Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 11 of 120
Found at i:3235250 original size:18 final size:18
Alignment explanation
Indices: 3235227--3235271 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3235217 ATCCCAATGA
3235227 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3235245 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3235263 TCACCACCA
1 TCGCCACCA
3235272 ACCATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:3236044 original size:63 final size:63
Alignment explanation
Indices: 3235908--3236030 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
3235898 AGGGTTTTAC
* * * * **
3235908 TAAAAATAATAACTAACTATAATAATAATACTAGTTTTTTACTAACTAGTTTATATTGGTAAA
1 TAAAAATAATAACTAACAATAATAATAATACTAGTTTTTTACTAACTAGATAATACTACTAAA
3235971 TAAAAATAATAACTAACAATAATAATAATACTAGTTTTTTACTAAC-A-ATAATACTACTAA
1 TAAAAATAATAACTAACAATAATAATAATACTAGTTTTTTACTAACTAGATAATACTACTAA
3236031 GTTAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 8 0.15
62 1 0.02
63 45 0.83
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (63 bp):
TAAAAATAATAACTAACAATAATAATAATACTAGTTTTTTACTAACTAGATAATACTACTAAA
Found at i:3236086 original size:3 final size:3
Alignment explanation
Indices: 3236080--3236123 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3236070 ACAACAACAG
3236080 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3236124 CTAACTAAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3236212 original size:9 final size:9
Alignment explanation
Indices: 3236200--3236224 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3236190 AAATATACAA
3236200 AACAATAAC
1 AACAATAAC
3236209 AACAATAAC
1 AACAATAAC
3236218 AACAATA
1 AACAATA
3236225 TAATCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.20, G:0.00, T:0.12
Consensus pattern (9 bp):
AACAATAAC
Found at i:3236269 original size:11 final size:11
Alignment explanation
Indices: 3236249--3236288 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
3236239 TTAAAAATAC
3236249 CTTCTTTTTCT
1 CTTCTTTTTCT
*
3236260 CTTCTCTTTCT
1 CTTCTTTTTCT
3236271 C-TCTTTTTCT
1 CTTCTTTTTCT
3236281 CTTCTTTT
1 CTTCTTTT
3236289 CCGCAGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:3236276 original size:21 final size:20
Alignment explanation
Indices: 3236251--3236289 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3236241 AAAAATACCT
3236251 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
3236272 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
3236290 CGCAGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:3236441 original size:10 final size:10
Alignment explanation
Indices: 3236426--3236463 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
3236416 GGTCTGATCA
3236426 AGCTTTTTGC
1 AGCTTTTTGC
*
3236436 AGCTTTTTCC
1 AGCTTTTTGC
3236446 AGCTTTTTGC
1 AGCTTTTTGC
*
3236456 AGGTTTTT
1 AGCTTTTT
3236464 TTTTGGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (10 bp):
AGCTTTTTGC
Found at i:3236451 original size:20 final size:20
Alignment explanation
Indices: 3236426--3236463 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3236416 GGTCTGATCA
3236426 AGCTTTTTGCAGCTTTTTCC
1 AGCTTTTTGCAGCTTTTTCC
*
3236446 AGCTTTTTGCAGGTTTTT
1 AGCTTTTTGCAGCTTTTT
3236464 TTTTGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (20 bp):
AGCTTTTTGCAGCTTTTTCC
Found at i:3236513 original size:30 final size:27
Alignment explanation
Indices: 3236474--3236543 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 27
3236464 TTTTGGTTTT
3236474 TTTAT-ATATTTTGGTAAATAATAAAAA
1 TTTATAATATTTTGGTAAATAA-AAAAA
3236501 TAATTATAATATTTTGGTAAATAAAAAAA
1 T--TTATAATATTTTGGTAAATAAAAAAA
3236530 TTTATAATATTTTG
1 TTTATAATATTTTG
3236544 ATTTTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
27 14 0.35
29 10 0.25
30 16 0.40
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTATAATATTTTGGTAAATAAAAAAA
Found at i:3236523 original size:27 final size:29
Alignment explanation
Indices: 3236474--3236543 Score: 94
Period size: 27 Copynumber: 2.5 Consensus size: 29
3236464 TTTTGGTTTT
3236474 TTTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTTATAATATTTTGGT-AATAATAAAAA-AA
3236504 -TTATAATATTTTGGT-A-AATAAAAAAA
1 TTTATAATATTTTGGTAATAATAAAAAAA
3236530 TTTATAATATTTTG
1 TTTATAATATTTTG
3236544 ATTTTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 2 0.05
27 21 0.55
28 1 0.03
29 4 0.11
30 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (29 bp):
TTTATAATATTTTGGTAATAATAAAAAAA
Found at i:3237033 original size:29 final size:32
Alignment explanation
Indices: 3237001--3237066 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
3236991 TTAGTCCTTT
3237001 AACTTTTTGAAT-TT-ACACTTTAACCCC-TC
1 AACTTTTTGAATATTCACACTTTAACCCCATC
*
3237030 AAC-TTTTGAATATTCACACTTTGACCCCATC
1 AACTTTTTGAATATTCACACTTTAACCCCATC
3237061 -ACTTTT
1 AACTTTT
3237067 CACTTCTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.25
29 5 0.16
30 14 0.44
31 5 0.16
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (32 bp):
AACTTTTTGAATATTCACACTTTAACCCCATC
Found at i:3244141 original size:20 final size:20
Alignment explanation
Indices: 3244116--3244154 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3244106 AAGTAGAAGT
*
3244116 AATAAATAAATAATATAAAC
1 AATAAATAAATAACATAAAC
3244136 AATAAATAAATAACATAAA
1 AATAAATAAATAACATAAA
