Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 132 of 253
Found at i:41996965 original size:11 final size:11
Alignment explanation
Indices: 41996949--41996973 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41996939 TTTTTAACAT
41996949 AAAAAAAAGAA
1 AAAAAAAAGAA
41996960 AAAAAAAAGAA
1 AAAAAAAAGAA
41996971 AAA
1 AAA
41996974 CTTACCTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:41997808 original size:14 final size:14
Alignment explanation
Indices: 41997789--41997817 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41997779 TACTTTTCGT
41997789 ACCTTGTGTTTGGA
1 ACCTTGTGTTTGGA
41997803 ACCTTGTGTTTGGA
1 ACCTTGTGTTTGGA
41997817 A
1 A
41997818 AGGGTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (14 bp):
ACCTTGTGTTTGGA
Found at i:42001213 original size:29 final size:29
Alignment explanation
Indices: 42001174--42001252 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
42001164 CTTAATAATC
*
42001174 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
42001204 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
42001233 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42001253 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:42004429 original size:27 final size:27
Alignment explanation
Indices: 42004398--42004565 Score: 221
Period size: 27 Copynumber: 6.2 Consensus size: 27
42004388 TAGTTTACAA
42004398 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
42004425 AATTACTCAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
42004452 AAATACCGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* * *
42004479 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
42004506 AATTACTAAAATA-CCTATGTAGGGTAG
1 AATTACTGAAATACCCT-TGTAGGGTAG
* * *
42004533 AATTACTGAGATACCCTTGTAGGGAAA
1 AATTACTGAAATACCCTTGTAGGGTAG
42004560 AATTAC
1 AATTAC
42004566 CATTTTACCC
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.02
27 119 0.96
28 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGTAGGGTAG
Found at i:42004915 original size:31 final size:32
Alignment explanation
Indices: 42004877--42004938 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
42004867 CTCGCTGCAA
*
42004877 TCTGGTGGCCTCGCCAC-ATATATATATCTGT
1 TCTGGTGGCCTAGCCACAATATATATATCTGT
*
42004908 TCTGGTGGCCTAGCCACAATATCTATATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
42004939 GTGACTTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:42005087 original size:6 final size:6
Alignment explanation
Indices: 42005078--42005165 Score: 83
Period size: 6 Copynumber: 14.3 Consensus size: 6
42005068 TTGCATTCAC
* *
42005078 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ACTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
42005127 -TCACCTG ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
42005166 AATGTTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
5 3 0.04
6 56 0.82
7 7 0.10
8 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
ATTCTG
Found at i:42005109 original size:25 final size:25
Alignment explanation
Indices: 42005081--42005151 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
42005071 CATTCACATT
42005081 CTGATTCTGATTCTGTTAC-CTGAT-A-
1 CTGATTCTGATTCTG--ACTCTG-TCAC
42005106 CTGATTCTGATTCTGACTCTGTCAC
1 CTGATTCTGATTCTGACTCTGTCAC
*
42005131 CTGATTCTGATTCTGATTCTG
1 CTGATTCTGATTCTGACTCTG
42005152 ATTCTAGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 3 0.07
24 4 0.10
25 35 0.83
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (25 bp):
CTGATTCTGATTCTGACTCTGTCAC
Found at i:42005113 original size:31 final size:31
Alignment explanation
Indices: 42005078--42005181 Score: 131
Period size: 31 Copynumber: 3.4 Consensus size: 31
42005068 TTGCATTCAC
42005078 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * *
42005109 ATTCTGATTCTGACTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
42005140 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
42005170 TTTCTTATTCTG
1 ATTCTGATTCTG
42005182 TAATGGGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
30 17 0.27
31 44 0.70
32 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.47
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:42007209 original size:27 final size:27
Alignment explanation
Indices: 42007116--42007201 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
42007106 TAGTTTACAA
*
42007116 AATTACTGAAATA-CCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
42007142 AAATACTGAAATACCCCTATAGGGAAG
1 AATTACTGAAATACCCCTGTAGGGTAG
42007169 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
42007196 AATTAC
1 AATTAC
42007202 CAAGATACGC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
26 12 0.23
27 40 0.77
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:42007221 original size:54 final size:53
Alignment explanation
Indices: 42007114--42007228 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 53
42007104 TTTAGTTTAC
* *
42007114 AAAATTACTGAAATACCTTGTAGGGTAGAAATACTGAAATACCCCTATAGGGA
1 AAAATTACTGAAATACCCTGTAGGGTAGAAATACTCAAATACCCCTATAGGGA
* * * * * *
42007167 AGAATTACTGAAATACCCCTGTAGGGTAGAATTAC-CAAGATACGCTTGTGGGGA
1 AAAATTACTGAAATA-CCCTGTAGGGTAGAAATACTCAA-ATACCCCTATAGGGA
42007221 AAAATTAC
1 AAAATTAC
42007229 CATTTTACCC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
53 16 0.31
54 35 0.69
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (53 bp):
AAAATTACTGAAATACCCTGTAGGGTAGAAATACTCAAATACCCCTATAGGGA
Found at i:42007578 original size:31 final size:32
Alignment explanation
Indices: 42007540--42007601 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
42007530 CTCACTGCAA
* *
42007540 TCTGGTGGCCTCGCCAC-ATATATATATCTGT
1 TCTGGTGGCCTAGCAACAATATATATATCTGT
*
42007571 TCTGGTGGCCTAGCAACAATATCTATATCTG
1 TCTGGTGGCCTAGCAACAATATATATATCTG
42007602 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (32 bp):
TCTGGTGGCCTAGCAACAATATATATATCTGT
Found at i:42010644 original size:40 final size:38
Alignment explanation
Indices: 42010600--42010760 Score: 191
Period size: 38 Copynumber: 4.2 Consensus size: 38
42010590 GAATCCAGCC
* * *
42010600 ACCAGCACAAAACTTGTCGGACTTTAAGCTCGGATATAAT
1 ACCAGCACAAAGCCTGTCGGA-TTTAA-CCCGGATATAAT
* *
42010640 ACCAGCACTAAGCCTGTGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGTCGGATTTAACCCGGATATAAT
* *
42010678 ACCAGCACGAAGCCTG-CGGGATTTAACCCGGATATATT
1 ACCAGCACAAAGCCTGTC-GGATTTAACCCGGATATAAT
*
42010716 ACCAGCACAAAGCCTG-CGGGATTCAACCCGGATATAAT
1 ACCAGCACAAAGCCTGTC-GGATTTAACCCGGATATAAT
*
42010754 TCCAGCA
1 ACCAGCA
42010761 TATAGCTTGC
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
38 86 0.80
39 5 0.05
40 17 0.16
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
ACCAGCACAAAGCCTGTCGGATTTAACCCGGATATAAT
Found at i:42010675 original size:38 final size:38
Alignment explanation
Indices: 42010630--42010789 Score: 212
Period size: 38 Copynumber: 4.2 Consensus size: 38
42010620 ACTTTAAGCT
* *
42010630 CGGATATAATACCAGCACTAAGCCTGTGGGATTTAACC
1 CGGATATAATACCAGCACAAAGCCTGCGGGATTTAACC
*
42010668 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
1 CGGATATAATACCAGCACAAAGCCTGCGGGATTTAACC
* *
42010706 CGGATATATTACCAGCACAAAGCCTGCGGGATTCAACC
1 CGGATATAATACCAGCACAAAGCCTGCGGGATTTAACC
* * * * *
42010744 CGGATATAATTCCAGCATATAGCTTGCGGGTCTTTAAGCC
1 CGGATATAATACCAGCACAAAGCCTGCGGG-ATTTAA-CC
42010784 CGGATA
1 CGGATA
42010790 CACATAAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
38 96 0.89
39 4 0.04
40 8 0.07
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (38 bp):
CGGATATAATACCAGCACAAAGCCTGCGGGATTTAACC
Found at i:42015583 original size:24 final size:23
Alignment explanation
Indices: 42015538--42015583 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
42015528 AGAACTTTTA
** *
42015538 ATCAGGAAGCTCATGAATAGCCT
1 ATCAGGAAGCTCACAAAGAGCCT
42015561 ATCAGGAATGCTCACAAAGAGCC
1 ATCAGGAA-GCTCACAAAGAGCC
42015584 ATGTAACAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAGAGCCT
Found at i:42016738 original size:27 final size:27
Alignment explanation
Indices: 42016700--42016753 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
42016690 AAAGAGTACG
*
42016700 ACAAATGAAGGGTATGCCTTAAAGTTT
1 ACAAATGAAGGGTATGCCTCAAAGTTT
42016727 ACAAATGAAGGGTATGCCTCAAAGTTT
1 ACAAATGAAGGGTATGCCTCAAAGTTT
42016754 TGGCTGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (27 bp):
ACAAATGAAGGGTATGCCTCAAAGTTT
Found at i:42020952 original size:20 final size:20
Alignment explanation
Indices: 42020927--42020965 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42020917 TTTATCCATA
* *
42020927 AAATTTTAGAATTTTTCATC
1 AAATTTTACAAATTTTCATC
42020947 AAATTTTACAAATTTTCAT
1 AAATTTTACAAATTTTCAT
42020966 TTTAGTCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATTTTACAAATTTTCATC
Found at i:42031706 original size:34 final size:34
Alignment explanation
Indices: 42031661--42031738 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
42031651 TGAACAGTCT
* * *
42031661 GGGCCTAAGCCC-ATATCAGTAGC-GATATTAGTGC
1 GGGCCTTAGCCCAATA-CAGTAGCAG-TATCAATGC
