Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 13 of 292
Found at i:3640439 original size:3 final size:3
Alignment explanation
Indices: 3640431--3640500 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
3640421 ATACCATATG
* * *
3640431 TAT TAT TAT CAT T-T TA- TAC TAT TAT TAT T-T ACAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
3640474 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3640501 CGTTTTCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.09
3 52 0.90
4 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3641891 original size:26 final size:25
Alignment explanation
Indices: 3641862--3641946 Score: 116
Period size: 26 Copynumber: 3.3 Consensus size: 25
3641852 TGGTACAAAT
3641862 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATG-GTTAGGTAAATGTTCCA
* *
3641888 TGATAATGGATTAGGTAAATATTCAA
1 TGATAATGG-TTAGGTAAATGTTCCA
3641914 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
3641940 TTATAAT
1 TGATAAT
3641947 AATGATAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.02
26 49 0.94
27 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:3641957 original size:61 final size:61
Alignment explanation
Indices: 3641887--3642007 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
3641877 TAAATGTTCC
*
3641887 ATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTAGGTAAATGTTCCATTATAATA
1 ATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTAGGTAAATGTTCCATGATAATA
*
3641948 ATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAAT
1 ATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTAGGTAAATGTTCCATGATAAT
3642008 GGTTTAGGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.36
Consensus pattern (61 bp):
ATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTAGGTAAATGTTCCATGATAATA
Found at i:3641963 original size:35 final size:35
Alignment explanation
Indices: 3641912--3641981 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3641902 GTAAATATTC
* * *
3641912 AATGATAATGGGTTAGGTAAATGTTCCATTATAAT
1 AATGATAATGGATTAGGTAAATATTCCATGATAAT
3641947 AATGATAATGGATTAGGTAAATATTCCATGATAAT
1 AATGATAATGGATTAGGTAAATATTCCATGATAAT
3641982 GGGTTAGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (35 bp):
AATGATAATGGATTAGGTAAATATTCCATGATAAT
Found at i:3641974 original size:87 final size:87
Alignment explanation
Indices: 3641862--3642027 Score: 271
Period size: 87 Copynumber: 1.9 Consensus size: 87
3641852 TGGTACAAAT
*
3641862 TGATAATGTGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTA
1 TGATAATGTGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTA
3641927 GGTAAATGTTCCATTATAATAA
66 GGTAAATGTTCCATTATAATAA
* * * *
3641949 TGATAATG-GATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTT
1 TGATAATGTG-TTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCAATGATAATGGGTT
3642013 AGGTAAATGTTCCAT
65 AGGTAAATGTTCCAT
3642028 GATGGGCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 72 0.99
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (87 bp):
TGATAATGTGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCAATGATAATGGGTTA
GGTAAATGTTCCATTATAATAA
Found at i:3641988 original size:26 final size:26
Alignment explanation
Indices: 3641948--3642030 Score: 139
Period size: 26 Copynumber: 3.2 Consensus size: 26
3641938 CATTATAATA
*
3641948 ATGATAATGGATTAGGTAAATATTCC
1 ATGATAATGGATTAGGTAAATGTTCC
*
3641974 ATGATAATGGGTTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
*
3642000 ATGATAATGGTTTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
3642026 ATGAT
1 ATGAT
3642031 GGGCATTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
ATGATAATGGATTAGGTAAATGTTCC
Found at i:3644061 original size:137 final size:137
Alignment explanation
Indices: 3643815--3644101 Score: 511
Period size: 137 Copynumber: 2.1 Consensus size: 137
3643805 GAGTAGTCTC
3643815 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
3643880 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
3643945 ACTGTTA
131 ACTGTTA
* *
3643952 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCTTATGGGTCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
3644017 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAATAGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
3644082 ACTGTTA
131 ACTGTTA
**
3644089 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3644102 AGGCCCAATA
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 143 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
ACTGTTA
Found at i:3649128 original size:26 final size:25
Alignment explanation
Indices: 3649099--3649261 Score: 211
Period size: 26 Copynumber: 6.2 Consensus size: 25
3649089 TGGTACAAAT
3649099 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATG-GTTAGGTAAATGTTCCA
*
3649125 TGATAATGGATTAGGTAAATATT-CA
1 TGATAATGG-TTAGGTAAATGTTCCA
3649150 TGATAATGGGTTAGGTAAATGTTCCATGATA
1 TGATAAT-GGTTAGGTAAATGTTCC-----A
*
3649181 TGATAATGGTTAGGTAAATATTCCA
1 TGATAATGGTTAGGTAAATGTTCCA
3649206 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
3649232 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
3649258 TGAT
1 TGAT
3649262 GGGCATTTCA
Statistics
Matches: 123, Mismatches: 4, Indels: 20
0.84 0.03 0.14
Matches are distributed among these distances:
25 32 0.26
26 67 0.54
30 16 0.13
31 8 0.07
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:3649163 original size:51 final size:51
Alignment explanation
Indices: 3649099--3649261 Score: 238
Period size: 56 Copynumber: 3.1 Consensus size: 51
3649089 TGGTACAAAT
*
3649099 TGATAATGTGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT-CA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGG-TTAGGTAAATATTCCA
3649150 TGATAATGGGTTAGGTAAATGTTCCATGATATGATAATGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCC-----ATGATAATGGTTAGGTAAATATTCCA
*
3649206 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGG-TTAGGTAAATATTCCA
3649258 TGAT
1 TGAT
3649262 GGGCATTTCA
Statistics
Matches: 103, Mismatches: 2, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
51 34 0.33
52 19 0.18
55 13 0.13
56 37 0.36
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (51 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATATTCCA
Found at i:3652340 original size:35 final size:35
Alignment explanation
Indices: 3652313--3652478 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
3652303 CATGGCAAAG
*
3652313 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
3652348 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
3652383 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
3652423 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
3652458 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
3652479 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:3652432 original size:75 final size:75
Alignment explanation
Indices: 3652313--3652483 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
3652303 CATGGCAAAG
** *
3652313 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
3652372 CCATACTGAGC
65 CCATACCGAGC
3652383 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
3652448 CATACCGAGT
66 CATACCGAGC
**
3652458 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
3652484 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:3653939 original size:136 final size:137
Alignment explanation
Indices: 3653695--3653980 Score: 493
Period size: 136 Copynumber: 2.1 Consensus size: 137
3653685 GAGTAGTCTC
3653695 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCATAC
*
3653760 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGG-CCAGTACC
66 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
3653824 ACTGTTA
131 ACTGTTA
* * *
3653831 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCTTATGGGTCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCATAC
* *
3653896 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAATAGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
3653961 ACTGTTA
131 ACTGTTA
**
3653968 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3653981 AGGCCCAATA
Statistics
Matches: 141, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
136 115 0.82
137 26 0.18
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGACTAAGGCCCAGTTTATTGTAATCTGAAAAGAGCTCTGGCCCAGTACC
ACTGTTA
Found at i:3654935 original size:35 final size:35
Alignment explanation
Indices: 3654896--3654983 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 35
3654886 TTAAGCCCCC
*
3654896 AAAAAACTAACCAAAAAAAAAAAAGAAGAAAAAAG
1 AAAAACCTAACCAAAAAAAAAAAAGAAGAAAAAAG
*
3654931 AAAAACCTAACC---CAAAAAAAAGAAGAAAAAAG
1 AAAAACCTAACCAAAAAAAAAAAAGAAGAAAAAAG
3654963 AAAAACCTAA-CAAAAAAAAAA
1 AAAAACCTAACCAAAAAAAAAA
3654984 CTAAAAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 1 0.02
32 29 0.62
34 6 0.13
35 11 0.23
ACGTcount: A:0.77, C:0.12, G:0.07, T:0.03
Consensus pattern (35 bp):
AAAAACCTAACCAAAAAAAAAAAAGAAGAAAAAAG
Found at i:3655268 original size:13 final size:13
Alignment explanation
Indices: 3655250--3655292 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3655240 TTCTTTCGAA
