Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 7 of 32
Found at i:3243567 original size:26 final size:25
Alignment explanation
Indices: 3243526--3243576 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
3243516 AAACTATTTT
*
3243526 TATATATATTTAATATATATGTTAA
1 TATATATATTTAATATATATATTAA
*
3243551 TATATAATATTTTATATATATATTAA
1 TATAT-ATATTTAATATATATATTAA
3243577 GAAGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATATATTTAATATATATATTAA
Found at i:3243793 original size:26 final size:25
Alignment explanation
Indices: 3243759--3243809 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3243749 AATTAATTTT
*
3243759 TATATATATTTAATATATATGTTAA
1 TATATATATTTAATATATATATTAA
**
3243784 TATATAATATTTTTTATATATATTAA
1 TATAT-ATATTTAATATATATATTAA
3243810 GAAGAATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATATATTTAATATATATATTAA
Found at i:3243847 original size:233 final size:234
Alignment explanation
Indices: 3243441--3243896 Score: 792
Period size: 233 Copynumber: 2.0 Consensus size: 234
3243431 TCAATTGATA
* **
3243441 TAAAATATTTAATTTAATCGATATTTTGATCGGTTATCGATTTTAAAATTTTTAAATTAATTTAT
1 TAAAATATTTAATTTAATCGATATTTTGATCGATTATCGATTTTAAAATTTTTAAACCAATTTAT
*
3243506 TTAAAAAATCAAACTATTTTTATATATATTTAATATATATGTTAATATATAATATTTTATATATA
66 TTAAAAAATAAAACTATTTTTATATATATTTAATATATATGTTAATATATAATATTTTATATATA
* *
3243571 TATTAAGAAGAATTGATAATAAATTAGATTATTAATATATTTTAAATATATTAATTTA-T-TATA
131 TATTAAGAAGAATTGATAATAAACTAAATTATTAATATATTTTAAATATATTAATTTATTATATA
3243634 TATACATATACAAATAAAAATTATAGTATTTTCTACTTT
196 TATACATATACAAATAAAAATTATAGTATTTTCTACTTT
3243673 TAAAATATTTAATTTAATC-AGTATTTTGATCGATTATCGATTTTAAAATTTTTAAACCAATTTA
1 TAAAATATTTAATTTAATCGA-TATTTTGATCGATTATCGATTTTAAAATTTTTAAACCAATTTA
* * *
3243737 TTTTAAAAATAAAATTAATTTTTATATATATTTAATATATATGTTAATATATAATATTTTTTATA
65 TTTAAAAAATAAAACT-ATTTTTATATATATTTAATATATATGTTAATATATAATATTTTATATA
3243802 TATATTAAGAAGAATTGATAATAAACTAAATTATTAATATATTTTAAATATATTAATTTATTATA
129 TATATTAAGAAGAATTGATAATAAACTAAATTATTAATATATTTTAAATATATTAATTTATTATA
3243867 TATATACATATACAAATAAAAATTATAGTA
194 TATATACATATACAAATAAAAATTATAGTA
3243897 ATTTAATTTT
Statistics
Matches: 211, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
231 1 0.00
232 72 0.34
233 105 0.50
234 1 0.00
235 32 0.15
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (234 bp):
TAAAATATTTAATTTAATCGATATTTTGATCGATTATCGATTTTAAAATTTTTAAACCAATTTAT
TTAAAAAATAAAACTATTTTTATATATATTTAATATATATGTTAATATATAATATTTTATATATA
TATTAAGAAGAATTGATAATAAACTAAATTATTAATATATTTTAAATATATTAATTTATTATATA
TATACATATACAAATAAAAATTATAGTATTTTCTACTTT
Found at i:3243871 original size:19 final size:19
Alignment explanation
Indices: 3243828--3243872 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3243818 GATAATAAAC
*
3243828 TAAAT-TATTAATATATTT
1 TAAATATATTAATATATTA
*
3243846 TAAATATATTAATTTATTA
1 TAAATATATTAATATATTA
*
3243865 TATATATA
1 TAAATATA
3243873 CATATACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATATATTAATATATTA
Found at i:3244097 original size:18 final size:18
Alignment explanation
Indices: 3244049--3244104 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 18
3244039 TACATCTTAG
3244049 TAATGTTTATAAATATA-A
1 TAATG-TTATAAATATATA
*
3244067 -AATGTTATGAATATATA
1 TAATGTTATAAATATATA
3244084 TAATAG-TATAAATATTATA
1 TAAT-GTTATAAATA-TATA
3244103 TA
1 TA
3244105 TATATATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 10 0.31
17 5 0.16
18 10 0.31
19 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (18 bp):
TAATGTTATAAATATATA
Found at i:3244123 original size:25 final size:23
Alignment explanation
Indices: 3244077--3244123 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3244067 AATGTTATGA
*
3244077 ATATATATAATAGTATAAATATT
1 ATATATATAATACTATAAATATT
*
3244100 ATATATATATATACTCATATATAT
1 ATATATATA-ATACT-ATAAATAT
3244124 ATTTAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATATATAATACTATAAATATT
Found at i:3246095 original size:7 final size:7
Alignment explanation
Indices: 3246083--3246112 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3246073 CAGCCATGTA
3246083 GAGAGAG
1 GAGAGAG
3246090 GAGAGAG
1 GAGAGAG
3246097 GAGAGAG
1 GAGAGAG
3246104 GAGAGAG
1 GAGAGAG
3246111 GA
1 GA
3246113 AGCTGGGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GAGAGAG
Found at i:3262717 original size:18 final size:18
Alignment explanation
Indices: 3262694--3262742 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3262684 CATTATCAAA
**
3262694 TAATAATAATATTTTAAT
1 TAATAATAATAAATTAAT
3262712 TAATAATAATAAATTAAT
1 TAATAATAATAAATTAAT
* *
3262730 TATTAATTATAAA
1 TAATAATAATAAA
3262743 AATTTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATAATAATAAATTAAT
Found at i:3262734 original size:21 final size:20
Alignment explanation
Indices: 3262692--3262747 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
3262682 GACATTATCA
3262692 AATAATAATAATATTTTAATT
1 AATAATAATAA-ATTTTAATT
3262713 AATAATAATAAATTAATT-ATT
1 AATAATAATAAATT--TTAATT
*
3262734 AATTATAA-AAATTT
1 AATAATAATAAATTT
3262748 ATTTTATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
20 8 0.25
21 21 0.66
22 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATAATAAATTTTAATT
Found at i:3276146 original size:3 final size:3
Alignment explanation
Indices: 3276138--3276187 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
3276128 GATCATTCAT
3276138 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3276184 TTA T
1 TTA T
3276188 ATAGAGTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3306648 original size:50 final size:50
Alignment explanation
Indices: 3306571--3306670 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
3306561 CCCTCCACGG
* * *
3306571 TGCAACTCAAATTTCCAAAAGATACCCTGTCAACAAAAGGACAGATTCAA
1 TGCAACTCAAATTTCCAAAAGACACCCTGTCAAAAAAAGGAAAGATTCAA
*
3306621 TGCAACTCAAATTTCCAAAAGACACCCTGTCAAAAAAAGGAAATATTCAA
1 TGCAACTCAAATTTCCAAAAGACACCCTGTCAAAAAAAGGAAAGATTCAA
3306671 ATACCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (50 bp):
TGCAACTCAAATTTCCAAAAGACACCCTGTCAAAAAAAGGAAAGATTCAA
Found at i:3312912 original size:2 final size:2
Alignment explanation
Indices: 3312905--3312930 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3312895 TCCATGGTTC
3312905 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
3312931 GGACGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3315831 original size:51 final size:51
Alignment explanation
Indices: 3315655--3316005 Score: 258
Period size: 51 Copynumber: 7.0 Consensus size: 51
3315645 GATCTCAAAT
* * * * *
3315655 AAATGATTTAGAGAATTCGCTTCAAGGGTCTCATGACTTGATATTAAATGAAC
1 AAATAATTTAGAGACTTCGCTTCAAGAGTCT--TGACTTGATCTTGAATGAAC
* * * * *
3315708 AAA-AGATTT-GAAAAATT-GCTTCAAGGGTCTTGATTTGATATTGAATGAAC
1 AAATA-ATTTAG-AGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAAC
* * *
3315758 ----GATTTAGAGACTTTGCTTCAAGAGTCTTAACTTGATCTTGAATGAAC
1 AAATAATTTAGAGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAAC
* * * *
3315805 AAACAATTTAGAGACTTCACTTCAAGAGTCTTGACTTGATATTAAATGAAC
1 AAATAATTTAGAGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAAC
* * * * *
3315856 AAATAATTTACAGACTTCGCTAT-ACAGATTTTATAACTTGATCTTGAATGAAT
1 AAATAATTTAGAGACTTCGCT-TCA-AGAGTCT-TGACTTGATCTTGAATGAAC
* * * * * * * * *
3315909 GAATGATTTGGAAACTTCCCTTTAAGAGTATTGACTTAATTTTGAATG---
1 AAATAATTTAGAGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAAC
* *
3315957 -AATGATTTAGAGACTTCGCTTCAAGGGTCTTGACTTGATCTTGAATGAA
1 AAATAATTTAGAGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAA
3316006 TGAACAATTT
Statistics
Matches: 239, Mismatches: 45, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
46 8 0.03
47 69 0.29
50 18 0.08
51 74 0.31
52 26 0.11
53 44 0.18
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATAATTTAGAGACTTCGCTTCAAGAGTCTTGACTTGATCTTGAATGAAC
Found at i:3315845 original size:98 final size:97
Alignment explanation
Indices: 3315659--3316079 Score: 346
Period size: 98 Copynumber: 4.2 Consensus size: 97
3315649 TCAAATAAAT
* * * * * * * *
3315659 GATTTAGAGAATTCGCTTCAAGGGTCTCATGACTTGATATTAAATGAA-CAAAAGATTTGAAAAA
1 GATTTAGAGACTTCGCTTCAAGAGTCT--TAACTTGATCTTGAATGAATGAACA-ATTTG-AAAC
* * *
3315723 TT-GCTTCAAGGGTCTTGATTTGATATTGAATGAAC
62 TTCACTTCAAGAGTCTTGACTTGATATTGAATGAAC
* ** *
3315758 GATTTAGAGACTTTGCTTCAAGAGTCTTAACTTGATCTTGAATGAACAAACAATTTAGAGACTTC
1 GATTTAGAGACTTCGCTTCAAGAGTCTTAACTTGATCTTGAATGAATGAACAATTT-GAAACTTC
*
3315823 ACTTCAAGAGTCTTGACTTGATATTAAATGAAC
65 ACTTCAAGAGTCTTGACTTGATATTGAATGAAC
* * * * **
3315856 AAATAATTTACAGACTTCGCTAT-ACAGATTTTATAACTTGATCTTGAATGAATGAATGATTTGG
1 ----GATTTAGAGACTTCGCT-TCA-AGAGTCT-TAACTTGATCTTGAATGAATGAACAATTT-G
* * * * * *
3315920 AAACTTCCCTTTAAGAGTATTGACTTAATTTTGAATGAAT
58 AAACTTCACTTCAAGAGTCTTGACTTGATATTGAATGAAC
* * *
3315960 GATTTAGAGACTTCGCTTCAAGGGTCTTGACTTGATCTTGAATGAATGAACAATTTGAAAATTTC
1 GATTTAGAGACTTCGCTTCAAGAGTCTTAACTTGATCTTGAATGAATGAACAATTTG-AAACTTC
* * * * *
3316025 ATTTTAAGAGTTTTTACTTGATCTTGAATGAAC
65 ACTTCAAGAGTCTTGACTTGATATTGAATGAAC
*
3316058 GATTT-GAATACTTCGCTTCAAG
1 GATTTAG-AGACTTCGCTTCAAG
3316080 TTTGCTTCGA
Statistics
Matches: 260, Mismatches: 49, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
97 26 0.10
98 110 0.42
99 29 0.11
100 16 0.06
102 15 0.06
103 6 0.02
104 58 0.22
