Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008152.1 Hibiscus syriacus cultivar Beakdansim tig00110718_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 877984
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 5
Found at i:399084 original size:29 final size:30
Alignment explanation
Indices: 399014--399084 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
399004 CAAACATTAT
399014 AATAATTAAATAATAAAAACATTAAAAAACAA
1 AATAA-TAAA-AATAAAAACATTAAAAAACAA
* * * *
399046 AAAAAT-AAAATTAAAACATT-ACAAACTA
1 AATAATAAAAATAAAAACATTAAAAAACAA
399074 AATAATAAAAA
1 AATAATAAAAA
399085 CGATTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 11 0.33
29 15 0.45
30 2 0.06
31 1 0.03
32 4 0.12
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AATAATAAAAATAAAAACATTAAAAAACAA
Found at i:399115 original size:19 final size:18
Alignment explanation
Indices: 399073--399115 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
399063 ATTACAAACT
399073 AAATAATAAAAACGATTA
1 AAATAATAAAAACGATTA
* *
399091 AAATAATTAAAACTATTA
1 AAATAATAAAAACGATTA
399109 AATATAA
1 AA-ATAA
399116 ACATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (18 bp):
AAATAATAAAAACGATTA
Found at i:399169 original size:25 final size:25
Alignment explanation
Indices: 399118--399169 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
399108 AAATATAAAC
* ** *
399118 ATTAAATACAAATGTTACAAAGAAA
1 ATTAAATAAAAACATTACAAACAAA
*
399143 ATTAAATAAAAACATTACAAACTAA
1 ATTAAATAAAAACATTACAAACAAA
399168 AT
1 AT
399170 AACTATATCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.25
Consensus pattern (25 bp):
ATTAAATAAAAACATTACAAACAAA
Found at i:402701 original size:22 final size:22
Alignment explanation
Indices: 402673--402924 Score: 378
Period size: 22 Copynumber: 11.5 Consensus size: 22
402663 ATAATAAATT
402673 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
402695 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*
402717 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*
402739 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
402761 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*
402783 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
402805 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
402827 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
402849 TTTTAAGACAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
402871 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
402893 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
402915 TTTTAAAATA
1 TTTTAAAATA
402925 TTAATGATTA
Statistics
Matches: 208, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 208 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:404979 original size:57 final size:57
Alignment explanation
Indices: 404886--405271 Score: 655
Period size: 57 Copynumber: 6.8 Consensus size: 57
404876 TAACTTTAAT
404886 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
* *
404943 ACAAACCATATAATATTTCTAACATAAACCAAAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
*
405000 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTTAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
* * *
405057 ATAAACCATATAATATTTCTAACATAAACCAAAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
* * * *
405114 ACAAACCATGTAATATTTCTAACATAGATCATAAACCATATAATGTTTTGAACATCA
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
* * *
405171 ACAAACCATATAATATTTCTAACTTAAACCATAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
405228 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAAT
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAAT
405272 ATTTCTTACA
Statistics
Matches: 306, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 306 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (57 bp):
ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTGAACATCG
Found at i:406380 original size:22 final size:22
Alignment explanation
Indices: 406349--406392 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
406339 GCATACACAA
406349 CAAATACATAACATACAAACAT
1 CAAATACATAACATACAAACAT
* *
406371 CAAATTCATAACATACATACAT
1 CAAATACATAACATACAAACAT
406393 ATATAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (22 bp):
CAAATACATAACATACAAACAT
Found at i:408121 original size:24 final size:25
Alignment explanation
Indices: 408094--408148 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
408084 ATTAATAAAA
408094 AATA-ACATCATCTATTTGTTATTG
1 AATACACATCATCTATTTGTTATTG
408118 AATAAACACATCATCTATTTGTTATTG
1 AAT--ACACATCATCTATTTGTTATTG
408145 AATA
1 AATA
408149 GACGATCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.11
25 1 0.04
26 1 0.04
27 23 0.82
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (25 bp):
AATACACATCATCTATTTGTTATTG
Found at i:408234 original size:29 final size:30
Alignment explanation
Indices: 408191--408297 Score: 110
Period size: 29 Copynumber: 3.5 Consensus size: 30
408181 TAAAGTTTAA
*
408191 TGAATAAATTAAAAATAATTAAAAATATAG
1 TGAATAAAATAAAAATAATTAAAAATATAG
*
408221 TGAATAAAAT-AAAATAGATAATAAAATTATGAAG
1 TGAATAAAATAAAAATA-AT--TAAAAATAT--AG
* * *
408255 TGAATAAATTGAAAAGAATT-AAAATATAG
1 TGAATAAAATAAAAATAATTAAAAATATAG
408284 TGAATAAAATAAAA
1 TGAATAAAATAAAA
408298 GAGATAACAA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
29 20 0.31
30 11 0.17
31 6 0.09
32 9 0.14
34 13 0.20
35 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (30 bp):
TGAATAAAATAAAAATAATTAAAAATATAG
Found at i:408258 original size:34 final size:30
Alignment explanation
Indices: 408191--408309 Score: 109
Period size: 31 Copynumber: 3.8 Consensus size: 30
408181 TAAAGTTTAA
*
408191 TGAAT-AAATTAAAA-ATAATTAAAAATATAG
1 TGAATAAAATAAAAAGATAA-T-AAAATATAG
408221 TGAATAAAATAAAATAGATAATAAAATTATGAAG
1 TGAATAAAATAAAA-AGATAATAAAA-TAT--AG
* * *
408255 TGAATAAATTGAAAAGA-ATTAAAATATAG
1 TGAATAAAATAAAAAGATAATAAAATATAG
*
408284 TGAATAAAATAAAAGAGATAACAAAA
1 TGAATAAAATAAAA-AGATAATAAAA
408310 ATTCTGAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
29 14 0.19
30 8 0.11
31 19 0.26
32 11 0.15
33 7 0.10
34 14 0.19
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.25
Consensus pattern (30 bp):
TGAATAAAATAAAAAGATAATAAAATATAG
Found at i:408311 original size:64 final size:64
Alignment explanation
Indices: 408191--408317 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 64
408181 TAAAGTTTAA
* * *
408191 TGAATAAATTAAAAATAATTAAAAATATAGTGAATAAAATAAAATAGATAATAAAATTATGAAG
1 TGAATAAATTAAAAAGAATTAAAAATATAGTGAATAAAATAAAAGAGATAAAAAAATTATGAAG
* *
408255 TGAATAAATTGAAAAGAATT-AAAATATAGTGAATAAAATAAAAGAGATAACAAAAATTCTGAA
1 TGAATAAATTAAAAAGAATTAAAAATATAGTGAATAAAATAAAAGAGATAA-AAAAATTATGAA
408318 TAAACGTGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 29 0.51
64 28 0.49
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (64 bp):
TGAATAAATTAAAAAGAATTAAAAATATAGTGAATAAAATAAAAGAGATAAAAAAATTATGAAG
Found at i:414768 original size:15 final size:16
Alignment explanation
Indices: 414734--414773 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
414724 ATAAATAAAT
*
414734 GAACATAAACGAACAC
1 GAACATAAACGAAAAC
414750 GAACATAAAC-AAAAC
1 GAACATAAACGAAAAC
414765 GAACATAAA
1 GAACATAAA
414774 TGAACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.62, C:0.20, G:0.10, T:0.07
Consensus pattern (16 bp):
GAACATAAACGAAAAC
Found at i:415037 original size:12 final size:12
Alignment explanation
Indices: 415008--415064 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
414998 CTCGAAACTC
415008 GAGCTCGA-T-T
1 GAGCTCGATTCT
415018 GAAGCTCGATTCT
1 G-AGCTCGATTCT
415031 GAGCTCGATTC-
1 GAGCTCGATTCT
*
415042 AAGCTCGATTCT
1 GAGCTCGATTCT
*
415054 GAGCTAGATTC
1 GAGCTCGATTC
415065 AAGCTCGACA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.03
11 17 0.43
12 20 0.50
13 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (12 bp):
GAGCTCGATTCT
Found at i:415037 original size:47 final size:46
Alignment explanation
Indices: 414984--415072 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 46
414974 AAAAATTTAA
* *
414984 GAGCTCGATTAAAACTCGAAACTCGAGCTCGATTGAAGCTCGATTCT
1 GAGCTCGATTAAAACTCGAAACT-GAGCTAGATTCAAGCTCGATTCT
* * **
415031 GAGCTCGATTCAAGCTCGATTCTGAGCTAGATTCAAGCTCGA
1 GAGCTCGATTAAAACTCGAAACTGAGCTAGATTCAAGCTCGA
415073 CATTACCCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 17 0.47
47 19 0.53
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (46 bp):
GAGCTCGATTAAAACTCGAAACTGAGCTAGATTCAAGCTCGATTCT
Found at i:415038 original size:23 final size:23
Alignment explanation
Indices: 414984--415072 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
414974 AAAAATTTAA
* * **
414984 GAGCTCGATTAAAACTCGAAACT
1 GAGCTCGATTCAAGCTCGATTCT
*
415007 CGAGCTCGATTGAAGCTCGATTCT
1 -GAGCTCGATTCAAGCTCGATTCT
415031 GAGCTCGATTCAAGCTCGATTCT
1 GAGCTCGATTCAAGCTCGATTCT
*
415054 GAGCTAGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
415073 CATTACCCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 40 0.68
24 19 0.32
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTCT
Found at i:415052 original size:11 final size:11
Alignment explanation
Indices: 415009--415072 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
414999 TCGAAACTCG
*
415009 AGCTCGATTGA
1 AGCTCGATTCA
*
415020 AGCTCGATTCTG
1 AGCTCGATTC-A
415032 AGCTCGATTCA
1 AGCTCGATTCA
*
415043 AGCTCGATTCTG
1 AGCTCGATTC-A
*
415055 AGCTAGATTCA
1 AGCTCGATTCA
