Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 104 of 199
Found at i:31670719 original size:21 final size:21
Alignment explanation
Indices: 31670658--31670719 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
31670648 ATTTGGGGCT
*
31670658 AATTTAAAAATGATTCAAAGATA
1 AATTT-AAAAT-ATTCAAAAATA
* * **
31670681 CATTAAAAATATAGAAAAATA
1 AATTTAAAATATTCAAAAATA
*
31670702 AATTTAAAATATTTAAAA
1 AATTTAAAATATTCAAAA
31670720 TTCCCCTTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 22 0.73
22 5 0.17
23 3 0.10
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (21 bp):
AATTTAAAATATTCAAAAATA
Found at i:31673276 original size:20 final size:20
Alignment explanation
Indices: 31673236--31673277 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31673226 CCTCTTTCTG
*
31673236 CATGGGCGTGTGTCCCTCCA
1 CATGGGCGTGTGACCCTCCA
31673256 CATGGGCGTGTTGACCC-CCA
1 CATGGGCGTG-TGACCCTCCA
31673276 CA
1 CA
31673278 CGAATAGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.21
Consensus pattern (20 bp):
CATGGGCGTGTGACCCTCCA
Found at i:31677197 original size:50 final size:50
Alignment explanation
Indices: 31677081--31677376 Score: 294
Period size: 50 Copynumber: 5.8 Consensus size: 50
31677071 ATAACAACAC
* * ** * *
31677081 GCCAAAGCCATGTCCCAGACATGGTCTTACCTGGGATGTTTCATGTAC--T
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGT
* * * **
31677130 GCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
** *
31677180 GCTC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GC-CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
** * *
31677230 GCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
*
31677280 GCCAACGCCATGTCCCTA-ACATGGTCTTACATGGGACCTCTCATGATCTCAAGGAT
1 GCCAATGCCATGTCCC-AGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG-T
* *
31677336 GTCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31677377 TTACCCAAAT
Statistics
Matches: 207, Mismatches: 28, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.00
49 38 0.18
50 124 0.60
51 2 0.01
53 2 0.01
55 3 0.01
56 37 0.18
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
Found at i:31684798 original size:50 final size:50
Alignment explanation
Indices: 31684649--31684945 Score: 285
Period size: 50 Copynumber: 5.8 Consensus size: 50
31684639 GATAATAACA
* ** * *
31684649 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * * * ** *
31684698 TACCGATGTCATATCCCAAATATGGTCTTACATGGGATTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
31684748 TGCCCATGCCATGTTCTAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
* *
31684798 TGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31684848 TGCCAACGCCATGTCCCTGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
31684903 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31684946 TTACCCAAAT
Statistics
Matches: 205, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.00
49 38 0.19
50 120 0.59
51 1 0.00
53 4 0.02
55 2 0.01
56 39 0.19
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31688322 original size:14 final size:14
Alignment explanation
Indices: 31688303--31688333 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31688293 TCTCTTCTTC
31688303 TTTTATTTCTTTCT
1 TTTTATTTCTTTCT
31688317 TTTTATTTCTTTCT
1 TTTTATTTCTTTCT
31688331 TTT
1 TTT
31688334 CTAATTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTCTTTCT
Found at i:31691599 original size:6 final size:6
Alignment explanation
Indices: 31691588--31691657 Score: 140
Period size: 6 Copynumber: 11.7 Consensus size: 6
31691578 ATTTTAAATC
31691588 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
31691636 TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTT
31691658 TCTTTCCAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:31692846 original size:13 final size:13
Alignment explanation
Indices: 31692830--31692876 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
31692820 GGGGGTAGGA
*
31692830 TTCTGTATATTTG
1 TTCTGTATATCTG
*
31692843 TTCTGCATATCTG
1 TTCTGTATATCTG
31692856 ATTCTGT-TATCTG
1 -TTCTGTATATCTG
31692869 TATCTGTA
1 T-TCTGTA
31692877 AAGGACTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 5 0.18
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:31702718 original size:44 final size:46
Alignment explanation
Indices: 31702618--31702719 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 46
31702608 CCTGAAACTA
* * * * *
31702618 CAGTGGAGCAAACTAAAGAAAAGCAAGTCTTATCCCCTTGAAGTTG
1 CAGTGGAGCAGACAAAAGAAAACCAAGTCCTATCCCCATGAAGTTG
*
31702664 CAGTGGAGCAGACAAAAG-AAACCAA-TCCTATCTCCATGAAGTTG
1 CAGTGGAGCAGACAAAAGAAAACCAAGTCCTATCCCCATGAAGTTG
31702708 -ATGTGGAGCAGA
1 CA-GTGGAGCAGA
31702720 TTAAAATCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.02
44 26 0.53
45 6 0.12
46 16 0.33
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (46 bp):
CAGTGGAGCAGACAAAAGAAAACCAAGTCCTATCCCCATGAAGTTG
Found at i:31702800 original size:129 final size:129
Alignment explanation
Indices: 31702643--31703016 Score: 585
Period size: 129 Copynumber: 2.9 Consensus size: 129
31702633 AAGAAAAGCA
*
31702643 AGTCTTATC-CCCTTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCCTATCTC-CATGAAGT
1 AGTCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACGAAAGAAACCAATCCTATCTCTC-TGAAGT
* *
31702706 TG-ATGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTACAT
64 TGCA-GTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
31702770 CC
128 CC
* *
31702772 AGTCTTATCTGCCTGAAGTTGCAGTGGAGCAGACGAAAGACACCAATCCTATCTCTCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTG
*
31702837 CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCC
66 CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCC
* * *
31702901 AGTTTTATCTCCCTGAACTTGTAGTGGAGCAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTG
* *
31702966 CAGTGGAGCGGATTAAAATCACAGATCTTATCTATTCT-AAGTTACAGTAGA
66 CAGTGGAGCGGATTAAAATCACAGATCTTATCT-CTCTGAAGTTGCAGTAGA
31703017 TCAGTTCGCA
Statistics
Matches: 228, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
129 221 0.97
130 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (129 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTG
CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCC
Found at i:31702910 original size:85 final size:85
Alignment explanation
Indices: 31702732--31702974 Score: 232
Period size: 85 Copynumber: 2.9 Consensus size: 85
31702722 AAAATCACAG
* *
31702732 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT-ACATC-CAG-TCTTATCTGC-CTGAAGTTG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCT-CTCTGAAGTTG
31702793 CAGTGGAGCAGACGAAAGACACCA
65 CAGTGGAGCAGAC---AGACACCA
* *
31702817 ATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
*
31702882 AGTAGAGCAGATC-G-CATCCA
66 AGTGGAGCAGA-CAGACA-CCA
* * * * * ** * *
31702902 GTTTTATCTCCCTGAACTTGTAGTGGAGCAGACGAAAGA-AACCA-ATCCTATCTCTCTGAAGTT
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-ATCA-CAGATCTTATCTCTCTGAAGTT
31702965 GCAGTGGAGC
64 GCAGTGGAGC
31702975 GGATTAAAAT
Statistics
Matches: 133, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
84 2 0.02
85 91 0.68
86 7 0.05
87 4 0.03
88 28 0.21
89 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (85 bp):
ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
AGTGGAGCAGACAGACACCA
Found at i:31703008 original size:44 final size:44
Alignment explanation
Indices: 31702656--31702998 Score: 293
Period size: 44 Copynumber: 7.9 Consensus size: 44
31702646 CTTATCCCCT
* ** *
31702656 TGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-ATCCTATCTC-C
1 TGAAGTTGCAGTGGAGCAGATTAAAA-TCA-CAGATCTTATCTCTC
31702699 ATGAAGTTG-ATGTGGAGCAGATTAAAATCACAGATCTTATCTCTC
1 -TGAAGTTGCA-GTGGAGCAGATTAAAATCACAGATCTTATCTCTC
* *
31702744 TGAAGTTGCAGTAGAGCAGATT-ACATC-CAG-TCTTATCTGC-C
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCT-CTC
** *
31702785 TGAAGTTGCAGTGGAGCAGACGAAAGA-CACCA-ATCCTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAA-ATCA-CAGATCTTATCTCTC
*
31702829 TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTC
* *** * *
31702873 TGAAGTTGCAGTAGAGCAGA-TCGCATC-CAG-TTTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTC
* * ** * *
31702914 TGAACTTGTAGTGGAGCAGACGAAAGA-AACCA-ATCCTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAA-ATCA-CAGATCTTATCTCTC
*
31702958 TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCT
31702999 ATTCTAAGTT
Statistics
Matches: 238, Mismatches: 40, Indels: 42
0.74 0.12 0.13
Matches are distributed among these distances:
41 54 0.23
42 9 0.04
43 20 0.08
44 149 0.63
45 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTC
Found at i:31703099 original size:129 final size:129
Alignment explanation
Indices: 31702672--31703060 Score: 462
Period size: 129 Copynumber: 3.0 Consensus size: 129
31702662 TGCAGTGGAG
* *
31702672 CAGACAAAAGAAACCAATCCTATCTC-CATGAAGTTG-ATGTGGAGCAGATTAAAATCACAGATC
1 CAGACGAAAGAAACCAATCCTATCTCTC-TGAAGTTGCA-GTGGAGCGGATTAAAATCACAGATC
* ** * * * ** **
31702735 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTACATCCAGTCTTATCTGCCTGAAGTTGCAGTGGA
