Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001741.1 Hibiscus syriacus cultivar Beakdansim tig00003525_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: 118030
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2951 original size:15 final size:15
Alignment explanation
Indices: 2931--2960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2921 TTAATTATTA
2931 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
2946 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
2961 TAAAAGCTCA
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:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:4230 original size:3 final size:3
Alignment explanation
Indices: 4222--4268 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
4212 GGCATGTTTG
**
4222 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
4267 TA
1 TA
4269 TCAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:13325 original size:125 final size:125
Alignment explanation
Indices: 13066--13325 Score: 333
Period size: 125 Copynumber: 2.1 Consensus size: 125
13056 AAAAAATATT
* * *
13066 TTTTGTTATTGTTATACATAATAAAATCAGTAAAAATTATAAAAAATATTATTATTTCTATCGGT
1 TTTTGTTATTGTTATACATAACAAAACCAGTAAAAATTATAAAAAATATTATTATTTCTACCGGT
* * * * *
13131 TTTATTATTAATTTGATATTTTACTTGGTTTCTTAATAAAATCGGTAAAAGCGCAATCGG
66 TTTATTATTAATTTGATATTTTACTCGGTTTCTTAATAAAACCGGTAAAAACGCAACCGA
* * * * ** *
13191 TTTTATTATTGTTGTGCATAACAAAACCGGTAAAAATTATCGAAAATATTATTATTTTTACCGGT
1 TTTTGTTATTGTTATACATAACAAAACCAGTAAAAATTATAAAAAATATTATTATTTCTACCGGT
* * * *
13256 TTTGTTATTATTTTGGTATTTTAC-CGGTTTTCTTAATAAAACCGGTAAAAACGCTACCGA
66 TTTATTATTAATTTGATATTTTACTCGG-TTTCTTAATAAAACCGGTAAAAACGCAACCGA
13316 TTTTGTTATT
1 TTTTGTTATT
13326 TTTTTATCGG
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
124 2 0.02
125 112 0.98
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (125 bp):
TTTTGTTATTGTTATACATAACAAAACCAGTAAAAATTATAAAAAATATTATTATTTCTACCGGT
TTTATTATTAATTTGATATTTTACTCGGTTTCTTAATAAAACCGGTAAAAACGCAACCGA
Found at i:13878 original size:21 final size:21
Alignment explanation
Indices: 13854--13906 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
13844 GTGCACGCAT
13854 AAAGTGTCGATACATTTATTA
1 AAAGTGTCGATACATTTATTA
13875 AAAGTGTCGATACATTTATTA
1 AAAGTGTCGATACATTTATTA
*
13896 AAAGTATCGAT
1 AAAGTGTCGAT
13907 CCAAAAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
AAAGTGTCGATACATTTATTA
Found at i:14588 original size:125 final size:126
Alignment explanation
Indices: 14459--14875 Score: 578
Period size: 125 Copynumber: 3.4 Consensus size: 126
14449 AATTTTAACA
* * * * * *
14459 GTAATTTTCACCGGATATGTTATGCACAACAATAATAAAATCAGTAGCGCTTTTACAGGTTTTGT
1 GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAATCGGTAGCGCTTTTACCGGTTTTGT
*
14524 TAAGAAACCCGGTAAAATGCCAAAATAATAACAAAA-CAGGTAGAAATAATGATATTTTCG
66 TAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCAGGTAGAAATAATGATGTTTTCG
* *
14584 GTAATTTTTACCGGTTTTGTTATGCACAACAATAAC-AAATCCGGTAGTGTTTTTACCGGTTTTG
1 GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAAT-CGGTAGCGCTTTTACCGGTTTTG
* *
14648 TTAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCA-GTAGATATAATGACGTTTTCG
65 TTAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCAGGTAGAAATAATGATGTTTTCG
* * * * *
14709 GTAATTTTTACCGGTTTTATTATGTACAACAATAACAAAACCGGTAGCACTTTTACCGATTTTG-
1 GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAATCGGTAGCGCTTTTACCGGTTTTGT
* * * * *
14773 T--GAAACCCGATAAAATACCAAAATAATAACAAAATC-GATAAAAATAATGATGTTTTCG
66 TAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCAGGTAGAAATAATGATGTTTTCG
*
14831 GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAACCGGT
1 GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAATCGGT
14876 GTAAATTTTA
Statistics
Matches: 261, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
122 92 0.35
124 5 0.02
125 159 0.61
126 5 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (126 bp):
