Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 10 of 143
Found at i:3068942 original size:18 final size:18
Alignment explanation
Indices: 3068915--3068954 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3068905 ATTACTTTTC
*
3068915 AAAAGTACTTTTAAGACA
1 AAAAGCACTTTTAAGACA
* *
3068933 AAAAGCACTTTTGAGATA
1 AAAAGCACTTTTAAGACA
3068951 AAAA
1 AAAA
3068955 TAAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (18 bp):
AAAAGCACTTTTAAGACA
Found at i:3069823 original size:7 final size:7
Alignment explanation
Indices: 3069811--3069850 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
3069801 CACCAGGTCG
3069811 TATATAA
1 TATATAA
3069818 TATATAA
1 TATATAA
3069825 TATATAA
1 TATATAA
3069832 TATATAA
1 TATATAA
3069839 TATATAA
1 TATATAA
3069846 TATAT
1 TATAT
3069851 GATTATGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:3077895 original size:27 final size:27
Alignment explanation
Indices: 3077833--3077898 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
3077823 CAGAATGCAT
* *
3077833 CACAAAGGCTATTCATTTAGAGTGTGC
1 CACAAAGGTTGTTCATTTAGAGTGTGC
3077860 CACAAAGGTTGTTCATTTAGAGTGTGC
1 CACAAAGGTTGTTCATTTAGAGTGTGC
*
3077887 CATAAAGGTTGT
1 CACAAAGGTTGT
3077899 AAATTCATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (27 bp):
CACAAAGGTTGTTCATTTAGAGTGTGC
Found at i:3077910 original size:27 final size:27
Alignment explanation
Indices: 3077851--3077920 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
3077841 CTATTCATTT
** *
3077851 AGAGTGTGCCACAAAGGTTGTTCATTT
1 AGAGTGTGCCACAAAGGTTGTAAATTC
*
3077878 AGAGTGTGCCATAAAGGTTGTAAATTC
1 AGAGTGTGCCACAAAGGTTGTAAATTC
* *
3077905 ATAGTGCGCCACAAAG
1 AGAGTGTGCCACAAAG
3077921 ACTGTTCTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (27 bp):
AGAGTGTGCCACAAAGGTTGTAAATTC
Found at i:3107704 original size:15 final size:15
Alignment explanation
Indices: 3107680--3107799 Score: 80
Period size: 15 Copynumber: 8.1 Consensus size: 15
3107670 TGGTGGTGGG
*
3107680 GTAGCTGGAGGAGGA
1 GTAGCCGGAGGAGGA
* *
3107695 GTAGCAGGAGGGGGA
1 GTAGCCGGAGGAGGA
* * * *
3107710 GAAGCAGGTGGTGGA
1 GTAGCCGGAGGAGGA
*
3107725 GTAGCCGGAGGTGGA
1 GTAGCCGGAGGAGGA
* *
3107740 GAAGCCGGTGG-GGA
1 GTAGCCGGAGGAGGA
* * * *
3107754 GTTGCGGGAGGTGGG
1 GTAGCCGGAGGAGGA
* *
3107769 GTAGCTGGGGGAGGA
1 GTAGCCGGAGGAGGA
*
3107784 GTAGCCGGTGGAGGA
1 GTAGCCGGAGGAGGA
3107799 G
1 G
3107800 AAGCTGGTGG
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
14 10 0.12
15 72 0.88
ACGTcount: A:0.21, C:0.09, G:0.57, T:0.12
Consensus pattern (15 bp):
GTAGCCGGAGGAGGA
Found at i:3107726 original size:30 final size:30
Alignment explanation
Indices: 3107682--3107812 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 30
3107672 GTGGTGGGGT
* * *
3107682 AGCTGGAGGAGGAGTAGCAGGAGGGGGAGA
1 AGCTGGTGGTGGAGTAGCCGGAGGGGGAGA
* *
3107712 AGCAGGTGGTGGAGTAGCCGGAGGTGGAGA
1 AGCTGGTGGTGGAGTAGCCGGAGGGGGAGA
* * * *
3107742 AGCCGGTGG-GGAGTTGCGGGAGGTGGG-GT
1 AGCTGGTGGTGGAGTAGCCGGAGG-GGGAGA
* * * *
3107771 AGCTGGGGGAGGAGTAGCCGGTGGAGGAGA
1 AGCTGGTGGTGGAGTAGCCGGAGGGGGAGA
3107801 AGCTGGTGGTGG
1 AGCTGGTGGTGG
3107813 GGAGCTAACG
Statistics
Matches: 79, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 22 0.28
30 57 0.72
ACGTcount: A:0.21, C:0.09, G:0.57, T:0.13
Consensus pattern (30 bp):
AGCTGGTGGTGGAGTAGCCGGAGGGGGAGA
Found at i:3107808 original size:15 final size:15
Alignment explanation
Indices: 3107771--3107809 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3107761 GAGGTGGGGT
* *
3107771 AGCTGGGGGAGGAGT
1 AGCTGGTGGAGGAGA
*
3107786 AGCCGGTGGAGGAGA
1 AGCTGGTGGAGGAGA
3107801 AGCTGGTGG
1 AGCTGGTGG
3107810 TGGGGAGCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.56, T:0.13
Consensus pattern (15 bp):
AGCTGGTGGAGGAGA
Found at i:3115602 original size:18 final size:19
Alignment explanation
Indices: 3115579--3115623 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3115569 TAAAAAAATA
3115579 TATAAATTTTGGAA-TTTT
1 TATAAATTTTGGAACTTTT
*
3115597 TATAAATATTTTGAACTTTT
1 TATAAAT-TTTGGAACTTTT
3115617 TA-AAATT
1 TATAAATT
3115624 ATTTTGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (19 bp):
TATAAATTTTGGAACTTTT
Found at i:3115637 original size:20 final size:19
Alignment explanation
Indices: 3115579--3115636 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
3115569 TAAAAAAATA
*
3115579 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
3115597 TATAAATATTTTGAACTTTT
1 TATAAATATTTTGAA-TTTT
3115617 TA-AAATTATTTTGAATTTT
1 TATAAA-TATTTTGAATTTT
3115636 T
1 T
3115637 TTAGAGAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 14 0.39
20 15 0.42
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:3116169 original size:34 final size:34
Alignment explanation
Indices: 3116126--3116201 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
3116116 GTTTCGTAAT
*
3116126 AATCGATTCAAAAGAA-TGATTATTCCAACATAAC
1 AATCGATTCAAAAGAAGT-AGTATTCCAACATAAC
* * *
3116160 AATCGATTCAAAAGAAGTAGTCTTTCAATATAAC
1 AATCGATTCAAAAGAAGTAGTATTCCAACATAAC
3116194 AATCGATT
1 AATCGATT
3116202 TAAACATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (34 bp):
AATCGATTCAAAAGAAGTAGTATTCCAACATAAC
Found at i:3116219 original size:55 final size:54
Alignment explanation
Indices: 3116155--3116293 Score: 154
Period size: 55 Copynumber: 2.5 Consensus size: 54
3116145 TTATTCCAAC
** * * * *
3116155 ATAACAATCGATTCAAAAGAAGTAGTCTTTCAATATAACAATCGATTTAAACAT
1 ATAACAATCGATTCAAAAGAAACAATATTCCAACATAACAATCGATTTAAACAT
*
3116209 ATAAGCAATCGATTCAAAAGAAACAATATTCCGACATAACAATCGATTTAAACAT
1 ATAA-CAATCGATTCAAAAGAAACAATATTCCAACATAACAATCGATTTAAACAT
* * *
3116264 AAAAATAATC-AATCTAAAAGAAACAATATT
1 -ATAACAATCGATTC-AAAAGAAACAATATT
3116294 TTTGAGAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
54 7 0.10
55 62 0.86
56 3 0.04
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (54 bp):
ATAACAATCGATTCAAAAGAAACAATATTCCAACATAACAATCGATTTAAACAT
Found at i:3116265 original size:18 final size:18
Alignment explanation
Indices: 3116189--3116265 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
3116179 GTCTTTCAAT
*
3116189 ATAACAATCGATTTAAAC
1 ATAACAATCGATTCAAAC
3116207 ATATAAGCAATCGATTCAAA-
1 --ATAA-CAATCGATTCAAAC
* **
3116227 AGAAACAAT--ATTCCGAC
1 A-TAACAATCGATTCAAAC
*
3116244 ATAACAATCGATTTAAAC
1 ATAACAATCGATTCAAAC
3116262 ATAA
1 ATAA
3116266 AAATAATCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
16 11 0.25
17 1 0.02
18 14 0.32
19 2 0.05
20 4 0.09
21 12 0.27
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.25
Consensus pattern (18 bp):
ATAACAATCGATTCAAAC
Found at i:3116520 original size:35 final size:35
Alignment explanation
Indices: 3116453--3116520 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3116443 GATATGTGAT
* * *
3116453 AATGTTTTGGGAGAGTAGGTGCAAATAGTTGTAAG
1 AATGTTTGGGGAGAGTAGGTGCAAACAATTGTAAG
*
3116488 AATGTTTGGGGAGAGTGGGTGCAAACAATTGTA
1 AATGTTTGGGGAGAGTAGGTGCAAACAATTGTA
3116521 TATCGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
AATGTTTGGGGAGAGTAGGTGCAAACAATTGTAAG
Found at i:3117426 original size:3 final size:3
Alignment explanation
Indices: 3117420--3117456 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3117410 TACCTCATAA
*
3117420 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3117457 AACATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3123804 original size:2 final size:2
Alignment explanation
Indices: 3123797--3123839 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3123787 CTATTCAAGA
* *
3123797 AT AT AT AT AC AT AT AT AG 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
3123839 A
1 A
3123840 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3124955 original size:111 final size:111
Alignment explanation
Indices: 3124754--3124965 Score: 304
Period size: 111 Copynumber: 1.9 Consensus size: 111
3124744 CAGCTCCGGG
* * *
3124754 AAGCCTCTCATTTGCTCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAATCCAT
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
3124819 AGCTCGAACCAAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
66 AGCTCGAACCAAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
* * *
3124865 AAGCCTCTCACTTGATCTCAAACTTTGCCTTCTTGAATTGCTTACACTGA-CTGCATTTAACCCA
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACAC-CATCTGCATTTAACCCA
* *
3124929 TTGCTCGATA-CAAGCTCG-CTGATACCTTCATCAAACC
65 TAGCTCGA-ACCAAGCTCGCCAG-TACCTTCATCAAACC
3124966 GCACTGATGC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
110 2 0.02
111 86 0.96
112 2 0.02
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.31
Consensus pattern (111 bp):
AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTTACACCATCTGCATTTAACCCAT
AGCTCGAACCAAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
Found at i:3130008 original size:34 final size:34
Alignment explanation
Indices: 3129970--3130035 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
3129960 TTACAAAAAA
3129970 AAAATTTA-AAATTTAAAATATTTATAAAAATTTC
1 AAAATTTATAAATTTAAAA-ATTTATAAAAATTTC
**
3130004 AAAATTTATATTTTTAAAAATTTATAAAAATT
1 AAAATTTATAAATTTAAAAATTTATAAAAATT
3130036 CTAAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAATTTATAAATTTAAAAATTTATAAAAATTTC
