Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003937.1 Hibiscus syriacus cultivar Beakdansim tig00008508_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: 51099
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:21533 original size:61 final size:64
Alignment explanation
Indices: 21421--21567 Score: 201
Period size: 61 Copynumber: 2.3 Consensus size: 64
21411 TAGCAGGTTT
* *
21421 ATATTAGCACTAGTGTGTAAGGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTTTCATATCC
1 ATATTAGCACTAGAGTGTAA-GACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
* * *
21486 ATATCAGCACTAGAGTGTAA-AC-CTA-GTGTAGGTGGTGGGCACGACCTTATGTGTCATATCC
1 ATATTAGCACTAGAGTGTAAGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
* *
21547 AGATTAGCACTAGAGGGTAAG
1 ATATTAGCACTAGAGTGTAAG
21568 CTCAGTGCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 50 0.68
62 3 0.04
63 2 0.03
65 18 0.25
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (64 bp):
ATATTAGCACTAGAGTGTAAGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
Found at i:29476 original size:21 final size:21
Alignment explanation
Indices: 29426--29481 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
29416 AGAAAAATGA
* *
29426 AGCAAGGGAAGCAGAGAGAGC
1 AGCAATGGAAGCAGACAGAGC
*
29447 AGCAATGGAAGCAGCCAGAGC
1 AGCAATGGAAGCAGACAGAGC
* *
29468 AGTAGTGGAAGCAG
1 AGCAATGGAAGCAG
29482 TTGCAACACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.39, T:0.05
Consensus pattern (21 bp):
AGCAATGGAAGCAGACAGAGC
Found at i:29919 original size:44 final size:43
Alignment explanation
Indices: 29841--29959 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 43
29831 TTATGTGTTA
**
29841 TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCGGTCC
1 TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCAATCC
* * * * *
29884 TTTAGCGTCGTTTGTATCCTAAAAACGCTGGTATATAGCAATCC
1 TTTAGCGGCGTTTGTA-ACAAAAAACGCTGCTATATACCAATCC
* * *
29928 TTTAGCGGCATTTGTGGA-AAAAAACGCCGCTA
1 TTTAGCGGCGTTTGT-AACAAAAAACGCTGCTA
29960 AATCTCAACA
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 26 0.43
44 34 0.57
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCAATCC
Found at i:29994 original size:43 final size:42
Alignment explanation
Indices: 29947--30113 Score: 126
Period size: 43 Copynumber: 3.9 Consensus size: 42
29937 ATTTGTGGAA
* *
29947 AAAAACGCCGCTAAATCTCAACACTTATTGCAGCGTTTGCGAT
1 AAAAACGCCGCTAAATCTCAACAC-TATTGCGGCGTTTGCGAG
* * * * *
29990 AAAAACGCTGCTAAA-CATCAACAACTACTGTGGCGTTTGTGGG
1 AAAAACGCCGCTAAATC-TCAAC-ACTATTGCGGCGTTTGCGAG
* * *
30033 AAAAATGCCGCTAAATATCAACACCTATTGCGGCGTTTG-GTG
1 AAAAACGCCGCTAAATCTCAACA-CTATTGCGGCGTTTGCGAG
* *
30075 AACAAACACAGCTATATATCGTC-AC-CTATTGCGGCGTTT
1 AA-AAACGCCGCTA-A-ATC-TCAACACTATTGCGGCGTTT
30114 TTTCTTCACG
Statistics
Matches: 99, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
42 6 0.06
43 84 0.85
44 3 0.03
45 4 0.04
46 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAATCTCAACACTATTGCGGCGTTTGCGAG
Found at i:30379 original size:25 final size:25
Alignment explanation
Indices: 30324--30379 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
30314 ATTTATGTAC
* **
30324 GTATATCATACCTACATACATGTAT
1 GTATATCATACATACATACATACAT
** *
30349 CAATATCATATATACATACATACAT
1 GTATATCATACATACATACATACAT
30374 GTATAT
1 GTATAT
30380 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (25 bp):
GTATATCATACATACATACATACAT
Found at i:31906 original size:31 final size:31
Alignment explanation
Indices: 31881--31992 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
31871 TCCATAGATT
* * *
31881 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
31912 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
31943 CCGATGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
31974 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
31993 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:33570 original size:3 final size:3
Alignment explanation
Indices: 33562--33587 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33552 CCATCTATAT
33562 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
33588 TTTTTAATCT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36412 original size:31 final size:31
Alignment explanation
Indices: 36374--36498 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
36364 CCCGAAGGAC
* * *
36374 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
36405 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
36436 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
36467 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
36498 C
1 C
36499 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:38578 original size:41 final size:41
Alignment explanation
Indices: 38527--38609 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
38517 ATTGTAATTA
* *
38527 ATATAGAAAGTAAATTTATTAACCAAATAATCATTATTAAT
1 ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
* * *
38568 ATATAGAAAGTAAATATATTAATCTAATAATTATAATTAAT
1 ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
38609 A
1 A
38610 AATTATTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (41 bp):
ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
Found at i:41740 original size:25 final size:25
Alignment explanation
Indices: 41702--41768 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
41692 TTTATTTTTG
41702 TTTC-TTAAAATTTTATAAACTATT
1 TTTCTTTAAAATTTTATAAACTATT
41726 TTTCTTTAAAATTTTATAAACTATT
1 TTTCTTTAAAATTTTATAAACTATT
41751 TTTCTTTAAAA-TTTATAA
1 TTTCTTTAAAATTTTATAA
41769 GTTTATCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 11 0.26
25 31 0.74
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTCTTTAAAATTTTATAAACTATT
Found at i:49663 original size:15 final size:15
Alignment explanation
Indices: 49640--49676 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
49630 ATAAGTGAGA
*
49640 CCTCCACCACCGTTC
1 CCTCAACCACCGTTC
49655 CCTCAACCACCGTTC
1 CCTCAACCACCGTTC
49670 CCTCAAC
1 CCTCAAC
49677 GATTGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.57, G:0.05, T:0.19
Consensus pattern (15 bp):
CCTCAACCACCGTTC
Done.