Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 115 of 168
Found at i:33592452 original size:2 final size:2
Alignment explanation
Indices: 33592445--33592469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33592435 ACAAGAACTG
33592445 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
33592470 ATCGATCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33593602 original size:55 final size:55
Alignment explanation
Indices: 33593536--33593644 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
33593526 GTCCCATGGA
* * *
33593536 ATGATAAATCATCACTTTTAATTTTAATAGTGCTTATGAATAATTAATTTGCAAG
1 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAAG
33593591 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAA
1 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAA
33593645 TCTATAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (55 bp):
ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAAG
Found at i:33596203 original size:43 final size:42
Alignment explanation
Indices: 33596142--33596305 Score: 185
Period size: 43 Copynumber: 3.9 Consensus size: 42
33596132 ATTTCGATAC
*
33596142 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
1 GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TT
* * *
33596185 GTGTTTACGTGTAAGACCATGTCTGGGACATTGACATCGTATT
1 GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATT
33596228 -TGATTT--GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATAT
1 GTG-TTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-T
* *
33596269 GTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
33596306 TGTTTGAGTC
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
40 2 0.02
41 29 0.28
42 5 0.05
43 64 0.63
44 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (42 bp):
GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGATT
Found at i:33596495 original size:16 final size:17
Alignment explanation
Indices: 33596466--33596497 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33596456 TGAATTGATG
33596466 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
33596483 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
33596498 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:33600115 original size:20 final size:20
Alignment explanation
Indices: 33600090--33600130 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
33600080 TTTCTTAAGA
33600090 TAGCCAAAAATCCTACAAAT
1 TAGCCAAAAATCCTACAAAT
33600110 TAGCCAAAAATCCTACAAAT
1 TAGCCAAAAATCCTACAAAT
33600130 T
1 T
33600131 CCTTTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (20 bp):
TAGCCAAAAATCCTACAAAT
Found at i:33604237 original size:14 final size:14
Alignment explanation
Indices: 33604215--33604244 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33604205 ATTTAATTTC
*
33604215 TTGTGAAGGATTAT
1 TTGTAAAGGATTAT
33604229 TTGTAAAGGATTAT
1 TTGTAAAGGATTAT
33604243 TT
1 TT
33604245 TAGTGTATTT
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:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTGTAAAGGATTAT
Found at i:33607410 original size:80 final size:80
Alignment explanation
Indices: 33607277--33607437 Score: 252
Period size: 80 Copynumber: 2.0 Consensus size: 80
33607267 AAGTTTGGAA
* *
33607277 AACTAGTCAACTTGTGACAACTTTTTGGATGGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
1 AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
33607342 GGTGTTCTAAGATCT
66 GGTGTTCTAAGATCT
** *
33607357 AACTAGCCAACTTGTGATGACTTTTTGGATAGAATTCA-GACATTTCTGGGTTAATATGTCTTCA
1 AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATG-CATTTCTGGGTTAATATGTCTTCA
*
33607421 TGTTGTTCTAAGATCT
65 TGGTGTTCTAAGATCT
33607437 A
1 A
33607438 CATCTTATCT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (80 bp):
AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
GGTGTTCTAAGATCT
Found at i:33608601 original size:13 final size:13
Alignment explanation
Indices: 33608583--33608617 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
33608573 TATTTATTGT
33608583 TTTTGAGAAGTGC
1 TTTTGAGAAGTGC
33608596 TTTTGAGAAGTGC
1 TTTTGAGAAGTGC
33608609 TTTTGAGAA
1 TTTTGAGAA
33608618 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (13 bp):
TTTTGAGAAGTGC
Found at i:33608823 original size:24 final size:23
Alignment explanation
Indices: 33608796--33608857 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
33608786 AATATTTTAA
33608796 TATATAATATTAATTTTAAATATT
1 TATA-AATATTAATTTTAAATATT
* * *
33608820 TATAAGTAATTAATATTAATTATT
1 TATAAAT-ATTAATTTTAAATATT
33608844 TATAAA-ATTTAATT
1 TATAAATA-TTAATT
33608858 AGAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 7 0.23
24 23 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATAAATATTAATTTTAAATATT
Found at i:33613507 original size:21 final size:21
Alignment explanation
Indices: 33613483--33613524 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33613473 TCACCTATGC
*
33613483 ACCATATAATCCAATAACAAT
1 ACCATATAATACAATAACAAT
33613504 ACCATATAATACAATAACAAT
1 ACCATATAATACAATAACAAT
33613525 TTATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCATATAATACAATAACAAT
Found at i:33613694 original size:20 final size:20
Alignment explanation
Indices: 33613669--33613707 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33613659 GATATTTTTA
33613669 AATTTT-AAATAACAAAAATT
1 AATTTTCAAATAA-AAAAATT
*
33613689 AATTTTCAATTAAAAAAAT
1 AATTTTCAAATAAAAAAAT
33613708 GTGGACGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTTCAAATAAAAAAATT
Found at i:33613953 original size:26 final size:26
Alignment explanation
Indices: 33613925--33613975 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
33613915 AAATAAGGTT
33613925 AAAATATTATTAAATGATAT-TAAATTA
1 AAAATA-TA-TAAATGATATATAAATTA
*
33613952 AAAATATATAAATTATATATAAAT
1 AAAATATATAAATGATATATAAAT
33613976 GTTGTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATATAAATGATATATAAATTA
Found at i:33614189 original size:9 final size:9
Alignment explanation
Indices: 33614177--33614291 Score: 50
Period size: 9 Copynumber: 11.4 Consensus size: 9
33614167 AAAATTACAA
*
33614177 AAAAAAATT
1 AAAAAATTT
33614186 AAAATAATTT
1 AAAA-AATTT
**
33614196 TTAAAATTT
1 AAAAAATTT
*
33614205 AAAATATTT
1 AAAAAATTT
*
33614214 AAAAAATTCA
1 AAAAAATT-T
33614224 AAATATATATTTTT
1 AAA-A-A-A--TTT
33614238 AAGAAAAATTCT
1 -A-AAAAATT-T
33614250 AAAAAATATAT
1 AAAAAAT-T-T
33614261 AAAAAATTT
1 AAAAAATTT
**
33614270 AAAATTTTT
1 AAAAAATTT
*
33614279 AAAAAAATT
1 AAAAAATTT
33614288 AAAA
1 AAAA
33614292 TAATAATTTG
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
9 40 0.50
10 16 0.20
11 13 0.16
12 2 0.03
13 2 0.03
14 1 0.01
15 4 0.05
16 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (9 bp):
AAAAAATTT
Found at i:33614229 original size:18 final size:17
Alignment explanation
Indices: 33614178--33614229 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
33614168 AAATTACAAA
33614178 AAAAAATTAAAATAATTTT
1 AAAAAATTAAAAT-A-TTT
* *
33614197 TAAAATTTAAAATATTT
1 AAAAAATTAAAATATTT
33614214 AAAAAATTCAAAATAT
1 AAAAAATT-AAAATAT
33614230 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 8 0.29
19 11 0.39
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAAATTAAAATATTT
Found at i:33614605 original size:18 final size:17
Alignment explanation
Indices: 33614564--33614605 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
33614554 CCTCTCTCAA
33614564 TTTTCTCCTTTTTTTTT
1 TTTTCTCCTTTTTTTTT
*
33614581 TCATTCTCCTTTTGTTTTT
1 T-TTTCTCCTTTT-TTTTT
33614600 TTTTCT
1 TTTTCT
33614606 TGGCTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCTCCTTTTTTTTT
Found at i:33625676 original size:29 final size:30
Alignment explanation
Indices: 33625635--33625700 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
33625625 ATTATAAATA
33625635 TAAATATATATAATTATTATT-TAACATAAG
1 TAAATATATATAA-TATTATTATAACATAAG
*
33625665 TAAATA-ATATAATATTTTTATAACATAA-
1 TAAATATATATAATATTATTATAACATAAG
*
33625693 TATATATA
1 TAAATATA
33625701 CGGGTCAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 11 0.34
29 15 0.47
30 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TAAATATATATAATATTATTATAACATAAG
Found at i:33626785 original size:31 final size:31
Alignment explanation
Indices: 33626698--33626786 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
33626688 AGTTTAAACT
* * *
33626698 CCAATGTGTGAATAACTACCAAGTTCAAGTC
1 CCAATGTGAGAATAATTACCAAGTTTAAGTC
* * *
33626729 CCAATATGAAAAGAATTACCAAGTTTAAGTC
1 CCAATGTGAGAATAATTACCAAGTTTAAGTC
* *
33626760 TCAATGTGAGAATAATTATCAAGTTTA
1 CCAATGTGAGAATAATTACCAAGTTTA
33626787 GGCCCGATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (31 bp):
CCAATGTGAGAATAATTACCAAGTTTAAGTC
Found at i:33627004 original size:50 final size:50
Alignment explanation
Indices: 33626929--33627024 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
33626919 GATATGAGAG
* *
33626929 TTATTGCCAAATTTAGGCAACTAATAGTGATTTAACCTTCCAACTTAGAA
1 TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
*
33626979 TTATTGCCAAATTTAGGCACCTAATAGTAATTTAACCTTCAAACTT
1 TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTT
33627025 TAAAGTGAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (50 bp):
TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
Found at i:33628568 original size:132 final size:131
Alignment explanation
Indices: 33627896--33628585 Score: 623
Period size: 136 Copynumber: 5.2 Consensus size: 131
33627886 GATGTTTTCT
* * *
33627896 TTAAAAGATCAATGCTT-ATTCATATTTGCTAATACT--GCGTTTTTGCAATGTAAAAACCAGAT
1 TTAAAAGATCAATG-TTCATTCATATTTGCTAATA-TAAGCGTCTTTGCAGTGTAAAAACCA-AA
* * *
33627958 CACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTAATGTTTCGTCACTTATGTCCAAGA
