Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 183 of 356
Found at i:59295678 original size:78 final size:77
Alignment explanation
Indices: 59295537--59295680 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 77
59295527 TTCAGTGATG
* * * *
59295537 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACCTAAGGTCCACAGGC
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGA-CTAAAGTCCACAGGC
59295602 TATGTGCTAGAAT
65 TATGTGCTAGAAT
* * * *
59295615 TATAACCGGACTTAAGGTCTGTAGGCTACGTGCTGGAAATATGTCTGGGA-TAAAGTCCTACAGG
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATC-CGGACTAAAGTCC-ACAGG
59295679 CT
64 CT
59295681 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 7 0.12
78 46 0.82
79 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (77 bp):
TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGTCCACAGGCT
ATGTGCTAGAAT
Found at i:59296308 original size:43 final size:43
Alignment explanation
Indices: 59296260--59296346 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
59296250 TAAGTCTGTT
59296260 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
1 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
59296303 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
1 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
59296346 T
1 T
59296347 GCTTAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (43 bp):
TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
Found at i:59303592 original size:39 final size:39
Alignment explanation
Indices: 59303537--59303662 Score: 162
Period size: 39 Copynumber: 3.2 Consensus size: 39
59303527 TTCAGTGATG
*
59303537 TATATCCGGACTTAAGGTCCGCAGGTTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
59303576 TATATCCGGACCTAAGGTCCGTAGGCTATATGCTAGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
59303615 TATAACCGGACTTAAGGTCTGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
59303654 TATGTCCGG
1 TATATCCGG
59303663 GATAAAGTCC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:59303679 original size:78 final size:77
Alignment explanation
Indices: 59303537--59303680 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 77
59303527 TTCAGTGATG
* * * * * *
59303537 TATATCCGGACTTAAGGTCCGCAGGTTATGTGCTGGAATTATATCCGGACCTAAGGTCCGTAGGC
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGA-CTAAAGTCCATAGGC
59303602 TATATGCTAGAAT
65 TATATGCTAGAAT
* *
59303615 TATAACCGGACTTAAGGTCTGCAGGCTACGTGCTGGAAATATGTCCGGGA-TAAAGTCCCATAGG
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTAAAGT-CCATAGG
59303679 CT
64 CT
59303681 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 5 0.09
78 48 0.86
79 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (77 bp):
TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGTCCATAGGCT
ATATGCTAGAAT
Found at i:59303829 original size:35 final size:35
Alignment explanation
Indices: 59303789--59303858 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
59303779 TAAGATTACG
59303789 ATATTGAATGTTCGCAGTAAACCATCATTGAGTAA
1 ATATTGAATGTTCGCAGTAAACCATCATTGAGTAA
59303824 ATATTGAATGTTCGCAGTAAACCATCATTGAGTAA
1 ATATTGAATGTTCGCAGTAAACCATCATTGAGTAA
59303859 GTACTATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (35 bp):
ATATTGAATGTTCGCAGTAAACCATCATTGAGTAA
Found at i:59305985 original size:22 final size:24
Alignment explanation
Indices: 59305960--59306016 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
59305950 GATACTTTTC
59305960 TTTTTTTTTCTTTC-T-TCCTAAA
1 TTTTTTTTTCTTTCTTCTCCTAAA
*
59305982 TTTTTTTGTTC-TTCTTCTCCTATA
1 TTTTTTT-TTCTTTCTTCTCCTAAA
*
59306006 TTTTGTTTTCT
1 TTTTTTTTTCT
59306017 CAATCAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 10 0.34
23 7 0.24
24 12 0.41
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTCTTTCTTCTCCTAAA
Found at i:59308847 original size:21 final size:22
Alignment explanation
Indices: 59308821--59308862 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
59308811 GACAAAAAAT
*
59308821 ATGTTTTTTT-TTGTTTTTTTA
1 ATGTTTTTTTCTTGTTGTTTTA
59308842 ATGTTTTTTTCTTGTTGTTTT
1 ATGTTTTTTTCTTGTTGTTTT
59308863 CTCCCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.79
Consensus pattern (22 bp):
ATGTTTTTTTCTTGTTGTTTTA
Found at i:59309115 original size:11 final size:11
Alignment explanation
Indices: 59309099--59309129 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
59309089 TATATATATT
59309099 TAAAAATTATA
1 TAAAAATTATA
*
59309110 TAAAAATAATA
1 TAAAAATTATA
59309121 TAAAAATTA
1 TAAAAATTA
59309130 ATACTGCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:59310200 original size:48 final size:47
Alignment explanation
Indices: 59310120--59310232 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 47
59310110 TGCTTTTTTT
* *
59310120 ACAATGCACT-GAAAATAATGCACTAAACCTATCTCAATGTTCGAAA
1 ACAATGCACTGGAAAATAATACACTAAACCTATCTAAATGTTCGAAA
* * * *
59310166 ATAATGCACTGGAAAAATAATACATTGAAGCTATCTAAATGTTCGAAA
1 ACAATGCACTGG-AAAATAATACACTAAACCTATCTAAATGTTCGAAA
*
59310214 ACAATGCACT-GTAAATAAT
1 ACAATGCACTGGAAAATAAT
59310233 GATTAAAACT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
46 16 0.28
47 2 0.04
48 39 0.68
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (47 bp):
ACAATGCACTGGAAAATAATACACTAAACCTATCTAAATGTTCGAAA
Found at i:59312352 original size:33 final size:33
Alignment explanation
Indices: 59312315--59312455 Score: 90
Period size: 33 Copynumber: 4.2 Consensus size: 33
59312305 GCCCAACCAC
* * *
59312315 GGTCTTACATTC-GTTGTGCCATAACCCTGTTAT
1 GGTCTTACATTCAG-AGTGCCATAACCCAGCTAT
*
59312348 GGTCTTATCA-TCAGAGTGCCATAGCCCAGCTAT
1 GGTCTTA-CATTCAGAGTGCCATAACCCAGCTAT
* * * *** * *
59312381 GGTCTTACATGTAAACATTGCCATGGTCCAACCAT
1 GGTCTTACAT-T-CAGAGTGCCATAACCCAGCTAT
* *
59312416 GGTCTTACATTC-GTAGTGCCACAACCCAGTTAT
1 GGTCTTACATTCAG-AGTGCCATAACCCAGCTAT
59312449 GGTCTTA
1 GGTCTTA
59312456 TCCGTCAATT
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
32 2 0.02
33 49 0.60
34 5 0.06
35 25 0.31
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (33 bp):
GGTCTTACATTCAGAGTGCCATAACCCAGCTAT
Found at i:59318268 original size:15 final size:15
Alignment explanation
Indices: 59318248--59318276 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59318238 GTATTGTTGT
59318248 TTGATAACACGATGA
1 TTGATAACACGATGA
59318263 TTGATAACACGATG
1 TTGATAACACGATG
59318277 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (15 bp):
TTGATAACACGATGA
Found at i:59320773 original size:19 final size:19
Alignment explanation
Indices: 59320714--59320773 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
59320704 AATCCTTTAA
*
59320714 AAATTAACAAAATACTATT
1 AAATTAACAAATTACTATT
*
59320733 AAGA-TAATC-ACTTACATATT
1 AA-ATTAA-CAAATTAC-TATT
59320753 AAATTAACAAATTACTATT
1 AAATTAACAAATTACTATT
59320772 AA
1 AA
59320774 GATAAGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATTAACAAATTACTATT
Found at i:59322003 original size:16 final size:16
Alignment explanation
Indices: 59321982--59322046 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
59321972 TTCGTTGTAT
59321982 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
59321998 TGGAATAGAAGTGTAA
1 TGGAATAGAGGCGTAA
59322014 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
59322030 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
59322046 T
1 T
59322047 AGCAATTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.40, C:0.05, G:0.34, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:59322023 original size:32 final size:32
Alignment explanation
Indices: 59321977--59322038 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
59321967 TTTGGTTCGT
*
59321977 TGTATTGGAATAGAGGCGTAATGGAATAGAAG
1 TGTAATGGAATAGAGGCGTAATGGAATAGAAG
59322009 TGTAATGGAATAGAGGCGTAATGGAATAGA
1 TGTAATGGAATAGAGGCGTAATGGAATAGA
59322039 GACGTAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.34, T:0.24
Consensus pattern (32 bp):
TGTAATGGAATAGAGGCGTAATGGAATAGAAG
Found at i:59322090 original size:45 final size:44
Alignment explanation
Indices: 59322026--59322122 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
59322016 GAATAGAGGC
59322026 GTAATGGAATAGAGACGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
59322071 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAAT
*
59322115 GGAATGGA
1 GTAATGGA
59322123 GGTGTAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.51
45 22 0.47
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:59322300 original size:18 final size:17
Alignment explanation
Indices: 59322277--59322313 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
59322267 AATTATTATT
59322277 AAATATAT-A-TTAATTA
1 AAATATATAATTTAA-TA
59322293 AAATATATAATTTAATA
1 AAATATATAATTTAATA
59322310 AAAT
1 AAAT
59322314 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAATTTAATA
Found at i:59322307 original size:14 final size:15
Alignment explanation
Indices: 59322270--59322309 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
59322260 TTAACATAAT
59322270 TATT-ATTAAATATA
1 TATTAATTAAATATA
59322284 TATTAATTAAA-ATA
1 TATTAATTAAATATA
*
59322298 TA-TAATTTAATA
1 TATTAATTAAATA
