Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 46 of 292
Found at i:12807161 original size:40 final size:40
Alignment explanation
Indices: 12807102--12807243 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
12807092 AAATTGAATG
* * *
12807102 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
12807142 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
12807182 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
12807222 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
12807244 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:12807244 original size:40 final size:39
Alignment explanation
Indices: 12807141--12807269 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
12807131 TGCTGGAAAT
* * *
12807141 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
12807181 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
12807221 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
12807261 TATATCCGG
1 TATATCCGG
12807270 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:12810094 original size:13 final size:13
Alignment explanation
Indices: 12810076--12810115 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
12810066 AGAGTAATAG
12810076 CACACAGGCGTGT
1 CACACAGGCGTGT
*
12810089 CACACAGGTGTGT
1 CACACAGGCGTGT
*
12810102 CACACGGGCGTGT
1 CACACAGGCGTGT
12810115 C
1 C
12810116 CCTTCCGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (13 bp):
CACACAGGCGTGT
Found at i:12822181 original size:40 final size:40
Alignment explanation
Indices: 12822126--12822224 Score: 180
Period size: 40 Copynumber: 2.5 Consensus size: 40
12822116 ACTTGACAAC
*
12822126 TTGTGTGAGTAGCCCGTGTAGTTACAACCTGACTGATAGT
1 TTGTGTGAGCAGCCCGTGTAGTTACAACCTGACTGATAGT
12822166 TTGTGTGAGCAGCCCGTGTAGTTACAACCTGACTGATAGT
1 TTGTGTGAGCAGCCCGTGTAGTTACAACCTGACTGATAGT
12822206 TTGTGTGAGCAGACCCGTG
1 TTGTGTGAGCAG-CCCGTG
12822225 AGTAGCTTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 51 0.89
41 6 0.11
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (40 bp):
TTGTGTGAGCAGCCCGTGTAGTTACAACCTGACTGATAGT
Found at i:12829357 original size:13 final size:13
Alignment explanation
Indices: 12829335--12829371 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
12829325 GTAATCGCAT
*
12829335 ACGGGTGTGTCAC
1 ACGGGCGTGTCAC
12829348 ACGGGCGTGTCAC
1 ACGGGCGTGTCAC
12829361 ACGGGCGTGTC
1 ACGGGCGTGTC
12829372 CCTACCGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.19
Consensus pattern (13 bp):
ACGGGCGTGTCAC
Found at i:12831719 original size:18 final size:18
Alignment explanation
Indices: 12831696--12831738 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12831686 AAGGAAATCA
12831696 ACCCTCCAGGTTTTCAAC
1 ACCCTCCAGGTTTTCAAC
*
12831714 ACCCTCCGGGTTTTCAAC
1 ACCCTCCAGGTTTTCAAC
*
12831732 AACCTCC
1 ACCCTCC
12831739 TTACCAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.42, G:0.12, T:0.26
Consensus pattern (18 bp):
ACCCTCCAGGTTTTCAAC
Found at i:12835096 original size:13 final size:13
Alignment explanation
Indices: 12835078--12835106 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12835068 TTTAGCTTAA
12835078 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12835091 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12835104 TTA
1 TTA
12835107 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:12837948 original size:31 final size:31
Alignment explanation
Indices: 12837906--12837965 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12837896 CCTTTTCATA
12837906 TTTCATATTTCATAATACTGGGCCGAAGCTT
1 TTTCATATTTCATAATACTGGGCCGAAGCTT
* * *
12837937 TTTCATGTTTCATATTTCTGGGCCGAAGC
1 TTTCATATTTCATAATACTGGGCCGAAGC
12837966 CTTTACTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCTT
Found at i:12838206 original size:24 final size:24
Alignment explanation
Indices: 12838160--12838278 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
12838150 GCTTTATCAT
*
12838160 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
12838185 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
12838209 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
**
12838232 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTA
12838256 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12838279 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 24 0.28
24 48 0.56
25 13 0.15
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12838239 original size:47 final size:48
Alignment explanation
Indices: 12838160--12838278 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
12838150 GCTTTATCAT
*
12838160 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
*
12838209 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
12838256 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12838279 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 2 0.03
47 43 0.65
48 9 0.14
49 12 0.18
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:12838354 original size:20 final size:20
Alignment explanation
Indices: 12838329--12838388 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
12838319 TATGATTACC
12838329 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
12838349 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
12838369 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12838389 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:12838359 original size:11 final size:11
Alignment explanation
Indices: 12838329--12838383 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12838319 TATGATTACC
12838329 TCATGTGCATA
1 TCATGTGCATA
*
12838340 TCA--TACATA
1 TCATGTGCATA
12838349 TCATGTGCATA
1 TCATGTGCATA
* *
12838360 TCA--TACATT
1 TCATGTGCATA
12838369 TCATGTGCATA
1 TCATGTGCATA
12838380 TCAT
1 TCAT
12838384 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:12838463 original size:25 final size:25
Alignment explanation
Indices: 12838431--12838478 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12838421 ATACATAAAC
* * *
12838431 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12838456 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12838479 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12840598 original size:22 final size:23
Alignment explanation
Indices: 12840573--12840618 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12840563 CAACCAAACC
12840573 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12840595 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12840618 A
1 A
12840619 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12840624 original size:23 final size:23
Alignment explanation
Indices: 12840580--12840624 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12840570 ACCAATTCAA
*
12840580 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12840603 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12840625 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12853249 original size:27 final size:26
Alignment explanation
Indices: 12853218--12853274 Score: 91
Period size: 24 Copynumber: 2.2 Consensus size: 26
12853208 GTTTTTCTTT
12853218 ATGTTTTGTATTCATTATTCTTCTGAG
1 ATGTTTT-TATTCATTATTCTTCTGAG
12853245 ATG--TTTATTCATTATTCTTCTGAG
1 ATGTTTTTATTCATTATTCTTCTGAG
12853269 ATGTTT
1 ATGTTT
12853275 ACCTTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 22 0.79
25 2 0.07
26 1 0.04
27 3 0.11
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (26 bp):
ATGTTTTTATTCATTATTCTTCTGAG
Found at i:12853255 original size:24 final size:24
Alignment explanation
Indices: 12853226--12853275 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
12853216 TTATGTTTTG
12853226 TATTCATTATTCTTCTGAGATGTT
1 TATTCATTATTCTTCTGAGATGTT
12853250 TATTCATTATTCTTCTGAGATGTT
1 TATTCATTATTCTTCTGAGATGTT
12853274 TA
1 TA
12853276 CCTTTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (24 bp):
TATTCATTATTCTTCTGAGATGTT
Found at i:12859520 original size:13 final size:14
Alignment explanation
Indices: 12859498--12859527 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12859488 CATAACTTAT
12859498 AAAACTATTTTTTA
1 AAAACTATTTTTTA
12859512 AAAAC-ATTTTTTA
1 AAAACTATTTTTTA
12859525 AAA
1 AAA
12859528 TCTTAGCCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAACTATTTTTTA
Found at i:12869259 original size:30 final size:30
Alignment explanation
Indices: 12869225--12869284 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
12869215 TTCCCGAGCC
12869225 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
12869255 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
12869285 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:12869757 original size:47 final size:47
Alignment explanation
Indices: 12869706--12869882 Score: 211
Period size: 47 Copynumber: 3.8 Consensus size: 47
12869696 TGGTTGAACA
*
12869706 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
12869753 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
*
12869800 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
12869846 CCCGAGCTCGTTGAATTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12869883 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 37 0.33
