Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 14 of 356
Found at i:4872663 original size:13 final size:14
Alignment explanation
Indices: 4872645--4872680 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4872635 ATATCTCATA
4872645 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
4872658 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
4872671 TCTC-ATTTCA
1 TCTCAATTTCA
4872681 TTCCAATAGC
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:4873337 original size:15 final size:15
Alignment explanation
Indices: 4873317--4873360 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4873307 TATTATATTT
4873317 CAATCAATATAAATC
1 CAATCAATATAAATC
* * * *
4873332 CAATCAAAATGATTT
1 CAATCAATATAAATC
4873347 CAATCAATATAAAT
1 CAATCAATATAAAT
4873361 TTGATAAATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (15 bp):
CAATCAATATAAATC
Found at i:4874876 original size:13 final size:14
Alignment explanation
Indices: 4874858--4874886 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4874848 GATTAACTTC
4874858 ATAAATATTTT-TA
1 ATAAATATTTTCTA
4874871 ATAAATATTTTCTA
1 ATAAATATTTTCTA
4874885 AT
1 AT
4874887 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:4875290 original size:16 final size:17
Alignment explanation
Indices: 4875271--4875309 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4875261 TATTTTTATT
4875271 AAATTATTA--TATAATA
1 AAATTATTAGTTAT-ATA
4875287 AAATTATTAGTTATATA
1 AAATTATTAGTTATATA
4875304 AAATTA
1 AAATTA
4875310 AAATTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 9 0.43
18 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTATTAGTTATATA
Found at i:4875414 original size:7 final size:7
Alignment explanation
Indices: 4875402--4875439 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
4875392 ACCAAGAGAA
4875402 AAACATT
1 AAACATT
4875409 AAACATT
1 AAACATT
4875416 AAACATT
1 AAACATT
*
4875423 AAATATT
1 AAACATT
*
4875430 AAATATT
1 AAACATT
4875437 AAA
1 AAA
4875440 AGCACCGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (7 bp):
AAACATT
Found at i:4879641 original size:51 final size:51
Alignment explanation
Indices: 4879578--4879680 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
4879568 GAAACTCTGT
* * *
4879578 CGGATCCGATTTCTCGTCAAACGTATGATTATGAATTGG-GCTTGGTTAATC
1 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAG-TTGGTTAATC
4879629 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
1 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
4879680 C
1 C
4879681 AATGGGGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (51 bp):
CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
Found at i:4883769 original size:21 final size:21
Alignment explanation
Indices: 4883745--4883800 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
4883735 AATAAAATTG
4883745 ATTTTTTATTTAATATGAT-TA
1 ATTTTTTATTTAAT-TGATATA
** *
4883766 ATTTTAAAATTTTATTGATATA
1 ATTTT-TTATTTAATTGATATA
4883788 ATTTTTTATTTAA
1 ATTTTTTATTTAA
4883801 AATAATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTTTATTTAATTGATATA
Found at i:4893893 original size:15 final size:16
Alignment explanation
Indices: 4893873--4893902 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4893863 TTAAATAACT
4893873 ATTTTGTAA-TTTTTC
1 ATTTTGTAAGTTTTTC
4893888 ATTTTGTAAGTTTTT
1 ATTTTGTAAGTTTTT
4893903 ATAATGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (16 bp):
ATTTTGTAAGTTTTTC
Found at i:4913846 original size:17 final size:15
Alignment explanation
Indices: 4913826--4913859 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
4913816 CCATTTTCAC
4913826 TTTGCTTCTTTTTTCTT
1 TTTGCTT-TTTTTT-TT
4913843 TTTGCTTTTTTTTTT
1 TTTGCTTTTTTTTTT
4913858 TT
1 TT
4913860 AATCTTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTGCTTTTTTTTTT
Found at i:4916167 original size:35 final size:35
Alignment explanation
Indices: 4916121--4916193 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
4916111 TCCCTTGTCA
4916121 ATCCTTTTGTCATCTTATAAAATATCGAATTCAAG
1 ATCCTTTTGTCATCTTATAAAATATCGAATTCAAG
4916156 ATCCTTTTGTCATCTTATAAAATATCGAATTCAAG
1 ATCCTTTTGTCATCTTATAAAATATCGAATTCAAG
4916191 ATC
1 ATC
4916194 AAGATTCGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (35 bp):
ATCCTTTTGTCATCTTATAAAATATCGAATTCAAG
Found at i:4922313 original size:5 final size:6
Alignment explanation
Indices: 4922296--4922320 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4922286 TGTCGATTTC
4922296 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
4922321 TTCTCGTATT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:4927882 original size:26 final size:26
Alignment explanation
Indices: 4927816--4927883 Score: 66
Period size: 31 Copynumber: 2.4 Consensus size: 26
4927806 TAGACGAAAA
*
4927816 TTTTAATATAATGATTAAATTATATTTT
1 TTTTATTATAATGATTAAATTATA--TT
4927844 TTCTTATCATATAATGATTAAATTATCA-T
1 TT-TTAT--TATAATGATTAAATTAT-ATT
4927873 TTTTATTATAA
1 TTTTATTATAA
4927884 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
26 5 0.14
28 6 0.17
29 6 0.17
31 17 0.49
32 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (26 bp):
TTTTATTATAATGATTAAATTATATT
Found at i:4930095 original size:20 final size:20
Alignment explanation
Indices: 4930066--4930109 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4930056 TGTAAACAAT
4930066 CCAAACCAAGTTTAATTGTA
1 CCAAACCAAGTTTAATTGTA
* *
4930086 CCAAATCAAGTTTAATTGTG
1 CCAAACCAAGTTTAATTGTA
4930106 CCAA
1 CCAA
4930110 TTAAATGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
CCAAACCAAGTTTAATTGTA
Found at i:4930917 original size:21 final size:21
Alignment explanation
Indices: 4930892--4930960 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4930882 TATAATGATT
4930892 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4930913 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4930933 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4930953 ATTATTAT
1 ATTATTAT
4930961 TAAATAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4931096 original size:8 final size:8
Alignment explanation
Indices: 4931083--4931108 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4931073 ATATTTGTTA
4931083 ATTAAATT
1 ATTAAATT
4931091 ATTAAATT
1 ATTAAATT
4931099 ATTAAATT
1 ATTAAATT
4931107 AT
1 AT
4931109 GAGATTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTAAATT
Found at i:4932099 original size:12 final size:12
Alignment explanation
Indices: 4932082--4932124 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4932072 AGAAAGAATG
4932082 TATGAACTAAAT
1 TATGAACTAAAT
* *
4932094 TATGAATTGAAT
1 TATGAACTAAAT
4932106 GTATGAACTAAAT
1 -TATGAACTAAAT
4932119 TATGAA
1 TATGAA
4932125 TTGAGTTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (12 bp):
TATGAACTAAAT
Found at i:4932105 original size:25 final size:25
Alignment explanation
Indices: 4932077--4932128 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4932067 GTACGAGAAA
4932077 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4932102 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4932127 GA
1 GA
4932129 GTTAGAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
GAATGTATGAACTAAATTATGAATT
Found at i:4932112 original size:13 final size:12
Alignment explanation
Indices: 4932077--4932124 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4932067 GTACGAGAAA
4932077 GAATGTATGAACT
1 GAAT-TATGAACT
* *
4932090 AAATTATGAATT
1 GAATTATGAACT
4932102 GAATGTATGAACT
1 GAAT-TATGAACT
*
