Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012801.1 Kokia drynarioides strain JFW-HI SEQ_127814, 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: 191530
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:134 original size:32 final size:33
Alignment explanation
Indices: 70--136 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
60 AATGTAGATG
*
70 AAAAAATAATGATATTTGAAATATTTTATATTTA
1 AAAAAATAATGATATTTGAAATA-TCTATATTTA
*
104 AAAATAATAATGATATTTGACATA-CT-TATTTA
1 AAAA-AATAATGATATTTGAAATATCTATATTTA
136 A
1 A
137 TTTTATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.23
33 1 0.03
34 4 0.13
35 18 0.60
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (33 bp):
AAAAAATAATGATATTTGAAATATCTATATTTA
Found at i:5390 original size:14 final size:15
Alignment explanation
Indices: 5365--5394 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5355 ATTATATAAA
5365 TTATATTTTAAATAT
1 TTATATTTTAAATAT
5380 TTATA-TTTAAATAT
1 TTATATTTTAAATAT
5394 T
1 T
5395 AGCACAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTTAAATAT
Found at i:5830 original size:15 final size:17
Alignment explanation
Indices: 5800--5842 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5790 TAATAAAAAT
5800 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
5817 ATAATTTATATT-TTTATA
1 ATAATTT-TATTATTT-TA
5835 A-AATTTTA
1 ATAATTTTA
5843 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 15 0.62
18 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:6994 original size:30 final size:31
Alignment explanation
Indices: 6960--7040 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 31
6950 TAAGATGAAG
**
6960 TTTTAGGTTTCTTAAAAATTGA-AGAATTT-T
1 TTTTAGGTCCCTTAAAAATTGATA-AATTTAT
*
6990 TTTTAGGTCCCTTAAAAGTTGATAAATTTATT
1 TTTTAGGTCCCTTAAAAATTGATAAATTTA-T
*
7022 TTTTTGG-CCCTTAAAAATT
1 TTTTAGGTCCCTTAAAAATT
7041 TTAAAAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 24 0.56
31 12 0.28
32 7 0.16
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTTAGGTCCCTTAAAAATTGATAAATTTAT
Found at i:16995 original size:15 final size:14
Alignment explanation
Indices: 16977--17014 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
16967 TAAAATTCGA
16977 AAAATATAAGAATTT
1 AAAATATAAGAA-TT
*
16992 AAAATATCA-AATT
1 AAAATATAAGAATT
17005 AAAATATAAG
1 AAAATATAAG
17015 TACTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 10 0.50
14 2 0.10
15 8 0.40
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (14 bp):
AAAATATAAGAATT
Found at i:18042 original size:20 final size:17
Alignment explanation
Indices: 18010--18058 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
18000 GTATTGTGTT
*
18010 TATATATTTTTTTATCATA
1 TATATAATTTTTT-T-ATA
*
18029 TATAATAATTTTTTTATT
1 TAT-ATAATTTTTTTATA
18047 TATATAATTTTT
1 TATATAATTTTT
18059 GTTTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.33
18 5 0.19
19 4 0.15
20 9 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATAATTTTTTTATA
Found at i:18050 original size:18 final size:19
Alignment explanation
Indices: 18010--18058 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
18000 GTATTGTGTT
18010 TATAT-ATTTTTTTATCATA
1 TATATAATTTTTTTAT-ATA
18029 TATAATAATTTTTTTAT-T-
1 TAT-ATAATTTTTTTATATA
18047 TATATAATTTTT
1 TATATAATTTTT
18059 GTTTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 4 0.14
20 2 0.07
21 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATAATTTTTTTATATA
