Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 187 of 295
Found at i:59255997 original size:42 final size:44
Alignment explanation
Indices: 59255932--59256040 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 44
59255922 CATCGACTTA
* * *
59255932 TGATTTACGTGTAAGACCATGTCTGGGACATTGGCAACG-TATT
1 TGATTTACGTGGAAGACCATGTCTGAGACAGTGGCAACGATATT
* *
59255975 TGATTT-CGTGGAAGACCTTGTCTGAGACAGTGGCATCGATATT
1 TGATTTACGTGGAAGACCATGTCTGAGACAGTGGCAACGATATT
* * *
59256018 TGA-TTACATGTAAGACCACGTCT
1 TGATTTACGTGGAAGACCATGTCT
59256041 TTCTAAGCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 29 0.53
43 26 0.47
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
TGATTTACGTGGAAGACCATGTCTGAGACAGTGGCAACGATATT
Found at i:59276855 original size:39 final size:40
Alignment explanation
Indices: 59276751--59277053 Score: 347
Period size: 39 Copynumber: 7.7 Consensus size: 40
59276741 TTGAATGATG
* *
59276751 TCCGGGCCAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* * *
59276790 ATCCGGACCAAGAT-CCGAAGGAATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
59276831 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
59276870 TCCGGACCAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
59276910 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
59276949 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
59276988 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
59277027 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
59277054 AACGAGGAGC
Statistics
Matches: 230, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
39 109 0.47
40 107 0.47
41 13 0.06
42 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:59276883 original size:79 final size:80
Alignment explanation
Indices: 59276751--59277018 Score: 368
Period size: 79 Copynumber: 3.4 Consensus size: 80
59276741 TTGAATGATG
* * *
59276751 TCCGGGCCAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AATATCCGGACCAAGATCCGAAGGAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAA-ATCCGGACCAAGATCCGAAGGCA
59276813 TTTGTGCGAGATACTAAT
63 TTTGTGCGAGATACTAAT
59276831 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAATCCGGACCAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACCAAGATCCGAAGGCATTT
59276895 GTGCGAGATACTAAT
66 GTGCGAGATACTAAT
* * * *
59276910 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACCAAGATCCGAAGGCATTT
* *
59276973 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAT
* *
59276988 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
59277019 ATTACTATAA
Statistics
Matches: 173, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
78 35 0.20
79 116 0.67
80 21 0.12
81 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACCAAGATCCGAAGGCATTT
GTGCGAGATACTAAT
Found at i:59276960 original size:118 final size:119
Alignment explanation
Indices: 59276751--59277053 Score: 375
Period size: 118 Copynumber: 2.6 Consensus size: 119
59276741 TTGAATGATG
* * * * * * * * *
59276751 TCCGGGCCAAGTCCCGAAGGC-TTTGTGCTAAGTGACAATATCCGGACCAAGAT-CCGAAGGAAT
1 TCCGGACCAAGTCCCAAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
59276814 TTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAA
* *
59276870 TCCGGACCAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 TCCGGACCAAG-TCCCAAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCA
*
59276931 TTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
63 TTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAA
*** *
59276988 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGACCAAGTCCCAAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
59277053 G
66 G
59277054 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 18
0.83 0.07 0.09
Matches are distributed among these distances:
117 2 0.01
118 104 0.65
119 45 0.28
120 9 0.06
121 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (119 bp):
TCCGGACCAAGTCCCAAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:59277025 original size:79 final size:79
Alignment explanation
Indices: 59276751--59277053 Score: 348
Period size: 79 Copynumber: 3.8 Consensus size: 79
59276741 TTGAATGATG
* * * * * *
59276751 TCCGGGCCAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AATATCCGGACCAAGATCCGAAGGAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT-TCCGGGCTAAGACCCGAAGGCA
59276813 TTTGTGCGAGATACTAAT
62 TTTGTGCGAGATACTAAT
* * * *
59276831 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACCAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTTG
59276896 TGCGAGATACTAAT
66 TGCGAGATACTAAT
59276910 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTTG
* *
59276974 TGCGAGTTACTAAA
66 TGCGAGATACTAAT
* * * * *
59276988 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAGACCCGAAGGCAT
59277051 TTG
63 TTG
59277054 AACGAGGAGC
Statistics
Matches: 202, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
78 38 0.19
79 128 0.63
80 35 0.17
81 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGATACTAAT
Found at i:59280632 original size:31 final size:31
Alignment explanation
Indices: 59280586--59280700 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
59280576 TTAGTCTTGA
*
59280586 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
59280616 TATATCACTGGACCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
59280647 CATATTACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
59280678 CATATCACTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
59280701 ACTGTAAACG
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
30 4 0.05
31 72 0.95
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:59280771 original size:42 final size:42
Alignment explanation
Indices: 59280724--59280815 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
59280714 TGGTCCTTAG
*
59280724 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
59280766 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
59280808 GCCCATTT
1 GCCCATTT
59280816 GGGGAGACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:59280996 original size:25 final size:25
Alignment explanation
Indices: 59280963--59281032 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
59280953 CTCTTTTAAT
*
59280963 AACTAGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
59280988 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
59281013 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
59281033 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 37 0.90
26 4 0.10
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:59281872 original size:27 final size:26
Alignment explanation
Indices: 59281842--59281908 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
59281832 GGGCATATTC
59281842 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACC-TACAAGGGCT-TTACG
* *
59281869 GTCACTTTAACCTACAGGGGCTTTACG
1 GTCA-TTTTACCTACAAGGGCTTTACG
* *
59281896 GTCTTTTTGCCTA
1 GTCATTTTACCTA
59281909 TTAGGGGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 7 0.21
27 19 0.58
28 7 0.21
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (26 bp):
GTCATTTTACCTACAAGGGCTTTACG
Found at i:59282030 original size:29 final size:28
Alignment explanation
Indices: 59281964--59282067 Score: 108
Period size: 27 Copynumber: 3.8 Consensus size: 28
59281954 ATCTACAAAC
*
59281964 CAAGGGTATTTC-AGTAA-TTTTGTAAAC
1 CAAGGGTATTTCTA-TAATTTTTGTAAAT
*
59281991 CAATGGTATTTCTATAATTTTTAG-AAAGT
1 CAAGGGTATTTCTATAATTTTT-GTAAA-T
*
59282020 CAAGGGTATTTCTGTAA-TTTTGTAAAT
1 CAAGGGTATTTCTATAATTTTTGTAAAT
* *
59282047 CAGGGGTATTTCGATAATTTT
1 CAAGGGTATTTCTATAATTTT
59282068 ACAAACTAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
27 30 0.47
28 18 0.28
29 16 0.25
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (28 bp):
CAAGGGTATTTCTATAATTTTTGTAAAT
Found at i:59282078 original size:27 final size:27
Alignment explanation
Indices: 59281995--59282084 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
59281985 GTAAACCAAT
* * *
59281995 GGTATTTCTATAATTTTTAGAAAGTCAAG
1 GGTATTTCGATAA-TTTTACAAA-TCAGG
**
59282024 GGTATTTCTG-TAATTTTGTAAATCAGG
1 GGTATTTC-GATAATTTTACAAATCAGG
59282051 GGTATTTCGATAATTTTACAAA-CTAGG
1 GGTATTTCGATAATTTTACAAATC-AGG
59282078 GGTATTT
1 GGTATTT
59282085 TGGTAATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.04
27 32 0.62
28 7 0.13
29 11 0.21
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACAAATCAGG
Found at i:59282192 original size:54 final size:54
Alignment explanation
Indices: 59282124--59282303 Score: 274
Period size: 54 Copynumber: 3.4 Consensus size: 54
59282114 GTAATTTCAC
* *
59282124 AATCGAGGGTAAAACGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTATA
*
59282178 AATCGAGTGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
* * *
59282232 AATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTGAAA-CGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
*
59282285 AATCGAGGGTAAAATGGTA
1 AATCGAGGGTAAAACGGTA
59282304 GTTCTACAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
53 29 0.25
54 87 0.74
55 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.29
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
Found at i:59282320 original size:27 final size:27
Alignment explanation
Indices: 59282124--59282303 Score: 247
Period size: 27 Copynumber: 6.7 Consensus size: 27
59282114 GTAATTTCAC
59282124 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
59282151 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
*
59282178 AATCGAGTGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
59282205 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
59282232 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * *
59282259 AATCAAGGGTGAAAC-GTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
59282285 AATCGAGGGTAAAATGGTA
1 AATCGAGGGTAAAACGGTA
59282304 GTTCTACAAA
Statistics
Matches: 133, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 22 0.17
27 110 0.83
28 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:59282333 original size:80 final size:81
Alignment explanation
Indices: 59282124--59282340 Score: 213
Period size: 81 Copynumber: 2.7 Consensus size: 81
59282114 GTAATTTCAC
* * ** * *** * *
59282124 AATCGAGGGTAAAACGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGTGT
1 AATCGAGGGTAAAATGGTAATTCTACAAATC-GAGGGCAAAACAATAATTTTGTAAATCAAGGGT
* *
59282188 AAAACGGTAATTTTGTA
65 AAAACGGTAATTCTATA
* * ** *
59282205 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGGCAAAACAATAATTTTGTAAATCAAGGGTA
59282270 AAAC-GTAATTCTATA
66 AAACGGTAATTCTATA
* *** *
59282285 AATCGAGGGTAAAATGGTAGTTCTACAAATCGAGGGCATTTCAATAATTTGGTAAA
1 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGGCAAAACAATAATTTTGTAAA
59282341 CTAAAGTATT
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
80 56 0.48
81 60 0.51
82 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGGCAAAACAATAATTTTGTAAATCAAGGGTA
AAACGGTAATTCTATA
