Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013163.1 Kokia drynarioides strain JFW-HI SEQ_128182, 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: 269659
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:3839 original size:7 final size:7
Alignment explanation
Indices: 3827--3859 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3817 ATTTTATATG
3827 GAATTTT
1 GAATTTT
3834 GAATTTT
1 GAATTTT
3841 GAATTTT
1 GAATTTT
3848 -AATTATT
1 GAATT-TT
3855 GAATT
1 GAATT
3860 AAAAGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (7 bp):
GAATTTT
Found at i:10902 original size:16 final size:16
Alignment explanation
Indices: 10881--10913 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10871 TTCATGTTGC
10881 TAAGATGTGGATGCAA
1 TAAGATGTGGATGCAA
10897 TAAGATGTGGATGCAA
1 TAAGATGTGGATGCAA
10913 T
1 T
10914 TTTTGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.27
Consensus pattern (16 bp):
TAAGATGTGGATGCAA
Found at i:18736 original size:13 final size:13
Alignment explanation
Indices: 18711--18761 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
18701 ATAAACTGAA
18711 AAACATT-AAAAT
1 AAACATTAAAAAT
18723 AAACATTAAAAAT
1 AAACATTAAAAAT
*
18736 AAACAAATTTAAAAT
1 AAAC--ATTAAAAAT
18751 --ACATTAAAAAT
1 AAACATTAAAAAT
18762 TCTTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 8 0.24
12 7 0.21
13 11 0.32
15 8 0.24
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (13 bp):
AAACATTAAAAAT
Found at i:18919 original size:12 final size:12
Alignment explanation
Indices: 18902--18954 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
18892 ACCAAAATAG
18902 CAAAAATAACAA
1 CAAAAATAACAA
*
18914 CAAAAACAACAA
1 CAAAAATAACAA
* * *
18926 CCAAAATAATAG
1 CAAAAATAACAA
*
18938 TAAAAATAACAA
1 CAAAAATAACAA
18950 CAAAA
1 CAAAA
18955 GTAATAGCAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.72, C:0.17, G:0.02, T:0.09
Consensus pattern (12 bp):
CAAAAATAACAA
Found at i:18942 original size:24 final size:24
Alignment explanation
Indices: 18915--18961 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18905 AAATAACAAC
18915 AAAAACAACAACCAAAA-TAATAGT
1 AAAAACAACAA-CAAAAGTAATAGT
*
18939 AAAAATAACAACAAAAGTAATAG
1 AAAAACAACAACAAAAGTAATAG
18962 CATCAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAACAACAACAAAAGTAATAGT
Found at i:18971 original size:23 final size:20
Alignment explanation
Indices: 18945--19014 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 20
18935 TAGTAAAAAT
18945 AACAACAAAAGTAATAGCATCAA
1 AACAACAAAA--AA-AGCATCAA
**
18968 AACAGTAAAAAAAGCATCAA
1 AACAACAAAAAAAGCATCAA
**
18988 AAC-AGTAAAAAAGCA-CTAA
1 AACAACAAAAAAAGCATC-AA
19007 AACAACAA
1 AACAACAA
19015 CCAAAACAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.37
20 13 0.34
21 2 0.05
23 8 0.21
ACGTcount: A:0.64, C:0.17, G:0.09, T:0.10
Consensus pattern (20 bp):
AACAACAAAAAAAGCATCAA
Found at i:19010 original size:19 final size:20
Alignment explanation
Indices: 18960--18999 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18950 CAAAAGTAAT
18960 AGCATCAAAACAGTAAAAAA
1 AGCATCAAAACAGTAAAAAA
18980 AGCATCAAAACAGTAAAAAA
1 AGCATCAAAACAGTAAAAAA
19000 GCACTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.10, T:0.10
Consensus pattern (20 bp):
AGCATCAAAACAGTAAAAAA
Found at i:19035 original size:20 final size:21
Alignment explanation
Indices: 19004--19064 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
18994 AAAAAAGCAC
*
19004 TAAAACAA-CAACCAAAACAG
1 TAAAAAAAGCAACCAAAACAG
19024 T-AAAAAAGCAACACCAAAACAG
1 TAAAAAAAGC-A-ACCAAAACAG
19046 TAAAAAAAGC-ACCAAAACA
1 TAAAAAAAGCAACCAAAACA
19065 ACAATATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 1 0.03
22 11 0.31
23 8 0.22
ACGTcount: A:0.66, C:0.23, G:0.07, T:0.05
Consensus pattern (21 bp):
TAAAAAAAGCAACCAAAACAG
Found at i:19035 original size:23 final size:21
Alignment explanation
Indices: 19005--19064 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
18995 AAAAAGCACT
19005 AAAACAACAACCAAAACAGTAA
1 AAAACAAC-ACCAAAACAGTAA
19027 AAAAGCAACACCAAAACAGTAA
1 AAAA-CAACACCAAAACAGTAA
*
19049 AAAA-AGCACCAAAACA
1 AAAACAACACCAAAACA
19065 ACAATATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 11 0.31
22 21 0.58
23 4 0.11
ACGTcount: A:0.67, C:0.23, G:0.07, T:0.03
Consensus pattern (21 bp):
AAAACAACACCAAAACAGTAA
Found at i:21687 original size:21 final size:19
Alignment explanation
Indices: 21661--21707 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
21651 TATTATTTTT
21661 TTAATTTTTTAAATATTTATA
1 TTAATTTTTT-AATATTTA-A
* *
21682 TTAATTATTTAGTATTTAA
1 TTAATTTTTTAATATTTAA
21701 -TAATTTT
1 TTAATTTT
21708 ATACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 6 0.26
19 1 0.04
20 7 0.30
21 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTAATTTTTTAATATTTAA
Found at i:23835 original size:57 final size:57
Alignment explanation
Indices: 23747--23874 Score: 211
Period size: 57 Copynumber: 2.2 Consensus size: 57
23737 CAATGAAGCA
23747 TCTACCGATAGAACGACTCCAACAGTAATATTTTGTAAAGTCGTCTACCCTGAGACT
1 TCTACCGATAGAACGACTCCAACAGTAATATTTTGTAAAGTCGTCTACCCTGAGACT
* * *
23804 TCTACCGATAGAATGACTCCTACAGTAATATTTTGTAAAGTCGTCTACCCTGGGACT
1 TCTACCGATAGAACGACTCCAACAGTAATATTTTGTAAAGTCGTCTACCCTGAGACT
**
23861 TCTATTGATAGAAC
1 TCTACCGATAGAAC
23875 TCCTCTTCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (57 bp):
TCTACCGATAGAACGACTCCAACAGTAATATTTTGTAAAGTCGTCTACCCTGAGACT
Found at i:23903 original size:20 final size:20
Alignment explanation
Indices: 23858--23904 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
23848 CTACCCTGGG
* *
23858 ACTTCTATTGATAGAACTCC
1 ACTTCTATTGATACAACTAC
*
23878 TCTTCTATTGATACAACTAC
1 ACTTCTATTGATACAACTAC
*
23898 AGTTCTA
1 ACTTCTA
23905 CCGATACAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (20 bp):
ACTTCTATTGATACAACTAC
Found at i:26089 original size:20 final size:20
Alignment explanation
Indices: 26066--26126 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
26056 AAAACTCCTC
*
26066 TTCTACTGATACAACTATAG
1 TTCTACCGATACAACTATAG
*
26086 TTCTACCGATACAAGTAT-G
1 TTCTACCGATACAACTATAG
*
26105 CTTCTACCGAAACAACTA-AG
1 -TTCTACCGATACAACTATAG
26125 TT
1 TT
26127 GCAGACTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (20 bp):