Found at i:18064 original size:16 final size:17
Alignment explanation
Indices: 18033--18065 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18023 ATCATATATA
*
18033 ATAATTTTTTTATTTAT
1 ATAATTTTTGTATTTAT
18050 ATAATTTTTGT-TTTAT
1 ATAATTTTTGTATTTAT
18066 TAAATTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATAATTTTTGTATTTAT
Found at i:18066 original size:20 final size:20
Alignment explanation
Indices: 18015--18054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18005 GTGTTTATAT
*
18015 ATTTTTTTATCATATATAATA
1 ATTTTTTTAT-TTATATAATA
18036 ATTTTTTTATTTATATAAT
1 ATTTTTTTATTTATATAAT
18055 TTTTGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTTATTTATATAATA
Found at i:18502 original size:21 final size:21
Alignment explanation
Indices: 18453--18493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18443 ATTTCTTTAT
*
18453 ATTATAAA--AAATTAAAATA
1 ATTATAAATTAAATAAAAATA
18472 ATTATAAATTAAATAAAAATA
1 ATTATAAATTAAATAAAAATA
18493 A
1 A
18494 ATTTTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTATAAATTAAATAAAAATA
Found at i:25670 original size:35 final size:35
Alignment explanation
Indices: 25622--25688 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
25612 CCCCTATTGA
25622 GGTATTTGAAAGATAGTA-GCATTTGTGCAACAGG
1 GGTATTTGAAAGATAGTAGGCATTTGTGCAACAGG
*
25656 GGTATTCTTAAAGATAGTAGGCATTTGTGCAAC
1 GGTATT-TGAAAGATAGTAGGCATTTGTGCAAC
25689 TATTTGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 6 0.20
35 11 0.37
36 13 0.43
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (35 bp):
GGTATTTGAAAGATAGTAGGCATTTGTGCAACAGG
Found at i:25988 original size:2 final size:2
Alignment explanation
Indices: 25981--26017 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25971 CAGCTTCACT
25981 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
26018 GAAGGATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:26545 original size:12 final size:12
Alignment explanation
Indices: 26528--26553 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26518 ATATGTGTAC
26528 ATGTATTTATAT
1 ATGTATTTATAT
26540 ATGTATTTATAT
1 ATGTATTTATAT
26552 AT
1 AT
26554 TCTTCCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
ATGTATTTATAT
Found at i:33790 original size:22 final size:22
Alignment explanation
Indices: 33762--33824 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 22
33752 GAAGTATTAA
33762 AATTAAATTATAAATTTTACAAT
1 AATTAAATTATAAATTTTA-AAT
* * *
33785 AATAAAAATATAATTTTTAAAT
1 AATTAAATTATAAATTTTAAAT
*
33807 AATTAAATCA-AAATTTTA
1 AATTAAATTATAAATTTTA
33825 TCATTTGTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 7 0.21
22 10 0.30
23 16 0.48
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTAAATTATAAATTTTAAAT
Found at i:34808 original size:19 final size:17
Alignment explanation
Indices: 34776--34811 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
34766 AGGGAACTTT
34776 TTATAAAAAAAAATAAA
1 TTATAAAAAAAAATAAA
34793 TTATACAAAAATAAATAAA
1 TTATA-AAAAA-AAATAAA
34812 AAATAATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
TTATAAAAAAAAATAAA
Found at i:40767 original size:17 final size:17
Alignment explanation
Indices: 40745--40778 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40735 AAGCAGGAAA
40745 ACAAACAAACCATAAGG
1 ACAAACAAACCATAAGG
*
40762 ACAAACAAAGCATAAGG
1 ACAAACAAACCATAAGG
40779 GCATGACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.21, G:0.15, T:0.06