Found at i:59289632 original size:10 final size:10
Alignment explanation
Indices: 59289617--59289654 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
59289607 AACCATTAAC
59289617 ATGATAGTGG
1 ATGATAGTGG
59289627 ATGATAGTGG
1 ATGATAGTGG
* *
59289637 AGGATAATGG
1 ATGATAGTGG
59289647 ATGATAGT
1 ATGATAGT
59289655 CAATTTTAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (10 bp):
ATGATAGTGG
Found at i:59290531 original size:42 final size:42
Alignment explanation
Indices: 59290318--59290538 Score: 228
Period size: 42 Copynumber: 5.2 Consensus size: 42
59290308 GTTTACAAAC
* * **
59290318 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTAA
* * * **
59290360 AAAAAAGCTGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTAA
59290402 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTT-TAA
* * * * ** **
59290444 AAAAATGCCACTAAAGACCATGTTCTTTAGTGGCATTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTAA
* * *
59290486 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTA-A
59290529 CAAAAACGCC
1 -AAAAACGCC
59290539 ACTATTTTTG
Statistics
Matches: 149, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
41 2 0.01
42 136 0.91
43 3 0.02
44 8 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTAA
Found at i:59290614 original size:14 final size:14
Alignment explanation
Indices: 59290591--59290624 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
59290581 GCCCTCCTGT
*
59290591 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
59290605 AGCAACATTTCAAA
1 AGCAACATTTCAAA
59290619 AGCAAC
1 AGCAAC
59290625 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:59292705 original size:11 final size:9
Alignment explanation
Indices: 59292657--59292744 Score: 64
Period size: 9 Copynumber: 9.9 Consensus size: 9
59292647 AATTGCAATG
59292657 GTAAGTTAT
1 GTAAGTTAT
59292666 GTAAGTTAT
1 GTAAGTTAT
59292675 GTAAGTTAAAT
1 GTAAGTT--AT
59292686 GT-A-TTAT
1 GTAAGTTAT
59292693 GTAAGTTAAAT
1 GTAAGTT--AT
59292704 GTAAG-T-T
1 GTAAGTTAT
59292711 GTAAGTTAT
1 GTAAGTTAT
*
59292720 -TATGTATTAT
1 GTAAG--TTAT
59292730 GTAAG-T-T
1 GTAAGTTAT
59292737 GTAAGTTA
1 GTAAGTTA
59292745 AATGTATTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
7 16 0.25
8 7 0.11
9 21 0.33
10 6 0.09
11 14 0.22
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:59292736 original size:26 final size:26
Alignment explanation
Indices: 59292702--59293098 Score: 498
Period size: 26 Copynumber: 16.1 Consensus size: 26
59292692 TGTAAGTTAA
59292702 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
59292728 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
59292753 GTGTAAGTTGTAAGTTA-AATGTA-T
1 ATGTAAGTTGTAAGTTATTATGTATT
59292777 -TGTAA---GT---T-ATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59292795 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
59292821 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59292846 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59292872 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
59292898 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59292924 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
59292950 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
59292975 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
59292993 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59293018 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
59293044 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
59293071 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
59293097 AT
1 AT
59293099 TTAATAAAAT
Statistics
Matches: 328, Mismatches: 21, Indels: 44
0.83 0.05 0.11
Matches are distributed among these distances:
16 1 0.00
17 6 0.02
18 13 0.04
19 6 0.02
20 2 0.01
21 3 0.01
22 5 0.02
23 5 0.02
24 2 0.01
25 96 0.29
26 165 0.50
27 15 0.05
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:59292794 original size:17 final size:16
Alignment explanation
Indices: 59292674--59292785 Score: 65
Period size: 18 Copynumber: 7.6 Consensus size: 16
59292664 ATGTAAGTTA
59292674 TGTAAGTTAAATGTATT
1 TGTAAGTTAAATGTA-T
59292691 ATGTAAGTTAAATGTAAGT
1 -TGTAAGTTAAATGT-A-T
59292710 TGTAAGTT--AT-TA-
1 TGTAAGTTAAATGTAT
59292722 TGT-A-TT--ATGTAAGT
1 TGTAAGTTAAATGT-A-T
59292736 TGTAAGTTAAATGTAT
1 TGTAAGTTAAATGTAT
59292752 TGT--G-T-AA-G--T
1 TGTAAGTTAAATGTAT
59292761 TGTAAGTTAAATGTAT
1 TGTAAGTTAAATGTAT
59292777 TGTAAGTTA
1 TGTAAGTTA
59292786 TTATGTATTA
Statistics
Matches: 77, Mismatches: 1, Indels: 34
0.69 0.01 0.30
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 4 0.05
12 7 0.09
13 3 0.04
14 6 0.08
15 2 0.03
16 18 0.23
17 1 0.01
18 26 0.34
19 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.45
Consensus pattern (16 bp):
TGTAAGTTAAATGTAT
Found at i:59292942 original size:19 final size:19
Alignment explanation
Indices: 59292662--59293094 Score: 109
Period size: 19 Copynumber: 23.4 Consensus size: 19
59292652 CAATGGTAAG
59292662 TTATGTAAGTTATGTAAGTTA
1 TTATGTAAG-T-TGTAAGTTA
* *
59292683 -AATGT-ATTATGTAAGTTA
1 TTATGTAAGT-TGTAAGTTA
*
59292701 -AATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
*
59292719 TTATGT-ATTATGTAAG---
1 TTATGTAAGT-TGTAAGTTA
*
59292735 -T-TGTAAG-T-TAAATGTA
1 TTATGTAAGTTGTAAGT-TA
*
59292751 TTGTGTAAGTTGTAAGTTAAA
1 TTATGTAAGTTGTAAGTT--A
* *
59292772 TGTATTGTAAGTTATTA-TGTA
1 T-TA-TGTAAGTTGTAAGT-TA
59292793 TTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
*
59292812 TTATGT-A-TTGT--GTAA
1 TTATGTAAGTTGTAAGTTA
* * *
59292827 GT-TGCAAG-T-TAAATGTA
1 TTATGTAAGTTGTAAGT-TA
59292844 TTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAG------T-TA
59292870 TTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
*
59292889 TTATGT-A-TTGT--GTAA
1 TTATGTAAGTTGTAAGTTA
* * *
59292904 GT-TGTAAGTTATTA-TGTA
1 TTATGTAAGTTGTAAGT-TA
59292922 TTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
*
59292941 TTATGT-A-TTGT--GTAA
1 TTATGTAAGTTGTAAGTTA
* *
59292956 GT-TGTAAG-T-TAAATGTA
1 TTATGTAAGTTGTAAGT-TA
* * *
59292973 TTATGTCAG-T-CAAATGTA
1 TTATGTAAGTTGTAAGT-TA
59292991 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAG-----T-TA
59293016 TTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
*
59293035 TTATGT-ATTATGTAAG-TA
1 TTATGTAAGT-TGTAAGTTA
*
59293053 --ATGTAAG-T-TAAATGTA
1 TTATGTAAGTTGTAAGT-TA
59293069 TTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTGTAAGTTA
59293088 TTATGTA
1 TTATGTA
59293095 TTATTTAATA
Statistics
Matches: 310, Mismatches: 42, Indels: 122
0.65 0.09 0.26
Matches are distributed among these distances:
12 3 0.01
13 1 0.00
14 16 0.05
15 20 0.06
16 11 0.04
17 19 0.06
18 75 0.24
19 85 0.27
20 23 0.07
21 4 0.01
22 2 0.01
23 11 0.04
25 20 0.06
26 20 0.06
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (19 bp):
TTATGTAAGTTGTAAGTTA
Found at i:59293022 original size:18 final size:18
Alignment explanation
Indices: 59292958--59293079 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
59292948 TTGTGTAAGT
59292958 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
* *
59292976 TGTCAGTCAAATGTATTATGTAA
1 TGTAAGTTAAATG---TAT-T-A
59292999 GTTGTAAGTTAAATGTATTA
1 --TGTAAGTTAAATGTATTA
*
59293019 TGTAAGTTGTAA-GTTATTA
1 TGTAAGTT-AAATG-TATTA
*
59293038 TGT-A-TT--ATGTAAGTAA
1 TGTAAGTTAAATGT-A-TTA
59293054 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
59293072 TGTAAGTT
1 TGTAAGTT
59293080 GTAAGTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 32
0.68 0.06 0.27
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 5 0.06
17 3 0.04
18 33 0.41
19 11 0.14
20 5 0.06
21 4 0.05
22 4 0.05
23 1 0.01
25 11 0.14
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:59293218 original size:73 final size:73
Alignment explanation
Indices: 59293135--59293284 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
59293125 ACATTACTAA
59293135 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
59293200 TATTTTTT
66 TATTTTTT
59293208 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
59293273 TATTTTTT
66 TATTTTTT
59293281 TATA
1 TATA
59293285 TTTTATTTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (73 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTT
Found at i:59293278 original size:35 final size:35
Alignment explanation
Indices: 59293166--59293278 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 35
59293156 ATAAAATAAC
59293166 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
1 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
* * **** *
59293201 ATTTT-TTTATAATTATTAATAATATTTAATAAAATA-AC
1 ATTTTATTT-TAA-TAGT--CAAT-TTTAATATTCCACAT
59293239 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
1 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
59293274 ATTTT
1 ATTTT
59293279 TTTATATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
34 11 0.19
35 17 0.30
36 3 0.05
37 3 0.05
38 12 0.21
39 11 0.19
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (35 bp):
ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
Found at i:59293449 original size:13 final size:13
Alignment explanation
Indices: 59293431--59293501 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
59293421 ATTTATAATT
59293431 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
59293444 ATTTAAGTAACAT
1 ATTTAAGTAATAA
59293457 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
59293470 ATTTAAGTAACAT
1 ATTTAAGTAATAA
59293483 ATTTAAGTAATAA
1 ATTTAAGTAATAA
59293496 ATTTAA
1 ATTTAA
59293502 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:59293460 original size:26 final size:26
Alignment explanation
Indices: 59293430--59293501 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
59293420 TATTTATAAT
59293430 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
59293456 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
59293482 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
59293502 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:59293546 original size:16 final size:17
Alignment explanation
Indices: 59293506--59293548 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
59293496 ATTTAAACAA
59293506 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
59293523 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
59293540 A-TTTAGTAA
1 ATTTTAGTAA
59293549 TAAATTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:59294868 original size:115 final size:114
Alignment explanation
Indices: 59294730--59295046 Score: 553
Period size: 115 Copynumber: 2.8 Consensus size: 114
59294720 AATAAACACC
59294730 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
* *
59294795 TAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGTAACATATTT
66 TAACA-TTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
* *
59294845 TGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACATA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGTAAACACAAA
* * *
