Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002340.1 Hibiscus syriacus cultivar Beakdansim tig00004777_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: 583550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:447616 original size:23 final size:23
Alignment explanation
Indices: 447572--447616 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
447562 ATTATTATAT
*
447572 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
447595 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
447617 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:448530 original size:22 final size:24
Alignment explanation
Indices: 448502--448559 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
448492 GACATGTGAA
*
448502 ATATGTCCCGAAGGA-C-CTATGC
1 ATATGTCCCGAAGGACCACTATCC
*
448524 ATATGTCTCGAAGGACCACTATCC
1 ATATGTCCCGAAGGACCACTATCC
*
448548 ATATGTTCCGAA
1 ATATGTCCCGAA
448560 TAACATAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.47
23 1 0.03
24 15 0.50
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (24 bp):
ATATGTCCCGAAGGACCACTATCC
Found at i:448581 original size:30 final size:30
Alignment explanation
Indices: 448545--448602 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
448535 AGGACCACTA
*
448545 TCCATATGT-TCCGAATAACATAGGTAACTG
1 TCCATATGTCT-CGAAGAACATAGGTAACTG
*
448575 TCCATATGTCTCGAAGGACATAGGTAAC
1 TCCATATGTCTCGAAGAACATAGGTAAC
448603 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCATATGTCTCGAAGAACATAGGTAACTG
Found at i:456000 original size:23 final size:23
Alignment explanation
Indices: 455957--456002 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
455947 ATGTTCATTT
*
455957 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
455980 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
456002 T
1 T
456003 TATATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:456391 original size:16 final size:16
Alignment explanation
Indices: 456367--456401 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
456357 ATATGAGAAA
456367 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
456383 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
456399 AAA
1 AAA
456402 ATAACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:458431 original size:25 final size:23
Alignment explanation
Indices: 458367--458441 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
458357 TTTTTATTTA
* *
458367 ATTTTTAAAATTTATTTAATCTG
1 ATTTTTAAAATTTATTTAATATT
** * *
458390 A-AATTAAATTTTATTTATTTATT
1 ATTTTTAAAATTTATTTA-ATATT
458413 ATTTTTAAAATTTAGTTTAATATT
1 ATTTTTAAAATTTA-TTTAATATT
458437 ATTTT
1 ATTTT
458442 CATTTATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
22 13 0.33
23 4 0.10
24 18 0.46
25 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (23 bp):
ATTTTTAAAATTTATTTAATATT
Found at i:458637 original size:21 final size:21
Alignment explanation
Indices: 458598--458637 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
458588 TTAATTAATT
*
458598 TAAATTATATTTATATATTCA
1 TAAATTATATTAATATATTCA
458619 TAAATTAATATTAAT-TATT
1 TAAATT-ATATTAATATATT
458638 TTTTCTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATTATATTAATATATTCA
Found at i:468872 original size:59 final size:59
Alignment explanation
Indices: 468799--468913 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 59
468789 GAATTTCAAT
* * *
468799 TTCATCCCTAAACTATGGCTA-TCATTCTATATTAATCCTCAAAC-TTTTGAACATTTTAG
1 TTCATCCCCAAACTAT-GATATTCATTCTAAATTAATCC-CAAACTTTTTGAACATTTTAG
**
468858 TTCATCCCCAAACTATGATATTCATTCTAAATTGGTCCCAAACTTTTTGAACATTT
1 TTCATCCCCAAACTATGATATTCATTCTAAATTAATCCCAAACTTTTTGAACATTT
468914 CAATTTCATC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.16
59 41 0.84
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (59 bp):
TTCATCCCCAAACTATGATATTCATTCTAAATTAATCCCAAACTTTTTGAACATTTTAG
Found at i:476802 original size:27 final size:27
Alignment explanation
Indices: 476772--476823 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
476762 ATTAAAATGC
*
476772 TTTAAGATAAAATGACTATTTAATCTA
1 TTTAAGATAAAATGACCATTTAATCTA
476799 TTTAAGATAAAATGACCATTTAATC
1 TTTAAGATAAAATGACCATTTAATC
476824 ACATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTAAGATAAAATGACCATTTAATCTA
Found at i:481039 original size:3 final size:3
Alignment explanation
Indices: 481028--481064 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
481018 TTTTTTATCG
481028 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
481065 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:481076 original size:13 final size:13
Alignment explanation
Indices: 481029--481072 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
481019 TTTTTATCGT
481029 TATT-TTATTAT-
1 TATTATTATTATG
*
481040 TATTATTATTATT
1 TATTATTATTATG
481053 TATTATTATTATG
1 TATTATTATTATG
481066 T-TTATTA
1 TATTATTA
481073 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:481076 original size:19 final size:19
Alignment explanation
Indices: 481035--481076 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
481025 TCGTTATTTT
*
481035 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
481054 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
481073 ATTA
1 ATTA
481077 CATATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:481178 original size:25 final size:25
Alignment explanation
Indices: 481149--481197 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
481139 CCCAACCCAT
481149 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
481174 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
481198 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:489202 original size:4 final size:4
Alignment explanation
Indices: 489193--489238 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
489183 GATCGAGAAA
*
489193 ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
489238 A
1 A
489239 AAATTTGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:489224 original size:18 final size:17
Alignment explanation
Indices: 489201--489236 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
489191 AAACATACAT
489201 ACATACATACATATATAC
1 ACATACATACATA-ATAC
489219 ACATACATACATAATAC
1 ACATACATACATAATAC
489236 A
1 A
489237 TAAAATTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (17 bp):
ACATACATACATAATAC
Found at i:489708 original size:36 final size:36
Alignment explanation
Indices: 489582--489718 Score: 143
Period size: 36 Copynumber: 3.8 Consensus size: 36
489572 TTTGAGAATT
* *
489582 TTAAAACAAATTTTCGTCTCGTTTGAGACAATTTCT-
1 TTAAAACAAA-TTTCGTCTCGCTTGAGACAAATTCTC
* * * **
489618 TTCAAAGCAAATTTTGTCTCGCTTGAAACAGCTT-TC
1 TT-AAAACAAATTTCGTCTCGCTTGAGACAAATTCTC
* *