TTCTACCGATACAACTATAG
Found at i:47581 original size:72 final size:72
Alignment explanation
Indices: 47504--47649 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
47494 TTATTTAAAT
47504 TTCACTAACTAATAATATTATTAATATATTATATTTTTACCTAAAAATTCTAAAAAAAAGTCAAA
1 TTCACTAACTAATAATATTATTAATATATTATATTTTTACCTAAAAATTCTAAAAAAAAGTCAAA
47569 TATATGA
66 TATATGA
47576 TTCACTAACTAATAATATTATTAATATATTATATTTTTACCTAAAAATTCTAAAAAAAAGTCAAA
1 TTCACTAACTAATAATATTATTAATATATTATATTTTTACCTAAAAATTCTAAAAAAAAGTCAAA
47641 TATATGA
66 TATATGA
47648 TT
1 TT
47650 TTGACATCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.40
Consensus pattern (72 bp):
TTCACTAACTAATAATATTATTAATATATTATATTTTTACCTAAAAATTCTAAAAAAAAGTCAAA
TATATGA
Found at i:49457 original size:141 final size:141
Alignment explanation
Indices: 49203--49485 Score: 548
Period size: 141 Copynumber: 2.0 Consensus size: 141
49193 TGACCAACTC
*
49203 TCTCCACCCTAATTTCTTTTGTTTTCACCCTAAACTTATGCATTCTTTTAGCGCCTTTGCTTGAT
1 TCTCCACCCTAATTTCTTTTGTTTTCACCCTAAACTTATGCATTCTTTTAGAGCCTTTGCTTGAT
49268 ATAGTATTTTCAATCCTACTTATCGACTAAAAAATATTGTTATTTCACATATAATCAGGCCGGTT
66 ATAGTATTTTCAATCCTACTTATCGACTAAAAAATATTGTTATTTCACATATAATCAGGCCGGTT
49333 CTTGATATTTT
131 CTTGATATTTT
*
49344 TCTCCGCCCTAATTTCTTTTGTTTTCACCCTAAACTTATGCATTCTTTTAGAGCCTTTGCTTGAT
1 TCTCCACCCTAATTTCTTTTGTTTTCACCCTAAACTTATGCATTCTTTTAGAGCCTTTGCTTGAT
49409 ATAGTATTTTCAATCCTACTTATCGACTAAAAAATATTGTTATTTCACATATAATCAGGCCGGTT
66 ATAGTATTTTCAATCCTACTTATCGACTAAAAAATATTGTTATTTCACATATAATCAGGCCGGTT
49474 CTTGATATTTT
131 CTTGATATTTT
49485 T
1 T
49486 GGGGCTCTAA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (141 bp):
TCTCCACCCTAATTTCTTTTGTTTTCACCCTAAACTTATGCATTCTTTTAGAGCCTTTGCTTGAT
ATAGTATTTTCAATCCTACTTATCGACTAAAAAATATTGTTATTTCACATATAATCAGGCCGGTT
CTTGATATTTT
Found at i:51312 original size:12 final size:12
Alignment explanation
Indices: 51297--51356 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
51287 CAACATTAAA
51297 AACAACAAAAAT
1 AACAACAAAAAT
51309 AACAACAAAAAT
1 AACAACAAAAAT
* *
51321 AACAGCAAAAAC
1 AACAACAAAAAT
*
51333 AAC-ACGAAAAT
1 AACAACAAAAAT
51344 AACAACAAAAAT
1 AACAACAAAAAT
51356 A
1 A
51357 GTAAAAAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 8 0.20
12 33 0.80
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:51312 original size:24 final size:23
Alignment explanation
Indices: 51297--51356 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
51287 CAACATTAAA
51297 AACAACAAAAATAACAACAAAAAT
1 AACAACAAAAATAACAAC-AAAAT
* *
51321 AACAGCAAAAACAAC-ACGAAAAT
1 AACAACAAAAATAACAAC-AAAAT
51344 AACAACAAAAATA
1 AACAACAAAAATA
51357 GTAAAAAAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (23 bp):
AACAACAAAAATAACAACAAAAT
Found at i:51391 original size:18 final size:18
Alignment explanation
Indices: 51348--51403 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
51338 GAAAATAACA
*
51348 ACAAAAATAGTAAAAAAGC
1 ACAAAAACAGTAAAAAA-C
*
51367 ACCAAAACAGTAAAAAAC
1 ACAAAAACAGTAAAAAAC
**
51385 ACAAAAACAACAAAAAAC
1 ACAAAAACAGTAAAAAAC
51403 A
1 A
51404 GCACTAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.71, C:0.18, G:0.05, T:0.05
Consensus pattern (18 bp):
ACAAAAACAGTAAAAAAC
Found at i:51418 original size:21 final size:20
Alignment explanation
Indices: 51359--51418 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
51349 CAAAAATAGT
**
51359 AAAAA-AGCACCAAAACAGTA
1 AAAAACAGCA-CAAAACAACA
51379 AAAAACA-CA-AAAACAACA
1 AAAAACAGCACAAAACAACA
51397 AAAAACAGCACTAAAACAACA
1 AAAAACAGCAC-AAAACAACA
51418 A
1 A
51419 TATAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 14 0.41
19 2 0.06
20 7 0.21
21 11 0.32
ACGTcount: A:0.70, C:0.22, G:0.05, T:0.03
Consensus pattern (20 bp):
AAAAACAGCACAAAACAACA
Found at i:54392 original size:42 final size:42
Alignment explanation
Indices: 54281--54385 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
54271 CTGATTGAGT
* * * * *
54281 TGTGCATGATATACAGGATCAACATGTAGTGTCTCATTAAGG
1 TGTGCAGGATGTACAGAATCAACATGTGGTGTCTCATCAAGG
* *
54323 TATGCAGGATGTACAGAATCAACATGTGGTGTCTTATCAAGG
1 TGTGCAGGATGTACAGAATCAACATGTGGTGTCTCATCAAGG
54365 TGTGCAGGATGTACAGAATCA
1 TGTGCAGGATGTACAGAATCA
54386 GTATGTGATG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTGCAGGATGTACAGAATCAACATGTGGTGTCTCATCAAGG
Found at i:63023 original size:45 final size:45
Alignment explanation
Indices: 62968--63056 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
62958 TTTTTGCTAG
62968 ACGTATGAATAATGGAGTTTTTAATAATGACTTTTTTATGCATAA
1 ACGTATGAATAATGGAGTTTTTAATAATGACTTTTTTATGCATAA
63013 ACGTATGAATAATGGAGTTTTTAATAATGACTTTTTTATGCATA
1 ACGTATGAATAATGGAGTTTTTAATAATGACTTTTTTATGCATA
63057 CTTTTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (45 bp):
ACGTATGAATAATGGAGTTTTTAATAATGACTTTTTTATGCATAA
Found at i:64202 original size:24 final size:24
Alignment explanation
Indices: 64170--64224 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
64160 GTATATTGGT
* * *
64170 TAACTATTCTAGGCTCGTAAGAGC
1 TAACCATTCTAGGCTCATAAAAGC
*
64194 TAACCATTCTAGGCTTATAAAAGC
1 TAACCATTCTAGGCTCATAAAAGC
64218 TAACCAT
1 TAACCAT
64225 CTTGGGCTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (24 bp):
TAACCATTCTAGGCTCATAAAAGC
Found at i:70925 original size:18 final size:19
Alignment explanation
Indices: 70904--70939 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
70894 GCAAATCTTC
70904 CTCTTT-TTCCAGATCTAA
1 CTCTTTGTTCCAGATCTAA
*
70922 CTCTTTGTTGCAGATCTA
1 CTCTTTGTTCCAGATCTA
70940 CGACGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.44
Consensus pattern (19 bp):
CTCTTTGTTCCAGATCTAA
Found at i:78669 original size:24 final size:24
Alignment explanation
Indices: 78627--78682 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
78617 TGGTTAAAAC
*
78627 TTAATAGTAAAAATTGTCAGTGCAAA
1 TTAATA-T-AAAATTGTCAGAGCAAA
78653 TGTAATATAAAA-TGTCAGAGCAAA
1 T-TAATATAAAATTGTCAGAGCAAA
78677 TTAATA
1 TTAATA
78683 AAAGATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 12 0.43
25 4 0.14
26 2 0.07
27 5 0.18
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.30
Consensus pattern (24 bp):
TTAATATAAAATTGTCAGAGCAAA
Found at i:79459 original size:19 final size:19
Alignment explanation
Indices: 79416--79460 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
