Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 90 of 276
Found at i:28178928 original size:32 final size:32
Alignment explanation
Indices: 28178855--28178931 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
28178845 GTAGCAGTAT
* * *
28178855 TATAATTGGCACAAAGCCATCAGTAACTATAA
1 TATAATCGGCACAAAGCCATCAGCAACGATAA
* *
28178887 TA-AGTTCGGCACATAGCCATCAGCAACGATAA
1 TATA-ATCGGCACAAAGCCATCAGCAACGATAA
28178919 TATAATCGGCACA
1 TATAATCGGCACA
28178932 CAACCATGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 1 0.03
32 35 0.95
33 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (32 bp):
TATAATCGGCACAAAGCCATCAGCAACGATAA
Found at i:28179055 original size:22 final size:22
Alignment explanation
Indices: 28179030--28179086 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
28179020 AATCAACATA
28179030 GCACAGAGCCATATTTAGGTTG
1 GCACAGAGCCATATTTAGGTTG
28179052 GCACAGAGCCATATTTAGGTTG
1 GCACAGAGCCATATTTAGGTTG
28179074 GCACAGAGCCATA
1 GCACAGAGCCATA
28179087 ATTTGATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (22 bp):
GCACAGAGCCATATTTAGGTTG
Found at i:28179471 original size:27 final size:27
Alignment explanation
Indices: 28179441--28179502 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28179431 CAAAATAGTC
* *
28179441 ATTTTACCCTACAACG-GTATTTCGATA
1 ATTTTACACTACAA-GAGTATTTCGACA
*
28179468 ATTTTACACTACAAGAGTATTTCGGCA
1 ATTTTACACTACAAGAGTATTTCGACA
28179495 ATTTTACA
1 ATTTTACA
28179503 AATTGAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
ATTTTACACTACAAGAGTATTTCGACA
Found at i:28179514 original size:27 final size:27
Alignment explanation
Indices: 28179484--28179692 Score: 237
Period size: 27 Copynumber: 7.8 Consensus size: 27
28179474 CACTACAAGA
* *
28179484 GTATTTCGGCAATTTTACAAATTGAGG
1 GTATTTCAGTAATTTTACAAATTGAGG
* *
28179511 GTATTTTAGTAATTTTATAAATTTG-GG
1 GTATTTCAGTAATTTTACAAA-TTGAGG
* * *
28179538 GTATTTCAATAATTTTACAAATCGGGG
1 GTATTTCAGTAATTTTACAAATTGAGG
** *
28179565 GTATTTTGGTAATTTTACAAATTAAGG
1 GTATTTCAGTAATTTTACAAATTGAGG
*
28179592 GTATTT-GGATAATTTTACAAATTGAGG
1 GTATTTCAG-TAATTTTACAAATTGAGG
* *
28179619 GTATTTTAGTAATTTTACAAA-TCAGG
1 GTATTTCAGTAATTTTACAAATTGAGG
*
28179645 GTATTTCAGTAATTTTATAAATT-AGGG
1 GTATTTCAGTAATTTTACAAATTGA-GG
28179672 GTATTTCAGTAATTTTACAAA
1 GTATTTCAGTAATTTTACAAA
28179693 CTGGAGTCTT
Statistics
Matches: 156, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.18
27 124 0.79
28 4 0.03
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATTGAGG
Found at i:28179579 original size:81 final size:79
Alignment explanation
Indices: 28179456--28179692 Score: 264
Period size: 81 Copynumber: 2.9 Consensus size: 79
28179446 ACCCTACAAC
* * * *
28179456 GGTATTTCGATAATTTTAC-ACTACAAGAGTATTTCGGCAATTTTACAAATTGAGGGTATTTTAG
1 GGTATTTCAATAATTTTACAAAT-C-AGGGTATTTCGGTAATTTTACAAATT-AGGGTATTTTAG
*
28179520 TAATTTTATAAATTTG-G
63 TAATTTTACAAA-TTGAG
* * *
28179537 GGTATTTCAATAATTTTACAAATCGGGGGTATTTTGGTAATTTTACAAATTAAGGGTA-TTTGGA
1 GGTATTTCAATAATTTTACAAATC-AGGGTATTTCGGTAATTTTACAAATT-AGGGTATTTTAG-
28179601 TAATTTTACAAATTGAG
63 TAATTTTACAAATTGAG
* * * * *
28179618 GGTATTTTAGTAATTTTACAAATCAGGGTATTTCAGTAATTTTATAAATTAGGGGTATTTCAGTA
1 GGTATTTCAATAATTTTACAAATCAGGGTATTTCGGTAATTTTACAAATTA-GGGTATTTTAGTA
28179683 ATTTTACAAA
65 ATTTTACAAA
28179693 CTGGAGTCTT
Statistics
Matches: 133, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 46 0.35
81 84 0.63
82 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (79 bp):
GGTATTTCAATAATTTTACAAATCAGGGTATTTCGGTAATTTTACAAATTAGGGTATTTTAGTAA
TTTTACAAATTGAG
Found at i:28186476 original size:16 final size:17
Alignment explanation
Indices: 28186440--28186476 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28186430 GTTATATTTA
*
28186440 ATTTTTGATATGTTTTT
1 ATTTTTGATATGTTTTC
28186457 ATTTTTGATATG-TTTC
1 ATTTTTGATATGTTTTC
28186473 ATTT
1 ATTT
28186477 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.68
Consensus pattern (17 bp):
ATTTTTGATATGTTTTC
Found at i:28186701 original size:14 final size:15
Alignment explanation
Indices: 28186682--28186711 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28186672 ATTTTAGTAT
28186682 ATTTTT-AAACTAAA
1 ATTTTTAAAACTAAA
28186696 ATTTTTAAAACTAAA
1 ATTTTTAAAACTAAA
28186711 A
1 A
28186712 ATAAAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTTAAAACTAAA
Found at i:28190671 original size:25 final size:26
Alignment explanation
Indices: 28190636--28190686 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
28190626 ATTGTAGAAT
28190636 AATTAAATTATTTGTTTCACTAATGA
1 AATTAAATTATTTGTTTCACTAATGA
28190662 AATT-AATTATTTGTTTCACTAATGA
1 AATTAAATTATTTGTTTCACTAATGA
28190687 TATTTTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (26 bp):
AATTAAATTATTTGTTTCACTAATGA
Found at i:28191510 original size:36 final size:36
Alignment explanation
Indices: 28191461--28191539 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
28191451 ATTCCAACTA
*
28191461 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
1 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
* * * *
28191497 AAACACACTAGATGCTCATACGAGCCAGTCCATTTG
1 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
28191533 ATAACAC
1 A-AACAC
28191540 CCAATAGCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 32 0.86
37 5 0.14
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (36 bp):
AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
Found at i:28198607 original size:40 final size:40
Alignment explanation
Indices: 28198555--28198826 Score: 454
Period size: 40 Copynumber: 6.8 Consensus size: 40
28198545 ATAACCACAA
* * * *
28198555 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28198595 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28198635 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28198675 GCACAAATGCCTTCGGGTCTTAGCCCAGATATATGTCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA--TCAACTC
28198717 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28198757 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28198797 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
28198827 GTATTCAAAT
Statistics
Matches: 219, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 180 0.82
42 39 0.18
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28198741 original size:122 final size:120
Alignment explanation
Indices: 28198555--28198822 Score: 455
Period size: 122 Copynumber: 2.2 Consensus size: 120
28198545 ATAACCACAA
* * * * *
28198555 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
28198620 CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
66 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28198675 GCACAAATGCCTTCGGGTCTTAGCCCAGATATATGTCAACTCGCACAAATGCCTTCGGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCAGATATA-G-CAACTCGCACAAATGCCTTCGGGTCTTAG
*
28198740 CCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
64 CCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28198797 GCACAAATGCCTTCGGGTCTTAGCCC
1 GCACAAATGCCTTCGGGTCTTAGCCC
28198823 GGATGTATTC
Statistics
Matches: 139, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 29 0.21
121 1 0.01
122 109 0.78
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (120 bp):
GCACAAATGCCTTCGGGTCTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28201696 original size:47 final size:47
Alignment explanation
Indices: 28201643--28202053 Score: 678
Period size: 47 Copynumber: 8.7 Consensus size: 47
28201633 CTTCCACTTC
* * * *
28201643 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
28201690 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28201737 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATT
28201786 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28201833 CATCACATTGGCCATTCGGCCTGATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28201880 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATT
* * * *
28201929 CATCACATTGGCCATTCGGCTTTATCATATATATATACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28201976 CATCACATTGGCCATTCGGCCTTATCACATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
28202023 CATCACATTGGCCATTCGGCCTTATCACATA
1 CATCACATTGGCCATTCGGCCTTATCACATA
28202054 TACATATCTT
Statistics
Matches: 341, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 251 0.74
49 90 0.26
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.33
Consensus pattern (47 bp):
CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
Found at i:28201805 original size:96 final size:96
Alignment explanation
Indices: 28201643--28202059 Score: 684
Period size: 96 Copynumber: 4.4 Consensus size: 96
28201633 CTTCCACTTC
* * *
28201643 CATCACATTGACCATTCGGCCTTAT--CATATATATATACTTTCACATTCATCACATTGGCCATT
1 CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATT
*
28201706 CGGCCTTATCACATACATACACTTTCACATT
66 CGGCCTTATCACATACATACACCTTCACATT
*
28201737 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATTCATCACATTGGCCATT
1 CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATT
*
28201802 CGGCCTTATCACATACATACACTTTCACATT
66 CGGCCTTATCACATACATACACCTTCACATT
*
28201833 CATCACATTGGCCATTCGGCCTGATCAC--ATACATACACTTTCACATTCATCACATTGGCCATT
1 CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATT
28201896 CGGCCTTATCACATATACATACACCTTCACATT
66 CGGCCTTATCAC--ATACATACACCTTCACATT
* * *
28201929 CATCACATTGGCCATTCGGCTTTAT--CATATATATATACTTTCACATTCATCACATTGGCCATT
1 CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATT
28201992 CGGCCTTATCACATACATACACCTTCACATT
66 CGGCCTTATCACATACATACACCTTCACATT
28202023 CATCACATTGGCCATTCGGCCTTATCACATATACATA
1 CATCACATTGGCCATTCGGCCTTATCACATATACATA
28202060 TCTTGTACAT
Statistics
Matches: 302, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
94 114 0.38
96 188 0.62
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (96 bp):
CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATT
CGGCCTTATCACATACATACACCTTCACATT
Found at i:28201901 original size:143 final size:143
Alignment explanation
Indices: 28201643--28202059 Score: 771
Period size: 143 Copynumber: 2.9 Consensus size: 143
28201633 CTTCCACTTC
*
28201643 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
28201708 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
28201773 ACACCTTCACATT
131 ACACCTTCACATT
* * *
28201786 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
*
28201851 GCCTGATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
28201916 ACACCTTCACATT
131 ACACCTTCACATT
*
28201929 CATCACATTGGCCATTCGGCTTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
*
28201994 GCCTTATCACATACATACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
28202059 A
131 A
28202060 TCTTGTACAT
Statistics
Matches: 263, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 263 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (143 bp):
CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
ACACCTTCACATT
Found at i:28206346 original size:27 final size:28
Alignment explanation
Indices: 28206262--28206359 Score: 144
Period size: 27 Copynumber: 3.5 Consensus size: 28
28206252 CATGAGATTG
* * *
28206262 GCACTAAGTGTGCGGGTTTAAATTGTATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
28206291 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28206319 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28206346 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28206360 GACTTAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 24 0.37
28 23 0.35
29 18 0.28
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28206370 original size:27 final size:27
Alignment explanation
Indices: 28206287--28206373 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 27
28206277 GTTTAAATTG
*
28206287 TATAGCACTAAGTGTGCGAGTTTGATTA
1 TATAGCACTAAGTGTGCGA-CTTGATTA
*
28206315 TATAGCACTAAGTGTGCGAGTTGATTA
1 TATAGCACTAAGTGTGCGACTTGATTA
* *
28206342 TATAGCACTGAGTGTGCGGACTTAATATA
1 TATAGCACTAAGTGTGC-GACTTGAT-TA
28206371 TAT
1 TAT
28206374 TTTTGAATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.43
28 25 0.47
29 5 0.09
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (27 bp):
TATAGCACTAAGTGTGCGACTTGATTA
Found at i:28210201 original size:15 final size:16
Alignment explanation
Indices: 28210181--28210218 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28210171 TAATTTGGTT
*
28210181 AATAAACAAAA-ATTA
1 AATAAACAAAAGATGA
28210196 AATAAA-AAAAGATGA
1 AATAAACAAAAGATGA
28210211 AATAAACA
1 AATAAACA
28210219 TCATCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AATAAACAAAAGATGA
Found at i:28211236 original size:25 final size:25
Alignment explanation
Indices: 28211190--28211259 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
28211180 GTGGATTCTC
* *
28211190 CATAGCTCATGTGACCAATTACAGT
1 CATAGCTCATGTGAACATTTACAGT
* * *
28211215 TATAGCTCGTGTGAACATTTACCGT
1 CATAGCTCATGTGAACATTTACAGT
* *
28211240 CAGAGCTCATGTGAGCATTT
1 CATAGCTCATGTGAACATTT
28211260 TCCTACATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (25 bp):
CATAGCTCATGTGAACATTTACAGT
Found at i:28213608 original size:23 final size:23
Alignment explanation
Indices: 28213565--28213608 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
28213555 AAAGGGTTTG
*
28213565 TATTATTTTAGTAAATTTTTTCA
1 TATTATTTTAGTAAATATTTTCA
*
28213588 TATTA-TTTGGTAAATAATTTT
1 TATTATTTTAGTAAAT-ATTTT
28213609 TTTTCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TATTATTTTAGTAAATATTTTCA
Found at i:28219157 original size:20 final size:20
Alignment explanation
Indices: 28219114--28219158 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28219104 TCATCTTTTG
* *
28219114 ATAAAAATACATAAGATTTA
1 ATAAAAATACATAAAAATTA
28219134 ATAAAAATACATACAAAATT-
1 ATAAAAATACATA-AAAATTA
28219154 ATAAA
1 ATAAA
28219159 TAAATGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAATACATAAAAATTA
Found at i:28220326 original size:19 final size:19
Alignment explanation
Indices: 28220279--28220315 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28220269 TTTCTAAAAG
* *
28220279 AATACCCAAATTTGTAACT
1 AATACCAAAACTTGTAACT
28220298 AATACCAAAACTTGTAAC
1 AATACCAAAACTTGTAAC
28220316 GTGATACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (19 bp):
AATACCAAAACTTGTAACT
Found at i:28220394 original size:18 final size:19
Alignment explanation
Indices: 28220373--28220412 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28220363 CAAAAATTGT
28220373 TAAT-GATAACAAAATTTC
1 TAATCGATAACAAAATTTC
* *
28220391 TAATCGATTACAATATTTC
1 TAATCGATAACAAAATTTC
28220410 TAA
1 TAA
28220413 CGTGATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATCGATAACAAAATTTC
Found at i:28222972 original size:48 final size:44
Alignment explanation
Indices: 28222808--28223170 Score: 248
Period size: 46 Copynumber: 7.8 Consensus size: 44
28222798 TAGGGTATAA
* * * ** *
28222808 TGCCAATGCCATGTCCCAAACATGGTCTTACACTGGCTTATCCATCA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGACACAT--ATCG
* * *
28222855 AGTCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCACATATCTG
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACT-G---ACACATATC-G
* *
28222905 TGCCGATGCCATGTTCCAGACATGGTCTTACACTGACAACTTTATACG
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGAC-AC-ATAT-CG
*
28222953 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCG
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGACACATATCG
* * *
28222998 TAGCCGATG-CATGTCCCAGACATATCTTACACTGGCTTACATCTCG
1 T-GCCGATGCCATGTCCCAGACATGTCTTACACTGAC--ACATATCG
* * * * * *
28223044 AGGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA
1 -TGCCGATGCCATGTCCCAGACATGTCTTACACT-G-ACACATATC-G
* *
28223091 TGCCGATGCTATGTCCCAGACATGGTCTTACACTGACTCTCATAAT-G
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGA--CACAT-ATCG
*
28223138 TGGCCGATG-CATGTCCCAAACATGTCTTACACT
1 T-GCCGATGCCATGTCCCAGACATGTCTTACACT
28223171 AGCACACAAA
Statistics
Matches: 261, Mismatches: 34, Indels: 43
0.77 0.10 0.13
Matches are distributed among these distances:
44 11 0.04
45 17 0.07
46 70 0.27
47 61 0.23
48 63 0.24
49 6 0.02
50 30 0.11
51 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (44 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACTGACACATATCG
Found at i:28223040 original size:46 final size:47
Alignment explanation
Indices: 28222858--28223170 Score: 274
Period size: 46 Copynumber: 6.6 Consensus size: 47
28222848 TCCATCAAGT
*
28222858 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCACATATCTGT-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGACTCT-ACATATC-GTAGC
* * **
28222908 CGATGCCATGTTCCAGACATGGTCTTACACTGACAACTTTATA-CGT-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGAC-TCTACATATCGTAGC
*
28222956 CGATGCCATGTCCCAGACATGGTCTTACACTGA--C-ACATCTCGTAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGACTCTACATATCGTAGC
* * *
28223002 CGATGCATGTCCCAGACATATCTTACACTGGCT-TACATCTCG-AGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGACTCTACATATCGTA-GC
* * *
28223048 CGATGCATGTCCCAGACATGTCTTACACT-AGCTCT-CGTCTC-AATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGA-CTCTACATATCGTA-GC
*
28223094 CGATGCTATGTCCCAGACATGGTCTTACACTGACTCT-CATAAT-GTGGC
1 CGATGC-ATGTCCCAGACAT-GTCTTACACTGACTCTACAT-ATCGTAGC
*
28223142 CGATGCATGTCCCAAACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
28223171 AGCACACAAA
Statistics
Matches: 227, Mismatches: 21, Indels: 34
0.80 0.07 0.12
Matches are distributed among these distances:
44 12 0.05
45 19 0.08
46 71 0.31
47 26 0.11
48 60 0.26
49 3 0.01
50 34 0.15
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACTCTACATATCGTAGC
Found at i:28223110 original size:138 final size:142
Alignment explanation
Indices: 28222802--28223170 Score: 407
Period size: 138 Copynumber: 2.6 Consensus size: 142
28222792 CAAACATAGG
* * * * * *
28222802 GTATAATGCCAATGCCATGTCCCAAACATGGTCTTACACTGGCTTATCCATC-AAGTCGATGCCA
1 GTATAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCAT-CATCGTAGCCGATG-CA
* *
28222866 TGTCCCAGACATAGTCTTACACTGGCTCTCACATATCTGTGCCGATGCCATGTTCCAGACATGGT
64 TGTCCCAGACATA-TCTTACACTGGCTCTCACATATCTGGGCCGATGCCATGTCCCAGACATGGT
28222931 CTTACACTGACAACT
128 CTTACACTGACAACT
* * *
28222946 TTATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATC-TCGTAGCCGATGCAT
1 GTATA-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCATCGTAGCCGATGCAT
*
28223010 GTCCCAGACATATCTTACACTGGCT-T-ACATCTC-GAGGCCGATG-CATGTCCCAGACAT-GTC
65 GTCCCAGACATATCTTACACTGGCTCTCACATATCTG-GGCCGATGCCATGTCCCAGACATGGTC
*
28223070 TTACACT-AGC-TCT
129 TTACACTGA-CAACT
* * * *
28223083 CGTCTCAATGCCGATGCTATGTCCCAGACATGGTCTTACACTGACTC-TCATAATGTGGCCGATG
1 -GTAT-AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCAT--CGTAGCCGATG
* *
28223147 CATGTCCCAAACATGTCTTACACT
62 CATGTCCCAGACATATCTTACACT
28223171 AGCACACAAA
Statistics
Matches: 194, Mismatches: 22, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
137 5 0.03
138 51 0.26
139 15 0.08
140 44 0.23
141 1 0.01
142 13 0.07
143 17 0.09
144 12 0.06
145 36 0.19
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (142 bp):
GTATAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCATCGTAGCCGATGCATG
TCCCAGACATATCTTACACTGGCTCTCACATATCTGGGCCGATGCCATGTCCCAGACATGGTCTT
ACACTGACAACT
Found at i:28223144 original size:94 final size:97
Alignment explanation
Indices: 28222806--28223173 Score: 313
Period size: 94 Copynumber: 3.9 Consensus size: 97
28222796 CATAGGGTAT
* * * * * *
28222806 AATGCCAATGCCATGTCCCAAACATGGTCTTACACTGGCTTATCCATCAA-GT--CGATGCCATG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACATCTACAT-AATGTGCCGATGCCATG
* *
28222868 TCCCAGACATAGTCTTACACTGGCTCTCACATATC
65 TCCCAGACATAGTCTTACACTAGCTCT--CATCTC
** * * ** *
28222903 TGTGCCGATGCCATGTTCCAGACATGGTCTTACACTGACAACTTTAT-ACGTGCCGATGCCATGT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACATCTACATAATGTGCCGATGCCATGT
* * *
28222967 CCCAGACATGGTCTTACACT-G-ACACATCTC
66 CCCAGACATAGTCTTACACTAGCTCTCATCTC
* * * * *
28222997 -GTAGCCGATG-CATGTCCCAGACAT-ATCTTACACTGGC-T-TACAT-CTCGAGGCCGATG-CA
1 AAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATCTACATAAT-G-TGCCGATGCCA
*
28223055 TGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTC
63 TGTCCCAGACATAGTCTTACACTAGCTCTCATCTC
*
28223089 AATGCCGATGCTATGTCCCAGACATGGTCTTACACTGAC-TCT-CATAATGTGGCCGATG-CATG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACATCTACATAATGT-GCCGATGCCATG
*
28223151 TCCCAAACAT-GTCTTACACTAGC
65 TCCCAGACATAGTCTTACACTAGC
28223174 ACACAAATAA
Statistics
Matches: 223, Mismatches: 34, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
90 13 0.06
91 16 0.07
92 31 0.14
93 29 0.13
94 61 0.27
95 3 0.01
96 3 0.01
97 37 0.17
98 30 0.13
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (97 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACATCTACATAATGTGCCGATGCCATGT
CCCAGACATAGTCTTACACTAGCTCTCATCTC
Found at i:28227576 original size:32 final size:32
Alignment explanation
Indices: 28227530--28227596 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
28227520 CGGTTCCCAT
28227530 TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
1 TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
28227562 TATATCTT-TCGGTTCCCATGTTGCTTCTTCAA
1 TATATCTTCT-GGTTCCCATGTTGCTTCTTCAA
28227594 TAT
1 TAT
28227597 TGTGACTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.48
Consensus pattern (32 bp):
TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
Found at i:28231970 original size:46 final size:44
Alignment explanation
Indices: 28231915--28232135 Score: 162
Period size: 46 Copynumber: 4.8 Consensus size: 44
