Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 187 of 206
Found at i:56782582 original size:18 final size:20
Alignment explanation
Indices: 56782543--56782584 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
56782533 AAGACTTCCA
*
56782543 AACATCTTATAAAATGTTTG
1 AACATCTTAGAAAATGTTTG
56782563 AACA-CTTAGAAAAT-TTTG
1 AACATCTTAGAAAATGTTTG
56782581 AACA
1 AACA
56782585 ATGTTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AACATCTTAGAAAATGTTTG
Found at i:56783711 original size:23 final size:23
Alignment explanation
Indices: 56783668--56783711 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
56783658 TGATCATTAT
* *
56783668 ATAAAAGAGATCAAGTTAGGTAG
1 ATAAAAGAGATCAAATCAGGTAG
56783691 ATAAAAGAGATCAAATCAGGT
1 ATAAAAGAGATCAAATCAGGT
56783712 GAACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (23 bp):
ATAAAAGAGATCAAATCAGGTAG
Found at i:56786737 original size:11 final size:11
Alignment explanation
Indices: 56786721--56786757 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56786711 AAATAAAACC
56786721 ATGTGCCTTTT
1 ATGTGCCTTTT
*
56786732 ATGTG-C-TTC
1 ATGTGCCTTTT
56786741 ATGTGCCTTTT
1 ATGTGCCTTTT
56786752 ATGTGC
1 ATGTGC
56786758 TTTCTTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.49
Consensus pattern (11 bp):
ATGTGCCTTTT
Found at i:56786745 original size:20 final size:20
Alignment explanation
Indices: 56786720--56786759 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56786710 GAAATAAAAC
56786720 CATGTGCCTTTTATGTGCTT
1 CATGTGCCTTTTATGTGCTT
56786740 CATGTGCCTTTTATGTGCTT
1 CATGTGCCTTTTATGTGCTT
56786760 TCTTGCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
CATGTGCCTTTTATGTGCTT
Found at i:56793701 original size:22 final size:22
Alignment explanation
Indices: 56793673--56793716 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
56793663 GTAGCTGAAG
56793673 GGCTAATAAAAACTACTCAAAC
1 GGCTAATAAAAACTACTCAAAC
56793695 GGCTAATAAAAACTACTCAAAC
1 GGCTAATAAAAACTACTCAAAC
56793717 ACATACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (22 bp):
GGCTAATAAAAACTACTCAAAC
Found at i:56798935 original size:15 final size:15
Alignment explanation
Indices: 56798911--56798941 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56798901 GTTAATTGTG
*
56798911 ATTAAGGTTTAATTA
1 ATTAAAGTTTAATTA
56798926 ATTAAAGTTTAATTA
1 ATTAAAGTTTAATTA
56798941 A
1 A
56798942 GTGATTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
ATTAAAGTTTAATTA
Found at i:56799541 original size:7 final size:7
Alignment explanation
Indices: 56799529--56799556 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
56799519 AATTTGTTTT
56799529 AAAAATA
1 AAAAATA
56799536 AAAAATA
1 AAAAATA
56799543 AAAAATA
1 AAAAATA
56799550 AAAAATA
1 AAAAATA
56799557 TTTTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:56803329 original size:30 final size:29
Alignment explanation
Indices: 56803293--56803388 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
56803283 TTAGCCCATA
*
56803293 TGAGCAACCTCGATATGATGTCAGCTTGTG
1 TGAGCAACCTCGATAT-ATGTCAACTTGTG
* *
56803323 TGAGCAA-CTCCGTTAAAATGTCAACTTGTG
1 TGAGCAACCT-CGAT-ATATGTCAACTTGTG
*
56803353 TGAGCAACC-CTGAAATACTGTCAACTTGTG
1 TGAGCAACCTC-GATATA-TGTCAACTTGTG
56803383 TGAGCA
1 TGAGCA
56803389 TTATATTCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
29 5 0.09
30 48 0.87
31 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (29 bp):
TGAGCAACCTCGATATATGTCAACTTGTG
Found at i:56806454 original size:6 final size:6
Alignment explanation
Indices: 56806442--56806483 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
56806432 ACGAAGGAAT
* *
56806442 GAGATG AAGATG AAGATG GAGATG GAGATG GAGATG GAGATG
1 GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG
56806484 AATGTGGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (6 bp):
GAGATG
Found at i:56806582 original size:27 final size:27
Alignment explanation
Indices: 56806552--56806639 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
56806542 TTGGTATTTT
* * *
56806552 CCAGTAGGCTTGGTGAGCAGGGGTTCG
1 CCAGAAGGCTTAGTAAGCAGGGGTTCG
*
56806579 CCAGAAGGCTTAGTAAGCAGAGGTTCG
1 CCAGAAGGCTTAGTAAGCAGGGGTTCG
*
56806606 CTAGAAGGCTTAGTAAGCAGGGGGTTCG
1 CCAGAAGGCTTAGTAAGCA-GGGGTTCG
56806634 CCAGAA
1 CCAGAA
56806640 AGCCTAGCGA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 41 0.77
28 12 0.23
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19
Consensus pattern (27 bp):
CCAGAAGGCTTAGTAAGCAGGGGTTCG
Found at i:56810345 original size:19 final size:21
Alignment explanation
Indices: 56810321--56810370 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
56810311 AGGCTATGTT
*
56810321 TATCGATAC-CT-TTGTAAAG
1 TATCGATACTCTGATGTAAAG
56810340 TATCGATACTCTGATGTAAAG
1 TATCGATACTCTGATGTAAAG
*
56810361 TACCGATACT
1 TATCGATACT
56810371 TTAGTCCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 16 0.59
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
TATCGATACTCTGATGTAAAG
Found at i:56812484 original size:50 final size:50
Alignment explanation
Indices: 56812265--56812553 Score: 305
Period size: 51 Copynumber: 5.7 Consensus size: 50
56812255 TATCAATGAA
* * ***
56812265 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * *
56812316 CACTTGTGTAGTACTAAGTGAAGGCTACAATGT-ATACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGA-ACCGTA-AAAC-TTGGT
* * *
56812367 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* *
56812418 CACGTGTGTAGTACTATGTGAAGGCTGCTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* * * *
56812468 CACTTGTGTAGTACTATGTGAAGGTTACTACGTGAACTGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* * *
56812518 CACGTATGTAGTATTATATGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
56812554 TCGAATGATA
Statistics
Matches: 205, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.00
50 86 0.42
51 114 0.56
52 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:56814928 original size:22 final size:22
Alignment explanation
Indices: 56814894--56814957 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
56814884 TCTTAAGGAA
** *
56814894 AGAGTACTGAAGTGCTAAATAG
1 AGAGTACAAAAGTGCTAAACAG
* * *
56814916 AGAGTACCAAAGTACTGAACAG
1 AGAGTACAAAAGTGCTAAACAG
* *
56814938 AGAGCACAAAATTGCTAAAC
1 AGAGTACAAAAGTGCTAAAC
56814958 CCGTACAAGC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (22 bp):
AGAGTACAAAAGTGCTAAACAG
Found at i:56816754 original size:10 final size:10
Alignment explanation
Indices: 56816739--56816773 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
56816729 TCCATTTCAC
*
56816739 CATTTTTATT
1 CATTTTTGTT
56816749 CATTTTTGTT
1 CATTTTTGTT
*
56816759 CATTTATGTT
1 CATTTTTGTT
56816769 CATTT
1 CATTT
56816774 GATTCAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (10 bp):
CATTTTTGTT
Found at i:56822658 original size:16 final size:16
Alignment explanation
Indices: 56822608--56822659 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
56822598 TTTGGTTCGC
56822608 TGTATT-GATTTAGAGG
1 TGTATTGGA-TTAGAGG
* *
56822624 TGAATTGGATTAAAGG
1 TGTATTGGATTAGAGG
56822640 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56822656 TGTA
1 TGTA
56822660 ATAGCAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56822918 original size:18 final size:17
Alignment explanation
Indices: 56822896--56822930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56822886 TTATTATTAA
*
56822896 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56822914 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56822931 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56823069 original size:16 final size:16
Alignment explanation
Indices: 56823032--56823073 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56823022 TTAATCATAT
*
56823032 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
56823048 TT-AAATATATTATAA
1 TTAAAATATATTATAA
56823063 TTAAAATATAT
1 TTAAAATATAT
56823074 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:56823074 original size:156 final size:157
Alignment explanation
Indices: 56822790--56823098 Score: 557
Period size: 156 Copynumber: 2.0 Consensus size: 157
56822780 CCCTTAACAT
* *
56822790 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAG
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* * *
56822855 TAATAAATATTTTAATCATATTTAAATATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
56822920 TTTAATAAAATTCTT-ATAATTAGCAG
131 TTTAATAAAATTCTTAATAATTAGCAG
*
56822946 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
56823011 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
56823076 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
56823099 ATATTCTTAT
Statistics
Matches: 146, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 139 0.95
157 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTAGCAG
Found at i:56823080 original size:14 final size:15
Alignment explanation
Indices: 56823041--56823082 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56823031 TTTAAACATA
*
56823041 ATTATTATTAAATAT
1 ATTATAATTAAATAT
56823056 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
56823070 A-TATAATTTAATA
1 ATTATAATTAAATA
56823083 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:56823200 original size:14 final size:15
Alignment explanation
Indices: 56823151--56823202 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56823141 GTAAAATATA
56823151 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
56823166 TATTAAATATATTAT
1 AATTAAATATATTAT
56823181 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
56823194 AATTTAATA
1 AATTAAATA
56823203 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:56823338 original size:120 final size:120
Alignment explanation
Indices: 56823030--56823320 Score: 537
Period size: 120 Copynumber: 2.4 Consensus size: 120
56823020 ATTTAATCAT
56823030 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