3655250 TCTTTTTTTTCTT
1 TCTTTTTTTTCTT
* *
3655263 TCTTTTTTGT-GT
1 TCTTTTTTTTCTT
*
3655275 TGTTTTTTTTCTT
1 TCTTTTTTTTCTT
3655288 TCTTT
1 TCTTT
3655293 ATATATACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (13 bp):
TCTTTTTTTTCTT
Found at i:3655796 original size:3 final size:3
Alignment explanation
Indices: 3655745--3655780 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3655735 TTATTGTAGA
3655745 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3655781 ATCATACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3666886 original size:42 final size:42
Alignment explanation
Indices: 3666818--3667020 Score: 130
Period size: 42 Copynumber: 4.7 Consensus size: 42
3666808 TATCATCAGC
*
3666818 CTTATCTTCACTAAGCAGGAGTGGAGCAGGTTATAGACTAGAT
1 CTTATCTTCACTGA-CAGGAGTGGAGCAGGTTATAGACTAGAT
*
3666861 CTTATCTTCACTGACAGGAGTGGAGCAGATCGAATT-TTGA-T-GAAT
1 CTTATCTTCACTGACAGGAGTGGAGCAG---G--TTATAGACTAG-AT
* * * * ** *
3666906 CTTATCTCCAC-GTACCGGCGATGGAGCAGATTCCA-ATCATCAG-C
1 CTTATCTTCACTG-ACAGGAG-TGGAGCAGGTTATAGA-C-T-AGAT
* * * *
3666950 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACCAGAT
1 CTTATCTTCACTGA-CAGGAGTGGAGCAGGTTATAGACTAGAT
3666993 CTTATCTTCACTGACAGGAGTGGAGCAG
1 CTTATCTTCACTGACAGGAGTGGAGCAG
3667021 ATCGAATTTT
Statistics
Matches: 124, Mismatches: 18, Indels: 37
0.69 0.10 0.21
Matches are distributed among these distances:
41 3 0.02
42 30 0.24
43 27 0.22
44 25 0.20
45 25 0.20
46 12 0.10
47 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (42 bp):
CTTATCTTCACTGACAGGAGTGGAGCAGGTTATAGACTAGAT
Found at i:3667046 original size:132 final size:132
Alignment explanation
Indices: 3666809--3667177 Score: 648
Period size: 132 Copynumber: 2.8 Consensus size: 132
3666799 GATTACAGAT
* * * *
3666809 ATCATCAGCCTTATCTTCACTAAGCAGGAGTGGAGCAGGTTATAGACTAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
3666874 ACAGGAGTGGAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC
66 ACAGGAGTGGAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC
3666939 CA
131 CA
*
3666941 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACCAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
*
3667006 ACAGGAGTGGAGCAGATCGAATTTTGATGAATTTTATCTCCACGTACCGGCGATGGAGCAGATTC
66 ACAGGAGTGGAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC
3667071 CA
131 CA
* *
3667073 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCGAAATACTAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
*
3667138 AACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT
66 -ACAGGAGTGGAGCAGATCGAATTTTGATGAATCTTATCT
3667178 TCGCTGAGCA
Statistics
Matches: 225, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
132 188 0.84
133 37 0.16
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (132 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
ACAGGAGTGGAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATTC
CA
Found at i:3667190 original size:46 final size:44
Alignment explanation
Indices: 3666818--3667211 Score: 229
Period size: 43 Copynumber: 8.9 Consensus size: 44
3666808 TATCATCAGC
* * * ***
3666818 CTTATCTTCACTAAGCAGGAGTGGAGCAGGT-TATAGACT-AGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGA-ATTTTGAGAT
3666861 CTTATCTTCACTGA-CAGGAGTGGAGCAGATCGAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGAATTTTGA-G-AT
* * * * ** * *
3666906 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCATCAG-C
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGA-TCGAATTTTGAGAT
* * *****
3666950 CTTATCTTCACTGAGCAGGAGTGGAGCAG-GCTAAACACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGAATTTTGAGAT
3666993 CTTATCTTCACTGA-CAGGAGTGGAGCAGATCGAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGAATTTTGA-G-AT
* * * * * ** * *
3667038 TTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCATCAG-C
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGA-TCGAATTTTGAGAT
* **
3667082 CTTATCTTCACTGAGCAGGAGTGGAGCAG-GCGAAATACT-AGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCG-AATTTTGAGAT
* *
3667125 CTTATCTTCACTGAACAGGAGTGAAGCAGATCGAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGAATTTTGA-G-AT
* *
3667171 CTTATCTTCGCTGAGCAGGAGCGGAGCAGATTCGAATTTTG
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGA-TCGAATTTTG
3667212 GTCTCCCTAT
Statistics
Matches: 270, Mismatches: 56, Indels: 46
0.73 0.15 0.12
Matches are distributed among these distances:
42 42 0.16
43 68 0.25
44 44 0.16
45 44 0.16
46 48 0.18
47 24 0.09
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGATCGAATTTTGAGAT
Found at i:3673817 original size:11 final size:13
Alignment explanation
Indices: 3673791--3673885 Score: 52
Period size: 12 Copynumber: 8.1 Consensus size: 13
3673781 ATAGGGTCTC
3673791 CAAATTCACATTT
1 CAAATTCACATTT
3673804 CAAA-TCAC-TTT
1 CAAATTCACATTT
3673815 C-AATGTCA-ATTT
1 CAAAT-TCACATTT
**
3673827 CACTTTCA-A-TT
1 CAAATTCACATTT
*
3673838 CAAATTCACAATT
1 CAAATTCACATTT
3673851 C-AATTCA-ATTCT
1 CAAATTCACATT-T
*
3673863 C--ATT--CAGTT
1 CAAATTCACATTT
3673872 CAAATTCACATTT
1 CAAATTCACATTT
3673885 C
1 C
3673886 CACTTTCTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 20 0.32
12 24 0.38
13 13 0.21
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (13 bp):
CAAATTCACATTT
Found at i:3673829 original size:18 final size:17
Alignment explanation
Indices: 3673808--3673860 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
3673798 ACATTTCAAA
3673808 TCACTTTCAATGTCAATT
1 TCACTTTCAAT-TCAATT
*
3673826 TCACTTTCAATTCAAAT
1 TCACTTTCAATTCAATT
*
3673843 TCACAATTCAATTCAATT
1 TCAC-TTTCAATTCAATT
3673861 CTCATTCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (17 bp):
TCACTTTCAATTCAATT
Found at i:3673840 original size:34 final size:34
Alignment explanation
Indices: 3673802--3673885 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
3673792 AAATTCACAT
3673802 TTCAAA-TCAC-TTTCAATGTCAATT-TCACTTTCAA
1 TTCAAATTCACATTTCAAT-TCAATTCTCA--TTCAA
* *
3673836 TTCAAATTCACAATTCAATTCAATTCTCATTCAG
1 TTCAAATTCACATTTCAATTCAATTCTCATTCAA
3673870 TTCAAATTCACATTTC
1 TTCAAATTCACATTTC
3673886 CACTTTCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 25 0.57
35 10 0.23
36 9 0.20
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (34 bp):
TTCAAATTCACATTTCAATTCAATTCTCATTCAA
Found at i:3673861 original size:17 final size:17
Alignment explanation
Indices: 3673802--3673883 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
3673792 AAATTCACAT
*
3673802 TTCAAA-TCACTTTCAA
1 TTCAAATTCACATTCAA
* *
3673818 TGTCAATTTCACTTTCAA
1 T-TCAAATTCACATTCAA
3673836 TTCAAATTCACAATTCAA
1 TTCAAATTCAC-ATTCAA
* *
3673854 TTC-AATTCTCATTCAG
1 TTCAAATTCACATTCAA
3673870 TTCAAATTCACATT
1 TTCAAATTCACATT
3673884 TCCACTTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 9 0.16
17 28 0.50
18 19 0.34
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (17 bp):
TTCAAATTCACATTCAA
Found at i:3674034 original size:15 final size:16
Alignment explanation
Indices: 3674014--3674046 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3674004 ATTCATAAAC
3674014 TAATTC-ATTTTTATT
1 TAATTCAATTTTTATT
3674029 TAATTCATATTTTTATT
1 TAATTCA-ATTTTTATT
3674046 T
1 T
3674047 CATTTTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTCAATTTTTATT
Found at i:3675126 original size:23 final size:23
Alignment explanation
Indices: 3675093--3675149 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
3675083 TTGGTATGTT
*
3675093 GCCTATGTGGCGTGA-TCTGCTA-A
1 GCCTTTGTGGCGT-ATTCTG-TATA
*
3675116 GCCTTTTTGGCGTATTCTGTATA
1 GCCTTTGTGGCGTATTCTGTATA
3675139 GCCTTTGTGGC
1 GCCTTTGTGGC
3675150 AAGTTCTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.39
Consensus pattern (23 bp):
GCCTTTGTGGCGTATTCTGTATA
Found at i:3679412 original size:20 final size:20
Alignment explanation
Indices: 3679387--3679480 Score: 99
Period size: 20 Copynumber: 4.8 Consensus size: 20
3679377 AAAAAAAAAG
*
3679387 AAATTGGGAAGAAGAAAGGA
1 AAATTGGGAAAAAGAAAGGA
3679407 AAATTGGGAAAAAG-AAGAGA
1 AAATTGGGAAAAAGAAAG-GA
*
3679427 AACA-AGGGAAAAA-AAA-G-
1 AA-ATTGGGAAAAAGAAAGGA
*
3679444 AAATTGGGAAGAAGAAAGGAA
1 AAATTGGGAAAAAGAAAGG-A
3679465 AAATTGGGAAAAAGAA
1 AAATTGGGAAAAAGAA
3679481 GAGAAACAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
16 1 0.02
17 9 0.15
18 4 0.07
19 4 0.07
20 27 0.44
21 16 0.26
ACGTcount: A:0.61, C:0.01, G:0.30, T:0.09
Consensus pattern (20 bp):
AAATTGGGAAAAAGAAAGGA
Found at i:3679440 original size:58 final size:58
Alignment explanation
Indices: 3679378--3679489 Score: 217
Period size: 57 Copynumber: 1.9 Consensus size: 58
3679368 TGTTTAGCAA
3679378 AAAAAAAAGAAATTGGGAAGAAGAAAGG-AAAATTGGGAAAAAGAAGAGAAACAAGGG
1 AAAAAAAAGAAATTGGGAAGAAGAAAGGAAAAATTGGGAAAAAGAAGAGAAACAAGGG
3679435 AAAAAAAAGAAATTGGGAAGAAGAAAGGAAAAATTGGGAAAAAGAAGAGAAACAA
1 AAAAAAAAGAAATTGGGAAGAAGAAAGGAAAAATTGGGAAAAAGAAGAGAAACAA
3679490 TGAAAAGACA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 28 0.52
58 26 0.48
ACGTcount: A:0.63, C:0.02, G:0.28, T:0.07
Consensus pattern (58 bp):
AAAAAAAAGAAATTGGGAAGAAGAAAGGAAAAATTGGGAAAAAGAAGAGAAACAAGGG
Found at i:3682167 original size:21 final size:22
