Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold22
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1964558
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 137786 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:13385 original size:4 final size:4
Alignment explanation
Indices: 13376--13437 Score: 52
Period size: 4 Copynumber: 14.0 Consensus size: 4
13366 ATAATGATGT
* *
13376 TTTG TTTG TTTGG TTTTG TTTTT TTTG TTAAG TTTG TTTTG TTTCG TTTG
1 TTTG TTTG TTT-G -TTTG -TTTG TTTG TT-TG TTTG -TTTG TTT-G TTTG
13426 TTTG TTTG TTTG
1 TTTG TTTG TTTG
13438 CTTTTTTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 29 0.59
5 17 0.35
6 3 0.06
ACGTcount: A:0.03, C:0.02, G:0.23, T:0.73
Consensus pattern (4 bp):
TTTG
Found at i:13391 original size:5 final size:5
Alignment explanation
Indices: 13373--13436 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
13363 AGTATAATGA
* * *
13373 TGTTT TG-TT TGTTT GGTTT TGTTT T-TTT TGTTA AG-TT TGTTT TGTTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT
*
13420 CG-TT TG-TT TG-TT TGTTT
1 TGTTT TGTTT TGTTT TGTTT
13437 GCTTTTTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
4 21 0.45
5 26 0.55
ACGTcount: A:0.03, C:0.02, G:0.22, T:0.73
Consensus pattern (5 bp):
TGTTT
Found at i:13391 original size:9 final size:9
Alignment explanation
Indices: 13373--13442 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
13363 AGTATAATGA
13373 TGTTTTGTT
1 TGTTTTGTT
*
13382 TGTTTGGTTT
1 TGTTTTG-TT
*
13392 TGTTTTTTT
1 TGTTTTGTT
**
13401 TGTTAAGTT
1 TGTTTTGTT
13410 TGTTTTGTT
1 TGTTTTGTT
13419 TCG-TTTGTT
1 T-GTTTTGTT
13428 TG-TTTGTT
1 TGTTTTGTT
13436 TGCTTTT
1 TG-TTTT
13443 TTTAACTGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
8 9 0.18
9 29 0.59
10 11 0.22
ACGTcount: A:0.03, C:0.03, G:0.21, T:0.73
Consensus pattern (9 bp):
TGTTTTGTT
Found at i:13393 original size:14 final size:14
Alignment explanation
Indices: 13373--13442 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
13363 AGTATAATGA
13373 TGTTTTGTTTGTTT
1 TGTTTTGTTTGTTT
* *
13387 GGTTTTGTTTTTTT
1 TGTTTTGTTTGTTT
**
13401 TGTTAAGTTTGTTT
1 TGTTTTGTTTGTTT
*
13415 TGTTTCGTTTG-TT
1 TGTTTTGTTTGTTT
13428 TG-TTTGTTTGCTTT
1 TGTTTTGTTTG-TTT
13442 T
1 T
13443 TTTAACTGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 34 0.76
ACGTcount: A:0.03, C:0.03, G:0.21, T:0.73
Consensus pattern (14 bp):
TGTTTTGTTTGTTT
Found at i:20264 original size:35 final size:35
Alignment explanation
Indices: 20215--20283 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
20205 GGATTTTCGT
* * *
20215 TGTGGCGTTTTAGTCACCTGTCTATGGATCTTTGC
1 TGTGGCGTTATAGTCACCTGGCTATGGAACTTTGC
*
20250 TGTGGCGTTATAGTCACCTGGCTATTGAACTTTG
1 TGTGGCGTTATAGTCACCTGGCTATGGAACTTTG
20284 TTTTCGTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.41
Consensus pattern (35 bp):
TGTGGCGTTATAGTCACCTGGCTATGGAACTTTGC
Found at i:20353 original size:41 final size:37
Alignment explanation
Indices: 20295--20435 Score: 124
Period size: 37 Copynumber: 3.7 Consensus size: 37
20285 TTTCGTGTAA
* *
20295 GGATTATTCGTTGTGGCGTTTTAGTCACCTGACTTGGTCTAT
1 GGATTATT-GTTGTGGCGTTTTAGTCACATGAC----TATAT
**
20337 GGATTATTGTTGTGGCGTTCGAGTCACATGACTATAT
1 GGATTATTGTTGTGGCGTTTTAGTCACATGACTATAT
* ** *
20374 GGATTTTTGTTGTGGCGTTTTAGTCATTTGAC--CAT
1 GGATTATTGTTGTGGCGTTTTAGTCACATGACTATAT
* * *
20409 GAATTTTTGTGGTGGCGTTTTAGTCAC
1 GGATTATTGTTGTGGCGTTTTAGTCAC
20436 CAATAAATTG
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
35 26 0.30
37 31 0.36
41 21 0.24
42 8 0.09
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.43
Consensus pattern (37 bp):
GGATTATTGTTGTGGCGTTTTAGTCACATGACTATAT
Found at i:33050 original size:2 final size:2
Alignment explanation
Indices: 33043--33067 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33033 TCATACTTAT
33043 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
33068 ATATTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35520 original size:13 final size:13
Alignment explanation
Indices: 35502--35527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35492 TTTGTTGTGG
35502 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
35515 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
35528 TTGGGGGGGG
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:47293 original size:1 final size:1
Alignment explanation
Indices: 47287--47319 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
47277 TGTGAGCCCT
47287 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
47320 AATACTCTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:58353 original size:2 final size:2
Alignment explanation
Indices: 58346--58429 Score: 141
Period size: 2 Copynumber: 42.0 Consensus size: 2
58336 TAATTAATAT
58346 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
58388 GA GA GA GA GA CA GA GA GA GA CA GA GA GA GA GA CA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
58430 AAATAAGTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.04, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:61857 original size:48 final size:48
Alignment explanation
Indices: 61801--61902 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 48
61791 TGTCAATTGT
61801 AATTATAGTGAGGTAAGATTTGACTATTGAA-GTCCATGTATAAAGATC
1 AATTATAGTGAGGTAAGATTTGACTATT-AAGGTCCATGTATAAAGATC
*
61849 AATTATAGTGAGGTAAGATTTGACTATTAAGGTCCATGTATATAGATC
1 AATTATAGTGAGGTAAGATTTGACTATTAAGGTCCATGTATAAAGATC
*
61897 AGTTAT
1 AATTAT
61903 TGAGGTCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
47 2 0.04
48 49 0.96
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (48 bp):
AATTATAGTGAGGTAAGATTTGACTATTAAGGTCCATGTATAAAGATC
Found at i:61950 original size:76 final size:75
Alignment explanation
Indices: 61825--61975 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 75
61815 AAGATTTGAC
* *
61825 TATTGAAGTCCATGTATAAAGATCAATTATAGTGAGGTAAGATTTGACTATTAAGGTCCATGTAT
1 TATTGAAGTCCATGTATAAAGATCAATTATAGTGAGGTAAAATTTGACTATTAAGGTCAATGTAT
61890 ATAGATCAGT
66 ATAGATCAGT
* * ** *
61900 TATTGAGGTCCATGTATATAGATCCTTTTATAGTGAGGTAAAATTTGACTATTGAGGTCAATGTA
1 TATTGAAGTCCATGTATAAAGAT-CAATTATAGTGAGGTAAAATTTGACTATTAAGGTCAATGTA
*
61965 TGTAGATCAGT
65 TATAGATCAGT
61976 CACAGTGAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
75 21 0.31
76 46 0.69
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (75 bp):
TATTGAAGTCCATGTATAAAGATCAATTATAGTGAGGTAAAATTTGACTATTAAGGTCAATGTAT
ATAGATCAGT
Found at i:62004 original size:48 final size:48
Alignment explanation
Indices: 61900--62662 Score: 1044
Period size: 48 Copynumber: 15.6 Consensus size: 48
61890 ATAGATCAGT
** * *
61900 TATTGAGGTCCATGTATATAGATCCTTTTATAGTGAGGTAAAATTTGAC
1 TATTGAGGTCCATGTATATAGAT-CAGTCATAGTGAGGTAAGATTTGAC
* * *
61949 TATTGAGGTCAATGTATGTAGATCAGTCACAGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* * * *
61997 TACTGAGGTCCATTTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAT
1 TATTGAGGTCCATGTATATAGATCAG-TCA-TA--GTGAGGTAAGATTTGAC
* * * * *
62049 TATTGAAGTTCATGTATATAGATCAGTTATAGTTAGGTAAGATTTCAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
*
62097 TATTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAG-TCA-TA--GTGAGGTAAGATTTGAC
*
62149 TATTGTA-GTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGAC
1 TATTG-AGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
*
62197 TATTGAGGTCCATGTATATAGATCAGTCACAGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* *
62245 TATTGAGGTCCATGTATGTAGATCAGTCACAGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* *
62293 TATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAATATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
*
62341 TATTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAG-TCA-TA--GTGAGGTAAGATTTGAC
* *
62393 TATTGAGGTCCATGTATATAGATCAGTCACAGTGAAGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
*
62441 TATTGAGGTCCATGTATATAGATCAGTCACAGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* *
62489 TATTGAGGTCCATGTATGTAGATCAGTCACAGTGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* *
62537 TATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGCAAGATTTGAC
1 TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
* * * *
62585 AATTGAGGTCCATGTAT-TAATATCAGTTATAATGAGGTAAGATTTGAC
1 TATTGAGGTCCATGTATAT-AGATCAGTCATAGTGAGGTAAGATTTGAC
* *
62633 TATCGAGGTTCATGTATATAGATCAGTCAT
1 TATTGAGGTCCATGTATATAGATCAGTCAT
62663 TGACCACCAA
Statistics
Matches: 643, Mismatches: 55, Indels: 33
0.88 0.08 0.05
Matches are distributed among these distances:
47 2 0.00
48 477 0.74
49 28 0.04
50 10 0.02
51 6 0.01
52 119 0.19
53 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (48 bp):
TATTGAGGTCCATGTATATAGATCAGTCATAGTGAGGTAAGATTTGAC
Found at i:62381 original size:244 final size:244
Alignment explanation
Indices: 61900--62659 Score: 1190
Period size: 244 Copynumber: 3.1 Consensus size: 244
61890 ATAGATCAGT
** * *
61900 TATTGAGGTCCATGTATATAGATCCTTTTATAGTGAGGTAAAATTTGACTATTGAGGTCAATGTA
1 TATTGAGGTCCATGTATATAGAT-CAGTTATAGTGAGGTAAGATTTGACTATTGAGGTCCATGTA
* * * * * *
61965 TGTAGATCAGTCACAGTGAGGTAAGATTTGACTACTGAGGTCCATTTATATAGATCAGTTAATTA
65 TATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAG-TCA-CA
* * * * *
62030 TTGTGAGGTAAGATTTGATTATTGAAGTTCATGTATATAGATCAGTTATAGTTAGGTAAGATTTC
128 --GTGAGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTG
62095 ACTATTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
191 ACTATTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
62149 TATTGTA-GTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTATTGAGGTCCATGTA
1 TATTG-AGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTATTGAGGTCCATGTA
62213 TATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAGTCACAGT
65 TATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAGTCACAGT
*
62278 GAGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAATATTTGACTA
130 GAGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTA
62343 TTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
195 TTGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
* * *
62393 TATTGAGGTCCATGTATATAGATCAGTCACAGTGAAGTAAGATTTGACTATTGAGGTCCATGTAT
1 TATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTATTGAGGTCCATGTAT
62458 ATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAGTCACAGTG
66 ATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAGTCACAGTG
* *
62523 AGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGCAAGATTTGACAAT
131 AGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTAT
* *
62588 TGAGGTCCATGTAT-TAATATCAGTT-A-TA--ATGAGGTAAGATTTGAC
196 TGAGGTCCATGTATAT-AGATCAGTTAATTATTGTGAGGTAAGATTTGAC
* *
62633 TATCGAGGTTCATGTATATAGATCAGT
1 TATTGAGGTCCATGTATATAGATCAGT
62660 CATTGACCAC
Statistics
Matches: 482, Mismatches: 26, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
240 41 0.09
242 2 0.00
243 3 0.01
244 320 0.66
246 1 0.00
247 2 0.00
248 91 0.19
249 21 0.04
250 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (244 bp):
TATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTATTGAGGTCCATGTAT
ATAGATCAGTCACAGTGAGGTAAGATTTGACTATTGAGGTCCATGTATGTAGATCAGTCACAGTG
AGGTAAGATTTGACTATTGAGGTCCATGTATATAGATCAGTTATAGTGAGGTAAGATTTGACTAT
TGAGGTCCATGTATATAGATCAGTTAATTATTGTGAGGTAAGATTTGAC
Found at i:71583 original size:2 final size:2
Alignment explanation
Indices: 71576--71625 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
71566 ACAAAACGCC
71576 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
71618 CT CT CT CT
1 CT CT CT CT
71626 ATTTTTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:73023 original size:2 final size:2
Alignment explanation
Indices: 73016--73069 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
73006 ATGCTAAACA
73016 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
73058 TC TC TC TC TC TC
1 TC TC TC TC TC TC
73070 ACAGCTATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:80935 original size:10 final size:9
Alignment explanation
Indices: 80920--80980 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
80910 CGGTTTTATA
80920 TTTGTGTTGT
1 TTTGTGTT-T
80930 TTTGTGTTT
1 TTTGTGTTT
** *
80939 TTAATTTTT
1 TTTGTGTTT
*
80948 TGTTTTGTTT
1 T-TTGTGTTT
*
80958 TGTTTTGTTT
1 T-TTGTGTTT
80968 TTTGTGTTT
1 TTTGTGTTT
80977 TTTG
1 TTTG
80981 GGGGGGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
9 19 0.44
10 24 0.56
ACGTcount: A:0.03, C:0.00, G:0.20, T:0.77
Consensus pattern (9 bp):
TTTGTGTTT
Found at i:80953 original size:5 final size:5
Alignment explanation
Indices: 80945--80977 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
80935 GTTTTTAATT
*
80945 TTTTG TTTTG TTTTG TTTTG TTTT- TTGTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
80978 TTGGGGGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:82248 original size:2 final size:2
Alignment explanation
Indices: 82243--82268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82233 TGTTTTTTGT
82243 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
82269 AATCACAAAA
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:92564 original size:31 final size:31
Alignment explanation
Indices: 92526--92587 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
92516 GAAAGGTATT
92526 CCGAGTGACTTTCGAACAGAGAAAAGATGTC
1 CCGAGTGACTTTCGAACAGAGAAAAGATGTC
*
92557 CCGAGTGACTTTCGAACAGAGGAAAGATGTC
1 CCGAGTGACTTTCGAACAGAGAAAAGATGTC
92588 AACATTCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.19
Consensus pattern (31 bp):
CCGAGTGACTTTCGAACAGAGAAAAGATGTC
Found at i:105524 original size:21 final size:21
Alignment explanation
Indices: 105498--105576 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
105488 TAGGATTTAA
*
105498 CTCGTAATAACGAGATCT-TCT
1 CTCGTAATTACGAGATCTAT-T
* *
105519 CTCGTAATTACGAGAACTGTT
1 CTCGTAATTACGAGATCTATT
105540 CTCGTAATTACGAG-TCATATAT
1 CTCGTAATTACGAGATC-TAT-T
105562 CTCGTAATTACGAGA
1 CTCGTAATTACGAGA
105577 AAAGATCTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.66
22 16 0.32
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (21 bp):
CTCGTAATTACGAGATCTATT
Found at i:105573 original size:43 final size:43
Alignment explanation
Indices: 105501--105627 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
105491 GATTTAACTC
* ** * *
105501 GTAATAACGAGATC--TTCTCTCGTAATTACGAGAACTGTTCTC
1 GTAATAACGAG-TCAATTATCTCGTAATTACGAGAAAAGATCTA
*
105543 GTAATTACGAGTC-ATATATCTCGTAATTACGAGAAAAGATCTA
1 GTAATAACGAGTCAAT-TATCTCGTAATTACGAGAAAAGATCTA
* * *
105586 GTAATAACGAGTTAATTATCTCGTTATTACGAGAAAAAATCT
1 GTAATAACGAGTCAATTATCTCGTAATTACGAGAAAAGATCT
105628 CGTTGTTACG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.03
42 11 0.15
43 57 0.79
44 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (43 bp):
GTAATAACGAGTCAATTATCTCGTAATTACGAGAAAAGATCTA
Found at i:105589 original size:21 final size:21
Alignment explanation
Indices: 105518--105692 Score: 98
Period size: 21 Copynumber: 8.1 Consensus size: 21
105508 CGAGATCTTC
** *
105518 TCTCGTAATTACGAGAACTGT
1 TCTCGTAATTACGAGAAAAGA
* * *
105539 TCTCGTAATTACGAGTCATATA
1 TCTCGTAATTACGAG-AAAAGA
105561 TCTCGTAATTACGAGAAAAGA
1 TCTCGTAATTACGAGAAAAGA
* * * **
105582 TCTAGTAATAACGAGTTAATTA
1 TCTCGTAATTACGAG-AAAAGA
* *
105604 TCTCGTTATTACGAGAAAAAA
1 TCTCGTAATTACGAGAAAAGA
** ** **
105625 TCTCGTTGTTACGAGTTTATTA
1 TCTCGTAATTACGAG-AAAAGA
* ** *
105647 TCTTGTCTTTTACAAGAAAAGA
1 TCTCGT-AATTACGAGAAAAGA
*
105669 TCTCGTTATTACGAGAAAAGA
1 TCTCGTAATTACGAGAAAAGA
105690 TCT
1 TCT
105693 AGTTTAAAAT
Statistics
Matches: 116, Mismatches: 34, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
21 64 0.55
22 45 0.39
23 7 0.06
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (21 bp):
TCTCGTAATTACGAGAAAAGA
Found at i:105675 original size:44 final size:43
Alignment explanation
Indices: 105518--105683 Score: 163
Period size: 43 Copynumber: 3.8 Consensus size: 43
105508 CGAGATCTTC
* ** * * *
105518 TCTCGTAATTACGAGAACTGTTCTCGTAATTACGAG-TCATATA
1 TCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAAT-TA
* * * *
105561 TCTCGTAATTACGAGAAAAGATCTAGTAATAACGAGTTAATTA
1 TCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATTA
* * *
105604 TCTCGTTATTACGAGAAAAAATCTCGTTGTTACGAGTTTATTA
1 TCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATTA
* * *
105647 TCTTGTCTTTTACAAGAAAAGATCTCGTTATTACGAG
1 TCTCGT-TATTACGAGAAAAGATCTCGTTATTACGAG
105684 AAAAGATCTA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
43 74 0.72
44 29 0.28
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (43 bp):
TCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATTA
Found at i:106373 original size:21 final size:21
Alignment explanation
Indices: 106322--106373 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
106312 ACGCAACATT
*
106322 TAATGTAGACCTTTTCTCGTAA
1 TAATG-AGATCTTTTCTCGTAA
**
106344 TAACAAGATCTTTTCTCGTAA
1 TAATGAGATCTTTTCTCGTAA
106365 TAATGAGAT
1 TAATGAGAT
106374 TATAAACACG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATGAGATCTTTTCTCGTAA
Found at i:106465 original size:43 final size:43
Alignment explanation
Indices: 106337--106466 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 43
106327 TAGACCTTTT
* * * * *
106337 CTCGTAATAACAAGATCTTTTCTCGTAATAATGAGATTATAAA
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAA
* * * *
106380 CACGTTATAACGAGATCTTTTCTCGTAAATACGAGAAAATTAA
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAA
* * * *
106423 CTCGTAATAACGATATCTTGTATCGTAATTACGAGATGATTAA
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAA
106466 C
1 C
106467 GAGATCTTTT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (43 bp):
CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAA
Found at i:106724 original size:21 final size:21
Alignment explanation
Indices: 106679--106725 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
106669 TGATAATTAA
*
106679 CTCGTAATTACGAGAAAAGAC
1 CTCGTAATTACGAGAAAAAAC
*
106700 CTCGTAATTACGAGAAAAAAT
1 CTCGTAATTACGAGAAAAAAC
106721 CTCGT
1 CTCGT
106726 TATGACGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
CTCGTAATTACGAGAAAAAAC
Found at i:106733 original size:21 final size:21
Alignment explanation
Indices: 106679--106733 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
106669 TGATAATTAA
* *
106679 CTCGTAATTACGAGAAAAGAC
1 CTCGTAATGACGAGAAAAAAC
* *
106700 CTCGTAATTACGAGAAAAAAT
1 CTCGTAATGACGAGAAAAAAC
*
106721 CTCGTTATGACGA
1 CTCGTAATGACGA
106734 CATCGTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (21 bp):
CTCGTAATGACGAGAAAAAAC
Found at i:106805 original size:21 final size:21
Alignment explanation
Indices: 106781--106990 Score: 161
Period size: 21 Copynumber: 9.9 Consensus size: 21
106771 TAATAATAAT
*
106781 TTTTCTCGTCATAACGAGATC
1 TTTTCTCGTAATAACGAGATC
* * **
106802 TTTTCTCATAATTACGAGAAAA
1 TTTTCTCGTAATAACGAG-ATC
** *
106824 TTAACTCGTAATAGCGAGATC
1 TTTTCTCGTAATAACGAGATC
* **
106845 -TTTCTCATAATAACGAAGAAA
1 TTTTCTCGTAATAACG-AGATC
**
106866 TTAACTCGTAATAACGAGATC
1 TTTTCTCGTAATAACGAGATC
* *
106887 TTTTCTCGTTATTACGAGATC
1 TTTTCTCGTAATAACGAGATC
* * * *
106908 GTTTCTCGTTATTACGGGATC
1 TTTTCTCGTAATAACGAGATC
*
106929 TTTTCTCGTAATAACGAGATAA
1 TTTTCTCGTAATAACGAGAT-C
** *
106951 TTAACTCGTAATAACGAGATA
1 TTTTCTCGTAATAACGAGATC
* *
106972 TTTTCTCGTATTTACGAGA
1 TTTTCTCGTAATAACGAGA
106991 AAAAAATATT
Statistics
Matches: 145, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
20 11 0.08
21 90 0.62
22 44 0.30
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTTCTCGTAATAACGAGATC
Found at i:106814 original size:106 final size:105
Alignment explanation
Indices: 106704--106923 Score: 241
Period size: 106 Copynumber: 2.1 Consensus size: 105
106694 AAAGACCTCG
* *
106704 TAATTACGAGAAAA-AATCTCGTTAT-GACGACATCGTTTCTCCTAATAACG-AGAAAATAAACT
1 TAATTACGAGAAAATAA-CTCGTAATAG-CGACATC-TTTCTCATAATAACGAAG-AAATAAACT
* * *
106766 CGTTATAATAATAAT-TTTTCTCGTCATAACGAGATCTTTTCTCA
62 CGTAATAACAA-AATCTTTTCTCGTCATAACGAGATCGTTTCTCA
* *
106810 TAATTACGAGAAAATTAACTCGTAATAGCGAGATCTTTCTCATAATAACGAAGAAATTAACTCGT
1 TAATTACGAGAAAA-TAACTCGTAATAGCGACATCTTTCTCATAATAACGAAGAAATAAACTCGT
* * * * *
106875 AATAACGAGATCTTTTCTCGTTATTACGAGATCGTTTCTCG
65 AATAACAAAATCTTTTCTCGTCATAACGAGATCGTTTCTCA
*
106916 TTATTACG
1 TAATTACG
106924 GGATCTTTTC
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
105 2 0.02
106 76 0.79
107 15 0.16
108 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (105 bp):
TAATTACGAGAAAATAACTCGTAATAGCGACATCTTTCTCATAATAACGAAGAAATAAACTCGTA
ATAACAAAATCTTTTCTCGTCATAACGAGATCGTTTCTCA
Found at i:106841 original size:22 final size:22
Alignment explanation
Indices: 106810--106884 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
106800 TCTTTTCTCA
*
106810 TAATTACGAGAAAATTAACTCG
1 TAATAACGAGAAAATTAACTCG
* ** * *
106832 TAATAGCGAG-ATCTT-TCTCA
