Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 18 of 130
Found at i:5053068 original size:12 final size:12
Alignment explanation
Indices: 5053049--5053085 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5053039 AAGTCTAGAG
5053049 AAAA-AAGAAAA
1 AAAAGAAGAAAA
*
5053060 AATAGAAGAAAA
1 AAAAGAAGAAAA
5053072 AAAAGAA-AAAA
1 AAAAGAAGAAAA
5053083 AAA
1 AAA
5053086 CTTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:5054055 original size:20 final size:21
Alignment explanation
Indices: 5054016--5054055 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5054006 TAAAAAATCT
* *
5054016 TAACCTTTTTAAATTCTCAAA
1 TAACCTTTTCAAAATCTCAAA
5054037 TAACC-TTTCAAAATCTCAA
1 TAACCTTTTCAAAATCTCAA
5054056 GCCCTTGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (21 bp):
TAACCTTTTCAAAATCTCAAA
Found at i:5054468 original size:33 final size:33
Alignment explanation
Indices: 5054390--5054487 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 33
5054380 AGCTAACATA
* *
5054390 TAATGAAGTTTTAAGCTCAACTTAATTGGC-CAC
1 TAATGAAGTTTTAAGCTCAGCTTAACTGGCAC-C
** * *
5054423 T-ATGAAAATTTAAACTCAGTTTAACTGGCACC
1 TAATGAAGTTTTAAGCTCAGCTTAACTGGCACC
* *
5054455 TAATGAAGTTTTAAGCCCAGCTTAGCTGGCACC
1 TAATGAAGTTTTAAGCTCAGCTTAACTGGCACC
5054488 CACAGATTAC
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
32 24 0.47
33 27 0.53
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (33 bp):
TAATGAAGTTTTAAGCTCAGCTTAACTGGCACC
Found at i:5054579 original size:32 final size:33
Alignment explanation
Indices: 5054509--5054583 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
5054499 TGACCCCAAA
5054509 AAAAATTTAAGTCAAGATTAGTTGGCACCTAAT
1 AAAAATTTAAGTCAAGATTAGTTGGCACCTAAT
*
5054542 AAAAATTTAAGTCCAA-ATTATTTGGC-CCTAAT
1 AAAAATTTAAGT-CAAGATTAGTTGGCACCTAAT
*
5054574 GAAAATTTAA
1 AAAAATTTAA
5054584 ACCCAATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
32 15 0.38
33 21 0.54
34 3 0.08
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAAATTTAAGTCAAGATTAGTTGGCACCTAAT
Found at i:5054599 original size:32 final size:33
Alignment explanation
Indices: 5054509--5054602 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 33
5054499 TGACCCCAAA
*
5054509 AAAAATTTAAG-TCAAGATTAGTTGGCACCTAAT
1 AAAAATTTAAGACCAA-ATTAGTTGGCACCTAAT
* *
5054542 AAAAATTTAAGTCCAAATTATTTGGC-CCTAAT
1 AAAAATTTAAGACCAAATTAGTTGGCACCTAAT
* *
5054574 GAAAATTTAA-ACCCAATGTAGTTGGCACC
1 AAAAATTTAAGACCAAAT-TAGTTGGCACC
5054603 CAAGTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
31 5 0.10
32 22 0.42
33 22 0.42
34 3 0.06
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
AAAAATTTAAGACCAAATTAGTTGGCACCTAAT
Found at i:5054672 original size:32 final size:32
Alignment explanation
Indices: 5054636--5054722 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 32
5054626 AACCCTGATA
* *
5054636 AAAATTTAAGCTTAGTTTAGCTGGCA-TAAAT
1 AAAATTTAAGCTTAGTTTAGCTGACACCAAAT
* * *
5054667 GAAAATTTTTAAGCTCAGTTTAGTTGACACCCAAT
1 -AAAA--TTTAAGCTTAGTTTAGCTGACACCAAAT
*
5054702 AAAATTTAAGCCTAGTTTAGC
1 AAAATTTAAGCTTAGTTTAGC
5054723 GATACCCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
32 18 0.41
34 23 0.52
35 3 0.07
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (32 bp):
AAAATTTAAGCTTAGTTTAGCTGACACCAAAT
Found at i:5054793 original size:35 final size:35
Alignment explanation
Indices: 5054749--5054911 Score: 167
Period size: 35 Copynumber: 4.8 Consensus size: 35
5054739 CTCAATTTAA
* *
5054749 CTGGCACCCAATGAAAAGTTTTAAGCGCAGCTTAG
1 CTGGCACCCAATGAAAAGATTTAAGCCCAGCTTAG
*
5054784 CTAGG-ACCCAAT--AAAGATTTAAACCCAGCTTAG
1 CT-GGCACCCAATGAAAAGATTTAAGCCCAGCTTAG
* * * * *
5054817 CTGGTATCTAAT-AAAGAGTTTTAAGCCCAACTTAG
1 CTGGCACCCAATGAAA-AGATTTAAGCCCAGCTTAG
** *
5054852 CTGGCATTCAATGAAAAGATTTAAGTCCAGCTTAG
1 CTGGCACCCAATGAAAAGATTTAAGCCCAGCTTAG
5054887 CTGGCACCCAATG-AAA-ATTTAAGCC
1 CTGGCACCCAATGAAAAGATTTAAGCC
5054912 TAGTATTAAC
Statistics
Matches: 106, Mismatches: 17, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
32 2 0.02
33 33 0.31
34 5 0.05
35 61 0.58
36 5 0.05
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (35 bp):
CTGGCACCCAATGAAAAGATTTAAGCCCAGCTTAG
Found at i:5054909 original size:68 final size:67
Alignment explanation
Indices: 5054749--5054911 Score: 170
Period size: 68 Copynumber: 2.4 Consensus size: 67
5054739 CTCAATTTAA
* *
5054749 CTGGCACCCAATGAAAAGTTTTAAGCGCAGCTTAGCTAGGACCCAATAAAGATTTAAACCCAGCT
1 CTGGCACCCAATGAAAAG-TTTAAGCCCAACTTAGCTAGGACCCAATAAAGATTTAAACCCAGCT
5054814 TAG
65 TAG
* * * ** **
5054817 CTGGTATCTAAT-AAAGAGTTTTAAGCCCAACTTAGCT-GGCATTCAATGAAAAGATTTAAGTCC
1 CTGGCACCCAATGAAA-AG-TTTAAGCCCAACTTAGCTAGG-ACCCAAT--AAAGATTTAAACCC
5054880 AGCTTAG
61 AGCTTAG
5054887 CTGGCACCCAATGAAAA-TTTAAGCC
1 CTGGCACCCAATGAAAAGTTTAAGCC
5054912 TAGTATTAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
67 5 0.06
68 41 0.53
70 29 0.37
71 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (67 bp):
CTGGCACCCAATGAAAAGTTTAAGCCCAACTTAGCTAGGACCCAATAAAGATTTAAACCCAGCTT
AG
Found at i:5054933 original size:33 final size:33
Alignment explanation
Indices: 5054896--5054960 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5054886 GCTGGCACCC
*
5054896 AATGAAAATTTAAGCCTAGTATTAACTAGCATT
1 AATGAAAATTTAAGCCCAGTATTAACTAGCATT
5054929 AATGAAAATTTAAGCCCAGTATTAACTAGCAT
1 AATGAAAATTTAAGCCCAGTATTAACTAGCAT
5054961 CAAGAAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (33 bp):
AATGAAAATTTAAGCCCAGTATTAACTAGCATT
Found at i:5055467 original size:6 final size:7
Alignment explanation
Indices: 5055443--5055494 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
5055433 AATAATAATA
*
5055443 AAAAATC
1 AAAAACC
**
5055450 AAAAATT
1 AAAAACC
5055457 AAAAACC
1 AAAAACC
5055464 AAAAACC
1 AAAAACC
5055471 AAAAACC
1 AAAAACC
*
5055478 AAAAAGC
1 AAAAACC
*
5055485 AAAAAGC
1 AAAAACC
5055492 AAA
1 AAA
5055495 TAATAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.73, C:0.17, G:0.04, T:0.06
Consensus pattern (7 bp):
AAAAACC
Found at i:5055501 original size:3 final size:3
Alignment explanation
Indices: 5055493--5055517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5055483 GCAAAAAGCA
5055493 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5055518 GGGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5056164 original size:26 final size:26
Alignment explanation
Indices: 5056128--5056191 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
5056118 AGGATTTGTA
* *
5056128 AAACTCTAAAATTAAAACCGTAAATG
1 AAACCCTAAAATTAAAACCCTAAATG
**
5056154 AAACCCTAAAATTAAGTCCCTAAATG
1 AAACCCTAAAATTAAAACCCTAAATG
*
5056180 AAATCCTAAAAT
1 AAACCCTAAAAT
5056192 GATCTAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (26 bp):
AAACCCTAAAATTAAAACCCTAAATG
Found at i:5059755 original size:51 final size:51
Alignment explanation
Indices: 5059699--5059856 Score: 142
Period size: 51 Copynumber: 3.1 Consensus size: 51
5059689 ACAAGAAAGA
* *
5059699 AAGATTCACCAGACTCCTAGTTTCGCAAAGGTTCTAAATTCGCAAAGATGC
1 AAGATTCACAAGACTCCTAGTTTCGCAAAGGTTCTAAATTCGCAAAGATAC
** * ** * * *
5059750 AAGATTCGTAA-AGTTTTAAGTTTTGCAAAGGTTTTAGATTCGCAAAGATAC
1 AAGATTCACAAGACTCCT-AGTTTCGCAAAGGTTCTAAATTCGCAAAGATAC
** * * *
5059801 AAGATTCACAAGGTTCCAAGTTTCGCAAAGG-TC-AAATTCACAAAAATAC
1 AAGATTCACAAGACTCCTAGTTTCGCAAAGGTTCTAAATTCGCAAAGATAC
*
5059850 AATATTC
1 AAGATTC
5059857 GTAAGGTTTC
Statistics
Matches: 82, Mismatches: 23, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
49 19 0.23
50 4 0.05
51 58 0.71
52 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (51 bp):
AAGATTCACAAGACTCCTAGTTTCGCAAAGGTTCTAAATTCGCAAAGATAC
Found at i:5059756 original size:17 final size:17
Alignment explanation
Indices: 5059720--5059830 Score: 64
Period size: 17 Copynumber: 6.5 Consensus size: 17
5059710 GACTCCTAGT
*
5059720 TTCGCAAAGGTTCTAA-A
1 TTCGCAAAGATTC-AAGA
*
5059737 TTCGCAAAGATGCAAGA
1 TTCGCAAAGATTCAAGA
* * * *
5059754 TTCGTAAAGTTTTAAGT
1 TTCGCAAAGATTCAAGA
* * **
5059771 TTTGCAAAGGTTTTAGA
1 TTCGCAAAGATTCAAGA
*
5059788 TTCGCAAAGATACAAGA
1 TTCGCAAAGATTCAAGA
* * *
5059805 TTCAC-AAGGTTCCAAGT
1 TTCGCAAAGATT-CAAGA
5059822 TTCGCAAAG
1 TTCGCAAAG
5059831 GTCAAATTCA
Statistics
Matches: 69, Mismatches: 22, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
16 6 0.09
17 60 0.87
18 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (17 bp):
TTCGCAAAGATTCAAGA
Found at i:5060141 original size:120 final size:121
Alignment explanation
Indices: 5059952--5060635 Score: 514
Period size: 119 Copynumber: 5.7 Consensus size: 121
5059942 AAATGAAGTA
* * * * * * * *
5059952 ACCAGGATCGAATTGAGGTAAAAAATGAATGA-CTGGGATGAAACCACGAA-TCATAAGAGATGA
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATC-AGGATGAAATCAC-AAGTCATAAGAAATGA
* * * * * * **
5060015 TTTAGATTGAGCCAAGATTGAATGACTGGGACAAAATCATGAGTTAAAAAATAAGGCG
64 TCTAGACTGAGCCAAGATCGAATGACCGGGATAAAATCACGAGTTAAAAAATAAAACG
* * * * * *
5060073 ACCAGGACCGAGTCGATGTCAAAAAT-AAT-AACCGAGATGAAATCACAAGTCATAAAAAATGAT
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAG-GATGAAATCACAAGTCATAAGAAATGAT
* ** ** * *
5060136 CTAGATTGAGCCAAGATCGGGTGACTAGGATAAAA-CTACAAGTT-AAAAATAAAATG
65 CTAGACTGAGCCAAGATCGAATGACCGGGATAAAATC-ACGAGTTAAAAAATAAAACG
* ** * * * * *
5060192 ACCAAGATCAAGTTAAGGTCTAAAAT-AATTATC-GAAATGAAATCACGAGTCATAAAAAATGAT
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAG-GATGAAATCACAAGTCATAAGAAATGAT
* * * * *
5060255 CTAGACTAAGCTAAGAT-TAGATGAACGGGATAAAATCACGAG-TCAAAAATAAAACG
65 CTAGACTGAGCCAAGATCGA-ATGACCGGGATAAAATCACGAGTTAAAAAATAAAACG
* * * * * * **
5060311 ACCAAGATTGAATCGAAGTAAAAAATAAATGACCAGGAT-AAAACTATGAGTCATAAGAAATGAT
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAGGATGAAATC-ACAAGTCATAAGAAATGAT
* * * * * **