59322310 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATTAAATATA
Found at i:59322411 original size:102 final size:102
Alignment explanation
Indices: 59322297--59322516 Score: 404
Period size: 102 Copynumber: 2.2 Consensus size: 102
59322287 TAATTAAAAT
*
59322297 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTATTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
* * *
59322362 AATACTATAAAATATAATTTAAAGTTATTATTATTAA
66 AATAATATAAAATATAATTTAAAATAATTATTATTAA
59322399 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
59322464 AATAATATAAAATATAATTTAAAATAATTATTATTAA
66 AATAATATAAAATATAATTTAAAATAATTATTATTAA
59322501 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
59322517 ATATATAATT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 114 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (102 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATAATATAAAATATAATTTAAAATAATTATTATTAA
Found at i:59322527 original size:120 final size:116
Alignment explanation
Indices: 59322399--59322703 Score: 531
Period size: 120 Copynumber: 2.6 Consensus size: 116
59322389 TTATTATTAA
59322399 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
59322464 AATAATATAAAATATAATTTAAAATAATTATTATTAAATATAATTTA-ATAAAAAT
66 AATAATACAAAATATAATTT--AA-AATTATTATTAAATATAA-TTAGAT-AAAAT
59322519 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
59322584 AATACTACAAAATATAATTTAAAATTATTATTAAATATAATTAGATAAAAT
66 AATAATACAAAATATAATTTAAAATTATTATTAAATATAATTAGATAAAAT
*
59322635 ATATAATTTAATAAAATTTTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
59322700 AATA
66 AATA
59322704 CTAAAATCAT
Statistics
Matches: 181, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
116 76 0.42
117 20 0.11
118 2 0.01
120 83 0.46
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (116 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATAATACAAAATATAATTTAAAATTATTATTAAATATAATTAGATAAAAT
Found at i:59322640 original size:17 final size:17
Alignment explanation
Indices: 59322618--59322651 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
59322608 TTATTATTAA
59322618 ATATAA-TTAGATAAAAT
1 ATATAATTTA-ATAAAAT
59322635 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
59322652 TTTTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:59322725 original size:23 final size:21
Alignment explanation
Indices: 59322681--59322721 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
59322671 TATATGAATT
59322681 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
59322702 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
59322722 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:59330151 original size:25 final size:25
Alignment explanation
Indices: 59330098--59330152 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
59330088 AACCCCAAAG
*
59330098 TTTTAATCATTTTTAATTTTAATCC
1 TTTTAATCATTTTTAATTTTAATCA
* *
59330123 TTTTATAT-ATTTTTAATTTTATTTA
1 TTTTA-ATCATTTTTAATTTTAATCA
59330148 TTTTA
1 TTTTA
59330153 GATACCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTAATCATTTTTAATTTTAATCA
Found at i:59330241 original size:5 final size:5
Alignment explanation
Indices: 59330217--59330322 Score: 58
Period size: 5 Copynumber: 21.0 Consensus size: 5
59330207 TATTTCCAAG
* * * *
59330217 TATA- TATAT TACTTT TATAT TATAT TA-ACA TATAT TATTT TATAT TTTAT
1 TATAT TATAT TA-TAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT
* * * * *
59330267 TAAAT GT-TAT ATATAT TATAT TATTT TATGT TTTAA TATA- TATAT ATATAT
1 TATAT -TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
59330318 TATAT
1 TATAT
59330323 ATTAGGATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
4 9 0.12
5 54 0.70
6 14 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:59330257 original size:25 final size:26
Alignment explanation
Indices: 59330220--59330269 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
59330210 TTCCAAGTAT
59330220 ATATATTACTTTTATATTATATTAAC
1 ATATATTACTTTTATATTATATTAAC
*
59330246 ATATATTA-TTTTATATTTTATTAA
1 ATATATTACTTTTATATTATATTAA
59330270 ATGTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATTACTTTTATATTATATTAAC
Found at i:59330323 original size:7 final size:7
Alignment explanation
Indices: 59330276--59330398 Score: 55
Period size: 7 Copynumber: 17.7 Consensus size: 7
59330266 TTAAATGTTA
59330276 TATATAT
1 TATATAT
59330283 TATATTAT
1 TATA-TAT
* *
59330291 TTTATGT
1 TATATAT
*
59330298 T-T-TAA
1 TATATAT
59330303 TATATAT
1 TATATAT
59330310 ATATATAT
1 -TATATAT
59330318 TATATAT
1 TATATAT
*
59330325 TAGGATAT
1 TA-TATAT
59330333 T-TCATAT
1 TAT-ATAT
59330340 T-T-TAT
1 TATATAT
59330345 TATATAT
1 TATATAT
59330352 TAT-TA-
1 TATATAT
59330357 TATATAAT
1 TATAT-AT
* *
59330365 TTTGAAATT
1 TAT-ATA-T
*
59330374 TATAAAT
1 TATATAT
59330381 TAT-TAT
1 TATATAT
*
59330387 TAAATAT
1 TATATAT
59330394 TATAT
1 TATAT
59330399 TTTTATTCAA
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
5 9 0.10
6 10 0.11
7 42 0.47
8 24 0.27
9 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:59330349 original size:10 final size:10
Alignment explanation
Indices: 59330246--59330361 Score: 55
Period size: 10 Copynumber: 11.6 Consensus size: 10
59330236 TTATATTAAC
59330246 ATATATTATT
1 ATATATTATT
*
59330256 TTATATT-TT
1 ATATATTATT
* *
59330265 AT-TAAATGTT
1 ATAT-ATTATT
59330275 ATATA-TATT
1 ATATATTATT
59330284 ATATTATT-TT
1 ATA-TATTATT
* * *
59330294 ATGTTTTAAT
1 ATATATTATT
59330304 ATATA-TATAT
1 ATATATTAT-T
59330314 ATATTATATATT
1 ATA-TAT-TATT
* *
59330326 AGGATATT-TC
1 A-TATATTATT
*
59330336 ATATTTTATT
1 ATATATTATT
59330346 ATATATTATT
1 ATATATTATT
59330356 ATATAT
1 ATATAT
59330362 AATTTTGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
8 1 0.01
9 20 0.26
10 43 0.55
11 5 0.06
12 5 0.06
13 4 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:59330489 original size:29 final size:29
Alignment explanation
Indices: 59330422--59330500 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
59330412 TTTAAACCTC
*
59330422 ATTTTATA-ATCTATATTATTACTTTATT
1 ATTTTATATATATATATTATTACTTTATT
* *
59330450 -CTTTATA-ATATATATTCTATTATTTTATT
1 ATTTTATATATATATA-T-TATTACTTTATT
*
59330479 ATTTTATATATATCTATTATTA
1 ATTTTATATATATATATTATTA
59330501 TGCATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.29
28 1 0.02
29 16 0.38
30 7 0.17
31 6 0.14
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTATATATATATATTATTACTTTATT
Found at i:59333947 original size:25 final size:23
Alignment explanation
Indices: 59333895--59333949 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
59333885 TATAAATAGT
59333895 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
59333918 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
59333943 AATAGTG
1 AATAGTG
59333950 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:59334069 original size:22 final size:22
Alignment explanation
Indices: 59334037--59334078 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59334027 TATAGTGCAA
*
59334037 AAAATACATACATAATATAATT
1 AAAATACATACATAAGATAATT
*
59334059 AAAATATATACATAAGATAA
1 AAAATACATACATAAGATAA
59334079 CATGTAGAAA
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:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATACATACATAAGATAATT
Found at i:59334540 original size:16 final size:16
Alignment explanation
Indices: 59334502--59334540 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
59334492 TCCAAAAAAA
*
59334502 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
59334518 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
59334534 AATAACT
1 AAAAACT
59334541 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:59334792 original size:30 final size:30
Alignment explanation
Indices: 59334702--59334800 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
59334692 TAGGTACAAG
59334702 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
59334732 AGGTAGTGAAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
59334762 TGTTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
59334792 TGGTGGTGG
1 TGGTGGTGG
59334801 CAAAGGCTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.18, C:0.06, G:0.47, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:59335690 original size:16 final size:16
Alignment explanation
Indices: 59335669--59335702 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
59335659 TTAATTTTTG
*
59335669 AAAAATATAAATTGAA
1 AAAAATAGAAATTGAA
59335685 AAAAATAGAAATTGAA
1 AAAAATAGAAATTGAA
59335701 AA
1 AA
59335703 TACCTTAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAATAGAAATTGAA
Found at i:59335744 original size:89 final size:89
Alignment explanation
Indices: 59335595--59335952 Score: 477
Period size: 89 Copynumber: 4.0 Consensus size: 89
59335585 ACTTAATTTG
** * * * * * *
59335595 AAAACAGATTTTGAAAATACTTC-GACATGTGCCCCGAGGCTCAACTCATCTCTCACAATATGAA
1 AAAACAGAAATTGAAAATACCTCAG-CATGT--CCTGAGGCTAAACTCACCTCTCGCAATATGAG
*
59335659 TTAATTTTTGAAAAATATAAATTGAAA
63 TTGATTTTTGAAAAATATAAATTGAAA
* * * *
59335686 AAAATAGAAATTGAAAATACCTTAGCGTGTCCTGAGGCTAAACTCACATCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
