Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 170 of 259
Found at i:55200863 original size:27 final size:27
Alignment explanation
Indices: 55200833--55200897 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
55200823 GTAATTTCAC
* * *
55200833 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
* * *
55200860 AATCGATGGTAAAATAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
55200887 AATCGAGGGTA
1 AATCGAGGGTA
55200898 CTTTGGTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:55202978 original size:31 final size:31
Alignment explanation
Indices: 55202940--55203003 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
55202930 CCTTTTCATA
55202940 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
55202971 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
55203002 TT
1 TT
55203004 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:55203248 original size:23 final size:23
Alignment explanation
Indices: 55203218--55203266 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
55203208 CCTAGCCTCT
55203218 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
55203241 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
55203264 TTT
1 TTT
55203267 TACACTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:55203382 original size:20 final size:20
Alignment explanation
Indices: 55203318--55203376 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
55203308 TATGATTACA
55203318 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
55203338 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
* *
55203358 TCATGCGCATGTCATACAT
1 TCATGTGCATATCATACAT
55203377 ACCATGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:55210843 original size:25 final size:24
Alignment explanation
Indices: 55210801--55210872 Score: 103
Period size: 23 Copynumber: 3.0 Consensus size: 24
55210791 GCTTTATCAT
*
55210801 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
55210826 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
55210849 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
55210873 CACTTCCTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
23 23 0.52
24 9 0.20
25 12 0.27
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:55210947 original size:20 final size:20
Alignment explanation
Indices: 55210922--55210960 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55210912 TATGATTACA
55210922 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
55210942 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
55210961 ACCCTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:55213659 original size:30 final size:28
Alignment explanation
Indices: 55213611--55213692 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 28
55213601 TCAGTCTCGA
55213611 CATATACTGGGCCGAAGCCTTTTCATAAAT
1 CATATACT-GGCC-AAGCCTTTTCATAAAT
55213641 CATATCACTAGGCCAAGCCTTTTCATAAAT
1 CATAT-ACT-GGCCAAGCCTTTTCATAAAT
*
55213671 CATATTACTGGTCGAAGCCTTT
1 CATA-TACTGG-CCAAGCCTTT
55213693 ACTGTAAGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 2 0.04
30 37 0.79
31 8 0.17
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (28 bp):
CATATACTGGCCAAGCCTTTTCATAAAT
Found at i:55213940 original size:25 final size:25
Alignment explanation
Indices: 55213912--55213981 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
55213902 CTCTTTTATT
*
55213912 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55213937 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55213962 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55213982 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:55214855 original size:26 final size:25
Alignment explanation
Indices: 55214794--55214866 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
55214784 ATATTCGTCA
55214794 TTTTACCATATAGGGGTATTACGGTC
1 TTTTACC-TATAGGGGTATTACGGTC
**
55214820 ACTTACCCTATAGGGGCT-TTACGGTC
1 TTTTA-CCTATAGGGG-TATTACGGTC
55214846 TTTTTACCTATTAGGGGTATT
1 -TTTTACCTA-TAGGGGTATT
55214867 TTAGTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (25 bp):
TTTTACCTATAGGGGTATTACGGTC
Found at i:55214937 original size:27 final size:27
Alignment explanation
Indices: 55214907--55215032 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 27
55214897 GTAAATCTAC
55214907 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
55214934 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
55214960 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
** * ** *
55214990 AAATTAGGGGTATTTTGGTAATTTTAT
1 AAACCAAGGGTATTTCAGTAATTTTGT
**
55215017 AAACTGAGGGTATTTC
1 AAACCAAGGGTATTTC
55215033 GGAAATTTCA
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
26 1 0.01
27 53 0.66
28 7 0.09
29 18 0.22
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:55215039 original size:27 final size:26
Alignment explanation
Indices: 55214969--55215093 Score: 115
Period size: 27 Copynumber: 4.7 Consensus size: 26
55214959 TAGAAAGTCA
* ** *
55214969 AGGGTATTTCTGTAATTTTGTAAATT
1 AGGGTATTTCGGTAATTTTACAAACT
* *
55214995 AGGGGTATTTTGGTAATTTTATAAACT
1 A-GGGTATTTCGGTAATTTTACAAACT
* * *
55215022 GAGGGTATTTCGGAAATTTCACAAACC
1 -AGGGTATTTCGGTAATTTTACAAACT
*
55215049 AGTGGTATTTTGGTAATTTTACAAACT
1 AG-GGTATTTCGGTAATTTTACAAACT
*
55215076 AGGAGTATTTTGGTAATT
1 AGG-GTATTTCGGTAATT
55215094 CTACCCTATA
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.05
27 77 0.94
28 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAAACT
Found at i:55216281 original size:56 final size:57
Alignment explanation
Indices: 55216152--55216303 Score: 243
Period size: 56 Copynumber: 2.6 Consensus size: 57
55216142 TCTCATACAG
* *
55216152 GGTCTTACTCGTACACATATATCGGAATCACATATCGATGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATC-A-GATGCCAACGTATTAAACGT
*
55216211 GGTCTTACTCGCACACATATATCGGAATCACATATC-GATGCCAACGTTTTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGT
*
55216267 GGTCTTACTTGCACACATATATCGGAATCACATATCA
1 GGTCTTACTCGCACACATATATCGGAATCACATATCA
55216304 CAAGTCGAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
56 53 0.60
59 35 0.40
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (57 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGT
Found at i:55236580 original size:40 final size:40
Alignment explanation
Indices: 55236506--55236726 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
55236496 AACCCAAGTA
* *
55236506 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
55236545 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
55236585 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * * *
55236625 CCTTCGGGACTTAGCCTGGGTATAGTCAATAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
55236665 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
55236704 CCTTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
55236727 CATCCGAATA
Statistics
Matches: 159, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
39 37 0.23
40 120 0.75
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:55240698 original size:53 final size:54
Alignment explanation
Indices: 55240635--55240742 Score: 200
Period size: 53 Copynumber: 2.0 Consensus size: 54
55240625 ATTTATAATG
55240635 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGAC-GTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
*
55240688 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACATTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
55240742 T
1 T
55240743 ACATTGTGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (54 bp):
TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
Found at i:55245149 original size:46 final size:45
Alignment explanation
Indices: 55245074--55245202 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 45
55245064 CATTAGGTGG
* *
55245074 TATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGACCACTT-
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCG-CCA-TTA
*
55245120 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATT-A
* * * *
55245166 GACGAGAGCTAGTGTAAGACATGTCTTGGACATGCAT
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCAT
55245203 TAGCCTCGGG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 70 0.95
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATTA
Found at i:55245355 original size:49 final size:49
Alignment explanation
Indices: 55245271--55245387 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 49
55245261 GTTTGTCAGG
* *
55245271 GTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAGAGCTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
* * * * *
55245320 GTAAGACCTGTCTGGGACGTGGCATTGGC-CTCGATATATGAAAGTTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAAAGCTAGT
* * *
55245369 GTAACACCTATATGGGACA
1 GTAAGACCTGTCTGGGACA
55245388 CAACATCGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 1 0.02
49 55 0.98
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (49 bp):
GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
Found at i:55246642 original size:20 final size:21
Alignment explanation
Indices: 55246603--55246642 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55246593 GTCAACAGGG
*
55246603 CCACACGGACGTGTTGCCCTT
1 CCACACGGACGTGATGCCCTT
*
55246624 CCACACGGGCGT-ATGCCCT
1 CCACACGGACGTGATGCCCT
55246643 GTTTTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (21 bp):
CCACACGGACGTGATGCCCTT
Found at i:55247657 original size:15 final size:16
Alignment explanation
Indices: 55247615--55247662 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
55247605 TAAAATCTTT
55247615 TTTGAATCCCTAACAATC
1 TTTGAATCCCT-A-AATC
*
55247633 TTTAAATCCCTAAATC
1 TTTGAATCCCTAAATC
55247649 -TTGAATCCCTAAAT
1 TTTGAATCCCTAAAT
55247663 AGTTAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 1 0.04
18 10 0.36
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (16 bp):
TTTGAATCCCTAAATC
Found at i:55247775 original size:23 final size:24
Alignment explanation
Indices: 55247734--55247779 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
55247724 CCTATAAAAA
*
55247734 TTAGAAACAAAATCGTGAAATCCC
1 TTAGAAACAAAATCATGAAATCCC
*
55247758 TTAG-AACCAAATCATGAAATCC
1 TTAGAAACAAAATCATGAAATCC
