Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1836538 original size:36 final size:36
Alignment explanation
Indices: 1836457--1836609 Score: 111
Period size: 36 Copynumber: 4.4 Consensus size: 36
1836447 ATTGAAAACA
** * * * *
1836457 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
1836493 TATCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* ** * **
1836529 TTTCTCTTGAAACACAA------AACCTTTGAGATTG
1 TTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAG
* *
1836560 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
1836596 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1836610 CAAAATCTTT
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
30 2 0.02
31 21 0.24
36 61 0.71
37 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:1836633 original size:67 final size:67
Alignment explanation
Indices: 1836495--1836642 Score: 228
Period size: 67 Copynumber: 2.2 Consensus size: 67
1836485 TGAGATAATA
*
1836495 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTG
1 TCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTG
1836560 TT
66 TT
* *
1836562 TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-ATT-
1 TCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTG
1836625 TAT
66 T-T
*
1836628 CTCCCTTAAAACAAA
1 -TCCCTTGAAACAAA
1836643 ATTTCGTTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 69 0.93
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (67 bp):
TCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTG
TT
Found at i:1836856 original size:36 final size:36
Alignment explanation
Indices: 1836776--1836871 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
1836766 CATCTCCCCG
* * * *
1836776 TGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTATCT
1836813 TGAGACAGTTTCTCTTGAAACAA-TTTTCGTCTATCT
1 TGAGACAGTTTCTCTTGAAACAAGTTTT-GTCTATCT
*
1836849 TGAGACAGTTTCCCTTGAAACAA
1 TGAGACAGTTTCTCTTGAAACAA
1836872 AATCTTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.08
36 31 0.58
37 18 0.34
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (36 bp):
TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTATCT
Found at i:1836934 original size:65 final size:67
Alignment explanation
Indices: 1836830--1836987 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
1836820 GTTTCTCTTG
** * * **
1836830 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
1836892 CTA
65 CTA
* *
1836895 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
1836960 TA
66 TA
*
1836962 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
1836988 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:1836964 original size:67 final size:65
Alignment explanation
Indices: 1836821--1836987 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
1836811 CTTGAGACAG
* * ** * * **
1836821 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
1836885 A
65 A
* *
1836886 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
1836951 TA
64 TA
*
1836953 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
1836988 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:1837768 original size:106 final size:105
Alignment explanation
Indices: 1837608--1838383 Score: 810
Period size: 105 Copynumber: 7.3 Consensus size: 105
1837598 GCCATCTGCG
* * *
1837608 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
*
1837673 GGGACGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * * **
1837717 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* **
1837782 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
1837822 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
1837887 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGACA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * * * *
1837927 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCATAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGAA
* * * * ** *
1837992 GGGACGACTGGTTATCAACGAACAACTTTTCAGTTTCA-TTCTCG
63 GGGACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGC-CA
* * * *
1838036 ATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGAA
* *
1838101 GGGACGGCTGGTTGTCAACAA-ACATTTTTCAAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAACAACA-ACTTCTC-AATTTCAGAGCCA
* * * *
1838145 ATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCATAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
1838210 ACGGCTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * * * *
1838245 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACATCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** * * * * *
1838310 GCGGCTGACTGTCAACAAACAATTTCCCAGTTTTAGAACCA
66 ACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
1838351 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCG
1838384 GAACAATATT
Statistics
Matches: 575, Mismatches: 78, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
100 80 0.14
101 2 0.00
102 1 0.00
103 4 0.01
104 3 0.01
105 147 0.26
106 134 0.23
107 8 0.01
108 52 0.09
109 143 0.25
110 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:1838907 original size:35 final size:35
Alignment explanation
Indices: 1838844--1838943 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
1838834 TTTCGTCCTA
*
1838844 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
1838881 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
1838916 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
1838944 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:1845422 original size:106 final size:104
Alignment explanation
Indices: 1845294--1845658 Score: 482
Period size: 106 Copynumber: 3.4 Consensus size: 104
1845284 CACCCACTTC
* * * * *
1845294 CAATACGAAAATTCATAGACTTATTATGAATTTATTAGTTTGTACACACAGTGTTAATACGAAAA
1 CAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAAT-TCAATACGAAAA
*
1845359 TTCATAAACTTATTATGAATTTCTTAGTTTGTACATAGTG
65 TTCATAAACTTATTATGAATTTCTTAATTTGTACATAGTG
* *
1845399 TCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACAC-CCATTACCAATACTAA
1 -CAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATT--CAATACGAA
* * ** * *
1845463 AATTCATAAACTTATTATGAATTTTTTAACTTCCACACAATG
63 AATTCATAAACTTATTATGAATTTCTTAATTTGTACATAGTG
*
1845505 CTAATGC-ATAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATTCCAATACGAA
1 C-AATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATT-CAATACGAA
1845569 AATTCATAAACTTATTATGAATTTCTTAATTTGTACACATAGTG
63 AATTCATAAACTTATTATGAATTTCTTAATTTGT--ACATAGTG
*
1845613 CCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAGTTTGCAC
1 -CAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCAC
1845659 TCATAATGCC
Statistics
Matches: 225, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
104 1 0.00
105 4 0.02
106 168 0.75
107 4 0.02
108 46 0.20
109 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (104 bp):
CAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATTCAATACGAAAAT
TCATAAACTTATTATGAATTTCTTAATTTGTACATAGTG
Found at i:1845566 original size:160 final size:159
Alignment explanation
Indices: 1845278--1845651 Score: 479
Period size: 160 Copynumber: 2.3 Consensus size: 159
1845268 GTTTACGTTG
* **
1845278 GTTT-CACACCCACTTCCAATACGAAAATTCATAGACTTATTATGAATTTATTAGTTTGTACACA
1 GTTTGCACACCCA-TTCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGACTGTACACA
* * * * *
1845342 CAGTGTTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGTACATAGTGTCAATACG
65 CAATGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACAATGTCAATACG
1845407 AAAATTCATAAACTTATTATGAATTTCTTA
130 AAAATTCATAAACTTATTATGAATTTCTTA
* * *
1845437 GTTTGCACACCCATTACCAATACTAAAATTCATAAACTTATTATGAATTTTTTA-ACT-TCCACA
1 GTTTGCACACCCATT-CCAATACGAAAATTCATAAACTTATTATGAATTTATTAGACTGTACACA
*
1845500 CAATGCTAATGC-ATAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAAT-TCCAA
65 CAATGCTAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTG--CACACAATGT-CAA
1845563 TACGAAAATTCATAAACTTATTATGAATTTCTTA
126 TACGAAAATTCATAAACTTATTATGAATTTCTTA
* * ** * * *
1845597 ATTTGTACACATAGTGCCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAG
1 GTTTGCACACCCA-TTCCAATACGAAAATTCATAAACTTATTATGAATTTATTAG
1845652 TTTGCACTCA
Statistics
Matches: 187, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
157 1 0.01
158 48 0.26
159 8 0.04
160 129 0.69
161 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (159 bp):
GTTTGCACACCCATTCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGACTGTACACAC
AATGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACAATGTCAATACGA
AAATTCATAAACTTATTATGAATTTCTTA
Found at i:1845669 original size:54 final size:54
Alignment explanation
Indices: 1845293--1845669 Score: 467
Period size: 54 Copynumber: 7.1 Consensus size: 54
1845283 ACACCCACTT
* * * *
1845293 CCAATACGAAAATTCATAGACTTATTATGAATTTATTAGTTTGTACACACAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
** * * *
1845347 TTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTG--TACATAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
* * * *
1845399 TCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACCCATTA
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
* * **
1845453 CCAATACTAAAATTCATAAACTTATTATGAATTTTTTAACTT-C-CACACAATG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
* * *
1845505 CTAATGC-ATAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATT
1 CCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
* * * *
1845559 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAATTTGTACACATAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
* * *
1845613 CCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAGTTTGCACTCATAATG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
1845667 CCA
1 CCA
1845670 TTTGGTAATC
Statistics
Matches: 279, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
51 1 0.00
52 90 0.32
53 2 0.01
54 185 0.66
55 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (54 bp):
CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAATG
Found at i:1846125 original size:19 final size:21
Alignment explanation
Indices: 1846087--1846126 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1846077 GTCTTAGTAT
1846087 CGATACTTCTATACTATGGTAC
1 CGATACTTCTATA-TATGGTAC
1846109 CGATAC-TCTAT-TATGGTA
1 CGATACTTCTATATATGGTA
1846127 TCGGTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (21 bp):
CGATACTTCTATATATGGTAC
Found at i:1850169 original size:81 final size:80
Alignment explanation
Indices: 1850037--1850718 Score: 783
Period size: 81 Copynumber: 8.4 Consensus size: 80
1850027 CATTTACCCG
* * * * * * * *
1850037 AAGGCATTTAGCCCTTCATCTAACTTGCATGATTGATACCTTTCTGCCAAATGCATAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGC-
* *
1850102 AATGATCTTTTACTCA
65 ATTAATCTTTTACTCA
* * * * *
1850118 AAGGTATTTAACCTTTCATCTAACTGGTATAACTAACACCTTTCTATCAAATGCACAGCTAGACC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAG-GC
* *
