Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 130 of 206
Found at i:39312014 original size:21 final size:21
Alignment explanation
Indices: 39311962--39312025 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
39311952 TCTTTAACTT
* *
39311962 TAGACCTTGAACCCTGGACCC
1 TAGACCTTGGACCCTGAACCC
* *
39311983 TAGACCATGGACCCTAAACCC
1 TAGACCTTGGACCCTGAACCC
*
39312004 TAGACCTTGGACCTTGAACCC
1 TAGACCTTGGACCCTGAACCC
39312025 T
1 T
39312026 TAAGTCTAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (21 bp):
TAGACCTTGGACCCTGAACCC
Found at i:39314212 original size:36 final size:36
Alignment explanation
Indices: 39314172--39314247 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
39314162 TGACATTATG
39314172 GAATA-AATTAATGA-ATGATTAATAGATAATTGAAGT
1 GAATATAA-TAATGAGATGATTAATAGATAA-TGAAGT
* * *
39314208 GAATATGATATTGAGTTGATTAATAGATAATGAAGT
1 GAATATAATAATGAGATGATTAATAGATAATGAAGT
39314244 GAAT
1 GAAT
39314248 GTGATATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 20 0.57
37 15 0.43
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (36 bp):
GAATATAATAATGAGATGATTAATAGATAATGAAGT
Found at i:39314220 original size:17 final size:17
Alignment explanation
Indices: 39314200--39314257 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
39314190 TTAATAGATA
39314200 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
39314217 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
* *
39314236 AATGAAGTGAATGTGAT
1 ATTGAAGTGAATATGAT
39314253 ATTGA
1 ATTGA
39314258 GTTATGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 3 0.09
19 10 0.31
20 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:39314253 original size:36 final size:37
Alignment explanation
Indices: 39314187--39314260 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
39314177 AATTAATGAA
39314187 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
39314224 TGATTAATAGATAA-TGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
39314260 T
1 T
39314261 ATGAAACGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 22 0.61
37 14 0.39
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.38
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:39314273 original size:20 final size:21
Alignment explanation
Indices: 39314248--39314293 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
39314238 TGAAGTGAAT
39314248 GTGATATTGAG-TTATGAAAC
1 GTGATATTGAGATTATGAAAC
*
39314268 GTGATATTGAGATTATGAAAT
1 GTGATATTGAGATTATGAAAC
39314289 GTGAT
1 GTGAT
39314294 TTTATGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (21 bp):
GTGATATTGAGATTATGAAAC
Found at i:39314417 original size:40 final size:40
Alignment explanation
Indices: 39314373--39314500 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
39314363 GGTTCATCCA
39314373 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
* * * * * *
39314413 ACTAGCGTTGGGCGCA--A---ATATCGTTGGTTTATCCA
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
* * *
39314448 ACTAAATCTGGGCTCACTATTTATATCGTCAGTTTA-TCTG
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTC-G
*
39314488 ACTAGCGCTGGGC
1 ACTAGAGCTGGGC
39314501 ACAAATATCG
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
35 26 0.41
37 1 0.02
38 1 0.02
39 1 0.02
40 35 0.55
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (40 bp):
ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
Found at i:39314448 original size:75 final size:75
Alignment explanation
Indices: 39314320--39314534 Score: 317
Period size: 75 Copynumber: 2.9 Consensus size: 75
39314310 TGAGTAATTG
* * * *
39314320 ATATTGTCGGTTCATTAGACTAGCGCTGGGCAC-AATCATCGTTGGTTCATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAAT-ATCGTTGGTTTATCCAACTAGAGCTGG
39314384 GCTCACTATTT
65 GCTCACTATTT
* * * *
39314395 ATATCGTCGGTTTATTCGACTAGCGTTGGGCGCAAATATCGTTGGTTTATCCAACTAAATCTGGG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGGG
39314460 CTCACTATTT
66 CTCACTATTT
*
39314470 ATATCGTCAGTTTA-TCTGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATTC-GACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGG
39314534 G
65 G
39314535 ATAACTGATT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 2 0.02
75 120 0.96
76 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (75 bp):
ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGGG
CTCACTATTT
Found at i:39314460 original size:35 final size:35
Alignment explanation
Indices: 39314344--39314534 Score: 105
Period size: 35 Copynumber: 5.2 Consensus size: 35
39314334 TTAGACTAGC
* *
39314344 GCTGGGCAC-AATCATCGTTGGTTCATCCAACTAGA
1 GCTGGGCACAAAT-ATCGTTGGTTTATCCAACTAAA
* * * * **
39314379 GCTGGGCTCACTATTTATATCGTCGGTTTATTCGACTAGC
1 GCTGGG--CAC-A--AATATCGTTGGTTTATCCAACTAAA
* *
39314419 GTTGGGCGCAAATATCGTTGGTTTATCCAACTAAA
1 GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
* * ** ** **
39314454 TCTGGGCTCACTATTTATATCGTCAGTTTATCTGACTAGC
1 GCTGGG--CAC-A--AATATCGTTGGTTTATCCAACTAAA
*
39314494 GCTGGGCACAAATATCGTTGGTTTATCCAACTAGA
1 GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
39314529 GCTGGG
1 GCTGGG
39314535 ATAACTGATT
Statistics
Matches: 114, Mismatches: 31, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
35 54 0.47
37 7 0.06
38 6 0.05
40 45 0.39
41 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (35 bp):
GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
Found at i:39344258 original size:21 final size:21
Alignment explanation
Indices: 39344233--39344276 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
39344223 ATCTTCGAGG
*
39344233 ATATGCAATCTTAGATATGAT
1 ATATGCAATCATAGATATGAT
39344254 ATATGCAATCATAGATATGAT
1 ATATGCAATCATAGATATGAT
39344275 AT
1 AT
39344277 GTAACCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGCAATCATAGATATGAT
Found at i:39344287 original size:19 final size:19
Alignment explanation
Indices: 39344232--39344287 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
39344222 AATCTTCGAG
39344232 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
39344251 GATATATGCAATCATAGATAT
1 G--ATATGCAATCTTAGATAT
* *
39344272 GATATGTAACCTTAGA
1 GATATGCAATCTTAGA
39344288 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39344294 original size:22 final size:23
Alignment explanation
Indices: 39344266--39344310 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39344256 ATGCAATCAT
39344266 AGATATGA-TATGTAACCTTAGA
1 AGATATGATTATGTAACCTTAGA
* *
39344288 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAACCTTAGA
39344311 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGTAACCTTAGA
Found at i:39344320 original size:22 final size:23
Alignment explanation
Indices: 39344276--39344320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39344266 AGATATGATA
*
39344276 TGTAACCTTAGAAGATATGATTT
1 TGTAACCTTAGAAGATATAATTT
* *
39344299 TGTAATCTTAG-AGATTTAATTT
1 TGTAACCTTAGAAGATATAATTT
39344321 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTAACCTTAGAAGATATAATTT
Found at i:39351398 original size:44 final size:44
Alignment explanation
Indices: 39351350--39351493 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 44
39351340 AATAGCAGAT
* *
39351350 CTTGCCTTCCTGCACTGACAGTGAAGTAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
*** * * * * * * *
39351394 CTTGCCTCCCTGGGTTG-CAGCGGAGCAG-GCTGAAAATAGCAGAT
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATC-GAAGACACCAG-C
* * * *
39351438 CTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGC
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
39351482 CTTGCCTCCCTG
1 CTTGCCTCCCTG
39351494 GGTTGCAGTG
Statistics
Matches: 69, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
42 1 0.01
43 16 0.23
44 36 0.52
45 15 0.22
46 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (44 bp):
CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
Found at i:39351844 original size:88 final size:88
Alignment explanation
Indices: 39351257--39351834 Score: 807
Period size: 88 Copynumber: 6.6 Consensus size: 88
39351247 GTGAAGATAA
* * * * * * ** *
39351257 CAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACTAGTCTTGCCTCCATCTGTG
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
39351322 GCAGCAGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
39351345 CAGATCTTGCCTTCCTGCACTGACAGTGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
39351410 GCAGCGGAGCAGGCTGAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
39351433 CAGATCTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
39351498 GCAGTGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
39351521 CAGATCTTGCCTTCCTTCACCGACAGCTAAGCATATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
39351586 GTAGCGGAGCAGGCTGAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
39351609 TAGATCTTGCCTTCCTGCACCGGA-AACGAAGCAAATCGAAGTCACCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCCTGCACC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
