Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 56 of 195
Found at i:11647043 original size:26 final size:26
Alignment explanation
Indices: 11647014--11647073 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
11647004 ACTTTAAGTT
**
11647014 TTTATTTTTTCTTTATTTAT-TTATTA
1 TTTATTTTTTCTAGA-TTATGTTATTA
*
11647040 TTTATTTTGTCTAGATTATGTTATTA
1 TTTATTTTTTCTAGATTATGTTATTA
11647066 -TTATTTTT
1 TTTATTTTT
11647074 CTACATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTATTTTTTCTAGATTATGTTATTA
Found at i:11647089 original size:26 final size:26
Alignment explanation
Indices: 11647031--11647096 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
11647021 TTTCTTTATT
*
11647031 TATTTATTATTTATTTTGTCTAGATTA
1 TATTTATTA-TTATTTTGTCTACATTA
*
11647058 T-GTTATTATTATTTT-TCTACATATA
1 TATTTATTATTATTTTGTCTACAT-TA
11647083 TATTTATTATTATT
1 TATTTATTATTATT
11647097 ATTATTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.18
25 10 0.29
26 17 0.50
27 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTTATTATTATTTTGTCTACATTA
Found at i:11647094 original size:3 final size:3
Alignment explanation
Indices: 11647086--11647111 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11647076 ACATATATAT
11647086 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11647112 TATTTTTTGC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11647452 original size:10 final size:9
Alignment explanation
Indices: 11647437--11647505 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 9
11647427 TACTTTGTAA
11647437 TTTTTTTTAG
1 TTTTTTTT-G
11647447 TTTTTTTAT-
1 TTTTTTT-TG
11647456 TTTTTTTT-
1 TTTTTTTTG
* *
11647464 TGTTTTATG
1 TTTTTTTTG
*
11647473 GTTTTTTTG
1 TTTTTTTTG
*
11647482 TTTTAGTTTG
1 TTTT-TTTTG
11647492 TTTTGTTTTG
1 TTTT-TTTTG
11647502 TTTT
1 TTTT
11647506 GTCTTTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
8 7 0.15
9 16 0.34
10 23 0.49
11 1 0.02
ACGTcount: A:0.06, C:0.00, G:0.13, T:0.81
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:11647477 original size:15 final size:15
Alignment explanation
Indices: 11647458--11647500 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
11647448 TTTTTTATTT
11647458 TTTTTTTGTTTTATGG
1 TTTTTTTGTTTTA-GG
11647474 TTTTTTTGTTTTA-G
1 TTTTTTTGTTTTAGG
11647488 TTTGTTTTGTTTT
1 TTT-TTTTGTTTT
11647501 GTTTTGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 13 0.50
ACGTcount: A:0.05, C:0.00, G:0.16, T:0.79
Consensus pattern (15 bp):
TTTTTTTGTTTTAGG
Found at i:11647573 original size:15 final size:15
Alignment explanation
Indices: 11647519--11647573 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
11647509 TTTTTTTTAA
11647519 TTTTTAATTTTTTG-C
1 TTTTT-ATTTTTTGCC
*
11647534 TTTTTACTTTTTGCC
1 TTTTTATTTTTTGCC
*
11647549 TTTTTATTTTTTTCC
1 TTTTTATTTTTTGCC
11647564 -TTTTATTTTT
1 TTTTTATTTTT
11647574 AAAACGACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.47
15 19 0.53
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTTTGCC
Found at i:11647816 original size:21 final size:21
Alignment explanation
Indices: 11647771--11647833 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
11647761 AATTTAATAT
*
11647771 GTGCCAGCT-AATTTGGCCTTTC
1 GTGCCAGCTAAATTAGG-C-TTC
11647793 GTGCCAGCTAAATTAGGCTTC
1 GTGCCAGCTAAATTAGGCTTC
*
11647814 GTGCCAGCTAAACTAGGCTT
1 GTGCCAGCTAAATTAGGCTT
11647834 GCATGAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 22 0.58
22 10 0.26
23 6 0.16
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (21 bp):
GTGCCAGCTAAATTAGGCTTC
Found at i:11647980 original size:32 final size:32
Alignment explanation
Indices: 11647935--11648180 Score: 132
Period size: 32 Copynumber: 7.8 Consensus size: 32
11647925 TGGGTGACAA
* * *
11647935 CTAAATTGGGCTTAAATTTTCATTGGTACTAG
1 CTAAACTGAGCTTAAATTTTCATTGGTGCTAG
* *
11647967 CTAAACTGAGCTTAAGA-CTT-ATTGATGCTAG
1 CTAAACTGAGCTTAA-ATTTTCATTGGTGCTAG
* * * * *
11647998 CTAATACTGGGCCTAAAATTT-A--GGTGCCAC
1 CTAA-ACTGAGCTTAAATTTTCATTGGTGCTAG
* * *
11648028 CTAAAC-CAGGCTTAAATTTTAATTAGTGCTAG
1 CTAAACTGA-GCTTAAATTTTCATTGGTGCTAG
* * * * *
11648060 CTAATCT-AGGTTTAAATTCTCATTGGTGCCAA
1 CTAAACTGA-GCTTAAATTTTCATTGGTGCTAG
* * * * *
11648092 CTAGACTGGGCCTGAATTTTCATTAGGTGCCAG
1 CTAAACTGAGCTTAAATTTTCATT-GGTGCTAG
* *
11648125 CTAAACTG-GTTTTAAATTTTTATTGGTGCTAG
1 CTAAACTGAG-CTTAAATTTTCATTGGTGCTAG
*
11648157 CTAAA-TCAAGCTTAAATTTTCATT
1 CTAAACT-GAGCTTAAATTTTCATT
11648181 AATGTTGGCT
Statistics
Matches: 159, Mismatches: 42, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
29 11 0.07
30 10 0.06
31 15 0.09
32 97 0.61
33 26 0.16
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (32 bp):
CTAAACTGAGCTTAAATTTTCATTGGTGCTAG
Found at i:11648015 original size:93 final size:93
Alignment explanation
Indices: 11647844--11648074 Score: 259
Period size: 93 Copynumber: 2.5 Consensus size: 93
11647834 GCATGAAACA
* * *
11647844 TAAACGGGGCTTAAATTTTCAATGGTGCTAGCT-AACTAGGCTTAAGATTTATCGATGCCAGCTA
1 TAAACCGGGCTTAAATTTTCATTGGTGCTAGCTAAACTAGGCTTAAGACTTATCGATGCCAGCTA
* * *
11647908 ATATTAGGCTTAAAACTTGGGTGACAAC
66 ATACTAGGCCTAAAACTTAGGTGACAAC
** * * *
11647936 TAAATTGGGCTTAAATTTTCATTGGTACTAGCTAAACT-GAGCTTAAGACTTATTGATGCTAGCT
1 TAAACCGGGCTTAAATTTTCATTGGTGCTAGCTAAACTAG-GCTTAAGACTTATCGATGCCAGCT
* * * *
11648000 AATACTGGGCCTAAAATTTAGGTGCCACC
65 AATACTAGGCCTAAAACTTAGGTGACAAC
* * * * *
11648029 TAAACCAGGCTTAAATTTTAATTAGTGCTAGCTAATCTAGGTTTAA
1 TAAACCGGGCTTAAATTTTCATTGGTGCTAGCTAAACTAGGCTTAA
11648075 ATTCTCATTG
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
92 30 0.26
93 83 0.73
94 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (93 bp):
TAAACCGGGCTTAAATTTTCATTGGTGCTAGCTAAACTAGGCTTAAGACTTATCGATGCCAGCTA
ATACTAGGCCTAAAACTTAGGTGACAAC
Found at i:11648433 original size:22 final size:22
Alignment explanation
Indices: 11648408--11648449 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11648398 AATCAAGGCT
*
11648408 TATGTGCCAGCTAAATTGGGCA
1 TATGTACCAGCTAAATTGGGCA
*
11648430 TATGTACCAGCTAATTTGGG
1 TATGTACCAGCTAAATTGGG
11648450 TTTGCATGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (22 bp):
TATGTACCAGCTAAATTGGGCA
Found at i:11649008 original size:13 final size:13
Alignment explanation
Indices: 11648990--11649022 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11648980 GAATGTCCAG
*
11648990 TTGTTGCTTTGAA
1 TTGTTGCTTCGAA
11649003 TTGTTGCTTCGAA
1 TTGTTGCTTCGAA
11649016 TTGTTGC
1 TTGTTGC
11649023 GGGTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (13 bp):
TTGTTGCTTCGAA
Found at i:11649677 original size:25 final size:24
Alignment explanation
Indices: 11649648--11649702 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
11649638 TATATATAAT
11649648 TATATATTTTTATATTTTAAAAAA
1 TATATATTTTTATATTTTAAAAAA
* *
11649672 TA-ATA-TTTTATATTTCAAAAGA
1 TATATATTTTTATATTTTAAAAAA
11649694 TA-ATATTTT
1 TATATATTTT
11649703 ACTAATTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 20 0.71
23 6 0.21
24 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TATATATTTTTATATTTTAAAAAA
Found at i:11649683 original size:22 final size:22
Alignment explanation
Indices: 11649655--11649703 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
11649645 AATTATATAT
*
11649655 TTTTATATTTTAAAAAATAATA
1 TTTTATATTTCAAAAAATAATA
*
11649677 TTTTATATTTCAAAAGATAATA
1 TTTTATATTTCAAAAAATAATA
11649699 TTTTA
1 TTTTA
11649704 CTAATTTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTATATTTCAAAAAATAATA
Found at i:11658893 original size:20 final size:21
Alignment explanation
Indices: 11658859--11658897 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11658849 AACCCTTTAA
11658859 TATATATTATATTATATATAC
1 TATATATTATATTATATATAC
*
11658880 TATA-ATTATTTTATATAT
1 TATATATTATATTATATAT
11658898 TTAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATTATATTATATATAC
Found at i:11658954 original size:19 final size:19
Alignment explanation
Indices: 11658930--11658966 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11658920 TCACATTAAA
11658930 ATTTTT-ATTTGTTAATTTT
1 ATTTTTAATTT-TTAATTTT
11658949 ATTTTTAATTTTTAATTT