56823095 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
56823151 AATTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
56823216 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* *
56823271 ATTTAACATAATTATTATTAAATATATTATAAGTAAAATATATTATTTAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAA
56823321 AATAATTTAA
Statistics
Matches: 165, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
120 162 0.98
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:56823414 original size:24 final size:25
Alignment explanation
Indices: 56823368--56823415 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
56823358 TATGAATTTG
56823368 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
56823394 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
56823416 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:56823420 original size:92 final size:92
Alignment explanation
Indices: 56823324--56823551 Score: 234
Period size: 92 Copynumber: 2.5 Consensus size: 92
56823314 TATTTAAAAT
* * *
56823324 AATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAA
1 AATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA
*
56823386 TTATTACATATAATTTAATAATTAATATTA
64 -TATTAAATATAATTTAATAATTAATATTA
* * * * *
56823416 AATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATA
* *
56823481 TTAAATATAATTTAAT-AGTCATA-TA
66 TTAAATATAATTTAATAATTAATATTA
* * *
56823506 TAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 -AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
56823552 CTAAAATCAA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 80 0.68
93 9 0.08
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATA
TTAAATATAATTTAATAATTAATATTA
Found at i:56828059 original size:9 final size:9
Alignment explanation
Indices: 56828045--56828073 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56828035 AACAAAATAT
56828045 AAACAGACC
1 AAACAGACC
56828054 AAACAGACC
1 AAACAGACC
56828063 AAACAGACC
1 AAACAGACC
56828072 AA
1 AA
56828074 GACACAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.31, G:0.10, T:0.00
Consensus pattern (9 bp):
AAACAGACC
Found at i:56831837 original size:49 final size:50
Alignment explanation
Indices: 56831782--56831904 Score: 146
Period size: 49 Copynumber: 2.5 Consensus size: 50
56831772 GAGTTCAGAG
* * *
56831782 TGGTTATAC-ATTCACGGGTTCAAGTATAACT-AGGGCTCCTAGTTGACAA
1 TGGTTATGCGATTCACGGGTTCAAGTATAACTCA-GGCCCCCAGTTGACAA
* * *
56831831 TGGTTATGCGATT-ACAGGTTGAAGTATAACTCAGGCCCCCAGTTGACGA
1 TGGTTATGCGATTCACGGGTTCAAGTATAACTCAGGCCCCCAGTTGACAA
*
56831880 TGGTTATGCGA-TCATGGGTTCAAGT
1 TGGTTATGCGATTCACGGGTTCAAGT
56831905 TTCATGATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
48 1 0.02
49 57 0.92
50 4 0.06
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TGGTTATGCGATTCACGGGTTCAAGTATAACTCAGGCCCCCAGTTGACAA
Found at i:56834388 original size:6 final size:6
Alignment explanation
Indices: 56834377--56834406 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
56834367 ATGTCTACCT
56834377 CAAACA CAAACA CAAACA CAAACA CAAACA
1 CAAACA CAAACA CAAACA CAAACA CAAACA
56834407 AATCTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACA
Found at i:56838260 original size:34 final size:34
Alignment explanation
Indices: 56838222--56838293 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
56838212 TCTTGAAGTG
56838222 ACTAAGGCCATATCGGAGAGACCCATAGGAGGAT
1 ACTAAGGCCATATCGGAGAGACCCATAGGAGGAT
56838256 ACTAAGGCCATATCGGAGAGACCCATAGGAGGAT
1 ACTAAGGCCATATCGGAGAGACCCATAGGAGGAT
56838290 -CTAA
1 ACTAA
56838294 TTCGACTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (34 bp):
ACTAAGGCCATATCGGAGAGACCCATAGGAGGAT
Found at i:56839531 original size:10 final size:10
Alignment explanation
Indices: 56839516--56839544 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
56839506 TCTCTCATAT
56839516 TTCCTCTCAA
1 TTCCTCTCAA
56839526 TTCCTCTCAA
1 TTCCTCTCAA
56839536 TTCCTCTCA
1 TTCCTCTCA
56839545 GTTTCCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.41, G:0.00, T:0.41
Consensus pattern (10 bp):
TTCCTCTCAA
Found at i:56839565 original size:22 final size:22
Alignment explanation
Indices: 56839534--56839589 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
56839524 AATTCCTCTC
*
56839534 AATTCCTCTCAGTTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
56839557 AATTCTCTCAATTTCCTTTCAA
1 AATTCTCTCAATTTCCTTCCAA
56839579 AATTCTCTCAA
1 AATTCTCTCAA
56839590 ATCCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.27, C:0.30, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:56839615 original size:29 final size:29
Alignment explanation
Indices: 56839583--56839669 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
56839573 TTTCAAAATT
56839583 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
* **
56839612 CTCTCAATTTCC-T-TCCAA----AA-TT-
1 CTCTCAA-ATCCATATTTAATTTCAATTTC
56839634 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
56839663 CTCTCAA
1 CTCTCAA
56839670 TTTCCCTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
21 3 0.07
22 8 0.19
23 5 0.12
24 2 0.05
27 2 0.05
28 5 0.12
29 15 0.35
30 3 0.07
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTCAATTTC
Found at i:56839620 original size:51 final size:51
Alignment explanation
Indices: 56839561--56839674 Score: 219
Period size: 51 Copynumber: 2.2 Consensus size: 51
56839551 TTCCAAAATT
*
56839561 CTCTCAATTTCCTTTCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
56839612 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
56839663 CTCTCAATTTCC
1 CTCTCAATTTCC
56839675 CTTTTTAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:56839621 original size:22 final size:22
Alignment explanation
Indices: 56839596--56839672 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
56839586 TCAAATCCAT
56839596 ATTTAATTTCAATTTCCTCTCA
1 ATTTAATTTCAATTTCCTCTCA
** * *
56839618 ATTTCCTTCCAAAATTCTCTCAAATCCA
1 ATTTAATTTC-AATTTC-CTC---T-CA
56839646 TATTTAATTTCAATTTCCTCTCA
1 -ATTTAATTTCAATTTCCTCTCA
56839669 ATTT
1 ATTT
56839673 CCCTTTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
22 11 0.28
23 7 0.17
24 4 0.10
27 4 0.10
28 7 0.17
29 7 0.17
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATTTCAATTTCCTCTCA
Found at i:56840830 original size:7 final size:7
Alignment explanation
Indices: 56840818--56840842 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56840808 AGTCGATTGA
56840818 TATTTAG
1 TATTTAG
56840825 TATTTAG
1 TATTTAG
56840832 TATTTAG
1 TATTTAG
56840839 TATT
1 TATT
56840843 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:56841520 original size:18 final size:18
Alignment explanation
Indices: 56841494--56841528 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56841484 AGGTGCGTTT
*
56841494 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
56841512 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
56841529 TCCTTTTCCG
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:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:56841998 original size:43 final size:45
Alignment explanation
Indices: 56841951--56842036 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
56841941 ATATTTTAAA
*
56841951 TATTTTGATATTATTTTATGTAA-AAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTAATGTAATAAAATAGAAATTTCTTTGAGT
*
56841994 TATTTTGATATTATTTAATGTAATAAAATAGAAGTTTCTTTGA
1 TATTTTGATATTATTTAATGTAATAAAATAGAAATTTCTTTGA
56842037 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (45 bp):
TATTTTGATATTATTTAATGTAATAAAATAGAAATTTCTTTGAGT
Found at i:56842104 original size:36 final size:36
Alignment explanation
Indices: 56841993--56842105 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
56841983 ATTTTTTGAG
56841993 TTATTTTGATATTATTTAATGTAATAAAATAGAAGT
1 TTATTTTGATATTATTTAATGTAATAAAATAGAAGT
* * * ** ** * *
56842029 TT-CTTTGATGTAATAAAATAAAAAAAAATTTCG-AG-
1 TTATTTTGATATTATTTAATGTAATAAAA--TAGAAGT
*
56842064 TTATTTTGATATTATTTGATGTAATAAAATAGAAGT
1 TTATTTTGATATTATTTAATGTAATAAAATAGAAGT
56842100 TTATTT
1 TTATTT
56842106 GATGTAATAA
Statistics
Matches: 53, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 2 0.04
35 22 0.42
36 27 0.51
37 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.45
Consensus pattern (36 bp):
TTATTTTGATATTATTTAATGTAATAAAATAGAAGT
Found at i:56842172 original size:23 final size:23
Alignment explanation
Indices: 56842113--56842750 Score: 337
Period size: 29 Copynumber: 25.0 Consensus size: 23
56842103 TTTGATGTAA
56842113 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
56842136 TAAAAAACCTTAACCTAATTTAAT
1 T-AAAAACCCTAACCTAATTTAAT
56842160 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
56842183 TAAAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
56842205 TAAAAA-CCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
* **
56842226 TACAAAACTCTAACCTAAACCCTAAT
1 TA-AAAACCCTAACCT-AA-TTTAAT
56842252 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
56842275 TAAAAACCCTACCCCTAACCTAATTTAAT
1 T-AAAA----A-CCCTAACCTAATTTAAT
*
56842304 TAAAAACACTACCTCTAACTTAATTTAAT
1 T--AAA-A--ACC-CTAACCTAATTTAAT
*
56842333 AAAAAACCCTACCCCTAACCTAATTTAAT
1 TAAAAA--C----CCTAACCTAATTTAAT
56842362 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
56842391 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
56842414 TAAAGACCCTAACCCTAACCTAAATTAAT
1 T-AA-A----AACCCTAACCTAATTTAAT
56842443 TAAAAATCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
*
56842472 TAAAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
*
56842494 TAAAAACCCTAAACTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
56842517 TAAAGACCCTAACCCTAACCTAAATTAAT
1 T-AA-A----AACCCTAACCTAATTTAAT
56842546 TAAAAACCTTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
* *
56842575 TCAAAACCCTAAACCCTTAACTTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
56842600 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