59335751 ATTTTTGAAAAATATAAATTGAAA
66 ATTTTTGAAAAATATAAATTGAAA
59335775 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
59335840 ATTTTTGAAAAATATAAATTGAAA
66 ATTTTTGAAAAATATAAATTGAAA
* * * * *
59335864 AAAACAGAACTTGAAAAGCACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTT
1 AAAACAGAAATTGAAAA-TACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTT
* * *
59335929 GA-TTTTGACAAACAGAAATTGAAA
65 GATTTTTGAAAAATATAAATTGAAA
59335953 TTACCTCAGC
Statistics
Matches: 240, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
89 172 0.72
90 45 0.19
91 22 0.09
92 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (89 bp):
AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAATATAAATTGAAA
Found at i:59336015 original size:73 final size:72
Alignment explanation
Indices: 59335865--59336310 Score: 644
Period size: 73 Copynumber: 6.1 Consensus size: 72
59335855 AAATTGAAAA
* ** * *
59335865 AAACAGAACTTGAAAAGCACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
1 AAACAGAAATTG-AAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
59335930 ATTTTGAC
65 TTTTTGAC
59335938 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGT
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGT
*
59336003 GTTTTGAA
66 -TTTTGAC
*
59336011 AAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
59336075 TTTTTGAC
65 TTTTTGAC
* * *
59336083 AAACAGAAATTGAAATTACATCAGCGTGACCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGT
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGT
59336148 GTTTTGAC
66 -TTTTGAC
* *
59336156 AAACAAAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
59336221 TTTTTGAC
65 TTTTTGAC
* * * **
59336229 AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
*
59336294 ATTTTGA-
65 TTTTTGAC
*
59336301 AAATAGAAAT
1 AAACAGAAAT
59336311 AAAAACATCA
Statistics
Matches: 341, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
72 123 0.36
73 217 0.64
74 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (72 bp):
AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGT
TTTTGAC
Found at i:59336146 original size:145 final size:146
Alignment explanation
Indices: 59335883--59336303 Score: 693
Period size: 145 Copynumber: 2.9 Consensus size: 146
59335873 CTTGAAAAGC
* *
59335883 ACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTGACAAACAGAAA
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
*
59335947 TTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
66 TTGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
*
59336012 AACATAAATTGAAATT
131 AACAAAAATTGAAATT
59336028 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGATTTTTGACAAACAGAAA
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
* * *
59336092 TTGAAATTACATCAGCGTGACCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGTGTTTTGACA
66 TTGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
59336157 AACAAAAATTGAAATT
131 AACAAAAATTGAAATT
*
59336173 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGACAAACAGAAA
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
* * * ** **
59336238 TTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAA
66 TTGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
59336303 A
131 A
59336304 TAGAAATAAA
Statistics
Matches: 257, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
144 12 0.05
145 161 0.63
146 84 0.33
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (146 bp):
ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
TTGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
AACAAAAATTGAAATT
Found at i:59336243 original size:218 final size:217
Alignment explanation
Indices: 59335886--59336310 Score: 665
Period size: 218 Copynumber: 2.0 Consensus size: 217
59335876 GAAAAGCACC
* * *
59335886 TCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTGACAAACAGAAATTGA
1 TCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGACAAACAAAAATTGA
*
59335951 AATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAAAACA
66 AATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGTGTTTTGAAAAACA
* * *
59336016 TAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGATTTTT
131 GAAATTGAAATTACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
59336080 GACAAACAGAAATTGAAATTACA
196 GA-AAACAGAAATTGAAATTACA
* * *
59336103 TCAGCGTGACCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGTGTTTTGACAAACAAAAATTG
1 TCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGACAAACAAAAATTG
*
59336168 AAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGAT-TTTTGACAAA
65 AAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTG-TGTTTTGAAAAA
* * **
59336232 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
129 CAGAAATTGAAATTACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATT
*
59336297 TTGAAAATAGAAAT
194 TTGAAAACAGAAAT
59336311 AAAAACATCA
Statistics
Matches: 189, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
217 40 0.21
218 130 0.69
219 19 0.10
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (217 bp):
TCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGACAAACAAAAATTGA
AATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGTGTTTTGAAAAACA
GAAATTGAAATTACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
GAAAACAGAAATTGAAATTACA
Found at i:59342569 original size:13 final size:13
Alignment explanation
Indices: 59342536--59342561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59342526 GAGGTGCATA
59342536 CTTCTCTTTCGTT
1 CTTCTCTTTCGTT
59342549 CTTCTCTTTCGTT
1 CTTCTCTTTCGTT
59342562 GGTTTCTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
CTTCTCTTTCGTT
Found at i:59348299 original size:25 final size:23
Alignment explanation
Indices: 59348247--59348301 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
59348237 TATAAATAGT
59348247 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
59348270 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
59348295 AATAGTG
1 AATAGTG
59348302 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:59348381 original size:26 final size:26
Alignment explanation
Indices: 59348352--59348407 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
59348342 ATATGTATGA
**
59348352 AATAGA-TATAAAAAAAATATGTACAT
1 AATAGAGTAT-AAAAAAATACATACAT
* *
59348378 AATATAGTGTAAAAAAATACATACAT
1 AATAGAGTATAAAAAAATACATACAT
59348404 AATA
1 AATA
59348408 TAATTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (26 bp):
AATAGAGTATAAAAAAATACATACAT
Found at i:59348382 original size:22 final size:22
Alignment explanation
Indices: 59348357--59348432 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
59348347 TATGAAATAG
*
59348357 ATATAAAAAAAATATGTACATA
1 ATATAAAAAAAATATATACATA
*
59348379 ATATAGTGTAAAAAAATACATACATA
1 ATATA----AAAAAAATATATACATA
**
59348405 ATATAATTAAAATATATACATA
1 ATATAAAAAAAATATATACATA
*
59348427 AGATAA
1 ATATAA
59348433 TATGTAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 24 0.55
26 20 0.45
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATAAAAAAAATATATACATA
Found at i:59348408 original size:26 final size:26
Alignment explanation
Indices: 59348362--59348464 Score: 86
Period size: 26 Copynumber: 3.9 Consensus size: 26
59348352 AATAGATATA
**
59348362 AAAAAAATATGTACATAATATAGTGT
1 AAAAAAATACATACATAATATAGTGT
*
59348388 AAAAAAATACATACATAATATAAT-T
1 AAAAAAATACATACATAATATAGTGT
* *
59348413 AAAATATATACATAAGATAATAT-GTAG-
1 AAAA-AAATACAT-ACATAATATAGT-GT
* *
59348440 AAAAAATATATATAAATAATATAGT
1 AAAAAA-ATACATACATAATATAGT
59348465 ATTAAAGATA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
25 5 0.08
26 38 0.61
27 19 0.31
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAAAAATACATACATAATATAGTGT
Found at i:59348435 original size:27 final size:27
Alignment explanation
Indices: 59348376--59348497 Score: 97
Period size: 26 Copynumber: 4.5 Consensus size: 27
59348366 AAATATGTAC
* * * *
59348376 ATAATATAGTGTAAAA-AAATACATAC
1 ATAATATAATATAAAATATATACATAA
59348402 ATAATATAAT-TAAAATATATACATAA
1 ATAATATAATATAAAATATATACATAA
* * * *
59348428 GATAATAT-GTAGAAAAAATATATATAA
1 -ATAATATAATATAAAATATATACATAA
*
59348455 ATAATATAGTATTAAAGATATATACATAAA
1 ATAATATAATA-TAAA-ATATATACAT-AA
*
59348485 ATAGTATAATATA
1 ATAATATAATATA
59348498 TATACGTAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
25 5 0.06
26 25 0.32
27 23 0.30
28 3 0.04
29 10 0.13
30 11 0.14
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (27 bp):
ATAATATAATATAAAATATATACATAA
Found at i:59348477 original size:29 final size:28
Alignment explanation
Indices: 59348376--59348484 Score: 104
Period size: 26 Copynumber: 4.0 Consensus size: 28
59348366 AAATATGTAC
* * *
59348376 ATAATATAGT-GTAAAA-AAATACATAC
1 ATAATATAGTATTAAAATATATACATAA
59348402 ATAATATA--ATTAAAATATATACATAA
1 ATAATATAGTATTAAAATATATACATAA
* * *
59348428 GATAATAT-GTA-GAAAAAATATATATAA
1 -ATAATATAGTATTAAAATATATACATAA
59348455 ATAATATAGTATTAAAGATATATACATAA
1 ATAATATAGTATTAAA-ATATATACATAA
59348484 A
1 A
59348485 ATAGTATAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
25 5 0.08
26 23 0.35
27 23 0.35
28 4 0.06
29 11 0.17