63 CACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATGTTTTGTCACTTATGTCTAAGA
33628023 TTCA
128 TTCA
* * * * * *
33628027 TTAAAAGATCAATGTCCATTCATGTATTGCTAATATAAGTGTCTGTGCAGTATAAAAACCAATCT
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAAC-
* * * * **
33628092 ACCA--TCTCAA---C-ATATTTGTTTGGATTTTATGTTGGTTTTTTTGTCACTTATGTCTGTGA
64 ACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTT-GATGTTTTGTCACTTATGTCTAAGA
33628151 TTCA
128 TTCA
* * * *
33628155 TTACAAGATCAATGTTTATTCATACATTGCTAATATAAGCGTCCTTGCAGTGTAAAAACCAAACC
1 TTAAAAGATCAATGTTCATTCATA-TTTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAA-C
* * * * * *
33628220 ACCGTGCATTAATCTCAATATATTTGTTTTGATTTTTATGTTGATGTTTTATTAATTATGTCTAA
64 ACCATGTATTAATCTC-A-ATATTTGTTTGGA-TTTTATGTTGATGTTTTGTCACTTATGTCTAA
33628285 GATTCA
126 GATTCA
* * * * * * * *
33628291 CTAAAAGATCAATTTTTATTCATATATTTCTAGTATAAGTGTCTGTGCAGTGTAAAAAACCAAGC
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATATAAGCGTCTTTGCAGTGT-AAAAACCAA-A
* * *
33628356 CATCATGTATTTATCTCAATATGTTTGTTTGGATTTTTATGTTGATAGTTTTGTCAGTTATGTCT
63 CACCATGTATTAATCTCAATA--TTTGTTTGGA-TTTTATGTTGAT-GTTTTGTCACTTATGTCT
*
33628421 AACATTCA
124 AAGATTCA
* * *
33628429 TTAAAAGAGATCAATGCTCATTCATATTTGCTAATAT-TGCGT-TTTCGCAATGTAAAAACCAGA
1 TT-AAA-AGATCAATGTTCATTCATATTTGCTAATATAAGCGTCTTT-GCAGTGTAAAAACCA-A
* * * * * *
33628492 ACACCATGTAATAATCTC-A-GTGTGTTAGGATTTTATGTTGATGTTTTTATCATTTATGTCTAA
62 ACACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATG-TTTTGTCACTTATGTCTAA
*
33628555 CATTCA
126 GATTCA
*
33628561 TTCAAAGATCAATGTTCATTCATAT
1 TTAAAAGATCAATGTTCATTCATAT
33628586 GTGTTTTGTC
Statistics
Matches: 453, Mismatches: 78, Indels: 57
0.77 0.13 0.10
Matches are distributed among these distances:
127 22 0.05
128 78 0.17
129 1 0.00
130 23 0.05
131 29 0.06
132 49 0.11
133 31 0.07
135 3 0.01
136 79 0.17
137 77 0.17
138 33 0.07
139 11 0.02
140 17 0.04
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (131 bp):
TTAAAAGATCAATGTTCATTCATATTTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAACAC
CATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATGTTTTGTCACTTATGTCTAAGATTC
A
Found at i:33629896 original size:2 final size:2
Alignment explanation
Indices: 33629889--33629922 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33629879 TTTTGAAGAA
33629889 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
33629923 GCCAGAACGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33646711 original size:51 final size:52
Alignment explanation
Indices: 33646649--33646873 Score: 217
Period size: 51 Copynumber: 4.4 Consensus size: 52
33646639 TTCGGTGGTT
* * * * *
33646649 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCAATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* ** * * * * *
33646700 TACACATAGTACTACACACGTGGTCA-AG-CTTTCCGGTTCACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* * * *
33646750 TGCACATAGTACTACACACGTGACCA-AGGCCATCCGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* * *
33646801 TGCAAATAGTACTACACATGTGACCATTATCTAT-CGATACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* *
33646852 TTCACTTAGTACTACACACGTG
1 TGCACATAGTACTACACACGTG
33646874 TTCATAGGTA
Statistics
Matches: 142, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
49 1 0.01
50 42 0.30
51 96 0.68
52 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (52 bp):
TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
Found at i:33649994 original size:50 final size:50
Alignment explanation
Indices: 33649926--33650043 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 50
33649916 AGTATGTAAA
* * ** * * *
33649926 CGGGAAGCTCTTGTGAGCCATTTATCGGGAAGCTCA-AGAGAGCCAAATAT
1 CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATA-AGAGCCAAACAG
* * *
33649976 CTGGAAGCTCGTGAGAGCCAAATATCAGGATGCTCATAAGAGCTAAACAG
1 CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATAAGAGCCAAACAG
33650026 CGGGAAGCTCGTGAGAGC
1 CGGGAAGCTCGTGAGAGC
33650044 TGTGGTGTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATAAGAGCCAAACAG
Found at i:33650044 original size:25 final size:25
Alignment explanation
Indices: 33649926--33650043 Score: 110
Period size: 25 Copynumber: 4.7 Consensus size: 25
33649916 AGTATGTAAA
* * **
33649926 CGGGAAGCTCTTGTGAGCCATTTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
*
33649951 CGGGAAGCTCAAGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
33649976 CTGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * * * *
33650001 CAGGATGCTCATAAGAGCTAAACAG
1 CGGGAAGCTCATGAGAGCCAAATAT
*
33650026 CGGGAAGCTCGTGAGAGC
1 CGGGAAGCTCATGAGAGC
33650044 TGTGGTGTAT
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:33650356 original size:22 final size:22
Alignment explanation
Indices: 33650331--33650375 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
33650321 ATATTAGGTT
33650331 TATCCGGATCTATATGAATGAA
1 TATCCGGATCTATATGAATGAA
33650353 TATCCGGATCTATATGAATGAA
1 TATCCGGATCTATATGAATGAA
33650375 T
1 T
33650376 TTAACTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
TATCCGGATCTATATGAATGAA
Found at i:33662873 original size:44 final size:44
Alignment explanation
Indices: 33662810--33662900 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
33662800 GTAGGTCAAA
* *
33662810 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
*
33662854 TAATATTAAAATAACCTACACTAATTAGAGCTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
33662898 TAA
1 TAA
33662901 AAACAGAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.27
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
Found at i:33665559 original size:16 final size:18
Alignment explanation
Indices: 33665526--33665566 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
33665516 GGGAAGGGAT
33665526 AAAAAATTGTCAGAAGAA
1 AAAAAATTGTCAGAAGAA
33665544 AAAAAATTG-CAG-AGAA
1 AAAAAATTGTCAGAAGAA
33665560 ACAAAAA
1 A-AAAAA
33665567 CGTGGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 9 0.41
ACGTcount: A:0.66, C:0.07, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAAATTGTCAGAAGAA
Found at i:33667858 original size:25 final size:25
Alignment explanation
Indices: 33667830--33667878 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
33667820 TCAAGCCTAA
33667830 TTTGATTTGGATCGTAGAGAGCAAC
1 TTTGATTTGGATCGTAGAGAGCAAC
33667855 TTTGATTTGGATCGTAGAGAGCAA
1 TTTGATTTGGATCGTAGAGAGCAA
33667879 TCTAACCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (25 bp):
TTTGATTTGGATCGTAGAGAGCAAC
Found at i:33670343 original size:41 final size:40
Alignment explanation
Indices: 33670298--33670541 Score: 262
Period size: 41 Copynumber: 6.0 Consensus size: 40
33670288 TTGTATAAAA
* * * *
33670298 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
* *
33670338 CCACCGGCACAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACA-TT
33670380 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGAAGTA-ATT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATT
* *
33670421 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* *
33670462 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* * *
33670503 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
33670542 CTTATTTTCA
Statistics
Matches: 186, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 173 0.93
42 6 0.03
43 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
Found at i:33670426 original size:82 final size:82
Alignment explanation
Indices: 33670298--33670541 Score: 316
Period size: 82 Copynumber: 3.0 Consensus size: 82
33670288 TTGTATAAAA
* * * * *
33670298 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG--ATACATTCCACCGGCA-CAAAGCCTGCTAG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATA-ATT-CACCGGCATC-AAGCCTGCTAG
* * *
33670360 ACATAAGGTCTGATACATTT
63 ACGTAAAGTCTGAAACATTT
*
33670380 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGGCATCAAGCCTGCTAGAC
1 CACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
* *
33670444 GTAAAGTCTGAAATAATT
65 GTAAAGTCTGAAACATTT
*
33670462 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
33670527 TAAAGTCTGAAACAT
66 TAAAGTCTGAAACAT
33670542 CTTATTTTCA
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
82 135 0.95
83 5 0.04
84 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (82 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
TAAAGTCTGAAACATTT
Found at i:33691461 original size:25 final size:25
Alignment explanation
Indices: 33691409--33691462 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
33691399 AAGCTCTTGC
**
33691409 GAGCCAAATATCGAGAAACTCATGA
1 GAGCCAAATATCGAGAAACTCAAAA
* * *
33691434 GAGCCAAGTATCGGGAAGCTCAAAA
1 GAGCCAAATATCGAGAAACTCAAAA
33691459 GAGC
1 GAGC
33691463 TATGGTGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (25 bp):
GAGCCAAATATCGAGAAACTCAAAA
Found at i:33693109 original size:35 final size:35
Alignment explanation
Indices: 33693041--33693108 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
33693031 CACAATGTTT
* *
33693041 GTTATGACCATTTAAAGAATTCAAACATATTTTTA
1 GTTATGACCATCTAAAGAATTCAAAAATATTTTTA
33693076 GTTATGACCATCTAAAGAATTCAAAAA-ATTTTT
1 GTTATGACCATCTAAAGAATTCAAAAATATTTTT
33693109 TCTTCACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (35 bp):
GTTATGACCATCTAAAGAATTCAAAAATATTTTTA
Found at i:33700212 original size:14 final size:14
Alignment explanation
Indices: 33700195--33700243 Score: 80
Period size: 14 Copynumber: 3.4 Consensus size: 14
33700185 CTGTAATTAG
33700195 TTTTTATTTATATTT
1 TTTTTATTTATA-TT
33700210 TTTTTATTTATATT
1 TTTTTATTTATATT
*
33700224 TATTTATTTATATT
1 TTTTTATTTATATT
33700238 TTTTTA
1 TTTTTA
