Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004540.1 Kokia drynarioides strain JFW-HI SEQ_117999, 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: 217929
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:3128 original size:61 final size:61
Alignment explanation
Indices: 3050--3569 Score: 422
Period size: 60 Copynumber: 8.6 Consensus size: 61
3040 TTTTTAGATA
* *
3050 AAATTTATTTTTGTGTTGGTCATTGCATGGCCGACACCCACTTTTTGTCAGATAAAATATTC
1 AAATTT-TTTTTGTGTTGGTCATTGCATGGCCGACACCCACTTTTTATCAGATAAAAAATTC
* ** * * *
3112 AAATTTTTTTGGTGTTGGTCA-TGCTATGGTTGACACCC-TTTTTTGTCAGATAAAAATTTC
1 AAATTTTTTTTGTGTTGGTCATTGC-ATGGCCGACACCCACTTTTTATCAGATAAAAAATTC
* ** * * *
3172 -AATTTTTTTTGTGTTGGCCATTGCATGATCGACACTCC-TTTTTTGTCAGATTAAAAATTC
1 AAATTTTTTTTGTGTTGGTCATTGCATGGCCGACAC-CCACTTTTTATCAGATAAAAAATTC
* * * * * *
3232 AAA-TTTTTTTGTGTTGATCA-TGCCATGACCAACACCCCCTTTTTATCTGATAAAAAAATC
1 AAATTTTTTTTGTGTTGGTCATTG-CATGGCCGACACCCACTTTTTATCAGATAAAAAATTC
* * * * * *
3292 AATTTTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTAATCTGACAAAAAATTC
1 AAATTTTTTTTGTGTTGGTCATTGCATGGCCGACACCCACTTTTT-ATCAGATAAAAAATTC
* * * *
3354 -AATTTTTTTTGTGTT-GTCCATTGCATGGTCGACA-CCACCTTTTTTTCTGATAAAAAATTT
1 AAATTTTTTTTGTGTTGGT-CATTGCATGGCCGACACCCA-CTTTTTATCAGATAAAAAATTC
* * * * * *
3414 GAA-TTTTTTGGTGTTGGTCA-TGCCATGGCTGACA-CCACCTATTTATCTGATAAAAAAATC
1 AAATTTTTTTTGTGTTGGTCATTG-CATGGCCGACACCCA-CTTTTTATCAGATAAAAAATTC
* ** * * * *
3474 -AATTTTTTTGGTGTTGACCATTGCATAGCCGACACCCCCTTTTTAATCTA-ACAAGAAATT-
1 AAATTTTTTTTGTGTTGGTCATTGCATGGCCGACACCCACTTTTT-ATC-AGATAAAAAATTC
* **
3534 GAATTTTTTTTGTGTTGACCATTGCATGGCCGACAC
1 AAATTTTTTTTGTGTTGGTCATTGCATGGCCGACAC
3570 TAATTTTCTT
Statistics
Matches: 384, Mismatches: 54, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
59 35 0.09
60 180 0.47
61 147 0.38
62 22 0.06
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (61 bp):
AAATTTTTTTTGTGTTGGTCATTGCATGGCCGACACCCACTTTTTATCAGATAAAAAATTC
Found at i:3994 original size:30 final size:30
Alignment explanation
Indices: 3960--4087 Score: 98
Period size: 30 Copynumber: 4.1 Consensus size: 30
3950 AAATAATAAT
3960 AATTAGAAA-TGAAATTTAAAATATAAACGA
1 AATTAGAAACT-AAATTTAAAATATAAACGA
* * *
3990 AATTAGAAATTAAAATTAAAATTAAAATATATAGGA
1 AATTAGAAACT-AAA-T----TTAAAATATAAACGA
* * *
4026 AATTAGAAACTATATTTAAAATAAAAATGA
1 AATTAGAAACTAAATTTAAAATATAAACGA
* *
4056 AATTACAAATTAAATTTAAAA-AGTAAACGA
1 AATTAGAAACTAAATTTAAAATA-TAAACGA
4086 AA
1 AA
4088 AAAATTAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
29 1 0.01
30 46 0.59
31 4 0.05
32 1 0.01
34 1 0.01
35 2 0.03
36 23 0.29
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (30 bp):
AATTAGAAACTAAATTTAAAATATAAACGA
Found at i:4013 original size:12 final size:13
Alignment explanation
Indices: 3989--4017 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3979 AATATAAACG
3989 AAATTAGAAATTA
1 AAATTAGAAATTA
4002 AAATTA-AAATTA
1 AAATTAGAAATTA
4014 AAAT
1 AAAT
4018 ATATAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AAATTAGAAATTA
Found at i:4020 original size:36 final size:36
Alignment explanation
Indices: 3960--4053 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
3950 AAATAATAAT
* *
3960 AATTAGAAATGAAATTTAAAATATAAACGAAATTAGA
1 AATTA-AAATTAAAATTAAAATATAAACGAAATTAGA
* *
3997 AATTAAAATTAAAATTAAAATATATAGGAAATTAGA
1 AATTAAAATTAAAATTAAAATATAAACGAAATTAGA
* * * *
4033 AACTATATTTAAAATAAAAAT
1 AATTAAAATTAAAATTAAAAT
4054 GAAATTACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 44 0.90
37 5 0.10
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (36 bp):
AATTAAAATTAAAATTAAAATATAAACGAAATTAGA
Found at i:4568 original size:12 final size:12
Alignment explanation
Indices: 4551--4607 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
4541 GTTAAGCCTG
**
4551 GGGCTCGTAATC
1 GGGCTCGTCCTC
*
4563 GGGCTCGTCCGC
1 GGGCTCGTCCTC
4575 GGGCTCGTCCTC
1 GGGCTCGTCCTC
* *
4587 TGGCTCGTACTC
1 GGGCTCGTCCTC
*
4599 AGGCTCGTC
1 GGGCTCGTC
4608 ATTGGGCTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.07, C:0.35, G:0.33, T:0.25
