Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:2009085 original size:22 final size:22
Alignment explanation
Indices: 2009031--2009091 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
2009021 AAATATGATA
*
2009031 TTAAAATAATATATAAAA-AAT
1 TTAAAATCATATATAAAATAAT
2009052 TTAAAATC-TATATAAAATAAT
1 TTAAAATCATATATAAAATAAT
2009073 TTATAAA-CATATATAAAAT
1 TTA-AAATCATATATAAAAT
2009092 TATAATAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 9 0.25
21 14 0.39
22 13 0.36
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAAATCATATATAAAATAAT
Found at i:2017519 original size:30 final size:30
Alignment explanation
Indices: 2017485--2017562 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
2017475 ATATTGATTT
* *
2017485 ATATTAAGAGTGTATTTAGA-TATAAATTAA
1 ATATTAAGAATGTATTT-GACAATAAATTAA
* *
2017515 ATATTAATAATTTATTTGACAATAAATTAA
1 ATATTAAGAATGTATTTGACAATAAATTAA
* *
2017545 ATATTAAAAATTTATTTG
1 ATATTAAGAATGTATTTG
2017563 GATGTAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 2 0.05
30 40 0.95
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (30 bp):
ATATTAAGAATGTATTTGACAATAAATTAA
Found at i:2017571 original size:30 final size:29
Alignment explanation
Indices: 2017497--2017605 Score: 121
Period size: 30 Copynumber: 3.6 Consensus size: 29
2017487 ATTAAGAGTG
2017497 TATTTAGATATAAATTAAATATTAATAATT
1 TATTT-GATATAAATTAAATATTAATAATT
* *
2017527 TATTTGACAATAAATTAAATATTAAAAATT
1 TATTTGA-TATAAATTAAATATTAATAATT
*
2017557 TATTTGGATGTAAATTTAAA-ATTAATAATT
1 TATTT-GATATAAA-TTAAATATTAATAATT
* *
2017587 TACTTAAGTATAAATTAAA
1 TATTTGA-TATAAATTAAA
2017606 AGTGAAATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
29 8 0.12
30 52 0.78
31 7 0.10
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (29 bp):
TATTTGATATAAATTAAATATTAATAATT
Found at i:2017618 original size:60 final size:60
Alignment explanation
Indices: 2017497--2017630 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
2017487 ATTAAGAGTG
* * *
2017497 TATTTAGATATAAATTAAATATTAATAATTTATTTGACAATAAATTAAATATTAAAAATT
1 TATTTAGATATAAATTAAATATTAATAATTTACTTAACAATAAATTAAATATGAAAAATT
* * ** *
2017557 TATTTGGATGTAAATTTAAA-ATTAATAATTTACTTAAGTATAAATTAAA-AGTGAAATATT
1 TATTTAGATATAAA-TTAAATATTAATAATTTACTTAACAATAAATTAAATA-TGAAAAATT
*
2017617 TATTTA-ATTTAAAT
1 TATTTAGATATAAAT
2017631 ATACAATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 1 0.02
59 7 0.11
60 49 0.79
61 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (60 bp):
TATTTAGATATAAATTAAATATTAATAATTTACTTAACAATAAATTAAATATGAAAAATT
Found at i:2017895 original size:2 final size:2
Alignment explanation
Indices: 2017888--2017916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2017878 TAGTATATGC
2017888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2017917 AATAAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2018315 original size:13 final size:13
Alignment explanation
Indices: 2018297--2018321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2018287 TATATATCTC
2018297 ATTTTATTTTTTT
1 ATTTTATTTTTTT
2018310 ATTTTATTTTTT
1 ATTTTATTTTTT
2018322 ATATATAAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTATTTTTTT
Found at i:2020243 original size:15 final size:14
Alignment explanation
Indices: 2020223--2020277 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
2020213 CAACAACAAC
2020223 AAGAAGATGAAGGTG
1 AAGAAGATGAA-GTG
*
2020238 AAGAAGAAGAA--G
1 AAGAAGATGAAGTG
*
2020250 ATGAAGATGAAGATG
1 AAGAAGATGAAG-TG
2020265 AAGAAGATGAAGT
1 AAGAAGATGAAGT
2020278 TATGAGCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 10 0.30
14 1 0.03
15 22 0.67
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.13
Consensus pattern (14 bp):
AAGAAGATGAAGTG
Found at i:2020249 original size:21 final size:21
Alignment explanation
Indices: 2020223--2020276 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2020213 CAACAACAAC
*
2020223 AAGAAGATGAAGGTGAAGAAG
1 AAGAAGATGAAGATGAAGAAG
*
2020244 AAGAAGATGAAGATGAAGATG
1 AAGAAGATGAAGATGAAGAAG
2020265 AAGAAGATGAAG
1 AAGAAGATGAAG
2020277 TTATGAGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.11
Consensus pattern (21 bp):
AAGAAGATGAAGATGAAGAAG
Found at i:2025832 original size:18 final size:18
Alignment explanation
Indices: 2025793--2025832 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2025783 CTAATTTTTT
***
2025793 TATTTAAAAATGTTATGC
1 TATTTAAAAATGTTAAAA
2025811 TATTTAAAAATGTTAAAA
1 TATTTAAAAATGTTAAAA
2025829 TATT
1 TATT
2025833 ACAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (18 bp):
TATTTAAAAATGTTAAAA
Found at i:2030171 original size:13 final size:13
Alignment explanation
Indices: 2030153--2030178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2030143 TGTTTTTCTC
2030153 AAGATTTCCAATT
1 AAGATTTCCAATT
2030166 AAGATTTCCAATT
1 AAGATTTCCAATT
2030179 TCCATCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAGATTTCCAATT
Found at i:2033296 original size:2 final size:2
Alignment explanation
Indices: 2033289--2033325 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2033279 GTACAGTAGT
*
2033289 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2033326 TGTTTGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2033352 original size:2 final size:2
Alignment explanation
Indices: 2033347--2033378 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2033337 GTGTGCGTGT
*
2033347 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2033379 ATAAGAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2043089 original size:26 final size:26
Alignment explanation
Indices: 2043053--2043102 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2043043 ATGGATGTGT
* *
2043053 AATGCTTTTGATTTTAAGTTTTGAGA
1 AATGCTCTTGATTTTAAATTTTGAGA
2043079 AATGCTCTTGATTTTAAATTTTGA
1 AATGCTCTTGATTTTAAATTTTGA
2043103 AGCTAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (26 bp):
AATGCTCTTGATTTTAAATTTTGAGA
Found at i:2046546 original size:17 final size:18
Alignment explanation
Indices: 2046511--2046551 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2046501 ATTGATTTGA
2046511 ATTAAAATAATTTTAAAT
1 ATTAAAATAATTTTAAAT
* *
2046529 ATTAAAAT-TTTTTTAAT
1 ATTAAAATAATTTTAAAT
2046546 ATTAAA
1 ATTAAA
2046552 TAAGTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAATAATTTTAAAT
Found at i:2054110 original size:3 final size:3
Alignment explanation
Indices: 2054102--2054136 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2054092 CTTGCAGCCA
2054102 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2054137 GTGCTTAATT
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2054726 original size:22 final size:22
Alignment explanation
Indices: 2054698--2054741 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2054688 TTATTTATAA
2054698 ATTTATATAAATTACATGACAT
1 ATTTATATAAATTACATGACAT
2054720 ATTTATATAAATTACATGACAT
1 ATTTATATAAATTACATGACAT
2054742 TAAAAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTTATATAAATTACATGACAT
Found at i:2054751 original size:22 final size:22
Alignment explanation
Indices: 2054704--2054753 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2054694 ATAAATTTAT
