Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001636.1 Hibiscus syriacus cultivar Beakdansim tig00003275_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: 128213
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1924 original size:21 final size:21
Alignment explanation
Indices: 1895--1950 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1885 ACCGTGATTG
*
1895 CGGCTGTCGCGGGCGCTATTA
1 CGGCCGTCGCGGGCGCTATTA
* *
1916 CGGTCGTCG-GGGACGCTATTG
1 CGGCCGTCGCGGG-CGCTATTA
1937 CGGCCGTCGCGGGC
1 CGGCCGTCGCGGGC
1951 AACTCGGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.07, C:0.30, G:0.43, T:0.20
Consensus pattern (21 bp):
CGGCCGTCGCGGGCGCTATTA
Found at i:14295 original size:26 final size:29
Alignment explanation
Indices: 14234--14300 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
14224 ATTTAGTTAC
** *
14234 ATTTTATTTTTTTTATTTTGATCACTTAA
1 ATTTTATTTTTTTTATAATCATCACTTAA
*
14263 ATATTATTTTTTTTA-AATCAT-ACTT-A
1 ATTTTATTTTTTTTATAATCATCACTTAA
*
14289 ATTTTATGTTTT
1 ATTTTATTTTTT
14301 ATGTCTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 11 0.34
27 4 0.12
28 3 0.09
29 14 0.44
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (29 bp):
ATTTTATTTTTTTTATAATCATCACTTAA
Found at i:19242 original size:43 final size:44
Alignment explanation
Indices: 19027--19304 Score: 202
Period size: 42 Copynumber: 6.5 Consensus size: 44
19017 TAATTTTATT
* * *
19027 TTTTTATCTTTATAATTGAGG-CCCTTAA--TTTTTCAATCCCAC
1 TTTTTACCTTTATAATTGAGGTCCC-TAATTTTTTTAAATCTCAC
* * * * * * *
19069 TTTGTACTTTTATAATTGAGCT-CCTAA-GTTTTTCAACCTTAC
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
* *
19111 TTTCTACCTTTATAATTGAGGTCCC-AAATTTTTT-AATCTCAC
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
* *** * *
19153 TTTTTACCTTTATAGTTG-CCCCCCTAATTTTTTTCAATCCCA-
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
* * *
19195 TTTTTA-CTTATATAATTTAGGTCCCTAATTTTTTT-ATTCTTAC
1 TTTTTACCTT-TATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
* * * * * * *
19238 TTTTTAGCTTTAAAATTAAGG-CCCTATTTTTTTTTAATTTGAC
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
19281 TTTTTACCTTTATAATTGAGGTCC
1 TTTTTACCTTTATAATTGAGGTCC
19305 TCAATCATAC
Statistics
Matches: 187, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
41 9 0.05
42 109 0.58
43 64 0.34
44 5 0.03
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (44 bp):
TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTAAATCTCAC
Found at i:24753 original size:21 final size:21
Alignment explanation
Indices: 24691--24753 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
24681 CAATATAATG
*
24691 AGTGATTCAAGTAAAATCTAA
1 AGTGATTTAAGTAAAATCTAA
* * * *
24712 ACT-ATATAAG-ATAATTTTAA
1 AGTGATTTAAGTA-AAATCTAA
24732 AGTGATTTAAGTAAAATCTAA
1 AGTGATTTAAGTAAAATCTAA
24753 A
1 A
24754 CTAATAGAGT
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
21 15 0.50
22 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (21 bp):
AGTGATTTAAGTAAAATCTAA
Found at i:25612 original size:3 final size:3
Alignment explanation
Indices: 25604--25677 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
25594 ATACATTGAT
25604 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25652 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
25678 GTAATGCAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:35675 original size:13 final size:13
Alignment explanation
Indices: 35659--35683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35649 TTTTTATTCC
35659 TTTTTTTTATAAT
1 TTTTTTTTATAAT
35672 TTTTTTTTATAA
1 TTTTTTTTATAA
35684 ATATTTCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTATAAT
Found at i:40834 original size:17 final size:15
Alignment explanation
Indices: 40798--40836 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40788 GGTGTGCAAA
*
40798 TCCGGGTACCCGATT
1 TCCGGGTACCCGACT
40813 TCCGGGTACCCGGAACT
1 TCCGGGTACCC-G-ACT
40830 TCCGGGT
1 TCCGGGT
40837 CGACGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 9 0.43
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.23
Consensus pattern (15 bp):
TCCGGGTACCCGACT