Alignment explanation
Indices: 3682143--3682187 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3682133 TACGGTTTTG
3682143 TTGTTCCA-TATGAGGGTTCTT
1 TTGTTCCATTATGAGGGTTCTT
*
3682164 TTGTTCCATTATGAGGTTTCTT
1 TTGTTCCATTATGAGGGTTCTT
3682186 TT
1 TT
3682188 CTTATTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (22 bp):
TTGTTCCATTATGAGGGTTCTT
Found at i:3687281 original size:18 final size:18
Alignment explanation
Indices: 3687258--3687293 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3687248 GACCATTTAT
3687258 GGCACTATTCACGTATAC
1 GGCACTATTCACGTATAC
*
3687276 GGCACTGTTCACGTATAC
1 GGCACTATTCACGTATAC
3687294 AGTAATTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (18 bp):
GGCACTATTCACGTATAC
Found at i:3692913 original size:26 final size:24
Alignment explanation
Indices: 3692884--3692932 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
3692874 AATAATTTAA
*
3692884 AATTATAAAAATATTCACAAAAAAAC
1 AATTATAAAAA-A-TCAAAAAAAAAC
3692910 AATTATAAAAAATCAAAAAAAAA
1 AATTATAAAAAATCAAAAAAAAA
3692933 GTAAGTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
26 11 0.50
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (24 bp):
AATTATAAAAAATCAAAAAAAAAC
Found at i:3694249 original size:26 final size:28
Alignment explanation
Indices: 3694220--3694282 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
3694210 TTATTCAAGA
*
3694220 TTTAGGGTTC-ATGGTTC-GGGTTTG-AG
1 TTTAGGGTTCAAT-GTTCAAGGTTTGTAG
3694246 TTTAGGGTTCAATGTTCAAGGTTTGTAG
1 TTTAGGGTTCAATGTTCAAGGTTTGTAG
3694274 TTTAGGGTT
1 TTTAGGGTT
3694283 TAAGGTCATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 14 0.42
27 8 0.24
28 11 0.33
ACGTcount: A:0.16, C:0.06, G:0.33, T:0.44
Consensus pattern (28 bp):
TTTAGGGTTCAATGTTCAAGGTTTGTAG
Found at i:3699545 original size:7 final size:7
Alignment explanation
Indices: 3699533--3699570 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
3699523 TTCATATTGA
3699533 ATTTTTT
1 ATTTTTT
3699540 ATTTTTT
1 ATTTTTT
3699547 A-TTTTT
1 ATTTTTT
3699553 A-TTTTT
1 ATTTTTT
3699559 ATTTTTT
1 ATTTTTT
3699566 ATTTT
1 ATTTT
3699571 ATATATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:3699551 original size:6 final size:6
Alignment explanation
Indices: 3699535--3699570 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
3699525 CATATTGAAT
3699535 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTTTA TTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA -TTTTTA TTTT
3699571 ATATATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:3699553 original size:13 final size:13
Alignment explanation
Indices: 3699533--3699570 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
3699523 TTCATATTGA
3699533 ATTTTTTATTTTT
1 ATTTTTTATTTTT
3699546 -TATTTTTATTTTT
1 AT-TTTTTATTTTT
3699559 ATTTTTTATTTT
1 ATTTTTTATTTT
3699571 ATATATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:3701769 original size:3 final size:3
Alignment explanation
Indices: 3701761--3701789 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3701751 AATGGTGGGG
3701761 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3701790 TACTTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3707520 original size:18 final size:18
Alignment explanation
Indices: 3707497--3707534 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3707487 AGAATAGAGT
3707497 ATGCATAATAAA-ATTAAA
1 ATGCATAA-AAATATTAAA
3707515 ATGCATAAAAATATTAAA
1 ATGCATAAAAATATTAAA
3707533 AT
1 AT
3707535 AAAGCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
ATGCATAAAAATATTAAA
Found at i:3715924 original size:20 final size:20
Alignment explanation
Indices: 3715899--3715941 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3715889 ACAGTTGCAA
3715899 CTTGCACTATAACTTGATTG
1 CTTGCACTATAACTTGATTG
3715919 CTTGCACTATAACTTGATTG
1 CTTGCACTATAACTTGATTG
3715939 CTT
1 CTT
3715942 TCTTGTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (20 bp):
CTTGCACTATAACTTGATTG
Found at i:3722439 original size:51 final size:52
Alignment explanation
Indices: 3722348--3722467 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 52
3722338 TCTTATTAAT
*
3722348 TTAAATTAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
1 TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
* * * *
3722400 TTAAAATAATTAAGTGAT-AATATTAAATGA-TTATTTTATCTTTAATT--AA
1 TTAAAATAATTAAGAGATAAATATTAAA-AATTTATATTATCATTAATTAAAA
*
3722449 TTAAATTAA-TAAGAGATAA
1 TTAAAATAATTAAGAGATAA
3722468 GTTGTAAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 7 0.12
49 11 0.19
51 24 0.41
52 17 0.29
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (52 bp):
TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
Found at i:3723938 original size:33 final size:33
Alignment explanation
Indices: 3723896--3723961 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3723886 TTCATGTGAT
3723896 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
3723929 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
3723962 CTTTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (33 bp):
TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
Found at i:3726123 original size:2 final size:2
Alignment explanation
Indices: 3726116--3726147 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3726106 ATCAATATTC
3726116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3726148 CGTTATTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3730247 original size:31 final size:31
Alignment explanation
Indices: 3730180--3730247 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3730170 TAATCGTAAT
** *
3730180 TTGAAAGTTGAAATTATTATTTGATTAAAAG
1 TTGAAAGTTGAAATTAAAATTTGATTAAAAC
* **
3730211 ATGAAAGTTGAAATTAAAATTTGATTAATTC
1 TTGAAAGTTGAAATTAAAATTTGATTAAAAC
3730242 TTGAAA
1 TTGAAA
3730248 AGGAAAATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.01, G:0.15, T:0.40
Consensus pattern (31 bp):
TTGAAAGTTGAAATTAAAATTTGATTAAAAC
Found at i:3730294 original size:17 final size:16
Alignment explanation
Indices: 3730261--3730291 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3730251 AAAATAATTT
*
3730261 AAAACTTTAAATTTTG
1 AAAACTTAAAATTTTG
3730277 AAAACTTAAAATTTT
1 AAAACTTAAAATTTT
3730292 TGAGAAACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:3730444 original size:20 final size:20
Alignment explanation
Indices: 3730419--3730457 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3730409 CCCTTACATC
3730419 ATTACATAATTGAAACTTTG
1 ATTACATAATTGAAACTTTG
*
3730439 ATTACATAATTGGAACTTT
1 ATTACATAATTGAAACTTT
3730458 TCAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTACATAATTGAAACTTTG
Found at i:3730560 original size:23 final size:23
Alignment explanation
Indices: 3730519--3730577 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
3730509 CTATTGATGT
* *
3730519 GCCAGAGAAT-CTTACTGTTCT-T
1 GCCAGAGAATATTTACTGTT-TAC
*
3730541 GCCAGGGAATATTTACTGTTTAC
1 GCCAGAGAATATTTACTGTTTAC
3730564 GCCAGAGAATATTT
1 GCCAGAGAATATTT
3730578 CTTGTTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (23 bp):
GCCAGAGAATATTTACTGTTTAC
Found at i:3737425 original size:42 final size:42
Alignment explanation
Indices: 3737366--3737483 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 42
3737356 TAGGATTAGT
*
3737366 TGAGATTACGTGTAAGACCATAACTGGGATATGACATC-AGTA
1 TGAGATTTCGTGTAAGACCATAACTGGGATATGACATCGA-TA
* * * * *
3737408 TGAGATTTCGCGTAAGACCATAGCTGGGCTATTGGCGTCGATA
1 TGAGATTTCGTGTAAGACCATAACTGGGATA-TGACATCGATA
* * *
3737451 TGAGATCTCATGTAAGACCATATCTGGGATATG
1 TGAGATTTCGTGTAAGACCATAACTGGGATATG
3737484 GCATTGGTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 29 0.46
43 33 0.52
44 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATAACTGGGATATGACATCGATA
Found at i:3739920 original size:28 final size:29
Alignment explanation
Indices: 3739888--3739950 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
3739878 ACTAAGAATG
3739888 AACAA-AATGTACTAAAAACATGCAAATT
1 AACAACAATGTACTAAAAACATGCAAATT
**
3739916 AACAACCTTGTACTAAAAACATGCAAATT
1 AACAACAATGTACTAAAAACATGCAAATT
3739945 AACAAC
1 AACAAC
3739951 CTATCCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.54, C:0.19, G:0.06, T:0.21
Consensus pattern (29 bp):
AACAACAATGTACTAAAAACATGCAAATT
Found at i:3739927 original size:29 final size:29
Alignment explanation
Indices: 3739895--3739952 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3739885 ATGAACAAAA
3739895 TGTACTAAAAACATGCAAATTAACAACCT
1 TGTACTAAAAACATGCAAATTAACAACCT
3739924 TGTACTAAAAACATGCAAATTAACAACCT
1 TGTACTAAAAACATGCAAATTAACAACCT
3739953 ATCCTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (29 bp):
TGTACTAAAAACATGCAAATTAACAACCT
Found at i:3739960 original size:28 final size:29
Alignment explanation
Indices: 3739897--3739960 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
3739887 GAACAAAATG
*
3739897 TACTAAAAACATGCAAATTAACAACCTTG
1 TACTAAAAACATGCAAATTAACAACCTTA
3739926 TACTAAAAACATGCAAATTAACAACC-TA
1 TACTAAAAACATGCAAATTAACAACCTTA
*
3739954 TCCTAAA
1 TACTAAA
3739961 CTCTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.50, C:0.22, G:0.05, T:0.23