1 ATTTTTAATTTTTAATTT
11658967 AAGTTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
ATTTTTAATTTTTAATTTT
Found at i:11658958 original size:12 final size:13
Alignment explanation
Indices: 11658932--11658960 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11658922 ACATTAAAAT
11658932 TTTTATTTGTTAA
1 TTTTATTTGTTAA
11658945 TTTTATTT-TTAA
1 TTTTATTTGTTAA
11658957 TTTT
1 TTTT
11658961 TAATTTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTATTTGTTAA
Found at i:11658961 original size:13 final size:14
Alignment explanation
Indices: 11658929--11658962 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
11658919 CTCACATTAA
11658929 AATTTTTATTTGTT
1 AATTTTTATTTGTT
11658943 AA-TTTTATTT-TT
1 AATTTTTATTTGTT
11658955 AATTTTTA
1 AATTTTTA
11658963 ATTTAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 13 0.68
14 2 0.11
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
AATTTTTATTTGTT
Found at i:11664195 original size:9 final size:9
Alignment explanation
Indices: 11664183--11664214 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11664173 TAGTTAAAGA
11664183 TGAAGATGT
1 TGAAGATGT
*
11664192 TGAAAATGT
1 TGAAGATGT
11664201 TGAAGATGT
1 TGAAGATGT
11664210 TGAAG
1 TGAAG
11664215 GAGAACCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (9 bp):
TGAAGATGT
Found at i:11664501 original size:18 final size:17
Alignment explanation
Indices: 11664462--11664515 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
11664452 TTATATATTT
*
11664462 AAATA-ATTTTTTATTA
1 AAATATATTTTTTAATA
*
11664478 ACATATATTTTTTCAATA
1 AAATATATTTTTT-AATA
*
11664496 AAATATATTATTATAATA
1 AAATATATT-TTTTAATA
11664514 AA
1 AA
11664516 TTTGAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 17 0.55
19 3 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATATTTTTTAATA
Found at i:11666088 original size:21 final size:21
Alignment explanation
Indices: 11666039--11666088 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
11666029 AGAATAGTCA
* *
11666039 ACTACTTCTTAAAGGCAGTTG
1 ACTACTTCCTAAAGGCAGTGG
* * *
11666060 ATTGCTTCCTGAAGGCAGTGG
1 ACTACTTCCTAAAGGCAGTGG
11666081 ACTACTTC
1 ACTACTTC
11666089 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTACTTCCTAAAGGCAGTGG
Found at i:11666736 original size:11 final size:12
Alignment explanation
Indices: 11666705--11666735 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11666695 AGAACAAATC
11666705 AACAAAAATCCT
1 AACAAAAATCCT
11666717 AACAAAAATCCT
1 AACAAAAATCCT
*
11666729 AGCAAAA
1 AACAAAA
11666736 TTCTCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.23, G:0.03, T:0.13
Consensus pattern (12 bp):
AACAAAAATCCT
Found at i:11669275 original size:22 final size:22
Alignment explanation
Indices: 11669247--11669297 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
11669237 TTTTTTCTTA
11669247 TATTTTTAGTATATT-TTTATTTT
1 TATTTTTAGTA-ATTATTTA-TTT
*
11669270 TATTTTTTGTAATTATTTATTT
1 TATTTTTAGTAATTATTTATTT
11669292 TATTTT
1 TATTTT
11669298 ATGTGTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (22 bp):
TATTTTTAGTAATTATTTATTT
Found at i:11669287 original size:36 final size:35
Alignment explanation
Indices: 11669214--11669297 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 35
11669204 TTTTTGGTAT
*
11669214 TTTTTATATTTTTTAGTGTTTTATTTTTTCTTATA
1 TTTTTATATTTTTTAGTGTTTTATTTTTTCTAATA
*
11669249 TTTTTAGTATATTTTTA-T-TTTTATTTTTTGTAATTA
1 TTTTTA-TAT-TTTTTAGTGTTTTATTTTTTCTAA-TA
*
11669285 TTTATTTTATTTT
1 TTT-TTATATTTT
11669298 ATGTGTTGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
35 22 0.52
36 12 0.29
37 8 0.19
ACGTcount: A:0.19, C:0.01, G:0.05, T:0.75
Consensus pattern (35 bp):
TTTTTATATTTTTTAGTGTTTTATTTTTTCTAATA
Found at i:11670046 original size:23 final size:23
Alignment explanation
Indices: 11670020--11670073 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
11670010 TTGAGGTAAG
11670020 AAAATATTTCTTAAATTTTTGCC
1 AAAATATTTCTTAAATTTTTGCC
11670043 AAAATATTTCTTAAATTTTTGCC
1 AAAATATTTCTTAAATTTTTGCC
11670066 AAAATATT
1 AAAATATT
11670074 AGAGTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (23 bp):
AAAATATTTCTTAAATTTTTGCC
Found at i:11671940 original size:2 final size:2
Alignment explanation
Indices: 11671933--11671960 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11671923 CACAAGGGTG
11671933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11671961 AAATATGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11676235 original size:3 final size:3
Alignment explanation
Indices: 11676227--11676256 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
11676217 AAACACCCAT
11676227 TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
11676257 TTTTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11677371 original size:18 final size:17
Alignment explanation
Indices: 11677341--11677379 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11677331 TTTAACATTT
11677341 AAAATAATGAATGAATAA
1 AAAATAATGAATGAA-AA
11677359 AAAATGAAT-AATGAAAA
1 AAAAT-AATGAATGAAAA
11677376 AAAA
1 AAAA
11677380 GCCTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 11 0.55
19 3 0.15
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATGAATGAAAA
Found at i:11683983 original size:15 final size:17
Alignment explanation
Indices: 11683963--11684000 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11683953 CAAATGCTAA
11683963 AAAAAGCT-AGG-AAAG
1 AAAAAGCTAAGGCAAAG
11683978 AAAAAGCTAAGGTCAAAG
1 AAAAAGCTAAGG-CAAAG
11683996 AAAAA
1 AAAAA
11684001 AAAAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 3 0.15
18 9 0.45
ACGTcount: A:0.63, C:0.08, G:0.21, T:0.08
Consensus pattern (17 bp):
AAAAAGCTAAGGCAAAG
Found at i:11689817 original size:51 final size:49
Alignment explanation
Indices: 11689746--11689868 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 49
11689736 ATGATTTAAA
** *
11689746 GTTGAGCCTTTTTTTAGAAGAGCCTTTTCCAAGATAAAAATTTTTAAAGTG
1 GTTGAGCCTTTACTTAGAAGAG-CTTTTCCAAGAT-AAAATTTTTAAAATG
* * * * *
11689797 GTTGAGCCTTTACTTGGAAGAGCTTTTTCGAGATGAAATTTTTAAAATT
1 GTTGAGCCTTTACTTAGAAGAGCTTTTCCAAGATAAAATTTTTAAAATG
* *
11689846 GTTGAGCCTCTACTTAGAGGAGC
1 GTTGAGCCTTTACTTAGAAGAGC
11689869 ATTTATTATC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 32 0.52
50 10 0.16
51 19 0.31
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (49 bp):
GTTGAGCCTTTACTTAGAAGAGCTTTTCCAAGATAAAATTTTTAAAATG
Found at i:11690180 original size:10 final size:10
Alignment explanation
Indices: 11690161--11690205 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
11690151 CATCTATTTA
*
11690161 TTTTCCTTTT
1 TTTTCTTTTT
11690171 TTTTCTTTTT
1 TTTTCTTTTT
11690181 TTTTCTTTTT
1 TTTTCTTTTT
*
11690191 CTTTCTTTCTT
1 TTTTCTTT-TT
11690202 TTTT
1 TTTT
11690206 GGCACCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 26 0.84
11 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:11691404 original size:19 final size:19
Alignment explanation
Indices: 11691380--11691419 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11691370 TTTAAGAACC
11691380 TTTTCTCTTCGGTTGGCCA
1 TTTTCTCTTCGGTTGGCCA
11691399 TTTTCTCTTCGGTTGGCCA
1 TTTTCTCTTCGGTTGGCCA
11691418 TT
1 TT
11691420 ACTATGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.25, G:0.20, T:0.50
Consensus pattern (19 bp):
TTTTCTCTTCGGTTGGCCA
Found at i:11692369 original size:2 final size:2
Alignment explanation
Indices: 11692364--11692394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11692354 ACACACACAC
11692364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11692395 CACACCTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11692680 original size:10 final size:10
Alignment explanation
Indices: 11692659--11692726 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
11692649 ACATTAAAAG
11692659 AAAATTTCTAA
1 AAAATTT-TAA
11692670 AAAATTTT-A
1 AAAATTTTAA
11692679 AAAATTTTAA
1 AAAATTTTAA
11692689 AAAATTTT--
1 AAAATTTTAA
*
11692697 CAAATTTTATTA
1 AAAATTTTA--A
* *
11692709 AAAGTTATAA
1 AAAATTTTAA
11692719 AAAATTTT
1 AAAATTTT
