Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 130 of 438
Found at i:38606550 original size:57 final size:58
Alignment explanation
Indices: 38606421--38606542 Score: 174
Period size: 57 Copynumber: 2.1 Consensus size: 58
38606411 GTGACGAGAT
* * ** *
38606421 CGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCATGCTGGAAATATATGACACTAAGTGTGCAAGCTGGAAAAATA
* *
38606479 AGGCACTAAGTGTGCATGCTGGAAA-ATATGACACTATGTGTGCAAGCTGGAAAAATA
1 CGGCACTAAGTGTGCATGCTGGAAATATATGACACTAAGTGTGCAAGCTGGAAAAATA
38606536 CGGCACT
1 CGGCACT
38606543 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 33 0.59
58 23 0.41
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (58 bp):
CGGCACTAAGTGTGCATGCTGGAAATATATGACACTAAGTGTGCAAGCTGGAAAAATA
Found at i:38614432 original size:29 final size:29
Alignment explanation
Indices: 38614399--38614529 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
38614389 TGACGAGATC
*
38614399 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
38614428 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
38614457 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
38614486 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
38614515 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
38614530 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:38621041 original size:3 final size:3
Alignment explanation
Indices: 38621033--38621063 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38621023 TCTAATTAGT
38621033 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38621064 CTTATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38629292 original size:19 final size:21
Alignment explanation
Indices: 38629268--38629306 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
38629258 TTGGGTTTAG
38629268 GGACTAAAT-AAA-AAAATTT
1 GGACTAAATCAAATAAAATTT
38629287 GGACTAAATCAAATAAAATT
1 GGACTAAATCAAATAAAATT
38629307 CAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (21 bp):
GGACTAAATCAAATAAAATTT
Found at i:38634127 original size:21 final size:20
Alignment explanation
Indices: 38634086--38634127 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
38634076 TTTTAGTTTA
*
38634086 TTTTCCTTTTTAAATACTTT
1 TTTTCCTTTTTAAATAATTT
*
38634106 TTTTCCTTTTTGAATCAATTT
1 TTTTCCTTTTTAAAT-AATTT
38634127 T
1 T
38634128 GATTTAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTCCTTTTTAAATAATTT
Found at i:38634969 original size:23 final size:24
Alignment explanation
Indices: 38634939--38635009 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 24
38634929 ATCTAATATG
38634939 ATATTAATTTAATA-TAAATTATT
1 ATATTAATTTAATATTAAATTATT
*
38634962 ATATTAATTTAATCACTTGATAAATATT
1 ATATTAATTTAAT-A-TT-A-AATTATT
38634990 ATATTAATTTAATATTAAAT
1 ATATTAATTTAATATTAAAT
38635010 CTTATTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
23 13 0.32
24 3 0.07
25 1 0.02
26 3 0.07
27 2 0.05
28 19 0.46
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATTAATTTAATATTAAATTATT
Found at i:38635014 original size:23 final size:23
Alignment explanation
Indices: 38634917--38635027 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 23
38634907 AATCACTTTA
* *
38634917 ATATTAAATTTAAT-CT-AATATG
1 ATATT-AATTTAATATTAAATATT
38634939 ATATTAATTTAATA-TAAATTATT
1 ATATTAATTTAATATTAAA-TATT
38634962 ATATTAATTTAATCACTTGATAAATATT
1 ATATTAATTTAAT-A--T--TAAATATT
*
38634990 ATATTAATTTAATATTAAAT-CT
1 ATATTAATTTAATATTAAATATT
*
38635012 -TATTAAGTTAATATTA
1 ATATTAATTTAATATTA
38635028 TTTTTAGAAG
Statistics
Matches: 77, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
21 24 0.31
22 8 0.10
23 21 0.27
24 1 0.01
25 1 0.01
27 1 0.01
28 17 0.22
29 4 0.05
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (23 bp):
ATATTAATTTAATATTAAATATT
Found at i:38637973 original size:29 final size:29
Alignment explanation
Indices: 38637934--38638008 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
38637924 GGTTGAGAGA
* *
38637934 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
38637963 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
38637992 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
38638009 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:38645621 original size:29 final size:29
Alignment explanation
Indices: 38645582--38645656 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
38645572 GGTTGAGAGA
* *
38645582 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
38645611 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
38645640 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
38645657 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:38647319 original size:15 final size:15
Alignment explanation
Indices: 38647299--38647330 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
38647289 TATGCATGCA
38647299 AAATATAAAAGACAT
1 AAATATAAAAGACAT
38647314 AAATATAAAAGACAT
1 AAATATAAAAGACAT
38647329 AA
1 AA
38647331 TAGTGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:38653005 original size:6 final size:6
Alignment explanation
Indices: 38652988--38653036 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
38652978 TCTGTTTCTA
* * * *
38652988 GAATTT GAATCT GGATCT GAATTT GAATCT GAATCT GAATCT GTATCT
1 GAATCT GAATCT GAATCT GAATCT GAATCT GAATCT GAATCT GAATCT
38653036 G
1 G
38653037 CTTCTAACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (6 bp):
GAATCT
Found at i:38653036 original size:18 final size:18
Alignment explanation
Indices: 38652988--38653027 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
38652978 TCTGTTTCTA
*
38652988 GAATTTGAATCTGGATCT
1 GAATTTGAATCTGAATCT
38653006 GAATTTGAATCTGAATCT
1 GAATTTGAATCTGAATCT
38653024 GAAT
1 GAAT
38653028 CTGTATCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (18 bp):
GAATTTGAATCTGAATCT
Found at i:38659292 original size:40 final size:40
Alignment explanation
Indices: 38659237--38659434 Score: 319
Period size: 40 Copynumber: 5.0 Consensus size: 40
38659227 ATTTATTGAT
38659237 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
38659277 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
* *
38659317 ATTTGTGCTAGTGACTACATTCGGGCTAAGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
* *
38659357 ATTTGTGCTAGTGACTATATCGGGGCTAAGACCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
* *
38659397 ATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 ATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGG
38659435 TACTTGGGTT
Statistics
Matches: 147, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.10
40 131 0.89
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC
Found at i:38659366 original size:22 final size:22
Alignment explanation
Indices: 38659301--38659366 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
38659291 CTATATCCGG
38659301 GCTAAGTCCCGAAGGCATTTGT
1 GCTAAGTCCCGAAGGCATTTGT
*** * *
38659323 GCT-AGT---GACTACATTCGG
1 GCTAAGTCCCGAAGGCATTTGT
38659341 GCTAAGTCCCGAAGGCATTTGT
1 GCTAAGTCCCGAAGGCATTTGT
38659363 GCTA
1 GCTA
38659367 GTGACTATAT
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
18 10 0.33
19 3 0.10
21 3 0.10
22 14 0.47
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (22 bp):
GCTAAGTCCCGAAGGCATTTGT
Found at i:38663800 original size:47 final size:47
Alignment explanation
Indices: 38663746--38664174 Score: 678
Period size: 47 Copynumber: 9.1 Consensus size: 47
38663736 TTAGGATTTT
** *
38663746 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38663793 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
38663840 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
38663887 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38663934 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
38663981 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
38664028 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38664075 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
38664122 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
38664169 ATGTGA
1 ATGTGA
38664175 AATATATATA
Statistics
Matches: 349, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 349 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:38663848 original size:25 final size:25
Alignment explanation
Indices: 38663773--38663848 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
38663763 GTGTATATAT
38663773 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
38663798 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
38663820 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
38663845 GTGA
1 GTGA
38663849 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:38663897 original size:141 final size:141
Alignment explanation
Indices: 38663745--38664174 Score: 797
Period size: 141 Copynumber: 3.0 Consensus size: 141
38663735 TTTAGGATTT
** *
38663745 TATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
38663810 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
66 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
38663875 GCCGAATGGCC
131 GCCGAATGGCC
38663886 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
38663951 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
66 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
38664016 GCCGAATGGCC
131 GCCGAATGGCC
38664027 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