42031695 GGGCCTTAGCCCAATACAGTAGCAGTATCAATGC
1 GGGCCTTAGCCCAATACAGTAGCAGTATCAATGC
42031729 GGGCCTTAGC
1 GGGCCTTAGC
42031739 TTACTTCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (34 bp):
GGGCCTTAGCCCAATACAGTAGCAGTATCAATGC
Found at i:42041936 original size:21 final size:21
Alignment explanation
Indices: 42041912--42041951 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42041902 TAATGCCTCC
42041912 ATGCATTATCTTAAT-TTTTAT
1 ATGCA-TATCTTAATCTTTTAT
*
42041933 ATGCATCTCTTAATCTTTT
1 ATGCATATCTTAATCTTTT
42041952 CATACCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (21 bp):
ATGCATATCTTAATCTTTTAT
Found at i:42053790 original size:30 final size:31
Alignment explanation
Indices: 42053738--42053795 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
42053728 CATCCATGGG
*
42053738 AAATAAAATAAAGAAAAGGATGA-AATTGGA
1 AAATAAAAAAAAGAAAAGGATGATAATTGGA
*
42053768 AAATGAAAAAAAATAAAA-GATGATAATT
1 AAAT-AAAAAAAAGAAAAGGATGATAATT
42053796 AATTAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (31 bp):
AAATAAAAAAAAGAAAAGGATGATAATTGGA
Found at i:42054087 original size:46 final size:46
Alignment explanation
Indices: 42054020--42054113 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
42054010 TTTGCCATGG
42054020 ATGAGTATGCTGAAATTTTGAAATTTATGGCAGAAAATGAAAGGTT
1 ATGAGTATGCTGAAATTTTGAAATTTATGGCAGAAAATGAAAGGTT
* *
42054066 ATGAGTATGTTGAAATTTTGAAATTTATGGTAGAAAATGAAAGGTT
1 ATGAGTATGCTGAAATTTTGAAATTTATGGCAGAAAATGAAAGGTT
42054112 AT
1 AT
42054114 TGATAGATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (46 bp):
ATGAGTATGCTGAAATTTTGAAATTTATGGCAGAAAATGAAAGGTT
Found at i:42063250 original size:29 final size:28
Alignment explanation
Indices: 42063185--42063324 Score: 124
Period size: 29 Copynumber: 4.9 Consensus size: 28
42063175 TACATACCAG
*
42063185 CATATGGGCCA-CTAGGCCCAATCTCA-TT
1 CATATGGCCCATC-AGGCCCAAT-TCACTT
* *
42063213 TATATGGCCCATCCGGCCCAATTCACGTT
1 CATATGGCCCATCAGGCCCAATTCAC-TT
*
42063242 CATATGGCCCATTAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAATTCAC-TT
* * *
42063271 CAAATGGCCCATTAGACCCAATCTCA-TT
1 CATATGGCCCATCAGGCCCAAT-TCACTT
* * *
42063299 TATATGGCCCATCTGGCCCAAATCAC
1 CATATGGCCCATCAGGCCCAATTCAC
42063325 ATTATATTCA
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
27 6 0.07
28 35 0.38
29 48 0.52
30 3 0.03
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATCAGGCCCAATTCACTT
Found at i:42063304 original size:57 final size:56
Alignment explanation
Indices: 42063185--42063327 Score: 146
Period size: 57 Copynumber: 2.5 Consensus size: 56
42063175 TACATACCAG
* * * * * * *
42063185 CATATGGGCCACTAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTCACGTT
1 CATATGGCCCATTAGGCCCAATCACATTCAAATGGCCCATCAGACCCAATTCAC-TT
*
42063242 CATATGGCCCATTAGGCCCAATTCACATTCAAATGGCCCATTAGACCCAATCTCA-TT
1 CATATGGCCCATTAGGCCCAA-TCACATTCAAATGGCCCATCAGACCCAAT-TCACTT
*
42063299 TATATGGCCCATCT-GGCCCAAATCACATT
1 CATATGGCCCAT-TAGGCCC-AATCACATT
42063328 ATATTCATGC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
57 44 0.60
58 26 0.36
59 3 0.04
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (56 bp):
CATATGGCCCATTAGGCCCAATCACATTCAAATGGCCCATCAGACCCAATTCACTT
Found at i:42072844 original size:16 final size:16
Alignment explanation
Indices: 42072810--42072844 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42072800 GTAGCCAAAC
*
42072810 TTTTGACTTTTCGGTA
1 TTTTGACTTTTCGGCA
*
42072826 TTTTGACTTTTTGGCA
1 TTTTGACTTTTCGGCA
42072842 TTT
1 TTT
42072845 CGGCTTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (16 bp):
TTTTGACTTTTCGGCA
Found at i:42073345 original size:24 final size:24
Alignment explanation
Indices: 42073318--42073366 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42073308 AAAGAGATAA
42073318 GGTACTTACACCAAAAGAGCAATC
1 GGTACTTACACCAAAAGAGCAATC
42073342 GGTACTTACACCAAAAGAGCAATC
1 GGTACTTACACCAAAAGAGCAATC
42073366 G
1 G
42073367 ACCTAAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (24 bp):
GGTACTTACACCAAAAGAGCAATC
Found at i:42074222 original size:18 final size:18
Alignment explanation
Indices: 42074199--42074235 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42074189 GGTAAGTTGG
42074199 TGTAACTCGAATGTAAAC
1 TGTAACTCGAATGTAAAC
42074217 TGTAACTCGAATGTAAAC
1 TGTAACTCGAATGTAAAC
42074235 T
1 T
42074236 ATCTTTAAAT
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:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (18 bp):
TGTAACTCGAATGTAAAC
Found at i:42081272 original size:28 final size:28
Alignment explanation
Indices: 42081232--42081302 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
42081222 TATAGTAAGT
*
42081232 TCGCACACTTAGTGCT-TAATAATCAAAC
1 TCGCACACTTAGTGCTAT-ACAATCAAAC
* *
42081260 TCGCATACTTAGTGCTATACAATTAAAC
1 TCGCACACTTAGTGCTATACAATCAAAC
*
42081288 TCGCACACTCAGTGC
1 TCGCACACTTAGTGC
42081303 CAATCTCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
TCGCACACTTAGTGCTATACAATCAAAC
Found at i:42087215 original size:40 final size:40
Alignment explanation
Indices: 42087130--42087355 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
42087120 TTTGAATGAT
* * * *
42087130 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
42087170 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* *
42087210 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
42087249 ATCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
42087289 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
42087330 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
42087356 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:42103797 original size:40 final size:40
Alignment explanation
Indices: 42103739--42103931 Score: 291
Period size: 40 Copynumber: 4.8 Consensus size: 40
42103729 TTATTTGATG
* *
42103739 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAAGCTTCGTGC
*
42103779 TGGAATTGTATCCAGGCTTAAAGACCCGCAAGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAAGCTTCGTGC
*
42103819 TGGAATTGTATCTGGGCTTAAAGACCCGCAAGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAAGCTTCGTGC
*
42103859 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAAGCTTCGTGC
* * *
42103899 TGGAA-TGACATCCGGG-TTAAAAACCTGCAAGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAAGCT
42103932 GTGCTAAATA
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.11
40 125 0.89
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAAGCTTCGTGC
Found at i:42106395 original size:28 final size:28
Alignment explanation
Indices: 42106355--42106425 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
42106345 TATAGTAAGT
*
42106355 TCGCACACTTAGTGCT-TAATAATCAAAC
1 TCGCACACTTAGTGCTAT-ACAATCAAAC
*
42106383 TCGCACACTTAGTGCTATACAATTAAAC
1 TCGCACACTTAGTGCTATACAATCAAAC
*
42106411 TCGTACACTTAGTGC
1 TCGCACACTTAGTGC
42106426 CAATCTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (28 bp):
TCGCACACTTAGTGCTATACAATCAAAC
Found at i:42132377 original size:22 final size:21
Alignment explanation
Indices: 42132332--42132385 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
42132322 CTATAGGCCT
42132332 TAAAT-CTCAAACCTTAAACTA
1 TAAATCCT-AAACCTTAAACTA
42132353 TAAATCCTAAACTCTTAAA-TCA
1 TAAATCCTAAAC-CTTAAACT-A
*
42132375 TAAACCCTAAA
1 TAAATCCTAAA
42132386 GTCGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAATCCTAAACCTTAAACTA
Found at i:42132393 original size:22 final size:22
Alignment explanation
Indices: 42132352--42132393 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42132342 ACCTTAAACT
* *
42132352 ATAAATCCTAAACTCTTAAATC
1 ATAAACCCTAAACTCGTAAATC
*
42132374 ATAAACCCTAAAGTCGTAAA
1 ATAAACCCTAAACTCGTAAA
42132394 AATAAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
ATAAACCCTAAACTCGTAAATC
Found at i:42134516 original size:24 final size:24
Alignment explanation
Indices: 42134484--42134547 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 24
42134474 AGTACCCCTA
*
42134484 GCAAAATTACCTACCCCTGTGTAT
1 GCAAAATTACCTACCCCTATGTAT
42134508 GCAAAATTACCATTATACCCCTATGTAT
1 GCAAAATTACC----TACCCCTATGTAT
*
42134536 GCAAAATGACCT
1 GCAAAATTACCT
42134548 CTATACCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 12 0.35
28 22 0.65
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (24 bp):
GCAAAATTACCTACCCCTATGTAT
Found at i:42134535 original size:28 final size:28
Alignment explanation
Indices: 42134495--42134558 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
42134485 CAAAATTACC
* *
42134495 TACCCCTGTGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
42134523 TACCCCTATGTATGCAAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
42134551 TACCCCTA
1 TACCCCTA
42134559 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:42134705 original size:28 final size:29
Alignment explanation
Indices: 42134664--42134726 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
42134654 AAGAAGCGTC
* *
42134664 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCCATGCCACAAAATATCTGTAT
*
42134692 CTGGTGGCCCTGCCACAAAATATCTGTAT