* *
39351673 TGTAGTGGAGCAGGCTAAAAATAG
65 TGCAGCGGAGCAGGCTAAAAATAG
*
39351697 CAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
39351762 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * * *
39351785 TAAATCTTGCCTTCCTGCACTGACAGCGAAGCAGATTGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
39351835 CTATCTCCCT
Statistics
Matches: 440, Mismatches: 48, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 2 0.00
88 436 0.99
89 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGCTAAAAATAG
Found at i:39351900 original size:44 final size:44
Alignment explanation
Indices: 39351834--39352165 Score: 367
Period size: 44 Copynumber: 7.7 Consensus size: 44
39351824 TGACCCCAGC
* *
39351834 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
39351878 CCTATCTCCTTGGACAGGAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
39351922 CCTATCTCCCTGGTCAACAGTGGAAGAGGTT-AA-A----GAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
39351960 CTTATCTCCCTGGACAGCAGTGGAATAGATTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
39352004 CCTATCTCCCTGGTA-AGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGG-ACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * * *
39352048 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * * * * *
39352092 CCTATCTCCCTAGTCAGCAGTGGAATAGGATGAAGATCGTGAAC
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
39352136 CCTATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 CCTATCTCCCTGGA-CAGCAGTGGAATAGGT
39352166 GGAAAATAGC
Statistics
Matches: 243, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
38 30 0.12
39 2 0.01
40 1 0.00
42 1 0.00
43 4 0.02
44 203 0.84
45 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:39351969 original size:38 final size:38
Alignment explanation
Indices: 39351918--39351995 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
39351908 TAAAGATTGT
* *
39351918 GAATCCTATCTCCCTGGTCAACAGTGGAAGAGGTTAAA
1 GAATCCTATCTCCCTGGACAACAGTGGAAGAGATTAAA
* * *
39351956 GAATCTTATCTCCCTGGACAGCAGTGGAATAGATTAAA
1 GAATCCTATCTCCCTGGACAACAGTGGAAGAGATTAAA
39351994 GA
1 GA
39351996 TTGTGAATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (38 bp):
GAATCCTATCTCCCTGGACAACAGTGGAAGAGATTAAA
Found at i:39352069 original size:126 final size:130
Alignment explanation
Indices: 39351834--39352165 Score: 406
Period size: 126 Copynumber: 2.6 Consensus size: 130
39351824 TGACCCCAGC
* * *
39351834 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGGACAGGAGT
1 CCTATCTCCCTAGTCAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGA-AGCAGT
* * *
39351899 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAACAGTGGAAGAGGTT-AA-A-G-A-A
65 GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTGAAGATGTAGA
39351959 T
130 T
* * *
39351960 CTTATCTCCCTGGACAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGT
1 CCTATCTCCCTAGTCAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGG-AAGCAGT
* * * *
39352025 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG
65 GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTGAAGA-TGTAG
*
39352090 GT
129 AT
* * * *
39352092 CCTATCTCCCTAGTCAGCAGTGGAATAGGA-TGAAGATCGTGAACCCTATCTCCCTGAGCAGCAG
1 CCTATCTCCCTAGTCAGCAGTGGAATA-GATTAAAGATTGTGAATCCTATCTCCCTG-GAAGCAG
*
39352156 TGGAGTAGGT
64 TGGAATAGGT
39352166 GGAAAATAGC
Statistics
Matches: 175, Mismatches: 22, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
126 104 0.59
127 3 0.02
128 1 0.01
130 1 0.01
131 1 0.01
132 62 0.35
133 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (130 bp):
CCTATCTCCCTAGTCAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGAAGCAGTG
GAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTGAAGATGTAGAT
Found at i:39352960 original size:17 final size:18
Alignment explanation
Indices: 39352946--39353029 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
39352936 ATAATCTTTG
39352946 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
39352964 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
*
39352983 TATGATATATGCAATCTTAGA
1 -A-G-GATATGCAATCTTAGA
* * *
39353004 TATGATATGTAACCTTAGA
1 -AGGATATGCAATCTTAGA
39353023 A-GATATG
1 AGGATATG
39353030 ATTTTGTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
17 6 0.11
18 1 0.02
19 32 0.57
21 17 0.30
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:39352972 original size:19 final size:19
Alignment explanation
Indices: 39352948--39353022 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
39352938 AATCTTTGAG
39352948 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39352967 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39352986 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
* *
39353007 GATATGTAACCTTAGA
1 GATATGCAATCTTAGA
39353023 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 33 0.63
21 19 0.37
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39352994 original size:21 final size:21
Alignment explanation
Indices: 39352949--39353011 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
39352939 ATCTTTGAGG
39352949 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
39352968 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
39352989 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
39353010 AT
1 AT
39353012 GTAACCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:39353029 original size:22 final size:23
Alignment explanation
Indices: 39353001--39353045 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39352991 ATGCAATCTT
39353001 AGATATGA-TATGTAACCTTAGA
1 AGATATGATTATGTAACCTTAGA
* *
39353023 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAACCTTAGA
39353046 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGTAACCTTAGA
Found at i:39353055 original size:22 final size:23
Alignment explanation
Indices: 39353011--39353055 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39353001 AGATATGATA
*
39353011 TGTAACCTTAGAAGATATGATTT
1 TGTAACCTTAGAAGATATAATTT
* *
39353034 TGTAATCTTAG-AGATTTAATTT
1 TGTAACCTTAGAAGATATAATTT
39353056 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTAACCTTAGAAGATATAATTT
Found at i:39353489 original size:3 final size:3
Alignment explanation
Indices: 39353469--39353511 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
39353459 ACTAATTTTG
* *
39353469 TTA TTT TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
39353512 ACCTACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:39356936 original size:2 final size:2
Alignment explanation
Indices: 39356929--39356955 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39356919 CAATAATAGA
39356929 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39356956 ATTTTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39363147 original size:46 final size:44
Alignment explanation
Indices: 39363080--39363169 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 44
39363070 AACAGATACA
*
39363080 CGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATGATATC
1 CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAATGATATC
* *
39363126 CGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAATGATATC
1 CGGT-GGATTCAGCACACAGCAACCACCTTATAATCAATGATATC
39363170 GGTTCACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 15 0.38
45 2 0.05
46 20 0.50
47 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (44 bp):
CGGTGGATTCAGCACACAGCAACCACCTTATAATCAATGATATC
Found at i:39368925 original size:16 final size:16
Alignment explanation
Indices: 39368904--39368935 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39368894 GTTCTGTTGC
*
39368904 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39368920 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39368936 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39369223 original size:51 final size:51
Alignment explanation
Indices: 39369168--39369346 Score: 181
Period size: 51 Copynumber: 3.5 Consensus size: 51
39369158 CACATAGTAG
* *
39369168 CATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAGTACTACACACGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
* * *
39369219 CATAGTACTACACACGTGATCGA--AGCTATCCAGTATGCA--TAGTAGCCTGTA
1 CATAGTACTACACACGTGA-CCATCA-CTAT-CAG-ATACACGTAGTAGCCTGCA
* * * * *
39369270 CATAGTACTACACATGCGACCTATCA-T-TCCGATAAACGTAGTAGCCTACA
1 CATAGTACTACACACGTGACC-ATCACTATCAGATACACGTAGTAGCCTGCA
39369320 CATAGTACTACACACGTGACCATCACT
1 CATAGTACTACACACGTGACCATCACT
39369347 TTCACTTTCA
Statistics
Matches: 103, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
48 3 0.03
49 6 0.06
50 33 0.32
51 52 0.50
52 4 0.04
53 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
CATAGTACTACACACGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
Found at i:39370942 original size:17 final size:17
