Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold270
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: 409424
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 3 of 4
Found at i:216886 original size:22 final size:25
Alignment explanation
Indices: 216854--216899 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
216844 TACGTATTAA
216854 ATTTTTAATTT-AT-TAAATAATAT
1 ATTTTTAATTTCATATAAATAATAT
216877 ATTTTT-ATTTCATATAAATAATA
1 ATTTTTAATTTCATATAAATAATA
216900 AATTAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTTAATTTCATATAAATAATAT
Found at i:217146 original size:20 final size:21
Alignment explanation
Indices: 217110--217156 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
217100 TGATTATTGT
* *
217110 AAATATTTATATAAAAATAAA
1 AAATATTAATATAAAAAGAAA
217131 AAATATTAAT-TAAAAAGAAA
1 AAATATTAATATAAAAAGAAA
*
217151 TAATAT
1 AAATAT
217157 GAGAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATATTAATATAAAAAGAAA
Found at i:217322 original size:16 final size:16
Alignment explanation
Indices: 217298--217329 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
217288 ATTTTATTAC
*
217298 TATTTATATTATAAAA
1 TATTGATATTATAAAA
217314 TATTGATATTATAAAA
1 TATTGATATTATAAAA
217330 AACTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTGATATTATAAAA
Found at i:217380 original size:35 final size:34
Alignment explanation
Indices: 217302--217386 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 34
217292 TATTACTATT
*
217302 TATATTATAAAATATTGATATTATAAAAAACTTA
1 TATATTATAAAATATTGATACTATAAAAAACTTA
* *
217336 TTTATTTATAAAAT-TTAGATACTA-AATATAAAGTTA
1 TATA-TTATAAAATATT-GATACTATAA-A-AAACTTA
217372 TATATTATATAAATA
1 TATATTATA-AAATA
217387 ACTAAAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
34 7 0.17
35 21 0.51
36 13 0.32
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (34 bp):
TATATTATAAAATATTGATACTATAAAAAACTTA
Found at i:217912 original size:24 final size:23
Alignment explanation
Indices: 217858--217914 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
217848 ATAGGTAAAA
*
217858 TTTTAAAAAATTAATTAAAAATT
1 TTTTAAAAAATTAAATAAAAATT
*
217881 TTCATAAAAAA-TAAATAAGATAATT
1 TT-TTAAAAAATTAAATAA-A-AATT
217906 TTTTAAAAA
1 TTTTAAAAA
217915 TTTTATATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 8 0.29
24 14 0.50
25 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTTAAAAAATTAAATAAAAATT
Found at i:218062 original size:4 final size:4
Alignment explanation
Indices: 218053--218084 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
218043 ATTTGTTTTA
218053 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
218085 CATTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:223318 original size:18 final size:20
Alignment explanation
Indices: 223295--223344 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 20
223285 CGATACATTA
223295 TATCGATACATGCTC-A-TG
1 TATCGATACATGCTCAATTG
*
223313 TATCGATACATACTCAATTG
1 TATCGATACATGCTCAATTG
223333 TATCGATACATG
1 TATCGATACATG
223345 AGATTGGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 13 0.46
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (20 bp):
TATCGATACATGCTCAATTG
Found at i:231416 original size:13 final size:13
Alignment explanation
Indices: 231398--231422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231388 CATTACGCTT
231398 TGTATCGATACAA
1 TGTATCGATACAA
231411 TGTATCGATACA
1 TGTATCGATACA
231423 TACTCAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:231436 original size:20 final size:20
Alignment explanation
Indices: 231411--231509 Score: 73
Period size: 20 Copynumber: 5.7 Consensus size: 20
231401 ATCGATACAA
231411 TGTATCGATACATACTCAAT
1 TGTATCGATACATACTCAAT
231431 TGTATC--T--ATA--C-AT
1 TGTATCGATACATACTCAAT
*
231444 TATATCGATACATACTCAAT
1 TGTATCGATACATACTCAAT
231464 TGTATC--T--ATA--C-AT
1 TGTATCGATACATACTCAAT
*
231477 TATATCGATACATACTCAAT
1 TGTATCGATACATACTCAAT
*
231497 TGTATCTATACAT
1 TGTATCGATACAT
231510 GAAACTGGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 28
0.65 0.05 0.30
Matches are distributed among these distances:
13 14 0.23
14 2 0.03
15 2 0.03
16 6 0.10
17 6 0.10
18 2 0.03
19 2 0.03
20 26 0.43
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTCAAT
Found at i:231509 original size:33 final size:33
Alignment explanation
Indices: 231380--231509 Score: 199
Period size: 33 Copynumber: 3.9 Consensus size: 33
231370 CATCTAGATG
* * * * *
231380 TATCGATACATTACGC-TTTGTATCGATACAATG
1 TATCGATACA-TACTCAATTGTATCTATACATTA
231413 TATCGATACATACTCAATTGTATCTATACATTA
1 TATCGATACATACTCAATTGTATCTATACATTA
231446 TATCGATACATACTCAATTGTATCTATACATTA
1 TATCGATACATACTCAATTGTATCTATACATTA
231479 TATCGATACATACTCAATTGTATCTATACAT
1 TATCGATACATACTCAATTGTATCTATACAT
231510 GAAACTGGCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 4 0.04
33 87 0.96
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (33 bp):
TATCGATACATACTCAATTGTATCTATACATTA
Found at i:232972 original size:13 final size:13
Alignment explanation
Indices: 232954--232980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
232944 TTTATCGAAT
232954 TAAATAAATAATC
1 TAAATAAATAATC
232967 TAAATAAATAATC
1 TAAATAAATAATC
232980 T
1 T
232981 GATTCATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAAATAATC
Found at i:233007 original size:16 final size:18
Alignment explanation
Indices: 232988--233024 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
232978 TCTGATTCAT
232988 AAAAT-TTTT-TATTAAA
1 AAAATATTTTCTATTAAA
*
233004 AAAATATTTTCTTTTAAA
1 AAAATATTTTCTATTAAA
233022 AAA
1 AAA
233025 TATACAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 9 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATATTTTCTATTAAA
Found at i:233267 original size:11 final size:11
Alignment explanation
Indices: 233251--233393 Score: 75
Period size: 11 Copynumber: 13.3 Consensus size: 11
233241 GAAAAAATTA
233251 AAATATAATAT
1 AAATATAATAT
233262 AAATATAAT-T
1 AAATATAATAT
* *
233272 TAATATATTAT
1 AAATATAATAT
*
233283 -AATAAAATAT
1 AAATATAATAT
*
233293 AAATATATTA-
1 AAATATAATAT
*
233303 AAAT-TTATAT
1 AAATATAATAT
*
233313 AATATATATTAT
1 AA-ATATAATAT
*
233325 TAATAT-AT-T
1 AAATATAATAT
* *
233334 AAATTTTATAT
1 AAATATAATAT
233345 AAATAT-ATAAT
1 AAATATAAT-AT
* *
233356 AAATTAAAACAT
1 AAA-TATAATAT
* *
233368 AATTATAATAAA
1 AAATATAAT-AT
*
233380 AAATATAATGT
1 AAATATAATAT
233391 AAA
1 AAA
233394 CTAATTAAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
9 8 0.08
10 27 0.28
11 41 0.42
12 20 0.21
13 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
AAATATAATAT
Found at i:233297 original size:21 final size:21
Alignment explanation
Indices: 233251--233375 Score: 77
Period size: 21 Copynumber: 6.1 Consensus size: 21
233241 GAAAAAATTA
*
233251 AAATATAATATAAATATAAT-T
1 AAATATATTAT-AATATAATAT
* *
233272 TAATATATTATAATAAAATAT
1 AAATATATTATAATATAATAT
* *
233293 AAATATATTAAAAT-TTATAT
1 AAATATATTATAATATAATAT
233313 AATATATATTATTAATAT-AT-T
1 AA-ATATATTA-TAATATAATAT
233334 AAAT-T-TTAT-ATA-AATAT
1 AAATATATTATAATATAATAT
* * *
233351 ATAATAAATTAAAACATAATTAT
1 A-AATATATTATAATATAA-TAT
233374 AA
1 AA
233376 TAAAAAATAT
Statistics
Matches: 81, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