28231905 ATTCGTGTGT
*
28231915 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGTC-ACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CGACA-TA-GA
*
28231961 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-A-TTGAGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCGACAT-AGA
* * * *
28232006 CGAGGACTAGTGTAAGACATGTCTGGGACGTGCATCGGCCTCGAGACAGA
1 -GA-G-CCAGTGTAAGACATGTCTGGGACATGCATCGG---CGACATAGA
* * *
28232056 -AGCCAGTGTAAGACATGTCTGGAACATGCATCGGCTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCGAC-ATA-GA
* * *
28232101 TAGCCAATGTAAGACCATGTCTGAGACATGGCATC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
28232136 AACTTGAGAT
Statistics
Matches: 144, Mismatches: 15, Indels: 30
0.76 0.08 0.16
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 5 0.03
46 64 0.44
47 43 0.30
48 23 0.16
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCGACATAGA
Found at i:28232145 original size:47 final size:48
Alignment explanation
Indices: 28231961--28232182 Score: 135
Period size: 47 Copynumber: 4.7 Consensus size: 48
28231951 CACATTATGA
* ** * * *
28231961 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACGAG
1 GAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAACTA-CGAGA-TAT
* * * ** *
28232010 GA-CTAGTGTAAGA-CATGTCTGGGACGT-GCATCGGCCT-CGAGACA-
1 GAGCCAGTGTAAGACCATGTCTGAGACATGGCATC-AACTACGAGATAT
**
28232054 GAAGCCAGTGTAAGA-CATGTCTG-GAACAT-GCATCGGCTACGAGATGAT
1 G-AGCCAGTGTAAGACCATGTCTGAG-ACATGGCATCAACTACGAGAT-AT
* *
28232102 -AGCCAATGTAAGACCATGTCTGAGACATGGCATCAACT-TGAGATAT
1 GAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAACTACGAGATAT
* *
28232148 GAGCTAGTGTAAGACCGTGTCT-AGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGA-GACATGGCATC
28232183 GGCACCTTAC
Statistics
Matches: 144, Mismatches: 16, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
44 1 0.01
45 6 0.04
46 55 0.38
47 62 0.43
48 18 0.12
49 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAACTACGAGATAT
Found at i:28234895 original size:49 final size:51
Alignment explanation
Indices: 28234827--28234969 Score: 186
Period size: 49 Copynumber: 2.8 Consensus size: 51
28234817 TGTAGACAAG
* *
28234827 GTTATCTGGTACGCATAGTAGCCTGCGCTTAGTACTACACATGTGAAC-AA
1 GTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
* * *
28234877 -TTATTC-GGTACAG-GTAGTAGCCTGCACTTAGTACTACACACGTGACCGAA
1 GTTA-TCGGGTAC-GCATAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
*
28234927 GTTATCGGGTACGCATAGTAGCTTGCACTTAGTACTACACATG
1 GTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATG
28234970 CAACCTCACA
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
49 38 0.47
50 8 0.10
51 34 0.43
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (51 bp):
GTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
Found at i:28235251 original size:27 final size:27
Alignment explanation
Indices: 28235221--28235274 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28235211 TCATACAACC
*
28235221 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
**
28235248 CATGTAATAATAATTTGCCATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
28235275 TCACATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (27 bp):
CATGTAATAATAATTTAACATTCAATT
Found at i:28238782 original size:30 final size:30
Alignment explanation
Indices: 28238737--28238795 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28238727 TCCTGAGCCC
28238737 AGGGGAAAAAGTGTAATTATGCAAAAGTTT
1 AGGGGAAAAAGTGTAATTATGCAAAAGTTT
* *
28238767 AGGGGCAAAAA-TGTAATTTTGCCAAAGTT
1 AGGGG-AAAAAGTGTAATTATGCAAAAGTT
28238796 CATATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (30 bp):
AGGGGAAAAAGTGTAATTATGCAAAAGTTT
Found at i:28241398 original size:24 final size:23
Alignment explanation
Indices: 28241354--28241398 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
28241344 TTTATCAGTG
28241354 AAAGATTTATTGATTAGAAGCGT
1 AAAGATTTATTGATTAGAAGCGT
*
28241377 AAAGAGTTTCTTGAATTA-AAGC
1 AAAGA-TTTATTG-ATTAGAAGC
28241399 AGGGGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
AAAGATTTATTGATTAGAAGCGT
Found at i:28241953 original size:21 final size:21
Alignment explanation
Indices: 28241927--28241972 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
28241917 GAGAGTTGAG
*
28241927 AAAGAAAAATTTTAGAATGTA
1 AAAGAAAAATTTCAGAATGTA
28241948 AAAGAAAAATTTCAGAATGTA
1 AAAGAAAAATTTCAGAATGTA
28241969 AAAG
1 AAAG
28241973 CTAGTGGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (21 bp):
AAAGAAAAATTTCAGAATGTA
Found at i:28246345 original size:30 final size:30
Alignment explanation
Indices: 28246309--28246366 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28246299 CCCGAGCCTA
*
28246309 GGGGCAAAAGTGTAATTATGCAAAAGTTTC
1 GGGGCAAAAATGTAATTATGCAAAAGTTTC
* *
28246339 GGGGCAAAAATGTAATTTTGCCAAAGTT
1 GGGGCAAAAATGTAATTATGCAAAAGTT
28246367 CGTATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGCAAAAGTTTC
Found at i:28249624 original size:18 final size:18
Alignment explanation
Indices: 28249601--28249637 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28249591 CATAACCAAA
28249601 ATATGCATACTCCATTCT
1 ATATGCATACTCCATTCT
* *
28249619 ATATGCGTACTCTATTCT
1 ATATGCATACTCCATTCT
28249637 A
1 A
28249638 ACTTTAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATGCATACTCCATTCT
Found at i:28252225 original size:22 final size:22
Alignment explanation
Indices: 28252184--28252225 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28252174 AACAACATGG
*
28252184 AGGCCCAAAATTATTTCATTGA
1 AGGCCCAAAATTATTCCATTGA
*
28252206 AGGCCCAAAATTGTTCCATT
1 AGGCCCAAAATTATTCCATT
28252226 TACCGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGCCCAAAATTATTCCATTGA
Found at i:28257024 original size:179 final size:178
Alignment explanation
Indices: 28256719--28257078 Score: 562
Period size: 179 Copynumber: 2.0 Consensus size: 178
28256709 TCAATTTGTG
* *
28256719 TTAAAGAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGTTGATTCTAACTAGGATGGT
1 TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGTTGATTCTAACTAGGATAGT
*
28256784 TAAGGTTGAAGGATTTGTATTGACTATTGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
66 TAAGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
* * *
28256849 GTTGCCATTTTTGGATCAAATTTTAGATAGACTTTTAGGACACAATTA
131 GTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
* * *
28256897 TTAAAAAAGGGAGGTGTTATAGTTGTAATGAATGAGAATAATGAGTTGATTAC-AACTAGGATAG
1 TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGTTGATT-CTAACTAGGATAG
* * *
28256961 TTACATGTTGAAGGATTTGTATTTATTATCGTAAGTTATATAAGGCAACTCA-AAATGATCATTT
65 TTA-AGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAA-GATCATTT
*
28257025 TTTGTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
128 TTCGTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
28257076 TTA
1 TTA
28257079 CTATTTCCTA
Statistics
Matches: 166, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
178 63 0.38
179 103 0.62
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (178 bp):
TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGTTGATTCTAACTAGGATAGT
TAAGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
GTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
Found at i:28267545 original size:17 final size:18
Alignment explanation
Indices: 28267523--28267557 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28267513 ATGTGGGCTG
*
28267523 TGTGGG-CCACATGGGCA
1 TGTGGGCCCACAAGGGCA
28267540 TGTGGGCCCACAAGGGCA
1 TGTGGGCCCACAAGGGCA
28267558 GGCCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (18 bp):
TGTGGGCCCACAAGGGCA
Found at i:28276895 original size:28 final size:28
Alignment explanation
Indices: 28276860--28276915 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28276850 CACGGGTTGA
28276860 GACACGGGCG-TGTCGAGGCCGTGTGAGG
1 GACACGGGCGATGTCGA-GCCGTGTGAGG
*
28276888 GACACGGGCGTATGTCTAGCCGTGTGAG
1 GACACGGGCG-ATGTCGAGCCGTGTGAG
28276916 AACCCCTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 10 0.40
30 5 0.20
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (28 bp):
GACACGGGCGATGTCGAGCCGTGTGAGG
Found at i:28282236 original size:40 final size:39
Alignment explanation
Indices: 28282177--28282300 Score: 113
Period size: 40 Copynumber: 3.1 Consensus size: 39
28282167 GCGTTTGGAT
* * * *
28282177 AAAAAAGCCGCTATTGATCGAGCATTAGTAGCGCTTTTTG
1 AAAAACGCCACTATAGATCGAACATTAGT-GCGCTTTTTG
* * * *
28282217 AGAAACGCCACTGTAGATCGAACATTAGCGGCGCTTTTTA
1 AAAAACGCCACTATAGATCGAACATTAG-TGCGCTTTTTG
* * * *
28282257 AAAAATGCCGCTATAGGTCGATCATTAGCTGCGCTTTTTG
1 AAAAACGCCACTATAGATCGAACATTAG-TGCGCTTTTTG
28282297 AAAA
1 AAAA
28282301 TGCCGAAAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (39 bp):
AAAAACGCCACTATAGATCGAACATTAGTGCGCTTTTTG
Found at i:28282405 original size:40 final size:40
Alignment explanation
Indices: 28282350--28282493 Score: 191
Period size: 40 Copynumber: 3.6 Consensus size: 40
28282340 AGCTTTAGTG
*
28282350 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
*
28282390 GCATTAGCAGCGCTTTTTG-AAAACGCCACTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * ** *
28282429 GCGTTAGCGGCGCTTTTTAAAAAAAACCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * *
28282469 GCTTTAGCGGCGCTTTATCAAAAAC
1 GCATTAGCGGCGCTTTTTGAAAAAC
28282494 ACCGCAATAA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 35 0.38
40 56 0.62
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
Found at i:28282820 original size:7 final size:7
Alignment explanation
Indices: 28282804--28282974 Score: 63
Period size: 7 Copynumber: 24.1 Consensus size: 7
28282794 TATCATTTTA
*
28282804 GTTTAGG
1 GTTTATG
28282811 GTTTATG
1 GTTTATG
*
28282818 GTTTAGG
1 GTTTATG
* *
28282825 GTATGTG
1 GTTTATG
*
28282832 GTTTAAG
1 GTTTATG
**
28282839 GTTTAAA
1 GTTTATG
*
28282846 GTTTAAG
1 GTTTATG
* *
28282853 AGTTAATA
1 -GTTTATG
* *
28282861 TTTTAAG
1 GTTTATG
*
28282868 GTTTAGG
1 GTTTATG
*
28282875 GATTATGG
1 GTTTAT-G
*
28282883 GTTTAGG
1 GTTTATG
*
28282890 GATTATG
1 GTTTATG
28282897 GTTTATG
1 GTTTATG
* *
28282904 TTTTAAG
1 GTTTATG
* **
28282911 GGTTGGG
1 GTTTATG
*
28282918 GTTTAAG
1 GTTTATG
*
28282925 GTTTAGG
1 GTTTATG
* *
28282932 GGTTAGG
1 GTTTATG
*
28282939 GTTTAGG
1 GTTTATG
28282946 GTTTATG
1 GTTTATG
*
28282953 TTTTATG
1 GTTTATG
* *
28282960 ATTTACG
1 GTTTATG
28282967 GTTTATG
1 GTTTATG
28282974 G
1 G
28282975 GGATAAGGGT
Statistics
Matches: 118, Mismatches: 44, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
7 109 0.92
8 9 0.08
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.46
Consensus pattern (7 bp):
GTTTATG
Found at i:28282823 original size:14 final size:14
Alignment explanation
Indices: 28282804--28282974 Score: 74
Period size: 14 Copynumber: 12.1 Consensus size: 14
28282794 TATCATTTTA