* *
38664092 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGGTAAA
66 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
*
38664157 GCCGAATGGTC
131 GCCGAATGGCC
*
38664168 AATGTGA
1 TATGTGA
38664175 AATATATATA
Statistics
Matches: 282, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 282 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (141 bp):
TATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGC
ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
GCCGAATGGCC
Found at i:38663989 original size:25 final size:25
Alignment explanation
Indices: 38663914--38663989 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
38663904 ATGCATATAT
38663914 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
38663939 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
38663961 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
38663986 GTGA
1 GTGA
38663990 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:38664130 original size:25 final size:25
Alignment explanation
Indices: 38664055--38664130 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
38664045 ATGCATATAT
38664055 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
38664080 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
38664102 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
38664127 GTGA
1 GTGA
38664131 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:38664523 original size:37 final size:37
Alignment explanation
Indices: 38664378--38664522 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
38664368 GGAAATATAT
*
38664378 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
38664415 TCCGGGTAAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
38664452 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
38664489 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
38664523 TCGTCTGAGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:38665869 original size:19 final size:20
Alignment explanation
Indices: 38665836--38665874 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
38665826 CGTGCTAGTG
38665836 ATATATCCGGGCTAAATCCC
1 ATATATCCGGGCTAAATCCC
38665856 ATATATCC-GGCTAAATCCC
1 ATATATCCGGGCTAAATCCC
38665875 GAAGAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (20 bp):
ATATATCCGGGCTAAATCCC
Found at i:38665889 original size:59 final size:59
Alignment explanation
Indices: 38665796--38665913 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
38665786 ATTGAGAGTG
38665796 ATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCC
1 ATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCT-AATCCC
38665856 ATATATCC-GGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATCCC
1 ATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATCCC
38665914 GAAGAGCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 6 0.10
59 44 0.76
60 8 0.14
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (59 bp):
ATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATCCC
Found at i:38666008 original size:40 final size:39
Alignment explanation
Indices: 38665856--38666040 Score: 257
Period size: 39 Copynumber: 4.7 Consensus size: 39
38665846 GCTAAATCCC
38665856 ATATATCCGGCTAAATCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGCTAAATCCCGAAGAGCATTCGTGCTAGTG
*
38665895 ATATATCCGGGCT-AATCCCGAAGAGCATTTGTGCTAGTG
1 ATATATCC-GGCTAAATCCCGAAGAGCATTCGTGCTAGTG
* *
38665934 ATGTATCCGGACTAAGT-CCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGG-CTAAATCCCGAAGAGCATTCGTGCTAGTG
*
38665973 ATATATCCAGGCTAAATCCTGAAGAGCATTCGTGCTAGTG
1 ATATATCC-GGCTAAATCCCGAAGAGCATTCGTGCTAGTG
* **
38666013 ATGTATCCGGGCTAGGTCCCGAAGAGCA
1 ATATATCC-GGCTAAATCCCGAAGAGCA
38666041 ATCATGCTGT
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.02
39 75 0.58
40 52 0.40
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
ATATATCCGGCTAAATCCCGAAGAGCATTCGTGCTAGTG
Found at i:38670102 original size:40 final size:40
Alignment explanation
Indices: 38669936--38670103 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
38669926 CATTTGAATG
* * *
38669936 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
38669976 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
38670016 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
38670056 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
38670096 GTATCCGG
1 ATATCCGG
38670104 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:38676072 original size:40 final size:40
Alignment explanation
Indices: 38676027--38676193 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
38676017 CGGAATACAA
38676027 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
38676067 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
38676107 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * * * *
38676147 CCGGATATAATTTCCAGCA-TAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
38676186 CCGGATAT
1 CCGGATAT
38676194 CATTCAATTG
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 25 0.23
40 82 0.77
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:38684150 original size:40 final size:40
Alignment explanation
Indices: 38684105--38684272 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
38684095 CGGAATACAA
38684105 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
38684145 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
38684185 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
38684225 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
38684265 CCGGATAT
1 CCGGATAT
38684273 CATTCAATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 102 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:38687568 original size:23 final size:23
Alignment explanation
Indices: 38687492--38687573 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
38687482 CCAAGCTGAT
*
38687492 AAACAATAAGCTCTATTGAGCTG
1 AAACAGTAAGCTCTATTGAGCTG
*
38687515 -AACAGTAAGCTCT-TTCAAGCT-
1 AAACAGTAAGCTCTATT-GAGCTG
* * *
38687536 ACATAGGTAAGCTCTAATGAGCTG
1 AAACA-GTAAGCTCTATTGAGCTG
38687560 AAACAGTAAGCTCT
1 AAACAGTAAGCTCT
38687574 TAGAAGCTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 2 0.04
22 18 0.39
23 22 0.48
24 4 0.09
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (23 bp):
AAACAGTAAGCTCTATTGAGCTG
Found at i:38687581 original size:23 final size:22
Alignment explanation
Indices: 38687492--38687584 Score: 66
Period size: 23 Copynumber: 4.1 Consensus size: 22
38687482 CCAAGCTGAT
* *
38687492 AAACAATAAGCTCTATTGAGCTG
1 AAACAGTAAGCTCT-TAGAGCTG
38687515 -AACAGTAAGCTCTTTCA-AGCT-
1 AAACAGTAAGCTC-TT-AGAGCTG
* * *
38687536 ACATAGGTAAGCTCTAATGAGCTG
1 AAACA-GTAAGCTCTTA-GAGCTG
38687560 AAACAGTAAGCTCTTAGAAGCTG
1 AAACAGTAAGCTCTTAG-AGCTG
38687583 AA
1 AA
38687585 TTAGTAAACT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
21 1 0.02
22 20 0.37
23 30 0.56
24 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (22 bp):
AAACAGTAAGCTCTTAGAGCTG
Found at i:38687602 original size:46 final size:45
Alignment explanation
Indices: 38687502--38687605 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 45
38687492 AAACAATAAG
* * *
38687502 CTCTATTGAGCTGAACAGTAAGCTCTTTCAAGCTACATAGGTAAG
1 CTCTAATGAGCTGAACAGTAAGCTCTTACAAGCTACATAGGTAAA
*
38687547 CTCTAATGAGCTGAAACAGTAAGCTCTTAGAAGCTGA-ATTA-GTAAA
1 CTCTAATGAGCTG-AACAGTAAGCTCTTACAAGCT-ACA-TAGGTAAA
38687593 CTCGT-ATGAGCTG
1 CTC-TAATGAGCTG
38687606 GGGTGAGTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
45 12 0.24
46 35 0.69
47 4 0.08
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
CTCTAATGAGCTGAACAGTAAGCTCTTACAAGCTACATAGGTAAA
Found at i:38687604 original size:23 final size:23
Alignment explanation
Indices: 38687552--38687605 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
38687542 GTAAGCTCTA
* *
38687552 ATGAGCTGAAACAGTAAGCTCTT
1 ATGAGCTGAAACAGTAAACTCGT
**
38687575 A-GAAGCTGAATTAGTAAACTCGT
1 ATG-AGCTGAAACAGTAAACTCGT
38687598 ATGAGCTG
1 ATGAGCTG
38687606 GGGTGAGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (23 bp):
ATGAGCTGAAACAGTAAACTCGT
Found at i:38697695 original size:28 final size:27
Alignment explanation
Indices: 38697598--38697711 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
38697588 AGCATGGCTG
* * *
38697598 CCAG-AACAGATATTGTGACAGAGTCA
1 CCAGAAACAGATATTGTGGCATAGCCA
* * *
38697624 CCAGATATAGATATTGTGGCAAAGCCA
1 CCAGAAACAGATATTGTGGCATAGCCA
*
38697651 CCAG-AACAGATATTTGTGGCGTAGCCA
1 CCAGAAACAGATA-TTGTGGCATAGCCA
38697678 CCAGAAACAGATATTTGTGGCATAGCCA
1 CCAGAAACAGATA-TTGTGGCATAGCCA
38697706 CCAGAA
1 CCAGAA
38697712 CTCTTCCTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
26 10 0.13
27 37 0.49
28 28 0.37
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGAAACAGATATTGTGGCATAGCCA
Found at i:38697711 original size:55 final size:53
Alignment explanation
Indices: 38697598--38697712 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 53
38697588 AGCATGGCTG
* * *
38697598 CCAGAACAGATATTGTGACAGAGTCACCAGATATAGATATTGTGGCAAAGCCA
1 CCAGAACAGATATTGTGACAGAGCCACCAGAAACAGATATTGTGGCAAAGCCA
* *
38697651 CCAGAACAGATATTTGTGGC-GTAGCCACCAGAAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGACAG-AGCCACCAGAAACAGATA-TTGTGGCAAAGCCA
38697706 CCAGAAC
1 CCAGAAC
38697713 TCTTCCTCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 13 0.24