33700244 AAAACTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:33700213 original size:15 final size:15
Alignment explanation
Indices: 33700195--33700242 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
33700185 CTGTAATTAG
33700195 TTTTTATTTATATTT
1 TTTTTATTTATATTT
33700210 TTTTTATTTATA-TT
1 TTTTTATTTATATTT
*
33700224 TATTTATTTATATTT
1 TTTTTATTTATATTT
33700239 TTTT
1 TTTT
33700243 AAAAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATATTT
Found at i:33700834 original size:19 final size:20
Alignment explanation
Indices: 33700804--33700844 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
33700794 ATATTTAATG
33700804 TAGCATCACATCATTTTTTT
1 TAGCATCACATCATTTTTTT
33700824 TAGCA-CACATCATTTTTTT
1 TAGCATCACATCATTTTTTT
33700843 TA
1 TA
33700845 CTCGATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.49
Consensus pattern (20 bp):
TAGCATCACATCATTTTTTT
Found at i:33702323 original size:6 final size:6
Alignment explanation
Indices: 33702312--33702347 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
33702302 CATATATGAA
* *
33702312 AAATAT AAATAT AAATAC AAATAC AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
33702348 CACATAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATAT
Found at i:33702339 original size:18 final size:18
Alignment explanation
Indices: 33702312--33702346 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33702302 CATATATGAA
*
33702312 AAATATAAATATAAATAC
1 AAATACAAATATAAATAC
33702330 AAATACAAATATAAATA
1 AAATACAAATATAAATA
33702347 TCACATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACAAATATAAATAC
Found at i:33702765 original size:5 final size:6
Alignment explanation
Indices: 33702750--33702774 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33702740 GTTTCAACAA
33702750 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
33702775 GAAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:33719729 original size:1 final size:1
Alignment explanation
Indices: 33719723--33719751 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
33719713 ACCAAAATAC
33719723 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33719752 GAAGAAGAAG
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33720874 original size:40 final size:40
Alignment explanation
Indices: 33720795--33720874 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
33720785 CATTATTCAA
* *
33720795 TTATAATATAATTATTAATTTATGTGCTTATTTTATTTAT
1 TTATAATATAATTATTAATTTATATGCTTATTATATTTAT
*
33720835 TTATAATATAATTATTAATACTTATATTC-TATTAT-TTTAT
1 TTATAATATAATTATTAAT--TTATATGCTTATTATATTTAT
33720875 ATCTAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 24 0.69
41 5 0.14
42 6 0.17
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (40 bp):
TTATAATATAATTATTAATTTATATGCTTATTATATTTAT
Found at i:33723095 original size:12 final size:12
Alignment explanation
Indices: 33723078--33723103 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33723068 ATTTAAACCT
33723078 AAAAAATTAGAA
1 AAAAAATTAGAA
33723090 AAAAAATTAGAA
1 AAAAAATTAGAA
33723102 AA
1 AA
33723104 CTATAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAATTAGAA
Found at i:33723380 original size:3 final size:3
Alignment explanation
Indices: 33723374--33723416 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
33723364 TCACATGTTG
33723374 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33723417 CTAAAGAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:33728803 original size:44 final size:42
Alignment explanation
Indices: 33728729--33728843 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
33728719 ATGTGATTTT
** * *
33728729 GTGTAAGACCACATCTGAGACGTTGACATCG-ACTAGAGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGACATCGTA-TA-AGA-TTAC
* *
33728773 GTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTAC
1 GTGTAAGACCATGTCTGGGACATTGACATCGTATAAGATTAC
* *
33728815 GTGTAAGACCTTGTCTGGGACAGTGACAT
1 GTGTAAGACCATGTCTGGGACATTGACAT
33728844 TGTTATTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 30 0.49
43 2 0.03
44 28 0.46
45 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATTGACATCGTATAAGATTAC
Found at i:33728830 original size:42 final size:43
Alignment explanation
Indices: 33728769--33728865 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 43
33728759 GACTAGAGAT
* *
33728769 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * *
33728811 TTACGTGTAAGACCTTGTCTGGGACAGTGACATTGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
*
33728854 TTACATGTAAGA
1 TTACGTGTAAGA
33728866 ACACATCTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 31 0.65
43 17 0.35
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:33729188 original size:30 final size:28
Alignment explanation
Indices: 33729154--33729272 Score: 103
Period size: 30 Copynumber: 4.0 Consensus size: 28
33729144 ATTAAATTTT
*
33729154 TTTTTAAAAATTTGCATTTTAACCCCTAAA
1 TTTTT-AAAA-TTACATTTTAACCCCTAAA
* *
33729184 TTTTTCTAAAATTACATTTTGATCCCTAAA
1 -TTTT-TAAAATTACATTTTAACCCCTAAA
*
33729214 CTTTCTTAAAATTACATTTCAACCCCTAAA
1 -TTT-TTAAAATTACATTTTAACCCCTAAA
* ** *
33729244 TTTCTCAAAATTATGTTTTGACCCCTAAA
1 TTT-TTAAAATTACATTTTAACCCCTAAA
33729273 CTTTCTCTGA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 24 0.32
30 40 0.54
31 9 0.12
32 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTTTAAAATTACATTTTAACCCCTAAA
Found at i:33729286 original size:30 final size:30
Alignment explanation
Indices: 33729170--33729306 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
33729160 AAAATTTGCA
* * *
33729170 TTTTAACCCCTAAA-TTTTTCTAAAATTACA
1 TTTTGACCCCTAAACTTTCTCT-AAATTACG
* *
33729200 TTTTGATCCCTAAACTTTCT-TAAAATTACA
1 TTTTGACCCCTAAACTTTCTCT-AAATTACG
** * *
33729230 TTTCAACCCCTAAA-TTTCTCAAAATTATG
1 TTTTGACCCCTAAACTTTCTCTAAATTACG
*
33729259 TTTTGACCCCTAAACTTTCTCTGAATTACG
1 TTTTGACCCCTAAACTTTCTCTAAATTACG
* *
33729289 TTTTGGCCCCAAAACTTT
1 TTTTGACCCCTAAACTTT
33729307 TGCTACATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
29 23 0.26
30 61 0.69
31 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTGACCCCTAAACTTTCTCTAAATTACG
Found at i:33729623 original size:17 final size:17
Alignment explanation
Indices: 33729586--33729629 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
33729576 CTCGCCACCG
* **
33729586 TCGCGCCACCACTATTG
1 TCGCGCCACCACCATCA
33729603 TCGCGCCACCACCATCA
1 TCGCGCCACCACCATCA
*
33729620 TCGCTCCACC
1 TCGCGCCACC
33729630 GCCGAAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.18, C:0.50, G:0.14, T:0.18
Consensus pattern (17 bp):
TCGCGCCACCACCATCA
Found at i:33729702 original size:14 final size:14
Alignment explanation
Indices: 33729665--33729708 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33729655 AAGCATAAAC
*
33729665 AAAAAAAATCAGCA
1 AAAAAAAAACAGCA
* * *
33729679 AACAAGAAACAACA
1 AAAAAAAAACAGCA
33729693 AAAAAAAAACAGCA
1 AAAAAAAAACAGCA
33729707 AA
1 AA
33729709 GAAGAAAAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.75, C:0.16, G:0.07, T:0.02
Consensus pattern (14 bp):
AAAAAAAAACAGCA
Found at i:33729807 original size:3 final size:3
Alignment explanation
Indices: 33729801--33729850 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
33729791 TAGGGTTCGT
*
33729801 GAA GAA GAA GAA GAA GAA GAA GAAA GAA GAA GAAA GAA GAA GAA AAA
1 GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA G-AA GAA GAA GAA GAA
33729848 GAA
1 GAA
33729851 AGAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33729851 original size:6 final size:6
Alignment explanation
Indices: 33729802--33729869 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
33729792 AGGGTTCGTG
* * * *
33729802 AAGAAG AAGAAG AAGAAG AAGAAA GAAGAAGA AAGAAG AAGAAA AAG--A
1 AAGAAA AAGAAA AAGAAA AAGAAA -AAGAA-A AAGAAA AAGAAA AAGAAA
33729850 AAGAAA AA-AAA AAGAGAA AA
1 AAGAAA AAGAAA AAGA-AA AA
33729870 AAGGAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
4 4 0.08
5 5 0.09
6 29 0.55
7 14 0.26
8 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:33729857 original size:10 final size:10
Alignment explanation
Indices: 33729801--33729855 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
33729791 TAGGGTTCGT
33729801 GAAG-AAGAA
1 GAAGAAAGAA
33729810 GAAG-AAGAA
1 GAAGAAAGAA
33729819 GAAGAAAGAA
1 GAAGAAAGAA
33729829 GAAGAAAGAA
1 GAAGAAAGAA
33729839 GAAGAAA-AA
1 GAAGAAAGAA
33729848 GAAAGAAA
1 G-AAGAAA
33729856 AAAAAAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
9 16 0.36
10 28 0.64
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:33729859 original size:13 final size:13
Alignment explanation
Indices: 33729820--33729871 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
33729810 GAAGAAGAAG
*
33729820 AAGAAAGAAGAAGA
1 AAGAAAGAA-AAAA
*
33729834 AAG-AAGAAGAAA
1 AAGAAAGAAAAAA
33729846 AAGAAAGAAAAAA
1 AAGAAAGAAAAAA
33729859 AA-AAGAGAAAAAA
1 AAGAA-AGAAAAAA
33729872 GGAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 7 0.21
13 23 0.70
14 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:33729862 original size:16 final size:16
Alignment explanation
Indices: 33729830--33729868 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
33729820 AAGAAAGAAG
* *
33729830 AAGAAAGAAGAAGAAA
1 AAGAAAGAAAAAAAAA
33729846 AAGAAAGAAAAAAAAA
1 AAGAAAGAAAAAAAAA
33729862 AGAGAAA
1 A-AGAAA
33729869 AAAGGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAAAAA
Found at i:33730717 original size:18 final size:18
Alignment explanation
Indices: 33730691--33731015 Score: 213
Period size: 17 Copynumber: 17.8 Consensus size: 18
33730681 TTAAAAAAAA
33730691 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
33730708 TCGTGTTTTCAAAAAAAATT
1 TCGTGTTTTC--AAAAATTT
* *
33730728 TCTTGTGTTTCAAAAACTT
