Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 34 of 335
Found at i:12527479 original size:25 final size:23
Alignment explanation
Indices: 12527435--12527518 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
12527425 ATTTTGATTT
*
12527435 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
12527459 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
* * *
12527483 ATATAAATTATAT-TTA-AATATA
1 AT-TTAATTATATAATATCATATA
12527505 A-TTAATTATATAAT
1 ATTTAATTATATAAT
12527519 TAAAACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.18
21 1 0.02
22 6 0.12
24 19 0.39
25 14 0.29
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:12527498 original size:35 final size:35
Alignment explanation
Indices: 12527443--12527522 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
12527433 TTATTTAATA
* * *
12527443 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATAATAAATT
*
12527477 CATATAATATAAATTAT-ATTTAAATATAATTAATT
1 -ATATAATATAAATTATAATTTAAATATAATAAATT
12527512 ATATAAT-TAAA
1 ATATAATATAAA
12527523 ACAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 24 0.60
36 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATAATAAATT
Found at i:12527516 original size:22 final size:22
Alignment explanation
Indices: 12527478--12527522 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12527468 TCATAAATTC
*
12527478 ATATAATATAAATTATATTTAA
1 ATATAATATAAATTATAATTAA
*
12527500 ATATAAT-TAATTATATAATTAA
1 ATATAATATAAAT-TATAATTAA
12527522 A
1 A
12527523 ACAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAATATAAATTATAATTAA
Found at i:12539875 original size:22 final size:21
Alignment explanation
Indices: 12539850--12539899 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12539840 TGAAAATTAC
*
12539850 TACATAATTGCTAAAACTTATA
1 TACAAAATT-CTAAAACTTATA
* *
12539872 TACAAAATTTTAAAATTTATA
1 TACAAAATTCTAAAACTTATA
*
12539893 TAAAAAA
1 TACAAAA
12539900 ACATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (21 bp):
TACAAAATTCTAAAACTTATA
Found at i:12540077 original size:16 final size:15
Alignment explanation
Indices: 12540048--12540087 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
12540038 GTTTGATTGT
12540048 ATAATT-TTTTTATA
1 ATAATTATTTTTATA
12540062 ATAATTATTCTTTATA
1 ATAATTATT-TTTATA
12540078 ATAATATATT
1 ATAAT-TATT
12540088 ATTCTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 11 0.48
17 4 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTATTTTTATA
Found at i:12554317 original size:6 final size:6
Alignment explanation
Indices: 12554297--12554345 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
12554287 CTGTCGCTTC
* * *
12554297 CACTGT CACTG- --CTGT CACTGT CACTAT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
12554342 CACT
1 CACT
12554346 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:12554334 original size:18 final size:18
Alignment explanation
Indices: 12554311--12554351 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12554301 GTCACTGCTG
*
12554311 TCACTGTCACTATCACTA
1 TCACTGCCACTATCACTA
*
12554329 TCACTGCCACTGTCACTA
1 TCACTGCCACTATCACTA
*
12554347 GCACT
1 TCACT
12554352 ATTTGCTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTATCACTA
Found at i:12554737 original size:43 final size:43
Alignment explanation
Indices: 12554676--12554767 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
12554666 CAAGAAACTA
*
12554676 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGCAGAGG
1 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
12554719 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
1 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
*
12554762 CACCAA
1 AACCAA
12554768 CCAACTTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (43 bp):
AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
Found at i:12561314 original size:28 final size:29
Alignment explanation
Indices: 12561276--12561330 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
12561266 AAGTTTATTT
12561276 AAAATAAAAATATTGAAT-TTAAATTTAA
1 AAAATAAAAATATTGAATATTAAATTTAA
* * *
12561304 AAAATAGAAATTTTTAATATTAAATTT
1 AAAATAAAAATATTGAATATTAAATTT
12561331 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAATAAAAATATTGAATATTAAATTTAA
Found at i:12561355 original size:10 final size:11
Alignment explanation
Indices: 12561328--12561353 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12561318 TAATATTAAA
12561328 TTTTTAAATTT
1 TTTTTAAATTT
12561339 TTTTTAAATTT
1 TTTTTAAATTT
12561350 TTTT
1 TTTT
12561354 AACTTTGATC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTAAATTT
Found at i:12561601 original size:21 final size:21
Alignment explanation
Indices: 12561577--12561631 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
12561567 TATAAAATTT
12561577 AAAAATTGTTATAAAAATAA-AA
1 AAAAATT-TTA-AAAAATAACAA
*
12561599 AAATAAATTTAAAAAAT-ACAA
1 AAA-AATTTTAAAAAATAACAA
12561620 AAAAA-TTTAAAA
1 AAAAATTTTAAAA
12561632 TTTAAATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 11 0.37
22 6 0.20
23 3 0.10
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAATTTTAAAAAATAACAA
Found at i:12561612 original size:19 final size:20
Alignment explanation
Indices: 12561590--12561632 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
12561580 AATTGTTATA
12561590 AAAATAA-A-AAAATAAATTT
1 AAAATAATACAAAA-AAATTT
12561609 AAAA-AATACAAAAAAATTT
1 AAAATAATACAAAAAAATTT
12561628 AAAAT
1 AAAAT
12561633 TTAAATACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.10
19 15 0.71
20 4 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAATACAAAAAAATTT
Found at i:12561723 original size:19 final size:19
Alignment explanation
Indices: 12561701--12561748 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
12561691 ATTTTAAAAC
12561701 TTTTTAAATA-TTTTTACAA
1 TTTTTAAATAGTTTTTAC-A
*
12561720 TTTTT-TATAGTTTTTACA
1 TTTTTAAATAGTTTTTACA
12561738 TTTTTATAATA
1 TTTTTA-AATA
12561749 ATATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 9 0.38
19 12 0.50
20 3 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTAAATAGTTTTTACA
Found at i:12561810 original size:16 final size:16
Alignment explanation
Indices: 12561789--12561821 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12561779 ATATCGTATT
*
12561789 TTTTTTGTAAATTTTA
1 TTTTTTCTAAATTTTA
12561805 TTTTTTCTAAATTTTA
1 TTTTTTCTAAATTTTA
12561821 T
1 T
12561822 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTTCTAAATTTTA
Found at i:12561865 original size:2 final size:2
Alignment explanation
Indices: 12561819--12561852 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12561809 TTCTAAATTT
12561819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12561853 AATTTGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12561871 original size:14 final size:14
Alignment explanation
Indices: 12561819--12561871 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
12561809 TTCTAAATTT
*
12561819 TATATATATATATA
1 TATATATATTTATA
*
12561833 TATATATATATATA
1 TATATATATTTATA
* *
12561847 TATATAAATTTGTA
1 TATATATATTTATA
*
12561861 TATATCTATTT
1 TATATATATTT
12561872 TCATTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATATATTTATA
Found at i:12567046 original size:21 final size:21
Alignment explanation
