Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold496
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: 765014
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 4 of 7
Found at i:265304 original size:32 final size:32
Alignment explanation
Indices: 265263--265325 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
265253 TTCAACAATT
*
265263 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
265295 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
265326 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:265384 original size:33 final size:33
Alignment explanation
Indices: 265347--265413 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
265337 TGCCAAGAAA
***
265347 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
265380 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
265413 T
1 T
265414 TGAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:265385 original size:13 final size:13
Alignment explanation
Indices: 265367--265392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
265357 CATTTTTCTG
265367 TGTATCGATACAT
1 TGTATCGATACAT
265380 TGTATCGATACAT
1 TGTATCGATACAT
265393 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:267983 original size:52 final size:51
Alignment explanation
Indices: 267865--268087 Score: 225
Period size: 52 Copynumber: 4.3 Consensus size: 51
267855 TTATTTCCGA
* * * * * *
267865 GGGGATACTCAAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATC
* * *
267916 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT-CACAATC
* ** *
267968 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTTC-CTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCAC---AATC
* * *
268021 GAGGATACTCCAACACCGATTTTATTTCCAAAA-ATATCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACA-CT-AATTTTTCACAATC
*
268073 GAGGATACTCCAACC
1 GGGGATACTCCAACC
268088 TCGTTATTTC
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
50 1 0.01
51 37 0.26
52 66 0.46
53 32 0.22
54 8 0.06
55 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATC
Found at i:268121 original size:28 final size:28
Alignment explanation
Indices: 268070--268151 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
268060 ATTTTTCACA
*
268070 ATCGAGGATACTCCAA-CCTCGTTATTTC
1 ATCGGGGATACTCCAACCCT-GTTATTTC
*
268098 ATCGGGGATACTCCAACCCTGTTACTTC
1 ATCGGGGATACTCCAACCCTGTTATTTC
* *
268126 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCTGTTATT
268152 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 38 0.83
29 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTGTTATTTC
Found at i:269873 original size:18 final size:17
Alignment explanation
Indices: 269850--269929 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 17
269840 TTAGATTATT
269850 TATTTAAATTTAAAAATA
1 TATTTAAATTTAAAAA-A
269868 TATTTAATATTTAAAAAA
1 TATTTAA-ATTTAAAAAA
*
269886 -ATTT-AA-GTAAAAAA
1 TATTTAAATTTAAAAAA
*
269900 TATAATT-TATTTAAAAAA
1 TAT--TTAAATTTAAAAAA
*
269918 TTAATTAAATTT
1 -TATTTAAATTT
269930 TAATTCTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
14 7 0.14
15 3 0.06
16 1 0.02
17 9 0.18
18 19 0.38
19 11 0.22
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TATTTAAATTTAAAAAA
Found at i:270398 original size:2 final size:2
Alignment explanation
Indices: 270391--270425 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
270381 TTGTTTTCAT
270391 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 T
270426 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:276131 original size:22 final size:22
Alignment explanation
Indices: 276103--276145 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
276093 AATAATTATT
276103 AAATATAATATTT-ATTTAATAA
1 AAATAT-ATATTTAATTTAATAA
276125 AAATATATATTTAATTTAATA
1 AAATATATATTTAATTTAATA
276146 GTATGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATATATTTAATTTAATAA
Found at i:276730 original size:19 final size:19
Alignment explanation
Indices: 276687--276732 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
276677 AAAAATTTGA
276687 TAATAT-TTAAAAATTATT
1 TAATATATTAAAAATTATT
276705 TAA-ATATTAATAAATTA-T
1 TAATATATTAA-AAATTATT
276723 TAATATATTA
1 TAATATATTA
276733 TGTAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATATATTAAAAATTATT
Found at i:276877 original size:21 final size:19
Alignment explanation
Indices: 276853--276898 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
276843 ATTTTATCGA
276853 TATTATATAATTTTTTAATAT
1 TATTATATAATTTTTT-AT-T
*
276874 TATTA-ATTATTTTTTATT
1 TATTATATAATTTTTTATT
276892 TATTATA
1 TATTATA
276899 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 9 0.39
21 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATATAATTTTTTATT
Found at i:276902 original size:17 final size:19
Alignment explanation
Indices: 276852--276903 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
276842 AATTTTATCG
276852 ATATTA-TATAATTTTTTA
1 ATATTATTATAATTTTTTA
*
276870 ATATTATTAATTATTTTTT-
1 ATATTATT-ATAATTTTTTA
276889 AT-TTATTATAATTTT
1 ATATTATTATAATTTT
276904 AAAATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.23
18 11 0.37
19 3 0.10
20 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTATTATAATTTTTTA
Found at i:277841 original size:17 final size:16
Alignment explanation
Indices: 277821--277877 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
277811 GTTAATTTAT
277821 TTTTAATATCAATATAA
1 TTTTAATAT-AATATAA
*
277838 TTTTAA-AT--TATTA
1 TTTTAATATAATATAA
*
277851 -TTTAAAATAAATATAA
1 TTTTAATAT-AATATAA
277867 TTTTAATATAA
1 TTTTAATATAA
277878 CTTTAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
16 8 0.25
17 13 0.41
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTAATATAATATAA
Found at i:277855 original size:29 final size:28
Alignment explanation
Indices: 277812--277872 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
277802 TTTTTAGTTG
* * *
277812 TTAATTTATTTTTAATATCAATATAATT
1 TTAAATTATTTTTAAAATAAATATAATT
277840 TTAAATTATTATTTAAAATAAATATAATT
1 TTAAATTATT-TTTAAAATAAATATAATT
277869 TTAA
1 TTAA
277873 TATAACTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAATTATTTTTAAAATAAATATAATT
Found at i:278439 original size:2 final size:2
Alignment explanation
Indices: 278432--278462 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
278422 AGCTAAGGTT
278432 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
278463 CATATGAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:279305 original size:17 final size:18
Alignment explanation
Indices: 279285--279322 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
279275 TTCGATATTT
*
279285 TTTAAACCTTAAAGTA-A
1 TTTAAAACTTAAAGTATA
*
279302 TTTAAAACTTGAAGTATA
1 TTTAAAACTTAAAGTATA
279320 TTT
1 TTT
279323 TGAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTAAAACTTAAAGTATA
Found at i:279350 original size:11 final size:11
Alignment explanation
Indices: 279334--279360 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
279324 GAAATTTAAA
279334 TTTTAATATAT
1 TTTTAATATAT
279345 TTTTAATATAT
1 TTTTAATATAT
279356 TTTTA
1 TTTTA
279361 TTTTACAAGA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:279895 original size:2 final size:2
Alignment explanation
Indices: 279890--279918 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
279880 GTGTGTATGC
279890 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 A
279919 ATTGTTGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:281277 original size:11 final size:11
Alignment explanation
Indices: 281173--281277 Score: 51
Period size: 11 Copynumber: 9.5 Consensus size: 11
281163 GTTTCAAAGA
* *
281173 AATATAATAAG
1 AATATAATTAT
*
281184 AATATAATAAT
1 AATATAATTAT
*
281195 AAAATAAATTAT
1 AATAT-AATTAT
281207 AATATGAA-TAT
1 AATAT-AATTAT
*
281218 ATTATTAA-TAT
1 AATA-TAATTAT
* *
281229 ATTAAAATT-T
1 AATATAATTAT
281239 ATATATAA--AT
1 A-ATATAATTAT
281249 ACATATAATT-T
1 A-ATATAATTAT
281260 AATTATAATTAT
1 AA-TATAATTAT
281272 AATATA
1 AATATA
281278 TCAAATGATA
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
10 13 0.17
11 47 0.63
12 15 0.20
