGTTATTGA
6106 AAATATTATTATTTTTTAATAAAAAATTATTT
1 AAATATTATTATTTTTTAATAAAAAATTATTT
*
6138 AAATATTATT-TTTTTTATTAAAAATATTATT
1 AAATATTATTATTTTTTAATAAAAA-ATTATT
6169 ATTGGGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
AAATATTATTATTTTTTAATAAAAAATTATTT
Found at i:6304 original size:19 final size:20
Alignment explanation
Indices: 6275--6315 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
6265 AGAAATCTTA
6275 AAAAAATTAATGTTTTAGGT
1 AAAAAATTAATGTTTTAGGT
6295 AAAAAA-TAATGTTTTAGGT
1 AAAAAATTAATGTTTTAGGT
6314 AA
1 AA
6316 TATTTACGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (20 bp):
AAAAAATTAATGTTTTAGGT
Found at i:6958 original size:10 final size:10
Alignment explanation
Indices: 6943--6968 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6933 TTAATAAATA
6943 AACGAATACG
1 AACGAATACG
6953 AACGAATACG
1 AACGAATACG
6963 AACGAA
1 AACGAA
6969 CATAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.08
Consensus pattern (10 bp):
AACGAATACG
Found at i:7265 original size:14 final size:16
Alignment explanation
Indices: 7246--7277 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
7236 ATGTCATCTT
7246 CGAACATA-AA-TGAA
1 CGAACATATAATTGAA
7260 CGAACATATAATTGAA
1 CGAACATATAATTGAA
7276 CG
1 CG
7278 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (16 bp):
CGAACATATAATTGAA
Found at i:13150 original size:41 final size:41
Alignment explanation
Indices: 13090--13171 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
13080 TCAATGCAAA
*
13090 TATTTACTTCCCATTAAAGAAATTAGGTAATAACAGATAAT
1 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
13131 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
1 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
13172 CATCTATCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (41 bp):
TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
Found at i:26409 original size:21 final size:19
Alignment explanation
Indices: 26373--26412 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
26363 ATGTTGATCC
*
26373 CTTGGTCCTTCTTACTACA
1 CTTGGTCCTTCCTACTACA
26392 CTTGGTCCTCTTCCTACTACA
1 CTTGGT-C-CTTCCTACTACA
26413 TGTGTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (19 bp):
CTTGGTCCTTCCTACTACA
Found at i:27263 original size:44 final size:44
Alignment explanation
Indices: 27210--27364 Score: 238
Period size: 44 Copynumber: 3.5 Consensus size: 44
27200 CGAGGTCTGA
* * ** * *
27210 GTCACATAGCATCGACACCTTATAAACTCTTTAGCTAGGTCAGG
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
*
27254 GTCATATAGCATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
*
27298 GTCATATAACACCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
27342 GTCATATAACATCGACACCTTGC
1 GTCATATAACATCGACACCTTGC
27365 CATGCCAGTC
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 103 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (44 bp):
GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
Found at i:33958 original size:10 final size:10
Alignment explanation
Indices: 33936--33978 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
33926 TTTTTAAATA
33936 AAATAATAT-
1 AAATAATATG
*
33945 AAATAATTTG
1 AAATAATATG
*
33955 AAATAATTATA
1 AAATAA-TATG
33966 AAATAATATG
1 AAATAATATG
33976 AAA
1 AAA
33979 CAGAATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 8 0.29
10 12 0.43
11 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (10 bp):
AAATAATATG
Found at i:33971 original size:21 final size:19
Alignment explanation
Indices: 33936--33978 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
33926 TTTTTAAATA
*
33936 AAATAATATAAATAATTTG
1 AAATAATATAAATAATATG
33955 AAATAATTATAAAATAATATG
1 AAATAA-TAT-AAATAATATG
33976 AAA
1 AAA
33979 CAGAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAATAATATAAATAATATG
Found at i:39100 original size:16 final size:16
Alignment explanation
Indices: 39079--39113 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39069 GAGGTTACCC
39079 TTATTTTCATTATCTG
1 TTATTTTCATTATCTG
* *
39095 TTATTTTTATTATTTG
1 TTATTTTCATTATCTG
39111 TTA
1 TTA
39114 CCAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTATTTTCATTATCTG
Found at i:40014 original size:174 final size:174
Alignment explanation
Indices: 39724--40071 Score: 480
Period size: 174 Copynumber: 2.0 Consensus size: 174
39714 AAAGCTTTTT
* * * * *
39724 CTAATTTGATTATTAGTAAAACGAGTCCTTCTGGGGTTGAGTCTGGTGGAATGGATGTTGATATT
1 CTAATTTGATTATTAGTAAAACGAGGCCTTCTGGGGTTGAGTCCGGTGAAAAGGATGTTGACATT
* * * * * *
39789 GGTACAGAAGATGAAAAGTGTTTAGAAGATGCCGATATTTCGGCATTATTGGGTGATAGTGGGGG
66 GGTACAGAAGATCAAAAGGGTGTAGAAGATGCCGATATTTCGGCATTATTGGATGATAATGAGGG
** * * **
39854 TAATGTGGCTGCTAATGATAGCAGTTCACTGGTACCTAGTAATG
131 TAATGTGGCCACTAAGGAGAGCAACTCACTGGTACCTAGTAATG
*
39898 CTAATTTGATTATTAGTGAAACGAGGCCTTCTGGGGTTGAGTCCGGTGAAAAGGATGTTGACATT
1 CTAATTTGATTATTAGTAAAACGAGGCCTTCTGGGGTTGAGTCCGGTGAAAAGGATGTTGACATT
* * * * *
39963 GGTACAGAAGCTCAAAAGGGTGTAGAAGATGCTGATATTTCTGCGTTATTGGATGGTAATGAGGG
66 GGTACAGAAGATCAAAAGGGTGTAGAAGATGCCGATATTTCGGCATTATTGGATGATAATGAGGG
*
40028 TATTGTGGCCACTAAGGAGAGCAACTCACTGGTACCTAGTAATG
131 TAATGTGGCCACTAAGGAGAGCAACTCACTGGTACCTAGTAATG
40072 TGAAGGAGTA
Statistics
Matches: 150, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.31
Consensus pattern (174 bp):
CTAATTTGATTATTAGTAAAACGAGGCCTTCTGGGGTTGAGTCCGGTGAAAAGGATGTTGACATT
GGTACAGAAGATCAAAAGGGTGTAGAAGATGCCGATATTTCGGCATTATTGGATGATAATGAGGG
TAATGTGGCCACTAAGGAGAGCAACTCACTGGTACCTAGTAATG
Found at i:48019 original size:2 final size:2
Alignment explanation
Indices: 48012--48059 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
48002 ATTTGATACG
48012 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
48054 AT AT AT
1 AT AT AT
48060 CGACAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49843 original size:2 final size:2
Alignment explanation
Indices: 49838--49879 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
49828 TGATGTGTGA
*
49838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
49880 GTAATCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50239 original size:23 final size:23
Alignment explanation
Indices: 50200--50283 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
50190 ACATCTTATA
50200 TGGCACTAT-GGTGCAATTCTACG
1 TGGCACT-TCGGTGCAATTCTACG
* *
50223 CGGAACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
50246 TGGCACTTCGGTACAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
50269 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
50284 TTTATATGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 1 0.02
23 52 0.98
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:51055 original size:13 final size:13
Alignment explanation
Indices: 51037--51071 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
51027 TGCGTCATAA
51037 ATTTATGACACGC
1 ATTTATGACACGC
*
51050 ATTTATGACGCGC
1 ATTTATGACACGC
51063 ATTTATGAC
1 ATTTATGAC
51072 TTACATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:51193 original size:85 final size:85
Alignment explanation
Indices: 51050--51215 Score: 260
Period size: 85 Copynumber: 2.0 Consensus size: 85
51040 TATGACACGC
* * * *
51050 ATTTATGACGCGCATTTATGACTTACATTGCACGTCATTGAAGCTCCCTTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCACGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
51115 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
** *
51135 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGG
1 ATTTATGACACGCATTTATGACTTACATTGCACGTCATTGAAGCCCCCGTCATAAATGAAAATGA
51200 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
51216 GTGATTGTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCACGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:57621 original size:24 final size:24
Alignment explanation
Indices: 57594--57691 Score: 162
Period size: 24 Copynumber: 4.1 Consensus size: 24
57584 GGCCGAGCAG
57594 CAGCAGCAATACCAGAACCAGGCA
1 CAGCAGCAATACCAGAACCAGGCA
57618 CAGCAGCAATACCAGAACCAGGCA
1 CAGCAGCAATACCAGAACCAGGCA
*
57642 CAGCAGCAATACCAGAACCAGGCG
1 CAGCAGCAATACCAGAACCAGGCA
*
57666 CAGCCA-CAATACCAGAATCAGGCA
1 CAG-CAGCAATACCAGAACCAGGCA
57690 CA
1 CA
57692 TGAATACGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
24 68 0.97
25 2 0.03
ACGTcount: A:0.41, C:0.34, G:0.20, T:0.05
Consensus pattern (24 bp):
CAGCAGCAATACCAGAACCAGGCA
Done.