Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009017.1 Hibiscus syriacus cultivar Beakdansim tig00112407_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: 1192163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:508264 original size:23 final size:22
Alignment explanation
Indices: 508238--508282 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
508228 TTCTATAAAA
508238 ATAA-TTAAAATAAATTAGGATAT
1 ATAATTTAAAA-AAA-TAGGATAT
*
508261 ATAATTTATAAAAATAGGATAT
1 ATAATTTAAAAAAATAGGATAT
508283 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAATTTAAAAAAATAGGATAT
Found at i:508571 original size:11 final size:11
Alignment explanation
Indices: 508564--508626 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
508554 GACTAATATA
508564 AAAATAATAAT
1 AAAATAATAAT
508575 AAAATAATAATT
1 AAAATAATAA-T
**
508587 AAAGCAATAATT
1 AAAATAATAA-T
*
508599 AAAGT-AT-A-
1 AAAATAATAAT
*
508607 AAAGTAATAAT
1 AAAATAATAAT
508618 AAAATAATA
1 AAAATAATA
508627 TTGCAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 5 0.11
9 2 0.05
10 2 0.05
11 20 0.45
12 15 0.34
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:509968 original size:3 final size:3
Alignment explanation
Indices: 509960--510020 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
509950 TATTTATTTA
* * **
509960 AAT AAT AAT AAT AAT ATAT AAT ATAT AAT GAT AAT GAT AAT TTT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
510007 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
510021 AATGAAATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:510444 original size:46 final size:45
Alignment explanation
Indices: 510192--510630 Score: 574
Period size: 45 Copynumber: 9.6 Consensus size: 45
510182 CGAAGGCTTT
* * *
510192 AACATCTTGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG---TTTTGAA
* * * * ** *
510240 AACATCCTGCATTGTAGGTCTTATGGATGACCCAAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
* * * * * ** *
510285 AACATCCTGTATTGTAGGTCTTATGGATGACCCAAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
* * *
510330 AACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
* *
510375 AA-ATCATGCACTGAAGGGATTACAAATGACCCGAAGGTTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAA
* *
510420 AACATCATGCAGTGAAGGGCTTACAGATGACCCAAAGGTTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAA
* *
510466 AACATCATGCACTGAAAGGCTTACAGATGGCCCGAAGGTTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAA
510512 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
510557 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
510602 AACATCATGCACTGAAGGGCTTACAGATG
1 AACATCATGCACTGAAGGGCTTACAGATG
510631 TGGGAAATAG
Statistics
Matches: 361, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
44 31 0.09
45 180 0.50
46 117 0.32
48 33 0.09
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
Found at i:511344 original size:22 final size:22
Alignment explanation
Indices: 511283--511344 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
511273 GAAATCCAAT
*
511283 AAATCT-T-ATCTTTGAAAAGA
1 AAATCTATCATCTTTGAAGAGA
*
511303 AAATCTATCATCTTTAAAGAGA
1 AAATCTATCATCTTTGAAGAGA
511325 AAATCTATCATCTTTGAAGA
1 AAATCTATCATCTTTGAAGA
511345 ATGTAGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 30 0.81
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATCTATCATCTTTGAAGAGA
Found at i:511801 original size:54 final size:54
Alignment explanation
Indices: 511712--511863 Score: 191
Period size: 54 Copynumber: 2.8 Consensus size: 54
511702 ATAATCACTG
* * * *
511712 GTTCGTAAAACATGTGATAATACATTCACCCTTTCTCGTGGTTTCT-GCACAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCATTTCTCGTGGTTTCTGGC-CAGAT
* *
511766 GTTCGTAAAACATTTGATAACACATTCATCATTTCTTGTGGCTTCTGGCCAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCATTTCTCGTGGTTTCTGGCCAGAT
* * *
511820 GTTCGTAAAGCATTTGACAACACATTTATCATTT-TCTGTGGTTT
1 GTTCGTAAAACATTTGATAACACATTCATCATTTCTC-GTGGTTT
511864 TTACATAGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 82 0.96
55 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGATAACACATTCATCATTTCTCGTGGTTTCTGGCCAGAT
Found at i:515977 original size:11 final size:9
Alignment explanation
Indices: 515949--515989 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
515939 CTTGGTTCAA
515949 TTTTTT-CT
1 TTTTTTCCT
515957 TTTTTTCCT
1 TTTTTTCCT
*
515966 TTTTTTCCC
1 TTTTTTCCT
*
515975 CTTTTTCCT
1 TTTTTTCCT
515984 TTTTTT
1 TTTTTT
515990 ATTTAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:518056 original size:19 final size:19
Alignment explanation
Indices: 518032--518070 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
518022 CGGGTAAGGA
518032 GGCAACAAAGGCTTAGCCT
1 GGCAACAAAGGCTTAGCCT
518051 GGCAACAAAGGCTTAGCCT
1 GGCAACAAAGGCTTAGCCT
518070 G
1 G
518071 ACATGGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.28, T:0.15
Consensus pattern (19 bp):
GGCAACAAAGGCTTAGCCT
Found at i:518797 original size:20 final size:21
Alignment explanation
Indices: 518758--518800 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
518748 TGCAAAATAT
*
518758 AAATACAAACGTAAAAATGAA
1 AAATACAAACATAAAAATGAA
*
518779 AAATACAAA-ATACAAATGAA
1 AAATACAAACATAAAAATGAA
518799 AA
1 AA
518801 TGTAAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (21 bp):
AAATACAAACATAAAAATGAA
Found at i:518800 original size:27 final size:27
Alignment explanation
Indices: 518737--518800 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
518727 GTAAATATGT
* *
518737 AAATGCAAAAATGCAAAATATAAATAC
1 AAATGCAAAAATGAAAAATAAAAATAC
* *
518764 AAACGTAAAAATGAAAAATACAAAATAC
1 AAATGCAAAAATGAAAAATA-AAAATAC
518792 AAATG-AAAA
1 AAATGCAAAA
518801 TGTAAATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.67, C:0.09, G:0.08, T:0.16
Consensus pattern (27 bp):
AAATGCAAAAATGAAAAATAAAAATAC
Found at i:519055 original size:43 final size:43
Alignment explanation
Indices: 518975--519060 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
518965 TTGTGCATCA
* *
518975 AACAAAACTTTACATATAGGGGACAACTTTCAGTCCTATCTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * *
519018 AACAAAACTTTACATATAGGGTATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
519061 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:520467 original size:22 final size:24
Alignment explanation
Indices: 520440--520483 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
520430 TTAATTCTTG
520440 AAAATA-AA-ATAAAAATATTAAT
1 AAAATAGAATATAAAAATATTAAT
520462 AAAATAGAATATAAAAATATTA
1 AAAATAGAATATAAAAATATTA
520484 TGAAAACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATAGAATATAAAAATATTAAT
Found at i:520489 original size:24 final size:23
Alignment explanation
Indices: 520438--520489 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
520428 ATTTAATTCT
520438 TGAAAATAAAATAAAAATATTAA
1 TGAAAATAAAATAAAAATATTAA
520461 T-AAAATAGAATATAAAAATATT-A
1 TGAAAATA-AA-ATAAAAATATTAA
520484 TGAAAA
1 TGAAAA
520490 CCATAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.23
23 5 0.19
24 15 0.58
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (23 bp):
TGAAAATAAAATAAAAATATTAA
Found at i:521495 original size:11 final size:11
Alignment explanation
Indices: 521479--521541 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
521469 GACTAAGATG
521479 AAAATAATAAT
1 AAAATAATAAT
521490 AAAATAATAATT
1 AAAATAATAA-T
**
521502 AAAGCAATAATT
1 AAAATAATAA-T
521514 AAAAT-AT-A-
1 AAAATAATAAT
*
521522 AAAGTAATAAT
1 AAAATAATAAT
521533 AAAATAATA
1 AAAATAATA
521542 TTGCAAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 20 0.48
12 14 0.33
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:521565 original size:16 final size:16
Alignment explanation
Indices: 521507--521568 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
521497 TAATTAAAGC
521507 AATAATTAAAAT--AT
1 AATAATTAAAATAAAT
*
521521 AA-AAGTAATAATAAAAT
1 AATAATTAA-AAT-AAAT
*
521538 AAT-ATTGCAAATAAAT
1 AATAATT-AAAATAAAT
521554 AATAATTAAAATAAA
1 AATAATTAAAATAAA
521569 AGAAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
16 14 0.38
17 12 0.32
18 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAATTAAAATAAAT
Found at i:522890 original size:3 final size:3
Alignment explanation
Indices: 522882--522922 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
522872 TATTTATTTA
* **
522882 AAT AAT AAT AAT AAT GAT AAT TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
522923 AATTAGATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:527355 original size:24 final size:24
Alignment explanation
Indices: 527310--527357 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
527300 ATTTGTCAAA
527310 TCAACATCACAAATGAGAAAAACT
1 TCAACATCACAAATGAGAAAAACT
* *
527334 TCAACATAGACAACTGAGAAAAAC
1 TCAACAT-CACAAATGAGAAAAAC
527358 CTCATAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (24 bp):