** *
2054704 ATAAATTACATGACATATTTAT
1 ATAAATTACATGACATATAAAG
2054726 ATAAATTACATGACAT-TAAAAG
1 ATAAATTACATGACATAT-AAAG
2054748 ATAAAT
1 ATAAAT
2054754 ATATCTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (22 bp):
ATAAATTACATGACATATAAAG
Found at i:2054800 original size:11 final size:11
Alignment explanation
Indices: 2054770--2054794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2054760 TTGTTTTTAT
2054770 ATTTATAATAA
1 ATTTATAATAA
2054781 ATTTATAATAA
1 ATTTATAATAA
2054792 ATT
1 ATT
2054795 ATTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTATAATAA
Found at i:2054807 original size:16 final size:17
Alignment explanation
Indices: 2054786--2054818 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2054776 AATAAATTTA
2054786 TAATAAA-TTATTAATT
1 TAATAAATTTATTAATT
2054802 TAATAAATTTATTAATT
1 TAATAAATTTATTAATT
2054819 AAATTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATAAATTTATTAATT
Found at i:2054857 original size:27 final size:28
Alignment explanation
Indices: 2054816--2054876 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
2054806 AAATTTATTA
*
2054816 ATTAAATTAATATCATTTAACTTATAAT
1 ATTAAATTAATATCATATAACTTATAAT
* **
2054844 ATTAAATTTA-ATCATATATTTTATAAT
1 ATTAAATTAATATCATATAACTTATAAT
*
2054871 AATAAA
1 ATTAAA
2054877 GACATAGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTAAATTAATATCATATAACTTATAAT
Found at i:2055800 original size:2 final size:2
Alignment explanation
Indices: 2055793--2055820 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2055783 AGAAGATAGC
2055793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2055821 TAGAAATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2056541 original size:64 final size:64
Alignment explanation
Indices: 2056440--2056567 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
2056430 TGTTTTCCCC
2056440 ACCATATCTAATGAAGCTCTTTGAAAATTATTCCAGAAATTAGTGACTCCATGACTATAAGGTT
1 ACCATATCTAATGAAGCTCTTTGAAAATTATTCCAGAAATTAGTGACTCCATGACTATAAGGTT
2056504 ACCATATCTAATGAAGCTCTTTGAAAATTATTCCAGAAATTAGTGACTCCATGACTATAAGGTT
1 ACCATATCTAATGAAGCTCTTTGAAAATTATTCCAGAAATTAGTGACTCCATGACTATAAGGTT
2056568 TCAATAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (64 bp):
ACCATATCTAATGAAGCTCTTTGAAAATTATTCCAGAAATTAGTGACTCCATGACTATAAGGTT
Found at i:2057466 original size:2 final size:2
Alignment explanation
Indices: 2057459--2057493 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2057449 CAGAAGATTT
*
2057459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2057494 TTTTGAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2059468 original size:18 final size:18
Alignment explanation
Indices: 2059445--2059482 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2059435 ACATACAATC
2059445 AAATTT-AAAATTCAATTA
1 AAATTTAAAAATT-AATTA
2059463 AAATTTAAAAATTAATTA
1 AAATTTAAAAATTAATTA
2059481 AA
1 AA
2059483 TTCACCGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAAAAATTAATTA
Found at i:2063528 original size:2 final size:2
Alignment explanation
Indices: 2063521--2063550 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2063511 AAGGGGAAAA
2063521 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2063551 GGGCAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2064412 original size:2 final size:2
Alignment explanation
Indices: 2064394--2064441 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2064384 TAAACGCGAA
* *
2064394 AG AG CG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2064436 AG AG AG
1 AG AG AG
2064442 GGAAGGAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2067161 original size:6 final size:6
Alignment explanation
Indices: 2067117--2067149 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2067107 TCTTTTTAGG
*
2067117 CAATAA CAATAA CAATAA CAATAA CAACAA CAA
1 CAATAA CAATAA CAATAA CAATAA CAATAA CAA
2067150 AAATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.12
Consensus pattern (6 bp):
CAATAA
Found at i:2067437 original size:15 final size:16
Alignment explanation
Indices: 2067417--2067450 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2067407 TTAGTATAAA
2067417 ATGTCTATTA-TTAAT
1 ATGTCTATTACTTAAT
2067432 ATGTCTATTACTTAAT
1 ATGTCTATTACTTAAT
2067448 ATG
1 ATG
2067451 ACTAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (16 bp):
ATGTCTATTACTTAAT
Found at i:2070151 original size:2 final size:2
Alignment explanation
Indices: 2070144--2070177 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2070134 TGAATTATTA
2070144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2070178 GCGATGGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2071149 original size:12 final size:12
Alignment explanation
Indices: 2071132--2071176 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2071122 AATATAAATA
2071132 ATTTAATATATT
1 ATTTAATATATT
2071144 ATTTAATA-ATT
1 ATTTAATATATT
*
2071155 A--TATTATATT
1 ATTTAATATATT
*
2071165 ATTAAATATATT
1 ATTTAATATATT
2071177 TGTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
9 4 0.15
10 4 0.15
11 4 0.15
12 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAATATATT
Found at i:2071164 original size:21 final size:20
Alignment explanation
Indices: 2071126--2071177 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2071116 TTTTAAAATA
2071126 TAAATAATTTAATATATTAT
1 TAAATAATTTAATATATTAT
* *
2071146 TTAATAATTATATTATATTAT
1 TAAATAATT-TAATATATTAT
2071167 TAAATATATTT
1 TAAATA-ATTT
2071178 GTTTTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 16 0.59
22 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAATAATTTAATATATTAT
Found at i:2075445 original size:16 final size:17
Alignment explanation
Indices: 2075426--2075471 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2075416 TTTATACATA
2075426 TATAAATTTTTAAAAT-
1 TATAAATTTTTAAAATC
** *
2075442 TATAAAAATTTAATATC
1 TATAAATTTTTAAAATC
2075459 TA-AAATTTTTAAA
1 TATAAATTTTTAAA
2075472 TATCAAATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAAATTTTTAAAATC
Found at i:2077095 original size:14 final size:15
Alignment explanation
Indices: 2077076--2077105 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2077066 CAAATAATTG
2077076 AGAT-AACCTAAAAT
1 AGATAAACCTAAAAT
2077090 AGATAAACCTAAAAT
1 AGATAAACCTAAAAT
2077105 A
1 A
2077106 ATGATACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
AGATAAACCTAAAAT
Found at i:2082696 original size:2 final size:2
Alignment explanation
Indices: 2082689--2082729 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2082679 ATGGAATGAT
2082689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2082730 GAAACTGTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2083006 original size:29 final size:29
Alignment explanation
Indices: 2082974--2083031 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2082964 AATTTTAGCC
*
2082974 TTTTTTTTT-TTGA-AAAAAAAATTGATG
1 TTTTTTTTTGTTCATAAAAAAAATTGATG
2083001 TTTTTTTTTGTTCATAAAAAAAATTGATG
1 TTTTTTTTTGTTCATAAAAAAAATTGATG
2083030 TT
1 TT
2083032 GAAATCTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 9 0.32
28 3 0.11
29 16 0.57
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTTTTTTTGTTCATAAAAAAAATTGATG