Indices: 12567022--12567069 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
12567012 TTCATCAATG
*
12567022 TTTTATTGTT-TTTTGTTATCA
1 TTTTA-TGTTGTTTTGCTATCA
12567043 TTTTGATGTTGTTTTGCTATCA
1 TTTT-ATGTTGTTTTGCTATCA
12567065 TTTTA
1 TTTTA
12567070 ATATTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTATGTTGTTTTGCTATCA
Found at i:12567063 original size:22 final size:21
Alignment explanation
Indices: 12567028--12567068 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12567018 AATGTTTTAT
*
12567028 TGTTTTTTGTTATCATTTTGA
1 TGTTTTTTGCTATCATTTTGA
12567049 TGTTGTTTTGCTATCATTTT
1 TGTT-TTTTGCTATCATTTT
12567069 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66
Consensus pattern (21 bp):
TGTTTTTTGCTATCATTTTGA
Found at i:12577330 original size:2 final size:2
Alignment explanation
Indices: 12577323--12577347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12577313 GTGTTTTCAA
12577323 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12577348 TCTCATATAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12579314 original size:13 final size:13
Alignment explanation
Indices: 12579306--12579357 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
12579296 AAAAAAAAAG
12579306 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
* *
12579319 TAAAAG-GAGGAAA
1 -AAAAGAAAAGAAA
*
12579332 AGAAAGAAGAGAAA
1 A-AAAGAAAAGAAA
12579346 AAAAGAAAAGAA
1 AAAAGAAAAGAA
12579358 TGTAGAGGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 1 0.03
13 19 0.63
14 10 0.33
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:12579323 original size:9 final size:9
Alignment explanation
Indices: 12579301--12579353 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
12579291 ATTTAAAAAA
12579301 AAAAGAAAAG
1 AAAAG-AAAG
*
12579311 AAAAGAAAT
1 AAAAGAAAG
* *
12579320 AAAAGGAGG
1 AAAAGAAAG
12579329 AAAAGAAAG
1 AAAAGAAAG
*
12579338 AAGAGAAA-
1 AAAAGAAAG
12579346 AAAAGAAA
1 AAAAGAAA
12579354 AGAATGTAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
8 7 0.20
9 23 0.66
10 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:12579369 original size:22 final size:22
Alignment explanation
Indices: 12579298--12579357 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
12579288 GGAATTTAAA
*
12579298 AAAAAAAGAAAAGAAAAGAA-AT
1 AAAAAAAGAAAAG-AAAGAAGAG
* *
12579320 AAAAGGAGGAAAAGAAAGAAGAG
1 AAAA-AAAGAAAAGAAAGAAGAG
12579343 AAAAAAAGAAAAGAA
1 AAAAAAAGAAAAGAA
12579358 TGTAGAGGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAGAAAGAAGAG
Found at i:12589069 original size:24 final size:24
Alignment explanation
Indices: 12589036--12589108 Score: 121
Period size: 24 Copynumber: 3.0 Consensus size: 24
12589026 AAAGGGGTCT
*
12589036 AAATTGAAAAAAATTCATTTCAAG
1 AAATTAAAAAAAATTCATTTCAAG
12589060 AAATTAAAAAAAAGTT-ATTTCAAG
1 AAATTAAAAAAAA-TTCATTTCAAG
12589084 AAATTAAAAAAAATTCATTTCAAG
1 AAATTAAAAAAAATTCATTTCAAG
12589108 A
1 A
12589109 GAGACCGAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
23 2 0.04
24 42 0.91
25 2 0.04
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATTAAAAAAAATTCATTTCAAG
Found at i:12593114 original size:47 final size:49
Alignment explanation
Indices: 12592992--12593171 Score: 200
Period size: 47 Copynumber: 3.8 Consensus size: 49
12592982 TGTAACCCGC
* * * *
12592992 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
12593038 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
*
12593088 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-CACAT
*
12593132 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
12593172 TCAACCATTC
Statistics
Matches: 114, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.04
45 1 0.01
46 37 0.32
47 58 0.51
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:12593160 original size:94 final size:93
Alignment explanation
Indices: 12593000--12593171 Score: 299
Period size: 94 Copynumber: 1.8 Consensus size: 93
12592990 GCCCATAAGT
* * *
12593000 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
12593065 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
12593093 GAACTCGGACTCAACTCAACGAGTTCGGACATTCCACATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATT-CACATCCATAAGTGAACTCGGACTCAACTCA
12593158 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
12593172 TCAACCATTC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 30 0.41
94 44 0.59
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:12596778 original size:2 final size:2
Alignment explanation
Indices: 12596773--12596804 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12596763 TGAGAATTTA
12596773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12596805 TCTAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12602343 original size:22 final size:22
Alignment explanation
Indices: 12602318--12602366 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
12602308 ATAATTAATT
* *
12602318 AATTTAAATTATTT-TTAAAGAA
1 AATTGAAATT-TTTCTTAAACAA
12602340 AATTGAAATTTTTCGTTAAACAA
1 AATTGAAATTTTTC-TTAAACAA
12602363 AATT
1 AATT
12602367 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 9 0.39
23 11 0.48
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
AATTGAAATTTTTCTTAAACAA
Found at i:12603213 original size:16 final size:17
Alignment explanation
Indices: 12603187--12603228 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
12603177 TAAGGTTGAG
12603187 TTAGAGTTTTATGGATT
1 TTAGAGTTTTATGGATT
*
12603204 TTAG-GTTTTATGGGTT
1 TTAGAGTTTTATGGATT
12603220 TT-GAGTTTT
1 TTAGAGTTTT
12603229 TTATTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 18 0.78
17 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (17 bp):
TTAGAGTTTTATGGATT
Found at i:12610116 original size:42 final size:43
Alignment explanation
Indices: 12610028--12610116 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 43
12610018 ATAGGACATG
* ****
12610028 TTTTAAAGGAATTTGACTTGGCATATTGCCGATATTACTTTTT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTACAGCCT
*
12610071 TTTTAAAGGAATTTGA-TTGGCATATTCCCGATATTCCAGCCT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTACAGCCT
12610113 TTTT
1 TTTT
12610117 TCTCCCACGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.45
Consensus pattern (43 bp):
TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTACAGCCT
Found at i:12610116 original size:43 final size:43
Alignment explanation
Indices: 12610028--12610117 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
12610018 ATAGGACATG
* ***
12610028 TTTTAAAGGAATTTGACTTGGCATATTGCCGATATTACTTTTT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTACGCCTT
*
12610071 TTTTAAAGGAATTTGA-TTGGCATATTCCCGATATTCCAGCCTT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTAC-GCCTT
12610114 TTTT
1 TTTT
12610118 CTCCCACGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 19 0.46
43 22 0.54
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (43 bp):
TTTTAAAGGAATTTGACTTGGCATATTCCCGATATTACGCCTT
Found at i:12613098 original size:50 final size:50
Alignment explanation
Indices: 12613044--12613145 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
12613034 GTGGTCTGGA
12613044 CTGCCTCTAATCCCGCGTGACTGCTACTTATTATACAATATGTATATGTT
1 CTGCCTCTAATCCCGCGTGACTGCTACTTATTATACAATATGTATATGTT
12613094 CTGCCTCTAATCCCGCGTGACTGCTACTTATTATACAATATGTATATGTT
