Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009896.1 Kokia drynarioides strain JFW-HI SEQ_124634, 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: 139409
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1376 original size:11 final size:11
Alignment explanation
Indices: 1360--1389 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1350 ATATATTTTT
1360 TAAAAATTATA
1 TAAAAATTATA
*
1371 TAAAAATAATA
1 TAAAAATTATA
1382 TAAAAATT
1 TAAAAATT
1390 TTAATACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:2042 original size:31 final size:31
Alignment explanation
Indices: 1972--2042 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
1962 TGAATTACTT
*
1972 ATTGATTTTTTAATTATTTTACGAGATCTTA
1 ATTGATTTTTTAATTATTTTACGAGATCGTA
*
2003 ATT-ATTTTTTAATTATTTTACGTGGA-CGTA
1 ATTGATTTTTTAATTATTTTACG-AGATCGTA
*
2033 ATTGCTTTTT
1 ATTGATTTTT
2043 AGAAATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.56
Consensus pattern (31 bp):
ATTGATTTTTTAATTATTTTACGAGATCGTA
Found at i:6884 original size:15 final size:15
Alignment explanation
Indices: 6864--6893 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6854 CAACGACACT
6864 TTCTCCAAATAGAAA
1 TTCTCCAAATAGAAA
6879 TTCTCCAAATAGAAA
1 TTCTCCAAATAGAAA
6894 AGCATATCCT
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:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
TTCTCCAAATAGAAA
Found at i:10266 original size:18 final size:18
Alignment explanation
Indices: 10243--10279 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10233 TTTGTGATCA
10243 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
10261 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
10279 A
1 A
10280 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:19047 original size:26 final size:26
Alignment explanation
Indices: 19018--19084 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
19008 ACCTTAAAAA
19018 CTTTGCATGTGATTAGG-TGAT-TTATT
1 CTTT-CATGTGATT-GGTTGATCTTATT
19044 CTTTACATGTGATTGGTTTGATCTTATT
1 CTTT-CATGTGATTGG-TTGATCTTATT
*
19072 CTTTCATATGATT
1 CTTTCATGTGATT
19085 CATACCAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 13 0.36
27 12 0.33
28 9 0.25
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.52
Consensus pattern (26 bp):
CTTTCATGTGATTGGTTGATCTTATT
Found at i:21946 original size:29 final size:27
Alignment explanation
Indices: 21914--22021 Score: 76
Period size: 28 Copynumber: 3.8 Consensus size: 27
21904 TTTTGCAAGT
21914 TTCGGGATCAAAAATGGAATTTTGGGAAG
1 TTCGGG-TC-AAAATGGAATTTTGGGAAG
* *
21943 TTCGAGGT-TAAATGATAATTTTTGGTGAA-
1 TTCG-GGTCAAAATG-GAA-TTTTGG-GAAG
*
21972 ATCGGGGTCAAAATGGAATTTTGGGAAG
1 TTC-GGGTCAAAATGGAATTTTGGGAAG
* * *
22000 TTTGGGGTTAAAATGTAATTTT
1 -TTCGGGTCAAAATGGAATTTT
22022 TGGTATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
27 8 0.13
28 24 0.39
29 19 0.31
30 11 0.18
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (27 bp):
TTCGGGTCAAAATGGAATTTTGGGAAG
Found at i:21956 original size:58 final size:57
Alignment explanation
Indices: 21893--22070 Score: 168
Period size: 58 Copynumber: 3.1 Consensus size: 57
21883 ACTCGGGGGC
*
21893 AAAATGATAATTTTTG-CAAGTTTCGGGATCAAAAATGGAATTTTGGGAAGTTCGAGGTT
1 AAAATGATAATTTTTGTCAA--ATCGGGATC-AAAATGGAATTTTGGGAAGTTCGAGGTT
* * * *
21952 -AAATGATAATTTTTGGTGAAATCGGGGTCAAAATGGAATTTTGGGAAGTTTGGGGTT
1 AAAATGATAATTTTT-GTCAAATCGGGATCAAAATGGAATTTTGGGAAGTTCGAGGTT
* * * *