55247780 TTATTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
TTAGAAACAAAATCATGAAATCCC
Found at i:55248771 original size:22 final size:22
Alignment explanation
Indices: 55248741--55248782 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55248731 TAAGCATATG
*
55248741 ATTTGGATAAATGTAATTTAAA
1 ATTTCGATAAATGTAATTTAAA
*
55248763 ATTTCGATAAATGTACTTTA
1 ATTTCGATAAATGTAATTTA
55248783 CAAAAGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTCGATAAATGTAATTTAAA
Found at i:55259995 original size:40 final size:40
Alignment explanation
Indices: 55259951--55260122 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
55259941 GGACTAAGAT
*
55259951 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
55259991 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
55260031 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
55260071 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
55260110 CCGAAGGCATTTG
1 CCGAAGGCATTTG
55260123 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:55260036 original size:80 final size:79
Alignment explanation
Indices: 55259951--55260122 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
55259941 GGACTAAGAT
*
55259951 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
55260015 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
55260031 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
55260096 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
55260110 CCGAAGGCATTTG
1 CCGAAGGCATTTG
55260123 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:55260140 original size:79 final size:80
Alignment explanation
Indices: 55259978--55260155 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
55259968 AGATACAAAT
* * * *
55259978 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
55260043 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
55260058 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
55260122 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
55260137 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55260156 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:55267940 original size:40 final size:40
Alignment explanation
Indices: 55267896--55268067 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
55267886 GGACTAAGAT
*
55267896 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
55267936 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
55267976 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
55268016 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
55268055 CCGAAGGCATTTG
1 CCGAAGGCATTTG
55268068 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:55267981 original size:80 final size:79
Alignment explanation
Indices: 55267896--55268067 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
55267886 GGACTAAGAT
*
55267896 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
55267960 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
55267976 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
55268041 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
55268055 CCGAAGGCATTTG
1 CCGAAGGCATTTG
55268068 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:55268085 original size:79 final size:80
Alignment explanation
Indices: 55267923--55268100 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
55267913 AGATACAAAT
* * * *
55267923 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
55267988 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
55268003 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
55268067 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
55268082 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55268101 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:55269943 original size:50 final size:48
Alignment explanation
Indices: 55269876--55269999 Score: 149
Period size: 48 Copynumber: 2.5 Consensus size: 48
55269866 AGGTGCCTAT
* ** *
55269876 GCCATGTCCCAGACATGGTCTTTCACAAGTTCTAGCATATATGTGCCGAA
1 GCCATGTCCCAGACATGGTCTTACACAAGCAC-AGC-TATACGTGCCGAA
* ** * *
55269926 GCCATGTCCCAGACATGGTCTTACGCTGGCACATCTATACGTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACAAGCACAGCTATACGTGCCGAA
55269974 GCCATGTCCCAGACATGGTCTTACAC
1 GCCATGTCCCAGACATGGTCTTACAC
55270000 TGACACATCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 36 0.56
49 2 0.03
50 26 0.41
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACAAGCACAGCTATACGTGCCGAA
Found at i:55269988 original size:48 final size:48
Alignment explanation
Indices: 55269868--55270137 Score: 195
Period size: 46 Copynumber: 5.7 Consensus size: 48
55269858 ATGGGGTCAG
* * ** ** * *
55269868 GTGCCTATGCCATGTCCCAGACATGGTCTTTCACAAGTTCTAGCATATAT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-ATC-TATAC
* *
55269918 GTGCCGAAGCCATGTCCCAGACATGGTCTTACGCTGGCACATCTATAC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACATCTATAC
*
55269966 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATC--T-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACATCTATAC
* * * *
55270011 GTAGCCGACG-CATGTCCCGGACAT-GTCTTACACTGGCTTACATC-ACAA
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC--ACATCTATAC
* * * * *
55270059 G-GCCAATG-CATGTCCTAGACAT-GTCTTACACTAGCTC-TCGTCT-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACATC-TATAC
* *
55270103 AATGTCGATGCCATGTCCCAGACAT-GTCTTACACT
1 -GTGCCGATGCCATGTCCCAGACATGGTCTTACACT
55270138 AGCTCACAAC
Statistics
Matches: 179, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.01
44 13 0.07
45 16 0.09
46 46 0.26
47 23 0.13
48 45 0.25
49 2 0.01
50 32 0.18
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACATCTATAC
Found at i:55270549 original size:29 final size:30
Alignment explanation
Indices: 55270489--55270549 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
55270479 TATTTTTGGC
** *
55270489 AAAATGACCATTTTGCCCTTAAATTTTGAA
1 AAAATGACCATTTTGCCCTTAAAGCTCGAA
*
55270519 AAAATGACCATTTTGCCCTT-AGGCTCGAA
1 AAAATGACCATTTTGCCCTTAAAGCTCGAA
55270548 AA
1 AA
55270550 TCAATTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (30 bp):
AAAATGACCATTTTGCCCTTAAAGCTCGAA
Found at i:55277659 original size:48 final size:46
Alignment explanation
Indices: 55277543--55277757 Score: 158
Period size: 48 Copynumber: 4.6 Consensus size: 46
55277533 TCAGGTGCCA
* * *
55277543 ATGCCATGTCCCAGACATGGTCTTTCACAAGTTCTAGCATATCTG-T-GCTG
1 ATGCCATGTCCCAGACATGGTC-TT-AC-A-TT-GA-CACATCTGATAGCCG
*
55277593 ATGCCATGTCCCAAACATGGTCTTACATTGACACATCT-ATACGTTCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATA-G--CCG
* *
55277641 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCTGGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATAGCCG
* * * **
55277687 ACG-CATGTCCCGGACAT-GTCTTACATTGGCTTACATCACA-ACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGAC--ACATCTGATA-GCCG
*
55277733 ATG-CATGTCCTAGACAT-GTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
55277758 CTAGCTCTCG
Statistics
Matches: 139, Mismatches: 17, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
44 18 0.13
45 15 0.11
46 39 0.28
47 1 0.01
48 41 0.29
49 4 0.03
50 21 0.15
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATAGCCG
Found at i:55277779 original size:46 final size:44
Alignment explanation
Indices: 55277683--55277857 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 44
55277673 ACATCTGGTA
* * * * * *
55277683 GCCGACGCATGTCCCGGACATGTCTTACATTGGCTTACATCACAAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-C-TCTCAAT
*
55277729 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT-TC-TCTCAAT
*
55277775 GCCGATGTCATGTCCTAGACATGGTCTTACACTAG-TTCTCAT-AATGT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTCTC-TCAA--T
55277822 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCT
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
55277858 CACAACAAGT
Statistics
Matches: 112, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
45 4 0.04
46 58 0.52
47 31 0.28
48 19 0.17
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCTCTCAAT
Found at i:55282280 original size:40 final size:40
Alignment explanation
Indices: 55282225--55282486 Score: 411
Period size: 40 Copynumber: 6.6 Consensus size: 40
55282215 TATTCGGATG
*
55282225 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
55282265 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
55282305 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
55282345 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
55282385 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
55282425 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* * *
55282465 AT-ATCTGGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
55282487 TACTTGGTTT
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
39 19 0.09
40 192 0.91
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:55290439 original size:38 final size:39
Alignment explanation
Indices: 55290393--55290633 Score: 342
Period size: 39 Copynumber: 6.4 Consensus size: 39
55290383 GATGATAACG
*
55290393 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-AC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
55290431 GGCTAAGT-CCGAA-G-----GTGCGAGTTACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
55290463 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
55290501 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
55290541 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
55290580 GGCTAAATCCCGAAGGCATTTGAG-GAG-TAGCTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
*
55290618 GGCTAATTCCCGAAGG
1 GGCTAAGTCCCGAAGG
55290634 TACTTGGTTT
Statistics
Matches: 187, Mismatches: 6, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.08
32 14 0.07
33 1 0.01
36 1 0.01
37 7 0.04
38 51 0.27
39 68 0.36
40 30 0.16
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:55290452 original size:31 final size:32
Alignment explanation
Indices: 55290414--55290556 Score: 117
Period size: 40 Copynumber: 4.0 Consensus size: 32
55290404 GAAGGCATTT
55290414 GTGCGAGTTACTATA-ACGGCTAAGTCCGAAG
1 GTGCGAGTTACTATATACGGCTAAGTCCGAAG
*