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (97 bp):
GATTTAGAGACTTCGCTTCAAGAGTCTTAACTTGATCTTGAATGAATGAACAATTTGAAACTTCA
CTTCAAGAGTCTTGACTTGATATTGAATGAAC
Found at i:3316006 original size:47 final size:47
Alignment explanation
Indices: 3315904--3316008 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 47
3315894 TGATCTTGAA
* * *
3315904 TGAATGAATGATTTGGAAACTTCCCTTTAAGAGTATTGACTTAATTT
1 TGAATGAATGATTTAGAAACTTCCCTTCAAGAGTATTGACTTAATCT
* * * * *
3315951 TGAATGAATGATTTAGAGACTTCGCTTCAAGGGTCTTGACTTGATCT
1 TGAATGAATGATTTAGAAACTTCCCTTCAAGAGTATTGACTTAATCT
3315998 TGAATGAATGA
1 TGAATGAATGA
3316009 ACAATTTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (47 bp):
TGAATGAATGATTTAGAAACTTCCCTTCAAGAGTATTGACTTAATCT
Found at i:3378943 original size:15 final size:15
Alignment explanation
Indices: 3378923--3378953 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3378913 ATACTACTCT
*
3378923 TAAAATAATTTAAAA
1 TAAAATAATATAAAA
3378938 TAAAATAATATAAAA
1 TAAAATAATATAAAA
3378953 T
1 T
3378954 TTAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATAATATAAAA
Found at i:3385274 original size:19 final size:20
Alignment explanation
Indices: 3385225--3385275 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3385215 TAAATTATAT
3385225 AAAAATTTATTGATTTTTAAA
1 AAAAATTTATT-ATTTTTAAA
*
3385246 ATTAATATTTATT-TTTTTAAA
1 A--AAAATTTATTATTTTTAAA
3385267 AAAAATTTA
1 AAAAATTTA
3385276 ATTAGATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 7 0.27
21 10 0.38
23 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAAAATTTATTATTTTTAAA
Found at i:3385499 original size:20 final size:20
Alignment explanation
Indices: 3385456--3385501 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3385446 TTTAAAATTT
* *
3385456 TTTTAAATATAATAATAATT
1 TTTTAAATATAATAAAAATA
3385476 TTTTAAAT-TAATAAAAAATA
1 TTTTAAATATAAT-AAAAATA
3385496 TTTTAA
1 TTTTAA
3385502 TTTTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAATATAATAAAAATA
Found at i:3398194 original size:44 final size:44
Alignment explanation
Indices: 3398131--3398308 Score: 306
Period size: 44 Copynumber: 4.1 Consensus size: 44
3398121 ACTTTCGTTT
3398131 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
1 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
*
3398175 CTGCTAAAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
1 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
3398219 CTGCTACAGCTA--GAGAGTTTAAAACATGCATACAGATTCATC
1 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
* **
3398261 CTGTTACAGCTAGTGAGAGTTTAAAATGTGCATACAGATTCATC
1 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
3398305 CTGC
1 CTGC
3398309 AGTACTTTTT
Statistics
Matches: 126, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
42 41 0.33
44 85 0.67
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATC
Found at i:3398278 original size:86 final size:87
Alignment explanation
Indices: 3398131--3398308 Score: 304
Period size: 86 Copynumber: 2.0 Consensus size: 87
3398121 ACTTTCGTTT
3398131 CTGCTACAGCTAGTGAGAGTTTAAAACATGCATACAGATTCATCCTGCTAAAGCTAGTGAGAGTT
1 CTGCTACAGCTAG-GAGAGTTTAAAACATGCATACAGATTCATCCTGCTAAAGCTAGTGAGAGTT
3398196 TAAAACATGCATACAGATTCATC
65 TAAAACATGCATACAGATTCATC
* *
3398219 CTGCTACAGCTA-GAGAGTTTAAAACATGCATACAGATTCATCCTGTTACAGCTAGTGAGAGTTT
1 CTGCTACAGCTAGGAGAGTTTAAAACATGCATACAGATTCATCCTGCTAAAGCTAGTGAGAGTTT
**
3398283 AAAATGTGCATACAGATTCATC
66 AAAACATGCATACAGATTCATC
3398305 CTGC
1 CTGC
3398309 AGTACTTTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
86 74 0.86
88 12 0.14
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (87 bp):
CTGCTACAGCTAGGAGAGTTTAAAACATGCATACAGATTCATCCTGCTAAAGCTAGTGAGAGTTT
AAAACATGCATACAGATTCATC
Found at i:3399434 original size:78 final size:78
Alignment explanation
Indices: 3399305--3399457 Score: 290
Period size: 78 Copynumber: 2.0 Consensus size: 78
3399295 AAAAATGCAT
3399305 GCAAAAGTTCTCAAACTGACCACTATATCAACATATTTCATTGAAATGCAAGTGCACACATACAC
1 GCAAAAGTTCTCAAACTGACCACTATATCAACATATTTCATTGAAATGCAAGTGCACACATACAC
3399370 ATTAGAACTTCAA
66 ATTAGAACTTCAA
3399383 GCAAAAGTTCTCAAACTGACCACTATATCAACATATTTCCA-TGAAATGCAAGTGCACACATACA
1 GCAAAAGTTCTCAAACTGACCACTATATCAACATATTT-CATTGAAATGCAAGTGCACACATACA
3399447 CATTAGAACTT
65 CATTAGAACTT
3399458 AGTAAATGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
78 72 0.97
79 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (78 bp):
GCAAAAGTTCTCAAACTGACCACTATATCAACATATTTCATTGAAATGCAAGTGCACACATACAC
ATTAGAACTTCAA
Found at i:3412690 original size:21 final size:21
Alignment explanation
Indices: 3412648--3412688 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3412638 TATTATTTTA
*
3412648 AACAAATCAAATAGTATAAAT
1 AACAAATCAAATAATATAAAT
*
3412669 AACAATTCAAATAAATATAA
1 AACAAATCAAAT-AATATAA
3412689 TATGGATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (21 bp):
AACAAATCAAATAATATAAAT
Found at i:3414515 original size:24 final size:25
Alignment explanation
Indices: 3414488--3414535 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3414478 CAAAGTCCAA
*
3414488 GAAAAA-AAGAATAACAA-AAAAAAT
1 GAAAAATAA-AATAAAAAGAAAAAAT
3414512 GAAAAATAAAATAAAAAGAAAAAA
1 GAAAAATAAAATAAAAAGAAAAAA
3414536 AAGAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.08
Consensus pattern (25 bp):
GAAAAATAAAATAAAAAGAAAAAAT
Found at i:3414527 original size:17 final size:16
Alignment explanation
Indices: 3414489--3414534 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3414479 AAAGTCCAAG
* *
3414489 AAAAAAAGAATAACAA
1 AAAAAAAGAAAAATAA
*
3414505 AAAAAATGAAAAATAA
1 AAAAAAAGAAAAATAA
3414521 AATAAAAAGAAAAA
1 AA-AAAAAGAAAAA
3414535 AAAGAAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.09
Consensus pattern (16 bp):
AAAAAAAGAAAAATAA
Found at i:3414960 original size:38 final size:38
Alignment explanation
Indices: 3414918--3414995 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3414908 GTAAAAAGAA
3414918 AAAAAATAAGTAATATTTTTTAATTTTTAAAAATGCAC
1 AAAAAATAAGTAATATTTTTTAATTTTTAAAAATGCAC
3414956 AAAAAATAAGTAATATTTTTTAATTTTTAAAAATGCAC
1 AAAAAATAAGTAATATTTTTTAATTTTTAAAAATGCAC
3414994 AA
1 AA
3414996 TTTTAGTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (38 bp):
AAAAAATAAGTAATATTTTTTAATTTTTAAAAATGCAC
Found at i:3419194 original size:1 final size:1
Alignment explanation
Indices: 3419188--3419246 Score: 91
Period size: 1 Copynumber: 59.0 Consensus size: 1
3419178 TCTTTCAACA
* * *
3419188 CCCCCCCCCCCCCCCGCCCCCCCCCCACCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3419247 TTCTCTCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.02, C:0.95, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:3425679 original size:2 final size:2
Alignment explanation
Indices: 3425672--3425696 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3425662 GCATAAAAAT
3425672 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3425697 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3428841 original size:24 final size:22
Alignment explanation
Indices: 3428797--3428842 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3428787 TAAATATGTG
*
3428797 TATATATAATATATGATTTTAT
1 TATATATAATATATGAATTTAT
3428819 TATATATATATATATGAAATTTAT
1 TATATATA-ATATATG-AATTTAT
3428843 GACATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 7 0.33
24 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATATATAATATATGAATTTAT
Found at i:3429014 original size:23 final size:22
Alignment explanation
Indices: 3428969--3429037 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
3428959 ATAAATTAAG
*
3428969 TTTATTATAAATTATAGTA-ATA
1 TTTATTATAAATTA-AATATATA
3428991 TTTATGTATAAATTAAATATATA
1 TTTAT-TATAAATTAAATATATA
* *
3429014 TAATATTTATACAATTATATATAT
1 T-TTA-TTATA-AATTAAATATAT
3429038 TCATAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.21
23 13 0.33
24 6 0.15
25 12 0.31
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (22 bp):
TTTATTATAAATTAAATATATA
Found at i:3461068 original size:17 final size:17
Alignment explanation
Indices: 3461046--3461082 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3461036 CATTGTCAAT
3461046 TTTGCCAGGATAGAGTC
1 TTTGCCAGGATAGAGTC
*
3461063 TTTGCCATGATAGAGTC
1 TTTGCCAGGATAGAGTC
3461080 TTT
1 TTT
3461083 CTTCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (17 bp):
TTTGCCAGGATAGAGTC
Found at i:3461314 original size:2 final size:2
Alignment explanation
Indices: 3461307--3461336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3461297 AAATATCTGA
3461307 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
3461337 GTAAAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3483764 original size:20 final size:21
Alignment explanation
Indices: 3483726--3483764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3483716 ATACTAAATG
3483726 GAAAAAAATGAAATGTCATGT
1 GAAAAAAATGAAATGTCATGT
*
3483747 GAAAAAAATTAAAT-TCAT
1 GAAAAAAATGAAATGTCAT
3483765 AAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (21 bp):
GAAAAAAATGAAATGTCATGT
Found at i:3504258 original size:11 final size:11
Alignment explanation
Indices: 3504242--3504266 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3504232 TTTCATCTAT
3504242 AAAAAAACAAA
1 AAAAAAACAAA
3504253 AAAAAAACAAA
1 AAAAAAACAAA
3504264 AAA
1 AAA