1 CTGGTGGCCATGCCACAAAATATCTGTAT
42134721 CTGGTG
1 CTGGTG
42134727 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCCATGCCACAAAATATCTGTAT
Found at i:42134737 original size:29 final size:28
Alignment explanation
Indices: 42134674--42134737 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
42134664 CTGGTGGCTA
* *
42134674 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACCC
*
42134702 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACCC
*
42134731 TGTCACA
1 TGCCACA
42134738 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACCC
Found at i:42142385 original size:27 final size:28
Alignment explanation
Indices: 42142346--42142433 Score: 123
Period size: 27 Copynumber: 3.3 Consensus size: 28
42142336 TGTACTAGAG
42142346 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
42142374 TA-CCCTATGTATG--AAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
*
42142399 TACCCCTATGTATGC-AAATGACC-TCTA
1 TACCCCTATGTATGCAAAATTACCAT-TA
42142426 TACCCCTA
1 TACCCCTA
42142434 GGGTTAATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
25 14 0.25
26 12 0.21
27 28 0.50
28 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATTACCATTA
Found at i:42142597 original size:27 final size:27
Alignment explanation
Indices: 42142539--42142628 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
42142529 AGGAAGCGTC
42142539 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
42142567 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
42142594 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
42142623 CTGGTG
1 CTGGTG
42142629 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:42143728 original size:7 final size:7
Alignment explanation
Indices: 42143698--42143810 Score: 54
Period size: 7 Copynumber: 16.0 Consensus size: 7
42143688 TAGTTTATAA
42143698 GGTTTAG
1 GGTTTAG
42143705 GGTATT-G
1 GGT-TTAG
42143712 GGTATT-G
1 GGT-TTAG
42143719 GGTTTAG
1 GGTTTAG
42143726 GGTTTAG
1 GGTTTAG
** *
42143733 TCTATAG
1 GGTTTAG
*
42143740 TGTTTAG
1 GGTTTAG
42143747 GGTTTAG
1 GGTTTAG
42143754 GGTATT-G
1 GGT-TTAG
* *
42143761 TGTATT-T
1 GGT-TTAG
42143768 GGTTTAG
1 GGTTTAG
42143775 GGTTTAG
1 GGTTTAG
** **
42143782 TCTACAG
1 GGTTTAG
42143789 GGTTTAG
1 GGTTTAG
*
42143796 GGTATTGG
1 GGT-TTAG
42143804 GGTTTAG
1 GGTTTAG
42143811 TGTATTGGTT
Statistics
Matches: 81, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
6 4 0.05
7 67 0.83
8 10 0.12
ACGTcount: A:0.16, C:0.03, G:0.37, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:42143729 original size:28 final size:27
Alignment explanation
Indices: 42143698--42143781 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 27
42143688 TAGTTTATAA
42143698 GGTTTAGGGTATTGGGTATTGGGTTTAG
1 GGTTTAGGGTATT-GGTATTGGGTTTAG
* * *
42143726 GGTTTA--G---T-CTATAGTGTTTAG
1 GGTTTAGGGTATTGGTATTGGGTTTAG
*
42143747 GGTTTAGGGTATTGTGTATTTGGTTTAG
1 GGTTTAGGGTATTG-GTATTGGGTTTAG
42143775 GGTTTAG
1 GGTTTAG
42143782 TCTACAGGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
21 16 0.38
23 2 0.05
26 2 0.05
28 22 0.52
ACGTcount: A:0.15, C:0.01, G:0.37, T:0.46
Consensus pattern (27 bp):
GGTTTAGGGTATTGGTATTGGGTTTAG
Found at i:42143729 original size:49 final size:49
Alignment explanation
Indices: 42143676--42143781 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 49
42143666 TTAAGGTATT
*
42143676 GGGTTTAGAATTTAGT-TTATAAGGTTTAGGGTATTGGGTATTGGGTTTA
1 GGGTTTAGAATATAGTGTT-TAAGGTTTAGGGTATTGGGTATTGGGTTTA
** * * *
42143725 GGGTTTAGTCTATAGTGTTTAGGGTTTAGGGTATTGTGTATTTGGTTTA
1 GGGTTTAGAATATAGTGTTTAAGGTTTAGGGTATTGGGTATTGGGTTTA
42143774 GGGTTTAG
1 GGGTTTAG
42143782 TCTACAGGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 48 0.96
50 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (49 bp):
GGGTTTAGAATATAGTGTTTAAGGTTTAGGGTATTGGGTATTGGGTTTA
Found at i:42143763 original size:21 final size:21
Alignment explanation
Indices: 42143699--42143802 Score: 88
Period size: 21 Copynumber: 5.0 Consensus size: 21
42143689 AGTTTATAAG
*
42143699 GTTTAGGGTATT-GGGTATTGG
1 GTTTAGGGT-TTAGGGTATTGT
** *
42143720 GTTTAGGGTTTAGTCTATAGT
1 GTTTAGGGTTTAGGGTATTGT
42143741 GTTTAGGGTTTAGGGTATTGT
1 GTTTAGGGTTTAGGGTATTGT
*
42143762 GTATT-TGGTTTAGGGT-TTAGT
1 GT-TTAGGGTTTAGGGTATT-GT
* **
42143783 CTACAGGGTTTAGGGTATTG
1 GTTTAGGGTTTAGGGTATTG
42143803 GGGTTTAGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.06
21 58 0.88
22 4 0.06
ACGTcount: A:0.16, C:0.03, G:0.36, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTATTGT
Found at i:42143772 original size:42 final size:42
Alignment explanation
Indices: 42143663--42143810 Score: 131
Period size: 42 Copynumber: 3.5 Consensus size: 42
42143653 TTAAGTTCAA
* ** *
42143663 GGTTTAAGGTATTGGGTTTAGAATTTAGTTTATAAG-GTTTAG
1 GGTTTAGGGTATTGGGTTTAGGGTTTAGTCTAT-AGTGTTTAG
42143705 GGTATT-GGGTATTGGGTTTAGGGTTTAGTCTATAGTGTTTAG
1 GGT-TTAGGGTATTGGGTTTAGGGTTTAGTCTATAGTGTTTAG
* * ** * * **
42143747 GGTTTAGGGTATTGTGTATT-TGGTTTAGGGTTTAGTCTACAG
1 GGTTTAGGGTATTGGGT-TTAGGGTTTAGTCTATAGTGTTTAG
42143789 GGTTTAGGGTATTGGGGTTTAG
1 GGTTTAGGGTATT-GGGTTTAG
42143811 TGTATTGGTT
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
41 4 0.05
42 75 0.87
43 7 0.08
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (42 bp):
GGTTTAGGGTATTGGGTTTAGGGTTTAGTCTATAGTGTTTAG
Found at i:42143782 original size:49 final size:49
Alignment explanation
Indices: 42143698--42143821 Score: 171
Period size: 49 Copynumber: 2.5 Consensus size: 49
42143688 TAGTTTATAA
* * * *
42143698 GGTTTAGGGTATTGGGTATTGGGTTTAGGGTTTAGTCTATAGTGTTTAG
1 GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTACAGGGTTTAG
42143747 GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTACAGGGTTTAG
1 GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTACAGGGTTTAG
*
42143796 GGTATTGGGGT-TTAGTGTA-TTGGTTT
1 GGT-TTAGGGTATT-GTGTATTTGGTTT
42143822 TGGGATTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
49 57 0.84
50 11 0.16
ACGTcount: A:0.15, C:0.02, G:0.36, T:0.46
Consensus pattern (49 bp):
GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTACAGGGTTTAG
Found at i:42143808 original size:15 final size:15
Alignment explanation
Indices: 42143788--42143818 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42143778 TTAGTCTACA
42143788 GGGTTTAGGGTATTG
1 GGGTTTAGGGTATTG
*
42143803 GGGTTTAGTGTATTG
1 GGGTTTAGGGTATTG
42143818 G
1 G
42143819 TTTTGGGATT
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:0.13, C:0.00, G:0.45, T:0.42
Consensus pattern (15 bp):
GGGTTTAGGGTATTG
Found at i:42144342 original size:84 final size:84
Alignment explanation
Indices: 42144150--42144331 Score: 303
Period size: 84 Copynumber: 2.2 Consensus size: 84
42144140 GGTAGTGGAT
* * **
42144150 TTAGTGGCGCTATCTTATAAACGCCACTAATAATATGAAAAATTGAATGAAAACTACGTCGTTTT
1 TTAGTGGCGCTATCTTATAAATGCCACTAAGAATATGAAAAACCGAATGAAAACTACGTCGTTTT
42144215 ATGTGGCGCGGTTTAGGAA
66 ATGTGGCGCGGTTTAGGAA
*
42144234 TTAGTGGCGCTATCTTATAAATGCCACTAAGAATATGAGAAACCGAATGAAAACTACGTCGTTTT
1 TTAGTGGCGCTATCTTATAAATGCCACTAAGAATATGAAAAACCGAATGAAAACTACGTCGTTTT
42144299 ATGTGGCAG-GGTTTAGGAA
66 ATGTGGC-GCGGTTTAGGAA
42144318 TTAGTGGCGCTATC
1 TTAGTGGCGCTATC
42144332 CTGAAAATGC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
84 91 0.99
85 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (84 bp):
TTAGTGGCGCTATCTTATAAATGCCACTAAGAATATGAAAAACCGAATGAAAACTACGTCGTTTT
ATGTGGCGCGGTTTAGGAA
Found at i:42144732 original size:16 final size:16
Alignment explanation
Indices: 42144707--42144739 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42144697 GGAATGCAGA
42144707 TTTCTATTGTTAATGC
1 TTTCTATTGTTAATGC
*
42144723 TTTCTGTTGTTAATGC
1 TTTCTATTGTTAATGC
42144739 T
1 T
42144740 CAGCACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (16 bp):
TTTCTATTGTTAATGC
Found at i:42147679 original size:9 final size:9
Alignment explanation
Indices: 42147667--42147748 Score: 69
Period size: 9 Copynumber: 9.1 Consensus size: 9
42147657 TATATCATAT
*
42147667 CATAAGTTA
1 CATAACTTA
42147676 CATAACTTA
1 CATAACTTA
*
42147685 CATACCTTA
1 CATAACTTA
*
42147694 CATAAATGTA
1 CATAACT-TA
* * *
42147704 TATCA-TAA
1 CATAACTTA
42147712 CATAACTTA
1 CATAACTTA
42147721 CATAACTTA
1 CATAACTTA
42147730 CA-AAGCTTA
1 CATAA-CTTA
*
42147739 CTTAACTTA
1 CATAACTTA
42147748 C
1 C
42147749 GTAATACATA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
8 6 0.10
9 45 0.78
10 7 0.12
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:42147739 original size:45 final size:45
Alignment explanation
Indices: 42147647--42147739 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
42147637 ACCCACATAA
* * *
42147647 TACATAAATATATATCATATCATAAGTTACATAACTTACATACCT
1 TACATAAATATATATCATAACATAACTTACATAACTTACAAACCT
* *
42147692 TACATAAATGTATATCATAACATAACTTACATAACTTACAAAGCT
1 TACATAAATATATATCATAACATAACTTACATAACTTACAAACCT
42147737 TAC
1 TAC
42147740 TTAACTTACG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (45 bp):
TACATAAATATATATCATAACATAACTTACATAACTTACAAACCT
