Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold335
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: 202493
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
File 2 of 2
Found at i:105790 original size:28 final size:27
Alignment explanation
Indices: 105728--105845 Score: 69
Period size: 28 Copynumber: 4.2 Consensus size: 27
105718 CATCTTATAT
* * * *
105728 TTAATAATTTTTAAAAATATT-TAATA
1 TTAATAAATTTTATATATATTAAAATA
*
105754 -TAATTAATTTTATATATATTAAAAATA
1 TTAATAAATTTTATATATATT-AAAATA
* * * *
105781 TTAATAAATTTAAAACATATTAAAATC
1 TTAATAAATTTTATATATATTAAAATA
*
105808 TTAAATAAAAATATATTATATATATTTAATATA
1 TT-AAT--AAAT-T-TTATATATA-TTAAAATA
105841 TTAAT
1 TTAAT
105846 TATAATTAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
25 16 0.24
27 11 0.16
28 19 0.28
30 4 0.06
31 1 0.01
32 9 0.13
33 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAATAAATTTTATATATATTAAAATA
Found at i:105806 original size:17 final size:19
Alignment explanation
Indices: 105772--105812 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
105762 TTTATATATA
105772 TTAAAAATATTAATAAAT-
1 TTAAAAATATTAATAAATC
105790 TTAAAACATATT-A-AAATC
1 TTAAAA-ATATTAATAAATC
105808 TTAAA
1 TTAAA
105813 TAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAAATATTAATAAATC
Found at i:105849 original size:18 final size:18
Alignment explanation
Indices: 105817--105854 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
105807 CTTAAATAAA
*
105817 AATATATTATATATATTT
1 AATATATTATATATAATT
105835 AATATATTA-ATTATAATT
1 AATATATTATA-TATAATT
105853 AA
1 AA
105855 ATTTATCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATATTATATATAATT
Found at i:106706 original size:21 final size:20
Alignment explanation
Indices: 106668--106707 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
106658 AATAAAAATA
* *
106668 TATTTATTTTTATTATATAC
1 TATTTATTTCTATCATATAC
106688 TATTTAATTTCTATCATATA
1 TATTT-ATTTCTATCATATA
106708 AAAGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTATTTCTATCATATAC
Found at i:106933 original size:2 final size:2
Alignment explanation
Indices: 106926--106965 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
106916 GATGTATCAA
106926 AT AT AT AT AT AT 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 AT AT AT AT AT AT
106966 TACACCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107865 original size:2 final size:2
Alignment explanation
Indices: 107858--107892 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
107848 ATCTCAACTC
107858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
107893 AGCTTATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:108128 original size:16 final size:16
Alignment explanation
Indices: 108107--108151 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
108097 TATATCATAA
*
108107 TTATATTTAAAATATT
1 TTATATTTAAAAAATT
108123 TTATATTTATAAAAATT
1 TTATATTTA-AAAAATT
108140 TTGATATGTTAA
1 TT-ATAT-TTAA
108152 TAATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 8 0.32
18 5 0.20
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
TTATATTTAAAAAATT
Found at i:108128 original size:29 final size:26
Alignment explanation
Indices: 108065--108129 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 26
108055 ATCTGACAAT
**
108065 TTTTATATTCATATTATATTTATGTA
1 TTTTATATTCATATTATATTTAAATA
108091 TTTTAATATATCATAATTATATTTAAAATA
1 TTTT-ATAT-TCAT-ATTATATTT-AAATA
108121 TTTTATATT
1 TTTTATATT
108130 TATAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 4 0.12
28 5 0.15
29 13 0.39
30 7 0.21
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTATATTCATATTATATTTAAATA
Found at i:108171 original size:32 final size:33
Alignment explanation
Indices: 108117--108178 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
108107 TTATATTTAA
*
108117 AATATTTTATATTTATAAAAATTTTGATATGTT
1 AATAATTTATATTTATAAAAATTTTGATATGTT
*
108150 AATAATTTATA-TTATATAAATTTTGATAT
1 AATAATTTATATTTATAAAAATTTTGATAT
108179 ATACGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (33 bp):
AATAATTTATATTTATAAAAATTTTGATATGTT
Found at i:112012 original size:23 final size:22
Alignment explanation
Indices: 111963--112010 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
111953 TTTTTATATG
*
111963 TAAATATTAATTTTAAAAATTA
1 TAAATATTAATATTAAAAATTA
111985 TAAATATTTAATATTAAAAATT-
1 TAAATA-TTAATATTAAAAATTA
112007 TAAA
1 TAAA
112011 ATCTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATTAATATTAAAAATTA
Found at i:112056 original size:24 final size:27
Alignment explanation
Indices: 112024--112072 Score: 77
Period size: 24 Copynumber: 1.9 Consensus size: 27
112014 TCATATAAAT
112024 AAAATATAT-ATAA-AT-TATTTTTAA
1 AAAATATATGATAATATATATTTTTAA
112048 AAAATATATGATAATATATATTTTT
1 AAAATATATGATAATATATATTTTT
112073 TTAGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 4 0.18
26 2 0.09
27 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAATATATGATAATATATATTTTTAA
Found at i:112503 original size:32 final size:32
Alignment explanation
Indices: 112467--112573 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
112457 AATGTATTGA
112467 TTTATTTCAAAATGTCAATATAATAAATATTT
1 TTTATTTCAAAATGTCAATATAATAAATATTT
** * * * *
112499 TTTATTT-ATTGATTTAAATATAATAAGTATTGA
1 TTTATTTCA-AAATGTCAATATAATAAATATT-T
*
112532 TTTATTTCAAAATCGATACGATATAATAAATATTT
1 TTTATTTCAAAAT-G-T-CAATATAATAAATATTT
112567 TTTATTT
1 TTTATTT
112574 ATTATTTTGT
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
31 1 0.02
32 24 0.43
33 9 0.16
34 1 0.02
35 8 0.14
36 13 0.23
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (32 bp):
TTTATTTCAAAATGTCAATATAATAAATATTT
Found at i:113365 original size:2 final size:2
Alignment explanation
Indices: 113358--113384 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
113348 TGTTTATAGA
113358 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
113385 AATTATGGAT
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:115685 original size:22 final size:22
Alignment explanation
Indices: 115660--115742 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
115650 ATTTGATTTG
115660 AATTATTATTTATTTAATTAAA
1 AATTATTATTTATTTAATTAAA
*
115682 AATTTTTATTTAAATTTAATTATAA
1 AATTATTATTT--ATTTAATTA-AA
*
115707 AA-TA-TATTAATATTAATATAAA