Found at i:3130019 original size:26 final size:25
Alignment explanation
Indices: 3129968--3130027 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3129958 GATTACAAAA
3129968 AAAAAATTTAAAATTTAAAATATTT
1 AAAAAATTTAAAATTTAAAATATTT
*
3129993 ATAAAAATTTCAAAATTT-ATAT-TTT
1 A-AAAAATTT-AAAATTTAAAATATTT
*
3130018 TAAAAATTTA
1 AAAAAATTTA
3130028 TAAAAATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 1 0.03
24 8 0.26
25 4 0.13
26 11 0.35
27 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAAATTTAAAATTTAAAATATTT
Found at i:3130048 original size:34 final size:35
Alignment explanation
Indices: 3129981--3130049 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 35
3129971 AAATTTAAAA
*
3129981 TTTAAAATATTTATAAAAATTTCAAAATTTATATT
1 TTTAAAATATTTATAAAAATTTCAAAATATATATT
*
3130016 TTTAAAA-ATTTATAAAAATTCTAAAGAATATATA
1 TTTAAAATATTTATAAAAATT-TCAA-AATATATA
3130050 AAAAAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 13 0.43
35 10 0.33
36 7 0.23
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTAAAATATTTATAAAAATTTCAAAATATATATT
Found at i:3133088 original size:21 final size:24
Alignment explanation
Indices: 3133047--3133098 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
3133037 TTGACAGAAT
3133047 ATATT-AATTTTTAAAAAGAAA-A
1 ATATTAAATTTTTAAAAAGAAAGA
*
3133069 A-ATTAAATTTTT-AAAGGAAAGA
1 ATATTAAATTTTTAAAAAGAAAGA
3133091 ATATTAAA
1 ATATTAAA
3133099 AAAAAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATTAAATTTTTAAAAAGAAAGA
Found at i:3135948 original size:20 final size:20
Alignment explanation
Indices: 3135923--3135961 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3135913 TCATTTCCAT
3135923 TGTTT-ATAAGTTGGGTTTTG
1 TGTTTAATAA-TTGGGTTTTG
*
3135943 TGTTTAATTATTGGGTTTT
1 TGTTTAATAATTGGGTTTT
3135962 TTTAATAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (20 bp):
TGTTTAATAATTGGGTTTTG
Found at i:3139167 original size:17 final size:18
Alignment explanation
Indices: 3139130--3139167 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3139120 ATTTCAAATT
*
3139130 AAAGGGATTAAATTGTAA
1 AAAGAGATTAAATTGTAA
3139148 AAAGAGATTAAATT-TAA
1 AAAGAGATTAAATTGTAA
3139165 AAA
1 AAA
3139168 TGAACGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (18 bp):
AAAGAGATTAAATTGTAA
Found at i:3142326 original size:19 final size:19
Alignment explanation
Indices: 3142304--3142340 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3142294 TGAAAAACAT
*
3142304 AAATATTATTAAATTAATA
1 AAATATTATTAAAATAATA
3142323 AAATATTATTAAAATAAT
1 AAATATTATTAAAATAAT
3142341 TATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTATTAAAATAATA
Found at i:3142344 original size:12 final size:12
Alignment explanation
Indices: 3142315--3142347 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3142305 AATATTATTA
*
3142315 AATTAATAAAAT
1 AATTATTAAAAT
3142327 -ATTATTAAAAT
1 AATTATTAAAAT
3142338 AATTATTAAA
1 AATTATTAAA
3142348 TTTATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTATTAAAAT
Found at i:3142344 original size:31 final size:31
Alignment explanation
Indices: 3142304--3142366 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
3142294 TGAAAAACAT
3142304 AAATATTATTAAATTAATAAA-ATATTATTA
1 AAATATTATTAAATTAATAAATATATTATTA
* *
3142334 AAATAATTATTAAATTTATAAATATATTTTTA
1 AAAT-ATTATTAAATTAATAAATATATTATTA
3142366 A
1 A
3142367 TTATGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 16 0.55
32 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATATTATTAAATTAATAAATATATTATTA
Found at i:3142348 original size:11 final size:10
Alignment explanation
Indices: 3142303--3142358 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
3142293 GTGAAAAACA
3142303 TAAATATTAT
1 TAAATATTAT
*
3142313 TAAAT-TAAT
1 TAAATATTAT
*
3142322 AAAATATTAT
1 TAAATATTAT
3142332 TAAAATAATTAT
1 T-AAAT-ATTAT
3142344 TAAAT-TTA-
1 TAAATATTAT
3142352 TAAATAT
1 TAAATAT
3142359 ATTTTTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 5 0.13
9 11 0.29
10 8 0.21
11 8 0.21
12 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAATATTAT
Found at i:3142794 original size:16 final size:16
Alignment explanation
Indices: 3142760--3142791 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3142750 ATTTTGTTTG
3142760 ATTAATTAAATATATA
1 ATTAATTAAATATATA
3142776 ATTAATTAAA-ATATA
1 ATTAATTAAATATATA
3142791 A
1 A
3142792 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAATTAAATATATA
Found at i:3147680 original size:19 final size:19
Alignment explanation
Indices: 3147653--3147707 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
3147643 GACTCAAATT
*
3147653 ATTTTTAAAATTATTA-TAA
1 ATTTATAAAA-TATTACTAA
3147672 ATTTATAAAATATTACTAAA
1 ATTTATAAAATATTACT-AA
*
3147692 AATTATAATAATATTA
1 ATTTATAA-AATATTA
3147708 AATAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.16
19 10 0.32
20 9 0.29
21 7 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTATAAAATATTACTAA
Found at i:3147691 original size:11 final size:10
Alignment explanation
Indices: 3147658--3147734 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 10
3147648 AAATTATTTT
3147658 TAAAATTATTA
1 TAAAA-TATTA
3147669 T-AAAT-TTA
1 TAAAATATTA
3147677 TAAAATATTA
1 TAAAATATTA
3147687 CTAAAA-ATTA
1 -TAAAATATTA
3147697 TAATAATATTAAA
1 TAA-AATATT--A
3147710 TAAAAT-TTA
1 TAAAATATTA
3147719 -AAACATATTA
1 TAAA-ATATTA
*
3147729 AAAAAT
1 TAAAAT
3147735 CAATTCTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
8 7 0.12
9 11 0.20
10 17 0.30
11 14 0.25
12 3 0.05
13 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATATTA
Found at i:3147694 original size:21 final size:21
Alignment explanation
Indices: 3147670--3147730 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
3147660 AAATTATTAT
*
3147670 AAATTTATAAAATATT-ACTA
1 AAATTTATAAAATATTAAATA
*
3147690 AAAATTATAATAATATTAAATA
1 AAATTTATAA-AATATTAAATA
3147712 AAATTTA-AAACATATTAAA
1 AAATTTATAAA-ATATTAAA
3147731 AAATCAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 10 0.29
21 16 0.46
22 9 0.26
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTATAAAATATTAAATA
Found at i:3159636 original size:2 final size:2
Alignment explanation
Indices: 3159629--3159655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3159619 GCTCCTTCCA
3159629 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 T
3159656 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3166422 original size:20 final size:20
Alignment explanation
Indices: 3166385--3166422 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3166375 AAATCAAGTT
*
3166385 TCCATAATTCATACTTATCA
1 TCCATAATTCATAATTATCA
3166405 TCCATAATT-ATTAATTAT
1 TCCATAATTCA-TAATTAT
3166423 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
TCCATAATTCATAATTATCA
Found at i:3171604 original size:125 final size:123
Alignment explanation
Indices: 3171371--3171622 Score: 387
Period size: 125 Copynumber: 2.0 Consensus size: 123
3171361 AAATCCTTGT
* *
3171371 AACTCGTTCATACAACTGTTTTCAACTATCTGGTCGTGGTTTTAGCATCGTATTTATCAAATCAT
1 AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAGCATCGTATTTATCAAATCAT
**
3171436 AGCCATGCTTTCATAGACAACATTGTTAGGAATTAATTTGATGAGAATGAAATCATCA
66 AGCCATGCTTTCATAGACAACATTGTTAGGAATTAACATGATGAGAATGAAATCATCA
* * * * *
3171494 AACTCGTTCATAGACAACTGTTTTCAACTATCTGATCATGGTTTTAGCTTTGTTTTTATTATATC
1 AACTCGTTCAT--ACAACTGTTTTCAACTATCTGATCATGGTTTTAGCATCGTATTTATCAAATC
* *
3171559 ATATCCATGCTTTCATAGACAACATTGTTAGGAATTAGCATGATGAGAATGAAATCATCA
64 ATAGCCATGCTTTCATAGACAACATTGTTAGGAATTAACATGATGAGAATGAAATCATCA
3171619 AACT
1 AACT
3171623 AGGACCTGGT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
123 11 0.09
125 105 0.91
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (123 bp):
AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAGCATCGTATTTATCAAATCAT
AGCCATGCTTTCATAGACAACATTGTTAGGAATTAACATGATGAGAATGAAATCATCA
Found at i:3188567 original size:38 final size:38
Alignment explanation
Indices: 3188508--3188596 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
3188498 AATTTTTCTC
*
3188508 GAGTTTCAAGTTTATGGTTTAAGGCTGATATCAAATTTT
1 GAGTTT-AAGTTTATGGTTTAAGACTGATATCAAATTTT
* * *
3188547 GAGTTTAAGTTTA-GGATTTAAGATTTATATCAAGTTTT
1 GAGTTTAAGTTTATGG-TTTAAGACTGATATCAAATTTT
*
3188585 GAGTTTGAGTTT
1 GAGTTTAAGTTT
3188597 CGTATTTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 2 0.05
38 36 0.82
39 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.46
Consensus pattern (38 bp):
GAGTTTAAGTTTATGGTTTAAGACTGATATCAAATTTT
Found at i:3195563 original size:7 final size:7
Alignment explanation
Indices: 3195551--3195588 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3195541 TGGAATTCAA
3195551 GTTTGAG
1 GTTTGAG
3195558 GTTTGAG
1 GTTTGAG
* *
3195565 ATTTAAG
1 GTTTGAG
3195572 GTTTG-G
1 GTTTGAG
3195578 GTTTGAG
1 GTTTGAG
3195585 GTTT
1 GTTT
3195589 AGGGTTCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
GTTTGAG
Found at i:3195580 original size:20 final size:21
Alignment explanation
Indices: 3195551--3195594 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3195541 TGGAATTCAA
3195551 GTTTGAGGTTTGAGATTTAAG
1 GTTTGAGGTTTGAGATTTAAG
* *
3195572 GTTTG-GGTTTGAGGTTTAGG