11692727 CAGAAAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.15
9 9 0.20
10 17 0.37
11 7 0.15
12 6 0.13
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:11692689 original size:19 final size:18
Alignment explanation
Indices: 11692659--11692705 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
11692649 ACATTAAAAG
11692659 AAAATTTCTAAAAAATTTT
1 AAAATTT-TAAAAAATTTT
11692678 AAAAATTTTAAAAAATTTT
1 -AAAATTTTAAAAAATTTT
*
11692697 CAAATTTTA
1 AAAATTTTA
11692706 TTAAAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTTAAAAAATTTT
Found at i:11692889 original size:17 final size:18
Alignment explanation
Indices: 11692869--11692911 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
11692859 TCAATTTTAG
*
11692869 AAAAATATCAAAAATTT-
1 AAAAAAATCAAAAATTTC
*
11692886 AAAAAAATCCAAAATTTC
1 AAAAAAATCAAAAATTTC
11692904 AAAAAAAT
1 AAAAAAAT
11692912 GAAGATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAAATCAAAAATTTC
Found at i:11692898 original size:18 final size:16
Alignment explanation
Indices: 11692864--11692911 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 16
11692854 AACCTTCAAT
11692864 TTTAGAAAAATATCAAAAA
1 TTTA-AAAAA-ATC-AAAA
11692883 TTTAAAAAAATCCAAAA
1 TTTAAAAAAAT-CAAAA
11692900 TTTCAAAAAAAT
1 TTT-AAAAAAAT
11692912 GAAGATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
18 14 0.52
19 4 0.15
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (16 bp):
TTTAAAAAAATCAAAA
Found at i:11693162 original size:18 final size:19
Alignment explanation
Indices: 11693139--11693196 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
11693129 AAAAAATTTA
11693139 TTTTTAGAATTATTT-AAT
1 TTTTTAGAATTATTTAAAT
11693157 TTTTTAGAATGT-TTTAAAT
1 TTTTTAGAAT-TATTTAAAT
*
11693176 TTTTTA-AATTATTAAAAT
1 TTTTTAGAATTATTTAAAT
11693194 TTT
1 TTT
11693197 CAAAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 1 0.03
18 25 0.69
19 10 0.28
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTTAGAATTATTTAAAT
Found at i:11693182 original size:9 final size:9
Alignment explanation
Indices: 11693139--11693196 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
11693129 AAAAAATTTA
11693139 TTTTTAGAAT
1 TTTTTA-AAT
*
11693149 TATTT-AAT
1 TTTTTAAAT
11693157 TTTTTAGAAT
1 TTTTTA-AAT
*
11693167 GTTTTAAAT
1 TTTTTAAAT
11693176 TTTTTAAAT
1 TTTTTAAAT
* *
11693185 TATTAAAAT
1 TTTTTAAAT
11693194 TTT
1 TTT
11693197 CAAAAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.18
9 20 0.51
10 12 0.31
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:11693299 original size:43 final size:45
Alignment explanation
Indices: 11693222--11693314 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
11693212 TTTTAAGAAC
11693222 TTTTTAAAAAAATTTCATATTTTTTAAACATTTTA-TATTTTTAAA
1 TTTTTAAAAAAATTTCATATTTTTTAAACATTTTACT-TTTTTAAA
* *
11693267 TTTTTAAAAAAACTTT-AGT-TTTTTT-AA-TTTTTACTTTTTTAAG
1 TTTTTAAAAAAA-TTTCA-TATTTTTTAAACATTTTACTTTTTTAAA
11693310 TTTTT
1 TTTTT
11693315 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
43 17 0.40
44 3 0.07
45 19 0.44
46 4 0.09
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (45 bp):
TTTTTAAAAAAATTTCATATTTTTTAAACATTTTACTTTTTTAAA
Found at i:11693325 original size:53 final size:53
Alignment explanation
Indices: 11693268--11693369 Score: 120
Period size: 53 Copynumber: 1.9 Consensus size: 53
11693258 ATTTTTAAAT
* *
11693268 TTTTAAAAAAACTTT-AGTTTT-TTT-AATTTTTACTTTTTTAAGTTTTTTTTTTA
1 TTTT-AAAAAACTTTAAGTTTTGTTTAAATTTTAAATTTTTT-A-TTTTTTTTTTA
* *
11693321 TTTTAAGAAAGTTTAAGTTTTGTTTAAATTTTAAATTTTTTATTTTTTT
1 TTTTAAAAAACTTTAAGTTTTGTTTAAATTTTAAATTTTTTATTTTTTT
11693370 AAATTTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
52 8 0.19
53 17 0.40
54 4 0.10
55 13 0.31
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (53 bp):
TTTTAAAAAACTTTAAGTTTTGTTTAAATTTTAAATTTTTTATTTTTTTTTTA
Found at i:11693374 original size:24 final size:26
Alignment explanation
Indices: 11693338--11693387 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
11693328 AAAGTTTAAG
*
11693338 TTTTGTTTAAATTTT-AAATTTTTTA
1 TTTTGTTTAAATTTTCAAAATTTTTA
11693363 TTTT-TTTAAATTTTCAAAATTTTTA
1 TTTTGTTTAAATTTTCAAAATTTTTA
11693388 AAAATTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTGTTTAAATTTTCAAAATTTTTA
Found at i:11693386 original size:19 final size:19
Alignment explanation
Indices: 11693370--11693407 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11693360 TTATTTTTTT
*
11693370 AAATTTTCAAAATTTTTAA
1 AAATTATCAAAATTTTTAA
*
11693389 AAATTATCATAATTTTTAA
1 AAATTATCAAAATTTTTAA
11693408 TTGTCTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTATCAAAATTTTTAA
Found at i:11693491 original size:19 final size:18
Alignment explanation
Indices: 11693467--11693508 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
11693457 AATTTTTAGA
11693467 TTTTTAGAATTCTTGTAAT
1 TTTTTAGAATT-TTGTAAT
*
11693486 TTTTTAGAATTTTTTAAT
1 TTTTTAGAATTTTGTAAT
11693504 TTTTT
1 TTTTT
11693509 TAAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTTAGAATTTTGTAAT
Found at i:11693498 original size:10 final size:10
Alignment explanation
Indices: 11693459--11693550 Score: 61
Period size: 10 Copynumber: 9.5 Consensus size: 10
11693449 TTATTAAAAA
11693459 TTTTTAG-A-
1 TTTTTAGAAT
11693467 TTTTTAGAA-
1 TTTTTAGAAT
*
11693476 TTCTT-GTAAT
1 TTTTTAG-AAT
11693486 TTTTTAGAAT
1 TTTTTAGAAT
*
11693496 TTTTTA-ATT
1 TTTTTAGAAT
*
11693505 TTTTTA-AAA
1 TTTTTAGAAT
* *
11693514 TTTTTAAAAA
1 TTTTTAGAAT
*
11693524 CTTTTAGAAT
1 TTTTTAGAAT
11693534 TTTTTAAGAAAT
1 TTTTT-AG-AAT
11693546 TTTTT
1 TTTTT
11693551 TATTTTTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
8 8 0.12
9 22 0.32
10 27 0.40
11 3 0.04
12 8 0.12
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:11693509 original size:19 final size:18
Alignment explanation
Indices: 11693429--11693540 Score: 84
Period size: 19 Copynumber: 5.9 Consensus size: 18
11693419 TTTTTCAAAA
11693429 TTTTTATGATATTTTTT-AT
1 TTTTTA-GA-ATTTTTTAAT
* *
11693448 TTTATTAAAAATTTTTAGA-
1 TTT-TTAGAATTTTTTA-AT
*
11693467 TTTTTAGAATTCTTGTAAT
1 TTTTTAGAATT-TTTTAAT
11693486 TTTTTAGAATTTTTTAATT
1 TTTTTAGAATTTTTTAA-T
* * *
11693505 TTTTTAAAATTTTTAAAAA
1 TTTTTAGAATTTTT-TAAT
*
11693524 CTTTTAGAATTTTTTAA
1 TTTTTAGAATTTTTTAA
11693541 GAAATTTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
18 20 0.27
19 48 0.65
20 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTTAGAATTTTTTAAT
Found at i:11694128 original size:22 final size:22
Alignment explanation
Indices: 11694079--11694128 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11694069 GTAACATCAG
*
11694079 TATTAAAAATTTTTTTAAAAAA
1 TATTAAAAATTTCTTTAAAAAA
*
11694101 TTTTAAAAA-TTCTTTAAAAAA
1 TATTAAAAATTTCTTTAAAAAA
11694122 TCATTAA
1 T-ATTAA
11694129 TTTTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAAAAATTTCTTTAAAAAA
Found at i:11694157 original size:20 final size:20
Alignment explanation
Indices: 11694084--11694159 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
11694074 ATCAGTATTA
* * *
11694084 AAAATTTTTTTAAAAAATTTT
1 AAAATATTTTTAAAAAA-ATC
11694105 AAAA-ATTCTTT-AAAAAATC
1 AAAATATT-TTTAAAAAAATC
* *
11694124 ATTAAT-TTTATAAAAAAATC
1 A-AAATATTTTTAAAAAAATC
11694144 AAAATATTTTTAAAAA
1 AAAATATTTTTAAAAA
11694160 TTAAAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
19 7 0.16
20 29 0.67
21 7 0.16
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTTTTAAAAAAATC
Found at i:11694230 original size:17 final size:18
Alignment explanation
Indices: 11694210--11694247 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11694200 AAAATTAAAG
11694210 AAAAT-TAAAAGATTCAA
1 AAAATCTAAAAGATTCAA
**
11694227 AAAATCTAAAATTTTCAA
1 AAAATCTAAAAGATTCAA
11694245 AAA
1 AAA
11694248 GTTTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATCTAAAAGATTCAA
Found at i:11694276 original size:29 final size:29
Alignment explanation
Indices: 11694198--11694289 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
11694188 TTATTCAAAT
*
11694198 AAAAAAT-TAAAGAAAATT-AAAAG-ATTC
1 AAAAAATCTAAA-AAAATTCAAAAGTTTTC
**
11694225 AAAAAATCT-AAAATTTTCAAAAAGTTTTC