56842626 TAAAGACCCTAACCCTAAACTAATTTAAT
1 T-AA-A----AACCCTAACCTAATTTAAT
*
56842655 TAAAAACCCTAAACCCTTAACTTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
56842680 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
56842706 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
56842729 TAAAAACCCTAAACTAAGTTAA
1 TAAAAACCCTAACCTAATTTAA
56842751 CAATGTTACA
Statistics
Matches: 506, Mismatches: 38, Indels: 142
0.74 0.06 0.21
Matches are distributed among these distances:
19 3 0.01
20 8 0.02
21 9 0.02
22 22 0.04
23 122 0.24
24 54 0.11
25 40 0.08
26 22 0.04
27 19 0.04
28 17 0.03
29 172 0.34
30 11 0.02
31 4 0.01
33 1 0.00
35 2 0.00
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:56842193 original size:18 final size:20
Alignment explanation
Indices: 56842124--56842282 Score: 72
Period size: 23 Copynumber: 7.0 Consensus size: 20
56842114 AAAAACCCTA
56842124 ACCTAATTTAATTAAAAAACC
1 ACCTAATTTAATT-AAAAACC
56842145 TTAACCTAATTTAATTAAAAACCC
1 ---ACCTAATTTAATTAAAAA-CC
56842169 TAACCTAATTTAATTAAAAA-C
1 --ACCTAATTTAATTAAAAACC
*
56842190 -CCTAAACCTTAACTTTAAAAACC
1 ACCT-AA-TTTAA--TTAAAAACC
56842213 TAACCTAATTTAA-TACAAAACTC
1 --ACCTAATTTAATTA-AAAAC-C
**
56842236 TAACCTAAACCCTAATTAAAAACCC
1 --ACCT-AA-TTTAATTAAAAA-CC
56842261 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
56842283 CTACCCCTAA
Statistics
Matches: 114, Mismatches: 6, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.03
19 2 0.02
20 4 0.04
21 3 0.03
22 14 0.12
23 43 0.38
24 23 0.20
25 16 0.14
26 6 0.05
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:56842255 original size:92 final size:92
Alignment explanation
Indices: 56842113--56842285 Score: 271
Period size: 92 Copynumber: 1.9 Consensus size: 92
56842103 TTTGATGTAA
**
56842113 TAAAAACCCTAACCTAATTTAATTAAAAAACCTTAACCTAATTTAATTAAAAACCCTAACCTAAT
1 TAAAAACCCTAACCTAATTTAATTAAAAAACCTTAACCTAACCTAATTAAAAACCCTAACCTAAT
56842178 TTAATTAAAAACCCTAAACCTTAACTT
66 TTAATTAAAAACCCTAAACCTTAACTT
*
56842205 TAAAAA-CCTAACCTAATTTAA-TACAAAA-CTCTAACCTAAACCCTAATTAAAAACCCTAACCT
1 TAAAAACCCTAACCTAATTTAATTAAAAAACCT-TAACCT-AA-CCTAATTAAAAACCCTAACCT
56842267 AATTTAATTAAAAACCCTA
63 AATTTAATTAAAAACCCTA
56842286 CCCCTAACCT
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
89 2 0.03
90 12 0.16
91 17 0.23
92 44 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (92 bp):
TAAAAACCCTAACCTAATTTAATTAAAAAACCTTAACCTAACCTAATTAAAAACCCTAACCTAAT
TTAATTAAAAACCCTAAACCTTAACTT
Found at i:56842298 original size:29 final size:29
Alignment explanation
Indices: 56842256--56842740 Score: 469
Period size: 29 Copynumber: 18.1 Consensus size: 29
56842246 CCTAATTAAA
56842256 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842285 ACCCCTAACCTAATTTAATTAAAAACACT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842314 -ACCTCTAACTTAATTTAATAAAAAACCCT
1 AACC-CTAACCTAATTTAATTAAAAACCCT
*
56842343 ACCCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
56842372 AACCCTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842395 AACCCTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842424 AACCCTAACCTAAATTAATTAAAAATCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
56842453 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842482 AAACCT----TAA-CT--TTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842504 -A----AA-CTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842527 AACCCTAACCTAAATTAATTAAAAACCTT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842556 AACCCTAACCTAATTTAATTCAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842585 AAACCCT----T-A---ACTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
* *
56842607 AACCTTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842636 AACCCTAAACTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
56842665 AAACCCT----T-A---ACTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
56842687 AACCTTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
56842710 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
56842739 AA
1 AA
56842741 ACTAAGTTAA
Statistics
Matches: 374, Mismatches: 38, Indels: 88
0.75 0.08 0.18
Matches are distributed among these distances:
20 3 0.01
21 12 0.03
22 34 0.09
23 49 0.13
24 2 0.01
25 12 0.03
26 4 0.01
27 6 0.02
28 4 0.01
29 234 0.63
30 14 0.04
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:56842537 original size:103 final size:103
Alignment explanation
Indices: 56842287--56842671 Score: 477
Period size: 103 Copynumber: 3.6 Consensus size: 103
56842277 AAAACCCTAC
* * * * * * *
56842287 CCCTAACCTAATTTAATTAAAAACACT-ACCTCTAACTTAATTTAATAAAAAACCCTACCCCTAA
1 CCCTAAACTAATTTAATTAAAGACCCTAACC-CTAACCTAAATTAATTAAAAACCCTAACCCTAA
* *
56842351 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAA
65 CCTAATTTAATTAAAAACCCTAAACCT----TAA-CT--TTAAAAA
* *
56842397 CCCTAACCTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAATCCTAACCCTAAC
1 CCCTAAACTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAACCCTAACCCTAAC
56842462 CTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAA
66 CTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAA
*
56842500 CCCTAAACTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAACCTTAACCCTAAC
1 CCCTAAACTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAACCCTAACCCTAAC
*
56842565 CTAATTTAATTCAAAACCCTAAACCCTTAAC-TTAAAAA
66 CTAATTTAATTAAAAACCCTAAA-CCTTAACTTTAAAAA
* *
56842603 CCCTAACCTTAACCTAATTTAATTAAAGACCCTAACCCTAAACTAATTTAATTAAAAACCCTAAA
1 CCCT-A----AA-CTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAACCCT-AA
56842668 CCCT
59 CCCT
56842672 TAACTTAAAA
Statistics
Matches: 250, Mismatches: 16, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
103 102 0.41
104 8 0.03
105 1 0.00
106 3 0.01
108 2 0.01
109 46 0.18
110 85 0.34
111 3 0.01
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (103 bp):
CCCTAAACTAATTTAATTAAAGACCCTAACCCTAACCTAAATTAATTAAAAACCCTAACCCTAAC
CTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAA
Found at i:56842610 original size:80 final size:79
Alignment explanation
Indices: 56842141--56842742 Score: 449
Period size: 80 Copynumber: 7.8 Consensus size: 79
56842131 TTAATTAAAA
56842141 AACCTTAACCTAATTTAATT--AAA---AACCCTAACCTAATTTAATTAAAAACCCTAAA-CCTT
1 AACCTTAACCTAATTTAATTAAAAACCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTT
*
56842200 AACTT-TAAA----
66 AACTTAAAAACCCT
*
56842209 AACC-TAACCTAATTTAA-TACAAAACTCTAA-CCTAAACC----CTAATTAAAAACCCT-AACC
1 AACCTTAACCTAATTTAATTA-AAAAC-CTAACCCT-AACCTAATTTAATTAAAAACCCTAAACC
*
56842266 TAATTTAA-TTAAAAACCCT
63 ---CTTAACTTAAAAACCCT
* * * *
56842285 ACCCCTAACCTAATTTAATTAAAAACACT-ACCTCTAACTTAATTTAATAAAAAACCCTACCCCT
1 AACCTTAACCTAATTTAATTAAAAAC-CTAACC-CTAACCTAATTTAATTAAAAACCCTA-----
*
56842349 AACCTAATTTAA-TTAAAAACCCT
59 AACC---CTTAACTTAAAAACCCT
* *
56842372 AACCCTAACCTAATTTAATT--AAA---AACCCTAACCTAATTTAATTAAAGACCCT-AACCCTA
1 AACCTTAACCTAATTTAATTAAAAACCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT-
* *
56842431 ACCTAAATTAATTAAAAATCCT
65 ---T--A--ACTTAAAAACCCT
* * * *
56842453 AACCCTAACCTAATTTAATTAAAAACCCTAAACCT----TAA-CT--TTAAAAACCCTAAACTAA
1 AACCTTAACCTAATTTAATTAAAAA-CCTAACCCTAACCTAATTTAATTAAAAACCCTAAAC--C
* *
56842511 TTTAA-TTAAAGACCCT
63 CTTAACTTAAAAACCCT
* * *
56842527 AACCCTAACCTAAATTAATTAAAAACCTTAACCCTAACCTAATTTAATTCAAAACCCTAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACC-TAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
56842592 TAACTTAAAAACCCT
65 TAACTTAAAAACCCT
* *
56842607 AACCTTAACCTAATTTAATTAAAGACCCTAACCCTAAACTAATTTAATTAAAAACCCTAAACCCT
1 AACCTTAACCTAATTTAATTAAA-AACCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
56842672 TAACTTAAAAACCCT
65 TAACTTAAAAACCCT
56842687 AACCTTAACCTAATTTAATT--AAA---AACCCTAACCTAATTTAATTAAAAACCCTAAAC
1 AACCTTAACCTAATTTAATTAAAAACCTAACCCTAACCTAATTTAATTAAAAACCCTAAAC
56842743 TAAGTTAACA
Statistics
Matches: 439, Mismatches: 35, Indels: 114
0.75 0.06 0.19
Matches are distributed among these distances:
66 1 0.00
67 13 0.03
68 6 0.01
69 18 0.04
71 2 0.00
72 11 0.03
73 8 0.02
74 71 0.16
75 5 0.01
76 5 0.01
77 26 0.06
78 9 0.02
79 6 0.01
80 112 0.26
81 85 0.19
82 4 0.01
83 7 0.02
85 3 0.01
87 47 0.11
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (79 bp):
AACCTTAACCTAATTTAATTAAAAACCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTT
AACTTAAAAACCCT
Found at i:56842738 original size:103 final size:103
Alignment explanation
Indices: 56842357--56842740 Score: 356
Period size: 103 Copynumber: 3.7 Consensus size: 103
56842347 CTAACCTAAT
56842357 TTAA-TTAAAAACCCTAACCC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAGA
1 TTAACTTAAAAACCCTAACCCTTAACCTAA-TTAATTAAAAACCCTAACCTAATTTAATTAAAGA
* *
56842420 CCCTAACCCTAACCTAAATTAATTAAAAATCCT-AACCC
65 CCCTAACCCTAAACTAAATTAATTAAAAACCCTAAACCC
* ***** * * *
56842458 -TAACCTAATTTAATTAAAAACCCTAAACCTTAACT--TTAAAAACCCTAAACTAATTTAATTAA
1 TTAACTTAA---AAACCCTAACCCTTAACC-TAATTAATTAAAAACCCTAACCTAATTTAATTAA
* *
56842520 AGACCCTAACCCTAACCTAAATTAATTAAAAA-CCTTAACCC
62 AGACCCTAACCCTAAACTAAATTAATTAAAAACCCTAAACCC
* * ***** *
56842561 TAACCTAATTTAATTCAAAACCCTAAACCCTTAACTTAA--AAACCCTAACCTTAACCTAATTTA
1 T----TAACTT-A---AAAACCCT-AACCCTTAACCTAATTAATTAAAAACCCTAACCTAATTTA
*
56842624 ATTAAAGACCCTAACCCTAAACTAATTTAATTAAAAACCCTAAACCC
57 ATTAAAGACCCTAACCCTAAACTAAATTAATTAAAAACCCTAAACCC
*
56842671 TTAACTTAAAAACCCTAA-CCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAA
1 TTAACTTAAAAACCCTAACCCTTAACCTAA-TTAATTAAAAACCCTAACCTAATTTAATTAAAGA
56842735 CCCTAA
65 CCCTAA
56842741 ACTAAGTTAA
Statistics
Matches: 223, Mismatches: 37, Indels: 44
0.73 0.12 0.14
Matches are distributed among these distances:
100 13 0.06
101 5 0.02
102 11 0.05
103 94 0.42
104 7 0.03
105 6 0.03
106 8 0.04
108 4 0.02
109 56 0.25
110 18 0.08
112 1 0.00
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (103 bp):