4932115 AAATTATGAA
1 GAATTATGAA
4932125 TTGAGTTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (12 bp):
GAATTATGAACT
Found at i:4938027 original size:21 final size:21
Alignment explanation
Indices: 4938002--4938070 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
4937992 TATAATGATT
4938002 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4938023 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* * *
4938043 A-CATTATGGTTTAATATTAG
1 ATTATTATGGTTTTATATTAA
4938063 ATTATTAT
1 ATTATTAT
4938071 TATTAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 2 0.06
19 10 0.28
20 3 0.08
21 18 0.50
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4938208 original size:8 final size:8
Alignment explanation
Indices: 4938195--4938220 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4938185 GATATTGTTA
4938195 ATTAAATT
1 ATTAAATT
4938203 ATTAAATT
1 ATTAAATT
4938211 ATTAAATT
1 ATTAAATT
4938219 AT
1 AT
4938221 GAGATTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTAAATT
Found at i:4938301 original size:24 final size:23
Alignment explanation
Indices: 4938241--4938310 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
4938231 TTTGAGAAAC
*
4938241 AAATTAAATA-ATG-ACAAATGT
1 AAATTAAATATGTGTACAAATGT
*
4938262 -AATAAAATTATG-GTACAAATGT
1 AAATTAAA-TATGTGTACAAATGT
*
4938284 AGAATTAAATATGTGTACAATTGT
1 A-AATTAAATATGTGTACAAATGT
4938308 AAA
1 AAA
4938311 ATATGTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 6 0.15
21 3 0.08
22 8 0.21
23 6 0.15
24 16 0.41
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (23 bp):
AAATTAAATATGTGTACAAATGT
Found at i:4939209 original size:12 final size:12
Alignment explanation
Indices: 4939192--4939234 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4939182 AGAAAGAATG
4939192 TATGAACTAAAT
1 TATGAACTAAAT
* *
4939204 TATGAATTGAAT
1 TATGAACTAAAT
4939216 GTATGAACTAAAT
1 -TATGAACTAAAT
4939229 TATGAA
1 TATGAA
4939235 TTGAGTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (12 bp):
TATGAACTAAAT
Found at i:4939215 original size:25 final size:25
Alignment explanation
Indices: 4939187--4939238 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4939177 GTACGAGAAA
4939187 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4939212 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4939237 GA
1 GA
4939239 GTTAGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
GAATGTATGAACTAAATTATGAATT
Found at i:4939222 original size:13 final size:12
Alignment explanation
Indices: 4939187--4939234 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4939177 GTACGAGAAA
4939187 GAATGTATGAACT
1 GAAT-TATGAACT
* *
4939200 AAATTATGAATT
1 GAATTATGAACT
4939212 GAATGTATGAACT
1 GAAT-TATGAACT
*
4939225 AAATTATGAA
1 GAATTATGAA
4939235 TTGAGTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (12 bp):
GAATTATGAACT
Found at i:4942778 original size:19 final size:19
Alignment explanation
Indices: 4942754--4942791 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4942744 CCTAAATGGA
4942754 TCAATGATATGTTATAAGG
1 TCAATGATATGTTATAAGG
*
4942773 TCAATGATATGTTGTAAGG
1 TCAATGATATGTTATAAGG
4942792 GTAACACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (19 bp):
TCAATGATATGTTATAAGG
Found at i:4950356 original size:27 final size:27
Alignment explanation
Indices: 4950305--4950356 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4950295 CCTACAGATG
*
4950305 TTAAAATATAATTTTTTATTAACTTTA
1 TTAAAATATAATTTTTTAATAACTTTA
* *
4950332 TTAATATATAATTTTTTAATGACTT
1 TTAAAATATAATTTTTTAATAACTT
4950357 AAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAAATATAATTTTTTAATAACTTTA
Found at i:4950365 original size:27 final size:27
Alignment explanation
Indices: 4950305--4950371 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
4950295 CCTACAGATG
* * *
4950305 TTAAAATATAATTTTTTATTAACTTTA
1 TTAATATATAATTTTTTAATAACTTAA
*
4950332 TTAATATATAATTTTTTAATGACTTAAA
1 TTAATATATAATTTTTTAATAACTT-AA
*
4950360 TT-ATATAAAATT
1 TTAATATATAATT
4950372 ATATAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (27 bp):
TTAATATATAATTTTTTAATAACTTAA
Found at i:4952114 original size:7 final size:7
Alignment explanation
Indices: 4952102--4952126 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4952092 TTCACTTAAC
4952102 TTTTCTA
1 TTTTCTA
4952109 TTTTCTA
1 TTTTCTA
4952116 TTTTCTA
1 TTTTCTA
4952123 TTTT
1 TTTT
4952127 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTA
Found at i:4957684 original size:14 final size:14
Alignment explanation
Indices: 4957655--4957683 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4957645 TTCTTTCTTC
4957655 TTCTTCTTTTTTTT
1 TTCTTCTTTTTTTT
4957669 TTCTT-TTTTTTTT
1 TTCTTCTTTTTTTT
4957682 TT
1 TT
4957684 TAAGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTCTTTTTTTT
Found at i:4958104 original size:15 final size:15
Alignment explanation
Indices: 4958084--4958121 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4958074 TTGAGAGAGG
*
4958084 AAAATTAACGATTAA
1 AAAATTAAAGATTAA
*
4958099 AAAATTAAATATTAA
1 AAAATTAAAGATTAA
4958114 AAAATTAA
1 AAAATTAA
4958122 GTACATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAATTAAAGATTAA
Found at i:4964286 original size:19 final size:20
Alignment explanation
Indices: 4964240--4964286 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4964230 AATAAGAAAT
4964240 AAAATATA-TTTAAATAATA
1 AAAATATATTTTAAATAATA
* *
4964259 TAACT-TATTTTAAATAA-A
1 AAAATATATTTTAAATAATA
4964277 AAAATATATT
1 AAAATATATT
4964287 AGTATAGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATATTTTAAATAATA
Found at i:4975329 original size:26 final size:26
Alignment explanation
Indices: 4975271--4975332 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
4975261 TTGGTCATTA
*
4975271 ACTTTTAGATTTTAATTAATTTACTT
1 ACTTTTGGATTTTAATTAATTTACTT
4975297 ACTTTTGGATTTTAATTAATTTACTT
1 ACTTTTGGATTTTAATTAATTTACTT
4975323 ACTTTTGGAT
1 ACTTTTGGAT
4975333 GGTAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (26 bp):
ACTTTTGGATTTTAATTAATTTACTT
Found at i:4975450 original size:17 final size:17
Alignment explanation
Indices: 4975415--4975454 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4975405 TTCATAAAAA
*
4975415 AAAATTAAAAATTTAAT
1 AAAATTAAAAAATTAAT
4975432 AAAATTAAAAAAATT-AT
1 AAAATT-AAAAAATTAAT
4975449 AAAATT
1 AAAATT
4975455 TTTTAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAAAAAATTAAT
Found at i:4977893 original size:15 final size:16
Alignment explanation
Indices: 4977863--4977901 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4977853 GAGCCGTAAT
*
4977863 TTTATTAATATTTTAA
1 TTTATAAATATTTTAA
4977879 TTTATAAAT-TTTTAA
1 TTTATAAATATTTTAA
*
4977894 TTTTTAAA
1 TTTATAAA
4977902 AGGTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAAATATTTTAA
Found at i:4982029 original size:6 final size:6
Alignment explanation
Indices: 4982013--4982063 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
4982003 GAAAATTGGA
* * * *
4982013 AAAAGG GAAAGG AAAAGA AAAAGA AAAAGC AAAA-- AAAAGG AAAAGG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
4982059 AAAAG
1 AAAAG
4982064 AAGTTGTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 4 0.10
6 35 0.90
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:4982050 original size:17 final size:18
Alignment explanation
Indices: 4982020--4982065 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
4982010 GGAAAAAGGG
*
4982020 AAAGGAAAAGAAAAAGAA
1 AAAGCAAAAGAAAAAGAA
*