Consensus pattern (12 bp):
GGGCTCGTCCTC
Found at i:4615 original size:24 final size:24
Alignment explanation
Indices: 4552--4616 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
4542 TTAAGCCTGG
* * * *
4552 GGCTCGTAATCGGGCTCGTCCGCG
1 GGCTCGTCATTGGGCTCGTACGCA
* *
4576 GGCTCGTCCTCT-GGCTCGTACTCA
1 GGCTCGTCAT-TGGGCTCGTACGCA
4600 GGCTCGTCATTGGGCTC
1 GGCTCGTCATTGGGCTC
4617 ATCTTCGGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.08, C:0.34, G:0.32, T:0.26
Consensus pattern (24 bp):
GGCTCGTCATTGGGCTCGTACGCA
Found at i:5249 original size:13 final size:13
Alignment explanation
Indices: 5231--5255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5221 ATTTCGAAAA
5231 TGTAAAAAATATG
1 TGTAAAAAATATG
5244 TGTAAAAAATAT
1 TGTAAAAAATAT
5256 CAGATTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TGTAAAAAATATG
Found at i:5685 original size:61 final size:60
Alignment explanation
Indices: 5561--5939 Score: 329
Period size: 60 Copynumber: 6.2 Consensus size: 60
5551 GATGGAAGAT
* * * * ** * *
5561 CAACACCAAAAAAAATTAAATTTTTTATCTGACAACCAGTATTGGTGTCGGTCAATGCATGAC
1 CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAG--GTGGTGTCGG-CCATGCATGAC
* **
5624 CAATACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGATCATGCAATGAC
1 CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGC-ATGAC
* * * *
5685 CAACACAAAAAAAAATTT-AATTTTTTGTCAGGTTAAAAAAGG-GGTGTCGGCCATACAATGAC
1 CAACAC-CAAAAAAATTTGAATTTTTTATCA-GAT-AAAAAGGTGGTGTCGGCCATGC-ATGAC
* * * * **
5747 TAACACCAAAAAAA-TTGATTTTTTTTATTAGATAAATAGGTGGTGTCGGCCATGGCATGGT
1 CAACACCAAAAAAATTTGA-ATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAT-GCATGAC
* * * * *
5808 CAACA-CAAAAAAAATTGAATTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGCATGGC
1 CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGGCCAT-GCATGAC
* * * * *
5868 CAACACC-AAAAAATTTGAATTTTTTATCTGACAAAAAGG-AGTGTCGGTCATGCAATGGC
1 CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGC-ATGAC
5927 CAACACCAAAAAA
1 CAACACCAAAAAA
5940 TTCTTTTTAT
Statistics
Matches: 265, Mismatches: 39, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.01
59 22 0.08
60 96 0.36
61 63 0.24
62 43 0.16
63 39 0.15
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (60 bp):
CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCATGAC
Found at i:5781 original size:123 final size:120
Alignment explanation
Indices: 5561--5974 Score: 380
Period size: 123 Copynumber: 3.4 Consensus size: 120
5551 GATGGAAGAT
* * ** ** *
5561 CAACACCAAAAAAAATTAAATTTTTTATCTGACAACCAGTATTGGTGTCGGTCAATG-CATGACC
1 CAACA-CAAAAAAAATTGAATTTTTTATCGGACAA--AAAAGGGGTGTCGG-CCATGACATGACC
* * * *
5625 AATACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGATCATGCAATGAC
62 AACACCAAAAAAA-TTGAATTTTTTATTAGATAAAAAGGTGGTGTCGGTCATGCAATGGC
* * ** *
5685 CAACACAAAAAAAAATTTAATTTTTTGTCAGGTTAAAAAAGGGGTGTCGGCCAT-ACAATGACTA
1 CAACAC-AAAAAAAATTGAATTTTTTATC-GGACAAAAAAGGGGTGTCGGCCATGAC-ATGACCA
* * * *
5749 ACACCAAAAAAATTGATTTTTTTTATTAGATAAATAGGTGGTGTCGGCCATGGC-ATGGT
63 ACACCAAAAAAATTGA-ATTTTTTATTAGATAAAAAGGTGGTGTCGGTCAT-GCAATGGC
* * * *
5808 CAACACAAAAAAAATTGAATTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGCATGGCCAACA
1 CAACACAAAAAAAATTGAATTTTTTATCGGACAAAAAAGGGGTGTCGGCCATGACATGACCAACA
* * *
5873 CCAAAAAATTTGAATTTTTTATCT-GACAAAAAGG-AGTGTCGGTCATGCAATGGC
66 CCAAAAAAATTGAATTTTTTAT-TAGATAAAAAGGTGGTGTCGGTCATGCAATGGC
* * * *
5927 CAACAC-CAAAAAATT---CTTTTTATCTGA-AAAAAAGGGGTGTCGACCATG
1 CAACACAAAAAAAATTGAATTTTTTATCGGACAAAAAAGGGGTGTCGGCCATG
5975 CATTTATTTG
Statistics
Matches: 242, Mismatches: 39, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
114 19 0.08
115 11 0.05
118 10 0.04
119 20 0.08
120 16 0.07
121 41 0.17
122 29 0.12
123 66 0.27
124 27 0.11
125 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (120 bp):
CAACACAAAAAAAATTGAATTTTTTATCGGACAAAAAAGGGGTGTCGGCCATGACATGACCAACA
CCAAAAAAATTGAATTTTTTATTAGATAAAAAGGTGGTGTCGGTCATGCAATGGC
Found at i:5818 original size:60 final size:60
Alignment explanation