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
ATAATATAGTATTAAAATATATACATAA
Found at i:59348552 original size:28 final size:28
Alignment explanation
Indices: 59348520--59348574 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
59348510 AGAATTTAGA
*
59348520 ATATACCTAAT-ATATTAAAAGAATATAT
1 ATATACATAATAATATTAAAA-AATATAT
*
59348548 ATATATATAATAATATTAAAAAATATA
1 ATATACATAATAATATTAAAAAATATA
59348575 ATAATAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (28 bp):
ATATACATAATAATATTAAAAAATATAT
Found at i:59348586 original size:18 final size:18
Alignment explanation
Indices: 59348552--59348588 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59348542 ATATATATAT
**
59348552 ATATAATAATATTAAAAA
1 ATATAATAATAACAAAAA
59348570 ATATAATAATAACAAAAA
1 ATATAATAATAACAAAAA
59348588 A
1 A
59348589 AAGAGGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
ATATAATAATAACAAAAA
Found at i:59349106 original size:30 final size:30
Alignment explanation
Indices: 59349060--59349158 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
59349050 TAGGTACAAG
*
59349060 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * **
59349090 AGGTAGTGGAGCAAGTGTGGCTAGTAAAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
59349120 TGTTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
59349150 TGGTGGTGG
1 TGGTGGTGG
59349159 CAAAGGCTAG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.20, C:0.05, G:0.46, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:59350097 original size:17 final size:17
Alignment explanation
Indices: 59350070--59350113 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
59350060 AATTAAACAT
* * *
59350070 TAAATTAATATATGTTA
1 TAAAATAATATATATCA
*
59350087 TAATATAATATATATCA
1 TAAAATAATATATATCA
59350104 TAAAATAATA
1 TAAAATAATA
59350114 ATAAGCCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAATAATATATATCA
Found at i:59351248 original size:56 final size:56
Alignment explanation
Indices: 59351157--59351308 Score: 180
Period size: 56 Copynumber: 2.7 Consensus size: 56
59351147 GAATATGTGG
* * *
59351157 CATCTATATGTGACTT-TGATATATGTGTGCAAGTAAGACCACGTTTAATACGTTGA
1 CATCGATATGTGA-TTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
* * * * *
59351213 CATTGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCATGTTTCATACATTGG
1 CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
* * * *
59351269 CATCGATATGTGATTCTGATTTGTGTTTACGAGTAAGACC
1 CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
59351309 CTGTCTGGGA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
55 2 0.02
56 79 0.98
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (56 bp):
CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
Found at i:59358724 original size:12 final size:12
Alignment explanation
Indices: 59358656--59358725 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
59358646 TGCTTTAATA
59358656 TTAA-ATTAAA-
1 TTAATATTAAAT
*
59358666 TTAATATTTAAT
1 TTAATATTAAAT
59358678 TTAATATTAAAT
1 TTAATATTAAAT
*
59358690 CT--TATTAAAT
1 TTAATATTAAAT
59358700 TAATAAGATATTAAAT
1 T--T-A-ATATTAAAT
59358716 TTAATATTAA
1 TTAATATTAA
59358726 GATAATCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
10 12 0.25
11 5 0.10
12 20 0.42
13 1 0.02
14 1 0.02
16 9 0.19
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (12 bp):
TTAATATTAAAT
Found at i:59361826 original size:10 final size:10
Alignment explanation
Indices: 59361811--59361836 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
59361801 TTCGATCGAG
59361811 TCGAGTCGGA
1 TCGAGTCGGA
59361821 TCGAGTCGGA
1 TCGAGTCGGA
59361831 TCGAGT
1 TCGAGT
59361837 TAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (10 bp):
TCGAGTCGGA
Found at i:59362690 original size:31 final size:31
Alignment explanation
Indices: 59362637--59362697 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
59362627 TATGGATATT
* *
59362637 TTTTTATTTTAGTTACTTAACTATTCAAAAG
1 TTTTTATTTAAGTTACTTAACTATTAAAAAG
*
59362668 TTTTTATTTAATTTA-TTAAACTATTAAAAA
1 TTTTTATTTAAGTTACTT-AACTATTAAAAA
59362698 ATCAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTTTATTTAAGTTACTTAACTATTAAAAAG
Found at i:59364814 original size:33 final size:34
Alignment explanation
Indices: 59364772--59364837 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
59364762 GTATTATTTT
59364772 AATTACTTATTAT-ATTTTTTTAAGGTTAACTCA
1 AATTACTTATTATAATTTTTTTAAGGTTAACTCA
59364805 AATTACTTATTATAAATTTTTTTAAGGTTAACT
1 AATTACTTATTAT-AATTTTTTTAAGGTTAACT
59364838 TAACACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 13 0.42
35 18 0.58
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (34 bp):
AATTACTTATTATAATTTTTTTAAGGTTAACTCA
Found at i:59365323 original size:29 final size:30
Alignment explanation
Indices: 59365278--59365367 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
59365268 TTGTAAGTAT
*
59365278 TGTTCTAGGAAAAATAATTTTGACAAGATAG
1 TGTTCT-GAAAAAATAATTTTGACAAGATAG
* ***
59365309 -GTTCTGAAAAAATAAATTTGATGTGAT-G
1 TGTTCTGAAAAAATAATTTTGACAAGATAG
* *
59365337 TGTTTTGAAAAAAAATATTTTGACAAGATAG
1 TGTTCTGAAAAAATA-ATTTTGACAAGATAG
59365368 ATTTTTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.64
30 14 0.31
31 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (30 bp):
TGTTCTGAAAAAATAATTTTGACAAGATAG
Found at i:59365501 original size:59 final size:59
Alignment explanation
Indices: 59365408--59365611 Score: 336
Period size: 59 Copynumber: 3.4 Consensus size: 59
59365398 CATAGTCAAT
* **
59365408 AATATATTTGTACAAAAGTATTCAAAAGAACTTCTATTTTATTAAATGAGGCAATATTAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
* *
59365468 AATAATTTGTACAAAATTATTCAAAAGAACTTCTATTGTATTAAATGAAACAATATTAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
* *
59365527 AATAATTTGTACAAAAATATTTAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
59365586 AATAATTTGTACAAAAATATTCAAAA
1 AATAATTTGTACAAAAATATTCAAAA
59365612 ATAAAACAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 131 0.97
60 4 0.03
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
Found at i:59369348 original size:25 final size:27
Alignment explanation
Indices: 59369320--59369376 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
59369310 CTAATTATCA
59369320 CATAAG-GA-CCTCCACTTTAATATTT
1 CATAAGCGATCCTCCACTTTAATATTT
*
59369345 CAT-AGCTATTTCCTCCACTTTAATATTT
1 CATAAGCGA--TCCTCCACTTTAATATTT
59369373 CATA
1 CATA
59369377 GCTATTAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.08
25 4 0.15
28 20 0.77
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (27 bp):
CATAAGCGATCCTCCACTTTAATATTT
Found at i:59369359 original size:28 final size:28
Alignment explanation
Indices: 59369328--59369382 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
59369318 CACATAAGGA
59369328 CCTCCACTTTAATATTTCATAGCTATTT
1 CCTCCACTTTAATATTTCATAGCTATTT
59369356 CCTCCACTTTAATATTTCATAGCTATT
1 CCTCCACTTTAATATTTCATAGCTATT
59369383 AGACACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.45
Consensus pattern (28 bp):
CCTCCACTTTAATATTTCATAGCTATTT
Found at i:59374304 original size:28 final size:29
Alignment explanation
Indices: 59374240--59374304 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
59374230 TTCACATTTA
* *
59374240 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAATTTAACCCCTCAATTGACACT
* * *
59374269 TTTCTCAATTTAA-TCCTTAATTGACATT
1 TTTCTCAATTTAACCCCTCAATTGACACT
*
59374297 TTTGTCAA
1 TTTCTCAA
59374305 AAATCACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTCTCAATTTAACCCCTCAATTGACACT
Found at i:59384777 original size:28 final size:29
Alignment explanation
Indices: 59384712--59384777 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
59384702 ACAGCCCATA
* *
59384712 TTTTCACAATTTAACCTCTCAATTTACAC
1 TTTTCTCAATTTAACCTCTCAATTGACAC
*
59384741 TTTTCTCAATTTAATCCT-T-AATTGACAT
1 TTTTCTCAATTTAA-CCTCTCAATTGACAC
*
59384769 TTTTGTCAA
1 TTTTCTCAA
59384778 AAATCACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 15 0.47
29 14 0.44
30 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTTCTCAATTTAACCTCTCAATTGACAC
Found at i:59394658 original size:27 final size:27
Alignment explanation
Indices: 59394626--59394766 Score: 164
Period size: 27 Copynumber: 5.2 Consensus size: 27
59394616 AGGAAGCGTC
* *
59394626 CTGGTGGTTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
59394653 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
59394679 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* *
59394707 CTGGTGGCTCTGTCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
59394734 TTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
59394761 CTGGTG
1 CTGGTG
59394767 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
26 11 0.11
27 82 0.85
28 4 0.04
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:59394776 original size:54 final size:54
Alignment explanation
Indices: 59394623--59394784 Score: 231
Period size: 54 Copynumber: 3.0 Consensus size: 54
59394613 TGGAGGAAGC
* *
59394623 GTCCTGGTGGTTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
59394677 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
