Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 90 of 186
Found at i:29174389 original size:46 final size:46
Alignment explanation
Indices: 29174194--29174603 Score: 285
Period size: 46 Copynumber: 8.7 Consensus size: 46
29174184 AGGGTATAAT
* * * ** *
29174194 GCCGATGCCAAGTCCCAGACATGGTCTTACACTGACTATCGAAGTTGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTC-ATCTCGAG
* * * * *
29174243 GCTGACGCCATGTCCCAGACATAGTCTTACACTAGCTCTCACATATCCG-T
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCT--CATCT-CGAG
** * * *
29174293 GTTGATGCCATGTCCTAGACATGGTCTTACACT-G-ACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCG-AG
*
29174339 GCCGATGAATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAG
* * * * *
29174385 GCCGATGCATGTCCCAGACATGTCTTACAATAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* * *
29174431 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAG
* * * * *
29174479 GTCGATGCATGTCCCAGACTTGTCTTACACTAGCTCTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* * * * *
29174525 GTCGATACCATGTCTCAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGAT-GCATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAG
*
29174573 GCCAATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
29174604 AGCACACACA
Statistics
Matches: 286, Mismatches: 58, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
44 10 0.03
45 17 0.06
46 94 0.33
47 53 0.19
48 44 0.15
49 35 0.12
50 31 0.11
51 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
Found at i:29174458 original size:94 final size:94
Alignment explanation
Indices: 29174250--29174606 Score: 390
Period size: 94 Copynumber: 3.8 Consensus size: 94
29174240 GAGGCTGACG
* * * ** *
29174250 CCATGTCCCAGACATAGTCTTACACTAGCTCTCACATATCCGT-GTTGATGCCATGTCCTAGACA
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT--GTGGCCGATG-CATGTCCCAGACA
* * *
29174314 TGGTCTTACACT-G-ACACATCTC-GTAGCCGATGA
62 T-GTCTTACACTAGCTCTCATCTCAATA-CCGAT-A
* *
29174347 --ATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGACATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGACATG
* * *
29174407 TCTTACAATAGCTCTCGTCTCAATACCGATG
64 TCTTACACTAGCTCTCATCTCAATACCGATA
* *
29174438 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGCATGTCCCAGACTTGTC
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
**
29174503 TTACACTAGCTCTCATCTCAATGTCGATA
66 TTACACTAGCTCTCATCTCAATACCGATA
* *
29174532 CCATGTCTCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCAATGCATGTCCCAGACATGTC
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
29174597 TTACACTAGC
66 TTACACTAGC
29174607 ACACACACAT
Statistics
Matches: 224, Mismatches: 26, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
90 9 0.04
91 16 0.07
92 17 0.08
93 16 0.07
94 151 0.67
95 15 0.07
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (94 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
TTACACTAGCTCTCATCTCAATACCGATA
Found at i:29174495 original size:140 final size:140
Alignment explanation
Indices: 29174296--29174564 Score: 330
Period size: 140 Copynumber: 1.9 Consensus size: 140
29174286 TATCCGTGTT
*
29174296 GATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATG
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATG
* * *
29174361 TCTTACACTGGCT-TACATCTCGAGGCCGAT-GCATGTCCCAGACAT-GTCTTACAATAGCTCTC
66 TCTTACACTAGCTCT-CATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTCTC
29174423 GTCTCAATACC
130 GTCTCAATACC
* * * * * *
29174434 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGGTCGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATC-T--CGTAGCCGATGAATGTCCCAGAC
* * * * * *
29174498 TTGTCTTACACTAGCTCTCATCTCAATGTCGATACCATGTCTCAGACATGGTCTTACACTGGCTC
63 ATGTCTTACACTAGCTCTCATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTC
29174563 TC
128 TC
29174565 ATAATGTGGC
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
137 2 0.02
138 33 0.30
140 45 0.41
141 14 0.13
142 15 0.14
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (140 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATG
TCTTACACTAGCTCTCATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTCTCG
TCTCAATACC
Found at i:29174583 original size:188 final size:187
Alignment explanation
Indices: 29174249--29174606 Score: 435
Period size: 188 Copynumber: 1.9 Consensus size: 187
29174239 TGAGGCTGAC
* *
29174249 GCCATGTCCCAGACATAGTCTTACACTAGCTCTCACATATCCGTGTTGATGCCATGTCCTAGACA
1 GCCATGTCCCAGACATAGTCTTACACTAGCTCTCACATAT-CGTGTCGATGCCATGTCCCAGACA
*
29174314 TGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATGTCTTACACTGGCTTACAT
65 TGGTCTTACACTGACACATCTCATAGCCGATGAATGTCCCAGACATGTCTTACACTGGCTTACAT
* *
29174379 CTCGAGGCCGATGCATGTCCCAGACATGTCTTACAATAGCTCTCGTCTCAATACCGAT
130 ATCGAGGCCAATGCATGTCCCAGACATGTCTTACAATAGCTCTCGTCTCAATACCGAT
* * *
29174437 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-GTGGTCGATG-CATGTCCCAGAC-
1 GCCATGTCCCAGACATAGTCTTACACTAGCTCTCACATATCGT-GTCGATGCCATGTCCCAGACA
* * * * *
29174498 TTGTCTTACACTAGCTCTCATCTCA-ATGTCGAT-ACCATGTCTCAGACATGGTCTTACACTGGC
65 TGGTCTTACACT-G-ACACATCTCATA-GCCGATGA--ATGTCCCAGACAT-GTCTTACACTGGC
* *
29174561 TCT-CATAAT-GTGGCCAATGCATGTCCCAGACATGTCTTACACTAGC
124 T-TACAT-ATCGAGGCCAATGCATGTCCCAGACATGTCTTACAATAGC
29174607 ACACACACAT
Statistics
Matches: 146, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
184 11 0.08
185 16 0.11
186 18 0.12
187 14 0.10
188 85 0.58
189 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (187 bp):
GCCATGTCCCAGACATAGTCTTACACTAGCTCTCACATATCGTGTCGATGCCATGTCCCAGACAT
GGTCTTACACTGACACATCTCATAGCCGATGAATGTCCCAGACATGTCTTACACTGGCTTACATA
TCGAGGCCAATGCATGTCCCAGACATGTCTTACAATAGCTCTCGTCTCAATACCGAT
Found at i:29184341 original size:7 final size:7
Alignment explanation
Indices: 29184329--29184384 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
29184319 ATAAAATAAT
29184329 ATTTTTA
1 ATTTTTA
29184336 ATTTTTA
1 ATTTTTA
29184343 ATTTTTA
1 ATTTTTA
29184350 ATTTTTA
1 ATTTTTA
29184357 ATTTTTA
1 ATTTTTA
29184364 ATTTTTA
1 ATTTTTA
29184371 ATTTTTA
1 ATTTTTA
29184378 ATTTTTA
1 ATTTTTA
29184385 TATATTATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:29184924 original size:131 final size:130
Alignment explanation
Indices: 29184618--29185014 Score: 385
Period size: 131 Copynumber: 3.0 Consensus size: 130
29184608 TGAAATTCAT
* * * *
29184618 GTTCGATTCCTTTCTTACTCACATTTGCATTTTTTATTTCAT-ATGCTTTAAGCTTTTTAAAATT
1 GTTCGATTCTTTTC-TACTCACATTTGTATTTTTTATTTCATGTTGCTTTAA-CTTTTTTAAATT
* * *
29184682 TTAATT-A-ATTTTTTATCATATTAGTTCTTTGGTTAGATAGTTAGATAATTGTAATTACATATT
64 TTAATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTAC-----
29184745 TAAGTCTCAA
124 --A-TCTCAA
* * * * *
29184755 GGTT-GATTTCTCTCCTACTCATATGTGTATTTTTTATTTCATGTTACTTTAACTTTTTTAAATT
1 -GTTCGA-TTCTTTTCTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAACTTTTTTAAATT
* * * *
29184819 TTGAATTAATATTTTTTAACATTTTAGTT-TTTCCTTAGATGGTTAAATAGTTGTAATTACATCT
64 TT-AATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTACATCT
29184883 CAA
128 CAA
* * * * *
29184886 GTTCGATTCTTTTACTAATCACATTTGTATTTTTTATTTTATGTTGCTTTAATTATTTTTTTATT
1 GTTCGATTCTTTT-CTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAA--CTTTTTTAAAT
*
29184951 TTTAATTAATA-TTTTTAACATATTAATTCATTTCGTTAGATGGTTAGATAATTGTGAA-TACAT
63 TTTAATTAATATTTTTTAACATATTAGTTC-TTTCGTTAGATGGTTAGATAATTGT-AATTACAT
29185014 C
126 C
29185015 CTTAAGACTA
Statistics
Matches: 216, Mismatches: 31, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
130 8 0.04
131 56 0.26
132 9 0.04
133 39 0.18
134 2 0.01
137 39 0.18
138 19 0.09
139 27 0.12
140 17 0.08
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.53
Consensus pattern (130 bp):
GTTCGATTCTTTTCTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAACTTTTTTAAATTTT
AATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTACATCTCAA
Found at i:29185124 original size:20 final size:20
Alignment explanation
Indices: 29185099--29185145 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29185089 TTTATTTTTA
29185099 ATTATTTT-TATAAGCATATT
1 ATTATTTTATATAAGCA-ATT
**
29185119 ATTATTTTATATTTGCAATT
1 ATTATTTTATATAAGCAATT
29185139 ATTATTT
1 ATTATTT
29185146 AATTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTATTTTATATAAGCAATT
Found at i:29202506 original size:12 final size:12
Alignment explanation
Indices: 29202489--29202537 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
29202479 TTTTTTAATA
29202489 AAATTTAATATT
1 AAATTTAATATT
*
29202501 AAATTTAAT-CT
1 AAATTTAATATT
29202512 AATATTT-ATATT
1 AA-ATTTAATATT
*
29202524 -AATGTAATATT
1 AAATTTAATATT
29202535 AAA
1 AAA
29202538 GTGATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.10
11 11 0.37
12 16 0.53
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
AAATTTAATATT
Found at i:29202516 original size:17 final size:18
Alignment explanation
Indices: 29202494--29202537 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
29202484 TAATAAAATT
29202494 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
29202511 TAATATT-TATATTAATG
1 TAATATTAAATATTAATC
29202528 TAATATTAAA
1 TAATATTAAA
29202538 GTGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:29222475 original size:25 final size:25
Alignment explanation
Indices: 29222441--29222499 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
29222431 GGCAAACAAA
**
29222441 ATCACAACAC-AGATCGGAGGAATTT
1 ATCA-AACACTAGATCAAAGGAATTT
*
29222466 ATCATAACACTGGATCAAAGGAATTT
1 ATCA-AACACTAGATCAAAGGAATTT
29222492 ATCAAACA
1 ATCAAACA
29222500 AAATCCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (25 bp):
ATCAAACACTAGATCAAAGGAATTT
Found at i:29238535 original size:33 final size:33
Alignment explanation
Indices: 29238497--29238560 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
29238487 TTGAGTGGGA
29238497 GTGTTTTGCTGCTGGACAGGAGCTGGAATGTGG