Consensus pattern (17 bp):
ACAAACAAACCATAAGG
Found at i:45061 original size:21 final size:22
Alignment explanation
Indices: 45028--45086 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
45018 TAAAAATGAT
* *
45028 AAAATTTTGATTTAATTAT-TTA
1 AAAATTAT-ATTTAATTATCGTA
*
45050 AAAATTATATTTTTATTATCGTA
1 AAAATTATA-TTTAATTATCGTA
*
45073 AAAATTATAATTAA
1 AAAATTATATTTAA
45087 ATTTCGACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.03
22 18 0.60
23 11 0.37
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (22 bp):
AAAATTATATTTAATTATCGTA
Found at i:45662 original size:15 final size:15
Alignment explanation
Indices: 45644--45673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45634 TTTTATTTTT
*
45644 ATAAATTTTAAATTA
1 ATAAATTTAAAATTA
45659 ATAAATTTAAAATTA
1 ATAAATTTAAAATTA
45674 CACTTTAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATTTAAAATTA
Found at i:48300 original size:28 final size:28
Alignment explanation
Indices: 48269--48322 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
48259 TATAGTGAAG
48269 TTTTTA-TTAAAATCCTTGAAGAATTTTT
1 TTTTTACTT-AAATCCTTGAAGAATTTTT
48297 TTTTTACTTAAATCCTTGAAGAATTT
1 TTTTTACTTAAATCCTTGAAGAATTT
48323 AGAATGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (28 bp):
TTTTTACTTAAATCCTTGAAGAATTTTT
Found at i:49611 original size:26 final size:26
Alignment explanation
Indices: 49561--49630 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
49551 CGAAGTACTA
*
49561 AACAGAGAGCACA-TAAGTGCTGGGC
1 AACAGAGAGCACACAAAGTGCTGGGC
49586 AACAGAGAGCACACAAAGTGCTGGGC
1 AACAGAGAGCACACAAAGTGCTGGGC
*
49612 AACAGAGAGTACACAAAGT
1 AACAGAGAGCACACAAAGT
49631 ATTGAGCACA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
25 13 0.31
26 29 0.69
ACGTcount: A:0.41, C:0.20, G:0.29, T:0.10
Consensus pattern (26 bp):
AACAGAGAGCACACAAAGTGCTGGGC
Found at i:49669 original size:23 final size:22
Alignment explanation
Indices: 49634--49800 Score: 174
Period size: 23 Copynumber: 7.2 Consensus size: 22
49624 ACAAAGTATT
49634 GAGCACACAAAGTGCTAATCAGA
1 GAGCACAC-AAGTGCTAATCAGA
* *
49657 GAACACATGAAGTGCTAATAGCAGA
1 GAGCACA-CAAGTGCTAAT--CAGA
* *
49682 GAGCACGAGACGTGCTAAAT-AGA
1 GAGCAC-ACAAGTGCT-AATCAGA
*
49705 GAGCACACACAGTGCTAGTCAGA
1 GAGCACACA-AGTGCTAATCAGA
*
49728 GAGCACACACAGTGCTAAACAGA
1 GAGCACACA-AGTGCTAATCAGA
*
49751 GAGCACACGAAGTGCTAAACAGA
1 GAGCACAC-AAGTGCTAATCAGA
49774 GAGCACACACAGTGCTAATCAGA
1 GAGCACACA-AGTGCTAATCAGA
49797 GAGC
1 GAGC
49801 GCGCTAGTGT
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
22 5 0.04
23 99 0.79
24 1 0.01
25 16 0.13
26 4 0.03
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (22 bp):
GAGCACACAAGTGCTAATCAGA
Found at i:49745 original size:46 final size:45
Alignment explanation
Indices: 49634--49800 Score: 194
Period size: 46 Copynumber: 3.6 Consensus size: 45
49624 ACAAAGTATT
* * *
49634 GAGCACACAAAGTGCTAATCAGAGAACACATGAAGTGCTAATAGCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACA-CAAGTGCTAAT--CAGA
* *
49682 GAGCACGAGAC-GTGCTAAAT-AGAGAGCACACACAGTGCTAGTCAGA
1 GAGCAC-ACACAGTGCT-AATCAGAGAGCACACA-AGTGCTAATCAGA
* *
49728 GAGCACACACAGTGCTAAACAGAGAGCACACGAAGTGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACAC-AAGTGCTAATCAGA
49774 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
49801 GCGCTAGTGT
Statistics
Matches: 103, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
45 5 0.05
46 63 0.61
47 2 0.02
48 28 0.27
49 5 0.05