Alignment explanation
Indices: 39370916--39370948 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39370906 TTTAAAAAGG
39370916 TTTTTTATAT-AGTGAT
1 TTTTTTATATGAGTGAT
39370932 TTTTGTTATATGAGTGA
1 TTTT-TTATATGAGTGA
39370949 GTTATTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TTTTTTATATGAGTGAT
Found at i:39372095 original size:20 final size:19
Alignment explanation
Indices: 39372048--39372096 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
39372038 TTTATTGAAA
*
39372048 ATGAATCAATATATATGTT
1 ATGAAACAATATATATGTT
*
39372067 AT-AATACAATTTATCATGTT
1 ATGAA-ACAATATAT-ATGTT
39372087 ATGAAACAAT
1 ATGAAACAAT
39372097 GTAAATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 12 0.48
21 2 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
ATGAAACAATATATATGTT
Found at i:39377427 original size:42 final size:42
Alignment explanation
Indices: 39377251--39377453 Score: 195
Period size: 42 Copynumber: 4.8 Consensus size: 42
39377241 AACTCACACA
* * * *
39377251 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATATCG
*
39377293 ATGCCAATAG--CCAG-CTATGGTCTTACAAGAATC-TCATATCG
1 ATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCAT-ATATCG
* * *
39377334 ATGCCAATGTCGCAGACATGGTCTCACACGAATC-TCATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCAT-ATATCG
*
39377376 ATGCTAATGTCCCAGACATGGTCTTACACGAATCATATAAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATAT-ATCG
* *
39377418 ATCCCAATGTCCCAGACATGGTGTTACACGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCA
39377454 CATCTCAGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.01
41 17 0.12
42 106 0.78
43 11 0.08
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATATCG
Found at i:39382685 original size:41 final size:41
Alignment explanation
Indices: 39382628--39382719 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
39382618 GGATTTCTTG
39382628 CTTGGGCTTGGAAAATTCTTATTGGGCCTTGCCTTCAAGAA
1 CTTGGGCTTGGAAAATTCTTATTGGGCCTTGCCTTCAAGAA
39382669 CTTGGGCTTGGAAAATTCTTATTGGGCCTTGCCTTCAAGAA
1 CTTGGGCTTGGAAAATTCTTATTGGGCCTTGCCTTCAAGAA
39382710 CTTGGGCTTG
1 CTTGGGCTTG
39382720 TGATCCATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (41 bp):
CTTGGGCTTGGAAAATTCTTATTGGGCCTTGCCTTCAAGAA
Found at i:39401627 original size:17 final size:18
Alignment explanation
Indices: 39401595--39401630 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39401585 TACTTCAATC
*
39401595 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAATATTCTTT
39401613 TCTTTTTCAA-ATTCTTT
1 TCTTTTTCAATATTCTTT
39401630 T
1 T
39401631 TCACTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTTTTCAATATTCTTT
Found at i:39401717 original size:22 final size:24
Alignment explanation
Indices: 39401666--39401718 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
39401656 TTTCACTCTC
*
39401666 TTTCGCTT-TTTCAATTTCTTGTT
1 TTTCGTTTCTTTCAATTTCTTGTT
39401689 TTT--TTTCTTTC-ATTTCTT-TT
1 TTTCGTTTCTTTCAATTTCTTGTT
39401709 TTTCGTTTCT
1 TTTCGTTTCT
39401719 CGATTTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 9 0.35
23 3 0.12
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTCGTTTCTTTCAATTTCTTGTT
Found at i:39406776 original size:29 final size:29
Alignment explanation
Indices: 39406734--39406795 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
39406724 CAACATCCTC
* *
39406734 GGTGATTTGAAGTCCACCCGACCTACCAA
1 GGTGATTTCAAGTCCACCCGACCCACCAA
* *
39406763 GGTGATTTCAAGTCCCCCCGACCCACCAC
1 GGTGATTTCAAGTCCACCCGACCCACCAA
39406792 GGTG
1 GGTG
39406796 CTTAACGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (29 bp):
GGTGATTTCAAGTCCACCCGACCCACCAA
Found at i:39407069 original size:23 final size:23
Alignment explanation
Indices: 39407043--39407093 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
39407033 CTATAAAAGT
39407043 AGACATAATTGTGCTATAGAAAC
1 AGACATAATTGTGCTATAGAAAC
39407066 AGACATAATTGTGCTATAGAAAC
1 AGACATAATTGTGCTATAGAAAC
39407089 AGACA
1 AGACA
39407094 AAACCATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
AGACATAATTGTGCTATAGAAAC
Found at i:39411476 original size:11 final size:12
Alignment explanation
Indices: 39411456--39411495 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
39411446 TAAATGGTTC
39411456 ATTTATATATTT
1 ATTTATATATTT
*
39411468 -TTTAAATATTT
1 ATTTATATATTT
39411479 ATTTATATATTAT
1 ATTTATATATT-T
39411492 ATTT
1 ATTT
39411496 TTAGCTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:39444675 original size:19 final size:19
Alignment explanation
Indices: 39444648--39444689 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
39444638 AAAATTAATT
*
39444648 TTAATCAAATTAAATT-AAA
1 TTAACCAAATT-AATTAAAA
39444667 TTAACCAAATTAATTAAAA
1 TTAACCAAATTAATTAAAA
39444686 TTAA
1 TTAA
39444690 TATGATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAACCAAATTAATTAAAA
Found at i:39445320 original size:25 final size:25
Alignment explanation
Indices: 39445278--39445325 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39445268 TTGTAGAGAG
39445278 AAAATTCTCTAAAGATATTATTTCAA
1 AAAATTCTCTAAAGATATT-TTTCAA
* *
39445304 AAAATT-TCTAGATATATTTTTC
1 AAAATTCTCTAAAGATATTTTTC
39445326 TTATTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (25 bp):
AAAATTCTCTAAAGATATTTTTCAA
Found at i:39451227 original size:49 final size:49
Alignment explanation
Indices: 39451155--39451252 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
39451145 TGAGTAACAT
39451155 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
1 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
39451204 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
1 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
39451253 ATCTTTCTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (49 bp):
GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
Found at i:39452834 original size:75 final size:75
Alignment explanation
Indices: 39452711--39452860 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 75
39452701 TCTATGCCTC
39452711 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
1 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
*
39452776 TGGCATATTA
66 TGACATATTA
* * * * *
39452786 TATCTTCTTAGAGTCATAAGCTTCGATGTTTAAGACAAAGCATCTCTCCAATTGGACTTGATAGA
1 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
39452851 TGACATATTA
66 TGACATATTA
39452861 GTCTTTCAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (75 bp):
TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
TGACATATTA
Found at i:39456943 original size:25 final size:24
Alignment explanation
Indices: 39456915--39456970 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
39456905 GCGAGCCATT
39456915 TATCGAGAAGCTCAAGAGAGTCAAA
1 TATCG-GAAGCTCAAGAGAGTCAAA
**
39456940 TATCGGAAAGCTCGTGAGAGTCAAA
1 TATCGG-AAGCTCAAGAGAGTCAAA
39456965 TATCGG
1 TATCGG
39456971 GATGCTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (24 bp):
TATCGGAAGCTCAAGAGAGTCAAA
Found at i:39458156 original size:21 final size:22
Alignment explanation
Indices: 39458115--39458157 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
39458105 TAAATAAATG
39458115 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
39458138 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
39458158 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:39458303 original size:26 final size:27
Alignment explanation
Indices: 39458252--39458308 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
39458242 ACAAAATAGC
* *
39458252 AAAATGAAAATAGGGGAGAAAGGAAAG
1 AAAAAGAAAATAGGGAAGAAAGGAAAG
39458279 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAATAGGGAA-GAAAGGAAAG
39458305 AAAA
1 AAAA
39458309 TTTGCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAATAGGGAAGAAAGGAAAG
Found at i:39459236 original size:21 final size:19
Alignment explanation
Indices: 39459190--39459245 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
39459180 AATCTTCAAG
*
39459190 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
39459209 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
39459228 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
39459246 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39459249 original size:24 final size:23
Alignment explanation
Indices: 39459203--39459268 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
39459193 ATGTAATCTT
*
39459203 AGATATGA-TATGCAGTCTT---
1 AGATATGATTATGCAATCTTAGA
39459222 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* *
39459246 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
39459269 GATTTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.21
21 10 0.26
23 12 0.31
24 9 0.23
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:39459267 original size:23 final size:24
Alignment explanation
Indices: 39459222--39459268 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39459212 ATGCAGTCTT
