Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 85 of 145
Found at i:28342639 original size:21 final size:21
Alignment explanation
Indices: 28342615--28342666 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
28342605 TATATAATAT
28342615 ATAAATACTTAGT-ATTGTACA
1 ATAAATACTTAGTAATTGTA-A
*
28342636 ATAAATA-TT-GTAATTGTAG
1 ATAAATACTTAGTAATTGTAA
28342655 ATAAA-ACTTAGT
1 ATAAATACTTAGT
28342667 GTTTGAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 10 0.37
21 7 0.26
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (21 bp):
ATAAATACTTAGTAATTGTAA
Found at i:28344024 original size:48 final size:48
Alignment explanation
Indices: 28343953--28344055 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 48
28343943 TTGAGTTTAC
28343953 ATAAACCTACACGAATAATGAATAATAGTGT-TTGGTTACCTGTTAGGG
1 ATAAACCTACACGAATAATGAATAATAGTGTCTT-GTTACCTGTTAGGG
* * * *
28344001 ATAAACTTACATGAATAGTGAATAATAGTGTCTTGTTACCTGTTTGGG
1 ATAAACCTACACGAATAATGAATAATAGTGTCTTGTTACCTGTTAGGG
*
28344049 TTAAACC
1 ATAAACC
28344056 CATATGATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (48 bp):
ATAAACCTACACGAATAATGAATAATAGTGTCTTGTTACCTGTTAGGG
Found at i:28349047 original size:106 final size:106
Alignment explanation
Indices: 28348859--28349068 Score: 375
Period size: 106 Copynumber: 2.0 Consensus size: 106
28348849 TAGTCCAGGG
*
28348859 TTAAGGTGTTCACAGATAAGCCATACCAATTTTGGGTTAATTCCCACCTAAATGGCTTCCTAAGG
1 TTAAGGTGTTCACAGATAAGCCATACCAATTTTGGGTTAATTCCCACCTAAATGACTTCCTAAGG
*
28348924 TCGTCAAGCCTAGGGTTTAAGTTCTTCCTCTCCCAAATAGC
66 TCGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAATAGC
*
28348965 TTAAGGTGTTCACAGATAAGCCATACCAATTTTGGGTTAATTCCCACCTAAATGACTTCCTAGGG
1 TTAAGGTGTTCACAGATAAGCCATACCAATTTTGGGTTAATTCCCACCTAAATGACTTCCTAAGG
* *
28349030 TCGTCAAGCGTAAGGTTTAATTTCTTCCTCTCCCAAATA
66 TCGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAATA
28349069 ACTAATCCAC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (106 bp):
TTAAGGTGTTCACAGATAAGCCATACCAATTTTGGGTTAATTCCCACCTAAATGACTTCCTAAGG
TCGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAATAGC
Found at i:28349552 original size:20 final size:18
Alignment explanation
Indices: 28349527--28349563 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28349517 ACGTAACACG
28349527 AATTAAATTTAAGCCATATT
1 AATTAAA-TTAAG-CATATT
28349547 AATTAAATTAAGCATAT
1 AATTAAATTAAGCATAT
28349564 CAACATCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAGCATATT
Found at i:28354186 original size:618 final size:618
Alignment explanation
Indices: 28353010--28354246 Score: 2384
Period size: 618 Copynumber: 2.0 Consensus size: 618
28353000 TTTGGACACG
*
28353010 CTGCCAAACTCACTTAGTATTTATAATAACTCGATAGGTCATTTCCCTGATGTAGTCTTGGCATC
1 CTGCCAAACTCACTTAGTATGTATAATAACTCGATAGGTCATTTCCCTGATGTAGTCTTGGCATC
*
28353075 GCTCCTCCTGGCGTAGACCCATACCAATTTACCTGTAATATAACACACAGATAAGTTCATAATAA
66 GCTCCTCCTGACGTAGACCCATACCAATTTACCTGTAATATAACACACAGATAAGTTCATAATAA
28353140 CTTAGCAAGCAACACATCATTTACCTAAGTCATATTTGCAGATCACAATTGATAACTTATATAAG
131 CTTAGCAAGCAACACATCATTTACCTAAGTCATATTTGCAGATCACAATTGATAACTTATATAAG
*
28353205 CGGTTTTATTGTTCTTAACCTTCAACCTTGTCTCTGGTGAATGCTTCCTCAAGTTTTATTCCTTT
196 CGGATTTATTGTTCTTAACCTTCAACCTTGTCTCTGGTGAATGCTTCCTCAAGTTTTATTCCTTT
28353270 TCACTTGTCCATTACTATACCTGACTCTGGAACATTTCCTTTTCTCAACAAAACATCTTCATTAC
261 TCACTTGTCCATTACTATACCTGACTCTGGAACATTTCCTTTTCTCAACAAAACATCTTCATTAC
* *
28353335 ATCAATTTCATCCTTCAATCACTGAGCCATCTCTTCATCACGATTCAAGAAGAAACACATACACA
326 ATCAATTTCATCCTTCAATCACTAAGCCATCTCTTCATCACGATTCAAGAAAAAACACATACACA
28353400 GATCACAGTTATATTTTCATGTCCTTAATCAGAATACATTTTCAATACTAACTCATTACTTCTTT
391 GATCACAGTTATATTTTCATGTCCTTAATCAGAATACATTTTCAATACTAACTCATTACTTCTTT
28353465 GTATCTCTTCAAGTCTTGTATAGTAGTTTATCATGTAGTCCATAGATATATTTTGTCCTTACAGA
456 GTATCTCTTCAAGTCTTGTATAGTAGTTTATCATGTAGTCCATAGATATATTTTGTCCTTACAGA
*
28353530 TTCCTCTGATTTTTTTTAAGAGCCATACAAAATTGCCCACCAGAGAAAATCTATTAGAATGTGCC
521 TTCCTCTGATATTTTTTAAGAGCCATACAAAATTGCCCACCAGAGAAAATCTATTAGAATGTGCC
28353595 ATGAAGGCCTTATCATTGGGAATCCTATTAAGA
586 ATGAAGGCCTTATCATTGGGAATCCTATTAAGA
28353628 CTGCCAAACTCACTTAGTATGTATAATAACTCGATAGGTCATTTCCCTGATGTAGTCTTGGCATC
1 CTGCCAAACTCACTTAGTATGTATAATAACTCGATAGGTCATTTCCCTGATGTAGTCTTGGCATC
*
28353693 GCTCCTCCTGACGTAGACCCTTACCAATTTACCTGTAATATAACACACAGATAAGTTCATAATAA
66 GCTCCTCCTGACGTAGACCCATACCAATTTACCTGTAATATAACACACAGATAAGTTCATAATAA
* *
28353758 CTTAGCAAGCAATACATCATTTACCTAAGTCATATTTGCATATCACAATTGATAACTTATATAAG
131 CTTAGCAAGCAACACATCATTTACCTAAGTCATATTTGCAGATCACAATTGATAACTTATATAAG
28353823 CGGATTTATTGTTCTTAACCTTCAACCTTGTCTCTGGTGAATGCTTCCTCAAGTTTTATTCCTTT
196 CGGATTTATTGTTCTTAACCTTCAACCTTGTCTCTGGTGAATGCTTCCTCAAGTTTTATTCCTTT
28353888 TCACTTGTCCATTACTATACCTGACTCTGGAACATTTCCTTTTCTCAACAAAACATCTTCATTAC
261 TCACTTGTCCATTACTATACCTGACTCTGGAACATTTCCTTTTCTCAACAAAACATCTTCATTAC
*
28353953 ATCAATTTCATCCTTCAATCACTAAGCCATCTCTTCATCACGATTCAAGAAAAAACACATACGCA
326 ATCAATTTCATCCTTCAATCACTAAGCCATCTCTTCATCACGATTCAAGAAAAAACACATACACA
28354018 GATCACAGTTATATTTTCATGTCCTTAATCAGAATACATTTTCAATACTAACTCATTACTTCTTT
391 GATCACAGTTATATTTTCATGTCCTTAATCAGAATACATTTTCAATACTAACTCATTACTTCTTT
28354083 GTATCTCTTCAAGTCTTGTATAGTAGTTTATCATGTAGTCCATAGATATATTTTGTCCTTACAGA
456 GTATCTCTTCAAGTCTTGTATAGTAGTTTATCATGTAGTCCATAGATATATTTTGTCCTTACAGA
28354148 TTCCTCTGATATTTTTTAAGAGCCATACAAAATTGCCCACCAGAGAAAATCTATTAGAATGTGCC
521 TTCCTCTGATATTTTTTAAGAGCCATACAAAATTGCCCACCAGAGAAAATCTATTAGAATGTGCC
28354213 ATGAAGGCCTTATCATTGGGAATCCTATTAAGA
586 ATGAAGGCCTTATCATTGGGAATCCTATTAAGA
28354246 C
1 C
28354247 ACGCCACAAG
Statistics
Matches: 609, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
618 609 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (618 bp):
CTGCCAAACTCACTTAGTATGTATAATAACTCGATAGGTCATTTCCCTGATGTAGTCTTGGCATC
GCTCCTCCTGACGTAGACCCATACCAATTTACCTGTAATATAACACACAGATAAGTTCATAATAA
CTTAGCAAGCAACACATCATTTACCTAAGTCATATTTGCAGATCACAATTGATAACTTATATAAG
CGGATTTATTGTTCTTAACCTTCAACCTTGTCTCTGGTGAATGCTTCCTCAAGTTTTATTCCTTT
TCACTTGTCCATTACTATACCTGACTCTGGAACATTTCCTTTTCTCAACAAAACATCTTCATTAC
ATCAATTTCATCCTTCAATCACTAAGCCATCTCTTCATCACGATTCAAGAAAAAACACATACACA
GATCACAGTTATATTTTCATGTCCTTAATCAGAATACATTTTCAATACTAACTCATTACTTCTTT
GTATCTCTTCAAGTCTTGTATAGTAGTTTATCATGTAGTCCATAGATATATTTTGTCCTTACAGA
TTCCTCTGATATTTTTTAAGAGCCATACAAAATTGCCCACCAGAGAAAATCTATTAGAATGTGCC
ATGAAGGCCTTATCATTGGGAATCCTATTAAGA
Found at i:28356290 original size:23 final size:23
Alignment explanation
Indices: 28356237--28356292 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
28356227 TATGACGCTT
28356237 TTGTGGCATATTCTATGTGAAGCC
1 TTGTGGCATATTCTATGTG-AGCC
* * *
28356261 TTATGGCATATTCTGTTTG-GCCC
1 TTGTGGCATATTCTATGTGAG-CC
28356284 TTGTGGCAT
1 TTGTGGCAT
28356293 GTTCCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 10 0.37
24 16 0.59
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (23 bp):
TTGTGGCATATTCTATGTGAGCC
Found at i:28360971 original size:17 final size:16
Alignment explanation
Indices: 28360949--28360980 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
28360939 TCATTTGACA
28360949 TTTTACTCTTTTTTTTT
1 TTTTACT-TTTTTTTTT
28360966 TTTTACTTTTTTTTT
1 TTTTACTTTTTTTTT
28360981 ATAATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTACTTTTTTTTTT
Found at i:28362739 original size:22 final size:22
Alignment explanation
Indices: 28362713--28362755 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28362703 GTTGTTTTAC
*
28362713 TTATAAATTAGTAAATAAATTT
1 TTATAAATGAGTAAATAAATTT
* *
28362735 TTATACATGAGTTAATAAATT
1 TTATAAATGAGTAAATAAATT
28362756 ATTCTTTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
TTATAAATGAGTAAATAAATTT
Found at i:28374418 original size:18 final size:17
Alignment explanation
Indices: 28374387--28374424 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
28374377 AAATGAATCG
*
28374387 AAAAAGAACGAAGAAGA
1 AAAAAGAACAAAGAAGA
28374404 AAAAAGTAACAAAGAAGA
1 AAAAAG-AACAAAGAAGA
28374422 AAA
1 AAA
28374425 GGAAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAAGAACAAAGAAGA
Found at i:28375160 original size:51 final size:51
Alignment explanation
Indices: 28375084--28375181 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
28375074 AATTGTGAGC
*
28375084 TCACTAAACCTGCGAGCTAACCAAATATGCAAGCTCTACAAAACTGTATGT
1 TCACTAAACCTGCAAGCTAACCAAATATGCAAGCTCTACAAAACTGTATGT
* *
28375135 TCACTAAACCTGCAAGCTCACCAAATATGCAAGGTCTACAAAACTGT
1 TCACTAAACCTGCAAGCTAACCAAATATGCAAGCTCTACAAAACTGT
28375182 GAGCCTACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (51 bp):
TCACTAAACCTGCAAGCTAACCAAATATGCAAGCTCTACAAAACTGTATGT
Found at i:28382569 original size:22 final size:21
Alignment explanation
Indices: 28382531--28382587 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
28382521 ATGCCTTTGA
28382531 AAATATTTACAAAAAGAG-ACATC
1 AAAT-TTTA-AAAAAGAGCA-ATC
*
28382554 TAATTTCTAAAAAAGAGCAATC
1 AAATTT-TAAAAAAGAGCAATC
28382576 AAATTTTAAAAA
1 AAATTTTAAAAA
28382588 TAGTTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.20
22 18 0.60
23 6 0.20
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (21 bp):
AAATTTTAAAAAAGAGCAATC
Found at i:28386150 original size:33 final size:33
Alignment explanation
Indices: 28386102--28386167 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
28386092 TGCTAGGAAA
*
28386102 GGCCTTCCTAGGATGATTGACACCTCTTTATCT
1 GGCCTTCCTAAGATGATTGACACCTCTTTATCT
*
28386135 GGCCTTTCTAAGATGATTGACACCTCTTTATCT
1 GGCCTTCCTAAGATGATTGACACCTCTTTATCT
28386168 ACTTCAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (33 bp):
GGCCTTCCTAAGATGATTGACACCTCTTTATCT
Found at i:28392291 original size:10 final size:10
Alignment explanation
Indices: 28392276--28392300 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28392266 AAATCTGTCG
28392276 AAAATAAATC
1 AAAATAAATC
28392286 AAAATAAATC
1 AAAATAAATC
28392296 AAAAT
1 AAAAT
28392301 TTATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATAAATC
Found at i:28392786 original size:22 final size:20
Alignment explanation
Indices: 28392745--28392792 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
28392735 GTCTTCAAGC
28392745 AAACAAAAAGAAGAAAAATG
1 AAACAAAAAGAAGAAAAATG
28392765 AAACTAAAAACGAA-AAATAATG
1 AAAC-AAAAA-GAAGAAA-AATG
*
28392787 ATACAA
1 AAACAA
28392793 GAAAATGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 10 0.42
22 10 0.42
ACGTcount: A:0.71, C:0.08, G:0.10, T:0.10
Consensus pattern (20 bp):
AAACAAAAAGAAGAAAAATG
Found at i:28393508 original size:56 final size:55
Alignment explanation
Indices: 28393383--28393523 Score: 144
Period size: 55 Copynumber: 2.6 Consensus size: 55
28393373 CTTAAAAAAA
* * * *
28393383 TTACTTCCCCCCAAA-CCCTAAAAC-TTTTTCCCTTTTACTTTCCCCCCAAAATTT
1 TTACTT-CGCCCAAACCCCAAAAACTTTTTTTCCTTTTACTTTCCCCCCAAAACTT
* * *
28393437 TTACTTCGCCCAAACCCCCCAAAACTTTTTTTCCTTTTTCTTT-CCCTCAAAACTT
1 TTACTTCGCCCAAA-CCCCAAAAACTTTTTTTCCTTTTACTTTCCCCCCAAAACTT
* * *
28393492 TTACTTCATCCTAAACCTCAAAAACTTTTTTT
1 TTACTTC-GCCCAAACCCCAAAAACTTTTTTT
28393524 TCGATTTTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
53 7 0.10
54 6 0.08
55 40 0.55
56 20 0.27
ACGTcount: A:0.25, C:0.35, G:0.01, T:0.40
Consensus pattern (55 bp):
TTACTTCGCCCAAACCCCAAAAACTTTTTTTCCTTTTACTTTCCCCCCAAAACTT
Found at i:28395232 original size:103 final size:103
Alignment explanation
Indices: 28395053--28395259 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
