Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 103 of 126
Found at i:31423325 original size:31 final size:30
Alignment explanation
Indices: 31423232--31423325 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
31423222 ATTCAATGCT
* * *
31423232 CAAATCAATTCGACAATATATATACATATA
1 CAAATCAATTCGGCAATGTATAAACATATA
* ** * *
31423262 CGAATCAAATTTAGCAATGTAT-ATCTACATA
1 CAAATC-AATTCGGCAATGTATAAAC-ATATA
31423293 CAAATCAATTCGGCAATGTATAAAACATATA
1 CAAATCAATTCGGCAATGTAT-AAACATATA
31423324 CA
1 CA
31423326 TTTAAATTCA
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
30 19 0.40
31 26 0.55
32 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATAAACATATA
Found at i:31425904 original size:190 final size:190
Alignment explanation
Indices: 31425666--31426044 Score: 695
Period size: 190 Copynumber: 2.0 Consensus size: 190
31425656 TGGTTGGGAT
* * *
31425666 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGTTGTGTGGAACTCATATATAAATGTAAGAATTAT
1 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
* *
31425731 TTCAAGTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCCTCATTTTTATAGAG
66 TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
31425796 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
131 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
*
31425856 GAGCATAGGCAGCTTGTTGTTGTTGAAGGTGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
1 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
*
31425921 TTCAACTCTTTATTATTTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
66 TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
31425986 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTG
131 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTG
31426045 CCATCTACGC
Statistics
Matches: 182, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 182 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (190 bp):
GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
Found at i:31426991 original size:12 final size:12
Alignment explanation
Indices: 31426976--31427020 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
31426966 TTCATATAAT
31426976 AATTATATTAAG
1 AATTATATTAAG
*
31426988 AATTTTATT-A-
1 AATTATATTAAG
31426998 AATTATATTAAG
1 AATTATATTAAG
*
31427010 AATTTTATTAA
1 AATTATATTAA
31427021 ATCATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
AATTATATTAAG
Found at i:31427001 original size:22 final size:22
Alignment explanation
Indices: 31426976--31427028 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
31426966 TTCATATAAT
31426976 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTTTATTA
31426998 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTTTATTA
*
31427020 AATCATATT
1 AATTATATT
31427029 TAATAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTATATTAAGAATTTTATTA
Found at i:31427089 original size:58 final size:60
Alignment explanation
Indices: 31426971--31427096 Score: 157
Period size: 58 Copynumber: 2.1 Consensus size: 60
31426961 TTTAATTCAT
* *
31426971 ATAATAATTATATTAAGAATTTTATTAAATTATATTAAGAATTTTATTAAATCATATTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
* * ** * * *
31427031 ATAATAATTATGTTAA-AATATGGTTAAATTAT-TTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
31427089 ATAATAAT
1 ATAATAAT
31427097 CGTATTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 29 0.51
59 13 0.23
60 15 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (60 bp):
ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
Found at i:31427295 original size:16 final size:16
Alignment explanation
Indices: 31427274--31427325 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
31427264 TAAATTACTG
31427274 ATTACAACTTTATTCC
1 ATTACAACTTTATTCC
* * *
31427290 ATTACAGCTCTATTCA
1 ATTACAACTTTATTCC
31427306 ATTACAA-TTCTATTCC
1 ATTACAACTT-TATTCC
31427322 ATTA
1 ATTA
31427326 TAGTGAACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTACAACTTTATTCC
Found at i:31428520 original size:14 final size:14
Alignment explanation
Indices: 31428479--31428586 Score: 81
Period size: 14 Copynumber: 7.7 Consensus size: 14
31428469 GTTTGTATAT
*
31428479 ATGCGACTCAATAC
1 ATGCGAGTCAATAC
* *
31428493 ATGCAAGTCTATAC
1 ATGCGAGTCAATAC
*
31428507 ATGCGAGCCAATAC
1 ATGCGAGTCAATAC
* * *
31428521 TTGTGAGTCAATAT
1 ATGCGAGTCAATAC
* * *
31428535 ATGTGAGACAACAC
1 ATGCGAGTCAATAC
* * *
31428549 CTACGATTCAATAC
1 ATGCGAGTCAATAC
*
31428563 ATGCGAGTCAATAT
1 ATGCGAGTCAATAC
*
31428577 ATGCAAGTCA
1 ATGCGAGTCA
31428587 TAAATCACAT
Statistics
Matches: 69, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (14 bp):
ATGCGAGTCAATAC
Found at i:31428644 original size:27 final size:26
Alignment explanation
Indices: 31428624--31428678 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
31428614 ACCCCTGCTT
31428624 GTGCGAACCTATGTGCAACCCCCTTA
1 GTGCGAACCTATGTGCAACCCCCTTA
* *
31428650 GGTGTGAACCTATGTGCGACCCCCCTTA
1 -GTGCGAACCTATGTGC-AACCCCCTTA
31428678 G
1 G
31428679 GTGTAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCGAACCTATGTGCAACCCCCTTA
Found at i:31428673 original size:28 final size:27
Alignment explanation
Indices: 31428628--31428687 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
31428618 CTGCTTGTGC
31428628 GAACCTATGTGCAACCCCCTTAGGTGT
1 GAACCTATGTGCAACCCCCTTAGGTGT
*
31428655 GAACCTATGTGCGACCCCCCTTAGGTGT
1 GAACCTATGTGC-AACCCCCTTAGGTGT
*
31428683 AAACC
1 GAACC
31428688 CCTAACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (27 bp):
GAACCTATGTGCAACCCCCTTAGGTGT
Found at i:31428792 original size:33 final size:34
Alignment explanation
Indices: 31428696--31428806 Score: 152
Period size: 34 Copynumber: 3.3 Consensus size: 34
31428686 CCCCTAACTA
* * *
31428696 TGCGAGCTTATATGTTATACGAACTCTAGGAATG
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
* *
31428730 TGCGACCCTATATGTTATGCGAACCCTAGGAATA
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
* *
31428764 TGTGAGCCTATATG-TATGTGAACCCTAGGAATG
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
31428797 TGCGAGCCTA
1 TGCGAGCCTA
31428807 CATGCGAACC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 26 0.39
34 41 0.61
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (34 bp):
TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
Found at i:31428816 original size:29 final size:31
Alignment explanation
Indices: 31428746--31428821 Score: 75
Period size: 33 Copynumber: 2.5 Consensus size: 31
31428736 CCTATATGTT
* *
31428746 ATGCGAACCCTAGGAATATGTGAGCCTATATGT
1 ATGCGAACCCTAGGAATATGCGAGCC-ATA-GC
* *
31428779 ATGTGAACCCTAGGAATGTGCGAGCC-TA-C
1 ATGCGAACCCTAGGAATATGCGAGCCATAGC
*
31428808 ATGCGAACCTTAGG
1 ATGCGAACCCTAGG
31428822 TACATGTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 12 0.32
31 2 0.05
33 23 0.62
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (31 bp):
ATGCGAACCCTAGGAATATGCGAGCCATAGC
Found at i:31430051 original size:21 final size:21
Alignment explanation
Indices: 31430025--31430071 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
31430015 AATACTAGTG
31430025 ATGTTACTAAAATGAAATATA
1 ATGTTACTAAAATGAAATATA
* *
31430046 ATGTTACTATAATGGAATATA
1 ATGTTACTAAAATGAAATATA
31430067 ATGTT
1 ATGTT
31430072 GGATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
ATGTTACTAAAATGAAATATA
Found at i:31434486 original size:69 final size:69
Alignment explanation
Indices: 31434386--31434521 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
31434376 TATACACTGC
*
31434386 CATGGTCCAACCATAGTATTACGTCTAAAAAACTATCATAGCCTCGCTATGGTCTTACATAAACA
1 CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
31434451 TTTT
66 TTTT
* * * * * *
31434455 CATGGTCCAGCCATGGTCTTGCGTCTGAAAAACTGCCATAGCCTCGCTATGGTCTTACATAAACA
1 CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
31434520 TT
66 TT
31434522 GCCGTAGTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (69 bp):
CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
TTTT
Found at i:31434532 original size:69 final size:69
Alignment explanation
Indices: 31434383--31434540 Score: 208
Period size: 69 Copynumber: 2.3 Consensus size: 69
31434373 ATATATACAC
* * * * *
31434383 TGCCATGGTCCAACCATAGTATTACGTCTAAAAAACTATCATAGCCTCGCTATGGTCTTACATAA
1 TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
31434448 ACAT
66 ACAT
** * * * *
31434452 TTTCATGGTCCAGCCATGGTCTTGCGTCTGAAAAACTGCCATAGCCTCGCTATGGTCTTACATAA
1 TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
31434517 ACAT
66 ACAT
*
31434521 TGCCGTAGTCCAACCATGGT
1 TGCCATAGTCCAACCATGGT
31434541 TTTGTACATT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (69 bp):
TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
ACAT
Found at i:31445697 original size:110 final size:111
Alignment explanation
Indices: 31445477--31445699 Score: 403
Period size: 111 Copynumber: 2.0 Consensus size: 111
31445467 ATGTTTAGCC
31445477 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
1 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
*
31445542 AATTTAATGTTTACTAAACTTATATATTTTCCCTTTATCAAAATTG
66 AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
* *
31445588 CAAACCTATTTTAAGTCTACCCATTTTATTTTTTTATTTTTTTGAAAAATATTTATA-TTTTTTT
1 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
*
31445652 AATTTAATGTTGACTAAATTTATATATTTTCCCTTTATCAAAATTG
66 AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
31445698 CA
1 CA
31445700 TATATGCAAC