1 GTTTGAGGTTTGAGATTTAAG
3195592 GTT
1 GTT
3195595 CGAGATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (21 bp):
GTTTGAGGTTTGAGATTTAAG
Found at i:3195593 original size:14 final size:13
Alignment explanation
Indices: 3195551--3195616 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
3195541 TGGAATTCAA
3195551 GTTTGAGGTTTGAG
1 GTTTGAGGTTTG-G
* *
3195565 ATTTAAGGTTTGG
1 GTTTGAGGTTTGG
3195578 GTTTGAGGTTTAGG
1 GTTTGAGGTTT-GG
* *
3195592 GTTCGAGATTATGG
1 GTTTGAGGTT-TGG
*
3195606 TTTTGA-GTTTG
1 GTTTGAGGTTTG
3195617 AAGTTTAAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
12 2 0.05
13 12 0.29
14 26 0.63
15 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.45
Consensus pattern (13 bp):
GTTTGAGGTTTGG
Found at i:3195600 original size:34 final size:34
Alignment explanation
Indices: 3195549--3195623 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
3195539 TTTGGAATTC
* *
3195549 AAGTTT-GAGGTTTGAGATTTAAGG-TTTGGGTTTG
1 AAGTTTAG-GGTTCGAGA-TTAAGGTTTTGAGTTTG
* *
3195583 AGGTTTAGGGTTCGAGATTATGGTTTTGAGTTTG
1 AAGTTTAGGGTTCGAGATTAAGGTTTTGAGTTTG
3195617 AAGTTTA
1 AAGTTTA
3195624 AGATTCAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
33 5 0.15
34 28 0.82
35 1 0.03
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.44
Consensus pattern (34 bp):
AAGTTTAGGGTTCGAGATTAAGGTTTTGAGTTTG
Found at i:3204523 original size:15 final size:17
Alignment explanation
Indices: 3204493--3204524 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3204483 GTTTCACATT
3204493 TCCCTCAAATATATGAA
1 TCCCTCAAATATATGAA
3204510 TCCCT-AAA-ATATGAA
1 TCCCTCAAATATATGAA
3204525 AAAGATGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (17 bp):
TCCCTCAAATATATGAA
Found at i:3204707 original size:13 final size:13
Alignment explanation
Indices: 3204689--3204714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3204679 AATAATCACC
3204689 TAATTATGAGTTA
1 TAATTATGAGTTA
3204702 TAATTATGAGTTA
1 TAATTATGAGTTA
3204715 GTTTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAATTATGAGTTA
Found at i:3222538 original size:16 final size:16
Alignment explanation
Indices: 3222487--3222541 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
3222477 AATTATTCTA
* *
3222487 ATTATTTTATGGATAT
1 ATTATTTTTTGAATAT
* *
3222503 ATTA-TTTTTCACT-T
1 ATTATTTTTTGAATAT
*
3222517 ACTATTTTTTGAATAT
1 ATTATTTTTTGAATAT
3222533 ATTATTTTT
1 ATTATTTTT
3222542 AATTAATAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 4 0.14
15 12 0.41
16 13 0.45
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTATTTTTTGAATAT
Found at i:3222554 original size:30 final size:30
Alignment explanation
Indices: 3222489--3222555 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
3222479 TTATTCTAAT
* * * *
3222489 TATTTTATGGATATATTATTTTTCACTTAC
1 TATTTTTTGAATATATTATTTTTCAATTAA
3222519 TATTTTTTGAATATATTATTTTT-AATTAA
1 TATTTTTTGAATATATTATTTTTCAATTAA
*
3222548 TAATTTTT
1 TATTTTTT
3222556 AGCTTTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTTTTGAATATATTATTTTTCAATTAA
Found at i:3225494 original size:10 final size:10
Alignment explanation
Indices: 3225488--3225519 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3225478 AATTTTTATT
3225488 TATTTTTAAA
1 TATTTTTAAA
3225498 TATTTTTAAA
1 TATTTTTAAA
*
3225508 CATTTTTAAA
1 TATTTTTAAA
3225518 TA
1 TA
3225520 ATATGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:3226471 original size:7 final size:8
Alignment explanation
Indices: 3226449--3226482 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
3226439 TTACTTAAGA
3226449 AAATTTTT
1 AAATTTTT
3226457 AAATTTTT
1 AAATTTTT
3226465 AAATTTTTTT
1 AAA--TTTTT
3226475 AAATTTTT
1 AAATTTTT
3226483 TATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
AAATTTTT
Found at i:3226472 original size:9 final size:9
Alignment explanation
Indices: 3226452--3226497 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 9
3226442 CTTAAGAAAA
3226452 TTTTTAAA-
1 TTTTTAAAT
3226460 TTTTTAAATT
1 TTTTTAAA-T
3226470 TTTTTAAAT
1 TTTTTAAAT
3226479 TTTTTATATAT
1 TTTTTA-A-AT
3226490 TTTTTAAA
1 TTTTTAAA
3226498 AATATAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.24
9 8 0.24
10 10 0.29
11 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:3226641 original size:9 final size:9
Alignment explanation
Indices: 3226627--3226651 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3226617 ACACAAATTT
3226627 ATTATTCAA
1 ATTATTCAA
3226636 ATTATTCAA
1 ATTATTCAA
3226645 ATTATTC
1 ATTATTC
3226652 GAACTGTGAA
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:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTATTCAA
Found at i:3228399 original size:33 final size:33
Alignment explanation
Indices: 3228362--3228443 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
3228352 AAATTATTTG
* * *
3228362 ATATTTCAATAATTTAATATAATGATACATAAA
1 ATATTTAAATAATTTAACATAATGACACATAAA
*
3228395 ATATTTAAATAATTTGACATAATGACACATAAA
1 ATATTTAAATAATTTAACATAATGACACATAAA
3228428 ATA--TAAATTAATTTAA
1 ATATTTAAA-TAATTTAA
3228444 TTTTTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.09
32 7 0.16
33 32 0.74
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (33 bp):
ATATTTAAATAATTTAACATAATGACACATAAA
Found at i:3228874 original size:27 final size:29
Alignment explanation
Indices: 3228839--3228896 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
3228829 AATTAGTAAA
* *
3228839 AAAATATATAAGAACTTAA-AAAAATTAT
1 AAAATATATAAAAACTTAAGAAAAAATAT
3228867 AAAA-ATATAAAAACTTAAGAAAAAATAT
1 AAAATATATAAAAACTTAAGAAAAAATAT
3228895 AA
1 AA
3228897 TATAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (29 bp):
AAAATATATAAAAACTTAAGAAAAAATAT
Found at i:3228877 original size:19 final size:20
Alignment explanation
Indices: 3228835--3228879 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
3228825 CCTTAATTAG
*
3228835 TAAAAAAATATATAAGAACT
1 TAAAAAAATATATAAGAAAT
3228855 TAAAAAAAT-TATAA-AAAT
1 TAAAAAAATATATAAGAAAT
3228873 ATAAAAA
1 -TAAAAA
3228880 CTTAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 9 0.39
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAAAATATATAAGAAAT
Found at i:3238442 original size:16 final size:16
Alignment explanation
Indices: 3238423--3238457 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3238413 AGAAATACCA
*
3238423 AAATCTAAAATCATTC
1 AAATCTAAAATAATTC
*
3238439 AAATTTAAAATAATTC
1 AAATCTAAAATAATTC
3238455 AAA
1 AAA
3238458 AAATCTAAAA
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:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATCTAAAATAATTC
Found at i:3238558 original size:1 final size:1
Alignment explanation
Indices: 3238552--3238580 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3238542 TCTCTTCAAT
3238552 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3238581 TCCTTGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3239149 original size:26 final size:24
Alignment explanation
Indices: 3239089--3239158 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 24
3239079 TTTCATATTT
*
3239089 TTTTATTT-TTTTAAATATTTATA
1 TTTTATTTATTTTTAATATTTATA
*
3239112 TTATA-TTA-TTTTAATATTTAATAA
1 TTTTATTTATTTTTAATATTT-AT-A
3239136 TTTTATTTATTTTT--TATTTATA
1 TTTTATTTATTTTTAATATTTATA
3239158 T
1 T
3239159 AAAATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
22 14 0.36
23 8 0.21
24 10 0.26
25 3 0.08
26 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATTTATTTTTAATATTTATA
Found at i:3239153 original size:24 final size:27
Alignment explanation
Indices: 3239112--3239160 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
3239102 AATATTTATA
3239112 TTATATTATTTTAATATTTA-ATAATT
1 TTATATTATTTTAATATTTATATAATT
*
3239138 TTAT-TTATTTT-TTATTTATATAA
1 TTATATTATTTTAATATTTATATAA
3239161 AATTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATATTATTTTAATATTTATATAATT
Found at i:3244955 original size:118 final size:115
Alignment explanation
Indices: 3244760--3244984 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 115
3244750 GTTGTATAAA
* *
3244760 GTCTTGATCAAAAGGGAATCACCAATTACCTATTTGAATCTTACTGCAAAATCATGATGCATAGT
1 GTCTTGATCAAAAGGGAATCACCAATTACCTATTTCAATCTTACTGCAAAATCATGATGCATACT
* * *
3244825 TGTCATTATTGTTCATTTTCCTAGATTTGCTTACAAAGGGCTATAGTGTAT
66 TGTCATCATTGTTCATCTT-CTAGATCTGCTTACAAAGGGCTATAGTGTAT
*
3244876 GTCTTGATC-AAAGGGCAATCACCAAATTACCTGTTTCAATCATTACTGCAAAATCATGATGCAT
1 GTCTTGATCAAAAGGG-AATCACC-AATTACCTATTTCAATC-TTACTGCAAAATCATGATGCAT
** * *
3244940 AACTT-TTGTCGTTGTTCATCTTCTAGATCTGCTTACTAAGGGCTA
63 -ACTTGTCATCATTGTTCATCTTCTAGATCTGCTTACAAAGGGCTA
3244985 CTGACATGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
115 6 0.06
116 16 0.17
117 36 0.38
118 34 0.36
119 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (115 bp):
GTCTTGATCAAAAGGGAATCACCAATTACCTATTTCAATCTTACTGCAAAATCATGATGCATACT
TGTCATCATTGTTCATCTTCTAGATCTGCTTACAAAGGGCTATAGTGTAT
Found at i:3248928 original size:25 final size:25
Alignment explanation
Indices: 3248893--3248941 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3248883 GAAACTGAAG
*
3248893 AAAATAGAAAA-AAAGAAAGTTAAAA
1 AAAATAGAAAAGAAA-AAAATTAAAA
*
3248918 AAAATATAAAAGAAAAAAATTAAA
