Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006979.1 Hibiscus syriacus cultivar Beakdansim tig00017980_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: 28580
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:9885 original size:37 final size:36
Alignment explanation
Indices: 9841--9963 Score: 140
Period size: 39 Copynumber: 3.2 Consensus size: 36
9831 ATTTTTTTCA
9841 AAAATATATATAATATATAGTCTTTGAAAACACTTTG
1 AAAATATATATAATATATAGT-TTTGAAAACACTTTG
* *
9878 AATATATATATGTAATATATAGTTTTTGAAAACATTTTG
1 AA-A-ATATATATAATATATAG-TTTTGAAAACACTTTG
* *
9917 AAAGCATATATATAATATATAATTTT-AAAACGCTTTTG
1 AAA--ATATATATAATATATAGTTTTGAAAACAC-TTTG
9955 AAAATATAT
1 AAAATATAT
9964 CATATGTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
36 6 0.08
37 7 0.09
38 13 0.18
39 47 0.64
40 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTGAAAACACTTTG
Found at i:14546 original size:20 final size:20
Alignment explanation
Indices: 14510--14547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14500 TGGTAGGAAT
**
14510 ATAATTATCATCTTTTTTTA
1 ATAATTATCATAATTTTTTA
14530 ATAATTATCATAATTTTT
1 ATAATTATCATAATTTTT
14548 CTCTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTATCATAATTTTTTA
Found at i:14989 original size:17 final size:16
Alignment explanation
Indices: 14969--15002 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
14959 CTTAAGAGAA
14969 TTGACCATTTAACTATG
1 TTGACCATTTAA-TATG
14986 TTGACCATTTAATATG
1 TTGACCATTTAATATG
15002 T
1 T
15003 AGCCCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (16 bp):
TTGACCATTTAATATG
Found at i:15442 original size:3 final size:3
Alignment explanation
Indices: 15434--15469 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15424 GGTTATAACC
15434 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15470 TACATACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:15526 original size:30 final size:30
Alignment explanation
Indices: 15485--15573 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
15475 ACAAAAAATA
15485 GGGCCCAAACCATTTACAAGA-CCCAAACCT
1 GGGCCCAAACCATTTACAA-ACCCCAAACCT
* * *
15515 GGGCACAAACCATTTACAAATCCCAAACTT
1 GGGCCCAAACCATTTACAAACCCCAAACCT
* *
15545 GGGCCCAAAACATTTATAAACCCCAAACC
1 GGGCCCAAACCATTTACAAACCCCAAACC
15574 CTAATAACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.39, C:0.34, G:0.11, T:0.16
Consensus pattern (30 bp):
GGGCCCAAACCATTTACAAACCCCAAACCT
Found at i:21040 original size:20 final size:21
Alignment explanation
Indices: 21001--21047 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
20991 GGCAAAACTC
*
21001 TATCTTTACACTATAAAAACAT
1 TATCTTTACAC-ACAAAAACAT
21023 TATCTTTACAC-CAAAAACAT
1 TATCTTTACACACAAAAACAT
*
21043 CATCT
1 TATCT
21048 AATGCAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (21 bp):
TATCTTTACACACAAAAACAT
Found at i:22920 original size:81 final size:79
Alignment explanation
Indices: 22787--22948 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 79
22777 TGAAAGAATC
*
22787 ATACCTATAAGAATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGGTTTATGATTA
1 ATACCTATAAGAATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGATTA
22852 TTAATGACATTATT
66 TTAATGACATTATT
22866 ATACCTATAAGAATATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGAT
1 ATACCTATAAG-A-ATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGAT
22931 TATTAATGACATTATT
64 TATTAATGACATTATT
22947 AT
1 AT
22949 TTTTAGCTAG
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 11 0.14
80 1 0.01
81 68 0.85
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (79 bp):
ATACCTATAAGAATGAGTTACAAAAGTAGGCACTAAATAGGACTTTCGAGAGTGATTTATGATTA
TTAATGACATTATT
Found at i:23929 original size:17 final size:18
Alignment explanation
Indices: 23909--23949 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23899 AAATTATATT
