Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 126 of 222
Found at i:40898348 original size:46 final size:46
Alignment explanation
Indices: 40898296--40898417 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
40898286 AGTGTTATTG
* *
40898296 ATCAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
40898342 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
40898388 ATCAGTGGTAGCTTTGGCTACATATCAGTG
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTG
40898418 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:40902048 original size:98 final size:97
Alignment explanation
Indices: 40901872--40902063 Score: 276
Period size: 98 Copynumber: 2.0 Consensus size: 97
40901862 GAAATCAGGC
* * * * *
40901872 TTTTATTTGAATCAAAGTATACGAGTCACGCATACATAGTCCATTATCCACTTAGGATTAAGGTA
1 TTTTATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGTA
*
40901937 TGACACACAATGAACGTCACAAGTGAATAAAA
66 TGACACACAATGAACGTCACAAATGAATAAAA
* * *
40901969 TTTTCATTTGCATCATAGTATACGAGCCACACATACATAGTCTATCATCCACTCAGAATTAAGGT
1 TTTT-ATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGT
* *
40902034 ATGACACACTATGAAGGTCACAAATGAATA
65 ATGACACACAATGAACGTCACAAATGAATA
40902064 GATCTATAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 4 0.05
98 79 0.95
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (97 bp):
TTTTATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGTA
TGACACACAATGAACGTCACAAATGAATAAAA
Found at i:40905405 original size:22 final size:22
Alignment explanation
Indices: 40905376--40905418 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
40905366 ACAGATACGC
*
40905376 GGATTCC-ACCCAAACACACCA
1 GGATTCCAACCAAAACACACCA
40905397 GGATATCCAACCAAAACACACC
1 GGAT-TCCAACCAAAACACACC
40905419 CGAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.42, C:0.40, G:0.09, T:0.09
Consensus pattern (22 bp):
GGATTCCAACCAAAACACACCA
Found at i:40909101 original size:11 final size:11
Alignment explanation
Indices: 40909081--40909112 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40909071 TTAATTAGTT
40909081 TAATATAATAA
1 TAATATAATAA
*
40909092 TAATAAAATAA
1 TAATATAATAA
40909103 TAATATAATA
1 TAATATAATA
40909113 TTACTTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAATAA
Found at i:40909247 original size:14 final size:13
Alignment explanation
Indices: 40909221--40909271 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
40909211 GTTTATTTGA
40909221 AATATAATAATAT
1 AATATAATAATAT
40909234 AATATAATTAATAT
1 AATATAA-TAATAT
* *
40909248 AAT-TTACAATAT
1 AATATAATAATAT
*
40909260 AATAAAATAATA
1 AATATAATAATA
40909272 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:40910838 original size:16 final size:16
Alignment explanation
Indices: 40910819--40910852 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40910809 AACCAGAATG
40910819 TTGTAGGCAAAATACC
1 TTGTAGGCAAAATACC
40910835 TTGTAGGCAAAATACC
1 TTGTAGGCAAAATACC
40910851 TT
1 TT
40910853 ACACCGTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
TTGTAGGCAAAATACC
Found at i:40913413 original size:51 final size:51
Alignment explanation
Indices: 40913353--40913507 Score: 265
Period size: 51 Copynumber: 3.0 Consensus size: 51
40913343 CGTACAAAAA
* *
40913353 CAACATTATCCAGTCCATTTAATGTTGCAAAATCACCAGCATATTCATCAG
1 CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
* *
40913404 CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAACATATTCATCAG
1 CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
*
40913455 CAACATTATCCACTCTATCTAATGTTGCAAAATCACCAGCATATTCATCAG
1 CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
40913506 CA
1 CA
40913508 GCAACTTCAC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 97 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.28
Consensus pattern (51 bp):
CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
Found at i:40913667 original size:33 final size:32
Alignment explanation
Indices: 40913611--40913723 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 32
40913601 GTAGCAGACA
* *
40913611 CACCCTCCCCATCAGCTTGTACCTCTCCTACAT
1 CACCCTCCCCATCAGATTCTACCTCTCC-ACAT
* * *
40913644 CACCCTCCCCACCAGATTCTACCTATCCCAGAT
1 CACCCTCCCCATCAGATTCTACCTCT-CCACAT
* ** * * *
40913677 CACCTTTACCATCATATTCTACCCCTTCATCAT
1 CACCCTCCCCATCAGATTCTACCTCTCCA-CAT
40913710 CACCCTCCCCATCA
1 CACCCTCCCCATCA
40913724 ACTTCCACCC
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.93
34 2 0.03
ACGTcount: A:0.22, C:0.48, G:0.04, T:0.27
Consensus pattern (32 bp):
CACCCTCCCCATCAGATTCTACCTCTCCACAT
Found at i:40920227 original size:22 final size:22
Alignment explanation
Indices: 40920199--40920275 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
40920189 TTTCTTTTAA
40920199 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
40920221 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
40920245 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
40920267 TTAGGAGAT
1 TTAGGAGAT
40920276 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:40920244 original size:46 final size:46
Alignment explanation
Indices: 40920194--40920288 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
40920184 TCTATTTTCT
40920194 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
40920240 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
40920286 TTT
1 TTT
40920289 CTATCTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:40924766 original size:46 final size:46
Alignment explanation
Indices: 40924716--40924810 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
40924706 TCTATTTTCT
*
40924716 TTTAATTATGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
40924762 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
40924808 TTT
1 TTT
40924811 TTATCTTTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:40924813 original size:22 final size:22
Alignment explanation
Indices: 40924742--40924813 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
40924732 GATGCTAAAG
40924742 TTTAGGAGATAATATTTTGGTT
1 TTTAGGAGATAATATTTTGGTT
* * ** ****
40924764 TAATTAGGAGATTAGATGCTAAAG
1 T--TTAGGAGATAATATTTTGGTT
40924788 TTTAGGAGATAATATTTTGGTT
1 TTTAGGAGATAATATTTTGGTT
40924810 TTTA
1 TTTA
40924814 TCTTTGTATT
Statistics
Matches: 32, Mismatches: 16, Indels: 4
0.62 0.31 0.08
Matches are distributed among these distances:
22 18 0.56
24 14 0.44
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.44
Consensus pattern (22 bp):
TTTAGGAGATAATATTTTGGTT
Found at i:40925543 original size:171 final size:170
Alignment explanation
Indices: 40925258--40925594 Score: 444
Period size: 171 Copynumber: 2.0 Consensus size: 170
40925248 ACAATTCAGA
* * * *
40925258 AACAAACTAAAAATGCATTAATTTGATCAAATTACTAAAATTTGCATCCTAATTGTGCCATCATC
1 AACAAACTAAAAATGCATTAACTTGATCAAATTACTAAAATTTACATCCTAATTATGACATCATC
** *
40925323 AAATCAACTTGATGATGAACACCAATCAACCAATAAACAACTGCCAAAAGTCCCAA-AAGACCCA
66 AAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTGCCAAAAGGCCCAAGAAG-CCCA
* * *
40925387 TCATATCAAATGATGCACGAAAGATCAAGTCTTAGATGCAAG
130 TCATATC-AATGATGCACAAAAGATAAAATCTTAGATGCAAG
** ** *
40925429 AACAAACTAGCAATGCATTAACTTGATCAAATTA-TAGAAATTTACATTTTAGTTATGACATCAT
1 AACAAACTAAAAATGCATTAACTTGATCAAATTACTA-AAATTTACATCCTAATTATGACATCAT
* * * *
40925493 CAAATCAACTTGACAATGAATATCAATCAACTAATAAACAACTGCCAAAAGGCCCAAGAAGCCTA
65 CAAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTGCCAAAAGGCCCAAGAAGCCCA
* *
40925558 TTATATCAATGATGCACAAAAGTTAAAATCTTAGATG
130 TCATATCAATGATGCACAAAAGATAAAATCTTAGATG
40925595 GACTTCCTCA
Statistics
Matches: 143, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
170 28 0.20
171 112 0.78
172 3 0.02
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (170 bp):
AACAAACTAAAAATGCATTAACTTGATCAAATTACTAAAATTTACATCCTAATTATGACATCATC
AAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTGCCAAAAGGCCCAAGAAGCCCAT
CATATCAATGATGCACAAAAGATAAAATCTTAGATGCAAG
Found at i:40932680 original size:16 final size:16
Alignment explanation
Indices: 40932659--40932718 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
40932649 TTTGGTTCGC
40932659 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40932675 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
40932691 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40932707 TGTATTAGATTA
1 TGTATTGGATTA
40932719 AATGTGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40932699 original size:32 final size:32
Alignment explanation
Indices: 40932659--40932726 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
40932649 TTTGGTTCGC
*
40932659 TGTATTGGATTAGAGGTGTATTGGATTAGAA-G
1 TGTATTGGATTAGAGGTGTATTAGATTA-AATG
40932691 TGTATTGGATTAGAGGTGTATTAGATTAAATG
1 TGTATTGGATTAGAGGTGTATTAGATTAAATG
40932723 TGTA
1 TGTA
40932727 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTAGATTAAATG
Found at i:40932725 original size:16 final size:16
Alignment explanation
Indices: 40932659--40932726 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
40932649 TTTGGTTCGC
*
40932659 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
40932675 TGTATTGGATTAGAA-G
1 TGTATTGGATTA-AAGG
*
40932691 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
* *
40932707 TGTATTAGATTAAATG
1 TGTATTGGATTAAAGG
40932723 TGTA
1 TGTA
40932727 ATAGCAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 43 0.96
17 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAAAGG
Found at i:40933050 original size:157 final size:157
Alignment explanation
Indices: 40932856--40933165 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 157
40932846 CCCTTAGCAT
*
40932856 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
40932921 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
40932986 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * *
40933013 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
40933078 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
40933143 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
40933166 ATATTCTTAT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:40933162 original size:82 final size:81
Alignment explanation
Indices: 40932919--40933168 Score: 186
Period size: 76 Copynumber: 3.1 Consensus size: 81
40932909 TATTATTATC
* * *
40932919 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTAT-ATTAAAATATAT
40932984 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
* * * * *
40933001 AATAATTACCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT-TTAAAT
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATATTAAAA
* * * * *
40933055 TTTGATAAGATT-AT-TAA-TATG
60 TAT-ATAA-TTTAATAAAATTCTT
40933076 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATA-TTAAAATATAT
