Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 275 of 290
Found at i:88175500 original size:5 final size:5
Alignment explanation
Indices: 88175490--88175514 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
88175480 GTGGTAAGAT
88175490 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
88175515 TAGGCCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:88181981 original size:10 final size:10
Alignment explanation
Indices: 88181968--88182097 Score: 69
Period size: 10 Copynumber: 13.5 Consensus size: 10
88181958 GTTTAATTAA
88181968 TTTTATAATT
1 TTTTATAATT
*
88181978 TTTT-TCAATA
1 TTTTAT-AATT
*
88181988 ATTTATTAATT
1 TTTTA-TAATT
88181999 TTTTAT-A-T
1 TTTTATAATT
88182007 TTTTATAA-T
1 TTTTATAATT
*
88182016 ATTTATAA-T
1 TTTTATAATT
* *
88182025 TTTAATAAAT
1 TTTTATAATT
*
88182035 TTATATCAA-T
1 TTTTAT-AATT
* *
88182045 TTTAATATTT
1 TTTTATAATT
88182055 TTTTAT-ATT
1 TTTTATAATT
**
88182064 TTTTATAACA
1 TTTTATAATT
**
88182074 TTTTACGATT
1 TTTTATAATT
88182084 TTTT-TAATT
1 TTTTATAATT
88182093 TTTTA
1 TTTTA
88182098 ATAAAAAATT
Statistics
Matches: 89, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.08
9 34 0.38
10 38 0.43
11 9 0.10
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:88181995 original size:29 final size:28
Alignment explanation
Indices: 88181963--88182076 Score: 90
Period size: 29 Copynumber: 4.0 Consensus size: 28
88181953 ATTAAGTTTA
*
88181963 ATTAATTTTATA-ATTTTTTTCAATAATTT
1 ATTAATTTTATATATTTTTAT-AAT-ATTT
*
88181992 ATTAATTTTTTATATTTTTATAATATTT
1 ATTAATTTTATATATTTTTATAATATTT
* *
88182020 A-TAATTTTAATAAATTTATATCAAT-TTT
1 ATTAATTTT-ATATATTTTTAT-AATATTT
* * * *
88182048 AATATTTTTTTATATTTTTTATAACATTT
1 ATTAATTTTATATA-TTTTTATAATATTT
88182077 TACGATTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
27 7 0.10
28 23 0.33
29 32 0.46
30 7 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTAATTTTATATATTTTTATAATATTT
Found at i:88182010 original size:9 final size:9
Alignment explanation
Indices: 88181985--88182099 Score: 65
Period size: 9 Copynumber: 12.6 Consensus size: 9
88181975 ATTTTTTTCA
*
88181985 ATAATTTAT
1 ATAATTTTT
88181994 -TAATTTTT
1 ATAATTTTT
88182002 -TATATTTTT
1 ATA-ATTTTT
*
88182011 ATAATATTT
1 ATAATTTTT
*
88182020 ATAATTTTA
1 ATAATTTTT
*
88182029 ATAAATTTAT
1 AT-AATTTTT
*
88182039 ATCAATTTTA
1 AT-AATTTTT
*
88182049 ATATTTTTTT
1 ATA-ATTTTT
*
88182059 ATATTTTTT
1 ATAATTTTT
*
88182068 ATAACATTTT
1 ATAA-TTTTT
**
88182078 ACGATTTTT
1 ATAATTTTT
*
88182087 TTAATTTTT
1 ATAATTTTT
88182096 -TAAT
1 ATAAT
88182100 AAAAAATTAG
Statistics
Matches: 82, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
8 13 0.16
9 40 0.49
10 29 0.35
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:88182019 original size:20 final size:20
Alignment explanation
Indices: 88181996--88182078 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 20
88181986 TAATTTATTA
*
88181996 ATTTTTTATATTTTTATAAT
1 ATTTTATATATTTTTATAAT
*
88182016 A-TTTATA-ATTTTAATAA-
1 ATTTTATATATTTTTATAAT
* *
88182033 A-TTTATATCAATTTTAATATT
1 ATTTTATAT--ATTTTTATAAT
* *
88182054 TTTTTATAT-TTTTTATAAC
1 ATTTTATATATTTTTATAAT
88182073 ATTTTA
1 ATTTTA
88182079 CGATTTTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
17 7 0.14
18 9 0.18
19 17 0.34
20 10 0.20
22 7 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATATATTTTTATAAT
Found at i:88182020 original size:17 final size:16
Alignment explanation
Indices: 88182000--88182040 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
88181990 TTATTAATTT
*
88182000 TTTATATTTTTATAATA
1 TTTATATTTTAATAA-A
88182017 TTTATAATTTTAATAAA
1 TTTAT-ATTTTAATAAA
88182034 TTTATAT
1 TTTATAT
88182041 CAATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTTAATAAA
Found at i:88182112 original size:29 final size:30
Alignment explanation
Indices: 88182051--88182112 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
88182041 CAATTTTAAT
* **
88182051 ATTTTTTTATATTTTTTATAACATTTTACG
1 ATTTTTTTATATTTTTTATAAAAAATTACG
88182081 ATTTTTTTA-ATTTTTTAATAAAAAATTA-G
1 ATTTTTTTATATTTTTT-ATAAAAAATTACG
88182110 ATT
1 ATT
88182113 AAACTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTTTTTATATTTTTTATAAAAAATTACG
Found at i:88196289 original size:15 final size:14
Alignment explanation
Indices: 88196263--88196304 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
88196253 AAATTTTGGT
88196263 TTTTGATATTTAAGG
1 TTTTGAT-TTTAAGG
88196278 TTTGTGATTTTAAGG
1 TTT-TGATTTTAAGG
*
88196293 TTTAGATTTTAA
1 TTTTGATTTTAA
88196305 AATTCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 13 0.52
16 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (14 bp):
TTTTGATTTTAAGG
Found at i:88199275 original size:28 final size:28
Alignment explanation
Indices: 88199238--88199293 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
88199228 AACAGAGAAG
88199238 AAAAAATATTACACAACAAAAATATGAT
1 AAAAAATATTACACAACAAAAATATGAT
*
88199266 AAAAAATATTACTCAACAAAAATATGAT
1 AAAAAATATTACACAACAAAAATATGAT
88199294 TTTCAATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.23
Consensus pattern (28 bp):
AAAAAATATTACACAACAAAAATATGAT
Found at i:88207089 original size:20 final size:19
Alignment explanation
Indices: 88207064--88207124 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
88207054 ATAATATTAT
88207064 TTTTTAAAATTTCAAATATA
1 TTTTTAAAATTT-AAATATA
88207084 TTTTTAAAA-TT--AT-T-
1 TTTTTAAAATTTAAATATA
88207098 TTTTTAAAATTTTAAATATA
1 TTTTTAAAA-TTTAAATATA
88207118 TTTTTAA
1 TTTTTAA
88207125 TAATATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 4 0.11
18 2 0.06
19 3 0.09
20 16 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATTTAAATATA
Found at i:88207099 original size:33 final size:34
Alignment explanation
Indices: 88207037--88207124 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
88207027 TTGGTTTTAA
* * * *
88207037 AAAATTTGAAATGT-TTTATAATATTA-TTTTTT
1 AAAATTTCAAATATATTTTTAAAATTATTTTTTT
88207069 AAAATTTCAAATATATTTTTAAAATTATTTTTTT
1 AAAATTTCAAATATATTTTTAAAATTATTTTTTT
*
88207103 AAAATTTTAAATATATTTTTAA
1 AAAATTTCAAATATATTTTTAA
88207125 TAATATAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
32 12 0.24
33 10 0.20
34 27 0.55
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (34 bp):
AAAATTTCAAATATATTTTTAAAATTATTTTTTT
Found at i:88207249 original size:14 final size:15
Alignment explanation
Indices: 88207224--88207255 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
88207214 TAATTTAACA
88207224 TATAATTTTTTAAAT
1 TATAATTTTTTAAAT
88207239 TATAA-TTTTTAAAT
1 TATAATTTTTTAAAT
88207253 TAT
1 TAT
88207256 TTTTAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATAATTTTTTAAAT
Found at i:88207367 original size:18 final size:19
Alignment explanation
Indices: 88207346--88207388 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
88207336 AATTAATTAG
88207346 AAAAAA-AATTTATTTGTT
1 AAAAAAGAATTTATTTGTT
*
88207364 AAAAAAGGATTTATTTGTT
1 AAAAAAGAATTTATTTGTT
88207383 AAAAAA
1 AAAAAA
88207389 TATAACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (19 bp):
AAAAAAGAATTTATTTGTT
Found at i:88210120 original size:30 final size:30
Alignment explanation
Indices: 88209994--88210103 Score: 168
Period size: 30 Copynumber: 3.7 Consensus size: 30
88209984 GTCGCAGAAC
88209994 AGTTCATATCACCCGGACATGGGCAGTTCG
1 AGTTCATATCACCCGGACATGGGCAGTTCG
* *
88210024 AGTTCATATCACCTGGACATGGGCGGCTT-G
1 AGTTCATATCACCCGGACATGGGCAG-TTCG
*
88210054 AGTTCATATCACCTGGACATGGGCAGTTCG
1 AGTTCATATCACCCGGACATGGGCAGTTCG
*
88210084 AGTTCATATCACCCAGACAT
1 AGTTCATATCACCCGGACAT
88210104 AAGCGGTTTG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
29 2 0.03
30 69 0.95
31 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATGGGCAGTTCG
Found at i:88210127 original size:60 final size:60
Alignment explanation
Indices: 88209994--88210120 Score: 200
Period size: 60 Copynumber: 2.1 Consensus size: 60
88209984 GTCGCAGAAC
* ** **
88209994 AGTTCATATCACCCGGACATGGGCAGTTCGAGTTCATATCACCTGGACATGGGCGGCTTG
1 AGTTCATATCACCTGGACATGGGCAGTTCGAGTTCATATCACCCAGACATAAGCGGCTTG
*
88210054 AGTTCATATCACCTGGACATGGGCAGTTCGAGTTCATATCACCCAGACATAAGCGGTTTG
1 AGTTCATATCACCTGGACATGGGCAGTTCGAGTTCATATCACCCAGACATAAGCGGCTTG
88210114 AGTTCAT
1 AGTTCAT
88210121 TCCACCTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (60 bp):
AGTTCATATCACCTGGACATGGGCAGTTCGAGTTCATATCACCCAGACATAAGCGGCTTG
Found at i:88212636 original size:39 final size:39
Alignment explanation