415066 AGCTCGA
1 AGCTCGA
415073 CATTACCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:415599 original size:24 final size:24
Alignment explanation
Indices: 415585--415640 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
415575 ATAAATTAAT
*
415585 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAAACGAAC
* *
415609 GAACATAAACGATCATAACCGAAC
1 GAACATAAACGAACATAAACGAAC
415633 GAACATAA
1 GAACATAA
415641 CTGAATGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAAACGAAC
Found at i:415609 original size:14 final size:14
Alignment explanation
Indices: 415592--415641 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
415582 AATGAACATA
415592 AACGAACATAACCG
1 AACGAACATAACCG
415606 AACGAACAT-A---
1 AACGAACATAACCG
*
415616 AACGATCATAACCG
1 AACGAACATAACCG
415630 AACGAACATAAC
1 AACGAACATAAC
415642 TGAATGTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.52, C:0.26, G:0.12, T:0.10
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:416723 original size:14 final size:14
Alignment explanation
Indices: 416701--416751 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
416691 AAATGGAGAG
*
416701 AAAAGAGATGAAAA
1 AAAAAAGATGAAAA
416715 AAAAAAGATGAAGGAA
1 AAAAAAGATGAA--AA
416731 GAAAAGAAGA-GAAAA
1 -AAAA-AAGATGAAAA
416746 AAAAAA
1 AAAAAA
416752 AAAAAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 2 0.06
14 15 0.47
15 2 0.06
16 2 0.06
17 7 0.22
18 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (14 bp):
AAAAAAGATGAAAA
Found at i:418943 original size:20 final size:20
Alignment explanation
Indices: 418920--418986 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
418910 CTAATGACGG
418920 GCAACGATTTGGAATGAATC
1 GCAACGATTTGGAATGAATC
* * **
418940 GCAACGCGAACTTCGCCT-A-TC
1 GCAA--CG-ATTTGGAATGAATC
418961 GCAACGATTTGGAATGAATC
1 GCAACGATTTGGAATGAATC
418981 GCAACG
1 GCAACG
418987 CGAACTTCGC
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 12 0.35
21 6 0.18
22 3 0.09
23 5 0.15
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
GCAACGATTTGGAATGAATC
Found at i:419026 original size:42 final size:41
Alignment explanation
Indices: 418920--419045 Score: 243
Period size: 41 Copynumber: 3.0 Consensus size: 41
418910 CTAATGACGG
418920 GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
1 GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
418961 GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
1 GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
419002 GCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
1 GCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
419044 GC
1 GC
419046 GTTGCGAATC
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 47 0.56
42 37 0.44
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (41 bp):
GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATC
Found at i:419505 original size:43 final size:43
Alignment explanation
Indices: 419458--419544 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
419448 AATGAAACTA
*
419458 AAACGTAAGCAAAATATAACGTTAGATATGATTTTAAAAAAGT
1 AAACGTAACCAAAATATAACGTTAGATATGATTTTAAAAAAGT
419501 AAACGTAACCAAAATATAACGTTAGATATGATTTTAAAAAAGT
1 AAACGTAACCAAAATATAACGTTAGATATGATTTTAAAAAAGT
419544 A
1 A
419545 GTCCAGTATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.28
Consensus pattern (43 bp):
AAACGTAACCAAAATATAACGTTAGATATGATTTTAAAAAAGT
Found at i:421052 original size:17 final size:18
Alignment explanation
Indices: 421020--421056 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
421010 AGCATATGAG
421020 TTAAAATAAATTATAAAT
1 TTAAAATAAATTATAAAT
*
421038 TTAAAAT-ATTTATAAAT
1 TTAAAATAAATTATAAAT
421055 TT
1 TT
421057 TTAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATAAATTATAAAT
Found at i:421635 original size:21 final size:20
Alignment explanation
Indices: 421592--421639 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
421582 TTACGTTTAC
*
421592 ATTATTAATCATTTAATGCT
1 ATTATTAATCATTTAATACT
* *
421612 ATTTATTAATCATTTATTATT
1 A-TTATTAATCATTTAATACT
421633 ATTATTA
1 ATTATTA
421640 TTATTTCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTATTAATCATTTAATACT
Found at i:422184 original size:42 final size:42
Alignment explanation
Indices: 422138--422220 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
422128 AATAACCAAC
* *
422138 AAATTCGCAACACAGTTTTTAAATTCGTAACGT-GAATTTCCA
1 AAATTCGCAACACAGTTTTGAAATTCGCAAC-TCGAATTTCCA
* *
422180 AAATTTGCAACTCAGTTTTGAAATTCGCAACTCGAATTTCC
1 AAATTCGCAACACAGTTTTGAAATTCGCAACTCGAATTTCC
422221 TTTTCGCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (42 bp):
AAATTCGCAACACAGTTTTGAAATTCGCAACTCGAATTTCCA
Found at i:422209 original size:20 final size:20
Alignment explanation
Indices: 422138--422212 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
422128 AATAACCAAC
* *
422138 AAATTCGCAACACAGTTTTT
1 AAATTCGCAACTCAGTTTTA
* * * *
422158 AAATTCGTAACGTGAATTTCCA
1 AAATTCGCAAC-TCAGTTT-TA
* *
422180 AAATTTGCAACTCAGTTTTG
1 AAATTCGCAACTCAGTTTTA
422200 AAATTCGCAACTC
1 AAATTCGCAACTC
422213 GAATTTCCTT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 22 0.55
21 9 0.22
22 9 0.22
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (20 bp):
AAATTCGCAACTCAGTTTTA
Found at i:422823 original size:14 final size:15
Alignment explanation
Indices: 422794--422826 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
422784 CTTGAAACTT
422794 AAATTCGCAACACGA
1 AAATTCGCAACACGA
*
422809 AAATT-GCAACTCGA
1 AAATTCGCAACACGA
422823 AAAT
1 AAAT
422827 GAAATTCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.18
Consensus pattern (15 bp):
AAATTCGCAACACGA
Found at i:422837 original size:20 final size:19
Alignment explanation
Indices: 422809--422846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
422799 CGCAACACGA
*
422809 AAATTGCAACTCGAAAATG
1 AAATTGCAACACGAAAATG
422828 AAATTCGCAACACGAAAAT
1 AAATT-GCAACACGAAAAT
422847 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (19 bp):
AAATTGCAACACGAAAATG
Found at i:422837 original size:34 final size:34
Alignment explanation
Indices: 422794--422872 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 34
422784 CTTGAAACTT
*
422794 AAATTCGCAACACGAAAATTGCAACT-CGAAAATG
1 AAATTCGCAACACGAAAATCGCAA-TGCGAAAATG
422828 AAATTCGCAACACGAAAATCGCAATGCGAAAATG
1 AAATTCGCAACACGAAAATCGCAATGCGAAAATG
422862 AAATTCGCAAC
1 AAATTCGCAAC
422873 GCGATTTTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 1 0.02
34 42 0.98
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.16
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCGCAATGCGAAAATG
Found at i:422907 original size:14 final size:14
Alignment explanation
Indices: 422884--422914 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
422874 CGATTTTAGT
422884 TTTCGCGTTGCGAA
1 TTTCGCGTTGCGAA
*
422898 TTTCGTGTTGCGAA
1 TTTCGCGTTGCGAA
422912 TTT
1 TTT
422915 TAATTTCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (14 bp):
TTTCGCGTTGCGAA
Found at i:422941 original size:34 final size:34
Alignment explanation
Indices: 422884--422948 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
422874 CGATTTTAGT
* * *
422884 TTTCGCGTTGCGAATTTCGTGTTGCGAATTTTAA
1 TTTCGAGTTACGAATTTCATGTTGCGAATTTTAA
*
422918 TTTCGAGTTACGATTTTCATGTTGCGAATTT
1 TTTCGAGTTACGAATTTCATGTTGCGAATTT
422949 AAGTTTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (34 bp):
TTTCGAGTTACGAATTTCATGTTGCGAATTTTAA
Found at i:424503 original size:42 final size:42
Alignment explanation
Indices: 424451--424554 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
424441 CCCCCACTCT
* * ** * *
424451 GACACCGAGAGCCATCATCTCATTGAGCCTCTTCTCCACTTC
1 GACACCGAGAGCCATCACCTCATCGAGCCGATTCTACACCTC
*
424493 GACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACCTC
1 GACACCGAGAGCCATCACCTCATCGAGCCGATTCTACACCTC
*
424535 GACACTGAGAGCCATCACCT
1 GACACCGAGAGCCATCACCT
424555 ATTCCATTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (42 bp):
GACACCGAGAGCCATCACCTCATCGAGCCGATTCTACACCTC
Found at i:424693 original size:21 final size:21
Alignment explanation
Indices: 424669--424739 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
424659 GTTAGGGGAG
424669 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTGCT
424690 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTGCT
*
424711 TTACGTAATGAGGTC-GTTGCT
1 TTACGTGATGAGGTCAG-TGCT
424732 TTACGTGA
1 TTACGTGA
424740 CGACAATGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 46 0.98
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTGCT
Found at i:425166 original size:21 final size:21
Alignment explanation
Indices: 425140--425201 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
425130 GAAGAAGCCC
425140 GATCCACCTACCATTGTTCAG
1 GATCCACCTACCATTGTTCAG
*
425161 GATCCACCTCCCATTGTTCAG
1 GATCCACCTACCATTGTTCAG
* * *
425182 GATTCACCTATCATCGTTCA
1 GATCCACCTACCATTGTTCA
425202 AGAGGCCCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.31
Consensus pattern (21 bp):
GATCCACCTACCATTGTTCAG
Found at i:425217 original size:21 final size:21
Alignment explanation
Indices: 425193--425243 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
425183 ATTCACCTAT
425193 CATCGTTCAAGAGGCCCATCC
1 CATCGTTCAAGAGGCCCATCC
*
425214 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCATCC
*
425235 TATCGTTCA
1 CATCGTTCA
425244 GGATCGACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCATCC
Found at i:426548 original size:20 final size:20