1 TCGTGT-TTTCAAAAATTT
* *
33730747 CCGTGTTTTAAAAAAAATTT
1 TCGTGTTTT--CAAAAATTT
*
33730767 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
33730785 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
33730802 TCGTGTTTTC-AAAA-TT
1 TCGTGTTTTCAAAAATTT
* *
33730818 CCAGAG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAATTT
33730836 TCGTGTTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* *
33730855 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* * *
33730874 CCGTATTTT-GAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
33730891 CCTTGTTTTCAAAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
* *
33730912 CCGTG-TTTCATAAA-TT
1 TCGTGTTTTCAAAAATTT
*
33730928 TCAGTGTTTTCAAAAAATTC
1 TC-GTGTTTTC-AAAAATTT
* *
33730948 CCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
33730965 TCGTGTTTTCAAGAAATTGA
1 TCGTGTTTTCAA-AAATT-T
* *
33730985 CCGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTT
33731002 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
33731016 AAAATCCTCA
Statistics
Matches: 241, Mismatches: 43, Indels: 48
0.73 0.13 0.14
Matches are distributed among these distances:
16 9 0.04
17 73 0.30
18 56 0.23
19 42 0.17
20 46 0.19
21 15 0.06
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:33730729 original size:20 final size:20
Alignment explanation
Indices: 33730700--33730781 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
33730690 ATCGTGTTTC
*
33730700 AAAAATTTTCGTGTTTTCAA
1 AAAAAATTTCGTGTTTTCAA
*
33730720 AAAAAATTTCTTGTGTTTC--
1 AAAAAATTTCGTGT-TTTCAA
* *
33730739 AAAAACTTCCGTGTTTT-AA
1 AAAAAATTTCGTGTTTTCAA
33730758 AAAAAATTTTCGTGTTTTCAA
1 AAAAAA-TTTCGTGTTTTCAA
33730779 AAA
1 AAA
33730782 TTCTCATGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
18 3 0.06
19 16 0.32
20 22 0.44
21 9 0.18
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAAAAATTTCGTGTTTTCAA
Found at i:33730888 original size:55 final size:54
Alignment explanation
Indices: 33730772--33731016 Score: 177
Period size: 55 Copynumber: 4.5 Consensus size: 54
33730762 AATTTTCGTG
* *
33730772 TTTTCAAAAATTCTCATG-TTTC-AAAAATCTT-CGTGTTTTC-AAAATTCCAG-A
1 TTTTC-AAAATTTTCGTGTTTTCAAAAAAT-TTCCGTGTTTTCAAAAATTCCAGTA
* *
33730823 GTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTCAAAAATTCCCGTA
1 TTTTC-AAAATTTTCGTGTTTTCAAAAAATTT-CCGTGTTTTCAAAAATTCCAGTA
* * * * * *
33730879 TTTTGAAAATTTCCTTGTTTTCAAAAAAAATTTCCGTG-TTTCATAAATTTCAGTG
1 TTTTCAAAATTTTCGTGTTTTC--AAAAAATTTCCGTGTTTTCAAAAATTCCAGTA
** ** *
33730934 TTTTCAAAAAATTCCCGTCTTTC-AAAAATTTTCGTGTTTTCAAGAAATTGACC-GT-
1 TTTTCAAAATTTTCGTGT-TTTCAAAAAATTTCCGTGTTTTCAA-AAATT--CCAGTA
*
33730989 GTTTCATAAATTTTCGTG-TTTCAAAAAA
1 TTTTCA-AAATTTTCGTGTTTTCAAAAAA
33731017 AAATCCTCAT
Statistics
Matches: 153, Mismatches: 26, Indels: 26
0.75 0.13 0.13
Matches are distributed among these distances:
51 15 0.10
52 6 0.04
53 18 0.12
54 18 0.12
55 64 0.42
56 22 0.14
57 10 0.07
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (54 bp):
TTTTCAAAATTTTCGTGTTTTCAAAAAATTTCCGTGTTTTCAAAAATTCCAGTA
Found at i:33731011 original size:36 final size:36
Alignment explanation
Indices: 33730692--33731016 Score: 168
Period size: 38 Copynumber: 8.9 Consensus size: 36
33730682 TAAAAAAAAT
* *
33730692 CGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
1 CGTGTTTCATAAATTTTCGTGTTTTC--AAAAAATTAC
* * * * * **
33730730 TTGTGTTTCAAAAACTTCCGTGTTTTAAAAAAAATTTT
1 -CGTGTTTCATAAATTTTCGTGTTTT-CAAAAAATTAC
* * * *
33730768 CGTGTTTTCAAAAATTCTCATG-TTTC-AAAAATCT-T
1 CGTG-TTTCATAAATTTTCGTGTTTTCAAAAAAT-TAC
* * **
33730803 CGTGTTTTCA-AAA-TTCCAGAG-TTTC-AAAAATTTT
1 CGTG-TTTCATAAATTTTC-GTGTTTTCAAAAAATTAC
* * *
33730837 CGTGTTTTCAAAAAATTTCCCGTGTTTTC-AAAAATTCC
1 CGTG-TTTC-ATAAATTT-TCGTGTTTTCAAAAAATTAC
* * * * *
33730875 CGTATTTTGA-AAATTTCCTTGTTTTCAAAAAAAATTTC
1 CGT-GTTTCATAAATTTTCGTGTTTTC--AAAAAATTAC
*
33730913 CGTGTTTCATAAA-TTTCAGTGTTTTCAAAAAATTCC
1 CGTGTTTCATAAATTTTC-GTGTTTTCAAAAAATTAC
* * *
33730949 CGTCTTTCAAAAATTTTCGTGTTTTCAAGAAATTGAC
1 CGTGTTTCATAAATTTTCGTGTTTTCAAAAAATT-AC
33730986 CGTGTTTCATAAATTTTCGTG-TTTCAAAAAA
1 CGTGTTTCATAAATTTTCGTGTTTTCAAAAAA
33731017 AAATCCTCAT
Statistics
Matches: 234, Mismatches: 34, Indels: 39
0.76 0.11 0.13
Matches are distributed among these distances:
33 3 0.01
34 24 0.10
35 27 0.12
36 54 0.23
37 42 0.18
38 62 0.26
39 22 0.09
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (36 bp):
CGTGTTTCATAAATTTTCGTGTTTTCAAAAAATTAC
Found at i:33731147 original size:33 final size:33
Alignment explanation
Indices: 33731110--33731172 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
33731100 AAAAATCTTG
* *
33731110 TGTTT-CATAAATTTTCGTTTTTTAAAAAAATTA
1 TGTTTCCA-AAATTCTCGTGTTTTAAAAAAATTA
33731143 TGTTTCCAAAATTCTCGTGTTTTAAAAAAA
1 TGTTTCCAAAATTCTCGTGTTTTAAAAAAA
33731173 AATCTCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (33 bp):
TGTTTCCAAAATTCTCGTGTTTTAAAAAAATTA
Found at i:33733737 original size:17 final size:17
Alignment explanation
Indices: 33733704--33733749 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
33733694 AACACGAAGA
33733704 TTTTTG-AAACA--ATT
1 TTTTTGAAAACACGATT
*
33733718 TTTTTGAAAATACGATT
1 TTTTTGAAAACACGATT
*
33733735 TTTTTTAAAACACGA
1 TTTTTGAAAACACGA
33733750 GAATTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 6 0.23
15 4 0.15
17 16 0.62
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTTTGAAAACACGATT
Found at i:33733800 original size:20 final size:20
Alignment explanation
Indices: 33733775--33733816 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
33733765 AAAATTCTTA
33733775 AAAACACGA-ATATTTTTTTG
1 AAAACACGACA-ATTTTTTTG
33733795 AAAACACGACAATTTTTTTG
1 AAAACACGACAATTTTTTTG
33733815 AA
1 AA
33733817 TATTTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAACACGACAATTTTTTTG
Found at i:33733949 original size:5 final size:5
Alignment explanation
Indices: 33733939--33733968 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
33733929 TAAAATTATT
33733939 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
33733969 AACATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:33734147 original size:8 final size:8
Alignment explanation
Indices: 33734129--33734196 Score: 66
Period size: 8 Copynumber: 7.8 Consensus size: 8
33734119 TTAAAACCCC
33734129 TTTTTTC-
1 TTTTTTCT
33734136 TTTTTTCT
1 TTTTTTCT
33734144 TTTTTTCT
1 TTTTTTCT
33734152 TCTTTTATCTT
1 T-TTTT-TC-T
33734163 CTTTTTTCCT
1 -TTTTTT-CT
33734173 CTCTTTTTCT
1 -T-TTTTTCT
33734183 TTTTTTCT
1 TTTTTTCT
33734191 TTTTTT
1 TTTTTT
33734197 TTCTGGACTG
Statistics
Matches: 54, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.13
8 22 0.41
9 5 0.09
10 8 0.15
11 11 0.20
12 1 0.02
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:33734156 original size:18 final size:18
Alignment explanation
Indices: 33734129--33734200 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
33734119 TTAAAACCCC
33734129 TTTT-TTCTTTTTTCTTT
1 TTTTCTTCTTTTTTCTTT
*
33734146 TTTTCTTCTTTTATCTTCTT
1 TTTTCTTCTTTTTTC-T-TT
*
33734166 TTTTCCTCTCTTTTTCTTT
1 TTTTCTTCT-TTTTTCTTT
*
33734185 TTTTCTTTTTTTTTCT
1 TTTTCTTCTTTTTTCT
33734201 GGACTGGGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.09
18 16 0.35
19 10 0.22
20 11 0.24
21 5 0.11
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTTTTTCTTT
Found at i:33734157 original size:10 final size:10
Alignment explanation
Indices: 33734129--33734200 Score: 73
Period size: 10 Copynumber: 7.6 Consensus size: 10
33734119 TTAAAACCCC
33734129 TTTT-TTCTT
1 TTTTCTTCTT
33734138 TTTTC-T-TT
1 TTTTCTTCTT
33734146 TTTTCTTCTT
1 TTTTCTTCTT
*
33734156 TTATCTTCTT
1 TTTTCTTCTT
*
33734166 TTTTCCTCTCT
1 TTTTCTTCT-T
33734177 TTTTC-T-TT
1 TTTTCTTCTT
*
33734185 TTTTCTTTTT
1 TTTTCTTCTT
33734195 TTTTCT
1 TTTTCT
33734201 GGACTGGGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
8 13 0.24
9 8 0.15
10 27 0.50
11 6 0.11
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:33734321 original size:23 final size:23
Alignment explanation
Indices: 33734294--33734363 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 23
33734284 TGCATTTGGG
33734294 CTGCTTCTTTCTTCTTCTCTTTT
1 CTGCTTCTTTCTTCTTCTCTTTT
*
33734317 CTGCTTCTTTCTTTCTTTCTTTTTT
1 CTGCTTCTTTC-TTC-TTCTCTTTT
* * *
33734342 CTGCTGC-TTCTTTTTCTGTTTT
1 CTGCTTCTTTCTTCTTCTCTTTT
33734364 GGTTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.20
23 13 0.32
24 6 0.15
25 14 0.34
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTCTTTT
Found at i:33734467 original size:13 final size:13
Alignment explanation
Indices: 33734449--33734504 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
33734439 TTTCTTTTTT
33734449 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
33734462 TC-TTTTTC-TTC
1 TCTTTTTTCTTTC
*
33734473 TCTCTTTTTCCTTC
1 TCT-TTTTTCTTTC
* *
33734487 TTTCTTTTTCTTTT
1 TCT-TTTTTCTTTC
33734501 TCTT
1 TCTT
33734505 CTTCTTCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 9 0.25
14 16 0.44
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:33734481 original size:14 final size:14
Alignment explanation
Indices: 33734449--33734495 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
33734439 TTTCTTTTTT
33734449 TCTTTTTTCTT-TC
1 TCTTTTTTCTTCTC
33734462 TC-TTTTTCTTCTC
1 TCTTTTTTCTTCTC
* *
33734475 TCTTTTTCCTTCTT
1 TCTTTTTTCTTCTC
33734489 TCTTTTT
1 TCTTTTT
33734496 CTTTTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 8 0.27
13 6 0.20
14 16 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTTTTCTTCTC
Found at i:33734491 original size:33 final size:32
Alignment explanation
Indices: 33734440--33734510 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
33734430 GCGGATATAT
