Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003892.1 Hibiscus syriacus cultivar Beakdansim tig00008407_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: 69729
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:11568 original size:2 final size:2
Alignment explanation
Indices: 11561--11597 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11551 TCATTCATGC
11561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11598 CACACACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14976 original size:3 final size:3
Alignment explanation
Indices: 14968--14993 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14958 TTTGTAACCA
14968 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
14994 ATAAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27612 original size:27 final size:26
Alignment explanation
Indices: 27574--27631 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
27564 AATTCTAAAA
*
27574 AAAAACCTTAAA-TTTCAGAAAATCTC
1 AAAAACCCTAAATTTTCA-AAAATCTC
*
27600 AAAAACTCCTAAATTTTTAAAAATCTC
1 AAAAAC-CCTAAATTTTCAAAAATCTC
27627 AAAAA
1 AAAAA
27632 ATATAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 18 0.64
28 4 0.14
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (26 bp):
AAAAACCCTAAATTTTCAAAAATCTC
Found at i:27795 original size:28 final size:28
Alignment explanation
Indices: 27736--27800 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
27726 AAAAATATCT
* ** *
27736 TAAATTCTAGAAAATCTCAAAAAACTCC
1 TAAATTCTAGAAAATCCCAAAAAAAGCA
27764 TAAATTCCTA-AAAATCCCAAAAAAAGCA
1 TAAATT-CTAGAAAATCCCAAAAAAAGCA
*
27792 TAAACTCTA
1 TAAATTCTA
27801 AATCATAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 3 0.10
28 25 0.81
29 3 0.10
ACGTcount: A:0.52, C:0.22, G:0.03, T:0.23
Consensus pattern (28 bp):
TAAATTCTAGAAAATCCCAAAAAAAGCA
Found at i:27892 original size:155 final size:152
Alignment explanation
Indices: 27537--27847 Score: 380
Period size: 157 Copynumber: 2.0 Consensus size: 152
27527 AAAAAGTTAC
* * * * *
27537 TTTCTAAAAAATCCATGAAATTATTAAAATTCTAAAAAA-AAACCTTAAATTTCAGAAAATCTCA
1 TTTCTAAAAAACCCCTTAAA-TATTAAAATTCAAAAAAATAAATCTTAAATTTCAGAAAATCTCA
** * * * *
27601 AAAACTCCTAAATTTTTAAAAATCTCAAAAAATATAAAATCGTAATCGTAATCTCTAAAAATCAT
65 AAAACTCCTAAATTCCTAAAAATCCCAAAAAACATAAAATCGTAATCATAATCCCTAAAAATCAT
27666 AAGATTCATTTTTAGGGAGTTTA
130 AAGATTCATTTTTAGGGAGTTTA
27689 TTTCTAAAAAACCCCTTGAAATTATTAAAATTCCCAAAAAAAT--ATCTTAAA-TTCTAGAAAAT
1 TTTCTAAAAAACCCCTT-AAA-TATTAAAATT--CAAAAAAATAAATCTTAAATTTC-AGAAAAT
*
27751 CTCAAAAAACTCCTAAATTCCTAAAAATCCCAAAAAAAGCATAAACTC-TAAATCATAATCCCTA
61 CTC-AAAAACTCCTAAATTCCTAAAAATCCC-AAAAAA-CATAAAATCGT-AATCATAATCCCTA
27815 AAAATCATAAGATTCATTTTTTAGGGAGTTTA
122 AAAATCATAAGATTCA-TTTTTAGGGAGTTTA
27847 T
1 T
27848 AATTTTTTGA
Statistics
Matches: 137, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
152 14 0.10
153 17 0.12
154 17 0.12
155 31 0.23
156 7 0.05
157 35 0.26
158 16 0.12
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (152 bp):
TTTCTAAAAAACCCCTTAAATATTAAAATTCAAAAAAATAAATCTTAAATTTCAGAAAATCTCAA
AAACTCCTAAATTCCTAAAAATCCCAAAAAACATAAAATCGTAATCATAATCCCTAAAAATCATA
AGATTCATTTTTAGGGAGTTTA
Found at i:37142 original size:15 final size:15
Alignment explanation
Indices: 37122--37151 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37112 GAGTCAGATA
37122 GCACATCATTAATAC
1 GCACATCATTAATAC
37137 GCACATCATTAATAC
1 GCACATCATTAATAC
37152 ACACTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
GCACATCATTAATAC
Found at i:48015 original size:22 final size:21
Alignment explanation
Indices: 47989--48035 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
47979 AAGGTCAAAA
*
47989 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
48011 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
48031 ATCAA
1 ATCAA
48036 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:52155 original size:61 final size:61
Alignment explanation
Indices: 52060--52181 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
52050 CAAACATAAA
*
52060 ACATAAGCTTGGGAAGCTCTGCTCTGCTTCACAATAAACTGAAATAAAATAGGAATACATT