55290445 GTGCGAGTTACTATATCCGGCTAAGTCCGAAGG
1 GTGCGAGTTACTATATACGGCTAAGTCCGAA-G
*
55290478 CATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGG
1 -----GTGCGAGTTACTATATAC-GGCTAAGT-CCGAA-G
*
55290518 CATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAG
1 -----GTGCGAGTTACTATATACGGCTAAGT-CCGAAG
55290556 G
1 G
55290557 CATTTGTGCG
Statistics
Matches: 102, Mismatches: 1, Indels: 16
0.86 0.01 0.13
Matches are distributed among these distances:
31 15 0.15
32 14 0.14
33 2 0.02
38 19 0.19
39 22 0.22
40 30 0.29
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (32 bp):
GTGCGAGTTACTATATACGGCTAAGTCCGAAG
Found at i:55294587 original size:28 final size:28
Alignment explanation
Indices: 55294555--55294649 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 28
55294545 ACATACATGC
* *
55294555 ATATGGCCCA-CTTGGCCCAATCTCATTT
1 ATATGGCCCATC-AGGCCCAATCACATTT
*
55294583 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAA-TCACATTT
*
55294612 ATATGGCCCATCAGGCCCAAATCACCTTT
1 ATATGGCCCATCAGGCCC-AATCACATTT
55294641 ATATGGCCC
1 ATATGGCCC
55294650 GTTAGGCCGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.29
29 40 0.68
30 2 0.03
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATCACATTT
Found at i:55294656 original size:29 final size:29
Alignment explanation
Indices: 55294580--55294667 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
55294570 CCCAATCTCA
* * *
55294580 TTTATATGGCCCATCAGGCCCAATTCACA
1 TTTATATGGCCCATCAGGCCCAAATAACC
* *
55294609 TTCATATGGCCCATCAGGCCCAAATCACC
1 TTTATATGGCCCATCAGGCCCAAATAACC
* * *
55294638 TTTATATGGCCCGTTAGGCCGAAATAACC
1 TTTATATGGCCCATCAGGCCCAAATAACC
55294667 T
1 T
55294668 CATATTCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (29 bp):
TTTATATGGCCCATCAGGCCCAAATAACC
Found at i:55294909 original size:16 final size:16
Alignment explanation
Indices: 55294883--55294925 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
55294873 GCAGCTAAAC
*
55294883 TTTCAGCTTTTCGGTA
1 TTTCGGCTTTTCGGTA
*
55294899 TTTTGGCTTTTCGGTA
1 TTTCGGCTTTTCGGTA
55294915 TTTCGGCTTTT
1 TTTCGGCTTTT
55294926 GCCGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.16, G:0.21, T:0.56
Consensus pattern (16 bp):
TTTCGGCTTTTCGGTA
Found at i:55301762 original size:16 final size:16
Alignment explanation
Indices: 55301741--55301783 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
55301731 GCCGCCAAAC
55301741 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
*
55301757 TTTCGACTTTTTGGCA
1 TTTCGACTTTTCGGCA
55301773 TTTCGACTTTT
1 TTTCGACTTTT
55301784 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:55303043 original size:16 final size:16
Alignment explanation
Indices: 55303022--55303053 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55303012 AAATTCAAAA
55303022 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
55303038 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
55303054 GCGCTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
TTTCAAGATTTTTGGG
Found at i:55308123 original size:34 final size:34
Alignment explanation
Indices: 55308084--55308149 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
55308074 AGCTCGAGCC
* *
55308084 CAGTGGGCCTAAGCCCTATTCAG-ATAACAGTACA
1 CAGTGGACCGAAGCCCTATTCAGAAT-ACAGTACA
*
55308118 CAGTGGACCGAAGCCCTTTTCAGAATACAGTA
1 CAGTGGACCGAAGCCCTATTCAGAATACAGTA
55308150 GCAAGGCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (34 bp):
CAGTGGACCGAAGCCCTATTCAGAATACAGTACA
Found at i:55311698 original size:44 final size:46
Alignment explanation
Indices: 55311586--55311699 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 46
55311576 CTAAAATTCA
* *
55311586 TATAACCTCTAAAACCTTAAACCCCAAAAAAATTATGAACACTAATC
1 TATAACCTCTAAAACCTTAAACCCCAAAAAAACTA-GAACACTAAAC
* * * **
55311633 TATAACCCCTAAAATAC-TAAACCCC-TAAACCCTA-AACACTAAAC
1 TATAACCTCTAAAA-CCTTAAACCCCAAAAAAACTAGAACACTAAAC
*
55311677 TATAACTTCTAAAACCTTAAACC
1 TATAACCTCTAAAACCTTAAACC
55311700 AAAAAACATC
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.02
44 27 0.49
46 5 0.09
47 21 0.38
48 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (46 bp):
TATAACCTCTAAAACCTTAAACCCCAAAAAAACTAGAACACTAAAC
Found at i:55312487 original size:7 final size:7
Alignment explanation
Indices: 55312477--55312578 Score: 102
Period size: 7 Copynumber: 14.3 Consensus size: 7
55312467 ACTCAAAAAA
55312477 TAAAATT
1 TAAAATT
55312484 TAAAAATT
1 T-AAAATT
55312492 TAAAAATT
1 T-AAAATT
55312500 TAAAATT
1 TAAAATT
55312507 TAAAAATT
1 T-AAAATT
55312515 TAAAATT
1 TAAAATT
55312522 TAAAATT
1 TAAAATT
*
55312529 TAAAAATA
1 T-AAAATT
*
55312537 AAAAATT
1 TAAAATT
55312544 TAAAA--
1 TAAAATT
55312549 -AAAATT
1 TAAAATT
*
55312555 AAAAATT
1 TAAAATT
*
55312562 TAATATT
1 TAAAATT
55312569 TAATAATT
1 TAA-AATT
55312577 TA
1 TA
55312579 GTCCATATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.05
7 45 0.56
8 32 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAAATT
Found at i:55312489 original size:15 final size:15
Alignment explanation
Indices: 55312471--55312551 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
55312461 AAATAAACTC
55312471 AAAAAATAAAATTTA
1 AAAAAATAAAATTTA
**
55312486 AAAATTTAAAAATTT-
1 AAAAAAT-AAAATTTA
**
55312501 AAAATTTAAAAATTT-
1 AAAAAAT-AAAATTTA
**
55312516 AAAATTTAAAATTTA
1 AAAAAATAAAATTTA
55312531 AAAATAA-AAAATTTA
1 AAAA-AATAAAATTTA
55312546 AAAAAA
1 AAAAAA
55312552 ATTAAAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
14 9 0.15
15 43 0.73
16 7 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAATAAAATTTA
Found at i:55312491 original size:8 final size:8
Alignment explanation
Indices: 55312478--55312578 Score: 113
Period size: 8 Copynumber: 13.0 Consensus size: 8
55312468 CTCAAAAAAT
55312478 AAAATTTA
1 AAAATTTA
55312486 AAAATTTA
1 AAAATTTA
55312494 AAAATTT-
1 AAAATTTA
55312501 AAAATTTA
1 AAAATTTA
55312509 AAAATTT-
1 AAAATTTA
55312516 AAAATTT-
1 AAAATTTA
55312523 AAAATTTA
1 AAAATTTA
*
55312531 AAAA-TAA
1 AAAATTTA
55312538 AAAATTTAAA
1 AAAATTT--A
*
55312548 AAAAATTA
1 AAAATTTA
55312556 AAAATTT-
1 AAAATTTA
*
55312563 AATATTTA
1 AAAATTTA
*
55312571 ATAATTTA
1 AAAATTTA
55312579 GTCCATATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
7 33 0.41
8 40 0.50
10 7 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTTA
Found at i:55312553 original size:18 final size:18
Alignment explanation
Indices: 55312530--55312564 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55312520 TTTAAAATTT
55312530 AAAAATAAAAAATTTAAA
1 AAAAATAAAAAATTTAAA
*
55312548 AAAAATTAAAAATTTAA
1 AAAAATAAAAAATTTAA
55312565 TATTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAAATTTAAA
Found at i:55312649 original size:18 final size:18
Alignment explanation
Indices: 55312628--55312667 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55312618 AATAAATTTC
55312628 AAAAAGAGAAAAATAAAA
1 AAAAAGAGAAAAATAAAA
* **
55312646 AAAATGTTAAAAATAAAA
1 AAAAAGAGAAAAATAAAA
55312664 AAAA
1 AAAA
55312668 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAGAGAAAAATAAAA
Found at i:55312665 original size:26 final size:26
Alignment explanation
Indices: 55312610--55312666 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
55312600 TTAAATATTC
* * *
55312610 AAAATTAAAATAAATTTCAAAAAGAG
1 AAAAATAAAAAAAATTTCAAAAAGAA
*
55312636 AAAAATAAAAAAAATGTT-AAAAATAA
1 AAAAATAAAAAAAAT-TTCAAAAAGAA
55312662 AAAAA
1 AAAAA
55312667 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (26 bp):
AAAAATAAAAAAAATTTCAAAAAGAA
Found at i:55312668 original size:18 final size:17
Alignment explanation
Indices: 55312636--55312674 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
55312626 TCAAAAAGAG
55312636 AAAAATAAAAAAAATGTT
1 AAAAATAAAAAAAAT-TT
55312654 AAAAATAAAAAAAATTT
1 AAAAATAAAAAAAATTT
55312671 AAAA
1 AAAA
55312675 TTAATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAAAAATTT
Found at i:55318262 original size:19 final size:19
Alignment explanation
Indices: 55318240--55318280 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
55318230 TTTATTGATA
55318240 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
55318258 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
55318277 TTTT
1 TTTT
55318281 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:55318551 original size:21 final size:21
Alignment explanation
Indices: 55318525--55318568 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
55318515 TGAATTTCAT
55318525 GACCTTTAGCGGCGTTTGTGG
1 GACCTTTAGCGGCGTTTGTGG
*
55318546 GACCTTTAGCGGCGTTTTTGG
1 GACCTTTAGCGGCGTTTGTGG
55318567 GA
1 GA
55318569 TCAGCGCCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.36, T:0.34
Consensus pattern (21 bp):
GACCTTTAGCGGCGTTTGTGG
Found at i:55319264 original size:16 final size:16
Alignment explanation
Indices: 55319243--55319288 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
55319233 AAATGCTAAC
55319243 GATTTAGGGATTTCAA
1 GATTTAGGGATTTCAA
* *
55319259 GATTTAAGGATTTGAA
1 GATTTAGGGATTTCAA
55319275 GATTGTTAGGGATT
1 GA-T-TTAGGGATT
55319289 CAATGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 16 0.64
17 1 0.04
18 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGATTTCAA
Found at i:55327153 original size:18 final size:20
Alignment explanation
Indices: 55327130--55327166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55327120 AATTATATTC
55327130 ATTTA-TTG-ATTTTTATAT
1 ATTTATTTGTATTTTTATAT
55327148 ATTTATTTGTATTTTTATA
1 ATTTATTTGTATTTTTATA
55327167 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTATTTGTATTTTTATAT
Found at i:55338463 original size:32 final size:33
Alignment explanation
Indices: 55338427--55338488 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
55338417 AATATTCCTT
*
55338427 TCAAAAATCTATCAAATTTC-ATTAAAATTTTC
1 TCAAAAATCTATCAAATTTCTATCAAAATTTTC
*
55338459 TCAAAATTCTATCAAATTTCTATCAAAATT
1 TCAAAAATCTATCAAATTTCTATCAAAATT
55338489 CTTTGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (33 bp):
TCAAAAATCTATCAAATTTCTATCAAAATTTTC
Found at i:55338484 original size:22 final size:23
Alignment explanation
Indices: 55338434--55338490 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