1 CTGCCTCTAATCCCGCGTGACTGCTACTTATTATACAATATGTATATGTT
12613144 CT
1 CT
12613146 TACTTTCTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (50 bp):
CTGCCTCTAATCCCGCGTGACTGCTACTTATTATACAATATGTATATGTT
Found at i:12623956 original size:18 final size:18
Alignment explanation
Indices: 12623920--12623958 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12623910 GAAGGTTGTT
*
12623920 TTTAATATTTTTTAGTAA
1 TTTAAAATTTTTTAGTAA
12623938 TTTAAAATTATTTTA-TAA
1 TTTAAAATT-TTTTAGTAA
12623956 TTT
1 TTT
12623959 TTAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAAAATTTTTTAGTAA
Found at i:12623968 original size:18 final size:19
Alignment explanation
Indices: 12623918--12623968 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
12623908 TTGAAGGTTG
*
12623918 TTTTTAATATTTTTTAGTAA
1 TTTTTAATA-ATTTTAGTAA
** *
12623938 TTTAAAATTATTTTA-TAA
1 TTTTTAATAATTTTAGTAA
12623956 TTTTTAATAATTT
1 TTTTTAATAATTT
12623969 ACTACTAGAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 13 0.54
19 5 0.21
20 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTAATAATTTTAGTAA
Found at i:12624998 original size:18 final size:18
Alignment explanation
Indices: 12624975--12625014 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12624965 GAAATATTTA
*
12624975 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
12624993 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
12625011 TTTT
1 TTTT
12625015 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:12629027 original size:19 final size:19
Alignment explanation
Indices: 12629003--12629046 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
12628993 GTTTGCTCTG
*
12629003 CCTTTTCTTCCTTTCTTTT
1 CCTTTTCTACCTTTCTTTT
*
12629022 CCTTTTGTACCTTTCTTTT
1 CCTTTTCTACCTTTCTTTT
12629041 CCTTTT
1 CCTTTT
12629047 GTATTCTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (19 bp):
CCTTTTCTACCTTTCTTTT
Found at i:12629047 original size:19 final size:19
Alignment explanation
Indices: 12629012--12629049 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12629002 GCCTTTTCTT
12629012 CCTTTCTTTTCCTTTTGTA
1 CCTTTCTTTTCCTTTTGTA
12629031 CCTTTCTTTTCCTTTTGTA
1 CCTTTCTTTTCCTTTTGTA
12629050 TTCTATCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.26, G:0.05, T:0.63
Consensus pattern (19 bp):
CCTTTCTTTTCCTTTTGTA
Found at i:12650315 original size:29 final size:29
Alignment explanation
Indices: 12650283--12650338 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12650273 AAATTAGATC
*
12650283 AAATT-AAAATTTCGTATATAAAATTATAA
1 AAATTCAAAA-TTCATATATAAAATTATAA
*
12650312 AAATTCAAAATTCATGTATAAAATTAT
1 AAATTCAAAATTCATATATAAAATTAT
12650339 TATAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (29 bp):
AAATTCAAAATTCATATATAAAATTATAA
Found at i:12658754 original size:31 final size:31
Alignment explanation
Indices: 12658713--12658773 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12658703 ATTAATAATT
12658713 TTAAATTAAATATTATAATT-ATTTTTAAATA
1 TTAAATTAAATA-TATAATTGATTTTTAAATA
* * *
12658744 TTAATTTAAATATATATTTGTTTTTTAAAT
1 TTAAATTAAATATATAATTGATTTTTAAAT
12658774 CTCATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTAAATTAAATATATAATTGATTTTTAAATA
Found at i:12659504 original size:78 final size:78
Alignment explanation
Indices: 12659417--12659573 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
12659407 TAACAGAAGA
12659417 AAGAAGAAGAAGAGTTGAAAGGTTAACTAACTGGCATGATGACCAAAGATTATAAGTTGATTGTT
1 AAGAAGAAGAAGAGTTGAAAGGTTAACTAACTGGCATGATGACCAAAGATTATAAGTTGATTGTT
12659482 TGATATTTTGTCT
66 TGATATTTTGTCT
12659495 AAGAAGAAGAAGAGTTGAAAGGTTAACTAACTGGCATGATGACCAAAGATTATAAGTTGATTGTT
1 AAGAAGAAGAAGAGTTGAAAGGTTAACTAACTGGCATGATGACCAAAGATTATAAGTTGATTGTT
12659560 TGATATTTTGTCT
66 TGATATTTTGTCT
12659573 A
1 A
12659574 CCACTTTCCT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (78 bp):
AAGAAGAAGAAGAGTTGAAAGGTTAACTAACTGGCATGATGACCAAAGATTATAAGTTGATTGTT
TGATATTTTGTCT
Found at i:12661425 original size:6 final size:6
Alignment explanation
Indices: 12661414--12661438 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12661404 GGAACGGCGG
12661414 ACATGC ACATGC ACATGC ACATGC A
1 ACATGC ACATGC ACATGC ACATGC A
12661439 TTGTACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACATGC
Found at i:12669114 original size:14 final size:14
Alignment explanation
Indices: 12669095--12669125 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12669085 TCAACTTTTC
12669095 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
12669109 TATTCTTTATTCAT
1 TATTCTTTACTCAT
12669123 TAT
1 TAT
12669126 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:12680210 original size:58 final size:58
Alignment explanation
Indices: 12680120--12680233 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
12680110 TTTCAAGGTT
12680120 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
1 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
**
12680178 AGCCAGTTTCCGTCCATTGATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
1 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
12680234 AATATCAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (58 bp):
AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
Found at i:12686346 original size:13 final size:13
Alignment explanation
Indices: 12686328--12686355 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12686318 CAAGCTAGAT
12686328 TAATATATATATA
1 TAATATATATATA
12686341 TAATATATATATA
1 TAATATATATATA
12686354 TA
1 TA
12686356 TAGTGCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATATATA
Found at i:12691540 original size:23 final size:23
Alignment explanation
Indices: 12691497--12691541 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12691487 AATTAATTTA
*
12691497 TTTTTATATTATATAAGTGTAAT
1 TTTTTATATTATATAAATGTAAT
*
12691520 TTTTTGTA-TATATAATATGTAA
1 TTTTTATATTATATAA-ATGTAA
12691542 ACATAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTTATATTATATAAATGTAAT
Found at i:12695257 original size:16 final size:16
Alignment explanation
Indices: 12695233--12695265 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12695223 TATAGATAAA
12695233 TTATATTTTAGTCACT
1 TTATATTTTAGTCACT
*
12695249 TTATGTTTTAGTCACT
1 TTATATTTTAGTCACT
12695265 T
1 T
12695266 ACATTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TTATATTTTAGTCACT
Found at i:12695788 original size:23 final size:23
Alignment explanation
Indices: 12695761--12695805 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12695751 GAAAGTAAGT
12695761 TTAAATAATGTAAAAGAAAAAAA
1 TTAAATAATGTAAAAGAAAAAAA
* * *
12695784 TTAAATTATTTAAAATAAAAAA
1 TTAAATAATGTAAAAGAAAAAA
12695806 TATCTCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
TTAAATAATGTAAAAGAAAAAAA
Found at i:12696239 original size:6 final size:6
Alignment explanation
Indices: 12696228--12696261 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
12696218 CGATTTAGAG
12696228 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
12696262 TTTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:12696985 original size:19 final size:17
Alignment explanation
Indices: 12696962--12697009 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
12696952 TTATTATTGT
12696962 GTTTTATAATATTAATTA
1 GTTTTATAATA-TAATTA
*
12696980 TTTTTTATCAAGTATAATTA
