Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold443
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: 318098
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 2 of 3
Found at i:123417 original size:20 final size:20
Alignment explanation
Indices: 123376--123417 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
123366 TAAAAAATAT
*
123376 ATTTTTCTATAATATTATAA
1 ATTTTTCTATAATATTAAAA
*
123396 ATTTTTTTATTAAT-TTAAAA
1 ATTTTTCTA-TAATATTAAAA
123416 AT
1 AT
123418 AAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTCTATAATATTAAAA
Found at i:123907 original size:20 final size:21
Alignment explanation
Indices: 123884--123967 Score: 75
Period size: 20 Copynumber: 4.0 Consensus size: 21
123874 AATTTAATTT
123884 AATTTAAATTTATTT-TTTAA
1 AATTTAAATTTATTTATTTAA
* *
123904 AATTAAAATTTAATTTATAATAA
1 AATTTAAATTT-ATTTAT-TTAA
* * *
123927 AAATTAAA-TTATTAATTTTTA
1 AATTTAAATTTATTTA-TTTAA
123948 AA-TTAAATTTATTTATTTAA
1 AATTTAAATTTATTTATTTAA
123968 TAAAAATTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
20 19 0.38
21 18 0.36
22 4 0.08
23 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTAAATTTATTTATTTAA
Found at i:123941 original size:25 final size:24
Alignment explanation
Indices: 123902--123984 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
123892 TTTATTTTTT
*
123902 AAAATTAAAAT-TTAATTTATAATA
1 AAAATTAAATTATTAATTT-TAATA
123926 AAAATTAAATTATTAATTTT--T-
1 AAAATTAAATTATTAATTTTAATA
*
123947 -AAATTAAATTTATTTA-TTTAATA
1 AAAATTAAA-TTATTAATTTTAATA
*
123970 AAAATTTAATTATTA
1 AAAATTAAATTATTA
123985 TTAAGCTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 11 0.22
21 6 0.12
22 2 0.04
23 5 0.10
24 18 0.37
25 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATTAAATTATTAATTTTAATA
Found at i:123954 original size:44 final size:44
Alignment explanation
Indices: 123897--123984 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
123887 TTAAATTTAT
123897 TTTTTAAAATTAAAATTTAATTTA-TAATAAAAATTAAATTATTAA
1 TTTTTAAAATT-AAATTT-ATTTATTAATAAAAATTAAATTATTAA
*
123942 TTTTT-AAATTAAATTTATTTATTTAATAAAAATTTAATTATTA
1 TTTTTAAAATTAAATTTATTTA-TTAATAAAAATTAAATTATTA
123985 TTAAGCTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 5 0.12
43 6 0.15
44 24 0.60
45 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (44 bp):
TTTTTAAAATTAAATTTATTTATTAATAAAAATTAAATTATTAA
Found at i:123995 original size:47 final size:43
Alignment explanation
Indices: 123903--124009 Score: 119
Period size: 47 Copynumber: 2.4 Consensus size: 43
123893 TTATTTTTTA
**
123903 AAATTAAAATTTAATTTA-TAATAAAAATTAAATTATTAATTTTT
1 AAATT-AAATTT-ATTTATTAATAAAAATTAAATTATTAAGCTTT
123947 AAATTAAATTTATTTATTTAATAAAAATTTAATTATTATTAAGCTTT
1 AAATTAAATTTATTTA-TTAATAAAAA-TTAA--ATTATTAAGCTTT
*
123994 AAATTTAA-TTATTTAT
1 AAATTAAATTTATTTAT
124010 GTTTAAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
42 5 0.09
43 6 0.11
44 14 0.25
45 5 0.09
46 7 0.13
47 18 0.33
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (43 bp):
AAATTAAATTTATTTATTAATAAAAATTAAATTATTAAGCTTT
Found at i:124006 original size:20 final size:20
Alignment explanation
Indices: 123938--124019 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 20
123928 AATTAAATTA
*
123938 TTAATT-TTTAA-ATTAAAT
1 TTAATTATTTAAGTTTAAAT
* **
123956 TTATTTATTTAA-TAAAAAT
1 TTAATTATTTAAGTTTAAAT
123975 TTAATTATTATTAAGCTTTAAAT
1 TTAATTA-T-TTAAG-TTTAAAT
*
123998 TTAATTATTTATGTTTAAAT
1 TTAATTATTTAAGTTTAAAT
124018 TT
1 TT
124020 GAACTTAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.10
19 15 0.29
20 10 0.20
21 8 0.16
22 1 0.02
23 12 0.24
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATTATTTAAGTTTAAAT
Found at i:124867 original size:2 final size:2
Alignment explanation
Indices: 124860--124891 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
124850 GGTTTATAAT
*
124860 TA TA TA TA CA 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
124892 AATTTTCATG
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):
TA
Found at i:128617 original size:23 final size:21
Alignment explanation
Indices: 128575--128627 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
128565 TAATTAAATC
128575 TATTTAAATATTTTATATTAA
1 TATTTAAATATTTTATATTAA
*
128596 TATTTATATATATTTATAATTAA
1 TATTTAAATAT-TTTAT-ATTAA
128619 -ATTTAAATA
1 TATTTAAATA
128628 AATTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 13 0.46
23 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTAAATATTTTATATTAA
Found at i:131115 original size:14 final size:14
Alignment explanation
Indices: 131096--131124 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
131086 ATTTTAATGC
131096 TTGGCTCAAGTAGA
1 TTGGCTCAAGTAGA
131110 TTGGCTCAAGTAGA
1 TTGGCTCAAGTAGA
131124 T
1 T
131125 CTTGAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (14 bp):
TTGGCTCAAGTAGA
Found at i:131583 original size:11 final size:11
Alignment explanation
Indices: 131558--131595 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
131548 TAAAATTTAA
*
131558 AAATAAAATTT
1 AAATTAAATTT
131569 -AATTAAATTT
1 AAATTAAATTT
131579 AAATTAAATTTT
1 AAATTAAA-TTT
131591 AAATT
1 AAATT
131596 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 7 0.29
12 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:131600 original size:19 final size:18
Alignment explanation
Indices: 131571--131607 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
131561 TAAAATTTAA
131571 TTAAATTTAAATTAAATT
1 TTAAATTTAAATTAAATT
131589 TTAAATTTTAAATTAAATT
1 TTAAA-TTTAAATTAAATT
131608 CGAGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAATTTAAATTAAATT
Found at i:131883 original size:22 final size:21
Alignment explanation
Indices: 131858--131927 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
131848 AAAACAATGC
131858 AAAATTAAATTAATTTGAA-TTT
1 AAAA-TAAATTAATTT-AATTTT
* *
131880 AAAATAATATAAATTAAAATTTT
1 AAAATAA-ATTAATT-TAATTTT
131903 AATAATAAATTAATTTAATTTT
1 AA-AATAAATTAATTTAATTTT
131925 AAA
1 AAA
131928 TTTAAATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.10
22 20 0.50
23 11 0.28
24 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
AAAATAAATTAATTTAATTTT
Found at i:131927 original size:16 final size:15
Alignment explanation
Indices: 131859--131967 Score: 50
Period size: 16 Copynumber: 7.3 Consensus size: 15
131849 AAACAATGCA
131859 AAATTAAATTAATTT
1 AAATTAAATTAATTT
* * *
131874 GAATTTAAAATAATAT
1 -AAATTAAATTAATTT
*
131890 AAATTAAA--ATTTT
1 AAATTAAATTAATTT
*
131903 AATAATAAATTAATTT
1 AA-ATTAAATTAATTT
131919 -AATT---TTAAATTT
1 AAATTAAATT-AATTT
* *
131931 AAATTGAAAATATTTT
1 AAATT-AAATTAATTT
* *
131947 AAATATAAAATAACTT
1 AAAT-TAAATTAATTT
131963 AAATT
1 AAATT
131968 TTATAATTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 21
0.67 0.12 0.20
Matches are distributed among these distances:
11 2 0.03
12 5 0.07
13 9 0.13
14 7 0.10
15 9 0.13
16 36 0.51
17 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (15 bp):
AAATTAAATTAATTT
Found at i:131933 original size:22 final size:22
Alignment explanation
Indices: 131862--131979 Score: 66
Period size: 22 Copynumber: 5.2 Consensus size: 22
131852 CAATGCAAAA
*
131862 TTAAATTAATTTGAATTTAAAAT
1 TTAAATTAATTT-AATTTTAAAT
131885 AATATAAATTAA---AATTTT-AAT
1 --T-TAAATTAATTTAATTTTAAAT
*
131906 AATAAATTAATTTAATTTTAAAT
1 -TTAAATTAATTTAATTTTAAAT
**
131929 TTAAATTGAAAAT-ATTTTAAAT
1 TTAAATT-AATTTAATTTTAAAT
* * *
131951 ATAAAATAACTTAAATTTTATAAT
1 TTAAATTAA-TTTAATTTTA-AAT
131975 TTAAA
1 TTAAA
131980 ATGATATGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
19 8 0.11
20 1 0.01
21 5 0.07
22 31 0.42
23 12 0.16
24 7 0.10