55338424 CTTTCAAAAA
*
55338434 TCTATCAAATTTC-ATTAAAATT
1 TCTATCAAAATTCTATTAAAATT
* *
55338456 T-TCTCAAAATTCTA-TCAAATT
1 TCTATCAAAATTCTATTAAAATT
55338477 TCTATCAAAATTCT
1 TCTATCAAAATTCT
55338491 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.44
Consensus pattern (23 bp):
TCTATCAAAATTCTATTAAAATT
Found at i:55338490 original size:11 final size:11
Alignment explanation
Indices: 55338404--55338490 Score: 68
Period size: 11 Copynumber: 7.9 Consensus size: 11
55338394 CTCATAATTC
* *
55338404 TCAACATTCTT
1 TCAAAATTCTA
* *
55338415 TCAATATTCCTT
1 TCAAAATT-CTA
*
55338427 TCAAAAATCTA
1 TCAAAATTCTA
*
55338438 TCAAATTTC-A
1 TCAAAATTCTA
* * *
55338448 TTAAAATTTTC
1 TCAAAATTCTA
55338459 TCAAAATTCTA
1 TCAAAATTCTA
*
55338470 TCAAATTTCTA
1 TCAAAATTCTA
55338481 TCAAAATTCT
1 TCAAAATTCT
55338491 TTGTTTAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
10 7 0.12
11 43 0.73
12 9 0.15
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.43
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:55344441 original size:20 final size:20
Alignment explanation
Indices: 55344416--55344488 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
55344406 TCTTGTATGT
55344416 ATCAATTAACCTTAAATTTA
1 ATCAATTAACCTTAAATTTA
* * *
55344436 ATCAATTAACCCTAAACCCTAA
1 ATCAATTAACCTTAAA--TTTA
*
55344458 ATCAA-T--CCAT-AATTTA
1 ATCAATTAACCTTAAATTTA
55344474 ATCAATTAACCTTAA
1 ATCAATTAACCTTAA
55344489 TACTCTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.17
17 1 0.03
18 2 0.05
19 6 0.15
20 16 0.40
21 1 0.03
22 7 0.17
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCAATTAACCTTAAATTTA
Found at i:55348155 original size:44 final size:45
Alignment explanation
Indices: 55348060--55348193 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 45
55348050 ACAGGACAGA
* *
55348060 ACAGAAATAAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * *
55348106 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
55348150 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
55348194 TAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:55354190 original size:18 final size:18
Alignment explanation
Indices: 55354164--55354198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55354154 CTTAGGGGAT
* *
55354164 TTACCAAATTCTCTAAGA
1 TTACAAAATACTCTAAGA
55354182 TTACAAAATACTCTAAG
1 TTACAAAATACTCTAAG
55354199 GTTATAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
TTACAAAATACTCTAAGA
Found at i:55355365 original size:17 final size:17
Alignment explanation
Indices: 55355343--55355375 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55355333 TTAGGAAATA
55355343 TTTATTTTAATGTTTTT
1 TTTATTTTAATGTTTTT
*
55355360 TTTATTTTGATGTTTT
1 TTTATTTTAATGTTTT
55355376 ATATATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTATTTTAATGTTTTT
Found at i:55359458 original size:3 final size:3
Alignment explanation
Indices: 55359452--55359485 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55359442 ATTAATAATA
55359452 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
55359486 ATGCGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:55361179 original size:15 final size:14
Alignment explanation
Indices: 55361161--55361198 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
55361151 CCTATCTTAT
55361161 TTCCTTCTTTCTTTC
1 TTCCTTCTTTC-TTC
55361176 TTCCTTCCTTTCTTC
1 TTCCTT-CTTTCTTC
55361191 TT-CTTCTT
1 TTCCTTCTT
55361199 GCTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 11 0.50
16 5 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCCTTCTTTCTTC
Found at i:55375262 original size:232 final size:234
Alignment explanation
Indices: 55374917--55375364 Score: 593
Period size: 232 Copynumber: 1.9 Consensus size: 234
55374907 TAACCGTGAA
* * *
55374917 TAAACCTCACAGCAGCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTTCAAAACAAAAG
1 TAAACCTCACAG-AGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAG
* * * * * *
55374982 ACTAAAACCTGCATAGTTTCTTGTACAGATACCTTAATTCAACCAAATTTC-TAGAACCTCGCAT
65 ACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCAT-GAAACTCGCAT
* * *
55375046 CTAATTACGAACTAACTTCCTCTAAGAAAGC-GATTTCAT-G-AAAGAGGTTTATGACGCCCTAT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTT-ATAGAAAAGAGGTTCATGACACCCTAT
*
55375108 TAAAACCCAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCAAG
193 TAAAACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
*
55375150 TAAACCTCACAG-GCTAGGAAGCTCGCTCAAATGAAGTAATTCAATTGAACTTTCAAAAAACAAA
1 TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAAC-TTCAAAAAA-AAA
* * *
55375214 TACGGAAACTTACAAAG-TTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCAT
64 GACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCAT
* * ** * *
55375278 CTAATTAGGAACTAGCTTCCTCTGGGAAAGCAAATTTATAGAAAAGAGGTTCATGATACCCTTTT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATT
*
55375343 AAAACCTAAAATACTAAGGAAA
194 AAAACCCAAAATACTAAGGAAA
55375365 CACAGAAAAA
Statistics
Matches: 185, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
231 35 0.19
232 79 0.43
233 32 0.17
234 39 0.21
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (234 bp):
TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAGA
CGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCATCT
AATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATTAA
AACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
Found at i:55376560 original size:168 final size:168
Alignment explanation
Indices: 55376359--55376663 Score: 540
Period size: 168 Copynumber: 1.8 Consensus size: 168
55376349 ACTTAATGAA
* *
55376359 TTAACAATTACCGTTTCGTAAGGATCAAAATTTTAAATTTTGAAAAGTACAGGGACTAAATATAA
1 TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATAA
55376424 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
66 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
55376489 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
131 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
55376527 TTAAAAATTACCGTTT-GATAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATA
1 TTAAAAATTACCGTTTCG-TAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATA
* * * *
55376591 ACCAAATTGAAGTAGAGAGATTAAATCAATAACTTTTGCAAAGTATAGGGACTGTGGTAGAGTTT
65 ACCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTT
55376656 AACCTTTT
130 AACCTTTT
55376664 CTTTTATATT
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
167 1 0.01
168 129 0.99
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (168 bp):
TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATAA
CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
Found at i:55378152 original size:24 final size:25
Alignment explanation
Indices: 55378117--55378192 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
55378107 TAAATATTTA
55378117 TTGGTAGAAAAAACTAATTAAATAT
1 TTGGTAGAAAAAACTAATTAAATAT
55378142 TTGGTAGAAAAAACTAATTAAATAT
1 TTGGTAGAAAAAACTAATTAAATAT
*
55378167 TTGGTAGAAAAAACTAATTAACTAT
1 TTGGTAGAAAAAACTAATTAAATAT
55378192 T
1 T
55378193 AAATGCGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (25 bp):
TTGGTAGAAAAAACTAATTAAATAT
Found at i:55380603 original size:47 final size:48
Alignment explanation
Indices: 55380530--55380794 Score: 255
Period size: 47 Copynumber: 5.7 Consensus size: 48
55380520 AAGGTGACCA
*
55380530 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCAT-ATCTCAAGTCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
* * * *
55380577 ATGCCATGTCCCAGACATGGTTTTACACTGACT-ATCATCTCGTAGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * * * *
55380625 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCAG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * *
55380671 ATG-CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAA-GCCG
* * ***
55380717 ATGCCATGTCCTAGACATGGTCTTACACTAGCTC-TCATAATGTGGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCAT-CTCAAGCCG
55380765 ATG-CATGTCCTAGACAT-GTCTTACACTGGC
1 ATGCCATGTCCTAGACATGGTCTTACACTGGC
55380795 CAAAAATAAC
Statistics
Matches: 186, Mismatches: 24, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
45 1 0.01
46 75 0.40
47 78 0.42
48 31 0.17
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
Found at i:55380786 original size:140 final size:140
Alignment explanation
Indices: 55380534--55380794 Score: 368
Period size: 140 Copynumber: 1.9 Consensus size: 140
55380524 TGACCAATGC
* * * *
55380534 CATGTCCTAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTT
1 CATGTCCTAGACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAGACATGGTC
*
55380599 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
66 TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
55380664 GAGGCAGATG
131 GAGGCAGATG
* *
55380674 CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCGATGCCATGTCCTAGACATGG
1 CATGTCCTAGACATGGTCTTACACTAGCACAT-ATCTCAA-GCCGATGCCATGTCCCAGACATGG
* * *
55380737 TCTTACACT-AGCTCTCATAAT-GTGGCCGATGCATGTCCTAGACATGTCTTACACTGGC
64 TCTTACACTGA-CTATCAT-ATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGC
55380795 CAAAAATAAC
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
138 1 0.01
139 20 0.19
140 85 0.79
141 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (140 bp):
CATGTCCTAGACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAGACATGGTC
TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
GAGGCAGATG
Found at i:55390895 original size:21 final size:21
Alignment explanation
Indices: 55390870--55390938 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
55390860 TATAATGATT
55390870 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
***
55390891 ATTATTACAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
55390911 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
55390931 ATTATTAT
1 ATTATTAT
55390939 TATTAGCATT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
18 3 0.09
19 9 0.26
20 3 0.09
21 17 0.49
22 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:55390951 original size:15 final size:14
Alignment explanation
Indices: 55390925--55390955 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
55390915 TATGGTTTTA
55390925 TATTAGATTATTAT