47 58 0.52
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:12872453 original size:31 final size:31
Alignment explanation
Indices: 12872415--12872477 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
12872405 ACATTAATGA
12872415 ATCAATATATGTAACCGTGGCATATCCACTT
1 ATCAATATATGTAACCGTGGCATATCCACTT
* * *
12872446 ATCAATATGTGTAATCGTGGTATATCCACTT
1 ATCAATATATGTAACCGTGGCATATCCACTT
12872477 A
1 A
12872478 GCACCATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (31 bp):
ATCAATATATGTAACCGTGGCATATCCACTT
Found at i:12876792 original size:27 final size:28
Alignment explanation
Indices: 12876733--12876797 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
12876723 CCATCACAGA
* *
12876733 AACAGTATCAAGTGGGCCTTAGCTCAAT
1 AACAGAATCAAGTGGGCCTTAGCCCAAT
12876761 AACAGAATCAAGTGGG-CTTAAGCCCAAT
1 AACAGAATCAAGTGGGCCTT-AGCCCAAT
12876789 -ACAGAATCA
1 AACAGAATCA
12876798 GTATCAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (28 bp):
AACAGAATCAAGTGGGCCTTAGCCCAAT
Found at i:12882415 original size:25 final size:25
Alignment explanation
Indices: 12882387--12882434 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12882377 TTATACCATG
* * *
12882387 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
12882412 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
12882435 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:12882537 original size:20 final size:20
Alignment explanation
Indices: 12882477--12882537 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
12882467 ATAAATATGG
*
12882477 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
12882497 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12882517 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12882537 T
1 T
12882538 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:12889422 original size:25 final size:25
Alignment explanation
Indices: 12889394--12889441 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12889384 TTATACCATG
* * *
12889394 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
12889419 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
12889442 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:12889544 original size:20 final size:20
Alignment explanation
Indices: 12889484--12889544 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
12889474 ATAAATATGG
*
12889484 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
12889504 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12889524 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12889544 T
1 T
12889545 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:12896971 original size:35 final size:35
Alignment explanation
Indices: 12896925--12896994 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
12896915 ATTAAGAAAG
*
12896925 TATGTAGATTTTTCTTGATGACTCATCCATGGAAT
1 TATGTAGATTTTTCTTGATGACTCATCCATAGAAT
12896960 TATGTAGATTTTTCTTGATGACTCATCCATAGAAT
1 TATGTAGATTTTTCTTGATGACTCATCCATAGAAT
12896995 CATGGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (35 bp):
TATGTAGATTTTTCTTGATGACTCATCCATAGAAT
Found at i:12903504 original size:20 final size:20
Alignment explanation
Indices: 12903481--12903523 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12903471 AAATCCAAAT
12903481 TAAAATACTAAAATTCAAGA
1 TAAAATACTAAAATTCAAGA
* * *
12903501 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAAGA
12903521 TAA
1 TAA
12903524 GAGTACTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:12904393 original size:16 final size:17
Alignment explanation
Indices: 12904357--12904393 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12904347 CAAACTTATT
12904357 TAATAATAAATGTTAAA
1 TAATAATAAATGTTAAA
*
12904374 -AATAAT-AATTTTAAA
1 TAATAATAAATGTTAAA
12904389 TAATA
1 TAATA
12904394 TTCATCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATGTTAAA
Found at i:12907247 original size:20 final size:20
Alignment explanation
Indices: 12907224--12907261 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12907214 GATATAATTG
*
12907224 TTATTCCCAGAAAATAAAAT
1 TTATACCCAGAAAATAAAAT
*
12907244 TTATACCTAGAAAATAAA
1 TTATACCCAGAAAATAAA
12907262 TTTCTCACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (20 bp):
TTATACCCAGAAAATAAAAT
Found at i:12909745 original size:23 final size:23
Alignment explanation
Indices: 12909719--12909764 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12909709 ACCATAAAAA
12909719 ATTTTGTTCAAATTAAAAACATT
1 ATTTTGTTCAAATTAAAAACATT
12909742 ATTTTGTTCAAATTAAAAACATT
1 ATTTTGTTCAAATTAAAAACATT
12909765 CATTCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTTTGTTCAAATTAAAAACATT
Found at i:12911588 original size:50 final size:50
Alignment explanation
Indices: 12911417--12911749 Score: 269
Period size: 51 Copynumber: 6.6 Consensus size: 50
12911407 AATTTTCATT
* * * *
12911417 CACATA-TA-CCTGCACTTAGTACCACATC-TGTGACCAAAACCATCGCT-TA
1 CACATAGTAGCCTGCACTTAGTACTACA-CATGTGACC-TAACTATC-TTGTA
* * * * * **
12911466 CACATAGTGGCCTGCATTTAGTACCACACATGTGATCGAAGCTATCGGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CTATCTTGTA
* *
12911517 CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTTGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTTGTA
* * * * * **
12911567 CACGTAGTAGCATGCATTTAGTACTACACATGTGACCTAAAACCATTTTAAA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACTATCTTGTA
* * * * * * **
12911619 CACATAGTGGCTTGCACTTAGTACCACGCATGTGATCGAAGCTATCGGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CTATCTTGTA
* * * * *
12911670 CGCATAGTAGCCTTCACTTAGTACTACACATGCGACCTAACCATCTTTTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTTGTA
*
12911720 CACGTAGTAGCCTGCACTTAGTACTACACA
1 CACATAGTAGCCTGCACTTAGTACTACACA
12911750 CGTTTTCTTA
Statistics
Matches: 221, Mismatches: 55, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
49 6 0.03
50 80 0.36
51 97 0.44
52 38 0.17
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTTGTA
Found at i:12911730 original size:153 final size:153
Alignment explanation
Indices: 12911427--12911749 Score: 501
Period size: 153 Copynumber: 2.1 Consensus size: 153
12911417 CACATATACC
* * *
12911427 TGCACTTAGTACCACATC-TGTGACC-AAAACCATCGCTT--ACACATAGTGGCCTGCATTTAGT
1 TGCACTTAGTACTACA-CATGTGACCTAAAACCAT--TTTAAACACATAGTGGCCTGCACTTAGT
12911488 ACCACACATGTGATCGAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGAC
63 ACCACACATGTGATCGAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGAC
*
12911553 CTAACTATCTTGTACACGTAGTAGCA
128 CTAACCATCTTGTACACGTAGTAGCA
* *
12911579 TGCATTTAGTACTACACATGTGACCTAAAACCATTTTAAACACATAGTGGCTTGCACTTAGTACC
1 TGCACTTAGTACTACACATGTGACCTAAAACCATTTTAAACACATAGTGGCCTGCACTTAGTACC
* *
12911644 ACGCATGTGATCGAAGCTATCGGGTACGCATAGTAGCCTTCACTTAGTACTACACATGCGACCTA
66 ACACATGTGATCGAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTA
* *
12911709 ACCATCTTTTACACGTAGTAGCC
131 ACCATCTTGTACACGTAGTAGCA
12911732 TGCACTTAGTACTACACA
1 TGCACTTAGTACTACACA
12911750 CGTTTTCTTA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
151 3 0.02
152 21 0.13
153 132 0.85
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (153 bp):
TGCACTTAGTACTACACATGTGACCTAAAACCATTTTAAACACATAGTGGCCTGCACTTAGTACC
ACACATGTGATCGAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTA
ACCATCTTGTACACGTAGTAGCA
Found at i:12915772 original size:15 final size:15
Alignment explanation
Indices: 12915731--12915782 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
12915721 TTTACCTTAA
12915731 TTTTTCCTT-TCTATT
1 TTTTTCCTTCTCTA-T
*
12915746 TTTTTCTATTCTCTAT
1 TTTTTC-CTTCTCTAT
*
12915762 TTTTTCCTTCTC-AC
1 TTTTTCCTTCTCTAT
12915776 TTTTTCC
1 TTTTTCC
12915783 CTCTTGATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 9 0.28
17 4 0.12
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTCCTTCTCTAT
Found at i:12918674 original size:31 final size:31
Alignment explanation
Indices: 12918631--12918696 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
12918621 AACCCTTCCT
*
12918631 GCATTAAATCCAACCAAAAACAGCAAATATA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
*
12918662 GCATGAAATCCAACCAAAAACAGCAAATGTA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
12918693 GCAT
1 GCAT
12918697 AAAAAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.23, G:0.11, T:0.15
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGCAAATATA
Found at i:12918977 original size:21 final size:21
Alignment explanation
Indices: 12918961--12919001 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12918951 GTTGCTGTCT
*
12918961 CTGCCTCTCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
12918982 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
12919002 TCCGCTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.51, G:0.20, T:0.29
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:12919437 original size:13 final size:14
Alignment explanation
Indices: 12919411--12919439 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12919401 ACTAACGATG
12919411 AATTAAACCATTAT
1 AATTAAACCATTAT
12919425 AATTAAA-CATTAT
1 AATTAAACCATTAT
12919438 AA
1 AA