64 TTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAGTTTTATCTCCCTAAAAATGCAGTAAA
*
31702800 G
129 A
*
31702801 CAGACGAAAGACACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTT
1 CAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTT
* * ** * ** *
31702866 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTTTTATCTCCCTGAACTTGTAGTGGAG
66 ATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAGTTTTATCTCCCTAAAAATGCAGTAAAA
31702930 CAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTT
1 CAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTT
* * * * * *
31702995 ATCTATTCT-AAGTTACAGTAGATCAGTTCGCAT-CAGATTTTATTTTCTTAAAAATGCAGTAAA
66 ATCT-CTCTGAAGTTACAGTAGAGCAGATCGCATCCAG-TTTTATCTCCCTAAAAATGCAGTAAA
31703058 A
129 A
31703059 CA
1 CA
31703061 AGTTGAAGCT
Statistics
Matches: 232, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
128 3 0.01
129 224 0.97
130 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (129 bp):
CAGACGAAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTT
ATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAGTTTTATCTCCCTAAAAATGCAGTAAAA
Found at i:31703298 original size:44 final size:44
Alignment explanation
Indices: 31703137--31703350 Score: 243
Period size: 44 Copynumber: 4.8 Consensus size: 44
31703127 CTCGAAGAGC
* * * * *
31703137 TACAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCACACCA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-A-GA
* *
31703182 TA-ATAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGA
1 TACA-AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * *
31703227 TAACAAACCTTATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGA
1 T-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* *
31703272 TACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
*
31703316 TACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
31703351 AATTAAAACG
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
44 72 0.50
45 39 0.27
46 31 0.21
47 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
Found at i:31703314 original size:89 final size:90
Alignment explanation
Indices: 31703137--31703350 Score: 272
Period size: 89 Copynumber: 2.4 Consensus size: 90
31703127 CTCGAAGAGC
* *
31703137 TACAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACACCATAATAAGTCTTATCTCCCTG
1 TACAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATCACACCATAACAAGTCTTATCTCCCTG
31703202 AAGTTGCAGTGGAACAGACTGAAGA
66 AAGTTGCAGTGGAACAGACTGAAGA
* * * * *
31703227 TAACAAACCTTATCTCTCTAAAGTTGCAGTGGAGCAGGTTGA-A-GATACCAA-TCTTATCTCCC
1 T-ACAAATCTTATCTCTCTAAAGTTGCAGTGGAGCA-GATCACACCATAACAAGTCTTATCTCCC
* * *
31703289 TGAAGTTGCAGTGGAGCAGATTGAAGC
64 TGAAGTTGCAGTGGAACAGACTGAAGA
* * *
31703316 TACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 TACAAATCTTATCTCTCTAAAGTTGCAGTGGAGCA
31703351 AATTAAAACG
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
88 30 0.28
89 36 0.33
90 6 0.06
91 33 0.31
92 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (90 bp):
TACAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATCACACCATAACAAGTCTTATCTCCCTG
AAGTTGCAGTGGAACAGACTGAAGA
Found at i:31703368 original size:44 final size:44
Alignment explanation
Indices: 31703189--31703371 Score: 154
Period size: 44 Copynumber: 4.1 Consensus size: 44
31703179 CCATAATAAG
* * * * ** *
31703189 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA-AATTAAAACGACTAA
* * * ** * * *
31703234 CCTTATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGA-TACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATT-AAAACGACTAA
* * * *
31703278 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACGACTAA
31703322 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACGA-TGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACGACT-AA
31703366 TCTTAT
1 TCTTAT
31703372 ACCTTTAAAG
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
43 2 0.02
44 83 0.73
45 29 0.25
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACGACTAA
Found at i:31704909 original size:3 final size:3
Alignment explanation
Indices: 31704896--31704937 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
31704886 TTAATTAATC
* * *
31704896 TAT TTT TAT TAT TAC TAT TAT TAT TAT TAG TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31704938 ATTTTTATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:31704919 original size:15 final size:15
Alignment explanation
Indices: 31704895--31704937 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
31704885 ATTAATTAAT
*
31704895 CTATTTTTATTATTA
1 CTATTATTATTATTA
31704910 CTATTATTATTATTA
1 CTATTATTATTATTA
*
31704925 GTATTATTATTAT
1 CTATTATTATTAT
31704938 ATTTTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (15 bp):
CTATTATTATTATTA
Found at i:31705070 original size:21 final size:21
Alignment explanation
Indices: 31705011--31705075 Score: 53
Period size: 23 Copynumber: 3.0 Consensus size: 21
31705001 ATTTAAAGTT
31705011 TTTTTTATATACTATTATCCTTTA
1 TTTTTTATATA-TATTAT--TTTA
** *
31705035 -AGTTTATAATGTATTATTTTA
1 TTTTTTAT-ATATATTATTTTA
31705056 TTTTTTATATATATT-TTTTA
1 TTTTTTATATATATTATTTTA
31705076 ATGATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.15
21 10 0.30
22 5 0.15
23 11 0.33
24 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTTATATATATTATTTTA
Found at i:31705175 original size:17 final size:18
Alignment explanation
Indices: 31705155--31705188 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31705145 TACATGAATA
*
31705155 TATTTTTTATA-ACATAC
1 TATTTTATATATACATAC
31705172 TATTTTATATATACATA
1 TATTTTATATATACATA
31705189 TATAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTATATATACATAC
Found at i:31708906 original size:9 final size:10
Alignment explanation
Indices: 31708884--31708908 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31708874 AAAGGAAAAG
31708884 AAAAGAAATA
1 AAAAGAAATA
31708894 AAAAGAAATA
1 AAAAGAAATA
31708904 AAAAG
1 AAAAG
31708909 GGGACGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAGAAATA
Found at i:31717460 original size:39 final size:40
Alignment explanation
Indices: 31717368--31717545 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
31717358 ACACACCAGG
* *
31717368 CAGAAGCTCATAAGAGCTGATCCAACCGAAATACACCAAA
1 CAGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAA
* * *
31717408 CAGAAGCTCATAAGAGCTGGTCCACCCGAAACATGCC-AA
1 CAGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAA
* *
31717447 CAGAAGCTCATAAGAGCTGATCCAACCGAAATATGCCAAA
1 CAGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAA
* *
31717487 CAGAAGCTCATAAGAGTTGGTCC-ACCTGAAACACGCC-AA
1 CAGAAGCTCATAAGAGCTGATCCAACC-GAAACACGCCAAA
*
31717526 CAGAAGCTCGTAAGAGCTGA
1 CAGAAGCTCATAAGAGCTGA
31717546 ACAGAAGCTC
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
39 58 0.48
40 63 0.52
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (40 bp):
CAGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAA
Found at i:31717486 original size:79 final size:79
Alignment explanation
Indices: 31717368--31717545 Score: 302
Period size: 79 Copynumber: 2.3 Consensus size: 79
31717358 ACACACCAGG
31717368 CAGAAGCTCATAAGAGCTGATCCAACCGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCAC
1 CAGAAGCTCATAAGAGCTGATCCAACCGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCAC
*
31717433 CCGAAACATGCCAA
66 CCGAAACACGCCAA
** *
31717447 CAGAAGCTCATAAGAGCTGATCCAACCGAAATATGCCAAACAGAAGCTCATAAGAGTTGGTCCAC
1 CAGAAGCTCATAAGAGCTGATCCAACCGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCAC
*
31717512 CTGAAACACGCCAA
66 CCGAAACACGCCAA
*
31717526 CAGAAGCTCGTAAGAGCTGA
1 CAGAAGCTCATAAGAGCTGA
31717546 ACAGAAGCTC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 93 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (79 bp):
CAGAAGCTCATAAGAGCTGATCCAACCGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCAC
CCGAAACACGCCAA
Found at i:31717550 original size:21 final size:21
Alignment explanation
Indices: 31717524--31717565 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31717514 GAAACACGCC
*
31717524 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
31717545 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
31717566 CTCCATTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:31726219 original size:20 final size:21
Alignment explanation
Indices: 31726196--31726236 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31726186 ATCAAATACC
*
31726196 TCCTCAAAAC-AACAAGGAAA
1 TCCTCAAAACTAAAAAGGAAA
*
31726216 TCCTTAAAACTAAAAAGGAAA
1 TCCTCAAAACTAAAAAGGAAA
31726237 ATACTAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.15
Consensus pattern (21 bp):
TCCTCAAAACTAAAAAGGAAA
Found at i:31728614 original size:12 final size:12
Alignment explanation
Indices: 31728597--31728622 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31728587 CTGTTTTTAA
31728597 ATTTCTTTGCAT
1 ATTTCTTTGCAT
31728609 ATTTCTTTGCAT
1 ATTTCTTTGCAT
31728621 AT
1 AT
31728623 ATTACTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (12 bp):
ATTTCTTTGCAT
Found at i:31752476 original size:22 final size:22
Alignment explanation