40933141 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
*
40933158 AATAATTAATA
1 AATAATAAATA
40933169 TTCTTATATG
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 10 0.08
76 21 0.17
77 6 0.05
78 8 0.07
79 8 0.07
80 6 0.05
81 21 0.17
82 20 0.17
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (81 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATATTAAAATATATA
ATTTAATAAAATTCTT
Found at i:40933239 original size:157 final size:155
Alignment explanation
Indices: 40932902--40933223 Score: 349
Period size: 157 Copynumber: 2.0 Consensus size: 155
40932892 TTAAATTTTA
* * * *
40932902 ATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * * * * ** *
40932967 TTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTACCAGAAATTTGTTTTGGTAAATT
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
* * * * *
40933032 ATTATTGTTATTGTTATTTAAATTTTG
131 ATAATTATTATTGATATATAAA--TAG
* *
40933059 ATAAGATTATTAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * **
40933124 TTATACTTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-A
40933189 AATCATAATATATTATATGATACTATAAA-AG
127 AATCATAAT-TATTAT-TGATA-TATAAATAG
40933220 ATAA
1 ATAA
40933224 TTTGAAATAA
Statistics
Matches: 137, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
157 102 0.74
159 4 0.03
160 4 0.03
161 13 0.09
162 5 0.04
163 4 0.03
164 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (155 bp):
ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
ATAATTATTATTGATATATAAATAG
Found at i:40934062 original size:13 final size:13
Alignment explanation
Indices: 40934044--40934073 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40934034 CAATCAGCTA
40934044 AATTCAGAAAAAC
1 AATTCAGAAAAAC
40934057 AATTCAGAAAAAC
1 AATTCAGAAAAAC
40934070 AATT
1 AATT
40934074 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:40937294 original size:114 final size:115
Alignment explanation
Indices: 40937058--40937316 Score: 290
Period size: 114 Copynumber: 2.3 Consensus size: 115
40937048 TTTGAAACCG
* * ** ** *
40937058 CCGCTATATATCAAGCA-TTAGCGGCGCGTCATGAAAAATGCCGCAAAAAGTTTAACGACAACGC
1 CCGCTATAGATCAAG-ATTTAGCGGCGCTTTTTGAAAAGCGCCGCAAAAAATTTAACGACAACGC
* * * **
40937122 CGTCATTTTATGTTGAGTTTTAGTGGCATTAGCGGTGCTTCTTGGAAAACA
65 CGTCATTTTAGGTTGAGCTTTAGTGGCATTAGCGGCGCTTCTTAAAAAACA
*
40937173 CCGCTATAGATCAAGATTTAGCGGC-CTTTTTGAAAAGCGCCGCAAAAAATTTAA-GCACAACGG
1 CCGCTATAGATCAAGATTTAGCGGCGCTTTTTGAAAAGCGCCGCAAAAAATTTAACG-ACAACGC
* * * **
40937236 CGTCGTTTTAGGTTGAGCTTTAGTGGCATTAGTGGCGCTTTTTAAAAAATG
65 CGTCATTTTAGGTTGAGCTTTAGTGGCATTAGCGGCGCTTCTTAAAAAACA
* * *
40937287 CCTCTATAGATCGAGCTTTAGCGGCGCTTT
1 CCGCTATAGATCAAGATTTAGCGGCGCTTT
40937317 GTAAAAAATG
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
113 1 0.01
114 93 0.77
115 26 0.22
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (115 bp):
CCGCTATAGATCAAGATTTAGCGGCGCTTTTTGAAAAGCGCCGCAAAAAATTTAACGACAACGCC
GTCATTTTAGGTTGAGCTTTAGTGGCATTAGCGGCGCTTCTTAAAAAACA
Found at i:40937616 original size:55 final size:53
Alignment explanation
Indices: 40937510--40937625 Score: 146
Period size: 55 Copynumber: 2.2 Consensus size: 53
40937500 AATAATTAAT
* * * *
40937510 GTTTAGAGTTTAGTGTTTGGTTTAGGTTGTAGGTTTATAGTTTAGTATTTAGG
1 GTTTAGGGTTTAGTGTTTGGTTTAGGGTGTAGGGTTAAAGTTTAGTATTTAGG
40937563 GTTTAGGGTTTAGTGTTTAGGGTTTATGGGT-TAGGGTTAAAGTTTA-TAGTTTAGG
1 GTTTAGGGTTTAGTGTTT--GGTTTA-GGGTGTAGGGTTAAAGTTTAGTA-TTTAGG
40937618 GTTTAGGG
1 GTTTAGGG
40937626 GCTTAGGATT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
53 17 0.31
54 2 0.04
55 33 0.60
56 3 0.05
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (53 bp):
GTTTAGGGTTTAGTGTTTGGTTTAGGGTGTAGGGTTAAAGTTTAGTATTTAGG
Found at i:40937621 original size:7 final size:7
Alignment explanation
Indices: 40937510--40937653 Score: 75
Period size: 7 Copynumber: 21.0 Consensus size: 7
40937500 AATAATTAAT
*
40937510 GTTTAGA
1 GTTTAGG
*
40937517 GTTTAGT
1 GTTTAGG
40937524 GTTT--G
1 GTTTAGG
40937529 GTTTA-G
1 GTTTAGG
40937535 GTTGTA-G
1 GTT-TAGG
**
40937542 GTTTATA
1 GTTTAGG
*
40937549 GTTTAGT
1 GTTTAGG
*
40937556 ATTTAGG
1 GTTTAGG
40937563 GTTTAGG
1 GTTTAGG
*
40937570 GTTTAGT
1 GTTTAGG
40937577 GTTTAGG
1 GTTTAGG
40937584 GTTTATGG
1 GTTTA-GG
40937592 G-TTAGG
1 GTTTAGG
**
40937598 G-TTAAA
1 GTTTAGG
**
40937604 GTTTATA
1 GTTTAGG
40937611 GTTTAGG
1 GTTTAGG
40937618 GTTTAGGG
1 GTTTA-GG
*
40937626 GCTTAGG
1 GTTTAGG
* **
40937633 ATTTATA
1 GTTTAGG
*
40937640 GTTTAGT
1 GTTTAGG
40937647 GTTTAGG
1 GTTTAGG
40937654 ATTTTAAACA
Statistics
Matches: 107, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
5 4 0.04
6 13 0.12
7 81 0.76
8 9 0.08
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:40938421 original size:39 final size:41
Alignment explanation
Indices: 40938366--40938450 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
40938356 AAAATGTAGT
** *
40938366 AAAAAGTAAGCAAATAGT-AGTTTTTTTAAAAAAACGCCGC
1 AAAAAGTAAGCAAATAGTGACATTTTTGAAAAAAACGCCGC
*
40938406 AAAAAGTAAGC-AATAGTGACATTTTTGAAAAAAACGCTGC
1 AAAAAGTAAGCAAATAGTGACATTTTTGAAAAAAACGCCGC
40938446 AAAAA
1 AAAAA
40938451 ATCATAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 6 0.15
40 34 0.85
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAAAGTAAGCAAATAGTGACATTTTTGAAAAAAACGCCGC
Found at i:40940151 original size:24 final size:24
Alignment explanation
Indices: 40940116--40940167 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
40940106 TTGTTTAAAC
*
40940116 ATTT-TTACCT-AATAAAACTAAT
1 ATTTCTTACCTAAAAAAAACTAAT
40940138 ATTTCTTACCCTAAAAAAAACTAAT
1 ATTTCTTA-CCTAAAAAAAACTAAT
40940163 ATTTC
1 ATTTC
40940168 AGTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 3 0.12
24 3 0.12
25 16 0.62
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTTCTTACCTAAAAAAAACTAAT
Found at i:40941066 original size:220 final size:229
Alignment explanation
Indices: 40940678--40941135 Score: 682
Period size: 220 Copynumber: 2.0 Consensus size: 229
40940668 TGACGTTTCA
** * * *
40940678 ATTTGGGATCATTGTCGTTGGGACTATTTTATTACTGTACATTTTTCAAGTTTATTACTGTACAT
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAC
*
40940743 TTTGAAATTGTGCTTCTTTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGT
66 TTTGAAATTGTGCTAC--TTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGT
40940808 TTTGATATTAACAATGTTTGATTTTAATA-TT-TAA-T-AAT-TTTTTAAAACTTATAAATATAT
129 TTTGATATTAACAATGTTTGATTTTAATATTTATAATTAAATGTTTTTAAAACTTATAAATATAT
40940868 TTTGTAAGAGAGTAATTTTAATCATTATTTAAATTT
194 TTTGTAAGAGAGTAATTTTAATCATTATTTAAATTT
*
40940904 ATTTGGGATCTTTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAC
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAC
* *
40940969 TTTG-AATT-TG-TAC-TTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAATTAATTTT
66 TTTGAAATTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
* *
40941030 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAATGTTTTTAAGACTTATAAATATT
131 TGATATTAACAATGTTTGATTTTAATATTT-ATAA--TTAAATGTTTTTAAAACTTATAAATATA
** *
40941095 TTTTGTGGGAGAGTAATTTTGATCATTATTTAAATTT
193 TTTTGTAAGAGAGTAATTTTAATCATTATTTAAATTT
40941132 ATTT
1 ATTT
40941136 TAATATAAAA
Statistics
Matches: 210, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
220 73 0.35
221 2 0.01
223 5 0.02
224 2 0.01
225 4 0.02
226 64 0.30
227 3 0.01
228 57 0.27
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (229 bp):
ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAC
TTTGAAATTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
TGATATTAACAATGTTTGATTTTAATATTTATAATTAAATGTTTTTAAAACTTATAAATATATTT
TGTAAGAGAGTAATTTTAATCATTATTTAAATTT
Found at i:40941178 original size:19 final size:19
Alignment explanation
Indices: 40941154--40941211 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
40941144 AAATCAAAAC
40941154 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
* *
40941173 TTACATAAC-TTACATAAT
1 TTACATAACTTTAAAGAAT
40941191 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
40941210 TT
1 TT
40941212 TCGATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (19 bp):
TTACATAACTTTAAAGAAT
Found at i:40941290 original size:8 final size:9
Alignment explanation
Indices: 40941151--40941499 Score: 125
Period size: 9 Copynumber: 36.2 Consensus size: 9
40941141 TAAAAATCAA
40941151 AACTTACAT
1 AACTTACAT
* *
40941160 AACTTTAAAG
1 AAC-TTACAT
*
40941170 AATTTACAT
1 AACTTACAT
40941179 AACTTACAT
1 AACTTACAT
*
40941188 AATTTACAT
1 AACTTACAT
* *
40941197 AACTTTAAAG
1 AAC-TTACAT
* *
40941207 AATTTTCGATTTT
1 AACTTAC-A---T
40941220 AACTTA-AT
1 AACTTACAT
*
40941228 AACTTATAT
1 AACTTACAT
*
40941237 ATATGTATATCAT
1 A-A-CT-TA-CAT
40941250 AACTTACAT
1 AACTTACAT
*
40941259 AACTCACATAT
1 AACTTAC--AT
40941270 AACTTACAT
1 AACTTACAT
40941279 AACTTA-AT
1 AACTTACAT
40941287 AACTTACAT
1 AACTTACAT
*
40941296 ATATCATATCAT
1 A-A-CTTA-CAT
40941308 AA-TTCACAT
1 AACTT-ACAT
40941317 AACTTA-AT
1 AACTTACAT
*
40941325 AACTTATATAT
1 AAC-T-TACAT
*
40941336 ATATCATATCAT
1 A-A-CTTA-CAT
40941348 AACTTACAT
1 AACTTACAT
* *
40941357 AACTCACAA
1 AACTTACAT
*
40941366 AACATACAT
1 AACTTACAT
*
40941375 AACATA-AT
1 AACTTACAT
*
40941383 AACTTATATAT
1 AAC-T-TACAT
*
40941394 ATATCATATCAT
1 A-A-CTTA-CAT
40941406 AACTTACAT
1 AACTTACAT
* *
40941415 AACTCATAT
1 AACTTACAT
* *
40941424 AACATATAT
1 AACTTACAT
* *
40941433 CATTTA-AT
1 AACTTACAT
*
40941441 AACTTATAT
1 AACTTACAT
*
40941450 ATATCATATCAT
1 A-A-CTTA-CAT
*
40941462 AACTTACGT
1 AACTTACAT
40941471 AACTTACAT
1 AACTTACAT
*
40941480 AACTCACAT
1 AACTTACAT
40941489 AACTTACAT
1 AACTTACAT
40941498 AA
1 AA
40941500 TACCTAAATA
Statistics
Matches: 254, Mismatches: 51, Indels: 70
0.68 0.14 0.19
Matches are distributed among these distances:
8 31 0.12
9 131 0.52
10 34 0.13
11 31 0.12
12 18 0.07
13 9 0.04
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (9 bp):
AACTTACAT
Found at i:40941349 original size:40 final size:38
Alignment explanation
Indices: 40941248--40941489 Score: 164
Period size: 40 Copynumber: 6.3 Consensus size: 38
40941238 TATGTATATC
*
40941248 ATAACTTACATA-ACTCACAT-ATAACTTACATAACTTA
1 ATAACTTACATATA-TCATATCATAACTTACATAACTTA
40941285 ATAACTTACATATATCATATCATAA-TTCACATAACTTA
1 ATAACTTACATATATCATATCATAACTT-ACATAACTTA
* *
40941323 ATAACTTATATATATATCATATCATAACTTACATAACTCA
1 ATAAC-T-TACATATATCATATCATAACTTACATAACTTA
* * * *
40941363 CAAAACATACATA-A-CATA--ATAACTTATATATATATCATATC
1 -ATAACTTACATATATCATATCATAAC-T-TACATA-A-C-T-TA
* * * *
40941404 ATAACTTACATA-A-C-TCAT-ATAACATATATCATTTA
1 ATAACTTACATATATCAT-ATCATAACTTACATAACTTA
* *
40941439 ATAACTTATATATATCATATCATAACTTACGTAACTTA
1 ATAACTTACATATATCATATCATAACTTACATAACTTA
