Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015318.1 Kokia drynarioides strain JFW-HI SEQ_130363, 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: 231499
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 203 characters in sequence are not A, C, G, or T
Found at i:3411 original size:24 final size:24
Alignment explanation
Indices: 3349--3399 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3339 AAAAATAATC
* * *
3349 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
3373 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
3397 TTT
1 TTT
3400 GATTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:23777 original size:11 final size:12
Alignment explanation
Indices: 23756--23785 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23746 TCTTATGCAT
23756 AAAGCAAAAAAA
1 AAAGCAAAAAAA
*
23768 AAAGAAAAAAAA
1 AAAGCAAAAAAA
23780 AAAGCA
1 AAAGCA
23786 CCCAAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAGCAAAAAAA
Found at i:24709 original size:22 final size:20
Alignment explanation
Indices: 24684--24737 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
24674 TCCTCATAAA
*
24684 TTTAAAATTCAATATTTATATT
1 TTTAAAATTCAAT-TTT-TAAT
*
24706 TTTAAAAATTTAATTTTTAAT
1 TTT-AAAATTCAATTTTTAAT
*
24727 TTTCAAATTCA
1 TTTAAAATTCA
24738 TATCTAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 6 0.22
21 6 0.22
22 6 0.22
23 9 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAAATTCAATTTTTAAT
Found at i:24724 original size:23 final size:22
Alignment explanation
Indices: 24687--24729 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
24677 TCATAAATTT
24687 AAAATTCAATATTTATATTTTTA
1 AAAATTCAATATTTA-ATTTTTA
* *
24710 AAAATTTAATTTTTAATTTT
1 AAAATTCAATATTTAATTTT
24730 CAAATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAAATTCAATATTTAATTTTTA
Found at i:29835 original size:16 final size:17
Alignment explanation
Indices: 29809--29850 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
29799 ATCGATATTG
*
29809 TAATATAAATATCTCAA
1 TAATATAAATACCTCAA
*
29826 -AATATCAATACCTCAA
1 TAATATAAATACCTCAA
29842 TAATA-AAAT
1 TAATATAAAT
29851 CTAGTAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATATAAATACCTCAA
Found at i:42655 original size:20 final size:18
Alignment explanation
Indices: 42631--42679 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
42621 TATCTAATTT
42631 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
42649 GTAATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
42669 T-TTAATTTAAT
1 TATTAATTTAAT
42680 GTTTATCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 4 0.15
20 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:62582 original size:12 final size:12
Alignment explanation
Indices: 62544--62587 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
62534 ATAAAGAGAC
62544 AGAAAGCAAATG
1 AGAAAGCAAATG
*
62556 ACAAAG-AGAATG
1 AGAAAGCA-AATG
*
62568 AGAAAGCAAAAG
1 AGAAAGCAAATG
62580 AGAAAGCA
1 AGAAAGCA
62588 TATTTTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.61, C:0.09, G:0.25, T:0.05
Consensus pattern (12 bp):
AGAAAGCAAATG
Found at i:69708 original size:4 final size:4
Alignment explanation
Indices: 69699--69725 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
69689 ATCTAACTTA
69699 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
69726 ATATTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:71920 original size:59 final size:59
Alignment explanation
Indices: 71827--71950 Score: 185
Period size: 59 Copynumber: 2.1 Consensus size: 59
71817 AATAAATATT
* *
71827 CAAAATAAATGTTTACCACTTTCAAATTAATTAAATATAAATTTATATTTTTTAATGTA
1 CAAAATAAATGTTTACCACTTTCAAATTAATTAAACATAAATTTATATTTCTTAATGTA
* * * * *
71886 TAAAATAAATGTTTATCATTTTCAACTTAGTTAAACATAAATTTATATTTCTTAATGTA
1 CAAAATAAATGTTTACCACTTTCAAATTAATTAAACATAAATTTATATTTCTTAATGTA
71945 CAAAAT
1 CAAAAT
71951 TAACAATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (59 bp):
CAAAATAAATGTTTACCACTTTCAAATTAATTAAACATAAATTTATATTTCTTAATGTA
Found at i:73220 original size:22 final size:21
Alignment explanation
Indices: 73168--73220 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
73158 TTCTCATTCT
73168 TTTTATAAAATATATTATATTA
1 TTTTA-AAAATATATTATATTA
*** *
73190 TTACGAAAATATTTTTATATTA
1 TTTTAAAAATA-TATTATATTA
73212 TTTTAAAAA
1 TTTTAAAAA
73221 ATTAACAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTAAAAATATATTATATTA
Found at i:75407 original size:17 final size:19
Alignment explanation
Indices: 75368--75413 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
75358 TTCAAACACG
75368 TTTACATTTATTTAAATTAT
1 TTTA-ATTTATTTAAATTAT
*
75388 TTTTATTT-TTTAAA-TAT
1 TTTAATTTATTTAAATTAT
75405 TTTAATTTA
1 TTTAATTTA
75414 CTATTTAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 4 0.17
20 3 0.13
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTATTTAAATTAT
Found at i:75530 original size:5 final size:5
Alignment explanation
Indices: 75511--75567 Score: 50
Period size: 5 Copynumber: 12.2 Consensus size: 5
75501 TTTAATTTTT
* * *
75511 ATATG ATATA A-ATA ATATA ATATA ATAT- ATA-A AAATA ATAAA ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
75557 ATATA TTATA A
1 ATATA ATATA A
75568 ATTGAAAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 13 0.31
5 29 0.69
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:75569 original size:23 final size:23
Alignment explanation
Indices: 75511--75569 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
75501 TTTAATTTTT
*
75511 ATATGATATAAATAATATAATATA
1 ATAT-ATATAAATAATAAAATATA
*
75535 ATATATAAAAATAATAAAATA-A
1 ATATATATAAATAATAAAATATA
75557 ATATATTATAAAT
1 ATATA-TATAAAT
75570 TGAAAACCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.19
23 21 0.68
24 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATATATAAATAATAAAATATA
Found at i:75996 original size:8 final size:8
Alignment explanation
Indices: 75985--76011 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
75975 AAAAAGATTG
75985 AATTTTAA
1 AATTTTAA
75993 AATTTTAA
1 AATTTTAA
76001 AATTTTAA
1 AATTTTAA
76009 AAT
1 AAT
76012 ATAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:76018 original size:16 final size:16
Alignment explanation
Indices: 75985--76020 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
75975 AAAAAGATTG
* *
75985 AATTTTAAAATTTTAA