28282804 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
* *
28282818 GTTTAGGGTATGTG
1 GTTTAGGGTTTATG
* **
28282832 GTTTAAGGTTTAAA
1 GTTTAGGGTTTATG
* * *
28282846 GTTTAAGAGTTAATA
1 GTTT-AGGGTTTATG
* * *
28282861 TTTTAAGGTTTAGG
1 GTTTAGGGTTTATG
* *
28282875 GATTATGGGTTTAGG
1 GTTTA-GGGTTTATG
* *
28282890 GATTATGGTTTATG
1 GTTTAGGGTTTATG
* **
28282904 TTTTAAGGG-TTGGG
1 GTTT-AGGGTTTATG
* *
28282918 GTTTAAGGTTTAGG
1 GTTTAGGGTTTATG
* *
28282932 GGTTAGGGTTTAGG
1 GTTTAGGGTTTATG
* *
28282946 GTTTATGTTTTATG
1 GTTTAGGGTTTATG
* *
28282960 ATTTACGGTTTATG
1 GTTTAGGGTTTATG
28282974 G
1 G
28282975 GGATAAGGGT
Statistics
Matches: 113, Mismatches: 40, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
13 3 0.03
14 85 0.75
15 25 0.22
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28282920 original size:21 final size:21
Alignment explanation
Indices: 28282862--28282950 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 21
28282852 GAGTTAATAT
* * *
28282862 TTTAAGGTTTAGGGATTATGGG
1 TTTAAGGGTTAGGGTTTA-AGG
* * * * *
28282884 TTTAGGGATTATGGTTTATGT
1 TTTAAGGGTTAGGGTTTAAGG
*
28282905 TTTAAGGGTTGGGGTTTAAGG
1 TTTAAGGGTTAGGGTTTAAGG
* *
28282926 TTTAGGGGTTAGGGTTTAGGG
1 TTTAAGGGTTAGGGTTTAAGG
28282947 TTTA
1 TTTA
28282951 TGTTTTATGA
Statistics
Matches: 52, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
21 38 0.73
22 14 0.27
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (21 bp):
TTTAAGGGTTAGGGTTTAAGG
Found at i:28283407 original size:21 final size:21
Alignment explanation
Indices: 28283361--28283407 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
28283351 TTAAGGTGTA
28283361 GTTTATGGTCTAGGATTTTAG
1 GTTTATGGTCTAGGATTTTAG
*
28283382 ATTTATGGTCTAGGA-TTTAGG
1 GTTTATGGTCTAGGATTTTA-G
28283403 GTTTA
1 GTTTA
28283408 GTGTTTGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (21 bp):
GTTTATGGTCTAGGATTTTAG
Found at i:28283441 original size:21 final size:21
Alignment explanation
Indices: 28283392--28283445 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
28283382 ATTTATGGTC
* *
28283392 TAGGATTTAGGGTTTAGTGTT
1 TAGGGTTTAGGGTTTAATGTT
* *
28283413 TGGGGTTTAGGGTTTAATTTT
1 TAGGGTTTAGGGTTTAATGTT
*
28283434 TAGTGTTTAGGG
1 TAGGGTTTAGGG
28283446 GTAAATACGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (21 bp):
TAGGGTTTAGGGTTTAATGTT
Found at i:28289581 original size:43 final size:42
Alignment explanation
Indices: 28289500--28289644 Score: 175
Period size: 43 Copynumber: 3.4 Consensus size: 42
28289490 TTAGTTTTTT
* *
28289500 TAAAGGTCATATTCTTTAGCGGCATTTGAGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCATTTG-GAGAAAAGCGCCGC
* * * *
28289543 TAAAGGTCATGTTCTTTAACGACGTTTGTGAGAGAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCATTTG-GAGAAAAGCGCCGC
* *
28289586 TAAAGGTCATGGTT-TTTAGCGGCATTTGCAGGAAAAGCGCTGC
1 TAAAGGTCAT-GTTCTTTAGCGGCATTTGGA-GAAAAGCGCCGC
28289629 TAAAGGTCATGTTCTT
1 TAAAGGTCATGTTCTT
28289645 GCGGGAAAAG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 4 0.05
43 79 0.92
44 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
TAAAGGTCATGTTCTTTAGCGGCATTTGGAGAAAAGCGCCGC
Found at i:28289665 original size:32 final size:32
Alignment explanation
Indices: 28289611--28289676 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
28289601 TTAGCGGCAT
28289611 TTGCAGGAAAAGCGCTGCTAAAGGTCATGTTC
1 TTGCAGGAAAAGCGCTGCTAAAGGTCATGTTC
* *
28289643 TTGCGGGAAAAGCG-TCGTTAAAGGTCATGTTC
1 TTGCAGGAAAAGCGCT-GCTAAAGGTCATGTTC
28289675 TT
1 TT
28289677 TAGCAGCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (32 bp):
TTGCAGGAAAAGCGCTGCTAAAGGTCATGTTC
Found at i:28291019 original size:94 final size:92
Alignment explanation
Indices: 28290900--28291070 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 92
28290890 TCATTTGTGC
28290900 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AT-TATGAGAACCAATGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATAT-A-AACCAATGTAAGA-CATG
28290963 TCTGGGACATGGCATCAACATTGAGACGAGA
63 TCTGGGACAT-GCATCAACATTGAGACGAGA
* * * *
28290994 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATATATAAGCCAGTGTAAGACATGTTT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATATAAACCAATGTAAGACATGTCT
28291059 GGGACATGCATC
66 GGGACATGCATC
28291071 GGCTACGAGA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
92 5 0.07
93 13 0.18
94 47 0.66
95 3 0.04
96 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATATAAACCAATGTAAGACATGTCT
GGGACATGCATCAACATTGAGACGAGA
Found at i:28291050 original size:46 final size:46
Alignment explanation
Indices: 28290903--28291116 Score: 179
Period size: 46 Copynumber: 4.6 Consensus size: 46
28290893 TTTGTGCGCT
* * *
28290903 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTATGAGAACC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-A-AGCC
* ** * * * * *
28290949 AATGTAAGACCATGTCTGGGACATGGCATCAACATTGAGACGA-GAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGA-TATAAGCC
*
28290997 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATATATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAGCC
* * *
28291043 AGTGTAAGACATGTTTGGGACATGCATCGG-CTACGAGATGT--GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATATAAGCC
28291087 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
28291117 TGTAATAGTC
Statistics
Matches: 134, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
44 11 0.08
45 16 0.12
46 61 0.46
47 28 0.21
48 16 0.12
49 1 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAGCC
Found at i:28293036 original size:46 final size:45
Alignment explanation
Indices: 28292968--28293104 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 45
28292958 TATATATACA
* * *
28292968 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACAT-TCGCATTAGCCATTCGGCTTTACCACATATC
*
28293014 CATCTCATACACGATTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACAC-ATTCGCATTAGCCATTCGGCTTTACCACATATC
* *
28293060 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACA-TTCGCATTAGCCATTCGGCTTTACCACATAT
28293105 ATACATGTTC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 79 0.96
47 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (45 bp):
CATCTCATACACATTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:28293139 original size:47 final size:47
Alignment explanation
Indices: 28293078--28293363 Score: 394
Period size: 47 Copynumber: 6.0 Consensus size: 47
28293068 ACACATTTCG
* * **
28293078 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* *
28293125 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* *
28293172 CATTGGCCATTCAGCCTTATCA-TTCATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACAT-ATACGCATGTTCACATTCATCA
*
28293219 CATTGGCCATTCGGCCTTATCTCATATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* ** *
28293266 CATTGGCCATTCGGCTTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ATATACGCATGTTCACATTCATCA
*
28293317 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
28293364 TATAAAATCC
Statistics
Matches: 212, Mismatches: 21, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
46 1 0.00
47 166 0.78
48 1 0.00
49 2 0.01
51 42 0.20
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
Found at i:28293398 original size:145 final size:141
Alignment explanation
Indices: 28293108--28293368 Score: 324
Period size: 145 Copynumber: 1.8 Consensus size: 141
28293098 CACATATATA
* * *
28293108 CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCAC
1 CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCGCATATATACAGGTTCACATTCATCAC
** ** *** ***
28293173 ATTGGCCATTCAGCCTTATCATTCATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
66 ATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAAGCCATAAAGCAAAA
* *
28293238 TCTCATATACG
131 TATCAAATACG
*
28293249 CATGTTCACATTCATCACATTGGCCATTCGGCTTTATCACGCATATATATACAGGTTCACATTCA
1 CATGTTCACATTCATCACATTGGCCATTCGGCCTTAT--CGC--ATATATACAGGTTCACATTCA
* *
28293314 TCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCATATAA
62 TCACATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAA
28293369 AATCCTAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
141 36 0.34
143 2 0.02
145 68 0.64
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (141 bp):
CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCGCATATATACAGGTTCACATTCATCAC
ATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAAGCCATAAAGCAAAA
TATCAAATACG
Found at i:28304203 original size:85 final size:85
Alignment explanation
Indices: 28304045--28304207 Score: 195
Period size: 85 Copynumber: 1.9 Consensus size: 85
28304035 GTCTGAGACA
* * * * **
28304045 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCAGGA
*
28304110 CATCGGCATTGTATCTGATT
66 CATAGGCATTGTATCTGATT
* * *
28304130 TCGTGTAAGACCCTGTTTGGGACAGAGGCATCGATATTGA-A-TTACATGTAAGACCACGTCCAG
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCG--ATTGAGATTTACATATAAGACCACGTCCAG
*
28304193 GACGTAGGCATTGTA
64 GACATAGGCATTGTA
28304208 CTTGTTTATG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 59 0.91
86 1 0.02
87 5 0.08
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (85 bp):
TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCAGGA
CATAGGCATTGTATCTGATT
Found at i:28306489 original size:49 final size:49
Alignment explanation
Indices: 28306107--28306481 Score: 480
Period size: 49 Copynumber: 7.5 Consensus size: 49
28306097 TGAGGTCACG
* *
28306107 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * *
28306156 TGTGTAGTATTAAGTGCAGGCTACTATGTGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
* *
28306207 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * *
28306256 TGTGTAGTATTAAGTGCAGGCTACTATGTGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
* *
28306307 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * *
28306356 TGTGTAGTATTAAGTGCAGGCTACTATGTGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
28306407 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
28306456 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28306482 TGCGTACCAG
Statistics
Matches: 274, Mismatches: 46, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
49 144 0.53
50 12 0.04
51 118 0.43
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:28306527 original size:100 final size:100
Alignment explanation
Indices: 28306102--28306494 Score: 741
Period size: 100 Copynumber: 3.9 Consensus size: 100
28306092 TATTGTGAGG
28306102 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
28306167 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
28306202 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
28306267 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
28306302 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
28306367 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