Indices: 88212582--88212661 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
88212572 ACCCGGGTTA
88212582 CTGAATAAAGGGCCATGAACATCTTCAAACTTCTCCGAG
1 CTGAATAAAGGGCCATGAACATCTTCAAACTTCTCCGAG
88212621 CTGAATAAAGGGCCATGAACATCTTCAAACTTCTCCGAG
1 CTGAATAAAGGGCCATGAACATCTTCAAACTTCTCCGAG
88212660 CT
1 CT
88212662 TTCATCAGCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (39 bp):
CTGAATAAAGGGCCATGAACATCTTCAAACTTCTCCGAG
Found at i:88213572 original size:30 final size:30
Alignment explanation
Indices: 88213538--88213613 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
88213528 TTTAAAATTA
*
88213538 ATTTAAAATTTTATAAT-TTATAAAAAATAT
1 ATTTAAAATTTTATAATATT-TAAAAAATAC
** * *
88213568 ATTTAAAATTAAAAAATATTTAAAATATAC
1 ATTTAAAATTTTATAATATTTAAAAAATAC
*
88213598 ATTTAAAATATTATAA
1 ATTTAAAATTTTATAA
88213614 AACAAATAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTTAAAATTTTATAATATTTAAAAAATAC
Found at i:88213581 original size:17 final size:17
Alignment explanation
Indices: 88213560--88213593 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
88213550 ATAATTTATA
88213560 AAAAATATATTTAAAATT
1 AAAAA-ATATTTAAAATT
88213578 AAAAAATATTTAAAAT
1 AAAAAATATTTAAAAT
88213594 ATACATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAATATTTAAAATT
Found at i:88213632 original size:120 final size:114
Alignment explanation
Indices: 88213522--88213808 Score: 305
Period size: 120 Copynumber: 2.5 Consensus size: 114
88213512 AAAACGTTTG
88213522 AATATCTTTAAAATTAATTTAAAATTTTATAATTTATAAAAAATATATTTAAAATTAAAAAATAT
1 AATATCTTTAAAATTAATTTAAAATTTTATAA-TTATAAAAAATATATTTAAAATTAAAAAAT-T
* *
88213587 TTAAAATAT-ACATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGT
64 TTAAAATATAAAATTTAAAATATTATAAAACAAATAATAAATTTTAAAGTT
*** * ** **
88213637 AATATCTTTAAAACTAATATATTTAAAAAAATAAAAAAATAAGAAAACTATA-AAACAAATTAAA
1 AATATCTTTAAAA-T--TA-ATTTAAAATTTTATAATTATAA-AAAA-TATATTTA-AAATTAAA
* * * *
88213701 AAATTTTAAATTTTAAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTT
59 AAATTTTAAAATATAAAATTTAAAATATTATAAAACAAATAATAAATTTTAAAGTT
* *
88213757 CATATCTTTAAAA-T-ATTTAAATATTTTAT-ATTATTAAAAATATATTTAAAAT
1 AATATCTTTAAAATTAATTTAAA-ATTTTATAATTATAAAAAATATATTTAAAAT
88213809 ATACATTTAA
Statistics
Matches: 138, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
112 8 0.06
113 5 0.04
114 11 0.08
115 16 0.12
116 2 0.01
118 6 0.04
119 25 0.18
120 65 0.47
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (114 bp):
AATATCTTTAAAATTAATTTAAAATTTTATAATTATAAAAAATATATTTAAAATTAAAAAATTTT
AAAATATAAAATTTAAAATATTATAAAACAAATAATAAATTTTAAAGTT
Found at i:88213818 original size:13 final size:13
Alignment explanation
Indices: 88213790--88213823 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
88213780 TTTTATATTA
*
88213790 TTAAAA-ATATAT
1 TTAAAATATACAT
88213802 TTAAAATATACAT
1 TTAAAATATACAT
88213815 TTAAAATAT
1 TTAAAATAT
88213824 TATAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAATATACAT
Found at i:88213831 original size:95 final size:96
Alignment explanation
Indices: 88213715--88214008 Score: 326
Period size: 95 Copynumber: 3.0 Consensus size: 96
88213705 TTTAAATTTT
88213715 AAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTTAAATA
1 AAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTTAAATA
88213780 TTTTATATTATTAAAAATATATTTAAAAT-A
66 TTTTATATTATTAAAAATATATTTAAAATAA
* * * * * * *
88213810 TACATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTA---ATAT
1 AAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAA-TATTTAAAT
* ** * **
88213872 ATTTTAAAAAATAAAAAAATAAGAAAACTATAAAACAAATTAA
65 ATTTTATATTAT-TAAAAAT------A-TAT-TTA-AAA-TAA
*
88213915 AAAATTTTAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTTAAATA
1 AAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTTAAATA
88213980 TTTTATATTATTAAAAATATATTTAAAAT
66 TTTTATATTATTAAAAATATATTTAAAAT
88214009 GTAAAAACTA
Statistics
Matches: 156, Mismatches: 27, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
93 12 0.08
94 6 0.04
95 49 0.31
96 3 0.02
97 3 0.02
98 1 0.01
99 3 0.02
100 2 0.01
101 3 0.02
102 1 0.01
103 3 0.02
104 3 0.02
105 49 0.31
106 6 0.04
107 12 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (96 bp):
AAAATTTAAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTTAAATA
TTTTATATTATTAAAAATATATTTAAAATAA
Found at i:88213934 original size:105 final size:105
Alignment explanation
Indices: 88213598--88213969 Score: 339
Period size: 105 Copynumber: 3.5 Consensus size: 105
88213588 TAAAATATAC
*
88213598 ATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTAATATATTTAA
1 ATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTAATATATTTTA
88213663 AAAAATAAAAAAATAAGAAAACTATAAAACAAATTAAAAA
66 AAAAATAAAAAAATAAGAAAACTATAAAACAAATTAAAAA
* ** * ** * * *
88213703 ATTTTAAAT-TT-T-AAA-ATTTAA-AATATTATAAAACTAATAATAAATTTGAAAGT--TCATA
1 ATTTAAAATATTATAAAACAAATAATAA-ATTTTAAAGGTAAT-AT--CTTTAAAACTAAT-ATA
* ** * *** * *
88213761 TCTTTAAAATATTTAAATAT-TTTATATTATTAAAA-ATATATTTAAAATATA
61 T-TTTAAAAAATAAAAAAATAAGAAAACTA-TAAAACA-A-A-TT-AAA-A-A
88213812 CATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTAATATATTTT
1 -ATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTAATATATTTT
88213877 AAAAAATAAAAAAATAAGAAAACTATAAAACAAATTAAAAA
65 AAAAAATAAAAAAATAAGAAAACTATAAAACAAATTAAAAA
* * * * *
88213918 ATTTTAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAA
1 ATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAA
88213970 TATTTAAATA
Statistics
Matches: 202, Mismatches: 42, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
100 2 0.01
101 15 0.07
102 6 0.03
103 10 0.05
104 28 0.14
105 56 0.28
106 3 0.01
107 4 0.02
108 4 0.02
109 3 0.01
110 9 0.04
111 29 0.14
112 10 0.05
113 6 0.03
114 15 0.07
115 2 0.01
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (105 bp):
ATTTAAAATATTATAAAACAAATAATAAATTTTAAAGGTAATATCTTTAAAACTAATATATTTTA
AAAAATAAAAAAATAAGAAAACTATAAAACAAATTAAAAA
Found at i:88214015 original size:20 final size:20
Alignment explanation
Indices: 88213990--88214060 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
88213980 TTTTATATTA
88213990 TTAAAAATATATTTAAAA-T
1 TTAAAAATATATTTAAAATT
* *
88214009 GTAAAAACTAATATTTAAATTT
1 TTAAAAA-T-ATATTTAAAATT
*
88214031 TTAAATATATATTTTAAAATT
1 TTAAAAATATA-TTTAAAATT
88214052 TTAAAAATA
1 TTAAAAATA
88214061 AATATTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.14
20 4 0.10
21 26 0.62
22 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (20 bp):
TTAAAAATATATTTAAAATT
Found at i:88214046 original size:21 final size:21
Alignment explanation
Indices: 88213977--88214056 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
88213967 AAATATTTAA
* * *
88213977 ATATTTTATATTATTAAAAAT
1 ATATTTTAAATTTTTAAATAT
* * **
88213998 ATATTTAAAATGTAAAAACTA-
1 ATATTTTAAATTTTTAAA-TAT
88214019 ATA-TTTAAATTTTTAAATAT
1 ATATTTTAAATTTTTAAATAT
*
88214039 ATATTTTAAAATTTTAAA
1 ATATTTTAAATTTTTAAA
88214057 AATAAATATT
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 28 0.64
22 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
ATATTTTAAATTTTTAAATAT
Found at i:88214050 original size:80 final size:78
Alignment explanation
Indices: 88213910--88214056 Score: 178
Period size: 80 Copynumber: 1.9 Consensus size: 78
88213900 TATAAAACAA
88213910 ATTAAAAAATTTTAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATATTT
1 ATTAAAAAATTTTAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAAT-TTT
88213975 AAATATTTTATATT
65 AAATATTTTATATT
* *
88213989 ATTAAAAATATATTTAAA-ATGTA-AAAACTAATATTTAAATTTTTAAA-TAT-ATAT-TTTAAA
1 ATTAAAAA-AT-TTTAAATAT-TATAAAACTAATA-ATAAA-TTTGAAAGT-TCATATCTTTAAA
88214049 ATTTTAAA
60 ATTTTAAA
88214057 AATAAATATT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
79 14 0.23
80 22 0.37
81 17 0.28
82 7 0.12
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (78 bp):
ATTAAAAAATTTTAAATATTATAAAACTAATAATAAATTTGAAAGTTCATATCTTTAAAATTTTA
AATATTTTATATT
Found at i:88222576 original size:52 final size:53
Alignment explanation
Indices: 88222504--88222609 Score: 196
Period size: 52 Copynumber: 2.0 Consensus size: 53
88222494 AAACTAGATG
88222504 AAAACACATGTCATTATACAATAAAAAAATATAATGCATAATTATGATGATAGT
1 AAAACACA-GTCATTATACAATAAAAAAATATAATGCATAATTATGATGATAGT
88222558 AAAACAC-GTCATTATACAATAAAAAAATATAATGCATAATTATGATGATAGT
1 AAAACACAGTCATTATACAATAAAAAAATATAATGCATAATTATGATGATAGT
88222610 TAATGTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 45 0.87