1 TAATAACGAGAAAATTAACTCG
106852 TAATAACGA-AGAAATTAACTCG
1 TAATAACGAGA-AAATTAACTCG
106874 TAATAACGAGA
1 TAATAACGAGA
106885 TCTTTTCTCG
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 11 0.29
21 6 0.16
22 20 0.53
23 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (22 bp):
TAATAACGAGAAAATTAACTCG
Found at i:106867 original size:42 final size:42
Alignment explanation
Indices: 106785--106993 Score: 188
Period size: 42 Copynumber: 4.9 Consensus size: 42
106775 AATAATTTTT
* *
106785 CTCGTCATAACGAGATCTTTTCTCATAATTACGAGAAAATTAA
1 CTCGTAATAACGAGATC-TTTCTCATAATAACGAGAAAATTAA
*
106828 CTCGTAATAGCGAGATCTTTCTCATAATAACGA-AGAAATTAA
1 CTCGTAATAACGAGATCTTTCTCATAATAACGAGA-AAATTAA
* * * *** *
106870 CTCGTAATAACGAGATCTTTTCTCGTTATTACGAGATCGTT-T
1 CTCGTAATAACGAGATC-TTTCTCATAATAACGAGAAAATTAA
* * * * *
106912 CTCGTTATTACGGGATCTTTTCTCGTAATAACGAGATAATTAA
1 CTCGTAATAACGAGATC-TTTCTCATAATAACGAGAAAATTAA
* * * *
106955 CTCGTAATAACGAGATATTTTCTCGTATTTACGAGAAAA
1 CTCGTAATAACGAGAT-CTTTCTCATAATAACGAGAAAA
106994 AAATATTTTT
Statistics
Matches: 135, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 72 0.53
43 61 0.45
44 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (42 bp):
CTCGTAATAACGAGATCTTTCTCATAATAACGAGAAAATTAA
Found at i:106880 original size:85 final size:85
Alignment explanation
Indices: 106785--106993 Score: 262
Period size: 85 Copynumber: 2.5 Consensus size: 85
106775 AATAATTTTT
* *
106785 CTCGTCATAACGAGATCTTTTCTCATAATTACGAGAAAATTAACTCG-TAATAGCGAGATC-TTT
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGAAAATT-ACTCGTTAATA-CGAGATCTTTT
106848 CTCATAATAACGAAGA-AATTAA
64 CTCATAATAACG-AGATAATTAA
* *** * * *
106870 CTCGTAATAACGAGATCTTTTCTCGTTATTACGAGATCGTTTCTCGTTATTACGGGATCTTTTCT
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGAAAATTACTCGTTAATACGAGATCTTTTCT
*
106935 CGTAATAACGAGATAATTAA
66 CATAATAACGAGATAATTAA
* *
106955 CTCGTAATAACGAGATATTTTCTCGTATTTACGAGAAAA
1 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGAAAA
106994 AAATATTTTT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
84 13 0.12
85 92 0.88
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (85 bp):
CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGAAAATTACTCGTTAATACGAGATCTTTTCT
CATAATAACGAGATAATTAA
Found at i:108739 original size:36 final size:35
Alignment explanation
Indices: 108695--108762 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
108685 GGGGTATTAC
108695 AGGGGCTGGTATCTCGCATTCCATTTTCTGTACAG
1 AGGGGCTGGTATCTCGCATTCCATTTTCTGTACAG
* * *
108730 AGGGAGCTGGTTTCTCGCTTTCCATTTTTTGTA
1 AGGG-GCTGGTATCTCGCATTCCATTTTCTGTA
108763 ATGTGACAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (35 bp):
AGGGGCTGGTATCTCGCATTCCATTTTCTGTACAG
Found at i:120622 original size:25 final size:25
Alignment explanation
Indices: 120588--120637 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
120578 AACAATAGTT
120588 CCTGCAGTTATCTTTCATTGTGACA
1 CCTGCAGTTATCTTTCATTGTGACA
*
120613 CCTGCGGTTATCTTTCATTGTGACA
1 CCTGCAGTTATCTTTCATTGTGACA
120638 TGGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (25 bp):
CCTGCAGTTATCTTTCATTGTGACA
Found at i:122470 original size:172 final size:172
Alignment explanation
Indices: 122184--122808 Score: 1043
Period size: 172 Copynumber: 3.6 Consensus size: 172
122174 GTATCGAGTC
* ** *
122184 TATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAACGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
* * *
122249 TAATGAAAATCTGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTCGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
*
122314 GAGTCATTATTGTGGTCAAAGTCCAATAACGCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* *
122356 TATCGACTAACGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAACGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
122421 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
* *
122486 GAGTCATGATTGTGGTCAAAGTCCCATAGCGCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* * *
122528 TATCGACTAACGCTGATTTTCAAACTTGACCAAGGTAATAGTGGTATAAATATTTGGTATAAATT
1 TATCGACCAACGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
122593 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
* * *
122658 GAGTCATTACTGCGGTCAAAGTCCCATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* * * *
122700 GATCGACCAATGCTGATTTTCGAACTTGACCAAGGTTATAGTGGTATAAACATTTGGTATAAATA
1 TATCGACCAACGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
*
122765 TAATGAAAATCCGTCAAAATTTGTAGACATGAGAGCGCTTACAA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
122809 AAAAGTGTGA
Statistics
Matches: 425, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
172 425 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (172 bp):
TATCGACCAACGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACA
GAGTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
Found at i:132614 original size:16 final size:14
Alignment explanation
Indices: 132574--132606 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
132564 CATCAAGGGA
132574 AGAATTTAAGGTGT
1 AGAATTTAAGGTGT
132588 AGAATTTAAGGTGT
1 AGAATTTAAGGTGT
132602 AGAAT
1 AGAAT
132607 AATTAAGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (14 bp):
AGAATTTAAGGTGT
Found at i:136331 original size:29 final size:29
Alignment explanation
Indices: 136184--136429 Score: 156
Period size: 29 Copynumber: 8.7 Consensus size: 29
136174 CTATTACATG
* *
136184 TACCTGTATGCAAGAGATGTCTTGTGTAT
1 TACCTGTATGTAAGAGATGTCTTGTCTAT
** * *
136213 TTTCTGTATGAAAGAGATGT-TTCGTCAAT
1 TACCTGTATGTAAGAGATGTCTT-GTCTAT
* * **
136242 TTCCTGTACACATGTAAGAGATGACCAGTCTAT
1 TACCTGT----ATGTAAGAGATGTCTTGTCTAT
* *
136275 TA--TCTATAT-A-AGATGTC-T-TCTAT
1 TACCTGTATGTAAGAGATGTCTTGTCTAT
* *
136298 AACCTGTTTGTAAGAGATGTCTTGTCTAT
1 TACCTGTATGTAAGAGATGTCTTGTCTAT
136327 TACCTGTATGT-AGATGATGTCTTGTCTAT
1 TACCTGTATGTAAGA-GATGTCTTGTCTAT
* *
136356 TACCTGTA-G---GAAATGTCTTGTTTAT
1 TACCTGTATGTAAGAGATGTCTTGTCTAT
* * *
136381 TACCTGTATGTAGGTGAGGTCTTGTCTAT
1 TACCTGTATGTAAGAGATGTCTTGTCTAT
* * *
136410 TACCAGTGTGTAAGAAATGT
1 TACCTGTATGTAAGAGATGT
136430 ATATTACCTG
Statistics
Matches: 166, Mismatches: 34, Indels: 34
0.71 0.15 0.15
Matches are distributed among these distances:
23 6 0.04
25 30 0.18
26 5 0.03
27 10 0.06
28 7 0.04
29 89 0.54
31 2 0.01
33 17 0.10
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (29 bp):
TACCTGTATGTAAGAGATGTCTTGTCTAT
Found at i:139935 original size:38 final size:38
Alignment explanation
Indices: 139884--140069 Score: 264
Period size: 38 Copynumber: 4.9 Consensus size: 38
139874 ATAAAACCTG
* *
139884 TTACCTGGTACTTTATGATATGACTGTAGACTGTTACA
1 TTACCTGGTACTTTATGATATGACTGTAGATTGTAACA
* * *
139922 TTACCTGGAACTTTTTGGTATGACTGTAGATTGTAACA
1 TTACCTGGTACTTTATGATATGACTGTAGATTGTAACA
* * * *
139960 TTACATGTTTCTTTTTGATATGACTGTAGATTGTAACA
1 TTACCTGGTACTTTATGATATGACTGTAGATTGTAACA
*
139998 TTACCTGGTACTTTTTGATATGACTGTAGATTGTAACA
1 TTACCTGGTACTTTATGATATGACTGTAGATTGTAACA
* *
140036 TTACCCGGTACTTTTTGATATGACTGTAGATTGT
1 TTACCTGGTACTTTATGATATGACTGTAGATTGT
140070 TACTTTTGAT
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 134 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (38 bp):
TTACCTGGTACTTTATGATATGACTGTAGATTGTAACA
Found at i:140109 original size:63 final size:63
Alignment explanation
Indices: 140010--140132 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
140000 ACCTGGTACT
*
140010 TTTTGATATGACTGTAGATTGTAACATTACCCGGTACTTTTTGATATGACTGTAGATTGTTAC
1 TTTTGATATGACTGTAGATTGTAACATTACCCGGTACTTTATGATATGACTGTAGATTGTTAC
*
140073 TTTTGATATGACTGTAGATTGTAACATTACCTGGTACTTTATGATATGACTGTAGATTGT
1 TTTTGATATGACTGTAGATTGTAACATTACCCGGTACTTTATGATATGACTGTAGATTGT
140133 AACATTACCC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (63 bp):
TTTTGATATGACTGTAGATTGTAACATTACCCGGTACTTTATGATATGACTGTAGATTGTTAC
Found at i:140120 original size:38 final size:38
Alignment explanation
Indices: 140070--140395 Score: 575
Period size: 38 Copynumber: 8.6 Consensus size: 38
140060 TGTAGATTGT
140070 TACTTT-TGATATGACTGTAGATTGTAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
*
140107 TACTTTATGATATGACTGTAGATTGTAACATTACCCGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
*
140145 TACATTT-TGATATGACTGTAAATTGTAACATTACCTGG
1 TAC-TTTATGATATGACTGTAGATTGTAACATTACCTGG
140183 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
140221 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
140259 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
140297 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
* * *
140335 TACTTTGTGATATGACCGTAGATTGCAACATTACCTGG
1 TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
*
140373 TACTTTTTGATATGACTGTAGAT
1 TACTTTATGATATGACTGTAGAT
140396 AGCTTCCTGA
Statistics
Matches: 277, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
37 9 0.03
38 265 0.96
39 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (38 bp):
TACTTTATGATATGACTGTAGATTGTAACATTACCTGG
Found at i:141073 original size:16 final size:16
Alignment explanation
Indices: 141052--141082 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
141042 AAGAAATTAC
*
141052 TTCGTTATATCCGTAA
1 TTCGTTATAACCGTAA
141068 TTCGTTATAACCGTA
1 TTCGTTATAACCGTA
141083 TAAGAAATTC
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:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TTCGTTATAACCGTAA
Found at i:141163 original size:15 final size:16
Alignment explanation
Indices: 141126--141163 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
141116 CCAAGATGAC
*
141126 TTCGCTATATCCGTGAA
1 TTCGCAATATCCGTG-A
141143 TTCGCAATATCCGTG-
1 TTCGCAATATCCGTGA
141158 TTCGCA
1 TTCGCA
141164 CTAAACGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (16 bp):
TTCGCAATATCCGTGA
Found at i:148305 original size:2 final size:2
Alignment explanation
Indices: 148300--148342 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
148290 TTTTTTTTAC
** *
148300 AG AG AG AG AG TT AG AG AG AG AA 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
148342 A
1 A
148343 TGCATTACAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (2 bp):
AG
Found at i:149147 original size:18 final size:17
Alignment explanation
Indices: 149124--149157 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
149114 ATTAAAAATA
149124 CACCATCTCCATCACCAT
1 CACCATCT-CATCACCAT
149142 CACCATCTCATCACCA
1 CACCATCTCATCACCA