28395043 TTTGGCCTGG
28395053 TACTCAATTGGTTAGTAAAATTTAGTTTTTTTTTTTAATTTTTATAATTTTGAGATCATGAAAGT
1 TACTCAATTGGTTAGTAAAATTTAGTTTTTTTTTTTAATTTTTATAATTTTGAGATCATGAAAGT
28395118 TTAATCTAGCTAACTCGTGTCTCAATTCGTTAAATTGT
66 TTAATCTAGCTAACTCGTGTCTCAATTCGTTAAATTGT
28395156 TACTCAATTGGTTAGTAAAATTTAGTTTTTTTTTTTAATTTTTATAATTTTGAGATCATGAAAGT
1 TACTCAATTGGTTAGTAAAATTTAGTTTTTTTTTTTAATTTTTATAATTTTGAGATCATGAAAGT
28395221 TTAATCTAGCTAACTCGTGTCTCAATTCGTTAAATTGT
66 TTAATCTAGCTAACTCGTGTCTCAATTCGTTAAATTGT
28395259 T
1 T
28395260 CAAGTTTCAA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.49
Consensus pattern (103 bp):
TACTCAATTGGTTAGTAAAATTTAGTTTTTTTTTTTAATTTTTATAATTTTGAGATCATGAAAGT
TTAATCTAGCTAACTCGTGTCTCAATTCGTTAAATTGT
Found at i:28403465 original size:59 final size:60
Alignment explanation
Indices: 28403373--28403492 Score: 233
Period size: 59 Copynumber: 2.0 Consensus size: 60
28403363 TTGACGAACC
28403373 CTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCC-AAAAATATGAAGGT
1 CTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAATATGAAGGT
28403432 CTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAATATGAAGGT
1 CTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAATATGAAGGT
28403492 C
1 C
28403493 CAAGTCTTAG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 45 0.75
60 15 0.25
ACGTcount: A:0.38, C:0.34, G:0.08, T:0.20
Consensus pattern (60 bp):
CTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAATATGAAGGT
Found at i:28409901 original size:134 final size:124
Alignment explanation
Indices: 28409743--28409984 Score: 331
Period size: 124 Copynumber: 1.9 Consensus size: 124
28409733 AATTAAACTG
*
28409743 GAGACTCAAAGATGTAATTACAACTATCTAACCATCTAACAAAAGTACTAATATGTTAAAAAATA
1 GAGACTCAAAGATATAATTACAACTATC-AA--A-C---CAAAA--ACTAATATGTTAAAAAA-A
**
28409808 TTAATTAAAAATTTAAAAAGCTTGAAGCAATGTAAAATAAAAAAAAATACAAAGAGATGAATCGA
56 TTAATTAAAAATTTAAAAAGCTTGAAGCAACATAAAATAAAAAAAAATACAAAGAGATGAATCGA
28409873 ATTC
121 ATTC
* * *
28409877 GAGACTCAATGATATAATTTCAACTATCAAACCAAAAACTAATATGTTAAAAAAATTATTTAAAA
1 GAGACTCAAAGATATAATTACAACTATCAAACCAAAAACTAATATGTTAAAAAAATTAATTAAAA
*
28409942 ATTTAAAAAGCTTGAAGCAACATGAAATAAAAAAAAATACAAA
66 ATTTAAAAAGCTTGAAGCAACATAAAATAAAAAAAAATACAAA
28409985 TGTAAGTAGG
Statistics
Matches: 101, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
124 50 0.50
125 17 0.17
127 5 0.05
130 1 0.01
131 1 0.01
133 2 0.02
134 25 0.25
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (124 bp):
GAGACTCAAAGATATAATTACAACTATCAAACCAAAAACTAATATGTTAAAAAAATTAATTAAAA
ATTTAAAAAGCTTGAAGCAACATAAAATAAAAAAAAATACAAAGAGATGAATCGAATTC
Found at i:28412946 original size:54 final size:57
Alignment explanation
Indices: 28412823--28412952 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 57
28412813 TTATATTAAA
* * * *
28412823 ATTTCTCATCCATAATGTACTTATTCTAGCTATATAAAAAAAAAGTTGTTATATTGT
1 ATTTCACATCAATAATATACTTATTCTAGCAATATAAAAAAAAAGTTGTTATATTGT
* * * *
28412880 ATTTTACATCAATAATATACTTATT-TA-CAATCTAAGAAAAAAA-TT-TTGTATTTT
1 ATTTCACATCAATAATATACTTATTCTAGCAATATAA-AAAAAAAGTTGTTATATTGT
*
28412934 ATTTCATATCAATAATATA
1 ATTTCACATCAATAATATA
28412953 TATCTATTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
54 24 0.39
55 8 0.13
56 9 0.15
57 21 0.34
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (57 bp):
ATTTCACATCAATAATATACTTATTCTAGCAATATAAAAAAAAAGTTGTTATATTGT
Found at i:28412961 original size:56 final size:56
Alignment explanation
Indices: 28412860--28412969 Score: 134
Period size: 54 Copynumber: 2.0 Consensus size: 56
28412850 AGCTATATAA
* *
28412860 AAAAAAAGTTGTTATATTGTATTTTACATCAATAATATACTTATTTACAATCTAAG
1 AAAAAAAGTTGTTATATTGTATTTCACATCAATAATATAATTATTTACAATCTAAG
* * * *
28412916 AAAAAAA-TT-TTGTATTTTATTTCATATCAATAATATATATCTATTTATAATCTA
1 AAAAAAAGTTGTTATATTGTATTTCACATCAATAATATA-AT-TATTTACAATCTA
28412970 CGAACTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 24 0.52
55 3 0.07
56 19 0.41
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (56 bp):
AAAAAAAGTTGTTATATTGTATTTCACATCAATAATATAATTATTTACAATCTAAG
Found at i:28420469 original size:9 final size:9
Alignment explanation
Indices: 28420445--28420498 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 9
28420435 TATCAAAATT
28420445 ATAATATAA
1 ATAATATAA
28420454 CATAATATAA
1 -ATAATATAA
28420464 ATAATATAA
1 ATAATATAA
28420473 ATAATTATAAA
1 ATAA-TAT-AA
28420484 ATAGATATATA
1 ATA-ATATA-A
28420495 ATAA
1 ATAA
28420499 GATTGGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 13 0.32
10 14 0.35
11 12 0.30
12 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAATATAA
Found at i:28420469 original size:19 final size:19
Alignment explanation
Indices: 28420445--28420498 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
28420435 TATCAAAATT
28420445 ATAATATAACATAA-TATAA
1 ATAATATAA-ATAATTATAA
28420464 ATAATATAAATAATTATAAA
1 ATAATATAAATAATTAT-AA
28420484 ATAGATATATAATAA
1 ATA-ATATA-AATAA
28420499 GATTGGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 5 0.16
21 5 0.16
22 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAATATAAATAATTATAA
Found at i:28420492 original size:11 final size:10
Alignment explanation
Indices: 28420445--28420498 Score: 58
Period size: 9 Copynumber: 5.4 Consensus size: 10
28420435 TATCAAAATT
*
28420445 ATAATATAAC
1 ATAATATAAA
28420455 ATAATAT-AA
1 ATAATATAAA
28420464 ATAATAT-AA
1 ATAATATAAA
28420473 ATAATTATAAA
1 ATAA-TATAAA
*
28420484 ATAGATATATA
1 ATA-ATATAAA
28420495 ATAA
1 ATAA
28420499 GATTGGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 14 0.36
10 11 0.28
11 13 0.33
12 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
ATAATATAAA
Found at i:28421427 original size:12 final size:12
Alignment explanation
Indices: 28421410--28421434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28421400 AATTAATTAC
28421410 TTTAATATTAAA
1 TTTAATATTAAA
28421422 TTTAATATTAAA
1 TTTAATATTAAA
28421434 T
1 T
28421435 ATATTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:28441576 original size:17 final size:17
Alignment explanation
Indices: 28441554--28441590 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28441544 TACTTATCAA
*
28441554 TTCATTTTTTTCATTCT
1 TTCATTTTATTCATTCT
*
28441571 TTCATTTTATTCCTTCT
1 TTCATTTTATTCATTCT
28441588 TTC
1 TTC
28441591 CACGCTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.68
Consensus pattern (17 bp):
TTCATTTTATTCATTCT
Found at i:28444791 original size:26 final size:26
Alignment explanation
Indices: 28444762--28444812 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28444752 ATTTTTTAAA
*
28444762 TTTAAGTAAATATTTAAACACAATTC
1 TTTAAATAAATATTTAAACACAATTC
* *
28444788 TTTAAATAAATATTTTAACATAATT
1 TTTAAATAAATATTTAAACACAATT
28444813 TTCTTCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
TTTAAATAAATATTTAAACACAATTC
Found at i:28447796 original size:20 final size:20
Alignment explanation
Indices: 28447718--28447789 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
28447708 AAAAATATAA
* *
28447718 ATTTTGAAAATTTTATAAA-T
1 ATTTTGAATATTTGA-AAATT
*
28447738 ATTTTGAAT-TTTAAAAATT
1 ATTTTGAATATTTGAAAATT
28447757 ATTTTGAATATTTGAAAATT
1 ATTTTGAATATTTGAAAATT
*
28447777 ATTTTGATTATTT
1 ATTTTGAATATTT
28447790 TGTAATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.07
19 14 0.30
20 29 0.63
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTTTGAATATTTGAAAATT
Found at i:28450535 original size:18 final size:18
Alignment explanation
Indices: 28450503--28450549 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28450493 AATTATATCA
*
28450503 TATAATTTA-TATTATTT
1 TATAATTCATTATTATTT
28450520 T-TAATATCATTATTATTT
1 TATAAT-TCATTATTATTT
28450538 TATAATTCATTA
1 TATAATTCATTA
28450550 AATTTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 3 0.12
18 15 0.58
19 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TATAATTCATTATTATTT
Found at i:28450554 original size:17 final size:19
Alignment explanation
Indices: 28450516--28450561 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
28450506 AATTTATATT
*
28450516 ATTTT-TAATATCATTATT
1 ATTTTATAATATCATTATA
28450534 ATTTTATAAT-TCATTA-A
1 ATTTTATAATATCATTATA
28450551 ATTTTAATAAT
1 ATTTT-ATAAT
28450562 CTAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 5 0.20
18 16 0.64
19 4 0.16
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTATAATATCATTATA
Found at i:28462122 original size:39 final size:37
Alignment explanation
Indices: 28462005--28462123 Score: 124
Period size: 39 Copynumber: 3.2 Consensus size: 37
28461995 AAAAGGGAAG
28462005 AAAAAGAAAAATCAAAATCAAAGTCAAAATGAAAATGA
1 AAAAAGAAAAATCAAAATCAAA-TCAAAATGAAAATGA
* *
28462043 AAAAATCAAAAATCAAAAT-AAA--AAAA--AACAA-CA
1 AAAAA-GAAAAATCAAAATCAAATCAAAATGAA-AATGA
*
28462076 AAGAAGAAAAATCAAAATCAAGATCAAAATGAAAATGA
1 AAAAAGAAAAATCAAAATCAA-ATCAAAATGAAAATGA
28462114 GAAAAAGAAA
1 -AAAAAGAAA
28462124 GAAGAATGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
32 12 0.18
33 9 0.14
34 3 0.05
35 4 0.06
36 4 0.06
37 2 0.03
38 11 0.17
39 20 0.31
ACGTcount: A:0.71, C:0.08, G:0.09, T:0.11
Consensus pattern (37 bp):
AAAAAGAAAAATCAAAATCAAATCAAAATGAAAATGA
Found at i:28463982 original size:86 final size:87
Alignment explanation
Indices: 28463759--28464293 Score: 813
Period size: 87 Copynumber: 6.2 Consensus size: 87
28463749 GTGAAGAAGT
* *
28463759 AGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAACGAAGCTTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
28463824 ATTGGAGCTGGTTAAAGATAGC
66 ATTGGAGCTGGTTAAAGATAGC
* * *
28463846 AGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAATGAAGCCTTGCCTCCATCGATTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
* *
28463911 AGTGGAGCTGGTTAAAGA-AGT
66 ATTGGAGCTGGTTAAAGATAGC
* * *
28463932 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGGTCAAAAACGAATCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
*
28463997 ATTGGAGCTGGTTAAAGATAGT
66 ATTGGAGCTGGTTAAAGATAGC
* *
28464019 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAACTAAGCATTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
*
28464083 ATTGGAGCTGGTTAAAGATAAC
66 ATTGGAGCTGGTTAAAGATAGC
*
28464105 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAATGAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
*
28464170 AGTGGAGCTGGTTAAAGATAGC
66 ATTGGAGCTGGTTAAAGATAGC
* * * * * *
28464192 AGATCTTACCTTTCTGCATTAACAACGAAGTAGATTGAAAACGAAGCCTTGCCTCCATCGGTTGT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
* * ***
28464257 AATAGAGCTAACTAAAGATAGC
66 ATTGGAGCTGGTTAAAGATAGC
28464279 AGATCTTGCCTTCCT
1 AGATCTTGCCTTCCT
28464294 AAGCACTAGT
Statistics
Matches: 407, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
86 159 0.39
87 248 0.61
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (87 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
ATTGGAGCTGGTTAAAGATAGC
Found at i:28463983 original size:43 final size:42
Alignment explanation
Indices: 28463854--28463985 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 42
28463844 GCAGATCTTA
* * *
28463854 CCTTCCTGCATTAACAGCGAAGCAGATCGAAAATGAAGCCTTG
1 CCTTCCTGCATTAACAGCGAAGCAGGTC-AAAAAGAATCCTTG
* * * * *
28463897 CC-TCCAT-CGATT-GCAGTGGAGCTGGTTAAAGAAGTAGAT-CTTG
1 CCTTCC-TGC-ATTAACAGCGAAGCAGGTCAAA-AAG-A-ATCCTTG
28463940 CCTTCCTGCATTAACAGCGAAGCAGGTCAAAAACGAATCCTTG
1 CCTTCCTGCATTAACAGCGAAGCAGGTCAAAAA-GAATCCTTG
28463983 CCT