5060375 CTTAGACTGAGCCAAGAACGAGTGACCAGGATAAAATCATGAGTCAAAAAATAAAGTG
65 C-TAGACTGAGCCAAGATCGAATGACCGGGATAAAATCACGAGTTAAAAAATAAAACG
* * * ** * ** **
5060433 ACCAAGGTCAAGTTGAGGTTTAAAATGAATGATCAGGACAAAATCATGAGTCATAAGAAATGAT-
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAGGATGAAATCACAAGTCATAAGAAATGATC
* ** *
5060497 TCAGACTGAGCTAAGATCGAATGACCGAAACAAAATCACGAG-TAAAAAATAAAACG
66 T-AGACTGAGCCAAGATCGAATGACCGGGATAAAATCACGAGTTAAAAAATAAAACG
* *
5060553 ATCAAGATCGAGTCGA-GTCAAAAATAAATGATCAGGATGAAACCACAAGTCATAAGAAATGATC
1 ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAGGATGAAATCACAAGTCATAAGAAATGATC
* *
5060617 TGGACTAAGCCAAGATCGA
66 TAGACTGAGCCAAGATCGA
5060636 GAAAGTGATA
Statistics
Matches: 441, Mismatches: 105, Indels: 36
0.76 0.18 0.06
Matches are distributed among these distances:
118 1 0.00
119 180 0.41
120 113 0.26
121 85 0.19
122 58 0.13
123 4 0.01
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (121 bp):
ACCAAGATCGAGTCGAGGTCAAAAATAAATGATCAGGATGAAATCACAAGTCATAAGAAATGATC
TAGACTGAGCCAAGATCGAATGACCGGGATAAAATCACGAGTTAAAAAATAAAACG
Found at i:5060423 original size:121 final size:119
Alignment explanation
Indices: 5060238--5060636 Score: 369
Period size: 121 Copynumber: 3.3 Consensus size: 119
5060228 ATGAAATCAC
* * *
5060238 GAGTCATAAAAAATGATCTAGACTAAGCTAAGATTA-GA-TGAACGGGATAAAATCACGAGTCAA
1 GAGTCATAAGAAATGATCTAGACTAAGCCAAGA--ACGAGTG-ACCGGATAAAATCACGAGTCAA
*
5060301 AAATAAAACGACCAAGATTGAATCGAAGTAAAAAATAAATGACCAGGATAAAACTAT
63 AAATAAAACGACCAAGATTGAATCGAAGTAAAAAATAAATGATCAGGATAAAACTAT
* *
5060358 GAGTCATAAGAAATGATCTTAGACTGAGCCAAGAACGAGTGACCAGGATAAAATCATGAGTCAAA
1 GAGTCATAAGAAATGATC-TAGACTAAGCCAAGAACGAGTGACC-GGATAAAATCACGAGTC-AA
** * * * * ** * *
5060423 AAATAAAGTGACCAAG-GTCAAGTTGAGGTTTAAAATGAATGATCAGGACAAAA-TCAT
63 AAATAAAACGACCAAGATTGAA-TCGAAGTAAAAAATAAATGATCAGGATAAAACT-AT
* * * * * * *
5060480 GAGTCATAAGAAATGAT-TCAGACTGAGCTAAGATCGAATGACCGAAACAAAATCACGAGTAAAA
1 GAGTCATAAGAAATGATCT-AGACTAAGCCAAGAACGAGTGACCG-GATAAAATCACGAGTCAAA
* * * * * * *
5060544 AATAAAACGATCAAGATCGAGTCG-AGTCAAAAATAAATGATCAGGATGAAACCAC
64 AATAAAACGACCAAGATTGAATCGAAGTAAAAAATAAATGATCAGGATAAAACTAT
* * *
5060599 AAGTCATAAGAAATGATCTGGACTAAGCCAAGATCGAG
1 GAGTCATAAGAAATGATCTAGACTAAGCCAAGAACGAG
5060637 AAAGTGATAA
Statistics
Matches: 223, Mismatches: 44, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
119 54 0.24
120 41 0.18
121 69 0.31
122 59 0.26
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (119 bp):
GAGTCATAAGAAATGATCTAGACTAAGCCAAGAACGAGTGACCGGATAAAATCACGAGTCAAAAA
TAAAACGACCAAGATTGAATCGAAGTAAAAAATAAATGATCAGGATAAAACTAT
Found at i:5060512 original size:242 final size:237
Alignment explanation
Indices: 5060045--5060636 Score: 631
Period size: 242 Copynumber: 2.5 Consensus size: 237
5060035 AATGACTGGG
* ** * * * * *
5060045 ACAAAATCATGAGTTAAAAAATAAGGCGACCAGGACCGAGTCGATGTCAAAAAT-AATAACC-GA
1 ACAAAATCACGAG-TAAAAAATAAAACGACCAAGATCGAATCGA-GTAAAAAATAAATGACCAG-
* * * * * *
5060108 GATGAAATCACAAGTCATAAAAAATGATCTAGATTGAGCCAAGATCGGGTGACTAGGATAAAACT
63 GATAAAACCACAAGTCATAAGAAATGATCTAGACTGAGCCAAGATCGAGTGACCAGGATAAAACT
* *
5060173 ACAAGTTAAAAATAAAATGACCAAGATCAAGTTAAGGTCTAAAATAATTATCGAAATGAAATCAC
128 ACAAGTAAAAAATAAAATGACCAAGATCAAGTTAAGGTCTAAAATAATGATCGAAA-GAAATCAC
**
5060238 GAGTCATAAAAAATGATCTAGACTAAGCTAAGATTAG-ATGAACGGG
192 GAGTCATAAAAAATGATCTAGACTAAGCTAAGA-TAGAATGAACGAA
* * *
5060284 ATAAAATCACGAGTCAAAAATAAAACGACCAAGATTGAATCGAAGTAAAAAATAAATGACCAGGA
1 ACAAAATCACGAGTAAAAAATAAAACGACCAAGATCGAATCG-AGTAAAAAATAAATGACCAGGA
* ** *
5060349 TAAAACTATGAGTCATAAGAAATGATCTTAGACTGAGCCAAGAACGAGTGACCAGGATAAAA-T-
65 TAAAACCACAAGTCATAAGAAATGATC-TAGACTGAGCCAAGATCGAGTGACCAGGATAAAACTA
* * * * *
5060412 CATGAGTCAAAAAATAAAGTGACCAAGGTCAAGTTGAGGTTTAAAATGAATGATCAGGACA-AAA
129 CA--AGT-AAAAAATAAAATGACCAAGATCAAGTTAAGGTCTAAAAT-AATGATC--GAAAGAAA
* * * * *
5060476 TCATGAGTCATAAGAAATGAT-TCAGACTGAGCTAAGATCGAATGACCGAA
188 TCACGAGTCATAAAAAATGATCT-AGACTAAGCTAAGATAGAATGAACGAA
* * * *
5060526 ACAAAATCACGAGTAAAAAATAAAACGATCAAGATCGAGTCGAGTCAAAAATAAATGATCAGGAT
1 ACAAAATCACGAGTAAAAAATAAAACGACCAAGATCGAATCGAGTAAAAAATAAATGACCAGGAT
* * *
5060591 GAAACCACAAGTCATAAGAAATGATCTGGACTAAGCCAAGATCGAG
66 AAAACCACAAGTCATAAGAAATGATCTAGACTGAGCCAAGATCGAG
5060637 AAAGTGATAA
Statistics
Matches: 292, Mismatches: 49, Indels: 23
0.80 0.13 0.06
Matches are distributed among these distances:
238 32 0.11
239 42 0.14
240 51 0.17
241 80 0.27
242 84 0.29
244 3 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.19
Consensus pattern (237 bp):
ACAAAATCACGAGTAAAAAATAAAACGACCAAGATCGAATCGAGTAAAAAATAAATGACCAGGAT
AAAACCACAAGTCATAAGAAATGATCTAGACTGAGCCAAGATCGAGTGACCAGGATAAAACTACA
AGTAAAAAATAAAATGACCAAGATCAAGTTAAGGTCTAAAATAATGATCGAAAGAAATCACGAGT
CATAAAAAATGATCTAGACTAAGCTAAGATAGAATGAACGAA
Found at i:5077321 original size:20 final size:20
Alignment explanation
Indices: 5077257--5077336 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
5077247 AAGAATTTTC
*
5077257 AAAA-ATTTT-AAAAATACT
1 AAAATATTTTAAAAAATTCT
* *
5077275 AAAAATAAATTCTAAAAAATTTTT
1 -AAAAT--ATTTTAAAAAA-TTCT
5077299 AAAA-ACTTTTAAAAAATTCT
1 AAAATA-TTTTAAAAAATTCT
*
5077319 AAAATATTTTCAAAAATT
1 AAAATATTTTAAAAAATT
5077337 ACAAACAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.08
20 19 0.40
21 10 0.21
22 4 0.08
23 9 0.19
24 2 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATATTTTAAAAAATTCT
Found at i:5077347 original size:31 final size:31
Alignment explanation
Indices: 5077257--5077354 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
5077247 AAGAATTTTC
* *
5077257 AAAAATTTTAAAAATAC-TAAAAATAAATTCTA
1 AAAAATTTTCAAAA-ACTTACAAA-AAATTCTA
* **
5077289 AAAAATTTTTAAAAACTTTTAAAAAATTCTA
1 AAAAATTTTCAAAAACTTACAAAAAATTCTA
*
5077320 AAATATTTTCAAAAA-TTACAAACAAATT-TA
1 AAAAATTTTCAAAAACTTACAAA-AAATTCTA
5077350 AAAAA
1 AAAAA
5077355 AGGTGATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.20
31 28 0.50
32 17 0.30
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAATTTTCAAAAACTTACAAAAAATTCTA
Found at i:5077434 original size:24 final size:24
Alignment explanation
Indices: 5077379--5077437 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
5077369 AGAAATTATA
* *
5077379 AAAACTAAAAAAATATTACAACTT
1 AAAATTAAAAAAATATTAAAACTT
* *
5077403 AAAATTAAAAAAATCTTAAAATTT
1 AAAATTAAAAAAATATTAAAACTT
* *
5077427 TAATTTAAAAA
1 AAAATTAAAAA
5077438 TCCAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATTAAAAAAATATTAAAACTT
Found at i:5077641 original size:10 final size:9
Alignment explanation
Indices: 5077615--5077654 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
5077605 CTTAATAATT
5077615 TTAAAAAAA
1 TTAAAAAAA
*
5077624 TTATAAAAAG
1 TTA-AAAAAA
5077634 TTAAAAAAA
1 TTAAAAAAA
5077643 TTTAAAAAAA
1 -TTAAAAAAA
5077653 TT
1 TT
5077655 GAAATATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 10 0.37
10 17 0.63
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:5077651 original size:19 final size:19
Alignment explanation
Indices: 5077615--5077650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5077605 CTTAATAATT
5077615 TTAAAAAAATTATAAAAAG
1 TTAAAAAAATTATAAAAAG
5077634 TTAAAAAAATT-TAAAAA
1 TTAAAAAAATTATAAAAA
5077651 AATTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TTAAAAAAATTATAAAAAG
Found at i:5077826 original size:20 final size:20
Alignment explanation
Indices: 5077809--5077854 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5077799 TTTGTAATTT
5077809 TTTTTACAATTTTTTAATAA
1 TTTTTACAATTTTTTAATAA
* * *
5077829 TTTTTAGATTTTTTTAAAAA
1 TTTTTACAATTTTTTAATAA
5077849 TTTTTA
1 TTTTTA
5077855 TATTTTTATT
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:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTACAATTTTTTAATAA
Found at i:5077832 original size:10 final size:9
Alignment explanation
Indices: 5077819--5077881 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 9
5077809 TTTTTACAAT
5077819 TTTTTAATAA
1 TTTTTAAT-A
*
5077829 TTTTTAGATT
1 TTTTTA-ATA
*
5077839 TTTTTAAAAA
1 TTTTT-AATA
5077849 TTTTT-ATA
1 TTTTTAATA
*
5077857 TTTTTATTA
1 TTTTTAATA
*
5077866 TTTTTAATT
1 TTTTTAATA
5077875 TTTTTAA
1 TTTTTAA
5077882 GTTCTTTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
8 7 0.16
9 16 0.37
10 17 0.40
11 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:5077859 original size:20 final size:20
Alignment explanation
Indices: 5077818--5077861 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5077808 TTTTTTACAA
*
5077818 TTTTTTAATAATTTTTAGAT
1 TTTTTTAAAAATTTTTAGAT
*
5077838 TTTTTTAAAAATTTTTATAT
1 TTTTTTAAAAATTTTTAGAT
5077858 TTTT
1 TTTT
5077862 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTTAAAAATTTTTAGAT
Found at i:5077905 original size:10 final size:10
Alignment explanation
Indices: 5077797--5077906 Score: 52
Period size: 10 Copynumber: 11.3 Consensus size: 10
5077787 AAATGAAAAG
*
5077797 TTTTTGTAAT
1 TTTTTTTAAT
5077807 TTTTTTTACA-
1 TTTTTTTA-AT
*
5077817 ATTTTTTAAT
1 TTTTTTTAAT
**
5077827 AATTTTTAGA-
1 TTTTTTTA-AT
*
5077837 TTTTTTTAAA
1 TTTTTTTAAT
**
5077847 AATTTTT-A-
1 TTTTTTTAAT
*
5077855 TATTTTT-AT
1 TTTTTTTAAT
*
5077864 TATTTTTAA-
1 TTTTTTTAAT
5077873 TTTTTTTAAGT
1 TTTTTTTAA-T
* *
5077884 TCTTTTGAAT
1 TTTTTTTAAT
5077894 TTTTTTTAAT
1 TTTTTTTAAT
5077904 TTT
1 TTT
5077907 ACAAAATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.09
9 18 0.23
10 45 0.57
11 9 0.11
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:5077960 original size:19 final size:18
Alignment explanation
Indices: 5077937--5077989 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
5077927 AAATTGTCAC
*
5077937 TTTTTGGATTTTTTAGAATG
1 TTTTTGGATTTTTTA-AA-A
5077957 TTTTTGGATTTTATTAAAA
1 TTTTTGGATTTT-TTAAAA
5077976 -TTTTGAGATTTTTT