Alignment explanation
Indices: 426525--426589 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
426515 TCGCATTGTA
*
426525 AATTTTAATTTCGAGTTATG
1 AATTTTAATTTCGAGTTACG
* * *
426545 AATTTTATTTTCGCGTTGCG
1 AATTTTAATTTCGAGTTACG
* *
426565 AATTTGAATATCGAGTTACG
1 AATTTTAATTTCGAGTTACG
426585 AATTT
1 AATTT
426590 GAGTTGCGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (20 bp):
AATTTTAATTTCGAGTTACG
Found at i:426555 original size:40 final size:40
Alignment explanation
Indices: 426511--426589 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
426501 TTGCGTAGCG
* * * *
426511 ATTTTCGCATTGTAAATTTTAATTTCGAGTTATGAATTTT
1 ATTTTCGCATTGCAAATTTGAATATCGAGTTACGAATTTT
* *
426551 ATTTTCGCGTTGCGAATTTGAATATCGAGTTACGAATTT
1 ATTTTCGCATTGCAAATTTGAATATCGAGTTACGAATTT
426590 GAGTTGCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (40 bp):
ATTTTCGCATTGCAAATTTGAATATCGAGTTACGAATTTT
Found at i:428928 original size:3 final size:3
Alignment explanation
Indices: 428920--428953 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
428910 TCTTCGGGGA
*
428920 CTT CTT CTT CTT CTT ATT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
428954 AGGGTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:429156 original size:24 final size:24
Alignment explanation
Indices: 429129--429181 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
429119 TGAAACATAT
*
429129 TCAAAATCCAAGTATTGACCAAGA
1 TCAAAATCCAAGTATTAACCAAGA
* *
429153 TCAAAGTCCAGGTATTAACCAAGA
1 TCAAAATCCAAGTATTAACCAAGA
429177 TCAAA
1 TCAAA
429182 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (24 bp):
TCAAAATCCAAGTATTAACCAAGA
Found at i:429328 original size:12 final size:12
Alignment explanation
Indices: 429307--429340 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
429297 GGTTGTGGGT
*
429307 TTTGAGATTGTG
1 TTTGATATTGTG
429319 TTTGATATTGTG
1 TTTGATATTGTG
*
429331 TTTGGTATTG
1 TTTGATATTG
429341 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:430274 original size:20 final size:20
Alignment explanation
Indices: 430249--430290 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
430239 GAAATTCGCC
430249 TTGCGAATTCAGAAATCGAG
1 TTGCGAATTCAGAAATCGAG
*
430269 TTGCGAATTGAGAAATCGAG
1 TTGCGAATTCAGAAATCGAG
430289 TT
1 TT
430291 ATGAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (20 bp):
TTGCGAATTCAGAAATCGAG
Found at i:430296 original size:20 final size:20
Alignment explanation
Indices: 430252--430297 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
430242 ATTCGCCTTG
*
430252 CGAATTCAGAAATCGAGTTG
1 CGAATTCAGAAATCGAGTTA
*
430272 CGAATTGAGAAATCGAGTTA
1 CGAATTCAGAAATCGAGTTA
*
430292 TGAATT
1 CGAATT
430298 TGAAATTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (20 bp):
CGAATTCAGAAATCGAGTTA
Found at i:430361 original size:20 final size:21
Alignment explanation
Indices: 430330--430443 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 21
430320 CAAATTCGCA
*
430330 TTGC-AAATTTGGAAACT-GCG
1 TTGCGAAA-TTGGAAACTCGTG
**
430350 TTGCGAAATTGG-AGTTCGTG
1 TTGCGAAATTGGAAACTCGTG
* * *
430370 TTGCGAATTTAGAAAATCGTG
1 TTGCGAAATTGGAAACTCGTG
* * * *
430391 TTACGAAA-AGGAAATTCGAG
1 TTGCGAAATTGGAAACTCGTG
*
430411 TTGCGAATTTGGAAACT-GTG
1 TTGCGAAATTGGAAACTCGTG
430431 TTGCGAAATTGGA
1 TTGCGAAATTGGA
430444 GTTCGCGTTG
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
19 2 0.03
20 48 0.68
21 21 0.30
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (21 bp):
TTGCGAAATTGGAAACTCGTG
Found at i:430379 original size:40 final size:40
Alignment explanation
Indices: 430330--430461 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
430320 CAAATTCGCA
* *
430330 TTGCAAATTTGGAAACTGCGTTGCGAAATTGGAGTTCGTG
1 TTGCAAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGAG
* * * * * *
430370 TTGCGAATTTAGAAAATCGTGTTACGAAA-AGGAAATTCGAG
1 TTGCAAATTTGGAAACT-GTGTTGCGAAATTGG-AGTTCGAG
* *
430411 TTGCGAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGCG
1 TTGCAAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGAG
430451 TTGCAAATTTG
1 TTGCAAATTTG
430462 TTGGTTATTT
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
40 42 0.57
41 32 0.43
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (40 bp):
TTGCAAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGAG
Found at i:430444 original size:81 final size:80
Alignment explanation
Indices: 430105--430461 Score: 253
Period size: 81 Copynumber: 4.4 Consensus size: 80
430095 CCAAAACATT
** * * *
430105 TGTGTTGCGAAATTAAAATTCGTGTTGCAAATTTGGAAATCGAGTTATGAAAACA-AAATTC-AT
1 TGTGTTGCGAAATTGGAATTCGTGTTGCAAATTTGAAAATCGTGTTACGAAAA-AGAAATTCGA-
* * *
430168 GTTACGAATTAGAAAATC
64 GTTGCGAATTTGGAAA-C
* * * * * *
430186 T-TGTTGCGAAA-AGTAAACTT-GTGTTGCAAATTTAAAAATCGTGTTGCTAAAAAGAAATTCGC
1 TGTGTTGCGAAATTG-GAA-TTCGTGTTGCAAATTTGAAAATCGTGTTACGAAAAAGAAATTCGA
* **
430248 CTTGCGAATTCAGAAA-
64 GTTGCGAATTTGGAAAC
* * * *** * * * **
430264 TCGAGTTGCG-AATTGAGAAATCGAGTTATGAATTTGAAATTTCGTGTTGCGAATATCAAATTCG
1 T-GTGTTGCGAAATTG-GAATTCGTGTTGCAAATTTGAAA-ATCGTGTTACGAAAAAGAAATTCG
*
430328 CA-TTGCAAATTTGGAAAC
63 -AGTTGCGAATTTGGAAAC
* * * *
430346 TGCGTTGCGAAATTGGAGTTCGTGTTGCGAATTTAGAAAATCGTGTTACGAAAAGGAAATTCGAG
1 TGTGTTGCGAAATTGGAATTCGTGTTGCAAATTT-GAAAATCGTGTTACGAAAAAGAAATTCGAG
430411 TTGCGAATTTGGAAAC
65 TTGCGAATTTGGAAAC
* *
430427 TGTGTTGCGAAATTGGAGTTCGCGTTGCAAATTTG
1 TGTGTTGCGAAATTGGAATTCGTGTTGCAAATTTG
430462 TTGGTTATTT
Statistics
Matches: 214, Mismatches: 48, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
78 1 0.00
79 4 0.02
80 79 0.37
81 120 0.56
82 10 0.05
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (80 bp):
TGTGTTGCGAAATTGGAATTCGTGTTGCAAATTTGAAAATCGTGTTACGAAAAAGAAATTCGAGT
TGCGAATTTGGAAAC
Found at i:430929 original size:21 final size:20
Alignment explanation
Indices: 430903--430952 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
430893 TTTCAAATTT
*
430903 GCAACGCGAATATCCAGATTC
1 GCAACGCGAATAT-AAGATTC
* *
430924 GCAACGCGATTGTAAGATTC
1 GCAACGCGAATATAAGATTC
430944 GCAACGCGA
1 GCAACGCGA
430953 TTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (20 bp):
GCAACGCGAATATAAGATTC
Found at i:430972 original size:20 final size:20
Alignment explanation
Indices: 430949--431002 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
430939 GATTCGCAAC
*
430949 GCGATTTTGAAAAATGTGTT
1 GCGATATTGAAAAATGTGTT
430969 GCGATAGTT--AAAATGTGTT
1 GCGATA-TTGAAAAATGTGTT
*
430988 GCGATAGTGAAAAAT
1 GCGATATTGAAAAAT
431003 CCAAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 10 0.34
21 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (20 bp):
GCGATATTGAAAAATGTGTT
Found at i:430983 original size:19 final size:19
Alignment explanation
Indices: 430959--431000 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
430949 GCGATTTTGA
*
430959 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
430978 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
430997 AAAA
1 AAAA
431001 ATCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:431461 original size:40 final size:40
Alignment explanation
Indices: 431406--431889 Score: 581
Period size: 40 Copynumber: 12.2 Consensus size: 40
431396 TTGTTGTGAT
431406 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
*
431446 TTTGGAAAATCGCAACGTGAACTTGGACTATCTCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* *
431486 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* **
431526 TTTGGAAAATCGCAAC--GAATTTGGAAAATCGCAACGTGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAAC--GAA
* ** * **
431566 CTTGGACTATCGCAAC--GAATTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAA--CGAA
* * **
431606 CTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* * * **
431646 TTTGG---A-C-TAACGTAAATTTGGAAAATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
*
431681 TTTGGAAAATCGCAACGACGCGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGC-A--ACGTGAACTTGGACTATCGCAACGAA
431724 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* *
431764 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* * *
431804 TTTGGAAAATCGCAATGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* *
431844 TTTGGAAAATTGCAACGTGAACTTGGACTATCGCAATGAA
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
431884 TTTGGA
1 TTTGGA
431890 CTAACGTAAA
Statistics
Matches: 393, Mismatches: 37, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.07
36 1 0.00
37 1 0.00
38 16 0.04
39 1 0.00
40 294 0.75
41 1 0.00
42 17 0.04
43 34 0.09
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
Found at i:431597 original size:139 final size:139
Alignment explanation
Indices: 431406--431818 Score: 647
Period size: 139 Copynumber: 3.0 Consensus size: 139
431396 TTGTTGTGAT
431406 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
*
431471 GACTATCTCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
66 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
431536 CGCAACGAA
131 CGCAACGAA
* *
431545 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
* ** * * * *
431610 GACTATCGCAACGTGAACTTGGACTATCGCAA--CGAATTTGGACTAACG-TA--AATTTGGAAA
66 GACTATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
431670 ATCGCAACGAA
129 ATCGCAACGAA
*
431681 TTTGGAAAATCGCAACGACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAAC
1 TTTGGAAAATCGC-A--ACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAAC
431746 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAA
63 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAA
431811 AATCGCAA
128 AATCGCAA
431819 TGCGAACTTC
Statistics
Matches: 244, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
136 34 0.14
137 16 0.07
138 1 0.00
139 160 0.66
140 1 0.00
141 15 0.06
142 17 0.07
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (139 bp):
TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
CGCAACGAA
Found at i:431667 original size:35 final size:35
Alignment explanation
Indices: 431619--431686 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
431609 CGACTATCGC
* **
431619 AACGTGAACTTGGACTATCGCAACGAATTTGGACT
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
*
431654 AACGTAAATTTGGAAAATCGCAACGAATTTGGA
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGA
431687 AAATCGCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (35 bp):
AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
Found at i:431709 original size:24 final size:24
Alignment explanation
Indices: 431677--431722 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
431667 AAAATCGCAA
*
431677 CGAATTTGGAAAATCGCAACGACG
1 CGAACTTGGAAAATCGCAACGACG
**
431701 CGAACTTGGACTATCGCAACGA
1 CGAACTTGGAAAATCGCAACGA
431723 ATTTGGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
CGAACTTGGAAAATCGCAACGACG
Found at i:431719 original size:179 final size:176
Alignment explanation
Indices: 431406--431935 Score: 567
Period size: 179 Copynumber: 3.0 Consensus size: 176
431396 TTGTTGTGAT
* * *
431406 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAAC-GAATTTGGAAAATCGCAACGTGAACTT
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGGAACTTGGAAAATCGCAACG-GAACTT
* ** *
431470 GGACTATCTCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAA
65 GGACTAACT-AAC-AATTTGGAAAATCGCAAC-CGAACTTCGAAAATCGCAACGAACTTGGAAAA
431535 TCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
127 TCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
** *
431585 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAAC-GAATTT
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACG-GAACTTGGAAAATCGCAACGGAACTT
* *
431649 GGACTAACGT-A-AATTTGGAAAATCGCAA-CGAATTTGGAAAATCGCAACGACGCGAACTTGGA
65 GGACTAAC-TAACAATTTGGAAAATCGCAACCGAACTTCGAAAATCGC-A--A--CGAACTTGGA
**
431711 CTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
124 AAATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
* *
431764 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC-GAATTTGGAAAATCGCAATGCGAACTT
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGGAACTTGGAAAATCGCAACG-GAACTT
* * * * * * ** * * *
431828 CGACTATCGCAACGAATTTGGAAAATTGCAACGTGAACTTGGACTATCGCAATGAATTTGGACTA
65 GGACTAAC-TAAC-AATTTGGAAAATCGCAAC-CGAACTTCGAAAATCGCAACGAACTTGGA-AA
* * * *
431893 A-CG-TA--AATTTAGAAAATCGCAACGCGAAGTTGGACTATCGCAA
126 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAA
431936 AATCGCGTTG
Statistics
Matches: 300, Mismatches: 35, Indels: 35
0.81 0.09 0.09
Matches are distributed among these distances:
174 13 0.04
175 1 0.00
176 52 0.17
177 16 0.05
178 2 0.01
179 166 0.55
180 3 0.01
181 17 0.06
182 16 0.05
183 1 0.00
184 13 0.04
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (176 bp):
TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGGAACTTGGAAAATCGCAACGGAACTTG
GACTAACTAACAATTTGGAAAATCGCAACCGAACTTCGAAAATCGCAACGAACTTGGAAAATCGC
AACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
Found at i:431849 original size:139 final size:138
Alignment explanation
Indices: 431406--431935 Score: 632
Period size: 139 Copynumber: 3.8 Consensus size: 138
431396 TTGTTGTGAT
431406 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
1 TTTGGAAAATCGCAACG-GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
*
431471 GACTATCTCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
65 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
431536 CGCAACGAA
130 CGCAACGAA
* *
431545 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 TTTGGAAAATCGCAACG-GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTG
* ** * * * *
431610 GACTATCGCAACGTGAACTTGGACTATCGCAA--CGAATTTGGACTAACG-TA--AATTTGGAAA
65 GACTATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
431670 ATCGCAACGAA
128 ATCGCAACGAA
431681 TTTGGAAAATCGCAACGACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAAC
1 TTTGGAAAATCGC-A--ACG-GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAAC
431746 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAA
62 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAA
431811 AATCGCAATGCGAA
127 AATCGCAA--CGAA
* * ** * ** * * ** *
431825 CTTCGACTATCGCAAC-GAATTTGGAAAATTGCAACGTGAACTTGGACTATCGCAA--TGAATTT
1 TTTGGAAAATCGCAACGGAACTTGGACTATCGCAAC--GAATTTGGAAAATCGCAACGTGAACTT
* * * * *
431887 GGACTAACG-TA--AATTTAGAAAATCGCAACGCGAAGTTGGACTATCGCAA
64 GGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
431936 AATCGCGTTG
Statistics
Matches: 340, Mismatches: 37, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
136 69 0.20
137 16 0.05
138 2 0.01
139 189 0.56
140 1 0.00
141 32 0.09
142 17 0.05
143 1 0.00
144 13 0.04
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (138 bp):
TTTGGAAAATCGCAACGGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGG
ACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATC
GCAACGAA
Found at i:431861 original size:238 final size:233
Alignment explanation
Indices: 431435--431916 Score: 671
Period size: 238 Copynumber: 2.0 Consensus size: 233
431425 AACTTGGACT
* *
431435 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCTCAACGAATTTGGAAAATCGCA
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCA
* *
431500 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGTGA
66 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGAACTTCGAAAATCGCAACG-GA
** * * **
431565 ACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTT
130 ACTTGGAAAATCGCAACGAACTTCGAAAATCGCAAC-CGAACTTCGAAAATCGCAACGTGAACTT
*
431630 GGACTATCGCAACGAATTTGGACTAACGTAAATTTGGAAA
194 GGACTATCGCAACGAATTTGGACTAACGTAAATTTAGAAA
431670 ATCGCAACGAATTTGGAAAATCGCAACGACGCGAACTTGGACTATCGCAACGAATTTGGAAAATC
1 ATCGCAACGAATTTGGAAAATCGC-A--ACGCGAACTTGGACTATCGCAACGAATTTGGAAAATC
* * **
431735 GCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
63 GCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAA--CGAACTTCGAAAATCGCAA
* ** * * *
431800 C-GAATTTGGAAAATCGCAATGCGAACTTCGACTATCGCAA-CGAATTTGGAAAATTGCAACGTG
126 CGGAACTTGGAAAATCGCAA--CGAACTTCGAAAATCGCAACCGAACTTCGAAAATCGCAACGTG
*
431863 AACTTGGACTATCGCAATGAATTTGGACTAACGTAAATTTAGAAA
189 AACTTGGACTATCGCAACGAATTTGGACTAACGTAAATTTAGAAA
431908 ATCGCAACG
1 ATCGCAACG
431917 CGAAGTTGGA
Statistics
Matches: 218, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
235 24 0.11
236 1 0.00
238 162 0.74
240 31 0.14
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (233 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCA
ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGAACTTCGAAAATCGCAACGGAA
CTTGGAAAATCGCAACGAACTTCGAAAATCGCAACCGAACTTCGAAAATCGCAACGTGAACTTGG
ACTATCGCAACGAATTTGGACTAACGTAAATTTAGAAA
Found at i:431910 original size:219 final size:214
Alignment explanation
Indices: 431534--431935 Score: 551
Period size: 219 Copynumber: 1.8 Consensus size: 214
431524 AATTTGGAAA
* *
431534 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCA
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
** *
431599 ACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGACTAACGTAAATT
66 ACGCGAACTTCGACTATCGCAACG-GAACTTGGAAAATCGCAACGAACTTGGACTAACGTAAATT
*
431664 TGGAAAATCGCAACGAATTTGGAAAATCGCAACGACGCGAACTTGGACTATCGCAACGAATTTGG
130 TGGAAAATCGCAAC-AATTTAGAAAATCGC-A--ACGCGAACTTGGACTATCGCAACGAATTTGG
431729 AAAATCGCAACGTGAACTTGGACT
191 AAAATCGCAACGTGAACTTGGACT
431753 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
* * * * *
431818 ATGCGAACTTCGACTATCGCAAC-GAATTTGGAAAATTGCAACGTGAACTTGGACTATCGCAATG
66 ACGCGAACTTCGACTATCGCAACGGAACTTGGAAAATCGCAAC--GAACTTGGACTAACG---TA
* * *
431882 AATTTGGACTAA-CG-TA-AATTTAGAAAATCGCAACGCGAAGTTGGACTATCGCAA
126 AATTTGGA-AAATCGCAACAATTTAGAAAATCGCAACGCGAACTTGGACTATCGCAA
431936 AATCGCGTTG
Statistics
Matches: 163, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
216 21 0.13
217 15 0.09
218 1 0.01
219 112 0.69
221 1 0.01
222 11 0.07
223 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (214 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
ACGCGAACTTCGACTATCGCAACGGAACTTGGAAAATCGCAACGAACTTGGACTAACGTAAATTT
GGAAAATCGCAACAATTTAGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAAT
CGCAACGTGAACTTGGACT
Found at i:435380 original size:27 final size:27
Alignment explanation
Indices: 435350--435402 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
435340 TCTCTTTTCA
435350 TCTTTTGCTT-TTTCATCTTCCTTGACT
1 TCTTTT-CTTGTTTCATCTTCCTTGACT
435377 TCTTTTCTTGTTTCATCTTCCTTGAC
1 TCTTTTCTTGTTTCATCTTCCTTGAC
435403 CTTGATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.08, C:0.26, G:0.08, T:0.58
Consensus pattern (27 bp):
TCTTTTCTTGTTTCATCTTCCTTGACT
Found at i:437999 original size:21 final size:21
Alignment explanation
Indices: 437975--438018 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
437965 TGCCGAAAGT
*
437975 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
437996 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
438017 AC
1 AC