Found at i:2083720 original size:2 final size:2
Alignment explanation
Indices: 2083707--2083738 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2083697 AATGAGAATC
*
2083707 TA TA TG 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
2083739 GGTAAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2085208 original size:22 final size:22
Alignment explanation
Indices: 2085183--2085225 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2085173 TTAAATAAAA
2085183 TTATATTTAATTTAA-ATTTAAG
1 TTATATTTAA-TTAATATTTAAG
*
2085205 TTATTTTTAATTAATATTTAA
1 TTATATTTAATTAATATTTAA
2085226 AATTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATATTTAATTAATATTTAAG
Found at i:2085506 original size:3 final size:3
Alignment explanation
Indices: 2085494--2085574 Score: 53
Period size: 3 Copynumber: 27.3 Consensus size: 3
2085484 ATAAAATATA
* * *
2085494 TAT T-T TAT TAT TAAT TTT TAT TA- TAT TAT TA- TAA TATT TAA TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * *
2085538 TAT TAT AAT AAT TAAC T-T TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
2085575 TTCATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
2 7 0.11
3 48 0.77
4 7 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2085524 original size:21 final size:21
Alignment explanation
Indices: 2085498--2085576 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
2085488 AATATATATT
2085498 TTATTATTAATTTTTATTATA
1 TTATTATTAATTTTTATTATA
*
2085519 TTATTA-TAATATTTA--ATA
1 TTATTATTAATTTTTATTATA
2085537 TTATTATAATAATTAACTTTATTATTA
1 TTATTAT--TAATT---TTTATTA-TA
2085564 TTATTATT-ATTTT
1 TTATTATTAATTTT
2085577 CATTTTTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
18 9 0.19
20 8 0.17
21 12 0.26
24 7 0.15
25 1 0.02
26 1 0.02
27 9 0.19
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTAATTTTTATTATA
Found at i:2085537 original size:18 final size:18
Alignment explanation
Indices: 2085516--2085561 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2085506 AATTTTTATT
*
2085516 ATATTATTATAATATTTA
1 ATATTATTATAATAATTA
2085534 ATATTATTATAATAATTA
1 ATATTATTATAATAATTA
2085552 ACT-TTATTAT
1 A-TATTATTAT
2085562 TATTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTATAATAATTA
Found at i:2086641 original size:20 final size:20
Alignment explanation
Indices: 2086618--2086655 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2086608 TTTAATTAAT
*
2086618 TAATTTTTATTTTTAAAATA
1 TAATTTTTATTATTAAAATA
2086638 TAATTTTTATTATTAAAA
1 TAATTTTTATTATTAAAA
2086656 AAGAATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATTTTTATTATTAAAATA
Found at i:2086662 original size:20 final size:20
Alignment explanation
Indices: 2086619--2086662 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2086609 TTAATTAATT
* * *
2086619 AATTTTTATTTTTAAAATAT
1 AATTTTTATTATTAAAAAAG
2086639 AATTTTTATTATTAAAAAAG
1 AATTTTTATTATTAAAAAAG
2086659 AATT
1 AATT
2086663 AGAGGTTAAA
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:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTTTTATTATTAAAAAAG
Found at i:2088147 original size:18 final size:19
Alignment explanation
Indices: 2088124--2088160 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2088114 ATAAGTTATG
2088124 TTATTTAA-ATGTTTATTT
1 TTATTTAATATGTTTATTT
*
2088142 TTATTTAATATTTTTATTT
1 TTATTTAATATGTTTATTT
2088161 AATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTATTTAATATGTTTATTT
Found at i:2088155 original size:13 final size:13
Alignment explanation
Indices: 2088137--2088165 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2088127 TTTAAATGTT
2088137 TATTTTTATTTAA
1 TATTTTTATTTAA
2088150 TATTTTTATTTAA
1 TATTTTTATTTAA
2088163 TAT
1 TAT
2088166 ATATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTTATTTAA
Found at i:2088703 original size:20 final size:20
Alignment explanation
Indices: 2088664--2088705 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2088654 TTATAATTAA
*
2088664 AATTAAATAAAATATTATTT
1 AATTAAATAAAATATAATTT
2088684 AATTAAAT-AAATAATAATTT
1 AATTAAATAAAAT-ATAATTT
2088704 AA
1 AA
2088706 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAAATAAAATATAATTT
Found at i:2089484 original size:26 final size:26
Alignment explanation
Indices: 2089426--2089518 Score: 70
Period size: 27 Copynumber: 3.7 Consensus size: 26
2089416 CTACCATTTG
2089426 TGTTTGTTAAAAAT-GAT-AGTTTCTTT
1 TGTTTGTTAAAAATAG-TGA-TTTCTTT
*
2089452 GTATTTGTTAAAAATAGTGATTTCTTT
1 -TGTTTGTTAAAAATAGTGATTTCTTT
* * **
2089479 TGTTTG-CAAAAA-ATTG-TGGCTTT
1 TGTTTGTTAAAAATAGTGATTTCTTT
*
2089502 TGTTTGTTAAAATTAGT
1 TGTTTGTTAAAAATAGT
2089519 AGCTAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 11 0.21
24 7 0.13
25 7 0.13
26 5 0.09
27 21 0.40
28 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (26 bp):
TGTTTGTTAAAAATAGTGATTTCTTT
Found at i:2092075 original size:21 final size:22
Alignment explanation
Indices: 2092046--2092091 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
2092036 TGTTCAGACA
*
2092046 AGTAGTACTCCATAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2092068 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2092089 AGT
1 AGT
2092092 TTCAACAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2094035 original size:25 final size:26
Alignment explanation
Indices: 2093969--2094040 Score: 119
Period size: 27 Copynumber: 2.8 Consensus size: 26
2093959 AAAAACTACC
*
2093969 CTTTGTGTTTGTCAAAAATAGTGGTTT
1 CTTTGTGTTTGTCAAAAAT-GTGGGTT
2093996 CTTTGTGTTTGTCAAAAATGTGGGTT
1 CTTTGTGTTTGTCAAAAATGTGGGTT
2094022 CTTT-TGTTTGTCAAAAATG
1 CTTTGTGTTTGTCAAAAATG
2094041 GTGGCTTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 15 0.34
26 10 0.23
27 19 0.43
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (26 bp):
CTTTGTGTTTGTCAAAAATGTGGGTT
Found at i:2094052 original size:24 final size:24
Alignment explanation
Indices: 2093969--2094068 Score: 105
Period size: 27 Copynumber: 4.0 Consensus size: 24
2093959 AAAAACTACC
*
2093969 CTTTGTGTTTGTCAAAAATAGTGGTTT
1 CTTT-TGTTTGTCAAAAATGGTGG--T
2093996 CTTTGTGTTTGTCAAAAAT-GTGGGTT
1 CTTT-TGTTTGTCAAAAATGGT-GG-T
2094022 CTTTTGTTTGTCAAAAATGGTGG-
1 CTTTTGTTTGTCAAAAATGGTGGT
*
2094045 CTTATTGTTTGTCAAAATTGGTGG
1 CTT-TTGTTTGTCAAAAATGGTGG
2094069 CTAATTCTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 9
0.87 0.01 0.11
Matches are distributed among these distances:
23 3 0.04
24 19 0.28
25 16 0.23
26 10 0.14
27 21 0.30
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (24 bp):
CTTTTGTTTGTCAAAAATGGTGGT
Found at i:2094069 original size:24 final size:24
Alignment explanation
Indices: 2093974--2094070 Score: 92
Period size: 24 Copynumber: 3.9 Consensus size: 24
2093964 CTACCCTTTG
*
2093974 TGTTTGTCAAAAATAGTGGTTTCTT-T
1 TGTTTGTCAAAAATGGTGG---CTTAT
2094000 GTGTTTGTCAAAAAT-GTGGGTTCTT-T
1 -TGTTTGTCAAAAATGGT-GG--CTTAT
2094026 TGTTTGTCAAAAATGGTGGCTTAT
1 TGTTTGTCAAAAATGGTGGCTTAT
*
2094050 TGTTTGTCAAAATTGGTGGCT
1 TGTTTGTCAAAAATGGTGGCT
2094071 AATTCTTATT
Statistics
Matches: 66, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
23 3 0.05
24 21 0.32
25 16 0.24
26 10 0.15
27 16 0.24