1 AATTTTAAAATATAAA
76001 AATTTTAAAATATAAA
1 AATTTTAAAATATAAA
76017 AATT
1 AATT
76021 AAGTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTAAAATATAAA
Found at i:76961 original size:4 final size:4
Alignment explanation
Indices: 76952--77017 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
76942 AAATAAACGG
* * *
76952 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
77002 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
77018 GTAATGTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.79
5 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:76974 original size:17 final size:16
Alignment explanation
Indices: 76952--77017 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
76942 AAATAAACGG
76952 GAAAGAAAGAAAGGAAA
1 GAAAG-AAGAAAGGAAA
76969 GAAAGAAAGAAAGG-AA
1 GAAAG-AAGAAAGGAAA
*
76985 G-AAG--GAGAGGAAA
1 GAAAGAAGAAAGGAAA
76998 GAAAGAAG-AAGGAAA
1 GAAAGAAGAAAGGAAA
77013 GAAAG
1 GAAAG
77018 GTAATGTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
12 5 0.12
13 3 0.07
14 3 0.07
15 14 0.33
16 4 0.09
17 14 0.33
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAAGAAGAAAGGAAA
Found at i:77018 original size:29 final size:31
Alignment explanation
Indices: 76951--77018 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
76941 CAAATAAACG
76951 GGAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
*
76981 GG-AAG-AAGGAGAGGAAAGAAAG-AAG-AA
1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
77008 GGAAAGAAAGG
1 GGAAAGAAAGG
77019 TAATGTGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 4 0.12
28 8 0.24
29 20 0.59
30 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (31 bp):
GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Found at i:84837 original size:29 final size:29
Alignment explanation
Indices: 84816--85136 Score: 278
Period size: 29 Copynumber: 11.0 Consensus size: 29
84806 TTTTGGATAC
*
84816 TCGGGGGTAAAAATGGAA-TTTTGGAAGT
1 TCGGGGGTAAAAATGTAATTTTTGGAAGT
84844 TCGGGGGTAAAAATGTAATTTTTGGAAGT
1 TCGGGGGTAAAAATGTAATTTTTGGAAGT
** *
84873 TTTGGGGTCAAAATGTAA-TTTTGGAAGT
1 TCGGGGGTAAAAATGTAATTTTTGGAAGT
84901 TCGGGGGTAAAAATGTAATTTTTGGAAGTT
1 TCGGGGGTAAAAATGTAATTTTTGGAAG-T
* * * * *
84931 TTGAGGTTGAAAATAG-AATTTTTGAAAGT
1 TCGGGGGTAAAAAT-GTAATTTTTGGAAGT
*
84960 TCGAGGGT-AAAATGTAATTTTTGGAAGT
1 TCGGGGGTAAAAATGTAATTTTTGGAAGT
**
84988 TTTGGGGTCAAAAATG-AATTTTTGGAAGT
1 TCGGGGGT-AAAAATGTAATTTTTGGAAGT
*
85017 TCGAGGGT-AAAATGGTAATTTTTGGAAGTT
1 TCGGGGGTAAAAAT-GTAATTTTTGGAAG-T
*** * ***
85047 TTATGGTTAAAAATGTAATCTTCAAGAAGT
1 TCGGGGGTAAAAATGTAAT-TTTTGGAAGT
** *
85077 TTAGGGGTAAAAATGTAATTTTTAGAAAGT
1 TCGGGGGTAAAAATGTAATTTTT-GGAAGT
** * *
85107 T-AAGGGTCAAAATATAATTTTTGGATAGT
1 TCGGGGGTAAAAATGTAATTTTTGGA-AGT
85136 T
1 T
85137 TAAGGACCTC
Statistics
Matches: 241, Mismatches: 38, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
27 6 0.02
28 67 0.28
29 95 0.39
30 61 0.25
31 12 0.05
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
TCGGGGGTAAAAATGTAATTTTTGGAAGT
Found at i:84886 original size:57 final size:57
Alignment explanation
Indices: 84819--85099 Score: 334
Period size: 57 Copynumber: 4.8 Consensus size: 57
84809 TGGATACTCG
84819 GGGGTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
* *
84876 GGGGTCAAAATGTAATTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
* * * * *
84933 GAGGTTGAAAATAGAATTTTTGAAAGTTCGAGGGT-AAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAA-TTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
*
84991 GGGGTCAAAAAT-GAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGT-AAAAATGGAA-TTTTGGAAGTTCGGGGGTAAAAAT-GTAATTTTTGGAAGTTTT
* * * ** **
85049 ATGGTTAAAAATGTAATCTTCAAGAAGTTTAGGGGTAAAAATGTAATTTTT
1 -GGGGTAAAAATGGAAT-TT-TGGAAGTTCGGGGGTAAAAATGTAATTTTT
85100 AGAAAGTTAA
Statistics
Matches: 196, Mismatches: 19, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
57 85 0.43
58 64 0.33
59 23 0.12
60 19 0.10
61 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (57 bp):
GGGGTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
Found at i:90076 original size:15 final size:17
Alignment explanation
Indices: 90046--90079 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
90036 GTATTATTAT
90046 ATATTTATTTATATTTA
1 ATATTTATTTATATTTA
90063 ATATTT-TTTA-ATTTA
1 ATATTTATTTATATTTA
90078 AT
1 AT
90080 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTTATTTATATTTA
Found at i:90093 original size:20 final size:20
Alignment explanation
Indices: 90047--90102 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
90037 TATTATTATA
*
90047 TATTTATTTATATTTAATATT
1 TATTAATTTA-ATTTAATATT
*
90068 TTTTAATTTAATTTAAT-TT
1 TATTAATTTAATTTAATATT
*
90087 TAATTAAATT-ATTTAA
1 T-ATTAATTTAATTTAA
90103 AATGATTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTAATTTAATTTAATATT
Found at i:90329 original size:27 final size:29
Alignment explanation
Indices: 90299--90357 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
90289 GAGTTTAAAA
*
90299 TTTAAAGTTC-AGAGTTTAAAGTT-CATG
1 TTTAAAGTTCAAAAGTTTAAAGTTACATG
* *
90326 TTTAAGGTTCAAAAGTTTAAGGTTACATG
1 TTTAAAGTTCAAAAGTTTAAAGTTACATG
90355 TTT
1 TTT
90358 TGGTTCAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 9 0.33
28 11 0.41
29 7 0.26
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (29 bp):
TTTAAAGTTCAAAAGTTTAAAGTTACATG
Found at i:90330 original size:13 final size:14
Alignment explanation
Indices: 90299--90336 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
90289 GAGTTTAAAA
90299 TTTAAAGTTCAGAG
1 TTTAAAGTTCAGAG
*
90313 TTTAAAGTTCA-TG
1 TTTAAAGTTCAGAG
*
90326 TTTAAGGTTCA
1 TTTAAAGTTCA
90337 AAAGTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (14 bp):
TTTAAAGTTCAGAG
Found at i:90343 original size:28 final size:28
Alignment explanation
Indices: 90311--90365 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
90301 TAAAGTTCAG
90311 AGTTTAAAGTT-CATGTTTAAGGTTCAAA
1 AGTTTAAAGTTACATGTTT-AGGTTCAAA
* *
90339 AGTTTAAGGTTACATGTTTTGGTTCAA
1 AGTTTAAAGTTACATGTTTAGGTTCAA
90366 GGTTCAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (28 bp):
AGTTTAAAGTTACATGTTTAGGTTCAAA
Found at i:91076 original size:10 final size:10
Alignment explanation
Indices: 91046--91089 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
91036 GTAATCCGGT
91046 AAAAATACTAA
1 AAAAATA-TAA