TTAACTTAAAAACCCTAACCCTTAACCTAATTAATTAAAAACCCTAACCTAATTTAATTAAAGAC
CCTAACCCTAAACTAAATTAATTAAAAACCCTAAACCC
Found at i:56842740 original size:18 final size:20
Alignment explanation
Indices: 56842694--56842736 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
56842684 CCTAACCTTA
56842694 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
56842715 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
56842737 CTAAACTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:56842890 original size:116 final size:116
Alignment explanation
Indices: 56842747--56842984 Score: 404
Period size: 116 Copynumber: 2.1 Consensus size: 116
56842737 CTAAACTAAG
* * * * * *
56842747 TTAACAATGTTACATTTACGTAATGTTAGATTTGGAAAATTTTTTTGACTGGTACTAACAATTAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTAGAAAAATGTTTTGACTGGTACTAACAATTAA
56842812 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
*
56842863 TTAATAATTTTACATTCACATAATGTTAGATTTAGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTAGAAAAATGTTTTGACTGGTACTAACAATTAA
*
56842928 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
56842979 TTAATA
1 TTAATA
56842985 CAATTTATCA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (116 bp):
TTAATAATGTTACATTCACATAATGTTAGATTTAGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:56843001 original size:17 final size:18
Alignment explanation
Indices: 56842960--56843001 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
56842950 TTTACTAACC
* *
56842960 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
56842978 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
56842995 ATTAATA
1 ATTAATA
56843002 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:56846423 original size:126 final size:123
Alignment explanation
Indices: 56846016--56846484 Score: 699
Period size: 123 Copynumber: 3.8 Consensus size: 123
56846006 AACATGCTAT
*
56846016 TGTAGCAAAAGCGCGTTCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
** *
56846081 AGCGATTTTATACTATTTGTTCAGAAACGTCAAAAAAAA-AATTCTTACATGACCTAC
66 AGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATATTTCTTACATGACCTAC
* *
56846138 TGCAGCAAAAGCGCGTCCACGAGAGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
* * *
56846203 AGCGATTTTATACTATTTGCTTAGAAACATCAAAAAAAATATTTCTTACATGACCTAC
66 AGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATATTTCTTACATGACCTAC
* * * * *
56846261 TGTAGCAAAAGTGCGTCCACGAGGCCGCAATTTCACAAATTCTTCTTAAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
* *
56846326 AGCGATTTTATACTATTTACTCAGAAACGTCAAAAAATTAATTATTTCTTCCGTGACCTAC
66 AGCGATTTTATACTATTTACTCAGAAACGTCAAAAAA--AA-TATTTCTTACATGACCTAC
* * *
56846387 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCCGCTAAA
1 TGTAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
* *
56846452 AGCGATTCTACACTATTTTA-TCAGAAACGTCAA
66 AGCGATTTTATACTA-TTTACTCAGAAACGTCAA
56846485 CTCAAAATTA
Statistics
Matches: 315, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
122 98 0.31
123 109 0.35
125 2 0.01
126 102 0.32
127 4 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (123 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
AGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATATTTCTTACATGACCTAC
Found at i:56855630 original size:20 final size:18
Alignment explanation
Indices: 56855607--56855659 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 18
56855597 GATAAAATAA
56855607 AGTTAAAATTGTTTCAATTG
1 AGTTAAAA-TGTTTCAA-TG
56855627 AGTTAAACAT-TTTCAATG
1 AGTTAAA-ATGTTTCAATG
56855645 ATGTTAAAACTGTTT
1 A-GTTAAAA-TGTTT
56855660 TTAAACAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 4 0.14
19 13 0.45
20 11 0.38
21 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (18 bp):
AGTTAAAATGTTTCAATG
Found at i:56857550 original size:22 final size:22
Alignment explanation
Indices: 56857492--56857550 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
56857482 GAATGGTATC
56857492 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
56857514 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
56857537 TACATATCAAATCT
1 TACAAATCAAATCT
56857551 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:56859740 original size:25 final size:25
Alignment explanation
Indices: 56859712--56859765 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
56859702 ACACGGGAAC
56859712 AATGCTCACACAAGCTGGGACAGTA
1 AATGCTCACACAAGCTGGGACAGTA
* *
56859737 AATGCTCACACAAGCTGTGACTGTA
1 AATGCTCACACAAGCTGGGACAGTA
56859762 AATG
1 AATG
56859766 TTTACGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
AATGCTCACACAAGCTGGGACAGTA
Found at i:56862091 original size:21 final size:22
Alignment explanation
Indices: 56862067--56862111 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
56862057 TGTATTAAAA
*
56862067 TTATCAAATTAATTTTT-AATT
1 TTATAAAATTAATTTTTAAATT
56862088 TTATAAAATTAATTTTTAAATT
1 TTATAAAATTAATTTTTAAATT
56862110 TT
1 TT
56862112 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAAAATTAATTTTTAAATT
Found at i:56864495 original size:10 final size:10
Alignment explanation
Indices: 56864474--56864515 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
56864464 CATACGAACC
56864474 AGAAAG-AAA
1 AGAAAGAAAA
56864483 AGAAAGAAAA
1 AGAAAGAAAA
*
56864493 AGAAAAAAAA
1 AGAAAGAAAA
56864503 AGAAAGAAGAA
1 AGAAAGAA-AA
56864514 AG
1 AG
56864516 GAGAAAGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 6 0.21
10 19 0.66
11 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:56864512 original size:7 final size:7
Alignment explanation
Indices: 56864482--56864523 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
56864472 CCAGAAAGAA
56864482 AAGAAAG
1 AAGAAAG
56864489 AA-AAAG
1 AAGAAAG
* *
56864495 AAAAAAA
1 AAGAAAG
56864502 AAGAAAG
1 AAGAAAG
56864509 AAGAAAG
1 AAGAAAG
*
56864516 GAGAAAG
1 AAGAAAG
56864523 A
1 A
56864524 CGCAAGGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:56880195 original size:102 final size:101
Alignment explanation
Indices: 56880081--56880282 Score: 332
Period size: 102 Copynumber: 2.0 Consensus size: 101
56880071 CCAATGAGTC
* * * *
56880081 GGGGAATTAGCACTTAGCAACCCCTTTCACATTTCAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCA
* *
56880146 CCAATGATTCGGGGAATCAGCACTTAGCAAGCCCTTG
66 CCAATGAGTCGGGGAATCAGCACTTAG-AAACCCTTG
*
56880183 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCA
56880248 CCAATGAGTCGGGGAATCAGCACTTAGAAACCCTT
66 CCAATGAGTCGGGGAATCAGCACTTAGAAACCCTT
56880283 TTCACATTTA
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 7 0.08
102 86 0.92
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (101 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCA
CCAATGAGTCGGGGAATCAGCACTTAGAAACCCTTG
Found at i:56880244 original size:42 final size:42
Alignment explanation
Indices: 56880185--56880321 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
56880175 AGCCCTTGGG
*
56880185 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGT
*
56880227 GGAATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGT
* **
56880260 GGAATCAGCACTTAGAAACCCTTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGT
*
56880302 GGAATCAGCACTTAGTAACC
1 GGAATCAGCACTTAGCAACC
56880322 ACCAATGAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
33 17 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.08
42 37 0.47
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGT
Found at i:56880280 original size:75 final size:75
Alignment explanation
Indices: 56880183--56880356 Score: 294
Period size: 75 Copynumber: 2.3 Consensus size: 75
56880173 CAAGCCCTTG
*
56880183 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGAAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
*
56880248 CCAATGAGTC
66 CCAATGAATC
** *
56880258 GGGGAATCAGCACTTAGAAACCCTTTTCACATTTAAGATACGGTGGAATCAGCACTTAGTAACCA
1 GGGGAATCAGCACTTAGAAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
56880323 CCAATGAATC
66 CCAATGAATC
*
56880333 GGGGAATCAACACTTAGAAACCCC
1 GGGGAATCAGCACTTAGAAACCCC
56880357 TTGGGAGAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.21
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGAAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATC
Found at i:56880349 original size:177 final size:177
Alignment explanation
Indices: 56880046--56880386 Score: 556
Period size: 177 Copynumber: 1.9 Consensus size: 177
56880036 TATCCGTTAT
* * * *
56880046 CGGTGGATTTAGCACTTAGCAACCACCAATGAGTCGGGGAATTAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGAAACCCCTTTCAC
* * * * *
56880111 ATTTCAGATACGGTGGGATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAA
66 ATTTAAGATACGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGAAA
* *
56880176 GCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
131 CCCCTTGGGAGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
*
56880223 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGAAACCCTTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGAAACCCCTTTCAC
* *
56880288 ATTTAAGATACGGTGGAATCAGCACTTAGTAACCACCAATGAATCGGGGAATCAACACTTAGAAA
66 ATTTAAGATACGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGAAA
56880353 CCCCTTGGGAGAATCAGCACTTAGCAACCCCCTT
131 CCCCTTGGGAGAATCAGCACTTAGCAACCCCCTT
56880387 TATATTCAAT
Statistics
Matches: 150, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 150 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (177 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGAAACCCCTTTCAC
ATTTAAGATACGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGAAA
CCCCTTGGGAGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
Found at i:56881272 original size:79 final size:79
Alignment explanation
Indices: 56881172--56881334 Score: 263
Period size: 79 Copynumber: 2.1 Consensus size: 79
56881162 GATGGCCTTG
* * *
56881172 AGATTGCTTGGAACTAAGGATATAAACAAGTTGCAACGGTAGTTGACTGCTTGTAGGCTATTAAT
