Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009223.1 Hibiscus syriacus cultivar Beakdansim tig00112815_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: 53976
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:895 original size:34 final size:33
Alignment explanation
Indices: 856--955 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 33
846 TGATGTTATT
* * *
856 GGCGTGATATTGTGATGGAATAT-GTGATAATATA
1 GGCGTGATATGGCGATGGAATATGGTGAT--GATA
*
890 GGCGTGATAATGGCGATGGACTATGGTGATGATA
1 GGCGTGAT-ATGGCGATGGAATATGGTGATGATA
* *
924 GGCGTGATAATGGAGATGGATTATGGTGATGA
1 GGCGTGAT-ATGGCGATGGAATATGGTGATGA
956 AAATAGTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 41 0.71
35 12 0.21
36 5 0.09
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (33 bp):
GGCGTGATATGGCGATGGAATATGGTGATGATA
Found at i:5243 original size:33 final size:33
Alignment explanation
Indices: 5201--5269 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5191 GTTGATGAAT
*
5201 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
5234 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
5267 GAA
1 GAA
5270 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:5274 original size:13 final size:12
Alignment explanation
Indices: 5255--5351 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
5245 TTATTGGCGT
5255 GATATGGTGATG
1 GATATGGTGATG
5267 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5279 GATATAGGCG-T-
1 GATAT-GGTGATG
5290 GATAATGGTGATG
1 GAT-ATGGTGATG
5303 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5315 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5326 GATAATGGAGATG
1 GAT-ATGGTGATG
5339 GATTATGGTGATG
1 GA-TATGGTGATG
5352 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5310 original size:36 final size:36
Alignment explanation
Indices: 5240--5352 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
5230 AATGGAAGGA
* *
5240 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
5275 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
5311 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
5347 TGATGA
1 TGATGA
5353 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:8911 original size:13 final size:13
Alignment explanation
Indices: 8889--8918 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8879 ACTAAACACC
8889 TTTC-ACATACCT
1 TTTCAACATACCT
8901 TTTCAACATACCT
1 TTTCAACATACCT
8914 TTTCA
1 TTTCA
8919 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:11289 original size:13 final size:14
Alignment explanation
Indices: 11269--11307 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
11259 GGAAAAAAAG
11269 GAAAAAAAGAATCA
1 GAAAAAAAGAATCA
11283 GAAAAAAAGAATCA
1 GAAAAAAAGAATCA
11297 GAAAAAAAGAA
1 GAAAAAAAGAA
11308 AAGAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (14 bp):
GAAAAAAAGAATCA
Found at i:11293 original size:8 final size:9
Alignment explanation
Indices: 11252--11277 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11242 TTGGAGTGCA
11252 AAAAAAAGG
1 AAAAAAAGG
11261 AAAAAAAGG
1 AAAAAAAGG
11270 AAAAAAAG
1 AAAAAAAG
11278 AATCAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:11315 original size:14 final size:14
Alignment explanation
Indices: 11269--11315 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
11259 GGAAAAAAAG
*
11269 GAAAAAAAGAATCA
1 GAAAAAAAGAATAA
*
11283 GAAAAAAAGAATCA
1 GAAAAAAAGAATAA
11297 GAAAAAAAGAA-AA
1 GAAAAAAAGAATAA
11310 GAAAAA
1 GAAAAA
11316 GAAATTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 7 0.22
14 25 0.78
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (14 bp):
GAAAAAAAGAATAA
Found at i:14713 original size:13 final size:13
Alignment explanation
Indices: 14691--14720 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14681 ACTAAACACC
14691 TTTC-ACATACCT
1 TTTCAACATACCT
14703 TTTCAACATACCT
1 TTTCAACATACCT
14716 TTTCA
1 TTTCA
14721 TTTTGGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:21321 original size:22 final size:18
Alignment explanation
Indices: 21275--21318 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
21265 GTCTCCTTCA
21275 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
21293 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
21311 AGCTAGCT
1 AGCTAGCT
21319 AGCAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:26376 original size:22 final size:23
Alignment explanation
Indices: 26348--26408 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 23
26338 ATTTATAAGT
26348 TGGTGATAATATGGGCGTGAT-A