*
91057 AAAAATTATAT
1 AAAAA-TATAA
*
91068 GAAAATATAA
1 AAAAATATAA
91078 AAAAATATAA
1 AAAAATATAA
91088 AA
1 AA
91090 GGGTGTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 15 0.54
11 11 0.39
12 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAATATAA
Found at i:91374 original size:20 final size:19
Alignment explanation
Indices: 91351--91454 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 19
91341 AAAGAGTACC
*
91351 AAAATATATGAGAGGATATA
1 AAAAAATATGAG-GGATATA
*
91371 AAAAAATATAAGGGAATATA
1 AAAAAATATGAGGG-ATATA
* * *
91391 AAAAAATACGAGAGAGTACAA
1 AAAAAATATGAGGGA-TA-TA
*
91412 AAAAAATATGAGGGATACA
1 AAAAAATATGAGGGATATA
91431 AAAAAATTATGAGGGATATA
1 AAAAAA-TATGAGGGATATA
91451 AAAA
1 AAAA
91455 TATAAGGGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.14
20 46 0.66
21 14 0.20
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (19 bp):
AAAAAATATGAGGGATATA
Found at i:91394 original size:60 final size:60
Alignment explanation
Indices: 91328--91454 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
91318 AAAAGTATTT
* * * *
91328 TAAAAAAATTATGAAAGAGTAC-CAAAATATATGAGAGGATATAAAAAAA-TATAAGGGAATA
1 TAAAAAAA-TACGAAAGAGTACAAAAAAAATATGAG-GGATACAAAAAAATTATAAGGG-ATA
* *
91389 TAAAAAAATACGAGAGAGTACAAAAAAAATATGAGGGATACAAAAAAATTATGAGGGATA
1 TAAAAAAATACGAAAGAGTACAAAAAAAATATGAGGGATACAAAAAAATTATAAGGGATA
91449 TAAAAA
1 TAAAAA
91455 TATAAGGGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 32 0.55
61 26 0.45
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (60 bp):
TAAAAAAATACGAAAGAGTACAAAAAAAATATGAGGGATACAAAAAAATTATAAGGGATA
Found at i:91404 original size:40 final size:40
Alignment explanation
Indices: 91351--91469 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
91341 AAAGAGTACC
*
91351 AAAATATATGAGAGGATATAAAAAAATATAAGGGAATATA
1 AAAAAATATGAGAGGATATAAAAAAATATAAGGGAATATA
* * * *
91391 AAAAAATACGAGA-GAGTACAAAAAAAATATGAGGG-ATACA
1 AAAAAATATGAGAGGA-TA-TAAAAAAATATAAGGGAATATA
91431 AAAAAATTATGAG-GGATAT--AAAAATATAAGGGAATATA
1 AAAAAA-TATGAGAGGATATAAAAAAATATAAGGGAATATA
91469 A
1 A
91470 GTGTGTACAG
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
37 12 0.18
38 5 0.08
39 2 0.03
40 25 0.38
41 21 0.32
ACGTcount: A:0.60, C:0.03, G:0.18, T:0.19
Consensus pattern (40 bp):
AAAAAATATGAGAGGATATAAAAAAATATAAGGGAATATA
Found at i:91415 original size:41 final size:38
Alignment explanation
Indices: 91370--91469 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 38
91360 GAGAGGATAT
91370 AAAAAAATATAAGGGAATATAAAAAAA-TACGAGAGAGTACA
1 AAAAAAATATAAGGGAATATAAAAAAATTACGAG-G-G-A-A
* * * *
91411 AAAAAAATATGAGGG-ATACAAAAAAATTATGAGGGAT
1 AAAAAAATATAAGGGAATATAAAAAAATTACGAGGGAA
*
91448 ATAAAAATATAAGGGAATATAA
1 AAAAAAATATAAGGGAATATAA
91470 GTGTGTACAG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
37 13 0.26
38 6 0.12
39 1 0.02
40 11 0.22
41 19 0.38
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (38 bp):
AAAAAAATATAAGGGAATATAAAAAAATTACGAGGGAA
Found at i:91453 original size:17 final size:18
Alignment explanation
Indices: 91413--91469 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
91403 AGAGTACAAA
* * *
91413 AAAAATATGAGGGATACAA
1 AAAAATATAAGGGA-ATAT
*
91432 AAAAATTATGAGGG-ATAT
1 AAAAA-TATAAGGGAATAT
91450 AAAAATATAAGGGAATAT
1 AAAAATATAAGGGAATAT
91468 AA
1 AA
91470 GTGTGTACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 7 0.21
18 13 0.39
19 5 0.15
20 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (18 bp):
AAAAATATAAGGGAATAT
Found at i:91780 original size:22 final size:21
Alignment explanation
Indices: 91746--91802 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
91736 AGAAATTTTA
*
91746 AGGGAATACCAAAAAAAATATG
1 AGGGAAT-GCAAAAAAAATATG
*
91768 AGGGAATGTC--AAAAATTATG
1 AGGGAATG-CAAAAAAAATATG
*
91788 AGGGAGTGCAAAAAA
1 AGGGAATGCAAAAAA
91803 TTCTAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 4 0.14
22 8 0.28
ACGTcount: A:0.53, C:0.07, G:0.25, T:0.16
Consensus pattern (21 bp):
AGGGAATGCAAAAAAAATATG
Found at i:91787 original size:20 final size:19
Alignment explanation
Indices: 91758--91803 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
91748 GGAATACCAA
91758 AAAAAATATGAGGGAATGTC
1 AAAAAATATGAGGGAATG-C
* *
91778 AAAAATTATGAGGGAGTGC
1 AAAAAATATGAGGGAATGC
91797 AAAAAAT
1 AAAAAAT
91804 TCTAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (19 bp):
AAAAAATATGAGGGAATGC
Found at i:92849 original size:17 final size:18
Alignment explanation
Indices: 92817--92851 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
92807 GTTTCTATAT
92817 ATATACTAATAAATTAAA
1 ATATACTAATAAATTAAA
*
92835 ATATATTAA-AAATTAAA
1 ATATACTAATAAATTAAA
92852 TAAATAGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATACTAATAAATTAAA
Found at i:95570 original size:20 final size:21
Alignment explanation
Indices: 95545--95595 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
95535 AAAAATACAT
* * *
95545 AAAAATTATTAATATTTT-TA
1 AAAAATTATAAAAATTTTAAA
95565 AAAAATTCATAAAAATTTTAAA
1 AAAAATT-ATAAAAATTTTAAA
95587 AAAAATTAT
1 AAAAATTAT
95596 CCAAGTCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTATAAAAATTTTAAA
Found at i:110590 original size:22 final size:20
Alignment explanation
Indices: 110557--110596 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
110547 TGATATTTTT
110557 ATTTTATAATTTTTATTAAA
1 ATTTTATAATTTTTATTAAA
110577 ATTTTAATATATTTTTATTA
1 ATTTT-ATA-ATTTTTATTA
110597 TTAATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATAATTTTTATTAAA
Found at i:123535 original size:5 final size:5
Alignment explanation
Indices: 123525--123556 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
123515 ATATTTGAAT
123525 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC
123557 TGAGTCGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:123747 original size:8 final size:8
Alignment explanation
Indices: 123734--123781 Score: 78
Period size: 8 Copynumber: 5.8 Consensus size: 8
123724 CAGCCACTCC
123734 TATTTTAT
1 TATTTTAT
123742 TATTTTAT
1 TATTTTAT
123750 TATTTTAT
1 TATTTTAT
123758 TATTTTTAT
1 TA-TTTTAT
123767 TATTTTTAT
1 TA-TTTTAT
123776 TATTTT
1 TATTTT
123782 TATGCTGGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 22 0.56
9 17 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTTTAT
Found at i:123752 original size:3 final size:3