1 GTGTTTTGCTGCTGGACAGGAGCTGGAATGTGG
*
29238530 GTGTTTTGTTGCTGGACAGGAGCTGGAATGT
1 GTGTTTTGCTGCTGGACAGGAGCTGGAATGT
29238561 CAAGAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.33
Consensus pattern (33 bp):
GTGTTTTGCTGCTGGACAGGAGCTGGAATGTGG
Found at i:29240101 original size:34 final size:34
Alignment explanation
Indices: 29240063--29240129 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
29240053 TTCAACAGGT
* * *
29240063 GATTCCTGATAATTATTTTTTCCATCCAGCTGTG
1 GATTCCTAAGAATTATTCTTTCCATCCAGCTGTG
29240097 GATTCCTAAGAATTATTCTTTCCATCCAGCTGT
1 GATTCCTAAGAATTATTCTTTCCATCCAGCTGT
29240130 CTTGCTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (34 bp):
GATTCCTAAGAATTATTCTTTCCATCCAGCTGTG
Found at i:29244179 original size:43 final size:43
Alignment explanation
Indices: 29244097--29244198 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 43
29244087 CAATGTGTTT
*
29244097 GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTGTAGATG-C
1 GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTATAGATGTC
* *
29244139 GCAAAACTGAGATGATAATAAGAACAA-GAAAACAC-ATAGATGTTT
1 GCAAAACTGAGAAGAT-ATAAGAA-AAGGAAAAC-CTATAGATG-TC
29244184 GCAAAACTGAGAAGA
1 GCAAAACTGAGAAGA
29244199 ACATATTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 15 0.29
43 19 0.37
44 3 0.06
45 14 0.27
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.16
Consensus pattern (43 bp):
GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTATAGATGTC
Found at i:29245306 original size:94 final size:94
Alignment explanation
Indices: 29245145--29245332 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
29245135 ACATCAAGAA
*
29245145 TGTTTCTCATAGTAATGATCTAGAGGAGCCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
1 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
29245210 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
66 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
*
29245239 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGATATTTTCCTTGA
1 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
29245304 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
66 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
29245333 GTAGTTACTG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (94 bp):
TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
GCTATAAGGTGGGCTTTTTTTTTTTTTTT
Found at i:29246012 original size:129 final size:129
Alignment explanation
Indices: 29245782--29246039 Score: 419
Period size: 129 Copynumber: 2.0 Consensus size: 129
29245772 AGGGGCCCTC
* *
29245782 AATTCAAGTCAAATATAAACAGTTAAATTAAAATAAAAACAAGAGTCTAAGTGTCTGTTCACTGA
1 AATTCAAGTCAAATATAAACAGTTAAATTAAAATAAAAACAACAGTCTAAGTGCCTGTTCACTGA
* ** * *
29245847 ATGGCTTCAGTGTTTTGGGAATTCATTCTCTTCTCA-TTCTCCCAACGCTAGAGTCATGCAACA
66 ATGGCTTCAGTGTATTGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
**
29245910 AATTCAAGTCAAATATAAACAGTTAAATTAAAATAGAAAACAACAGTCTAAGTGCCTGTTCTGTG
1 AATTCAAGTCAAATATAAACAGTTAAATTAAAATA-AAAACAACAGTCTAAGTGCCTGTTCACTG
29245975 AATGGCTTCAGTGTATTGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
65 AATGGCTTCAGTGTATTGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
29246040 GATGAGGCCT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
128 35 0.29
129 59 0.50
130 25 0.21
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (129 bp):
AATTCAAGTCAAATATAAACAGTTAAATTAAAATAAAAACAACAGTCTAAGTGCCTGTTCACTGA
ATGGCTTCAGTGTATTGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
Found at i:29248913 original size:28 final size:28
Alignment explanation
Indices: 29248874--29248968 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 28
29248864 TTTATTTCTT
29248874 TTAAAATATTATAAATTTGTAAAAAATTA
1 TTAAAA-ATTATAAATTTGTAAAAAATTA
* *
29248903 TTAAAAATTATAAA-ATGTTAAATAAAAT-
1 TTAAAAATTATAAATTTG-TAAA-AAATTA
* * * * *
29248931 TTAAAAATAAAAAATTTATTAAAAATCA
1 TTAAAAATTATAAATTTGTAAAAAATTA
29248959 TTCAAAAATT
1 TT-AAAAATT
29248969 TAATTTTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
27 5 0.10
28 29 0.57
29 17 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TTAAAAATTATAAATTTGTAAAAAATTA
Found at i:29249498 original size:31 final size:31
Alignment explanation
Indices: 29249463--29249525 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29249453 TTTAAAACTT
29249463 TATATAATTTAAAAAAATCTTCTTGAATGAA
1 TATATAATTTAAAAAAATCTTCTTGAATGAA
29249494 TATATAATTTAAAAAAATCTTCTTGAATGAA
1 TATATAATTTAAAAAAATCTTCTTGAATGAA
29249525 T
1 T
29249526 TTGGACATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (31 bp):
TATATAATTTAAAAAAATCTTCTTGAATGAA
Found at i:29249974 original size:27 final size:27
Alignment explanation
Indices: 29249944--29250019 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
29249934 GACTAATCGA
* *
29249944 GCCTTTCTCTGAGGCGCAAATGATTGT
1 GCCTATCTCAGAGGCGCAAATGATTGT
*
29249971 GCCTATCTCAGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGATTGT
* *
29249998 GCCTATCCCAAAGGCGCAAATG
1 GCCTATCTCAGAGGCGCAAATG
29250020 GTGGGGCCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAAATGATTGT
Found at i:29255476 original size:31 final size:31
Alignment explanation
Indices: 29255438--29255496 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
29255428 ATTAAATATT
29255438 TTTAATACAGGTAACACAATATGATTGGCTC
1 TTTAATACAGGTAACACAATATGATTGGCTC
* ** *
29255469 TTTAATACATGTGGCATAATATGATTGG
1 TTTAATACAGGTAACACAATATGATTGG
29255497 TTGACATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (31 bp):
TTTAATACAGGTAACACAATATGATTGGCTC
Found at i:29256430 original size:20 final size:20
Alignment explanation
Indices: 29256401--29256442 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29256391 GAAAGAAAGG
29256401 AAAGAAAGAAAAGAAAAGAA
1 AAAGAAAGAAAAGAAAAGAA
* *
29256421 AAAGAGAGAAAAGAAAATAA
1 AAAGAAAGAAAAGAAAAGAA
29256441 AA
1 AA
29256443 GTTTTCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAAGAAAAGAA
Found at i:29260191 original size:45 final size:44
Alignment explanation
Indices: 29260133--29260251 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 44
29260123 AGACATCATG
*
29260133 ATAAAGATGAGTAAGACCATAACTGAAAGATGTTATGGCATCACC
1 ATAAAGATGAGTAAGACCATAACTGAAAGATGCTATGGCATCA-C
* *
29260178 ATAAAGATCAGTAAGACCATAGAC-GAAACG-TGCTATGGCATCAT
1 ATAAAGATGAGTAAGACCATA-ACTGAAA-GATGCTATGGCATCAC
**
29260222 ATATAA-ATGAGTAAGACCATGGCTGAAAGA
1 ATA-AAGATGAGTAAGACCATAACTGAAAGA
29260252 CACTATGGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
43 2 0.03
44 20 0.32
45 38 0.60
46 3 0.05
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (44 bp):
ATAAAGATGAGTAAGACCATAACTGAAAGATGCTATGGCATCAC
Found at i:29260423 original size:27 final size:26
Alignment explanation
Indices: 29260393--29260460 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
29260383 ACAGTTCGCA
*
29260393 GGGACATTAAACACGGGACAGTCCGAT
1 GGGACACTAAACAC-GGACAGTCCGAT
** *
29260420 GGGACACTAAACATCGGATGGTCCGCT
1 GGGACACTAAACA-CGGACAGTCCGAT
*
29260447 GGGACAGTAAACAC
1 GGGACACTAAACAC
29260461 CGGGTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.03
27 33 0.94
28 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (26 bp):
GGGACACTAAACACGGACAGTCCGAT
Found at i:29264233 original size:38 final size:38
Alignment explanation
Indices: 29264191--29264264 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
29264181 CCAGTTGACC
* *
29264191 CCTTAGTAGGGGATAAAATACTTGAAAATGAGTATACT
1 CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATACT
*
29264229 CCTTAGTTGGGGACAAAATACTTGAAAAGGAGTATA
1 CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATA
29264265 TTTTACATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (38 bp):
CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATACT
Found at i:29265151 original size:45 final size:43
Alignment explanation
Indices: 29265084--29265304 Score: 176
Period size: 45 Copynumber: 4.9 Consensus size: 43
29265074 AGTTGTAAGC
*
29265084 ATAAAATGAGTAAGACCATAGCTAAATGATTCTATGTCATCATG
1 ATAAAATGAGTAAGACCATAGCTAAA-GATTCTATGACATCATG
* *
29265128 ATAAAGATGAGTAAGATCGTAGCTAAAAGATGT-TATGACATCACT-
1 ATAAA-ATGAGTAAGACCATAGCT-AAAGAT-TCTATGACATCA-TG
* * *
29265173 ATAAAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATG
1 AT-AAAATGAGTAAGACCATAGCT-AAAGATTCTATGACATCATG
* * * * *
29265218 ATATAAATGAATAAGACCATGGCTGAAAGATGCCATGGCATCATG
1 ATA-AAATGAGTAAGACCATAGCT-AAAGATTCTATGACATCATG
* * * * **
29265263 GTAAACAAGACTAAAACCATAGCTGAAAGACACTATGACATC
1 ATAAA-ATGAGTAAGACCATAGCT-AAAGATTCTATGACATC
29265305 CTAGTAGTCT
Statistics
Matches: 146, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
44 9 0.06
45 129 0.88
46 8 0.05
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (43 bp):
ATAAAATGAGTAAGACCATAGCTAAAGATTCTATGACATCATG
Found at i:29265247 original size:90 final size:90
Alignment explanation
Indices: 29265086--29265292 Score: 233
Period size: 90 Copynumber: 2.3 Consensus size: 90
29265076 TTGTAAGCAT
* * * * * *
29265086 AAAATGAGTAAGACCATAGCT-AAATGATTCTATGTCATCATGATAAAGATGAGTAAGATCGTAG
1 AAAATGAGTAAAACCATAGCTGAAA-GATGCTATGGCATCATGATAAAGATGAATAAGACCATAG
**
29265150 CTAAAAGATGTTATGACATCACT-ATA
65 CTAAAAGATGCCATGACATCA-TGATA
*
29265176 AAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATGATATAA-ATGAATAAGACCATGG
1 AAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATGATA-AAGATGAATAAGACCATAG
* * *
29265240 CTGAAAGATGCCATGGCATCATGGTA
65 CTAAAAGATGCCATGACATCATGATA
*
29265266 AACAA-GACTAAAACCATAGCTGAAAGA
1 AA-AATGAGTAAAACCATAGCTGAAAGA
29265293 CACTATGACA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
89 1 0.01
90 92 0.92
91 7 0.07
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (90 bp):
AAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATGATAAAGATGAATAAGACCATAGC
TAAAAGATGCCATGACATCATGATA
Found at i:29267679 original size:18 final size:18
Alignment explanation