1 AAAATAGAAAAGAAAAAAATTAAA
3248942 TTGCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (25 bp):
AAAATAGAAAAGAAAAAAATTAAAA
Found at i:3249105 original size:15 final size:15
Alignment explanation
Indices: 3249085--3249135 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3249075 ATAACATGTT
3249085 AACGTAAGTGACTAA
1 AACGTAAGTGACTAA
*
3249100 AACGTAACGT--TTAA
1 AACGTAA-GTGACTAA
*
3249114 AACATAAGTGACTAA
1 AACGTAAGTGACTAA
*
3249129 AATGTAA
1 AACGTAA
3249136 TCTAAGTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (15 bp):
AACGTAAGTGACTAA
Found at i:3251806 original size:26 final size:24
Alignment explanation
Indices: 3251764--3251815 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
3251754 TTTAATCAGT
*
3251764 AAATATATATTTTTAAAATATAAA
1 AAATATATATTTATAAAATATAAA
*
3251788 AAATATATGATTTAATAAAATTTAAA
1 AAATATAT-ATTT-ATAAAATATAAA
3251814 AA
1 AA
3251816 TAAATACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 4 0.17
26 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATATTTATAAAATATAAA
Found at i:3257229 original size:20 final size:20
Alignment explanation
Indices: 3257204--3257246 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3257194 AATCTGTTAG
*
3257204 TGAATTAACGGAATTTTTAA
1 TGAATTAACGAAATTTTTAA
*
3257224 TGAATTAATGAAATTTTTAA
1 TGAATTAACGAAATTTTTAA
3257244 TGA
1 TGA
3257247 TTTTAATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (20 bp):
TGAATTAACGAAATTTTTAA
Found at i:3264231 original size:17 final size:17
Alignment explanation
Indices: 3264185--3264296 Score: 60
Period size: 17 Copynumber: 6.8 Consensus size: 17
3264175 TAGTATTTTA
3264185 TTAATTTAATATTAAAGT
1 TTAATTTAATATTAAA-T
*
3264203 GATTATTTTAATATTAAAT
1 --TTAATTTAATATTAAAT
* *
3264222 TTAATTTAATGTT-TAT
1 TTAATTTAATATTAAAT
*
3264238 TT--TGTAGATA--AATAT
1 TTAATTTA-ATATTAA-AT
*
3264253 TTTA-TTAAT-TT-AAT
1 TTAATTTAATATTAAAT
**
3264267 AAAATTTAATATTAAAT
1 TTAATTTAATATTAAAT
3264284 TTAATTTAATATT
1 TTAATTTAATATT
3264297 TATCTTGATA
Statistics
Matches: 69, Mismatches: 13, Indels: 23
0.66 0.12 0.22
Matches are distributed among these distances:
14 6 0.09
15 14 0.20
16 8 0.12
17 25 0.36
19 1 0.01
20 15 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAATTTAATATTAAAT
Found at i:3264278 original size:62 final size:59
Alignment explanation
Indices: 3264209--3264326 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 59
3264199 AAGTGATTAT
* * *
3264209 TTTAATATTAAATTTAATTTAATGTTTATTTTGTAGATAAATATTTTATTAATTTAATAAAA
1 TTTAATATTAAATTTAATTTAATATTTA-TCT-T-GATAAATATTATATTAATTTAATAAAA
*
3264271 TTTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATTATATTAATTTAATA
3264327 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 2 0.04
62 27 0.52
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (59 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATTATATTAATTTAATAAAA
Found at i:3284417 original size:2 final size:2
Alignment explanation
Indices: 3284410--3284437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3284400 TACAACTCTC
3284410 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
3284438 CTATGTTTTT
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:3284681 original size:110 final size:111
Alignment explanation
Indices: 3284537--3284748 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 111
3284527 ACCTGTCCTT
* * * **
3284537 TTTGTGGAATAGGTTTAAGATCAACAGTAAACTTTTGAAAATGGTTCAATC-TATTTATTTTACT
1 TTTGTGGAATAGCTTTAAGATCAACAATAAACTTTTGAAAAGGGCACAATCTTATTTATTTTACT
3284601 CATTACAAAGGAATCTTGTCAGAAAACAAATAGATGTGATGTTTTTC
66 CATTACAAAGGAA-CTTGTCAGAAAACAAATAGATGTGATGTTTTTC
**
3284648 TTTGTGG-ATAGCTTTAAGATCAACAATTTACTTTTGAAAAGGGCACAATCTATTTATTTATTTT
1 TTTGTGGAATAGCTTTAAGATCAACAATAAACTTTTGAAAAGGGCACAATC---TTATTTATTTT
* *
3284712 ACTCATTACAAAGGAACTTGTCAGGAAACAAGTAGAT
63 ACTCATTACAAAGGAACTTGTCAGAAAACAAATAGAT
3284749 CTAATGCTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
110 36 0.41
111 7 0.08
113 19 0.22
114 26 0.30
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (111 bp):
TTTGTGGAATAGCTTTAAGATCAACAATAAACTTTTGAAAAGGGCACAATCTTATTTATTTTACT
CATTACAAAGGAACTTGTCAGAAAACAAATAGATGTGATGTTTTTC
Found at i:3291295 original size:8 final size:8
Alignment explanation
Indices: 3291282--3291306 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3291272 TGATGCAATA
3291282 GTATTGAT
1 GTATTGAT
3291290 GTATTGAT
1 GTATTGAT
3291298 GTATTGAT
1 GTATTGAT
3291306 G
1 G
3291307 ACAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (8 bp):
GTATTGAT
Found at i:3302157 original size:98 final size:99
Alignment explanation
Indices: 3302055--3302276 Score: 235
Period size: 99 Copynumber: 2.3 Consensus size: 99
3302045 GCCATTGTGA
* * * * *
3302055 CTTAAACCTTTCCCTTTGCAT-CTTC-GTGGTAC-TGGATTTACCGTTGCGGCTTAAACCTTTCC
1 CTTAAATCTTTCCCTTT-CATGCTTCTGAGGTACAAGG-TTCACCGTTGCGACTTAAACCTTT-C
*
3302117 CTTTGCA-T-C-TTCGTGGTACTGGATTCGCCGTTGCGG
63 CTTT-CATTCCATT-GTGGTACTAGATTCGCCGTTGCGG
* *
3302153 CTTAAATCTTTCCC-TTCGTGCTTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCTT
1 CTTAAATCTTTCCCTTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCTT
*
3302217 TTATTGCCATTGTGGTACTAGATTCGCCGTTGCGG
66 TCATT-CCATTGTGGTACTAGATTCGCCGTTGCGG
*
3302252 CTTAAATTTTTCCC-TTCATGTCTTC
1 CTTAAATCTTTCCCTTTCATG-CTTC
3302277 ATGGTAATGA
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
96 3 0.03
97 12 0.11
98 40 0.38
99 44 0.42
100 6 0.06
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (99 bp):
CTTAAATCTTTCCCTTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCTT
TCATTCCATTGTGGTACTAGATTCGCCGTTGCGG
Found at i:3302264 original size:50 final size:49
Alignment explanation
Indices: 3301983--3302267 Score: 206
Period size: 49 Copynumber: 5.8 Consensus size: 49
3301973 AATGTTTTCA
* * * *
3301983 TGGTACTAGATTTGCCATTGCGGCTTAAATCTTTCCCTTCA-TGCTTTTG
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTT-AGTGCATCTG
* * * * * *
3302032 AGGTA-TAAAGTTCGCCATTGTGACTTAAACCTTTCCCTT--TGCATCTTCG
1 TGGTACTAGA-TTCGCCGTTGCGGCTTAAATCTTTCCCTTAGTGCATC-T-G
* ** *
3302081 TGGTACTGGATTTACCGTTGCGGCTTAAACCTTTCCCTT--TGCATCTTCG
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTAGTGCATC-T-G
* * *
3302130 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTGCTTCTG
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTAGTGCATCTG
* * * ** * * * *
3302179 AGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCTTTTATTGCCAT-TG
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCC-CTTAGTG-CATCTG
*
3302229 TGGTACTAGATTCGCCGTTGCGGCTTAAATTTTTCCCTT
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
3302268 CATGTCTTCA
Statistics
Matches: 187, Mismatches: 41, Indels: 16
0.77 0.17 0.07
Matches are distributed among these distances:
47 4 0.02
48 4 0.02
49 135 0.72
50 37 0.20
51 7 0.04
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (49 bp):
TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTAGTGCATCTG
Found at i:3317961 original size:16 final size:17
Alignment explanation
Indices: 3317940--3317977 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3317930 AAACTGAAAT
3317940 AAATAAATTAA-ATTAA
1 AAATAAATTAACATTAA
* *
3317956 AAATAATTTAACATTTA
1 AAATAAATTAACATTAA
3317973 AAATA
1 AAATA
3317978 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAAATTAACATTAA
Found at i:3318219 original size:29 final size:29
Alignment explanation
Indices: 3318186--3318268 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
3318176 AATTAAGTAA
* *
3318186 CAAATTTAAAAAATATCAAATTTAGATA-
1 CAAATTAAAAAAATATCAAATTTAAATAT
* *
3318214 CTAAATTAAAAAAAATGTCAAATTCAAATAT
1 C-AAATT-AAAAAAATATCAAATTTAAATAT
*
3318245 CAAACTAAAAAAATATCAAATTTA
1 CAAATTAAAAAAATATCAAATTTA
3318269 TATTAAGGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.02
29 21 0.47
30 22 0.49
31 1 0.02
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (29 bp):
CAAATTAAAAAAATATCAAATTTAAATAT
Found at i:3320162 original size:6 final size:6
Alignment explanation
Indices: 3320151--3320245 Score: 53
Period size: 6 Copynumber: 16.8 Consensus size: 6
3320141 TGGCCCAATA
* * * * *
3320151 AAATTT AAATTT -ATTTT AAATTT AAGTTT ATA-TT AAGTTT AAATCT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
3320197 --ATTT GGAATTT AAATTT --ATTAT AAATTT AAGTTT AAATTT --ATTT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT AAATTT
3320241 AAATT
1 AAATT
3320246 AATAATATCC
Statistics
Matches: 66, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
4 10 0.15
5 8 0.12
6 41 0.62
7 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:3320173 original size:17 final size:17
Alignment explanation
Indices: 3320151--3320231 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 17
3320141 TGGCCCAATA
3320151 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
3320168 AAATTTAAGTTTATATT
1 AAATTTAAATTTATTTT
* * *
3320185 AAGTTTAAATCTATTTG
1 AAATTTAAATTTATTTT
* *
3320202 GAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
*
3320219 AAATTTAAGTTTA
1 AAATTTAAATTTA
3320232 AATTTATTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:3321980 original size:30 final size:30
Alignment explanation
Indices: 3321942--3322179 Score: 115