22009 AAAATG-TAATTTTTGGT-ATAATCAAGG-TCAAAAATGGAATTTTGGAAAATTCGAGGGT
1 AAAATGATAATTTTT-GTCA-AATC-GGGATC-AAAATGGAATTTTGGGAAGTTCGAGGTT
22067 AAAA
1 AAAA
22071 ATGTTATTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
56 1 0.01
57 43 0.42
58 55 0.54
59 1 0.01
60 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (57 bp):
AAAATGATAATTTTTGTCAAATCGGGATCAAAATGGAATTTTGGGAAGTTCGAGGTT
Found at i:22070 original size:29 final size:29
Alignment explanation
Indices: 21923--22138 Score: 103
Period size: 29 Copynumber: 7.5 Consensus size: 29
21913 TTTCGGGATC
* *
21923 AAAAATGGAATTTTGGGAAGTTCGA-GGT
1 AAAAATGGAATTTTGGAAAATTCGAGGGT
* * *
21951 -TAAATGATAATTTTTGGTGAAA-TCG-GGGT
1 AAAAATG-GAA-TTTTGG-AAAATTCGAGGGT
* * * *
21980 CAAAATGGAATTTTGGGAAGTTTG-GGGT
1 AAAAATGGAATTTTGGAAAATTCGAGGGT
* * * *
22008 TAAAATGTAATTTTTGGTATAA-TC-AAGGT
1 AAAAATGGAA-TTTTGG-AAAATTCGAGGGT
22037 CAAAAATGGAATTTTGGAAAATTCGAGGGT
1 -AAAAATGGAATTTTGGAAAATTCGAGGGT
* *
22067 AAAAATGTTATTTTTGGAAAAATT--AGGGT
1 AAAAATG-GAATTTTGG-AAAATTCGAGGGT
* *
22096 CAAAAAT-GAATTTTGGAAAGTT-TAGGGGT
1 -AAAAATGGAATTTTGGAAAATTCGA-GGGT
*
22125 AAAAATGTAATTTT
1 AAAAATGGAATTTT
22139 TGAGAAGTTT
Statistics
Matches: 146, Mismatches: 24, Indels: 35
0.71 0.12 0.17
Matches are distributed among these distances:
27 13 0.09
28 39 0.27
29 54 0.37
30 34 0.23
31 6 0.04
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAATTCGAGGGT
Found at i:22107 original size:58 final size:59
Alignment explanation
Indices: 21921--22140 Score: 254
Period size: 58 Copynumber: 3.8 Consensus size: 59
21911 AGTTTCGGGA
* * * *
21921 TCAAAAATGGAATTTTGGGAAGTTCGA-GGT-TAAATGATAATTTTTGGTGAAATCGGGG
1 TCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATG-TAATTTTTGGTAAAATCAGGG
* * * * *
21979 TC-AAAATGGAATTTTGGGAAGTTTG-GGGTTAAAATGTAATTTTTGGTATAATCAAGG
1 TCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGTAAAATCAGGG
* * * *
22036 TCAAAAATGGAATTTTGGAAAATTCGAGGGTAAAAATGTTATTTTTGGAAAAATTAGGG
1 TCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGTAAAATCAGGG
*
22095 TCAAAAAT-GAATTTTGGAAAGTT-TAGGGGTAAAAATGTAATTTTTG
1 TCAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAAATGTAATTTTTG
22141 AGAAGTTTAA
Statistics
Matches: 139, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
57 45 0.32
58 60 0.43
59 34 0.24
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (59 bp):
TCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGTAAAATCAGGG
Found at i:23179 original size:12 final size:12
Alignment explanation
Indices: 23144--23189 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
23134 TTTTTTTTAA
*
23144 TTATTATTAATA
1 TTATTATTAATG
23156 TTATTATTAATG
1 TTATTATTAATG
23168 TTATTATTAATG
1 TTATTATTAATG
* *
23180 ATAGTATTAA
1 TTATTATTAA
23190 GATAACATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (12 bp):
TTATTATTAATG
Found at i:23941 original size:17 final size:18
Alignment explanation
Indices: 23916--23963 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
23906 TAAATAGATT
*
23916 TAAACTTAAATTTATAA-
1 TAAATTTAAATTTATAAG
23933 TAAATTTAAATTT-TAAG
1 TAAATTTAAATTTATAAG
23950 TAAATTTAAATTTA
1 TAAATTTAAATTTA
23964 AATTCTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TAAATTTAAATTTATAAG
Found at i:23942 original size:6 final size:6
Alignment explanation
Indices: 23913--23967 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
23903 ATTTAAATAG
* * *