1 CCT
28463986 CCATCGGTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
41 3 0.05
42 17 0.26
43 27 0.41
44 19 0.29
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CCTTCCTGCATTAACAGCGAAGCAGGTCAAAAAGAATCCTTG
Found at i:28464041 original size:173 final size:174
Alignment explanation
Indices: 28463759--28464293 Score: 815
Period size: 173 Copynumber: 3.1 Consensus size: 174
28463749 GTGAAGAAGT
* *
28463759 AGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAACGAAGCTTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
28463824 ATTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAATG
66 ATTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAATG
* * *
28463889 AAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGA-AGT
131 AAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGC
* * *
28463932 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGGTCAAAAACGAATCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
* *
28463997 ATTGGAGCTGGTTAAAGATAGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAACT
66 ATTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAA-T
* * *
28464061 -AAGCATTGCCTCCATCGGTTGCATTGGAGCTGGTTAAAGATAAC
130 GAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGC
*
28464105 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAATGAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
* * * * * *
28464170 AGTGGAGCTGGTTAAAGATAGCAGATCTTACCTTTCTGCATTAACAACGAAGTAGATTGAAAACG
66 ATTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAATG
* * ***
28464235 AAGCCTTGCCTCCATCGGTTGTAATAGAGCTAACTAAAGATAGC
131 AAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGC
28464279 AGATCTTGCCTTCCT
1 AGATCTTGCCTTCCT
28464294 AAGCACTAGT
Statistics
Matches: 326, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
172 41 0.13
173 230 0.71
174 55 0.17
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (174 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCATCGGTTGC
ATTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAATG
AAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGC
Found at i:28472305 original size:23 final size:23
Alignment explanation
Indices: 28472279--28472331 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
28472269 ATAAGTGCCA
28472279 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28472302 CACTGATATGTAGCCGAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
28472325 CACTGAT
1 CACTGAT
28472332 CAATAACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28480363 original size:132 final size:132
Alignment explanation
Indices: 28480125--28481182 Score: 1670
Period size: 132 Copynumber: 8.0 Consensus size: 132
28480115 GTGAAACACT
* * * *
28480125 AAGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAGGATCGTAGATCTTATCTCTCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
28480190 TAGTGGAGTAGATCAAGGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28480255 CC
131 CC
*
28480257 AAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * *
28480322 TAGTGCAGCAGATCAAAGATGGCAAATCTTAT-TTTGTCAAGATAGTGGGAAGCAGATTTAAGCC
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTT-CCAAGATAGTGGGAAGTAGATTTAAGCC
*
28480386 ACT
130 ACC
28480389 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
28480454 TAGTGGAGTAGATCAAGGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATGTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28480519 CC
131 CC
* * * *
28480521 AAGCCTTGTCTCCTTGAGCAGCAGCCGAGGAGGATGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
28480586 TAGTGGAGTAGATCAAGGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATGTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28480651 CC
131 CC
* * * *
28480653 AAGCCTTGTCTCCTTGAGCAGCAGCCGAGGAGGATGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
28480718 TAGTGGAGTAGATCAAGGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATGTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28480783 CC
131 CC
* * * *
28480785 AAGCCTTGTCTCCTTGAGCAGCAGCCGAGGAGGATGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * *
28480850 TAGTAGAGAAGATCGAAGATGGCAAATCTTATCTTTCAAAGATAGTGGGAAGTAGATTTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28480915 CC
131 CC
*
28480917 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAA
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
28480982 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGGCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
28481047 CC
131 CC
* * * *
28481049 AAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGCTAAAGATTGTAGATCTTATCTCCCTAAGTAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * *
28481114 TAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGA-TTAAGCCA
66 TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
*
28481178 GC
131 CC
28481180 AAG
1 AAG
28481183 TCTTATCCTC
Statistics
Matches: 871, Mismatches: 53, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
131 14 0.02
132 854 0.98
133 3 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
CC
Found at i:28480462 original size:44 final size:44
Alignment explanation
Indices: 28480265--28480466 Score: 117
Period size: 44 Copynumber: 4.6 Consensus size: 44
28480255 CCAAGCCTTG
* * *
28480265 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCTTA
* * ** * * *
28480309 TCTCCCTAAGCAGTAGTGCAGCAGATCAAAGATGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCTTA
*** * * * * * *
28480353 T-TTTGTCAAG-A-TAGTGGGAAGCAGATTTAAGCCACT-AAG-CCTTG
1 TCTCCCT-AAGCAGTAGT-GG-AGTAGATTGAAG--ATTGTAGATCTTA
* * * *
28480397 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCTTA
28480441 TCTCCCTAAGCAGTAGTGGAGTAGAT
1 TCTCCCTAAGCAGTAGTGGAGTAGAT
28480467 CAAGGACGGC
Statistics
Matches: 109, Mismatches: 39, Indels: 20
0.65 0.23 0.12
Matches are distributed among these distances:
42 6 0.06
43 6 0.06
44 88 0.81
45 6 0.06
46 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCTTA
Found at i:28480483 original size:44 final size:44
Alignment explanation
Indices: 28480435--28480751 Score: 136
Period size: 44 Copynumber: 7.2 Consensus size: 44
28480425 AAGATTGTAG
28480435 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
* * *
28480479 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATGTAAGCCAC--CAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGAT-CAAG-GACGGCAA
** * * * * ** * * ** * *
28480523 GCCTTGTCTCCTTGAGCAGCAGCCGAGGAGGATGAA-GATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GATCAAGGACGGCAA
28480567 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
* * *
28480611 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATGTAAGCCAC--CAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGAT-CAAG-GACGGCAA
** * * * * ** * * ** * *
28480655 GCCTTGTCTCCTTGAGCAGCAGCCGAGGAGGATGAA-GATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GATCAAGGACGGCAA
28480699 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
28480743 ATCTTATCT
1 ATCTTATCT
28480752 TTCCAAGATA
Statistics
Matches: 185, Mismatches: 64, Indels: 48
0.62 0.22 0.16
Matches are distributed among these distances:
42 10 0.05
43 20 0.11
44 125 0.68
45 22 0.12
46 8 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAGGACGGCAA
Found at i:28481212 original size:44 final size:44
Alignment explanation
Indices: 28481164--28481264 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
28481154 GATAGTGGGA
28481164 AGCAGATT-AAGCCAGCAAGTCTTATC-CTCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGCCA-CAAGTCTTATCTC-CCTGAAGTTGCAGTGG
* * *
28481208 AGCAGATTAAAACTATAAGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGCCACAAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
28481252 AGTAGATTGAAGC
1 AGCAGATTAAAGC
28481265 ACGAATTCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
AGCAGATTAAAGCCACAAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:28481517 original size:21 final size:21
Alignment explanation
Indices: 28481468--28481560 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
28481458 ATTTTCGAGG
*
28481468 ATATACAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
28481489 A-A-GCAATCTTAGATATCAT
1 ATATGCAATCTTAGATATGAT
* *
28481508 ATATGCAATCTTAGACATGGT
1 ATATGCAATCTTAGATATGAT
*
28481529 ATATGTAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
28481550 ATATACAATCT
1 ATATGCAATCT
28481561 CAGAAGATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.27
20 2 0.03
21 42 0.70
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:28481856 original size:25 final size:25
Alignment explanation
Indices: 28481805--28481856 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
28481795 AATTTTGTTA
**
28481805 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
28481830 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
28481855 AT
1 AT
28481857 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:28481961 original size:33 final size:30
Alignment explanation
Indices: 28481922--28481982 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
28481912 TTTTCGCATA
*
28481922 TTTATTTTCTTAATATGAGGTAATTATTTTTAT
1 TTTATTTTATTAATAT-A--TAATTATTTTTAT
*
28481955 TTTATTTTATTTATATATAATTATTTTT
1 TTTATTTTATTAATATATAATTATTTTT
28481983 TTATAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
32 1 0.04
33 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTATTTTATTAATATATAATTATTTTTAT
Found at i:28482456 original size:19 final size:20
Alignment explanation
Indices: 28482415--28482456 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28482405 ATTTCTAGGC
* *
28482415 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
28482435 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
28482454 CAT
1 CAT
28482457 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:28484620 original size:20 final size:20
Alignment explanation
Indices: 28484585--28484634 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
28484575 CTTTGCTACA
28484585 TGATTT-GTTGTTGTTTGAT
1 TGATTTAGTTGTTGTTTGAT
* *
28484604 TGATTTAGTTTTTGTTTGCT
1 TGATTTAGTTGTTGTTTGAT
28484624 TGATTTAGTTG
1 TGATTTAGTTG
28484635 CTGCAGCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.12, C:0.02, G:0.24, T:0.62
Consensus pattern (20 bp):
TGATTTAGTTGTTGTTTGAT
Found at i:28485333 original size:20 final size:19
Alignment explanation
Indices: 28485271--28485333 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
28485261 TAAATATTTA
* *
28485271 TTTTCTTTTTTCTTTACTT
1 TTTTCCTTTTTCTTTTCTT
28485290 TTTTCCTATTTTCCCTTCTTCTT
1 TTTTCCT-TTTT--CTT-TTCTT
28485313 TTTTCCTTTTTCTTATTCTT
1 TTTTCCTTTTTCTT-TTCTT
28485333 T
1 T
28485334 CCCTTCCCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.16
20 13 0.35
22 7 0.19
23 11 0.30
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCCTTTTTCTTTTCTT
Found at i:28486616 original size:19 final size:20
Alignment explanation
Indices: 28486588--28486626 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28486578 TATTAGTGAT
*
28486588 TACATGTGTAAAT-TTAATA
1 TACATATGTAAATATTAATA
*
28486607 TACATATGTATATATTAATA
1 TACATATGTAAATATTAATA
28486627 AAATATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
TACATATGTAAATATTAATA
Found at i:28487719 original size:41 final size:40
Alignment explanation
Indices: 28487623--28487758 Score: 161
Period size: 41 Copynumber: 3.5 Consensus size: 40