1 -GTTTTAT-AA-TATAATTA
12697000 GTTTTATAAT
1 GTTTTATAAT
12697010 TTATGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.04
18 2 0.08
19 12 0.48
20 8 0.32
21 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
GTTTTATAATATAATTA
Found at i:12700705 original size:32 final size:32
Alignment explanation
Indices: 12700680--12700775 Score: 174
Period size: 32 Copynumber: 3.0 Consensus size: 32
12700670 ATTTCACCAC
12700680 TTTAATAGTCTATATCTTTATAATTTTTAAAG
1 TTTAATAGTCTATATCTTTATAATTTTTAAAG
* *
12700712 TTTAATAGTTTTTATCTTTATAATTTTTAAAG
1 TTTAATAGTCTATATCTTTATAATTTTTAAAG
12700744 TTTAATAGTCTATATCTTTATAATTTTTAAAG
1 TTTAATAGTCTATATCTTTATAATTTTTAAAG
12700776 AATTAAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTAATAGTCTATATCTTTATAATTTTTAAAG
Found at i:12706930 original size:3 final size:3
Alignment explanation
Indices: 12706917--12706945 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12706907 AAATAGACAC
12706917 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12706946 CAAGGGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12707101 original size:2 final size:2
Alignment explanation
Indices: 12707096--12707130 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12707086 CATCTCTCGT
12707096 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12707131 TCCCCACTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12707494 original size:14 final size:14
Alignment explanation
Indices: 12707475--12707522 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
12707465 ACTTAGTTGG
12707475 TTTTTTTTT-GTTT
1 TTTTTTTTTGGTTT
12707488 TTTTTTTTTGGTTT
1 TTTTTTTTTGGTTT
* *
12707502 TTTGTCTTTGGATTT
1 TTTTTTTTTGG-TTT
12707517 TTTTTT
1 TTTTTT
12707523 CTTTTTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 9 0.31
14 13 0.45
15 7 0.24
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTGGTTT
Found at i:12707667 original size:6 final size:6
Alignment explanation
Indices: 12707632--12707663 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12707622 CTTTATGTTC
*
12707632 CAGCAA CAGCAA CAGCAA CAGCAA CAACAA CA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA
12707664 ACAAGTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.34, G:0.12, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:12708487 original size:65 final size:65
Alignment explanation
Indices: 12708383--12708517 Score: 270
Period size: 65 Copynumber: 2.1 Consensus size: 65
12708373 TGTGGAACCC
12708383 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
1 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
12708448 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
1 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
12708513 TCTTC
1 TCTTC
12708518 ATTTATTGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (65 bp):
TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
Found at i:12711175 original size:22 final size:22
Alignment explanation
Indices: 12711150--12711195 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12711140 AAAATATAAA
*
12711150 GGATTTATTATTAAACTCGTTC
1 GGATTTATTACTAAACTCGTTC
12711172 GGATTTATTACTAAACTCGTTC
1 GGATTTATTACTAAACTCGTTC
12711194 GG
1 GG
12711196 GTAGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (22 bp):
GGATTTATTACTAAACTCGTTC
Found at i:12714217 original size:7 final size:6
Alignment explanation
Indices: 12714190--12714214 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12714180 TTGTTTTTAT
12714190 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
12714215 ATACAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:12714865 original size:18 final size:18
Alignment explanation
Indices: 12714842--12714880 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12714832 CAATTAGTAT
12714842 TTTATAAAAAAATTGTAA
1 TTTATAAAAAAATTGTAA
* * *
12714860 TTTATATAAATATTTTAA
1 TTTATAAAAAAATTGTAA
12714878 TTT
1 TTT
12714881 CAGTAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATAAAAAAATTGTAA
Found at i:12715505 original size:2 final size:2
Alignment explanation
Indices: 12715498--12715524 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12715488 TTTGCTAGCT
12715498 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12715525 GGTTTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12724941 original size:26 final size:26
Alignment explanation
Indices: 12724911--12724961 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12724901 TTCAAAGAAT
*
12724911 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
12724937 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
12724962 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:12739050 original size:5 final size:5
Alignment explanation
Indices: 12739040--12739064 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12739030 TTCTCTGTTT
12739040 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
12739065 GCATTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:12739838 original size:21 final size:21
Alignment explanation
Indices: 12739814--12739853 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12739804 ATCTTTTTTA
*
12739814 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
12739835 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
12739854 CATTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:12747187 original size:22 final size:21
Alignment explanation
Indices: 12747148--12747190 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12747138 TTAAATATAT
12747148 ATTAAAATAAAAAATAAAAAA
1 ATTAAAATAAAAAATAAAAAA
* *
12747169 ATTATAAATATAAACTAAAAAA
1 ATTA-AAATAAAAAATAAAAAA
12747191 TCAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
ATTAAAATAAAAAATAAAAAA
Found at i:12747187 original size:29 final size:27
Alignment explanation
Indices: 12747140--12747207 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
12747130 GTAACACATT
*
12747140 AAATATATAT-TAAAATAAAAAATAAAA
1 AAATATAAATATAAAATAAAAAAT-AAA
* *
12747167 AAATTATAAATATAAACTAAAAAATCAA
1 AAA-TATAAATATAAAATAAAAAATAAA
*
12747195 ATATATAAATATA
1 AAATATAAATATA
12747208 TATTTTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.37
28 10 0.29
29 12 0.34
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (27 bp):
AAATATAAATATAAAATAAAAAATAAA
Found at i:12749562 original size:22 final size:22
Alignment explanation
Indices: 12749530--12749571 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
12749520 TTTTGATGAA
12749530 TATTTATATTTATCTTGTAAATG
1 TATTTATATTTAT-TTGTAAATG
12749553 TATTT-TATTTATTTGTAAA
1 TATTTATATTTATTTGTAAA
12749572 GGCAACGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TATTTATATTTATTTGTAAATG
Found at i:12761368 original size:25 final size:25
Alignment explanation
Indices: 12761339--12761388 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12761329 CAAATAATAT
12761339 GATTTTCAGATTCTAAAAGAGAGAA
1 GATTTTCAGATTCTAAAAGAGAGAA
*
12761364 GATTTTCAGATTTTAAAAGAGAGAA
1 GATTTTCAGATTCTAAAAGAGAGAA
12761389 ATACTATTGA
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:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (25 bp):
GATTTTCAGATTCTAAAAGAGAGAA
Found at i:12769306 original size:50 final size:50
Alignment explanation
Indices: 12769247--12769348 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