TCAACATCACAAATGAGAAAAACT
Found at i:529648 original size:42 final size:42
Alignment explanation
Indices: 529590--529682 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
529580 TCACGTTATG
* *
529590 AAAAA-ATGCTTAAATGTCATGTGAAATGTAAATATGAAAAT
1 AAAAAGATGCTTAAATGTCATGTGAAATGCAAAGATGAAAAT
*
529631 AAAAAGATGCTTAAATGTCATGTGAAATGCATAGATGAAAAT
1 AAAAAGATGCTTAAATGTCATGTGAAATGCAAAGATGAAAAT
*
529673 ACAAAGATGC
1 AAAAAGATGC
529683 AAATGCAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 5 0.11
42 42 0.89
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (42 bp):
AAAAAGATGCTTAAATGTCATGTGAAATGCAAAGATGAAAAT
Found at i:529696 original size:14 final size:14
Alignment explanation
Indices: 529655--529697 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
529645 ATGTCATGTG
* *
529655 AAATGCATAGATGA
1 AAATGCAAAGATGC
*
529669 AAATACAAAGATGC
1 AAATGCAAAGATGC
*
529683 AAATGCAAATATGC
1 AAATGCAAAGATGC
529697 A
1 A
529698 GATAAAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (14 bp):
AAATGCAAAGATGC
Found at i:530172 original size:11 final size:11
Alignment explanation
Indices: 530156--530180 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
530146 TTCAAATAAG
530156 AAAGAATACCA
1 AAAGAATACCA
530167 AAAGAATACCA
1 AAAGAATACCA
530178 AAA
1 AAA
530181 AAATGACCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAATACCA
Found at i:532331 original size:21 final size:21
Alignment explanation
Indices: 532307--532346 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
532297 TTCACTTTAG
* *
532307 TTTATTTTTTGCTATATAATT
1 TTTATGTTTTACTATATAATT
*
532328 TTTATGTTTTACTGTATAA
1 TTTATGTTTTACTATATAA
532347 AAATAATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTATGTTTTACTATATAATT
Found at i:533936 original size:21 final size:21
Alignment explanation
Indices: 533903--533954 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
533893 CAAAGAGAAG
*
533903 GATCGATCATGTTTCACGAGA
1 GATCGATCCTGTTTCACGAGA
* *
533924 GATTGATCCTGTTTCACGGGA
1 GATCGATCCTGTTTCACGAGA
533945 GATCGATCCT
1 GATCGATCCT
533955 TTATAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
GATCGATCCTGTTTCACGAGA
Found at i:541262 original size:20 final size:20
Alignment explanation
Indices: 541239--541285 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
541229 TCTAAACACG
541239 CCAATCACTTCTTTAAGACA
1 CCAATCACTTCTTTAAGACA
* *
541259 CCAACCACTTCTTTAAGGCA
1 CCAATCACTTCTTTAAGACA
541279 CCAATCA
1 CCAATCA
541286 ATATTTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (20 bp):
CCAATCACTTCTTTAAGACA
Found at i:550783 original size:20 final size:21
Alignment explanation
Indices: 550735--550791 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
550725 GATCCCTTAG
* *
550735 CAAAAGGATCAACCCCATTGA
1 CAAAATGATCAATCCCATTGA
*
550756 CCAAATGATCAATCCCATTGA
1 CAAAATGATCAATCCCATTGA
*
550777 -AAAATGATCGATCCC
1 CAAAATGATCAATCCC
550792 TTAGATTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.19
Consensus pattern (21 bp):
CAAAATGATCAATCCCATTGA
Found at i:550861 original size:21 final size:20
Alignment explanation
Indices: 550814--550885 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
550804 AGGTTTGGGT
*
550814 TCGATCCCTTCA-CAAAAGGA
1 TCGATCCC-TCAGCAAAAGAA
** *
550834 TAAATCCCTCAAGGAAAAGAA
1 TCGATCCCTC-AGCAAAAGAA
*
550855 TCGATCCCCTCAGCAAAAGGA
1 TCGAT-CCCTCAGCAAAAGAA
*
550876 TCGAACCCTC
1 TCGATCCCTC
550886 GATGAAAATG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 21 0.52
22 5 0.12
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGATCCCTCAGCAAAAGAA
Found at i:552909 original size:25 final size:24
Alignment explanation
Indices: 552875--552927 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
552865 TATGGTGACA
552875 AATTTTGTAACTATAAGTGTTAACT
1 AATTTTGTAACTATAAGTGTTAA-T
*
552900 AATTTTGTAACTATAATTGTTAAT
1 AATTTTGTAACTATAAGTGTTAAT
552924 AATT
1 AATT
552928 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
AATTTTGTAACTATAAGTGTTAAT
Found at i:556931 original size:32 final size:32
Alignment explanation
Indices: 556895--556959 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
556885 ATTGTTTCAG
556895 ATGATACCCTATATCGGTATTTGTAACCTGCA
1 ATGATACCCTATATCGGTATTTGTAACCTGCA
*
556927 ATGATACCCTATATCGGTATTTGTGACCTGCA
1 ATGATACCCTATATCGGTATTTGTAACCTGCA
556959 A
1 A
556960 GAAAGATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (32 bp):
ATGATACCCTATATCGGTATTTGTAACCTGCA
Found at i:557141 original size:22 final size:22
Alignment explanation
Indices: 557115--557171 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
557105 ATAATCAATT
557115 ATAACAAATTTATTTAGTCACA-
1 ATAACAAATTTATTTAGTCA-AG
* *
557137 ATAACATATTAAATTTAGTCAAG
1 ATAACAAATT-TATTTAGTCAAG
557160 ATAA-AAATTTAT
1 ATAACAAATTTAT
557172 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 13 0.45
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAG
Found at i:557320 original size:33 final size:33
Alignment explanation
Indices: 557236--557320 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 33
557226 ATTTAATCAA
* * * *
557236 AATAACAATTTATAATAAATATTAATTTCTCAT
1 AATAACAAATTATAACAAATATAAATTTCTCAC
* * * *
557269 TATAAAAAATTGTGACAAATAATAAATTT-TCAC
1 AATAACAAATTATAACAAAT-ATAAATTTCTCAC
557302 AATAACAAATTATAACAAA
1 AATAACAAATTATAACAAA
557321 ATTATTTAGT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.34
Consensus pattern (33 bp):
AATAACAAATTATAACAAATATAAATTTCTCAC
Found at i:557361 original size:31 final size:32
Alignment explanation
Indices: 557298--557361 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
557288 TAATAAATTT
* *
557298 TCACAATAACAAATTATAACAAAATTATTTAG
1 TCACAATAAAAAATTATAACAAAAATATTTAG
*
557330 TCACAGTAAAAAATTATAA-AAAAATATTTAG
1 TCACAATAAAAAATTATAACAAAAATATTTAG
557361 T
1 T
557362 GACGAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (32 bp):
TCACAATAAAAAATTATAACAAAAATATTTAG
Found at i:557468 original size:21 final size:19
Alignment explanation
Indices: 557442--557484 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
557432 TTAATGTTAT
*
557442 AATTTAACTTATCTGTGATGA
1 AATTT-ACTT-TCTGTGATAA
*
557463 AATTTACTTTTTGTGATAA
1 AATTTACTTTCTGTGATAA
557482 AAT
1 AAT
557485 AATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTTACTTTCTGTGATAA
Found at i:559448 original size:21 final size:21
Alignment explanation
Indices: 559424--559464 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
559414 TTTTCCAAAA
559424 AAAAAAGGATCAATCCCTTTG
1 AAAAAAGGATCAATCCCTTTG
* * *
559445 AAAAATGTATCGATCCCTTT
1 AAAAAAGGATCAATCCCTTT
559465 TTATGATAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAAGGATCAATCCCTTTG
Found at i:561178 original size:20 final size:19
Alignment explanation
Indices: 561153--561206 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
561143 CATACACATG
561153 AAGTTTTGAAACTTTGATGA
1 AAGTTTTGAAACTTTG-TGA
**
561173 AAGTTTCAAAACTATTGTGA
1 AAGTTTTGAAACT-TTGTGA
*
561193 AAATTTTGAAACTT
1 AAGTTTTGAAACTT
561207 CTAAACACGG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.04
20 24 0.86
21 3 0.11
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (19 bp):
AAGTTTTGAAACTTTGTGA
Found at i:565018 original size:65 final size:65
Alignment explanation
Indices: 564944--565108 Score: 206
Period size: 65 Copynumber: 2.6 Consensus size: 65
564934 ACCTAATTTA
* * * *
564944 ATTG-AACATCGAATGCATTATGTGTACCGATGCACATACCATGCATCGATGCACTCCAGGTTGT
1 ATTGAAACATCGAATGCATTATGTGTACCGATGCACAGACCATACATCGATGCACTCCAGGCTCT
* * * * *
565008 ATTGAAACATCGGATGCATTTTATGTACCGATGCATAGACCATACATCGATGCACTCCTGGCTCT
1 ATTGAAACATCGAATGCATTATGTGTACCGATGCACAGACCATACATCGATGCACTCCAGGCTCT
* * * *
565073 TTTGAAACATCGAATGTAATAAGTGTACCGATGCAC
1 ATTGAAACATCGAATGCATTATGTGTACCGATGCAC
565109 CCCAAGGGTA
Statistics
Matches: 83, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
64 4 0.05
65 79 0.95
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (65 bp):
ATTGAAACATCGAATGCATTATGTGTACCGATGCACAGACCATACATCGATGCACTCCAGGCTCT
Found at i:570994 original size:20 final size:20
Alignment explanation
Indices: 570943--570994 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
570933 TTGAATGTGC
*
570943 ATCGATACACTATGCAGTGT
1 ATCGATACACTCTGCAGTGT
570963 ATCGATACACTCTGCAGTGT
1 ATCGATACACTCTGCAGTGT
570983 ATCGATACACTC
1 ATCGATACACTC
570995 GTCGGGTTTT
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:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCGATACACTCTGCAGTGT
Found at i:571436 original size:18 final size:20
Alignment explanation
Indices: 571393--571436 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
571383 AGATTTTTTT
571393 TTGTTTTAATTGAATTGATG
1 TTGTTTTAATTGAATTGATG
*
571413 TT-TTTT-ATTTAATT-ATG
1 TTGTTTTAATTGAATTGATG
571430 TTGTTTT
1 TTGTTTT
571437 TCATAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 4 0.18