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (45 bp):
GAGCACACACAGTGCTAATCAGAGAGCACACAAGTGCTAATCAGA
Found at i:49784 original size:69 final size:71
Alignment explanation
Indices: 49634--49800 Score: 234
Period size: 69 Copynumber: 2.4 Consensus size: 71
49624 ACAAAGTATT
* * * *
49634 GAGCACACAAAGTGCTAATCAGAGAACACATGAAGTGCTAATAGCAGAGAGCACGAGACGTGCTA
1 GAGCACACACAGTGCTAATCAGAGAGCACATCAAGTGCTAATAGCAGAGAGCACGAGAAGTGCTA
*
49699 AATAGA
66 AACAGA
*
49705 GAGCACACACAGTGCTAGTCAGAGAGCACA-CACAGTGCTAA-A-CAGAGAGCAC-ACGAAGTGC
1 GAGCACACACAGTGCTAATCAGAGAGCACATCA-AGTGCTAATAGCAGAGAGCACGA-GAAGTGC
49766 TAAACAGA
64 TAAACAGA
49774 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
49801 GCGCTAGTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
68 1 0.01
69 49 0.56
70 2 0.02
71 35 0.40
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (71 bp):
GAGCACACACAGTGCTAATCAGAGAGCACATCAAGTGCTAATAGCAGAGAGCACGAGAAGTGCTA
AACAGA
Found at i:70213 original size:22 final size:20
Alignment explanation
Indices: 70188--70233 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 20
70178 AAGAAAAATG
70188 AGAGTGAGGAAGCTCATTTGA
1 AGAG-GAGGAAGCTCATTTGA
70209 A-A-GAGGAAGCTCATTTGAA
1 AGAGGAGGAAGCTCATTTG-A
70228 AGAGGA
1 AGAGGA
70234 AGTCCGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 15 0.68
19 2 0.09
20 2 0.09
21 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.20
Consensus pattern (20 bp):
AGAGGAGGAAGCTCATTTGA
Found at i:70216 original size:18 final size:18
Alignment explanation
Indices: 70193--70235 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
70183 AAATGAGAGT
70193 GAGGAAGCTCATTTGAAA
1 GAGGAAGCTCATTTGAAA
70211 GAGGAAGCTCATTTGAAA
1 GAGGAAGCTCATTTGAAA
70229 GAGGAAG
1 GAGGAAG
70236 TCCGAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.19
Consensus pattern (18 bp):
GAGGAAGCTCATTTGAAA
Found at i:85645 original size:27 final size:27
Alignment explanation
Indices: 85593--85647 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
85583 ATTAAAAATA
* * *
85593 ATAAAATATAATTTTATATTAATATTT
1 ATAAAATATAAATTTAAATAAATATTT
85620 ATAAAAT-TAAATTTAAATAAATTATTT
1 ATAAAATATAAATTTAAATAAA-TATTT
85647 A
1 A
85648 ATTTAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAAATATAAATTTAAATAAATATTT
Found at i:93555 original size:26 final size:27
Alignment explanation
Indices: 93521--93573 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
93511 TTACAATTAA
93521 TTTT-AAAA-AAATCAACATATAATTTT
1 TTTTAAAAAGAAATCAACATA-AATTTT
* *
93547 TTTTTAAAAGAAATCAATATAAATTTT
1 TTTTAAAAAGAAATCAACATAAATTTT
93574 ATCCTTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 10 0.42
28 10 0.42
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTAAAAAGAAATCAACATAAATTTT
Found at i:95862 original size:2 final size:2
Alignment explanation
Indices: 95855--95882 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
95845 GATATGATTA
95855 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
95883 TGAACAATTT
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:99816 original size:20 final size:20
Alignment explanation
Indices: 99793--99832 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
99783 TTATTTATTC
99793 TTTATAATTTTTTTAAAAAT
1 TTTATAATTTTTTTAAAAAT
99813 TTTATAATTTTTTTAAAAAT
1 TTTATAATTTTTTTAAAAAT
99833 ATAAATTTTG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATAATTTTTTTAAAAAT
Found at i:103138 original size:31 final size:30