1 AATTATTATTTAT-TTAAT-TAAA
* *
115729 AATAATAATTTATT
1 AATTATTATTTATT
115743 ATTTTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
21 2 0.04
22 19 0.40
23 8 0.17
24 15 0.31
25 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATTATTTATTTAATTAAA
Found at i:117224 original size:18 final size:18
Alignment explanation
Indices: 117185--117226 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
117175 CCTTTCAATT
*
117185 TTAAAATATAAATATCTA
1 TTAAAATATAAATATCAA
*
117203 TTAAAATAT-ACTATCAA
1 TTAAAATATAAATATCAA
117220 CTTAAAA
1 -TTAAAA
117227 AACTACTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAATATAAATATCAA
Found at i:117297 original size:16 final size:17
Alignment explanation
Indices: 117259--117296 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
117249 TTAACTTATT
*
117259 TTTTTTAAAAATAATTA
1 TTTTTAAAAAATAATTA
117276 TTTTTAAAAAATAATTA
1 TTTTTAAAAAATAATTA
117293 TTTT
1 TTTT
117297 ACTTACCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTAAAAAATAATTA
Found at i:117787 original size:16 final size:16
Alignment explanation
Indices: 117764--117902 Score: 66
Period size: 16 Copynumber: 8.8 Consensus size: 16
117754 TAAAATAAAG
117764 TATA-AAATATAAAAT
1 TATATAAATATAAAAT
*
117779 TATATAAATACAATATAAT
1 TATATAAAT---ATAAAAT
* *
117798 TATATAATATTTTAAAT
1 TATATAA-ATATAAAAT
*
117815 TTTATATAATA-AAAAT
1 TATATA-AATATAAAAT
117831 TATA-AATATATTAAAATT
1 TATATAA-ATA-TAAAA-T
*
117849 TATATAAATAT-TAA-
1 TATATAAATATAAAAT
117863 T-T-T-AA-ATAAAAT
1 TATATAAATATAAAAT
*
117875 TATA-ATATAATAAAA-
1 TATATAAAT-ATAAAAT
117890 TATATAAATATAA
1 TATATAAATATAA
117903 TATAATTATA
Statistics
Matches: 93, Mismatches: 12, Indels: 38
0.65 0.08 0.27
Matches are distributed among these distances:
10 2 0.02
11 4 0.04
12 2 0.02
13 2 0.02
14 3 0.03
15 16 0.17
16 22 0.24
17 16 0.17
18 9 0.10
19 15 0.16
20 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATATAAAAT
Found at i:117845 original size:18 final size:19
Alignment explanation
Indices: 117774--117862 Score: 61
Period size: 18 Copynumber: 5.1 Consensus size: 19
117764 TATAAAATAT
*
117774 AAAATTATATAA-ATA-CA
1 AAAATTATATAATATATTA
117791 ATATAATTATATAATAT-TT-
1 A-A-AATTATATAATATATTA
* *
117810 TAAATT-T-T-ATATAATA
1 AAAATTATATAATATATTA
117826 AAAATTATA-AATATATTA
1 AAAATTATATAATATATTA
*
117844 AAATTTATATAA-ATATTA
1 AAAATTATATAATATATTA
117862 A
1 A
117863 TTTAAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 19
0.69 0.07 0.23
Matches are distributed among these distances:
14 4 0.07
15 2 0.04
16 6 0.11
17 6 0.11
18 24 0.43
19 12 0.21
20 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTATATAATATATTA
Found at i:117857 original size:10 final size:10
Alignment explanation
Indices: 117764--117929 Score: 77
Period size: 10 Copynumber: 16.7 Consensus size: 10
117754 TAAAATAAAG
117764 TATAAA-ATA
1 TATAAATATA
117773 TA-AAAT-TA
1 TATAAATATA
*
117781 TATAAATACA
1 TATAAATATA
117791 -ATATAAT-TA
1 TATA-AATATA
117800 TAT-AATAT-
1 TATAAATATA
*
117808 TTTAAATTTTATA
1 TATAAA---TATA
*
117821 TAATAAAAAT-
1 T-ATAAATATA
117831 TATAAATATA
1 TATAAATATA
*
117841 T-TAAAATTTA
1 TAT-AAATATA
117851 TATAAATATTAA
1 TATAAATA-T-A
*
117863 TTTAAATA-A
1 TATAAATATA
*
117872 AATTATAATATA
1 TA-TA-AATATA
117884 -ATAAA-ATA
1 TATAAATATA
117892 TATAAATATAA
1 TATAAATAT-A
*
117903 TATAATTATA
1 TATAAATATA
*
117913 TATATATATA
1 TATAAATATA
117923 TATAAAT
1 TATAAAT
117930 TTATTTTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 45
0.66 0.08 0.25
Matches are distributed among these distances:
8 15 0.13
9 29 0.24
10 40 0.34
11 18 0.15
12 12 0.10
13 1 0.01
14 4 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
TATAAATATA
Found at i:117859 original size:6 final size:6
Alignment explanation
Indices: 117850--117929 Score: 51
Period size: 6 Copynumber: 13.3 Consensus size: 6
117840 ATTAAAATTT
* * *
117850 ATATAA ATATTA ATTTAA ATA-AA AT-TATA ATAT-A ATAAAA TATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATATAA ATATAA -ATATAA
* *
117897 ATAT-A ATATAA TTATATAT ATATAT ATATAA AT
1 ATATAA ATATAA --ATATAA ATATAA ATATAA AT
117930 TTATTTTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
5 14 0.24
6 33 0.57
7 6 0.10
8 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAA
Found at i:117869 original size:32 final size:31
Alignment explanation
Indices: 117790--117934 Score: 95
Period size: 32 Copynumber: 4.6 Consensus size: 31
117780 ATATAAATAC
* *
117790 AATATAATTATATAATATTTTAAATTTTATAT
1 AATATAATTATA-AATATATTAAAATTTATAT
*
117822 AATAAAAATTATAAATATATTAAAATTTATAT
1 AAT-ATAATTATAAATATATTAAAATTTATAT
** *
117854 AA-AT-ATTA-ATTTA-AATAAAATTATAATAT
1 AATATAATTATAAATATATTAAAATT-T-ATAT
* * *
117883 AATAAAATATATAAATATAATATAA-TTATAT
1 AATATAAT-TATAAATATATTAAAATTTATAT
*
117914 -ATATATATATATAAATTTATT
1 AATATA-AT-TATAAATATATT
117935 TTTTCTCCCA
Statistics
Matches: 90, Mismatches: 14, Indels: 19
0.73 0.11 0.15
Matches are distributed among these distances:
27 8 0.09
28 4 0.04
29 10 0.11
30 6 0.07
31 19 0.21
32 25 0.28
33 12 0.13
34 6 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AATATAATTATAAATATATTAAAATTTATAT
Found at i:117901 original size:18 final size:18
Alignment explanation
Indices: 117818--117920 Score: 73
Period size: 18 Copynumber: 5.3 Consensus size: 18
117808 TTTAAATTTT
117818 ATATAATAAAA-ATTATAA
1 ATATAATAAAATA-TATAA
*
117836 ATATATTAAAATTTATATAA
1 ATATAATAAAA--TATATAA
* *
117856 ATATTAATTTAAATAAAATTATA
1 ATA-TAA-TAAAAT-ATA-TA-A
117879 ATATAATAAAATATATAA
1 ATATAATAAAATATATAA
* *
117897 ATATAATATAATTATATAT
1 ATATAATA-AAATATATAA
117916 ATATA
1 ATATA
117921 TATATAAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
18 19 0.28
19 15 0.22
20 11 0.16
21 10 0.15
22 9 0.13
23 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATAAAATATATAA
Found at i:117901 original size:23 final size:23
Alignment explanation
Indices: 117875--117924 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
117865 TAAATAAAAT
117875 TATAATATAATAAAATATATAAA
1 TATAATATAATAAAATATATAAA
* * *
117898 TATAATATAATTATATATATATA
1 TATAATATAATAAAATATATAAA
117921 TATA
1 TATA
117925 TAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAATATAATAAAATATATAAA
Found at i:118257 original size:34 final size:36
Alignment explanation