GTAATTTTTACCGGTTTTGTTATGCACAACAATAACAAAATCGGTAGCGCTTTTACCGGTTTTGT
TAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCAGGTAGAAATAATGATGTTTTCG
Found at i:15301 original size:28 final size:29
Alignment explanation
Indices: 15269--15323 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
15259 AAATAACAAG
15269 TTTTG-AACATATGAATAGCTAG-GGACCA
1 TTTTGTAAC-TATGAATAGCTAGAGGACCA
* *
15297 TTTTGTAACTATTAATAGTTAGAGGAC
1 TTTTGTAACTATGAATAGCTAGAGGAC
15324 TCAACAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (29 bp):
TTTTGTAACTATGAATAGCTAGAGGACCA
Found at i:15686 original size:30 final size:31
Alignment explanation
Indices: 15648--15721 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
15638 CTTGAATTCG
* *
15648 TAGA-AAAATATTAATATAA-TCTTAAATTT
1 TAGATAAAATATTAATATAACTCATAAACTT
*
15677 TAGATAAAATATTAATTTAACTCATAAACTT
1 TAGATAAAATATTAATATAACTCATAAACTT
*
15708 TAAATAAAATATTA
1 TAGATAAAATATTA
15722 TTTTTTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 4 0.10
30 14 0.36
31 21 0.54
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
TAGATAAAATATTAATATAACTCATAAACTT
Found at i:28907 original size:15 final size:16
Alignment explanation
Indices: 28875--28913 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28865 ACGTATTTAA
*
28875 ATAATATTTTTAAATT
1 ATAATAATTTTAAATT
28891 ATAATAATTTT-AATT
1 ATAATAATTTTAAATT
*
28906 ATATTAAT
1 ATAATAAT
28914 CTTCGAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAATAATTTTAAATT
Found at i:29636 original size:23 final size:25
Alignment explanation
Indices: 29604--29650 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
29594 TAATTTAATA
29604 TATTATCATCTCTA-ATTAT-TTTTG
1 TATTATCATCT-TATATTATATTTTG
29628 TATT-TCATCTTATATTATATTTT
1 TATTATCATCTTATATTATATTTT
29651 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.10
23 11 0.52
24 8 0.38
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTATCATCTTATATTATATTTTG
Found at i:35183 original size:29 final size:29
Alignment explanation
Indices: 35141--35196 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
35131 CGACACTCGA
35141 CAGGGATGGATAATTTAAGTGTGCATAAG
1 CAGGGATGGATAATTTAAGTGTGCATAAG
35170 CAGGGATGGATAATTTAAGTGTGCATA
1 CAGGGATGGATAATTTAAGTGTGCATA
35197 GTGTCACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (29 bp):
CAGGGATGGATAATTTAAGTGTGCATAAG
Found at i:35816 original size:66 final size:66
Alignment explanation
Indices: 35709--35833 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
35699 CGGGAACTCG
* *
35709 AACGAGTCGACTGCTACCGAGGGACGTGGGAAAGAAACTGCACCCACCAACCTGAAGAAGAGCAC
1 AACGAGTCGACTGCTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAAGAGCAC
35774 C
66 C
* * * *
35775 AACGAGTCGACTGTTACTGAGGAACGTGGGAGAGAAGCTGCACCCACCAACCAGAAGAA
1 AACGAGTCGACTGCTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAA
35834 AAAAAGGGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.35, C:0.26, G:0.28, T:0.10
Consensus pattern (66 bp):
AACGAGTCGACTGCTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAAGAGCAC
C
Found at i:54527 original size:88 final size:92
Alignment explanation
Indices: 54355--54530 Score: 220
Period size: 92 Copynumber: 1.9 Consensus size: 92
54345 AAAATAGGGC
** *
54355 CCTTTTTGCCCTAAAATGAAATGTTGGGGAGCCAAAATGCTCCACACACAAAAAAAGCAAGGGTC
1 CCTTTTTGCCCTAAAATGAAATGTACGGGAGCCAAAATGCTCCACACACAAAAAAA-CAAGGGCC
* *
54420 AAAGTGACTATTTAGTCAAACGTTACGG
65 AAAATGACTATTTACTCAAACGTTACGG
* *
54448 CCTTTTTG-CCTCAAAATGAAA-GTACGGGAGCCAAAATGCTCCA-A-A-AAAATAA-TAGGGAC
1 CCTTTTTGCCCT-AAAATGAAATGTACGGGAGCCAAAATGCTCCACACACAAAAAAACAAGGG-C
54507 CAAAATGACTATTTACTCAAACGT
64 CAAAATGACTATTTACTCAAACGT
54531 AAAGAGTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
87 4 0.05
88 22 0.30
89 6 0.08
90 1 0.01
91 1 0.01
92 23 0.31
93 17 0.23
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (92 bp):
CCTTTTTGCCCTAAAATGAAATGTACGGGAGCCAAAATGCTCCACACACAAAAAAACAAGGGCCA