4982038 AAAGC-AAA-AAAAAGGA
1 AAAGCAAAAGAAAAAGAA
*
4982054 AAAGGAAAAGAA
1 AAAGCAAAAGAA
4982066 GTTGTGAGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 11 0.48
17 6 0.26
18 6 0.26
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAGCAAAAGAAAAAGAA
Found at i:4986845 original size:5 final size:5
Alignment explanation
Indices: 4986837--4986864 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4986827 ATCTGATTGG
4986837 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
4986865 GGTGAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:4990863 original size:13 final size:13
Alignment explanation
Indices: 4990825--4990863 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
4990815 TATAAAACTG
4990825 TTTAATAT-ATTA
1 TTTAATATAATTA
*
4990837 TTTAAAATTAATTA
1 TTTAATA-TAATTA
4990851 TTTAATATAATTA
1 TTTAATATAATTA
4990864 AATTATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 7 0.30
14 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAATATAATTA
Found at i:4993639 original size:64 final size:63
Alignment explanation
Indices: 4993535--4993671 Score: 256
Period size: 64 Copynumber: 2.2 Consensus size: 63
4993525 GGTCAAAGTG
*
4993535 CAATTTACCATCAAATTGAAATAAAGCATTATGATTCTCTCTCTTTTCTTGTATAAAAAAAATA
1 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTCTTGTAT-AAAAAAATA
4993599 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTCTTGTATAAAAAAATA
1 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTCTTGTATAAAAAAATA
4993662 CAATTTACCA
1 CAATTTACCA
4993672 ATATATAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 19 0.26
64 53 0.74
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (63 bp):
CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTCTTGTATAAAAAAATA
Found at i:4995651 original size:14 final size:16
Alignment explanation
Indices: 4995632--4995666 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4995622 AAATTAATTA
4995632 TAAAATA-TACA-AAT
1 TAAAATATTACATAAT
4995646 TAAAATATTACATAAT
1 TAAAATATTACATAAT
4995662 TAAAA
1 TAAAA
4995667 ATGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 8 0.42
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATATTACATAAT
Found at i:5000515 original size:12 final size:12
Alignment explanation
Indices: 5000500--5000524 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5000490 TTTTTAAAAA
5000500 TATTTTATTTTT
1 TATTTTATTTTT
5000512 TATTTTATTTTT
1 TATTTTATTTTT
5000524 T
1 T
5000525 GTCTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:5002023 original size:11 final size:10
Alignment explanation
Indices: 5002006--5002053 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
5001996 CAAATATATA
5002006 ATATAAAATT
1 ATATAAAATT
5002016 ATTATAAAA-T
1 A-TATAAAATT
* *
5002026 ATAAAAAAGT
1 ATATAAAATT
5002036 ATA-AAAATT
1 ATATAAAATT
5002045 ATATAAAAT
1 ATATAAAAT
5002054 ATAAAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 14 0.42
10 12 0.36
11 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
ATATAAAATT
Found at i:5002943 original size:10 final size:10
Alignment explanation
Indices: 5002930--5002972 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
5002920 TCATATTAAC
5002930 AAATATAAAA
1 AAATATAAAA
5002940 AAATATAATAA
1 AAATATAA-AA
*
5002951 AAATATATAA
1 AAATATAAAA
5002961 AAATATAAAA
1 AAATATAAAA
5002971 AA
1 AA
5002973 GGTTACACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATATAAAA
Found at i:5002954 original size:21 final size:20
Alignment explanation
Indices: 5002930--5002972 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
5002920 TCATATTAAC
5002930 AAATATAAAAAAATATAATAA
1 AAATATAAAAAAATATAA-AA
*
5002951 AAATATATAAAAATATAAAA
1 AAATATAAAAAAATATAAAA
5002971 AA
1 AA
5002973 GGTTACACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATATAAAAAAATATAAAA
Found at i:5004652 original size:2 final size:2
Alignment explanation
Indices: 5004645--5004695 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5004635 TTCTAAAATT
5004645 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5004687 TC TC TC TC T
1 TC TC TC TC T
5004696 GTGTCTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5004947 original size:19 final size:19
Alignment explanation
Indices: 5004923--5004962 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5004913 TATTTTGAAT
5004923 TTCAATTTCTCTTCATACC
1 TTCAATTTCTCTTCATACC
5004942 TTCAATTTCTCTTCATACC
1 TTCAATTTCTCTTCATACC
5004961 TT
1 TT
5004963 TTAACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTTCTCTTCATACC
Found at i:5010547 original size:13 final size:14
Alignment explanation
Indices: 5010517--5010554 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5010507 GTTTGCCAGT
5010517 AAAATAATTTCCGA
1 AAAATAATTTCCGA
*
5010531 AAAATAATTTCTGA
1 AAAATAATTTCCGA
*
5010545 AAAATGATTT
1 AAAATAATTT
5010555 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (14 bp):
AAAATAATTTCCGA
Found at i:5010569 original size:19 final size:20
Alignment explanation
Indices: 5010538--5010582 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
5010528 CGAAAAATAA
5010538 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
5010558 TTTCTG-AAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
5010577 TTTCTG
1 TTTCTG
5010583 GTGTTTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:5015751 original size:15 final size:16
Alignment explanation
Indices: 5015715--5015749 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5015705 TTAAAAAGTT
5015715 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
5015731 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
5015747 TTT
1 TTT
5015750 AAGGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:5020857 original size:19 final size:20
Alignment explanation
Indices: 5020822--5020863 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
5020812 CAGAAAATGA
5020822 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
5020842 TTTCTGG-AAATTATTTACT
1 TTTCTGGAAAATGATTTACT
5020861 TTT
1 TTT
5020864 ATTGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5020969 original size:16 final size:16
Alignment explanation
Indices: 5020942--5020976 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5020932 GAAAAGTTGT
5020942 TTTAAGAAATTTATATA
1 TTTAAGAAATTTAT-TA
5020959 TTTAA-AAATTTATTA
1 TTTAAGAAATTTATTA
5020974 TTT
1 TTT
5020977 TTTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAGAAATTTATTA
Found at i:5022515 original size:14 final size:14
Alignment explanation
Indices: 5022496--5022535 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5022486 TTGTTTGGCA
5022496 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5022510 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5022524 GGAAAATGTTTT
1 GTAAAATGTTTT
5022536 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5022544 original size:20 final size:20
Alignment explanation
Indices: 5022519--5022558 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5022509 CGTAAAATGA
*
5022519 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5022539 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5022559 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5022548 original size:34 final size:35
Alignment explanation
Indices: 5022504--5022570 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5022494 CAGTAAAATG
*
5022504 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
5022538 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