Found at i:42152861 original size:13 final size:14
Alignment explanation
Indices: 42152845--42152873 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42152835 TTCTAAATAT
42152845 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
42152858 TTATAATTGTTTAA
1 TTATAATTGTTTAA
42152872 TT
1 TT
42152874 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:42153828 original size:43 final size:43
Alignment explanation
Indices: 42153729--42153853 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 43
42153719 TTTGTGGGAA
* * ***
42153729 AAACGCCGCTAAAAGTTATGGCTTTTAGCGGCGCTTTCCCAAC
1 AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCACTTTTTTAAC
* * * **
42153772 AAATGCCGTTAAAAGCCATGGCTTTTAGCGGCACTTTTTTTTC
1 AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCACTTTTTTAAC
* * *
42153815 GAACGCCGCTAAAAGTCATGACTTTTAGTGGCA-TTTTTT
1 AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCACTTTTTT
42153854 GCGGCGTTTA
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 6 0.09
43 60 0.91
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCACTTTTTTAAC
Found at i:42156551 original size:16 final size:17
Alignment explanation
Indices: 42156510--42156554 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
42156500 CATGACTATA
*
42156510 AAACCAAAA-TGAGCAT
1 AAACCAAAATTTAGCAT
*
42156526 AAACC-GAATTTAGCAT
1 AAACCAAAATTTAGCAT
42156542 -AACCAAAATTTAG
1 AAACCAAAATTTAG
42156555 AAATATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (17 bp):
AAACCAAAATTTAGCAT
Found at i:42157418 original size:43 final size:43
Alignment explanation
Indices: 42157353--42157436 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
42157343 AAATCGTACA
* *
42157353 ATGCCAACGTCCCAGACGTGGTCTTACAT-GTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTAC-TCGTAAACACATATCG
42157396 ATGCC-ACTGTCCCAGACATGGTCTTACTCGTAAACACATAT
1 ATGCCAAC-GTCCCAGACATGGTCTTACTCGTAAACACATAT
42157437 TAGAATCACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACTCGTAAACACATATCG
Found at i:42161405 original size:27 final size:28
Alignment explanation
Indices: 42161375--42161428 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
42161365 ACATAGGGGT
42161375 AAAACAATCATCTTACCATATA-AGGGA
1 AAAACAATCATCTTACCATATATAGGGA
* * * *
42161402 AAAATAGTCATTTTATCATATATAGGG
1 AAAACAATCATCTTACCATATATAGGG
42161429 GGTCTAGGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (28 bp):
AAAACAATCATCTTACCATATATAGGGA
Found at i:42165616 original size:27 final size:27
Alignment explanation
Indices: 42165586--42165651 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
42165576 TGGATAAGTT
42165586 GTAGAAATACCAAAATACCCTTGTAGG
1 GTAGAAATACCAAAATACCCTTGTAGG
* * * *
42165613 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAAATACCAAAATACCCTTGTAGG
42165640 GTA-AAACTACCA
1 GTAGAAA-TACCA
42165652 TTTTCCCCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
GTAGAAATACCAAAATACCCTTGTAGG
Found at i:42166330 original size:27 final size:26
Alignment explanation
Indices: 42166290--42166341 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
42166280 CTCGCTGCAA
*
42166290 TCTGGTGGCCTCGTCACATATATCTGT
1 TCTGGTGACCTCGTCACA-ATATCTGT
*
42166317 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGTCACAATATCTG
42166342 GTAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACCTCGTCACAATATCTGT
Found at i:42166418 original size:27 final size:26
Alignment explanation
Indices: 42166380--42166439 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
42166370 CCACATATAT
* *
42166380 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
42166406 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
42166433 ATATCTG
1 ATATCTG
42166440 ATAGCTTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:42170436 original size:79 final size:80
Alignment explanation
Indices: 42170268--42170448 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
42170258 GCTACTCATT
* * *
42170268 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCATCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCTGGAAT-TAGTAACTCGCACAAATGCCATCGGGACTTAACCCG
* *
42170332 GATTTAGTAACTCGCAC
64 GATATAGTAACTAGCAC
* * ** *
42170349 CAATGCCTTCGGG-CTTAGCCTGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCTGG
1 CAAAGCCTTCGGGACTTAGCCTGGAATTAGTAACTCGCACAAATGCCATCGGGA-CTTAACCCGG
* *
42170412 ATATGGTCACTTAGCA-
65 ATATAGTAAC-TAGCAC
42170428 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
42170449 CGGATATCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.04
79 56 0.67
80 21 0.25
81 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCTGGAATTAGTAACTCGCACAAATGCCATCGGGACTTAACCCGGA
TATAGTAACTAGCAC
Found at i:42170454 original size:40 final size:40
Alignment explanation
Indices: 42170268--42170455 Score: 213
Period size: 40 Copynumber: 4.7 Consensus size: 40
42170258 GCTACTCATT
* *
42170268 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
42170308 CAAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
42170348 CCAATGCCTTCGGG-CTTAGCCTGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
42170387 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
42170428 CAAA-GCCTTCGGGACTTAGCCCGGATAT
1 CAAATGCCTTCGGGACTTAGCCCGGATAT
42170456 CATTCGAATA
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 80 0.64
41 12 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:42177615 original size:40 final size:40
Alignment explanation
Indices: 42177571--42177754 Score: 171
Period size: 40 Copynumber: 4.6 Consensus size: 40
42177561 GCTACTCGTT
* *
42177571 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
42177611 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * * *
42177651 CCAATGCCTTCAGG-CTTAGCCCGG-AATTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* ** * * * *
42177690 CAAATGCCTTC-GGATCTTAGTCTTGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
42177731 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
42177755 ACATCATTCG
Statistics
Matches: 116, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 71 0.61
41 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:42177685 original size:39 final size:40
Alignment explanation
Indices: 42177599--42177708 Score: 152
Period size: 39 Copynumber: 2.8 Consensus size: 40
42177589 AGCCCGGTTA
* *
42177599 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAAT
* *
42177639 TAGTAACTCGCACCAATGCCTTCAGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAAT
*
42177678 TAGTAACTCGTACAAATGCCTTC-GGATCTTA
1 TAGTAACTCGCACAAATGCCTTCAGGA-CTTA
42177709 GTCTTGATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.52
40 28 0.45
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAAT
Found at i:42183161 original size:40 final size:40
Alignment explanation
Indices: 42183091--42183228 Score: 235
Period size: 40 Copynumber: 3.5 Consensus size: 40
42183081 AAACCAAGTA
*
42183091 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
42183130 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42183170 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
42183210 CCTTCAGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42183229 TAACCATCCG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
39 14 0.15
40 81 0.85
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42191339 original size:40 final size:40
Alignment explanation
Indices: 42191267--42191482 Score: 355
Period size: 40 Copynumber: 5.4 Consensus size: 40
42191257 AAACCAACTA
* *
42191267 CCTTCGGTATTTAG-CCGGATATAGCT-ACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
42191306 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
42191346 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
42191386 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
42191426 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42191466 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
42191483 AGTTACCATC
Statistics
Matches: 165, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
39 13 0.08
40 152 0.92
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42195258 original size:27 final size:27
Alignment explanation
Indices: 42195214--42195278 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
42195204 TGGATAAGTT
42195214 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
42195241 GTAGAATTACTGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
42195268 GTAAAATTACC
1 GTAGAATTACC
42195279 ATTTCCCCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:42197678 original size:40 final size:40
Alignment explanation
Indices: 42197622--42197886 Score: 270
Period size: 40 Copynumber: 6.7 Consensus size: 40
42197612 TAACGGGGTC
* * *
42197622 AAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCT
*
42197662 AAGTCCCGAAGGCATTTGTGCGAGTTACTACA-TCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTGACTA-ATTCCGGGCT
* * * *
42197702 AAGTCCCGAAGGCAATTGTGCGAGTTACTAATTTCGGGCC
1 AAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCT
* * * *