12919440 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:12924467 original size:42 final size:43
Alignment explanation
Indices: 12924403--12924515 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 43
12924393 CTATTCGAGC
* ** *
12924403 CTTCGAGCCTAGCAGGCTATAATGCTGGTGATTTAATAT-GGG
1 CTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATATCGGG
* *
12924445 TTTTAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATATCGGG
1 CTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATATCGGG
* *
12924488 CTTCGAGCCTAGCAGGC-GTAATGCCAGT
1 CTTCAAGCCTAGCAGGCTATAATGCCAGT
12924516 CAATGAATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 43 0.72
43 17 0.28
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
CTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATATCGGG
Found at i:12930363 original size:17 final size:18
Alignment explanation
Indices: 12930330--12930363 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12930320 ATAGGTTAAT
*
12930330 TTGTAGTGGCCAAATAAA
1 TTGTAGTGGCAAAATAAA
12930348 TTGTAGT-GCAAAATAA
1 TTGTAGTGGCAAAATAA
12930364 GAGGATTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (18 bp):
TTGTAGTGGCAAAATAAA
Found at i:12930752 original size:24 final size:24
Alignment explanation
Indices: 12930720--12930768 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12930710 TCGAGGTAAG
12930720 TTTTAAGTAGTTAAACATAAATAA
1 TTTTAAGTAGTTAAACATAAATAA
12930744 TTTTAAGTAGTTAAACATAAATAA
1 TTTTAAGTAGTTAAACATAAATAA
12930768 T
1 T
12930769 ATTCGATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (24 bp):
TTTTAAGTAGTTAAACATAAATAA
Found at i:12931177 original size:43 final size:43
Alignment explanation
Indices: 12931110--12931230 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
12931100 ACAGTGTTAT
* * *
12931110 TCGGGCCTTCGAGCCTAGCA-GCTATAATGCCGGTGATTTAATA
1 TCGGG-CTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATA
*
12931153 TCGGGCTTTAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATA
* * * *
12931196 TTGGGCTTCGAGCCTAGAAGGC-GTAATGCCAGTGA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATGCCAGTGA
12931231 ATGAATTCAG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 24 0.35
43 44 0.65
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (43 bp):
TCGGGCTTCAAGCCTAGCAGGCTATAATGCCAGTGAGTTAATA
Found at i:12933154 original size:9 final size:9
Alignment explanation
Indices: 12933134--12933372 Score: 95
Period size: 9 Copynumber: 26.8 Consensus size: 9
12933124 ATGTATTACA
*
12933134 TAAGTTAAG
1 TAAGTTATG
12933143 TAAGCTT-TG
1 TAAG-TTATG
12933152 TAAGTTATG
1 TAAGTTATG
12933161 TAAGTTATG
1 TAAGTTATG
* * *
12933170 TTA-TGATA
1 TAAGTTATG
*
12933178 TACATTTATG
1 TA-AGTTATG
*
12933188 TAAGGTATG
1 TAAGTTATG
12933197 TAAGTTATG
1 TAAGTTATG
* ** *
12933206 ATATGGCATA
1 -TAAGTTATG
*
12933216 T-ATTTATG
1 TAAGTTATG
12933224 T-A-TTATG
1 TAAGTTATG
*
12933231 TAAGTTGTG
1 TAAGTTATG
12933240 TAAGTTATG
1 TAAGTTATG
* * *
12933249 ATATGATATA
1 -TAAGTTATG
*
12933259 T-ATTTATG
1 TAAGTTATG
12933267 T-A-TTATG
1 TAAGTTATG
* *
12933274 TTAGTTGTG
1 TAAGTTATG
12933283 TAAGTTATG
1 TAAGTTATG
* * *
12933292 ATATGATATA
1 -TAAGTTATG
*
12933302 T-ATTTATG
1 TAAGTTATG
*
12933310 ATATATATTTATG
1 ---TA-AGTTATG
12933323 T-A-TTATG
1 TAAGTTATG
*
12933330 TAAGTTTTG
1 TAAGTTATG
*
12933339 TAAGTTTTG
1 TAAGTTATG
12933348 TAAGTTATG
1 TAAGTTATG
12933357 TAAGTTATG
1 TAAGTTATG
12933366 TAAGTTA
1 TAAGTTA
12933373 CTATATGATA
Statistics
Matches: 172, Mismatches: 40, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
7 18 0.10
8 22 0.13
9 99 0.58
10 25 0.15
11 1 0.01
13 7 0.04
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12933197 original size:36 final size:36
Alignment explanation
Indices: 12933150--12933309 Score: 158
Period size: 43 Copynumber: 4.1 Consensus size: 36
12933140 AAGTAAGCTT
* *
12933150 TGTAAGTTATGTAAGTTATGTTATGATATACATTTA
1 TGTAAGTTATGTAAGTTATGATATGATATATATTTA
*
12933186 TGTAAGGTATGTAAGTTATGATATGGCATATATTTATGTATTA
1 TGTAAGTTATGTAAGTTATGATAT-G-ATATA--TA--T-TTA
*
12933229 TGTAAGTTGTGTAAGTTATGATATGATATATATTTA
1 TGTAAGTTATGTAAGTTATGATATGATATATATTTA
12933265 TGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTA
1 TGTA--A-GTTA----TGTAAGTTATGATATGATATATATTTA
12933308 TG
1 TG
12933310 ATATATATTT
Statistics
Matches: 104, Mismatches: 6, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
36 29 0.28
37 2 0.02
38 6 0.06
39 5 0.05
40 1 0.01
41 5 0.05
42 2 0.02
43 54 0.52
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.47
Consensus pattern (36 bp):
TGTAAGTTATGTAAGTTATGATATGATATATATTTA
Found at i:12933242 original size:43 final size:43
Alignment explanation
Indices: 12933183--12933309 Score: 209
Period size: 43 Copynumber: 3.0 Consensus size: 43
12933173 TGATATACAT
* * **
12933183 TTATGTAAGGTATGTAAGTTATGATATGGCATATATTTATGTA
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
12933226 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
*
12933269 TTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATG
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATG
12933310 ATATATATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (43 bp):
TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
Found at i:12933311 original size:13 final size:13
Alignment explanation
Indices: 12933293--12933322 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12933283 TAAGTTATGA
12933293 TATGATATATATT
1 TATGATATATATT
12933306 TATGATATATATT
1 TATGATATATATT
12933319 TATG
1 TATG
12933323 TATTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:12933365 original size:56 final size:54
Alignment explanation
Indices: 12933229--12933358 Score: 165
Period size: 56 Copynumber: 2.4 Consensus size: 54
12933219 TTATGTATTA
* *
12933229 TGTAAGTTGTGTAAGTTATG-A-TATGATATATATTTATGTATTATGTTAGTTG
1 TGTAAGTTATGTAAGTTATGTATTATGATATATATTTATGTATTATGTAAGTTG
* * * *
12933281 TGTAAGTTATGATATGATATATATTTATGATATATATTTATGTATTATGTAAGTTT
1 TGTAAGTTATG-TAAGTTATGTA-TTATGATATATATTTATGTATTATGTAAGTTG
*
12933337 TGTAAGTTTTGTAAGTTATGTA
1 TGTAAGTTATGTAAGTTATGTA
12933359 AGTTATGTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
52 10 0.16
53 6 0.09
54 1 0.02
55 8 0.12
56 39 0.61
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (54 bp):
TGTAAGTTATGTAAGTTATGTATTATGATATATATTTATGTATTATGTAAGTTG
Found at i:12933870 original size:8 final size:8
Alignment explanation
Indices: 12933857--12933886 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
12933847 ATTAATTGAT
12933857 AAATATTG
1 AAATATTG
12933865 AAATATTG
1 AAATATTG
12933873 AAATATTG
1 AAATATTG
12933881 AAATAT
1 AAATAT
12933887 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (8 bp):
AAATATTG
Found at i:12936891 original size:59 final size:59
Alignment explanation
Indices: 12936796--12936911 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
12936786 AAAATGGGAA
* * ** * *
12936796 ATTATTTTAGGGTTTCGAATTAGGGAAAATGGGGGAAATAAACTAGGGAGAAGGGGGTG
1 ATTATTTTAGGGATTCGAAGTAGGGAAAATAAGGGAAATAAACCAGAGAGAAGGGGGTG
12936855 ATTATTTTAGGGATTC-AGAGTAGGGAAAATAAGGGAAATAAACCAGAGAGAAGGGGG
1 ATTATTTTAGGGATTCGA-AGTAGGGAAAATAAGGGAAATAAACCAGAGAGAAGGGGG
12936912 AAAATGAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 1 0.02
59 49 0.98
ACGTcount: A:0.38, C:0.04, G:0.35, T:0.22
Consensus pattern (59 bp):
ATTATTTTAGGGATTCGAAGTAGGGAAAATAAGGGAAATAAACCAGAGAGAAGGGGGTG
Found at i:12937413 original size:114 final size:114
Alignment explanation
Indices: 12937016--12937588 Score: 550
Period size: 114 Copynumber: 5.0 Consensus size: 114
12937006 TTGCTATAGG
* * * * ** *
12937016 CAAACCAATTGCGGTGTTTTAACAT-AAATGCCACTAAAAAT-CAAACAAAACGATGCCATTTTG
1 CAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAA-AAAACGACACCGTTTTG
* * * * *
12937079 ATATAAATAGAATAAACTTTAGTGGCGTTTTTCCCCTAGCGCCGCTAAAGG
65 ATATAAACAGAATAAACATTAGTGGCGTTTATACCCTAGCGCCGCTAAA-T
* *
12937130 CAAATCTATTGCGGCG-TTTAACCCTAAAACGCCACTAAAAATCCAAAAAAAAACGAGGA-CGTT
1 CAAACCTATTGCGGCGTTTTAA-CCTAAAACGCCACTAAAAATCC--AAAAAAACGA-CACCGTT
* * * * * * * *
12937193 TTCATATAAATAGAAT-AACATTTAGTGGCGTTTTTTCTCCAAGCGTCACTAAAGG
62 TTGATATAAACAGAATAAACA-TTAGTGGCGTTTATAC-CCTAGCGCCGCTAAA-T
* * * *
12937248 CGAAA-CTATTGCGGCGTTTTACCCTAAAACGCCACTAACAATCCAATAAAACTACACCGTTTTG
1 C-AAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTG
* * *
12937312 ATATAAACAAAATAACCATTAGTGGCGTTTATACCCTAGGGCCGCTAAAT
65 ATATAAACAGAATAAACATTAGTGGCGTTTATACCCTAGCGCCGCTAAAT
* * * * *
12937362 CAAACCTATTGTGGCTTTTTAACCTAAACCGCCACTAAAAATCCAAAAAAACTACATCGTTTTGA
1 CAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGA
* * *
12937427 TATAAACAAAATAAACATTAGTGGCGTTTATAACCTAGTGCCGCTAAAT
66 TATAAACAGAATAAACATTAGTGGCGTTTATACCCTAGCGCCGCTAAAT
* * * *** * * *
12937476 CAAACCTATTGTGGCGTTTTAACCTAAAACGCCATTAAAGATCCAAAAAAACGATGTCATCTAG-
1 CAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGA
* * * *
12937540 TAT-AACAGAATAACCTTTAGCGGCGTTTATACCCTAGGGCCGCTAAAT
66 TATAAACAGAATAAACATTAGTGGCGTTTATACCCTAGCGCCGCTAAAT
12937588 C
1 C
12937589 CAATGTTTTT
Statistics
Matches: 390, Mismatches: 56, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