Indices: 29267651--29267697 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
29267641 AATTGATCGG
* *
29267651 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTAAA
*
29267669 TTATTCGGTAACAGTAAA
1 TTATTCAGTAACAGTAAA
29267687 TTATTCAGTAA
1 TTATTCAGTAA
29267698 TAATCAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAGTAAA
Found at i:29267940 original size:45 final size:45
Alignment explanation
Indices: 29267883--29267993 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 45
29267873 AATAGTAAAA
* ***
29267883 GTAACAGTAACAGTAACAGTATTCAACATACAAAGTGTTGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
* * *
29267928 TTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCAAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
*
29267973 GTAATAGTAACAGTAACAGTA
1 GTAACAGTAACAGTAACAGTA
29267994 ACAGTAGTCG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
Found at i:29269590 original size:64 final size:64
Alignment explanation
Indices: 29269509--29269692 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
29269499 AGACATTATG
* *
29269509 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
29269573 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAATAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29269638 AA
63 AA
* * * *
29269640 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GCACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29269693 CGAACTATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 21 0.22
65 8 0.08
66 16 0.17
67 30 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29280105 original size:27 final size:27
Alignment explanation
Indices: 29280063--29280141 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
29280053 GTCACTAGAT
29280063 ACAGATAT-TGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
29280089 ACAGATATATGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
* *
29280116 TCAGATA-ATTGTGGCATAGCCACCAG
1 ACAGATATA-TGTGGCAGAGCCACCAG
29280142 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
26 9 0.18
27 40 0.82
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
ACAGATATATGTGGCAGAGCCACCAGA
Found at i:29281793 original size:26 final size:26
Alignment explanation
Indices: 29281762--29281895 Score: 214
Period size: 26 Copynumber: 5.2 Consensus size: 26
29281752 TGAAATGCCC
*
29281762 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29281788 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
29281814 ATCATGGAATATATACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29281840 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29281866 ATCATGGAACATTTTCCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29281892 ATCA
1 ATCA
29281896 ATTTGTATCA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 98 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29282815 original size:15 final size:18
Alignment explanation
Indices: 29282787--29282828 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
29282777 TCATCCTTTC
29282787 TTTCTTTATCTATT-CTT
1 TTTCTTTATCTATTCCTT
29282804 TTTCTTT-T-TATTCCTT
1 TTTCTTTATCTATTCCTT
*
29282820 TTACTTTAT
1 TTTCTTTAT
29282829 ATATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTATCTATTCCTT
Found at i:29286259 original size:38 final size:38
Alignment explanation
Indices: 29286217--29286293 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
29286207 GGTTTTAGGT
*
29286217 ACAAGAATGGCTCTCATACTTTCTTATAATCCATTGGG
1 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
29286255 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
1 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
29286293 A
1 A
29286294 TCCCAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (38 bp):
ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
Found at i:29291430 original size:62 final size:62
Alignment explanation
Indices: 29291330--29291455 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
29291320 TAGATTCTTA
29291330 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
1 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
* * *
29291392 GTATCGCTCAGCAAGGTTCCTTGTGGTCTATTATGAAGCTCCGTAGTTAACTGACCCATTTG
1 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
29291454 GT
1 GT
29291456 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (62 bp):
GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
Found at i:29294652 original size:131 final size:131
Alignment explanation
Indices: 29294512--29294749 Score: 282
Period size: 131 Copynumber: 1.8 Consensus size: 131
29294502 TGAAAACCTA
* * * *
29294512 AAGGAATATTCGATTGTTTTGAGCAAACG-AGAAATCACAACCCAGCACGGTAGGGCATGATTCC
1 AAGGAATATTCGATTATTTTGAGCAAACGCA-AAATCACAACCCAACACGGTAGAGCACGATTCC
* *
29294576 -CAAATTGTCAAACGCCAAATATTGCCTTCGTTTTAAATGAATTTTAGAAGACATGAGTGAAATT
65 ACAAATTGTCAAACACCAAATATCGCCTTCGTTTTAAAT-AATTTTAGAAGACATGAGTGAAATT
29294640 TTG
129 TTG
* * * * ** *
29294643 AAGGGATATTTGATTATTTTGAGTAAGCGCAAAATTGCAACCCAACACGTTAGAGCACGATTCCA
1 AAGGAATATTCGATTATTTTGAGCAAACGCAAAATCACAACCCAACACGGTAGAGCACGATTCCA
* * * * *
29294708 CGAATTTTCAAATATCGAATATCGCCTTCGTTTTAAATAATT
66 CAAATTGTCAAACACCAAATATCGCCTTCGTTTTAAATAATT
29294750 GTGAAACTAG
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
131 55 0.63
132 32 0.37
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (131 bp):
AAGGAATATTCGATTATTTTGAGCAAACGCAAAATCACAACCCAACACGGTAGAGCACGATTCCA
CAAATTGTCAAACACCAAATATCGCCTTCGTTTTAAATAATTTTAGAAGACATGAGTGAAATTTT
G
Found at i:29295445 original size:27 final size:27
Alignment explanation
Indices: 29295415--29295469 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
29295405 AAGATCAAGC
*
29295415 ACATCCTTATATTAAAACATTTAAAAA
1 ACATCCTTATATTAAAACATTAAAAAA
29295442 ACATCCTTATATTAAAACATTAAAAAA
1 ACATCCTTATATTAAAACATTAAAAAA
29295469 A
1 A
29295470 ATAGGCTATA
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:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (27 bp):
ACATCCTTATATTAAAACATTAAAAAA
Found at i:29295460 original size:16 final size:16
Alignment explanation
Indices: 29295415--29295461 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
29295405 AAGATCAAGC
29295415 ACATCCTTATATTAAA
1 ACATCCTTATATTAAA
29295431 ACAT--TTA-A--AAA
1 ACATCCTTATATTAAA
29295442 ACATCCTTATATTAAA
1 ACATCCTTATATTAAA
29295458 ACAT
1 ACAT
29295462 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
11 7 0.27
13 4 0.15
14 4 0.15
16 11 0.42
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (16 bp):
ACATCCTTATATTAAA
Found at i:29295559 original size:23 final size:23
Alignment explanation
Indices: 29295515--29295559 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29295505 AAGAGACATT
*
29295515 CAAAAATAATAATTTTATAATTA
1 CAAAAATAATAATTTTAAAATTA
*
29295538 CAAAAATGA-AATTTCTAAAATT
1 CAAAAATAATAATTT-TAAAATT
29295560 GTTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CAAAAATAATAATTTTAAAATTA
Found at i:29309960 original size:23 final size:23
Alignment explanation
Indices: 29309916--29309960 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29309906 AGGAGACATT
*
29309916 CAAAAATAATAATTTTATAATTA
1 CAAAAATAATAATTTTAAAATTA
*
29309939 CAAAAATGA-AATTTCTAAAATT
1 CAAAAATAATAATTT-TAAAATT
29309961 GTTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CAAAAATAATAATTTTAAAATTA
Found at i:29319163 original size:30 final size:30
Alignment explanation
Indices: 29319129--29319189 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29319119 TCCTTAACTC
29319129 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29319159 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29319189 A
1 A
29319190 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29327240 original size:42 final size:42
Alignment explanation
Indices: 29327174--29327274 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
29327164 TATGGACGCC
* *
29327174 ACACGGGTGTGTGGTCGCCCGTGTGGTAGGCCGTGTGCCCTA
1 ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
* *
29327216 ACACGGGCGTGTGGTCACCTGTGTGGTAGGCTGTGTGCCCTA
1 ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
*
29327258 ACACGGGCGTGTAGTCA
1 ACACGGGCGTGTGGTCA
29327275 ACGAGACTAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.13, C:0.25, G:0.39, T:0.24
Consensus pattern (42 bp):
ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
Found at i:29327957 original size:34 final size:35
Alignment explanation
Indices: 29327900--29327969 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
29327890 ACTGATGATA
29327900 TGATAGGCTAAGGCCCTAATGCATA-CTGATACTG
1 TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
* ** * *
29327934 TGATGGGCTAAGGCTTTACTGCATATTTGATACTG
1 TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
29327969 T
1 T
29327970 ATTGAGATGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 21 0.70
35 9 0.30
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (35 bp):
TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
Found at i:29328471 original size:18 final size:18
Alignment explanation
Indices: 29328448--29328489 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29328438 TCGACTAAAT
*
29328448 AAATAAAATGATTTTTGG
1 AAATAAAACGATTTTTGG
*
29328466 AAATAATACGATTTTTGG
1 AAATAAAACGATTTTTGG
29328484 AAATAA
1 AAATAA
29328490 TAAGATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (18 bp):
AAATAAAACGATTTTTGG
Found at i:29328490 original size:18 final size:18
Alignment explanation
Indices: 29328457--29328491 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29328447 TAAATAAAAT
29328457 GATTTTTGGAAATAATAC
1 GATTTTTGGAAATAATAC
29328475 GATTTTTGGAAATAATA
1 GATTTTTGGAAATAATA
29328492 AGATCTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (18 bp):
GATTTTTGGAAATAATAC
Found at i:29336121 original size:43 final size:43
Alignment explanation
Indices: 29336073--29336179 Score: 169
Period size: 43 Copynumber: 2.5 Consensus size: 43