5022571 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:5022574 original size:14 final size:15
Alignment explanation
Indices: 5022498--5022574 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5022488 GTTTGGCAGT
* *
5022498 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
5022512 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
5022526 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
5022546 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
5022561 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
5022575 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:5022676 original size:14 final size:14
Alignment explanation
Indices: 5022657--5022684 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5022647 TTTTTACATA
5022657 TATTAATATATATT
1 TATTAATATATATT
5022671 TATTAATATATATT
1 TATTAATATATATT
5022685 AATAAATTGT
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:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:5024006 original size:35 final size:36
Alignment explanation
Indices: 5023960--5024028 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
5023950 ATTCAACCAT
5023960 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
5023995 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
5024029 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:5024026 original size:27 final size:28
Alignment explanation
Indices: 5023996--5024065 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
5023986 AATAATAAAT
*
5023996 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
5024023 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
5024051 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
5024066 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:5025577 original size:15 final size:16
Alignment explanation
Indices: 5025557--5025589 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5025547 AGTACCACTT
5025557 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
5025572 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
5025588 AA
1 AA
5025590 GTTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:5028022 original size:25 final size:25
Alignment explanation
Indices: 5027983--5028034 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5027973 AAAATGTCTG
5027983 CTGCTTAGAAGAGAACAGAAAATGT
1 CTGCTTAGAAGAGAACAGAAAATGT
**
5028008 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAACAGAAAATGT
5028033 CT
1 CT
5028035 TACCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
CTGCTTAGAAGAGAACAGAAAATGT
Found at i:5034869 original size:15 final size:16
Alignment explanation
Indices: 5034833--5034867 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5034823 TTAAAAAGTT
5034833 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
5034849 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
5034865 TTT
1 TTT
5034868 AAGGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:5035080 original size:28 final size:27
Alignment explanation
Indices: 5035049--5035109 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
5035039 ATAAAAATAA
*
5035049 AAAAAATCAAATA-CGAAATTTGAAATCC
1 AAAAAATCAAA-ACCAAAATTTGAAA-CC
**
5035077 AAAACCTCAAAACCAAAATTTGAAACC
1 AAAAAATCAAAACCAAAATTTGAAACC
5035104 AAAAAA
1 AAAAAA
5035110 ATTAAACCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAAATCAAAACCAAAATTTGAAACC
Found at i:5036785 original size:5 final size:5
Alignment explanation
Indices: 5036775--5036801 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5036765 AATATTAAAT
5036775 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
5036802 AGCACCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:5046445 original size:37 final size:37
Alignment explanation
Indices: 5046395--5046468 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
5046385 AAGGACATAT
*
5046395 ACAGAGACTGAGCAAATCATACAATCCAAACAGCAAA
1 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
5046432 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
1 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
5046469 TAAAGGAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.11
Consensus pattern (37 bp):
ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
Found at i:5046673 original size:61 final size:61
Alignment explanation
Indices: 5046578--5046705 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
5046568 ACATGGTAGG
5046578 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
1 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
*
5046639 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGTTTCATGCCAACTTCCAA
1 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
5046700 ATAAAC
1 A-AAAC
5046706 TTCCGAATCA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 61 0.94
62 4 0.06
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (61 bp):
AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
Found at i:5046679 original size:33 final size:33
Alignment explanation
Indices: 5046581--5046679 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
5046571 TGGTAGGAAA
5046581 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
1 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
** * * * * *
5046614 ACAAT-GGGTTCA--TGC--CAACTTCCAAAA-A
1 ACAATAAAGATAATTTGCAGGAAC-TGCAAAATG
5046642 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
1 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
5046675 ACAAT
1 ACAAT
5046680 GGTTTCATGC
Statistics
Matches: 45, Mismatches: 14, Indels: 14
0.62 0.19 0.19
Matches are distributed among these distances:
28 8 0.18
29 9 0.20
30 3 0.07
31 3 0.07
32 9 0.20
33 13 0.29
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (33 bp):
ACAATAAAGATAATTTGCAGGAACTGCAAAATG
Found at i:5049928 original size:24 final size:24
Alignment explanation
Indices: 5049896--5049949 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5049886 TTGGTAAATT
*
5049896 TCAATACAATAGCAATAAATTTCA
1 TCAATACAATAGCAATAAACTTCA
*
5049920 TCAATACAATAGCAATCAACTTCA
1 TCAATACAATAGCAATAAACTTCA
*
5049944 TTAATA
1 TCAATA
5049950 TTTTAATACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (24 bp):
TCAATACAATAGCAATAAACTTCA
Found at i:5050416 original size:24 final size:25
Alignment explanation
Indices: 5050381--5050440 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
5050371 AAAGAATTAA
5050381 ATTAAAATTTTTTTATTTTTAGAAG
1 ATTAAAATTTTTTTATTTTTAGAAG
*
5050406 ATTAAAATTTTTTTATTTTTAGAGG
1 ATTAAAATTTTTTTATTTTTAGAAG
*
5050431 ATCAAAATTT
1 ATTAAAATTT
5050441 ACTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (25 bp):
ATTAAAATTTTTTTATTTTTAGAAG
Found at i:5051649 original size:31 final size:31
Alignment explanation
Indices: 5051611--5051670 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
5051601 TGATTATTTT
5051611 ATATTATTTCTTTTTATTTTT-TTAAAATAAA
1 ATATTATTT-TTTTTATTTTTATTAAAATAAA
5051642 ATATTATTTTTTTTATTTTTATTAAAATA
1 ATATTATTTTTTTTATTTTTATTAAAATA
5051671 TTTAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (31 bp):
ATATTATTTTTTTTATTTTTATTAAAATAAA
Found at i:5052047 original size:28 final size:29
Alignment explanation
Indices: 5051976--5052049 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
5051966 GTCCACACCG
5051976 AAAGAAAG-AAAAAAA-AAGAGAGAGAGA
1 AAAGAAAGAAAAAAAAGAAGAGAGAGAGA
*
5052003 AAGGAGAAGAAAAAAAAAGAAGA-AGA-AGA
1 AAAGA-AAG-AAAAAAAAGAAGAGAGAGAGA
5052032 AGAAGAAAGAAAAAAAAG
1 A-AAGAAAGAAAAAAAAG
5052050 GTAATGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 4 0.10