3504267 CCACTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:3505233 original size:3 final size:3
Alignment explanation
Indices: 3505225--3505252 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3505215 GTACTTAAGG
3505225 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3505253 AATAGACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3508809 original size:14 final size:12
Alignment explanation
Indices: 3508778--3508807 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3508768 TATGAAGAAA
3508778 AATTA-AAAAAT
1 AATTATAAAAAT
3508789 AATTATAAAAAT
1 AATTATAAAAAT
3508801 AATTATA
1 AATTATA
3508808 TATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTATAAAAAT
Found at i:3509054 original size:16 final size:17
Alignment explanation
Indices: 3509035--3509072 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3509025 AAGTAAATTT
*
3509035 TATTAAAAAC-TTTATA
1 TATTAAAAACATTTAAA
*
3509051 TATTAATAACATTTAAA
1 TATTAAAAACATTTAAA
3509068 TATTA
1 TATTA
3509073 TCAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAAAACATTTAAA
Found at i:3509079 original size:36 final size:35
Alignment explanation
Indices: 3509045--3509124 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 35
3509035 TATTAAAAAC
3509045 TTTATATATTAATAACATTTAAATATTATCAAAAAATAA
1 TTTATATATTAAT---ATTTAAATATTATC-AAAAATAA
*
3509084 TTTATATATTAATATTTAAATATTA-CATAAAAAAA
1 TTTATATATTAATATTTAAATATTATCA-AAAATAA
3509119 TTTATA
1 TTTATA
3509125 ATTTAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
34 1 0.03
35 13 0.33
36 12 0.31
39 13 0.33
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (35 bp):
TTTATATATTAATATTTAAATATTATCAAAAATAA
Found at i:3509093 original size:39 final size:35
Alignment explanation
Indices: 3509039--3509124 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 35
3509029 AAATTTTATT
*
3509039 AAAAACTTTATATATTAATAACATTTAAATATTATCA-A
1 AAAAAATTTATATATTAAT---ATTTAAATATTA-CATA
3509077 AAAATAATTTATATATTAATATTTAAATATTACATA
1 AAAA-AATTTATATATTAATATTTAAATATTACATA
3509113 AAAAAATTTATA
1 AAAAAATTTATA
3509125 ATTTAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
35 10 0.22
36 17 0.38
38 4 0.09
39 14 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAAAATTTATATATTAATATTTAAATATTACATA
Found at i:3512176 original size:2 final size:2
Alignment explanation
Indices: 3512169--3512203 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3512159 GATTGAATAT
3512169 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3512204 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3514919 original size:14 final size:13
Alignment explanation
Indices: 3514900--3514942 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3514890 AAAAATATAG
3514900 AAATATATTATTAA
1 AAATATATT-TTAA
3514914 AAATAT-TTTTAA
1 AAATATATTTTAA
* *
3514926 TAGTATATTTTAA
1 AAATATATTTTAA
3514939 AAAT
1 AAAT
3514943 GTACAATCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.33
13 10 0.42
14 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AAATATATTTTAA
Found at i:3527927 original size:16 final size:15
Alignment explanation
Indices: 3527895--3527947 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
3527885 ATATATTTTA
3527895 TTTTAAATTAAATTAAT
1 TTTTAAATT-AA-TAAT
3527912 TTTTATAATTAATAAT
1 TTTTA-AATTAATAAT
* *
3527928 TAATTAAAATAATAAT
1 T-TTTAAATTAATAAT
3527944 TTTT
1 TTTT
3527948 TTATCACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.48
17 10 0.32
18 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAATTAATAAT
Found at i:3531076 original size:14 final size:14
Alignment explanation
Indices: 3531045--3531110 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
3531035 GTAAGTTTGG
*
3531045 TTTATTTATTATTAT
1 TTTATTT-TTAATAT
3531060 TTTATTTTTAATATT
1 TTTATTTTTAATA-T
* *
3531075 TTTAATTTTAAAAT
1 TTTATTTTTAATAT
*
3531089 TTT-TATTTAATAAT
1 TTTATTTTTAAT-AT
3531103 TTCTATTT
1 TT-TATTT
3531111 AGAGATAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.12
14 13 0.32
15 20 0.50
16 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTTTTAATAT
Found at i:3531514 original size:26 final size:23
Alignment explanation
Indices: 3531485--3531541 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 23
3531475 AACATTGAAA
3531485 ATAATAATAATATTATTAAATTATTT
1 ATAATAATAATA--ATT-AATTATTT
*
3531511 ATAATTATAATAATTAATTATTT
1 ATAATAATAATAATTAATTATTT
3531534 -TAAATAAT
1 AT-AATAAT
3531542 TTTCAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 1 0.04
23 13 0.46
24 3 0.11
26 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATAATAATAATTAATTATTT
Found at i:3550415 original size:277 final size:276
Alignment explanation
Indices: 3550000--3550499 Score: 654
Period size: 277 Copynumber: 1.8 Consensus size: 276
3549990 GGCATTATTA
3550000 TACCTTAATGTATAATAAGAATGCCATATGCCCACACCTTAAAGTTTATTTATTTCTCCAAACAC
1 TACCTTAATGTATAATAAGAATGCCATATGCCCACACCTTAAAGTTTATTTATTTCTCCAAACAC
* *
3550065 AACAACGTGGTTTTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAAAAATAAATT
66 AACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAAAAAGAAATT
* * *
3550130 CCCAATTGACACCATTGTGCTTTAATGTACAATT-GAAAAGTCAAATTAACATATCA-AGCTACA
131 CCCAATTGACACCATTGTACCTTAATGTACAATTAGAAAA-TCAAATTAACACATCAGA-CTACA
* * *
3550193 TGTTCATATAAGCACTATTGTGCCTTTATTGTTCAATAGGAATGTCATGTCGAATATTTTAAACA
194 TGTTCACATAAGCACCATTATGCCTTTATTGTTCAATAGGAATGTCATGTCGAATATTTTAAACA
3550258 TGTATTTTTCCCCAATTC
259 TGTATTTTTCCCCAATTC
* * *
3550276 TACCTTTAATTGTATAATAGGAATGGCCACATATGCGCACATC-TAATAGTTTATTTATTTCT-C
1 TACC-TTAA-TGTATAATAAGAAT-G-C-CATATGCCCACACCTTAA-AGTTTATTTATTTCTCC
* * * ** * *
3550339 TAA-AC-ATAA-GTGGTTCTCACCTTAAGTTAACCAACCAAATCCATCATGACAATGAAACAAAA
60 AAACACAACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAAAAA
* * * * * *
3550401 GGAATTCTCAATTGACACCATTTTACCTTAATGTACAATTAGAATATCAAATTAAGACATCCGAC
125 GAAATTCCCAATTGACACCATTGTACCTTAATGTACAATTAGAAAATCAAATTAACACATCAGAC
*
3550466 TATATGTTCACATAAGCACCATTATGCCTTTATT
190 TACATGTTCACATAAGCACCATTATGCCTTTATT
3550500 ACACAATAAG
Statistics
Matches: 191, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
276 4 0.02
277 129 0.68
278 21 0.11
279 3 0.02
280 7 0.04
281 27 0.14
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (276 bp):
TACCTTAATGTATAATAAGAATGCCATATGCCCACACCTTAAAGTTTATTTATTTCTCCAAACAC
AACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAAAAAGAAATT
CCCAATTGACACCATTGTACCTTAATGTACAATTAGAAAATCAAATTAACACATCAGACTACATG
TTCACATAAGCACCATTATGCCTTTATTGTTCAATAGGAATGTCATGTCGAATATTTTAAACATG
TATTTTTCCCCAATTC
Found at i:3550585 original size:277 final size:280
Alignment explanation
Indices: 3549996--3550585 Score: 623
Period size: 277 Copynumber: 2.1 Consensus size: 280
3549986 TATTGGCATT
* *
3549996 ATTATACC-TTAAT-GTATAATAAGAATG--C-CATATGCCCACACCTTAAAGTTTATTTATTTC
1 ATTATACCTTTAATGGTAAAATACGAATGACCACATATGCCCACACCTTAAAGTTTATTTATTTC
*
3550056 TCCAAACACAACAACGTGGTTTTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAA
66 TCCAAACACAACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAA
* * * *
3550121 AAATAAATTCCCAATTGACACCATTGTGCTTTAATGTACAATTGAAAAGTCAAATTAACATATCA
131 AAAGAAATTCCCAATTGACACCATTGTACCTTAATGTACAATTGAAAAGTCAAATTAACACATCA
* * * *** * * *
3550186 AGCTACATGTTCATATAAGCACTATTGTGCCTTTATTGTTCAATAGGAATGTCATGTCGAATATT
196 AGCTACATGTTCACATAAGCACCATTATGCCTTTATTACACAATAAGAATGCCATG-CGAATATA
* *
3550251 TTAAACATGTATTTTTCCCCA
260 TTAAACATCTATTTTTCCACA
* * * * * * *
3550272 ATTCTACCTTTAATTGTATAATAGGAATGGCCACATATGCGCACATC-TAATAGTTTATTTATTT
1 ATTATACCTTTAATGGTAAAATACGAATGACCACATATGCCCACACCTTAA-AGTTTATTTATTT
* * * ** * *
3550336 CT-CTAA-AC-ATAA-GTGGTTCTCACCTTAAGTTAACCAACCAAATCCATCATGACAATGAAAC
65 CTCCAAACACAACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAA
* * * * *
3550397 AAAAGGAATTCTCAATTGACACCATTTTACCTTAATGTACAATTAGAATA-TCAAATTAAGACAT
130 AAAAGAAATTCCCAATTGACACCATTGTACCTTAATGTACAATT-GAAAAGTCAAATTAACACAT
* *
3550461 C-CGACTATATGTTCACATAAGCACCATTATGCCTTTATTACACAATAAGAATGCCATAG-GAAA
194 CAAG-CTACATGTTCACATAAGCACCATTATGCCTTTATTACACAATAAGAATGCCAT-GCG-AA
* * **
3550524 TATATTAAATATCTA-TTTTGCATT
256 TATATTAAACATCTATTTTTCCACA
*
3550548 ATTATACCTTTGATGGTAAAATACGAATGCACCACATA
1 ATTATACCTTTAATGGTAAAATACGAATG-ACCACATA
3550586 CTAAGATGTT
Statistics
Matches: 259, Mismatches: 44, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
276 38 0.15
277 164 0.63
278 21 0.08
279 2 0.01
280 7 0.03
281 27 0.10
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (280 bp):
ATTATACCTTTAATGGTAAAATACGAATGACCACATATGCCCACACCTTAAAGTTTATTTATTTC
TCCAAACACAACAACGTGGTTCTCACCTTAAGCTAACCAACCAAATCCATCACAACAATAAAAAA
AAAGAAATTCCCAATTGACACCATTGTACCTTAATGTACAATTGAAAAGTCAAATTAACACATCA
AGCTACATGTTCACATAAGCACCATTATGCCTTTATTACACAATAAGAATGCCATGCGAATATAT
TAAACATCTATTTTTCCACA
Found at i:3551708 original size:277 final size:275
Alignment explanation
Indices: 3551210--3551790 Score: 779
Period size: 277 Copynumber: 2.1 Consensus size: 275
3551200 TATTGGTATT
* * * *
3551210 ATTATACCTTAATGTATAATAGGAATGTCACATACCCCACACCTTATAATTTATTTATTTCTCCG
1 ATTATACCTTAATGTATAATAGGAATGCCACATAACCCACACCTAATAATTTATTTATTTCTCCA
* *
3551275 AACACAAAAATGTGGTTTTTCCCTTAAGCTAACCAACCAAATCTATCAAGACAATAAAAAAAATG
66 AACACAAAAATGTGGTTTCTCCCTTAAGCTAACCAACCAAATCTATCAAGACAATAAAAAAAACG
* * * ** *
3551340 AATTCTCAACTGACATCATTATACCTTAATGTACAATTGGAATATCAAATTAACATATCAAGCTA