Consensus pattern (29 bp):
TACTAAAAACATGCAAATTAACAACCTTA
Found at i:3747606 original size:8 final size:8
Alignment explanation
Indices: 3747593--3747621 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3747583 AATTTGTGAA
3747593 AAAAAAAT
1 AAAAAAAT
3747601 -AAAAAAT
1 AAAAAAAT
3747608 AAAAAAAT
1 AAAAAAAT
3747616 AAAAAA
1 AAAAAA
3747622 CACACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3747613 original size:15 final size:15
Alignment explanation
Indices: 3747593--3747621 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3747583 AATTTGTGAA
3747593 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
3747608 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
3747622 CACACAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:3755985 original size:2 final size:2
Alignment explanation
Indices: 3755978--3756008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3755968 TTATTATACC
3755978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3756009 AACACCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3762137 original size:36 final size:36
Alignment explanation
Indices: 3762090--3762160 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
3762080 CATGTAGCAG
*
3762090 TTCTACCTAGTATGCTATAATCAATGATGGGGGAAA
1 TTCTACCTAGTATGCTATAATCAATAATGGGGGAAA
3762126 TTCTACCTAGTATGCTATAATCAATAATGGGGGAA
1 TTCTACCTAGTATGCTATAATCAATAATGGGGGAA
3762161 TTTTTTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (36 bp):
TTCTACCTAGTATGCTATAATCAATAATGGGGGAAA
Found at i:3766292 original size:30 final size:30
Alignment explanation
Indices: 3766256--3766317 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3766246 CAGCAGCCAA
3766256 CCATAACAACCTGATCTGATGGTCTTGCAT
1 CCATAACAACCTGATCTGATGGTCTTGCAT
3766286 CCATAACAACCTGATCTGATGGTCTTGCAT
1 CCATAACAACCTGATCTGATGGTCTTGCAT
3766316 CC
1 CC
3766318 TGAATAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (30 bp):
CCATAACAACCTGATCTGATGGTCTTGCAT
Found at i:3770663 original size:19 final size:19
Alignment explanation
Indices: 3770628--3770678 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3770618 ACACACATGT
3770628 CTTTTT-TTTTATCTTTCCC
1 CTTTTTCTTTT-TCTTTCCC
* **
3770647 CTTTTTCTTTTTTTTTCTT
1 CTTTTTCTTTTTCTTTCCC
*
3770666 CATTTTCTTTTTC
1 CTTTTTCTTTTTC
3770679 CCTATTTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTTTCTTTTTCTTTCCC
Found at i:3772693 original size:13 final size:13
Alignment explanation
Indices: 3772675--3772708 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3772665 ACAGATTTGT
*
3772675 AAAGGATAATAAC
1 AAAGGACAATAAC
*
3772688 AAAGGACAATGAC
1 AAAGGACAATAAC
3772701 AAAGGACA
1 AAAGGACA
3772709 GTGAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.09
Consensus pattern (13 bp):
AAAGGACAATAAC
Found at i:3777595 original size:2 final size:2
Alignment explanation
Indices: 3777573--3777613 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
3777563 CAAATTCTAA
* *
3777573 AT AT AA AT AGT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3777614 TTAAAGGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3783200 original size:2 final size:2
Alignment explanation
Indices: 3783193--3783222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3783183 AAACGTATTA
3783193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3783223 TGAACTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3783383 original size:18 final size:18
Alignment explanation
Indices: 3783362--3783614 Score: 165
Period size: 18 Copynumber: 13.6 Consensus size: 18
3783352 GAACAATTAT
3783362 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
3783380 TTATGCGGTAACAATCAA
1 TTATTCAGTAACAGTCAA
* * ** *
3783398 ATATTCAGTAATAACCAG
1 TTATTCAGTAACAGTCAA
*
3783416 TTATTCAGTATC-GATCAA
1 TTATTCAGTAACAG-TCAA
3783434 TTGATCGGTTATCCAGTAACAGTCAA
1 TT-A-----T-T-CAGTAACAGTCAA
*
3783460 TTATTCAGTAA-AATCAA
1 TTATTCAGTAACAGTCAA
* *
3783477 ATATTCAGTAACAGTTAA
1 TTATTCAGTAACAGTCAA
*
3783495 GTTATTTAGTAACAGTC-A
1 -TTATTCAGTAACAGTCAA
* * *
3783513 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAA
*
3783532 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
3783550 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
3783568 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
*
3783587 -TATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
3783604 TTATTCAGTAA
1 TTATTCAGTAA
3783615 TAATCAGTTA
Statistics
Matches: 178, Mismatches: 39, Indels: 36
0.70 0.15 0.14
Matches are distributed among these distances:
17 19 0.11
18 124 0.70
19 18 0.10
20 1 0.01
24 1 0.01
25 2 0.01
26 12 0.07
27 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:3783826 original size:23 final size:23
Alignment explanation
Indices: 3783744--3783830 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
3783734 CCTGATCAGT
*
3783744 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
3783766 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
3783786 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
3783809 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
3783831 TCAATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:3784204 original size:15 final size:15
Alignment explanation
Indices: 3784179--3784234 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
3784169 TAATGTATAT
3784179 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
3784195 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
3784210 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3784225 TATAAATTCA
1 TATAAATTCA
3784235 TCGTATACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3785502 original size:5 final size:5
Alignment explanation
Indices: 3785492--3785526 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
3785482 TTACTTATTT
3785492 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
3785527 TATTTTAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:3787988 original size:25 final size:27
Alignment explanation
Indices: 3787951--3788003 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3787941 TCAAACATGC
3787951 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
3787977 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
3788003 A
1 A
3788004 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:3789523 original size:26 final size:26
Alignment explanation
Indices: 3789487--3789596 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
3789477 CATGATATTC
3789487 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
3789513 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3789539 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3789565 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3789591 TTATCA
1 TTATCA
3789597 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3792731 original size:18 final size:18
Alignment explanation
Indices: 3792710--3792962 Score: 165
Period size: 18 Copynumber: 13.6 Consensus size: 18
3792700 GAACAATTAT
3792710 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
3792728 TTATGCGGTAACAATCAA
1 TTATTCAGTAACAGTCAA
* * ** *
3792746 ATATTCAGTAATAACCAG
1 TTATTCAGTAACAGTCAA
*
3792764 TTATTCAGTATC-GATCAA
1 TTATTCAGTAACAG-TCAA
3792782 TTGATCGGTTATCCAGTAACAGTCAA
1 TT-A-----T-T-CAGTAACAGTCAA
*
3792808 TTATTCAGTAA-AATCAA
1 TTATTCAGTAACAGTCAA
* *
3792825 ATATTCAGTAACAGTTAA
1 TTATTCAGTAACAGTCAA
*
3792843 GTTATTTAGTAACAGTC-A
1 -TTATTCAGTAACAGTCAA
* * *
3792861 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAA
*
3792880 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
3792898 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
3792916 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
*
3792935 -TATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
3792952 TTATTCAGTAA
1 TTATTCAGTAA
3792963 TAATCAGTTA
Statistics
Matches: 178, Mismatches: 39, Indels: 36
0.70 0.15 0.14
Matches are distributed among these distances:
17 19 0.11
18 124 0.70
19 18 0.10
20 1 0.01
24 1 0.01
25 2 0.01
26 12 0.07
27 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:3793174 original size:23 final size:23
Alignment explanation
Indices: 3793092--3793178 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
3793082 CCTGATCAGT
*
3793092 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
3793114 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
3793134 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
3793157 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
3793179 TCAATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:3793552 original size:15 final size:15
Alignment explanation
Indices: 3793527--3793582 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
3793517 TAATGTATAT
3793527 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
3793543 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
3793558 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3793573 TATAAATTCA
1 TATAAATTCA
3793583 TCGTATACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3794854 original size:5 final size:5
Alignment explanation