16 5 0.06
17 3 0.04
18 6 0.07
19 1 0.01
20 18 0.22
21 35 0.43
22 8 0.10
23 5 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATATTATAATATAATAT
Found at i:233297 original size:42 final size:43
Alignment explanation
Indices: 233252--233351 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 43
233242 AAAAAATTAA
*
233252 AATATAATATAAATATAATTTAATATAT-TATAATAAAATA-TA
1 AATATAATATAAATATAATATAATATATAT-TAATAAAATATTA
* * * *
233294 AATATATTA-AAAT-TTATATAATATATATTATTAATATATTA
1 AATATAATATAAATATAATATAATATATATTAATAAAATATTA
* *
233335 AATTTTATATAAATATA
1 AATATAATATAAATATA
233352 TAATAAATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
40 19 0.42
41 13 0.29
42 12 0.27
43 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (43 bp):
AATATAATATAAATATAATATAATATATATTAATAAAATATTA
Found at i:233342 original size:18 final size:18
Alignment explanation
Indices: 233253--233352 Score: 61
Period size: 20 Copynumber: 5.6 Consensus size: 18
233243 AAAAATTAAA
*
233253 ATATAATATAAATATAATTT
1 ATATAATAT-ATTA-AATTT
* * *
233273 AATATATTATAATAAA-AT
1 -ATATAATATATTAAATTT
233291 ATA-AATATATTAAAATTT
1 ATATAATATATT-AAATTT
233309 ATATAATATA-T--A-TT
1 ATATAATATATTAAATTT
233323 AT-TAATATATTAAATTTT
1 ATATAATATATTAAA-TTT
233341 ATATAAATATAT
1 ATAT-AATATAT
233353 AATAAATTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
13 7 0.11
14 5 0.08
15 1 0.02
16 7 0.11
17 6 0.09
18 10 0.16
19 9 0.14
20 11 0.17
21 8 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATATATTAAATTT
Found at i:233345 original size:52 final size:52
Alignment explanation
Indices: 233224--233352 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
233214 GGTAAACATA
* * *
233224 ATATTATTATAAAATACGAAA-AAATTAAAATATAATATAAATATAATTTAAT
1 ATATTATAATAAAATA-TAAATATATTAAAATATAATATAAATATAATTTAAT
* *
233276 ATATTATAATAAAATATAAATATATTAAAAT-TTATATAATATATATTATTAAT
1 ATATTATAATAAAATATAAATATATTAAAATATAATATAA-ATATAAT-TTAAT
***
233329 ATATTA-AATTTTATATAAATATAT
1 ATATTATAATAAAATATAAATATAT
233353 AATAAATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
51 10 0.15
52 45 0.68
53 11 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (52 bp):
ATATTATAATAAAATATAAATATATTAAAATATAATATAAATATAATTTAAT
Found at i:233358 original size:22 final size:20
Alignment explanation
Indices: 233308--233360 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
233298 TATTAAAATT
* *
233308 TATATAATATATATTATTAA
1 TATATAATAAATTTTATTAA
233328 TATAT--TAAATTTTATATAAA
1 TATATAATAAATTTTAT-T-AA
233348 TATATAATAAATT
1 TATATAATAAATT
233361 AAAACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.30
19 1 0.04
20 12 0.44
22 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATAATAAATTTTATTAA
Found at i:234026 original size:15 final size:15
Alignment explanation
Indices: 234008--234088 Score: 51
Period size: 18 Copynumber: 5.1 Consensus size: 15
233998 TATATATAAA
234008 ATATAAATTATTAAT
1 ATATAAATTATTAAT
* *
234023 ATATCAAAATTTATAAAA
1 ATAT--AAA-TTATTAAT
*
234041 ATAAAAATATATTAA-
1 ATATAAAT-TATTAAT
234056 ATAT-AATTA-TAAT
1 ATATAAATTATTAAT
234069 ATTATAATATCTATTAAT
1 A-TATAA-AT-TATTAAT
234087 AT
1 AT
234089 GATATAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 6 0.12
15 9 0.18
16 10 0.20
17 6 0.12
18 14 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAAATTATTAAT
Found at i:234103 original size:8 final size:8
Alignment explanation
Indices: 233999--234105 Score: 56
Period size: 8 Copynumber: 12.2 Consensus size: 8
233989 TTCAATATTT
233999 ATATATAA
1 ATATATAA
234007 A-ATATAA
1 ATATATAA
*
234014 AT-TATTA
1 ATATATAA
234021 ATATATCAAA
1 ATATAT--AA
*
234031 ATTTATAA
1 ATATATAA
* *
234039 AAATAAAA
1 ATATATAA
234047 ATATATTAA
1 ATATA-TAA
234056 ATATAATTATA
1 ATAT-A-TA-A
234067 ATATTATAA
1 ATA-TATAA
*
234076 TATCTATTAA
1 -ATATA-TAA
234086 TATGATATAA
1 -AT-ATATAA
234096 ATATATAA
1 ATATATAA
234104 AT
1 AT
234106 TATCGAATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
7 13 0.17
8 23 0.29
9 11 0.14
10 23 0.29
11 7 0.09
12 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (8 bp):
ATATATAA
Found at i:234838 original size:11 final size:12
Alignment explanation
Indices: 234822--234876 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
234812 ATATGATTAA
234822 ATAAT-ATAAAT
1 ATAATAATAAAT
234833 ATAAT-ATAAAT
1 ATAATAATAAAT
*
234844 AAAATAATTAAAAT
1 ATAATAA-T-AAAT
234858 ATAATAATAAA-
1 ATAATAATAAAT
234869 A-AATAATA
1 ATAATAATA
234877 TTGAACATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 7 0.18
11 16 0.41
12 4 0.10
13 2 0.05
14 10 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:234844 original size:20 final size:20
Alignment explanation
Indices: 234819--234877 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
234809 ATCATATGAT
234819 TAAATAATATAAATATAATA
1 TAAATAATATAAATATAATA
* * *
234839 TAAATAAAATAATTAAAATA
1 TAAATAATATAAATATAATA
*
234859 T-AATAATA-AAAAATAATA
1 TAAATAATATAAATATAATA
234877 T
1 T
234878 TGAACATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 18 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATAATATAAATATAATA
Found at i:234848 original size:25 final size:25
Alignment explanation
Indices: 234820--234877 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
234810 TCATATGATT
234820 AAATAATAT-AAATATAAT-ATAAATA
1 AAATAATATAAAATATAATAAT-AA-A
234845 AAATAAT-TAAAATATAATAATAAA
1 AAATAATATAAAATATAATAATAAA
234869 AAATAATAT
1 AAATAATAT
234878 TGAACATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.30
25 19 0.63
26 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAATATAAAATATAATAATAAA
Found at i:234870 original size:14 final size:14
Alignment explanation
Indices: 234821--234876 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
234811 CATATGATTA
*
234821 AATAATATAAATAT
1 AATAATAAAAATAT
*
234835 AAT-AT--AAATAA
1 AATAATAAAAATAT
*
234846 AATAATTAAAATAT
1 AATAATAAAAATAT
234860 AATAATAAAAA-AT
1 AATAATAAAAATAT
234873 AATA
1 AATA
234877 TTGAACATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 8 0.22
12 2 0.06
13 8 0.22
14 18 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAAAAATAT
Found at i:236780 original size:2 final size:2
Alignment explanation
Indices: 236773--236815 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
236763 GGGTATATTT
236773 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
236815 T
1 T
236816 TACTTCAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:237024 original size:31 final size:32
Alignment explanation
Indices: 236967--237030 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
236957 ATAGATTATT
* * *
236967 ATTTATTTAATAAAAAATAATTTTTTATTTAA
1 ATTTAATTAATAAAAAATAATATTTTAATTAA
236999 ATTTAATT-ATAAAAATATAA-ATTTTAATTAA
1 ATTTAATTAATAAAAA-ATAATATTTTAATTAA
237030 A
1 A
237031 AATATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTTAATTAATAAAAAATAATATTTTAATTAA
Found at i:237411 original size:21 final size:21
Alignment explanation
Indices: 237385--237424 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
237375 AATGTTAGAA
*
237385 TTTTATATTCGTGTTTTTATT
1 TTTTATATTAGTGTTTTTATT
*
237406 TTTTATATTAGTTTTTTTA
1 TTTTATATTAGTGTTTTTA
237425 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTATATTAGTGTTTTTATT
Found at i:237430 original size:21 final size:21
Alignment explanation
Indices: 237383--237430 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
237373 AAAATGTTAG
*
237383 AATTTTATATTCGTGTTTTTA
1 AATTTTATATTAGTGTTTTTA
** *
237404 TTTTTTATATTAGTTTTTTTA
1 AATTTTATATTAGTGTTTTTA
237425 AATTTT
1 AATTTT
237431 TAAATATAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
AATTTTATATTAGTGTTTTTA
Found at i:238040 original size:21 final size:22
Alignment explanation
Indices: 238016--238073 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
238006 ATTAATTTAA
* * *
238016 TTAAAAATTTTATTT-TATTAT
1 TTAAAAATTATATTTAAAATAT
238037 TT-AAAATTATATTTAAAATAT
1 TTAAAAATTATATTTAAAATAT
* *
238058 TTAAAAAATATTTTTA
1 TTAAAAATTATATTTA
238074 TATTAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.37
21 8 0.27
22 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATTATATTTAAAATAT
Found at i:238663 original size:28 final size:27
Alignment explanation
Indices: 238631--238695 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
238621 AAATAAATTC
238631 TAAAAAT-TCTAAAAAAAATAAAAAAAA
1 TAAAAATATCTAAAAAAAA-AAAAAAAA
** *
238658 TAAAAATATCTAAAAGTAAAAATAAAA
1 TAAAAATATCTAAAAAAAAAAAAAAAA
238685 TAAAAA-ATCTA
1 TAAAAATATCTA
238696 GTTTTACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.15
27 20 0.59
28 9 0.26
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (27 bp):
TAAAAATATCTAAAAAAAAAAAAAAAA
Found at i:238904 original size:17 final size:17
Alignment explanation
Indices: 238884--238930 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
238874 TTTTTAAAAA
238884 AATATTAAATTTATATT
1 AATATTAAATTTATATT
* *
238901 AATATT-AATATATTTT
1 AATATTAAATTTATATT
*
238917 TATAATTAAATTTA
1 AAT-ATTAAATTTA
238931 AATAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTAAATTTATATT
Found at i:238924 original size:23 final size:22
Alignment explanation
Indices: 238893--238956 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
238883 AAATATTAAA
238893 TTTATATT-AATATT-AATATATT
1 TTTATATTAAAT-TTAAATA-ATT
238915 TTTATAATTAAATTTAAATAATT
1 TTTAT-ATTAAATTTAAATAATT
238938 TTTATATTAAA--TAAATAAT
1 TTTATATTAAATTTAAATAAT
238957 AATTCAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.21
22 11 0.28
23 13 0.33
24 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATATTAAATTTAAATAATT
Found at i:239310 original size:10 final size:10
Alignment explanation
Indices: 239297--239419 Score: 62
Period size: 11 Copynumber: 12.3 Consensus size: 10
239287 ATTAATATAA
239297 ATATATAAAT
1 ATATATAAAT
239307 ATAT-TAAA-
1 ATATATAAAT
*
239315 ATTTATATAAT
1 ATATATA-AAT
* *
239326 ATAAATTAAT
1 ATATATAAAT
239336 AATATATAAAATT
1 -ATATAT-AAA-T
*
239349 TTATATAAAT
1 ATATATAAAT
*
239359 TTATAT-AAT
1 ATATATAAAT
* *
239368 GT-TTTAAAT
1 ATATATAAAT
239377 ATA-ATTATAAT
1 ATATA-TA-AAT
239388 ATATA-AAAT
1 ATATATAAAT
*
239397 -TATATAAAC
1 ATATATAAAT
239406 ATAATATAAAT
1 AT-ATATAAAT
239417 ATA
1 ATA
239420 CGAATTTTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
8 9 0.10
9 20 0.23
10 21 0.24
11 27 0.31
12 8 0.09
13 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (10 bp):
ATATATAAAT
Found at i:239343 original size:22 final size:21
Alignment explanation
Indices: 239279--239347 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
239269 TTTTTTTAAG
* *
239279 ATAAAAAAATTAATATAAATAT
1 ATAAATAAATTAATA-ATATAT
* *
239301 ATAAATATATTAA-AATTTAT
1 ATAAATAAATTAATAATATAT
239321 ATAATATAAATTAATAATATAT
1 ATAA-ATAAATTAATAATATAT
239343 A-AAAT
1 ATAAAT
239348 TTTATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.26
21 11 0.28
22 18 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATAAATTAATAATATAT
Found at i:239352 original size:32 final size:33
Alignment explanation
Indices: 239289--239356 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
239279 ATAAAAAAAT
239289 TAATATAAATATATAAATATATTAAAATTTATA
1 TAATATAAATATATAAATATATTAAAATTTATA
239322 TAATATAAAT-TA-ATAATATA-TAAAATTTTATA
1 TAATATAAATATATA-AATATATTAAAA-TTTATA
239354 TAA
1 TAA
239357 ATTTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
31 6 0.18
32 17 0.52
33 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TAATATAAATATATAAATATATTAAAATTTATA
Found at i:239625 original size:22 final size:22
Alignment explanation
Indices: 239587--239631 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
239577 TTAAAATTTT
*
239587 ATTTTTAATTAATATTTATATA
1 ATTTTTAATTAATATTTAAATA
239609 ATTTTATAATTAA-ATTTAAATA
1 ATTTT-TAATTAATATTTAAATA
239631 A
1 A
239632 AAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTAATTAATATTTAAATA
Found at i:241136 original size:15 final size:15
Alignment explanation
Indices: 241089--241138 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
241079 TATTTTATTT
*
241089 AAAT-TTAATTAT-A
1 AAATATTAAATATAA
* *
241102 AAATAATAAATATAT
1 AAATATTAAATATAA
*
241117 TAATATTAAATATAA
1 AAATATTAAATATAA
241132 AAATATT
1 AAATATT
241139 TTTTTATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 18 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATTAAATATAA
Found at i:241668 original size:24 final size:26
Alignment explanation
Indices: 241604--241658 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
241594 ACATATGTCG
*
241604 TAATT-TTAAATATAATAAAA-TTATA
1 TAATTATTAAA-ATATTAAAATTTATA
241629 TAATTATTAAAATATTAAAATTTATA
1 TAATTATTAAAATATTAAAATTTATA
241655 TAAT
1 TAAT
241659 ATATAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTATTAAAATATTAAAATTTATA
Found at i:241673 original size:24 final size:26
Alignment explanation
Indices: 241619--241673 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
241609 TTAAATATAA
*
241619 TAAAATTATATAATTATTAAAATATT
1 TAAATTTATATAATTATTAAAATATT
* *
241645 AAAATTTATATAA-TA-TATAATATT
1 TAAATTTATATAATTATTAAAATATT
241669 TAAAT
1 TAAAT
241674 ATAATTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 12 0.48
25 2 0.08
26 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAATTTATATAATTATTAAAATATT
Found at i:241686 original size:24 final size:23
Alignment explanation
Indices: 241626--241693 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
241616 TAATAAAATT
*
241626 ATATAATTAT-TAAAATATTAAA
1 ATATAATTATATATAATATTAAA
* * *
241648 ATTTATATAATATATAATATTTAA
1 ATATA-ATTATATATAATATTAAA
241672 ATATAATTATGATAT-ATATTAA
1 ATATAATTAT-ATATAATATTAA
241694 TAACATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 4 0.11
23 14 0.39
24 18 0.50
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATAATTATATATAATATTAAA
Found at i:245201 original size:2 final size:2
Alignment explanation
Indices: 245179--245215 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
245169 ATTTTTAATG
*
245179 AT AT AT AC AT AT A- AT AT -T 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 AT AT A
245216 AAGTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:245641 original size:2 final size:2
Alignment explanation
Indices: 245634--245667 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
245624 TCAAACCACC
245634 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
245668 TGGTCACTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246152 original size:12 final size:11