1850183 ATTACTCTTTTACACA
65 ATTAATCTTTTACTCA
* *
1850199 AAGGGATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG-C
1850264 ATTAATCTTTTACTCA
65 ATTAATCTTTTACTCA
* ** * * * * *
1850280 AAGGTATTTAACCTTTAATCTAACTAACAAAATTGACATCTTTCTGTCAAATGCACAACAAAGAC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGC-TAGGC
**
1850345 ATTAATCTTTTTTTTCA
65 ATTAATC-TTTTACTCA
** * * *
1850362 AAGGTATTTAACCTTTCATCTAACTAACAAAATTGACATCTTTCTGTCAAAATGCACAGCTAGTC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AAATGCACAGCTAG-G
*
1850427 CATTAATCTTTTACTTA
64 CATTAATCTTTTACTCA
* * * *
1850444 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGCCACATTTCTCTCAAATGCACAGATAGGCC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG-C
*
1850509 ATTAATATTTTACTCA
65 ATTAATCTTTTACTCA
* * * *
1850525 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGAACAACCAGGTC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG-C
*
1850590 ATTAATCTTTTACTTA
65 ATTAATCTTTTACTCA
* * * * * *
1850606 AAGATATTTAACCTTTCTTCTAACTGGCATAATTGACACATTTCTATCAAATGTACA-ATAGGTC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG-C
1850670 ATTAATCTTTTACTCA
65 ATTAATCTTTTACTCA
* *
1850686 AAGGGATTTAACCTTT-ATCTAACTGCCATAATT
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATT
1850719 TATTCTTTTA
Statistics
Matches: 516, Mismatches: 78, Indels: 16
0.85 0.13 0.03
Matches are distributed among these distances:
79 15 0.03
80 34 0.07
81 343 0.66
82 106 0.21
83 18 0.03
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (80 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
TTAATCTTTTACTCA
Found at i:1850496 original size:245 final size:243
Alignment explanation
Indices: 1850106--1850718 Score: 833
Period size: 245 Copynumber: 2.5 Consensus size: 243
1850096 TAGGCAAATG
* * *
1850106 ATCTTTTAC-TCAAAGGTATTTAACCTTTCATCTAACTGGTATAACTAACACCTTTCTATCAAAT
1 ATCTTTTACTTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTATCAAAT
* * *
1850170 GCACAGCTAGACCATTACTCTTTTACACAAAGGGATTTAACCTTTCATCTAACTGGCATAATTGA
65 GCACAGCTAGTCCATTAATCTTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATAATTGA
* * *
1850235 CACCTTTCTGTCAAATGCACA-ACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTAAT
130 CACATTTCTCTCAAATGCACAGA-TAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTAAT
* *
1850299 CTAACTAACAAAATTGACATCTTTCTGTCAAATGCACAACAAAGACATTA
194 CTAACTAACAAAATTGACACCTTTCTGTCAAATGAACAACAAAGACATTA
** ** * *
1850349 ATCTTTTTTTTCAAAGGTATTTAACCTTTCATCTAACTAACAAAATTGACATCTTTCTGTCAAAA
1 ATCTTTTACTTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTATC-AAA
* *
1850414 TGCACAGCTAGTCCATTAATCTTTTACTTAAAGGTATTTAACCTTTCATCTAACTGGCATAATTG
64 TGCACAGCTAGTCCATTAATCTTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATAATTG
* *
1850479 CCACATTTCTCTCAAATGCACAGATAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCAT
129 ACACATTTCTCTCAAATGCACAGATAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTAAT
** * * * * *
1850544 CTAACTGGCATAATTGACACCTTTTTGTCAAATGAACAACCAGGTCATTA
194 CTAACTAACAAAATTGACACCTTTCTGTCAAATGAACAACAAAGACATTA
* *
1850594 ATCTTTTACTT-AAAGATATTTAACCTTTCTTCTAACTGGCATAATTGACACATTTCTATCAAAT
1 ATCTTTTACTTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC-TTTCTATCAAAT
* * *
1850658 GTACA-ATAGGT-CATTAATCTTTTACTCAAAGGGATTTAACCTTT-ATCTAACTGCCATAATT
65 GCACAGCTA-GTCCATTAATCTTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATAATT
1850719 TATTCTTTTA
Statistics
Matches: 323, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
241 16 0.05
242 33 0.10
243 18 0.06
244 84 0.26
245 171 0.53
246 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (243 bp):
ATCTTTTACTTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTCTATCAAATG
CACAGCTAGTCCATTAATCTTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATAATTGAC
ACATTTCTCTCAAATGCACAGATAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTAATCT
AACTAACAAAATTGACACCTTTCTGTCAAATGAACAACAAAGACATTA
Found at i:1854238 original size:13 final size:13
Alignment explanation
Indices: 1854150--1854241 Score: 100
Period size: 13 Copynumber: 7.3 Consensus size: 13
1854140 AACCCAACCC
1854150 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1854163 TACCCGACCAGTT
1 GACCCGACCCGTT
* *
1854176 TACCCGACCAGTT
1 GACCCGACCCGTT
*
1854189 TACCCGACCC---
1 GACCCGACCCGTT
*
1854199 GACACGACCCGTT
1 GACCCGACCCGTT
*
1854212 GATCCGACCCGTT
1 GACCCGACCCGTT
1854225 GACCCGACCCGTT
1 GACCCGACCCGTT
1854238 GACC
1 GACC
1854242 GACGTTGACA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.12
13 60 0.88
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1856569 original size:24 final size:24
Alignment explanation
Indices: 1856542--1856627 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
1856532 TCAAATTTGA
* * *
1856542 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACATGACATGG
* * *
1856566 ATTCTGATCTGATA-TTAACATGG
1 ATTCTGATATGATACATGACATGG
*
1856589 ATTCTGATCTGATACATGACATGG
1 ATTCTGATATGATACATGACATGG
1856613 ATTCTGATATGATAC
1 ATTCTGATATGATAC
1856628 TTAACTTGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.38
24 33 0.62
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACATGG
Found at i:1856614 original size:47 final size:48
Alignment explanation
Indices: 1856542--1856632 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
1856532 TCAAATTTGA
* * * *
1856542 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTAACATGG
1 ATTCTGATATGATACATGACATGGATTCTGATATGATACTTAACATGG
*
1856589 ATTCTGATCTGATACATGACATGGATTCTGATATGATACTTAAC
1 ATTCTGATATGATACATGACATGGATTCTGATATGATACTTAAC
1856633 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACATGGATTCTGATATGATACTTAACATGG
Found at i:1858764 original size:13 final size:13
Alignment explanation
Indices: 1858745--1858781 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1858735 GTCATAACCC
1858745 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1858758 TACCCGACCCGTT
1 GACCCGACCCGTT
1858771 GACCCGACCCG
1 GACCCGACCCG
1858782 ACCTGTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1858779 original size:31 final size:31
Alignment explanation
Indices: 1858741--1858805 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1858731 ATCGGTCATA
*
1858741 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
* *
1858772 ACCCGACCCGACCTGTTGATCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1858803 ACC
1 ACC
1858806 TGTTGACCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:1858780 original size:18 final size:18
Alignment explanation
Indices: 1858759--1858799 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1858749 CGACCCGTTT
1858759 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
* *
1858777 ACCCGACCTGTTGATCCG
1 ACCCGACCCGTTGACCCG
1858795 ACCCG
1 ACCCG
1858800 TTGACCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1858821 original size:18 final size:20
Alignment explanation
Indices: 1858781--1858823 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1858771 GACCCGACCC
1858781 GACCTGTTGATCCGACCCGTT
1 GACCTGTTGATCCGA-CCGTT
1858802 GACCTGTTGA-CCGA-CGTT
1 GACCTGTTGATCCGACCGTT
1858820 GACC
1 GACC
1858824 ACTATTGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
20 4 0.18
21 10 0.45
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (20 bp):
GACCTGTTGATCCGACCGTT
Found at i:1861133 original size:23 final size:24
Alignment explanation
Indices: 1861086--1861176 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
1861076 TCAAATTTGA
* * *
1861086 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
1861110 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
* *
1861133 ATTTTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
1861157 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1861177 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:1865954 original size:81 final size:81
Alignment explanation
Indices: 1865898--1866474 Score: 760
Period size: 81 Copynumber: 7.1 Consensus size: 81
1865888 TACGTAGATG
* * * *
1865898 ATCTTTTACTCAAAGATATTTAACCTTTCATTTAAATGGCATAATTGACACATTTCTATCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
* *
1865963 CAAAGCTAGGACATTA
66 CACAGCTAGGCCATTA
* * * * ** * *
1865979 ATCTTTTACTCAAATGAATTTAGCATTTCATCTAACTCACATAATTGACACCTTTTTGTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
*
1866044 CATAGCTAGGCCATTA
66 CACAGCTAGGCCATTA
* * * * *
1866060 ATTTTTTACTCAAAGGTATTTAACATTTCATATAACTGGAATAATTGACACATTTATGTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
**
1866125 CACAATTAGGCCATTA
66 CACAGCTAGGCCATTA
* * *
1866141 ATTTTTTACTCAAAGGTATTTAACCTTTCCTCTAACTGGAATAATTGACA-ACTTTCTGTCAAAT
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACA-TTTCTGTCAAAT
**
1866205 GCATTGCTAGGCCATTA
65 GCACAGCTAGGCCATTA
* * * * * *
1866222 ATCTTTTATTCATAGGTATTTAACCTTTCATCTAACTGTCATAATTGAAACCTTTTTGTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
*
1866287 CACAGCTAGGTCATTA
66 CACAGCTAGGCCATTA
*
1866303 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTTTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
1866368 CACAGCTAGGCCATTA
66 CACAGCTAGGCCATTA
** * * *
1866384 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTACCATAATTGAAACATTTCTATCAAATA
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
* *
1866449 CACAACTAAGCCATTA
66 CACAGCTAGGCCATTA
1866465 ATCTTTTACT
1 ATCTTTTACT
1866475 TTAAAATAAT
Statistics
Matches: 432, Mismatches: 62, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 431 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (81 bp):
ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATG
CACAGCTAGGCCATTA
Found at i:1870205 original size:12 final size:12
Alignment explanation
Indices: 1870188--1870218 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1870178 TCGTTACTCT
1870188 ATGTTGTAGGTA
1 ATGTTGTAGGTA
1870200 ATGTTGTAGGTA
1 ATGTTGTAGGTA
1870212 ATGTTGT
1 ATGTTGT
1870219 GATAGGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (12 bp):
ATGTTGTAGGTA
Found at i:1873812 original size:22 final size:22
Alignment explanation
Indices: 1873785--1873826 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1873775 CTTATCGTTT
*
1873785 TATATGATGTTTATCATGAACA
1 TATATGATATTTATCATGAACA
1873807 TATATGATATTTATCATGAA
1 TATATGATATTTATCATGAA
1873827 TGATATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (22 bp):
TATATGATATTTATCATGAACA
Found at i:1878730 original size:30 final size:33
Alignment explanation
Indices: 1878690--1878771 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 33
1878680 TCGGATTATC
1878690 ACTATAGTGTGTAAGGACACCTAGTG-A-A-GT
1 ACTATAGTGTGTAAGGACACCTAGTGCATAGGT
* *
1878720 ACTCTAGTGTGTAAGGACACTTAGTGCATATGGT
1 ACTATAGTGTGTAAGGACACCTAGTGCATA-GGT
1878754 ACTATAGTGTGTAAGGAC
1 ACTATAGTGTGTAAGGAC
1878772 TCTTAGTACA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 24 0.53