28 12 0.30
29 7 0.17
30 13 0.32
31 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (29 bp):
AAAGAAAGAAAAAAAAGAAGAGAGAGAGA
Found at i:5052047 original size:29 final size:27
Alignment explanation
Indices: 5051976--5052048 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
5051966 GTCCACACCG
5051976 AAAGAAAGAAAAAAAAAGAGAGAGAGA
1 AAAGAAAGAAAAAAAAAGAGAGAGAGA
*
5052003 AAGGAGAAGAAAAAAAAAGA-AGAAGAAGA
1 AAAGA-AAGAAAAAAAAAGAGAG-AG-AGA
5052032 AGAAGAAAGAAAAAAAA
1 A-AAGAAAGAAAAAAAA
5052049 GGTAATGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 6 0.15
28 16 0.40
29 15 0.38
30 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (27 bp):
AAAGAAAGAAAAAAAAAGAGAGAGAGA
Found at i:5052250 original size:33 final size:32
Alignment explanation
Indices: 5052207--5052314 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 32
5052197 GTTTTTTATA
*
5052207 ATTATTTTAAAATTAATTTGTTAGTGATTTAGG
1 ATTATGTTAAAATTAATTT-TTAGTGATTTAGG
*
5052240 ATTATGTTAAAA--AA-TTTT-GTG-TTT-GTA
1 ATTATGTTAAAATTAATTTTTAGTGATTTAG-G
* * *
5052267 ATTATTTTAAAATTAATTTATTAGTAAATTAGG
1 ATTATGTTAAAATTAATTT-TTAGTGATTTAGG
*
5052300 ATTAAGTTATAAATT
1 ATTATGTTA-AAATT
5052315 GTTGTGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
26 1 0.02
27 14 0.24
28 3 0.05
29 4 0.07
30 4 0.07
31 4 0.07
32 2 0.03
33 20 0.34
34 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (32 bp):
ATTATGTTAAAATTAATTTTTAGTGATTTAGG
Found at i:5052291 original size:60 final size:60
Alignment explanation
Indices: 5052205--5052323 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
5052195 TTGTTTTTTA
* * * *
5052205 TAATTATTTTAAAATTAATTTGTTAGTGATTTAGGATTATGTTAAAAAATT-TTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAAATTAGGATTAAGTT-AAAAATTGTTGTGTTTG
*
5052265 TAATTATTTTAAAATTAATTTATTAGTAAATTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAAATTAGGATTAAGTTAAAAATTGTTGTGTTT
5052324 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.51
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAAATTAGGATTAAGTTAAAAATTGTTGTGTTTG
Found at i:5052659 original size:15 final size:15
Alignment explanation
Indices: 5052639--5052671 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5052629 ATTTGATCCG
5052639 TAAAATTGAAATCTT
1 TAAAATTGAAATCTT
5052654 TAAAATTGAAATCTT
1 TAAAATTGAAATCTT
5052669 TAA
1 TAA
5052672 TTTTATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
TAAAATTGAAATCTT
Found at i:5054556 original size:5 final size:5
Alignment explanation
Indices: 5054530--5054587 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5054520 ATGTGTTAAA
* *
5054530 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
5054579 ATATT ATAT
1 ATATT ATAT
5054588 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:5054566 original size:10 final size:9
Alignment explanation
Indices: 5054531--5054588 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
5054521 TGTGTTAAAA
5054531 TATATATAT
1 TATATATAT
*
5054540 TAAAT-TAT
1 TATATATAT
5054548 TAT-TATAT
1 TATATATAT
5054556 TATAGTATAT
1 TATA-TATAT
5054566 TATAT-TA-
1 TATATATAT
5054573 TATATTATAT
1 TATA-TATAT
5054583 TATATA
1 TATATA
5054589 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:5054578 original size:12 final size:12
Alignment explanation
Indices: 5054533--5054588 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5054523 TGTTAAAATA
*
5054533 TATATATTAAAT
1 TATATATTATAT
5054545 TAT-TATTATATT
1 TATATATTATA-T
5054557 ATAGTATATTATAT
1 -TA-TATATTATAT
5054571 TATATATTATAT
1 TATATATTATAT
5054583 TATATA
1 TATATA
5054589 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5055925 original size:18 final size:19
Alignment explanation
Indices: 5055904--5055942 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5055894 ATATATAGAT
5055904 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5055922 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5055941 AT
1 AT
5055943 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5056291 original size:39 final size:39
Alignment explanation
Indices: 5056181--5056315 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
5056171 GACCTCGAGT
* * * * *
5056181 CGATAAGACACTGGGTGTCATTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5056222 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5056260 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5056299 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5056316 CCATATTGGT
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5056459 original size:18 final size:19
Alignment explanation
Indices: 5056438--5056478 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5056428 AATGAAATGA
5056438 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5056456 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5056475 GAAA
1 GAAA
5056479 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5068583 original size:70 final size:72
Alignment explanation
Indices: 5068469--5068619 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
5068459 GGGGAATCAT
* *
5068469 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
5068533 GATATCG
66 GATATCG
***
5068540 CACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
5068604 GATATCG
66 GATATCG
5068611 CACTTAGCA
1 CACTTAGCA
5068620 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 34 0.46
71 40 0.54
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:5068648 original size:103 final size:102
Alignment explanation
Indices: 5068539--5068758 Score: 352
Period size: 103 Copynumber: 2.1 Consensus size: 102
5068529 AATGGATATC
5068539 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
5068604 GAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
65 GATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
5068642 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAA-CCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
5068707 GATCACGCACATAGCACCACCCATAAATCGGGGAATCA
65 GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
5068745 GCACACAGCAACCC
1 GCACTTAGCAACCC
5068759 CTTTTATATA
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
102 3 0.03
103 100 0.92
104 6 0.06
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (102 bp):
GCACTTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
ATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:5068662 original size:26 final size:26
Alignment explanation
Indices: 5068632--5068682 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5068622 ACCAATGAAC
*
5068632 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
5068658 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
5068683 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:5069122 original size:29 final size:29
Alignment explanation
Indices: 5069089--5069152 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
5069079 TAATCCACCA
5069089 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
5069118 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
5069148 CCCAA
1 CCCAA
5069153 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:5069126 original size:30 final size:30
Alignment explanation
Indices: 5069096--5069152 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5069086 CCACCCAACT
5069096 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
5069125 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
5069153 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:5075071 original size:18 final size:19