112 40 0.10
113 11 0.03
114 169 0.43
115 27 0.07
116 43 0.11
117 43 0.11
118 50 0.13
119 7 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (114 bp):
CAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGA
TATAAACAGAATAAACATTAGTGGCGTTTATACCCTAGCGCCGCTAAAT
Found at i:12938000 original size:14 final size:14
Alignment explanation
Indices: 12937981--12938090 Score: 62
Period size: 14 Copynumber: 7.7 Consensus size: 14
12937971 TCCAAACTCT
12937981 TAAACCATAAACCC
1 TAAACCATAAACCC
*
12937995 TAAACCCTAAACCC
1 TAAACCATAAACCC
* * *
12938009 ATAATCTATAAACCT
1 -TAAACCATAAACCC
*
12938024 TAAA--ATAGTAACTCA
1 TAAACCATA--AAC-CC
* **
12938039 TACACTTTAAACCC
1 TAAACCATAAACCC
*
12938053 TAAACCATATACCC
1 TAAACCATAAACCC
* *
12938067 TAAGCCATAATCCC
1 TAAACCATAAACCC
*
12938081 TAAACTATAA
1 TAAACCATAA
12938091 TGATAATTAA
Statistics
Matches: 71, Mismatches: 19, Indels: 12
0.70 0.19 0.12
Matches are distributed among these distances:
12 3 0.04
14 49 0.69
15 17 0.24
17 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:12938027 original size:7 final size:7
Alignment explanation
Indices: 12937867--12938008 Score: 69
Period size: 7 Copynumber: 20.1 Consensus size: 7
12937857 ACTAATTACT
12937867 CTAAACC
1 CTAAACC
*
12937874 TTAAACCC
1 CTAAA-CC
12937882 CT-AACC
1 CTAAACC
**
12937888 CTATCCC
1 CTAAACC
12937895 CTAAACC
1 CTAAACC
*
12937902 CTAAATC
1 CTAAACC
* *
12937909 ATAAAAC
1 CTAAACC
* * *
12937916 ATAATCT
1 CTAAACC
12937923 CTAAACC
1 CTAAACC
12937930 CTAAAACC
1 CT-AAACC
12937938 CT-AACAC
1 CTAAAC-C
* *
12937945 TTAACCC
1 CTAAACC
*
12937952 CTAACCC
1 CTAAACC
12937959 CT-AACC
1 CTAAACC
12937965 TCT-AACTC
1 -CTAAAC-C
12937973 C-AAACTC
1 CTAAAC-C
*
12937980 TTAAACC
1 CTAAACC
*
12937987 ATAAACC
1 CTAAACC
12937994 CTAAACC
1 CTAAACC
12938001 CTAAACC
1 CTAAACC
12938008 C
1 C
12938009 ATAATCTATA
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
6 10 0.10
7 77 0.74
8 17 0.16
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:12938327 original size:15 final size:15
Alignment explanation
Indices: 12938307--12938338 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12938297 AATAATAATA
*
12938307 ATTTATATTTATCTT
1 ATTTATATTTATATT
12938322 ATTTATATTTATATT
1 ATTTATATTTATATT
12938337 AT
1 AT
12938339 AAAAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTATATTTATATT
Found at i:12938408 original size:7 final size:7
Alignment explanation
Indices: 12938398--12938427 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
12938388 AACCCCTAAC
12938398 CCCAAAT
1 CCCAAAT
12938405 CCCAAAT
1 CCCAAAT
12938412 CCCAAAT
1 CCCAAAT
12938419 CCCAAAT
1 CCCAAAT
12938426 CC
1 CC
12938428 AAAACCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.13
Consensus pattern (7 bp):
CCCAAAT
Found at i:12938453 original size:14 final size:14
Alignment explanation
Indices: 12938387--12938455 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
12938377 ATTTACCCTT
* *
12938387 AAACCCCTAACCCC
1 AAACCCCAAACCAC
*
12938401 AAATCCCAAATCC-C
1 AAACCCCAAA-CCAC
*
12938415 AAATCCCAAATCCA-
1 AAACCCCAAA-CCAC
**
12938429 AAACCTTAAACCAC
1 AAACCCCAAACCAC
12938443 AAACCCCAAACCA
1 AAACCCCAAACCA
12938456 TAAATCTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
13 3 0.07
14 40 0.89
15 2 0.04
ACGTcount: A:0.46, C:0.43, G:0.00, T:0.10
Consensus pattern (14 bp):
AAACCCCAAACCAC
Found at i:12938466 original size:21 final size:21
Alignment explanation
Indices: 12938415--12938467 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
12938405 CCCAAATCCC
* * *
12938415 AAATCCCAAATCCAAAACCTT
1 AAATCACAAACCCAAAACCAT
* *
12938436 AAACCACAAACCCCAAACCAT
1 AAATCACAAACCCAAAACCAT
*
12938457 AAATCTCAAAC
1 AAATCACAAAC
12938468 TATAAATCAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.36, G:0.00, T:0.13
Consensus pattern (21 bp):
AAATCACAAACCCAAAACCAT
Found at i:12938508 original size:21 final size:21
Alignment explanation
Indices: 12938477--12938528 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
12938467 CTATAAATCA
* * *
12938477 TAAACCCTAAACTCCAAGCCC
1 TAAACCATAAACTACAAACCC
* *
12938498 TAAACTATAAACTATAAACCC
1 TAAACCATAAACTACAAACCC
12938519 TAAACCATAA
1 TAAACCATAA
12938529 CCCATAAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (21 bp):
TAAACCATAAACTACAAACCC
Found at i:12938535 original size:21 final size:21
Alignment explanation
Indices: 12938495--12938542 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12938485 AAACTCCAAG
* *
12938495 CCCTAAACTATAAACTATAAA
1 CCCTAAACCATAAACCATAAA
*
12938516 CCCTAAACCATAACCCATAAA
1 CCCTAAACCATAAACCATAAA
*
12938537 CTCTAA
1 CCCTAA
12938543 TGATAGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
CCCTAAACCATAAACCATAAA
Found at i:12938845 original size:40 final size:39
Alignment explanation
Indices: 12938763--12938847 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 39
12938753 TTTTTAAGAA
12938763 CGCCGCTAATGCTTGATCTTTTGCGGCGTTTTTTACATAAG
1 CGCCGCTAATGC-TGATCTTTTGCGGCGTTTTTTACA-AAG
12938804 CGCCGCTAATAG-TGATCTTTTGCGGCGTTTGTTTTAC-AAG
1 CGCCGCTAAT-GCTGATCTTTTGCGGCG-TT-TTTTACAAAG
12938844 CGCC
1 CGCC
12938848 ACTATAGCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
40 22 0.54
41 12 0.29
42 7 0.17
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (39 bp):
CGCCGCTAATGCTGATCTTTTGCGGCGTTTTTTACAAAG
Found at i:12946071 original size:55 final size:55
Alignment explanation
Indices: 12946007--12946115 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
12945997 TTATGCACTC
*
12946007 AAAAATAAAATTGAATTCTCAATGAGGTAAGAATTAATCTTGTGAGTCCTTTAGG
1 AAAAATAAAATTGAATTCTCAATAAGGTAAGAATTAATCTTGTGAGTCCTTTAGG
12946062 AAAAATAAAATTGAATTCTCAATAAGGTAAGAATTAATCTTGTGAGTCCTTTAG
1 AAAAATAAAATTGAATTCTCAATAAGGTAAGAATTAATCTTGTGAGTCCTTTAG
12946116 AAGTATTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (55 bp):
AAAAATAAAATTGAATTCTCAATAAGGTAAGAATTAATCTTGTGAGTCCTTTAGG
Found at i:12947360 original size:15 final size:16
Alignment explanation
Indices: 12947331--12947360 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12947321 ATTCCCCCTC
12947331 CAAGAAAAAGACTTGG
1 CAAGAAAAAGACTTGG
12947347 CAAGAAAAAG-CTTG
1 CAAGAAAAAGACTTG
12947361 CAGATGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (16 bp):
CAAGAAAAAGACTTGG
Found at i:12952210 original size:6 final size:6
Alignment explanation
Indices: 12952199--12952246 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
12952189 AACAGAAAGG
* * *
12952199 TAAAAT TAAAAT TAAAAA TAAAAA TAAAAA TAAAAA TAAAAG TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
12952247 GAAAGGGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
TAAAAA
Found at i:12957729 original size:39 final size:40
Alignment explanation
Indices: 12957609--12957798 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 40
12957599 GCTGATCGTT
* * * *** * *
12957609 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAGCCCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* * *
12957649 CAAAGGCCTTCGGGACTTAACCCGGATATCGCAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* * *
12957689 CAATTGCCTTCGGG-CTTAGCCCGGATATCACAATTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* * *
12957728 CAAATGCCTTCGGGTCTTAGCCCGGATGT-AGTC-ACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCA--CAACTCGCA
*
12957768 CAAATGTCC-TCGAGACTTAGCCCGGATATCA
1 CAAATG-CCTTCGGGACTTAGCCCGGATATCA
12957799 TTCAATTGCT
Statistics
Matches: 124, Mismatches: 21, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
39 35 0.28
40 85 0.69
41 4 0.03
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
Found at i:12957729 original size:79 final size:80
Alignment explanation
Indices: 12957646--12957798 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 80
12957636 ATGGTAGCCC
* * * *
12957646 GCACAAAGGCCTTCGGGACTTAACCCGGATATCG-CAACTCGCACAATTG-CCTTCG-GGCTTAG
1 GCACAAAGGCCTTCGGGACTTAACCCGGATATAGTC-ACTAGCACAAATGTCC-TCGAGACTTAG
12957708 CCCGGATATCACAATTT
64 CCCGGATATCACAATTT
* * * *
12957725 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTAGCACAAATGTCCTCGAGACTTAGCC
1 GCACAAAGGCCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGTCCTCGAGACTTAGCC
12957790 CGGATATCA
66 CGGATATCA
12957799 TTCAATTGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
79 43 0.68
80 20 0.32
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
GCACAAAGGCCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGTCCTCGAGACTTAGCC
CGGATATCACAATTT
Found at i:12961839 original size:43 final size:43
Alignment explanation
Indices: 12961792--12961937 Score: 231
Period size: 43 Copynumber: 3.4 Consensus size: 43
12961782 TTTAATGTAC
* *
12961792 TGGCATTAAGTGTGCGATACAATTATAGCTTTGGCTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
*
12961835 TGGCACTAAGTGTGC-AGTACAATTATAGCTTCGACTAATTAAT
1 TGGCACTAAGTGTGCGA-TACAATTATAGCTTCGGCTAATTAAT
*
12961878 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGTTAATTAAT
1 TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
*
12961921 TAGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
12961938 GTTCATTGAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 93 0.98