23913 ATTTAA ACTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
23959 ATTTAA ATT
1 ATTTAA ATT
23968 CTGTTGGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.05
5 5 0.13
6 30 0.77
7 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:26875 original size:2 final size:2
Alignment explanation
Indices: 26870--26895 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26860 GAAAAAAATA
26870 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
26896 GGGTAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32300 original size:24 final size:23
Alignment explanation
Indices: 32272--32316 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
32262 TGTGTTTGAC
*
32272 CTAAATTTATAAAGAGATTAAATT
1 CTAAATTTAGAAAGAG-TTAAATT
32296 CTAAATTTAGAAAGAGTTAAA
1 CTAAATTTAGAAAGAGTTAAA
32317 GTCACGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (23 bp):
CTAAATTTAGAAAGAGTTAAATT
Found at i:32479 original size:19 final size:19
Alignment explanation
Indices: 32455--32493 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32445 AATTTAATCG
32455 TAATTACAAA-TATAAATAA
1 TAATTA-AAACTATAAATAA
*
32474 TAATTAAAACTATAATTAA
1 TAATTAAAACTATAAATAA
32493 T
1 T
32494 TAATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATTAAAACTATAAATAA
Found at i:48105 original size:22 final size:21
Alignment explanation
Indices: 48080--48191 Score: 88
Period size: 20 Copynumber: 5.3 Consensus size: 21
48070 ATTATATTGT
*
48080 TGTTTTGGTGCTGTTTTTTTGC
1 TGTTTTGATG-TGTTTTTTTGC
*
48102 TGTTTT--TGTGTTTTTTTAC
1 TGTTTTGATGTGTTTTTTTGC
* *
48121 TGTTTTGATG-CTTTTTTTAC
1 TGTTTTGATGTGTTTTTTTGC
*
48141 TGTTTTGAT-TGTTATTTTCGTGT
1 TGTTTTGATGTGTT-TTTT--TGC
* *
48164 TGTTTTGCTGTTATTTTTTTGC
1 TGTTTTGATG-TGTTTTTTTGC
48186 TGTTTT
1 TGTTTT
48192 TGTTGTTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
19 16 0.22
20 22 0.30
21 6 0.08
22 14 0.19
23 9 0.12
24 4 0.05
25 3 0.04
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (21 bp):
TGTTTTGATGTGTTTTTTTGC
Found at i:48220 original size:22 final size:21
Alignment explanation
Indices: 48161--48222 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
48151 GTTATTTTCG
* *
48161 TGTTGTTTTGCTGTTATTTTTT
1 TGTTG-TTTGCTGTTGTTTTTA
* *
48183 TGCTGTTT-TTGTTGTTTTTAA
1 TGTTGTTTGCTGTTGTTTTT-A
48204 TGTTGTTTGCTGTTGTTTT
1 TGTTGTTTGCTGTTGTTTT
48223 GGTTATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.28
21 10 0.31
22 13 0.41
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.69
Consensus pattern (21 bp):
TGTTGTTTGCTGTTGTTTTTA
Found at i:48256 original size:21 final size:21
Alignment explanation
Indices: 48214--48255 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
48204 TGTTGTTTGC
*
48214 TGTTGTTTTGGTTATTATTTT
1 TGTTGTTTTGGATATTATTTT
*
48235 TGTTG-TTTGGATGTTATTTT
1 TGTTGTTTTGGATATTATTTT
48255 T
1 T
48256 TATGCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (21 bp):
TGTTGTTTTGGATATTATTTT
Found at i:50014 original size:19 final size:20
Alignment explanation
Indices: 49981--50019 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
49971 TAGTATATAG
*
49981 TAAAATTGTA-CTTTTATCT
1 TAAAATTGAATCTTTTATCT
*
50000 TAAAATTGAATTTTTTATCT
1 TAAAATTGAATCTTTTATCT
50020 AATCTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
TAAAATTGAATCTTTTATCT
Found at i:52517 original size:30 final size:30
Alignment explanation
Indices: 52483--52547 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