Indices: 5561--5974 Score: 283
Period size: 61 Copynumber: 6.9 Consensus size: 60
5551 GATGGAAGAT
* * ** ** * *
5561 CAACACCAAAAAAAATTAAATTTTTTATCTGACAACCAGTATTGGTGTCGGTCAAT-GCATGAC
1 CAACACC-AAAAAAATTGATTTTTTTATCTGACAAAAAG--GGGGTGTCGG-CCATGGCATGGC
* * * * * ** *
5624 CAATACCAAAAAAATTTGAATTTTTTATCAGATAAAAAGGTGGTGTCGATCAT-GCAATGAC
1 CAACACCAAAAAAA-TTGATTTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGC-ATGGC
* * * * * ** * * *
5685 CAACACAAAAAAAAATTTAATTTTTTGTCAGGTTAAAAAAGGGGTGTCGGCCAT-ACAATGAC
1 CAACAC-CAAAAAAATTGATTTTTTTATC-TGACAAAAAGGGGGTGTCGGCCATGGC-ATGGC
* * * * *
5747 TAACACCAAAAAAATTGATTTTTTTTAT-TAGATAAATAGGTGGTGTCGGCCATGGCATGGT
1 CAACACCAAAAAAATTGA-TTTTTTTATCT-GACAAAAAGGGGGTGTCGGCCATGGCATGGC
* *
5808 CAACACAAAAAAAATTGAATTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGCATGGC
1 CAACACCAAAAAAATTGATTTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGCATGGC
* * * *
5868 CAACACCAAAAAATTTGAATTTTTTATCTGACAAAAA-GGAGTGTCGGTCAT-GCAATGGC
1 CAACACCAAAAAAATTGATTTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGC-ATGGC
* * *
5927 CAACACC-AAAAAA-T--TCTTTTTATCTGA-AAAAAAGGGGTGTCGACCATG
1 CAACACCAAAAAAATTGATTTTTTTATCTGACAAAAAGGGGGTGTCGGCCATG
5975 CATTTATTTG
Statistics
Matches: 289, Mismatches: 51, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
54 5 0.02
55 22 0.08
57 1 0.00
58 7 0.02
59 24 0.08
60 74 0.26
61 79 0.27
62 52 0.18
63 25 0.09
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (60 bp):
CAACACCAAAAAAATTGATTTTTTTATCTGACAAAAAGGGGGTGTCGGCCATGGCATGGC
Found at i:6974 original size:15 final size:14
Alignment explanation
Indices: 6949--6999 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
6939 AAAAAATGAC
6949 ATATTTATAT-ATA
1 ATATTTATATAATA
6962 AGTATTCTATATAATA
1 A-TATT-TATATAATA
6978 ATATTTATA-ACATAA
1 ATATTTATATA-AT-A
6993 ATATTTA
1 ATATTTA
7000 ACCAAAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.06
14 10 0.30
15 17 0.52
16 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
ATATTTATATAATA
Found at i:9683 original size:40 final size:40
Alignment explanation
Indices: 9628--9707 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
9618 TACTATTACC
9628 ATAGAAGTAAGTTCTATGAATACCTCTAAATACAGATTAA
1 ATAGAAGTAAGTTCTATGAATACCTCTAAATACAGATTAA
9668 ATAGAAGTAAGTTCTATGAATACCTCTAAATACAGATTAA
1 ATAGAAGTAAGTTCTATGAATACCTCTAAATACAGATTAA
9708 CTTCCCAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (40 bp):
ATAGAAGTAAGTTCTATGAATACCTCTAAATACAGATTAA
Found at i:10649 original size:2 final size:2
Alignment explanation
Indices: 10642--10669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10632 AAATTAATTA
10642 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
10670 TTCTAAATAA
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:14629 original size:7 final size:7
Alignment explanation
Indices: 14617--14644 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
14607 TAAACTTGAT
14617 AAATATA
1 AAATATA
14624 AAATATA
1 AAATATA
14631 AAATATA
1 AAATATA
14638 AAATATA
1 AAATATA
14645 TTAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:15691 original size:21 final size:21
Alignment explanation
Indices: 15665--15707 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
15655 TAAAATATCA
*
15665 TTTTTTTAA-TCTCTAAGATTT
1 TTTTTTTAACTCT-TAAAATTT
15686 TTTTTTTAACTCTTAAAATTT
1 TTTTTTTAACTCTTAAAATTT
15707 T
1 T
15708 GAAATTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTTTAACTCTTAAAATTT
Found at i:22288 original size:2 final size:2
Alignment explanation
Indices: 22281--22319 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
22271 TGGTATGCAT
* *
22281 AC AC AC AC AC AT GC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22320 TGATCTGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.46, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:23964 original size:164 final size:164
Alignment explanation
Indices: 23758--24083 Score: 539
Period size: 164 Copynumber: 2.0 Consensus size: 164
23748 GAAGATTACG
* * * *