1 TATTAGATTATTAT
55390939 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
55390954 TA
1 TA
55390956 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:55391294 original size:14 final size:14
Alignment explanation
Indices: 55391270--55391302 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55391260 AAGAATTAAG
55391270 GAAACAAAGAAACA
1 GAAACAAAGAAACA
55391284 -AAACAAAAGAAACA
1 GAAAC-AAAGAAACA
55391298 GAAAC
1 GAAAC
55391303 GAAGTAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAACAAAGAAACA
Found at i:55398558 original size:26 final size:26
Alignment explanation
Indices: 55398468--55398566 Score: 128
Period size: 26 Copynumber: 3.8 Consensus size: 26
55398458 TCCCCATTTT
55398468 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
* * * * *
55398494 GGATAGTCCTCAC-AAGCTTCTACCAA
1 AGATAGTCCTGACGGA-CTTCCACAAA
55398520 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
*
55398546 AGATAGTCTTGACGGACTTCC
1 AGATAGTCCTGACGGACTTCC
55398567 CACATAATAG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.02
26 58 0.97
27 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (26 bp):
AGATAGTCCTGACGGACTTCCACAAA
Found at i:55399490 original size:23 final size:23
Alignment explanation
Indices: 55399438--55399483 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
55399428 ACAAGATTTC
55399438 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
55399461 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
55399484 GTCTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
CAATTTCTAAGACTTAGATCTTA
Found at i:55402381 original size:46 final size:46
Alignment explanation
Indices: 55402321--55402586 Score: 325
Period size: 46 Copynumber: 6.0 Consensus size: 46
55402311 TTTGACGTGA
* * * * * *
55402321 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * **
55402367 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACCT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
55402413 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
55402459 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
55402505 TGCCATGATATCTTTCAACCATGGTCTTACACA---C--AT---GT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55402543 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
55402587 AGAGCACACT
Statistics
Matches: 192, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
38 34 0.18
41 3 0.02
43 3 0.02
45 4 0.02
46 148 0.77
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:55402555 original size:38 final size:38
Alignment explanation
Indices: 55402503--55402575 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
55402493 TTCATATCAG
55402503 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
*
55402541 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACA
55402576 TTTCATATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (38 bp):
GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
Found at i:55414050 original size:13 final size:13
Alignment explanation
Indices: 55414032--55414058 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55414022 GAAGAAATCG
55414032 CATACGGGCATGT
1 CATACGGGCATGT
55414045 CATACGGGCATGT
1 CATACGGGCATGT
55414058 C
1 C
55414059 CTTGTTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (13 bp):
CATACGGGCATGT
Found at i:55421550 original size:47 final size:47
Alignment explanation
Indices: 55421495--55421625 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
55421485 CTCAACTGAA
*
55421495 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * * * *
55421542 GAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCCTCTCT
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * **
55421589 AAATACCTATACCATGACCCGTATTCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
55421626 TTATTTGCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
Found at i:55436142 original size:23 final size:23
Alignment explanation
Indices: 55436116--55436162 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
55436106 CATTCTATTG
*
55436116 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
55436139 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
55436162 T
1 T
55436163 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:55437448 original size:23 final size:23
Alignment explanation
Indices: 55437397--55437449 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
55437387 ATGATGATGT
*
55437397 TTAA-TTTTATTTTATCTTTATT
1 TTAATTTTTATTTTATCTTTATA
* * *
55437419 TTTATTTTTATTTTATGTTTGTA
1 TTAATTTTTATTTTATCTTTATA
55437442 TTAATTTT
1 TTAATTTT
55437450 ACCTTTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (23 bp):
TTAATTTTTATTTTATCTTTATA
Found at i:55443982 original size:48 final size:49
Alignment explanation
Indices: 55443911--55444074 Score: 160
Period size: 49 Copynumber: 3.4 Consensus size: 49
55443901 AGCTAACACT
* * *
55443911 ATGTCCCA-AGCAGGTCTTACACTAGCT-TGTAT-ATCCCGAGGCCGATGC
1 ATGTCCCAGA-CATGTCTTACACTAGCTCT-CATCATCCCAAGGCCGATGC
* * * *
55443959 ATGTCTCAGACATGTCTTACACTAGCTCTCATCGTCTCAATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
* * ** *
55444008 ATGTCCCAGACATGTCTTACACTGGCTCTCATAAT---GTGGCTGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
55444054 ATGTCCCAGACATGTCTTACA
1 ATGTCCCAGACATGTCTTACA
55444075 TTGGCTCACA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
46 28 0.29
48 25 0.26
49 45 0.46
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
Found at i:55444070 original size:46 final size:47
Alignment explanation
Indices: 55443949--55444086 Score: 170
Period size: 49 Copynumber: 2.9 Consensus size: 47
55443939 GTATATCCCG
* * **
55443949 AGGCCGATGCATGTCTCAGACATGTCTTACACTAGCTCTCATCGTCT
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
* *
55443996 CAATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGT
1 --AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
* * *
55444045 -GGCTGATGCATGTCCCAGACATGTCTTACATTGGCTCACATA
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATA
55444087 CCACCCAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
46 38 0.48
49 41 0.52
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (47 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
Found at i:55446493 original size:17 final size:16
Alignment explanation
Indices: 55446466--55446500 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
55446456 TTACAATCAA
55446466 ACAAAACGTATATTCC
1 ACAAAACGTATATTCC
55446482 ACAAATACGTATATTCC
1 ACAAA-ACGTATATTCC
55446499 AC
1 AC
55446501 TTATTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
ACAAAACGTATATTCC
Found at i:55448437 original size:999 final size:999
Alignment explanation
Indices: 55446501--55448940 Score: 4605
Period size: 999 Copynumber: 2.4 Consensus size: 999
55446491 TATATTCCAC
**
55446501 TTATTCTATCTATCATCTAGTCTCTTGGTGTTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
* *
55446566 ATTTTTGTAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
*
55446631 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCTAACTTATTGCTAGATCTTCTCCTAAAT
131 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
55446696 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
196 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
55446761 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
261 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
55446826 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
326 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
55446891 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
391 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
55446956 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
456 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
55447021 ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
521 ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
55447086 CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
586 CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
55447151 TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
651 TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
55447216 TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
716 TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
*
55447281 TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATTCCTATTGGTGTTGAATT
781 TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAATT
55447346 TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
846 TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
55447411 TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
911 TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
55447476 CAGGTTTTAAAGTACTAGCACCAG
976 CAGGTTTTAAAGTACTAGCACCAG
55447500 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
55447565 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
* *
55447630 TACTTCTGCAGTATTTGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTTTCCTAAAT
131 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
55447695 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
196 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
55447760 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
261 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
55447825 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
326 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
55447890 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
391 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
55447955 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
456 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
55448020 ACGGCTCTAATTGGATTTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACT
521 ACGGCTCTAATTGGA-TTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACT
55448085 ACTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAA
585 ACTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAA
55448150 ATGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTT-AAAATGTAATAACATCACTA
650 ATGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTA
55448214 TTTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGA
715 TTTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGA
55448279 ATTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAAT
780 ATTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAAT
55448344 TTGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTT
845 TTGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTT
55448409 GTATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTT
910 GTATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTT
55448474 ACAGGTTTTAAAGTACTAGCACCAG
975 ACAGGTTTTAAAGTACTAGCACCAG
55448499 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
55448564 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
* * *
55448629 TACCTT-TGCAGTATTAGTATATTCATTAATAGAAGTCCAACTTATTCCTAGATCTTCTGCTAAA
131 TA-CTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAA
* * * * *
55448693 TCATTTATTTCAGAATTTTTTATCTGAATTCTCAAACATAAACACTTTTCTATTAAAGGGTCTGT
195 TCATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGT
* * * * *
55448758 GATAGGTATAAAGTAATTTTGTTTAACTTTAAAACTTATTACACCGGTATGTAAATTAGACTAAA
260 GATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAA
* * *
55448823 TACCTCCAATAAGTGATTTTATTGTATTTTCAAATCTTTTATCTAATAAAATTGCTATTATAGGT
325 TACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATA-GT
* *
55448888 ATATCATGACCTTTTCTAAATAAAGTTCTAATTGTTATCATAATTATACCTAA
389 ATATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAA
55448941 ATGTATATAT
Statistics
Matches: 1410, Mismatches: 28, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
999 1196 0.85
1000 214 0.15
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (999 bp):
TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAATT
TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
CAGGTTTTAAAGTACTAGCACCAG
Found at i:55451544 original size:15 final size:14
Alignment explanation
Indices: 55451516--55451559 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
55451506 ATTAATACTA
55451516 TTACAAAG-AAAGT
1 TTACAAAGAAAAGT
55451529 TTACAAATGAAAAGT
1 TTACAAA-GAAAAGT
55451544 TTAC-AAGAAAAGT
1 TTACAAAGAAAAGT
55451557 TTA
1 TTA
55451560 AAAAAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.59
14 3 0.10
15 9 0.31
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (14 bp):
TTACAAAGAAAAGT
Found at i:55452434 original size:22 final size:21
Alignment explanation
Indices: 55452406--55452450 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
55452396 TAATATAGTA
* *
55452406 TTAATAATTGCAGGAAAATCTT
1 TTAATAATTGAAAGAAAAT-TT
55452428 TTAATAATTGAAAGAAAATTT
1 TTAATAATTGAAAGAAAATTT
55452449 TT
1 TT
55452451 GAACTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (21 bp):
TTAATAATTGAAAGAAAATTT
Found at i:55455545 original size:23 final size:23
Alignment explanation
Indices: 55455519--55455846 Score: 109
Period size: 23 Copynumber: 14.3 Consensus size: 23
55455509 ATAAAACATC
* *
55455519 TCAATTTTCAGCAACTAAACAAT
1 TCAATTTACAGCAACTAAACACT
* *
55455542 TCAATTTGCAG-TACTTAAAACACT
1 TCAATTTACAGCAAC-T-AAACACT
* **
55455566 TCAATTTACAACATTTAAACACT
1 TCAATTTACAGCAACTAAACACT
** * *
55455589 TCAATTTACAGCATTTTAACGCT
1 TCAATTTACAGCAACTAAACACT
* * ** *
55455612 TCAATTCACATCATTTAAACGCT
1 TCAATTTACAGCAACTAAACACT
* * * *
55455635 TCAATTTGCAAC-ACTTTAGCACT
1 TCAATTTACAGCAAC-TAAACACT
* *
55455658 TCAATTTACAGC-ATTTAACACT
1 TCAATTTACAGCAACTAAACACT
* *
55455680 TCAATTTGCAGC-ACTTTAACA-T
1 TCAATTTACAGCAAC-TAAACACT
* * ** * *
55455702 CTCAATTAACAACATTTATACACC
1 -TCAATTTACAGCAACTAAACACT
* *
55455726 TCAA-TTATAGCGA-TAAA-ACAT
1 TCAATTTACAGCAACTAAACAC-T
* *
55455747 CTCAATTTCCAGCAACTAAACAAT
1 -TCAATTTACAGCAACTAAACACT
* * *
55455771 TCAACTTGCAG-TACTTAAAACACT
1 TCAATTTACAGCAAC-T-AAACACT
* * **
55455795 TCAATTTATAACATTTAAACACT
1 TCAATTTACAGCAACTAAACACT
* *
55455818 TCAATTTGCAGC-ACTTTAACACT
1 TCAATTTACAGCAAC-TAAACACT
55455841 TCAATT
1 TCAATT
55455847 CACAACATTT
Statistics
Matches: 224, Mismatches: 64, Indels: 34
0.70 0.20 0.11
Matches are distributed among these distances:
20 2 0.01
21 3 0.01
22 32 0.14
23 151 0.67
24 35 0.16
25 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
TCAATTTACAGCAACTAAACACT
Found at i:55455628 original size:46 final size:46
Alignment explanation
Indices: 55455534--55455957 Score: 364
Period size: 46 Copynumber: 9.2 Consensus size: 46
55455524 TTTCAGCAAC
* * * *
55455534 TAAACAATTCAATTTGCAGTACTTAAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTGCAGCACTT-TAACACTTCAATTCACAACATT
* * * *
55455581 TAAACACTTCAATTTACAGCATTTTAACGCTTCAATTCACATCATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
* * * * *
55455627 TAAACGCTTCAATTTGCAACACTTTAGCACTTCAATTTACAGCATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
*
55455673 T-AACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACACT-TCAATTCACAACATT
* * ** * **
55455718 TATACACCTCAATTAT--AGCGA-TAAAACA-TCTCAATTTC-CAGCAAC
1 TAAACACTTCAATT-TGCAGC-ACTTTAACACT-TCAA-TTCACAACATT
* * * * * *
55455763 TAAACAATTCAACTTGCAGTACTTAAAACACTTCAATTTATAACATT
1 TAAACACTTCAATTTGCAGCACTT-TAACACTTCAATTCACAACATT
55455810 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
* ** *
55455856 TAAACAGTACTTCAATGTGCAATACTTTAACACTTCAAATT-AAAACATT
1 TAAAC---ACTTCAATTTGCAGCACTTTAACACTTC-AATTCACAACATT
*
55455905 TAAACACTTCAATTTGTAGCACTTTAACATCTT-AATT-AGCAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACA-CTTCAATTCA-CAACATT
*
55455951 TATACAC
1 TAAACAC
55455958 CTGAATTACA
Statistics
Matches: 304, Mismatches: 56, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.01
45 72 0.24
46 131 0.43
47 57 0.19
48 1 0.00
49 37 0.12
50 4 0.01
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (46 bp):
TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
Found at i:55455861 original size:23 final size:23
Alignment explanation
Indices: 55455559--55456082 Score: 247
Period size: 23 Copynumber: 22.7 Consensus size: 23
55455549 GCAGTACTTA
55455559 AAACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
*
55455582 AAACACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
* * * *
55455605 TAACGCTTCAATTCACATCATTT
1 AAACACTTCAATTTACAACATTT
* *
55455628 AAACGCTTCAATTTGCAACACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
55455652 -AGCACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
* *
55455674 -AACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
*
55455697 -AACA-TCTCAATTAACAACATTT
1 AAACACT-TCAATTTACAACATTT
* * * * *
55455719 ATACACCTCAA-TTATAGCGA-TA
1 AAACACTTCAATTTACAAC-ATTT
* * **
55455741 AAACA-TCTCAATTTCCAGCAACT
1 AAACACT-TCAATTTACAACATTT
* * * *
55455764 AAACAATTCAACTTGCAGTAC-TTA
1 AAACACTTCAATTTACA--ACATTT
*
55455788 AAACACTTCAATTTATAACATTT
1 AAACACTTCAATTTACAACATTT
* *
55455811 AAACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
*
55455835 -AACACTTCAATTCACAACATTT
1 AAACACTTCAATTTACAACATTT
* * *
55455857 AAACAGTACTTCAATGTGCAATACTTT
1 AAAC---ACTTCAATTTACAACA-TTT
* *
55455884 -AACACTTCAAATTAAAACATTT
1 AAACACTTCAATTTACAACATTT
** *
55455906 AAACACTTCAATTTGTAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
55455930 -AACATCTT-AA-TTAGCAACATTT
1 AAACA-CTTCAATTTA-CAACATTT
* * * * * *
55455952 ATACACCTGAA-TTACAGCAATA
1 AAACACTTCAATTTACAACATTT
* **
55455974 AAACA-TCTCAATTT-CTAGCAACT
1 AAACACT-TCAATTTAC-AACATTT
* *
55455997 AAGCACTTCAATTTACAACATGT
1 AAACACTTCAATTTACAACATTT
** * *
55456020 GTACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
55456044 -AACA-TCTCAATTAACAACGTTT
1 AAACACT-TCAATTTACAACATTT
* *
55456066 ATACACCTCAATTTACA
1 AAACACTTCAATTTACA
55456083 GAAATAAAAC
Statistics
Matches: 376, Mismatches: 91, Indels: 68
0.70 0.17 0.13
Matches are distributed among these distances:
22 70 0.19
23 257 0.68
24 30 0.08
25 1 0.00
26 15 0.04
27 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:55456643 original size:15 final size:15
Alignment explanation
Indices: 55456623--55456655 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55456613 GTGTTTTAAG
55456623 ACAACATAAATACTT
1 ACAACATAAATACTT
*
55456638 ACAACATGAATACTT
1 ACAACATAAATACTT
55456653 ACA
1 ACA
55456656 TTTTAATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.21, G:0.03, T:0.24
Consensus pattern (15 bp):
ACAACATAAATACTT
Found at i:55458356 original size:24 final size:24
Alignment explanation
Indices: 55458302--55458367 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
55458292 TGCTCTCTGT
* * *
55458302 GAGCTTCCTGATATGGTTCTTTAT
1 GAGCTTCCCGATATGGCTCTTTAC
*
55458326 GAACTTCCCGATTATGGCTC-TTAC
1 GAGCTTCCCGA-TATGGCTCTTTAC
*
55458350 GAGCTTCTCGATATGGCT
1 GAGCTTCCCGATATGGCT
55458368 ATGTCTGAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 7 0.20
24 21 0.60
25 7 0.20
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGATATGGCTCTTTAC
Found at i:55459148 original size:18 final size:16
Alignment explanation
Indices: 55459118--55459173 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
55459108 TAGTAGTATT
*
55459118 AAATCAAAACAAATAA
1 AAATCCAAACAAATAA
*
55459134 AAATCCCAAATCAAAGATA
1 AAAT-CCAAA-CAAATA-A
55459153 AAATCCAAACACAATAA
1 AAATCCAAACA-AATAA
55459170 AAAT
1 AAAT
55459174 ACCGCAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 4 0.12
17 11 0.33
18 13 0.39
19 5 0.15
ACGTcount: A:0.66, C:0.18, G:0.02, T:0.14
Consensus pattern (16 bp):
AAATCCAAACAAATAA
Found at i:55462301 original size:40 final size:40
Alignment explanation
Indices: 55462241--55462424 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
55462231 TATTCGAATG
*
55462241 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
55462281 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * * *
55462321 ATATCTGGGCTAAGACCCGAAGGAATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
55462361 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGTTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
55462401 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
55462425 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 117 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:55462374 original size:80 final size:80
Alignment explanation
Indices: 55462241--55462423 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 80