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (24 bp):
TGTTTGTCAAAAATGGTGGCTTAT
Found at i:2096861 original size:2 final size:2
Alignment explanation
Indices: 2096854--2096881 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2096844 CATGCTAATA
2096854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2096882 GAAGGAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2100702 original size:19 final size:20
Alignment explanation
Indices: 2100665--2100703 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2100655 TAATTCTAAA
2100665 AGTTATTTTGTTTGTTATAT
1 AGTTATTTTGTTTGTTATAT
* *
2100685 AGTTTTTTTTTTTG-TATAT
1 AGTTATTTTGTTTGTTATAT
2100704 TTAAATGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (20 bp):
AGTTATTTTGTTTGTTATAT
Found at i:2101441 original size:5 final size:5
Alignment explanation
Indices: 2101433--2101469 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
2101423 AACAACACAA
2101433 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
2101470 GTTAATAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:2101807 original size:3 final size:3
Alignment explanation
Indices: 2101799--2101840 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2101789 CCAACGTCAA
*
2101799 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2101841 TAAGTTCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2101949 original size:15 final size:15
Alignment explanation
Indices: 2101929--2101974 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
2101919 ATTTATAAAT
2101929 TTATATATCATATTA
1 TTATATATCATATTA
2101944 TTATATATCAT-TT-
1 TTATATATCATATTA
* *
2101957 TTATTTATTATA-TA
1 TTATATATCATATTA
2101971 TTAT
1 TTAT
2101975 TTGTTAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.37
14 6 0.22
15 11 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATATCATATTA
Found at i:2103652 original size:87 final size:87
Alignment explanation
Indices: 2103547--2103707 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 87
2103537 GCATACTCTC
*
2103547 GCTTAGTTGACCTCTGTTTTAGCTCGTAAATGAACTCTGAATGAAATCAGTCTGACACTGATTTT
1 GCTTAATTGACCTCTGTTTTAGCTCGTAAATGAACTCTGAATGAAATCAGTCTGACACTGATTTT
*
2103612 TTCTGGAATTATAATGATTATA
66 TTATGGAATTATAATGATTATA
* *
2103634 GCTTAATTGACCTTTGTTTTAGCTCGTAAGTGAACTCTGAATGAAATCAGTCTGACACTGATTTT
1 GCTTAATTGACCTCTGTTTTAGCTCGTAAATGAACTCTGAATGAAATCAGTCTGACACTGATTTT
2103699 TTATGGAAT
66 TTATGGAAT
2103708 CCAGATTTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (87 bp):
GCTTAATTGACCTCTGTTTTAGCTCGTAAATGAACTCTGAATGAAATCAGTCTGACACTGATTTT
TTATGGAATTATAATGATTATA
Found at i:2104664 original size:2 final size:2
Alignment explanation
Indices: 2104657--2104681 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2104647 TAAGATTGAA
2104657 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2104682 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2108292 original size:14 final size:14
Alignment explanation
Indices: 2108273--2108323 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2108263 GACTTAATTT
2108273 TTTAATAATAAAAA
1 TTTAATAATAAAAA
*
2108287 TTTAATAAT-ATAA
1 TTTAATAATAAAAA
*
2108300 TTTAAAAAATTAAAAA
1 TTT-AATAA-TAAAAA
2108316 TTT-ATAAT
1 TTTAATAAT
2108324 TTATATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 7 0.23
14 16 0.53
15 1 0.03
16 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAATAAAAA
Found at i:2108307 original size:21 final size:22
Alignment explanation
Indices: 2108281--2108326 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2108271 TTTTTAATAA
* *
2108281 TAAAAATTTAATAA-TATAATT
1 TAAAAAATTAAAAATTATAATT
2108302 TAAAAAATTAAAAATTTATAATT
1 TAAAAAATTAAAAA-TTATAATT
2108325 TA
1 TA
2108327 TATAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
23 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAAAATTAAAAATTATAATT
Found at i:2109122 original size:17 final size:17
Alignment explanation
Indices: 2109079--2109124 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2109069 AAAATAACAT
* *
2109079 AATTTATCTAAAAATTA
1 AATTTATTTATAAATTA
2109096 AATTTATTTATAAATTA
1 AATTTATTTATAAATTA
2109113 AGATTT-TTTATA
1 A-ATTTATTTATA
2109125 TTTATAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTATTTATAAATTA
Found at i:2109237 original size:25 final size:25
Alignment explanation
Indices: 2109209--2109285 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
2109199 TTGATTAATA
* * *
2109209 AAAATAATATTTTAAATTTATTTTT
1 AAAATAATAATATAAAATTATTTTT
*
2109234 AAAATATTAATATAAAATTATTTTT
1 AAAATAATAATATAAAATTATTTTT
**
2109259 AAAA-AA-AATAT-AAATTAAATTT
1 AAAATAATAATATAAAATTATTTTT
2109281 AAAAT
1 AAAAT
2109286 TTTAATAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 13 0.30
23 5 0.11
24 1 0.02
25 25 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATAATAATATAAAATTATTTTT
Found at i:2109281 original size:22 final size:23
Alignment explanation
Indices: 2109242--2109284 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2109232 TTAAAATATT
**
2109242 AATATAAAATTATTTTTAAAAAA
1 AATATAAAATTAAATTTAAAAAA
2109265 AATAT-AAATTAAATTTAAAA
1 AATATAAAATTAAATTTAAAA
2109285 TTTTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATATAAAATTAAATTTAAAAAA
Found at i:2111243 original size:24 final size:26
Alignment explanation
Indices: 2111209--2111284 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 26
2111199 TAAAAATTAG
* *
2111209 CCACCAATTTTGACAAACAACAA-G-
1 CCACCATTTTTGACAAACAAAAAGGA
* *
2111233 CTACCATTTTTTACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGG-A
*
2111260 CCACCATTTTTGACAAACATAAAGG
1 CCACCATTTTTGACAAACAAAAAGG
2111285 GTGGCTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 19 0.45
25 1 0.02
27 22 0.52
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (26 bp):
CCACCATTTTTGACAAACAAAAAGGA
Found at i:2115829 original size:27 final size:27
Alignment explanation
Indices: 2115754--2115822 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
2115744 AACAAGTCAC
*
2115754 CATTTTTGACAAATAAAAAGAAACCAT
1 CATTTTTTACAAATAAAAAGAAACCAT
* *
2115781 CATTTTTTATAAACAAAAAGAAACCA-
1 CATTTTTTACAAATAAAAAGAAACCAT
2115807 CTATTTTTTACAAATA
1 C-ATTTTTTACAAATA
2115823 TACAGAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (27 bp):
CATTTTTTACAAATAAAAAGAAACCAT
Found at i:2122855 original size:2 final size:2
Alignment explanation
Indices: 2122843--2122874 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2122833 ACATAGATAC
*
2122843 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2122875 GGATGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2123172 original size:16 final size:16
Alignment explanation
Indices: 2123141--2123175 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2123131 TTTAATTAAC
**
2123141 AAAAAAAAAAGGAAGG
1 AAAAAAAAAAAAAAGG
2123157 AAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAGG
2123173 AAA
1 AAA
2123176 TGAGAATCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGG
Found at i:2128428 original size:25 final size:24
Alignment explanation
Indices: 2128400--2128449 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2128390 TATTTTACAA
2128400 ATAAAATAA-TATATATTTTTATTTT
