Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006130.1 Hibiscus syriacus cultivar Beakdansim tig00014534_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: 63599
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:443 original size:21 final size:23
Alignment explanation
Indices: 410--452 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
400 TGATTTGGTC
410 TTATCTCAATTAAAT-GAATATT
1 TTATCTCAATTAAATGGAATATT
* *
432 TTAT-TCATTTAAGTGGAATAT
1 TTATCTCAATTAAATGGAATAT
453 AATGTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TTATCTCAATTAAATGGAATATT
Found at i:2129 original size:45 final size:45
Alignment explanation
Indices: 2042--2172 Score: 212
Period size: 45 Copynumber: 2.9 Consensus size: 45
2032 GTAATCATGC
2042 AAATAAGCTTACAAGCTTAT-GGACT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGGA-TAAATGGTAAGTATATTGGTA
* *
2086 AATTAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGGTA
*
2131 AAATAAGCTTACAAGCTTGTGGGATAAATGGTAAGTATATTG
1 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTG
2173 ATAAGAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
44 19 0.24
45 61 0.76
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:6856 original size:13 final size:13
Alignment explanation
Indices: 6838--6876 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6828 ATGGGCGTGA
*
6838 ATGGTGATGGAGG
1 ATGGTGATGGAAG
*
6851 ATGGTGATTGAAAG
1 ATGGTGA-TGGAAG
6865 ATGGTGATGGAA
1 ATGGTGATGGAA
6877 ATAGATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:6869 original size:14 final size:14
Alignment explanation
Indices: 6838--6877 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6828 ATGGGCGTGA
*
6838 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
*
6851 ATGGTGATTGAAAG
1 ATGGTGATGGAAAG
6865 ATGGTGATGGAAA
1 ATGGTGATGGAAA
6878 TAGATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:10862 original size:13 final size:13
Alignment explanation
Indices: 10839--10882 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
10829 TTTGTAGGAG
10839 TCTTTTC-TTTTC
1 TCTTTTCTTTTTC
*
10851 TCTTTTGTTTTTC
1 TCTTTTCTTTTTC
10864 ATC-TTTCTTTTTC
1 -TCTTTTCTTTTTC
10877 TCTTTT
1 TCTTTT
10883 TGTTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 8 0.30
13 17 0.63
14 2 0.07
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.75
Consensus pattern (13 bp):
TCTTTTCTTTTTC
Found at i:14822 original size:61 final size:61
Alignment explanation
Indices: 14726--14841 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
14716 GTGTTAAACC
14726 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
1 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
* * * * * * *
14787 TACACTAGGTTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCC
1 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCC
14842 TCCACCTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (61 bp):
TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
Found at i:18596 original size:12 final size:12
Alignment explanation
Indices: 18579--18604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18569 ATAGAACAAA
18579 ATATTTCTATGT
1 ATATTTCTATGT
18591 ATATTTCTATGT
1 ATATTTCTATGT
18603 AT
1 AT
18605 TTATACTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (12 bp):
ATATTTCTATGT
Found at i:21283 original size:17 final size:18
Alignment explanation
Indices: 21251--21286 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
21241 ATCAGTGCTC
21251 AACAATGGCTATAACATT
1 AACAATGGCTATAACATT
*
21269 AACAATGTC-ATAACATT
1 AACAATGGCTATAACATT
21286 A
1 A
21287 GTATATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (18 bp):
AACAATGGCTATAACATT
Found at i:31861 original size:21 final size:21
Alignment explanation