54 7 0.13
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.29
Consensus pattern (53 bp):
AAAACACAGTCATTATACAATAAAAAAATATAATGCATAATTATGATGATAGT
Found at i:88230128 original size:30 final size:31
Alignment explanation
Indices: 88230094--88230162 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
88230084 TTAGTAATGG
* *
88230094 TAAAACTACACTTTAACCTCTT-AAAAATTA
1 TAAAAATACAATTTAACCTCTTAAAAAATTA
** *
88230124 TAAAAATTTAATTTAACCTTTTAAAAAATTA
1 TAAAAATACAATTTAACCTCTTAAAAAATTA
88230155 TAAAAATA
1 TAAAAATA
88230163 TAGACTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (31 bp):
TAAAAATACAATTTAACCTCTTAAAAAATTA
Found at i:88230741 original size:27 final size:30
Alignment explanation
Indices: 88230695--88230752 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
88230685 ATGACTTTTC
*
88230695 AAAAATTCATACATGATTTAACTT-TAAAA
1 AAAAATTCATACAAGATTTAACTTATAAAA
*
88230724 AAAAATT-ATACAAG-TTTAAGTTATAAAA
1 AAAAATTCATACAAGATTTAACTTATAAAA
88230752 A
1 A
88230753 TTATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 12 0.46
29 7 0.27
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAATTCATACAAGATTTAACTTATAAAA
Found at i:88230835 original size:20 final size:21
Alignment explanation
Indices: 88230806--88230849 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
88230796 TGATAAAAAA
88230806 AAATCT-AAAAT-TATATTAT
1 AAATCTAAAAATATATATTAT
88230825 AAATACTAAAAATATATATTAT
1 AAAT-CTAAAAATATATATTAT
88230847 AAA
1 AAA
88230850 AAAATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 2 0.09
21 5 0.23
22 11 0.50
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATCTAAAAATATATATTAT
Found at i:88232381 original size:7 final size:7
Alignment explanation
Indices: 88232369--88232420 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
88232359 TTGTAAACAT
88232369 TTTTATA
1 TTTTATA
88232376 TTTTATA
1 TTTTATA
88232383 TTTTATA
1 TTTTATA
88232390 TTTTATAA
1 TTTTAT-A
88232398 TTATATATA
1 TT-T-TATA
*
88232407 TTTTGTAA
1 TTTTAT-A
88232415 TTTTAT
1 TTTTAT
88232421 TTCTTTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 22 0.56
8 10 0.26
9 4 0.10
10 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTTATA
Found at i:88232388 original size:14 final size:15
Alignment explanation
Indices: 88232369--88232420 Score: 70
Period size: 14 Copynumber: 3.4 Consensus size: 15
88232359 TTGTAAACAT
88232369 TTTTATATTTTAT-A
1 TTTTATATTTTATAA
88232383 TTTTATATTTTATAA
1 TTTTATATTTTATAA
*
88232398 TTATATATATTTTGTAA
1 TT-T-TATATTTTATAA
88232415 TTTTAT
1 TTTTAT
88232421 TTCTTTTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 13 0.38
15 6 0.18
16 2 0.06
17 13 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTATATTTTATAA
Found at i:88232527 original size:28 final size:29
Alignment explanation
Indices: 88232496--88232556 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
88232486 CTTTTCTATA
**
88232496 TTTTTAATAATTTTAATAAATTTTAA-AT
1 TTTTTAATAATGGTAATAAATTTTAATAT
* * *
88232524 TTTTTTATTATGGTAATAATTTTTAATAT
1 TTTTTAATAATGGTAATAAATTTTAATAT
88232553 TTTT
1 TTTT
88232557 CTGTAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTTAATAATGGTAATAAATTTTAATAT
Found at i:88234483 original size:41 final size:41
Alignment explanation
Indices: 88234420--88234530 Score: 204
Period size: 41 Copynumber: 2.7 Consensus size: 41
88234410 CCTTCCGGGG
**
88234420 CTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
88234461 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
88234502 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
88234531 AAAAACATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:88234921 original size:22 final size:23
Alignment explanation
Indices: 88234871--88234921 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
88234861 ATATGATTTA
88234871 GAGTTTAAGGTTTAGGAGTTACT
1 GAGTTTAAGGTTTAGGAGTTACT
*
88234894 -ATTTTAAGGTTTATGGA-TTA-T
1 GAGTTTAAGGTTTA-GGAGTTACT
88234915 GAGTTTA
1 GAGTTTA
88234922 GGGGTTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (23 bp):
GAGTTTAAGGTTTAGGAGTTACT
Found at i:88235004 original size:34 final size:34
Alignment explanation
Indices: 88234938--88235018 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
88234928 ATAGTTTACA
*
88234938 GTTTATGGTTTAAGATATAGGGTTTAAGGGTTGCG
1 GTTTATGGTTTAAGATATA-GGATTAAGGGTTGCG
* *
88234973 GTTTATGGTTTAAGGTTATA-GATTAAGGGTTGGG
1 GTTTATGGTTTAA-GATATAGGATTAAGGGTTGCG
*
88235007 GTTTAAGGTTTA
1 GTTTATGGTTTA
88235019 GGGGTTGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
34 23 0.56
35 13 0.32
36 5 0.12
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.42
Consensus pattern (34 bp):
GTTTATGGTTTAAGATATAGGATTAAGGGTTGCG
Found at i:88235189 original size:16 final size:17
Alignment explanation
Indices: 88235170--88235211 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
88235160 AAATTCTTTA
88235170 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
88235186 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
88235203 TAAAATAAT
1 T-AAATAAT
88235212 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:88235422 original size:21 final size:22
Alignment explanation
Indices: 88235404--88235444 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
88235394 ATGGTTTATT
88235404 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
*
88235425 GTTTAGGGGTTAGGGATTTA
1 GTTTAAGGGTTAGGGATTTA
88235445 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:88235698 original size:23 final size:23
Alignment explanation
Indices: 88235670--88235716 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
88235660 AACTAATAAT
88235670 TTTTAACAAATAAAATAAA-AAAA
1 TTTTAACAAAT-AAATAAATAAAA
88235693 TTTTAACAAATAAATAAATAAAA
1 TTTTAACAAATAAATAAATAAAA
88235716 T
1 T
88235717 CACTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
TTTTAACAAATAAATAAATAAAA
Found at i:88235802 original size:38 final size:39
Alignment explanation
Indices: 88235719--88235803 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
88235709 AATAAAATCA
*
88235719 CTAAAAATAAGCATTAGCGGCGCTTTTCGGAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
* * *
88235758 CTAAAAATGAGCATTAGTGGCG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAA-CGCCG
*
88235797 CAAAAAA
1 CTAAAAA
88235804 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
Found at i:88236674 original size:38 final size:38
Alignment explanation
Indices: 88236594--88236675 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
88236584 GGTTACAAAC
* * * *
88236594 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
88236632 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
88236670 TTTATC
1 TTTATC
88236676 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:88239440 original size:43 final size:43
Alignment explanation
Indices: 88239393--88239577 Score: 273
Period size: 43 Copynumber: 4.3 Consensus size: 43
88239383 TTTGTTTTTT
* * *
88239393 AAGCGTCGCTAAAGGTCAGGGTCTTTAGCGGCATTTGTCGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
* * * *
88239436 AAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGAAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
*
88239479 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
* *
88239522 AAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGT-GGGA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
88239564 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
88239578 TTAGCGACGC
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 17 0.13
43 113 0.87
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
Found at i:88239448 original size:85 final size:85
Alignment explanation
Indices: 88239332--88239577 Score: 264
Period size: 86 Copynumber: 2.9 Consensus size: 85
88239322 AAAGCCATGT
** * * *****
88239332 TTTAGCGGCGTTTGTTAAAAAGCGCCGCTAAAACTCATCTTCATT-GTGGCGTTTGTTTTTTAAG
1 TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAAG
*
88239396 CGTCGCTAAAGGTCAGGGTC
66 CGCCGCTAAAGGTCAGGGTC
* * * *
88239416 TTTAGCGGCATTTGTCGGAAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGAAAAA
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAA
*
88239481 GCGCCGCTAAAGGTCATGGTC
65 GCGCCGCTAAAGGTCAGGGTC
** * **
88239502 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT-GATCTTTAGCGGCGTTTGT-GGGAA
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAACTCATCG-TCATTAGCGGCGTTTGTCGAAAA
88239565 AGCGCCGCTAAAG