1 ATAAAATAATTAT-TA-TTTTATTTT
*
2128425 ATAAATTAATTATTATTTTATTTT
1 ATAAAATAATTATTATTTTATTTT
2128449 A
1 A
2128450 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 10 0.43
26 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATAAAATAATTATTATTTTATTTT
Found at i:2128463 original size:12 final size:12
Alignment explanation
Indices: 2128411--2128469 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
2128401 TAAAATAATA
*
2128411 TATATTTTTATTT
1 TATAATTTTA-TT
* *
2128424 TATAA-ATTAAT
1 TATAATTTTATT
*
2128435 TATTATTTTATT
1 TATAATTTTATT
*
2128447 T-TAATTTTTTT
1 TATAATTTTATT
2128458 TATAATTTTATT
1 TATAATTTTATT
2128470 AATTAAATTG
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
11 14 0.40
12 17 0.49
13 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATAATTTTATT
Found at i:2129580 original size:2 final size:2
Alignment explanation
Indices: 2129573--2129599 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2129563 GCAGTAATGA
2129573 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2129600 ACGTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2132202 original size:26 final size:26
Alignment explanation
Indices: 2132172--2132223 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2132162 CTCTTGTCGA
*
2132172 TCCGAATAACATAGACCGTAAGTTTC
1 TCCGAATAACATAGACCGTAAATTTC
* *
2132198 TCCGAGTAACATAGGCCGTAAATTTC
1 TCCGAATAACATAGACCGTAAATTTC
2132224 CTTTTGCCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (26 bp):
TCCGAATAACATAGACCGTAAATTTC
Found at i:2133419 original size:13 final size:16
Alignment explanation
Indices: 2133387--2133430 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2133377 GTAAAGGATG
2133387 ATTTATAAATATTAAA
1 ATTTATAAATATTAAA
2133403 ATTTA-AAAT-TT-AA
1 ATTTATAAATATTAAA
2133416 ATTTATTAAATATTA
1 ATTTA-TAAATATTA
2133431 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.29
14 2 0.08
15 8 0.33
16 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATAAATATTAAA
Found at i:2134610 original size:15 final size:15
Alignment explanation
Indices: 2134587--2134616 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2134577 TAGTGAAGTG
*
2134587 TATGTCTACATTAAA
1 TATGACTACATTAAA
2134602 TATGACTACATTAAA
1 TATGACTACATTAAA
2134617 CAGACATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (15 bp):
TATGACTACATTAAA
Found at i:2135659 original size:16 final size:16
Alignment explanation
Indices: 2135635--2135666 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2135625 AACACCATTT
2135635 TCTTAGCTAACTGCTG
1 TCTTAGCTAACTGCTG
*
2135651 TCTTGGCTAACTGCTG
1 TCTTAGCTAACTGCTG
2135667 GCTTCTGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (16 bp):
TCTTAGCTAACTGCTG
Found at i:2136975 original size:34 final size:34
Alignment explanation
Indices: 2136911--2137093 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
2136901 ACCAACAAAA
* *
2136911 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
2136944 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2136978 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2137012 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2137046 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2137080 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2137094 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.08
34 123 0.92
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2137086 original size:102 final size:101
Alignment explanation
Indices: 2136911--2137093 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
2136901 ACCAACAAAA
2136911 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
2136976 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
2137012 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
2137077 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
2137094 TGGTTTTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 12 0.16
102 65 0.84
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2141575 original size:34 final size:34
Alignment explanation
Indices: 2141509--2141693 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
2141499 AAGTGGGAGA
* *
2141509 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2141542 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2141576 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2141610 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2141644 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2141678 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2141694 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2141684 original size:102 final size:101
Alignment explanation
Indices: 2141509--2141693 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
2141499 AAGTGGGAGA
2141509 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
2141574 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2141610 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
2141675 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
2141694 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2142257 original size:16 final size:16
Alignment explanation
Indices: 2142236--2142268 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2142226 TGTACAATAA
*
2142236 AAATAAATATTTAAAC
1 AAATAAAAATTTAAAC
2142252 AAATAAAAATTTAAAC
1 AAATAAAAATTTAAAC
2142268 A
1 A
2142269 TCATATTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAAAATTTAAAC
Found at i:2144182 original size:2 final size:2
Alignment explanation
Indices: 2144175--2144199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2144165 TGCATGATTC
2144175 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2144200 CACATGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2146487 original size:113 final size:117
Alignment explanation
Indices: 2146277--2146490 Score: 285
Period size: 113 Copynumber: 1.9 Consensus size: 117
2146267 ATATATGATA
* * *
2146277 ATTTTTTTATAAAATAGTAAAAAATTATTTAATAATTATATATTTTTCGTTAACACATAGGTATT
1 ATTTTTTTATAAAATAGTAAAAAATTATTGAATAACTATATATTTTTC-ATAACACATAGGTATT
*
2146342 TGACAATTCATTAAAAAAGAGTGATTAAATTATGTTTTTGTAATATATTACAT
65 TGACAATTCATTAAAAAAGAATGATTAAATTATGTTTTTGTAATATATTACAT
* * *
2146395 ATTTTTTTATACAATAGT-GAAAGTTATTGAATAACTATAT-TTTTT-AT-ACACATA-GTATTT
1 ATTTTTTTATAAAATAGTAAAAAATTATTGAATAACTATATATTTTTCATAACACATAGGTATTT
* * *
2146455 GAGAATTCCTTTTAAAAAGAATGATTAAATTATGTT
66 GACAATT-CATTAAAAAAGAATGATTAAATTATGTT
2146491 ATCGTAAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
112 12 0.14
113 32 0.38
114 1 0.01
116 5 0.06
117 18 0.21
118 17 0.20
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (117 bp):
ATTTTTTTATAAAATAGTAAAAAATTATTGAATAACTATATATTTTTCATAACACATAGGTATTT
GACAATTCATTAAAAAAGAATGATTAAATTATGTTTTTGTAATATATTACAT
Found at i:2146738 original size:28 final size:27
Alignment explanation
Indices: 2146707--2146829 Score: 80
Period size: 28 Copynumber: 4.5 Consensus size: 27
2146697 TATTCCTTCC
2146707 TAATATATTTATATATTTTATTATATTA
1 TAATATATTTATATATTTTATTA-ATTA
*
2146735 TAATTATATTTAAAATATTTTA-TAGA-TA
1 TAA-TATATTT-ATATATTTTATTA-ATTA
* *
2146763 TAA-AT-TTTACTAGTA-ATTAGTAATTA
1 TAATATATTTA-TA-TATTTTATTAATTA