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (11 bp):
AATATAATTAT
Found at i:281909 original size:17 final size:16
Alignment explanation
Indices: 281887--281941 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 16
281877 ATATTAAAAT
281887 ATTTTATATTTATATTA
1 ATTTTATA-TTATATTA
281904 ATTTTA-A-TATATTA
1 ATTTTATATTATATTA
*
281918 ATAATTTATATTATATAA
1 AT--TTTATATTATATTA
281936 ATTTTA
1 ATTTTA
281942 ATATATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 9 0.27
16 9 0.27
17 7 0.21
18 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTATATTA
Found at i:281916 original size:14 final size:14
Alignment explanation
Indices: 281897--281947 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
281887 ATTTTATATT
281897 TATATTAATTTTAA
1 TATATTAATTTTAA
281911 TATATTAATAATTTATA
1 TATATTAAT--TTTA-A
*
281928 TTATATAAATTTTAA
1 -TATATTAATTTTAA
281943 TATAT
1 TATAT
281948 GTATTTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 14 0.44
15 1 0.03
16 8 0.25
17 1 0.03
18 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATTAATTTTAA
Found at i:281932 original size:32 final size:33
Alignment explanation
Indices: 281884--281947 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
281874 ATCATATTAA
* *
281884 AATATTTTATATTTATATTAATTTTAATATATT
1 AATAATTTATATTTATATAAATTTTAATATATT
281917 AATAATTTATA-TTATATAAATTTTAATATAT
1 AATAATTTATATTTATATAAATTTTAATATAT
281948 GTATTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAATATATT
Found at i:282275 original size:12 final size:12
Alignment explanation
Indices: 282258--282282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282248 AAAATAATTA
282258 AAAATTTTATAT
1 AAAATTTTATAT
282270 AAAATTTTATAT
1 AAAATTTTATAT
282282 A
1 A
282283 TTCATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTTATAT
Found at i:282551 original size:12 final size:12
Alignment explanation
Indices: 282534--282558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282524 AAAATAATTA
282534 AAAATTTTATAT
1 AAAATTTTATAT
282546 AAAATTTTATAT
1 AAAATTTTATAT
282558 A
1 A
282559 TTCGTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTTATAT
Found at i:282836 original size:12 final size:12
Alignment explanation
Indices: 282819--282843 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282809 AAAATAATTA
282819 AAAATTTTATAT
1 AAAATTTTATAT
282831 AAAATTTTATAT
1 AAAATTTTATAT
282843 A
1 A
282844 TTCATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTTATAT
Found at i:282837 original size:285 final size:282
Alignment explanation
Indices: 281994--283649 Score: 2423
Period size: 269 Copynumber: 6.0 Consensus size: 282
281984 TTATTAATGT
* * * ** *
281994 TATATTCGTATAATCATATTTAAAATTATTAGATTTTATTAAAATAAAAGAACAAATATTTATAT
1 TATATTCGTATAAT-TTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGT
*
282059 TATATAATATATATAAAAGTATGAATGTAATTTTTTTTAAATTGATAAAAACAAATATGATTATT
65 TTTATAATATATATAAAAGTATGAATGTAA-TTTTTTTAAATTGATAAAAACAAATATGATTATT
* * *
282124 TAAAATATTTTTATTTTGTCATTTTAAATATTTATTATTAAAAAGTTTTTTTGGATGAAATATTA
129 TAAAATATTTCTATTTCGTCATTTTAAATATTTATTATT-AAAATTTTTTTTGGATGAAATATTA
*
282189 TTAAAAAGTTTTAATTTCATTAAAATAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATA
193 TTAAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATA
282254 ATTAAAAATTTTATATAAAATTTTA
258 ATTAAAAATTTTATATAAAATTTTA
* * *
282279 TATATTCATATAATTTTATTTAAAATTATTAAATCTTATTGAAATAAAAGAACACGTATTCATG-
1 TATATTCGTATAA-TTTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGT
* * *
282343 ---------TATGTAAAAGTACGAATGTAATTTTTTTTAAATTGATAAAAACAAATACGATTATT
65 TTTATAATATATATAAAAGTATGAATGTAA-TTTTTTTAAATTGATAAAAACAAATATGATTATT
* * *
282399 TAGAATAGTTCTATTTTGTCATTTTAAATATTTATTATTAAAATGTTTTTTTTGGATGAAATATT
129 TAAAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAA--TTTTTTTTGGATGAAATATT
** *
282464 ATTAAAAAGTTTTAATTTTGTTAAAACAGCTTCATAAATGGATTAATTTGATAATAAATAAAAAT
192 ATTAAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAAT
282529 AATTAAAAATTTTATATAAAATTTTA
257 AATTAAAAATTTTATATAAAATTTTA
*
282555 TATATTCGTATAATTTTATTTAAAATTATTAGATTTTATTGAAATAAAAGAACACGTATTTATGT
1 TATATTCGTATAA-TTTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGT
*
282620 TATATAATATATATAAAAGTATGAATGTAATTTTTTTAAAATTGATAAAAACAAATATGATTATT
65 TTTATAATATATATAAAAGTATGAATGTAATTTTTTT-AAATTGATAAAAACAAATATGATTATT
* * **
282685 TAACATATTTATATTTTTTCATTTTAAATATTTATTATTAAAATGTTTTTTTGGATGAAATATTA
129 TAAAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAAT-TTTTTTTGGATGAAATATTA
* *
282750 TTAAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATCAATTTGATAATAAATTAAAATA
193 TTAAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATA
282815 ATTAAAAATTTTATATAAAATTTTA
258 ATTAAAAATTTTATATAAAATTTTA
* * * * * **
282840 TATATTCATATAATCATATTAAAAATTATTAGATTTTATTGAAATAAAAGGATGCGTATTTATGT
1 TATATTCGTATAAT-TTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGT
*
282905 TTTATAATATATATACAAGTATGAATGTAATTTTTTTAAATTGATAAAAACAAATATGATTATTT
65 TTTATAATATATATAAAAGTATGAATGTAATTTTTTTAAATTGATAAAAACAAATATGATTATTT
* *
282970 AAAATATTTCTATTTCATCATTTTAAATA-TTATTATT-AAATTTTTTTTCGATGAAATATTATT
130 AAAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAATTTTTTTTGGATGAAATATTATT
283033 AAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAAT
195 AAAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAAT
*
283098 TAAAAATTTTATAT---A-TTCA
260 TAAAAATTTTATATAAAATTTTA
* *
283117 TATAATCG--T-A-TTA---AAAATTATTAGATCTTATTGAAATAAAAGAACAAGTATTTATGTT
1 TATATTCGTATAATTTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGTT
* * *
283175 TTATAATATATATACAAGTATGAATGTAATTTTTTAAAATTAATAAAAACAAATATGATTATTTA
66 TTATAATATATATAAAAGTATGAATGTAATTTTTTTAAATTGATAAAAACAAATATGATTATTTA
*
283240 AAATATTTCTATTTCATCATTTTAAATATTTATTATTAAAA-TTTTTTTGGATGAAATATTATTA
131 AAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAATTTTTTTTGGATGAAATATTATTA
*
283304 AAAAGTTTTAATTTCATTAAAACCGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAATT
196 AAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAATT
283369 AAAAATTTTATAT---A-TTTA
261 AAAAATTTTATATAAAATTTTA
* * * *
283387 TATAATCG--T-A-TTA---AAAATTAGTAAATCTTATTGAAATAAAAGAACGCGTATTTATGTT
1 TATATTCGTATAATTTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGTT
*
283445 TTATAATATATATACAAGTATGAATGTAATTTTTTTAAATTGATAAAAA-AAATATGATTATTTA
66 TTATAATATATATAAAAGTATGAATGTAATTTTTTTAAATTGATAAAAACAAATATGATTATTTA
* *
283509 AAATATTTTTATTTCGTCATTTTAAATATTTATTATTAAAA-TTCTTTTGGATGAAATATTATTA
131 AAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAATTTTTTTTGGATGAAATATTATTA
* * *
283573 AAAAGTTTTAATTTCATTAAAACAGTTTTATAAATAGATTAATTTGATAATAAATAAAAGTAATT
196 AAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAATT
283638 AAAAATTTTATA
261 AAAAATTTTATA
283650 GGGAATTGTT
Statistics
Matches: 1274, Mismatches: 79, Indels: 52
0.91 0.06 0.04
Matches are distributed among these distances:
269 280 0.22
270 212 0.17
271 3 0.00
272 2 0.00
274 5 0.00
275 90 0.07
276 166 0.13
277 9 0.01
278 1 0.00
281 98 0.08
282 4 0.00
283 8 0.01
284 55 0.04
285 257 0.20
286 84 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (282 bp):
TATATTCGTATAATTTATTTAAAATTATTAGATCTTATTGAAATAAAAGAACACGTATTTATGTT
TTATAATATATATAAAAGTATGAATGTAATTTTTTTAAATTGATAAAAACAAATATGATTATTTA
AAATATTTCTATTTCGTCATTTTAAATATTTATTATTAAAATTTTTTTTGGATGAAATATTATTA
AAAAGTTTTAATTTCATTAAAACAGTTTCATAAATGGATTAATTTGATAATAAATAAAAATAATT
AAAAATTTTATATAAAATTTTA
Found at i:283777 original size:35 final size:37
Alignment explanation
Indices: 283737--283806 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
283727 AATTAAAATG
283737 TATAATTCAA-TATTTT-TCTT-GATAATTAATTTTTT
1 TATAATTCAATTATTTTATCTTAG-TAATTAATTTTTT
* *
283772 TATAATTGAATTTTTTTATCTTAGTAATTAATTTT
1 TATAATTCAATTATTTTATCTTAGTAATTAATTTT
283807 ACATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 9 0.30
36 5 0.17
37 15 0.50
38 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (37 bp):
TATAATTCAATTATTTTATCTTAGTAATTAATTTTTT
Found at i:283778 original size:15 final size:16
Alignment explanation