39459222 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
39459246 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
39459269 GATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:39459497 original size:23 final size:23
Alignment explanation
Indices: 39459453--39459497 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39459443 TCTTATTTTG
* *
39459453 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
39459476 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
39459498 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:39459814 original size:23 final size:21
Alignment explanation
Indices: 39459765--39459830 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
39459755 TTTTTATGTA
39459765 ATATATATATATA-TATTGTTT
1 ATATATATATATACTA-TGTTT
*
39459786 -TTTATATAGTATACGTATGTTT
1 ATATATATA-TATAC-TATGTTT
*
39459808 ATATATATTTTATACATATGTTT
1 ATATATA-TATATAC-TATGTTT
39459831 TTATTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.19
21 4 0.11
22 5 0.14
23 19 0.53
24 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (21 bp):
ATATATATATATACTATGTTT
Found at i:39459959 original size:2 final size:2
Alignment explanation
Indices: 39459948--39460001 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
39459938 TTTCTAATGA
39459948 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39459989 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
39460002 CGCACATGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39461883 original size:50 final size:50
Alignment explanation
Indices: 39461771--39462017 Score: 201
Period size: 50 Copynumber: 4.8 Consensus size: 50
39461761 ATTTGGGTAA
* *
39461771 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* * *
39461827 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
39461877 AGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * ** *
39461927 AGAACTCCCATGTATGACCATATCTGGGATACGGCATTGGCA-TTATA-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
39461975 AAAACATCCCATGTAAGACCATGTCTAGGACATGGCCTTGGCA
1 -AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39462018 TGTTATTGTC
Statistics
Matches: 158, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 79 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39464261 original size:39 final size:38
Alignment explanation
Indices: 39464141--39464274 Score: 105
Period size: 39 Copynumber: 3.4 Consensus size: 38
39464131 GACCTTGAGT
* *
39464141 CGATGAGACACTGAGTGTCATACTGTTACTTCGAA-TAGATT
1 CGATGAGACACTGGGTGTCA-ACT-TTACTTCGAACT--ATC
** ** *
39464182 CGATGAGGTACTGGGTACCAAC-TTACTTCG-GCT-TGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTAT--C
39464219 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACT-TTACTTCGAACTATC
*
39464258 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
39464275 CCATTCTGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
35 1 0.01
37 18 0.25
38 9 0.12
39 25 0.34
40 4 0.05
41 16 0.22
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
Found at i:39471145 original size:35 final size:36
Alignment explanation
Indices: 39471079--39471154 Score: 136
Period size: 35 Copynumber: 2.1 Consensus size: 36
39471069 TTTATTACCA
*
39471079 GTTTAAGGTTTAGTTAGTATTTTTATCAAAAAAAAG
1 GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
39471115 GTTTAAGGTTTAGTCAGTA-TTTTATCAAAAAAAAG
1 GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
39471150 GTTTA
1 GTTTA
39471155 GGCAGTAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 21 0.54
36 18 0.46
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (36 bp):
GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
Found at i:39471182 original size:14 final size:14
Alignment explanation
Indices: 39471163--39471206 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
39471153 TAGGCAGTAG
*
39471163 AAGAAGAAAAGAAA
1 AAGAAGAAGAGAAA
* *
39471177 AAGAAGAGGAGAAG
1 AAGAAGAAGAGAAA
39471191 AAGAAGAAGAGAAA
1 AAGAAGAAGAGAAA
39471205 AA
1 AA
39471207 AATGGAAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAGAAA
Found at i:39471943 original size:26 final size:26
Alignment explanation
Indices: 39471907--39471958 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
39471897 CAAATTGCAG
39471907 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
39471933 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
39471959 CCTTAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
ATGAAAAATACCAATTGGTTTCTAAC
Found at i:39472310 original size:3 final size:3
Alignment explanation
Indices: 39472297--39472332 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39472287 TTTTACAGTC
*
39472297 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
39472333 GTTATTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:39472974 original size:27 final size:26
Alignment explanation
Indices: 39472915--39472974 Score: 61
Period size: 27 Copynumber: 2.2 Consensus size: 26
39472905 TATTTAAAAA
*
39472915 ATAAAAAATCATAAAATTTATTAAAT
1 ATAAAAAATCATAAAATTGATTAAAT
39472941 ATGAAAAAAT-A-AAAATTGATATAAACTT
1 AT-AAAAAATCATAAAATTGAT-TAAA--T
39472969 ATAAAA
1 ATAAAA
39472975 TTTATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 8 0.28
26 7 0.24
27 11 0.38
28 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAAAAAATCATAAAATTGATTAAAT
Found at i:39473016 original size:45 final size:44
Alignment explanation
Indices: 39472925--39473020 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
39472915 ATAAAAAATC
39472925 ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
1 ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
* * *
39472969 ATAAAATTTA-TAAATATTATAAAAATATAAAATTTATAATGAA-TT
1 ATAAAATTTATTAAATATGA-AAAAATA-AAAATTGAT-ATAAACTT
39473014 ATAAAAT
1 ATAAAAT
39473021 CAATAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 8 0.17
44 17 0.37
45 17 0.37
46 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (44 bp):
ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
Found at i:39473027 original size:45 final size:43
Alignment explanation
Indices: 39472936--39473027 Score: 105
Period size: 45 Copynumber: 2.1 Consensus size: 43
39472926 TAAAATTTAT
**
39472936 TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATTTA
1 TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATCAA
* * *
39472979 TAAATATTATAAAAATATAAAATTTATAATGAA-TTATAAAATCAA
1 TAAATATGA-AAAAATA-AAAATTGAT-ATAAACTTATAAAATCAA
39473024 TAAA
1 TAAA
39473028 AAATATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 8 0.20
44 7 0.17
45 22 0.54
46 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (43 bp):
TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATCAA
Found at i:39473049 original size:21 final size:20
Alignment explanation
Indices: 39472989--39473073 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
39472979 TAAATATTAT
39472989 AAAAATA-TAAAATT-TATA
1 AAAAATATTAAAATTCTATA
** *
39473007 ATGAAT-TATAAAA-TCAATA
1 AAAAATAT-TAAAATTCTATA
*
39473026 AAAAATATTTAAAATTTTATA
1 AAAAATA-TTAAAATTCTATA
39473047 AAAACATATTAAAATTCTATA
1 AAAA-ATATTAAAATTCTATA
39473068 AAAAAT
1 AAAAAT
39473074 CACAAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 5 0.10
19 12 0.23
20 7 0.13
21 25 0.48
22 3 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAAATATTAAAATTCTATA
Found at i:39473089 original size:20 final size:20
Alignment explanation
Indices: 39473066--39473110 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39473056 TAAAATTCTA
*
39473066 TAAAAAATCACAAAAATTAT
1 TAAAAAATCACAAAAAGTAT
* * *
39473086 TAAAAGATTATAAAAAGTAT
1 TAAAAAATCACAAAAAGTAT
39473106 TAAAA
1 TAAAA
39473111 TTGATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAAAATCACAAAAAGTAT
Found at i:39473604 original size:19 final size:20
Alignment explanation
Indices: 39473582--39473623 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
39473572 TTTATATCAA
*
39473582 TTTTAATATTTTTA-TATTT
1 TTTTAACATTTTTATTATTT
*
39473601 TTTTACCATTTTTATTATTT
1 TTTTAACATTTTTATTATTT
39473621 TTT
1 TTT
39473624 AAGAATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTAACATTTTTATTATTT
Found at i:39473744 original size:27 final size:26
Alignment explanation
Indices: 39473700--39473827 Score: 92
Period size: 27 Copynumber: 5.0 Consensus size: 26
39473690 TATTAGAACT
*
39473700 TATTTGAAT-TTTTATATTTTTATTA
1 TATTTTAATATTTTATATTTTTATTA
*
39473725 TATTTATAATATTTTATATTTTTTATAA
1 TATTT-TAATATTTTATA-TTTTTATTA
***
39473753 TATTTT-ATCATTTTAATAAGGTTA-TA
1 TATTTTAAT-ATTTT-ATATTTTTATTA
39473779 TAATTTTAATATTTT-TA--TTT-TTA
1 T-ATTTTAATATTTTATATTTTTATTA
39473802 T-TTTTAATATTTAATATATTTTTATT
1 TATTTTAATATTT--TATATTTTTATT
39473828 TTTTTCTACT
Statistics
Matches: 82, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
21 11 0.13
23 6 0.07
24 2 0.02
25 7 0.09
26 10 0.12
27 28 0.34
28 18 0.22