Alignment explanation
Indices: 5075048--5075086 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5075038 ATATATAGAT
5075048 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5075066 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5075085 AT
1 AT
5075087 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5075436 original size:39 final size:39
Alignment explanation
Indices: 5075326--5075460 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
5075316 GACCTCGAGT
* * * * *
5075326 CGATAAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5075367 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5075405 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5075444 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5075461 CCATATTGGT
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5075604 original size:18 final size:19
Alignment explanation
Indices: 5075583--5075623 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5075573 AATTAAATGA
5075583 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5075601 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5075620 GAAA
1 GAAA
5075624 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5081208 original size:21 final size:21
Alignment explanation
Indices: 5081184--5081242 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
5081174 AATACATTAA
*
5081184 AAATATTTAAAAAATAAAAGT
1 AAATATTTAAAAAATAAAAAT
5081205 AAATATTTTTTAAGAAAATAAAAAT
1 AAATA---TTTAA-AAAATAAAAAT
5081230 AAAT-TTTAAAAAA
1 AAATATTTAAAAAA
5081243 CACGTAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 4 0.12
21 10 0.30
24 5 0.15
25 14 0.42
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
AAATATTTAAAAAATAAAAAT
Found at i:5083162 original size:19 final size:18
Alignment explanation
Indices: 5083122--5083164 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5083112 TACCGTAATA
*
5083122 TAAAAATTAAAAAATTCC
1 TAAAAATTAAAAAATTAC
* *
5083140 TAAAAATTAATATAATTAT
1 TAAAAATTAA-AAAATTAC
5083159 TAAAAA
1 TAAAAA
5083165 AATAATTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATTAAAAAATTAC
Found at i:5098915 original size:33 final size:35
Alignment explanation
Indices: 5098878--5098974 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
5098868 ATGGTTATAT
5098878 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
5098911 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
5098946 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
5098975 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:5103224 original size:13 final size:14
Alignment explanation
Indices: 5103202--5103233 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5103192 AAAATTTAAT
5103202 TAAATAAAAATATC
1 TAAATAAAAATATC
5103216 TAAATAAAAATATC
1 TAAATAAAAATATC
5103230 -AAAT
1 TAAAT
5103234 GTACTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATAAAAATATC
Found at i:5104321 original size:11 final size:11
Alignment explanation
Indices: 5104307--5104347 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5104297 TATTTTCTCT
5104307 CTATTTTGCTA
1 CTATTTTGCTA
*
5104318 CTATTTTACTA
1 CTATTTTGCTA
* *
5104329 TTATATTGCTA
1 CTATTTTGCTA
5104340 CTATTTTG
1 CTATTTTG
5104348 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:5104431 original size:30 final size:29
Alignment explanation
Indices: 5104387--5104445 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
5104377 TATTTTATTA
5104387 TTAATTTTTTATTATTTTA-AAGACATTTG
1 TTAATTTTTTATTATTTTAGAA-ACATTTG
5104416 TTAATTTTGTTATTATTTTAGAAACATTTG
1 TTAATTTT-TTATTATTTTAGAAACATTTG
5104446 CTTATTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.29
30 18 0.64
31 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (29 bp):
TTAATTTTTTATTATTTTAGAAACATTTG
Found at i:5104584 original size:11 final size:11
Alignment explanation
Indices: 5104568--5104596 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5104558 TATATATTAT
5104568 AAAATTATATA
1 AAAATTATATA
5104579 AAAATTATATA
1 AAAATTATATA
5104590 AAAATTA
1 AAAATTA
5104597 ATATGGACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTATATA
Found at i:5107387 original size:15 final size:15
Alignment explanation
Indices: 5107367--5107396 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5107357 CTCACATTGG
5107367 ATATAATAAAAATAA
1 ATATAATAAAAATAA
*
5107382 ATATAATAATAATAA
1 ATATAATAAAAATAA
5107397 TAATAAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAATAAAAATAA
Found at i:5122375 original size:27 final size:27
Alignment explanation
Indices: 5122313--5122387 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
5122303 TGGTCCATTT
* *
5122313 TAAT-TTTAACTGAT-GTATAATTTTAA
1 TAATATTTAACTGATAAT-TAATTTAAA
* *
5122339 TATTAATTAACTGATAATTAATTTAAA
1 TAATATTTAACTGATAATTAATTTAAA
5122366 TAATATTTAA-T-ATTAATTAATT
1 TAATATTTAACTGA-TAATTAATT
5122388 AATATTACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 13 0.32
27 25 0.62
28 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATATTTAACTGATAATTAATTTAAA
Found at i:5123363 original size:20 final size:20
Alignment explanation
Indices: 5123314--5123365 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
5123304 TTATGCCACA
5123314 TTAGTATTCTTATCCTAAATT
1 TTAGTATT-TTATCCTAAATT
* *
5123335 TCA-TGATTTTATCCTGAATT
1 TTAGT-ATTTTATCCTAAATT
5123355 TTAGTATTTTA
1 TTAGTATTTTA
5123366 ATTTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.54
Consensus pattern (20 bp):
TTAGTATTTTATCCTAAATT
Found at i:5130949 original size:18 final size:19
Alignment explanation
Indices: 5130910--5130953 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5130900 AACTTTCTTT
*
5130910 TTTAT-TTTATTTCATATT
1 TTTATATTTATTTCATATA
*
5130928 TTTATATTTATTTTATA-A
1 TTTATATTTATTTCATATA
5130946 TTTATATT
1 TTTATATT
5130954 CGGGATTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATATTTATTTCATATA
Found at i:5147773 original size:210 final size:210
Alignment explanation
Indices: 5147226--5148284 Score: 1562
Period size: 210 Copynumber: 5.1 Consensus size: 210
5147216 CTTCATCGGG
* * * * *
5147226 GCAGATCTAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCATATCAAAGATATAGTTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCTG
5147291 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * * * *
5147356 AAACGAATCGAAGTTTGGTATCTT-CACTTTGATGG-AGAGCAGACACATAGCAGATCTGACCTT
131 GAACAAATCGAAGTCTGGCAT-TTCCACTTTGATGGAAG-GCAGACACATAGCAGATCTTACCTT
*
5147419 CAGAAGTTTATGCTGAA
194 CAGATGTTTATGCTGAA
* *** * * * ** * * * *
5147436 GCGGATCCAAGATGGTTTG-GCAT-TC-CT-TGTGTT-TACAAGGAACAAAT-GAAGACATAGCT
1 GCAGATCCAAGAT-GACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCT
* *
5147495 GATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAG
*
5147560 AGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAAACACATAGCAGATCTTACCTTC
130 AGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTC
*
5147625 AGATGTTTACGCTGAA
195 AGATGTTTATGCTGAA
* *
5147641 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAAGGAGCAGATCGAAGATATAGTTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCTG
*
5147706 ATTTGGCTTTCACGTGTTTACGATGAGGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* *
5147771 GAACAAATTGAAGGCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCA
131 GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCA
5147836 GATGTTTATGCTGAA
196 GATGTTTATGCTGAA
*
5147851 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGTAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCTG
*
5147916 ATTTGGCTTTCACGTGTTTTCGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
*
5147981 GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCCTCA
131 GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCA
*
5148046 GATGTTTACGCTGAA
196 GATGTTTATGCTGAA
*
5148061 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCTG
* * *
5148126 ATTTGGCTTTCACATGTTTTCGATGAAGCAAATCTAAGATGATTTGTTGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * * * **
5148191 GAACGAATCAAAGTTTGGCATCTT-CACTTTGATGG-AGAGCAGACACATAGCAGATATCGCCTT
131 GAACAAATCGAAGTCTGGCAT-TTCCACTTTGATGGAAG-GCAGACACATAGCAGATCTTACCTT
*
5148254 CGGATGTTTATGCTGAA
194 CAGATGTTTATGCTGAA
*
5148271 GCGGATCCAAGATG
1 GCAGATCCAAGATG
5148285 GTTTGGCATC
Statistics
Matches: 768, Mismatches: 70, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
204 4 0.01
205 153 0.20
206 12 0.02
207 7 0.01
208 7 0.01
209 14 0.02
210 567 0.74
211 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (210 bp):
GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGCTG
ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCA
GATGTTTATGCTGAA
Found at i:5148092 original size:420 final size:414
Alignment explanation
Indices: 5147226--5148403 Score: 1668
Period size: 420 Copynumber: 2.8 Consensus size: 414
5147216 CTTCATCGGG
* * * *
5147226 GCAGATCTAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCATATCAAAGATATAGTTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGTTG
5147291 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * *
5147356 AAACGAATCGAAGTTTGGTATCTTCACTTTGATGGAGAGCAGACACATAGCAGATCTGACCTTCA
131 GAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCA
* *** * *
5147421 GAAGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATTCCTTGTGTTTACAAGGAACAAATGAA
196 GATGTTTATGCTGAAGCGGATCCAAGAT-GACAGGCATTCCTTGTATTGACAAGGAACAAATGAA
*
5147486 GACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGATTTGTCGTCTCTG
260 GACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGATTTGTCGTCTCTG
5147551 TATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAAACACATAGCAGAT
325 TATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAAACACATAGCAGAT
*
5147616 CTTACCTTCAGATGTTTACGCTGAA
390 CTTACCCTCAGATGTTTACGCTGAA
*
5147641 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAAGGAGCAGATCGAAGATATAGTTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGTTG
*
5147706 ATTTGGCTTTCACGTGTTTACGATGAGGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * ** *
5147771 GAACAAATTGAAGGCTGGCAT-TTCCACTTTGATGGA-AGGCAGACACATAGCAGATCTTACCTT
131 GAACGAATCGAAGTTTGGCATCTT-CACTTTGATGGAGA-GCAGACACATAGCAGATCTCACCTT
* * * * * **
5147834 CAGATGTTTATGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGTA
194 CAGATGTTTATGCTGAAGCGGATCCAAGATGACAG-GCAT-TC-CT-TGTATT-GACAAGGAACA
* * * *
5147899 GATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTTCGATGAAGCAAATCTAAGATGATTTGTC
254 AAT-GAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGATTTGTC
*
5147964 GTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAGACACAT
318 GTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAAACACAT
5148029 AGCAGATCTTACCCTCAGATGTTTACGCTGAA
383 AGCAGATCTTACCCTCAGATGTTTACGCTGAA
* *
5148061 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGTTG
* * *
5148126 ATTTGGCTTTCACATGTTTTCGATGAAGCAAATCTAAGATGATTTGTTGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * * *
5148191 GAACGAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCAGACACATAGCAGATATCGCCTTCG
131 GAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCA
*** * *
5148256 GATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCA-TCCTTATGCTT-ACAA-GAACCAAATC
196 GATGTTTATGCTGAAGCGGATCCAAGAT-GACAGGCATTCCTTGT-ATTGACAAGGAA-CAAAT-
* * * * * * **
5148318 GAA-TCATAGTTGATTTGGCTTTCACGTGCTTAC-ATTAAAGCAAATCTAAAATGATTTGGCACC
257 GAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAA-CAAATCTAAGATGATTTGTCGTC
*
5148381 TCTGTATTGTCAGGGAACAAATC
321 TCTGTATTGTCAGAGAACAAATC
5148404 AAAGAAACAG
Statistics
Matches: 675, Mismatches: 74, Indels: 29
0.87 0.10 0.04
Matches are distributed among these distances:
413 4 0.01
414 73 0.11
415 214 0.32
416 4 0.01
417 6 0.01
418 7 0.01
419 8 0.01
420 354 0.52
421 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (414 bp):
GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAGTTG
ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
GAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCA
GATGTTTATGCTGAAGCGGATCCAAGATGACAGGCATTCCTTGTATTGACAAGGAACAAATGAAG
ACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGATTTGTCGTCTCTGT
ATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATGGAAGGCAAACACATAGCAGATC
TTACCCTCAGATGTTTACGCTGAA
Found at i:5148536 original size:44 final size:45
Alignment explanation
Indices: 5148482--5148589 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
5148472 AGTTTGCAAT
* * *
5148482 GAGCAAATTGAAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGG
1 GAGCAGATTGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* * *
5148526 GAGCAGATTGAAGATAATAGATTTGTCGTCTCTGTAGTAGACGGG
1 GAGCAGATTGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* **
5148571 GGGCAGATCAAAGATAACA
1 GAGCAGATTGAAGATAACA
5148590 GATATTGCCT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
44 13 0.25
45 40 0.75
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (45 bp):
GAGCAGATTGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
Found at i:5148559 original size:45 final size:45
Alignment explanation
Indices: 5148501--5148592 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
5148491 GAAGAAGCAA
* ** *
5148501 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATTGAAGATAATAG
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAACAG
* *
5148546 ATTTGTCGTCTCTGTAGTAGACGGGGGGCAGATCAAAGATAACAG
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAACAG
5148591 AT
1 AT
5148593 ATTGCCTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (45 bp):
ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAACAG
Found at i:5149954 original size:38 final size:38
Alignment explanation
Indices: 5149819--5149968 Score: 194
Period size: 39 Copynumber: 3.9 Consensus size: 38
5149809 ATAAAGTATG
* * *
5149819 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGCATG-GGGAGTA
* *
5149858 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGG-AGTA
5149897 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGT-
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGTA
* * *
5149934 GTTTTTGATTAATAATAAAACAAAGTAGCATGGGG
1 G-TTTTAATTAACAATAAAACAAAATAGCATGGGG
5149969 GAGTGGAATC
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
37 1 0.01
38 34 0.34
39 66 0.65
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGTA
Found at i:5149970 original size:78 final size:78
Alignment explanation
Indices: 5149819--5149968 Score: 214
Period size: 77 Copynumber: 1.9 Consensus size: 78
5149809 ATAAAGTATG
* *
5149819 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
*
5149884 GTATGGGGAAATA
66 GCATGGGGAAATA
* * * *
5149897 GTTTTAATTAACAATAAAACAAAATAGCATG-GGGAGT-GTTTTTGATTAATAATAAAACAAAGT
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAG-TTTTAATTAACAATAAAACAAAAT
5149960 AGCATGGGG
65 AGCATGGGG
5149969 GAGTGGAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
76 1 0.02
77 34 0.53
78 29 0.45