Alignment explanation
Indices: 246135--246175 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
246125 AAAAATTTTA
246135 AAATTTAATTAT
1 AAATTTAATT-T
246147 AAATTTAAATTT
1 AAATTT-AATTT
246159 AAATTT-ATTT
1 AAATTTAATTT
246169 -AATTTAA
1 AAATTTAA
246176 AAAGTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 5 0.19
12 13 0.48
13 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:246253 original size:20 final size:19
Alignment explanation
Indices: 246206--246265 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
246196 AAAATTGTAA
*
246206 AATAATTTTAATTAATATT
1 AATAATTTTAATTAATAAT
* *
246225 TATATATTTTAATTATTAAAT
1 AATA-ATTTTAATTAAT-AAT
*
246246 AATAATTTAAATTAA-AAT
1 AATAATTTTAATTAATAAT
246264 AA
1 AA
246266 ATAAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 20 0.61
21 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTTAATTAATAAT
Found at i:246269 original size:22 final size:22
Alignment explanation
Indices: 246241--246285 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
246231 TTTTAATTAT
*
246241 TAAATAATAATTTAAATTAAAA
1 TAAATAAAAATTTAAATTAAAA
*
246263 TAAATAAAAATTTAAATTTAAA
1 TAAATAAAAATTTAAATTAAAA
246285 T
1 T
246286 TTAATTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATAAAAATTTAAATTAAAA
Found at i:246933 original size:22 final size:21
Alignment explanation
Indices: 246896--246938 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
246886 ACAAAGACAA
*
246896 AAAAATTAGAAAT-AAATTTT
1 AAAAATTAAAAATAAAATTTT
246916 AAAAATTAAATAAGTAAAATTTT
1 AAAAATTAAA-AA-TAAAATTTT
246939 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 1 0.05
23 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAAATAAAATTTT
Found at i:248824 original size:26 final size:25
Alignment explanation
Indices: 248795--248851 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
248785 TATAATATGA
* *
248795 ATTTATATAATATAAATTTTTTTATT
1 ATTTATATAATA-AAATTGTTTAATT
*
248821 ATTTGATATTATAAAATTGTTTAATT
1 ATTT-ATATAATAAAATTGTTTAATT
248847 ATTTA
1 ATTTA
248852 AAAATTGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 19 0.70
27 7 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTTATATAATAAAATTGTTTAATT
Found at i:249373 original size:21 final size:20
Alignment explanation
Indices: 249340--249379 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
249330 AAGTTTGAAT
* *
249340 TTTAATAATAAAATTAATTA
1 TTTAAGAATAAAATAAATTA
249360 TTTAAGAATAAAAATAAATT
1 TTTAAGAAT-AAAATAAATT
249380 TAAATTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TTTAAGAATAAAATAAATTA
Found at i:249420 original size:41 final size:42
Alignment explanation
Indices: 249371--249460 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
249361 TTAAGAATAA
** *
249371 AAATAAATTTAAATTTATCAAATATTAT-TTTTAAAATAATT
1 AAATAAATTTAAAAATATCAAATATCATCTTTTAAAATAATT
*
249412 AAATAAA-TTAAAAATATTAAATATCATCTTTTAAAATAATT
1 AAATAAATTTAAAAATATCAAATATCATCTTTTAAAATAATT
249453 AAATAAAT
1 AAATAAAT
249461 CAAAGATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 16 0.37
41 27 0.63
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (42 bp):
AAATAAATTTAAAAATATCAAATATCATCTTTTAAAATAATT
Found at i:250307 original size:13 final size:13
Alignment explanation
Indices: 250279--250315 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
250269 AGTTGTTAAG
250279 TTTAATTAA-A-T
1 TTTAATTAATATT
*
250290 TTTAATTATTATT
1 TTTAATTAATATT
250303 TTTAATTAATATT
1 TTTAATTAATATT
250316 AAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTAATATT
Found at i:251514 original size:24 final size:26
Alignment explanation
Indices: 251455--251516 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
251445 TATTTTCATT
*
251455 TAAATTTATTTATAAATATTAATAAAA
1 TAAATTT-TTAATAAATATTAATAAAA
*
251482 -AATAATTTTAATAAA-A-TAATAAAA
1 TAA-ATTTTTAATAAATATTAATAAAA
251506 TAAATTTTTAA
1 TAAATTTTTAA
251517 GTCTGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 15 0.50
25 3 0.10
26 9 0.30
27 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTTTTAATAAATATTAATAAAA
Found at i:251875 original size:2 final size:2
Alignment explanation
Indices: 251868--251903 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
251858 GCACATTTCA
251868 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
251904 TACCCGTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252131 original size:8 final size:8
Alignment explanation
Indices: 252111--252192 Score: 60
Period size: 8 Copynumber: 9.2 Consensus size: 8
252101 CGTAATTTTT
252111 TATTTA-A
1 TATTTATA
252118 TAATTTATA
1 T-ATTTATA
252127 TATTTATA
1 TATTTATA
252135 TTTTATTTATA
1 ---TATTTATA
252146 TATTTTATTA
1 TA-TTTA-TA
252156 TATTATAATTA
1 TATT-T-A-TA
252167 TATTTATGA
1 TATTTAT-A
252176 TATTT-TA
1 TATTTATA
252183 TATTTATA
1 TATTTATA
252191 TA
1 TA
252193 ATTTTTGATA
Statistics
Matches: 64, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
7 7 0.11
8 20 0.31
9 15 0.23
10 6 0.09
11 16 0.25
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:252136 original size:6 final size:6
Alignment explanation
Indices: 252125--252191 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
252115 TAATAATTTA
* *
252125 TATATT TATATT T-TATT TATATAT TTTA-T TATA-T TATAAT TATATT
1 TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT TATATT
252171 TATGA-- TAT-TT TATATT TATAT
1 TAT-ATT TATATT TATATT TATAT
252192 AATTTTTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
5 20 0.39
6 26 0.51
7 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:252140 original size:27 final size:27
Alignment explanation
Indices: 252108--252191 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 27
252098 TGACGTAATT
252108 TTTTATTTAATAATTTATATATTTATA
1 TTTTATTTAATAATTTATATATTTATA
*
252135 TTTTATTTATATATTTTAT-TATATTATAA
1 TTTTATTTA-ATAATTTATATAT-TTAT-A
*
252164 TTATATTT-ATGATATTT-TATATTTATA
1 TTTTATTTAAT-A-ATTTATATATTTATA
252191 T
1 T
252192 AATTTTTGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
27 16 0.33
28 18 0.38
29 14 0.29
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTATTTAATAATTTATATATTTATA
Found at i:252205 original size:27 final size:28
Alignment explanation
Indices: 252109--252206 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 28
252099 GACGTAATTT
252109 TTTATTTA-ATAATTTATATATTTATAT--
1 TTTATTTATAT-ATTT-TATATTTATATAA
*
252136 TTTATTTATATATTTTAT-TATATTATAA
1 TTTATTTATATATTTTATATTTA-TATAA
252164 TTATATTTATGATATTTTATATTTATATAA
1 TT-TATTTAT-ATATTTTATATTTATATAA
*
252194 TTT-TTGATATATT
1 TTTATTTATATATT
252207 AATAATTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.05
26 6 0.10
27 17 0.28
28 8 0.13
29 8 0.13
30 16 0.26
31 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATTTATATATTTTATATTTATATAA
Found at i:252211 original size:18 final size:17
Alignment explanation
Indices: 252103--252231 Score: 69
Period size: 16 Copynumber: 7.5 Consensus size: 17
252093 AATTGTGACG
252103 TAATTTTT-TATTTA-A
1 TAATTTTTATATTTATA
*
252118 TAATTTATATATTTATA
1 TAATTTTTATATTTATA
* *
252135 T-TTTATTTATATATTTTA
1 TAATT-TTTATAT-TTATA
252153 TTATATTATAATTATATTTATGA
1 -TA-ATT-T--TTATATTTAT-A
252176 T-A-TTTTATATTTATA
1 TAATTTTTATATTTATA
252191 TAATTTTTGATATATTA-A