54 21 0.39
55 20 0.37
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (53 bp):
CCAGAACAGATATTGTGACAGAGCCACCAGAAACAGATATTGTGGCAAAGCCA
Found at i:38698119 original size:8 final size:8
Alignment explanation
Indices: 38698108--38698134 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38698098 CTCTTCGGCA
38698108 TTTCGACT
1 TTTCGACT
38698116 TTTCGACT
1 TTTCGACT
38698124 TTTCGACT
1 TTTCGACT
38698132 TTT
1 TTT
38698135 GCCGATCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTCGACT
Found at i:38701945 original size:28 final size:28
Alignment explanation
Indices: 38701905--38701983 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
38701895 GCAATCAAAT
* * *
38701905 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
**
38701933 ATGGCACTTAGTGTGCGAGGTATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
38701961 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
38701984 CGAATGATTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:38708987 original size:40 final size:40
Alignment explanation
Indices: 38708923--38709072 Score: 169
Period size: 39 Copynumber: 3.8 Consensus size: 40
38708913 GCTACTCGTT
* * * ***
38708923 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
* *
38708963 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
* ***
38709003 CAATTGCCTTCGGG-CTTAGCCCGGATATCACAATTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
*
38709042 CAATTGCCTTCGGG-CTTAGCCCGGATATCAC
1 CAAATGCCTTCGGGACTTAGCCCGGATATCAC
38709073 TCGAACATTC
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 53 0.54
40 45 0.46
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
Found at i:38709043 original size:39 final size:39
Alignment explanation
Indices: 38708959--38709072 Score: 183
Period size: 39 Copynumber: 2.9 Consensus size: 39
38708949 TATGGTAACC
* *
38708959 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
*
38708999 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38709038 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38709073 TCGAACATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
39 53 0.76
40 17 0.24
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:38716441 original size:40 final size:39
Alignment explanation
Indices: 38716377--38716564 Score: 232
Period size: 39 Copynumber: 4.8 Consensus size: 39
38716367 GCTACTCGTT
* * * ** *
38716377 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
38716417 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
38716457 CAATTGCCTTCGGGCTTAGCCCGGATATCATAGCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
38716496 CAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
*
38716535 CAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCA
38716565 CTCGAACATT
Statistics
Matches: 133, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 88 0.66
40 45 0.34
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
Found at i:38716494 original size:39 final size:39
Alignment explanation
Indices: 38716413--38716565 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
38716403 TATGGTAACC
* *
38716413 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
38716453 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38716492 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
38716531 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38716566 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:38719566 original size:28 final size:28
Alignment explanation
Indices: 38719520--38719583 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
38719510 TATGGTAGAA
* *
38719520 CCACCAG-AATAGATATTTGTGGCGTAG
1 CCACCAGAAACAGATATTTGTGGCATAG
38719547 CCACCAGAAACAGATATTTGTGGCATAG
1 CCACCAGAAACAGATATTTGTGGCATAG
38719575 CCACCAGAA
1 CCACCAGAA
38719584 CTCTTCCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (28 bp):
CCACCAGAAACAGATATTTGTGGCATAG
Found at i:38729612 original size:22 final size:22
Alignment explanation
Indices: 38729570--38729612 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38729560 CAAGTTGATA
* *
38729570 AACAGTAAGCTCTATTGAGCTG
1 AACAATAAGCTCTATTAAGCTG
38729592 AACAATAAGCTCT-TTCAAGCT
1 AACAATAAGCTCTATT-AAGCT
38729613 AAATAGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (22 bp):
AACAATAAGCTCTATTAAGCTG
Found at i:38729667 original size:23 final size:23
Alignment explanation
Indices: 38729609--38729682 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
38729599 AGCTCTTTCA
*
38729609 AGCT-AAATAGGTAAGCTCCA-ATG
1 AGCTGAAATA-GTAAGCT-CATACG
* **
38729632 AGCTGAAATAGTAGGCTTTTACG
1 AGCTGAAATAGTAAGCTCATACG
38729655 AGCTG-AATCAGTAAGCTCATACG
1 AGCTGAAAT-AGTAAGCTCATACG
38729678 AGCTG
1 AGCTG
38729683 GGGTGAGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 3 0.07
23 33 0.80
24 5 0.12
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
AGCTGAAATAGTAAGCTCATACG
Found at i:38736541 original size:110 final size:110
Alignment explanation
Indices: 38736236--38736546 Score: 402
Period size: 108 Copynumber: 2.9 Consensus size: 110
38736226 TTTGTTTGTT
* * * * *
38736236 TTGGCCTTCTAATGGCCGGCAAC-AGTACAAAAAAAAATTC-AATTTTTTTGGTGCAGGCCTTAT
1 TTGGTCTTCTAATGGCCGGCACCAAGTAC-GAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGT
* *
38736299 AATGG-TCGGCACTAGAGTACCAGTATTTAAAAAAAAAATTTGGTAC
65 AATGGCT-GGCACTAGAGTACCAATATTTAAAAAAAAAAATTGGTAC
* *
38736345 -TGGTCTTCTAATGGCCGGCACCAAGTATG-AAAAAATTCAAATTTTTTTGGTGATGGCCTTGTA
1 TTGGTCTTCTAATGGCCGGCACCAAGTACGAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGTA
** * *
38736408 ATGGCCAGCAC-CGAACTACCAATATTTAAAAAAAAAAATTGGT-C
66 ATGGCTGGCACTAG-AGTACCAATATTTAAAAAAAAAAATTGGTAC
* *
38736452 TTGGTCTTCTAATGGCTGGCACCAAGTACGAAAAAAATTCAAATTTTTTTTTGTGCTGGCCTTGT
1 TTGGTCTTCTAATGGCCGGCACCAAGTACGAAAAAAATTCAAA-TTTTTTTGGTGCTGGCCTTGT
38736517 AATGGCTGGCACTAGAGTACCAATATTTAA
65 AATGGCTGGCACTAGAGTACCAATATTTAA
38736547 TTTTTTTTTA
Statistics
Matches: 173, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
107 11 0.06
108 102 0.59
109 16 0.09
110 43 0.25
111 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (110 bp):
TTGGTCTTCTAATGGCCGGCACCAAGTACGAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGTA
ATGGCTGGCACTAGAGTACCAATATTTAAAAAAAAAAATTGGTAC
Found at i:38742621 original size:6 final size:6
Alignment explanation
Indices: 38742607--38742649 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
38742597 TTCAACTTTT
* *
38742607 TTTTCA TTTTAA -TTTAA TTTTAA TTTTAA -TTTAA TTTCAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
38742650 CATTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:38742624 original size:5 final size:5
Alignment explanation
Indices: 38742614--38742666 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
38742604 TTTTTTTCAT
* * *
38742614 TTTAA TTTAA TTTTAA TTTTAA TTTAA TTTCAA TTTCA TTTCA TTTCA
1 TTTAA TTTAA -TTTAA -TTTAA TTTAA TTT-AA TTTAA TTTAA TTTAA
38742662 TTTAA
1 TTTAA
38742667 ATTATTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:38742626 original size:11 final size:11
Alignment explanation
Indices: 38742612--38742649 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
38742602 CTTTTTTTTC
38742612 ATTTTAATTTA
1 ATTTTAATTTA
38742623 ATTTTAATTTTA
1 ATTTTAA-TTTA
38742635 A-TTTAATTTCA
1 ATTTTAATTT-A
38742646 ATTT
1 ATTT
38742650 CATTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.12
11 14 0.58
12 7 0.29
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTTAATTTA
Found at i:38742632 original size:17 final size:17
Alignment explanation
Indices: 38742607--38742649 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
38742597 TTCAACTTTT
*
38742607 TTTTCATTTTAATTTAA
1 TTTTAATTTTAATTTAA
38742624 TTTTAATTTTAATTTAA
1 TTTTAATTTTAATTTAA
*
38742641 TTTCAATTT
1 TTTTAATTT
38742650 CATTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATTTTAATTTAA
Found at i:38742796 original size:18 final size:17
Alignment explanation
Indices: 38742773--38742843 Score: 81
Period size: 18 Copynumber: 4.1 Consensus size: 17
38742763 AATATAAAAT
* *
38742773 TTTTCATATTATTTTTTA
1 TTTTCAT-TTAATATTTA
38742791 TTTTCATTTAAATATTTA
1 TTTTCATTT-AATATTTA
*
38742809 TTTTCATTTTAGTATTTA
1 TTTTCA-TTTAATATTTA
38742827 TTTTCATTTAA-ATTTA
1 TTTTCATTTAATATTTA
38742843 T
1 T
38742844 AAAATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.13
17 6 0.13
18 32 0.68
19 3 0.06
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (17 bp):
TTTTCATTTAATATTTA
Found at i:38742863 original size:14 final size:14
Alignment explanation
Indices: 38742844--38742870 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38742834 TTAAATTTAT
38742844 AAAATTTTATATTC
1 AAAATTTTATATTC
38742858 AAAATTTTATATT
1 AAAATTTTATATT
38742871 TTATTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAATTTTATATTC
Found at i:38744828 original size:28 final size:28
Alignment explanation
Indices: 38744796--38744894 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
38744786 GCAATAAGCC
*
38744796 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
38744824 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
38744852 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
38744881 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38744895 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:38747936 original size:110 final size:107