59294910 ATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTT
65 ATAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
59294960 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
59295025 TAACATTTTTGCGGCGTTTTAA
66 TAACATTTTTGCGGCGTTTTAA
59295047 TAAAAACGCC
Statistics
Matches: 190, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
114 50 0.26
115 105 0.55
116 35 0.18
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (114 bp):
TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
TAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
Found at i:59294873 original size:40 final size:40
Alignment explanation
Indices: 59294795--59294873 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
59294785 AAACACAAAA
* * * * * *
59294795 TAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
59294835 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
59294874 TACATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (40 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
Found at i:59294988 original size:40 final size:39
Alignment explanation
Indices: 59294911--59294988 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
59294901 AAACACATAA
* * *
59294911 TAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAG
1 TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
*
59294950 TAACATCTTTTGCGGCGTTTTAACAA-AAACGCCACTAAA
1 TAACAT-TTTTGCGGCATTTTAA-AAGAAACGCCACTAAA
59294989 TACATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.18
40 25 0.76
41 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (39 bp):
TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
Found at i:59295137 original size:75 final size:74
Alignment explanation
Indices: 59294950--59295121 Score: 308
Period size: 75 Copynumber: 2.3 Consensus size: 74
59294940 GCCGCTAAAG
59294950 TAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGT
1 TAACAT-TTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGT
59295015 AAACACAAAA
65 AAACACAAAA
*
59295025 TAACATTTTTGCGGCGTTTTAATAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGT
1 TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGT
59295090 AAACACAAAA
65 AAACACAAAA
*
59295100 TAACATTCTTGCGGCGTTTTAA
1 TAACATTTTTGCGGCGTTTTAA
59295122 GATAAGCGCC
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
74 36 0.38
75 58 0.62
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (74 bp):
TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTA
AACACAAAA
Found at i:59295162 original size:189 final size:189
Alignment explanation
Indices: 59294835--59295213 Score: 589
Period size: 189 Copynumber: 2.0 Consensus size: 189
59294825 GCCGCTAAAG
59294835 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * * *
59294900 TAAACACATAATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTTTGCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
* * *
59294965 CGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACAT-AAAAACGATCACGTTTCGGTAAACACAAAA
* *
59295025 TAACAT-TTTTGCGGCGTTTTAATAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * *
59295089 TAAACACAAAATAACATTCTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGCAAGATCTTTTCCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
** *
59295154 CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATTTCGTTTCGGTCAACACAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATCACGTTTCGGTAAACACAAAA
59295213 T
1 T
59295214 CCAACAAAAC
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 26 0.15
189 140 0.81
190 6 0.03
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (189 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATCACGTTTCGGTAAACACAAAA
Found at i:59295410 original size:113 final size:115
Alignment explanation
Indices: 59295273--59295488 Score: 312
Period size: 114 Copynumber: 1.9 Consensus size: 115
59295263 TTTCCAACGC
* * *
59295273 AGCGCCGCTAAAGGCTGACGTTTT-CGGCGTTTTACAAAAAACGCCACTAATAAATCCTACACCA
1 AGCGCCGCTAAAGGATGACGTTTTCCGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACAA
* *
59295337 CGGCAGCG-TTTTATTAAAACAGAATCACATTTTGCGGCATTTTTGACAT
66 CGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCATTTTTGACAT
* * * *
59295386 AGCGCCGCTAAAGGATGATC-TTTTCCGGCGTTTTACCAAAAACGCCAGTAAGAAATCTTACAGA
1 AGCGCCGCTAAAGGATGA-CGTTTTCCGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACA
*
59295450 ACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGG
65 ACGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGG
59295489 TGTTTTACCC
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
113 21 0.23
114 42 0.47
115 27 0.30
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (115 bp):
AGCGCCGCTAAAGGATGACGTTTTCCGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACAA
CGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCATTTTTGACAT
Found at i:59295505 original size:75 final size:75
Alignment explanation
Indices: 59295406--59295551 Score: 179
Period size: 75 Copynumber: 1.9 Consensus size: 75
59295396 AAGGATGATC
* *
59295406 TTTTCCGGCGTTTTACCAAAAACGCCAGTAAGAAATCTTACAG-A-ACGGCAACGTTTTTATTGA
1 TTTTCCGGCGTTTTACCAAAAACGCCACTAAGAAATCCTACAGAACACGGC--CGTTTTTATTGA
59295469 AACAAAATCACA
64 AACAAAATCACA
* * * * * * *
59295481 TTTTGCGGTGTTTTACCCAAAACGCCACTAATATATCCTATAGAACACTGCCGTTTTTATTGAAA
1 TTTTCCGGCGTTTTACCAAAAACGCCACTAAGAAATCCTACAGAACACGGCCGTTTTTATTGAAA
59295546 CAAAAT
66 CAAAAT
59295552 TCCTTTAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
75 55 0.92
76 1 0.02
77 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (75 bp):
TTTTCCGGCGTTTTACCAAAAACGCCACTAAGAAATCCTACAGAACACGGCCGTTTTTATTGAAA
CAAAATCACA
Found at i:59296010 original size:7 final size:7
Alignment explanation
Indices: 59295998--59296171 Score: 51
Period size: 7 Copynumber: 25.1 Consensus size: 7
59295988 ACTAATCAAT
59295998 CTAAACC
1 CTAAACC
*
59296005 CTAAACA
1 CTAAACC
59296012 C-ATAACC
1 CTA-AACC
59296019 CTTAAATCC
1 C-TAAA-CC
59296028 CTTAAACC
1 C-TAAACC
59296036 CTAAACC
1 CTAAACC
*
59296043 C-AAATC
1 CTAAACC
* *
59296049 ATAATCC
1 CTAAACC
59296056 CTAAA-C
1 CTAAACC
*
59296062 CT--AGC
1 CTAAACC
*
59296067 CTAGACC
1 CTAAACC
*
59296074 CTGAACC
1 CTAAACC
*
59296081 C-CAACC
1 CTAAACC
59296087 CGTAAACC
1 C-TAAACC
*
59296095 TTAAACC
1 CTAAACC
*
59296102 C-CAACC
1 CTAAACC
*
59296108 C-CAACC
1 CTAAACC
59296114 CGTAAACC
1 C-TAAACC
*
59296122 TTAAACC
1 CTAAACC
*
59296129 C-CAACTC
1 CTAAAC-C
*
59296136 ATAAACC
1 CTAAACC
*
59296143 CTAAACT
1 CTAAACC
*
59296150 GTAAACC
1 CTAAACC
* * *
59296157 ATAATCA
1 CTAAACC
59296164 CTAAACC
1 CTAAACC
59296171 C
1 C
59296172 ATAATTTGCA
Statistics
Matches: 121, Mismatches: 32, Indels: 28
0.67 0.18 0.15
Matches are distributed among these distances:
4 1 0.01
5 3 0.02
6 27 0.22
7 65 0.54
8 16 0.13
9 9 0.07
ACGTcount: A:0.40, C:0.39, G:0.03, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:59296107 original size:27 final size:27
Alignment explanation
Indices: 59296077--59296133 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
59296067 CTAGACCCTG
59296077 AACCCCAACCCGTAAACCTTAAACCCC
1 AACCCCAACCCGTAAACCTTAAACCCC
59296104 AACCCCAACCCGTAAACCTTAAACCCC
1 AACCCCAACCCGTAAACCTTAAACCCC
59296131 AAC
1 AAC
59296134 TCATAAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.47, G:0.04, T:0.11
Consensus pattern (27 bp):
AACCCCAACCCGTAAACCTTAAACCCC
Found at i:59296128 original size:21 final size:21
Alignment explanation
Indices: 59296096--59296148 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
59296086 CCGTAAACCT
* *
59296096 TAAACCC-CAACCCCAACCCG
1 TAAACCCTAAACCCCAACCCA
* *
59296116 TAAACCTTAAACCCCAACTCA
1 TAAACCCTAAACCCCAACCCA
59296137 TAAACCCTAAAC
1 TAAACCCTAAAC
59296149 TGTAAACCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.42, C:0.43, G:0.02, T:0.13
Consensus pattern (21 bp):
TAAACCCTAAACCCCAACCCA
Found at i:59296884 original size:113 final size:112
Alignment explanation
Indices: 59296639--59296965 Score: 388
Period size: 113 Copynumber: 2.9 Consensus size: 112
59296629 TTAGGCTTTT
* * **
59296639 GCGGCGCTTTTACAAAAACGCCACTAAAGCCTCCCAAACTAAGAAAAACGATGTCGTTGGGCTTC
1 GCGGCGC-TTTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTT-
* * * * * * *
59296704 AGTTTTTTGTGGCGATTTTTAAAAAATGCCGCTAAAACATTGAGCATTA
64 AGGTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* *
59296753 GCGGCGCTTTCCCGAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAATGATGTCGTTGGGCTTA
1 GCGGCGCTTT-CCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
* * *
59296817 GGTCTTTTGCGGCGCTTTTTAAGAAACGCTGCTAAAGCCCTGAGAATTA
65 GGT-TTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* * * *
59296866 -CTTGCGCTTCTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTTGGTTT
1 GC-GGCGCTT-TCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTT
*
59296930 AGGTTTTTAGCGGCACTTTTTAAGAAACGCCGCTAA
64 AGGTTTTT-GCGGCGCTTTTTAAGAAACGCCGCTAA
59296966 TGCTCATTAT
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
112 4 0.02
113 99 0.54
114 80 0.44
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (112 bp):
GCGGCGCTTTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTAG
GTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
Found at i:59297000 original size:39 final size:39
Alignment explanation
Indices: 59296957--59297085 Score: 116
Period size: 41 Copynumber: 3.2 Consensus size: 39
59296947 TTTTAAGAAA
* *
59296957 CGCCGCTAATGCTCATTATTAGCGGCGTTTTTGTAAAAG
1 CGCCGCTAATGCTAATTATTAGCGGCGTTTTTGTAAAAT
* * * * *
59296996 CGCCGGTAATACTGA-TATTTAGCGGCGTTTTTTTTTAAAT
1 CGCCGCTAATGCTAATTA-TTAGCGGCG-TTTTTGTAAAAT
* * **
59297036 CACCGCTAATGCTTAATTTTTAGCGGCGTTTGTTGTCCAAT
1 CGCCGCTAATGC-TAATTATTAGCGGCGTTT-TTGTAAAAT
59297077 CGCCGCTAA
1 CGCCGCTAA
59297086 AAGCGCCGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
38 2 0.03
39 21 0.30
40 21 0.30
41 25 0.36
42 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (39 bp):
CGCCGCTAATGCTAATTATTAGCGGCGTTTTTGTAAAAT
Found at i:59297083 original size:41 final size:39
Alignment explanation
Indices: 59296933--59297085 Score: 128
Period size: 39 Copynumber: 3.8 Consensus size: 39
59296923 TTGGTTTAGG
** * *
59296933 TTTTTAGCGGCACTTTT-TAAGAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTGTAA-AATCGCCGCTAATGCTAA
* * * * *
59296972 TTATTAGCGGCGTTTTTGTAAAAGCGCCGGTAATACTGA
1 TTTTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTAA
* * * *
59297011 TATTTAGCGGCGTTTTTTTTTAAATCACCGCTAATGCTTAA
1 TTTTTAGCGGCG-TTTTTGTAAAATCGCCGCTAATGC-TAA
**
59297052 TTTTTAGCGGCGTTTGTTGTCCAATCGCCGCTAA
1 TTTTTAGCGGCGTTT-TTGTAAAATCGCCGCTAA
59297086 AAGCGCCGCT
Statistics
Matches: 89, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
39 38 0.43
40 24 0.27
41 27 0.30
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTAA
Found at i:59299571 original size:15 final size:15
Alignment explanation
Indices: 59299551--59299584 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