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTTAATATTTTATATTTTTATTA
Found at i:39473766 original size:19 final size:18
Alignment explanation
Indices: 39473707--39473802 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
39473697 ACTTATTTGA
39473707 ATTTTTAT-AT-TTTTATT
1 ATTTTTATAATATTTTA-T
*
39473724 ATATTTATAATATTTTAT
1 ATTTTTATAATATTTTAT
39473742 ATTTTTTATAATATTTTAT
1 A-TTTTTATAATATTTTAT
* ** *
39473761 CATTTTAATAAGGTTATAT
1 -ATTTTTATAATATTTTAT
*
39473780 A-ATTT-TAATATTTT-T
1 ATTTTTATAATATTTTAT
39473795 ATTTTTAT
1 ATTTTTAT
39473803 TTTTAATATT
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.03
16 9 0.15
17 10 0.16
18 5 0.08
19 34 0.56
20 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTATAATATTTTAT
Found at i:39475381 original size:27 final size:27
Alignment explanation
Indices: 39475343--39475433 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
39475333 GGCCATGACA
*
39475343 TACTTTGAATGGATCGCCTTTGTGGCG
1 TACTCTGAATGGATCGCCTTTGTGGCG
* **
39475370 TACTCTGAATGGTTCGCCTTAATGGCG
1 TACTCTGAATGGATCGCCTTTGTGGCG
* * * * *
39475397 TACTTTGTAT-GATTGCCTGTGTGGTG
1 TACTCTGAATGGATCGCCTTTGTGGCG
*
39475423 TATTCTGAATG
1 TACTCTGAATG
39475434 AAGGCTTTAT
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
26 17 0.35
27 31 0.65
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.40
Consensus pattern (27 bp):
TACTCTGAATGGATCGCCTTTGTGGCG
Found at i:39480916 original size:14 final size:14
Alignment explanation
Indices: 39480897--39480923 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39480887 ATGGAAAAAA
39480897 AATTTAGGTACCAG
1 AATTTAGGTACCAG
39480911 AATTTAGGTACCA
1 AATTTAGGTACCA
39480924 ATCTGGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
AATTTAGGTACCAG
Found at i:39485129 original size:25 final size:25
Alignment explanation
Indices: 39485099--39485148 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39485089 AAGTAATCCA
39485099 CCCACTGAGAATTGCAAAGATCAAG
1 CCCACTGAGAATTGCAAAGATCAAG
39485124 CCCACTGAGAATTGCAAAGATCAAG
1 CCCACTGAGAATTGCAAAGATCAAG
39485149 TATTGGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
CCCACTGAGAATTGCAAAGATCAAG
Found at i:39486043 original size:16 final size:16
Alignment explanation
Indices: 39486024--39486055 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39486014 TCATGAGTAG
39486024 GGGTGTTCATTCGGTT
1 GGGTGTTCATTCGGTT
39486040 GGGTGTTCATTCGGTT
1 GGGTGTTCATTCGGTT
39486056 AACCGACCCG
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:0.06, C:0.12, G:0.38, T:0.44
Consensus pattern (16 bp):
GGGTGTTCATTCGGTT
Found at i:39486238 original size:9 final size:9
Alignment explanation
Indices: 39486224--39486272 Score: 89
Period size: 9 Copynumber: 5.4 Consensus size: 9
39486214 TTTGGTTAAA
39486224 AATTAACCG
1 AATTAACCG
39486233 AATTAACCG
1 AATTAACCG
39486242 AATTAACCG
1 AATTAACCG
*
39486251 AATTACCCG
1 AATTAACCG
39486260 AATTAACCG
1 AATTAACCG
39486269 AATT
1 AATT
39486273 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:39486324 original size:12 final size:13
Alignment explanation
Indices: 39486292--39486339 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
39486282 CATAATTAAA
* *
39486292 TTATTTTTGGACT
1 TTATTTTTAGATT
*
39486305 TTAGTTTTAG-TT
1 TTATTTTTAGATT
39486317 TTATTTTTAGAATT
1 TTATTTTTAG-ATT
39486331 TTATTTTTA
1 TTATTTTTA
39486340 TTTATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (13 bp):
TTATTTTTAGATT
Found at i:39487261 original size:27 final size:27
Alignment explanation
Indices: 39487231--39487295 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
39487221 GCCTATCAAT
39487231 GCGCCAATGAAGGTGCCTCACAGAGAG
1 GCGCCAATGAAGGTGCCTCACAGAGAG
*
39487258 GCGCCAATGAAGGTGCCTCATAGAGAG
1 GCGCCAATGAAGGTGCCTCACAGAGAG
39487285 GCGCCAATGAA
1 GCGCCAATGAA
39487296 TATTGTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.32, T:0.12
Consensus pattern (27 bp):
GCGCCAATGAAGGTGCCTCACAGAGAG
Found at i:39487437 original size:19 final size:19
Alignment explanation
Indices: 39487291--39487407 Score: 80
Period size: 19 Copynumber: 5.8 Consensus size: 19
39487281 AGAGGCGCCA
39487291 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
39487310 ATGAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
39487330 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
39487354 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
39487371 ATGAATATTGTAATTTTTTGT
1 ATGAATATTGTAA--TTTTGT
39487392 ATGAATATTGTAATTT
1 ATGAATATTGTAATTT
39487408 ATAATTTTGT
Statistics
Matches: 77, Mismatches: 8, Indels: 26
0.69 0.07 0.23
Matches are distributed among these distances:
17 5 0.06
18 4 0.05
19 22 0.29
20 13 0.17
21 20 0.26
22 5 0.06
23 4 0.05
24 3 0.04
25 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:39487439 original size:27 final size:26
Alignment explanation
Indices: 39487364--39487450 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 26
39487354 TTGGATTAGT
39487364 ATTTTGTATGAATATTGTAA--T-T-
1 ATTTTGTATGAATATTGTAATTTATA
39487386 -TTTTGTATGAATATTGTAATTTATA
1 ATTTTGTATGAATATTGTAATTTATA
*
39487411 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAA-TTTATA
39487438 ATTTTGTATGAAT
1 ATTTTGTATGAAT
39487451 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
21 19 0.33
23 1 0.02
24 1 0.02
26 19 0.33
27 18 0.31
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (26 bp):
ATTTTGTATGAATATTGTAATTTATA
Found at i:39487794 original size:60 final size:60
Alignment explanation
Indices: 39487701--39487822 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
39487691 TGTATGAATA
* * * * * *
39487701 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAATAATTTAGGATTAAGCTATAAATTGTTGTGT
*
39487761 TTGTAATTA-TTTAAAATTTAATTTATTAATAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAATAATTTAGGATTAAGCTATAAATTGTTGTGT
39487821 TT
1 TT
39487823 AGGTTAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAATAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:39487900 original size:38 final size:38
Alignment explanation
Indices: 39487855--39487936 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
39487845 CATATAAAGT
39487855 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
*
39487893 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
39487931 TTATAA
1 TTATAA
39487937 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
Found at i:39488014 original size:15 final size:15
Alignment explanation
Indices: 39487973--39488014 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
39487963 GTTAACTAAT
*
39487973 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
39487988 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
39488004 TTAAATTTTAT
1 TTAAATTTTAT
39488015 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:39488182 original size:8 final size:8
Alignment explanation
Indices: 39488164--39488214 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
39488154 ACAATATTCA
39488164 TACAA-AT
1 TACAATAT
39488171 TACAATAT
1 TACAATAT
39488179 TACAATATT
1 TACAATA-T
*
39488188 CATACAAAAT
1 --TACAATAT
*
39488198 TATAATAT
1 TACAATAT
39488206 TACAATAT
1 TACAATAT
39488214 T
1 T
39488215 CATAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 5 0.14
8 23 0.64
9 1 0.03
10 1 0.03
11 6 0.17
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
TACAATAT
Found at i:39488197 original size:27 final size:27
Alignment explanation
Indices: 39488151--39488254 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 27
39488141 TTATAAAATA
39488151 ATTACAATATTCATAC-AAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
39488177 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
39488204 ATTACAATATTCATAAAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
39488231 ATT-C-ATA--CA-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
39488252 ATT
1 ATT
39488255 CATACAAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.19
22 1 0.01
23 2 0.03
25 3 0.04
26 17 0.23
27 37 0.50
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:39488199 original size:19 final size:19
Alignment explanation
Indices: 39488150--39488264 Score: 100
Period size: 19 Copynumber: 6.2 Consensus size: 19
39488140 ATTATAAAAT
39488150 AATTACAATATTCATAC-A
1 AATTACAATATTCATACAA
39488168 AATTACAATA-T--TACAA
1 AATTACAATATTCATACAA
* *
39488184 TATTCATACAAAATT-AT--AA
1 -AAT--TACAATATTCATACAA
* *
39488203 TATTACAATATTCATAAAA
1 AATTACAATATTCATACAA
39488222 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
39488243 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
39488262 AAT
1 AAT
39488265 ACTAATCCAA
Statistics
Matches: 79, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
15 3 0.04
16 9 0.11
17 5 0.06
18 11 0.14
19 30 0.38
20 1 0.01
21 20 0.25
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:39488244 original size:21 final size:21
Alignment explanation