Found at i:40884 original size:17 final size:17
Alignment explanation
Indices: 40862--40933 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
40852 CCGTGTCCCG
* *
40862 ACCCGGATGTTACGGGT
1 ACCCGGATTTTGCGGGT
**
40879 ACCCGG-TAAT-CGGGT
1 ACCCGGATTTTGCGGGT
40894 ACCCGGATTTTGCGGGT
1 ACCCGGATTTTGCGGGT
40911 ACCCGGATTTTGCGGGT
1 ACCCGGATTTTGCGGGT
40928 ACCCGG
1 ACCCGG
40934 TAATCGGGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.22
16 4 0.08
17 34 0.69
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.24
Consensus pattern (17 bp):
ACCCGGATTTTGCGGGT
Found at i:42907 original size:21 final size:22
Alignment explanation
Indices: 42865--42907 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42855 AATTCAATGA
*
42865 TTATTTGTATATATATTGAAGG
1 TTATTTGTATATATATTAAAGG
42887 TTATTTAGTA-AT-TATTAAAGG
1 TTATTT-GTATATATATTAAAGG
42908 AAATTAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
TTATTTGTATATATATTAAAGG
Found at i:43486 original size:21 final size:21
Alignment explanation
Indices: 43460--43504 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43450 GATTTCTGGG
* *
43460 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
43481 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
43502 CAA
1 CAA
43505 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:44364 original size:31 final size:31
Alignment explanation
Indices: 44326--44481 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
44316 AGGGTCGAGG
*
44326 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
44357 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
44388 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
44419 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
44450 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
44481 G
1 G
44482 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:48293 original size:23 final size:23
Alignment explanation
Indices: 48262--48313 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 23
48252 CAATTCTGCC
48262 TAAACTAGACATAACTAGCTTTAA
1 TAAA-TAGACATAACTAGCTTTAA
48286 TAAATAGACATAACTAGCTTTAA
1 TAAATAGACATAACTAGCTTTAA
48309 TAAAT
1 TAAAT
48314 GTGAAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (23 bp):
TAAATAGACATAACTAGCTTTAA
Found at i:54850 original size:41 final size:41
Alignment explanation
Indices: 54802--54883 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
54792 ACTTTTGACA
54802 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
1 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
54843 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
1 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
54884 ATTCTCATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (41 bp):
GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
Found at i:65304 original size:23 final size:22
Alignment explanation
Indices: 65261--65304 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
65251 GATCCCATAT
* **
65261 AAAATAAAGATTTAATTAAATA
1 AAAATAAAAATTTAAAAAAATA
65283 AAAATAAAAATTTTAAAAAAAT
1 AAAATAAAAA-TTTAAAAAAAT
65305 TATATTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATAAAAATTTAAAAAAATA
Found at i:68846 original size:17 final size:17
Alignment explanation
Indices: 68824--68862 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
68814 TTAAGGTTAG
68824 GATTTGAGGATTTTATA
1 GATTTGAGGATTTTATA
* *
68841 GATTTGGGGATTTTATG
1 GATTTGAGGATTTTATA
68858 GATTT
1 GATTT
68863 AGGGGGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (17 bp):
GATTTGAGGATTTTATA
Found at i:73548 original size:2 final size:2
Alignment explanation
Indices: 73541--73567 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73531 ATTCAAAGCG
73541 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
73568 TTGAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76169 original size:21 final size:21
Alignment explanation
Indices: 76143--76207 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
76133 TTGATAACAC
76143 CTAATTTGTCTAATATTTAAA
1 CTAATTTGTCTAATATTTAAA
* *
76164 CTAATTTATAC-AAGA--TAATA
1 CTAATTTGT-CTAATATTTAA-A
76184 CATAATTTGTCTAATATTTAAA