79406 TCACTTGTAA
**
79416 TTGCAGATCTTCCTCTTTT
1 TTGCAGATCTAACTCTTTT
79435 TT-CAGATCTAACTCTTTT
1 TTGCAGATCTAACTCTTTT
79453 TTGCAGAT
1 TTGCAGAT
79461 GTAAAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TTGCAGATCTAACTCTTTT
Found at i:89015 original size:27 final size:26
Alignment explanation
Indices: 88985--89047 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
88975 TATCATCCTT
88985 ATTTTACTCCCGATAAAATTTTGATG
1 ATTTTACTCCCGATAAAATTTTGATG
*
89011 AATTTTACCCCCGATAAAATTTTGATG
1 -ATTTTACTCCCGATAAAATTTTGATG
89038 ATTTTA-TCCC
1 ATTTTACTCCC
89048 TAATCAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 3 0.09
26 6 0.18
27 25 0.74
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (26 bp):
ATTTTACTCCCGATAAAATTTTGATG
Found at i:89056 original size:26 final size:27
Alignment explanation
Indices: 88985--89058 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
88975 TATCATCCTT
* *
88985 ATTTTACTCCCGATAAAATTTTGATGA
1 ATTTTACCCCCAATAAAATTTTGATGA
*
89012 ATTTTACCCCCGATAAAATTTTGATG-
1 ATTTTACCCCCAATAAAATTTTGATGA
* * *
89038 ATTTTATCCCTAATCAAATTT
1 ATTTTACCCCCAATAAAATTT
89059 CTAGAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 17 0.40
27 25 0.60
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (27 bp):
ATTTTACCCCCAATAAAATTTTGATGA
Found at i:90349 original size:34 final size:34
Alignment explanation
Indices: 90306--90374 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
90296 TATTTACTTT
90306 ACTTTTTGTGGGAAAGTAAAAGTCTCTCTAATAG
1 ACTTTTTGTGGGAAAGTAAAAGTCTCTCTAATAG
90340 ACTTTTTGTGGGAAAGTAAAAGTCTCTCTAATAG
1 ACTTTTTGTGGGAAAGTAAAAGTCTCTCTAATAG
90374 A
1 A
90375 AACTGGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (34 bp):
ACTTTTTGTGGGAAAGTAAAAGTCTCTCTAATAG
Found at i:90795 original size:16 final size:16
Alignment explanation
Indices: 90764--90808 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
90754 TTATTTACTA
90764 AATTAA-TTTT-AATT
1 AATTAATTTTTCAATT
90778 AATTAATTTTTCAATT
1 AATTAATTTTTCAATT
90794 AATTAATTTTCTCAA
1 AATTAATTTT-TCAA
90809 CCAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.21
15 4 0.14
16 14 0.50
17 4 0.14
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAATTTTTCAATT
Found at i:95239 original size:28 final size:28
Alignment explanation
Indices: 95194--95545 Score: 202
Period size: 27 Copynumber: 12.6 Consensus size: 28
95184 GTCCTTGTTT
*
95194 GCCAC-AAGGCCTCATTTATCAAAGATC
1 GCCACAAAGGCTTCATTTATCAAAGATC
* * * * *
95221 GCTACAAAGGTTTCCTTTATCAAAAATT
1 GCCACAAAGGCTTCATTTATCAAAGATC
* *
95249 GCCACAAAGGCTTCTTTTAAT-AAAGATT
1 GCCACAAAGGCTTCATTT-ATCAAAGATC
95277 GCCACAAA-GCTTCATTTATCAAAGATC
1 GCCACAAAGGCTTCATTTATCAAAGATC
* *
95304 TTTCCATAAA-GCTTCATTTATCAAAGATC
1 --GCCACAAAGGCTTCATTTATCAAAGATC
* * * ** * *
95333 ACCAAAAAGTCTTCCGTT-TCAGATATC
1 GCCACAAAGGCTTCATTTATCAAAGATC
** * *
95360 ATCGCAAAGGCTTCCATTTGTCAAAGATC
1 GCCACAAAGGCTT-CATTTATCAAAGATC
* **
95389 GACACAAAGGCTTCCGTT-TCAAAGATC
1 GCCACAAAGGCTTCATTTATCAAAGATC
* * * *
95416 ACCACAAATGCTTCTAGTTGTCAAAGATC
1 GCCACAAAGGCTTC-ATTTATCAAAGATC
* *
95445 GCCATAAAGGCTTTCA-TT-TCATAGATC
1 GCCACAAAGGC-TTCATTTATCAAAGATC
* * * * *
95472 ACCGCAAAAGCTTTTATTTATCAAAGATT
1 GCCACAAAGGC-TTCATTTATCAAAGATC
* * *
95501 GCCATAAAGGCTTTCATTT-T-AGAGATT
1 GCCACAAAGGC-TTCATTTATCAAAGATC
**
95528 GCCACAAAGATTTCATTT
1 GCCACAAAGGCTTCATTT
95546 CCTAACATGT
Statistics
Matches: 254, Mismatches: 58, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
26 9 0.04
27 93 0.37
28 66 0.26
29 83 0.33
30 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (28 bp):
GCCACAAAGGCTTCATTTATCAAAGATC
Found at i:95397 original size:29 final size:29
Alignment explanation
Indices: 95364--95457 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
95354 GATATCATCG
*
95364 CAAAGGCTTCCATTTGTCAAAGATCGACA
1 CAAAGGCTTCCAGTTGTCAAAGATCGACA
95393 CAAAGGCTTCC-GTT-TCAAAGATC-ACCA
1 CAAAGGCTTCCAGTTGTCAAAGATCGA-CA
* * *
95420 CAAATGCTTCTAGTTGTCAAAGATCGCCA
1 CAAAGGCTTCCAGTTGTCAAAGATCGACA
*
95449 TAAAGGCTT
1 CAAAGGCTT
95458 TCATTTCATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
26 1 0.02
27 20 0.36
28 5 0.09
29 29 0.53
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (29 bp):
CAAAGGCTTCCAGTTGTCAAAGATCGACA
Found at i:95514 original size:56 final size:56
Alignment explanation
Indices: 95311--95519 Score: 204
Period size: 56 Copynumber: 3.8 Consensus size: 56
95301 ATCTTTCCAT
* * * * * * *
95311 AAAGCTT-CATTTATCAAAGATCACCAAAAAGTCTTCCGTTTCAGATATCATCGCA
1 AAAGCTTCCATTTATCAAAGATCGCCATAAAGGCTTCCATTTCAAAGATCACCGCA
* * * * * *
95366 AAGGCTTCCATTTGTCAAAGATCGACACAAAGGCTTCCGTTTCAAAGATCACCACA
1 AAAGCTTCCATTTATCAAAGATCGCCATAAAGGCTTCCATTTCAAAGATCACCGCA
* * * * * *
95422 AATGCTTCTAGTTGTCAAAGATCGCCATAAAGGCTTTCATTTCATAGATCACCGCA
1 AAAGCTTCCATTTATCAAAGATCGCCATAAAGGCTTCCATTTCAAAGATCACCGCA
** * *
95478 AAAGCTTTTATTTATCAAAGATTGCCATAAAGGCTTTCATTT
1 AAAGCTTCCATTTATCAAAGATCGCCATAAAGGCTTCCATTT
95520 TAGAGATTGC
Statistics
Matches: 129, Mismatches: 24, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
55 6 0.05
56 123 0.95
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (56 bp):
AAAGCTTCCATTTATCAAAGATCGCCATAAAGGCTTCCATTTCAAAGATCACCGCA
Found at i:97446 original size:6 final size:6
Alignment explanation
Indices: 97426--97464 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
97416 TGTTTGATCC
** *
97426 ATTGTT ATTAAT ATTGTT ATTGTT GTTGTT ATTGTT ATT
1 ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATT
97465 TATTAAAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (6 bp):
ATTGTT
Found at i:114358 original size:23 final size:23
Alignment explanation
Indices: 114328--114382 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
114318 TCATCCTTGC
114328 TGACTAGACCTTCTAGAAGCTAA
1 TGACTAGACCTTCTAGAAGCTAA
* **
114351 TGACTAGATCTTCTAGAAGCTGC
1 TGACTAGACCTTCTAGAAGCTAA
114374 TGACTAGAC
1 TGACTAGAC
114383 GCCACTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (23 bp):
TGACTAGACCTTCTAGAAGCTAA
Found at i:115139 original size:13 final size:12
Alignment explanation
Indices: 115120--115148 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
115110 TTTTTTTTTA
115120 TTTTCTC-CTTT
1 TTTTCTCTCTTT
115131 TTTTCTCTCTTT
1 TTTTCTCTCTTT