31 1 0.02
32 1 0.02
34 19 0.42
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (33 bp):
ACTATAGTGTGTAAGGACACCTAGTGCATAGGT
Found at i:1878762 original size:34 final size:30
Alignment explanation
Indices: 1878690--1878778 Score: 115
Period size: 34 Copynumber: 2.8 Consensus size: 30
1878680 TCGGATTATC
*
1878690 ACTATAGTGTGTAAGGACACCTAGTGAAGT
1 ACTATAGTGTGTAAGGACACTTAGTGAAGT
*
1878720 ACTCTAGTGTGTAAGGACACTTAGTGCATATGGT
1 ACTATAGTGTGTAAGGACACTTAGTG-A-A--GT
*
1878754 ACTATAGTGTGTAAGGACTCTTAGT
1 ACTATAGTGTGTAAGGACACTTAGT
1878779 ACAAATTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.47
31 1 0.02
32 1 0.02
34 25 0.49
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTGAAGT
Found at i:1878778 original size:17 final size:17
Alignment explanation
Indices: 1878694--1878778 Score: 54
Period size: 17 Copynumber: 5.2 Consensus size: 17
1878684 ATTATCACTA
* *
1878694 TAGTGTGTAAGGACACC
1 TAGTGTGTAAGGACTCT
*
1878711 TA--GTG-AAGTACTC-
1 TAGTGTGTAAGGACTCT
*
1878724 TAGTGTGTAAGGACACT
1 TAGTGTGTAAGGACTCT
** * *
1878741 TAGTGCATATGGTACT-A
1 TAGTGTGTAAGG-ACTCT
1878758 TAGTGTGTAAGGACTCT
1 TAGTGTGTAAGGACTCT
1878775 TAGT
1 TAGT
1878779 ACAAATTGTA
Statistics
Matches: 49, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
13 2 0.04
14 6 0.12
15 6 0.12
16 9 0.18
17 24 0.49
18 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (17 bp):
TAGTGTGTAAGGACTCT
Found at i:1880127 original size:47 final size:47
Alignment explanation
Indices: 1880060--1880273 Score: 324
Period size: 47 Copynumber: 4.6 Consensus size: 47
1880050 TAAAAATCTT
* * * *
1880060 TTACCATTT--ATCCCATAAGCTCGTAAGCTTCTTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
* *
1880105 ATACCATTTAAATTCCATAAGCTCGTAAGCTTAATTTTATCAACATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTT-ATTTTATCAATATAC
1880153 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
* *
1880200 TTATCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
*
1880247 TTGCCATTTAAATTCCATAAGCTCGTA
1 TTACCATTTAAATTCCATAAGCTCGTA
1880274 GACAATAGCC
Statistics
Matches: 154, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 8 0.05
47 103 0.67
48 43 0.28
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
Found at i:1880177 original size:95 final size:94
Alignment explanation
Indices: 1880060--1880273 Score: 324
Period size: 95 Copynumber: 2.3 Consensus size: 94
1880050 TAAAAATCTT
* *
1880060 TTACCATTT--ATCCCATAAGCTCGTAAGCTTCTTTTACCAAAATACATACCATTTAAATTCCAT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACATACCATTTAAATTCCAT
*
1880123 AAGCTCGTAAGCTTAATTTTATCAACATAC
66 AAGCTCATAAGCTT-ATTTTATCAACATAC
* * * *
1880153 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTATCATTTAAATTCCAT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACATACCATTTAAATTCCAT
*
1880218 AAGCTCATAAGCTTATTTTATCAATATAC
66 AAGCTCATAAGCTTATTTTATCAACATAC
*
1880247 TTGCCATTTAAATTCCATAAGCTCGTA
1 TTACCATTTAAATTCCATAAGCTCGTA
1880274 GACAATAGCC
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
93 9 0.08
94 40 0.36
95 61 0.55
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (94 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACATACCATTTAAATTCCAT
AAGCTCATAAGCTTATTTTATCAACATAC
Found at i:1884057 original size:5 final size:5
Alignment explanation
Indices: 1884047--1884134 Score: 63
Period size: 6 Copynumber: 16.4 Consensus size: 5
1884037 TCTCTCATTT
* *
1884047 TTTTC TTTTC TTTTC ATTTTC TATT- ATTT- TTTTC ATTTTC ATTTTC
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC
*
1884093 ATTTTC TTCTTT TTTTC TATTTTC TTTTC TTTTC TGTTTC TT
1 -TTTTC TT-TTC TTTTC --TTTTC TTTTC TTTTC T-TTTC TT
1884135 CATTTCTGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
4 5 0.07
5 29 0.41
6 31 0.44
7 5 0.07
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:1884066 original size:18 final size:19
Alignment explanation
Indices: 1884057--1884139 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 19
1884047 TTTTCTTTTC
*
1884057 TTTTCATTTTCTATT-ATTT
1 TTTTCATTTTCTTTTCA-TT
1884076 TTTTCATTTTCATTTTCATT
1 TTTTCATTTTC-TTTTCATT
*
1884096 TTCTTC--TTT-TTTTC-TA
1 TT-TTCATTTTCTTTTCATT
1884112 TTTTC-TTTTCTTTTC-TGT
1 TTTTCATTTTCTTTTCAT-T
1884130 TTCTTCATTT
1 TT-TTCATTT
1884140 CTGTGTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
15 3 0.06
16 6 0.11
17 11 0.21
18 2 0.04
19 17 0.32
20 10 0.19
21 4 0.08
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTCATTTTCTTTTCATT
Found at i:1884134 original size:11 final size:10
Alignment explanation
Indices: 1884047--1884134 Score: 63
Period size: 11 Copynumber: 8.2 Consensus size: 10
1884037 TCTCTCATTT
1884047 TTTTCTTTTC
1 TTTTCTTTTC
1884057 TTTTCATTTTC
1 TTTTC-TTTTC
* *
1884068 TATT-ATTT-
1 TTTTCTTTTC
1884076 TTTTCATTTTC
1 TTTTC-TTTTC
1884087 ATTTTCATTTTC
1 -TTTTC-TTTTC
*
1884099 TTCTTTTTTTC
1 TT-TTCTTTTC
1884110 TATTTTCTTTTC
1 --TTTTCTTTTC
1884122 TTTTCTGTTTC
1 TTTTCT-TTTC
1884133 TT
1 TT
1884135 CATTTCTGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 14 0.22
11 21 0.33
12 20 0.32
13 2 0.03
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:1884134 original size:31 final size:29
Alignment explanation
Indices: 1884044--1884127 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
1884034 TCATCTCTCA
*
1884044 TTTTTTTC-TTTTCTTTTCATTTTCTATTA
1 TTTTTTTCATTTTCTTTTCATTTTCT-TTC
1884073 TTTTTTTCATTTTCATTTTCATTTTC-TTC
1 TTTTTTTCATTTTC-TTTTCATTTTCTTTC
1884102 TTTTTTTCTATTTTCTTTTC-TTTTCT
1 TTTTTTTC-ATTTTCTTTTCATTTTCT
1884128 GTTTCTTCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
28 5 0.10
29 23 0.46
30 11 0.22
31 11 0.22
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTTTTTCATTTTCTTTTCATTTTCTTTC
Found at i:1884160 original size:2 final size:2
Alignment explanation
Indices: 1884150--1884201 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1884140 CTGTGTTTTT
1884150 TA TA T- 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
1884191 TA TA TA TA TA T
1 TA TA TA TA TA T
1884202 TGAGCTCTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1886458 original size:20 final size:20
Alignment explanation
Indices: 1886419--1886458 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1886409 ATTTATTCTC
* *
1886419 TATAAAATTATAATTGATAT
1 TATAAAAATATAATTCATAT
*
1886439 TATAAAAATATCATTCATAT
1 TATAAAAATATAATTCATAT
1886459 AATTTATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TATAAAAATATAATTCATAT
Found at i:1887062 original size:47 final size:47
Alignment explanation
Indices: 1886989--1887202 Score: 315
Period size: 47 Copynumber: 4.6 Consensus size: 47
1886979 TAAAAATCTT
* * * *
1886989 TTACCATTT--ATCCCATAAGCTAGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
* *
1887034 TTACCATTTAAATTCCATAAGCTCGTAAGCTTAATTTTATCAACATAT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTT-ATTTTATCAATATAC
1887082 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
* * *
1887129 TTGCCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCGATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
*
1887176 TTGCCATTTAAATTCCATAAGCTCGTA
1 TTACCATTTAAATTCCATAAGCTCGTA
1887203 GACAATAGCC
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
45 9 0.06
47 102 0.66
48 44 0.28
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
Found at i:1887386 original size:61 final size:61
Alignment explanation
Indices: 1887272--1887386 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
1887262 GTAGTGCTAA
* * *** *
1887272 ACCTGCACTAAGCTTATGCCATAGTGCTAATCTGGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAAACATGACACATAAGGTCGTGCCCACC
* *
1887333 ACCTACACTAAGCTTACGCTATAGTGCTAATCCAAACATGATACATTAA-GTCGT
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAAACATGACACA-TAAGGTCGT
1887387 ATCCACCTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 42 0.93
62 3 0.07
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCAAACATGACACATAAGGTCGTGCCCACC
Found at i:1888152 original size:14 final size:14
Alignment explanation
Indices: 1888116--1888152 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1888106 AGTTGATCAA
*
1888116 CAGAATCTATTTTG
1 CAGAATCTGTTTTG
1888130 CAGAATCTGTTTTG
1 CAGAATCTGTTTTG
1888144 CAGAATCTG
1 CAGAATCTG
1888153 CTGTCCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (14 bp):
CAGAATCTGTTTTG
Found at i:1889273 original size:30 final size:29
Alignment explanation
Indices: 1889212--1889285 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
1889202 ATTTTTAATT
* * *
1889212 TTTCCAAATTTACATTTTGATCCCTAAAC
1 TTTCCAAATTTATACTTTAATCCCTAAAC
1889241 TTTCCAAAGTTTATACTTTAATCACC-AAAC
1 TTTCCAAA-TTTATACTTTAATC-CCTAAAC
1889271 TTTACCAAATTTATA
1 TTT-CCAAATTTATA
1889286 ATTTGGTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.21
30 24 0.62
31 7 0.18
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTCCAAATTTATACTTTAATCCCTAAAC
Found at i:1890774 original size:18 final size:18
Alignment explanation
Indices: 1890751--1890794 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1890741 GCCCATTATC
*
1890751 TGTGCATTGAGAGTTCTA
1 TGTGCATTGAGAGTCCTA
1890769 TGTGCATTGAGAGTCCTA
1 TGTGCATTGAGAGTCCTA
*
1890787 GGTGCATT
1 TGTGCATT
1890795 TCGACATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (18 bp):
TGTGCATTGAGAGTCCTA
Found at i:1891072 original size:138 final size:138
Alignment explanation
Indices: 1890817--1891072 Score: 361
Period size: 138 Copynumber: 1.9 Consensus size: 138
1890807 GTATGCATTG
* * * *
1890817 GTTATCGATCGATTTTGTTTAATGCATGACAGTGCATTTTCGTATCAGTACTATGTGTACTTTTG
1 GTTATCAATCGATTTTGTTTAATGCATAACAGCGCATTTTCGTATCAGTACTATGTGCACTTTTG
* * * *
1890882 GCACTAAATGTGCAATCATGGTATTCATAATGAGTTTGTGAATTTCCTTTTCGATATACATATGT
66 GCACTAAATGTGCAATCATGGAATTCATAATAAGTTTGTGAATTTACATTTCGATATACATATGT
1890947 ATATAAAA
131 ATATAAAA
* * * ** *
1890955 GTTATCAATCGTTTTTGTTTAATTCATAACGGCGCATTTTCGTATCAGTGTTGTGTGCACTTTTG
1 GTTATCAATCGATTTTGTTTAATGCATAACAGCGCATTTTCGTATCAGTACTATGTGCACTTTTG
*
1891020 GCACTATATGTGC-ATCCATGGAATTCATAATAAGTTTGTGAATTTACATTTCG
66 GCACTAAATGTGCAAT-CATGGAATTCATAATAAGTTTGTGAATTTACATTTCG
1891073 GCACTTCGGT
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
137 2 0.02
138 100 0.98
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (138 bp):
GTTATCAATCGATTTTGTTTAATGCATAACAGCGCATTTTCGTATCAGTACTATGTGCACTTTTG
GCACTAAATGTGCAATCATGGAATTCATAATAAGTTTGTGAATTTACATTTCGATATACATATGT
ATATAAAA
Found at i:1895899 original size:39 final size:39
Alignment explanation
Indices: 1895856--1895933 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1895846 ATTATGCTAG
1895856 CAAAACATTGAATGATTATGAAGTTAATCATACAAAAAA
1 CAAAACATTGAATGATTATGAAGTTAATCATACAAAAAA
1895895 CAAAACATTGAATGATTATGAAGTTAATCATACAAAAAA
1 CAAAACATTGAATGATTATGAAGTTAATCATACAAAAAA
1895934 TAATTGCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (39 bp):
CAAAACATTGAATGATTATGAAGTTAATCATACAAAAAA
