Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007033.1 Hibiscus syriacus cultivar Beakdansim tig00018213_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: 75069
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4366 original size:18 final size:18
Alignment explanation
Indices: 4343--4382 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4333 TTCATTATAA
* *
4343 AAATTATAAATGAAAAAG
1 AAATTACAAATCAAAAAG
*
4361 AAATTACAAATCAAAAAT
1 AAATTACAAATCAAAAAG
4379 AAAT
1 AAAT
4383 ATTATTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATTACAAATCAAAAAG
Found at i:10038 original size:23 final size:22
Alignment explanation
Indices: 9995--10038 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
9985 AATATTTAAA
* *
9995 AAAATTATTAAATATATATTTC
1 AAAATTATTAAATAAAGATTTC
*
10017 AAAATTACTTAATTAAAGATTT
1 AAAATTA-TTAAATAAAGATTT
10039 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTATTAAATAAAGATTTC
Found at i:19869 original size:14 final size:14
Alignment explanation
Indices: 19850--19877 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19840 TCAAAATAAA
19850 TATACAATTTACGT
1 TATACAATTTACGT
19864 TATACAATTTACGT
1 TATACAATTTACGT
19878 GATCGGTTAT
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:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TATACAATTTACGT
Found at i:21438 original size:16 final size:16
Alignment explanation
Indices: 21394--21454 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
21384 ACTCGATCCG
**
21394 AAAGTAACATGAACTA
1 AAAGTAACCCGAACTA
*
21410 AAATTAACCCGAACTA
1 AAAGTAACCCGAACTA
** *
21426 AAAGTAATTCGAATTGA
1 AAAGTAACCCGAACT-A
21443 AAA-TAACCCGAA
1 AAAGTAACCCGAA
21455 TCGAAAGCAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
16 31 0.89
17 4 0.11
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAGTAACCCGAACTA
Found at i:21958 original size:2 final size:2
Alignment explanation
Indices: 21951--21984 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21941 CAAATAAAGA
21951 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
21985 TCACTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24443 original size:23 final size:23
Alignment explanation
Indices: 24388--24444 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
24378 CTCATATAAA
* *
24388 TGCACCGAAGTGCCACATAGAGT
1 TGCACCGTAGTGCCACATAGAAT
* *
24411 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
24434 TGCACTGTAGT
1 TGCACCGTAGT
24445 ACCATATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:24635 original size:103 final size:103
Alignment explanation
Indices: 24464--24784 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
24454 TAATGTCCAA
* * *
24464 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
24529 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
24567 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCAAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
*
24632 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
24670 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
24735 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
24773 AAGGACCACATA
1 AAGGACCACATA
24785 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:29763 original size:23 final size:23
Alignment explanation
Indices: 29737--29797 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
29727 CTCATATAAA
*
29737 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
29760 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
29783 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
29798 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:29987 original size:103 final size:103
Alignment explanation
Indices: 29813--30133 Score: 527
Period size: 103 Copynumber: 3.1 Consensus size: 103
29803 TAATGTCCAA
* * * *
29813 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
29878 GGCTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
29916 AAGGACCACATATCATTCCATAAGAATCATATATATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* * *
29981 GACTTCAAACATATTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
30019 AAGAACCACATATCATTCCTTAAGAATC-TAATACATATGCCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCAT-ATACATATGCCAAGGATCAAGTATGTGTCTCACC
30083 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