3244155 ATGATAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
AATAAATAAATAACATAAAC
Found at i:3245678 original size:19 final size:21
Alignment explanation
Indices: 3245640--3245679 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3245630 ATTTAATTTT
*
3245640 GATATTAATTTTAAATTTTGA
1 GATATTAATTTTAAAGTTTGA
3245661 GATATTAA-TTT-AAGTTTGA
1 GATATTAATTTTAAAGTTTGA
3245680 TGCTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
GATATTAATTTTAAAGTTTGA
Found at i:3253619 original size:2 final size:2
Alignment explanation
Indices: 3253612--3253672 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
3253602 CAAACTTTGT
* * * * * *
3253612 TA TA TA TA TA TA CA TA CA TA CA TT TG TT 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
3253654 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3253673 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3253789 original size:2 final size:2
Alignment explanation
Indices: 3253782--3253814 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3253772 NTACGTTCAT
3253782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3253815 GCATACGTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3256645 original size:85 final size:86
Alignment explanation
Indices: 3256434--3256699 Score: 462
Period size: 86 Copynumber: 3.1 Consensus size: 86
3256424 GATGAGAAAA
*
3256434 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGGCAACCATGGTGGATTGCTCCTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGATTGCTCCTACC
3256499 ACACATGGATGGTCATTTTTT
66 ACACATGGATGGTCATTTTTT
* * *
3256520 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAGCCATGGTGGACTGCTACTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGATTGCTCCTACC
*
3256585 ACACATGGATGGT-ACTTTTT
66 ACACATGGATGGTCATTTTTT
*
3256605 TAGAAGAATGTTGCATTGAAGTTACCTCAAAACATAGAGGACAACCATGGTGGATTGCTCCTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGATTGCTCCTACC
*
3256670 AGACATGGATGGTCATTTTTT
66 ACACATGGATGGTCATTTTTT
3256691 TAGAAGAAT
1 TAGAAGAAT
3256700 TGAATGACTA
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 79 0.47
86 89 0.53
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (86 bp):
TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGATTGCTCCTACC
ACACATGGATGGTCATTTTTT
Found at i:3256747 original size:37 final size:37
Alignment explanation
Indices: 3256696--3256772 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
3256686 TTTTTTAGAA
* *
3256696 GAATTGAATGACTACAACATTTTCGTACAATAAATGC
1 GAATTGAATAACTACAACATTTTCATACAATAAATGC
*
3256733 GAATTGAATAACTACAACATTTTCATACAATGAATGC
1 GAATTGAATAACTACAACATTTTCATACAATAAATGC
3256770 GAA
1 GAA
3256773 AGGAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (37 bp):
GAATTGAATAACTACAACATTTTCATACAATAAATGC
Found at i:3257467 original size:26 final size:28
Alignment explanation
Indices: 3257438--3257490 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
3257428 GGTTATAAAA
3257438 TATTTTAT-AATATAAAATGAA-AACAT
1 TATTTTATAAATATAAAATGAACAACAT
* *
3257464 TATTTTTTAAATGTAAAATGAACAACA
1 TATTTTATAAATATAAAATGAACAACA
3257491 AATAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (28 bp):
TATTTTATAAATATAAAATGAACAACAT
Found at i:3263078 original size:20 final size:20
Alignment explanation
Indices: 3263045--3263106 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
3263035 AAAAATACTA
*
3263045 AATTTCTTATAGAATTATTG
1 AATTTCTTACAGAATTATTG
*
3263065 AATTTTTTACAGAATTATTG
1 AATTTCTTACAGAATTATTG
* * *
3263085 AATCTCTTACAAAATTGTTG
1 AATTTCTTACAGAATTATTG
3263105 AA
1 AA
3263107 CCTCTTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (20 bp):
AATTTCTTACAGAATTATTG
Found at i:3263111 original size:20 final size:20
Alignment explanation
Indices: 3263057--3263113 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
3263047 TTTCTTATAG
** * *
3263057 AATTATTGAATTTTTTACAG
1 AATTATTGAACCTCTTACAA
*
3263077 AATTATTGAATCTCTTACAA
1 AATTATTGAACCTCTTACAA
*
3263097 AATTGTTGAACCTCTTA
1 AATTATTGAACCTCTTA
3263114 TAACATTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (20 bp):
AATTATTGAACCTCTTACAA
Found at i:3266767 original size:13 final size:15
Alignment explanation
Indices: 3266737--3266768 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3266727 ATATTTATAA
3266737 AAATAATTATATTTG
1 AAATAATTATATTTG
3266752 AAATAATTA-A-TTG
1 AAATAATTATATTTG
3266765 AAAT
1 AAAT
3266769 TTTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
AAATAATTATATTTG
Found at i:3266831 original size:15 final size:14
Alignment explanation
Indices: 3266811--3266844 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3266801 GTAAGTGAAA
3266811 AAATAACGATTTTTG
1 AAATAA-GATTTTTG
*
3266826 AAATAAGTTTTTTG
1 AAATAAGATTTTTG
3266840 AAATA
1 AAATA
3266845 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (14 bp):
AAATAAGATTTTTG
Found at i:3267074 original size:20 final size:20
Alignment explanation
Indices: 3267049--3267088 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3267039 ATATTAGAAT
3267049 TTACCATACCTATAACGGAC
1 TTACCATACCTATAACGGAC
3267069 TTACCATACCTATAACGGAC
1 TTACCATACCTATAACGGAC
3267089 GTGAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (20 bp):
TTACCATACCTATAACGGAC
Found at i:3267231 original size:2 final size:2
Alignment explanation