** * *
59394731 GTTTTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACT-TCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCT-GTCACATATATCT
59394784 G
1 G
59394785 GCAGCTTCGC
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
53 14 0.14
54 86 0.86
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
Found at i:59394777 original size:27 final size:27
Alignment explanation
Indices: 59394639--59394784 Score: 149
Period size: 27 Copynumber: 5.4 Consensus size: 27
59394629 GTGGTTATGC
*
59394639 CACAATTATCTG-ATCTGGTGGCTCTGC
1 CACAA-TATCTGTATCTGGTGGCTCTGT
* * *
59394666 CACATATATCTGT-CCTGGTGGCTATGC
1 CACA-ATATCTGTATCTGGTGGCTCTGT
59394693 CACAATTATCTG-ATCTGGTGGCTCTGT
1 CACAA-TATCTGTATCTGGTGGCTCTGT
* *
59394720 CACATATATCTGT-TTTGGTGGCTCTGC
1 CACA-ATATCTGTATCTGGTGGCTCTGT
*
59394747 CACAATATCTGTATCTGGTGACT-TCGT
1 CACAATATCTGTATCTGGTGGCTCT-GT
59394774 CACAATATCTG
1 CACAATATCTG
59394785 GCAGCTTCGC
Statistics
Matches: 101, Mismatches: 10, Indels: 16
0.80 0.08 0.13
Matches are distributed among these distances:
26 10 0.10
27 89 0.88
28 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
CACAATATCTGTATCTGGTGGCTCTGT
Found at i:59396750 original size:49 final size:49
Alignment explanation
Indices: 59396689--59396789 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
59396679 TTGTCAAAAG
* *
59396689 TCACTTTACAAATGTTGTTTATCTAACAACAAGCATACATTTTCTATTA
1 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
59396738 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
1 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
59396787 TCA
1 TCA
59396790 AACATCAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (49 bp):
TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
Found at i:59398384 original size:16 final size:17
Alignment explanation
Indices: 59398358--59398393 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
59398348 TATCCAATTA
59398358 TTTTGAATTTTTTGATG
1 TTTTGAATTTTTTGATG
*
59398375 TTTT-AATTTTTTGGTG
1 TTTTGAATTTTTTGATG
59398391 TTT
1 TTT
59398394 CTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (17 bp):
TTTTGAATTTTTTGATG
Found at i:59401180 original size:22 final size:22
Alignment explanation
Indices: 59401155--59401198 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59401145 TAGTCATATA
59401155 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
59401177 ATAATTTATTACTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
59401199 TAATTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:59401236 original size:13 final size:14
Alignment explanation
Indices: 59401218--59401259 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
59401208 TTTCAATTTT
59401218 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
59401231 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
59401246 ATTTTAAATAATAT
1 ATTTT-AATAATAT
59401260 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:59401244 original size:16 final size:16
Alignment explanation
Indices: 59401222--59401258 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
59401212 AATTTTATTT
59401222 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
59401239 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
59401254 TAATA
1 TAATA
59401259 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:59401311 original size:15 final size:15
Alignment explanation
Indices: 59401291--59401347 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
59401281 ATTCAATATT
59401291 AATATTTTAATAATA
1 AATATTTTAATAATA
*
59401306 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
59401325 AATATATTAATAATA
1 AATATTTTAATAATA
*
59401340 AATGTTTT
1 AATATTTT
59401348 GTATATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:59401723 original size:28 final size:28
Alignment explanation
Indices: 59401692--59401754 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
59401682 AATGTATGTT
**
59401692 TATTTAATTGAAAACAACTTTTATAAAA
1 TATTTAAGGGAAAACAACTTTTATAAAA
59401720 TATTTTTAAGGGAAAACAACTTTTATAAAA
1 TA--TTTAAGGGAAAACAACTTTTATAAAA
59401750 TATTT
1 TATTT
59401755 TTAAGAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
30 26 0.84
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (28 bp):
TATTTAAGGGAAAACAACTTTTATAAAA
Found at i:59401728 original size:30 final size:30
Alignment explanation
Indices: 59401701--59401759 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
59401691 TTATTTAATT
59401701 GAAAACAACTTTTATAAAATATTTTTAAGG
1 GAAAACAACTTTTATAAAATATTTTTAAGG
59401731 GAAAACAACTTTTATAAAATATTTTTAAG
1 GAAAACAACTTTTATAAAATATTTTTAAG
59401760 AAATCTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.37
Consensus pattern (30 bp):
GAAAACAACTTTTATAAAATATTTTTAAGG
Found at i:59401855 original size:14 final size:14
Alignment explanation
Indices: 59401836--59401874 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
59401826 CCAGAAAAGT
59401836 AAATCA-TTTTCTAA
1 AAATCATTTTTC-AA
59401850 AAATCATTTTTCAA
1 AAATCATTTTTCAA
59401864 AAATCATTTTT
1 AAATCATTTTT
59401875 AGTGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:59403734 original size:27 final size:27
Alignment explanation
Indices: 59403703--59403756 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
59403693 AACAGAAAGG
59403703 CTAAAACTAACTAATCATGAAGAAGTT
1 CTAAAACTAACTAATCATGAAGAAGTT
59403730 CTAAAACTAACTAATCATGAAGAAGTT
1 CTAAAACTAACTAATCATGAAGAAGTT
59403757 AAATATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
CTAAAACTAACTAATCATGAAGAAGTT
Found at i:59405187 original size:15 final size:15
Alignment explanation
Indices: 59405167--59405196 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59405157 AAAATTTGAT
*
59405167 TCGAGTTGAATTAAA
1 TCGAGTTAAATTAAA
59405182 TCGAGTTAAATTAAA
1 TCGAGTTAAATTAAA
59405197 ATAATTGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
TCGAGTTAAATTAAA
Found at i:59406025 original size:17 final size:17
Alignment explanation
Indices: 59405999--59406033 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59405989 CCTAATTGTA
59405999 AAAAACTAAAAATATAT
1 AAAAACTAAAAATATAT
* *
59406016 AAAAATTAAAATTATAT
1 AAAAACTAAAAATATAT
59406033 A
1 A
59406034 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAACTAAAAATATAT
Found at i:59406521 original size:16 final size:16
Alignment explanation
Indices: 59406500--59406534 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
59406490 TATTAGCAAT
59406500 AATCTCCAAAATAAAA
1 AATCTCCAAAATAAAA
59406516 AATCTCCAAAATAAAA
1 AATCTCCAAAATAAAA
59406532 AAT
1 AAT
59406535 GCTAAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (16 bp):
AATCTCCAAAATAAAA
Found at i:59409776 original size:20 final size:20
Alignment explanation
Indices: 59409751--59409794 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
59409741 AAGGACTAAA
* *
59409751 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
59409771 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
59409791 ATGA
1 ATGA
59409795 TTACATTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:59413472 original size:22 final size:22
Alignment explanation
Indices: 59413447--59413500 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
59413437 TATAAGTAAA
*
59413447 TATTATTTTATTATT-AAATTGT
1 TATTATATTA-TATTAAAATTGT
*
59413469 TATTATATTATATTAAAATTTT
1 TATTATATTATATTAAAATTGT
59413491 TATTATATTA
1 TATTATATTA
59413501 ATATAAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTATATTATATTAAAATTGT
Found at i:59413595 original size:13 final size:13
Alignment explanation
Indices: 59413577--59413601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59413567 AAAGAGTCAG
59413577 ATATTAATATATA
1 ATATTAATATATA
59413590 ATATTAATATAT
1 ATATTAATATAT
59413602 GGAAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTAATATATA
Found at i:59413800 original size:15 final size:13
Alignment explanation
Indices: 59413753--59413792 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
59413743 AAATGGAATT
59413753 GAAACGAAAAGAGA
1 GAAAC-AAAAGAGA
59413767 GAAACAAAAGAGA
1 GAAACAAAAGAGA
59413780 GAAACAAAAGAGA
1 GAAACAAAAGAGA
59413793 AAGAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (13 bp):
GAAACAAAAGAGA
Found at i:59414792 original size:37 final size:38
Alignment explanation
Indices: 59414676--59414792 Score: 110
Period size: 37 Copynumber: 3.0 Consensus size: 38
59414666 TGTTCATGGA
* *
59414676 TACTTCGACCTTGAGTCGATGAGACACTAGGAGTCATACTGT
1 TACTTCG-GCTTGAGTCGATGAGACACTAGGTGTCA-AC--T
* * * * **
59414718 TACTTCGGATAGATTCGATGAGGCACTAGGTACCAACT
1 TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
*
59414756 TACTTCGGCTTG-GTCGATGAGACACTGGGTGTCAACT
1 TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
59414793 ATTGCTTCGA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
37 20 0.33
38 11 0.18
40 2 0.03
41 20 0.33
42 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (38 bp):
TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
Found at i:59416202 original size:25 final size:25
Alignment explanation
Indices: 59416173--59416224 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