438019 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:438840 original size:23 final size:23
Alignment explanation
Indices: 438810--438853 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
438800 GAGTAGAGGG
438810 TCTACGTGGTCCTTCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAT
438833 TCTACGTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
438854 TATATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAT
Found at i:441435 original size:21 final size:20
Alignment explanation
Indices: 441408--441506 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
441398 AATCAGTTTC
441408 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
441429 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
441450 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
441470 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
441491 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
441507 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:441499 original size:20 final size:20
Alignment explanation
Indices: 441474--441666 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
441464 GATTTTCCAG
* ** *
441474 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
441494 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
441514 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
441534 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
441554 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
441574 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
441594 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
441614 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
441635 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
441655 AATCGCAACGCG
1 AATCGCAACGCG
441667 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:442075 original size:14 final size:14
Alignment explanation
Indices: 442056--442112 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
442046 TTTCATTTCA
442056 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
442070 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
442089 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
442103 CGTTGCGATT
1 CGTTGCGATT
442113 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:442086 original size:33 final size:33
Alignment explanation
Indices: 442046--442116 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
442036 TTCACTTAGA
442046 TTTCATTTCACGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCACGTTGCGATTCTCTCGTTGCGAT
* *
442079 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCACGTTGCGATTCTCTCGTTGCGAT
442112 TTTCA
1 TTTCA
442117 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCACGTTGCGATTCTCTCGTTGCGAT
Found at i:442220 original size:21 final size:21
Alignment explanation
Indices: 442196--442272 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
442186 TGCAGAAGAG
*
442196 TCGCAATGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
442217 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
442237 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
442259 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
442273 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.20
21 28 0.61
22 9 0.20
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:442276 original size:14 final size:14
Alignment explanation
Indices: 442257--442313 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
442247 GAAAAATGAA
442257 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
442271 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
442290 AATCGCAACGAGAG
1 AATCGCAACGAGAG
442304 AATCGCAACG
1 AATCGCAACG
442314 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:442288 original size:33 final size:33
Alignment explanation
Indices: 442250--442329 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
442240 GCAACGAGAA
442250 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
442283 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
442316 AAACCAAAATCGCA
1 AAATGAAAATCGCA
442330 TTGCAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:442381 original size:21 final size:21
Alignment explanation
Indices: 442355--442419 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
442345 CGCGTTGCGA
442355 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
442376 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
442396 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
442417 TTC
1 TTC
442420 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:442416 original size:20 final size:20
Alignment explanation
Indices: 442354--442417 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
442344 TCGCGTTGCG
442354 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
442374 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
442395 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
442415 ATT
1 ATT
442418 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:444383 original size:33 final size:33
Alignment explanation
Indices: 444330--444453 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
444320 TCTTTTACTT
* * *
444330 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
444364 TCGTAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
444397 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
444430 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
444454 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:444390 original size:19 final size:18
Alignment explanation
Indices: 444362--444453 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 18
444352 GCAACGAGAG
*
444362 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
444381 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
444395 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
444414 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
444428 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
444447 AATCGCA
1 AATCGCA
444454 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 25 0.42
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:444400 original size:14 final size:14
Alignment explanation
Indices: 444379--444437 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
444369 ACGCGAAATG
444379 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
444393 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
444412 AAAATCGCAACGAC
1 AAAATCGCAACGAC
444426 AAAATCGCAACG
1 AAAATCGCAACG
444438 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:444471 original size:19 final size:19
Alignment explanation
Indices: 444449--444621 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
444439 GAAACCAAAA
*
444449 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
444468 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
444482 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
444501 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
444517 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
444534 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
444553 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
444572 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
444591 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
444611 TCGTGTTGCGA
1 TCGCGTTGCGA
444622 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:444490 original size:14 final size:14
Alignment explanation
Indices: 444471--444527 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
444461 TTTCATTTCG
444471 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
444485 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
444502 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
444518 CGTTGCGATT
1 CGTTGCGATT
444528 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:444579 original size:38 final size:38
Alignment explanation
Indices: 444449--444621 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
444439 GAAACCAAAA
*
444449 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
444484 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
444517 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
444553 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
444591 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
444622 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:445098 original size:21 final size:21
Alignment explanation
Indices: 445074--445140 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
445064 TCATTCCTCG
*
445074 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCATTCA
* * * * *
445095 AGAGGCCACTGCCATCATTGA
1 AGAGTCCCCTCCCACCATTCA
445116 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
445137 AGAG
1 AGAG
445141 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.18
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:446563 original size:14 final size:14
Alignment explanation
Indices: 446544--446579 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
446534 ATTGTTTAAT
446544 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
446558 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
446572 TGATTTGT
1 TGATTTGT
446580 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:446721 original size:19 final size:19
Alignment explanation
Indices: 446686--446784 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
446676 AAAAATGACT
446686 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