489654 TAAAAACAAATTTTGTCTCGCTTGAGACAAATTCTC
1 TTAAAACAAATTTCGTCTCGCTTGAGACAAATTCTC
* *
489690 TTGAAACAAACTTCGTCTCGCTTGAGACA
1 TTAAAACAAATTTCGTCTCGCTTGAGACA
489719 TTTTTCCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
35 28 0.34
36 48 0.58
37 7 0.08
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (36 bp):
TTAAAACAAATTTCGTCTCGCTTGAGACAAATTCTC
Found at i:489958 original size:36 final size:35
Alignment explanation
Indices: 489876--489960 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
489866 ACAAAGTTGA
**
489876 TCTCACTTGAGATCGTTTTCTCAAAAATAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCAAAAATAAACTTTG
** *
489912 TCTTGCTTGAGACAATTTCTCTAAAAATAAATTTTG
1 TCTCACTTGAGACAATTTCTC-AAAAATAAACTTTG
*
489948 TCTCATTTGAGAC
1 TCTCACTTGAGAC
489961 TATATCTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 7 0.17
36 33 0.82
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (35 bp):
TCTCACTTGAGACAATTTCTCAAAAATAAACTTTG
Found at i:490277 original size:28 final size:28
Alignment explanation
Indices: 490245--490400 Score: 210
Period size: 28 Copynumber: 5.6 Consensus size: 28
490235 TTTCTTTTGA
490245 GAAAAAAATCTTTGAGTTTGTTTCTCTT
1 GAAAAAAATCTTTGAGTTTGTTTCTCTT
490273 GAAAAAAATCTTTGAGTTTGTTTCTCTT
1 GAAAAAAATCTTTGAGTTTGTTTCTCTT
490301 GAAAAAAATCTTTGAGTTTG-TTCATCTT
1 GAAAAAAATCTTTGAGTTTGTTTC-TCTT
*** *
490329 G-AAAAAATCTTTGAGTTTGCCCCTTTT
1 GAAAAAAATCTTTGAGTTTGTTTCTCTT
* *
490356 GAATAAAAATCTTTTAG-TTGTTTCTTTT
1 GAA-AAAAATCTTTGAGTTTGTTTCTCTT
*
490384 GAAAAATATCTTTGAGT
1 GAAAAAAATCTTTGAGT
490401 CTACTTATTT
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
27 36 0.32
28 66 0.58
29 12 0.11
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (28 bp):
GAAAAAAATCTTTGAGTTTGTTTCTCTT
Found at i:490336 original size:83 final size:83
Alignment explanation
Indices: 490247--490400 Score: 229
Period size: 83 Copynumber: 1.9 Consensus size: 83
490237 TCTTTTGAGA
***
490247 AAAAAATCTTTGAGTTTGTTTCTCTTGAA-AAAAATCTTTGAGTTTGTTTCTCTTGAAAAAAATC
1 AAAAAATCTTTGAGTTTGCCCCTCTTGAATAAAAATCTTTGAG-TTGTTTCTCTTGAAAAAAATC
490311 TTTGAGTTTGTTCATCTTG
65 TTTGAGTTTGTTCATCTTG
* * * *
490330 AAAAAATCTTTGAGTTTGCCCCTTTTGAATAAAAATCTTTTAGTTGTTTCTTTTGAAAAATATCT
1 AAAAAATCTTTGAGTTTGCCCCTCTTGAATAAAAATCTTTGAGTTGTTTCTCTTGAAAAAAATCT
490395 TTGAGT
66 TTGAGT
490401 CTACTTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 51 0.81
84 12 0.19
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (83 bp):
AAAAAATCTTTGAGTTTGCCCCTCTTGAATAAAAATCTTTGAGTTGTTTCTCTTGAAAAAAATCT
TTGAGTTTGTTCATCTTG
Found at i:490412 original size:56 final size:54
Alignment explanation
Indices: 490236--490425 Score: 204
Period size: 56 Copynumber: 3.4 Consensus size: 54
490226 TAAAGACAAT
*
490236 TTCTTTTGAGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAAATCTTTGAGTTTGT
1 TTCTTTT--GAAAAAAATCTTTGAG-TTGTTTCTCTTG-AAAAAATCTTTGAGTTTGC
*
490294 TTCTCTTGAAAAAAATCTTTGAGTT-TGTTCATCTTGAAAAAATCTTTGAGTTTGC
1 TTCTTTTGAAAAAAATCTTTGAGTTGT-TTC-TCTTGAAAAAATCTTTGAGTTTGC
** * * * *
490349 CCCTTTTGAATAAAAATCTTTTAGTTGTTTCTTTTGAAAAATATCTTTGAGTCTAC
1 TTCTTTTGAA-AAAAATCTTTGAGTTGTTTCTCTTGAAAAA-ATCTTTGAGTTTGC
*
490405 TTATTTTGAAACAAAAT-TTTG
1 TTCTTTTGAAA-AAAATCTTTG
490426 TCTCTTGAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
54 1 0.01
55 43 0.38
56 62 0.55
57 1 0.01
58 6 0.05
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (54 bp):
TTCTTTTGAAAAAAATCTTTGAGTTGTTTCTCTTGAAAAAATCTTTGAGTTTGC
Found at i:491010 original size:15 final size:15
Alignment explanation
Indices: 490987--491030 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
490977 TTTTGAGTCG
*
490987 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
491002 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
491017 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
491031 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:491353 original size:35 final size:36
Alignment explanation
Indices: 491287--491361 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
491277 TATTTCTTTG
* *
491287 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
491323 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
491358 GAAA
1 GAAA
491362 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:491684 original size:28 final size:28
Alignment explanation
Indices: 491634--491687 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
491624 TCAAAATCCA
* *
491634 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
491662 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
491688 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:491850 original size:43 final size:43
Alignment explanation
Indices: 491790--492041 Score: 181
Period size: 43 Copynumber: 5.8 Consensus size: 43
491780 TCATTCCCCG
* *
491790 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
* * * * *
491833 ACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATA
* * * * * **
491879 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
*
491919 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
* * * * *
491962 ACCAG-CCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATA
* * *
492008 GCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
1 ACC-AGACCTCCTCATCACGTAGGAGCCGTGTCA
492042 CCTTTAGACG
Statistics
Matches: 159, Mismatches: 36, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
40 33 0.21
42 2 0.01
43 55 0.35
44 2 0.01
45 6 0.04
46 36 0.23
47 24 0.15
48 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
Found at i:491934 original size:129 final size:129
Alignment explanation
Indices: 491699--492041 Score: 625
Period size: 129 Copynumber: 2.7 Consensus size: 129
491689 ATTATCCTAG
491699 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
491764 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* *
491828 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
491893 TCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
491957 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
*
492022 ATCACGTAGGAGCCGTGTCA
65 ATCACGTATGAGCCGTGTCA
492042 CCTTTAGACG
Statistics
Matches: 206, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
128 5 0.02
129 172 0.83
130 29 0.14
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:491935 original size:40 final size:40
Alignment explanation
Indices: 491751--491951 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 40
491741 CTTTAGATGG
*
491751 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * **
491791 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * * * *
491834 CCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
*
491877 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