28487613 CGACTTCGAA
* * *
28487623 TCGATGAGGCACTAGGTGTCAA-TT--TACTTCGGTTTAA
1 TCGATGAGACACTAGGTGTCAATTTACTACTTCGATTTAT
* *
28487660 TCGATGAGACACTGGGTGTCAATTTACTACTTTGATTTTAT
1 TCGATGAGACACTAGGTGTCAATTTACTACTTCGA-TTTAT
*
28487701 TCGATGAGACACTAGGTGTCAATTTACTACTTCGAATTAT
1 TCGATGAGACACTAGGTGTCAATTTACTACTTCGATTTAT
* * *
28487741 CCGATGAGGCACTGGGTG
1 TCGATGAGACACTAGGTG
28487759 CTAAACTGGT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 20 0.24
38 2 0.02
40 25 0.30
41 37 0.44
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (40 bp):
TCGATGAGACACTAGGTGTCAATTTACTACTTCGATTTAT
Found at i:28490073 original size:20 final size:20
Alignment explanation
Indices: 28489992--28490074 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
28489982 TACACCACAC
*
28489992 CAGAGGCATCAAAGATGCGTAA-
1 CAGAGGCACCAAAG-TGC--AAT
*
28490014 CAGAGGCACCAAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAT
*
28490034 AAGAGGCA-CAAATGTGCAAT
1 CAGAGGCACCAAA-GTGCAAT
*
28490054 CATAGGCACCAAAGTGCAAT
1 CAGAGGCACCAAAGTGCAAT
28490074 C
1 C
28490075 CCGTACAAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.11
20 27 0.51
21 7 0.13
22 13 0.25
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAT
Found at i:28492968 original size:17 final size:17
Alignment explanation
Indices: 28492946--28492984 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
28492936 ACGTTATACT
28492946 TAATTGTAACAAATTTA
1 TAATTGTAACAAATTTA
28492963 TAATTGTAACAAATTTA
1 TAATTGTAACAAATTTA
28492980 TAATT
1 TAATT
28492985 AAATTCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
TAATTGTAACAAATTTA
Found at i:28498094 original size:42 final size:42
Alignment explanation
Indices: 28498030--28498112 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
28498020 GTTTTCCTTC
* *
28498030 CCTTCAATTTCGACAAGCAGTTGAATAAAGAAGAAATTTTTT
1 CCTTCAATCTCGACAAGAAGTTGAATAAAGAAGAAATTTTTT
28498072 CCTTCAATCTCGACAAGAAGTTGAATAAAGAAGAAATTTTT
1 CCTTCAATCTCGACAAGAAGTTGAATAAAGAAGAAATTTTT
28498113 ACTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (42 bp):
CCTTCAATCTCGACAAGAAGTTGAATAAAGAAGAAATTTTTT
Found at i:28506844 original size:138 final size:137
Alignment explanation
Indices: 28506665--28506936 Score: 413
Period size: 138 Copynumber: 2.0 Consensus size: 137
28506655 ATTTTCTACC
* * * *
28506665 ATCAAACATCAAAACACATACACATTCCTCAATGTTTAAACCTTAATACTTTACCAGTTTCAGAA
1 ATCAAACATCAAAACACA-ACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
*
28506730 ATGAATCCCCCCGGCTAGCTAGGTTCA-TCCTCAACGACTCCAAAAACATAGAAATCATTAAAAA
65 ATGAAT-CCCCCGGCTAGCTAGGTT-AGTCCACAACGACTCCAAAAACATAG-AATCATTAAAAA
28506794 CGGAGTATAAA
127 CGGAGTATAAA
28506805 ATCAAACATCAAAACAC-ACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAAA
1 ATCAAACATCAAAACACAACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAAA
* * **
28506869 TGAGTCGCTGGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGGA
66 TGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGGA
28506934 GTA
131 GTA
28506937 CAAAGTCACT
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
136 20 0.16
137 38 0.31
138 47 0.39
140 17 0.14
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (137 bp):
ATCAAACATCAAAACACAACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAAA
TGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGGA
GTATAAA
Found at i:28508575 original size:137 final size:137
Alignment explanation
Indices: 28508408--28508682 Score: 421
Period size: 137 Copynumber: 2.0 Consensus size: 137
28508398 ATTTTCTACC
* * *
28508408 ATCAAACATCGAAACACATACACATTCATCAATGTTTAAACCTTAATACTTTAACAGTTTCAGAA
1 ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
* *
28508473 ATGAATCCCCCCGGCTAGCTAGGTTCGTCCACAACGACTTC-AAAACATAGAAATCATTAAAAAC
66 ATGAAT-CCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAG-AATCATTAAAAAC
28508537 GGAGTATAAA
129 GGAGTA-AAA
28508547 ATCAAACATC-AAA-ACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
1 ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
* * **
28508610 ATGAGTCGCTGGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
66 ATGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
28508675 AGTAAAA
131 AGTAAAA
28508682 A
1 A
28508683 GTCACTTACA
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
135 4 0.03
136 48 0.38
137 61 0.48
138 3 0.02
139 10 0.08
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (137 bp):
ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
ATGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
AGTAAAA
Found at i:28510180 original size:137 final size:137
Alignment explanation
Indices: 28510013--28510287 Score: 421
Period size: 137 Copynumber: 2.0 Consensus size: 137
28510003 ATTTTCTACC
* * *
28510013 ATCAAACATCGAAACACATACACATTCATCAATGTTTAAACCTTAATACTTTAACAGTTTCAGAA
1 ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
* *
28510078 ATGAATCCCCCCGGCTAGCTAGGTTCGTCCACAACGACTTC-AAAACATAGAAATCATTAAAAAC
66 ATGAAT-CCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAG-AATCATTAAAAAC
28510142 GGAGTATAAA
129 GGAGTA-AAA
28510152 ATCAAACATC-AAA-ACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
1 ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
* * **
28510215 ATGAGTCGCTGGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
66 ATGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
28510280 AGTAAAA
131 AGTAAAA
28510287 A
1 A
28510288 GTCACTTACA
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
135 4 0.03
136 48 0.38
137 61 0.48
138 3 0.02
139 10 0.08
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (137 bp):
ATCAAACATCGAAACACACACACATTCATCAATGTTAAAACCTTAATACTTTAACAGTTTCACAA
ATGAATCCCCCGGCTAGCTAGGTTAGTCCACAACGACTCCAAAAACATAGAATCATTAAAAACGG
AGTAAAA
Found at i:28520646 original size:21 final size:21
Alignment explanation
Indices: 28520617--28520665 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28520607 ATCTACGTAA
* *
28520617 TCAAATTTAACT-AATTGAAT
1 TCAAATTTTACTCAATTCAAT
*
28520637 TCATATTTTACTCAATTCAAT
1 TCAAATTTTACTCAATTCAAT
28520658 TCAAATTT
1 TCAAATTT
28520666 CAAGTTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
TCAAATTTTACTCAATTCAAT
Found at i:28522245 original size:21 final size:21
Alignment explanation
Indices: 28522218--28522264 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28522208 CTACGTAATA
*
28522218 AAATTTAACT-AATTGAATTC
1 AAATTTTACTCAATTGAATTC
* *
28522238 ATATTTTACTCAATTTAATTC
1 AAATTTTACTCAATTGAATTC
28522259 AAATTT
1 AAATTT
28522265 CAAGTTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTTTACTCAATTGAATTC
Found at i:28527612 original size:20 final size:21
Alignment explanation
Indices: 28527575--28527618 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28527565 ATAAAGAAGA
*
28527575 AATTTTTACTTTATTTTACTT
1 AATTTTTACTTTATTTTAATT
28527596 AATTTTT-CTTT-TATTTAATT
1 AATTTTTACTTTAT-TTTAATT
28527616 AAT
1 AAT
28527619 AACATAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 13 0.62
21 7 0.33
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTTTTACTTTATTTTAATT
Found at i:28533521 original size:20 final size:21
Alignment explanation
Indices: 28533476--28533521 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
28533466 AATAAAGAAG
*
28533476 AAATTTTTACTTTATTTTACT
1 AAATTTTTACTTTATTTTAAT
*
28533497 TAATTTTT-CTTT-TATTTAAT
1 AAATTTTTACTTTAT-TTTAAT
28533517 AAATT
1 AAATT
28533522 AAATAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.62
21 7 0.33
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
AAATTTTTACTTTATTTTAAT
Found at i:28537420 original size:20 final size:21
Alignment explanation
Indices: 28537375--28537420 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
28537365 AATAAAGAAG
*
28537375 AAATTTTTACTTTATTTTACT
1 AAATTTTTACTTTATTTTAAT
*
28537396 TAATTTTT-CTTT-TATTTAAT
1 AAATTTTTACTTTAT-TTTAAT
28537416 AAATT
1 AAATT
28537421 AAATAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.62
21 7 0.33
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
AAATTTTTACTTTATTTTAAT
Found at i:28547640 original size:13 final size:13
Alignment explanation
Indices: 28547622--28547646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28547612 TTCTTGCTAG
28547622 ATCTATCAATTAA
1 ATCTATCAATTAA
28547635 ATCTATCAATTA
1 ATCTATCAATTA
28547647 TTATTCTTTT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
ATCTATCAATTAA
Found at i:28550087 original size:110 final size:110
Alignment explanation
Indices: 28549894--28550447 Score: 813
Period size: 110 Copynumber: 5.0 Consensus size: 110
28549884 CATGGACTTA
* * *
28549894 TACATA-AGTTCATGTATCGTGATATGTCATTTCGATTCATACACTATCGAAGGCTACACCATGA
1 TACATACA-TTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGA
28549958 ATATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
65 ATATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
* * *
28550004 TACATACATTCATGTATCGTGACCTACCATTTCAATTCATACACTATTGAAGGCTACACCATGAA
1 TACATACATTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGAA
28550069 TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
66 TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
* * * * * * *
28550114 TACACACATACATGTATCATGATCTGCCATTTCGATTCATGCATTATCGAAGGCTACTCCATGAA
1 TACATACATTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGAA
* * *
28550179 TATAAATACAGACATATCATGTCATGGGTCTTAACCACATGATCT
66 TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
* * * * *
28550224 TACATGCATTTATGTATTGTGATCTGCTATTTCAATTCATACACTATCGAAGGCTACTCCATGAA
1 TACATACATTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGAA
* * *
28550289 TATAAATACAGACATATCATGTCATGGGTCTTAACCACATGGTTT
66 TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
* * * * *
28550334 TACACACATTTATTTATCGTGATCTGCTATTTAAATTCATACACTATCGAAGGCTACACCATGAA
1 TACATACATTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGAA
* *
28550399 TATAAATACAAGCATATCATGCCATGGGTCTTAACCACATGGTTT
66 TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
28550444 TACA
1 TACA
28550448 CTTGTTTTCA
Statistics
Matches: 403, Mismatches: 40, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
110 402 1.00
111 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (110 bp):
TACATACATTCATGTATCGTGATCTGCCATTTCAATTCATACACTATCGAAGGCTACACCATGAA
TATAAATACAAACATATCATGCCATGGGTCTTAACCACATGGTCT
Found at i:28551841 original size:3 final size:3
Alignment explanation
Indices: 28551833--28551857 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28551823 AAGGGAAATC
28551833 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
28551858 TTTGTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28554715 original size:98 final size:98
Alignment explanation
Indices: 28554605--28555309 Score: 1401
Period size: 98 Copynumber: 7.2 Consensus size: 98
28554595 TATATAAAAA
28554605 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28554670 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28554703 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28554768 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28554801 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28554866 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28554899 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28554964 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28554997 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28555062 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28555095 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28555160 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28555193 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