20 2 0.09
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (20 bp):
TTGTTTTAATTGAATTGATG
Found at i:573283 original size:15 final size:16
Alignment explanation
Indices: 573255--573287 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
573245 GGGGGAGTAA
573255 TTTTCAAAATTGATTT
1 TTTTCAAAATTGATTT
*
573271 TTTTTAAAA-TGATTT
1 TTTTCAAAATTGATTT
573286 TT
1 TT
573288 CATAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTCAAAATTGATTT
Found at i:573708 original size:65 final size:64
Alignment explanation
Indices: 573635--573756 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 64
573625 ACCTAATTTA
* *
573635 ATTGAACATCGAATCCATTATGTGTACCGATGCACATACCATACATCGATGCACTCCAGGTTTT
1 ATTGAACATCGAATCCATTATATGTACCGATGCACAGACCATACATCGATGCACTCCAGGTTTT
* *
573699 ATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACCATACATCGATGCACTCC
1 ATTG-AACATCGAATCCATTATATGTACCGATGCACAGACCATACATCGATGCACTCC
573757 TCGCTCTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
64 4 0.08
65 49 0.92
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
ATTGAACATCGAATCCATTATATGTACCGATGCACAGACCATACATCGATGCACTCCAGGTTTT
Found at i:573769 original size:65 final size:65
Alignment explanation
Indices: 573635--573796 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
573625 ACCTAATTTA
* * * * * *
573635 ATTG-AACATCGAATCCATTATGTGTACCGATGCACATACCATACATCGATGCACTCCAGGTTTT
1 ATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACCATACATCGATGCACTCCAGCTCTT
*
573699 ATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACCATACATCGATGCACTCCTCGCTCT
1 ATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACCATACATCGATGCACTCC-AGCTCT
573764 T
65 T
* * *
573765 -TTGAAACATCAAATGTA-ATTAGTGTACCGATG
1 ATTGAAACATCGAATGCATTTTA-TGTACCGATG
573797 TACCCCAAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 7 0.08
65 74 0.87
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (65 bp):
ATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACCATACATCGATGCACTCCAGCTCTT
Found at i:575695 original size:26 final size:28
Alignment explanation
Indices: 575666--575717 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
575656 AGGATACTAA
575666 TTTGAAAA-AAA-ATGATATCAATTTAT
1 TTTGAAAACAAATATGATATCAATTTAT
575692 TTTGAAAACAAATATGATATCAATTT
1 TTTGAAAACAAATATGATATCAATTT
575718 TTGGTATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 8 0.33
27 3 0.12
28 13 0.54
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (28 bp):
TTTGAAAACAAATATGATATCAATTTAT
Found at i:576575 original size:20 final size:18
Alignment explanation
Indices: 576539--576586 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
576529 TCAAAATCAT
**
576539 TTTTCAAAATTTCTTTTGG
1 TTTTCAAAATTAATTTT-G
576558 TTTTCAAAATCTAATTTTG
1 TTTTCAAAAT-TAATTTTG
*
576577 CTTTCAAAAT
1 TTTTCAAAAT
576587 AAAATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTTCAAAATTAATTTTG
Found at i:578105 original size:20 final size:20
Alignment explanation
Indices: 578056--578105 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
578046 ATAGTATTTT
578056 CATATTTTAAAAGCTTTAAA
1 CATATTTTAAAAGCTTTAAA
*
578076 CACATTTTAAACA-CTTTAAA
1 CATATTTTAAA-AGCTTTAAA
*
578096 CATATCTTAA
1 CATATTTTAA
578106 TTAACTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (20 bp):
CATATTTTAAAAGCTTTAAA
Found at i:578731 original size:22 final size:22
Alignment explanation
Indices: 578687--578732 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
578677 ATTTAAATAA
* *
578687 TTTGGAATTATTAATTTCTATT
1 TTTGGAATTAATAATTTCGATT
578709 TTTGGAAATTAATAATTT-GATT
1 TTTGG-AATTAATAATTTCGATT
578731 TT
1 TT
578733 ACTAGGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTGGAATTAATAATTTCGATT
Found at i:580681 original size:20 final size:20
Alignment explanation
Indices: 580656--580707 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
580646 GTTGCCTGGC
* *
580656 ATCGATACCCTTACCATGGT
1 ATCGATACCCATACAATGGT
580676 ATCGATACTACCATACAATGGT
1 ATCGATAC--CCATACAATGGT
*
580698 ACCGATACCC
1 ATCGATACCC
580708 CTTTTTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (20 bp):
ATCGATACCCATACAATGGT
Found at i:585332 original size:46 final size:46
Alignment explanation
Indices: 585235--585325 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
585225 CATTAAATTT
* ** *
585235 CATTTTATTTATGGCATCCTTTCATGCCTTAATGTTTTCTTTCATA
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATA
585281 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCAT
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCAT
585326 GAATTTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (46 bp):
CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATA
Found at i:585431 original size:79 final size:78
Alignment explanation
Indices: 585290--585735 Score: 633
Period size: 79 Copynumber: 5.6 Consensus size: 78
585280 ACATTTTATT
* * * * * * *
585290 TATGGCATCATTTCATGCC-TTAATGCATCCTTTCATGAATTTTTCTTTTATGCCAATAATGCAC
1 TATGGCATCCTTTCATGCCAATAATGCA-CC-AT-ATGCATTATTCTTTTATGTCGATAATGCAC
*
585354 CCATATGCTTTTCAGC
63 CCATATGCATTTCAGC
*
585370 TATGGCATCCTTTCATGCCCATAATGCACCAATATGCATTATTCTTTTATGTCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACC-ATATGCATTATTCTTTTATGTCGATAATGCACCC
*
585435 ATATGCATTTCAAC
65 ATATGCATTTCAGC
* *
585449 TATGGCATCCTTTCATACCAATAATGCACCCATATGCATTATTCTTTTATGTAGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCA-CCATATGCATTATTCTTTTATGTCGATAATGCACCC
585514 ATATGCATTTCAGC
65 ATATGCATTTCAGC
585528 TATGGCATCCTTTCATGCCAATAATGCACTCATATGCATTATTCTTTTATGTCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCAC-CATATGCATTATTCTTTTATGTCGATAATGCACCC
*
585593 ATATGCATTTCAGT
65 ATATGCATTTCAGC
* * * *
585607 TATGGCATCCTTTTATGCCAATAATGTACCCATATGCATTATTCTTTTATATTGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCA-CCATATGCATTATTCTTTTATGTCGATAATGCACCC
585672 ATATGCATTTCAGC
65 ATATGCATTTCAGC
* * *
585686 TATGGCATCCTTTCATGCCAATATTGCTCTCATATGCGTTATTCTTTTAT
1 TATGGCATCCTTTCATGCCAATAATGCAC-CATATGCATTATTCTTTTAT
585736 TCATTCGTTC
Statistics
Matches: 334, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
78 2 0.01
79 301 0.90
80 24 0.07
81 7 0.02
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (78 bp):
TATGGCATCCTTTCATGCCAATAATGCACCATATGCATTATTCTTTTATGTCGATAATGCACCCA
TATGCATTTCAGC
Found at i:585433 original size:34 final size:34
Alignment explanation
Indices: 585390--585680 Score: 168
Period size: 34 Copynumber: 7.6 Consensus size: 34
585380 TTTCATGCCC
*
585390 ATAATGCACCAATATGCATTATTCTTTTATGTCG
1 ATAATGCACCCATATGCATTATTCTTTTATGTCG
** *
585424 ATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATACCA
1 ATAATGCACCCATATGCA-TT--A-T-T--C-T--TTT-ATGTCG
*
585469 ATAATGCACCCATATGCATTATTCTTTTATGTAG
1 ATAATGCACCCATATGCATTATTCTTTTATGTCG
* *
585503 ATAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT-ATGTCG
*
585548 ATAATGCACTCATATGCATTATTCTTTTATGTCG
1 ATAATGCACCCATATGCATTATTCTTTTATGTCG
* *
585582 ATAATGCACCCATATGCATTTCAGTTATGGCATCCTTTTATGCCA
1 ATAATGCACCCATATG-----CA-TTAT----T-CTTTTATGTCG
* * *
585627 ATAATGTACCCATATGCATTATTCTTTTATATTG
1 ATAATGCACCCATATGCATTATTCTTTTATGTCG
585661 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
585681 TCAGCTATGG
Statistics
Matches: 201, Mismatches: 23, Indels: 66
0.69 0.08 0.23
Matches are distributed among these distances:
34 82 0.41
35 11 0.05
36 1 0.00
37 3 0.01
38 4 0.02
39 8 0.04
40 8 0.04
41 4 0.02
42 3 0.01
43 1 0.00
44 11 0.05
45 65 0.32
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (34 bp):
ATAATGCACCCATATGCATTATTCTTTTATGTCG
Found at i:585622 original size:45 final size:44
Alignment explanation
Indices: 585571--585698 Score: 125
Period size: 45 Copynumber: 3.1 Consensus size: 44
585561 ATGCATTATT
585571 CTTTTATGTCGATAATGCACCCATATGCATTTCAGTTATGGCATC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAG-TATGGCATC
* * *
585616 CTTTTATGCCAATAATGTACCCATATGCA-TT-A-T-T--C-T-
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAGTATGGCATC
585652 -TTTATAT-T-GATAATGCACCCATATGCATTTCAGCTATGGCATC
1 CTTT-TATGTCGATAATGCACCCATATGCATTTCAG-TATGGCATC
585695 CTTT
1 CTTT
585699 CATGCCAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
34 17 0.26
35 5 0.08
36 4 0.06
37 1 0.02
38 2 0.03
39 1 0.02
40 1 0.02
41 2 0.03
42 1 0.02
43 1 0.02
44 5 0.08
45 26 0.39
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (44 bp):
CTTTTATGTCGATAATGCACCCATATGCATTTCAGTATGGCATC
Found at i:590930 original size:20 final size:20
Alignment explanation
Indices: 590902--590941 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
590892 TGTTGGGCTT
* *
590902 GATATTACTGTAGCAGTATC
1 GATACTACTGTAGCAATATC
590922 GATACTACTGTAGCAATATC
1 GATACTACTGTAGCAATATC
590942 AGTACCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
GATACTACTGTAGCAATATC