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (78 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
GCATGGGGAAATA
Found at i:5150703 original size:18 final size:20
Alignment explanation
Indices: 5150680--5150718 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
5150670 TTAATAGTTG
5150680 TTTCTAATAT-TATG-ATTA
1 TTTCTAATATGTATGTATTA
5150698 TTTCTAATATGTATGTATTA
1 TTTCTAATATGTATGTATTA
5150718 T
1 T
5150719 GTATTTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTCTAATATGTATGTATTA
Found at i:5158099 original size:23 final size:23
Alignment explanation
Indices: 5158073--5158146 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
5158063 ATCTGATTTG
5158073 TTATTTCATACAATCCTTTTTCA
1 TTATTTCATACAATCCTTTTTCA
* * *
5158096 TTATTGT-AGAAAAAT--TTGATTT-G
1 TTATT-TCA-TACAATCCTT--TTTCA
5158119 TTATTTCATACAATCCTTTTTCA
1 TTATTTCATACAATCCTTTTTCA
5158142 TTATT
1 TTATT
5158147 GTAGACTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
22 10 0.27
23 17 0.46
24 10 0.27
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (23 bp):
TTATTTCATACAATCCTTTTTCA
Found at i:5158116 original size:46 final size:46
Alignment explanation
Indices: 5158059--5158151 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
5158049 GTTTAAAAGT
5158059 AAAAATCTGATTTGTTATTTCATACAATCCTTTTTCATTATTGTAG
1 AAAAATCTGATTTGTTATTTCATACAATCCTTTTTCATTATTGTAG
*
5158105 AAAAATTTGATTTGTTATTTCATACAATCCTTTTTCATTATTGTAG
1 AAAAATCTGATTTGTTATTTCATACAATCCTTTTTCATTATTGTAG
5158151 A
1 A
5158152 CTTGAATGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (46 bp):
AAAAATCTGATTTGTTATTTCATACAATCCTTTTTCATTATTGTAG
Found at i:5164358 original size:21 final size:21
Alignment explanation
Indices: 5164332--5164372 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5164322 AGATGAGCAA
* *
5164332 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5164353 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5164373 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5172292 original size:21 final size:20
Alignment explanation
Indices: 5172260--5172301 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
5172250 TTAATTTGTT
5172260 ATAAATTATATAATATATAAA
1 ATAAATTATATAA-ATATAAA
*
5172281 ATAAA-TATTATAAATTTAAA
1 ATAAATTA-TATAAATATAAA
5172301 A
1 A
5172302 ATGGATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATTATATAAATATAAA
Found at i:5175855 original size:14 final size:14
Alignment explanation
Indices: 5175836--5175878 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5175826 AAACCAAATC
5175836 AAATTTATATATAA
1 AAATTTATATATAA
* *
5175850 AAATTTATAACATTA
1 AAATTTAT-ATATAA
*
5175865 AAATTCATATATAA
1 AAATTTATATATAA
5175879 TATTACACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTTATATATAA
Found at i:5184304 original size:28 final size:29
Alignment explanation
Indices: 5184245--5184312 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
5184235 TTAGACGCTT
* * * *
5184245 TTTAAAATTTTGAAAACTCACATTATATC
1 TTTAAAATTTTAAAAAATCACATTAAAAC
*
5184274 TTTAAATTTTTAAAAAATCA-ATTAAAAC
1 TTTAAAATTTTAAAAAATCACATTAAAAC
5184302 TTTTAAAATTT
1 -TTTAAAATTT
5184313 ATTATTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (29 bp):
TTTAAAATTTTAAAAAATCACATTAAAAC
Found at i:5190436 original size:17 final size:18
Alignment explanation
Indices: 5190393--5190439 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
5190383 TTTAATATAA
5190393 TTATTCAGTAATCATCAG
1 TTATTCAGTAATCATCAG
*
5190411 TTATTCAGTAAT-ATTAG
1 TTATTCAGTAATCATCAG
5190428 TCT-TTCAGTAAT
1 T-TATTCAGTAAT
5190440 TATTTAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
TTATTCAGTAATCATCAG
Found at i:5192344 original size:3 final size:3
Alignment explanation
Indices: 5192329--5192391 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
5192319 TTAATTTATT
* * * *
5192329 TAA TAA CAA TAA TAA TAA TAA TAA TAA TATA TAG TTA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
5192375 TAC TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
5192392 TGCCGTCAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5193780 original size:24 final size:24
Alignment explanation
Indices: 5193753--5193804 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5193743 TTAGTAAGTC
*
5193753 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5193777 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5193801 AAAT
1 AAAT
5193805 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5195749 original size:24 final size:24
Alignment explanation
Indices: 5195722--5195773 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5195712 TTAGTAAGTC
*
5195722 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5195746 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5195770 AAAT
1 AAAT
5195774 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5204324 original size:42 final size:41
Alignment explanation
Indices: 5204237--5204327 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
5204227 TTTAGTCTCT
*
5204237 ATATTTATATTTTTAGATTTTAAATTTAGGTCTAATTATTA
1 ATATTTTTATTTTTAGATTTTAAATTTAGGTCTAATTATTA
** * *
5204278 ATATTTTTATTTTTATTTTGTTAAGTTTAGGT-TAATTATATC
1 ATATTTTTATTTTTAGATT-TTAAATTTAGGTCTAATTAT-TA
5204320 ATATTTTT
1 ATATTTTT
5204328 TAATTACACG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (41 bp):
ATATTTTTATTTTTAGATTTTAAATTTAGGTCTAATTATTA
Found at i:5224462 original size:20 final size:18
Alignment explanation
Indices: 5224428--5224464 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
5224418 GCAACTCATA
5224428 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
5224446 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
5224465 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:5225456 original size:45 final size:45
Alignment explanation
Indices: 5225404--5225651 Score: 174
Period size: 45 Copynumber: 5.6 Consensus size: 45
5225394 TAAAATCTAA
*
5225404 TCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCGATCTGC
1 TCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCAATCTGC
** *
5225449 TCCATAGCCGATACATGGAGATAAGA-TCCGTAATTTTCAGTCTGC
1 TCCATAGCCGATACATGGAGATAAGACT-CGCCATTTTCAATCTGC
* * * * * *
5225494 TTCC-T-G-CAACTTCA-GGAAGATAAGACTTG-TATCTTCAACCTGC
1 -TCCATAGCCGA-TACATGG-AGATAAGACTCGCCATTTTCAATCTGC
* * * ** ** **
5225537 TCCACT-G-CAACTTCA-GAGAGATAAGGCT-GGTAGCTAAAATCTGC
1 TCCA-TAGCCGA-TACATG-GAGATAAGACTCGCCATTTTCAATCTGC
* *
5225581 TCCATAGCCGATACATGGAGATAAGACTCGCCATTTCCGATCTGC
1 TCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCAATCTGC
5225626 TCCATAGCCGATACATGGAGATAAGA
1 TCCATAGCCGATACATGGAGATAAGA
5225652 AAACGACAGG
Statistics
Matches: 164, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
42 3 0.02
43 16 0.10
44 62 0.38
45 80 0.49
46 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (45 bp):
TCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCAATCTGC
Found at i:5225581 original size:44 final size:44
Alignment explanation
Indices: 5225489--5225584 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
5225479 TAATTTTCAG
* * * **
5225489 TCTGCTTC-CTGCAACTTCAGGAAGATAAGACTTGTATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGACTGGTAGCTAAAA
* *
5225532 CCTGCTCCACTGCAACTTCA-GAGAGATAAGGCTGGTAGCTAAAA
1 TCTGCTCCACTGCAACTTCAGGA-AGATAAGACTGGTAGCTAAAA
5225576 TCTGCTCCA
1 TCTGCTCCA
5225585 TAGCCGATAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
43 8 0.19
44 35 0.81
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGAAGATAAGACTGGTAGCTAAAA
Done.