*
2146789 T-ATAAATTTATTATATTTTATGTAATTA
1 TAATATATTTA-TATATTTTAT-TAATTA
*
2146817 TATTATA-TTATAT
1 TAATATATTTATAT
2146830 TATAATTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
24 1 0.01
25 9 0.12
26 12 0.16
27 12 0.16
28 18 0.24
29 13 0.18
30 9 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (27 bp):
TAATATATTTATATATTTTATTAATTA
Found at i:2146809 original size:20 final size:20
Alignment explanation
Indices: 2146786--2146838 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2146776 TAATTAGTAA
2146786 TTATATAAATT-TATTATATT
1 TTATAT-AATTATATTATATT
*
2146806 TTATGTAATTATATTATATT
1 TTATATAATTATATTATATT
*
2146826 ATATTATAATTAT
1 TTA-TATAATTAT
2146839 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATATAATTATATTATATT
Found at i:2146821 original size:5 final size:5
Alignment explanation
Indices: 2146785--2146838 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
2146775 GTAATTAGTA
* *
2146785 ATTAT A-TAA ATT-T ATTAT ATTTT ATGTA- ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT
2146833 AATTAT
1 -ATTAT
2146839 TTTTTTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
4 8 0.20
5 26 0.65
6 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:2146864 original size:14 final size:13
Alignment explanation
Indices: 2146798--2146865 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
2146788 ATATAAATTT
2146798 ATTATATTTTATGTA
1 ATTATATTTTA--TA
2146813 ATTATA--TTAT-
1 ATTATATTTTATA
2146823 ATTATA--TTATA
1 ATTATATTTTATA
*
2146834 ATTAT-TTTTTTA
1 ATTATATTTTATA
2146846 A-TATACTTTTATA
1 ATTATA-TTTTATA
2146859 ATTATAT
1 ATTATAT
2146866 ATAATATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
10 10 0.22
11 9 0.20
12 5 0.11
13 11 0.24
14 4 0.09
15 6 0.13
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (13 bp):
ATTATATTTTATA
Found at i:2147387 original size:15 final size:15
Alignment explanation
Indices: 2147369--2147421 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2147359 ATTTAATTTT
* *
2147369 TTATAAATTTAAGTA
1 TTATAAATATAAATA
2147384 TTATAAATATAAATA
1 TTATAAATATAAATA
* *
2147399 TTATTTGAATATAGATA
1 TTA--TAAATATAAATA
2147416 TTATAA
1 TTATAA
2147422 TTATTATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 18 0.58
17 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
TTATAAATATAAATA
Found at i:2147750 original size:23 final size:23
Alignment explanation
Indices: 2147688--2147792 Score: 88
Period size: 23 Copynumber: 4.4 Consensus size: 23
2147678 TAATATTATT
* *
2147688 TAATTTAAATTTAAATAGTAATA
1 TAATTTAAATTTAAATAATAAAA
*
2147711 TAAATTT-AATATAAATAATAAAA
1 T-AATTTAAATTTAAATAATAAAA
***
2147734 TAATTTAAATTTTAATATAATTTTA
1 TAATTTAAA-TTTAA-ATAATAAAA
*
2147759 TAATTTAAATTTAAATATTATAAA
1 TAATTTAAATTTAAATAATA-AAA
2147783 -AATTATAAAT
1 TAATT-TAAAT
2147793 ATTTCCAGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
22 5 0.08
23 25 0.38
24 20 0.31
25 15 0.23
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
TAATTTAAATTTAAATAATAAAA
Found at i:2147753 original size:17 final size:16
Alignment explanation
Indices: 2147688--2147766 Score: 58
Period size: 18 Copynumber: 4.9 Consensus size: 16
2147678 TAATATTATT
2147688 TAATTTAAATTTAAATA
1 TAATTTAAATTT-AATA
*
2147705 GTAATATAAATTTAATA
1 -TAATTTAAATTTAATA
* *
2147722 TAA-AT-AA--TAAAA
1 TAATTTAAATTTAATA
2147734 TAATTTAAATTTTAATA
1 TAATTTAAA-TTTAATA
2147751 TAATTTTATAATTTAA
1 TAA-TTTA-AATTTAA
2147767 ATTTAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
12 7 0.14
13 1 0.02
14 4 0.08
15 2 0.04
16 3 0.06
17 11 0.22
18 20 0.40
19 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
TAATTTAAATTTAATA
Found at i:2147753 original size:25 final size:25
Alignment explanation
Indices: 2147688--2147783 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 25
2147678 TAATATTATT
*
2147688 TAATTTAAATTTAAATAGTAAT-ATA
1 TAATTTAAATTTAAATA-TAATAAAA
*
2147713 -AATTT-AATAT-AA-ATAATAAAA
1 TAATTTAAATTTAAATATAATAAAA
* ***
2147734 TAATTTAAATTTTAATATAATTTTA
1 TAATTTAAATTTAAATATAATAAAA
*
2147759 TAATTTAAATTTAAATATTATAAAA
1 TAATTTAAATTTAAATATAATAAAA
2147784 ATTATAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
20 4 0.07
21 3 0.05
22 7 0.13
23 8 0.15
24 7 0.13
25 26 0.47
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
TAATTTAAATTTAAATATAATAAAA
Found at i:2150457 original size:34 final size:33
Alignment explanation
Indices: 2150409--2150629 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
2150399 TGGTAAAAAC
*
2150409 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
2150442 CTACCATTTAGTCAACAATGGTAAGCC-ACTAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
2150476 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2150510 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
2150544 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
2150578 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
2150612 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2150630 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2150525 original size:68 final size:68
Alignment explanation
Indices: 2150411--2150629 Score: 298
Period size: 68 Copynumber: 3.2 Consensus size: 68
2150401 GTAAAAACCA
* * * *
2150411 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACTAAA
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
2150475 TCAC
65 TCAC
* * * *
2150479 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
2150544 CTC
66 CAC
* * * *
2150547 CCATTTAGTCAACAATGGCAAACCACCAAATCACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
2150612 CA-
66 CAC
2150614 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2150630 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
67 17 0.13
68 115 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:2150553 original size:102 final size:101
Alignment explanation
Indices: 2150409--2150629 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
2150399 TGGTAAAAAC
* * *
2150409 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACTAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
2150474 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
2150510 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
2150575 AATCACTCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2150612 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2150630 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2155082 original size:34 final size:33
Alignment explanation
Indices: 2155034--2155252 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 33
2155024 TGGTAAAAAC
*
2155034 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
2155067 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
2155101 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
2155135 TTCTCATTTAATCAACAATTGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
2155169 CTCCCATTTAGTCAACAATGATAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGGT-AACCTACCAAAT
* *
2155203 CACCCATTTAATCAACAATGATAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
2155237 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2155253 TAAATAATAA
Statistics