*
40941477 CATAACTCACATA
1 -ATAACTTACATA
40941490 ACTTACATAA
Statistics
Matches: 162, Mismatches: 23, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
35 17 0.10
36 3 0.02
37 31 0.19
38 36 0.22
39 23 0.14
40 41 0.25
41 11 0.07
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (38 bp):
ATAACTTACATATATCATATCATAACTTACATAACTTA
Found at i:40941375 original size:58 final size:58
Alignment explanation
Indices: 40941313--40941535 Score: 299
Period size: 58 Copynumber: 3.8 Consensus size: 58
40941303 ATCATAATTC
*
40941313 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACAAAACAT
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* *
40941371 ACATAACATAATAACTTATATATATATCATATCATAACTTACATAACTCATATAACAT
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* * * * *
40941429 ATATCATTTAATAAC-T-TATATATATCATATCATAACTTACGTAACTTACATAAC-T
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* *
40941484 CACATAACTTACATAATACCTAAATATATATCATATCATAACTTACATAACT
1 -ACATAACTTA-AT-A-ACTTATATATATATCATATCATAACTTACATAACT
40941536 TGTTTATACT
Statistics
Matches: 144, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.01
56 42 0.29
57 3 0.02
58 67 0.47
59 2 0.01
60 1 0.01
61 28 0.19
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.35
Consensus pattern (58 bp):
ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
Found at i:40941453 original size:21 final size:21
Alignment explanation
Indices: 40941427--40941467 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40941417 CTCATATAAC
*
40941427 ATATATCATTTAATAACTTAT
1 ATATATCATATAATAACTTAT
*
40941448 ATATATCATATCATAACTTA
1 ATATATCATATAATAACTTA
40941468 CGTAACTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATCATATAATAACTTAT
Found at i:40941481 original size:65 final size:61
Alignment explanation
Indices: 40941345--40941536 Score: 200
Period size: 61 Copynumber: 3.1 Consensus size: 61
40941335 TATATCATAT
* * *
40941345 CATAACTTACATAACTCACAAAACATACATAACATAA-TAACTTATATAT-ATATCAT-A--T-
1 CATAACTTACATAACTCACATAACTTACAT-A-ATAACTAA-ATATATATCATATCATAACTTA
* *
40941403 CATAACTTACATAACTCATATAACATATATCATTTAATAACT-TATATATATCATATCATAACTT
1 CATAACTTACATAACTCACATAAC-T-TA-CA--TAATAACTAAATATATATCATATCATAACTT
40941467 A
61 A
* *
40941468 CGTAACTTACATAACTCACATAACTTACATAATACCTAAATATATATCATATCATAACTTA
1 CATAACTTACATAACTCACATAACTTACATAATAACTAAATATATATCATATCATAACTTA
40941529 CATAACTT
1 CATAACTT
40941537 GTTTATACTT
Statistics
Matches: 112, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
58 22 0.20
60 16 0.14
61 42 0.38
62 5 0.04
63 3 0.03
64 2 0.02
65 22 0.20
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (61 bp):
CATAACTTACATAACTCACATAACTTACATAATAACTAAATATATATCATATCATAACTTA
Found at i:40943261 original size:12 final size:12
Alignment explanation
Indices: 40943244--40943279 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
40943234 AATATCAATG
40943244 GATGAATCTGAT
1 GATGAATCTGAT
40943256 GATGAATCTGAT
1 GATGAATCTGAT
*
40943268 GATGAATTTGAT
1 GATGAATCTGAT
40943280 AAAGATGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:40943288 original size:18 final size:18
Alignment explanation
Indices: 40943265--40943308 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
40943255 TGATGAATCT
*
40943265 GATGATGAATTTGATAAA
1 GATGATGAATCTGATAAA
40943283 GATGATGAATCTGATAAA
1 GATGATGAATCTGATAAA
40943301 GATGATGA
1 GATGATGA
40943309 CTTAATGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30
Consensus pattern (18 bp):
GATGATGAATCTGATAAA
Found at i:40944250 original size:16 final size:16
Alignment explanation
Indices: 40944202--40944255 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
40944192 TTTGGTTTGC
*
40944202 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
40944218 CGCAATGGAATAGAGG
1 TGTAATGGAATAGAGG
40944234 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
40944250 TGTAAT
1 TGTAAT
40944256 AGCAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:40944285 original size:45 final size:44
Alignment explanation
Indices: 40944234--40944324 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
40944224 GGAATAGAGG
*
40944234 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
40944279 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
40944323 TG
1 TG
40944325 GAATAGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:40944531 original size:51 final size:51
Alignment explanation
Indices: 40944476--40944655 Score: 135
Period size: 51 Copynumber: 3.2 Consensus size: 51
40944466 TATTTAAACA
40944476 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
** * **
40944527 TAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
1 TAATAAT---TATT-AAATAT--A-TTA-T--AAT-TTAA-ATAT-ATA--ATTTAATA-AAATT
40944592 AACT
50 --CT
* *
40944596 TAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
40944647 TAATAATTA
1 TAATAATTA
40944656 ATATTCTTAT
Statistics
Matches: 98, Mismatches: 13, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
51 17 0.17
53 5 0.05
54 10 0.10
55 4 0.04
56 3 0.03
57 5 0.05
58 5 0.05
59 4 0.04
61 4 0.04
62 6 0.06
63 5 0.05
64 3 0.03
65 4 0.04
66 10 0.10
67 5 0.05
69 8 0.08
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (51 bp):
TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
Found at i:40944637 original size:14 final size:15
Alignment explanation
Indices: 40944598--40944639 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40944588 AATTAACTTA
*
40944598 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40944613 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40944627 A-TATAATTTAATA
1 ATTATAATTAAATA
40944640 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40944694 original size:120 final size:120
Alignment explanation
Indices: 40944472--40944884 Score: 729
Period size: 120 Copynumber: 3.4 Consensus size: 120
40944462 ATCATATTTA
* * *
40944472 AACATAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40944537 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
40944592 AACTTAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40944657 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
40944712 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
40944777 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * *
40944832 GAA-ATAATTAATATTAAATATATTTTATTTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
40944885 TAAAATAATT
Statistics
Matches: 282, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 280 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:40944757 original size:14 final size:15
Alignment explanation
Indices: 40944708--40944759 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40944698 ATAAAATATA
40944708 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40944723 TATTAAATATATTAT
1 AATTAAATATATTAT
40944738 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40944751 AATTTAATA
1 AATTAAATA
40944760 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40944935 original size:47 final size:46
Alignment explanation
Indices: 40944866--40945033 Score: 139
Period size: 47 Copynumber: 3.7 Consensus size: 46
40944856 TTATTTAAAA
*
40944866 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * * *
40944913 TATATGAATTTGTATAATTTAAAATAGTTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
40944958 TA-AT-AATAATATATAATTTCATAA-AATTATTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTA-TAATAATAAATTATCT
*
40945004 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
40945034 ATATTAAATA
Statistics
Matches: 92, Mismatches: 21, Indels: 16
0.71 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:40944938 original size:101 final size:91
Alignment explanation
Indices: 40944881--40945107 Score: 289
Period size: 91 Copynumber: 2.5 Consensus size: 91
40944871 GATTTAATAA
* * *
40944881 AATTTAA-AATAATTA-TAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAGTTAT
1 AATTTAATAA-AATTATTAA-TAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAA
*
40944944 TATTACATATAATTTAATAATAATATAT
64 TATTAAATATAATTTAATAATAATATAT
* * * *
40944972 AATTTCATAAAATTATTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTAATAAAATTATTAATAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAATA
*
40945037 TTAAATATAATTTAATAATGATATAT
66 TTAAATATAATTTAATAATAATATAT
* * *
40945063 AATTTTATAAATTTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 AATTTAATAAAATTATTAATAAT-AAAT-TATCTTATATGAATTTA
40945108 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
91 95 0.80
92 23 0.19
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
AATTTAATAAAATTATTAATAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATAATAATATAT
Found at i:40944988 original size:44 final size:42
Alignment explanation
Indices: 40944925--40945073 Score: 106
Period size: 44 Copynumber: 3.3 Consensus size: 42
40944915 TATGAATTTG
40944925 TATAATTTA-AAATAGTTATTATTACATATAATTTAATAATAATA
1 TATAATTTATAAA-A-TTATTATTA-ATATAATTTAATAATAATA
**
40944969 TATAATTTCATAAAATTATTGA-TAATA-AATTTTCTTATATGAATTTA
1 TATAATTT-ATAAAATTATT-ATTAATATAA-TTTAATA-AT-AA--TA
* * * *
40945016 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTATAA-AATTATTATT-AATATAATTTAATAATAATA
40945060 TATAATTTTATAAA
1 TATAA-TTTATAAA
40945074 TTTCTTAATA
Statistics
Matches: 82, Mismatches: 10, Indels: 26
0.69 0.08 0.22
Matches are distributed among these distances:
42 2 0.02
43 8 0.10
44 24 0.29
45 11 0.13
46 8 0.10
47 18 0.22
48 9 0.11
49 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (42 bp):
TATAATTTATAAAATTATTATTAATATAATTTAATAATAATA
Found at i:40948208 original size:33 final size:33
Alignment explanation
Indices: 40948169--40948244 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
40948159 ATTATAAAGC
*
40948169 ATGTATAATTGACCTAAAATTAATTGTTAGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTAGTAT
*
40948202 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTAGTAT
40948235 ATGTATAATT
1 ATGTATAATT
40948245 CAAGTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTAGTAT
Found at i:40948342 original size:37 final size:37
Alignment explanation
Indices: 40948287--40948373 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
40948277 GTATAAATAT
* * *
40948287 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
40948324 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
40948361 ATTGATTAGTTTA
1 ATTGATTAGTTTA
40948374 TTTATTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
Found at i:40949650 original size:69 final size:69
Alignment explanation
Indices: 40949540--40949679 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
40949530 AATCAAGTTC
*