Indices: 3267188--3267221 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3267178 TAACGTAATG
3267188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3267222 TCATTATATA
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):
AT
Found at i:3268702 original size:13 final size:12
Alignment explanation
Indices: 3268674--3268717 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 12
3268664 AAGATAATGT
3268674 AAAATAAAGAAA
1 AAAATAAAGAAA
3268686 AAAATAAAGTTAAA
1 AAAATAAAG--AAA
3268700 AAACATAAAAGAAA
1 AAA-AT-AAAGAAA
3268714 AAAA
1 AAAA
3268718 ATTAAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 9 0.32
13 1 0.04
14 12 0.43
15 2 0.07
16 4 0.14
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAATAAAGAAA
Found at i:3270228 original size:3 final size:3
Alignment explanation
Indices: 3270220--3270256 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3270210 TAATATTAGA
* *
3270220 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
3270257 CTTGTTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3288055 original size:24 final size:23
Alignment explanation
Indices: 3287982--3288048 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 23
3287972 GTTATTAGGG
*
3287982 TTACCGATACTTAGCTCGGAAGAGC
1 TTACCGTTA-TTAGCTC-GAAGAGC
*
3288007 TTACCGTTATTCAGCTCAGAGGAGC
1 TTACCGTTATT-AGCTC-GAAGAGC
3288032 TTACCGTT-TATAGCTCG
1 TTACCGTTAT-TAGCTCG
3288049 TATGAGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 1 0.03
24 8 0.22
25 28 0.76
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (23 bp):
TTACCGTTATTAGCTCGAAGAGC
Found at i:3291676 original size:19 final size:20
Alignment explanation
Indices: 3291646--3291699 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
3291636 CAAGAATACA
*
3291646 TATTTGGTATCGATAATTTT
1 TATTTAGTATCGATAATTTT
* *
3291666 T-TTTAGTATCGGTATTTTT
1 TATTTAGTATCGATAATTTT
3291685 TAATTTA-TATCGATA
1 T-ATTTAGTATCGATA
3291700 CCTTGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 16 0.57
20 8 0.29
21 4 0.14
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.56
Consensus pattern (20 bp):
TATTTAGTATCGATAATTTT
Found at i:3294802 original size:4 final size:4
Alignment explanation
Indices: 3294793--3294817 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3294783 CTATTATTGC
3294793 CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
3294818 CTAGTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:3304031 original size:42 final size:42
Alignment explanation
Indices: 3303981--3304080 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
3303971 TTATATGAAC
3303981 GGCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAG
1 GGCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTGAATAAAG
* * * *
3304023 GGCACTAAGTGTGCAAAATTAAAATGGAGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAG
3304065 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
3304081 TACCGAGAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 50 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAG
Found at i:3304857 original size:2 final size:2
Alignment explanation
Indices: 3304850--3304874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3304840 AATAATACTA
3304850 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 A
3304875 GGATTCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3307056 original size:31 final size:30
Alignment explanation
Indices: 3307016--3307077 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3307006 AGTAAATCTC
* *
3307016 AAATTTATATATCAATTTTGATTTAATGTA
1 AAATTTATATATCAACTTTAATTTAATGTA
* *
3307046 AAATTGTATATATGAACTTTAATTTGATGTA
1 AAATT-TATATATCAACTTTAATTTAATGTA
3307077 A
1 A
3307078 TTATACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (30 bp):
AAATTTATATATCAACTTTAATTTAATGTA
Found at i:3308235 original size:25 final size:24
Alignment explanation
Indices: 3308206--3308266 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
3308196 AATTTTGGAA
3308206 ATTTTCATATTTTAAAAATATTTTT
1 ATTTTCATATTTTAAAAA-ATTTTT
* * *
3308231 ATTTTTGA-ATTTTAAAGAGTTTTT
1 A-TTTTCATATTTTAAAAAATTTTT
3308255 -TTTTCATATTTT
1 ATTTTCATATTTT
3308267 TAGTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 5 0.17
25 10 0.33
26 5 0.17
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (24 bp):
ATTTTCATATTTTAAAAAATTTTT
Found at i:3310557 original size:3 final size:3
Alignment explanation
Indices: 3310551--3310586 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3310541 CCTCCTACTC
3310551 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3310587 TTTCATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3323053 original size:17 final size:17
Alignment explanation
Indices: 3323033--3323109 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
3323023 TCAAACCTTT
3323033 AACTTAAGCATGTTTTG
1 AACTTAAGCATGTTTTG
**
3323050 AACTTAAAG-AAATTTTG
1 AACTT-AAGCATGTTTTG
**
3323067 GGCTTAAGCAAAT-TTTTG
1 AACTTAAGC--ATGTTTTG
**
3323085 AACTTAAATATGTTTTG
1 AACTTAAGCATGTTTTG
3323102 AACTTAAG
1 AACTTAAG
3323110 TAAATTCTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
16 5 0.11
17 26 0.58
18 13 0.29
19 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (17 bp):
AACTTAAGCATGTTTTG
Found at i:3323101 original size:35 final size:34
Alignment explanation
Indices: 3323033--3323123 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 34