Indices: 118213--118293 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 36
118203 ATTATATCTC
*
118213 ATAAAT-TTAAAAT-AATATTATGAAAAA-A-ATAAT
1 ATAAATATTAAAATAAATA-TATAAAAAATATATAAT
118246 ATAAATATT-AAATAAATATATAAAAAATTATATAAT
1 ATAAATATTAAAATAAATATATAAAAAA-TATATAAT
118282 ATAAATTATTAA
1 ATAAA-TATTAA
118294 TATATCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
33 18 0.45
34 6 0.15
35 1 0.03
36 10 0.25
37 4 0.10
38 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (36 bp):
ATAAATATTAAAATAAATATATAAAAAATATATAAT
Found at i:118275 original size:20 final size:21
Alignment explanation
Indices: 118239--118284 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
118229 ATTATGAAAA
*
118239 AAATA-ATATAAATATTAAAT
1 AAATATATATAAAAATTAAAT
*
118259 AAATATATA-AAAAATTATAT
1 AAATATATATAAAAATTAAAT
118279 -AATATA
1 AAATATA
118285 AATTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 14 0.61
21 3 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATATATAAAAATTAAAT
Found at i:118292 original size:17 final size:17
Alignment explanation
Indices: 118241--118322 Score: 53
Period size: 17 Copynumber: 4.7 Consensus size: 17
118231 TATGAAAAAA
118241 ATAATATAAA-TATTAAAT
1 ATAATATAAATTATT--AT
* **
118259 AAATATATAAAAAATTAT
1 ATA-ATATAAATTATTAT
118277 ATAATATAAATTATTA-
1 ATAATATAAATTATTAT
*
118293 AT-ATATCAAAATTTTTAT
1 ATAATAT--AAATTATTAT
*
118311 AAAATATAAATT
1 ATAATATAAATT
118323 GAATTAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.08
16 2 0.04
17 24 0.47
18 7 0.14
19 11 0.22
20 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATATAAATTATTAT
Found at i:118296 original size:32 final size:31
Alignment explanation
Indices: 118236--118322 Score: 79
Period size: 34 Copynumber: 2.7 Consensus size: 31
118226 AATATTATGA
*
118236 AAAAAATAATATAAATATTAAA-TAAATATAT-
1 AAAAAATTATAT-AATA-TAAATTAAATATATC
118267 AAAAAATTATATAATATAAATTATTAATATATC
1 AAAAAATTATATAATATAAATTA--AATATATC
** *
118300 AAAATTTTTATAAAATATAAATT
1 AAAA-AATTATATAATATAAATT
118323 GAATTAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.09
30 6 0.13
31 11 0.23
32 7 0.15
33 4 0.09
34 15 0.32
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
AAAAAATTATATAATATAAATTAAATATATC
Found at i:121490 original size:2 final size:2
Alignment explanation
Indices: 121483--121520 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
121473 TATTTGAGAA
121483 AT AT AT AT AT 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 AT AT AT AT AT
121521 TTGCATGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127301 original size:2 final size:2
Alignment explanation
Indices: 127294--127332 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
127284 ATATCGAAAA
127294 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
127333 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:127337 original size:2 final size:2
Alignment explanation
Indices: 127332--127368 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
127322 TCTCTCTCTC
127332 TA TA TA TA TA 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 TA TA TA TA TA T
127369 CATTGTCACT
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:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128062 original size:21 final size:21
Alignment explanation
Indices: 128037--128105 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
128027 AACTACTCAT
128037 TTAAAAAAAATTCATTTATTC
1 TTAAAAAAAATTCATTTATTC
* * *
128058 TTAAAAACTAA-CCATATATT-
1 TTAAAAA-AAATTCATTTATTC
* *
128078 TTTAAAAAATTTCAATTTATTC
1 TTAAAAAAAATTC-ATTTATTC
128100 TTAAAA
1 TTAAAA
128106 GTTACTCACT
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
19 1 0.03
20 7 0.20
21 20 0.57
22 7 0.20
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAAAATTCATTTATTC
Found at i:128314 original size:17 final size:16
Alignment explanation
Indices: 128282--128362 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
128272 TGGGTTCAAA
128282 ATTTTCAAATTTAATTT
1 ATTTT-AAATTTAATTT
128299 ATTTTAAATTTGAATTGT
1 ATTTTAAATTT-AATT-T
* *
128317 -TTTTAAATTTAAATC
1 ATTTTAAATTTAATTT
* *
128332 ATTTTAAAGTTAA-AT
1 ATTTTAAATTTAATTT
*
128347 -TTTTAAATTGAATTT
1 ATTTTAAATTTAATTT
128362 A
1 A
128363 ATCAAGGCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 20 0.39
17 19 0.37
18 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTTAAATTTAATTT
Found at i:130091 original size:2 final size:2
Alignment explanation
Indices: 130084--130125 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
130074 CTTATTCCCC
130084 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
130126 GTATGTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137645 original size:24 final size:24
Alignment explanation
Indices: 137582--137651 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
137572 CATATGAAAG
*
137582 TATATATTATAATTTAAAATAATATT
1 TATA-ATTA-AATTTAAATTAATATT
* * ** *
137608 AAAAATTATTTTTATATTAATATT
1 TATAATTAAATTTAAATTAATATT
137632 TATAATTAAATTTAAATTAA
1 TATAATTAAATTTAAATTAA
137652 AAAAATTTAT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
24 27 0.82
25 4 0.12
26 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAATTAAATTTAAATTAATATT
Found at i:138445 original size:2 final size:2
Alignment explanation
Indices: 138438--138463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
138428 ATATTTGTAT
138438 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
138464 AAATATGATC
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):
TA
Found at i:143375 original size:4 final size:4
Alignment explanation
Indices: 143368--143420 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
143358 CCGGCAGGAG
* * *
143368 AGAA AGAA AGAA AGAA A-AA AAAA AGAA AG-G AGAA AAAA AGAA A-AA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
143413 A-AA AGAA A
1 AGAA AGAA A
143421 AATATTTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
3 11 0.27
4 30 0.73
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:143394 original size:15 final size:15
Alignment explanation
Indices: 143374--143421 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
143364 GGAGAGAAAG
143374 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
* *
143389 AAAGAAAGGAGAAAA
1 AAAGAAAGAAAAAAA
143404 AAAGAAA-AAAAAAGA