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
110 53 0.49
111 55 0.51
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (111 bp):
CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
Found at i:31447915 original size:18 final size:18
Alignment explanation
Indices: 31447892--31447927 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31447882 AGCCTCGTCT
* *
31447892 ATCACACGCCCGTGTTCG
1 ATCACAAGCCCATGTTCG
31447910 ATCACAAGCCCATGTTCG
1 ATCACAAGCCCATGTTCG
31447928 GTCATATGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (18 bp):
ATCACAAGCCCATGTTCG
Found at i:31449559 original size:45 final size:45
Alignment explanation
Indices: 31449508--31449598 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
31449498 GGTGTTTAGT
31449508 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
1 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
31449553 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
1 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
31449598 T
1 T
31449599 CCTTATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (45 bp):
TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
Found at i:31453046 original size:5 final size:5
Alignment explanation
Indices: 31453036--31453060 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31453026 TTTGGTATAT
31453036 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
31453061 AGGTAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:31454081 original size:20 final size:20
Alignment explanation
Indices: 31454052--31454089 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31454042 CTTGTACGAG
* *
31454052 ATTTGTACTTCGATGCCCTT
1 ATTTGCACTTCAATGCCCTT
31454072 ATTTGCACTTCAATGCCC
1 ATTTGCACTTCAATGCCC
31454090 CTGTATACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.39
Consensus pattern (20 bp):
ATTTGCACTTCAATGCCCTT
Found at i:31454158 original size:20 final size:20
Alignment explanation
Indices: 31454123--31454173 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31454113 TTCGCACTAC
* *
31454123 GGTGCCCATGTTTGCACATTT
1 GGTGCCCCTGTCTGCA-ATTT
*
31454144 -GTGCCCCTGTCTGCATTTT
1 GGTGCCCCTGTCTGCAATTT
31454163 GGTGCCCCTGT
1 GGTGCCCCTGT
31454174 TATGCATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.08, C:0.29, G:0.25, T:0.37
Consensus pattern (20 bp):
GGTGCCCCTGTCTGCAATTT
Found at i:31457009 original size:32 final size:32
Alignment explanation
Indices: 31456965--31457028 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
31456955 ATATATTCCT
*
31456965 AGTTCTATATGTCGATGACATTTTGCTTGCCA
1 AGTTCTAGATGTCGATGACATTTTGCTTGCCA
* *
31456997 AGTTCTAGATGTCGTTGATATTTTGCTTGCCA
1 AGTTCTAGATGTCGATGACATTTTGCTTGCCA
31457029 CTAATGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (32 bp):
AGTTCTAGATGTCGATGACATTTTGCTTGCCA
Found at i:31460340 original size:29 final size:27
Alignment explanation
Indices: 31460294--31460348 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
31460284 ATATAGATAT
31460294 GAAAATATTCATTAAAAATATAAATATAG
1 GAAAATATTCATTAAAAA-A-AAATATAG
** *
31460323 GAAAATATTTGTTGAAAAAAAATATA
1 GAAAATATTCATTAAAAAAAAATATA
31460349 AATTTATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 1 0.04
29 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (27 bp):
GAAAATATTCATTAAAAAAAAATATAG
Found at i:31461545 original size:18 final size:18
Alignment explanation
Indices: 31461522--31461556 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31461512 TTTTGGGTCG
* *
31461522 CGTTTGTAATTGGGCCAC
1 CGTTTGAAATCGGGCCAC
31461540 CGTTTGAAATCGGGCCA
1 CGTTTGAAATCGGGCCA
31461557 TGTATTTTGT
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:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTTTGAAATCGGGCCAC
Found at i:31462006 original size:44 final size:44
Alignment explanation
Indices: 31461942--31462053 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
31461932 GATCTACTCT
* * **
31461942 ACTGTGACTTCAGCGAGATAAGATCCA-TGATTTTAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGAT-CATTGACCTTAATCCGCTCC
* * * *
31461986 ACTGTAACTTTAGGGAGATAAGATTATTGGCCTTAATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCATTGACCTTAATCCGCTCC
*
31462030 ACTGCAACTTCAGGGAGATAAGAT
1 ACTGTAACTTCAGGGAGATAAGAT
31462054 TCGCCCACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 56 0.98
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGATCATTGACCTTAATCCGCTCC
Found at i:31462275 original size:42 final size:42
Alignment explanation
Indices: 31462080--31463237 Score: 427
Period size: 44 Copynumber: 26.5 Consensus size: 42
31462070 GCCTCACTGC
* * * *
31462080 CAATATAAGAAGACAAGATCTGCTATTTTCAATCCACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * *
31462124 CAATACATGAAGACAAGATCTGCTTTCCTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * *
31462169 CAATAT-GGAAACACAAGATCTGCATCTTCGATCTACTTCGCCAC
1 CAATATAGG-AAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* *
31462213 CAATATGGGAAGACAAGATCTAGTCTTCGATCCACTTC-CTAA
1 CAATATAGGAAGACAAGATCT-GTCTTCGATCCACTTCGCCAA
* *
31462255 TAATATAGGAAGACAGGATCTG-C-T--AT---CTTCG-C--
1 CAATATAGGAAGACAAGATCTGTCTTCGATCCACTTCGCCAA
* * * *
31462287 CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * *
31462332 CAATATGGGAAGACAAGATCTAGTCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCT-GTCTTCGATCCACTTCGCCAA
* * *
31462374 CAATATAGGAAGACAGGATCTGCTATCTTCAATCTACTTCATG-C--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTC--GCCAA
* * * **
31462418 CAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTCGCCGC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * * *
31462463 CAGTATGGGAAGACAAGATCTACATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCT--GTCTTCGATCCACTTCGCCAA
* * *
31462507 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * * *
31462551 CAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * *
31462596 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
31462640 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * * *
31462684 CAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * *
31462729 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
31462773 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * ** * * *
31462817 CAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCACTAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * * * * * *
31462862 CAGTATGGGAAGTCAAAATCTGCATCTTTGATCCACTTCACTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
31462906 CAATATAGGAAGACAAGATCTATTATCTTTGATCTACTTCACGCCAA
1 CAATATAGGAAGACAAGATC---TGTCTTCGATCCACTT--CGCCAA
* * *
31462953 -TATATA--AATG-CAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 CAATATAGGAA-GACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * *
31462995 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
31463039 CAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * * * *
31463083 CAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCACCAC
1 CAATATAGGAAGAC-A-AGAT-CTGTCTTCGATCCACTTCGCCAA
* * * *
31463128 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
31463172 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* *
31463216 CAATACATGAAGACAAGATCTG
1 CAATATAGGAAGACAAGATCTG
31463238 CTGCTTTTTA
Statistics
Matches: 869, Mismatches: 176, Indels: 138
0.73 0.15 0.12
Matches are distributed among these distances:
32 18 0.02
34 4 0.00
36 1 0.00
37 3 0.00
39 3 0.00
40 1 0.00
41 3 0.00
42 55 0.06
43 40 0.05
44 507 0.58
45 220 0.25
46 8 0.01
47 6 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
CAATATAGGAAGACAAGATCTGTCTTCGATCCACTTCGCCAA
Found at i:31462555 original size:133 final size:133
Alignment explanation
Indices: 31462284--31463239 Score: 1605
Period size: 133 Copynumber: 7.2 Consensus size: 133
31462274 CTGCTATCTT
*
31462284 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
* *
31462349 ATCT--AGTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCAATCTAC
66 ATCTGCA-TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTAC
31462411 TTCA
130 TTCA
* * * * *
31462415 TGCCAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTCGCCGCCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
*
31462480 ATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
31462545 TCA
131 TCA
* *
31462548 CGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
31462613 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
31462678 TCA
131 TCA
* *
31462681 CGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
31462746 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
31462811 TCA
131 TCA
* * * * *
31462814 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCACTACCAGTATGGGAAGTCAAA
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
* * * * *
31462879 ATCTGCATCTTTGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTTTGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
31462944 TCA
131 TCA
* *
31462947 CGCCAATATATAAATG-CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 CGCCAATACATGAA-GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
*
31463011 GATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTAC
65 GATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTAC
31463076 TTCA
130 TTCA
* * *
31463080 CGCCAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
31463145 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
31463210 TCA
131 TCA
31463213 CGCCAATACATGAAGACAAGATCTGCT