29336063 GATAAACGGA
**
29336073 TCTCCAAAAACAACCAATATAATGTGTAGCATAAAGCTATCAC
1 TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
* *
29336116 TCTCCAAGCACAGCTAATATAATGTGTAGCATAAAGCTATCAC
1 TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
*
29336159 ACTCCAAGCACAACCAATATA
1 TCTCCAAGCACAACCAATATA
29336180 CCCTCCAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.22
Consensus pattern (43 bp):
TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
Found at i:29336185 original size:22 final size:22
Alignment explanation
Indices: 29336160--29336283 Score: 78
Period size: 22 Copynumber: 5.7 Consensus size: 22
29336150 AGCTATCACA
29336160 CTCCAAGCACAACCAATATACC
1 CTCCAAGCACAACCAATATACC
* * *
29336182 CTCCAAACACAACTAATATAAC
1 CTCCAAGCACAACCAATATACC
* ** * *
29336204 AT-GTAGCATAA--AGCTATCACC
1 CTCCAAGCACAACCA-ATAT-ACC
*
29336225 CTCTAAGCACAACCAATATACC
1 CTCCAAGCACAACCAATATACC
* *
29336247 CTCCAAACACAACTAATAT-CTC
1 CTCCAAGCACAACCAATATAC-C
29336269 CTCCACA-CACAACCA
1 CTCCA-AGCACAACCA
29336284 TAAAGTGGTG
Statistics
Matches: 76, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 9 0.12
22 58 0.76
23 4 0.05
24 1 0.01
ACGTcount: A:0.42, C:0.36, G:0.04, T:0.18
Consensus pattern (22 bp):
CTCCAAGCACAACCAATATACC
Found at i:29336221 original size:65 final size:65
Alignment explanation
Indices: 29336117--29336265 Score: 244
Period size: 65 Copynumber: 2.3 Consensus size: 65
29336107 AGCTATCACT
* * **
29336117 CTCCAAGCACAGCTAATATAATGTGTAGCATAAAGCTATCACACTCCAAGCACAACCAATATACC
1 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCCAAGCACAACCAATATACC
* *
29336182 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACCCTCTAAGCACAACCAATATACC
1 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCCAAGCACAACCAATATACC
29336247 CTCCAAACACAACTAATAT
1 CTCCAAACACAACTAATAT
29336266 CTCCTCCACA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 78 1.00
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.20
Consensus pattern (65 bp):
CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCCAAGCACAACCAATATACC
Found at i:29336600 original size:19 final size:19
Alignment explanation
Indices: 29336550--29336600 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
29336540 TGACATTTTC
*
29336550 ACATCACATATAATCATAT
1 ACATCACATATAAACATAT
* **
29336569 -CAACTTATCATAAACATAT
1 ACATCACAT-ATAAACATAT
29336588 ACATCACATATAA
1 ACATCACATATAA
29336601 GCTTTATTTG
Statistics
Matches: 23, Mismatches: 7, Indels: 4
0.68 0.21 0.12
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (19 bp):
ACATCACATATAAACATAT
Found at i:29339163 original size:127 final size:127
Alignment explanation
Indices: 29338932--29339194 Score: 472
Period size: 127 Copynumber: 2.1 Consensus size: 127
29338922 TTCCTCCCTT
* *
29338932 TTTCAAATCAGTCCTTTTGTTTAATTAAAATATATATTCTTAATTATTTTCAAATTGGGTTCCGT
1 TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
29338997 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
66 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
* *
29339059 TTTCTAATCAGTCCTTTTGTTTAATTAAGACATATATTCTTAATTATTTTCAAATTGGGTTTCGT
1 TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
* *
29339124 TTTTAAAATCCATTTTAAACAAATGAATTCCCGAACACTTAATTTTAATTTTCCCTATTAAA
66 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
29339186 TTTCTAATC
1 TTTCTAATC
29339195 CCAAATATTA
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 130 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (127 bp):
TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
Found at i:29342448 original size:22 final size:22
Alignment explanation
Indices: 29342423--29342466 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29342413 TAGTCATATA
29342423 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
29342445 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
29342467 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:29342502 original size:13 final size:14
Alignment explanation
Indices: 29342486--29342527 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
29342476 TTTCAATTTT
29342486 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
29342499 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
29342514 ATTTTACATAATAT
1 ATTTTA-ATAATAT
29342528 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 9 0.38
16 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:29343121 original size:15 final size:14
Alignment explanation
Indices: 29343076--29343121 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
29343066 CTAGAAAAAT
29343076 AAATTATTTTCTA-A
1 AAATTATTTT-TAGA
*
29343090 AAATTATTTTTCGA
1 AAATTATTTTTAGA
29343104 AAATTATTTTTAGTA
1 AAATTATTTTTAG-A
29343119 AAA
1 AAA
29343122 CAAATGGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 1 0.04
14 23 0.82
15 4 0.14
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (14 bp):
AAATTATTTTTAGA
Found at i:29343944 original size:22 final size:22
Alignment explanation
Indices: 29343894--29343959 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
29343884 ATCAGTTTTT
* *
29343894 TTTTAATTTTTTATTTTAATTA
1 TTTTAATTTTTAATTTTAATAA
*
29343916 TTGTAATTTTTGAATTTTAA-AA
1 TTTTAATTTTT-AATTTTAATAA
* *
29343938 TTTTAA-TTTCAATTTAAATAA
1 TTTTAATTTTTAATTTTAATAA
29343959 T
1 T
29343960 AGTAAACTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 7 0.19
21 6 0.17
22 16 0.44
23 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTTAATTTTTAATTTTAATAA
Found at i:29348184 original size:24 final size:24
Alignment explanation
Indices: 29348157--29348205 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
29348147 TTAAATTCTT
* *
29348157 TAAAATATAATTATATGGATTAAA
1 TAAAATATAAATATACGGATTAAA
29348181 TAAAATATAAATATACGGATTAAA
1 TAAAATATAAATATACGGATTAAA
29348205 T
1 T
29348206 TTCAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
TAAAATATAAATATACGGATTAAA
Found at i:29354069 original size:18 final size:18
Alignment explanation
Indices: 29354036--29354070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29354026 TACAAGGTGC
*
29354036 GTATCCTAGCCATTATAT
1 GTATCCTAACCATTATAT
*
29354054 GTATCCTAACCCTTATA
1 GTATCCTAACCATTATA
29354071 AGTTTTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (18 bp):
GTATCCTAACCATTATAT
Found at i:29354365 original size:21 final size:22
Alignment explanation
Indices: 29354329--29354371 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29354319 CAACCAGAAT
*
29354329 AACCACAACATTCGCCA-AAGC
1 AACCACAACATCCGCCAGAAGC
*
29354350 AACCACAACCTCCGCCAGAAGC
1 AACCACAACATCCGCCAGAAGC
29354372 TGAATCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.42, G:0.12, T:0.07
Consensus pattern (22 bp):
AACCACAACATCCGCCAGAAGC
Found at i:29357850 original size:126 final size:127
Alignment explanation
Indices: 29357617--29358139 Score: 653
Period size: 126 Copynumber: 4.1 Consensus size: 127
29357607 GGCTAAGCAG
* **
29357617 GAACTACTGTAGAAAAGGAGCGTCCACATGGAAGCTTTTTTTTTGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTTCAGTAATTTTGCTGACAGTGCAT
* *
29357682 CCTGCTTGAAGCGTTTTTTAAACTATTTTTTCATAA-TCGTCTTCTCAAAATTATTTTTTTAA
66 CCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACT-GTCTTCTCAAAATTATTTTTTTAA
* * *
29357744 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAG-TTTTTTTCAGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTTCAGTAATTTTGCTGACAGTGCAT
* * * *
29357808 CCTGCTTGAAGCCTTTTTTACACTATTTTCTCAAAACTGTCTTCTCAAAATTATTTTTTCAG
66 CCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTTTAA
* * * * * * *
29357870 GAACTACTATAGAAAAAGAGCATCCACGTGGGAGC-TTTTTTCAATAATTTTGCTAACAGCGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTTCAGTAATTTTGCTGACAGTGCAT
* * * * *
29357934 CTTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTATTTTCAAAATTATTTTTTTAG
66 CCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTTTAA
* *
29357996 GAACTACTGTAGAGAAAGAGCGTTCACATGGAAGCTTTTTTT-AGTAATTTTGCTGACAGTTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTTCAGTAATTTTGCTGACAG-TGCA
* * * * * * * * *
29358060 TCCTGCTTGAAACATTCTTAACATTATCTTTTT-AGAACCGTCTTCTCAAAATTAATTTTTCTGA
65 TCCTGCTTGAAGCGTTTTTTACACTAT-TTTTTCAAAACTGTCTTCTCAAAATT-ATTTTTTTAA
29358124 -AACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
29358140 AAAACAAAAT
Statistics
Matches: 342, Mismatches: 48, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
126 238 0.70
127 92 0.27
128 12 0.04
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (127 bp):
GAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTTCAGTAATTTTGCTGACAGTGCAT
CCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTTTAA
Found at i:29358281 original size:33 final size:33
Alignment explanation
Indices: 29358237--29358353 Score: 132
Period size: 33 Copynumber: 3.5 Consensus size: 33
29358227 ATTTTTTAAA
29358237 AAAAAAC-TAAACCCTAATTTAATTAATTTTTT
1 AAAAAACTTAAACCCTAATTTAATTAATTTTTT
*
29358269 AAAAAACTTAAACCTTAATTTAATTAATTTATTT
1 AAAAAACTTAAACCCTAATTTAATTAATTT-TTT
** * **
29358303 AAAACCCCTCAAA-CCTAATTTAATTAA-TTTAA
1 AAAA-AACTTAAACCCTAATTTAATTAATTTTTT
29358335 AAAAAACTCTAAACCCTAA
1 AAAAAACT-TAAACCCTAA
29358354 ATTTTTATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
31 2 0.03
32 15 0.21
33 28 0.40
34 20 0.29
35 5 0.07
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (33 bp):
AAAAAACTTAAACCCTAATTTAATTAATTTTTT
Found at i:29369467 original size:18 final size:18
Alignment explanation
Indices: 29369432--29369474 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29369422 CGCATAAAAA
* * *
29369432 GAAAGCAAATAAATAAAT
1 GAAAGAAAAGAAACAAAT
29369450 GAAAGAAAAGAAACAAAT
1 GAAAGAAAAGAAACAAAT
29369468 GAAAGAA
1 GAAAGAA
29369475 GGGGGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (18 bp):
GAAAGAAAAGAAACAAAT
Found at i:29369561 original size:5 final size:5
Alignment explanation