* * *
28306402 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
* *
28306467 AAGTGCAGGCTACTATGCGTACCAGATA
66 AAGTGCAGGCTACTATGTGTACCCGATA
28306495 GTTTTGGCTA
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 288 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGTATGTGTAGTATT
AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
Found at i:28308569 original size:21 final size:21
Alignment explanation
Indices: 28308545--28308603 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
28308535 AATAGCGGTG
**
28308545 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGAAACTGTA
28308566 GCGGTGAGATTAGAAACTGTA
1 GCGGTGAGATTAGAAACTGTA
28308587 GCGGTGAGATTAGAAAC
1 GCGGTGAGATTAGAAAC
28308604 AATGGTGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.34, T:0.25
Consensus pattern (21 bp):
GCGGTGAGATTAGAAACTGTA
Found at i:28308880 original size:19 final size:19
Alignment explanation
Indices: 28308858--28308896 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28308848 TAAAATGATA
28308858 ATTATTTTAAATTTTTTAT
1 ATTATTTTAAATTTTTTAT
28308877 ATTATTTTAAATTTTTTAT
1 ATTATTTTAAATTTTTTAT
28308896 A
1 A
28308897 GTTAAATATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTTTAAATTTTTTAT
Found at i:28308893 original size:9 final size:10
Alignment explanation
Indices: 28308857--28308894 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
28308847 ATAAAATGAT
28308857 AATTATTTTA
1 AATTATTTTA
28308867 AATT-TTTTA
1 AATTATTTTA
*
28308876 TATTATTTTA
1 AATTATTTTA
28308886 AATT-TTTTA
1 AATTATTTTA
28308895 TAGTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTATTTTA
Found at i:28312889 original size:33 final size:33
Alignment explanation
Indices: 28312840--28312919 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
28312830 CCCTAAATCA
28312840 TGTTT-TC-ATCAA-AAATCACTTTGTAAAAGT
1 TGTTTATCTATCAATAAATCACTTTGTAAAAGT
28312870 TGTTTATCTATCAATAAATCACTTTGTAAAAGT
1 TGTTTATCTATCAATAAATCACTTTGTAAAAGT
28312903 TGTTTATCTATCAATAA
1 TGTTTATCTATCAATAA
28312920 TCTTTCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
30 5 0.11
31 2 0.04
32 5 0.11
33 35 0.74
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (33 bp):
TGTTTATCTATCAATAAATCACTTTGTAAAAGT
Found at i:28329741 original size:342 final size:343
Alignment explanation
Indices: 28328786--28329815 Score: 1882
Period size: 343 Copynumber: 3.0 Consensus size: 343
28328776 TGAAACCCAG
*
28328786 AAATGTGACAATGATTTGTAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
* *
28328851 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCGAAAAATGATGAACTTA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
* * *
28328916 TTCAGAAAATTCTTCATGAAGCATATAATGGTTATTTATCTATACATCCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
* *
28328981 TATAATGACTTGAAGAAAATGTATTGGTAGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
* * *
28329046 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTAACTTTGGGTTTACTTCAGCCAC
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
28329111 TGATGGTACCCGAGTGGA
326 TGATGGTACCCGAGTGGA
*
28329129 AAATTTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
*
28329194 TGTCGGATTCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
28329259 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
28329324 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
* *
28329389 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCGAGTACCTTCGGGTTTACTTCAGCTAG
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
*
28329454 TGATGGTACCCGAGTAGA
326 TGATGGTACCCGAGTGGA
28329472 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
* * *
28329537 TGTCGGATCCGTTGATTGTTTGAT-ATTTGAGGTAGAATTTATGTACCAAAAAATGATGAACTCA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
28329601 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
28329666 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
28329731 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
28329796 TGATGGTACCCGAGTGGA
326 TGATGGTACCCGAGTGGA
28329814 AA
1 AA
28329816 TGGGATAGGA
Statistics
Matches: 663, Mismatches: 24, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
342 250 0.38
343 413 0.62
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (343 bp):
AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATCCGGGTAGTACAAAAATG
TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
TGATGGTACCCGAGTGGA
Found at i:28335327 original size:43 final size:42
Alignment explanation
Indices: 28335230--28335351 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 42
28335220 TAGGGTTAGT
*
28335230 TGAGATTACC-TGTAACACCATATCTGGGATATGGCATCGATA
1 TGAGATT-CCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
28335272 TGAGACTT-CGTGTAAGACCATAGCTGGGCTATTTGCATCGATA
1 TGAGA-TTCCGTGTAAGACCATATCTGGGATA-TGGCATCGATA
28335315 TGAGATTCCGTGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTCCGTGTAAGACCATATCTGGGATATGGCAT
28335352 TGGTATGGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 1 0.01
42 30 0.43
43 38 0.55
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
TGAGATTCCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:28335462 original size:20 final size:20
Alignment explanation
Indices: 28335434--28335480 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28335424 TGGCAATGTT
28335434 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
28335454 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
28335474 TAAGTTG
1 TAAGTTG
28335481 CAAGTTGATA
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:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:28341427 original size:28 final size:28
Alignment explanation
Indices: 28341364--28341489 Score: 209
Period size: 28 Copynumber: 4.5 Consensus size: 28
28341354 ATATTAAGTC
* *
28341364 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28341391 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28341419 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
28341447 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28341475 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28341490 GTACAATTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.23
28 72 0.77
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:28344406 original size:24 final size:25
Alignment explanation
Indices: 28344372--28344504 Score: 109
Period size: 24 Copynumber: 5.5 Consensus size: 25
28344362 TCCCAGCTAT
*
28344372 ATAAT-GGGAAGCTCA-TAAGAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
* *
28344395 ATAATCGGGAAGTTCACAAAGAACC
1 ATAATCGGGAAGCTCACAAAGAGCC
* *
28344420 AT-ATCGGGAAGGTCACAAAAAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
*
28344444 -T-ATCAGGAAGCTCACAAAGAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
* * *
28344467 ATGTAA-GGGGAAGCTC-CGAATAGCC
1 A--TAATCGGGAAGCTCACAAAGAGCC
28344492 ATATATCGGGAAG
1 ATA-ATCGGGAAG
28344505 TTCAAGCGAG
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
23 27 0.31
24 29 0.33
25 22 0.25
26 9 0.10
27 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (25 bp):
ATAATCGGGAAGCTCACAAAGAGCC
Found at i:28347737 original size:9 final size:9
Alignment explanation
Indices: 28347705--28347731 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28347695 GTCCGTCTAA
28347705 GTATGAAAT
1 GTATGAAAT
28347714 GTATGAAAT
1 GTATGAAAT
28347723 GTATGAAAT
1 GTATGAAAT
28347732 TAATGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (9 bp):
GTATGAAAT
Found at i:28348610 original size:25 final size:25
Alignment explanation
Indices: 28348582--28348631 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28348572 ATAAACAAGA
28348582 TTGGTAAGTTTAGTTTCTGTTATAC
1 TTGGTAAGTTTAGTTTCTGTTATAC
28348607 TTGGTAAGTTTAGTTTCTGTTATAC
1 TTGGTAAGTTTAGTTTCTGTTATAC
28348632 GAACTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (25 bp):
TTGGTAAGTTTAGTTTCTGTTATAC
Found at i:28352172 original size:30 final size:30
Alignment explanation
Indices: 28352138--28352200 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
28352128 ATGATATGTG
28352138 ATTGCCAAATGTGATTGTTAAGTGAATAAT
1 ATTGCCAAATGTGATTGTTAAGTGAATAAT
28352168 ATTGCCAAATGTGATTGTTAAGTGAATAAT
1 ATTGCCAAATGTGATTGTTAAGTGAATAAT
28352198 ATT
1 ATT
28352201 AGTTAAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (30 bp):
ATTGCCAAATGTGATTGTTAAGTGAATAAT
Found at i:28353193 original size:48 final size:48
Alignment explanation
Indices: 28353122--28353325 Score: 318
Period size: 48 Copynumber: 4.2 Consensus size: 48
28353112 CAAGATAAAT
* * *
28353122 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
28353170 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
28353218 ATAAATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 AT--ATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
28353268 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
28353316 ATGTGTATAT
1 ATATGTATAT
28353326 ATTGTGGCCG
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
48 98 0.69
50 44 0.31
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:28353327 original size:98 final size:98
Alignment explanation
Indices: 28353124--28353317 Score: 343
Period size: 98 Copynumber: 2.0 Consensus size: 98
28353114 AGATAAATAT
* *
28353124 ATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
28353189 CCGAATGGCTAACATGAAATATGTATGAGATAA
66 CCGAATGGCTAACATGAAATATGTATGAGATAA
*
28353222 ATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
**
28353287 CCGAATGGCTAATGTGAAATATGTATGAGAT
66 CCGAATGGCTAACATGAAATATGTATGAGAT
28353318 GTGTATATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.31
Consensus pattern (98 bp):
ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
CCGAATGGCTAACATGAAATATGTATGAGATAA
Found at i:28353550 original size:36 final size:37
Alignment explanation
Indices: 28353458--28353566 Score: 184
Period size: 37 Copynumber: 3.0 Consensus size: 37
28353448 GGAAATATAT
28353458 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
28353495 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28353532 TCCGGGT-AGACCCGATGACTACGTGTGGGGATTAT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
28353567 TCGAGCTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 26 0.39
37 41 0.61
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28360475 original size:15 final size:15
Alignment explanation
Indices: 28360455--28360484 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28360445 ATTTATTTGC
28360455 ATTATTATTACTATT
1 ATTATTATTACTATT
*
28360470 ATTATTATTTCTATT
1 ATTATTATTACTATT
28360485 TTTTTAACAT
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:28361064 original size:27 final size:26
Alignment explanation
Indices: 28361022--28361092 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 26