59299541 GATTTAGTTT
59299551 TTTTCTTCTATTTTC
1 TTTTCTTCTATTTTC
* *
59299566 TTTTCTTTTTTTTTC
1 TTTTCTTCTATTTTC
59299581 TTTT
1 TTTT
59299585 TTCCTCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTCTATTTTC
Found at i:59299585 original size:10 final size:10
Alignment explanation
Indices: 59299548--59299586 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
59299538 TAGGATTTAG
59299548 TTTTTTTCTTC
1 TTTTTTT-TTC
59299559 TATTTTCTTTTC
1 T-TTTT-TTTTC
59299571 TTTTTTTTTC
1 TTTTTTTTTC
59299581 TTTTTT
1 TTTTTT
59299587 CCTCTCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 11 0.42
11 5 0.19
12 8 0.31
13 2 0.08
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:59299594 original size:22 final size:23
Alignment explanation
Indices: 59299548--59299594 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
59299538 TAGGATTTAG
* *
59299548 TTTTTTTCTTCTATTTTCTTTTC
1 TTTTTTTCTTCTATTTTCCTCTC
*
59299571 TTTTTTT-TTCTTTTTTCCTCTC
1 TTTTTTTCTTCTATTTTCCTCTC
59299593 TT
1 TT
59299595 CATCTACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTTCTTCTATTTTCCTCTC
Found at i:59299783 original size:22 final size:22
Alignment explanation
Indices: 59299755--59299815 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
59299745 AGCCAAACCC
59299755 TCCGATTCTTCTCTATCTTGTG
1 TCCGATTCTTCTCTATCTTGTG
*
59299777 TCTGATTCTTCTCTATCTTGTG
1 TCCGATTCTTCTCTATCTTGTG
59299799 TCCGATTCTT-TCT-TCTT
1 TCCGATTCTTCTCTATCTT
59299816 CTAAACCCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 30 0.81
ACGTcount: A:0.08, C:0.26, G:0.11, T:0.54
Consensus pattern (22 bp):
TCCGATTCTTCTCTATCTTGTG
Found at i:59305402 original size:27 final size:23
Alignment explanation
Indices: 59305372--59305426 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 23
59305362 AAATAAAATA
59305372 TATATATCAAAGTAGATCAGCATAAC
1 TATATA-CAAA-T-GATCAGCATAAC
*
59305398 T-TATACATATGATCAGCATAAC
1 TATATACAAATGATCAGCATAAC
59305420 T-TATACA
1 TATATACA
59305427 TATGTCGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.68
23 1 0.04
24 3 0.11
25 4 0.14
26 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (23 bp):
TATATACAAATGATCAGCATAAC
Found at i:59305411 original size:22 final size:22
Alignment explanation
Indices: 59305386--59305430 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59305376 TATCAAAGTA
59305386 GATCAGCATAACTTATACATAT
1 GATCAGCATAACTTATACATAT
59305408 GATCAGCATAACTTATACATAT
1 GATCAGCATAACTTATACATAT
59305430 G
1 G
59305431 TCGAACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (22 bp):
GATCAGCATAACTTATACATAT
Found at i:59305439 original size:22 final size:22
Alignment explanation
Indices: 59305386--59305439 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
59305376 TATCAAAGTA
*
59305386 GATCAGCATAACTTATACATAT
1 GATCAACATAACTTATACATAT
*
59305408 GATCAGCATAACTTATACATAT
1 GATCAACATAACTTATACATAT
59305430 G-TCGAACATA
1 GATC-AACATA
59305440 TAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (22 bp):
GATCAACATAACTTATACATAT
Found at i:59307187 original size:56 final size:55
Alignment explanation
Indices: 59307130--59307337 Score: 281
Period size: 56 Copynumber: 3.7 Consensus size: 55
59307120 CATACAAGGT
* *
59307130 CTTACTCGTACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGT
1 CTTACTCGCACACATATATC-AAATCACATATCGATGCCAACGTATTAAACGTGGA
* * * * *
59307186 CTTACTCACACACATATATCAGAGTCACATATCGATGCCAACATATGAAACGTAGA
1 CTTACTCGCACACATATATCA-AATCACATATCGATGCCAACGTATTAAACGTGGA
* * *
59307242 CTTACTCGCACACATATATCGGAATCACATATCAATGCCAACGTATTAAATGTGGA
1 CTTACTCGCACACATATATC-AAATCACATATCGATGCCAACGTATTAAACGTGGA
*
59307298 CTTACTCGCACACTTATATCAAAGTCACATATCGATGCCA
1 CTTACTCGCACACATATATCAAA-TCACATATCGATGCCA
59307338 CATATACTTC
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
55 3 0.02
56 128 0.98
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (55 bp):
CTTACTCGCACACATATATCAAATCACATATCGATGCCAACGTATTAAACGTGGA
Found at i:59307302 original size:112 final size:111
Alignment explanation
Indices: 59307130--59307342 Score: 345
Period size: 112 Copynumber: 1.9 Consensus size: 111
59307120 CATACAAGGT
* * *
59307130 CTTACTCGTACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCAC
1 CTTACTCGCACACATATATCGAAATCACATATCAATGCCAACGTATTAAACGTGGACTTACTCAC
*
59307195 ACACATATATCAGAGTCACATATCGATGCCAACATATGAAACGTAGA
66 ACACATATATCAAAGTCACATATCGATGCC-ACATATGAAACGTAGA
* * *
59307242 CTTACTCGCACACATATATCGGAATCACATATCAATGCCAACGTATTAAATGTGGACTTACTCGC
1 CTTACTCGCACACATATATCGAAATCACATATCAATGCCAACGTATTAAACGTGGACTTACTCAC
*
59307307 ACACTTATATCAAAGTCACATATCGATGCCACATAT
66 ACACATATATCAAAGTCACATATCGATGCCACATAT
59307343 ACTTCCAGGT
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 6 0.06
112 87 0.94
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27
Consensus pattern (111 bp):
CTTACTCGCACACATATATCGAAATCACATATCAATGCCAACGTATTAAACGTGGACTTACTCAC
ACACATATATCAAAGTCACATATCGATGCCACATATGAAACGTAGA
Found at i:59317133 original size:45 final size:45
Alignment explanation
Indices: 59317067--59317191 Score: 135
Period size: 45 Copynumber: 2.8 Consensus size: 45
59317057 TACGATGCTG
* * * *
59317067 ATGTCCCAGACATGGTTTTACACGTAACCACATATATCGA-TGCCA
1 ATGTCCCAGACGTGGTCTTACACGAAAACACATATATC-ATTGCCA
* *
59317112 ATGTTCCAGACGTGGTCTTACACGAAAACACATATATCATTTCCA
1 ATGTCCCAGACGTGGTCTTACACGAAAACACATATATCATTGCCA
* * * * *
59317157 ACGTCCCAAACGTGGTCTTACTCAAAAATACATAT
1 ATGTCCCAGACGTGGTCTTACACGAAAACACATAT
59317192 CAAAATCCTA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 66 0.99
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (45 bp):
ATGTCCCAGACGTGGTCTTACACGAAAACACATATATCATTGCCA
Found at i:59320433 original size:27 final size:27
Alignment explanation
Indices: 59320396--59320752 Score: 437
Period size: 27 Copynumber: 13.3 Consensus size: 27
59320386 AAAATTAGTT
* ** *
59320396 AAATGATCGTAATGCCTTTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
59320423 AAATGACCGTAATACCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
59320450 AAATGATCGTAAT-ACCCTGTAGGATA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
59320476 AAATGATCGTAATGCTCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
59320503 AAATGATCGTAATACCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
59320530 AAATGACCGTAATGCCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
59320557 AAATGACCGTAATACCCCTGTAGGGAA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
59320584 AAATGATCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
59320611 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* **
59320638 AAATGACTGTAATATCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
** *
59320665 AAATGATTGTAATGCCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
59320692 AAATGACTGTAATGCCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
59320719 AAATGACCGTAATACCCCTGTATGTTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
59320746 AAATGAC
1 AAATGAC
59320753 AATTATGACA
Statistics
Matches: 287, Mismatches: 42, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
26 24 0.08
27 263 0.92
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAGGGTA
Found at i:59325272 original size:46 final size:46
Alignment explanation
Indices: 59325222--59325388 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 46
59325212 AGCATCCAAA
* *
59325222 CTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCAAATGTCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAG
* * * * *
59325268 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG--TCCGAG
* *
59325315 CTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-AATCGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT-GTCCGAG
*
59325361 CTCGTTGAGTTGAGTTCGAGTTCACTTA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTA
59325389 GGGGCGGGTT
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 52 0.53
47 28 0.29
48 3 0.03
49 1 0.01
50 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAG
Found at i:59325372 original size:93 final size:93
Alignment explanation
Indices: 59325213--59325383 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
59325203 GGATGGTTGA
* *
59325213 GCATCCAAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCAAATGTCTGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCAAATGCCCGAGCTCGTTGAGT
59325278 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
59325306 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-AATCGCCCGAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCAAAT-GCCCGAGCTCGTTGAG
*
59325370 TTGAGTTCGAGTTC
65 TTGAGTCCGAGTTC
59325384 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCAAATGCCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59340433 original size:93 final size:92
Alignment explanation
Indices: 59340275--59340444 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 92
59340265 GGATGGTTGA
* * * *
59340275 GCATCCGAACTCGTTGAGTTGAGTCCAGTTCACTTATGGATGCAAATGTCTGAGCTTGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGTT
59340340 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* *
59340367 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCC-AGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
59340432 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
59340445 ACTTAGGGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 26 0.37
93 45 0.63
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59340441 original size:46 final size:46
Alignment explanation
Indices: 59340279--59340449 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
59340269 GGTTGAGCAT
* *
59340279 CCGAACTCGTTGAGTTGAGTCC-AGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * * * * *
59340324 CTGAGCTTGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
* *
59340369 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
*
59340417 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59340450 GGGGTGGGTT
Statistics
Matches: 100, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
43 6 0.06
45 23 0.23
46 36 0.36
47 25 0.25
48 5 0.05
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:59343667 original size:55 final size:55
Alignment explanation
Indices: 59343606--59343730 Score: 171
Period size: 55 Copynumber: 2.3 Consensus size: 55
59343596 ATATTAAGTC
* * *
59343606 CGCACACTCAGTGCTATATAATC-AGCTCGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACCTAGTGCTACATAATC-AACT
* * *
59343661 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACCTAGTGCTACATAATCAACT
*
59343716 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
59343731 GCACAATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 38 0.61
56 24 0.39
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACCTAGTGCTACATAATCAACT
Found at i:59343672 original size:28 final size:27
Alignment explanation
Indices: 59343606--59343730 Score: 169
Period size: 28 Copynumber: 4.6 Consensus size: 27