23909 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
23926 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
23944 ATTAAA
1 AGTAAA
23950 TACATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:28228 original size:74 final size:76
Alignment explanation
Indices: 28058--28546 Score: 472
Period size: 74 Copynumber: 6.5 Consensus size: 76
28048 AGCCAGTTCT
* * *
28058 TGGTGCCCAACATCAATGTTCAAACCAGTTTTCTTTACCCTTATGATCTCCTATGTTGGTGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAG-TTTCTTTACCCTTATGAT-TTCTATGTTGGGGTAGG
*
28123 CTTATTA-AATCC
64 CTTATTAGTATCC
*
28135 TGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACCCTTATGA-TTCTATGTTGGGTGTAGG-
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATTTCTATGTTGGG-GTAGGC
* *
28198 TT-TTAGGATTC
65 TTATTAGTATCC
* ** * *
28209 TGGGGGCCAACATCAATGTTTGAACCAGTTTCTTT--CCTTATGATTTTTATATTGGGGTAGGCT
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATTTCTATGTTGGGGTAGGCT
28272 TATTAGTATCC
66 TATTAGTATCC
* * * *
28283 TGGTGGCCAACATCGATGTTCGAACCAG-TTCTTTACCCTTTTGATCTTCTATACTT-GGGTAGG
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGAT-TTCTAT-GTTGGGGTAGG
* * *
28346 -ATATTTGCAT-C
64 CTTATTAGTATCC
** * * * * * * *
28357 TCCATGGCTAACAGCAA-GTCCAAATCAGCTCCTTTACCCTTGTGATCTTCTATG-TGGGTGTAG
1 T-GGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGAT-TTCTATGTTGGG-GTAG
28420 GCTTATTAGTATCC
63 GCTTATTAGTATCC
* * * *
28434 TGGTGGCCAACATCAATGTTCAAAACTAGTTTCTTTACCCTTTTGA--TCTTTCTTGGGGTCAGG
1 TGGTGGCCAACATCAATGTTC-AAACCAGTTTCTTTACCCTTATGATTTCTATGTTGGGGT-AGG
28497 CTTATTAGTATCC
64 CTTATTAGTATCC
*
28510 TGGTTGCCAA-ATCAATGTTC-AA-CAGTTTCTTTACCCT
1 TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCT
28547 CTTGATCTTT
Statistics
Matches: 342, Mismatches: 51, Indels: 43
0.78 0.12 0.10
Matches are distributed among these distances:
72 27 0.08
73 24 0.07
74 90 0.26
75 73 0.21
76 76 0.22
77 33 0.10
78 19 0.06
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (76 bp):
TGGTGGCCAACATCAATGTTCAAACCAGTTTCTTTACCCTTATGATTTCTATGTTGGGGTAGGCT
TATTAGTATCC
Found at i:28345 original size:148 final size:152
Alignment explanation
Indices: 28064--28483 Score: 459
Period size: 151 Copynumber: 2.8 Consensus size: 152
28054 TTCTTGGTGC
* *
28064 CCAACATCAATGTTCAAACCAGTTTTCTTTACCCTTATGATCTCCTATGTTGGTGTAGGCTTATT
1 CCAACATCAATGTTCAAACCAG-TTTCTTTA-CCTTATGATCTTCTAT-TTGGGGTAGGCTTATT
* * *
28129 A-AATCCTGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACCCTTATGA--TTCTATGTTGG
63 AGTATCCTGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACCCTTTTGATCTTCTATCTTGG
* **
28191 GTGTAGG-T-TTTAGGAT-TCTGGGGG
128 GTGTAGGATATTT-GCATCTC-CAGGG
** *
28215 CCAACATCAATGTTTGAACCAGTTTCTTT-CCTTATGAT-TTTTATATTGGGGTAGGCTTATTAG
1 CCAACATCAATGTTCAAACCAGTTTCTTTACCTTATGATCTTCTAT-TTGGGGTAGGCTTATTAG
*
28278 TATCCTGGTGGCCAACATCGATGTTCGAACCAG-TTCTTTACCCTTTTGATCTTCTATACTT-GG
65 TATCCTGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACCCTTTTGATCTTCTAT-CTTGGG
*
28341 -GTAGGATATTTGCATCTCCATGG
129 TGTAGGATATTTGCATCTCCAGGG
* * * * * * * *
28364 CTAACAGCAA-GTCCAAATCAGCTCCTTTACCCTTGTGATCTTCTATGTGGGTGTAGGCTTATTA
1 CCAACATCAATGTTCAAACCAGTTTCTTTA-CCTTATGATCTTCTATTTGGG-GTAGGCTTATTA
* *
28428 GTATCCTGGTGGCCAACATCAATGTTCAAAACTAGTTTCTTTACCCTTTTGATCTT
64 GTATCCTGGTGGCCAACATCGATGTTC-AAACCAGTTTCTTTACCCTTTTGATCTT
28484 TCTTGGGGTC
Statistics
Matches: 228, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
147 35 0.15
148 57 0.25
149 22 0.10
150 26 0.11
151 63 0.28
152 5 0.02
153 20 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (152 bp):
CCAACATCAATGTTCAAACCAGTTTCTTTACCTTATGATCTTCTATTTGGGGTAGGCTTATTAGT
ATCCTGGTGGCCAACATCGATGTTCAAACCAGTTTCTTTACCCTTTTGATCTTCTATCTTGGGTG
TAGGATATTTGCATCTCCAGGG
Done.