59416163 ATGGTAAAAG
** *
59416173 GTTATTGCTTTTTGATTAACTTGAT
1 GTTATTGCCATTTGATGAACTTGAT
*
59416198 GTTATTGCCATTTGATGAATTTGAT
1 GTTATTGCCATTTGATGAACTTGAT
59416223 GT
1 GT
59416225 GATCTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (25 bp):
GTTATTGCCATTTGATGAACTTGAT
Found at i:59419954 original size:38 final size:38
Alignment explanation
Indices: 59419912--59419988 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
59419902 TTATCAAGGT
*
59419912 ATGAAAATAGGCCATAGATTTATCATGCTTGAAATTAG
1 ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
* *
59419950 ATGAAAATAGGCCATGGATTTATTATGCTCGAAATTAG
1 ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
59419988 A
1 A
59419989 AATTTATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (38 bp):
ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
Found at i:59430117 original size:15 final size:14
Alignment explanation
Indices: 59430093--59430123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
59430083 GGAGAAATTA
59430093 TTTTTAATATTATT
1 TTTTTAATATTATT
59430107 TTTTTATATATTATT
1 TTTTTA-ATATTATT
59430122 TT
1 TT
59430124 ATGTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTAATATTATT
Found at i:59431305 original size:48 final size:47
Alignment explanation
Indices: 59431253--59431640 Score: 292
Period size: 48 Copynumber: 7.9 Consensus size: 47
59431243 GTGTGCTAGT
*
59431253 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATT-ATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG--CGCATTGATGAGA
* *
59431301 GCTAGTGTAAGACCATGTTTGAGACATGGCATCG-GCATTGA-GACAAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTGATG---AGA
59431349 GCTAGTGTAAGACCATGTCTGGGACATGGCATCCAGACATGGCATTGGCATTGAGACTAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT-C-G-C---GCATT-G-A-T--G---AGA
* * * *
59431410 GCTAGTGTAAGACCATGTCTGTGACATGGCATCG-GCCTCGACATGTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTG--ATGAGA
* * * *
59431458 GCCAGTGTAAGACCATGTTTGGGACATGGCATTG-GCATTGAGATAAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATT--GATGAGA
** *
59431506 GCTAGTGTAAGACCATGTCTAGTTA-ATGGCATCG-GCATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCT-GGGACATGGCATCGCGCATT--GATGAGA
* *
59431554 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG-GCCTCGACATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTG--ATG-AGA
*
59431602 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG-GCATT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATT
59431641 TTACCCTATT
Statistics
Matches: 282, Mismatches: 33, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
45 5 0.02
46 2 0.01
47 2 0.01
48 213 0.76
49 4 0.01
50 2 0.01
51 1 0.00
53 2 0.01
54 5 0.02
55 5 0.02
56 1 0.00
57 1 0.00
59 1 0.00
60 1 0.00
61 37 0.13
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTGATGAGA
Found at i:59431417 original size:61 final size:61
Alignment explanation
Indices: 59431322--59431442 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
59431312 ACCATGTTTG
59431322 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
1 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
* * *
59431383 AGACATGGCATTGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATC
1 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
59431443 GGCCTCGACA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (61 bp):
AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
Found at i:59431561 original size:96 final size:95
Alignment explanation
Indices: 59431384--59431640 Score: 329
Period size: 96 Copynumber: 2.7 Consensus size: 95
59431374 ATGGCATCCA
* *
59431384 GACATGGCATTGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCCTC
1 GACATGGCATTGGCATTGAGA-TAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCATT
* * *
59431449 GACATGTGAGCCAGTGTAAGACCATGTTTGG
65 GACACGAGAGCCAGTGTAAGACCATGTCTGG
*
59431480 GACATGGCATTGGCATTGAGATAAGAGCTAGTGTAAGACCATGTCTAGTTA-ATGGCATCGGCAT
1 GACATGGCATTGGCATTGAGAT-AGAGCTAGTGTAAGACCATGTCT-GTGACATGGCATCGGCAT
* *
59431544 TGAGACGAGAGCTAGTGTAAGACCATGTCTGG
64 TGACACGAGAGCCAGTGTAAGACCATGTCTGG
* * * * * *
59431576 GACATGGCATCGGCCTCGACAT-GTAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 GACATGGCATTGGCATTGAGATAG--AGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCAT
59431640 T
64 T
59431641 TTACCCTATT
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
94 1 0.01
95 3 0.02
96 134 0.95
97 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
GACATGGCATTGGCATTGAGATAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCATTG
ACACGAGAGCCAGTGTAAGACCATGTCTGG
Found at i:59442673 original size:94 final size:93
Alignment explanation
Indices: 59442512--59442682 Score: 209
Period size: 94 Copynumber: 1.8 Consensus size: 93
59442502 ATACTGACGC
* ** * *
59442512 CATGTCCCAGACACGTCTTACACTGGCTTGTATATCGCGAGGGATTTGCATGTCCCAAACATGTC
1 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGGGA-TCGCATGTCCCAAACATATC
59442577 TTACACTAGCTCTCGTCTCAATGCTGATG
65 TTACACTAGCTCTCGTCTCAATGCTGATG
* * * *
59442606 CATGTCCCAGACAAGTCTTATACTGGCTTAAATATCTCGAGGCCGA-CGCATGTCCGAGACATAT
1 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGG--GATCGCATGTCCCAAACATAT
* *
59442670 CTTATACTGGCTC
64 CTTACACTAGCTC
59442683 CTATACTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
94 62 0.97
96 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGGGATCGCATGTCCCAAACATATCT
TACACTAGCTCTCGTCTCAATGCTGATG
Found at i:59442719 original size:46 final size:48
Alignment explanation
Indices: 59442558--59442719 Score: 127
Period size: 46 Copynumber: 3.5 Consensus size: 48
59442548 GCGAGGGATT
* * * * *
59442558 TGCATGTCCCAAACATGTCTTACACTAGCTC---TCGTCTCAATGCTGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAAT-ATCTCGATGCTGA
* * * *
59442604 TGCATGTCCCAGACAAGTCTTATACTGGCTTAAATATCTCGAGGCCGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
* * * ** *
59442652 CGCATGTCCGAGACATATCTTATACTGGCTCCTATA-CT-GTTGCTGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
* *
59442698 TGCATGTCCTAGCCATGTCTTA
1 TGCATGTCCCAGACATGTCTTA
59442720 CACTAGCACA
Statistics
Matches: 90, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
46 49 0.54
47 2 0.02
48 38 0.42
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (48 bp):
TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
Found at i:59448995 original size:21 final size:20
Alignment explanation
Indices: 59448966--59449004 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
59448956 TCCTGTAACA
59448966 GGGCACATGCCCGTGTGGAT
1 GGGCACATGCCCGTGTGGAT
59448986 GGGCAACATGCCCGTGTGG
1 GGGC-ACATGCCCGTGTGG
59449005 TCATTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (20 bp):
GGGCACATGCCCGTGTGGAT
Found at i:59450297 original size:48 final size:48
Alignment explanation
Indices: 59450240--59450408 Score: 191
Period size: 48 Copynumber: 3.6 Consensus size: 48
59450230 AAGCTGACGC
* **
59450240 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGG-TCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCT-GATG
* * *
59450288 CATGTCCCAGACATGTCTTATACTGGCTTAAATATCTCGAGGCTGACG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
* * * *** *
59450336 CATGTCCCAGACTTGTCTTACACTGGATCCCATA-CT-GTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
59450382 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
59450409 ACACACCTCA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 32 0.31
47 2 0.02
48 68 0.66
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
Found at i:59451929 original size:28 final size:27
Alignment explanation
Indices: 59451888--59451986 Score: 74
Period size: 28 Copynumber: 3.6 Consensus size: 27
59451878 AATGTGGCAG
* *
59451888 AAAAAGATAAAAAAAATTTAAATTAAT
1 AAAAATATTAAAAAAATTTAAATTAAT
* **
59451915 AAAAATTATT-AAAAAATATAGAAAAATAT
1 AAAAA-TATTAAAAAAATTTA-AATTA-AT
* * * *
59451944 AAAAATATTAAAAATATTAAAAATTTAG
1 AAAAATATTAAAAAAATT-TAAATTAAT
59451972 AAAAATATTAAAAAA
1 AAAAATATTAAAAAA
59451987 TAAAATATAT
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
27 14 0.26
28 24 0.44
29 15 0.28
30 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATATTAAAAAAATTTAAATTAAT
Found at i:59451929 original size:37 final size:37
Alignment explanation
Indices: 59451888--59452001 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 37
59451878 AATGTGGCAG
* *
59451888 AAAAAGATA-AAAAAAAT-TTAAATTAATAAAAATTATT
1 AAAAA-ATATAAAAAAATATAAAAATAATAAAAA-TATT
* *
59451925 AAAAAATATAGAAAAATATAAAAATATTAAAAATATT
1 AAAAAATATAAAAAAATATAAAAATAATAAAAATATT
* * *
59451962 -AAAAATTTAGAAAAATATTAAAA-AAT-AAAATATAT
1 AAAAAATATAAAAAAATATAAAAATAATAAAAATAT-T
59451997 AAAAA
1 AAAAA
59452002 TGTAGAAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.11
35 3 0.05
36 28 0.42
37 16 0.24
38 12 0.18
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (37 bp):
AAAAAATATAAAAAAATATAAAAATAATAAAAATATT
Found at i:59451939 original size:9 final size:8
Alignment explanation
Indices: 59451926--59452002 Score: 66
Period size: 9 Copynumber: 8.8 Consensus size: 8
59451916 AAAATTATTA
59451926 AAAAATAT