3323023 TCAAACCTTT
**
3323033 AACTTAAGCATGTTTTGAACTTAAAGAAATTTTG
1 AACTTAAGCAAATTTTGAACTTAAAGAAATTTTG
** * **
3323067 GGCTTAAGCAAATTTTTGAACTTAAATATGTTTTG
1 AACTTAAGCAAA-TTTTGAACTTAAAGAAATTTTG
* *
3323102 AACTTAAGTAAATTCTGAACTT
1 AACTTAAGCAAATTTTGAACTT
3323124 GAGTAAACTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
34 17 0.38
35 28 0.62
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (34 bp):
AACTTAAGCAAATTTTGAACTTAAAGAAATTTTG
Found at i:3325381 original size:26 final size:26
Alignment explanation
Indices: 3325337--3325387 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3325327 TCTAAACTTA
* *
3325337 ATTTTTTTAATTCTAATTTTTTTAAT
1 ATTTTTTTAATCCTAATTTATTTAAT
3325363 ATTTTATTTAATCCT-ATTTATTTAA
1 ATTTT-TTTAATCCTAATTTATTTAA
3325388 ATTATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTTTTAATCCTAATTTATTTAAT
Found at i:3328194 original size:48 final size:48
Alignment explanation
Indices: 3328105--3328197 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
3328095 ACCAAGTTTG
* * * *
3328105 TTTCTTTTCTCATTTCTATCTCGAATCCATTGACCCGTTTTATATTTA
1 TTTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTA
* * **
3328153 TTTCTTTTTTCATTTCTATTTCAAATCCACTAATTCATTTTATAT
1 TTTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATAT
3328198 CCACCTCAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.03, T:0.55
Consensus pattern (48 bp):
TTTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTA
Found at i:3328397 original size:28 final size:31
Alignment explanation
Indices: 3328348--3328408 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
3328338 AAAGTTTTGT
3328348 TTGATCAATTTTAGCCTTTATACTTTT-AAA
1 TTGATCAATTTTAGCCTTTATACTTTTCAAA
3328378 TTGATC-A-TTTAGTCC-TTATACTTTTCAAA
1 TTGATCAATTTTAG-CCTTTATACTTTTCAAA
3328407 TT
1 TT
3328409 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 15 0.52
29 8 0.28
30 6 0.21
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (31 bp):
TTGATCAATTTTAGCCTTTATACTTTTCAAA
Found at i:3337312 original size:9 final size:9
Alignment explanation
Indices: 3337287--3337327 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3337277 TTATTTATCG
3337287 AATTAATTA
1 AATTAATTA
* *
3337296 AATAAATTT
1 AATTAATTA
3337305 AATTAATTA
1 AATTAATTA
*
3337314 ACTTAATTA
1 AATTAATTA
3337323 AATTA
1 AATTA
3337328 TATTCTTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:3342559 original size:15 final size:15
Alignment explanation
Indices: 3342541--3342574 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3342531 CCAACACCCT
*
3342541 AAATTTTTCCAAAAA
1 AAATTTATCCAAAAA
*
3342556 AAATTTATCCAAACA
1 AAATTTATCCAAAAA
3342571 AAAT
1 AAAT
3342575 AATCACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTTATCCAAAAA
Found at i:3348298 original size:14 final size:13
Alignment explanation
Indices: 3348279--3348312 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3348269 TTTTCAAACC
3348279 AAAAAAATAGAAAA
1 AAAAAAATA-AAAA
*
3348293 AAAAAAGTAAAAA
1 AAAAAAATAAAAA
3348306 AAAAAAA
1 AAAAAAA
3348313 CTTTAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAATAAAAA
Found at i:3349729 original size:19 final size:19
Alignment explanation
Indices: 3349707--3349743 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3349697 AAATTCAAGA
3349707 TTCA-AAAAATTATAAAAAG
1 TTCATAAAAATT-TAAAAAG
3349726 TTCATAAAAATTTAAAAA
1 TTCATAAAAATTTAAAAA
3349744 ATAGCATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
TTCATAAAAATTTAAAAAG
Found at i:3353417 original size:2 final size:2
Alignment explanation
Indices: 3353410--3353445 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3353400 CACTTGAACC
3353410 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
3353446 CACACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3353772 original size:27 final size:27
Alignment explanation
Indices: 3353734--3353789 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3353724 GTGGCATGTA
3353734 CATAGAATGTCCTTTGTAAGTAATGCT
1 CATAGAATGTCCTTTGTAAGTAATGCT
3353761 CATAGAATGTCCTTTGTAAGTAATGCT
1 CATAGAATGTCCTTTGTAAGTAATGCT
3353788 CA
1 CA
3353790 AACTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (27 bp):
CATAGAATGTCCTTTGTAAGTAATGCT
Found at i:3355535 original size:23 final size:23
Alignment explanation
Indices: 3355505--3355551 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3355495 AAGATATTCT
3355505 ATGAGGGTAACACATTTATAATA
1 ATGAGGGTAACACATTTATAATA
3355528 ATGAGGGTAACACATTTATAATA
1 ATGAGGGTAACACATTTATAATA
3355551 A
1 A
3355552 AGCCATTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (23 bp):
ATGAGGGTAACACATTTATAATA
Found at i:3357886 original size:25 final size:25
Alignment explanation
Indices: 3357808--3357966 Score: 113
Period size: 25 Copynumber: 6.4 Consensus size: 25
3357798 CGCTCTTATG
*
3357808 AGCTTCTCGATATTTAGCTCACATA
1 AGCTTCCCGATATTTAGCTCACATA
** * *
3357833 AAATTCTCAATATTTAGCTCACATA
1 AGCTTCCCGATATTTAGCTCACATA
**
3357858 AGCTTCCCGATATTTAGCTCACACG
1 AGCTTCCCGATATTTAGCTCACATA
* * * *
3357883 AGCTTCCAGATACTTAGCTCGCATG
1 AGCTTCCCGATATTTAGCTCACATA
* * * ** * *
3357908 GGTTTCCCGTTATACAGCTCGCATG
1 AGCTTCCCGATATTTAGCTCACATA
* * *
3357933 AGCTTCCC-ATTATTCAGCTCAGAAA
1 AGCTTCCCGA-TATTTAGCTCACATA
3357958 AGCTTCCCG
1 AGCTTCCCG
3357967 TTTACAGCTC
Statistics