Found at i:594289 original size:44 final size:44
Alignment explanation
Indices: 594169--594290 Score: 199
Period size: 44 Copynumber: 2.8 Consensus size: 44
594159 CTACTTTAAA
* *
594169 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAAGGTGCC
* *
594213 ATAAATGAAAATGCATAACAGTGCATTATTGGTAGAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAAGGTGCC
*
594257 ATAAAAGAAAATGCATAACGGTGCATTATTGGTA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTA
594291 TAAAATGTGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAAGGTGCC
Found at i:594404 original size:19 final size:18
Alignment explanation
Indices: 594380--594427 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
594370 TTATTTAACA
594380 TATATTGGGCAAAATAAAG
1 TATATTGGGCAAAAT-AAG
594399 TATATTTGGG-AAAATAAG
1 TATA-TTGGGCAAAATAAG
*
594417 TATGTTGGGCA
1 TATATTGGGCA
594428 TACTAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 9 0.35
20 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (18 bp):
TATATTGGGCAAAATAAG
Found at i:594419 original size:18 final size:21
Alignment explanation
Indices: 594379--594419 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
594369 CTTATTTAAC
594379 ATATATTGGGCAAAATAAAGT
1 ATATATTGGGCAAAATAAAGT
594400 ATAT-TTGGG-AAAAT-AAGT
1 ATATATTGGGCAAAATAAAGT
594418 AT
1 AT
594420 GTTGGGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 5 0.25
21 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (21 bp):
ATATATTGGGCAAAATAAAGT
Found at i:595087 original size:20 final size:21
Alignment explanation
Indices: 595062--595116 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
595052 TTTTTTGTTC
*
595062 AAAGGATCGATCCC-TTAGCA
1 AAAGGATCGATCCCTTTAACA
* *
595082 AAAGGATCTATCCCTTTAACC
1 AAAGGATCGATCCCTTTAACA
*
595103 AAAGGATTGATCCC
1 AAAGGATCGATCCC
595117 CTTGAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTAACA
Found at i:595223 original size:37 final size:36
Alignment explanation
Indices: 595161--595233 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
595151 ATTTGGGATT
*
595161 GATCCCTTCCCAAAAGGATCGATCCCTTGAGGAAAA
1 GATCCCTTCCCAAAAGGATCGATCCCTCGAGGAAAA
* * *
595197 GATCCCTTCACCGAAAGGATCTATCCCTCGATGAAAA
1 GATCCCTTC-CCAAAAGGATCGATCCCTCGAGGAAAA
595234 TGACTGATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (36 bp):
GATCCCTTCCCAAAAGGATCGATCCCTCGAGGAAAA
Found at i:609632 original size:14 final size:15
Alignment explanation
Indices: 609593--609633 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
609583 ATTTAATTAT
*
609593 TAAATTAAAA-ATTA
1 TAAATTAAAATATAA
609607 TAAATTATAAATATAA
1 TAAATTA-AAATATAA
609623 TAAA-TAAAATA
1 TAAATTAAAATA
609634 AGAAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 5 0.21
16 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATTAAAATATAA
Found at i:612634 original size:28 final size:29
Alignment explanation
Indices: 612563--612635 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 29
612553 ACGGTAGCCG
*
612563 ATCGAACCAAA-TTATCATTAACCGAATTA
1 ATCGAACCAAATTTTTCATTAACCG-ATTA
**** *
612592 ATCGAACTTTTTTTTTCTTTAACCG-TTA
1 ATCGAACCAAATTTTTCATTAACCGATTA
612620 ATCGAACCAAATTTTT
1 ATCGAACCAAATTTTT
612636 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
28 15 0.45
29 7 0.21
30 11 0.33
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (29 bp):
ATCGAACCAAATTTTTCATTAACCGATTA
Found at i:618351 original size:12 final size:12
Alignment explanation
Indices: 618336--618380 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
618326 CGGTTTTTTT
*
618336 ACCGGATAAAAA
1 ACCGGTTAAAAA
618348 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
618362 ACCGGTTAAAAA
1 ACCGGTTAAAAA
618374 ACCGGTT
1 ACCGGTT
618381 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:618362 original size:14 final size:13
Alignment explanation
Indices: 618342--618381 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
618332 TTTTACCGGA
618342 TAAAAAACCGGTT
1 TAAAAAACCGGTT
618355 TGAAAAAACCGG-T
1 T-AAAAAACCGGTT
618368 TAAAAAACCGGTT
1 TAAAAAACCGGTT
618381 T
1 T
618382 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:623980 original size:106 final size:106
Alignment explanation
Indices: 623843--624751 Score: 1498
Period size: 106 Copynumber: 8.6 Consensus size: 106
623833 AAGTTGTCTT
* *
623843 TCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATGGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
623908 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * * *
623949 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
624014 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
624055 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
624120 ACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
624161 TCAACAAACAACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
624226 ACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * *
624267 TCAACGAACAACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
624332 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
624373 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
624438 ACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * * *
624479 TCAACAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
624544 ACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
624585 TCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
624649 ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
66 ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
** * * * * *
624690 TCAACAAATGATTTCCCGATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
624752 GGAACAATGC
Statistics
Matches: 766, Mismatches: 35, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
105 98 0.13
106 668 0.87
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
ACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTG
Found at i:625377 original size:17 final size:17
Alignment explanation
Indices: 625355--625393 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
625345 TCTATTAAAA
625355 TATTTTATT-GTATTATT
1 TATTTTATTAGTATTA-T
*
625372 TATTTTATTATTATTAT
1 TATTTTATTAGTATTAT
625389 TATTT
1 TATTT
625394 CTTTTATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTATTAGTATTAT
Found at i:626550 original size:28 final size:29
Alignment explanation
Indices: 626513--626571 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
626503 ATTTTGGCCC
*
626513 TTTTATTTAT-TTATTTAC-TTTTTTAAT
1 TTTTATTTATCTTATTAACATTTTTTAAT
*
626540 TTTTATTTTATCTTCTTAACATTTTTTAAT
1 TTTTA-TTTATCTTATTAACATTTTTTAAT
626570 TT
1 TT
626572 CAAACCTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 5 0.19
29 6 0.22
30 11 0.41
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTATTTATCTTATTAACATTTTTTAAT
Found at i:626617 original size:16 final size:16
Alignment explanation
Indices: 626587--626624 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
626577 CTTAGCCTTT
*
626587 TTTTTCATTTCTTTTA
1 TTTTTCATTTATTTTA
626603 TATTTT-ATTTATTTTA
1 T-TTTTCATTTATTTTA
626619 TTTTTC
1 TTTTTC
626625 CCCTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTATTTTA
Found at i:629022 original size:18 final size:19
Alignment explanation
Indices: 628985--629022 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
628975 TATAACTTTA
628985 TTTCAATTATCGTAAACTTG
1 TTTCAATTATCG-AAACTTG
629005 TTTCAATTATCG-AACTTG
1 TTTCAATTATCGAAACTTG
629023 AAGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTCAATTATCGAAACTTG
Found at i:629064 original size:33 final size:33
Alignment explanation
Indices: 629011--629109 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
629001 CTTGTTTCAA
629011 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
629043 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
629076 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
629109 T
1 T
629110 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:629138 original size:13 final size:13
Alignment explanation
Indices: 629095--629149 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
629085 TTGGAAGTAT
629095 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
629108 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
629122 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
629135 TTAAGTATTTGAA
1 TTAAGTATTTCAA
629148 TT
1 TT
629150 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:629587 original size:17 final size:17
Alignment explanation
Indices: 629567--629629 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
629557 TTTTTATAAT
629567 CGGTTTTTTAAAAAAAC
1 CGGTTTTTTAAAAAAAC
* * *
629584 CGGTTTTTT--TATAAT
1 CGGTTTTTTAAAAAAAC
629599 CGGTTTTTTAAAAAAAC
1 CGGTTTTTTAAAAAAAC
629616 CGGTTTTTTTAAAA
1 CGG-TTTTTTAAAA
629630 CCGAAACCGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 12 0.32
17 15 0.41
18 10 0.27
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (17 bp):