Indices: 31752448--31752491 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
31752438 TTCCTTACTA
31752448 GTTTTTAATGTTATCTAGTCTT
1 GTTTTTAATGTTATCTAGTCTT
31752470 GTTTTTAATGTTATCTAGTCTT
1 GTTTTTAATGTTATCTAGTCTT
31752492 TTAAATAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (22 bp):
GTTTTTAATGTTATCTAGTCTT
Found at i:31758990 original size:19 final size:20
Alignment explanation
Indices: 31758959--31759022 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
31758949 TAAAAAACAA
*
31758959 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AATTTTTAAAAATT
31758979 ATTTTAAA-TTTTAAAAATT
1 ATTTTAAATTTTTAAAAATT
* *
31758998 ATTTTCAATTTTTGAAAATT
1 ATTTTAAATTTTTAAAAATT
31759018 ATTTT
1 ATTTT
31759023 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 21 0.54
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTAAATTTTTAAAAATT
Found at i:31759015 original size:20 final size:18
Alignment explanation
Indices: 31758966--31759029 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
31758956 CAAATTTTAG
31758966 AATTTTTATAAA-TATTTT
1 AATTTTTA-AAATTATTTT
*
31758984 AAATTTTAAAAATTATTTT
1 -AATTTTTAAAATTATTTT
31759003 CAATTTTTGAAAATTATTTT
1 -AATTTTT-AAAATTATTTT
*
31759023 GATTTTT
1 AATTTTT
31759030 TTTGTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 3 0.08
19 25 0.64
20 11 0.28
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (18 bp):
AATTTTTAAAATTATTTT
Found at i:31759796 original size:3 final size:3
Alignment explanation
Indices: 31759788--31759831 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
31759778 ATTCGATCCT
31759788 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31759832 TAATTAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31762155 original size:42 final size:42
Alignment explanation
Indices: 31762089--31762561 Score: 622
Period size: 42 Copynumber: 11.3 Consensus size: 42
31762079 CTTCATATAC
* *
31762089 AATGCAATGAAAAGTAAATGGACCTCCACACTTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * ** *
31762131 AATTCAATGAAAATTAAACAGACCTCCACACCTGGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
31762173 AATGCAATGAAAAGCAAATGGACCTCCACGCCTGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
31762215 AATGCAATAAAAAGCAAATAGACCTCCACACCTGGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
31762257 AATGTAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
31762299 AATGCAATGAAAAGTGAATGGACCTCCATACCTGCGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* *
31762341 AATGCAATGAAAAGTAAACGGATCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
31762383 AATGCAACGAAAAGTAAATGGACCTCCACACTTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
** *
31762425 AATGCAATGAAAAGTAAACAGACCTCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* **
31762467 AATGCAACGAAAAGTAAATGGACCTCCACACCTGGATCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
31762509 AATGCAATTACAAGTAAATGGGCCTCTACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
31762551 AATGCAATGAA
1 AATGCAATGAA
31762562 TGCTTTCCTT
Statistics
Matches: 371, Mismatches: 60, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 371 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:31762982 original size:12 final size:12
Alignment explanation
Indices: 31762967--31763009 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
31762957 ATTTTTTTAT
31762967 TTTTTTGGTTTC
1 TTTTTTGGTTTC
*
31762979 TTTTTTGGTTTG
1 TTTTTTGGTTTC
*
31762991 TTGTTTTGTTGTTC
1 TT-TTTTGGT-TTC
31763005 TTTTT
1 TTTTT
31763010 ATTTAGGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 13 0.50
13 9 0.35
14 4 0.15
ACGTcount: A:0.00, C:0.05, G:0.19, T:0.77
Consensus pattern (12 bp):
TTTTTTGGTTTC
Found at i:31770872 original size:51 final size:51
Alignment explanation
Indices: 31770811--31770921 Score: 213
Period size: 51 Copynumber: 2.2 Consensus size: 51
31770801 CACATATCAC
31770811 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTT
*
31770862 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTT
31770913 ATCACTTGT
1 ATCACTTGT
31770922 TACTGAATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTT
Found at i:31771043 original size:19 final size:17
Alignment explanation
Indices: 31771001--31771043 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
31770991 TTTTATTCTC
31771001 AATTCATCAACAAATAT
1 AATTCATCAACAAATAT
31771018 -ATCTCATCATACATAATAT
1 AAT-TCATCA-ACA-AATAT
31771037 AATTCAT
1 AATTCAT
31771044 GAAATTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 3 0.14
19 9 0.41
20 2 0.09
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTCATCAACAAATAT
Found at i:31773286 original size:21 final size:21
Alignment explanation
Indices: 31773262--31773303 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31773252 ATCCAAATCT
*
31773262 GATTTTATTAAAGAGAAATTA
1 GATTTCATTAAAGAGAAATTA
*
31773283 GATTTCGTTAAAGAGAAATTA
1 GATTTCATTAAAGAGAAATTA
31773304 CACGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (21 bp):
GATTTCATTAAAGAGAAATTA
Found at i:31776580 original size:13 final size:13
Alignment explanation
Indices: 31776562--31776586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31776552 ATTTTTTTCA
31776562 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
31776575 AAAAAAGAAAAA
1 AAAAAAGAAAAA
31776587 ACCTCTTCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:31776820 original size:30 final size:31
Alignment explanation
Indices: 31776759--31776820 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
31776749 TACTTTTCTT
* * *
31776759 AAAAATTAAAACTTTATTTCGAAATAGTTAA
1 AAAAATCAAAACTTTATTTCGAAAAACTTAA
*
31776790 AAAAATCAAAACTTTATTT-TAAAAACTTAA
1 AAAAATCAAAACTTTATTTCGAAAAACTTAA
31776820 A
1 A
31776821 CTTTCCTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAAATCAAAACTTTATTTCGAAAAACTTAA
Found at i:31776968 original size:147 final size:145
Alignment explanation
Indices: 31776706--31777050 Score: 466
Period size: 147 Copynumber: 2.4 Consensus size: 145
31776696 CCGGATTTTT
* * *
31776706 TTTTTTTTTTTGCAAAATC-AAAGTTT-TC-TTTAGAAAAAATCATTACTTTTCTTAAAAATTAA
1 TTTTTATTTTT-CAAAATCTAAACTTTCTCTTTTA-AAAAAATCAATACTTTTCTTAAAAATTAA
31776768 AACTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTTAAAAACTTAAACTTTCCTTTAAA
64 AACTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTTAAAAACTTAAACTTTCCTTTAAA
31776833 ATGACTTAAAAAAAAG-A
129 ATGAC-TAAAAAAAAGTA
* *
31776850 TTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTAAAAAAA-CAATATTTTTCTTAAAGATTAAA
1 TTTTTATTTTTCAAAATCTAAACTTTCT-CTTTTAAAAAAATCAATACTTTTCTTAAAAATTAAA
* * * **
31776914 ACTTTTATTTGGAAATAGTTGAAAAAAATCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAA
65 AC-TTTATTTCGAAATAGTT-AAAAAAATCAAAACTTTATTTTAAAAACTTAAACTTTCCTTTAA
*
31776979 AATGACTAAAAAAACGTA
128 AATGACTAAAAAAAAGTA
* * *
31776997 TTTTTATTTTTTAAAATCTAAACTTTCTATTTTAAAAAAAATCAAAACTTTTCT
1 TTTTTATTTTTCAAAATCTAAACTTTCTCTTTT-AAAAAAATCAATACTTTTCT
31777051 CAGAATCAAG
Statistics
Matches: 177, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
143 7 0.04
144 16 0.09
145 23 0.13
146 36 0.20
147 85 0.48
148 10 0.06
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (145 bp):
TTTTTATTTTTCAAAATCTAAACTTTCTCTTTTAAAAAAATCAATACTTTTCTTAAAAATTAAAA
CTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTTAAAAACTTAAACTTTCCTTTAAAAT
GACTAAAAAAAAGTA
Found at i:31788232 original size:11 final size:11
Alignment explanation
Indices: 31788211--31788243 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
31788201 TGATCTTTTC
31788211 AAAACTCATTTG
1 AAAA-TCATTTG
31788223 AAAATCATTTG
1 AAAATCATTTG
31788234 AAAATCATTT
1 AAAATCATTT
31788244 TAAAGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (11 bp):
AAAATCATTTG
Found at i:31792004 original size:17 final size:16
Alignment explanation
Indices: 31791971--31792001 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31791961 TTGTAAAGTA
31791971 AAATATGAGTATATTT
1 AAATATGAGTATATTT
31791987 AAATATGAG-ATATTT
1 AAATATGAGTATATTT
31792002 TTATTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
AAATATGAGTATATTT
Found at i:31794599 original size:2 final size:2
Alignment explanation
Indices: 31794592--31794654 Score: 117
Period size: 2 Copynumber: 31.0 Consensus size: 2
31794582 AGATAACTTT
31794592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31794634 TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA -TA TA
31794655 AGATGAAACA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31794884 original size:5 final size:5
Alignment explanation
Indices: 31794876--31794906 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31794866 TTTTCAGTGT
31794876 TAATA TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA TAATA T
31794907 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:31795816 original size:2 final size:2
Alignment explanation
Indices: 31795809--31795846 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31795799 GCCAAAATAG
31795809 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31795847 ACTCACTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31802137 original size:14 final size:14