23758 ATCGAGCCAAAATCTTTTACCATACGAAGTAAAGCCAATAAAATATAA-ATGTTGGACA-TGGAT
1 ATCGAGCCAAAATCTTTTACCATACAAAGTAAAGCAAATAAAAAATAATA-GTTGGACACAGG-T
*
23821 TTAATTGCTTTCAATGGCTATTTATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGTG
64 TTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGTG
23886 CTACCTATGTTGCTCCAACTCTACTTTTCTTGAACA
129 CTACCTATGTTGCTCCAACTCTACTTTTCTTGAACA
23922 ATCGAGCCAAAATCTTTTACCATACAAAGTAAAGCAAATAAAAAATAATAGTTGGACACAGGTTT
1 ATCGAGCCAAAATCTTTTACCATACAAAGTAAAGCAAATAAAAAATAATAGTTGGACACAGGTTT
* *
23987 AATTGCTTTCCATGGCTATTCATCATCTAAATCTTTGACATGATTGAACAGTTCAATCAGGTGCT
66 AATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGTGCT
* *
24052 ACCTATGTTGCTCCGACTCTACTTTTTTTGAA
131 ACCTATGTTGCTCCAACTCTACTTTTCTTGAA
24084 GTATCCGTGT
Statistics
Matches: 151, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
164 148 0.98
165 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (164 bp):
ATCGAGCCAAAATCTTTTACCATACAAAGTAAAGCAAATAAAAAATAATAGTTGGACACAGGTTT
AATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGTGCT
ACCTATGTTGCTCCAACTCTACTTTTCTTGAACA
Found at i:45035 original size:85 final size:85
Alignment explanation
Indices: 44892--45059 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
44882 ATCAACTACG
*
44892 TAAGCATATAATGCTTAGTAAGTCATAACCAGAATCCACTTACCAAAATACATACTCCACAAGAA
1 TAAGCATATAATGCTTAGTAAGTCATAACCAGAATCAACTTACCAAAATACATACTCCACAAGAA
44957 ATGTTGTTAACATTTCTTAC
66 ATGTTGTTAACATTTCTTAC
44977 TAAGCATATAATGCTTAGTAAGTCATAACCAGAATCAACTTACCAAAATACATACTCCACAAGAA
1 TAAGCATATAATGCTTAGTAAGTCATAACCAGAATCAACTTACCAAAATACATACTCCACAAGAA
45042 ATGTTGTTAACATTTCTT
66 ATGTTGTTAACATTTCTT
45060 TCTATAATTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (85 bp):
TAAGCATATAATGCTTAGTAAGTCATAACCAGAATCAACTTACCAAAATACATACTCCACAAGAA
ATGTTGTTAACATTTCTTAC
Found at i:48104 original size:95 final size:95
Alignment explanation
Indices: 47941--48134 Score: 388
Period size: 95 Copynumber: 2.0 Consensus size: 95
47931 TATATGTTAA
47941 TAAGAAATGAATTACACCTTTTCCTTTTTAAAATTATGTAATTATTGAGAAATATTAATTTTAAA
1 TAAGAAATGAATTACACCTTTTCCTTTTTAAAATTATGTAATTATTGAGAAATATTAATTTTAAA
48006 AATATATTTTAACATGTCTATATTATTTAT
66 AATATATTTTAACATGTCTATATTATTTAT
48036 TAAGAAATGAATTACACCTTTTCCTTTTTAAAATTATGTAATTATTGAGAAATATTAATTTTAAA
1 TAAGAAATGAATTACACCTTTTCCTTTTTAAAATTATGTAATTATTGAGAAATATTAATTTTAAA
48101 AATATATTTTAACATGTCTATATTATTTAT
66 AATATATTTTAACATGTCTATATTATTTAT
48131 TAAG
1 TAAG
48135 TGTTTTATTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (95 bp):
TAAGAAATGAATTACACCTTTTCCTTTTTAAAATTATGTAATTATTGAGAAATATTAATTTTAAA
AATATATTTTAACATGTCTATATTATTTAT
Found at i:48126 original size:46 final size:46
Alignment explanation
Indices: 47981--48127 Score: 111
Period size: 46 Copynumber: 3.1 Consensus size: 46
47971 AAATTATGTA
47981 ATTATTGAGAAATATTAATTTTAAAAATATATTTTAACATGTCTAT
1 ATTATTGAGAAATATTAATTTTAAAAATATATTTTAACATGTCTAT
* * * * *** * * * * *
48027 ATTATTTATTAAGAAATGAA--TTACACCTTTTCCTTTTTAAAAT-TATGT
1 ATTATTGA-GAA-ATATTAATTTTA-AAAATAT--ATTTTAACATGTCTAT
48075 AATTATTGAGAAATATTAATTTTAAAAATATATTTTAACATGTCTAT
1 -ATTATTGAGAAATATTAATTTTAAAAATATATTTTAACATGTCTAT
48122 ATTATT
1 ATTATT
48128 TATTAAGTGT
Statistics
Matches: 68, Mismatches: 24, Indels: 18
0.62 0.22 0.16
Matches are distributed among these distances:
46 24 0.35
47 13 0.19
48 13 0.19
49 18 0.26
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (46 bp):
ATTATTGAGAAATATTAATTTTAAAAATATATTTTAACATGTCTAT
Found at i:55118 original size:3 final size:3
Alignment explanation
Indices: 55110--55139 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55100 CCTAGAGTTG
55110 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55140 GATTCGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59980 original size:3 final size:3
Alignment explanation
Indices: 59972--60015 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
59962 GATGTAAAGT
59972 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
60016 TTCTTTCCGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:60058 original size:29 final size:29