1 TTTTTG-GATTTTTT
5077990 TAATTGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.23
19 6 0.20
20 14 0.47
21 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (18 bp):
TTTTTGGATTTTTTAAAA
Found at i:5079612 original size:17 final size:17
Alignment explanation
Indices: 5079590--5079625 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5079580 TCTGTTTTTA
*
5079590 TTTTATTTTTTTTAATT
1 TTTTATTTTATTTAATT
*
5079607 TTTTATTTTATTTCATT
1 TTTTATTTTATTTAATT
5079624 TT
1 TT
5079626 ATTTTAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTTATTTAATT
Found at i:5079629 original size:22 final size:22
Alignment explanation
Indices: 5079584--5079685 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 22
5079574 CTGTTTTCTG
*
5079584 TTTTTATTTTATTT-TTTTTAAT
1 TTTTTATTTTATTTCATTTT-AT
5079606 TTTTTATTTTATTTCATTTTAT
1 TTTTTATTTTATTTCATTTTAT
** * *
5079628 TTTAGATTTT-TTTTATTTTTAC
1 TTTTTATTTTATTTCA-TTTTAT
* *
5079650 TTGTTATTATTATTTTCATCTTTAG
1 TTTTTATT-TTA-TTTCAT-TTTAT
*
5079675 TTATTATTTTA
1 TTTTTATTTTA
5079686 CTCATCACTT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.06
22 34 0.54
23 6 0.10
24 4 0.06
25 15 0.24
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTATTTTATTTCATTTTAT
Found at i:5079641 original size:16 final size:14
Alignment explanation
Indices: 5079585--5079646 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
5079575 TGTTTTCTGT
5079585 TTTTATTTTATTTT-
1 TTTTATTTT-TTTTA
*
5079599 TTTTA-ATTTTTTA
1 TTTTATTTTTTTTA
*
5079612 TTTTATTTCATTTTA
1 TTTTATTT-TTTTTA
5079627 TTTTAGATTTTTTTTA
1 TTTT--ATTTTTTTTA
5079643 TTTT
1 TTTT
5079647 TACTTGTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.10
13 7 0.18
14 6 0.15
15 9 0.23
16 9 0.23
17 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:5081140 original size:4 final size:4
Alignment explanation
Indices: 5081131--5081158 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5081121 ATAAGTTTGC
5081131 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
5081159 TCATTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:5081214 original size:20 final size:20
Alignment explanation
Indices: 5081159--5081215 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
5081149 TTATTTATTT
5081159 TCATTCATTTCATACATCTCAC
1 TCATTCA-TTCAT-CATCTCAC
**
5081181 TCATTCATAGATCATCATCA-
1 TCATTCATTCATCATC-TCAC
5081201 TCATTCATTCATCAT
1 TCATTCATTCATCAT
5081216 GTCATTGCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 17 0.57
21 6 0.20
22 7 0.23
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (20 bp):
TCATTCATTCATCATCTCAC
Found at i:5086454 original size:62 final size:62
Alignment explanation
Indices: 5086352--5086470 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
5086342 TCTAGGTAAA
* *
5086352 ATTCTTAAGTCTTTCGAGCTGAATCTATTTTAAAATTAAGATTTATAAGACTTTCGGATAAG
1 ATTCATAAGTCTTTCGAGCTAAATCTATTTTAAAATTAAGATTTATAAGACTTTCGGATAAG
* * * * *
5086414 ATTCATAAGTTTTTCGAGTTAAATTTATTTT-AGATATAAGATTTGTAAGACTTTCGG
1 ATTCATAAGTCTTTCGAGCTAAATCTATTTTAAAAT-TAAGATTTATAAGACTTTCGG
5086471 GCCTAATCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 3 0.06
62 46 0.94
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (62 bp):
ATTCATAAGTCTTTCGAGCTAAATCTATTTTAAAATTAAGATTTATAAGACTTTCGGATAAG
Found at i:5086562 original size:84 final size:84
Alignment explanation
Indices: 5086411--5086567 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
5086401 ACTTTCGGAT
* * * * * *
5086411 AAGATTCATAAGTTTTTCGAGTTAAATTTATTTTAGATATAAGATTTGTAAGACTTTCGGGCCTA
1 AAGATTCATAAGTTTTTCGAGCTAAATCTATTTTAGATACAAGATTTATAAGACGTTCAGGCCTA
5086476 ATCTCTAAGTCTTCCAAGC
66 ATCTCTAAGTCTTCCAAGC
* *
5086495 AAGATTCATAAGTCTTTT-GAGCTGAATCTATTTTAGAGT-CAAGATTTATAAGACGTTCAGGCG
1 AAGATTCATAAGT-TTTTCGAGCTAAATCTATTTTAGA-TACAAGATTTATAAGACGTTCAGGCC
5086558 TAATCTCTAA
64 TAATCTCTAA
5086568 TACCTCTGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 58 0.92
85 5 0.08
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (84 bp):
AAGATTCATAAGTTTTTCGAGCTAAATCTATTTTAGATACAAGATTTATAAGACGTTCAGGCCTA
ATCTCTAAGTCTTCCAAGC
Found at i:5087818 original size:6 final size:5
Alignment explanation
Indices: 5087795--5087842 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
5087785 CATCCTATTT
* *
5087795 TTTTA TTTTA -TTTA TTTTA CTTT- TTCTA TTTTA TTTTCA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT
5087843 TAGATTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 6 0.17
5 25 0.69
6 5 0.14
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:5090872 original size:78 final size:79
Alignment explanation
Indices: 5090790--5090946 Score: 289
Period size: 78 Copynumber: 2.0 Consensus size: 79
5090780 AAGCGCAACA
* *
5090790 AAAAAATAAAATAAAATAAGTTTTGTTTTTGGACCTTTTTTAATTTTT-TTTTTTTTCTTCTATT
1 AAAAAATAAAATAAAATAAGTTTTGTTTTTGGACCTTGTTTAATTTTTCCTTTTTTTCTTCTATT
5090854 TATATTTTGTTTAC
66 TATATTTTGTTTAC
5090868 AAAAAATAAAATAAAATAAGTTTTGTTTTTGGACCTTGTTTAATTTTTCCTTTTTTTCTTCTATT
1 AAAAAATAAAATAAAATAAGTTTTGTTTTTGGACCTTGTTTAATTTTTCCTTTTTTTCTTCTATT
5090933 TATATTTTGTTTAC
66 TATATTTTGTTTAC
5090947 TTGTCCTTCT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 47 0.62
79 29 0.38
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (79 bp):
AAAAAATAAAATAAAATAAGTTTTGTTTTTGGACCTTGTTTAATTTTTCCTTTTTTTCTTCTATT
TATATTTTGTTTAC
Found at i:5095048 original size:18 final size:17
Alignment explanation
Indices: 5095021--5095054 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5095011 AATTAAATAA
5095021 AAACTAAAATTAAAATC
1 AAACTAAAATTAAAATC
*
5095038 AAACTATAAATTGAAAT
1 AAACTA-AAATTAAAAT
5095055 GTTTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (17 bp):
AAACTAAAATTAAAATC
Found at i:5096635 original size:16 final size:18
Alignment explanation
Indices: 5096604--5096636 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5096594 GATAATTTAA
5096604 AATATAACATTATGATAT
1 AATATAACATTATGATAT
5096622 AATATAA-A-TATGATA
1 AATATAACATTATGATA
5096637 AAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (18 bp):
AATATAACATTATGATAT
Found at i:5097295 original size:11 final size:12
Alignment explanation
Indices: 5097272--5097297 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5097262 ATGATTTTGG
5097272 ATTGATTTAAAA
1 ATTGATTTAAAA
5097284 ATTGATTTAAAA
1 ATTGATTTAAAA
5097296 AT
1 AT
5097298 CGACGTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTGATTTAAAA
Found at i:5102401 original size:28 final size:28
Alignment explanation
Indices: 5102370--5102431 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5102360 TATTAGATAA
* * *
5102370 TATTTTTATTATATTAA-ATTAATAAAAT
1 TATTTTT-TGATATAAACATTAACAAAAT
*
5102398 TATTTCTTGATATAAACATTAACAAAAT
1 TATTTTTTGATATAAACATTAACAAAAT
5102426 TATTTT
1 TATTTT
5102432 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTTTTTGATATAAACATTAACAAAAT
Found at i:5104253 original size:21 final size:21
Alignment explanation
Indices: 5104223--5104266 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5104213 GTTTTAACTT
5104223 AAAAACAGTCTTTTCAACAAA
1 AAAAACAGTCTTTTCAACAAA
*
5104244 AAAAATAGTCTTTTCAACAAA
1 AAAAACAGTCTTTTCAACAAA
5104265 AA
1 AA
5104267 CTATTTTTTA
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:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAACAGTCTTTTCAACAAA
Found at i:5104328 original size:25 final size:25
Alignment explanation
Indices: 5104281--5104329 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5104271 TTTTTATCTT
* *
5104281 AAAACTTTATTTTTATTGAATTTTG
1 AAAACTATATTTTTATTCAATTTTG
5104306 AAAACTATATTTTT-TTCATATTTT
1 AAAACTATATTTTTATTCA-ATTTT
5104330 CAATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
AAAACTATATTTTTATTCAATTTTG
Found at i:5104899 original size:129 final size:129
Alignment explanation
Indices: 5104745--5105011 Score: 525
Period size: 129 Copynumber: 2.1 Consensus size: 129
5104735 ATTTATATAA
5104745 TTTGAAAATACAATTAAATGAGGTTAAATAAGAAAAATTTTTCACTTTCTCTCTAAAATCTTAAA
1 TTTGAAAATACAATTAAATGAGGTTAAATAAGAAAAATTTTTCACTTTCTCTCTAAAATCTTAAA
5104810 AATCTCAGGGAGAAAGAGTTTTTTATTTTTTCCTACTTTCTTACTTTTTAATATTGTTAAAAAT
66 AATCTCAGGGAGAAAGAGTTTTTTATTTTTTCCTACTTTCTTACTTTTTAATATTGTTAAAAAT
5104874 TTTGAAAATACAATTAAATGAGGTTAAATAAGAAAAATTTTTCACTTTCTCTCTAAAATCTTAAA
1 TTTGAAAATACAATTAAATGAGGTTAAATAAGAAAAATTTTTCACTTTCTCTCTAAAATCTTAAA
5104939 AATCTCAGGGAGAAAGAGTTTTTTATTTTTTCCTACTTTCTTACTTTTTAATATTGTTAAAAAT
66 AATCTCAGGGAGAAAGAGTTTTTTATTTTTTCCTACTTTCTTACTTTTTAATATTGTTAAAAAT
*
5105003 TTTAAAAAT
1 TTTGAAAAT
5105012 TTTTAAAAAT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 137 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (129 bp):
TTTGAAAATACAATTAAATGAGGTTAAATAAGAAAAATTTTTCACTTTCTCTCTAAAATCTTAAA
AATCTCAGGGAGAAAGAGTTTTTTATTTTTTCCTACTTTCTTACTTTTTAATATTGTTAAAAAT
Found at i:5107234 original size:18 final size:18
Alignment explanation
Indices: 5107211--5107250 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5107201 GGGTAGAAAG
* *
5107211 TTTTTTTT-TTATTTTTA
1 TTTTTTTTGTTATATATA
5107228 TTTTTTTTGTTATATATA
1 TTTTTTTTGTTATATATA
5107246 TTTTT
1 TTTTT
5107251 GTATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTTTGTTATATATA
Found at i:5110772 original size:31 final size:31
Alignment explanation
Indices: 5110734--5110795 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5110724 AAATTGTAAG
5110734 CAAGGCCCACACTGAATTAAACATTCTACAA
1 CAAGGCCCACACTGAATTAAACATTCTACAA
*
5110765 CAAGGCCCACACTGAATTAGACATTCTACAA
1 CAAGGCCCACACTGAATTAAACATTCTACAA
5110796 TGACATGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.19
Consensus pattern (31 bp):
CAAGGCCCACACTGAATTAAACATTCTACAA
Found at i:5114281 original size:22 final size:21
Alignment explanation