1 AAAGAAAGAAAAAA-A
143419 AAA
1 AAA
143422 ATATTTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:143407 original size:26 final size:25
Alignment explanation
Indices: 143372--143420 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
143362 CAGGAGAGAA
*
143372 AGAAAGAAAGAAAAAAAAAAGAAAGG
1 AGAAAAAAAG-AAAAAAAAAGAAAGG
143398 AGAAAAAAAGAAAAAAAAAGAAA
1 AGAAAAAAAGAAAAAAAAAGAAA
143421 AATATTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AGAAAAAAAGAAAAAAAAAGAAAGG
Found at i:143489 original size:135 final size:133
Alignment explanation
Indices: 143296--143561 Score: 398
Period size: 135 Copynumber: 2.0 Consensus size: 133
143286 TTATCTATAT
* *
143296 ATAATATTAAAATTAACTACGTATGAGGTGTTGACACGTGGCACCTCCTTTGATTTTTTTTTCCG
1 ATAATATTAAAATTAACTACATACGAGGTGTTGACACGTGGCACCT-CTTTGATTTTTTTTTCCG
143361 GCAGGAGAGAAAGAAAGAAAGAAAAAAAAAAGAAAGGAGAAAAAAAGAAA-AAAAAA-GAAAAAT
65 GCAGGAGAGAAAGAAAGAAAG--AAAAAAAAGAAAGGAGAAAAAAA-AAAGAAAAAAGGAAAAAT
143424 ATTTTAC
127 ATTTTAC
*
143431 ATAATATTAAAATTAACTACACAAATACGAGGTGTTGACACGTGGCA-CT-TTT-TTTTTTTTTT
1 ATAATATTAAAATTAACT--AC--ATACGAGGTGTTGACACGTGGCACCTCTTTGATTTTTTTTT
143493 CCGGCAGGAGAGAAAGAAAGAAAGAAAAAAAAGAAAGGAGAAAAAAAAAAGAAAAAAGGAAAAAT
62 CCGGCAGGAGAGAAAGAAAGAAAGAAAAAAAAGAAAGGAGAAAAAAAAAAGAAAAAAGGAAAAAT
143558 ATTT
127 ATTT
143562 GTATTTATAT
Statistics
Matches: 122, Mismatches: 3, Indels: 13
0.88 0.02 0.09
Matches are distributed among these distances:
132 3 0.02
133 29 0.24
134 11 0.09
135 51 0.42
136 3 0.02
137 2 0.02
138 2 0.02
139 21 0.17
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (133 bp):
ATAATATTAAAATTAACTACATACGAGGTGTTGACACGTGGCACCTCTTTGATTTTTTTTTCCGG
CAGGAGAGAAAGAAAGAAAGAAAAAAAAGAAAGGAGAAAAAAAAAAGAAAAAAGGAAAAATATTT
TAC
Found at i:143527 original size:13 final size:13
Alignment explanation
Indices: 143509--143549 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
143499 GGAGAGAAAG
143509 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
143522 AAAGAAAGGAGAAAA
1 AAAGAAA-GA-AAAA
143537 AAA-AAAGAAAAA
1 AAAGAAAGAAAAA
143549 A
1 A
143550 GGAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 5 0.19
15 7 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAA
Found at i:143540 original size:18 final size:17
Alignment explanation
Indices: 143505--143556 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
143495 GGCAGGAGAG
143505 AAAGAAAGAAAGAAAAA
1 AAAGAAAGAAAGAAAAA
143522 AAAGAAAGGAGAA-AAAAA
1 AAAGAAA-GA-AAGAAAAA
143540 AAAGAAA-AAAGGAAAAA
1 AAAGAAAGAAA-GAAAAA
143557 TATTTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 12 0.39
18 14 0.45
19 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAAA
Found at i:144543 original size:11 final size:11
Alignment explanation
Indices: 144527--144572 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
144517 TTGTCAAGAG
144527 AAAAAGAAAAA
1 AAAAAGAAAAA
* *
144538 AAAAAGATAGA
1 AAAAAGAAAAA
* *
144549 AAAAAGGAGAA
1 AAAAAGAAAAA
144560 AAAAAGAAAAA
1 AAAAAGAAAAA
144571 AA
1 AA
144573 TTATGTATTC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:144559 original size:10 final size:8
Alignment explanation
Indices: 144522--144572 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
144512 TATTTTTGTC
*
144522 AAGAGAAA
1 AAGAAAAA
144530 AAGAAAAA
1 AAGAAAAA
*
144538 AA-AAAGA
1 AAGAAAAA
*
144545 TAGAAAAA
1 AAGAAAAA
144553 AGGAGAAAAA
1 A--AGAAAAA
144563 AAGAAAAA
1 AAGAAAAA
144571 AA
1 AA
144573 TTATGTATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 5 0.14
8 22 0.63
10 8 0.23
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:144870 original size:23 final size:25
Alignment explanation
Indices: 144843--144903 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
144833 GTATTCTTAC
144843 TGTGTTTATATTATTTT-T-TATGT
1 TGTGTTTATATTATTTTATATATGT
144866 TGTGTTT-TAATT-TTTTATATATGT
1 TGTGTTTAT-ATTATTTTATATATGT
* *
144890 TGAGTTTATGTTAT
1 TGTGTTTATATTAT
144904 ATCTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 13 0.42
25 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (25 bp):
TGTGTTTATATTATTTTATATATGT
Found at i:145638 original size:16 final size:17
Alignment explanation
Indices: 145611--145651 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
145601 ATTTTTAAAT
145611 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
145626 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
145643 AAATTTTAT
1 AAATTTTAT
145652 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:146157 original size:34 final size:34
Alignment explanation
Indices: 146118--146193 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
146108 TATATTTAAT
*
146118 ATTAA-TA-TATTATATTATTTTTATTTAAAAATAA
1 ATTAATTACTATTATATTAATTTT-TTTAAAAA-AA
*
146152 ATTAATTACTATTATTTTAATTTTTTTAAAAAAA
1 ATTAATTACTATTATATTAATTTTTTTAAAAAAA
*
146186 ATTGATTA
1 ATTAATTA
146194 AAATATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 14 0.38
35 10 0.27
36 13 0.35
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (34 bp):
ATTAATTACTATTATATTAATTTTTTTAAAAAAA
Found at i:146159 original size:25 final size:28
Alignment explanation
Indices: 146098--146168 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
146088 TTAAATTCAT
*
146098 TTATA-TATTTTATATTTAATATTAATATA
1 TTATATTATTTT-TATTTAATA-TAATAAA
146127 TTATATTATTTTTATTTAA-A-AATAAA
1 TTATATTATTTTTATTTAATATAATAAA
* *
146153 TTA-ATTACTATTATTT
1 TTATATTATTTTTATTT
146169 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 11 0.29
26 8 0.21
28 1 0.03
29 12 0.32
30 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TTATATTATTTTTATTTAATATAATAAA
Found at i:146572 original size:12 final size:13
Alignment explanation
Indices: 146555--146589 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
146545 CTTATTATTA
146555 TCATCATCATCT-
1 TCATCATCATCTG
146567 TCATCATCAT-TG
1 TCATCATCATCTG
146579 TCATCATCATC
1 TCATCATCATC
146590 AATGCTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.95
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (13 bp):
TCATCATCATCTG
Found at i:146735 original size:17 final size:16
Alignment explanation
Indices: 146703--146738 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
146693 GCTTTAAATT
146703 ATTATTTAAATAAAAA
1 ATTATTTAAATAAAAA
* *
146719 ATTATTTTAATATAAA