Alignment explanation
Indices: 103103--103167 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 30
103093 TTTTAAGAGT
103103 TGGTTTTATATTATATATAGATGAGAAGGGA
1 TGGTTTTATATTATATATAGATGAGAA-GGA
*
103134 TGGTTTTATATTATATATGGATGAGAAGGA
1 TGGTTTTATATTATATATAGATGAGAAGGA
103164 TGGT
1 TGGT
103168 ATGAGCTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (30 bp):
TGGTTTTATATTATATATAGATGAGAAGGA
Found at i:105517 original size:2 final size:2
Alignment explanation
Indices: 105510--105536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105500 TAACTTTTTA
105510 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 A
105537 AAACCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113116 original size:17 final size:17
Alignment explanation
Indices: 113094--113132 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
113084 AGGCGGAGAA
* *
113094 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
113111 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
113128 CTTGT
1 CTTGT
113133 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:113332 original size:15 final size:15
Alignment explanation
Indices: 113312--113341 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
113302 ACGTTACTTC
113312 TATTAGTTGTTGATT
1 TATTAGTTGTTGATT
113327 TATTAGTTGTTGATT
1 TATTAGTTGTTGATT
113342 GGAATAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (15 bp):
TATTAGTTGTTGATT
Found at i:118557 original size:2 final size:2
Alignment explanation
Indices: 118552--118586 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
118542 ATATAAAGTC
118552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118587 CAGCATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:118727 original size:20 final size:18
Alignment explanation
Indices: 118702--118740 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
118692 AGTGACAGAC
118702 ATAAATAAAATAAAAAATAT
1 ATAAAT-AAAT-AAAAATAT
*
118722 ATAAATTAATAAAAATAT
1 ATAAATAAATAAAAATAT
118740 A
1 A
118741 ATTTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAATAAATAAAAATAT
Found at i:119234 original size:63 final size:63
Alignment explanation
Indices: 119167--119296 Score: 233
Period size: 63 Copynumber: 2.1 Consensus size: 63
119157 GATTTGAGTA
*
119167 TTTTACGAAAGTTTTTTTAATACTCCAAGTGTTTTAAAAATGTTTCTAACTCTAAAATTGTTT
1 TTTTACGAAAGTTTTTTTAATACTCCAAGTGTTTTAAAAATGTTTATAACTCTAAAATTGTTT
* *
119230 TTTTACGAAAGTTTTTTTAATACTCCAAGTGTTTTAAAAATGTTTATAACTCTAAATTTTTTT
1 TTTTACGAAAGTTTTTTTAATACTCCAAGTGTTTTAAAAATGTTTATAACTCTAAAATTGTTT
119293 TTTT
1 TTTT
119297 CCAGGTCTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (63 bp):
TTTTACGAAAGTTTTTTTAATACTCCAAGTGTTTTAAAAATGTTTATAACTCTAAAATTGTTT
Found at i:120727 original size:16 final size:17
Alignment explanation
Indices: 120696--120729 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
120686 ATGTGAAAAG
*
120696 ATTTATATCGTTTTTAA
1 ATTTATATCATTTTTAA
120713 ATTTATAT-ATTTTTAA
1 ATTTATATCATTTTTAA
120729 A
1 A
120730 GATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTATATCATTTTTAA
Found at i:123405 original size:22 final size:24
Alignment explanation
Indices: 123361--123406 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
123351 CAAAGTATAT
*
123361 TAATAATCCAAAATCAAATTAATAG
1 TAATAAT-CAAAATCAAAATAATAG
123386 TAATAAT-AAAAT-AAAATAATA
1 TAATAATCAAAATCAAAATAATA
123407 TAAATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
25 7 0.35