30122 AAGGACCACATA
1 AAGGACCACATA
30134 GACCCTCGAC
Statistics
Matches: 200, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
102 1 0.00
103 199 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:35319 original size:3 final size:3
Alignment explanation
Indices: 35311--35336 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35301 TATCTTAAAA
35311 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
35337 AATGACATTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35657 original size:19 final size:20
Alignment explanation
Indices: 35612--35658 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
35602 AATTACTAGT
35612 TATTTTATATAATATTATACA
1 TATTTT-TATAATATTATACA
35633 TA-TTTTATAATACTT-TA-A
1 TATTTTTATAATA-TTATACA
35651 TATTTTTA
1 TATTTTTA
35659 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 5 0.21
21 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTATAATATTATACA
Found at i:35952 original size:31 final size:31
Alignment explanation
Indices: 35917--35977 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
35907 TTAAAATACG
35917 GATTAAATATTA-AGTGATTGTATTGTAAATA
1 GATTAAATATTAGAG-GATTGTATTGTAAATA
35948 GATTAAATATTAGAGGATTGTATTGTAAAT
1 GATTAAATATTAGAGGATTGTATTGTAAAT
35978 TTTAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (31 bp):
GATTAAATATTAGAGGATTGTATTGTAAATA
Found at i:43068 original size:14 final size:16
Alignment explanation
Indices: 43030--43070 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
43020 AATCTTCTTG
43030 AAATATTTAATTTATAA
1 AAATATTT-ATTTATAA
43047 AAATTATTT-TTT-TAA
1 AAA-TATTTATTTATAA
43062 AAATATTTA
1 AAATATTTA
43071 GAATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 3 0.14
17 3 0.14
18 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATTTATTTATAA
Found at i:44469 original size:26 final size:25
Alignment explanation
Indices: 44427--44482 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
44417 TGCTAATAAG
* *
44427 TTTATGAATTCCTTTTTCAATTTTT
1 TTTATGAATTCCATTTTCAATTTTA
*
44452 TTTATAGATTTCCATTTTCAATTTTA
1 TTTAT-GAATTCCATTTTCAATTTTA
44478 TTTAT
1 TTTAT
44483 TTATGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.23, C:0.11, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTATGAATTCCATTTTCAATTTTA
Found at i:48860 original size:20 final size:21
Alignment explanation
Indices: 48832--48873 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48822 TGATTGATAT
*
48832 TGATAACAC-ATACATTGAAC
1 TGATAACACAAAACATTGAAC
*
48852 TGATGACACAAAACATTGAAC
1 TGATAACACAAAACATTGAAC
48873 T
1 T
48874 ATGTACGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (21 bp):
TGATAACACAAAACATTGAAC
Found at i:60721 original size:23 final size:23
Alignment explanation
Indices: 60678--60725 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
60668 TTTATTTTTG
*
60678 TTTTTTATTCATTACTATTATTAT
1 TTTTTTATT-ATTAATATTATTAT
60702 TTTTTTATT-TTAATACTTATTAT
1 TTTTTTATTATTAATA-TTATTAT
60725 T
1 T
60726 ACTATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTATTATTAATATTATTAT
Found at i:60914 original size:10 final size:10
Alignment explanation
Indices: 60894--60932 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
60884 TTTTATGTGA
60894 TTGTATTTTT
1 TTGTATTTTT
*
60904 TT-CATTTTT
1 TTGTATTTTT
60913 TTGTATTTTT
1 TTGTATTTTT
60923 TTGTATTTTT
1 TTGTATTTTT
60933 CTCATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (10 bp):
TTGTATTTTT
Found at i:60958 original size:29 final size:29
Alignment explanation
Indices: 60894--60952 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
60884 TTTTATGTGA
* *
60894 TTGTATTTTTTTCATTTTTTTGTATTTTT
1 TTGTATTTTTCTCATTATTTTGTATTTTT
*
60923 TTGTATTTTTCTCATTATTTT-TATTGTT
1 TTGTATTTTTCTCATTATTTTGTATTTTT
60951 TT
1 TT
60953 ATTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (29 bp):
TTGTATTTTTCTCATTATTTTGTATTTTT
Found at i:64336 original size:23 final size:23
Alignment explanation
Indices: 64310--64356 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
64300 AAGTCTACCA
64310 CGCAAGCATTAAATATGCATCAC
1 CGCAAGCATTAAATATGCATCAC
64333 CGCAAGCATTAAATATGCATCAC
1 CGCAAGCATTAAATATGCATCAC
64356 C
1 C
64357 CGCACAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (23 bp):
CGCAAGCATTAAATATGCATCAC
Done.