1 ATTATTTAAATAAAAA
146735 ATTA
1 ATTA
146739 ATTGCAAATA
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):
ATTATTTAAATAAAAA
Found at i:147598 original size:15 final size:14
Alignment explanation
Indices: 147565--147612 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
147555 TCGATTAATT
147565 ATATTAAA-AAAATA
1 ATATTAAATAAAA-A
147579 ATATTAAATATAAAA
1 ATATTAAATA-AAAA
*
147594 ATATTTAATAAAAA
1 ATATTAAATAAAAA
147608 TATAT
1 -ATAT
147613 ATTTGATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.40
15 15 0.50
16 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATTAAATAAAAA
Found at i:148853 original size:21 final size:21
Alignment explanation
Indices: 148815--148854 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
148805 TATATAAGTT
*
148815 TAAATCACGTTTTTATATAAC
1 TAAATCACGTTTTCATATAAC
148836 TAAATCA-GTTTTGCATATA
1 TAAATCACGTTTT-CATATA
148855 TTTCAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
TAAATCACGTTTTCATATAAC
Found at i:150124 original size:19 final size:20
Alignment explanation
Indices: 150100--150159 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
150090 TTTGAATTTC
150100 AACAAT-TTGTATCGATACA
1 AACAATATTGTATCGATACA
*
150119 AACAATAAATGTATCGATACA
1 AACAAT-ATTGTATCGATACA
* * *
150140 TA-AGTGTTGTATCGATACA
1 AACAATATTGTATCGATACA
150159 A
1 A
150160 TGTATCGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
AACAATATTGTATCGATACA
Found at i:150213 original size:20 final size:20
Alignment explanation
Indices: 150188--150225 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
150178 CTGCCAAGGA
*
150188 AATGTATCGATATATTATTT
1 AATGTATCGATACATTATTT
150208 AATGTATCGATACATTAT
1 AATGTATCGATACATTAT
150226 CGATACATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (20 bp):
AATGTATCGATACATTATTT
Found at i:153449 original size:32 final size:32
Alignment explanation
Indices: 153384--153478 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 32
153374 TATAATTATG
* *
153384 TAAAAATTTATAT-AATATAAATTATTAAAAAA
1 TAAAAATTTATATAAATATAAAATATT-ATAAA
*
153416 TAAAAATTTATATAAATATAAAATATTTTAAA
1 TAAAAATTTATATAAATATAAAATATTATAAA
* * *
153448 T-ATAA-TTATA-AAATAAAAAATAATATAAA
1 TAAAAATTTATATAAATATAAAATATTATAAA
153477 TA
1 TA
153479 CATAAATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 17 0.31
30 5 0.09
31 3 0.06
32 17 0.31
33 12 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAATTTATATAAATATAAAATATTATAAA
Found at i:153646 original size:16 final size:14
Alignment explanation
Indices: 153615--153654 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
153605 TTATTTTTTA
153615 TAAAAAAATTTAAT
1 TAAAAAAATTTAAT
153629 TAAAAAAA-TTAAT
1 TAAAAAAATTTAAT
**
153642 TATTAAAATTTAA
1 TAAAAAAATTTAA
153655 ATTTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAAAATTTAAT
Found at i:154982 original size:2 final size:2
Alignment explanation
Indices: 154975--154999 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
154965 TATTAGTATG
154975 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 T
155000 GTTAGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:155202 original size:34 final size:33
Alignment explanation
Indices: 155154--155272 Score: 157
Period size: 34 Copynumber: 3.5 Consensus size: 33
155144 TGGTAAAAAC
*
155154 CACCATTTAATCAACAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* * * * * *
155187 CTCTCATTTAGTCAACAATAGCAAACCATCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
155221 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
155255 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
155273 TCTCCCACTT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
33 18 0.25
34 52 0.73
35 1 0.01
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:162259 original size:30 final size:29
Alignment explanation
Indices: 162218--162275 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
162208 TAAATAGATT
*
162218 AAATTTAAAGTTTAATTTTAATTTATTTAA
1 AAATATAAAGTTTAATTTT-ATTTATTTAA
* *
162248 AAATATAAAGTTTGATTTTATTTTTTTA
1 AAATATAAAGTTTAATTTTATTTATTTA
162276 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (29 bp):
AAATATAAAGTTTAATTTTATTTATTTAA
Found at i:163478 original size:26 final size:26
Alignment explanation
Indices: 163449--163502 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
163439 TTAATTAGTA
163449 TTTAATGACACTAATTAA-A-ATTATTT
1 TTTAA-GACA-TAATTAATACATTATTT
*
163475 TTTAAGATATAATTAATACATTATTT
1 TTTAAGACATAATTAATACATTATTT
163501 TT
1 TT
163503 CTTGAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 4 0.16
26 14 0.56
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
TTTAAGACATAATTAATACATTATTT
Found at i:163810 original size:18 final size:16
Alignment explanation
Indices: 163784--163822 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
163774 AATGGGAGAA
163784 AAAAAGATATGATTTTTT
1 AAAAAGATA-G-TTTTTT
*
163802 AAAATGATAGTTTTTT
1 AAAAAGATAGTTTTTT
163818 AAAAA
1 AAAAA
163823 TTGATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (16 bp):
AAAAAGATAGTTTTTT
Found at i:164382 original size:35 final size:31
Alignment explanation
Indices: 164348--164442 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 31
164338 ATTTTTATTA
*
164348 ATATATTAATTTATATAA-TTATATCATA-T-
1 ATATATTAATTTATATAATTTAAAT-ATATTA
164377 ATATTATTATATTTATA-AATTTAAATATATTA
1 ATA-TATTA-ATTTATATAATTTAAATATATTA
* *
164409 ATA-ATTATTTTATATAAATTTTAATATAATTA
1 ATATATTAATTTATAT-AATTTAAATAT-ATTA
164441 AT
1 AT
164443 TAAATAATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
29 9 0.16
30 14 0.25
31 23 0.42
32 9 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATATTAATTTATATAATTTAAATATATTA
Found at i:164793 original size:14 final size:14
Alignment explanation
Indices: 164774--164800 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
164764 TGATTTTTTT
164774 TTTAAATATATAAC
1 TTTAAATATATAAC
164788 TTTAAATATATAA
1 TTTAAATATATAA
164801 ATTATGGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAATATATAAC
Found at i:165175 original size:21 final size:21
Alignment explanation
Indices: 165133--165176 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
165123 TCATATATCG
* **
165133 TATTTTATAATTATATTTAAT
1 TATTATATAATTATATAAAAT
*
165154 TATTATATATTTATATAAAAT