1 TGGTGATAATATGGGCGTGATAA
* *
26370 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATGGGCGTGATAA
26393 TGGTGATGAACTATGG
1 TGGTGAT-AA-TATGG
26409 TGATGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 19 0.59
23 8 0.25
24 1 0.03
25 4 0.12
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (23 bp):
TGGTGATAATATGGGCGTGATAA
Found at i:26391 original size:36 final size:38
Alignment explanation
Indices: 26368--26436 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
26358 ATGGGCGTGA
26368 TATGGTGATGATATAGGCGTGAT-A-ATGGTGATGAAC
1 TATGGTGATGATATAGGCGTGATAATATGGTGATGAAC
26404 TATGGTGATGATATAGGCGTGAT-A-ATGGTGATG
1 TATGGTGATGATATAGGCGTGATAATATGGTGATG
26437 GACAGATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (38 bp):
TATGGTGATGATATAGGCGTGATAATATGGTGATGAAC
Found at i:32080 original size:13 final size:12
Alignment explanation
Indices: 32061--32146 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
32051 ATATGGGCGT
32061 GATATGGTGATG
1 GATATGGTGATG
32073 GAATATGGTGAT-
1 G-ATATGGTGATG
*
32085 GATATAGGCG-T-
1 GATAT-GGTGATG
32096 GATAATGGTGATG
1 GAT-ATGGTGATG
32109 GACTATGGTGAT-
1 GA-TATGGTGATG
*
32121 GATATAGGCG-T-
1 GATAT-GGTGATG
32132 GATAATGGTGATG
1 GAT-ATGGTGATG
32145 GA
1 GA
32147 CAGATTATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:32116 original size:36 final size:36
Alignment explanation
Indices: 32043--32147 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
32033 ATTTATAAGT
* * *
32043 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
32078 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
32114 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
32148 AGATTATATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:33969 original size:15 final size:15
Alignment explanation
Indices: 33933--33962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33923 GTGCTTCAAC
33933 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
33947 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
33962 T
1 T
33963 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:34014 original size:29 final size:26
Alignment explanation
Indices: 33957--34014 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
33947 TTTCTTTGCT
*
33957 TTTCTTCTTTTTGAATGCTGAATTTC
1 TTTCTTCTTTTTGAATGCTCAATTTC
*
33983 TTTCTTTCTTTTTAGAGTGCTTCAATTTC
1 TTTC-TTCTTTTT-GAATGC-TCAATTTC
34012 TTT
1 TTT
34015 TCTGATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 8 0.30
28 5 0.19
29 10 0.37
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTTGAATGCTCAATTTC
Found at i:34017 original size:30 final size:28
Alignment explanation
Indices: 33955--34017 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
33945 CTTTTCTTTG
*
33955 CTTTTC-TTCTTTTTGAATGCTGAATTT
1 CTTTTCTTTCTTTTTGAATGCTCAATTT
*
33982 C-TTTCTTTCTTTTTAGAGTGCTTCAATTT
1 CTTTTCTTTCTTTTT-GAATGC-TCAATTT
34011 CTTTTCT
1 CTTTTCT
34018 GATTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 9 0.30
28 5 0.17
29 7 0.23
30 5 0.17
ACGTcount: A:0.13, C:0.17, G:0.10, T:0.60
Consensus pattern (28 bp):
CTTTTCTTTCTTTTTGAATGCTCAATTT
Found at i:38027 original size:5 final size:5
Alignment explanation
Indices: 38017--38042 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38007 CTTCAACTTG
38017 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
38043 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:47477 original size:24 final size:21
Alignment explanation
Indices: 47443--47485 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
47433 TCCACAAGAC
*
47443 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
47465 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
47486 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:50279 original size:30 final size:31
Alignment explanation
Indices: 50224--50285 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
50214 TTTACTTAGC
***
50224 TTTATTATGTTTACATATGTTTTAGAT-TCA
1 TTTATTATGTTTACATATCACTTAGATATCA
*
50254 TTTATTATGTTTTCATATCACTTAGATATCA
1 TTTATTATGTTTACATATCACTTAGATATCA
50285 T
1 T
50286 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (31 bp):
TTTATTATGTTTACATATCACTTAGATATCA
Found at i:52286 original size:24 final size:21
Alignment explanation
Indices: 52251--52293 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
52241 GGCTCATTCT
*
52251 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
52274 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
52294 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Done.