64 AGCGCCGCTAAAG
88239578 TTAGCGACGC
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
84 14 0.10
85 41 0.30
86 83 0.60
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAAG
CGCCGCTAAAGGTCAGGGTC
Found at i:88254454 original size:12 final size:12
Alignment explanation
Indices: 88254437--88254484 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
88254427 TGGGAGTAAA
88254437 GTTTTATATTTG
1 GTTTTATATTTG
*
88254449 GTTTTATATGTTAAA
1 GTTTTATAT-TT--G
88254464 GTTTTATATTTG
1 GTTTTATATTTG
88254476 GTTTTATAT
1 GTTTTATAT
88254485 GTTAATGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
GTTTTATATTTG
Found at i:88254467 original size:27 final size:27
Alignment explanation
Indices: 88254433--88254489 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
88254423 TTAATGGGAG
88254433 TAAAGTTTTATATTTGGTTTTATATGT
1 TAAAGTTTTATATTTGGTTTTATATGT
88254460 TAAAGTTTTATATTTGGTTTTATATGT
1 TAAAGTTTTATATTTGGTTTTATATGT
88254487 TAA
1 TAA
88254490 TGACATATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (27 bp):
TAAAGTTTTATATTTGGTTTTATATGT
Found at i:88256345 original size:25 final size:24
Alignment explanation
Indices: 88256306--88256353 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
88256296 TCTGTAATTC
88256306 AATTTTTATTTGTATTATTAGTTGG
1 AATTTTTATTTGTA-TATTAGTTGG
*
88256331 AATTTTT-TTTCGTATGTTAGTTG
1 AATTTTTATTT-GTATATTAGTTG
88256354 TCTACAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (24 bp):
AATTTTTATTTGTATATTAGTTGG
Found at i:88265589 original size:43 final size:43
Alignment explanation
Indices: 88265528--88265613 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
88265518 TATATGATTG
* *
88265528 ATATTGAAATGACAAATATGATAAGTGAATATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
* *
88265571 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
88265614 TGAGATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.26
Consensus pattern (43 bp):
ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:88267636 original size:18 final size:18
Alignment explanation
Indices: 88267613--88267676 Score: 110
Period size: 18 Copynumber: 3.6 Consensus size: 18
88267603 TAAATAAATA
88267613 TACTGAATAACTGACTGC
1 TACTGAATAACTGACTGC
*
88267631 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGC
*
88267649 TACTGGATAACTGACTGC
1 TACTGAATAACTGACTGC
88267667 TACTGAATAA
1 TACTGAATAA
88267677 TTTATCGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (18 bp):
TACTGAATAACTGACTGC
Found at i:88267704 original size:18 final size:18
Alignment explanation
Indices: 88267613--88267704 Score: 105
Period size: 18 Copynumber: 5.1 Consensus size: 18
88267603 TAAATAAATA
*
88267613 TACTGAATAACTGACTGC
1 TACTGAATAACTGACTGT
88267631 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGT
* *
88267649 TACTGGATAACTGACTGC
1 TACTGAATAACTGACTGT
* *
88267667 TACTGAATAATTTA-TCGT
1 TACTGAATAACTGACT-GT
* *
88267685 TATTGAATAATTGACTGT
1 TACTGAATAACTGACTGT
88267703 TA
1 TA
88267705 AAGAGTGATT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 1 0.02
18 61 0.97
19 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGACTGT
Found at i:88267757 original size:18 final size:18
Alignment explanation
Indices: 88267683--88267765 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
88267673 ATAATTTATC
* *
88267683 GTTATTGAATAATTGACT
1 GTTATTGAATGATTGAAT
** *
88267701 GTTAAAGAGTGATTGAAT
1 GTTATTGAATGATTGAAT
* * *
88267719 ATTATTGAACGACT-AATT
1 GTTATTGAATGATTGAA-T
88267737 GTTATTGAATGATTGAAT
1 GTTATTGAATGATTGAAT
*
88267755 GTTACTGAATG
1 GTTATTGAATG
88267766 CAACTGACAA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
17 2 0.04
18 44 0.92
19 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (18 bp):
GTTATTGAATGATTGAAT
Found at i:88276106 original size:22 final size:23
Alignment explanation
Indices: 88276063--88276106 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
88276053 TCCAATTCAA
* *
88276063 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAAATAAAGTCATG
*
88276086 CATATTTT-AAAATAACGTCAT
1 CATATTTTCAAAATAAAGTCAT
88276107 CACATACCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
CATATTTTCAAAATAAAGTCATG
Found at i:88279867 original size:49 final size:49
Alignment explanation
Indices: 88279786--88279879 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
88279776 TCAAGAAGGG
* * * *
88279786 ATAAATAGTGATCAGAGTGTAAACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAAACAATAGAAGACCAAGTTTAGCAATGT
*
88279835 ATAAATAGTGATAAGAGTGTAGAA-AATAGAAGACCAATTTTAGCA
1 ATAAATAGTGATAAGAGTGTA-AACAATAGAAGACCAAGTTTAGCA
88279880 TTGCATAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 37 0.95
50 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAAACAATAGAAGACCAAGTTTAGCAATGT
Found at i:88280799 original size:32 final size:32
Alignment explanation
Indices: 88280758--88280821 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
88280748 TAGTAAGTTC
88280758 ATAGGAATAAATCATAAATCTTACCAAACATT
1 ATAGGAATAAATCATAAATCTTACCAAACATT
88280790 ATAGGAATAAATCATAAATCTTACCAAACATT
1 ATAGGAATAAATCATAAATCTTACCAAACATT
88280822 CATACTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (32 bp):
ATAGGAATAAATCATAAATCTTACCAAACATT
Found at i:88288520 original size:11 final size:10
Alignment explanation
Indices: 88288483--88288631 Score: 81
Period size: 10 Copynumber: 14.7 Consensus size: 10
88288473 TTTTTATTAG
*
88288483 AATTTATTAT
1 AATTTTTTAT
88288493 AA-TTTTTAT
1 AATTTTTTAT
**
88288502 AAACTTTTAT
1 AATTTTTTAT
88288512 GAATTTTTTAAT
1 -AATTTTTT-AT
*
88288524 AATATTTTAT
1 AATTTTTTAT
*
88288534 AAGTTTTTAT
1 AATTTTTTAT
* *
88288544 AAGTTTATAT
1 AATTTTTTAT
88288554 AATTTTTT-T
1 AATTTTTTAT
** *
88288563 AAGATTTAAT
1 AATTTTTTAT
*
88288573 -ATTTTTAAT
1 AATTTTTTAT
*
88288582 GA-TTTTTAT
1 AATTTTTTAT
88288591 GAAATTATTTTTAT
1 --AA-T-TTTTTAT
*
88288605 AATTTTTAAT
1 AATTTTTTAT
*
88288615 AAATTTTTAT
1 AATTTTTTAT
*
88288625 GATTTTT
1 AATTTTT
88288632 AAATAAAAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
9 27 0.25
10 54 0.50
11 15 0.14
12 4 0.04
14 7 0.07
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.60
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:88288542 original size:32 final size:31
Alignment explanation
Indices: 88288472--88288569 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 31
88288462 ATACACTTTT
88288472 ATTTTTATTAGAATTTATTATAATTTTTATAA
1 ATTTTTA-TAGAATTTATTATAATTTTTATAA
* *
88288504 ACTTTTAT-GAATTTTTTAATAATATTTTATAA
1 ATTTTTATAGAATTTATT-ATAAT-TTTTATAA
* * *
88288536 GTTTTTATA-AGTTTA-TATAATTTTTTTAA
1 ATTTTTATAGAATTTATTATAATTTTTATAA
88288565 GATTT
1 -ATTT
88288570 AATATTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
29 7 0.13
30 16 0.30
31 7 0.13
32 24 0.44
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (31 bp):
ATTTTTATAGAATTTATTATAATTTTTATAA
Found at i:88288565 original size:19 final size:20
Alignment explanation
Indices: 88288472--88288579 Score: 84
Period size: 22 Copynumber: 5.3 Consensus size: 20
88288462 ATACACTTTT
*
88288472 ATTTTTATTAGAATTTATTATA
1 ATTTTTATAAG-ATTTA-TATA
88288494 ATTTTTATAA-ACTTT-TATGA
1 ATTTTTATAAGA-TTTATAT-A
*
88288514 ATTTTTTAATAATATTT-TATA
1 A-TTTTT-ATAAGATTTATATA
88288535 AGTTTTTATAAG-TTTATATA
1 A-TTTTTATAAGATTTATATA
*
88288555 ATTTTTTTAAGATTTA-AT-
1 ATTTTTATAAGATTTATATA
88288573 ATTTTTA
1 ATTTTTA
88288580 ATGATTTTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.08
19 17 0.23
20 16 0.22
21 15 0.20
22 19 0.26
23 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTTTTATAAGATTTATATA
Found at i:88288577 original size:16 final size:17
Alignment explanation
Indices: 88288553--88288586 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
88288543 TAAGTTTATA
*
88288553 TAATTTTTTTAA-GATT
1 TAATATTTTTAATGATT
88288569 TAATATTTTTAATGATT
1 TAATATTTTTAATGATT
88288586 T
1 T
88288587 TTATGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TAATATTTTTAATGATT
Found at i:88288579 original size:29 final size:28
Alignment explanation
Indices: 88288516--88288590 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
88288506 TTTTATGAAT
* *
88288516 TTTTTAATAATATTTTATAAGTTTTTATA
1 TTTTTAATAAT-TTTTATAAGATTTAATA
** *
88288545 AGTTTATATAATTTTTTTAAGATTTAATA
1 TTTTTA-ATAATTTTTATAAGATTTAATA
*
88288574 TTTTTAATGATTTTTAT
1 TTTTTAATAATTTTTAT
88288591 GAAATTATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
28 9 0.25
29 22 0.61