Indices: 29369551--29369582 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
29369541 AAGCTGTGAA
29369551 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29369583 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29369576 original size:9 final size:9
Alignment explanation
Indices: 29369552--29369582 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29369542 AGCTGTGAAA
29369552 AAATAAAAT
1 AAATAAAAT
29369561 AAAATAAAAT
1 -AAATAAAAT
29369571 AAATAAAAT
1 AAATAAAAT
29369580 AAA
1 AAA
29369583 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:29381147 original size:2 final size:2
Alignment explanation
Indices: 29381140--29381184 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
29381130 TAAATAAGTG
* * *
29381140 CT CT CT CT CT CT CT CT CT CT CC CC CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29381182 CT C
1 CT C
29381185 CCATACCCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
CT
Found at i:29381159 original size:14 final size:14
Alignment explanation
Indices: 29381140--29381184 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
29381130 TAAATAAGTG
*
29381140 CTCTCTCTCTCTCT
1 CTCTCTCTCCCTCT
*
29381154 CTCTCTCCCCCTCT
1 CTCTCTCTCCCTCT
29381168 CTCTCTCTCCCTCT
1 CTCTCTCTCCCTCT
29381182 CTC
1 CTC
29381185 CCATACCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (14 bp):
CTCTCTCTCCCTCT
Found at i:29382280 original size:2 final size:2
Alignment explanation
Indices: 29382273--29382338 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
29382263 CTTATTTGTA
* * * *
29382273 CT CT CT CT CT CC CT C- CC CC CT CT CT CT CT CT CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
29382314 CT CT CT CT CT CT CT CT CC CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
29382339 ATGCAAAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:29387104 original size:20 final size:20
Alignment explanation
Indices: 29387058--29387095 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29387048 CCAATTTTTT
*
29387058 TTACTTTCATTTGCATTTCA
1 TTACTTTCAATTGCATTTCA
29387078 TTACTTTCAATTGCATTT
1 TTACTTTCAATTGCATTT
29387096 ACTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (20 bp):
TTACTTTCAATTGCATTTCA
Found at i:29390280 original size:25 final size:20
Alignment explanation
Indices: 29390232--29390271 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29390222 CTCTTTTCCA
29390232 TAACTTTTCATCTAATCTAT
1 TAACTTTTCATCTAATCTAT
29390252 TAACTTTTCATCTAATCTAT
1 TAACTTTTCATCTAATCTAT
29390272 ACATTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (20 bp):
TAACTTTTCATCTAATCTAT
Found at i:29396618 original size:16 final size:16
Alignment explanation
Indices: 29396599--29396629 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29396589 CTTCTTCACT
29396599 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
29396615 TACTTACTTACTTAA
1 TACTCACTTACTTAA
29396630 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:29396635 original size:20 final size:20
Alignment explanation
Indices: 29396596--29396635 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29396586 AAACTTCTTC
* *
29396596 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
29396616 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
29396636 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:29404169 original size:24 final size:24
Alignment explanation
Indices: 29404110--29404170 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
29404100 ACGTACCGGT
29404110 ACTTATAGAATACGCCACAAAGGC
1 ACTTATAGAATACGCCACAAAGGC
* * *
29404134 ATTTACACAATACGCCACAAAGGC
1 ACTTATAGAATACGCCACAAAGGC
29404158 ACTTATAGAATAC
1 ACTTATAGAATAC
29404171 CCTGCCTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.20
Consensus pattern (24 bp):
ACTTATAGAATACGCCACAAAGGC
Found at i:29404893 original size:30 final size:30
Alignment explanation
Indices: 29404828--29404911 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
29404818 AGCACGACAT
29404828 TCATCGGCTTCTGTCAGACACAATCAGTAG
1 TCATCGGCTTCTGTCAGACACAATCAGTAG
* *
29404858 CCATCGGCTTCTGTCAGACGCAATC-GATAG
1 TCATCGGCTTCTGTCAGACACAATCAG-TAG
** * *
29404888 TCATCGATTTTTGTCACACACAAT
1 TCATCGGCTTCTGTCAGACACAAT
29404912 TGGTAGTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 44 0.98
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TCATCGGCTTCTGTCAGACACAATCAGTAG
Found at i:29410551 original size:47 final size:48
Alignment explanation
Indices: 29410497--29410591 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 48
29410487 AACATAAAAG
29410497 TTTCAAACATTCCAAGTTGAGTATTTAATCAAGCAAA-ATAGGTGTCT
1 TTTCAAACATTCCAAGTTGAGTATTTAATCAAGCAAACATAGGTGTCT
* *
29410544 TTTCAAACATTCTAAGTTGAGTATTTAATCATGCAAACATAGGTGTCT
1 TTTCAAACATTCCAAGTTGAGTATTTAATCAAGCAAACATAGGTGTCT
29410592 CTCTGCATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 35 0.78
48 10 0.22
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (48 bp):
TTTCAAACATTCCAAGTTGAGTATTTAATCAAGCAAACATAGGTGTCT
Found at i:29423783 original size:17 final size:17
Alignment explanation
Indices: 29423757--29423798 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
29423747 TTGATTGTAT
*
29423757 ATTGAAATGGAATTGAA
1 ATTGAAATGGAAATGAA
*
29423774 ATTGATATGGAAATGAA
1 ATTGAAATGGAAATGAA
29423791 ATTGAAAT
1 ATTGAAAT
29423799 AAAAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (17 bp):
ATTGAAATGGAAATGAA
Found at i:29423786 original size:23 final size:24
Alignment explanation
Indices: 29423750--29423798 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
29423740 TATTGAATTG
* *
29423750 ATTGTATATTGAAATGGAATTGAA
1 ATTGTATATGGAAATGAAATTGAA
29423774 ATTG-ATATGGAAATGAAATTGAA
1 ATTGTATATGGAAATGAAATTGAA
29423797 AT
1 AT
29423799 AAAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (24 bp):
ATTGTATATGGAAATGAAATTGAA
Found at i:29424001 original size:28 final size:29
Alignment explanation
Indices: 29423948--29424004 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29423938 CACTCTGTGC
29423948 TATTCTGGTGTGTTTTAGATGGATTATAT
1 TATTCTGGTGTGTTTTAGATGGATTATAT
29423977 TATTCTGGTGTG-TTTAGGA-GGATTATAT
1 TATTCTGGTGTGTTTTA-GATGGATTATAT
29424005 GATATTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (29 bp):
TATTCTGGTGTGTTTTAGATGGATTATAT
Found at i:29424013 original size:28 final size:29
Alignment explanation
Indices: 29423949--29424020 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
29423939 ACTCTGTGCT
*
29423949 ATTCTGGTGTGTTTTAGATGGATTATATT
1 ATTCTGGTGTGTTTTAGATGGATTATATG
29423978 ATTCTGGTGTG-TTTAGGA-GGATTATATG
1 ATTCTGGTGTGTTTTA-GATGGATTATATG
*
29424006 ATAT-TGGTGTATTTT
1 AT-TCTGGTGTGTTTT
29424021 GGAAGAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (29 bp):
ATTCTGGTGTGTTTTAGATGGATTATATG
Found at i:29429475 original size:13 final size:14
Alignment explanation
Indices: 29429452--29429481 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29429442 TTTGAGAAGA
29429452 GATTTGGAGATG-T
1 GATTTGGAGATGCT
29429465 GATTTGGAGATGCT
1 GATTTGGAGATGCT
29429479 GAT
1 GAT
29429482 GTTTATATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.37, T:0.37
Consensus pattern (14 bp):
GATTTGGAGATGCT
Found at i:29429564 original size:29 final size:29
Alignment explanation
Indices: 29429521--29429624 Score: 114
Period size: 28 Copynumber: 3.8 Consensus size: 29
29429511 GCACTCTGTG
*
29429521 TTATTCTGGTGTGTTTTGGATGGATTATA
1 TTATTCTGGTGTGTTTTGGATGGATTACA
* *
29429550 TTATTCTGGTATGTTTGGGA-GGATTACA
1 TTATTCTGGTGTGTTTTGGATGGATTACA
* *
29429578 TTATACTGGTGTGTTTTGGTTGG---ACA
1 TTATTCTGGTGTGTTTTGGATGGATTACA
29429604 TT-TT-TGGTGTG-TTTGGATGGA
1 TTATTCTGGTGTGTTTTGGATGGA
29429625 ATCCGTGTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
23 8 0.12
24 7 0.11
25 1 0.02
26 5 0.08
28 23 0.36
29 20 0.31
ACGTcount: A:0.16, C:0.05, G:0.31, T:0.48
Consensus pattern (29 bp):
TTATTCTGGTGTGTTTTGGATGGATTACA
Found at i:29441155 original size:19 final size:19
Alignment explanation
Indices: 29441110--29441147 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29441100 CATGGGAAAT
29441110 CAACACGGCCTGGACTTCC
1 CAACACGGCCTGGACTTCC
29441129 CAACACGGCCTGGACTTCC
1 CAACACGGCCTGGACTTCC
29441148 TCACACGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.16
Consensus pattern (19 bp):
CAACACGGCCTGGACTTCC
Found at i:29442397 original size:13 final size:13
Alignment explanation
Indices: 29442381--29442405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29442371 TTAAATTTTT
29442381 ATTTTATTTTCTA
1 ATTTTATTTTCTA
29442394 ATTTTATTTTCT
1 ATTTTATTTTCT
29442406 TTTATTCGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTATTTTCTA
Found at i:29442402 original size:24 final size:23
Alignment explanation
Indices: 29442351--29442411 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
29442341 TTACTTTAGC
*
29442351 AATTTTACTTTATTTGCAATTTA
1 AATTTTATTTTATTTGCAATTTA
*
29442374 AATTTTTATTTTATTTTCTAATTT-
1 AA-TTTTATTTTATTTGC-AATTTA
* *
29442398 TATTTTCTTTTATT
1 AATTTTATTTTATT
29442412 CGCTCCTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 13 0.41
24 14 0.44
25 5 0.16
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (23 bp):
AATTTTATTTTATTTGCAATTTA
Found at i:29453721 original size:29 final size:26
Alignment explanation
Indices: 29453681--29453752 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
29453671 TTATTTTCAC
29453681 TTTTATCTTTATTTATCTTCTTTAAGTATT-
1 TTTTAT-TTTATTT-TC--CTTTAA-TATTA
29453711 TTTTATTTTATTTTCCTTTAATATTA
1 TTTTATTTTATTTTCCTTTAATATTA
29453737 TTTTAATTTTAGTTTT
1 TTTT-ATTTTA-TTTT
29453753 TATAATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.10
26 10 0.26
27 6 0.15
28 6 0.15
29 7 0.18
30 6 0.15
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTATTTTATTTTCCTTTAATATTA
Found at i:29463857 original size:55 final size:53
Alignment explanation
Indices: 29463764--29463892 Score: 134