1 AAAAAATCTAAAAAAATTC-AAAAGTTTTC
*
11694254 AAAAAATCTAAAAAAATTCAAAA-TTTTA
1 AAAAAATCTAAAAAAATTCAAAAGTTTTC
11694282 ACAAAAAT
1 A-AAAAAT
11694290 AAATTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.08
27 9 0.17
28 11 0.21
29 22 0.42
30 7 0.13
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (29 bp):
AAAAAATCTAAAAAAATTCAAAAGTTTTC
Found at i:11694330 original size:21 final size:22
Alignment explanation
Indices: 11694301--11694353 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
11694291 AATTTTTTTT
11694301 AAATTTAAAAAATTCAAA-AAA
1 AAATTTAAAAAATTCAAATAAA
* * *
11694322 AACTTTAAAATATTTAAATAAA
1 AAATTTAAAAAATTCAAATAAA
11694344 AAATTTAAAA
1 AAATTTAAAA
11694354 TTCTTGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATTTAAAAAATTCAAATAAA
Found at i:11694500 original size:30 final size:29
Alignment explanation
Indices: 11694440--11694532 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
11694430 TAAGATTTTC
* *
11694440 TTTTTTTATAATTT-TTTAATTTTTCA-AAA
1 TTTTTTT-GAATTTCTTT-ATTTTTAAGAAA
*
11694469 TTTTTTTGAACTTTCTTTATTTTTATGAAA
1 TTTTTTTGAA-TTTCTTTATTTTTAAGAAA
** * *
11694499 TTATTTTTTTATTTTTTTATTTTTAAGGAA
1 TT-TTTTTGAATTTCTTTATTTTTAAGAAA
11694529 TTTT
1 TTTT
11694533 GTTAATGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.04
29 18 0.35
30 26 0.50
31 6 0.12
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (29 bp):
TTTTTTTGAATTTCTTTATTTTTAAGAAA
Found at i:11694822 original size:10 final size:10
Alignment explanation
Indices: 11694807--11694871 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
11694797 AAAATATTTC
11694807 ATTTTTTAAA
1 ATTTTTTAAA
*
11694817 ATTTTTTATA
1 ATTTTTTAAA
*
11694827 A--TTTAAAA
1 ATTTTTTAAA
*
11694835 ACTTTTTTAGA
1 A-TTTTTTAAA
11694846 ATTTTTTAAA
1 ATTTTTTAAA
** *
11694856 AAATTTTACA
1 ATTTTTTAAA
11694866 ATTTTT
1 ATTTTT
11694872 AAAGACAGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
8 6 0.15
10 29 0.71
11 6 0.15
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:11694831 original size:17 final size:17
Alignment explanation
Indices: 11694783--11694849 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 17
11694773 ATTAACATAA
11694783 TTTTTATAATTTTTAAAAT
1 TTTTTATAA--TTTAAAAT
* * **
11694802 ATTTCATTTTTTAAAAT
1 TTTTTATAATTTAAAAT
11694819 TTTTTATAATTTAAAAACT
1 TTTTTATAATTT-AAAA-T
*
11694838 TTTTTAGAATTT
1 TTTTTATAATTT
11694850 TTTAAAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 16 0.43
18 4 0.11
19 17 0.46
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTTTATAATTTAAAAT
Found at i:11694842 original size:19 final size:18
Alignment explanation
Indices: 11694814--11694849 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11694804 TTCATTTTTT
*
11694814 AAAATTTTTTATAATTTA
1 AAAATTTTTTAGAATTTA
11694832 AAAACTTTTTTAGAATTT
1 AAAA-TTTTTTAGAATTT
11694850 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
AAAATTTTTTAGAATTTA
Found at i:11694872 original size:19 final size:19
Alignment explanation
Indices: 11694784--11694874 Score: 55
Period size: 17 Copynumber: 4.8 Consensus size: 19
11694774 TTAACATAAT
* *
11694784 TTTTATAATTTTTAAAATA
1 TTTTACAATTTTTAAAAAA
* **
11694803 -TTT-CATTTTTTAAAATT
1 TTTTACAATTTTTAAAAAA
* *
11694820 TTTTATAA--TTTAAAAACTT
1 TTTTACAATTTTTAAAAA--A
*
11694839 TTTTAGAATTTTTTAAAAAA
1 TTTTACAA-TTTTTAAAAAA
11694859 TTTTACAATTTTTAAA
1 TTTTACAATTTTTAAA
11694875 GACAGTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 18 0.32
18 6 0.11
19 17 0.30
20 7 0.12
22 8 0.14
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (19 bp):
TTTTACAATTTTTAAAAAA
Found at i:11696557 original size:15 final size:15
Alignment explanation
Indices: 11696534--11696572 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11696524 GGTTTGATTA
*
11696534 ATTTTAAATTAAATT
1 ATTTAAAATTAAATT
11696549 ATTTAAAATTAAATT
1 ATTTAAAATTAAATT
*
11696564 AATTAAAAT
1 ATTTAAAAT
11696573 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTAAAATTAAATT
Found at i:11696615 original size:28 final size:28
Alignment explanation
Indices: 11696561--11696616 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 28
11696551 TTAAAATTAA
11696561 ATTAATTAAAATATTTTATTTTATTTTT
1 ATTAATTAAAATATTTTATTTTATTTTT
11696589 ATTAATT-AAAT-TTTTATTTTTATTTTT
1 ATTAATTAAAATATTTTA-TTTTATTTTT
11696616 A
1 A
11696617 AAAATTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 5 0.19
27 15 0.56
28 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
ATTAATTAAAATATTTTATTTTATTTTT
Found at i:11696622 original size:27 final size:27
Alignment explanation
Indices: 11696564--11696624 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
11696554 AAATTAAATT
**
11696564 AATTAAAATATTTTATTTTATTTTTATT
1 AATT-AAATATTTTATTTTATTTTTAAA
11696592 AATTAAAT-TTTTATTTTTATTTTTAAA
1 AATTAAATATTTTA-TTTTATTTTTAAA
11696619 AATTAA
1 AATTAA
11696625 CCGACCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 21 0.70
28 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
AATTAAATATTTTATTTTATTTTTAAA
Found at i:11697186 original size:9 final size:10
Alignment explanation
Indices: 11697172--11697218 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
11697162 GCGGTGCGTT
11697172 TTAATTT-AA
1 TTAATTTCAA
11697181 TTAATTTCAA
1 TTAATTTCAA
11697191 TTAATTATTCAA
1 TTAA-T-TTCAA
*
11697203 TTAA-TTCGA
1 TTAATTTCAA
11697212 TTAATTT
1 TTAATTT
11697219 GATTTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 15 0.45
10 8 0.24
11 1 0.03
12 9 0.27
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (10 bp):
TTAATTTCAA
Found at i:11697526 original size:16 final size:18
Alignment explanation
Indices: 11697505--11697537 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
11697495 CCCTTTAATC
11697505 TTATTTT-TT-AAAATTT
1 TTATTTTATTCAAAATTT
11697521 TTATTTTATTCAAAATT
1 TTATTTTATTCAAAATT
11697538 ATAAAATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTTTATTCAAAATTT
Found at i:11698260 original size:15 final size:15
Alignment explanation
Indices: 11698218--11698260 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
11698208 GCCTGCCACG
*
11698218 ACAAGACTCAAGCCA
1 ACAAAACTCAAGCCA
11698233 A-AAAA-TCAA-CCA
1 ACAAAACTCAAGCCA
11698245 ACAAAACTCAAGCCA
1 ACAAAACTCAAGCCA
11698260 A
1 A
11698261 AAACGACCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 7 0.29
15 5 0.21
ACGTcount: A:0.56, C:0.30, G:0.07, T:0.07
Consensus pattern (15 bp):
ACAAAACTCAAGCCA
Found at i:11704118 original size:15 final size:15
Alignment explanation
Indices: 11704106--11704136 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11704096 GTTAATTTTG
11704106 AATTAAATTATTTAA
1 AATTAAATTATTTAA
*
11704121 AATTAAATTAATTAA
1 AATTAAATTATTTAA
11704136 A
1 A
11704137 TTATTTTATT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATTATTTAA
Found at i:11704769 original size:24 final size:24
Alignment explanation
Indices: 11704740--11704786 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11704730 GGTTAGGGAG
*
11704740 AAGTGAGGGTGGACAGTGTGAAGA
1 AAGTGAGGATGGACAGTGTGAAGA
* *
11704764 AAGTGAGGATTGACCGTGTGAAG
1 AAGTGAGGATGGACAGTGTGAAG
11704787 GAGGGAGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.43, T:0.19
Consensus pattern (24 bp):
AAGTGAGGATGGACAGTGTGAAGA
Found at i:11704894 original size:25 final size:24
Alignment explanation
Indices: 11704841--11704892 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
11704831 GTATAGTACT
*
11704841 AAATTTGAACTTAAATTTGATTCG
1 AAATTTGAACTTAAATTCGATTCG
11704865 AAATTTGAAACTTAAAATTCGATTCG
1 AAATTTG-AACTT-AAATTCGATTCG
11704891 AA
1 AA
11704893 TTCAATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 13 0.52
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (24 bp):
AAATTTGAACTTAAATTCGATTCG
Found at i:11705507 original size:23 final size:23
Alignment explanation
Indices: 11705445--11705507 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
11705435 TCAAATTGAT
*
11705445 TTAATTTGATTAAATTTTGATTAA
1 TTAATTTAATTAAA-TTTGATTAA
* * *
11705469 TTAAATTAAATCAATTTGATTAA
1 TTAATTTAATTAAATTTGATTAA