1 ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
* * *
52121 ACATAAGCTTGGGATGCTCTGCTATGCTTCACAATAACCTGAAATAGAATAGGAATACATT
1 ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
52182 TTCAGGCTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (61 bp):
ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
Found at i:58501 original size:2 final size:2
Alignment explanation
Indices: 58496--58555 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
58486 AGTGTGTGTG
58496 TA TA TA TA TA TA TA TA TA TA -A 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
58537 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
58556 TAAGAAGAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59622 original size:21 final size:21
Alignment explanation
Indices: 59599--59637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59589 TGTTTAATGA
59599 AAAAT-ATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
59619 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
59638 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:62657 original size:21 final size:21
Alignment explanation
Indices: 62631--62681 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
62621 CCCATAACAT
62631 GGTGCATTGGTGCACTATCAA
1 GGTGCATTGGTGCACTATCAA
*
62652 GGTGCATCGGTGCACTATCAA
1 GGTGCATTGGTGCACTATCAA
62673 GGTGCATTG
1 GGTGCATTG
62682 ATACCCCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (21 bp):
GGTGCATTGGTGCACTATCAA
Found at i:67824 original size:2 final size:2
Alignment explanation
Indices: 67817--67854 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
67807 GTACTCATTT
* *
67817 TA TA TA TA AA TA TA TA TC TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67855 CATCAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:68579 original size:43 final size:44
Alignment explanation
Indices: 68532--68645 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 44
68522 TTACAACATA
68532 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAAAAGGTATTGATATT
* *
68575 TAGC-GCG-TTTATCATTA-AAACGCCGCAATAGGTTTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAAAAGGTATTGATATT
* ** *
68617 TAACGGC-ATTTGGCAGACAAACGCCGCAA
1 TAGCGGCGATTTATCATACAAACGCCGCAA
68646 TAGTCGTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
40 1 0.02
41 5 0.08
42 30 0.51
43 23 0.39
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAAAAGGTATTGATATT
Found at i:68646 original size:43 final size:43
Alignment explanation
Indices: 68548--68648 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 43
68538 CGATTGTTCA
* * * * *
68548 ACAAACGCCGCAAAAGGTATTGATATTTAGCGCGTTTATCATT
1 ACAAACGCCGCAATAGGTATTGATATTTAACGCATTTAGCATG
* *
68591 A-AAACGCCGCAATAGGTTTTGATATTTAACGGCATTTGGCA-G
1 ACAAACGCCGCAATAGGTATTGATATTTAAC-GCATTTAGCATG
68633 ACAAACGCCGCAATAG
1 ACAAACGCCGCAATAG
68649 TCGTTGATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
42 27 0.55
43 22 0.45
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTATTGATATTTAACGCATTTAGCATG
Found at i:69132 original size:21 final size:21
Alignment explanation
Indices: 69095--69155 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
69085 ATATATTACT
*
69095 TCTCTCTGTTC-GCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
* *
69115 TCTCTCTGTGCTGCCGCTACT
1 TCTCTCTGTGCTGCCGCTGCC
* *
69136 TCTCTCTCTGCTTCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
69156 TGCTCTAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.02, C:0.43, G:0.18, T:0.38
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:69198 original size:21 final size:21
Alignment explanation
Indices: 69107--69192 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
69097 TCTCTGTTCG
* *
69107 CCGCTGCCT-CTCTCTGTGCTG
1 CCGCTG-CTGCTCTCTCTGCTT
* *
69128 CCGCTACTTCTCTCTCTGCTT
1 CCGCTGCTGCTCTCTCTGCTT
**
69149 CCGCTGCTGCTCTAGCTGCTT
1 CCGCTGCTGCTCTCTCTGCTT
*
69170 CCGCTGCTGCTCTCTCTGTTT
1 CCGCTGCTGCTCTCTCTGCTT
69191 CC
1 CC
69193 CTTGCTTCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.04
21 52 0.96
ACGTcount: A:0.02, C:0.42, G:0.19, T:0.37
Consensus pattern (21 bp):
CCGCTGCTGCTCTCTCTGCTT
Done.