AAATGACTATTTACTCAAACGTTACGG
Found at i:56591 original size:60 final size:62
Alignment explanation
Indices: 56521--56665 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 62
56511 AATTTTTAAT
* * * * *
56521 CATTTCAATTTCATCCCT-AAATTTTGA-CTATCATTCTAAATT-AGTCTTCACAC-ATTTGAA
1 CATTTCAATTTCATCCCTCAAACTATGACCT-TCATTCAAAATTGA-TCCTCAAACTATTTGAA
* *
56581 CATTTTAATTTCA-CCCTCAAACTATGACCTTCATTCAAAATTGATCCTCAAACTTTTTGAA
1 CATTTCAATTTCATCCCTCAAACTATGACCTTCATTCAAAATTGATCCTCAAACTATTTGAA
*
56642 CATTTCAGTTTCAT-CC-CAAACTAT
1 CATTTCAATTTCATCCCTCAAACTAT
56666 ACATATATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
59 4 0.06
60 45 0.63
61 22 0.31
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (62 bp):
CATTTCAATTTCATCCCTCAAACTATGACCTTCATTCAAAATTGATCCTCAAACTATTTGAA
Found at i:56880 original size:20 final size:20
Alignment explanation
Indices: 56857--56915 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
56847 CAAATTCGCG
56857 TTGCATTTCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATT
56877 TTGCATTTCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATT
*
56897 TTCCATTTCGCGTTGCGAT
1 TTGCATTTCGCGTTGCGAT
56916 AGTCTACAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGCATTTCGCGTTGCGATT
Found at i:56935 original size:22 final size:22
Alignment explanation
Indices: 56907--56970 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
56897 TTCCATTTCG
56907 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
56929 CGTTGCGAT-TTC-CCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
56948 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
56970 C
1 C
56971 AAAATTCTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 10 0.32
20 5 0.16
21 5 0.16
22 11 0.35
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:57062 original size:6 final size:6
Alignment explanation
Indices: 57051--57130 Score: 160
Period size: 6 Copynumber: 13.3 Consensus size: 6
57041 GACACGTATT
57051 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
57099 ACCACG ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG AC
57131 GGCGGCGGCG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:57773 original size:22 final size:22
Alignment explanation
Indices: 57745--57797 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
57735 AATTTGGAAA
57745 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* *
57767 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
57789 ATCGCAACG
1 ATCGCAACG
57798 CGAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:58054 original size:12 final size:12
Alignment explanation
Indices: 58037--58063 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58027 TTCACATTGG
58037 GATGAATTTGAA
1 GATGAATTTGAA
58049 GATGAATTTGAA
1 GATGAATTTGAA
58061 GAT
1 GAT
58064 TTATAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (12 bp):
GATGAATTTGAA
Found at i:78107 original size:15 final size:16
Alignment explanation
Indices: 78082--78115 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
78072 TGATCTTGTT
78082 TAAAGAATTATTCAGA
1 TAAAGAATTATTCAGA
*
78098 TAAA-AATTATTCATA
1 TAAAGAATTATTCAGA
78113 TAA
1 TAA
78116 GATGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAGAATTATTCAGA
Found at i:86497 original size:3 final size:3
Alignment explanation
Indices: 86489--86513 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
86479 CCACTAACAA
86489 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
86514 CTTGTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:105250 original size:20 final size:20
Alignment explanation
Indices: 105210--105255 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
105200 TTTACTAGTT
* * *
105210 TTATATTTTTATATTTGTAA
1 TTATATTTTTAAATATCTAA
105230 TTATATTTTTAAATATCTAA
1 TTATATTTTTAAATATCTAA
105250 TT-TATT
1 TTATATT
105256 AAAATGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATATTTTTAAATATCTAA
Done.