1 ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
28555258 TATGTTTTAATTTTTATCTCATTATAAAATTAT
66 TATGTTTTAATTTTTATCTCATTATAAAATTAT
28555291 ATTATGTTTTTAAATTTTA
1 ATTATG-TTTTAAATTTTA
28555310 ATACTTAATT
Statistics
Matches: 606, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
98 594 0.98
99 12 0.02
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (98 bp):
ATTATGTTTTAAATTTTATTTGTGTCATTTATAATTCTGACATTTGTTCATACTTCCGATCATAT
TATGTTTTAATTTTTATCTCATTATAAAATTAT
Found at i:28554722 original size:17 final size:17
Alignment explanation
Indices: 28554667--28554722 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28554657 CTTCCGATCA
*
28554667 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28554684 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28554702 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28554719 TATT
1 TATT
28554723 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28554820 original size:17 final size:17
Alignment explanation
Indices: 28554765--28554820 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28554755 CTTCCGATCA
*
28554765 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28554782 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28554800 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28554817 TATT
1 TATT
28554821 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28554918 original size:17 final size:17
Alignment explanation
Indices: 28554863--28554918 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28554853 CTTCCGATCA
*
28554863 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28554880 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28554898 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28554915 TATT
1 TATT
28554919 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28555016 original size:17 final size:17
Alignment explanation
Indices: 28554961--28555016 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28554951 CTTCCGATCA
*
28554961 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28554978 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28554996 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28555013 TATT
1 TATT
28555017 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28555114 original size:17 final size:17
Alignment explanation
Indices: 28555059--28555114 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28555049 CTTCCGATCA
*
28555059 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28555076 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28555094 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28555111 TATT
1 TATT
28555115 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28555212 original size:17 final size:17
Alignment explanation
Indices: 28555157--28555212 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
28555147 CTTCCGATCA
*
28555157 TATTATGTTTTAATTTT
1 TATTATGTTTTAAATTT
* * *
28555174 TATCTCAT-TATAAAATTA
1 TAT-T-ATGTTTTAAATTT
28555192 TATTATGTTTTAAATTT
1 TATTATGTTTTAAATTT
28555209 TATT
1 TATT
28555213 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATGTTTTAAATTT
Found at i:28556196 original size:22 final size:20
Alignment explanation
Indices: 28556164--28556203 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
28556154 TGAAAATGAT
*
28556164 TATATAATAAATTTGTAAAA
1 TATATAATAAATATGTAAAA
28556184 TATATAAGTTAAATATGTAA
1 TATATAA--TAAATATGTAA
28556204 GTTGGGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
TATATAATAAATATGTAAAA
Found at i:28557439 original size:14 final size:16
Alignment explanation
Indices: 28557423--28557452 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28557413 TATCGAGTTT
28557423 AAATA-ATAATTTTTA
1 AAATATATAATTTTTA
28557438 AAATATATAATTTTT
1 AAATATATAATTTTT
28557453 TTTAAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATATATAATTTTTA
Found at i:28560024 original size:42 final size:42
Alignment explanation
Indices: 28559965--28560056 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
28559955 TTTCTTGTCT
*
28559965 ACACGGCCTAAGACACGGGCGTGTGTCTCAGCAATGTATGAC
1 ACACGGCCTAAAACACGGGCGTGTGTCTCAGCAATGTATGAC
* * ** *
28560007 ACACGGCTTAAAACACGGGGGTGTGTCTCAGCCGTGTGTGAC
1 ACACGGCCTAAAACACGGGCGTGTGTCTCAGCAATGTATGAC
28560049 ACACGGCC
1 ACACGGCC
28560057 AGGTGACACG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.18
Consensus pattern (42 bp):
ACACGGCCTAAAACACGGGCGTGTGTCTCAGCAATGTATGAC
Found at i:28564110 original size:40 final size:40
Alignment explanation
Indices: 28564055--28564135 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
28564045 GGATTCTCCG
28564055 ATGCCAATTGGATATTTGATATTCAAGATACCAAAGGCAC
1 ATGCCAATTGGATATTTGATATTCAAGATACCAAAGGCAC
28564095 ATGCCAATTGGATATTTGATATTCAAGATACCAAAGGCAC
1 ATGCCAATTGGATATTTGATATTCAAGATACCAAAGGCAC
28564135 A
1 A
28564136 AGTGGATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (40 bp):
ATGCCAATTGGATATTTGATATTCAAGATACCAAAGGCAC
Found at i:28578989 original size:6 final size:7
Alignment explanation
Indices: 28578973--28578999 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28578963 ATATTAATCC
28578973 TTTTTAT
1 TTTTTAT
28578980 TTTTTAT
1 TTTTTAT
28578987 TTTTTAT
1 TTTTTAT
28578994 TTTTTA
1 TTTTTA
28579000 AAAAGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:28582794 original size:9 final size:9
Alignment explanation
Indices: 28582780--28582808 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28582770 TCATTTTTTC
28582780 TTTTTATTT
1 TTTTTATTT
28582789 TTTTTATTT
1 TTTTTATTT
28582798 TTTTT-TTT
1 TTTTTATTT
28582806 TTT
1 TTT
28582809 GGCTTCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTATTT
Found at i:28582808 original size:15 final size:15
Alignment explanation
Indices: 28582773--28582807 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28582763 CTGGGTTTCA
*
28582773 TTTTTTCTTTTTATT
1 TTTTTTATTTTTATT
28582788 TTTTTTATTTTT-TT
1 TTTTTTATTTTTATT
28582802 TTTTTT
1 TTTTTT
28582808 TGGCTTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTTATTTTTATT
Found at i:28585549 original size:18 final size:18
Alignment explanation
Indices: 28585528--28585562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28585518 AGGTATGTTT
* *
28585528 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
28585546 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
28585563 TCCTTTTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:28586088 original size:29 final size:29
Alignment explanation
Indices: 28586048--28587139 Score: 1985
Period size: 29 Copynumber: 37.6 Consensus size: 29
28586038 AAAACACTAA
*
28586048 CCTAA-CCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586076 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
28586105 CCTAACCCTAACCTAAATTATTTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
* *
28586134 CCTAACCCTAACCTAACCTAACCTAAATAAAAAC
1 CCTAACCCTAACCT-A---AA-TTAATTAAAAAC
*
28586168 CCTAACCCTAACCTAACTTAACCTT--AAAC
1 CCTAACCCTAACCTAAATTAA--TTAAAAAC
* *
28586197 CCTAGCCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
* *
28586226 CCTAATCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
28586255 CCTAA-CCTAACCTAAATTAATTAAAAAT
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
28586283 CGTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
28586312 CGTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586341 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586370 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586399 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586428 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586457 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586486 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586515 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586544 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586573 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586602 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586631 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586660 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586689 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586718 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586747 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586776 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586805 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586834 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586863 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586892 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586921 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586950 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28586979 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28587008 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28587037 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28587066 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28587095 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
28587124 CCTAACCCTAACCTAA
1 CCTAACCCTAACCTAA
28587140 CNNNNNNNNN
Statistics
Matches: 1037, Mismatches: 16, Indels: 21
0.97 0.01 0.02
Matches are distributed among these distances:
27 2 0.00
28 30 0.03
29 976 0.94
30 2 0.00
31 1 0.00
33 3 0.00
34 23 0.02
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.24
Consensus pattern (29 bp):
CCTAACCCTAACCTAAATTAATTAAAAAC
Found at i:28593725 original size:10 final size:10
Alignment explanation
Indices: 28593708--28593789 Score: 60
Period size: 10 Copynumber: 8.2 Consensus size: 10
28593698 AAAAATCAAT
28593708 AAAATTTATA
1 AAAATTTATA
*
28593718 AAATTTTAATA
1 AAAATTT-ATA
*
28593729 AAAATATATA
1 AAAATTTATA
* * *
28593739 TAAATTAGAAA
1 AAAATT-TATA
*
28593750 AAAATTTAAA
1 AAAATTTATA
*
28593760 AAAAATTAT-
1 AAAATTTATA
28593769 AAAA-TTATA
1 AAAATTTATA
*
28593778 AAATTTTATA
1 AAAATTTATA
28593788 AA
1 AA
28593790 GTCGTAAGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
8 4 0.07
9 7 0.12
10 30 0.54
11 15 0.27
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAATTTATA
Found at i:28594021 original size:13 final size:13
Alignment explanation
Indices: 28594005--28594030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28593995 ACTTTAATAA
28594005 TTAATGGTTAAAG
1 TTAATGGTTAAAG
28594018 TTAATGGTTAAAG
1 TTAATGGTTAAAG
28594031 GACCTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TTAATGGTTAAAG
Found at i:28594059 original size:10 final size:10
Alignment explanation
Indices: 28594046--28594096 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
28594036 TTTTGATGCA
28594046 TTTTATAATT
1 TTTTATAATT
*
28594056 TTTTATGA-T
1 TTTTATAATT
**
28594065 TTTTATAAAA
1 TTTTATAATT
*
28594075 TTTTACAATTT
1 TTTTATAA-TT
28594086 TTTTATAATT
1 TTTTATAATT
28594096 T
1 T
28594097 CATNNNNNNN
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 8 0.25
10 17 0.53
11 7 0.22
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:28594402 original size:25 final size:21
Alignment explanation