Alignment explanation
Indices: 31802076--31802176 Score: 55
Period size: 14 Copynumber: 7.1 Consensus size: 14
31802066 CTTTCTTCCT
31802076 AAATTCTCAATCTTC
1 AAATT-TCAATCTTC
*
31802091 AATATTT-AATC-CC
1 AA-ATTTCAATCTTC
* *
31802104 CAATTTCCAAT-TTT
1 AAATTT-CAATCTTC
31802118 ATAATTTCAATCTTC
1 A-AATTTCAATCTTC
* *
31802133 AAATTTTAATTTTC
1 AAATTTCAATCTTC
* * *
31802147 AATTTTCAATTTTG
1 AAATTTCAATCTTC
* *
31802161 AATTTTCAATCCTC
1 AAATTTCAATCTTC
31802175 AA
1 AA
31802177 TCCTCAAATA
Statistics
Matches: 66, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
12 4 0.06
13 2 0.03
14 46 0.70
15 11 0.17
16 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.47
Consensus pattern (14 bp):
AAATTTCAATCTTC
Found at i:31802145 original size:6 final size:7
Alignment explanation
Indices: 31802104--31802170 Score: 66
Period size: 7 Copynumber: 9.6 Consensus size: 7
31802094 ATTTAATCCC
*
31802104 CAATTTC
1 CAATTTT
31802111 CAATTTT
1 CAATTTT
*
31802118 -ATAATTT
1 CA-ATTTT
*
31802125 CAATCTT
1 CAATTTT
31802132 CAAATTTT
1 C-AATTTT
31802140 -AATTTT
1 CAATTTT
31802146 CAATTTT
1 CAATTTT
31802153 CAATTTT
1 CAATTTT
*
31802160 GAATTTT
1 CAATTTT
31802167 CAAT
1 CAAT
31802171 CCTCAATCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
6 7 0.14
7 36 0.73
8 6 0.12
ACGTcount: A:0.33, C:0.13, G:0.01, T:0.52
Consensus pattern (7 bp):
CAATTTT
Found at i:31802176 original size:21 final size:20
Alignment explanation
Indices: 31802077--31802177 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 20
31802067 TTTCTTCCTA
*
31802077 AATTCTCAATCTTCAATATTT
1 AATTTTCAATCTTCAAT-TTT
***
31802098 AATCCCCAAT-TTCCAATTTT
1 AATTTTCAATCTT-CAATTTT
*
31802118 ATAATTTCAATCTTCAAATTTT
1 A-ATTTTCAATCTTC-AATTTT
*
31802140 AATTTTCAATTTTCAATTTT
1 AATTTTCAATCTTCAATTTT
*
31802160 GAATTTTCAATCCTCAAT
1 -AATTTTCAATCTTCAAT
31802178 CCTCAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
20 12 0.18
21 44 0.68
22 9 0.14
ACGTcount: A:0.33, C:0.19, G:0.01, T:0.48
Consensus pattern (20 bp):
AATTTTCAATCTTCAATTTT
Found at i:31803819 original size:2 final size:2
Alignment explanation
Indices: 31803812--31803839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31803802 ACTAACCTTA
31803812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31803840 GTTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31804986 original size:2 final size:2
Alignment explanation
Indices: 31804934--31804967 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31804924 ATGTATATTC
31804934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31804968 AAAGATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31805808 original size:19 final size:19
Alignment explanation
Indices: 31805784--31805894 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
31805774 AATCTTCAGG
31805784 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31805803 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
* **
31805822 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31805841 GATATTCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
31805860 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31805879 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
31805895 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31805893 original size:38 final size:38
Alignment explanation
Indices: 31805791--31805894 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
31805781 AGGGATATGC
*
31805791 AATCTTAGATATGATATGCAATCTTAAATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
* *
31805829 AATCTTAGATATGATATTCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
31805867 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
31805895 AGATATGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:31805920 original size:22 final size:21
Alignment explanation
Indices: 31805784--31805920 Score: 107
Period size: 19 Copynumber: 6.9 Consensus size: 21
31805774 AATCTTCAGG
*
31805784 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31805803 GATATGCAATCTTA-A-ATAT
1 GATATGTAATCTTAGAGATAT
* *
31805822 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
31805841 GATAT-TCAATCTT--AGATAT
1 GATATGT-AATCTTAGAGATAT
*
31805860 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31805879 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
31805901 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
31805921 TTAATTTGTA
Statistics
Matches: 102, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
18 2 0.02
19 75 0.74
20 2 0.02
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:31807736 original size:41 final size:41
Alignment explanation
Indices: 31807582--31807725 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 41
31807572 TTTCGACACT
*
31807582 AGACATTACGTCTAGCAGGCTTGATGCCGATGAAACATACC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* * *
31807623 AGAAATTACGTTTAGCAGGCTTGATGCCAGTGAAACATACC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* * *
31807664 AGACTTTACATCTAGCAGGCTTGATGCCGGTGAAACATATC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* *
31807705 AGACTTTATGTCTAGCAGGCT
1 AGACATTACGTCTAGCAGGCT
31807726 AAGTGCCGGT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
Found at i:31820700 original size:18 final size:19
Alignment explanation
Indices: 31820679--31820725 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
31820669 TTTGATTTAA
*
31820679 TTATTTAATTGTTCA-ATT
1 TTATTTAATTGTTAATATT
*
31820697 TTA-TGAATTGTTAATATT
1 TTATTTAATTGTTAATATT
31820715 TTATTCTAATT
1 TTATT-TAATT
31820726 AAATTTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.39
18 9 0.39
19 1 0.04
20 4 0.17
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (19 bp):
TTATTTAATTGTTAATATT
Found at i:31829784 original size:27 final size:27
Alignment explanation
Indices: 31829715--31829978 Score: 261
Period size: 27 Copynumber: 9.8 Consensus size: 27
31829705 CCCCAAAATA
* *
31829715 GGTAAAATGACCAAAATACCCCCATA-
1 GGTAAAATGACCGAAATACCCTCATAG
* **
31829741 GGTAAAATAACTAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCTCATAG
** *
31829768 GGTAAAATGACCGAAATACCCAAATAA
1 GGTAAAATGACCGAAATACCCTCATAG
*
31829795 GGTAAAATGACCGAAATTCCC-CTATAG
1 GGTAAAATGACCGAAATACCCTC-ATAG
*
31829822 GGTAAAATGACTGAAATA-CCTCTATAG
1 GGTAAAATGACCGAAATACCCTC-ATAG
* * *
31829849 GGTAGAATGTCCAAAATA-CCTCTATAG
1 GGTAAAATGACCGAAATACCCTC-ATAG
* *
31829876 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCTCATAG
* *
31829903 GATAAAATGACTGAAATACCC-CTATAG
1 GGTAAAATGACCGAAATACCCTC-ATAG
*
31829930 GGTAGAATGACCGAAATACACC-CATAG
1 GGTAAAATGACCGAAATAC-CCTCATAG
**
31829957 GGTAAAATGACATAAATACCCT
1 GGTAAAATGACCGAAATACCCT
31829979 GATTTGCGAA
Statistics
Matches: 199, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
26 28 0.14
27 165 0.83
28 6 0.03
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCTCATAG
Found at i:31829866 original size:81 final size:79
Alignment explanation
Indices: 31829714--31829977 Score: 323
Period size: 81 Copynumber: 3.3 Consensus size: 79
31829704 ACCCCAAAAT
* * * *
31829714 AGGTAAAATGACCAAAATACCCCCATA-GGTAAAATAACTAAAATACCCTCATAGGGTAAAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCT-ATAGGGTAGAATGA
31829778 CCGAAATACCCAAATA
65 CCGAAATACCC-AATA
* * *
31829794 AGGTAAAATGACCGAAATTCCCCTATAGGGTAAAATGACTGAAATACCTCTATAGGGTAGAATGT
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACC-CTATAGGGTAGAATGA
* *
31829859 CCAAAATACCTCTATA
65 CCGAAATACC-CAATA
* * *
31829875 GGGTAAAATGATCGAAATACCCCCATAGGATAAAATGACTGAAATACCCCTATAGGGTAGAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATA-CCCTATAGGGTAGAATGA
*
31829940 CCGAAATACACCCATA
65 CCGAAATAC-CCAATA
* **
31829956 GGGTAAAATGACATAAATACCC
1 AGGTAAAATGACCGAAATACCC
31829978 TGATTTGCGA
Statistics
Matches: 159, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
80 24 0.15
81 129 0.81
82 6 0.04
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (79 bp):
AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCTATAGGGTAGAATGAC
CGAAATACCCAATA
Found at i:31831375 original size:27 final size:27
Alignment explanation
Indices: 31831344--31831731 Score: 407
Period size: 27 Copynumber: 14.4 Consensus size: 27
31831334 CCCCAAATTA
*
31831344 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** *
31831371 GGTAAAATGACTAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
31831398 GTTAAAATGATCGAAATACCCCTACAG
1 GGTAAAATGACCGAAATACCCCCATAG
*** * *
31831425 GGTAAAATGATTAAAATACCCCTAGAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831452 GGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * * ** *
31831479 GGTAAGATAATCGAAATATCCTAATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
31831506 GGTAGAATGACCGAAATATCTCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831533 GGTAGAATGACGGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831560 GGTAAAATGACCAAAATACCCCCAAAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
31831587 GATAAAATGACCAAAATACCCTCATCG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831614 GATAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831641 GGTAAAATAACCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* *