Alignment explanation
Indices: 38747760--38748170 Score: 529
Period size: 108 Copynumber: 3.7 Consensus size: 107
38747750 AAAAAGTCCC
* * *
38747760 TGGTGCCGGCCATTAGAAAACCAGAACCAATTTTTTTTTAAATACTGGTACTCTGGTGTCGGCCA
1 TGGTGCCGGCCATTAGAAGACCAGGACCAATTTTTTTTTAAATACTGGTACTCTGGTGCCGGCCA
*
38747825 TTACAAGGCCAGCACTAAAAAAATTTGAATTTTTTTTCTTGCT
66 TTACAAGGCCAGCAC-AAAAAAATTTGAATTTTTTTTCTTACT
* *
38747868 TGGTGCCGGCCATTAGAAGACCAGGACCAAATTTCTTTTTTAAATATTGGTACTCTGGTGCCGAC
1 TGGTGCCGGCCATTAGAAGACCAGGACC-AATTT-TTTTTTAAATACTGGTACTCTGGTGCCGGC
*
38747933 CATTACAAGGCCAGCACAAAAAAAATTGAATTTTTTTT-TGTACT
64 CATTACAAGGCCAGCACAAAAAAATTTGAATTTTTTTTCT-TACT
** * * *
38747977 TGGTGCTAGCCATTAGTAGACCAGGACCAATTTTTTTTTTAAATACTAGTAGTCTGGTGCCGGCC
1 TGGTGCCGGCCATTAGAAGACCAGGACCAA-TTTTTTTTTAAATACTGGTACTCTGGTGCCGGCC
* *
38748042 ATTACAAGGCCAGCACAAAAAATTTTGAATTTTTTTTCGTACT
65 ATTACAAGGCCAGCACAAAAAAATTTGAATTTTTTTTCTTACT
* * *
38748085 TGGTGCCGGCCATTAGTAGACCAAGACCAAAAAAATATATTTTTTAAATACTGGTAGC-CTGGTG
1 TGGTGCCGGCCATTAGAAGACCAGGACC-----AAT-TTTTTTTTAAATACTGGTA-CTCTGGTG
* *
38748149 CAGGCCATTACAAGGCCGGCAC
59 CCGGCCATTACAAGGCCAGCAC
38748171 TAATTTTTTT
Statistics
Matches: 266, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
108 120 0.45
109 56 0.21
110 44 0.17
112 1 0.00
113 45 0.17
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (107 bp):
TGGTGCCGGCCATTAGAAGACCAGGACCAATTTTTTTTTAAATACTGGTACTCTGGTGCCGGCCA
TTACAAGGCCAGCACAAAAAAATTTGAATTTTTTTTCTTACT
Found at i:38748011 original size:217 final size:218
Alignment explanation
Indices: 38747768--38748170 Score: 587
Period size: 217 Copynumber: 1.8 Consensus size: 218
38747758 CCTGGTGCCG
* *
38747768 GCCATTAGAAAACCAGAACCAA-TTTTTTTTTAAATACTGGTACTCTGGTGTCGGCCATTACAAG
1 GCCATTAGAAAACCAGAACCAATTTTTTTTTTAAATACTAGTACTCTGGTGCCGGCCATTACAAG
* * *
38747832 GCCAGCACTAAAAAAATTTGAATTTTTTTTCTTGCTTGGTGCCGGCCATTAGAAGACCAGGACC-
66 GCCAGCAC-AAAAAAATTTGAATTTTTTTTCGTACTTGGTGCCGGCCATTAGAAGACCAAGACCA
* * * *
38747896 AAATTTCTTTTTTAAATATTGGTA-CTCTGGTGCCGACCATTACAAGGCCAGCACAAAAAAAATT
130 AAATATATTTTTTAAATACTGGTAGC-CTGGTGCAGACCATTACAAGGCCAGCACAAAAAAAATT
38747960 GAATTTTTTTTTGTACTTGGTGCTA
194 GAATTTTTTTTTGTACTTGGTGCTA
* * * *
38747985 GCCATTAGTAGACCAGGACCAATTTTTTTTTTAAATACTAGTAGTCTGGTGCCGGCCATTACAAG
1 GCCATTAGAAAACCAGAACCAATTTTTTTTTTAAATACTAGTACTCTGGTGCCGGCCATTACAAG
* *
38748050 GCCAGCACAAAAAATTTTGAATTTTTTTTCGTACTTGGTGCCGGCCATTAGTAGACCAAGACCAA
66 GCCAGCACAAAAAAATTTGAATTTTTTTTCGTACTTGGTGCCGGCCATTAGAAGACCAAGACC--
* *
38748115 AAAAATATATTTTTTAAATACTGGTAGCCTGGTGCAGGCCATTACAAGGCCGGCAC
129 -AAAATATATTTTTTAAATACTGGTAGCCTGGTGCAGACCATTACAAGGCCAGCAC
38748171 TAATTTTTTT
Statistics
Matches: 163, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
217 69 0.42
218 47 0.29
221 46 0.28
222 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (218 bp):
GCCATTAGAAAACCAGAACCAATTTTTTTTTTAAATACTAGTACTCTGGTGCCGGCCATTACAAG
GCCAGCACAAAAAAATTTGAATTTTTTTTCGTACTTGGTGCCGGCCATTAGAAGACCAAGACCAA
AATATATTTTTTAAATACTGGTAGCCTGGTGCAGACCATTACAAGGCCAGCACAAAAAAAATTGA
ATTTTTTTTTGTACTTGGTGCTA
Found at i:38748117 original size:54 final size:54
Alignment explanation
Indices: 38747807--38748117 Score: 137
Period size: 54 Copynumber: 5.7 Consensus size: 54
38747797 TTAAATACTG
* * * * *
38747807 GTACTCTGGTGTCGGCCATTACAAGGCC-AGCACTAAAAAAATTTGAATTTTTTTTC
1 GTACT-TGGTGCCGGCCATTAGAAGACCAAG-AC-CAAAAATTTTGAATTTTTTTTC
* * * *
38747863 TTGCTTGGTGCCGGCCATTAGAAGACCAGGACC--AAATTTCT---TTTTTAAATATTG
1 GTACTTGGTGCCGGCCATTAGAAGACCAAGACCAAAAATTT-TGAATTTTT---T-TTC
* * * * ** *
38747917 GTACTCTGGTGCCGACCATTACAAGGCC-AGCACAAAAAAAATTGAATTTTTTTTT
1 GTACT-TGGTGCCGGCCATTAGAAGACCAAG-ACCAAAAATTTTGAATTTTTTTTC
** * * *
38747972 GTACTTGGTGCTAGCCATTAGTAGACCAGGACC---AATTTT---TTTTTTAAATACTA
1 GTACTTGGTGCCGGCCATTAGAAGACCAAGACCAAAAATTTTGAATTTTTT---T--TC
* * * *
38748025 GTAGTCTGGTGCCGGCCATTACAAGGCC-AGCACAAAAAATTTTGAATTTTTTTTC
1 GTACT-TGGTGCCGGCCATTAGAAGACCAAG-ACCAAAAATTTTGAATTTTTTTTC
*
38748080 GTACTTGGTGCCGGCCATTAGTAGACCAAGACCAAAAA
1 GTACTTGGTGCCGGCCATTAGAAGACCAAGACCAAAAA
38748118 AATATATTTT
Statistics
Matches: 183, Mismatches: 44, Indels: 58
0.64 0.15 0.20
Matches are distributed among these distances:
48 6 0.03
50 5 0.03
51 5 0.03
52 5 0.03
53 8 0.04
54 69 0.38
55 57 0.31
56 6 0.03
57 11 0.06
59 5 0.03
60 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (54 bp):
GTACTTGGTGCCGGCCATTAGAAGACCAAGACCAAAAATTTTGAATTTTTTTTC
Found at i:38758716 original size:40 final size:40
Alignment explanation
Indices: 38758606--38758716 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 40
38758596 TAGCACTAAG
* *
38758606 GTGCTCCTGTTAGCATTACAATGCTCTTGATGACACATCC
1 GTGCTCCTGTTAGCATTACAGTGCTCTTGATCACACATCC
* * * * * *
38758646 GTGCTCTTGTTAGCACTATAGTGCTTTTGATCCCACATCT
1 GTGCTCCTGTTAGCATTACAGTGCTCTTGATCACACATCC
* * *
38758686 GTGCTCCTATTAGCATTACGGTACTCTTGAT
1 GTGCTCCTGTTAGCATTACAGTGCTCTTGAT
38758717 AGCATATTCA
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
GTGCTCCTGTTAGCATTACAGTGCTCTTGATCACACATCC
Found at i:38765799 original size:27 final size:26
Alignment explanation
Indices: 38765743--38765799 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
38765733 TAACCTTAAC
* * *
38765743 CCTAGGGGTATATTAGTAATTTTGCT
1 CCTAGGGGTAAATTAGTAATTTTCCA
38765769 CCTAGGGGTAAATCT-GTAAATTTTCCA
1 CCTAGGGGTAAAT-TAGT-AATTTTCCA
38765796 CCTA
1 CCTA
38765800 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (26 bp):
CCTAGGGGTAAATTAGTAATTTTCCA
Found at i:38769104 original size:30 final size:30
Alignment explanation
Indices: 38769068--38769128 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
38769058 GGGGATGGTC
38769068 ATTCTTTCGAGAATTTTTCGTCAAATCCTT
1 ATTCTTTCGAGAATTTTTCGTCAAATCCTT
38769098 ATTCTTTCGAGAATTTTTCGTCAAATCCTT
1 ATTCTTTCGAGAATTTTTCGTCAAATCCTT
38769128 A
1 A
38769129 GTCAGTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (30 bp):
ATTCTTTCGAGAATTTTTCGTCAAATCCTT
Found at i:38774239 original size:41 final size:41
Alignment explanation
Indices: 38774193--38774276 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
38774183 CACATGCGAC
*
38774193 CAATTATCCGGTACATGTAGTAGCCTGCACTTAGTACTACA
1 CAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
*
38774234 CAATTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACA
1 CAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
38774275 CA
1 CA
38774277 CGTGATCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
CAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
Found at i:38774326 original size:92 final size:90
Alignment explanation
Indices: 38774148--38774327 Score: 234
Period size: 90 Copynumber: 2.0 Consensus size: 90
38774138 TAGCCAAAGC
* * * **
38774148 TATCTGGTACGCATAGTAGCCTGCACATAGTACTGCACATGCGACCAATTATCCGGTACATGTAG
1 TATCTGGTACACATAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAG
38774213 TAGCCTGCACTTAGTACTACACAAT
66 TAGCCTGCACTTAGTACTACACAAT
* * * * * * *
38774238 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCAT
1 TATCTGGTACACATAGTAGCCTGCACATAGTACTACACACGCGA-C-CAATTATCCGGTACACAT
38774303 AGTAGCCTGCACTTAGTACTACACA
64 AGTAGCCTGCACTTAGTACTACACA
38774328 TGCGACCTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
90 38 0.50
91 1 0.01
92 37 0.49
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (90 bp):
TATCTGGTACACATAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAG
TAGCCTGCACTTAGTACTACACAAT
Found at i:38776142 original size:30 final size:30
Alignment explanation
Indices: 38776108--38776171 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
38776098 AAACATTTGG
38776108 CCAAATCAATTATGAAACATAACAAAATGA
1 CCAAATCAATTATGAAACATAACAAAATGA
38776138 CCAAATCAATTATGAAACATAACAAAATGA
1 CCAAATCAATTATGAAACATAACAAAATGA
38776168 CCAA
1 CCAA
38776172 GTCCTCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (30 bp):
CCAAATCAATTATGAAACATAACAAAATGA
Found at i:38778020 original size:42 final size:41
Alignment explanation
Indices: 38777974--38778138 Score: 181
Period size: 42 Copynumber: 3.9 Consensus size: 41
38777964 ACATTAGGGT
* * *
38777974 TATGAGTTTACGTGTAAGACCATAT-TCGGGATATGACATCGC
1 TATGAGATT-CGTGTAAGACCATATCT-GGGATATGGCATCGA
* *
38778016 TATGAGATTTCGTGTAAGACCATATCTGGGACATGGCATTGA
1 TATGAGA-TTCGTGTAAGACCATATCTGGGATATGGCATCGA
* *
38778058 TATGAGAATCGTGTAAGACCATAGT-TGGGCTATTGGCATCGA
1 TATGAGATTCGTGTAAGACCATA-TCTGGGATA-TGGCATCGA
* *
38778100 TATGAGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TATGAGAT-TCGTGTAAGACCATATCTGGGATATGGCAT
38778139 TGGAATGATT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
41 20 0.19
42 62 0.60
43 22 0.21
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (41 bp):
TATGAGATTCGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:38778098 original size:84 final size:83
Alignment explanation
Indices: 38777984--38778140 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 83
38777974 TATGAGTTTA
* ** *
38777984 CGTGTAAGACCATATTCGGGATATGACATCGCTATGAGATTTCGTGTAAGACCATATCTGGGACA
1 CGTGTAAGACCATATTCGGGATATGACATCGATATGAGATCCCATGTAAGACCATATCTGGGACA
38778049 TGGCATTGATATGAGAAT
66 TGGCATTGATATGAGAAT
* *
38778067 CGTGTAAGACCATAGTT-GGGCTATTGGCATCGATATGAGATCCCATGTAAGACCATATCTGGGA
1 CGTGTAAGACCATA-TTCGGGATA-TGACATCGATATGAGATCCCATGTAAGACCATATCTGGGA