Alignment explanation
Indices: 123734--123784 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
123724 CAGCCACTCC
* *
123734 TAT T-T TAT TAT T-T TAT TAT T-T TAT TAT TTT TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
123779 TTT TAT
1 TAT TAT
123785 GCTGGTCTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (3 bp):
TAT
Found at i:123766 original size:9 final size:9
Alignment explanation
Indices: 123736--123784 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
123726 GCCACTCCTA
123736 TTTTATTA-
1 TTTTATTAT
123744 TTTTATTA-
1 TTTTATTAT
123752 TTTTATTAT
1 TTTTATTAT
123761 TTTTATTAT
1 TTTTATTAT
123770 TTTTATTAT
1 TTTTATTAT
123779 TTTTAT
1 TTTTAT
123785 GCTGGTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 16 0.40
9 24 0.60
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTAT
Found at i:124588 original size:26 final size:26
Alignment explanation
Indices: 124559--124610 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
124549 TTCTATTTTA
124559 TTTTAATAT-TTAATAATTTTATATAT
1 TTTTAATATATTAA-AATTTTATATAT
* * *
124585 TTTTTATTTATTAAAATTTTTTATAT
1 TTTTAATATATTAAAATTTTATATAT
124611 GGTCATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTAATATATTAAAATTTTATATAT
Found at i:125016 original size:341 final size:341
Alignment explanation
Indices: 124340--125024 Score: 1070
Period size: 341 Copynumber: 2.0 Consensus size: 341
124330 GGGCGCTTTG
* * * * *
124340 GTTTTGTGCAAGGCTAACTTGAGATTTGGATTAGAAATGTTCTTGAGTCGAGTTGGATTAGATCT
1 GTTTTGTGCAAGGCTAACTTGAGACTCGGATTAGAAATATTCATGAGTCGAGTCGGATTAGATCT
* ** *** * *
124405 AAATATTATATTAATATATATATTTGTTTAAATTTGATTTGATTCGAAATATAGATTTAAAATTT
66 AAATATTATATTAACATATATATTTGTTTAAATCAGACCCGACTCGAAATATAGACTTAAAATTT
* *
124470 TATACAAACTCATTTATATTTACAAAAGATTAATTCAATCTCATTCATATTATTTTTTAATTTTT
131 TATACAAACTCATTTATATTTACAAAAAATTAATTCAAGCTCATTCATATTATTTTTTAATTTTT
*
124535 TTAAAAAATATTTATTCTATTTTATTTTAATATTTAATAATTTTATATATTTTTTATTTATTAAA
196 TTAAAAAATATTTATTCTATTTTATTTTAATAGTTAATAATTTTATATATTTTTTATTTATTAAA
*
124600 ATTTTTTATATGGTCATCTTAACATTATTTTAACGTTTACATTAAATTAGTATTATTTATTTAGT
261 ATTTTTTATATGATCATCTTAACATTATTTTAACGTTTACATTAAATTAGTATTATTTATTTAGT
124665 ATAGTTTTTTTAATGT
326 ATAGTTTTTTTAATGT
* *
124681 GTTTTGTGCAAGGCTAACTTGGGACTCGGATTAGAAATATTCATGAGTCGAGTCGGATTAGATTT
1 GTTTTGTGCAAGGCTAACTTGAGACTCGGATTAGAAATATTCATGAGTCGAGTCGGATTAGATCT
* * * *
124746 AAGTATTATATTAACATATATATTTGTTTATATCAGACCCGACTCGAAATATGGGCTTAAAATTT
66 AAATATTATATTAACATATATATTTGTTTAAATCAGACCCGACTCGAAATATAGACTTAAAATTT
* *
124811 TGTACAAACTCATTTATATTTACAAAAAATTAATTCAAGCTCATTCATATTATATTTTTTA-TTT
131 TATACAAACTCATTTATATTTACAAAAAATTAATTCAAGCTCATTCATATTAT-TTTTTAATTTT
124875 TTTAAAAAATATTTATTCTATTTTATTTTAATAGTTAATAA-TTT-TATATTTTTTATTTATTAA
195 TTTAAAAAATATTTATTCTATTTTATTTTAATAGTTAATAATTTTATATATTTTTTATTTATTAA
* * *
124938 ATTTTTTTATATGATCATCTTAACATTATTTTAATGTTTATATTAAATTAGTATTATTTATTTAG
260 AATTTTTTATATGATCATCTTAACATTATTTTAACGTTTACATTAAATTAGTATTATTTATTTAG
125003 TATAGTTTTTTTTTAATGT
325 TATAG--TTTTTTTAATGT
125022 GTT
1 GTT
125025 CTAAATTACA
Statistics
Matches: 313, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
339 85 0.27
340 3 0.01
341 219 0.70
342 6 0.02
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (341 bp):
GTTTTGTGCAAGGCTAACTTGAGACTCGGATTAGAAATATTCATGAGTCGAGTCGGATTAGATCT
AAATATTATATTAACATATATATTTGTTTAAATCAGACCCGACTCGAAATATAGACTTAAAATTT
TATACAAACTCATTTATATTTACAAAAAATTAATTCAAGCTCATTCATATTATTTTTTAATTTTT
TTAAAAAATATTTATTCTATTTTATTTTAATAGTTAATAATTTTATATATTTTTTATTTATTAAA
ATTTTTTATATGATCATCTTAACATTATTTTAACGTTTACATTAAATTAGTATTATTTATTTAGT
ATAGTTTTTTTAATGT
Found at i:147247 original size:17 final size:17
Alignment explanation
Indices: 147225--147257 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
147215 ACACTTAATT
147225 TTAATTTCTTAA-CCTAA
1 TTAATTT-TTAATCCTAA
147242 TTAATTTTTAATCCTA
1 TTAATTTTTAATCCTA
147258 GTTATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTTTTAATCCTAA
Found at i:152384 original size:5 final size:5
Alignment explanation
Indices: 152374--152400 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
152364 ATAATTTCTC
152374 TAATT TAATT TAATT TAATT TAATT TA
1 TAATT TAATT TAATT TAATT TAATT TA
152401 CTTAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:153724 original size:64 final size:64
Alignment explanation
Indices: 153623--153751 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
153613 ACCAAAATAC
153623 CTCTTGTTCCTCTGTCTCCATATCACATACAAATATGCACTCCAAGCAAGCTTGAATATAGTAA
1 CTCTTGTTCCTCTGTCTCCATATCACATACAAATATGCACTCCAAGCAAGCTTGAATATAGTAA
*
153687 CTCTTGTTCCTCTGTCTCCATATCACATACAAATATGCACTCCAAGCAAGCTTTAATATAGTAA
1 CTCTTGTTCCTCTGTCTCCATATCACATACAAATATGCACTCCAAGCAAGCTTGAATATAGTAA
153751 C
1 C
153752 AAGCAAGGGC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (64 bp):
CTCTTGTTCCTCTGTCTCCATATCACATACAAATATGCACTCCAAGCAAGCTTGAATATAGTAA
Found at i:154697 original size:3 final size:3
Alignment explanation
Indices: 154689--154723 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
154679 TATACCGTGA
154689 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
154724 CATCATCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:154872 original size:15 final size:16
Alignment explanation
Indices: 154847--154876 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
154837 TATAAGTTCT
154847 TTTTAAAATTTTAAAA
1 TTTTAAAATTTTAAAA
154863 TTTT-AAATTTTAAA
1 TTTTAAAATTTTAAA
154877 TAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATTTTAAAA
Found at i:154877 original size:7 final size:8
Alignment explanation
Indices: 154847--154876 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
154837 TATAAGTTCT
154847 TTTTAAAA
1 TTTTAAAA
154855 TTTTAAAA
1 TTTTAAAA
154863 TTTT-AAA
1 TTTTAAAA
154870 TTTTAAA
1 TTTTAAA
154877 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:166112 original size:21 final size:24
Alignment explanation
Indices: 166087--166137 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
166077 AAACTACATG
166087 ATTTT-AATTTT-TT-ATAATAAA
1 ATTTTAAATTTTATTAATAATAAA
166108 ATTTTAAAATTTTATTAATAATAAA
1 ATTTT-AAATTTTATTAATAATAAA
*
166133 GTTTT
1 ATTTT
166138 TAAAATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
23 6 0.24
24 2 0.08
25 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTAAATTTTATTAATAATAAA
Found at i:166126 original size:22 final size:21
Alignment explanation
Indices: 166087--166128 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
166077 AAACTACATG
**
166087 ATTTTAATTTTTTATAATAAA
1 ATTTTAAAATTTTATAATAAA
166108 ATTTTAAAATTTTATTAATAA
1 ATTTTAAAATTTTA-TAATAA
166129 TAAAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAAAATTTTATAATAAA
Found at i:166137 original size:25 final size:24
Alignment explanation
Indices: 166092--166144 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
166082 ACATGATTTT
166092 AATTTTTTATAATAAAA-TTTTAA
1 AATTTTTTATAATAAAATTTTTAA
*
166115 AATTTTATTAATAATAAAGTTTTTAA
1 AATTTT-TT-ATAATAAAATTTTTAA
166141 AATT
1 AATT
166145 ACAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 8 0.31
26 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTTTTTATAATAAAATTTTTAA
Found at i:170118 original size:19 final size:19
Alignment explanation
Indices: 170081--170119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
170071 ATTTGAACAT
*
170081 ATTTTATTAATTGAAATTA
1 ATTTTATTAATTCAAATTA
170100 ATTTT-TTAATTCAATATTA
1 ATTTTATTAATTCAA-ATTA
170119 A
1 A
170120 AATGTCGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTATTAATTCAAATTA
Found at i:173356 original size:18 final size:18
Alignment explanation
Indices: 173335--173380 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
173325 ATAATTTTAT
173335 TTTTGTAAACAATA-AAAA
1 TTTT-TAAACAATATAAAA
173353 -TTTTAAACAATATTAAAA
1 TTTTTAAACAATA-TAAAA
173371 -TTTTAAACAA
1 TTTTTAAACAA
173381 ATATTAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (18 bp):
TTTTTAAACAATATAAAA
Found at i:173361 original size:16 final size:17
Alignment explanation
Indices: 173340--173380 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
173330 TTTATTTTTG
173340 TAAACAATA-AAAATTT
1 TAAACAATATAAAATTT
173356 TAAACAATATTAAAATTT
1 TAAACAATA-TAAAATTT
173374 TAAACAA
1 TAAACAA
173381 ATATTAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAACAATATAAAATTT
Found at i:173369 original size:19 final size:20
Alignment explanation
Indices: 173347--173387 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
173337 TTGTAAACAA
173347 TAAAAATTTTAAAC-AATAT
1 TAAAAATTTTAAACAAATAT
173366 T-AAAATTTTAAACAAATAT
1 TAAAAATTTTAAACAAATAT
173385 TAA
1 TAA
173388 TGTACATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.60
19 7 0.35
20 1 0.05
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATTTTAAACAAATAT
Found at i:174451 original size:22 final size:22
Alignment explanation
Indices: 174423--174467 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
174413 ATTAGAGAAA
174423 GGAAATTGTAGGTGACATATGT
1 GGAAATTGTAGGTGACATATGT
174445 GGAAATTGTAGGTGACATATGT
1 GGAAATTGTAGGTGACATATGT
174467 G
1 G
174468 TGATAATAAT
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:0.31, C:0.04, G:0.33, T:0.31
Consensus pattern (22 bp):
GGAAATTGTAGGTGACATATGT
Found at i:174682 original size:22 final size:22
Alignment explanation
Indices: 174616--174682 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
174606 TCTCCATTTA
* *
174616 TTAGCAAGTGTAGTGCTCTCCGA
1 TTAGCACGT-TAGTGCTCTCCGT
174639 TTAGCACGTTAGTGCTCTCCGT
1 TTAGCACGTTAGTGCTCTCCGT
* *
174661 TTAGCACTTTGGTGCTCTCCGT
1 TTAGCACGTTAGTGCTCTCCGT
174683 ATATTTGTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 32 0.80
23 8 0.20
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCCGT
Found at i:177234 original size:2 final size:2
Alignment explanation
Indices: 177227--177253 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
177217 ATCATTTGTG
177227 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
177254 GAAGTTTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:177837 original size:29 final size:27
Alignment explanation
Indices: 177792--178108 Score: 174
Period size: 30 Copynumber: 10.9 Consensus size: 27
177782 GGATACTTTG
*
177792 AGGGTAAAATAGTAATTTTT-GAAGGTTC
1 AGGGTAAAAT-GGAATTTTTGGAA-GTTC
*
177820 AGGGTCAAAAATGGAATTTTTGGACA-TCTA
1 AGGGT--AAAATGGAATTTTTGGA-AGT-TC
* *
177850 AGGCTAAAATGTTAATTTTTGGAAGTTC
1 AGGGTAAAATG-GAATTTTTGGAAGTTC
177878 AGGAGTAAAATGGTAATTTTTGGAAAGTTC
1 AGG-GTAAAATGG-AATTTTTGG-AAGTTC
* * *
177908 GAGGTTAAAATGGAATTTTTGGAAATTT
1 -AGGGTAAAATGGAATTTTTGGAAGTTC
*
177936 AGGGGTAAAATGGTAATTTTTGGAAAGTTT
1 A-GGGTAAAATGG-AATTTTTGG-AAGTTC
* *
177966 AGTGTCAAAAATGGAATTTTTGTGAAGTTTG
1 AGGGT--AAAATGGAATTTTTG-GAAG-TTC
** * * *
177997 AGCTTAAAAATGTAATTTTTGGAAATTT
1 AGGGT-AAAATGGAATTTTTGGAAGTTC
*
178025 AGGGGT-AAATGATAATTTTTGGAAGGTTC
1 A-GGGTAAAATG-GAATTTTTGGAA-GTTC
* *
178054 -GAGGTAAAAAATGTAATATTTGTGAAGTTC
1 AG-GGT--AAAATGGAATTTTTG-GAAGTTC
* *
178084 GTGGGTAAAAATGTAATTTTTGGAA
1 -AGGGT-AAAATGGAATTTTTGGAA
178109 AGTATGGGGT
Statistics
Matches: 236, Mismatches: 25, Indels: 55
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.03
28 48 0.20
29 67 0.28
30 85 0.36
31 28 0.12
32 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (27 bp):
AGGGTAAAATGGAATTTTTGGAAGTTC
Found at i:178041 original size:88 final size:87
Alignment explanation
Indices: 177826--178153 Score: 328
Period size: 88 Copynumber: 3.7 Consensus size: 87
177816 GTTCAGGGTC
* * * * *
177826 AAAAATGGAATTTTTGGACATCTAAGGCTAAAATGTTAATTTTTGG-AAGTTCAGG-AGTAAAAT
1 AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGATAATTTTTGGAAAGTTCAGGTA--AAAAT
177889 GGTAATTTTTG-GAAAGTTCGAGGTT
64 GG-AATTTTTGTG-AAGTTCGAGGTT
* *
177914 -AAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTAGTGTCAAAAAT
1 AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGATAATTTTTGGAAAGTTCAG-GT-AAAAAT
* *
177978 GGAATTTTTGTGAAGTTTGAGCTT
64 GGAATTTTTGTGAAGTTCGAGGTT
* *
178002 AAAAATGTAATTTTTGGAAATTTAGGGGT-AAATGATAATTTTTGGAAGGTTCGAGGTAAAAAAT
1 AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGATAATTTTTGGAAAGTTC-AGGT-AAAAAT
* * * *
178066 GTAATATTTGTGAAGTTCGTGGGT
64 GGAATTTTTGTGAAGTTCGAGGTT
* * ** *
178090 AAAAATGTAATTTTTGGAAA-GTATGGGGTCAAAATG-TAATTTTTAAAAAGTTCGAGGTCAAAA
1 AAAAATGGAATTTTTGGAAATTTA-GGGGT-AAAATGATAATTTTTGGAAAGTTC-AGGTAAAAA
178153 T
63 T
178154 ATGATTTCTG
Statistics
Matches: 206, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
87 42 0.20
88 101 0.49
89 57 0.28
90 5 0.02
91 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (87 bp):
AAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGATAATTTTTGGAAAGTTCAGGTAAAAATGG