*
33734440 TTCTT-TTTTT-CTTTTTTCTTTCTCTTTTTC
1 TTCTTCTTTTTCCTTCTTTCTTTCTCTTTTTC
*
33734470 TTCTCTCTTTTTCCTTCTTTCTTTTTCTTTTTC
1 TTCT-TCTTTTTCCTTCTTTCTTTCTCTTTTTC
33734503 TTCTTCTT
1 TTCTTCTT
33734511 CTTCGGGCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 4 0.11
31 1 0.03
32 9 0.25
33 22 0.61
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (32 bp):
TTCTTCTTTTTCCTTCTTTCTTTCTCTTTTTC
Found at i:33734498 original size:6 final size:6
Alignment explanation
Indices: 33734445--33734510 Score: 69
Period size: 6 Copynumber: 10.3 Consensus size: 6
33734435 TATATTTCTT
* *
33734445 TTTTTC TTTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC
*
33734497 TTTTTC TTCTTC TT
1 TTTTTC TTTTTC TT
33734511 CTTCGGGCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
6 31 0.61
7 17 0.33
8 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:33735097 original size:4 final size:4
Alignment explanation
Indices: 33735090--33735119 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
33735080 TTTTTGTATT
33735090 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
33735120 ATTGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:33735106 original size:27 final size:27
Alignment explanation
Indices: 33735074--33735139 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
33735064 CTAACATGTA
*
33735074 ATTTATTTTTTGTATTT-TTATT-TATTT
1 ATTTATTTATT-TATTTATTATTGT-TTT
33735101 ATTTATTTATTTATTTATTATTGTTTT
1 ATTTATTTATTTATTTATTATTGTTTT
*
33735128 ATTAATATTATT
1 ATTTAT-TTATT
33735140 AAAACATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 5 0.15
27 23 0.68
28 6 0.18
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTATTTATTTATTTATTATTGTTTT
Found at i:33735895 original size:160 final size:153
Alignment explanation
Indices: 33735612--33735948 Score: 435
Period size: 160 Copynumber: 2.1 Consensus size: 153
33735602 NGTTATTTTT
* **
33735612 GAAAAACAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACATCTGTATATGA
1 GAAAAA-A-AAATTT-AAA-AAATACCTCAGCATGACCCGAGGCTCAACTCACATCTGTATATGA
* *
33735677 GTTGTATTTAAAAAAAGACATAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCT
62 GTTGTATTTAAAAAAAAAAATAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCT
*
33735742 GTATTATGAGTTGA-TTTTTGAAAAAA
127 ATATTATGAGTTGATTTTTTGAAAAAA
* *
33735768 GAAAAAAAAATTTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 GAAAAAAAAATTTAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACATCTGTA-TATGAGTT
* *
33735833 GATTTTTTGAAAAAACAAAAATTAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
65 G--TATTT-AAAAAA-AAAAA-TAAATT--AAAAATACCTCAGCATGACCCGAGGCTCAACTCAC
33735898 CTCTATATTATGAGTTGATTTTTTGAAAAAA
123 CTCTATATTATGAGTTGATTTTTTGAAAAAA
* * *
33735929 -AAAACAGAATTTTAAAAATA
1 GAAAAAAAAATTTAAAAAATA
33735949 TTTCTTGAAA
Statistics
Matches: 159, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
152 35 0.22
153 12 0.08
154 6 0.04
155 5 0.03
156 12 0.08
157 3 0.02
158 6 0.04
160 68 0.43
161 12 0.08
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (153 bp):
GAAAAAAAAATTTAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACATCTGTATATGAGTTG
TATTTAAAAAAAAAAATAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTATAT
TATGAGTTGATTTTTTGAAAAAA
Found at i:33735897 original size:81 final size:78
Alignment explanation
Indices: 33735625--33735932 Score: 419
Period size: 81 Copynumber: 3.9 Consensus size: 78
33735615 AAACAGAAAT
* ** * *
33735625 TTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACATCTGTA-TATGAGTTG-TATTT-A
1 TTAAAA-AAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGA
* *
33735687 AAAAAAGACATAAA
65 AAAAAAAAAATAAA
33735701 TT--AAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAA
1 TTAAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAA
*
33735764 AAAAGAAAAAAAAA
66 AAAA-AAAAATAAA
* *
33735778 TTTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGA
1 TTAAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGA
33735843 AAAAACAAAAATTAAA
65 AAAAA-AAAAA-TAAA
* *
33735859 TTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGA
1 TTAAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGA
33735924 AAAAAAAAA
65 AAAAAAAAA
33735933 CAGAATTTTA
Statistics
Matches: 211, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
73 36 0.17
74 11 0.05
75 4 0.02
76 8 0.04
77 8 0.04
79 52 0.25
80 21 0.10
81 71 0.34
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (78 bp):
TTAAAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAA
AAAAAAAAATAAA
Found at i:33736793 original size:6 final size:6
Alignment explanation
Indices: 33736779--33736826 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
33736769 TTCATCTTAA
*
33736779 TTTTT- TTTTTG TTTTTG -TTTTG TTTTTG TGTTT- TTTTTG TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
33736823 TTTT
1 TTTT
33736827 CAGGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 18 0.47
6 20 0.53
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:33736799 original size:11 final size:10
Alignment explanation
Indices: 33736779--33736826 Score: 62
Period size: 11 Copynumber: 4.7 Consensus size: 10
33736769 TTCATCTTAA
33736779 TTTTTTT-TT
1 TTTTTTTGTT
*
33736788 TGTTTTTGTT
1 TTTTTTTGTT
33736798 TTGTTTTTGTGT
1 TT-TTTTTGT-T
33736810 TTTTTTTGTT
1 TTTTTTTGTT
33736820 TTTTTTT
1 TTTTTTT
33736827 CAGGCATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 6 0.18
10 11 0.32
11 14 0.41
12 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:33739369 original size:29 final size:29
Alignment explanation
Indices: 33739306--33739363 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
33739296 ACAAAGTTTC
33739306 TGGGGTAAAAGTATAATTTTTGCAAAAATA
1 TGGGGTAAAA-TATAATTTTTGCAAAAATA
33739336 TGGGGTTAAAATATAATTTTTG-AAAAAT
1 TGGGG-TAAAATATAATTTTTGCAAAAAT
33739364 TCGGGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 6 0.22
30 16 0.59
31 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (29 bp):
TGGGGTAAAATATAATTTTTGCAAAAATA
Found at i:33739381 original size:29 final size:30
Alignment explanation
Indices: 33739306--33739383 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
33739296 ACAAAGTTTC
33739306 TGGGG-TAAAAGTATAATTTTTGCAAAAATA
1 TGGGGCTAAAA-TATAATTTTTGCAAAAATA
*
33739336 TGGGGTTAAAATATAATTTTTG-AAAAAT-
1 TGGGGCTAAAATATAATTTTTGCAAAAATA
* *
33739364 TCGGGGCTAACATGTAATTT
1 T-GGGGCTAAAATATAATTT
33739384 ATTTTTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 16 0.37
31 5 0.12
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
TGGGGCTAAAATATAATTTTTGCAAAAATA
Found at i:33739404 original size:19 final size:19
Alignment explanation
Indices: 33739380--33739438 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
33739370 CTAACATGTA
*
33739380 ATTTATTTTTTGTATTT-TT
1 ATTTATTTATT-TATTTATT
33739399 ATTTATTTATTTATTTATT
1 ATTTATTTATTTATTTATT
*
33739418 ATTGT-TTTATTAATATTATT
1 ATT-TATTTATTTAT-TTATT
33739438 A
1 A
33739439 AAACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 5 0.14
19 23 0.66
20 7 0.20
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTATTTATTTATTTATT
Found at i:33744948 original size:10 final size:10
Alignment explanation
Indices: 33744933--33744962 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33744923 GGCATATATC
33744933 TCATATCATT
1 TCATATCATT
*
33744943 TCATATCATC
1 TCATATCATT
33744953 TCATATCATT
1 TCATATCATT
33744963 GTGTGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (10 bp):
TCATATCATT
Found at i:33744955 original size:20 final size:19
Alignment explanation
Indices: 33744925--33744962 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
33744915 CCTTTTCCGG
33744925 CATATATCTCATATCATTT
1 CATATATCTCATATCATTT
33744944 CATATCATCTCATATCATT
1 CATAT-ATCTCATATCATT
33744963 GTGTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (19 bp):
CATATATCTCATATCATTT
Found at i:33748496 original size:13 final size:13
Alignment explanation
Indices: 33748478--33748554 Score: 79
Period size: 13 Copynumber: 6.1 Consensus size: 13
33748468 TATTATGCCT
33748478 AAAAAAAACAAAC
1 AAAAAAAACAAAC
*
33748491 -AAAAAAACAAAAT
1 AAAAAAAAC-AAAC
33748504 AAAAAAAAC-AAC
1 AAAAAAAACAAAC
*
33748516 AAAAAAAACAAAG
1 AAAAAAAACAAAC
* *
33748529 AAACAAAACAAAG
1 AAAAAAAACAAAC
*
33748542 AAACAAAA-AAAC
1 AAAAAAAACAAAC
33748554 A
1 A
33748555 GAAGAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
12 23 0.41
13 25 0.45
14 8 0.14
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:33748500 original size:8 final size:8
Alignment explanation
Indices: 33748478--33748554 Score: 65
Period size: 8 Copynumber: 9.9 Consensus size: 8
33748468 TATTATGCCT
33748478 AAAAA-AA
1 AAAAACAA
*
33748485 ACAAACAA
1 AAAAACAA
33748493 AAAAACAA
1 AAAAACAA
33748501 AATAAA-AA
1 AA-AAACAA
33748509 AAACAACAAA
1 AAA-AAC-AA
33748519 AAAAACAA
1 AAAAACAA
*
33748527 AGAAAC--
1 AAAAACAA
33748533 -AAAACAA
1 AAAAACAA
*
33748540 AGAAACAA
1 AAAAACAA
33748548 AAAAACA
1 AAAAACA
33748555 GAAGAAAAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
5 4 0.07
7 5 0.09
8 36 0.64
9 6 0.11
10 5 0.09
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (8 bp):
AAAAACAA
Found at i:33748513 original size:26 final size:26
Alignment explanation
Indices: 33748477--33748563 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
33748467 ATATTATGCC
33748477 TAAAAAAAACAAACAAAAAAACAAAA
1 TAAAAAAAACAAACAAAAAAACAAAA
33748503 TAAAAAAAAC-AACAAAAAAAACAAAGA
1 TAAAAAAAACAAAC-AAAAAAACAAA-A
* * *
33748530 AACAAAACAAAGAAACAAAAAAACAGAA
1 TA-AAAA-AAACAAACAAAAAAACAAAA
*
33748558 GAAAAA
1 TAAAAA
33748564 GAAAAATCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.06
26 21 0.40
27 6 0.12