11705492 TTAATTTAATTAAATT
1 TTAATTTAATTAAATT
11705508 CGAACTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
TTAATTTAATTAAATTTGATTAA
Found at i:11706023 original size:13 final size:15
Alignment explanation
Indices: 11705993--11706034 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
11705983 TCTCTTATTT
*
11705993 AATATTATTACATATAA
1 AATATTATT-TATA-AA
11706010 AATATT-TTTATAAA
1 AATATTATTTATAAA
11706024 AATATTATTTA
1 AATATTATTTA
11706035 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 7 0.30
16 2 0.09
17 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTATTTATAAA
Found at i:11706081 original size:27 final size:29
Alignment explanation
Indices: 11706039--11706112 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 29
11706029 TATTTAATAT
* *
11706039 ATATATATATAATAATTTTA-ATAATTTTAA
1 ATATATAT-TATTAATTTTATA-AATATTAA
11706069 AT-TAT-TTATTAATTTTATAAATATTAA
1 ATATATATTATTAATTTTATAAATATTAA
*
11706096 ATATATATTATAAATTT
1 ATATATATTATTAATTT
11706113 CATTATACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 19 0.50
28 5 0.13
29 12 0.32
30 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATATATTATTAATTTTATAAATATTAA
Found at i:11706529 original size:22 final size:21
Alignment explanation
Indices: 11706499--11706539 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11706489 ATATCACCTA
* *
11706499 TAATTATAATATTACAATTAAC
1 TAATCATAAT-TTAAAATTAAC
11706521 TAATCATAATTTAAAATTA
1 TAATCATAATTTAAAATTA
11706540 TATAAAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATCATAATTTAAAATTAAC
Found at i:11708002 original size:31 final size:31
Alignment explanation
Indices: 11707960--11708027 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11707950 TTTTGGGTAG
* * * *
11707960 TTTGAATTTTTTTTATTGAATTTTTTAATAAC
1 TTTGAATTTTTTTAATAGAATTTTCT-ACAAC
11707992 TTTGAA-TTTTTTAATAGAATTTTCTACAAC
1 TTTGAATTTTTTTAATAGAATTTTCTACAAC
11708022 TTTGAA
1 TTTGAA
11708028 CTTGTCAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 10 0.31
31 16 0.50
32 6 0.19
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTGAATTTTTTTAATAGAATTTTCTACAAC
Found at i:11708004 original size:30 final size:30
Alignment explanation
Indices: 11707960--11708045 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
11707950 TTTTGGGTAG
* * * *
11707960 TTTGAATTTTTTTTATTGAATTTTTTAATAAC
1 TTTGAA-TTTTTTAATAGAATTTTCT-ACAAC
11707992 TTTGAATTTTTTAATAGAATTTTCTACAAC
1 TTTGAATTTTTTAATAGAATTTTCTACAAC
* * * *
11708022 TTTGAACTTGTCAATTGAATTTTC
1 TTTGAATTTTTTAATAGAATTTTC
11708046 AAGCGACTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 24 0.52
31 16 0.35
32 6 0.13
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (30 bp):
TTTGAATTTTTTAATAGAATTTTCTACAAC
Found at i:11713262 original size:7 final size:8
Alignment explanation
Indices: 11713243--11713290 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
11713233 AACTTTTATT
11713243 AAAAAATG
1 AAAAAATG
11713251 AAAAAATG
1 AAAAAATG
11713259 AAAAAAATGG
1 -AAAAAAT-G
11713269 AAAAAAATG
1 -AAAAAATG
*
11713278 AAAAGAT-
1 AAAAAATG
11713285 AAAAAA
1 AAAAAA
11713291 GTTGAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 5 0.14
8 14 0.39
9 8 0.22
10 9 0.25
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:11713264 original size:10 final size:9
Alignment explanation
Indices: 11713243--11713281 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
11713233 AACTTTTATT
11713243 AAAAAATG-
1 AAAAAATGA
11713251 AAAAAATGA
1 AAAAAATGA
11713260 AAAAAATGGA
1 AAAAAAT-GA
11713270 AAAAAATGA
1 AAAAAATGA
11713279 AAA
1 AAA
11713282 GATAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.28
9 12 0.41
10 9 0.31
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:11713279 original size:27 final size:26
Alignment explanation
Indices: 11713243--11713299 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
11713233 AACTTTTATT
11713243 AAAAAATGAAAAAATGAAAAAAATGGA
1 AAAAAATGAAAAAAT-AAAAAAATGGA
* * *
11713270 AAAAAATGAAAAGATAAAAAAGTTGA
1 AAAAAATGAAAAAATAAAAAAATGGA
11713296 AAAA
1 AAAA
11713300 TAAGGCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (26 bp):
AAAAAATGAAAAAATAAAAAAATGGA
Found at i:11713643 original size:29 final size:29
Alignment explanation
Indices: 11713584--11713644 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
11713574 TGAATGAAGC
** *
11713584 AAAAATGATGAGTGAAAGAAAAAAATGAA
1 AAAAATGATGAGAAAAAGAAAAAAATAAA
11713613 AAAAATGATGAGAAATAAGAAAAAAA-AAA
1 AAAAATGATGAGAAA-AAGAAAAAAATAAA
11713642 AAA
1 AAA
11713645 GAAAAAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.11
Consensus pattern (29 bp):
AAAAATGATGAGAAAAAGAAAAAAATAAA
Found at i:11713776 original size:3 final size:3
Alignment explanation
Indices: 11713770--11713865 Score: 116
Period size: 3 Copynumber: 34.3 Consensus size: 3
11713760 TAGTATACTC
*
11713770 ATT ATT ATT ATT ATT ATT A-T ATT ATT -GT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
11713815 ATT ATT ATT ATT A-T ATT ATT -GT ATT A-T ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11713860 A-T ATT A
1 ATT ATT A
11713866 CTGTACTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
2 12 0.15
3 68 0.85
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:11713786 original size:39 final size:37
Alignment explanation
Indices: 11713717--11713861 Score: 152
Period size: 39 Copynumber: 3.9 Consensus size: 37
11713707 TAGGACCAAT
* * * *
11713717 TTATTAGTGTTATATTACTA-TAGTA-TATTATCTTGTA
1 TTATT-GTATTATATTATTATTATTATTATTAT-TTATA
* * *
11713754 TTATTATAGTATACTCATTATTATTATTATTA-TTATA
1 TTATTGTATTATA-TTATTATTATTATTATTATTTATA
11713791 TTATTGTATTATATTATTATTATTATTATTATTATTATA
1 TTATTGTATTATATTATTATTATTATTATTA-T-TTATA
*
11713830 TTATTGTATTATATTATTATTACTATTATTAT
1 TTATTGTATTATATTATTATTATTATTATTAT
11713862 ATTACTGTAC
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
36 22 0.24
37 24 0.26
38 5 0.05
39 40 0.44
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (37 bp):
TTATTGTATTATATTATTATTATTATTATTATTTATA
Found at i:11713789 original size:42 final size:39
Alignment explanation
Indices: 11713768--11713865 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
11713758 TATAGTATAC
11713768 TCATTATTATTATTATTATTATATTATTGTATTATATTA
1 TCATTATTATTATTATTATTATATTATTGTATTATATTA
*
11713807 TTATTATTATTATTATTATTATATTATTGTATTATATTA
1 TCATTATTATTATTATTATTATATTATTGTATTATATTA
* *
11713846 TTATTACTATTATTA-TATTA
1 TCATTATTATTATTATTATTA
11713866 CTGTACTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
38 5 0.09
39 52 0.91
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (39 bp):
TCATTATTATTATTATTATTATATTATTGTATTATATTA
Found at i:11713807 original size:33 final size:33
Alignment explanation
Indices: 11713775--11713876 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 33
11713765 TACTCATTAT
*
11713775 TATTATTATTATTA-TATTAT-TGTATTATATTA
1 TATTATTATTATTATTATTATAT-TATTGTATTA
11713807 TTATTATTATTATTATTATTATATTATTGTATTA
1 -TATTATTATTATTATTATTATATTATTGTATTA
* * *
11713841 TATTATTATTACTATTATTATATTACTGTACTA
1 TATTATTATTATTATTATTATATTATTGTATTA
11713874 TAT
1 TAT
11713877 ATTTTTTTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
33 47 0.75
34 15 0.24
35 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (33 bp):
TATTATTATTATTATTATTATATTATTGTATTA
Found at i:11714272 original size:20 final size:20
Alignment explanation
Indices: 11714247--11714292 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
11714237 TAGGTTTAGA
*
11714247 TTTTTGGCTTT-GATTTGAAG
1 TTTTTGGATTTGGATTT-AAG
11714267 TTTTTGGATTTGGATTTAAG
1 TTTTTGGATTTGGATTTAAG
11714287 TTTTTG
1 TTTTTG
11714293 CAGCTTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.15, C:0.02, G:0.24, T:0.59
Consensus pattern (20 bp):
TTTTTGGATTTGGATTTAAG
Found at i:11714303 original size:21 final size:21
Alignment explanation
Indices: 11714253--11714309 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
11714243 TAGATTTTTG
* *
11714253 GCTTTGATTTGAAGTTTTTGGA
1 GCTTAGATTT-AAGTTTTTGCA
* *
11714275 -TTTGGATTTAAGTTTTTGCA
1 GCTTAGATTTAAGTTTTTGCA
*