149158 ATGTACCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (17 bp):
CACCATCTCATCACCAT
Found at i:151097 original size:177 final size:177
Alignment explanation
Indices: 150794--151113 Score: 534
Period size: 177 Copynumber: 1.8 Consensus size: 177
150784 GAGAAGAAGA
* * *
150794 TTTTTAAAGATTTACTCTATATATTCCTATGTAAAAGTTCGACCCCCCATTGTGGCCCCACCATA
1 TTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCACCCATTGTGGCCCAACCATA
*
150859 CACCCGGGGGCCATGATTTTCACAACTTTGTATCTACACTACCTGAGAATGCTTTCACACAAGTT
66 CACCCGGGGGCCATGATTTTCACAACTTTGTATCTACACTACCTGAGAATGCTTCCACACAAGTT
150924 TCAGCTTTCCTGGCTGATAAGTTTCTAAGAAGAAGATTTTTTAATTT
131 TCAGCTTTCCTGGCTGATAAGTTTCTAAGAAGAAGATTTTTTAATTT
* * *
150971 TTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGATCACCCATTGTGGCCCAACCCTT
1 TTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCACCCATTGTGGCCCAACCATA
* * *
151036 CCCCCGGGGGCCATGATTTTCACAACTTT-TAATCTACACTACCTGAGGATGCTTCCACACAATT
66 CACCCGGGGGCCATGATTTTCACAACTTTGT-ATCTACACTACCTGAGAATGCTTCCACACAAGT
151100 TTCAGCTTTCCTGG
130 TTCAGCTTTCCTGG
151114 TTTTATGGTT
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 1 0.01
177 131 0.99
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (177 bp):
TTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCACCCATTGTGGCCCAACCATA
CACCCGGGGGCCATGATTTTCACAACTTTGTATCTACACTACCTGAGAATGCTTCCACACAAGTT
TCAGCTTTCCTGGCTGATAAGTTTCTAAGAAGAAGATTTTTTAATTT
Found at i:151321 original size:4 final size:4
Alignment explanation
Indices: 151312--151357 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
151302 TGAAAAGTTT
* *
151312 ACAG ACAG ACGG ACAG ACAG ACAG ACAG ACAG ACGG AC-G ACAG ACA
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACA
151358 AAATGTGATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.46, C:0.26, G:0.28, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:151329 original size:12 final size:12
Alignment explanation
Indices: 151312--151356 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
151302 TGAAAAGTTT
151312 ACAGACAGACGG
1 ACAGACAGACGG
*
151324 ACAGACAGACAG
1 ACAGACAGACGG
151336 ACAGACAGACGG
1 ACAGACAGACGG
151348 AC-GACAGAC
1 ACAGACAGAC
151357 AAAATGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.44, C:0.27, G:0.29, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:163445 original size:5 final size:5
Alignment explanation
Indices: 163425--163501 Score: 88
Period size: 5 Copynumber: 15.0 Consensus size: 5
163415 CCTACAGACT
163425 TTTTG TTTGGTG TTTTG TTTTTG TTTTTG TTTTG TTTT- TTTTG TTTTG
1 TTTTG TTT--TG TTTTG -TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG
163473 TTTTG TTTTTG TTTTG TTTT- TTTT- TTTTG
1 TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG
163502 GGGGGGGGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.18
5 33 0.50
6 16 0.24
7 5 0.08
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:163451 original size:11 final size:11
Alignment explanation
Indices: 163424--163497 Score: 93
Period size: 11 Copynumber: 6.9 Consensus size: 11
163414 GCCTACAGAC
*
163424 TTTTTGTTTGG
1 TTTTTGTTTTG
163435 TGTTTTGTTTTTG
1 T-TTTTG-TTTTG
163448 TTTTTGTTTTG
1 TTTTTGTTTTG
163459 -TTTT-TTTTG
1 TTTTTGTTTTG
163468 -TTTTGTTTTG
1 TTTTTGTTTTG
163478 TTTTTGTTTTG
1 TTTTTGTTTTG
163489 TTTTT-TTTT
1 TTTTTGTTTT
163498 TTTGGGGGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
9 9 0.16
10 13 0.22
11 21 0.36
12 10 0.17
13 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:163479 original size:30 final size:31
Alignment explanation
Indices: 163435--163501 Score: 120
Period size: 30 Copynumber: 2.2 Consensus size: 31
163425 TTTTGTTTGG
163435 TGTTTTGTTTTTGTTTTTGTTTTGTTTTTTT
1 TGTTTTGTTTTTGTTTTTGTTTTGTTTTTTT
163466 TGTTTTG-TTTTGTTTTTGTTTTGTTTTTTT
1 TGTTTTGTTTTTGTTTTTGTTTTGTTTTTTT
163496 T-TTTTG
1 TGTTTTG
163502 GGGGGGGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 5 0.14
30 24 0.67
31 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (31 bp):
TGTTTTGTTTTTGTTTTTGTTTTGTTTTTTT
Found at i:163500 original size:6 final size:6
Alignment explanation
Indices: 163424--163498 Score: 70
Period size: 6 Copynumber: 12.8 Consensus size: 6
163414 GCCTACAGAC
* *
163424 TTTTTG -TTTGG TGTTTTG TTTTTG TTTTTG -TTTTG TTTTT- TTTGTTT
1 TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTT-TTG
163471 TGTTTTG TTTTTG -TTTTG TTTTT- TTTTT
1 T-TTTTG TTTTTG TTTTTG TTTTTG TTTTT
163499 TTGGGGGGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
5 22 0.37
6 26 0.44
7 9 0.15
8 2 0.03
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:163500 original size:36 final size:37
Alignment explanation
Indices: 163424--163501 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 37
163414 GCCTACAGAC
163424 TTTTTGTTTGGTGTTTTGTTTTTGTTTTTGTTTTGTTT
1 TTTTTGTTT-GTGTTTTGTTTTTGTTTTTGTTTTGTTT
163462 TTTTTGTTT-TGTTTTGTTTTTG-TTTTGTTTT-TTT
1 TTTTTGTTTGTGTTTTGTTTTTGTTTTTGTTTTGTTT
163496 TTTTTG
1 TTTTTG
163502 GGGGGGGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
34 9 0.22
35 9 0.22
36 13 0.32
38 9 0.22
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (37 bp):
TTTTTGTTTGTGTTTTGTTTTTGTTTTTGTTTTGTTT
Found at i:164786 original size:32 final size:32
Alignment explanation
Indices: 164745--164815 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
164735 CTAGCCATCT
164745 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
1 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
*
164777 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT
1 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
164809 TTCCCCC
1 TTCCCCC
164816 AGGGAAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (32 bp):
TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
Found at i:164832 original size:33 final size:32
Alignment explanation
Indices: 164745--164835 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
164735 CTAGCCATCT
*
164745 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
1 TTCCCCCCGGAAAAATGACTATATAGCAGTTC
* *
164777 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT
1 TTCCCCCCGGAAAAATGACTATATAGCAGTTC
* **
164809 TTCCCCCAGGGAAAGCTGACTATATAG
1 TTCCCCC-CGGAAAAATGACTATATAG
164836 TGGGCTTTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 38 0.72
33 15 0.28
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (32 bp):
TTCCCCCCGGAAAAATGACTATATAGCAGTTC
Found at i:166126 original size:16 final size:16
Alignment explanation
Indices: 166105--166155 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
166095 TTTCCTCTGC
166105 GTCCGTCAGTCCGTCT
1 GTCCGTCAGTCCGTCT
166121 GTCCGT-ACGTCCGTCT
1 GTCCGTCA-GTCCGTCT
* *
166137 GTCTGTCCGTCCGTCT
1 GTCCGTCAGTCCGTCT
166153 GTC
1 GTC
166156 TGTCCCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.04, C:0.37, G:0.25, T:0.33
Consensus pattern (16 bp):
GTCCGTCAGTCCGTCT
Found at i:166156 original size:16 final size:16
Alignment explanation
Indices: 166113--166160 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
166103 GCGTCCGTCA
* *
166113 GTCCGTCTGTCCGTAC
1 GTCCGTCTGTCTGTCC
166129 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
166145 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
166161 CACTTCAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.02, C:0.38, G:0.25, T:0.35
Consensus pattern (16 bp):
GTCCGTCTGTCTGTCC
Found at i:166160 original size:12 final size:12
Alignment explanation
Indices: 166105--166160 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
166095 TTTCCTCTGC
* *
166105 GTCCGTCAGTCC
1 GTCCGTCCGTCT
*
166117 GTCTGTCCGTAC-
1 GTCCGTCCGT-CT
*
166129 GTCCGTCTGTCT
1 GTCCGTCCGTCT
166141 GTCCGTCCGTCT
1 GTCCGTCCGTCT
*
166153 GTCTGTCC
1 GTCCGTCC
166161 CACTTCAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.04, C:0.38, G:0.25, T:0.34
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:170005 original size:32 final size:33
Alignment explanation
Indices: 169948--170024 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
169938 GAATCCGGGT
* * *
169948 GGTTTCGCTCCG-ATCGCTTGTTCGCCCTGAGA
1 GGTTTCGCTCCGAATCGCATGATCGCCCCGAGA
*
169980 GGTTTCGCTCCGAAT-GCATGATCGCCCCGAGT
1 GGTTTCGCTCCGAATCGCATGATCGCCCCGAGA
* *
170012 GGATTCGCCCCGA
1 GGTTTCGCTCCGA
170025 TTGTATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (33 bp):
GGTTTCGCTCCGAATCGCATGATCGCCCCGAGA
Found at i:171808 original size:2 final size:2
Alignment explanation
Indices: 171801--171825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
171791 ATGTATTTTC
171801 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
171826 TAAATTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:172102 original size:10 final size:10
Alignment explanation
Indices: 172075--172108 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
172065 TGTAATGCTG
* *
172075 GCATTACATG
1 GCATTACTTT
172085 GCATTACTTT
1 GCATTACTTT
172095 GCATTACTTT
1 GCATTACTTT
172105 GCAT
1 GCAT
172109 ATTTATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (10 bp):
GCATTACTTT
Found at i:172663 original size:24 final size:24
Alignment explanation
Indices: 172625--172670 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
172615 TTTCTCTCTC
** *
172625 TTTCTCTCTGTCTCTGTCTCTTTG
1 TTTCTCTCTCCCTCTCTCTCTTTG
172649 TTTCTCTCTCCCTCTCTCTCTT
1 TTTCTCTCTCCCTCTCTCTCTT
172671 GTATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.00, C:0.37, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTCTCTCTCCCTCTCTCTCTTTG
Found at i:176234 original size:11 final size:11
Alignment explanation
Indices: 176218--176243 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
176208 TACTGAAATC
176218 TAATTGGTTTA
1 TAATTGGTTTA
176229 TAATTGGTTTA
1 TAATTGGTTTA
176240 TAAT
1 TAAT
176244 CCATTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (11 bp):
TAATTGGTTTA
Found at i:187150 original size:57 final size:57
Alignment explanation
Indices: 187062--187349 Score: 531
Period size: 57 Copynumber: 5.1 Consensus size: 57
187052 AAACAATTTT
* *
187062 CATGTTTGGTGATAAAGGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
1 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
187119 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
1 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
187176 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
1 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