Indices: 283748--283790 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
283738 ATAATTCAAT
283748 ATTTTTCTTGATAATT-A
1 ATTTTT-TT-ATAATTGA
283765 ATTTTTTTATAATTGA
1 ATTTTTTTATAATTGA
283781 ATTTTTTTAT
1 ATTTTTTTAT
283791 CTTAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.24
16 13 0.52
17 6 0.24
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (16 bp):
ATTTTTTTATAATTGA
Found at i:284609 original size:3 final size:3
Alignment explanation
Indices: 284601--284631 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
284591 TATGAGTTAT
284601 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
284632 GATATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:285179 original size:24 final size:22
Alignment explanation
Indices: 285151--285217 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
285141 TAAAAACATC
285151 ATTTTTATTATTAATATTTAAATA
1 ATTTTTATTATTAA-A-TTAAATA
*
285175 A-TTTTATAATTAAATTAAATA
1 ATTTTTATTATTAAATTAAATA
285196 A-TTTT-TTATT-AATTAAATA
1 ATTTTTATTATTAAATTAAATA
285215 ATT
1 ATT
285218 ATTCAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.25
20 5 0.12
21 12 0.30
22 1 0.03
23 11 0.28
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTATTATTAAATTAAATA
Found at i:285180 original size:23 final size:22
Alignment explanation
Indices: 285153--285217 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 22
285143 AAAACATCAT
285153 TTTTATTATTAATATTTAAATAA
1 TTTTATTATTAATA-TTAAATAA
*
285176 TTTTATAATTAA-ATTAAATAA
1 TTTTATTATTAATATTAAATAA
285197 TTTT-TTATT-A-ATTAAATAA
1 TTTTATTATTAATATTAAATAA
285216 TT
1 TT
285218 ATTCAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.30
20 4 0.10
21 12 0.30
22 1 0.03
23 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATTATTAATATTAAATAA
Found at i:287211 original size:52 final size:55
Alignment explanation
Indices: 287150--287255 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 55
287140 TTATATGTTA
287150 TTAATTATTTATGTAA-ATTATAA-ATATTAAATTTTAAATA-A-ATTAAAAATAT
1 TTAATTATTTATGTAATATTA-AATATATTAAATTTTAAATATATATTAAAAATAT
* * * *
287202 TTAATTATTTATTTAATATTAAATTTTTTAATTTTTAAATATATATTAAAAATA
1 TTAATTATTTATGTAATATTAAATATATTAAATTTTAAATATATATTAAAAATA
287256 ATAATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 17 0.37
53 18 0.39
54 1 0.02
55 10 0.22
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (55 bp):
TTAATTATTTATGTAATATTAAATATATTAAATTTTAAATATATATTAAAAATAT
Found at i:287346 original size:21 final size:23
Alignment explanation
Indices: 287320--287374 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
287310 ACATAATAAA
*
287320 TAATAATTATATTATT-AAAT-T
1 TAATAATTATAATATTAAAATAT
*
287341 TAATAATTAAAATATTAAAATAT
1 TAATAATTATAATATTAAAATAT
287364 TAAT-ATTATAA
1 TAATAATTATAA
287375 AAATTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.48
22 10 0.34
23 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAATTATAATATTAAAATAT
Found at i:287380 original size:23 final size:22
Alignment explanation
Indices: 287336--287380 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
287326 TTATATTATT
*
287336 AAATTTAATAATTAAAATATTA
1 AAATTTAATAATTAAAAAATTA
287358 AAATATTAAT-ATTATAAAAATTA
1 AAAT-TTAATAATTA-AAAAATTA
287381 TATAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAATAATTAAAAAATTA
Found at i:287801 original size:22 final size:23
Alignment explanation
Indices: 287759--287801 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
287749 AAATTTATTA
* *
287759 TTATTTAAATTATATTTAAATTG
1 TTATTTAAATAATATTAAAATTG
287782 TTATTTAAA-AATATTAAAAT
1 TTATTTAAATAATATTAAAAT
287802 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATTTAAATAATATTAAAATTG
Found at i:288815 original size:21 final size:21
Alignment explanation
Indices: 288767--288812 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
288757 AAAATATTTT
* *
288767 TAAATATTAAAAATGATAATA
1 TAAATATTAAAAATAAAAATA
288788 TAAATATTAAAAAATAAAAATA
1 TAAATATT-AAAAATAAAAATA
288810 TAA
1 TAA
288813 TATGATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAATATTAAAAATAAAAATA
Found at i:288860 original size:22 final size:23
Alignment explanation
Indices: 288811--288898 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 23
288801 ATAAAAATAT
288811 AATATGATATTAATAT-AT-TTTTAA
1 AATAT-ATA-TAATATAATATTTT-A
288835 AATATATATAATATAA-ATTATT-
1 AATATATATAATATAATATT-TTA
*
288857 AATATAAATAATA-AATATTTTA
1 AATATATATAATATAATATTTTA
288879 AATATAATTATAATATAATA
1 AATAT-A-TATAATATAATA
288899 AAATATATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
21 4 0.07
22 26 0.48
23 7 0.13
24 13 0.24
25 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
AATATATATAATATAATATTTTA
Found at i:289339 original size:16 final size:16
Alignment explanation
Indices: 289267--289347 Score: 81
Period size: 16 Copynumber: 4.9 Consensus size: 16
289257 CTTAATAAAA
* *
289267 TTATTATTATAATTATT
1 TTATT-TTATTATAATT
* *
289284 TTATTTAATTTTAATT
1 TTATTTTATTATAATT
**
289300 TTATTTTATTATCAAAA
1 TTATTTTATTAT-AATT
*
289317 ATATTTTATTATAATT
1 TTATTTTATTATAATT
289333 TTATTTTATTATAAT
1 TTATTTTATTATAAT
289348 AAATTAAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 33 0.65
17 18 0.35
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:295013 original size:2 final size:2
Alignment explanation
Indices: 295006--295037 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
294996 GAGAGGCCTC
*
295006 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295038 TTATCTTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:301303 original size:116 final size:116
Alignment explanation
Indices: 301172--301400 Score: 431
Period size: 116 Copynumber: 2.0 Consensus size: 116
301162 TAAGATTTAT
*
301172 TTGGATGGGCAGTAAATTTAATTTCAGTAAGATAAAAAACTATAAGGGTGATAAGATTAATTTTT
1 TTGGATGGGCAGTAAAATTAATTTCAGTAAGATAAAAAACTATAAGGGTGATAAGATTAATTTTT
**
301237 GTAATAGTAAGATTAAAATTAATGGTGATGTATTTTGATGCAAAGTAGAGG
66 GTAATAACAAGATTAAAATTAATGGTGATGTATTTTGATGCAAAGTAGAGG
301288 TTGGATGGGCAGTAAAATTAATTTCAGTAAGATAAAAAACTATAAGGGTGATAAGATTAATTTTT
1 TTGGATGGGCAGTAAAATTAATTTCAGTAAGATAAAAAACTATAAGGGTGATAAGATTAATTTTT
301353 GTAATAACAAGATTAAAATTAATGGTGATGTATTTTGATGCAAAGTAG
66 GTAATAACAAGATTAAAATTAATGGTGATGTATTTTGATGCAAAGTAG
301401 TGGCAATGAG
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (116 bp):
TTGGATGGGCAGTAAAATTAATTTCAGTAAGATAAAAAACTATAAGGGTGATAAGATTAATTTTT
GTAATAACAAGATTAAAATTAATGGTGATGTATTTTGATGCAAAGTAGAGG
Found at i:302258 original size:15 final size:15
Alignment explanation
Indices: 302216--302278 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
302206 TTTAGATTTG
302216 ATAATTTATATATTTA
1 ATAATTTATATA-TTA
302232 TATTATATTTATATATTA
1 -A-TA-ATTTATATATTA
*
302250 ATAATTTATA-ATTT
1 ATAATTTATATATTA
302264 ATAAATTTATGATAT
1 AT-AATTTAT-ATAT
302279 ATTTATATCG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 5 0.12
15 14 0.35
16 3 0.08
17 4 0.10
18 5 0.12
19 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATAATTTATATATTA
Found at i:302286 original size:8 final size:8
Alignment explanation
Indices: 302219--302278 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
302209 AGATTTGATA
302219 ATTTATAT
1 ATTTATAT
302227 ATTTATATTAT
1 A-TT-TA-TAT
302238 ATTTATAT
1 ATTTATAT
*
302246 ATTAATA-
1 ATTTATAT
302253 ATTTATA-
1 ATTTATAT
*
302260 ATTTATAA
1 ATTTATAT
302268 ATTTATGAT
1 ATTTAT-AT
302277 AT
1 AT
302279 ATTTATATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
7 13 0.30
8 16 0.36
9 7 0.16
10 4 0.09
11 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:302661 original size:6 final size:6
Alignment explanation
Indices: 302651--302687 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
302641 ATATGATTGG
* *
302651 AAAATG AAAATA AAAATG AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
302688 TATTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:302668 original size:12 final size:12
Alignment explanation
Indices: 302651--302687 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
302641 ATATGATTGG
302651 AAAATGAAAATA
1 AAAATGAAAATA
302663 AAAATGAAAATA