Indices: 3794844--3794883 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
3794834 TTACTTATTT
3794844 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
3794884 TATTTTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:3797731 original size:40 final size:40
Alignment explanation
Indices: 3797671--3797882 Score: 252
Period size: 40 Copynumber: 5.3 Consensus size: 40
3797661 CCTTTGGGGT
* *
3797671 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGTTATAG-TAACTCGCACAAATGCCTTCGGGAC
3797710 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
*
3797750 TCAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
* * * * *
3797790 TTAGCCCGGATGTAATAACTCGCACAATTTGCCTTTGGG-C
1 TTAGCCCGGTTATAGTAACTCGCACAA-ATGCCTTCGGGAC
* * * * *
3797830 TTAGCCCGG-AATTAGTCATTAGCACAAATGCCTTTGGGAC
1 TTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGAC
3797870 TTAGCCCGGTTAT
1 TTAGCCCGGTTAT
3797883 CATCCGAATA
Statistics
Matches: 150, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
39 15 0.10
40 125 0.83
41 10 0.07
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:3804841 original size:22 final size:22
Alignment explanation
Indices: 3804813--3804856 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3804803 CAATGTGTGC
*
3804813 CATGCATCTCATATGAAGATAT
1 CATGCATCTCATATGAAAATAT
3804835 CATGCATCTCATATGAAAATAT
1 CATGCATCTCATATGAAAATAT
3804857 TTACCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
CATGCATCTCATATGAAAATAT
Found at i:3805759 original size:19 final size:20
Alignment explanation
Indices: 3805719--3805761 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3805709 ATTTTGCAAG
3805719 AAAAAAATTATATAATAAATT
1 AAAAAAATTATATAAT-AATT
3805740 AAAATAAATT-TATAAT-ATT
1 AAAA-AAATTATATAATAATT
3805759 AAA
1 AAA
3805762 CATATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAAATTATATAATAATT
Found at i:3806546 original size:6 final size:6
Alignment explanation
Indices: 3806535--3806618 Score: 95
Period size: 6 Copynumber: 14.7 Consensus size: 6
3806525 AATAAATTAT
*
3806535 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAAA-C AAAAGC
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC
* * * *
3806582 AATAGC AATATC --AACC AAAACC AAAACC AAAA-C AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAAA
3806619 GCAATAGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
4 2 0.03
5 10 0.14
6 59 0.83
ACGTcount: A:0.67, C:0.27, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAACC
Found at i:3806598 original size:39 final size:39
Alignment explanation
Indices: 3806555--3806631 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
3806545 CCAAAACCAA
3806555 AACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATC
1 AACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATC
3806594 AACCAAAACCAAAACCAAAACAAAAGCAATAGCAATAT
1 AACCAAAACCAAAACCAAAACAAAAGCAATAGCAATAT
3806632 TAAGTTGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.62, C:0.25, G:0.05, T:0.08
Consensus pattern (39 bp):
AACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATC
Found at i:3806603 original size:33 final size:33
Alignment explanation
Indices: 3806561--3806624 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
3806551 CCAAAACCAA
*
3806561 AACCAAAACCAAAA-CAAAAGCAATAGCAATATC
1 AACCAAAACCAAAACCAAAA-CAAAAGCAATATC
3806594 AACCAAAACCAAAACCAAAACAAAAGCAATA
1 AACCAAAACCAAAACCAAAACAAAAGCAATA
3806625 GCAATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.64, C:0.25, G:0.05, T:0.06
Consensus pattern (33 bp):
AACCAAAACCAAAACCAAAACAAAAGCAATATC
Found at i:3807151 original size:28 final size:28
Alignment explanation
Indices: 3807111--3807165 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3807101 ATTCATCATA
3807111 AACCAGATGTCTTCTTAAAGAACAAATT
1 AACCAGATGTCTTCTTAAAGAACAAATT
* *
3807139 AACCAGATGTCTTCTTGAAGAATAAAT
1 AACCAGATGTCTTCTTAAAGAACAAAT
3807166 CATCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (28 bp):
AACCAGATGTCTTCTTAAAGAACAAATT
Found at i:3807790 original size:14 final size:15
Alignment explanation
Indices: 3807771--3807810 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3807761 CTGTTGTGTT
3807771 TTTTAGTTTTA-GAC
1 TTTTAGTTTTAGGAC
*
3807785 TTTTAGTTTTAGGAT
1 TTTTAGTTTTAGGAC
*
3807800 TTTTATTTTTA
1 TTTTAGTTTTA
3807811 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (15 bp):
TTTTAGTTTTAGGAC
Found at i:3812203 original size:7 final size:8
Alignment explanation
Indices: 3812177--3812202 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3812167 CTTATAAATT
3812177 AAATATTA
1 AAATATTA
3812185 AAATATTA
1 AAATATTA
3812193 AAATATTA
1 AAATATTA
3812201 AA
1 AA
3812203 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATTA
Found at i:3814226 original size:12 final size:12
Alignment explanation
Indices: 3814209--3814235 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3814199 ATTCTATTTT
3814209 TTAGGATTATTG
1 TTAGGATTATTG
3814221 TTAGGATTATTG
1 TTAGGATTATTG
3814233 TTA
1 TTA
3814236 TATTGTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (12 bp):
TTAGGATTATTG
Found at i:3816091 original size:21 final size:21
Alignment explanation
Indices: 3816067--3816116 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3816057 TTCATATAAC
3816067 ATTATTATTTTGAATCATTGA
1 ATTATTATTTTGAATCATTGA
* *
3816088 ATTATTATTTTGACTCGTTGA
1 ATTATTATTTTGAATCATTGA
3816109 ATCTATTA
1 AT-TATTA
3816117 GAACTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (21 bp):
ATTATTATTTTGAATCATTGA
Found at i:3816249 original size:22 final size:22
Alignment explanation
Indices: 3816222--3816263 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3816212 GCTAAAAACG
3816222 GGAAGCTCTATT-GAGCTGAATA
1 GGAAGCTCT-TTCGAGCTGAATA
3816244 GGAAGCTCTTTCGAGCTGAA
1 GGAAGCTCTTTCGAGCTGAA
3816264 CGAGAAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (22 bp):
GGAAGCTCTTTCGAGCTGAATA
Found at i:3816270 original size:22 final size:22
Alignment explanation
Indices: 3816218--3816282 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
3816208 ATGAGCTAAA
*
3816218 AACGGGAAGCTCTATT-GAGCTG
1 AACGAGAAGCTCT-TTCGAGCTG
*
3816240 AA-TAGGAAGCTCTTTCGAGCTG
1 AACGA-GAAGCTCTTTCGAGCTG
* *
3816262 AACGAGAAGCTCATACGAGCT
1 AACGAGAAGCTCTTTCGAGCT
3816283 ATGGTGAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (22 bp):
AACGAGAAGCTCTTTCGAGCTG
Found at i:3821669 original size:14 final size:15
Alignment explanation
Indices: 3821650--3821689 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3821640 CTGTCGAGTT
3821650 TTTTAGTTTTA-GAC
1 TTTTAGTTTTAGGAC
*
3821664 TTTTAGTTTTAGGAT
1 TTTTAGTTTTAGGAC
*
3821679 TTTTATTTTTA
1 TTTTAGTTTTA
3821690 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (15 bp):
TTTTAGTTTTAGGAC
Found at i:3826371 original size:21 final size:22
Alignment explanation
Indices: 3826346--3826387 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3826336 TTAATAAAAT
3826346 TTTATAA-TTTTATAAGTTTTG
1 TTTATAATTTTTATAAGTTTTG
*
3826367 TTTATAATTTTTATAATTTTT
1 TTTATAATTTTTATAAGTTTT
3826388 TAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTATAATTTTTATAAGTTTTG
Found at i:3828818 original size:20 final size:20
Alignment explanation
Indices: 3828793--3828838 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3828783 CGAGGTCATT
*
3828793 AATGCACTGTCAAGGCCATC
1 AATGCACTGTCAAGCCCATC
*
3828813 AATGCACTGTCGAGCCCATC
1 AATGCACTGTCAAGCCCATC
3828833 AATGCA
1 AATGCA
3828839 TCTTTTCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGCACTGTCAAGCCCATC
Found at i:3830099 original size:23 final size:22
Alignment explanation
Indices: 3830063--3830114 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3830053 TACATAATAC
* * *
3830063 TATTTTATATTTTATTATTATAT
1 TATTTTACACTTTAATA-TATAT
*
3830086 TATTTTACACTTTAATATATGT
1 TATTTTACACTTTAATATATAT
3830108 TATTTTA
1 TATTTTA
3830115 TATTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTTTACACTTTAATATATAT
Found at i:3830319 original size:13 final size:13
Alignment explanation
Indices: 3830281--3830320 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3830271 TTTTTTTTTC
3830281 ATTA-CATACA-T
1 ATTATCATACATT
*
3830292 ATTATC-TATATT
1 ATTATCATACATT
3830304 ATTATCATACATT
1 ATTATCATACATT
3830317 ATTA
1 ATTA
3830321 AATATGGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.29
12 8 0.33
13 9 0.38
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATCATACATT
Found at i:3830432 original size:18 final size:17
Alignment explanation
Indices: 3830398--3830434 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3830388 GTATTAAATC
*
3830398 TTTTATATATTTTTATA
1 TTTTATATATTTATATA
3830415 TTTTATATTATTTATATA
1 TTTTATA-TATTTATATA
3830433 TT
1 TT
3830435 AAATGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATATATTTATATA
Found at i:3834326 original size:14 final size:14
Alignment explanation
Indices: 3834307--3834344 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3834297 AATATATTAT
3834307 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
3834321 TTTTCTAAATAAGG
1 TTTTCTAAATAAAG