Indices: 5114250--5114301 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
5114240 CGCTAATTAC
5114250 TTAAAATTTTTAAATCAT-TTTT
1 TTAAAA-TTTTAAA-CATATTTT
*
5114272 TTAAACTTTTAAACATATTTT
1 TTAAAATTTTAAACATATTTT
5114293 TTAAAATTT
1 TTAAAATTT
5114302 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 19 0.70
22 5 0.19
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTTTAAACATATTTT
Found at i:5115801 original size:19 final size:20
Alignment explanation
Indices: 5115772--5115809 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5115762 TTGTTTATTT
5115772 ATTAGTTTATTATAATAAAA
1 ATTAGTTTATTATAATAAAA
*
5115792 ATTA-TTTATTATATTAAA
1 ATTAGTTTATTATAATAAA
5115810 TTAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTAGTTTATTATAATAAAA
Found at i:5124623 original size:14 final size:14
Alignment explanation
Indices: 5124604--5124638 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5124594 GTATATCACA
5124604 TATAATT-ATTATAT
1 TATAATTAATTA-AT
5124618 TATAATTAATTAAT
1 TATAATTAATTAAT
5124632 TATAATT
1 TATAATT
5124639 TAAAATTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATAATTAATTAAT
Found at i:5127877 original size:14 final size:14
Alignment explanation
Indices: 5127858--5127884 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5127848 ACTGTGAATC
5127858 CATTTTGAGTTTCA
1 CATTTTGAGTTTCA
5127872 CATTTTGAGTTTC
1 CATTTTGAGTTTC
5127885 TCTGTGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
CATTTTGAGTTTCA
Found at i:5128394 original size:16 final size:17
Alignment explanation
Indices: 5128373--5128407 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5128363 TAAATTATTT
5128373 TTTAA-TTTTAAATTAA
1 TTTAATTTTTAAATTAA
*
5128389 TTTAATTTTTAATTTAA
1 TTTAATTTTTAAATTAA
5128406 TT
1 TT
5128408 ATTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAATTTTTAAATTAA
Found at i:5128441 original size:21 final size:19
Alignment explanation
Indices: 5128409--5128457 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
5128399 AATTTAATTA
* *
5128409 TTTATTATTATTATTATTT
1 TTTATTATTATTAATATAT
5128428 TTTAGTTATCTATTAATATAT
1 TTTA-TTAT-TATTAATATAT
*
5128449 TTTACTATT
1 TTTATTATT
5128458 TATCTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATTATTATTAATATAT
Found at i:5128441 original size:24 final size:24
Alignment explanation
Indices: 5128410--5128479 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
5128400 ATTTAATTAT
5128410 TTAT-TATTATTATTATTTTTTAG
1 TTATCTATTATTATTATTTTTTAG
* * *
5128433 TTATCTATTAATA-TATTTTACTAT
1 TTATCTATTATTATTATTTT-TTAG
* *
5128457 TTATCTATTTTTTTTTATTTTTT
1 TTATCTA-TTATTATTATTTTTT
5128480 TTGATCAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
23 10 0.28
24 16 0.44
25 4 0.11
26 6 0.17
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (24 bp):
TTATCTATTATTATTATTTTTTAG
Found at i:5129258 original size:5 final size:5
Alignment explanation
Indices: 5129248--5129280 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
5129238 TGATTCAAGG
5129248 TTTAT TTTAT TTTAT TTTA- TTTAT TATTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTT
5129281 TTAATTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:5129509 original size:107 final size:111
Alignment explanation
Indices: 5129381--5129588 Score: 268
Period size: 111 Copynumber: 1.9 Consensus size: 111
5129371 AAAAATTTTT
* * *
5129381 AAAAAATAATATTTTGAGAAAAAGTT-ACAAGTATCAATTTTTCTTAAAGAT-AA-A-TTTAAAA
1 AAAAAATAATATTTTGAGAAAAAGTTGA-AAGTATCAATTTCTCTGAAAAATAAAGATTTTAAAA
**
5129442 AATATATTTTTGAAG-AAAAGCTGATTGTATCAATTTCCTTTGAACAC
65 AATATATTTTT-AAGAAAAAGCTGAAAGTATCAATTTCCTTTGAACAC
*
5129489 AAAAAAT-AT-TTTTTAGGAAAAAGTTGAAAGTATCAATTTCTCTGAAAAATAAAAGATTTTAAA
1 AAAAAATAATATTTTGA-GAAAAAGTTGAAAGTATCAATTTCTCTGAAAAAT-AAAGATTTTAAA
*
5129552 AAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTT
64 AAATATATTTTTAAGAAAAAGCTGAAAGTATCAATTT
5129589 TTCTCAAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
106 5 0.06
107 31 0.36
108 8 0.09
109 2 0.02
110 4 0.05
111 36 0.42
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (111 bp):
AAAAAATAATATTTTGAGAAAAAGTTGAAAGTATCAATTTCTCTGAAAAATAAAGATTTTAAAAA
ATATATTTTTAAGAAAAAGCTGAAAGTATCAATTTCCTTTGAACAC
Found at i:5129554 original size:61 final size:60
Alignment explanation
Indices: 5129489--5129678 Score: 202
Period size: 61 Copynumber: 3.0 Consensus size: 60
5129479 CTTTGAACAC
* * *
5129489 AAAAAATAT-TTTTTAGGAAAAAGTTGAAAGTATCAATTTCTCTGAAAAATAAAAGATTTT
1 AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCT-AAAAATAAAAAATTTA
* *
5129549 AAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAGAATTTCAAAATT
1 AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCT-AAAA--ATAA----AAAATT
*
5129614 AA
59 TA
* * * *
5129616 AAAAATATATATTTTTGGGAAAAAGTTGAAAGTACCAATTTTTCTTAAAATAAAAACTTTA
1 AAAAA-ATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTAAAAATAAAAAATTTA
5129677 AA
1 AA
5129679 TGCTTAAAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
60 9 0.08
61 44 0.41
63 3 0.03
65 3 0.03
67 13 0.12
68 36 0.33
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (60 bp):
AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTAAAAATAAAAAATTTA
Found at i:5129627 original size:68 final size:62
Alignment explanation
Indices: 5129489--5129671 Score: 201
Period size: 68 Copynumber: 2.9 Consensus size: 62
5129479 CTTTGAACAC
* * * * **
5129489 AAAAAATAT-TTTTTAGGAAAAAGTTGAAAGTATCAATTTCTCTGAAAA-ATAAAAGATTTT
1 AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTCAAAATAGAAAAAATTAA
*
5129549 AAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAGAATTTCAAAATT
1 AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTCAAAA-TAGAA----AAAATT
5129614 AA
61 AA
* * *
5129616 AAAAATATATATTTTTGGGAAAAAGTTGAAAGTACCAATTTTTCTTAAAATA-AAAA
1 AAAAA-ATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTCAAAATAGAAAA
5129672 CTTTAAATGC
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
60 9 0.09
61 36 0.35
62 2 0.02
63 3 0.03
66 2 0.02
67 12 0.12
68 40 0.38
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (62 bp):
AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTCAAAATAGAAAAAATTAA
Found at i:5141724 original size:12 final size:12
Alignment explanation
Indices: 5141696--5141732 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5141686 CTAATTTTTC
5141696 TTTTTAATTTTAA
1 TTTTTAA-TTTAA
5141709 --TTTAATTTAA
1 TTTTTAATTTAA
5141719 TTTTTAATTTAA
1 TTTTTAATTTAA
5141731 TT
1 TT
5141733 ATTTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.23
11 5 0.23
12 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:5141725 original size:17 final size:16
Alignment explanation
Indices: 5141698--5141732 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
5141688 AATTTTTCTT
5141698 TTTAATTTTAATTTAA
1 TTTAATTTTAATTTAA
5141714 TTTAATTTTTAATTTAA
1 TTTAA-TTTTAATTTAA
5141731 TT
1 TT
5141733 ATTTTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATTTTAATTTAA
Found at i:5141748 original size:3 final size:3
Alignment explanation
Indices: 5141730--5141837 Score: 89
Period size: 3 Copynumber: 35.0 Consensus size: 3
5141720 TTTTAATTTA
* *
5141730 ATT ATT TTT CATT ATT ATT ATT ATT ATT ATT ATT ATTT ATCT ATT AAT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT
* *
5141778 ATT -TT -TT ATTT ATCT ATT ATT ATT ATT ATT TTT AGTT ATCT ATT AAT
1 ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT
5141825 A-T ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT
5141838 TATCTTTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
2 8 0.09
3 60 0.68
4 20 0.23
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5141860 original size:50 final size:47
Alignment explanation
Indices: 5141727--5141834 Score: 157
Period size: 47 Copynumber: 2.3 Consensus size: 47
5141717 AATTTTTAAT
* * *
5141727 TTAATTATTTTTCA-TTAT-TATTATTATTATTATTATTATTTATCTA
1 TTAA-TATTTTTTATTTATCTATTATTATTATTATTTTTAGTTATCTA
5141773 TTAATATTTTTTATTTATCTATTATTATTATTATTTTTAGTTATCTA
1 TTAATATTTTTTATTTATCTATTATTATTATTATTTTTAGTTATCTA
*
5141820 TTAATATATTTTATT
1 TTAATATTTTTTATT
5141835 ATTTATCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 8 0.14
46 8 0.14
47 40 0.71
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.66
Consensus pattern (47 bp):
TTAATATTTTTTATTTATCTATTATTATTATTATTTTTAGTTATCTA
Found at i:5142692 original size:18 final size:17
Alignment explanation
Indices: 5142669--5142706 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5142659 CAAGGTTTCT
5142669 TTTATTTTATT-TTATTTA
1 TTTA-TTTATTATTA-TTA
5142687 TTTATTTATTATTATTA
1 TTTATTTATTATTATTA
5142704 TTT
1 TTT
5142707 TAATTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTATTATTA
Found at i:5142842 original size:59 final size:60
Alignment explanation
Indices: 5142772--5142973 Score: 196
Period size: 59 Copynumber: 3.3 Consensus size: 60
5142762 TCAATAATTT
*
5142772 TTTTTCCCAAAA-AAAAATTTCAAAAAATAAATATTTTGAGAAAAAGTTGAAAGTATCAA
1 TTTTTCTCAAAATAAAAATTTCAAAAAATAAATATTTTGAGAAAAAGTTGAAAGTATCAA
* * * * *
5142831 TTTTTCTCAAAATTAGAATTTTAAAATAAAAAATATATATTTTTTG-GAAAAAGTTGGAAGTATC
1 TTTTTCTCAAAA-TAAAAATTT----CAAAAAATA-A-ATATTTTGAGAAAAAGTTGAAAGTATC
5142895 AA
59 AA
* * * * *
5142897 TTTTTTTTAAAATAAAAATTATC-AAGAA-AAATATTTTAAGGAAAAGTTGAAAGTATCAA
1 TTTTTCTCAAAATAAAAATT-TCAAAAAATAAATATTTTGAGAAAAAGTTGAAAGTATCAA
*
5142956 TTTTTCTTAAAATAAAAA
1 TTTTTCTCAAAATAAAAA
5142974 CTCTAAATGC
Statistics
Matches: 116, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
58 6 0.05
59 47 0.41
60 1 0.01
61 10 0.09
65 14 0.12
66 31 0.27
67 7 0.06
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (60 bp):
TTTTTCTCAAAATAAAAATTTCAAAAAATAAATATTTTGAGAAAAAGTTGAAAGTATCAA
