Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 43 of 214
Found at i:11844288 original size:29 final size:29
Alignment explanation
Indices: 11844256--11844318 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
11844246 TTTTCTTTTC
11844256 TTTTTTGATCATTTTTA-TTTTTTGAAATA
1 TTTTTTGAT-ATTTTTATTTTTTTGAAATA
*
11844285 TTTTTTGATTTTTTTATTTTTTTGAAATA
1 TTTTTTGATATTTTTATTTTTTTGAAATA
11844314 TTTTT
1 TTTTT
11844319 GATTGGATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (29 bp):
TTTTTTGATATTTTTATTTTTTTGAAATA
Found at i:11846267 original size:16 final size:16
Alignment explanation
Indices: 11846242--11846272 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11846232 TTATGATGAA
11846242 AATGCAATGCAATCAT
1 AATGCAATGCAATCAT
*
11846258 AATGCCATGCAATCA
1 AATGCAATGCAATCA
11846273 AAACAACACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (16 bp):
AATGCAATGCAATCAT
Found at i:11848172 original size:3 final size:3
Alignment explanation
Indices: 11848164--11848210 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
11848154 ATAACCAAAT
* *
11848164 ATA ATA AT- ATCA ATA ATA ATA AGA GTA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
11848210 A
1 A
11848211 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11848182 original size:15 final size:13
Alignment explanation
Indices: 11848164--11848210 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 13
11848154 ATAACCAAAT
11848164 ATAATAATATCAATA
1 ATAATAA-AT-AATA
11848179 ATAATAAGAGTAATA
1 ATAATAA-A-TAATA
11848194 ATAATAAATAATA
1 ATAATAAATAATA
11848207 ATAA
1 ATAA
11848211 ATTAATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 9 0.30
14 1 0.03
15 19 0.63
16 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:11849429 original size:20 final size:21
Alignment explanation
Indices: 11849389--11849440 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
11849379 CACAATAAAT
11849389 AAATATAT-AAAA-TAGAAAA
1 AAATATATAAAAATTAGAAAA
11849408 AAATATATAAAAATTAGGAAAA
1 AAATATATAAAAATTA-GAAAA
11849430 AAATATATAAA
1 AAATATATAAA
11849441 TTATAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
21 2 0.07
22 16 0.53
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATATATAAAAATTAGAAAA
Found at i:11849574 original size:11 final size:11
Alignment explanation
Indices: 11849526--11849584 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
11849516 ATATTTTTAC
11849526 AAAAAAATGTA
1 AAAAAAATGTA
*
11849537 AAAGAAATTGT-
1 AAA-AAAATGTA
* *
11849548 -AAAAATTATA
1 AAAAAAATGTA
*
11849558 ATAAAAATGTA
1 AAAAAAATGTA
*
11849569 AAAAAAATTTA
1 AAAAAAATGTA
11849580 AAAAA
1 AAAAA
11849585 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 6 0.16
10 2 0.05
11 24 0.63
12 6 0.16
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (11 bp):
AAAAAAATGTA
Found at i:11849629 original size:15 final size:16
Alignment explanation
Indices: 11849600--11849646 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
11849590 AAATATATTT
* *
11849600 TTATCTAATTATAAAA
1 TTATATAATTCTAAAA
11849616 -TATATAATTCTAAAA
1 TTATATAATTCTAAAA
* *
11849631 TTCTAAAATTCTAAAA
1 TTATATAATTCTAAAA
11849647 AGGTATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
TTATATAATTCTAAAA
Found at i:11849634 original size:8 final size:8
Alignment explanation
Indices: 11849621--11849646 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11849611 TAAAATATAT
11849621 AATTCTAA
1 AATTCTAA
11849629 AATTCTAA
1 AATTCTAA
11849637 AATTCTAA
1 AATTCTAA
11849645 AA
1 AA
11849647 AGGTATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTCTAA
Found at i:11851295 original size:30 final size:27
Alignment explanation
Indices: 11851249--11851303 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
11851239 TATAGAGTTG
*
11851249 CCACAGAGGCTTTCCTTTGACAGAGATCA
1 CCACAAAGGCTTTCCTTT--CAGAGATCA
11851278 CCACAAAGGCGTTTCCTTTCAGAGAT
1 CCACAAAGGC-TTTCCTTTCAGAGAT
11851304 TTGCCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTTTCCTTTCAGAGATCA
Found at i:11852951 original size:25 final size:25
Alignment explanation
Indices: 11852923--11852992 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
11852913 TGGCTCTCAT
*
11852923 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATGGCTCTTGC
* **
11852948 GAGCTTTCCGATTA-ATGGCTCTTTT
1 GAGCTTCCCG-TTATATGGCTCTTGC
*
11852973 AAGCTTCCCGTT-TATGGCTC
1 GAGCTTCCCGTTATATGGCTC
11852993 CTCGGAGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 9 0.24
25 25 0.68
26 3 0.08
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCTTGC
Found at i:11853050 original size:25 final size:25
Alignment explanation
Indices: 11852987--11853053 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
11852977 TTCCCGTTTA
* * *
11852987 TGGCTCCTCGGAGCTTTTCAATAAT
1 TGGCTCTTAGGAGCTTCTCAATAAT
*
11853012 TGGCTTTTAGGAGCTTCTCAATAAT
1 TGGCTCTTAGGAGCTTCTCAATAAT
11853037 TGGCTCTT-GTGAGCTTC
1 TGGCTCTTAG-GAGCTTC
11853054 CTGGTTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (25 bp):
TGGCTCTTAGGAGCTTCTCAATAAT
Found at i:11853171 original size:25 final size:25
Alignment explanation
Indices: 11853046--11853207 Score: 104
Period size: 24 Copynumber: 6.6 Consensus size: 25
11853036 TTGGCTCTTG
*
11853046 TGAGCTTCCTGGTTA-ATGGCTCTTCA
1 TGAGCTTCCT-GTTATATGGCTC-ACA
* *
11853072 -GAGCTT-CTAGATAT-TGGCTCACT
1 TGAGCTTCCT-GTTATATGGCTCACA
* * **
11853095 TGAACTTCCTGATAT-TGGCTTGCA
1 TGAGCTTCCTGTTATATGGCTCACA
* * * *
11853119 TGAGCTTCCTG-AATTTGGCTCTCT
1 TGAGCTTCCTGTTATATGGCTCACA
*
11853143 TGAGCTTCTTGTTATATGGCTCACA
1 TGAGCTTCCTGTTATATGGCTCACA
*
11853168 TGAGCTTCCCGTTATATGGCTCGA-A
1 TGAGCTTCCTGTTATATGGCTC-ACA
* *
11853193 AGAGCTTCCCGTTAT
1 TGAGCTTCCTGTTAT
11853208 GTGCTCGTAT
Statistics
Matches: 109, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.03
24 53 0.49
25 52 0.48
26 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (25 bp):
TGAGCTTCCTGTTATATGGCTCACA
Found at i:11853174 original size:49 final size:50
Alignment explanation
Indices: 11853035--11853176 Score: 127
Period size: 48 Copynumber: 2.9 Consensus size: 50
11853025 CTTCTCAATA
* *
11853035 ATTGGCTCT-TGTGAGCTTCCTGGTTA-ATGGCTCTTCA-GAGCTT-CTAGAT
1 ATTGGCTCTCT-TGAGCTT-CTTGTTATATGGCTC-ACATGAGCTTCCTAGAT
* * * * **
11853084 ATTGGCTCACTTGAACTTCCTGATAT-TGGCTTGCATGAGCTTCCT-GA-
1 ATTGGCTCTCTTGAGCTTCTTGTTATATGGCTCACATGAGCTTCCTAGAT
11853131 ATTTGGCTCTCTTGAGCTTCTTGTTATATGGCTCACATGAGCTTCC
1 A-TTGGCTCTCTTGAGCTTCTTGTTATATGGCTCACATGAGCTTCC
11853177 CGTTATATGG
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
47 3 0.04
48 38 0.51
49 32 0.43
50 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (50 bp):
ATTGGCTCTCTTGAGCTTCTTGTTATATGGCTCACATGAGCTTCCTAGAT
Found at i:11866068 original size:27 final size:27
Alignment explanation
Indices: 11866030--11866163 Score: 119
Period size: 27 Copynumber: 5.0 Consensus size: 27
11866020 TCGCAATTGG
*
11866030 CGGACTGGCTCGCGAACAGGAGACTGA
1 CGGACTGCCTCGCGAACAGGAGACTGA
*
11866057 CGGACTGTCTCGCGAACA-GAGGACTGA
1 CGGACTGCCTCGCGAACAGGA-GACTGA
* * *
11866084 CGGATTGCCTCGCGAATAGGTGACTGA
1 CGGACTGCCTCGCGAACAGGAGACTGA
* * * * *
11866111 TGGATTGCCTTGCAAACAGGGGACT-A
1 CGGACTGCCTCGCGAACAGGAGACTGA
* * *
11866137 GCGGACTGCCTTGTGAACAGGGGACTG
1 -CGGACTGCCTCGCGAACAGGAGACTG
11866164 GTGGATTGTC
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.03
27 85 0.96
28 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.35, T:0.18
Consensus pattern (27 bp):
CGGACTGCCTCGCGAACAGGAGACTGA
Found at i:11866129 original size:54 final size:54
Alignment explanation
Indices: 11866029--11866196 Score: 149
Period size: 54 Copynumber: 3.1 Consensus size: 54
11866019 CTCGCAATTG
* * * * *
11866029 GCGGACTGGCTCGCGAACAGGAGACTGACGGACTGTCTCGCGAACAGAGGACT-
1 GCGGACTGCCTCGCGAACAGGAGACTGATGGATTGCCTCGCAAACAGAGGACTA
* * * * *
11866082 GACGGATTGCCTCGCGAATAGGTGACTGATGGATTGCCTTGCAAACAGGGGACTA
1 G-CGGACTGCCTCGCGAACAGGAGACTGATGGATTGCCTCGCAAACAGAGGACTA
* * * * * ** *
11866137 GCGGACTGCCTTGTGAACAGGGGACTGGTGGATTGTCTCATAAACAGATGACTA
1 GCGGACTGCCTCGCGAACAGGAGACTGATGGATTGCCTCGCAAACAGAGGACTA
*
11866191 ACGGAC
1 GCGGAC
11866197 AACTGAGAGC
Statistics
Matches: 90, Mismatches: 23, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
53 1 0.01
54 88 0.98
55 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (54 bp):