11714295 GCTTAGATTGAAGTT
1 GCTTAGATTTAAGTT
11714310 ATGGCAGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.21, C:0.05, G:0.25, T:0.49
Consensus pattern (21 bp):
GCTTAGATTTAAGTTTTTGCA
Found at i:11714727 original size:7 final size:7
Alignment explanation
Indices: 11714704--11714743 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
11714694 CGTAGGATTT
11714704 TTTTAT-
1 TTTTATA
11714710 TTTTATTTA
1 TTTTA--TA
11714719 TTTTATA
1 TTTTATA
11714726 TTTTATA
1 TTTTATA
11714733 TTTTATA
1 TTTTATA
11714740 TTTT
1 TTTT
11714744 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 1 0.03
9 5 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTATA
Found at i:11714734 original size:14 final size:15
Alignment explanation
Indices: 11714704--11714753 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
11714694 CGTAGGATTT
11714704 TTTTAT-TTTTATTTA
1 TTTTATATTTTA-TTA
11714719 TTTTATATTTTA-TA
1 TTTTATATTTTATTA
*
11714733 TTTTATATTTTTTTAA
1 TTTTATATTTTATT-A
11714749 TTTTA
1 TTTTA
11714754 GTTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 13 0.42
15 7 0.23
16 11 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATATTTTATTA
Found at i:11714736 original size:23 final size:22
Alignment explanation
Indices: 11714704--11714759 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
11714694 CGTAGGATTT
11714704 TTTTATTTTTAT-TTATTTTATA
1 TTTTATTTTTATATTATTTTA-A
*
11714726 TTTTATATTTTATATTTTTTTAA
1 TTTTAT-TTTTATATTATTTTAA
11714749 TTTTAGTTTTT
1 TTTTA-TTTTT
11714760 TTTTTCCTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.20
23 16 0.53
24 8 0.27
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTTTTATATTATTTTAA
Found at i:11714763 original size:17 final size:17
Alignment explanation
Indices: 11714702--11714762 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
11714692 ATCGTAGGAT
*
11714702 TTTTTTATTTTTATT-TA
1 TTTTATATTTTT-TTATA
11714719 TTTTATA---TTTTATA
1 TTTTATATTTTTTTATA
11714733 TTTTATATTTTTTTA-A
1 TTTTATATTTTTTTATA
11714749 TTTTAGT-TTTTTTT
1 TTTTA-TATTTTTTT
11714763 TTCCTGACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.05
14 11 0.29
16 13 0.34
17 12 0.32
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTATATTTTTTTATA
Found at i:11717841 original size:86 final size:86
Alignment explanation
Indices: 11717697--11718135 Score: 422
Period size: 86 Copynumber: 5.1 Consensus size: 86
11717687 TTTGCAAATT
* * * * * *
11717697 TTGAAATCTTGCAAATCTTTCTTACTTGTGAATCTAAAAATTTTTGTAAACTTAGAATCTTTGAA
1 TTGAAATCTTGCAAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAGAATCTTTGAG
*
11717762 AATTTAGAACCTTTATGAAAC
66 AATCTAGAACCTTTATGAAAC
* * * * * * * * *
11717783 TTGAAATCTTACAAATATTTCTTTCCTGTGAATTTAAAAGTCCTTGCGAACCTGGAATCTTT-AT
1 TTGAAATCTTGCAAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAGAATCTTTGA-
*
11717847 GAACCTAGAACCTTTATGAAAC
65 GAATCTAGAACCTTTATGAAAC
* ** * * *
11717869 TTGAATTCTTGTGAATCTTTCTTTCTTAAGAATCTAAAAATCTTTGTGAA-CTTGAAATCTTTGC
1 TTGAAATCTTGCAAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAG-AATCTTTGA
* **
11717933 GAATCTATAACCTTTGCGAAAC
65 GAATCTAGAACCTTTATGAAAC
* ** * * *
11717955 TAGAAATCTTGTGAATCTTTCTTTCTTACGAATCTAAAAGTCTTTGTGAACCTAGAATCTTTGCG
1 TTGAAATCTTGCAAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAGAATCTTTGAG
*
11718020 -ATCTAGAACCTTTGTGAAAC
66 AATCTAGAACCTTTATGAAAC
* ** *
11718040 TTGAAATCTT-CTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTACGAA-CTTGAAATCTTT-
1 TTGAAATCTTGC-AAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAG-AATCTTTG
* * *
11718102 ATGAATCTATAACCTTTACGAATC
64 A-GAATCTAGAACCTTTATGAAAC
*
11718126 TTGGAATCTT
1 TTGAAATCTT
11718136 TCAACTTCTA
Statistics
Matches: 292, Mismatches: 53, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
84 3 0.01
85 73 0.25
86 213 0.73
87 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (86 bp):
TTGAAATCTTGCAAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACCTAGAATCTTTGAG
AATCTAGAACCTTTATGAAAC
Found at i:11717852 original size:17 final size:17
Alignment explanation
Indices: 11717830--11717866 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11717820 AAGTCCTTGC
* *
11717830 GAACCTGGAATCTTTAT
1 GAACCTAGAACCTTTAT
11717847 GAACCTAGAACCTTTAT
1 GAACCTAGAACCTTTAT
11717864 GAA
1 GAA
11717867 ACTTGAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (17 bp):
GAACCTAGAACCTTTAT
Found at i:11717996 original size:172 final size:171
Alignment explanation
Indices: 11717697--11718123 Score: 509
Period size: 172 Copynumber: 2.5 Consensus size: 171
11717687 TTTGCAAATT
* * * * *
11717697 TTGAAATCTTGC-AAATCTTTCTTACTTGTGAATCTAAAAATTTTTGTAAACTT-AGAATCTTTG
1 TTGAAATCTT-CTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACTTGA-AATCTTTG
* * * * * ** *
11717760 AAAATTTAGAACCTTTATGAAACTTGAAATCTTACAAATATTTCTTTCCTGTGAATTTAAAAGTC
64 AGAATCTATAACCTTTACGAAACTAGAAATCTTACAAATATTTCTTTCCTACGAATCTAAAAGTC
* *
11717825 CTTGCGAACCTGGAATCTTTATGAACCTAGAACCTTTATGAAAC
129 CTTGCGAACCTAGAATCTTTACG-ACCTAGAACCTTTATGAAAC
* * * *
11717869 TTGAATTCTTGTGAATCTTTCTTTCTTAAGAATCTAAAAATCTTTGTGAACTTGAAATCTTTGCG
1 TTGAAATCTTCTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACTTGAAATCTTTGAG
* *** * * *
11717934 AATCTATAACCTTTGCGAAACTAGAAATCTTGTGAATCTTTCTTTCTTACGAATCTAAAAGTCTT
66 AATCTATAACCTTTACGAAACTAGAAATCTTACAAATATTTCTTTCCTACGAATCTAAAAGTCCT
* * * *
11717999 TGTGAACCTAGAATCTTTGCGATCTAGAACCTTTGTGAAAC
131 TGCGAACCTAGAATCTTTACGACCTAGAACCTTTATGAAAC
**
11718040 TTGAAATCTTCTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTACGAACTTGAAATCTTT-AT
1 TTGAAATCTTCTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACTTGAAATCTTTGA-
11718104 GAATCTATAACCTTTACGAA
65 GAATCTATAACCTTTACGAA
11718124 TCTTGGAATC
Statistics
Matches: 215, Mismatches: 37, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
171 94 0.44
172 120 0.56
173 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (171 bp):
TTGAAATCTTCTGAATCTTTCTTTCTTATGAATCTAAAAATCTTTGTGAACTTGAAATCTTTGAG
AATCTATAACCTTTACGAAACTAGAAATCTTACAAATATTTCTTTCCTACGAATCTAAAAGTCCT
TGCGAACCTAGAATCTTTACGACCTAGAACCTTTATGAAAC
Found at i:11718015 original size:17 final size:17
Alignment explanation
Indices: 11717995--11718037 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
11717985 AATCTAAAAG
11717995 TCTTTGTGAACCTAGAA
1 TCTTTGTGAACCTAGAA
* *
11718012 TCTTTGCG-ATCTAGAA
1 TCTTTGTGAACCTAGAA
*
11718028 CCTTTGTGAA
1 TCTTTGTGAA
11718038 ACTTGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (17 bp):
TCTTTGTGAACCTAGAA
Found at i:11718083 original size:17 final size:18
Alignment explanation
Indices: 11718065--11718110 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
11718055 TCTTTCTTTC
11718065 TTATGAATCTAAAAATCT
1 TTATGAATCTAAAAATCT
* **
11718083 TTACGAA-CTTGAAATCT
1 TTATGAATCTAAAAATCT
11718100 TTATGAATCTA
1 TTATGAATCTA
11718111 TAACCTTTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (18 bp):
TTATGAATCTAAAAATCT
Found at i:11718106 original size:35 final size:35
Alignment explanation
Indices: 11718065--11718136 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
11718055 TCTTTCTTTC
*
11718065 TTATGAATCTAAAAATCTTTACGAA-CTTGAAATCT
1 TTATGAATCT-AAAACCTTTACGAATCTTGAAATCT
* *
11718100 TTATGAATCTATAACCTTTACGAATCTTGGAATCT
1 TTATGAATCTAAAACCTTTACGAATCTTGAAATCT
11718135 TT
1 TT
11718137 CAACTTCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 12 0.36
35 21 0.64
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (35 bp):
TTATGAATCTAAAACCTTTACGAATCTTGAAATCT
Found at i:11719742 original size:6 final size:6
Alignment explanation
Indices: 11719739--11719830 Score: 62
Period size: 6 Copynumber: 14.3 Consensus size: 6
11719729 TCTTTTTTCA
* *
11719739 TTTTAT TTTTAT TTTTAT TTTT-T TATTTAA TTTTATT TTTTAT TTTATTT
1 TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTA-T TTTTAT TTT-TAT
* *
11719789 ATTTTAT TTTCAAT ATTTA- TTTTATT GATTTTAT TTTTAT TT
1 -TTTTAT TTT-TAT TTTTAT TTTTA-T --TTTTAT TTTTAT TT
11719831 AATAAATTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
5 6 0.09
6 39 0.57