25 1 0.01
26 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAATTAATTTAATTTTAAAT
Found at i:132253 original size:19 final size:17
Alignment explanation
Indices: 132219--132259 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
132209 TCAATATTAA
132219 ATATTAATAATATTATT
1 ATATTAATAATATTATT
*
132236 ATATTATATAAATTTTATT
1 ATATTA-AT-AATATTATT
132255 ATATT
1 ATATT
132260 TATTTTATAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTAATAATATTATT
Found at i:132255 original size:31 final size:32
Alignment explanation
Indices: 132220--132295 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
132210 CAATATTAAA
132220 TATTAATA-ATATTATTATATTAT-ATAAATTT
1 TATTAATATATATT-TTATATTATAATAAATTT
* * *
132251 TATT-ATATTTATTTTATATTTTAATTAATTT
1 TATTAATATATATTTTATATTATAATAAATTT
*
132282 TATTATATTTATAT
1 TATTA-ATATATAT
132296 AATCATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
30 11 0.31
31 19 0.53
33 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTAATATATATTTTATATTATAATAAATTT
Found at i:132293 original size:9 final size:10
Alignment explanation
Indices: 132231--132291 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
132221 ATTAATAATA
132231 TTATTATATT
1 TTATTATATT
* *
132241 ATA-TAAATT
1 TTATTATATT
132250 TTATTATATT
1 TTATTATATT
*
132260 TATTTTATATT
1 T-TATTATATT
132271 TTAATTA-ATT
1 TT-ATTATATT
132281 TTATTATATT
1 TTATTATATT
132291 T
1 T
132292 ATATAATCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
9 11 0.27
10 18 0.44
11 12 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATATT
Found at i:140391 original size:12 final size:12
Alignment explanation
Indices: 140376--140430 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
140366 AGGTTATATA
* *
140376 TTAATTTTTTTT
1 TTAAATTTTTAT
140388 TTAAATTTTTAT
1 TTAAATTTTTAT
*
140400 TTAAATTTATGAGT
1 TTAAATTT-TTA-T
*
140414 TTAAATTATTAT
1 TTAAATTTTTAT
140426 TTAAA
1 TTAAA
140431 AATATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 24 0.67
13 4 0.11
14 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (12 bp):
TTAAATTTTTAT
Found at i:143515 original size:24 final size:22
Alignment explanation
Indices: 143464--143516 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
143454 ATATTTATTT
143464 TTATATAATAAAAATTATATAA
1 TTATATAATAAAAATTATATAA
143486 -TATATAAATATAAAATTAATATAAA
1 TTATAT-AATA-AAAATT-ATAT-AA
143511 TTATAT
1 TTATAT
143517 GATTGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 6 0.23
24 4 0.15
25 2 0.08
26 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTATATAATAAAAATTATATAA
Found at i:144802 original size:13 final size:12
Alignment explanation
Indices: 144782--144852 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
144772 TATTTATTCG
144782 ATTTATAATTAA
1 ATTTATAATTAA
144794 ATTTAATAATT-A
1 ATTT-ATAATTAA
*
144806 TTTTAT-ATTAA
1 ATTTATAATTAA
144817 TATTTATATATT--
1 -ATTTATA-ATTAA
144829 -TTTATAATTAA
1 ATTTATAATTAA
144840 ATTTA-AA-TAA
1 ATTTATAATTAA
144850 ATT
1 ATT
144853 ATTATTTAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
9 3 0.06
10 15 0.31
11 5 0.10
12 17 0.35
13 6 0.12
14 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTATAATTAA
Found at i:144811 original size:24 final size:24
Alignment explanation
Indices: 144783--144855 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 24
144773 ATTTATTCGA
144783 TTTATAATTAAATTTAATAATTAT
1 TTTATAATTAAATTTAATAATTAT
144807 TTTAT-ATTAATATTT-AT-A-TATT
1 TTTATAATTAA-ATTTAATAATTA-T
144829 TTTATAATTAAATTTAAATAAATTAT
1 TTTATAATTAAATTT-AAT-AATTAT
144855 T
1 T
144856 ATTTAAGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
21 2 0.05
22 11 0.27
23 12 0.29
24 11 0.27
26 3 0.07
27 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATAATTAAATTTAATAATTAT
Found at i:146593 original size:29 final size:29
Alignment explanation
Indices: 146535--146612 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 29
146525 AAAATGAATC
*
146535 AATATTGAAATAT-ATATATAGATTTGTAT
1 AATATT-AAATATAAAATATAGATTTGTAT
* *
146564 AAATATTAAATATAAAATA-AGTTTTTTAT
1 -AATATTAAATATAAAATATAGATTTGTAT
*
146593 ATTATTTAAATAATAAAATA
1 AATA-TTAAAT-ATAAAATA
146613 GGTAGTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.07
29 20 0.49
30 18 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
AATATTAAATATAAAATATAGATTTGTAT
Found at i:147120 original size:2 final size:2
Alignment explanation
Indices: 147113--147152 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
147103 AATATAAACG
147113 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
147153 TTGGAAGCTA
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:148397 original size:17 final size:15
Alignment explanation
Indices: 148348--148408 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 15
148338 TCATTTAATC
* *
148348 AAATATATTTTATTA
1 AAATTTATTATATTA
148363 AATATTTATTATATTTA
1 AA-ATTTATTATA-TTA
148380 AAATTTATTTACTATTA
1 AAATTTA-TTA-TATTA
148397 AAATTTTATTAT
1 AAA-TTTATTAT
148409 TCTAACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 2 0.05
16 14 0.36
17 17 0.44
18 6 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATTTATTATATTA
Found at i:148450 original size:17 final size:17
Alignment explanation
Indices: 148360--148451 Score: 57
Period size: 17 Copynumber: 5.3 Consensus size: 17
148350 ATATATTTTA
148360 TTAAATATTTAT-TATAT
1 TTAAATATTTATATAT-T
* *
148377 TTAAA-ATTTATTTACTA
1 TTAAATATTTATATA-TT
148394 TTAAA-ATTT-TATTATT
1 TTAAATATTTATA-TATT
* * *
148410 CTAACTATATATATAATTTT
1 TTAA--ATATTTAT-ATATT
148430 TTAAATATTTATATATT
1 TTAAATATTTATATATT
148447 TTAAA
1 TTAAA
148452 ATAACTTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
16 11 0.19
17 27 0.47
18 9 0.16
19 3 0.05
20 7 0.12
21 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAATATTTATATATT
Found at i:148453 original size:18 final size:18
Alignment explanation
Indices: 148350--148454 Score: 60
Period size: 18 Copynumber: 5.8 Consensus size: 18
148340 ATTTAATCAA
148350 ATATATTTTATTAAATATTT
1 ATATATTTTA--AAATATTT
148370 AT-TATATTT-AAA-ATTT
1 ATATAT-TTTAAAATATTT
* *
148386 ATTTACTATTAAAAT-TTT
1 ATATA-TTTTAAAATATTT
* * *
148404 AT-TATTCT-AACTATAT
1 ATATATTTTAAAATATTT
*
148420 ATATAATTTTTTAAATATTT
1 ATAT-A-TTTTAAAATATTT
148440 ATATATTTTAAAATA
1 ATATATTTTAAAATA
148455 ACTTGAAACT
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
15 3 0.05
16 12 0.18
17 10 0.15
18 19 0.29
19 7 0.11
20 15 0.23
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTTTAAAATATTT
Found at i:148593 original size:19 final size:19
Alignment explanation
Indices: 148569--148686 Score: 81
Period size: 19 Copynumber: 6.3 Consensus size: 19
148559 TTAGATAATA
148569 ATTTATAAATTTATATTAT
1 ATTTATAAATTTATATTAT
*
148588 ATTTATATATTT-TATTAT
1 ATTTATAAATTTATATTAT
*
148606 A-TTAT-AA-TTATATAAAT
1 ATTTATAAATTTATAT-TAT
*
148623 ATTT-TATATTTATA-TA-
1 ATTTATAAATTTATATTAT
* *
148639 AATTATAATTATTAATAATTAAT
1 ATTTATAA--ATTTAT-ATT-AT
148662 ATTATATAAATTT-TATTAT
1 ATT-TATAAATTTATATTAT
148681 ATTTAT
1 ATTTAT
148687 TTTATATTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
15 2 0.03
16 7 0.09
17 11 0.14
18 13 0.17
19 26 0.34
20 4 0.05
21 2 0.03
22 4 0.05
23 2 0.03
24 5 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATAAATTTATATTAT
Found at i:148606 original size:31 final size:29
Alignment explanation
Indices: 148572--148729 Score: 94
Period size: 31 Copynumber: 5.2 Consensus size: 29
148562 GATAATAATT
148572 TATAAATTTATATTATATTTATATATTTTA
1 TATAAATTTATATTATATTTATATA-TTTA
* *
148602 TTATATTATAATTATATAAATATTT-TATATTTA
1 -TATA--A-ATTTATAT-TATATTTATATATTTA
*