Indices: 31831--31878 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
31821 TAGAATAAGT
*
31831 GATTTGGCATAACCAAAATTA
1 GATTTTGCATAACCAAAATTA
31852 GATTTTGCATAACCAAAATTA
1 GATTTTGCATAACCAAAATTA
31873 GATTTT
1 GATTTT
31879 AGTTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
GATTTTGCATAACCAAAATTA
Found at i:33243 original size:21 final size:21
Alignment explanation
Indices: 33203--33243 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33193 AATGATTTAC
*
33203 GACTCGATCAACAGTTAACAT
1 GACTCGATCAACAGTCAACAT
*
33224 GACTCGATCAACGGTCAACA
1 GACTCGATCAACAGTCAACA
33244 CGGCTCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (21 bp):
GACTCGATCAACAGTCAACAT
Found at i:35873 original size:2 final size:2
Alignment explanation
Indices: 35866--35919 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
35856 AAATGAGCAT
35866 TA TA TA TA TA 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 TA TA TA TA TA
*
35908 TA TA TG TA TA TA
1 TA TA TA TA TA TA
35920 ATGGATGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39118 original size:22 final size:22
Alignment explanation
Indices: 39092--39145 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
39082 GCTATGAATT
39092 ATTAAGAAAATT-AATGAAC-ATA
1 ATTAA-AAAATTAAAT-AACAATA
*
39114 ATTAAATAATTAAATAACAATA
1 ATTAAAAAATTAAATAACAATA
39136 ATTAAAAAAT
1 ATTAAAAAAT
39146 AAAAAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
ATTAAAAAATTAAATAACAATA
Found at i:41067 original size:136 final size:135
Alignment explanation
Indices: 40850--41818 Score: 819
Period size: 136 Copynumber: 7.1 Consensus size: 135
40840 CTTTCTTCTA
* * * ** * * * * * **
40850 GAAATATTGATCCCTCAAGTGAGGTGTGTCTG-ATTCAAAGTGTTATGAATCGAACAATAGGTCA
1 GAAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATG-TGTGAATCGAGCGATAGGTTG
* *
40914 AACAAGCTCTTCTCATTATGAACTTCCTCTCCCTCCGTCGGATGAGTTCTTCTCATTATGAACTC
65 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-CATCGGATGAGTTCTTCTCATTATGAACTC
40979 TCCA-TT
129 TCCATTT
* ** * **
40985 GAAAATGTCAATCCCTCAAATGAGGTGTCACTGAA-TCGAAATGATGTGAATCGAGTTATAGGTT
1 G-AAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATG-TGTGAATCGAGCGATAGGTT
* * *
41049 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTTTCGGATGAGTTCTTCTCATTATAAACT
64 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACT
41114 CTCCATTT
128 CTCCATTT
* * * * * * *
41122 GAAATGTTAATACCTCAAGCGAGGCGTCACTG-ATTTAAAATGTCATAAATCAAGCGATAGGTTG
1 GAAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATGT-GTGAATCGAGCGATAGGTTG
*
41186 AACAAACTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
65 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * *
41251 CTACTA
130 CCATTT
* * * * * * * * *
41257 GAAATATTAATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCAACCGA-AG
1 GAAATGTTAATCCCTCAAGCGAGGTG-T-C--ACTGAACTCAAAATGTG-TGAATCGAGCGATAG
* * * *
41321 GTTGAACAAGTTATTCTCATTTTGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
61 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
**** *
41386 CTCTTTGCTG
126 CTCTCCATTT
* * * * * * * * *
41396 GAAATGTTGA-CCGTTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA-A
1 GAAATGTTAATCC-CTCAAGCGAGGTG-T-C--ACTGAACTCAAAATGTG-TGAATCGAGCGATA
* * *
41459 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTGTGA
60 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGA
*
41524 ACTCTTCATTT
125 ACTCTCCATTT
* * * * * * * * *
41535 GAAATGTTAATCCATTAAGCAAGGTGTCACTGATC-CAAAAT-TCCATGAATTGAGTGATTGGTC
1 GAAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATGT--GTGAATCGAGCGATAGGTT
* * * * * *
41598 GAATAATCTCTTCTCATTATGAACTTATTCTCCCTCTGTTGGATGAGTTCTACTCATTATGAACT
64 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACT
41663 CTCCATTT