1 AGATGGCTTGGAACAAAGGATATAAACAAGTTGCAACGGTAGTTGACTACTTGTAGGCTATTAAT
56881237 TTGATTACTACACT
66 TTGATTACTACACT
* ***
56881251 AGATGGCTTGGAACAAAGGATATAGACAAGTTGCTGTGGTAGTTGACTACTTGTAGGCTATTAAT
1 AGATGGCTTGGAACAAAGGATATAAACAAGTTGCAACGGTAGTTGACTACTTGTAGGCTATTAAT
56881316 TTGATTACTACACT
66 TTGATTACTACACT
56881330 AGATG
1 AGATG
56881335 CGCATAGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (79 bp):
AGATGGCTTGGAACAAAGGATATAAACAAGTTGCAACGGTAGTTGACTACTTGTAGGCTATTAAT
TTGATTACTACACT
Found at i:56887364 original size:18 final size:18
Alignment explanation
Indices: 56887341--56887377 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56887331 GCTTTTAGTC
56887341 CTACTCTTAAAAAATTAT
1 CTACTCTTAAAAAATTAT
56887359 CTACTCTTAAAAAATTAT
1 CTACTCTTAAAAAATTAT
56887377 C
1 C
56887378 CTAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (18 bp):
CTACTCTTAAAAAATTAT
Found at i:56887581 original size:14 final size:14
Alignment explanation
Indices: 56887536--56887590 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
56887526 GGATGCGCCG
56887536 GGCCTAACATATCT
1 GGCCTAACATATCT
** *
56887550 GGCGGATA-AT-TGT
1 GGCCTA-ACATATCT
56887563 GGCCTAACATATCT
1 GGCCTAACATATCT
*
56887577 GGCCTAGCATATCT
1 GGCCTAACATATCT
56887591 TTGTGGGTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
12 1 0.03
13 8 0.26
14 21 0.68
15 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (14 bp):
GGCCTAACATATCT
Found at i:56895490 original size:26 final size:24
Alignment explanation
Indices: 56895445--56895495 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
56895435 AAAATGTGCA
56895445 AAAAAGAAAAAATATAGAAAAAGT
1 AAAAAGAAAAAATATAGAAAAAGT
* *
56895469 AAAAAGTAAAAATGAGTGGAAAAAGT
1 AAAAAGAAAAAAT-A-TAGAAAAAGT
56895495 A
1 A
56895496 TTGAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 1 0.04
26 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.14
Consensus pattern (24 bp):
AAAAAGAAAAAATATAGAAAAAGT
Found at i:56897754 original size:20 final size:20
Alignment explanation
Indices: 56897729--56897792 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
56897719 ATGCGACTAC
*
56897729 AATAATACCAATTTTATAAT
1 AATAATATCAATTTTATAAT
56897749 AATAATATCAATTTTATAAT
1 AATAATATCAATTTTATAAT
*
56897769 AATAATATCGATTTTAATAAT
1 AATAATATCAATTTT-ATAAT
56897790 AAT
1 AAT
56897793 GGTATTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 33 0.80
21 8 0.20
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (20 bp):
AATAATATCAATTTTATAAT
Found at i:56901493 original size:215 final size:215
Alignment explanation
Indices: 56900885--56901530 Score: 1100
Period size: 215 Copynumber: 3.0 Consensus size: 215
56900875 AACCAATCTT
56900885 CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTT-TCTCTAA
1 CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTTCTCTCTAA
* * *
56900949 GAAGGTAATCAATGCGATACCTTCTATTGTCTCAGTATAAACAATGCCCTCCAATAATTCAGTAT
66 GAAGGTAATCAATGGGATACCTTCTATTGTCTCAGTATAAACACTGCCCTCCAATAATTCAATAT
* * *
56901014 -TTCCTCATTTAGTGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCTAG
131 CTTCCTCAATTAATGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCCAG
*
56901078 AAAGAGACTCGGGCTCCTCC
196 AAAGAGACTCGGGTTCCTCC
*
56901098 CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTTTATTAAAAAATGGA-TTCTCTCTAA
1 CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTTCTCTCTAA
* *
56901162 GAAGGTAATCAATGGGACACCTTCTATTGTCTCATTATAAACACTGCCCTCCAATAATTCAATAT
66 GAAGGTAATCAATGGGATACCTTCTATTGTCTCAGTATAAACACTGCCCTCCAATAATTCAATAT
56901227 CTTCCTCAATTAATGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCCAG
131 CTTCCTCAATTAATGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCCAG
56901292 AAAGAGACTCGGGTTCCTCC
196 AAAGAGACTCGGGTTCCTCC
* *
56901312 GTAGTAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTTCTCTCTAA
1 CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTTCTCTCTAA
* *
56901377 GAAAGTAATCAATGGGATACCTTCTATTATCTCAGTATAAACACTGCCCTCCAATAATTCAATAT
66 GAAGGTAATCAATGGGATACCTTCTATTGTCTCAGTATAAACACTGCCCTCCAATAATTCAATAT
* * *
56901442 CTTCCTCAGTTAATGCCTTCGTTGAACGATTTGCTTCCATCGAAAATCCCATCAACATGTCCCAG
131 CTTCCTCAATTAATGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCCAG
56901507 AAAGAGACTCGGGCCTTCCTCC
196 AAAGAGACTCGGG--TTCCTCC
56901529 CT
1 CT
56901531 TCAGCGCACC
Statistics
Matches: 407, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
212 2 0.00
213 120 0.29
214 131 0.32
215 146 0.36
217 8 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (215 bp):
CTAATAACTTGATAGTCACCGATTGATCCATACTCTTCTCTATTAAAAAATGGATTTCTCTCTAA
GAAGGTAATCAATGGGATACCTTCTATTGTCTCAGTATAAACACTGCCCTCCAATAATTCAATAT
CTTCCTCAATTAATGCCTTCATTGAACGATTTGCTTCCATCGGAAATCCCATCAACATGTCCCAG
AAAGAGACTCGGGTTCCTCC
Found at i:56909286 original size:13 final size:14
Alignment explanation
Indices: 56909228--56909287 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
56909218 ATACATAAAC
56909228 AAATAGTAATAATAA
1 AAATAGTAA-AATAA
*
56909243 TAGATA-TAATAATAA
1 -AAATAGTAA-AATAA
* *
56909258 ATATAGTAAAAGAA
1 AAATAGTAAAATAA
56909272 AAATAG-AAAATAA
1 AAATAGTAAAATAA
56909285 AAA
1 AAA
56909288 AAAACAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.24
14 13 0.34
15 12 0.32
16 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.23
Consensus pattern (14 bp):
AAATAGTAAAATAA
Found at i:56910913 original size:44 final size:44
Alignment explanation
Indices: 56910865--56911153 Score: 188
Period size: 44 Copynumber: 6.4 Consensus size: 44
56910855 TACTCTACTA
* *
56910865 CAACTTCAGAGAGATGAGATTTGTAATTTCAACCAGCTCCACTG
1 CAACTTCAGAGAGATAAGATTTGTAATTTCAACCTGCTCCACTG
* ** ** * * *
56910909 CAACTTCAGGGAGATAAGGCTTGTAGCTTCAACTTGCACTACTG
1 CAACTTCAGAGAGATAAGATTTGTAATTTCAACCTGCTCCACTG
* * * * * *
56910953 CAACTTCAGAGAGATAAGGTTTG--ATAT-GATCTGCTCTACTA
1 CAACTTCAGAGAGATAAGATTTGTAATTTCAACCTGCTCCACTG
* * * *
56910994 CAACTTTAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGTTCCACTG
1 CAACTTCAGAGAGATAAGATTTGTAA-TT-T--C---AACCTGCTCCACTG
* * *
56911045 CAGCTTCAGGGAAATAAGATTTGGTAATTTCAACCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTT-GTAATTTCAACCTGCTCCACTG
* * * * * *
56911090 CAACTTCAGGGAGATAAGGTTTGCGTATTTTTATCCTACTCCACTG
1 CAACTTCAGAGAGATAAGATTT--GTAATTTCAACCTGCTCCACTG
* *
56911136 CAGCTTCAGGGAGATAAG
1 CAACTTCAGAGAGATAAG
56911154 GATTGTGGCT
Statistics
Matches: 189, Mismatches: 44, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
41 29 0.15
42 1 0.01
43 1 0.01
44 56 0.30
45 32 0.17
46 35 0.19
48 1 0.01
50 1 0.01
51 29 0.15
52 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTTGTAATTTCAACCTGCTCCACTG
Found at i:56911143 original size:46 final size:45
Alignment explanation
Indices: 56911038--56911154 Score: 162
Period size: 46 Copynumber: 2.6 Consensus size: 45
56911028 TTTAATCTGT
* * *
56911038 TCCACTGCAGCTTCAGGGAAATAAGATTTGGTAATTTCAACCTGC
1 TCCACTGCAGCTTCAGGGAGATAAGGTTTGGTAATTTCAACCTAC
* * * *
56911083 TCCACTGCAACTTCAGGGAGATAAGGTTTGCGTATTTTTATCCTAC
1 TCCACTGCAGCTTCAGGGAGATAAGGTTTG-GTAATTTCAACCTAC
56911129 TCCACTGCAGCTTCAGGGAGATAAGG
1 TCCACTGCAGCTTCAGGGAGATAAGG
56911155 ATTGTGGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 27 0.43
46 36 0.57
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (45 bp):
TCCACTGCAGCTTCAGGGAGATAAGGTTTGGTAATTTCAACCTAC
Found at i:56922617 original size:15 final size:16
Alignment explanation
Indices: 56922585--56922620 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
56922575 TCAAAGAAAA
*
56922585 AATAAATTAAATTAAT
1 AATAAAATAAATTAAT
56922601 AATAAAATAAA-TAAT
1 AATAAAATAAATTAAT
56922616 AATAA
1 AATAA
56922621 TGATAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAATAAATTAAT
Found at i:56922621 original size:21 final size:21
Alignment explanation
Indices: 56922583--56922632 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
56922573 AATCAAAGAA
*
56922583 AAAATAAATTAAATTAATAAT
1 AAAATAAATTAAAATAATAAT
*
56922604 AAAATAAA-TAATAATAATGAT
1 AAAATAAATTAA-AATAATAAT
56922625 AACAATAA
1 AA-AATAA
56922633 TAGTTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATAAATTAAAATAATAAT
Found at i:56922913 original size:18 final size:18
Alignment explanation
Indices: 56922887--56922921 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56922877 AACAAAAAAA
56922887 TATAAATATAAATAAATG
1 TATAAATATAAATAAATG
*
56922905 TATATATATAAATAAAT
1 TATAAATATAAATAAAT
56922922 ACAAAGAAAA
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:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TATAAATATAAATAAATG
Found at i:56926649 original size:72 final size:72
Alignment explanation
Indices: 56926559--56926693 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
56926549 AAATAAGATA
* * * * * *
56926559 ATTAAGTTTATTTGCTCAT-GATTTCTAATATGGTAAAGTTGTCATGACTTTGACAAAATTAAAT
1 ATTAAATTTATTTACTCATAGATTT-TAATATGATAAAATCGTCATGACTTTAACAAAATTAAAT
56926623 TTGAGTAG
65 TTGAGTAG
*
56926631 ATTAAATTTATTTACTCATAGATTTTAATATGATAAAATCGTCATGACTTTAACGAAATTAAA
1 ATTAAATTTATTTACTCATAGATTTTAATATGATAAAATCGTCATGACTTTAACAAAATTAAA
56926694 ATTGGATTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 50 0.91
73 5 0.09
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (72 bp):
ATTAAATTTATTTACTCATAGATTTTAATATGATAAAATCGTCATGACTTTAACAAAATTAAATT
TGAGTAG
Found at i:56935046 original size:42 final size:42
Alignment explanation
Indices: 56934964--56935074 Score: 181
Period size: 42 Copynumber: 2.7 Consensus size: 42
56934954 CACCGGCACG
* *
56934964 AAGCCTGCTAGACAT-AAGGTCTGAA-ATAATTCACTAGCATT
1 AAGCCTGCTAGGCATCAA-GCCTGAATATAATTCACTAGCATT
56935005 AAGCCTGCTAGGCATCAAGCCTGAATATAATTCACTAGCATT
1 AAGCCTGCTAGGCATCAAGCCTGAATATAATTCACTAGCATT
56935047 AAGCCTGCTAGGCATCAAGCCTGAATAT
1 AAGCCTGCTAGGCATCAAGCCTGAATAT
56935075 CACAGATAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 20 0.30
42 46 0.70
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (42 bp):