42197742 AAGTCCCGAAGGCATTGGTGTGAGTTACTAATTCTGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCT
*
42197782 AAGTCCCGAAGGCATTTGTGCAAGTTG-CT-ATATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAG-TGACTAAT-TCCGGGCT
* * * * *
42197822 AAGACCCAAAGACATTTGTGCTAGTGAC-CATATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCT
* * *
42197862 AAGACCCGACGGC-CTTGTGCGAGTG
1 AAGTCCCGAAGGCATTTGTGCGAGTG
42197887 GTTATATCCG
Statistics
Matches: 192, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
39 15 0.08
40 175 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
AAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCT
Found at i:42197841 original size:120 final size:120
Alignment explanation
Indices: 42197621--42197842 Score: 320
Period size: 120 Copynumber: 1.9 Consensus size: 120
42197611 CTAACGGGGT
* * *
42197621 CAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 CAAGTCCCGAAGACATTGGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG
* * *
42197686 TTACTACATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAATTTCGGGC
66 TTACTACATCCGGGCTAAGACCCAAAGACAATTGTGCGAGTTACTAATTTCGGGC
* * *
42197741 CAAGTCCCGAAGGCATTGGTG-TGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCAA
1 CAAGTCCCGAAGACATTGGTGCT-AGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAA
* * *
42197805 GTTGCTATATCCGGGCTAAGACCCAAAGACATTTGTGC
65 GTTACTACATCCGGGCTAAGACCCAAAGACAATTGTGC
42197843 TAGTGACCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
119 1 0.01
120 88 0.99
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (120 bp):
CAAGTCCCGAAGACATTGGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG
TTACTACATCCGGGCTAAGACCCAAAGACAATTGTGCGAGTTACTAATTTCGGGC
Found at i:42197860 original size:120 final size:120
Alignment explanation
Indices: 42197621--42197870 Score: 306
Period size: 120 Copynumber: 2.1 Consensus size: 120
42197611 CTAACGGGGT
* * *
42197621 CAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 CAAGTCCCGAAGACATTGGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG
* * * * * *
42197686 TTACTACATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAATTTCGGGC
66 TTACTACATCCGGGCTAAGACCCAAAGACAATTGTGCGAGTGACCAATTCCGGGC
* * *
42197741 CAAGTCCCGAAGGCATTGGTG-TGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCAA
1 CAAGTCCCGAAGACATTGGTGCT-AGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAA
* * * *
42197805 GTTGCTATATCCGGGCTAAGACCCAAAGACATTTGTGCTAGTGACC-ATATCCGGGC
65 GTTACTACATCCGGGCTAAGACCCAAAGACAATTGTGCGAGTGACCAAT-TCCGGGC
* *
42197861 TAAGACCCGA
1 CAAGTCCCGA
42197871 CGGCCTTGTG
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
119 3 0.03
120 107 0.97
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (120 bp):
CAAGTCCCGAAGACATTGGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG
TTACTACATCCGGGCTAAGACCCAAAGACAATTGTGCGAGTGACCAATTCCGGGC
Found at i:42212174 original size:28 final size:29
Alignment explanation
Indices: 42212134--42212188 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42212124 CACGAGAAAT
42212134 GACACGAGCGTGT-CTAGGCCATGTGAGG
1 GACACGAGCGTGTGCTAGGCCATGTGAGG
*
42212162 GACACG-GACGTGTGCTCGGCCATGTGA
1 GACACGAG-CGTGTGCTAGGCCATGTGA
42212189 AAACCCCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 11 0.46
29 12 0.50
ACGTcount: A:0.20, C:0.24, G:0.38, T:0.18
Consensus pattern (29 bp):
GACACGAGCGTGTGCTAGGCCATGTGAGG
Found at i:42214430 original size:40 final size:40
Alignment explanation
Indices: 42214365--42214549 Score: 214
Period size: 40 Copynumber: 4.7 Consensus size: 40
42214355 TCGAATGATA
42214365 ACCGGGCTAAGTCCCGAA-GCAATTTGTGCGAGCTACTAAT
1 ACCGGGCTAAGTCCCGAAGGC-ATTTGTGCGAGCTACTAAT
* * * *
42214405 TCCGGGCTAAGTTCCAAAGGCATTTGTGCGAGCTAATAAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT
** * * *
42214445 TTCGGGCTAAGTCCCGAAGGCATTTTTGCGAGTTA-TTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT
* * *
42214484 ACCGGGCTAAGTCCCGAAGGTATTTGTGCAAGTTACT-AT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT
*
42214523 AACCAGGCTAAGTCCCGAAGGCATTTG
1 -ACCGGGCTAAGTCCCGAAGGCATTTG
42214550 AGCTAGTGGC
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
39 35 0.28
40 88 0.70
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (40 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT
Found at i:42214532 original size:79 final size:78
Alignment explanation
Indices: 42214362--42214549 Score: 218
Period size: 79 Copynumber: 2.4 Consensus size: 78
42214352 TGTTCGAATG
* *
42214362 ATAACCGGGCTAAGTCCCGAA-GCAATTTGTGCGAGCTACTAATTCCGGGCTAAGTTCCAAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGC-ATTTGTGCGAGCTACTAATACCGGGCTAAGTCCCAAAGGC
*
42214426 ATTTGTGCGAGCTA
65 ATTTGTGCAAGCTA
* * * * *
42214440 ATAATTTCGGGCTAAGTCCCGAAGGCATTTTTGCGAGTTA-TTATACCGGGCTAAGTCCCGAAGG
1 ATAA--CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATACCGGGCTAAGTCCCAAAGG
* *
42214504 TATTTGTGCAAGTTA
64 CATTTGTGCAAGCTA
*
42214519 CTATAACCAGGCTAAGTCCCGAAGGCATTTG
1 --ATAACCGGGCTAAGTCCCGAAGGCATTTG
42214550 AGCTAGTGGC
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 4 0.04
79 54 0.59
80 28 0.30
81 6 0.07
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATACCGGGCTAAGTCCCAAAGGCA
TTTGTGCAAGCTA
Found at i:42214563 original size:40 final size:39
Alignment explanation
Indices: 42214362--42214572 Score: 158
Period size: 40 Copynumber: 5.3 Consensus size: 39
42214352 TGTTCGAATG
* *
42214362 ATAACCGGGCTAAGTCCCGAA-GCAATTTGTGCGAGCTACT
1 ATAACC-GGCTAAGTCCCGAAGGC-ATTTGTGCAAGTTACT
* * * * * *
42214402 A-ATTCCGGGCTAAGTTCCAAAGGCATTTGTGCGAGCTAAT
1 ATA-ACC-GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * * * *
42214442 AATTTCGGGCTAAGTCCCGAAGGCATTTTTGCGAGTTATT
1 -ATAACCGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
42214482 AT-ACCGGGCTAAGTCCCGAAGGTATTTGTGCAAGTTACT
1 ATAACC-GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * **
42214521 ATAACCAGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT
1 ATAACC-GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
42214561 ATATCCGGCTAA
1 ATAACCGGCTAA
42214573 ACTCGGAAGG
Statistics
Matches: 141, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
38 1 0.01
39 40 0.28
40 95 0.67
41 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (39 bp):
ATAACCGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:42222497 original size:40 final size:39
Alignment explanation
Indices: 42222435--42222662 Score: 254
Period size: 40 Copynumber: 5.8 Consensus size: 39
42222425 CGGATGATAA
* *
42222435 CCGGGCTAAGTCCC-AAGAGCATTTGAGCTAGTGGCTAATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-ACTAATT
42222475 CCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TACTAATT
*
42222515 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAATT
* *
42222555 CCGGGCTAAGTCCCGAA-GCATTTGTGCGAGT--TATTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTAAT-T
* * *
42222592 ACGGGCTAAGT-CCGAAGGCATTTGTGCAAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAAT-T
*
42222631 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT
42222663 GGCTATATCC
Statistics
Matches: 167, Mismatches: 11, Indels: 21
0.84 0.06 0.11
Matches are distributed among these distances:
36 8 0.05
37 23 0.14
38 2 0.01
39 27 0.16
40 103 0.62
41 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTAATT
Found at i:42225634 original size:16 final size:16
Alignment explanation
Indices: 42225610--42225655 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
42225600 GTAAATCCTG
42225610 AAATGCCGAAAAGCCA
1 AAATGCCGAAAAGCCA
* **
42225626 AAATACCGAAAAGTTA
1 AAATGCCGAAAAGCCA
42225642 AAATGCCGAAAAGC
1 AAATGCCGAAAAGC
42225656 TGAATGTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.52, C:0.20, G:0.17, T:0.11
Consensus pattern (16 bp):
AAATGCCGAAAAGCCA
Found at i:42230351 original size:79 final size:81
Alignment explanation
Indices: 42230209--42230391 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
42230199 TCGAATGATG
* *
42230209 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAAGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAAGCATT
42230273 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
42230288 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAAGCA
*
42230350 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
42230368 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42230392 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 56 0.64
80 30 0.34
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAAGCATT
TGTGCGAGATACTATA
Found at i:42230400 original size:40 final size:40
Alignment explanation
Indices: 42230209--42230393 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
42230199 TCGAATGATG
* * * *
42230209 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
42230249 TCCGGACTAAGAT-CCGAAAGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42230289 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42230328 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42230369 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42230394 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 33 0.27