30 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTAATAATTTTTATAAGATTTAATA
Found at i:88288622 original size:20 final size:20
Alignment explanation
Indices: 88288472--88288638 Score: 81
Period size: 20 Copynumber: 8.6 Consensus size: 20
88288462 ATACACTTTT
*
88288472 ATTTTTATTAGAATTTATTATA
1 ATTTTTAATA-AATTT-TTATA
*
88288494 ATTTTT-ATAAACTTTTATGA
1 ATTTTTAATAAATTTTTAT-A
88288514 ATTTTTTAAT-AATATTTTATA
1 A-TTTTTAATAAAT-TTTTATA
* *
88288535 AGTTTTT-ATAAGTTTATATA
1 A-TTTTTAATAAATTTTTATA
* *
88288555 ATTTTT-TTAAGA-TTTAAT-
1 ATTTTTAATAA-ATTTTTATA
* *
88288573 ATTTTTAAT-GATTTTTATG
1 ATTTTTAATAAATTTTTATA
*
88288592 A-----AAT-TATTTTTATA
1 ATTTTTAATAAATTTTTATA
*
88288606 ATTTTTAATAAATTTTTATG
1 ATTTTTAATAAATTTTTATA
88288626 ATTTTTAAATAAA
1 ATTTTT-AATAAA
88288639 AAATATAATA
Statistics
Matches: 112, Mismatches: 17, Indels: 33
0.69 0.10 0.20
Matches are distributed among these distances:
14 12 0.11
17 1 0.01
18 11 0.10
19 21 0.19
20 29 0.26
21 24 0.21
22 14 0.12
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTTAATAAATTTTTATA
Found at i:88288631 original size:21 final size:20
Alignment explanation
Indices: 88288597--88288638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
88288587 TTATGAAATT
*
88288597 ATTTTTATAATTTTTAATAA
1 ATTTTTATAATTTTAAATAA
*
88288617 ATTTTTATGATTTTTAAATAA
1 ATTTTTAT-AATTTTAAATAA
88288638 A
1 A
88288639 AAATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTTATAATTTTAAATAA
Found at i:88292468 original size:29 final size:30
Alignment explanation
Indices: 88292436--88292502 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
88292426 TTAAGAATAA
* *
88292436 GTAT-ATTTATCATTTAAAAAAAATCAAAT
1 GTATAATTAATCATTTAAAAAAAATAAAAT
* *
88292465 GTATAATTAATTATTTAAAACAAATAAAAT
1 GTATAATTAATCATTTAAAAAAAATAAAAT
*
88292495 -TTTAATTA
1 GTATAATTA
88292503 CATTTCAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (30 bp):
GTATAATTAATCATTTAAAAAAAATAAAAT
Found at i:88293681 original size:28 final size:29
Alignment explanation
Indices: 88293650--88293714 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
88293640 TAGAAGGTTT
*
88293650 AAATATTATTTAAAATAT-AAAAATATAA
1 AAATATTATTGAAAATATAAAAAATATAA
* *
88293678 AAATTATT-TTGAAATTATAAAAAATATAT
1 AAA-TATTATTGAAAATATAAAAAATATAA
*
88293707 AATTATTA
1 AAATATTA
88293715 AAAAAATCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AAATATTATTGAAAATATAAAAAATATAA
Found at i:88301088 original size:22 final size:22
Alignment explanation
Indices: 88301044--88301088 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
88301034 TAGCAAACAA
* *
88301044 ATATAAATATAAATAATTGTAT
1 ATATAAATATAAAAAATTATAT
88301066 ATATAAATA-AAAAAATTA-AT
1 ATATAAATATAAAAAATTATAT
88301086 ATA
1 ATA
88301089 AGCAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATAAATATAAAAAATTATAT
Found at i:88306497 original size:12 final size:13
Alignment explanation
Indices: 88306482--88306513 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
88306472 ATAACACATT
88306482 TCAAAAC-ATGCA
1 TCAAAACTATGCA
88306494 TCAAAACTATGCA
1 TCAAAACTATGCA
88306507 -CAAAACT
1 TCAAAACT
88306514 TAACATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:88317167 original size:100 final size:100
Alignment explanation
Indices: 88316994--88317191 Score: 342
Period size: 100 Copynumber: 2.0 Consensus size: 100
88316984 AGACGGCAAT
* *
88316994 GAGAATGTGCGATTTTCGAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCTTTTACATCATG
1 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG
88317059 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC
66 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC
**
88317094 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATTGTG
1 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG
* *
88317159 TCAATAGGCGTTTAAACCACGTGCCTTCCGGTT
66 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTT
88317192 TTAGCCCACT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (100 bp):
GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG
TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC
Found at i:88317331 original size:29 final size:30
Alignment explanation
Indices: 88317296--88317352 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
88317286 TGGTTTAATA
*
88317296 TGTAATTGTATATATG-AATTTTAATTTTG
1 TGTAATTGTATACATGAAATTTTAATTTTG
* *
88317325 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTGTATACATGAAATTTTAATTT
88317353 GATCCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTAATTGTATACATGAAATTTTAATTTTG
Found at i:88317559 original size:31 final size:30
Alignment explanation
Indices: 88317491--88317547 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
88317481 GACTAAATCA
*
88317491 AAATTAAAATTTCATGTGTATAATTGCATC
1 AAATTAAAATTTCATGTATATAATTGCATC
88317521 AAATTAAAA-TTCATGTATATAATTGCA
1 AAATTAAAATTTCATGTATATAATTGCA
88317548 CATTAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (30 bp):
AAATTAAAATTTCATGTATATAATTGCATC
Found at i:88317790 original size:20 final size:22
Alignment explanation
Indices: 88317746--88317806 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
88317736 AAAGTTTTTA
* *
88317746 AAATACAATTTTATTAAATAAT
1 AAATATAATTTTATTAAACAAT
*
88317768 AAATA-AATTTT-TTAAACAGT
1 AAATATAATTTTATTAAACAAT
88317788 AAATATTAATTTTATTAAA
1 AAATA-TAATTTTATTAAA
88317807 AATTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 12 0.35
21 6 0.18
22 11 0.32
23 5 0.15
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATAATTTTATTAAACAAT
Found at i:88317828 original size:23 final size:22
Alignment explanation
Indices: 88317752--88317828 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
88317742 TTTAAAATAC
88317752 AATTTTATTAAATAA-TAAATA--
1 AATTTT-TTAAA-AAGTAAATATT
*
88317773 AATTTTTTAAACAGTAAATATT
1 AATTTTTTAAAAAGTAAATATT
* *
88317795 AATTTTATTAAAAATTATATTATT
1 AATTTT-TTAAAAAGTA-AATATT
88317819 AATTTTTTAA
1 AATTTTTTAA
88317829 TGCAATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 11 0.23
21 6 0.13
22 6 0.13
23 12 0.26
24 11 0.23
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AATTTTTTAAAAAGTAAATATT
Found at i:88332110 original size:22 final size:22
Alignment explanation
Indices: 88332085--88332128 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
88332075 TAGTCATATA
88332085 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* *
88332107 ATAAATTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
88332129 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:88332174 original size:16 final size:16
Alignment explanation
Indices: 88332152--88332188 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
88332142 AATTTTATTT
88332152 TAATAATAAACTTTAAA
1 TAATAATAAA-TTTAAA
88332169 -AATAATAAATTTAAA
1 TAATAATAAATTTAAA
88332184 TAATA
1 TAATA
88332189 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAAATTTAAA
Found at i:88332497 original size:29 final size:29
Alignment explanation
Indices: 88332456--88332518 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
88332446 TTTTTAAATA
88332456 AAAAATAATCATTTAGTAGTCATGTAATT
1 AAAAATAATCATTTAGTAGTCATGTAATT
*
88332485 AAAAATACTCATTTAGTAGTCATGTAATT
1 AAAAATAATCATTTAGTAGTCATGTAATT
88332514 AAAAA
1 AAAAA
88332519 ATGACGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (29 bp):
AAAAATAATCATTTAGTAGTCATGTAATT
Found at i:88332945 original size:18 final size:18
Alignment explanation
Indices: 88332922--88332963 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
88332912 TTCAAGGTGT
88332922 AATTAATTTAAAATT-TTC
1 AATTAA-TTAAAATTATTC
*
88332940 AATTAATTAAATTTATTC
1 AATTAATTAAAATTATTC
88332958 AATTAA
1 AATTAA
88332964 AAATCTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAAAATTATTC
Found at i:88341848 original size:16 final size:16
Alignment explanation
Indices: 88341827--88341863 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
88341817 CTAAGAAATT
*
88341827 AAACACATATAATTGA
1 AAACACACATAATTGA
88341843 AAACACACATAATTGA
1 AAACACACATAATTGA
*
88341859 GAACA
1 AAACA
88341864 AGATCTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (16 bp):
AAACACACATAATTGA
Found at i:88344940 original size:19 final size:19
Alignment explanation
Indices: 88344859--88344940 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
88344849 CACCAGGATA
* *
88344859 CACTTCGTGTGCCAAGATG
1 CACTTTGTGTGCCAATATG
** *
88344878 CACTACGTGTGCCAGTATG
1 CACTTTGTGTGCCAATATG
* *
88344897 CACTTTGTGCGTCAATATG