187233 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
1 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
* * *
187290 CATGTTTAGTGATAAAGGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
1 CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
187347 CAT
1 CAT
187350 TTTTTATATA
Statistics
Matches: 226, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 226 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (57 bp):
CATGTTTGGTGAAAAAAGGTGTTACTGAGTAATGTTTAAATGTATTACAAATTTATC
Found at i:187920 original size:42 final size:42
Alignment explanation
Indices: 187883--188005 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
187873 AGGCATCGTT
*
187883 GGAAGCTGCTGTTGCATCATGGGAGGCTGCTGTGGCATTGTG
1 GGAAGTTGCTGTTGCATCATGGGAGGCTGCTGTGGCATTGTG
* * **
187925 GGAAATTGGTG-TGACATCACT-GGAGGCTGCACTGGCATTGTG
1 GGAAGTTGCTGTTG-CATCA-TGGGAGGCTGCTGTGGCATTGTG
** * *
187967 GGTGGTTGCTGTTGCATTATGGGAGGCTGTTGTGGCATT
1 GGAAGTTGCTGTTGCATCATGGGAGGCTGCTGTGGCATT
188006 CTAGGAGGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
41 3 0.05
42 58 0.91
43 3 0.05
ACGTcount: A:0.15, C:0.15, G:0.39, T:0.31
Consensus pattern (42 bp):
GGAAGTTGCTGTTGCATCATGGGAGGCTGCTGTGGCATTGTG
Found at i:187926 original size:21 final size:21
Alignment explanation
Indices: 187887--188005 Score: 78
Period size: 21 Copynumber: 5.7 Consensus size: 21
187877 ATCGTTGGAA
* *
187887 GCTGCTGTTGCATCATGGGAG
1 GCTGCTGTGGCATTATGGGAG
* *
187908 GCTGCTGTGGCATTGTGGGAA
1 GCTGCTGTGGCATTATGGGAG
** * * *
187929 ATTGGTGTGACATCACT-GGAG
1 GCTGCTGTGGCATTA-TGGGAG
** * *
187950 GCTGCACTGGCATTGTGGGTG
1 GCTGCTGTGGCATTATGGGAG
* *
187971 GTTGCTGTTGCATTATGGGAG
1 GCTGCTGTGGCATTATGGGAG
*
187992 GCTGTTGTGGCATT
1 GCTGCTGTGGCATT
188006 CTAGGAGGAT
Statistics
Matches: 67, Mismatches: 29, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.14, C:0.15, G:0.39, T:0.32
Consensus pattern (21 bp):
GCTGCTGTGGCATTATGGGAG
Found at i:188879 original size:21 final size:22
Alignment explanation
Indices: 188839--188879 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
188829 AAAAATAAAC
188839 AATTTACTGGAATGAAATTTGA
1 AATTTACTGGAATGAAATTTGA
188861 AATTTACTGGAAT-AAATTT
1 AATTTACTGGAATGAAATTT
188880 CAAAGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (22 bp):
AATTTACTGGAATGAAATTTGA
Found at i:190346 original size:2 final size:2
Alignment explanation
Indices: 190339--190419 Score: 110
Period size: 2 Copynumber: 40.0 Consensus size: 2
190329 AAACTACTTT
*
190339 TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
190381 TC TC TC TC TC TC TC ATC -C TT TG TNC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC -TC TC TC TC T-C TC TC TC TC TC TC TC
190420 AGCCTTTGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
1 1 0.01
2 67 0.94
3 3 0.04
ACGTcount: A:0.02, C:0.47, G:0.01, T:0.48
Consensus pattern (2 bp):
TC
Found at i:190722 original size:69 final size:68
Alignment explanation
Indices: 190638--190774 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 68
190628 ATATACAGGG
190638 TTATTTTCACCCCGTGTTGTTTTCGCCCTGGTGCACTTTCAAACAGTTTCACCACATCTTGAATT
1 TTATTTTCACCCCGTGTTGTTTTCGCCCTGGTGCACTTTCAAACAGTTTCACCACATCTTGAATT
190703 TGC
66 TGC
*
190706 NTTATTTTCACTCCGTGTTGTTTTCGCCCTGGTGCACTTTCAAACAGTTTCACCACATCTTGAAT
1 -TTATTTTCACCCCGTGTTGTTTTCGCCCTGGTGCACTTTCAAACAGTTTCACCACATCTTGAAT
190771 TTGC
65 TTGC
190775 CAAGAAACAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (68 bp):
TTATTTTCACCCCGTGTTGTTTTCGCCCTGGTGCACTTTCAAACAGTTTCACCACATCTTGAATT
TGC
Found at i:190987 original size:21 final size:21
Alignment explanation
Indices: 190961--191101 Score: 120
Period size: 21 Copynumber: 6.7 Consensus size: 21
190951 TACAAGATAA
190961 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
* *
190982 ACGATAGGATAGCATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
191003 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * *
191024 ACGAAAGGATAGCATTTACGC
1 ACGATAGGATAGGATTCACGC
* * * *
191045 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * **
191066 ACGATATGATAGGATTGATAC
1 ACGATAGGATAGGATTCACGC
*
191087 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
191102 AAACGATGTT
Statistics
Matches: 91, Mismatches: 29, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 91 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:191093 original size:42 final size:42
Alignment explanation
Indices: 190977--191077 Score: 175
Period size: 42 Copynumber: 2.4 Consensus size: 42
190967 GGATAGGATT
190977 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
* *
191019 CACGCACGAAAGGATAGCATTTACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
*
191061 CACGCACGATATGATAG
1 CACGCACGATAGGATAG
191078 GATTGATACA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (42 bp):
CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
Found at i:192113 original size:21 final size:21
Alignment explanation
Indices: 192089--192201 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 21
192079 CGATAAACCT
*
192089 GATAGGATAAACGCACGTTAG
1 GATAGGATAAACGCACGATAG
* *
192110 GATATGATTAACGCACGATAG
1 GATAGGATAAACGCACGATAG
* * * *
192131 AACAGTATACACGCACGATAG
1 GATAGGATAAACGCACGATAG
* * *
192152 GATAGAATTAATGCACGAT-G
1 GATAGGATAAACGCACGATAG
* * * * *
192172 AAACAGTATACACGCACGATAC
1 -GATAGGATAAACGCACGATAG
192194 GATAGGAT
1 GATAGGAT
192202 TGATACACGA
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.98
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (21 bp):
GATAGGATAAACGCACGATAG
Found at i:192146 original size:42 final size:42
Alignment explanation
Indices: 192099--192198 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
192089 GATAGGATAA
*
192099 ACGCACGTTAGGATATG-ATTAACGCACGAT-AGAACAGTATAC
1 ACGCACGATAGGATA-GAATTAACGCACGATGA-AACAGTATAC
*
192141 ACGCACGATAGGATAGAATTAATGCACGATGAAACAGTATAC
1 ACGCACGATAGGATAGAATTAACGCACGATGAAACAGTATAC
*
192183 ACGCACGATACGATAG
1 ACGCACGATAGGATAG
192199 GATTGATACA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.02
42 51 0.96
43 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (42 bp):
ACGCACGATAGGATAGAATTAACGCACGATGAAACAGTATAC
Found at i:192211 original size:42 final size:42
Alignment explanation
Indices: 192131--192212 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
192121 CGCACGATAG
* *
192131 AACAGTATACACGCACGATAGGATAGAATTAATGCACGATGA
1 AACAGTATACACGCACGATACGATAGAATTAATACACGATGA
* *
192173 AACAGTATACACGCACGATACGATAGGATTGATACACGAT
1 AACAGTATACACGCACGATACGATAGAATTAATACACGAT
192213 ACGATAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (42 bp):
AACAGTATACACGCACGATACGATAGAATTAATACACGATGA
Found at i:192643 original size:25 final size:25
Alignment explanation
Indices: 192609--192729 Score: 217
Period size: 25 Copynumber: 4.8 Consensus size: 25
192599 TACCATATCT
192609 GTGACCTATAAATTGAGTTTTACCG
1 GTGACCTATAAATTGAGTTTTACCG
192634 GTGACCTATAAATTGAGTTTTACCG
1 GTGACCTATAAATTGAGTTTTACCG
*
192659 GTGACCTATAAATTGAGTTTTACAG
1 GTGACCTATAAATTGAGTTTTACCG
192684 GTGACCTATAAATTGAGTTTTACCG
1 GTGACCTATAAATTGAGTTTTACCG
192709 GTGACCTATAAA-TGAAGTTTT
1 GTGACCTATAAATTG-AGTTTT
192730 TACCTGTGGG
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
24 2 0.02
25 91 0.98
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (25 bp):
GTGACCTATAAATTGAGTTTTACCG
Found at i:198864 original size:55 final size:55
Alignment explanation
Indices: 198790--199574 Score: 1150
Period size: 55 Copynumber: 14.2 Consensus size: 55
198780 TGACAACATT
* *
198790 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAGA-CATCAGGCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATA-ACCATCTGCCCAC
* * *
198845 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTGA-CATTTGTCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACA-TAACCATCTGCCCAC
* *
198900 AGAGAGGGACACTATGTCACTGACTGATCCTTAACTGACATAACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
* *
198955 AGAGAGAGAGACACCATGTCACTGGCTGATCCTTTACTGACATAACCATCTGCCCAC
1 --AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
* * * * *
199012 AGAGAGAGAGACACCATGTCACTGGCTGATCCTTTACTGACATTGA-CATTTGTCCAC
1 --AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACA-TAACCATCTGCCCAC
*
199069 AGAGAGGGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
*
199124 AGAGAGAGACACTATGTCACTAACTGATCCTTTACTGACATAACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
*
199179 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTTCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
199234 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
199289 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
* * *
199344 AGAGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGA-CATCAGGCCAC
1 --AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATA-ACCATCTGCCCAC
* * * *
199401 AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATAGA-CATCAGGCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATA-ACCATCTGCCCAC
*
199456 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTACCATCTGCCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
* * * * *
199511 AGAGAGAGACACCATGCCACTGACTGATCCTTTACTGACATTGA-CATTTGTCCAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACA-TAACCATCTGCCCAC
199566 AGAGAGAGA
1 AGAGAGAGA
199575 GAGAGAGAGA
Statistics
Matches: 678, Mismatches: 41, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
54 5 0.01
55 515 0.76
56 3 0.00
57 152 0.22
58 3 0.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (55 bp):
AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
Found at i:198996 original size:167 final size:165
Alignment explanation
Indices: 198790--199574 Score: 1245
Period size: 167 Copynumber: 4.7 Consensus size: 165
198780 TGACAACATT
* *
198790 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAGA-CATCAGGCCACAGAGAGAGA
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATA-ACCATCTGCCCACAGAGAGAGA
* *
198854 CACTATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGGGACACTATGTCA
65 CACCATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGACACTATGTCA
*
198919 CTGACTGATCCTTAACTGACATAACCATCTGCCCAC
130 CTGACTGATCCTTTACTGACATAACCATCTGCCCAC
* *
198955 AGAGAGAGAGACACCATGTCACTGGCTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAG
1 --AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC--AGAGAG
* *
199020 AGACACCATGTCACTGGCTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGGGACACTATG
62 AGACACCATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGACACTATG
199085 TCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
127 TCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
*
199124 AGAGAGAGACACTATGTCACTAACTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAGAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAGAC
* * *
199189 ACTATGTCACTGACTGATCCTTTACTGACA-TAACCATCTT-CCCACAGAGAGAGACACTATGTC
66 ACCATGTCACTGACTGATCCTTTACTGACATTGA-CAT-TTGTCCACAGAGAGAGACACTATGTC
199252 ACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
129 ACTGACTGATCCTTTACTGACATAACCATCTGCCCAC
199289 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAGAG
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCAC--AGAGAGAG
* ** * *
199354 ACACCATGTCACTGACTGATCCTTTACTGACATAGACATCAGGCCACAGAGAGAGACACCATGTC
64 ACACCATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGACACTATGTC
* * *
199419 ACTAACTGATCCTTTACTGACATAGA-CATCAGGCCAC
129 ACTGACTGATCCTTTACTGACATA-ACCATCTGCCCAC
*
199456 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTACCATCTGCCCACAGAGAGAGAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAGAC
*
199521 ACCATGCCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGA
66 ACCATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGA
199575 GAGAGAGAGA
Statistics
Matches: 576, Mismatches: 32, Indels: 22
0.91 0.05 0.03
Matches are distributed among these distances:
164 2 0.00
165 212 0.37
166 3 0.01
167 250 0.43
168 2 0.00
169 107 0.19
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (165 bp):
AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATAACCATCTGCCCACAGAGAGAGAC
ACCATGTCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGACACTATGTCAC
TGACTGATCCTTTACTGACATAACCATCTGCCCAC
Found at i:199573 original size:2 final size:2
Alignment explanation
Indices: 199566--199604 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
199556 ATTTGTCCAC
199566 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
199605 CTGTGTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:199617 original size:138 final size:138
Alignment explanation
Indices: 199456--199712 Score: 390
Period size: 138 Copynumber: 1.9 Consensus size: 138
199446 ATCAGGCCAC
199456 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATT-ACCATCTGCCCACAGAGAGAGA
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTGA-CATCTGCCCACAGAGAGAGA
* ** * *
199520 CACCATGCCACTGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGAGAGAGAGAGA
65 CACCATGCCACTAACTGATCCTTTACTGACATACACATCTGCCCACAGAGAGAGAGAGAGAGAGA
199585 GAGAGAGAG
130 GAGAGAGAG
* * ** * *
199594 AGAGAGAGAGACTGTGTCACTGACTGATTGTTTACTGACATTGACATTTGTCCACAGAGAGAGAC
1 AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTGACATCTGCCCACAGAGAGAGAC
*
199659 ACCATGTCACTAACTGATCCTTTACTGACATACACATCTGCCCACAGAGAGAGA
66 ACCATGCCACTAACTGATCCTTTACTGACATACACATCTGCCCACAGAGAGAGA
199713 CACTGTGTCA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
138 105 0.99
139 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (138 bp):
AGAGAGAGACACTATGTCACTGACTGATCCTTTACTGACATTGACATCTGCCCACAGAGAGAGAC
ACCATGCCACTAACTGATCCTTTACTGACATACACATCTGCCCACAGAGAGAGAGAGAGAGAGAG
AGAGAGAG
Found at i:199683 original size:55 final size:55
Alignment explanation
Indices: 199594--199819 Score: 229
Period size: 55 Copynumber: 4.1 Consensus size: 55
199584 AGAGAGAGAG
* ** ** * * *
199594 AGAGAGAGAGACTGTGTCACTGACTGATTGTTTACTGACATTGACATTTGTCCAC
1 AGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGACATCTGACCAC
* * *
199649 AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATACACATCTGCCCAC
1 AGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGACATCTGACCAC
** * * * * * *
199704 AGAGAGAGACACTGTGTCACTCACTGATCCTTCACTTATATAGACCTCTTACCAC
1 AGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGACATCTGACCAC
* * * * *
199759 AGA-AAAAACACCATATCACTGTCTGATCCTTTACTGACATAGACATCTGACAAC
1 AGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGACATCTGACCAC
199813 AGAGAGA
1 AGAGAGA
199820 AACCTATCAA
Statistics
Matches: 136, Mismatches: 34, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
54 41 0.30
55 95 0.70
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (55 bp):
AGAGAGAGACACCATGTCACTGACTGATCCTTTACTGACATAGACATCTGACCAC
Found at i:199761 original size:193 final size:193
Alignment explanation
Indices: 199401--199761 Score: 492
Period size: 193 Copynumber: 1.9 Consensus size: 193
199391 ATCAGGCCAC
199401 AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATAGACATCAGGCCACAGAGAGAGAC
1 AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATAGACATCAGGCCACAGAGAGAGAC
* *
199466 ACTATGTCACTGACTGATCCTTTACTGACATTACCATCTGCCCACAGAGAGAGACACCATGCCAC
66 ACCATGTCACTAACTGATCCTTTACTGACATTACCATCTGCCCACAGAGAGAGACACCATGCCAC
* * * *
199531 TGACTGATCCTTTACTGACATTGACATTTGTCCACAGAGAGAGAGAGAGAGAGAGAGAGAGAG
131 TCACTGATCCTTCACTGACATAGACATTTGACCACAGAGAGAGAGAGAGAGAGAGAGAGAGAG
* ** * ** * ** *
199594 AGAGAGAGAGACTGTGTCACTGACTGATTGTTTACTGACATTGACATTTGTCCACAGAGAGAGAC
1 AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATAGACATCAGGCCACAGAGAGAGAC
** *
199659 ACCATGTCACTAACTGATCCTTTACTGACA-TACACATCTGCCCACAGAGAGAGACACTGTGTCA
66 ACCATGTCACTAACTGATCCTTTACTGACATTAC-CATCTGCCCACAGAGAGAGACACCATGCCA
* * *
199723 CTCACTGATCCTTCACTTATATAGACCTCTT-ACCACAGA
130 CTCACTGATCCTTCACTGACATAGACAT-TTGACCACAGA
199762 AAAAACACCA
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
192 3 0.02
193 139 0.97
194 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (193 bp):
AGAGAGAGACACCATGTCACTAACTGATCCTTTACTGACATAGACATCAGGCCACAGAGAGAGAC
ACCATGTCACTAACTGATCCTTTACTGACATTACCATCTGCCCACAGAGAGAGACACCATGCCAC
TCACTGATCCTTCACTGACATAGACATTTGACCACAGAGAGAGAGAGAGAGAGAGAGAGAGAG
Found at i:208372 original size:8 final size:8
Alignment explanation
Indices: 208359--208402 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
208349 GGAATCACCT
208359 TGTCCGTC
1 TGTCCGTC
208367 TGTCCGTC
1 TGTCCGTC
* *
208375 CGTCTGTC
1 TGTCCGTC
*
208383 CGTCCGTC
1 TGTCCGTC
208391 TGTCCGTC
1 TGTCCGTC
208399 TGTC
1 TGTC
208403 TGTGCAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.00, C:0.39, G:0.25, T:0.36
Consensus pattern (8 bp):
TGTCCGTC
Found at i:208377 original size:12 final size:12
Alignment explanation
Indices: 208360--208405 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
208350 GAATCACCTT
208360 GTCCGTCTGTCC
1 GTCCGTCTGTCC
208372 GTCCGTCTGTCC
1 GTCCGTCTGTCC
208384 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
208396 GTCTGTCTGT
1 GTCCGTCTGT
208406 GCAATCGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:208405 original size:4 final size:4
Alignment explanation
Indices: 208360--208398 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
208350 GAATCACCTT
* * *
208360 GTCC GTCT GTCC GTCC GTCT GTCC GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
208399 TGTCTGTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.41, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:208675 original size:146 final size:146
Alignment explanation
Indices: 208410--209066 Score: 889
Period size: 146 Copynumber: 4.5 Consensus size: 146
208400 GTCTGTGCAA
* *
208410 TCGTGTCCGGTCCATATCTTTCTTATAGAGAAACATTGGAATTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
208475 TTATGACCTAAGGATGTGTCATGACCTTGACCCAATGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
208540 AGAAAAAATACAAAAT
131 AGAAAAAATACAAAAT
* *
208556 CCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
208621 TTATGACCTAAGGGTGTGTCATGACCTTGATCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
208686 AGAAAAAATACAAAAT
131 AGAAAAAATACAAAAT
* ** *
208702 TTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGCCAGTCCTTTA-TTCACACAAAGATTG
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTC-TTACTTCACACAAAGATTG
* * * * * **
208766 CTTATGACCTAAGGTTGTGCCATGACTTTTATCCAAGGTCATTTGGGCAAGGTCAAGGTCGTTAG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT-G
* *
208831 G-A-AAAATAGTGCAAAAT
129 GCAGAAAA-AATACAAAAT
* * *
208848 TCGTGTCCAGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTC-TAGCTTCACACAAATAT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTA-CTTCACACAAAGAT
* * * *
208910 TGCTTAGGACCAAAAGGTGTGTCCTGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT
63 TGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT
* *
208975 GGCAGAAAAAGTGCAAAAT
128 GGCAGAAAAAATACAAAAT
* * * *
208994 TTGTGTCCGGT-CATTATTTTTCTTATGGAGAAGCATT-GAATGTTCTTACTTCACACAAATATT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
209057 GCTTATGACC
64 GCTTATGACC
209067 AACAGTTTAA
Statistics
Matches: 458, Mismatches: 43, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
144 2 0.00
145 9 0.02
146 436 0.95
147 11 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATACAAAAT
Found at i:211320 original size:49 final size:49
Alignment explanation
Indices: 211241--211505 Score: 449
Period size: 49 Copynumber: 5.4 Consensus size: 49
211231 CAAGCATTAA
** * *
211241 ACAGAGAGTAAATCACCATTACCCACAGCACATACCATATATCCACTTT
1 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
* * * *
211290 ACAGAGAGTAAATCACCAACACCAAGAGCACATACCATAAAACCACTAT
1 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
*
211339 ACGGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
1 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
211388 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
1 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
211437 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
1 ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
211486 ACAGAGAGTAAATCACCACC
1 ACAGAGAGTAAATCACCACC
211506 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 203 1.00
ACGTcount: A:0.43, C:0.32, G:0.09, T:0.15
Consensus pattern (49 bp):
ACAGAGAGTAAATCACCACCACCCACAGCACATACCATATAACCACTAT
Found at i:211384 original size:24 final size:24
Alignment explanation
Indices: 211356--211482 Score: 64
Period size: 24 Copynumber: 5.2 Consensus size: 24
211346 GTAAATCACC
211356 ACCACCCACAGCACATACCATATA
1 ACCACCCACAGCACATACCATATA
** * * **
211380 ACCACTATACAG-AGAGTA-AATCACC
1 ACCAC-CCACAGCACA-TACCAT-ATA
211405 ACCACCCACAGCACATACCATATA
1 ACCACCCACAGCACATACCATATA
** * * **
211429 ACCACTATACAG-AGAGTA-AATCACC
1 ACCAC-CCACAGCACA-TACCAT-ATA
211454 ACCACCCACAGCACATACCATATA