7 14 0.21
8 4 0.06
9 5 0.07
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:11719746 original size:5 final size:5
Alignment explanation
Indices: 11719733--11719830 Score: 69
Period size: 5 Copynumber: 18.6 Consensus size: 5
11719723 GGTTTTTCTT
*
11719733 TTTTCA TTTTA TTTTTA TTTT- TATTT- TTTTA TTTAA TTTTA TTTTTTA
1 TTTT-A TTTTA -TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA --TTTTA
*
11719781 TTTTA -TTTA TTTTA TTTTCAA TATTTA TTTTA -TTGA TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTT--A T-TTTA TTTTA TTTTA TTTTA -TTTTA
11719828 TTT
1 TTT
11719831 AATAAATTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 23
0.74 0.04 0.22
Matches are distributed among these distances:
4 11 0.14
5 40 0.52
6 16 0.21
7 7 0.09
8 3 0.04
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:11719747 original size:13 final size:12
Alignment explanation
Indices: 11719726--11719830 Score: 72
Period size: 13 Copynumber: 8.2 Consensus size: 12
11719716 GATCGTAGGT
*
11719726 TTTTCTTTTTTCA
1 TTTTATTTTTT-A
11719739 TTTTA-TTTTTA
1 TTTTATTTTTTA
11719750 TTTTTATTTTTTTA
1 -TTTTA-TTTTTTA
*
11719764 TTTAATTTTATT-
1 TTTTATTTT-TTA
11719776 TTTTATTTTATTTA
1 TTTTA-TTT-TTTA
**
11719790 TTTTATTTTCAA
1 TTTTATTTTTTA
11719802 TATTTATTTTATTGA
1 T-TTTATTTT-TT-A
11719817 TTTTA-TTTTTA
1 TTTTATTTTTTA
11719828 TTT
1 TTT
11719831 AATAAATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
11 5 0.07
12 23 0.31
13 29 0.39
14 16 0.21
15 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:11719753 original size:18 final size:17
Alignment explanation
Indices: 11719732--11719830 Score: 76
Period size: 18 Copynumber: 5.5 Consensus size: 17
11719722 AGGTTTTTCT
11719732 TTTTTCATTTTATTTTTA
1 TTTTT-ATTTTATTTTTA
*
11719750 TTTTTATTTTTTTATTTA
1 TTTTTATTTTATT-TTTA
*
11719768 ATTTTATTTT-TTATTT-
1 TTTTTATTTTATT-TTTA
* *
11719784 TATTTATTTTATTTTCAA
1 TTTTTATTTTATTTT-TA
*
11719802 TATTTATTTTATTGATTTTA
1 TTTTTATTTTA-T--TTTTA
11719822 TTTTTATTT
1 TTTTTATTT
11719831 AATAAATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
16 10 0.15
17 15 0.22
18 29 0.43
19 1 0.01
20 9 0.13
21 3 0.04
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTATTTTTA
Found at i:11719791 original size:9 final size:9
Alignment explanation
Indices: 11719738--11719824 Score: 69
Period size: 9 Copynumber: 10.0 Consensus size: 9
11719728 TTCTTTTTTC
11719738 ATTTTATTT
1 ATTTTATTT
11719747 -TTATT-TTT
1 ATT-TTATTT
11719755 ATTTT-TTT
1 ATTTTATTT
*
11719763 ATTTAATTT
1 ATTTTATTT
11719772 -TATTT-TTT
1 AT-TTTATTT
11719780 ATTTTATTT
1 ATTTTATTT
11719789 ATTTTATTT
1 ATTTTATTT
**
11719798 -TCAATATTT
1 AT-TTTATTT
*
11719807 ATTTTATTG
1 ATTTTATTT
11719816 ATTTTATTT
1 ATTTTATTT
11719825 TTATTTAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 22 0.35
9 39 0.63
10 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (9 bp):
ATTTTATTT
Found at i:11722875 original size:16 final size:16
Alignment explanation
Indices: 11722854--11722884 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11722844 TTTGTTTTCA
11722854 TGAAGAGATTTCATCT
1 TGAAGAGATTTCATCT
11722870 TGAAGAGATTTCATC
1 TGAAGAGATTTCATC
11722885 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (16 bp):
TGAAGAGATTTCATCT
Found at i:11723531 original size:15 final size:16
Alignment explanation
Indices: 11723481--11723531 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
11723471 TAATCATGCC
*
11723481 AAAA-AAAATAAATAGA
1 AAAATAAAATAAACA-A
11723497 ATAAATAAAATAAACAA
1 A-AAATAAAATAAACAA
11723514 AAAATAAAA-AAACCAA
1 AAAATAAAATAAA-CAA
11723530 AA
1 AA
11723532 CAGGAAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 14 0.45
17 5 0.16
18 9 0.29
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAATAAAATAAACAA
Found at i:11724321 original size:16 final size:17
Alignment explanation
Indices: 11724300--11724334 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11724290 TCTTTTCTTC
11724300 TAATTTTT-TTAATTTT
1 TAATTTTTATTAATTTT
*
11724316 TAATTTTTATTTATTTT
1 TAATTTTTATTAATTTT
11724333 TA
1 TA
11724335 TTAACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TAATTTTTATTAATTTT
Found at i:11725073 original size:29 final size:29
Alignment explanation
Indices: 11725041--11725102 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
11725031 AAATAAAACT
*
11725041 AATTAC-A-TTTTGATTACTTAATTTTGAA
1 AATTACTATTTTTG-TTACTCAATTTTGAA
*
11725069 GAATTTCTATTTTTGTTACTCAATTTTGAA
1 -AATTACTATTTTTGTTACTCAATTTTGAA
11725099 AATT
1 AATT
11725103 TAAAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.31
30 15 0.52
31 5 0.17
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (29 bp):
AATTACTATTTTTGTTACTCAATTTTGAA
Found at i:11727666 original size:3 final size:3
Alignment explanation
Indices: 11727658--11727682 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11727648 CAAGACCTCG
11727658 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
11727683 GCAACAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11727705 original size:3 final size:3
Alignment explanation
Indices: 11727697--11727731 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11727687 CAATAACAAG
11727697 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
11727732 TTAATGATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11728213 original size:8 final size:8
Alignment explanation
Indices: 11728200--11728224 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11728190 AAAGAAATAT
11728200 ATATATAC
1 ATATATAC
11728208 ATATATAC
1 ATATATAC
11728216 ATATATAC
1 ATATATAC
11728224 A
1 A
11728225 CACAAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:11728251 original size:2 final size:2
Alignment explanation
Indices: 11728244--11728287 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
11728234 ATGTGTACAT
11728244 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11728286 AG
1 AG
11728288 TGAAAGGAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11730482 original size:6 final size:6
Alignment explanation
Indices: 11730471--11730502 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
11730461 GCTTACATGG
11730471 TTTCTT TTTCTT TTTCTT TTT-TT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
11730503 TTATTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:11730495 original size:11 final size:11
Alignment explanation
Indices: 11730471--11730504 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
11730461 GCTTACATGG
11730471 TTTCTTTTTCTT
1 TTTCTTTTT-TT
11730483 TTTCTTTTTTT
1 TTTCTTTTTTT
11730494 TTTCTTTTTTT
1 TTTCTTTTTTT
11730505 ATTTGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:11731662 original size:9 final size:9
Alignment explanation
Indices: 11731637--11731687 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
11731627 TGCATACTTA
11731637 AAAAATGAA-
1 AAAAA-GAAG
11731646 AAACAAGAAG
1 AAA-AAGAAG
*
11731656 AAGAAGAAG
1 AAAAAGAAG
11731665 AAAAAGAAG
1 AAAAAGAAG
*
11731674 AAAAA-AAA
1 AAAAAGAAG
11731682 AAAAAG
1 AAAAAG
11731688 GAAAGAGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.19
9 25 0.69
10 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:11732223 original size:2 final size:2
Alignment explanation
Indices: 11732218--11732242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11732208 GAAAAAAAAA
11732218 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11732243 GTATCCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11733225 original size:12 final size:12
Alignment explanation
Indices: 11733208--11733250 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
11733198 ACCTATTTAT
11733208 TGTTCATGAATA
1 TGTTCATGAATA
11733220 TGTTCATGTATATA
1 TGTTCATG-A-ATA
* *
11733234 TATTTATGAATA
1 TGTTCATGAATA
11733246 TGTTC
1 TGTTC
11733251 GTTTTAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 14 0.56
13 2 0.08
14 9 0.36
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (12 bp):
TGTTCATGAATA
Found at i:11738439 original size:80 final size:78
Alignment explanation
Indices: 11738298--11738547 Score: 322