31831668 GGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
31831695 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
31831722 GGTAAAATGA
1 GGTAAAATGA
31831732 TATAAATACC
Statistics
Matches: 303, Mismatches: 58, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 303 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:31832510 original size:24 final size:24
Alignment explanation
Indices: 31832462--31832508 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
31832452 ATTGGTCATA
*
31832462 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
31832486 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
31832509 GGGATTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:31833233 original size:27 final size:27
Alignment explanation
Indices: 31833211--31833397 Score: 232
Period size: 27 Copynumber: 7.0 Consensus size: 27
31833201 TAAAATAATT
*
31833211 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
*
31833238 GAAATACCCCCATAGGGTAGAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
* * * * *
31833265 AAAATACCTCTATAGGATAGAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
*
31833292 GAAATACCCCCATGGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
*
31833319 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *
31833346 GAAATA-CCCAATAGGGTAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
* * * *
31833372 AAAATACCCTCATAAGGTAGAATGAC
1 GAAATACCCCCATAGGGTAAAATGAC
31833398 TGTTTACCCC
Statistics
Matches: 136, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 22 0.16
27 114 0.84
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACC
Found at i:31835689 original size:15 final size:15
Alignment explanation
Indices: 31835669--31835698 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31835659 TAGGTGCAAT
31835669 GAAGGAAAATACAAA
1 GAAGGAAAATACAAA
*
31835684 GAAGGAAAATGCAAA
1 GAAGGAAAATACAAA
31835699 CATAGGTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.23, T:0.07
Consensus pattern (15 bp):
GAAGGAAAATACAAA
Found at i:31836671 original size:9 final size:9
Alignment explanation
Indices: 31836659--31836690 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
31836649 ATATGTGGAG
31836659 TTTTATATA
1 TTTTATATA
31836668 TTTTATATA
1 TTTTATATA
*
31836677 TTTTAAATA
1 TTTTATATA
31836686 TTTTA
1 TTTTA
31836691 AATTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:31836708 original size:32 final size:32
Alignment explanation
Indices: 31836672--31836764 Score: 96
Period size: 33 Copynumber: 2.9 Consensus size: 32
31836662 TATATATTTT
* *
31836672 ATATATTTTAAATATTTTAAATTTAATTTTAG
1 ATATATTTTAAATATTTTAAATTAAATTCTAG
* * * *
31836704 ATATATTTTTAAAAATTTAAAATAAAATTCTAT
1 ATATA-TTTTAAATATTTTAAATTAAATTCTAG
* * *
31836737 ATATACTTTAAATAATTTAAATTGAATT
1 ATATATTTTAAATATTTTAAATTAAATT
31836765 GAATATAATT
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
32 22 0.46
33 26 0.54
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (32 bp):
ATATATTTTAAATATTTTAAATTAAATTCTAG
Found at i:31836771 original size:32 final size:32
Alignment explanation
Indices: 31836671--31836789 Score: 91
Period size: 32 Copynumber: 3.7 Consensus size: 32
31836661 TTATATATTT
* * *
31836671 TATATATTTTAAATATTTTAAATTTAATTTTAGA
1 TATATATTTTAAATAATTTAAA-TTAAATTCA-A
* *
31836705 TATAT-TTTTAAA-AATTTAAAATAAAATTCTA
1 TATATATTTTAAATAATTT-AAATTAAATTCAA
* * *
31836736 TATATACTTTAAATAATTTAAATTGAATTGAA
1 TATATATTTTAAATAATTTAAATTAAATTCAA
*
31836768 TATA-ATTTAAAAATAAATTTAA
1 TATATATTT-TAAAT-AATTTAA
31836790 CAAAATTTCT
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
31 9 0.13
32 32 0.47
33 22 0.32
34 5 0.07
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.47
Consensus pattern (32 bp):
TATATATTTTAAATAATTTAAATTAAATTCAA
Found at i:31848732 original size:45 final size:45
Alignment explanation
Indices: 31848665--31848777 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 45
31848655 CACGGTGGAT
* * *
31848665 CAGCACACAGC-ACCACCCTTATAGTCAATAGTACTCAGTGAAAG
1 CAGCACACAGCAACCACCTTTATACTCAATAGTACACAGTGAAAG
* * ** *
31848709 CAGCACAGAGCAACCACCTTTATACTCAATGGTACAGGGTGAAAT
1 CAGCACACAGCAACCACCTTTATACTCAATAGTACACAGTGAAAG
* * *
31848754 CAACACATAGCAACCACCTATATA
1 CAGCACACAGCAACCACCTTTATA
31848778 ACTATTAGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 10 0.18
45 47 0.82
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (45 bp):
CAGCACACAGCAACCACCTTTATACTCAATAGTACACAGTGAAAG
Found at i:31848795 original size:45 final size:45
Alignment explanation
Indices: 31848702--31848866 Score: 161
Period size: 45 Copynumber: 3.7 Consensus size: 45
31848692 ATAGTACTCA
* * * * * ** *
31848702 GTGAAAGCAGCACAGAGCAACCACCTTTATACTCAATGGTACAGG
1 GTGAAATCAACACATAGCAACCACCTATATACTCATTAATACCGG
* * *
31848747 GTGAAATCAACACATAGCAACCACCTATATAACT-ATTAGTATCTG
1 GTGAAATCAACACATAGCAACCACCTATAT-ACTCATTAATACCGG
* * **
31848792 GTGAAATCAACACATAGCAACCAACTTTATTTTCATTAATACCGG
1 GTGAAATCAACACATAGCAACCACCTATATACTCATTAATACCGG
* *
31848837 GTGGAATCAACACATAGCATCCACCTATAT
1 GTGAAATCAACACATAGCAACCACCTATAT
31848867 TTCCAACGAT
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
44 1 0.01
45 94 0.96
46 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (45 bp):
GTGAAATCAACACATAGCAACCACCTATATACTCATTAATACCGG
Found at i:31861498 original size:75 final size:74
Alignment explanation
Indices: 31861419--31861558 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 74
31861409 AATATAATGG
* * *
31861419 TGTGCCAAACACTAGTC-AGATAAA-CTGACAAAGTTTGCACCCAGCGCTATTCGGATAAACCAA
1 TGTGCCAAACACTAGTCGA-ATAAATC-GACAAAGATTGCACCCAGCGCTAGTCGAAT-AACCAA
31861482 CAAGTATGATAT
63 CAAGTATGATAT
* * * *
31861494 TGTGCCTAGCACTAGTCGAATAAATCGACAAAGATTGCGCCCAGTGCTAGTCGAATAACCAACAA
1 TGTGCCAAACACTAGTCGAATAAATCGACAAAGATTGCACCCAGCGCTAGTCGAATAACCAACAA
31861559 TAGTTGATCC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
74 9 0.16
75 45 0.80
76 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (74 bp):
TGTGCCAAACACTAGTCGAATAAATCGACAAAGATTGCACCCAGCGCTAGTCGAATAACCAACAA
GTATGATAT
Found at i:31861813 original size:24 final size:24
Alignment explanation
Indices: 31861781--31861830 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
31861771 TGTCACATAG
*
31861781 AAGTGTTCTATAAAATCAAATTCT
1 AAGTGTTCTATAAAATCAAAGTCT
* *
31861805 AAGTGTTCTATGAAATCGAAGTCT
1 AAGTGTTCTATAAAATCAAAGTCT
31861829 AA
1 AA
31861831 CGAAGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (24 bp):
AAGTGTTCTATAAAATCAAAGTCT
Found at i:31862010 original size:21 final size:22
Alignment explanation
Indices: 31861978--31862022 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
31861968 TTTTGAAGTT
31861978 AAAAATACGTGTTTGTCT-TGAA
1 AAAAATACGTGTTTGT-TGTGAA
31862000 AAAAATA-GTGTTTGTTGTGAA
1 AAAAATACGTGTTTGTTGTGAA
31862021 AA
1 AA
31862023 CTTATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (22 bp):
AAAAATACGTGTTTGTTGTGAA
Found at i:31862351 original size:33 final size:36
Alignment explanation
Indices: 31862308--31862375 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 36
31862298 GAGCCCTTTC
*
31862308 CAGTATCAGTGTAGGCCTTAG-CCCAATA-CATTAT
1 CAGTATCAGTGCAGGCCTTAGCCCCAATAGCATTAT
*
31862342 CAGTA-CAGTGCGGGCCTTAGCCCCAATAGCATTA
1 CAGTATCAGTGCAGGCCTTAGCCCCAATAGCATTA
31862376 GTGTGGGCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 12 0.40
35 5 0.17
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (36 bp):
CAGTATCAGTGCAGGCCTTAGCCCCAATAGCATTAT
Found at i:31862807 original size:27 final size:27
Alignment explanation
Indices: 31862775--31862914 Score: 157
Period size: 26 Copynumber: 5.3 Consensus size: 27
31862765 ACCCTTCTGG
31862775 GGGTATTTCAATAATTTTGCCCTA-CG-
1 GGGTATTTCAATAATTTT-CCCTATCGA
** *
31862801 GAGGTATTTCGGTAA-TTTACCTATCGA
1 G-GGTATTTCAATAATTTTCCCTATCGA
*
31862828 GGGTATTTCGATAATTTTCCC-ATCGA
1 GGGTATTTCAATAATTTTCCCTATCGA
*
31862854 GGGTATTTCAATAATTTACCC-ATCGA
1 GGGTATTTCAATAATTTTCCCTATCGA
* *
31862880 GGGTATTTCGATAATTTGCCC-ATCGA
1 GGGTATTTCAATAATTTTCCCTATCGA
31862906 GGGTATTTC
1 GGGTATTTC
31862915 GGTTAACACC
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
25 4 0.04
26 80 0.79
27 17 0.17
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTCCCTATCGA
Found at i:31862837 original size:26 final size:26
Alignment explanation
Indices: 31862803--31862915 Score: 181
Period size: 26 Copynumber: 4.3 Consensus size: 26
31862793 GCCCTACGGA
* *
31862803 GGTATTTCGGTAATTTACCTATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
*
31862829 GGTATTTCGATAATTTTCCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
*
31862855 GGTATTTCAATAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
*
31862881 GGTATTTCGATAATTTGCCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
31862907 GGTATTTCG
1 GGTATTTCG
31862916 GTTAACACCG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (26 bp):
GGTATTTCGATAATTTACCCATCGAG
Found at i:31862873 original size:52 final size:52
Alignment explanation
Indices: 31862775--31862914 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 52