CGGTTTTTTAAAAAAAC
Found at i:629589 original size:32 final size:32
Alignment explanation
Indices: 629547--629626 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
629537 CTGAAATATT
*
629547 AAAATCGGTTTTTTTATAATCGGTTTTTTAAA
1 AAAACCGGTTTTTTTATAATCGGTTTTTTAAA
629579 AAAACCGGTTTTTTTATAATCGGTTTTTTAAA
1 AAAACCGGTTTTTTTATAATCGGTTTTTTAAA
629611 AAAACCGGTTTTTTTA
1 AAAACCGGTTTTTTTA
629627 AAACCGAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
AAAACCGGTTTTTTTATAATCGGTTTTTTAAA
Found at i:629629 original size:15 final size:15
Alignment explanation
Indices: 629545--629632 Score: 77
Period size: 15 Copynumber: 5.6 Consensus size: 15
629535 ATCTGAAATA
*
629545 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
629560 TTATAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
629575 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
* *
629592 TTATAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
629607 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
629624 TTAAAACCG
1 TTAAAACCG
629633 AAACCGGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
15 34 0.59
17 24 0.41
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:631039 original size:31 final size:31
Alignment explanation
Indices: 631004--631096 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
630994 GGTGAAAAGG
631004 TTGGAATGCAATGAGTAAATCGATTGGTTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
631035 TTGGAATGCAATGAGTAAATCGATTGGTTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
*
631066 TTGGAATGCAATGAGTAAATCGATTGATTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
631097 CGCTAAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (31 bp):
TTGGAATGCAATGAGTAAATCGATTGGTTTT
Found at i:638399 original size:196 final size:198
Alignment explanation
Indices: 638064--638458 Score: 670
Period size: 196 Copynumber: 2.0 Consensus size: 198
638054 GGTAAGACCA
*
638064 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTCTTGGTCCATAA
1 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
*
638129 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTTTAAGTTTC
66 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
* *
638194 ATAGAGTTTTTTATATGA-TTTTA-GGCT-TTGAAACATTAAAGCCTAGTATCTTAAAGATTAAT
131 ATAGAGTTTTTTATATGATTTTTATGG-TATTGAAACATTAAAGCCTAATACCTTAAAGATTAAT
638256 ATTT
195 ATTT
** *
638260 TAATCTTAGTTTTCTTTTGGTACTAATTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
1 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
*
638325 ACCCTAACTTAAAAGGTTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
66 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
* *
638390 ATGGAGTTTTTTCTATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
131 ATAGAGTTTTTTATATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
638455 TTT
196 TTT
638458 T
1 T
638459 CATGTTTATT
Statistics
Matches: 186, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
196 140 0.75
197 6 0.03
198 40 0.22
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (198 bp):
TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
ATAGAGTTTTTTATATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
TTT
Found at i:639414 original size:23 final size:23
Alignment explanation
Indices: 639369--639446 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
639359 CACCGAAGTC
* * *
639369 CCACATAGAATTTGTCCCGAAGGA
1 CCACATAG-GTTTGTCTCAAAGGA
639393 CCACATAGGTTTGTCTCAAAGGA
1 CCACATAGGTTTGTCTCAAAGGA
*
639416 CTACATAGGTTTGTCTCAAAGGA
1 CCACATAGGTTTGTCTCAAAGGA
*
639439 CTACATAG
1 CCACATAG
639447 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 42 0.84
24 8 0.16
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CCACATAGGTTTGTCTCAAAGGA
Found at i:645584 original size:20 final size:20
Alignment explanation
Indices: 645559--645603 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
645549 GATTTTTAAC
645559 TTTTAGTTGGCATGCACACT
1 TTTTAGTTGGCATGCACACT
*
645579 TTTTAGTTGGCATGTACACT
1 TTTTAGTTGGCATGCACACT
645599 TTTTA
1 TTTTA
645604 AAACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (20 bp):
TTTTAGTTGGCATGCACACT
Found at i:646356 original size:23 final size:22
Alignment explanation
Indices: 646324--646385 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 22
646314 AGAATATGTC
646324 CCGAAGGACCACATAGGTTTGTT
1 CCGAAGGACCACATAGGTTTG-T
*
646347 CCGAATGACCACATAGGTTTGT
1 CCGAAGGACCACATAGGTTTGT
646369 CTCGAAGGACCACATAG
1 C-CGAAGGACCACATAG
646386 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (22 bp):
CCGAAGGACCACATAGGTTTGT
Found at i:647080 original size:20 final size:20
Alignment explanation
Indices: 647036--647086 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
647026 TTTTCGATAA
*
647036 CAGTATCGATACCTTCCTCT
1 CAGTATCGATACCTTCCTAT
*
647056 TAGTATCGATACC-TCCATAT
1 CAGTATCGATACCTTCC-TAT
647076 CAGTATCGATA
1 CAGTATCGATA
647087 TTACTTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGTATCGATACCTTCCTAT
Found at i:655135 original size:21 final size:22
Alignment explanation
Indices: 655109--655164 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
655099 AAACCATTCA
655109 GGGGGGAATCGGTACCCCCTTG
1 GGGGGGAATCGGTACCCCCTTG
* *
655131 GGGGGGAATCGGTA-CCCTTTT
1 GGGGGGAATCGGTACCCCCTTG
655152 GGGGGGAATCGGT
1 GGGGGGAATCGGT
655165 TCCCTCTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.14, C:0.20, G:0.45, T:0.21
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCCTTG
Found at i:657002 original size:21 final size:22
Alignment explanation
Indices: 656972--657012 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
656962 TTAGGATCAA
*
656972 TGGGATTAGGAATAGGATTTAG
1 TGGGATTAGGAAGAGGATTTAG
*
656994 TGGGA-TAGGAGGAGGATTT
1 TGGGATTAGGAAGAGGATTT
657013 GGAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTAG
Found at i:660476 original size:21 final size:22
Alignment explanation
Indices: 660446--660486 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
660436 TTAGGATCAA
*
660446 TGGGATTAGGAATAGGATTTAG
1 TGGGATTAGGAAGAGGATTTAG
*
660468 TGGGA-TAGGAGGAGGATTT
1 TGGGATTAGGAAGAGGATTT
660487 GGAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTAG
Found at i:665096 original size:22 final size:21
Alignment explanation
Indices: 665054--665093 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
665044 GAGTTTATTT
*
665054 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
665075 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
665094 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:668528 original size:353 final size:352
Alignment explanation
Indices: 667878--668583 Score: 1331
Period size: 353 Copynumber: 2.0 Consensus size: 352
667868 TCACTCCTTG
667878 ATGATTAATGGTGGAATGATCGTAGATAAGATTCTACAACTGTATCATTTCTCCGATCAAAGGAT
1 ATGATTAATGGTGGAATGATCGTAGATAAGATTCTACAACTGTATCATTTCTCCGATCAAAGGAT
667943 CTCTATTCAAATCTTCAATGTCATTATATTAGTCAACTCTTATGTGCAACTTTAATGCGAGCTTC
66 CTCTATTCAAATCTTCAATGTCATTATATTAGTCAACTCTTATGTGCAACTTTAATGCGAGCTTC
*
668008 CTCCTTGTTCTCTAAGCTTCGTTATCAGTGCATGTCTGTGTATGTGGTTACTTGATTGAAAACTT
131 CTCCTTGTTCTCAAAGCTTCGTTATCAGTGCATGTCTGTGTATGTGGTTACTTGATTGAAAACTT
*
668073 TCCCCCTTATGAAATTTTTTACTTAGATAATCACTTATGGATCAATACTTTCACATTATGTCGCG
196 TCCCCCTTATGAAATATTTTACTTAGATAATCACTTATGGATCAATACTTTCACATTATGTCGCG
*
668138 ATGATACAATGTAAAAAGGCGAAAAATGACAAAAACTAAGAAAAATGAGTTAGTACAGGTAAGAC
261 ATGATACAATGTAAAAAGGCAAAAAATGACAAAAACTAAGAAAAATGAGTTAGTACAGGTAAGAC
668203 AATAGATAAAGATAAAAAATGATATTC
326 AATAGATAAAGATAAAAAATGATATTC
*
668230 ATGATTAATGGTGGAATGATCGTAGATAATATTCTACAACTGTATCATTTCTCCGATCAAAGGAT
1 ATGATTAATGGTGGAATGATCGTAGATAAGATTCTACAACTGTATCATTTCTCCGATCAAAGGAT
668295 CTCTATTCAAATCTTCAATGTCATTATATTAGTCAACTCTTATGTGCAACTTTAATGCGAGCTTC
66 CTCTATTCAAATCTTCAATGTCATTATATTAGTCAACTCTTATGTGCAACTTTAATGCGAGCTTC
668360 CTCCTTGTTCTCAAAGCTTTCGTTATCAGTGCATGTCTGTGTATGTGGTTACTTGATTGAAAACT
131 CTCCTTGTTCTCAAAGC-TTCGTTATCAGTGCATGTCTGTGTATGTGGTTACTTGATTGAAAACT
* * *
668425 TTCCCCCTTATGAAATATTTTACTTAGATAATCACTTGTGGATTAATACTTTCACATTTTGTCGC
195 TTCCCCCTTATGAAATATTTTACTTAGATAATCACTTATGGATCAATACTTTCACATTATGTCGC
*
668490 GATGATACAATGTAAAAAGGCAAAAAATGACAAAAACTAAGAACAATGAGTTAGTACAGGTAAGA
260 GATGATACAATGTAAAAAGGCAAAAAATGACAAAAACTAAGAAAAATGAGTTAGTACAGGTAAGA
668555 CAATAGATAAAGATAAAAAATGATATTC
325 CAATAGATAAAGATAAAAAATGATATTC
668583 A
1 A
668584 AAGATGAATA
Statistics
Matches: 345, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
352 145 0.42
353 200 0.58
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (352 bp):
ATGATTAATGGTGGAATGATCGTAGATAAGATTCTACAACTGTATCATTTCTCCGATCAAAGGAT
CTCTATTCAAATCTTCAATGTCATTATATTAGTCAACTCTTATGTGCAACTTTAATGCGAGCTTC
CTCCTTGTTCTCAAAGCTTCGTTATCAGTGCATGTCTGTGTATGTGGTTACTTGATTGAAAACTT
TCCCCCTTATGAAATATTTTACTTAGATAATCACTTATGGATCAATACTTTCACATTATGTCGCG
ATGATACAATGTAAAAAGGCAAAAAATGACAAAAACTAAGAAAAATGAGTTAGTACAGGTAAGAC