1 CGCCAATACATGAAGACAAGATCTGCT
31463240 GCTTTTTAGC
Statistics
Matches: 771, Mismatches: 49, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 63 0.08
132 16 0.02
133 691 0.90
134 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (133 bp):
CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
TCA
Found at i:31463020 original size:399 final size:397
Alignment explanation
Indices: 31462088--31463239 Score: 1660
Period size: 399 Copynumber: 2.9 Consensus size: 397
31462078 GCCAATATAA
* * * * * * * *
31462088 GAAGACAAGATCTGCTATTTTCAATCCACTTCAC-GCCAATACATGAAGACAAGATCTGCTT-TC
1 GAAGACAAAATCTAC-ATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGATCT-ATTATC
* * * ** * *
31462151 CTCGATCTACTTCGCCACCAATATGGAAACACAAGATCTGC-ATCTTCGATCTACTTCGCCACCA
64 TTCGATCTACTTC-ACGCCAATATATAAA-GCAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
* **
31462215 ATATGGGAAGACAAGATCT--AGTCTTCGATCCACTTC-CTAATAATATAGGAAGACAGGATCTG
127 GTATGGGAAGACAAGATCTGCA-TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG
*
31462277 ---C-T--A--T-CTT--CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
191 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTCTTCGATCTACTTCGCCA
*
31462331 CCAATATGGGAAGACAAGATCT--AGTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGAT
256 CCAGTATGGGAAGACAAGATCTGCA-TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGAT
* * * * * *
31462393 CTGCTATCTTCAATCTACTTCATGCCAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTC
320 CTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
* *
31462458 GCCGCCAGTATGG
385 ACCACCAGTATGG
* * * *
31462471 GAAGACAAGATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTT
1 GAAGACAAAATCTACATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTT
* * * *
31462536 CGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCAGTA
66 CGATCTACTTCACGCCAATATATAAAG-CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
31462601 TGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTAT
130 TGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG-TAT
*
31462666 CTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCA
194 CTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTCTTCGATCTACTTCGCCACCA
31462731 GTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGT
259 GTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGT
* *
31462796 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCACTA
324 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCA
31462861 CCAGTATGG
389 CCAGTATGG
* * *
31462870 GAAGTCAAAATCTGCATCTTTGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTT
1 GAAGACAAAATCTACATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTT
*
31462935 TGATCTACTTCACGCCAATATATAAATGCAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
66 CGATCTACTTCACGCCAATATATAAA-GCAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
31463000 TGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTAT
130 TGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG-TAT
* * *
31463065 CTTCGATCTACTTCACGCCAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCACCACCA
194 CTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTCTTCGATCTACTTCGCCACCA
31463130 GTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGT
259 GTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGT
31463195 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
324 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
31463240 GCTTTTTAGC
Statistics
Matches: 693, Mismatches: 53, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
382 35 0.05
383 86 0.12
384 15 0.02
385 25 0.04
389 1 0.00
390 1 0.00
392 1 0.00
394 1 0.00
395 3 0.00
397 66 0.10
398 15 0.02
399 443 0.64
400 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (397 bp):
GAAGACAAAATCTACATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTT
CGATCTACTTCACGCCAATATATAAAGCAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
GGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTATCT
TCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTTTCTTCGATCTACTTCGCCACCAGT
ATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTA
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
AGTATGG
Found at i:31473796 original size:23 final size:23
Alignment explanation
Indices: 31473766--31473811 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
31473756 GGTACCCGAA
31473766 CCAGCAGATTCCTCGATCTTCAC
1 CCAGCAGATTCCTCGATCTTCAC
31473789 CCAGCAGATTCCTCGATCTTCAC
1 CCAGCAGATTCCTCGATCTTCAC
31473812 AACAAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.26
Consensus pattern (23 bp):
CCAGCAGATTCCTCGATCTTCAC
Found at i:31475097 original size:19 final size:19
Alignment explanation
Indices: 31475073--31475147 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
31475063 AATCATATTT
31475073 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
* *
31475092 TCTAAGATTGCATATATCAAA
1 TCTAAGATT--ACATATCATA
*
31475113 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
31475132 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
31475148 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:31475110 original size:21 final size:21
Alignment explanation
Indices: 31475084--31475146 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
31475074 CTAAGATTAC
31475084 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
31475105 ATATCAAATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
31475124 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
31475145 AT
1 AT
31475147 CCTTGAAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.47
21 20 0.53
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:31479782 original size:120 final size:120
Alignment explanation
Indices: 31479569--31480061 Score: 871
Period size: 120 Copynumber: 4.1 Consensus size: 120
31479559 ATTTTCAATT
* * * * * * *
31479569 TAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGA
1 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
* * *
31479634 ATATTTAA-TATTAAGAATTTTACTAAATTATATATTTTTATTAAATTATATTTAA
66 ATA-TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
31479689 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
1 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
31479754 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
*
31479809 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGA
1 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
31479874 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
31479929 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
1 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
31479994 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
31480049 TAATAATTATGTT
1 TAATAATTATGTT
31480062 TAAATATGAT
Statistics
Matches: 360, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 4 0.01
120 356 0.99
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
Found at i:31479798 original size:18 final size:17
Alignment explanation
Indices: 31479770--31479804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31479760 ATTATTAAGA
*
31479770 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31479787 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31479805 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31479918 original size:18 final size:17
Alignment explanation
Indices: 31479890--31479924 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31479880 ATTATTAAGA
*
31479890 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31479907 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31479925 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31480038 original size:18 final size:17
Alignment explanation
Indices: 31480010--31480044 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31480000 ATTATTAAGA
*
31480010 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31480027 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31480045 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31480258 original size:44 final size:45
Alignment explanation
Indices: 31480209--31480299 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
31480199 AACTCTATTC
* * *
31480209 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
31480253 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
31480298 CA
1 CA
31480300 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:31480301 original size:16 final size:16
Alignment explanation
Indices: 31480280--31480348 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
31480270 GATTAGCTAT
31480280 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31480296 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
31480313 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31480329 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
31480345 TACA
1 TACA
31480349 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31480322 original size:33 final size:32
Alignment explanation
Indices: 31480280--31480348 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
31480270 GATTAGCTAT
31480280 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
31480313 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
31480345 TACA
1 TACA
31480349 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:31494401 original size:24 final size:24
Alignment explanation