148635 TATAAATTATAATTATTAATAATTA-ATA-TTA
1 TATAAATT-T-A-TATT-ATATTTATATATTTA
148666 TATAAATTT-TATTATATTTATTTTATATTT-
1 TATAAATTTATATTATATTTA---TATATTTA
* * *
148696 TAATTAATTT-TATTATATTTATATAATCA
1 T-ATAAATTTATATTATATTTATATATTTA
148725 TATAA
1 TATAA
148730 TATTATCACC
Statistics
Matches: 101, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
26 6 0.06
27 4 0.04
28 8 0.08
29 3 0.03
30 7 0.07
31 36 0.36
32 15 0.15
33 5 0.05
34 11 0.11
35 6 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TATAAATTTATATTATATTTATATATTTA
Found at i:148612 original size:36 final size:34
Alignment explanation
Indices: 148571--148714 Score: 100
Period size: 34 Copynumber: 4.1 Consensus size: 34
148561 AGATAATAAT
148571 TTATAAATTTATATTATATTTATATATTTTATTATA
1 TTAT-AATTTATATTATATTT-TATATTTTATTATA
* *
148607 TTATAA-TTATATAAATATTTTATA-TTTATATAAA
1 TTATAATTTATAT-TATATTTTATATTTTAT-TATA
*
148641 TTATAATTATTAATAATTAATATTATATAAATTTTATTATA
1 TTATAA-T-TT-AT-ATT-ATATT-T-TATATTTTATTATA
* * *
148682 TT-TATTTTATATTTTA-ATTA-ATTTTATTATA
1 TTATAATTTATATTATATTTTATATTTTATTATA
148713 TT
1 TT
148715 TATATAATCA
Statistics
Matches: 89, Mismatches: 8, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
31 13 0.15
32 2 0.02
33 6 0.07
34 19 0.21
35 10 0.11
36 7 0.08
37 4 0.04
38 4 0.04
39 8 0.09
40 3 0.03
41 8 0.09
42 5 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TTATAATTTATATTATATTTTATATTTTATTATA
Found at i:148687 original size:9 final size:10
Alignment explanation
Indices: 148671--148715 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
148661 TATTATATAA
148671 ATTTTATTAT
1 ATTTTATTAT
*
148681 ATTTATTTTAT
1 ATTT-TATTAT
148692 ATTTTAATTA-
1 ATTTT-ATTAT
148702 ATTTTATTAT
1 ATTTTATTAT
148712 ATTT
1 ATTT
148716 ATATAATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 4 0.13
10 14 0.47
11 12 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:148722 original size:19 final size:19
Alignment explanation
Indices: 148569--148722 Score: 59
Period size: 19 Copynumber: 7.6 Consensus size: 19
148559 TTAGATAATA
148569 ATTTATA-AATTTATATTAT
1 ATTTATATAATTT-TATTAT
148588 ATTTATAT-ATTTTATTATATT
1 ATTTATATAATTTTA-T-TA-T
*
148609 ATAATTATATAAATATT-TTAT
1 AT--TTATAT-AATTTTATTAT
* *
148630 ATTTATATAA-ATTATAATT
1 ATTTATATAATTTTATTA-T
* * *
148649 ATTAATAATTAATATTATATAA
1 ATTTAT-A-TAATTTTAT-TAT
*
148671 ATTT-TATTATATTTATTTTAT
1 ATTTATA-TA-ATTT-TATTAT
148692 ATTT-TAATTAATTTTATTAT
1 ATTTAT-A-TAATTTTATTAT
148712 ATTTATATAAT
1 ATTTATATAAT
148723 CATATAATAT
Statistics
Matches: 107, Mismatches: 10, Indels: 36
0.70 0.07 0.24
Matches are distributed among these distances:
17 3 0.03
18 6 0.06
19 28 0.26
20 17 0.16
21 25 0.23
22 16 0.15
23 8 0.07
25 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTATATAATTTTATTAT
Found at i:150165 original size:13 final size:13
Alignment explanation
Indices: 150147--150172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150137 AGTTTAAATT
150147 ATTTTAAATTATG
1 ATTTTAAATTATG
150160 ATTTTAAATTATG
1 ATTTTAAATTATG
150173 TTAAGTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTTAAATTATG
Found at i:150170 original size:39 final size:40
Alignment explanation
Indices: 150121--150198 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
150111 AAGTTATTAA
* * * *
150121 ATTTTGAATTATTTTAAGTTTAAAT-TATTTTAAATTATG
1 ATTTTAAATTATGTTAAGTATAAATAAATTTTAAATTATG
150160 ATTTTAAATTATGTTAAGTATAAATAAATTTTAAATTAT
1 ATTTTAAATTATGTTAAGTATAAATAAATTTTAAATTAT
150199 TTTAACTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (40 bp):
ATTTTAAATTATGTTAAGTATAAATAAATTTTAAATTATG
Found at i:156841 original size:210 final size:207
Alignment explanation
Indices: 156493--156876 Score: 483
Period size: 210 Copynumber: 1.8 Consensus size: 207
156483 TGTTGAGGAA
* * * *
156493 GGTGAAATAGTTTGTCTTAGTTCTCAACTTACAACTCCCGCGACAAATGCTGCTTCCACTGAAGG
1 GGTGAAAAAGTTTATCTTAGTTCTCAACTTACAACTCCCACAACAAATGCTGCTTCCACTGAAGG
*
156558 ATTGTTAACTCCAAAGAAGGCTCTATGTGCTGCAACGCGAAAAAGCTGTTCTGCAAAAATTATTT
66 ATTGTTAACTCCAAAGAAGGCTCTATGTGCTGCAACGCGAAAAAGCCGTTCTGCAAAAATTATTT
156623 CGAAAGCTCAACAGAAGATCAAGACACGACTTGATAATAGTGAGAAAGCTGATCCAGCTCTGAAT
131 CGAAAGCTCAACAGAAGATCAAG--AC-ACTTGATAATAGTGAGAAAGCTGATCCAGCTCTGAAT
156688 GACGACTTTGAAAAG
193 GACGACTTTGAAAAG
* * * *
156703 GGTGAAAAAGTTTATCTTATTTCTCAATTTACAACTCCCACAACAGATGCTGCTTCGACTGAAGG
1 GGTGAAAAAGTTTATCTTAGTTCTCAACTTACAACTCCCACAACAAATGCTGCTTCCACTGAAGG
* * * * * *
156768 ATTGTT-ATTTCAGAAGAAGGCTCT-TCGTGCTGCAATGCTG-AAATGCCGTTTTGCAGCCACAA
66 ATTGTTAACTCCA-AAGAAGGCTCTAT-GTGCTGCAACGC-GAAAAAGCCGTTCTGCA---AAAA
* * *
156830 -T-TTTC-AAAGCTCAGCAGATGATCAAGACACTTGATAATGGTGAGAAA
125 TTATTTCGAAAGCTCAACAGAAGATCAAGACACTTGATAATAGTGAGAAA
156877 ACCAATCCAG
Statistics
Matches: 150, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
207 18 0.12
208 2 0.01
209 5 0.03
210 116 0.77
211 5 0.03
212 1 0.01
213 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (207 bp):
GGTGAAAAAGTTTATCTTAGTTCTCAACTTACAACTCCCACAACAAATGCTGCTTCCACTGAAGG
ATTGTTAACTCCAAAGAAGGCTCTATGTGCTGCAACGCGAAAAAGCCGTTCTGCAAAAATTATTT
CGAAAGCTCAACAGAAGATCAAGACACTTGATAATAGTGAGAAAGCTGATCCAGCTCTGAATGAC
GACTTTGAAAAG
Found at i:159444 original size:26 final size:26
Alignment explanation
Indices: 159415--159469 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
159405 TTCATAGGAT
*
159415 TAGGCTCATTTCTGATTTCAGACTAA
1 TAGGCTCATTTCTGATTTCAAACTAA
159441 TAGGCTCATTTCTGATTTCAAACTAA
1 TAGGCTCATTTCTGATTTCAAACTAA
159467 TAG
1 TAG
159470 TAGTAACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (26 bp):
TAGGCTCATTTCTGATTTCAAACTAA
Found at i:160261 original size:17 final size:19
Alignment explanation
Indices: 160226--160271 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
160216 TTAGCTTCAG
160226 TTATTATTTAATTAATAAAA
1 TTATTATTTAATT-ATAAAA
*
160246 TTATT-TTTAATT-TAAAT
1 TTATTATTTAATTATAAAA
160263 TTAATTATT
1 TT-ATTATT
160272 AAAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
19 9 0.39
20 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTTAATTATAAAA
Found at i:160297 original size:22 final size:22
Alignment explanation
Indices: 160258--160299 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
160248 ATTTTTAATT
*
160258 TAAATTTAATTATTAAAATATA
1 TAAATTTAATTATAAAAATATA
160280 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
160300 ATTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:160322 original size:16 final size:16
Alignment explanation
Indices: 160301--160331 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
160291 ATAAAAATAA
*
160301 TTTTATAATATTTTAT
1 TTTTATAATAATTTAT
160317 TTTTATAATAATTTA
1 TTTTATAATAATTTA
160332 AGTTTACGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATAATAATTTAT
Found at i:160636 original size:19 final size:18
Alignment explanation
Indices: 160600--160638 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
160590 TTTTATTTTT
* *
160600 ATTTTAAATTAAATTTAA
1 ATTTTAAAATAAAATTAA
160618 ATTTTAAAAATAAAATTAA
1 ATTTT-AAAATAAAATTAA
160637 AT
1 AT
160639 GAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTAAAATAAAATTAA
Found at i:161196 original size:29 final size:28
Alignment explanation
Indices: 161164--161229 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
161154 TCACAATTCA
*
161164 TATATTTA-AATTATATTTATATATTATTT
1 TATATTTATAATTATATTTA-A-AATATTT
*
161193 TATA-TTATAGTTATATTTAAAATATTT
1 TATATTTATAATTATATTTAAAATATTT
161220 TATATTTATA
1 TATATTTATA
161230 TAAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 10 0.30
28 9 0.27
29 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TATATTTATAATTATATTTAAAATATTT