1 AAAATGAAAATA
*
302675 AAAATAAAAATA
1 AAAATGAAAATA
302687 A
1 A
302688 TATTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:302673 original size:18 final size:18
Alignment explanation
Indices: 302650--302685 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
302640 GATATGATTG
*
302650 GAAAATGAAAATAAAAAT
1 GAAAATAAAAATAAAAAT
302668 GAAAATAAAAATAAAAAT
1 GAAAATAAAAATAAAAAT
302686 AATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
GAAAATAAAAATAAAAAT
Found at i:303125 original size:17 final size:18
Alignment explanation
Indices: 303103--303140 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
303093 TATATAACAC
* *
303103 AAATTATTTACATAT-TA
1 AAATTATATAAATATATA
303120 AAATTATATAAATATATA
1 AAATTATATAAATATATA
303138 AAA
1 AAA
303141 CCTTAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTATATAAATATATA
Found at i:303333 original size:18 final size:18
Alignment explanation
Indices: 303310--303364 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
303300 AATGTCTTAA
*
303310 AAATTATTTATATAATAT
1 AAATTATTTAAATAATAT
* *
303328 AAATTATTTACATATTA-
1 AAATTATTTAAATAATAT
*
303345 AAATTATATAAAT-ATAT
1 AAATTATTTAAATAATAT
303362 AAA
1 AAA
303365 ACCTTAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 15 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTATTTAAATAATAT
Found at i:303408 original size:225 final size:225
Alignment explanation
Indices: 303017--303471 Score: 777
Period size: 225 Copynumber: 2.0 Consensus size: 225
303007 TATATTTTTT
*
303017 ATTAAAATACGACATAAAATATAATAAAATATAAAAAATAATTCAATACGAATATATAAATATTT
1 ATTAAAATACGACATAAAATATAATAAAATATAAAAAATAATTCAATACGAATATATAAATATCT
*
303082 TAAAATTTATTTATATAACACAAATTATTTACATATTAAAATTATATAAATATATAAAACCTTAA
66 TAAAAATTATTTATATAACACAAATTATTTACATATTAAAATTATATAAATATATAAAACCTTAA
* *
303147 ACAATAGATTAAAAAAAGCTTTCTCTATATTTAAGAACTTAAAATCATCTTATTCTAACGCCTTC
131 ACAAAAGATTAAAAAAAGCTTTCTCTATATTTAAGAACTTAAAATCATCTTATTCCAACGCCTTC
* *
303212 GACATTAAGATTATGTAAAACTAAGGTTTG
196 AACATTAAGATTATGCAAAACTAAGGTTTG
* *
303242 ATTAAAATACGACATAAAATATAATAAAATATAAAAAATAATTCAATATGAATATATAAATGTCT
1 ATTAAAATACGACATAAAATATAATAAAATATAAAAAATAATTCAATACGAATATATAAATATCT
* *
303307 TAAAAATTATTTATATAATATAAATTATTTACATATTAAAATTATATAAATATATAAAACCTTAA
66 TAAAAATTATTTATATAACACAAATTATTTACATATTAAAATTATATAAATATATAAAACCTTAA
*
303372 ACAAAAGATTAAAAAATA-CTTTCTCTATATTTAAGAACTTAAAATCATCTTATTCCAATGCCTT
131 ACAAAAGATTAAAAAA-AGCTTTCTCTATATTTAAGAACTTAAAATCATCTTATTCCAACGCCTT
*
303436 CAACATTAAGATTATGCAAAACTAGGGTTTG
195 CAACATTAAGATTATGCAAAACTAAGGTTTG
*
303467 GTTAA
1 ATTAA
303472 TATAATTACA
Statistics
Matches: 216, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
225 215 1.00
226 1 0.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.35
Consensus pattern (225 bp):
ATTAAAATACGACATAAAATATAATAAAATATAAAAAATAATTCAATACGAATATATAAATATCT
TAAAAATTATTTATATAACACAAATTATTTACATATTAAAATTATATAAATATATAAAACCTTAA
ACAAAAGATTAAAAAAAGCTTTCTCTATATTTAAGAACTTAAAATCATCTTATTCCAACGCCTTC
AACATTAAGATTATGCAAAACTAAGGTTTG
Found at i:303496 original size:2 final size:2
Alignment explanation
Indices: 303491--303531 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
303481 AAAAAATTTT
303491 TA 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 TA T
303532 TCATCAACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:304712 original size:33 final size:32
Alignment explanation
Indices: 304650--304712 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
304640 TTAAATATGA
*
304650 TTATATAAATAAAATATTGAATATATAAAAAT
1 TTATATAAATAAAATATTAAATATATAAAAAT
*
304682 TTATATAAAATAAAATTTTAAAGTAT-TAAAA
1 TTATAT-AAATAAAATATTAAA-TATATAAAA
304713 TAATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 18 0.67
34 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (32 bp):
TTATATAAATAAAATATTAAATATATAAAAAT
Found at i:305408 original size:2 final size:2
Alignment explanation
Indices: 305401--305436 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
305391 ATTTTAAATG
305401 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
305437 GGCAAATAAA
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:305478 original size:2 final size:2
Alignment explanation
Indices: 305471--305499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
305461 CAAGAAAGGA
305471 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 A
305500 AATAGGCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:305966 original size:2 final size:2
Alignment explanation
Indices: 305959--305987 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
305949 TTTATGGTTT
305959 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
305988 TTATTGTTAA
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:306190 original size:17 final size:17
Alignment explanation
Indices: 306168--306200 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
306158 GTTTTTATTA
306168 TTTTAA-ATATTTAATTC
1 TTTTAACAT-TTTAATTC
306185 TTTTAACATTTTAATT
1 TTTTAACATTTTAATT
306201 ACTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAACATTTTAATTC
Found at i:306562 original size:2 final size:2
Alignment explanation
Indices: 306550--306582 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
306540 AAGGGGCTCC
*
306550 AT AT TT 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 A
306583 AACAAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:306906 original size:22 final size:22
Alignment explanation
Indices: 306881--306930 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
306871 AATATATTAA
* *
306881 AATTTTA-AATTAATATTTATAT
1 AATTTTATAAATAA-ATTTAAAT
306903 AATTTTATAAATAAATTTAAAT
1 AATTTTATAAATAAATTTAAAT
306925 AATTTT
1 AATTTT
306931 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTATAAATAAATTTAAAT
Found at i:308941 original size:17 final size:16
Alignment explanation
Indices: 308921--308964 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
308911 AAAATATTTA
308921 TCAATATAAATTTATAT
1 TCAATATAAATTTA-AT
*
308938 TCAATTTAAATTTAAT
1 TCAATATAAATTTAAT
*
308954 TTAATCATAAA
1 TCAAT-ATAAA
308965 AAAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (16 bp):
TCAATATAAATTTAAT
Found at i:310525 original size:19 final size:18
Alignment explanation
Indices: 310477--310527 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
310467 CTAGCTCAGC
310477 ATAA-ATAA-TATTTTTT
1 ATAATATAATTATTTTTT
* *
310493 ATTATAAAATTTATATTTTT
1 ATAATATAA-TTAT-TTTTT
310513 ATAATATAATTATTT
1 ATAATATAATTATTT
310528 ATATTACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.11
17 3 0.11
18 2 0.07
19 7 0.26
20 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATATAATTATTTTTT
Found at i:310531 original size:23 final size:21
Alignment explanation
Indices: 310484--310532 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
310474 AGCATAAATA
*
310484 ATATTTTTTATTATAAAATTT
1 ATATTTTTTAATATAAAATTT
*
310505 ATATTTTTATAATATAATTATTT
1 ATATTTTT-TAATATAA-AATTT
310528 ATATT
1 ATATT
310533 ACATTTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTTTAATATAAAATTT
Found at i:310658 original size:24 final size:23
Alignment explanation
Indices: 310595--310669 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 23
310585 TAAAAGTTTT
* *
310595 AAAAATTAGTAATTTTTTGAATA
1 AAAAATAAGTAATTTTTTAAATA
* * *
310618 AATAAGAAGTTATTTTTTTAAATA
1 AAAAATAAG-TAATTTTTTAAATA
* **
310642 AGAAAATAAGTAGTTTTTTTTATA
1 A-AAAATAAGTAATTTTTTAAATA
310666 AAAA
1 AAAA
310670 GAAAAATTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
23 9 0.22
24 25 0.62
25 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAAATAAGTAATTTTTTAAATA
Found at i:310676 original size:28 final size:28
Alignment explanation
Indices: 310617--310674 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
310607 TTTTTTGAAT
*
310617 AAATAAGAAGTTATTTTTTTAAATAAGA
1 AAATAAGTAGTTATTTTTTTAAATAAGA
310645 AAATAAGTAGTT-TTTTTTATAAA-AAGA
1 AAATAAGTAGTTATTTTTT-TAAATAAGA
310672 AAA
1 AAA
310675 ATTAGATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (28 bp):
AAATAAGTAGTTATTTTTTTAAATAAGA