Period size: 55 Copynumber: 2.4 Consensus size: 53
29463754 TGCGACATGG
* * * * *
29463764 CCGTGGGCAAACCTGCCAAAACAACACGTGCGTTCGACAGGCCCATGCCTCGA-AA
1 CCGTGGGCGAACCTGTC-AAACAACACGGGCGTGCGACACGCCCATGCC-C-ACAA
* * *
29463819 CCGTGGGCGAACCTGTCAAACTAGCACGGGCGTGCGACACGCCCTTGCCCATCAT
1 CCGTGGGCGAACCTGTCAAAC-AACACGGGCGTGCGACACGCCCATGCCCA-CAA
29463874 CCGTGGGCGAACCTGTCAA
1 CCGTGGGCGAACCTGTCAA
29463893 GTTAACACGG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 1 0.02
54 5 0.08
55 57 0.90
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (53 bp):
CCGTGGGCGAACCTGTCAAACAACACGGGCGTGCGACACGCCCATGCCCACAA
Found at i:29468704 original size:13 final size:13
Alignment explanation
Indices: 29468686--29468710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29468676 GGGCCGTGTG
29468686 AGGGACACGGGCC
1 AGGGACACGGGCC
29468699 AGGGACACGGGC
1 AGGGACACGGGC
29468711 GTGTGCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.48, T:0.00
Consensus pattern (13 bp):
AGGGACACGGGCC
Found at i:29481661 original size:37 final size:37
Alignment explanation
Indices: 29481611--29481685 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
29481601 ATTCAGAGAT
*
29481611 GTTCATCGTGTTCATCTTCAGTCCTCTAATACACTAG
1 GTTCATCGTGTTCATCTTCAGTCCTCGAATACACTAG
29481648 GTTCATCGTGTTCATCTTCAGTCCTCGAATACACTAG
1 GTTCATCGTGTTCATCTTCAGTCCTCGAATACACTAG
29481685 G
1 G
29481686 ATGTCATCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (37 bp):
GTTCATCGTGTTCATCTTCAGTCCTCGAATACACTAG
Found at i:29488026 original size:5 final size:5
Alignment explanation
Indices: 29488016--29488058 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
29488006 CGAACATCTA
29488016 TTTAT TTTAT TTTAT TTTAT TTTACT ATTTAT TATTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T -TTTAT T-TTAT TTTAT
29488059 AATCTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 24 0.69
6 7 0.20
7 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:29488047 original size:22 final size:21
Alignment explanation
Indices: 29488021--29488071 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
29488011 ATCTATTTAT
**
29488021 TTTATTTTATTTTATTTTACTA
1 TTTATTTTATTTTATAAT-CTA
29488043 TTTATTATTATTTTATAATCTA
1 TTTATT-TTATTTTATAATCTA
29488065 TTTATTT
1 TTTATTT
29488072 ATTCATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.58
23 10 0.38
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTTATTTTATAATCTA
Found at i:29488066 original size:18 final size:17
Alignment explanation
Indices: 29488011--29488071 Score: 51
Period size: 18 Copynumber: 3.8 Consensus size: 17
29488001 TTCATCGAAC
29488011 ATCTA-TTTATTTTA-T
1 ATCTATTTTATTTTACT
*
29488026 -TTTATTTTATTTTACT
1 ATCTATTTTATTTTACT
*
29488042 ATTTATTATTATTTTA-T
1 ATCTATT-TTATTTTACT
29488059 AATCTA-TTTATTT
1 -ATCTATTTTATTT
29488072 ATTCATTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.08
15 9 0.23
16 7 0.18
17 8 0.21
18 12 0.31
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
ATCTATTTTATTTTACT
Found at i:29488149 original size:63 final size:63
Alignment explanation
Indices: 29488042--29488171 Score: 172
Period size: 63 Copynumber: 2.1 Consensus size: 63
29488032 TTATTTTACT
*
29488042 ATTTATTATTATTTTATAATCTATTTATTTATTCATTCATTCTTTTACATTTTAAATACTTAA
1 ATTTAATATTATTTTATAATCTATTTATTTATTCATTCATTCTTTTACATTTTAAATACTTAA
* * * ** * *
29488105 ATTTAATATTATTTGTTTCATCTATTTATTTATTTATT-ATTCTTTTATTTTTTTAATATTTAA
1 ATTTAATATTATTT-TATAATCTATTTATTTATTCATTCATTCTTTTACATTTTAAATACTTAA
29488168 ATTT
1 ATTT
29488172 GATACTACTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 38 0.66
64 20 0.34
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (63 bp):
ATTTAATATTATTTTATAATCTATTTATTTATTCATTCATTCTTTTACATTTTAAATACTTAA
Found at i:29492725 original size:12 final size:12
Alignment explanation
Indices: 29492708--29492732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29492698 ACCAATACCG
29492708 ATTGAATCAACC
1 ATTGAATCAACC
29492720 ATTGAATCAACC
1 ATTGAATCAACC
29492732 A
1 A
29492733 AGTCGGTCTT
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:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
ATTGAATCAACC
Found at i:29499328 original size:24 final size:24
Alignment explanation
Indices: 29499296--29499343 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29499286 GGGAAAGGTT
29499296 CTCCACGACTGTCATTTCTTGATC
1 CTCCACGACTGTCATTTCTTGATC
29499320 CTCCACGACTGTCATTTCTTGATC
1 CTCCACGACTGTCATTTCTTGATC
29499344 GACCATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.12, T:0.38
Consensus pattern (24 bp):
CTCCACGACTGTCATTTCTTGATC
Found at i:29506352 original size:15 final size:15
Alignment explanation
Indices: 29506295--29506352 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
29506285 GAGATGACAT
*
29506295 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* * *
29506310 GAAGTCCAGGATAAT
1 GAAATCCAAGATAAA
* *
29506325 GAAATTCATGATAAA
1 GAAATCCAAGATAAA
29506340 GAAATCCAAGATA
1 GAAATCCAAGATA
29506353 CAATATCACA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.53, C:0.12, G:0.17, T:0.17
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:29542199 original size:45 final size:45
Alignment explanation
Indices: 29542057--29543062 Score: 572
Period size: 45 Copynumber: 21.6 Consensus size: 45
29542047 AATTAAAAAT
* * * * * *
29542057 AAATCTTATCGCCCTGAAGTTGTATTGGAGCAGTTTGAAAATAAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * *
29542102 AAA-CCTATCTCCCTGAAGTTGTAGTGCAGCAGATTGAAAATAAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * *
29542146 AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * * *
29542191 GAATCTTATTTCCCTTAAGTTACAGTGGAAG-AAATTAAAGCTACAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGG-AGCAGATTGAAG--A-TAG---C
* * * **
29542242 AAATCTTATCTCCTTGAAGTTACAGTGGAGTAGATTGAAGCCA-C
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * *
29542286 AAATCTTACCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * * *
29542331 GAATCTTATCTCCTTGAAGTTACAGTGGAGTAGATTTAAAATAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * *
29542376 GAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAG---C
* * * * *
29542427 AAATCTTCTCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATACC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * * *
29542472 TAATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGCTACAAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAGC
* *
29542520 TACTAATCTTATCTCCCTGAAGCTGCAGTGGAGCATATTGAAGATAGC
1 -A--AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * * *
29542568 AAACCTTATCTCCTTGGATTTGGAGTGGAGAAAATTGAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * *
29542613 AAATCTTATTTCCCTGAAATTGCAGTGGAGCAGATT-AAGCTA-C
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* ** * * *
29542656 GAATCTTATCTCTTTGAAGTTGTAGTGGAGTAGATTGAAGTTA-C
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * *
29542700 AAATCTTATCTCCCTAAAGTTGTAGTGGAGAAGATTGAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * *
29542745 GAATCTTATGTCCCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAG---C
* * *** * *
29542796 AAATCTTATTTCCCTGAAATTGCAGTGGAATTGATTAAAGCTGAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--AG---C
* * * *
29542846 AAATCTTATCTTCCTGAAGTTGTAGTGGAGCAAATTGAAGATAGA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * *
29542891 AAATCTTATTTCTCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAG---C
* * * * * * *
29542942 AAATCTTATTTCCCTAAAATTGTAGTGGAACAGAAT-AAGGCTACAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-G--A-TAG---C
* **
29542993 AAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGA-C
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
*
29543037 AATTCTTATAC-CCCTGAAGTTGCAGT
1 AAATCTTAT-CTCCCTGAAGTTGCAGT
29543063 AGGTTAGAAT
Statistics
Matches: 759, Mismatches: 161, Indels: 83
0.76 0.16 0.08
Matches are distributed among these distances:
43 30 0.04
44 148 0.19
45 300 0.40
46 2 0.00
47 6 0.01
48 18 0.02
49 2 0.00
50 42 0.06
51 209 0.28
52 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
Found at i:29542261 original size:96 final size:96
Alignment explanation
Indices: 29542057--29543062 Score: 604
Period size: 96 Copynumber: 10.7 Consensus size: 96
29542047 AATTAAAAAT
* * * * * * * *
29542057 AAATCTTATCGCCCTGAAGTTGTATTGGAGCAGTTTGAAAATAAC-AAACCTATCTCCCTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* * * *
29542121 TGTAGT-GCAGCAGATT---G--A-AAATAAC
66 TGCAGTGGAAG-AGATTAAAGCTACAAGTTAC
* * * * *
29542146 AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAATCTTATTTCCCTTAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* *
29542211 TACAGTGGAAGAAATTAAAGCTACAAGTTAC
66 TGCAGTGGAAGAGATTAAAGCTACAAGTTAC
* * * ** * *
29542242 AAATCTTATCTCCTTGAAGTTACAGTGGAGTAGATTGAAGCCA-CAAATCTTACCTCCCTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* * *
29542306 TGCAGTAG-AGCAGATTGAAG--A-TAG-T--
66 TGCAGTGGAAG-AGATTAAAGCTACAAGTTAC
* * * * * * * *
29542331 GAATCTTATCTCCTTGAAGTTACAGTGGAGTAGATTTAAAATAGTGAATCTTATTTCCCTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* * *
29542396 TACAGTGGAACAGATTAAAGCTACGAGTTAC
66 TGCAGTGGAAGAGATTAAAGCTACAAGTTAC
* * * * * * * *
29542427 AAATCTTCTCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATACCTAATCTTATTTCCCTAAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* * *
29542492 TGTAGTGGAACAGATTAAAGCTACAAGCTAC
66 TGCAGTGGAAGAGATTAAAGCTACAAGTTAC
* * * * * * * *
29542523 TAATCTTATCTCCCTGAAGCTGCAGTGGAGCATATTGAAGATAGCAAACCTTATCTCCTTGGATT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
* ** *
29542588 TGGAGT-G--GAGA--AAA--TTGAAGATAGC
66 TGCAGTGGAAGAGATTAAAGCTACAAGTTA-C
* * * **
29542613 AAATCTTATTTCCCTGAAATTGCAGTGGAGCAGATT-AAGCTA-CGAATCTTATCTCTTTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
*
29542676 TGTAGTGG-AGTAGATT---G----AAGTTAC