28361012 TACTTTGTGA
28361022 ATTATTTATCTT-AATTT-ATTTAACAT
1 ATTATTTAT-TTAAATTTGATTT-ACAT
* *
28361048 ATTATTTATTTGAAATTTGCTTTATAT
1 ATTATTTATTT-AAATTTGATTTACAT
28361075 ATTATGTTATTTCAAATT
1 ATTAT-TTATTT-AAATT
28361093 GTTTTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 9 0.24
27 13 0.34
28 14 0.37
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTATTTATTTAAATTTGATTTACAT
Found at i:28361098 original size:27 final size:27
Alignment explanation
Indices: 28361046--28361107 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28361036 TTTATTTAAC
*
28361046 ATATTATTTATTTGAAATTTGCTTTAT
1 ATATTATTTATTTCAAATTTGCTTTAT
*
28361073 ATATTATGTTATTTCAAA-TTGTTTTAT
1 ATATTAT-TTATTTCAAATTTGCTTTAT
*
28361100 ATTTTATT
1 ATATTATT
28361108 CATGTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (27 bp):
ATATTATTTATTTCAAATTTGCTTTAT
Found at i:28362476 original size:20 final size:20
Alignment explanation
Indices: 28362451--28362495 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28362441 AGGGACTAAA
* *
28362451 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
28362471 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
28362491 ATGAA
1 ATGAA
28362496 TACAAGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28369701 original size:3 final size:3
Alignment explanation
Indices: 28369693--28370102 Score: 768
Period size: 3 Copynumber: 136.0 Consensus size: 3
28369683 ACTATTTTCG
* *
28369693 TAT TAT TAT TAT TAT TAACG TAT T-T TAC TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT
28369740 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28369788 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28369836 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28369884 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28369932 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28369980 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28370028 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28370076 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
28370103 ATATATATAC
Statistics
Matches: 399, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
2 2 0.01
3 391 0.98
4 5 0.01
5 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28370878 original size:142 final size:142
Alignment explanation
Indices: 28370588--28370871 Score: 532
Period size: 142 Copynumber: 2.0 Consensus size: 142
28370578 AACCTAAATA
*
28370588 AACGGAATATTCTTTTAAATCACGATACGAGTCTAAAAAATGCTTATTTTCGGAGCTTCGAGGTG
1 AACGGAATATTCTTTTAAATCACGATACGAGTCTAAAAAATACTTATTTTCGGAGCTTCGAGGTG
28370653 TGGTGCCCTAACTTACCGGGTATGACATTTTGATACCTCGAAATAAGATCTTTTGCAAATAAAGG
66 TGGTGCCCTAACTTACCGGGTATGACATTTTGATACCTCGAAATAAGATCTTTTGCAAATAAAGG
28370718 CAATGTTCGGTG
131 CAATGTTCGGTG
*
28370730 AACGGAATATTCTTTTAAATCACGATACGAGTCTAAAAAATACTTATTTTTGGAGCTTCGAGGTG
1 AACGGAATATTCTTTTAAATCACGATACGAGTCTAAAAAATACTTATTTTCGGAGCTTCGAGGTG
*
28370795 TGGTGCCCTAACTTACTGGGTATGACATTTTGATACCTCGAAATAAGATCTTTTGCAAATAAAGG
66 TGGTGCCCTAACTTACCGGGTATGACATTTTGATACCTCGAAATAAGATCTTTTGCAAATAAAGG
*
28370860 CCATGTTCGGTG
131 CAATGTTCGGTG
28370872 TTCGGAAGTT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (142 bp):
AACGGAATATTCTTTTAAATCACGATACGAGTCTAAAAAATACTTATTTTCGGAGCTTCGAGGTG
TGGTGCCCTAACTTACCGGGTATGACATTTTGATACCTCGAAATAAGATCTTTTGCAAATAAAGG
CAATGTTCGGTG
Found at i:28371652 original size:337 final size:337
Alignment explanation
Indices: 28371033--28371706 Score: 1294
Period size: 337 Copynumber: 2.0 Consensus size: 337
28371023 TAACTCACTA
*
28371033 GATATGACGTATCGTTGCCTCGAGACGAGAATGTCTTTAACATTTTAATGTTTATTTTACAAAAG
1 GATATGACGTATCGTTGCCTCGAAACGAGAATGTCTTTAACATTTTAATGTTTATTTTACAAAAG
28371098 AGGGATTGTAGTTCAAGGTCTTTCAAGTTCTCAATTTTCGACAATTAAGACACTAATTAATTAAC
66 AGGGATTGTAGTTCAAGGTCTTTCAAGTTCTCAATTTTCGACAATTAAGACACTAATTAATTAAC
*
28371163 TAGGTACCAATTCTGGGCGTATCGGGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACT
131 TAGGTACCAATTCTAGGCGTATCGGGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACT
28371228 CATTTTCTGATTTTCGTAGACTAAAAATTATCGTTTTAGTAAATCTTAACTTTTATTAAAATGAT
196 CATTTTCTGATTTTCGTAGACTAAAAATTATCGTTTTAGTAAATCTTAACTTTTATTAAAATGAT
28371293 TAATTTAAAGGTGACCCGATCACACCTCGTCAAAAATGATTGGTGGCGACTCCCGTTATTTAGTT
261 TAATTTAAAGGTGACCCGATCACACCTCGTCAAAAATGATTGGTGGCGACTCCCGTTATTTAGTT
28371358 TTCAAATCCAAG
326 TTCAAATCCAAG
28371370 GATATGACGTATCGTTGCCTCGAAACGAGAATGTCTTTAACATTTTAATGTTTATTTTACAAAAG
1 GATATGACGTATCGTTGCCTCGAAACGAGAATGTCTTTAACATTTTAATGTTTATTTTACAAAAG
*
28371435 AGGGATTGTATTTCAAGGTCTTTCAAGTTCTCAATTTTCGACAATTAAGACACTAATTAATTAAC
66 AGGGATTGTAGTTCAAGGTCTTTCAAGTTCTCAATTTTCGACAATTAAGACACTAATTAATTAAC
*
28371500 TAGGTACCAATTCTAGGCGTATCGGGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCTGAACT
131 TAGGTACCAATTCTAGGCGTATCGGGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACT
*
28371565 CATTTTCTGATTTTCGTAGACTAAAAATTATTGTTTTAGTAAATCTTAACTTTTATTAAAATGAT
196 CATTTTCTGATTTTCGTAGACTAAAAATTATCGTTTTAGTAAATCTTAACTTTTATTAAAATGAT
*
28371630 TAATTTAAAGGTGACTCGATCACACCTCGTCAAAAATGATTGGTGGCGACTCCCGTTATTTAGTT
261 TAATTTAAAGGTGACCCGATCACACCTCGTCAAAAATGATTGGTGGCGACTCCCGTTATTTAGTT
28371695 TTCAAATCCAAG
326 TTCAAATCCAAG
28371707 TCGATCCCCG
Statistics
Matches: 331, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
337 331 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (337 bp):
GATATGACGTATCGTTGCCTCGAAACGAGAATGTCTTTAACATTTTAATGTTTATTTTACAAAAG
AGGGATTGTAGTTCAAGGTCTTTCAAGTTCTCAATTTTCGACAATTAAGACACTAATTAATTAAC
TAGGTACCAATTCTAGGCGTATCGGGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACT
CATTTTCTGATTTTCGTAGACTAAAAATTATCGTTTTAGTAAATCTTAACTTTTATTAAAATGAT
TAATTTAAAGGTGACCCGATCACACCTCGTCAAAAATGATTGGTGGCGACTCCCGTTATTTAGTT
TTCAAATCCAAG
Found at i:28375191 original size:9 final size:9
Alignment explanation
Indices: 28375177--28375208 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
28375167 CAACGCTTTT
28375177 TTGCATTCA
1 TTGCATTCA
28375186 TTGCATTCA
1 TTGCATTCA
28375195 TTGCATTCA
1 TTGCATTCA
28375204 -TGCAT
1 TTGCAT
28375209 CGGCATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:28381742 original size:51 final size:51
Alignment explanation
Indices: 28381666--28381769 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
28381656 GTTACAAAAT
28381666 CGGCAGTTAGCAAGTTCCTAAAAAAGGAAATCATTTGTCGATATGGAATGC
1 CGGCAGTTAGCAAGTTCCTAAAAAAGGAAATCATTTGTCGATATGGAATGC
28381717 CGGCAGTTAGCAAGTTCCTAAAAAAGGAAATCATTTGTCGATATGGAATGC
1 CGGCAGTTAGCAAGTTCCTAAAAAAGGAAATCATTTGTCGATATGGAATGC
28381768 CG
1 CG
28381770 AAAAGGATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (51 bp):
CGGCAGTTAGCAAGTTCCTAAAAAAGGAAATCATTTGTCGATATGGAATGC
Found at i:28383428 original size:43 final size:44
Alignment explanation
Indices: 28383348--28383458 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
28383338 ATCCTGTCTT
* * * * * *
28383348 CCTGAAGCCTCAGCGAAGCAGATTGAAGTCACTAGTCTTATCTC
1 CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
* * *
28383392 CCTGAAG-TGCAGTGGAGTAGACTGAAGTTACAAGTCTCATCTC
1 CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
*
28383435 CTTGAAGCCGCAGTGGAGCAGACT
1 CCTGAAGCCGCAGTGGAGCAGACT
28383459 AAATGTACAG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 33 0.61
44 21 0.39
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (44 bp):
CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
Found at i:28390714 original size:2 final size:2
Alignment explanation
Indices: 28390707--28390736 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28390697 AACGCCTTAA
28390707 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28390737 TCCCCCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28397834 original size:23 final size:23
Alignment explanation
Indices: 28397800--28397854 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
28397790 ATTTGATTTT
* *
28397800 TAAT-TTTTGAATTACTTAGTGA
1 TAATATTTAGAATTACTTAATGA
*
28397822 TAATATTTAGAATTATTTAATGA
1 TAATATTTAGAATTACTTAATGA
28397845 TAATATTTAG
1 TAATATTTAG
28397855 GAAAAATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (23 bp):
TAATATTTAGAATTACTTAATGA
Found at i:28400556 original size:34 final size:34
Alignment explanation
Indices: 28400512--28400586 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
28400502 ATAAATGTAT
* *
28400512 ATATATATTCA-TCTTCGGTTATATCAAACCATAC
1 ATATATATTCACT-TTCGATTATACCAAACCATAC
* * *
28400546 ATATGTATTCACTTTCTATTATACCAAACTATAC
1 ATATATATTCACTTTCGATTATACCAAACCATAC
28400580 ATATATA
1 ATATATA
28400587 ATTATGTACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (34 bp):
ATATATATTCACTTTCGATTATACCAAACCATAC
Found at i:28408242 original size:103 final size:103
Alignment explanation
Indices: 28408063--28408268 Score: 403
Period size: 103 Copynumber: 2.0 Consensus size: 103
28408053 GCTCCATATG
*
28408063 CCTATATGAATCCTTATATATCTTCATTTCACAATTAACTTCCCATTTAACAATTTATTTCATTT
1 CCTATATGAATCCTTACATATCTTCATTTCACAATTAACTTCCCATTTAACAATTTATTTCATTT
28408128 TCATACCATAAACACAAAATCACCTAACATTTAAATTT
66 TCATACCATAAACACAAAATCACCTAACATTTAAATTT
28408166 CCTATATGAATCCTTACATATCTTCATTTCACAATTAACTTCCCATTTAACAATTTATTTCATTT
1 CCTATATGAATCCTTACATATCTTCATTTCACAATTAACTTCCCATTTAACAATTTATTTCATTT
28408231 TCATACCATAAACACAAAATCACCTAACATTTAAATTT
66 TCATACCATAAACACAAAATCACCTAACATTTAAATTT
28408269 AAACCTTAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (103 bp):
CCTATATGAATCCTTACATATCTTCATTTCACAATTAACTTCCCATTTAACAATTTATTTCATTT
TCATACCATAAACACAAAATCACCTAACATTTAAATTT
Found at i:28419123 original size:41 final size:41
Alignment explanation
Indices: 28419024--28419116 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
28419014 TTATAGCTAA
*
28419024 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAGCGCCG
1 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
*
28419065 CTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAACGCCG
1 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
*
28419106 CTATTGCTCTG
1 CTAATGCTCTG
28419117 TATTTTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (41 bp):
CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
Found at i:28419804 original size:6 final size:6
Alignment explanation
Indices: 28419793--28419822 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
28419783 ACTGCATTTG
28419793 AAAATA AAAATA AAAATA AAAATA ATAAAT
1 AAAATA AAAATA AAAATA AAAATA A-AAAT
28419823 TGATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:28428209 original size:54 final size:54
Alignment explanation
Indices: 28428025--28428221 Score: 229
Period size: 55 Copynumber: 3.6 Consensus size: 54
28428015 AACATACCAT
* * *
28428025 TGCCATGTCTTGACATGGTCTTA-AGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACA-TGATATCCTTGCCTTATAGAACTCATCAA
