Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004616.1 Hibiscus syriacus cultivar Beakdansim tig00010326_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: 46473
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4746 original size:13 final size:13
Alignment explanation
Indices: 4709--4738 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4699 TAATACATTT
4709 AATAATAATAATA
1 AATAATAATAATA
*
4722 AATAATTATAATA
1 AATAATAATAATA
4735 AATA
1 AATA
4739 TAACTAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:4872 original size:5 final size:5
Alignment explanation
Indices: 4862--4934 Score: 51
Period size: 5 Copynumber: 14.0 Consensus size: 5
4852 AGTTAATAAG
* * *
4862 AAATA AAATA ATAAT- GA-TA AAATAA AAATG AGATA AAATA AAATA AAATAA
1 AAATA AAATA A-AATA AAATA AAAT-A AAATA AAATA AAATA AAATA AAAT-A
*
4913 AAATA ACAAAA AAATGA AAATA
1 AAATA A-AATA AAAT-A AAATA
4935 GAATTAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 28 0.53
6 22 0.42
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4883 original size:14 final size:15
Alignment explanation
Indices: 4864--4904 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
4854 TTAATAAGAA
*
4864 ATAAAATAATAAT-G
1 ATAAAATAAAAATAG
4878 ATAAAATAAAAATGAG
1 ATAAAATAAAAAT-AG
4894 ATAAAATAAAA
1 ATAAAATAAAA
4905 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (15 bp):
ATAAAATAAAAATAG
Found at i:4915 original size:11 final size:11
Alignment explanation
Indices: 4856--4960 Score: 63
Period size: 11 Copynumber: 9.1 Consensus size: 11
4846 AATAGAAGTT
4856 AATAAGAAATAA
1 AATAA-AAATAA
4868 AATAATAATGATAA
1 AATAA-AA--ATAA
*
4882 AATAAAAATGA
1 AATAAAAATAA
*
4893 GAT-AAAATAA
1 AATAAAAATAA
4903 AAT-AAAATAAA
1 AATAAAAAT-AA
4914 AATAACAAA-AA
1 AATAA-AAATAA
*
4925 AATGAAAATAGA
1 AATAAAAATA-A
* *
4937 ATTAAAAATTA
1 AATAAAAATAA
*
4948 AAGAAAATATAA
1 AATAAAA-ATAA
4960 A
1 A
4961 TTGGATGAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
10 16 0.22
11 23 0.32
12 20 0.27
13 5 0.07
14 9 0.12
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:4932 original size:17 final size:16
Alignment explanation
Indices: 4856--4934 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
4846 AATAGAAGTT
*
4856 AATAAGAAATAAAATAAT
1 AATAA-AAATAAAA-AAA
*
4874 AATGATAAAATAAAAATGA
1 AAT-A-AAAATAAAAA-AA
* *
4893 GAT-AAAATAAAATAA
1 AATAAAAATAAAAAAA
4908 AATAAAAATAACAAAAA
1 AATAAAAATAA-AAAAA
*
4925 AATGAAAATA
1 AATAAAAATA
4935 GAATTAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 3 0.06
16 16 0.33
17 13 0.27
18 4 0.08
19 11 0.23
20 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:4961 original size:28 final size:27
Alignment explanation
Indices: 4878--4945 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
4868 AATAATAATG
* * *
4878 ATAAAATAAAAATGA-GATAAAATAAA
1 ATAAAATAAAAATAACAAAAAAATAAA
4904 ATAAAATAAAAATAACAAAAAAATGAAA
1 ATAAAATAAAAATAACAAAAAAAT-AAA
*
4932 ATAGAATTAAAAAT
1 ATA-AAATAAAAAT
4946 TAAAGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.40
27 6 0.17
28 6 0.17
29 9 0.26
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (27 bp):
ATAAAATAAAAATAACAAAAAAATAAA
Found at i:6012 original size:25 final size:25
Alignment explanation
Indices: 5978--6044 Score: 134
Period size: 25 Copynumber: 2.7 Consensus size: 25
5968 TTATGTTATT
5978 GAACGAATTTATAATATCTTAGAAG
1 GAACGAATTTATAATATCTTAGAAG
6003 GAACGAATTTATAATATCTTAGAAG
1 GAACGAATTTATAATATCTTAGAAG
6028 GAACGAATTTATAATAT
1 GAACGAATTTATAATAT
6045 TTTAAGAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (25 bp):
GAACGAATTTATAATATCTTAGAAG
Found at i:9951 original size:28 final size:28
Alignment explanation
Indices: 9891--9967 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