Matches: 157, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 130 0.83
35 6 0.04
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2155179 original size:102 final size:101
Alignment explanation
Indices: 2155034--2155252 Score: 321
Period size: 102 Copynumber: 2.2 Consensus size: 101
2155024 TGGTAAAAAC
* *
2155034 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGATAAACCACCAA
* * * *
2155099 ATCACCCATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * * * *
2155135 TTCTCATTTAATCAACAATTGTAAGCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGATAAACCACCA
2155200 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
2155237 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2155253 TAAATAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 14 0.14
102 89 0.86
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGATAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:2160419 original size:24 final size:22
Alignment explanation
Indices: 2160387--2160455 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
2160377 ATTATTTAAA
* *
2160387 ATTATTTTACATAAATATTTTT
1 ATTAATTTAAATAAATATTTTT
2160409 AATTAAATTTAAATAAAAAATATTTTT
1 -ATT-AATTTAAAT---AAATATTTTT
2160436 ATTAA-TTAAATAAATATTTT
1 ATTAATTTAAATAAATATTTT
2160456 GAATCAGATC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 9 0.22
23 3 0.08
24 13 0.32
25 2 0.05
26 3 0.08
27 10 0.25
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAATTTAAATAAATATTTTT
Found at i:2160434 original size:27 final size:24
Alignment explanation
Indices: 2160399--2160449 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 24
2160389 TATTTTACAT
2160399 AAATATTTTTAATTAAATTTAAATAAA
1 AAATATTTTT-ATT-AA-TTAAATAAA
2160426 AAATATTTTTATTAATTAAATAAA
1 AAATATTTTTATTAATTAAATAAA
2160450 TATTTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 2 0.08
26 3 0.12
27 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATATTTTTATTAATTAAATAAA
Found at i:2160440 original size:20 final size:21
Alignment explanation
Indices: 2160417--2160455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2160407 TTAATTAAAT
2160417 TTAAATAAA-AAATATTTTTA
1 TTAAATAAATAAATATTTTTA
*
2160437 TTAATTAAATAAATATTTT
1 TTAAATAAATAAATATTTT
2160456 GAATCAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATAAATAAATATTTTTA
Found at i:2162638 original size:2 final size:2
Alignment explanation
Indices: 2162631--2162659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2162621 TGATGACTAT
2162631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2162660 GTTTTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2162975 original size:31 final size:30
Alignment explanation
Indices: 2162940--2163007 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
2162930 AATAAAAAAT
* *
2162940 ATTTAAATTATTATAAAA-TAAATTATTTTAA
1 ATTTAAATAATT-TAAAATTAAAAT-TTTTAA
2162971 ATTTAAATAATTTAAAATTTAAAATTTTTAA
1 ATTTAAATAATTTAAAA-TTAAAATTTTTAA
2163002 ATTTAA
1 ATTTAA
2163008 TGTTATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 5 0.15
31 23 0.70
32 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAAATAATTTAAAATTAAAATTTTTAA
Found at i:2162983 original size:16 final size:16
Alignment explanation
Indices: 2162940--2163007 Score: 68
Period size: 15 Copynumber: 4.4 Consensus size: 16
2162930 AATAAAAAAT
* *
2162940 ATTTAAATTATTATAA
1 ATTTAAATAATTTTAA
* *
2162956 A-ATAAATTATTTTAA
1 ATTTAAATAATTTTAA
*
2162971 ATTTAAATAATTTAAA
1 ATTTAAATAATTTTAA
*
2162987 ATTTAAA-ATTTTTAA
1 ATTTAAATAATTTTAA
2163002 ATTTAA
1 ATTTAA
2163008 TGTTATAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 25 0.57
16 19 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAATAATTTTAA
Found at i:2164179 original size:7 final size:7
Alignment explanation
Indices: 2164138--2164187 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
2164128 GGGTTAAAGA
2164138 AAAATAT
1 AAAATAT
*
2164145 AATATA-
1 AAAATAT
2164151 AAAATAAT
1 AAAAT-AT
*
2164159 TAAAT-T
1 AAAATAT
*
2164165 ATAATAT
1 AAAATAT
2164172 AAAATAT
1 AAAATAT
2164179 AAAATAT
1 AAAATAT
2164186 AA
1 AA
2164188 TATACATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 8 0.24
7 22 0.65
8 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:2164268 original size:27 final size:27
Alignment explanation
Indices: 2164142--2164292 Score: 86
Period size: 27 Copynumber: 5.5 Consensus size: 27
2164132 TAAAGAAAAA
2164142 TATAATATAAAAATA-AT---TA-AAT
1 TATAATATAAAAATATATAAATATAAT
2164164 TATAATAT-AAAATATA-AAATATAA-
1 TATAATATAAAAATATATAAATATAAT
*
2164188 TATACATATAAAAAATTTTATATAATATAAAT
1 TATA-ATAT-AAAAA-TATATA-AATAT-AAT
*
2164220 TATTAATCTATTAAAATTTATATAAATATAAT
1 TA-TAA--TA-TAAAA-ATATATAAATATAAT
* * *
2164252 TTTAATATAAAAATATAAAAATAT-TT
1 TATAATATAAAAATATATAAATATAAT
*
2164278 TATAAATATATAAAT
1 TAT-AATATAAAAAT
2164293 TATCAAAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
21 6 0.06
22 9 0.09
24 6 0.06
25 6 0.06
26 3 0.03
27 24 0.24
28 8 0.08
29 3 0.03
30 5 0.05
31 5 0.05
32 7 0.07
33 7 0.07
34 11 0.11
35 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
TATAATATAAAAATATATAAATATAAT
Found at i:2164893 original size:2 final size:2
Alignment explanation
Indices: 2164886--2164920 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2164876 CATTTAGACT
*
2164886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2164921 TGTAAGAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2165110 original size:19 final size:18
Alignment explanation
Indices: 2165082--2165129 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
2165072 TAAATATAAA
2165082 TTTA-TATATTTATATAT
1 TTTACTATATTTATATAT
*
2165099 TTATACTATATTTATTTAT
1 TT-TACTATATTTATATAT
*
2165118 TTTATTATATTT
1 TTTACTATATTT
2165130 TAATTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTACTATATTTATATAT
Found at i:2165131 original size:19 final size:19
Alignment explanation
Indices: 2165083--2165156 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
2165073 AAATATAAAT
*
2165083 TTATATATTTATATATTTATA
1 TTATAT-TTTATTTATTT-TA
*
2165104 CTATA-TTTATTTATTTTA
1 TTATATTTTATTTATTTTA
*
2165122 TTATATTTTAATTATATTTA
1 TTATATTTTATTTAT-TTTA
**
2165142 AAATATTTATATTTA
1 TTATATTT-TATTTA
2165157 AATAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 6 0.14
19 18 0.42
20 10 0.23
21 9 0.21
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTTTATTTATTTTA
Found at i:2165137 original size:11 final size:10
Alignment explanation
Indices: 2165083--2165140 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
2165073 AAATATAAAT
2165083 TTATATATTTA
1 TTATAT-TTTA
2165094 -TATATTTATA
1 TTATATTT-TA
*
2165104 CTATA-TTTA
1 TTATATTTTA
2165113 TT-TATTTTA
1 TTATATTTTA
2165122 TTATATTTTAA
1 TTATATTTT-A
2165133 TTATATTT
1 TTATATTT
2165141 AAAATATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.05
9 11 0.27
10 15 0.37
11 13 0.32
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATTTTA
Found at i:2165214 original size:32 final size:31
Alignment explanation
Indices: 2165143--2165216 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
2165133 TTATATTTAA
*
2165143 AATATTTATATTTAAATAAATTTTAACAAATT