Found at i:1896323 original size:27 final size:27
Alignment explanation
Indices: 1896292--1896347 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1896282 ATCGTAAAGG
1896292 AAGAATTTTTTTCTTCTTGATGTTATA
1 AAGAATTTTTTTCTTCTTGATGTTATA
1896319 AAGAATTTTTTTCTTCTTGATGTTATA
1 AAGAATTTTTTTCTTCTTGATGTTATA
1896346 AA
1 AA
1896348 ATACCATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
AAGAATTTTTTTCTTCTTGATGTTATA
Found at i:1902644 original size:83 final size:83
Alignment explanation
Indices: 1902505--1902670 Score: 305
Period size: 83 Copynumber: 2.0 Consensus size: 83
1902495 ATTATTTTCG
1902505 ATAAAAAACAGTAACATGGCCCGATGGTTAAGACATAGTTGGCCACTACATGGGTCAAGGGTTCA
1 ATAAAAAACAGTAACATGGCCCGATGGTTAAGACATAGTTGGCCACTACATGGGTCAAGGGTTCA
1902570 AAACCCCATGACCACCCA
66 AAACCCCATGACCACCCA
** *
1902588 ATAAAAAACAGTAACATGGCTTGATGGTTAAGACATGGTTGGCCACTACATGGGTCAAGGGTTCA
1 ATAAAAAACAGTAACATGGCCCGATGGTTAAGACATAGTTGGCCACTACATGGGTCAAGGGTTCA
1902653 AAACCCCATGACCACCCA
66 AAACCCCATGACCACCCA
1902671 TTATTTTATT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (83 bp):
ATAAAAAACAGTAACATGGCCCGATGGTTAAGACATAGTTGGCCACTACATGGGTCAAGGGTTCA
AAACCCCATGACCACCCA
Found at i:1907782 original size:30 final size:30
Alignment explanation
Indices: 1907712--1907800 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
1907702 AATGGATTTA
* * *
1907712 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGGGACCAAAGTATAAATTTGGAAAAG
*
1907742 CTT-GGTGACCAAAGTATAAACTTT-GAAAAG
1 TTTAGG-GACCAAAGTATAAA-TTTGGAAAAG
* * *
1907772 TTTAGGGACCAAAATGTAATTTTGGAAAA
1 TTTAGGGACCAAAGTATAAATTTGGAAAA
1907801 ATTACAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
29 4 0.09
30 38 0.81
31 5 0.11
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (30 bp):
TTTAGGGACCAAAGTATAAATTTGGAAAAG
Found at i:1909962 original size:45 final size:44
Alignment explanation
Indices: 1909890--1909983 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
1909880 ATAAACATAT
* * * *
1909890 AAATAAGCTTATGAGCTTATTAGATAAATGTTATGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGAGATAAATGGTAAGTATA-TAGTA
*
1909935 AAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATGAG-ATAAATGGTAAGTATATAGTA
1909979 AAATA
1 AAATA
1909984 TTGGATATGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.23
45 33 0.77
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAGATAAATGGTAAGTATATAGTA
Found at i:1916943 original size:24 final size:25
Alignment explanation
Indices: 1916861--1916946 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 25
1916851 AATATTTTAG
* *
1916861 TATTA-TTTTAATAAAATATTATT-
1 TATTACTTTTAATAATATAATATTA
1916884 TATTACACTATTTAA-AATAT-A-ATTA
1 TATT--ACT-TTTAATAATATAATATTA
* *
1916909 TGAATATTTTTAATAATATAATATTA
1 T-ATTACTTTTAATAATATAATATTA
1916935 TATTA-TTTTAAT
1 TATTACTTTTAAT
1916947 TTGAAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
23 9 0.18
24 17 0.35
25 6 0.12
26 12 0.24
27 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (25 bp):
TATTACTTTTAATAATATAATATTA
Found at i:1920048 original size:101 final size:101
Alignment explanation
Indices: 1919853--1920048 Score: 281
Period size: 101 Copynumber: 1.9 Consensus size: 101
1919843 AGTGTTTATA
*
1919853 TATGTGATATGAGTCGAAAGAAAAATATTGTTTAATGAGTAATCAGATTTGGCACTATATGCTTA
1 TATGTAATATGAGTCGAAAGAAAAATATTGTTTAATGAGTAATCAGATTTGGCACTATATGCTTA
*
1919918 TACATGTGCTAAAGAATGATTTTTCAGGTTTCTTCC
66 TACATGTGCTAAAGAATGACTTTTCAGGTTTCTTCC
* * * *
1919954 TATGTAATATGAG-CTGAAAGAAAACTATTGTTTACTGAGTATTCAGATTTGGCATTATATGCTT
1 TATGTAATATGAGTC-GAAAGAAAAATATTGTTTAATGAGTAATCAGATTTGGCACTATATGCTT
*
1920018 ATACTTGTGCT-AAGTAATGAACTTTT-AGGTT
65 ATACATGTGCTAAAG-AATG-ACTTTTCAGGTT
1920049 CAATTTCATT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
100 4 0.05
101 76 0.89
102 5 0.06
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (101 bp):
TATGTAATATGAGTCGAAAGAAAAATATTGTTTAATGAGTAATCAGATTTGGCACTATATGCTTA
TACATGTGCTAAAGAATGACTTTTCAGGTTTCTTCC
Found at i:1923251 original size:23 final size:23
Alignment explanation
Indices: 1923225--1923274 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1923215 ATTGGTGAAT
*
1923225 ATAAGGATTAAATAGAATAGAAG
1 ATAAGGATTAAATAGAACAGAAG
*
1923248 ATAAGGATTAAATAGAACAGATG
1 ATAAGGATTAAATAGAACAGAAG
1923271 ATAA
1 ATAA
1923275 AAGTTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (23 bp):
ATAAGGATTAAATAGAACAGAAG
Found at i:1923386 original size:3 final size:3
Alignment explanation
Indices: 1923378--1923418 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1923368 GTCCGAGTCG
*
1923378 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT TTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT A
1923419 CATTTTGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1924705 original size:2 final size:2
Alignment explanation
Indices: 1924687--1924730 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1924677 CCTGTTTAAG
* *
1924687 TA TA TA AA TC TA T- 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
1924728 TA T
1 TA T
1924731 GAATATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1925100 original size:2 final size:2
Alignment explanation
Indices: 1925093--1925120 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1925083 ATTACTGTTA
1925093 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
1925121 TTGTTTGTCT
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:1930690 original size:13 final size:13
Alignment explanation
Indices: 1930674--1930737 Score: 71
Period size: 12 Copynumber: 4.9 Consensus size: 13
1930664 CATCAGAAGA
1930674 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
1930687 -AAAAAAAGAGAAG
1 AAAAAAAAGA-AAG
1930700 -AAAAAAAGAAA-
1 AAAAAAAAGAAAG
*
1930711 AGAAAAAAGAAAAG
1 AAAAAAAAG-AAAG
1930725 AAAATAAAAGAAA
1 AAAA-AAAAGAAA
1930738 TTGAATTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 18 0.41
13 15 0.34
14 6 0.14
15 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:1930692 original size:12 final size:12
Alignment explanation
Indices: 1930675--1930728 Score: 74
Period size: 12 Copynumber: 4.3 Consensus size: 12
1930665 ATCAGAAGAA
1930675 AAAAAAAGAAAG
1 AAAAAAAGAAAG
1930687 AAAAAAAGAGAAG
1 AAAAAAAGA-AAG
1930700 AAAAAAAGAAA-
1 AAAAAAAGAAAG
1930711 AGAAAAAAGAAAAG
1 A-AAAAAAG-AAAG
1930725 AAAA
1 AAAA
1930729 TAAAAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.03
12 18 0.47
13 18 0.47
14 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:1930709 original size:25 final size:25
Alignment explanation
Indices: 1930668--1930737 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 25
1930658 CTCATCCATC
*
1930668 AGAAGAAAAAAAAAGAAAGAAAAAAAG
1 AGAAGAAAAAAAGA-AAAG-AAAAAAG
1930695 AGAAGAAAAAAAGAAAAGAAAAAAG
1 AGAAGAAAAAAAGAAAAGAAAAAAG
*
1930720 AAAAGAAAATAAAAGAAA
1 AGAAG-AAA-AAAAGAAA
1930738 TTGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 11 0.28
26 7 0.18
27 21 0.54
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (25 bp):
AGAAGAAAAAAAGAAAAGAAAAAAG
Found at i:1930711 original size:5 final size:5
Alignment explanation
Indices: 1930670--1930737 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
1930660 CATCCATCAG
* *
1930670 AAGAA AAAAA AAG-A AAGAA AA-AA AGAGAA GAAAAA AAGAA AAGAAAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA A-AGAA -AAGAA AAGAA AAG--AA
*
1930717 AAGAA AAGAA AATAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA A
1930738 TTGAATTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 7 0.14
5 33 0.65
6 5 0.10
7 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (5 bp):
AAGAA
Found at i:1930714 original size:30 final size:28
Alignment explanation
Indices: 1930668--1930737 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
1930658 CTCATCCATC
1930668 AGAAGAAAAA-AAAAGAAAGAAAAAAAGAGA
1 AGAA-AAAAAGAAAAGAAA-AAAAAAA-AGA
*
1930698 AGAAAAAAAGAAAAGAAAAAAGAAAAGA
1 AGAAAAAAAGAAAAGAAAAAAAAAAAGA
*
1930726 A-AATAAAAGAAA
1 AGAAAAAAAGAAA
1930738 TTGAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 10 0.27
28 4 0.11
29 11 0.30
30 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (28 bp):
AGAAAAAAAGAAAAGAAAAAAAAAAAGA
Found at i:1933999 original size:40 final size:40
Alignment explanation
Indices: 1933661--1933996 Score: 496
Period size: 40 Copynumber: 8.4 Consensus size: 40
1933651 CTTATTTAAT
**
1933661 ACAGAAGATTTTATCTCGTTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
1933701 ACAGAAGATTTTATCTCACTCAAGATAGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
1933741 ACA-AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1933780 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
1933820 ACATAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * *
1933860 AAAAAAGATTTTATCTTACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * * * *
1933900 ACAAAATATTTTTTCTCATTCAAGATTGTTTTTCCTTAAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
1933940 ACAGAAGATTTTATCTCGCTCAAGATTGGTTTTT-CTCGAA
1 ACAGAAGATTTTATCTCACTCAAGATT-GTTTTTCCTTGAA
*
1933980 ACAGGAGATTTTATCTC
1 ACAGAAGATTTTATCTC
1933997 GCTTGAGATA
Statistics
Matches: 268, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
39 37 0.14
40 225 0.84
41 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (40 bp):
ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
Found at i:1934038 original size:35 final size:36
Alignment explanation
Indices: 1933987--1934163 Score: 140
Period size: 36 Copynumber: 5.1 Consensus size: 36
1933977 GAAACAGGAG
*
1933987 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAA
* *
1934023 ATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACA-A
*
1934059 A----A-CT---TTGA-AAATGTTTCCCTTGAAACAA
1 ATTTTATCTCGCTTGAGACA-GTTTCCCTTGAAACAA
* * * * *
1934087 ATTTTGTCTCTCTTGAGACATTTTCCCTTTAAACGA
1 ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAA
* * * *
1934123 ATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAA
1 ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAA
*
1934159 GTTTT
1 ATTTT
1934164 TGAGACAATT
Statistics
Matches: 113, Mismatches: 17, Indels: 22
0.74 0.11 0.14
Matches are distributed among these distances:
28 4 0.04
29 18 0.16
31 2 0.02
33 2 0.02
35 22 0.19
36 63 0.56
37 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (36 bp):
ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1934158 original size:15 final size:15
Alignment explanation
Indices: 1934134--1934186 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
1934124 TTTTGTCTCC
*
1934134 CTTGAGACAATTTCT
1 CTTGAAACAATTTCT
*
1934149 CTTGAAACAAGTT-T
1 CTTGAAACAATTTCT
*
1934163 -TTGAGACAATTTCT
1 CTTGAAACAATTTCT
1934177 CTTGAAACAA
1 CTTGAAACAA
1934187 AGTTGTCTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 19 0.61
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (15 bp):
CTTGAAACAATTTCT
Found at i:1934166 original size:100 final size:100
Alignment explanation