131 AATTCTCAACTGACACCATTAAAACTTAATGTACAATCAGAATATCAAATTAACACATCAAGCTA
* * * * ** *
3551405 TATGTTCACATAAGCACCACTGTGCCTTTATTGCAAAATAGGAATGTCATATCAAATATTTTAAA
196 TATCTTCACACAAGCACCACTGTGCCTTTATTACAAAATAGGAATGCCATAAAAAATATATTAAA
3551470 TATCTATTTTGCACC
261 TATCTATTTTGCACC
* * *
3551485 ATTATACCTTAATGTATAATAGGAATGCCGCATATACCCACACCTAATAGTTTATTTATTTCTCT
1 ATTATACCTTAATGTATAATAGGAATGCCACATA-ACCCACACCTAATAATTTATTTATTTCTCC
* * *
3551550 AAACACTACAAA-GTGG-TTCTCACCTTAAGCTAACCAACCAAATCTATCATGACAATGAAACAA
65 AAACAC-AAAAATGTGGTTTCTC-CCTTAAGCTAACCAACCAAATCTATCAAGACAAT-AAAAAA
* *
3551613 AACGAATTCTCAATTGACACCATTAAAACTTAATGTACAATCAGAATATCAAATTAACACGTCAA
127 AACGAATTCTCAACTGACACCATTAAAACTTAATGTACAATCAGAATATCAAATTAACACATCAA
** * * *
3551678 TTTTTATCTTCACACAAGCACCATTGTGCCTTTATTACACAATAGGAATGCCATAAAAAATATAT
192 GCTATATCTTCACACAAGCACCACTGTGCCTTTATTACAAAATAGGAATGCCATAAAAAATATAT
*
3551743 TAAATATCTATTTTGCACT
257 TAAATATCTATTTTGCACC
* *
3551762 ATTATACCTTTGATGGTAAAATAGGAATG
1 ATTATACC-TTAAT-GTATAATAGGAATG
3551791 TATCACATAA
Statistics
Matches: 265, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
275 36 0.14
276 68 0.26
277 144 0.54
278 4 0.02
279 13 0.05
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (275 bp):
ATTATACCTTAATGTATAATAGGAATGCCACATAACCCACACCTAATAATTTATTTATTTCTCCA
AACACAAAAATGTGGTTTCTCCCTTAAGCTAACCAACCAAATCTATCAAGACAATAAAAAAAACG
AATTCTCAACTGACACCATTAAAACTTAATGTACAATCAGAATATCAAATTAACACATCAAGCTA
TATCTTCACACAAGCACCACTGTGCCTTTATTACAAAATAGGAATGCCATAAAAAATATATTAAA
TATCTATTTTGCACC
Found at i:3552061 original size:340 final size:338
Alignment explanation
Indices: 3551478--3552587 Score: 1130
Period size: 341 Copynumber: 3.3 Consensus size: 338
3551468 AATATCTATT
* * *
3551478 TTGCACCATTATACCTTAATGTATAATAGGAATGCCGCATATACCCACACCTAATAGTTTATTTA
1 TTGCACCATTATACCTTAATGTATAATAGGAATGCCACATATGCCCACACCTTATAGTTTATTTA
* *
3551543 TTTC-TCTAAACACTACAAAGTGGTTCTCACCTTAAGCTAACCAACCAAATCTATCATGACAATG
66 TTTCTTC-AAACAC-ACAAAGTGGTTCT---CTTAAACTAACCAACCAAATCCATCATGACAAT-
* * *
3551607 AAACAAAAC--GAATTCTCAATTGACACCATTAAAACTTAATGTACAATCAGAATATCAAATTAA
125 AAAAAAAACAAGAATTCTCAATTGACACCATTATAACTTAATGTACAATCAGAATGT-AAATTAA
* * ** * * * *
3551670 CACGTCAATTTTTATCTTCACACAAGCACCATTGTGCCTTTATTACACAATAGGAATGCCATAAA
189 TACATCAAGCTATATGTTCACATAAGCACCATTGTGCCTTTATTGCACAATAGGAATGCCAT-AA
* * *
3551735 AAATATATTAAATATCTATTTTGCACTATTATACCTTTGATGGTAAAATAGGAATGTATCACATA
253 AAATATATTAAATATCAATTTTGCACCATTATACCTTTGATGGTAAAATAGGAATGCATCACATA
3551800 ACAAGATATTAGATTTATATA
318 ACAAGATATTAGATTTATATA
** *
3551821 TTAGCACCATTATACCTTAATACATAATAGAAATGCCACA-ATGCCCACACCTTATAGTTTATTT
1 TT-GCACCATTATACCTTAATGTATAATAGGAATGCCACATATGCCCACACCTTATAGTTTATTT
* *
3551885 ATTTCTTCAAACACAACAATGTGGTT-T-TTAAACTAACCAACCAAATCCATGATGACAATAAAA
65 ATTTCTTCAAACAC-ACAAAGTGGTTCTCTTAAACTAACCAACCAAATCCATCATGACAATAAAA
* * * *
3551948 AAAACAATGAATTCCCAATTGACACCATTATACCTTAATGTATAATCAAAATGTAATATTAATAC
129 AAAACAA-GAATTCTCAATTGACACCATTATAACTTAATGTACAATCAGAATGTAA-ATTAATAC
**
3552013 ATCAAGCTATATGTTCACATAAGCACCATTGTGCCTTTATTGCACAATAGGAATGCCATTTAAAT
192 ATCAAGCTATATGTTCACATAAGCACCATTGTGCCTTTATTGCACAATAGGAATGCCATAAAAAT
** * * * *
3552078 AT-TTAAAATATCAATAATGCACCATTACACCTTTGACGGAAAAATGGGAATGCATCACA-AACC
257 ATATT-AAATATCAATTTTGCACCATTATACCTTTGATGGTAAAATAGGAATGCATCACATAA-C
*
3552141 AAGATGTTAGATTTATATA
320 AAGATATTAGATTTATATA
* * * * ** *
3552160 TGGGCATCATTATACCTTAATG--T-ATAGGAATGTCACATATGCCCACACCTTACAAATTCTTT
1 T-TGCACCATTATACCTTAATGTATAATAGGAATGCCACATATGCCCACACCTTATAGTTTATTT
* * * *
3552222 ATTGCTCCAAACAGCACAAAATGGTTCTCACCTTAAACTTAACCAACCAAATTCATCATGACAAT
65 ATTTCTTCAAACA-CACAAAGTGGTTCT---CTTAAAC-TAACCAACCAAATCCATCATGACAAT
* ** * * * * * **
3552287 GAAGTAAA-AGGAATTCTCGATTGATACCATTGTATCTTAATGTACAATTGGAATGTAAAATTAA
125 AAAAAAAACAAGAATTCTCAATTGACACCATTATAACTTAATGTACAATCAGAATGT-AAATTAA
* * *
3552351 TATATTAAGCTATATGTTCACATAAGCACTATTGTGCCTTTATTAG-ACAATAGGAATGCCATGA
189 TACATCAAGCTATATGTTCACATAAGCACCATTGTGCCTTTATT-GCACAATAGGAATGCCAT-A
* * * * * **
3552415 CAAATATATTCAATATGAATTTTTCACCATAATACCTTTGAT--TAAATCATAGGAATGCATCTT
252 AAAATATATTAAATATCAATTTTGCACCATTATACCTTTGATGGTAAA--ATAGGAATGCATCAC
* * *
3552478 ATAACAGGATA--AGATTCAAATA
315 ATAACAAGATATTAGATTTATATA
* *
3552500 TTGACACCATTATACC-T-ATGTATAATAGGAATGCCACACA--CCCACACCTTTAAAGTTTATT
1 TTG-CACCATTATACCTTAATGTATAATAGGAATGCCACATATGCCCACACC-TTATAGTTTA-T
*
3552561 TTATTTC-TCTAAACAACACAAGGTGGT
63 TTATTTCTTC-AAAC-ACACAAAGTGGT
3552588 GCTCACCTTT
Statistics
Matches: 636, Mismatches: 99, Indels: 66
0.79 0.12 0.08
Matches are distributed among these distances:
336 12 0.02
337 49 0.08
338 38 0.06
339 100 0.16
340 131 0.21
341 133 0.21
342 60 0.09
343 78 0.12
344 35 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (338 bp):
TTGCACCATTATACCTTAATGTATAATAGGAATGCCACATATGCCCACACCTTATAGTTTATTTA
TTTCTTCAAACACACAAAGTGGTTCTCTTAAACTAACCAACCAAATCCATCATGACAATAAAAAA
AACAAGAATTCTCAATTGACACCATTATAACTTAATGTACAATCAGAATGTAAATTAATACATCA
AGCTATATGTTCACATAAGCACCATTGTGCCTTTATTGCACAATAGGAATGCCATAAAAATATAT
TAAATATCAATTTTGCACCATTATACCTTTGATGGTAAAATAGGAATGCATCACATAACAAGATA
TTAGATTTATATA
Found at i:3557720 original size:10 final size:9
Alignment explanation
Indices: 3557705--3557729 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3557695 ATCACCCATA
3557705 TTTTTTTGT
1 TTTTTTTGT
3557714 TTTTTTTGT
1 TTTTTTTGT
3557723 TTTTTTT
1 TTTTTTT
3557730 CTAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:3558303 original size:2 final size:2
Alignment explanation
Indices: 3558296--3558321 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3558286 TGTGGACCCC
3558296 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
3558322 GAACAGCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3564969 original size:204 final size:203
Alignment explanation
Indices: 3564620--3565031 Score: 716
Period size: 204 Copynumber: 2.0 Consensus size: 203
3564610 GTCTATTAGA
3564620 ATTCACAATTAAAAAAAGAAATGACCAGTTATTCTGGGTGAAAACAAAAGAACCTACTATGGACA
1 ATTCACAATTAAAAAAAGAAATGACCAGTTATTCTGGGTGAAAACAAAAGAACCTACTATGGACA
3564685 AATTAGTGGCCAAACATAAAACAAAATACCAATTAGTTTGAGATTTAACCAGAAACAGTAAAATC
66 AATTAGTGGCCAAACATAAAACAAAATACCAATTAGTTTGAGATTTAACCAGAAACAGTAAAATC
* * *
3564750 CACTATATAGTAACAAAGGTATGCTATATTCACATCTTCTCAGTACAGGTACAGCTTATGTCAAA
131 CACTATACAGTAACAAACGTATACTATATTCACATCTTCTCAGTACAGGTACAGCTTATGTCAAA
*
3564815 GCTTGCGC
196 GCTTGAGC
*
3564823 ATTCACAATTAAAAAAAGAAATGACCATTTATTCTGGGTGAAAACAAAAGAACCTACTATGGACA
1 ATTCACAATTAAAAAAAGAAATGACCAGTTATTCTGGGTGAAAACAAAAGAACCTACTATGGAC-
* * * *
3564888 AAATTAGTGGTCAAACATAAAACATAATACCCATTAGTTTGAGATTTAACCAGCAACAGTAAAAT
65 AAATTAGTGGCCAAACATAAAACAAAATACCAATTAGTTTGAGATTTAACCAGAAACAGTAAAAT
*
3564953 CCACTATACAGTAACAAACGTATACTATATTCACATCTTGTCAGTACAGGTACAGCTTATGTCAA
130 CCACTATACAGTAACAAACGTATACTATATTCACATCTTCTCAGTACAGGTACAGCTTATGTCAA
*
3565018 AGTTTGAGC
195 AGCTTGAGC
3565027 ATTCA
1 ATTCA
3565032 TGTTACAATG
Statistics
Matches: 197, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
203 63 0.32
204 134 0.68
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (203 bp):
ATTCACAATTAAAAAAAGAAATGACCAGTTATTCTGGGTGAAAACAAAAGAACCTACTATGGACA
AATTAGTGGCCAAACATAAAACAAAATACCAATTAGTTTGAGATTTAACCAGAAACAGTAAAATC
CACTATACAGTAACAAACGTATACTATATTCACATCTTCTCAGTACAGGTACAGCTTATGTCAAA
GCTTGAGC
Found at i:3569488 original size:19 final size:18
Alignment explanation
Indices: 3569454--3569501 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
3569444 CAAATTTAGA
3569454 ATAA-AAAA-TTATAAAT
1 ATAATAAAATTTATAAAT
*
3569470 ATAATAATATTTATCAAAT
1 ATAATAAAATTTAT-AAAT
3569489 ATAATAAAATTTA
1 ATAATAAAATTTA
3569502 ATAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 3 0.11
18 4 0.15
19 16 0.59
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAAAATTTATAAAT
Found at i:3575296 original size:26 final size:26
Alignment explanation
Indices: 3575228--3575288 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
3575218 GATGCCTTTT
*
3575228 TATTTTTGTCCATTTTTCCTGACCTC
1 TATTTTTGTCCATTTTTCCTGACCAC
*
3575254 TAATTTTGTCCATTTTTCCTGACCAC
1 TATTTTTGTCCATTTTTCCTGACCAC
*
3575280 TCTTTTTGT
1 TATTTTTGT
3575289 TAATTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.13, C:0.25, G:0.08, T:0.54
Consensus pattern (26 bp):
TATTTTTGTCCATTTTTCCTGACCAC
Found at i:3578972 original size:61 final size:62
Alignment explanation
Indices: 3578869--3578989 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 62
3578859 CTTCTGAGTT
* ***
3578869 CGACTCTTCCAACCCAGATGTGTTATATGGCTTTGACTCTCCACTTGACACTAGTGATGCTC
1 CGACTCTTCCAACACAGATGTGTTATATGGCTTTGACTCTCCACCCAACACTAGTGATGCTC
* *
3578931 CGACTCTTCGAACACAGATGTCG-TCT-TGGCTTTGACTCTCCACCCAACACTAGTGATGC
1 CGACTCTTCCAACACAGATGT-GTTATATGGCTTTGACTCTCCACCCAACACTAGTGATGC
3578990 AGCCTCTGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 30 0.58
62 21 0.40
63 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (62 bp):
CGACTCTTCCAACACAGATGTGTTATATGGCTTTGACTCTCCACCCAACACTAGTGATGCTC
Found at i:3596596 original size:2 final size:2
Alignment explanation
Indices: 3596589--3596615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3596579 AATTTAAATT
3596589 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3596616 TCTTACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3622067 original size:2 final size:2