59343596 ATATTAAGTC
* * *
59343606 CGCACACTCAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTACATAATCAACT
*
59343633 CGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
59343661 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
59343689 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
*
59343716 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
59343731 GCACAATTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 37 0.42
28 52 0.58
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:59343749 original size:56 final size:56
Alignment explanation
Indices: 59343633--59343755 Score: 149
Period size: 56 Copynumber: 2.2 Consensus size: 56
59343623 ATAATCAGCT
* * * *
59343633 CGCACACCTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCACACACTTAGTGCTACACAATCAAACC
* * * *
59343689 CGCACACTTAGTGCTACATAGTC-AATTCACACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAAACTCACACACTTAGTGCTACACAA-TCAAACC
*
59343745 CGCACTCTTAG
1 CGCACACTTAG
59343756 CGCCAATCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 21 0.37
56 36 0.63
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCACACACTTAGTGCTACACAATCAAACC
Found at i:59351315 original size:19 final size:19
Alignment explanation
Indices: 59351279--59351314 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
59351269 TCAAATTAGT
59351279 TTTTCTAAAAATATTTTTG
1 TTTTCTAAAAATATTTTTG
*
59351298 TTTTCT-AGAATATTTTT
1 TTTTCTAAAAATATTTTT
59351315 TTCCTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTCTAAAAATATTTTTG
Found at i:59353587 original size:51 final size:51
Alignment explanation
Indices: 59353511--59353613 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
59353501 TGTTGGAAGT
* * *
59353511 CGGCAAAAGCCGAAAAGCTAAAACCTCGGCATTCGGGGCCTCACAAGCGTG
1 CGGCAAAAGCCGAAAAGCCAAAACCTCGACATTCAGGGCCTCACAAGCGTG
*
59353562 CGGCAAAAGCTGAAAAGCCAAAACCTCGACATTCAGGGCCTCACAAGCGTG
1 CGGCAAAAGCCGAAAAGCCAAAACCTCGACATTCAGGGCCTCACAAGCGTG
59353613 C
1 C
59353614 AAACGCACGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.30, G:0.25, T:0.12
Consensus pattern (51 bp):
CGGCAAAAGCCGAAAAGCCAAAACCTCGACATTCAGGGCCTCACAAGCGTG
Found at i:59354124 original size:27 final size:27
Alignment explanation
Indices: 59354093--59354166 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
59354083 CCTAATATTG
* * *
59354093 GTAAAATTATCGAAATACCCTTATAGT
1 GTAAAATGACCGAAATACCCTTATAGA
* *
59354120 GTAAAATGACCGTAATGCCCTTATAGA
1 GTAAAATGACCGAAATACCCTTATAGA
*
59354147 GTAAAATGACCGTAATACCC
1 GTAAAATGACCGAAATACCC
59354167 CTGTATGGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTTATAGA
Found at i:59368336 original size:43 final size:43
Alignment explanation
Indices: 59368283--59368481 Score: 317
Period size: 43 Copynumber: 4.6 Consensus size: 43
59368273 GCTGGTATTA
* *
59368283 TATTTGGGCCTTCGTGCCTAGCAGGCTTTGTGTCGGTGATGTG
1 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
59368326 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCTGTGATGTG
1 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
59368369 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
59368412 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCTGGTGATGTG
1 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
59368455 TATTTGGGCCTTCGTGCCTAGTAGGCT
1 TATTTGGGCCTTCGTGCCTAGCAGGCT
59368482 ATGATGCTGA
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 145 1.00
ACGTcount: A:0.10, C:0.22, G:0.33, T:0.35
Consensus pattern (43 bp):
TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:59369603 original size:46 final size:46
Alignment explanation
Indices: 59369536--59369630 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
59369526 GGTGATTACG
59369536 GATATCCAGAGGACTCTGTCATAACCCGAATGAACAAATTTGGCAT
1 GATATCCAGAGGACTCTGTCATAACCCGAATGAACAAATTTGGCAT
59369582 GATATCCAGAGGACTCTGTCATAACCCGAATGAACAAATTTGGCAT
1 GATATCCAGAGGACTCTGTCATAACCCGAATGAACAAATTTGGCAT
59369628 GAT
1 GAT
59369631 TTCAGGTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (46 bp):
GATATCCAGAGGACTCTGTCATAACCCGAATGAACAAATTTGGCAT
Found at i:59374619 original size:31 final size:31
Alignment explanation
Indices: 59374584--59374646 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
59374574 GCCAAAATCG
59374584 GACAAGACGAGCTACTTTCAAGATCTACACA
1 GACAAGACGAGCTACTTTCAAGATCTACACA
*
59374615 GACAAGACGAGCTACTTTCAGGATCTACACA
1 GACAAGACGAGCTACTTTCAAGATCTACACA
59374646 G
1 G
59374647 TCCACACGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (31 bp):
GACAAGACGAGCTACTTTCAAGATCTACACA
Found at i:59381847 original size:46 final size:46
Alignment explanation
Indices: 59381737--59381962 Score: 201
Period size: 46 Copynumber: 4.9 Consensus size: 46
59381727 CATTGTTGTT
* * * * *
59381737 ATGTGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGA-
1 ATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG
*** * *
59381782 AACAAGAGCTAGTGCAAGACATGTTTGGGACATGCATCGGCCTCGAG
1 ATGTA-AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG
* *
59381829 ATGTAAGCAAGTGTAAGACATGTCTGGAACATGCATCGG-CTACGAG
1 ATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAG
* *
59381875 ATGT--GCTAGTGTAAGACATGTCTGGGACATGCATCGGCAC-GGAT
1 ATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCGAG
* * *
59381919 ATGTGAGAGCCAGTGTAAGACCATATCTGGGATATGGCATCGGC
1 ATGT-A-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
59381963 ATCAATATGT
Statistics
Matches: 146, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
44 37 0.25
45 3 0.02
46 73 0.50
47 2 0.01
48 11 0.08
49 12 0.08
50 8 0.05
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
ATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG
Found at i:59381934 original size:92 final size:92
Alignment explanation
Indices: 59381737--59381964 Score: 250
Period size: 92 Copynumber: 2.5 Consensus size: 92
59381727 CATTGTTGTT
*
59381737 ATGT-GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGAAACAAGAGCTAGTGCAAGA
1 ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCA-TGAAACAAGAGCTAGTGCAAGA
*
59381801 CATGTTTGGGACATGCATCGGCCTCGAG
65 CATGTCTGGGACATGCATCGGCCTCGAG
* * * * * * *
59381829 ATGTA-AGCAAGTGTAAGACATGTCTGGAACATGCATCGGC-T-ACGAGATGTGCTAGTGTAAGA
1 ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATGA-AACAAGAGCTAGTGCAAGA
* *
59381891 CATGTCTGGGACATGCATCGGCAC-GGAT
65 CATGTCTGGGACATGCATCGGC-CTCGAG
* *
59381919 ATGTGAGAGCCAGTGTAAGACCATATCTGGGATATGGCATCGGCAT
1 ATGT-AGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAT
59381965 CAATATGTGT
Statistics
Matches: 113, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
89 1 0.01
90 42 0.37
91 2 0.02
92 48 0.42
93 11 0.10
94 8 0.07
95 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (92 bp):
ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATGAAACAAGAGCTAGTGCAAGAC
ATGTCTGGGACATGCATCGGCCTCGAG
Found at i:59386260 original size:12 final size:11
Alignment explanation
Indices: 59386243--59386273 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
59386233 TCCATAATTC
59386243 AAAAAAAAAGT
1 AAAAAAAAAGT
59386254 GAAAAAAAAAGT
1 -AAAAAAAAAGT
59386266 AAAAAAAA
1 AAAAAAAA
59386274 TATATGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAGT
Found at i:59387154 original size:30 final size:30
Alignment explanation
Indices: 59387120--59387176 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
59387110 TGGCCATTCC
*
59387120 CACACGGGCTGAG-CACACGCCTGTGTGAGA
1 CACACGGGCTG-GCCACACGCCTATGTGAGA
59387150 CACACGGGCTGGCCACACGCCTATGTG
1 CACACGGGCTGGCCACACGCCTATGTG
59387177 CCAGTCCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (30 bp):
CACACGGGCTGGCCACACGCCTATGTGAGA
Found at i:59390686 original size:15 final size:15
Alignment explanation
Indices: 59390666--59390697 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
59390656 ACATTTATCA
59390666 AATAAAGCTTAACTT
1 AATAAAGCTTAACTT
59390681 AATAAAGCTTAACTT
1 AATAAAGCTTAACTT
59390696 AA
1 AA
59390698 CATGAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (15 bp):
AATAAAGCTTAACTT
Found at i:59392523 original size:31 final size:31
Alignment explanation
Indices: 59392485--59392547 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
59392475 GGTTAAAGTG
*
59392485 TAAGAATAGTTACTCAATTGTTGAATTAATT
1 TAAGAATAGTTACTCAATTGTTCAATTAATT
59392516 TAAGAATAGTTACTCAATTGTTCAATTAATT
1 TAAGAATAGTTACTCAATTGTTCAATTAATT
59392547 T
1 T
59392548 TATTTTAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (31 bp):
TAAGAATAGTTACTCAATTGTTCAATTAATT
Found at i:59392775 original size:62 final size:63
Alignment explanation
Indices: 59392675--59392792 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 63
59392665 GCCTAATAAT
* * *
59392675 AAATTTAGCCCTCTAATTTTTACACGTTCTCTCAATTTGATCCTAAGTCTAAAAAAATTAAAC
1 AAATTTAGCCCTCCAATGTTTACACATTCTCTCAATTTGATCCTAAGTCTAAAAAAATTAAAC
59392738 AAATTTAGCCCTCCAATGTTT-CACATTCTCTCAATTTGATCCTAAGTCTAAAAAA
1 AAATTTAGCCCTCCAATGTTTACACATTCTCTCAATTTGATCCTAAGTCTAAAAAA
59392793 TTATAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 33 0.63
63 19 0.37
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (63 bp):
AAATTTAGCCCTCCAATGTTTACACATTCTCTCAATTTGATCCTAAGTCTAAAAAAATTAAAC
Found at i:59399189 original size:13 final size:13
Alignment explanation
Indices: 59399159--59399183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59399149 ATAAACGGTA
59399159 AATTTAATATTTC
1 AATTTAATATTTC
59399172 AATTTAATATTT
1 AATTTAATATTT
59399184 ATATTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAATATTTC
Found at i:59412168 original size:454 final size:450
Alignment explanation
Indices: 59411322--59412208 Score: 1375
Period size: 454 Copynumber: 2.0 Consensus size: 450
59411312 GACTAAATCA
*
59411322 AATAATTTGCAAAACTTGCATTCTAGAAGTTTTTAGTATGAAATTGCTTTGGAATATTAATTAGG
1 AATAATTTGCAAAACTTGCATTATAGAAGTTTTTAGTATGAAATTGCTTTGGAATATTAATTAGG
*
59411387 AGGGTTTAAATAACAATTTGACCAATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAATTT
66 AGGGTTTAAATAAAAATTTGACCAATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAATTT
* *
59411452 TGAAAGTTTAATAAGGAAGGGCATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGAAAAAT
131 TGAAAGTTTAATAAGGAAGGGCATTTTGGTCATTTAGATATTAAATGAAATAAAAA-GCAAAAAT
* * *
59411517 AACACAAAATTCATCATCTTCTTCATTAGCACGAAATTTCAAGGGTTCTTCATAGCTAAGGTTTG
195 AAAACAAAATTCATCATCTTCTTCATTAGCACAAAATTTCAAGGGTTCTCCATAGCTAAGGTTTG
* *
59411582 TTTCAAGCTTTCAAGCTCCAAAGCAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTT
260 TTTCAAGCTTTCAAACTCCAAAGCAAGTGATTCCAAGCCCCGTTTTTAATGATCTTTACGTTTTT
* * * *
59411647 GGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAAGGTTCATATTTGGAAA
325 GGAGTCCCGATAACTCGATAAAGCTTATGCTAGCAATAATTCAAGTTAAGGTTCATATTTGGAAA
*
59411712 AATACCCATAGGTGAAAAGTGTTTATTTTGATGTTTTATGATAACATCAAATTCAAACTCT
390 AATACCCATAGGTGAAAAGTGTGTATTTTGATGTTTTATGATAACATCAAATTCAAACTCT
59411773 AATAATTTGCAAAACTTGCATTATAGAAGTTTTTAGTATGAAATTGCTTTGGAATATTAATTAGG