Indices: 1933987--1934201 Score: 258
Period size: 100 Copynumber: 2.2 Consensus size: 100
1933977 GAAACAGGAG
* * * *
1933987 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAGTTTCTCTTG
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAATTTCTCTTG
1934052 AAACATAAACTTTGA-A-AATGTTTCCCTTGAAACAA
66 AAACATAAACTTTGAGACAA--TTTCCCTTGAAACAA
* * * *
1934087 ATTTTGTCTCTCTTGAGACATTTTCCCTTTAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCT-CCTTGAGACAATTTCTCTT
*** *
1934152 GAAACA-AGTTTTTGAGACAATTTCTCTTGAAACAA
65 GAAACATAAACTTTGAGACAATTTCCCTTGAAACAA
*
1934187 A-GTTGTCTCCCTTGA
1 ATTTTGTCTCCCTTGA
1934202 AATGGTTTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
99 12 0.12
100 60 0.61
101 25 0.25
102 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (100 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAATTTCTCTTG
AAACATAAACTTTGAGACAATTTCCCTTGAAACAA
Found at i:1934253 original size:15 final size:15
Alignment explanation
Indices: 1934233--1934273 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1934223 CTTCTTCTGG
1934233 CTTGAGACAGTCTCC
1 CTTGAGACAGTCTCC
*
1934248 CTTGAGACAGTCTCG
1 CTTGAGACAGTCTCC
*
1934263 TTTGAGACAGT
1 CTTGAGACAGT
1934274 TTTCAGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (15 bp):
CTTGAGACAGTCTCC
Found at i:1934941 original size:20 final size:21
Alignment explanation
Indices: 1934885--1934943 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
1934875 TCCAATGGAG
*
1934885 AGTTCATAATGAGAAGAACTC
1 AGTTCATAATGAGAAGAACTA
*
1934906 A--TCA-AACGAGGAAGAA-TA
1 AGTTCATAATGA-GAAGAACTA
1934924 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1934944 TGTTCAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 9 0.30
21 6 0.20
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTTCATAATGAGAAGAACTA
Found at i:1934948 original size:20 final size:20
Alignment explanation
Indices: 1934886--1934949 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1934876 CCAATGGAGA
1934886 GTTCATAATGAGAAGAAC-T
1 GTTCATAATGAGAAGAACTT
** * *
1934905 CATCA-AACGAGGAAGAA-TAA
1 GTTCATAATGA-GAAGAACT-T
1934925 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1934945 GTTCA
1 GTTCA
1934950 ACTTCACATC
Statistics
Matches: 32, Mismatches: 8, Indels: 9
0.65 0.16 0.18
Matches are distributed among these distances:
18 4 0.12
19 9 0.28
20 14 0.44
21 5 0.16
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1934984 original size:91 final size:92
Alignment explanation
Indices: 1934866--1935040 Score: 255
Period size: 91 Copynumber: 1.9 Consensus size: 92
1934856 AAAGAGATGG
* * *
1934866 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT-C-AAACGAGGAAGAATAAGTTC
1 ATCAACATTTCCAAAGGAGAGTTCATAATGAGAAGAACTCATCCGAAA-AAGGAAGAAGAAGTTC
1934929 ATAATGAGAAGAACTTGTTCAACTTCAC
65 ATAATGAGAAGAACTTGTTCAACTTCAC
* * * *
1934957 ATCAACATTTTCAAAGGAGAGTTCATAATGAGAATAACTCATCCGAAAAAGGGAGAGGAAGTTCA
1 ATCAACATTTCCAAAGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAAGAAGAAGTTCA
*
1935022 TAATGAGAAGAGCTTGTTC
66 TAATGAGAAGAACTTGTTC
1935041 GACCTATCAC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 39 0.53
92 32 0.43
93 3 0.04
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (92 bp):
ATCAACATTTCCAAAGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCAC
Found at i:1935233 original size:332 final size:331
Alignment explanation
Indices: 1934625--1935281 Score: 982
Period size: 332 Copynumber: 2.0 Consensus size: 331
1934615 AGATAAACAG
* *
1934625 ATCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCA
1 ATCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAAAAGTTCA
* *
1934690 TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATCAGTGATACCTCGCT
66 TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATAAGTGACACCTCGCT
* * * *
1934755 TGAGGGATTGGCATTTTCAGAATAGTTCATAATGAGAAAAACTCATCCTAAAGGAGAAAGTTCAT
131 TGAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAGGAGAAAGTTCAT
* * * *
1934820 AATGAGAAGAACTTGTTCCTTTCAAGTCCATCACCAAAAGAGATGGATCAACATTTCCAATGGAG
196 AATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAAAAAAAGATGGATCAACATTTCCAATGAAG
* *
1934885 AGTTCATAATGAGAAGAACTCATCAAACGAG-GAAGAATAAGTTCATAATGAGAAGAACTTGTTC
261 AGTTCATAAAGAGAAGAACTCATC-AACGAGAG-AGAAGAAGTTCATAATGAGAAGAACTTGTTC
1934949 AACTTCAC
324 AACTTCAC
* * **
1934957 ATCAACATTTTCAA-AGGAGAGTTCATAATGAGAATAACTCATCCGAAAAAGGGAGAGGAAGTTC
1 ATCAACATTTCCAATA-GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAAAAGTTC
* *
1935021 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATAAGTGACGCCTCG-
65 ATAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATAAGTGACACCTCGC
* * * *
1935085 TTAGAGGGATTGACATTTCCAAAAGAGTTTATAATTAGAATAACTCATCTTAAAGGAGAAAGTTC
130 TT-GAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAGGAGAAAGTTC
* *
1935150 ATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAAAAATAAG-T-GACTCAACATTTTCAGT
194 ATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAAAAA-AAGATGGA-TCAACATTTCCAAT
*
1935213 GAAGAGTTCATAAAGAGAAGAACTCATCCACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
257 GAAGAGTTCATAAAGAGAAGAACTCATCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
1935278 TCAA
322 TCAA
1935282 TCCAACGACG
Statistics
Matches: 293, Mismatches: 27, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
331 42 0.14
332 249 0.85
333 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (331 bp):
ATCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAAAAGTTCA
TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATAAGTGACACCTCGCT
TGAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAGGAGAAAGTTCAT
AATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAAAAAAAGATGGATCAACATTTCCAATGAAG
AGTTCATAAAGAGAAGAACTCATCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CTTCAC
Found at i:1936792 original size:13 final size:13
Alignment explanation
Indices: 1936774--1936803 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1936764 ATTATTTGCT
1936774 GCATTATGTGTAA
1 GCATTATGTGTAA
*
1936787 GCATTATGTGTAG
1 GCATTATGTGTAA
1936800 GCAT
1 GCAT
1936804 ATAAAACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (13 bp):
GCATTATGTGTAA
Found at i:1937084 original size:2 final size:2
Alignment explanation
Indices: 1937077--1937146 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1937067 ATTACTGTTA
1937077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1937119 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
1937147 TTGTTTGTCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1938374 original size:22 final size:22
Alignment explanation
Indices: 1938343--1938401 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
1938333 ACACGTTCAT
*
1938343 GAACAAATAAATGAATGCTAAA
1 GAACATATAAATGAATGCTAAA
1938365 GAACATATAAATGAATGCTAAA
1 GAACATATAAATGAATGCTAAA
1938387 GAACATATAAATGAA
1 GAACATATAAATGAA
1938402 AATGTTCGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (22 bp):
GAACATATAAATGAATGCTAAA
Found at i:1938424 original size:23 final size:24
Alignment explanation
Indices: 1938387--1938444 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1938377 GAATGCTAAA
1938387 GAACATATAAATGAAAATGTTCGC
1 GAACATATAAATGAAAATGTTCGC
* **
1938411 GAACAT-TAAATGAACATGTTCAT
1 GAACATATAAATGAAAATGTTCGC
1938434 GAACA-ATAAAT
1 GAACATATAAAT
1938445 AAACTGACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (24 bp):
GAACATATAAATGAAAATGTTCGC
Found at i:1939467 original size:29 final size:29
Alignment explanation
Indices: 1939421--1939669 Score: 230
Period size: 29 Copynumber: 8.6 Consensus size: 29
1939411 TCTATAGAGG
1939421 ATCCCATGCAGAATCAAGACGGGGATATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
*
1939450 ATCTCATGCAGAATCAAGACGGGGATATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
* ***
1939479 ATCCCATGCTGAATCAAGATATGGATATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
* * * *
1939508 ATCTCATGAAGAATCAGGACGGGAATATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
** * * *
1939537 ATTTCATGCAAAATCAAGATGGGGTTATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
* * **
1939566 ATCCCATGCCA-AATTACGACAAGGATATA
1 ATCCCATG-CAGAATCAAGACGGGGATATA
* * * *
1939595 ATCCCATGCAGAATCAGGATGGGGAAACA
1 ATCCCATGCAGAATCAAGACGGGGATATA
* ** **
1939624 ATCCCATGTAGAATCGGGATAGGGATATA
1 ATCCCATGCAGAATCAAGACGGGGATATA
*
1939653 ATCTCATGCAGAATCAA
1 ATCCCATGCAGAATCAA
1939670 AAATACATCA
Statistics
Matches: 173, Mismatches: 45, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
28 2 0.01
29 169 0.98
30 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (29 bp):
ATCCCATGCAGAATCAAGACGGGGATATA
Found at i:1939511 original size:58 final size:58
Alignment explanation
Indices: 1939421--1939669 Score: 259
Period size: 58 Copynumber: 4.3 Consensus size: 58
1939411 TCTATAGAGG
* * * *
1939421 ATCCCATGCAGAATCAAGACGGGGATATAATCTCATGCAGAATCAAGACGGGGATATA
1 ATCCCATGCAGAATCAAGATGGGGATATAATCCCATGCAGAATCAGGACAGGGATATA
* ** * *
1939479 ATCCCATGCTGAATCAAGATATGGATATAATCTCATGAAGAATCAGGAC-GGGAATATA
1 ATCCCATGCAGAATCAAGATGGGGATATAATCCCATGCAGAATCAGGACAGGG-ATATA
** * * * * *
1939537 ATTTCATGCAAAATCAAGATGGGGTTATAATCCCATGCCA-AATTACGACAAGGATATA
1 ATCCCATGCAGAATCAAGATGGGGATATAATCCCATG-CAGAATCAGGACAGGGATATA
* * * * * *
1939595 ATCCCATGCAGAATCAGGATGGGGAAACAATCCCATGTAGAATCGGGATAGGGATATA
1 ATCCCATGCAGAATCAAGATGGGGATATAATCCCATGCAGAATCAGGACAGGGATATA
*
1939653 ATCTCATGCAGAATCAA
1 ATCCCATGCAGAATCAA
1939670 AAATACATCA
Statistics
Matches: 154, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
57 4 0.03
58 147 0.95
59 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (58 bp):
ATCCCATGCAGAATCAAGATGGGGATATAATCCCATGCAGAATCAGGACAGGGATATA
Found at i:1939592 original size:87 final size:87
Alignment explanation
Indices: 1939421--1939613 Score: 260
Period size: 87 Copynumber: 2.2 Consensus size: 87
1939411 TCTATAGAGG
* * *
1939421 ATCCCATGCAGAATCAAGACGGGGATATAATCTCATGCAGAATCAAGACGGGGATATAATCCCAT
1 ATCCCATGCAGAATCAGGACGGGAATATAATCTCATGCAAAATCAAGACGGGGATATAATCCCAT
** * *
1939486 GCTGAATCAAGATATGGATATA
66 GCCAAATCAAGACAAGGATATA
* * * * *
1939508 ATCTCATGAAGAATCAGGACGGGAATATAATTTCATGCAAAATCAAGATGGGGTTATAATCCCAT
1 ATCCCATGCAGAATCAGGACGGGAATATAATCTCATGCAAAATCAAGACGGGGATATAATCCCAT
* *
1939573 GCCAAATTACGACAAGGATATA
66 GCCAAATCAAGACAAGGATATA
1939595 ATCCCATGCAGAATCAGGA
1 ATCCCATGCAGAATCAGGA
1939614 TGGGGAAACA
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (87 bp):
ATCCCATGCAGAATCAGGACGGGAATATAATCTCATGCAAAATCAAGACGGGGATATAATCCCAT
GCCAAATCAAGACAAGGATATA
Found at i:1939653 original size:87 final size:86
Alignment explanation
Indices: 1939421--1939669 Score: 257
Period size: 87 Copynumber: 2.9 Consensus size: 86
1939411 TCTATAGAGG
* * *
1939421 ATCCCATGCAGAATCAAGACGGGGATATAATCTCATGCAGAATCAAGACGGGGATATAATCCCAT
1 ATCCCATGCAGAATCAGGA-GGGGAAATAATCTCATGCAGAATCAAGATGGGGATATAATCCCAT