Alignment explanation
Indices: 3622060--3622084 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3622050 ATCTGTCATT
3622060 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3622085 TATGGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3630254 original size:20 final size:20
Alignment explanation
Indices: 3630231--3630270 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3630221 AATCATAGCA
*
3630231 ATTTA-TTATTAATTATGTAT
1 ATTTATTTATAAATT-TGTAT
3630251 ATTTATTTATAAATTTGTAT
1 ATTTATTTATAAATTTGTAT
3630271 TAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTATTTATAAATTTGTAT
Found at i:3630496 original size:22 final size:23
Alignment explanation
Indices: 3630431--3630496 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
3630421 TGTATAAATA
*
3630431 TATTATATATACATATATT-TAATT
1 TATTA-ATAAACAT-TATTATAATT
* *
3630455 TATTTATAAACATTACTATAATT
1 TATTAATAAACATTATTATAATT
*
3630478 TA-TAATAAACTTTATTATA
1 TATTAATAAACATTATTATA
3630497 TGATTACATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 17 0.49
23 14 0.40
24 4 0.11
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATAAACATTATTATAATT
Found at i:3630801 original size:220 final size:218
Alignment explanation
Indices: 3630427--3631053 Score: 733
Period size: 207 Copynumber: 2.9 Consensus size: 218
3630417 TAATTGTATA
** *
3630427 AATATATTATATATACATATATTTAATTTATTTATAAACATTACTATAATTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTTTA
*
3630492 -TTATATGATTACATTTAATAACTTTTTATTAGTTATCATCC-TAGATTTTATAATATATTGTTT
66 TTTATATGATTACACTTAATAAC--TTTATTAGTTATCA-CCTTAGATTTTATAATATATTGTTT
* * * **
3630555 ATAATTAGTTATTGTTTATTCAAACTTTGATATTAAACATTATAGTATATAAGTTATGTTATTAA
128 ATAATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTTATTAA
*
3630620 TTTCATATATGTATCTATATAATAAAGC
193 TTTCATAT-T-TATCTATATAATAAAAC
* * *
3630648 CATATATTATATATACATATATTTAATTTATACATAAGA-ATTACAATAACTTATAATAGACTTT
1 AATATATTATATATACATATATTTAATTTATACATAA-ACATTACTATAACTTATAATAAACTTT
* * *
3630712 ATTTACATGATTACACTTAATAACTTAATTAGTTATCACCTTAGATTTTATAATATATTGTTTAC
65 ATTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAATATATTGTTTAT
* *
3630777 AATTAGTTATTATTTATACAAACTTTGATATAAAACATTTTAACATATAA-TT-TG-TA-TCA-T
130 AATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTTATTAATT
* *
3630837 T-A-ATTTATTTATATAATAAAAT
195 TCATATTTATCTATATAATAAAAC
*
3630859 AATATATTATATATAC----ATTTAATTTATACATAAATATTACTATAACTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTTTA
*********** * * * * *
3630920 TTTATATGGNNNNNNNNNNTAAGTTTATTAGCTATCACCTTAGATTTTATAAAACATTATTTATA
66 TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAATATATTGTTTATA
* * * *
3630985 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACACATAAGTCATATCATTAATTT
131 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTTATTAATTT
3631050 CATA
196 CATA
3631054 NNNNNNNNNN
Statistics
Matches: 347, Mismatches: 48, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
206 1 0.00
207 134 0.39
208 1 0.00
209 1 0.00
210 1 0.00
211 31 0.09
212 3 0.01
213 3 0.01
214 2 0.01
215 2 0.01
216 2 0.01
217 2 0.01
218 2 0.01
219 4 0.01
220 80 0.23
221 57 0.16
222 21 0.06
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.45
Consensus pattern (218 bp):
AATATATTATATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTTTA
TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAATATATTGTTTATA
ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTTATTAATTT
CATATTTATCTATATAATAAAAC
Found at i:3637679 original size:33 final size:33
Alignment explanation
Indices: 3637637--3637700 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
3637627 TAAAATTTTC
3637637 TTATATAAAAAAT-TTTGCTATTTCTAAAAAAAAA
1 TTATATAAAAAATATTT-CTATTT-TAAAAAAAAA
*
3637671 TTAT-TAAAAAATATTTTTATTTTAAAAAAA
1 TTATATAAAAAATATTTCTATTTTAAAAAAA
3637701 TTAAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 8 0.29
33 13 0.46
34 7 0.25
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (33 bp):
TTATATAAAAAATATTTCTATTTTAAAAAAAAA
Found at i:3638992 original size:13 final size:13
Alignment explanation
Indices: 3638974--3639000 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3638964 ATGAATAATA
3638974 AATATTATTTTTC
1 AATATTATTTTTC
3638987 AATATTATTTTTC
1 AATATTATTTTTC
3639000 A
1 A
3639001 TTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTATTTTTC
Found at i:3649150 original size:86 final size:85
Alignment explanation
Indices: 3648985--3649152 Score: 209
Period size: 85 Copynumber: 2.0 Consensus size: 85
3648975 CATCCGTTTC
* *
3648985 GTCCTGTTAAAACAGTTTATTCCTTCCCTGAACTTGAGACTGAGAGGATTTTCTATTTAGGCATA
1 GTCCTGTTAAAACAGTTTATCCCTTCCCTGAACTTGAGACTGAGAGGATTTTCAATTTAGGCATA
*
3649050 TCAAATAAAGCACAAAATTTT
66 -CAAATAAAACACAAAATTTT
* *
3649071 GTCCTGTT-AAACAGTTTATCCCTTCTCTGTACTTGAGACT-A-AGGAGTATTTCAATTTTAGGC
1 GTCCTGTTAAAACAGTTTATCCCTTCCCTGAACTTGAGACTGAGAGGA-T-TTTCAA-TTTAGGC
3649133 ATA-AAAGGTAAAACACAAAA
63 ATACAAA--TAAAACACAAAA
3649153 GTCTTTTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
83 4 0.06
84 5 0.07
85 34 0.47
86 29 0.40
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (85 bp):
GTCCTGTTAAAACAGTTTATCCCTTCCCTGAACTTGAGACTGAGAGGATTTTCAATTTAGGCATA
CAAATAAAACACAAAATTTT
Found at i:3660658 original size:25 final size:25
Alignment explanation
Indices: 3660630--3660693 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
3660620 ATATTAAAGT
3660630 ATAATATATAATATAAG-AATTAGAA
1 ATAATATATAATATAAGAAATTA-AA
* *
3660655 ATAAAATAAAATATAAGAAATTAAA
1 ATAATATATAATATAAGAAATTAAA
*
3660680 AT-TTATATAATATA
1 ATAATATATAATATA
3660694 GGTGAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 9 0.27
25 19 0.58
26 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (25 bp):
ATAATATATAATATAAGAAATTAAA
Found at i:3660692 original size:49 final size:49
Alignment explanation
Indices: 3660634--3660737 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 49
3660624 TAAAGTATAA
*
3660634 TATATAATATA-AGAATTAGAAA-TAAAATAAAATATA-AGAAATTAAAATT
1 TATATAATATAGAGAA--AGAAATTAAAATAAAATATATA-AAATAAAAATT
* *
3660683 TATATAATATAGGTGAAAGAAATTAAAATAAAATATATAATATAAAAATT
1 TATATAATATA-GAGAAAGAAATTAAAATAAAATATATAAAATAAAAATT
3660733 TATAT
1 TATAT
3660738 TAAAGAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
49 16 0.33
50 28 0.58
51 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (49 bp):
TATATAATATAGAGAAAGAAATTAAAATAAAATATATAAAATAAAAATT
Found at i:3664823 original size:16 final size:16
Alignment explanation
Indices: 3664800--3664838 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3664790 ATTTGGTAGG
*
3664800 TAAAAAAAACTTGAGAA
1 TAAAAAAAA-TAGAGAA
3664817 TAAAAAAAATAGAGAA
1 TAAAAAAAATAGAGAA
3664833 TAAAAA
1 TAAAAA
3664839 GAAAAAGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (16 bp):
TAAAAAAAATAGAGAA
Found at i:3664909 original size:27 final size:28
Alignment explanation
Indices: 3664879--3664944 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
3664869 ATTTATTTTT
*
3664879 ATTTTAT-A-TTATTTTTAAATATTAATA
1 ATTTTATAATTTA-TTTAAAATATTAATA
3664906 A-TTTATAATTTATTTAAAATATTAATA
1 ATTTTATAATTTATTTAAAATATTAATA
*
3664933 A-TTGATAATTTA
1 ATTTTATAATTTA
3664945 AAAATTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 5 0.14
27 27 0.77
28 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTATAATTTATTTAAAATATTAATA
Found at i:3665094 original size:152 final size:152
Alignment explanation
Indices: 3664923--3665318 Score: 571
Period size: 152 Copynumber: 2.6 Consensus size: 152
3664913 ATTTATTTAA
* *
3664923 AATATTAATAATTGATAATTTAAAAATTAATATTTTATTTATAATTTAAATATAATTATGATTAA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAATATTATTATGATTAA
* * * * *
3664988 AACATAAATAATTTTAATCAATTTTTAAATTTAAAATA-TA-TTTTATAATATATTATTAAAAAT
66 AATATAAATAATTTTAATTAATTTTTAAAATTAAAATATTATTTTTATAACATATAATTAAAAAT
* *
3665051 TTAAACTTTCTTCTTTTTTAAAAT
131 TAAAAATTT-TTC-TTTTTAAAAT
* * *
3665075 AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTGAAATGTTGTTATGATTAA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAATATTATTATGATTAA
* * *
3665140 AATATAATTAATTTTAATTAATTTTGAAAATTAAAATATTATTTTTATGACATATAATTAAAAAT
66 AATATAAATAATTTTAATTAATTTTTAAAATTAAAATATTATTTTTATAACATATAATTAAAAAT
*
3665205 TAAAAATTTTTCTTTTTATAAT
131 TAAAAATTTTTCTTTTTAAAAT
* *
3665227 AATACTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAATATTATTATGATTCA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAATATTATTATGATTAA
* * *
3665292 AATATTAATTATTTTAATTATTTTTTA
66 AATATAAATAATTTTAATTAATTTTTA
3665319 TAATATATAA
Statistics
Matches: 216, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
152 184 0.85
153 5 0.02
154 27 0.12
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (152 bp):
AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAATATTATTATGATTAA
AATATAAATAATTTTAATTAATTTTTAAAATTAAAATATTATTTTTATAACATATAATTAAAAAT
TAAAAATTTTTCTTTTTAAAAT
Found at i:3669730 original size:2 final size:2
Alignment explanation
Indices: 3669723--3669757 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3669713 AGGATGTGAC
3669723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3669758 GTAATGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3670647 original size:37 final size:35