Indices: 28594353--28594411 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
28594343 NNNNNNNNNN
28594353 TATGTATGTTTAATAATTAAA
1 TATGTATGTTTAATAATTAAA
28594374 TATGTATGTTTAATAATTAAA
1 TATGTATGTTTAATAATTAAA
28594395 TATGTATGTTTAATAAT
1 TATGTATGTTTAATAAT
28594412 ATTAAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TATGTATGTTTAATAATTAAA
Found at i:28601274 original size:100 final size:101
Alignment explanation
Indices: 28601159--28601361 Score: 390
Period size: 100 Copynumber: 2.0 Consensus size: 101
28601149 ACATAATTTT
28601159 TTAATGTATAAAATTTTATTTTTAAAATAATTAAATATAATTTTCTTTTATTTTTAGGGTCAAAA
1 TTAATGTATAAAATTTTATTTTTAAAATAATTAAATATAATTTTCTTTTATTTTTAGGGTCAAAA
28601224 TATAATTTTACCATAAATTACTTTA-AATTTAATCA
66 TATAATTTTACCATAAATTACTTTATAATTTAATCA
*
28601259 TTAATGTATTAAATTTTATTTTTAAAATAATTAAATATAATTTTCTTTTATTTTTAGGGTCAAAA
1 TTAATGTATAAAATTTTATTTTTAAAATAATTAAATATAATTTTCTTTTATTTTTAGGGTCAAAA
28601324 TATAATTTTACCATAAATTACTTTATAATTTAATCA
66 TATAATTTTACCATAAATTACTTTATAATTTAATCA
28601360 TT
1 TT
28601362 TTAAATAGCA
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 89 0.88
101 12 0.12
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (101 bp):
TTAATGTATAAAATTTTATTTTTAAAATAATTAAATATAATTTTCTTTTATTTTTAGGGTCAAAA
TATAATTTTACCATAAATTACTTTATAATTTAATCA
Found at i:28603625 original size:43 final size:43
Alignment explanation
Indices: 28603577--28603725 Score: 192
Period size: 43 Copynumber: 3.4 Consensus size: 43
28603567 CACTACACCA
*
28603577 TCCCACAAACGCCGCTAAAGACCA-GTACCTTTAACGGCGCTTT
1 TCCCACAAACGCCGCTAAAGACCATG-ACCTTTAGCGGCGCTTT
* * *
28603620 TCCCACAAACGCCGCTATAGACCATGACCTTTAGCAGCACTTTT
1 TCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTT
* * *
28603664 TCCCGCAAACGCTGCTAAAGACCATGACCTTTAGCGACGCTTT
1 TCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTT
* *
28603707 TCACAAAAACGCCGCTAAA
1 TCCCACAAACGCCGCTAAA
28603726 AACTTATCTT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 52 0.58
44 38 0.42
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (43 bp):
TCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTT
Found at i:28608055 original size:6 final size:6
Alignment explanation
Indices: 28608017--28608063 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
28608007 AAAAATACAC
* * *
28608017 ATTTTA ATTTTA ATTTTT -TTCTT ATTATTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT-TTT ATTTTT ATTTTT ATTTT
28608064 GCAGGGAGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:28611050 original size:114 final size:114
Alignment explanation
Indices: 28610868--28611397 Score: 853
Period size: 114 Copynumber: 4.7 Consensus size: 114
28610858 CGTTTTCCAA
* * ** * * *
28610868 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACACCGTTTTCAGAGTTTTTGGGGATTTAGCGACG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
*
28610932 TTTTTAAGAAAGCGCCGCTAATGGTCAGGGCTTTAGCGGCGTTTTTGAG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* *
28610981 AAAGCGTCGCAAAAAAACATAAGTCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
*
28611046 TTTTTAAGAAAGCGCCGCTAATGGTCAGGGCTTTAGCGGCGTTTTTGAG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
28611095 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGT--G-----GGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
* *
28611153 TTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTGAG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
28611202 AAAGCGCCGC-AAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
* * *
28611266 TTTTTAAGAAAGCGCCACTAATGCTTAGTGCTTTAGCGGCGTTTTTGAG
66 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
28611315 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
28611380 TTTTTAAGAAAGCGCCGC
66 TTTTTAAGAAAGCGCCGC
28611398 AAAAAAACAT
Statistics
Matches: 390, Mismatches: 18, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
106 31 0.08
107 71 0.18
108 1 0.00
112 1 0.00
113 80 0.21
114 206 0.53
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (114 bp):
AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
Found at i:28611281 original size:220 final size:221
Alignment explanation
Indices: 28610868--28611395 Score: 799
Period size: 220 Copynumber: 2.3 Consensus size: 221
28610858 CGTTTTCCAA
* * * *
28610868 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACACCGTTTTCAGAGTTTTTGGGGATTTAGCGACG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTT----G---TGGGGGATTTAGCGGCG
* * * *
28610932 TTTTTAAGAAAGCGCCGCTAATGGTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAA
59 TTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAA
*
28610997 ACATAAGTCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCC
124 ACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCC
* *
28611062 GCTAATGGTCAGGGCTTTAGCGGCGTTTTTGAG
189 ACTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
28611095 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGGGATTTAGCGGCGTTTTTAA
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGGGATTTAGCGGCGTTTTTAA
28611160 GAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAAGCGCCGC-AAAAAACATAAG
66 GAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACATAAG
28611224 CCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATG
131 CCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATG
* *
28611289 CTTAGTGCTTTAGCGGCGTTTTTGAG
196 CTCAGGGCTTTAGCGGCGTTTTTGAG
28611315 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGT--G-----GGGGATTTAGCGGCG
28611380 TTTTTAAGAAAGCGCC
59 TTTTTAAGAAAGCGCC
28611396 GCAAAAAAAC
Statistics
Matches: 280, Mismatches: 13, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
220 140 0.50
221 70 0.25
222 1 0.00
224 1 0.00
227 41 0.15
228 27 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (221 bp):
AAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGGGATTTAGCGGCGTTTTTAA
GAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACATAAG
CCCAACGACGCCGTTTTGTGGGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATG
CTCAGGGCTTTAGCGGCGTTTTTGAG
Found at i:28611418 original size:73 final size:73
Alignment explanation
Indices: 28611297--28611470 Score: 294
Period size: 73 Copynumber: 2.4 Consensus size: 73
28611287 TGCTTAGTGC
* * *
28611297 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
**
28611362 TTTGGGGA
66 TTCAGGGA
28611370 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
28611435 TTCAGGGA
66 TTCAGGGA
*
28611443 TTTAGCGGCGTTTTTAAGAAGGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
28611471 TAATGCTTAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
TTCAGGGA
Found at i:28611426 original size:187 final size:186
Alignment explanation
Indices: 28611184--28611565 Score: 611
Period size: 187 Copynumber: 2.0 Consensus size: 186
28611174 TGCTCAGGGC
* * *
28611184 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCTT
** * * *
28611249 TTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGTGCTTTAGCGGCGTTTTTGA
66 TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCTTTAGCAGCGTTTGTGA
* *
28611314 GAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
131 GAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCTTTCGGGGA
*
28611370 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGC-AAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
* *
28611435 TTCAGGGATTTAGCGGCGTTTTTAAGAAGGCGCCGCTAATGCTTAGGGCTTTAGCAGCGTTTGTG
65 TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCTTTAGCAGCGTTTGTG
* * *
28611500 AGTAAGCGCCGCAAAAAAACCTAATCCCAACGACGCCGTTTTGTGAGCTTTCGGGGA
130 AGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCTTTCGGGGA
28611557 TTTAGCGGC
1 TTTAGCGGC
28611566 CAAAAAAATA
Statistics
Matches: 179, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
186 26 0.15
187 153 0.85
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (186 bp):
TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCTT
TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCTTTAGCAGCGTTTGTGA
GAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGCTTTCGGGGA
Found at i:28612558 original size:31 final size:31
Alignment explanation
Indices: 28612522--28612587 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
28612512 AAAACGCCGC
*
28612522 AAAATACAAGCAATAGCGGCGTTTTTTTTAA
1 AAAATACAAGCAATAGCGGCGTTTTTATTAA
28612553 AAAATACAAGCAATAGCGGCGTTTTTATTAA
1 AAAATACAAGCAATAGCGGCGTTTTTATTAA
28612584 AAAA
1 AAAA
28612588 ACGCCGCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (31 bp):
AAAATACAAGCAATAGCGGCGTTTTTATTAA
Found at i:28612676 original size:102 final size:102
Alignment explanation
Indices: 28612564--28612803 Score: 294
Period size: 100 Copynumber: 2.3 Consensus size: 102
28612554 AAATACAAGC
*
28612564 AATAGCGGCGTTTTTATTAAAAAAACGCCGCAAAAAATAAATCAATTTTA-AAAAAATCAAAAAA
1 AATAGCGGCGTTTTTATTAAAAAAACGCCACAAAAAATAAATCAA-TTTACAAAAAAT-AAAAAA
* * *
28612628 AAA-GGCATAGCAAAACGACGTCATTTTGTTCAAA-ATGA
64 AAATAGCATAGCAAAACGACGTCATTTTGCT-AAAGAAGA
* * *
28612666 AATAGCGGCG-TTTT-TTATAAAAATGCCACAAAATATAAATCAATTTACTAAAAAATAAAAAAA
1 AATAGCGGCGTTTTTATTAAAAAAACGCCACAAAAAATAAATCAATTTAC-AAAAAATAAAAAAA
* *
28612729 AATTAGCATAGCAAAACGGCGTCATTTTGCTAAAGGTAAGC
65 AA-TAGCATAGCAAAACGACGTCATTTTGCTAAA-G-AAGA
28612770 AATAGCGGCGTTTTTA-TAAAAAAACGCCACAAAA
1 AATAGCGGCGTTTTTATTAAAAAAACGCCACAAAA
28612804 TAATTTTACT
Statistics
Matches: 118, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
99 4 0.03
100 34 0.29
101 14 0.12
102 34 0.29
104 12 0.10
105 20 0.17
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.24
Consensus pattern (102 bp):
AATAGCGGCGTTTTTATTAAAAAAACGCCACAAAAAATAAATCAATTTACAAAAAATAAAAAAAA
ATAGCATAGCAAAACGACGTCATTTTGCTAAAGAAGA
Found at i:28612821 original size:102 final size:99
Alignment explanation
Indices: 28612560--28612821 Score: 269
Period size: 102 Copynumber: 2.6 Consensus size: 99
28612550 TAAAAAATAC
* * *
28612560 AAGCAATAGCGGCGTTTTTATTAAAAAAACGCCGCAAAAAATAAATCAATTTTAAAAAAATCAAA
1 AAGCAATAGCGGCGTTTTTA-TAAAAAAACG-C-CACAAAATAAATTAAATTTAAAAAAATCAAA
* *
28612625 AAAAAAGGCATAGCAAAACGACGTCATTTTGTTCAAA
63 AAAAAAAGCATAGCAAAACGACGTCATTTTGCTCAAA
* * * * * *
28612662 ATGAAATAGCGGCGTTTTT-TATAAAAATGCCACAAAATATAAATCAATTTACTAAAAAAT-AAA
1 AAGCAATAGCGGCGTTTTTATAAAAAAACGCCACAAAATA-AATTAAATTTA--AAAAAATCAAA
*
28612725 AAAAAATTAGCATAGCAAAACGGCGTCATTTTGCT-AAA
63 AAAAAA--AGCATAGCAAAACGACGTCATTTTGCTCAAA
* * *
28612763 GGTAAGCAATAGCGGCGTTTTTATAAAAAAACGCCACAAAATAATTTTACTTTAAAAAA
1 ---AAGCAATAGCGGCGTTTTTATAAAAAAACGCCACAAAATAAATTAAATTTAAAAAA
28612822 TAGCCCCCTT
Statistics
Matches: 131, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
98 8 0.06
99 8 0.06
100 17 0.13
101 10 0.08
102 46 0.35
104 24 0.18
105 18 0.14
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (99 bp):
AAGCAATAGCGGCGTTTTTATAAAAAAACGCCACAAAATAAATTAAATTTAAAAAAATCAAAAAA
AAAAGCATAGCAAAACGACGTCATTTTGCTCAAA
Found at i:28612927 original size:149 final size:149
Alignment explanation
Indices: 28612756--28613107 Score: 580
Period size: 149 Copynumber: 2.4 Consensus size: 149
28612746 GGCGTCATTT
28612756 TGCTAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAAACGCCACAAAATAATTTTACTTT-AAAA
1 TGCTAAAGGTAAGCAATAGCGGCGTTTTTAT-AAAAAACGCCACAAAATAATTTTACTTTAAAAA
* * * *
28612820 AATAGCCCCCTTTCAGCATAGTATAGCAAAACGGCGTAGTTTTGTTTAAAATGAAAATTTTTTGC
65 AATAGACCCCTTTCAGCATAGCATAACAAAACGGCGTAGTTTTCTTTAAAATGAAAATTTTTTGC