Alignment explanation
Indices: 60025--60080 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
60015 ATTCTTTCCG
60025 TGAAGAGGTGAGCTTTGAAAGGGCTATGC
1 TGAAGAGGTGAGCTTTGAAAGGGCTATGC
60054 TGAAGAGGTGAGCTTTGAAAGGGCTAT
1 TGAAGAGGTGAGCTTTGAAAGGGCTAT
60081 ATGGGACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.38, T:0.25
Consensus pattern (29 bp):
TGAAGAGGTGAGCTTTGAAAGGGCTATGC
Found at i:61452 original size:21 final size:21
Alignment explanation
Indices: 61428--61495 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
61418 GTTTCATTTG
61428 TTGTTTTGAATCG-TTTGTTTA
1 TTGTTTTGAATCGATTT-TTTA
*
61449 TTG-TTTGAATCGATTTATTA
1 TTGTTTTGAATCGATTTTTTA
* * *
61469 TTATTTTAAATCGATTTTTTT
1 TTGTTTTGAATCGATTTTTTA
61490 TTGTTT
1 TTGTTT
61496 AATTCGATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.63
Consensus pattern (21 bp):
TTGTTTTGAATCGATTTTTTA
Found at i:61469 original size:20 final size:20
Alignment explanation
Indices: 61432--61504 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
61422 CATTTGTTGT
61432 TTTGAATCG-TTTGTTTATTG
1 TTTGAATCGATTT-TTTATTG
* *
61452 TTTGAATCGATTTATTATTAT
1 TTTGAATCGATTTTTTATT-G
* *
61473 TTTAAATCGATTTTTTTTTG
1 TTTGAATCGATTTTTTATTG
61493 TTT-AATTCGATT
1 TTTGAA-TCGATT
61505 AAAACTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 23 0.52
21 19 0.43
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.60
Consensus pattern (20 bp):
TTTGAATCGATTTTTTATTG
Found at i:61924 original size:17 final size:18
Alignment explanation
Indices: 61888--61927 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
61878 GTGTCTCGTA
**
61888 AGAAAAAAAAAAAGTGAG
1 AGAAAAAAAAAAAGAAAG
61906 AGAAAAAAAAAAA-AAAG
1 AGAAAAAAAAAAAGAAAG
61923 AGAAA
1 AGAAA
61928 TGGTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAAAAGAAAG
Found at i:63314 original size:22 final size:22
Alignment explanation
Indices: 63289--63337 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
63279 ACACTCATCG
63289 ACTCGTATTCGAAGTAACTCCT
1 ACTCGTATTCGAAGTAACTCCT
63311 ACTCGTATTCGAAGTAACTCCT
1 ACTCGTATTCGAAGTAACTCCT
63333 ACTCG
1 ACTCG
63338 ACCTATCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (22 bp):
ACTCGTATTCGAAGTAACTCCT
Found at i:81761 original size:6 final size:7
Alignment explanation
Indices: 81744--81770 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
81734 TTGAAATGTA
81744 AAAAAAT
1 AAAAAAT
81751 AAAAAAT
1 AAAAAAT
81758 AAAAAAT
1 AAAAAAT
81765 AAAAAA
1 AAAAAA
81771 ACTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:84004 original size:18 final size:20
Alignment explanation
Indices: 83982--84031 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
83972 ATTTTAATTT
83982 TTTTTATTTTTTTATAA-CA
1 TTTTTATTTTTTTATAATCA
* * *
84001 TTTTCA-ATTTTTATAATTA
1 TTTTTATTTTTTTATAATCA
84020 TTTTTATTTTTT
1 TTTTTATTTTTT
84032 AAAACTTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 9 0.38
19 11 0.46
20 4 0.17
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTATTTTTTTATAATCA
Found at i:92530 original size:33 final size:36
Alignment explanation
Indices: 92492--92557 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
92482 TATAGAATTT
92492 AAATTTATTA-T-TATA-TTTTTGAAAATATTTTTA
1 AAATTTATTATTATATATTTTTTGAAAATATTTTTA
92525 AAATTTATTATTATATATTTTTTGAAAATATTT
1 AAATTTATTATTATATATTTTTTGAAAATATTT
92558 ATGTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 10 0.33
34 1 0.03
35 4 0.13
36 15 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (36 bp):
AAATTTATTATTATATATTTTTTGAAAATATTTTTA
Found at i:92559 original size:24 final size:24
Alignment explanation
Indices: 92519--92567 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
92509 TTTGAAAATA
*
92519 TTTTTAAAATTTATTAT-TATATAT
1 TTTTTAAAATATATTATGTAT-TAT
92543 TTTTTGAAAATAT-TTATGTATTAT
1 TTTTT-AAAATATATTATGTATTAT
92567 T
1 T
92568 CTATATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTTAAAATATATTATGTATTAT
Found at i:92875 original size:3 final size:3
Alignment explanation