Matches: 104, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
25 104 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGATATTTAGCTCACATA
Found at i:3357984 original size:24 final size:24
Alignment explanation
Indices: 3357911--3357984 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
3357901 TCGCATGGGT
*
3357911 TTCCCGTTATACAGCTCGCATGAGC
1 TTCCCGTTATACAGCTCG-ATAAGC
* * *
3357936 TTCCCATTATTCAGCTCAGAAAAGC
1 TTCCCGTTATACAGCTC-GATAAGC
3357961 TTCCCGTT-TACAGCTCGTATAAGC
1 TTCCCGTTATACAGCTCG-ATAAGC
3357985 ATACATGCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.03
24 12 0.30
25 26 0.65
26 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (24 bp):
TTCCCGTTATACAGCTCGATAAGC
Found at i:3365330 original size:42 final size:42
Alignment explanation
Indices: 3365278--3365359 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
3365268 TGATTAGTAT
3365278 ACGACACACGAGGTGCCTGATACGACACATAAAGTGCCTGTA
1 ACGACACACGAGGTGCCTGATACGACACATAAAGTGCCTGTA
3365320 ACGACACACGAGGTGCCTGATACGACACATAAAGTGCCTG
1 ACGACACACGAGGTGCCTGATACGACACATAAAGTGCCTG
3365360 AGATACGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (42 bp):
ACGACACACGAGGTGCCTGATACGACACATAAAGTGCCTGTA
Found at i:3365383 original size:23 final size:22
Alignment explanation
Indices: 3365276--3365382 Score: 121
Period size: 21 Copynumber: 5.0 Consensus size: 22
3365266 CCTGATTAGT
** *
3365276 ATACGACACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTGG
*
3365297 ATACGACACATAAAGTGCCTGT
1 ATACGACACATAAAGTGCCTGG
** *
3365319 A-ACGACACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTGG
3365339 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTG-G
3365362 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
3365383 ATCGGCAAAG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.01
21 47 0.66
22 1 0.01
23 22 0.31
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGG
Found at i:3366589 original size:15 final size:16
Alignment explanation
Indices: 3366571--3366602 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3366561 TTAATTAATA
3366571 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
3366586 TAATTTAATAATATTT
1 TAATTTAATAATATTT
3366602 T
1 T
3366603 TATAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:3371093 original size:17 final size:17
Alignment explanation
Indices: 3371073--3371108 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3371063 TTAATTAATA
3371073 TTTATA-AAATTTAAAAT
1 TTTATAGAAA-TTAAAAT
3371090 TTTATAGAAATTAAAAT
1 TTTATAGAAATTAAAAT
3371107 TT
1 TT
3371109 CTGGTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTATAGAAATTAAAAT
Found at i:3389239 original size:2 final size:2
Alignment explanation
Indices: 3389232--3389279 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3389222 ATCGAAATGA
3389232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3389274 AT AT AT
1 AT AT AT
3389280 GATAGTCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3389420 original size:1 final size:1
Alignment explanation
Indices: 3389414--3389440 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3389404 AGGAATGAGG
3389414 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3389441 ATGATCTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3398915 original size:97 final size:97
Alignment explanation
Indices: 3398749--3398944 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 97
3398739 TTTCTTAAAA
* *
3398749 TATAACAGATTTTGTAGTAAGCTTTTGAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
3398814 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
*
3398846 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTTACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
3398911 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
3398943 TA
1 TA
3398945 GGTTTTAGTC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (97 bp):
TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
GATTACATTTTAGTCACTTATGTTTGAAATGT
Found at i:3399358 original size:23 final size:23
Alignment explanation
Indices: 3399324--3399367 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3399314 TTTATCCAAT
*
3399324 TTTTAATAAATAAATTTAATATA
1 TTTTAATAAATAAATATAATATA
* *
3399347 TTTTAATTAATATATATAATA
1 TTTTAATAAATAAATATAATA
3399368 CAAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATAAATAAATATAATATA
Found at i:3401685 original size:74 final size:72
Alignment explanation
Indices: 3401544--3401715 Score: 245
Period size: 74 Copynumber: 2.4 Consensus size: 72
3401534 GAAAATAATC
* *
3401544 ATTAGCGACGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACATCGTTTCCCGAGCTT
1 ATTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACACCGTTTCCCGAGCTT
3401609 TCGGGGA
66 TCGGGGA
* * ***
3401616 ATTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACCATAAGCCCAACGACGCCGTTTTGTGAGC
1 ATTAGCGGCGTTTTTGAGAAAGCGCCAC-AAAAAACC-TAAGCCCAACGACACCGTTTCCCGAGC
3401681 TTTCGGGGA
64 TTTCGGGGA
* *
3401690 TTTAGCGGCGTTTTTAAGAAAGCGCC
1 ATTAGCGGCGTTTTTGAGAAAGCGCC
3401716 GCTAATGCTT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 26 0.30
73 8 0.09
74 54 0.61
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (72 bp):
ATTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACACCGTTTCCCGAGCTT
TCGGGGA
Found at i:3401818 original size:114 final size:114