52473 TTAATAAAAG
52483 TAAAA-TTGTATTCAGATATTCTAAAAATGA
1 TAAAATTTGTATTCA-ATATTCTAAAAATGA
* * * *
52513 TAAAATTTTTATTTAATATTTTAAAAATTA
1 TAAAATTTGTATTCAATATTCTAAAAATGA
52543 TAAAA
1 TAAAA
52548 ATATAAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
TAAAATTTGTATTCAATATTCTAAAAATGA
Found at i:62782 original size:3 final size:3
Alignment explanation
Indices: 62774--62799 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62764 TTTAGAAGTA
62774 CGG CGG CGG CGG CGG CGG CGG CGG CG
1 CGG CGG CGG CGG CGG CGG CGG CGG CG
62800 AGGGAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.65, T:0.00
Consensus pattern (3 bp):
CGG
Found at i:74913 original size:22 final size:22
Alignment explanation
Indices: 74885--74929 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
74875 AATCCTATAG
74885 GAAAGCTCAGAAACCTTCAAAA
1 GAAAGCTCAGAAACCTTCAAAA
74907 GAAAGCTCAGAAACCTTCAAAA
1 GAAAGCTCAGAAACCTTCAAAA
74929 G
1 G
74930 TTTGTACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (22 bp):
GAAAGCTCAGAAACCTTCAAAA
Found at i:81714 original size:5 final size:5
Alignment explanation
Indices: 81704--81736 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
81694 TCTCAACAAA
*
81704 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAC AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
81737 ACTAAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:81724 original size:14 final size:13
Alignment explanation
Indices: 81701--81731 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
81691 CCCTCTCAAC
81701 AAAAAAATAAAAT
1 AAAAAAATAAAAT
81714 AAAATAAATAAAAT
1 AAAA-AAATAAAAT
81728 AAAA
1 AAAA
81732 CAAAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:88650 original size:17 final size:18
Alignment explanation
Indices: 88613--88665 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
88603 ACATGAAATG
* *
88613 ATAAAAATATCTTTAAAATA
1 ATAAATATAT-TTTATAA-A
*
88633 ATATAATCTATTTTATAAA
1 ATA-AATATATTTTATAAA
88652 ATAAATATATTTTA
1 ATAAATATATTTTA
88666 ATTATTACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 10 0.36
19 4 0.14
20 9 0.32
21 5 0.18
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAATATATTTTATAAA
Found at i:101318 original size:34 final size:34
Alignment explanation
Indices: 101279--101346 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
101269 AGATCCCCAC
101279 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
1 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
101313 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
1 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
101347 CTTATTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (34 bp):
TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
Found at i:103153 original size:15 final size:15
Alignment explanation
Indices: 103133--103222 Score: 144
Period size: 15 Copynumber: 6.0 Consensus size: 15
103123 AGACCACTGG
*
103133 GAACCAAGGAGGTCC
1 GAACCAAGGGGGTCC
103148 GAACCAAGGGGGTCC
1 GAACCAAGGGGGTCC
103163 GAACCAAGGGGGTCC
1 GAACCAAGGGGGTCC
*
103178 AAACCAAGGGGGTCC
1 GAACCAAGGGGGTCC
*
103193 GAACCAAGGGGATCC
1 GAACCAAGGGGGTCC
*
103208 GATCCAAGGGGGTCC
1 GAACCAAGGGGGTCC
103223 AACTCAAAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.37, T:0.08
Consensus pattern (15 bp):
GAACCAAGGGGGTCC
Found at i:103745 original size:9 final size:9
Alignment explanation