AAGCCTGCTAGGCATCAAGCCTGAATATAATTCACTAGCATT
Found at i:56935328 original size:61 final size:61
Alignment explanation
Indices: 56935262--56935432 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 61
56935252 TCAGCTTATA
* * * *
56935262 AAACTCAAAACATACATTCGGCTAACAGATATATATTTTATAAAATTTCTTTCAAC-TCAT-
1 AAACTCAAAACATACATTCGGCTAACATATTTATATTTCATAAAATTACTTTCAACAT-ATC
* * *
56935322 AGAACTCAAAACATACACTT--GCTAACATATTTATAATTCATACAATTAGTTTCAACATATC
1 A-AACTCAAAACATACA-TTCGGCTAACATATTTATATTTCATAAAATTACTTTCAACATATC
* *
56935383 AAACTTAAAATATACATTCGGCTAACATATTTATATAATTCATAAAATTA
1 AAACTCAAAACATACATTCGGCTAACATATTTATAT--TTCATAAAATTA
56935433 AATTCAGCTT
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
59 2 0.02
60 45 0.49
61 32 0.35
62 2 0.02
63 11 0.12
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.35
Consensus pattern (61 bp):
AAACTCAAAACATACATTCGGCTAACATATTTATATTTCATAAAATTACTTTCAACATATC
Found at i:56935398 original size:60 final size:58
Alignment explanation
Indices: 56935227--56935438 Score: 192
Period size: 61 Copynumber: 3.5 Consensus size: 58
56935217 TAAGATATAT
* * *
56935227 ATATATATAATTCATACAATTAAATTCAGCTTATAAAACTCAAAACATACATTCGGCTAAC
1 ATATATATAATTCATAAAATTAATTTCAAC-TAT-AAACTCAAAACATACATTC-GCTAAC
* * * **
56935288 AGATATATATTTTATAAAATTTCTTTCAACTCATAGAACTCAAAACATACACTT-GCTAAC
1 ATATATATAATTCATAAAATTAATTTCAACT-ATA-AACTCAAAACATACA-TTCGCTAAC
* * * * *
56935348 ATATTTATAATTCATACAATTAGTTTCAACATATCAAACTTAAAATATACATTCGGCTAAC
1 ATATATATAATTCATAAAATTAATTTCAAC-TAT-AAACTCAAAACATACATTC-GCTAAC
*
56935409 ATATTTATATAATTCATAAAATTAAATTCA
1 ATA--TATATAATTCATAAAATTAATTTCA
56935439 GCTTATAGAA
Statistics
Matches: 121, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
59 2 0.02
60 46 0.38
61 50 0.41
62 2 0.02
63 21 0.17
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (58 bp):
ATATATATAATTCATAAAATTAATTTCAACTATAAACTCAAAACATACATTCGCTAAC
Found at i:56937344 original size:28 final size:29
Alignment explanation
Indices: 56937306--56937378 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
56937296 ACAAAACTTC
*
56937306 TCTCGTCAAAATTATTTCTTCAGAACCCA
1 TCTCGTCAAAATTATTTCTTAAGAACCCA
*
56937335 TCTC-TCAAAATTATTTTTTAAGAACCCA
1 TCTCGTCAAAATTATTTCTTAAGAACCCA
*
56937363 TCTTGT-ACAAATTATT
1 TCTCGTCA-AAATTATT
56937379 ATTTTCAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (29 bp):
TCTCGTCAAAATTATTTCTTAAGAACCCA
Found at i:56937452 original size:32 final size:32
Alignment explanation
Indices: 56937411--56937472 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
56937401 TAATTAATAA
56937411 ACTTAAAAATAAATAAAACCCTAAA-CCTAAAT
1 ACTTAAAAATAAA-AAAACCCTAAATCCTAAAT
* * *
56937443 ACTTTAAAATTAAAAAACCTTAAATCCTAA
1 ACTTAAAAATAAAAAAACCCTAAATCCTAA
56937473 CCCTTATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (32 bp):
ACTTAAAAATAAAAAAACCCTAAATCCTAAAT
Found at i:56941049 original size:6 final size:6
Alignment explanation
Indices: 56941039--56941074 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
56941029 AGAATTTAGC
*
56941039 TTTTAC TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
56941075 CTTCTCAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:56944546 original size:16 final size:16
Alignment explanation
Indices: 56944519--56944555 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
56944509 CCAGAATTAC
56944519 AGGAAA-AAAATAAAA
1 AGGAAATAAAATAAAA
56944534 AGGAAATAAAATAAAA
1 AGGAAATAAAATAAAA
56944550 A-GAAAT
1 AGGAAAT
56944556 CCTCCCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
AGGAAATAAAATAAAA
Found at i:56945964 original size:29 final size:27
Alignment explanation
Indices: 56945876--56945964 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 27
56945866 CGAAAAAAAT
*
56945876 ATATAAATAAAAATTATAAAAACTATTAAA
1 ATATAAA-AAAAATTAT-AAATC-ATTAAA
* * * *
56945906 TTTTAAGAAAATATATATAAATCATAAAA
1 ATATAA-AAAAAAT-TATAAATCATTAAA
56945935 ATATAAAAAAAATTATCAAATGCATTAAA
1 ATATAAAAAAAATTAT-AAAT-CATTAAA
56945964 A
1 A
56945965 AGACCCTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 3 0.07
28 10 0.22
29 16 0.35
30 13 0.28
31 4 0.09
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
ATATAAAAAAAATTATAAATCATTAAA
Found at i:56946452 original size:16 final size:17
Alignment explanation
Indices: 56946421--56946453 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56946411 ACACACACAG
56946421 AAACAACAGCAAATAGAA
1 AAACAACAGC-AATAGAA
56946439 AAACAACAGC-ATAGA
1 AAACAACAGCAATAGA
56946454 GGTGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.64, C:0.18, G:0.12, T:0.06
Consensus pattern (17 bp):
AAACAACAGCAATAGAA
Found at i:56948837 original size:10 final size:8
Alignment explanation
Indices: 56948825--56948920 Score: 56
Period size: 8 Copynumber: 11.6 Consensus size: 8
56948815 TCTTTTCTAT
56948825 ATTTCTATA
1 ATTT-TATA
56948834 TATTTTATA
1 -ATTTTATA
56948843 ATTTTATA
1 ATTTTATA
*
56948851 ATTTTTTA
1 ATTTTATA
56948859 ATATTT-T-
1 AT-TTTATA
* *
56948866 -TATTAAA
1 ATTTTATA
*
56948873 ATTTAATA
1 ATTTTATA
56948881 ATTTTTATA
1 A-TTTTATA
56948890 ATTTTTATTGA
1 A-TTTTA-T-A
56948901 ATTTTAT-
1 ATTTTATA
*
56948908 TTTTTATA
1 ATTTTATA
56948916 ATTTT
1 ATTTT
56948921 TTTCCATATG
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 2 0.03
6 1 0.01
7 6 0.09
8 27 0.39
9 21 0.30
10 10 0.14
11 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (8 bp):
ATTTTATA
Found at i:56948868 original size:19 final size:19
Alignment explanation
Indices: 56948823--56948896 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
56948813 TTTCTTTTCT
*
56948823 ATATTTCTAT-ATATTTT-
1 ATATTTTTATAATATTTTA
* *
56948840 ATAATTTTATAATTTTTTA
1 ATATTTTTATAATATTTTA
*
56948859 ATATTTTTATTAA-AATTTA
1 ATATTTTTA-TAATATTTTA
56948878 ATAATTTTTATAAT-TTTTA
1 AT-ATTTTTATAATATTTTA
56948897 TTGAATTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
17 8 0.18
18 6 0.13
19 21 0.47
20 10 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTTATAATATTTTA
Found at i:56948887 original size:29 final size:30
Alignment explanation
Indices: 56948842--56948921 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 30
56948832 TATATTTTAT
*
56948842 AATTTTATAATTTTTTA-ATATTTTTATTAA
1 AATTTAATAATTTTTTATA-ATTTTTATTAA
*
56948872 AATTTAATAA-TTTTTATAATTTTTATT-G
1 AATTTAATAATTTTTTATAATTTTTATTAA
56948900 AATTT--T-ATTTTTTATAATTTTT
1 AATTTAATAATTTTTTATAATTTTT
56948922 TTCCATATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.02
26 15 0.33
28 5 0.11
29 15 0.33
30 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTAATAATTTTTTATAATTTTTATTAA
Found at i:56948905 original size:11 final size:9
Alignment explanation
Indices: 56948836--56948921 Score: 65
Period size: 9 Copynumber: 9.4 Consensus size: 9
56948826 TTTCTATATA
56948836 TTTTATAA-
1 TTTTATAAT
56948844 TTTTATAAT
1 TTTTATAAT
56948853 TTTT-TAATAT
1 TTTTAT-A-AT
*
56948863 TTTTATTAAAA
1 TTTTA-T-AAT
*
56948874 TTTAATAAT
1 TTTTATAAT
56948883 TTTTATAAT
1 TTTTATAAT
56948892 TTTTATTGAA-
1 TTTTA-T-AAT
56948902 TTTTAT--T
1 TTTTATAAT
56948909 TTTTATAAT
1 TTTTATAAT
56948918 TTTT
1 TTTT
56948922 TTCCATATGT
Statistics
Matches: 64, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
7 6 0.09
8 9 0.14
9 26 0.41
10 13 0.20
11 7 0.11
12 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:56952383 original size:45 final size:45
Alignment explanation
Indices: 56952318--56952411 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
56952308 AAAGATACGG
**
56952318 GCAAACAAACAATCTGGTTTCATAATTAACCTCCAACCTTGTTTT
1 GCAAACAAACAATCCAGTTTCATAATTAACCTCCAACCTTGTTTT
56952363 GCAAACAAACAATCCAGTTTCATAATTAACCTCCAACCTTGTTTT
1 GCAAACAAACAATCCAGTTTCATAATTAACCTCCAACCTTGTTTT
56952408 GCAA
1 GCAA
56952412 GCAACACTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.31
Consensus pattern (45 bp):
GCAAACAAACAATCCAGTTTCATAATTAACCTCCAACCTTGTTTT
Found at i:56952549 original size:32 final size:32
Alignment explanation
Indices: 56952508--56952571 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
56952498 TGAATTCCCT
*
56952508 TTCCTATTTTAGAATTTCTCTACTAAAATTTA
1 TTCCTATTTTAGAATTTCTCCACTAAAATTTA
*
56952540 TTCCTATTTTAGAATTTCTCCACTAACATTTA
1 TTCCTATTTTAGAATTTCTCCACTAAAATTTA
56952572 CTAATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (32 bp):
TTCCTATTTTAGAATTTCTCCACTAAAATTTA
Found at i:56968204 original size:39 final size:39
Alignment explanation
Indices: 56968150--56968227 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
56968140 TATTATACAC
*
56968150 ATTAACTAATTGAACTAATTAGTCTACAATTACGAATAA
1 ATTAACTAATTGAACTAATTAGTCTACAATTAAGAATAA
56968189 ATTAACTAATTGAACTAATTAGTCTACAATTAAGAATAA
1 ATTAACTAATTGAACTAATTAGTCTACAATTAAGAATAA
56968228 GAAATTATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (39 bp):
ATTAACTAATTGAACTAATTAGTCTACAATTAAGAATAA
Found at i:56970391 original size:16 final size:16
Alignment explanation
Indices: 56970362--56970395 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56970352 AAAAATACTA
* *
56970362 TATAACTAATTAAATT
1 TATAAATAAATAAATT
56970378 TATAAATAAATAAATT
1 TATAAATAAATAAATT
56970394 TA
1 TA
56970396 AAAACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAATAAATAAATT
Found at i:56970657 original size:14 final size:13
Alignment explanation
Indices: 56970631--56970664 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56970621 TCATTTTGAT
56970631 TTTCTAAACAAAA
1 TTTCTAAACAAAA
*
56970644 TTTCTGAACAAAA
1 TTTCTAAACAAAA
*
56970657 ATTCTAAA
1 TTTCTAAA
56970665 AAATTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (13 bp):
TTTCTAAACAAAA
Found at i:56972237 original size:20 final size:19
Alignment explanation
Indices: 56972214--56972252 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
56972204 AAATAACTCA
*
56972214 TATTATTTACAATTAAAAAT
1 TATTAATTACAA-TAAAAAT
*
56972234 TATTAATTAGAATAAAAAT
1 TATTAATTACAATAAAAAT