115143 TTTTCT
1 TTTTCT
115149 TTTCGAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTCTCTTT
Found at i:115169 original size:8 final size:8
Alignment explanation
Indices: 115158--115187 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
115148 TTTTCGAACC
115158 TTTTTCTTT
1 TTTTTC-TT
115167 TTTTTCTT
1 TTTTTCTT
115175 TTTTTCTT
1 TTTTTCTT
115183 TTTTT
1 TTTTT
115188 TGCTGTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:115175 original size:15 final size:15
Alignment explanation
Indices: 115157--115207 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
115147 CTTTTCGAAC
115157 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
115172 CTTTTTTTCTTTTTTTT
1 C--TTTTTCTTTTTTTT
*
115189 GC-TGTTCTTTTTTCTT
1 -CTTTTTCTTTTTT-TT
115205 CTT
1 CTT
115208 CTTTATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
15 12 0.40
16 3 0.10
17 14 0.47
18 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:115207 original size:10 final size:9
Alignment explanation
Indices: 115158--115188 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
115148 TTTTCGAACC
115158 TTTTTCTTT
1 TTTTTCTTT
115167 TTTTTC-TT
1 TTTTTCTTT
115175 TTTTTCTTT
1 TTTTTCTTT
115184 TTTTT
1 TTTTT
115189 GCTGTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:116127 original size:4 final size:4
Alignment explanation
Indices: 116106--116174 Score: 66
Period size: 4 Copynumber: 15.8 Consensus size: 4
116096 AAATAAGCAA
* *
116106 AAAT AAAAT AATAT AAAT AAAT AAAAT AAAT TAAT AACGAA AAAT AAAAT
1 AAAT -AAAT AA-AT AAAT AAAT -AAAT AAAT AAAT AA--AT AAAT -AAAT
116156 AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
116175 AACAATTGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
4 36 0.65
5 16 0.29
6 3 0.05
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:116131 original size:23 final size:23
Alignment explanation
Indices: 116105--116175 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
116095 AAAATAAGCA
116105 AAAATAAAATAATATAAATAAAT
1 AAAATAAAATAATATAAATAAAT
*
116128 AAAATAAATTAATA-ACGAA-AAAT
1 AAAATAAAATAATATA--AATAAAT
116151 AAAAT-AAATAA-ATAAATAAAT
1 AAAATAAAATAATATAAATAAAT
116172 AAAA
1 AAAA
116176 ACAATTGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 2 0.05
21 9 0.21
22 7 0.17
23 22 0.52
24 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (23 bp):
AAAATAAAATAATATAAATAAAT
Found at i:121829 original size:17 final size:17
Alignment explanation
Indices: 121807--121840 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
121797 CTAAGAATTT
121807 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
121824 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
121841 GTATTAGTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:122724 original size:23 final size:23
Alignment explanation
Indices: 122672--122725 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
122662 AGTCCATCCT
* *
122672 TGCTGACTAGACCTTTTAGAAGC
1 TGCTGATTAGACCTTCTAGAAGC
*
122695 TGCTGATTAGATCTTCTAGAAGC
1 TGCTGATTAGACCTTCTAGAAGC
122718 TGCTGATT
1 TGCTGATT
122726 GGATGCCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (23 bp):
TGCTGATTAGACCTTCTAGAAGC
Found at i:124663 original size:29 final size:27
Alignment explanation
Indices: 124595--124672 Score: 113
Period size: 29 Copynumber: 2.9 Consensus size: 27
124585 TAAGGTGTTC
124595 TTACAAAG-TTGCCACGAAGGCTTCCT
1 TTACAAAGATTGCCACGAAGGCTTCCT
*
124621 TTACAAAGATTGCCACAAAGGCATTCCT
1 TTACAAAGATTGCCACGAAGGC-TTCCT
*
124649 TATTCAAAGATTGCCACGAAGGCT
1 T-TACAAAGATTGCCACGAAGGCT
124673 ATTTTTTAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 8 0.17
27 12 0.26
28 7 0.15
29 19 0.41
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (27 bp):
TTACAAAGATTGCCACGAAGGCTTCCT
Found at i:124754 original size:56 final size:56
Alignment explanation
Indices: 124681--124891 Score: 242
Period size: 56 Copynumber: 3.8 Consensus size: 56
124671 CTATTTTTTA
* * * * *
124681 ACAGAGAACACCTCAAAGGCCTTCCTGTCTGGAGTTTGCCACAGAGGCTTTCATTT
1 ACAGAGAACGCCACAAAGGCTTTCCTGTCTAGAGTTTGCCACAGAGGCTTTCCTTT
* * * * * * * *
124737 ACAGAGAATGTCACAAAGGTTTTCCTGTCCAAAGTTTTCCACAAAGACTTTCCTTT
1 ACAGAGAACGCCACAAAGGCTTTCCTGTCTAGAGTTTGCCACAGAGGCTTTCCTTT
* * * *
124793 ACAGAGAACGCCACGAAGGATTTCCTGTCTATAGTTTGCCACAGATGCTTTCCTTT
1 ACAGAGAACGCCACAAAGGCTTTCCTGTCTAGAGTTTGCCACAGAGGCTTTCCTTT
* * *
124849 ATAGAGAACGCCACAAAGGCTTTCTTGTCTAGAATTTGCCACA
1 ACAGAGAACGCCACAAAGGCTTTCCTGTCTAGAGTTTGCCACA
124892 AAGACATTTC
Statistics
Matches: 126, Mismatches: 29, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 126 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (56 bp):
ACAGAGAACGCCACAAAGGCTTTCCTGTCTAGAGTTTGCCACAGAGGCTTTCCTTT
Found at i:124775 original size:15 final size:17
Alignment explanation
Indices: 124745--124776 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
124735 TTACAGAGAA
124745 TGTCACAAAGGTTTTCC
1 TGTCACAAAGGTTTTCC
124762 TGTC-CAAA-GTTTTCC
1 TGTCACAAAGGTTTTCC
124777 ACAAAGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (17 bp):
TGTCACAAAGGTTTTCC
Found at i:124806 original size:28 final size:28
Alignment explanation
Indices: 124775--124872 Score: 67
Period size: 28 Copynumber: 3.5 Consensus size: 28
124765 CCAAAGTTTT
124775 CCACAAAGACTTTCCTTTACAGAGAACG
1 CCACAAAGACTTTCCTTTACAGAGAACG
* * * ***
124803 CCACGAAGGA-TTTCCTGT-CTATAGTTTG
1 CCAC-AAAGACTTTCCTTTAC-AGAGAACG
* *
124831 CCACAGATG-CTTTCCTTTATAGAGAACG
1 CCACA-AAGACTTTCCTTTACAGAGAACG
*
124859 CCACAAAGGCTTTC
1 CCACAAAGACTTTC
124873 TTGTCTAGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
27 4 0.08
28 42 0.84
29 4 0.08
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (28 bp):
CCACAAAGACTTTCCTTTACAGAGAACG
Found at i:124829 original size:112 final size:113
Alignment explanation
Indices: 124659--124911 Score: 289
Period size: 112 Copynumber: 2.2 Consensus size: 113
124649 TATTCAAAGA
* * * * * ** *
124659 TTGCCACGAAGGCTATTT-TTTAACAGAGAACACCTCAAAGGCCTTCCTGTCTGGAGTTTGCCAC
1 TTGCCACAAAGAC-ATTTCTTTAACAGAGAACGCCACGAAGGATTTCCTGTCTAGAGTTTGCCAC
* * *
124723 AGAGGCTTTCATTTACAGAGAATGTCACAAAGGTTTTCCTGTCCA-AAGT
65 AGAGGCTTTCATTTACAGAGAACGCCACAAAGGCTTTCCTGTCCAGAA-T
* *
124772 TTTCCACAAAGAC-TTTCCTTT-ACAGAGAACGCCACGAAGGATTTCCTGTCTATAGTTTGCCAC