*
38778131 TATGGCATTG
64 CATGGCATTG
38778141 GAATGATTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 19 0.29
84 46 0.71
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (83 bp):
CGTGTAAGACCATATTCGGGATATGACATCGATATGAGATCCCATGTAAGACCATATCTGGGACA
TGGCATTGATATGAGAAT
Found at i:38785346 original size:28 final size:28
Alignment explanation
Indices: 38785306--38785398 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
38785296 ATGTACTAGA
38785306 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
38785334 ATACCCCTATGTACGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* *
38785362 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
38785390 ATACCCCTA
1 ATACCCCTA
38785399 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:38785562 original size:27 final size:27
Alignment explanation
Indices: 38785505--38785593 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 27
38785495 GGAAGCGTCT
38785505 TGGTGGCTA-TGCCACAAATTATCTGTTC
1 TGGTGGC-ACTGCCACAAA-TATCTGTTC
* *
38785533 TGGTGGCCCTGCCACATATATCTGTTC
1 TGGTGGCACTGCCACAAATATCTGTTC
38785560 TGGTGGCACTGCCACAAAATATCTGTATC
1 TGGTGGCACTGCCAC-AAATATCTGT-TC
38785589 TGGTG
1 TGGTG
38785594 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.43
28 24 0.44
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (27 bp):
TGGTGGCACTGCCACAAATATCTGTTC
Found at i:38785612 original size:55 final size:56
Alignment explanation
Indices: 38785505--38785618 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 56
38785495 GGAAGCGTCT
* *
38785505 TGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-TC
1 TGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATC
* * *
38785560 TGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTATC
1 TGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTATC
38785616 TGG
1 TGG
38785619 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
TGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATC
Found at i:38786699 original size:11 final size:10
Alignment explanation
Indices: 38786671--38786704 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38786661 AGCCTGTAAG
38786671 TATTCTGAAT
1 TATTCTGAAT
*
38786681 TTTTCTGAAT
1 TATTCTGAAT
38786691 ATATTCTGAAT
1 -TATTCTGAAT
38786702 TAT
1 TAT
38786705 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:38792057 original size:8 final size:8
Alignment explanation
Indices: 38792044--38792091 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
38792034 CTAGATCGGC
*
38792044 AAAAGCTG
1 AAAAGCCG
38792052 AAAAGCCG
1 AAAAGCCG
38792060 AAATA-CCG
1 AAA-AGCCG
38792068 AAAAGCCG
1 AAAAGCCG
38792076 AAATA-CCG
1 AAA-AGCCG
38792084 AAAAGCCG
1 AAAAGCCG
38792092 GTATTTTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 2 0.06
8 31 0.89
9 2 0.06
ACGTcount: A:0.50, C:0.23, G:0.21, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:38792072 original size:16 final size:16
Alignment explanation
Indices: 38792051--38792091 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
38792041 GGCAAAAGCT
38792051 GAAAAGCCGAAATACC
1 GAAAAGCCGAAATACC
38792067 GAAAAGCCGAAATACC
1 GAAAAGCCGAAATACC
38792083 GAAAAGCCG
1 GAAAAGCCG
38792092 GTATTTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.22, T:0.05
Consensus pattern (16 bp):
GAAAAGCCGAAATACC
Found at i:38792378 original size:28 final size:28
Alignment explanation
Indices: 38792338--38792430 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
38792328 ATGTACTAGA
*
38792338 ATACCCCTATGTATGTAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* *
38792366 ATACCCCTTTGTACGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
** * *
38792394 ATACTTCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
38792422 ATACCCCTA
1 ATACCCCTA
38792431 GGGTTAATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:38792594 original size:27 final size:27
Alignment explanation
Indices: 38792536--38792625 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
38792526 AGGAAGCGTC
38792536 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
38792564 CTGGTGGCCCTGCCACATATATCTATT
1 CTGGTGGCACTGCCACAAATATCTGTT
38792591 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
38792620 CTGGTG
1 CTGGTG
38792626 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 24 0.45
29 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:38792644 original size:55 final size:56
Alignment explanation
Indices: 38792536--38792650 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
38792526 AGGAAGCGTC
* *
38792536 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTAT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTATAT
* * *
38792591 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTATAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTATAT
38792647 CTGG
1 CTGG
38792651 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTATAT
Found at i:38795448 original size:42 final size:40
Alignment explanation
Indices: 38795390--38795553 Score: 143
Period size: 42 Copynumber: 4.0 Consensus size: 40
38795380 ACATTAGGGT
* *
38795390 TATGAGTTTACGTGTAAAACCATATCTGGGATATGGCATCA
1 TATGAGATT-CGTGTAAGACCATATCTGGGATATGGCATCA
* * * *
38795431 TTATGAGATTTCGTGTAAGACCATGTCT-GGACATGGAATTGA
1 -TATGAGA-TTCGTGTAAGACCATATCTGGGATATGGCA-TCA
* * *
38795473 TATGAGAATCGTGTAAGACCATAGT-TGAGCTATTGGCATCGA
1 TATGAGATTCGTGTAAGACCATA-TCTGGGATA-TGGCATC-A
* *
38795515 TATGAGATCCTATGTAAGACCATATCTGGGATATGGCAT
1 TATGAGATTC-GTGTAAGACCATATCTGGGATATGGCAT
38795554 TGGAATGATT
Statistics
Matches: 96, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
40 15 0.16
41 19 0.20
42 43 0.45
43 19 0.20
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (40 bp):
TATGAGATTCGTGTAAGACCATATCTGGGATATGGCATCA
Found at i:38800827 original size:23 final size:23
Alignment explanation
Indices: 38800801--38800844 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
38800791 CGAAGGCGGA
38800801 TGTAAGCCTACGGGCTAGGCATT
1 TGTAAGCCTACGGGCTAGGCATT
38800824 TGTAAGCCTACGGGCTAGGCA
1 TGTAAGCCTACGGGCTAGGCA
38800845 CTTAGTGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (23 bp):
TGTAAGCCTACGGGCTAGGCATT
Found at i:38804234 original size:25 final size:25
Alignment explanation
Indices: 38804200--38804254 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
38804190 ATATTTTAAT
38804200 TAACCTTATTATCAAATTACAAAAC
1 TAACCTTATTATCAAATTACAAAAC
38804225 TAACCTTATTATCAAATTACAAAAC
1 TAACCTTATTATCAAATTACAAAAC
38804250 TAACC
1 TAACC
38804255 ATTTAAGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (25 bp):
TAACCTTATTATCAAATTACAAAAC
Found at i:38815167 original size:13 final size:13
Alignment explanation
Indices: 38815135--38815168 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
38815125 ATTTTGGGTG
*
38815135 AGAAATAAAGCTA
1 AGAAATGAAGCTA
38815148 AGAAATGAAGCTA
1 AGAAATGAAGCTA
38815161 AGAAATGA
1 AGAAATGA
38815169 CTTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (13 bp):
AGAAATGAAGCTA
Found at i:38816307 original size:12 final size:12
Alignment explanation
Indices: 38816290--38816354 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
38816280 CCACATGCCT
38816290 GTGTGCCAGGCC
1 GTGTGCCAGGCC
* *
38816302 GTGTGCTAGGCT
1 GTGTGCCAGGCC
* *
38816314 GTGTGCCGGGCT
1 GTGTGCCAGGCC
* *
38816326 GTGTGCTAGCCC
1 GTGTGCCAGGCC
*
38816338 GTGT-CTCAAGCC
1 GTGTGC-CAGGCC
38816350 GTGTG
1 GTGTG
38816355 GACCCAAATT
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
11 1 0.03
12 39 0.98
ACGTcount: A:0.08, C:0.26, G:0.40, T:0.26
Consensus pattern (12 bp):
GTGTGCCAGGCC
Found at i:38816320 original size:24 final size:24
Alignment explanation
Indices: 38816288--38816334 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38816278 CCCCACATGC
38816288 CTGTGTGCCAGGCCGTGTGCTAGG
1 CTGTGTGCCAGGCCGTGTGCTAGG
* *
38816312 CTGTGTGCCGGGCTGTGTGCTAG
1 CTGTGTGCCAGGCCGTGTGCTAG
38816335 CCCGTGTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.23, G:0.43, T:0.28
Consensus pattern (24 bp):
CTGTGTGCCAGGCCGTGTGCTAGG
Found at i:38816341 original size:24 final size:24
Alignment explanation
Indices: 38816290--38816354 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
38816280 CCACATGCCT
* *
38816290 GTGTGCCAGGCCGTGTGCTAGGCT
1 GTGTGCCAGGCCGTGTGCTAGCCC
* *
38816314 GTGTGCCGGGCTGTGTGCTAGCCC
1 GTGTGCCAGGCCGTGTGCTAGCCC
*
38816338 GTGT-CTCAAGCCGTGTG
1 GTGTGC-CAGGCCGTGTG
38816355 GACCCAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.08, C:0.26, G:0.40, T:0.26
Consensus pattern (24 bp):
GTGTGCCAGGCCGTGTGCTAGCCC
Found at i:38817192 original size:15 final size:15
Alignment explanation
Indices: 38817172--38817201 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38817162 TTTATCATTC
*
38817172 TTGCTTAGTGTTCTA
1 TTGCTTACTGTTCTA
38817187 TTGCTTACTGTTCTA
1 TTGCTTACTGTTCTA
38817202 CCTAGCCCAT
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:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (15 bp):
TTGCTTACTGTTCTA
Found at i:38819685 original size:17 final size:17
Alignment explanation
Indices: 38819663--38819697 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38819653 ACTGAGTATG
38819663 TTGAATTTGATAATATA
1 TTGAATTTGATAATATA
38819680 TTGAATTTGATAATATA
1 TTGAATTTGATAATATA
38819697 T
1 T