9881 TATGGGTTAA
*
9891 AAAAATCAAACA-TTTTAAATTTTTTTT
1 AAAAATAAAACATTTTTAAATTTTTTTT
**
9918 AAAAATATTACATTTTTAAATTTTTGTTT
1 AAAAATAAAACATTTTTAAATTTTT-TTT
* *
9947 -TAAATAAAAGATTTTTAAATT
1 AAAAATAAAACATTTTTAAATT
9968 ATCAAAATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 9 0.22
28 29 0.71
29 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (28 bp):
AAAAATAAAACATTTTTAAATTTTTTTT
Found at i:12414 original size:45 final size:45
Alignment explanation
Indices: 12350--12442 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
12340 GTTTCAAGTT
12350 ATTCAAATTGACAGGTCATATTTTATGACTCAAACTTAATAAGAA
1 ATTCAAATTGACAGGTCATATTTTATGACTCAAACTTAATAAGAA
12395 ATTCAAATTGACAGGTCATATTTTATGACTCAAACTTAATAAGAA
1 ATTCAAATTGACAGGTCATATTTTATGACTCAAACTTAATAAGAA
12440 ATT
1 ATT
12443 TTTTCAGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (45 bp):
ATTCAAATTGACAGGTCATATTTTATGACTCAAACTTAATAAGAA
Found at i:12553 original size:2 final size:2
Alignment explanation
Indices: 12546--12621 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
12536 TACTCTTACC
12546 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A- 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
12586 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
12622 CTTTTCACAT
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12736 original size:14 final size:14
Alignment explanation
Indices: 12717--12755 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
12707 TCAAGGGGCT
12717 TATATATATGA-TAA
1 TATATATAT-ATTAA
12731 TATATATATATTAA
1 TATATATATATTAA
12745 TATATAGTATA
1 TATATA-TATA
12756 GTTTTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (14 bp):
TATATATATATTAA
Found at i:12811 original size:38 final size:39
Alignment explanation
Indices: 12756--12897 Score: 141
Period size: 38 Copynumber: 3.6 Consensus size: 39
12746 ATATAGTATA
* *
12756 GTTTTTGAAGAA-TTATAATATATAATTTTTTTTAAAATT
1 GTTTTTGAA-AACATATAATATATAATTTTTTTTAAAAGT
*
12795 G-TTTTGAAAACATATAATATATAGTTTTTTTTTTAAAAAAAGT
1 GTTTTTGAAAACATATAATATATA--ATTTTTTTT---AAAAGT
*
12838 GTTTTTGAAAACATATAATATAT-A--TTTTTTAAAAGG
1 GTTTTTGAAAACATATAATATATAATTTTTTTTAAAAGT
12874 GTTTTTGAAAACCTATATAATATA
1 GTTTTTGAAAA-C-ATATAATATA
12898 GTTTTGAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
36 16 0.18
37 3 0.03
38 28 0.31
39 7 0.08
40 8 0.09
43 6 0.07
44 21 0.24
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (39 bp):
GTTTTTGAAAACATATAATATATAATTTTTTTTAAAAGT
Found at i:13157 original size:5 final size:5
Alignment explanation
Indices: 12950--13153 Score: 309
Period size: 5 Copynumber: 40.8 Consensus size: 5
12940 AAAAAAAAAT
* * *
12950 TATGT TATGT TATGT TATGC TATGC TATGC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
13000 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
* *
13050 TATGC TATGC TATGC TATGT TATGC TATTC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
* * * * * *
13100 TATGC TATGC TATGC TATGC TATGT TATGT TATGT TATGT TATGT TATGT
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
13150 TATG
1 TATG
13154 TTATATATTA
Statistics
Matches: 193, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 193 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (5 bp):
TATGC
Found at i:15351 original size:20 final size:21
Alignment explanation
Indices: 15313--15353 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
15303 TGTTGTGGCC
*
15313 TTTTCTAGCTGTTGGGGATGA
1 TTTTCTAGCTGTTGAGGATGA
*
15334 TTTT-TAGCTTTTGAGGATGA
1 TTTTCTAGCTGTTGAGGATGA
15354 AATATATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.17, C:0.07, G:0.29, T:0.46
Consensus pattern (21 bp):
TTTTCTAGCTGTTGAGGATGA
Found at i:16444 original size:17 final size:17