1 TTGCCACAAAGACATTT-CTTTAACAGAGAACGCCACGAAGGATTTCCTGTCTAGAGTTTGCCAC
* * * * *
124835 AGATGCTTTCCTTTATAGAGAACGCCACAAAGGCTTTCTTGTCTAGAAT
65 AGAGGCTTTCATTTACAGAGAACGCCACAAAGGCTTTCCTGTCCAGAAT
124884 TTGCCACAAAGACATTTCTTTAACAGAG
1 TTGCCACAAAGACATTTCTTTAACAGAG
124912 GTTGCCATAA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
111 3 0.03
112 89 0.77
113 24 0.21
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (113 bp):
TTGCCACAAAGACATTTCTTTAACAGAGAACGCCACGAAGGATTTCCTGTCTAGAGTTTGCCACA
GAGGCTTTCATTTACAGAGAACGCCACAAAGGCTTTCCTGTCCAGAAT
Found at i:124881 original size:28 final size:28
Alignment explanation
Indices: 124795--124881 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 28
124785 TTTCCTTTAC
* * *
124795 AGAGAACGCCACGAAGGATTTCCTGTCT
1 AGAGAACGCCACAAAGGCTTTCTTGTCT
* *** * * *
124823 ATAGTTTGCCACAGATGCTTTCCTT-TAT
1 AGAGAACGCCACAAAGGCTTT-CTTGTCT
124851 AGAGAACGCCACAAAGGCTTTCTTGTCT
1 AGAGAACGCCACAAAGGCTTTCTTGTCT
124879 AGA
1 AGA
124882 ATTTGCCACA
Statistics
Matches: 40, Mismatches: 17, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
27 3 0.08
28 35 0.88
29 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (28 bp):
AGAGAACGCCACAAAGGCTTTCTTGTCT
Found at i:124916 original size:29 final size:29
Alignment explanation
Indices: 124884--125058 Score: 133
Period size: 29 Copynumber: 6.0 Consensus size: 29
124874 TGTCTAGAAT
* *
124884 TTGCCACAAAGACATTTCTTTAACAGAGG
1 TTGCCATAAAGACATTTCTTTAACAGAGA
* *
124913 TTGCCATAAAGACATTTTTTTAACAAAGA
1 TTGCCATAAAGACATTTCTTTAACAGAGA
* ** *
124942 TCGCCATAAA-AGTGTTTCCTTT-ATAGAGA
1 TTGCCATAAAGA-CATTT-CTTTAACAGAGA
* *
124971 TTGCCAAAGAAG-CATTTCTTTAATAGAGA
1 TTGCCATA-AAGACATTTCTTTAACAGAGA
* * *
125000 TTACCACAAAGACATTTCCTTT-ATAGAGA
1 TTGCCATAAAGACATTT-CTTTAACAGAGA
* * * *
125029 TTGTCATTAAGGCATTTCTTTAACAAAGA
1 TTGCCATAAAGACATTTCTTTAACAGAGA
125058 T
1 T
125059 CACCACAAAC
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
28 12 0.10
29 94 0.82
30 9 0.08
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (29 bp):
TTGCCATAAAGACATTTCTTTAACAGAGA
Found at i:125064 original size:58 final size:57
Alignment explanation
Indices: 124887--125067 Score: 179
Period size: 58 Copynumber: 3.1 Consensus size: 57
124877 CTAGAATTTG
* * * * *
124887 CCACAAAGACATTT-CTTTAACAGAGGTTGCCATAAAGACATTTTTTTAACAAAGATCG
1 CCACAAAGACATTTCCTTT-ATAGAGATTGCCAT-AAGGCATTTCTTTAACAAAGATCA
* ** * * *
124945 CCATAAA-AGTGTTTCCTTTATAGAGATTGCCA-AAGAAGCATTTCTTTAATAGAGATTA
1 CCACAAAGA-CATTTCCTTTATAGAGATTGCCATAAG--GCATTTCTTTAACAAAGATCA
*
125003 CCACAAAGACATTTCCTTTATAGAGATTGTCATTAAGGCATTTCTTTAACAAAGATCA
1 CCACAAAGACATTTCCTTTATAGAGATTGCCA-TAAGGCATTTCTTTAACAAAGATCA
125061 CCACAAA
1 CCACAAA
125068 CCACAAAGGC
Statistics
Matches: 98, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
56 3 0.03
57 1 0.01
58 86 0.88
59 5 0.05
60 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (57 bp):
CCACAAAGACATTTCCTTTATAGAGATTGCCATAAGGCATTTCTTTAACAAAGATCA
Found at i:128562 original size:16 final size:16
Alignment explanation
Indices: 128543--128592 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
128533 TGATAATAAA
*
128543 TAATTTAATCATATTT
1 TAATTTAATTATATTT
*
128559 TAATATAATTAT-TTT
1 TAATTTAATTATATTT
*
128574 TATTTTAAATTATATTT
1 TAATTT-AATTATATTT
128591 TA
1 TA
128593 TATTAAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 7 0.25
16 16 0.57
17 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTAATTATATTT
Found at i:128593 original size:17 final size:16
Alignment explanation
Indices: 128565--128599 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
128555 ATTTTAATAT
*
128565 AATTATTTTTATTTTA
1 AATTATTTTTATATTA
128581 AATTATATTTTATATTA
1 AATTAT-TTTTATATTA
128598 AA
1 AA
128600 ACATTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTATTTTTATATTA
Found at i:131029 original size:16 final size:17
Alignment explanation
Indices: 130987--131029 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
130977 TAATTGAAGC
130987 AATTTTTTAAGATCTATA
1 AATTTTTT-AGATCTATA
**
131005 AATCATTTAGA-CTATA
1 AATTTTTTAGATCTATA
131021 AATTTTTTA
1 AATTTTTTA
131030 TAGTGGATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (17 bp):
AATTTTTTAGATCTATA
Found at i:133111 original size:17 final size:17
Alignment explanation
Indices: 133083--133132 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
133073 CTCACTATTT
*
133083 TCAAGGAAAATAATATC
1 TCAAGAAAAATAATATC
*
133100 TCAGGAAAAATAACAATATC
1 TCAAGAAAAAT---AATATC
133120 TCAAGAAAAATAA
1 TCAAGAAAAATAA
133133 CAATATCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.41
20 16 0.59
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.20
Consensus pattern (17 bp):
TCAAGAAAAATAATATC
Found at i:133119 original size:20 final size:20
Alignment explanation
Indices: 133094--133143 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
133084 CAAGGAAAAT
*
133094 AATATCTCAGGAAAAATAAC
1 AATATCTCAAGAAAAATAAC
133114 AATATCTCAAGAAAAATAAC
1 AATATCTCAAGAAAAATAAC
133134 AATATCTCAA
1 AATATCTCAA
133144 AGTTGTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (20 bp):
AATATCTCAAGAAAAATAAC
Found at i:135015 original size:19 final size:19
Alignment explanation
Indices: 134978--135015 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
134968 GTCTTGAGAA
**
134978 TTGACAAAATTACTCTTTT
1 TTGACAAAATTACAATTTT
134997 TTGACAAAATTACAATTTT
1 TTGACAAAATTACAATTTT
135016 ACCCTTTTAC
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:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (19 bp):
TTGACAAAATTACAATTTT
Found at i:136496 original size:18 final size:17
Alignment explanation
Indices: 136469--136504 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
136459 CTTTCTCAAG
136469 TATTATTAATATTTTTT
1 TATTATTAATATTTTTT
*
136486 TATTAATTAATGTTTTTT
1 TATT-ATTAATATTTTTT
136504 T
1 T
136505 TTAGAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTATTAATATTTTTT
Found at i:137028 original size:20 final size:20
Alignment explanation
Indices: 136996--137033 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
136986 ACTTTTAATA
136996 TTTATTAAACATA-AATATT
1 TTTATTAAACATATAATATT
*
137015 TTTATTTAATCATATAATA
1 TTTA-TTAAACATATAATA
137034 AATTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATTAAACATATAATATT
Found at i:138182 original size:20 final size:20
Alignment explanation
Indices: 138157--138197 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
138147 GTTTATATAT
138157 TGCATACATAAATAGTTGTA
1 TGCATACATAAATAGTTGTA
138177 TGCATACATAAATAGTTGTA
1 TGCATACATAAATAGTTGTA
138197 T
1 T
138198 TTATCTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCATACATAAATAGTTGTA
Found at i:140068 original size:24 final size:24
Alignment explanation
Indices: 140040--140090 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
140030 AGAAATAATC
* *
140040 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
140064 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
140088 TTT
1 TTT
140091 AAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:142054 original size:24 final size:24
Alignment explanation
Indices: 142021--142095 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
142011 AGAAATAATC
* * *
142021 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
142045 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
142069 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
142093 TTT
1 TTT
142096 GAGTCAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:147354 original size:20 final size:21
Alignment explanation
Indices: 147314--147360 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
147304 CTGCTATTAC
* **
147314 CTTTTTTCTTTTTCTTTAATT
1 CTTTTTTCTTTCTCTAAAATT
147335 -TTTTTTCTTTCTCTAAAATT
1 CTTTTTTCTTTCTCTAAAATT
147355 CTTTTT
1 CTTTTT
147361 GTTTGATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTTCTTTCTCTAAAATT
Found at i:150747 original size:4 final size:4
Alignment explanation
Indices: 150738--150769 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
150728 CGCACACACG
150738 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
150770 TGTTTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:164275 original size:37 final size:37
Alignment explanation
Indices: 164232--164335 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 37
164222 TTCGAAGCAA
164232 TAAAGTGACACCCAGTGTCTCATCGACCTAGCCAAAG
1 TAAAGTGACACCCAGTGTCTCATCGACCTAGCCAAAG
** ** * * *
164269 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCG-ACCTAGCCAAAG
*
164307 TAAAATAATGACA-CCAGTGTCTCATCGAC
1 T--AA-AGTGACACCCAGTGTCTCATCGAC
164336 TCAAGGTCGA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
37 21 0.42
38 10 0.20
39 1 0.02
40 14 0.28
41 4 0.08
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (37 bp):
TAAAGTGACACCCAGTGTCTCATCGACCTAGCCAAAG
Found at i:171251 original size:29 final size:29
Alignment explanation
Indices: 171218--171332 Score: 167
Period size: 29 Copynumber: 4.0 Consensus size: 29
171208 CCTGTGTGCA
* * *
171218 ACACACGGTTTAGCACATGCTCGTATGTG
1 ACACACGGTCTAGCACACGCTCGTGTGTG
* * *
171247 ACACACGATCTAGCACATGCCCGTGTGTG
1 ACACACGGTCTAGCACACGCTCGTGTGTG
*
171276 ACACACGGTCAAGCACACGCTCGTGTGTG
1 ACACACGGTCTAGCACACGCTCGTGTGTG
171305 ACACACGGTCTAGCACACGCTCGTGTGT
1 ACACACGGTCTAGCACACGCTCGTGTGT
171333 TTGGCCCGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (29 bp):
ACACACGGTCTAGCACACGCTCGTGTGTG
Found at i:171473 original size:56 final size:56
Alignment explanation
Indices: 171364--171474 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
171354 CCTTTAATTA
* *
171364 CAAAACAGTATACACATACGGTTTGGAACACACCCGTGTGCCCAGCCCGTGTGTCT
1 CAAAACAGTATACACACACGGTTTGGAACACACCCGTGTGCCCAGCCCATGTGTCT
* * * * ***
171420 CAAAACATTATACACACATGGTTTGGCACACGCCCGTGTGCTTGGCCCATGTGTC
1 CAAAACAGTATACACACACGGTTTGGAACACACCCGTGTGCCCAGCCCATGTGTC
171475 CTCTGTACCT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (56 bp):
CAAAACAGTATACACACACGGTTTGGAACACACCCGTGTGCCCAGCCCATGTGTCT
Found at i:172122 original size:17 final size:18
Alignment explanation
Indices: 172100--172133 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
172090 ATTAAGTAAG
172100 GAAGATGAA-AAAAAAAC
1 GAAGATGAACAAAAAAAC
172117 GAAGATGAACAAAAAAA
1 GAAGATGAACAAAAAAA
172134 AAAGAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.06
Consensus pattern (18 bp):
GAAGATGAACAAAAAAAC
Found at i:172138 original size:17 final size:17
Alignment explanation
Indices: 172101--172138 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
172091 TTAAGTAAGG
*
172101 AAGATGAAAAAAAAACG
1 AAGATGAAAAAAAAACA
172118 AAGATGAACAAAAAAA-A
1 AAGATGAA-AAAAAAACA
172135 AAGA
1 AAGA
172139 AACAATTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (17 bp):
AAGATGAAAAAAAAACA
Found at i:178673 original size:22 final size:22
Alignment explanation
Indices: 178645--178688 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
178635 GCTTTGATTC
*
178645 CATGATGAAATTAGAGGTGAAT
1 CATGATGAAATTAGAGATGAAT
178667 CATGATGAAATTAGAGATGAAT
1 CATGATGAAATTAGAGATGAAT
178689 ACTCTAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (22 bp):
CATGATGAAATTAGAGATGAAT
Found at i:191257 original size:3 final size:3
Alignment explanation
Indices: 191249--191281 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
191239 ACACGTTTTA
191249 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
191282 TTGGTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:194751 original size:30 final size:30
Alignment explanation
Indices: 194659--194771 Score: 151
Period size: 29 Copynumber: 3.8 Consensus size: 30
194649 GAGACAAGAT
194659 AACCACTTGAAAATGT-AGGGGTGTCCTAG
1 AACCACTTGAAAATGTGAGGGGTGTCCTAG
* * *
194688 AACCACTT-AGAAATGTG-GGGATCTCCTAA
1 AACCACTTGA-AAATGTGAGGGGTGTCCTAG
*
194717 AACCACTTGGAAATGTGAGGGGTGTCCTAG
1 AACCACTTGAAAATGTGAGGGGTGTCCTAG
*
194747 AACCACTTGAAAATGTGGGGGGTGT
1 AACCACTTGAAAATGTGAGGGGTGT
194772 ATTGTTTACA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 38 0.54
30 32 0.45
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
AACCACTTGAAAATGTGAGGGGTGTCCTAG
Found at i:200916 original size:10 final size:11
Alignment explanation
Indices: 200895--200925 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
200885 TTCTGACTTT
200895 GAAAAATCATA
1 GAAAAATCATA
200906 GAAAAAT-ATA
1 GAAAAATCATA
200916 GAAAAATCAT
1 GAAAAATCAT
200926 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (11 bp):
GAAAAATCATA
Found at i:201371 original size:23 final size:23
Alignment explanation