Indices: 31494345--31494457 Score: 77
Period size: 24 Copynumber: 4.8 Consensus size: 24
31494335 AATCTATACT
*
31494345 TGAACCCCCATGTGAACCCCCATG
1 TGAACCCCCATGCGAACCCCCATG
** * *
31494369 CAAAACCCCATGCGAACCCCCTTG
1 TGAACCCCCATGCGAACCCCCATG
* * * *
31494393 TGAACCCCC-TACAAACTCTCATG
1 TGAACCCCCATGCGAACCCCCATG
* * * *
31494416 CGAACACCCTTGCAAACCCCCATG
1 TGAACCCCCATGCGAACCCCCATG
* *
31494440 CGAA-CACCATGCGAACCC
1 TGAACCCCCATGCGAACCC
31494458 ATGTAAACGA
Statistics
Matches: 66, Mismatches: 22, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
23 26 0.39
24 40 0.61
ACGTcount: A:0.29, C:0.43, G:0.13, T:0.14
Consensus pattern (24 bp):
TGAACCCCCATGCGAACCCCCATG
Found at i:31494402 original size:12 final size:12
Alignment explanation
Indices: 31494345--31494401 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
31494335 AATCTATACT
31494345 TGAACCCCCATG
1 TGAACCCCCATG
31494357 TGAACCCCCATG
1 TGAACCCCCATG
** *
31494369 CAAAACCCCATG
1 TGAACCCCCATG
* *
31494381 CGAACCCCCTTG
1 TGAACCCCCATG
31494393 TGAACCCCC
1 TGAACCCCC
31494402 TACAAACTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.26, C:0.46, G:0.14, T:0.14
Consensus pattern (12 bp):
TGAACCCCCATG
Found at i:31494426 original size:35 final size:36
Alignment explanation
Indices: 31494346--31494457 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 36
31494336 ATCTATACTT
* *
31494346 GAACCCCCATGTGAACCCCCATGCAAAACCCCATGC
1 GAACCCCCTTGTGAACCCCCATACAAAACCCCATGC
*
31494382 GAACCCCCTTGTGAACCCCC-TAC-AAACTCTCATGC
1 GAACCCCCTTGTGAACCCCCATACAAAAC-CCCATGC
* ** * * *
31494417 GAACACCCTTGCAAACCCCCATGC-GAACACCATGC
1 GAACCCCCTTGTGAACCCCCATACAAAACCCCATGC
31494452 GAACCC
1 GAACCC
31494458 ATGTAAACGA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 4 0.06
35 35 0.56
36 24 0.38
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (36 bp):
GAACCCCCTTGTGAACCCCCATACAAAACCCCATGC
Found at i:31496137 original size:24 final size:25
Alignment explanation
Indices: 31496080--31496147 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 25
31496070 AGGTTCTTCG
* * *
31496080 TGAGCTTCCCGATTAAATGTTCTTTA
1 TGAGCTTCCTGATTATA-GCTCTTTA
*
31496106 TGAACTTCCTGATTATAGCTC-TTA
1 TGAGCTTCCTGATTATAGCTCTTTA
*
31496130 TGAGCTTCCT-AATATAGC
1 TGAGCTTCCTGATTATAGC
31496148 CCAGATAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 7 0.19
24 12 0.33
25 3 0.08
26 14 0.39
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (25 bp):
TGAGCTTCCTGATTATAGCTCTTTA
Found at i:31499204 original size:17 final size:17
Alignment explanation
Indices: 31499144--31499195 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
31499134 AATTAAAATT
31499144 AAATAATAAAA-ATTACA
1 AAATAA-AAAATATTACA
* *
31499161 TAATATTAAAAATATTATA
1 -AA-ATAAAAAATATTACA
31499180 AAATAAAAAATATTAC
1 AAATAAAAAATATTAC
31499196 CAATTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 12 0.43
18 8 0.29
19 8 0.29
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAAAAATATTACA
Found at i:31502355 original size:16 final size:17
Alignment explanation
Indices: 31502328--31502361 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31502318 TAGAATTGGG
*
31502328 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
31502345 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
31502361 T
1 T
31502362 ATAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:31502368 original size:9 final size:9
Alignment explanation
Indices: 31502350--31502398 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
31502340 TTTAATTGAG
31502350 AAATTAATT
1 AAATTAATT
31502359 -AATATAATT
1 AAAT-TAATT
31502368 AAATTAATT
1 AAATTAATT
31502377 AAATTAATT
1 AAATTAATT
* *
31502386 GAA-TAAAT
1 AAATTAATT
31502394 AAATT
1 AAATT
31502399 TTTTTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 9 0.26
9 22 0.65
10 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
AAATTAATT
Found at i:31509202 original size:14 final size:14
Alignment explanation
Indices: 31509183--31509210 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31509173 AAGATATTCA
31509183 AATAGCAGATAGAC
1 AATAGCAGATAGAC
31509197 AATAGCAGATAGAC
1 AATAGCAGATAGAC
31509211 TGCGATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
AATAGCAGATAGAC
Found at i:31510247 original size:69 final size:69
Alignment explanation
Indices: 31510131--31510266 Score: 200
Period size: 69 Copynumber: 2.0 Consensus size: 69
31510121 TGTCATCTGT
* * *
31510131 AAAATTAAGGTTCGCATGCGAAGAGCCGTGACCTCCAGCACAATTAGCGAGAGTAAAGCTCCCAG
1 AAAATTAAGGTTCGCAAGCGAAGAGCCGCGACCTCCAGCACAATTAGCGAGAGCAAAGCTCCCAG
31510196 CTAA
66 CTAA
* * * * *
31510200 AAAATTAAGGTTCGCAAGTGAAGAGCTGCGACCTCTAGCACAGTTAGCGAGAGCAAAGCTCTCAG
1 AAAATTAAGGTTCGCAAGCGAAGAGCCGCGACCTCCAGCACAATTAGCGAGAGCAAAGCTCCCAG
31510265 CT
66 CT
31510267 GTAAACTATG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (69 bp):
AAAATTAAGGTTCGCAAGCGAAGAGCCGCGACCTCCAGCACAATTAGCGAGAGCAAAGCTCCCAG
CTAA
Found at i:31513175 original size:42 final size:43
Alignment explanation
Indices: 31513064--31513179 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 43
31513054 CTCGTACAAT
* * * *
31513064 GCCAACGTCCCAGACG-TGGTCTTACATGTAATCAAACAATGAT
1 GCCAATGTCCCAGA-GATGGTCTTACACGTAATCAAACAACGAC
* * * * * *
31513107 GCCACTGTCTCAGACAGGGTCTTACACGTAATCATA-TACGAC
1 GCCAATGTCCCAGAGATGGTCTTACACGTAATCAAACAACGAC
31513149 GCCAATGTCCCAGAGATGGTCTTACACGTAA
1 GCCAATGTCCCAGAGATGGTCTTACACGTAA
31513180 ATATCAAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
GCCAATGTCCCAGAGATGGTCTTACACGTAATCAAACAACGAC
Found at i:31518128 original size:19 final size:20
Alignment explanation
Indices: 31518072--31518129 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 20
31518062 TGTTATAATT
31518072 TTTTTAAAATATAAATTTTAGAA
1 TTTTTAAAA-AT--ATTTTAGAA
*
31518095 TTTTTATAAATATTTTA-AA
1 TTTTTAAAAATATTTTAGAA
31518114 -TTTTAAAAATCATTTT
1 TTTTTAAAAAT-ATTTT
31518130 GAAAATTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 6 0.19
22 2 0.06
23 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATATTTTAGAA
Found at i:31533820 original size:25 final size:25
Alignment explanation
Indices: 31533781--31533831 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
31533771 ATGATATAAT
*
31533781 ACTTATTATAATCTTTTAAATTATA
1 ACTTATCATAATCTTTTAAATTATA
*
31533806 ACTTATCATATTCTTTTAAATTATA
1 ACTTATCATAATCTTTTAAATTATA
31533831 A
1 A
31533832 TTTTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (25 bp):
ACTTATCATAATCTTTTAAATTATA
Found at i:31536296 original size:18 final size:17
Alignment explanation
Indices: 31536235--31536298 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
31536225 TGTCACCTCA
*
31536235 ATAAATAATTT-AAAATT
1 ATAAA-AATTTAAAAAAT
*
31536252 ATAAAAATATTCAAAAAT
1 ATAAAAAT-TTAAAAAAT
*
31536270 AAAAGAAATTTAAAAAAT
1 ATAA-AAATTTAAAAAAT
31536288 GATAAAAATTT
1 -ATAAAAATTT
31536299 TATTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 22 0.56
19 7 0.18
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAAATTTAAAAAAT
Found at i:31542980 original size:30 final size:29
Alignment explanation
Indices: 31542944--31543010 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
31542934 TTTAATTAAT
* *
31542944 TTTTTAAAATTTA-AAAAATATTTTTATAAG
1 TTTTTAAAACTTATAAAAATA-TTTTA-AAA
31542974 TTTTT-AAACTTATAAAAATATTTTAAAA
1 TTTTTAAAACTTATAAAAATATTTTAAAA
31543002 TTTTTAAAA
1 TTTTTAAAA
31543011 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 14 0.42
30 12 0.36
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTTTAAAACTTATAAAAATATTTTAAAA
Found at i:31544068 original size:20 final size:19
Alignment explanation
Indices: 31544032--31544070 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
31544022 ATTAAAGGAG
* *
31544032 AAATTAAATTAATTTGATT
1 AAATTAAATCAAATTGATT
31544051 AAATTCAAATCAAATTGATT
1 AAATT-AAATCAAATTGATT
31544071 TGAATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
AAATTAAATCAAATTGATT
Found at i:31545339 original size:21 final size:21
Alignment explanation
Indices: 31545315--31545357 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
31545305 ACCTAAACCC
31545315 TAAACTTATAAAAATA-TTTTT
1 TAAA-TTATAAAAATAGTTTTT
*
31545336 TAAATTTTAAAAATAGTTTTT
1 TAAATTATAAAAATAGTTTTT
31545357 T
1 T
31545358 TTATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAAATTATAAAAATAGTTTTT
Found at i:31546982 original size:60 final size:60
Alignment explanation
Indices: 31546889--31547010 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
31546879 TGATAAAGGG
31546889 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
1 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
*
31546949 AAAGAAATAACTATCCAAACAGAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
1 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
31547009 AA
1 AA
31547011 TGCTTAGCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (60 bp):
AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
Found at i:31550961 original size:21 final size:21
Alignment explanation
Indices: 31550937--31550976 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31550927 TTTTTTAAGC
31550937 CAACACACCAATTTTGACTAT
1 CAACACACCAATTTTGACTAT
** *
31550958 CAACATGCCTATTTTGACT
1 CAACACACCAATTTTGACT
31550977 GGCATAATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (21 bp):
CAACACACCAATTTTGACTAT
Found at i:31552292 original size:20 final size:19
Alignment explanation