56972253 AATTTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTAATTACAATAAAAAT
Found at i:56972945 original size:16 final size:16
Alignment explanation
Indices: 56972924--56972970 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
56972914 GGTAAGACGA
56972924 AAATTTAAATTTTTTT
1 AAATTTAAATTTTTTT
* ** *
56972940 AAATTTCAATAATGTT
1 AAATTTAAATTTTTTT
56972956 AAATTTAAATTTTTT
1 AAATTTAAATTTTTT
56972971 AATTTGAAAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
AAATTTAAATTTTTTT
Found at i:56974935 original size:27 final size:27
Alignment explanation
Indices: 56974836--56974938 Score: 73
Period size: 27 Copynumber: 3.6 Consensus size: 27
56974826 TATATTTACA
**
56974836 AAATATATAAAAAAA-ATGTAAATATAT
1 AAATATA-AAAAAAATATGTATGTATAT
* *
56974863 AATATATAAATAAACTATGAAGATATGTATAT
1 AA-ATATAAA-AAA-AAT-ATG-TATGTATAT
* *
56974895 ATATGTAAAAAAAATATGTATGTATAT
1 AAATATAAAAAAAATATGTATGTATAT
56974922 AAATATATATAAAAAAT
1 AAATATA-A-AAAAAAT
56974939 GAAATATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
27 18 0.31
28 11 0.19
29 10 0.17
30 3 0.05
31 8 0.14
32 8 0.14
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATATAAAAAAAATATGTATGTATAT
Found at i:56974953 original size:27 final size:27
Alignment explanation
Indices: 56974837--56974956 Score: 100
Period size: 29 Copynumber: 4.3 Consensus size: 27
56974827 ATATTTACAA
*
56974837 AATATATAAAAAAAATGTAA-ATATAT
1 AATATATAAAAAAAATGAAATATATAT
* *
56974863 AATATATAAATAAACTATGAAGATATGTAT
1 AATATATAAA-AAA-AATGAA-ATATATAT
* * *
56974893 ATATATGTAAAAAAAAT-ATGTATGTATAT
1 A-ATATATAAAAAAAATGA--AATATATAT
*
56974922 AAATATATATAAAAAATGAAATATATAT
1 -AATATATAAAAAAAATGAAATATATAT
56974950 AATATAT
1 AATATAT
56974957 GTATATATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
26 10 0.14
27 10 0.14
28 12 0.16
29 22 0.30
30 11 0.15
31 8 0.11
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (27 bp):
AATATATAAAAAAAATGAAATATATAT
Found at i:56975391 original size:3 final size:3
Alignment explanation
Indices: 56975383--56975465 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
56975373 TTTATGGTTG
56975383 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
56975431 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
56975466 TTAAACTTAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56975764 original size:49 final size:48
Alignment explanation
Indices: 56975711--56975809 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 48
56975701 TGAAAAGGAT
56975711 TAAAA-ACA-TAAATAACCCATAAAT-AAAACCCCATTTCATTTGCAGCCAA
1 TAAAACACATTAAA-AACCC-T-AATCAAAACCCCATTTCATTTGCAG-CAA
* **
56975760 TAAAACCCATTTCAAACCCTAATCAAAACCCCATTTCATTTGCAGCAA
1 TAAAACACATTAAAAACCCTAATCAAAACCCCATTTCATTTGCAGCAA
56975808 TA
1 TA
56975810 GCAGCACAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
48 8 0.18
49 27 0.61
50 7 0.16
51 2 0.05
ACGTcount: A:0.44, C:0.27, G:0.04, T:0.24
Consensus pattern (48 bp):
TAAAACACATTAAAAACCCTAATCAAAACCCCATTTCATTTGCAGCAA
Found at i:56976236 original size:21 final size:21
Alignment explanation
Indices: 56976188--56976237 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
56976178 ATGCGCTGAA
*
56976188 GCACGGGGCAACGTGCACGAC
1 GCACGGGGCAACGTGCACAAC
** * *
56976209 GTGCGGGGCGACGTGCGCAAC
1 GCACGGGGCAACGTGCACAAC
56976230 GCACGGGG
1 GCACGGGG
56976238 GGCTGTTGTG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.30, G:0.46, T:0.06
Consensus pattern (21 bp):
GCACGGGGCAACGTGCACAAC
Found at i:56979917 original size:29 final size:30
Alignment explanation
Indices: 56979863--56979928 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
56979853 CTTTCAAAAT
*
56979863 ACCCTAATCCCTAAAAAACCATAAACCCTA
1 ACCCTAATCCCTAAAAAACCAAAAACCCTA
* *
56979893 ACCCTAA-CCCTAATAAAA-TAAAAACTCTA
1 ACCCTAATCCCTAA-AAAACCAAAAACCCTA
56979922 ACCCTAA
1 ACCCTAA
56979929 AAAAAAAGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (30 bp):
ACCCTAATCCCTAAAAAACCAAAAACCCTA
Found at i:56980968 original size:2 final size:2
Alignment explanation
Indices: 56980963--56980998 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56980953 CCTCTCACCG
56980963 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56980999 CAGTCTCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:56987345 original size:44 final size:46
Alignment explanation
Indices: 56987297--56987383 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
56987287 CAACACCTAT
56987297 TCCATTAAACCAAAC-ATAAAAATACT-ATTACAATTTTATTCTAC
1 TCCATTAAACCAAACAATAAAAATACTAATTACAATTTTATTCTAC
* ** *
56987341 TCCATTAAACCAAGCAATTGAATTACTAATTACAATTTTATTC
1 TCCATTAAACCAAACAATAAAAATACTAATTACAATTTTATTC
56987384 CATTCACCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 14 0.38
45 8 0.22
46 15 0.41
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.36
Consensus pattern (46 bp):
TCCATTAAACCAAACAATAAAAATACTAATTACAATTTTATTCTAC
Found at i:56998491 original size:22 final size:24
Alignment explanation
Indices: 56998460--56998510 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
56998450 AATAAATAAC
*
56998460 CCCAAACCCAA-ATCAAA-AC-AG
1 CCCAAACCCAATAACAAACACTAG
56998481 CCCAATACCCAATAACAAACACTAG
1 CCCAA-ACCCAATAACAAACACTAG
56998506 CCCAA
1 CCCAA
56998511 CAACAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 6 0.24
23 5 0.20
24 2 0.08
25 7 0.28
ACGTcount: A:0.49, C:0.39, G:0.04, T:0.08
Consensus pattern (24 bp):
CCCAAACCCAATAACAAACACTAG
Found at i:56999748 original size:3 final size:3
Alignment explanation
Indices: 56999740--56999818 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
56999730 ATGTTCGCTG
* * * * *
56999740 TTA TTA TTA TCA TTC TTA TCT- TCA TTA TTA CTA TT- TCTA TTA TCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA
* * *
56999785 ATA TTA TTA TTA TTA TTA TTA CTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56999819 ATTTTTATAA
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:57000472 original size:20 final size:20
Alignment explanation
Indices: 57000447--57000487 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57000437 AGAAATAAGA
57000447 TGACCAAAATTTTTTAGTTT
1 TGACCAAAATTTTTTAGTTT
57000467 TGACCAAAATTTTTTAGTTT
1 TGACCAAAATTTTTTAGTTT
57000487 T
1 T
57000488 CAAATTAATA
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:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TGACCAAAATTTTTTAGTTT
Found at i:57012303 original size:132 final size:132
Alignment explanation
Indices: 57012064--57012671 Score: 790
Period size: 132 Copynumber: 4.6 Consensus size: 132
57012054 AGATAACAAG
* * * * * *
57012064 TCCTATTTCCCTGAGCAACAGTGGAGTAGGTTGAATATTATAGATCCT-GTCTCTCTAAGCAGTA
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGAT-CTGGTCTCCCTAAGCAGTA
* * *
57012128 GCGGAGCAGATCGAAGAA-GTTGAGTCTTATCTTCCCAAAGTAGTAGGGAAGCAGATTTAAGCCA
65 GCGGAGCAGATCGAA-AATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
57012192 CCAA
129 CCAA
* *
57012196 TCCTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAATGTGGATCTGGTCTCCCTAAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
* *
57012261 CGGAGCAGATCGAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
66 CGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACC
57012326 AA
131 AA
57012328 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
* * * * * *
57012393 CAGAGCAAATCGAACATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAGGCTACT
66 CGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACC
57012458 AA
131 AA
* * * * *
57012460 T-CTCATCTGCCTGAGCACCAGTGGATTAGGTTGAAGAATGTAGATCTTGTCTCCTTAAGCAGTA
1 TCCT-ATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTA
* * ** * *
57012524 GTGGAGTAGATAAAAAAATGGTGAATTTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
65 GCGGAGCAGAT-CGAAAATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
57012589 CCAA
129 CCAA
* * * * ** * *
57012593 TCCTATCTCCCTGAGCAGTAGTAGAGTAGGTTGAAGATTGCAGATCACGTCTCCTTGAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
** *
57012658 TAGAGCGGATCGAA
66 CGGAGCAGATCGAA
57012672 GACAGCAAAT
Statistics
Matches: 419, Mismatches: 52, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
131 6 0.01
132 303 0.72
133 108 0.26
134 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
CGGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACC
AA
Found at i:57012743 original size:51 final size:51
Alignment explanation
Indices: 57012669--57012777 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
57012659 AGAGCGGATC
* * ** **
57012669 GAAGACAGCAAATTTTATTTCCCTGGCGTTGCAGTGGAACGGATTAAAGCT
1 GAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCT
* * *
57012720 GAAGGCAGTAAATCTTATTTCCCTGGCGTTGTAACGGAACAAATTAAAGTT
1 GAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCT
57012771 GAAGGCA
1 GAAGGCA
57012778 ACGAATCTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (51 bp):
GAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCT
Found at i:57012785 original size:51 final size:51
Alignment explanation
Indices: 57012677--57012794 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 51
57012667 TCGAAGACAG
* ** ** *
57012677 CAAATTTTATTTCCCTGGCGTTGCAGTGGAACGGATTAAAGCTGAAGGCAG
1 CAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCTGAAGGCAA
* * *
57012728 TAAATCTTATTTCCCTGGCGTTGTAACGGAACAAATTAAAGTTGAAGGCAA
1 CAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCTGAAGGCAA
* * *
57012779 CGAATCTCATCTCCCT
1 CAAATCTTATTTCCCT
57012795 AACATTTAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (51 bp):
CAAATCTTATTTCCCTGGCGTTGCAACGGAACAAATTAAAGCTGAAGGCAA
Found at i:57014408 original size:3 final size:3
Alignment explanation
Indices: 57014400--57014478 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
57014390 ATGTTCGCTG
* * * * *
57014400 TTA TTA TTA TCA TTC TTA TCT- TCA TTA TTA CTA TT- TCTA TTA TCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA
* * *