AATTTTTGTGAAGTTCGAGGTT
Found at i:178118 original size:29 final size:29
Alignment explanation
Indices: 177793--178173 Score: 237
Period size: 29 Copynumber: 13.0 Consensus size: 29
177783 GATACTTTGA
* *
177793 GGGT-AAAATAGTAATTTTT-GAAGGTTCA
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTCG
* * **
177821 GGGTCAAAAATGGAATTTTTGGACA-TCTAA
1 GGGT-AAAAATGTAATTTTTGGAAAGT-TCG
*
177851 GGCT-AAAATGTTAATTTTTGG-AAGTTCAG
1 GGGTAAAAATG-TAATTTTTGGAAAGTTC-G
*
177880 GAGT-AAAATGGTAATTTTTGGAAAGTTCG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTCG
* * * * *
177909 AGGTTAAAATGGAATTTTTGGAAATTTAG
1 GGGTAAAAATGTAATTTTTGGAAAGTTCG
**
177938 GGGT-AAAATGGTAATTTTTGGAAAGTTTA
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTCG
* * *
177967 GTGTCAAAAATGGAATTTTTGTG-AAGTTTG
1 GGGT-AAAAATGTAATTTTTG-GAAAGTTCG
** * *
177997 AGCTTAAAAATGTAATTTTTGGAAATTTAG
1 -GGGTAAAAATGTAATTTTTGGAAAGTTCG
*
178027 GGGT--AAATGATAATTTTTGGAAGGTTCG
1 GGGTAAAAATG-TAATTTTTGGAAAGTTCG
* *
178055 AGGTAAAAAATGTAATATTTGTG-AAGTTCG
1 GGGT-AAAAATGTAATTTTTG-GAAAGTTCG
178085 TGGGTAAAAATGTAATTTTTGGAAAGTAT-G
1 -GGGTAAAAATGTAATTTTTGGAAAGT-TCG
* **
178115 GGGTCAAAATGTAATTTTTAAAAAGTTCG
1 GGGTAAAAATGTAATTTTTGGAAAGTTCG
* * * * * *
178144 AGGTCAAAATATGATTTCTGGATAGTTCG
1 GGGTAAAAATGTAATTTTTGGAAAGTTCG
178173 G
1 G
178174 TGACCTTCTG
Statistics
Matches: 278, Mismatches: 50, Indels: 49
0.74 0.13 0.13
Matches are distributed among these distances:
27 5 0.02
28 36 0.13
29 126 0.45
30 93 0.33
31 18 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTCG
Found at i:179174 original size:24 final size:24
Alignment explanation
Indices: 179128--179172 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
179118 ATTATCACTA
*
179128 TATTTATTTATTAATATACTTTAT
1 TATTTATTTATTAACATACTTTAT
*
179152 TATTTATTTATTACCAT-CTTT
1 TATTTATTTATTAACATACTTT
179173 TAAATGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTATTTATTAACATACTTTAT
Found at i:179359 original size:46 final size:46
Alignment explanation
Indices: 179306--179393 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
179296 AATGGTATAC
179306 CTTTGCTAATATCAAATGCGAAAATGCTTGGTGGTATGCCCTTTGT
1 CTTTGCTAATATCAAATGCGAAAATGCTTGGTGGTATGCCCTTTGT
* *
179352 CTTTGCTAATATCAAATGTGAAAATGTTTGGTGGTATGCCCT
1 CTTTGCTAATATCAAATGCGAAAATGCTTGGTGGTATGCCCT
179394 CTATCTGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (46 bp):
CTTTGCTAATATCAAATGCGAAAATGCTTGGTGGTATGCCCTTTGT
Found at i:179611 original size:28 final size:28
Alignment explanation
Indices: 179571--179626 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
179561 CTTTGCAGGT
179571 GTGGCAGTGGTGGCTGGTGTAGAGGGCG
1 GTGGCAGTGGTGGCTGGTGTAGAGGGCG
179599 GTGGCAGTGGTGGCTGGTGTAGAGGGCG
1 GTGGCAGTGGTGGCTGGTGTAGAGGGCG
179627 TGCTGACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.11, C:0.11, G:0.57, T:0.21
Consensus pattern (28 bp):
GTGGCAGTGGTGGCTGGTGTAGAGGGCG
Found at i:179818 original size:28 final size:25
Alignment explanation
Indices: 179774--179830 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 25
179764 TTGGGCCCCA
*
179774 ATTTGGGTTGTAATTTTGGACATTTGT
1 ATTTGGGTTATAATTTTGGAC-TTT-T
179801 ATTTGGGCTTATAATTTTGGACTTTT
1 ATTTGGG-TTATAATTTTGGACTTTT
179827 ATTT
1 ATTT
179831 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 10 0.36
28 13 0.46
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.54
Consensus pattern (25 bp):
ATTTGGGTTATAATTTTGGACTTTT
Found at i:179870 original size:18 final size:17
Alignment explanation
Indices: 179831--179958 Score: 152
Period size: 18 Copynumber: 7.4 Consensus size: 17
179821 ACTTTTATTT
*
179831 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
*
179848 TTTTAAATTTAAATATAA
1 ATTTAAATTTAAA-ATAA
* * *
179866 ATTTAAACTTACATTAA
1 ATTTAAATTTAAAATAA
*
179883 ATTTAAATTTTAAAACAA
1 ATTTAAA-TTTAAAATAA
179901 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
179919 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
179935 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
179952 ATTTAAA
1 ATTTAAA
179959 ATGGGTTTAG
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
15 3 0.03
16 12 0.13
17 34 0.36
18 45 0.48
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:179896 original size:7 final size:6
Alignment explanation
Indices: 179831--179958 Score: 92
Period size: 6 Copynumber: 22.2 Consensus size: 6
179821 ACTTTTATTT
* * * *
179831 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA ATATAA ATTTAA ACTTAC
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** **
179878 A-TTAA ATTTAA ATTTTAA A-ACAA ATTTAA ATTTAA AAATAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
179925 ATTTAA A--TAA ATTT-A ATCTTAA A-ATAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA A
179959 ATGGGTTTAG
Statistics
Matches: 94, Mismatches: 17, Indels: 22
0.71 0.13 0.17
Matches are distributed among these distances:
4 5 0.05
5 16 0.17
6 63 0.67
7 10 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:180646 original size:173 final size:173
Alignment explanation
Indices: 180352--180725 Score: 676
Period size: 173 Copynumber: 2.2 Consensus size: 173
180342 GATGAATTTG
180352 ATCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATC
1 ATCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATC
*
180417 TCATCAGGAAGTTAGAGTTCGAAGATTTGCTTACTTTGAGCCTTGGTTTCTTTGATTTGGTCTAT
66 TCATCAGGAAGTTAGAGTTCGAAGATTTGCTTACTTTGAGCCTTAGTTTCTTTGATTTGGTCTAT
180482 TTCTCTGTATCTCATCAAGAACATGACCGCATCGCTTGTTTCA
131 TTCTCTGTATCTCATCAAGAACATGACCGCATCGCTTGTTTCA
* * * *
180525 ATCCGCTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTGCTTCTCAGTATC
1 ATCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATC
* *
180590 TCATCAGGAAGTTGGGGTTCGAAGATTTGCTTACTTTGAGCCTTAGTTTCTTTGATTTGGTCTAT
66 TCATCAGGAAGTTAGAGTTCGAAGATTTGCTTACTTTGAGCCTTAGTTTCTTTGATTTGGTCTAT
180655 TTCTCTGTATCTCATCAAGAACATGACCGCATCGCTTGTTTCA
131 TTCTCTGTATCTCATCAAGAACATGACCGCATCGCTTGTTTCA
*
180698 ATCCACTTCTCTGTATCTCATCAAGAAG
1 ATCCACTTCTCAGTATCTCATCAAGAAG
180726 ACGAATTTGG
Statistics
Matches: 190, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 190 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (173 bp):
ATCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATC
TCATCAGGAAGTTAGAGTTCGAAGATTTGCTTACTTTGAGCCTTAGTTTCTTTGATTTGGTCTAT