* *
491920 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
491952 ACCATAGATA
Statistics
Matches: 127, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
39 2 0.02
40 60 0.47
42 1 0.01
43 31 0.24
44 1 0.01
45 2 0.02
46 29 0.23
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
Found at i:492083 original size:43 final size:44
Alignment explanation
Indices: 491737--492083 Score: 118
Period size: 43 Copynumber: 8.0 Consensus size: 44
491727 AACCGTGTTA
* * * *
491737 TCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
*** * *
491780 TCA---TTCCCCGACC-AGATCTCTTCATCACGTAGGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
* ** * * * *
491820 TCAACC-ATAGATAACC-AG-CCGTCCTCATCACGTAGGAACCATGTTA
1 TC-ACCTTTAGACGACCAAGAAC-TCTTCATCACGTAGG-AGCA-G-TG
* * * *
491866 TCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
** * * *
491909 TCATCC---CCA-GACC-AGATCTCCTCATCACGTAGGAGCCGTG
1 TCA-CCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
* ** * * * * *
491949 TCAACC-ATAGATAACC-AG-CCGTCCTCGTCACGTAGGAACCGTG
1 TC-ACCTTTAGACGACCAAGAAC-TCTTCATCACGTAGGAGCAGTG
* * *
491992 TTATCACCTTTAGATGGCCAAGAACTCTTCATCACGTAGGAGCCGTG
1 ---TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
* * *
492039 TCACCTTTAGACGACCCA-AACTCTTCATCATGTATGAGCAGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
492082 TC
1 TC
492084 GTCCCCAACA
Statistics
Matches: 231, Mismatches: 52, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
40 63 0.27
41 3 0.01
42 3 0.01
43 76 0.33
44 20 0.09
45 9 0.04
46 34 0.15
47 22 0.10
48 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (44 bp):
TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCAGTG
Found at i:492252 original size:3 final size:3
Alignment explanation
Indices: 492241--492277 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
492231 TTTTTTATCG
492241 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
492278 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:492289 original size:13 final size:13
Alignment explanation
Indices: 492242--492285 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
492232 TTTTTATCGT
492242 TATT-TTATTAT-
1 TATTATTATTATG
*
492253 TATTATTATTATT
1 TATTATTATTATG
492266 TATTATTATTATG
1 TATTATTATTATG
492279 T-TTATTA
1 TATTATTA
492286 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:492289 original size:19 final size:19
Alignment explanation
Indices: 492248--492289 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
492238 TCGTTATTTT
*
492248 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
492267 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
492286 ATTA
1 ATTA
492290 CATATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:492391 original size:25 final size:25
Alignment explanation
Indices: 492362--492410 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
492352 CCCAACCCAT
492362 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
492387 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
492411 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:496852 original size:19 final size:17
Alignment explanation
Indices: 496809--496853 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
496799 AGATAAATTG
*
496809 AAAATAAAGAAAATAAA
1 AAAATAAAGAAAACAAA
496826 ATAAATAAGAGATAAACAAA
1 A-AAATAA-AGA-AAACAAA
496846 AAAATAAA
1 AAAATAAA
496854 TAAATACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 9 0.38
20 7 0.29
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (17 bp):
AAAATAAAGAAAACAAA
Found at i:498660 original size:106 final size:106
Alignment explanation
Indices: 498426--498848 Score: 626
Period size: 106 Copynumber: 4.0 Consensus size: 106
498416 TGTATTGTTC
* * * *
498426 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
*
498490 AACCAACCG-----TC-TTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
498526 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
498591 ACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
**
498632 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
498697 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
498738 TAAGTCCAACATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTCGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
498803 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
498844 CGAGT
1 CGAGT
498849 GGCGCGATAT
Statistics
Matches: 293, Mismatches: 23, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
100 67 0.23
101 1 0.00
105 1 0.00
106 224 0.76
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:499558 original size:37 final size:37
Alignment explanation
Indices: 499476--499560 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
499466 GTTTCATGAG
* * * * **
499476 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
499513 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
499549 TAAATTGTCTCA
1 -AAACTGTCTCA
499561 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:501329 original size:21 final size:20
Alignment explanation
Indices: 501305--501370 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 20
501295 TTTTGTCCCT
501305 TTTTCTTTTCCTTTTTGCTTC
1 TTTTCTTTT-CTTTTTGCTTC
* *
501326 TTTTCTTTT-TTGTT-CTTG
1 TTTTCTTTTCTTTTTGCTTC
*
501344 TTTT-TTCT-TTTTTGCTTC
1 TTTTCTTTTCTTTTTGCTTC
501362 TTTTCTTTT
1 TTTTCTTTT
501371 TTGTTCTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.19
18 14 0.38
19 7 0.19
21 9 0.24
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTGCTTC
Found at i:501357 original size:36 final size:36
Alignment explanation
Indices: 501310--501379 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
501300 TCCCTTTTTC
501310 TTTTCCTTTTTGCTTCTTTTCTTTTTTGTTCTTGTT
1 TTTTCCTTTTTGCTTCTTTTCTTTTTTGTTCTTGTT
*
501346 TTTTCTTTTTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTTCCTTTTTGCTTCTTTTCTTTTTTGTTCTTG
501380 ATTAAATCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.76
Consensus pattern (36 bp):
TTTTCCTTTTTGCTTCTTTTCTTTTTTGTTCTTGTT
Found at i:501377 original size:15 final size:16
Alignment explanation
Indices: 501307--501378 Score: 83
Period size: 16 Copynumber: 4.3 Consensus size: 16
501297 TTGTCCCTTT
*
501307 TTCTTTTCCTTTTTGC
1 TTCTTTTCTTTTTTGC
501323 TTCTTTTCTTTTTTGTTC
1 TTCTTTTCTTTTTTG--C
*
501341 TTGTTTTTTCTTTTTTGC
1 -T-TCTTTTCTTTTTTGC
501359 TTCTTTTCTTTTTTG-
1 TTCTTTTCTTTTTTGC
501374 TTCTT
1 TTCTT
501379 GATTAAATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.10
16 27 0.55
17 1 0.02
18 2 0.04
19 1 0.02
20 13 0.27
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (16 bp):
TTCTTTTCTTTTTTGC
Found at i:501378 original size:10 final size:10
Alignment explanation