44 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (43 bp):
TGGCACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTAAT
Found at i:12970649 original size:43 final size:42
Alignment explanation
Indices: 12970583--12970712 Score: 102
Period size: 43 Copynumber: 3.0 Consensus size: 42
12970573 TATAGGATTT
* *
12970583 TCGATATGTGTTCT-CATGTAAGACTACGTCTGGGATGTTGGCA
1 TCGATATGTG-ACTACATGCAAGAC-ACGTCTGGGATGTTGGCA
* * * * *
12970626 TCGATATGTGACTACGTGCAAGACCCTGTCCGAGACAG-TGGCA
1 TCGATATGTGACTACATGCAAGACAC-GTCTGGGA-TGTTGGCA
* * * *
12970669 TCTATATGTGATTACATGTAAGACCACGTCTCGGATGTTGGCA
1 TCGATATGTGACTACATGCAAGA-CACGTCTGGGATGTTGGCA
12970712 T
1 T
12970713 TGTACGATAT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
42 4 0.06
43 59 0.89
44 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (42 bp):
TCGATATGTGACTACATGCAAGACACGTCTGGGATGTTGGCA
Found at i:12973227 original size:43 final size:43
Alignment explanation
Indices: 12973174--12973322 Score: 262
Period size: 43 Copynumber: 3.5 Consensus size: 43
12973164 TTATTTGAAA
*
12973174 AAACGCCGCTAAAGGTCATGGCTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
* *
12973217 AAACGTCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
12973260 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
12973303 AAACGCTGCTAAAGGTCATG
1 AAACGCCGCTAAAGGTCATG
12973323 AAATTTTAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:12973449 original size:6 final size:6
Alignment explanation
Indices: 12973438--12973488 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
12973428 ATTCATTATC
* *
12973438 AAATAA AAATAA AAATAA AAATATA GAATCAA AACT-A AAATAA ATAATAA
1 AAATAA AAATAA AAATAA AAATA-A AAAT-AA AAATAA AAATAA A-AATAA
12973488 A
1 A
12973489 CATTAGATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.11
6 19 0.51
7 13 0.35
8 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:12976449 original size:37 final size:37
Alignment explanation
Indices: 12976394--12976485 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
12976384 CTTATTACGA
*
12976394 AGTCTTACCCGGACATAATCTCCACACGTAGTCATCG
1 AGTCCTACCCGGACATAATCTCCACACGTAGTCATCG
*
12976431 AGTCCTACCCGGTCATAATCTCCACACGTAGTCATCG
1 AGTCCTACCCGGACATAATCTCCACACGTAGTCATCG
*
12976468 GGT-CTCACCCGGAACATA
1 AGTCCT-ACCCGG-ACATA
12976486 TTCCAAGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.04
37 43 0.88
38 4 0.08
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (37 bp):
AGTCCTACCCGGACATAATCTCCACACGTAGTCATCG
Found at i:12976640 original size:49 final size:49
Alignment explanation
Indices: 12976581--12976848 Score: 473
Period size: 49 Copynumber: 5.5 Consensus size: 49
12976571 TTTTACATTA
*
12976581 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
12976630 GCCGTTAGGCCTTATCACATATACATACACTTTCACATTCACCACCTCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
12976679 GCCGTTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
12976728 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
12976777 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACCTCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
12976826 GCCATTAGGCCTTATCACATATA
1 GCCATTAGGCCTTATCACATATA
12976849 TATATCTCAT
Statistics
Matches: 211, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 211 1.00
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:12980173 original size:81 final size:81
Alignment explanation
Indices: 12980037--12980187 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 81
12980027 ATTCTGAAGT
* * * * * * * *
12980037 CAACAGCCAAGATACACAAGCATGTGATAAACATCTGCAAAATTTTCCCATTGAAAATTTATTAC
1 CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
12980102 AAATTAAACAATGTAC
66 AAATTAAACAATGTAC
*
12980118 CAACAGCCAAGATACACAAGTAAGTGACAAAGAATAT-CAATAA-ATTCCCACTGAAAATCTATC
1 CAACAGCCAAGATACACAAGCAAGTGACAAA-AATATGCAA-AATATTCCCACTGAAAATCTATC
12980181 ACAAATT
64 ACAAATT
12980188 CAAAAAGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
81 54 0.92
82 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (81 bp):
CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
AAATTAAACAATGTAC
Found at i:12983136 original size:24 final size:24
Alignment explanation
Indices: 12983108--12983156 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12983098 CCAAAATAAC
12983108 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
12983132 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
12983156 A
1 A
12983157 TAAATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:12983159 original size:11 final size:12
Alignment explanation
Indices: 12983115--12983160 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
12983105 AACAATTAAT
12983115 TTTTATATAAAC
1 TTTTATATAAAC
* * *
12983127 TTTTAAATTAAT
1 TTTTATATAAAC
12983139 TTTTATATAAAC
1 TTTTATATAAAC
12983151 TTTTA-ATAAA
1 TTTTATATAAA
12983161 TATATGAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTATATAAAC
Found at i:12983814 original size:41 final size:41
Alignment explanation
Indices: 12983769--12984060 Score: 365
Period size: 41 Copynumber: 7.1 Consensus size: 41
12983759 TTACATGACT
* * *
12983769 TTTAGTGGCATTTTACCAAAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
*
12983810 TTTAGCAGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
* * * *
12983851 CTTAGCGGCGTTTCACCAAAAGCGCCGCTGATGCTCTGGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
* * *
12983892 TTTAGCGGCGTTTCACCAAAAGCACCGCTGATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
* * *
12983933 TTTAGCGGCGTTTCACCAAAAGCACCGCTGATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
* * *
12983974 TTTAGAGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
* * *
12984014 TTTAGCGGCGTTTTAACAAAAAACGCCGCT-ATTGCTC-AGTT
1 TTTAGCGGCGTTTT-ACCAAAAGCGCCGCTGA-TGCTCTAGTC
12984055 TTTAGC
1 TTTAGC
12984061 AAAAATGCCG
Statistics
Matches: 228, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
40 16 0.07
41 212 0.93
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTGATGCTCTAGTC
Found at i:12984088 original size:30 final size:31
Alignment explanation
Indices: 12984023--12984088 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
12984013 TTTTAGCGGC
12984023 GTTTTAACAAAAAACGCCGCTATTGCTCAGT
1 GTTTTAACAAAAAACGCCGCTATTGCTCAGT
* * **
12984054 -TTTTAGC-AAAAATGCCGCTATTGCTTTGT
1 GTTTTAACAAAAAACGCCGCTATTGCTCAGT
12984083 GTTTTA
1 GTTTTA
12984089 CAATTTTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (31 bp):
GTTTTAACAAAAAACGCCGCTATTGCTCAGT
Found at i:12985361 original size:25 final size:25
Alignment explanation
Indices: 12985333--12985392 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
12985323 CTTTATAATA
12985333 TGAAAATGACTATTTTGCCCCTAGG
1 TGAAAATGACTATTTTGCCCCTAGG
12985358 TGAAAATGACTATTTTGCCCCTAGG
1 TGAAAATGACTATTTTGCCCCTAGG
*
12985383 TAAAAATGAC
1 TGAAAATGAC
12985393 CATTATACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (25 bp):
TGAAAATGACTATTTTGCCCCTAGG
Found at i:12985468 original size:20 final size:20
Alignment explanation
Indices: 12985435--12985489 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
12985425 ATACGTGGGA
12985435 TATGATAT--ACATGA-ATG
1 TATGATATGCACATGATATG
*
12985452 ATATGATGTGCACATGATATG
1 -TATGATATGCACATGATATG
12985473 TATGATATGCACATGAT
1 TATGATATGCACATGAT
12985490 GTAATCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.22
20 22 0.69
21 3 0.09
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:12985617 original size:52 final size:50
Alignment explanation
Indices: 12985539--12985661 Score: 194
Period size: 52 Copynumber: 2.4 Consensus size: 50
12985529 GAGGAAGTGC
12985539 AAAAGGGCTTATGACCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATG-CCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
12985591 AAAAGGGCTTATGCCCTAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCC-AGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
*
12985642 AAAAAGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATG-CCCAGTT
12985662 ATTAAAGAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
50 6 0.09
51 30 0.44
52 32 0.47
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (50 bp):
AAAAGGGCTTATGCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:12985636 original size:25 final size:26
Alignment explanation
Indices: 12985539--12985661 Score: 169
Period size: 26 Copynumber: 4.8 Consensus size: 26
12985529 GAGGAAGTGC
* **
12985539 AAAAGGGCTTATGACCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
12985565 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
12985591 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
12985617 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
12985642 AAAAAGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
12985662 ATTAAAGAGG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 31 0.36
26 56 0.64
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:12990375 original size:44 final size:44
Alignment explanation
Indices: 12990312--12990399 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
12990302 ATATGGCTAT
**
12990312 GAGTAATGTATGATGAGACTTAACGTGGTAAACTCCCCGTTGAA