28 6 0.12
29 13 0.25
30 3 0.06
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (26 bp):
TAAAAAAAACAAACAAAAAAACAAAA
Found at i:33748563 original size:13 final size:12
Alignment explanation
Indices: 33748479--33748552 Score: 75
Period size: 12 Copynumber: 6.3 Consensus size: 12
33748469 ATTATGCCTA
33748479 AAAAAAACAAAC
1 AAAAAAACAAAC
33748491 AAAAAAACAAA-
1 AAAAAAACAAAC
*
33748502 ATAAAAA-AAAC
1 AAAAAAACAAAC
33748513 AACAAAAA-AAAC
1 AA-AAAAACAAAC
*
33748525 AAAGAAACAAAAC
1 AAAAAAAC-AAAC
*
33748538 AAAGAAACAAA-
1 AAAAAAACAAAC
33748549 AAAA
1 AAAA
33748553 CAGAAGAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
10 3 0.06
11 14 0.26
12 25 0.46
13 12 0.22
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:33748569 original size:17 final size:16
Alignment explanation
Indices: 33748482--33748561 Score: 69
Period size: 17 Copynumber: 4.9 Consensus size: 16
33748472 ATGCCTAAAA
*
33748482 AAAACAAACAAAAAAAC
1 AAAA-AAACAAAGAAAC
*
33748499 AAAATAAA-AAAAACAAC
1 AAAA-AAACAAAGA-AAC
33748516 AAAAAAAACAAAGAAAC
1 -AAAAAAACAAAGAAAC
33748533 ---AAAACAAAGAAAC
1 AAAAAAACAAAGAAAC
33748546 AAAAAAACAGAAGAAA
1 AAAAAAACA-AAGAAA
33748562 AAGAAAAATC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 13 0.24
16 11 0.20
17 22 0.41
18 8 0.15
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.01
Consensus pattern (16 bp):
AAAAAAACAAAGAAAC
Found at i:33749513 original size:77 final size:74
Alignment explanation
Indices: 33749405--33749602 Score: 272
Period size: 74 Copynumber: 2.6 Consensus size: 74
33749395 TTCTGTTTTT
*
33749405 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTC
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATA--T-
33749470 TTTTAAATTTC-TA
62 TTTTAAA-TTCATA
** *
33749483 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATATTTTT
* *
33749548 CAATTCATG
66 AAATTCATA
* *
33749557 TTTTTCAAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGG
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
33749603 GGCACATGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
73 3 0.03
74 51 0.46
75 1 0.01
77 50 0.45
78 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (74 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATATTTTT
AAATTCATA
Found at i:33749664 original size:75 final size:73
Alignment explanation
Indices: 33749413--33749690 Score: 281
Period size: 77 Copynumber: 3.7 Consensus size: 73
33749403 TTTTTTTCAA
** * * *
33749413 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTA--T-TTTTCAA-
*
33749478 TTC-TATTTTTC
62 TTCATGTTTTTC
*
33749489 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTCAATTC
33749554 ATGTTTTTC
65 ATGTTTTTC
* * *
33749563 AAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGGGCACATGTCGAGGTA-TTTTCGAT
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTTCAAT
**
33749627 TTTTGTTTTTC
63 TCATGTTTTTC
* * * * * *
33749638 GAAGATCAACTCATAATCCAAGAGGTGAGTTGAGCTTCGAGTCGCACGCCGAG
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-G-GGCACGCCGAG
33749691 CTTTTCACTA
Statistics
Matches: 174, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
73 7 0.04
74 51 0.29
75 51 0.29
76 12 0.07
77 53 0.30
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTCAATTCA
TGTTTTTC
Found at i:33749686 original size:151 final size:149
Alignment explanation
Indices: 33749405--33749690 Score: 351
Period size: 149 Copynumber: 1.9 Consensus size: 149
33749395 TTCTGTTTTT
*
33749405 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTC
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGACCATGCCGAGATA--T-
* * * *
33749470 TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
63 TTTTAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCACG
33749535 CCGAGGTATTTTTCAATTCATG
128 CCGAGGTATTTTTCAATTCATG
* * * *
33749557 TTTTTC-AAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGGGCACATGTCGAGGTA-T
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTC-GGAC-CATGCCGAGATATT
** * * * * *
33749620 TTTCGATTTTTGTTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGCTTCGAGTCGCAC
64 TTTAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGT--CAC
33749685 GCCGAG
127 GCCGAG
33749691 CTTTTCACTA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
149 50 0.44
151 45 0.39
152 9 0.08
153 10 0.09
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (149 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGACCATGCCGAGATATTTT
TAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCACGCCG
AGGTATTTTTCAATTCATG
Found at i:33750014 original size:30 final size:31
Alignment explanation
Indices: 33749891--33750006 Score: 141
Period size: 30 Copynumber: 3.9 Consensus size: 31
33749881 AAAAAATTTG
* *
33749891 CATTTTGACCCCTACA-TTTTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
*
33749921 CATTTTGATCCCTAAACTTTCTC-AAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
**
33749951 CATTTAAACCCCTAAAC-TTCT-TAAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
**
33749980 TGTTTTGACCCCTAAACTTTCTCTAAA
1 CATTTTGACCCCTAAACTTTCTCTAAA
33750007 TTATGTTTCG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 24 0.33
30 39 0.54
31 9 0.12
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (31 bp):
CATTTTGACCCCTAAACTTTCTCTAAAATTA
Found at i:33750508 original size:3 final size:3
Alignment explanation
Indices: 33750502--33750595 Score: 145
Period size: 3 Copynumber: 31.0 Consensus size: 3
33750492 TAGGGTTCAT
33750502 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
33750550 GAA GAA GAA GAA GAAA GAA GAA GAA -AA AAA GAAA GAA GAA AAA GAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA
33750596 AGAAAAAAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.02
3 77 0.91
4 6 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33750601 original size:9 final size:10
Alignment explanation
Indices: 33750502--33750614 Score: 127
Period size: 9 Copynumber: 12.1 Consensus size: 10
33750492 TAGGGTTCAT
33750502 GAAGAAG-AA
1 GAAGAAGAAA
33750511 GAAGAAG-AA
1 GAAGAAGAAA
33750520 GAAGAAG-AA
1 GAAGAAGAAA
33750529 GAAGAAG-AA
1 GAAGAAGAAA
33750538 GAAGAAG-AA
1 GAAGAAGAAA
33750547 GAAGAAG-AA
1 GAAGAAGAAA
33750556 GAAGAAGAAA
1 GAAGAAGAAA
33750566 GAAGAAGAAA
1 GAAGAAGAAA
33750576 -AA-AAGAAA
1 GAAGAAGAAA
33750584 GAAGAA-AAA
1 GAAGAAGAAA
*
33750593 GAAAGAAAAAA
1 G-AAGAAGAAA
* *
33750604 AAAGAAAAAA
1 GAAGAAGAAA
33750614 G
1 G
33750615 GAAAAAATAT
Statistics
Matches: 97, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
8 6 0.06
9 60 0.62
10 28 0.29
11 3 0.03
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:33750610 original size:14 final size:14
Alignment explanation
Indices: 33750563--33750610 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
33750553 GAAGAAGAAG
33750563 AAAG-AAGAAGAAAA
1 AAAGAAAGAA-AAAA
*
33750577 AAAGAAAG-AAGAA
1 AAAGAAAGAAAAAA
33750590 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
33750604 AAAGAAA
1 AAAGAAA
33750611 AAAGGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 11 0.37
14 16 0.53
15 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAAA
Found at i:33750619 original size:13 final size:13
Alignment explanation
Indices: 33750512--33750620 Score: 67
Period size: 15 Copynumber: 7.6 Consensus size: 13
33750502 GAAGAAGAAG
*
33750512 AAGAAGAAGAAGAA
1 AAGAAAAAGAA-AA
*
33750526 GAAGAAGAAGAAGAA
1 -AAGAAAAAGAA-AA
*
33750541 GAAGAAGAAGAAGAA
1 -AAGAAAAAGAA-AA
33750556 GAAGAAGAAAGAAGAA
1 -AAGAA-AAAGAA-AA
*
33750572 GAA-AAAAAGAAAG
1 -AAGAAAAAGAAAA
33750585 AAGAAAAAGAAAGA
1 AAGAAAAAGAAA-A
*
33750599 AAAAAAAAGAAAA
1 AAGAAAAAGAAAA
33750612 AAGGAAAAA
1 AA-GAAAAA
33750621 ATATAAAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
12 2 0.02
13 13 0.15
14 22 0.26
15 37 0.44
16 11 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:33750739 original size:20 final size:21
Alignment explanation
Indices: 33750714--33750763 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
33750704 CAGCAACCCC
* *
33750714 AAAAAAAAGAAACG-GGCCCA
1 AAAAAAAAGAAAAGTAGCCCA
**
33750734 AAAAAAGGGAAAAGTAGCCCA
1 AAAAAAAAGAAAAGTAGCCCA
33750755 AAAAAAAAG
1 AAAAAAAAG
33750764 GAGACAGCAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.64, C:0.14, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAAAGTAGCCCA
Found at i:33751461 original size:18 final size:18
Alignment explanation
Indices: 33751435--33751738 Score: 198
Period size: 17 Copynumber: 16.8 Consensus size: 18
33751425 TTAAAAAAAA
33751435 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
33751452 TCGTGTTTTCAAAAACTT
1 TCGTGTTTTCAAAAATTT
* * **
33751470 CCGTGTTTTAAAAAAAAAAT
1 TCGTGTTTT--CAAAAATTT
*
33751490 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
33751508 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
33751525 TCGTGTTTTC-AAAA-TT
1 TCGTGTTTTCAAAAATTT
33751541 TCAGTG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAATTT
33751559 TCGTGTTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* *
33751578 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* *
33751597 CCGT-ATTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
33751614 CCTTGTTTTCAAAAAAAAAAT
1 TCGTGTTTTC---AAAAATTT
* *
33751635 CCGTG-TTTCATAAA-TT
1 TCGTGTTTTCAAAAATTT
*
33751651 TCAGTGTTTTCAAAAAATTC
1 TC-GTGTTTTC-AAAAATTT
* *
33751671 CCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
33751688 TCGTGTTTTCAAGAAATTGA
1 TCGTGTTTTCAA-AAATT-T
* * *
33751708 CCGTG-TTTCATAGATTT
1 TCGTGTTTTCAAAAATTT
33751725 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
33751739 AAAATCCTCA
Statistics
Matches: 224, Mismatches: 42, Indels: 42
0.73 0.14 0.14
Matches are distributed among these distances:
16 9 0.04