Indices: 501328--501365 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
501318 TTTGCTTCTT
501328 TTCTTTTTTG
1 TTCTTTTTTG
501338 TTCTTGTTTT-
1 TTCTT-TTTTG
501348 TTCTTTTTTG
1 TTCTTTTTTG
501358 CTTCTTTT
1 -TTCTTTT
501366 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:504267 original size:19 final size:19
Alignment explanation
Indices: 504243--504282 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
504233 TTACCCATCT
504243 TTCGTCAACCCCAACAACC
1 TTCGTCAACCCCAACAACC
*
504262 TTCGTCAACCCCAGCAACC
1 TTCGTCAACCCCAACAACC
504281 TT
1 TT
504283 GGCTAGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.45, G:0.07, T:0.20
Consensus pattern (19 bp):
TTCGTCAACCCCAACAACC
Found at i:504842 original size:10 final size:10
Alignment explanation
Indices: 504823--504874 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
504813 ACATTTAGTA
504823 AAATAAAAAT
1 AAATAAAAAT
*
504833 AAATAGAAATAG
1 AAATA-AAA-AT
504845 AAATAAAAAT
1 AAATAAAAAT
504855 -AATAAATAAT
1 AAATAAA-AAT
504865 AAA-AAAAAT
1 AAATAAAAAT
504874 A
1 A
504875 GATGGCAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 10 0.28
10 12 0.33
11 8 0.22
12 6 0.17
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:504865 original size:22 final size:21
Alignment explanation
Indices: 504821--504872 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
504811 AAACATTTAG
*
504821 TAAAATAAAAATAAATAGAAA
1 TAAAATAAAAATAAATAAAAA
504842 TAGAAATAAAAAT-AATAAATAA
1 TA-AAATAAAAATAAATAAA-AA
504864 TAAAA-AAAA
1 TAAAATAAAA
504873 TAGATGGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
21 10 0.36
22 14 0.50
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAAATAAAAATAAATAAAAA
Found at i:509098 original size:20 final size:19
Alignment explanation
Indices: 509061--509098 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
509051 AACCCAACCC
*
509061 GACCCATTGACTTTGACCT
1 GACCCATTGACGTTGACCT
509080 GACCCATTGACCGTTGACC
1 GACCCATTGA-CGTTGACC
509099 AATCTGACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.26
Consensus pattern (19 bp):
GACCCATTGACGTTGACCT
Found at i:509317 original size:17 final size:18
Alignment explanation
Indices: 509268--509317 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
509258 TTTAGCTTCG
* *
509268 GATTCAATTTGGTTTTTC
1 GATTAAATTTAGTTTTTC
*
509286 GATTAAGTTTAGTTTTT-
1 GATTAAATTTAGTTTTTC
509303 GATGTAAATTT-GTTT
1 GAT-TAAATTTAGTTT
509318 GCTATGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (18 bp):
GATTAAATTTAGTTTTTC
Found at i:521101 original size:209 final size:212
Alignment explanation
Indices: 520723--521141 Score: 691
Period size: 209 Copynumber: 2.0 Consensus size: 212
520713 CTTTAGAGGT
520723 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAGTATATATTATTTTAATCAA
1 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAGTATATATTATTTTAATCAA
* * ***
520788 TACTTTTTTAATTTGAAAATTTAGAATAAAAGGTTGACATTGGTTTCTTACCCACGTCAAAGAGC
66 TACTTTTTTAATTTAAAAATTTAGAATAAAAGGTTGAAATTAACTTCTTACCCACGTCAAAGAGC
* *
520853 ACAAAGCTCAAGAAATAGGTGTGCAAAATTTTTAACTCTTAATATAATATATTAAATATTGATAC
131 ACAAAGCTCAAGAAATAGGTGTGCAAAATTTTAAACTCTTAATAAAATATATTAAATATTGATAC
520918 TTTTT-AAGGAAAATGA
196 TTTTTAAAGGAAAATGA
* * *
520934 GAGAAAGT-AAAAATGTGAGATGAATTGTTGTAAAAGGTAAAATGGTATATATTATTTTAATCAA
1 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAGTATATATTATTTTAATCAA
*
520998 TA-TTTTTTAATTTAAAAATTTAGAATAAAAGGTTGAAATTAACTTCTTACTCACGTCAAAGAGC
66 TACTTTTTTAATTTAAAAATTTAGAATAAAAGGTTGAAATTAACTTCTTACCCACGTCAAAGAGC
* * *
521062 ACAAAGCTCAAGAAATATGTGTGCATAATTTTAAACTCTTAATAAAATATATTAAATGTTGATAC
131 ACAAAGCTCAAGAAATAGGTGTGCAAAATTTTAAACTCTTAATAAAATATATTAAATATTGATAC
521127 TTTTTAAAGGAAAAT
196 TTTTTAAAGGAAAAT
521142 AGGTATGCAT
Statistics
Matches: 193, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
209 121 0.63
210 64 0.33
211 8 0.04
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (212 bp):
GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAGTATATATTATTTTAATCAA
TACTTTTTTAATTTAAAAATTTAGAATAAAAGGTTGAAATTAACTTCTTACCCACGTCAAAGAGC
ACAAAGCTCAAGAAATAGGTGTGCAAAATTTTAAACTCTTAATAAAATATATTAAATATTGATAC
TTTTTAAAGGAAAATGA
Found at i:525475 original size:23 final size:22
Alignment explanation
Indices: 525438--525499 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
525428 CAGCTCCTAT
*
525438 AAATGCACCGGAGTGCAACGTAG
1 AAATGCACCGAAGTGC-ACGTAG
* *
525461 AATTGCACCGAAGTGTCGCGTAG
1 AAATGCACCGAAGTG-CACGTAG
*
525484 AAATGCACCGTAGTGC
1 AAATGCACCGAAGTGC
525500 CATATAAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.18
Consensus pattern (22 bp):
AAATGCACCGAAGTGCACGTAG
Found at i:526301 original size:2 final size:2
Alignment explanation
Indices: 526247--526285 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
526237 ACTTATAAAC
*
526247 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
526286 TATTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:527607 original size:21 final size:21
Alignment explanation
Indices: 527583--527636 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
527573 TTGATGTTTA
527583 AAGCTTATATAAGCTTTCCTT
1 AAGCTTATATAAGCTTTCCTT
527604 AAGCTTATATAAGCTTTCCTT
1 AAGCTTATATAAGCTTTCCTT
527625 AAGCTTATATAA
1 AAGCTTATATAA
527637 TACTCAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
AAGCTTATATAAGCTTTCCTT
Found at i:530400 original size:14 final size:15
Alignment explanation
Indices: 530381--530409 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
530371 TTTTATCTTA
530381 ATATATATA-CACAT
1 ATATATATATCACAT
530395 ATATATATATCACAT
1 ATATATATATCACAT
530410 CACCAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATATATCACAT
Found at i:530592 original size:23 final size:22
Alignment explanation
Indices: 530536--530602 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
530526 CATCATAGCT
* *
530536 CGTATAAATGCACCGGAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
530558 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
530580 GCGTAGAAATGCACCGTAGTGCC
1 -CGTAGAAATGCACCGAAGTGCC
530603 ATAAGATGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:532838 original size:23 final size:23
Alignment explanation
Indices: 532812--532885 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
532802 CACAGCTCAG
532812 ATAATTGCACCGAAGTGCCACAT
1 ATAATTGCACCGAAGTGCCACAT
* *
532835 ATAATTGCACCGAAGTGCCGCGT
1 ATAATTGCACCGAAGTGCCACAT
* * *
532858 AGAA-TGCACCGTAGTGCCATAT
1 ATAATTGCACCGAAGTGCCACAT
532880 AATAAT
1 -ATAAT
532886 GTCCATAAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 14 0.34
23 27 0.66
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (23 bp):
ATAATTGCACCGAAGTGCCACAT
Found at i:533009 original size:18 final size:18