TTCTCTGTATCTCATCAAGAACATGACCGCATCGCTTGTTTCA
Found at i:193137 original size:88 final size:88
Alignment explanation
Indices: 193017--193423 Score: 314
Period size: 88 Copynumber: 4.6 Consensus size: 88
193007 GTTCGAGGTC
* * * * *
193017 AAAAATGGATTTTTTGGATATCCGAGGGTAAAATGGTAACTTTTGGAAGTTCGAGG-GAAAAATG
1 AAAAATGGATTTTTTAGAAATTCAAGGGTAAAATGGTAATTTTTGGAAGTTCGAGGTGAAAAAT-
*
193081 GTAATTTCTGGAAAGTTTGGGGTT
65 GTAATTTTTGGAAAGTTTGGGGTT
* * * *
193105 AAAAATGGATTTTTTAGAAATTTAAGGGTAAAATGGAAATTTTTGGAAAGTTTG-GGTCAAAAAT
1 AAAAATGGATTTTTTAGAAATTCAAGGGTAAAATGGTAATTTTTGG-AAGTTCGAGGTGAAAAAT
* *
193169 GGAATTTTTGGAAA-TCTAGGGG-T
65 GTAATTTTTGGAAAGT-TTGGGGTT
* * * * * *
193192 -AAAATGGTAATTTTTTGTGAAGTTTAAGGGTAAAAAT-GTAATTTTTAGAAAGTTTAGAGGT-T
1 AAAAATGG--ATTTTTT-AGAAATTCAAGGGT-AAAATGGTAATTTTT-GGAAG-TTCGAGGTGA
* * *
193254 AAAATGTAATTTTTAGAAAATTTGAGGTT
60 AAAATGTAATTTTTGGAAAGTTTGGGGTT
* * * **
193283 -AAAATGTAATTTTTGGAAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTGAAAAAT
1 AAAAATGGATTTTTTAGAAATTCAAGGGTAAAATGGTAATTTTTGGAA-GTTCGAGGTGAAAAAT
* *
193347 GTAA-TTTTGTG-AAGTTCGGGGGT
65 GTAATTTTTG-GAAAGTTTGGGGTT
* * * * *
193370 AAAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAT-ATGATTTTTGGATAGTTC
1 AAAAATGGATTTTTTAGAAA-TTCAAGGGT-AAAATGGTAATTTTTGGA-AGTTC
193424 AGAGACCTCC
Statistics
Matches: 258, Mismatches: 41, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
86 7 0.03
87 29 0.11
88 112 0.43
89 63 0.24
90 36 0.14
91 11 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (88 bp):
AAAAATGGATTTTTTAGAAATTCAAGGGTAAAATGGTAATTTTTGGAAGTTCGAGGTGAAAAATG
TAATTTTTGGAAAGTTTGGGGTT
Found at i:193366 original size:59 final size:59
Alignment explanation
Indices: 193046--193397 Score: 288
Period size: 59 Copynumber: 5.9 Consensus size: 59
193036 ATCCGAGGGT
* * * * * *
193046 AAAATGGTAACTTTTGGAAGTTCGAGGGAAAAATGGTAATTTCTGGAAAGTTTGGGGTTA
1 AAAAT-GTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTGA
* * * ** * *
193106 AAAATGGATTTTTTAGAAATTTAAGGGTAAAATGGAAATTTTTGGAAAGTTTG-GGTCA
1 AAAATGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTGA
* * * * *
193164 AAAATGGAATTTTTGGAA-ATCTAGGGGTAAAATGGTAATTTTTTGTG-AAGTTTAAGG-GTA
1 AAAATGTAATTTTTAGAAGTTCGA-GGGTAAAATGGTAA-TTTTTG-GAAAGTTTGAGGTG-A
* * * * *
193224 AAAATGTAATTTTTAGAAAGTTTAGAGGTTAAAAT-GTAATTTTTAGAAAATTTGAGGT-T
1 AAAATGTAATTTTTAG-AAG-TTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTGA
* * * * *
193283 AAAATGTAATTTTTGGAAATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTGA
1 AAAATGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTGA
* * *
193342 AAAATGTAATTTTGT-GAAGTTCGGGGGTAAAAAT-GTAATTTTTAGAAAGTTCGAGG
1 AAAATGTAATTTT-TAGAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTTGAGG
193398 GTCAAAATAT
Statistics
Matches: 236, Mismatches: 42, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
57 13 0.06
58 54 0.23
59 111 0.47
60 42 0.18
61 6 0.03
62 8 0.03
63 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTGA
Found at i:193394 original size:30 final size:30
Alignment explanation
Indices: 192931--193423 Score: 228
Period size: 29 Copynumber: 16.8 Consensus size: 30
192921 CAGACTGGAT
* *
192931 AAAATGTAATTTTTGGATA-CTCGGGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* * *
192959 AAAATAATAATTTTAT--ACACTTCGGGGGT-
1 AAAAT-GTAATTTT-TGGAAAGTTCGGGGGTA
* *
192988 AAAATAGTAA-TTTT-CAAAGGTTC-GAGGTCA
1 AAAAT-GTAATTTTTGGAAA-GTTCGGGGGT-A
* * * * *
193018 AAAATGGATTTTTTGGATA-TCCGAGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* *
193046 AAAATGGTAACTTTTGG-AAGTTCGAGGG-A
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGGTA
* * *
193075 AAAATGGTAATTTCTGGAAAGTTTGGGGTTA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGGTA
* * * ***
193106 AAAATGGATTTTTTAGAAA-TTTAAGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* *
193134 AAAATGGAAATTTTTGGAAAGTT--TGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGGT-A
* *
193164 AAAATGGAATTTTTGGAAA--TCTAGGGGT-
1 AAAATGTAATTTTTGGAAAGTTC-GGGGGTA
***
193192 AAAATGGTAATTTTTTGTG-AAGTTTAAGGGTA
1 AAAAT-GTAA-TTTTTG-GAAAGTTCGGGGGTA
* ** * *
193224 AAAATGTAATTTTTAGAAAGTTTAGAGGTT
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* * * * *
193254 AAAATGTAATTTTTAGAAAATT-TGAGGTT
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
193283 AAAATGTAATTTTTGGAAA-TTCGGGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* *
193311 AAAATGGTAATTTTTGGAAGGTTC-GAGGTGA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGGT-A
193342 AAAATGTAA-TTTTGTG-AAGTTCGGGGGTA
1 AAAATGTAATTTTTG-GAAAGTTCGGGGGTA
* * *
193371 AAAATGTAATTTTTAGAAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAAGTTCGGGGGTA
* * *
193401 AAAATATGATTTTTGGATAGTTC
1 AAAATGTAATTTTTGGAAAGTTC
193424 AGAGACCTCC
Statistics
Matches: 367, Mismatches: 60, Indels: 74
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.01
28 43 0.12
29 161 0.44
30 132 0.36
31 23 0.06
32 6 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGGGGGTA
Found at i:194433 original size:3 final size:3
Alignment explanation
Indices: 194420--194506 Score: 140
Period size: 3 Copynumber: 29.3 Consensus size: 3
194410 CTCTTTTTAT
** *
194420 TTA TT- TTA TTA TTA AAA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
194467 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
194507 ATTTATTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:195134 original size:27 final size:28
Alignment explanation
Indices: 195104--195158 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
195094 TTGAGCCTCA
* *
195104 ATTTGGG-TTGTAATTTTTGACATTTAT
1 ATTTGGGCCTGTAATTTTGGACATTTAT
*
195131 ATTTGGGCCTGTAATTTTGGACTTTTAT
1 ATTTGGGCCTGTAATTTTGGACATTTAT
195159 TTACTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (28 bp):
ATTTGGGCCTGTAATTTTGGACATTTAT
Found at i:195185 original size:17 final size:17
Alignment explanation
Indices: 195163--195258 Score: 92
Period size: 17 Copynumber: 5.8 Consensus size: 17
195153 TTTTATTTAC
* *
195163 TTAAATTTAGAATAATT
1 TTAAATTTAAAATAAAT
195180 TTAAATTTAAATATAAAT
1 TTAAATTTAAA-ATAAAT
* * *
195198 TTAAACTTACATTAAAT
1 TTAAATTTAAAATAAAT
195215 TTAAATTT----TAAAT
1 TTAAATTTAAAATAAAT
*
195228 TTATATTTTAAAATAAAT
1 TTA-AATTTAAAATAAAT
195246 TTAAATTTAAAAT
1 TTAAATTTAAAAT