GCGGACTGCCTCGCGAACAGGAGACTGATGGATTGCCTCGCAAACAGAGGACTA
Found at i:11869067 original size:26 final size:26
Alignment explanation
Indices: 11869029--11869079 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11869019 ATAACTTACA
*
11869029 ACTTAACTACTGCAGTAGTTCATTCT
1 ACTTAACTACTGCAGCAGTTCATTCT
* *
11869055 ACTTAACTGCTGCTGCAGTTCATTC
1 ACTTAACTACTGCAGCAGTTCATTC
11869080 CTTAACATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (26 bp):
ACTTAACTACTGCAGCAGTTCATTCT
Found at i:11875560 original size:17 final size:17
Alignment explanation
Indices: 11875530--11875562 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11875520 ATAGAAACAA
11875530 ACAAACAAACACCAAAC
1 ACAAACAAACACCAAAC
11875547 ACAAGACAAA-ACCAAA
1 ACAA-ACAAACACCAAA
11875563 ACTCTCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (17 bp):
ACAAACAAACACCAAAC
Found at i:11877964 original size:9 final size:9
Alignment explanation
Indices: 11877946--11878021 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
11877936 TTTGGTTAAA
11877946 AATTAACCG
1 AATTAACCG
*
11877955 AATTACCCG
1 AATTAACCG
*
11877964 AATTAACCT
1 AATTAACCG
11877973 AATTAACCG
1 AATTAACCG
11877982 AATTAACCG
1 AATTAACCG
* *
11877991 GATTAATCG
1 AATTAACCG
* *
11878000 GATTACCCG
1 AATTAACCG
11878009 AATTAACCG
1 AATTAACCG
11878018 AATT
1 AATT
11878022 GAATCACTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:11878123 original size:5 final size:5
Alignment explanation
Indices: 11878113--11878158 Score: 65
Period size: 5 Copynumber: 8.6 Consensus size: 5
11878103 ATTTTTATGA
11878113 TTGGG TTGGG TTGGG TTGGG TAATTGGG TTGGG TTGGG TTGGG TTG
1 TTGGG TTGGG TTGGG TTGGG ---TTGGG TTGGG TTGGG TTGGG TTG
11878159 AATACTTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 33 0.87
8 5 0.13
ACGTcount: A:0.04, C:0.00, G:0.54, T:0.41
Consensus pattern (5 bp):
TTGGG
Found at i:11878142 original size:23 final size:23
Alignment explanation
Indices: 11878112--11878156 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
11878102 AATTTTTATG
11878112 ATTGGGTTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTTGGGTA
11878135 ATTGGGTTGGGTTGGGTTGGGT
1 ATTGGGTTGGGTTGGGTTGGGT
11878157 TGAATACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.07, C:0.00, G:0.53, T:0.40
Consensus pattern (23 bp):
ATTGGGTTGGGTTGGGTTGGGTA
Found at i:11878189 original size:29 final size:28
Alignment explanation
Indices: 11878113--11878191 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
11878103 ATTTTTATGA
* * ** *
11878113 TTGGGTTGGGTTGGGTTGGGTAATTGGG
1 TTGGATTGGGTTAGGTTGAATACTTGGG
* *
11878141 TTGGGTTGGGTTGGGTTGAATACTTGGG
1 TTGGATTGGGTTAGGTTGAATACTTGGG
11878169 TTTGGATTGGGTTTAGG-TGAATA
1 -TTGGATTGGG-TTAGGTTGAATA
11878192 GTGAGCCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 25 0.57
29 15 0.34
30 4 0.09
ACGTcount: A:0.13, C:0.01, G:0.46, T:0.41
Consensus pattern (28 bp):
TTGGATTGGGTTAGGTTGAATACTTGGG
Found at i:11884852 original size:2 final size:2
Alignment explanation
Indices: 11884845--11884871 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11884835 AGCATGAATA
11884845 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
11884872 AAGTGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11889466 original size:33 final size:33
Alignment explanation
Indices: 11889424--11889489 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11889414 GAGCAAGCAG
11889424 ACAAAATGTCAGTACAGTATCAGATATATAGTC
1 ACAAAATGTCAGTACAGTATCAGATATATAGTC
11889457 ACAAAATGTCAGTACAGTATCAGATATATAGTC
1 ACAAAATGTCAGTACAGTATCAGATATATAGTC
11889490 TGGGCTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
ACAAAATGTCAGTACAGTATCAGATATATAGTC
Found at i:11895039 original size:13 final size:13
Alignment explanation
Indices: 11895021--11895045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11895011 AATGCTAGGT
11895021 TGGGCACAAAAAG
1 TGGGCACAAAAAG
11895034 TGGGCACAAAAA
1 TGGGCACAAAAA
11895046 CTGAGACAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
TGGGCACAAAAAG
Found at i:11896225 original size:15 final size:16
Alignment explanation
Indices: 11896197--11896226 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11896187 TAAATTCATA
11896197 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
11896213 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
11896227 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:11896246 original size:18 final size:17
Alignment explanation
Indices: 11896218--11896252 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11896208 ATTATTAAGA
*
11896218 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
11896235 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
11896253 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:11896294 original size:59 final size:59
Alignment explanation
Indices: 11896231--11896416 Score: 180
Period size: 59 Copynumber: 3.1 Consensus size: 59
11896221 TTATTAAATT
11896231 ATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATC
1 ATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATC
* * ** * * * * * * * *
11896290 ATATATTATGATTTTAGTAAATTCATATAAGAA-TATTT-ATTATTAAGAATTTTATTA-AATT
1 ATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCA-AATT-A-TATTTTA-TAGTATC
* *
11896351 ATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTACC
1 ATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATC
11896410 ATATATT
1 ATATATT
11896417 ATGATTTTAG
Statistics
Matches: 92, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
58 3 0.03
59 39 0.42
60 14 0.15
61 33 0.36
62 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (59 bp):
ATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATC
Found at i:11896335 original size:120 final size:120
Alignment explanation
Indices: 11896155--11896506 Score: 677
Period size: 120 Copynumber: 2.9 Consensus size: 120
11896145 TTAATTAAAA
11896155 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
11896220 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
66 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
11896275 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
*
11896340 TTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAATT
66 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
*
11896395 ATATTTTATAGTACCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
1 ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
*
11896460 TTTATTAAATTATATATTTTAATTAATATATATTTAATAATAATTAT
66 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
11896507 GTTAAAATAT
Statistics
Matches: 228, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 228 1.00
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
ATATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAAT
TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATT
Found at i:11896345 original size:15 final size:16
Alignment explanation
Indices: 11896317--11896346 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11896307 TAAATTCATA
11896317 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
11896333 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
11896347 AATTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:11896364 original size:18 final size:18
Alignment explanation
Indices: 11896337--11896372 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11896327 TATTATTAAG
* *
11896337 AATTTTATTAAATTATAT
1 AATTTAATTAAAATATAT
11896355 AATTTAATTAAAATATAT
1 AATTTAATTAAAATATAT
11896373 TTAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAATTAAAATATAT
Found at i:11896465 original size:15 final size:16
Alignment explanation
Indices: 11896437--11896466 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11896427 TAAATTCATA
11896437 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
11896453 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
11896467 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:11896488 original size:14 final size:15
Alignment explanation
Indices: 11896462--11896501 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
11896452 TTAAGAATTT
*
11896462 TATTAAATT-ATATA
1 TATTTAATTAATATA
11896476 T-TTTAATTAATATA
1 TATTTAATTAATATA
11896490 TATTTAA-TAATA
1 TATTTAATTAATA
11896502 ATTATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTAATATA
Found at i:11896491 original size:18 final size:17
Alignment explanation
Indices: 11896458--11896494 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
11896448 ATTATTAAGA
11896458 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
11896475 ATTTTAATT-AA-TATAT
1 ATTTT-ATTAAATTATAT
11896491 ATTT
1 ATTT
11896495 AATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 7 0.37
18 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:11896684 original size:39 final size:41
Alignment explanation
Indices: 11896639--11896744 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
11896629 TTTCCTTATG
*
11896639 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACACAAGAATTAC
*
11896679 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAGAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACACAAGAATTAC
11896724 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
11896745 ACACATCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.40
45 4 0.07
46 10 0.18
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACACAAGAATTAC
Found at i:11896719 original size:44 final size:46
Alignment explanation
Indices: 11896652--11896744 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
11896642 TTACACCTCT
11896652 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
*
11896696 ATTCCATTCAACCAAACAGAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
11896742 ATT
1 ATT
11896745 ACACATCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 23 0.50
45 4 0.09
46 19 0.41
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
Found at i:11896753 original size:16 final size:16
Alignment explanation
Indices: 11896726--11896795 Score: 122
Period size: 16 Copynumber: 4.4 Consensus size: 16
11896716 AGAATTACCT
*
11896726 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
11896742 ATTACACATCTATTCC
1 ATTACACCTCTATTCC
11896758 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
11896774 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
11896790 ATTACA
1 ATTACA
11896796 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.27, C:0.34, G:0.01, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:11899541 original size:27 final size:27
Alignment explanation
Indices: 11899483--11899544 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
11899473 AAGTGTTTGC
* * *
11899483 AATATAGTCTACCTATAGTAGTCTTAG
1 AATATACTATACCTATAGCAGTCTTAG
*
11899510 TATATACTATACCTATAGCAGT-TTCAG
1 AATATACTATACCTATAGCAGTCTT-AG
11899537 AATATACT
1 AATATACT
11899545 TGGTGTACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (27 bp):
AATATACTATACCTATAGCAGTCTTAG
Found at i:11901130 original size:14 final size:15
Alignment explanation
Indices: 11901111--11901144 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
11901101 ACGATTCAAG
*
11901111 ATTAAACCAATAAC-
1 ATTAAACCAAAAACA
11901125 ATTAAACCAAAAACA
1 ATTAAACCAAAAACA
11901140 ATTAA
1 ATTAA
11901145 TCTCCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (15 bp):
ATTAAACCAAAAACA
Found at i:11915736 original size:19 final size:20
Alignment explanation
Indices: 11915704--11915741 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11915694 CGGCGCCGAT
11915704 TCTGTAAGTATTTT-AAAAC
1 TCTGTAAGTATTTTGAAAAC
11915723 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTATTTTGAAAA
11915742 TATGAGTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (20 bp):
TCTGTAAGTATTTTGAAAAC
Found at i:11927434 original size:27 final size:26
Alignment explanation
Indices: 11927404--11927540 Score: 98
Period size: 27 Copynumber: 5.1 Consensus size: 26
11927394 TCGATATCTA
11927404 GACCGAAATACCCTCGAAGGATAAAAT
1 GACCGAAATACCCT-GAAGGATAAAAT
* * * *
11927431 GACCAAAATACCCTTAATGGGTAATAT
1 GACCGAAATACCCTGAA-GGATAAAAT
* *
11927458 GATCGAAATACTCCTGTAGG-TAAGAAT
1 GACCGAAATAC-CCTGAAGGATAA-AAT
* * * *
11927485 -ACTGAAATACCCTCATAAGTTAAAAT
1 GACCGAAATACCCTGA-AGGATAAAAT
* *
11927511 GACCGTAATACTCCTGTAGGATAAAAT
1 GACCGAAATAC-CCTGAAGGATAAAAT
11927538 GAC
1 GAC
11927541 TGTAATGCCC
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
25 3 0.04
26 18 0.22
27 55 0.66
28 7 0.08
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (26 bp):
GACCGAAATACCCTGAAGGATAAAAT
Found at i:11927545 original size:27 final size:27
Alignment explanation
Indices: 11927464--11927594 Score: 108
Period size: 27 Copynumber: 4.9 Consensus size: 27
11927454 ATATGATCGA
* *
11927464 AATACTCCTGTAGG-TAAGAAT-ACTGA
1 AATACCCCTGTAGGTTAA-AATGACTGT
* * *
11927490 AATA-CCCTCATAAGTTAAAATGACCGT
1 AATACCCCT-GTAGGTTAAAATGACTGT
* *
11927517 AATACTCCTGTAGGATAAAATGACTGT
1 AATACCCCTGTAGGTTAAAATGACTGT
* *
11927544 AATGCCCCTGTAGGGTAAAATGA-TCGT
1 AATACCCCTGTAGGTTAAAATGACT-GT
* *
11927571 AATGCCCCTATAGGTTAAAATGAC
1 AATACCCCTGTAGGTTAAAATGAC
11927595 CATAATGCTC
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
25 3 0.04
26 11 0.13
27 67 0.80
28 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
AATACCCCTGTAGGTTAAAATGACTGT
Found at i:11927573 original size:54 final size:53
Alignment explanation
Indices: 11927425--11927594 Score: 148
Period size: 54 Copynumber: 3.2 Consensus size: 53
11927415 CCTCGAAGGA
** * * *
11927425 TAAAATGACCAAAATACCCTTA-ATGGGTAATATGATCGAAATACTCCTGTAGG
1 TAAAATGACTGAAATACCCTCATA-GGGTAAAATGATCGTAATACTCCTGTAGG
* * *
11927478 TAAGAAT-ACTGAAATACCCTCATAAGTTAAAATGACCGTAATACTCCTGTAGG
1 TAA-AATGACTGAAATACCCTCATAGGGTAAAATGATCGTAATACTCCTGTAGG
* * * * * *
11927531 ATAAAATGACTGTAATGCCC-CTGTAGGGTAAAATGATCGTAATGCCCCTATAGG
1 -TAAAATGACTGAAATACCCTC-ATAGGGTAAAATGATCGTAATACTCCTGTAGG
11927585 TTAAAATGAC
1 -TAAAATGAC
11927595 CATAATGCTC
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 43 0.46
54 51 0.54
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (53 bp):
TAAAATGACTGAAATACCCTCATAGGGTAAAATGATCGTAATACTCCTGTAGG
Found at i:11927600 original size:27 final size:27
Alignment explanation
Indices: 11927494--11927602 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 27
11927484 TACTGAAATA
* *
11927494 CCCTCATAAGTTAAAATGACCGTAATAC
1 CCCT-ATAGGTTAAAATGACCGTAATGC
* * * *
11927522 TCCTGTAGGATAAAATGACTGTAATGC
1 CCCTATAGGTTAAAATGACCGTAATGC
* * *
11927549 CCCTGTAGGGTAAAATGATCGTAATGC
1 CCCTATAGGTTAAAATGACCGTAATGC
*
11927576 CCCTATAGGTTAAAATGACCATAATGC
1 CCCTATAGGTTAAAATGACCGTAATGC
11927603 TCTGGTGGGT
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 64 0.96
28 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (27 bp):
CCCTATAGGTTAAAATGACCGTAATGC
Found at i:11927893 original size:32 final size:33
Alignment explanation
Indices: 11927840--11928022 Score: 146
Period size: 32 Copynumber: 5.7 Consensus size: 33
11927830 GCTGCGATGC
* **
11927840 TACTGATGGCTTTGTATCGATCATAGT-ACCGT
1 TACTGATGGCTGTGTGCCGATCATAGTCACCGT
* *
11927872 TACT-AGTGGCTGTGTGCCGATCAT-TTCACTGT
1 TACTGA-TGGCTGTGTGCCGATCATAGTCACCGT
* ** * *
11927904 TACTGATGGTTGTGTGATGATCATA-TCACTGC
1 TACTGATGGCTGTGTGCCGATCATAGTCACCGT
* *
11927936 TACTGATGGCTTTGTG-CGAATCAT-GTTACCGT
1 TACTGATGGCTGTGTGCCG-ATCATAGTCACCGT
* * *
11927968 TACTGATGGTTGTGTGCCGATCATA-TCACTGC
1 TACTGATGGCTGTGTGCCGATCATAGTCACCGT
* *
11928000 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTGTGTGCCGATCA
11928023 CATTACTGTA
Statistics
Matches: 120, Mismatches: 23, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
31 3 0.03
32 114 0.95
33 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (33 bp):
TACTGATGGCTGTGTGCCGATCATAGTCACCGT
Found at i:11927928 original size:64 final size:64
Alignment explanation
Indices: 11927840--11928022 Score: 189
Period size: 64 Copynumber: 2.9 Consensus size: 64
11927830 GCTGCGATGC
*
11927840 TACTGATGGCTT-TGT-ATCGATCATAGT-ACCGTTACT-AGTGGCTGTGTGCCG-ATCAT-TTC
1 TACTGATGG-TTGTGTGAT-GATCATA-TCACCGCTACTGA-TGGCTGTGTG-CGAATCATGTT-
*
11927899 ACTGT
60 ACCGT
* *
11927904 TACTGATGGTTGTGTGATGATCATATCACTGCTACTGATGGCTTTGTGCGAATCATGTTACCGT
1 TACTGATGGTTGTGTGATGATCATATCACCGCTACTGATGGCTGTGTGCGAATCATGTTACCGT
** * * *
11927968 TACTGATGGTTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGTGCCAATCA
1 TACTGATGGTTGTGTGATGATCATATCACCGCTACTGATGGCTGTGTGCGAATCA
11928023 CATTACTGTA
Statistics
Matches: 106, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
63 5 0.05
64 96 0.91
65 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (64 bp):