40949540 CAGTTTCATATTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
40949605 AGAA
66 AGAA
* * * * * *
40949609 CAGTTTCATCTTCTACTCACTAACAAATTAATAACATTTTCCAGCAGACTATCAAAACAATTTCC
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
40949674 AGAA
66 AGAA
40949678 CA
1 CA
40949680 AATCAACAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.26
Consensus pattern (69 bp):
CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
AGAA
Found at i:40951122 original size:36 final size:36
Alignment explanation
Indices: 40951037--40951159 Score: 147
Period size: 36 Copynumber: 3.3 Consensus size: 36
40951027 GGCAGAAACT
* **
40951037 GAGCAAATCGGCCGAAAAAGAAAAGAAAAGAAACGGGGG
1 GAGCAAATCGGCAG-AAAAGAAAAGAAAAGAAAC--AAG
* *
40951076 GAGCAAATCGGCAGAAAAGAAAAGAAAATAAACTAG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAAG
*
40951112 GAGCAAATCGGCAGAAAAGAAAAGCAAAGAAACAAG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAAG
*
40951148 TAAGCAAATCGG
1 -GAGCAAATCGG
40951160 ATGAAGCTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 34 0.45
37 10 0.13
38 18 0.24
39 13 0.17
ACGTcount: A:0.54, C:0.13, G:0.27, T:0.06
Consensus pattern (36 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAAG
Found at i:40953245 original size:26 final size:26
Alignment explanation
Indices: 40953209--40953258 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
40953199 GTAGTAGAGG
*
40953209 TTTGCTTTAGA-GCTCTCGGATAATAA
1 TTTGCTTTAGATG-TCTCAGATAATAA
40953235 TTTGCTTTAGATGTCTCAGATAAT
1 TTTGCTTTAGATGTCTCAGATAAT
40953259 TTTGTCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (26 bp):
TTTGCTTTAGATGTCTCAGATAATAA
Found at i:40954731 original size:42 final size:42
Alignment explanation
Indices: 40954615--40954755 Score: 196
Period size: 43 Copynumber: 3.3 Consensus size: 42
40954605 GAACGGTACT
* *
40954615 TTTAGCGGTGTTTGTGAAAAAG-GCTTCGCTAAATGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAGTGC-T-GCTAAAGGTCATGTTC
*
40954658 TTTAGCGGCGTTTGTGAAAAAGGTGCCGCTAAAGGTCATGTT-
1 TTTAGCGGCGTTTGTGAAAAA-GTGCTGCTAAAGGTCATGTTC
40954700 TTTAGCGGCGTTTGTGATAAAAGTGCTGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGA-AAAAGTGCTGCTAAAGGTCATGTTC
*
40954743 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
40954756 ATGTGAAAGA
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
42 36 0.40
43 50 0.56
44 1 0.01
45 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.36
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAAAAAGTGCTGCTAAAGGTCATGTTC
Found at i:40959004 original size:19 final size:19
Alignment explanation
Indices: 40958930--40959006 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 19
40958920 ATATGTCAAG
*
40958930 ATGCACTTTGTGTGCTAGAT
1 ATGCACTTTGTGTGCCAG-T
** * * *
40958950 ATATACTTTCTATGCCAAT
1 ATGCACTTTGTGTGCCAGT
*
40958969 ATGCACTTTGTGCGCCAGT
1 ATGCACTTTGTGTGCCAGT
*
40958988 ATGCACTTTATGTGCCAGT
1 ATGCACTTTGTGTGCCAGT
40959007 TTACCCTACT
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (19 bp):
ATGCACTTTGTGTGCCAGT
Found at i:40959963 original size:28 final size:28
Alignment explanation
Indices: 40959932--40960014 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
40959922 TCCTATTCAA
* *
40959932 TTTCAACATAATAAGTGTAGACACTTAT
1 TTTCAACATAATAAATGAAGACACTTAT
* *
40959960 TTTCAACATAATAAAT-ACGGAAACTTAT
1 TTTCAACATAATAAATGA-AGACACTTAT
*
40959988 TTCCAACATAATAAATGAAGACACTTA
1 TTTCAACATAATAAATGAAGACACTTA
40960015 ATCAATCACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (28 bp):
TTTCAACATAATAAATGAAGACACTTAT
Found at i:40960368 original size:14 final size:14
Alignment explanation
Indices: 40960349--40960375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40960339 CTTGGAATCA
40960349 TCAGGATAAGTTCG
1 TCAGGATAAGTTCG
40960363 TCAGGATAAGTTC
1 TCAGGATAAGTTC
40960376 TTTTCATAAC
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:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (14 bp):
TCAGGATAAGTTCG
Found at i:40963293 original size:55 final size:54
Alignment explanation
Indices: 40963129--40963294 Score: 185
Period size: 55 Copynumber: 3.0 Consensus size: 54
40963119 CGGATATTCT
* * * *
40963129 TATATATGTTAAACTATGACTTTGTAGAGGCTTGGGTCGGTTGTA-CAGAGATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCTT-GGTAGGTTGTATGA-AGATTTC
* * *
40963184 TATATATGTTAAATTATGGCTTTACAGAGGCTTAGGTAGGCTGT-TCAGAA-ATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCTT-GGTAGGTTGTAT--GAAGATTTC
*
40963239 TATATATGTTAAATTATGACTTTGCAGAGGCTTGGTTGGGTTGTATGAAGATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCTTGG-TAGGTTGTATGAAGATTTC
40963294 T
1 T
40963295 CAGTGTATTA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
54 5 0.05
55 85 0.91
56 2 0.02
57 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.40
Consensus pattern (54 bp):
TATATATGTTAAATTATGACTTTGCAGAGGCTTGGTAGGTTGTATGAAGATTTC
Found at i:40969114 original size:25 final size:26
Alignment explanation
Indices: 40969058--40969116 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
40969048 TAAACAACCT
*
40969058 AAAAAAATTAAAAATAAATGGAACAA
1 AAAAAAATTAAAAATAAATGAAACAA
* *
40969084 ATAAAAA-TAAAAATAAAT-AAATAA
1 AAAAAAATTAAAAATAAATGAAACAA
*
40969108 ACAAAAATT
1 AAAAAAATT
40969117 TTACTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.36
25 12 0.43
26 6 0.21
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAAAAATTAAAAATAAATGAAACAA
Found at i:40969218 original size:16 final size:16
Alignment explanation
Indices: 40969176--40969211 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40969166 TAAACCCTGA
40969176 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
40969192 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
40969208 AACC
1 AACC
40969212 TTCAAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.17, G:0.11, T:0.06
Consensus pattern (16 bp):
AACCAGAAAAATAAAG
Found at i:40972362 original size:28 final size:28
Alignment explanation
Indices: 40972322--40972410 Score: 142
Period size: 28 Copynumber: 3.2 Consensus size: 28
40972312 TAGTAGTAGT
40972322 ACAGTGTGGGCCTTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* *
40972350 ATAGTGTGAGCCTTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* *
40972378 ACAGTGTGGGCCTTAGCCCAATATAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
40972406 ACAGT
1 ACAGT
40972411 CTAGTGCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Found at i:40972817 original size:56 final size:56
Alignment explanation
Indices: 40972731--40972850 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
40972721 ACAAGGGATG
40972731 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40972787 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40972843 ATGGGCAA
1 ATGGGCAA
40972851 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40975526 original size:22 final size:22
Alignment explanation
Indices: 40975498--40975619 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
40975488 TTCCACATCC
40975498 ATCACATTGGCCATTCGGCATT
1 ATCACATTGGCCATTCGGCATT
** * *
40975520 ATCACATATATACACTTTC-TCATT
1 ATCACAT-T-GGC-CATTCGGCATT
*
40975544 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCATT
* * *
40975567 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCATT
*
40975591 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCATT
40975614 ATCACA
1 ATCACA
40975620 CATACACATG
Statistics
Matches: 71, Mismatches: 17, Indels: 24
0.63 0.15 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 13 0.18
25 20 0.28
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCATT
Found at i:40975533 original size:47 final size:47
Alignment explanation
Indices: 40975470--40975726 Score: 347
Period size: 47 Copynumber: 5.4 Consensus size: 47
40975460 CCCTTCGGGA
* * *
40975470 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40975517 ATTATCACATATATACACTTTCTCATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40975564 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
40975611 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
40975658 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40975707 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
40975727 GTACATCAAC
Statistics
Matches: 188, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
46 1 0.01
47 146 0.78
49 40 0.21
50 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:40978729 original size:40 final size:40
Alignment explanation
Indices: 40978498--40978722 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
40978488 TCGAATGATG
* * * *
40978498 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40978538 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40978578 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40978617 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40978657 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40978698 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40978723 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40978744 original size:119 final size:119
Alignment explanation
Indices: 40978498--40978755 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
40978488 TCGAATGATG
* *
40978498 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
40978563 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACCAAA
* * * **
40978617 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
40978680 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCCATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CCAAA
* *
40978737 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40978756 TATGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.72
120 30 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACCAAA
Found at i:40986671 original size:40 final size:40
Alignment explanation
Indices: 40986440--40986664 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
40986430 TCGAATGATG
* * * *
40986440 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40986480 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
40986520 TCCGGGCTAAG-CCCGAAGGCAGTGGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40986559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40986599 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40986640 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40986665 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.20
40 119 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40986686 original size:119 final size:119
Alignment explanation
Indices: 40986440--40986697 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
40986430 TCGAATGATG
* *
40986440 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