17 75 0.33
18 66 0.29
19 31 0.14
20 33 0.15
21 10 0.04
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:33751495 original size:38 final size:36
Alignment explanation
Indices: 33751451--33751696 Score: 166
Period size: 36 Copynumber: 6.8 Consensus size: 36
33751441 TTCAAAAATT
*
33751451 TTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAAAA
1 TTCGTGTTTTCAAAAATTTCCGTGTTTT--AAAAAAAA
* * **
33751489 TTCGTGTTTTCAAAAA-TTCTCATG-TTTCAAAAATC
1 TTCGTGTTTTCAAAAATTTC-CGTGTTTTAAAAAAAA
* * **
33751524 TTCGTGTTTTC-AAAATTTCAGTG-TTTCAAAAATT
1 TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
*
33751558 TTCGTGTTTTCAAAAAATTTCCCGTGTTTT--CAAAAA
1 TTCGTGTTTTC-AAAAATTT-CCGTGTTTTAAAAAAAA
** *
33751594 TTCCCGTATTTCAAAAATTTCCTTGTTTTCAAAAAAAAAA
1 TTCGTGT-TTTCAAAAATTTCCGTGTTTT---AAAAAAAA
* * * *
33751634 TCCGTG-TTTCATAAATTTCAGTGTTTT-CAAAAAA
1 TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
** *
33751668 TTCCCGTCTTTCAAAAATTTTCGTGTTTT
1 TTCGTGT-TTTCAAAAATTTCCGTGTTTT
33751697 CAAGAAATTG
Statistics
Matches: 166, Mismatches: 28, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
34 36 0.22
35 27 0.16
36 41 0.25
37 14 0.08
38 40 0.24
40 8 0.05
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (36 bp):
TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
Found at i:33751503 original size:21 final size:21
Alignment explanation
Indices: 33751462--33751504 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
33751452 TCGTGTTTTC
*
33751462 AAAAACTTCCGTGTTTTAAAA
1 AAAAAATTCCGTGTTTTAAAA
*
33751483 AAAAAATT-CGTGTTTTCAAA
1 AAAAAATTCCGTGTTTTAAAA
33751503 AA
1 AA
33751505 TTCTCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAAAATTCCGTGTTTTAAAA
Found at i:33751573 original size:89 final size:88
Alignment explanation
Indices: 33751435--33751627 Score: 223
Period size: 89 Copynumber: 2.2 Consensus size: 88
33751425 TTAAAAAAAA
33751435 TCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAAAATT-CGTGTTT
1 TCGTGTTTTC-AAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTT--AAAAAAAATTCCGTGTTT
* *
33751498 TCAAAAATTCTCATGTTTCAAAAATCT
63 TCAAAAATTCCCATATTTCAAAAAT-T
* * * *
33751525 TCGTGTTTTCAAAA-TTTCAGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTT
1 TCGTGTTTTCAAAATTTTC-GTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAATT-CCGTGTTTT
*
33751588 CAAAAATTCCCGTATTTCAAAAATT
64 CAAAAATTCCCATATTTCAAAAATT
*
33751613 TCCTTGTTTTCAAAA
1 T-CGTGTTTTCAAAA
33751628 AAAAAATCCG
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
87 8 0.09
88 2 0.02
89 64 0.71
90 12 0.13
91 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (88 bp):
TCGTGTTTTCAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAATTCCGTGTTTTCA
AAAATTCCCATATTTCAAAAATT
Found at i:33751610 original size:36 final size:35
Alignment explanation
Indices: 33751531--33751738 Score: 154
Period size: 36 Copynumber: 5.8 Consensus size: 35
33751521 ATCTTCGTGT
* ** *
33751531 TTTC-AAAATTTCAGTG-TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGTTTTCAAAAATTCCCGT-A
33751565 TTTCAAAAAATTTCCCGTGTTTTCAAAAATTCCCGTA
1 TTTC-AAAAATTT-CCGTGTTTTCAAAAATTCCCGTA
* * *
33751602 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAAT-CCGTG
1 TTTCAAAAATTTCCGTGTTTTC----AAAAATTCCCGTA
* * *
33751640 TTTCATAAATTTCAGTGTTTTCAAAAAATTCCCGTC
1 TTTCAAAAATTTCCGTGTTTTC-AAAAATTCCCGTA
* * *
33751676 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGACCGTG
1 TTTCAAAAATTTCCGTGTTTTCAA-AAATT-CCCGTA
* * *
33751713 TTTCATAGATTTTCGTG-TTTCAAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAA
33751739 AAAATCCTCA
Statistics
Matches: 144, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
34 4 0.03
35 21 0.15
36 49 0.34
37 27 0.19
38 37 0.26
39 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (35 bp):
TTTCAAAAATTTCCGTGTTTTCAAAAATTCCCGTA
Found at i:33751650 original size:55 final size:55
Alignment explanation
Indices: 33751517--33751631 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 55
33751507 CTCATGTTTC
* * * * *
33751517 AAAAATCTTCGTGTTTTC-AAAATTTCAGTGTTTCAAAAATTTTCGTGTTTTCAAA
1 AAAAATC-CCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
** *
33751572 AAATTTCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCTTGTTTTCAAA
1 AAAAATCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
33751627 AAAAA
1 AAAAA
33751632 AATCCGTGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
54 9 0.18
55 40 0.82
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (55 bp):
AAAAATCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
Found at i:33751666 original size:73 final size:74
Alignment explanation
Indices: 33751437--33751699 Score: 251
Period size: 74 Copynumber: 3.6 Consensus size: 74
33751427 AAAAAAAATC
** * *
33751437 GTGTTTCAAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTT-AAAAAAAAAATTCGTGTTTTCA
1 GTGTTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTCA
33751501 AAAATTCTCA
66 AAAATT-TCA
* * ** *
33751511 -TGTTTCAAAAA-TCTTCGTGTTTTC-AAAATTTCAGTG-TTTC---AAAAATTTTCGTGTTTTC
1 GTGTTTCAAAAATTC-CCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTC
*
33751569 AAAAAATTTCCC
65 -AAAAATTT-CA
* *
33751581 GTGTTTTCAAAAATTCCCGT-ATTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATCCGTG-TTTC
1 GTG-TTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTC
*
33751644 ATAAATTTCA
65 AAAAATTTCA
* *
33751654 GTGTTTTCAAAAAATTCCCGT-CTTTCAAAAATTTTCGTGTTTTCAA
1 GTG-TTTC-AAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAA
33751700 GAAATTGACC
Statistics
Matches: 158, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
69 17 0.11
70 8 0.05
71 9 0.06
72 33 0.21
73 36 0.23
74 41 0.26
75 4 0.03
76 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (74 bp):
GTGTTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTCA
AAAATTTCA
Found at i:33751726 original size:37 final size:35
Alignment explanation
Indices: 33751580--33751739 Score: 135
Period size: 37 Copynumber: 4.4 Consensus size: 35
33751570 AAAAATTTCC
* * * *
33751580 CGTGTTTTC-AAAAATTCCCGTATTTCAAAAATTTC
1 CGTGTTTTCAAAAAATTACCGTGTTTC-ATAATTTT
* ** *
33751615 CTTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTT
1 CGTGTTTTC-AAAAAATTA-CCGTGTTTCATAATTTT
* * *
33751652 CAGTGTTTTCAAAAAATTCCCGTCTTTCAAAAATTTT
1 C-GTGTTTTCAAAAAATTACCGTGTTTC-ATAATTTT
*
33751689 CGTGTTTTCAAGAAATTGACCGTGTTTCATAGATTTT
1 CGTGTTTTCAAAAAATT-ACCGTGTTTCATA-ATTTT
33751726 CGTG-TTTCAAAAAA
1 CGTGTTTTCAAAAAA
33751740 AAATCCTCAT
Statistics
Matches: 98, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
35 8 0.08
36 34 0.35
37 41 0.42
38 15 0.15
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (35 bp):
CGTGTTTTCAAAAAATTACCGTGTTTCATAATTTT
Found at i:33751741 original size:74 final size:74
Alignment explanation
Indices: 33751458--33751739 Score: 230
Period size: 74 Copynumber: 3.9 Consensus size: 74
33751448 ATTTTCGTGT
* * *
33751458 TTTCAAAAACTTCCGTGTTTT-AAAAAAAAAATTCGTGTTTTCAAAAATTCTCA-TG-TTTCAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTG-TTTCATAAATT-TCAGTGTTTTCAAA
* **
33751520 AATCTTCGTGT-
64 AA-ATTCCCGTA
* ** * * *
33751531 TTTC-AAAATTTCAGTG-TTTC---AAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC-A
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTG-TTTC-ATAAATTT-CAGTGTTTTCAA
33751590 AAAATTCCCGTA
63 AAAATTCCCGTA
*
33751602 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
*
33751667 ATTCCCGTC
66 ATTCCCGTA
* * *** *
33751676 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGA-CCGTGTTTCATAGATTTTC-GTG-TTTCAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATA-AATTTCAGTGTTTTCAAAA
33751738 AA
65 AA
33751740 AAATCCTCAT
Statistics
Matches: 173, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
69 17 0.10
70 13 0.08
71 13 0.08
72 34 0.20
73 32 0.18
74 50 0.29
75 4 0.02
76 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
ATTCCCGTA
Found at i:33751846 original size:38 final size:38
Alignment explanation
Indices: 33751602--33751911 Score: 173
Period size: 38 Copynumber: 8.1 Consensus size: 38
33751592 AATTCCCGTA
* * *
33751602 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATC-CGTG
1 TTTCATAAATTTTCGTGTTTTC-AAAAAAAAATCTCGTG
* * *
33751640 TTTCATAAA-TTTCAGTGTTTTC--AAAAAATTCCCGTC
1 TTTCATAAATTTTC-GTGTTTTCAAAAAAAAATCTCGTG
* ***
33751676 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGA-C-CGTG
1 TTTCATAAATTTTCGTGTTTTCAA-AAAAAAATCTCGTG
*
33751713 TTTCATAGATTTTCGTG-TTTCAAAAAAAAATCCTCATGTTTCG
1 TTTCATAAATTTTCGTGTTTTCAAAAAAAAAT-CTC--G--T-G
* ** *
33751756 TACTTTATTAAAATTTTTATGTTTTCAAAAACAAAT-TCGGTG
1 T--TTCA-T-AAATTTTCGTGTTTTCAAAAAAAAATCTC-GTG
*
33751798 TCTTGA-AAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
1 T-TTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
* ** *
33751836 TTTCATAAATTTT--TATTTTTTAAAAAAAAT-T-ATG
1 TTTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
* *
33751870 TTTACA-AAATTCTCGTGTTTT-AAAAAAAAATCTCATG
1 TTT-CATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
33751907 TTTCA
1 TTTCA
33751912 ATCGGCTCGC
Statistics
Matches: 212, Mismatches: 34, Indels: 54
0.71 0.11 0.18
Matches are distributed among these distances:
34 11 0.05
35 24 0.11
36 47 0.22
37 35 0.17
38 51 0.24
39 5 0.02
40 1 0.00
41 4 0.02
42 3 0.01
43 3 0.01
45 4 0.02
46 3 0.01
47 8 0.04
48 13 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (38 bp):
TTTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
Found at i:33757563 original size:43 final size:40
Alignment explanation
Indices: 33757484--33757564 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
33757474 TATTTTTATC
*
33757484 TATTTTATAATTTGTATACGTATAATTATATCTACATACA