66 TGCAGTGGAAG-AGATTAAAGCTACAAGTTAC
* * * * *
29542700 AAATCTTATCTCCCTAAAGTTGTAGTGGAGAAGATTGAAGATAGCGAATCTTATGTCCCTGAAAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
*
29542765 TGCAGTGGAACAGATTAAAGCTACAAGTTAC
66 TGCAGTGGAAGAGATTAAAGCTACAAGTTAC
* * *** * * * *
29542796 AAATCTTATTTCCCTGAAATTGCAGTGGAATTGATTAAAGCTGAAGTTACAAATCTTATCTTCCT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--AG---CGAATCTTATCTCCCT
* * * *
29542861 GAAGTTGTAGTGG-AGCAAATTGAAG--A-TAG--A-
61 GAAGTTGCAGTGGAAG-AGATTAAAGCTACAAGTTAC
* * * * * * * *
29542891 AAATCTTATTTCTCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAG---CGAATCTTATCTCCC
* * * * * *
29542956 TAAAATTGTAGTGGAACAGAATAAGGCTACAAGTTAC
60 TGAAGTTGCAGTGGAAGAGATTAAAGCTACAAGTTAC
* **
29542993 AAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGA-C-AATTCTTATAC-CCCTGAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAA-TCTTAT-CTCCCTGAA
29543055 GTTGCAGT
64 GTTGCAGT
29543063 AGGTTAGAAT
Statistics
Matches: 709, Mismatches: 156, Indels: 98
0.74 0.16 0.10
Matches are distributed among these distances:
87 32 0.05
88 31 0.04
89 115 0.16
90 88 0.12
91 11 0.02
92 4 0.01
93 7 0.01
94 5 0.01
95 88 0.12
96 250 0.35
97 1 0.00
98 5 0.01
99 4 0.01
100 1 0.00
101 32 0.05
102 35 0.05
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (96 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATCTCCCTGAAGT
TGCAGTGGAAGAGATTAAAGCTACAAGTTAC
Found at i:29542550 original size:51 final size:51
Alignment explanation
Indices: 29542377--29543038 Score: 376
Period size: 51 Copynumber: 13.9 Consensus size: 51
29542367 TAAAATAGTG
* * *
29542377 AATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * * *
29542428 AATCTTCTCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATAC------CT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
29542473 AATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGCTACAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
29542524 AATCTTATCTCCCTGAAGCTGCAGTGGAGCATATTGAAG--A-TAG---CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * * ** *
29542569 AACCTTATCTCCTTGGATTTGGAGTGG---AGA--AAA--TTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTA-CA
* * *
29542614 AATCTTATTTCCCTGAAATTGCAGTGGAGCAGATT-AAGCTAC--G-----
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
** * **
29542657 AATCTTATCTCTTTGAAGTTGTAGTGGAGTAGATT---G----AAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
29542701 AATCTTATCTCCCTAAAGTTGTAGTGGAGA-AGATTGAAG--A-TAG---CG
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-ACAGATTAAAGCTACAAGTTACA
* *
29542746 AATCTTATGTCCCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * ** *
29542797 AATCTTATTTCCCTGAAATTGCAGTGGAATTGATTAAAGCT-GAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * * *
29542847 AATCTTATCTTCCTGAAGTTGTAGTGGAGCAAATTGAAG--A-TAG--A-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * *
29542892 AATCTTATTTCTCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * * *
29542943 AATCTTATTTCCCTAAAATTGTAGTGGAACAGAATAAGGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * *
29542994 AATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGACAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAA
29543039 TTCTTATACC
Statistics
Matches: 467, Mismatches: 99, Indels: 90
0.71 0.15 0.14
Matches are distributed among these distances:
39 1 0.00
40 2 0.00
41 3 0.01
42 2 0.00
43 29 0.06
44 31 0.07
45 146 0.31
46 1 0.00
47 3 0.01
48 13 0.03
49 4 0.01
50 39 0.08
51 193 0.41
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
Found at i:29542915 original size:95 final size:96
Alignment explanation
Indices: 29542796--29542970 Score: 273
Period size: 95 Copynumber: 1.8 Consensus size: 96
29542786 TACAAGTTAC
** *
29542796 AAATCTTATTTCCCTGAAATTGCAGTGGAATTGATTAAAGCT-GAAGTTACAAATCTTATCTT-C
1 AAATCTTATTTCCCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTAT-TTCC
* *
29542859 CTGAAGTTGTAGTGGAGCAAATTGAAGATAGA
65 CTAAAATTGTAGTGGAGCAAATTGAAGATAGA
*
29542891 AAATCTTATTTCTCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCC
1 AAATCTTATTTCCCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCC
29542956 TAAAATTGTAGTGGA
66 TAAAATTGTAGTGGA
29542971 ACAGAATAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
95 41 0.57
96 31 0.43
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (96 bp):
AAATCTTATTTCCCTGAAATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCC
TAAAATTGTAGTGGAGCAAATTGAAGATAGA
Found at i:29543080 original size:146 final size:144
Alignment explanation
Indices: 29542144--29543062 Score: 581
Period size: 146 Copynumber: 6.5 Consensus size: 144
29542134 ATTGAAAATA
* * * * * * *
29542144 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAATCTTATTTCCCTTAA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGA-C-AATCTTATATCCCTGAA
* * * * * * * * * **
29542209 GTTACAGTGGAAGAAATTAAAGCTACAAGTTACAAATCTTATCTCCTTGAAGTTACAGTGGAGTA
64 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAACA
* *
29542274 GATTGAAGC-C-----
129 GAATAAAGCTCAAGTT
* * * ** * *
29542284 ACAAATCTTACCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATAGTGAATCTTATCTCCTTGAA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAG--AGACAATCTTATATCCCTGAA
* * ** * * * * *
29542349 GTTACAGTGGAGTAGATTTAAA---A-TAG-T--GAATCTTATTTCCCTGAAGTTACAGTGGAAC
64 ATTGCAGTGGAACAGA-TTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAAC
* *
29542407 AGATTAAAGCTACGAGTT
128 AGAATAAAGCT-CAAGTT
* * * * * * *
29542425 ACAAATCTTCTCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATACCTAATCTTATTTCCCT-AA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGA-C-AATCTTATATCCCTGAA
* * * * * ** *
29542489 AGTTGTAGTGGAACAGATTAAAGCTACAAGCTACTAATCTTATCTCCCTGAAGCTGCAGTGGAGC
64 A-TTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAAC
* * * *
29542554 ATATTGAAGAT--AG--
128 AGAATAAAGCTCAAGTT
* * * * * * * * *
29542567 -CAAACCTTATCTCCTTGGATTTGGAGTGGAGAAAATTGAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGA-C-AATCTTATATCCCTGAA
* * ** * * *
29542631 ATTGCAGTGGAGCAGATT-AAGCTAC--G-----AATCTTATCTCTTTGAAGTTGTAGTGG---A
64 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAACA
* * *
29542685 G--TAGA-TTGAAGTT
129 GAATAAAGCTCAAGTT
* * * *
29542698 ACAAATCTTATCTCCCTAAAGTTGTAGTGGAGAAGATTGAAGATAGCGAATCTTATGTCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGA-C-AATCTTATATCCCTGAA
* **
29542763 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTGAAATTGCAGTGGAATT
64 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAACA
* *
29542828 GATTAAAGCTGAAGTT
129 GAATAAAGCTCAAGTT
* * * * *
29542844 ACAAATCTTATCTTCCTGAAGTTGTAGTGGAGCAAATTGAAGATAGAAAATCTTATTTCTCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAG--AGACAATCTTATATCCCTGAA
*
29542909 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGTAGTGGAACA
64 ATTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAACA
*
29542974 GAATAAGGCTACAAGTT
129 GAATAAAGCT-CAAGTT
* * * * *
29542991 ACAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGACAATTCTTATACCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGACAA-TCTTATATCCCTGAAA
29543056 TTGCAGT
65 TTGCAGT
29543063 AGGTTAGAAT
Statistics
Matches: 625, Mismatches: 110, Indels: 82
0.76 0.13 0.10
Matches are distributed among these distances:
127 1 0.00
128 2 0.00
129 2 0.00
130 1 0.00
132 72 0.12
133 30 0.05
134 35 0.06
135 1 0.00
136 2 0.00
137 2 0.00
138 2 0.00
139 1 0.00
140 100 0.16
141 129 0.21
142 4 0.01
143 2 0.00
144 4 0.01
145 8 0.01
146 148 0.24
147 77 0.12
148 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (144 bp):
ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAGACAATCTTATATCCCTGAAAT
TGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCCCTAAAATTGCAGTGGAACAGA
ATAAAGCTCAAGTT
Found at i:29543675 original size:22 final size:22
Alignment explanation
Indices: 29543647--29543707 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
29543637 AAAAGAAAGG
29543647 TGATTTTTTTTTATATTTTCAT
1 TGATTTTTTTTTATATTTTCAT
29543669 TGA-TTTTTTTTATATTTTCAT
1 TGATTTTTTTTTATATTTTCAT
* *
29543690 T-CTTTATTTTT-TATTTTC
1 TGATTTTTTTTTATATTTTC
29543708 GAAAACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.19
21 26 0.72
22 3 0.08
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (22 bp):
TGATTTTTTTTTATATTTTCAT
Found at i:29544808 original size:15 final size:15
Alignment explanation
Indices: 29544773--29544805 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
29544763 TGTTAATTCT
29544773 TTTATTTTTTATTTA
1 TTTATTTTTTATTTA
29544788 TTTATTTTCTTATTTA
1 TTTATTTT-TTATTTA
29544804 TT
1 TT
29544806 ATTCCTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTATTTA
Found at i:29544814 original size:23 final size:24
Alignment explanation
Indices: 29544774--29544819 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
29544764 GTTAATTCTT
* *
29544774 TTATTTTTTATTTATTTA-TTTTC
1 TTATTTATTATTCATTTACTTTTC
*
29544797 TTATTTATTATTCCTTTACTTTT
1 TTATTTATTATTCATTTACTTTT
29544820 TGTTATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (24 bp):
TTATTTATTATTCATTTACTTTTC
Found at i:29544889 original size:21 final size:22
Alignment explanation
Indices: 29544865--29544919 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
29544855 CGAACATCTA
*
29544865 TTATTTATTTTATT-TTAGTAT
1 TTATTTATTTTATTAGTAGTAT
*
29544886 TTATTACTATTTTATTAGTATTAT
1 TTATT--TATTTTATTAGTAGTAT
*
29544910 CTATTTATTT
1 TTATTTATTT
29544920 ATTCATTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.18
22 5 0.18
23 9 0.32
24 9 0.32
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTTATTTTATTAGTAGTAT
Found at i:29545731 original size:27 final size:27
Alignment explanation
Indices: 29545689--29545741 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29545679 AACTAGGTAC
*
29545689 CTATTTTGGGCGTTACGAGGGTGCTAT