1 C-TAATTTGTCTAATATTTAAA
76206 CT
1 CT
76208 TACAATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 22 0.65
22 3 0.09
23 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.43
Consensus pattern (21 bp):
CTAATTTGTCTAATATTTAAA
Found at i:76462 original size:17 final size:17
Alignment explanation
Indices: 76440--76472 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
76430 ATCACTGATG
76440 ATAACATAATAATACAC
1 ATAACATAATAATACAC
*
76457 ATAACATACTAATACA
1 ATAACATAATAATACA
76473 TTGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAACATAATAATACAC
Found at i:78609 original size:78 final size:79
Alignment explanation
Indices: 78509--78655 Score: 199
Period size: 80 Copynumber: 1.9 Consensus size: 79
78499 GGTAGAACCT
* * *
78509 AATATTAACATTTCCGGAAG-AAAAATAATATTTTAGGTAACGCTTTACCATAAATGTTAAACAT
1 AATATTAACATTTCCGGAAGAAAAAATAATATTTTAAGTAACGCTTTACCAGAAATGTTAAAAAT
78573 TTTGGGTAGCGCCC
66 TTTGGGTAGCGCCC
* * * *
78587 AATATTAACAATTT-CGGTAGAAAAAAATAATGTTTTAAGTAGCGTTTTACCAGAAATGTTAAAA
1 AATATTAAC-ATTTCCGGAAG-AAAAAATAATATTTTAAGTAACGCTTTACCAGAAATGTTAAAA
78651 ATTTT
64 ATTTT
78656 TAACATTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
78 14 0.24
79 4 0.07
80 41 0.69
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (79 bp):
AATATTAACATTTCCGGAAGAAAAAATAATATTTTAAGTAACGCTTTACCAGAAATGTTAAAAAT
TTTGGGTAGCGCCC
Found at i:91875 original size:24 final size:24
Alignment explanation
Indices: 91847--91894 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
91837 ACACTTTTGG
91847 TTGGACATCGATTTAACAAATAAA
1 TTGGACATCGATTTAACAAATAAA
91871 TTGGACATCGATTTAACAAATAAA
1 TTGGACATCGATTTAACAAATAAA
91895 CTGTAGATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (24 bp):
TTGGACATCGATTTAACAAATAAA
Found at i:92772 original size:82 final size:82
Alignment explanation
Indices: 92635--92800 Score: 332
Period size: 82 Copynumber: 2.0 Consensus size: 82
92625 AAAACTAGGA
92635 GAAAATGTACGTACATGGCATGTAAGAACAAGTAGGGTCCATAAATATTGACCAATCGCATCACG
1 GAAAATGTACGTACATGGCATGTAAGAACAAGTAGGGTCCATAAATATTGACCAATCGCATCACG
92700 AAGTCGATCTTCCTGGT
66 AAGTCGATCTTCCTGGT
92717 GAAAATGTACGTACATGGCATGTAAGAACAAGTAGGGTCCATAAATATTGACCAATCGCATCACG
1 GAAAATGTACGTACATGGCATGTAAGAACAAGTAGGGTCCATAAATATTGACCAATCGCATCACG
92782 AAGTCGATCTTCCTGGT
66 AAGTCGATCTTCCTGGT
92799 GA
1 GA
92801 GATTAGTGTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (82 bp):
GAAAATGTACGTACATGGCATGTAAGAACAAGTAGGGTCCATAAATATTGACCAATCGCATCACG
AAGTCGATCTTCCTGGT
Found at i:94077 original size:18 final size:17
Alignment explanation
Indices: 94051--94089 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
94041 TTTTTTTTCT
*
94051 TTTATGTAGAATGTCTAC
1 TTTAAGTAG-ATGTCTAC
*
94069 TTTAAGTAGATTTCTAC
1 TTTAAGTAGATGTCTAC
94086 TTTA
1 TTTA
94090 TAAATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (17 bp):
TTTAAGTAGATGTCTAC
Found at i:98192 original size:2 final size:2
Alignment explanation
Indices: 98185--98222 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
98175 TCTTTTTAAA
98185 AT 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 AT
98223 CCCCATCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98444 original size:24 final size:24
Alignment explanation
Indices: 98417--98540 Score: 90
Period size: 24 Copynumber: 5.2 Consensus size: 24
98407 TATATCAAAA
98417 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
98441 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
98465 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
98489 ATCAGATCAGAATCTATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * *
98513 ATCAAATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
98537 ATCA
1 ATCA
98541 GATCAGAATT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.07
24 80 0.91
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:98545 original size:24 final size:24
Alignment explanation
Indices: 98434--98549 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
98424 CATAAATCAG
* * *
98434 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
98458 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