1 TAATTTTT-ATAT-TTATA
252209 TAA--TTTATA-TTATA
1 TAATTTTTATATTTATA
*
252223 TAAATTTTA
1 TAATTTTTA
252232 AAAATATATT
Statistics
Matches: 91, Mismatches: 6, Indels: 33
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.03
14 4 0.04
15 12 0.13
16 26 0.29
17 12 0.13
18 13 0.14
19 5 0.05
20 1 0.01
21 4 0.04
22 4 0.04
23 7 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTTTTATATTTATA
Found at i:252214 original size:27 final size:25
Alignment explanation
Indices: 252168--252218 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
252158 TTATAATTAT
*
252168 ATTTATGATATTTTATATTTATATA
1 ATTTATGATATTTAATATTTATATA
*
252193 ATTTTTGATATATTAATAATTTATAT
1 ATTTATGATAT-TTAAT-ATTTATAT
252219 TATATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
ATTTATGATATTTAATATTTATATA
Found at i:252218 original size:15 final size:14
Alignment explanation
Indices: 252111--252219 Score: 64
Period size: 15 Copynumber: 7.3 Consensus size: 14
252101 CGTAATTTTT
252111 TATTTAATAATTTA
1 TATTTAATAATTTA
*
252125 TATATTTAT-ATTT-
1 TAT-TTAATAATTTA
*
252138 TATTTATATATTTTA
1 TATTTA-ATAATTTA
252153 TTATATT-ATAA-TTA
1 -TAT-TTAATAATTTA
*
252167 TATTTATGATATTTTA
1 TATTTA--ATAATTTA
252183 TATTTATATAATTTTTGA
1 TATTTA-ATAA--TTT-A
252201 TATATTAATAATTTA
1 TAT-TTAATAATTTA
252216 TATT
1 TATT
252220 ATATAAATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 28
0.68 0.06 0.26
Matches are distributed among these distances:
12 4 0.05
13 8 0.11
14 14 0.19
15 17 0.23
16 15 0.20
17 5 0.07
18 8 0.11
19 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TATTTAATAATTTA
Found at i:252500 original size:19 final size:17
Alignment explanation
Indices: 252468--252508 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
252458 TTTTATATTA
252468 TAAATAATAATTAAATC
1 TAAATAATAATTAAATC
*
252485 TAAATAGATAAATTAAATT
1 TAAATA-AT-AATTAAATC
252504 TAAAT
1 TAAAT
252509 TTAATATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATAATAATTAAATC
Found at i:252742 original size:19 final size:19
Alignment explanation
Indices: 252718--252754 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
252708 TTCGTTTTAT
*
252718 TATTTAAATAATATTAAAA
1 TATTTAAAAAATATTAAAA
*
252737 TATTTAAAAAATTTTAAA
1 TATTTAAAAAATATTAAA
252755 TTTAGATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTTAAAAAATATTAAAA
Found at i:252949 original size:11 final size:11
Alignment explanation
Indices: 252930--252982 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
252920 ATTAAAAATT
252930 TAAATATAAAA
1 TAAATATAAAA
* *
252941 TAAAAATAATA
1 TAAATATAAAA
252952 TAAATATAAAA
1 TAAATATAAAA
*
252963 -ATATATTAAAA
1 TAAATA-TAAAA
*
252974 TATATATAA
1 TAAATATAA
252983 TTATATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 4 0.11
11 26 0.74
12 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAATATAAAA
Found at i:252953 original size:16 final size:16
Alignment explanation
Indices: 252932--252975 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
252922 TAAAAATTTA
252932 AATATAAAATAAAAAT
1 AATATAAAATAAAAAT
252948 AATATAAATATAAAAAT
1 AATATAAA-ATAAAAAT
252965 -ATATTAAAATA
1 AATA-TAAAATA
252976 TATATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATAAAATAAAAAT
Found at i:252972 original size:17 final size:17
Alignment explanation
Indices: 252932--252965 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
252922 TAAAAATTTA
252932 AATATAAA-ATAAAAAT
1 AATATAAATATAAAAAT
252948 AATATAAATATAAAAAT
1 AATATAAATATAAAAAT
252965 A
1 A
252966 TATTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATATAAATATAAAAAT
Found at i:253245 original size:10 final size:10
Alignment explanation
Indices: 253223--253256 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
253213 AAATTCGATA
253223 TTAATATTA-T
1 TTAAT-TTATT
253233 TTAATTTATT
1 TTAATTTATT
253243 TTAATTTATT
1 TTAATTTATT
253253 TTAA
1 TTAA
253257 AATGTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 3 0.13
10 20 0.87
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTAATTTATT
Found at i:254870 original size:27 final size:30
Alignment explanation
Indices: 254851--254912 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
254841 AAAATTAATA
254851 AAAATA-TAAAATATTTTAAAAATAATTAT
1 AAAATAGTAAAATATTTTAAAAATAATTAT
* * *
254880 AATATAGTAAAATA-TGTAAATATAA-TAT
1 AAAATAGTAAAATATTTTAAAAATAATTAT
254908 AAAAT
1 AAAAT
254913 TTTAAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.25
29 14 0.50
30 7 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATAGTAAAATATTTTAAAAATAATTAT
Found at i:256621 original size:14 final size:14
Alignment explanation
Indices: 256604--256630 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
256594 TTCAATAATT
256604 AAAAATGAATGAAA
1 AAAAATGAATGAAA
256618 AAAAATGAATGAA
1 AAAAATGAATGAA
256631 GATTAAACAA
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATGAATGAAA
Found at i:257787 original size:24 final size:25
Alignment explanation
Indices: 257750--257805 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
257740 TTAATCTATT
*
257750 AATTTAATTAAAAAATT-TACATAA-A
1 AATTAAATT-AAAAATTATA-ATAATA
257775 AATTAAATT-AAAATTATAATAATA
1 AATTAAATTAAAAATTATAATAATA
257799 AATTAAA
1 AATTAAA
257806 ATCAAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.36
24 10 0.36
25 8 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTAAATTAAAAATTATAATAATA
Found at i:258308 original size:13 final size:13
Alignment explanation
Indices: 258269--258311 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
258259 TGTGTTATCC
258269 TTCTTTGATATTAT
1 TTCTTTGATATT-T
*
258283 TTCAATTTTATATTT
1 TTC--TTTGATATTT
258298 TTCTTTGATATTT
1 TTCTTTGATATTT
258311 T
1 T
258312 AATTTGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 4 0.16
16 8 0.32
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (13 bp):
TTCTTTGATATTT
Found at i:258795 original size:2 final size:2
Alignment explanation
Indices: 258788--258822 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
258778 TGCATTATTT
258788 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 T
258823 TGAAAGAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259782 original size:5 final size:5
Alignment explanation
Indices: 259768--259806 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
259758 GACAATAGAC
* *
259768 AAATA AAACA AAACA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT
259807 CCCATGTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:260413 original size:11 final size:11
Alignment explanation
Indices: 260357--260415 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
260347 CAATTGAGTA
*
260357 AATATAAATAC
1 AATATAAATAT
260368 AATATAAAT-T
1 AATATAAATAT
260378 -AT-TAAATAT
1 AATATAAATAT
* * *
260387 ATTAAAAATTT
1 AATATAAATAT
260398 AAATATAAATAT
1 -AATATAAATAT
260410 AATATA
1 AATATA
260416 TATTAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
8 5 0.14
9 3 0.08
10 1 0.03
11 20 0.54
12 8 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:260424 original size:23 final size:22
Alignment explanation
Indices: 260355--260456 Score: 70
Period size: 23 Copynumber: 4.6 Consensus size: 22
260345 ATCAATTGAG
*
260355 TAAATATAAATACAATATAAAT
1 TAAATATAAATATAATATAAAT
* *