Found at i:312535 original size:27 final size:29
Alignment explanation
Indices: 312488--312571 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
312478 TATATATTTT
* *
312488 TATATATTATA-ATTATATTTAATAT-ATTA
1 TATATATTATATA-AAT-TTTAATATAATAA
312517 TATAT-TTATATAAATTTTAATATAATAA
1 TATATATTATATAAATTTTAATATAATAA
* *
312545 TTTATATTATTTAAATTTTAATA-AATA
1 TATATATTATATAAATTTTAATATAATA
312572 TTTATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 8 0.17
28 18 0.38
29 22 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATTATATAAATTTTAATATAATAA
Found at i:312551 original size:37 final size:36
Alignment explanation
Indices: 312474--312554 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
312464 TATTAATAAA
* * *
312474 ATATTATATATTTTTATATATTATAATTATATTTAAT
1 ATATTATATATTTATATAAATTATAATTATAATT-AT
*
312511 ATATTATATATTTATATAAATTTTAATATAATAATT-T
1 ATATTATATATTTATATAAATTATAAT-T-ATAATTAT
312548 ATATTAT
1 ATATTAT
312555 TTAAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 32 0.84
38 1 0.03
39 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
ATATTATATATTTATATAAATTATAATTATAATTAT
Found at i:312557 original size:22 final size:22
Alignment explanation
Indices: 312457--312558 Score: 58
Period size: 22 Copynumber: 4.7 Consensus size: 22
312447 AGATACGATG
*
312457 ATTTATA-TA-TTAATAAAAT-
1 ATTTATATTATTTAATATAATA
*
312476 ATTATATATT-TTTATATATTATA
1 ATT-TATATTATTTA-ATATAATA
312499 A--T-TA-TATTTAATATATTATA
1 ATTTATATTATTTAATATA--ATA
*
312519 TATTTATATAAATTTTAATATAATA
1 -ATTTATAT-TA-TTTAATATAATA
312544 ATTTATATTATTTAA
1 ATTTATATTATTTAA
312559 ATTTTAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 27
0.66 0.05 0.28
Matches are distributed among these distances:
18 5 0.08
19 9 0.14
20 8 0.13
21 5 0.08
22 10 0.16
23 3 0.05
24 10 0.16
25 3 0.05
26 1 0.02
27 9 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTATATTATTTAATATAATA
Found at i:313062 original size:3 final size:3
Alignment explanation
Indices: 313054--313079 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
313044 TTTTTGTCAT
313054 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
313080 GACAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:313841 original size:56 final size:57
Alignment explanation
Indices: 313749--313859 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 57
313739 TGCAAAAAGA
* ** * *
313749 GTTTAACTTTGTCGTAATGCTGGATCTAGATTGCAAGAACGTCTTGGTG-TTTTTGG
1 GTTTAACTTTGTCGTAATGCTAGAAATAGATCGCAAGAACGTCATGGTGATTTTTGG
* *
313805 GTTTAACTTTG-CTGTAGTGCTAGAAATAGATCGCAAGAATGTCATGGTGATTTTT
1 GTTTAACTTTGTC-GTAATGCTAGAAATAGATCGCAAGAACGTCATGGTGATTTTT
313860 TTCTTCTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 1 0.02
56 40 0.87
57 5 0.11
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (57 bp):
GTTTAACTTTGTCGTAATGCTAGAAATAGATCGCAAGAACGTCATGGTGATTTTTGG
Found at i:314606 original size:16 final size:16
Alignment explanation
Indices: 314585--314616 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
314575 GTTCACATTA
314585 ATGATCCTGCACTCTT
1 ATGATCCTGCACTCTT
314601 ATGATCCTGCACTCTT
1 ATGATCCTGCACTCTT
314617 CCTATGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGATCCTGCACTCTT
Found at i:317574 original size:2 final size:2
Alignment explanation
Indices: 317567--317592 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
317557 GCTCTCAATT
317567 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
317593 GCTGCTATGT
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:323200 original size:2 final size:2
Alignment explanation
Indices: 323193--323233 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
323183 ACAAAGAGGC
323193 AT AT AT 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 AT AT AT A
323234 CACACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:324641 original size:25 final size:25
Alignment explanation
Indices: 324613--324662 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
324603 CTTTTCAATT
324613 TTTAAAATTATTTTCGAATTTAAAA
1 TTTAAAATTATTTTCGAATTTAAAA
324638 TTTAAAATTATTTTCGAATTTAAAA
1 TTTAAAATTATTTTCGAATTTAAAA
324663 ACTTGAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TTTAAAATTATTTTCGAATTTAAAA
Found at i:328413 original size:172 final size:171
Alignment explanation
Indices: 327780--328823 Score: 855
Period size: 172 Copynumber: 6.0 Consensus size: 171
327770 AAAATGTAAT
*
327780 ATGGTAATTAACTACTATTTAATATGTCAAATATCATCACAAATAAGATGGGTTATACACTTGGA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGAT--GTTATACACTTGGA
* * ** * * * *
327845 TATTAAAATC-ATTTATACAAAAGCAATGCCAAAATCTACTAAAATCAAATAATTATATATGAT-
64 TATTAAAATCAATTT-TACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATG-TC
* * * * *
327908 ATTTAAATTTTATGAAAACTATCATTTGATGAACATCGTAATAAG
127 ATTCAAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
* *
327953 ATGGTAATTAACTACTATTTAATATGTCAAATATCATCATAAATAAGATGGATTATACACTTGGA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGAT-G-TTATACACTTGGA
* * * * * * *
328018 TATTAAAATCAATTTTATAAGAAGCAACAACAACAAAATTTAGTAAAATCTAA-TATTACTAAAT
64 TATTAAAATCAATTTTA-CA-AA--AACGATAACAAAATCTAATAAAATC-AAGTAATAATAAAT
* * * *
328082 GGT-ATTCAAATTTAATGAAAACTATCGTATAACGAACATTCTAATAAG
124 -GTCATTCAAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
* * * * * * * * *
328130 ATGTTAATTAACTACTATTTAATATGTCAACAATCATTACAAAGATGGT-TTATAAAATTAGATA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGATGTTATACACTTGGATA
* * * * ** * * ** * *
328194 TTAAAATAAATTTTATAAAACCGACAGTAAAATCTAGTAAAATCAAGTGATAATACGTGTTATTT
66 TTAAAATCAATTTTACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATGTCATTC
* * * * *
328259 AAATTTTATGAAGATTGTTATCTAACGAACATCCTAGTAAG
131 AAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
* * * * * * *
328300 ATGGTAATCAACTACCATTCAGTATGCCAAAAATCATCACAAACAAGGTAGTATATACACTTGGA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGAT-GT-TATACACTTGGA
* * *
328365 TATTAAAATCAATTTTACAAAAACGATAA-TAAATCTAATAAAATCAAGTGATAATATATGTCAT
64 TATTAAAATCAATTTTACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATGTCAT
** *** *
328429 AT-AAATTTTATGAGGACTATTGCCTAATGAACATCCTAATAAG
129 -TCAAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
* * * * * * * * *
328472 ATAGTAATTAGCCATTACTTAATAGGTCAAAAATCATCACAAATAAGATGATCTATTCACCTAGA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGATG-T-TATACACTTGGA
* * * ****
328537 TATTAAAATAAATTTTACAAAAACGATAACAAAAT-TAATAAAATTAAATAATAATGCGCGTCAT
64 TATTAAAATCAATTTTACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATGTCAT
* *** * *
328601 TCAAATTTTAT-AAAGACAATTGCCTAACGAACTTCCTAAGAAG
129 TCAAATTTTATGAAA-ACTATCATCTAACGAACATCCTAATAAG
* * * * * ** * *
328644 ATAGTAATTAGCTACTACTCAATATGTCAAAACTCATCACAAGCAAAATGATCTATTCACTTGGA
1 ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGATG-T-TATACACTTGGA
* * * * *
328709 TATTAAAATCAATTTTACAAAAACGAAAACAAAATCTATTAAAATCAAGTAATAATAAGTGGCAC
64 TATTAAAATCAATTTTACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATGTCAT
* * * * *
328774 TCAAATTTTATGAAAATTGTCATCTAATGAACATTCTATTAAG
129 TCAAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
328817 ATGGTAA
1 ATGGTAA
328824 CCATTTAACA
Statistics
Matches: 704, Mismatches: 147, Indels: 40
0.79 0.16 0.04
Matches are distributed among these distances:
169 4 0.01
170 100 0.14
171 3 0.00
172 286 0.41
173 167 0.24
174 34 0.05
175 2 0.00
177 105 0.15
178 3 0.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (171 bp):
ATGGTAATTAACTACTATTTAATATGTCAAAAATCATCACAAATAAGATGTTATACACTTGGATA
TTAAAATCAATTTTACAAAAACGATAACAAAATCTAATAAAATCAAGTAATAATAAATGTCATTC
AAATTTTATGAAAACTATCATCTAACGAACATCCTAATAAG
Found at i:329317 original size:2 final size:2
Alignment explanation
Indices: 329310--329342 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
329300 AAATTTGTAA
329310 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 T
329343 GTTTTTTTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:335355 original size:16 final size:16
Alignment explanation
Indices: 335336--335413 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