1 AATAATTTGCAAAACTTGCATTATAGAAGTTTTTAGTATGAAATTGCTTTGGAATATTAATTAGG
59411838 AGGGTTTAAATAAAAATTTGACCAATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAATTT
66 AGGGTTTAAATAAAAATTTGACCAATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAA-TT
* * * *
59411903 TTGAAAGTTTAATAAGGAAGGGCATTTTGGTTATTTAGTTATTAAAATGAATTAAAAA-CAAAAT
130 TTGAAAGTTTAATAAGGAAGGGCATTTTGGTCATTTAGATATT-AAATGAAATAAAAAGCAAAAA
** ** * *
59411967 TAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGACAAAATTTCAAGGGTTCTCCATAGCTAGGG
194 TAAAA--CAAAATTCAT-CATCTTCTTCATTAGCACAAAATTTCAAGGGTTCTCCATAGCTAAGG
* * *
59412032 TTTGTTTCAAGCTTTCAAACTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATCTTTATGT
256 TTTGTTTCAAGCTTTCAAACTCCAAAGCAAGTGATTCCAAGCCCCGTTTTTAATGATCTTTACGT
* * * *
59412097 TTTTGGAGTCCCGATAACTTGATTAAGCTTATTCTAGCAATAATTCAACG-TAGGGTTCATATAT
321 TTTTGGAGTCCCGATAACTCGATAAAGCTTATGCTAGCAATAATTCAA-GTTAAGGTTCATAT-T
** *
59412161 T-GAAAAATACCCATAGGTGAAATTTGTGTATTTTGGTGTTTTATGATA
384 TGGAAAAATACCCATAGGTGAAAAGTGTGTATTTTGATGTTTTATGATA
59412209 GAATATGAGG
Statistics
Matches: 395, Mismatches: 34, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
451 133 0.34
452 42 0.11
453 19 0.05
454 198 0.50
455 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (450 bp):
AATAATTTGCAAAACTTGCATTATAGAAGTTTTTAGTATGAAATTGCTTTGGAATATTAATTAGG
AGGGTTTAAATAAAAATTTGACCAATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAATTT
TGAAAGTTTAATAAGGAAGGGCATTTTGGTCATTTAGATATTAAATGAAATAAAAAGCAAAAATA
AAACAAAATTCATCATCTTCTTCATTAGCACAAAATTTCAAGGGTTCTCCATAGCTAAGGTTTGT
TTCAAGCTTTCAAACTCCAAAGCAAGTGATTCCAAGCCCCGTTTTTAATGATCTTTACGTTTTTG
GAGTCCCGATAACTCGATAAAGCTTATGCTAGCAATAATTCAAGTTAAGGTTCATATTTGGAAAA
ATACCCATAGGTGAAAAGTGTGTATTTTGATGTTTTATGATAACATCAAATTCAAACTCT
Found at i:59432651 original size:50 final size:50
Alignment explanation
Indices: 59432521--59432651 Score: 201
Period size: 50 Copynumber: 2.6 Consensus size: 50
59432511 ATATGTGTCA
* *
59432521 GTGTAAGACCAT-TTTGGGACATGGCATCGACACAGATATGCTAGAGCCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGCTAGAGCCT
* * *
59432570 ATGTAAAACCATGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGCTAGAGCCT
*
59432620 GTGTAAGACCATGTCTGGGACATGGCTTCGGC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC
59432652 TCCTTACCCC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 10 0.14
50 63 0.86
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGCTAGAGCCT
Found at i:59434877 original size:14 final size:16
Alignment explanation
Indices: 59434858--59434890 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
59434848 ATTATGTGAT
59434858 AATGAATGT-A-ATTG
1 AATGAATGTGAGATTG
59434872 AATGAATGTGAGATTG
1 AATGAATGTGAGATTG
59434888 AAT
1 AAT
59434891 AAGTGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (16 bp):
AATGAATGTGAGATTG
Found at i:59444002 original size:14 final size:16
Alignment explanation
Indices: 59443983--59444015 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
59443973 ATTATGTGAT
59443983 AATGAATGT-A-ATTG
1 AATGAATGTGAGATTG
59443997 AATGAATGTGAGATTG
1 AATGAATGTGAGATTG
59444013 AAT
1 AAT
59444016 AAGTGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (16 bp):
AATGAATGTGAGATTG
Found at i:59449370 original size:48 final size:48
Alignment explanation
Indices: 59449291--59449391 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 48
59449281 CACAAGATAG
*
59449291 GATGCCAATGCCATATCCCAGATATCATCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATCATCTTACATGGGATCACATATC
* **
59449339 GATGCCAATGCCATGTCCCAGACATTGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATCATCTTACATGGGATCACATATC
59449387 GATGC
1 GATGC
59449392 TGATAGCCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATCATCTTACATGGGATCACATATC
Found at i:59451629 original size:22 final size:21
Alignment explanation
Indices: 59451604--59451668 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
59451594 GTAAATACGT
59451604 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
* *
59451626 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
59451648 TTAGCACAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
59451669 AATAATTGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:59451870 original size:41 final size:41
Alignment explanation
Indices: 59451812--59451932 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
59451802 AAAGCCACCG
* *
59451812 GTGGATCCACGGTCGTCAAGTAACCATGCGATCCTTAATC-
1 GTGGATCCACGATCGTCAAGTAACCATGCGATCCTCAATCT
* *
59451852 GATGGATCCACGTTCGTCAA-TAAACCATCCGATCCTCAATCT
1 G-TGGATCCACGATCGTCAAGT-AACCATGCGATCCTCAATCT
* *
59451894 GTGGATCCACGATCATGAAGTAACCATGCGATCCTCAAT
1 GTGGATCCACGATCGTCAAGTAACCATGCGATCCTCAAT
59451933 TTCTTCCTCC
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
40 2 0.03
41 66 0.94
42 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
GTGGATCCACGATCGTCAAGTAACCATGCGATCCTCAATCT
Found at i:59452294 original size:27 final size:27
Alignment explanation
Indices: 59452179--59452520 Score: 198
Period size: 27 Copynumber: 12.6 Consensus size: 27
59452169 TTAGTAAATC
*
59452179 TACAAACCAAGGGTATTTC-AGTAATTT
1 TACAAATCAAGGGTATTTCTA-TAATTT
* ** *
59452206 TGCAAGCCAATGGTATTTCTATAATTT
1 TACAAATCAAGGGTATTTCTATAATTT
** * **
59452233 TTGAAAGTCAAGGGTATTTTTGCAATTT
1 TACAAA-TCAAGGGTATTTCTATAATTT
*
59452261 TATAAATCAAGGGTATTTCTATAATTT
1 TACAAATCAAGGGTATTTCTATAATTT
* *
59452288 TCCAAATTAAGGGTATTT-TGATAATTT
1 TACAAATCAAGGGTATTTCT-ATAATTT
* * *
59452315 TCCAAATCAGGGGTATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCT-ATAATTT
*
59452342 TACAAATCGAGGGTATTT-TGATAATTT
1 TACAAATCAAGGGTATTTCT-ATAATTT
* * * *
59452369 TAGAAGTCGAGGGTATTTCGATAATTT
1 TACAAATCAAGGGTATTTCTATAATTT
* **
59452396 TACAACTTGAGGGTATTTC-AGTAATTT
1 TACAAATCAAGGGTATTTCTA-TAATTT
* * * * *
59452423 CATAAATTAGGGGTATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCT-ATAATTT
* *
59452450 TACAAA-CTAGGGGTATTT-TGGTAATTT
1 TACAAATC-AAGGGTATTTCT-ATAATTT
* * *
59452477 TGCTAATCGAGGGTATTT-TGATAATTT
1 TACAAATCAAGGGTATTTCT-ATAATTT
** *
59452504 TGTAAACCAAGGGTATT
1 TACAAATCAAGGGTATT
59452521 CAGTAATTCT
Statistics
Matches: 256, Mismatches: 50, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.01
27 232 0.91
28 22 0.09
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCTATAATTT
Found at i:59452322 original size:54 final size:54
Alignment explanation
Indices: 59452242--59452504 Score: 244
Period size: 54 Copynumber: 4.9 Consensus size: 54
59452232 TTTGAAAGTC
* * *
59452242 AAGGGTATTTTTG-CAATTTTATAAATCAAGGGTATTTCT-ATAATTTTCCAAATT
1 AAGGGTA-TTTTGATAATTTTACAAATCAAGGGTATTT-TGATAATTTTACAAATT
* * * *
59452296 AAGGGTATTTTGATAATTTTCCAAATCAGGGGTATTTTGGTAATTTTACAAATC
1 AAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGATAATTTTACAAATT
* * * * * *
59452350 GAGGGTATTTTGATAATTTTAGAAGTCGAGGGTATTTCGATAATTTTACAACTT
1 AAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGATAATTTTACAAATT
* * * * * * * *
59452404 GAGGGTA-TTTCAGTAATTTCATAAATTAGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGA-TAATTTTACAAATCAAGGGTATTTTGATAATTTTACAAATT
* * * * *
59452458 AGGGGTATTTTGGTAATTTTGCTAATCGAGGGTATTTTGATAATTTT
1 AAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGATAATTTT
59452505 GTAAACCAAG
Statistics
Matches: 165, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
53 10 0.06
54 152 0.92
55 3 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (54 bp):
AAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGATAATTTTACAAATT
Found at i:59452366 original size:81 final size:82
Alignment explanation
Indices: 59452217--59452520 Score: 278
Period size: 81 Copynumber: 3.7 Consensus size: 82
59452207 GCAAGCCAAT
** * *
59452217 GGTATTTCT-ATAATTTTTGAAAGTCA-AGGGTATTTTTGCAATTTTATAAATCAAGGGTATTTC
1 GGTATTT-TGATAATTTTACAAA-TCAGAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTT-
*
59452280 T-ATAATTTTCCAAATTAAG
63 TGATAATTTTACAAATTAAG
* * *
59452299 GGTATTTTGATAATTTTCCAAATCAG-GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGA
1 GGTATTTTGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGA
* * **
59452363 TAATTTTAGAAGTCGAG
66 TAATTTTACAAATTAAG
* * * ** * * * *
59452380 GGTATTTCGATAATTTTACAACT-TGAGGGTATTTCAGTAATTTCATAAATTAGGGGTATTTTGG
1 GGTATTTTGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGA
* *
59452444 TAATTTTACAAACTAGG
66 TAATTTTACAAATTAAG
* * * * * *
59452461 GGTATTTTGGTAATTTTGCTAATC-GAGGGTATTTTGATAATTTTGTAAACCAAGGGTATT
1 GGTATTTTGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTATAAATCAAGGGTATT
59452521 CAGTAATTCT
Statistics
Matches: 175, Mismatches: 42, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
80 2 0.01
81 155 0.89
82 18 0.10
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (82 bp):
GGTATTTTGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGA
TAATTTTACAAATTAAG
Found at i:59452393 original size:108 final size:105
Alignment explanation
Indices: 59452243--59452528 Score: 301
Period size: 108 Copynumber: 2.7 Consensus size: 105
59452233 TTGAAAGTCA
* * * * * *
59452243 AGGGTATTTTTGCAATTTTATAAATCAAGGGTATTTCTATAATTTTCCAAATTAAGGGTATTT-T
1 AGGGTA-TTTTGTAATTTTA-GAATCGAGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCA
59452307 GATAATTTTC-CAAATCAGGGGTATTTTGGTAATTTTACAAATCG
64 G-TAA-TTTCACAAATCAGGGGTATTTTGGTAATTTTACAAA-CG
* *
59452351 AGGGTATTTTGATAATTTTAGAAGTCGAGGGTATTTCGATAATTTTACAACTTGAGGGTATTTCA
1 AGGGTATTTTG-TAATTTTAGAA-TCGAGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCA
* * *
59452416 GTAATTTCATAAATTAGGGGTATTTTGGTAATTTTACAAACT
64 GTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACG
* ** **
59452458 AGGGGTATTTTGGTAATTTT-GCTAATCGAGGGTATTTTGATAATTTTGTAAACCAAGGGTA-TT
1 A-GGGTATTTT-GTAATTTTAG--AATCGAGGGTATTTCGATAATTTTACAAATTAAGGGTATTT
59452521 CAGTAATT
62 CAGTAATT
59452529 CTATCCTACA
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
107 24 0.16
108 124 0.82
109 4 0.03
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (105 bp):
AGGGTATTTTGTAATTTTAGAATCGAGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCAGT
AATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACG
Found at i:59452543 original size:26 final size:27
Alignment explanation
Indices: 59452514--59452565 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
59452504 TGTAAACCAA
* *
59452514 GGGTA-TTCAGTAATTCTATCCTACAG
1 GGGTATTTCAGTAATACTAGCCTACAG
*
59452540 GGGTATTTTAGTAATACTAGCCTACA
1 GGGTATTTCAGTAATACTAGCCTACA
59452566 AATATGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (27 bp):
GGGTATTTCAGTAATACTAGCCTACAG
Found at i:59453850 original size:43 final size:42
Alignment explanation
Indices: 59453788--59453940 Score: 168
Period size: 42 Copynumber: 3.6 Consensus size: 42
59453778 TATTACACCA
* *
59453788 ATGCCATATCCCAGATATGGTCTTACATAG-GATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACA-AGAAATCTCATATCG
* * *