Found at i:161868 original size:19 final size:19
Alignment explanation
Indices: 161838--161886 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
161828 TTATATATGC
161838 ATTTAA-AA-TTTTAATAT
1 ATTTAATAATTTTTAATAT
*
161855 ATTTAATAATTTTTATTAT
1 ATTTAATAATTTTTAATAT
*
161874 ACTT-AT-ATTTTTA
1 ATTTAATAATTTTTA
161887 TAACTGATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 13 0.46
18 4 0.14
19 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAATAATTTTTAATAT
Found at i:163365 original size:17 final size:17
Alignment explanation
Indices: 163335--163367 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
163325 TTTTTTTAAG
163335 ATTTATATATAATATAT
1 ATTTATATATAATATAT
163352 ATTTA-ATATGAATATA
1 ATTTATATAT-AATATA
163368 AAAATATAAA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATTTATATATAATATAT
Found at i:165160 original size:27 final size:25
Alignment explanation
Indices: 165117--165176 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
165107 TGTTAATTTT
*
165117 TATTATAATTATATTTAAAATATTATA
1 TATT-TAAATATATTTAAAATATTA-A
*
165144 TATTTAAATATAGTTTAATATATTAA
1 TATTTAAATATA-TTTAAAATATTAA
*
165170 TAATTAA
1 TATTTAA
165177 TTTCATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TATTTAAATATATTTAAAATATTAA
Found at i:165871 original size:21 final size:23
Alignment explanation
Indices: 165806--165910 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 23
165796 AATTATTTTT
* *
165806 TTATATTATAATTATGTTTCACATA
1 TTATATTAT-ATTATATTTTA-ATA
* *
165831 TTATATATTTATATAAATTTTAATA
1 TTATAT-TATAT-TATATTTTAATA
* * *
165856 -TGTA-TGTATTATATTTTTATA
1 TTATATTATATTATATTTTAATA
*
165877 TTATATTATATTATATTTT-ACA
1 TTATATTATATTATATTTTAATA
*
165899 TTATATTTTATT
1 TTATATTATATT
165911 TTTATTCATT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
21 10 0.16
22 20 0.31
23 12 0.19
24 3 0.05
25 11 0.17
26 8 0.12
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (23 bp):
TTATATTATATTATATTTTAATA
Found at i:165880 original size:5 final size:5
Alignment explanation
Indices: 165862--165893 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
165852 AATATGTATG
165862 TATTA TATT- T-TTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
165894 TTACATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.08
4 2 0.08
5 21 0.84
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:165903 original size:12 final size:12
Alignment explanation
Indices: 165862--165909 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
165852 AATATGTATG
165862 TATTATATTTTTA
1 TATTATA-TTTTA
165875 TATTATA--TTA
1 TATTATATTTTA
165885 TATTATATTTTA
1 TATTATATTTTA
*
165897 CATTATATTTTA
1 TATTATATTTTA
165909 T
1 T
165910 TTTTATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.32
12 14 0.45
13 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:170645 original size:39 final size:39
Alignment explanation
Indices: 170570--170647 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
170560 GCTGAAATTG
* * *
170570 TTAAAGTTGCATTTAATTTATACCGCAAAAAGACCAAAT
1 TTAAAGTTACATTTAATTCATACCACAAAAAGACCAAAT
*
170609 TTAAAGTTACATTTAATTCATATCACTAAAAA-ACCAAAT
1 TTAAAGTTACATTTAATTCATACCAC-AAAAAGACCAAAT
170648 GTCAAAGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (39 bp):
TTAAAGTTACATTTAATTCATACCACAAAAAGACCAAAT
Found at i:172470 original size:27 final size:27
Alignment explanation
Indices: 172407--172475 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 27
172397 TGATTCGTGA
* *
172407 TATTAATTTA-ATAAAATTTTATATTT
1 TATTAATTTATATAAAATTTTAAACTT
*
172433 TA-AAATATTATA-AAAATTTTTAAACTT
1 TATTAAT-TTATATAAAA-TTTTAAACTT
*
172460 TATTAATTTATTTAAA
1 TATTAATTTATATAAA
172476 TAAACTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
25 3 0.09
26 9 0.27
27 15 0.45
28 6 0.18
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
TATTAATTTATATAAAATTTTAAACTT
Found at i:172514 original size:29 final size:29
Alignment explanation
Indices: 172462--172546 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
172452 TTAAACTTTA
* **
172462 TTAATT-TATTTAAATAAACTTTTATATTT
1 TTAATTGTACTTAAATAAGTTTTTAT-TTT
172491 TT-ATTGTACTTAAATAA-TTATTTATTTT
1 TTAATTGTACTTAAATAAGTT-TTTATTTT
* *
172519 TTAATTTTATTTAAATAAGTTTTTATTT
1 TTAATTGTACTTAAATAAGTTTTTATTT
172547 CAAATGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 9 0.19
29 37 0.77
30 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTAATTGTACTTAAATAAGTTTTTATTTT
Found at i:172884 original size:29 final size:30
Alignment explanation
Indices: 172832--172913 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
172822 CTATAGAATG
*
172832 TATTTATGTATAAATTT-AAGATTATAA-GTT
1 TATTTATGTAT-AATTTAAAAATTA-AATGTT
172862 T-TTTATGTATAATTTAAAAATTAAATGTT
1 TATTTATGTATAATTTAAAAATTAAATGTT
** *
172891 TATTTACATATAAATTAAAAATT
1 TATTTATGTATAATTTAAAAATT
172914 GAAGTCCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.16
29 19 0.42
30 19 0.42
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (30 bp):
TATTTATGTATAATTTAAAAATTAAATGTT
Found at i:173863 original size:16 final size:16
Alignment explanation
Indices: 173827--173883 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
173817 ATATCACTTA
*
173827 ATTAAATATATATTCAT
1 ATTAAATATTTATT-AT
173844 ATTAAATATTTATTAT
1 ATTAAATATTTATTAT
173860 ATTAAATATTTATTTACT
1 ATTAAATATTTA-TTA-T
173878 ATTAAA
1 ATTAAA
173884 ATTATATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
16 14 0.38
17 16 0.43
18 7 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAAATATTTATTAT
Found at i:174421 original size:20 final size:20
Alignment explanation
Indices: 174396--174436 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
174386 GAACTGAATA
*
174396 TAAATTTTTTTAATTTAAAT
1 TAAATTATTTTAATTTAAAT
* *
174416 TAAATTATTTTGATTTGAAT
1 TAAATTATTTTAATTTAAAT
174436 T
1 T
174437 GATATTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TAAATTATTTTAATTTAAAT
Found at i:176864 original size:22 final size:22
Alignment explanation
Indices: 176839--176880 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
176829 TTTTTTTATT
176839 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
*
176861 TAAATATTAATGTAAAAATA
1 TAAATATTAATATAAAAATA
176881 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:177363 original size:15 final size:17
Alignment explanation
Indices: 177343--177376 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
177333 CTAGTATTTT
177343 TATTTAT-AT-ATTATA
1 TATTTATAATAATTATA
177358 TATTTATAATAATTATA
1 TATTTATAATAATTATA
177375 TA
1 TA
177377 GATAAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATAATAATTATA
Found at i:178430 original size:25 final size:21
Alignment explanation
Indices: 178384--178428 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
178374 TTAAATTGGA
178384 TACATATTAATATCCAAAACT
1 TACATATTAATATCCAAAACT
178405 TACATATTAATATCCAAAACT
1 TACATATTAATATCCAAAACT
178426 TAC
1 TAC
178429 TTTTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
TACATATTAATATCCAAAACT
Found at i:179030 original size:2 final size:2
Alignment explanation
Indices: 179023--179051 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
179013 AACACTCTCG
179023 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
179052 AAATGAGTTG
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:179295 original size:16 final size:16
Alignment explanation
Indices: 179270--179315 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
179260 TGATAACTTG
* *
179270 AAATTGAAAATAATTT
1 AAATTTAAAATAATTC
179286 AAATTTAAAATAATTC
1 AAATTTAAAATAATTC
*
179302 AAACTTAAAATAAT