Alignment explanation
Indices: 532986--533021 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
532976 GAATACATAT
532986 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
533004 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
533022 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:533111 original size:121 final size:120
Alignment explanation
Indices: 532883--533124 Score: 430
Period size: 121 Copynumber: 2.0 Consensus size: 120
532873 GCCATATAAT
* * * *
532883 AATGTCCATAAGGACACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 AATGTCCAGAAGGACACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTA
532948 TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
533003 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCAGAAGGA-CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
533068 ATCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
65 ATCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
533124 A
1 A
533125 TAGACCCTCG
Statistics
Matches: 116, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
120 12 0.10
121 104 0.90
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (120 bp):
AATGTCCAGAAGGACACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTA
TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:533986 original size:64 final size:62
Alignment explanation
Indices: 533862--533999 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 62
533852 TTAATGAAGG
** *
533862 TATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGATGCATCGATGCACTACT
1 TATGCATCGATGCACTAATTGCATTCGATGTTT-CTTATTAAAAGATGCATCGATGCACTACC
533925 TATGCATCGATGCAC-AATTGCATTCGATGTATT-TTATTTTAAAAGAGTGCATCGATGCACTAC
1 TATGCATCGATGCACTAATTGCATTCGATGT-TTCTTA--TTAAAAGA-TGCATCGATGCACTAC
533988 C
62 C
*
533989 AATGCATCGAT
1 TATGCATCGAT
534000 ACACCTTCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.04
62 15 0.22
63 23 0.34
64 26 0.39
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (62 bp):
TATGCATCGATGCACTAATTGCATTCGATGTTTCTTATTAAAAGATGCATCGATGCACTACC
Found at i:535871 original size:26 final size:24
Alignment explanation
Indices: 535824--535871 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
535814 CCACGTTTTT
*
535824 ATATTCCTTAAAAAGAGAATAAAA
1 ATATTCCTTAAAAAGACAATAAAA
*
535848 ATATTCTCTTAGAAAAGACCATAA
1 ATATTC-CTTA-AAAAGACAATAA
535872 TACCCTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 4 0.20
26 10 0.50
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (24 bp):
ATATTCCTTAAAAAGACAATAAAA
Found at i:538861 original size:7 final size:7
Alignment explanation
Indices: 538849--538975 Score: 175
Period size: 7 Copynumber: 17.9 Consensus size: 7
538839 GTGGTTATCG
538849 TTCTTCT
1 TTCTTCT
538856 TTCTTCT
1 TTCTTCT
538863 TTCTTCT
1 TTCTTCT
538870 TTCTTCTTT
1 TTCTTC--T
538879 CTTCTTCT
1 -TTCTTCT
*
538887 TTCTCCT
1 TTCTTCT
*
538894 TTCCTCT
1 TTCTTCT
538901 TTCTTCT
1 TTCTTCT
538908 TTCTTCT
1 TTCTTCT
538915 TTCTTCT
1 TTCTTCT
*
538922 TTCTCCT
1 TTCTTCT
538929 TTCTTCT
1 TTCTTCT
538936 TTCTTCT
1 TTCTTCT
538943 TTCTTCT
1 TTCTTCT
538950 TTCTTCT
1 TTCTTCT
*
538957 TTCTAC-
1 TTCTTCT
*
538963 TTCTGCT
1 TTCTTCT
538970 TTCTTC
1 TTCTTC
538976 GATTAGGTTC
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
6 5 0.05
7 94 0.88
8 1 0.01
9 1 0.01
10 6 0.06
ACGTcount: A:0.01, C:0.31, G:0.01, T:0.67
Consensus pattern (7 bp):
TTCTTCT
Found at i:539287 original size:17 final size:18
Alignment explanation
Indices: 539255--539288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
539245 TTTAAATGCT
539255 TTTATTGAATAATTTAAA
1 TTTATTGAATAATTTAAA
*
539273 TTTATTTAA-AATTTAA
1 TTTATTGAATAATTTAA
539289 TTAATTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTATTGAATAATTTAAA
Found at i:539507 original size:19 final size:18
Alignment explanation
Indices: 539478--539514 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
539468 AGGTGAGAAA
539478 ATAATCACCATTAAATTT
1 ATAATCACCATTAAATTT
539496 ATAATGCACCATTAAATTT
1 ATAAT-CACCATTAAATTT
539515 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATCACCATTAAATTT
Found at i:541155 original size:20 final size:23
Alignment explanation
Indices: 541091--541155 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
541081 CATCGATGCA
*
541091 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAATGCATCGATGCAC-TGT
* * *
541115 TAAGGGATGCATCGGTACACTG-
1 TAAGGAATGCATCGATGCACTGT
541137 T-A-GAATGCATCGATGCACT
1 TAAGGAATGCATCGATGCACT
541156 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 1 0.03
23 2 0.06
24 16 0.47
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (23 bp):
TAAGGAATGCATCGATGCACTGT
Found at i:541669 original size:21 final size:22
Alignment explanation
Indices: 541628--541669 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
541618 ATAGGAGAAC
*
541628 AAATATAAGTCATATGATAATG
1 AAATATAAGACATATGATAATG
*
541650 AAATATAAGAC-TATGTTAAT
1 AAATATAAGACATATGATAAT
541670 ACATGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATATAAGACATATGATAATG
Found at i:542689 original size:18 final size:18
Alignment explanation
Indices: 542666--542738 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
542656 GGGGATTATC
*
542666 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
542684 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
542703 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
542722 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
542739 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:542714 original size:38 final size:38
Alignment explanation
Indices: 542663--542739 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
542653 CGAGGGGATT
*
542663 ATCAGTGGTCCTTCGAGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
* *
542701 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
542739 A
1 A
542740 ATATTCAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
Found at i:543930 original size:2 final size:2
Alignment explanation
Indices: 543923--543972 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
543913 CAATAACATG
543923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
543964 TA TA TA TA T
1 TA TA TA TA T
543973 TAGAAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:548806 original size:21 final size:21
Alignment explanation
Indices: 548780--548819 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
548770 CAGAACCCCA
*
548780 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
548801 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
548820 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:548852 original size:18 final size:19
Alignment explanation
Indices: 548824--548860 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