TACTGATGGTTGTGTGATGATCATATCACCGCTACTGATGGCTGTGTGCGAATCATGTTACCGT
Found at i:11928307 original size:28 final size:28
Alignment explanation
Indices: 11928273--11928339 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
11928263 TAACGGGCAG
11928273 AGGCCCACACTATTTCTATATTGGGCTA
1 AGGCCCACACTATTTCTATATTGGGCTA
*
11928301 AGGCCCACACTATTTCTGTATTGGGCTA
1 AGGCCCACACTATTTCTATATTGGGCTA
11928329 AGGCCCACACT
1 AGGCCCACACT
11928340 GTACTATTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (28 bp):
AGGCCCACACTATTTCTATATTGGGCTA
Found at i:11931235 original size:17 final size:17
Alignment explanation
Indices: 11931194--11931242 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
11931184 TCATTTATAT
*
11931194 ACATATAATATATATAC
1 ACATATAATATATACAC
*
11931211 ACACATAATATATACAC
1 ACATATAATATATACAC
11931228 A-ATTATAATAATATA
1 ACA-TATAAT-ATATA
11931243 AAAAATATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 21 0.78
18 5 0.19
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
ACATATAATATATACAC
Found at i:11934695 original size:21 final size:21
Alignment explanation
Indices: 11934662--11934710 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
11934652 ATCATGTTAT
*
11934662 TTAT-TTTTATTTGATTTTG-
1 TTATGTTTTATTTGAATTTGA
11934681 TTATGTTTATATTTGAATTTGAA
1 TTATGTTT-TATTTGAATTTG-A
11934704 TTATGTT
1 TTATGTT
11934711 AGCACCACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 11 0.44
23 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.65
Consensus pattern (21 bp):
TTATGTTTTATTTGAATTTGA
Found at i:11935688 original size:23 final size:23
Alignment explanation
Indices: 11935662--11935707 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11935652 GAGTGTATAA
*
11935662 ATGTATGCATATGAAT-TATTTTG
1 ATGTATGAAT-TGAATGTATTTTG
*
11935685 ATGTTTGAATTGAATGTATTTTG
1 ATGTATGAATTGAATGTATTTTG
11935708 TTATAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (23 bp):
ATGTATGAATTGAATGTATTTTG
Found at i:11936829 original size:14 final size:14
Alignment explanation
Indices: 11936810--11936843 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11936800 ATTTTCTTCA
11936810 CTTGAACCCTGCAC
1 CTTGAACCCTGCAC
*
11936824 CTTGAATCCTGCAC
1 CTTGAACCCTGCAC
11936838 CTTGAA
1 CTTGAA
11936844 ACTTAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (14 bp):
CTTGAACCCTGCAC
Found at i:11937027 original size:18 final size:19
Alignment explanation
Indices: 11937001--11937038 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11936991 TTAGAGTCCA
*
11937001 AAATGACATAAAAT-ATTG
1 AAATAACATAAAATAATTG
*
11937019 AAATAACATTAAATAATTG
1 AAATAACATAAAATAATTG
11937038 A
1 A
11937039 TAAAAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
AAATAACATAAAATAATTG
Found at i:11940504 original size:3 final size:3
Alignment explanation
Indices: 11940496--11940521 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11940486 ACAACCTTGA
11940496 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
11940522 AACAAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11944416 original size:43 final size:43
Alignment explanation
Indices: 11944371--11944631 Score: 177
Period size: 43 Copynumber: 6.1 Consensus size: 43
11944361 GGACAGGACG
* * *
11944371 AAGTAATTATACTGGTACACATAGTACATCATTGGATAAACCG
1 AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
* ** ** ** *
11944414 AAGCAATTATGTTGGCACGTA-AGTGCATCATTGGATGTACCG
1 AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
* * * ** * *
11944456 AAGAAAATATA-TCG-ACATGTAAGTGCATCATAGGATATACCA
1 AAGTAATTATACTGGCACACAT-AGTGCATCATTGGATAAACCA
* ** * * * **
11944498 AAGCAATTATACTAACACACATAGTGCATTATCGGACAAGTCA
1 AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
* * * * ***
11944541 AATTAATTATACTAGCACACACAGTGCATCATTGGACAAGGTA
1 AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
* *
11944584 AAGTAATTATACTGGCACACATAGTGCATCATTGGGTAAATCA
1 AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
11944627 AAGTA
1 AAGTA
11944632 TAAATTGTAC
Statistics
Matches: 168, Mismatches: 46, Indels: 8
0.76 0.21 0.04
Matches are distributed among these distances:
40 3 0.02
41 2 0.01
42 53 0.32
43 106 0.63
44 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (43 bp):
AAGTAATTATACTGGCACACATAGTGCATCATTGGATAAACCA
Found at i:11944449 original size:42 final size:42
Alignment explanation
Indices: 11944397--11944508 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 42
11944387 ACACATAGTA
* * * *
11944397 CATCATTGGATAAACCGAAGCAATTATGTTGGCACGTAAGTG
1 CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
* * * *
11944439 CATCATTGGATGTACCGAAGAAAATATATCGACATGTAAGTG
1 CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
* *
11944481 CATCATAGGATATACCAAAGCAATTATA
1 CATCATTGGATATACCGAAGCAATTATA
11944509 CTAACACACA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (42 bp):
CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
Found at i:11949288 original size:46 final size:47
Alignment explanation
Indices: 11949224--11949314 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 47
11949214 CTTTGAATTG
* *
11949224 CGAACTCAAATCTCAAACCATAAATTTCAAATCTCAAAC-TCGAACT
1 CGAACTCAAATCTCAAACCATAAATCTCAAACCTCAAACTTCGAACT
* * *
11949270 CGAACTCGAA-CTCTAAACCTTAAATCTCAAACCTTAAACTTCGAA
1 CGAACTCAAATCTC-AAACCATAAATCTCAAACCTCAAACTTCGAA
11949315 ACTTAAACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 3 0.08
46 30 0.79
47 5 0.13
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (47 bp):
CGAACTCAAATCTCAAACCATAAATCTCAAACCTCAAACTTCGAACT
Found at i:11951207 original size:14 final size:14
Alignment explanation
Indices: 11951190--11951216 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11951180 AAATTAAAAA
11951190 AAAATATTAGAATT
1 AAAATATTAGAATT
11951204 AAAATATTAGAAT
1 AAAATATTAGAAT
11951217 CACAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAATATTAGAATT
Found at i:11951223 original size:14 final size:14
Alignment explanation
Indices: 11951190--11951223 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11951180 AAATTAAAAA
*
11951190 AAAATATTAGAATT
1 AAAATATTAGAATC
11951204 AAAATATTAGAATC
1 AAAATATTAGAATC
*
11951218 ACAATA
1 AAAATA
11951224 AAACAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
AAAATATTAGAATC
Found at i:11952210 original size:7 final size:7
Alignment explanation
Indices: 11952169--11952213 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
11952159 TAGTTGAACA
*
11952169 AATTGCA
1 AATTGCT
*
11952176 AATTGCA
1 AATTGCT
11952183 AATTGCT
1 AATTGCT
11952190 AATTGCT
1 AATTGCT
11952197 AATTGCT
1 AATTGCT
11952204 AATTGCT
1 AATTGCT
11952211 AAT
1 AAT
11952214 CGCTTAGCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (7 bp):
AATTGCT
Found at i:11953583 original size:31 final size:30
Alignment explanation
Indices: 11953526--11953588 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
11953516 AAATTCTATT
*
11953526 TTTTCGAAAAATTTAAAATTTTAAAAAATA
1 TTTTCGAAAAATTTAAAATTTAAAAAAATA
* *
11953556 TTTTCTAAAAATTTTAATAA-TTAAAAAATTA
1 TTTTCGAAAAA-TTTAA-AATTTAAAAAAATA
11953587 TT
1 TT
11953589 AAATTTTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.36
31 16 0.57
32 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTTCGAAAAATTTAAAATTTAAAAAAATA
Found at i:11955706 original size:14 final size:14
Alignment explanation
Indices: 11955695--11955724 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11955685 TTAAAATGTT
11955695 TTTC-GGAAAATGA
1 TTTCTGGAAAATGA
11955708 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
11955722 TTT
1 TTT
11955725 ACTTTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:11955868 original size:20 final size:20
Alignment explanation
Indices: 11955845--11955883 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11955835 ATTTTTACAT
11955845 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
11955865 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
11955884 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:11956133 original size:38 final size:38
Alignment explanation
Indices: 11956090--11956176 Score: 174
Period size: 38 Copynumber: 2.3 Consensus size: 38
11956080 TCCAAACCAC
11956090 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
1 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