55462231 TATTCGAATG
* ** *
55462241 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGAATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
55462305 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* * *
55462321 ATATCTGGGCTAAGACCCGAAGGAATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGAATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
**
55462386 TTTATGTTAGTGACC
66 TTTATGCGAGTGACC
55462401 ATATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGG
55462424 CCTTGTGCGA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.03
80 86 0.97
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGAATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:55472462 original size:23 final size:23
Alignment explanation
Indices: 55472395--55472454 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
55472385 ACATCGCTAC
55472395 GTTACTATTAGCAGCTTTGCTGT
1 GTTACTATTAGCAGCTTTGCTGT
*
55472418 GTTACTACTAGCAGCTTTGCTGT
1 GTTACTATTAGCAGCTTTGCTGT
55472441 GTTACTATTAGCAG
1 GTTACTATTAGCAG
55472455 TTACGCTGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (23 bp):
GTTACTATTAGCAGCTTTGCTGT
Found at i:55473439 original size:21 final size:21
Alignment explanation
Indices: 55473398--55473441 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55473388 AAGTTGTTTA
*
55473398 TCTATCAAAAACTTTTCATTT
1 TCTATCAAAAACTTTTAATTT
*
55473419 TCTATCATAAA-TTTTAAATTT
1 TCTATCAAAAACTTTT-AATTT
55473440 TC
1 TC
55473442 AGCATATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (21 bp):
TCTATCAAAAACTTTTAATTT
Found at i:55479090 original size:44 final size:44
Alignment explanation
Indices: 55479040--55479197 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 44
55479030 TATGTGTTTT
55479040 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* *
55479084 CGTGTAAGACCATGTCTAGGACATTGGCATCG-TATATGATTT-
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* * * * *
55479126 CGTGTAAGACC-CTGCCTAGGGCAGTGTCATCAATATT-TGA-TTA
1 CGTGTAAGACCAC-GTCTAGGACATTGGCATCGAT-TTATGATTTA
* * *
55479169 CATGTAAGACCACGTCTGGGACGTTGGCA
1 CGTGTAAGACCACGTCTAGGACATTGGCA
55479198 CTGTACGAGC
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
42 27 0.29
43 33 0.35
44 33 0.35
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
Found at i:55479167 original size:86 final size:85
Alignment explanation
Indices: 55479037--55479197 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 85
55479027 CGATATGTGT
* * * * *
55479037 TTTCGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTACGTGTAAGACCATGTCTA
1 TTTCGTGTAAGACCACGCCTAGGACAGTGGCATCAATTTATGA-TTACATGTAAGACCACGTCTA
55479102 GGACATTGGCATCGTATATGA
65 GGACATTGGCATCGTATATGA
* *
55479123 TTTCGTGTAAGACC-CTGCCTAGGGCAGTGTCATCAATATT-TGATTACATGTAAGACCACGTCT
1 TTTCGTGTAAGACCAC-GCCTAGGACAGTGGCATCAAT-TTATGATTACATGTAAGACCACGTCT
* *
55479186 GGGACGTTGGCA
64 AGGACATTGGCA
55479198 CTGTACGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 29 0.45
86 33 0.52
87 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (85 bp):
TTTCGTGTAAGACCACGCCTAGGACAGTGGCATCAATTTATGATTACATGTAAGACCACGTCTAG
GACATTGGCATCGTATATGA
Found at i:55485793 original size:44 final size:43
Alignment explanation
Indices: 55485730--55485881 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 43
55485720 TGTGTTTTCG
* *
55485730 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTTAAA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATTT-TGATTTACA
* * *
55485774 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGAT-TTTGATTTACA
* * **
55485816 TGTAAGACCCTGTCTAGGAC-TGTGTTATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGGGACGT-TGGCATCGAT-TTTGATTTACA
55485859 TGTAAGACCATGTCTGGGACGTT
1 TGTAAGACCATGTCTGGGACGTT
55485882 CACATTGTAC
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 33 0.37
44 30 0.33
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTTACA
Found at i:55487182 original size:23 final size:23
Alignment explanation
Indices: 55487155--55487200 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
55487145 ATTGAAATTG
55487155 GCTGAAATTA-TAGTGCAATTGTA
1 GCTGAAATTACT-GTGCAATTGTA
55487178 GCTGAAATTACTGTGCAATTGTA
1 GCTGAAATTACTGTGCAATTGTA
55487201 CTTGGTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (23 bp):
GCTGAAATTACTGTGCAATTGTA
Found at i:55495978 original size:46 final size:47
Alignment explanation
Indices: 55495795--55496100 Score: 158
Period size: 46 Copynumber: 6.6 Consensus size: 47
55495785 TGATATGTGT
* * * *
55495795 GCCAGTGTAAGACATGTCTGGAACATGCATTG-GCTGCATTATG-AGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTA-A
* * *
55495841 GCCAGTGTAAGACCATGTTTGGGACATGGCATCG-GCATTGAGACGA-GT--
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGAGC--T-ACATGATGTAA
* * * * * *
55495889 GCTACTATAAGACATGTCTGGGACATGCATTGACCT-CAGGATGTAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTAA
55495935 GCCAGTGTAAGACATGTCTGGGACATGCATCGA-CTACGA-GATGT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTAC-ATGATGTAA
* * * * **
55495979 GTCAGTGTAAGACCATGTTTGGAACATGGCGTC-AGC-ACGGAT-ATGTGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGAGCTAC--ATGATGTAA
* * * * *
55496027 GCTAGTGTAAGACACGTCTAGGACATGCATC-AGCCACATCG-TGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACAT-GATGTAA
*
55496073 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGA-CATGTCTGGGACATG
55496101 GCTTGATATG
Statistics
Matches: 202, Mismatches: 35, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
43 3 0.01
44 13 0.06
45 20 0.10
46 84 0.42
47 52 0.26
48 26 0.13
50 2 0.01
51 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTAA
Found at i:55496051 original size:138 final size:139
Alignment explanation
Indices: 55495843--55496100 Score: 324
Period size: 138 Copynumber: 1.9 Consensus size: 139
55495833 TTATGAGAGC
* * ** *
55495843 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTGCTACTATAAGACATGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACACGTCT
* * * * *
55495908 GGGACATGCAT-TGACCTCA-GGATGTAAGCCAGTGTAAGA-CATGTCTGGGACATGCATCGACT
66 AGGACATGCATCAG-CCACATCG-TGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACT
55495970 ACGAGATGTGT
129 ACGAGATGTGT
* * * * * *
55495981 CAGTGTAAGACCATGTTTGGAACATGGCGTCAGCACGGATATGTGTGCTAGTGTAAGACACGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACACGTCT
*
55496046 AGGACATGCATCAGCCACATCGTGAAAGCTAGTGTAAGACCATGTCTGGGACATG
66 AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATG
55496101 GCTTGATATG
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
138 83 0.83
139 17 0.17
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (139 bp):
CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACACGTCT
AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTAC
GAGATGTGT
Found at i:55502553 original size:9 final size:9
Alignment explanation
Indices: 55502539--55502563 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55502529 TAAGGTTGCA
55502539 CAAGTCGCC
1 CAAGTCGCC
55502548 CAAGTCGCC
1 CAAGTCGCC
55502557 CAAGTCG
1 CAAGTCG
55502564 ACTGTGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (9 bp):
CAAGTCGCC
Found at i:55504093 original size:32 final size:32
Alignment explanation
Indices: 55504027--55504093 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
55504017 TTAAAAATCT
* *
55504027 AAAGTTAAAATATGTTATAATATTATTACTTA
1 AAAGTTAAAATATATTATAATATTATTACATA
*
55504059 AAAGTT-AAGTATATTATATATATTATATA-ATA
1 AAAGTTAAAATATATTATA-ATATTAT-TACATA
55504091 AAA
1 AAA
55504094 ACAAACAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 10 0.33
32 18 0.60
33 2 0.07
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (32 bp):
AAAGTTAAAATATATTATAATATTATTACATA
Found at i:55505065 original size:25 final size:25
Alignment explanation
Indices: 55505034--55505117 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
55505024 GAACTTTAGC
55505034 GCGCTCTCTGATTATTAGCACGTTA
1 GCGCTCTCTGATTATTAGCACGTTA
* *
55505059 GCGCTCTATGATTATTAGCACGCTA
1 GCGCTCTCTGATTATTAGCACGTTA
* * *
55505084 GTGTTCTCCGATTATTAGCACGTTA
1 GCGCTCTCTGATTATTAGCACGTTA
*
55505109 GTGCTCTCT
1 GCGCTCTCT
55505118 ATTTAGCACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (25 bp):
GCGCTCTCTGATTATTAGCACGTTA
Found at i:55505126 original size:22 final size:22
Alignment explanation
Indices: 55505048--55505164 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
55505038 TCTCTGATTA
* *
55505048 TTAGCACGTTAGCGCTCTATGATT
1 TTAGCACGTTAGTGCTCTCT-A-T
* * *
55505072 ATTAGCACGCTAGTGTTCTCCGATT
1 -TTAGCACGTTAGTGCTCT-CTA-T
55505097 ATTAGCACGTTAGTGCTCTCTAT
1 -TTAGCACGTTAGTGCTCTCTAT
* * *
55505120 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTAT
*
55505142 ATAGCAC-TTCAGTGCTCTCTAT
1 TTAGCACGTT-AGTGCTCTCTAT
55505164 T
1 T
55505165 CATTAGTGCA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
21 2 0.03
22 35 0.47
23 1 0.01
24 2 0.03
25 35 0.47
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTAT
Found at i:55505285 original size:31 final size:31
Alignment explanation
Indices: 55505248--55505310 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
55505238 AAGAATATGA
*
55505248 GATAGTGAATTGAAAATAGAAGGTGAAATAT
1 GATAGTGAATTGAAAATAGAAAGTGAAATAT
55505279 GATAGTGAATTGAAAATAGAAAGTGAAATAT
1 GATAGTGAATTGAAAATAGAAAGTGAAATAT
55505310 G
1 G
55505311 TTGTAAATAC
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:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (31 bp):
GATAGTGAATTGAAAATAGAAAGTGAAATAT
Found at i:55505303 original size:18 final size:18
Alignment explanation
Indices: 55505251--55505305 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
55505241 AATATGAGAT
55505251 AGTGAATTGAAAATAG-A
1 AGTGAATTGAAAATAGAA
*
55505268 AG-G---TG-AAATATGAT
1 AGTGAATTGAAAATA-GAA
55505282 AGTGAATTGAAAATAGAA
1 AGTGAATTGAAAATAGAA
55505300 AGTGAA
1 AGTGAA
55505306 ATATGTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 10 0.34
19 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (18 bp):
AGTGAATTGAAAATAGAA
Found at i:55505858 original size:18 final size:19
Alignment explanation
Indices: 55505820--55505858 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55505810 GACGATATGA