548814 TCCCCTTCAA
*
548824 AGGGGGAATCGGTTCCCTC
1 AGGGGGAATCGATTCCCTC
548843 AGGGGG-ATCGATTCCCTC
1 AGGGGGAATCGATTCCCTC
548861 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.16, C:0.27, G:0.35, T:0.22
Consensus pattern (19 bp):
AGGGGGAATCGATTCCCTC
Found at i:559524 original size:68 final size:68
Alignment explanation
Indices: 559415--559543 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
559405 AGAACAAATT
*
559415 TAAGCATTTCAAGAGAAATATATGCATGATTCTGTTAGCATAACTAGGTGCAATCATATCCATTT
1 TAAGCATTTCAAGAGAAATATATGCATGATTCTGTTAGCATAACTAGGTGAAATCATATCCATTT
559480 CTG
66 CTG
* *
559483 TAAGCATTGT-AAGAGAAATA-A-GCATATGATTCTGTTAGCATAGCTAGTTGAAATCATATCC
1 TAAGCATT-TCAAGAGAAATATATGC--ATGATTCTGTTAGCATAACTAGGTGAAATCATATCC
559544 GTTTAATCTG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
66 2 0.04
67 1 0.02
68 51 0.93
69 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (68 bp):
TAAGCATTTCAAGAGAAATATATGCATGATTCTGTTAGCATAACTAGGTGAAATCATATCCATTT
CTG
Found at i:560158 original size:2 final size:2
Alignment explanation
Indices: 560146--560181 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
560136 ACATTTTCTT
560146 TA TA T- 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
560182 TGAAAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:561296 original size:16 final size:16
Alignment explanation
Indices: 561277--561308 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
561267 TCAACAGCAA
561277 CAAACAGCTAATGATT
1 CAAACAGCTAATGATT
*
561293 CAAATAGCTAATGATT
1 CAAACAGCTAATGATT
561309 ATTTCCGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
CAAACAGCTAATGATT
Found at i:561735 original size:19 final size:19
Alignment explanation
Indices: 561711--561782 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
561701 CATATTCGCA
561711 TTGCGATAGTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
* *
561730 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
561751 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
561772 TTGCGATAGTC
1 TTGCGATAGTC
561783 TAAAATCACA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 19 0.44
21 16 0.37
23 8 0.19
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:562410 original size:21 final size:21
Alignment explanation
Indices: 562384--562424 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
562374 GACTATCGTA
562384 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
562405 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTCCCAAATTCGC
562425 AACGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:562446 original size:20 final size:19
Alignment explanation
Indices: 562421--562507 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 19
562411 TTTTCCTAAT
562421 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGT-AA
* *
562441 TCGCAACGCGAATACATAT
1 TCGCAACGCGAATACGTAA
** *
562460 TCGCATTGCGATTTACGTAA
1 TCGCAACGCGA-ATACGTAA
**
562480 TCGCATTGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GT-AA
562500 TCGCAACG
1 TCGCAACG
562508 AGATTCTGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.02
19 13 0.24
20 40 0.74
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (19 bp):
TCGCAACGCGAATACGTAA
Found at i:563394 original size:24 final size:24
Alignment explanation
Indices: 563367--563420 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
563357 GTATTCGAAA
563367 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
563391 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
563415 TTTGAT
1 TTTGAT
563421 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:563640 original size:14 final size:14
Alignment explanation
Indices: 563611--563647 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
563601 AGAAAAAAAA
563611 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
563626 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
563640 GAAGAAAA
1 GAAGAAAA
563648 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:565998 original size:33 final size:33
Alignment explanation
Indices: 565961--566141 Score: 236
Period size: 33 Copynumber: 5.3 Consensus size: 33
565951 GGAAATTACT
565961 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * * *
565994 ATCGCAACGTGAAAATCGCAACGCGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
*
566028 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
566067 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
566100 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
566133 ATCGCAACG
1 ATCGCAACG
566142 CGAATTTAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
33 83 0.64
34 12 0.09
35 2 0.02
36 4 0.03
37 3 0.02
38 1 0.01
39 12 0.09
40 12 0.09
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:566008 original size:14 final size:14
Alignment explanation
Indices: 565989--566016 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
565979 CAATGCGAAA
565989 TGAAAATCGCAACG
1 TGAAAATCGCAACG
566003 TGAAAATCGCAACG
1 TGAAAATCGCAACG
566017 CGAATATGAA
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:566026 original size:20 final size:19
Alignment explanation
Indices: 565974--566145 Score: 131
Period size: 19 Copynumber: 9.7 Consensus size: 19
565964 GCAACGAGAG
*
565974 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
565993 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
566007 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
566027 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
566047 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
566066 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
566080 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
566099 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
566113 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
566132 AATCGCAACGCGAA
1 AATCGCAACGCGAA
566146 TTTAATTTCG
Statistics
Matches: 124, Mismatches: 12, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
14 31 0.25
15 2 0.02
16 6 0.05
17 6 0.05
18 2 0.02
19 46 0.37
20 28 0.23
21 3 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:566068 original size:73 final size:66
Alignment explanation
Indices: 565941--566141 Score: 240
Period size: 73 Copynumber: 2.9 Consensus size: 66
565931 CTTAATGTCT
* ** * *
565941 ATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGTGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGA
566006 AA
65 AA
* *
566008 ATCGCAACGCGAATATGAATATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCA
1 ATCGCAACGCGAA-ATGAAAATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAAATCGCA
*
566073 ACGAGAGA
59 ACGAGAAA
* *
566081 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