11956128 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
1 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
11956166 AATTAATACTA
1 AATTAATACTA
11956177 ATACAACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (38 bp):
AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
Found at i:11956134 original size:22 final size:22
Alignment explanation
Indices: 11956109--11956173 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
11956099 TAGAAATTAA
11956109 TAATATTATCCAAATGCATAAT
1 TAATATTATCCAAATGCATAAT
* *
11956131 TAATACTA--GAAAT---TAA-
1 TAATATTATCCAAATGCATAAT
11956147 TAATATTATCCAAATGCATAAT
1 TAATATTATCCAAATGCATAAT
11956169 TAATA
1 TAATA
11956174 CTAATACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 7 0.21
17 3 0.09
18 4 0.12
20 4 0.12
21 3 0.09
22 12 0.36
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (22 bp):
TAATATTATCCAAATGCATAAT
Found at i:11956188 original size:38 final size:38
Alignment explanation
Indices: 11956090--11956189 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 38
11956080 TCCAAACCAC
**
11956090 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
1 AATTAATACTAGAAACAAATAATATTATCCAAATGCAT
**
11956128 AATTAATACTAGAAATTAATAATATTATCCAAATGCAT
1 AATTAATACTAGAAACAAATAATATTATCCAAATGCAT
*
11956166 AATTAATACTA-ATACAACATAATA
1 AATTAATACTAGAAACAA-ATAATA
11956190 ACAACAACAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 3 0.05
38 55 0.95
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (38 bp):
AATTAATACTAGAAACAAATAATATTATCCAAATGCAT
Found at i:11957227 original size:32 final size:32
Alignment explanation
Indices: 11957181--11957245 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
11957171 TGTCAATCAT
11957181 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
11957213 TTCAATATCTAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
11957245 T
1 T
11957246 ATCTAACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:11957248 original size:27 final size:29
Alignment explanation
Indices: 11957184--11957253 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 29
11957174 CAATCATTTC
*
11957184 AATATCCAACAAGCTTAAAACATAATAAATT
1 AATATCTAACAAGCTTAAAACATAAT-AA-T
11957215 CAATATCTAACAAGCTTAAAACATAAT-A-
1 -AATATCTAACAAGCTTAAAACATAATAAT
11957243 AATATCTAACA
1 AATATCTAACA
11957254 TTCAAGACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 11 0.30
30 1 0.03
32 25 0.68
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (29 bp):
AATATCTAACAAGCTTAAAACATAATAAT
Found at i:11958868 original size:22 final size:21
Alignment explanation
Indices: 11958824--11958869 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
11958814 AGATGCAAGC
*
11958824 TATTAAAAGCAAAAGATATAA
1 TATTAAAAGCAAAAGAAATAA
11958845 TATTAAAAGCTAAAA-AAATGAA
1 TATTAAAAGC-AAAAGAAAT-AA
11958867 TAT
1 TAT
11958870 AGCTCATGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (21 bp):
TATTAAAAGCAAAAGAAATAA
Found at i:11963103 original size:24 final size:24
Alignment explanation
Indices: 11963069--11963120 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11963059 TTTCTAGAAG
* **
11963069 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
11963093 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
11963117 ATTT
1 ATTT
11963121 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:11966688 original size:19 final size:18
Alignment explanation
Indices: 11966664--11966699 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
11966654 CATGCTTTCT
11966664 ATTCACATTTTCATATTCA
1 ATTCACATTTT-ATATTCA
11966683 ATTCACATTTTATATTC
1 ATTCACATTTTATATTC
11966700 CACAATCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCACATTTTATATTCA
Found at i:11967926 original size:22 final size:21
Alignment explanation
Indices: 11967901--11967941 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
11967891 TCTTTTTCTA
11967901 TTTGTTTTATCTATTTATTTGT
1 TTTGTTTTATCT-TTTATTTGT
11967923 TTTGTTTTATCTTTTATTT
1 TTTGTTTTATCTTTTATTT
11967942 TACTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTGTTTTATCTTTTATTTGT
Found at i:11968115 original size:31 final size:31
Alignment explanation
Indices: 11968080--11968148 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
11968070 TATTTATCAT
11968080 ATAAAA-ATAT-TTTACTAATTAATAATAAATA
1 ATAAAATATATGTTTACTAATT-AT-ATAAATA
* *
11968111 ATAAAATATCTGTTTACTAATTATATATATA
1 ATAAAATATATGTTTACTAATTATATAAATA
11968142 ATAAAAT
1 ATAAAAT
11968149 GTACTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 19 0.56
32 5 0.15
33 10 0.29
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
ATAAAATATATGTTTACTAATTATATAAATA
Found at i:11968247 original size:29 final size:29
Alignment explanation
Indices: 11968205--11968261 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
11968195 ATCTTTTCTT
*
11968205 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
11968234 AATTTAATTT-ATAATATAATAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
11968262 AACAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:11968282 original size:37 final size:37
Alignment explanation
Indices: 11968215--11968285 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
11968205 AATTTATTTC
* * *
11968215 ATAATATAATAATATAATCAATTTAATTTATAATATA
1 ATAAAATAATAAAATAATCAATATAATTTATAATATA
*
11968252 ATAAAATAATAACAATAAT-AATATATTTTATAAT
1 ATAAAATAATAA-AATAATCAATATAATTTATAAT
11968286 TAAACAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (37 bp):
ATAAAATAATAAAATAATCAATATAATTTATAATATA
Found at i:11971683 original size:38 final size:38
Alignment explanation
Indices: 11971641--11971715 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
11971631 TCTTTTCACA
11971641 GCAATCCAAAATCACTCCATGTTCAGATAACCAATCCG
1 GCAATCCAAAATCACTCCATGTTCAGATAACCAATCCG
11971679 GCAATCCAAAATCACTCCATGTTCAGATAACCAATCC
1 GCAATCCAAAATCACTCCATGTTCAGATAACCAATCC
11971716 ATCCCTAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.32, G:0.09, T:0.21
Consensus pattern (38 bp):
GCAATCCAAAATCACTCCATGTTCAGATAACCAATCCG
Found at i:11974181 original size:19 final size:18
Alignment explanation
Indices: 11974157--11974192 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
11974147 CATGCTTTCT
11974157 ATTCACATTTTCATATTCA
1 ATTCACATTTT-ATATTCA
11974176 ATTCACATTTTATATTC
1 ATTCACATTTTATATTC
11974193 CACAATCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCACATTTTATATTCA
Found at i:11975434 original size:22 final size:22
Alignment explanation
Indices: 11975406--11975447 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
11975396 TCTTTTTCTA
11975406 TTTG-TTTTATCTATTTATTTGT
1 TTTGTTTTTATCT-TTTATTTGT
11975428 TTTGTTTTTATCTTTTATTT
1 TTTGTTTTTATCTTTTATTT
11975448 TACTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTGTTTTTATCTTTTATTTGT
Found at i:11980463 original size:24 final size:24
Alignment explanation
Indices: 11980429--11980480 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11980419 TTTCAAGAAG
* **
11980429 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
11980453 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
11980477 ATTT
1 ATTT
11980481 GAATTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:11980491 original size:24 final size:24
Alignment explanation
Indices: 11980446--11980491 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
11980436 ATTTATGAGT
*
11980446 ATAATATATTTAGCATTTATTAAC
1 ATAATATATTTAGAATTTATTAAC
11980470 ATAATATATTT-GAATTTGATTA
1 ATAATATATTTAGAATTT-ATTA
11980492 GAATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAGAATTTATTAAC
Found at i:11982793 original size:51 final size:52
Alignment explanation
Indices: 11982738--11982960 Score: 217
Period size: 51 Copynumber: 4.4 Consensus size: 52
11982728 TTCGGTGGGT
* * *
11982738 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * * * *
11982789 TGCACATAGTACT--ACACGTGATCA-AG-CTTTTCGGTTCACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * * * * *
11982837 TACACATAGTACTACACACATGACCA-AGGCCATCCGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * *
11982888 TGCACATAGTACTACACATGTGATCATTATCTAT-CGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
*
11982939 TGCACTTAGTACTACACACGTG
1 TGCACATAGTACTACACACGTG
11982961 TTCATAGGTA
Statistics
Matches: 138, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