Indices: 103731--103755 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
103721 ACAAAGAGCT
103731 GCAGCTTTA
1 GCAGCTTTA
103740 GCAGCTTTA
1 GCAGCTTTA
103749 GCAGCTT
1 GCAGCTT
103756 CATTTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (9 bp):
GCAGCTTTA
Found at i:106409 original size:20 final size:20
Alignment explanation
Indices: 106384--106422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
106374 TAAAAATTTT
106384 ATTTTTTTAAACAATAAATA
1 ATTTTTTTAAACAATAAATA
* *
106404 ATTTTTTTATACATTAAAT
1 ATTTTTTTAAACAATAAAT
106423 TTTAATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTTTAAACAATAAATA
Found at i:111417 original size:42 final size:42
Alignment explanation
Indices: 111358--111443 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
111348 CAACTTTCGT
111358 AAAATGCAGGGACTAATAATAGATTTTAACCAATGTAAATGA
1 AAAATGCAGGGACTAATAATAGATTTTAACCAATGTAAATGA
111400 AAAATGCAGGGACTAATAATAGATTTTAACCAATGTAAATGA
1 AAAATGCAGGGACTAATAATAGATTTTAACCAATGTAAATGA
111442 AA
1 AA
111444 TAAACAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAATGCAGGGACTAATAATAGATTTTAACCAATGTAAATGA
Found at i:112132 original size:101 final size:101
Alignment explanation
Indices: 111949--112149 Score: 294
Period size: 101 Copynumber: 2.0 Consensus size: 101
111939 TTTATAATTC
* * * **
111949 GTGAGTAATTATAAATATGGATGACAATAGAGTAAGGCGAAACGAATGTTGCTAAATCCACCATT
1 GTGAGTAATCATAAATATGGATGACAATAGAGTAAAGCGAAACGAATGTTACTAAATCCACCACC
* *
112014 ACTCCATAGTTGGCACGCTCTGCTTCACAATCTACT
66 ACTCCATAATTGACACGCTCTGCTTCACAATCTACT
* ** **
112050 GTGAGTAATCATAAATATGGATGGCAATAGAGTAAAGCGGGACGAATGTTACTAAATTTACCACC
1 GTGAGTAATCATAAATATGGATGACAATAGAGTAAAGCGAAACGAATGTTACTAAATCCACCACC
112115 ACTCCATAATTGACACGCTCTGCTTCACAATCTAC
66 ACTCCATAATTGACACGCTCTGCTTCACAATCTAC
112150 CTCACCCCTA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 88 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (101 bp):
GTGAGTAATCATAAATATGGATGACAATAGAGTAAAGCGAAACGAATGTTACTAAATCCACCACC
ACTCCATAATTGACACGCTCTGCTTCACAATCTACT
Found at i:113105 original size:21 final size:21
Alignment explanation
Indices: 113072--113111 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
113062 AAAGAGTTAA
* * *
113072 CATTTATTGTTTAGAAAATAT
1 CATTTACTATTTAAAAAATAT
113093 CATTTACTATTTAAAAAAT
1 CATTTACTATTTAAAAAAT
113112 TTAACATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (21 bp):
CATTTACTATTTAAAAAATAT
Found at i:115528 original size:14 final size:14
Alignment explanation
Indices: 115497--115535 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
115487 TTCGTTAGCG
115497 GGTATG-TT-TTTT
1 GGTATGTTTATTTT
*
115509 GATATGTTTATTTT
1 GGTATGTTTATTTT
115523 GGTATGTTTATTT
1 GGTATGTTTATTT
115536 ATTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 16 0.70
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (14 bp):
GGTATGTTTATTTT
Found at i:127581 original size:2 final size:2
Alignment explanation
Indices: 127574--127603 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
127564 TACATGCTAG
*
127574 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127604 GTATGTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127608 original size:10 final size:10
Alignment explanation
Indices: 127574--127612 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
127564 TACATGCTAG
*
127574 ATATATATAT
1 ATATGTATAT
*
127584 ATATATATAT
1 ATATGTATAT
127594 ATATGTATAT
1 ATATGTATAT
*