1 TATTATATAATTATATAAAAT
165175 TA
1 TA
165177 CATCAAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATATAATTATATAAAAT
Found at i:166049 original size:23 final size:23
Alignment explanation
Indices: 166023--166106 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
166013 AAAAATTATT
166023 TATTTATTTTAATATTTAAAATA
1 TATTTATTTTAATATTTAAAATA
* **
166046 TATTAAAATTAATATTTAAAA-A
1 TATTTATTTTAATATTTAAAATA
* *
166068 TATATA-TTTCATATTTTATAAATA
1 TATTTATTTTAATA-TTTA-AAATA
166092 T-TTATATATTTAATA
1 TATT-TAT-TTTAATA
166107 ATTATATTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
21 5 0.11
22 9 0.20
23 22 0.48
24 4 0.09
26 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTATTTTAATATTTAAAATA
Found at i:166067 original size:14 final size:13
Alignment explanation
Indices: 166031--166076 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
166021 TTTATTTATT
166031 TTAATATTTAAAA
1 TTAATATTTAAAA
166044 -T-ATA-TTAAAA
1 TTAATATTTAAAA
166054 TTAATATTTAAAA
1 TTAATATTTAAAA
*
166067 ATATATATTT
1 TTA-ATATTT
166077 CATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
12 4 0.14
13 8 0.29
14 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATATTTAAAA
Found at i:168454 original size:21 final size:20
Alignment explanation
Indices: 168430--168471 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
168420 TATTTTTATT
* *
168430 TAAATTTAATTATAAAATATA
1 TAAATATAAATATAAAA-ATA
168451 TAAATATAAATATAAAAATA
1 TAAATATAAATATAAAAATA
168471 T
1 T
168472 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATAAATATAAAAATA
Found at i:169395 original size:244 final size:247
Alignment explanation
Indices: 168966--170041 Score: 903
Period size: 240 Copynumber: 4.4 Consensus size: 247
168956 TTGAGTTTTA
*
168966 AATAAAATAATATTTTTATTTAAATTTATTATAAAAATTATAAATATTAATAAAATAATATTTTA
1 AATAAAATAATATTTTTA--TAAATTAATTATAAAAATTATAAATATTAATAAAATAATATTTTA
* * *
169031 ATAACATAATAAATAATAAAAAAG---TTAAATCAGATA-TTTATAAGTTATAATTAAATTTATT
64 ATAATATAATGAATAATAAAAAAGTTTTTAAATCAGATATTTTATAAATTATAATTAAATTTATT
* ** * *
169092 T-AAAGTCAAGTTATTTATTTAGACTAGATTATTCATTCGACTTACTCAATTGATCTTATATTAT
129 TAAAAGTCAAGTTATTT-GTTAGGTTAGATTATTCACTCGACTTACTCAATTGATCTTATATGAT
* * * * *
169156 CCAAGCT-TTGGATACGATTTTGT-T-GA-TTGAAAATAGCTTGAATTATTATTTAAT
193 CCAAG-TATTGGATAAGATTTT-TATGGAGTCG-AAATAGCTTAAATCACTATTTAAT
* * *
169210 AATAAAAAAATATTTTTA-AAATTAATTA-AAAATTTA-AAAGTATTAATAAAATGATATTTTAA
1 AATAAAATAATATTTTTATAAATTAATTATAAAAATTATAAA-TATTAATAAAATAATATTTTAA
* ** *
169272 TAATATAATGAATAATAAAAAAGTTTTTAAGTTGGATATTTTATAAATTATAATTAAAATTATTT
65 TAATATAATGAATAATAAAAAAGTTTTTAAATCAGATATTTTATAAATTATAATTAAATTTATTT
* ** * *
169337 AAAAGTCAAGTTATTTGTTAGGTTAAATTATTGGCTCGACTTACTCAACTT-ATCTTATATGGTT
130 AAAAGTCAAGTTATTTGTTAGGTTAGATTATTCACTCGACTTACTCAA-TTGATCTTATATGATC
** * *
169401 TGAGTATTGGATAAGATTTTTATGGAGTCGAAATGGTTTAAATCACTATTTAAT
194 CAAGTATTGGATAAGATTTTTATGGAGTCGAAATAGCTTAAATCACTATTTAAT
* * *
169455 AATAAAAGTAATGTTTTTATTTGAATTTAATTATAAAAATTATAAATATTAATAAATTAATATTT
1 AATAAAA-TAATATTTTTA--T-AAATTAATTATAAAAATTATAAATATTAATAAAATAATATTT
* * *
169520 TAGTGATGTAATGAATAATAAACAAAAGTTTTTCAAATCAGATATTTTATAAATTATAA-TAAAT
62 TAATAATATAATGAATAAT-AA-AAAAGTTTTT-AAATCAGATATTTTATAAATTATAATTAAAT
* * * *
169584 TTCTTTAAAAGTCAA-TTATTTGTTTAGGTTAGATTATTTAATTGACCTTA-T--A-TG--C-T-
124 TTATTTAAAAGTCAAGTTATTTG-TTAGGTTAGATTATTCACTCGA-CTTACTCAATTGATCTTA
* * * * * * * * ** * *
169640 T-TG-----AGCATTGGATAAGATCTATCTGAATTTGAAACT-TCTCGAATAATTATTTAAT
187 TATGATCCAAGTATTGGATAAGATTTTTATGGAGTCGAAA-TAGCTTAAATCACTATTTAAT
169695 AATAAAAATAATATTTTTATTTAAATTTAATTATAAAAATTATAAATATTAATAAAATAATATTT
1 AAT-AAAATAATATTTTTA--TAAA-TTAATTATAAAAATTATAAATATTAATAAAATAATATTT
* * * * * * * * *
169760 TAATAATAAAATAAATAATAAAAAAAGTTTTCAAGTAAAAAATTTTGTAAGTTATAATTAAATTT
62 TAATAATATAATGAATAAT-AAAAAAGTTTTTAAATCAGATATTTTATAAATTATAATTAAATTT
* * * * *
169825 ATTTAAAAATCAA-TTATTTATTTAGGTTAGATTATTCACTTGACTTACTCAACT-AACTTTATA
126 ATTTAAAAGTCAAGTTATTT-GTTAGGTTAGATTATTCACTCGACTTACTCAATTGATC-TTATA
* * * * ** * * * *
169888 TGGT--GAGTGTTGGATAAAATTTTTATAAATTTGAAACAGCTTAAATCATTATTTAAT
189 TGATCCAAGTATTGGATAAGATTTTTATGGAGTCGAAATAGCTTAAATCACTATTTAAT
* * *
169945 GA-AAAATAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTGATAAAATAATATTTT
1 AATAAAATAATATTTTTA--TAAA-TTAATTATAAAAATTATAAATATTAATAAAATAATATTTT
* *
170009 AATAATATAATAAATATTACAAAAA--TTTTAAAT
63 AATAATATAATGAATAATA-AAAAAGTTTTTAAAT
170042 TAAATTTAAT
Statistics
Matches: 687, Mismatches: 101, Indels: 86
0.79 0.12 0.10
Matches are distributed among these distances:
238 23 0.03
239 59 0.09
240 157 0.23
241 15 0.02
242 1 0.00
243 12 0.02
244 92 0.13
245 48 0.07
246 19 0.03
247 4 0.01
248 82 0.12
249 1 0.00
250 49 0.07
251 41 0.06
252 12 0.02
253 46 0.07
254 26 0.04
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (247 bp):
AATAAAATAATATTTTTATAAATTAATTATAAAAATTATAAATATTAATAAAATAATATTTTAAT
AATATAATGAATAATAAAAAAGTTTTTAAATCAGATATTTTATAAATTATAATTAAATTTATTTA
AAAGTCAAGTTATTTGTTAGGTTAGATTATTCACTCGACTTACTCAATTGATCTTATATGATCCA
AGTATTGGATAAGATTTTTATGGAGTCGAAATAGCTTAAATCACTATTTAAT
Found at i:170061 original size:492 final size:484
Alignment explanation
Indices: 168966--170037 Score: 1132
Period size: 491 Copynumber: 2.2 Consensus size: 484
168956 TTGAGTTTTA
*
168966 AATAAAA-TAATATTTTTATTTAAATTT-ATTATAAAAATTATAAATATTAATAAAATAATATTT
1 AATAAAAGTAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTAATAAAATAATATTT
* * *
169029 TAATAACATAATAAATAAT--A-AAAAA--GTT-AAATCAGATA-TTTA-TAAGT-TATAATTAA
66 TAATAATATAATAAATAATAAACAAAAATTTTTCAAATCAGATATTTTATTAAATCTA-AA-TAA
* * *
169085 ATTTATTT-AAAGTCAAGTTATTTATTTAGACTAGATTATTCATTCGACTTACTCAATTGATCTT
129 ATTT-TTTAAAAGTCAA-TTATTTGTTTAG----G-TTA--GATT--A-TT--T-AATTGACCTT
** *** * * * * * * * *
169149 ATATTATCCAAGCTTTGGATACGAT-TTTGTTG-A-TTGAAAATAGCTTGAATTATTATTTAATA
179 ATATGCTTTGAGCATTGGATAAGATCTAT-CTGAATTTGAAACT-TCTCGAATAATTATTTAATA
* *
169211 ATAAAAAAATATTTTTAAAATTAATTAAAAATTTAAAAGTATTAATAAAATGATATTTTAATAAT
242 ATAAAAAAATATTTTTAAAATTAATTAAAAAATTAAAAGTATTAATAAAATAATATTTTAATAAT
* * * *** *
169276 ATAATGAATAATAAAAAAGTTTTTAAGTTGGATATTTTATAAATTATAATTAAAATTATTTAAAA
307 AAAATAAATAATAAAAAAGTTTTCAAGTAAAAAATTTTATAAATTATAATTAAAATTATTTAAAA
* ** *