40986505 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCAGTGGTGCGAGTTATTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCAGTGGAACGAGTTACTAAA
* * * **
40986559 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
40986622 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCAGTGGAACGAGTTA-CTAAA
* *
40986679 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40986698 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.72
120 29 0.25
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCAGTGGAACGAGTTACTAAA
Found at i:40988199 original size:26 final size:26
Alignment explanation
Indices: 40988126--40988212 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
40988116 CCAATATCGC
* * *
40988126 AGCAAAGCTGTCAGTAATAGCATTGC
1 AGCAAAGCTGCCAGTAATAGTATTGT
*
40988152 AGCAGAGCTGCCAGT-ATCAGTATTGT
1 AGCAAAGCTGCCAGTAAT-AGTATTGT
40988178 AGCAAAGCTGCCAGTAATAGTATATGT
1 AGCAAAGCTGCCAGTAATAGTAT-TGT
*
40988205 GGCAAAGC
1 AGCAAAGC
40988213 CACCAGTAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
25 2 0.04
26 38 0.73
27 12 0.23
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAGTATTGT
Found at i:40988218 original size:27 final size:27
Alignment explanation
Indices: 40988162--40988220 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
40988152 AGCAGAGCTG
**
40988162 CCAGT-ATCAGTATTGTAGCAAAGCTG
1 CCAGTAATCAGTATTGTAGCAAAGCCA
*
40988188 CCAGTAAT-AGTATATGTGGCAAAGCCA
1 CCAGTAATCAGTAT-TGTAGCAAAGCCA
40988215 CCAGTA
1 CCAGTA
40988221 GGTCTACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
CCAGTAATCAGTATTGTAGCAAAGCCA
Found at i:40988610 original size:80 final size:81
Alignment explanation
Indices: 40988408--40988747 Score: 329
Period size: 80 Copynumber: 4.2 Consensus size: 81
40988398 GCCATAACAG
* * *
40988408 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-AGGGGTATTTCAGTCATGTTACC
1 TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGA-GGGTATTTCAGTCATTTTA-C
* *
40988472 CTATG-A-GGGTATTTTGA
64 C-ATGTAGGGGTAATTAGA
* * ** * * *
40988489 TCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTCGGTTATTTTACCA
1 TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCA
40988554 TGTAGGGGTAATTAG-
66 TGTAGGGGTAATTAGA
* * * *
40988569 TTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAAGGTAATTCAGTCATTTTACCT
1 TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCA
*
40988634 TGTGGGGGTAATTTA-A
66 TGTAGGGGTAA-TTAGA
* * * * * * *
40988650 T-AATTTCCCCTGTGAGGGTAATTTGGTCATTTTACCTTGTGAGGGTAATTT-AGT-AATTT-CC
1 TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGT-ATTTCAGTCATTTTACC
* *
40988711 ATTGTGGGGGTAATTCGA
65 A-TGTAGGGGTAATTAGA
40988729 TCATTTTACCCTGTGGGGG
1 TCATTTTACCCTGTGGGGG
40988748 GGGGGGGGTA
Statistics
Matches: 216, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
78 4 0.02
79 20 0.09
80 122 0.56
81 70 0.32
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCA
TGTAGGGGTAATTAGA
Found at i:40988644 original size:27 final size:27
Alignment explanation
Indices: 40988405--40988747 Score: 275
Period size: 27 Copynumber: 12.8 Consensus size: 27
40988395 AAGGCCATAA
* *
40988405 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * * *
40988432 CGGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * *
40988459 CAGTCATGTTACCCTATGAGGGT-ATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
** * *
40988485 TTGATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTGTGGGGGTAATT
* * *
40988513 TAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * * *
40988540 CGGTTATTTTACCATGTAGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
40988567 -AGTTATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * **
40988593 CGGTCATTTTACCCTATGAAGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
40988620 CAGTCATTTTACCTTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * * * *
40988647 TAAT-AATTTCCCCTGTGAGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
** * *
40988673 TGGTCATTTTACCTTGTGAGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* * *
40988700 TAGT-AATTT-CCATTGTGGGGGTAATT
1 CAGTCATTTTACC-CTGTGGGGGTAATT
40988726 C-GATCATTTTACCCTGTGGGGG
1 CAG-TCATTTTACCCTGTGGGGG
40988748 GGGGGGGGTA
Statistics
Matches: 258, Mismatches: 50, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
25 3 0.01
26 64 0.25
27 185 0.72
28 6 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTGTGGGGGTAATT
Found at i:40988686 original size:53 final size:53
Alignment explanation
Indices: 40988515--40988747 Score: 202
Period size: 53 Copynumber: 4.4 Consensus size: 53
40988505 GGGTATTTTA
* * * * * *
40988515 GTCATTTTACCCTATGGGGGT-ATTTCGGTTATTTTACCATGT-AGGGGTAATT-A
1 GTCATTTTACCCTGTGGGGGTAATTT-AG-TAATTTCCCCTGTGA-GGGTAATTCG
* ** * * * * *
40988568 GTTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAAGGTAATTCA
1 GTCATTTTACCCTGTGGGGGTAATTTAGT-AATTTCCCCTGTGAGGGTAATTCG
* * *
40988622 GTCATTTTACCTTGTGGGGGTAATTTAATAATTTCCCCTGTGAGGGTAATTTG
1 GTCATTTTACCCTGTGGGGGTAATTTAGTAATTTCCCCTGTGAGGGTAATTCG
* * ** *
40988675 GTCATTTTACCTTGTGAGGGTAATTTAGTAATTTCCATTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTTAGTAATTTCCCCTGTGAGGGTAATTCG
*
40988728 ATCATTTTACCCTGTGGGGG
1 GTCATTTTACCCTGTGGGGG
40988748 GGGGGGGGTA
Statistics
Matches: 150, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.01
53 120 0.80
54 29 0.19
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (53 bp):
GTCATTTTACCCTGTGGGGGTAATTTAGTAATTTCCCCTGTGAGGGTAATTCG
Found at i:40989461 original size:24 final size:24
Alignment explanation
Indices: 40989436--40989482 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40989426 CCCAAATCCC
40989436 AATATTCTCTCCTCAAATCTCTCCA
1 AATA-TCTCTCCTCAAATCTCTCCA
* *
40989461 AATATCTCTCCTTAATTCTCTC
1 AATATCTCTCCTCAAATCTCTC
40989483 TATGACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATCTCTCCTCAAATCTCTCCA
Found at i:40990995 original size:105 final size:100
Alignment explanation
Indices: 40990886--40991078 Score: 224
Period size: 105 Copynumber: 1.9 Consensus size: 100
40990876 TTTGTAGTGC
* * * * *
40990886 CATAACCCAATTATGATCTTATCATCATAATGTCATATCCCAACTATGGTCTTACACATGTATAT
1 CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATT--ACAT-T-TAA
* *
40990951 ATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTCT
62 ACACTACCATGGTCCAA-CATGGTCTTACGTTCAAGGTCT
* * * * * *
40990991 CATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAACCTAGCTATGGTATTACATTTAAACAC
1 CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATTACATTTAAACAC
40991056 TACCATGGTCCAACATGGTCTTA
66 TACCATGGTCCAACATGGTCTTA
40991079 TCCGCCAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
100 10 0.13
101 17 0.23
102 1 0.01
103 4 0.05
105 43 0.57
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (100 bp):
CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATTACATTTAAACAC
TACCATGGTCCAACATGGTCTTACGTTCAAGGTCT
Found at i:40998250 original size:18 final size:17
Alignment explanation
Indices: 40998221--40998284 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
40998211 AAGAAAACTT
40998221 TTTGAAATTGAATAACGA
1 TTTGAAA-TGAATAACGA
* *
40998239 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAACGA
*
40998257 TTTGGAAACGAATGACACGA
1 TTT-GAAATGAAT-A-ACGA
40998277 TTTGAAAT
1 TTTGAAAT
40998285 TAACATAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 22 0.61
19 9 0.25
20 5 0.14
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (17 bp):
TTTGAAATGAATAACGA
Found at i:41006272 original size:21 final size:21
Alignment explanation
Indices: 41006248--41006287 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41006238 CGACATGGCC
41006248 GTGT-ATTTCAGCCACACGAGT
1 GTGTGATTT-AGCCACACGAGT
41006269 GTGTGATTTAGCCACACGA
1 GTGTGATTTAGCCACACGA
41006288 CCGTGTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGTGATTTAGCCACACGAGT
Found at i:41006293 original size:21 final size:21
Alignment explanation
Indices: 41006246--41006293 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41006236 AACGACATGG
41006246 CCGTGTATTTCAGCCACACGA
1 CCGTGTATTTCAGCCACACGA
**
41006267 GTGTGTGATTT-AGCCACACGA
1 CCGTGT-ATTTCAGCCACACGA
41006288 CCGTGT
1 CCGTGT
41006294 CTACTCTGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (21 bp):
CCGTGTATTTCAGCCACACGA
Found at i:41006423 original size:21 final size:21
Alignment explanation
Indices: 41006399--41006451 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41006389 GTCTCAGTCG
41006399 CACGGCCGTGTGCT-TCACTTA
1 CACGGCCGTGTG-TATCACTTA
* *
41006420 CACGGGCGTGTGTATCATTTA
1 CACGGCCGTGTGTATCACTTA
*
41006441 CACGGTCGTGT
1 CACGGCCGTGT
41006452 ACCTTTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CACGGCCGTGTGTATCACTTA
Found at i:41009268 original size:30 final size:30
Alignment explanation
Indices: 41009234--41009319 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
41009224 ATTAAAGCAT
*
41009234 GCATGTATTTAGGGAGTTGAATGGGGGCAC
1 GCATGTATTTAGGGAGCTGAATGGGGGCAC
* *
41009264 GCATGTATTTAGGGAGCTGAAT-GGAGCAT
1 GCATGTATTTAGGGAGCTGAATGGGGGCAC
* *
41009293 GCATGTAATTGAAGGAGCTGAATGGGG
1 GCATGT-ATTTAGGGAGCTGAATGGGG
41009320 ATGCTAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.23
30 35 0.73
31 2 0.04
ACGTcount: A:0.27, C:0.09, G:0.38, T:0.26
Consensus pattern (30 bp):
GCATGTATTTAGGGAGCTGAATGGGGGCAC
Found at i:41009315 original size:60 final size:60
Alignment explanation
Indices: 41009206--41009319 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
41009196 GGTTCGGCCA
* * * * *
41009206 ATGTGTTTATGGAGCTGAATTAAAGCATGCATGTATTTAGGGAGTTGAATGGGGGCACGC
1 ATGTATTTAGGGAGCTGAATTAAAGCATGCATGTATTGAAGGAGCTGAATGGGGGCACGC
**
41009266 ATGTATTTAGGGAGCTGAA-TGGAGCATGCATGTAATTGAAGGAGCTGAATGGGG
1 ATGTATTTAGGGAGCTGAATTAAAGCATGCATGT-ATTGAAGGAGCTGAATGGGG
41009320 ATGCTAGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 12 0.26
60 34 0.74
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (60 bp):
ATGTATTTAGGGAGCTGAATTAAAGCATGCATGTATTGAAGGAGCTGAATGGGGGCACGC
Found at i:41011562 original size:21 final size:21
Alignment explanation
Indices: 41011535--41011581 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
41011525 GCTACATGGG
41011535 TGTGTGATTTAGCCACACAGGC
1 TGTGTGATTTAGCCACAC-GGC
41011557 -GTGTGATTTAGCCACACGGC
1 TGTGTGATTTAGCCACACGGC
41011577 TGTGT
1 TGTGT
41011582 CTACTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTGTGATTTAGCCACACGGC
Found at i:41026199 original size:22 final size:22
Alignment explanation
Indices: 41026148--41026313 Score: 140
Period size: 22 Copynumber: 7.5 Consensus size: 22
41026138 TACACCACAC
*
41026148 TAGTAGGCACCGAAGTGCTTAAA
1 TAGTAGGCACCGAAGTGC-TAAT