Found at i:5144918 original size:29 final size:29
Alignment explanation
Indices: 5144876--5144938 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5144866 AAGAAAGATT
* *
5144876 AATAACTACGTTAATCT-GATACACATATA
1 AATAACTACATTAATCTCG-CACACATATA
5144905 AATAACTACATTAATCTCGCACACATATA
1 AATAACTACATTAATCTCGCACACATATA
5144934 AATAA
1 AATAA
5144939 TATAAGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (29 bp):
AATAACTACATTAATCTCGCACACATATA
Found at i:5148459 original size:24 final size:24
Alignment explanation
Indices: 5148430--5148500 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
5148420 ATTCTTAAAT
*
5148430 TTAAAAAGATATATATGTAAATTA
1 TTAAAAAGATATATATTTAAATTA
* **
5148454 TTAAAAAAAT-TA-ATTTTAAAGGA
1 TTAAAAAGATATATA-TTTAAATTA
5148477 -TAAAAAGATATATATTTAAATTA
1 TTAAAAAGATATATATTTAAATTA
5148500 T
1 T
5148501 ATAGATCTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 9 0.25
23 17 0.47
24 10 0.28
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (24 bp):
TTAAAAAGATATATATTTAAATTA
Found at i:5148776 original size:101 final size:107
Alignment explanation
Indices: 5148590--5148801 Score: 287
Period size: 101 Copynumber: 2.0 Consensus size: 107
5148580 TTATTAGTAA
* * *
5148590 ATTAATTTTAGAAGATAAAAATATATATTTAAATTATATATATTATTATAAAATTATTTGAAAAA
1 ATTAATTTTAAAAGATAAAAAGATATA-TT-AATTATATATATTATTATAAAATTATTAGAAAAA
*
5148655 TTAATTTTGGTAACTTATAATTTTTAAAT-ATTTTATTTATTTG
64 TTAATTTTGGTAACTAATAATTTTTAAATAATTTTATTTATTTG
5148698 ATTAATTTTAAAAGATAAAAAGATATA-T-ATT-TA-A-ATTA-TATATAAATTATTAG-AAAAT
1 ATTAATTTTAAAAGATAAAAAGATATATTAATTATATATATTATTATA-AAATTATTAGAAAAAT
*
5148756 TAATTTTGGATAACTAATAATTTTTAACTAATTTTATTTATTTG
65 TAATTTTGG-TAACTAATAATTTTTAAATAATTTTATTTATTTG
5148800 AT
1 AT
5148802 AAATACCATA
Statistics
Matches: 96, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
100 18 0.19
101 30 0.31
102 17 0.18
103 2 0.02
104 3 0.03
106 1 0.01
108 25 0.26
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (107 bp):
ATTAATTTTAAAAGATAAAAAGATATATTAATTATATATATTATTATAAAATTATTAGAAAAATT
AATTTTGGTAACTAATAATTTTTAAATAATTTTATTTATTTG
Found at i:5148822 original size:71 final size:71
Alignment explanation
Indices: 5148741--5148874 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
5148731 AATTATATAT
* * *
5148741 AAATTATTAGAAAATTAATTTTGGATAACTAATAATTTTTAACTAATTTTATTTATTTGATAAAT
1 AAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGATAAAT
5148806 ACCATA
66 ACCATA
*
5148812 AAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATATTTTTATTTAGTTGATAA
1 AAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGATAA
5148875 GCACTATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (71 bp):
AAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGATAAAT
ACCATA
Found at i:5148884 original size:71 final size:71
Alignment explanation
Indices: 5148736--5148885 Score: 228
Period size: 71 Copynumber: 2.1 Consensus size: 71
5148726 ATTTAAATTA
* * *
5148736 TATATAAATTATTAGAAAATTAATTTTGGATAACTAATAATTTTTAACTAATTTTATTTATTTGA
1 TATA-AAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGA
*
5148801 TAAATAC
65 TAAACAC
* *
5148808 CATAAAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATATTTTTATTTAGTTGAT
1 TATAAAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGAT
*
5148873 AAGCAC
66 AAACAC
5148879 TATAAAA
1 TATAAAA
5148886 CTAGATCTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 67 0.96
72 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (71 bp):
TATAAAATTATTAGAAAATTAATTTTGAATAACTAATAATTTTTAAATAATTTTATTTAGTTGAT
AAACAC
Found at i:5149517 original size:22 final size:22
Alignment explanation
Indices: 5149492--5149538 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
5149482 CCTTGTGTGC
*
5149492 TTTTGTGATCCTCCTGACTATA
1 TTTTGTGATCCTCCGGACTATA
*
5149514 -TTT-TGATCCTCCGGACTGTA
1 TTTTGTGATCCTCCGGACTATA
5149534 TTTTG
1 TTTTG
5149539 ACCCTGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (22 bp):
TTTTGTGATCCTCCGGACTATA
Found at i:5149522 original size:20 final size:20
Alignment explanation
Indices: 5149497--5149539 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5149487 TGTGCTTTTG
*
5149497 TGATCCTCCTGACTATATTT
1 TGATCCTCCGGACTATATTT
*
5149517 TGATCCTCCGGACTGTATTT
1 TGATCCTCCGGACTATATTT
5149537 TGA
1 TGA
5149540 CCCTGCTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (20 bp):
TGATCCTCCGGACTATATTT
Found at i:5149640 original size:3 final size:3
Alignment explanation
Indices: 5149632--5149669 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5149622 TAAATAAATA
5149632 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5149670 AAGGTCTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5149832 original size:51 final size:53
Alignment explanation
Indices: 5149742--5149850 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 53
5149732 TACTATATTA
*
5149742 AAAAAAGAATCAAAGTTAAAAACAAATGACATTCTATAAACACT-TACAAAAAG
1 AAAAAAGAATCAAAGTTAAAAACAAATGACATTCCATAAACA-TGTACAAAAAG
* * * *
5149795 AAAAAAG-AT-AAAGTTAAAGACAAATGA-GTTACCATAAATATGTATAAAAAG
1 AAAAAAGAATCAAAGTTAAAAACAAATGACATT-CCATAAACATGTACAAAAAG
5149846 AAAAA
1 AAAAA
5149851 TAATACTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
50 3 0.06
51 37 0.76
52 2 0.04
53 7 0.14
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.19
Consensus pattern (53 bp):
AAAAAAGAATCAAAGTTAAAAACAAATGACATTCCATAAACATGTACAAAAAG
Found at i:5150107 original size:22 final size:22
Alignment explanation
Indices: 5150082--5150148 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
5150072 AATATATATC
5150082 TAAATTATTAAAAAATTAATTT
1 TAAATTATTAAAAAATTAATTT
** *
5150104 TAAAGGA-TAAAAGA-TATATATT
1 TAAATTATTAAAAAATTA-AT-TT
*
5150126 TAAATTATTAGAAAATTAATTT
1 TAAATTATTAAAAAATTAATTT
5150148 T
1 T
5150149 GGATAACTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 15 0.44
23 7 0.21
24 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (22 bp):
TAAATTATTAAAAAATTAATTT
Found at i:5150774 original size:17 final size:18
Alignment explanation
Indices: 5150754--5150787 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5150744 TGTAATTATA
5150754 ATTTGAAT-AATTTTAAT
1 ATTTGAATAAATTTTAAT
5150771 ATTTGAATAAATTTTAA
1 ATTTGAATAAATTTTAA
5150788 ATGATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTGAATAAATTTTAAT
Found at i:5150869 original size:301 final size:300
Alignment explanation
Indices: 5150322--5150923 Score: 1012
Period size: 301 Copynumber: 2.0 Consensus size: 300
5150312 TTGATTAATT
5150322 TTAAAAGATAAAAAGATATATATATATTTCAATTATATACATGAATTATTAGAAATTTAATTTTG
1 TTAAAAGATAAAAAGATATATATATATTTCAATTATATACATGAATTATTAGAAATTTAATTTTG
*
5150387 ATTATATATTTTTCATTTTTTTAATTTTAAAAAACTTATCCAAGATTGATCTAGTTTGTAATTAT
66 ATTATATATTTTTCATATTTTTAATTTTAAAAAACTTATCCAAGATTGATCTAGTTTGTAATTAT
* *
5150452 AATTTGAATAATTTTAATATTTGAATAAATTTTAGATGATTTAATTTAGAATTAAAAGAAAGCTA
131 AATTTGAATAATTTTAATATTTGAATAAATTTTAAATGATTAAATTTAGAATTAAAAGAAAGCTA
** **
5150517 TTTTATTTAAAAATCTATCTTATGTGTCATCTCAAAAAGTTATTCATATAATTCATTTAATAAAT
196 TTTTATTTAAAAATCTATCTTACATGTCATCGAAAAAAGTTATTCATATAATTCATTTAATAAAT
* *
5150582 CTTATCAATATATTTATGTATATTATAATATATATATATA
261 CTTATCAAGATATCTATGTATATTATAATATATATATATA
*
5150622 TTAAAAGATAAAAAGATATATATATATTTCAATTATTTATATATGAATTATTAGAAATTTAATTT
1 TTAAAAGATAAAAAGATATATATATATTTCAATTA--TATACATGAATTATTAGAAATTTAATTT
* *
5150687 TGATTATATATTTTTCATATTTTTAATTTTAAAAAACTTATCCAATATTGATTTAG-TTGTAATT
64 TGATTATATATTTTTCATATTTTTAATTTTAAAAAACTTATCCAAGATTGATCTAGTTTGTAATT
5150751 ATAATTTGAATAATTTTAATATTTGAATAAATTTTAAATGATTAAATTT-GTAATTAAAAGAAAG
129 ATAATTTGAATAATTTTAATATTTGAATAAATTTTAAATGATTAAATTTAG-AATTAAAAGAAAG
* * *
5150815 TTATTTTATTTAAAAATTTATTTTACATGTCATCGAAAAAAGTTA-TCTATATAATTCATTTAAT
193 CTATTTTATTTAAAAATCTATCTTACATGTCATCGAAAAAAGTTATTC-ATATAATTCATTTAAT
5150879 AAATCTTATCAAGATATCTATGTATATTATAATATATATATATA
257 AAATCTTATCAAGATATCTATGTATATTATAATATATATATATA
5150923 T
1 T
5150924 GTATATATGT
Statistics
Matches: 283, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
300 38 0.13
301 165 0.58
302 80 0.28
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (300 bp):
TTAAAAGATAAAAAGATATATATATATTTCAATTATATACATGAATTATTAGAAATTTAATTTTG
ATTATATATTTTTCATATTTTTAATTTTAAAAAACTTATCCAAGATTGATCTAGTTTGTAATTAT
AATTTGAATAATTTTAATATTTGAATAAATTTTAAATGATTAAATTTAGAATTAAAAGAAAGCTA
TTTTATTTAAAAATCTATCTTACATGTCATCGAAAAAAGTTATTCATATAATTCATTTAATAAAT
CTTATCAAGATATCTATGTATATTATAATATATATATATA
Found at i:5150928 original size:12 final size:12
Alignment explanation
Indices: 5150892--5150939 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
5150882 TCTTATCAAG
*
5150892 ATATCTATGTAT
1 ATATATATGTAT
*
5150904 AT-TATAATATAT
1 ATATAT-ATGTAT
5150916 ATATATATGTAT
1 ATATATATGTAT
*
5150928 ATATGTATGTAT
1 ATATATATGTAT
5150940 GTGTATGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.83
13 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:5152418 original size:25 final size:25
Alignment explanation
Indices: 5152387--5152440 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
5152377 AATAAAATAT
5152387 TATTT-TAAATATAAATATAAATTAAA
1 TATTTATAAA-ATAAATAT-AATTAAA
*
5152413 TATTTATAAAATATATATAATTAAA
1 TATTTATAAAATAAATATAATTAAA
5152438 TAT
1 TAT
5152441 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 10 0.38
26 12 0.46
27 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTTATAAAATAAATATAATTAAA
Found at i:5157095 original size:20 final size:20
Alignment explanation
Indices: 5157066--5157104 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5157056 AAGTAAAGTT
5157066 GTTATAAATATTTGATTTTA
1 GTTATAAATATTTGATTTTA
* *
5157086 GTTATTAATATTTTATTTT
1 GTTATAAATATTTGATTTT
5157105 TTAAAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
