Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:3362989 original size:19 final size:19
Alignment explanation
Indices: 3362965--3363073 Score: 157
Period size: 19 Copynumber: 5.7 Consensus size: 19
3362955 AGTCGGGTCG
*
3362965 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
3362984 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
3363003 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
3363022 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
3363041 GATCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
3363061 GGTCAAACCGGTT
1 GGTCAAACCGGTT
3363074 TTCCAGCAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
18 1 0.01
19 67 0.82
20 14 0.17
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:3363056 original size:10 final size:10
Alignment explanation
Indices: 3362967--3363073 Score: 107
Period size: 9 Copynumber: 11.1 Consensus size: 10
3362957 TCGGGTCGGG
*
3362967 TCAACCCGGT
1 TCAAACCGGT
*
3362977 TCAGACCGG-
1 TCAAACCGGT
3362986 TCAAACCGGT
1 TCAAACCGGT
*
3362996 TCAGACCGG-
1 TCAAACCGGT
3363005 TCAAACCGGT
1 TCAAACCGGT
*
3363015 TCAGACCGG-
1 TCAAACCGGT
3363024 TCAAACCGGT
1 TCAAACCGGT
* *
3363034 TCGAACC-GA
1 TCAAACCGGT
3363043 TCAAACCGGT
1 TCAAACCGGT
*
3363053 TCAAAACTGG-
1 TC-AAACCGGT
3363063 TCAAACCGGT
1 TCAAACCGGT
3363073 T
1 T
3363074 TTCCAGCAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
9 37 0.47
10 35 0.45
11 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:3364781 original size:2 final size:2
Alignment explanation
Indices: 3364774--3364810 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3364764 TGATAAATTT
3364774 TA TA TA TA TA 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 TA TA TA TA TA T
3364811 TTATTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3369271 original size:25 final size:24
Alignment explanation
Indices: 3369227--3369273 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3369217 CTATGGTTCC
3369227 ATGGGGATTTGAGAGAGAAAGATT
1 ATGGGGATTTGAGAGAGAAAGATT
* *
3369251 ATGGGGCATTTGGGAGGGAAAGA
1 ATGGGG-ATTTGAGAGAGAAAGA
3369274 CGACAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.34, C:0.02, G:0.43, T:0.21
Consensus pattern (24 bp):
ATGGGGATTTGAGAGAGAAAGATT
Found at i:3370276 original size:18 final size:18
Alignment explanation
Indices: 3370255--3370297 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3370245 CTCATCTCTG
3370255 TCCTCACCAACATCTTCA
1 TCCTCACCAACATCTTCA
** *
3370273 TCCTCGTCATCATCTTCA
1 TCCTCACCAACATCTTCA
*
3370291 TCATCAC
1 TCCTCAC
3370298 TGTCAAAATC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.42, G:0.02, T:0.33
Consensus pattern (18 bp):
TCCTCACCAACATCTTCA
Found at i:3388581 original size:17 final size:17
Alignment explanation
Indices: 3388542--3388582 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3388532 TAAGAACTCA
* *
3388542 AGTCGAGCTCGAGTTTG
1 AGTCGAACTCGAGTTCG
*
3388559 ATTCGAACTCGAGTTCG
1 AGTCGAACTCGAGTTCG
3388576 AGTCGAA
1 AGTCGAA
3388583 TCCATTCGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (17 bp):
AGTCGAACTCGAGTTCG
Found at i:3391642 original size:15 final size:16
Alignment explanation
Indices: 3391622--3391662 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3391612 GTTTATTTCA
*
3391622 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
3391637 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
3391653 GAATGATTCA
1 GAATGATTCA
3391663 GAGGCTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:3395345 original size:2 final size:2
Alignment explanation
Indices: 3395338--3395364 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3395328 ATCGAAACAT
3395338 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
3395365 TGTAGTTAAT
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:3398902 original size:20 final size:20
Alignment explanation
Indices: 3398808--3399176 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3398798 GATTTTCCAT
* ** *
3398808 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3398828 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3398848 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3398868 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3398888 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3398908 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3398928 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3398948 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3398968 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3398988 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3399008 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3399028 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3399048 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3399068 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3399088 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3399108 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3399128 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3399148 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3399168 AATCACAAC
1 AATCGCAAC
3399177 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3399887 original size:24 final size:24
Alignment explanation
Indices: 3399848--3399894 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3399838 AAATTTGGTC