Alignment explanation
Indices: 3670596--3670665 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 35
3670586 ATCAAACATT
3670596 TTAATAATTTTTTTAAAATTTCTCGTAACATTTCC
1 TTAATAATTTTTTTAAAATTTCTCGTAACATTTCC
*
3670631 TTAATATATTGTTTTTAAAATTTCTTGTAACATTT
1 TTAATA-ATT-TTTTTAAAATTTCTCGTAACATTT
3670666 ATAGTTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 6 0.19
36 3 0.09
37 23 0.72
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (35 bp):
TTAATAATTTTTTTAAAATTTCTCGTAACATTTCC
Found at i:3681933 original size:26 final size:25
Alignment explanation
Indices: 3681891--3681946 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
3681881 TATTATTTTT
* *
3681891 TAAAAAATTAAAATAAATATATAATA
1 TAAAAAATTAAAATAAAAATA-AAAA
* *
3681917 TAAAAAATTATATTAAAAATAAAAA
1 TAAAAAATTAAAATAAAAATAAAAA
3681942 TAAAA
1 TAAAA
3681947 TATATAAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAAATAAAAA
Found at i:3681966 original size:32 final size:33
Alignment explanation
Indices: 3681900--3681982 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
3681890 TTAAAAAATT
* * * *
3681900 AAAATAAATATATAATATAAAAAATTAT-ATTA
1 AAAATAAAAATAAAATATAAAAAACTATAATAA
* *
3681932 AAAATAAAAATAAAATATATAAGACTATAATAA
1 AAAATAAAAATAAAATATAAAAAACTATAATAA
*
3681965 AAAATAAAAATGAAATAT
1 AAAATAAAAATAAAATAT
3681983 CTGATATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 23 0.53
33 20 0.47
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAACTATAATAA
Found at i:3683148 original size:69 final size:70
Alignment explanation
Indices: 3683062--3683209 Score: 208
Period size: 74 Copynumber: 2.1 Consensus size: 70
3683052 CAATGCAATA
* * *
3683062 AAATTTTTAATT-TTTTTAAACTTGATTGCAGTTTGATTTAATGACAAACAAAATTAAGACATAA
1 AAATTCTTAATTATTTTAAAACTTGATTGCAGTTTGATTTAATGACAAACAAAATTAAAACATAA
*
3683126 TCTAT
66 TATAT
*
3683131 AAATTCTTAATTATTTTAAAAAAAACTTGATTGCAGTTTGATTTAATGACAAACAAGATTAAAAC
1 AAATTCTTAATTATTTT----AAAACTTGATTGCAGTTTGATTTAATGACAAACAAAATTAAAAC
3683196 ATAATATAT
62 ATAATATAT
3683205 AAATT
1 AAATT
3683210 ACTTCACGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
69 11 0.16
70 4 0.06
74 54 0.78
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (70 bp):
AAATTCTTAATTATTTTAAAACTTGATTGCAGTTTGATTTAATGACAAACAAAATTAAAACATAA
TATAT
Found at i:3683918 original size:44 final size:44
Alignment explanation
Indices: 3683868--3683952 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
3683858 CCGCCCATAA
* * *
3683868 ACTAGATGTATAAGAAATTATATTGTTATTTGTAGTTATTAAAT
1 ACTAGATCTATAAGAAATTATATTATTATTTATAGTTATTAAAT
*
3683912 ACTAGATCTATAGGAAATTATATTATTATTTATAGTTATTA
1 ACTAGATCTATAAGAAATTATATTATTATTTATAGTTATTA
3683953 TTATTAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (44 bp):
ACTAGATCTATAAGAAATTATATTATTATTTATAGTTATTAAAT
Found at i:3683953 original size:16 final size:14
Alignment explanation
Indices: 3683932--3683965 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
3683922 TAGGAAATTA
3683932 TATTATTATTTATAGT
1 TATTATTA-TTA-AGT
3683948 TATTATTATTAAGT
1 TATTATTATTAAGT
3683962 TATT
1 TATT
3683966 TTGAAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTATTATTAAGT
Found at i:3684221 original size:2 final size:2
Alignment explanation
Indices: 3684214--3684239 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3684204 GAGAAAATTA
3684214 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
3684240 TTACAGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3686593 original size:70 final size:70
Alignment explanation
Indices: 3686480--3686620 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
3686470 GAAGAAGGTC
*
3686480 TTGGATTTCCCCTTCTTGGACCAATGTGGATATGGAAGCTTAGTTTGCCCAAGCTCTGCAACGTT
1 TTGGATTTCCCCTTCTTGGACCAATATGGATATGGAAGCTTAGTTTGCCCAAGCTCTGCAACGTT
3686545 ATCCA
66 ATCCA
*
3686550 TTGGATTTCCCCTTCTTGGACCAATATGGATATGGCAGCTTAGTTTGCCCAAGCTCTGCAACGTT
1 TTGGATTTCCCCTTCTTGGACCAATATGGATATGGAAGCTTAGTTTGCCCAAGCTCTGCAACGTT
3686615 ATCCA
66 ATCCA
3686620 T
1 T
3686621 ATCCTTGAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (70 bp):
TTGGATTTCCCCTTCTTGGACCAATATGGATATGGAAGCTTAGTTTGCCCAAGCTCTGCAACGTT
ATCCA
Found at i:3692645 original size:29 final size:31
Alignment explanation
Indices: 3692612--3692682 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 31
3692602 TATTAATTAT
3692612 AAAAATTTATTTGATTAAA-AAT-AAAAATA
1 AAAAATTTATTTGATTAAATAATAAAAAATA
*
3692641 TAAAA---ATTTGATTAAATGTAATAAAAAATA
1 AAAAATTTATTTGATTAAA--TAATAAAAAATA
3692671 AAAAATTTATTT
1 AAAAATTTATTT
3692683 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
26 11 0.33
29 7 0.21
30 11 0.33
33 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (31 bp):
AAAAATTTATTTGATTAAATAATAAAAAATA
Found at i:3692645 original size:30 final size:29
Alignment explanation
Indices: 3692609--3692684 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
3692599 AATTATTAAT
*
3692609 TATAAAAATTTATTTGAT-TAAAAATAAAAA
1 TATAAAAATTTATTTAATGT-AAAA-AAAAA
* *
3692639 TATAAAAATTTGATTAAATGTAATAAAAAA
1 TATAAAAATTT-ATTTAATGTAAAAAAAAA
3692669 TA-AAAAATTTATTTAA
1 TATAAAAATTTATTTAA
3692685 AATTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.12
29 8 0.20
30 18 0.45
31 8 0.20
32 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (29 bp):
TATAAAAATTTATTTAATGTAAAAAAAAA
Found at i:3696151 original size:28 final size:29
Alignment explanation
Indices: 3696088--3696151 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
3696078 AAATATTACG
3696088 CATATTGCCCAAAAAAAAACTTGATATGA
1 CATATTGCCCAAAAAAAAACTTGATATGA
* * * *
3696117 CACATTGCCC-CAAAAAACCTTGATATGC
1 CATATTGCCCAAAAAAAAACTTGATATGA
3696145 CATATTG
1 CATATTG
3696152 TGCAGATCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (29 bp):
CATATTGCCCAAAAAAAAACTTGATATGA
Found at i:3698594 original size:13 final size:12
Alignment explanation
Indices: 3698578--3698620 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
3698568 AAAAATAAAA
3698578 ATATTACATAATC
1 ATATTACAT-ATC
*
3698591 ATATTATCATGTC
1 ATATTA-CATATC
3698604 ATATTAACATATC
1 ATATT-ACATATC
3698617 ATAT
1 ATAT
3698621 CATTACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (12 bp):
ATATTACATATC
Found at i:3698721 original size:29 final size:29
Alignment explanation
Indices: 3698699--3698753 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3698689 TATTTAATTT
3698699 AAAAT-AAAATATAAAATTTTATTTAAAC
1 AAAATAAAAATATAAAATTTTATTTAAAC
* *
3698727 ACAATAAAAATATAAAATTTAATTTAA
1 AAAATAAAAATATAAAATTTTATTTAA
3698754 CTTTTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATAAAAATATAAAATTTTATTTAAAC
Found at i:3698722 original size:24 final size:26
Alignment explanation
Indices: 3698690--3698754 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 26
3698680 AATCAAATTT
3698690 ATTTAATTTAA-AAT-AAAATATAAA
1 ATTTAATTTAACAATAAAAATATAAA
*
3698714 ATTTTATTTAAACACAATAAAAATATAAA
1 ATTTAATTT--A-ACAATAAAAATATAAA
3698743 ATTTAATTTAAC
1 ATTTAATTTAAC
3698755 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 8 0.24
26 3 0.09
27 2 0.06
28 3 0.09
29 18 0.53
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTTAATTTAACAATAAAAATATAAA
Found at i:3707791 original size:23 final size:21
Alignment explanation
Indices: 3707756--3707798 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
3707746 CTGTCCATTA
3707756 TATTTAATTAAAATTAATTTT
1 TATTTAATTAAAATTAATTTT
3707777 TATTATAATTAAAAATTAATTT
1 TATT-TAATT-AAAATTAATTT
3707799 CATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAATTAAAATTAATTTT
Found at i:3707811 original size:19 final size:19
Alignment explanation
Indices: 3707761--3707822 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 19
3707751 CATTATATTT
*
3707761 AATTAAAATTAATTTTTATTA
1 AATTAAAATTAA-TTTCA-TA
3707782 TAATTAAAAATTAATTTCATA
1 -AATT-AAAATTAATTTCATA
*
3707803 AATTAAAATT-AGTTCATA
1 AATTAAAATTAATTTCATA
3707821 AA
1 AA
3707823 AATAAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 9 0.24
19 6 0.16
20 4 0.11
21 2 0.05
22 8 0.22
23 8 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTAAAATTAATTTCATA
Found at i:3710230 original size:20 final size:20
Alignment explanation
Indices: 3710205--3710245 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3710195 AAATTCTAAC
3710205 TTTTCCATACATGGGAAGTT
1 TTTTCCATACATGGGAAGTT
3710225 TTTTCCATACATGGGAAGTT
1 TTTTCCATACATGGGAAGTT
3710245 T
1 T
3710246 ATTATAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTTCCATACATGGGAAGTT
Found at i:3723464 original size:27 final size:27
Alignment explanation
Indices: 3723405--3723695 Score: 210
Period size: 27 Copynumber: 10.7 Consensus size: 27
3723395 TGATAATTTT
* *
3723405 TTAAAAA-TTAATTTTTATATATTATG
1 TTAAAAATTTAATTATTATATATTATA
* *
3723431 TTAAAAAATATAATTATTATATGTTATA
1 TT-AAAAATTTAATTATTATATATTATA
* * *
3723459 TTAAAATTTTAATTATTATATATCATG
1 TTAAAAATTTAATTATTATATATTATA
* * *
3723486 TTAAAAAATATAATTATTATAAATTATG
1 TT-AAAAATTTAATTATTATATATTATA
* * * * *
3723514 TTAAAGATTTAGTTGTTATACATCATA
1 TTAAAAATTTAATTATTATATATTATA
* * * *
3723541 TTAAAAAATATAATTATTACA-AGTCATG
1 TT-AAAAATTTAATTATTATATA-TTATA
* * *
3723569 TTAAAAATTTAGTTATTGTATATTATG
1 TTAAAAATTTAATTATTATATATTATA
* ** *
3723596 TTAAAAATTTAATTATTACACGTTGTA
1 TTAAAAATTTAATTATTATATATTATA
* ** *
3723623 TTAAAAAATATAATTAACATAAATTA-A