127604 GTATGTATA
1 ATATGTATA
127613 CTAAAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (10 bp):
ATATGTATAT
Found at i:131006 original size:13 final size:13
Alignment explanation
Indices: 130990--131015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
130980 ATACTTTTAC
130990 AATTAAAATATAA
1 AATTAAAATATAA
131003 AATTAAAATATAA
1 AATTAAAATATAA
131016 TAAAAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAATATAA
Found at i:131271 original size:21 final size:22
Alignment explanation
Indices: 131240--131289 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
131230 TTGATATCTG
*
131240 TAAATATATTTATATAAATATA-T
1 TAAATAT-TTTA-AAAAATATAGT
131263 TAAATATTTTAAAAAATATAGT
1 TAAATATTTTAAAAAATATAGT
131285 TAAAT
1 TAAAT
131290 TCGAAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 10 0.40
23 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAATATTTTAAAAAATATAGT
Found at i:135081 original size:39 final size:39
Alignment explanation
Indices: 135034--135249 Score: 140
Period size: 39 Copynumber: 5.6 Consensus size: 39
135024 CTATAATCTA
*
135034 CCCCAGGCTCGAGGTAAGAGATTAGCTGATGGTGATTTG
1 CCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATTTG
* * * *
135073 CCCTAGGCTCG-GAGTAAAAGA-T--CGGATGGCTACAATTTG
1 CCCCAGGCTCGAG-GTAAGAGATTGGCTGATGG-T--GATTTG
* * * *
135112 TCCCAGGCTC-AGGGTAAGAGATTGGTTGATGGTGATCTA
1 CCCCAGGCTCGA-GGTAAGAGATTGGCTGATGGTGATTTG
* * * ** ** *
135151 CCCCAAGCTCGGGGTAAGAGATCGAATG-TTATAATTTG
1 CCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATTTG
* * *
135189 CCCTAGGCTC-AGGGTAAGAGATTGGTTGATGGTGATCTG
1 CCCCAGGCTCGA-GGTAAGAGATTGGCTGATGGTGATTTG
*
135228 CCCCAAGCTCGAGGTAAGAGAT
1 CCCCAGGCTCGAGGTAAGAGAT
135250 CGAATGTTAC
Statistics
Matches: 129, Mismatches: 35, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
36 6 0.05
37 1 0.01
38 28 0.22
39 85 0.66
40 3 0.02
41 1 0.01
42 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
CCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATTTG
Found at i:135212 original size:77 final size:78
Alignment explanation
Indices: 134949--135290 Score: 413
Period size: 78 Copynumber: 4.4 Consensus size: 78
134939 TGGATAATTG
* * *
134949 CAATCTACCCCAGGCTCGGGGT-AGAAGATTGGTTGATGGTGATCTGCCCCAAGTTCGGGGTAAA
1 CAATCTGCCCCAGGCTCAGGGTAAG-AGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAA
*
135013 AGATCGGATGGCTA
65 AGATCGAATGGCTA
* * * * * * * *
135027 TAATCTACCCCAGGCTC-GAGGTAAGAGATTAGCTGATGGTGATTTGCCCTAGGCTCGGAGTAAA
1 CAATCTGCCCCAGGCTCAG-GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAA
*
135091 AGATCGGATGGCTA
65 AGATCGAATGGCTA
* * * *
135105 CAATTTGTCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTACCCCAAGCTCGGGGTAAGA
1 CAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAA
*
135170 GATCGAAT-GTTA
66 GATCGAATGGCTA
* * * * *
135182 TAATTTGCCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAGA
1 CAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAA
*
135247 GATCGAAT-GTTA
66 GATCGAATGGCTA
*
135259 CAATCTGCCCCAGGCTCATGGTAAGAGATTGG
1 CAATCTGCCCCAGGCTCAGGGTAAGAGATTGG
135291 CTTATGTAAC
Statistics
Matches: 230, Mismatches: 31, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
77 104 0.45
78 123 0.53
79 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
CAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAA
GATCGAATGGCTA
Found at i:135709 original size:49 final size:47
Alignment explanation