Period size: 29 Copynumber: 8.1 Consensus size: 30
3321932 CCTAAAAGGT
3321942 CCCT-GAACTATCCAAAAA-T-CATATTTTAA
1 CCCTCGAACT-TCCAAAAATTCCAT-TTTTAA
* *
3321971 CCCTCGAACTTCTCAAAAATTGCATTTTT-G
1 CCCTCGAACTTC-CAAAAATTCCATTTTTAA
*
3322001 CCCTCGAACTTCTAAAAATTCCATTTTTAA
1 CCCTCGAACTTCCAAAAATTCCATTTTTAA
* * *
3322031 -CCTCTAATTTTCAAAAAATTCCA-TTTT-A
1 CCCTCGAA-CTTCCAAAAATTCCATTTTTAA
* * * * * *
3322059 CCCCCG-AGTGTCAAAAAATTACAATTTTGA
1 CCCTCGAACT-TCCAAAAATTCCATTTTTAA
* * *
3322089 CCCT-GAACTTTCTAAAATTACCA-TTTTAC
1 CCCTCGAACTTCCAAAAATT-CCATTTTTAA
* ** **
3322118 CCCT-GAA-TGTCCAAAAAATAAATTTTTGT
1 CCCTCGAACT-TCCAAAAATTCCATTTTTAA
** *
3322147 CCCT-GAGTTTCCAAAAATTCCATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTTAA
3322176 CCCT
1 CCCT
3322180 AAACTTTCCA
Statistics
Matches: 163, Mismatches: 31, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.01
28 16 0.10
29 93 0.57
30 45 0.28
31 5 0.03
32 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (30 bp):
CCCTCGAACTTCCAAAAATTCCATTTTTAA
Found at i:3321988 original size:29 final size:31
Alignment explanation
Indices: 3321965--3322057 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 31
3321955 AAAAATCATA
* *
3321965 TTTTAACCCTCGAACTTCTCAAAAATTGCAT
1 TTTTAACCCTCGAACTTCTAAAAAATTCCAT
*
3321996 TTTT-GCCCTCGAACTTCT-AAAAATTCCAT
1 TTTTAACCCTCGAACTTCTAAAAAATTCCAT
* *
3322025 TTTTAA-CCTCTAA-TTTTCAAAAAATTCCAT
1 TTTTAACCCTCGAACTTCT-AAAAAATTCCAT
3322055 TTT
1 TTT
3322058 ACCCCCGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
28 3 0.06
29 20 0.37
30 27 0.50
31 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (31 bp):
TTTTAACCCTCGAACTTCTAAAAAATTCCAT
Found at i:3322105 original size:29 final size:29
Alignment explanation
Indices: 3321942--3322206 Score: 97
Period size: 29 Copynumber: 9.1 Consensus size: 29
3321932 CCTAAAAGGT
* *
3321942 CCCTGAACTATCCAAAAA-T-CATATTTTAA
1 CCCTGAACT-TTCAAAAATTACA-ATTTTGA
* *
3321971 CCCTCGAACTTCTCAAAAATTGCATTTTTG-
1 CCCT-GAACTT-TCAAAAATTACAATTTTGA
* * *
3322001 CCCTCGAAC-TTCTAAAAATTCCATTTTTAA
1 CCCT-GAACTTTC-AAAAATTACAATTTTGA
* *
3322031 CCTCT-AATTTTCAAAAAATT-CCATTTT-A
1 CC-CTGAACTTTC-AAAAATTACAATTTTGA
* * *
3322059 CCCCCG-AGTGTCAAAAAATTACAATTTTGA
1 -CCCTGAACTTTC-AAAAATTACAATTTTGA
* *
3322089 CCCTGAACTTTCTAAAATTACCATTTT-A
1 CCCTGAACTTTCAAAAATTACAATTTTGA
* * *
3322117 CCCCTGAA-TGTCCAAAAAATA-AATTTTTGT
1 -CCCTGAACT-TTCAAAAATTACAA-TTTTGA
* * *
3322147 CCCTG-AGTTTCCAAAAATTCCATTTTTGA
1 CCCTGAACTTT-CAAAAATTACAATTTTGA
* * * *
3322176 CCCTAAACTTTCCACAATTACTATTTT-A
1 CCCTGAACTTTCAAAAATTACAATTTTGA
3322204 CCC
1 CCC
3322207 CAGGCGTCCA
Statistics
Matches: 180, Mismatches: 35, Indels: 43
0.70 0.14 0.17
Matches are distributed among these distances:
28 25 0.14
29 104 0.58
30 42 0.23
31 7 0.04
32 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCTGAACTTTCAAAAATTACAATTTTGA
Found at i:3322133 original size:87 final size:86
Alignment explanation
Indices: 3321985--3322207 Score: 211
Period size: 87 Copynumber: 2.6 Consensus size: 86
3321975 CGAACTTCTC
* * * *
3321985 AAAAATTGCATTTTTG-CCCTCGAAC-TTCTAAAAATT-CCATTTTTAACCTCTAATTTTCAAAA
1 AAAAATTACATTTTTGACCCT-GAACTTTCT-AAAATTACCA-TTTT-ACCCCTAATGTCCAAAA
**
3322047 AATTCCA-TTTTACCCCCGAGTGTCA
62 AA-TAAATTTTTACCCCCGAGTGTCA
*
3322072 AAAAATTACAATTTTGACCCTGAACTTTCTAAAATTACCATTTTACCCCTGAATGTCCAAAAAAT
1 AAAAATTACATTTTTGACCCTGAACTTTCTAAAATTACCATTTTACCCCT-AATGTCCAAAAAAT
** * * *
3322137 AAATTTTTGTCCCTGAGTTTCC
65 AAATTTTTACCCCCGAGTGTCA
* * * * *
3322159 AAAAATTCCATTTTTGACCCTAAACTTTCCACAATTACTATTTTACCCC
1 AAAAATTACATTTTTGACCCTGAACTTTCTAAAATTACCATTTTACCCC
3322208 AGGCGTCCAA
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
86 7 0.06
87 95 0.84
88 11 0.10
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (86 bp):
AAAAATTACATTTTTGACCCTGAACTTTCTAAAATTACCATTTTACCCCTAATGTCCAAAAAATA
AATTTTTACCCCCGAGTGTCA
Found at i:3322164 original size:58 final size:58
Alignment explanation
Indices: 3321964--3322172 Score: 162
Period size: 58 Copynumber: 3.6 Consensus size: 58
3321954 CAAAAATCAT
* * * * * *
3321964 ATTTTAACCCTCGAAC-TTCTCAAAAATTGCATTTTTGCCCTCGAACT-TCTAAAAATTCCA
1 ATTTTGACCCT-GAACTTTC-CAAAAATTCCA-TTTTACCCCCGAA-TGTCAAAAAATTACA
* * * * *
3322024 TTTTTAACCTCT-AATTTTCAAAAAATTCCATTTTACCCCCGAGTGTCAAAAAATTACA
1 ATTTTGACC-CTGAACTTTCCAAAAATTCCATTTTACCCCCGAATGTCAAAAAATTACA
* *
3322082 ATTTTGACCCTGAACTTT-CTAAAATTACCATTTTACCCCTGAATGTCCAAAAAA-TA-A
1 ATTTTGACCCTGAACTTTCCAAAAATT-CCATTTTACCCCCGAATGT-CAAAAAATTACA
* *
3322139 ATTTTTGTCCCTG-AGTTTCCAAAAATTCCATTTT
1 A-TTTTGACCCTGAACTTTCCAAAAATTCCATTTT
3322173 TGACCCTAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
57 22 0.18
58 69 0.57
59 18 0.15
60 11 0.09
61 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (58 bp):
ATTTTGACCCTGAACTTTCCAAAAATTCCATTTTACCCCCGAATGTCAAAAAATTACA
Found at i:3325371 original size:119 final size:119
Alignment explanation
Indices: 3325152--3325388 Score: 393
Period size: 119 Copynumber: 2.0 Consensus size: 119
3325142 ATTGAGGGAA
3325152 ATGCATGTGAATGTCAGAGGTTTGTTAACGTGAAGTCGCAACTTCGAGTTTGACTATAGCCATGC
1 ATGCATGTGAATGTCAGAGGTTTGTTAACGTGAAGTCGCAACTTCGAGTTTGACTATAGCCATGC
* ** * *
3325217 ATGGTAGTAATTGAGACCCTAACCGGTGATAGTGTCGAGTTTTGGGTGTTACAT
66 AAGGTAGTAACCGAGACCCTAACCGGCGACAGTGTCGAGTTTTGGGTGTTACAT
*
3325271 ATGCATGTGAATGTCAGAGGTTTGTTAACGTGAAGTCGCAACTTCGAGTTTGACTATAGCTATGC
1 ATGCATGTGAATGTCAGAGGTTTGTTAACGTGAAGTCGCAACTTCGAGTTTGACTATAGCCATGC
* * *
3325336 AAGGTAGTAACCGGGACCCTAACCGGCGACGGTGTCGGGTTTTGGGTGTTACA
66 AAGGTAGTAACCGAGACCCTAACCGGCGACAGTGTCGAGTTTTGGGTGTTACA
3325389 ACAACCATCT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 109 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (119 bp):
ATGCATGTGAATGTCAGAGGTTTGTTAACGTGAAGTCGCAACTTCGAGTTTGACTATAGCCATGC
AAGGTAGTAACCGAGACCCTAACCGGCGACAGTGTCGAGTTTTGGGTGTTACAT
Found at i:3327142 original size:21 final size:20
Alignment explanation
Indices: 3327108--3327146 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3327098 CACCAATTCA
*
3327108 ATAAAAATATTAAATATTTTT
1 ATAAAAATAATAAA-ATTTTT
*
3327129 ATAAATATAATAAAATTT
1 ATAAAAATAATAAAATTT
3327147 AAAGTAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAAATAATAAAATTTTT
Found at i:3335097 original size:2 final size:2
Alignment explanation
Indices: 3335086--3335118 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3335076 CTTTTACTAC
3335086 TA TA -A 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
3335119 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3336290 original size:21 final size:21
Alignment explanation
Indices: 3336266--3336305 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3336256 AACCATACCC
*
3336266 ATTTTTAAAATCTAATATCTA
1 ATTTTAAAAATCTAATATCTA
*
3336287 ATTTTAAAAATCTAGTATC
1 ATTTTAAAAATCTAATATC
3336306 ATAGAGGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTTTAAAAATCTAATATCTA
Found at i:3344025 original size:13 final size:13
Alignment explanation
Indices: 3343994--3344023 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3343984 CACCTGTTAA
3343994 AGAAATAAAATAT
1 AGAAATAAAATAT
3344007 AGAAATAAAATA-
1 AGAAATAAAATAT
3344019 AGAAA
1 AGAAA
3344024 ATTTGTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (13 bp):
AGAAATAAAATAT
Found at i:3348060 original size:29 final size:29
Alignment explanation
Indices: 3348025--3348095 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
3348015 AACGATAATT
3348025 TAAGTGACTAAAACGTAACATTTCAAACA
1 TAAGTGACTAAAACGTAACATTTCAAACA
3348054 TAAGTGACTAAAACGTAACATTTCAAACA
1 TAAGTGACTAAAACGTAACATTTCAAACA
*
3348083 TAAGTGACAAAAA
1 TAAGTGACTAAAA
3348096 ATGTAATCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAACATTTCAAACA
Found at i:3349281 original size:11 final size:11
Alignment explanation
Indices: 3349265--3349294 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3349255 GCCCAGATCA
3349265 GTTGTTTTGTT
1 GTTGTTTTGTT
*
3349276 GTTGTTTCGTT
1 GTTGTTTTGTT
3349287 GTTGTTTT
1 GTTGTTTT
3349295 TCTAACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.27, T:0.70
Consensus pattern (11 bp):
GTTGTTTTGTT
Found at i:3354873 original size:18 final size:18
Alignment explanation
Indices: 3354852--3354908 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 18
3354842 TTATAGTTTC
*
3354852 TTATATTTTTTATAAATT
1 TTATATTTTTAATAAATT
3354870 TTATATTTTGTAATAAATTT
1 TTATATTTT-TAATAAA-TT
*
3354890 TTACATTTTTAATAAATT
1 TTATATTTTTAATAAATT
3354908 T
1 T
3354909 CTAATTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 12 0.34
19 13 0.37
20 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTATATTTTTAATAAATT
Found at i:3355968 original size:29 final size:26
Alignment explanation
Indices: 3355934--3355988 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 26
3355924 ACCAAAATAA
3355934 CATTTTATTTATTATATTTTTAATAATTT
1 CATTTTATTTATT-T-TTTTT-ATAATTT
*
3355963 CATTTTTTTTATTTTTTTTATAATTT
1 CATTTTATTTATTTTTTTTATAATTT
3355989 GAATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 5 0.20
28 1 0.04
29 12 0.48
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (26 bp):
CATTTTATTTATTTTTTTTATAATTT