260377 T--AT-TAAATATATTAAAAATT
1 TAAATATAAATATAATATAAA-T
*
260397 TAAATATAAATATAATATATAT
1 TAAATATAAATATAATATAAAT
* *
260419 TAAA-ATATTATATTAATCAT-ATT
1 TAAATATA-AATA-TAAT-ATAAAT
260442 TAAATATATAATATA
1 TAAATATA-AATATA
260457 GCGTGTTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
19 12 0.19
20 4 0.06
21 3 0.05
22 11 0.18
23 23 0.37
24 9 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATAAATATAATATAAAT
Found at i:260431 original size:17 final size:17
Alignment explanation
Indices: 260372--260431 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
260362 AAATACAATA
* *
260372 TAAATTATTAAATATAT
1 TAAAATATTATATATAT
*
260389 TAAAA-ATT-TAAATA-
1 TAAAATATTATATATAT
*
260403 T-AAATATAATATATAT
1 TAAAATATTATATATAT
260419 TAAAATATTATAT
1 TAAAATATTATAT
260432 TAATCATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 9 0.27
16 4 0.12
17 14 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATTATATATAT
Found at i:260431 original size:22 final size:23
Alignment explanation
Indices: 260394--260456 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
260384 TATATTAAAA
260394 ATTTAAATATA-AATATAAT-AT
1 ATTTAAATATATAATATAATCAT
*
260415 ATATTAAA-ATATTATATTAATCAT
1 AT-TTAAATATATAATA-TAATCAT
260439 ATTTAAATATATAATATA
1 ATTTAAATATATAATATA
260457 GCGTGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 5 0.14
22 8 0.23
23 11 0.31
24 11 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAATATATAATATAATCAT
Found at i:261032 original size:2 final size:2
Alignment explanation
Indices: 261027--261058 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
261017 AAAAGGTCAA
261027 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
261059 TGGGACTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261420 original size:28 final size:27
Alignment explanation
Indices: 261377--261462 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 27
261367 GAAATGTTTC
* *
261377 AATTTAAAAATCTTTTTTAATATTTAA
1 AATTAAAAAATATTTTTTAATATTTAA
*
261404 AATATAAAAAATA--TTTTAATATTTTTAT
1 AAT-TAAAAAATATTTTTTAATA--TTTAA
*
261432 AATTAAATTAAATATTTTGTTATTATTTAA
1 AATTAAA--AAATATTTT-TTAATATTTAA
261462 A
1 A
261463 GAATAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
26 8 0.17
27 7 0.15
28 14 0.30
29 5 0.11
30 5 0.11
31 2 0.04
32 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTAAAAAATATTTTTTAATATTTAA
Found at i:262399 original size:3 final size:3
Alignment explanation
Indices: 262385--262439 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
262375 AGAAAAAGAT
* *
262385 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
262433 ATA ATA A
1 ATA ATA A
262440 AAGAAAGCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:262985 original size:14 final size:14
Alignment explanation
Indices: 262945--262987 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
262935 TGGATTTGAT
262945 TAAATTGAAATTT-
1 TAAATTGAAATTTA
**
262958 TAAATAAAATATTTA
1 TAAATTGAA-ATTTA
262973 TAAATTGAAATTTA
1 TAAATTGAAATTTA
262987 T
1 T
262988 TTATTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
TAAATTGAAATTTA
Found at i:264189 original size:14 final size:14
Alignment explanation
Indices: 264170--264204 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
264160 TATTTTAAAT
264170 ATATATTTAATTTA
1 ATATATTTAATTTA
*
264184 ATATATTTTATTTA
1 ATATATTTAATTTA
264198 AT-TATTT
1 ATATATTT
264205 TGTCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATATTTAATTTA
Found at i:264316 original size:21 final size:22
Alignment explanation
Indices: 264289--264352 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
264279 AAACAATATC
264289 TATTATTATAAAAATATATAAT
1 TATTATTATAAAAATATATAAT
264311 TA-TATTATAAAAATATA-AA-
1 TATTATTATAAAAATATATAAT
* * *
264330 TATTATAATAAAAAAACATAAT
1 TATTATTATAAAAATATATAAT
264352 T
1 T
264353 TGTGTTGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
21 17 0.47
22 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TATTATTATAAAAATATATAAT
Found at i:264326 original size:19 final size:18
Alignment explanation
Indices: 264292--264337 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 18
264282 CAATATCTAT
264292 TATTATAAAAATATATAATTA
1 TATTAT-AAAATATATAA--A
264313 TATTATAAAA-ATATAAA
1 TATTATAAAATATATAAA
264330 TATTATAA
1 TATTATAA
264338 TAAAAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
19 6 0.24
20 4 0.16
21 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATTATAAAATATATAAA
Found at i:264334 original size:22 final size:22
Alignment explanation
Indices: 264283--264350 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
264273 AAAATAAAAC
264283 AATATCTATTATTATAAAAATATA
1 AATAT-TA-TATTATAAAAATATA
*
264307 TA-ATTATATTATAAAAATATA
1 AATATTATATTATAAAAATATA
* * *
264328 AATATTATAATAAAAAAACATA
1 AATATTATATTATAAAAATATA
264350 A
1 A
264351 TTTGTGTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 16 0.42
22 19 0.50
23 2 0.05
24 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATTATATTATAAAAATATA
Found at i:264342 original size:19 final size:19
Alignment explanation
Indices: 264292--264342 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
264282 CAATATCTAT
264292 TATTATAAAAATATATAATTA
1 TATTATAAAAA-ATATAA-TA
264313 TATTAT-AAAAATATAA-A
1 TATTATAAAAAATATAATA
264330 TATTATAATAAAA
1 TATTATAA-AAAA
264343 AAACATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
19 10 0.36
20 4 0.14
21 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTATAAAAAATATAATA
Found at i:264422 original size:22 final size:22
Alignment explanation
Indices: 264396--264439 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
264386 TCTTTGTCTA
264396 AGACTTGATTTTTT-TTCTAAAT
1 AGACTTGATTTTTTGTT-TAAAT
264418 AGACTTGATTTTTTGTTTAAAT
1 AGACTTGATTTTTTGTTTAAAT
264440 TTATTTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (22 bp):
AGACTTGATTTTTTGTTTAAAT
Found at i:265594 original size:26 final size:27
Alignment explanation
Indices: 265565--265618 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
265555 TTAAATTATT
* *
265565 ATTTAATAATAAAATTTTTAAT-TTAA
1 ATTTAATAATAAAAATATTAATATTAA
*
265591 ATTTAATTATAAAAATATTAATATTAA
1 ATTTAATAATAAAAATATTAATATTAA
265618 A
1 A
265619 ATATTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTAATAATAAAAATATTAATATTAA
Found at i:268159 original size:2 final size:2
Alignment explanation
Indices: 268154--268201 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
268144 CCATTTGAAC
*
268154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
268196 AT AT AT
1 AT AT AT
268202 GCAGCATGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:268522 original size:18 final size:17
Alignment explanation
Indices: 268467--268522 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
268457 CGGTTTAACT
268467 TATTTTT-TA-ATTATA
1 TATTTTTATATATTATA
*
268482 TAATTTTTAT-TATCTTTA
1 T-ATTTTTATATAT-TATA
268500 TATTTTTATATATTATA
1 TATTTTTATATATTATA
268517 TCATTT
1 T-ATTT
268523 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.03
16 6 0.18
17 15 0.45
18 11 0.33
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTATATATTATA
Found at i:268535 original size:23 final size:24
Alignment explanation