Indices: 92869--92893 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
92859 TAATAATGGT
92869 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
92894 AGCTTTTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:109281 original size:37 final size:39
Alignment explanation
Indices: 109219--109307 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
109209 TTAGAAAAAC
* *
109219 AAAAATTATTATATTTTCAATAAAA-TATTCTAAAATTTA
1 AAAAACTATTATATTTTCAAAAAAATTATT-TAAAATTTA
*
109258 AAAAACTA-TATATTTT-AAAAAAATTATTTAAAATTTTC
1 AAAAACTATTATATTTTCAAAAAAATTATTTAAAA-TTTA
109296 AAAAAC-ATTATA
1 AAAAACTATTATA
109308 AAATAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 12 0.27
38 25 0.57
39 7 0.16
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (39 bp):
AAAAACTATTATATTTTCAAAAAAATTATTTAAAATTTA
Found at i:111091 original size:28 final size:31
Alignment explanation
Indices: 111058--111117 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 31
111048 TGATCCGATC
111058 TGCAATT-TGATACA-T-AACTTTGATT-TGG
1 TGCAATTAT-ATACATTGAACTTTGATTGTGG
111086 TGCAATTATATACATTGAACTTTGATTGTGG
1 TGCAATTATATACATTGAACTTTGATTGTGG
111117 T
1 T
111118 TCAAATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 12 0.43
29 2 0.07
30 10 0.36
31 4 0.14
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (31 bp):
TGCAATTATATACATTGAACTTTGATTGTGG
Found at i:112150 original size:116 final size:116
Alignment explanation
Indices: 111946--112179 Score: 468
Period size: 116 Copynumber: 2.0 Consensus size: 116
111936 GTCAGGGCTG
111946 TTGCCACCATTGAGATCCTAATGGCCCTAGGAGAATCGGAGTATATTTAATAAATAGCTAGATAT
1 TTGCCACCATTGAGATCCTAATGGCCCTAGGAGAATCGGAGTATATTTAATAAATAGCTAGATAT
112011 TACGTATACCCCACTGAAATTGAGAAGAAAAATGATATGCATATTACATGT
66 TACGTATACCCCACTGAAATTGAGAAGAAAAATGATATGCATATTACATGT
112062 TTGCCACCATTGAGATCCTAATGGCCCTAGGAGAATCGGAGTATATTTAATAAATAGCTAGATAT
1 TTGCCACCATTGAGATCCTAATGGCCCTAGGAGAATCGGAGTATATTTAATAAATAGCTAGATAT
112127 TACGTATACCCCACTGAAATTGAGAAGAAAAATGATATGCATATTACATGT
66 TACGTATACCCCACTGAAATTGAGAAGAAAAATGATATGCATATTACATGT
112178 TT
1 TT
112180 ATAAATGTTT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (116 bp):
TTGCCACCATTGAGATCCTAATGGCCCTAGGAGAATCGGAGTATATTTAATAAATAGCTAGATAT
TACGTATACCCCACTGAAATTGAGAAGAAAAATGATATGCATATTACATGT
Found at i:115787 original size:45 final size:45
Alignment explanation
Indices: 115737--115825 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
115727 CTGATAAAAT
* **
115737 GAAGAAAGAGAAGGTC-GTGACAGTAAATAGCTCAGTTGAGAAGAG
1 GAAGAAAGAGAAGG-CAATGACAGTAAATAGCTCAACTGAGAAGAG
* *
115782 GAAGAAAGAGATGGCAATGGCAGTAAATAGCTCAACTGAGAAGA
1 GAAGAAAGAGAAGGCAATGACAGTAAATAGCTCAACTGAGAAGA
115826 TGAGTCGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.44, C:0.10, G:0.31, T:0.15
Consensus pattern (45 bp):
GAAGAAAGAGAAGGCAATGACAGTAAATAGCTCAACTGAGAAGAG
Found at i:117623 original size:16 final size:16
Alignment explanation
Indices: 117598--117632 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
117588 TTGAAATTTT
*
117598 TATAATTTTTAAAAAA
1 TATAAATTTTAAAAAA
*
117614 TATAAATTTTGAAAAA
1 TATAAATTTTAAAAAA
117630 TAT
1 TAT
117633 TTTGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TATAAATTTTAAAAAA
Found at i:118456 original size:12 final size:12
Alignment explanation
Indices: 118439--118463 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
118429 AAATATTGAG
118439 ATATGGAAGATC
1 ATATGGAAGATC
118451 ATATGGAAGATC
1 ATATGGAAGATC
118463 A
1 A
118464 AGAAGCTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
ATATGGAAGATC
Found at i:128967 original size:16 final size:16
Alignment explanation
Indices: 128941--128982 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
128931 ATTATTTTAA
128941 CATTTTATTTAAT-TTT
1 CATTTT-TTTAATCTTT
128957 CATTTCTTTTAATCTTT
1 CATTT-TTTTAATCTTT
*
128974 GATTTTTTT
1 CATTTTTTT
128983 TTTTGTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (16 bp):
CATTTTTTTAATCTTT
Found at i:131919 original size:18 final size:18
Alignment explanation