1 GAGTAATGTATGATGAGACTTAACGTCATAAACTCCCCGTTGAA
*
12990356 GAGTAATGTATGATGAGACTTAACGTCATAAACTCCCGGTTGAA
1 GAGTAATGTATGATGAGACTTAACGTCATAAACTCCCCGTTGAA
12990400 CCTTGAGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (44 bp):
GAGTAATGTATGATGAGACTTAACGTCATAAACTCCCCGTTGAA
Found at i:12990529 original size:50 final size:48
Alignment explanation
Indices: 12990453--12990626 Score: 170
Period size: 50 Copynumber: 3.6 Consensus size: 48
12990443 CATGTGTGCT
* *
12990453 AGTGTAAGA-CAAGTCTAGGACATGGCATCGGCATTGACAGAGAAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-AGAG-AGAGCC
* * * *
12990502 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-AGA-GAGAGCC
* * * * * * * *
12990552 ATTGTAGGACCATGTCTGGGACATGGCATCGACTTTGATGTGTGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAAGAGAGAGCC
*
12990600 AGTGTAAGACAATGTCTGGGACATGGC
1 AGTGTAAGACCATGTCTGGGACATGGC
12990627 GTTGGCATCT
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 28 0.27
49 9 0.09
50 64 0.63
51 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAAGAGAGAGCC
Found at i:13010430 original size:206 final size:205
Alignment explanation
Indices: 13010065--13010620 Score: 806
Period size: 206 Copynumber: 2.7 Consensus size: 205
13010055 GCAGATCTGG
*
13010065 CTAAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAATAAATCGAAGACATAGCT
1 CTAAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA-ACATAGCT
* * *
13010130 GATTTGGCTTTCACGTGCTTACGATAAAGTAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
64 GATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
13010195 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACAGAGAGTAGATACATAGCAGATCTAGCCTT
129 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTT
* *
13010260 CAGATGTTTATA
194 CAGATGATTAGA
* *
13010272 CTAAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAATCATAGCTG
1 CTAAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAA-CATAGCTG
* * *
13010337 ACTTAGCTTTCACGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGA
65 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * *
13010402 GAACAAATCGAAGTTTGGCATTTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
130 GAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTTC
13010467 AGATGATTAGA
195 AGATGATTAGA
* * * * *
13010478 CTGAAGCAAATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCAAAGACATAGCTG
1 CTAAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA-ACATAGCTG
* ** * *
13010543 ATTTGGTTTTTGCGTGCTAACGCTGAAGCAAATCTAAGATGATTTGACATCTCTGTATTGTCAGA
65 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
13010608 GAACAAATTGAAG
130 GAACAAATCGAAG
13010621 AAGCATATTT
Statistics
Matches: 312, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
205 1 0.00
206 303 0.97
207 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (205 bp):
CTAAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAACATAGCTGA
TTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
AACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTTCA
GATGATTAGA
Found at i:13016076 original size:138 final size:138
Alignment explanation
Indices: 13015821--13016097 Score: 473
Period size: 138 Copynumber: 2.0 Consensus size: 138
13015811 AAACAAAGAG
* * *
13015821 TGGTTTGTTTTATAGTCCAAAAGAGCAAACAGTAATAGTGTCGACTCATGCTATTTTCCTTGAGG
1 TGGTTTATTTTATAGTCCAAAAGAGCAAACAGTAATAGTGTCAACTCATGCTACTTTCCTTGAGG
* *
13015886 AAAGTTACATGAACGACTTTAAACCTCCAAGTAAAAAAGTACTCGAGGAACTTTTGGGAAATACA
66 AAAATTACATGAACGACTTTAAACCTCCAAGTAAAAAAGTACTCGAGAAACTTTTGGGAAATACA
13015951 CAAAGCCC
131 CAAAGCCC
*
13015959 TGGTTTATTTTATAGTCCAAAAGAGCAAATAGTAATAGTGTCAACTCATGCTACTTTCCTTGAGG
1 TGGTTTATTTTATAGTCCAAAAGAGCAAACAGTAATAGTGTCAACTCATGCTACTTTCCTTGAGG
* * *
13016024 AAAATTACATGAATGACTTTAAACCTCGAAGTAAAAAAGTACTTGAGAAACTTTTGGGAAATACA
66 AAAATTACATGAACGACTTTAAACCTCCAAGTAAAAAAGTACTCGAGAAACTTTTGGGAAATACA
13016089 CAAAGCCC
131 CAAAGCCC
13016097 T
1 T
13016098 ATAGAAATGG
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (138 bp):
TGGTTTATTTTATAGTCCAAAAGAGCAAACAGTAATAGTGTCAACTCATGCTACTTTCCTTGAGG
AAAATTACATGAACGACTTTAAACCTCCAAGTAAAAAAGTACTCGAGAAACTTTTGGGAAATACA
CAAAGCCC
Found at i:13019057 original size:28 final size:28
Alignment explanation
Indices: 13018992--13019092 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
13018982 ATAGTGAATC
*
13018992 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
13019021 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
13019049 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
13019079 CGCACACTTAGTGC
1 CGCACACTTAGTGC
13019093 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13019141 original size:29 final size:29
Alignment explanation
Indices: 13019080--13019210 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
13019070 TTTTAAACCC
*** *
13019080 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
13019108 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
13019138 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
13019167 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
13019196 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
13019211 ATCTCGTCAC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:13022103 original size:40 final size:40
Alignment explanation
Indices: 13022058--13022225 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
13022048 CGGAATATAA
*
13022058 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
13022098 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
13022138 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
13022178 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
13022218 CCGGATAT
1 CCGGATAT
13022226 CATTCAATTT
Statistics
Matches: 103, Mismatches: 24, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
40 102 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:13022208 original size:80 final size:80
Alignment explanation
Indices: 13022074--13022223 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
13022064 ATAACCATGT
* *
13022074 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
13022139 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
13022154 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
13022217 CCCGGAT
64 CCCGGAT
13022224 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:13030101 original size:40 final size:40
Alignment explanation
Indices: 13030056--13030222 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
13030046 CGGAATATAA
*
13030056 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
13030096 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
13030136 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
13030176 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
13030215 CCGGATAT
1 CCGGATAT
13030223 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 13 0.13
40 89 0.86
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:13038162 original size:28 final size:28
Alignment explanation
Indices: 13038095--13038196 Score: 114
Period size: 30 Copynumber: 3.5 Consensus size: 28
13038085 ATAGTGAATC
* *
13038095 CGCACACTTAGTGCTATATGTATTCAGACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
13038125 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
13038153 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
13038183 CGCACACTTAGTGC
1 CGCACACTTAGTGC
13038197 CATACCCTNG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
28 27 0.42
30 37 0.58
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13045607 original size:14 final size:14
Alignment explanation
Indices: 13045584--13045613 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13045574 TTGAAAATAT
13045584 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
13045598 GTTGATTTGGATTG
1 GTTGAATTGGATTG
13045612 GT
1 GT
13045614 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:13063073 original size:39 final size:39
Alignment explanation
Indices: 13063019--13063108 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
13063009 ACTCAGTGAT
* *
13063019 GAATTATATCTGGACTTAAGGTCCACAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCACAGGCTATATGCTG
*
13063058 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCACAGGCTATATGCTG
*
13063097 G-ATTACGTCCGG
1 GAATTATGTCCGG
13063109 GCTAAAGTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 10 0.21
39 37 0.79
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (39 bp):
GAATTATGTCCGGACTTAAGGTCCACAGGCTATATGCTG
Found at i:13063122 original size:38 final size:39
Alignment explanation
Indices: 13063030--13063126 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 39
13063020 AATTATATCT
* * *
13063030 GGACTTAAGGTCCACAGGCTATATGCTGGAATTATGTCC
1 GGACTTAAAGTCCGCAGGCTATATGCTGGAATTACGTCC
*
13063069 GGACTTAAGGTCCGCAGGCTATATGCTGG-ATTACGTCC
1 GGACTTAAAGTCCGCAGGCTATATGCTGGAATTACGTCC
*
13063107 GGGC-TAAAGTCCCGCAGGCT
1 GGACTTAAAGT-CCGCAGGCT
13063127 TCGAGCTGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.09
38 20 0.38
39 28 0.53
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
GGACTTAAAGTCCGCAGGCTATATGCTGGAATTACGTCC