Indices: 201345--201551 Score: 260
Period size: 23 Copynumber: 9.0 Consensus size: 23
201335 ACACTAGCGC
201345 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCACTGTGTGT
201368 GCTTACTGATTCGCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
*
201391 GCTTACTGGATT-GCACTATGTGT
1 GCTTACT-GATTCGCACTGTGTGT
*
201414 GCTTACTG-TTCAGCACTATGTGT
1 GCTTACTGATTC-GCACTGTGTGT
*
201437 GCTTACTG-TTCAGCATTGTGTGT
1 GCTTACTGATTC-GCACTGTGTGT
* *
201460 GCTTACTGATTCGCACTATATGT
1 GCTTACTGATTCGCACTGTGTGT
*
201483 GCTTACTGATTTGCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
* *
201506 GCTTACTGTTTTGCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
* *
201529 GCATACTGATTTGCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
201552 TTACTGTTTC
Statistics
Matches: 167, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
21 2 0.01
22 1 0.01
23 154 0.92
24 10 0.06
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (23 bp):
GCTTACTGATTCGCACTGTGTGT
Found at i:202147 original size:13 final size:13
Alignment explanation
Indices: 202129--202156 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
202119 AGGGTGTTAC
202129 AAATTTAATATTA
1 AAATTTAATATTA
202142 AAATTTAATATTA
1 AAATTTAATATTA
202155 AA
1 AA
202157 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTTAATATTA
Found at i:206743 original size:22 final size:23
Alignment explanation
Indices: 206712--206776 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 23
206702 TTATCTTTTC
206712 CCATTTCTTGTTCTTGTTCTAGA
1 CCATTTCTTGTTCTTGTTCTAGA
***
206735 CC-TTTCTTGTTCTTGTTCTTTC
1 CCATTTCTTGTTCTTGTTCTAGA
*
206757 CCATTTCTTATTCTTGTTCT
1 CCATTTCTTGTTCTTGTTCT
206777 CGATTTAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.08, C:0.25, G:0.09, T:0.58
Consensus pattern (23 bp):
CCATTTCTTGTTCTTGTTCTAGA
Found at i:212583 original size:24 final size:23
Alignment explanation
Indices: 212531--212588 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
212521 TTTAAAAATT
*
212531 GTTATTTTATTATTTTATTATTC
1 GTTATTTTATTATTTTAATATTC
*
212554 GTTTATTTTATTCTTATTAAT-TTC
1 G-TTATTTTATTATT-TTAATATTC
212578 AGTTATGTTTA
1 -GTTAT-TTTA
212589 GTTTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 9 0.31
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (23 bp):
GTTATTTTATTATTTTAATATTC
Found at i:213556 original size:59 final size:59
Alignment explanation
Indices: 213484--213602 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
213474 GTAGGTGAGA
213484 GAAGGAGATAAAAGGCGGTGAGCTTGGATGAGACATTAAGGGGGAAGAGAGGGAACAAT
1 GAAGGAGATAAAAGGCGGTGAGCTTGGATGAGACATTAAGGGGGAAGAGAGGGAACAAT
213543 GAAGGAGATAAAAGGCGGTGAGCTTGGATGAGACATTAAGGGGGAAGAGAGGGAACAAT
1 GAAGGAGATAAAAGGCGGTGAGCTTGGATGAGACATTAAGGGGGAAGAGAGGGAACAAT
213602 G
1 G
213603 TCATTGCCTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.39, C:0.07, G:0.41, T:0.13
Consensus pattern (59 bp):
GAAGGAGATAAAAGGCGGTGAGCTTGGATGAGACATTAAGGGGGAAGAGAGGGAACAAT
Found at i:221471 original size:18 final size:18
Alignment explanation
Indices: 221438--221522 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
221428 CGCGGAAGGA
221438 AGAGCATACT-GCTCATT
1 AGAGCATACTGGCTCATT
*
221455 AGAGCATATTGGCTCATT
1 AGAGCATACTGGCTCATT
* * *
221473 AGAGCACACTAGCTCGTT
1 AGAGCATACTGGCTCATT
221491 AGAGCATACTGGCTCGATT
1 AGAGCATACTGGCTC-ATT
*
221510 -GAGCATACAGGCT
1 AGAGCATACTGGCT
221523 TGTAAGAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.16
18 46 0.81
19 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (18 bp):
AGAGCATACTGGCTCATT
Found at i:223895 original size:18 final size:18
Alignment explanation
Indices: 223872--223907 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
223862 GATCTGATAT
223872 TGCTCAAACGAGCCAGTA
1 TGCTCAAACGAGCCAGTA
*
223890 TGCTCAAACGAGTCAGTA
1 TGCTCAAACGAGCCAGTA
223908 CGCTATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (18 bp):
TGCTCAAACGAGCCAGTA
Found at i:228507 original size:4 final size:4
Alignment explanation
Indices: 228500--228536 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
228490 TATATATATA
228500 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
228537 GACTGAGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:229153 original size:34 final size:34
Alignment explanation
Indices: 229092--229161 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
229082 TGACACATGG
* * * *
229092 AAATGCAATGATAATGCAGATGAAGTGATAATTA
1 AAATGCAATGACAAAGCAAATGAAGTGACAATTA
* *
229126 AAATGCAATGACAAAGGAAATGTAGTGACAATTA
1 AAATGCAATGACAAAGCAAATGAAGTGACAATTA
229160 AA
1 AA
229162 TTACATCTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (34 bp):
AAATGCAATGACAAAGCAAATGAAGTGACAATTA
Found at i:240973 original size:19 final size:19
Alignment explanation
Indices: 240949--240985 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
240939 ATGAACAACC
240949 TCTATGCACTTGAGTTGTT
1 TCTATGCACTTGAGTTGTT
240968 TCTATGCACTTGAGTTGT
1 TCTATGCACTTGAGTTGT
240986 ATCGGTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (19 bp):
TCTATGCACTTGAGTTGTT
Found at i:241014 original size:30 final size:30
Alignment explanation
Indices: 240980--241039 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
240970 TATGCACTTG
240980 AGTTGTATCGGTAGTTGAATAACAAGTATC
1 AGTTGTATCGGTAGTTGAATAACAAGTATC
* *
241010 AGTTGTATCGGTAGTTGTATAACAGGTATC
1 AGTTGTATCGGTAGTTGAATAACAAGTATC
241040 GGTAGTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (30 bp):
AGTTGTATCGGTAGTTGAATAACAAGTATC
Found at i:241737 original size:80 final size:80
Alignment explanation
Indices: 241593--241778 Score: 273
Period size: 80 Copynumber: 2.3 Consensus size: 80
241583 GTTACCAGTA
* * *
241593 TACGATGCTGCTCACACTAAGCTGACAAGGACTCACATTACATGTGGTACCTCAACCATCGATAC
1 TACGATGCTGCTCACACTAAGCTGACAAGGACTCACATCACATGCGGTACCTCAACCATAGATAC
241658 GGTATAACTATTCCC
66 GGTATAACTATTCCC
* * *
241673 TATGATGCTGCTCACACTAAGCTGACAAGGACTCACATCACATGCGGTACCTCAGCTATAGATAC
1 TACGATGCTGCTCACACTAAGCTGACAAGGACTCACATCACATGCGGTACCTCAACCATAGATAC
* * *
241738 GGTATAATTGTTCTC
66 GGTATAACTATTCCC
* *
241753 TACGATGTTGCTCACATTAAGCTGAC
1 TACGATGCTGCTCACACTAAGCTGAC
241779 GAGAATATGC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 94 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (80 bp):