* **
28428078 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCATTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* * * * *
28428133 TGCCATGTCTTGAAATGGTCTTACATGATTTCCTTGCCTTTTAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* *
28428187 TTCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTT
28428222 ATCTTACCGA
Statistics
Matches: 122, Mismatches: 17, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
52 2 0.02
53 34 0.28
54 41 0.34
55 43 0.35
56 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:28430700 original size:44 final size:44
Alignment explanation
Indices: 28430650--28430734 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
28430640 TACATTAACT
* *
28430650 GTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCC
1 GTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCC
* *
28430694 GTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
28430735 GAGATATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (44 bp):
GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCC
Found at i:28431758 original size:58 final size:58
Alignment explanation
Indices: 28431677--28431791 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 58
28431667 ATAACGGACT
28431677 TACTATTGAGATTGGAAAGCTTGGAAACCCTAACCATGGCTTCCCCCATGCTATATTG
1 TACTATTGAGATTGGAAAGCTTGGAAACCCTAACCATGGCTTCCCCCATGCTATATTG
* *
28431735 TACTATTGAGCTTGGAAAGCTTGGAAACCCTAACCATGGCTTCCCCTATGCTATATT
1 TACTATTGAGATTGGAAAGCTTGGAAACCCTAACCATGGCTTCCCCCATGCTATATT
28431792 CGGCCTCCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (58 bp):
TACTATTGAGATTGGAAAGCTTGGAAACCCTAACCATGGCTTCCCCCATGCTATATTG
Found at i:28437121 original size:55 final size:54
Alignment explanation
Indices: 28436975--28437169 Score: 182
Period size: 55 Copynumber: 3.6 Consensus size: 54
28436965 CATACCATTG
* * * * *
28436975 CCATGTCTTAACATGGTCTCACGTGGTATCCTTGCCTTAT-GAACTCA-CTAATT
1 CCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATC-AATT
* * ** * *
28437028 CCATGCCTTGGCATGCTCTTACATGGGA-CCTTTACCTTATAGTAAGTCATCAATT
1 CCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAATT
* * * *
28437083 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAGAACTTATCAATT
1 CCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATT
*
28437137 CCATGCCTTTG-CATGATCTTACATGATATCCTT
1 CCATGCC-TTGACATGGTCTTACATGATATCCTT
28437170 ATCTTACCAA
Statistics
Matches: 114, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
52 2 0.02
53 29 0.25
54 37 0.32
55 43 0.38
56 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (54 bp):
CCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATT
Found at i:28437410 original size:44 final size:44
Alignment explanation
Indices: 28437359--28437445 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
28437349 GTATCCTTAA
* *
28437359 CCGTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTT
* *
28437403 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
28437446 GAGATATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (44 bp):
CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTT
Found at i:28442909 original size:55 final size:55
Alignment explanation
Indices: 28442843--28443008 Score: 314
Period size: 55 Copynumber: 3.0 Consensus size: 55
28442833 AACCCTAATC
28442843 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
1 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
28442898 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
1 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
* *
28442953 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAAAGCTATGGTT
1 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
28443008 T
1 T
28443009 AGTTAGTTCT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 109 1.00
ACGTcount: A:0.20, C:0.04, G:0.34, T:0.42
Consensus pattern (55 bp):
TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
Found at i:28464371 original size:12 final size:12
Alignment explanation
Indices: 28464354--28464391 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28464344 TTATTATAGT
28464354 AAATGATAATTA
1 AAATGATAATTA
28464366 AAATGATAATT-
1 AAATGATAATTA
*
28464377 AAATGA-AAATA
1 AAATGATAATTA
28464388 AAAT
1 AAAT
28464392 ACAAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 10 0.42
12 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (12 bp):
AAATGATAATTA
Found at i:28464673 original size:20 final size:20
Alignment explanation
Indices: 28464624--28464673 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28464614 ATGTGTATTT
*
28464624 TGAAGTTTCTTGATAGATTA
1 TGAAGTTTGTTGATAGATTA
*
28464644 TGAATATTTGTTGATAG-TTA
1 TGAA-GTTTGTTGATAGATTA
28464664 TGTAAGTTTG
1 TG-AAGTTTG
28464674 GTAAAGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (20 bp):
TGAAGTTTGTTGATAGATTA
Found at i:28469278 original size:25 final size:26
Alignment explanation
Indices: 28469220--28469279 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
28469210 TAGAGCGTAT
28469220 TTAGA-TAGATTTGTTGTTGTGTTTA
1 TTAGACTAGATTTGTTGTTGTGTTTA
28469245 TTGACGACTAGATTTGTTGTTGTGTTTA
1 TT-A-GACTAGATTTGTTGTTGTGTTTA
28469273 TT-GACTA
1 TTAGACTA
28469280 CATTCTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 2 0.06
28 22 0.69
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (26 bp):
TTAGACTAGATTTGTTGTTGTGTTTA
Found at i:28475248 original size:14 final size:14
Alignment explanation
Indices: 28475231--28475269 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
28475221 TCAAAACAAG
28475231 AATTTAGAACACAT
1 AATTTAGAACACAT
28475245 AATTTAGAACACAT
1 AATTTAGAACACAT
*
28475259 AATTAAGAACA
1 AATTTAGAACA
28475270 AGTCAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (14 bp):
AATTTAGAACACAT
Found at i:28477618 original size:43 final size:43
Alignment explanation
Indices: 28477470--28477627 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 43
28477460 TATGTGTTTT
28477470 CATGTAAGACCACGTCTGGGACGTTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGA-TATATGA-TTA
** * ** ** * *
28477514 TGTGTAA-ACCATGTCTGGGATATCAGCATCG-TATTTGATTT
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
**
28477555 TGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATATGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTA
*
28477598 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
28477628 TGTATGAGCG
Statistics
Matches: 88, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
41 10 0.11
42 22 0.25
43 50 0.57
44 6 0.07
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
Found at i:28479151 original size:12 final size:12
Alignment explanation
Indices: 28479134--28479171 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28479124 TTATTATAGT
28479134 AAATGATAATTA
1 AAATGATAATTA
28479146 AAATGATAATT-
1 AAATGATAATTA
*
28479157 AAATGA-AAATA
1 AAATGATAATTA
28479168 AAAT
1 AAAT
28479172 ACAAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 10 0.42
12 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (12 bp):
AAATGATAATTA
Found at i:28486296 original size:40 final size:40
Alignment explanation
Indices: 28486229--28486501 Score: 350
Period size: 40 Copynumber: 6.8 Consensus size: 40
28486219 ATTACCACAA
* * * ** *
28486229 GCACAATTGCCTTCAGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28486269 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
28486309 GCACAATTGCCTTCGGGTCTTAGCCTTGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCC-CG-GATATATCAACTC
* *
28486351 GCACAAATGCCTGCGGGTCTTAGCCCGGATAAATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28486391 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28486431 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
28486471 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
28486502 AAATTCAAAT
Statistics
Matches: 206, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.00
40 165 0.80
41 6 0.03
42 34 0.17
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28486446 original size:122 final size:120
Alignment explanation
Indices: 28486263--28486503 Score: 365
Period size: 122 Copynumber: 2.0 Consensus size: 120
28486253 CCGGGCATAG
* * * *
28486263 CAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTTCGGGTC
1 CAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
** * * *
28486328 TTAGCCTTGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATAAAT
66 TTAGCCCGGATA-AAATC-ACTAGCACAAATGCCTGCGGGACTTAGCCCGGATAAAT
28486385 CAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 CAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
* *
28486450 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAAA
66 TTAGCCCGGATAAAATCACTAGCACAAATGCCTGCGGGACTTAGCCCGGATAAA
28486504 ATTCAAATGC
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
120 33 0.31
121 4 0.04
122 71 0.66
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (120 bp):
CAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
TTAGCCCGGATAAAATCACTAGCACAAATGCCTGCGGGACTTAGCCCGGATAAAT
Found at i:28489089 original size:18 final size:21
Alignment explanation
Indices: 28489051--28489089 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
28489041 AGTATGTCAG
28489051 TTGTGGAATATGAACGTAAGT
1 TTGTGGAATATGAACGTAAGT
28489072 TTGT-GAATAT-AA-GTAAGT
1 TTGTGGAATATGAACGTAAGT
28489090 ATGCTCGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 6 0.33
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGTGGAATATGAACGTAAGT
Found at i:28498867 original size:16 final size:16
Alignment explanation
Indices: 28498846--28498877 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28498836 CGTGTGACCC
28498846 ACATGGCCGGGACACA
1 ACATGGCCGGGACACA
*
28498862 ACATGGCCTGGACACA
1 ACATGGCCGGGACACA
28498878 TAGGTGTGTC
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:0.31, C:0.31, G:0.28, T:0.09
Consensus pattern (16 bp):
ACATGGCCGGGACACA
Found at i:28498933 original size:5 final size:5
Alignment explanation
Indices: 28498923--28498998 Score: 59
Period size: 5 Copynumber: 14.6 Consensus size: 5
28498913 TCACCCCCAT
* *
28498923 TTTTA TTTTA TTTTA TTTTA -TTTA TTATTTG TTTTA TTATT- TATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -T-TTTA TTTTA TT-TTA TTTTA
28498969 -TTTA TTTTA CTAATTTA TTTTA TTTTA TTT
1 TTTTA TTTTA -T--TTTA TTTTA TTTTA TTT
28498999 ATTATTCTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
4 9 0.16
5 37 0.64
6 4 0.07
7 4 0.07
8 4 0.07
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:28500893 original size:55 final size:55
Alignment explanation
Indices: 28500705--28500959 Score: 262
Period size: 55 Copynumber: 4.8 Consensus size: 55
28500695 ACACGGGTAC
* * * * *
28500705 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA----T-CCTT-TCGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