*
41026171 TAGTAGGCACCGAAGTGCTGAT
1 TAGTAGGCACCGAAGTGCTAAT
*
41026193 TAGTAGGCACC-ATAGTGCAAAT
1 TAGTAGGCACCGA-AGTGCTAAT
* * * *
41026215 CAGTAGGTACCGAAGTGCTGAG
1 TAGTAGGCACCGAAGTGCTAAT
* *
41026237 TAGTAGGCA-CTATAGTGCAAAT
1 TAGTAGGCACCGA-AGTGCTAAT
* * *
41026259 TAGTACGCACTGTAGTGCTAAT
1 TAGTAGGCACCGAAGTGCTAAT
* *
41026281 TAGTAGGCA-CTATAGTGCAAAT
1 TAGTAGGCACCGA-AGTGCTAAT
*
41026303 CAGTAGGCACC
1 TAGTAGGCACC
41026314 ATAATGCTAA
Statistics
Matches: 111, Mismatches: 26, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
21 3 0.03
22 88 0.79
23 20 0.18
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (22 bp):
TAGTAGGCACCGAAGTGCTAAT
Found at i:41026232 original size:44 final size:44
Alignment explanation
Indices: 41026148--41026313 Score: 210
Period size: 44 Copynumber: 3.8 Consensus size: 44
41026138 TACACCACAC
41026148 TAGTAGGCACCGA-AGTGCTTAAAT-AGTAGGCACCGAAGTGCTGAT
1 TAGTAGGCACC-ATAGTGC--AAATCAGTAGGCACCGAAGTGCTGAT
* *
41026193 TAGTAGGCACCATAGTGCAAATCAGTAGGTACCGAAGTGCTGAG
1 TAGTAGGCACCATAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
* * * * * *
41026237 TAGTAGGCACTATAGTGCAAATTAGTACGCACTGTAGTGCTAAT
1 TAGTAGGCACCATAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
*
41026281 TAGTAGGCACTATAGTGCAAATCAGTAGGCACC
1 TAGTAGGCACCATAGTGCAAATCAGTAGGCACC
41026314 ATAATGCTAA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
43 4 0.04
44 86 0.81
45 16 0.15
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (44 bp):
TAGTAGGCACCATAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
Found at i:41026261 original size:66 final size:67
Alignment explanation
Indices: 41026149--41026290 Score: 162
Period size: 66 Copynumber: 2.1 Consensus size: 67
41026139 ACACCACACT
** *
41026149 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCTGATTAGTAGGCACCATAGTGCAAA
1 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCAAATTAGTACGCACCATAGTGCAAA
41026214 TC
66 TC
* * * * ** *
41026216 AGTAGGTACCGAAGTGC-TGAGTAGTAGGCA-CTATAGTGCAAATTAGTACGCACTGTAGTGCTA
1 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGA-AGTGCAAATTAGTACGCACCATAGTGCAA
*
41026279 ATT
65 ATC
41026282 AGTAGGCAC
1 AGTAGGCAC
41026291 TATAGTGCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
65 2 0.03
66 44 0.71
67 16 0.26
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (67 bp):
AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCAAATTAGTACGCACCATAGTGCAAA
TC
Found at i:41037738 original size:19 final size:20
Alignment explanation
Indices: 41037711--41037754 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41037701 GTTGGTAAAT
*
41037711 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
41037730 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
41037750 A-ATAT
1 ACATAT
41037755 ATATTGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:41037746 original size:20 final size:19
Alignment explanation
Indices: 41037721--41037759 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
41037711 ACATGTGTAA
*
41037721 TAATAATAAACATATGTATT
1 TAATAATAAA-ATATATATT
41037741 TAATAATAAAATATATATT
1 TAATAATAAAATATATATT
41037760 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
TAATAATAAAATATATATT
Found at i:41037793 original size:24 final size:26
Alignment explanation
Indices: 41037749--41037796 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
41037739 TTTAATAATA
*
41037749 AAATATATATTGCTTATTAATTAAGT
1 AAATATATATTGATTATTAATTAAGT
41037775 AAATATATATT-ATTA-TAATTAA
1 AAATATATATTGATTATTAATTAA
41037797 AACAAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
AAATATATATTGATTATTAATTAAGT
Found at i:41038823 original size:41 final size:38
Alignment explanation
Indices: 41038767--41038905 Score: 138
Period size: 40 Copynumber: 3.6 Consensus size: 38
41038757 AAGTTTGAGT
* *
41038767 CGATGAGACACTGGGTGTCAATTTATTACTTTAGATTAATT
1 CGATGAGACACTGGGTGCCAA-TTATTACTTT-GATT-ATC
* * * *
41038808 CGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGCCAATTATTACTT-TGATTATC
*
41038845 CGATGAGACACTGGGTGGCAAATTATTACTTTGAATTATC
1 CGATGAGACACTGGGT-GCCAATTATTACTTTG-ATTATC
*
41038885 CGATGAGGCACTGGGTGCCAA
1 CGATGAGACACTGGGTGCCAA
41038906 ACTGGTGTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
37 16 0.20
38 13 0.16
39 7 0.09
40 25 0.31
41 19 0.24
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGCCAATTATTACTTTGATTATC
Found at i:41039312 original size:18 final size:19
Alignment explanation
Indices: 41039257--41039313 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
41039247 GATACTAGAC
*
41039257 ATTAATATGTCCTTATAAT
1 ATTAATATGTCTTTATAAT
* *
41039276 -TTAAT-TGTGTTTATTAT
1 ATTAATATGTCTTTATAAT
41039293 ATTAATATGTCTTTA-AAT
1 ATTAATATGTCTTTATAAT
41039311 ATT
1 ATT
41039314 CAGATTATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.29
18 15 0.48
19 7 0.23
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTAATATGTCTTTATAAT
Found at i:41045187 original size:25 final size:27
Alignment explanation
Indices: 41045159--41045211 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41045149 ACAGTCATAC
41045159 ATAACATA-AAGCAT-ACAGTCATTTT
1 ATAACATAGAAGCATAACAGTCATTTT
**
41045184 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAGAAGCATAACAGTCATTTT
41045211 A
1 A
41045212 CCACGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 4 0.17
27 12 0.50
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (27 bp):
ATAACATAGAAGCATAACAGTCATTTT
Found at i:41045207 original size:27 final size:27
Alignment explanation
Indices: 41045169--41045240 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
41045159 ATAACATAAA
41045169 GCAT-ACAGTCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
** * *
41045195 GCATAACAGTCATTTTACCACGTGGGG
1 GCATAACAGTCATTTTATAACATAGGG
*
41045222 GCATAACAATCATTTTATA
1 GCATAACAGTCATTTTATA
41045241 TCAGTTTGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 4 0.11
27 34 0.89
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (27 bp):
GCATAACAGTCATTTTATAACATAGGG
Found at i:41056011 original size:156 final size:156
Alignment explanation
Indices: 41055690--41056004 Score: 486
Period size: 156 Copynumber: 2.0 Consensus size: 156
41055680 TCAATCTTTC
* ** * * **
41055690 TAGGATAAATTCAAATTGCCTCAACAGAAACCACGTGCCCTAGAAAAGTCACCTCTCGTAACCAG
1 TAGGATAAACTCAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
* *
41055755 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAACACTACTCTAAT
66 AACTCACACTTGATCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAACACTACTCTAAG
*
41055820 ATGTTCATCATGCTCATCCTCGGTCT
131 ATATTCATCATGCTCATCCTCGGTCT
* * *
41055846 TAGGATAAACTCAAATCACCTCAGCAGAAACTACGTACCCCAGAAAAGTCACCTCTCACAACTAG
1 TAGGATAAACTCAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
* *
41055911 AACTCACACTTGATCAACTTAGCGTAGAGTTGTTTCTCTCGAAGTATCTGAAGCACTACTCTAAG
66 AACTCACACTTGATCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAACACTACTCTAAG
*
41055976 ATATTCATCATGTTCATCCTCGGTCT
131 ATATTCATCATGCTCATCCTCGGTCT
41056002 TAG
1 TAG
41056005 AGTAAACCAA
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
156 143 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (156 bp):
TAGGATAAACTCAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
AACTCACACTTGATCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAACACTACTCTAAG
ATATTCATCATGCTCATCCTCGGTCT
Found at i:41060696 original size:16 final size:16
Alignment explanation
Indices: 41060675--41060730 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
41060665 CAGGGCATTA
*
41060675 CATTACAACTCTATTC
1 CATTACAGCTCTATTC
*
41060691 CATTACAGCTCTATTG
1 CATTACAGCTCTATTC
* *
41060707 AATTACAGCCCTATTC
1 CATTACAGCTCTATTC
41060723 CATTACAG
1 CATTACAG
41060731 TAAACCAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (16 bp):
CATTACAGCTCTATTC
Found at i:41068386 original size:36 final size:35
Alignment explanation
Indices: 41068326--41068425 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 35
41068316 AGTCTCAGAT
* *
41068326 ATTACAATTATATGTTTATTTTTTTATTAGTCCAAAA
1 ATTACAATTATGTG-TTA-TTTTTTATTACTCCAAAA
*
41068363 GATTACAATTATGTGCTTATTTTTTATTACTCCTAAA
1 -ATTACAATTATGTG-TTATTTTTTATTACTCCAAAA
* * *
41068400 ATTATAATTATGCGTTAATTTTTATT
1 ATTACAATTATGTGTTATTTTTTATT
41068426 TAATAGAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
35 11 0.20
36 12 0.22
37 16 0.29
38 16 0.29
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (35 bp):
ATTACAATTATGTGTTATTTTTTATTACTCCAAAA
Found at i:41071167 original size:44 final size:44
Alignment explanation
Indices: 41071099--41071189 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
41071089 GTAGGTCAAA
* *
41071099 TAATATTGAAATAACCTACACTAATAAGAGTTTAAGTG-GAAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAG-AAAC
* *
41071143 TAATATTAAAAAAACCTACGCTAATTAGAGTTTAAGTGAGAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
41071187 TAA
1 TAA
41071190 AAACGTAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.27
Consensus pattern (44 bp):
TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
Found at i:41083809 original size:30 final size:30
Alignment explanation
Indices: 41083769--41083838 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
41083759 TTAGATATAA
* *
41083769 ATTATGTTAAACTAATTTAAAACAATAATT
1 ATTATATTAAACCAATTTAAAACAATAATT
41083799 ATTATATTAAACCAATTTAAAACAATAATT
1 ATTATATTAAACCAATTTAAAACAATAATT
41083829 ATTATATTAA
1 ATTATATTAA
41083839 GAAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (30 bp):
ATTATATTAAACCAATTTAAAACAATAATT
Found at i:41083936 original size:18 final size:19
Alignment explanation
Indices: 41083915--41083950 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41083905 ACATGTGTAA
41083915 TAATAA-ACAACATGTATT
1 TAATAATACAACATGTATT
*
41083933 TAATAATACAATATGTAT
1 TAATAATACAACATGTAT
41083951 GGCTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (19 bp):
TAATAATACAACATGTATT
Found at i:41085151 original size:23 final size:23
Alignment explanation
Indices: 41085125--41085179 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
41085115 AGACACTTTA
*
41085125 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* *
41085148 TGTGTTGTA--TCAGGCACTTCG
1 TGTGTCGTATTTCAGGCACCTCG
41085169 TGTGTCGTATT
1 TGTGTCGTATT
41085180 AGGCAGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 18 0.69
23 8 0.31
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:41085162 original size:21 final size:21
Alignment explanation
Indices: 41085138--41085184 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41085128 GTCGTATTTT
*
41085138 AGGCACCTCGTGTGTTGTATC
1 AGGCACCTCGTGTGTCGTATC
* *
41085159 AGGCACTTCGTGTGTCGTATT