128 CTCCATTT
* * * * * * *
41671 GAAGTGTTAATCCCTTAAGCGAGGCGTCACT-AATTCAAAATGACGTGAATCGAGTGATAGGTCG
1 GAAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATG-TGTGAATCGAGCGATAGGTTG
* * *
41735 AACAAGCTCTTCTCATTATGAACTTCTT-TCCC-CTTTGTTAGATGAGTTATTCTCATTATGAAC
65 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCG---GATGAGTTCTTCTCATTATGAAC
*
41798 TCTCCACTT
127 TCTCCATTT
41807 GAAATGTTAATC
1 GAAATGTTAATC
41819 GGTTCATCTT
Statistics
Matches: 690, Mismatches: 120, Indels: 47
0.81 0.14 0.05
Matches are distributed among these distances:
133 4 0.01
134 14 0.02
135 100 0.14
136 335 0.49
137 6 0.01
138 3 0.00
139 209 0.30
140 19 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (135 bp):
GAAATGTTAATCCCTCAAGCGAGGTGTCACTGAACTCAAAATGTGTGAATCGAGCGATAGGTTGA
ACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTC
CATTT
Found at i:42759 original size:6 final size:6
Alignment explanation
Indices: 42748--42814 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
42738 TCTCCTCTTC
* * * * * *
42748 TTTTAT TTTTATT TTTTCT TTTTCT TTTCAT TTTCAT TTTCAT TTTAAT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
42797 TTTTAAT TTTTAAT TTTT
1 TTTT-AT TTTT-AT TTTT
42815 TTTCTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
6 36 0.67
7 18 0.33
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:42793 original size:18 final size:17
Alignment explanation
Indices: 42761--42799 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
42751 TATTTTTATT
* *
42761 TTTTCTTTTTCTTTTCA
1 TTTTCATTTTCTTTTAA
42778 TTTTCATTTTCATTTTAA
1 TTTTCATTTTC-TTTTAA
42796 TTTT
1 TTTT
42800 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCATTTTCTTTTAA
Found at i:42802 original size:7 final size:7
Alignment explanation
Indices: 42790--42814 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42780 TTCATTTTCA
42790 TTTTAAT
1 TTTTAAT
42797 TTTTAAT
1 TTTTAAT
42804 TTTTAAT
1 TTTTAAT
42811 TTTT
1 TTTT
42815 TTTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:46342 original size:14 final size:14
Alignment explanation
Indices: 46323--46350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46313 TGGAATGGAA
46323 AGAATAAAGAATAT
1 AGAATAAAGAATAT
46337 AGAATAAAGAATAT
1 AGAATAAAGAATAT
46351 GATGCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
AGAATAAAGAATAT
Found at i:49566 original size:21 final size:22
Alignment explanation
Indices: 49536--49579 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
49526 AACATTAGAT
*
49536 TAATTCATAAAAA-TCAAAGAA
1 TAATTAATAAAAATTCAAAGAA
*
49557 TAATTAATAAAAATTTAAAGAA
1 TAATTAATAAAAATTCAAAGAA
49579 T
1 T
49580 CGAATGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (22 bp):
TAATTAATAAAAATTCAAAGAA
Found at i:56500 original size:114 final size:116
Alignment explanation
Indices: 56313--56537 Score: 341
Period size: 114 Copynumber: 2.0 Consensus size: 116
56303 TAATCAGTGC
* *
56313 ATTTTAAATTGATATTTCTAGGTCTTTTATTATTATTTTTTAAATTCTGAACTTCAGCTATGATC
1 ATTTTAAATTGATATTTCTAAGTCTTTTATTATTATTTTTTAAATTCTAAACTTCAGCTATGATC
* *
56378 CAAACAATAACAGTTAATTTTGATAGATCAATTTCTGGTATTAATTAATGT
66 CAAACAATAACAGTTAAATTTGATAGATCAATTTCTGGCATTAATTAATGT
* *
56429 ATTTT-AATTGATATTTCTAATTCTTTTATTATT-TTTTTTAAATTC-AAATTTTCAG-TCATGA
1 ATTTTAAATTGATATTTCTAAGTCTTTTATTATTATTTTTTAAATTCTAAA-CTTCAGCT-ATGA
*
56490 TCTAAACAATAACAGTTAAATTTGATAGATCAATTTCTGGCATTAATT
64 TCCAAACAATAACAGTTAAATTTGATAGATCAATTTCTGGCATTAATT
56538 CACTTGTTAA
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
113 3 0.03
114 66 0.66
115 26 0.26
116 5 0.05
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (116 bp):
ATTTTAAATTGATATTTCTAAGTCTTTTATTATTATTTTTTAAATTCTAAACTTCAGCTATGATC
CAAACAATAACAGTTAAATTTGATAGATCAATTTCTGGCATTAATTAATGT
Done.