446706 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
446725 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
446739 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
446758 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
446778 ATCGCAA
1 ATCGCAA
446785 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 2 0.03
18 1 0.01
19 29 0.42
20 25 0.36
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:446774 original size:53 final size:53
Alignment explanation
Indices: 446686--446803 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 53
446676 AAAAATGACT
*
446686 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
446739 ATCGCAATGC-AAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
446792 ATCGCAATGCGA
1 ATCGCAATGCGA
446804 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
52 18 0.29
53 43 0.69
54 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:446838 original size:20 final size:19
Alignment explanation
Indices: 446793--446964 Score: 176
Period size: 19 Copynumber: 9.7 Consensus size: 19
446783 AACGAGAGAA
*
446793 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
446812 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
446831 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
446848 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
446865 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
446884 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
446901 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
446918 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
446936 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
446952 TCGCATTGCGATT
1 TCGCATTGCGATT
446965 CTCTCGTTGC
Statistics
Matches: 128, Mismatches: 7, Indels: 36
0.75 0.04 0.21
Matches are distributed among these distances:
14 23 0.18
16 12 0.09
17 11 0.09
18 9 0.07
19 41 0.32
20 32 0.25
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:446862 original size:53 final size:53
Alignment explanation
Indices: 446799--446936 Score: 267
Period size: 53 Copynumber: 2.6 Consensus size: 53
446789 AGAATCGCAA
446799 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
446852 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
446905 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
446937 GTTGGGATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
53 67 0.80
54 17 0.20
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:446913 original size:34 final size:34
Alignment explanation
Indices: 446870--446997 Score: 179
Period size: 34 Copynumber: 3.8 Consensus size: 34
446860 TCATTTCGCA
446870 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
446904 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCG
*
446938 TTGGGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* * **
446971 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCCGCATTGCGAT
446998 AGTCAAATGC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.01
33 27 0.33
34 54 0.65
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:449280 original size:12 final size:12
Alignment explanation
Indices: 449263--449287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
449253 TCTTCGGGGA
449263 CTTTTTCTTCTT
1 CTTTTTCTTCTT
449275 CTTTTTCTTCTT
1 CTTTTTCTTCTT
449287 C
1 C
449288 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:449496 original size:24 final size:24
Alignment explanation
Indices: 449462--449508 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
449452 CTGAAACATC
449462 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
449486 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
449509 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:450226 original size:20 final size:20
Alignment explanation
Indices: 450201--450386 Score: 210
Period size: 20 Copynumber: 9.3 Consensus size: 20
450191 AAATTTCAGT
*
450201 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
450221 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
450241 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
450261 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
450281 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
450301 GTTGCGATTTACGGATGCGC
1 GTTGCGATTTACGGATTCTC
* * *
450321 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
450341 GTTACGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * * *
450361 GTTACGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
450381 GTTGCG
1 GTTGCG
450387 TACTACTTCT
Statistics
Matches: 148, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 148 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:450930 original size:20 final size:20
Alignment explanation
Indices: 450902--451130 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
450892 AAATTTCAGT
* ** *
450902 GTTGTGATTTACATATTCTC
1 GTTGCGATTTACGGATTCGC
*
450922 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
450942 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
450962 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
450982 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
451002 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
451022 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
451042 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
451062 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
451082 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
451102 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
451122 GTTGCGATT
1 GTTGCGATT
451131 CTGGAAAATC
Statistics
Matches: 182, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:451029 original size:701 final size:701
Alignment explanation
Indices: 449686--451087 Score: 2678
Period size: 701 Copynumber: 2.0 Consensus size: 701
449676 GACCCAACAA
449686 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
1 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
449751 AATCGTTCAACATCTTCATTATCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
66 AATCGTTCAACATCTTCATTATCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
449816 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTA
131 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTA
449881 ACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAAGCATATATTGTAAAACACCATGA
196 ACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAAGCATATATTGTAAAACACCATGA
449946 ACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCAT
261 ACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCAT
*
450011 GGTTGTAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAACCTATTGCCGGATTGGGAAGG
326 GGTTGTAAATTAATTTACTAAACAGACAAGCTGCGAAACTAAAACCTATTGCCGGATTGGGAAGG
*
450076 ATGTCATTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCG
391 ATGTCATTGGATATAGGAACGGATGTCACCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCG
450141 ATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATAACCAAAATTTCAGTGTTGC
456 ATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATAACCAAAATTTCAGTGTTGC
450206 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTT
521 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTT
* *
450271 ACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATGCGCATTGCGATTTACGGA
586 ACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGA
450336 TACGCGTTACGATTTACGGATACACGTTACGGTTTACGGATACGCGTTGCG
651 TACGCGTTACGATTTACGGATACACGTTACGGTTTACGGATACGCGTTGCG
450387 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
1 TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
*
450452 AATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
66 AATCGTTCAACATCTTCATTATCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
450517 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTA
131 AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTA
450582 ACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAAGCATATATTGTAAAACACCATGA
196 ACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAAGCATATATTGTAAAACACCATGA
450647 ACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCAT
261 ACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCAT
*
450712 GGTTGTAAATTAATTTACTAAACAGACAAGCTGCGAAACTAAAACCTGTTGCCGGATTGGGAAGG
326 GGTTGTAAATTAATTTACTAAACAGACAAGCTGCGAAACTAAAACCTATTGCCGGATTGGGAAGG
*
450777 ATGTCGTTGGATATAGGAACGGATGTCACCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCG
391 ATGTCATTGGATATAGGAACGGATGTCACCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCG
* *
450842 ATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATACCCAAAATTTCAGTGTTGT
456 ATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATAACCAAAATTTCAGTGTTGC
* *
450907 GATTTACATATTCTCGTTGCGATTTACGGATTCTCGTTGCGATTTACAGATTCTCGTTGCGATTT
521 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTT
450972 ACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGA
586 ACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGA
* * *
451037 TACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCG
651 TACGCGTTACGATTTACGGATACACGTTACGGTTTACGGATACGCGTTGCG
451088 ATTTATGTGT
Statistics
Matches: 687, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
701 687 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (701 bp):
TACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGTGAAACACTAATGTAAGCAATG
AATCGTTCAACATCTTCATTATCGGTTAACAAATAAACTTTACCATTTCTCTGATAAGATAGCCT
AAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTAGCATTAGAGTTTCATAAGTTA
ACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAAGCATATATTGTAAAACACCATGA
ACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAACATTAGATGATTTCAT
GGTTGTAAATTAATTTACTAAACAGACAAGCTGCGAAACTAAAACCTATTGCCGGATTGGGAAGG
ATGTCATTGGATATAGGAACGGATGTCACCGGAGAGAGTGATAGATGGAGATGGAATGAGTTGCG
ATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATATAACCAAAATTTCAGTGTTGC
GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTTGCGATTT
ACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGA
TACGCGTTACGATTTACGGATACACGTTACGGTTTACGGATACGCGTTGCG
Found at i:452794 original size:23 final size:24
Alignment explanation
Indices: 452754--452800 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
452744 AACATTGAAA
452754 TTTAATTTTATGGATGTTGATATT
1 TTTAATTTTATGGATGTTGATATT
* * *
452778 TTTATTTTTA-GGTTGTTGGTATT
1 TTTAATTTTATGGATGTTGATATT
452801 ATAAATGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (24 bp):
TTTAATTTTATGGATGTTGATATT
Found at i:454160 original size:15 final size:15
Alignment explanation
Indices: 454140--454168 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
454130 TTAATATTAT
454140 ATAAAATAAACCTAC
1 ATAAAATAAACCTAC
454155 ATAAAATAAACCTA
1 ATAAAATAAACCTA
454169 AAATAGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAATAAACCTAC
Found at i:456567 original size:64 final size:65
Alignment explanation
Indices: 456494--456655 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
456484 ATTGTTTGAA
* *** *
456494 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAAT-AAATAAACATCGAATGCAAT
456557 T
65 T
* * * *
456558 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAATAAACATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAATAAACATCGAATGCAAT
456621 T
65 T
** * *
456622 TATGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
456656 CGATAGGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 5 0.06
64 71 0.91
65 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAATAAACATCGAATGCAATT
Found at i:457673 original size:103 final size:103
Alignment explanation
Indices: 457449--457665 Score: 380
Period size: 103 Copynumber: 2.1 Consensus size: 103
457439 TGAATATATG
457449 ATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGCGAGACACATACT
1 ATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGCGAGACACATACT
* * *
457514 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGAT
66 TGATCCCTAGCATATGTATATGATTCTTAAAGAATGAT
* *
457552 ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 ATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGCGAGACACATACT
*
457617 TGATCCCTAGTATATGTATATGATTCTTAAAGAATGAT
66 TGATCCCTAGCATATGTATATGATTCTTAAAGAATGAT
457655 ATGTGGTCCTT
1 ATGTGGTCCTT
457666 ATAGACATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (103 bp):
ATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGCGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAAGAATGAT
Found at i:457715 original size:23 final size:23
Alignment explanation
Indices: 457682--457744 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
457672 ATTATTATAT
457682 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
457705 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
457728 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
457745 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:463347 original size:103 final size:103
Alignment explanation
Indices: 463163--463388 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
463153 GTCGAGGGTC
*
463163 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
463228 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
463266 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACGTAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
463331 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
463369 TATGTGGTCCTTAT-GGACAT
1 TATGTGGTCCTT-TGGGACAT
463389 TATTATATGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 116 0.99
104 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:463430 original size:23 final size:23
Alignment explanation
Indices: 463397--463459 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
463387 ATTATTATAT
463397 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
463420 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
463443 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
463460 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:503404 original size:22 final size:22
Alignment explanation
Indices: 503379--503443 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
503369 GATTTATAGG
503379 CTAAATCTTAGGTATTAGAAGA
1 CTAAATCTTAGGTATTAGAAGA
* * *
503401 CT-AA-C-TA--AAATAGAATA
1 CTAAATCTTAGGTATTAGAAGA
*
503418 CTATATCTTAGGTATTAGAAGA
1 CTAAATCTTAGGTATTAGAAGA
503440 CTAA
1 CTAA
503444 TTAAAATAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 9 0.30
18 1 0.03
19 3 0.10
20 3 0.10
21 2 0.07
22 12 0.40
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (22 bp):
CTAAATCTTAGGTATTAGAAGA
Found at i:503437 original size:39 final size:39
Alignment explanation
Indices: 503383--503460 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
503373 TATAGGCTAA
503383 ATCTTAGGTATTAGAAGACTAACTAAAATAGAATACTAT
1 ATCTTAGGTATTAGAAGACTAACTAAAATAGAATACTAT
*
503422 ATCTTAGGTATTAGAAGACTAATTAAAATAGAATACTAT
1 ATCTTAGGTATTAGAAGACTAACTAAAATAGAATACTAT
503461 GTTACCTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (39 bp):
ATCTTAGGTATTAGAAGACTAACTAAAATAGAATACTAT
Found at i:505835 original size:39 final size:36
Alignment explanation
Indices: 505789--505879 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 36
505779 TTTTTGGGCC
*
505789 ACCCGACCCGACCCGA-GAAGAA-AGGGTTTTTCACCCGTG
1 ACCCGACCCGACCCGACGAA-AATAAGG--TTTCACCC--G
505828 ACCCGACCCGACCCGACGAAAATAAGGTTTCACCCG
1 ACCCGACCCGACCCGACGAAAATAAGGTTTCACCCG
505864 ACCCGACCCGACCCGA
1 ACCCGACCCGACCCGA
505880 ATATATGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 17 0.35
38 8 0.16
39 18 0.37
40 6 0.12
ACGTcount: A:0.27, C:0.40, G:0.22, T:0.11
Consensus pattern (36 bp):
ACCCGACCCGACCCGACGAAAATAAGGTTTCACCCG
Found at i:516949 original size:10 final size:10
Alignment explanation
Indices: 516934--516961 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
516924 AATTCAAGAT
516934 TCCCACCCTA
1 TCCCACCCTA
516944 TCCCACCCTA
1 TCCCACCCTA
516954 TCCCACCC
1 TCCCACCC
516962 AAATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.64, G:0.00, T:0.18
Consensus pattern (10 bp):
TCCCACCCTA
Found at i:531642 original size:22 final size:22
Alignment explanation
Indices: 531609--531651 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
531599 AAACCAAAAG
531609 CACAGCTCCTAA-CAATATCCTC
1 CACAGCTCCTAACCAAT-TCCTC
531631 CACAG-TCACTAACCAATTCCT
1 CACAGCTC-CTAACCAATTCCT
531652 GACTTAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.33, C:0.40, G:0.05, T:0.23
Consensus pattern (22 bp):
CACAGCTCCTAACCAATTCCTC
Found at i:541313 original size:20 final size:20
Alignment explanation
Indices: 541278--541356 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
541268 CACTGAATAT
*
541278 TTGTCCCAAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
541298 TTGTTCCGAAGAACCA-TTA
1 TTGTCCCGAAGGACCACTGA
*
541317 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
541336 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
541356 T
1 T
541357 AATCCCTCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 13 0.27
19 3 0.06
20 32 0.67
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:541330 original size:38 final size:38
Alignment explanation
Indices: 541279--541351 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
541269 ACTGAATATT
*
541279 TGTCCCAAAGGACCACTGATTGTTCCGAAGAACCATTA
1 TGTCCCAAAGGACCACTGATTGTCCCGAAGAACCATTA
* * *
541317 TGTCCCGAAGGACCACTGTTTGTCCCGAAGGACCA
1 TGTCCCAAAGGACCACTGATTGTCCCGAAGAACCA
541352 CTGATAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (38 bp):
TGTCCCAAAGGACCACTGATTGTCCCGAAGAACCATTA
Found at i:541362 original size:20 final size:20
Alignment explanation
Indices: 541319--541362 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
541309 AACCATTATG
* **
541319 TCCCGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTGATAA
541339 TCCCGAAGGACCACTGATAA
1 TCCCGAAGGACCACTGATAA
541359 TCCC
1 TCCC
541363 TCAAATCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATAA
Found at i:545191 original size:15 final size:15
Alignment explanation
Indices: 545167--545208 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
545157 CGGGCTTTTT
545167 AGCCCGCTCCGTTTA
1 AGCCCGCTCCGTTTA
*
545182 AGCCCTCTCCGTTTA
1 AGCCCGCTCCGTTTA
*
545197 AGCCCGCACCGT
1 AGCCCGCTCCGT
545209 CAAAACCCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.14, C:0.43, G:0.19, T:0.24
Consensus pattern (15 bp):
AGCCCGCTCCGTTTA
Found at i:546934 original size:29 final size:29
Alignment explanation
Indices: 546861--546927 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
546851 CCATTTTACG
* *
546861 AAAATAGCATCATTTTCAAAAAAAATACC
1 AAAATATCACCATTTTCAAAAAAAATACC
* * *
546890 AAAATATCACCATTTTCAAAATAATTACT
1 AAAATATCACCATTTTCAAAAAAAATACC
546919 AAAATATCA
1 AAAATATCA
546928 TTTTTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.28
Consensus pattern (29 bp):
AAAATATCACCATTTTCAAAAAAAATACC