Indices: 31552267--31552316 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
31552257 TAATATATTT
31552267 TATTATTAAAATATTAAAAA
1 TATTATTAAAAT-TTAAAAA
* *
31552287 TATTATTTAAACTTTAAAAT
1 TATTA-TTAAAATTTAAAAA
31552307 TATTAATTAA
1 TATT-ATTAA
31552317 CGTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTATTAAAATTTAAAAA
Found at i:31552322 original size:19 final size:20
Alignment explanation
Indices: 31552280--31552323 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31552270 TATTAAAATA
* *
31552280 TTAAAAATATTATTTAAACT
1 TTAAAAATATTAATTAAACG
*
31552300 TTAAAATTATTAATT-AACG
1 TTAAAAATATTAATTAAACG
31552319 TTAAA
1 TTAAA
31552324 TTTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAAATATTAATTAAACG
Found at i:31555786 original size:43 final size:43
Alignment explanation
Indices: 31555722--31555904 Score: 294
Period size: 43 Copynumber: 4.3 Consensus size: 43
31555712 TTCTAAAAAT
* *
31555722 GCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAATC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* * *
31555765 GCCACTAAAGATCAAAACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*
31555808 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTCTTCCCACAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
31555851 GCCGCTAAAGAACAAGACTTTTAGCGGCGCTTTTCCCATAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
31555894 GCCGCTAAAGA
1 GCCGCTAAAGA
31555905 TTATGACCTT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:31559336 original size:21 final size:22
Alignment explanation
Indices: 31559289--31559359 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 22
31559279 GAAATATCAA
*
31559289 AATAAAAATCAACTG-AAAT-CC
1 AATAAAAA-CAACTGAAAATAAC
*
31559310 AAATAAAAAGAAC-GAAAATTAAC
1 -AATAAAAACAACTGAAAA-TAAC
31559333 -AT-AAAACAACTGAAAATAAC
1 AATAAAAACAACTGAAAATAAC
31559353 AATAAAA
1 AATAAAA
31559360 CGGGGGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
20 12 0.30
21 15 0.38
22 12 0.30
23 1 0.03
ACGTcount: A:0.66, C:0.13, G:0.06, T:0.15
Consensus pattern (22 bp):
AATAAAAACAACTGAAAATAAC
Found at i:31559984 original size:9 final size:9
Alignment explanation
Indices: 31559970--31560022 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
31559960 GTTTAAATTT
31559970 TTTTTAAAA
1 TTTTTAAAA
31559979 TTTTTAAAA
1 TTTTTAAAA
**
31559988 AATTTAAAA
1 TTTTTAAAA
31559997 TCTTTTAAAA
1 T-TTTTAAAA
31560007 TTCATTTTAAAA
1 -T--TTTTAAAA
31560019 TTTT
1 TTTT
31560023 AAATCACGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 19 0.53
10 7 0.19
11 2 0.06
12 8 0.22
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:31560394 original size:21 final size:18
Alignment explanation
Indices: 31560352--31560407 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
31560342 CAAAACACGC
*
31560352 AAAAAACTGAACTGGATA
1 AAAAAACTGAACCGGATA
31560370 AAAAAACTGAACCGAGCACTA
1 AAAAAACTGAACCG-G-A-TA
* *
31560391 AAAATACTGAACGGGAT
1 AAAAAACTGAACCGGAT
31560408 GGGAGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 2 0.06
21 14 0.44
ACGTcount: A:0.52, C:0.16, G:0.18, T:0.14
Consensus pattern (18 bp):
AAAAAACTGAACCGGATA
Found at i:31560633 original size:21 final size:21
Alignment explanation
Indices: 31560609--31560648 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31560599 TTTAACACAT
*
31560609 AACCTCTAAACCTTAAACCCC
1 AACCTCTAAACCATAAACCCC
*
31560630 AACCTTTAAACCATAAACC
1 AACCTCTAAACCATAAACC
31560649 ATAAACCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAAACCATAAACCCC
Found at i:31560653 original size:14 final size:14
Alignment explanation
Indices: 31560636--31560689 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
31560626 CCCCAACCTT
31560636 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
31560650 TAAACCATAACCCC
1 TAAACCATAAACCA
* *
31560664 TAAACCCATAATCTA
1 TAAA-CCATAAACCA
*
31560679 TAAACCTTAAA
1 TAAACCATAAA
31560690 ATGGTAACAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:31560719 original size:14 final size:14
Alignment explanation
Indices: 31560699--31560747 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
31560689 AATGGTAACA
*
31560699 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
31560713 TCTAAACCATATAC
1 CCTAAACCATAAAC
* *
31560727 CCTAAACCAAAAAA
1 CCTAAACCATAAAC
31560741 CCTAAAC
1 CCTAAAC
31560748 TATAGTGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:31560996 original size:41 final size:41
Alignment explanation
Indices: 31560929--31561296 Score: 477
Period size: 41 Copynumber: 9.0 Consensus size: 41
31560919 TTTAAATCCT
31560929 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * *
31560970 TGAGCATTAGTGGCGTTTTTTAAAAAACGCCGCTAAAG-CC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * * * *
31561010 TAAGCATTAGCGGCGCTTCCCCAAAAACGCCACTAAGGCTC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
31561051 TGAGCATTAGCGGCGCTTCCCCAAAAACGCCACTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * *
31561092 TGACCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAACCT
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
31561133 TGAGCATTAGCGACGCTTCCTCAAAAACGCCGCTAAAGCCT
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
31561174 TAAGCATTAGCGGTGCTTTCTCAAAAACGCCGCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* ** * *
31561215 TGATCATTAGCGATGCTTTCTCAAAAACGCCTCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
31561256 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
31561297 CGGAAGCTCA
Statistics
Matches: 284, Mismatches: 42, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
40 31 0.11
41 253 0.89
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
Found at i:31573518 original size:18 final size:19
Alignment explanation
Indices: 31573497--31573534 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
31573487 ATCAATATTT
31573497 TTAT-AAAAATATCGATAC
1 TTATAAAAAATATCGATAC
31573515 TTATGAAAAAATATCGATAC
1 TTAT-AAAAAATATCGATAC
31573535 CACGGGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTATAAAAAATATCGATAC
Found at i:31575922 original size:29 final size:30
Alignment explanation
Indices: 31575890--31576079 Score: 116
Period size: 29 Copynumber: 6.6 Consensus size: 30
31575880 TTTTTTCGAG
* *
31575890 TTTTATAGTTCTGCCATTA-TTTTCTAGAA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* *
31575919 TTTTATAGTTTTGCCCCTAGTTTTCT-GGA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* * * * *
31575948 TTTTTTAATTATGCCACTATTTTTCTAG-T
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* *
31575977 TTTTATAGTTTTGCCACTGGTTTTCCA-AA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
** *
31576006 GTTTTCA-A-TTCAGCCACT--TTTTTTAG-A
1 -TTTT-ATAGTTTTGCCACTAGTTTTCTAGAA
* **
31576033 TTTTACAAATTTGCCACTA-TTTT-TAAGAA
1 TTTTATAGTTTTGCCACTAGTTTTCT-AGAA
31576062 -TTTATAGTTTTGCCACTA
1 TTTTATAGTTTTGCCACTA
31576080 TTCTTCAAAA
Statistics
Matches: 123, Mismatches: 27, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 5 0.04
27 14 0.11
28 21 0.17
29 69 0.56
30 12 0.10
31 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.51
Consensus pattern (30 bp):
TTTTATAGTTTTGCCACTAGTTTTCTAGAA
Found at i:31576022 original size:58 final size:57
Alignment explanation
Indices: 31575901--31576056 Score: 147
Period size: 58 Copynumber: 2.7 Consensus size: 57
31575891 TTTATAGTTC
* *** * *
31575901 TGCCA-TTATTTTCTAGAATTTTATAGTTTTGCCCCTAGTTTTCTGGATTTTTTAATTA
1 TGCCACTT-TTTTCTAG-ATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATTA
* *
31575959 TGCCACTATTTTTCTAGTTTTTATAGTTTTGCCACTGGTTTTCCAAAGTTTTCAATTCA
1 TGCCACT-TTTTTCTAGATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATT-A
* ** *
31576018 -GCCACTTTTTT-TAGATTTTACAAATTTGCCACTATTTTT
1 TGCCACTTTTTTCTAGATTTTATAGTTTTGCCACTAGTTTT
31576057 AAGAATTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
56 22 0.27
57 5 0.06
58 43 0.53
59 10 0.12
60 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (57 bp):
TGCCACTTTTTTCTAGATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATTA
Found at i:31576055 original size:28 final size:28
Alignment explanation
Indices: 31576018--31576081 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
31576008 TTTCAATTCA
* *
31576018 GCCACT-TTTTTTAGATTTTACAAATTT
1 GCCACTATTTTTAAGAATTTACAAATTT
* **
31576045 GCCACTATTTTTAAGAATTTATAGTTTT
1 GCCACTATTTTTAAGAATTTACAAATTT
31576073 GCCACTATT
1 GCCACTATT
31576082 CTTCAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (28 bp):
GCCACTATTTTTAAGAATTTACAAATTT
Found at i:31577112 original size:37 final size:36
Alignment explanation
Indices: 31577031--31577120 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 36
31577021 TTGAACCGTA
* *
31577031 TTGAATTGATTGATATACGAGACTGTTTGTTATCATG
1 TTGAATTGATTGATATACGAAACTGTTTGTCAT-ATG
* **
31577068 TTAAATTGATTGATATGTGAAACTGTTTGTCAT-TG
1 TTGAATTGATTGATATACGAAACTGTTTGTCATATG
31577103 TACTGAATTGATTGATAT
1 T--TGAATTGATTGATAT
31577121 TACTGTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 3 0.07
37 42 0.93
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (36 bp):
TTGAATTGATTGATATACGAAACTGTTTGTCATATG
Found at i:31578134 original size:20 final size:20
Alignment explanation
Indices: 31578109--31578170 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
31578099 ACAATTTTAA
* *
31578109 AATCAAGTGAAAATGATTTT
1 AATCAAGTCAAAATAATTTT
*
31578129 AATCAAGTCAAAATAATTTC