1 AAAAATAT
59451934 AGAAAAATAT
1 --AAAAATAT
59451944 AAAAATATT
1 AAAAATA-T
59451953 AAAAATATT
1 AAAAATA-T
*
59451962 AAAAATTTAG
1 AAAAA--TAT
59451972 AAAAATATT
1 AAAAATA-T
59451981 AAAAA-AT
1 AAAAATAT
59451988 AAAATATAT
1 AAAA-ATAT
59451997 AAAAAT
1 AAAAAT
59452003 GTAGAAAGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
7 5 0.08
8 13 0.22
9 26 0.44
10 13 0.22
11 2 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:59451973 original size:36 final size:35
Alignment explanation
Indices: 59451899--59452043 Score: 125
Period size: 37 Copynumber: 4.0 Consensus size: 35
59451889 AAAAGATAAA
*
59451899 AAAAAT-TTAAATTAATAAAAATTATTAAAAAATATAG
1 AAAAATATTAAA-AAATAAAAA-TATT-AAAAATATAG
*
59451936 AAAAATA-TAAAAATATTAAAAATATTAAAAATTTAG
1 AAAAATATTAAAAA-A-TAAAAATATTAAAAATATAG
*
59451972 AAAAATATTAAAAAAT-AAAATATATAAAAATGTAG
1 AAAAATATTAAAAAATAAAAATAT-TAAAAATATAG
** * *
59452007 AAAGTTCATTAACAATATAAAAAAATTTAAAAATATA
1 AAAAAT-ATTAA-AAAATAAAAATA-TTAAAAATATA
59452044 AATTTATACG
Statistics
Matches: 91, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
34 7 0.08
35 15 0.16
36 23 0.25
37 25 0.27
38 20 0.22
39 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (35 bp):
AAAAATATTAAAAAATAAAAATATTAAAAATATAG
Found at i:59451975 original size:10 final size:10
Alignment explanation
Indices: 59451914--59451988 Score: 81
Period size: 10 Copynumber: 7.9 Consensus size: 10
59451904 TTTAAATTAA
*
59451914 TAAAAATTAT
1 TAAAAAATAT
59451924 TAAAAAATA-
1 TAAAAAATAT
59451933 TAGAAAAATA-
1 TA-AAAAATAT
59451943 T-AAAAATAT
1 TAAAAAATAT
59451952 T-AAAAATAT
1 TAAAAAATAT
59451961 T-AAAAAT-T
1 TAAAAAATAT
59451969 TAGAAAAATAT
1 TA-AAAAATAT
59451980 TAAAAAATA
1 TAAAAAATA
59451989 AAATATATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
8 9 0.15
9 18 0.31
10 29 0.49
11 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:59452001 original size:10 final size:10
Alignment explanation
Indices: 59451913--59452002 Score: 74
Period size: 10 Copynumber: 9.8 Consensus size: 10
59451903 ATTTAAATTA
59451913 ATAAAAAT-T
1 ATAAAAATAT
59451922 ATTAAAAA-AT
1 A-TAAAAATAT
59451932 ATAGAAAA-AT
1 ATA-AAAATAT
59451942 ATAAAAATAT
1 ATAAAAATAT
59451952 -TAAAAATAT
1 ATAAAAATAT
*
59451961 -TAAAAATTT
1 ATAAAAATAT
*
59451970 AGAAAAATAT
1 ATAAAAATAT
59451980 -T-AAAA-A-
1 ATAAAAATAT
59451986 AT-AAAATAT
1 ATAAAAATAT
59451995 ATAAAAAT
1 ATAAAAAT
59452003 GTAGAAAGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
7 6 0.09
8 5 0.07
9 26 0.38
10 31 0.46
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:59452044 original size:18 final size:18
Alignment explanation
Indices: 59451897--59452045 Score: 81
Period size: 18 Copynumber: 8.2 Consensus size: 18
59451887 GAAAAAGATA
59451897 AAAAAAATTTAAATTAATA-
1 AAAAAAATTTAAA--AATAT
** *
59451916 AAAATTATTAAAAAATAT
1 AAAAAAATTTAAAAATAT
* *
59451934 AGAAAAATATAAAAATAT
1 AAAAAAATTTAAAAATAT
* *
59451952 -TAAAAATATTAAAAATTT
1 AAAAAAAT-TTAAAAATAT
*
59451970 AGAAAAATATTAAAAA-AT
1 AAAAAAAT-TTAAAAATAT
* * *
59451988 -AAAATATATAAAAATGT
1 AAAAAAATTTAAAAATAT
* ** *
59452005 AGAAAGTTCATTAACAATAT
1 AAAAAAAT--TTAAAAATAT
59452025 AAAAAAATTTAAAAATAT
1 AAAAAAATTTAAAAATAT
59452043 AAA
1 AAA
59452046 TTTATACGAT
Statistics
Matches: 96, Mismatches: 27, Indels: 15
0.70 0.20 0.11
Matches are distributed among these distances:
16 6 0.06
17 16 0.17
18 38 0.40
19 24 0.25
20 12 0.12
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAAATTTAAAAATAT
Found at i:59452173 original size:11 final size:12
Alignment explanation
Indices: 59452150--59452181 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
59452140 ACATAGGGAA
59452150 ATATAAAAA-TT
1 ATATAAAAATTT
59452161 AT-TAAAAATTT
1 ATATAAAAATTT
59452172 ATATAAAAAT
1 ATATAAAAAT
59452182 ATAGAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.32
11 6 0.32
12 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAAAAATTT
Found at i:59452231 original size:10 final size:10
Alignment explanation
Indices: 59452218--59452250 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
59452208 TAAATTATGG
59452218 AAAATATTAAA
1 AAAAT-TTAAA
59452229 AAAATTTAAA
1 AAAATTTAAA
59452239 AAAATTTAAA
1 AAAATTTAAA
59452249 AA
1 AA
59452251 GTTATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:59452389 original size:19 final size:18
Alignment explanation
Indices: 59452329--59452388 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
59452319 TTTTTAGTAA
59452329 ATTTTT-ATAATTTTTAT
1 ATTTTTAATAATTTTTAT
*
59452346 ACTTTTAATAATTTATTAT
1 ATTTTTAATAATTT-TTAT
*
59452365 ATTTTTAATAACTTTTAT
1 ATTTTTAATAATTTTTAT
59452383 ATTTTT
1 ATTTTT
59452389 TTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.13
18 17 0.45
19 16 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTAATAATTTTTAT
Found at i:59452464 original size:9 final size:9
Alignment explanation
Indices: 59452328--59452388 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
59452318 GTTTTTAGTA
59452328 AATTTTTAT
1 AATTTTTAT
59452337 AATTTTTAT
1 AATTTTTAT
* *
59452346 ACTTTTAAT
1 AATTTTTAT
59452355 AATTTATTAT
1 AATTT-TTAT
59452365 -ATTTTTAAT
1 AATTTTT-AT
*
59452374 AACTTTTAT
1 AATTTTTAT
59452383 -ATTTTT
1 AATTTTT
59452389 TTTCTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
8 7 0.16
9 28 0.65
10 8 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:59456637 original size:3 final size:3
Alignment explanation
Indices: 59456629--59456657 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59456619 TTGAATTATG
59456629 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59456658 TGTAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59464857 original size:41 final size:41
Alignment explanation
Indices: 59464808--59464993 Score: 203
Period size: 41 Copynumber: 4.5 Consensus size: 41
59464798 AAATGTAAAC
** *
59464808 AGGGGCATGTATATGTTATTCAAGGGTACCGAAGTACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * * *
59464849 AGGTGCATGTATATGCAATTTAAGGGTACAAAAGTACAAAC
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * *
59464890 AGGGGCATGTATGTGCAATACAGGGGTACCAAAGTACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * * *
59464931 AGGGGCACGTATGTGCAATTTAAGGGTACTGAAA-TACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTAC-CAAAGTACAAAT
** *
59464972 AGGGGCACATATGTGCAATTCA
1 AGGGGCATGTATATGCAATTCA
59464994 GGCTATAATT
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
41 120 0.98
42 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (41 bp):
AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
Found at i:59464948 original size:82 final size:82
Alignment explanation
Indices: 59464804--59464995 Score: 251
Period size: 82 Copynumber: 2.3 Consensus size: 82
59464794 ATCGAAATGT
* ** * * * *
59464804 AAACAGGGGCATGTATATGTTATTCAAGGGTACCGAAGTACAAATAGGTGCATGTATATGCAATT
1 AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
59464869 TAAGGGTAC-AAAAGTAC
66 TAAGGGTACTAAAA-TAC
* *
59464886 AAACAGGGGCATGTATGTGCAATACAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATT
1 AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
*
59464951 TAAGGGTACTGAAATAC
66 TAAGGGTACTAAAATAC
* **
59464968 AAATAGGGGCACATATGTGCAATTCAGG
1 AAACAGGGGCATGTATGTGCAATTCAGG
59464996 CTATAATTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
82 92 0.97
83 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (82 bp):
AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
TAAGGGTACTAAAATAC
Found at i:59476211 original size:20 final size:20
Alignment explanation
Indices: 59476169--59476215 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
59476159 TAGAGACATA
* *
59476169 GGCGTGTCCCAAGCCATATG
1 GGCGTGTCCCAAGCCACACG
*
59476189 GGCGTGTCCCAAGCCGCACG
1 GGCGTGTCCCAAGCCACACG
59476209 GGCGTGT
1 GGCGTGT
59476216 GACCCCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (20 bp):
GGCGTGTCCCAAGCCACACG
Found at i:59479535 original size:12 final size:12
Alignment explanation
Indices: 59479518--59479547 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59479508 AATATTATAC
59479518 ATATATATGCAT
1 ATATATATGCAT
59479530 ATATATATGCAT
1 ATATATATGCAT
*
59479542 ACATAT
1 ATATAT
59479548 GTGTGATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (12 bp):
ATATATATGCAT
Found at i:59482681 original size:16 final size:16
Alignment explanation
Indices: 59482650--59482694 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
59482640 AAATATCGTA
59482650 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
59482664 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
59482680 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
59482695 CTTGATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:59482692 original size:17 final size:16
Alignment explanation
Indices: 59482648--59482694 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
59482638 ATAAATATCG
59482648 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
59482663 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
59482679 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