335326 GACTCGAATA
335336 CGAAATGACCTGAACT
1 CGAAATGACCTGAACT
*
335352 CGAAATGATCC--AACC
1 CGAAATGA-CCTGAACT
*
335367 CGAAATGATCTGAAC-
1 CGAAATGACCTGAACT
* ** *
335382 CTGAAATAACCCAAATT
1 C-GAAATGACCTGAACT
335399 CGAAATGACCTGAAC
1 CGAAATGACCTGAAC
335414 CTGAAAATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.26
16 30 0.65
17 3 0.07
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (16 bp):
CGAAATGACCTGAACT
Found at i:335374 original size:31 final size:32
Alignment explanation
Indices: 335336--335425 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
335326 GACTCGAATA
* *
335336 CGAAATGACCTGAA-CTCGAAATGATCC-AACC
1 CGAAATGACCTGAACCT-GAAATAACCCAAACC
* **
335367 CGAAATGATCTGAACCTGAAATAACCCAAATT
1 CGAAATGACCTGAACCTGAAATAACCCAAACC
335399 CGAAATGACCTGAACCTGAAAATAACC
1 CGAAATGACCTGAACCTG-AAATAACC
335426 TGAAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.42
32 21 0.42
33 8 0.16
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (32 bp):
CGAAATGACCTGAACCTGAAATAACCCAAACC
Found at i:335419 original size:16 final size:16
Alignment explanation
Indices: 335337--335429 Score: 59
Period size: 16 Copynumber: 5.8 Consensus size: 16
335327 ACTCGAATAC
335337 GAAATGACCTGAA-CT
1 GAAATGACCTGAACCT
*
335352 CGAAATGATCC--AACCC
1 -GAAATGA-CCTGAACCT
*
335368 GAAATGATCTGAACCT
1 GAAATGACCTGAACCT
* * **
335384 GAAATAACC-CAAATT
1 GAAATGACCTGAACCT
335399 CGAAATGACCTGAACCT
1 -GAAATGACCTGAACCT
*
335416 GAAAATAACCTGAA
1 G-AAATGACCTGAA
335430 AATTTTAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
14 1 0.02
15 12 0.21
16 28 0.49
17 16 0.28
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (16 bp):
GAAATGACCTGAACCT
Found at i:335893 original size:25 final size:25
Alignment explanation
Indices: 335840--335892 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
335830 AAAATTTTAT
*
335840 AAAATTAATTATTTTTAAAAAACTA
1 AAAATTAATTATATTTAAAAAACTA
* *
335865 AAAATTAA-TATATTTGAAAATCTA
1 AAAATTAATTATATTTAAAAAACTA
335889 AAAA
1 AAAA
335893 AAAGAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAATTAATTATATTTAAAAAACTA
Found at i:339086 original size:21 final size:21
Alignment explanation
Indices: 339038--339096 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
339028 TGAAAATATA
* **
339038 TTTTTGAATAAAATGATGCAT
1 TTTTTGGATAAAAAAATGCAT
**
339059 TGGTTGGATAAAAAAATGCAT
1 TTTTTGGATAAAAAAATGCAT
*
339080 TTTTTGGATGAAAAAAT
1 TTTTTGGATAAAAAAAT
339097 ACAACTTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTTTGGATAAAAAAATGCAT
Found at i:339105 original size:21 final size:21
Alignment explanation
Indices: 339062--339105 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
339052 GATGCATTGG
* **
339062 TTGGATAAAAAAATGCATTTT
1 TTGGATAAAAAAATACAACTT
*
339083 TTGGATGAAAAAATACAACTT
1 TTGGATAAAAAAATACAACTT
339104 TT
1 TT
339106 AATAACCAAA
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:0.07, G:0.14, T:0.36
Consensus pattern (21 bp):
TTGGATAAAAAAATACAACTT
Found at i:339533 original size:24 final size:22
Alignment explanation
Indices: 339483--339555 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
339473 TTTCCCTAAC
* *
339483 ATATA-TAAATATATTAAAATTT
1 ATATATTAAATATA-TAATATAT
339505 ATATAATGTAAATTATATATATATAT
1 ATAT-AT-TAAA-TATATA-ATATAT
*
339531 ATATATTAAATATATAATATTT
1 ATATATTAAATATATAATATAT
339553 ATA
1 ATA
339556 CACAATTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 12 0.28
23 7 0.16
24 4 0.09
25 8 0.19
26 12 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
ATATATTAAATATATAATATAT
Found at i:339678 original size:3 final size:3
Alignment explanation
Indices: 339672--339705 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
339662 CATCTTTTTT
339672 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
339706 TAAAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:339852 original size:13 final size:14
Alignment explanation
Indices: 339825--339867 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
339815 ATGTTTTAAA
339825 TTAAA-AATAATTT
1 TTAAATAATAATTT
339838 TTAAATAATAATTTT
1 TTAAATAATAA-TTT
*
339853 TTAAAATAAAAATTT
1 TT-AAATAATAATTT
339868 AAATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 8 0.31
16 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAATAATAATTT
Found at i:339859 original size:16 final size:15
Alignment explanation
Indices: 339825--339867 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
339815 ATGTTTTAAA
339825 TTAAA-AATAA-TTT
1 TTAAATAATAATTTT
339838 TTAAATAATAATTTT
1 TTAAATAATAATTTT
*
339853 TTAAAATAAAAATTT
1 TT-AAATAATAATTT
339868 AAATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 5 0.19
16 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATAATAATTTT
Found at i:343886 original size:2 final size:2
Alignment explanation
Indices: 343881--343912 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
343871 AAATTGTGTG
343881 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
343913 AAATTTCCAA
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):
TA
Found at i:344003 original size:17 final size:16
Alignment explanation
Indices: 343977--344016 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
343967 CGGCAGCAAA
*
343977 ATAAATAAAACATAAT
1 ATAAATAAAAAATAAT
343993 ATAATATAAAAAATAAT
1 ATAA-ATAAAAAATAAT
344010 ATAAATA
1 ATAAATA
344017 TTTATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATAAAAAATAAT
Found at i:345264 original size:17 final size:17
Alignment explanation
Indices: 345231--345277 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
345221 AATAAAATTT
*
345231 TTTTAAATAT-ATAATA
1 TTTTAAAAATAATAATA
*
345247 TTTTAAAAATAATTATA
1 TTTTAAAAATAATAATA
**
345264 TTAAAAAAATAATA
1 TTTTAAAAATAATA
345278 TAAATATGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTTAAAAATAATAATA
Found at i:345487 original size:19 final size:19
Alignment explanation
Indices: 345441--345488 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
345431 TATATTTAAT
*
345441 ATTTTATAATTATATATAAA
1 ATTTTA-AATTATACATAAA
* *
345461 ATTATAAATTTTACATAAA
1 ATTTTAAATTATACATAAA
*
345480 CTTTTAAAT
1 ATTTTAAAT
345489 CTATTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTAAATTATACATAAA
Found at i:345676 original size:15 final size:14
Alignment explanation
Indices: 345634--345696 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
345624 AAAATTTGGA
*
345634 TAATTAAAATGATT
1 TAATTAAAATAATT
*
345648 TAAATCAAAATAATT
1 T-AATTAAAATAATT
*
345663 TGAATTAAATTAATT
1 T-AATTAAAATAATT
**
345678 TAATTTTAA-AATT
1 TAATTAAAATAATT
345691 TAATTA
1 TAATTA
345697 TTTAGATTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 9 0.23
14 6 0.15
15 24 0.62
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (14 bp):
TAATTAAAATAATT
Found at i:345710 original size:21 final size:21
Alignment explanation
Indices: 345658--345710 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
345648 TAAATCAAAA
345658 TAATTTG-AATTAAATTAATT
1 TAATTTGAAATTAAATTAATT
* *
345678 TAATTTTAAAATTTAATT-ATT
1 TAA-TTTGAAATTAAATTAATT
345699 TAGATTTGAAAT
1 TA-ATTTGAAAT
345711 GATACAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
TAATTTGAAATTAAATTAATT
Found at i:345746 original size:22 final size:22
Alignment explanation
Indices: 345715--345756 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
345705 TGAAATGATA
*
345715 CAAATCTAAATAGTTTAACTCT
1 CAAATCTAAAAAGTTTAACTCT
* *
345737 CAAATTTAAAAATTTTAACT
1 CAAATCTAAAAAGTTTAACT
345757 TAAAATGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
CAAATCTAAAAAGTTTAACTCT
Found at i:345956 original size:19 final size:19
Alignment explanation
Indices: 345932--345979 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
345922 TAGATACAAA
* **
345932 ATATTTTTAATATTTTAAT
1 ATATTTTTAATAATAAAAT
*
345951 ATATTTTAAATAATAAAAT
1 ATATTTTTAATAATAAAAT
345970 ATATTTTTAA
1 ATATTTTTAA
345980 ATCTAAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTTTAATAATAAAAT
Found at i:346413 original size:22 final size:20
Alignment explanation
Indices: 346372--346428 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