1 AATCAAGTCAAAATAATTTT
* *
31578149 AATCAAGTTAAAATTATTTT
1 AATCAAGTCAAAATAATTTT
31578169 AA
1 AA
31578171 GACATCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
AATCAAGTCAAAATAATTTT
Found at i:31578189 original size:40 final size:40
Alignment explanation
Indices: 31578109--31578196 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
31578099 ACAATTTTAA
*
31578109 AATCAAGTGAAAATGATTTTAATCAAGTCAAAATAATTTC
1 AATCAAGTGAAAATGATTTTAAACAAGTCAAAATAATTTC
* * *
31578149 AATCAAGTTAAAATTATTTTAAGAC-A-TCAAAATGATTTTC
1 AATCAAGTGAAAATGATTTTAA-ACAAGTCAAAAT-AATTTC
*
31578189 AAACAAGT
1 AATCAAGT
31578197 CAGGATTGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 7 0.17
40 33 0.80
41 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (40 bp):
AATCAAGTGAAAATGATTTTAAACAAGTCAAAATAATTTC
Found at i:31579446 original size:25 final size:25
Alignment explanation
Indices: 31579400--31579447 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31579390 CACACGGCCG
* *
31579400 TGTGAAATAATGTAGGCCGTGTGCT
1 TGTGAAATAATGTAGACAGTGTGCT
31579425 TGTGAAATCAA-GTAGACAGTGTG
1 TGTGAAAT-AATGTAGACAGTGTG
31579448 GACCACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (25 bp):
TGTGAAATAATGTAGACAGTGTGCT
Found at i:31585183 original size:18 final size:21
Alignment explanation
Indices: 31585155--31585194 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
31585145 ATATATATGT
31585155 ATTATTTTAAAA-AT-AAAAA
1 ATTATTTTAAAATATGAAAAA
31585174 ATTA-TTTAAAATATGAAAAA
1 ATTATTTTAAAATATGAAAAA
31585194 A
1 A
31585195 ATAAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTATTTTAAAATATGAAAAA
Found at i:31585647 original size:15 final size:16
Alignment explanation
Indices: 31585614--31585649 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
31585604 TGAATGGGTC
*
31585614 TCAACCTCTTTTATTA
1 TCAACCCCTTTTATTA
31585630 TCAACCCCTTTT-TTA
1 TCAACCCCTTTTATTA
31585645 TCAAC
1 TCAAC
31585650 AACTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (16 bp):
TCAACCCCTTTTATTA
Found at i:31588472 original size:51 final size:51
Alignment explanation
Indices: 31588355--31588842 Score: 400
Period size: 51 Copynumber: 9.6 Consensus size: 51
31588345 AAAGGGATGG
* * * * *
31588355 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGAT-AGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-TTCA-A
* *
31588405 TCGCATGTGTAGTACTACT-TGCAGGCTACTATGCGTACTGGATAGTTTCAA
1 TCACGTGTGTAGTACTA-TGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* * * * *
31588456 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGAT-AGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-TTCA-A
* *
31588506 TCGCATGTGTAGTACTACT-TGCAGGCTACTATGCGTACTGGATAGTTTCAA
1 TCACGTGTGTAGTACTA-TGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* * * * *
31588557 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGAT-AGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-TTCA-A
* *
31588607 TCGCATGTGTAGTACTACT-TGCAGGCTACTATGCGTACTGGATAGTTTCAA
1 TCACGTGTGTAGTACTA-TGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* * * * *
31588658 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGAT-AGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-TTCA-A
* *
31588708 TCGCATGTGTAGTACTACT-TGCAGGCTACTATGCGTACTGGATAGTTTCAA
1 TCACGTGTGTAGTACTA-TGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* * * * * **
31588759 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCAGATGGTAAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACT-GGATAGT-TTCAA
*
31588810 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
31588843 TGAACCGAAC
Statistics
Matches: 350, Mismatches: 60, Indels: 55
0.75 0.13 0.12
Matches are distributed among these distances:
49 6 0.02
50 151 0.43
51 184 0.53
52 9 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
Found at i:31588475 original size:101 final size:101
Alignment explanation
Indices: 31588355--31588842 Score: 899
Period size: 101 Copynumber: 4.8 Consensus size: 101
31588345 AAAGGGATGG
31588355 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31588420 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
66 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
31588456 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31588521 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
66 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
31588557 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31588622 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
66 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
31588658 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31588723 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
66 TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* * * *
31588759 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGGTAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
31588823 ACTA-TGTGCAGGCTACTATG
64 ACTACT-TGCAGGCTACTATG
31588843 TGAACCGAAC
Statistics
Matches: 380, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
100 4 0.01
101 344 0.91
102 32 0.08
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
TACTTGCAGGCTACTATGCGTACTGGATAGTTTCAA
Found at i:31588844 original size:26 final size:26
Alignment explanation
Indices: 31588764--31588844 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
31588754 TTCAATCACG
31588764 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
31588790 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
31588815 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
31588841 TGTG
1 TGTG
31588845 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:31588902 original size:45 final size:45
Alignment explanation
Indices: 31588846--31588940 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
31588836 TACTATGTGA
* *
31588846 ACCGAACATCATTGATTAGTAAAGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
* *
31588891 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
31588936 ACCGA
1 ACCGA
31588941 GTATCTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
Found at i:31591645 original size:50 final size:50
Alignment explanation
Indices: 31591586--31591697 Score: 208
Period size: 50 Copynumber: 2.3 Consensus size: 50
31591576 CATTCAAAAT
31591586 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
1 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
*
31591636 TAACCATTCAAGAGCTTCAAACACTTAACAAGACACATATACATATCATA
1 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
31591686 TAACCA-TCAAGA
1 TAACCATTCAAGA
31591698 ACAAGTATTA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 6 0.10
50 55 0.90
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (50 bp):
TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
Found at i:31592293 original size:22 final size:20
Alignment explanation
Indices: 31592272--31592348 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
31592262 CTGAGTAGTA
*
31592272 GGCACCGAAGTGCGAATCAGT
1 GGCACCGAAGTGC-AAACAGT
** *
31592293 AAACACCGAAATGCAAACAGT
1 -GGCACCGAAGTGCAAACAGT
*
31592314 GGCACCAAAGTGCAAACAGT
1 GGCACCGAAGTGCAAACAGT
**
31592334 GGCATTGAAGTGCAA
1 GGCACCGAAGTGCAA
31592349 TCTCATACAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 28 0.64
21 6 0.14
22 10 0.23
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (20 bp):
GGCACCGAAGTGCAAACAGT
Found at i:31593327 original size:22 final size:20
Alignment explanation
Indices: 31593291--31593349 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
31593281 GACCCGATCC
31593291 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
31593313 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
31593334 AAATATTTTAAAAATA
1 ATTTATTTTAAAAATA
31593350 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:31593346 original size:11 final size:11
Alignment explanation
Indices: 31593332--31593474 Score: 79
Period size: 11 Copynumber: 14.4 Consensus size: 11
31593322 AAAAATTAAA
31593332 AAAAATATTTT
1 AAAAATATTTT
31593343 AAAAATATTTT
1 AAAAATATTTT
31593354 --AAA-A--TT
1 AAAAATATTTT
*
31593360 AAAAA-A-ATT
1 AAAAATATTTT
31593369 AAAAAGTATTTT
1 AAAAA-TATTTT
31593381 AAAAATATTTT
1 AAAAATATTTT
31593392 --AAA-A--TT
1 AAAAATATTTT
*
31593398 AAAAA-A-ATT
1 AAAAATATTTT
31593407 AAAAAGTATTTT
1 AAAAA-TATTTT
31593419 AAAAATATTTT
1 AAAAATATTTT
*
31593430 --AAA-A-TTA
1 AAAAATATTTT
* **
31593437 AAAAATAATAA
1 AAAAATATTTT
31593448 AAAAAGTATTTT
1 AAAAA-TATTTT
31593460 AAAAATATTTT
1 AAAAATATTTT
31593471 AAAA
1 AAAA
31593475 TTAAAAAAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
6 4 0.04
7 2 0.02
8 11 0.10
9 26 0.24
10 1 0.01
11 42 0.39
12 22 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:31593363 original size:38 final size:37
Alignment explanation
Indices: 31593331--31593484 Score: 245
Period size: 38 Copynumber: 4.0 Consensus size: 37
31593321 TAAAAATTAA
*
31593331 AAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA-T
31593369 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA-T
31593407 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATT-AAAAA-AAT
31593446 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
1 --AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
31593485 TTAAAAAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
38 66 0.59
39 9 0.08
40 7 0.06
41 29 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (37 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