AATAGATAAAGATAAAAAATGATATTC
Found at i:669848 original size:8 final size:8
Alignment explanation
Indices: 669831--669871 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
669821 GTAAATGAAC
669831 AATAAAAT
1 AATAAAAT
*
669839 AATAACAT
1 AATAAAAT
669847 AATAAAAT
1 AATAAAAT
669855 AA-AATAA-
1 AATAA-AAT
669862 AATAAAAT
1 AATAAAAT
669870 AA
1 AA
669872 AATACATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AATAAAAT
Found at i:669855 original size:5 final size:5
Alignment explanation
Indices: 669831--669875 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
669821 GTAAATGAAC
* *
669831 AATAA AATAA TAACAT AATAA AATAA AATAA AATAA AATAA AATA
1 AATAA AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATA
669876 CATGTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 32 0.91
6 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:670946 original size:21 final size:19
Alignment explanation
Indices: 670908--670953 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
670898 AATTAATCCT
670908 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
670928 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
670949 A-TAAT
1 ACTAAT
670954 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:679533 original size:21 final size:20
Alignment explanation
Indices: 679495--679536 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
679485 AATTAATCCT
679495 ACTAAGTATTAAAGCTAAGA
1 ACTAAGTATTAAAGCTAAGA
679515 ACTAA-TATTAAGGAGCTAAGA
1 ACTAAGTATTAA--AGCTAAGA
679536 A
1 A
679537 TAACAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
ACTAAGTATTAAAGCTAAGA
Found at i:687279 original size:2 final size:2
Alignment explanation
Indices: 687272--687317 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
687262 AAATACATAC
687272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
687314 AT AT
1 AT AT
687318 TGTATCTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:687716 original size:21 final size:21
Alignment explanation
Indices: 687692--687734 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
687682 TAATCAAAAG
* *
687692 GTTATGACCTTTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
*
687713 GTTAAGATCATTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
687734 G
1 G
687735 ATTTATTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (21 bp):
GTTAAGACCATTTGATGAAGA
Found at i:688953 original size:21 final size:22
Alignment explanation
Indices: 688914--688955 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
688904 AATAACATTT
688914 ATGATAAATATCATATGTAATC
1 ATGATAAATATCATATGTAATC
* *
688936 ATGAT-AATATTATGTGTAAT
1 ATGATAAATATCATATGTAAT
688956 GAAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
ATGATAAATATCATATGTAATC
Found at i:690312 original size:31 final size:31
Alignment explanation
Indices: 690269--690338 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
690259 ATCTACAATA
* * * * *
690269 TTTCCAAAATTATTGATTTGGTCCCCCAACTT
1 TTTCTAAAATTATAGA-ATGGTCCCCAAAATT
690301 TTT-TAAAATTATAGAATGGTCCCCAAAATT
1 TTTCTAAAATTATAGAATGGTCCCCAAAATT
690331 TTTCTAAA
1 TTTCTAAA
690339 GCCTGTAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 15 0.47
31 14 0.44
32 3 0.09
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (31 bp):
TTTCTAAAATTATAGAATGGTCCCCAAAATT
Found at i:703059 original size:22 final size:24
Alignment explanation
Indices: 703031--703076 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
703021 AATATATGAT
703031 GATTTATTATCTT-TTA-GAATTA
1 GATTTATTATCTTATTATGAATTA
*
703053 GATTTATTATTTTATTATGAATTA
1 GATTTATTATCTTATTATGAATTA
703077 AGATAGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 3 0.14
24 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (24 bp):
GATTTATTATCTTATTATGAATTA
Found at i:705327 original size:19 final size:20
Alignment explanation
Indices: 705303--705343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
705293 CCAGAATGCT
705303 CATA-GGGAACCGATTCCCC
1 CATAGGGGAACCGATTCCCC
*
705322 CATAGGGGGTACCGATTCCCC
1 CATA-GGGGAACCGATTCCCC
705343 C
1 C
705344 TTGTATAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.17
Consensus pattern (20 bp):
CATAGGGGAACCGATTCCCC
Found at i:710452 original size:21 final size:23
Alignment explanation
Indices: 710428--710477 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
710418 AGGTAATCGA
*
710428 TCCCCCCTTG-A-GGGAACTGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
710449 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
710472 TCCCCC
1 TCCCCC
710478 ACAGGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 1 0.04
23 15 0.60
ACGTcount: A:0.18, C:0.38, G:0.22, T:0.22
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:710503 original size:19 final size:20
Alignment explanation
Indices: 710460--710497 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
710450 CCCCCTTTGA
*
710460 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
710480 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
710498 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:716205 original size:18 final size:18
Alignment explanation
Indices: 716168--716223 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
716158 GGGCACTTAA
716168 CACT-TGTCCCGAATGG-C
1 CACTATGTCCCGAA-GGAC
*
716185 CACTATGTCCTGAAGGAC
1 CACTATGTCCCGAAGGAC
716203 CACTATGTCCCGAAGGAC
1 CACTATGTCCCGAAGGAC
716221 CAC
1 CAC
716224 GTAGAACCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
17 6 0.17
18 29 0.83
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.20
Consensus pattern (18 bp):
CACTATGTCCCGAAGGAC
Found at i:717668 original size:31 final size:30
Alignment explanation
Indices: 717598--717666 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
717588 CAACCATTCA
* *
717598 CAAATTTTCCAAAATTACTAAATTGGTCTCC
1 CAAATTTTCAAAAATTACTAAAATGGTC-CC
* *
717629 TAACTTTTCAAAAATTAC-AAAATGGTCCCC
1 CAAATTTTCAAAAATTACTAAAATGGT-CCC
717659 CAAATTTT
1 CAAATTTT
717667 TCTAAGGCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
CAAATTTTCAAAAATTACTAAAATGGTCCC
Found at i:718655 original size:29 final size:31
Alignment explanation
Indices: 718602--718665 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
718592 TTTGTTCCCT
* *
718602 AAACTTTTTCAAAGTTTATACTTTGGTCACC
1 AAACTTTTACAAAGTTTATAATTTGGTCACC
*
718633 AAAC-TTTACAAA-TTTATAATTTGGTCACT
1 AAACTTTTACAAAGTTTATAATTTGGTCACC
718662 AAAC
1 AAAC
718666 AAAATCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 19 0.63
30 7 0.23
31 4 0.13
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (31 bp):
AAACTTTTACAAAGTTTATAATTTGGTCACC
Found at i:718700 original size:18 final size:18
Alignment explanation
Indices: 718666--718712 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
718656 GTCACTAAAC
718666 AAAATCCATTTATGGAAT
1 AAAATCCATTTATGGAAT
* *
718684 AAAATTCATTT-TGGGA-
1 AAAATCCATTTATGGAAT
718700 AAAATACCATTTA
1 AAAAT-CCATTTA
718713 GGTCTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 10 0.42
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAATCCATTTATGGAAT
Found at i:718956 original size:10 final size:11
Alignment explanation
Indices: 718943--718974 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
718933 AAATATTTGA
718943 AAAAAT-TAAT
1 AAAAATATAAT
718953 AAAAATATAA-
1 AAAAATATAAT
718963 AAAAATATAAT
1 AAAAATATAAT
718974 A
1 A
718975 TAGAAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAAATATAAT
Found at i:720012 original size:102 final size:102
Alignment explanation
Indices: 719906--720097 Score: 262
Period size: 106 Copynumber: 1.9 Consensus size: 102
719896 TTTTTAATTT
* * *
719906 AAATTG-A-TAATTTACATTCTTGATTCAGTATGATACTTATGATTTCTTTCAGTTAAATACATT
1 AAATTGAACTAATTTAAATTCTTGATTCAATATGATACTTATGATTTCTTTCAATTAAATACATT
719969 TATTTGATTCACTGATATCTAAATTGAATTTTTTTAAAA
66 TATTTGATTCACTGAT-T-TAAATTGAATTTTTTTAAAA
* * * *
720008 AAATTGATACTTAATTTAAATTCTTGATTCAATATGGTAGTTATGATTTTTTTTAATTAAATACA
1 AAATTGA-AC-TAATTTAAATTCTTGATTCAATATGATACTTATGATTTCTTTCAATTAAATACA
*
720073 TTTATTTGATTCATTGATTTAAATT
64 TTTATTTGATTCACTGATTTAAATT
720098 AAGTATTTAG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
102 6 0.08
104 7 0.09
105 1 0.01
106 64 0.82
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (102 bp):
AAATTGAACTAATTTAAATTCTTGATTCAATATGATACTTATGATTTCTTTCAATTAAATACATT
TATTTGATTCACTGATTTAAATTGAATTTTTTTAAAA
Found at i:722726 original size:20 final size:22
Alignment explanation
Indices: 722701--722752 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
722691 GGCTTATGGG
*
722701 TATCGATACTCC-ATGAACA-A
1 TATCGATACTCCTAAGAACATA
*
722721 TATCGATA-TCCTAAGAACATG
1 TATCGATACTCCTAAGAACATA
722742 TATCGATACTC
1 TATCGATACTC
722753 TTCTCACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 8 0.30
22 2 0.07