57014445 ATA TTA TTA TTA TTA TTA TTA CTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
57014479 ATTTTTATAA
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:57016120 original size:8 final size:8
Alignment explanation
Indices: 57016107--57016531 Score: 473
Period size: 8 Copynumber: 53.6 Consensus size: 8
57016097 CCCTATTTCA
57016107 TATGTATG
1 TATGTATG
57016115 TATGTATG
1 TATGTATG
57016123 TATGTATG
1 TATGTATG
57016131 TATGTATG
1 TATGTATG
57016139 TATGTATG
1 TATGTATG
* *
57016147 TGTGTGTG
1 TATGTATG
*
57016155 TATGTGTG
1 TATGTATG
*
57016163 TATGTGTG
1 TATGTATG
*
57016171 TATGTGTG
1 TATGTATG
*
57016179 TATGTGTG
1 TATGTATG
*
57016187 TATGTGTG
1 TATGTATG
*
57016195 TATGTGTG
1 TATGTATG
*
57016203 TATGTGTG
1 TATGTATG
*
57016211 TATGTGTG
1 TATGTATG
*
57016219 TATGTGTG
1 TATGTATG
*
57016227 TATGTGTG
1 TATGTATG
*
57016235 TATGTGTG
1 TATGTATG
*
57016243 TATGTGTG
1 TATGTATG
*
57016251 TATGTGTG
1 TATGTATG
57016259 TATGTATG
1 TATGTATG
*
57016267 TATGTGTG
1 TATGTATG
57016275 TATGTATG
1 TATGTATG
57016283 TATGTATG
1 TATGTATG
57016291 TATGTATG
1 TATGTATG
** *
57016299 TA-ACATT
1 TATGTATG
*
57016306 TATCTA-G
1 TATGTATG
*
57016313 -ACTGCATG
1 TA-TGTATG
*
57016321 TGTGTATG
1 TATGTATG
*
57016329 TGTGTATG
1 TATGTATG
*
57016337 TGTGTATG
1 TATGTATG
*
57016345 TGTGTATG
1 TATGTATG
*
57016353 TGTGTATG
1 TATGTATG
*
57016361 TGTGTATG
1 TATGTATG
*
57016369 TGTGTATG
1 TATGTATG
*
57016377 TGTGTATG
1 TATGTATG
*
57016385 TGTGTATG
1 TATGTATG
* *
57016393 TGTGTGTG
1 TATGTATG
57016401 TATGTATG
1 TATGTATG
*
57016409 TGTGTATG
1 TATGTATG
57016417 TATGTATG
1 TATGTATG
*
57016425 TGTGTATG
1 TATGTATG
57016433 TATG--TG
1 TATGTATG
*
57016439 TGTGTATG
1 TATGTATG
57016447 TATGTATG
1 TATGTATG
*
57016455 TGTGTATG
1 TATGTATG
57016463 TATGTATG
1 TATGTATG
*
57016471 TGTGTATG
1 TATGTATG
57016479 TATGTATG
1 TATGTATG
57016487 TATGTATG
1 TATGTATG
57016495 TATGTATG
1 TATGTATG
57016503 TATGTATG
1 TATGTATG
57016511 TATGTATG
1 TATGTATG
57016519 TATGTATG
1 TATGTATG
57016527 TATGT
1 TATGT
57016532 TTTGAAGTTA
Statistics
Matches: 382, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
6 6 0.02
7 6 0.02
8 370 0.97
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (8 bp):
TATGTATG
Found at i:57020524 original size:18 final size:19
Alignment explanation
Indices: 57020483--57020524 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
57020473 AAATAAAAAT
57020483 TATATAAAAATATTTTGAA
1 TATATAAAAATATTTTGAA
* * *
57020502 AATAT-AAAATGTTTTTAA
1 TATATAAAAATATTTTGAA
57020520 TATAT
1 TATAT
57020525 GTTATTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATAAAAATATTTTGAA
Found at i:57022380 original size:5 final size:5
Alignment explanation
Indices: 57022370--57022405 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
57022360 TTATTTGTTT
57022370 TAATA TAATA TAATA TAATA TAATA TAATA T-ATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
57022406 CTTAATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:57023539 original size:10 final size:10
Alignment explanation
Indices: 57023504--57023546 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
57023494 CGAGACTAAA
57023504 TAGAAAACATT
1 TAGAAAA-ATT
*
57023515 TAG-AAAGTT
1 TAGAAAAATT
57023524 TAAGAAAAATT
1 T-AGAAAAATT
57023535 TAGAAAAATT
1 TAGAAAAATT
57023545 TA
1 TA
57023547 TACTGCAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 3 0.11
10 16 0.57
11 9 0.32
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (10 bp):
TAGAAAAATT
Found at i:57023546 original size:21 final size:21
Alignment explanation
Indices: 57023505--57023546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57023495 GAGACTAAAT
*
57023505 AGAAAACATTTAGAAAGTTTA
1 AGAAAACATTTAGAAAATTTA
57023526 AGAAAA-ATTTAGAAAAATTTA
1 AGAAAACATTTAG-AAAATTTA
57023547 TACTGCAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (21 bp):
AGAAAACATTTAGAAAATTTA
Found at i:57024929 original size:39 final size:39
Alignment explanation
Indices: 57024826--57024940 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 39
57024816 AAATCAACCG
* **
57024826 AACACACCAGACAGAAGCTCATAAGAGCTTATCCAATTGA
1 AACACACCA-ACAGAAGCTCATAAGAGCTGATCCACCTGA
* * *
57024866 AATACTCCAAACAGAAGCTCATAAGAGCTGGTCCACCTGA
1 AACACACC-AACAGAAGCTCATAAGAGCTGATCCACCTGA
*
57024906 AACACACCAACAGAAGCTCATAAGAGATGATCCAC
1 AACACACCAACAGAAGCTCATAAGAGCTGATCCAC
57024941 TCGGAACACG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 25 0.39
40 38 0.59
41 1 0.02
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.16
Consensus pattern (39 bp):
AACACACCAACAGAAGCTCATAAGAGCTGATCCACCTGA
Found at i:57024949 original size:39 final size:39
Alignment explanation
Indices: 57024826--57024954 Score: 143
Period size: 40 Copynumber: 3.3 Consensus size: 39
57024816 AAATCAACCG
* * *
57024826 AACACACCAGACAGAAGCTCATAAGAGCTTATCCAATTGA
1 AACACACCA-ACAGAAGCTCATAAGAGCTGATCCACTCGA
* * *
57024866 AATACTCCAAACAGAAGCTCATAAGAGCTGGTCCAC-CTGA
1 AACACACC-AACAGAAGCTCATAAGAGCTGATCCACTC-GA
* *
57024906 AACACACCAACAGAAGCTCATAAGAGATGATCCACTCGG
1 AACACACCAACAGAAGCTCATAAGAGCTGATCCACTCGA
*
57024945 AACACGCCAA
1 AACACACCAA
57024955 ATAGAAAGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
39 35 0.47
40 38 0.51
41 1 0.01
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (39 bp):
AACACACCAACAGAAGCTCATAAGAGCTGATCCACTCGA
Found at i:57026410 original size:28 final size:28
Alignment explanation
Indices: 57026379--57026434 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
57026369 TAGGTTGTTG
57026379 TAGGAACTCACTAAGTTTAATTGAACTT
1 TAGGAACTCACTAAGTTTAATTGAACTT
57026407 TAGGAACTCACTAAGTTTAATTGAACTT
1 TAGGAACTCACTAAGTTTAATTGAACTT
57026435 ACTCCATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
TAGGAACTCACTAAGTTTAATTGAACTT
Found at i:57028098 original size:38 final size:38
Alignment explanation
Indices: 57028023--57028099 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
57028013 GACTTAGGTC
**
57028023 ACACGGCCAAGCCAAACGCTTGTGTGCTAGGTTGTGTG
1 ACACGGCCAAGCCAAACGCTTGTGTGCTAGGCCGTGTG
57028061 ACACGGCCAAGCCAAACGCTTGTGTGCTAGGCCGTGTG
1 ACACGGCCAAGCCAAACGCTTGTGTGCTAGGCCGTGTG
57028099 A
1 A
57028100 AAAATGGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.21
Consensus pattern (38 bp):
ACACGGCCAAGCCAAACGCTTGTGTGCTAGGCCGTGTG
Found at i:57028218 original size:66 final size:66
Alignment explanation
Indices: 57028065--57028223 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 66
57028055 TGTGTGACAC
* * *
57028065 GGCCAAGCCAAACGCTTGTGTGCTAGGCCGTGTGAAAAATGGTGAGCATACTGACTTATGACACA
1 GGCCAAGCCAAACGCCTGTGTGCTAGGACGTGTGAAAAATAGTGAGCATACTGACTTATGACACA
57028130 T
66 T
* * * * * * *
57028131 GGCCAAGCCACACG-CTCGTGTGCTAGGATGTGTGAAAAATAGTGGGTATACTGACTTGTGTCGC
1 GGCCAAGCCAAACGCCT-GTGTGCTAGGACGTGTGAAAAATAGTGAGCATACTGACTTATGACAC
57028195 ACT
65 A-T
* *
57028198 -GCCAAGTCAAATGCCTGTGTGCTAGG
1 GGCCAAGCCAAACGCCTGTGTGCTAGG
57028224 CCATTTGAGG
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
65 1 0.01
66 73 0.95
67 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (66 bp):
GGCCAAGCCAAACGCCTGTGTGCTAGGACGTGTGAAAAATAGTGAGCATACTGACTTATGACACA
T
Found at i:57028321 original size:30 final size:30
Alignment explanation
Indices: 57028287--57028352 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
57028277 TGTCACCTGG
* * *
57028287 CCGTGTGTCACATACCGCTGAGACACATGC
1 CCGTGTGTCACACACCGATGACACACATGC
*
57028317 CCGTGTGTCACACACGGATGACACACATGC
1 CCGTGTGTCACACACCGATGACACACATGC
57028347 CCGTGT
1 CCGTGT
57028353 CTCTGCCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (30 bp):
CCGTGTGTCACACACCGATGACACACATGC
Found at i:57029105 original size:22 final size:22
Alignment explanation
Indices: 57029054--57029096 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
57029044 TTTATTGTTC
57029054 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
57029076 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
57029097 TAGCCATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:57037573 original size:26 final size:25
Alignment explanation
Indices: 57037505--57037579 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 25
57037495 CTCAAAAGAT
*
57037505 AAAAGCTTGATTAAAAACTTGATG-
1 AAAAACTTGATTAAAAACTTGATGA
*
57037529 -AAAACTTGCTTAAAAACTTGATGA
1 AAAAACTTGATTAAAAACTTGATGA
* *
57037553 AAAACACTTGATGAAAGACTTGATGA
1 AAAA-ACTTGATTAAAAACTTGATGA
57037579 A
1 A
57037580 TAAATGAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 21 0.49
25 3 0.07
26 19 0.44
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (25 bp):
AAAAACTTGATTAAAAACTTGATGA
Found at i:57037577 original size:12 final size:12
Alignment explanation
Indices: 57037505--57037579 Score: 80
Period size: 12 Copynumber: 6.2 Consensus size: 12
57037495 CTCAAAAGAT
* *
57037505 AAAAGCTTGATT
1 AAAAACTTGATG
57037517 AAAAACTTGATG
1 AAAAACTTGATG
* *
57037529 -AAAACTTGCTT
1 AAAAACTTGATG
57037540 AAAAACTTGATG
1 AAAAACTTGATG
57037552 AAAAACACTTGATG
1 -AAAA-ACTTGATG
*
57037566 AAAGACTTGATG
1 AAAAACTTGATG
57037578 AA
1 AA
57037580 TAAATGAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
11 9 0.17
12 29 0.55
13 7 0.13
14 8 0.15
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (12 bp):
AAAAACTTGATG
Found at i:57041585 original size:19 final size:19
Alignment explanation
Indices: 57041561--57041659 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 19
57041551 AATCTTCAAG
57041561 GATATGAAATCTTAGATAT
1 GATATGAAATCTTAGATAT
* *
57041580 GATATGTAATCTTAGATGT
1 GATATGAAATCTTAGATAT
*
57041599 GATATGCAATCTTAGATAT
1 GATATGAAATCTTAGATAT
*
57041618 GATATGTAATCTTAGATAT
1 GATATGAAATCTTAGATAT
*
57041637 GATATGCAAT-TTAGA-A-
1 GATATGAAATCTTAGATAT
57041653 GATATGA
1 GATATGA
57041660 TTTTGTAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.08
17 1 0.01
18 5 0.07
19 61 0.84
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGAAATCTTAGATAT
Done.