12769237 TTTGCCAGCT
12769247 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTC
* *
12769297 CAACATTAGCATCTGCAAAAACAATTAAAAATATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTC
12769347 CA
1 CA
12769349 CCTTGTTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.23
Consensus pattern (50 bp):
CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTC
Found at i:12773888 original size:137 final size:138
Alignment explanation
Indices: 12773641--12773916 Score: 448
Period size: 137 Copynumber: 2.0 Consensus size: 138
12773631 AACAGCTAAA
* * *
12773641 AAAATGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAACA
1 AAAATGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACA
* * *
12773706 CTAGCTACAAAAGTAATTTAACAATATCATGTGGTAACAAGTTCACATGAAAGTG-AGATATGAA
66 CTAACTACAAAAGTAACTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCA-ATATGAA
*
12773770 AGATATGCC
130 AGACATGCC
* *
12773779 AAAATGAAATCATTTATAGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACA
1 AAAATGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACA
12773843 CTAACTACAAAAGTAACTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
66 CTAACTACAAAAGTAACTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
12773908 GACATGCC
131 GACATGCC
12773916 A
1 A
12773917 TTTTCTGAAA
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
137 87 0.68
138 41 0.32
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (138 bp):
AAAATGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACA
CTAACTACAAAAGTAACTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
GACATGCC
Found at i:12776353 original size:16 final size:16
Alignment explanation
Indices: 12776328--12776364 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12776318 TTTTTCAAAT
*
12776328 TTTAAAATTTATTTAAA
1 TTTAAATTTTA-TTAAA
12776345 TTTAAATTTTATTAAA
1 TTTAAATTTTATTAAA
12776361 TTTA
1 TTTA
12776365 TCGGTGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATTTTATTAAA
Found at i:12776443 original size:18 final size:18
Alignment explanation
Indices: 12776407--12776465 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
12776397 AATAATTATG
*
12776407 TAATTAA-AAAAAATT-A
1 TAATTAATATAAAATTAA
12776423 TAATTAACT-TAAAATTAA
1 TAATTAA-TATAAAATTAA
*
12776441 TAA-TAATAATAACATTAA
1 TAATTAAT-ATAAAATTAA
12776459 TAATTAA
1 TAATTAA
12776466 ACCTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.23
17 9 0.26
18 15 0.43
19 3 0.09
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTAATATAAAATTAA
Found at i:12776446 original size:21 final size:22
Alignment explanation
Indices: 12776395--12776465 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 22
12776385 TAAAAATTAT
* *
12776395 TTAATAATTATGTAA-TTAAAA
1 TTAATAATAATATAACTTAAAA
** *
12776416 AAAATTATAAT-TAACTTAAAA
1 TTAATAATAATATAACTTAAAA
12776437 TTAATAATAATAATAACATTAATAA
1 TTAATAATAAT-ATAAC-TTAA-AA
12776462 TTAA
1 TTAA
12776466 ACCTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 3 0.08
21 21 0.55
23 4 0.11
24 4 0.11
25 6 0.16
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
TTAATAATAATATAACTTAAAA
Found at i:12778419 original size:14 final size:15
Alignment explanation
Indices: 12778381--12778441 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
12778371 TTTAATTATT
* *
12778381 TAAAAATTATAAAATA
1 TAAAAATTACAATA-A
*
12778397 TAAATAATTAAAATAA
1 TAAA-AATTACAATAA
*
12778413 T-AAAATTACTATAA
1 TAAAAATTACAATAA
12778427 TAAAAATTACAATAA
1 TAAAAATTACAATAA
12778442 CGGTGCTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.26
15 14 0.37
16 6 0.16
17 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTACAATAA
Found at i:12778426 original size:23 final size:23
Alignment explanation
Indices: 12778381--12778433 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12778371 TTTAATTATT
*
12778381 TAAAAATTATAAAATATAAATAA
1 TAAAAATAATAAAATATAAATAA
* *
12778404 TTAAAATAATAAAAT-TACTATAA
1 TAAAAATAATAAAATATA-AATAA
12778427 TAAAAAT
1 TAAAAAT
12778434 TACAATAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAATAATAAAATATAAATAA
Found at i:12783909 original size:2 final size:2
Alignment explanation
Indices: 12783892--12783925 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12783882 GAACCCTTCA
* *
12783892 AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12783926 CTGTGCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12785620 original size:16 final size:15
Alignment explanation
Indices: 12785599--12785628 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12785589 AAAATGTGAA
12785599 AAACAAAAAGAAAAAC
1 AAACAAAAA-AAAAAC
12785615 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
12785629 GCTTACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAAAAC
Found at i:12790165 original size:7 final size:6
Alignment explanation
Indices: 12790113--12790166 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
12790103 CTTCTTCTTC
12790113 TTTTTG TTTTTTG TTTTTTG TTTTTG TTTTTG TTTTT- TTTTT- TTTTTG
1 TTTTTG -TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
12790161 GTTTTG
1 TTTTTG
12790167 GGTTTAAAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
5 10 0.22
6 22 0.49
7 13 0.29
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:12790747 original size:19 final size:20
Alignment explanation
Indices: 12790709--12790753 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
12790699 GCTTTTTTTT
* *
12790709 TTAAATTACATATGATAAAA
1 TTAAATTACAAATAATAAAA
12790729 TTAAATT-CAAATAATAAAA
1 TTAAATTACAAATAATAAAA
*
12790748 TAAAAT
1 TTAAAT
12790754 ACATAAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAATTACAAATAATAAAA
Found at i:12791957 original size:15 final size:16
Alignment explanation
Indices: 12791927--12791957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12791917 TTAAGAAGTT
12791927 AATTTAATTATTAATA
1 AATTTAATTATTAATA
12791943 AATTTAATT-TTAATA
1 AATTTAATTATTAATA
12791958 GCCAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAATTATTAATA
Found at i:12793857 original size:41 final size:41
Alignment explanation
Indices: 12793789--12794030 Score: 290
Period size: 41 Copynumber: 6.0 Consensus size: 41
12793779 GCGTTTGTCC
* * * *
12793789 AAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCA
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
* * *
12793830 AAAACACCACTAAAAACTGGTCAATAGCGGCGTTTTTCGC-
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
* * *** *
12793870 CAAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTAATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
* * ** *
12793911 CAAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
* *
12793952 AAAACGCCACTAAAAACTGATCAATTGTGGCGTTTTTGG-A
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
12793992 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG
12794031 TCCAAACGCC
Statistics
Matches: 176, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
40 70 0.40
41 106 0.60
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCA
Found at i:12793887 original size:81 final size:81
Alignment explanation
Indices: 12793774--12794040 Score: 331
Period size: 81 Copynumber: 3.3 Consensus size: 81
12793764 TAATAAACAC
* * * * * *
12793774 TAGCGGCGTTTGTC-CAAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCAAAAACACC
1 TAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTTGGCAAAAACGCC
*
12793838 ACTAAAAACTGGTCAA
66 ACTAAAAACTGATCAA
*** **
12793854 TAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTAATCCCAAACGCC
1 TAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTTGGCAAAAACGCC
12793919 ACTAAAAACTGATCAA
66 ACTAAAAACTGATCAA
* ** * * *
12793935 TTGCGGCGTTTTTATCCAAAACGCCACTAAAAACTGATCAATTGTGGCGTTTTTGG-AAAAACGC
1 TAGCGGCGTTTTTCGCC-AAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTTGGCAAAAACGC
12793999 CACTAAAAACTGATCAA
65 CACTAAAAACTGATCAA
*
12794016 TAGCGGCGTTTTTGGTCCAAACGCC
1 TAGCGGCGTTTTTCG-CCAAACGCC
12794041 GCAAAAAGTT
Statistics
Matches: 158, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
80 13 0.08
81 111 0.70
82 34 0.22
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (81 bp):
TAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTTGGCAAAAACGCC
ACTAAAAACTGATCAA
Found at i:12793956 original size:122 final size:121
Alignment explanation
Indices: 12793774--12794027 Score: 330
Period size: 122 Copynumber: 2.1 Consensus size: 121
12793764 TAATAAACAC
* * * *
12793774 TAGCGGCG-TTTGTCCAAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCAAAAACACC
1 TAGCGGCGTTTTATCCAAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTAGCAAAAACACC
* ** *
12793838 ACTAAAAACTGGTCAATAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAA
66 ACTAAAAACTGATCAATAGCGGCGTTTTTCGAAAAACGCCACTAAAAACTGATCAA
* * * * * * *
12793894 TAGCGGCGTTTTAATCCCAAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCCAAAACGC
1 TAGCGGCGTTTT-ATCCAAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTAGCAAAAACAC
* * *
12793959 CACTAAAAACTGATCAATTGTGGCGTTTTTGGAAAAACGCCACTAAAAACTGATCAA
65 CACTAAAAACTGATCAATAGCGGCGTTTTTCGAAAAACGCCACTAAAAACTGATCAA
12794016 TAGCGGCGTTTT
1 TAGCGGCGTTTT
12794028 TGGTCCAAAC
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
120 8 0.07
121 3 0.03
122 103 0.90
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (121 bp):
TAGCGGCGTTTTATCCAAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTAGCAAAAACACC
ACTAAAAACTGATCAATAGCGGCGTTTTTCGAAAAACGCCACTAAAAACTGATCAA
Found at i:12794373 original size:29 final size:29
Alignment explanation
Indices: 12794325--12794380 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12794315 TGGCTTTTTG
*
12794325 TAAACCCTTAAATCTTAAACATTAAACCC
1 TAAACCCTTAAATCTTAAACATAAAACCC
*
12794354 TAAACCC-TAAATTTTAAAACATAAAAC
1 TAAACCCTTAAATCTT-AAACATAAAAC
12794381 ATAAACACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (29 bp):
TAAACCCTTAAATCTTAAACATAAAACCC
Found at i:12794385 original size:28 final size:28
Alignment explanation
Indices: 12794325--12794391 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
12794315 TGGCTTTTTG
* *
12794325 TAAACCCTTAAATCTTAAACATTAAACCC
1 TAAACCC-TAAATCTTAAACATTAAAACA
*
12794354 TAAACCCTAAATTTTAAAACA-TAAAACA
1 TAAACCCTAAATCTT-AAACATTAAAACA
*
12794382 TAAACACTAA
1 TAAACCCTAA
12794392 TCCATAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAATCTTAAACATTAAAACA
Found at i:12794638 original size:43 final size:44
Alignment explanation
Indices: 12794572--12794661 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 44
12794562 TATGGTTTAG
* * *
12794572 GGTTCAATGGTACGTAGAATATATTTTAAGTTTATGGTTTAGGCC
1 GGTTCAATGGTAC-TAGAATATATATTAAGTTAATGGTATAGGCC
* *
12794617 GGTTCAATGGTA-TAGTATATATATTAAGTTAATGGTATGGGCC
1 GGTTCAATGGTACTAGAATATATATTAAGTTAATGGTATAGGCC
12794660 GG
1 GG
12794662 GTTTGTTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 28 0.70
45 12 0.30
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.38
Consensus pattern (44 bp):
GGTTCAATGGTACTAGAATATATATTAAGTTAATGGTATAGGCC
Found at i:12795785 original size:40 final size:42
Alignment explanation
Indices: 12795709--12795803 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 42
12795699 GCGTTTTTAC
* * * *
12795709 AAAAATGCCACTAAAAAATAGAGAATTAGTGGCGCTTTCATA
1 AAAAACGCCACTAAAAAATAGAGAAATAGCGACGCTTTCATA
* *
12795751 AAAAACGCCAC-AAAAACT-GAGAAATAGCGACGCTTT--TG
1 AAAAACGCCACTAAAAAATAGAGAAATAGCGACGCTTTCATA
*
12795789 TAAAACGCCACTAAA
1 AAAAACGCCACTAAA
12795804 TGTTTAATTG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
38 11 0.24
39 3 0.07
40 15 0.33
41 6 0.13
42 10 0.22
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (42 bp):
AAAAACGCCACTAAAAAATAGAGAAATAGCGACGCTTTCATA
Found at i:12796662 original size:2 final size:2
Alignment explanation
Indices: 12796655--12796689 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12796645 TAATAGGAGT
12796655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12796690 TTATCCGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12796794 original size:14 final size:15
Alignment explanation
Indices: 12796775--12796804 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12796765 TGTGTTTATA
12796775 TAAATACAT-AATTC
1 TAAATACATAAATTC
12796789 TAAATACATAAATTC
1 TAAATACATAAATTC
12796804 T
1 T
12796805 GAAGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATACATAAATTC
Found at i:12799621 original size:2 final size:2
Alignment explanation
Indices: 12799614--12799646 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12799604 GTCAAATTGT
12799614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12799647 GTTATTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12800765 original size:9 final size:9
Alignment explanation
Indices: 12800742--12800869 Score: 114
Period size: 9 Copynumber: 13.6 Consensus size: 9
12800732 AGTATTAATT
*
12800742 ACTTAAATA
1 ACTTACATA
*
12800751 AATTACATA
1 ACTTACATA
12800760 ACTTACATA
1 ACTTACATA
* *
12800769 ACTCATATA
1 ACTTACATA
12800778 ACTTACATA
1 ACTTACATA
*
12800787 ATTTACATAACA
1 ACTTACAT---A
12800799 ACTTACATA
1 ACTTACATA
*
12800808 ACTCACATA
1 ACTTACATA
12800817 ACTTACATA
1 ACTTACATA
*
12800826 ATTTACATA
1 ACTTACATA
*
12800835 ACTCACATA
1 ACTTACATA
12800844 A-TGTACATAACA
1 ACT-TACAT---A
12800856 ACTTACATA
1 ACTTACATA
12800865 ACTTA
1 ACTTA
12800870 ACTAATACAT
Statistics
Matches: 96, Mismatches: 15, Indels: 16
0.76 0.12 0.13
Matches are distributed among these distances:
8 1 0.01
9 79 0.82
12 15 0.16
13 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:12800811 original size:39 final size:39
Alignment explanation
Indices: 12800759--12800836 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12800749 TAAATTACAT
*
12800759 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
12800798 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
12800837 TCACATAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:12800818 original size:57 final size:57
Alignment explanation
Indices: 12800755--12800867 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
12800745 TAAATAAATT
* * *
12800755 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAATGTACATAACAACTTACATAACTC
* *
12800812 ACATAACTTACATAATTTACATAACTCACATAATGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAATGTACATAACAACTTACATAACT
12800868 TAACTAATAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAATGTACATAACAACTTACATAACTC
Found at i:12806762 original size:33 final size:33
Alignment explanation
Indices: 12806720--12806801 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