Indices: 135655--136471 Score: 419
Period size: 49 Copynumber: 16.7 Consensus size: 47
135645 CACAGTACTG
*
135655 GATTCGCCATTGCAGCTTAAATCTTTCCCTTCATGCTGTTGAGGTACAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCT-TTGAGGTACAA
* * * * * * * * **
135704 AATTCGTCGTTGCAACTTAAACCTTTCCCTCCATATCTTCGTGGTACTG
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCAT-GCTTTGAGGTACAA
* *
135753 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCTT-TGAGGTACAA
* * * * * * * * **
135802 GGTTTGTCGTTACGACTTAAACCTTTCCTTTTAAAT-CTTCT-TGGTACTG
1 GATTCGCCGTTGCG-CTTAAATCTTTCC-CTT-CATGCTT-TGAGGTACAA
* * *
135851 GATTCGCCATTGCAGCTTCAATCTTTCCCTTCCTGCTTCTGAGGTACAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCTT-TGAGGTACAA
* * * * * * * * *
135900 GGTTCGTCGTTACGACTTAAACCTTTCCTTTCAT-ATCTCGTGGTACAG
1 GATTCGCCGTTGCG-CTTAAATCTTTCCCTTCATGCT-TTGAGGTACAA
* *
135948 GATTCGTCGTTATG-GCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAA
1 GATTCGCCG-T-TGCGCTTAAATCTTTCCCTTCATGC-TTTGAGGTACAA
* * * * * * *
135997 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTAAAT-CTTCGTGGTACTA
1 GATTCGCCGTTGCG-CTTAAATCTTTCCC-TT-CATGCTTTGAGGTACAA
* *
136046 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCTT-TGAGGTACAA
* * * * * * * **
136095 GGTTCGTCATTGCGACTTAAACCTTTCCCTCCAT-ATCTTCATGGTACTG
1 GATTCGCCGTTGCG-CTTAAATCTTTCCCTTCATGCT-TTGA-GGTACAA
136144 GATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCTT-TGAGGTACAA
* * * * * * * **
136193 GGTTCGTCATTGCAACTTAAACCTTTCCCTTTAAAT-CTTTGTGGTACTG
1 GATTCGCCGTTGC-GCTTAAATCTTTCCC-TT-CATGCTTTGAGGTACAA
* * *
136242 GATTTGTCGTTGCAGCTTAAATATTTCCCTTCATGCTTCTGAGGTACAA
1 GATTCGCCGTTGC-GCTTAAATCTTTCCCTTCATGCTT-TGAGGTACAA
* * * * * * *
136291 GGTTCGCCGTTTCGACTTAAACCTTTCCCTTCATGTCCTCGTGGTACTA
1 GATTCGCCGTTGCG-CTTAAATCTTTCCCTTCATG-CTTTGAGGTACAA
* * *
136340 GATTCGCCGTTGTGGCTTAAATCTTTCCCTTCATGCTCCTGAGGTGCAA
1 GATTCGCCGTTG-CGCTTAAATCTTTCCCTTCATGCT-TTGAGGTACAA
* * * * * * * *
136389 GGTTCACCATTGCGACTTAAA-CATTTCCCTCCATATCTTCGTGGTAC-T
1 GATTCGCCGTTGCG-CTTAAATC-TTTCCCTTCAT-GCTTTGAGGTACAA
**
136437 GAATTCGTTGTTGCGGCTTAAATCTTTCCCTTCAT
1 G-ATTCGCCGTTGC-GCTTAAATCTTTCCCTTCAT
136472 ATCTTTGCGG
Statistics
Matches: 570, Mismatches: 157, Indels: 82
0.70 0.19 0.10
Matches are distributed among these distances:
47 7 0.01
48 65 0.11
49 460 0.81
50 32 0.06
51 6 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (47 bp):
GATTCGCCGTTGCGCTTAAATCTTTCCCTTCATGCTTTGAGGTACAA
Found at i:135729 original size:98 final size:97
Alignment explanation
Indices: 135572--136471 Score: 1077
Period size: 98 Copynumber: 9.2 Consensus size: 97
135562 CGCCATTGTA
* * * * * * *
135572 GCTTAAAT-TTTTCTTTCATGCTTCTTAGGTATAAAGTTCGCCATTGCGACTTAAACCTTTCCCC
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTT-CCC
* * *** * *
135636 TTGTGTCTTCACAGTACTGGATTCGCCATTGCA
65 TTATATCTTCGTGGTACTGGATTCGCCGTTGCG
** *
135669 GCTTAAATCTTTCCCTTCATGCTGT-TGAGGTACAAAATTCGTCGTTGCAACTTAAACCTTTCCC
1 GCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCC
* *
135733 TCCATATCTTCGTGGTACTGGATTCGCCGTTACG
65 T-TATATCTTCGTGGTACTGGATTCGCCGTTGCG
* * * *
135767 GCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTTGTCGTTACGACTTAAACCTTTCCTT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCC-C
* * * *
135832 TTAAATCTTCTTGGTACTGGATTCGCCATTGCA
65 TTATATCTTCGTGGTACTGGATTCGCCGTTGCG
* * * *