** * *
1939486 GCTGAATCAAGATATGGATATA
65 GCCAAATCAAGACAAGGATATA
* * * * * *
1939508 ATCTCATGAAGAATCAGGACGGGAATATAATTTCATGCAAAATCAAGATGGGGTTATAATCCCAT
1 ATCCCATGCAGAATCAGGAGGGGAA-ATAATCTCATGCAGAATCAAGATGGGGATATAATCCCAT
* *
1939573 GCCAAATTACGACAAGGATATA
65 GCCAAATCAAGACAAGGATATA
* * * ** * *
1939595 ATCCCATGCAGAATCAGGATGGGGAAACAATCCCATGTAGAATCGGGATAGGGATATAATCTCAT
1 ATCCCATGCAGAATCAGGA-GGGGAAATAATCTCATGCAGAATCAAGATGGGGATATAATCCCAT
1939660 G-CAGAATCAA
65 GCCA-AATCAA
1939670 AAATACATCA
Statistics
Matches: 129, Mismatches: 30, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
86 6 0.05
87 118 0.91
88 5 0.04
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (86 bp):
ATCCCATGCAGAATCAGGAGGGGAAATAATCTCATGCAGAATCAAGATGGGGATATAATCCCATG
CCAAATCAAGACAAGGATATA
Found at i:1945771 original size:21 final size:22
Alignment explanation
Indices: 1945746--1945790 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1945736 GTTTACTTAA
1945746 TTTATTATATATAT-TTTTATT
1 TTTATTATATATATATTTTATT
* *
1945767 TTTATTATGTATTTATTTTATT
1 TTTATTATATATATATTTTATT
1945789 TT
1 TT
1945791 CATTTTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTATATATATATTTTATT
Found at i:1946157 original size:20 final size:20
Alignment explanation
Indices: 1946096--1946288 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1946086 GATTTTCCAG
* ** *
1946096 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1946116 AATCGCAACGCG-AGCACATA
1 AATCGCAACGCGTATC-CGTA
1946136 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1946156 AATCGAAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1946176 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1946196 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1946216 TATCACAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1946236 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
*
1946257 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1946277 AATCGCAACGCG
1 AATCGCAACGCG
1946289 ATTTTTAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 125 0.86
21 19 0.13
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1946707 original size:33 final size:33
Alignment explanation
Indices: 1946668--1946738 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1946658 TTCACTTAGA
1946668 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1946701 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1946734 TTTCA
1 TTTCA
1946739 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1946855 original size:20 final size:21
Alignment explanation
Indices: 1946818--1946893 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1946808 TGCAGAAGAG
1946818 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* ***
1946839 TCGCAACGTGA-AAATGACTG
1 TCGCAACGAGAGAAATGAAAA
1946859 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1946880 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1946894 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1946910 original size:33 final size:33
Alignment explanation
Indices: 1946870--1946950 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
1946860 CGCAACGAGA
*
1946870 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
*
1946903 GAAATGAAAATCGCAACGATAGAATCGCAAAGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
**
1946936 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1946951 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
Found at i:1946968 original size:19 final size:19
Alignment explanation
Indices: 1946946--1947073 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1946936 GAAACCAAAA
*
1946946 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1946965 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1946979 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1946998 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1947012 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1947032 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1947052 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1947072 TC
1 TC
1947074 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1946987 original size:14 final size:14
Alignment explanation
Indices: 1946968--1947024 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1946958 TTTCATTTCG
1946968 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1946982 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1947001 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1947015 CGTTGCGATT
1 CGTTGCGATT
1947025 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1946993 original size:33 final size:33
Alignment explanation
Indices: 1946951--1947073 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1946941 CAAAATCGCA
1946951 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1946984 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1947017 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1947058 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1947074 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1947035 original size:21 final size:21
Alignment explanation
Indices: 1947009--1947073 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1946999 CGCGTTGCGA
1947009 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1947030 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1947050 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1947071 TTC
1 TTC
1947074 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1948966 original size:91 final size:92
Alignment explanation
Indices: 1948754--1948974 Score: 390
Period size: 93 Copynumber: 2.4 Consensus size: 92
1948744 TAGATTGCTT
* *
1948754 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1948819 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 -TTGTATTTGTTTTGTCTTTTGGTTGAA
1948847 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1948912 -TGTATTTGTTTTGTCTTTTGGTTGAA
66 TTGTATTTGTTTTGTCTTTTGGTTGAA
*
1948938 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1948975 AATACCCTGA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 61 0.49
93 63 0.51
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTATTTGTTTTGTCTTTTGGTTGAA
Found at i:1949128 original size:19 final size:18
Alignment explanation
Indices: 1949099--1949195 Score: 66
Period size: 19 Copynumber: 5.7 Consensus size: 18
1949089 AAATCGCAAC
*
1949099 AAGAGAATCGCAACGCGA
1 AAGAAAATCGCAACGCGA
1949117 AATGAAAATCGCAA--CGA
1 AA-GAAAATCGCAACGCGA
*
1949134 CAG--AATCGCAACGCGA
1 AAGAAAATCGCAACGCGA
*
1949150 AACCAAAATCGCAA--CG-
1 AA-GAAAATCGCAACGCGA
*
1949166 -ACAAAATCGCAACGCGA
1 AAGAAAATCGCAACGCGA
*
1949183 AACCAAAATCGCA
1 AA-GAAAATCGCA
1949196 TTGCGATTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.30
15 1 0.02
16 7 0.11
17 6 0.09
18 3 0.05
19 28 0.44
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (18 bp):
AAGAAAATCGCAACGCGA
Found at i:1949130 original size:33 final size:33
Alignment explanation
Indices: 1949072--1949195 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1949062 TAGTTTACTT
* * * *
1949072 TCGCAACACGAAACTTAAAATCGCAACAAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
1949106 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
1949139 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
1949172 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1949196 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:1949142 original size:14 final size:14
Alignment explanation
Indices: 1949121--1949179 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1949111 ACGCGAAATG
1949121 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1949135 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1949154 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1949168 AAAATCGCAACG
1 AAAATCGCAACG
1949180 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1949218 original size:19 final size:19
Alignment explanation
Indices: 1949191--1949347 Score: 145
Period size: 19 Copynumber: 8.8 Consensus size: 19
1949181 GAAACCAAAA
*
1949191 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1949210 TCGAGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1949224 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1949243 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1949259 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1949276 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1949295 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1949314 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
1949333 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1949348 AAGTTTTGTG
Statistics
Matches: 111, Mismatches: 17, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
14 16 0.14
16 8 0.07
17 8 0.07
19 79 0.71
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1949321 original size:38 final size:38
Alignment explanation
Indices: 1949191--1949347 Score: 154
Period size: 33 Copynumber: 4.4 Consensus size: 38
1949181 GAAACCAAAA
* *
1949191 TCGCATTGCGATTTTCATTTCGAGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1949226 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
1949259 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
1949295 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
1949333 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1949348 AAGTTTTGTG
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.50
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.43
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:1951309 original size:14 final size:14
Alignment explanation
Indices: 1951290--1951325 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1951280 ATTGTTTAAT
1951290 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1951304 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1951318 TGATTTGT
1 TGATTTGT
1951326 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1951448 original size:19 final size:19
Alignment explanation
Indices: 1951432--1951481 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1951422 AAAAATGACT
1951432 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1951451 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1951470 ATCGCAATGCGA
1 ATCGCAATGCGA
1951482 TTTTCATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1951500 original size:20 final size:19
Alignment explanation
Indices: 1951471--1951714 Score: 251
Period size: 19 Copynumber: 13.7 Consensus size: 19
1951461 GAAATGAAAA
*
1951471 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1951490 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
*
1951507 TCG--TTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