1 CACTTTGTGTGCCAATATG
* *
88344916 CGCTTTGTGTACCAATATG
1 CACTTTGTGTGCCAATATG
88344935 CACTTT
1 CACTTT
88344941 ACATGCCAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (19 bp):
CACTTTGTGTGCCAATATG
Found at i:88350913 original size:9 final size:9
Alignment explanation
Indices: 88350883--88350963 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 9
88350873 ACTTTCATTA
88350883 AATTTTAA-
1 AATTTTAAT
88350891 AATTTATAAT
1 AATTT-TAAT
88350901 -ATTTTAAT
1 AATTTTAAT
*
88350909 AATTTCTTAT
1 AATTT-TAAT
*
88350919 CATTTTTAAT
1 -AATTTTAAT
* *
88350929 AACTTCAAT
1 AATTTTAAT
88350938 AAATTTTAAT
1 -AATTTTAAT
*
88350948 -ATTTTATAA
1 AATTTTA-AT
88350957 AATTTTA
1 AATTTTA
88350964 TTTGAAAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 15 0.27
9 18 0.32
10 19 0.34
11 4 0.07
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTTAAT
Found at i:88350951 original size:28 final size:27
Alignment explanation
Indices: 88350876--88350952 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 27
88350866 TGATTTTACT
* * * *
88350876 TTCATTAAATTTTAAAATTTATAATAT
1 TTCAATAAATTTTAATATTTTTAATAC
* *
88350903 TTTAAT-AATTTCTTATCATTTTTAATAAC
1 TTCAATAAATTT-TAAT-ATTTTTAAT-AC
88350932 TTCAATAAATTTTAATATTTT
1 TTCAATAAATTTTAATATTTT
88350953 ATAAAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
26 5 0.13
27 6 0.16
28 13 0.34
29 9 0.24
30 5 0.13
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (27 bp):
TTCAATAAATTTTAATATTTTTAATAC
Found at i:88351453 original size:19 final size:19
Alignment explanation
Indices: 88351429--88351468 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
88351419 CTTCTTCTTT
* *
88351429 TTTCACTATTTTGCTACTA
1 TTTCACAATTATGCTACTA
*
88351448 TTTCACAATTATGTTACTA
1 TTTCACAATTATGCTACTA
88351467 TT
1 TT
88351469 ATTTTGTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTCACAATTATGCTACTA
Found at i:88356397 original size:19 final size:19
Alignment explanation
Indices: 88356375--88356412 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
88356365 AAAGCGATAC
88356375 GATAAATGCATTTTCTTAT
1 GATAAATGCATTTTCTTAT
88356394 GATAAATGCATTTTCTTAT
1 GATAAATGCATTTTCTTAT
88356413 ATGTTTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
GATAAATGCATTTTCTTAT
Found at i:88357546 original size:18 final size:18
Alignment explanation
Indices: 88357525--88357560 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
88357515 TCTCTTTATC
88357525 CTCTCTAAA-CTCTCAAAT
1 CTCTC-AAATCTCTCAAAT
88357543 CTCTCAAATCTCTCAAAT
1 CTCTCAAATCTCTCAAAT
88357561 TTTTTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCTCAAATCTCTCAAAT
Found at i:88364251 original size:20 final size:20
Alignment explanation
Indices: 88364226--88364267 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
88364216 ATCCGGAAAC
88364226 TATCCGCAGGTAATAAGTGT
1 TATCCGCAGGTAATAAGTGT
88364246 TATCCGCAGGTAATAAGTGT
1 TATCCGCAGGTAATAAGTGT
88364266 TA
1 TA
88364268 GTCTACCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCCGCAGGTAATAAGTGT
Found at i:88368100 original size:32 final size:32
Alignment explanation
Indices: 88368059--88368122 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
88368049 GATTTTTTGT
88368059 CTCCACCTATGTCCAAATATGTACTTAGTTAA
1 CTCCACCTATGTCCAAATATGTACTTAGTTAA
88368091 CTCCACCTATGTCCAAATATGTACTTAGTTAA
1 CTCCACCTATGTCCAAATATGTACTTAGTTAA
88368123 TATTATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (32 bp):
CTCCACCTATGTCCAAATATGTACTTAGTTAA
Found at i:88368560 original size:17 final size:18
Alignment explanation
Indices: 88368534--88368567 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88368524 TCGCTGATGG
*
88368534 CCCTTTATTTT-TTTGTT
1 CCCTTGATTTTCTTTGTT
88368551 CCCTTGATTTTCTTTGT
1 CCCTTGATTTTCTTTGT
88368568 AGGTTTCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.06, C:0.21, G:0.09, T:0.65
Consensus pattern (18 bp):
CCCTTGATTTTCTTTGTT
Found at i:88371674 original size:16 final size:17
Alignment explanation
Indices: 88371648--88371687 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
88371638 AAGGAATTTA
*
88371648 ACAACAAAGAATAAAAAG
1 ACAA-AAAGAAAAAAAAG
88371666 A-AAAAAGAAAAAAAAG
1 ACAAAAAGAAAAAAAAG
88371682 ACAAAA
1 ACAAAA
88371688 TGGAAGATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 13 0.65
17 6 0.30
18 1 0.05
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (17 bp):
ACAAAAAGAAAAAAAAG
Found at i:88371813 original size:9 final size:9
Alignment explanation
Indices: 88371801--88371844 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
88371791 ACAATATCTA
88371801 AAATAACTT
1 AAATAACTT
88371810 AAATAACTCTT
1 AAATAA--CTT
88371821 AAATAACTT
1 AAATAACTT
88371830 AAA-ATACTT
1 AAATA-ACTT
88371839 AAATAA
1 AAATAA
88371845 TATCCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 20 0.65
10 1 0.03
11 9 0.29
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATAACTT
Found at i:88372714 original size:23 final size:23
Alignment explanation
Indices: 88372681--88372734 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
88372671 AATTCATAAC
*
88372681 CAAATATACACATATTTATAGTT
1 CAAATACACACATATTTATAGTT
88372704 CAAATACACACATATTTATAGTT
1 CAAATACACACATATTTATAGTT
88372727 CAAATACA
1 CAAATACA
88372735 TAACAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (23 bp):
CAAATACACACATATTTATAGTT
Found at i:88372743 original size:23 final size:23
Alignment explanation
Indices: 88372681--88372744 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
88372671 AATTCATAAC
* *
88372681 CAAATATACACATATTTATAGTT
1 CAAATACAAACATATTTATAGTT
*
88372704 CAAATACACACATATTTATAGTT
1 CAAATACAAACATATTTATAGTT
88372727 CAAATACATAACA-ATTTA
1 CAAATACA-AACATATTTA
88372745 AACACGACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (23 bp):
CAAATACAAACATATTTATAGTT
Found at i:88373521 original size:15 final size:15
Alignment explanation
Indices: 88373491--88373541 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
88373481 GAAGATTAAT
**
88373491 TTAATTAAACCCTAA
1 TTAATTAAACTATAA
88373506 TTAATTAAACTATAA
1 TTAATTAAACTATAA
*
88373521 TCCTAATT-AACTAAAA
1 T--TAATTAAACTATAA
88373537 TTAAT
1 TTAAT
88373542 GGGTTATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 4 0.13
15 14 0.45
16 8 0.26
17 5 0.16
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAATTAAACTATAA
Found at i:88380633 original size:13 final size:13
Alignment explanation
Indices: 88380607--88380650 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
88380597 TTCCTGTAAA
*
88380607 CATTTCATACAAC
1 CATTTCATATAAC
*
88380620 CATTTTATATAAC
1 CATTTCATATAAC
*
88380633 CAATTCATATAAC
1 CATTTCATATAAC
88380646 CATTT
1 CATTT
88380651 GTCATCTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (13 bp):
CATTTCATATAAC
Found at i:88380655 original size:15 final size:14
Alignment explanation
Indices: 88380609--88380655 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
88380599 CCTGTAAACA
*
88380609 TTTCATACAACCAT
1 TTTCATATAACCAT
88380623 TTT-ATATAACCA-
1 TTTCATATAACCAT
*
88380635 ATTCATATAACCAT
1 TTTCATATAACCAT
88380649 TTGTCAT
1 TT-TCAT
88380656 CTGGTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 2 0.07
13 17 0.63
14 4 0.15
15 4 0.15
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (14 bp):
TTTCATATAACCAT
Found at i:88380799 original size:46 final size:46
Alignment explanation
Indices: 88380733--88381083 Score: 340
Period size: 46 Copynumber: 7.9 Consensus size: 46
88380723 TTATCTTCGA
* * * *
88380733 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* * *
88380779 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-TCTGT
*
88380826 CATGTTGCCATGGTATCTTTCAACCATGG------TC---TTGTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* *
88380863 -A--TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCT-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* *
88380905 CATTTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGT
* * * * *
88380951 CACGTTGCCATGGAATCTTTCAACCATGGTCTTCCACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGT
* *
88380997 CATGTTGCCATGGTATCTTTCTACCATGGTCTTA-TACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTTC-TGT
* * *
88381043 CATGTTACCATGGTATCTTTCAACCATAGTCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
88381084 CATTTCAGAA
Statistics
Matches: 258, Mismatches: 28, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
34 25 0.10
36 1 0.00
37 2 0.01
38 1 0.00
40 2 0.01