1 AAATTTAAAATAAT
179316 ATGAACTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTTAAAATAATTC
Found at i:180220 original size:20 final size:20
Alignment explanation
Indices: 180170--180221 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
180160 GATTGTTGGT
*
180170 TCTTCTTCCTTT--TTCTTTT
1 TCTTCTT-CTTTCCTTCTTTA
**
180189 TCTTCTGGTTTCCTTCTTTA
1 TCTTCTTCTTTCCTTCTTTA
180209 TCTTCTTCTTTCC
1 TCTTCTTCTTTCC
180222 AATTGCATCC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.12
19 6 0.23
20 17 0.65
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.65
Consensus pattern (20 bp):
TCTTCTTCTTTCCTTCTTTA
Found at i:180651 original size:29 final size:28
Alignment explanation
Indices: 180591--180653 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
180581 ATTAAAAAAT
*
180591 TTAAATATTAAATAAATATTAAATTTAG
1 TTAAATATTAAAAAAATATTAAATTTAG
*
180619 -TAAATATTTAAAAATAATA-TATATTTAG
1 TTAAATA-TTAAAAA-AATATTAAATTTAG
180647 TTAAATA
1 TTAAATA
180654 AAATAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.20
28 14 0.47
29 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
TTAAATATTAAAAAAATATTAAATTTAG
Found at i:184028 original size:12 final size:13
Alignment explanation
Indices: 183989--184022 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
183979 AAACATAACA
183989 AAAAATTAAATTATT
1 AAAAATTAAA-T-TT
184004 AAAAATTAAATTT
1 AAAAATTAAATTT
184017 AAAAAT
1 AAAAAT
184023 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 1 0.05
15 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:185805 original size:2 final size:2
Alignment explanation
Indices: 185800--185836 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
185790 TATATGCGCT
185800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
185837 GCACTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:186821 original size:15 final size:15
Alignment explanation
Indices: 186803--186832 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
186793 GAAAGAAAGG
186803 TTGAGGAAAGGAAAA
1 TTGAGGAAAGGAAAA
186818 TTGAGGAAAGGAAAA
1 TTGAGGAAAGGAAAA
186833 GAAATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (15 bp):
TTGAGGAAAGGAAAA
Found at i:187091 original size:29 final size:29
Alignment explanation
Indices: 187046--187106 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
187036 ACATAATGTA
187046 AAAGTTAAAGGCATATTTGGA-TACAAATT
1 AAAGTTAAAGGCATATTT-GATTACAAATT
* *
187075 AAAGTT-AAGAGCTTATTTGATTATAAATT
1 AAAGTTAAAG-GCATATTTGATTACAAATT
187104 AAA
1 AAA
187107 AGATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAGTTAAAGGCATATTTGATTACAAATT
Found at i:187144 original size:16 final size:17
Alignment explanation
Indices: 187119--187159 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
187109 ATTAAAAATT
187119 TATTTAAATATAAA-AA
1 TATTTAAATATAAATAA
*
187135 TATTTGAATATAAATAA
1 TATTTAAATATAAATAA
187152 TATATTAA
1 TAT-TTAA
187160 CTTATCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 13 0.62
17 5 0.24
18 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TATTTAAATATAAATAA
Found at i:189171 original size:17 final size:19
Alignment explanation
Indices: 189145--189179 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
189135 CCTAACTTTG
189145 AAATATAAAA-GACATTGA
1 AAATATAAAAGGACATTGA
189163 AAATA-AAAAGGACATTG
1 AAATATAAAAGGACATTG
189180 CTCTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (19 bp):
AAATATAAAAGGACATTGA
Found at i:189199 original size:2 final size:2
Alignment explanation
Indices: 189186--189226 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
189176 ATTGCTCTTT
* *
189186 TA TA TA TT TA TA TA CA 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
189227 TAAATAGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:189478 original size:20 final size:20
Alignment explanation
Indices: 189450--189524 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
189440 TTTTACCCAG
189450 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
189470 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
189490 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
189510 ATGTATCGATACATT
1 ATGTATCGATACATT
189525 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:189510 original size:40 final size:39
Alignment explanation
Indices: 189450--189527 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
189440 TTTTACCCAG
*
189450 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
189490 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
189528 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:193357 original size:21 final size:21
Alignment explanation
Indices: 193333--193389 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
193323 TTAAATTATT
*
193333 ATTTAATAATAAAA-AATTTAA
1 ATTTAAT-ATAAAACAATATAA
*
193354 ATTTAATTATAAAACTATATAA
1 ATTTAA-TATAAAACAATATAA
193376 ATATTAATATAAAA
1 AT-TTAATATAAAA
193390 TATAAGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 12 0.39
22 15 0.48
23 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAATATAAAACAATATAA
Found at i:193386 original size:22 final size:21
Alignment explanation
Indices: 193333--193393 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
193323 TTAAATTATT
* * *
193333 ATTTAATAATAAAAAATTTAA
1 ATTTAATTATAAAATATATAA
193354 ATTTAATTATAAAACTATATAA
1 ATTTAATTATAAAA-TATATAA
193376 ATATTAA-TATAAAATATA
1 AT-TTAATTATAAAATATA
193394 AGTGATCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.49
22 14 0.40
23 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAATTATAAAATATATAA
Found at i:195669 original size:2 final size:2
Alignment explanation
Indices: 195662--195688 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
195652 AATGCCAACA
195662 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
195689 AATTAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196436 original size:25 final size:25
Alignment explanation
Indices: 196408--196457 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
196398 TTATGCTTTG
196408 AATAAT-AA-TTAAAAATATATTAAAA
1 AATAATCAACTTAAAAAT-T-TTAAAA
196433 AATAATCAACTTAAAAATTTTAAAA
1 AATAATCAACTTAAAAATTTTAAAA
196458 GAGAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 12 0.52
26 3 0.13
27 8 0.35
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAATCAACTTAAAAATTTTAAAA
Found at i:198807 original size:11 final size:11
Alignment explanation
Indices: 198793--198868 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
198783 TATATAATGA
198793 TATATTTATAT
1 TATATTTATAT
*
198804 TATATTTAATAA
1 TATATTT-ATAT
198816 TATATTCATATAT
1 TATATT--TATAT
198829 TATTATTT-TAT
1 TA-TATTTATAT
*
198840 AATATTT-TA-
1 TATATTTATAT
198849 TAT-TTTA-AT
1 TATATTTATAT
*
198858 TATTTTTATAT
1 TATATTTATAT
198869 CAATATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 4 0.08
9 5 0.09
10 11 0.21
11 13 0.25
12 10 0.19
13 5 0.09
14 5 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:198818 original size:23 final size:24
Alignment explanation
Indices: 198782--198852 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
198772 ATTATAAATT
* *
198782 TTATATAATGATATATTTATATTA
1 TTATTTAATAATATATTTATATTA
198806 -TATTTAATAATATATTCATATATTA
1 TTATTTAATAATATATT--TATATTA
*
198831 TTATTTTATAATAT-TTTATATT
1 TTATTTAATAATATATTTATATT
198853 TTAATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 20 0.49
25 9 0.22
26 12 0.29
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
TTATTTAATAATATATTTATATTA
Found at i:198851 original size:25 final size:26
Alignment explanation
Indices: 198792--198863 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