169341 GTCAAGTTATTTGTTAGGTTAAATTATTGGCTCGACTTACTCAACTTATCTTATATGGTTTGAGT
372 ATCAAGTTATTTGTTAGGTTAAATTATTCACTCGACTTACTCAACTAATCTTATATGG-TTGAGT
* ** ** *
169406 ATTGGATAAGATTTTTATGGAGTCGAAATGGTTTAAATCACTATTTAAT
436 ATTGGATAAAATTTTTATAAAGTCGAAACAGCTTAAATCACTATTTAAT
* * * *
169455 AATAAAAGTAATGTTTTTATTTGAATTTAATTATAAAAATTATAAATATTAATAAATTAATATTT
1 AATAAAAGTAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTAATAAAATAATATTT
* * * * *
169520 TAGTGATGTAATGAATAATAAACAAAAGTTTTTCAAATCAGATATTTTA-TAAAT-TATAATAAA
66 TAATAATATAATAAATAATAAACAAAAATTTTTCAAATCAGATATTTTATTAAATCTA-AATAAA
169583 TTTCTTTAAAAGTCAATTATTTGTTTAGGTTAGATTATTTAATTGACCTTATATGCTTTGAGCAT
130 TTT-TTTAAAAGTCAATTATTTGTTTAGGTTAGATTATTTAATTGACCTTATATGCTTTGAGCAT
169648 TGGATAAGATCTATCTGAATTTGAAACTTCTCGAATAATTATTTAATAATAAAAATAATATTTTT
194 TGGATAAGATCTATCTGAATTTGAAACTTCTCGAATAATTATTTAATAATAAAAA-AATATTTTT
169713 ATTTAAATTTAATTATAAAAATTATAAA-TATTAATAAAATAATATTTTAATAATAAAATAAATA
258 A---AAA-TTAATTA-AAAAATTA-AAAGTATTAATAAAATAATATTTTAATAATAAAATAAATA
* * *
169777 ATAAAAAAAGTTTTCAAGTAAAAAATTTTGTAAGTTATAATTAAATTTATTTAAAAATCAA-TTA
317 AT-AAAAAAGTTTTCAAGTAAAAAATTTTATAAATTATAATTAAAATTATTTAAAAATCAAGTTA
* * * *
169841 TTTATTTAGGTTAGATTATTCACTTGACTTACTCAACTAA-CTTTATATGG-TGAGTGTTGGATA
381 TTT-GTTAGGTTAAATTATTCACTCGACTTACTCAACTAATC-TTATATGGTTGAGTATTGGATA
* * *
169904 AAATTTTTATAAATTTGAAACAGCTTAAATCATTATTTAAT
444 AAATTTTTATAAAGTCGAAACAGCTTAAATCACTATTTAAT
* *
169945 GA-AAAA-TAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTGATAAAATAATATTT
1 AATAAAAGTAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTAATAAAATAATATTT
*
170008 TAATAATATAATAAAT-AT-TACAAAAATTTT
66 TAATAATATAATAAATAATAAACAAAAATTTT
170038 AAATTAAATT
Statistics
Matches: 491, Mismatches: 69, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
484 29 0.06
485 28 0.06
486 27 0.05
487 4 0.01
488 65 0.13
489 14 0.03
490 73 0.15
491 98 0.20
492 93 0.19
493 2 0.00
494 4 0.01
496 2 0.00
497 31 0.06
498 21 0.04
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (484 bp):
AATAAAAGTAATATTTTTATTTAAATTTAATTATAAAAATTAAAAATATTAATAAAATAATATTT
TAATAATATAATAAATAATAAACAAAAATTTTTCAAATCAGATATTTTATTAAATCTAAATAAAT
TTTTTAAAAGTCAATTATTTGTTTAGGTTAGATTATTTAATTGACCTTATATGCTTTGAGCATTG
GATAAGATCTATCTGAATTTGAAACTTCTCGAATAATTATTTAATAATAAAAAAATATTTTTAAA
ATTAATTAAAAAATTAAAAGTATTAATAAAATAATATTTTAATAATAAAATAAATAATAAAAAAG
TTTTCAAGTAAAAAATTTTATAAATTATAATTAAAATTATTTAAAAATCAAGTTATTTGTTAGGT
TAAATTATTCACTCGACTTACTCAACTAATCTTATATGGTTGAGTATTGGATAAAATTTTTATAA
AGTCGAAACAGCTTAAATCACTATTTAAT
Found at i:172607 original size:26 final size:25
Alignment explanation
Indices: 172567--172618 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
172557 AAGAAGCTTG
172567 AGTTCGGTTTAAAATTCAAGACTTTA
1 AGTTCGGTTTAAAATTCAAGA-TTTA
* *
172593 AGTTTGGTTTGAAATTCAAGATTTA
1 AGTTCGGTTTAAAATTCAAGATTTA
172618 A
1 A
172619 CATTAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (25 bp):
AGTTCGGTTTAAAATTCAAGATTTA
Found at i:177630 original size:2 final size:2
Alignment explanation
Indices: 177625--177673 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
177615 AAAATTATTT
*
177625 TA TA TA TA TA TA TA TA TA TGA -A GTT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA
177668 TA TA TA
1 TA TA TA
177674 GGGGAGAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:178111 original size:2 final size:2
Alignment explanation
Indices: 178104--178162 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
178094 GCAATTCACT
178104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
178146 TA TA -A GA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
178163 CTTATGATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:178214 original size:18 final size:19
Alignment explanation
Indices: 178178--178216 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
178168 GATTTTTTTA
178178 TATTTATATAATACGTTAAT
1 TATTTATATAATAC-TTAAT
*
178198 TATTTATATTATA-TTAAT
1 TATTTATATAATACTTAAT
178216 T
1 T
178217 TTATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TATTTATATAATACTTAAT
Found at i:179182 original size:17 final size:18
Alignment explanation
Indices: 179150--179183 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
179140 ATACGAACTC
*
179150 ATATCTTTTAGATAAATT
1 ATATATTTTAGATAAATT
179168 ATATATTTT-GATAAAT
1 ATATATTTTAGATAAAT
179184 AAAATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATATTTTAGATAAATT
Found at i:179997 original size:20 final size:21
Alignment explanation
Indices: 179959--179999 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
179949 TCGTAGTTGG
*
179959 TAAATATTTATTTTATTTAAA
1 TAAATATTTATTTCATTTAAA
*
179980 TAAATA-TTATTTCGTTTAAA
1 TAAATATTTATTTCATTTAAA
180000 CACCTGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAAATATTTATTTCATTTAAA
Found at i:180710 original size:2 final size:2
Alignment explanation
Indices: 180703--180731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
180693 TTTCTTTGCT
180703 TA 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 TA T
180732 TATGCCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:181434 original size:21 final size:23
Alignment explanation
Indices: 181402--181452 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
181392 AATTTTTAAT
*
181402 AATATA-AAATTATTA-TTGA-C
1 AATATATAAATTAATACTTGATC
*
181422 AATATATAAATTAATACTTTATC
1 AATATATAAATTAATACTTGATC
181445 AATATATA
1 AATATATA
181453 TATATACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 3 0.12
23 9 0.35
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (23 bp):
AATATATAAATTAATACTTGATC
Found at i:181993 original size:33 final size:33
Alignment explanation
Indices: 181931--181995 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
181921 TAGCCAAACT
**
181931 TGTATCGATACACAAAGTATGTATCCGATACAA
1 TGTATCGATACACAAAAAATGTATCCGATACAA
181964 TGTATCGATACACAAAAAATTGTAT-CGATACA
1 TGTATCGATACACAAAAAA-TGTATCCGATACA
181996 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATGTATCCGATACAA
Found at i:184225 original size:21 final size:21
Alignment explanation
Indices: 184192--184241 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
184182 TTGCAAGTTG
*
184192 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