Found at i:31593480 original size:17 final size:17
Alignment explanation
Indices: 31593458--31593504 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
31593448 AAAAAGTATT
*
31593458 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
31593475 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
31593492 ATAAATATATTTA
1 TTAAAAATATTTA
31593505 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:31594708 original size:12 final size:12
Alignment explanation
Indices: 31594687--31594722 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
31594677 AAGATCTCTC
31594687 CATA-TCTTTTG
1 CATATTCTTTTG
31594698 CATATTCTTTTG
1 CATATTCTTTTG
31594710 CATATTCTTTTG
1 CATATTCTTTTG
31594722 C
1 C
31594723 TTACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (12 bp):
CATATTCTTTTG
Found at i:31595443 original size:12 final size:13
Alignment explanation
Indices: 31595426--31595458 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
31595416 TTCCCTTTTA
31595426 TTTAACATAA-TT
1 TTTAACATAAGTT
31595438 TTTAAC-TAAGTT
1 TTTAACATAAGTT
31595450 TTTAACATA
1 TTTAACATA
31595459 TAAACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 14 0.74
13 2 0.11
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (13 bp):
TTTAACATAAGTT
Found at i:31595721 original size:29 final size:30
Alignment explanation
Indices: 31595686--31595745 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
31595676 ACAAATGTTT
*
31595686 ACTAAAAATATTTACAAGCTCAGTTT-ATA
1 ACTAAAAATAATTACAAGCTCAGTTTCATA
*
31595715 ACTAAAAATAATTACAAGCTTAGTTTCATA
1 ACTAAAAATAATTACAAGCTCAGTTTCATA
31595745 A
1 A
31595746 ATAAGGTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
ACTAAAAATAATTACAAGCTCAGTTTCATA
Found at i:31597146 original size:5 final size:5
Alignment explanation
Indices: 31597136--31597160 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31597126 TAGTCTCTAC
31597136 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
31597161 GCTAATGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:31598320 original size:24 final size:24
Alignment explanation
Indices: 31598293--31598348 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
31598283 TATCATGTAC
* *
31598293 TATTATTTTA-AGTTTTTCATATAT
1 TATTATTTTAGA-TTTATCACATAT
*
31598317 TATTATTTTGGATTTATCACATAT
1 TATTATTTTAGATTTATCACATAT
31598341 TATTATTT
1 TATTATTT
31598349 AATTTCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (24 bp):
TATTATTTTAGATTTATCACATAT
Found at i:31610054 original size:27 final size:27
Alignment explanation
Indices: 31610018--31610427 Score: 455
Period size: 27 Copynumber: 15.2 Consensus size: 27
31610008 AGAGGTCTAT
*
31610018 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31610045 AAATGACCGAAATACCCCCATAGGGT-
1 AAATGACCGAAATACCCCCATAGGGTA
* ** ** *
31610071 AAATAACTAAAATACCCTTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
31610098 AAATGATTGAAATACTCTCCATAGGGTA
1 AAATGACCGAAATAC-CCCCATAGGGTA
* ** *
31610126 GAATGATAGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31610153 GAATGACCGAAATACACCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
31610180 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31610207 GAATGATCGAAATA-CCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31610233 AATTGACCGAAATACCCCGATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31610260 AAATGACTGAAATACCCCTATAGGGTT
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31610287 AAATAATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31610314 GAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
31610341 AAATGACCAAAATGCCCTCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
*
31610368 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31610395 AAATAACCGAAATACCCCCATAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31610422 AAATGA
1 AAATGA
31610428 TTGTTATACC
Statistics
Matches: 322, Mismatches: 58, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 42 0.13
27 259 0.80
28 21 0.07
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:31610864 original size:29 final size:31
Alignment explanation
Indices: 31610822--31610888 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
31610812 AACTACATAT
* *
31610822 CTGCACTGATTAATGATATT-GTACTG-TTA
1 CTGCATTGATTAATGATATTAATACTGTTTA
31610851 CTGCATTGATTAATGATATTACATACTGTTTA
1 CTGCATTGATTAATGATATTA-ATACTGTTTA
31610883 CTGCAT
1 CTGCAT
31610889 GACTGATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 5 0.15
32 9 0.27
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (31 bp):
CTGCATTGATTAATGATATTAATACTGTTTA
Found at i:31622566 original size:22 final size:20
Alignment explanation
Indices: 31622530--31622588 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
31622520 GACCCAGCCC
31622530 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
31622552 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
31622573 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
31622589 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:31622759 original size:29 final size:29
Alignment explanation
Indices: 31622738--31622798 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
31622728 AAAGTATTTT
31622738 AAAAA-TATTTTAAAATTAAAAAATAATA
1 AAAAAGTATTTTAAAATTAAAAAATAATA
*
31622766 AAAAAGTATTTTAAAATTAAAAAA-AATT
1 AAAAAGTATTTTAAAATTAAAAAATAATA
31622794 AAAAA
1 AAAAA
31622799 CTAAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAATAATA
Found at i:31622782 original size:39 final size:39
Alignment explanation
Indices: 31622571--31622781 Score: 386
Period size: 39 Copynumber: 5.4 Consensus size: 39
31622561 AAAAATTAAA
31622571 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
31622610 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
31622649 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
31622688 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
* **
31622727 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAT-TTTG
31622767 AAAAGTATTTTAAAA
1 AAAAGTATTTTAAAA
31622782 TTAAAAAAAA
Statistics
Matches: 168, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
39 152 0.90
40 16 0.10
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (39 bp):
AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTG
Found at i:31623293 original size:17 final size:17
Alignment explanation
Indices: 31623271--31623305 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31623261 ATTTTTATAG
31623271 TTTAATAATAATTTTAA
1 TTTAATAATAATTTTAA
* *
31623288 TTTAATACTTATTTTAA
1 TTTAATAATAATTTTAA
31623305 T
1 T
31623306 AGTATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATAATAATTTTAA
Found at i:31625999 original size:17 final size:18
Alignment explanation
Indices: 31625963--31626001 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31625953 CCATCGTCCT
* *
31625963 CTAAGGGGAAATAGATAA
1 CTAAGGGAAAAAAGATAA
31625981 CTAAGGGAAAAAAGA-AA
1 CTAAGGGAAAAAAGATAA
31625998 CTAA
1 CTAA
31626002 CTAAGTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.56, C:0.08, G:0.23, T:0.13
Consensus pattern (18 bp):
CTAAGGGAAAAAAGATAA
Found at i:31628887 original size:16 final size:15
Alignment explanation
Indices: 31628852--31628887 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
31628842 CATTCATTCA
*
31628852 TGCATTTAGATTATT
1 TGCATTTAGATTAAT
31628867 TGCATTTAGATTTAAT
1 TGCATTTAGA-TTAAT
31628883 TGCAT
1 TGCAT
31628888 AGGGATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (15 bp):
TGCATTTAGATTAAT
Found at i:31631628 original size:45 final size:47
Alignment explanation
Indices: 31631575--31631666 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
31631565 ATTTATACCT
*
31631575 GAATACATAGCTAATACCTACATTCG-A-ATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
31631620 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
31631667 ATCATATACA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 25 0.57
46 1 0.02
47 18 0.41
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (47 bp):
GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
Found at i:31631647 original size:25 final size:25
Alignment explanation
Indices: 31631575--31631649 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
31631565 ATTTATACCT
*
31631575 GAATACATAGCTAATACCTACATTC
1 GAATACATAGCTAATACATACATTC
*
31631600 GAATATATA--T-ATACAT--ATTC
1 GAATACATAGCTAATACATACATTC
31631620 GAATACATAGCTAATACATACATTC
1 GAATACATAGCTAATACATACATTC
31631645 GAATA
1 GAATA
31631650 TATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 12 0.29
22 6 0.14
23 7 0.17
25 17 0.40
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (25 bp):
GAATACATAGCTAATACATACATTC
Found at i:31631662 original size:20 final size:20
Alignment explanation
Indices: 31631593--31631662 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
31631583 AGCTAATACC
31631593 TACATTCGAATATATATATA
1 TACATTCGAATATATATATA
* * *
31631613 CATATTCGAATACATAGCTAATACA
1 TACATTCGAAT--ATA--T-ATATA
31631638 TACATTCGAATATATATATA
1 TACATTCGAATATATATATA
31631658 TACAT
1 TACAT
31631663 ATTCATCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 18 0.46
21 1 0.03
22 3 0.08
23 3 0.08
24 1 0.03
25 13 0.33
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (20 bp):
TACATTCGAATATATATATA
Found at i:31632037 original size:16 final size:16
Alignment explanation