GTTATAAATATTTGATTTTA
Found at i:5158198 original size:15 final size:16
Alignment explanation
Indices: 5158173--5158203 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5158163 AAGACGTGGG
5158173 GAAAAAGAAAAAGAAA
1 GAAAAAGAAAAAGAAA
5158189 GAAAAA-AAAAAGAAA
1 GAAAAAGAAAAAGAAA
5158204 AAAGAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
GAAAAAGAAAAAGAAA
Found at i:5158203 original size:27 final size:27
Alignment explanation
Indices: 5158173--5158239 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
5158163 AAGACGTGGG
5158173 GAAAAAGAAAAAGAAAGAAAAAAAAAA
1 GAAAAAGAAAAAGAAAGAAAAAAAAAA
* * *
5158200 GAAAAA-AGAAAGGAAAGAGAAAAATAA
1 GAAAAAGA-AAAAGAAAGAAAAAAAAAA
*
5158227 GAAGGAAGAAAAA
1 GAA-AAAGAAAAA
5158240 TGATGAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
27 25 0.78
28 5 0.16
29 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (27 bp):
GAAAAAGAAAAAGAAAGAAAAAAAAAA
Found at i:5158215 original size:12 final size:11
Alignment explanation
Indices: 5158176--5158239 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
5158166 ACGTGGGGAA
5158176 AAAG-AAAAAG
1 AAAGAAAAAAG
*
5158186 AAAGAAAAAAA
1 AAAGAAAAAAG
5158197 AAAGAAAAAAG
1 AAAGAAAAAAG
* *
5158208 AAAGGAAAGAG
1 AAAGAAAAAAG
5158219 AAA-AATAAGAAG
1 AAAGAA-AA-AAG
*
5158231 GAAGAAAAA
1 AAAGAAAAA
5158240 TGATGAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.12
11 30 0.70
12 6 0.14
13 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:5158220 original size:18 final size:18
Alignment explanation
Indices: 5158174--5158223 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5158164 AGACGTGGGG
*
5158174 AAAAAGAAAAAGAAAGAAA
1 AAAAAGAGAAA-AAAGAAA
*
5158193 AAAAAAAGAAAAAAGAAA
1 AAAAAGAGAAAAAAGAAA
**
5158211 GGAAAGAGAAAAA
1 AAAAAGAGAAAAA
5158224 TAAGAAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAAAGAAA
Found at i:5159133 original size:16 final size:16
Alignment explanation
Indices: 5159095--5159133 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5159085 GTTAATTAGT
5159095 AAAAAAAATAAAAAAG
1 AAAAAAAATAAAAAAG
***
5159111 GGTAAAAATAAAAAAG
1 AAAAAAAATAAAAAAG
5159127 AAAAAAA
1 AAAAAAA
5159134 TGTGAAATTT
Statistics
Matches: 17, Mismatches: 6, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (16 bp):
AAAAAAAATAAAAAAG
Found at i:5159659 original size:32 final size:30
Alignment explanation
Indices: 5159623--5159690 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
5159613 GAATAACTTT
* *
5159623 TATATATTTAATTACATATTTTGCATGGTTTA
1 TATATATTT-ATTACATA-ATTGCATGATTTA
*
5159655 TATATTATTTCTTACATAATTGCATGATTTA
1 TATA-TATTTATTACATAATTGCATGATTTA
5159686 TATAT
1 TATAT
5159691 TATTATTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 15 0.47
32 11 0.34
33 5 0.16
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.53
Consensus pattern (30 bp):
TATATATTTATTACATAATTGCATGATTTA
Found at i:5159686 original size:31 final size:32
Alignment explanation
Indices: 5159634--5159694 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5159624 ATATATTTAA
* *
5159634 TTACATATTTTGCATGGTTTATATATTATTTC
1 TTACATATATTGCATGATTTATATATTATTTC
5159666 TTACATA-ATTGCATGATTTATATATTATT
1 TTACATATATTGCATGATTTATATATTATT
5159695 ATTTGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (32 bp):
TTACATATATTGCATGATTTATATATTATTTC
Found at i:5159720 original size:55 final size:55
Alignment explanation
Indices: 5159674--5159850 Score: 218
Period size: 55 Copynumber: 3.2 Consensus size: 55
5159664 TCTTACATAA
* *
5159674 TTGCATGATTTATATATTATTATTTGTATGACTATGTATTTAATTTCATGTTTAT
1 TTGCATGATTTATATATTATTATTTGTATGATTATGTATTTAATTTCATATTTAT
* *
5159729 TTGCATGATTTATATATTACTATTTACGTA--ATTATAG-ATTTAATTGCATATTTAT
1 TTGCATGATTTATATATTATTATTT--GTATGATTAT-GTATTTAATTTCATATTTAT
* * * *
5159784 TTGCATGGTTTATATATTTTTATTTGTATGATTATATATTTAATTGT-ATGTTTAT
1 TTGCATGATTTATATATTATTATTTGTATGATTATGTATTTAATT-TCATATTTAT
5159839 TTGCATGATTTA
1 TTGCATGATTTA
5159851 CATTGTTAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
53 3 0.03
55 97 0.93
56 1 0.01
57 3 0.03
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.55
Consensus pattern (55 bp):
TTGCATGATTTATATATTATTATTTGTATGATTATGTATTTAATTTCATATTTAT
Found at i:5159821 original size:22 final size:23
Alignment explanation
Indices: 5159779--5159824 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
5159769 TAATTGCATA
*
5159779 TTTATTTGCATGGTTTATATATT
1 TTTATTTGCATGGATTATATATT
*
5159802 TTTATTTGTAT-GATTATATATT
1 TTTATTTGCATGGATTATATATT
5159824 T
1 T
5159825 AATTGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (23 bp):
TTTATTTGCATGGATTATATATT
Found at i:5159825 original size:20 final size:20
Alignment explanation
Indices: 5159776--5159838 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
5159766 ATTTAATTGC
*
5159776 ATATTTATTTGCATGGTTTAT
1 ATATTTATTTGTAT-GTTTAT
*
5159797 ATATTTTTATTTGTATGATTAT
1 ATA--TTTATTTGTATGTTTAT
*
5159819 ATATTTAATTGTATGTTTAT
1 ATATTTATTTGTATGTTTAT
5159839 TTGCATGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 15 0.42
21 3 0.08
22 8 0.22
23 10 0.28
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (20 bp):
ATATTTATTTGTATGTTTAT
Found at i:5159892 original size:53 final size:55
Alignment explanation
Indices: 5159770--5159892 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 55
5159760 TTATAGATTT
* * * * * * *
5159770 AATTGCAT-ATTTATTTGCATGGTTTATATATTTTTATTTGTATGATTATATATTT
1 AATTGCATGA-TTATTTGCATGGATTATACATTGTTAATTGCATGATTAAATATTA
* * *
5159825 AATTGTATGTTTATTTGCAT-GATT-TACATTGTTAATTGCATGGTTAAATATTA
1 AATTGCATGATTATTTGCATGGATTATACATTGTTAATTGCATGATTAAATATTA
5159878 AATTGCATGATTATT
1 AATTGCATGATTATT
5159893 AATTAATTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
53 35 0.64
54 3 0.05
55 17 0.31
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (55 bp):
AATTGCATGATTATTTGCATGGATTATACATTGTTAATTGCATGATTAAATATTA
Found at i:5160027 original size:24 final size:24
Alignment explanation
Indices: 5159973--5160034 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
5159963 TTATTATTGC
*
5159973 ATAATTTTATATTTATTACATGAT
1 ATAATATTATATTTATTACATGAT
* *
5159997 ATGATATTATATGTTATTGCATGAT
1 ATAATATTATAT-TTATTACATGAT
5160022 -TAATATTATATTT
1 ATAATATTATATTT
5160035 GAATGATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.06
24 20 0.61
25 11 0.33
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (24 bp):
ATAATATTATATTTATTACATGAT
Found at i:5160184 original size:18 final size:18
Alignment explanation
Indices: 5160155--5160249 Score: 84
Period size: 18 Copynumber: 5.0 Consensus size: 18
5160145 AATAAATGGT
*
5160155 TATTAATATATTTGTATGA
1 TATT-ATATATTTGCATGA
*
5160174 TATTTTATATTTGCATGA
1 TATTATATATTTGCATGA
* *
5160192 TATTATATATTTACATAA
1 TATTATATATTTGCATGA
*
5160210 TTATTAT-TATTATTGTATGA
1 -TATTATATA-T-TTGCATGA
5160230 TAATTAATATATTTGCATGA
1 T-ATT-ATATATTTGCATGA
5160250 AATTCTTGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
18 29 0.48
19 12 0.20
20 15 0.25
21 3 0.05
22 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (18 bp):
TATTATATATTTGCATGA
Found at i:5160191 original size:58 final size:57
Alignment explanation
Indices: 5160095--5160249 Score: 142
Period size: 58 Copynumber: 2.7 Consensus size: 57
5160085 ATTATACATA
* * *
5160095 ATTACTAATATATTTGTGTGATTATATTT-GATTT-CATGATTATATATTTGA-ATAAATG
1 ATTATTAATATATTTGTATGA-TAT-TTTATATTTGCATGATTATATATTT-ACAT-AATG
* *
5160153 GTTATTAATATATTTGTATGATATTTTATATTTGCATGATATTATATATTTACATAATT
1 ATTATTAATATATTTGTATGATATTTTATATTTGCATG--ATTATATATTTACATAATG
*
5160212 ATTATT-AT-TA-TTGTATGATAATTAATATATTTGCATGA
1 ATTATTAATATATTTGTATGAT-ATT-TTATATTTGCATGA
5160250 AATTCTTGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
56 13 0.16
57 12 0.14
58 36 0.43
59 9 0.11
60 13 0.16
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (57 bp):
ATTATTAATATATTTGTATGATATTTTATATTTGCATGATTATATATTTACATAATG
Found at i:5160276 original size:14 final size:13
Alignment explanation
Indices: 5160235--5160276 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
5160225 TATGATAATT
5160235 AATATATTTGCATG
1 AATAT-TTTGCATG
5160249 AA-ATTCTTGCATG
1 AATATT-TTGCATG
5160262 AATATTTTAGCATG
1 AATATTTT-GCATG
5160276 A
1 A
5160277 TGTAGGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 13 0.52
14 11 0.44
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (13 bp):
AATATTTTGCATG
Found at i:5161480 original size:26 final size:26
Alignment explanation
Indices: 5161445--5161497 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5161435 TGTTCTTTTA
*
5161445 TTTTTTAGGAAAATATCTTCATTACT
1 TTTTTTAGGAAAACATCTTCATTACT
5161471 TTTTTTAGGAAAACATCTTCATTACT
1 TTTTTTAGGAAAACATCTTCATTACT
5161497 T
1 T
5161498 ATTCTATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTTTTAGGAAAACATCTTCATTACT
Found at i:5161633 original size:35 final size:35
Alignment explanation
Indices: 5161579--5161768 Score: 127
Period size: 35 Copynumber: 5.3 Consensus size: 35
5161569 ATTTTCTTAA
*
5161579 TTTTTTTAGATAAACACTCTTATTACTTGTTCTCC
1 TTTTTTTAGAGAAACACTCTTATTACTTGTTCTCC
* * * *
5161614 TTTTTTTA-AGAAAAGACTCTCATTATTTATTCTCC
1 TTTTTTTAGAG-AAACACTCTTATTACTTGTTCTCC
* *
5161649 TATTTTTAGAGAAACACT-TTCATTACTTGTTCTTC
1 TTTTTTTAGAGAAACACTCTT-ATTACTTGTTCTCC
* * ** * *
5161684 TATTTTTTA-AGGAAATATTCACATTACTTGGTCTCT
1 T-TTTTTTAGA-GAAACACTCTTATTACTTGTTCTCC
* *
5161720 TATTTTTCGTAAGGGAAACACTCTTATTACTAT-TTTTCC
1 T-TTTTT--T-AGAGAAACACTCTTATTACT-TGTTCTCC
5161759 TATTTTTTAG
1 T-TTTTTTAG
5161769 GGAAGCATTC
Statistics
Matches: 117, Mismatches: 27, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
34 2 0.02
35 54 0.46
36 34 0.29
37 1 0.01
38 1 0.01
39 24 0.21