184214 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
184235 AAATAAA
1 AAATAAA
184242 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:188164 original size:13 final size:13
Alignment explanation
Indices: 188146--188180 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
188136 TTTTCTTTGT
188146 ATCGATACAATGG
1 ATCGATACAATGG
* *
188159 ATCGATACACTGT
1 ATCGATACAATGG
188172 ATCGATACA
1 ATCGATACA
188181 GAGGGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (13 bp):
ATCGATACAATGG
Found at i:189974 original size:19 final size:19
Alignment explanation
Indices: 189950--189997 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
189940 AGAGAAAATA
189950 GATATGCAA-ATAAATTTTT
1 GATATG-AATATAAATTTTT
189969 GATATGAATTATAAATTTTT
1 GATATGAA-TATAAATTTTT
189989 GATATGAAT
1 GATATGAAT
189998 TACTTGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 18 0.67
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (19 bp):
GATATGAATATAAATTTTT
Found at i:189984 original size:20 final size:20
Alignment explanation
Indices: 189959--189999 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
189949 AGATATGCAA
189959 ATAAATTTTTGATATGAATT
1 ATAAATTTTTGATATGAATT
189979 ATAAATTTTTGATATGAATT
1 ATAAATTTTTGATATGAATT
189999 A
1 A
190000 CTTGATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
ATAAATTTTTGATATGAATT
Found at i:190774 original size:13 final size:13
Alignment explanation
Indices: 190756--190781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190746 TACACAAAGT
190756 ATGTATCGATACA
1 ATGTATCGATACA
190769 ATGTATCGATACA
1 ATGTATCGATACA
190782 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:190779 original size:32 final size:33
Alignment explanation
Indices: 190738--190801 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
190728 TAGCCAAACT
**
190738 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
190770 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
190802 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:192051 original size:4 final size:4
Alignment explanation
Indices: 192042--192068 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
192032 ACCATTAGAT
192042 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
192069 GCAACGTAAT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:192306 original size:29 final size:29
Alignment explanation
Indices: 192252--192309 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
192242 TAAAAAATTT
* * *
192252 TCATTTTATTTTGATTTTGTTAAATTTTA
1 TCATTGTATTTTAATTTTATTAAATTTTA
*
192281 TCATTGTACTTTTAATTTTATTAATTTTT
1 TCATTGTA-TTTTAATTTTATTAAATTTT
192310 TAATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (29 bp):
TCATTGTATTTTAATTTTATTAAATTTTA
Found at i:192856 original size:33 final size:31
Alignment explanation
Indices: 192786--192848 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
192776 TAATTATGTT
* * *
192786 TAATATATTTTATATAAATTTTAATTTTTAA
1 TAATTTATATTATATAAATTTTAATATTTAA
192817 TAATTTATATTATATAAATTATTAAATATTTA
1 TAATTTATATTATATAAATT-TT-AATATTTA
192849 TGTATTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 18 0.67
32 2 0.07
33 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TAATTTATATTATATAAATTTTAATATTTAA
Found at i:194037 original size:24 final size:24
Alignment explanation
Indices: 194010--194056 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
194000 ATAATTTTAC
194010 CATA-TAAAGAATAAATATATATAT
1 CATATTAAA-AATAAATATATATAT
*
194034 CATATTTAAAATAAATATATATA
1 CATATTAAAAATAAATATATATA
194057 ATATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
CATATTAAAAATAAATATATATAT
Found at i:197436 original size:24 final size:23
Alignment explanation
Indices: 197409--197470 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
197399 AATAAACAAA
*
197409 AATATTTATATCTTTTTAAAATTT
1 AATATTTAT-TCTTTTTAAAATAT
*
197433 AATATGTATGTCTTTTTTAAAATAT
1 AATATTTAT-TC-TTTTTAAAATAT
197458 -ATATTTATTCTTT
1 AATATTTATTCTTT
197471 GAAAACTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 2 0.06
24 17 0.52
25 11 0.33
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (23 bp):
AATATTTATTCTTTTTAAAATAT
Found at i:197803 original size:19 final size:19
Alignment explanation
Indices: 197778--197825 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
197768 TATTTTTTAA
*
197778 AATAAATTATT-ATATATT
1 AATAAATTATTAAAATATT
197796 ATATAAATT-TTAAAATATT
1 A-ATAAATTATTAAAATATT
*
197815 AATAACTTATT
1 AATAAATTATT
197826 TCATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAAATTATTAAAATATT
Found at i:198061 original size:33 final size:32
Alignment explanation
Indices: 197987--198071 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
197977 TATAAATCGA
* * *
197987 ATATAATATAAATATATTAATATTTTAAAATCT
1 ATATAATATAAAT-TATTAACATATCAAAATCT
* *
198020 ATATAATATAAATTATTAACATATCAAATTTT
1 ATATAATATAAATTATTAACATATCAAAATCT
198052 ATATAAATATAAAATTATTA
1 ATAT-AATAT-AAATTATTA
198072 CGAAATTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 18 0.40
33 18 0.40
34 9 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTATTAACATATCAAAATCT
Found at i:198753 original size:41 final size:42
Alignment explanation
Indices: 198699--198777 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
198689 TTGTTTCTTC
*
198699 TTAATTAAAATAATAAT-ATTTAAATATGATATTTAATTTAA
1 TTAATTAAAATAATAATAATTAAAATATGATATTTAATTTAA
* * * *
198740 TTAATTCATATAATTATAATTAAAATATTATATTTAAT
1 TTAATTAAAATAATAATAATTAAAATATGATATTTAAT
198778 AAATTTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (42 bp):
TTAATTAAAATAATAATAATTAAAATATGATATTTAATTTAA
Found at i:198782 original size:22 final size:22
Alignment explanation
Indices: 198757--198800 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
198747 ATATAATTAT
*
198757 AATTAAAATATT-ATATTTAATA
1 AATTAAAAT-TTAAAATTTAATA
*
198779 AATTTAAATTTAAAATTTAATA
1 AATTAAAATTTAAAATTTAATA
198801 TTAAATTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAAATTTAAAATTTAATA
Found at i:200656 original size:2 final size:2
Alignment explanation
Indices: 200649--200681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
200639 GCAAGTAGCA
200649 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
200682 CGAAGGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.