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
TAATAATCAAAATCAAAATAATAG
Found at i:124386 original size:11 final size:11
Alignment explanation
Indices: 124370--124400 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
124360 ACGGTTAAAT
*
124370 GATCAACGGTC
1 GATCAACAGTC
124381 GATCAACAGTC
1 GATCAACAGTC
124392 GATCAACAG
1 GATCAACAG
124401 CTGGTCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (11 bp):
GATCAACAGTC
Found at i:124551 original size:24 final size:24
Alignment explanation
Indices: 124523--124576 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
124513 GATTTTTAAA
124523 GGGTTTAAAAAGATTTGGGTTATT
1 GGGTTTAAAAAGATTTGGGTTATT
* * *
124547 GGGTTTTTAAAGGATTTGGGTTGTT
1 GGG-TTTAAAAAGATTTGGGTTATT
124572 GGGTT
1 GGGTT
124577 AGTGACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.44
Consensus pattern (24 bp):
GGGTTTAAAAAGATTTGGGTTATT
Found at i:130449 original size:22 final size:24
Alignment explanation
Indices: 130405--130450 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
130395 CAAAGTATAT
*
130405 TAATAATCCAAAATCAAATTAATAG
1 TAATAAT-CAAAATCAAAATAATAG
130430 TAATAAT-AAAAT-AAAATAATA
1 TAATAATCAAAATCAAAATAATA
130451 TAAATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
25 7 0.35
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
TAATAATCAAAATCAAAATAATAG
Found at i:131548 original size:13 final size:13
Alignment explanation
Indices: 131530--131558 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
131520 TTTTTCGGAA
131530 AAAGTCAACGGTC
1 AAAGTCAACGGTC
131543 AAAGTCAACGGTC
1 AAAGTCAACGGTC
131556 AAA
1 AAA
131559 CGATCAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:133330 original size:18 final size:18
Alignment explanation
Indices: 133307--133344 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
133297 CAAATTCTGC
133307 CCTTATTAGACGTATCCA
1 CCTTATTAGACGTATCCA
133325 CCTTATTAGACGTATCCA
1 CCTTATTAGACGTATCCA
133343 CC
1 CC
133345 CTCTTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (18 bp):
CCTTATTAGACGTATCCA
Found at i:140560 original size:16 final size:17
Alignment explanation
Indices: 140539--140572 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
140529 ACTAAACTAT
140539 AAAACCCT-AAAAATAA
1 AAAACCCTCAAAAATAA
140555 AAAACCCTCAAAAATAA
1 AAAACCCTCAAAAATAA
140572 A
1 A
140573 CACTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.21, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAACCCTCAAAAATAA
Found at i:140910 original size:52 final size:52
Alignment explanation
Indices: 140832--140937 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
140822 TGTGCTTAGA
140832 AGCTGGAAGTCTTCTAGCTTCGACTTATGCACTGCCAAATCAAAACTAACTC
1 AGCTGGAAGTCTTCTAGCTTCGACTTATGCACTGCCAAATCAAAACTAACTC
140884 AGCTGGAAGTCTTCTAGCTTCGACTTATGCACTGCCAAATCAAAACTAACTC
1 AGCTGGAAGTCTTCTAGCTTCGACTTATGCACTGCCAAATCAAAACTAACTC
140936 AG
1 AG
140938 GTTTGATTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (52 bp):
AGCTGGAAGTCTTCTAGCTTCGACTTATGCACTGCCAAATCAAAACTAACTC
Found at i:141488 original size:24 final size:24
Alignment explanation
Indices: 141461--141529 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
141451 AGTTTGACTC
* *
141461 AAACAAATAAATAGTGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
141485 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
141509 AAACAATTAAACAGGGTTTAA
1 AAACAAATAAACAGAGTTTAA