47 1 0.01
48 29 0.21
49 8 0.06
50 11 0.08
51 86 0.62
52 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (52 bp):
TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
Found at i:11990728 original size:54 final size:54
Alignment explanation
Indices: 11990663--11990857 Score: 250
Period size: 54 Copynumber: 3.5 Consensus size: 54
11990653 CCTTACAGCG
11990663 GGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCA
1 GGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCA
* * * *
11990717 GGATTACCAGTCCAGGCTAAATCCCCTGCAATGACAATTACTC-TAATGAGCT-TGGATCT
1 GGATTACCAGTCCAGGCTAAATCCCCTGTAAT-ATAA--ACTCAT-A-GAG-TATTG-TCA
* * *
11990776 GAATTACCAGTCCAGGATAAATCCCCTGTAATATAAACTCATAGAGTATTGTCG
1 GGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCA
11990830 GGATTACCAGTCCAGGCTAAATCCCCTG
1 GGATTACCAGTCCAGGCTAAATCCCCTG
11990858 CAATGACAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
54 60 0.50
55 8 0.07
56 6 0.05
57 6 0.05
58 8 0.07
59 32 0.27
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (54 bp):
GGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCA
Found at i:11990863 original size:113 final size:113
Alignment explanation
Indices: 11990665--11990910 Score: 474
Period size: 113 Copynumber: 2.2 Consensus size: 113
11990655 TTACAGCGGG
11990665 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCC
1 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCC
11990730 AGGCTAAATCCCCTGCAATGACAATTACTCTAATGAGCTTGGATCTGA
66 AGGCTAAATCCCCTGCAATGACAATTACTCTAATGAGCTTGGATCTGA
* *
11990778 ATTACCAGTCCAGGATAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTACCAGTCC
1 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCC
11990843 AGGCTAAATCCCCTGCAATGACAATTACTCTAATGAGCTTGGATCTGA
66 AGGCTAAATCCCCTGCAATGACAATTACTCTAATGAGCTTGGATCTGA
11990891 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
11990911 TCAGACCCTA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 130 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (113 bp):
ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCC
AGGCTAAATCCCCTGCAATGACAATTACTCTAATGAGCTTGGATCTGA
Found at i:12001082 original size:50 final size:50
Alignment explanation
Indices: 12001014--12001201 Score: 216
Period size: 51 Copynumber: 3.7 Consensus size: 50
12001004 TGTCATCCGA
*
12001014 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAGCTTTCAGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGCTTTCAGG
* * *
12001064 TGCACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGGCATTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAA-GCTTTCAGG
* ** * * * *
12001115 TACACATAGTAGCCTGGACATAGTACTACACATGTGACCATTATCTATCA-A
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCA--AGCTTTCAGG
* * *
12001166 TACACGTAGTAGGCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
12001202 CTCACAGGTA
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
50 39 0.34
51 73 0.63
52 3 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (50 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGCTTTCAGG
Found at i:12003864 original size:46 final size:46
Alignment explanation
Indices: 12003797--12003884 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
12003787 ATATGTGCAG
* *
12003797 TGTGGGCCTTAGCTAATTACAGT-ATCAGAATCAGAAATAGAATACA
1 TGTGGGCCTAAGCCAATTACAGTGA-CAGAATCAGAAATAGAATACA
*
12003843 TGTGGGCCTAAGCCCAA-TACAGTGACAGAATCAGTAATAGAA
1 TGTGGGCCTAAG-CCAATTACAGTGACAGAATCAGAAATAGAA
12003885 ATGCAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 33 0.89
47 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (46 bp):
TGTGGGCCTAAGCCAATTACAGTGACAGAATCAGAAATAGAATACA
Found at i:12004155 original size:32 final size:31
Alignment explanation
Indices: 12004100--12004238 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 31
12004090 GAATGACTAC
* * *
12004100 AAGCCATAAGTACAGTAATATGATTGGCACA
1 AAGCCATCAGTACAGTAATATGATCGACACA
* *
12004131 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTA-CAGTAATATGATCGACACA
* * *
12004163 TAGGCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGT-ACAGTAATATGATCGACACA
12004195 AAGCCATCAGTA-ATGATAATATGATCGACACA
1 AAGCCATCAGTACA-G-TAATATGATCGACACA
12004227 AAGCCATCAGTA
1 AAGCCATCAGTA
12004239 GCATCGTAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
31 13 0.14
32 79 0.85
33 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (31 bp):
AAGCCATCAGTACAGTAATATGATCGACACA
Found at i:12004435 original size:11 final size:11
Alignment explanation
Indices: 12004419--12004461 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12004409 AATCAGTCAT
12004419 ACAAATCACAA
1 ACAAATCACAA
*
12004430 ACAAATCAGTCAT
1 ACAAATCA--CAA
*
12004443 ACCAATCACAA
1 ACAAATCACAA
12004454 ACAAATCA
1 ACAAATCA
12004462 GTCATTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.56, C:0.28, G:0.02, T:0.14
Consensus pattern (11 bp):
ACAAATCACAA
Found at i:12004441 original size:24 final size:24
Alignment explanation
Indices: 12004409--12004466 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
12004399 CCATGCTCAG
12004409 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATACAAATCACAAACA
*
12004433 AATCAGTCATACCAATCACAAACA
1 AATCAGTCATACAAATCACAAACA
12004457 AATCAGTCAT
1 AATCAGTCAT
12004467 TTACATCACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAAACA
Found at i:12004474 original size:24 final size:24
Alignment explanation
Indices: 12004409--12004495 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
12004399 CCATGCTCAG
** *
12004409 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATTTACATCACAAACA
12004433 AATCAGTCA--TACCAATCACAAACA
1 AATCAGTCATTTA-C-ATCACAAACA
**
12004457 AATCAGTCATTTACATCACCGACA
1 AATCAGTCATTTACATCACAAACA
*
12004481 AATCAATCATTTACA
1 AATCAGTCATTTACA
12004496 CTCGAGGGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
24 50 0.93
25 1 0.02
26 2 0.04
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.22
Consensus pattern (24 bp):
AATCAGTCATTTACATCACAAACA
Found at i:12004568 original size:27 final size:28
Alignment explanation
Indices: 12004532--12004603 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
12004522 CTCTAGGGGC
* *
12004532 ATTACGGTCATTTTACCTGAA-AAGGGT
1 ATTACAGTCATTTTACCTCAATAAGGGT
* *
12004559 ATTTCAGTCATTTTACC-CAATGAGGGT
1 ATTACAGTCATTTTACCTCAATAAGGGT
12004586 ATTACAGTCATTTTACCT
1 ATTACAGTCATTTTACCT
12004604 TACAGGGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (28 bp):
ATTACAGTCATTTTACCTCAATAAGGGT
Found at i:12004616 original size:27 final size:27
Alignment explanation
Indices: 12004526--12004638 Score: 79
Period size: 27 Copynumber: 4.1 Consensus size: 27
12004516 TTTACCCTCT
* * *
12004526 AGGGGCATTACGGTCATTTTACCTGAA
1 AGGGGCATTACAGTCATTTTACCTTAC
* * * *
12004553 AAGGGTATTTCAGTCATTTTACC-CA-
1 AGGGGCATTACAGTCATTTTACCTTAC
*
12004578 ATGAGGGTATTACAGTCATTTTACCTTAC
1 A-G-GGGCATTACAGTCATTTTACCTTAC
* *
12004607 AGGGGCATTA-TGATCATTTTACCCTAC
1 AGGGGCATTACAG-TCATTTTACCTTAC
12004634 GAGGG
1 -AGGG
12004639 TATTTCGATC
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 59 0.86
28 6 0.09
29 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (27 bp):
AGGGGCATTACAGTCATTTTACCTTAC
Found at i:12004648 original size:27 final size:27
Alignment explanation
Indices: 12004554--12004921 Score: 385
Period size: 27 Copynumber: 13.7 Consensus size: 27
12004544 TTACCTGAAA
12004554 AGGGTATTTC-AGTCATTTTACCCAAT-G
1 AGGGTATTTCGA-TCATTTTACCC-ATCG
* *
12004581 AGGGTATTAC-AGTCATTTTA-CCTTAC-
1 AGGGTATTTCGA-TCATTTTACCCAT-CG
*
12004607 AGGGGCATTAT-GATCATTTTACCC-TACG
1 A-GGGTATT-TCGATCATTTTACCCAT-CG
*
12004635 AGGGTATTTCGATCATTTTACCGATCG
1 AGGGTATTTCGATCATTTTACCCATCG
* * *
12004662 AGGATATTT-TAGTAATTTTACCCATCG
1 AGGGTATTTCGA-TCATTTTACCCATCG
** **
12004689 AGGGTATTTTAATCATTTTATTCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
* *
12004716 AGGGTATTTCAATAATTTTACCCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
*
12004743 AGGGTAGTTCGATCATTTTACCCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
* *
12004770 AGGGTATTTTGGTCATTTTACCCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
*
12004797 AGGGTATTTCAATCATTTTACCCATC-
1 AGGGTATTTCGATCATTTTACCCATCG
*
12004823 AGGGTATTTCGATCATTTTACCCAGCG
1 AGGGTATTTCGATCATTTTACCCATCG