Alignment explanation
Indices: 3401617--3401920 Score: 470
Period size: 114 Copynumber: 2.7 Consensus size: 114
3401607 TTTCGGGGAA
* * *
3401617 TTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACCATAAGCCCAACGACGCCGTTTTGTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
3401682 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTT-TGGGCT
65 TTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATG-TTCAGGGCT
*
3401732 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
3401797 TCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTCAGGGCT
66 TCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTCAGGGCT
* * *
3401846 TTAGCGGTGTTTTTGAGAAAGCGCTGCAAAAATTA--TAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA-AACCTAAGCCCAACGACGCCGTTTTCTGAGCT
3401909 TTCGGGGATTTA
65 TTCGGGGATTTA
3401921 GCGGCCAAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
113 42 0.24
114 100 0.57
115 34 0.19
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTCAGGGCT
Found at i:3402261 original size:14 final size:14
Alignment explanation
Indices: 3402242--3402273 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3402232 AAGTATGGGT
3402242 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3402256 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3402270 TTAG
1 TTAG
3402274 AGGTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:3402301 original size:7 final size:7
Alignment explanation
Indices: 3402291--3402339 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3402281 GATTTAAGGT
3402291 TTAGGGG
1 TTAGGGG
3402298 TTAGAGGG
1 TTAG-GGG
3402306 TTAGGGG
1 TTAGGGG
3402313 TTTAGGGG
1 -TTAGGGG
*
3402321 TTAGACGTG
1 TTAG--GGG
3402330 TTAGGGG
1 TTAGGGG
3402337 TTA
1 TTA
3402340 AAAGTTAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 16 0.44
8 14 0.39
9 6 0.17
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:3402311 original size:15 final size:15
Alignment explanation
Indices: 3402291--3402339 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
3402281 GATTTAAGGT
3402291 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
3402306 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
3402321 TTAGACGTGTTAGGGG
1 TTAGGGGT-TTAGGGG
3402337 TTA
1 TTA
3402340 AAAGTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:3402315 original size:23 final size:24
Alignment explanation
Indices: 3402288--3402338 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
3402278 TGGGATTTAA
3402288 GGTTTAGGGGTTAGA-GGGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
*
3402311 GGTTTAGGGGTTAGACGTGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
3402335 GGTT
1 GGTT
3402339 AAAAGTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.16, C:0.02, G:0.49, T:0.33
Consensus pattern (24 bp):
GGTTTAGGGGTTAGACGGGTTAGG
Found at i:3402596 original size:21 final size:22
Alignment explanation
Indices: 3402566--3402606 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3402556 AGGGATTATG
*
3402566 GTTTAAGGGTTGGGA-TTTAAT
1 GTTTAAGGGTTAGGAGTTTAAT
*
3402587 GTTTAGGGGTTAGGAGTTTA
1 GTTTAAGGGTTAGGAGTTTA
3402607 GGGGTTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (22 bp):
GTTTAAGGGTTAGGAGTTTAAT
Found at i:3402623 original size:14 final size:13
Alignment explanation
Indices: 3402589--3402637 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
3402579 GATTTAATGT
3402589 TTAGGGGTTAGGAG
1 TTAGGGGTTA-GAG
3402603 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGA-G
3402618 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
3402632 TTAGGG
1 TTAGGG
3402638 ATTTAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:3402645 original size:15 final size:15
Alignment explanation
Indices: 3402625--3402655 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3402615 ATGTTAGGGG
3402625 TTAAGAGTTAGGGAT
1 TTAAGAGTTAGGGAT
*
3402640 TTAAGATTTAGGGAT
1 TTAAGAGTTAGGGAT
3402655 T
1 T
3402656 CAGGGGTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (15 bp):
TTAAGAGTTAGGGAT
Found at i:3402747 original size:303 final size:299
Alignment explanation
Indices: 3402120--3402751 Score: 959
Period size: 303 Copynumber: 2.1 Consensus size: 299
3402110 ATTATTTAAA
* *
3402120 ATAATTGTAAAAGAGATAATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTA
1 ATAATTGTAAAAGAG---ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAA
* *
3402185 TTTAAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGGTTTAGGGAT
63 TTTAAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAAT
*
3402250 TATGGATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTT
128 TATGAATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTT
* * *
3402315 TAGGGGTTAGACGTGTTAGGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTT
193 TAGGGGTTAGACGAGTTAGGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTT
3402380 AGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
258 AGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
3402422 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
* *
3402487 AAGATTTAAGGCTGGTTTAGGAGTTCATATTTTAAGGTTTAGGG-AGTATGGATTTAGGAATTAT
66 AAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTAT
* * *
3402551 GAATTAGGGATTATGGTTTA-AGGGTTGGGATTTAATGTTTAGGGGTTAG-GAGTTTAGGGGTTA
131 GAATTAGGGATTATGGATTAGA-GGTTGGGATTTAAGGTTTAGGGGTTAGAG-GGTTA-GGG---