12806710 TTAGAATTAA
* *
12806720 TGTTTTTGGTTGTATTTTTTATGTTAAATTTGC
1 TGTTTTTGGTTGCATTTTTTATATTAAATTTGC
* *
12806753 TGTTTTTGGTTGCA--TTTTATATTATATTTGT
1 TGTTTTTGGTTGCATTTTTTATATTAAATTTGC
* *
12806784 TGTATTTGGTTGGATTTT
1 TGTTTTTGGTTGCATTTT
12806802 AATGCAGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 26 0.63
33 15 0.37
ACGTcount: A:0.15, C:0.02, G:0.20, T:0.63
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTTATATTAAATTTGC
Found at i:12806949 original size:16 final size:16
Alignment explanation
Indices: 12806928--12806959 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12806918 ACGCCGCTAA
12806928 AAGCCTTGACCTTTAG
1 AAGCCTTGACCTTTAG
12806944 AAGCCTTGACCTTTAG
1 AAGCCTTGACCTTTAG
12806960 CGGCGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
AAGCCTTGACCTTTAG
Found at i:12807814 original size:23 final size:24
Alignment explanation
Indices: 12807780--12807830 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
12807770 ATCTTTTATC
* *
12807780 ATAATT-ATTTAAAGTCTATTTTA
1 ATAATTAATTAAAAATCTATTTTA
12807803 ATAATTAATTAAAAAATCTATTTTA
1 ATAATTAATT-AAAAATCTATTTTA
12807828 ATA
1 ATA
12807831 TCTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 3 0.12
25 15 0.62
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATAATTAATTAAAAATCTATTTTA
Found at i:12809609 original size:26 final size:25
Alignment explanation
Indices: 12809580--12809631 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
12809570 TTAAACTTTG
* *
12809580 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAA-TTTAAAAAATAGTAAA
12809606 ATTTATAAATTTAAAAAATAGTAAA
1 ATTTATAAATTTAAAAAATAGTAAA
12809631 A
1 A
12809632 ATTAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTTATAAATTTAAAAAATAGTAAA
Found at i:12809632 original size:26 final size:26
Alignment explanation
Indices: 12809580--12809634 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
12809570 TTAAACTTTG
* *
12809580 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAAGTTTAAAAAATATAAAA
12809606 ATTTATAAA-TTTAAAAAATAGTAAAA
1 ATTTATAAAGTTTAAAAAATA-TAAAA
12809632 ATT
1 ATT
12809635 AGTTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTATAAAGTTTAAAAAATATAAAA
Found at i:12818053 original size:93 final size:93
Alignment explanation
Indices: 12817941--12818111 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
12817931 CCCATAAGTG
* *
12817941 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
12818006 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
*
12818034 AACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
12818099 GAGTTCGGATGCC
66 GAGTTCGGATGCC
12818112 CAAATATCCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:12818107 original size:46 final size:46
Alignment explanation
Indices: 12817932--12818107 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
12817922 TGTAACCCGC
* * *
12817932 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
12817978 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
*
12818028 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
12818071 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12818108 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
46 67 0.60
47 31 0.28
50 5 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:12820442 original size:13 final size:14
Alignment explanation
Indices: 12820426--12820461 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12820416 CAATCTCATA
12820426 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
12820439 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
12820452 TCTC-ATTTCA
1 TCTCAATTTCA
12820462 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:12820451 original size:18 final size:19
Alignment explanation
Indices: 12820413--12820453 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12820403 TGGTTCATGT
12820413 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12820432 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12820450 TTTC
1 TTTC
12820454 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12820643 original size:21 final size:21
Alignment explanation
Indices: 12820617--12820701 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
12820607 TGATCAGTAT
*
12820617 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
12820638 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
12820659 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
12820681 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
12820702 TCGGTAAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:12820667 original size:23 final size:22
Alignment explanation
Indices: 12820615--12820689 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
12820605 CCTGATCAGT
** *
12820615 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
12820636 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
12820657 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
12820680 ATACGACACA
1 ATACGACACA
12820690 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:12821178 original size:2 final size:2
Alignment explanation
Indices: 12821171--12821210 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
12821161 ATATCTCATT
*
12821171 CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12821211 TATATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:12821215 original size:2 final size:2
Alignment explanation
Indices: 12821210--12821245 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12821200 ACACACACAC
*
12821210 AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12821246 ATTCAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12822048 original size:13 final size:13
Alignment explanation
Indices: 12822030--12822057 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12822020 CCTCCTTTTA
12822030 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
12822043 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
12822056 TT
1 TT
12822058 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:12823939 original size:46 final size:46
Alignment explanation
Indices: 12823886--12824061 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
12823876 TATTTGGGCA
12823886 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
12823932 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
12823979 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
12824025 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12824062 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:12824041 original size:93 final size:93
Alignment explanation
Indices: 12823882--12824053 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
12823872 GGGATATTTG
* *
12823882 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12823947 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
12823975 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12824040 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
12824054 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:12833083 original size:3 final size:3
Alignment explanation
Indices: 12833075--12833100 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12833065 TGATTGGTAC
12833075 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