346362 TATAATAAAA
*
346372 AATTTATATAAATATAATAT
1 AATTTAAATAAATATAATAT
*
346392 AATTTAAATATAATCATGATAT
1 AATTTAAATA-AAT-ATAATAT
*
346414 AA--AAAATAAATATAA
1 AATTTAAATAAATATAA
346429 CATGAATCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 14 0.45
21 3 0.10
22 8 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATATAATAT
Found at i:348492 original size:2 final size:2
Alignment explanation
Indices: 348485--348516 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
348475 GTGTGCGTGC
348485 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
348517 GTATCATATG
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:348918 original size:2 final size:2
Alignment explanation
Indices: 348911--348946 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
348901 TGTCTCTATT
348911 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
348947 GTGATTTTCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:350943 original size:16 final size:17
Alignment explanation
Indices: 350901--350947 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
350891 GTTTGATAAT
*
350901 TTATATATTTGTATTGTA
1 TTATATATTT-TATTATA
350919 -TATATATTTTATTATA
1 TTATATATTTTATTATA
350935 TTATA-ATTTTATT
1 TTATATATTTTATT
350948 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTATATATTTTATTATA
Found at i:356037 original size:16 final size:17
Alignment explanation
Indices: 355996--356041 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
355986 ATTTGATACG
*
355996 TTATTATTATTATTTAA
1 TTATTATTAATATTTAA
* *
356013 TAATT-TTAATATTT-T
1 TTATTATTAATATTTAA
356028 TTATTATTAATATT
1 TTATTATTAATATT
356042 GTGATCGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTAATATTTAA
Found at i:357218 original size:20 final size:19
Alignment explanation
Indices: 357179--357218 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
357169 ACAATACAAT
*
357179 TTAAAAAACTTTATAAATA
1 TTAAAAAACTTTAAAAATA
*
357198 TTAAATAACTTATAAAAATA
1 TTAAAAAACTT-TAAAAATA
357218 T
1 T
357219 AATTGTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAAACTTTAAAAATA
Found at i:361509 original size:10 final size:10
Alignment explanation
Indices: 361453--361502 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
361443 GAACATTATC
*
361453 ATAATAAATT
1 ATAATAAATA
361463 ATAATAAAT-
1 ATAATAAATA
361472 ATAAATAAATA
1 AT-AATAAATA
361483 ATAAT-AATA
1 ATAATAAATA
361492 ATAATAAATA
1 ATAATAAATA
361502 A
1 A
361503 AATTAAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 11 0.30
10 24 0.65
11 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATAAATA
Found at i:363709 original size:16 final size:16
Alignment explanation
Indices: 363669--363710 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
363659 ACATATTAAA
363669 ATATTTTAAAAATTAT
1 ATATTTTAAAAATTAT
* * *
363685 TTATATTAATAATTAT
1 ATATTTTAAAAATTAT
363701 ATATTTTAAA
1 ATATTTTAAA
363711 TTTATAATTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTTAAAAATTAT
Found at i:363759 original size:16 final size:16
Alignment explanation
Indices: 363721--363781 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
363711 TTTATAATTA
363721 AATTTAAATAAATATT
1 AATTTAAATAAATATT
* *
363737 -TTATTAATTAAATATT
1 AAT-TTAAATAAATATT
363753 AATTTAAATCAAATCAAATT
1 AATTTAAAT-AAAT---ATT
363773 AATTTAAAT
1 AATTTAAAT
363782 TTAAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 17 0.49
17 5 0.14
20 12 0.34
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAATAAATATT
Found at i:364097 original size:2 final size:2
Alignment explanation
Indices: 364090--364129 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
364080 AATAAAGACA
364090 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
364130 TACAATAAAA
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:366264 original size:21 final size:21
Alignment explanation
Indices: 366240--366291 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
366230 CTCAGGCCCC
*
366240 TCCTACATATTTCTCCATTTA
1 TCCTTCATATTTCTCCATTTA
366261 TCCTTCATATTTCTCCATTTA
1 TCCTTCATATTTCTCCATTTA
366282 TCCTTCATAT
1 TCCTTCATAT
366292 CTATTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (21 bp):
TCCTTCATATTTCTCCATTTA
Found at i:373275 original size:55 final size:54
Alignment explanation
Indices: 373211--373392 Score: 188
Period size: 55 Copynumber: 3.3 Consensus size: 54
373201 TACGACTCTG
** *
373211 AGTGACACCAAGTCACTACAATCCTGATCGCCACTGTGGCATTATCACAACATTA
1 AGTGACACCAAGTCACTACAA-CCTGATCGCCACCATGGCATCATCACAACATTA
* * * * * * *
373266 GGTGGCACCATGTCACTCCAAACTGAATCACCGCCATGGCATCATCACAACATTA
1 AGTGACACCAAGTCACTACAACCTG-ATCGCCACCATGGCATCATCACAACATTA
* * *
373321 AGTGACACCAAGTCACTAAGAACCTGATCGCCACCAAGGCATCAAT-ATAAC-TTCA
1 AGTGACACCAAGTCACT-ACAACCTGATCGCCACCATGGCATC-ATCACAACATT-A
373376 AGTGACACCAAGTCACT
1 AGTGACACCAAGTCACT
373393 CAAAATTTGA
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
54 5 0.05
55 91 0.88
56 7 0.07
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.20
Consensus pattern (54 bp):
AGTGACACCAAGTCACTACAACCTGATCGCCACCATGGCATCATCACAACATTA
Found at i:377698 original size:9 final size:9
Alignment explanation
Indices: 377684--377718 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
377674 TTATGAGTTC
377684 ATAAATAAA
1 ATAAATAAA
*
377693 ATAAATAAT
1 ATAAATAAA
*
377702 ATATATAAA
1 ATAAATAAA
377711 ATAAATAA
1 ATAAATAA
377719 TCATAAGCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAATAAA
Found at i:379133 original size:20 final size:20
Alignment explanation
Indices: 379100--379191 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
379090 AAAAAAGATC
*
379100 ACCTAGTATGATTACATTCA
1 ACCTAATATGATTACATTCA
* *
379120 ACCTAATATAATTACATTCC
1 ACCTAATATGATTACATTCA
*
379140 ACCTAATATGTTTACATTCAA
1 ACCTAATATGATTACATTC-A
*
379161 ACC--ATATGATGACATTCA
1 ACCTAATATGATTACATTCA
*
379179 A-ATAATATGATTA
1 ACCTAATATGATTA
379192 TTCAAACAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
18 2 0.03
19 20 0.34
20 34 0.58
21 3 0.05
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (20 bp):
ACCTAATATGATTACATTCA
Found at i:379186 original size:19 final size:19
Alignment explanation
Indices: 379106--379191 Score: 82
Period size: 19 Copynumber: 4.4 Consensus size: 19
379096 GATCACCTAG
*
379106 TATGATTACATTCAACCTAA
1 TATGATTACATTCAA-ATAA
* **
379126 TATAATTACATTCCACCTAA
1 TATGATTACATT-CAAATAA
* **
379146 TATGTTTACATTCAAACCA
1 TATGATTACATTCAAATAA
*
379165 TATGATGACATTCAAATAA
1 TATGATTACATTCAAATAA
379184 TATGATTA
1 TATGATTA
379192 TTCAAACAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
19 25 0.48
20 25 0.48
21 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (19 bp):
TATGATTACATTCAAATAA
Found at i:379204 original size:20 final size:20
Alignment explanation
Indices: 379179--379219 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
379169 ATGACATTCA
* *
379179 AATAATATGATTATTCAAAC
1 AATAATATAATGATTCAAAC
379199 AATAATATAATGATTCAAAC
1 AATAATATAATGATTCAAAC
379219 A
1 A
379220 TTCAAACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (20 bp):
AATAATATAATGATTCAAAC
Found at i:382665 original size:119 final size:119
Alignment explanation
Indices: 382480--382719 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 119
382470 TGGCAAGAAC
*
382480 AACATCAACAGATAGAGCGAAGCACATTAAGTCGACTTTCTTCTATGATTAATTCCTTGATCACA
1 AACATCAACAGATAGAGCGAAGAACATTAAGTCGACTTTCTTCTATGATTAATTCCTTGATCACA
*
382545 GTGTCAAGTGTTGGTAAGGAACCTCTATGAAGAAGAGAACTATGAATGGATTCA
66 GTGTCAAGTGTTGGCAAGGAACCTCTATGAAGAAGAGAACTATGAATGGATTCA
*
382599 AACATCAACAGATAGAGCGAAGAACATTAAGTCGACTTTCTTCTATGATTAATTTCTTGATCACA
1 AACATCAACAGATAGAGCGAAGAACATTAAGTCGACTTTCTTCTATGATTAATTCCTTGATCACA
382664 GTGTCAAGTGTTGGCAAGGAACCTCTATGAAGAAGAGAACTATGAATGGATTCA
66 GTGTCAAGTGTTGGCAAGGAACCTCTATGAAGAAGAGAACTATGAATGGATTCA
382718 AA
1 AA
382720 TTCTTCTTGA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (119 bp):
AACATCAACAGATAGAGCGAAGAACATTAAGTCGACTTTCTTCTATGATTAATTCCTTGATCACA
GTGTCAAGTGTTGGCAAGGAACCTCTATGAAGAAGAGAACTATGAATGGATTCA
Found at i:383963 original size:20 final size:20