3834335 TTTTCTAAAT
1 TTTTCTAAAT
3834345 GAGATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:3838466 original size:16 final size:15
Alignment explanation
Indices: 3838430--3838481 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
3838420 CTTCTATTTC
*
3838430 AAAAAAAAG-GAAA-
1 AAAAAAAAGAAAAAG
*
3838443 AAAGAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
3838458 AGAAAAAAATAAAAAG
1 A-AAAAAAAGAAAAAG
3838474 AAAAAAAA
1 AAAAAAAA
3838482 TATGGAGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.25
14 3 0.09
15 8 0.25
16 13 0.41
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:3839525 original size:44 final size:44
Alignment explanation
Indices: 3839381--3839829 Score: 349
Period size: 44 Copynumber: 10.2 Consensus size: 44
3839371 GGGACAATGT
* *
3839381 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * * **
3839425 AGATCTGACA-CTCCTTTGCTTACAGCGAAGC-AGATTGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
3839470 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* *
3839513 AGATTTGGCATCCCTATGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * ***
3839557 AGATCTGACATTCCTGTGCTTACAGCGAAGC-AGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
3839602 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * *
3839645 AGATTTGGCATCCCTGTGTTTATAAGGAACAAATCAAAGATAGA
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * * ** **
3839689 AGATCTGACATTCCTATGCTTACAGCGAAGTAGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAG-TCGAAGATAGC
* *
3839734 AGCA--TGGCATCCCTGTGTTTATAGGGAAAAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * *
3839777 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAAC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
3839821 AGATCTGGC
1 AGATTTGGC
3839830 GTCTCCATAT
Statistics
Matches: 309, Mismatches: 78, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
42 3 0.01
43 33 0.11
44 239 0.77
45 31 0.10
46 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
Found at i:3839618 original size:132 final size:132
Alignment explanation
Indices: 3839381--3839827 Score: 768
Period size: 132 Copynumber: 3.4 Consensus size: 132
3839371 GGGACAATGT
* * * *
3839381 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGTAGATCTGACACTCCTTTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
*
3839446 ACAGCGAAGCAGATTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3839511 GC
131 GC
* * *
3839513 AGATTTGGCATCCCTATGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
*
3839578 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3839643 GC
131 GC
* *
3839645 AGATTTGGCATCCCTGTGTTTATAAGGAACAAATCAAAGATAGAAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
* *
3839710 ACAGCGAAGTAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAAAAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3839775 GC
131 GC
*
3839777 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAACAGATCTG
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTG
3839828 GCGTCTCCAT
Statistics
Matches: 298, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 298 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:3840187 original size:206 final size:206
Alignment explanation
Indices: 3839831--3840230 Score: 640
Period size: 206 Copynumber: 1.9 Consensus size: 206
3839821 AGATCTGGCG
** * *
3839831 TCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAG
1 TCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAG
* *
3839896 ATCCAAGGTGGTTTGGCATCCTTATGCTTACAAGGAACAAATCAAAGACATAGTTGATTTGGCTT
66 ATCCAAGATGGTTTGGCATCCTTATGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTT
*
3839961 TCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATC
131 TCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATC
3840026 GAAGTTTAGCA
196 GAAGTTTAGCA
* *
3840037 TCTCCATATTCGACGGAGGGCAGACATATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAG
1 TCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAG
* * * * *
3840102 ATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTT
66 ATCCAAGATGGTTTGGCATCCTTATGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTT
* *
3840167 TCGCGTGCTTAC-ACTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAAT
131 TCACGTGCTTACGA-TGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAACAAAT
3840231 AAAAGAAGCA
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
205 1 0.01
206 176 0.99
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (206 bp):
TCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAG
ATCCAAGATGGTTTGGCATCCTTATGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTT
TCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATC
GAAGTTTAGCA
Found at i:3840759 original size:20 final size:20
Alignment explanation
Indices: 3840734--3840790 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3840724 GCTCCCCGAA
*
3840734 TCAAGGTCATCAATGCACTG
1 TCAAGGCCATCAATGCACTG
3840754 TCAAGGCCATCAATGCACTG
1 TCAAGGCCATCAATGCACTG
*
3840774 TCGAGGCCATCAATGCA
1 TCAAGGCCATCAATGCA
3840791 TCTTCTCAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (20 bp):
TCAAGGCCATCAATGCACTG
Found at i:3842021 original size:24 final size:25
Alignment explanation
Indices: 3841964--3842136 Score: 71
Period size: 24 Copynumber: 6.8 Consensus size: 25
3841954 AAAAAAACTT
*
3841964 TATTTA-TATATTATTATTCACCTA
1 TATTTATTATATTATTATTCACATA
3841988 TATCTATATTATATT-TTATT-ACATAA
1 TAT-T-TATTATATTATTATTCACAT-A
* *
3842014 TATTTATTATACTATT-TT-ATAT-
1 TATTTATTATATTATTATTCACATA
*
3842036 TTTATTATTATATTATT-TTACACTTTAATA
1 TAT-TTATTATATTATTATT-CAC----ATA
3842066 TATGTTATTTTATATTATTATT-ACATCA
1 TAT-TTA--TTATATTATTATTCACAT-A
* **
3842094 TATTTATTAT-GTATT-TTCGTATA
1 TATTTATTATATTATTATTCACATA
3842117 T-TATTATCTATATTATTATT
1 TAT-TTAT-TATATTATTATT
3842137 TTGATAGATT
Statistics
Matches: 115, Mismatches: 12, Indels: 42
0.68 0.07 0.25
Matches are distributed among these distances:
22 3 0.03
23 22 0.19
24 25 0.22
25 16 0.14
26 13 0.11
27 11 0.10
28 4 0.03
29 2 0.02
30 5 0.04
31 2 0.02
32 10 0.09
33 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTTATTATATTATTATTCACATA
Found at i:3842047 original size:23 final size:23
Alignment explanation
Indices: 3842017--3842088 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
3842007 TACATAATAT
*
3842017 TTATTATACTATTTTATATTTTA
1 TTATTATATTATTTTATATTTTA
* *
3842040 TTATTATATTATTTTACACTTTA
1 TTATTATATTATTTTATATTTTA
* *
3842063 ATA-TATGTTATTTTATATTATTA
1 TTATTATATTATTTTATATT-TTA
3842086 TTA
1 TTA
3842089 CATCATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 13 0.32
23 27 0.68
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (23 bp):
TTATTATATTATTTTATATTTTA
Found at i:3842105 original size:35 final size:31
Alignment explanation
Indices: 3842028--3842110 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 31
3842018 TATTATACTA
*
3842028 TTTTA-TATTTTATTATTATATTATTTTACAC
1 TTTTATTATGTTATT-TTATATTATTTTACAC
*
3842059 TTTAATATATGTTATTTTATATTATTATTACATC
1 TTTTAT-TATGTTATTTTATATTATT-TTACA-C
3842093 ATATTTATTATG-TATTTT
1 -T-TTTATTATGTTATTTT
3842111 CGTATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
31 4 0.09
32 10 0.23
33 13 0.30
34 7 0.16
35 5 0.12
36 4 0.09
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTATTATGTTATTTTATATTATTTTACAC
Found at i:3842283 original size:13 final size:13
Alignment explanation
Indices: 3842245--3842284 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3842235 TTTTTTTTTC
3842245 ATTA-CATACA-T
1 ATTATCATACATT
*
3842256 ATTATC-TATATT
1 ATTATCATACATT
3842268 ATTATCATACATT
1 ATTATCATACATT
3842281 ATTA
1 ATTA
3842285 AATATGGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.29
12 8 0.33
13 9 0.38
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATCATACATT
Found at i:3843699 original size:44 final size:44
Alignment explanation
Indices: 3843636--3843724 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3843626 AACTTACTGT
3843636 GTCAGAGGCTGTCGAGCCCAAGAGATGAAATGGTGTGACATTCG
1 GTCAGAGGCTGTCGAGCCCAAGAGATGAAATGGTGTGACATTCG
3843680 GTCAGAGGCTGTCGAGCCCAAGAGATGAAATGGTGTGACATTCG
1 GTCAGAGGCTGTCGAGCCCAAGAGATGAAATGGTGTGACATTCG
3843724 G
1 G
3843725 CATTAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (44 bp):
GTCAGAGGCTGTCGAGCCCAAGAGATGAAATGGTGTGACATTCG
Found at i:3850096 original size:25 final size:25
Alignment explanation
Indices: 3850060--3850116 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3850050 GTTATCGATT
*
3850060 TCAGCTCTTATGAGCTTACTGATAC
1 TCAGCTCTTATGACCTTACTGATAC
* *
3850085 TCAGCT-TGTATGACCTTACTGTTAT
1 TCAGCTCT-TATGACCTTACTGATAC
3850110 TCAGCTC
1 TCAGCTC
3850117 GGAGGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (25 bp):
TCAGCTCTTATGACCTTACTGATAC
Found at i:3850127 original size:25 final size:25
Alignment explanation
Indices: 3850071--3850153 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
3850061 CAGCTCTTAT
* * * * *
3850071 GAGCTTACTGATACTCAGCTTGTAT
1 GAGCTTACTGTTATTCAGCTCGGAA
* *
3850096 GACCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACTGTTATTCAGCTCGGAA
*
3850121 GAGCTTACCGTTATTCAGCTCGGAA
1 GAGCTTACTGTTATTCAGCTCGGAA
3850146 GAGCTTAC
1 GAGCTTAC
3850154 CGTTTATAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGCTCGGAA
Found at i:3850154 original size:25 final size:25
Alignment explanation
Indices: 3850099--3850157 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
3850089 CTTGTATGAC
* *
3850099 CTTACTGTTATTCAGCTCGGAGGAG
1 CTTACCGTTATTCAGCTCGGAAGAG
3850124 CTTACCGTTATTCAGCTCGGAAGAG
1 CTTACCGTTATTCAGCTCGGAAGAG
3850149 CTTACCGTT
1 CTTACCGTT
3850158 TATAGCTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (25 bp):
CTTACCGTTATTCAGCTCGGAAGAG
Found at i:3852765 original size:12 final size:12
Alignment explanation
Indices: 3852748--3852772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3852738 ATAGATAAGT
3852748 ATGGTCAATCCC
1 ATGGTCAATCCC
3852760 ATGGTCAATCCC
1 ATGGTCAATCCC
3852772 A
1 A
3852773 CAGGGACTGA
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:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGGTCAATCCC
Found at i:3855771 original size:42 final size:41
Alignment explanation
Indices: 3855711--3855836 Score: 126
Period size: 43 Copynumber: 3.0 Consensus size: 41
3855701 CTGTTTTAAG
* * *
3855711 TGTAAGGCCATGTTTGGGACATCGGCATCGTATCTGATTTCA
1 TGTAAGACCATGTCTGGGACAT-GGCATCGTATATGATTTCA
* * * *
3855753 TGTAAGACCTTGTCTGGGACAGTGGCATCGATGTTTGATTACA
1 TGTAAGACCATGTCTGGGACA-TGGCATCG-TATATGATTTCA
* * *
3855796 TGTAAGACCACGTCTAGGACATTGGCATTGTATATGATTTC
1 TGTAAGACCATGTCTGGGACA-TGGCATCGTATATGATTTC
3855837 CAAGCTTTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 33 0.49
43 35 0.51
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATGGCATCGTATATGATTTCA
Found at i:3857858 original size:26 final size:26
Alignment explanation
Indices: 3857829--3857936 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3857819 TGATACAAAT
* *
3857829 TGATAATGGGTTAGGTAAATCTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3857855 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3857881 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3857907 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3857933 TGAT
1 TGAT
3857937 TGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3864665 original size:40 final size:36
Alignment explanation
Indices: 3864620--3864726 Score: 137
Period size: 35 Copynumber: 2.9 Consensus size: 36
3864610 AAGATTACAA
* *
3864620 AATCATATCTTTTAAGATTGTATATCATATCTAAGTTTGC
1 AATCATATC--TTAAGATTG--TATCATATCTAAGATAGC
3864660 AATCATATC-TAAGATTGTATCATATCTAAGATAGC
1 AATCATATCTTAAGATTGTATCATATCTAAGATAGC
*
3864695 AATCATATC-TAAAATTGTATCATATCTAAGAT
1 AATCATATCTTAAGATTGTATCATATCTAAGAT
3864727 TGCATGTCAC
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
35 47 0.73
37 8 0.12
40 9 0.14
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (36 bp):
AATCATATCTTAAGATTGTATCATATCTAAGATAGC
Found at i:3864683 original size:17 final size:18
Alignment explanation
Indices: 3864632--3864755 Score: 135
Period size: 17 Copynumber: 6.8 Consensus size: 18
3864622 TCATATCTTT
*
3864632 TAAGATTGTATATCATATC
1 TAAGATTG-CTATCATATC
* *
3864651 TAAGTTTGCAATCATATC
1 TAAGATTGCTATCATATC
3864669 TAAGATTG-TATCATATC
1 TAAGATTGCTATCATATC
* *
3864686 TAAGATAGCAATCATATC
1 TAAGATTGCTATCATATC
*
3864704 TAAAATTG-TATCATATC
1 TAAGATTGCTATCATATC
* *
3864721 TAAGATTGCATGTCACATC
1 TAAGATTGC-TATCATATC
3864740 TAAGATTGCATATCAT
1 TAAGATTGC-TATCAT
3864756 TGAAGATTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
17 30 0.34
18 29 0.33
19 28 0.32
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TAAGATTGCTATCATATC
Found at i:3864687 original size:35 final size:35
Alignment explanation
Indices: 3864632--3864747 Score: 160
Period size: 35 Copynumber: 3.2 Consensus size: 35
3864622 TCATATCTTT
*
3864632 TAAGATTGTATATCATATCTAAGTTTGCAATCATATC
1 TAAGATTG--TATCATATCTAAGATTGCAATCATATC
*
3864669 TAAGATTGTATCATATCTAAGATAGCAATCATATC
1 TAAGATTGTATCATATCTAAGATTGCAATCATATC
* * *
3864704 TAAAATTGTATCATATCTAAGATTGCATGTCACATC
1 TAAGATTGTATCATATCTAAGATTGCA-ATCATATC
3864740 TAAGATTG
1 TAAGATTG
3864748 CATATCATTG
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
35 50 0.70
36 13 0.18
37 8 0.11
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (35 bp):
TAAGATTGTATCATATCTAAGATTGCAATCATATC
Found at i:3865645 original size:207 final size:207
Alignment explanation
Indices: 3865146--3866272 Score: 1891
Period size: 207 Copynumber: 5.5 Consensus size: 207
3865136 AAATTTGCTT
* * * *
3865146 CTTCAATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCATAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
* * *
3865211 GAGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * ** * *
3865276 GGATC-TGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTGTCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3865340 GGAGACGCCAAA
196 GGAGACGCCAAA
*
3865352 CTTCGATTTGTTCTCTGAC-ATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
3865416 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
3865481 GGATCTTGCTTCAGTATACACATTTGAAGGCCAGATTTGCTATGTGTCTGCCCTCCGTCAAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3865546 GGAGACGCCAAA
196 GGAGACGCCAAA
*
3865558 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
*
3865623 GTGAAAGCCAAATCAGCTATGTCTTCAATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
3865688 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3865753 GGAGACGCCAAA
196 GGAGACGCCAAA
*
3865765 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
* *
3865830 GTGAAAGCCAAATCAACTATGTCTTCAATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
3865895 AGATCTTGCTTCAGTATAAACATCTAAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
*
3865960 AGAGACGCCAAA
196 GGAGACGCCAAA
*
3865972 CTTCGATTTGTTCTCTGACAATACA-AGGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACA
1 CTTCGATTTGTTCTCTGACAATACAGA-GATGCCAAATCATCTTAGACTTGCTTCAACATAAACA
*
3866036 CATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
3866101 TGGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATA
130 TGGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATA
3866166 TGGAGACGCCAAA
195 TGGAGACGCCAAA
* * * * * *
3866179 CTTTGATTTGTTCTCTAACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCATAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
*
3866244 GTGAAATCCAAATCAGCTATGTCTTCGAT
66 GTGAAAGCCAAATCAGCTATGTCTTCGAT
3866273 CTGCTCTCCG
Statistics
Matches: 867, Mismatches: 50, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
205 109 0.13
206 97 0.11
207 660 0.76
208 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
GGAGACGCCAAA
Found at i:3866502 original size:87 final size:87
Alignment explanation
Indices: 3866397--3866605 Score: 275
Period size: 87 Copynumber: 2.4 Consensus size: 87
3866387 TCTACTATAC
*
3866397 TTTAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCA-TC-T-TGGATCTGCTCCACTACTGC
1 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCAGTCGTCTGGATCTGCTCCACTACTGC
3866459 TTAGGGAGATAAGATCCGCAAT
66 TTAGGGAGATAAGATCCGCAAT
* ** * * *
3866481 TTT-GACCTGTTACCCTACTACTTAAAGGATTAAGGCG-AGTCGTCGTTGATCTGTTCCACTACT
1 TTTAG-CCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCAGTCGTC-TGGATCTGCTCCACTACT
* *
3866544 GCTTAGGGAGATAAGATCTGTAAT
64 GCTTAGGGAGATAAGATCCGCAAT
*
3866568 TTTAGCCTGTTACCCTACTGCTTTGGGGGTTAAGGCGC
1 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGC
3866606 TGAATTTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
83 1 0.01
84 33 0.32
85 1 0.01
87 68 0.65
88 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (87 bp):
TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCAGTCGTCTGGATCTGCTCCACTACTGC
TTAGGGAGATAAGATCCGCAAT
Found at i:3867571 original size:24 final size:23
Alignment explanation
Indices: 3867540--3867621 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 23
3867530 TCCATTTTCC
3867540 TTTTTTTTTCTCTCTTTTTTCTT
1 TTTTTTTTTCTCTCTTTTTTCTT
*
3867563 TTTTCTTTTTTTCTCTTTTTAT-TT
1 TTTT-TTTTTCTCTCTTTTT-TCTT
3867587 TCTTTTTTTTCT-TCTTTTTCTTCTT
1 T-TTTTTTTTCTCTC-TTTT-TTCTT
3867612 CTTTTTTTTT
1 -TTTTTTTTT
3867622 TTGAAATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
23 6 0.12
24 28 0.56
25 15 0.30
26 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTCTCTCTTTTTTCTT
Found at i:3867575 original size:37 final size:35
Alignment explanation
Indices: 3867534--3867622 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 35
3867524 GGCCTCTCCA
*
3867534 TTTTCCTTTTTTTTTCTCTCTTTTTTCTT-TTTTCTTT
1 TTTTCCTTTTTTTTTCT-T-TTTTTTCTTCTTTT-TCT
3867571 TTTTCTCTTTTTATTTTCTTTTTTTTCTTCTTTTTCT
1 TTTTC-CTTTTT-TTTTCTTTTTTTTCTTCTTTTTCT
* *
3867608 TCTTCTTTTTTTTTT
1 TTTTCCTTTTTTTTT
3867623 TGAAATAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
35 4 0.09
36 5 0.11
37 20 0.43
38 11 0.24
39 6 0.13
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (35 bp):
TTTTCCTTTTTTTTTCTTTTTTTTCTTCTTTTTCT
Found at i:3867880 original size:22 final size:24
Alignment explanation
Indices: 3867852--3867897 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3867842 CAAGGTTTCC