198782 TTATATAATG
*
198792 ATATATT--TATATTA-TATTTAATA
1 ATATATTCATATATTATTATTTTATA
198815 ATATATTCATATATTATTATTTTATA
1 ATATATTCATATATTATTATTTTATA
* *
198841 ATAT-TTTATATTTTAATTATTTT
1 ATATATTCATATATT-ATTATTTT
198864 TATATCAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.17
25 15 0.36
26 20 0.48
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATATTCATATATTATTATTTTATA
Found at i:199207 original size:18 final size:20
Alignment explanation
Indices: 199174--199224 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
199164 ATTATTGATT
199174 TATTTTAACTATAAAAATT-A
1 TATTTTAA-TATAAAAATTAA
199194 TATTTTAATA-AAAAATTAAA
1 TATTTTAATATAAAAATT-AA
199214 TATTTTAATAT
1 TATTTTAATAT
199225 TTTTAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 19 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTAATATAAAAATTAA
Found at i:201459 original size:2 final size:2
Alignment explanation
Indices: 201452--201480 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
201442 TGATTTTAAC
201452 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
201481 GAGAGAGAGA
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:201485 original size:2 final size:2
Alignment explanation
Indices: 201480--201531 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
201470 ATATATATAT
201480 AG AG AG 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 AG AG AG
201522 AG AG AG AG AG
1 AG AG AG AG AG
201532 CAGCAGCAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:207321 original size:46 final size:46
Alignment explanation
Indices: 207271--207365 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
207261 TACTGAGATT
**
207271 TTAATTAAATTTATTAAA--TATTATATTTTAAAAATAATTATATTAA
1 TTAATTAAATAAATTAAATTTATTA-ATTTTAAAAAT-ATTATATTAA
* **
207317 TTAATTAAATAAATTTAATTTATTAATTTTTTAAATATTATATTAA
1 TTAATTAAATAAATTAAATTTATTAATTTTAAAAATATTATATTAA
207363 TTA
1 TTA
207366 GTGTCAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 28 0.67
47 9 0.21
48 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (46 bp):
TTAATTAAATAAATTAAATTTATTAATTTTAAAAATATTATATTAA
Found at i:207331 original size:22 final size:21
Alignment explanation
Indices: 207302--207344 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
207292 TATATTTTAA
207302 AAATAA-TTATATTAATTAATT
1 AAATAATTTA-ATTAATTAATT
*
207323 AAATAAATTTAATTTATTAATT
1 AAAT-AATTTAATTAATTAATT
207345 TTTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATTTAATTAATTAATT
Found at i:207345 original size:13 final size:14
Alignment explanation
Indices: 207305--207345 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
207295 ATTTTAAAAA
207305 TAATTATATTAA-T
1 TAATTATATTAATT
* *
207318 TAATTAAATAAATT
1 TAATTATATTAATT
207332 TAATT-TATTAATT
1 TAATTATATTAATT
207345 T
1 T
207346 TTTAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATTATATTAATT
Found at i:207983 original size:12 final size:12
Alignment explanation
Indices: 207954--207992 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
207944 TAATTATCTA
* *
207954 ATATAAAAAATA
1 ATATAAAATATG
207966 AT-TAAAATATG
1 ATATAAAATATG
207977 ATATAAAATATG
1 ATATAAAATATG
207989 ATAT
1 ATAT
207993 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
ATATAAAATATG
Found at i:215619 original size:20 final size:20
Alignment explanation
Indices: 215596--215634 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
215586 ATTAATGTTT
215596 AAAAATATTCAAATATTAAA
1 AAAAATATTCAAATATTAAA
* **
215616 AAAATTATTTTAATATTAA
1 AAAAATATTCAAATATTAA
215635 TTTATATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATATTCAAATATTAAA
Found at i:220609 original size:15 final size:17
Alignment explanation
Indices: 220579--220610 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
220569 TTAAAAATAA
220579 TTTATAATATTAAATTT
1 TTTATAATATTAAATTT
220596 TTTATAA-A-TAAATTT
1 TTTATAATATTAAATTT
220611 AAATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATAATATTAAATTT
Found at i:220642 original size:33 final size:32
Alignment explanation
Indices: 220597--220676 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 32
220587 ATTAAATTTT
220597 TTATAAATAAATTTAAATAAAATATTT-TTTAAA
1 TTATAAA-AAATTTAAATAAAAT-TTTATTTAAA
*
220630 TTAGTAAAAAATTTAAATTAAATTTTAATTTAAA
1 TTA-TAAAAAATTTAAATAAAATTTT-ATTTAAA
*
220664 TTATAAAATATTT
1 TTATAAAAAATTT
220677 TATCCAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 3 0.07
33 26 0.62
34 13 0.31
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
TTATAAAAAATTTAAATAAAATTTTATTTAAA
Found at i:220678 original size:17 final size:17
Alignment explanation
Indices: 220624--220678 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
220614 TAAAATATTT
220624 TTTAAATTAGTAAAA-AA
1 TTTAAATTA-TAAAATAA
**
220641 TTTAAATTA-AATTTTAA
1 TTTAAATTATAA-AATAA
*
220658 TTTAAATTATAAAATAT
1 TTTAAATTATAAAATAA
220675 TTTA
1 TTTA
220679 TCCAAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAATTATAAAATAA
Found at i:221024 original size:15 final size:16
Alignment explanation
Indices: 220987--221027 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
220977 ATATTTAAAT
*
220987 TTTAAA-TATTAATTG
1 TTTAAATTATTAATTA
221002 TTTAAAATTATTAA-TA
1 TTT-AAATTATTAATTA
221018 TTTAAATTAT
1 TTTAAATTAT
221028 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTAATTA
Found at i:222851 original size:22 final size:20
Alignment explanation
Indices: 222826--222865 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
222816 ATAGTATATA
222826 AATATTAAATATTAAATATAAT
1 AATATTAAATA--AAATATAAT
*
222848 AATATTTAATAAAATATA
1 AATATTAAATAAAATATA
222866 TATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATTAAATAAAATATAAT
Found at i:222865 original size:40 final size:38
Alignment explanation
Indices: 222811--222903 Score: 91
Period size: 40 Copynumber: 2.4 Consensus size: 38
222801 GAATAAAAAA
**
222811 TTTTAATAGTATATAAATA-TTAAATAT-TAAATATAAT
1 TTTTAATAAAATATAAATATTTAAATATGT-AATATAAT
* *
222848 AATATTTAATAAAATATATATATTTAATTATGTAATATAAT
1 --T-TTTAATAAAATATAAATATTTAAATATGTAATATAAT
222889 TTTTAATATAAATAT
1 TTTTAATA-AAATAT
222904 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 7 0.15
39 8 0.17
40 15 0.33
41 15 0.33
42 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATATAAATATTTAAATATGTAATATAAT
Found at i:222902 original size:18 final size:18
Alignment explanation
Indices: 222821--222903 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
222811 TTTTAATAGT
222821 ATATAAATATTAA-ATATTA
1 ATATAAATA-TAATAT-TTA
*
222840 A-ATATA-ATAATATTTA
1 ATATAAATATAATATTTA
222856 ATA-AAATATATATATTTA
1 ATATAAATATA-ATATTTA
* *
222874 ATTATGTAATATAATTTTTA
1 A-TAT-AAATATAATATTTA
222894 ATATAAATAT
1 ATATAAATAT
222904 TTAATTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
16 9 0.17
17 7 0.13
18 17 0.33
19 6 0.12
20 7 0.13
21 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
ATATAAATATAATATTTA
Found at i:222971 original size:33 final size:33
Alignment explanation
Indices: 222934--223026 Score: 125
Period size: 33 Copynumber: 2.7 Consensus size: 33
222924 AAAAAATTAA
222934 AATTAATTTTTTATTTTTTATTTTTATCAATTC
1 AATTAATTTTTTATTTTTTATTTTTATCAATTC
* *
222967 AATTAA-ATTTTATTATTTTATTTTTATCAATTT
1 AATTAATTTTTTATT-TTTTATTTTTATCAATTC
223000 AATTAAATTTTTATATTTTTTTATTTT
1 AATT-AATTTTT-TA-TTTTTTATTTT
223027 ATGATATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.13
33 27 0.52
34 2 0.04
35 3 0.06
36 11 0.21
37 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
AATTAATTTTTTATTTTTTATTTTTATCAATTC
Found at i:224100 original size:35 final size:34