Found at i:3355997 original size:26 final size:26
Alignment explanation
Indices: 3355939--3356011 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
3355929 AATAACATTT
* *
3355939 TATTTATTATATTTTTAATAATTTCAT
1 TATTT-TTATTTTTTTAATAATTTCAA
* * *
3355966 TTTTTTTATTTTTTTTATAATTTGAA
1 TATTTTTATTTTTTTAATAATTTCAA
* *
3355992 TATTTTAATTATTTTCAATA
1 TATTTTTATT-TTTTTAATA
3356012 GGCATAACGG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 25 0.69
27 11 0.31
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (26 bp):
TATTTTTATTTTTTTAATAATTTCAA
Found at i:3357211 original size:29 final size:30
Alignment explanation
Indices: 3357178--3357258 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
3357168 GGTATCTAAT
* *
3357178 TTTTTTTAATTTTATACTTAAATTTGACA-
1 TTTTTTTAATTTGATACTTAAACTTGACAC
* *
3357207 TTTTTTTAATTTGCTATTTAAACTTGACAC
1 TTTTTTTAATTTGATACTTAAACTTGACAC
* *
3357237 TTTTTCTTAAGTTGGTACTTAA
1 TTTTT-TTAATTTGATACTTAA
3357259 TCTTATCGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 25 0.58
30 5 0.12
31 13 0.30
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTTTTTAATTTGATACTTAAACTTGACAC
Found at i:3357332 original size:25 final size:24
Alignment explanation
Indices: 3357283--3357332 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
3357273 AATTTTGTAC
* *
3357283 TTGAACTTGATTTTTTTTCCTAAT
1 TTGAACTTAATTTTTTTTCCAAAT
3357307 TTGATACTTAATTTTTTTAT-CAAAT
1 TTGA-ACTTAATTTTTTT-TCCAAAT
3357332 T
1 T
3357333 GGTACTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 17 0.77
26 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (24 bp):
TTGAACTTAATTTTTTTTCCAAAT
Found at i:3357777 original size:18 final size:19
Alignment explanation
Indices: 3357753--3357806 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
3357743 TAAAAAAAAT
3357753 TAAATATTAAATTAAA-AA
1 TAAATATTAAATTAAATAA
* *
3357771 TATATATTAAATTTAAATAT
1 TAAATATTAAA-TTAAATAA
*
3357791 TAAATATTATATTAAA
1 TAAATATTAAATTAAA
3357807 GAGTTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 10 0.33
20 10 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATATTAAATTAAATAA
Found at i:3357781 original size:13 final size:13
Alignment explanation
Indices: 3357751--3357806 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
3357741 GATAAAAAAA
*
3357751 ATTAAATAT-TAA
1 ATTAAATATATAT
*
3357763 ATTAAAAATATAT
1 ATTAAATATATAT
* *
3357776 ATTAAATTTAAAT
1 ATTAAATATATAT
3357789 ATTAAATAT-TAT
1 ATTAAATATATAT
3357801 ATTAAA
1 ATTAAA
3357807 GAGTTTAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 16 0.44
13 20 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTAAATATATAT
Found at i:3357788 original size:6 final size:7
Alignment explanation
Indices: 3357751--3357799 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
3357741 GATAAAAAAA
3357751 ATTAAAT
1 ATTAAAT
3357758 ATT-AA-
1 ATTAAAT
3357763 ATTAAA-
1 ATTAAAT
* *
3357769 AATATAT
1 ATTAAAT
3357776 ATTAAAT
1 ATTAAAT
3357783 -TTAAAT
1 ATTAAAT
3357789 ATTAAAT
1 ATTAAAT
3357796 ATTA
1 ATTA
3357800 TATTAAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 3 0.09
6 14 0.40
7 18 0.51
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTAAAT
Found at i:3357801 original size:25 final size:25
Alignment explanation
Indices: 3357751--3357806 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
3357741 GATAAAAAAA
3357751 ATTAAATATTAAATTAAAAATATAT
1 ATTAAATATTAAATTAAAAATATAT
*
3357776 ATTAAAT-TTAAA-TATTAAATATTAT
1 ATTAAATATTAAATTA-AAAATA-TAT
3357801 ATTAAA
1 ATTAAA
3357807 GAGTTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 10 0.36
25 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTAAATATTAAATTAAAAATATAT
Found at i:3358815 original size:14 final size:14
Alignment explanation
Indices: 3358792--3358821 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3358782 TATTATTTCG
3358792 TTATTATATTGTTA
1 TTATTATATTGTTA
*
3358806 TTATTTTATTGTTA
1 TTATTATATTGTTA
3358820 TT
1 TT
3358822 GTTTGGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTATTATATTGTTA
Found at i:3363315 original size:19 final size:22
Alignment explanation
Indices: 3363291--3363335 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3363281 AATAACAAAA
3363291 AAAATTC-AAA-TTA-ATTTTT
1 AAAATTCAAAACTTATATTTTT
3363310 AAAATTCAAAACTTATATTTTT
1 AAAATTCAAAACTTATATTTTT
3363332 AAAA
1 AAAA
3363336 AATTATACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 3 0.13
22 10 0.43
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTCAAAACTTATATTTTT
Found at i:3377440 original size:2 final size:2
Alignment explanation
Indices: 3377433--3377478 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3377423 TGCAATCAGC
3377433 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
3377475 AT AT
1 AT AT
3377479 TGTTTTCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3380495 original size:31 final size:33
Alignment explanation
Indices: 3380376--3380498 Score: 110
Period size: 32 Copynumber: 3.5 Consensus size: 33
3380366 TTAGAGGTAT
3380376 AAATTATTAAAATATTTTTATTTGTATTAATTATTTA
1 AAATTATTAAAATATTTTTA--TGTATT-A-TATTTA
3380413 AAATT-TTAGATTAATTTATATTTTATGTATTATATATT-
1 AAATTATTA-A--AA--TAT-TTTTATGTATTATAT-TTA
*
3380451 AAATTATTTAAATATTTTTAT-TATTATATTTA
1 AAATTATTAAAATATTTTTATGTATTATATTTA
3380483 AAATT-TTAAAATATTT
1 AAATTATTAAAATATTT
3380499 CATGTGTAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
31 12 0.16
32 13 0.17
33 6 0.08
34 3 0.04
36 5 0.07
37 6 0.08
38 9 0.12
39 7 0.09
40 6 0.08
41 3 0.04
42 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
AAATTATTAAAATATTTTTATGTATTATATTTA
Found at i:3380497 original size:22 final size:22
Alignment explanation
Indices: 3380455--3380497 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3380445 TATATTAAAT
* *
3380455 TATTTAAATATTTTTATTATTA
1 TATTTAAATATTTTAAATATTA
3380477 TATTTAAA-ATTTTAAAATATT
1 TATTTAAATATTTT-AAATATT
3380498 TCATGTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTAAATATTTTAAATATTA
Found at i:3380873 original size:25 final size:23
Alignment explanation
Indices: 3380821--3380867 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3380811 CACGAGACAA
*
3380821 TTTCTT-CTTTTTTTTTCTTCCC
1 TTTCTTCCATTTTTTTTCTTCCC
3380843 -TTCTTCCATTTTTTTTCTTCCC
1 TTTCTTCCATTTTTTTTCTTCCC
3380865 TTT
1 TTT
3380868 TTCTTCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCTTCCATTTTTTTTCTTCCC
Found at i:3380963 original size:11 final size:11
Alignment explanation
Indices: 3380947--3380971 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3380937 CCTTCTTTCA
3380947 TTTTTTTCCAT
1 TTTTTTTCCAT
3380958 TTTTTTTCCAT
1 TTTTTTTCCAT
3380969 TTT
1 TTT
3380972 CTTCACTGTT
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTCCAT
Found at i:3381088 original size:30 final size:30
Alignment explanation
Indices: 3381054--3381110 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3381044 TTTTATAAAT
3381054 AATTAATATTT-AT-TATTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
3381084 AATTAATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
3381111 AACAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 19 0.76
31 4 0.16
32 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:3383032 original size:17 final size:17
Alignment explanation
Indices: 3382999--3383031 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3382989 TATCACTTGA
*
3382999 AAATTTTTAATAATTTT
1 AAATTTTAAATAATTTT
3383016 AAATTTTAAAT-ATTTT
1 AAATTTTAAATAATTTT
3383032 TTTAATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATTTTAAATAATTTT
Found at i:3386569 original size:14 final size:14
Alignment explanation
Indices: 3386533--3386574 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3386523 GTTATTTTAA
*
3386533 TATAC-TTAAATTT
1 TATACTTTAATTTT
*
3386546 GATA-TTTAATTTT
1 TATACTTTAATTTT
3386559 TATACTTTAATTTT
1 TATACTTTAATTTT
3386573 TA
1 TA
3386575 ACATAGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (14 bp):
TATACTTTAATTTT
Found at i:3389964 original size:17 final size:17
Alignment explanation
Indices: 3389944--3389977 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3389934 TTCCATAAAT
3389944 TATGGATAGCCATGAAA
1 TATGGATAGCCATGAAA
3389961 TATGGATAGCCATGAAA
1 TATGGATAGCCATGAAA
3389978 AAGGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TATGGATAGCCATGAAA
Found at i:3390250 original size:31 final size:31
Alignment explanation
Indices: 3390199--3390263 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3390189 CATAAAATGA
* * *
3390199 TCACTTAACTCTTCAGAAGTTTTTATTTAAG
1 TCACTGAACTATTCAAAAGTTTTTATTTAAG
3390230 TCACTGAACTATTCAAAAGTTTTTATTTAAG
1 TCACTGAACTATTCAAAAGTTTTTATTTAAG
3390261 TCA
1 TCA
3390264 TTGGATTTTT
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:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (31 bp):
TCACTGAACTATTCAAAAGTTTTTATTTAAG
Found at i:3391906 original size:20 final size:21
Alignment explanation
Indices: 3391878--3391916 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3391868 TATTTTACAT
*
3391878 TTTTACCT-CAAACCTTTTTA
1 TTTTACCTCCAAAACTTTTTA
*
3391898 TTTTCCCTCCAAAACTTTT
1 TTTTACCTCCAAAACTTTT