1951524 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1951543 TACGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1951560 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1951577 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1951596 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1951613 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1951630 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1951649 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1951668 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
1951686 T-G--TTG-GTATTTTCATT
1 TCGCATTGCG-ATTTTCATT
1951702 TCGCATTGCGATT
1 TCGCATTGCGATT
1951715 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 9, Indels: 52
0.76 0.04 0.21
Matches are distributed among these distances:
13 1 0.01
14 27 0.14
16 17 0.09
17 19 0.10
18 10 0.05
19 70 0.37
20 46 0.24
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1951589 original size:72 final size:71
Alignment explanation
Indices: 1951513--1951714 Score: 250
Period size: 72 Copynumber: 2.8 Consensus size: 71
1951503 TCTCTCGTTA
* *
1951513 CGATTTTCATTT-CGCATTGCGATTTTCATTTACGCA-TTGCGATTCTCTCGTTGCGATTTTCAT
1 CGATTTTCATTTCCGCATTGCGATTTTCATTTACG-ATTTGC-ATT-TCGCATTGCGATTTTCAT
1951576 TTCGCATTG
63 TTCGCATTG
* * *
1951585 CGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 CGATTTTCATTTCCGCATTGCGATT-T-TCATTTACGATTTGCATTTCGCATTGCGATTTTCATT
1951649 TCGCATTG
64 TCGCATTG
* *
1951657 CGATTTTCATTTCCGCATTGCGATTTTCATGTT-GGTATTTTCATTTCGCATTGCGATT
1 CGATTTTCATTTCCGCATTGCGATTTTCAT-TTACG-ATTTGCATTTCGCATTGCGATT
1951715 CTCTCGTTGC
Statistics
Matches: 116, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
70 2 0.02
71 2 0.02
72 86 0.74
73 16 0.14
74 8 0.07
75 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (71 bp):
CGATTTTCATTTCCGCATTGCGATTTTCATTTACGATTTGCATTTCGCATTGCGATTTTCATTTC
GCATTG
Found at i:1951743 original size:53 final size:53
Alignment explanation
Indices: 1951471--1951728 Score: 361
Period size: 53 Copynumber: 4.9 Consensus size: 53
1951461 GAAATGAAAA
* *
1951471 TCGCAATGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTACGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1951524 TCGCATTGCGATTTTCATTTACGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1951577 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1951630 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
1951686 T-G--TTG-GTATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCG-ATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1951729 GTAATTTCCG
Statistics
Matches: 192, Mismatches: 6, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 11 0.06
53 145 0.76
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.06
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1954028 original size:12 final size:12
Alignment explanation
Indices: 1954011--1954035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1954001 TCTTCGGGGA
1954011 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1954023 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1954035 C
1 C
1954036 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1954244 original size:24 final size:24
Alignment explanation
Indices: 1954210--1954256 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1954200 CTGAAACATC
1954210 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1954234 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1954257 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1954977 original size:20 final size:20
Alignment explanation
Indices: 1954949--1955178 Score: 208
Period size: 20 Copynumber: 11.4 Consensus size: 20
1954939 AAATTTTAGT
* * *
1954949 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1954969 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1954989 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
1955009 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1955029 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1955049 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1955069 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1955089 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1955109 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
1955129 GTTGCGATAGTACAAATTCGC
1 GTTGCGAT-TTACGGATTCGC
* **
1955150 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1955170 GTTGCGATT
1 GTTGCGATT
1955179 CTGGAAAATC
Statistics
Matches: 180, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
20 164 0.91
21 16 0.09
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1958054 original size:30 final size:30
Alignment explanation
Indices: 1957967--1958043 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
1957957 CATCATATGT
* *
1957967 ACTAAGTGTCCTTACACACTACAGTGCTGG
1 ACTAAGTGTCCTTACACACAACAGTGCTGC
*
1957997 ACTAAGTGTCCTTACACACAACGGTGCTGC
1 ACTAAGTGTCCTTACACACAACAGTGCTGC
1958027 ACTAAGTGTCCTTACAC
1 ACTAAGTGTCCTTACAC
1958044 GCCATAGTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (30 bp):
ACTAAGTGTCCTTACACACAACAGTGCTGC
Found at i:1959471 original size:19 final size:20
Alignment explanation
Indices: 1959447--1959492 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1959437 AAAAATTATC
* *
1959447 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCAAACAT
1959466 CAATTTCAACACTCAAACAT
1 CAATTTCAACACTCAAACAT
*
1959486 TAATTTC
1 CAATTTC
1959493 CAGCATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCAAACAT
Found at i:1960797 original size:25 final size:24
Alignment explanation
Indices: 1960720--1960797 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
1960710 ACTAAACATT
*
1960720 CAAAATTTATATTTTGGGCCTAAC
1 CAAAATTTATATTTTGGTCCTAAC
1960744 CAAAATTTATATTTTGGTCCTAAC
1 CAAAATTTATATTTTGGTCCTAAC
1960768 CAAAATTTATATTTTGGTCACTAAC
1 CAAAATTTATATTTTGGTC-CTAAC
*
1960793 AAAAA
1 CAAAA
1960798 ATTTGGGGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 42 0.82
25 9 0.18
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
CAAAATTTATATTTTGGTCCTAAC
Found at i:1972512 original size:30 final size:30
Alignment explanation
Indices: 1972467--1972524 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1972457 GCTTACCATA
* * *
1972467 TGTACCAAGTTTCCTTGCACACTATAGTGT
1 TGTACCAAGTGTCCTTACACACAATAGTGT
*
1972497 TGTACTAAGTGTCCTTACACACAATAGT
1 TGTACCAAGTGTCCTTACACACAATAGT
1972525 ACAAATACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (30 bp):
TGTACCAAGTGTCCTTACACACAATAGTGT
Found at i:1975698 original size:19 final size:18
Alignment explanation
Indices: 1975663--1975702 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1975653 AAAAGGTTCG
1975663 AAAGAAAAAATCAAAAATA
1 AAAGAAAAAATCAAAAA-A
*
1975682 AAAGAAAAAAGTTAAAAAA
1 AAAGAAAAAA-TCAAAAAA
1975701 AA
1 AA
1975703 GTTGTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAGAAAAAATCAAAAAA
Found at i:1976925 original size:13 final size:13
Alignment explanation
Indices: 1976875--1976917 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1976865 TAAATATCAG
*
1976875 ATGACGCGCATTT
1 ATGACGCACATTT
*
1976888 ATGACACACATTT
1 ATGACGCACATTT
1976901 ATGACTG-ACATTT
1 ATGAC-GCACATTT
1976914 ATGA
1 ATGA
1976918 TGCGCATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (13 bp):
ATGACGCACATTT
Found at i:1978981 original size:202 final size:195
Alignment explanation
Indices: 1978625--1979021 Score: 731
Period size: 202 Copynumber: 2.0 Consensus size: 195
1978615 AAAATGTTAG
1978625 CATGAAACCCCATTTTTTTGTAAATTTTAGGGTATCTATTGTATGCACCTTTTTTCCTTTTTAGG
1 CATGAAACCCCATTTTTTTGTAAATTTTAGGGTATCTATTGTATGCACCTTTTTTCCTTTTTAGG
1978690 CTTTTGAAAGAAAATTAAATCTAGGAATTCTCAATCTTACTTCTTCAGCTGTGGGTGATCTTTTG
66 CTTTTGAAAGAAAATTAAATCTAGGAATTCTCAATCTTACTTCTTCAGCTGTGGGTGATCTTTTG
1978755 GATCAAATGCAAGTAAGAGCTCAAGTAGGCGAAGAGCCTCGGGATCCACATTAGGGAACTTCTGT
131 GATCAAATGCAAGTAAGAGCTCAAGTAGGCGAAGAGCCTCGGGATCCACATTAGGGAACTTCTGT
1978820 CATGAAACCCCATTTTTTTGTAAATTTTAGGGTTATCTATTGTATGCATACCTTTTTTCCTTTTT
1 CATGAAACCCCATTTTTTTGTAAATTTTAGGG-TATCTATTGTATGC--ACCTTTTTTCCTTTTT
1978885 AGTGCTTTTGAAAGAAAAATTAAATACTAGGAATTCTCAATCTTACTTCTTCAGCTGTGGGATGA
63 AG-GCTTTTGAAAG-AAAATTAAAT-CTAGGAATTCTCAATCTTACTTCTTCAGCTGTGGG-TGA
1978950 TCTTTTGGATCAAATGCAAGTAAGAGCTCAAGTAGGCGAAGAGCCTCGGGATCCACATTAGGGAA
124 TCTTTTGGATCAAATGCAAGTAAGAGCTCAAGTAGGCGAAGAGCCTCGGGATCCACATTAGGGAA
1979015 CTTCTGT
189 CTTCTGT
1979022 GAGAAAGGAA
Statistics
Matches: 195, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
195 32 0.16
196 14 0.07
198 18 0.09
199 11 0.06
200 10 0.05
201 35 0.18
202 75 0.38
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (195 bp):
CATGAAACCCCATTTTTTTGTAAATTTTAGGGTATCTATTGTATGCACCTTTTTTCCTTTTTAGG
CTTTTGAAAGAAAATTAAATCTAGGAATTCTCAATCTTACTTCTTCAGCTGTGGGTGATCTTTTG
GATCAAATGCAAGTAAGAGCTCAAGTAGGCGAAGAGCCTCGGGATCCACATTAGGGAACTTCTGT
Found at i:1984714 original size:45 final size:45
Alignment explanation
Indices: 1984631--1984900 Score: 228
Period size: 45 Copynumber: 6.0 Consensus size: 45
1984621 TTTTCATTTG
* * * *
1984631 TAACATCCATTTATGTTTATAA--TACACCATTATACATTTTAAACTC
1 TAACATACTTTTATGTTGATAATGTAC-CCA-TATACA-TTTCAACTC
* *
1984677 TAACAT-CTTTTATGTTGATAAT-TCACCCATATGCATTTCAACTA
1 TAACATACTTTTATGTTGATAATGT-ACCCATATACATTTCAACTC
** * * *
1984721 TATTATACTTTTATATTGATAATGTACCCATACACATCTCAAC-C
1 TAACATACTTTTATGTTGATAATGTACCCATATACATTTCAACTC
** *
1984765 GTAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTC
1 -TAACATACTTTTATGTTGATAATGTACCCATATACATTTCAACTC
* * * * * *
1984811 TAGCAT-TTTTTCTGTTGATAATGCACCCATATGCATTTCAACTA
1 TAACATACTTTTATGTTGATAATGTACCCATATACATTTCAACTC
** * * *
1984855 TAGTATATTTTTTTGTTGATAATGTACCCATATGCATTTCAACTC
1 TAACATACTTTTATGTTGATAATGTACCCATATACATTTCAACTC
1984900 T
1 T
1984901 GGCATCCTTT
Statistics
Matches: 191, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
44 50 0.26
45 127 0.66
46 12 0.06
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.42
Consensus pattern (45 bp):
TAACATACTTTTATGTTGATAATGTACCCATATACATTTCAACTC
Found at i:1984872 original size:89 final size:89
Alignment explanation
Indices: 1984683--1984933 Score: 279
Period size: 89 Copynumber: 2.8 Consensus size: 89
1984673 ACTCTAACAT
* ** * * *
1984683 CTTTTATGTTGATAAT-TCACCCATATGCATTTCAACTATATTATACTTTTATATTGATAATGTA
1 CTTTTATGTTGATAATGT-ACCCATATGCATTTCAACTCTAGCAT-CTTTTCTGTTGATAATGCA
** *
1984747 CCCATACACATCTCAACCGTAGTATA
64 CCCATATGCATCTCAACCATAGTATA
* * *
1984773 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATTTTTTCTGTTGATAATGCACC
1 CTTTTATGTTGATAATGTACCCATATGCATTTCAACTCTAGCATCTTTTCTGTTGATAATGCACC
* *
1984838 CATATGCATTTCAACTATAGTATA
66 CATATGCATCTCAACCATAGTATA
* * * * ***
1984862 TTTTTTTGTTGATAATGTACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGTTGATAATGTACCCATATGCATTTCAACTCTAGCATCTTTTC-TGTTGATAATGCAC
1984927 CCATATG
65 CCATATG
1984934 TATTATTCTG
Statistics
Matches: 136, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
89 80 0.59
90 55 0.40
91 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (89 bp):