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.29
Consensus pattern (22 bp):
TATCGATACTCCTAAGAACATA
Found at i:724765 original size:170 final size:174
Alignment explanation
Indices: 724389--724988 Score: 750
Period size: 181 Copynumber: 3.4 Consensus size: 174
724379 TGTCGGTTTA
* *
724389 CGATACTTTATAA-AACTGTATCGATCCAC-ATCAATATAACAAGTAAAAATATGACAAAACCGG
1 CGATACTTTATAACAA-TGTATCGATCCACAAT-GATATAACAGGTAAAAATATGACAAAACCGG
* * * * * *
724452 TCTCAAAAAGACAAAATCG-GTAAATCGGTATCAGATATATTGAAAGTATCGATACTTTAATATA
64 TCTC-TAAAG---GAACCGAG-AGA---G-ACCAGATATATTGAAAGTGTCGATACTTTAATATA
* *
724516 AGTATCGACATTTTGTG-ATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGT
120 AGTATCGACACTTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGT
*
724570 CGATACTTTATAACAATGTATCGATCCACAATGATATAATAGGTAAAAATATGACAAAACCGGTC
1 CGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTC
**
724635 TCTAAAGG-A-C-AGAGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
66 TCTAAAGGAACCGAGAGAGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
* *
724697 TTTGTGAATTTTAAAGAGAATCAGTTTTAGCG-CTATAAAGTAT
131 TTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGT
* * *
724740 CGATACTTTATAACAATGTATCGATCCACAATAATATAACAGGTAAAAACATGACAAAACCAGTC
1 CGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTC
724805 TCTAAAGGACAAAACCGGTATAGAGAGACC-GAATATATTGAAAGTGTCGATACTTTAATATAAG
66 TCTAAAGG----AACC-G---AGAGAGACCAG-ATATATTGAAAGTGTCGATACTTTAATATAAG
*
724869 TATCGATACTTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGT
122 TATCGACACTTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGT
* * * *
724922 CGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAATCGGTC
1 CGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTC
724987 TC
66 TC
724989 GAACTGACAA
Statistics
Matches: 372, Mismatches: 30, Indels: 33
0.86 0.07 0.08
Matches are distributed among these distances:
170 128 0.34
171 23 0.06
174 1 0.00
175 3 0.01
176 2 0.01
180 5 0.01
181 136 0.37
182 74 0.20
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (174 bp):
CGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTC
TCTAAAGGAACCGAGAGAGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
TTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGT
Found at i:724865 original size:181 final size:182
Alignment explanation
Indices: 724656--725046 Score: 622
Period size: 182 Copynumber: 2.2 Consensus size: 182
724646 GAGCTACCAG
*
724656 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTTAAAGAGAATCAG
1 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAATCAG
* *
724721 TTTTAGCG-CTATAAAGTATCGATACTTTATAACAATGTATCGATCCACAATAATATAACAGGTA
66 TTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTA
* *
724785 AAAACATGACAAAACCAGTCTCTAAAGGACAAAACCGGTATAGAGAGACCGA
131 AAAACATGACAAAACCAGTCTCGAAAGGACAAAACCGGTAAAGAGAGACCGA
*
724837 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGATACTTTGTGAATTTAAAAGAGAATCAG
1 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAATCAG
* * *
724902 TTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTA
66 TTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTA
* * * ** * **
724967 AAAATATGACAAAATCGGTCTCGAACTGACAAAACCGGTAAAGCGCTACCGA
131 AAAACATGACAAAACCAGTCTCGAAAGGACAAAACCGGTAAAGAGAGACCGA
725019 ATATATTGAAAGTGTCGATACTTTAATA
1 ATATATTGAAAGTGTCGATACTTTAATA
725047 AGTACGTGTA
Statistics
Matches: 192, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
181 71 0.37
182 121 0.63
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (182 bp):
ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAATCAG
TTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTA
AAAACATGACAAAACCAGTCTCGAAAGGACAAAACCGGTAAAGAGAGACCGA
Found at i:727421 original size:6 final size:6
Alignment explanation
Indices: 727387--727445 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
727377 CAAGAGGTCA
* * * * *
727387 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATT ATGATG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
*
727435 ATTATG ATGAT
1 ATGATG ATGAT
727446 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.39, C:0.02, G:0.29, T:0.31
Consensus pattern (6 bp):
ATGATG
Found at i:727428 original size:15 final size:15
Alignment explanation
Indices: 727410--727445 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
727400 TGACGATGAA
727410 GATGATGATGATTAT
1 GATGATGATGATTAT
727425 GATGATGATGATTAT
1 GATGATGATGATTAT
727440 GATGAT
1 GATGAT
727446 CCAAACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (15 bp):
GATGATGATGATTAT
Found at i:728797 original size:24 final size:24
Alignment explanation
Indices: 728746--728798 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
728736 TTTCATATGT
* * *
728746 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
728770 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
728794 AATTT
1 AATTT
728799 TGGTTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:730032 original size:19 final size:19
Alignment explanation
Indices: 730008--730056 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
729998 AATGTAGGGT
730008 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
** *
730027 TAATTTTACATACGATTTA
1 TAATTTTGTATAAGATTTA
730046 TAATTTTGTAT
1 TAATTTTGTAT
730057 GTGAATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:733476 original size:19 final size:20
Alignment explanation
Indices: 733445--733482 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
733435 ATTAATTTGG
733445 AATAAATTAATCA-ATTTTC
1 AATAAATTAATCATATTTTC
733464 AATAAA-TAGATCATATTTT
1 AATAAATTA-ATCATATTTT
733483 AACTTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 10 0.59
20 5 0.29
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
AATAAATTAATCATATTTTC
Found at i:734610 original size:35 final size:35
Alignment explanation
Indices: 734561--734732 Score: 220
Period size: 35 Copynumber: 4.9 Consensus size: 35
734551 GTGAATAGAT
* * *
734561 TAGAATGAAGGGAAGCATCACACTTTCCATTCAAG
1 TAGAACGAAAGGAAGCATCACACTTTCGATTCAAG
* **
734596 TAGAAC-AGAAGGAAGTATCGTACTTTCGATTCAAG
1 TAGAACGA-AAGGAAGCATCACACTTTCGATTCAAG
* * **
734631 TAGAACGGAAGGAAGCATCGCACTTTTAATTCAAG
1 TAGAACGAAAGGAAGCATCACACTTTCGATTCAAG
* *
734666 TAGAATGAAAGGAAGCATCACAATTTCGATTCAAG
1 TAGAACGAAAGGAAGCATCACACTTTCGATTCAAG
734701 TAGAACGAAAGGAAGCATCACACTTTCGATTC
1 TAGAACGAAAGGAAGCATCACACTTTCGATTC
734733 TAGTGTTCCT
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
34 1 0.01
35 115 0.99
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (35 bp):
TAGAACGAAAGGAAGCATCACACTTTCGATTCAAG
Found at i:740528 original size:17 final size:17
Alignment explanation
Indices: 740487--740531 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
740477 CACTACTTTA
740487 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
740504 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
740521 TTAAATATTTA
1 TTAAATATTTA
740532 TTTTGACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:741387 original size:23 final size:23
Alignment explanation
Indices: 741360--741404 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
741350 TTAAACTGAC
*
741360 TATTTTTATACAAGGAGCCTTTG
1 TATTTGTATACAAGGAGCCTTTG
*
741383 TATTTGTATACATGGAGCCTTT
1 TATTTGTATACAAGGAGCCTTT
741405 AAAAGATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (23 bp):
TATTTGTATACAAGGAGCCTTTG
Found at i:741876 original size:5 final size:6
Alignment explanation
Indices: 741846--741880 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
741836 GACACGTATT
741846 ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
741881 GACGGCGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.37, C:0.46, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:742407 original size:6 final size:6
Alignment explanation
Indices: 742398--742422 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
742388 GTCGTGGTCG
742398 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
742423 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:742564 original size:21 final size:21
Alignment explanation
Indices: 742538--742737 Score: 221
Period size: 21 Copynumber: 9.6 Consensus size: 21
742528 GATTTACATA
742538 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
742559 TTCGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCGAAG
* *
742580 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
742601 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* * *
742622 TTTGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
742643 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
742663 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
* *
742684 TTCGCATTGCGATATTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
742704 TATCGCATTGCGATAGTCTAAG
1 T-TCGCATTGCGATAGTCGAAG
*
742726 TTCGCGTTGCGA
1 TTCGCATTGCGA