28612885 GACGTTTTTATGAAAAACGC
130 GACGTTTTTATGAAAAACGC
*
28612905 TGCTAAAGTTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTTAAAAAA
1 TGCTAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTTAAAAAA
* *
28612970 ATAGACCCCTTTCAGCATAGCATAACAAAACGGCGTAGTTTTCTTTAAAATGAAATTTTTTTGTG
66 ATAGACCCCTTTCAGCATAGCATAACAAAACGGCGTAGTTTTCTTTAAAATGAAAATTTTTTGCG
28613035 ACGTTTTTATGAAAAACGC
131 ACGTTTTTATGAAAAACGC
* * * *
28613054 CGCTAAAGGTAAGCAATAGCGGCGTTGTTAGAGAAAACGCCACAAAAATAATTT
1 TGCTAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCAC-AAAATAATTT
28613108 CACTCCATTT
Statistics
Matches: 189, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
148 28 0.15
149 151 0.80
150 10 0.05
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (149 bp):
TGCTAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTTAAAAAA
ATAGACCCCTTTCAGCATAGCATAACAAAACGGCGTAGTTTTCTTTAAAATGAAAATTTTTTGCG
ACGTTTTTATGAAAAACGC
Found at i:28613451 original size:96 final size:96
Alignment explanation
Indices: 28613346--28613538 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
28613336 AAGCTCATTC
28613346 AGTTTTTTCCTTTAAATGTTTTTGCGGGTCAAATTTTTTTACCGTCCATTTGTTCATCTACAACT
1 AGTTTTTTCCTTTAAATGTTTTTGCGGGTCAAATTTTTTTACCGTCCATTTGTTCATCTACAACT
28613411 TTTTTGATCCTGGGTTTTGTCTAATATTAAT
66 TTTTTGATCCTGGGTTTTGTCTAATATTAAT
28613442 AGTTTTTTCCTTTAAATGTTTTTGCGGGTCAAATTTTTTTACCGTCCATTTGTTCATCTACAACT
1 AGTTTTTTCCTTTAAATGTTTTTGCGGGTCAAATTTTTTTACCGTCCATTTGTTCATCTACAACT
28613507 TTTTTGATCCTGGGTTTTGTCTAATATTAAT
66 TTTTTGATCCTGGGTTTTGTCTAATATTAAT
28613538 A
1 A
28613539 AAAAAATCTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (96 bp):
AGTTTTTTCCTTTAAATGTTTTTGCGGGTCAAATTTTTTTACCGTCCATTTGTTCATCTACAACT
TTTTTGATCCTGGGTTTTGTCTAATATTAAT
Found at i:28617238 original size:81 final size:82
Alignment explanation
Indices: 28617148--28617310 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
28617138 AAATATTTAT
28617148 CATAAAAATAAATATTATTTGATTAAAATAATTTTTTTAAAGCTTATGTCTTTAGTGGCGTTTTT
1 CATAAAAATAAATATTATTTGATTAAAATAATTTTTTTAAAGCTTATGTCTTTAGTGGCGTTTTT
28617213 GCTAC-AGCGTCGCTAA
66 GCTACAAGCGTCGCTAA
28617229 CATAAAAATAAATATTATTTGATTAAAATAATTTTTTTAAAGCTTATGTCTTTAGTGGCGTTTTT
1 CATAAAAATAAATATTATTTGATTAAAATAATTTTTTTAAAGCTTATGTCTTTAGTGGCGTTTTT
28617294 GCTACAAGCGTCGCTAA
66 GCTACAAGCGTCGCTAA
28617311 AGGTCATGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 70 0.86
82 11 0.14
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (82 bp):
CATAAAAATAAATATTATTTGATTAAAATAATTTTTTTAAAGCTTATGTCTTTAGTGGCGTTTTT
GCTACAAGCGTCGCTAA
Found at i:28618049 original size:19 final size:20
Alignment explanation
Indices: 28618012--28618051 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28618002 ATTTGGCAGA
*
28618012 GATTTCGAAGGGGAGTTAGG
1 GATTTCGAAGGGGAATTAGG
*
28618032 GATTTGGAA-GGGAATTAGG
1 GATTTCGAAGGGGAATTAGG
28618051 G
1 G
28618052 CCTGGGTGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.28, C:0.03, G:0.45, T:0.25
Consensus pattern (20 bp):
GATTTCGAAGGGGAATTAGG
Found at i:28619725 original size:50 final size:50
Alignment explanation
Indices: 28619650--28619776 Score: 254
Period size: 50 Copynumber: 2.5 Consensus size: 50
28619640 NNNNNNNNNN
28619650 GACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCA
1 GACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCA
28619700 GACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCA
1 GACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCA
28619750 GACATGGTCTTACATGGGACCTCTCAT
1 GACATGGTCTTACATGGGACCTCTCAT
28619777 GATTTCAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.25
Consensus pattern (50 bp):
GACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCA
Found at i:28620185 original size:30 final size:30
Alignment explanation
Indices: 28620150--28620206 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28620140 CCTCGACTCT
*
28620150 AACTTTTTCAAAATTACAATTTTGCCCTTA
1 AACTTTTACAAAATTACAATTTTGCCCTTA
* *
28620180 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
28620207 CAAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCTTA
Found at i:28621826 original size:7 final size:7
Alignment explanation
Indices: 28621816--28621855 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
28621806 AATTAAAAAA
28621816 TAAACCC
1 TAAACCC
28621823 TAAACCC
1 TAAACCC
28621830 TAAACCC
1 TAAACCC
28621837 TAAACCC
1 TAAACCC
28621844 TAAACCC
1 TAAACCC
28621851 TAAAC
1 TAAAC
28621856 AGCTAAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.45, C:0.40, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:28622044 original size:20 final size:20
Alignment explanation
Indices: 28622009--28622047 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28621999 AAAGCCTTAA
*
28622009 ACCCTAAACCATAAATATAC
1 ACCCTAAACCAGAAATATAC
*
28622029 ACCCTAAACCCGAAATATA
1 ACCCTAAACCAGAAATATA
28622048 GATATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.31, G:0.03, T:0.18
Consensus pattern (20 bp):
ACCCTAAACCAGAAATATAC
Found at i:28622122 original size:13 final size:13
Alignment explanation
Indices: 28622104--28622131 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28622094 ATCTCCAAAT
28622104 CCCAAACCCTAAA
1 CCCAAACCCTAAA
28622117 CCCAAACCCTAAA
1 CCCAAACCCTAAA
28622130 CC
1 CC
28622132 ATACACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.50, G:0.00, T:0.07
Consensus pattern (13 bp):
CCCAAACCCTAAA
Found at i:28623055 original size:41 final size:41
Alignment explanation
Indices: 28622910--28623267 Score: 335
Period size: 41 Copynumber: 8.7 Consensus size: 41
28622900 AAATGTTTTT
*
28622910 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * * * * *
28622951 GCAGC-ATTTTCCAAGAAGCACCGCTATAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAA-AAACGCCGCTAAAGGCCCGAGCATTA
* * * * * * *
28622992 GCAGC-ATTTTCCAAGAAGCGCTGCTATAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAA-AAACGCCGCTAAAGGCCCGAGCATTA
* **
28623033 GCGGCGCTTTTTCAAAAACGCTGCTAAATCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * **
28623074 GCGGTGTTTTTTTGGAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCG-CTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * *
28623116 GTGGCGCTTTTTCAAAAACGTCGCTAAAGGACCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * * ** *
28623157 GCGGCACTTTTTTAAAAACGCCACTAAAGACTGGAGCATTG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
28623198 GTGCCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
28623239 GCGGCGC-TTTTCTAAAAGCGCCACTAAAG
1 GCGGCGCTTTTTC-AAAAACGCCGCTAAAG
28623268 CCTCGAAAGG
Statistics
Matches: 260, Mismatches: 53, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
40 12 0.05
41 208 0.80
42 40 0.15
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
Found at i:28624562 original size:3 final size:3
Alignment explanation
Indices: 28624554--28624582 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28624544 TGGCGATGGC
28624554 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
28624583 GCCGAAACCC
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:28626161 original size:86 final size:86
Alignment explanation
Indices: 28626016--28626273 Score: 471
Period size: 86 Copynumber: 3.0 Consensus size: 86
28626006 CATCCTAGGC
*
28626016 CTATCTCTCGTACATGGATGTGTCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
1 CTATCTCTCGTACATGGATGTGCCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
28626081 TACATGACTTGAATGTCCAAA
66 TACATGACTTGAATGTCCAAA
* * *
28626102 CTATCTCTCATACATGGATTTGCCATCAATTTGGACTATTAGCTTACAATACCAAAATGCTTCAA
1 CTATCTCTCGTACATGGATGTGCCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
28626167 TACATGACTTGAATGTCCAAA
66 TACATGACTTGAATGTCCAAA
28626188 CTATCTCTCGTACATGGATGTGCCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
1 CTATCTCTCGTACATGGATGTGCCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
*
28626253 TACATTACTTGAATGTCCAAA
66 TACATGACTTGAATGTCCAAA
28626274 AAAGACTATG
Statistics
Matches: 164, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 164 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (86 bp):
CTATCTCTCGTACATGGATGTGCCATCAATTTGGACTATTAGCTTACAGTACCAAAATGCTTCAA
TACATGACTTGAATGTCCAAA
Found at i:28628233 original size:18 final size:18
Alignment explanation
Indices: 28628189--28628238 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
28628179 ATTATCGGTT
28628189 TCAACTTCCTCTTCGTTC
1 TCAACTTCCTCTTCGTTC
** *
28628207 TCATTTTCCTCTTTGTTC
1 TCAACTTCCTCTTCGTTC
*
28628225 TCAACTTCCCCTTC
1 TCAACTTCCTCTTC
28628239 ATTATCAACC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.10, C:0.38, G:0.04, T:0.48
Consensus pattern (18 bp):
TCAACTTCCTCTTCGTTC
Found at i:28629773 original size:9 final size:9
Alignment explanation
Indices: 28629756--28629792 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28629746 TGAGTTTTCA
28629756 AATTCGAAT
1 AATTCGAAT
*
28629765 AACTCGAAT
1 AATTCGAAT
28629774 AATTCGAAT
1 AATTCGAAT
28629783 AATTCGAAT
1 AATTCGAAT
28629792 A
1 A
28629793 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28629905 original size:28 final size:28
Alignment explanation
Indices: 28629845--28629900 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
28629835 CTTTTTATTT
* *
28629845 TTCCCTCAAAACTTTTACTTCTTCCCAC
1 TTCCCTCAAAACTTTTACTCCCTCCCAC
28629873 TTCCCTCCAAAACTTTTACTCCCCTCCC
1 TTCCCT-CAAAACTTTTACT-CCCTCCC
28629901 CTCCCCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 13 0.54
30 5 0.21
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.36
Consensus pattern (28 bp):
TTCCCTCAAAACTTTTACTCCCTCCCAC
Found at i:28636767 original size:13 final size:13
Alignment explanation
Indices: 28636749--28636775 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28636739 GAGGGGAAAA
28636749 AATATTTTGTTTT
1 AATATTTTGTTTT
28636762 AATATTTTGTTTT
1 AATATTTTGTTTT
28636775 A
1 A
28636776 CCGCTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (13 bp):
AATATTTTGTTTT
Found at i:28638630 original size:19 final size:21
Alignment explanation
Indices: 28638608--28638654 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
28638598 AAAAAACTTA
28638608 TATATTAATTAAA-A-TTTAC
1 TATATTAATTAAATATTTTAC
*
28638627 TATATTTATTAAATATTTTAC
1 TATATTAATTAAATATTTTAC
28638648 TATATTA
1 TATATTA
28638655 TTGAAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 1 0.04
21 11 0.46
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTAATTAAATATTTTAC
Found at i:28638714 original size:27 final size:28
Alignment explanation
Indices: 28638654--28638721 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 28
28638644 TTACTATATT
*
28638654 ATTGAAGTAATATGAATATACATATTACAT
1 ATTGAA-TAATATGAATATA-ATATTACAC
28638684 ATTGAATAATATGAATAT-ATATTACAC
1 ATTGAATAATATGAATATAATATTACAC
28638711 ATTGAATAATA
1 ATTGAATAATA
28638722 ATTATATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 19 0.51
29 12 0.32
30 6 0.16
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (28 bp):
ATTGAATAATATGAATATAATATTACAC
Found at i:28639253 original size:17 final size:18
Alignment explanation
Indices: 28639231--28639264 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28639221 GTAGTTGATT
*
28639231 TAGATATTG-ATATTAAC
1 TAGATAATGAATATTAAC
28639248 TAGATAATGAATATTAA
1 TAGATAATGAATATTAA
28639265 TTAGGGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (18 bp):