Alignment explanation
Indices: 224038--224115 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 34
224028 TATAATTAAT
* *
224038 TTTTTA-TTTTTATCTATTCAATCAAATTTTACA
1 TTTTTATTTTTTATCAATTAAATCAAATTTTACA
* *
224071 TTTTATATTTTTTATCAATTAAATTAAATTTTATA
1 TTTT-TATTTTTTATCAATTAAATCAAATTTTACA
224106 TTTTTATTTT
1 TTTTTATTTT
224116 AAAAAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
33 4 0.10
34 8 0.21
35 27 0.69
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTTTATTTTTTATCAATTAAATCAAATTTTACA
Found at i:224731 original size:17 final size:17
Alignment explanation
Indices: 224706--224739 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
224696 TTAATTATAA
224706 AATTATTTTTAAAAAAT
1 AATTATTTTTAAAAAAT
*
224723 AATTTTTTTTAAAAAAT
1 AATTATTTTTAAAAAAT
224740 TTGAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTATTTTTAAAAAAT
Found at i:225078 original size:35 final size:35
Alignment explanation
Indices: 225038--225117 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
225028 TTAAATTAAA
* *
225038 TTTTTTATTTTTTATTGATTCAATTAA-ATTTTTTAT
1 TTTTTTA-TTTTTATTAATTCAATTAATA-TTTATAT
*
225074 TTTTTTATTTTTATTAATTTAATTAATATTTATAT
1 TTTTTTATTTTTATTAATTCAATTAATATTTATAT
225109 TTTTTTATT
1 TTTTTTATT
225118 CTATGATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 32 0.80
36 8 0.20
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (35 bp):
TTTTTTATTTTTATTAATTCAATTAATATTTATAT
Found at i:226292 original size:39 final size:39
Alignment explanation
Indices: 226214--226292 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
226204 TATATTTAGT
* **
226214 TATTTAATATATTTATTAATAAAAATATTAAAATTTAAA
1 TATTTAATATATTTATAAATAAAAATATTAAAAAATAAA
*
226253 TATTTAAT-T-TTTATAAAATAAAAATTTTTAAAAAATAAA
1 TATTTAATATATTTAT-AAATAAAAA-TATTAAAAAATAAA
226292 T
1 T
226293 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 5 0.15
38 9 0.26
39 20 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTTAATATATTTATAAATAAAAATATTAAAAAATAAA
Found at i:226293 original size:15 final size:17
Alignment explanation
Indices: 226258--226291 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
226248 TTAAATATTT
226258 AATTTTTATAAAATAAA
1 AATTTTTATAAAATAAA
*
226275 AATTTTTAAAAAATAAA
1 AATTTTTATAAAATAAA
226292 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTTTATAAAATAAA
Found at i:226650 original size:22 final size:22
Alignment explanation
Indices: 226625--226684 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
226615 GATTATTATG
226625 ATATAATAAAATATAATTAAAA
1 ATATAATAAAATATAATTAAAA
* * *
226647 ATATAAT-ATATATATTTTAAA
1 ATATAATAAAATATAATTAAAA
* *
226668 AT-TTATATAATATAATT
1 ATATAATAAAATATAATT
226685 TTTATTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.10
21 20 0.67
22 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAATAAAATATAATTAAAA
Found at i:226724 original size:19 final size:19
Alignment explanation
Indices: 226687--226724 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
226677 ATATAATTTT
*
226687 TATTTTAAAATATATATAA
1 TATTTTAAAATATAAATAA
226706 TATTTT-AAATATGAAATAA
1 TATTTTAAAATAT-AAATAA
226725 AATAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TATTTTAAAATATAAATAA
Found at i:227741 original size:15 final size:15
Alignment explanation
Indices: 227721--227751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
227711 TATATTGCGT
227721 CTTACTTCATTCGGG
1 CTTACTTCATTCGGG
*
227736 CTTACTTCATTTGGG
1 CTTACTTCATTCGGG
227751 C
1 C
227752 GAGTGCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.42
Consensus pattern (15 bp):
CTTACTTCATTCGGG
Found at i:228070 original size:3 final size:3
Alignment explanation
Indices: 228062--228093 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
228052 TTTGATCATG
228062 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
228094 TAGTTACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:229206 original size:19 final size:19
Alignment explanation
Indices: 229179--229215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
229169 TATATTTAAT
* *
229179 ATTTTAAAAATTTTTATAC
1 ATTTAAAAAATCTTTATAC
229198 ATTTAAAAAATCTTTATA
1 ATTTAAAAAATCTTTATA
229216 AGATCATATC
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:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAAAAATCTTTATAC
Found at i:236270 original size:30 final size:29
Alignment explanation
Indices: 236206--236271 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
236196 GGTCAAAAAC
* *
236206 TTTT-TTTAGTATAATTTAAAAGTTGAAG
1 TTTTATTTAGTATAAATTAAAAATTGAAG
**
236234 GCTTATTTAAGTATAAATTAAAAATTGAAG
1 TTTTATTT-AGTATAAATTAAAAATTGAAG
236264 TTTTATTT
1 TTTTATTT
236272 GGATGCAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.07
29 3 0.10
30 25 0.83
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTTATTTAGTATAAATTAAAAATTGAAG
Found at i:236621 original size:6 final size:6
Alignment explanation
Indices: 236581--236619 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
236571 AAATTCGTAC
* *
236581 AAAATA AAAATA AAAATA AAAATA AAATTA AAATTA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
236620 TTTCAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:237436 original size:92 final size:92
Alignment explanation
Indices: 237287--237474 Score: 306
Period size: 92 Copynumber: 2.1 Consensus size: 92
237277 ATTTTTTTAA
* **
237287 TTTT-TTATTTTAATGTAATTGATCTACTAAACGGATCTAACCTATTAGATTGATAACCGAAAGT
1 TTTTATTATTTTAATATAATTGATCTACTAAACCAATCTAACCTATTAGATTGATAACCGAAAGT
*
237351 ATCACCAATTTAACCTCTAATTTAATT
66 ATCACCAACTTAACCTCTAATTTAATT
* *
237378 TTTTATTATTTTAATATAATTGATCTATTAAACCAATCTAACTTATTAGATTGATAACCGAAAGT
1 TTTTATTATTTTAATATAATTGATCTACTAAACCAATCTAACCTATTAGATTGATAACCGAAAGT
*
237443 ATCACCAACTTAACCTCTAATTTATTT
66 ATCACCAACTTAACCTCTAATTTAATT
237470 TTTTA
1 TTTTA
237475 AATCTTGACT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 4 0.04
92 85 0.96
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (92 bp):
TTTTATTATTTTAATATAATTGATCTACTAAACCAATCTAACCTATTAGATTGATAACCGAAAGT
ATCACCAACTTAACCTCTAATTTAATT
Found at i:240007 original size:2 final size:2
Alignment explanation
Indices: 240000--240026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239990 AAAATAAAAT
240000 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
240027 TCAGTACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240863 original size:19 final size:18
Alignment explanation
Indices: 240814--240859 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
240804 ATACAATTTA
*
240814 ATTTAAATTATTATTTTT
1 ATTTAAATTAATATTTTT
* *
240832 ATAATAAAATAATATTTTT
1 AT-TTAAATTAATATTTTT
240851 ATTTAAATT
1 ATTTAAATT
240860 TAATTATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAAATTAATATTTTT
Found at i:241244 original size:44 final size:44
Alignment explanation
Indices: 241196--241281 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
241186 ATATAAGATT
*
241196 CATATTTATTTAATTTTACTATTGTATTCCATCTTCTATTCAAG
1 CATATTTATTTAATTTGACTATTGTATTCCATCTTCTATTCAAG
** *
241240 CATATTTATTTAATTTGACTATTGTATTTTATCTTTTATTCA
1 CATATTTATTTAATTTGACTATTGTATTCCATCTTCTATTCA
241282 CGTAAATCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.56
Consensus pattern (44 bp):
CATATTTATTTAATTTGACTATTGTATTCCATCTTCTATTCAAG
Found at i:242465 original size:2 final size:2
Alignment explanation
Indices: 242458--242489 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
242448 AGCAGGTCTA
242458 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
242490 TAATATTATA
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:243430 original size:13 final size:13