1 ACCACCCACAGCACATACCATATA
211478 ACCAC
1 ACCAC
211483 TATACAGAGA
Statistics
Matches: 69, Mismatches: 24, Indels: 20
0.61 0.21 0.18
Matches are distributed among these distances:
24 37 0.54
25 32 0.46
ACGTcount: A:0.43, C:0.37, G:0.07, T:0.13
Consensus pattern (24 bp):
ACCACCCACAGCACATACCATATA
Found at i:211406 original size:22 final size:22
Alignment explanation
Indices: 211380--211504 Score: 56
Period size: 22 Copynumber: 5.2 Consensus size: 22
211370 ATACCATATA
211380 ACCACTATACAGAGAGTAAATC
1 ACCACTATACAGAGAGTAAATC
* * * *
211402 ACCACCACCCACAGCACA-TACCATATA
1 ACCACTA--TACAG-AGAGTA--A-ATC
211429 ACCACTATACAGAGAGTAAATC
1 ACCACTATACAGAGAGTAAATC
* * * *
211451 ACCACCACCCACAGCACA-TACCATATA
1 ACCACTA--TACAG-AGAGTA--A-ATC
211478 ACCACTATACAGAGAGTAAATC
1 ACCACTATACAGAGAGTAAATC
211500 ACCAC
1 ACCAC
211505 CNNNNNNNNN
Statistics
Matches: 73, Mismatches: 16, Indels: 28
0.62 0.14 0.24
Matches are distributed among these distances:
22 21 0.29
23 2 0.03
24 16 0.22
25 16 0.22
26 2 0.03
27 16 0.22
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.14
Consensus pattern (22 bp):
ACCACTATACAGAGAGTAAATC
Found at i:213717 original size:97 final size:97
Alignment explanation
Indices: 213213--213710 Score: 978
Period size: 97 Copynumber: 5.1 Consensus size: 97
213203 NNNNNNNNNN
213213 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
1 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
213278 CAGAATCAAATCACCACCACCCACAGCACATA
66 CAGAATCAAATCACCACCACCCACAGCACATA
213310 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
1 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
213375 CAGAATCAAATCACCACCACCCACAGCACATA
66 CAGAATCAAATCACCACCACCCACAGCACATA
213407 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
1 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
213472 CAGAATCAAATCACCACCACCCACAGCACATA
66 CAGAATCAAATCACCACCACCCACAGCACATA
213504 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
1 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
213569 CAGAATCAAATCACCACCACCCACAGCACATA
66 CAGAATCAAATCACCACCACCCACAGCACATA
213601 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
1 CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
*
213666 CAGAATCAAATCACCACCACCCACAGCACTTA
66 CAGAATCAAATCACCACCACCCACAGCACATA
*
213698 CCATATATCCACT
1 CCATATAACCACT
213711 TTACAGACAG
Statistics
Matches: 399, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 399 1.00
ACGTcount: A:0.42, C:0.35, G:0.08, T:0.15
Consensus pattern (97 bp):
CCATATAACCACTAAACAGAGAGTAGATCACAACCACCTACAGCTCACGCCATATAACCACTATA
CAGAATCAAATCACCACCACCCACAGCACATA
Found at i:216486 original size:2 final size:2
Alignment explanation
Indices: 216481--216507 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
216471 CACAGTGTGT
216481 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
216508 GTCCATTGTG
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:219544 original size:24 final size:24
Alignment explanation
Indices: 219517--219566 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
219507 TCCTGTGTCT
*
219517 GTTCCAGTGCCGGTACCTGTTCCA
1 GTTCCAGTGCCGGTACCAGTTCCA
* * *
219541 GTTCCGGTGTCTGTACCAGTTCCA
1 GTTCCAGTGCCGGTACCAGTTCCA
219565 GT
1 GT
219567 GCCCGTTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.30, G:0.26, T:0.32
Consensus pattern (24 bp):
GTTCCAGTGCCGGTACCAGTTCCA
Found at i:219736 original size:18 final size:18
Alignment explanation
Indices: 219499--219737 Score: 253
Period size: 18 Copynumber: 13.3 Consensus size: 18
219489 GTTAGTTCCT
* * *
219499 GTTCCAGTTCCTGTGTCT
1 GTTCCAGTTCCGGTGCCC
* * *
219517 GTTCCAGTGCCGGTACCT
1 GTTCCAGTTCCGGTGCCC
* *
219535 GTTCCAGTTCCGGTGTCT
1 GTTCCAGTTCCGGTGCCC
* *
219553 GTACCAGTTCCAGTGCCC
1 GTTCCAGTTCCGGTGCCC
*
219571 GTTCCAGTTCCGGTGTCC
1 GTTCCAGTTCCGGTGCCC
* *
219589 GTGCCAGTTCCGGTTCCC
1 GTTCCAGTTCCGGTGCCC
* * *
219607 GTGCCAGTTCCTGTTCCC
1 GTTCCAGTTCCGGTGCCC
* *
219625 GTACCAGTTCCTGTGCCC
1 GTTCCAGTTCCGGTGCCC
*
219643 GTTCCAGTTCCGGTGTCC
1 GTTCCAGTTCCGGTGCCC
* *
219661 GTGCCAGTTCCTGTGCCC
1 GTTCCAGTTCCGGTGCCC
*
219679 GTTCCAGTTCCTGTGCCC
1 GTTCCAGTTCCGGTGCCC
*
219697 GTTCCAGTTCCGGTTCCC
1 GTTCCAGTTCCGGTGCCC
* *
219715 GTTCCAGTCCCGGTGCCA
1 GTTCCAGTTCCGGTGCCC
219733 GTTCC
1 GTTCC
219738 TCCACTATAT
Statistics
Matches: 189, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 189 1.00
ACGTcount: A:0.08, C:0.36, G:0.25, T:0.31
Consensus pattern (18 bp):
GTTCCAGTTCCGGTGCCC
Found at i:221314 original size:2 final size:2
Alignment explanation
Indices: 221301--221345 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
221291 GCAGACAGAC
* * *
221301 AG AG AT AG AG AG AG AG AG AC AG AA 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
221343 AG A
1 AG A
221346 TGATAGCTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.02, G:0.42, T:0.02
Consensus pattern (2 bp):
AG
Found at i:221320 original size:24 final size:24
Alignment explanation
Indices: 221293--221343 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
221283 TAAAACAGGC
* *
221293 AGACAGACAGAGATAGAGAGAGAG
1 AGACAGAAAGAGAGAGAGAGAGAG
221317 AGACAGAAAGAGAGAGAGAGAGAG
1 AGACAGAAAGAGAGAGAGAGAGAG
221341 AGA
1 AGA
221344 GATGATAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.06, G:0.39, T:0.02
Consensus pattern (24 bp):
AGACAGAAAGAGAGAGAGAGAGAG
Found at i:225107 original size:20 final size:20
Alignment explanation
Indices: 225082--225121 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
225072 TACTCAGAGT
225082 CGCACGGATTAGTCGACAGG
1 CGCACGGATTAGTCGACAGG
225102 CGCACGGATTAGTCGACAGG
1 CGCACGGATTAGTCGACAGG
225122 AGCATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (20 bp):
CGCACGGATTAGTCGACAGG
Found at i:227703 original size:20 final size:20
Alignment explanation
Indices: 227657--227705 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
227647 TGAATTAGTT
* *
227657 ATTTGTTCGGACGAATTGAG
1 ATTTATTCGGACAAATTGAG
*
227677 ATGTATTCGGACAAATT-AGG
1 ATTTATTCGGACAAATTGA-G
227697 ATTTATTCG
1 ATTTATTCG
227706 TCTGAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTATTCGGACAAATTGAG
Found at i:229045 original size:2 final size:2
Alignment explanation
Indices: 229038--229086 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
229028 CAAACAAGTC
* *
229038 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AA AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
229079 AG AG AG AG
1 AG AG AG AG
229087 GGGGGAATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:230699 original size:2 final size:2
Alignment explanation
Indices: 230692--230742 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
230682 GAATGAACGN
230692 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
230734 AG AG AG AG A
1 AG AG AG AG A
230743 AGAAATTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:233726 original size:170 final size:169
Alignment explanation
Indices: 233315--233782 Score: 658
Period size: 169 Copynumber: 2.8 Consensus size: 169
233305 AAAGAGTAAG
* * *
233315 ATTTTTAAAGATTTAATATA-TTTTTGCTGTATGGCCATATTGGCCCCACCCTAGAGCCTGAACC
1 ATTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACC
* *
233379 CTTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGATGGCTTCAT-GAATATCATAATCATGC
66 CATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGA-GGCTTCATGGACT-TCATAATCATGC
*
233443 ATTTAGTTTTACACAAATATATATTGAAGTAGAGAAGAAGA
129 ATTTAGTTTTACACAAATATACATTGAAGTAGAGAAGAAGA
*
233484 ATTTCT-AAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACC
1 ATTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACC
* * * * *
233548 CCTGACCCAGGGGTCATAAATTTCAGAATTTTGGTAGAGAACTTCGTGGACTTCATAATCATGCA
66 CATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAG-GCTTCATGGACTTCATAATCATGCA
* * * *
233613 TTTGGTTTTTA-ACAAATTTACATTGGAGTAGAGAATAA-A
130 TTTAG-TTTTACACAAATATACATTGAAGTAGAGAAGAAGA
*
233652 ATTTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAAC
1 A-TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAAC
* * * *
233717 CCATGACCCAGGGGCCATGAATTTCACAATTTTTGTAGAGGGCTTCATGGACATCATAACCATGC
65 CCATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGA-GGCTTCATGGACTTCATAATCATGC
233782 A
129 A
233783 ACCAGTTTTT
Statistics
Matches: 266, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
168 15 0.06
169 131 0.49
170 119 0.45
171 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (169 bp):
ATTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACC
CATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGCTTCATGGACTTCATAATCATGCAT
TTAGTTTTACACAAATATACATTGAAGTAGAGAAGAAGA
Found at i:233815 original size:170 final size:168
Alignment explanation
Indices: 233316--233835 Score: 611
Period size: 170 Copynumber: 3.1 Consensus size: 168
233306 AAGAGTAAGA
* * *
233316 TTTTTAAAGATTTAATATA-TTTTTGCTGTATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
1 TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
* * * * *
233380 TTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGATGGCTTCATGAATATCATAATCATGCAT
66 ATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCAA
* *
233445 TTAG-TTTTACACAAATATATATTGAAGTAGAGAAGAAGAA-
131 TTAGTTTTTCCAC-AA-ATATA-TGGAGTAGAGAAGAA-AAT
*
233485 TTTCT-AAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
1 TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
* * * ** * * *
233549 CTGACCCAGGGGTCATAAATTTCAGAATTTTGGTAGAGAACTTCGTGGACTTCATAATCATGCAT
66 ATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCAA
* * * *
233614 TTGGTTTTT-AACAAATTTACATTGGAGTAGAGAATAAAAT
131 TTAGTTTTTCCACAAA--TATA-TGGAGTAGAGAAGAAAAT
*
233654 TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCC
1 TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
* * *
233719 ATGACCCAGGGGCCATGAATTTCACAATTTTTGTAGAGGGCTTCATGGACATCATAACCATGCAA
66 ATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCAA
** * * * *
233784 CCAGTTTTTTCCTCACATGTATGGCAGTAGAGAAGAAGAT
131 TTAG-TTTTTCCACAAATATATGG-AGTAGAGAAGAAAAT
*
233824 TTTTGAAA-ATTT
1 TTTTTAAAGATTT
233836 GGCTTTTTTG
Statistics
Matches: 299, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
167 1 0.00
168 16 0.05
169 135 0.45
170 139 0.46
171 5 0.02
172 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (168 bp):
TTTTTAAAGATTTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCC
ATGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCAA
TTAGTTTTTCCACAAATATATGGAGTAGAGAAGAAAAT
Found at i:235365 original size:7 final size:7
Alignment explanation
Indices: 235349--235388 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
235339 AGAACAAAAA
235349 TTCA-TG
1 TTCATTG
235355 TTCATTG
1 TTCATTG
235362 TTCA-TG
1 TTCATTG
235368 TTCATTG
1 TTCATTG
*
235375 TTCAATG
1 TTCATTG
235382 TTCATTG
1 TTCATTG
235389 AAATGTCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (7 bp):
TTCATTG
Found at i:235367 original size:13 final size:13
Alignment explanation
Indices: 235349--235388 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
235339 AGAACAAAAA
235349 TTCATGTTCATTG
1 TTCATGTTCATTG
235362 TTCATGTTCATTG
1 TTCATGTTCATTG
235375 TTCAATGTTCATTG
1 TTC-ATGTTCATTG
235389 AAATGTCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (13 bp):
TTCATGTTCATTG
Found at i:235378 original size:20 final size:19
Alignment explanation
Indices: 235349--235386 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
235339 AGAACAAAAA
*
235349 TTCATGTTCATTGTTCATG
1 TTCATGTTCAATGTTCATG
235368 TTCATTGTTCAATGTTCAT
1 TTCA-TGTTCAATGTTCAT
235387 TGAAATGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (19 bp):
TTCATGTTCAATGTTCATG
Found at i:239419 original size:52 final size:52
Alignment explanation
Indices: 239267--239476 Score: 171
Period size: 51 Copynumber: 4.1 Consensus size: 52
239257 TCATACTCTT
* * * * **
239267 AGTAAAACTTTGTCAATGTT-TATGCGATTG-CTAGTTAGATTTTAAACTGTC
1 AGTAACACTTTGTCAATGTTGCAAGAGATTGTC-AGTTAGATTAAAAACTGTC
* * ** * * * *
239318 AGTAACAGTTTATCAATGTTTTAA-AGGTTTTCAGTTAGATTAGAGACTGTC
1 AGTAACACTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAAAAACTGTC
**
239369 -GATAACTTTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAAAAACTGTC
1 AG-TAACACTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAAAAACTGTC
** * *
239421 AGTAACACTTTGTCAATGTTTTAAGAGGTTGTCAGTT--ATTAACAGACTGTC
1 AGTAACACTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAA-AAACTGTC
239472 AGTAA
1 AGTAA
239477 GTCCTTTTCA
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
50 6 0.05
51 65 0.51
52 56 0.44
53 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (52 bp):
AGTAACACTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAAAAACTGTC
Found at i:239494 original size:51 final size:51
Alignment explanation
Indices: 239310--239508 Score: 147
Period size: 52 Copynumber: 3.9 Consensus size: 51
239300 GTTAGATTTT
* * * * * *
239310 AAACTGTCAGTAACAGTTTATCAATGTTTTAA-AGGTTTTCAGTTAGATTAG
1 AAACTGTCAGTAACACTTTGTCAATCTTTTAAGAGATTGTCAGTTA-ATTAA
* ** * **
239361 AGACTGTC-GATAACTTTTTGTCAATGTTGCAAGAGATTGTCAGTTAGATTAA
1 AAACTGTCAG-TAACACTTTGTCAATCTTTTAAGAGATTGTCAGTTA-ATTAA
* *
239413 AAACTGTCAGTAACACTTTGTCAATGTTTTAAGAGGTTGTCAGTT-ATTAA
1 AAACTGTCAGTAACACTTTGTCAATCTTTTAAGAGATTGTCAGTTAATTAA
* * * *
239463 CAGACTGTCAGTAAGTC-CTTT-TCATTCTTTTAAAAGATTATCAGTT
1 -AAACTGTCAGTAA--CACTTTGTCAATCTTTTAAGAGATTGTCAGTT
239509 CTATTAAGGC
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
50 6 0.05
51 56 0.46
52 57 0.47
53 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (51 bp):
AAACTGTCAGTAACACTTTGTCAATCTTTTAAGAGATTGTCAGTTAATTAA
Found at i:239515 original size:103 final size:102
Alignment explanation
Indices: 239299--239508 Score: 228
Period size: 103 Copynumber: 2.0 Consensus size: 102
239289 TGCGATTGCT
** * * *
239299 AGTTAGATTTTAAACTGTCAGTAACAGTTTATCAATGTTTTAAAGGTTTTCAGTTAGATTAGAGA
1 AGTTAGATTAAAAACTGTCAGTAACACTTTATCAATGTTTTAAAGGTTGTCAGTTA-ATTACAGA
* * * *
239364 CTGTCGATAACTTTTTGTCAATGTTGCAAGAGATTGTC
65 CTGTCGATAACTCTTTGTCAATCTTGCAAAAGATTATC
*
239402 AGTTAGATTAAAAACTGTCAGTAACACTTTGTCAATGTTTTAAGAGGTTGTCAGTT-ATTAACAG
1 AGTTAGATTAAAAACTGTCAGTAACACTTTATCAATGTTTTAA-AGGTTGTCAGTTAATT-ACAG
* * **
239466 ACTGTC-AGTAAGTCCTTT-TCATTCTTTTAAAAGATTATC
64 ACTGTCGA-TAACT-CTTTGTCAATCTTGCAAAAGATTATC
239505 AGTT
1 AGTT
239509 CTATTAAGGC
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
102 4 0.04
103 71 0.80
104 14 0.16
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (102 bp):
AGTTAGATTAAAAACTGTCAGTAACACTTTATCAATGTTTTAAAGGTTGTCAGTTAATTACAGAC
TGTCGATAACTCTTTGTCAATCTTGCAAAAGATTATC
Found at i:241784 original size:89 final size:89
Alignment explanation
Indices: 241633--241800 Score: 302
Period size: 89 Copynumber: 1.9 Consensus size: 89
241623 CGTATCATTA
*
241633 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGAAGTTGATCTGTGAATGTG
1 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGAAGTTGATCCGTGAATGTG
241698 TGACTGGGGCATTAACGATTATTT
66 TGACTGGGGCATTAACGATTATTT
*
241722 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCGT-GGAGTTGATCCGTGAATGT
1 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACC-TAGAAGTTGATCCGTGAATGT
241786 GTGACTGGGGCATTA
65 GTGACTGGGGCATTA
241801 GAGATGTCTT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
89 75 0.99
90 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (89 bp):
GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGAAGTTGATCCGTGAATGTG
TGACTGGGGCATTAACGATTATTT
Found at i:243910 original size:12 final size:12
Alignment explanation
Indices: 243893--243923 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
243883 TAAATCTGAG
243893 AGAGAGACAGAC
1 AGAGAGACAGAC
243905 AGAGAGACAGAC
1 AGAGAGACAGAC
243917 AGAGAGA
1 AGAGAGA
243924 TCTAAGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.13, G:0.35, T:0.00
Consensus pattern (12 bp):
AGAGAGACAGAC
Found at i:254051 original size:2 final size:2
Alignment explanation
Indices: 254044--254092 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
254034 NNNNNNNNNN
254044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
254086 TC TC TC T
1 TC TC TC T
254093 ATATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:255492 original size:2 final size:2
Alignment explanation
Indices: 255485--255593 Score: 175
Period size: 2 Copynumber: 55.0 Consensus size: 2
255475 CCATACTTCA
255485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
** * *
255526 TC TC TC TC NN TC TC TC TC CC TC TC TC TC CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
255568 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
255594 ACCTGAAACA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 97 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:257648 original size:21 final size:22
Alignment explanation
Indices: 257622--257666 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
257612 AAACTCAATC
*
257622 AAACAA-ACAAAACAACAAAAA
1 AAACAAGACAAAAAAACAAAAA
* *
257643 AAACAAGCCAAAAAAATAAAAA
1 AAACAAGACAAAAAAACAAAAA
257665 AA
1 AA
257667 TAAAAGTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.80, C:0.16, G:0.02, T:0.02
Consensus pattern (22 bp):
AAACAAGACAAAAAAACAAAAA
Found at i:272361 original size:1 final size:1
Alignment explanation
Indices: 272355--272398 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
272345 TTGTTATTTA
* * **
272355 TTTTTTTGTTTTTTATTTTTTTGGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
272399 GGAAGCAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:272388 original size:22 final size:23
Alignment explanation
Indices: 272356--272400 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
272346 TGTTATTTAT
272356 TTTTTTGTTTTTTATTTTTTTGG
1 TTTTTTGTTTTTTATTTTTTTGG
*
272379 TTTTTT-TTTTTTTTTTTTTTGG
1 TTTTTTGTTTTTTATTTTTTTGG
272401 AAGCAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (23 bp):
TTTTTTGTTTTTTATTTTTTTGG
Found at i:272398 original size:15 final size:15
Alignment explanation
Indices: 272344--272397 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
272334 CGTATTATTA
*
272344 TTTGTTATTTATTTT
1 TTTGTTTTTTATTTT
272359 TTTGTTTTTTATTTT
1 TTTGTTTTTTATTTT
272374 TTTGGTTTTTT-TTTT
1 TTT-GTTTTTTATTTT
272389 TTT-TTTTTT
1 TTTGTTTTTT
272398 TGGAAGCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 6 0.16
15 24 0.65
16 7 0.19
ACGTcount: A:0.06, C:0.00, G:0.07, T:0.87
Consensus pattern (15 bp):
TTTGTTTTTTATTTT
Found at i:280958 original size:19 final size:18
Alignment explanation
Indices: 280933--280970 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
280923 TAATGATACG
280933 TACCAAACTAGAACTCTT
1 TACCAAACTAGAACTCTT
280951 TNACCAAACTAGAACTCTT
1 T-ACCAAACTAGAACTCTT
280970 T
1 T
280971 CCCTTGCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.29
Consensus pattern (18 bp):
TACCAAACTAGAACTCTT
Found at i:298756 original size:19 final size:19
Alignment explanation
Indices: 298732--298770 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
298722 TAATCACACA
*
298732 TGTTGTTTTAATAAATAAT
1 TGTTGTTATAATAAATAAT
298751 TGTTGTTATAATAAATAAT
1 TGTTGTTATAATAAATAAT
298770 T
1 T
298771 ACACTTGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (19 bp):
TGTTGTTATAATAAATAAT
Found at i:299243 original size:20 final size:20
Alignment explanation
Indices: 299213--299264 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
299203 ACTTTATTTC
299213 CCAGTATTTCCCGGGAAATA
1 CCAGTATTTCCCGGGAAATA
* * *
299233 GCAGTAATTCCCGGGAATTA
1 CCAGTATTTCCCGGGAAATA
299253 CCAGTATTTCCC
1 CCAGTATTTCCC
299265 ATCGTCCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
CCAGTATTTCCCGGGAAATA
Found at i:302312 original size:2 final size:2
Alignment explanation
Indices: 302305--302351 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
302295 ACTTACTTAA
*
302305 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
302347 TC TC T
1 TC TC T
302352 TTTGTATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:306495 original size:28 final size:28
Alignment explanation
Indices: 306459--306514 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
306449 TGTAAACAAG
306459 GCACAATTTTCATTGTTGTTATTTGTTA
1 GCACAATTTTCATTGTTGTTATTTGTTA
306487 GCACAATTTTCATTGTTGTTATTTGTTA
1 GCACAATTTTCATTGTTGTTATTTGTTA
306515 CTTTTTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (28 bp):
GCACAATTTTCATTGTTGTTATTTGTTA
Found at i:309876 original size:20 final size:20
Alignment explanation
Indices: 309851--309897 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
309841 TGACATCACA
* *
309851 GGGTCAGGGGTCGGGACGTG
1 GGGTCAGGGGTCGGGAAGAG
309871 GGGTCAGGGGTCGGGAAGAG
1 GGGTCAGGGGTCGGGAAGAG
309891 GGGTCAG
1 GGGTCAG
309898 AGGATCAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.60, T:0.13
Consensus pattern (20 bp):
GGGTCAGGGGTCGGGAAGAG
Done.