41 2 0.01
42 3 0.01
43 2 0.01
44 3 0.01
45 33 0.13
46 150 0.58
47 34 0.13
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
Found at i:88383196 original size:31 final size:29
Alignment explanation
Indices: 88383142--88383210 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
88383132 ATACTAATAA
*
88383142 AATAATAATAATATATCTTATTAAAATATT
1 AATAA-AATAATATATCTAATTAAAATATT
* *
88383172 AATAAAATAATATTTATCTAATTAAATTGTT
1 AATAAAATAATA--TATCTAATTAAAATATT
88383203 -ATAAAATA
1 AATAAAATA
88383211 TCAAAATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.21
30 13 0.38
31 14 0.41
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
AATAAAATAATATATCTAATTAAAATATT
Found at i:88385964 original size:11 final size:11
Alignment explanation
Indices: 88385948--88385982 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
88385938 AACATAATAT
88385948 AAAAATTATAA
1 AAAAATTATAA
88385959 AAAAATTATAA
1 AAAAATTATAA
88385970 AACAAATATATAA
1 AA-AAAT-TATAA
88385983 GGATATGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 4 0.18
13 5 0.23
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:88395998 original size:23 final size:22
Alignment explanation
Indices: 88395947--88395998 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
88395937 CCTCGTCTTT
*
88395947 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
88395969 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
88395992 TTCTTTT
1 TTCTTTT
88395999 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:88397980 original size:9 final size:8
Alignment explanation
Indices: 88397957--88397996 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
88397947 CAGCACAAGT
88397957 AGAAATAA
1 AGAAATAA
88397965 AGAAATAA
1 AGAAATAA
88397973 ATGAAATAGCA
1 A-GAAATA--A
88397984 AGAAATAA
1 AGAAATAA
88397992 AGAAA
1 AGAAA
88397997 GTCCTAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 15 0.52
9 6 0.21
10 6 0.21
11 2 0.07
ACGTcount: A:0.70, C:0.03, G:0.15, T:0.12
Consensus pattern (8 bp):
AGAAATAA
Found at i:88402763 original size:66 final size:66
Alignment explanation
Indices: 88402598--88402835 Score: 361
Period size: 66 Copynumber: 3.5 Consensus size: 66
88402588 TTCGAATAAA
* *
88402598 AAAAGACAAAACTACGTCGTTTTGATGAA-TGTTTACTTTTTTAAAAGTTAAAATTCGAAATAAT
1 AAAAGGCAAAACTACGTCGTTTTGAT-AAGTGTTTACTTTTTAAAAAGTTAAAATTC--AA-AA-
*
88402662 TAAGTT
61 TAATTT
* *
88402668 AAACGGCAAAACTACGTCGTTTTGATAAGTGTGTACTTTTTAAAAAGTTAAAATTCAAAATAATT
1 AAAAGGCAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATT
88402733 T
66 T
*
88402734 AAAAGGCAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAATTAAAATTCAAAATAATT
1 AAAAGGCAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATT
88402799 T
66 T
*
88402800 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTAC
1 AAAAGGCAAAACTACGTCGTTTTGATAAGTGTTTAC
88402836 CCATTAAGTT
Statistics
Matches: 158, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
66 103 0.65
67 2 0.01
68 2 0.01
69 2 0.01
70 49 0.31
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (66 bp):
AAAAGGCAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATT
T
Found at i:88404035 original size:31 final size:31
Alignment explanation
Indices: 88403986--88404058 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
88403976 AGCCTGTTAG
** * *
88403986 AGTGCGACCCTGTTGAAGATAGTAAGCCAAA
1 AGTGCGAGTCTGTCGAAGACAGTAAGCCAAA
88404017 AGTGCGAGTCTGTCGAAGACAGTAAGCCAAA
1 AGTGCGAGTCTGTCGAAGACAGTAAGCCAAA
*
88404048 AGTGCAAGTCT
1 AGTGCGAGTCT
88404059 ATTGAAGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.19
Consensus pattern (31 bp):
AGTGCGAGTCTGTCGAAGACAGTAAGCCAAA
Found at i:88404066 original size:31 final size:31
Alignment explanation
Indices: 88403998--88404066 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
88403988 TGCGACCCTG
* * *
88403998 TTGAAGATAGTAAGCCAAAAGTGCGAGTCTG
1 TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA
*
88404029 TCGAAGACAGTAAGCCAAAAGTGCAAGTCTA
1 TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA
88404060 TTGAAGA
1 TTGAAGA
88404067 GTGAGCCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (31 bp):
TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA
Found at i:88412971 original size:12 final size:12
Alignment explanation
Indices: 88412954--88412978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88412944 ACTCAAAACC
88412954 CTTAGCCCAAAA
1 CTTAGCCCAAAA
88412966 CTTAGCCCAAAA
1 CTTAGCCCAAAA
88412978 C
1 C
88412979 ATTAACTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:88413079 original size:37 final size:38
Alignment explanation
Indices: 88413025--88413111 Score: 149
Period size: 37 Copynumber: 2.3 Consensus size: 38
88413015 ATCCTAATCT
88413025 CACCTACTCCACCACCCTTGTTGGCCACCCACCTTGGC
1 CACCTACTCCACCACCCTTGTTGGCCACCCACCTTGGC
*
88413063 CACCTACT-CACCACCCTTGTTGGCCACCCACCTTGGT
1 CACCTACTCCACCACCCTTGTTGGCCACCCACCTTGGC
*
88413100 CACCTACACCAC
1 CACCTACTCCAC
88413112 TATGCCACCA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 35 0.76
38 11 0.24
ACGTcount: A:0.18, C:0.49, G:0.11, T:0.21
Consensus pattern (38 bp):
CACCTACTCCACCACCCTTGTTGGCCACCCACCTTGGC
Found at i:88413883 original size:52 final size:52
Alignment explanation
Indices: 88413808--88413909 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
88413798 GTATATATTA
* *
88413808 TATTGCTTTTATTATTACCATTATTAAATA-TTCTTATTATTACTATTATTTT
1 TATTCCTTTTATTATTACCATTA-TAAATATTTATTATTATTACTATTATTTT
*** * *
88413860 TATTCCTTTTATTATTGTTATTATCAATATTTATTATTATTGCTATTATT
1 TATTCCTTTTATTATTACCATTATAAATATTTATTATTATTACTATTATT
88413910 GCTATTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 5 0.12
52 37 0.88
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (52 bp):
TATTCCTTTTATTATTACCATTATAAATATTTATTATTATTACTATTATTTT
Found at i:88414092 original size:3 final size:3
Alignment explanation
Indices: 88414086--88414129 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
88414076 TTTTGTATCT
88414086 TTA TTA TTA TTA 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 TT
88414130 TCGCTATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:88414216 original size:22 final size:22
Alignment explanation
Indices: 88414191--88414232 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
88414181 TAACATGCTA
* *
88414191 TTATTACTATTATTTTTATTTT
1 TTATTACCATTATTGTTATTTT
88414213 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
88414233 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTACCATTATTGTTATTTT
Found at i:88425425 original size:43 final size:44
Alignment explanation
Indices: 88425371--88425465 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
88425361 GCCTCAGTGA
* *
88425371 AGCAGATTGAAGTCACTAGCCTTATCTCCCTGAAGT-GCAGAGG
1 AGCAGACTGAAGTCACAAGCCTTATCTCCCTGAAGTCGCAGAGG
* * * *
88425414 AGCAGACTGAAGTTACAAGTCTTATCTCCTTGAAGTCGCAGTGG
1 AGCAGACTGAAGTCACAAGCCTTATCTCCCTGAAGTCGCAGAGG
88425458 AGCAGACT
1 AGCAGACT
88425466 AAATGTACAG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 31 0.69
44 14 0.31
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
AGCAGACTGAAGTCACAAGCCTTATCTCCCTGAAGTCGCAGAGG
Found at i:88425885 original size:42 final size:44
Alignment explanation
Indices: 88425827--88425945 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
88425817 ATTTTCAAAC
* *
88425827 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGA-GTTTAC-AGAT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAG-T
* * **
88425870 C-TAAACCCCTAAGCAGTAGGGAAACAGATCAATGATGACAAGT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAGT
*
88425913 CTTAACCCCCTAAGCAGTAGGGTAACAGGTTGA
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGA
88425946 AAATCAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
42 27 0.44
43 7 0.11
44 28 0.45
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAGT
Found at i:88427325 original size:12 final size:12
Alignment explanation
Indices: 88427310--88427357 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
88427300 TATTTCTCTC
88427310 TTTATATTTATG
1 TTTATATTTATG
88427322 TTTATATTTTATG
1 TTTATA-TTTATG
** *
88427335 TATTATACCTATT
1 T-TTATATTTATG
88427348 TTTATATTTA
1 TTTATATTTA
88427358 CGCATGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:88427550 original size:22 final size:22
Alignment explanation
Indices: 88427525--88427566 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
88427515 TAACGTGCTA