59453830 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACAAGAAATCTCATATCG
* * *
59453873 ATACCATATCCCAGATATGGTCTTACACGAAGTCTCATCAT-G
1 ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCAT-ATCG
* *
59453915 ATGTCATATCCCATATAT-GTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
59453941 CCTAAACTTA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
41 8 0.08
42 52 0.54
43 36 0.38
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCATATCG
Found at i:59457375 original size:26 final size:26
Alignment explanation
Indices: 59457339--59457391 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
59457329 CAACTCGCAC
* *
59457339 AAATGCCTTCGGGTCTTAGCCTGGAT
1 AAATGCCTTCGGGACTTAGCCCGGAT
59457365 AAATGCCTTCGGGACTTAGCCCGGAT
1 AAATGCCTTCGGGACTTAGCCCGGAT
59457391 A
1 A
59457392 TAGTCGCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (26 bp):
AAATGCCTTCGGGACTTAGCCCGGAT
Found at i:59457503 original size:40 final size:40
Alignment explanation
Indices: 59457365--59457496 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
59457355 TAGCCTGGAT
*
59457365 AAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC
* *
59457405 AAATGCCTTCGGGACTTAGCCCGGGTATAGTCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC
* * *
59457445 AAATGCTTTCGGGACTTAGCCCGGATATA-CCAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCAC
*
59457485 AAATTCCTTCGG
1 AAATGCCTTCGG
59457497 ATCTTAGTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 80 0.99
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC
Found at i:59466496 original size:20 final size:21
Alignment explanation
Indices: 59466430--59466498 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
59466420 TCACTTCGTT
59466430 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
59466451 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
59466472 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
59466493 -CTTTTT
1 TCTTTTT
59466499 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:59477301 original size:65 final size:65
Alignment explanation
Indices: 59477194--59477325 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
59477184 TGAGCCAGAG
* * * *
59477194 TAAGACCATGTCTAGGACATGTCATCGGCAACATACCTTATGTTTGAGGTTTAGTGAATATTTGA
1 TAAGACCATGTCTAGGACATGGCATCGACAACATACCCTATGTTTGAGGTTTAATGAATATTTGA
*
59477259 TAAGACCATGTCTAGGACATGGCATCGACATCATACCCTATGTTTGAGGTTTAATGAATATTTGA
1 TAAGACCATGTCTAGGACATGGCATCGACAACATACCCTATGTTTGAGGTTTAATGAATATTTGA
59477324 TA
1 TA
59477326 GTATTCCAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (65 bp):
TAAGACCATGTCTAGGACATGGCATCGACAACATACCCTATGTTTGAGGTTTAATGAATATTTGA
Found at i:59483956 original size:46 final size:46
Alignment explanation
Indices: 59483889--59484064 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
59483879 TATTTGGGCA
* *
59483889 TCCGAACTCGTTGAGTTGAGTCCGCGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59483935 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
59483982 TGCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
59484028 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59484065 TCGGGTTACA
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 59 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59484044 original size:93 final size:93
Alignment explanation
Indices: 59483885--59484057 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 93
59483875 AGGATATTTG
* * * *
59483885 GGCATCCGAACTCGTTGAGTTGAGTCCGCGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCATTGAG
59483950 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
59483978 GGCATGCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG-CCTGAGCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCC-GAACTCATTGA
59484042 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
59484058 CTTATGGTCG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:59487007 original size:15 final size:15
Alignment explanation
Indices: 59486987--59487042 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
59486977 GTATCTTAGG
59486987 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
59487002 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
59487017 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
59487032 TTTCTTTATTC
1 TTTCTTTATTC
59487043 AGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:59489914 original size:27 final size:27
Alignment explanation
Indices: 59489884--59490061 Score: 153
Period size: 27 Copynumber: 6.6 Consensus size: 27
59489874 ATATTGAGCC
* *
59489884 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
59489911 CGCACGCTTAGTGCCACGTAATCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
*
59489938 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
59489966 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
59489993 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
59490020 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
59490047 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
59490062 GTACAATTTA
Statistics
Matches: 124, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 98 0.79
28 25 0.20
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:59490044 original size:54 final size:53
Alignment explanation
Indices: 59489884--59490060 Score: 178
Period size: 54 Copynumber: 3.3 Consensus size: 53
59489874 ATATTGAGCC
* * * *
59489884 CGCACACTCAGTGCTAT-ATAATCAACTCGCACGCTTAGTGCCACGTAATCGAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCCACATAGTC-AAT
* * *
59489938 CGCACACTTAGTGC-TACATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCA-ACTCGCACACTTAGTGCCACATAGTCAA-T
* ** *
59489993 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCCACATAGTC-AAT
*
59490047 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
59490061 TGTACAATTT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 1 0.01
54 56 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCCACATAGTCAAT
Found at i:59497966 original size:27 final size:27
Alignment explanation
Indices: 59497848--59498023 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 27
59497838 ATATTGAGCC
* * * * *
59497848 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
59497875 CGCACGCTTAGTGC-ACGTAATCGAA-T
1 CGCACACTTAGTGCAACATAGTC-AATT
* *
59497901 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCAACATAGTCA-ATT
** *
59497929 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
59497956 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAATT
*
59497983 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCAACATAGTCAATT
*
59498010 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
59498024 TGTACAATTT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.17
27 81 0.65
28 22 0.18
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAATT
Found at i:59514549 original size:13 final size:13
Alignment explanation
Indices: 59514531--59514562 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
59514521 GTTTCTTAAA
59514531 TTTATTCCCACCC
1 TTTATTCCCACCC
59514544 TTTATTCCCACCC
1 TTTATTCCCACCC
59514557 TTTATT
1 TTTATT
59514563 GTATAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTATTCCCACCC
Found at i:59515984 original size:130 final size:129
Alignment explanation
Indices: 59515752--59515990 Score: 293
Period size: 130 Copynumber: 1.8 Consensus size: 129
59515742 AGAATGCTTA
* * * *
59515752 AAAACGAAGACGATGTTCAATGTTTGGCGATTGAGAATCGTGCCCTATTGTGCTGGGTTGCACTT
1 AAAACGAAGACGATGTTCAATGTTTGGCAATTAAGAATCGAGCCCTATCGTGCTGGGTTGCACTT
* * *
59515817 TTTCATTGGTTCGAAACAATTGAACATCCCTACGGAATTTCACTCACATTTCCTAAAATCTTTC
66 TTTCATTGGTCCAAAACAATCGAACATCCCTACGGAATTTCACTCACATTTCCTAAAATCTTTC
* * * * *
59515881 AAAATGAAGGCGATGTTCGATGTTTGGCAATTTAAGAATCGAGCCCTATCGTGTTGGGTTGCGCT
1 AAAACGAAGACGATGTTCAATGTTTGGCAA-TTAAGAATCGAGCCCTATCGTGCTGGGTTGCACT
* * * *
59515946 TTCTT-ATTTGTCCAAAATAATCGAATATCTCCT-TGGAATTTCACT
65 TT-TTCATTGGTCCAAAACAATCGAACATC-CCTACGGAATTTCACT
59515991 TATATTCTCT
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
129 26 0.29
130 60 0.66
131 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (129 bp):
AAAACGAAGACGATGTTCAATGTTTGGCAATTAAGAATCGAGCCCTATCGTGCTGGGTTGCACTT
TTTCATTGGTCCAAAACAATCGAACATCCCTACGGAATTTCACTCACATTTCCTAAAATCTTTC
Found at i:59527083 original size:93 final size:93
Alignment explanation
Indices: 59526970--59527141 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
59526960 CGCCCATAAG
* *
59526970 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCTATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59527035 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
59527063 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59527128 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
59527142 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:59527138 original size:46 final size:46
Alignment explanation
Indices: 59526963--59527138 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
59526953 TGTAACCCGC
* *
59526963 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
59527009 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
59527059 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
59527102 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
59527139 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59534608 original size:93 final size:93
Alignment explanation
Indices: 59534479--59534650 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
59534469 CGCCCATAAG
* * *
59534479 CGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAGTGAGCTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59534544 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
59534572 CGAACTCGGACTCAACTGAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59534637 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
59534651 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:59534647 original size:46 final size:46
Alignment explanation
Indices: 59534472--59534647 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
59534462 TGTAACCCGC
* * * *
59534472 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
59534518 CCATAAGTGAGCTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
59534568 -C-TCA-CGAACTCGGACTCAACTGAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
59534611 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
59534648 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.57
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59538314 original size:44 final size:44
Alignment explanation
Indices: 59537789--59538294 Score: 726
Period size: 44 Copynumber: 11.5 Consensus size: 44
59537779 GGTAAATCCT
*
59537789 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
59537833 GCAGATTTGGCGTCTCGGTATTGGCAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
59537877 GCAGACTTGACATCTCTGTATTGGCGGAGAACAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * *
59537921 GCAGAATTGGCATCTCTGTATTGGCGGAGAGTAGATCGAAGGTC
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
59537965 GCAGATTTGGCATCTCTGTATTGGCGGAGAGTAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * *
59538009 GCAGATTTGGCATCTCTGTATTGGCGGAGAACGGGTCGAAAATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
59538053 GCAAATTTGGCATCTCTGTATTGGCGGAGAGCAGATTGAAGATC
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
59538097 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
59538141 GTAGATTTGGAATCTCTGTATTGGCGGAGAAG-AGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAG-AGCAGATCGAAGATA
* * * * *
59538185 GCAGAATCGACATCTCTGTATTGGCGGAGAGCAGATCGAAGGTC
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
59538229 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
59538273 GCAGATTTGGCATCTCTATATT
1 GCAGATTTGGCATCTCTGTATT
59538295 TACAAAGAGC
Statistics
Matches: 409, Mismatches: 51, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
43 2 0.00
44 405 0.99
45 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (44 bp):
GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
Found at i:59543209 original size:80 final size:80
Alignment explanation
Indices: 59543093--59543309 Score: 321
Period size: 80 Copynumber: 2.7 Consensus size: 80
59543083 ACCCAAGTAT
* * *
59543093 CTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
59543157 CACTTGCATAAATGC
66 CACTAGCATAAATGC
* * *
59543172 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
59543236 TCACTAGCATAAATGC
65 TCACTAGCATAAATGC
* * *
59543252 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
59543310 TTATCATCCG
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
79 13 0.11
80 109 0.89
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCATAAATGC
Found at i:59543304 original size:40 final size:40
Alignment explanation
Indices: 59543093--59543297 Score: 281
Period size: 40 Copynumber: 5.2 Consensus size: 40
59543083 ACCCAAGTAT
* * *
59543093 CTTCGGGATTTAG-CCGGATATCG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
59543132 CTTCGGGTCTTAGCCCGGATATAGTCACTTGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
59543172 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
59543212 CTTCGGGACTTAGCCCGGGTATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
59543252 CTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
59543292 CTTCGG
1 CTTCGG
59543298 ATCTTAGTCC
Statistics
Matches: 148, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 12 0.08
40 135 0.91
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:59565589 original size:16 final size:15
Alignment explanation
Indices: 59565570--59565624 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 15
59565560 AAAACTTTTT
59565570 TTTATATTTTTATTAA
1 TTTA-ATTTTTATTAA
59565586 TTTATATTTTTATT--
1 TTTA-ATTTTTATTAA
59565600 TTTAATTTTTATTATA
1 TTTAATTTTTATTA-A
59565616 TTTAATTTT
1 TTTAATTTT
59565625 ATAATAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
16 23 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTAATTTTTATTAA
Found at i:59565608 original size:29 final size:30
Alignment explanation
Indices: 59565568--59565624 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
59565558 TAAAAACTTT
59565568 TTTTTATATTTTTATTA-ATTTATATTTTTA
1 TTTTTATATTTTTATTATATTTA-ATTTTTA
59565598 TTTTTA-ATTTTTATTATATTTAATTTT
1 TTTTTATATTTTTATTATATTTAATTTT
59565625 ATAATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTTATATTTTTATTATATTTAATTTTTA
Found at i:59585016 original size:27 final size:27
Alignment explanation
Indices: 59584985--59585161 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
59584975 TAAATTGTAC
59584985 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
59585012 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59585038 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
59585066 GGCACTAAGT-TGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
59585093 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59585120 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59585147 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59585162 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.04
27 117 0.92
28 5 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59585125 original size:81 final size:81
Alignment explanation
Indices: 59584986--59585140 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
59584976 AAATTGTACA
* *
59584986 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
59585051 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
59585067 GCACTAAGT-TGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
*
59585130 GTGCGAGTTGA
64 GTGCGAATTGA
59585141 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 6 0.09
81 60 0.91
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59585152 original size:81 final size:81
Alignment explanation
Indices: 59584982--59585161 Score: 220
Period size: 81 Copynumber: 2.2 Consensus size: 81
59584972 GATTAAATTG
* *
59584982 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59585047 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59585063 TGCGGCACTAAGT-TGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59585126 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59585144 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59585162 GACTCAATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 6 0.07
81 72 0.88
82 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59590812 original size:30 final size:30
Alignment explanation
Indices: 59590778--59590837 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
59590768 TCCTTAACTC
59590778 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
59590808 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
59590838 GGGCTCGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:59604916 original size:16 final size:16
Alignment explanation
Indices: 59604895--59604951 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
59604885 TTTGGTTCGC
*
59604895 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
59604911 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
59604927 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
59604943 TGTAATGGA
1 TGTAATGGA
59604952 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:59605218 original size:18 final size:17
Alignment explanation
Indices: 59605197--59605231 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59605187 TTATTATTAA
*
59605197 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
59605215 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
59605232 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:59605368 original size:16 final size:16
Alignment explanation
Indices: 59605331--59605372 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
59605321 TTAATCATAT
*
59605331 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
59605347 TT-AAATATATTATAA
1 TTAAAATATATTATAA
59605362 TTAAAATATAT
1 TTAAAATATAT
59605373 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:59605370 original size:154 final size:156
Alignment explanation
Indices: 59605084--59605397 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 156
59605074 TAGAATACCC
59605084 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
59605149 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
59605214 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAAAAA
* *
59605241 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
59605304 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
59605369 ATATAATTTAATAAAATTCTTAAAAA
131 ATATAATTTAATAAAATTCTTAAAAA
59605395 TTA
1 TTA
59605398 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
154 92 0.60
155 1 0.01
157 60 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAAA
Found at i:59605379 original size:14 final size:15
Alignment explanation
Indices: 59605340--59605381 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
59605330 TTTAAACATA
*
59605340 ATTATTATTAAATAT
1 ATTATAATTAAATAT
59605355 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
59605369 A-TATAATTTAATA
1 ATTATAATTAAATA
59605382 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:59605468 original size:120 final size:121
Alignment explanation
Indices: 59605329--59605625 Score: 462
Period size: 120 Copynumber: 2.5 Consensus size: 121
59605319 ATTTAATCAT
*
59605329 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-A
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
59605393 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 AA-TAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
59605451 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
59605514 AATAAAATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
59605570 ATTTCAA-ATAATTAATATTAAATATGATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATT
59605626 TAAAATTATT
Statistics
Matches: 165, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
119 24 0.15
120 130 0.79
121 10 0.06
122 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:59605499 original size:14 final size:15
Alignment explanation
Indices: 59605450--59605501 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
59605440 GTAAAATATA
59605450 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
59605465 TATTAAATATATTAT
1 AATTAAATATATTAT
59605480 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
59605493 AATTTAATA
1 AATTAAATA
59605502 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:59605516 original size:44 final size:43
Alignment explanation
Indices: 59605427--59605517 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
59605417 CTCAAATCAT
* * *
59605427 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
59605470 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
59605514 AATA
1 AATA
59605518 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:59605552 original size:59 final size:59
Alignment explanation
Indices: 59605369--59605552 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
59605359 TAATTAAAAT
59605369 ATATAATTTAATAAAATTCTTAA-AAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
59605428 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
59605488 T-
58 TA
* *
59605489 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
59605548 ATATA
1 ATATA
59605553 TGATACTATA
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 11 0.12
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:59605606 original size:15 final size:15
Alignment explanation
Indices: 59605586--59605624 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
59605576 AATAATTAAT
59605586 ATTAAATATGATTTA
1 ATTAAATATGATTTA
59605601 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
59605618 ATAAAAT
1 ATTAAAT
59605625 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Done.