1 TATTTTATAATTTGTATAAGTATAATTATATCTACATACA
* * *
33757524 TATTTTCTAAATTTTTATAAGTATATATTTATATGTACATA
1 TATTTTAT-AATTTGTATAAGTATA-A-TTATATCTACATA
33757565 TGTTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 7 0.21
41 14 0.41
42 1 0.03
43 12 0.35
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (40 bp):
TATTTTATAATTTGTATAAGTATAATTATATCTACATACA
Found at i:33759656 original size:15 final size:16
Alignment explanation
Indices: 33759630--33759659 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33759620 GCATTGAATA
33759630 AAATATTTATAATTTT
1 AAATATTTATAATTTT
33759646 AAATA-TTATAATTT
1 AAATATTTATAATTT
33759660 GACTTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTTATAATTTT
Found at i:33766491 original size:43 final size:43
Alignment explanation
Indices: 33766426--33766590 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
33766416 TACCGTAACA
* * * *
33766426 ATGCCAA-ATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
* * *** *
33766468 ATGCCAATAGCCCAGCCACGGTCTTACAAAAAATCACATATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
33766511 ATGCCAAT-GTCCCAGACATGGTCTTACACG-AAGTCTCATATCG
1 ATGCCAATAG-CCCAGACATGGTCTTACACGTAA-TCTCATATCG
* *
33766554 ATGCC-ATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCA
33766591 GTAACCCTAA
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 36 0.35
43 66 0.65
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
Found at i:33767940 original size:16 final size:18
Alignment explanation
Indices: 33767905--33767947 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
33767895 CTCCTTGCTA
*
33767905 CTTCTTTTTTTCCTTATT
1 CTTCTTTTTTTCCATATT
33767923 CTTCTTTTTTT-CAT-TT
1 CTTCTTTTTTTCCATATT
33767939 CTTCCTTTT
1 CTT-CTTTT
33767948 AGTTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 11 0.48
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTCTTTTTTTCCATATT
Found at i:33768685 original size:64 final size:64
Alignment explanation
Indices: 33768606--33768731 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
33768596 AGTGCAGGGG
* * *
33768606 TCACACAGGCCAAGGACACGGGTGTGTGTCTAGGCCGTGTAACTCACTGATTACAAAATAAGAA
1 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAGAA
* *
33768670 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCTGTGTAACCCACTGATTATAAAATAAG
1 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAG
33768732 GACCATACGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (64 bp):
TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAGAA
Found at i:33771203 original size:11 final size:11
Alignment explanation
Indices: 33771187--33771213 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33771177 TTGACGAATG
33771187 AAAACAAACCC
1 AAAACAAACCC
33771198 AAAACAAACCC
1 AAAACAAACCC
33771209 AAAAC
1 AAAAC
33771214 CGAAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAACCC
Found at i:33772102 original size:32 final size:32
Alignment explanation
Indices: 33772036--33772103 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
33772026 CACGCCCCTA
* *
33772036 TGGCCCACACGGCCTAAATGACCTAACCCGTG
1 TGGCCCACACGGCCCAAATGACCTAACCCATG
*
33772068 TGGCCCACATGGCCCAAAT-AGCCTAGA-CCATG
1 TGGCCCACACGGCCCAAATGA-CCTA-ACCCATG
33772100 TGGC
1 TGGC
33772104 TTACAAGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 1 0.03
32 29 0.94
33 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (32 bp):
TGGCCCACACGGCCCAAATGACCTAACCCATG
Found at i:33778852 original size:8 final size:8
Alignment explanation
Indices: 33778841--33778886 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
33778831 GCTAAATGTT
33778841 TGTTTATA
1 TGTTTATA
33778849 TGTTTATA
1 TGTTTATA
*
33778857 TATTTATA
1 TGTTTATA
33778865 TG-TT-T-
1 TGTTTATA
*
33778870 CGTTTATA
1 TGTTTATA
33778878 TGTTTATA
1 TGTTTATA
33778886 T
1 T
33778887 CGGAATAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
5 1 0.03
6 3 0.10
7 3 0.10
8 24 0.77
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (8 bp):
TGTTTATA
Found at i:33779782 original size:42 final size:42
Alignment explanation
Indices: 33779731--33779850 Score: 197
Period size: 42 Copynumber: 2.9 Consensus size: 42
33779721 CAATTTTTAT
33779731 TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
***
33779773 TATTTATAACAAATTAATA-ACAAATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAA-AGAGTTATTAATTTAAAATTCTATA
33779815 TATTTATAACAAATTAAAGAGTTATTAATTTAAAAT
1 TATTTATAACAAATTAAAGAGTTATTAATTTAAAAT
33779851 ATTTAATAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (42 bp):
TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
Found at i:33782348 original size:9 final size:9
Alignment explanation
Indices: 33782302--33782356 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
33782292 GGTTGCAAAA
*
33782302 AGGACAATG
1 AGGACGATG
*
33782311 ATGACGATG
1 AGGACGATG
*
33782320 ACGACGATG
1 AGGACGATG
*
33782329 ACGACGATG
1 AGGACGATG
33782338 AGGACGATG
1 AGGACGATG
*
33782347 AGGATGATG
1 AGGACGATG
33782356 A
1 A
33782357 TGTTTCTTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.36, T:0.15
Consensus pattern (9 bp):
AGGACGATG
Found at i:33782423 original size:22 final size:22
Alignment explanation
Indices: 33782398--33782462 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
33782388 CTTCTAAATA
33782398 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
* *
33782420 TGTT-AT-GA-AA-TTA-AATA
1 TGTTGATGGACAATTTATATTT
33782437 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
33782459 TGTT
1 TGTT
33782463 ATGAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (22 bp):
TGTTGATGGACAATTTATATTT
Found at i:33782431 original size:19 final size:19
Alignment explanation
Indices: 33782409--33782470 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
33782399 GTTGATGGAC
33782409 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
33782428 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
33782447 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
33782467 AATT
1 AATT
33782471 AAATATGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 8 0.24
20 4 0.12
21 5 0.15
22 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:33782435 original size:39 final size:39
Alignment explanation
Indices: 33782392--33782485 Score: 188
Period size: 39 Copynumber: 2.4 Consensus size: 39
33782382 GCTTTCCTTC
33782392 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
33782431 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
33782470 TAAATATGTTGATGGA
1 TAAATATGTTGATGGA
33782486 TTAATGTATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (39 bp):
TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
Found at i:33782504 original size:39 final size:38
Alignment explanation
Indices: 33782392--33782504 Score: 120
Period size: 39 Copynumber: 2.9 Consensus size: 38
33782382 GCTTTCCTTC
* * *
33782392 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TATATTATGAAAT
* * *
33782431 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TATATTATGAAAT
*
33782470 TAAATATGTTGATGGATTAATGTATGA-ATATTATG
1 TAAATATGTTGATGGA-CAATGTAT-ATATATTATG
33782505 GTTTGTTGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
39 61 0.90
40 6 0.09
41 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (38 bp):
TAAATATGTTGATGGACAATGTATATATATTATGAAAT
Found at i:33785197 original size:55 final size:55
Alignment explanation
Indices: 33785113--33785226 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 55
33785103 GAAAGTGGCG
* *
33785113 AGCACTCATAACGGGTGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
1 AGCACTCACAACGGGAGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
*** *
33785168 AGCACTCACAACGGGCAG-GCTCTTAGGGAGCTCGTTAGAGCCTACGTGTCAAGCG
1 AGCACTCACAACGGG-AGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
33785223 AGCA
1 AGCA
33785227 GGGTTTACGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 51 0.98
56 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (55 bp):
AGCACTCACAACGGGAGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
Found at i:33791989 original size:25 final size:25
Alignment explanation
Indices: 33791907--33792140 Score: 174
Period size: 25 Copynumber: 9.5 Consensus size: 25
33791897 AGTTGTATAA
* *
33791907 CGGGAAGCT--TGCGAGCCAATTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
33791930 CGGGAAGCTCAT-ACGAGCCATAA-A-
1 CGGGAAGCTCATGA-GAGCCA-AATAT
* *
33791954 CAGGAAGCTCATGCGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * *
33791979 TGGGAAGCTCATGAGAGTCATATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * *
33792004 CGGGAAGCTCGTGAGAGACATATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* ** *
33792029 CGGGAAGCTCAAGAGAATC-ATTAAT
1 CGGGAAGCTCATGAGAGCCAAAT-AT
* * *
33792054 CGAGAAGCTCATGAGAGCTAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
*
33792079 CGGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
** * *
33792104 TAGAAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
33792129 AGGGACGCTCAT
1 CGGGAAGCTCAT
33792141 AATAGTTATG
Statistics
Matches: 163, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
23 11 0.07
24 19 0.12
25 130 0.80
26 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:33794518 original size:31 final size:31
Alignment explanation
Indices: 33794483--33794547 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
33794473 TATAAAATGA
* *
33794483 TCACTAAATTATTCAAAAATTTTCATTTAAG
1 TCACTAAACTACTCAAAAATTTTCATTTAAG
* * *
33794514 TCACTGAACTACTCAAAAGTTTTTATTTAAG
1 TCACTAAACTACTCAAAAATTTTCATTTAAG
33794545 TCA
1 TCA
33794548 TTGGTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (31 bp):
TCACTAAACTACTCAAAAATTTTCATTTAAG
Done.