40 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.49
Consensus pattern (35 bp):
TTTTTTTAGAGAAACACTCTTATTACTTGTTCTCC
Found at i:5161709 original size:36 final size:36
Alignment explanation
Indices: 5161526--5161778 Score: 144
Period size: 36 Copynumber: 6.9 Consensus size: 36
5161516 AAATGTTTTT
*
5161526 ATTACTTATTCTCCTATTTTCTTAAAGGAAACA--C-C
1 ATTACTTGTTCTCCTATTTT-TT-AAGGAAACATTCTC
* * * * * * *
5161561 AATTACTTATTTTCTTAATTTTTTTAGATAAACACTCTT
1 -ATTACTTGTTCTCCT-ATTTTTTAAG-GAAACATTCTC
* * *
5161600 ATTACTTGTTCTCCT-TTTTTTAAGAAAAGACTCTC
1 ATTACTTGTTCTCCTATTTTTTAAGGAAACATTCTC
* *
5161635 ATTATTTATTCTCCTA-TTTTT-AGAGAAACACTT-TC
1 ATTACTTGTTCTCCTATTTTTTAAG-GAAACA-TTCTC
* * *
5161670 ATTACTTGTTCTTCTATTTTTTAAGGAAATATTCAC
1 ATTACTTGTTCTCCTATTTTTTAAGGAAACATTCTC
* * * *
5161706 ATTACTTGGTCTCTTATTTTTCGTAAGGGAAACACTCTT
1 ATTACTTGTTCTCCTATTTTT--TAA-GGAAACATTCTC
* * *
5161745 ATTACTAT-TTTTCCTATTTTTTAGGGAAGCATTC
1 ATTACT-TGTTCTCCTATTTTTTAAGGAAACATTC
5161779 CCATCACATA
Statistics
Matches: 167, Mismatches: 35, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
34 2 0.01
35 49 0.29
36 66 0.40
37 9 0.05
38 16 0.10
39 24 0.14
40 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (36 bp):
ATTACTTGTTCTCCTATTTTTTAAGGAAACATTCTC
Found at i:5161866 original size:48 final size:48
Alignment explanation
Indices: 5161795--5162174 Score: 261
Period size: 48 Copynumber: 8.0 Consensus size: 48
5161785 CATATTCATT
5161795 TTTTCCTAATTTTCTAA-GAAAACACTCCATTACCTATTCCTTTTAATAA
1 TTTTCCT-ATTTT-TAAGGAAAACACTCCATTACCTATTCCTTTTAATAA
* * * *
5161844 TTTTCCTATTTTTAAGTAAAACATTCCCTTACCTATTCCTTTTAATAT
1 TTTTCCTATTTTTAAGGAAAACACTCCATTACCTATTCCTTTTAATAA
* * * * * * *
5161892 TTCTTCCTATTTTTTAGGGAAGCATTCCCATCACATATT-C-----AT-T
1 TT-TTCCTATTTTTAAGGAAAACACT-CCATTACCTATTCCTTTTAATAA
*
5161935 TTTTCCTAATTTTCTAA-GAAAACACTCCATTACCTATTCCTTTTAATAG
1 TTTTCCT-ATTTT-TAAGGAAAACACTCCATTACCTATTCCTTTTAATAA
* * *
5161984 TTTTCTTATTTTTAAGTG-AAACACTTCC-TTAACTATTCCTTTTAATAT
1 TTTTCCTATTTTTAAG-GAAAACAC-TCCATTACCTATTCCTTTTAATAA
* * * *
5162032 TTCTTTC-ATTTTTTAGGAAAACGCTCTC-TTGCCTATTCCTTTTAAT-A
1 TT-TTCCTATTTTTAAGGAAAACACTC-CATTACCTATTCCTTTTAATAA
* * * *
5162079 TTTCTTCTATTTTT-AGGAAAATAATCCCTTACCTATTCCTTTTAATAA
1 TTT-TCCTATTTTTAAGGAAAACACTCCATTACCTATTCCTTTTAATAA
* * ** * *
5162127 TTTACCTTTTTTTTTTTGAAAATACACT-CATTACCTATACCTTTTAAT
1 TTTTCC--TATTTTTAAGGAAA-ACACTCCATTACCTATTCCTTTTAAT
5162175 TTTTCTAATT
Statistics
Matches: 264, Mismatches: 41, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
42 15 0.06
43 15 0.06
44 4 0.02
46 2 0.01
47 41 0.16
48 108 0.41
49 45 0.17
50 31 0.12
51 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (48 bp):
TTTTCCTATTTTTAAGGAAAACACTCCATTACCTATTCCTTTTAATAA
Found at i:5161906 original size:140 final size:140
Alignment explanation
Indices: 5161750--5162048 Score: 523
Period size: 140 Copynumber: 2.1 Consensus size: 140
5161740 CTCTTATTAC
5161750 TATTT-TTCCTATTTTTTAGGGAAGCATTCCCATCACATATTCATTTTTTCCTAATTTTCTAAGA
1 TATTTCTTCCTATTTTTTAGGGAAGCATTCCCATCACATATTCATTTTTTCCTAATTTTCTAAGA
*
5161814 AAACACTCCATTACCTATTCCTTTTAATAATTTTCCTATTTTTAAGTAAAACA-TTCCCTTACCT
66 AAACACTCCATTACCTATTCCTTTTAATAATTTTCCTATTTTTAAGTAAAACACTT-CCTTAACT
5161878 ATTCCTTTTAA
130 ATTCCTTTTAA
5161889 TATTTCTTCCTATTTTTTAGGGAAGCATTCCCATCACATATTCATTTTTTCCTAATTTTCTAAGA
1 TATTTCTTCCTATTTTTTAGGGAAGCATTCCCATCACATATTCATTTTTTCCTAATTTTCTAAGA
* * *
5161954 AAACACTCCATTACCTATTCCTTTTAATAGTTTTCTTATTTTTAAGTGAAACACTTCCTTAACTA
66 AAACACTCCATTACCTATTCCTTTTAATAATTTTCCTATTTTTAAGTAAAACACTTCCTTAACTA
5162019 TTCCTTTTAA
131 TTCCTTTTAA
*
5162029 TATTTCTTTC-ATTTTTTAGG
1 TATTTCTTCCTATTTTTTAGG
5162049 AAAACGCTCT
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
139 15 0.10
140 136 0.89
141 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.47
Consensus pattern (140 bp):
TATTTCTTCCTATTTTTTAGGGAAGCATTCCCATCACATATTCATTTTTTCCTAATTTTCTAAGA
AAACACTCCATTACCTATTCCTTTTAATAATTTTCCTATTTTTAAGTAAAACACTTCCTTAACTA
TTCCTTTTAA
Found at i:5163401 original size:2 final size:2
Alignment explanation
Indices: 5163394--5163438 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5163384 TCTTGAACCT
5163394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5163436 TA T
1 TA T
5163439 GAGTTTTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5174552 original size:25 final size:25
Alignment explanation
Indices: 5174524--5174572 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5174514 TAAAAATGCA
*
5174524 AGAAGGATGACTAGTTATAATTTCC
1 AGAAGCATGACTAGTTATAATTTCC
5174549 AGAAGCATGACTAGTTATAATTTC
1 AGAAGCATGACTAGTTATAATTTC
5174573 TAACTTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
AGAAGCATGACTAGTTATAATTTCC
Found at i:5177217 original size:17 final size:17
Alignment explanation
Indices: 5177192--5177229 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5177182 TATATTTTAT
5177192 ATATATTTAGTAAATAA
1 ATATATTTAGTAAATAA
* *
5177209 ATATTTTTATTAAAT-A
1 ATATATTTAGTAAATAA
5177225 ATATA
1 ATATA
5177230 AATTATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATTTAGTAAATAA
Found at i:5179094 original size:13 final size:14
Alignment explanation
Indices: 5179076--5179107 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5179066 AAATTATTCA
5179076 AAAAATTTAAAAT-
1 AAAAATTTAAAATG
5179089 AAAAATTTAAAATG
1 AAAAATTTAAAATG
5179103 AAAAA
1 AAAAA
5179108 GAAGAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
AAAAATTTAAAATG
Found at i:5180476 original size:55 final size:55
Alignment explanation
Indices: 5180329--5180466 Score: 188
Period size: 55 Copynumber: 2.5 Consensus size: 55
5180319 ACGCTTAACA
* * * *
5180329 TCAGTATAGACTCATATTTTTTAATTTTCTTACTTATATCGACGGTTCAAAATTG
1 TCAGTATAGACTTATATGTTTTAATTTTCTTACTTATATCAACGGTTAAAAATTG
* * *
5180384 TCAGTATAGAATTGTATGCTTTAATTTTCTTACTTATA-CTAACGGTTAAAAATTG
1 TCAGTATAGACTTATATGTTTTAATTTTCTTACTTATATC-AACGGTTAAAAATTG
*
5180439 TCAGTATAGACTTATAGGTTTTAATTTT
1 TCAGTATAGACTTATATGTTTTAATTTT
5180467 TTTTATTATA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 1 0.01
55 70 0.99
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (55 bp):
TCAGTATAGACTTATATGTTTTAATTTTCTTACTTATATCAACGGTTAAAAATTG
Found at i:5182643 original size:3 final size:3
Alignment explanation
Indices: 5182635--5182669 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5182625 AAAGAAAAGC
5182635 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5182670 AGTAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5183346 original size:18 final size:19
Alignment explanation
Indices: 5183314--5183383 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
5183304 AAGCCAAACA
5183314 ATAAACAATTATATATAAT
1 ATAAACAATTATATATAAT
*
5183333 ATAAACAA-TATATA-AACA
1 ATAAACAATTATATATAA-T
5183351 ATAAACAATTATATATAAT
1 ATAAACAATTATATATAAT
*
5183370 GTAAACAA-TATATA
1 ATAAACAATTATATA
5183384 AACAATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
17 2 0.04
18 20 0.44
19 21 0.47
20 2 0.04
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.31
Consensus pattern (19 bp):
ATAAACAATTATATATAAT
Found at i:5183355 original size:37 final size:37
Alignment explanation
Indices: 5183309--5183389 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
5183299 TAAAAAAGCC
5183309 AAACAATAAACAATTATATATAATATAAACAATATAT
1 AAACAATAAACAATTATATATAATATAAACAATATAT
*
5183346 AAACAATAAACAATTATATATAATGTAAACAATATAT
1 AAACAATAAACAATTATATATAATATAAACAATATAT
5183383 AAACAAT
1 AAACAAT
5183390 TATATAAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (37 bp):
AAACAATAAACAATTATATATAATATAAACAATATAT
Found at i:5183395 original size:12 final size:11
Alignment explanation
Indices: 5183331--5183398 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
5183321 ATTATATATA
5183331 ATATAAACAAT
1 ATATAAACAAT
5183342 ATATAAACAAT
1 ATATAAACAAT
* * *
5183353 AAACAATTATATAT
1 ATATAA--ACA-AT
*
5183367 AATGTAAACAAT
1 -ATATAAACAAT
5183379 ATATAAACAATT
1 ATATAAACAA-T
5183391 ATATAAAC
1 ATATAAAC
5183399 CTTATTATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
11 24 0.55
12 11 0.25
13 4 0.09
14 2 0.05
15 3 0.07
ACGTcount: A:0.60, C:0.09, G:0.01, T:0.29
Consensus pattern (11 bp):
ATATAAACAAT
Found at i:5186464 original size:17 final size:16
Alignment explanation
Indices: 5186429--5186472 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
5186419 ATTCTAAAAA
5186429 TTTTATATTTTTATGT
1 TTTTATATTTTTATGT
5186445 TTTTATTATTTTTAAT-T
1 TTTTA-TATTTTT-ATGT
5186462 TTTTA-ATTTTT
1 TTTTATATTTTT
5186473 TTGGTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 13 0.50
18 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATATTTTTATGT
Found at i:5187615 original size:82 final size:81
Alignment explanation
Indices: 5187496--5187760 Score: 343
Period size: 82 Copynumber: 3.2 Consensus size: 81
5187486 AGGCTTAACG
* * * *
5187496 ACTTTGAAAATCAAAATGCTCCTCTAAACAAAGGCACCGTAAATTTTGAAAAGTAAATTGCTCCT
1 ACTTTGAAAGT-AAATTGCTCCTCTAAACAGAGGCACC-TAACTTTTGAAAAGTAAATTGCTCCT
5187561 CTAAATAGAGGCACCACA
64 CTAAATAGAGGCACCACA
5187579 ACTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCTCAACTTTTGAAAAGTAAATTGCTCCTC
1 ACTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCT-AACTTTTGAAAAGTAAATTGCTCCTC
*
5187644 TAAATAGAGGCATCACA
65 TAAATAGAGGCACCACA
* * * * * *
5187661 ACTTTTGAAAGTAAATTACTCCTCTAAATAGAAGTACCACAACTTTTG-AAAGTAAATTGCTCTT
1 AC-TTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACC-TAACTTTTGAAAAGTAAATTGCTCCT
**
5187725 CTAAATAGAGGCAACCATG
64 CTAAATAGAGGC-ACCACA
5187744 ACTTTGAAAAGTAAATT
1 ACTTTG-AAAGTAAATT
5187761 ACTCTTTAAC
Statistics
Matches: 163, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
81 1 0.01
82 98 0.60
83 64 0.39