Indices: 39488218--39488263 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
39488208 CAATATTCAT
39488218 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
39488239 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
39488260 AAAA
1 AAAA
39488264 TACTAATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:39488316 original size:19 final size:19
Alignment explanation
Indices: 39488297--39488334 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39488287 AAATTTAATT
39488297 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
39488317 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
39488335 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Found at i:39488466 original size:9 final size:10
Alignment explanation
Indices: 39488445--39488474 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
39488435 ATTTTTTTAA
39488445 AAAAAATATT
1 AAAAAATATT
*
39488455 AAAAAATATA
1 AAAAAATATT
39488465 AAAAAATATT
1 AAAAAATATT
39488475 TTATTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAAATATT
Found at i:39490819 original size:44 final size:44
Alignment explanation
Indices: 39490766--39490974 Score: 151
Period size: 44 Copynumber: 4.8 Consensus size: 44
39490756 AATCCACCAT
*
39490766 CTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAA
1 CTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAA
* * * *
39490810 CTTCAATCTATTCCACTGCTGCCCAGGGAGAT-AGAATTACTG---G
1 CTTCAATCTACTCCACTACTGCCTAGGGAGATAAG-A-T-CTGTAAA
* * * * * ** *
39490853 CTTCAATGC-ACTCCACT-GTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAAT-CTACTCCACTACT-GCCT-AGGGAGATAAGATCTGTAAA
* * *
39490898 CTTCGATCTGCTCCACTACTGCCTAAGGAGATAAGATCTGTAAA
1 CTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAA
* * *
39490942 CTTCAATCTATTCCACTGCTGCCCAGGGAGATA
1 CTTCAATCTACTCCACTACTGCCTAGGGAGATA
39490975 GAATTACTTT
Statistics
Matches: 123, Mismatches: 30, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
42 3 0.02
43 19 0.15
44 79 0.64
45 18 0.15
46 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (44 bp):
CTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAA
Found at i:39490901 original size:132 final size:132
Alignment explanation
Indices: 39490704--39490982 Score: 506
Period size: 132 Copynumber: 2.1 Consensus size: 132
39490694 GCAACTTCAA
*
39490704 GGAGATAGGAA-TACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCT
1 GGAGATA-GAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCT
*
39490768 TCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCC
65 TCGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCC
39490833 CAG
130 CAG
*
39490836 GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
*
39490901 CGATCTGCTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
66 CGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
39490966 AG
131 AG
39490968 GGAGATAGAATTACT
1 GGAGATAGAATTACT
39490983 TTCTTCGATC
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
131 3 0.02
132 139 0.98
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
CGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
AG
Found at i:39491036 original size:44 final size:44
Alignment explanation
Indices: 39490981--39491380 Score: 372
Period size: 44 Copynumber: 9.0 Consensus size: 44
39490971 GATAGAATTA
* *
39490981 CTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * ***
39491025 CTTTATTCGATCTACTTCGACACCAGTATGGGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTG
* * *
39491070 GTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* ***
39491114 CTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTG
* * *
39491159 GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * *** *
39491203 CTTTCTTCGATCTGCTTCACCACCAGTATGGGAAGACAATATCTG
1 CTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTG
* * ** * *
39491248 GTATCTTTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * * * *** *
39491292 CTTTCTTTGACCTGCTTTGC-CACCAGTATGGGAAGGCAAGATCTG
1 CTTTCTTCGATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTG
* * *
39491337 GTATC-TCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTG
1 CTTTCTTC-GATCTACTTCACGCCAGTACATGAAGACAAGATCTG
39491381 TTATCTTTGA
Statistics
Matches: 277, Mismatches: 72, Indels: 14
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.00
44 142 0.51
45 133 0.48
46 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
Found at i:39491390 original size:89 final size:89
Alignment explanation
Indices: 39490984--39491380 Score: 607
Period size: 89 Copynumber: 4.5 Consensus size: 89
39490974 AGAATTACTT
* * * *
39490984 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTGCTTTATTCGATCTACTTCGA-CAC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACCAC
39491048 CAGTATGGGAAGACAAGATCTGGTA
65 CAGTATGGGAAGACAAGATCTGGTA
* *
39491073 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
39491138 AGTATGGGAAGACAAGATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
*
39491162 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
*
39491227 AGTATGGGAAGACAATATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* * * * * * **
39491251 TCTTTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTTTGACCTGCTTTGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
*
39491316 AGTATGGGAAGGCAAGATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* *
39491340 TCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTG
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
39491381 TTATCTTTGA
Statistics
Matches: 287, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 1 0.00
89 286 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (89 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
AGTATGGGAAGACAAGATCTGGTA
Found at i:39491397 original size:22 final size:22
Alignment explanation
Indices: 39491366--39491408 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39491356 CTCCAGTACA
*
39491366 TGAAGACAAGATCTGTTATCTT
1 TGAAGACAAGATCTGGTATCTT
*
39491388 TGAAGGCAAGATCTGGTATCT
1 TGAAGACAAGATCTGGTATCT
39491409 CTGATCTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (22 bp):
TGAAGACAAGATCTGGTATCTT
Found at i:39491429 original size:66 final size:66
Alignment explanation
Indices: 39491323--39491456 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
39491313 ACCAGTATGG
*
39491323 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTT
39491388 T
66 T
*
39491389 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTT
39491454 T
66 T
39491455 GA
1 GA
39491457 CCTGCTTCGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (66 bp):
GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTT
T
Found at i:39491525 original size:155 final size:155
Alignment explanation
Indices: 39491234--39491543 Score: 530
Period size: 155 Copynumber: 2.0 Consensus size: 155
39491224 ACCAGTATGG
* *
39491234 GAAGACAATATCTGGTATCTTTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGGTATCTCTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTT
* *
39491299 TGACCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTA
66 TGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTA
39491364 CATGAAGACAAGATCTGTTATCTTT
131 CATGAAGACAAGATCTGTTATCTTT
* * * * *
39491389 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGGTATCTCTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTT
*
39491454 TGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTTATCTACTTCACGCCAGTA
66 TGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTA
39491519 CATGAAGACAAGATCTGTTATCTTT
131 CATGAAGACAAGATCTGTTATCTTT
39491544 CAACCTTCTC
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
155 145 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (155 bp):
GAAGACAAGATCTGGTATCTCTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTT
TGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTA
CATGAAGACAAGATCTGTTATCTTT
Found at i:39491531 original size:44 final size:44
Alignment explanation
Indices: 39491388--39491541 Score: 166
Period size: 44 Copynumber: 3.5 Consensus size: 44
39491378 CTGTTATCTT
* *
39491388 TGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACA
1 TGAAGACAAGATCTGGTATCTCTTATCTACTTCACGCCAGTACA
* * * * * * **
39491432 TGAAGACAAGATCTGTTTTCT-TTGACCTGCTTCGCCACCAGTATG
1 TGAAGACAAGATCTGGTATCTCTT-ATCTACTTC-ACGCCAGTACA
* *
39491477 GGAAGGCAAGATCTGGTATCTCTTATCTACTTCACGCCAGTACA
1 TGAAGACAAGATCTGGTATCTCTTATCTACTTCACGCCAGTACA
*
39491521 TGAAGACAAGATCTGTTATCT
1 TGAAGACAAGATCTGGTATCT
39491542 TTCAACCTTC
Statistics
Matches: 84, Mismatches: 23, Indels: 6
0.74 0.20 0.05
Matches are distributed among these distances:
43 1 0.01
44 50 0.60
45 31 0.37
46 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TGAAGACAAGATCTGGTATCTCTTATCTACTTCACGCCAGTACA
Found at i:39499627 original size:20 final size:20
Alignment explanation