* * *
3402614 GATGTTAGGGGTTA-A-GAGTTAGGGATTTAAGATTTAGGGATTCAGGGGTCGAGTTAAGGTTTT
190 G-T-TTAGGGGTTAGACGAGTTAGGG-GTTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTT
3402677 GAGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
252 GAGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
* *
3402725 ATAATTGTAAAATAGGTAATAATAAAT
1 ATAATTGTAAAAGAGATAATAATAAAT
3402752 CAAATATATT
Statistics
Matches: 303, Mismatches: 18, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
297 2 0.01
298 66 0.22
299 93 0.31
302 24 0.08
303 108 0.36
304 10 0.03
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.41
Consensus pattern (299 bp):
ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
AAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTAT
GAATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAG
GGGTTAGACGAGTTAGGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGA
TTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
Found at i:3402952 original size:106 final size:106
Alignment explanation
Indices: 3402764--3402961 Score: 308
Period size: 106 Copynumber: 1.9 Consensus size: 106
3402754 AATATATTGA
* * *
3402764 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAAAAATAAAATAAAAATTTTTAGCATA
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
* * *
3402829 GCAAAACGGCGTTATTTTGTTGAAAATTAAATAGCGGCGTT
66 GCAAAACAGCGTCATTTTGTTCAAAATTAAATAGCGGCGTT
* *
3402870 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAATAAATTAAAAAAATTTTAGCAG
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAAT-AAAAAATTTTAGCAG
3402934 AGCAAAACAGCGTCATTTTGTTCAAAAT
65 AGCAAAACAGCGTCATTTTGTTCAAAAT
3402962 GAAAAAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 11 0.13
106 72 0.87
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (106 bp):
TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
GCAAAACAGCGTCATTTTGTTCAAAATTAAATAGCGGCGTT
Found at i:3403021 original size:152 final size:148
Alignment explanation
Indices: 3402858--3403146 Score: 422
Period size: 154 Copynumber: 1.9 Consensus size: 148
3402848 TTGAAAATTA
*
3402858 AATAGCGGCG-TTTTTATAAAAAACGCCGCAAAAAATAAATCAATTTAT-AAA-AAATAAATTAA
1 AATAGCGGCGTTTTTTAT-AAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAA
*
3402920 AAAAATTTTAGCAGAGCAAAACAGCGTCATTTTGTTCAAAATGAAAAAAAATTTGCGGCGTTTTT
65 AAAAATTTTAGCAGAACAAAACAGCGTCATTTTGTTCAAAATG-----AAA-TTGCGGCGTTTTT
3402985 CATAAAAACGCCGCTAAAGGTAAGC
124 CATAAAAACGCCGCTAAAGGTAAGC
*
3403010 AATAGCGGCGTTTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAA
1 AATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAA
* ** * *
3403075 AAAATTTTAGCATAACAAAATGGCGTCATTTTGTTGAAAATGAAATTGCGGCGTTTTTTATAAAA
66 AAAATTTTAGCAGAACAAAACAGCGTCATTTTGTTCAAAATGAAATTGCGGCGTTTTTCATAAAA
3403140 ACGCCGC
131 ACGCCGC
3403147 AAAAAATAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
148 26 0.21
149 3 0.02
152 39 0.31
153 10 0.08
154 48 0.38
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (148 bp):
AATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAA
AAAATTTTAGCAGAACAAAACAGCGTCATTTTGTTCAAAATGAAATTGCGGCGTTTTTCATAAAA
ACGCCGCTAAAGGTAAGC
Found at i:3403126 original size:108 final size:104
Alignment explanation
Indices: 3403014--3403223 Score: 321
Period size: 104 Copynumber: 2.0 Consensus size: 104
3403004 GTAAGCAATA
*
3403014 GCGGCGTTTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAAA
1 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTAT--AA-AAA-AAAATAAAAAAA
* * * *
3403079 TTTTAGCATAACAAAATGGCGTCATTTTGTTGAAAATGAAATT
62 TTTTAGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAATT
*
3403122 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAAATAAAAAATTTTT
1 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAAATAAAAAAATTTT
*
3403187 AGCAGAGCAAAACGACGTCATTTTGTTCAAAATGAAA
66 AGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAA
3403224 AAATTTTTGC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
104 47 0.49
105 3 0.03
106 2 0.02
108 43 0.45
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.28
Consensus pattern (104 bp):
GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAAATAAAAAAATTTT
AGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAATT
Found at i:3403369 original size:57 final size:59
Alignment explanation
Indices: 3403272--3403381 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 59
3403262 TTTTTATAAA
*
3403272 AAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATA-AAATTTTTTTAGCAT
1 AAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATATAAAATTTTTTAGCAT
*
3403330 AAACGCCGCAAAAAATAAATCAATTTATAAAA-AAATAAAATATAAAATTTTT
1 AAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATATAAAATTTTT
3403382 AAATATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
57 10 0.20
58 39 0.80
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (59 bp):
AAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATATAAAATTTTTTAGCAT
Found at i:3404638 original size:30 final size:31
Alignment explanation
Indices: 3404577--3404641 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
3404567 ATCTCCAAAC
* *
3404577 TATATATGAACTTTGATTTTATGTATAATTT
1 TATATAGGAACTTTGATTTTATGAATAATTT
*
3404608 TATATAGGAAC-TTGATTTTGTGCAAT-ATTT
1 TATATAGGAACTTTGATTTTATG-AATAATTT
3404638 TATA
1 TATA