* * * *
12004850 GGGGCATTTTGGTCATTTTACCCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
*
12004877 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATCATTTTACCCATCG
*
12004904 AGGGTTTTTCGATCATTT
1 AGGGTATTTCGATCATTT
12004922 AACAAATATT
Statistics
Matches: 287, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.00
26 29 0.10
27 251 0.87
28 6 0.02
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATCATTTTACCCATCG
Found at i:12006692 original size:40 final size:41
Alignment explanation
Indices: 12006633--12006724 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 41
12006623 GATTCCCTTC
12006633 CATTTTCTGTCTGT-TTGTTTCTAGTTAATCCGGGTAACTT
1 CATTTTCTGTCTGTCTTGTTTCTAGTTAATCCGGGTAACTT
* *
12006673 CATTTTCTGTCTAGCTGTTTGTTTCTGGTTAATCCGGGTAACTT
1 CATTTTCTGTCT-G-T-CTTGTTTCTAGTTAATCCGGGTAACTT
12006717 CATTTTCT
1 CATTTTCT
12006725 TGTTCTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 12 0.26
41 1 0.02
42 1 0.02
44 33 0.70
ACGTcount: A:0.14, C:0.18, G:0.17, T:0.50
Consensus pattern (41 bp):
CATTTTCTGTCTGTCTTGTTTCTAGTTAATCCGGGTAACTT
Found at i:12007896 original size:12 final size:12
Alignment explanation
Indices: 12007879--12007911 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12007869 TTTTCCAAAC
12007879 TTGTTTTTTTTT
1 TTGTTTTTTTTT
12007891 TTGTTTTTGTTTT
1 TTGTTTTT-TTTT
12007904 TT-TTTTTT
1 TTGTTTTTT
12007912 GCGTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 13 0.65
13 6 0.30
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:12008495 original size:5 final size:5
Alignment explanation
Indices: 12008485--12008509 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12008475 TTGCTTTTAG
12008485 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
12008510 TCTTTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:12010648 original size:22 final size:23
Alignment explanation
Indices: 12010623--12010677 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12010613 TGTACTATGA
*
12010623 TGCCTACTGATTCA-CACTTCGG
1 TGCCTACTGATTAATCACTTCGG
* *
12010645 TGCCTACT-ACTAATCACTTTGG
1 TGCCTACTGATTAATCACTTCGG
12010667 TGCCTACTGAT
1 TGCCTACTGAT
12010678 ATGGTGTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (23 bp):
TGCCTACTGATTAATCACTTCGG
Found at i:12011322 original size:16 final size:16
Alignment explanation
Indices: 12011301--12011331 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12011291 TTCATTAGTA
*
12011301 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
12011317 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
12011332 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:12012918 original size:14 final size:14
Alignment explanation
Indices: 12012896--12012927 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12012886 AGGTCATTTA
*
12012896 GCCCCACCAAACTG
1 GCCCAACCAAACTG
12012910 GCCCAACCAAACTG
1 GCCCAACCAAACTG
12012924 GCCC
1 GCCC
12012928 GGTGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.50, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:12018037 original size:14 final size:14
Alignment explanation
Indices: 12018018--12018049 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12018008 AGGTCATTTA
12018018 GCCCAACCAAACTG
1 GCCCAACCAAACTG
12018032 GCCCAACCAAACTG
1 GCCCAACCAAACTG
12018046 GCCC
1 GCCC
12018050 GATGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:12026425 original size:68 final size:70
Alignment explanation
Indices: 12026316--12026444 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 70
12026306 TTTTAATAGT
*
12026316 TTAATATTAAATTAAATTTAATACTTATATTAATAGCATTTT-ATTA-ATTTAATATTAAAGTAA
1 TTAATATTAAATTAAATTTAATACTTATATTAATAGCATTTTAATAAGATTTAATATTAAAGTAA
12026379 TTATC
66 TTATC
** * ** *
12026384 TTAATATTAAATTAAATTTAATGTTTATCATT-CTATTATTTTAATAAGATTTACTATTAAA
1 TTAATATTAAATTAAATTTAATACTTAT-ATTAATAGCATTTTAATAAGATTTAATATTAAA
12026445 TTTAATCTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
68 33 0.65
69 6 0.12
70 12 0.24
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (70 bp):
TTAATATTAAATTAAATTTAATACTTATATTAATAGCATTTTAATAAGATTTAATATTAAAGTAA
TTATC
Found at i:12026507 original size:15 final size:17
Alignment explanation
Indices: 12026446--12026506 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
12026436 ACTATTAAAT
12026446 TTAATCTAATATTTATC
1 TTAATCTAATATTTATC
12026463 TTAATCTAATATTTATC
1 TTAATCTAATATTTATC
* * *
12026480 TTGAT-AAATA-TTATA
1 TTAATCTAATATTTATC
12026495 TTAAT-TAATATT
1 TTAATCTAATATT
12026507 AAAGTGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 12 0.32
16 5 0.13
17 21 0.55
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAATCTAATATTTATC
Found at i:12053987 original size:29 final size:29
Alignment explanation
Indices: 12053951--12054014 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
12053941 AGCTCCATCC
12053951 AACAAATAGGTGTTCTACAGCTTCTACCA
1 AACAAATAGGTGTTCTACAGCTTCTACCA
12053980 AACAAATAGGTGTTCTACAGCTTCTACCA
1 AACAAATAGGTGTTCTACAGCTTCTACCA
12054009 AACAAA
1 AACAAA
12054015 GCTTCGAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (29 bp):
AACAAATAGGTGTTCTACAGCTTCTACCA
Found at i:12064502 original size:36 final size:37
Alignment explanation
Indices: 12064428--12064612 Score: 239
Period size: 36 Copynumber: 5.0 Consensus size: 37
12064418 AAAAAAATAA
12064428 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
* * *
12064465 TACTGATTATATTGAAAGTGCTC-AATGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
* * * * *
12064501 TATTGATCCTACTGAATGTGCTCAAATGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
12064538 TACTGATTCTACTG-AAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
* * *
12064574 TACTAATTCTACTGAATAGTTGCTCAAACAAGCATTATC
1 TACTGATTCTACTGAA-AG-TGCTCAAACGAGCAATATC
12064613 CATTGATTAT
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
36 62 0.49
37 46 0.36
38 2 0.02
39 17 0.13
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (37 bp):
TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATC
Found at i:12064568 original size:73 final size:73
Alignment explanation
Indices: 12064428--12064625 Score: 245
Period size: 73 Copynumber: 2.7 Consensus size: 73
12064418 AAAAAAATAA
* * *
12064428 TACTGATTCTACTGAAAGTGCTCAAACGAGCAATATCTACTGATTATATTGAAAGTGCTCAATGA
1 TACTGATTCTACTGAATGTGCTCAAACGAGCAATATCTACTGATTATACTGAAAGTGCTCAACGA
12064493 GCAATATC
66 GCAATATC
* * * * *
12064501 TATTGATCCTACTGAATGTGCTCAAATGAGCAATGTCTACTGATTCTACTG-AAGTGCTCAAACG
1 TACTGATTCTACTGAATGTGCTCAAACGAGCAATATCTACTGATTATACTGAAAGTGCTC-AACG
12064565 AGCAATATC
65 AGCAATATC
* * * * *
12064574 TACTAATTCTACTGAATAGTTGCTCAAACAAGCATTATCCATTGATTATACT
1 TACTGATTCTACTGAAT-G-TGCTCAAACGAGCAATATCTACTGATTATACT
12064626 AAATAAGATT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
72 8 0.08
73 70 0.67
74 1 0.01
75 25 0.24
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (73 bp):
TACTGATTCTACTGAATGTGCTCAAACGAGCAATATCTACTGATTATACTGAAAGTGCTCAACGA
GCAATATC
Found at i:12066111 original size:24 final size:24
Alignment explanation
Indices: 12066084--12066132 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
12066074 CTTGAAACCA
12066084 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
12066108 TTTCCACAGCTCTTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
12066132 T
1 T
12066133 CTTCACCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:12073294 original size:23 final size:22
Alignment explanation
Indices: 12073238--12073298 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
12073228 AAAAATACAT
*
12073238 GAGCA-CATAAGTGCTAAATCGG
1 GAGCACCA-AAGTGCTAAATCAG
12073260 GAGCACCAAAGTGCTAAATTCAG
1 GAGCACCAAAGTGCTAAA-TCAG
* *
12073283 TAGCACCGAAGTGCTA
1 GAGCACCAAAGTGCTA
12073299 GTTTCAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (22 bp):
GAGCACCAAAGTGCTAAATCAG
Found at i:12073304 original size:23 final size:23
Alignment explanation
Indices: 12073246--12073298 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
12073236 ATGAGCACAT
* *
12073246 AAGTGCTAAA-TCGGGAGCACCA
1 AAGTGCTAAATTCAGTAGCACCA
*
12073268 AAGTGCTAAATTCAGTAGCACCG
1 AAGTGCTAAATTCAGTAGCACCA
12073291 AAGTGCTA
1 AAGTGCTA
12073299 GTTTCAAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (23 bp):
AAGTGCTAAATTCAGTAGCACCA