3391917 ACTCCCTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTACCTCCAAAACTTTTTA
Found at i:3394813 original size:31 final size:31
Alignment explanation
Indices: 3394778--3394849 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
3394768 TGCATATGCA
3394778 TTCATGCATTCATAAAATTTCGCATCACATT
1 TTCATGCATTCATAAAATTTCGCATCACATT
* * **
3394809 TTCATGCATTCATAAAGTTTTGCATTGCATT
1 TTCATGCATTCATAAAATTTCGCATCACATT
3394840 TTCATGCATT
1 TTCATGCATT
3394850 AAAAGTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (31 bp):
TTCATGCATTCATAAAATTTCGCATCACATT
Found at i:3399614 original size:50 final size:50
Alignment explanation
Indices: 3399560--3399666 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
3399550 AGAGAAACAA
* * * * * *
3399560 ATTGAAGCCACGATGGCGAATCTCATAT-ACCTAAAGCTGTAGAGGGGTAT
1 ATTGAAGCCACAATGGCAAATCTCAT-TCACCTAAAGCTATAGAAGGGCAG
*
3399610 ATTGAAGCCGCAATGGCAAATCTCATTCACCTAAAGCTATAGAAGGGCAG
1 ATTGAAGCCACAATGGCAAATCTCATTCACCTAAAGCTATAGAAGGGCAG
3399660 ATTGAAG
1 ATTGAAG
3399667 TCGTAAGAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (50 bp):
ATTGAAGCCACAATGGCAAATCTCATTCACCTAAAGCTATAGAAGGGCAG
Found at i:3399813 original size:40 final size:40
Alignment explanation
Indices: 3399746--3400309 Score: 246
Period size: 40 Copynumber: 14.3 Consensus size: 40
3399736 CGACCATGGG
* * *
3399746 GCAGATTGAAG-CAATCCAATCTTTTACCCTAATTAGAGA
1 GCAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
* *
3399785 GTAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGG
1 GCAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
* *
3399825 GCAGATTGAAGACTA-TCAAATCTTTTACTCTAATCAGAGG
1 GCAGATTGAAGACTATTC-AATCTTTTACCCTAATCAGAGA
* *
3399865 GTAGATTGAAGACTA-TCAAATCTTTTACCCTAATTAGAGA
1 GCAGATTGAAGACTATTC-AATCTTTTACCCTAATCAGAGA
* * * ** *
3399905 GCAGATTGAAGACCATCCAATCTCTTACCCCGATCATAG-
1 GCAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
* * * *
3399944 GACAGATTGAAGACCA-TCTAATCTCTTTTCCC-GATCATG-GG
1 G-CAGATTGAAGACTATTC-AATCT-TTTACCCTAATCA-GAGA
* * * * * *
3399985 GCAGATTAAAGACCATCCAAT-TTCTTA-CCTCGACCATG-GG
1 GCAGATTGAAGACTATTCAATCTT-TTACCCT-AATCA-GAGA
* *
3400025 GCATATTGAAG-CAATTCAATCTTTTACCCTAA-CTAGAG-
1 GCAGATTGAAGACTATTCAATCTTTTACCCTAATC-AGAGA
* * ** * * * *
3400063 GCCAGATTGAAGACCATCCGGTCTATTA-TCTCGACCATG-G-
1 G-CAGATTGAAGACTATTCAATCTTTTACCCT-AATCA-GAGA
* *
3400103 GCAGATTGAA-A-TAATTCAATCTTTTACCCTAACCAGAGG
1 GCAGATTGAAGACT-ATTCAATCTTTTACCCTAATCAGAGA
* * * ** * *
3400142 GCAGATTGAAGACCA-TCTGATCTCTTACCCCGACCATG-GG
1 GCAGATTGAAGACTATTC-AATCTTTTACCCTAATCA-GAGA
* * *
3400182 GCA-ATTTGAAG-C-AATCTAATCTTTTACCCTAACCAGAGG
1 GCAGA-TTGAAGACTATTC-AATCTTTTACCCTAATCAGAGA
* * * * * * *
3400221 GCAAATTGAAGACCATCCGATCTCTTACCCTAACCAG-GG
1 GCAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
* * *
3400260 GACAGATTGAA-ACAATCCAATCTTTTACCCTACT-AGA-A
1 G-CAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
3400298 GGCAGATTGAAG
1 -GCAGATTGAAG
3400310 CCATCAGATC
Statistics
Matches: 419, Mismatches: 67, Indels: 78
0.74 0.12 0.14
Matches are distributed among these distances:
37 1 0.00
38 34 0.08
39 116 0.28
40 255 0.61
41 13 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (40 bp):
GCAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGA
Found at i:3399869 original size:80 final size:79
Alignment explanation
Indices: 3399744--3400370 Score: 475
Period size: 80 Copynumber: 7.9 Consensus size: 79
3399734 CCCGACCATG
* * * ** * *
3399744 GGGCAGATTGAAG-CAATCCAATCTTTTACCCTAATTAGAGAGTAGATTGAAGACTATTCAATCT
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCAG-GGGCAGATTGAAGACTATTCAATCT
3399808 TTTACCCTAATCAGA
65 TTTACCCTAATCAGA
* * * * * * *
3399823 GGGCAGATTGAAGACTATCAAATCTTTTACTCTAATCAGAGGGTAGATTGAAGACTA-TCAAATC
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCAG-GGGCAGATTGAAGACTATTC-AATC
*
3399887 TTTTACCCTAATTAGA
64 TTTTACCCTAATCAGA
* * * * * *
3399903 GAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATAGGACAGATTGAAGACCA-TCTAATC
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCA-GGGGCAGATTGAAGACTATTC-AATC
* *
3399967 TCTTTTCCC-GATCATG-
64 T-TTTACCCTAATCA-GA
* * * *
3399983 GGGCAGATTAAAGACCATCCAATTTCTTA-CCTCGACCATGGGGCATATTGAAG-CAATTCAATC
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCT-GACCA-GGGGCAGATTGAAGACTATTCAATC
3400046 TTTTACCCTAA-CTAGA
64 TTTTACCCTAATC-AGA
* ** * * *
3400062 GGCCAGATTGAAGACCATCCGGTCTATTA-TCTCGACCATGGGCAGATTGAA-A-TAATTCAATC
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCT-GACCAGGGGCAGATTGAAGACT-ATTCAATC
*
3400124 TTTTACCCTAACCAGA
64 TTTTACCCTAATCAGA
** * *
3400140 GGGCAGATTGAAGACCATCTGATCTCTTACCCCGACCATGGGGCA-ATTTGAAG-C-AATCTAAT
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCA-GGGGCAGA-TTGAAGACTATTC-AAT
*
3400202 CTTTTACCCTAACCAGA
63 CTTTTACCCTAATCAGA
* * * * *
3400219 GGGCAAATTGAAGACCATCCGATCTCTTACCCTAACCAGGGGACAGATTGAA-ACAATCCAATCT
1 GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCAGGGG-CAGATTGAAGACTATTCAATCT
*
3400283 TTTACCCTACT-AGA
65 TTTACCCTAATCAGA
* * * * *
3400297 AGGCAGATTGAAG-CCAT-CAGATCTCTTA-CCTCGACCATGAGGCAGGTTGAAG-CAATCCAAT
1 GGGCAGATTGAAGACCATCCA-ATCTCTTACCCT-GACCA-GGGGCAGATTGAAGACTATTCAAT
*
3400358 ATTTTACCTCTAA
63 CTTTTACC-CTAA
3400371 AACTATAGAA
Statistics
Matches: 454, Mismatches: 66, Indels: 57
0.79 0.11 0.10
Matches are distributed among these distances:
76 4 0.01
77 40 0.09
78 99 0.22
79 145 0.32
80 159 0.35
81 7 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (79 bp):
GGGCAGATTGAAGACCATCCAATCTCTTACCCTGACCAGGGGCAGATTGAAGACTATTCAATCTT
TTACCCTAATCAGA
Found at i:3399991 original size:120 final size:120
Alignment explanation
Indices: 3399717--3400370 Score: 406
Period size: 120 Copynumber: 5.5 Consensus size: 120
3399707 CGAAGTTACA
* * *
3399717 ACCATCTGATCTCTTACCCCGACCATGGGGCAGATTGAAG-CAATCCAATCTTTTACCCTAATTA
1 ACCATCTAATCTCTTATCCCGACCATGGGGCAGATTGAAGACTATCCAATCTTTTACCCTAATTA
* * * * ** *
3399781 GAGAGTAGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
66 GAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCAGAGGACAGATTGAAG
* * * ** * * *
3399836 ACTATCAAATCTTTTA-CTCTAATCA-GAGGGTAGATTGAAGACTATCAAATCTTTTACCCTAAT
1 ACCATCTAATCTCTTATC-CCGACCATG-GGGCAGATTGAAGACTATCCAATCTTTTACCCTAAT
*
3399899 TAGAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATAGGACAGATTGAAG
64 TAGAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCAGAGGACAGATTGAAG
* * * * *
3399956 ACCATCTAATCTCTTTTCCCGATCATGGGGCAGATTAAAGACCATCCAAT-TTCTTACCTCGACC
1 ACCATCTAATCTCTTATCCCGACCATGGGGCAGATTGAAGACTATCCAATCTT-TTACC-CTA--
* * * * * * * *
3400020 A-T-G-GGGCATATTGAAG-CAATTCAATCTTTTA-CCCTAACTAGAGGCCAGATTGAAG
62 ATTAGAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATC-AGAGGACAGATTGAAG
*** * * * **
3400075 ACCATCCGGTCTATTATCTCGACCAT-GGGCAGATTGAA-A-TAATTCAATCTTTTACCCTAACC
1 ACCATCTAATCTCTTATCCCGACCATGGGGCAGATTGAAGACT-ATCCAATCTTTTACCCTAATT
* ** * *
3400137 AGAGGGCAGATTGAAGACCATCTGATCTCTTACCCCGACCATG-GGGCA-ATTTGAAG
65 AGAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCA-GAGGACAGA-TTGAAG
* * * * * * * *
3400193 -CAATCTAATCTTTTA-CCCTAACCA-GAGGGCAAATTGAAGACCATCCGATCTCTTACCCTAAC
1 ACCATCTAATCTCTTATCCC-GACCATG-GGGCAGATTGAAGACTATCCAATCTTTTACCCTAAT
* * * * *
3400255 CAG-GGGACAGATTGAA-ACAATCCAATCTTTTA-CCCTA-CTAGAAGG-CAGATTGAAG
64 TAGAGAG-CAGATTGAAGACCATCCAATCTCTTACCCCGATC-AG-AGGACAGATTGAAG
* * * *
3400310 -CCATC-AGATCTCTTA-CCTCGACCATGAGGCAGGTTGAAG-CAATCCAATATTTTACCTCTAA
1 ACCATCTA-ATCTCTTATCC-CGACCATGGGGCAGATTGAAGACTATCCAATCTTTTACC-CTAA
3400371 AACTATAGAA
Statistics
Matches: 416, Mismatches: 86, Indels: 68
0.73 0.15 0.12
Matches are distributed among these distances:
114 1 0.00
116 21 0.05
117 83 0.20
118 72 0.17
119 111 0.27
120 121 0.29
121 5 0.01
122 1 0.00
123 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (120 bp):
ACCATCTAATCTCTTATCCCGACCATGGGGCAGATTGAAGACTATCCAATCTTTTACCCTAATTA
GAGAGCAGATTGAAGACCATCCAATCTCTTACCCCGATCAGAGGACAGATTGAAG
Found at i:3400096 original size:79 final size:79
Alignment explanation
Indices: 3399787--3400370 Score: 537
Period size: 79 Copynumber: 7.4 Consensus size: 79
3399777 ATTAGAGAGT
* * * ** *
3399787 AGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACTATCAAATCTTTTA
1 AGATTGAAG-CAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
* * *
3399852 -CTCTAATCA-GAGGGT
65 CCTC-GACCATG-GGGC
* ** * *
3399867 AGATTGAAG-ACTATCAAATCTTTTACCCTAATTAGAGAGCAGATTGAAGACCATCCAATCTCTT
1 AGATTGAAGCAAT-TC-AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTT
* * * *
3399931 ACCCCGATCATAGGAC
64 ACCTCGACCATGGGGC
* * * * * * *
3399947 AGATTGAAGACCA-TCTAATCTCTTTTCCC-GATCATG-GGGCAGATTAAAGACCATCCAATTTC
1 AGATTGAAG-CAATTC-AATCT-TTTACCCTAACCA-GAGGGCAGATTGAAGACCATCCGATCTC
3400009 TTACCTCGACCATGGGGC
62 TTACCTCGACCATGGGGC
* * * * * *
3400027 ATATTGAAGCAATTCAATCTTTTACCCTAACTAGAGGCCAGATTGAAGACCATCCGGTCTATTAT
1 AGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTAC
3400092 CTCGACCAT-GGGC
66 CTCGACCATGGGGC
** *
3400105 AGATTGAAATAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCTGATCTCTTAC
1 AGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTAC
*
3400170 CCCGACCATGGGGC
66 CTCGACCATGGGGC
*