3867852 TTTATGAA-TTT-TTTTGGACGAA
1 TTTATGAATTTTATTTTGGACGAA
3867874 TTTATGAATTTTATTTTGGACGAA
1 TTTATGAATTTTATTTTGGACGAA
3867898 CCTTCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
24 11 0.50
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (24 bp):
TTTATGAATTTTATTTTGGACGAA
Found at i:3873425 original size:17 final size:18
Alignment explanation
Indices: 3873374--3873497 Score: 144
Period size: 17 Copynumber: 6.8 Consensus size: 18
3873364 TCATATCTTT
*
3873374 TAAGATTGTATATCATATC
1 TAAGATTG-CTATCATATC
* *
3873393 TAATATTGCAATCATATC
1 TAAGATTGCTATCATATC
3873411 TAAGATTG-TATCATATC
1 TAAGATTGCTATCATATC
*
3873428 TAAGATTGCAATCATATC
1 TAAGATTGCTATCATATC
* *
3873446 TAAAATTG-TACCATATC
1 TAAGATTGCTATCATATC
*
3873463 TAAGATTGCATATCACATC
1 TAAGATTGC-TATCATATC
3873482 TAAGATTGCATATCAT
1 TAAGATTGC-TATCAT
3873498 TGAAGATTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
17 30 0.34
18 30 0.34
19 29 0.33
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TAAGATTGCTATCATATC
Found at i:3873429 original size:35 final size:35
Alignment explanation
Indices: 3873374--3873489 Score: 169
Period size: 35 Copynumber: 3.2 Consensus size: 35
3873364 TCATATCTTT
*
3873374 TAAGATTGTATATCATATCTAATATTGCAATCATATC
1 TAAGATTG--TATCATATCTAAGATTGCAATCATATC
3873411 TAAGATTGTATCATATCTAAGATTGCAATCATATC
1 TAAGATTGTATCATATCTAAGATTGCAATCATATC
* * *
3873446 TAAAATTGTACCATATCTAAGATTGCATATCACATC
1 TAAGATTGTATCATATCTAAGATTGCA-ATCATATC
3873482 TAAGATTG
1 TAAGATTG
3873490 CATATCATTG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 51 0.70
36 14 0.19
37 8 0.11
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (35 bp):
TAAGATTGTATCATATCTAAGATTGCAATCATATC
Found at i:3873505 original size:17 final size:18
Alignment explanation
Indices: 3873374--3873494 Score: 65
Period size: 18 Copynumber: 6.7 Consensus size: 18
3873364 TCATATCTTT
* *
3873374 TAAGATTGTATATCATATC
1 TAAGATTGCATAT-ACATC
* *
3873393 TAATATTGCA-ATCATATC
1 TAAGATTGCATAT-ACATC
*
3873411 TAAGATTG--TATCATATC
1 TAAGATTGCATAT-ACATC
*
3873428 TAAGATTGCA-ATCATATC
1 TAAGATTGCATAT-ACATC
* * *
3873446 TAAAATTG--TACCATATC
1 TAAGATTGCATA-TACATC
3873463 TAAGATTGCATATCACATC
1 TAAGATTGCATAT-ACATC
3873482 TAAGATTGCATAT
1 TAAGATTGCATAT
3873495 CATTGAAGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
17 29 0.34
18 30 0.35
19 27 0.31
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TAAGATTGCATATACATC
Found at i:3873827 original size:84 final size:84
Alignment explanation
Indices: 3873686--3873864 Score: 268
Period size: 84 Copynumber: 2.1 Consensus size: 84
3873676 AGTGTCTACA
* * * *
3873686 AAAATAAAATTAGATAAAATCTTGTTAAACGGCGGGAGTAAATCCCCAAACAGATTTTATTTTAT
1 AAAATAAAATCAAATAAAATCATGTTAAACGGCGGGAATAAATCCCCAAACAGATTTTATTTTAT
* *
3873751 TTAATTCTAATTTGGAAAC
66 TTAATTATAATTTAGAAAC
** *
3873770 AAAATAAAATCAAATAAAATCATGTTAAACGGCGGGAATAAATCCTGAAATAGATTTTATTTTAT
1 AAAATAAAATCAAATAAAATCATGTTAAACGGCGGGAATAAATCCCCAAACAGATTTTATTTTAT
*
3873835 TTAATTATAATTTAGAAAT
66 TTAATTATAATTTAGAAAC
3873854 AAAATAAAATC
1 AAAATAAAATC
3873865 TTGTTAAACG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.33
Consensus pattern (84 bp):
AAAATAAAATCAAATAAAATCATGTTAAACGGCGGGAATAAATCCCCAAACAGATTTTATTTTAT
TTAATTATAATTTAGAAAC
Found at i:3874104 original size:88 final size:86
Alignment explanation
Indices: 3873916--3874289 Score: 328
Period size: 87 Copynumber: 4.3 Consensus size: 86
3873906 GAAGAAATCA
* * * * * *
3873916 GAAACAAATTTTAATTTAGTTTTAATAC-TCATTTTGAAAATAACATCAAAAT-TGGAATAAATT
1 GAAACAGATTTT-ATTTAATTTTAAT-CTTCGTTTTGGAAATAAAAT-AAAATATGGAATAAAAT
* *
3873979 CGTTAAACGGAGAGAATAAATCTT
63 CGTTAAACGGTGAGAATAAATCCT
* *
3874003 GAAACAGATTTTATTTTAATTTTAATACTT-GTTTTGGAAATAAAATCAAAATTTGAAATAAAAT
1 GAAACAGATTTTA-TTTAATTTTAAT-CTTCGTTTTGGAAATAAAAT-AAAATATGGAATAAAAT
* * *
3874067 CGTTGAACGGTGGGAATCAATCCT
63 CGTTAAACGGTGAGAATAAATCCT
* ** * * *
3874091 GAAACAAATTTTATTTACCTTTAATTTTCCG-TTTGGAAATAAAATAAAAAATGGAATAAAATAG
1 GAAACAGATTTTATTTAATTTTAATCTT-CGTTTTGGAAATAAAATAAAATATGGAATAAAATCG
* * * *
3874155 TTGAACGGTAAGAATCAATCTT
65 TTAAACGGTGAGAATAAATCCT
* * **
3874177 GAAACAGATTTTA-TTAACCTTTAATTTTCCATTTGGAAAT-AAATAAAAGTAATGGAATAAAAT
1 GAAACAGATTTTATTTAA-TTTTAATCTTCGTTTTGGAAATAAAATAAAA-T-ATGGAATAAAAT
* * *
3874240 CCGTTAAACGGCGGGAATAAATCCC
63 -CGTTAAACGGTGAGAATAAATCCT
*
3874265 GAAACAGATTTTATTTACTTTTAAT
1 GAAACAGATTTTATTTAATTTTAAT
3874290 TTGGAAAAAA
Statistics
Matches: 239, Mismatches: 37, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
85 12 0.05
86 68 0.28
87 79 0.33
88 77 0.32
89 3 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (86 bp):
GAAACAGATTTTATTTAATTTTAATCTTCGTTTTGGAAATAAAATAAAATATGGAATAAAATCGT
TAAACGGTGAGAATAAATCCT
Found at i:3874177 original size:174 final size:174
Alignment explanation
Indices: 3873903--3874291 Score: 423
Period size: 174 Copynumber: 2.2 Consensus size: 174
3873893 CATTGAATGA
* * * ** * * *
3873903 CGGGAAGAAAT-CAGAAACAAATTTTAATTTAGTTTTAATACTCATTTTGAAAATAACATCAAAA
1 CGGGAATAAATCCCGAAACAAATTTT-ATTTACTTTTAATTTTCAGTTTGAAAATAAAATAAAAA
* * * *
3873967 TTGGAATAAATTCGTTAAACGGAGAGAATAAATCTTGAAACAGATTTTATTTTAA-TTTTAATAC
65 ATGGAATAAAATAGTTAAACGGAGAGAATAAATCTTGAAACAGATTTTA--TTAACCTTTAAT-C
** * *
3874031 TT-GTTTTGGAAATAAAATCAAAA-T-TTGAAATAAAAT-CGTTGAACGG
127 TTCCATTTGGAAAT-AAAT-AAAAGTAATGAAATAAAATCCGTTAAACGG
* * * * * *
3874077 TGGGAATCAATCCTGAAACAAATTTTATTTACCTTTAATTTTCCGTTTGGAAATAAAATAAAAAA
1 CGGGAATAAATCCCGAAACAAATTTTATTTACTTTTAATTTTCAGTTTGAAAATAAAATAAAAAA
* * *
3874142 TGGAATAAAATAGTTGAACGGTA-AGAATCAATCTTGAAACAGATTTTATTAACCTTTAATTTTC
66 TGGAATAAAATAGTTAAACGG-AGAGAATAAATCTTGAAACAGATTTTATTAACCTTTAATCTTC
*
3874206 CATTTGGAAATAAATAAAAGTAATGGAATAAAATCCGTTAAACGG
130 CATTTGGAAATAAATAAAAGTAATGAAATAAAATCCGTTAAACGG
*
3874251 CGGGAATAAATCCCGAAACAGATTTTATTTACTTTTAATTT
1 CGGGAATAAATCCCGAAACAAATTTTATTTACTTTTAATTT
3874292 GGAAAAAAAA
Statistics
Matches: 178, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
171 4 0.02
172 11 0.06
173 25 0.14
174 124 0.70
175 14 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (174 bp):
CGGGAATAAATCCCGAAACAAATTTTATTTACTTTTAATTTTCAGTTTGAAAATAAAATAAAAAA
TGGAATAAAATAGTTAAACGGAGAGAATAAATCTTGAAACAGATTTTATTAACCTTTAATCTTCC
ATTTGGAAATAAATAAAAGTAATGAAATAAAATCCGTTAAACGG
Found at i:3874290 original size:88 final size:87
Alignment explanation
Indices: 3873968--3874291 Score: 350
Period size: 88 Copynumber: 3.7 Consensus size: 87
3873958 ACATCAAAAT
* * * ** *
3873968 TGGAATAAATTCGTTAAACGGAGAGAATAAATCTTGAAACAGATTTTATTTTAATTTTAATACTT
1 TGGAATAAAATCGTTAAACGGTGAGAATAAATCCTGAAACAGATTTTA-TTTACCTTTAAT-TTT
** *
3874033 -GTTTTGGAAATAAAATCAAAAT-T
64 CCATTTGGAAATAAAAT-AAAATAA
* * * * *
3874056 TGAAATAAAATCGTTGAACGGTGGGAATCAATCCTGAAACAAATTTTATTTACCTTTAATTTTCC
1 TGGAATAAAATCGTTAAACGGTGAGAATAAATCCTGAAACAGATTTTATTTACCTTTAATTTTCC
*
3874121 GTTTGGAAATAAAATAAAA-AA
66 ATTTGGAAATAAAATAAAATAA
* * * * * *
3874142 TGGAATAAAATAGTTGAACGGTAAGAATCAATCTTGAAACAGATTTTATTAACCTTTAATTTTCC
1 TGGAATAAAATCGTTAAACGGTGAGAATAAATCCTGAAACAGATTTTATTTACCTTTAATTTTCC
3874207 ATTTGGAAAT-AAATAAAAGTAA
66 ATTTGGAAATAAAATAAAA-TAA
* * * *
3874229 TGGAATAAAATCCGTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACTTTTAATTT
1 TGGAATAAAAT-CGTTAAACGGTGAGAATAAATCCTGAAACAGATTTTATTTACCTTTAATTT
3874292 GGAAAAAAAA
Statistics
Matches: 199, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
85 8 0.04
86 73 0.37
87 37 0.19
88 81 0.41
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
TGGAATAAAATCGTTAAACGGTGAGAATAAATCCTGAAACAGATTTTATTTACCTTTAATTTTCC
ATTTGGAAATAAAATAAAATAA
Found at i:3877509 original size:13 final size:13
Alignment explanation
Indices: 3877491--3877555 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
3877481 ATTAAACCAA
*
3877491 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
3877504 ACTTTT-AAAATC
1 ACTTTTCAAAAGC
*
3877516 ACTTTTCCAAAGC
1 ACTTTTCAAAAGC
*
3877529 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
3877542 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
3877555 A
1 A
3877556 ATGCTAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 10 0.23
13 33 0.77
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3877526 original size:26 final size:26
Alignment explanation
Indices: 3877491--3877555 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
3877481 ATTAAACCAA
* *
3877491 ACTTTTCAAAAGTAC-TTTTAAAATC
1 ACTTTTCAAAAGCACTTTTTAAAAGC
*
3877516 ACTTTTCCAAAGCACTTTTTAAAAGC
1 ACTTTTCAAAAGCACTTTTTAAAAGC
*
3877542 ACTTCTCAAAAGCA
1 ACTTTTCAAAAGCA
3877556 ATGCTAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTTTTAAAAGC
Found at i:3877815 original size:13 final size:13
Alignment explanation
Indices: 3877776--3877826 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
3877766 TTTGGCAATA
3877776 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* * *
3877789 CTGTGGAAATGTG
1 CTTTTGAAAAGTG
*
3877802 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
3877815 CTTTTGAAAAGT
1 CTTTTGAAAAGT
3877827 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Done.