Found at i:12077295 original size:11 final size:11
Alignment explanation
Indices: 12077281--12077313 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12077271 GAAAAAGTGC
12077281 AGAGAAAACTA
1 AGAGAAAACTA
*
12077292 AGAG-AAACTT
1 AGAGAAAACTA
12077302 AGAGAAAACTA
1 AGAGAAAACTA
12077313 A
1 A
12077314 ACCTAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.61, C:0.09, G:0.18, T:0.12
Consensus pattern (11 bp):
AGAGAAAACTA
Found at i:12082479 original size:194 final size:193
Alignment explanation
Indices: 12082150--12082536 Score: 720
Period size: 194 Copynumber: 2.0 Consensus size: 193
12082140 CTATCTACCC
12082150 AAAGTTTTGGTAGACTCTTGATTTTGTTTGGTTCGATCGAAGTGGCATGTATATAGATAGTTGGT
1 AAAGTTTTGGTAGACTCTTGATTTTGTTTGGTTCGATCGAAGTGGCATGTATATAGATAGTTGGT
*
12082215 TATTTGTAAATAAATGTGTTAAATTTAGAAGTTGATTGCTTTGGAATCTGTTGATGTATATAAAT
66 TATTTGTAAACAAATGTGTTAAATTTAGAAGTTGATTGCTTTGGAATCTGTTGATGTATATAAAT
*
12082280 AAAATGAACTCAGGTTCTGTTATGTTCCGCATTATAAGTTTTGCGGGATCTATCGCAGTTTGGG
131 AAAATGAACTCA-GATCTGTTATGTTCCGCATTATAAGTTTTGCGGGATCTATCGCAGTTTGGG
*
12082344 AAAGTTTTGGTAGACTCTTGATTTTTTTTGGTTCGATCGAAGTGGCATGTATATAGATAGTTGGT
1 AAAGTTTTGGTAGACTCTTGATTTTGTTTGGTTCGATCGAAGTGGCATGTATATAGATAGTTGGT
12082409 TATTTGTAAACAAATGTGTTAAATTTAGAAGTTGATTGCTTTGGAATCTGTTGATGTATATAAAT
66 TATTTGTAAACAAATGTGTTAAATTTAGAAGTTGATTGCTTTGGAATCTGTTGATGTATATAAAT
* *
12082474 AAAATGAACTCAGATCTGTTATGTTTCGCATTATAAGTTTTGCGGGATCTATTGCAGTTTGGG
131 AAAATGAACTCAGATCTGTTATGTTCCGCATTATAAGTTTTGCGGGATCTATCGCAGTTTGGG
12082537 GTATTCGTAG
Statistics
Matches: 188, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
193 48 0.26
194 140 0.74
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (193 bp):
AAAGTTTTGGTAGACTCTTGATTTTGTTTGGTTCGATCGAAGTGGCATGTATATAGATAGTTGGT
TATTTGTAAACAAATGTGTTAAATTTAGAAGTTGATTGCTTTGGAATCTGTTGATGTATATAAAT
AAAATGAACTCAGATCTGTTATGTTCCGCATTATAAGTTTTGCGGGATCTATCGCAGTTTGGG
Found at i:12083512 original size:22 final size:22
Alignment explanation
Indices: 12083487--12083556 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
12083477 AAATGTCACA
*
12083487 ACATTGAAGGTCAGATGTTGCG
1 ACATTGAAGGTCGGATGTTGCG
* * *
12083509 ACATTGCAGGTCGGATGTTACA
1 ACATTGAAGGTCGGATGTTGCG
* *
12083531 ACATTGAAGGTTGGATGTCGCG
1 ACATTGAAGGTCGGATGTTGCG
12083553 ACAT
1 ACAT
12083557 CAGAGACAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (22 bp):
ACATTGAAGGTCGGATGTTGCG
Found at i:12084240 original size:23 final size:23
Alignment explanation
Indices: 12084196--12084282 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
12084186 AATAGCACAT
**
12084196 AAGTGCTAAA-TCGGGAGCACCA
1 AAGTGCTAAATTCAAGAGCACCA
12084218 AAGTGCTAAATTCAAGAGCACCA
1 AAGTGCTAAATTCAAGAGCACCA
* ** **
12084241 AAGTCCTAGTTTCAAGAGCATTA
1 AAGTGCTAAATTCAAGAGCACCA
* *
12084264 GAGTGCTAAATTCATGAGC
1 AAGTGCTAAATTCAAGAGC
12084283 GCGTTATGGA
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 10 0.19
23 42 0.81
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
AAGTGCTAAATTCAAGAGCACCA
Found at i:12087092 original size:30 final size:30
Alignment explanation
Indices: 12087057--12087117 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12087047 AGATGTTATT
12087057 TTTAATGAAACTTTTATGTTGTCTAACTTA
1 TTTAATGAAACTTTTATGTTGTCTAACTTA
12087087 TTTAATGAAACTTTTATGTTGTCTAACTTA
1 TTTAATGAAACTTTTATGTTGTCTAACTTA
12087117 T
1 T
12087118 CTCTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (30 bp):
TTTAATGAAACTTTTATGTTGTCTAACTTA
Found at i:12096140 original size:35 final size:35
Alignment explanation
Indices: 12096089--12096155 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
12096079 ATATGATGAC
*
12096089 TAAGTCACTTCCTATAACCAAGTTTGAGCATTACT
1 TAAGTCACTTCCTATAACCAAGTTTAAGCATTACT
*
12096124 TAAGTCACTTCTTATAACCAAGTTTAAGCATT
1 TAAGTCACTTCCTATAACCAAGTTTAAGCATT
12096156 GCTTGGACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (35 bp):
TAAGTCACTTCCTATAACCAAGTTTAAGCATTACT
Found at i:12096541 original size:28 final size:28
Alignment explanation
Indices: 12096510--12096565 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12096500 GATTTCTACG
12096510 TAAAATCTGTGTGTTTTATTTTTCCTTT
1 TAAAATCTGTGTGTTTTATTTTTCCTTT
12096538 TAAAATCTGTGTGTTTTATTTTTCCTTT
1 TAAAATCTGTGTGTTTTATTTTTCCTTT
12096566 CTTTTTTGCT
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:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (28 bp):
TAAAATCTGTGTGTTTTATTTTTCCTTT
Found at i:12102319 original size:13 final size:14
Alignment explanation
Indices: 12102286--12102325 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
12102276 AAGAAAGTTG
* *
12102286 TAAAAGATAGACAA
1 TAAAAAATATACAA
12102300 TAAAAAATATACAA
1 TAAAAAATATACAA
12102314 -AAAAAATATACA
1 TAAAAAATATACA
12102326 GAGGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.17
Consensus pattern (14 bp):
TAAAAAATATACAA
Found at i:12102986 original size:5 final size:5
Alignment explanation
Indices: 12102971--12103010 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
12102961 TTTTTCTTTA
*
12102971 ATTTT ATTTTT GTTTT ATTTT ATTTT ATTTT -TTTT ATTTT
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
12103011 TATTGATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (5 bp):
ATTTT
Found at i:12102991 original size:10 final size:9
Alignment explanation
Indices: 12102959--12103011 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
12102949 CTAGTCCTCC
12102959 TATTTTTCTT
1 TATTTTT-TT
* *
12102969 TAATTTTAT
1 TATTTTTTT
*
12102978 T-TTTGTTT
1 TATTTTTTT
12102986 TATTTTATTT
1 TATTTT-TTT
12102996 TATTTTTTT
1 TATTTTTTT
12103005 TATTTTT
1 TATTTTT
12103012 ATTGATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 5 0.14
9 15 0.43
10 15 0.43
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (9 bp):
TATTTTTTT
Found at i:12102995 original size:21 final size:19
Alignment explanation
Indices: 12102961--12103010 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
12102951 AGTCCTCCTA
* *
12102961 TTTTTCTTTAATTTTATTTT
1 TTTTTATTTTATTTTA-TTT
12102981 TGTTTTATTTTATTTTATTT
1 T-TTTTATTTTATTTTATTT
12103001 TTTTTATTTT
1 TTTTTATTTT
12103011 TATTGATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTATTTTATTT
Found at i:12103002 original size:16 final size:16
Alignment explanation
Indices: 12102959--12103014 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
12102949 CTAGTCCTCC
* *
12102959 TATTTTTCTTTAATTT
1 TATTTTTATTTTATTT
*
12102975 TATTTTTGTTTTATTT
1 TATTTTTATTTTATTT
12102991 TA-TTTTATTTT-TTT
1 TATTTTTATTTTATTT
12103005 TATTTTTATT
1 TATTTTTATT
12103015 GATTTGATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.14
15 15 0.42
16 16 0.44
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (16 bp):
TATTTTTATTTTATTT
Found at i:12112182 original size:29 final size:31
Alignment explanation
Indices: 12112133--12112192 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
12112123 TAAGGCCTCG
12112133 TTTATCTAAATAAAAAATAAAGGGTTTATTT
1 TTTATCTAAATAAAAAATAAAGGGTTTATTT
*
12112164 TTTATC-AAA-AATAAATAAAGGGTTTATTT
1 TTTATCTAAATAAAAAATAAAGGGTTTATTT
12112193 AGTATATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 19 0.68
30 3 0.11
31 6 0.21
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTATCTAAATAAAAAATAAAGGGTTTATTT
Found at i:12115578 original size:24 final size:23
Alignment explanation
Indices: 12115534--12115578 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12115524 TAATAATTTT
**
12115534 ATTTTTATGATACATTTTTTTAA
1 ATTTTTATGATACATGCTTTTAA
*
12115557 ATTTTTATGTATATATGCTTTT
1 ATTTTTATG-ATACATGCTTTT
12115579 GTGCTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (23 bp):
ATTTTTATGATACATGCTTTTAA
Found at i:12119702 original size:39 final size:38
Alignment explanation
Indices: 12119653--12119749 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 38
12119643 GATATAATTT
* *
12119653 AATGAAATACATAAATATAATA-ATACATGATA-ATGCATG
1 AATGAAATACATAAATATAATACATA-ATAATATAT--ATA
*
12119692 AATGCAATACATAAATATAATACATAATAATATATATA
1 AATGAAATACATAAATATAATACATAATAATATATATA
*
12119730 AATGTAATACATAAATATAA
1 AATGAAATACATAAATATAA
12119750 CAAGGATAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 21 0.40
39 26 0.50
40 5 0.10
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (38 bp):
AATGAAATACATAAATATAATACATAATAATATATATA
Done.