1 AGGCACCTCGTGTGTCGTATC
41085180 AGGCA
1 AGGCA
41085185 GTTATGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:41097123 original size:26 final size:26
Alignment explanation
Indices: 41097072--41097133 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
41097062 TACCTATAGT
*
41097072 AGTTTCAAAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
41097098 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
41097124 AGTTTCAGAA
1 AGTTTCAGAA
41097134 CACTTACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:41103923 original size:27 final size:27
Alignment explanation
Indices: 41103893--41103952 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
41103883 GCATCATAGT
*
41103893 TAGTCTGACAGGACATTAAACACGAGA
1 TAGTCTGACAGGACAATAAACACGAGA
*
41103920 TAGTCTGACGGGACAATAAACACGAGA
1 TAGTCTGACAGGACAATAAACACGAGA
41103947 TAGTCT
1 TAGTCT
41103953 ATAGGGGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (27 bp):
TAGTCTGACAGGACAATAAACACGAGA
Found at i:41105438 original size:533 final size:533
Alignment explanation
Indices: 41104379--41105965 Score: 2724
Period size: 533 Copynumber: 3.0 Consensus size: 533
41104369 CATCTTGAAG
*
41104379 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGCAAACAAAAGAAGGTTTATCCG
1 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAA-AAAAGAAGGTTTATCCG
* *
41104444 AGGATCACAGATAAAGATCCACCAATAATAACCACCAAAGGGTGCTTAGTGAAAACCTACATGTT
65 AGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTT
41104509 AGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
130 AGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
* * *
41104574 CAGAGTGAGTCACACAGAGGGATATATCGAGTAACAAATATGTCTGTTAATACTATTCCTCTTTA
195 CAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
* * * *
41104639 AGGGGATTATGTTGCGAAGTACTCACCAAATGGGTAGTTCCATGGGAACCAACATGTAAGAGGAA
260 AGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAA
*
41104704 TCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAATCCATAGTTGATGGGCATG
325 TCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATG
* *
41104769 TTATGTATAAGAGTAAGGTAACGCATGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAA
390 TTATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAA
* * *
41104834 ACCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAATTATTCCAATAAATGGTGT
455 ACCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGT
41104899 GGGATCTCATCAAT
520 GGGATCTCATCAAT
* *
41104913 TATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGTAAAAAAACAAGGTTTATCCGA
1 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAAAGAAGGTTTATCCGA
* *
41104978 GGATCACAGATAAAGATCCACCAATAAGAACCACCAAAAGGTGCTCAGTGAAAACCTACATGTTA
66 GGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTTA
*** * * *
41105043 GAGATTGAGCATAAATACGACAACTAGTCCATTGAATAAAGAGGTTTTAGCTAGAAGCCATAGTT
131 GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
41105108 AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
196 AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
41105173 GGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAAT
261 GGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAAT
* * *
41105238 CGTGAACTTAAATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAATTGATGGTCATGT
326 CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATGT
41105303 TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAAA
391 TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAAA
*
41105368 CCCAATTTCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGTG
456 CCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGTG
*
41105433 GGATCTCATCAGT
521 GGATCTCATCAAT
* *
41105446 TATTCAAGAACAATAAACACACTATTAGGTGCCTGGTGTATAGGTAAAAAAAAAAGAAGGTTTAT
1 TATTCATGAACAAT-AACACACTAGTAGGTGCCTGGTGTATAGGT---AAAAAAAGAAGGTTTAT
*
41105511 CCGAGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTGCAT
62 CCGAGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACAT
41105576 GTTAGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCAT
127 GTTAGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCAT
* *
41105641 AGTCAGAGAGAGTCACACAAAGGGATATATCAAGTGACAAATATGTCTGTTAAGACTATTCCTCT
192 AGTCAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCT
* *
41105706 TTAAGGGGATTATGTTGTGAAGTACTAGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCG
257 TTAAGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCG
* *
41105771 AAATCGTGAACTTAGATGACAATTATCTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGC
322 GAATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGC
* *
41105836 ATGTTATGTATAAGAGTGAGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTAT
387 ATGTTATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTAT
* * *
41105901 TAAACCCAATTGCTATTTAGTTTGCCAGAGTGGTGTGAGATCTCATCAGTTATTCCAACAAATGG
452 TAAACCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGG
41105966 AATGTGAGTA
Statistics
Matches: 991, Mismatches: 58, Indels: 5
0.94 0.06 0.00
Matches are distributed among these distances:
533 471 0.48
534 73 0.07
537 447 0.45
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (533 bp):
TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAAAGAAGGTTTATCCGA
GGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTTA
GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
GGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAAT
CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATGT
TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAAA
CCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGTG
GGATCTCATCAAT
Found at i:41110479 original size:38 final size:38
Alignment explanation
Indices: 41110428--41110505 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
41110418 ATAAAACAAG
* *
41110428 TATGTCATTACAATCATCTCATGACTGGTCTTTGGGCA
1 TATGTCATTACAATCATCTCATGACTGGTCCTTGGCCA
*
41110466 TATGTTATTACAATCATCTCATGACTGGTCCTTGGCCA
1 TATGTCATTACAATCATCTCATGACTGGTCCTTGGCCA
41110504 TA
1 TA
41110506 CTCCATTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (38 bp):
TATGTCATTACAATCATCTCATGACTGGTCCTTGGCCA
Found at i:41125545 original size:39 final size:39
Alignment explanation
Indices: 41125489--41125576 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
41125479 TAATGAAGTT
41125489 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
*
41125528 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
41125567 GGTGAGGGTG
1 GGTGAGGGTG
41125577 AGGGTGGTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.18, C:0.02, G:0.52, T:0.27
Consensus pattern (39 bp):
GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
Found at i:41125574 original size:45 final size:44
Alignment explanation
Indices: 41125489--41125616 Score: 158
Period size: 45 Copynumber: 3.0 Consensus size: 44
41125479 TAATGAAGTT
*
41125489 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAA-T-GT---GGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGTGGTGAGGGTGAG
41125528 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAA-GTGGTGAGGGTGAG
* * * *
41125573 GGTGAGGGTGGTGAGGTTGCTGACAGTAGAGGTGGTGAGAGTGA
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTA-AAGTGGTGAGGGTGA
41125617 TAGAAGTGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
39 29 0.38
41 1 0.01
42 2 0.03
45 44 0.57
46 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.52, T:0.26
Consensus pattern (44 bp):
GGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGTGGTGAGGGTGAG
Found at i:41125610 original size:39 final size:39
Alignment explanation
Indices: 41125489--41125616 Score: 139
Period size: 39 Copynumber: 3.1 Consensus size: 39
41125479 TAATGAAGTT
* * *
41125489 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
*
41125528 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGT--A-GAGGT---GGTGAG
* *
41125573 GGTGAGGGTGGTGAGGTTGCTGACAGTAGAGGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
*
41125612 AGTGA
1 GGTGA
41125617 TAGAAGTGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
39 36 0.48
41 1 0.01
42 6 0.08
43 1 0.01
45 31 0.41
ACGTcount: A:0.20, C:0.03, G:0.52, T:0.26
Consensus pattern (39 bp):
GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
Found at i:41128285 original size:82 final size:82
Alignment explanation
Indices: 41128157--41128359 Score: 318
Period size: 82 Copynumber: 2.5 Consensus size: 82
41128147 TTGAGATTGT
* *
41128157 TAACATATTTTATTTGTTTTTTGAAATGATTTGCTGAAATGGTTGGTTAACAACTTACTAG-TAT
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTA-TAGCTAT
41128221 AGGATCATTTTGTTAGCA
65 AGGATCATTTTGTTAGCA
* * * *
41128239 TAACATATTTTGTTTGTTTTTTTAAATGATTTGTTGAAATGATTGGTTAACATCTTATTGCTATA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTATAGCTATA
*
41128304 GGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGCA
*
41128321 TAACATATTTTATTTGTTTTTTGGAATGATTTGTTGAAA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAA
41128360 GATGTATACC
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 2 0.02
82 108 0.98
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.49
Consensus pattern (82 bp):
TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTATAGCTATA
GGATCATTTTGTTAGCA
Found at i:41129856 original size:115 final size:112
Alignment explanation
Indices: 41129699--41129909 Score: 325
Period size: 115 Copynumber: 1.9 Consensus size: 112
41129689 TACTCTAATA
*
41129699 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAAAGAATC-CCCAA
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAAT-AAAAAAT-AAAAAA-AATCACACAA
* *
41129763 TTTCTTATGAACCTTAAAATAAATCGGCTAAATATGCTTACCCGAATACAT
63 TTTCTTATGAACCCTAAAACAAAT-GGCTAAATATGCTTACCCGAATACAT
* * *
41129814 TTCATGCATGGGAAAGAAATGTTTCATTAATATCCAATTAAAAAATAAAAAAAATCACACAATTT
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAATAAAAAAAATCACACAATTT
41129879 CTTATGAACCCTAAAACAAATGGCTAAATAT
66 CTTATGAACCCTAAAACAAATGGCTAAATAT
41129910 ACAGTGATTA
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 14 0.16
113 32 0.36
114 7 0.08
115 36 0.40
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (112 bp):
TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAATAAAAAAAATCACACAATTT
CTTATGAACCCTAAAACAAATGGCTAAATATGCTTACCCGAATACAT
Found at i:41130403 original size:18 final size:18
Alignment explanation
Indices: 41130370--41130408 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
41130360 TTAAATATTT
*
41130370 TTTTTTAATTTTAATT-A
1 TTTTTTAATTTAAATTCA
41130387 TTTTTTAAGTTTAAATTCA
1 TTTTTTAA-TTTAAATTCA
41130406 TTT
1 TTT
41130409 GCTGATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTTAAATTCA
Found at i:41132605 original size:16 final size:16