3399848 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3399872 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3399895 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3400087 original size:13 final size:13
Alignment explanation
Indices: 3400069--3400093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3400059 ATATAATCCT
3400069 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
3400082 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3400094 GTCCCCGAAG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:3402420 original size:19 final size:19
Alignment explanation
Indices: 3402398--3402685 Score: 304
Period size: 19 Copynumber: 16.4 Consensus size: 19
3402388 CGGAAAATAC
*
3402398 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3402417 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3402431 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3402451 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3402465 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3402484 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3402498 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3402517 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
* *
3402535 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
3402549 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3402568 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
3402587 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3402606 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3402625 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3402639 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
3402659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3402678 AATCGCAA
1 AATCGCAA
3402686 CGAGATAATC
Statistics
Matches: 229, Mismatches: 13, Indels: 54
0.77 0.04 0.18
Matches are distributed among these distances:
14 45 0.20
15 4 0.02
16 17 0.07
17 15 0.07
18 10 0.04
19 114 0.50
20 24 0.10
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3402470 original size:14 final size:14
Alignment explanation
Indices: 3402451--3402505 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3402441 CGGAAATGAA
3402451 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3402465 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3402484 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3402498 AATCGCAA
1 AATCGCAA
3402506 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3402485 original size:33 final size:33
Alignment explanation
Indices: 3402398--3402666 Score: 260
Period size: 33 Copynumber: 7.8 Consensus size: 33
3402388 CGGAAAATAC
* *
3402398 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
3402431 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
*
3402465 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
3402498 AATCGCAATGCGAAATGAAAATCGCAATGCG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* ** *
3402530 AAT-GAAAT-CGAACCGACATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGA-A-AATCGCAA--CG--A-GAA
*
3402568 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
3402606 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
3402638 GAATCGCAATGCGGAAATGAAAATCGCAA
1 -AATCGCAATGC-GAAATGAAAATCGCAA
3402667 TGCGAAATGA
Statistics
Matches: 205, Mismatches: 17, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
30 6 0.03
31 5 0.02
32 13 0.06
33 72 0.35
34 47 0.23
35 1 0.00
36 2 0.01
38 48 0.23
39 5 0.02
40 6 0.03
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:3402558 original size:32 final size:35
Alignment explanation
Indices: 3402465--3402707 Score: 181
Period size: 33 Copynumber: 6.9 Consensus size: 35
3402455 GCAACGAGAG
* *
3402465 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-
1 AATCGCAATACGAAAT--AAATCGCAATGCGAAATGA
*
3402498 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATACGAAAT--AAATCGCAATGCGAAATGA
* * *
3402535 AATCG-AA-CCGACAT-AATCGCAATGCGAAATTAA
1 AATCGCAATACGAAATAAATCGCAATGCGAAA-TGA
3402568 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATACGAAAT--AAATCGCAATGCGAAATG-A
*
3402606 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G-
1 AATCGCAATACGAAAT--AAATCGCAATGCGAAATGA
*
3402639 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATAC-GAAAT--AAATCGCAATGCGAAATG-A
*
3402678 AATCGC-A-ACGAGAT-AATCGCAATGCGAAAT
1 AATCGCAATACGAAATAAATCGCAATGCGAAAT
3402708 TATAAACGCA
Statistics
Matches: 183, Mismatches: 10, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
32 15 0.08
33 61 0.33
34 18 0.10
35 15 0.08
36 17 0.09
37 8 0.04
38 43 0.23
39 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (35 bp):
AATCGCAATACGAAATAAATCGCAATGCGAAATGA
Found at i:3402559 original size:51 final size:55
Alignment explanation
Indices: 3402392--3402685 Score: 254
Period size: 53 Copynumber: 5.6 Consensus size: 55
3402382 GCAACACGGA
* * *
3402392 AAATACAATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGG
1 AAATA-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAT-CCG
*
3402444 AAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA--CG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATCCG
* *
3402494 AGA-GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCG-AA-CCG
1 AAATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATCCG
* * * *
3402545 ACAT-AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCG
1 AAATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATCCG
*
3402599 AAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGG
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAT-CCG
3402652 AAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAA
3402686 CGAGATAATC
Statistics
Matches: 207, Mismatches: 14, Indels: 41
0.79 0.05 0.16
Matches are distributed among these distances:
47 8 0.04
48 9 0.04
49 3 0.01
50 6 0.03
51 47 0.23
52 38 0.18
53 58 0.28
54 7 0.03
55 5 0.02
57 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (55 bp):
AAATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATCCG
Found at i:3402823 original size:19 final size:19
Alignment explanation
Indices: 3402714--3402815 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3402704 AAATTATAAA
3402714 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3402733 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3402753 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3402769 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3402786 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3402805 CGCATTGCGAT
1 CGCATTGCGAT
3402816 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3402941 original size:14 final size:14
Alignment explanation
Indices: 3402922--3402958 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3402912 CATCAATTAC
3402922 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3402936 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3402950 ACAAATCAA
1 ACAAATCAA
3402959 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3402986 original size:37 final size:37
Alignment explanation
Indices: 3402939--3403009 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
3402929 AACTTTTACA
*
3402939 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
3402976 AATCAACTTTTACAAATCAATTAAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAA
3403010 AACAATCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
Found at i:3403017 original size:37 final size:37
Alignment explanation
Indices: 3402939--3403018 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
3402929 AACTTTTACA
* ***
3402939 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
3402976 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
3403013 AATCAA
1 AATCAA
3403019 TTAAACTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
Found at i:3404899 original size:14 final size:14
Alignment explanation
Indices: 3404880--3404936 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3404870 GCGAAATGAA
*
3404880 AATCGCAACGACAG
1 AATCGCAACGAAAG
3404894 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3404911 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3404927 AATCGCAACG
1 AATCGCAACG
3404937 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3404907 original size:33 final size:33
Alignment explanation
Indices: 3404861--3404953 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3404851 GCGAAACCAA
*
3404861 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3404894 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3404927 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3404954 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3404918 original size:19 final size:19
Alignment explanation
Indices: 3404824--3404958 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3404814 TAGTTTACTT
* *
3404824 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3404844 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3404863 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3404882 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3404896 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3404915 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3404929 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3404948 TCGCAATGCGA
1 TCGCAACGCGA
3404959 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3404976 original size:19 final size:19
Alignment explanation
Indices: 3404954--3405082 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3404944 AAAATCGCAA
3404954 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3404973 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3404987 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3405006 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3405020 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3405039 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3405058 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3405078 TGCGA
1 TGCGA
3405083 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3404996 original size:33 final size:33
Alignment explanation
Indices: 3404954--3405045 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3404944 AAAATCGCAA
3404954 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3404987 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3405020 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3405046 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3405416 original size:92 final size:93
Alignment explanation
Indices: 3405126--3405504 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
3405116 TTGAATGGAT
3405126 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3405191 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3405219 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3405284 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3405312 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3405376 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3405404 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3405468 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3405496 AAATTTACT