566142 CGAATTTAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
66 30 0.26
67 24 0.21
68 2 0.02
71 2 0.02
72 16 0.14
73 43 0.37
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (66 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAA
A
Found at i:566087 original size:106 final size:106
Alignment explanation
Indices: 565934--566143 Score: 314
Period size: 106 Copynumber: 2.0 Consensus size: 106
565924 CAATTATCTT
* * **
565934 AATGTCTATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
* * *
565999 AACGTGAAAATCGCAACGCGAATATGAATATCGCAACGCGGA
66 AACGAGAAAATCGCAAAGCGAA-ATGAAAATCGCAACGCGGA
*
566041 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
**
566105 AACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCG
66 AACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCG
566144 AATTTAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
105 16 0.17
106 62 0.67
107 15 0.16
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.15
Consensus pattern (106 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCGGA
Found at i:566195 original size:33 final size:33
Alignment explanation
Indices: 566150--566230 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
566140 CGCGAATTTA
* * *
566150 ATTTCGCGTTGCGATTTTGTCGTTACGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTACGATTTTC
*
566183 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTACGATTTTC
566216 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
566231 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTACGATTTTC
Found at i:566229 original size:19 final size:19
Alignment explanation
Indices: 566175--566230 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
566165 TTTGTCGTTA
566175 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
566194 CGA--TTC-TCTCG--TTG
1 CGATTTTCATTTCGCATTG
566208 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
566227 CGAT
1 CGAT
566231 AGTCATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.20
16 7 0.23
17 7 0.23
19 10 0.33
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:566238 original size:19 final size:17
Alignment explanation
Indices: 566180--566230 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
566170 CGTTACGATT
566180 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
566197 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
566211 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
566230 T
1 T
566231 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:567792 original size:42 final size:42
Alignment explanation
Indices: 567746--567825 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
567736 CGATGACAGT
* * *
567746 GGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTTGAGGAATGATAGG
* *
567788 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTTGAGGAATGA
567826 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTTGAGGAATGATAGG
Found at i:568450 original size:94 final size:93
Alignment explanation
Indices: 568289--568495 Score: 360
Period size: 94 Copynumber: 2.2 Consensus size: 93
568279 GAATCGCAAC
*
568289 GCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT
1 GCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT
**
568354 AAAGAATGCACAGTTTAGCAGAATTGGCA
65 AAAGAATAAACAGTTTAGCAGAATTGGCA
568383 GCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT
1 GCAACCGAATAAATTTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTT
*
568448 AAAGAATAAACAGTTTAGCAGTATTGGCA
65 AAAGAATAAACAGTTTAGCAGAATTGGCA
568477 GCAACCGAATAAATTTACT
1 GCAACCGAATAAATTTACT
568496 AAGCAATCTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
93 19 0.18
94 89 0.82
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (93 bp):
GCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTA
AAGAATAAACAGTTTAGCAGAATTGGCA
Found at i:570272 original size:19 final size:19
Alignment explanation
Indices: 570204--570302 Score: 126
Period size: 19 Copynumber: 5.1 Consensus size: 19
570194 TCTTTTGGTT
* *
570204 GAAATGAAAATCGTAACGA
1 GAAATGAAAATCGCAACGC
**
570223 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
570243 GGAAATGAAAATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
570263 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
570282 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
570301 GA
1 GA
570303 TTTTGGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 39 0.57
20 28 0.41
21 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:570357 original size:38 final size:37
Alignment explanation
Indices: 570309--570380 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
570299 GCGATTTTGG
570309 TTTCGCGTTGCGATTTTCATTTCTC-TCGTTGCGATCAT
1 TTTCGCGTTGCGATTTTCATTT-TCAT-GTTGCGATCAT
*
570347 TTTCGTGTTGCGATTTTCATTTTCATGTTGCGAT
1 TTTCGCGTTGCGATTTTCATTTTCATGTTGCGAT
570381 TTTAAGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.31
38 22 0.69
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.50
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTCATTTTCATGTTGCGATCAT
Found at i:570368 original size:20 final size:20
Alignment explanation
Indices: 570309--570383 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
570299 GCGATTTTGG
*
570309 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
570329 TTCTC-TCGTTGCGA---TCAT
1 TT-TCGT-GTTGCGATTTTCAT
570347 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
570367 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
570384 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
17 9 0.19
18 7 0.15
20 22 0.47
21 9 0.19
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:570947 original size:20 final size:20
Alignment explanation
Indices: 570922--571135 Score: 180
Period size: 20 Copynumber: 10.6 Consensus size: 20
570912 CTTTAAAAAT
*
570922 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
570942 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
570962 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
570983 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
571003 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
571023 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * **
571043 CTCGTTGCAATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
571063 CGTGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
571083 TGTTGTTGCGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
571104 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
571125 CTCGTTGCGAT
1 CGCGTTGCGAT
571136 AGTCAGAATC
Statistics
Matches: 150, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
20 100 0.67
21 50 0.33
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:571008 original size:40 final size:41