31862765 ACCCTTCTGG
* ** *
31862775 GGGTATTTCAATAATTTTGCCC-TACG-GAGGTATTTCGGTAATTTACCTATCGA
1 GGGTATTTCGATAATTTT-CCCAT-CGAG-GGTATTTCAATAATTTACCCATCGA
31862828 GGGTATTTCGATAATTTTCCCATCGAGGGTATTTCAATAATTTACCCATCGA
1 GGGTATTTCGATAATTTTCCCATCGAGGGTATTTCAATAATTTACCCATCGA
*
31862880 GGGTATTTCGATAATTTGCCCATCGAGGGTATTTC
1 GGGTATTTCGATAATTTTCCCATCGAGGGTATTTC
31862915 GGTTAACACC
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
52 61 0.76
53 19 0.24
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (52 bp):
GGGTATTTCGATAATTTTCCCATCGAGGGTATTTCAATAATTTACCCATCGA
Found at i:31870297 original size:26 final size:27
Alignment explanation
Indices: 31870267--31870355 Score: 112
Period size: 26 Copynumber: 3.4 Consensus size: 27
31870257 CTACCCTTCT
31870267 GGGGGTATTTCAGTAATTTTGCCTTA-C
1 GGGGGTATTTCAGTAA-TTTGCCTTATC
* * *
31870294 GGGGGTATTTTAGTAATTT-ACTCATC
1 GGGGGTATTTCAGTAATTTGCCTTATC
31870320 GGGGGTATTTCAGTAATTTGCC-TATC
1 GGGGGTATTTCAGTAATTTGCCTTATC
*
31870346 GAGGGTATTT
1 GGGGGTATTT
31870356 TGGCAATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
25 3 0.06
26 34 0.64
27 16 0.30
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.40
Consensus pattern (27 bp):
GGGGGTATTTCAGTAATTTGCCTTATC
Found at i:31870364 original size:52 final size:52
Alignment explanation
Indices: 31870253--31870406 Score: 152
Period size: 52 Copynumber: 2.9 Consensus size: 52
31870243 GTGTATTGGT
* * *
31870253 CAATCTACCCTTCTGGGGGTATTTCAGTAATTTTGCCT-TACGGGGGTATTTTAG
1 CAATTTACCCATC-GGGGGTATTTCAGTAA-TTTGCCTAT-CGAGGGTATTTTAG
* * *
31870307 TAATTTACTCATCGGGGGTATTTCAGTAATTTGCCTATCGAGGGTATTTTGG
1 CAATTTACCCATCGGGGGTATTTCAGTAATTTGCCTATCGAGGGTATTTTAG
* * * * *
31870359 CAATTTACCCATC-GAGTTATTTC-GATCATTTACCCATCGAGGGTATTT
1 CAATTTACCCATCGGGGGTATTTCAG-TAATTTGCCTATCGAGGGTATTT
31870407 CGGTCAACAT
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 28 0.33
52 30 0.35
53 17 0.20
54 9 0.11
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (52 bp):
CAATTTACCCATCGGGGGTATTTCAGTAATTTGCCTATCGAGGGTATTTTAG
Found at i:31872717 original size:27 final size:27
Alignment explanation
Indices: 31872682--31872735 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31872672 AACTTCAACA
31872682 ACTCAAATTTCTCAAAGATAACATTTT
1 ACTCAAATTTCTCAAAGATAACATTTT
31872709 ACTCAAATTTCTCAAAGATAACATTTT
1 ACTCAAATTTCTCAAAGATAACATTTT
31872736 CCACAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (27 bp):
ACTCAAATTTCTCAAAGATAACATTTT
Found at i:31872751 original size:27 final size:27
Alignment explanation
Indices: 31872685--31872751 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
31872675 TTCAACAACT
** *
31872685 CAAATTTCTCAAAGATAACATTTTACT
1 CAAATTTAACAAAGATAACATTTTACA
** *
31872712 CAAATTTCTCAAAGATAACATTTTCCA
1 CAAATTTAACAAAGATAACATTTTACA
31872739 CAACA-TTAACAAA
1 CAA-ATTTAACAAA
31872752 TCTAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (27 bp):
CAAATTTAACAAAGATAACATTTTACA
Found at i:31872995 original size:17 final size:17
Alignment explanation
Indices: 31872975--31873009 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31872965 TTTTTTATTA
31872975 TCATTTTCATTTCATTT
1 TCATTTTCATTTCATTT
* *
31872992 TCATTTTCTTTTTATTT
1 TCATTTTCATTTCATTT
31873009 T
1 T
31873010 ATTCGAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (17 bp):
TCATTTTCATTTCATTT
Found at i:31883979 original size:35 final size:34
Alignment explanation
Indices: 31883903--31883984 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
31883893 TAAACCTACG
* **
31883903 AACAATCATATTTGGACAATATTATAACATGTAA
1 AACAACCATATTTGGACAATATTATAACATACAA
* *
31883937 AAAAACCATATTTGGGAC-ATCTTTATAACATACAA
1 AACAACCATATTT-GGACAAT-ATTATAACATACAA
*
31883972 AACAACCACATTT
1 AACAACCATATTT
31883985 AATTATTCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 13 0.33
35 26 0.67
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (34 bp):
AACAACCATATTTGGACAATATTATAACATACAA
Found at i:31890605 original size:83 final size:83
Alignment explanation
Indices: 31890452--31890606 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 83
31890442 ATGCATGATT
* *** * *
31890452 ACATGTCCAGACCAAAATAGATTCAGTGTGACATTTGTCTGAAATGAATAAAAGAGTATATACAC
1 ACATGTCCAGACCAAAATAGATTCAGAGTGACAAGGGTCTGAAAAGAATAAAAGAGTAAATACAC
*
31890517 TAACATACATGCATGCAC
66 CAACATACATGCATGCAC
* * **
31890535 ACATGTCCAGTA-CAACATAGATTCAGAGTGACAAGGGTCTGAAAAGAATAAAAGGGTAAATGTA
1 ACATGTCCAG-ACCAAAATAGATTCAGAGTGACAAGGGTCTGAAAAGAATAAAAGAGTAAATACA
31890599 CCAACATA
65 CCAACATA
31890607 AATATATGCT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 59 0.98
84 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.23
Consensus pattern (83 bp):
ACATGTCCAGACCAAAATAGATTCAGAGTGACAAGGGTCTGAAAAGAATAAAAGAGTAAATACAC
CAACATACATGCATGCAC
Found at i:31911751 original size:41 final size:41
Alignment explanation
Indices: 31911684--31911762 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
31911674 AAACAATTGA
*
31911684 GAATCGATTTAAACAATAATAGATCGATTCAAAATAGCAAT
1 GAATCGATTTAAACAATAATAAATCGATTCAAAATAGCAAT
*
31911725 GAATCGATTTAAAC-ATCAA-ACAATCGATTCAAAGTAGC
1 GAATCGATTTAAACAAT-AATA-AATCGATTCAAAATAGC
31911763 TACAACACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.09
41 31 0.91
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (41 bp):
GAATCGATTTAAACAATAATAAATCGATTCAAAATAGCAAT
Found at i:31913070 original size:54 final size:55
Alignment explanation
Indices: 31913012--31913138 Score: 150
Period size: 55 Copynumber: 2.3 Consensus size: 55
31913002 TGTTTTAAAT
* *
31913012 CGTGTAACTCACTGAGTTAG-GTCACACAGTCGTGTC-GCAAGCCGTGTGCTAGAC
1 CGTGTAACTCACTGACTT-GCGACACACAGTCGTGTCGGCAAGCCGTGTGCTAGAC
** * * * *
31913066 CGTGTAACTCTTTGACTTGCGACACACGGTCTTGTCGGTAGGCCGTGTGCTAGAC
1 CGTGTAACTCACTGACTTGCGACACACAGTCGTGTCGGCAAGCCGTGTGCTAGAC
*
31913121 CGTGTAACACACTGACTT
1 CGTGTAACTCACTGACTT
31913139 AATACATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.02
54 28 0.47
55 31 0.52
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (55 bp):
CGTGTAACTCACTGACTTGCGACACACAGTCGTGTCGGCAAGCCGTGTGCTAGAC
Found at i:31917423 original size:20 final size:20
Alignment explanation
Indices: 31917395--31917470 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
31917385 AAATAATATA
31917395 GAATCGATTTAAACAAGAAT
1 GAATCGATTTAAACAAGAAT
*
31917415 GAATTGATTTAAA-ATAGCAAT
1 GAATCGATTTAAACA-AG-AAT
* *
31917436 GAATCAATTTAAATAAGAAT
1 GAATCGATTTAAACAAGAAT
*
31917456 GAATTGATTTAAACA
1 GAATCGATTTAAACA
31917471 TCAAACAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 29 0.62
21 16 0.34
22 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (20 bp):
GAATCGATTTAAACAAGAAT
Found at i:31921662 original size:21 final size:21
Alignment explanation
Indices: 31921636--31921680 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
31921626 TTTGTTTGAT
31921636 TGGTGAGAAAACTAAAGAAAA
1 TGGTGAGAAAACTAAAGAAAA
*
31921657 TGGTGAGAAAACTGAAGAAAA
1 TGGTGAGAAAACTAAAGAAAA
31921678 TGG
1 TGG
31921681 ATTTCATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (21 bp):
TGGTGAGAAAACTAAAGAAAA
Found at i:31922678 original size:22 final size:22
Alignment explanation
Indices: 31922653--31922694 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31922643 TCCAAACAAT
*
31922653 AACAACATAATAGTAAAAAAAC
1 AACAACAAAATAGTAAAAAAAC
*
31922675 AACAAGAAAATAGTAAAAAA
1 AACAACAAAATAGTAAAAAA
31922695 TTGTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (22 bp):
AACAACAAAATAGTAAAAAAAC
Found at i:31924884 original size:2 final size:2
Alignment explanation
Indices: 31924877--31924910 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31924867 TTGAGTGCAC
31924877 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31924911 CTTAATTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31927977 original size:26 final size:26
Alignment explanation
Indices: 31927943--31927995 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31927933 GGCTCAATGA
31927943 TTTTGGCGACGTTATATCATGAGCTT
1 TTTTGGCGACGTTATATCATGAGCTT
31927969 TTTTGGCGACGTTATATCATGAGCTT
1 TTTTGGCGACGTTATATCATGAGCTT
31927995 T
1 T
31927996 GTCATGCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (26 bp):
TTTTGGCGACGTTATATCATGAGCTT
Found at i:31932098 original size:27 final size:27
Alignment explanation
Indices: 31932068--31932150 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
31932058 ACTTATGAAC
31932068 CTTTATTAATATGATATGAGAACACAA
1 CTTTATTAATATGATATGAGAACACAA
* * ** **
31932095 CTTT-TATAATCATTA-ATTA-TTC-TTA
1 CTTTAT-TAAT-ATGATATGAGAACACAA
31932120 CTTTATTAATATGATATGAGAACACAA
1 CTTTATTAATATGATATGAGAACACAA
31932147 CTTT
1 CTTT
31932151 TATAATCATT
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
24 3 0.08
25 12 0.32
26 4 0.11
27 16 0.42
28 3 0.08
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (27 bp):
CTTTATTAATATGATATGAGAACACAA
Found at i:31932130 original size:52 final size:52
Alignment explanation
Indices: 31932068--31932179 Score: 215
Period size: 52 Copynumber: 2.1 Consensus size: 52
31932058 ACTTATGAAC
31932068 CTTTATTAATATGATATGAGAACACAACTTTTATAATCATTAATTATTCTTA