98482 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
98506 GTC-AGATATCAAATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
98530 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
98550 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:99679 original size:18 final size:18
Alignment explanation
Indices: 99658--99693 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
99648 ATTCCATCCG
*
99658 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
99676 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
99694 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:102742 original size:29 final size:29
Alignment explanation
Indices: 102700--102764 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
102690 AATGAAAATA
*
102700 TTGTTATTGAGGGAGTAATCATTGGTAAT
1 TTGTTGTTGAGGGAGTAATCATTGGTAAT
102729 TTGTTGTTGAGGGAGTAATCATTGGTAAT
1 TTGTTGTTGAGGGAGTAATCATTGGTAAT
102758 TTGTTGT
1 TTGTTGT
102765 GCCTTGGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.45
Consensus pattern (29 bp):
TTGTTGTTGAGGGAGTAATCATTGGTAAT
Found at i:122407 original size:2 final size:2
Alignment explanation
Indices: 122400--122429 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
122390 ATTCGATCTG
*
122400 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122430 TAGTCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:123377 original size:17 final size:16
Alignment explanation
Indices: 123347--123382 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
123337 ATATATATTT
123347 AAAATTATAAAATTAA
1 AAAATTATAAAATTAA
*
123363 AAAATATATATAATTAA
1 AAAAT-TATAAAATTAA
123380 AAA
1 AAA
123383 CAAAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTATAAAATTAA
Found at i:123387 original size:29 final size:28
Alignment explanation
Indices: 123334--123389 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
123324 TGACAATTTT
*
123334 AAAATATATATTTAAAATTATAAAATTAA
1 AAAATATATATTTAAAA-TACAAAATTAA
123363 AAAATATATATAATTAAAA-ACAAAATT
1 AAAATATATAT--TTAAAATACAAAATT
123390 TTGAAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 18 0.75
31 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAATATATATTTAAAATACAAAATTAA
Found at i:127114 original size:143 final size:141
Alignment explanation
Indices: 126646--127171 Score: 605
Period size: 143 Copynumber: 3.7 Consensus size: 141
126636 ATCTTATCAT
* *
126646 GTTGGAACTGCCAAGAATGCTGGAACTGTATTCAAGAATAAGCTTCCTTT-CGGTAGATCGGCTG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTT-CTTTCCGGTAGATCGGCTG
* ** * * * * * * *
126710 ACC-AACACCAGCCCTGGTGCCGGAGGCTGGTTTCTCCCTTCTCTTACTAGGCCGTATTTATTT-
65 GCCGAA-ACCAGCATTGGTGCCGGAGGCCGGCTCCCCCCCTCTCATACTAGGTCGTATTTATTTA
* *
126773 GTGTCTTTATGAA
129 TTATCTTTATGAA
* * * * *
126786 GTTGGACCTGCCGAGAATGCTGAAACTGT-TTCATGAATAAGCTTCATTCCGGTAGATTGGATGG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCCGGTAGATCGGCTGG
* * * * * *
126850 CTGAAACC-GGACTTGGTGTCGGAGGCCGGCTCCCCTCCTCTCATAATAGGTTGTATTTATTTAT
66 CCGAAACCAGCA-TTGGTGCCGGAGGCCGGCTCCCCCCCTCTCATACTAGGTCGTATTTATTTAT
*
126914 GTATCTTTACGAA
130 -TATCTTTATGAA
*
126927 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCCGGTAGATTGGCTGG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCCGGTAGATCGGCTGG
** * * *
126992 CCGAAACTGGCATTGGTGTCGGAGGCCGGCTCCTCCCCCCTCTCGTACTAGGTCGTATTTCTTTA
66 CCGAAACCAGCATTGGTGCCGGAGGCCGGCT-C-CCCCCCTCTCATACTAGGTCGTATTTATTTA
127057 TTATCTTTATGAA
129 TTATCTTTATGAA
* * *
127070 GTTGGACCTGCCAAGAATGCTGGAATTTTATTCATGAATAAGCTT-TGTTTCGGTAGATCGGCTG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCT-TTCCGGTAGATCGGCTG
* * *
127134 GCCGACACCAGCCTTGGTGCCGGAGGCCCGCTCCCCCC
65 GCCGAAACCAGCATTGGTGCCGGAGGCCGGCTCCCCCC
127172 TCCCCCCCCC
Statistics
Matches: 327, Mismatches: 49, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
138 4 0.01
139 68 0.21
140 28 0.09
141 42 0.13
142 60 0.18
143 98 0.30
144 27 0.08
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (141 bp):
GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCCGGTAGATCGGCTGG
CCGAAACCAGCATTGGTGCCGGAGGCCGGCTCCCCCCCTCTCATACTAGGTCGTATTTATTTATT
ATCTTTATGAA
Done.