Alignment explanation
Indices: 570924--571135 Score: 284
Period size: 41 Copynumber: 5.2 Consensus size: 41
570914 TTAAAAATCG
* *
570924 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
570965 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
571005 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* ** * *
571045 CGTTGCAATTTATAGATACGTGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
571086 TGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
571127 CGTTGCGAT
1 CGTTGCGAT
571136 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 74 0.49
41 77 0.51
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:571167 original size:20 final size:20
Alignment explanation
Indices: 571144--571196 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
571134 ATAGTCAGAA
*
571144 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
571164 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
571184 TCACGTTGCGATT
1 TCGCGTTGCGATT
571197 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:571845 original size:21 final size:21
Alignment explanation
Indices: 571818--572081 Score: 233
Period size: 21 Copynumber: 12.7 Consensus size: 21
571808 CGTTGCGATT
*
571818 TTGGACTATTGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
571839 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
571858 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
571881 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
571900 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
571923 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
571944 TTGGTCTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * *
571963 TTGGAATAAATCGTAACACGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
571986 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
572005 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
572026 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
572045 TTGGAATAAATCGCAACACGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
572068 TTAGACTATCGCAA
1 TTGGACTATCGCAA
572082 TGAATTTGGA
Statistics
Matches: 197, Mismatches: 28, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
19 56 0.28
21 104 0.53
23 37 0.19
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:572022 original size:82 final size:82
Alignment explanation
Indices: 571909--572091 Score: 294
Period size: 82 Copynumber: 2.2 Consensus size: 82
571899 CTTGGAATAA
* *
571909 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGTCTATCGCAACGAATTTGGAATAAAT
1 ATCGCAA--CGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAAT
* *
571974 CGTAACACGAACTTCGACT
64 CGCAACACGAACTTAGACT
571993 ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
1 ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
572058 CAACACGAACTTAGACT
66 CAACACGAACTTAGACT
* *
572075 ATCGCAATGAATTTGGA
1 ATCGCAACGAACTTGGA
572092 AAATCGCATT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 86 0.92
84 7 0.08
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (82 bp):
ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
CAACACGAACTTAGACT
Found at i:572087 original size:42 final size:42
Alignment explanation
Indices: 571930--572099 Score: 231
Period size: 42 Copynumber: 4.1 Consensus size: 42
571920 AACTTCGACT
* *
571930 ATCGCAACGCGAACTTGGTCTATCGCAACGAATTTGGAATAA
1 ATCGCAACACGAACTTGGACTATCGCAACGAATTTGGAATAA
* * * *
571972 ATCGTAACACGAACTTCGACTATCGCAACGAACTTGGACT--
1 ATCGCAACACGAACTTGGACTATCGCAACGAATTTGGAATAA
*
572012 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACACGAACTTGGACTATCGCAACGAATTTGGAATAA
* *
572054 ATCGCAACACGAACTTAGACTATCGCAATGAATTTGG-A-AA
1 ATCGCAACACGAACTTGGACTATCGCAACGAATTTGGAATAA
572094 ATCGCA
1 ATCGCA
572100 TTGCGATAGT
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
40 43 0.38
41 1 0.01
42 68 0.61
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACACGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:572124 original size:21 final size:21
Alignment explanation
Indices: 572095--572147 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
572085 ATTTGGAAAA
*
572095 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
572116 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
572137 TCGCGTTGCGA
1 TCGCGTTGCGA
572148 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:575718 original size:15 final size:15
Alignment explanation
Indices: 575698--575759 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 15
575688 GAAAGGGTAG
575698 TATCGATACCATAGT
1 TATCGATACCATAGT
*
575713 TATCGATACCGAAAGGGGT
1 TATCGATACC-ATA---GT
575732 AGTATCGATACCATAGT
1 --TATCGATACCATAGT
575749 TATCGATACCA
1 TATCGATACCA
575760 ACAAGAAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
15 21 0.54
16 2 0.05
17 2 0.05
19 2 0.05
20 2 0.05
21 10 0.26
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (15 bp):
TATCGATACCATAGT
Found at i:575724 original size:35 final size:36
Alignment explanation
Indices: 575678--575758 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
575668 CTTCATGAGG
575678 TATCGATACCGAAA-GGGTAGTATCGATACCATAGT
1 TATCGATACCGAAAGGGGTAGTATCGATACCATAGT
575713 TATCGATACCGAAAGGGGTAGTATCGATACCATAGT
1 TATCGATACCGAAAGGGGTAGTATCGATACCATAGT
575749 TATCGATACC
1 TATCGATACC
575759 AACAAGAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 14 0.31
36 31 0.69
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (36 bp):
TATCGATACCGAAAGGGGTAGTATCGATACCATAGT
Found at i:576826 original size:23 final size:24
Alignment explanation
Indices: 576791--576839 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
576781 CCACTAGGGG
*
576791 CTATGAATTTGTCCCAAATGACCA
1 CTATGAATATGTCCCAAATGACCA
*
576815 CTATGAA-ATGTCCCGAATGACCA
1 CTATGAATATGTCCCAAATGACCA
576838 CT
1 CT
576840 GTATGTCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (24 bp):
CTATGAATATGTCCCAAATGACCA
Found at i:576847 original size:20 final size:20
Alignment explanation
Indices: 576822--576876 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
576812 CCACTATGAA
*
576822 ATGTCCCGAATGACCACTGT
1 ATGTCCCGAAGGACCACTGT
576842 ATGTCCCGAAGGACCACTGT
1 ATGTCCCGAAGGACCACTGT
*
576862 ATGTTCCGAAGGACC
1 ATGTCCCGAAGGACC
576877 TATGAACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (20 bp):
ATGTCCCGAAGGACCACTGT
Found at i:579775 original size:16 final size:17
Alignment explanation
Indices: 579748--579781 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
579738 TTCTTCCTTC
579748 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
579765 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
579781 T
1 T
579782 GACACCTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Done.