TAGATAATGAATATTAAC
Found at i:28640127 original size:18 final size:18
Alignment explanation
Indices: 28640027--28640132 Score: 61
Period size: 18 Copynumber: 5.6 Consensus size: 18
28640017 CATTAAAACG
28640027 TATAAAAATAGAAATAAATA
1 TATAAAAATA-AAA-AAATA
* ** *
28640047 TATAAAAGTTCACAAATA
1 TATAAAAATAAAAAAATA
* * * *
28640065 TATATAATATCTAGAAAACA
1 TATA-AAAAT-AAAAAAATA
* *
28640085 TATAAATTATAAAAAAATT
1 TATAAA-AATAAAAAAATA
28640104 TATAAAAATAAAAAAATA
1 TATAAAAATAAAAAAATA
28640122 -ATTAAAAATAA
1 TA-TAAAAATAA
28640133 TTAAAATATT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
17 1 0.02
18 28 0.42
19 17 0.26
20 20 0.30
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (18 bp):
TATAAAAATAAAAAAATA
Found at i:28640138 original size:21 final size:20
Alignment explanation
Indices: 28640088--28640138 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
28640078 GAAAACATAT
*
28640088 AAATTATAAAAAAATTTATAA
1 AAATTA-AAAAAAATTTAAAA
*
28640109 AAA-TAAAAAAATAATTAAAA
1 AAATTAAAAAAA-ATTTAAAA
28640129 ATAATTAAAA
1 A-AATTAAAA
28640139 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 5 0.20
22 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATTAAAAAAAATTTAAAA
Found at i:28640140 original size:9 final size:10
Alignment explanation
Indices: 28640106--28640138 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
28640096 AAAAAATTTA
28640106 TAAAAATAA-
1 TAAAAATAAT
28640115 -AAAAATAAT
1 TAAAAATAAT
28640124 TAAAAATAAT
1 TAAAAATAAT
28640134 TAAAA
1 TAAAA
28640139 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:28660942 original size:129 final size:129
Alignment explanation
Indices: 28660739--28661008 Score: 405
Period size: 129 Copynumber: 2.1 Consensus size: 129
28660729 TTGACAGTGA
* **
28660739 AGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAAGGATC
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATC
***
28660804 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTATCTCCCTGAGATTACAGCGG
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGATCTTATCTCCCTGAGATTACAGCGG
* *
28660868 AGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTATAGTGGAGTGGATTAAAACCAAGGATC
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATC
* * * * *
28660933 TTATCTCTCTGAAGTTATAGTAGAGTAGATCGCACCAGGTCTTATTTCTCTGAGATTACAGTGG
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGATCTTATCTCCCTGAGATTACAGCGG
* *
28660997 AACAGACTGAAG
1 AGCAGATTGAAG
28661009 AATTTCAGAT
Statistics
Matches: 126, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (129 bp):
AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATC
TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGATCTTATCTCCCTGAGATTACAGCGG
Found at i:28661046 original size:175 final size:175
Alignment explanation
Indices: 28660838--28661183 Score: 548
Period size: 175 Copynumber: 2.0 Consensus size: 175
28660828 GTAGATCGTG
* *
28660838 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
28660903 TTATAGTGGAGTGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCAC
66 TTACAGTAGAGTGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
* * *
28660968 CAGGTCTTATTTCTCTGAGATTACAGTGGAACAGACTGAAGAATT
131 CAGGTCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAGAATT
28661013 TCAGATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* ** **
28661078 TTACAGTAGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGT
66 TTACAGTAGAGTGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
* * *
28661143 TAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
131 CAGGTCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAG
28661184 CTAGTAATCC
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
175 155 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (175 bp):
TCAGATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTAGAGTGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
CAGGTCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAGAATT
Found at i:28661168 original size:129 final size:129
Alignment explanation
Indices: 28661020--28661396 Score: 691
Period size: 129 Copynumber: 2.9 Consensus size: 129
28661010 ATTTCAGATA
28661020 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
28661085 AGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTTAGGTC
66 AGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGGTC
28661149 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
28661214 GGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGGTC
66 AGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGGTC
* * *
28661278 TTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGTTAGTAATCCTATCTTCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
* *
28661343 AGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
66 AGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
28661397 NNNNNNNNNN
Statistics
Matches: 240, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 240 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (129 bp):
TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
AGAGTGGATTGAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGGTC
Found at i:28661292 original size:304 final size:304
Alignment explanation
Indices: 28660739--28661297 Score: 974
Period size: 304 Copynumber: 1.8 Consensus size: 304
28660729 TTGACAGTGA
* *
28660739 AGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAAGGATC
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTAGAGTGGATTAAAATGAAGGATC
*
28660804 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTATCTCCCTGAGATTACAGCGGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGATCTTATCTCCCTGAGATTACAGCGGA
* *
28660869 GCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTATAGTGGAGTGGATTAAAACCAAGGATCT
131 GCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATCT
* * *
28660934 TATCTCTCTGAAGTTATAGTAGAGTAGATCGCACCAGGTCTTATTTCTCTGAGATTACAGTGGAA
196 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGAA
28660999 CAGACTGAAGAATTTCAGATATTATCTCCCTGAGATTACAGCGG
261 CAGACTGAAGAATTTCAGATATTATCTCCCTGAGATTACAGCGG
*
28661043 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTAGAGTGGATTGAAATGAAGGATC
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTAGAGTGGATTAAAATGAAGGATC
* *
28661108 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTTAGGTCTTATCTCCCTGAGATTACAGCGGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGATCTTATCTCCCTGAGATTACAGCGGA
* **
28661173 GCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTGAAATGAAGGATCT
131 GCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATCT
**
28661238 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGGTCTTATCTCCCTGAGATTACAG
196 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAG
28661298 CGGAGCAAAT
Statistics
Matches: 239, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
304 239 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (304 bp):
AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTAGAGTGGATTAAAATGAAGGATC
TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAGATCTTATCTCCCTGAGATTACAGCGGA
GCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAACCAAGGATCT
TATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGAA
CAGACTGAAGAATTTCAGATATTATCTCCCTGAGATTACAGCGG
Found at i:28661371 original size:44 final size:44
Alignment explanation
Indices: 28660757--28661395 Score: 320
Period size: 44 Copynumber: 14.8 Consensus size: 44
28660747 GAAGCTAGTA
* * *
28660757 ATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
* * *
28660801 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG---TGTCA-G
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATTGAAATG-AAGG
** * * * *
28660842 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGT-TAGTA
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAG-G
* * * * * **
28660886 ATCCTATCTCCCTGAGATTATAGTGGAGTGGATTAAAACCAAGG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
* * * * **
28660930 ATCTTATCTCTCTGA-AGTTATAGTAGAGTAGATCG-CA-CCAGG
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATTGAAATGAAGG
* * * ** * **
28660972 -TCTTATTTCTCTGAGATTACAGTGGAACAGACTGAAGAATTTCA-G
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTG-A-AA-TGAAGG
* ** * * *
28661017 ATATTATCTCCCTGAGATTACAGCGGAGCAGATTG-AA-GCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATG-AAG-G
* *
28661061 ATCCTATCTCCCTGAGATTACAGTAGAGTGGATTGAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
* * ** *
28661105 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-CGT-TAGG
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATTGAAATGAAGG
** * * *
28661147 -TCTTATCTCCCTGAGATTACAGCGGAGCAGATTG-AA-GCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATG-AAG-G
* * *
28661190 ATCCTATCTCCCTGAGATTACAGTGGAGTGGATTGAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
* * ** *
28661234 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-CGT-CAGG
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATTGAAATGAAGG
** * * * * *
28661276 -TCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGT-TAGTA
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAG-G
* * * *
28661319 ATCCTATCTTCCTGAGATTACAGTAGAGTGGATTAAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
* *
28661363 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGAT
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGAT
28661396 CNNNNNNNNN
Statistics
Matches: 447, Mismatches: 111, Indels: 74
0.71 0.18 0.12
Matches are distributed among these distances:
41 109 0.24
42 24 0.05
43 10 0.02
44 259 0.58
45 13 0.03
46 32 0.07
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAATGAAGG
Found at i:28663133 original size:50 final size:50
Alignment explanation
Indices: 28663075--28663176 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
28663065 TTTTTTTTTC
28663075 AAAGGGAAAAGAAAGAATGAAGATTTTTTTAAAAAAAATTGGGTTTAAAT
1 AAAGGGAAAAGAAAGAATGAAGATTTTTTTAAAAAAAATTGGGTTTAAAT
*
28663125 AAAGGGAAAAGAAAGAATGAAGATTTTTTTAAAAAAATTTGGGTTTAAAT
1 AAAGGGAAAAGAAAGAATGAAGATTTTTTTAAAAAAAATTGGGTTTAAAT
28663175 AA
1 AA
28663177 CCCCATAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (50 bp):
AAAGGGAAAAGAAAGAATGAAGATTTTTTTAAAAAAAATTGGGTTTAAAT
Found at i:28663308 original size:55 final size:55
Alignment explanation
Indices: 28663241--28663349 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
28663231 TTTTGGCCTT
*
28663241 GACCCGCGCGGTGACCCGACCCAGAGGGGAGGATCTGCGTGTTTTCTTAAAGGGA
1 GACCCGCGCGGTGACCCGACCCAGAGGGGAGGATCCGCGTGTTTTCTTAAAGGGA
*
28663296 GACCCGCTCGGTGACCCGACCCAGAGGGGAGGATCCGCGTGTTTTCTTAAAGGG
1 GACCCGCGCGGTGACCCGACCCAGAGGGGAGGATCCGCGTGTTTTCTTAAAGGG
28663350 GGTATTTACG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.18
Consensus pattern (55 bp):
GACCCGCGCGGTGACCCGACCCAGAGGGGAGGATCCGCGTGTTTTCTTAAAGGGA
Found at i:28663664 original size:3 final size:3
Alignment explanation
Indices: 28663656--28663720 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
28663646 GTATTATCAT
*
28663656 TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA TGTA -TA TTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA
*
28663701 TTA CTTA TCA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA TTA T
28663721 GTGATAGCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 3 0.06
3 44 0.83
4 6 0.11
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Done.