Indices: 268509--268560 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
268499 ATATTTTTAT
*
268509 ATATTATATCAT-TTAAAAAATAA
1 ATATTATATAATATTAAAAAATAA
* *
268532 ATA-TATATAATATTATAATATAA
1 ATATTATATAATATTAAAAAATAA
268555 ATATTA
1 ATATTA
268561 AAAACTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTATATAATATTAAAAAATAA
Found at i:268609 original size:21 final size:20
Alignment explanation
Indices: 268583--268628 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
268573 AGTTATATAT
268583 ATTTTAAAATTTAGTAAAAA-A
1 ATTTT-AAA-TTAGTAAAAATA
*
268604 ATTTTAAATTATTAAAAATA
1 ATTTTAAATTAGTAAAAATA
268624 ATTTT
1 ATTTT
268629 TTAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTAAATTAGTAAAAATA
Found at i:268665 original size:10 final size:10
Alignment explanation
Indices: 268650--268704 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
268640 ATATAATATG
268650 AATAAATTTA
1 AATAAATTTA
268660 AATAAATTTA
1 AATAAATTTA
*
268670 AATTATCTATTT-
1 AA-TA--AATTTA
*
268682 -ATAAATATA
1 AATAAATTTA
268691 AATAAATTTA
1 AATAAATTTA
268701 AATA
1 AATA
268705 TAAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
8 3 0.08
10 26 0.72
11 3 0.08
13 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
AATAAATTTA
Found at i:268715 original size:18 final size:16
Alignment explanation
Indices: 268652--268718 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
268642 ATAATATGAA
*
268652 TAAATTTAAATAAATT
1 TAAATATAAATAAATT
** *
268668 TAAAT-TATCT-ATTT
1 TAAATATAAATAAATT
268682 ATAAATATAAATAAATT
1 -TAAATATAAATAAATT
268699 TAAATATAAAATAAAATT
1 TAAATAT-AAAT-AAATT
268717 TA
1 TA
268719 TATTTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.08
15 8 0.20
16 15 0.38
17 7 0.17
18 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATAAATAAATT
Found at i:268728 original size:18 final size:17
Alignment explanation
Indices: 268683--268733 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
268673 TATCTATTTA
268683 TAAATA-TAAATAAATT
1 TAAATATTAAATAAATT
*
268699 TAAATATAAAATAAAATT
1 TAAATATTAAAT-AAATT
* *
268717 TATATTTTAAATTAAAT
1 TAAATATTAAA-TAAAT
268734 CAAATTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 17 0.61
19 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATAAATT
Found at i:268728 original size:41 final size:42
Alignment explanation
Indices: 268632--268741 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 42
268622 TAATTTTTTA
* * * *
268632 ATATATGTATATAATATGAATAAATTT-AAATAAATTTAAATT
1 ATATATTTATA-AATATAAATAAATTTAAAATAAAATAAAATT
*
268674 ATCTATTTATAAATATAAATAAATTTAAATATAAAATAAAATT
1 ATATATTTATAAATATAAATAAATTTAAA-ATAAAATAAAATT
268717 -TATATTT-TAAAT-TAAATCAAATTTA
1 ATATATTTATAAATATAAAT-AAATTTA
268742 CTCATCCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.08
41 26 0.44
42 17 0.29
43 11 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
ATATATTTATAAATATAAATAAATTTAAAATAAAATAAAATT
Found at i:270004 original size:16 final size:17
Alignment explanation
Indices: 269983--270015 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
269973 ATAAGGTTGG
269983 AACAAA-AAAAAACAAA
1 AACAAACAAAAAACAAA
269999 AACAAACAAAAAACAAA
1 AACAAACAAAAAACAAA
270016 GAACTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AACAAACAAAAAACAAA
Found at i:274375 original size:13 final size:14
Alignment explanation
Indices: 274344--274381 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
274334 CTTCTTACTC
274344 ATATCAAA-AT-AT
1 ATATCAAATATAAT
274356 ATATCAAATATAAT
1 ATATCAAATATAAT
274370 -TATCAAATATAA
1 ATATCAAATATAA
274382 ATTCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 14 0.58
14 2 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATCAAATATAAT
Found at i:274608 original size:31 final size:32
Alignment explanation
Indices: 274573--274661 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 32
274563 ATATTATAAT
274573 TATATTTAAAATATTTTTTATATAAAATTT-A
1 TATATTTAAAATATTTTTTATATAAAATTTAA
*
274604 TATA-TTAATAAT-TTATATTATATAAAATTTAA
1 TATATTTAA-AATATT-TTTTATATAAAATTTAA
*
274636 AATATTTAAATATATTTATATTATAT
1 TATATTTAAA-ATATTT-T-TTATAT
274662 TTTAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
30 6 0.13
31 21 0.45
32 5 0.11
33 7 0.15
34 2 0.04
35 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTTAAAATATTTTTTATATAAAATTTAA
Found at i:275518 original size:13 final size:13
Alignment explanation
Indices: 275468--275520 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
275458 AATTTTTAAT
*
275468 AAAAATTTTAATA
1 AAAAATTTAAATA
* *
275481 AAAAAATCAAATTA
1 AAAAATTTAAA-TA
275495 AATTAAATTTAAATA
1 AA--AAATTTAAATA
275510 AAAAATTTAAA
1 AAAAATTTAAA
275521 AATTCGGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 17 0.53
14 4 0.12
15 4 0.12
16 7 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTTAAATA
Found at i:276824 original size:16 final size:15
Alignment explanation
Indices: 276774--276816 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
276764 TTATTATATA
* *
276774 TAATAATATTATAATT
1 TAATAATA-TAAAAAT
276790 TAATAATATAAAAAT
1 TAATAATATAAAAAT
276805 TAATAA-ATAAAA
1 TAATAATATAAAA
276817 TTATTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAATATAAAAAT
Found at i:277047 original size:21 final size:20
Alignment explanation
Indices: 277023--277070 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
277013 ATTTTAAAAA
277023 TTATAA-TAATATTTATATATT
1 TTATAATTAA-ATTTA-ATATT
277044 TTATAATTAAATTTAAT-TT
1 TTATAATTAAATTTAATATT
277063 TT-TAATTA
1 TTATAATTA
277071 TTAAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 4 0.15
20 2 0.08
21 11 0.42
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATAATTAAATTTAATATT
Found at i:277311 original size:17 final size:15
Alignment explanation
Indices: 277276--277305 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
277266 ATTTAAATTT
*
277276 ATATTCATAAACTTA
1 ATATTAATAAACTTA
277291 ATATTAATAAACTTA
1 ATATTAATAAACTTA
277306 TAATATACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTAATAAACTTA
Found at i:278051 original size:40 final size:39
Alignment explanation
Indices: 277974--278052 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
277964 TTAAAAAAAA
*
277974 TCTTAAAATAATTAAAAAGTAAATAAGTTTTTGTTTTTT
1 TCTTAAAATAATTAAAAAATAAATAAGTTTTTGTTTTTT
* *
278013 TCTTAAAATAATTAAAAAATAAATGAGTTTTTATTTTTT
1 TCTTAAAATAATTAAAAAATAAATAAGTTTTTGTTTTTT
278052 T
1 T
278053 GATCTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (39 bp):
TCTTAAAATAATTAAAAAATAAATAAGTTTTTGTTTTTT
Found at i:278813 original size:18 final size:18
Alignment explanation
Indices: 278790--278824 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
278780 ATGTAATATT
*
278790 ATATAATATAAATAAAAA
1 ATATAAAATAAATAAAAA
*
278808 ATATAAAATAATTAAAA
1 ATATAAAATAAATAAAA
278825 TATAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATAAAATAAATAAAAA
Found at i:278831 original size:11 final size:11
Alignment explanation
Indices: 278815--278841 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
278805 AAAATATAAA
278815 ATAATTAAAAT
1 ATAATTAAAAT
278826 ATAATTAAAAT
1 ATAATTAAAAT
278837 ATAAT
1 ATAAT
278842 ATATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:278882 original size:29 final size:30