141530 CCGTAAGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:145268 original size:226 final size:226
Alignment explanation
Indices: 144874--145295 Score: 754
Period size: 226 Copynumber: 1.9 Consensus size: 226
144864 TATGACTTAT
*
144874 ATATATATATATATTTAAACTTAATGGTTTCTTTTGGATGGATTCTTCACTTTTTCAATTTAACA
1 ATATATATATATATTTAAACTTAATGGTTTCTTTTGGATGGATTCTTCACTTTTTCAATGTAACA
144939 ACTCCTTGCCACTGGAACAAGGTGAATTGCAAATATTGAATATGCTCGTGGTGTTCAAATGATGG
66 ACTCCTTGCCACTGGAACAAGGTGAATTGCAAATATTGAATATGCTCGTGGTGTTCAAATGATGG
*
145004 TTCCTTATCTATTTCTTCTTTGCTGATCTGTCTTTTTGTGCATGCCTAGTTCCATGTGCTTCAAA
131 TTCCTTATCTATTGCTTCTTTGCTGATCTGTCTTTTTGTGCATGCCTAGTTCCATGTGCTTCAAA
145069 TTTTTGCATGACTTACATATATCATATATAC
196 TTTTTGCATGACTTACATATATCATATATAC
*
145100 ATATATATATATGTTTAAACTTAATGGTTTCTTTTGGATGGATTCTTCACTTTTTCAATGTAACA
1 ATATATATATATATTTAAACTTAATGGTTTCTTTTGGATGGATTCTTCACTTTTTCAATGTAACA
* ** *
145165 ACTCCTTGCTACTGGAACAAGGTGAATTGCAAATATTGAATATGCTTTTGGTGTTTAAATGATGG
66 ACTCCTTGCCACTGGAACAAGGTGAATTGCAAATATTGAATATGCTCGTGGTGTTCAAATGATGG
* * *
145230 TTCCTTATCTATTGCTTCTTTGCTGGTCTGTCTTTTTGTGCATGCCTAGTTTCATGTGCTTTAAA
131 TTCCTTATCTATTGCTTCTTTGCTGATCTGTCTTTTTGTGCATGCCTAGTTCCATGTGCTTCAAA
145295 T
196 T
145296 GTTTAAACTC
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
226 186 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (226 bp):
ATATATATATATATTTAAACTTAATGGTTTCTTTTGGATGGATTCTTCACTTTTTCAATGTAACA
ACTCCTTGCCACTGGAACAAGGTGAATTGCAAATATTGAATATGCTCGTGGTGTTCAAATGATGG
TTCCTTATCTATTGCTTCTTTGCTGATCTGTCTTTTTGTGCATGCCTAGTTCCATGTGCTTCAAA
TTTTTGCATGACTTACATATATCATATATAC
Found at i:160584 original size:21 final size:19
Alignment explanation
Indices: 160558--160610 Score: 52
Period size: 23 Copynumber: 2.6 Consensus size: 19
160548 TATTTGTTTG
*
160558 TATAAATTTTTTATAATCGCA
1 TATAAATTTTATATAAT--CA
*
160579 TATAAAATTGTTATATAATTA
1 TAT-AAATT-TTATATAATCA
160600 TATAAATTTTA
1 TATAAATTTTA
160611 AAATGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.18
21 7 0.25
22 5 0.18
23 8 0.29
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (19 bp):
TATAAATTTTATATAATCA
Found at i:167462 original size:15 final size:15
Alignment explanation
Indices: 167442--167480 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
167432 AATCAAAATA
167442 TAATTTTATTTTTAT
1 TAATTTTATTTTTAT
*
167457 TAATTTAAATTTTTAT
1 TAATTT-TATTTTTAT
*
167473 AAATTTTA
1 TAATTTTA
167481 AAGTAACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTTAT
Found at i:167614 original size:18 final size:18
Alignment explanation
Indices: 167574--167619 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
167564 GTAAACAAAT
**
167574 TAAATATATTGTCATATTA
1 TAAATATATT-TCATAAAA
167593 -AAATATATTTCATAAAA
1 TAAATATATTTCATAAAA
167610 TAAAT-TATTT
1 TAAATATATTT
167620 ATTCGATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
TAAATATATTTCATAAAA
Found at i:168211 original size:30 final size:29
Alignment explanation
Indices: 168175--168233 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
168165 AAAAAGTATA
168175 TTTAATACAATAAAACATTTATTAATATTT
1 TTTAATACAATAAAACATTTATT-ATATTT
*
168205 TTTAATATAATAAAACATTTATTATATTT
1 TTTAATACAATAAAACATTTATTATATTT
168234 ATGGTAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAATACAATAAAACATTTATTATATTT
Found at i:168354 original size:13 final size:13
Alignment explanation
Indices: 168336--168360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168326 ATTTTTTTAA