Indices: 39499602--39499641 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39499592 TAAAGGTCTA
*
39499602 TAATGCATATAATGTGATGC
1 TAATGCATATAATGCGATGC
*
39499622 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCGATGC
39499642 ATGAGATGAA
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:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:39505759 original size:31 final size:29
Alignment explanation
Indices: 39505690--39505759 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
39505680 ACCTCAGATT
* *
39505690 ACATTTTAGTCACTTATATTTGAAATGTT
1 ACATTTTAGTCACTTACATTTGAAATGTA
* * *
39505719 ATATTTTAGTCACTTACATTATCGTATTGTA
1 ACATTTTAGTCACTTACATT-T-GAAATGTA
39505750 ACATTTTAGT
1 ACATTTTAGT
39505760 TACTGAGCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.55
30 1 0.03
31 14 0.42
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTACATTTGAAATGTA
Found at i:39506101 original size:203 final size:204
Alignment explanation
Indices: 39505752--39506163 Score: 781
Period size: 203 Copynumber: 2.0 Consensus size: 204
39505742 GTATTGTAAC
*
39505752 ATTTTAGTTACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
39505817 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
39505882 AGCAATTTAATTTTTTCTTTTATGTTTTTCAAC-TTTTTTTTCTTATTTTCCATTATCTTTTGTT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTTCTTATTTTCCATTATCTTTTGTT
39505946 TCTCCCTCT
196 TCTCCCTCT
39505955 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
*
39506020 TTATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
* *
39506085 AGCAATTTAATTTTTTCTTTTATGTTTTTTAACTTTTTTTTTCTTATTTTCCATTCTCTTTTGTT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTTCTTATTTTCCATTATCTTTTGTT
39506150 TCTCCCTCT
196 TCTCCCTCT
39506159 ATTTT
1 ATTTT
39506164 CCTCCCTTTT
Statistics
Matches: 204, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
203 160 0.78
204 44 0.22
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.50
Consensus pattern (204 bp):
ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTTCTTATTTTCCATTATCTTTTGTT
TCTCCCTCT
Found at i:39511062 original size:17 final size:17
Alignment explanation
Indices: 39511036--39511075 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39511026 GAATGGAGGT
*
39511036 AAATTAAGATCATTTTG
1 AAATTCAGATCATTTTG
39511053 AAATTCAGATCATTTTG
1 AAATTCAGATCATTTTG
39511070 AAATTC
1 AAATTC
39511076 TACTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (17 bp):
AAATTCAGATCATTTTG
Found at i:39512664 original size:20 final size:20
Alignment explanation
Indices: 39512627--39512665 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39512617 AATGACTTGG
*
39512627 AAAATTTTAATTTCGAGACC
1 AAAATTTTAAATTCGAGACC
39512647 AAAATTTTTAAATT-GAGAC
1 AAAA-TTTTAAATTCGAGAC
39512666 GTTTCGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAATTCGAGACC
Found at i:39518514 original size:27 final size:27
Alignment explanation
Indices: 39518446--39518517 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
39518436 GGAAATCATA
* *
39518446 TAGAGTACGCCACCAAGGCATTCCATT
1 TAGAGTTCGCCACAAAGGCATTCCATT
* * ** * *
39518473 CAGAATTTTCTACAAAGGCATTCCTTT
1 TAGAGTTCGCCACAAAGGCATTCCATT
39518500 TAGAGTTCGCCACAAAGG
1 TAGAGTTCGCCACAAAGG
39518518 TTATTCTTAC
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (27 bp):
TAGAGTTCGCCACAAAGGCATTCCATT
Found at i:39523972 original size:14 final size:14
Alignment explanation
Indices: 39523953--39523991 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
39523943 ATAACGGTGA
39523953 TAATAATAATAAAT
1 TAATAATAATAAAT
*
39523967 TAATAATAATAGAT
1 TAATAATAATAAAT
39523981 TAATAATAATA
1 TAATAATAATA
39523992 TTACTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:39523974 original size:17 final size:17
Alignment explanation
Indices: 39523952--39523991 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39523942 AATAACGGTG
39523952 ATAATAATA-ATAAATTA
1 ATAATAATAGATAAA-TA
*
39523969 ATAATAATAGATTAATA
1 ATAATAATAGATAAATA
39523986 ATAATA
1 ATAATA
39523992 TTACTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAATAGATAAATA
Found at i:39524612 original size:23 final size:20
Alignment explanation
Indices: 39524569--39524618 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 20
39524559 TTTCCTAAAC
39524569 AAAGAAACTGAAAAAAAGAA
1 AAAGAAACTGAAAAAAAGAA
*
39524589 AAAGAACAGTGAAGAAAAACGAA
1 AAAGAA-ACTGAA-AAAAA-GAA
39524612 AAAGAAA
1 AAAGAAA
39524619 AAAACGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 5 0.19
22 6 0.23
23 9 0.35
ACGTcount: A:0.72, C:0.06, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAGAAACTGAAAAAAAGAA
Found at i:39525072 original size:17 final size:15
Alignment explanation
Indices: 39525041--39525075 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
39525031 AAAACTGAAC
39525041 ATTTTATTATTATTT
1 ATTTTATTATTATTT
39525056 ATTTTA-TA-TATTT
1 ATTTTATTATTATTT
39525069 ATTTTAT
1 ATTTTAT
39525076 ATCTGGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.58
14 2 0.11
15 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:39536840 original size:36 final size:36
Alignment explanation
Indices: 39536787--39536858 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
39536777 GAATTCTTTC
39536787 TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
1 TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
39536823 TTCTTGA-TTTTCTAGCTCCTGTCCAGCAGCCAAACA
1 TTCTTGATTTTTC-AGCTCCTGTCCAGCAGCCAAACA
39536859 CTCAGTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 5 0.14
36 30 0.86
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (36 bp):
TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
Found at i:39538876 original size:10 final size:10
Alignment explanation
Indices: 39538861--39538889 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
39538851 GAATTAGTCT
39538861 GTTTCCTAAA
1 GTTTCCTAAA
39538871 GTTTCCTAAA
1 GTTTCCTAAA
39538881 GTTTCCTAA
1 GTTTCCTAA
39538890 GTTAGGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (10 bp):
GTTTCCTAAA
Found at i:39546991 original size:11 final size:13
Alignment explanation
Indices: 39546975--39547007 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39546965 ATTTCACGGA
39546975 AAAATTTCG-T-G
1 AAAATTTCGTTCG
39546986 AAAATTTCGTTCG
1 AAAATTTCGTTCG
39546999 AAAATTTCG
1 AAAATTTCG
39547008 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:39547711 original size:28 final size:30
Alignment explanation
Indices: 39547675--39547730 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
39547665 TCCGAGATTT
*
39547675 GGGGAAAAAT-GTAAATTTGC-AAAGTTTA
1 GGGGAAAAATCATAAATTTGCTAAAGTTTA
* *
39547703 GGGGCAAAATCATAATTTTGCTAAAGTT
1 GGGGAAAAATCATAAATTTGCTAAAGTT
39547731 CGAGTCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 8 0.35
30 6 0.26
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGAAAAATCATAAATTTGCTAAAGTTTA
Found at i:39548264 original size:51 final size:51
Alignment explanation
Indices: 39548200--39548537 Score: 391
Period size: 51 Copynumber: 6.7 Consensus size: 51
39548190 TATCGATGAA
* * * *
39548200 CACGTGTGTAGTACTGTGTGAAGGCTATTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * * * * *
39548251 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATGTTGGT
* * *
39548302 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * *
39548353 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
* ** *
39548404 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
*
39548454 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-GCTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG-TTGGT
39548504 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
39548538 TATCGAATGA
Statistics
Matches: 245, Mismatches: 35, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.00
50 89 0.36
51 154 0.63
52 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
Found at i:39548376 original size:102 final size:101
Alignment explanation
Indices: 39548200--39548543 Score: 503
Period size: 102 Copynumber: 3.4 Consensus size: 101
39548190 TATCGATGAA
* *
39548200 CACGTGTGTAGTACTGTGTGAAGGCTATTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
39548265 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
*
39548302 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
39548367 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * *** * *
39548404 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * *
39548468 TATGTGAAGGCTACTACGTGAACCGTAAAGC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
*
39548504 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
39548544 ATGATAAAAG
Statistics
Matches: 222, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
100 40 0.18
101 47 0.21
102 134 0.60
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:39550445 original size:22 final size:22
Alignment explanation