1 TT-AAAAATTTAATTATTATATATTATA
* *
3723650 GTTGATAATTTAATTATTATATATTATA
1 -TTAAAAATTTAATTATTATATATTATA
*
3723678 TTAAAAATTTAACTATTA
1 TTAAAAATTTAATTATTA
3723696 CACGTCATAA
Statistics
Matches: 202, Mismatches: 54, Indels: 17
0.74 0.20 0.06
Matches are distributed among these distances:
26 2 0.01
27 121 0.60
28 79 0.39
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (27 bp):
TTAAAAATTTAATTATTATATATTATA
Found at i:3723594 original size:82 final size:83
Alignment explanation
Indices: 3723407--3723704 Score: 241
Period size: 82 Copynumber: 3.6 Consensus size: 83
3723397 ATAATTTTTT
* * * * ** * * *
3723407 AAAAAT-TAATTTTTATATATTATGTTAAAAAATATAATTATTATATGTTATATT-AAAATTTTA
1 AAAAATATAATTATTATAAATTATGTT-AAAAATTTAATTATTACACATCATATTAAAAAATATA
*
3723470 ATTATTATATATCATGTTA
65 ATTATTACATATCATGTTA
* * * *
3723489 AAAAATATAATTATTATAAATTATGTTAAAGATTTAGTTGTTATACATCATATTAAAAAATATAA
1 AAAAATATAATTATTATAAATTATGTTAAAAATTTAATTATTACACATCATATTAAAAAATATAA
3723554 TTATTACA-AGTCATGTT-
66 TTATTACATA-TCATGTTA
* * * * * **
3723571 AAAAATTTAGTTATTGTATATTATGTTAAAAATTTAATTATTACACGTTGTATTAAAAAATATAA
1 AAAAATATAATTATTATAAATTATGTTAAAAATTTAATTATTACACATCATATTAAAAAATATAA
* *
3723636 TTA--ACATAAATTAAGTT-
66 TTATTACAT--ATCATGTTA
* * * * * * *
3723653 GATAATTTAATTATTATATATTATATTAAAAATTTAACTATTACACGTCATA
1 AAAAATATAATTATTATAAATTATGTTAAAAATTTAATTATTACACATCATA
3723705 ATAAGATTAT
Statistics
Matches: 177, Mismatches: 33, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
80 3 0.02
82 133 0.75
83 41 0.23
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (83 bp):
AAAAATATAATTATTATAAATTATGTTAAAAATTTAATTATTACACATCATATTAAAAAATATAA
TTATTACATATCATGTTA
Found at i:3723631 original size:55 final size:55
Alignment explanation
Indices: 3723405--3723629 Score: 247
Period size: 55 Copynumber: 4.1 Consensus size: 55
3723395 TGATAATTTT
* * * * *
3723405 TTAAAAA-TTAATTTTTATATATTATGTTAAAAAATATAATTATTATATGTTATA
1 TTAAAAATTTAGTTATTATATATCATGTTAAAAAATATAATTATTACAAGTTATA
* * * * *
3723459 TTAAAATTTTAATTATTATATATCATGTTAAAAAATATAATTATTATAAATTATG
1 TTAAAAATTTAGTTATTATATATCATGTTAAAAAATATAATTATTACAAGTTATA
* * * * * *
3723514 TTAAAGATTTAGTTGTTATACATCATATTAAAAAATATAATTATTACAAGTCATG
1 TTAAAAATTTAGTTATTATATATCATGTTAAAAAATATAATTATTACAAGTTATA
* * * * *
3723569 TTAAAAATTTAGTTATTGTATATTATGTT-AAAAATTTAATTATTACACGTTGTA
1 TTAAAAATTTAGTTATTATATATCATGTTAAAAAATATAATTATTACAAGTTATA
3723623 TTAAAAA
1 TTAAAAA
3723630 ATATAATTAA
Statistics
Matches: 144, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
54 33 0.23
55 111 0.77
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (55 bp):
TTAAAAATTTAGTTATTATATATCATGTTAAAAAATATAATTATTACAAGTTATA
Found at i:3726939 original size:2 final size:2
Alignment explanation
Indices: 3726932--3726976 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3726922 AGAGAATTGT
3726932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3726974 TA T
1 TA T
3726977 TCTTAACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3737417 original size:142 final size:142
Alignment explanation
Indices: 3737161--3737447 Score: 520
Period size: 142 Copynumber: 2.0 Consensus size: 142
3737151 TTTTTTGTGG
* *
3737161 TATCATTGAAAATGAGGTAAAACATGAGAAATTTTTTAACTTTATTGATTCTATTTGTCTTTCTA
1 TATCATTGAAAATGAGGTAAAACATGAGAAATTTTTGAACTTTATTGATTCTATTTGTCTTGCTA
* * *
3737226 TGAAACTGTTTGTCAATTCCATCTATTTGTCTATGTGAAGTTTAAACTTTATTTTGAACTTCACT
66 TGAAACTGTGTATCAATTCCATCTATTTATCTATGTGAAGTTTAAACTTTATTTTGAACTTCACT
3737291 TAATATAATTCT
131 TAATATAATTCT
3737303 TATCATTGAAAATGAGGTAAAACATGAGAAATTTTTGAACTTTATTGATTCTATTTGTCTTGCTA
1 TATCATTGAAAATGAGGTAAAACATGAGAAATTTTTGAACTTTATTGATTCTATTTGTCTTGCTA
*
3737368 TGAAACTGTGTATCAATTCCATCTGTTTATCTATGTGAAGTTTAAACTTTATTTTGAACTTCACT
66 TGAAACTGTGTATCAATTCCATCTATTTATCTATGTGAAGTTTAAACTTTATTTTGAACTTCACT
3737433 TAATATAATTCT
131 TAATATAATTCT
3737445 TAT
1 TAT
3737448 GGATGATATG
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (142 bp):
TATCATTGAAAATGAGGTAAAACATGAGAAATTTTTGAACTTTATTGATTCTATTTGTCTTGCTA
TGAAACTGTGTATCAATTCCATCTATTTATCTATGTGAAGTTTAAACTTTATTTTGAACTTCACT
TAATATAATTCT
Found at i:3737657 original size:24 final size:24
Alignment explanation
Indices: 3737630--3737686 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
3737620 AGAGTGAGCC
3737630 TGGACGTGGAGGAGGCCGTGGTGG
1 TGGACGTGGAGGAGGCCGTGGTGG
3737654 TGGACGTGGAGGAGGCCGTGGTGG
1 TGGACGTGGAGGAGGCCGTGGTGG
3737678 TGGACGTGG
1 TGGACGTGG
3737687 TGGCAGTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.12, G:0.58, T:0.18
Consensus pattern (24 bp):
TGGACGTGGAGGAGGCCGTGGTGG
Found at i:3737661 original size:12 final size:12
Alignment explanation
Indices: 3737630--3737689 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
3737620 AGAGTGAGCC
*
3737630 TGGACGTGGAGG
1 TGGACGTGGTGG
* *
3737642 AGGCCGTGGTGG
1 TGGACGTGGTGG
*
3737654 TGGACGTGGAGG
1 TGGACGTGGTGG
* *
3737666 AGGCCGTGGTGG
1 TGGACGTGGTGG
3737678 TGGACGTGGTGG
1 TGGACGTGGTGG
3737690 CAGTGGGTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.12, C:0.12, G:0.58, T:0.18
Consensus pattern (12 bp):
TGGACGTGGTGG
Found at i:3746042 original size:14 final size:15
Alignment explanation
Indices: 3746013--3746042 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3746003 AAATATTAAT
3746013 AGAAAAAATTATCAA
1 AGAAAAAATTATCAA
3746028 AGAAAAAATTA-CAA
1 AGAAAAAATTATCAA
3746042 A
1 A
3746043 TGTCCTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (15 bp):
AGAAAAAATTATCAA
Found at i:3754295 original size:17 final size:17
Alignment explanation
Indices: 3754262--3754295 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3754252 ATTATTATTT
*
3754262 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
3754279 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
3754296 ATAACATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:3754732 original size:34 final size:34
Alignment explanation
Indices: 3754655--3754758 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 34
3754645 TATTTATGAC
* *
3754655 AATATTAAATTATAAATAAAATATTAGTATTTAAA
1 AATATTAATTTAT-AATAAAATATTAATATTTAAA
* *
3754690 AATCTTAATTTATAATAAAATATTAATATTTAAC
1 AATATTAATTTATAATAAAATATTAATATTTAAA
* *
3754724 CATATTAATGTTTTAATAATTAATCATTAATATTT
1 AATATTAAT-TTATAATAA--AAT-ATTAATATTT
3754759 TAATTAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 26 0.45
35 19 0.33
37 3 0.05
38 10 0.17
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
AATATTAATTTATAATAAAATATTAATATTTAAA
Found at i:3754746 original size:24 final size:22
Alignment explanation
Indices: 3754712--3754762 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
3754702 TAATAAAATA
* *
3754712 TTAATATTTAACCATATTAATGTT
1 TTAATAATTAACC--ATTAATATT
*
3754736 TTAATAATTAATCATTAATATT
1 TTAATAATTAACCATTAATATT
3754758 TTAAT
1 TTAAT
3754763 TAAATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
24 11 0.46
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAATAATTAACCATTAATATT
Found at i:3766490 original size:27 final size:27
Alignment explanation
Indices: 3766418--3766492 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
3766408 GAGAGCTTAT
* * * *
3766418 TGATGGGCTTGGTGCCATAGGGGTAGA
1 TGATGGGCTAGGAGCCATTGGAGTAGA
* * * *
3766445 TGACGGGCTCGGGGCCATTGGAGTTGA
1 TGATGGGCTAGGAGCCATTGGAGTAGA
3766472 TGATGGGCTAGGAGCCATTGG
1 TGATGGGCTAGGAGCCATTGG
3766493 GCTTGTTGGA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.17, C:0.15, G:0.44, T:0.24
Consensus pattern (27 bp):
TGATGGGCTAGGAGCCATTGGAGTAGA
Found at i:3795957 original size:51 final size:51
Alignment explanation
Indices: 3795902--3796053 Score: 133
Period size: 51 Copynumber: 3.0 Consensus size: 51
3795892 GCTGGCAGCA
*
3795902 ATGCAACAACAGGCCTTGCTTGAGAAAGCTGAAGCTGAGAAAATAGCAAAC
1 ATGCAACAACAAGCCTTGCTTGAGAAAGCTGAAGCTGAGAAAATAGCAAAC
*****************
3795953 ATGCAACAACAAGCCNNNNNNNNNNNNNNNNNAGCTGAGAAAATAGCAAAC
1 ATGCAACAACAAGCCTTGCTTGAGAAAGCTGAAGCTGAGAAAATAGCAAAC
*
3796004 ATGCAACAACAAGCCTTGCTTGAGAAAGCTGAAGCGGAGAAAATAGCAAA
1 ATGCAACAACAAGCCTTGCTTGAGAAAGCTGAAGCTGAGAAAATAGCAAA
3796054 TACGCATCAA
Statistics
Matches: 65, Mismatches: 36, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.12
Consensus pattern (51 bp):
ATGCAACAACAAGCCTTGCTTGAGAAAGCTGAAGCTGAGAAAATAGCAAAC
Found at i:3796721 original size:16 final size:16
Alignment explanation
Indices: 3796702--3796735 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3796692 TTCGATAAAT
3796702 AAATTA-TTAATTATAA
1 AAATTATTTAATT-TAA
3796718 AAATTATTTAATTTAA
1 AAATTATTTAATTTAA
3796734 AA
1 AA
3796736 TAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTATTTAATTTAA
Found at i:3799495 original size:15 final size:15
Alignment explanation
Indices: 3799475--3799532 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
3799465 CTCCTAAATG
3799475 TTTTGGAGGGAAAAC
1 TTTTGGAGGGAAAAC
3799490 TTTTGGAGGGAAAAGC
1 TTTTGGAGGGAAAA-C
3799506 -TTTGGAGGGAAAAC
1 TTTTGGAGGGAAAAC
3799520 TTTTGGAGGGAAA
1 TTTTGGAGGGAAA
3799533 TGTGGGGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.02
15 39 0.95
16 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (15 bp):
TTTTGGAGGGAAAAC
Found at i:3799512 original size:30 final size:30
Alignment explanation
Indices: 3799476--3799532 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