38819698 AGACCAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TTGAATTTGATAATATA
Found at i:38820070 original size:23 final size:23
Alignment explanation
Indices: 38820002--38820077 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
38819992 TGTTGCAAAC
*
38820002 TACCGTTTCA-TCTCTTATGAGCT
1 TACCGTTTCAGTC-CTTAGGAGCT
* *
38820025 TACC-ATTCAGAT-CTTCGGAGCT
1 TACCGTTTCAG-TCCTTAGGAGCT
*
38820047 TACCGTTTCAGTCCTTAGGGGCT
1 TACCGTTTCAGTCCTTAGGAGCT
38820070 TACCGTTT
1 TACCGTTT
38820078 TATCTCTACG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 17 0.40
23 25 0.58
24 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (23 bp):
TACCGTTTCAGTCCTTAGGAGCT
Found at i:38823558 original size:16 final size:16
Alignment explanation
Indices: 38823537--38823570 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38823527 CCTTTACATA
38823537 TATATTTTGATTCATT
1 TATATTTTGATTCATT
38823553 TATATTTTGATTCATT
1 TATATTTTGATTCATT
38823569 TA
1 TA
38823571 CATCAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TATATTTTGATTCATT
Found at i:38829015 original size:24 final size:24
Alignment explanation
Indices: 38828983--38829189 Score: 342
Period size: 24 Copynumber: 8.6 Consensus size: 24
38828973 TATCTCAAAT
*
38828983 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38829007 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38829031 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38829055 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
38829079 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38829103 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38829127 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38829151 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
*
38829175 GCTCTATGTGTGCGA
1 GCACTATGTGTGCGA
38829190 ACATAATAAG
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 177 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:38832913 original size:24 final size:24
Alignment explanation
Indices: 38832881--38833063 Score: 294
Period size: 24 Copynumber: 7.6 Consensus size: 24
38832871 TATCTCAAAT
*
38832881 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38832905 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38832929 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38832953 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38832977 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38833001 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38833025 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
*
38833049 GCTCTATGTGTGCGA
1 GCACTATGTGTGCGA
38833064 ACATAATAAG
Statistics
Matches: 153, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 153 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:38832957 original size:72 final size:72
Alignment explanation
Indices: 38832881--38833085 Score: 295
Period size: 72 Copynumber: 2.8 Consensus size: 72
38832871 TATCTCAAAT
* *
38832881 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
*
38832946 CACTATG
66 CACTATA
38832953 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
**
38833018 TGCTATA
66 CACTATA
* * * ** *
38833025 GCACTATGTGTGCGATTTGCTATAGCTCTATGTGTGCGAACATAATA-AGCACTATGTGTGC
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ATTTACTATAGCACTATGTGTGC
38833086 CACATTCGGT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
72 116 0.96
73 5 0.04
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (72 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
CACTATA
Found at i:38833076 original size:48 final size:48
Alignment explanation
Indices: 38832881--38833085 Score: 286
Period size: 48 Copynumber: 4.3 Consensus size: 48
38832871 TATCTCAAAT
* *
38832881 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
* *
38832929 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
* *
38832977 GCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
** * ** *
38833025 GCACTATGTGTGCGATTTGCTATAGCTCTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCG-ATTTACTATA
38833073 GCACTATGTGTGC
1 GCACTATGTGTGC
38833086 CACATTCGGT
Statistics
Matches: 146, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
48 142 0.97
49 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (48 bp):
GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
Found at i:38840625 original size:24 final size:24
Alignment explanation
Indices: 38840593--38840775 Score: 294
Period size: 24 Copynumber: 7.6 Consensus size: 24
38840583 TATCTCAAAT
*
38840593 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38840617 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38840641 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTTACTATG
38840665 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
38840689 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38840713 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
* *
38840737 GCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTTACTATG
*
38840761 GCTCTATGTGTGCGA
1 GCACTATGTGTGCGA
38840776 ACATAATAAG
Statistics
Matches: 153, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 153 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:38840669 original size:72 final size:72
Alignment explanation
Indices: 38840593--38840797 Score: 295
Period size: 72 Copynumber: 2.8 Consensus size: 72
38840583 TATCTCAAAT
* *
38840593 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
*
38840658 CACTATG
66 CACTATA
38840665 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
**
38840730 TGCTATA
66 CACTATA
* * * ** *
38840737 GCACTATGTGTGCGATTTGCTATAGCTCTATGTGTGCGAACATAATA-AGCACTATGTGTGC
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ATTTACTATAGCACTATGTGTGC
38840798 CACATTCGGT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
72 116 0.96
73 5 0.04
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (72 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATT
CACTATA
Found at i:38840788 original size:48 final size:48
Alignment explanation
Indices: 38840593--38840797 Score: 286
Period size: 48 Copynumber: 4.3 Consensus size: 48
38840583 TATCTCAAAT
* *
38840593 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
* *
38840641 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
* *
38840689 GCACTATGTGTGCGATTTACTATAGCACTATGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
** * ** *
38840737 GCACTATGTGTGCGATTTGCTATAGCTCTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCG-ATTTACTATA
38840785 GCACTATGTGTGC
1 GCACTATGTGTGC
38840798 CACATTCGGT
Statistics
Matches: 146, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
48 142 0.97
49 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (48 bp):
GCACTATGTGTGCGATTCACTATAGCACTATGTGTGCGATTTACTATA
Found at i:38845639 original size:20 final size:20
Alignment explanation
Indices: 38845611--38845661 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
38845601 CAGGGGTTAC
*
38845611 CGCCCGTGTGGTTTGGGACA
1 CGCCCGTGTGGATTGGGACA
*
38845631 CGCCTGTGTGGATTGGGACA
1 CGCCCGTGTGGATTGGGACA
*
38845651 CGCCCATGTGG
1 CGCCCGTGTGG
38845662 GCAGACCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.25, G:0.39, T:0.24
Consensus pattern (20 bp):
CGCCCGTGTGGATTGGGACA
Found at i:38854616 original size:20 final size:20
Alignment explanation
Indices: 38854573--38854616 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38854563 GCTGTTTTGT
38854573 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
38854593 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
38854612 TATGG
1 TATGG
38854617 CTAAGGCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:38856790 original size:49 final size:49
Alignment explanation
Indices: 38856735--38856949 Score: 367
Period size: 49 Copynumber: 4.4 Consensus size: 49
38856725 TTTTACATTA
*
38856735 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
38856784 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
*
38856833 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* * *
38856882 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
* *
38856931 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTCATCACA
38856950 CATATATGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 160 1.00
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.28
Consensus pattern (49 bp):
GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38859715 original size:40 final size:41
Alignment explanation
Indices: 38859671--38859769 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
38859661 TCGATTGTCC
* * **
38859671 TCGGGACATAGCCCGG-TTATAGTTA-TTCGCACAATTGCCT
1 TCGGGACATAGCCCGGATT-TAGTAACTTAGCACAAAAGCCT
38859711 TCGGGA-ATTAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
1 TCGGGACA-TAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
*
38859752 TCGGGACTTAGCCCGGAT
1 TCGGGACATAGCCCGGAT
38859770 ACCATTCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 19 0.38
41 30 0.60
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (41 bp):
TCGGGACATAGCCCGGATTTAGTAACTTAGCACAAAAGCCT
Found at i:38860288 original size:29 final size:29
Alignment explanation
Indices: 38860252--38860502 Score: 484
Period size: 29 Copynumber: 8.7 Consensus size: 29
38860242 TGTTGAAAAA
* *