Alignment explanation
Indices: 41132573--41132610 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
41132563 TAAATTAGAA
41132573 AAAAAATAAAAATTAT
1 AAAAAATAAAAATTAT
*
41132589 ATAAAATTAAAAA-TAT
1 A-AAAAATAAAAATTAT
41132605 AAAAAA
1 AAAAAA
41132611 ATCTTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 4 0.21
16 5 0.26
17 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATAAAAATTAT
Found at i:41132610 original size:27 final size:26
Alignment explanation
Indices: 41132552--41132612 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
41132542 AAAGTTATTC
41132552 AAAAAATTATATAAATTAGAAAAAAA
1 AAAAAATTATATAAATTAGAAAAAAA
*
41132578 ATAAAAATTATATAAAATTA-AAAATATA
1 A-AAAAATTATAT-AAATTAGAAAA-AAA
41132606 AAAAAAT
1 AAAAAAT
41132613 CTTTACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AAAAAATTATATAAATTAGAAAAAAA
Found at i:41133023 original size:17 final size:16
Alignment explanation
Indices: 41132949--41133040 Score: 67
Period size: 16 Copynumber: 5.4 Consensus size: 16
41132939 TTTATTAATA
* *
41132949 ATTTTATATATTTTAT
1 ATTTTTTATAATTTAT
* *
41132965 ATATTTTTAAAAATTCAT
1 AT-TTTTT-ATAATTTAT
*
41132983 AATTTTTTACAAGTTTTAT
1 -ATTTTTTATAA--TTTAT
**
41133002 ATTTTTCCTAATTTAT
1 ATTTTTTATAATTTAT
*
41133018 ATTTTTTATAAATTAT
1 ATTTTTTATAATTTAT
41133034 ATTTTTT
1 ATTTTTT
41133041 TTATTTTTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
16 27 0.46
17 7 0.12
18 19 0.32
19 6 0.10
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (16 bp):
ATTTTTTATAATTTAT
Found at i:41133041 original size:17 final size:17
Alignment explanation
Indices: 41132961--41133041 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 17
41132951 TTTATATATT
* *
41132961 TTATATATTTTTAAAAA
1 TTATATTTTTTTATAAA
* * *
41132978 TTCATAATTTTTTACAAG
1 TT-ATATTTTTTTATAAA
* ** *
41132996 TTTTATATTTTTCCTAAT
1 TTATAT-TTTTTTATAAA
41133014 TTATA-TTTTTTATAAA
1 TTATATTTTTTTATAAA
41133030 TTATATTTTTTT
1 TTATATTTTTTT
41133042 TATTTTTAAT
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
16 13 0.28
17 10 0.21
18 24 0.51
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (17 bp):
TTATATTTTTTTATAAA
Found at i:41133172 original size:18 final size:19
Alignment explanation
Indices: 41133130--41133173 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41133120 TTTTAACTTG
* *
41133130 AAATTTTTTATAAATTTAT
1 AAATTATTTATAAATATAT
41133149 AAATTATTTATAAA-ATAT
1 AAATTATTTATAAATATAT
*
41133167 ATATTAT
1 AAATTAT
41133174 GATTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTATTTATAAATATAT
Found at i:41135580 original size:109 final size:108
Alignment explanation
Indices: 41135417--41135631 Score: 279
Period size: 109 Copynumber: 2.0 Consensus size: 108
41135407 AGTAATAAAC
* * * *
41135417 TCAACTTCACATGTCGGTGAATTCATCAAGTTCGTCTCAATAGGACCACTCAAATCCTAGGATAT
1 TCAACCTCACATGTCAGTGAATACATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATAT
41135482 GAATTCATTAAAAGTGAGAACTCAACCTTATGCATGTACATCAT
66 GAATTCATTAAAAGTGAGAACTCAACCTTATGC-TGTACATCAT
* * * * *
41135526 TCAACCTCACTTGTCAGTGAATACATCAAG-TCTGTCTTAATTGGACCACCCAAATCTTGGGATA
1 TCAACCTCACATGTCAGTGAATACATCAAGTTC-GTCTCAATAGGACCACCCAAATCCTAGGATA
* * * * *
41135590 TTATTTTATTAAGAGTGAGAACTCAACCTTATGCTTTACATC
65 TGAATTCATTAAAAGTGAGAACTCAACCTTATGCTGTACATC
41135632 GTTTTCCATA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
108 9 0.10
109 82 0.90
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (108 bp):
TCAACCTCACATGTCAGTGAATACATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATAT
GAATTCATTAAAAGTGAGAACTCAACCTTATGCTGTACATCAT
Found at i:41140701 original size:17 final size:17
Alignment explanation
Indices: 41140679--41140718 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41140669 GTTATACAAA
41140679 CTTACTAAGATTAATTG
1 CTTACTAAGATTAATTG
** *
41140696 CTTACTCTGTTTAATTG
1 CTTACTAAGATTAATTG
41140713 CTTACT
1 CTTACT
41140719 CTCATTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (17 bp):
CTTACTAAGATTAATTG
Found at i:41141303 original size:55 final size:54
Alignment explanation
Indices: 41141148--41141310 Score: 184
Period size: 55 Copynumber: 3.0 Consensus size: 54
41141138 CTAATGGAAG
* * * *
41141148 CAAGTCATTGAGTTACATGGGCTAGTCACATTGGCGTGTGGTTGGCCATGTGACC
1 CAAGTCAGTGAGTTACATGGGCTAG-CACATAGGCGTGTGGTTGACCGTGTGACC
* * * *
41141203 CAAGTCAGTGAGTTACACGGGCTAGTCCCACAAGCGTGTGGTTGACCGTGTGACC
1 CAAGTCAGTGAGTTACATGGGCTAG-CACATAGGCGTGTGGTTGACCGTGTGACC
* **
41141258 CAAGTCAGTGAGTTACATGGCCTAAG-ACATAGGCGTGTCTCTTGACCGTGTGA
1 CAAGTCAGTGAGTTACATGGGCT-AGCACATAGGCGTGT-GGTTGACCGTGTGA
41141311 GACACACGGC
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
54 9 0.10
55 80 0.88
56 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACATGGGCTAGCACATAGGCGTGTGGTTGACCGTGTGACC
Found at i:41143393 original size:16 final size:16
Alignment explanation
Indices: 41143372--41143402 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41143362 AAGCCTATAC
41143372 ATATACATCAAACAAT
1 ATATACATCAAACAAT
41143388 ATATACATCAAACAA
1 ATATACATCAAACAA
41143403 GTTAGCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATACATCAAACAAT
Found at i:41143720 original size:25 final size:25
Alignment explanation
Indices: 41143682--41143782 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 25
41143672 ATGTACATGT
* * * *
41143682 ATGCTCATATGAGCTATGAATTGGA
1 ATGCTCACACGAGCTATAAATCGGA
* * *
41143707 ATGCTCACTCGAGCTGTAAATCGGT
1 ATGCTCACACGAGCTATAAATCGGA
* *
41143732 ATGCTCTCACGAGCTATAAATCGGC
1 ATGCTCACACGAGCTATAAATCGGA
**
41143757 ATGCTCACACGAGCTGCAAATCGGA
1 ATGCTCACACGAGCTATAAATCGGA
41143782 A
1 A
41143783 CATAGCTACA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
ATGCTCACACGAGCTATAAATCGGA
Found at i:41156395 original size:370 final size:370
Alignment explanation
Indices: 41155677--41156419 Score: 1012
Period size: 370 Copynumber: 2.0 Consensus size: 370
41155667 TTAAGCAAGC
* * *
41155677 ATCCTGCTCATGGAATCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATGTAG
1 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATATAG
* * * **
41155742 ATGAACATTGTGTTTACAAATATTTAGGGGATCAAAAGGTGGTCTTTCTTGTTCTATATGTCGAT
66 ATGAACATTGTGTTTACAAACATTTAGGAGATCAAAAGGTGATCTTTCTCATTCTATATGTCGAT
* * ** *
41155807 GACATTCAACTCATTAGAAATTATGTAGGGACATTGTCATCAGTTAAACTGTGGTTAACCCAACA
131 GACATTCAACTCATTAGAAATTATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCCAAAA
* * ** ** * * *
41155872 GTTTAGCATGAAGGACTCGAGAGAATTTAATTTTTTTCTAGGTATTCGAATCTTAATGGATCGAA
196 ATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCGAAACCTAAGGGATCGAA
* *
41155937 AGAACAAAGTGATAGCACTGTCTCATGCTTCATAAATAGATAAGATATTGGAACATTATACAATG
261 AGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATACAATA
* *
41156002 ACTGATTCAATAAAGGGAAATCAACC-TTCTGTATCGGGATTTCAT
326 ACTGATTCAATAAAGGAAAATCAACCTTTC-GTATCGAGATTTCAT
*
41156047 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGACTTTTGGATTTGAGA-AAAATATA
1 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGA-ACAAAATATA
*
41156111 GATGAACCTTGTGTTTACAAACATTTAGGAGAT-AGAAAGGTGATCTTTCTCATTCTATATGTCG
65 GATGAACATTGTGTTTACAAACATTTAGGAGATCA-AAAGGTGATCTTTCTCATTCTATATGTCG
* * **
41156175 ATGACATTCTACTCATT-GAAAATGT-TGTAGAGACATTGTTATTGGTTAAACTATGACTAACCC
129 ATGACATTCAACTCATTAG-AAAT-TATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCC
* * *
41156238 AAAAATTTAGCATGAATGACTTGGGAAAAGCTAATTTCATTCTAGGTATTCGAAACCTAAGGGAT
192 AAAAATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCGAAACCTAAGGGAT
* * * * *
41156303 CGAAAGAACAAAGTGATAGCACTGTCTCAGGTTTCATACATAGATAAGATATTGGAGCGTTATGC
257 CGAAAGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATAC
* *
41156368 AATAATTGATTCGAA-AAAGGAAAATCAACCTTTCGTATCGAGATTTCGT
322 AATAACTGATTC-AATAAAGGAAAATCAACCTTTCGTATCGAGATTTCAT
41156417 ATC
1 ATC
41156420 TCTTTATAGG
Statistics
Matches: 325, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
369 2 0.01
370 316 0.97
371 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (370 bp):
ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATATAG
ATGAACATTGTGTTTACAAACATTTAGGAGATCAAAAGGTGATCTTTCTCATTCTATATGTCGAT
GACATTCAACTCATTAGAAATTATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCCAAAA
ATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCGAAACCTAAGGGATCGAA
AGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATACAATA
ACTGATTCAATAAAGGAAAATCAACCTTTCGTATCGAGATTTCAT
Found at i:41157082 original size:25 final size:25
Alignment explanation
Indices: 41157026--41157086 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
41157016 ACATATTTTT
*
41157026 TCAAAATTTTACAAGGGAAAAATCA
1 TCAAAATTTTACAAGGCAAAAATCA
* *
41157051 TCAAAATTTTACAAGAGCTAAAATCG
1 TCAAAATTTTACAAG-GCAAAAATCA
*
41157077 TCAAATTTTT
1 TCAAAATTTT
41157087 GTTAGGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACAAGGCAAAAATCA
Found at i:41158412 original size:26 final size:26
Alignment explanation
Indices: 41158374--41158457 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
41158364 CTCTGACCAG
* *
41158374 CTCATACTAAAGGGTCTTCGAACCCA
1 CTCAAACTCAAGGGTCTTCGAACCCA
* * *
41158400 CTCAAACTCAAGGGACATCCAACCCA
1 CTCAAACTCAAGGGTCTTCGAACCCA
* *
41158426 TTTCAAACTCAAGGGTCCTT-GAGCCCA
1 -CTCAAACTCAAGGGT-CTTCGAACCCA
41158453 CTCAA
1 CTCAA
41158458 TCTTATTAGG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 25 0.56
27 18 0.40
28 2 0.04
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.20
Consensus pattern (26 bp):
CTCAAACTCAAGGGTCTTCGAACCCA
Found at i:41160312 original size:27 final size:27
Alignment explanation
Indices: 41160222--41160312 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
41160212 AGGTATAACA
* *
41160222 GTCATTTTACCCTAT-AGGGGTATCTCG
1 GTCATTTTATCCTATGA-GGGTATTTCG
*
41160249 GTCATTTTA-CCATATGGGGGTATTTCG
1 GTCATTTTATCC-TATGAGGGTATTTCG
*
41160276 GTCATTTTATCCTATGAAGGTATTTCG
1 GTCATTTTATCCTATGAGGGTATTTCG
41160303 GTCATTTTAT
1 GTCATTTTAT
41160313 TTATTTTAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.04
27 53 0.93
28 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTATCCTATGAGGGTATTTCG
Found at i:41162663 original size:30 final size:31
Alignment explanation
Indices: 41162629--41162697 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
41162619 AACTTTTAAC
41162629 TCAGTCACTCAA-ATT-TTAAAAAAT-AACAAA
1 TCAGTCACT-AACATTATTAAAAAATGAA-AAA
* *
41162659 TCAGTCACTAACATTATTGAAAAGTGAAAAA
1 TCAGTCACTAACATTATTAAAAAATGAAAAA
41162690 TCAGTCAC
1 TCAGTCAC
41162698 CCACTAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 12 0.35
31 18 0.53
32 2 0.06
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (31 bp):
TCAGTCACTAACATTATTAAAAAATGAAAAA
Done.