CTTTTATGTTGATAATGTACCCATATGCATTTCAACTCTAGCATCTTTTCTGTTGATAATGCACC
CATATGCATCTCAACCATAGTATA
Found at i:1984922 original size:45 final size:44
Alignment explanation
Indices: 1984672--1984933 Score: 229
Period size: 45 Copynumber: 5.9 Consensus size: 44
1984662 ATACATTTTA
* * * *
1984672 AACTCTAACATCTTTTATGTTGATAATTCACCCATATGCATTTC
1 AACTCTAGCATATTTTCTGTTGATAATGCACCCATATGCATTTC
* ** * * * ** *
1984716 AACTATATTATACTTTTATATTGATAATGTACCCATACACATCTC
1 AACTCTAGCATA-TTTTCTGTTGATAATGCACCCATATGCATTTC
* * *
1984761 AAC-CGTAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTC-TAGCATA-TTTTCTGTTGATAATGCACCCATATGCATTTC
*
1984806 AACTCTAGCATTTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTCTAGCATATTTTCTGTTGATAATGCACCCATATGCATTTC
* * * *
1984850 AACTATAGTATATTTTTTTGTTGATAATGTACCCATATGCATTTC
1 AACTCTAGCATA-TTTTCTGTTGATAATGCACCCATATGCATTTC
* ** ***
1984895 AACTCTGGCATCCTTTCATGCCAATAATGCACCCATATG
1 AACTCTAGCATATTTTC-TGTTGATAATGCACCCATATG
1984934 TATTATTCTG
Statistics
Matches: 178, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
44 50 0.28
45 127 0.71
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (44 bp):
AACTCTAGCATATTTTCTGTTGATAATGCACCCATATGCATTTC
Found at i:1984922 original size:134 final size:135
Alignment explanation
Indices: 1984661--1984932 Score: 334
Period size: 134 Copynumber: 2.0 Consensus size: 135
1984651 AATACACCAT
* *
1984661 TATACATTTTAAACTCTAACATCTTTTATGTTGATAATTCACCCATATGCATTTCAACTATATTA
1 TATACATTTTAAACTCTAACATCTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTA
* * *** *
1984726 TACTTTTATATTGATAATGTACCCATACACATCTCAACCGTAGTATACTTTTCTGTTGATAATGT
66 TACTTTTATATTGATAATGTACCCATACACATCTCAACCGTAGCATACCTTTCTGCCAATAATGC
1984791 ACCCA
131 ACCCA
* * * *
1984796 TATACA-TTTCAACTCTAGCATTTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTA
1 TATACATTTTAAACTCTAACATCTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTA
* * * ** * *
1984860 TATTTTTTTGTTGATAATGTACCCATATGCATTTCAACTC-TGGCAT-CCTTTCATGCCAATAAT
66 TACTTTTATATTGATAATGTACCCATACACATCTCAAC-CGTAGCATACCTTTC-TGCCAATAAT
1984923 GCACCCA
129 GCACCCA
1984930 TAT
1 TAT
1984933 GTATTATTCT
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
133 5 0.04
134 104 0.90
135 7 0.06
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (135 bp):
TATACATTTTAAACTCTAACATCTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTA
TACTTTTATATTGATAATGTACCCATACACATCTCAACCGTAGCATACCTTTCTGCCAATAATGC
ACCCA
Found at i:1984966 original size:79 final size:79
Alignment explanation
Indices: 1984871--1985104 Score: 319
Period size: 78 Copynumber: 3.0 Consensus size: 79
1984861 ATTTTTTTGT
* * ** *
1984871 TGATAATGTACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATGTA
1 TGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCA
*
1984936 TTATTCTGTTATGC
66 TTATTCTTTTATGC
* * * *
1984950 TGATAATGTACCCATATACATATCAGCTAAGGCAT-CTTTCCATACCACTAATGCACCCATATGG
1 TGATAATGTACCCATATACATATCAACTAAGGCATCCTTT-CATGCCAATAATGCACCCATATGC
1985014 ATTATT-TTTTATGC
65 ATTATTCTTTTATGC
* * * *
1985028 CGATAATGTACCCATATACATATCAACTAAGGCATCCTTTTATGCCAATAATGAATCCATATGCA
1 TGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCA
1985093 TTATTCTTTTAT
66 TTATTCTTTTAT
1985105 TCATTAGTTT
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 68 0.50
79 67 0.50
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (79 bp):
TGATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCA
TTATTCTTTTATGC
Found at i:1985490 original size:20 final size:20
Alignment explanation
Indices: 1985465--1985518 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1985455 TAGCCCTCTA
*
1985465 GTATCGATACCCGTATTAGG
1 GTATCGATACCCCTATTAGG
1985485 GTATCGATACCCCTATTAGG
1 GTATCGATACCCCTATTAGG
1985505 GTATCGATACCCCT
1 GTATCGATACCCCT
1985519 TCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTATTAGG
Found at i:1985528 original size:18 final size:20
Alignment explanation
Indices: 1985465--1985533 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1985455 TAGCCCTCTA
* *
1985465 GTATCGATACCCGTATTAGG
1 GTATCGATACCCCTATCAGG
*
1985485 GTATCGATACCCCTATTAGG
1 GTATCGATACCCCTATCAGG
*
1985505 GTATCGATACCCCT-TCA-T
1 GTATCGATACCCCTATCAGG
1985523 GTATCGATACC
1 GTATCGATACC
1985534 AAAATTAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 11 0.24
19 2 0.04
20 33 0.72
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTATCAGG
Found at i:1986074 original size:107 final size:107
Alignment explanation
Indices: 1985888--1986101 Score: 419
Period size: 107 Copynumber: 2.0 Consensus size: 107
1985878 TACTAATTTG
1985888 TTATTTCACTTAACTAATGCTTCTAATCTTTCATTTACCTTAATGACAAGTCAATTTTACCAACA
1 TTATTTCACTTAACTAATGCTTCTAATCTTTCATTTACCTTAATGACAAGTCAATTTTACCAACA
1985953 AACCTCAACACACCTTCATATATTAACATATCATGATAAAAC
66 AACCTCAACACACCTTCATATATTAACATATCATGATAAAAC
*
1985995 TTATTTCACTTAACTAATGCTTCTAATCTTTCATTTACCTTAATGACAAGTCAATTTTACCAATA
1 TTATTTCACTTAACTAATGCTTCTAATCTTTCATTTACCTTAATGACAAGTCAATTTTACCAACA
1986060 AACCTCAACACACCTTCATATATTAACATATCATGATAAAAC
66 AACCTCAACACACCTTCATATATTAACATATCATGATAAAAC
1986102 CCATTTTCTA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (107 bp):
TTATTTCACTTAACTAATGCTTCTAATCTTTCATTTACCTTAATGACAAGTCAATTTTACCAACA
AACCTCAACACACCTTCATATATTAACATATCATGATAAAAC
Found at i:1988721 original size:29 final size:29
Alignment explanation
Indices: 1988689--1988913 Score: 157
Period size: 29 Copynumber: 7.8 Consensus size: 29
1988679 AACAAGATAT
*
1988689 GGATATAATCCCATGTAGAACCAGGACGG
1 GGATATAATCCCATGTAGAATCAGGACGG
* * * *
1988718 GGATATAATCCCATGCAAAATTAGGACATG
1 GGATATAATCCCATGTAGAATCAGGAC-GG
* *
1988748 GG-TATAA-CCTCATGTAGAATCAAGACGA
1 GGATATAATCC-CATGTAGAATCAGGACGG
* * * * *
1988776 GAATATAATCCTATGTAGAATCAGAATGA
1 GGATATAATCCCATGTAGAATCAGGACGG
*** * * *
1988805 GGATATAATATAATGCAGAATTAGGATGG
1 GGATATAATCCCATGTAGAATCAGGACGG
* * * *
1988834 GGATATAATCTCATGAAAAATCAGGATGG
1 GGATATAATCCCATGTAGAATCAGGACGG
* *** *
1988863 GGATATAATCTCACACAGAATCAGGACAG
1 GGATATAATCCCATGTAGAATCAGGACGG
* *
1988892 GGATATGATCCCATGTTGAATC
1 GGATATAATCCCATGTAGAATC
1988914 TGAAATACAT
Statistics
Matches: 151, Mismatches: 41, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
28 3 0.02
29 143 0.95
30 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (29 bp):
GGATATAATCCCATGTAGAATCAGGACGG
Found at i:1988856 original size:87 final size:86
Alignment explanation
Indices: 1988691--1988856 Score: 190
Period size: 87 Copynumber: 1.9 Consensus size: 86
1988681 CAAGATATGG
* * * *
1988691 ATATAATCCCATGTAGAACCAGGACGGGGATATAATCCCATGCAAAATTAGGACATGGGTATAAC
1 ATATAATCCCATGTAGAACCAGAACGAGGATATAATACAATGCAAAATTAGGA-ATGGGTATAAC
* *
1988756 CTCATGTAGAATCAAGACGAGA
65 CTCATGAAAAATCAAGACGAGA
* * * * *
1988778 ATATAATCCTATGTAGAATCAGAATGAGGATATAATATAATGCAGAATTAGG-ATGGGGATATAA
1 ATATAATCCCATGTAGAACCAGAACGAGGATATAATACAATGCAAAATTAGGAAT-GGG-TATAA
*
1988842 TCTCATGAAAAATCA
64 CCTCATGAAAAATCA
1988857 GGATGGGGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 2 0.03
86 3 0.05
87 60 0.92
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (86 bp):
ATATAATCCCATGTAGAACCAGAACGAGGATATAATACAATGCAAAATTAGGAATGGGTATAACC
TCATGAAAAATCAAGACGAGA
Found at i:1998359 original size:29 final size:29
Alignment explanation
Indices: 1998133--1998359 Score: 129
Period size: 29 Copynumber: 7.8 Consensus size: 29
1998123 AACATGATAT
* * *
1998133 GGATATAATCTCATGTAGAATCAGGACAG
1 GGATATAATCCCATGCAGAATCAGGACAA
* * * **
1998162 GGATAAAATCACATGCAGAATCACGACGT
1 GGATATAATCCCATGCAGAATCAGGACAA
* ** * **
1998191 GGATATAACCCCATATAAAATCAGGATGA
1 GGATATAATCCCATGCAGAATCAGGACAA
* * * * *
1998220 GAATATAATCCTATGTAGAATCATG-CTGA
1 GGATATAATCCCATGCAGAATCAGGAC-AA
* * * *
1998249 GGATATAATCTCGTACAGAATCAGTG--TA
1 GGATATAATCCCATGCAGAATCAG-GACAA
* * * *
1998277 GCGATATAATCTCATGCAGAATCAAGATAT
1 G-GATATAATCCCATGCAGAATCAGGACAA
* *
1998307 GGGTATAA-CCCTATGCAAAATCAGGACAA
1 GGATATAATCCC-ATGCAGAATCAGGACAA
1998336 GGATATAATCCCATGCAGAATCAG
1 GGATATAATCCCATGCAGAATCAG
1998360 AAAAACATCA
Statistics
Matches: 148, Mismatches: 43, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
28 5 0.03
29 138 0.93
30 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (29 bp):
GGATATAATCCCATGCAGAATCAGGACAA
Found at i:2003552 original size:2 final size:2
Alignment explanation
Indices: 2003545--2003598 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2003535 GTCCTTAATA
2003545 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2003586 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2003599 AAGAATGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2010857 original size:21 final size:20
Alignment explanation
Indices: 2010802--2010859 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2010792 TTTTGGTGCA
*
2010802 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
2010822 GAGGGAACCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
*
2010842 GAGTGAACCGATTCCCCC
1 GAGGGAACCGA-TCCCCC
2010860 TTTGAATGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 29 0.83
21 6 0.17
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:2013150 original size:13 final size:13
Alignment explanation
Indices: 2013132--2013163 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
2013122 AAAGGGGGAG
2013132 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
2013145 AA--GTGTGTTTT
1 AAGTGTGTGTTTT
2013156 AAGTGTGT
1 AAGTGTGT
2013164 TTTAAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:2013152 original size:11 final size:11
Alignment explanation
Indices: 2013136--2013179 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
2013126 GGGGAGAAGT
2013136 GTGTGTTTTAA
1 GTGTGTTTTAA
2013147 GTGTGTTTTAA
1 GTGTGTTTTAA
2013158 GTGTGTTTTAA
1 GTGTGTTTTAA
*
2013169 ATGTGTTTTAA
1 GTGTGTTTTAA
2013180 AATGATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:2032251 original size:30 final size:30
Alignment explanation
Indices: 2032160--2032382 Score: 125
Period size: 30 Copynumber: 7.5 Consensus size: 30
2032150 TATTAAAACC
* * **
2032160 ATTTTAGT-CTCTTAAGTTTCTATTTTTTTT
1 ATTTTAGTCCT-TTAAGTTTTTGTTTTTGCT
* * *
2032190 ATTTTAGTTCCTTTAA-TGTCTATTTTTGCT
1 ATTTTAG-TCCTTTAAGTTTTTGTTTTTGCT
* * * *
2032220 ATTTTGGTCCTTTGATTTTTTGTTTTAGCT
1 ATTTTAGTCCTTTAAGTTTTTGTTTTTGCT
* *
2032250 A-TTTAGTCCCTTAAGTTTTTGTTTTTGTT
1 ATTTTAGTCCTTTAAGTTTTTGTTTTTGCT
* * *
2032279 ATTTTAGTCCTTTAAATGTCTGTATTTT-CT
1 ATTTTAGTCCTTTAAGTTTTTGT-TTTTGCT
* ** * *
2032309 A-TTTAGACAATTAAGTTTATGTTTTTACT
1 ATTTTAGTCCTTTAAGTTTTTGTTTTTGCT
* * * * *
2032338 AATTTAG-CCATTTAAGTTTCTATTTTTTCC
1 ATTTTAGTCC-TTTAAGTTTTTGTTTTTGCT
*
2032368 ATTTTAATCCTTTAA
1 ATTTTAGTCCTTTAA
2032383 ATTCTTAATT
Statistics
Matches: 150, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
28 4 0.03
29 49 0.33
30 84 0.56
31 11 0.07
32 2 0.01
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAGTTTTTGTTTTTGCT
Done.