Alignment explanation
Indices: 16424--16462 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
16414 CATTTGCATT
16424 GAAAATCAATTTTGACC
1 GAAAATCAATTTTGACC
16441 GAAAATCAATTTTGACC
1 GAAAATCAATTTTGACC
16458 -AAAAT
1 GAAAAT
16463 TCATTATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (17 bp):
GAAAATCAATTTTGACC
Found at i:23461 original size:31 final size:31
Alignment explanation
Indices: 23420--23478 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
23410 AGAGTCGAGG
*
23420 GTTACCTATGTCCTTCGGGACATATGGACAA
1 GTTACATATGTCCTTCGGGACATATGGACAA
*
23451 GTTACATATGTCCTTTGGGACATATGGA
1 GTTACATATGTCCTTCGGGACATATGGA
23479 TAGGTCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (31 bp):
GTTACATATGTCCTTCGGGACATATGGACAA
Found at i:23514 original size:20 final size:19
Alignment explanation
Indices: 23458--23514 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 19
23448 CAAGTTACAT
23458 ATGTCCTTTGGGACATATGG
1 ATGT-CTTTGGGACATATGG
23478 ATAGGTCTTTCGGGACATATGTG
1 AT--GTCTTT-GGGACATATG-G
23501 -TGTCATTTGGGACA
1 ATGTC-TTTGGGACA
23515 AATTCTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
20 11 0.34
21 7 0.22
22 13 0.41
23 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
ATGTCTTTGGGACATATGG
Found at i:30202 original size:192 final size:191
Alignment explanation
Indices: 29870--30238 Score: 729
Period size: 192 Copynumber: 1.9 Consensus size: 191
29860 TTGAGAAAGT
29870 TTTCAATCCAAGCCGAAAGGACTGGTCGCCAAAGCTAGATGAAGCATTATGGGCTTATCGCACAT
1 TTTCAATCCAAGCCGAAAGGACTGGTCGCCAAAGCTAGATGAAGCATTATGGGCTTATCGCACAT
29935 CGTTTAGACACCGCTATGAATGTCCCCATTCAAACTCGTTTACGGTAAAGAATGCCATTTGCCTG
66 CGTTTAGACACCGCTATGAATGTCCCCATTCAAACTCGTTTACGGTAAAGAATGCCATTTGCCTG
30000 TGGAAAGCGAACATAAAGCTTATTGGGCCATCAAGAAATTAAACATGGATGCTCAGCTCGC
131 TGGAAAGCGAACATAAAGCTTATTGGGCCATCAAGAAATTAAACATGGATGCTCAGCTCGC
30061 TTTCAATCCAAGCCGAAAGGACTGGTCGCCAAAGCTAGATGAAGCATTATGGGCTTATCGCACAT
1 TTTCAATCCAAGCCGAAAGGACTGGTCGCCAAAGCTAGATGAAGCATTATGGGCTTATCGCACAT
30126 CGTTTAAGACACCGCTATGAATGTCCCCATTCAAACTCGTTTACGGTAAAGAATGCCATTTGCCT
66 CGTTT-AGACACCGCTATGAATGTCCCCATTCAAACTCGTTTACGGTAAAGAATGCCATTTGCCT
30191 GTGGAAAGCGAACATAAAGCTTATTGGGCCATCAAGAAATTAAACATG
130 GTGGAAAGCGAACATAAAGCTTATTGGGCCATCAAGAAATTAAACATG
30239 AGCCCACGCT
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
191 70 0.40
192 107 0.60
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (191 bp):
TTTCAATCCAAGCCGAAAGGACTGGTCGCCAAAGCTAGATGAAGCATTATGGGCTTATCGCACAT
CGTTTAGACACCGCTATGAATGTCCCCATTCAAACTCGTTTACGGTAAAGAATGCCATTTGCCTG
TGGAAAGCGAACATAAAGCTTATTGGGCCATCAAGAAATTAAACATGGATGCTCAGCTCGC
Found at i:34684 original size:53 final size:52
Alignment explanation
Indices: 34620--34738 Score: 202
Period size: 53 Copynumber: 2.3 Consensus size: 52
34610 ACAATGATTA
*
34620 TAGTTTATGCTGAGAGGTATTGCTACAACAACAGTCTGACAAACCAAGGGTTG
1 TAGTTTATGCTGAGAGGTATTGCTACAAAAACAGTCTGACAAA-CAAGGGTTG
34673 TAGTTTATGCTGAGAGGTATTGCTACAAAAACAGTCTGACAAACAAGGGTTG
1 TAGTTTATGCTGAGAGGTATTGCTACAAAAACAGTCTGACAAACAAGGGTTG
* *
34725 TAATTAATGCTGAG
1 TAGTTTATGCTGAG
34739 TAGTACTGCC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
52 21 0.33
53 42 0.67
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (52 bp):
TAGTTTATGCTGAGAGGTATTGCTACAAAAACAGTCTGACAAACAAGGGTTG
Found at i:40483 original size:12 final size:13
Alignment explanation
Indices: 40466--40498 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
40456 TAAGATTTTC
40466 TTTGAAAAT-AAT
1 TTTGAAAATCAAT
40478 TTTG-AAATCAAT
1 TTTGAAAATCAAT
40490 TTTGAAAAT
1 TTTGAAAAT
40499 TACTCCCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 11 0.58
13 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTGAAAATCAAT
Done.