Found at i:13063135 original size:38 final size:39
Alignment explanation
Indices: 13063105--13063178 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
13063095 TGGATTACGT
13063105 CCGGG-CTAAAGTCCCGCAGGCTTCGAGCTGGTATTATA
1 CCGGGTCTAAAGTCCCGCAGGCTTCGAGCTGGTATTATA
* * *
13063143 CCGGGTTTAAATTCCCGCAGGCTT-GTGCTGGTATTA
1 CCGGGTCTAAAGTCCCGCAGGCTTCGAGCTGGTATTA
13063179 ATTTCAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 16 0.50
39 16 0.50
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (39 bp):
CCGGGTCTAAAGTCCCGCAGGCTTCGAGCTGGTATTATA
Found at i:13071149 original size:40 final size:40
Alignment explanation
Indices: 13071090--13071231 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
13071080 AAATTGAATG
* * *
13071090 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
13071130 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
13071170 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
13071210 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
13071232 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:13071232 original size:40 final size:39
Alignment explanation
Indices: 13071129--13071257 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
13071119 TGCTGGAAAT
* * *
13071129 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
13071169 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
13071209 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ATGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
13071249 TATATCCGG
1 TATATCCGG
13071258 TTATATTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:13079153 original size:40 final size:40
Alignment explanation
Indices: 13079094--13079235 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
13079084 AAATTGAATG
* * *
13079094 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
13079134 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
13079174 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
13079214 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
13079236 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:13079236 original size:40 final size:39
Alignment explanation
Indices: 13079133--13079261 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
13079123 TGCTGGAAAT
* * *
13079133 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
13079173 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
13079213 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
13079253 TATATCCGG
1 TATATCCGG
13079262 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:13084783 original size:28 final size:28
Alignment explanation
Indices: 13084718--13084818 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
13084708 ATAGTGAATC
*
13084718 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
13084747 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
13084775 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
13084805 CGCACACTTAGTGC
1 CGCACACTTAGTGC
13084819 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13084867 original size:29 final size:29
Alignment explanation
Indices: 13084806--13084936 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
13084796 TTTTAAACCC
*** *
13084806 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
13084834 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
13084864 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
13084893 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
13084922 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
13084937 ATCTCGTCAC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:13094076 original size:46 final size:46
Alignment explanation
Indices: 13093933--13094076 Score: 122
Period size: 46 Copynumber: 3.1 Consensus size: 46
13093923 CCCACCCATA
* *
13093933 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTC-A---ACCATC-CT
* * *
13093982 --TGAACTCGGACTCAACTCAACGAGTTCAGACAT-TTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCAG--ATGCT-CAACCATCCT
13094026 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
13094072 AGTGA
1 AGTGA
13094077 CATGTCACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
44 8 0.10
45 1 0.01
46 34 0.44
47 30 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
Found at i:13100777 original size:17 final size:18
Alignment explanation
Indices: 13100740--13100783 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
13100730 GTTGGAAGAT
*
13100740 AAAAGTAAATAAACAATG
1 AAAAGTAAATAAACAAAG
*
13100758 AAAAG-AAATAAATAAAG
1 AAAAGTAAATAAACAAAG
*
13100775 AAAAATAAA
1 AAAAGTAAA
13100784 CAAATGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAGTAAATAAACAAAG
Found at i:13103123 original size:17 final size:18
Alignment explanation
Indices: 13103101--13103134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13103091 CACATTGAAG
13103101 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
13103118 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
13103135 CTTCTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:13107555 original size:37 final size:37
Alignment explanation
Indices: 13107502--13107678 Score: 327
Period size: 37 Copynumber: 4.8 Consensus size: 37
13107492 TCGAATAGTC
* *
13107502 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
13107539 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
13107576 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
13107613 CCACACGTAGTCATCGGGTCTTACTCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
13107650 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
13107679 ATATATTTCC
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:13107905 original size:48 final size:48
Alignment explanation
Indices: 13107848--13108399 Score: 978
Period size: 48 Copynumber: 11.5 Consensus size: 48
13107838 CTAGCCGAAT
* **
13107848 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTTG
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* * *
13107896 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* * * *
13107944 CATTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* * *
13107992 CATTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108040 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108088 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
*
13108136 CATTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108184 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108232 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108280 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108328 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13108376 CACTAGCCATTCGGCTTTACCACA
1 CACTAGCCATTCGGCTTTACCACA
13108400 CACATATATA
Statistics
Matches: 495, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 495 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (48 bp):
CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
Found at i:13111988 original size:29 final size:29
Alignment explanation
Indices: 13111935--13112064 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
13111925 TGATTTCGCA
* * *
13111935 CACACATAGCG-CTCGATTATAGAACTCG
1 CACACATAGTGCCTCAATTAAAGAACTCG
13111963 CACACATAGTGCCTCAATTAAAGAACTCG
1 CACACATAGTGCCTCAATTAAAGAACTCG
* *
13111992 CACACATAGTGCCTCAATTACCA-ATCTCG
1 CACACATAGTGCCTCAATTA-AAGAACTCG
* * * *
13112021 CACACATAGCG-CTCGATTGAAGAACTTG
1 CACACATAGTGCCTCAATTAAAGAACTCG
*
13112049 CACACACAGTGCCTCA
1 CACACATAGTGCCTCA
13112065 TAATTCCAGC
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.01
28 29 0.35
29 53 0.63
30 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (29 bp):
CACACATAGTGCCTCAATTAAAGAACTCG
Found at i:13112000 original size:57 final size:57
Alignment explanation
Indices: 13111935--13112064 Score: 138
Period size: 57 Copynumber: 2.3 Consensus size: 57
13111925 TGATTTCGCA
* * *
13111935 CACACATAGCG-CTCGATTA-TAGAACTCGCACACATAGTGCCTCAATTAAAGAACTCG
1 CACACATAGCGCCTCAATTACCA-AACTCGCACACATAGCG-CTCAATTAAAGAACTCG
* * * * *
13111992 CACACATAGTGCCTCAATTACCAATCTCGCACACATAGCGCTCGATTGAAGAACTTG
1 CACACATAGCGCCTCAATTACCAAACTCGCACACATAGCGCTCAATTAAAGAACTCG
* *
13112049 CACACACAGTGCCTCA
1 CACACATAGCGCCTCA
13112065 TAATTCCAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 39 0.63
58 22 0.35
59 1 0.02
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (57 bp):
CACACATAGCGCCTCAATTACCAAACTCGCACACATAGCGCTCAATTAAAGAACTCG
Found at i:13112137 original size:40 final size:40
Alignment explanation
Indices: 13112072--13112306 Score: 348
Period size: 40 Copynumber: 5.9 Consensus size: 40
13112062 TCATAATTCC
*
13112072 AGCACGAATGC-CTTCGAGG-TTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCACT
*
13112111 AGCACGAATGCTCTTCGGGACTTAGCCCAGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
*
13112151 AGCACGAATGCTCTTCAGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* * * *
13112191 ACCACGAATGCTCTTCGGGACTTAGCCCGGACATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* * *
13112231 AGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
*
13112271 AGCACGAATGCTCTTCGGGACTTAGCCCGGCTATAT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