1 AAATTTACT
3405505 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 22 0.08
92 131 0.46
93 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3407223 original size:14 final size:14
Alignment explanation
Indices: 3407204--3407293 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3407194 TTGAAATGAA
3407204 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3407218 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3407235 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3407251 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3407270 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3407284 AATCGCAACG
1 AATCGCAACG
3407294 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3407241 original size:33 final size:33
Alignment explanation
Indices: 3407196--3407310 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3407186 TCTTTTGGTT
3407196 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3407229 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3407262 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3407295 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3407311 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3407242 original size:19 final size:18
Alignment explanation
Indices: 3407203--3407315 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
3407193 GTTGAAATGA
3407203 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3407218 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3407235 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3407251 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3407268 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
3407284 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3407301 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3407316 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3407346 original size:14 final size:14
Alignment explanation
Indices: 3407327--3407381 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3407317 TTTGGTTTCG
3407327 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3407341 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
3407360 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3407374 CGTTGCGA
1 CGTTGCGA
3407382 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3407544 original size:33 final size:33
Alignment explanation
Indices: 3407502--3407572 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3407492 AATACTAACT
*
3407502 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3407535 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3407568 TGAAA
1 TGAAA
3407573 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3407805 original size:22 final size:22
Alignment explanation
Indices: 3407753--3407807 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3407743 TGGTTGTGAG
**
3407753 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3407775 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3407797 GGATTTCTTCG
1 GGATTTCTTCG
3407808 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3407976 original size:20 final size:20
Alignment explanation
Indices: 3407951--3408143 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
3407941 CTTTAAATAT
3407951 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3407971 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3407993 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3408012 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3408032 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3408052 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3408072 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3408092 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3408112 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3408132 CGCGTTGCGATT
1 CGCGTTGCGATT
3408144 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3408138 original size:60 final size:60
Alignment explanation
Indices: 3407951--3408143 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3407941 CTTTAAATAT
**
3407951 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3408012 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3408072 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3408132 CGCGTTGCGATT
1 CGCGTTGCGATT
3408144 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3408224 original size:20 final size:20
Alignment explanation
Indices: 3408199--3408250 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3408189 AAGAATCGCG
*
3408199 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3408219 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3408239 TTGCGATTCTGG
1 TTGCGATTCTGG
3408251 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3410541 original size:18 final size:17
Alignment explanation
Indices: 3410520--3410575 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
3410510 TTAAACTCTG
3410520 ATTTCCTTTTTCTCTCTC
1 ATTTCCTTTTTCTCTC-C
3410538 ATTTACTCTCTTTT-TC-CC
1 ATTT-C-CT-TTTTCTCTCC
*
3410556 CTTTCCTTTTTCTCTCC
1 ATTTCCTTTTTCTCTCC
3410573 ATT
1 ATT
3410576 CTCCATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 5 0.16
18 8 0.26
19 2 0.06
20 4 0.13
21 4 0.13
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTCCTTTTTCTCTCC
Found at i:3423962 original size:18 final size:18
Alignment explanation
Indices: 3423901--3423970 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
3423891 TTGTATATTA
*
3423901 AAAAATTAATAAATTAGT
1 AAAAATTAATAAATTAAT
* * * *
3423919 GATAATT-ATTAATCAAT
1 AAAAATTAATAAATTAAT
**
3423936 AATTTATTAATAAATTAAT
1 AA-AAATTAATAAATTAAT
3423955 AAAAATTAATAAATTA
1 AAAAATTAATAAATTA
3423971 GGAAAAATAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
17 8 0.21
18 21 0.54
19 10 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAAATTAATAAATTAAT
Found at i:3423976 original size:18 final size:18
Alignment explanation
Indices: 3423941--3423978 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3423931 TCAATAATTT
*
3423941 ATTAATAAATTAATAAAA
1 ATTAATAAATTAAGAAAA
*
3423959 ATTAATAAATTAGGAAAA
1 ATTAATAAATTAAGAAAA
3423977 AT
1 AT
3423979 AATTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTAATAAATTAAGAAAA
Found at i:3424541 original size:20 final size:20
Alignment explanation
Indices: 3424497--3424590 Score: 93
Period size: 20 Copynumber: 4.6 Consensus size: 20
3424487 ACTTCGACTA
* *
3424497 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
*
3424518 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
3424538 TCGCATTGCGA-TAATCGA-AGT
1 TCGCATTGCGATTTA-C-ATA-T
*
3424559 TCGCTTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
3424579 TCGCATTGCGAT
1 TCGCATTGCGAT
3424591 AGTCGAAGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.03
20 32 0.53
21 24 0.40
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:3424549 original size:41 final size:41
Alignment explanation
Indices: 3424497--3424606 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
3424487 ACTTCGACTA
**
3424497 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
* * *
3424538 TCGCATTGCGATAATCGAAGTTCGCTTTGCGATTTACATAT
1 TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
* * *
3424579 TCGCATTGCGATAGTCGAAGTTCGCGTT
1 TCGCATTGCGATAATCCAAATTCGCGTT
3424607 ACCCAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
Found at i:3425463 original size:21 final size:21
Alignment explanation
Indices: 3425434--3425565 Score: 89
Period size: 21 Copynumber: 6.5 Consensus size: 21
3425424 GCGATTTTGG
*
3425434 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
*
3425455 GCAATGCGAA-TAT-GTA-AATC
1 GCAATGCGAACT-TCG-ACTATC
** *
3425475 GCAACACGAACTTCAAACTATC
1 GCAATGCGAACTTC-GACTATC
* * **
3425497 GCAA--CGAATTTGGAAAATC
1 GCAATGCGAACTTCGACTATC
*
3425516 GCAA--CGAACTCCGACTATC
1 GCAATGCGAACTTCGACTATC
*
3425535 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
3425556 GCAATGCGAA
1 GCAATGCGAA
3425566 TATGTAAATC
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
19 22 0.26
20 20 0.24
21 36 0.42
22 7 0.08
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
GCAATGCGAACTTCGACTATC
Found at i:3425515 original size:41 final size:40
Alignment explanation
Indices: 3425434--3425544 Score: 111
Period size: 41 Copynumber: 2.8 Consensus size: 40
3425424 GCGATTTTGG
* * *
3425434 GCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATC
1 GCAACACGAACTTCAACTATCGCAA-GCGAATATGAAAATC
*
3425475 GCAACACGAACTTCAAACTATCGCAA-CGAATTTGGAAAATC
1 GCAACACGAACTTC-AACTATCGCAAGCGAATAT-GAAAATC
* *
3425516 GC-A-ACGAACTCCGACTATCGCAATGCGAA
1 GCAACACGAACTTCAACTATCGCAA-GCGAA
3425545 CTTGGACTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
38 10 0.17
39 8 0.13
40 11 0.18
41 21 0.35
42 10 0.17
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (40 bp):
GCAACACGAACTTCAACTATCGCAAGCGAATATGAAAATC
Found at i:3425518 original size:19 final size:19
Alignment explanation
Indices: 3425494--3425599 Score: 70
Period size: 19 Copynumber: 5.4 Consensus size: 19
3425484 ACTTCAAACT
3425494 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* ** **
3425513 ATCGCAACGAACTCCGACT
1 ATCGCAACGAATTTGGAAA
* **
3425532 ATCGCAATGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
* *
3425553 ATCGCAATGCGAATAT-GTAA
1 ATCGCAA--CGAATTTGGAAA
3425573 ATCGCAACAGAATTTGGAAA
1 ATCGCAAC-GAATTTGGAAA
3425593 ATCGCAA
1 ATCGCAA
3425600 TGCGATAGTC
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
18 1 0.01
19 26 0.38
20 18 0.26
21 24 0.35
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:3425557 original size:40 final size:38
Alignment explanation
Indices: 3425440--3425559 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 38
3425430 TTGGGCAACG
* *
3425440 CGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAACA
1 CGAACTCCGACTATCGCAATGCGAAT-TGGAAATCGC-A-A
**
3425481 CGAACTTCAAACTATCGCAA--CGAATTTGGAAAATCGCAA
1 CGAAC-TCCGACTATCGCAATGCGAA-TTGG-AAATCGCAA
*
3425520 CGAACTCCGACTATCGCAATGCGAACTTGGACTATCGCAA
1 CGAACTCCGACTATCGCAATGCGAA-TTGGA-AATCGCAA
3425560 TGCGAATATG
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
38 12 0.18
39 7 0.11
40 22 0.34
41 13 0.20
42 11 0.17
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (38 bp):
CGAACTCCGACTATCGCAATGCGAATTGGAAATCGCAA
Found at i:3425655 original size:21 final size:21
Alignment explanation
Indices: 3425600--3425646 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3425590 AAAATCGCAA
*
3425600 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAATTCGCGT
3425621 TGCGATAGTCGAAATTCGCGT
1 TGCGATAGTCGAAATTCGCGT
3425642 TGCGA
1 TGCGA
3425647 ATCTAGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAATTCGCGT
Done.