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42230425 original size:79 final size:78
Alignment explanation
Indices: 42230256--42230426 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 78
42230246 ATATCCGGAC
* * **
42230256 TAAGATCCGAAAGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGT
42230321 TACTAAATCCGGGT
65 TACTAAATCCGGGT
* * *
42230335 TAAGTCTCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTC-CGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGA
*
42230399 G-TAGCTATATCC-GGT
63 GTTA-CTAAATCCGGGT
*
42230414 TAAATTCCGAAGG
1 T-AAGTCCGAAGG
42230427 TACGTGATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
78 4 0.05
79 46 0.59
80 28 0.36
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTT
ACTAAATCCGGGT
Found at i:42232718 original size:16 final size:16
Alignment explanation
Indices: 42232697--42232739 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
42232687 GCAAATCCCG
42232697 AAATGCTAAAAAGCCA
1 AAATGCTAAAAAGCCA
*
42232713 AAATGCTGAAAAGCCA
1 AAATGCTAAAAAGCCA
*
42232729 AAATGCCAAAA
1 AAATGCTAAAA
42232740 TGCCGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.12
Consensus pattern (16 bp):
AAATGCTAAAAAGCCA
Found at i:42232723 original size:24 final size:24
Alignment explanation
Indices: 42232689--42232750 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
42232679 GTAGATCGGC
* * *
42232689 AAATCCCGAAATGCTAAAAAGCCA
1 AAATGCCGAAAAGCCAAAAAGCCA
* *
42232713 AAATGCTGAAAAGCCAAAATGCCA
1 AAATGCCGAAAAGCCAAAAAGCCA
42232737 AAATGCCGAAAAGC
1 AAATGCCGAAAAGC
42232751 TGAAAGTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (24 bp):
AAATGCCGAAAAGCCAAAAAGCCA
Found at i:42233016 original size:28 final size:29
Alignment explanation
Indices: 42232967--42233034 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
42232957 GAAAGCATGT
42232967 ATATGAATGTAATTTGGGCCTAATGGGCC
1 ATATGAATGTAATTTGGGCCTAATGGGCC
*
42232996 ATATGAATG-AGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTA-ATTTGGGCCTAATGGGCC
*
42233024 ATATGCATGTA
1 ATATGAATGTA
42233035 TGGAGACGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (29 bp):
ATATGAATGTAATTTGGGCCTAATGGGCC
Found at i:42245023 original size:13 final size:13
Alignment explanation
Indices: 42245005--42245030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42244995 AAATAATCTA
42245005 ACACAGGCGTGTC
1 ACACAGGCGTGTC
42245018 ACACAGGCGTGTC
1 ACACAGGCGTGTC
42245031 CCTACCGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACAGGCGTGTC
Found at i:42247336 original size:30 final size:30
Alignment explanation
Indices: 42247302--42247361 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
42247292 GGACAGAGAA
42247302 GTGTTAGTAGAGTTTCAAAAAGTTAAAGAC
1 GTGTTAGTAGAGTTTCAAAAAGTTAAAGAC
42247332 GTGTTAGTAGAGTTTCAAAAAGTTAAAGAC
1 GTGTTAGTAGAGTTTCAAAAAGTTAAAGAC
42247362 ATTGCTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (30 bp):
GTGTTAGTAGAGTTTCAAAAAGTTAAAGAC
Found at i:42260579 original size:27 final size:26
Alignment explanation
Indices: 42260546--42260630 Score: 125
Period size: 27 Copynumber: 3.2 Consensus size: 26
42260536 CATGGCTGCT
* *
42260546 AGAACAGATATTGTGACAGAGTCACC
1 AGAACAGATATTGTGGCAGAGCCACC
*
42260572 AGATACAGATATTGTGGCAGAGCCACT
1 AGA-ACAGATATTGTGGCAGAGCCACC
42260599 AGAACAGATATTTGTGGCAGAGCCACC
1 AGAACAGATA-TTGTGGCAGAGCCACC
42260626 AGAAC
1 AGAAC
42260631 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.19
27 43 0.81
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (26 bp):
AGAACAGATATTGTGGCAGAGCCACC
Found at i:42260786 original size:25 final size:25
Alignment explanation
Indices: 42260730--42260787 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
42260720 CAAAATTAAC
* **
42260730 CCTAGGGGTATAATGGTAATTTTGCA
1 CCTA-GGGTATAATAGTAATTTCACA
*
42260756 CCTAGGGTATAATAGTAATTTCATA
1 CCTAGGGTATAATAGTAATTTCACA
*
42260781 CTTAGGG
1 CCTAGGG
42260788 GTATTTTACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (25 bp):
CCTAGGGTATAATAGTAATTTCACA
Found at i:42274707 original size:48 final size:48
Alignment explanation
Indices: 42274553--42274700 Score: 233
Period size: 48 Copynumber: 3.1 Consensus size: 48
42274543 ATATATACAC
* * **
42274553 ATCTCATACATATTTCACATAAGCCATTTGGCTTTACCACATATGCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
**
42274601 GGCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
*
42274649 ATCTCATACATATTTTACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
42274697 ATCT
1 ATCT
42274701 TGTACATCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.37
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
Found at i:42276182 original size:23 final size:23
Alignment explanation
Indices: 42276150--42276193 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42276140 AAAATTTCAC
* *
42276150 ACATGTAATTTCACATATAATAG
1 ACATGAAATTTAACATATAATAG
*
42276173 ACATGAAATTTAACATTTAAT
1 ACATGAAATTTAACATATAAT
42276194 TATTTTTGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
ACATGAAATTTAACATATAATAG
Found at i:42276327 original size:12 final size:12
Alignment explanation
Indices: 42276310--42276335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42276300 TTACTAATGA
42276310 ATAAGTTCAGAT
1 ATAAGTTCAGAT
42276322 ATAAGTTCAGAT
1 ATAAGTTCAGAT
42276334 AT
1 AT
42276336 CGTTCTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAAGTTCAGAT
Found at i:42277167 original size:40 final size:40
Alignment explanation
Indices: 42277112--42277228 Score: 191
Period size: 40 Copynumber: 3.0 Consensus size: 40
42277102 ATTTTGTCAA
* *
42277112 AGCACGAATGC-CTTCGGGGCTTAGCCCGGATACATCACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACAACACC
*
42277151 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACAACACC
*
42277191 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACAACA
42277229 TACTAAACTT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 11 0.15
40 63 0.85
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATACAACACC
Found at i:42279326 original size:48 final size:48
Alignment explanation
Indices: 42279172--42279319 Score: 242
Period size: 48 Copynumber: 3.1 Consensus size: 48
42279162 ATATATACAC
* **
42279172 ATCTCATACATATTTCACATTAGCCATTTGGCTTTACCACATATGCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
**
42279220 GGCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
*
42279268 ATCTCATACATATTTTACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
42279316 ATCT
1 ATCT
42279320 TGTACATCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
Found at i:42284030 original size:40 final size:40
Alignment explanation
Indices: 42283946--42284170 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
42283936 TGAATGATTG
* * * *
42283946 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42283986 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42284026 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42284065 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42284105 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42284146 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42284171 AAACGAGGAG
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42284193 original size:80 final size:80
Alignment explanation
Indices: 42283946--42284204 Score: 235
Period size: 80 Copynumber: 3.2 Consensus size: 80
42283936 TGAATGATTG
* * * * * * *
42283946 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
** *
42284009 TTGTGCGAGAT-ACTAAT
64 TTGAACGAG-TGACTAAA
* *
42284026 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
** *
42284090 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
* *
42284105 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
42284169 TGAAACGAG-GAGCTATA
65 TG-AACGAGTGA-CTAAA
* *
42284186 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42284205 TACGTGATTT
Statistics
Matches: 154, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
78 2 0.01
79 59 0.38
80 80 0.52
81 13 0.08
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:42292058 original size:40 final size:40
Alignment explanation
Indices: 42291974--42292198 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
42291964 TTGAATGATG
* * * *
42291974 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42292014 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42292054 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42292093 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42292133 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42292174 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42292199 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42292220 original size:119 final size:119
Alignment explanation
Indices: 42291974--42292231 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
42291964 TTGAATGATG
* *