Indices: 131879--131921 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
131869 ATTCAAGGTG
131879 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
131897 AAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
131915 TAATTAA
1 TAATTAA
131922 AGATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:136905 original size:22 final size:26
Alignment explanation
Indices: 136857--136914 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 26
136847 TATTTTTTAA
*
136857 ATTATTTTTTAATATATTTTTGGCTT
1 ATTATTTTTTAATATATTTTTGACTT
136883 ATTA-TTTTTAAT-T-TTTTT-ACTT
1 ATTATTTTTTAATATATTTTTGACTT
136905 A-TATCTTTTT
1 ATTAT-TTTTT
136915 GTAAATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.07
22 4 0.14
23 10 0.34
24 1 0.03
25 8 0.28
26 4 0.14
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (26 bp):
ATTATTTTTTAATATATTTTTGACTT
Found at i:143050 original size:16 final size:16
Alignment explanation
Indices: 143017--143059 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
143007 AGTTGAAAGC
*
143017 ATATATAT-ATAATGT
1 ATATATATAATAATAT
143032 ATAGTA-ATAATAATAT
1 ATA-TATATAATAATAT
143048 ATATATATAATA
1 ATATATATAATA
143060 CATGACAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
ATATATATAATAATAT
Found at i:146341 original size:20 final size:20
Alignment explanation
Indices: 146318--146381 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
146308 ATTTAATCTA
146318 ATTTTGAAATTTTTATAAA-T
1 ATTTTGAAATTTTTA-AAATT
146338 ATTTTG-AATTTTTAAAATT
1 ATTTTGAAATTTTTAAAATT
*
146357 ATTTTGAAAATTTTAAAATT
1 ATTTTGAAATTTTTAAAATT
146377 ATTTT
1 ATTTT
146382 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 3 0.07
19 15 0.37
20 23 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAATT
Found at i:146912 original size:109 final size:110
Alignment explanation
Indices: 146664--146971 Score: 313
Period size: 109 Copynumber: 2.8 Consensus size: 110
146654 TATTATCCGA
* * * * * *
146664 ATATCTAATCAGTTTCGAGGTGAGGGACAATTTTACATGGAGGTTGATAAT-GAGAGAGTTTGGG
1 ATATCTAACCAATTCCGAGGTGAAGGATAATTCTACA-GGAGGTTGATAATGGA-AGAGTTTGGG
* * * *
146728 ACTCGAAATTTCATCCAGCTAGATGCACTTTCTTGTTGAGTCCCGAG
64 ACTCGAAATTTCGTCCAGCTAGACGCACTTTCCTGTTGAGTCCCAAG
* * ** * ** * *
146775 ATATGTAATCAATTCCGAGGTGCTGGATAATTTTA-TTGAGGTTGTTAATGGAAGAGTTTAGGAC
1 ATATCTAACCAATTCCGAGGTGAAGGATAATTCTACAGGAGGTTGATAATGGAAGAGTTTGGGAC
* * * *
146839 TCGAAATTTTGTCTAGCTAGACGCTCTTTCCTGTTGAGTCGCAAG
66 TCGAAATTTCGTCCAGCTAGACGCACTTTCCTGTTGAGTCCCAAG
146884 ATATCTAACCAAATT-CG-GGTTGAAGGATAATTCTACAGGAGGTTGATAATGG-AGAGTTTGGG
1 ATATCTAACC-AATTCCGAGG-TGAAGGATAATTCTACAGGAGGTTGATAATGGAAGAGTTTGGG
*
146946 A-TCCGAAATTTCGTCCAACTAGACGC
64 ACT-CGAAATTTCGTCCAGCTAGACGC
146972 GTTTTCTTGA
Statistics
Matches: 162, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
108 3 0.02
109 111 0.69
110 19 0.12
111 29 0.18
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (110 bp):
ATATCTAACCAATTCCGAGGTGAAGGATAATTCTACAGGAGGTTGATAATGGAAGAGTTTGGGAC
TCGAAATTTCGTCCAGCTAGACGCACTTTCCTGTTGAGTCCCAAG
Found at i:162259 original size:23 final size:23
Alignment explanation
Indices: 162216--162259 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
162206 CTCATATCTT
*
162216 GGAATTTTAATATACATTAAATA
1 GGAATTTTAATATACAATAAATA
162239 GGAATTTTGAATATA-AATAAA
1 GGAATTTT-AATATACAATAAA
162260 AAGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (23 bp):
GGAATTTTAATATACAATAAATA
Found at i:169916 original size:17 final size:17
Alignment explanation
Indices: 169878--169921 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
169868 AAAAAAATAT
*
169878 TTTTTATAAATTTTATAC
1 TTTTTA-AAATTTTATAA
169896 TTTTTAAATATTTT-TAA
1 TTTTTAAA-ATTTTATAA
169913 TTTTTAAAA
1 TTTTTAAAA
169922 AAATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAAATTTTATAA
Found at i:171656 original size:8 final size:8
Alignment explanation
Indices: 171639--171673 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
171629 TAACAGCATC
*
171639 AAGAGGGA
1 AAGAGAGA
171647 AAGAGAGA
1 AAGAGAGA
171655 AAGAGAGA
1 AAGAGAGA
171663 AAGAGGAGA