59482695 CTTGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:59492182 original size:47 final size:47
Alignment explanation
Indices: 59491968--59492229 Score: 172
Period size: 47 Copynumber: 5.6 Consensus size: 47
59491958 CACTTGTGTG
* *
59491968 AGCTAGTGTAAGA-CATGTCTGGGACATG-TATC-AGC-C-ACATTATGA
1 AGCTAGTGTAAGACCATGTCTGGGACATGCT-TCGA-CTCGAGATGAT-A
* * * * * *
59492013 GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGT-
1 -AGCTAGTGTAAGACCATGTCTGGGACAT-GCTTCGAC-TCGAGATGA-TA
* *
59492063 -GCTAGTGTAAGA-CATGTCTGGGACATGCATTAGCCTCGAGATG-TA
1 AGCTAGTGTAAGACCATGTCTGGGACATGC-TTCGACTCGAGATGATA
* * *
59492108 AGCTAGTGTAA-AACATGTATGGGACATGCTTCGGCTACGAGATGAT-
1 AGCTAGTGTAAGACCATGTCTGGGACATGCTTCGACT-CGAGATGATA
* * * * *
59492154 AG-TCAGAGTAAGACCATGTCTGGGACATGGCATCGAATTGAGAT-ATG
1 AGCT-AGTGTAAGACCATGTCTGGGACAT-GCTTCGACTCGAGATGATA
59492201 AGCTAGTGTAAGACCATGTCTGGGACATG
1 AGCTAGTGTAAGACCATGTCTGGGACATG
59492230 ACATCATCAC
Statistics
Matches: 171, Mismatches: 26, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
44 1 0.01
45 7 0.04
46 63 0.37
47 74 0.43
48 22 0.13
51 3 0.02
52 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGCTTCGACTCGAGATGATA
Found at i:59492220 original size:140 final size:140
Alignment explanation
Indices: 59491968--59492229 Score: 343
Period size: 140 Copynumber: 1.9 Consensus size: 140
59491958 CACTTGTGTG
* * * *
59491968 AGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTGTAAGACCATGT
1 AGCTAGTGTAAAACATGTATGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGT
* * *
59492033 CCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGCATTAGCC
66 CCGGGACATGGCATCGGAATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCC
59492098 TCGAGATGTA
131 TCGAGATGTA
* * * *
59492108 AGCTAGTGTAAAACATGTATGGGACATGCT-TCGGCTACGA-GATGATAGTCAGAGTAAGACCAT
1 AGCTAGTGTAAAACATGTATGGGACATG-TATCAGCCAC-ATGATGAGAGCCAGAGTAAGACCAT
* *
59492171 GTCTGGGACATGGCATC-GAATTGAGA-TATGAGCTAGTGTAAGACCATGTCTGGGACATG
64 GTCCGGGACATGGCATCGGAATTGAGACGA-GAGCTAGTGTAAGA-CATGTCTGGGACATG
59492230 ACATCATCAC
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
138 1 0.01
139 21 0.20
140 81 0.77
141 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (140 bp):
AGCTAGTGTAAAACATGTATGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGT
CCGGGACATGGCATCGGAATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCC
TCGAGATGTA
Found at i:59492984 original size:41 final size:41
Alignment explanation
Indices: 59492937--59493045 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 41
59492927 CACGGGTAGA
*
59492937 CACACGGGCATGTGTCTAGGCCGTGTGTGACACAC-AGCCAGG
1 CACACGGGC-TGTGTC-AGGCCGTGTGAGACACACGAGCCAGG
* * ** *
59492979 -TCACGGGC-GTGTCGAGGCCGTGAGAGGGACACGGGCCAGG
1 CACACGGGCTGTGTC-AGGCCGTGTGAGACACACGAGCCAGG
59493019 CACACGGGCGTGTGTCAGGCCGTGTGA
1 CACACGGGC-TGTGTCAGGCCGTGTGA
59493046 AAACCACTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 19 0.35
40 6 0.11
41 14 0.26
42 10 0.19
43 5 0.09
ACGTcount: A:0.18, C:0.27, G:0.40, T:0.15
Consensus pattern (41 bp):
CACACGGGCTGTGTCAGGCCGTGTGAGACACACGAGCCAGG
Found at i:59497824 original size:18 final size:18
Alignment explanation
Indices: 59497801--59497842 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
59497791 AGGTATTTTT
*
59497801 GAAAGTTTCTCTGCGGAG
1 GAAAGTTTCTCCGCGGAG
*
59497819 GAAAGTTTCTCCGTGGAG
1 GAAAGTTTCTCCGCGGAG
59497837 GAAAGT
1 GAAAGT
59497843 CCTCAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.26
Consensus pattern (18 bp):
GAAAGTTTCTCCGCGGAG
Found at i:59499484 original size:46 final size:47
Alignment explanation
Indices: 59499426--59499595 Score: 158
Period size: 46 Copynumber: 3.6 Consensus size: 47
59499416 TCACTTGTGT
*
59499426 GAGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATT-ATGA-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGA-GAC
* * *
59499472 GAGCCAGTGTAAGACCATGTCCGGGACATGGCATC-G--GCATTGAGAC
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATTGAGAC
* *
59499518 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-C-C-TCGAGAT
1 GA--GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGAC
*
59499564 GTATGCTAGTGTAATACATGTCTGGGACATGC
1 G-A-GCTAGTGTAAGACATGTCTGGGACATGC
59499596 TTCGGCTACG
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
45 6 0.06
46 55 0.52
47 30 0.28
48 15 0.14
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGAC
Found at i:59499608 original size:46 final size:45
Alignment explanation
Indices: 59499428--59499694 Score: 193
Period size: 47 Copynumber: 5.7 Consensus size: 45
59499418 ACTTGTGTGA
* * * *
59499428 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGA-T
* * * * * *
59499474 GCCAGTGTAAGACCATGTCCGGGACATGGCATCGGCATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGA-T
59499522 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGTAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATG-AT
* * *
59499568 GCTAGTGTAATACATGTCTGGGACATGCTTC-GGCTACGAGATGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGAT
* * *
59499613 AG-TCAGAGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGAT-AT
1 -GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGAT
* * *
59499659 GAGTCAGTGTAAGACCATGTTTAGGACATGGCATCA
1 G-CT-AGTGTAAGA-CATGTCTGGGACAT-GCATCA
59499695 AAACCTTTCC
Statistics
Matches: 182, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
45 7 0.04
46 71 0.39
47 75 0.41
48 28 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGAT
Found at i:59499686 original size:140 final size:141
Alignment explanation
Indices: 59499428--59499694 Score: 339
Period size: 140 Copynumber: 1.9 Consensus size: 141
59499418 ACTTGTGTGA
* *
59499428 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
* *
59499493 CGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCC
66 CGGGACATGGCATCGACATTGAGACGAGTGCTAGTGTAAGACATGTCTAGGACATGGCATCAGCC
59499557 TCGAGATGTAT
131 TCGAGATGTAT
* * * * *
59499568 GCTAGTGTAATACATGTCTGGGACATGCT-TCGGCTACGA-GATGATAGTCAGAGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATG-TATCAGCCAC-ATGATGAGAGCCAGAGTAAGACCATG
* * *
59499631 TCTGGGACATGGCATCGAC-TTGAGATATGAGT-C-AGTGTAAGACCATGTTTAGGACATGGCAT
64 TCCGGGACATGGCATCGACATTGAG--ACGAGTGCTAGTGTAAGA-CATGTCTAGGACATGGCAT
59499693 CA
126 CA
59499695 AAACCTTTCC
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
139 14 0.13
140 82 0.75
141 13 0.12
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (141 bp):
GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
CGGGACATGGCATCGACATTGAGACGAGTGCTAGTGTAAGACATGTCTAGGACATGGCATCAGCC
TCGAGATGTAT
Found at i:59501742 original size:37 final size:37
Alignment explanation
Indices: 59501678--59501751 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
59501668 TTACAAGCCA
59501678 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
59501715 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
59501752 GACATCGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 4 0.12
37 28 0.85
38 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:59506500 original size:13 final size:13
Alignment explanation
Indices: 59506482--59506510 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
59506472 ATTCAATTAC
59506482 AACAACAATAATA
1 AACAACAATAATA
59506495 AACAACAATAATA
1 AACAACAATAATA
59506508 AAC
1 AAC
59506511 TCATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (13 bp):
AACAACAATAATA
Found at i:59507396 original size:15 final size:16
Alignment explanation
Indices: 59507373--59507413 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
59507363 TTCCTCTTTT
*
59507373 AATATAAAATAAA-AA
1 AATAAAAAATAAATAA
59507388 AATAAAAAATAAATAA
1 AATAAAAAATAAATAA
59507404 ATATAAAAAA
1 A-ATAAAAAA
59507414 AAACTCACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
16 3 0.13
17 8 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAAAAAATAAATAA
Found at i:59508866 original size:13 final size:14
Alignment explanation
Indices: 59508835--59508866 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
59508825 AGTGTATTTC
59508835 ATTT-ATTAAATGA
1 ATTTAATTAAATGA
59508848 ATTTAATTAAAT-A
1 ATTTAATTAAATGA
59508861 ATTTAA
1 ATTTAA
59508867 AGTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTTAATTAAATGA
Found at i:59509050 original size:23 final size:22
Alignment explanation
Indices: 59509000--59509050 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
59508990 TAGAATTTGA
59509000 ATTTTATATTTTTATTTTTAGG
1 ATTTTATATTTTTATTTTTAGG
*
59509022 AATTTAGT-TTTTCTATTGTTTA-G
1 ATTTTA-TATTTT-TATT-TTTAGG
59509045 ATTTTA
1 ATTTTA
59509051 AAATTCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 9 0.38
23 11 0.46
24 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (22 bp):
ATTTTATATTTTTATTTTTAGG
Found at i:59509614 original size:13 final size:13
Alignment explanation
Indices: 59509580--59509618 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
59509570 ATTAAATTAT
59509580 TAAAAAATAAAAA
1 TAAAAAATAAAAA
* * *
59509593 TATATAATAACAA
1 TAAAAAATAAAAA
59509606 TAAAAAATAAAAA
1 TAAAAAATAAAAA
59509619 AAACTTTTGC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAAATAAAAA
Done.