*
55505820 TTAAATTATGATGTGAATG
1 TTAAATAATGATGTGAATG
*
55505839 TTAAATAATTATGT-AATG
1 TTAAATAATGATGTGAATG
55505857 TT
1 TT
55505859 TGTATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
TTAAATAATGATGTGAATG
Found at i:55509747 original size:183 final size:183
Alignment explanation
Indices: 55509439--55509777 Score: 624
Period size: 183 Copynumber: 1.9 Consensus size: 183
55509429 TTTCATGAAC
*
55509439 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTA
* *
55509504 TCTAAGGAGATTGAAACTTAAGCGGGACTGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCAGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
55509569 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
55509622 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTA
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTA
*
55509687 TCTAAGGATATTGAAACTTAAGCAGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCAGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
* *
55509752 AATGTAATTTGTTAAGCAGAAATTTT
131 AATGTAATTTGTTAAGAAAAAATTTT
55509778 TAAATTTTTA
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 150 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (183 bp):
TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTA
TCTAAGGAGATTGAAACTTAAGCAGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
Found at i:55511673 original size:183 final size:183
Alignment explanation
Indices: 55511365--55511701 Score: 638
Period size: 183 Copynumber: 1.8 Consensus size: 183
55511355 TAAAAATTTA
55511365 AAAATTTCTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTCTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
* *
55511430 CCTGCTTAAGTTTCAATATCCTTAGATAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATATCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
55511495 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
*
55511548 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTCTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
*
55511613 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATATCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
55511678 TAATTATTTATTTATTTAAAAAAT
131 TAATTATTTATTTATTTAAAAAAT
55511702 GAGTTCATGA
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 150 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (183 bp):
AAAATTTCTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
CCCGCTTAAGTTTCAATATCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
Found at i:55514237 original size:39 final size:40
Alignment explanation
Indices: 55514129--55514313 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
55514119 TTGAATGATG
* * *
55514129 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
55514168 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55514209 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55514248 TCCGGGTTAAGTCCCGATGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55514287 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55514314 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:55514273 original size:79 final size:81
Alignment explanation
Indices: 55514129--55514311 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 81
55514119 TTGAATGATG
* * *
55514129 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
55514193 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
55514208 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGATGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
55514270 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
55514288 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
55514312 TGAACGAGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.64
80 30 0.34
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:55514335 original size:79 final size:79
Alignment explanation
Indices: 55514190--55514336 Score: 174
Period size: 79 Copynumber: 1.9 Consensus size: 79
55514180 ATCCGAAGGT
* ** *
55514190 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGT
1 ATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAATCCGGGT
55514255 TAAGTCCCGATGGC
66 TAAGTCCCGATGGC
* * * *
55514269 ATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-
1 ATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAATCCG
55514331 GGTTAA
63 GGTTAA
55514337 ATTCCGAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
78 2 0.04
79 31 0.54
80 24 0.42
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
ATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAATCCGGGT
TAAGTCCCGATGGC
Found at i:55521407 original size:30 final size:30
Alignment explanation
Indices: 55521371--55521430 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
55521361 AACATGTTTG
55521371 GTGAAGTTATGTACTTA-GCAAATGGCCATA
1 GTGAAGTTATGTAC-TAGGCAAATGGCCATA
55521401 GTGAAGTTATGTACTAGGCAAATGGCCATA
1 GTGAAGTTATGTACTAGGCAAATGGCCATA
55521431 TAGTATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (30 bp):
GTGAAGTTATGTACTAGGCAAATGGCCATA
Found at i:55521758 original size:16 final size:16
Alignment explanation
Indices: 55521737--55521769 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55521727 TTTATTTTGA
55521737 TTTAATTGAGTTATGT
1 TTTAATTGAGTTATGT
55521753 TTTAATTGAGTTATGT
1 TTTAATTGAGTTATGT
55521769 T
1 T
55521770 AAACATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTAATTGAGTTATGT
Found at i:55533564 original size:21 final size:20
Alignment explanation
Indices: 55533537--55533595 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
55533527 TTTTTCACAT
55533537 AAATTTAATATTAAATAATA
1 AAATTTAATATTAAATAATA
*
55533557 ACAATTT-ATATTAGAAGAATA
1 A-AATTTAATATTA-AATAATA
* *
55533578 ATATTTAAATATAAAATA
1 AAATTT-AATATTAAATA
55533596 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 11 0.35
21 15 0.48
22 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTTAATATTAAATAATA
Found at i:55536272 original size:19 final size:19
Alignment explanation
Indices: 55536250--55536323 Score: 52
Period size: 22 Copynumber: 4.1 Consensus size: 19
55536240 AATATAATGG
55536250 ATAATATATATAAATAAAA
1 ATAATATATATAAATAAAA
**
55536269 ATAATAACTAATATTTATAAAA
1 ATAAT-A-T-ATATAAATAAAA
55536291 ATAA-ATA-AT--ATAAAA
1 ATAATATATATAAATAAAA
*
55536306 A-AATATTTA-AAATAAAA
1 ATAATATATATAAATAAAA
55536323 A
1 A
55536324 AGGATTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.04
15 9 0.20
16 1 0.02
17 9 0.20
18 1 0.02
19 6 0.13
20 2 0.04
21 1 0.02
22 14 0.31
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATATATATAAATAAAA
Found at i:55536272 original size:26 final size:26
Alignment explanation
Indices: 55536251--55536300 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
55536241 ATATAATGGA
55536251 TAATATATATAAATAA-AAATAATAAC
1 TAATATATATAAA-AATAAATAATAAC
*
55536277 TAATATTTATAAAAATAAATAATA
1 TAATATATATAAAAATAAATAATA
55536301 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATATATATAAAAATAAATAATAAC
Found at i:55536275 original size:22 final size:23
Alignment explanation
Indices: 55536250--55536302 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
55536240 AATATAATGG
55536250 ATAATATATATAAATAAAAAT-A
1 ATAATATATATAAATAAAAATAA
**
55536272 ATAACTA-ATATTTATAAAAATAA
1 ATAA-TATATATAAATAAAAATAA
55536295 ATAATATA
1 ATAATATA
55536303 AAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATATATATAAATAAAAATAA
Found at i:55538285 original size:206 final size:206
Alignment explanation
Indices: 55537759--55538300 Score: 809
Period size: 204 Copynumber: 2.6 Consensus size: 206
55537749 CTGCTTTTTC
* * **
55537759 GATTTGTTCTCTGACAATACAGAGATGCCAAATCCTCTTAGATTTGCTTCAGCGTAAGCATGCAA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTGA
* * * * *
55537824 AAACCAAATCAGGTATGTCTTCGATTTGCTCCTTGTAAGCACGAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * * * ** *
55537889 CTGCTTCAGTCTAATCATTTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAAAATGGAGA
131 CTACTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTGTCTGCTCTCCGTCGAAAATGGAGA
*
55537954 CGCCAAACTTT
196 CACCAAACTTT
* *
55537965 GATTTGTTCTCTGACAAT--AGAGATGCCAAATCATCTTGGACTTGCTTCAGCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTGA
* * *
55538028 AAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
** *
55538093 CTACTTCAGTATAAACATCTGAAGGCCAGATATTTTATGTGTCTGCTCTCCGTCGAATATGGAGA
131 CTACTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTGTCTGCTCTCCGTCGAAAATGGAGA
55538158 CACCAAACTTT
196 CACCAAACTTT
* * *
55538169 GATTTGTTCCCTGACAATACAGATATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTGA
*
55538234 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAATGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
55538299 CT
131 CT
55538301 TGCTTCAGCC
Statistics
Matches: 300, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
204 178 0.59
206 122 0.41
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTACTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTGTCTGCTCTCCGTCGAAAATGGAGA
CACCAAACTTT
Found at i:55560009 original size:20 final size:20
Alignment explanation
Indices: 55559984--55560024 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55559974 TCAAGTTAGG
55559984 AGAATGAGAAAATAGCGTGA
1 AGAATGAGAAAATAGCGTGA
55560004 AGAATGAGAAAATAGCGTGA
1 AGAATGAGAAAATAGCGTGA
55560024 A
1 A
55560025 AAATAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.29, T:0.15
Consensus pattern (20 bp):
AGAATGAGAAAATAGCGTGA
Found at i:55560865 original size:40 final size:41
Alignment explanation
Indices: 55560777--55560887 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
55560767 ACATAGTTTT
55560777 GGCTATATATTTGGCACTTAGTGTGTGAGAATAAGATAGCTTA
1 GGCTATATA--TGGCACTTAGTGTGTGAGAATAAGATAGCTTA
* ** * *
55560820 TGCTATATATGGCACTTAGTGTGTGA-TTTGAGATAGCTTC
1 GGCTATATATGGCACTTAGTGTGTGAGAATAAGATAGCTTA
* ***
55560860 GGCTATGTACATCACTTAGTGTGTGAGA
1 GGCTATATATGGCACTTAGTGTGTGAGA
55560888 TATTGAGTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 31 0.55
41 17 0.30
43 8 0.14
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (41 bp):
GGCTATATATGGCACTTAGTGTGTGAGAATAAGATAGCTTA
Done.