Found at i:546997 original size:29 final size:29
Alignment explanation
Indices: 546956--547027 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
546946 ATTTTTTTTA
* *
546956 AATTACGAAAATAGCACAAATTTCAAAAT
1 AATTACCAGAATAGCACAAATTTCAAAAT
* *** *
546985 AATTACCAGAATAACACCTTTTTCTAAAT
1 AATTACCAGAATAGCACAAATTTCAAAAT
547014 AATTACCAGAATAG
1 AATTACCAGAATAG
547028 TAGTCGGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.28
Consensus pattern (29 bp):
AATTACCAGAATAGCACAAATTTCAAAAT
Found at i:549724 original size:18 final size:18
Alignment explanation
Indices: 549701--549735 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
549691 TTGCAGTTTA
549701 AACGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCGGGTC
*
549719 AACGGGTTGGGTCGGGT
1 AACGGGTCGGGTCGGGT
549736 TGTAACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.17, G:0.51, T:0.20
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTC
Found at i:553356 original size:38 final size:37
Alignment explanation
Indices: 553278--553386 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 37
553268 TGGATATTTA
553278 TCCCGAAGGACCACTA-TG-TCCTGAAGGACCACTATG
1 TCCCGAAGGACCACTATTGTTCC-GAAGGACCACTATG
*
553314 TCCCGAAGGACCACTAATTGTTCCGAAGAACCACTATG
1 TCCCGAAGGACCACT-ATTGTTCCGAAGGACCACTATG
* *
553352 TCCCGAAGGACCACTGTTTGTCCCGAAGGACCACT
1 TCCCGAAGGACCACT-ATTGTTCCGAAGGACCACT
553387 GATAATCCCT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 15 0.23
37 1 0.02
38 46 0.71
39 3 0.05
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (37 bp):
TCCCGAAGGACCACTATTGTTCCGAAGGACCACTATG
Found at i:553395 original size:20 final size:18
Alignment explanation
Indices: 553278--553386 Score: 146
Period size: 18 Copynumber: 5.8 Consensus size: 18
553268 TGGATATTTA
553278 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
553296 TCCTGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
553314 TCCCGAAGGACCACTAATTG
1 TCCCGAAGGACCACT-A-TG
* *
553334 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
*
553352 TCCCGAAGGACCACTGTTTG
1 TCCCGAAGGACCAC--TATG
553372 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
553387 GATAATCCCT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
18 46 0.57
19 2 0.03
20 32 0.40
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:555551 original size:13 final size:13
Alignment explanation
Indices: 555533--555557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
555523 ACGGGAGGAG
555533 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
555546 AGGAAGAAGAAG
1 AGGAAGAAGAAG
555558 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:557498 original size:27 final size:27
Alignment explanation
Indices: 557467--557536 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
557457 TCAACATAAG
557467 AGTATTTTCATAATTTTACCTAATCGA
1 AGTATTTTCATAATTTTACCTAATCGA
*
557494 AGTATTCTCATAATTTTACCTAATCGA
1 AGTATTTTCATAATTTTACCTAATCGA
557521 AGTATTTTCATAATTT
1 AGTATTTTCATAATTT
557537 ATCATCCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (27 bp):
AGTATTTTCATAATTTTACCTAATCGA
Found at i:559015 original size:15 final size:15
Alignment explanation
Indices: 558995--559076 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
558985 TTTCGAAAAA
*
558995 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
559010 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
559025 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
559040 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
559055 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
559069 TGAATTAC
1 TGAATTAC
559077 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:559040 original size:45 final size:44
Alignment explanation
Indices: 558991--559076 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
558981 GGTTTTTCGA
* **
558991 AAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACTGG
1 AAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTGG
559036 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
559077 ATTTCTGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (44 bp):
AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTGG
Found at i:559074 original size:29 final size:30
Alignment explanation
Indices: 558995--559076 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
558985 TTTCGAAAAA
***
558995 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
559025 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
559055 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
559077 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:559082 original size:20 final size:20
Alignment explanation
Indices: 559059--559108 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
559049 GGAATTTGAA
559059 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
559079 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
559099 TTCTGGAAAA
1 TTCTGGAAAA
559109 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:559353 original size:28 final size:28
Alignment explanation
Indices: 559308--559409 Score: 100
Period size: 28 Copynumber: 3.5 Consensus size: 28
559298 TTTACTAAAA
559308 TATTATTGAAATATATAAATAATATTATT
1 TATTATT-AAATATATAAATAATATTATT
* *
559337 TATTATTAAATATATAAAAAATTTATTATA
1 TATTATTAAATATATAAATAA--TATTATT
* *
559367 TATTATTAAA-ATA-AAATAAAATATCTT
1 TATTATTAAATATATAAATAATAT-TATT
559394 ATATTATTATAATATA
1 -TATTATTA-AATATA
559410 ATTGATTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
26 2 0.03
27 2 0.03
28 26 0.43
29 12 0.20
30 19 0.31
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TATTATTAAATATATAAATAATATTATT
Found at i:559364 original size:30 final size:29
Alignment explanation
Indices: 559308--559403 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
559298 TTTACTAAAA
*
559308 TATTATTGAAATATATAAATAA-TATTATT
1 TATTATT-AAATATATAAAAAATTATTATT
*
559337 TATTATTAAATATATAAAAAATTTATTATA
1 TATTATTAAATATATAAAAAA-TTATTATT
* *
559367 TATTATTAAA-ATAAAATAAAATATCTTATAT
1 TATTATTAAATATATAA-AAAAT-TATTAT-T
559398 TATTAT
1 TATTAT
559404 AATATAATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
28 13 0.23
29 13 0.23
30 25 0.44
31 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TATTATTAAATATATAAAAAATTATTATT
Found at i:559423 original size:28 final size:28
Alignment explanation
Indices: 559307--559425 Score: 84
Period size: 28 Copynumber: 4.1 Consensus size: 28
559297 CTTTACTAAA
559307 ATATTATTGAAATATATAAAT-AA-TATTATT
1 ATATTATT-AAA-ATA-AAATAAATTATT-TT
*
559337 -TATTATTAAATATATAAA-AAATTTATTAT
1 ATATTATTAAA-ATA-AAATAAA-TTATTTT
* *
559366 ATATTATTAAAATAAAATAAAATATCTT
1 ATATTATTAAAATAAAATAAATTATTTT
* * **
559394 ATATTATTATAATATAATTGATTATTTT
1 ATATTATTAAAATAAAATAAATTATTTT
559422 ATAT
1 ATAT
559426 AAATATTAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
28 46 0.62
29 14 0.19
30 14 0.19
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (28 bp):
ATATTATTAAAATAAAATAAATTATTTT
Found at i:559454 original size:22 final size:23
Alignment explanation
Indices: 559422--559499 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
559412 TGATTATTTT
559422 ATATAA-A-TATTAAAAATA-TA
1 ATATAATATTATTAAAAATATTA
*
559442 ATATAATATTATTATAAATATTA
1 ATATAATATTATTAAAAATATTA
* * *
559465 ATA-AATATATTTTAAATATTTTA
1 ATATAATAT-TATTAAAAATATTA
559488 ATAATTAATATT
1 AT-A-TAATATT
559500 TTGATGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.13
21 1 0.02
22 15 0.33
23 17 0.37
24 1 0.02
25 1 0.02
26 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATAATATTATTAAAAATATTA
Found at i:559475 original size:21 final size:22
Alignment explanation
Indices: 559422--559484 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
559412 TGATTATTTT
*
559422 ATATAA-ATATTAAAAATA-TA
1 ATATAATATATTATAAATATTA
559442 ATATAATATTATTATAAATATTA
1 ATATAATA-TATTATAAATATTA
*
559465 ATA-AATATATTTTAAATATT
1 ATATAATATATTATAAATATT
559485 TTAATAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 6 0.16
21 13 0.34
22 14 0.37
23 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAATATATTATAAATATTA
Found at i:559489 original size:23 final size:21
Alignment explanation
Indices: 559435--559484 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
559425 TAAATATTAA
*
559435 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
559457 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
559478 AAATATT
1 AAATATT
559485 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:559727 original size:42 final size:42
Alignment explanation
Indices: 559673--559787 Score: 205
Period size: 42 Copynumber: 2.7 Consensus size: 42
559663 ATGAATTACA
*
559673 TTCCGGAAAACGAATTACGTGAAACAAACAC-GAGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACAG-GAAAACATT
559715 TTCCGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
559757 TTCCGAAAAACGAATTACGTGAAACAAACAC
1 TTCCGAAAAACGAATTACGTGAAACAAACAC
559788 TGAAATTCGG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.17
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
Found at i:567266 original size:28 final size:28
Alignment explanation
Indices: 567211--567267 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
567201 CATACATGCA
*
567211 TTTGCATTGTATAATTTGCATTCCCATT
1 TTTGCATTGTATAATTTGCATTCACATT
567239 TTTGCATT-TATCATATTTGCA-TCACATT
1 TTTGCATTGTAT-A-ATTTGCATTCACATT
567267 T
1 T
567268 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTGCATTGTATAATTTGCATTCACATT
Done.