135865 GCTTCAATCTTTCCCTTCCTGCTTCTGAGGTACAAGGTTCGTCGTTACGACTTAAACCTTTCCTT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
* * **
135930 TCATATC-TCGTGGTACAGGATTCGTCGTTATG
66 T-ATATCTTCGTGGTACTGGATTCGCCGTTGCG
* *
135962 GCTTAAATCTTTCCCTTTATGCTTTTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCC-
* * *
136027 TTAAATCTTCGTGGTACTAGATTCGCCATTGCG
65 TTATATCTTCGTGGTACTGGATTCGCCGTTGCG
* *
136060 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
* *
136125 CCATATCTTCATGGTACTGGATTCGCCGTTGCG
66 -TATATCTTCGTGGTACTGGATTCGCCGTTGCG
* *
136158 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCAACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCC-
* * * * *
136223 TTAAATCTTTGTGGTACTGGATTTGTCGTTGCA
65 TTATATCTTCGTGGTACTGGATTCGCCGTTGCG
* * *
136256 GCTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTTCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
* * * *
136321 TCATGTCCTCGTGGTACTAGATTCGCCGTTGTG
66 T-ATATCTTCGTGGTACTGGATTCGCCGTTGCG
* * ** * *
136354 GCTTAAATCTTTCCCTTCATGCTCCTGAGGTGCAAGGTTCACCATTGCGACTTAAACATTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
* * **
136419 CCATATCTTCGTGGTACTGAATTCGTTGTTGCG
66 -TATATCTTCGTGGTACTGGATTCGCCGTTGCG
136452 GCTTAAATCTTTCCCTTCAT
1 GCTTAAATCTTTCCCTTCAT
136472 ATCTTTGCGG
Statistics
Matches: 689, Mismatches: 102, Indels: 23
0.85 0.13 0.03
Matches are distributed among these distances:
97 99 0.14
98 587 0.85
99 3 0.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (97 bp):
GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
TATATCTTCGTGGTACTGGATTCGCCGTTGCG
Found at i:137454 original size:22 final size:23
Alignment explanation
Indices: 137429--137474 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
137419 TTCTTCTTCT
*
137429 TCTTCTTCTTTTTT-TTTATTTC
1 TCTTCTTATTTTTTATTTATTTC
* *
137451 TCTTTTTATTTTTTATTTTTTTC
1 TCTTCTTATTTTTTATTTATTTC
137474 T
1 T
137475 TCATTGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (23 bp):
TCTTCTTATTTTTTATTTATTTC
Found at i:138324 original size:19 final size:18
Alignment explanation
Indices: 138300--138343 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
138290 TTCATCTTGA
138300 CTTTTTCTTTCCTTTCTTT
1 CTTTTTCTTT-CTTTCTTT
* *
138319 CTTTTTTCTTTTTTTTTTT
1 C-TTTTTCTTTCTTTCTTT
138338 CTTTTT
1 CTTTTT
138344 TTTTAAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
CTTTTTCTTTCTTTCTTT
Found at i:138334 original size:11 final size:11
Alignment explanation
Indices: 138312--138347 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
138302 TTTTCTTTCC
*
138312 TTTCTTTCTTT
1 TTTCTTTTTTT
138323 TTTCTTTTTTTT
1 TTTC-TTTTTTT
138335 TTTCTTTTTTT
1 TTTCTTTTTTT
138346 TT
1 TT
138348 AAATGCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:138337 original size:12 final size:12
Alignment explanation
Indices: 138320--138347 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
138310 CCTTTCTTTC
138320 TTTTTTCTTTTT
1 TTTTTTCTTTTT
138332 TTTTTTCTTTTT
1 TTTTTTCTTTTT
138344 TTTT
1 TTTT
138348 AAATGCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:138345 original size:20 final size:20
Alignment explanation
Indices: 138301--138344 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
138291 TCATCTTGAC
138301 TTTTTCTTTCCTTTCTTTCT
1 TTTTTCTTTCCTTTCTTTCT
* *
138321 TTTTTCTTT-TTTTTTTTCT
1 TTTTTCTTTCCTTTCTTTCT
138340 TTTTT
1 TTTTT
138345 TTTAAATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTCCTTTCTTTCT
Done.