Period size: 80 Copynumber: 3.1 Consensus size: 78
11738288 AGAAATATCA
* * *
11738298 TTCAACAAACCATTCAATATATGATTCAACCCCCCAATATCATACAAAACCATTCAGCAAAACAA
1 TTCAGCAAACCATTCAGTATATGATTC-AGCCCCCAATATCATACAAAA-CATTCAGCAAAACAA
11738363 TATCAGACAACAAGG
64 TATCAGACAACAAGG
* * * *
11738378 TTCAGCAAACCATTTAGCATATGATTCAGCCCTTCAATATCATAGAAGAACATTC-GACAAAACA
1 TTCAGCAAACCATTCAGTATATGATTCAGCCC-CCAATATCATACAA-AACATTCAG-CAAAACA
*
11738442 ATATCAAACAACAAGG
63 ATATCAGACAACAAGG
* * *
11738458 TTCAGCAAACCATTCAGTATACGATTCAGCCCCCTAATATCATACAATACCATTCAGTAAAACAA
1 TTCAGCAAACCATTCAGTATATGATTCAGCCCCC-AATATCATACAA-AACATTCAGCAAAACAA
11738523 TATCAGACAACAAGG
64 TATCAGACAACAAGG
*
11738538 TTTAGCAAAC
1 TTCAGCAAAC
11738548 TATAATATTT
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
79 6 0.04
80 138 0.94
81 3 0.02
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (78 bp):
TTCAGCAAACCATTCAGTATATGATTCAGCCCCCAATATCATACAAAACATTCAGCAAAACAATA
TCAGACAACAAGG
Found at i:11739618 original size:22 final size:22
Alignment explanation
Indices: 11739593--11739635 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11739583 TTTTAGAGGA
*
11739593 AAATTACTGAAGGTGTTTATTG
1 AAATTACTGAAGGCGTTTATTG
*
11739615 AAATTATTGAAGGCGTTTATT
1 AAATTACTGAAGGCGTTTATT
11739636 ATCAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (22 bp):
AAATTACTGAAGGCGTTTATTG
Found at i:11739660 original size:146 final size:145
Alignment explanation
Indices: 11739469--11739755 Score: 466
Period size: 146 Copynumber: 2.0 Consensus size: 145
11739459 TTTTATAAGA
11739469 AAATTATTGAAGGCGTTTATTATCAATAAACACCTTCAATATTTATGTAAAAAATTTAAAAGAAA
1 AAATTATTGAAGGCGTTTATTATCAATAAACACCTTCAATATTTATGTAAAAAATTTAAAAGAAA
* *
11739534 TTATTAAAGGCATTTGTCAGTAGAAGACACCTTTAATAATCCTAAACTTTTTTAGAGGAAAATTA
66 TTATTAAAGGCATTTGTCAGTAGAAGACACCTTTAATAATCCTAAAATTTTTTAGA-AAAAATTA
*
11739599 CTGAAGGTGTTTATTG
130 CTAAAGGTGTTTATTG
* * *
11739615 AAATTATTGAAGGCGTTTATTATCAATAAACACCTTTAATTTTTATGTAAAAAATTTAAAAGGAA
1 AAATTATTGAAGGCGTTTATTATCAATAAACACCTTCAATATTTATGTAAAAAATTTAAAAGAAA
* ** * *
11739680 TTATTGAAGGTGTTTGTCAGTAGAAGACGCCTTTAATAATCCTAAAATTTTTTAGAAAAAATTAT
66 TTATTAAAGGCATTTGTCAGTAGAAGACACCTTTAATAATCCTAAAATTTTTTAGAAAAAATTAC
11739745 TAAAGGTGTTT
131 TAAAGGTGTTT
11739756 GTTATTAACA
Statistics
Matches: 130, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
145 17 0.13
146 113 0.87
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (145 bp):
AAATTATTGAAGGCGTTTATTATCAATAAACACCTTCAATATTTATGTAAAAAATTTAAAAGAAA
TTATTAAAGGCATTTGTCAGTAGAAGACACCTTTAATAATCCTAAAATTTTTTAGAAAAAATTAC
TAAAGGTGTTTATTG
Found at i:11747744 original size:33 final size:33
Alignment explanation
Indices: 11747681--11747745 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
11747671 TATCTCAAAG
**
11747681 ATACAAATGCCTCTAATATAGAGGTGTTTTCAA
1 ATACAAATGCCTCTAATATAGAGGCATTTTCAA
11747714 ATACAAATGCCTCTAA-AGTA-ATGGCATTTTCA
1 ATACAAATGCCTCTAATA-TAGA-GGCATTTTCA
11747746 GTTACAAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
ATACAAATGCCTCTAATATAGAGGCATTTTCAA
Found at i:11749412 original size:2 final size:2
Alignment explanation
Indices: 11749405--11749432 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11749395 CTCAACTTTC
11749405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11749433 TGTGGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11749744 original size:27 final size:28
Alignment explanation
Indices: 11749714--11749770 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
11749704 AATAACATAT
*
11749714 TTAGTTCTTGGAAGGTGAAGAAG-TGTC
1 TTAGTTCTTAGAAGGTGAAGAAGTTGTC
*
11749741 TTAGTTCTTAGAAGGTGAAGGAGTTGTC
1 TTAGTTCTTAGAAGGTGAAGAAGTTGTC
11749769 TT
1 TT
11749771 TAGCAGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.37
Consensus pattern (28 bp):
TTAGTTCTTAGAAGGTGAAGAAGTTGTC
Found at i:11751610 original size:14 final size:13
Alignment explanation
Indices: 11751576--11751615 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
11751566 AAAAATTAAC
11751576 ATAAATAATCAAA
1 ATAAATAATCAAA
*
11751589 ATAAATAATCCAA
1 ATAAATAATCAAA
11751602 A-AAAT-AT-AAA
1 ATAAATAATCAAA
11751612 ATAA
1 ATAA
11751616 CCAAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 4 0.17
12 4 0.17
13 13 0.54
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATAATCAAA
Found at i:11751647 original size:11 final size:10
Alignment explanation
Indices: 11751622--11751655 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
11751612 ATAACCAAGT
*
11751622 AAAAAATAGA
1 AAAAAATAAA
11751632 AAAAAATAAA
1 AAAAAATAAA
11751642 ACAAAAATAAA
1 A-AAAAATAAA
11751653 AAA
1 AAA
11751656 GAAAGCAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:11751975 original size:30 final size:31
Alignment explanation
Indices: 11751941--11752006 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
11751931 TATCAACAAG
* *
11751941 AAATTCAAAGTCAC-GTAAAATTTAATCGAA
1 AAATTCAAAGTCACTGAAAAATTTAATCAAA
* *
11751971 AAATTCAAAGTTACTGAAAAATTTAGTCAAA
1 AAATTCAAAGTCACTGAAAAATTTAATCAAA
11752002 AAATT
1 AAATT
11752007 TAAAATTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (31 bp):
AAATTCAAAGTCACTGAAAAATTTAATCAAA
Found at i:11752786 original size:43 final size:42
Alignment explanation
Indices: 11752728--11752925 Score: 208
Period size: 43 Copynumber: 4.6 Consensus size: 42
11752718 GTAGGTGCAC
11752728 AACAACTTTG-AAAATATAAAAGGCTCTTTTCATCAAAGGCTT
1 AACAACTTTGAAAAATATAAAAGGCT-TTTTCATCAAAGGCTT
* * * *
11752770 AATAACTTTAAAAAATATAAAAGG-TTTCTTTATCAAAAGCTT
1 AACAACTTTGAAAAATATAAAAGGCTTT-TTCATCAAAGGCTT
* * * *
11752812 AAAAACTTTTGAAAAATATAAAAGACTTTTCCTATCATAAGG-TC
1 AACAAC-TTTGAAAAATATAAAAGGCTTTTTC-ATCA-AAGGCTT
*
11752856 AACAACTTTGAAAAAT-TATAAAGGCTTTTTTCACCAAAGGCTT
1 AACAACTTTGAAAAATATA-AAAGGC-TTTTTCATCAAAGGCTT
11752899 AACAACTTTGAAAAATA-AAAAGAGCTT
1 AACAACTTTGAAAAATATAAAAG-GCTT
11752926 CTCTAATTAG
Statistics
Matches: 129, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
41 2 0.02
42 38 0.29
43 68 0.53
44 18 0.14
45 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (42 bp):
AACAACTTTGAAAAATATAAAAGGCTTTTTCATCAAAGGCTT
Found at i:11754814 original size:13 final size:14
Alignment explanation
Indices: 11754780--11754815 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
11754770 ATTTATGATT
11754780 TGTTATTTGCATGA
1 TGTTATTTGCATGA
11754794 T-TTATTTGCATGA
1 TGTTATTTGCATGA
11754807 TGTT-TTTGC
1 TGTTATTTGC
11754816 TTGTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.17, C:0.08, G:0.19, T:0.56
Consensus pattern (14 bp):
TGTTATTTGCATGA
Found at i:11756322 original size:139 final size:138
Alignment explanation
Indices: 11756148--11756543 Score: 542
Period size: 139 Copynumber: 2.8 Consensus size: 138
11756138 TTTGAACATT
* * * *
11756148 TTTTGGAATATGAATTCTTGTTGTTACCATCTATTGTATACATGTATTTGCATATATATTTTTAT
1 TTTT-GAATATGAATTCTTGTTGTTACTATATATTGCATACATGTATTTGCATATACATTTTTAT
* * * *
11756213 CCATATAAATATTTTTGTATGTACATTGTTTCATTTATTTGGGGACAATCTTTG-TCTTTTCAGT
65 CCATGTAAACATTTTTCTATGTACATTGTTTCATTTGTTTGGGG-CAATCTTTGCT-TTTTCAGT
*
11756277 TTTATATATAG
128 TTTATACATAG
* * * * *
11756288 TTTTGAATATGAATTCTTATTATTATTATGTATTGCATACATGTATTTGTATATACATTTTTATC
1 TTTTGAATATGAATTCTTGTTGTTACTATATATTGCATACATGTATTTGCATATACATTTTTATC
11756353 CATGTAAACATTTTTCTATGTACATTGTTTCATTTGTTTAGGGGCAATCTTTGCTTTTTCAGTTT
66 CATGTAAACATTTTTCTATGTACATTGTTTCATTTGTTT-GGGGCAATCTTTGCTTTTTCAGTTT
*
11756418 TGTACATAG
130 TATACATAG
* * *
11756427 TTTTGAATATTAATTATTGTTGTTACTATATATGGCATACATGTATTTGCATATACATTTTTATC
1 TTTTGAATATGAATTCTTGTTGTTACTATATATTGCATACATGTATTTGCATATACATTTTTATC
* * * * *
11756492 CATGTAAACATTTTTTTATGTATATTATTTCATTTGTTTAGGGCTATCTTTG
66 CATGTAAACATTTTTCTATGTACATTGTTTCATTTGTTTGGGGCAATCTTTG
11756544 GTATACAAAT
Statistics
Matches: 227, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
138 11 0.05
139 207 0.91
140 9 0.04
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (138 bp):
TTTTGAATATGAATTCTTGTTGTTACTATATATTGCATACATGTATTTGCATATACATTTTTATC
CATGTAAACATTTTTCTATGTACATTGTTTCATTTGTTTGGGGCAATCTTTGCTTTTTCAGTTTT
ATACATAG
Done.