TACGATGCTGCTCACACTAAGCTGACAAGGACTCACATCACATGCGGTACCTCAACCATAGATAC
GGTATAACTATTCCC
Found at i:245463 original size:18 final size:17
Alignment explanation
Indices: 245439--245486 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
245429 TGATTTAAAT
245439 TTTTTTAATTTTAATTATA
1 TTTTTTAATTTTAA-TA-A
*
245458 TTTTTAAAATATTTAATAA
1 TTTTT-TAAT-TTTAATAA
245477 TTTTTTAATT
1 TTTTTTAATT
245487 AAATCAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.04
18 3 0.12
19 11 0.44
20 5 0.20
21 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTAATTTTAATAA
Found at i:245481 original size:20 final size:19
Alignment explanation
Indices: 245436--245484 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
245426 GGTTGATTTA
*
245436 AATTTTTT-TAATTTTAAT
1 AATTTTTTAAAATTTTAAT
*
245454 TATATTTTTAAAATATTTAAT
1 AAT-TTTTTAAAAT-TTTAAT
245475 AATTTTTTAA
1 AATTTTTTAA
245485 TTAAATCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 10 0.40
21 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTTAAAATTTTAAT
Found at i:245636 original size:30 final size:30
Alignment explanation
Indices: 245602--245660 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
245592 TTAATACAAC
* *
245602 ATTTGATATTTGAACTTGATATTTTTTTTA
1 ATTTGATACTTAAACTTGATATTTTTTTTA
*
245632 ATTTGGTACTTAAACTTGATATTTTTTTT
1 ATTTGATACTTAAACTTGATATTTTTTTT
245661 TCTAATTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (30 bp):
ATTTGATACTTAAACTTGATATTTTTTTTA
Found at i:246903 original size:6 final size:6
Alignment explanation
Indices: 246892--246922 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
246882 TTGATAATAA
246892 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
246923 AAATATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:247183 original size:15 final size:15
Alignment explanation
Indices: 247133--247183 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
247123 ATTCAATATT
247133 AATAT-TTAATAATA
1 AATATATTAATAATA
*
247147 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
247166 AATATATTAATAATA
1 AATATATTAATAATA
247181 AAT
1 AAT
247184 GTTTTGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 1 0.03
17 6 0.20
19 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:247871 original size:15 final size:16
Alignment explanation
Indices: 247851--247880 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247841 ATTTTATTTT
247851 AAATATTTAA-AATTA
1 AAATATTTAATAATTA
247866 AAATATTTAATAATT
1 AAATATTTAATAATT
247881 GAATGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATTTAATAATTA
Found at i:253741 original size:22 final size:22
Alignment explanation
Indices: 253698--253741 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
253688 TATAAAAAAA
*
253698 AATTTATTTTAGTTTTTCATTT
1 AATTTATTTTAGTTTTTAATTT
*
253720 AATTT-TTTTATTTCTTTAATTT
1 AATTTATTTTAGTT-TTTAATTT
253742 TTAAAGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (22 bp):
AATTTATTTTAGTTTTTAATTT
Found at i:254888 original size:20 final size:19
Alignment explanation
Indices: 254865--254909 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
254855 TTATTTATTC
254865 AATTTTAAAATT-TATAAAA
1 AATTTT-AAATTATATAAAA
254884 TAATTATTAAATTATATAAAA
1 -AATT-TTAAATTATATAAAA
254905 AATTT
1 AATTT
254910 CATTTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTTAAATTATATAAAA
Found at i:257665 original size:19 final size:19
Alignment explanation
Indices: 257637--257678 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
257627 AAGCTCCATG
257637 AAAA-ATGGTTGTTGAGGA
1 AAAATATGGTTGTTGAGGA
257655 AAAATATGGTTGTTGAGGA
1 AAAATATGGTTGTTGAGGA
257674 AAAAT
1 AAAAT
257679 GGTGCTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (19 bp):
AAAATATGGTTGTTGAGGA
Found at i:263489 original size:18 final size:19
Alignment explanation
Indices: 263466--263504 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
263456 TCATTTGTTT
263466 TTATTAA-TTTACAATT-TA
1 TTATTAACTTTA-AATTGTA
263484 TTATTAACTTTAAATTGTA
1 TTATTAACTTTAAATTGTA
263503 TT
1 TT
263505 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAACTTTAAATTGTA
Found at i:266258 original size:44 final size:45
Alignment explanation
Indices: 266190--266280 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 45
266180 TGTTTTAGAA
*
266190 ATTCTTAGGTTTTCTTCCCCCTTTTTGGACGATAATGGAGAATAG
1 ATTCTTAGGTTTTCTTCCCCCTTTTTGGACGACAATGGAGAATAG
*
266235 ATTCTTAGG-TTTCTTCCCTCTTTTTGGACGACAATGGAGAATAG
1 ATTCTTAGGTTTTCTTCCCCCTTTTTGGACGACAATGGAGAATAG
266279 AT
1 AT
266281 GAAAAAGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (45 bp):
ATTCTTAGGTTTTCTTCCCCCTTTTTGGACGACAATGGAGAATAG
Found at i:266606 original size:30 final size:30
Alignment explanation
Indices: 266572--266631 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
266562 TTAATTAGGA
*
266572 AAAATTATCAAACCAATATTTAATATATAT
1 AAAATTATCAAACCAATATTTAACATATAT
*
266602 AAAATTGTCAAACCAATATTTAACATATAT
1 AAAATTATCAAACCAATATTTAACATATAT
266632 TTATATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTATCAAACCAATATTTAACATATAT
Found at i:268019 original size:17 final size:17
Alignment explanation
Indices: 267999--268034 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
267989 TTTTTTTAGA
267999 ATTGAGCCTTAGCCTAG
1 ATTGAGCCTTAGCCTAG
268016 ATTGAGCCTTAGCCTAG
1 ATTGAGCCTTAGCCTAG
268033 AT
1 AT
268035 ATAGACAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (17 bp):
ATTGAGCCTTAGCCTAG
Found at i:268270 original size:19 final size:20
Alignment explanation
Indices: 268245--268295 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
268235 AAAAAATTAC
*
268245 ATATTTTTTGAAA-TTTTAT
1 ATATTTTTTGAAACTTCTAT
*
268264 GTA-TTTTTGCAAACTTCTAT
1 ATATTTTTTG-AAACTTCTAT
268284 ATATTTTTTGAA
1 ATATTTTTTGAA
268296 TTTGAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.23
19 5 0.19
20 9 0.35
21 6 0.23
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (20 bp):
ATATTTTTTGAAACTTCTAT
Found at i:269634 original size:2 final size:2
Alignment explanation
Indices: 269627--269659 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
269617 TTCTTCTTGA
269627 AT 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 AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.