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (81 bp):
ACTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCTAACTTTTGAAAAGTAAATTGCTCCTCT
AAATAGAGGCACCACA
Found at i:5187766 original size:42 final size:41
Alignment explanation
Indices: 5187391--5187760 Score: 325
Period size: 42 Copynumber: 8.9 Consensus size: 41
5187381 AACAAAGCTT
* * ** * *
5187391 CTCTAAATAGAGGCTCAATGACTTTTGAAAATAAATAAAGCTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAAT--TGCTC
* * * * * *
5187434 CTCTAAATTGAGGCTCAACGAC-TTTGAAAATAAATAAAGCTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAAT--TGCTC
* * *** * * *
5187476 TTCTAAACAGAGGCTTAACGAC-TTTGAAAATCAAAATGCTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGT-AAATTGCTC
* * ** *
5187517 CTCTAAACAAAGGCACCGTAAATTTTGAAAAGTAAATTGCTC
1 CTCTAAATAGAGGCACCACAACTTTTG-AAAGTAAATTGCTC
5187559 CTCTAAATAGAGGCACCACAAC-TTTGAAAGTAAATTGCTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATTGCTC
* *
5187599 CTCTAAACAGAGGCACCTCAACTTTTGAAAAGTAAATTGCTC
1 CTCTAAATAGAGGCACCACAACTTTTG-AAAGTAAATTGCTC
* *
5187641 CTCTAAATAGAGGCATCACAACTTTTGAAAGTAAATTACTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATTGCTC
* *
5187682 CTCTAAATAGAAGTACCACAACTTTTGAAAGTAAATTGCTC
1 CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATTGCTC
* **
5187723 TTCTAAATAGAGGCAACCATGAC-TTTGAAAAGTAAATT
1 CTCTAAATAGAGGC-ACCACAACTTTTG-AAAGTAAATT
5187761 ACTCTTTAAC
Statistics
Matches: 281, Mismatches: 39, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
40 34 0.12
41 90 0.32
42 130 0.46
43 27 0.10
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (41 bp):
CTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATTGCTC
Found at i:5188117 original size:43 final size:42
Alignment explanation
Indices: 5188041--5188146 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
5188031 TTCAAGGCTT
* ** *
5188041 TTCAAAGGTTTTCATTTGGCAAACTTGGAATTCATATCCAAAAA
1 TTCAAAGCTTTTCATTT-G-AATTTTGGAATTCACATCCAAAAA
*
5188085 -TCTAAAGCTTTTTATTTGAATTTTGGAGATTCACATCCAAAAA
1 TTC-AAAGCTTTTCATTTGAATTTTGGA-ATTCACATCCAAAAA
*
5188128 TTCAGAGCTTTTCATTTGA
1 TTCAAAGCTTTTCATTTGA
5188147 GTTCAAAGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
42 7 0.13
43 31 0.60
44 14 0.27
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (42 bp):
TTCAAAGCTTTTCATTTGAATTTTGGAATTCACATCCAAAAA
Found at i:5189546 original size:12 final size:12
Alignment explanation
Indices: 5189516--5189547 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
5189506 TTTTTCCTCC
5189516 TTTCATCTTTTT
1 TTTCATCTTTTT
5189528 TTT--TCTTTTT
1 TTTCATCTTTTT
5189538 TTTCATCTTT
1 TTTCATCTTT
5189548 CACCTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.56
12 8 0.44
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCATCTTTTT
Found at i:5189547 original size:29 final size:29
Alignment explanation
Indices: 5189506--5189579 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
5189496 TAAGTCTTCA
* *
5189506 TTTTTCCTCCTTTCATCTTT-TTTTTTCTTT
1 TTTTTCAT-CTTTCATCTTTAATTTTT-TTT
*
5189536 TTTTTCATCTTTCACCTTTAATTTTTTTT
1 TTTTTCATCTTTCATCTTTAATTTTTTTT
5189565 TTTTT-ATCTTTCATC
1 TTTTTCATCTTTCATC
5189580 CATTGTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.23
29 18 0.46
30 12 0.31
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTCATCTTTCATCTTTAATTTTTTTT
Found at i:5191278 original size:28 final size:28
Alignment explanation
Indices: 5191221--5191280 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
5191211 TTATAGAGAA
* **
5191221 CATAGGAGCAAAACGACGTCATTTTGAG
1 CATAGGACCAAAACGACGTCATTTCAAG
*
5191249 CATAGGACCAAAACGACGTCGTTTCAAG
1 CATAGGACCAAAACGACGTCATTTCAAG
5191277 CATA
1 CATA
5191281 AGAGGATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (28 bp):
CATAGGACCAAAACGACGTCATTTCAAG
Found at i:5191891 original size:109 final size:110
Alignment explanation
Indices: 5191705--5191934 Score: 444
Period size: 109 Copynumber: 2.1 Consensus size: 110
5191695 AATAATTTCA
5191705 CCTAGATGTTGAGAAATTATTATTAATAAATTTTCATAAAAAAGAAATATATAAGAAAATTTTGA
1 CCTAGATGTTGAGAAATTATTATTAATAAATTTTCATAAAAAAGAAATATATAAGAAAATTTTGA
5191770 TTAATTTTCAAAAATAGCTAAAATCGAACTTGCTCTGAAAATTCG
66 TTAATTTTCAAAAATAGCTAAAATCGAACTTGCTCTGAAAATTCG
*
5191815 CCTAGATGTTGAGAATTTATTATTAATAAATTTT-ATAAAAAAGAAATATATAAGAAAATTTTGA
1 CCTAGATGTTGAGAAATTATTATTAATAAATTTTCATAAAAAAGAAATATATAAGAAAATTTTGA
5191879 TTAATTTTCAAAAATAGCTAAAATCGAACTTGCTCTGAAAATTCG
66 TTAATTTTCAAAAATAGCTAAAATCGAACTTGCTCTGAAAATTCG
5191924 CCTAGATGTTG
1 CCTAGATGTTG
5191935 GAGATTTTTA
Statistics
Matches: 119, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
109 86 0.72
110 33 0.28
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (110 bp):
CCTAGATGTTGAGAAATTATTATTAATAAATTTTCATAAAAAAGAAATATATAAGAAAATTTTGA
TTAATTTTCAAAAATAGCTAAAATCGAACTTGCTCTGAAAATTCG
Found at i:5192025 original size:30 final size:29
Alignment explanation
Indices: 5191989--5192119 Score: 97
Period size: 30 Copynumber: 4.4 Consensus size: 29
5191979 AACACTAATT
* *
5191989 CTTAAATCCAAACTCCTAAAATTCAAACTC
1 CTTAAATCCAAACTCCTAAAATCCAAA-AC
5192019 CTTAAATCCAAAAC-CCTAAAATCCAAAAC
1 CTTAAATCC-AAACTCCTAAAATCCAAAAC
* * * *
5192048 CTTAAAATCCTAACT-TTTAAATCCAAACC
1 CTT-AAATCCAAACTCCTAAAATCCAAAAC
** * *
5192077 CCAAAATTCAAAACCCCTAAAATCC-AAAC
1 CTTAAA-TCCAAACTCCTAAAATCCAAAAC
*
5192106 CTTTAAATCAAAAC
1 C-TTAAATCCAAAC
5192120 CCCAAACCTC
Statistics
Matches: 79, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
28 3 0.04
29 35 0.44
30 37 0.47
31 4 0.05
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (29 bp):
CTTAAATCCAAACTCCTAAAATCCAAAAC
Found at i:5192098 original size:44 final size:43
Alignment explanation
Indices: 5191992--5192125 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 43
5191982 ACTAATTCTT
* * *
5191992 AAATCC-AAACTCCTAAAATTCAAACTCCTTAAATCCAAAACCCTA
1 AAATCCAAAAC-CCTAAAATCCAAAC-CTTTAAATCC-AAACCCCA
* * *
5192037 AAATCCAAAACCTTAAAATCCTAACTTTTAAATCCAAACCCCA
1 AAATCCAAAACCCTAAAATCCAAACCTTTAAATCCAAACCCCA
* *
5192080 AAATTCAAAACCCCTAAAATCCAAACCTTTAAATCAAAACCCCA
1 AAATCCAAAA-CCCTAAAATCCAAACCTTTAAATCCAAACCCCA
5192124 AA
1 AA
5192126 CCTCAAATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
43 16 0.21
44 39 0.51
45 17 0.22
46 4 0.05
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (43 bp):
AAATCCAAAACCCTAAAATCCAAACCTTTAAATCCAAACCCCA
Found at i:5192106 original size:15 final size:15
Alignment explanation
Indices: 5191992--5192106 Score: 99
Period size: 15 Copynumber: 7.7 Consensus size: 15
5191982 ACTAATTCTT
*
5191992 AAATCCAAACTCCTA
1 AAATCCAAACCCCTA
* * *
5192007 AAATTCAAACTCCTT
1 AAATCCAAACCCCTA
*
5192022 AAATCCAAAACCCTA
1 AAATCCAAACCCCTA
* *
5192037 AAATCCAAAACCTTA
1 AAATCCAAACCCCTA
* ** *
5192052 AAATCCTAA-CTTTT
1 AAATCCAAACCCCTA
5192066 AAATCCAAACCCC-A
1 AAATCCAAACCCCTA
*
5192080 AAATTCAAAACCCCTA
1 AAA-TCCAAACCCCTA
5192096 AAATCCAAACC
1 AAATCCAAACC
5192107 TTTAAATCAA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
14 14 0.17
15 63 0.78
16 4 0.05
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:5192112 original size:15 final size:14
Alignment explanation
Indices: 5191992--5192228 Score: 118
Period size: 14 Copynumber: 16.2 Consensus size: 14
5191982 ACTAATTCTT
5191992 AAATCCAAACTCCTA
1 AAATCCAAAC-CCTA
* *
5192007 AAATTCAAACTCCTT
1 AAATCCAAAC-CCTA
5192022 AAATCCAAAACCCTA
1 AAATCC-AAACCCTA
*
5192037 AAATCCAAAACCTTA
1 AAATCC-AAACCCTA
* ** *
5192052 AAATCCTAACTTTT
1 AAATCCAAACCCTA
*
5192066 AAATCCAAACCCCA
1 AAATCCAAACCCTA
*
5192080 AAATTCAAAACCCCTA
1 AAA-TCCAAA-CCCTA
* *
5192096 AAATCCAAACCTTT
1 AAATCCAAACCCTA
* *
5192110 AAATCAAAACCC-C
1 AAATCCAAACCCTA
* ***
5192123 AAACCTCAAATTTTAA
1 AAATC-CAAACCCT-A
*
5192139 AAATCAAAACCCTA
1 AAATCCAAACCCTA
* * **
5192153 AAAACGAAATTCTA
1 AAATCCAAACCCTA
* *
5192167 AATTTTCCAAACCTTA
1 AA--ATCCAAACCCTA
* *
5192183 AAAT-TAAACCTTA
1 AAATCCAAACCCTA
5192196 AAACTTCCAAACCCTA
1 AAA--TCCAAACCCTA
5192212 AAATCCAAACCCTA
1 AAATCCAAACCCTA
5192226 AAA
1 AAA
5192229 AAAAAACTCT
Statistics
Matches: 165, Mismatches: 46, Indels: 23
0.71 0.20 0.10
Matches are distributed among these distances:
13 15 0.09
14 61 0.37
15 56 0.34
16 33 0.20
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATCCAAACCCTA
Found at i:5192284 original size:72 final size:72
Alignment explanation
Indices: 5192138--5192278 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 72
5192128 TCAAATTTTA
** * *
5192138 AAAATCAAAACCCTAAAAACGAAATTCTAAATTTTCCAAACCTTAAAATTAAACCTTAAAACTTC
1 AAAATCAAAACCCTAAAAAAAAAACTCTAAATTTTCCAAACCCTAAAATTAAACCTTAAAACTT-
5192203 CAAACCCT
65 CAAACCCT
* * *
5192211 AAAATCCAAACCCTAAAAAAAAAACTCT-AATTTTTCAAACCCTAAAATTAAACCTTAAACCTT-
1 AAAATCAAAACCCTAAAAAAAAAACTCTAAATTTTCCAAACCCTAAAATTAAACCTTAAAACTTC
5192274 AAACC
66 AAACC
5192279 TCCTAACCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 5 0.08
72 32 0.52
73 24 0.39
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (72 bp):
AAAATCAAAACCCTAAAAAAAAAACTCTAAATTTTCCAAACCCTAAAATTAAACCTTAAAACTTC
AAACCCT
Found at i:5192465 original size:14 final size:14
Alignment explanation
Indices: 5192397--5192493 Score: 67
Period size: 14 Copynumber: 6.9 Consensus size: 14
5192387 CTCCAAACCT
5192397 TCAAACCCTAAAAT-
1 TCAAACCCT-AAATC
*
5192411 T-AAACCATAAATCC
1 TCAAACCCTAAAT-C
*
5192425 TCTAAACCCTAAAAC
1 TC-AAACCCTAAATC
**
5192440 -CAAAACTTTAAATC
1 TC-AAACCCTAAATC
5192454 TCAAACCCTAAAAT-
1 TCAAACCCT-AAATC
* *
5192468 TAAAACCCCAAATC
1 TCAAACCCTAAATC
5192482 TCAAACCCTAAA
1 TCAAACCCTAAA
5192494 ATCAAAAACC
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
12 4 0.06
13 10 0.16
14 34 0.54
15 6 0.10
16 9 0.14
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (14 bp):
TCAAACCCTAAATC
Done.