3799466 TCCTAAATGT
3799476 TTTGGAGGGAAAACTTTTGGAGGGAAAAGC
1 TTTGGAGGGAAAACTTTTGGAGGGAAAAGC
3799506 TTTGGAGGGAAAACTTTTGGAGGGAAA
1 TTTGGAGGGAAAACTTTTGGAGGGAAA
3799533 TGTGGGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.37, T:0.25
Consensus pattern (30 bp):
TTTGGAGGGAAAACTTTTGGAGGGAAAAGC
Found at i:3803417 original size:13 final size:13
Alignment explanation
Indices: 3803375--3803432 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
3803365 AAATTCATAT
*
3803375 AAATAAATTTTAA
1 AAATTAATTTTAA
**
3803388 AAATT-ATTCAAA
1 AAATTAATTTTAA
3803400 AAATTAATTTTAA
1 AAATTAATTTTAA
* *
3803413 TAATTTATTTTAA
1 AAATTAATTTTAA
3803426 AAATTAA
1 AAATTAA
3803433 CTAGTATAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTAATTTTAA
Found at i:3803420 original size:26 final size:25
Alignment explanation
Indices: 3803375--3803432 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
3803365 AAATTCATAT
*
3803375 AAATAAATTTTAAAAATTATTCAAA
1 AAATTAATTTTAAAAATTATTCAAA
* **
3803400 AAATTAATTTTAATAATTTATTTTAA
1 AAATTAATTTTAA-AAATTATTCAAA
3803426 AAATTAA
1 AAATTAA
3803433 CTAGTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATTAATTTTAAAAATTATTCAAA
Found at i:3805228 original size:15 final size:15
Alignment explanation
Indices: 3805208--3805238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3805198 GTGTGGAATG
3805208 GGGCCGCTCCTATGA
1 GGGCCGCTCCTATGA
*
3805223 GGGCCGCTTCTATGA
1 GGGCCGCTCCTATGA
3805238 G
1 G
3805239 AATTGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.23
Consensus pattern (15 bp):
GGGCCGCTCCTATGA
Found at i:3810047 original size:15 final size:15
Alignment explanation
Indices: 3810027--3810057 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3810017 ACCATCTCTC
3810027 TTTCTTTCTCTTTCT
1 TTTCTTTCTCTTTCT
3810042 TTTCTTTCTCTTTCT
1 TTTCTTTCTCTTTCT
3810057 T
1 T
3810058 CCCATTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTCTCTTTCT
Found at i:3819518 original size:23 final size:25
Alignment explanation
Indices: 3819473--3819519 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3819463 AAATTTTATT
*
3819473 TATTTATTATATTCAATCAAATATA
1 TATTTATTATATTAAATCAAATATA
*
3819498 TATTT-TTTTATTAAAT-AAATAT
1 TATTTATTATATTAAATCAAATAT
3819520 TTATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTATTATATTAAATCAAATATA
Found at i:3821113 original size:16 final size:16
Alignment explanation
Indices: 3821094--3821128 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3821084 TTGAATTTTA
*
3821094 AAAATATTAAAAAATT
1 AAAATATTAAAAAAAT
*
3821110 AAAATTTTAAAAAAAT
1 AAAATATTAAAAAAAT
3821126 AAA
1 AAA
3821129 CACAAGAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTAAAAAAAT
Found at i:3837996 original size:34 final size:32
Alignment explanation
Indices: 3837950--3838037 Score: 83
Period size: 34 Copynumber: 2.6 Consensus size: 32
3837940 GTCATAGAAT
3837950 TTTATTTG-ATTTAAAATAAAAATATGATTCAAAG-
1 TTTA-TTGAATTTAAAATAAAAATAT-A-T-AAAGA
3837984 TTTATTGAATTTAAAA-AAGAAATATATAAAGA
1 TTTATTGAATTTAAAATAA-AAATATATAAAGA
*
3838016 TTTGATTGAATATAATAATAAA
1 TTT-ATTGAATTTAA-AATAAA
3838038 TAAACTTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
31 4 0.09
32 4 0.09
33 16 0.34
34 21 0.45
35 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (32 bp):
TTTATTGAATTTAAAATAAAAATATATAAAGA
Found at i:3842700 original size:42 final size:42
Alignment explanation
Indices: 3842646--3842729 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
3842636 AACACCCAGC
* * *
3842646 TACATCATGGTACACTGCTTGGTGACATATATAAAACACTAG
1 TACATCACGGTACACTGCTTCGTAACATATATAAAACACTAG
*
3842688 TACATCACGGTACATTGCTTCGTAACATATATAAAACACTAG
1 TACATCACGGTACACTGCTTCGTAACATATATAAAACACTAG
3842730 AAGCCACGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (42 bp):
TACATCACGGTACACTGCTTCGTAACATATATAAAACACTAG
Found at i:3848629 original size:46 final size:46
Alignment explanation
Indices: 3848572--3848666 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
3848562 GTCCCTACTG
3848572 TAGTTCTTGTGGCGGCTATACTGATTGCAACAGCCACCTACCAGGC
1 TAGTTCTTGTGGCGGCTATACTGATTGCAACAGCCACCTACCAGGC
*
3848618 TAGTTCTTGTGGTGGCTATACTGATTGCAACAGCCACCTACCAGGC
1 TAGTTCTTGTGGCGGCTATACTGATTGCAACAGCCACCTACCAGGC
3848664 TAG
1 TAG
3848667 ACTTAGCCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.27
Consensus pattern (46 bp):
TAGTTCTTGTGGCGGCTATACTGATTGCAACAGCCACCTACCAGGC
Found at i:3896047 original size:44 final size:44
Alignment explanation
Indices: 3895992--3896085 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
3895982 ATAACACATT
*
3895992 AAACAACAGAGTAATAGACATGTCATTCAAGTGACCATAACTAC
1 AAACAACAGAGTAATAGACATGCCATTCAAGTGACCATAACTAC
* *
3896036 AAACCACAGAGTAATAGACATGCCATTCAGGTGACCATAACTAC
1 AAACAACAGAGTAATAGACATGCCATTCAAGTGACCATAACTAC
3896080 AAACAA
1 AAACAA
3896086 AAAAAAAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.18
Consensus pattern (44 bp):
AAACAACAGAGTAATAGACATGCCATTCAAGTGACCATAACTAC
Found at i:3928672 original size:16 final size:17
Alignment explanation
Indices: 3928651--3928685 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3928641 GAGAGGGAAA
*
3928651 GGAGGAGG-GATTTGAG
1 GGAGGAGGAGAATTGAG
3928667 GGAGGAGGAGAATTGAG
1 GGAGGAGGAGAATTGAG
3928684 GG
1 GG
3928686 GAGTGGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (17 bp):
GGAGGAGGAGAATTGAG
Found at i:3953606 original size:16 final size:16
Alignment explanation
Indices: 3953569--3953606 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
3953559 AACCTAGAAT
3953569 AATAAACAAAATAAAA
1 AATAAACAAAATAAAA
3953585 ACATAAA-AAAATAAATA
1 A-ATAAACAAAATAAA-A
3953602 AATAA
1 AATAA
3953607 TTTAAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (16 bp):
AATAAACAAAATAAAA
Found at i:3964470 original size:39 final size:39
Alignment explanation
Indices: 3964388--3964471 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
3964378 AGCTAGAAGG
* * *
3964388 AGTAACCAAAGGTTAAGCTCCAAATCATACTTACAAAAG
1 AGTAATCAAAGGTTAACCTCCAAATCATACTTACAAAAC
**
3964427 AGTAATCAAAGGTTAACCTCCAAATCATACTTATGAAAC
1 AGTAATCAAAGGTTAACCTCCAAATCATACTTACAAAAC
3964466 AGTAAT
1 AGTAAT
3964472 GTAATTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (39 bp):
AGTAATCAAAGGTTAACCTCCAAATCATACTTACAAAAC
Found at i:3969790 original size:2 final size:2
Alignment explanation
Indices: 3969783--3969810 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3969773 ACAGCAAATT
3969783 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
3969811 AGTAAAAGGA
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):
TA
Found at i:3971466 original size:23 final size:23
Alignment explanation
Indices: 3971440--3971492 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3971430 TGTTAAATGG
3971440 ATTAAATAAA-AATAATTTTAAAA
1 ATTAAA-AAATAATAATTTTAAAA
*
3971463 ATTAAAAAATTATAATTTTAAAA
1 ATTAAAAAATAATAATTTTAAAA
3971486 A-TAAAAA
1 ATTAAAAA
3971493 CTAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTAAAAAATAATAATTTTAAAA
Found at i:3972363 original size:27 final size:27
Alignment explanation
Indices: 3972311--3972363 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3972301 TATTTGATTA
** *
3972311 TTATATTTAATTTTAATTTATGAATAT
1 TTATATTTAATTTTAATCGATAAATAT
*
3972338 TTATATTTAATTTTGATCGATAAATA
1 TTATATTTAATTTTAATCGATAAATA
3972364 AAAATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (27 bp):
TTATATTTAATTTTAATCGATAAATAT
Found at i:3976322 original size:29 final size:27
Alignment explanation
Indices: 3976288--3976404 Score: 78
Period size: 29 Copynumber: 4.0 Consensus size: 27
3976278 TAAAAAATAT
3976288 TTAAATAAGTTTTTTATTATTTTATTATA
1 TTAAATAA-TTTTTTATTATTTTATTA-A
*
3976317 TTAAATTAA-ATTTTA-TATTTTTATTTAAA
1 TTAAA-TAATTTTTTATTA-TTTTA-TT-AA
* * *
3976346 TAAAATAATTTTTTATAATTGATAATTAA
1 TTAAATAATTTTTTATTATT--TTATTAA
3976375 TTAAA-AATATTATTTATTATTTTATATAA
1 TTAAATAAT-TT-TTTATTATTTTAT-TAA
3976404 T
1 T
3976405 GTAATATTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
27 2 0.03
28 19 0.28
29 31 0.45
30 15 0.22
31 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAATAATTTTTTATTATTTTATTAA
Found at i:3979132 original size:18 final size:18
Alignment explanation
Indices: 3979084--3979132 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 18
3979074 TTAATATGAT
3979084 ATTAATTATATATTAATTA
1 ATTAATTAT-TATTAATTA
3979103 ATT--TT-TTA-TAATTA
1 ATTAATTATTATTAATTA
3979117 ATTAATTATTATTAAT
1 ATTAATTATTATTAAT
3979133 CAAAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 3 0.12
17 5 0.19
18 4 0.15
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTAATTATTATTAATTA
Found at i:3982042 original size:3 final size:3
Alignment explanation
Indices: 3982034--3982071 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3982024 TTCGGAGAAG
3982034 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA AC
3982072 GACAGCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3987909 original size:3 final size:3
Alignment explanation
Indices: 3987903--3987946 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
3987893 GGAGGAGGAG
* * * *
3987903 GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA GAG GAA GAG GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3987947 TGAGCATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (3 bp):
GAA
Done.