Alignment explanation
Indices: 243412--243437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243402 CTCTCCAGAA
243412 TATATATATATGT
1 TATATATATATGT
243425 TATATATATATGT
1 TATATATATATGT
243438 GGTGGATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TATATATATATGT
Found at i:247671 original size:27 final size:28
Alignment explanation
Indices: 247606--247683 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
247596 AATTCCATCC
247606 TTTGTATTTGTCAAATATGGTGGTTTCT
1 TTTGTATTTGTCAAATATGGTGGTTTCT
247634 TTTGTATTTGTCAAATATGGTGGTTAT-T
1 TTTGTATTTGTCAAATATGGTGGTT-TCT
* * *
247662 TTT-TGTTTGTAAAAAATGGTGG
1 TTTGTATTTGTCAAATATGGTGG
247684 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.35
28 29 0.63
29 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.23, T:0.51
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTGGTTTCT
Found at i:247691 original size:24 final size:24
Alignment explanation
Indices: 247664--247709 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
247654 TGGTTATTTT
247664 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
247688 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
247710 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:248435 original size:35 final size:33
Alignment explanation
Indices: 248377--248457 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
248367 ATGTAAACAT
* **
248377 TAAAAAATATATTAAATATTTATATTTTAAATCA
1 TAAAAAAAATATTAAATATTTATAAATTAAAT-A
248411 TAATAAAAAATATTAAAT-TATTATAAATTAAATA
1 TAA-AAAAAATATTAAATAT-TTATAAATTAAATA
*
248445 TAAAAAATATATT
1 TAAAAAAAATATT
248458 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.22
34 8 0.20
35 24 0.59
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAAAAAATATTAAATATTTATAAATTAAATA
Found at i:248578 original size:16 final size:15
Alignment explanation
Indices: 248557--248588 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
248547 ATTATAATTA
248557 AATCTAACTTAAACTT
1 AATCTAACTT-AACTT
248573 AATCTAACTTAACTT
1 AATCTAACTTAACTT
248588 A
1 A
248589 TAAACATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCTAACTTAACTT
Found at i:249078 original size:20 final size:19
Alignment explanation
Indices: 249028--249104 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
249018 TTTTACCTTG
*
249028 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATCA
* * *
249048 ATATATTGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
249068 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
249088 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
249105 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:249099 original size:40 final size:39
Alignment explanation
Indices: 249028--249105 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
249018 TTTTACCTTG
* * *
249028 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
249068 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
249106 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:250052 original size:23 final size:23
Alignment explanation
Indices: 250016--250071 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
250006 AGCCTTTGAC
250016 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
250038 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
250061 CATGCATTTTT
1 CATGCATTTTT
250072 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:250078 original size:20 final size:21
Alignment explanation
Indices: 250016--250078 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
250006 AGCCTTTGAC
**
250016 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
250038 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTAACATGTTT
250061 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
250079 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.26
22 6 0.16
23 22 0.58
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:256253 original size:21 final size:21
Alignment explanation
Indices: 256229--256276 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
256219 AAATGAAAAG
256229 AAAAAGTGCAAAAAC-AAAATAA
1 AAAAAG-G-AAAAACAAAAATAA
*
256251 AAAAAGGAACAACAAAAATAA
1 AAAAAGGAAAAACAAAAATAA
256272 AAAAA
1 AAAAA
256277 TGAGGACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.06
Consensus pattern (21 bp):
AAAAAGGAAAAACAAAAATAA
Found at i:256533 original size:9 final size:9
Alignment explanation
Indices: 256519--256544 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
256509 CCAATCCTAA
256519 AAAAAAAAC
1 AAAAAAAAC
256528 AAAAAAAAC
1 AAAAAAAAC
256537 AAAAAAAA
1 AAAAAAAA
256545 AAACCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:257600 original size:27 final size:27
Alignment explanation
Indices: 257561--258579 Score: 1536
Period size: 27 Copynumber: 37.2 Consensus size: 27
257551 AGTGTGACCT
* * *
257561 CTTTAAAGCCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
257588 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
257615 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
257642 CTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
257670 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
257697 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
*
257725 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
257752 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
257780 CTTTTAAGACCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
257807 CTTTTAAGTCCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
257834 CTTTTAAGTCCACAACTCCGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
**
257862 CTTTTAAGTCCACAACTCCGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
257890 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
257917 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
257945 GTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
257972 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
258000 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
258027 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
258054 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
258081 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
258108 CTTTTTAAGTCCACAACTCCGTGGCATCC
1 C-TTTTAAGTCCACAACTCCGTGGCA-CC
*
258137 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
258164 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
258191 CTTTTAAGTCCACAACCCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
258219 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
258246 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
258273 CTTTTAAGTCCATAACTCCATGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
258301 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
258328 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
258356 CTTTTTAA-TCCATAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
*
258383 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
258410 CTTTTAAGTCCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
258437 CTTTTAAGACCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
258464 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
258492 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
258519 CTTTTAAAATCCACAACTCTGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
258547 CTTTTAAAATCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
258575 CTTTT
1 CTTTT
258580 CAAAGCCCAC
Statistics
Matches: 916, Mismatches: 61, Indels: 29
0.91 0.06 0.03
Matches are distributed among these distances:
26 6 0.01
27 527 0.58
28 376 0.41
29 7 0.01
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Done.