1 CTATTTTGGGCATTACGAGGGTGCTAT
29545716 CTATTTTGGGCATTACGAGGGTGCTA
1 CTATTTTGGGCATTACGAGGGTGCTA
29545742 ACCCTTCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (27 bp):
CTATTTTGGGCATTACGAGGGTGCTAT
Found at i:29548028 original size:26 final size:26
Alignment explanation
Indices: 29547827--29548012 Score: 345
Period size: 26 Copynumber: 7.2 Consensus size: 26
29547817 TGATACAAAT
*
29547827 TGATAATGGGTTAGGTAACTGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29547853 TGATAATGGGCTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29547879 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29547905 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29547931 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29547957 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29547983 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29548009 TGAT
1 TGAT
29548013 TATACTTAAG
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 155 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29555479 original size:26 final size:26
Alignment explanation
Indices: 29555443--29555524 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
29555433 TGATACAAAT
*
29555443 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTCAGGTAAATGTTCCA
29555469 TGATAATGGGTCAGGTAAATGTTCCA
1 TGATAATGGGTCAGGTAAATGTTCCA
29555495 TGATAATGGGTCAGGTAAATGTTCCA
1 TGATAATGGGTCAGGTAAATGTTCCA
29555521 TGAT
1 TGAT
29555525 GGGAATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (26 bp):
TGATAATGGGTCAGGTAAATGTTCCA
Found at i:29558132 original size:39 final size:39
Alignment explanation
Indices: 29558078--29558157 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
29558068 GGGTGTTACA
* *
29558078 TTTCCAGCATGTAGCCTGCGGACCTCAGGTCCGGATATG
1 TTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATATG
29558117 TTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATATG
1 TTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATATG
29558156 TT
1 TT
29558158 CCAAATATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (39 bp):
TTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATATG
Found at i:29564656 original size:5 final size:5
Alignment explanation
Indices: 29564646--29564675 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
29564636 TAGTTAATAA
29564646 TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
29564676 GAAAGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:29566491 original size:18 final size:18
Alignment explanation
Indices: 29566468--29566503 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29566458 TGAGAATTTC
*
29566468 TGATACCGTGACTGAATG
1 TGATACCGTGACTAAATG
*
29566486 TGATACTGTGACTAAATG
1 TGATACCGTGACTAAATG
29566504 CGTTACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (18 bp):
TGATACCGTGACTAAATG
Found at i:29568110 original size:18 final size:18
Alignment explanation
Indices: 29568087--29568124 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
29568077 AAAAATCACT
29568087 TAACAA-AATACTTATAAA
1 TAACAATAATACTTA-AAA
29568105 TAACAATTAATACTTAAAA
1 TAACAA-TAATACTTAAAA
29568124 T
1 T
29568125 TCATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
TAACAATAATACTTAAAA
Found at i:29570752 original size:50 final size:49
Alignment explanation
Indices: 29570653--29570753 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 49
29570643 TAGTTTTATT
* * * *
29570653 AAAATTATATATATATCCAATAATTTTTTTTATTAATATTAAAGAATTA
1 AAAATAATATATATATCCAAAAATTTTTATTATAAATATTAAAGAATTA
*
29570702 AAAATAATA-ATATAT-CAAAAATATTTTATTATAAATATAATAAATAATTA
1 AAAATAATATATATATCCAAAAAT-TTTTATTATAAATAT--TAAAGAATTA
29570752 AA
1 AA
29570754 TTTTATTGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
47 6 0.14
48 19 0.43
49 8 0.18
50 11 0.25
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (49 bp):
AAAATAATATATATATCCAAAAATTTTTATTATAAATATTAAAGAATTA
Found at i:29571924 original size:37 final size:37
Alignment explanation
Indices: 29571865--29571935 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
29571855 AGACATCTTG
* *
29571865 TTTCGATACTAAACTGAAATAATAAGTCTAGATTTCA
1 TTTCAATACTAAACTAAAATAATAAGTCTAGATTTCA
*
29571902 TTTCAATATTAAACTAAAATAATAAGTCTAGATT
1 TTTCAATACTAAACTAAAATAATAAGTCTAGATT
29571936 CTGTTTCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (37 bp):
TTTCAATACTAAACTAAAATAATAAGTCTAGATTTCA
Found at i:29572142 original size:24 final size:24
Alignment explanation
Indices: 29572115--29572174 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
29572105 ATCTTCCAAT
* **
29572115 ATATACATATATTAAATTTATTTA
1 ATATACATATATAAAATAAATTTA
* *
29572139 ATATATAAATATAAAATAAATTTA
1 ATATACATATATAAAATAAATTTA
29572163 AT-TAGCATATAT
1 ATATA-CATATAT
29572175 GTATACATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATACATATATAAAATAAATTTA
Found at i:29572831 original size:13 final size:13
Alignment explanation
Indices: 29572797--29572837 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
29572787 TTGGGGTTCG
*
29572797 GAGTTCAATGTTT
1 GAGTTCAAGGTTT
*
29572810 AAGGTTCAAGGTTT
1 GA-GTTCAAGGTTT
29572824 GAGTTCAAGGTTT
1 GAGTTCAAGGTTT
29572837 G
1 G
29572838 GAATTTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.39
Consensus pattern (13 bp):
GAGTTCAAGGTTT
Found at i:29573222 original size:22 final size:22
Alignment explanation
Indices: 29573197--29573240 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29573187 AAATAATTGC
29573197 AGGAATAAATTTCAAAAGTTGT
1 AGGAATAAATTTCAAAAGTTGT
29573219 AGGAATAAATTTCAAAAGTTGT
1 AGGAATAAATTTCAAAAGTTGT
29573241 GAAGTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (22 bp):
AGGAATAAATTTCAAAAGTTGT
Found at i:29575502 original size:2 final size:2
Alignment explanation
Indices: 29575495--29575526 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29575485 ACAGTAAATA
29575495 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29575527 TGATGGGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29582189 original size:13 final size:13
Alignment explanation
Indices: 29582171--29582209 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
29582161 AGATATTATT
29582171 TTATTTAGTTTTA
1 TTATTTAGTTTTA
29582184 TTATTTA-TTTTA
1 TTATTTAGTTTTA
*
29582196 TTAATTTAGCTTTA
1 TT-ATTTAGTTTTA
29582210 GCATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:29584614 original size:13 final size:13
Alignment explanation
Indices: 29584596--29584634 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
29584586 AGATATTATT
29584596 TTATTTAGTTTTA
1 TTATTTAGTTTTA
29584609 TTATTTA-TTTTA
1 TTATTTAGTTTTA
*
29584621 TTAATTTAGCTTTA
1 TT-ATTTAGTTTTA
29584635 GCATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:29587959 original size:68 final size:67
Alignment explanation
Indices: 29587887--29588036 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29587877 CATCATGTGT
* * * *
29587887 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29587949 ATGTAG
62 ATGTAG
** * *
29587955 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29588020 AG
66 AG
29588022 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29588037 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:29587992 original size:64 final size:64
Alignment explanation
Indices: 29587911--29588094 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
29587901 AGACATTATG
* *
29587911 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29587975 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29588040 AA
63 AA
* * * *
29588042 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29588095 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29592168 original size:21 final size:21
Alignment explanation
Indices: 29592144--29592184 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29592134 ACCTTTTCTA
29592144 AAGTTAAAA-GTCAAAACCATT
1 AAGTTAAAAGGT-AAAACCATT
29592165 AAGTTAAAAGGTAAAACCAT
1 AAGTTAAAAGGTAAAACCAT
29592185 GTTATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACCATT
Found at i:29592192 original size:70 final size:67
Alignment explanation
Indices: 29592100--29592232 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
29592090 TCTAAATAAG
* ** *
29592100 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACCACGTCATTTTGATAAATGTTTA-CTAAT-T-AAGTTAAAAGGCAAAACCATT
29592165 AAGTT
63 AAGTT
* * *
29592170 AAAAGGTAAAACCATGTTATTTTGATAAATGTTTACTAATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACCACGTCATTTTGATAAATGTTTACTAATTAAGTTAAAAGGCAAAACCATTA
29592233 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 3 0.05
70 31 0.55
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACCACGTCATTTTGATAAATGTTTACTAATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:29595725 original size:27 final size:28
Alignment explanation
Indices: 29595695--29595756 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 28
29595685 GTGACGAAGT
29595695 CACCAGATACAGATAT-TATGGCAGAGC
1 CACCAGATACAGATATATATGGCAGAGC
*
29595722 CACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGATACAGATATATATGGCAGAGC
29595749 CACCAGAT
1 CACCAGAT
29595757 CANNNNNNNN
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (28 bp):
CACCAGATACAGATATATATGGCAGAGC
Found at i:29597354 original size:26 final size:26
Alignment explanation
Indices: 29597325--29597451 Score: 209
Period size: 26 Copynumber: 4.9 Consensus size: 26
29597315 TTCTTTAATA
*
29597325 AACATTTACCTAACCCATTATTATGG
1 AACATTTACCTAACCCATTATCATGG
*
29597351 AACATTTACCTAAACCATTATCATGG
1 AACATTTACCTAACCCATTATCATGG
*
29597377 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGG
* *
29597403 AATATTTACCTAATCCATTATCATGG
1 AACATTTACCTAACCCATTATCATGG
29597429 AACATTTACCTAACCCATTATCA
1 AACATTTACCTAACCCATTATCA
29597452 ATTTGTACCG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 92 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCATGG
Done.