42291974 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
42292039 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
42292093 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
42292156 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
42292213 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42292232 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:42294297 original size:43 final size:42
Alignment explanation
Indices: 42294163--42294323 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 42
42294153 AGGATTTCTG
* *
42294163 ATATGTGATTTCGTGTAAGACCACGTCTGGGA-CGCTGGCATC
1 ATATTTGATTTCGTGTAAGACCACGTCTGGGATAG-TGGCATC
* * * *
42294205 A-ATTTGAGATTTACGTTTAAGACCATGTTTGGGATATTGGCATC
1 ATATTT--GATTT-CGTGTAAGACCACGTCTGGGATAGTGGCATC
42294249 ATATTTGATTTCGTGTAAGACC-CTGTCTGGGATAGTGGCATC
1 ATATTTGATTTCGTGTAAGACCAC-GTCTGGGATAGTGGCATC
* * *
42294291 GATATTTGATTACATGTAAAACCACGTCTGGGA
1 -ATATTTGATTTCGTGTAAGACCACGTCTGGGA
42294324 CGTTGGCATT
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
41 3 0.03
42 27 0.28
43 37 0.38
44 27 0.28
45 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
ATATTTGATTTCGTGTAAGACCACGTCTGGGATAGTGGCATC
Found at i:42296056 original size:43 final size:43
Alignment explanation
Indices: 42296008--42296175 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 43
42295998 AGGATTTCCT
* *
42296008 ATATGTGTTATCGAGTAAGACCATGTCTGGGATGTTGGCATCG
1 ATATGTGATATCGAGTAAGACCATGTCTGGGACGTTGGCATCG
* * *
42296051 ATATGTGGT-TACGAGTAAGACCATGTCTGGGACATCGGCATC-
1 ATATGTGATAT-CGAGTAAGACCATGTCTGGGACGTTGGCATCG
* * * *
42296093 ATATTTGAT-TCGTGTAAGACCCTGTCTGGGATAG-TGGCATCG
1 ATATGTGATATCGAGTAAGACCATGTCTGGGA-CGTTGGCATCG
* * * *
42296135 ATATGAGATAGC-ATGTAAGACCACGTCTTGGACGTTGGCAT
1 ATATGTGATATCGA-GTAAGACCATGTCTGGGACGTTGGCAT
42296176 TGTATGGTAT
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
41 25 0.25
42 17 0.17
43 58 0.58
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
ATATGTGATATCGAGTAAGACCATGTCTGGGACGTTGGCATCG
Found at i:42296628 original size:14 final size:14
Alignment explanation
Indices: 42296609--42296646 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42296599 GTTTGTCAGT
*
42296609 AAAATGTTTTCTAG
1 AAAATGATTTCTAG
*
42296623 AAAATGATTTCTGG
1 AAAATGATTTCTAG
42296637 AAAATGATTT
1 AAAATGATTT
42296647 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (14 bp):
AAAATGATTTCTAG
Found at i:42301984 original size:6 final size:6
Alignment explanation
Indices: 42301969--42302017 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
42301959 GTCAAGGATG
* * *
42301969 GGGGAA GGGGAG GGGGAA GGGGAA GGGGAA TGGAAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
42302017 G
1 G
42302018 CAGAAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.65, T:0.02
Consensus pattern (6 bp):
GGGGAA
Found at i:42303931 original size:34 final size:34
Alignment explanation
Indices: 42303893--42303960 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
42303883 TGACAGTGTA
* *
42303893 TGAGCGAAAATTCATGAGACTCAGTCAGTATGCT
1 TGAGCAAAAATTCATAAGACTCAGTCAGTATGCT
** *
42303927 TGAGCAAAAATTTGTAAGACTCGGTCAGTATGCT
1 TGAGCAAAAATTCATAAGACTCAGTCAGTATGCT
42303961 CGAGAGTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (34 bp):
TGAGCAAAAATTCATAAGACTCAGTCAGTATGCT
Found at i:42305770 original size:28 final size:28
Alignment explanation
Indices: 42305738--42305802 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
42305728 ATTTACTAGA
42305738 ATACCCCTATGTATACAAAACT-ACCATT
1 ATACCCCTATGTATACAAAA-TGACCATT
* * *
42305766 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATACAAAATGACCATT
42305794 ATACCCCTA
1 ATACCCCTA
42305803 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATACAAAATGACCATT
Found at i:42305949 original size:28 final size:29
Alignment explanation
Indices: 42305908--42305970 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
42305898 AGGAAGCGTC
** *
42305908 CTGGTGGCTTTGCCACAAATTATCTGT-T
1 CTGGTGGCACTGCCACAAAATATCTGTAT
42305936 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGTAT
42305965 CTGGTG
1 CTGGTG
42305971 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (29 bp):
CTGGTGGCACTGCCACAAAATATCTGTAT
Found at i:42305981 original size:29 final size:28
Alignment explanation
Indices: 42305918--42305981 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
42305908 CTGGTGGCTT
* *
42305918 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
42305946 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
42305975 TGTCACA
1 TGCCACA
42305982 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:42309459 original size:34 final size:34
Alignment explanation
Indices: 42309416--42309483 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42309406 AAGCGAGCTC
42309416 AATGTGAATAGAATGTTGAATTCGAGTTTCGAGT
1 AATGTGAATAGAATGTTGAATTCGAGTTTCGAGT
42309450 AATGTGAATAGAATGTTGAATTCGAGTTTCGAGT
1 AATGTGAATAGAATGTTGAATTCGAGTTTCGAGT
42309484 TGATGCTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (34 bp):
AATGTGAATAGAATGTTGAATTCGAGTTTCGAGT
Found at i:42322747 original size:11 final size:11
Alignment explanation
Indices: 42322731--42322755 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42322721 GAAGCTTAAA
42322731 AATGTAAGTGT
1 AATGTAAGTGT
42322742 AATGTAAGTGT
1 AATGTAAGTGT
42322753 AAT
1 AAT
42322756 TGTCTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (11 bp):
AATGTAAGTGT
Found at i:42324009 original size:26 final size:27
Alignment explanation
Indices: 42323969--42324047 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 27
42323959 TTGTATTAGA
42323969 GCTAGGATTGGTTAATTTGTTAGGTT-T
1 GCTAGG-TTGGTTAATTTGTTAGGTTCT
* *
42323996 GCTAGGTTGATTAACTTGTTAGGTTCT
1 GCTAGGTTGGTTAATTTGTTAGGTTCT
* *
42324023 -CTAGGTTGGTTAATCTGTTAAGTTC
1 GCTAGGTTGGTTAATTTGTTAGGTTC
42324048 GGCAGGTCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 38 0.84
27 7 0.16
ACGTcount: A:0.19, C:0.09, G:0.27, T:0.46
Consensus pattern (27 bp):
GCTAGGTTGGTTAATTTGTTAGGTTCT
Found at i:42329967 original size:25 final size:25
Alignment explanation
Indices: 42329938--42329985 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
42329928 TTATAACATG
* *
42329938 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
42329963 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
42329986 GTTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:42330087 original size:20 final size:20
Alignment explanation
Indices: 42330022--42330087 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
42330012 ATTTTGATAG
*
42330022 ACATG-TATGTATGATTTGC
1 ACATGATATGTATGATATGC
*
42330041 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42330061 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42330081 ACATGAT
1 ACATGAT
42330088 GTAATCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42330223 original size:45 final size:46
Alignment explanation
Indices: 42330138--42330231 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
42330128 AGGAAATGAA
*
42330138 AAAGGGCTTATGCCCCAGTTATTAAATGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
42330184 AAAGGGCTTATG-CCCAGTTATTAAAAGGGCTTTTG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
42330229 AAA
1 AAA
42330232 AGAGGCTAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 23 0.51
46 22 0.49
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:42330232 original size:23 final size:24
Alignment explanation
Indices: 42330137--42330252 Score: 152
Period size: 23 Copynumber: 5.0 Consensus size: 24
42330127 GAGGAAATGA
42330137 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42330161 -AAATGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42330184 -AAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42330206 AAAAGGGCTTTTG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42330229 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42330253 ATGATAAAGC
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
22 10 0.12
23 61 0.73
24 4 0.05
25 8 0.10
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:42330479 original size:31 final size:31
Alignment explanation
Indices: 42330444--42330507 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
42330434 CGTTTACAGT
42330444 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
42330475 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42330506 AA
1 AA
42330508 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42338802 original size:20 final size:20
Alignment explanation
Indices: 42338736--42338802 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
42338726 ATTTTGATAG
*
42338736 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* * *
42338756 ACATGACAGGTATGATATGT
1 ACATGATATGTATGATATGC
42338776 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42338796 ACATGAT
1 ACATGAT
42338803 GTAATCATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42338883 original size:23 final size:23
Alignment explanation
Indices: 42338853--42338947 Score: 156