12833101 GACAACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12837388 original size:47 final size:46
Alignment explanation
Indices: 12837270--12837443 Score: 189
Period size: 45 Copynumber: 3.8 Consensus size: 46
12837260 GGGATATTTG
*
12837270 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
12837317 TG--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
12837362 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCG-A
* *
12837410 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
12837444 TATGGGCGGG
Statistics
Matches: 108, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 4 0.04
44 2 0.02
45 32 0.30
46 30 0.28
47 31 0.29
48 5 0.05
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:12837439 original size:46 final size:46
Alignment explanation
Indices: 12837275--12837448 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
12837265 ATTTGGGCAT
* *
12837275 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-ATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
12837320 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
12837365 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
12837413 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12837449 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
42 5 0.05
44 2 0.02
45 29 0.26
46 35 0.32
47 28 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:12840431 original size:15 final size:15
Alignment explanation
Indices: 12840392--12840470 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
12840382 GTATCTTGGG
*
12840392 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
12840407 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
12840422 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
12840437 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
12840452 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
12840465 TTTCTT
1 TTTCTT
12840471 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
13 6 0.11
14 4 0.08
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:12840478 original size:30 final size:30
Alignment explanation
Indices: 12840383--12840469 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
12840373 CATAGTATCG
* * * *
12840383 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGGTTTCTC
12840413 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGGTTTCTC
12840443 TATCTTGGATTTCTTTATT-C-GGTTTCT
1 TATCTTGGATTTCTTTATTCCGGGTTTCT
12840470 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
28 7 0.14
29 2 0.04
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGGTTTCTC
Found at i:12842906 original size:46 final size:46
Alignment explanation
Indices: 12842853--12843028 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
12842843 TATTTGGGCA
12842853 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12842899 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
12842944 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
12842992 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12843029 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12843008 original size:93 final size:93
Alignment explanation
Indices: 12842849--12843020 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
12842839 GGGATATTTG
* *
12842849 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12842914 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
12842942 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12843007 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
12843021 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:12850099 original size:47 final size:47
Alignment explanation
Indices: 12849990--12850100 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
12849980 CCGGGATAAG
* *
12849990 CACATAGTGCTTCATCGGAATAAATCCGAAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
12850037 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
12850084 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
12850101 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:12858593 original size:24 final size:24
Alignment explanation
Indices: 12858528--12858594 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
12858518 ACGTAATATG
* * *
12858528 TAATTTGATATATAAATTTTAATTT
1 TAATTTAAT-TATACATATTAATTT
* *
12858553 T-ATATAAATATACATATTAATTT
1 TAATTTAATTATACATATTAATTT
12858576 TAATTTAATTATACATATT
1 TAATTTAATTATACATATT
12858595 TAAAGAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 14 0.41
24 19 0.56
25 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (24 bp):
TAATTTAATTATACATATTAATTT
Found at i:12867508 original size:21 final size:21
Alignment explanation
Indices: 12867469--12867508 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12867459 CGCCCCTCGG
* *
12867469 TTTTTTTTTCCATTGTTTTTC
1 TTTTTCTTTCCATTATTTTTC
*
12867490 TTTTTCTTTCCTTTATTTT
1 TTTTTCTTTCCATTATTTT
12867509 ACTTGCTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTCCATTATTTTTC
Found at i:12877841 original size:2 final size:2
Alignment explanation
Indices: 12877836--12877860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12877826 GTGTGTGTGT
12877836 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
12877861 GGGGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12878739 original size:136 final size:135
Alignment explanation
Indices: 12878597--12878861 Score: 453
Period size: 137 Copynumber: 2.0 Consensus size: 135
12878587 AGACGACACA
12878597 TTAGCTTTTAATTA-TTTTTAAATTTAAAAAAAAATTAAAAAAA-TTTGTAATTTTTAAATAAAT
1 TTAGCTTTTAATTAGTTTTTAAATTT-AAAAAAAATTAAAAAAAGTTTGTAATTTTTAAATAAAT
*
12878660 TTAATTCTTTCTCATTTTTAAAAATAGTTTTCATATTTTTTGAATTTTTAAATTTTAAAAAATTA
65 TTAATTCTTTCTCATTTTT-AAAATAGTTTTCATA-TTTTCGAATTTTTAAATTTTAAAAAATTA
12878725 ATCCCACG
128 ATCCCACG
* *
12878733 TTAGCTTTTTATTAGTTTTTAAATTTAAAAAAATTTAAAAAAAGTTTGTAATTTTTAAATAAATT
1 TTAGCTTTTAATTAGTTTTTAAATTTAAAAAAAATTAAAAAAAGTTTGTAATTTTTAAATAAATT
*
12878798 TAATTCTTTTTCATTTTTAAAATAGTTTTCATATTTTCGAATTTTTAAATTTTAAAAAATTAAT
66 TAATTCTTTCTCATTTTTAAAATAGTTTTCATATTTTCGAATTTTTAAATTTTAAAAAATTAAT
12878862 TGCTTACGTG
Statistics
Matches: 123, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
135 30 0.24
136 44 0.36
137 49 0.40
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (135 bp):
TTAGCTTTTAATTAGTTTTTAAATTTAAAAAAAATTAAAAAAAGTTTGTAATTTTTAAATAAATT
TAATTCTTTCTCATTTTTAAAATAGTTTTCATATTTTCGAATTTTTAAATTTTAAAAAATTAATC
CCACG
Found at i:12880158 original size:14 final size:14
Alignment explanation
Indices: 12880139--12880166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12880129 AAATCCTACT
12880139 TAATATGATCGACA
1 TAATATGATCGACA
12880153 TAATATGATCGACA
1 TAATATGATCGACA
12880167 AATGAGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TAATATGATCGACA
Found at i:12895671 original size:13 final size:13
Alignment explanation
Indices: 12895612--12895670 Score: 91
Period size: 13 Copynumber: 4.5 Consensus size: 13
12895602 TTTAGCAATA
12895612 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
12895625 TTTTTGAAAAATG
1 CTTTTGAAAAGTG
12895638 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
12895651 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
12895664 CTTTTGA
1 CTTTTGA
12895671 GTGTTTAGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Done.