1 AATATTT-TATATAAATAAATTTTAACAAATT
* *
2165175 AAAATTTTATATAATATAAATGTTTAA-ATATT
1 AATATTTTATATAA-ATAAAT-TTTAACAAATT
*
2165207 TATATTTTAT
1 AATATTTTAT
2165217 TATTATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 6 0.17
32 24 0.69
33 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
AATATTTTATATAAATAAATTTTAACAAATT
Found at i:2171251 original size:16 final size:17
Alignment explanation
Indices: 2171230--2171263 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2171220 TCAAACCCGA
2171230 TAAAAATATT-AATAAT
1 TAAAAATATTAAATAAT
2171246 TAAAAATATTAAATAAT
1 TAAAAATATTAAATAAT
2171263 T
1 T
2171264 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATATTAAATAAT
Found at i:2171562 original size:24 final size:23
Alignment explanation
Indices: 2171525--2171573 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
2171515 TGATATAATT
* *
2171525 AAATAACATAAATATAATACAAA
1 AAATAAAATAAATATAAAACAAA
2171548 AAATAAAATATAATATAAAACAAA
1 AAATAAAATA-AATATAAAACAAA
2171572 AA
1 AA
2171574 TAACACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAAATAAATATAAAACAAA
Found at i:2171583 original size:24 final size:24
Alignment explanation
Indices: 2171525--2171584 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
2171515 TGATATAATT
*
2171525 AAATAACATA-AATATAATACAAA
1 AAATAACATATAATATAAAACAAA
*
2171548 AAATAAAATATAATATAAAAC-AA
1 AAATAACATATAATATAAAACAAA
2171571 AAATAACACTATAA
1 AAATAACA-TATAA
2171585 AAATATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (24 bp):
AAATAACATATAATATAAAACAAA
Found at i:2171661 original size:20 final size:20
Alignment explanation
Indices: 2171636--2171677 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2171626 AACCTATTAA
*
2171636 AATTTATATA-AATATATAAT
1 AATTTAAATATAAT-TATAAT
2171656 AATTTAAATATAATTATAAT
1 AATTTAAATATAATTATAAT
2171676 AA
1 AA
2171678 AAATAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTAAATATAATTATAAT
Found at i:2176793 original size:14 final size:14
Alignment explanation
Indices: 2176774--2176811 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
2176764 TAACCTTATC
2176774 TTTTATTTTTATTA
1 TTTTATTTTTATTA
2176788 TTTTA-TTTTATTA
1 TTTTATTTTTATTA
*
2176801 ATTTATTTTTA
1 TTTTATTTTTA
2176812 ATATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:2177523 original size:174 final size:174
Alignment explanation
Indices: 2177301--2177629 Score: 577
Period size: 174 Copynumber: 1.9 Consensus size: 174
2177291 ATTTACAAGA
* *
2177301 AGGAAACTCCTTTTACTTTTCGTGCCGTACGCGTAGTACATACCGGTGGAAGAACTATAGAACTA
1 AGGAAACTCCTTTTACTTTTCATGCCGTACGCGCAGTACATACCGGTGGAAGAACTATAGAACTA
2177366 ACCAAGGAAGTTTGTGGCAGCCGCATGATCACATTTCTTTAACCACCAAAAAGAATCTCCATTTT
66 ACCAAGGAAGTTTGTGGCAGCCGCATGATCACATTTCTTTAACCACCAAAAAGAATCTCCATTTT
*
2177431 CAGATTCTCCCTCGAATACATGCAGAAGGAAGGTTTCACGTGCT
131 CAGATTCTCCCTCAAATACATGCAGAAGGAAGGTTTCACGTGCT
* *
2177475 AGGAAACTTCTTTTACTTTTCATGCCGTACGTGCAGTACATACCGGTGGAAGAACTATAGAACTA
1 AGGAAACTCCTTTTACTTTTCATGCCGTACGCGCAGTACATACCGGTGGAAGAACTATAGAACTA
* * *
2177540 ACCAAGGAAGTTTGTGGCAGCCGCATGATCATATTTCTTTGACCACCAAAAAGAGTCTCCATTTT
66 ACCAAGGAAGTTTGTGGCAGCCGCATGATCACATTTCTTTAACCACCAAAAAGAATCTCCATTTT
*
2177605 CAGATTCTCCTTCAAATACATGCAG
131 CAGATTCTCCCTCAAATACATGCAG
2177630 CTTCGATCGA
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 146 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (174 bp):
AGGAAACTCCTTTTACTTTTCATGCCGTACGCGCAGTACATACCGGTGGAAGAACTATAGAACTA
ACCAAGGAAGTTTGTGGCAGCCGCATGATCACATTTCTTTAACCACCAAAAAGAATCTCCATTTT
CAGATTCTCCCTCAAATACATGCAGAAGGAAGGTTTCACGTGCT
Found at i:2181486 original size:46 final size:40
Alignment explanation
Indices: 2181396--2181474 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
2181386 GATCTTAGTT
*
2181396 TTTTATTTATATATTATTAATATAAATAAAATTTTAATAA
1 TTTTATTTATATATTATTAACATAAATAAAATTTTAATAA
2181436 TTTTATTTAT-TATTATTTAACATAAATATAAA-TTTAATA
1 TTTTATTTATATATTA-TTAACATAAATA-AAATTTTAATA
2181475 TATATAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 5 0.14
40 28 0.78
41 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (40 bp):
TTTTATTTATATATTATTAACATAAATAAAATTTTAATAA
Found at i:2181514 original size:24 final size:25
Alignment explanation
Indices: 2181461--2181525 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
2181451 TTTAACATAA
*
2181461 ATATAAA-TTTAATATATATAATTTT
1 ATATAAATTTTAAT-TATATAATTAT
*
2181486 A-ATAAATTTTAATTAT-TTATTAT
1 ATATAAATTTTAATTATATAATTAT
2181509 ATATAAATATTTTAATT
1 ATAT-AA-ATTTTAATT
2181526 TAATTCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 6 0.18
24 10 0.29
25 9 0.26
26 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATAAATTTTAATTATATAATTAT
Found at i:2181642 original size:21 final size:21
Alignment explanation
Indices: 2181616--2181656 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2181606 ATACATATTT
2181616 AATTATTAAT-TTTAATTTTAA
1 AATTA-TAATATTTAATTTTAA
*
2181637 AATTATAGTATTTAATTTTA
1 AATTATAATATTTAATTTTA
2181657 TTATTATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTATAATATTTAATTTTAA
Found at i:2181803 original size:20 final size:20
Alignment explanation
Indices: 2181772--2181821 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2181762 TTTTTAATTA
2181772 ATTAAAAA-TATATTAAAAT
1 ATTAAAAATTATATTAAAAT
*
2181791 ATTAAAAATTATATTAATAT
1 ATTAAAAATTATATTAAAAT
2181811 -TTATAAAATTA
1 ATTA-AAAATTA
2181822 AATAAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAAAATTATATTAAAAT
Found at i:2183022 original size:2 final size:2
Alignment explanation
Indices: 2183015--2183046 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2183005 CAATGAAGAA
2183015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2183047 GTGGTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2183618 original size:2 final size:2
Alignment explanation
Indices: 2183611--2183635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2183601 ACTCTCAAAG
2183611 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2183636 AAATACCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2184227 original size:34 final size:34
Alignment explanation
Indices: 2184161--2184345 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
2184151 AACAAAGAAA
* *
2184161 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2184194 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2184228 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2184262 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2184296 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2184330 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2184346 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2184336 original size:102 final size:101
Alignment explanation
Indices: 2184161--2184345 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
2184151 AACAAAGAAA
2184161 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
2184226 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2184262 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
2184327 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
2184346 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Done.