Alignment explanation
Indices: 278823--278883 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
278813 AAATAATTAA
***
278823 AATATAATTAAAATATAATATATATTTATT
1 AATATAATTAAAATATAATATATACAAATT
278853 AATAT-ATTAAAATAT-ATATGATACAAATT
1 AATATAATTAAAATATAATAT-ATACAAATT
278882 AA
1 AA
278884 GAATTATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
AATATAATTAAAATATAATATATACAAATT
Found at i:279318 original size:24 final size:24
Alignment explanation
Indices: 279291--279336 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
279281 TTATTTAATT
279291 AATATTTCAAAATTTTAA-ATATTA
1 AATATTT-AAAATTTTAACATATTA
*
279315 AATATTTATAATTTTAACATAT
1 AATATTTAAAATTTTAACATAT
279337 ACATTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTAAAATTTTAACATATTA
Found at i:280163 original size:16 final size:15
Alignment explanation
Indices: 280142--280191 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
280132 GAAATTATAA
280142 AATATTATTTTAATAT
1 AATATT-TTTTAATAT
*
280158 AATA-TTCTTAATAT
1 AATATTTTTTAATAT
280172 ATATAATTTTTTAAT-T
1 A-AT-ATTTTTTAATAT
280188 AATA
1 AATA
280192 AAAAAATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.34
15 5 0.17
16 7 0.24
17 7 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTTTTTAATAT
Found at i:280414 original size:26 final size:25
Alignment explanation
Indices: 280381--280449 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
280371 TTATATATTG
280381 ATAT-TTTTATAATAATATATGTTAT
1 ATATATTTTATAATAATATAT-TTAT
*
280406 A-ATTATTTTAAAATATTATATATTTAT
1 ATA-TATTTTATAATA--ATATATTTAT
280433 ATATATTTT-TAA-AATAT
1 ATATATTTTATAATAATAT
280450 TTATTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
23 4 0.11
24 1 0.03
25 3 0.08
26 11 0.30
27 11 0.30
28 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (25 bp):
ATATATTTTATAATAATATATTTAT
Found at i:280459 original size:18 final size:18
Alignment explanation
Indices: 280436--280471 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
280426 TATTTATATA
280436 TATTTTTAAAATATTTAT
1 TATTTTTAAAATATTTAT
**
280454 TATTTTTATTATATTTAT
1 TATTTTTAAAATATTTAT
280472 ATTAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTAAAATATTTAT
Found at i:280467 original size:29 final size:28
Alignment explanation
Indices: 280381--280469 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
280371 TTATATATTG
*
280381 ATATTTTTATAATA--ATATATGTTATA-
1 ATATTTTTAAAATATTATATAT-TTATAT
280407 AT-TATTTTAAAATATTATATATTTATAT
1 ATAT-TTTTAAAATATTATATATTTATAT
*
280435 ATATTTTTAAAATATT-TATTATTTTTATT
1 ATATTTTTAAAATATTATA-TATTTATA-T
280464 ATATTT
1 ATATTT
280470 ATATTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.02
26 11 0.20
27 7 0.13
28 27 0.50
29 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
ATATTTTTAAAATATTATATATTTATAT
Found at i:280473 original size:39 final size:39
Alignment explanation
Indices: 280424--280504 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
280414 TAAAATATTA
*
280424 TATATTTATA-TATATTTTTA-A-AATATTTATTATTTTTAT
1 TATATTTATATTA-ATTTTTATATAATA-TTA-TATTTTAAT
280463 TATATTTATATTAATTTTTATATAATATTATATTTTAAT
1 TATATTTATATTAATTTTTATATAATATTATATTTTAAT
280502 TAT
1 TAT
280505 TTTTTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
39 28 0.74
40 6 0.16
41 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (39 bp):
TATATTTATATTAATTTTTATATAATATTATATTTTAAT
Found at i:280483 original size:18 final size:19
Alignment explanation
Indices: 280424--280498 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 19
280414 TAAAATATTA
280424 TATATTTATA-TATATTTT
1 TATATTTATATTATATTTT
* *
280442 TAAAATATT-TATTATTTTTAT
1 T-ATAT-TTATATTATATTT-T
280463 TATATTTATATTA-ATTTT
1 TATATTTATATTATATTTT
*
280481 TATA-TAATATTATATTTT
1 TATATTTATATTATATTTT
280499 AATTATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 7 0.15
18 11 0.24
19 10 0.22
20 16 0.35
21 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTTATATTATATTTT
Found at i:280928 original size:16 final size:18
Alignment explanation
Indices: 280901--280933 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
280891 TTTAACAGAA
280901 AAAAAATCAATT-TTTTT
1 AAAAAATCAATTATTTTT
280918 AAAAAAT-AATTATTTT
1 AAAAAATCAATTATTTT
280934 CTATTTTTTA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAAATCAATTATTTTT
Found at i:281762 original size:8 final size:8
Alignment explanation
Indices: 281731--281789 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
281721 TTTATTTATT
281731 TAATATAA
1 TAATATAA
*
281739 -ATTATAA
1 TAATATAA
*
281746 -AAAATAA
1 TAATATAA
281753 TAATATAA
1 TAATATAA
281761 TAATATAA
1 TAATATAA
281769 TAATAT-A
1 TAATATAA
281776 -AATATAA
1 TAATATAA
*
281783 AAATATA
1 TAATATA
281790 TTAAATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
6 5 0.11
7 13 0.30
8 26 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TAATATAA
Found at i:281768 original size:16 final size:15
Alignment explanation
Indices: 281732--281789 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
281722 TTATTTATTT
*
281732 AATATAA-ATTATAA
1 AATATAATAATATAA
*
281746 AAAATAATAATATAA
1 AATATAATAATATAA
281761 TAATATAATAATAT-A
1 -AATATAATAATATAA
*
281776 AATATAAAAATATA
1 AATATAATAATATA
281790 TTAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 18 0.49
15 7 0.19
16 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAATAATATAA
Found at i:281773 original size:22 final size:20
Alignment explanation
Indices: 281731--281789 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 20
281721 TTTATTTATT
*
281731 TAATATAAATTATAAAAAATAA
1 TAATATAAAATAT-AAAAAT-A
*
281753 TAATATAATAATATAATAATA
1 TAATATAA-AATATAAAAATA
281774 TAAATATAAAAATATA
1 T-AATAT-AAAATATA
281790 TTAAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
22 24 0.75
23 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATATAAAATATAAAAATA
Found at i:290557 original size:2 final size:2
Alignment explanation
Indices: 290550--290596 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
290540 ACTCTGTTCC
290550 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
290592 TA TA T
1 TA TA T
290597 TCATGCATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:297023 original size:15 final size:15
Alignment explanation
Indices: 297000--297029 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
296990 CGGTTCGATT
297000 AATTGATTAATTAAA
1 AATTGATTAATTAAA
*
297015 AATTTATTAATTAAA
1 AATTGATTAATTAAA
297030 TTAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
AATTGATTAATTAAA
Found at i:299668 original size:2 final size:2
Alignment explanation
Indices: 299661--299699 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
299651 CCCATAAATT
299661 TA 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 TA T
299700 TCTTTTTCCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:300102 original size:29 final size:29
Alignment explanation
Indices: 300070--300125 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
300060 AAGATGAAAA
300070 TAAATATTA-TAAATATTAAAATTTAAATT
1 TAAAT-TTACTAAATATTAAAATTTAAATT
* * *
300099 TAAATTTACTGAATATTACATTTTAAA
1 TAAATTTACTAAATATTAAAATTTAAA
300126 AATAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTACTAAATATTAAAATTTAAATT
Done.