742738 ATCTGGAAAC
Statistics
Matches: 153, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
19 1 0.01
20 17 0.11
21 132 0.86
22 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:755824 original size:15 final size:15
Alignment explanation
Indices: 755806--755835 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
755796 ATATCAGCAC
755806 ATATAATAACATAAA
1 ATATAATAACATAAA
*
755821 ATATAATACCATAAA
1 ATATAATAACATAAA
755836 TTTAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
ATATAATAACATAAA
Found at i:759396 original size:172 final size:172
Alignment explanation
Indices: 759110--759453 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
759100 TTTTGAATGT
759110 CATTCTAATATAGAGCTCACCATCAACACATTGGTTGTATGGCTCAAATTGTGGAAGTTATTAAA
1 CATTCTAATATAGAGCTCACCATCAACACATTGGTTGTATGGCTCAAATTGTGGAAGTTATTAAA
759175 ATTCTAGAGCGTTCAAAGGTTCCATATCAACCGTTGTGAAGTGTGATGGTATTTGAAAATAAGAA
66 ATTCTAGAGCGTTCAAAGGTTCCATATCAACCGTTGTGAAGTGTGATGGTATTTGAAAATAAGAA
759240 ACATGAGGTGCAACATGTGGAATATCATCATCATTCGCTTCC
131 ACATGAGGTGCAACATGTGGAATATCATCATCATTCGCTTCC
759282 CATTCTAATATAGAGCTCACCATCAACACATTGGTTGTATGGCTCAAATTGTGGAAGTTATTAAA
1 CATTCTAATATAGAGCTCACCATCAACACATTGGTTGTATGGCTCAAATTGTGGAAGTTATTAAA
759347 ATTCTAGAGCGTTCAAAGGTTCCATATCAACCGTTGTGAAGTGTGATGGTATTTGAAAATAAGAA
66 ATTCTAGAGCGTTCAAAGGTTCCATATCAACCGTTGTGAAGTGTGATGGTATTTGAAAATAAGAA
759412 ACATGAGGTGCAACATGTGGAATATCATCATCATTCGCTTCC
131 ACATGAGGTGCAACATGTGGAATATCATCATCATTCGCTTCC
759454 ACCAGCATGT
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (172 bp):
CATTCTAATATAGAGCTCACCATCAACACATTGGTTGTATGGCTCAAATTGTGGAAGTTATTAAA
ATTCTAGAGCGTTCAAAGGTTCCATATCAACCGTTGTGAAGTGTGATGGTATTTGAAAATAAGAA
ACATGAGGTGCAACATGTGGAATATCATCATCATTCGCTTCC
Found at i:761189 original size:103 final size:103
Alignment explanation
Indices: 760980--761290 Score: 435
Period size: 104 Copynumber: 3.0 Consensus size: 103
760970 AATTACCAAA
** * * *
760980 GTAAGTTCCAAACACTATTATGAAAACAAAATGTGATATACATGCCCCCTTGTTACACATGTATC
1 GTAAGTTCCAAATGCTAATATGAAAACAAAATGTGACATACATGCCCCC-TATTACACATGTATC
* **
761045 GTACTCATAAGCAATGCTGGAGGAACTCCCATTACCAAT
65 GTACTCATAAGCAATGCTAGAGGAACTCCCATTACTGAT
* * * *
761084 GTAAGTTCCAGATGCTAATATGAAAACAAAATGTGACATACATGCCCCCTATTACATATGTACCA
1 GTAAGTTCCAAATGCTAATATGAAAACAAAATGTGACATACATGCCCCCTATTACACATGTATCG
*
761149 TACTCATAAGCAATGCTTGAGGAACTCCCATTACTGAT
66 TACTCATAAGCAATGCTAGAGGAACTCCCATTACTGAT
* *
761187 GTAAGTTCCAAATGCTAATATGAAAACAAAATGTGACATACATGTCCCCTTATTACACATGTATT
1 GTAAGTTCCAAATGCTAATATGAAAACAAAATGTGACATACATG-CCCCCTATTACACATGTATC
* *
761252 GTACTCGTAAGCAATG-TCAGAGGAACGCCCATTACTGAT
65 GTACTCATAAGCAATGCT-AGAGGAACTCCCATTACTGAT
761291 CGACATTGGT
Statistics
Matches: 184, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
103 91 0.49
104 93 0.51
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (103 bp):
GTAAGTTCCAAATGCTAATATGAAAACAAAATGTGACATACATGCCCCCTATTACACATGTATCG
TACTCATAAGCAATGCTAGAGGAACTCCCATTACTGAT
Found at i:762654 original size:24 final size:24
Alignment explanation
Indices: 762623--762669 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
762613 ATTTGATTTT
762623 AATAAG-TTTTGTCTA-TTTATTAC
1 AATAAGTTTTTGT-TATTTTATTAC
762646 AATAGAGTTTTTGTTATTTTATTA
1 AATA-AGTTTTTGTTATTTTATTA
762670 TATGTTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 13 0.62
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (24 bp):
AATAAGTTTTTGTTATTTTATTAC
Found at i:763450 original size:505 final size:506
Alignment explanation
Indices: 762486--763463 Score: 1539
Period size: 505 Copynumber: 1.9 Consensus size: 506
762476 GCAATTGCGG
*
762486 TAACAACTATCCATGTAATTCAATCGACCAAGTTTGGCAACCAATGAACAACATATGTACTTGTT
1 TAACAACTATCCACGTAATTCAATCGACCAAGTTTGGCAACCAATGAACAACATATGTACTTGTT
* * * *
762551 ATGATTCTTGTTTTTGGAACCATGAAGCAACTTTGTTTAGTACCATGTTATATTAGAATGAAATT
66 ATGATTCTTATTTTTGGAACCATGAAGCAACATTGTTTAGTAACATGTTATATTAAAATGAAATT
*
762616 TGATTTTAATAAGTTTTGTCTATTTATTACAATAGAGTTTTTGTTATTTTATTATATGTTATACA
131 TGATTTTAATAAGTTTTGTCTATTTATTACAATAGAGTTTTTGTTATTTTATTATATGCTATACA
* *
762681 ATAAAAATATAATCATTAATTTATATTTATAAAATAGTTTGGTCACATTGGAGCTCGCGTTAAGC
196 ATAAAAATATAATCATTAATTTATATTTATAAAATAGTTTGGTCACAATGGACCTCGCGTTAAGC
* * * *
762746 ACACAGGGAGATCTATTCAAAAGATGTGATACTTAAAATTCTTGGGGAAGTTTCATTATCTCGGA
261 ACACAGGGAGATCCATTCAAAAGATGTGATACTTAAAATTCTCGGGGAAGTTCCAATATCTCGGA
* * * * *
762811 TACCTTTCGTTTGATTTAACGCGAGGTCATTTATCAAAATATTAAATTGTATTATCTGAAAAGTG
326 TACCTTTAGTTTGATATAACACGAGGTCATTAATCAAAATATTAAATTGTATTATCTGAAAAATG
* *
762876 TTTCTACATTAGATGAGACTCGCGTTCTATGGAACATGAGGTCTTTAAACGCGTTTTGTATGACA
391 TTTCCACATTAGATGAGACTCGCGTTCTATGGAACATGAGGTCTTTAAACGCGTTTTGTAGGACA
762941 CGACGTAGTCCTACGTGTACATTTTGAAAAAAAATCCAATTAAGATTGTAA
456 CGACGTAGTCCTACGTGTACATTTTGAAAAAAAATCCAATTAAGATTGTAA
* **
762992 TAACAACTATCCGCGTAATTCAATCGACCAAGTTTGGCAACCAATGAAC-ATTTATGTACTTGTT
1 TAACAACTATCCACGTAATTCAATCGACCAAGTTTGGCAACCAATGAACAACATATGTACTTGTT
* *
763056 ATGATTCTTATTTTTGGAACCATGAAGTAACATTGTTTTGTAACATGTTATATTAAAATGAAATT
66 ATGATTCTTATTTTTGGAACCATGAAGCAACATTGTTTAGTAACATGTTATATTAAAATGAAATT
763121 TGATTTTAATAAGTTTTGTCTATTTATTACAATAGAGTTTTTTGTTATTTTATTATATGCTATAC
131 TGATTTTAATAAGTTTTGTCTATTTATTACAATAGAG-TTTTTGTTATTTTATTATATGCTATAC
* * *
763186 AATAAAAATATAATCATTAATTTATATTTATTAAATA-TTTTGTCACAATGGACCTCGCGTTACG
195 AATAAAAATATAATCATTAATTTATATTTATAAAATAGTTTGGTCACAATGGACCTCGCGTTAAG
* * *
763250 CACTC-GGCGAGGTCCATTCAAAAGATGTGATACTTCAAATTCTCGGGGAAGTTCCAATATCTCG
260 CACACAGG-GAGATCCATTCAAAAGATGTGATACTTAAAATTCTCGGGGAAGTTCCAATATCTCG
* * * *
763314 GGTACCTTTAGTTTGATATAGCACGAGGTCATTAATCGAAATATTAAATTGTATTCTCTGAAAAA
324 GATACCTTTAGTTTGATATAACACGAGGTCATTAATCAAAATATTAAATTGTATTATCTGAAAAA
** * * * * * *
763379 TGTTTCCATGTTAGATGAGATTCGCGTTTTATGGAACGTGAGGTCTTTAAACGTGTTTTTTAGGG
389 TGTTTCCACATTAGATGAGACTCGCGTTCTATGGAACATGAGGTCTTTAAACGCGTTTTGTAGGA
763444 CACGACGTAGTCCTACGTGT
454 CACGACGTAGTCCTACGTGT
763464 GCAATTTAAA
Statistics
Matches: 428, Mismatches: 42, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
504 2 0.00
505 317 0.74
506 109 0.25
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (506 bp):
TAACAACTATCCACGTAATTCAATCGACCAAGTTTGGCAACCAATGAACAACATATGTACTTGTT
ATGATTCTTATTTTTGGAACCATGAAGCAACATTGTTTAGTAACATGTTATATTAAAATGAAATT
TGATTTTAATAAGTTTTGTCTATTTATTACAATAGAGTTTTTGTTATTTTATTATATGCTATACA
ATAAAAATATAATCATTAATTTATATTTATAAAATAGTTTGGTCACAATGGACCTCGCGTTAAGC
ACACAGGGAGATCCATTCAAAAGATGTGATACTTAAAATTCTCGGGGAAGTTCCAATATCTCGGA
TACCTTTAGTTTGATATAACACGAGGTCATTAATCAAAATATTAAATTGTATTATCTGAAAAATG
TTTCCACATTAGATGAGACTCGCGTTCTATGGAACATGAGGTCTTTAAACGCGTTTTGTAGGACA
CGACGTAGTCCTACGTGTACATTTTGAAAAAAAATCCAATTAAGATTGTAA
Found at i:764403 original size:20 final size:20
Alignment explanation
Indices: 764378--764431 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
764368 ATGCCACCTT
** *
764378 TATATTATTTAAATTTTTTA
1 TATATTATTTAAAAATTTAA
*
764398 TATATTTTTTAAAAATTTAA
1 TATATTATTTAAAAATTTAA
*
764418 AATATTATTTAAAA
1 TATATTATTTAAAA
764432 CAATATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTATTTAAAAATTTAA
Found at i:764613 original size:20 final size:20
Alignment explanation
Indices: 764588--764625 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
764578 ATTTGGGTAA
764588 TAGATTTAGAGATTTAAGTT
1 TAGATTTAGAGATTTAAGTT
*
764608 TAGATTTATAGATTTAAG
1 TAGATTTAGAGATTTAAG
764626 GGGATTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (20 bp):
TAGATTTAGAGATTTAAGTT
Found at i:770015 original size:43 final size:42
Alignment explanation
Indices: 769922--770017 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
769912 TTCCCCGAAA
**
769922 TTCCGTGTTTGTTTCATGTAATCTGTTTTTCGGAAAATGTTT
1 TTCCGTGTTTGTTTCACATAATCTGTTTTTCGGAAAATGTTT
*
769964 TTCCGTGTTTGTTTCACATAAT-TCGTTTTTTTGGAAAATG-TT
1 TTCCGTGTTTGTTTCACATAATCT-G-TTTTTCGGAAAATGTTT
770006 TTCCAGTGTTTG
1 TTCC-GTGTTTG
770018 ATTGGAGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.02
42 27 0.56
43 20 0.42
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (42 bp):
TTCCGTGTTTGTTTCACATAATCTGTTTTTCGGAAAATGTTT
Found at i:770275 original size:26 final size:26
Alignment explanation
Indices: 770222--770333 Score: 66
Period size: 23 Copynumber: 4.5 Consensus size: 26
770212 CAAAATATTA
*
770222 ATTATTAAAATATT-TAA-AATAT-AT
1 ATTATTAATAT-TTATAATAATATAAT
770246 -TTATTAATATTTATAATAATATAAT
1 ATTATTAATATTTATAATAATATAAT
*
770271 ATTATATTTTAATA-TTATAATAAAATAAT
1 A-T-TA--TTAATATTTATAATAATATAAT
*
770300 CA--ATT-ATA-TTATAATAATATAAG
1 -ATTATTAATATTTATAATAATATAAT
770323 A-TA-TAATATTT
1 ATTATTAATATTT
770334 TTATTTTAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
22 4 0.06
23 32 0.44
24 9 0.12
25 2 0.03
26 1 0.01
27 1 0.01
28 2 0.03
29 14 0.19
30 7 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATTATTAATATTTATAATAATATAAT
Done.