38860252 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860281 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860310 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860339 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860368 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860397 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860426 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860455 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
38860484 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
38860503 AATCATTCGC
Statistics
Matches: 220, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 220 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:38862611 original size:37 final size:37
Alignment explanation
Indices: 38862558--38862648 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
38862548 TATAAAAGAA
38862558 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
38862595 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
38862632 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
38862649 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:38862799 original size:49 final size:49
Alignment explanation
Indices: 38862744--38862958 Score: 385
Period size: 49 Copynumber: 4.4 Consensus size: 49
38862734 TTTTACATTA
38862744 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
38862793 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
38862842 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
38862891 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
38862940 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
38862959 CATATATGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 160 1.00
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:38868661 original size:39 final size:39
Alignment explanation
Indices: 38868618--38868694 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
38868608 TTTATATGCT
38868618 TAAATTCCTTATTAAGTCTAGTTTTATATGAAACAGGTC
1 TAAATTCCTTATTAAGTCTAGTTTTATATGAAACAGGTC
* *
38868657 TAAATTCCTTATTGAGTTTAGTTTTATATGAAACAGGT
1 TAAATTCCTTATTAAGTCTAGTTTTATATGAAACAGGT
38868695 TTCATGGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (39 bp):
TAAATTCCTTATTAAGTCTAGTTTTATATGAAACAGGTC
Found at i:38875188 original size:46 final size:46
Alignment explanation
Indices: 38875136--38875311 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
38875126 TGGTTGAGCA
38875136 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * *
38875182 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
38875227 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
38875275 CCCGAGCTCGTTGATTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38875312 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 60 0.56
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:38875294 original size:93 final size:93
Alignment explanation
Indices: 38875133--38875304 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
38875123 GGATGGTTGA
* **
38875133 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
38875198 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
38875226 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATGCCCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
38875291 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
38875305 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38878610 original size:14 final size:13
Alignment explanation
Indices: 38878587--38878632 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
38878577 TAATTTAACC
38878587 ATTTTTTATTTTA
1 ATTTTTTATTTTA
38878600 ATTTTTCTATTTTA
1 ATTTTT-TATTTTA
*
38878614 A-TTTTTAATTT-
1 ATTTTTTATTTTA
38878625 ATTTTTTA
1 ATTTTTTA
38878633 CATTCTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.03
12 11 0.37
13 10 0.33
14 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTTATTTTA
Found at i:38881828 original size:42 final size:41
Alignment explanation
Indices: 38881748--38881897 Score: 153
Period size: 41 Copynumber: 3.6 Consensus size: 41
38881738 GAGCCTGGTC
38881748 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* *
38881789 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
38881831 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
* *
38881872 TCGAAGGGCTTTTGAGTCGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
38881898 GAGTTGGACT
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
39 4 0.04
40 9 0.10
41 36 0.40
42 28 0.31
43 12 0.13
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:38881880 original size:41 final size:40
Alignment explanation
Indices: 38881728--38881883 Score: 131
Period size: 41 Copynumber: 3.8 Consensus size: 40
38881718 GCTAATCGGG
* * *
38881728 GTCTAAATCCGAGCCTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTAGAGCCAGT
* *
38881769 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC--TTTAGAGCCAGT
* *
38881812 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTAGAGCCAGT
*
38881852 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTT
38881884 TGAGTCGGTG
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
39 3 0.03
40 15 0.16
41 40 0.43
42 19 0.20
43 12 0.13
44 1 0.01
45 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTAGAGCCAGT
Found at i:38891551 original size:10 final size:10
Alignment explanation
Indices: 38891538--38891577 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
38891528 TTCATGTTAT
38891538 TTTAAAAAAA
1 TTTAAAAAAA
38891548 TTTAAAAAAA
1 TTTAAAAAAA
* *
38891558 CTCAAAAAAA
1 TTTAAAAAAA
38891568 TTTTAAAAAA
1 -TTTAAAAAA
38891578 GGGTGTACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:38891921 original size:13 final size:15
Alignment explanation
Indices: 38891903--38891934 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
38891893 GGGTAATTCG
38891903 ACACGACC-TGT-GC
1 ACACGACCGTGTGGC
38891916 ACACGACCGTGTGGC
1 ACACGACCGTGTGGC
38891931 ACAC
1 ACAC
38891935 ATAACCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (15 bp):
ACACGACCGTGTGGC
Found at i:38892025 original size:6 final size:6
Alignment explanation
Indices: 38892014--38892101 Score: 58
Period size: 6 Copynumber: 14.0 Consensus size: 6
38892004 CCAAAGCCTC
38892014 ATTTTT ATTTTT ATTTATT -TTTTT ATTTTCT ATATTCATAT ATTTTT
1 ATTTTT ATTTTT ATTT-TT ATTTTT ATTTT-T AT-TT--T-T ATTTTT
* *
38892061 ATTTTT ATTTACTT -TATTT ATTTTT -TTATT -TTTTT ATTTTT
1 ATTTTT ATTT--TT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
38892102 TGGATTTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
5 12 0.18
6 37 0.55
7 8 0.12
8 4 0.06
9 2 0.03
10 4 0.06
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:38892040 original size:8 final size:8
Alignment explanation
Indices: 38892015--38892102 Score: 70
Period size: 8 Copynumber: 10.5 Consensus size: 8
38892005 CAAAGCCTCA
38892015 TTTTTATTT
1 TTTTTA-TT
38892024 TTATTTATT
1 TT-TTTATT
38892033 TTTTTATT
1 TTTTTATT
*
38892041 TTCTATATT
1 TT-TTTATT
** *
38892050 CATATATT
1 TTTTTATT
38892058 TTTATT-TT
1 TTT-TTATT
*
38892066 TATTTACTT
1 TTTTTA-TT
*
38892075 TATTTATT
1 TTTTTATT
38892083 TTTTTATT
1 TTTTTATT
38892091 TTTTTATT
1 TTTTTATT
38892099 TTTT
1 TTTT
38892103 GGATTTATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
7 2 0.03
8 40 0.61
9 20 0.30
10 4 0.06
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:38892058 original size:25 final size:26
Alignment explanation
Indices: 38892029--38892092 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
38892019 TATTTTTATT
*
38892029 TATTTTTTTATTTTCTATA-TTCATA
1 TATTTTTTTATTTTATATACTTCATA
* * * *
38892054 TATTTTTAT-TTTTATTTACTTTATT
1 TATTTTTTTATTTTATATACTTCATA
38892079 TATTTTTTTATTTT
1 TATTTTTTTATTTT
38892093 TTTATTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 20 0.65
26 4 0.13
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTTTTTTATTTTATATACTTCATA
Found at i:38892108 original size:29 final size:27
Alignment explanation
Indices: 38892017--38892122 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 27
38892007 AAGCCTCATT
38892017 TTTATTTTTATTTATTTTTTTATTTTCTATA
1 TTTA-TTTT-TTTATTTTTTTATTTT-T-TA
*
38892048 TTCATATATTTTTA--TTTTTATTTACTTTA
1 TT--TATTTTTTTATTTTTTTATTT--TTTA
38892077 TTTATTTTTTTATTTTTTTATTTTTTGGA
1 TTTATTTTTTTATTTTTTTATTTTTT--A
*
38892106 TTTATATCTTTTATTTT
1 TTTAT-TTTTTTATTTT
38892123 ATTTTATTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
27 12 0.19
29 28 0.44
30 11 0.17
31 7 0.11
32 3 0.05
33 2 0.03
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTATTTTTTTATTTTTTTATTTTTTA
Found at i:38893812 original size:10 final size:11
Alignment explanation
Indices: 38893786--38893823 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
38893776 GCATTTGGGA
38893786 GAAAAATGAGC
1 GAAAAATGAGC
* *
38893797 AAAAAATGAGT
1 GAAAAATGAGC
38893808 GAAAAATGAGC
1 GAAAAATGAGC
38893819 GAAAA
1 GAAAA
38893824 CTAGAGCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.61, C:0.05, G:0.24, T:0.11
Consensus pattern (11 bp):
GAAAAATGAGC
Found at i:38912986 original size:138 final size:138
Alignment explanation
Indices: 38912738--38913017 Score: 542
Period size: 138 Copynumber: 2.0 Consensus size: 138
38912728 ATGCTTCTTT
*
38912738 TGAACAAGGGGCTAATGTTGATGCCCTCATGAAAGATGGCAACAATGCGTTACACCTCACGGTTG
1 TGAACAAGGGGCTAATGTTGATGCCCTCACGAAAGATGGCAACAATGCGTTACACCTCACGGTTG