Indices: 39550418--39550459 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39550408 TTAACTATAC
39550418 TTTTTAGCACATATTCCTTTGT
1 TTTTTAGCACATATTCCTTTGT
* *
39550440 TTTTTAGCACGTTTTCCTTT
1 TTTTTAGCACATATTCCTTT
39550460 CTCTTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (22 bp):
TTTTTAGCACATATTCCTTTGT
Found at i:39555609 original size:7 final size:6
Alignment explanation
Indices: 39555593--39555640 Score: 69
Period size: 6 Copynumber: 7.7 Consensus size: 6
39555583 TCACATATTT
*
39555593 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AATAAAG AGCAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG A-AAAAG AAAA
39555641 GTTTAATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:39563319 original size:51 final size:50
Alignment explanation
Indices: 39563192--39563379 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
39563182 TATCATTCGA
* * * * **
39563192 TACACGTATTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
* * *
39563242 TTCACGTAGTAGCCTACACATAGTACTAGACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * * *
39563293 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATC-TCTCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AACCTTC-CGG
*
39563344 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
39563380 GTTATAGGCA
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
50 39 0.34
51 76 0.66
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:39566860 original size:35 final size:35
Alignment explanation
Indices: 39566814--39566885 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
39566804 CCCGGAAAAC
39566814 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
1 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
*
39566849 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCTAA
1 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
39566884 TT
1 TT
39566886 AATAATTGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (35 bp):
TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
Found at i:39570744 original size:50 final size:51
Alignment explanation
Indices: 39570682--39570865 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
39570672 TATTATTCGA
** * ** *
39570682 TACACGTAGTAGCCTTAACATAGTACTACACACT-TGATCAAAATTTTCGGT
1 TACACGTAGTAGCCTGCACATAGTACTACACA-TGTGACCAAAACCTTCCGT
*
39570733 T-CATGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
* ** * *
39570783 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCT-TCCGT
* * *
39570834 TACAAGTAATAGCCTGCACTTAGTACTACACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
39570866 CGTGTTTATA
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 41 0.36
51 70 0.62
52 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
Found at i:39577575 original size:33 final size:37
Alignment explanation
Indices: 39577506--39577599 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 37
39577496 GGGCACAGAA
*
39577506 AGTGCATACTGGCACATAAAGTGCATATTGACACACAT
1 AGTGCATACTGGCACATATAGTG-ATATTGACACACAT
*
39577544 TGTGCATACTGGCACATATAGTG-TA-T-A-ACACAT
1 AGTGCATACTGGCACATATAGTGATATTGACACACAT
* *
39577577 AGTGCATATTGGCACACATAGTG
1 AGTGCATACTGGCACATATAGTG
39577600 CATCATCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 26 0.51
34 1 0.02
35 1 0.02
36 2 0.04
38 21 0.41
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (37 bp):
AGTGCATACTGGCACATATAGTGATATTGACACACAT
Found at i:39577595 original size:19 final size:19
Alignment explanation
Indices: 39577401--39577602 Score: 101
Period size: 19 Copynumber: 10.9 Consensus size: 19
39577391 AAGTCAATAT
39577401 TGGCACACATAGTGCATAC
1 TGGCACACATAGTGCATAC
** * ** *
39577420 TAACACA-AAATGTTAATAT
1 TGGCACACATA-GTGCATAC
***
39577439 TGGCACACATAACACATAC
1 TGGCACACATAGTGCATAC
* * * * *
39577458 TAGAACATAAAGTGCATGC
1 TGGCACACATAGTGCATAC
* * *
39577477 TAGCACAAATAGTTCATAC
1 TGGCACACATAGTGCATAC
* * *
39577496 GGGCACAGAAAGTGCATAC
1 TGGCACACATAGTGCATAC
* * *
39577515 TGGCACATAAAGTGCATAT
1 TGGCACACATAGTGCATAC
* *
39577534 TGACACACATTGTGCATAC
1 TGGCACACATAGTGCATAC
*
39577553 TGGCACATATAGTG--TA-
1 TGGCACACATAGTGCATAC
* *
39577569 T--AACACATAGTGCATAT
1 TGGCACACATAGTGCATAC
39577586 TGGCACACATAGTGCAT
1 TGGCACACATAGTGCAT
39577603 CATCGGATAA
Statistics
Matches: 130, Mismatches: 46, Indels: 14
0.68 0.24 0.07
Matches are distributed among these distances:
14 9 0.07
16 3 0.02
17 3 0.02
18 2 0.02
19 111 0.85
20 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (19 bp):
TGGCACACATAGTGCATAC
Found at i:39585766 original size:11 final size:11
Alignment explanation
Indices: 39585750--39585774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39585740 GTTTAGATGA
39585750 AATTAACTATT
1 AATTAACTATT
39585761 AATTAACTATT
1 AATTAACTATT
39585772 AAT
1 AAT
39585775 ACCTCCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAACTATT
Found at i:39597680 original size:37 final size:37
Alignment explanation
Indices: 39597639--39597712 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
39597629 CACAATTAAC
39597639 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
1 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
39597676 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
1 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
39597713 TAACTCCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (37 bp):
CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
Found at i:39599528 original size:20 final size:20
Alignment explanation
Indices: 39599503--39599568 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
39599493 ATCAGGAAGC
*
39599503 TTTGGTAACTTGTCTGCAAT
1 TTTGGTAACTTGTCTACAAT
**
39599523 TTTGGTGGCTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
** * *
39599543 ACTGGCAATTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
*
39599563 TCTGGT
1 TTTGGT
39599569 GGCTTGTTAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGGTAACTTGTCTACAAT
Found at i:39599575 original size:20 final size:20
Alignment explanation
Indices: 39599511--39599575 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
39599501 GCTTTGGTAA
* *
39599511 CTTGTCTGCAATTTTGGTGG
1 CTTGTCTACAATTCTGGTGG
* ***
39599531 CTTGTCTACAATACTGGCAA
1 CTTGTCTACAATTCTGGTGG
*
39599551 TTTGTCTACAATTCTGGTGG
1 CTTGTCTACAATTCTGGTGG
39599571 CTTGT
1 CTTGT
39599576 TAATCTACCA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (20 bp):
CTTGTCTACAATTCTGGTGG
Found at i:39603760 original size:27 final size:26
Alignment explanation
Indices: 39603728--39603864 Score: 130
Period size: 27 Copynumber: 5.1 Consensus size: 26
39603718 AACACGTTAG
* *
39603728 GAAAGAAAATCCTTTGTGATAAACTTT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
*
39603755 GAAAGAAAACCTTCTGTGGCGAACTTT
1 GAAAGAAAACCTT-TGTGGTGAACTTT
* *
39603782 GAAAGAAAGCCTTTGTGGTGAACTCT
1 GAAAGAAAACCTTTGTGGTGAACTTT
* * *
39603808 AAAAGAAAACCCTTGGCGGTGAACTTT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
* * * *
39603835 CAAAAAAAACCCTTTGTGGCGAACTCT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
39603862 GAA
1 GAA
39603865 TGGACTGTCC
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 22 0.24
27 68 0.76
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
GAAAGAAAACCTTTGTGGTGAACTTT
Found at i:39613492 original size:16 final size:16
Alignment explanation
Indices: 39613438--39613492 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
39613428 GTAAATTTCG
* **
39613438 CAAGTTAAGTATCCAC
1 CAAGTAAAGTATCTGC
39613454 CAAGTAAAGT-T-TG-
1 CAAGTAAAGTATCTGC
*
39613467 CAAGTCAAGTATCTGC
1 CAAGTAAAGTATCTGC
39613483 CAAGTAAAGT
1 CAAGTAAAGT
39613493 TCCCAAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
15 3 0.10
16 18 0.58
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (16 bp):
CAAGTAAAGTATCTGC
Found at i:39613503 original size:29 final size:29
Alignment explanation
Indices: 39613412--39613514 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
39613402 AAGGGAGGAG
** *
39613412 GTCAAGTATCCAACAAGTAAATTTCGCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* * *
39613441 GTTAAGTATCCACCAAGTAAAGTTTGCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* *
39613470 GTCAAGTATCTGCCAAGTAAAGTTCCCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* *
39613499 ATCAAGTGTCCGCCAA
1 GTCAAGTATCCGCCAA
39613515 ATGCACTTGC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (29 bp):
GTCAAGTATCCGCCAAGTAAAGTTCGCAA
Found at i:39625747 original size:27 final size:27
Alignment explanation
Indices: 39625709--39625763 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
39625699 GAGTTAGTGC
39625709 GTGAATTCTATGCGAATTTAACCTCAA
1 GTGAATTCTATGCGAATTTAACCTCAA
*
39625736 GTGACTTCTATGCGAATTTAACCTCAA
1 GTGAATTCTATGCGAATTTAACCTCAA
39625763 G
1 G
39625764 CGAGTTGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
GTGAATTCTATGCGAATTTAACCTCAA
Done.