13112307 AACTCTCAAT
Statistics
Matches: 181, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 13 0.07
40 168 0.93
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
Found at i:13113633 original size:37 final size:37
Alignment explanation
Indices: 13113580--13113804 Score: 380
Period size: 37 Copynumber: 6.1 Consensus size: 37
13113570 CGAATAGTCC
*
13113580 CCACACGTAG-CTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTC-ATCGGGTCTTACCCGGACATAATCT
* *
13113617 CTACACGTAGTCATCGGGACTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
13113654 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
13113691 CCACATGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
13113728 CCACACGTAGTCATCGGGTCTTACTCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
13113765 CTACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
13113802 CCA
1 CCA
13113805 AGTTTCATGT
Statistics
Matches: 176, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
37 175 0.99
38 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:13114020 original size:48 final size:48
Alignment explanation
Indices: 13113963--13114562 Score: 1092
Period size: 48 Copynumber: 12.5 Consensus size: 48
13113953 CTAGCCGAAT
* *
13113963 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* * *
13114011 CATTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* *
13114059 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
* *
13114107 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114155 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114203 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114251 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
*
13114299 CACTAGCCATTCGGTTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114347 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114395 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
13114443 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
*
13114491 CATTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
*
13114539 CATTAGCCATTCGGCTTTACCACA
1 CACTAGCCATTCGGCTTTACCACA
13114563 CACATATATA
Statistics
Matches: 543, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 543 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.32
Consensus pattern (48 bp):
CACTAGCCATTCGGCTTTACCACATATACACATCTCATACATATTTCA
Found at i:13116888 original size:29 final size:28
Alignment explanation
Indices: 13116786--13116888 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 28
13116776 GTGACAAGAT
*
13116786 TGGCACTAAGTGTGCAAGCTTGAAA-AGTA
1 TGGCACTAAGTGTGCGAGCTT-AAATA-TA
**
13116815 TGGCACTAAGTGTGCGAATTTAAATTATA
1 TGGCACTAAGTGTGCGAGCTTAAA-TATA
* *
13116844 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCGAGCTTAAAT-ATA
13116873 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
13116889 TGATCGATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.06
29 58 0.92
30 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTAAATATA
Found at i:13120580 original size:13 final size:13
Alignment explanation
Indices: 13120558--13120590 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13120548 AAGGGTTTGT
13120558 TTAT-TAAACTAA
1 TTATCTAAACTAA
13120570 TTATCTAAACTAA
1 TTATCTAAACTAA
*
13120583 TTAACTAA
1 TTATCTAA
13120591 TTTAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:13125161 original size:29 final size:28
Alignment explanation
Indices: 13125119--13125210 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
13125109 ATCCATACTT
* *
13125119 ATTCATTTGGCCCATTTAGGCCCAATCTC
1 ATTCATATGGCCCA-TCAGGCCCAATCTC
* * *
13125148 ATTCATATGGCCCATCAGACCTAATCAC
1 ATTCATATGGCCCATCAGGCCCAATCTC
* *
13125176 TTTCATATGGCCCGTCAGGCCCAATCAT-
1 ATTCATATGGCCCATCAGGCCCAATC-TC
13125204 ATTCATA
1 ATTCATA
13125211 GTCATGCAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 38 0.75
29 13 0.25
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (28 bp):
ATTCATATGGCCCATCAGGCCCAATCTC
Found at i:13133015 original size:28 final size:28
Alignment explanation
Indices: 13132979--13133053 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
13132969 TCGCCCCTTT
*
13132979 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* * **
13133007 AGGCCCAATCACTTTCATATGGTCGGTC
1 AGGCCCAATCACATTCATATGGCCCATC
*
13133035 AAGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
13133054 GTCATGGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:13133290 original size:16 final size:16
Alignment explanation
Indices: 13133269--13133300 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13133259 CCAAACTTCT
13133269 AGCTTTTCGGCATTTC
1 AGCTTTTCGGCATTTC
13133285 AGCTTTTCGGCATTTC
1 AGCTTTTCGGCATTTC
13133301 TGGATTTGCC
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:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
AGCTTTTCGGCATTTC
Found at i:13137968 original size:57 final size:58
Alignment explanation
Indices: 13137902--13138038 Score: 168
Period size: 57 Copynumber: 2.4 Consensus size: 58
13137892 CATATAACAT
** * *
13137902 GATTACCAGTCCAGGCTAAATCCTTTTTGTAATATATGCTCAAAAGAG-CTCAATTAG
1 GATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCAAAAGAGACTCAATCAG
* * * * **
13137959 GATTACCAGTCCAGGCCAAATCCTAATTGTAACATATGCTCAAGAGGGATTTTATCAG
1 GATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCAAAAGAGACTCAATCAG
*
13138017 GATTACCGGTCCAGGCTAAATC
1 GATTACCAGTCCAGGCTAAATC
13138039 TCGTCAGCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 42 0.63
58 25 0.37
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (58 bp):
GATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCAAAAGAGACTCAATCAG
Found at i:13138433 original size:13 final size:13
Alignment explanation
Indices: 13138415--13138439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13138405 TGAAGAAGAC
13138415 ATAAAATAAGATG
1 ATAAAATAAGATG
13138428 ATAAAATAAGAT
1 ATAAAATAAGAT
13138440 TATATTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
ATAAAATAAGATG
Found at i:13146463 original size:17 final size:17
Alignment explanation
Indices: 13146441--13146478 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
13146431 CATTAGCGAG
* *
13146441 TGTGTGACACATAATCC
1 TGTGTGACACACAATCA
13146458 TGTGTGACACACAATCA
1 TGTGTGACACACAATCA
13146475 TGTG
1 TGTG
13146479 CCAAACTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (17 bp):
TGTGTGACACACAATCA
Found at i:13152264 original size:38 final size:40
Alignment explanation
Indices: 13152152--13152335 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
13152142 TCGAATGATG
* *
13152152 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
13152192 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
13152232 TTCGGGCTAAG-CCTGAAGGCA-TGGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
13152270 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
13152311 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
13152336 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 23 0.19
39 17 0.14
40 71 0.59
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:13152316 original size:78 final size:79
Alignment explanation
Indices: 13152153--13152332 Score: 213
Period size: 78 Copynumber: 2.3 Consensus size: 79
13152143 CGAATGATGT
* * * * *
13152153 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATGGTGC-GAGTTATTAAATCCGGACTAAGATCCGAAGGCATTTG
*
13152218 TGCGAGTTACTAATT
65 TGCGAGTTACTAATA
* * **
13152233 TCGGGCTAAG-CCTGAAGGCATGGTGCGAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATGGTGCGAGTTATTAAATCCGGACTAAGAT-CCGAAGGCATTTG
13152296 TGCGAGTTACT-ATAA
65 TGCGAGTTACTAAT-A
*
13152311 CCGGGCTATGTCCCGAAGGCAT
1 CCGGGCTAAGTCCCGAAGGCAT
13152333 TTGAACGAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 3 0.04
78 49 0.58
79 23 0.27
80 9 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATGGTGCGAGTTATTAAATCCGGACTAAGATCCGAAGGCATTTGT
GCGAGTTACTAATA
Found at i:13152368 original size:118 final size:118
Alignment explanation
Indices: 13152152--13152368 Score: 246
Period size: 118 Copynumber: 1.8 Consensus size: 118
13152142 TCGAATGATG
13152152 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
** * * * *
13152217 GTGCGAGTTACTAATTTCGGGCTAAGCCTGAAGGCATGGTGCGAGTTATTAAA
66 GAACGAGTTACTAATATCCGGCTAAACCCGAAGGCATGGTGCGAGTTATTAAA
* * * * *
13152270 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTA-AATCCGGACTAAGAT-CCGAAGGCA
*
13152332 TTTGAACGAG-TAGCT-ATATCCGGTTAAACTCCGAAGG
63 TTTGAACGAGTTA-CTAATATCCGGCTAAAC-CCGAAGG
13152369 TACGTGATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
117 13 0.16
118 60 0.73
119 9 0.11
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAATATCCGGCTAAACCCGAAGGCATGGTGCGAGTTATTAAA
Found at i:13163106 original size:14 final size:14
Alignment explanation
Indices: 13163087--13163116 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13163077 AGTAAATCGT
13163087 AATAAACAGCATAA
1 AATAAACAGCATAA
*
13163101 AATAAACAGTATAA
1 AATAAACAGCATAA
13163115 AA
1 AA
13163117 CAACAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (14 bp):
AATAAACAGCATAA
Done.