195259 GGGTTTAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
13 8 0.12
14 4 0.06
17 31 0.48
18 22 0.34
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:195226 original size:7 final size:6
Alignment explanation
Indices: 195179--195256 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
195169 TTAGAATAAT
* * *
195179 TTTAAA TTTAAA TATAAA TTTAAA CTTACA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* *
195227 TTTATAT TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
195257 ATGGGTTTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
5 8 0.14
6 40 0.68
7 11 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:202131 original size:16 final size:16
Alignment explanation
Indices: 202110--202142 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
202100 TTTCAGAGTT
*
202110 TAACAATTTAACAATG
1 TAACAATCTAACAATG
202126 TAACAATCTAACAATG
1 TAACAATCTAACAATG
202142 T
1 T
202143 TAAAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (16 bp):
TAACAATCTAACAATG
Found at i:203036 original size:27 final size:27
Alignment explanation
Indices: 203006--203069 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
202996 GTTGTTACAA
203006 AGGGAGATAGGAAGGAAGCTGTTTCAG
1 AGGGAGATAGGAAGGAAGCTGTTTCAG
* *
203033 AGGGAGATAGGGAGGAAGTTGTTTCAG
1 AGGGAGATAGGAAGGAAGCTGTTTCAG
203060 AGGGAGATAG
1 AGGGAGATAG
203070 TGATGGTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.44, T:0.19
Consensus pattern (27 bp):
AGGGAGATAGGAAGGAAGCTGTTTCAG
Found at i:209847 original size:25 final size:25
Alignment explanation
Indices: 209818--209868 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
209808 GTTGATTGTT
209818 CCTCAATCAACCTTTCCTCTTCTTC
1 CCTCAATCAACCTTTCCTCTTCTTC
209843 CCTCAATCAACCTTTCCTCTTCTTC
1 CCTCAATCAACCTTTCCTCTTCTTC
209868 C
1 C
209869 AACAAATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.45, G:0.00, T:0.39
Consensus pattern (25 bp):
CCTCAATCAACCTTTCCTCTTCTTC
Found at i:214591 original size:22 final size:22
Alignment explanation
Indices: 214563--214621 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
214553 GATAATATCA
214563 TTAAATCTTGTCAAATTCAAGT
1 TTAAATCTTGTCAAATTCAAGT
214585 TTAAATCTTGTCAAATTCAAGT
1 TTAAATCTTGTCAAATTCAAGT
214607 TTAAATCTTGTCAAA
1 TTAAATCTTGTCAAA
214622 ATTATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (22 bp):
TTAAATCTTGTCAAATTCAAGT
Found at i:214797 original size:232 final size:232
Alignment explanation
Indices: 214387--214821 Score: 852
Period size: 232 Copynumber: 1.9 Consensus size: 232
214377 AAAATATAAA
*
214387 AAAATTATTAAATGGGTACAACTTGGTCAACTTTAGATTTTTATATTTGTTTTCTATTTTTACCA
1 AAAATTATTAAATCGGTACAACTTGGTCAACTTTAGATTTTTATATTTGTTTTCTATTTTTACCA
214452 ATTTCAAATAATATTTGAGTCAATCAGATCAACCTCTTTGTTCAGACCATTATATTGATTAGTTC
66 ATTTCAAATAATATTTGAGTCAATCAGATCAACCTCTTTGTTCAGACCATTATATTGATTAGTTC
*
214517 TCGGTTCATCCAGTCCAGTCTTGTTCTATTAACATTGATAATATCATTAAATCTTGTCAAATTCA
131 TCGGTTCATCCAGTCCAGTCTTGTTCTATTAACATTGATAACATCATTAAATCTTGTCAAATTCA
214582 AGTTTAAATCTTGTCAAATTCAAGTTTAAATCTTGTC
196 AGTTTAAATCTTGTCAAATTCAAGTTTAAATCTTGTC
214619 AAAATTATTAAATCGGTACAACTTGGTCAACTTTAGATTTTTATATTTGTTTTCTATTTTTACCA
1 AAAATTATTAAATCGGTACAACTTGGTCAACTTTAGATTTTTATATTTGTTTTCTATTTTTACCA
214684 ATTTCAAATAATATTTGAGTCAATCAGATCAACCTCTTTGTTCAGACCATTATATTGATTAGTTC
66 ATTTCAAATAATATTTGAGTCAATCAGATCAACCTCTTTGTTCAGACCATTATATTGATTAGTTC
214749 TCGGTTCATCCAGTCCAGTCTTGTTCTATTAACATTGATAACATCATTAAATCTTGTCAAATTCA
131 TCGGTTCATCCAGTCCAGTCTTGTTCTATTAACATTGATAACATCATTAAATCTTGTCAAATTCA
214814 AGTTTAAA
196 AGTTTAAA
214822 GATCAAAATA
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 201 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (232 bp):
AAAATTATTAAATCGGTACAACTTGGTCAACTTTAGATTTTTATATTTGTTTTCTATTTTTACCA
ATTTCAAATAATATTTGAGTCAATCAGATCAACCTCTTTGTTCAGACCATTATATTGATTAGTTC
TCGGTTCATCCAGTCCAGTCTTGTTCTATTAACATTGATAACATCATTAAATCTTGTCAAATTCA
AGTTTAAATCTTGTCAAATTCAAGTTTAAATCTTGTC
Found at i:216084 original size:17 final size:18
Alignment explanation
Indices: 216062--216099 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
216052 TAGTAATCAT
216062 ATTATTTAAAAT-TTAAA
1 ATTATTTAAAATGTTAAA
**
216079 ATTATTTTTAATGTTAAA
1 ATTATTTAAAATGTTAAA
216097 ATT
1 ATT
216100 TATTATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTATTTAAAATGTTAAA
Found at i:218296 original size:212 final size:211
Alignment explanation
Indices: 217929--218354 Score: 771
Period size: 212 Copynumber: 2.0 Consensus size: 211
217919 CACTTCCTCC
*
217929 TTTATACAATTCCTACCCAATGCAAATGCAAATCTCAAATAACAGATAGTAAGGTCGCATATATA
1 TTTATACAATTCCTACCCAATGCAAATGCAAATCTCAAATAACAAATAGTAAGGTCGCATATATA
*
217994 GTTATTCATTTACAGTTTATGCTCAAACAGATTATATCAATACCAAAAATGATTATCACATGCAG
66 GTTATTCATTTACAGTTTATGCTCAAACAGATTATATCAATACCAAAAATGATTATCACATGCAC
*
218059 ATATTAAGTACTCAGTTCAAATCATGGTATAGCAATTTATATAGTCTAATTCAGTTCATACGGAC
131 ATATTAAGTACTCAGTTCAAATCATGGTATAGCAA-TTATATAGTCTAATTCAATTCATACGGAC
218124 ACTACAGAAGGCCTACA
195 ACTACAGAAGGCCTACA
*
218141 TTTATACAATTCCTACCCAATGCAAATGCAAATTTCAAATAACAAATAGTAAGGTCGCATATATA
1 TTTATACAATTCCTACCCAATGCAAATGCAAATCTCAAATAACAAATAGTAAGGTCGCATATATA
*
218206 GTTATTCATTTACAGTTTATGCTCAGACAGATTATATCAATACCAAAAATGATTATCACATGCAC
66 GTTATTCATTTACAGTTTATGCTCAAACAGATTATATCAATACCAAAAATGATTATCACATGCAC
* *
218271 ATATTCAGTACTCAGTTCAAATCATGGTATAGCAATTATATAGTCTAATTCAATTCATATGGACA
131 ATATTAAGTACTCAGTTCAAATCATGGTATAGCAATTATATAGTCTAATTCAATTCATACGGACA
*
218336 CTACAGAAGGCTTACA
196 CTACAGAAGGCCTACA
218352 TTT
1 TTT
218355 GTCCCAAATG
Statistics
Matches: 206, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
211 46 0.22
212 160 0.78
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (211 bp):
TTTATACAATTCCTACCCAATGCAAATGCAAATCTCAAATAACAAATAGTAAGGTCGCATATATA
GTTATTCATTTACAGTTTATGCTCAAACAGATTATATCAATACCAAAAATGATTATCACATGCAC
ATATTAAGTACTCAGTTCAAATCATGGTATAGCAATTATATAGTCTAATTCAATTCATACGGACA
CTACAGAAGGCCTACA
Found at i:226833 original size:23 final size:23
Alignment explanation
Indices: 226806--226854 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
226796 GTCATAAAAC
226806 AAAAACATACCACAAGATAGAGA
1 AAAAACATACCACAAGATAGAGA
* * *
226829 AAAAACGTGCCACAAGATAGATA
1 AAAAACATACCACAAGATAGAGA
226852 AAA
1 AAA
226855 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.10
Consensus pattern (23 bp):
AAAAACATACCACAAGATAGAGA
Done.