Indices: 31632016--31632050 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31632006 CACCGGCTTT
31632016 TAGCCTGCTAGACCTA
1 TAGCCTGCTAGACCTA
31632032 TAGCCTGCTAGACCTA
1 TAGCCTGCTAGACCTA
31632048 TAG
1 TAG
31632051 TCCGAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (16 bp):
TAGCCTGCTAGACCTA
Found at i:31632107 original size:41 final size:41
Alignment explanation
Indices: 31632033--31632141 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
31632023 CTAGACCTAT
* * * * * * *
31632033 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
*
31632074 AGCCTGTTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
* *
31632115 AGTCTGCTAGACGTAAAGTCTGTATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTA
31632142 CATTCGATCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
Found at i:31634809 original size:27 final size:27
Alignment explanation
Indices: 31634770--31634922 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 27
31634760 AGAGGCCAGT
31634770 AAATGA-CATAAATACCCCCATAGGGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* *
31634797 AAATGACCAAAATACCCTCATAGGGAA
1 AAATGACCAAAATACCCCCATAGGGTA
* * * *
31634824 AAATAACCGAAATACCTCCATAGGATA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
31634851 AAATGACCAAAATACCCCCATAAGATA
1 AAATGACCAAAATACCCCCATAGGGTA
** *
31634878 AAATGACTGAAATACCCTCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
31634905 AAATAACTAAAATACCCC
1 AAATGACCAAAATACCCC
31634923 TTATAGGAGA
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
27 103 0.98
28 2 0.02
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:31634908 original size:81 final size:81
Alignment explanation
Indices: 31634770--31634920 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
31634760 AGAGGCCAGT
* * *
31634770 AAATGACATAAATACCCCCATAGGGTAAAATGACCAAAATACCCTCATAGGGAAAAATAACCGAA
1 AAATGACATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAAA
31634835 ATACCTCCATAGGATA
66 ATACCTCCATAGGATA
** * *
31634851 AAATGACCA-AAATACCCCCATAAGATAAAATGACTGAAATACCCTCATAGGGTAAAATAACTAA
1 AAATGA-CATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAA
31634915 AATACC
65 AATACC
31634921 CCTTATAGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 60 0.97
82 2 0.03
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (81 bp):
AAATGACATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAAA
ATACCTCCATAGGATA
Found at i:31635134 original size:26 final size:26
Alignment explanation
Indices: 31635105--31635158 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
31635095 TTGCCACATT
*
31635105 TACTGTTACTGGCAGCTTCGCTGCGA
1 TACTATTACTGGCAGCTTCGCTGCGA
*
31635131 TACTATTACTGGCAGCTTTGCTGCGA
1 TACTATTACTGGCAGCTTCGCTGCGA
31635157 TA
1 TA
31635159 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTCGCTGCGA
Found at i:31635324 original size:28 final size:28
Alignment explanation
Indices: 31635266--31635329 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
31635256 ACTGTACTGA
* *
31635266 TACTGTATTGGGCTAAAGCCCACATTGT
1 TACTGTATTGGGCTAAAGCCCACACTAT
* * * *
31635294 TACTGTATTGGGCTCAGGCTCAGACTAT
1 TACTGTATTGGGCTAAAGCCCACACTAT
31635322 TACTGTAT
1 TACTGTAT
31635330 GTCGTATACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (28 bp):
TACTGTATTGGGCTAAAGCCCACACTAT
Found at i:31639411 original size:17 final size:18
Alignment explanation
Indices: 31639381--31639423 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31639371 TCCCTCACCT
**
31639381 TTTCTTTTTTGTTCT-TC
1 TTTCTTTTCGGTTCTCTC
31639398 TTTCTTTTCGGTTCTCTC
1 TTTCTTTTCGGTTCTCTC
31639416 TTCTCTTT
1 TT-TCTTT
31639424 GATTGTCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 4 0.18
19 5 0.23
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCGGTTCTCTC
Found at i:31641255 original size:9 final size:9
Alignment explanation
Indices: 31641241--31641319 Score: 104
Period size: 9 Copynumber: 8.6 Consensus size: 9
31641231 TTTGGTTAAA
*
31641241 AATTACTCG
1 AATTACCCG
*
31641250 AATTACCTG
1 AATTACCCG
31641259 AATTACCCG
1 AATTACCCG
31641268 AATTACCCG
1 AATTACCCG
31641277 AATTACCCG
1 AATTACCCG
*
31641286 AAAATTACCCA
1 --AATTACCCG
*
31641297 AATTACCAG
1 AATTACCCG
31641306 AATTACCCG
1 AATTACCCG
31641315 AATTA
1 AATTA
31641320 AATCACTACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
9 53 0.87
11 8 0.13
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:31644415 original size:62 final size:57
Alignment explanation
Indices: 31644331--31644463 Score: 178
Period size: 62 Copynumber: 2.3 Consensus size: 57
31644321 TCCAAAAATA
* * *
31644331 ATATTATTTTAAT-TGTTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATT
1 ATATTATTTTAATATATTTAATATTAAATTTAATCTAAT-ATTATC-T-T-GATAAATATT
31644391 ATATTATTTTAATAATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
1 ATATTATTTTAAT-ATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
*
31644449 ATATTAATTTAATAT
1 ATATTATTTTAATAT
31644464 TAAAGTGATT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
57 2 0.03
58 22 0.33
59 1 0.01
60 14 0.21
61 5 0.07
62 23 0.34
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (57 bp):
ATATTATTTTAATATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
Found at i:31644460 original size:58 final size:62
Alignment explanation
Indices: 31644346--31644462 Score: 179
Period size: 58 Copynumber: 2.0 Consensus size: 62
31644336 ATTTTAATTG
* * *
31644346 TTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTATATTATTTTAATAATA
1 TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATAATA
31644408 TTTAATATTAAATTTAATCTAAT-ATTATC-T-T-GATAAATATTATATTAATTTAATA
1 TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATA
31644463 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 23 0.44
59 1 0.02
60 1 0.02
61 5 0.10
62 22 0.42
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (62 bp):
TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATAATA
Found at i:31645589 original size:9 final size:9
Alignment explanation
Indices: 31645575--31645626 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
31645565 TTTGGTTAAA
31645575 AATTACCCG
1 AATTACCCG
31645584 AATTACCCG
1 AATTACCCG
*
31645593 AAAATTACCCA
1 --AATTACCCG
*
31645604 AAATACCCG
1 AATTACCCG
*
31645613 AATTACCCA
1 AATTACCCG
31645622 AATTA
1 AATTA
31645627 AATCACTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 28 0.78
11 8 0.22
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:31645598 original size:20 final size:20
Alignment explanation
Indices: 31645573--31645626 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
31645563 TTTTTGGTTA
*
31645573 AAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCG
*
31645593 AAAATTACCCAAAATACCCG
1 AAAATTACCCAAATTACCCG
31645613 --AATTACCCAAATTA
1 AAAATTACCCAAATTA
31645627 AATCACTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.42
20 18 0.58
ACGTcount: A:0.46, C:0.28, G:0.06, T:0.20
Consensus pattern (20 bp):
AAAATTACCCAAATTACCCG
Found at i:31646782 original size:16 final size:16
Alignment explanation
Indices: 31646761--31646800 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
31646751 CCTAAGAAAA
31646761 AAATTGGGCT-GGATTT
1 AAATTGGGCTAGG-TTT
31646777 AAATTGGGCTAGGTTT
1 AAATTGGGCTAGGTTT
31646793 AAATTGGG
1 AAATTGGG
31646801 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTAGGTTT
Found at i:31647722 original size:16 final size:16
Alignment explanation
Indices: 31647698--31647728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31647688 CTTTATATAT
*
31647698 TAAATTATTATATTAA
1 TAAAATATTATATTAA
31647714 TAAAATATTATATTA
1 TAAAATATTATATTA
31647729 TGTTAATTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:31651739 original size:26 final size:27
Alignment explanation
Indices: 31651684--31651743 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
31651674 TATTTTCTTG
*
31651684 AAATTTTACCAAATGGAAAAATCATCA
1 AAATTTTACCAAAGGGAAAAATCATCA
* * *
31651711 AAATTTTACC-AAGGGTAAAATCGTTA
1 AAATTTTACCAAAGGGAAAAATCATCA
31651737 AAATTTT
1 AAATTTT
31651744 GATGGGGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (27 bp):
AAATTTTACCAAAGGGAAAAATCATCA
Found at i:31656848 original size:3 final size:3
Alignment explanation
Indices: 31656836--31656865 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31656826 AACTCATTTA
31656836 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
31656866 AAAACTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:31661391 original size:3 final size:3
Alignment explanation
Indices: 31661383--31661429 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
31661373 TAGTCACCTT
*
31661383 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31661430 TTGGCATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31663371 original size:2 final size:2
Alignment explanation
Indices: 31663364--31663390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31663354 TACTTGTGGT
31663364 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31663391 GAGTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31671029 original size:2 final size:2
Alignment explanation
Indices: 31671022--31671105 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
31671012 ATTTCTTTCA
31671022 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31671064 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31671106 TTATTATTCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.