3400184 A-ATTTGAAGCAA-TCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCGATCTCTT
1 AGA-TTGAAGCAATTC-AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTT
*
3400247 ACC-CTAACCA-GGGGAC
64 ACCTC-GACCATGGGG-C
* * * * *
3400263 AGATTGAAACAATCCAATCTTTTACCCT-ACTAGAAGGCAGATTGAAG-CCATCAGATCTCTTAC
1 AGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTAC
*
3400326 CTCGACCATGAGGC
66 CTCGACCATGGGGC
* * *
3400340 AGGTTGAAGCAATCCAATATTTTACCTCTAA
1 AGATTGAAGCAATTCAATCTTTTACC-CTAA
3400371 AACTATAGAA
Statistics
Matches: 418, Mismatches: 64, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
77 44 0.11
78 106 0.25
79 132 0.32
80 127 0.30
81 9 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (79 bp):
AGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTAC
CTCGACCATGGGGC
Found at i:3400178 original size:157 final size:156
Alignment explanation
Indices: 3399787--3400370 Score: 551
Period size: 157 Copynumber: 3.7 Consensus size: 156
3399777 ATTAGAGAGT
* * * *
3399787 AGATTGAAGACTATTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACTATCAAATCTTTTA
1 AGATTGAA-ACAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCAAATCTCTTA
* ** * * * *
3399852 CTCTAATCA-GAGGGTAGATTGAAG-ACTATCAAATCTTTTACCCTAATTAGAGAGCAGATTGAA
65 CCCCGACCATG-GGGCAGATTGAAGCAAT-TCAAATCTTTTACCCTAACTAGAG-GCAGATTGAA
* * *
3399915 GACCATCCAATCTCTTACCCCGATCATAGGAC
127 GACCATCCGATCTCTTA-CCCGACCAT-GGGC
* * * * * * *
3399947 AGATTGAAGACCA-TCTAATCTCTTTTCCC-GATCATG-GGGCAGATTAAAGACCATCCAATTTC
1 AGATTGAA-ACAATTC-AATCT-TTTACCCTAACCA-GAGGGCAGATTGAAGACCATCAAATCTC
* *
3400009 TTACCTCGACCATGGGGCATATTGAAGCAATTC-AATCTTTTACCCTAACTAGAGGCCAGATTGA
62 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAAATCTTTTACCCTAACTAGAGG-CAGATTGA
* * *
3400073 AGACCATCCGGTCTATTATCTCGACCATGGGC
126 AGACCATCCGATCTCTTA-CCCGACCATGGGC
* **
3400105 AGATTGAAATAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCTGATCTCTTAC
1 AGATTGAAACAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCAAATCTCTTAC
* * *
3400170 CCCGACCATGGGGCA-ATTTGAAGCAA-TCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAGA
66 CCCGACCATGGGGCAGA-TTGAAGCAATTCAAATCTTTTACCCTAACTAGA-GGCAGATTGAAGA
* *
3400233 CCATCCGATCTCTTACCCTAACCAGGGGAC
129 CCATCCGATCTCTTACCC-GACCATGGG-C
* * * *
3400263 AGATTGAAACAATCCAATCTTTTACCCT-ACTAGAAGGCAGATTGAAG-CCATCAGATCTCTTAC
1 AGATTGAAACAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCAAATCTCTTAC
* * * * *
3400326 CTCGACCATGAGGCAGGTTGAAGCAA-TCCAATATTTTACCTCTAA
66 CCCGACCATGGGGCAGATTGAAGCAATTCAAATCTTTTACC-CTAA
3400371 AACTATAGAA
Statistics
Matches: 357, Mismatches: 51, Indels: 35
0.81 0.12 0.08
Matches are distributed among these distances:
156 61 0.17
157 129 0.36
158 43 0.12
159 52 0.15
160 62 0.17
161 10 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (156 bp):
AGATTGAAACAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCAAATCTCTTAC
CCCGACCATGGGGCAGATTGAAGCAATTCAAATCTTTTACCCTAACTAGAGGCAGATTGAAGACC
ATCCGATCTCTTACCCGACCATGGGC
Found at i:3400815 original size:67 final size:63
Alignment explanation
Indices: 3400643--3400812 Score: 215
Period size: 63 Copynumber: 2.7 Consensus size: 63
3400633 TTCTTATTAT
3400643 TTTTATTTATTTATTTATTATTTTTATGAAT-ATAAATAAATAAATATAAAATAATAATTATTTA
1 TTTTA-TTATTTATTTATTA-TTTTATGAATAATAAATAAATAAATATAAAATAATAATTATTTA
* * * * *
3400707 TTAT-TTATTTATTTATTATTGTATGAA-CATAAATAAATAAATGTAAAATAAT-ATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATAATAAATAAATAAATATAAAATAATAATT-A-TTTA
*
3400769 TTTTATTATTTATTTATTATTTTATGAAT-ATAGATAAATAAATA
1 TTTTATTATTTATTTATTATTTTATGAATAATAAATAAATAAATA
3400813 AATAACAAAC
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
60 3 0.03
61 32 0.34
62 20 0.22
63 35 0.38
64 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (63 bp):
TTTTATTATTTATTTATTATTTTATGAATAATAAATAAATAAATATAAAATAATAATTATTTA
Found at i:3406992 original size:31 final size:30
Alignment explanation
Indices: 3406927--3406990 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
3406917 ATACCAAAAC
*
3406927 TATACATGAATTATGGTTTAATGTGTAATTA
1 TATACATGAATTATGATTT-ATGTGTAATTA
* *
3406958 TATACATGAATTTTGATTT-TGTGTAATTT
1 TATACATGAATTATGATTTATGTGTAATTA
3406987 TATA
1 TATA
3406991 TATTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (30 bp):
TATACATGAATTATGATTTATGTGTAATTA
Found at i:3407007 original size:29 final size:29
Alignment explanation
Indices: 3406948--3407007 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3406938 TATGGTTTAA
* *
3406948 TGTGTAATTATATACATGAATTTTGATTT
1 TGTGTAATTATATACATAAATTTTGAATT
* *
3406977 TGTGTAATTTTATATATTAAATTTT-AATT
1 TGTGTAATTATATACA-TAAATTTTGAATT
3407006 TG
1 TG
3407008 ATCCAATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (29 bp):
TGTGTAATTATATACATAAATTTTGAATT
Found at i:3407777 original size:82 final size:82
Alignment explanation
Indices: 3407640--3407890 Score: 493
Period size: 82 Copynumber: 3.1 Consensus size: 82
3407630 CCAATACAAT
*
3407640 AAGCTCTACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
1 AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
3407705 AACAAGTAACACTATAC
66 AACAAGTAACACTATAC
3407722 AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
1 AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
3407787 AACAAGTAACACTATAC
66 AACAAGTAACACTATAC
3407804 AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
1 AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
3407869 AACAAGTAACACTATAC
66 AACAAGTAACACTATAC
3407886 AAGCT
1 AAGCT
3407891 CTGTTCATCA
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 168 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (82 bp):
AAGCTATACCCTATGTCAACATCCTTCCGAAGAACGGTGGTTCATTGCACAGCAGTGCAAATTGT
AACAAGTAACACTATAC
Found at i:3408729 original size:111 final size:108
Alignment explanation
Indices: 3408596--3408817 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 108
3408586 TGCTCTGTTG
3408596 CATCAGTTTCAGCTTCTGGAACCAGCTCCGAGCTTTTAAAATCTTCTTGTTCTTCATCTTTACCT
1 CATCAGTTTCAGCTTCTGGAACCAGCTCCGAGCTTTTAAAATCTTCTTGTTCTTCATCTTTACCT
3408661 GCATCGGTTTCTTCTTCTATCTCTTCTTCATCTTCATCTACTGCCT
66 GCATCGGTTTCTTCTTCTA--TC-TCTTCATCTTCATCTACTGCCT
3408707 CATCAGTTTCAGCTTCTGGAACCAGCTCCGAGCTTTTAAAATCTTCTTGTTCTTCATCTTTACCT
1 CATCAGTTTCAGCTTCTGGAACCAGCTCCGAGCTTTTAAAATCTTCTTGTTCTTCATCTTTACCT
3408772 GCATCGGTTTCTTCTTCTATCTCTTCATCTTCATCTACTGCCT
66 GCATCGGTTTCTTCTTCTATCTCTTCATCTTCATCTACTGCCT
3408815 CAT
1 CAT
3408818 TGGCTTCAAC
Statistics
Matches: 111, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
108 25 0.23
109 2 0.02
111 84 0.76
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.43
Consensus pattern (108 bp):
CATCAGTTTCAGCTTCTGGAACCAGCTCCGAGCTTTTAAAATCTTCTTGTTCTTCATCTTTACCT
GCATCGGTTTCTTCTTCTATCTCTTCATCTTCATCTACTGCCT
Found at i:3411945 original size:14 final size:13
Alignment explanation
Indices: 3411926--3411964 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3411916 ACCATCCTTG
*
3411926 CAAATAAAACGACA
1 CAAATAAAAC-AAA
3411940 CAAATAATAACAAA
1 CAAATAA-AACAAA
3411954 CAAATAAAACA
1 CAAATAAAACA
3411965 CGTGAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (13 bp):
CAAATAAAACAAA
Found at i:3416523 original size:21 final size:22
Alignment explanation
Indices: 3416484--3416525 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3416474 AGTTAGATGC
3416484 ATATATTTATCATAATTTATTAT
1 ATATATTTA-CATAATTTATTAT
*
3416507 ATATATTTA-ATATTTTATT
1 ATATATTTACATAATTTATT
3416526 TAAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTTACATAATTTATTAT
Found at i:3422866 original size:17 final size:17
Alignment explanation
Indices: 3422844--3422914 Score: 67
Period size: 17 Copynumber: 4.1 Consensus size: 17
3422834 TAAATTTTGA
*
3422844 ATTTAAATTTTGAATTT
1 ATTTAAATTTTAAATTT
3422861 ATTTAAA-TTTAAATTT
1 ATTTAAATTTTAAATTT
3422877 ATTTTAAA-TTTAAATTCAACT
1 A-TTTAAATTTTAAATT----T
3422898 ATTTAAA-TTTAAATTT
1 ATTTAAATTTTAAATTT
3422914 A
1 A
3422915 AATTTAAATC
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
16 11 0.23
17 21 0.44
20 14 0.29
21 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTTAAATTT
Found at i:3422870 original size:6 final size:6
Alignment explanation
Indices: 3422832--3422923 Score: 91
Period size: 6 Copynumber: 15.2 Consensus size: 6
3422822 ACTTTTATGT
* * *
3422832 TTTAAA TTTTGAA TTTAAA TTTTGAA TTT--A TTTAAA TTTAAA TTT-AT
1 TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
3422879 TTTAAA TTTAAA TTCAACTA TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA T
3422924 CAAATTATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
4 4 0.06
5 4 0.06
6 49 0.68
7 10 0.14
8 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:3423644 original size:22 final size:20
Alignment explanation
Indices: 3423605--3423655 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
3423595 CTCATTGAAT
3423605 ATTTTAAAT-GCATTAATTA
1 ATTTTAAATAGCATTAATTA
*
3423624 ATGTTTTAAATAGTATTAATTA
1 A--TTTTAAATAGCATTAATTA
3423646 ATTTTAAATA
1 ATTTTAAATA
3423656 AAAGCATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
21 8 0.29
22 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTTTAAATAGCATTAATTA
Done.