38912803 AGAATAGAAACGGAGTTTACACACATTTGTTATTAGCTAACAGTGTCGTTCTCGGTGTTCGAAAT
66 AGAATAGAAACGGAGTTTACACACATTTGTTATTAGCTAACAGTGTCGTTCTCGGTGTTCGAAAT
38912868 ACTCAAGA
131 ACTCAAGA
38912876 TGAACAAGGGGCTAATGTTGATGCCCTCACGAAAGATGGCAACAATGCGTTACACCTCACGGTTG
1 TGAACAAGGGGCTAATGTTGATGCCCTCACGAAAGATGGCAACAATGCGTTACACCTCACGGTTG
*
38912941 AGAATAGAAACGGAGTTTACACACATTTGTTATTAGCTAACAGTGTTGTTCTCGGTGTTCGAAAT
66 AGAATAGAAACGGAGTTTACACACATTTGTTATTAGCTAACAGTGTCGTTCTCGGTGTTCGAAAT
38913006 ACTCAAGA
131 ACTCAAGA
38913014 TGAA
1 TGAA
38913018 GATTTCTTAC
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (138 bp):
TGAACAAGGGGCTAATGTTGATGCCCTCACGAAAGATGGCAACAATGCGTTACACCTCACGGTTG
AGAATAGAAACGGAGTTTACACACATTTGTTATTAGCTAACAGTGTCGTTCTCGGTGTTCGAAAT
ACTCAAGA
Found at i:38920987 original size:27 final size:27
Alignment explanation
Indices: 38920957--38921051 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
38920947 CATCCTATTA
* *
38920957 GCCTTTATGGTGTACTCTAAAAGGAAT
1 GCCTTTGTGGCGTACTCTAAAAGGAAT
* * * *
38920984 GCCTTTGCGGCATATTCTGAAAGGAAT
1 GCCTTTGTGGCGTACTCTAAAAGGAAT
* * * *
38921011 GTCTTTGTAGTGTACTCTAAAAAGAAT
1 GCCTTTGTGGCGTACTCTAAAAGGAAT
38921038 GCCTTTGTGGCGTA
1 GCCTTTGTGGCGTA
38921052 TCCTAAATGG
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (27 bp):
GCCTTTGTGGCGTACTCTAAAAGGAAT
Found at i:38926201 original size:28 final size:28
Alignment explanation
Indices: 38926132--38926232 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
38926122 GACAAGATTG
* * * *
38926132 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
38926162 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
38926190 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
38926219 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38926233 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:38929518 original size:16 final size:16
Alignment explanation
Indices: 38929486--38929518 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38929476 TGATAGATCT
38929486 TTGACGAGCTTCGAAA
1 TTGACGAGCTTCGAAA
38929502 TTGATCGAGCTTC-AAA
1 TTGA-CGAGCTTCGAAA
38929518 T
1 T
38929519 AATCTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (16 bp):
TTGACGAGCTTCGAAA
Found at i:38933087 original size:54 final size:54
Alignment explanation
Indices: 38933005--38933113 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
38932995 AACGGGAGTT
*
38933005 AGAATCATACCATGCAAGGTAGAAGTAGAAATTGAATGCTCCCCCCTTTCAAAA
1 AGAATCATACCATGCAAGGTAGAAGTAGAAATTGAATGCTCCCACCTTTCAAAA
38933059 AGAATCATACCATGCAAGGTAGAAGTAGAAATTGAATGCTCCCACCTTTCAAAA
1 AGAATCATACCATGCAAGGTAGAAGTAGAAATTGAATGCTCCCACCTTTCAAAA
38933113 A
1 A
38933114 TGGTGAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (54 bp):
AGAATCATACCATGCAAGGTAGAAGTAGAAATTGAATGCTCCCACCTTTCAAAA
Found at i:38936304 original size:22 final size:22
Alignment explanation
Indices: 38936276--38936342 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
38936266 ACACACACAT
38936276 AGTCCATCATCTACTCAGGATA
1 AGTCCATCATCTACTCAGGATA
38936298 AGTCCATCATCTACTCAGGATA
1 AGTCCATCATCTACTCAGGATA
*
38936320 AGTCCATCATCTACTCAAGATA
1 AGTCCATCATCTACTCAGGATA
38936342 A
1 A
38936343 AGTTATGTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (22 bp):
AGTCCATCATCTACTCAGGATA
Found at i:38948038 original size:5 final size:5
Alignment explanation
Indices: 38948028--38948071 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
38948018 TTGCATACCC
* * *
38948028 ATCCA ATCCA ATCCA ATCCA ATGCA ATGCA ATGCA ATCCA ATCC
1 ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATCC
38948072 TCACGGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.39, C:0.34, G:0.07, T:0.20
Consensus pattern (5 bp):
ATCCA
Found at i:38952041 original size:37 final size:37
Alignment explanation
Indices: 38951985--38952063 Score: 133
Period size: 37 Copynumber: 2.1 Consensus size: 37
38951975 ATCTGTAAAA
38951985 TGAGAAAACTAAAAGGGGTGAGCTAAAAAGCTCAGTG
1 TGAGAAAACTAAAAGGGGTGAGCTAAAAAGCTCAGTG
*
38952022 TGAGAAAACT-AAAGAGGGTGAGCTAGAAAGCTCAGTG
1 TGAGAAAACTAAAAG-GGGTGAGCTAAAAAGCTCAGTG
38952059 TGAGA
1 TGAGA
38952064 TTATCCTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 4 0.10
37 36 0.90
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.16
Consensus pattern (37 bp):
TGAGAAAACTAAAAGGGGTGAGCTAAAAAGCTCAGTG
Found at i:38954587 original size:24 final size:24
Alignment explanation
Indices: 38954555--38954654 Score: 146
Period size: 24 Copynumber: 4.0 Consensus size: 24
38954545 TGACATTGTG
*
38954555 CTAAGTGAAATAAGACCATGGCAT
1 CTAAGTGAAATAAGTCCATGGCAT
38954579 CTAAGTGAAATAAGTCCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGC-A--T
*
38954606 GTTAAGTGAAATAAGTCCATGGCAT
1 -CTAAGTGAAATAAGTCCATGGCAT
38954631 CTAAGTGAAATAAGTCCATGGCAT
1 CTAAGTGAAATAAGTCCATGGCAT
38954655 TGTGTTAAGT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
24 44 0.64
25 2 0.03
27 2 0.03
28 21 0.30
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (24 bp):
CTAAGTGAAATAAGTCCATGGCAT
Found at i:38954620 original size:28 final size:27
Alignment explanation
Indices: 38954551--38954666 Score: 145
Period size: 24 Copynumber: 4.4 Consensus size: 27
38954541 GATATGACAT
*
38954551 TGTGCTAAGTGAAATAAGACCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGCA
38954578 --T-CTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAAGTCCATGGC-A
*
38954603 TGTGTTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGCA
38954630 --T-CTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGCA
*
38954654 TTGTGTTAAGTGA
1 -TGTGCTAAGTGA
38954667 GAAATTTCCC
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
24 43 0.56
25 3 0.04
27 3 0.04
28 28 0.36
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (27 bp):
TGTGCTAAGTGAAATAAGTCCATGGCA
Found at i:38954634 original size:52 final size:52
Alignment explanation
Indices: 38954551--38954666 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
38954541 GATATGACAT
*
38954551 TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAA
1 TGTGTTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAA
* *
38954603 TGTGTTAAGTGAAATAAGTCCATGGCATCTAAGTGAAATAAGTCCATGGCAT
1 TGTGTTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAA
38954655 TGTGTTAAGTGA
1 TGTGTTAAGTGA
38954667 GAAATTTCCC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (52 bp):
TGTGTTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAA
Found at i:38954920 original size:52 final size:52
Alignment explanation
Indices: 38954842--38954945 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
38954832 GTGTAAATGA
38954842 ATATGACTATGTGATGATTAAATGTGAAAGAATTATGAACCAATAATATTAT
1 ATATGACTATGTGATGATTAAATGTGAAAGAATTATGAACCAATAATATTAT
38954894 ATATGACTATGTGATGATTAAATGTGAAAGAATTATGAACCAATAATATTAT
1 ATATGACTATGTGATGATTAAATGTGAAAGAATTATGAACCAATAATATTAT
38954946 TTAATGTTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (52 bp):
ATATGACTATGTGATGATTAAATGTGAAAGAATTATGAACCAATAATATTAT
Found at i:38963036 original size:181 final size:180
Alignment explanation
Indices: 38962732--38963386 Score: 958
Period size: 180 Copynumber: 3.6 Consensus size: 180
38962722 CCCACAACTG
* *
38962732 CTTCAA-TCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC--GCAAACCTGC
1 CTTCAATTC-TCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-C-ATCTTTC-AACTTGC
* * * * *
38962794 TTTCTTGCTACCTCAGAGAGATAAGGC-TAGTGGCTTAAATCTACTCCATTGCTGATACATGGAG
62 TCTCTTGCTACCTCAGAGAAATAAGGCTTAGTGG-TAAAATCTGCTCCATTGCCGATACATGGAG
* * * * *
38962858 ATAAGATTCACCATCTGCGAAGATCTACTCCACTGCAATCTTAGAAAGATAAAAT
126 ATAAGAGTCACCATCTGCGAAGATTTGCTCTACTGCAATCTTAGAGAGATAAAAT
38962913 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCCATCTTTCAACTTGCTCT
1 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-CATCTTTCAACTTGCTCT
* * *
38962978 TTTTCTACCTCAGAGAAATAAGGCTTGGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAA
65 CTTGCTACCTCAGAGAAATAAGGCTTAGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAA
* * * *
38963043 GAGTCACCATTTGCGAAGATTTGCTCTGCTGCAATCTCAGTGAGATAAAAT
130 GAGTCACCATCTGCGAAGATTTGCTCTACTGCAATCTTAGAGAGATAAAAT
38963094 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATCTTTCAACTTGCTCTC
1 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATCTTTCAACTTGCTCTC
* * * * *
38963159 TTACTACCTTAGAGAAATAAGGCTTGGTGCTAAAATATGCTCCATTGCCGATACATGGAGATAAG
66 TTGCTACCTCAGAGAAATAAGGCTTAGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAG
* *
38963224 AGTCACCATCTACGAAGATTTGCTCTACTGCAATCTTAGGGAGATAAAAT
131 AGTCACCATCTGCGAAGATTTGCTCTACTGCAATCTTAGAGAGATAAAAT
*
38963274 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTTTTCAACTTGCTCTC
1 CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATCTTTCAACTTGCTCTC
* * *
38963339 TTGCTACCTCAGAGAGATAAGGCTTAGTGGTAAGATCTGCTCCGTTGC
66 TTGCTACCTCAGAGAAATAAGGCTTAGTGGTAAAATCTGCTCCATTGC
38963387 AACTTTAGGG
Statistics
Matches: 431, Mismatches: 39, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
180 231 0.54
181 192 0.45
182 8 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (180 bp):
CTTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATCTTTCAACTTGCTCTC
TTGCTACCTCAGAGAAATAAGGCTTAGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAG
AGTCACCATCTGCGAAGATTTGCTCTACTGCAATCTTAGAGAGATAAAAT
Done.