Period size: 23 Copynumber: 4.1 Consensus size: 23
42338843 AGGAAGTGAA
42338853 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
42338876 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
42338899 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
42338921 AAAAGGGATTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
42338945 AAA
1 AAA
42338948 AGAGGCTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
22 10 0.15
23 48 0.71
24 10 0.15
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:42339198 original size:31 final size:31
Alignment explanation
Indices: 42339162--42339225 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
42339152 CGTTTACAGT
* *
42339162 AAAGGCTTCGGCCTAGTAATATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
**
42339193 AAAGGCTTCGACCCAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
42339224 AA
1 AA
42339226 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGA
Found at i:42342407 original size:27 final size:27
Alignment explanation
Indices: 42342377--42342439 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
42342367 CCCCAAAATA
*
42342377 GGTAAAATGATCATAAGGCCCCTGTAG
1 GGTAAAATGATCATAAGGCCCCCGTAG
* *
42342404 GGTAAAATGATCGTAATGCCCCCGTAG
1 GGTAAAATGATCATAAGGCCCCCGTAG
42342431 GGTAAAATG
1 GGTAAAATG
42342440 GCCGTAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (27 bp):
GGTAAAATGATCATAAGGCCCCCGTAG
Found at i:42342445 original size:27 final size:27
Alignment explanation
Indices: 42342377--42342464 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
42342367 CCCCAAAATA
* * *
42342377 GGTAAAATGATCATAAGGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
42342404 GGTAAAATGATCGTAATGCCCCCGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
42342431 GGTAAAATGGCCGTAAT-ACCCTGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAG
42342457 GGTAAAAT
1 GGTAAAAT
42342465 AACGATTATG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 14 0.26
27 39 0.74
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:42349032 original size:47 final size:47
Alignment explanation
Indices: 42348977--42349318 Score: 522
Period size: 47 Copynumber: 7.3 Consensus size: 47
42348967 ACAAGGAGTG
** *
42348977 TATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
42349024 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTG
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
42349071 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
42349118 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTTAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
42349165 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * *
42349212 TATATGAGATAAGACCTAATGGCCAATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
42349259 TATATGAGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
42349306 TAAATGTGATAAG
1 TATATGTGATAAG
42349319 TCCCGAAGGG
Statistics
Matches: 268, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 268 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:42351223 original size:40 final size:40
Alignment explanation
Indices: 42351168--42351559 Score: 615
Period size: 40 Copynumber: 9.8 Consensus size: 40
42351158 TAGTATGTTA
42351168 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
42351208 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* * *
42351248 TATCCGGACTAAGTTCCAAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
42351288 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* * *
42351328 TATCTGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* * *
42351368 TATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGCTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* ** *
42351408 TATCCAGATTAAGTTCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* *
42351448 TATCCGGGCTAAGTCCCGAAGAGTATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
42351488 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
42351528 TATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
42351560 TGGACAAAAT
Statistics
Matches: 317, Mismatches: 35, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 11 0.03
40 306 0.97
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
Found at i:42355568 original size:47 final size:47
Alignment explanation
Indices: 42355485--42355876 Score: 599
Period size: 47 Copynumber: 8.4 Consensus size: 47
42355475 GATGTACAAG
* * *
42355485 GTGTGTATATGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
42355531 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
42355578 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
42355625 GTGTATATATGTGATAAGGCCG-ATGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
42355671 GTGTATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
42355718 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
42355765 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
42355812 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
42355859 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
42355877 TCCCGAAGGG
Statistics
Matches: 319, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 61 0.19
47 258 0.81
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:42355660 original size:140 final size:140
Alignment explanation
Indices: 42355485--42355876 Score: 631
Period size: 140 Copynumber: 2.8 Consensus size: 140
42355475 GATGTACAAG
* *
42355485 GTGTGTATATGTGATAAGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
1 GTGTATATATGTGATAAGGCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * *
42355550 CCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGAT
66 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCAATGTGAT
42355615 GAATGTGAAA
131 GAATGTGAAA
* * * *
42355625 GTGTATATATGTGATAAGGCCGATGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAGGG
1 GTGTATATATGTGATAAGGCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
42355690 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAATGGCCAATGTGAT
66 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCAATGTGAT
42355755 GAATGTGAAA
131 GAATGTGAAA
* * * *
42355765 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTATATATGTGATAAG
1 GTGTATATATGTGATAAGGCC-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
* *
42355830 GCCGAATGGCCAATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
65 GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42355877 TCCCGAAGGG
Statistics
Matches: 230, Mismatches: 21, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
140 149 0.65
141 81 0.35
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (140 bp):
GTGTATATATGTGATAAGGCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCAATGTGAT
GAATGTGAAA
Found at i:42359769 original size:27 final size:27
Alignment explanation
Indices: 42359739--42359842 Score: 138
Period size: 27 Copynumber: 3.9 Consensus size: 27
42359729 CCCTAAAATA
*
42359739 GGTAAAATGACTGTAATGCCCCTGTAG
1 GGTAAAATGACTGTAATGCCCTTGTAG
* *
42359766 GGTAAAATGACCGTAACGCCCTTGTAG
1 GGTAAAATGACTGTAATGCCCTTGTAG
* *
42359793 GGTAAAATGACTGTAATACCCTTGTAT
1 GGTAAAATGACTGTAATGCCCTTGTAG
*
42359820 GGTAAAATGA-TGATTATGCCCTT
1 GGTAAAATGACTG-TAATGCCCTT
42359843 ATGTCTCGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 2 0.03
27 65 0.97
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (27 bp):
GGTAAAATGACTGTAATGCCCTTGTAG
Found at i:42360211 original size:33 final size:33
Alignment explanation
Indices: 42360174--42360249 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
42360164 CTTGGGCCCA
* * * *
42360174 CTCTGCTATTGTATAGGGCAAAAGCCTAGACTG
1 CTCTGCTACTCTATAGGGCAAAAGCCCAAACTG
* *
42360207 CTCTGTTACTCTATAGGGCTAAAGCCCAAACTG
1 CTCTGCTACTCTATAGGGCAAAAGCCCAAACTG
*
42360240 CTCTGTTACT
1 CTCTGCTACT
42360250 GAATAAGGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (33 bp):
CTCTGCTACTCTATAGGGCAAAAGCCCAAACTG
Found at i:42360260 original size:33 final size:33
Alignment explanation
Indices: 42360194--42360260 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
42360184 GTATAGGGCA
* * * *
42360194 AAAGCCTAGACTGCTCTGTTACTCTATAGGGCT
1 AAAGCCCAAACTGCTCTGTTACTCAATAAGGCT
*
42360227 AAAGCCCAAACTGCTCTGTTACTGAATAAGGCT
1 AAAGCCCAAACTGCTCTGTTACTCAATAAGGCT
42360260 A
1 A
42360261 TGGCGCAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (33 bp):
AAAGCCCAAACTGCTCTGTTACTCAATAAGGCT
Found at i:42362428 original size:47 final size:48
Alignment explanation
Indices: 42362359--42362453 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 48
42362349 ATTCAATGCC
* *
42362359 AGAATAGGGTTATGAAGCATTATCAGACTTATAAAA-AATTAAACATT
1 AGAATAGGGTTACGAAGCATTATCACACTTATAAAACAATTAAACATT
42362406 AGAATAGGGTTACGAAGCATTATCACACTTATAAAACAATTAAACATT
1 AGAATAGGGTTACGAAGCATTATCACACTTATAAAACAATTAAACATT
42362454 CATTTCACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 34 0.76
48 11 0.24
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (48 bp):
AGAATAGGGTTACGAAGCATTATCACACTTATAAAACAATTAAACATT
Done.