* *
88427525 TTATTACTATTATTTTTATTTT
1 TTATTACCATTATTGTTATTTT
88427547 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
88427567 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTACCATTATTGTTATTTT
Found at i:88439544 original size:20 final size:20
Alignment explanation
Indices: 88439521--88439558 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
88439511 TAAAGAAAGT
88439521 AAATGCAA-TGTAAAGTAATG
1 AAATGCAAGTG-AAAGTAATG
88439541 AAATGCAAGTGAAAGTAA
1 AAATGCAAGTGAAAGTAA
88439559 GCAAATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
AAATGCAAGTGAAAGTAATG
Found at i:88439564 original size:20 final size:19
Alignment explanation
Indices: 88439507--88439564 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
88439497 GTTGTTATTT
* *
88439507 AAGTTAAAGAAAGTAAATGC
1 AAGTGAAAGTAAG-AAATGC
88439527 AA-TGTAAAGTAATGAAATGC
1 AAGTG-AAAGTAA-GAAATGC
88439547 AAGTGAAAGTAAGCAAAT
1 AAGTGAAAGTAAG-AAAT
88439565 TTGGAAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 27 0.84
21 3 0.09
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AAGTGAAAGTAAGAAATGC
Found at i:88442873 original size:21 final size:21
Alignment explanation
Indices: 88442843--88442888 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
88442833 TCAACAAATT
88442843 TACTTACCTTGTATAATTT-AA
1 TACTTACCTTG-ATAATTTAAA
* *
88442864 TACTTGCCTTGATACTTTAAA
1 TACTTACCTTGATAATTTAAA
88442885 TACT
1 TACT
88442889 CATATTACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
TACTTACCTTGATAATTTAAA
Found at i:88447036 original size:15 final size:15
Alignment explanation
Indices: 88447016--88447045 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
88447006 TGTTGAAATC
88447016 ATTGTGTGAGATGTG
1 ATTGTGTGAGATGTG
88447031 ATTGTGTGAGATGTG
1 ATTGTGTGAGATGTG
88447046 CTTGGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
ATTGTGTGAGATGTG
Found at i:88450550 original size:15 final size:15
Alignment explanation
Indices: 88450530--88450565 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
88450520 GAATTAAACT
88450530 CACCACCGCC-ACCGC
1 CACCACC-CCAACCGC
88450545 CACCACCCCAACCGC
1 CACCACCCCAACCGC
88450560 CACCAC
1 CACCAC
88450566 TGCCGCCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.25, C:0.67, G:0.08, T:0.00
Consensus pattern (15 bp):
CACCACCCCAACCGC
Found at i:88452971 original size:18 final size:19
Alignment explanation
Indices: 88452934--88452970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
88452924 AAAAAAATAA
*
88452934 AACTGATTTTATATTTTTT
1 AACTGATTTTAGATTTTTT
*
88452953 AACTTATTTTAGATTTTT
1 AACTGATTTTAGATTTTT
88452971 ATGAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
AACTGATTTTAGATTTTTT
Found at i:88453378 original size:36 final size:36
Alignment explanation
Indices: 88453331--88453401 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
88453321 ATCTTTTTCA
88453331 GGCTAAACTAAATGAATAACGATTTTCAAATTTAAG
1 GGCTAAACTAAATGAATAACGATTTTCAAATTTAAG
88453367 GGCTAAACTAAATGAATAACGATTTTCAAATTTAA
1 GGCTAAACTAAATGAATAACGATTTTCAAATTTAA
88453402 AAGTTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (36 bp):
GGCTAAACTAAATGAATAACGATTTTCAAATTTAAG
Found at i:88458598 original size:10 final size:9
Alignment explanation
Indices: 88458567--88458695 Score: 86
Period size: 9 Copynumber: 14.1 Consensus size: 9
88458557 ATGAAAAAAT
88458567 AATTATAAA
1 AATTATAAA
88458576 AA--ATAAA
1 AATTATAAA
*
88458583 AGTTATAAA
1 AATTATAAA
88458592 AATTTATTAAA
1 AA-TTA-TAAA
**
88458603 TTTTAATAAA
1 AATT-ATAAA
* *
88458613 AAATATATA
1 AATTATAAA
*
88458622 AATTAAAAA
1 AATTATAAA
88458631 AATTATAAA
1 AATTATAAA
88458640 AATCGTA-AAA
1 AAT--TATAAA
*
88458650 AAATA-AAA
1 AATTATAAA
*
88458658 AATTGTAAA
1 AATTATAAA
*
88458667 ATTTATAAA
1 AATTATAAA
*
88458676 AATCATAAAA
1 AATTAT-AAA
88458686 AATTATAAA
1 AATTATAAA
88458695 A
1 A
88458696 TGCATCAAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 18
0.71 0.16 0.14
Matches are distributed among these distances:
7 6 0.07
8 8 0.09
9 47 0.52
10 23 0.25
11 7 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AATTATAAA
Found at i:88458649 original size:19 final size:19
Alignment explanation
Indices: 88458627--88458695 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
88458617 ATATAAATTA
88458627 AAAAAATTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
* *
88458646 AAAAAAATA-AAAAATTGT
1 AAAAAATTATAAAAATCGT
* *
88458664 -AAAATTTATAAAAATCAT
1 AAAAAATTATAAAAATCGT
88458682 AAAAAATTATAAAA
1 AAAAAATTATAAAA
88458696 TGCATCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 6 0.15
18 15 0.37
19 20 0.49
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:88458696 original size:18 final size:18
Alignment explanation
Indices: 88458608--88458706 Score: 69
Period size: 18 Copynumber: 5.4 Consensus size: 18
88458598 TTAAATTTTA
*
88458608 ATAAAAAA-TATATAAATT
1 ATAAAAAATTATA-AAATC
88458626 A-AAAAAATTATAAAAATC
1 ATAAAAAATTAT-AAAATC
* * * *
88458644 GTAAAAAAATAAAAAATT
1 ATAAAAAATTATAAAATC
* *
88458662 GT-AAAATTTATAAAAATC
1 ATAAAAAATTAT-AAAATC
88458680 ATAAAAAATTATAAAATGC
1 ATAAAAAATTATAAAAT-C
88458699 ATCAAAAA
1 AT-AAAAA
88458707 GACCCTATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
17 12 0.19
18 26 0.41
19 20 0.32
20 5 0.08
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTATAAAATC
Found at i:88458696 original size:36 final size:35
Alignment explanation
Indices: 88458608--88458696 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 35
88458598 TTAAATTTTA
88458608 ATAAAAAATATATAAATTAAAAAAATTATAAAAATC
1 ATAAAAAATATA-AAATTAAAAAAATTATAAAAATC
* * ** *
88458644 GTAAAAAAATAAAAAATTGTAAAATTTATAAAAATC
1 AT-AAAAAATATAAAATTAAAAAAATTATAAAAATC
88458680 ATAAAAAATTATAAAAT
1 ATAAAAAA-TATAAAAT
88458697 GCATCAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 6 0.14
36 29 0.66
37 9 0.20
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (35 bp):
ATAAAAAATATAAAATTAAAAAAATTATAAAAATC
Found at i:88458915 original size:10 final size:10
Alignment explanation
Indices: 88458902--88459052 Score: 68
Period size: 9 Copynumber: 15.6 Consensus size: 10
88458892 TTTTTACGAA
88458902 TTTTATAATT
1 TTTTATAATT
88458912 TTTTATAA-T
1 TTTTATAATT
88458921 TTTTATAATT
1 TTTTATAATT
** *
88458931 TTCTTACGACT
1 TT-TTATAATT
* *
88458942 TTATAAAATT
1 TTTTATAATT
*
88458952 TTGTAT--TT
1 TTTTATAATT
88458960 TTTCTAT-A-T
1 TTT-TATAATT
* *
88458969 TTCTAT-ATA
1 TTTTATAATT
88458978 TTTTATAATT
1 TTTTATAATT
*
88458988 TTTTATGA-T
1 TTTTATAATT
**
88458997 TTTTATAAAAA
1 TTTTAT-AATT
*
88459008 ATTTATAATT
1 TTTTATAATT
* *
88459018 TTTAATAA-A
1 TTTTATAATT
*
88459027 TTTTAAATATT
1 TTTTATA-ATT
88459038 TTTTAT-ATT
1 TTTTATAATT
88459047 TTTTAT
1 TTTTAT
88459053 TAAAATTTAA
Statistics
Matches: 104, Mismatches: 27, Indels: 21
0.68 0.18 0.14
Matches are distributed among these distances:
8 8 0.08
9 41 0.39
10 38 0.37
11 17 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:88459000 original size:19 final size:19
Alignment explanation
Indices: 88458880--88459004 Score: 87
Period size: 19 Copynumber: 6.5 Consensus size: 19
88458870 GGTATAATAG
*
88458880 TTTTTATAACTTTTTTTACGA
1 TTTTTATAA--TTTTTTATGA
* *
88458901 ATTTTATAATTTTTTATAA
1 TTTTTATAATTTTTTATGA
*
88458920 TTTTTATAATTTTCTTACGA
1 TTTTTATAATTTT-TTATGA
* * *
88458940 CTTTATAAAATTTTGTAT--
1 -TTTTTATAATTTTTTATGA
* *
88458958 TTTTTCT-ATATTTCTAT-A
1 TTTTTATAAT-TTTTTATGA
88458976 TATTTTATAATTTTTTATGA
1 T-TTTTATAATTTTTTATGA
88458996 TTTTTATAA
1 TTTTTATAA
88459005 AAAATTTATA
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
16 2 0.02
17 10 0.12
18 1 0.01
19 39 0.48
20 10 0.12
21 19 0.23
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTTATGA
Found at i:88459000 original size:38 final size:37
Alignment explanation
Indices: 88458880--88459004 Score: 112
Period size: 40 Copynumber: 3.2 Consensus size: 37
88458870 GGTATAATAG
*
88458880 TTTTTATAACTTTTTTTACGAATTTTATAATTTTTTATAA
1 TTTTTATAA-TTTTCTTACG-ATTTTATAATTTTTTAT-A
* *
88458920 TTTTTATAATTTTCTTACGACTTTATAAAATTTTGTAT-
1 TTTTTATAATTTTCTTACGA-TTT-TATAATTTTTTATA
* *
88458958 TTTTTCT-ATATTTCTATA-TATTTTATAATTTTTTATGA
1 TTTTTATAAT-TTTCT-TACGATTTTATAATTTTTTAT-A
88458996 TTTTTATAA
1 TTTTTATAA
88459005 AAAATTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
36 11 0.16
37 5 0.07
38 19 0.27
39 15 0.21
40 20 0.29
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (37 bp):
TTTTTATAATTTTCTTACGATTTTATAATTTTTTATA
Done.