1 AAGA-GAGA
171672 AA
1 AA
171674 AACAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AAGAGAGA
Found at i:180840 original size:16 final size:17
Alignment explanation
Indices: 180821--180858 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
180811 ATTTCCTAAT
* *
180821 TTTATTGAC-TTTTTTA
1 TTTATTAACATTTTATA
180837 TTTATTAACATTTTATA
1 TTTATTAACATTTTATA
180854 TTTAT
1 TTTAT
180859 ATATTAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTATTAACATTTTATA
Found at i:189890 original size:12 final size:13
Alignment explanation
Indices: 189873--189901 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
189863 AATATTTAAA
189873 ATTAATA-AAAAT
1 ATTAATATAAAAT
189885 ATTAATATAAAAT
1 ATTAATATAAAAT
189898 ATTA
1 ATTA
189902 TAATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAATATAAAAT
Found at i:194654 original size:95 final size:95
Alignment explanation
Indices: 194545--194736 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
194535 AGTTAATTAA
194545 AAAAGAGAACCACCACCATTAACAGATTTAAGGAAACAAAATTAGTGCAAGAAAGGCATTTATAA
1 AAAAGAGAACCACCACCATTAACAGATTTAAGGAAACAAAATTAGTGCAAGAAAGGCATTTATAA
194610 TTAGTCTGGTGTAACTAGATTTAGTTTTAT
66 TTAGTCTGGTGTAACTAGATTTAGTTTTAT
194640 AAAAGAGAACCACCACCATTAACAGATTTAAGGAAACAAAATTAGTGCAAGAAAGGCATTTATAA
1 AAAAGAGAACCACCACCATTAACAGATTTAAGGAAACAAAATTAGTGCAAGAAAGGCATTTATAA
194705 TTAGTCTGGTGTAACTAGATTTAGTTTTAT
66 TTAGTCTGGTGTAACTAGATTTAGTTTTAT
194735 AA
1 AA
194737 TTCAAAGATT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (95 bp):
AAAAGAGAACCACCACCATTAACAGATTTAAGGAAACAAAATTAGTGCAAGAAAGGCATTTATAA
TTAGTCTGGTGTAACTAGATTTAGTTTTAT
Found at i:204375 original size:172 final size:172
Alignment explanation
Indices: 204089--204433 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
204079 ACATCCCGTC
204089 TTATTGTACACGTAAGTTGCTTGATGATATTGTTAGTTCTTTCTTTATACGGTTCTAAAATATGT
1 TTATTGTACACGTAAGTTGCTTGATGATATTGTTAGTTCTTTCTTTATACGGTTCTAAAATATGT
204154 TTTCATAATGTCATATTTACTTTTGGTTCAATACTCGGAAGGGGAGTAGTTGTAGTAATCGGAAA
66 TTTCATAATGTCATATTTACTTTTGGTTCAATACTCGGAAGGGGAGTAGTTGTAGTAATCGGAAA
204219 CAAGGTTGTATACACCATACAACCTAGAGGGGCTCCTTAGTG
131 CAAGGTTGTATACACCATACAACCTAGAGGGGCTCCTTAGTG
204261 TTATTGTACACGTAAGTTGCTTGATGATATTGTTAGTTCTTTCTTTATACGGTTCTAAAATATGT
1 TTATTGTACACGTAAGTTGCTTGATGATATTGTTAGTTCTTTCTTTATACGGTTCTAAAATATGT
204326 TTTCATAATGTCATATTTACTTTTGGTTCAATACTCGGAAGGGGAGTAGTTGTAGTAATCGGAAA
66 TTTCATAATGTCATATTTACTTTTGGTTCAATACTCGGAAGGGGAGTAGTTGTAGTAATCGGAAA
204391 CAAGGTTGTATACACCATACAACCTAGAGGGGCTCCTTAGTG
131 CAAGGTTGTATACACCATACAACCTAGAGGGGCTCCTTAGTG
204433 T
1 T
204434 ATCTTGTTTG
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (172 bp):
TTATTGTACACGTAAGTTGCTTGATGATATTGTTAGTTCTTTCTTTATACGGTTCTAAAATATGT
TTTCATAATGTCATATTTACTTTTGGTTCAATACTCGGAAGGGGAGTAGTTGTAGTAATCGGAAA
CAAGGTTGTATACACCATACAACCTAGAGGGGCTCCTTAGTG
Found at i:205596 original size:3 final size:3
Alignment explanation
Indices: 205588--205612 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
205578 CTGAGGTATT
205588 TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC T
205613 TGTTATTAAC
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:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:209547 original size:29 final size:30
Alignment explanation
Indices: 209486--209548 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
209476 AAGTATAACC
*
209486 ATATTAGGTCATTTACGCAAAAAAAGTAAAA
1 ATATTAGGTCATTTAC-CAAAAAAAGAAAAA
** *
209517 ATATTAGGTCATTTA-TTAAAAACGAAAAA
1 ATATTAGGTCATTTACCAAAAAAAGAAAAA
209546 ATA
1 ATA
209549 AGGATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.46
31 15 0.54
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (30 bp):
ATATTAGGTCATTTACCAAAAAAAGAAAAA
Found at i:213468 original size:3 final size:3
Alignment explanation
Indices: 213460--213484 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
213450 ATGCAAGTTC
213460 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
213485 TGACTGATAC
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Done.