* * * *
28500754 CTTACCATTGCCATGTCTCGACAAGGTCTTACATGGTATCCTTGCCTTAT-G-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
* * *
28500807 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAGAAA
* * *
28500862 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-T-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
*
28500915 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28500960 AAATCCTAAT
Statistics
Matches: 172, Mismatches: 22, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
49 33 0.19
52 2 0.01
53 49 0.28
54 14 0.08
55 72 0.42
56 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (55 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAA
Found at i:28500896 original size:108 final size:110
Alignment explanation
Indices: 28500750--28500952 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 110
28500740 GTATCCTTTC
* *
28500750 GAAACTTACCATTGCCATGTCTCGACAAGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGCCATGTCTCGACAAGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACC
28500813 AA-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
65 AATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
* * * *
28500858 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGCCATGTCTCGACAAGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
28500923 ATTGCCATGCCTTGGCATGGTCTTACATGG
66 ATTGCCATGCCTTGGCATGGTCTTACATGG
28500953 TATCCTTAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.58
109 7 0.08
110 28 0.33
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (110 bp):
GAAACTTACCAATGCCATGTCTCGACAAGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
ATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
Found at i:28504356 original size:47 final size:47
Alignment explanation
Indices: 28504292--28504455 Score: 160
Period size: 47 Copynumber: 3.5 Consensus size: 47
28504282 CATTCATAGG
*
28504292 TGAACTCGAACCCAACTCAACGAGCTTGGATGCCTAGTTACATATCA
1 TGAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATATCA
* * *
28504339 TGAACTCGGACTCAACTCAACAAG-TTCGGATGTTCGC-AG--CCATA--A
1 TGAACTCGAACTCAACTCAACGAGCTT-GGATG--C-CTAGTTACATATCA
* * *
28504384 GTGAACTCGAACTCAACTCAACGAGCTCGAATGCCTAGTTACATCTCA
1 -TGAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATATCA
* *
28504432 CGAACTCGGACTCAACTCAACGAG
1 TGAACTCGAACTCAACTCAACGAG
28504456 TTCAGACGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 22
0.73 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 31 0.33
47 53 0.56
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (47 bp):
TGAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATATCA
Found at i:28504399 original size:46 final size:45
Alignment explanation
Indices: 28504338--28504509 Score: 143
Period size: 46 Copynumber: 3.7 Consensus size: 45
28504328 GTTACATATC
*
28504338 ATGAACTCGGACTCAACTCAACAAGTTCGGATGTTCGCAGCCATA
1 ATGAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCATA
* * * * *
28504383 AGTGAACTCGAACTCAACTCAACGAGCTCGAATG--C-CTAGTTACATCTC
1 A-TGAACTCGAACTCAACTCAACAAGTTCGGATGTTCGC-AG--CCA--TA
* * * * * * *
28504431 ACGAACTCGGACTCAACTCAACGAGTTCAGACGTTTGCATCCATAA
1 ATGAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCAT-A
28504477 ATGAACTCGAACTCAACTCAACAAGTTCGGATG
1 ATGAACTCGAACTCAACTCAACAAGTTCGGATG
28504510 CCCAAATATC
Statistics
Matches: 96, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 58 0.60
47 28 0.29
48 2 0.02
49 1 0.01
50 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (45 bp):
ATGAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCATA
Found at i:28504405 original size:93 final size:93
Alignment explanation
Indices: 28504246--28504511 Score: 354
Period size: 93 Copynumber: 2.9 Consensus size: 93
28504236 CGCCCATAAG
* * * * * * *
28504246 TGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCCCATTCATAGGTGAACTCGAACCCAACTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
28504311 ACGAGCTTGGATGCCTAGTTACATATCA
66 ACGAGCTTGGATGCCTAGTTACATATCA
* * *
28504339 TGAACTCGGACTCAACTCAACAAGTTCGGATGTTCGCAGCCATAAGTGAACTCGAACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
* * *
28504404 ACGAGCTCGAATGCCTAGTTACATCTCA
66 ACGAGCTTGGATGCCTAGTTACATATCA
* * * *
28504432 CGAACTCGGACTCAACTCAACGAGTTCAGACGTTTGCATCCATAAATGAACTCGAACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
28504497 ACAAG-TTCGGATGCC
66 ACGAGCTT-GGATGCC
28504512 CAAATATCCG
Statistics
Matches: 149, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
92 1 0.01
93 148 0.99
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGCTTGGATGCCTAGTTACATATCA
Found at i:28512096 original size:27 final size:27
Alignment explanation
Indices: 28512065--28512242 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
28512055 TAAATTGTAC
28512065 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *** *
28512092 TGCACTAAGTGTGCGAAACGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28512118 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28512146 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28512174 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28512201 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28512228 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28512243 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28512206 original size:82 final size:81
Alignment explanation
Indices: 28512066--28512221 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28512056 AAATTGTACA
* *
28512066 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
28512131 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
*** *
28512147 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACTAAGT
*
28512211 GTGCGAGTTGA
64 GTGCGAATTGA
28512222 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28512233 original size:82 final size:81
Alignment explanation
Indices: 28512062--28512242 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28512052 GATTAAATTG
* *
28512062 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
28512127 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * *** *
28512143 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACT
* **
28512207 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28512225 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28512243 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28513858 original size:16 final size:16
Alignment explanation
Indices: 28513837--28513874 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28513827 CATTCTAAAC
28513837 CATTGCAGATATTCAG
1 CATTGCAGATATTCAG
*
28513853 CATTGCAGATATTTAG
1 CATTGCAGATATTCAG
28513869 CATTGC
1 CATTGC
28513875 GATGTGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (16 bp):
CATTGCAGATATTCAG
Found at i:28515298 original size:27 final size:29
Alignment explanation
Indices: 28515230--28515300 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
28515220 TAGATCAAGT
* *
28515230 ATAACACATATAAAACGTTGAATCAAATA
1 ATAACACACATAAAGCGTTGAATCAAATA
28515259 ATAACACACATAAAGCGTTGAATC-AAT-
1 ATAACACACATAAAGCGTTGAATCAAATA
* *
28515286 GTAACACGCATAAAG
1 ATAACACACATAAAG
28515301 TGCAGGATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 13 0.34
28 3 0.08
29 22 0.58
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (29 bp):
ATAACACACATAAAGCGTTGAATCAAATA
Found at i:28519438 original size:37 final size:37
Alignment explanation
Indices: 28519381--28519525 Score: 166
Period size: 37 Copynumber: 3.9 Consensus size: 37
28519371 ATCCAACCGA
28519381 AACACGCCAATCGC-CTATAAGAGCTAATCCACCCAAT
1 AACACGCCAATCGCTC-ATAAGAGCTAATCCACCCAAT
* * * *
28519418 AACATGCCAATTGCTCATAAGATCTAATCCACCCGAT
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
* * * *
28519455 AACCCACTAATCGGTCATAAGAGCTAATCCACCCAAT
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
* * * *
28519492 AACACGACAATCGCTCACAAAAGCCAATCCACCC
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCC
28519526 GGTAACACAC
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 86 0.99
38 1 0.01
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (37 bp):
AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
Found at i:28520429 original size:36 final size:36
Alignment explanation
Indices: 28520382--28520451 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
28520372 GTGTATTCGG
28520382 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
1 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
* *
28520418 TTATGAAGAAGAGAAATGAAGACGAAAGTAGCTT
1 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTT
28520452 TTACTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.21
Consensus pattern (36 bp):
TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
Found at i:28525971 original size:29 final size:29
Alignment explanation
Indices: 28525939--28526022 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
28525929 TACACACAGC
* * *
28525939 CATGTCACATGTCGTGGGTGGCACATGGA
1 CATGTCACAGGTCGTGTGTGGCACACGGA
*
28525968 CATGTCGCAGGTCGTGTGTGGCACACGGA
1 CATGTCACAGGTCGTGTGTGGCACACGGA
*
28525997 CATGTTACAGGTCGTGTGTGGCACAC
1 CATGTCACAGGTCGTGTGTGGCACAC
28526023 AGCCAAGTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.24
Consensus pattern (29 bp):
CATGTCACAGGTCGTGTGTGGCACACGGA
Found at i:28526038 original size:31 final size:29
Alignment explanation
Indices: 28525931--28526038 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
28525921 TGACTTAATA
* * * *
28525931 CACACAGCCATGTCACATGTCGTGGGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
** * *
28525960 CACATGGACATGTCGCAGGTCGTGTGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
* **
28525989 CACACGGACATGTTACAGGTCGTGTGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
*
28526018 CACACAGCCAAGTGGCACAGG
1 CACACAGAC-A-TGGCACAGG
28526039 CCTGTCCCAG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 56 0.88
30 1 0.02
31 7 0.11
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.19
Consensus pattern (29 bp):
CACACAGACATGGCACAGGTCGTGTGTGG
Found at i:28527019 original size:65 final size:65
Alignment explanation
Indices: 28526910--28527045 Score: 256
Period size: 65 Copynumber: 2.1 Consensus size: 65
28526900 ATTTTGGGAG
28526910 TGAAT-AAAGCTTTCGACCATAGTAGTCAATAAAGAATATGGCTGTTGTTTCATATTAATTTGGA
1 TGAATCAAAGCTTTCGACCATAGTAGTCAATAAAGAATATGGCTGTTGTTTCATATTAATTTGGA
*
28526974 TGAATCAAAGCTTTCGGCCATAGTAGTCAATAAAGAATATGGCTGTTGTTTCATATTAATTTGGA
1 TGAATCAAAGCTTTCGACCATAGTAGTCAATAAAGAATATGGCTGTTGTTTCATATTAATTTGGA
28527039 TGAATCA
1 TGAATCA
28527046 TGGTGGATGG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 5 0.07
65 65 0.93
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (65 bp):
TGAATCAAAGCTTTCGACCATAGTAGTCAATAAAGAATATGGCTGTTGTTTCATATTAATTTGGA
Done.