Alignment explanation
Indices: 383903--383950 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
383893 AAAAAAGATC
383903 ACCTAATATAATTACATTCA
1 ACCTAATATAATTACATTCA
383923 ACCTAATATAATTACATTCA
1 ACCTAATATAATTACATTCA
383943 ACCTAATA
1 ACCTAATA
383951 CGATTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ACCTAATATAATTACATTCA
Found at i:383999 original size:17 final size:18
Alignment explanation
Indices: 383955--384000 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
383945 CTAATACGAT
*
383955 TATATTCAAACCATATGA
1 TATATTCAAACAATATGA
*
383973 TGACATTCAAACAATATGA
1 T-ATATTCAAACAATATGA
383992 T-TATTCAAA
1 TATATTCAAA
384001 TATTCAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 16 0.67
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (18 bp):
TATATTCAAACAATATGA
Found at i:384819 original size:21 final size:20
Alignment explanation
Indices: 384795--384922 Score: 100
Period size: 21 Copynumber: 6.1 Consensus size: 20
384785 TTTGGTAACC
384795 TTTGATAGTCTTTGATATAAT
1 TTTGATAGT-TTTGATATAAT
*
384816 TTTGATAGTTTTTAGTATAAT
1 TTTGATAGTTTTGA-TATAAT
*
384837 TTTAGTAATA-TTTT-ATATGAT
1 TTT-G--ATAGTTTTGATATAAT
*
384858 TTT-ATTAGCTTTTAATATAAT
1 TTTGA-TAG-TTTTGATATAAT
* *
384879 TTTGATAAATTTTGGTATAAT
1 TTTGAT-AGTTTTGATATAAT
*
384900 TTTGATAAGTTTTGACATAAT
1 TTTGAT-AGTTTTGATATAAT
384921 TT
1 TT
384923 CAATACTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
20 8 0.09
21 66 0.75
22 4 0.05
23 4 0.05
24 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTGATAGTTTTGATATAAT
Found at i:384889 original size:10 final size:10
Alignment explanation
Indices: 384876--384914 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
384866 CTTTTAATAT
384876 AATTTTGATA
1 AATTTTGATA
*
384886 AATTTTGGTA
1 AATTTTGATA
384896 TAATTTTGATA
1 -AATTTTGATA
*
384907 AGTTTTGA
1 AATTTTGA
384915 CATAATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (10 bp):
AATTTTGATA
Found at i:384902 original size:42 final size:43
Alignment explanation
Indices: 384805--384906 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 43
384795 TTTGATAGTC
* *
384805 TTTGATATAATTTTGATAGTTTTTAGTATAATTTTAGTAATAT
1 TTTGATATAATTTTGATAGCTTTTAATATAATTTTAGTAATAT
*
384848 TTT-ATATGATTTT-ATTAGCTTTTAATATAATTTT-GATAA-AT
1 TTTGATATAATTTTGA-TAGCTTTTAATATAATTTTAG-TAATAT
*
384889 TTTGGTATAATTTTGATA
1 TTTGATATAATTTTGATA
384907 AGTTTTGACA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
41 7 0.14
42 39 0.78
43 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (43 bp):
TTTGATATAATTTTGATAGCTTTTAATATAATTTTAGTAATAT
Found at i:384920 original size:42 final size:42
Alignment explanation
Indices: 384805--384922 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
384795 TTTGATAGTC
*
384805 TTTGATATAATTTTGATAGTTTTTAGTATAATTTTAGTAATAT
1 TTTGATATAATTTTGATAG-TTTTAATATAATTTTAGTAATAT
*
384848 TTT-ATATGATTTT-ATTAGCTTTTAATATAATTTT-GATAA-AT
1 TTTGATATAATTTTGA-TAG-TTTTAATATAATTTTAG-TAATAT
* * *
384889 TTTGGTATAATTTTGATAAGTTTTGACATAATTT
1 TTTGATATAATTTTGAT-AGTTTTAATATAATTT
384923 CAATACTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
41 7 0.11
42 50 0.79
43 6 0.10
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (42 bp):
TTTGATATAATTTTGATAGTTTTAATATAATTTTAGTAATAT
Found at i:384960 original size:21 final size:21
Alignment explanation
Indices: 384936--385064 Score: 65
Period size: 21 Copynumber: 6.2 Consensus size: 21
384926 TACTTTTTAG
384936 TAACTTTCATTATAATTTTGA
1 TAACTTTCATTATAATTTTGA
* *
384957 TAACTTTTGA-TATACTTTTG-
1 TAAC-TTTCATTATAATTTTGA
* * **
384977 TTACTTCTTAACATAATTTTGA
1 TAACTT-TCATTATAATTTTGA
*
384999 TAAC--ACATGATATAATTTTGA
1 TAACTTTCAT--TATAATTTTGA
*
385020 TAACCTTT-AATATAATTTTGA
1 TAA-CTTTCATTATAATTTTGA
* *
385041 TAA--TACATATAAAATTTTGA
1 TAACTTTCAT-TATAATTTTGA
385061 TAAC
1 TAAC
385065 GTTTGAGATA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 18 0.22
21 48 0.60
22 8 0.10
23 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (21 bp):
TAACTTTCATTATAATTTTGA
Found at i:384993 original size:42 final size:42
Alignment explanation
Indices: 384947--385084 Score: 136
Period size: 42 Copynumber: 3.3 Consensus size: 42
384937 AACTTTCATT
*** * * *
384947 ATAATTTTGATAACTTTTGATATACTTTTG-TTACTTCTTAAC
1 ATAATTTTGATAACACATGATATAATTTTGATAACCT-TTAAC
*
384989 ATAATTTTGATAACACATGATATAATTTTGATAACCTTTAAT
1 ATAATTTTGATAACACATGATATAATTTTGATAACCTTTAAC
* * * * *
385031 ATAATTTTGATAATACAT-ATAAAATTTTGATAACGTTTGAG
1 ATAATTTTGATAACACATGATATAATTTTGATAACCTTTAAC
*
385072 ATAATTTAGATAA
1 ATAATTTTGATAA
385085 TCTTCTATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 31 0.38
42 47 0.57
43 4 0.05
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (42 bp):
ATAATTTTGATAACACATGATATAATTTTGATAACCTTTAAC
Found at i:385076 original size:41 final size:42
Alignment explanation
Indices: 384984--385085 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 42
384974 TTGTTACTTC
* * *
384984 TTAACATAATTTTGATAACACATGATATAATTTTGATAACCT
1 TTAAGATAATTTTGATAATACATGATAAAATTTTGATAACCT
* *
385026 TTAATATAATTTTGATAATACAT-ATAAAATTTTGATAACGT
1 TTAAGATAATTTTGATAATACATGATAAAATTTTGATAACCT
* *
385067 TTGAGATAATTTAGATAAT
1 TTAAGATAATTTTGATAAT
385086 CTTCTATATA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 32 0.60
42 21 0.40
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (42 bp):
TTAAGATAATTTTGATAATACATGATAAAATTTTGATAACCT
Found at i:385095 original size:62 final size:61
Alignment explanation
Indices: 384991--385106 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 61
384981 TTCTTAACAT
* *
384991 AATTTTGATAACACATGATATAATTTTGATAACCTTTAATATAATTTTGATAATACATATAA
1 AATTTTGATAACACATGAGATAATTTAGATAACCTTTAATATAATTTTG-TAATACATATAA
*** *
385053 AATTTTGATAACGTTTGAGATAATTTAGATAATCTTCT-ATATAATTTTGTAATA
1 AATTTTGATAACACATGAGATAATTTAGATAACCTT-TAATATAATTTTGTAATA
385107 GTTCTGATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 5 0.11
62 41 0.87
63 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.44
Consensus pattern (61 bp):
AATTTTGATAACACATGAGATAATTTAGATAACCTTTAATATAATTTTGTAATACATATAA
Found at i:386643 original size:14 final size:14
Alignment explanation
Indices: 386624--386661 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
386614 TATTTGATAT
386624 TATTATAAAAAAAA
1 TATTATAAAAAAAA
*
386638 TATTAT-AAAAATA
1 TATTATAAAAAAAA
386651 TATGTATAAAA
1 TAT-TATAAAA
386662 TAACAAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 9 0.43
15 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
TATTATAAAAAAAA
Found at i:389668 original size:44 final size:42
Alignment explanation
Indices: 389581--389675 Score: 104
Period size: 46 Copynumber: 2.2 Consensus size: 42
389571 TAATTTATTT
*
389581 ATATTATTAATATTTATTATTTATAATTAATAATAATTTTAAAAA
1 ATATT-TTAATATTTATTATTTATAATTAATAATAA-TAT-AAAA
*
389626 ATATTTTAATATTTATATATTTTATAATTAA-ATTTAA-ATAAAA
1 ATATTTTAATATTTAT-TA-TTTATAATTAATA-ATAATATAAAA
389669 ATATTTT
1 ATATTTT
389676 TTAATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
43 11 0.24
44 12 0.27
45 8 0.18
46 14 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
ATATTTTAATATTTATTATTTATAATTAATAATAATATAAAA
Found at i:390236 original size:12 final size:12
Alignment explanation
Indices: 390213--390246 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
390203 ATAATTAGTA
390213 AAAAATT-A-TT
1 AAAAATTAATTT
390223 AAAAATTAATTT
1 AAAAATTAATTT
390235 AAAAATTAATTT
1 AAAAATTAATTT
390247 TATATCGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 1 0.05
12 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAAATTAATTT
Found at i:390522 original size:11 final size:11
Alignment explanation
Indices: 390493--390543 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
390483 TTTTCACTAC
390493 AAAATAAAAA-
1 AAAATAAAAAT
*
390503 AAATTTAAAAAT
1 AAA-ATAAAAAT
390515 AAAATAAAAAT
1 AAAATAAAAAT
* *
390526 ATAATAAATAAA
1 AAAATAAA-AAT
390538 AAAATA
1 AAAATA
390544 TCTTTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 3 0.09
11 20 0.61
12 10 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATAAAAAT
Done.