1 CTTTATTAATATGATATGAGAACACAACTTTTATAATCATTAATTATTCTTA
31932120 CTTTATTAATATGATATGAGAACACAACTTTTATAATCATTAATTATTCTTA
1 CTTTATTAATATGATATGAGAACACAACTTTTATAATCATTAATTATTCTTA
31932172 CATTTATT
1 C-TTTATT
31932180 TACAAATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 53 0.90
53 6 0.10
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.46
Consensus pattern (52 bp):
CTTTATTAATATGATATGAGAACACAACTTTTATAATCATTAATTATTCTTA
Found at i:31932740 original size:12 final size:12
Alignment explanation
Indices: 31932723--31932756 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
31932713 TTAGCCTTTG
31932723 TCCAAAAATATA
1 TCCAAAAATATA
31932735 TCCAAAAATATA
1 TCCAAAAATATA
31932747 TCCAAAAATA
1 TCCAAAAATA
31932757 GTAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (12 bp):
TCCAAAAATATA
Found at i:31933808 original size:14 final size:14
Alignment explanation
Indices: 31933770--31933812 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
31933760 CAAAATGTAC
31933770 AATATAATTAAA-T
1 AATATAATTAAATT
31933783 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
31933798 AA-ATAATTTAATT
1 AATATAATTAAATT
31933811 AA
1 AA
31933813 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:31943570 original size:2 final size:2
Alignment explanation
Indices: 31943563--31943597 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31943553 CTCTATATGA
31943563 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
31943598 GATTCATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:31949270 original size:15 final size:16
Alignment explanation
Indices: 31949239--31949272 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
31949229 TAAAAATTAA
31949239 AAAATAAGATAAATTG
1 AAAATAAGATAAATTG
*
31949255 AAAATAA-ATTAATTG
1 AAAATAAGATAAATTG
31949270 AAA
1 AAA
31949273 TTTGATAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAATAAGATAAATTG
Found at i:31950303 original size:24 final size:23
Alignment explanation
Indices: 31950260--31950310 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
31950250 AAATTAATAA
* *
31950260 TATAAAAATATTTTATAAAATTT
1 TATAAAAATATATTAAAAAATTT
31950283 TATAAAAATAATATTAAAAAATTT
1 TATAAAAAT-ATATTAAAAAATTT
31950307 TATA
1 TATA
31950311 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAAAAATATATTAAAAAATTT
Found at i:31950423 original size:21 final size:20
Alignment explanation
Indices: 31950399--31950437 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31950389 ATATTTTTTT
31950399 ATAATTTAATAAAATTTTACA
1 ATAATTTAA-AAAATTTTACA
*
31950420 ATAATTTAAATAATTTTA
1 ATAATTTAAAAAATTTTA
31950438 ATTTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTTAAAAAATTTTACA
Found at i:31950746 original size:16 final size:15
Alignment explanation
Indices: 31950715--31950755 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
31950705 TATTTTATTG
*
31950715 TAATTTTTATTTTTA
1 TAATTTATATTTTTA
31950730 TAATTTATATGTTTTA
1 TAATTTATAT-TTTTA
*
31950746 TAAATTATAT
1 TAATTTATAT
31950756 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TAATTTATATTTTTA
Found at i:31950778 original size:20 final size:19
Alignment explanation
Indices: 31950732--31950784 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
31950722 TATTTTTATA
31950732 ATTTATATGTTTTATAAATT
1 ATTTATAT-TTTTATAAATT
* *
31950752 ATATATATTTTTATGAATTT
1 ATTTATATTTTTAT-AAATT
*
31950772 TTTTATATTTTTA
1 ATTTATATTTTTA
31950785 ATGTGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTATATTTTTATAAATT
Found at i:31955559 original size:18 final size:18
Alignment explanation
Indices: 31955518--31955562 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
31955508 TTATAGTTTA
31955518 TATATTTTTTATATACATT
1 TATATTTTTTATATA-ATT
*
31955537 CATATTTTTTATGAT-ATT
1 TATATTTTTTAT-ATAATT
31955555 TATATTTT
1 TATATTTT
31955563 CATGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 11 0.48
20 2 0.09
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTTTATATAATT
Found at i:31956869 original size:22 final size:21
Alignment explanation
Indices: 31956844--31956888 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
31956834 TTTTGAGCAA
* *
31956844 TTTAATTTTTCTTTTATGTTCT
1 TTTAACTTTCCTTTT-TGTTCT
*
31956866 TTTAACTTTCCTTTTTTTTCT
1 TTTAACTTTCCTTTTTGTTCT
31956887 TT
1 TT
31956889 ATTTTCTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTAACTTTCCTTTTTGTTCT
Found at i:31957180 original size:10 final size:10
Alignment explanation
Indices: 31957130--31957180 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
31957120 AAAAGAGAAT
*
31957130 GAAAAATAAA
1 GAAAAAAAAA
31957140 G-AAAAAAAA
1 GAAAAAAAAA
31957149 GAAAAATTAAAA
1 GAAAAA--AAAA
* *
31957161 GAACATAAAA
1 GAAAAAAAAA
31957171 GAAAAAAAAA
1 GAAAAAAAAA
31957181 TTAAATTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 8 0.24
10 17 0.52
12 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:31960295 original size:18 final size:18
Alignment explanation
Indices: 31960272--31960309 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31960262 GTAGATTGTA
*
31960272 ACACCCCTATCTATATTT
1 ACACCCCTACCTATATTT
31960290 ACACCCCTACCTATATTT
1 ACACCCCTACCTATATTT
31960308 AC
1 AC
31960310 GAGGTAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (18 bp):
ACACCCCTACCTATATTT
Found at i:31960391 original size:16 final size:16
Alignment explanation
Indices: 31960348--31960383 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31960338 ATTATCGGAG
*
31960348 TTTTTCAAATTAATTT
1 TTTTTCGAATTAATTT
31960364 TTTTTCGAATTAATTT
1 TTTTTCGAATTAATTT
31960380 TTTT
1 TTTT
31960384 CGTTATTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTTCGAATTAATTT
Found at i:31971379 original size:19 final size:19
Alignment explanation
Indices: 31971355--31971393 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31971345 GAATCAAGGG
*
31971355 TGTTAGTGGAATTATCTAA
1 TGTTAGTAGAATTATCTAA
31971374 TGTTAGTAGAATTATCTAA
1 TGTTAGTAGAATTATCTAA
31971393 T
1 T
31971394 TTTTCCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (19 bp):
TGTTAGTAGAATTATCTAA
Found at i:31979032 original size:25 final size:26
Alignment explanation
Indices: 31978996--31979074 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
31978986 AAGTTCAAGC
*
31978996 GAGCCA-T-ATCAGGAAGCTCTGGAAA
1 GAGCCATTAATCAGGAAGCTC-AGAAA
31979021 G-G-CATTAATCAGGAAGCTCAGAAA
1 GAGCCATTAATCAGGAAGCTCAGAAA
* * **
31979045 GAGCCTTTAATCGGGAAGCTCCCAAA
1 GAGCCATTAATCAGGAAGCTCAGAAA
31979071 GAGC
1 GAGC
31979075 TATATATCGG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.04
24 7 0.16
25 14 0.31
26 22 0.49
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCAGAAA
Found at i:31979061 original size:26 final size:25
Alignment explanation
Indices: 31979025--31979102 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
31979015 TGGAAAGGCA
* *
31979025 TTAATCAGGAAGCTCAGAAAGAGCCT
1 TTAATCGGGAAGCTCACAAAGAG-CT
*
31979051 TTAATCGGGAAGCTCCCAAAGAGCT
1 TTAATCGGGAAGCTCACAAAGAGCT
* * *
31979076 ATATATCGGGACGCTCA-TAAGAGCT
1 TTA-ATCGGGAAGCTCACAAAGAGCT
31979101 TT
1 TT
31979103 GGTGTGTCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
25 12 0.28
26 31 0.72
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
TTAATCGGGAAGCTCACAAAGAGCT
Found at i:31989552 original size:16 final size:16
Alignment explanation
Indices: 31989531--31989564 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31989521 TTTTCGTCTA
31989531 TTAATTACAAAATTAT
1 TTAATTACAAAATTAT
* *
31989547 TTAATTATATAATTAT
1 TTAATTACAAAATTAT
31989563 TT
1 TT
31989565 TGCTAAGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTACAAAATTAT
Found at i:31991857 original size:10 final size:10
Alignment explanation
Indices: 31991844--31991877 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31991834 AAAAATACAT
31991844 AAATATTTTA
1 AAATATTTTA
31991854 AAATATTTTA
1 AAATATTTTA
*
31991864 AATATATATTA
1 AA-ATATTTTA
31991875 AAA
1 AAA
31991878 GTTTTTGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATATTTTA
Found at i:32016696 original size:3 final size:3
Alignment explanation
Indices: 32016688--32016747 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
32016678 ATGCGTGTAT
32016688 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32016735 TATA AT- ATA ATA A
1 -ATA ATA ATA ATA A
32016748 CAAATTAAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32018292 original size:50 final size:50
Alignment explanation
Indices: 32018238--32018863 Score: 343
Period size: 50 Copynumber: 12.5 Consensus size: 50
32018228 AAGATCTGTT
* *
32018238 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACCAGATCCGTC
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* ** * * * * **
32018288 GTTGTGAG-TTCAAT-CTGCTCCACTGCACTGCCAGGGAAGTAAGATCCGCC
1 GTTGTG-GCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * *
32018338 GTTGTGGCTTCAATCTTTTTAATTGTGCTGTCGGGGAAACCAGATCCGCC
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * ** * * * * ** * *
32018388 GTTGTGACTTCAAT-CTGCTCCACTACACCGTCGGGGAAGTAAGACCCGCT
1 GTTGTGGCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * *
32018438 GTTGTGGCTTCAATCTTTTTAATTACGCTGTCGGGGAAACCAGATCCGCC
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * ** * * * * * *
32018488 GTTGTGACTTCAAT-CTGCTCCACTGCACCGCCAGGGAAATAAGATCCGCC
1 GTTGTGGCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * * *
32018538 GTTGAGGCTTCAATCTTTTTAATTGCGCTGTCGGGAAAACTAGA-CCTGCC
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCC-GCC
* * ** * * * * * **
32018588 GTTGTGACTTCAAT-CTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCC
1 GTTGTGGCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * * *
32018638 GTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACCAGATCCACT
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * ** * * * * * ** *
32018688 GTTGTGACTTCAAT-CTGCTCCACTGCACCGCCAGGGAAGTAAGACCCGCC
1 GTTGTGGCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
* * *
32018738 GTTGTGGCTTCAATCTTTTTAATTGCGCTGTCAGGAAAACCAA-ATCCGCC
1 GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAA-CAAGATCCGCC
* * ** * * * * * **
32018788 GTTGTGACTTCAAT-CTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCC
1 GTTGTGGCTTCAATCCT-TTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
*
32018838 GTTGTGGCTTCAATCTTTTTAATTGC
1 GTTGTGGCTTCAATCCTTTTAATTGC
32018864 TATGTCGAGA
Statistics
Matches: 403, Mismatches: 155, Indels: 36
0.68 0.26 0.06
Matches are distributed among these distances:
49 12 0.03
50 380 0.94
51 11 0.03
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (50 bp):
GTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACAAGATCCGCC
Found at i:32018300 original size:100 final size:100
Alignment explanation
Indices: 32018195--32018863 Score: 1061
Period size: 100 Copynumber: 6.7 Consensus size: 100
32018185 ACCGTCGTAG
* * * * * * ** *
32018195 CTTCAATCTGTTCAACTGCACCGCTAAGGAGGTAAGATCTGTTGTTGTGGCTTCAATCCTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
32018260 TTGCGCTGTCGGGGAAACCAGATCCGTCGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
* *
32018295 GTTCAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
32018360 TTGTGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
* * * * *
32018395 CTTCAATCTGCTCCACTACACCGTCGGGGAAGTAAGACCCGCTGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
32018460 TTACGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
* *
32018495 CTTCAATCTGCTCCACTGCACCGCCAGGGAAATAAGATCCGCCGTTGAGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
32018560 TTGCGCTGTCGGGAAAACTAGA-CCTGCCGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCC-GCCGTTGTGA
32018595 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
32018660 TTGCGCTGTCGGGGAAACCAGATCCACTGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
*
32018695 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGACCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* * *
32018760 TTGCGCTGTCAGGAAAACCAAATCCGCCGTTGTGA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
32018795 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
32018860 TTGC
66 TTGC
32018864 TATGTCGAGA
Statistics
Matches: 522, Mismatches: 45, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 2 0.00
100 518 0.99
101 2 0.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (100 bp):
CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGA
Found at i:32020244 original size:15 final size:15
Alignment explanation
Indices: 32020224--32020277 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
32020214 CCTTAGCCTC
32020224 TCCATTTTTATTTTT
1 TCCATTTTTATTTTT
32020239 TCCATTTTTCA--TTT
1 TCCATTTTT-ATTTTT
* *
32020253 TACATTTTCATTTTT
1 TCCATTTTTATTTTT
32020268 TCACATTTTT
1 TC-CATTTTT
32020278 TTACATCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
13 1 0.03
14 10 0.32
15 13 0.42
16 7 0.23
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TCCATTTTTATTTTT
Found at i:32020800 original size:24 final size:24
Alignment explanation
Indices: 32020769--32020841 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
32020759 CCGTAAAGTT
32020769 TTTTTTTGTTTTTTTTTGTTTTTG
1 TTTTTTTGTTTTTTTTTGTTTTTG
* *
32020793 TTTTTTTGTTCTTTTTTGTTCTTCTT
1 TTTTTTTGTTTTTTTTTGTT-TT-TG
*
32020819 TTTTTATTGTTTTCTTTT-TTTTT
1 TTTTT-TTGTTTTTTTTTGTTTTT
32020842 CCCTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 20 0.48
25 4 0.10
26 8 0.19
27 10 0.24
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.85
Consensus pattern (24 bp):
TTTTTTTGTTTTTTTTTGTTTTTG
Found at i:32020842 original size:10 final size:10
Alignment explanation
Indices: 32020767--32020842 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
32020757 CCCCGTAAAG
32020767 TTTTTTT-TT
1 TTTTTTTCTT
*
32020776 GTTTTTT-TT
1 TTTTTTTCTT
* *
32020785 TGTTTTTGTT
1 TTTTTTTCTT
32020795 TTTTTGTTCTT
1 TTTTT-TTCTT
*
32020806 TTTTGTTCTT
1 TTTTTTTCTT
* *
32020816 CTTTTTT-TA
1 TTTTTTTCTT
*
32020825 TTGTTTTCTT
1 TTTTTTTCTT
32020835 TTTTTTTC
1 TTTTTTTC
32020843 CCTTTTTTAA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
9 19 0.37
10 24 0.47
11 8 0.16
ACGTcount: A:0.01, C:0.07, G:0.08, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:32020850 original size:1 final size:1
Alignment explanation
Indices: 32020767--32020841 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
32020757 CCCCGTAAAG
* * * * * * * * * *
32020767 TTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTGTTCTTTTTTGTTCTTCTTTTTTTATTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
32020832 CTTTTTTTTT
1 TTTTTTTTTT
32020842 CCCTTTTTTA
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:32023482 original size:16 final size:16
Alignment explanation
Indices: 32023461--32023495 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32023451 TCTAAGATGC
32023461 AAATGCAATGCAATCA
1 AAATGCAATGCAATCA
* *
32023477 AAATGCCATGCAGTCA
1 AAATGCAATGCAATCA
32023493 AAA
1 AAA
32023496 CACAACAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (16 bp):
AAATGCAATGCAATCA
Found at i:32024856 original size:2 final size:2
Alignment explanation
Indices: 32024851--32024883 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32024841 TAAAATGATA
32024851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32024884 AAACAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32025032 original size:13 final size:14
Alignment explanation
Indices: 32025007--32025037 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
32024997 AAAGAAAAAC
32025007 AATATATATATATA
1 AATATATATATATA
32025021 AATATA-ATATATA
1 AATATATATATATA
32025034 AATA
1 AATA
32025038 AACTAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATATATATATA
Found at i:32025110 original size:18 final size:19
Alignment explanation
Indices: 32025087--32025132 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
32025077 TATATAAATG
*
32025087 TATATATAAAAAATG-AAA
1 TATATATAAAAAACGTAAA
*
32025105 TATATA-ACAAAAACGTAAG
1 TATATATA-AAAAACGTAAA
32025124 TATATATAA
1 TATATATAA
32025133 CCTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.04
18 12 0.52
19 9 0.39
20 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (19 bp):
TATATATAAAAAACGTAAA
Found at i:32025351 original size:3 final size:3
Alignment explanation
Indices: 32025343--32025412 Score: 124
Period size: 3 Copynumber: 23.3 Consensus size: 3
32025333 ATGCGTGTAT
32025343 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32025391 ATA ATA ATA TATA AT- ATA ATA A
1 ATA ATA ATA -ATA ATA ATA ATA A
32025413 CAAATTAAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:32027263 original size:21 final size:21
Alignment explanation
Indices: 32027238--32027281 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
32027228 ATCTTCGAGG
32027238 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
32027259 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
32027280 AT
1 AT
32027282 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:32027287 original size:19 final size:19
Alignment explanation
Indices: 32027237--32027292 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
32027227 AATCTTCGAG
32027237 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
32027256 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
32027277 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
32027293 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:32027299 original size:22 final size:23
Alignment explanation
Indices: 32027250--32027315 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
32027240 ATGCAATCTT
*
32027250 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
32027271 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
32027293 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
32027316 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:32027325 original size:22 final size:23
Alignment explanation
Indices: 32027281--32027325 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
32027271 AGATATGATA
*
32027281 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
32027304 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
32027326 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Done.