168336 CTAAAAAATCAAT
1 CTAAAAAATCAAT
168349 CTAAAAAATCAA
1 CTAAAAAATCAA
168361 ATATGAATAG
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
CTAAAAAATCAAT
Found at i:168719 original size:22 final size:21
Alignment explanation
Indices: 168669--168719 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
168659 TCATTAATTT
168669 TTAATT-TTAATTATCAAATA
1 TTAATTATTAATTATCAAATA
168689 TT--TTATTAATATATC-AATAA
1 TTAATTATTAAT-TATCAAAT-A
168709 TTAATTATTAA
1 TTAATTATTAA
168720 ACTGATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.08
19 8 0.31
20 9 0.35
22 7 0.27
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATTATTAATTATCAAATA
Found at i:169984 original size:18 final size:16
Alignment explanation
Indices: 169965--169995 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
169955 TAATACAAAT
169965 TATTA-AAAAATTAAA
1 TATTATAAAAATTAAA
169980 TATTATAAAAATTAAA
1 TATTATAAAAATTAAA
169996 AAATTTGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTATAAAAATTAAA
Found at i:171648 original size:13 final size:13
Alignment explanation
Indices: 171627--171671 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
171617 CTTTTGATTC
*
171627 TTTTCTTTTCTTT
1 TTTTTTTTTCTTT
171640 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
171653 TTTTTTTTTGCATTT
1 TTTTTTTTT-C-TTT
171668 TTTT
1 TTTT
171672 AAGGTGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 21 0.72
14 1 0.03
15 7 0.24
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:171650 original size:18 final size:17
Alignment explanation
Indices: 171627--171661 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
171617 CTTTTGATTC
171627 TTTTCTTTTCTTTTTTTT
1 TTTTCTTTT-TTTTTTTT
171645 TTTTCTTTTTTTTTTTT
1 TTTTCTTTTTTTTTTTT
171662 GCATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTCTTTTTTTTTTTT
Found at i:172249 original size:48 final size:48
Alignment explanation
Indices: 172186--172278 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
172176 TGTTCAATAA
172186 CATGTATTAACTTTGTCCCAAGAACACGTTAAACCTGTCTATGTTTTT
1 CATGTATTAACTTTGTCCCAAGAACACGTTAAACCTGTCTATGTTTTT
*
172234 CATGTTTTAACTTTGTCCCAAGAACACGTTAAACCTGTCTATGTT
1 CATGTATTAACTTTGTCCCAAGAACACGTTAAACCTGTCTATGTT
172279 CTTACTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (48 bp):
CATGTATTAACTTTGTCCCAAGAACACGTTAAACCTGTCTATGTTTTT
Found at i:183233 original size:30 final size:31
Alignment explanation
Indices: 183186--183243 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
183176 CCAATATTTT
*
183186 TTTTACCAACTTTTTAAGGGACCTGAAAAAAA
1 TTTTACCAACTTTTTAAGGAACCT-AAAAAAA
183218 TTTT-CCAAC-TTTTAAGGAACCTAAAA
1 TTTTACCAACTTTTTAAGGAACCTAAAA
183244 TCTCATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 12 0.48
31 5 0.20
32 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (31 bp):
TTTTACCAACTTTTTAAGGAACCTAAAAAAA
Found at i:187741 original size:43 final size:44
Alignment explanation
Indices: 187693--187777 Score: 127
Period size: 43 Copynumber: 1.9 Consensus size: 44
187683 AGAGCCGATT
* *
187693 TTTGGATAGTGAAAAAATG-CGTATGTTTAAGGTTCCAAATGTA
1 TTTGGATAGTGAAAAAATGACATATATTTAAGGTTCCAAATGTA
*
187736 TTTGGATAGTGAAAAAATGTATATATATTTAAGGTTCCAAAT
1 TTTGGATAGTGAAAAAATG-ACATATATTTAAGGTTCCAAAT
187778 ATAGCATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 19 0.51
45 18 0.49
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (44 bp):
TTTGGATAGTGAAAAAATGACATATATTTAAGGTTCCAAATGTA
Done.