3404642 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATAGGAACTTTGATTTTATGAATAATTT
Found at i:3404814 original size:31 final size:31
Alignment explanation
Indices: 3404778--3404838 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3404768 ATTTTTTTAA
*
3404778 ATGTATATAATTGAA-TCAAAATTAAAGTTTT
1 ATGTATACAATTGAACT-AAAATTAAAGTTTT
* *
3404809 ATGTATACATTTGAACTACAATTAAAGTTT
1 ATGTATACAATTGAACTAAAATTAAAGTTT
3404839 CACGTGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
ATGTATACAATTGAACTAAAATTAAAGTTTT
Found at i:3418330 original size:22 final size:23
Alignment explanation
Indices: 3418278--3418335 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
3418268 TTATAGTAAC
* * *
3418278 AATAAAAATAAGAGAATAATAAG
1 AATAAAGATGAGAGAATAACAAG
3418301 AATAAAGATGAGAGAAT-ACAAG
1 AATAAAGATGAGAGAATAACAAG
3418323 ACAT-AAGATGAGA
1 A-ATAAAGATGAGA
3418336 TGGTTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.62, C:0.03, G:0.19, T:0.16
Consensus pattern (23 bp):
AATAAAGATGAGAGAATAACAAG
Found at i:3423655 original size:20 final size:21
Alignment explanation
Indices: 3423632--3423675 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3423622 AAAAATTACA
3423632 AAAAAATT-AAAATAATTTTC
1 AAAAAATTCAAAATAATTTTC
*
3423652 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTC
3423672 AAAA
1 AAAA
3423676 TTGAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTC
Found at i:3423657 original size:19 final size:19
Alignment explanation
Indices: 3423633--3423703 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
3423623 AAAATTACAA
3423633 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
3423651 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
3423671 TAAAATTGAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
3423690 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
3423704 TAAAGAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 25 0.56
20 16 0.36
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:3423766 original size:9 final size:9
Alignment explanation
Indices: 3423754--3423783 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3423744 TTTTTTGAAT
3423754 TTAAATAAG
1 TTAAATAAG
3423763 TT-AATAAG
1 TTAAATAAG
3423771 TTAAATAAG
1 TTAAATAAG
3423780 TTAA
1 TTAA
3423784 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (9 bp):
TTAAATAAG
Found at i:3427222 original size:20 final size:19
Alignment explanation
Indices: 3427199--3427266 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
3427189 TTACAAATAG
3427199 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTT-AAA
* *
3427219 AATTCAAAATAATTTTTAA
1 AATTTAAAATAATTTTAAA
*
3427238 AATTGAAAAT-ATTTGTAAA
1 AATTTAAAATAATTT-TAAA
3427257 AATTCTAAAA
1 AATT-TAAAA
3427267 ATTCTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTAAAATAATTTTAAA
Found at i:3427258 original size:19 final size:19
Alignment explanation
Indices: 3427199--3427276 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
3427189 TTACAAATAG
*
3427199 AATTTAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
3427219 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
*
3427238 AATTGAAAAT-ATTTGTAAA
1 AATTCAAAATAATTT-TAAA
* *
3427257 AATTCTAAA-AATTCTAAA
1 AATTCAAAATAATTTTAAA
3427275 AA
1 AA
3427277 AAAAAGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 10 0.20
19 24 0.49
20 15 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:3430742 original size:40 final size:40
Alignment explanation
Indices: 3430691--3430771 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3430681 AATTAGTAAA
3430691 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3430731 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3430771 T
1 T
3430772 CGAGAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
Found at i:3430782 original size:40 final size:40
Alignment explanation
Indices: 3430688--3430782 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
3430678 TTAAATTAGT
*
3430688 AAATT-GAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
* *
3430727 AAATTTGAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
3430767 AAATTCGAGA-AAAATA
1 AAATTCGA-ATAAAATA
3430783 GAAATTTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 5 0.10
40 46 0.88
41 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (40 bp):
AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
Found at i:3444426 original size:6 final size:6
Alignment explanation
Indices: 3444415--3444505 Score: 102
Period size: 6 Copynumber: 16.0 Consensus size: 6
3444405 ACAATTACAC
* *
3444415 ATTTTA ATTTTA ATTTTA ATTTTT ATTTTT A-TTT- ATTTTA A-TTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
* * *
3444460 ATTTTT A-TAT- ATTTTA ATTTTA ATTTTA ATTTTA ATTTTT ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
3444506 CATGTAGACA
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
4 2 0.03
5 15 0.20
6 57 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:3444465 original size:21 final size:22
Alignment explanation
Indices: 3444427--3444505 Score: 97
Period size: 21 Copynumber: 3.5 Consensus size: 22
3444417 TTTAATTTTA
*
3444427 ATTTTAATTTTTATTTTTATTT
1 ATTTTAATTTTAATTTTTATTT
*
3444449 ATTTTAA-TTTAATTTTTATAT
1 ATTTTAATTTTAATTTTTATTT
*
3444470 ATTTTAATTTTAATTTTAATTTT
1 ATTTTAATTTTAATTTTTA-TTT
*
3444493 AATTTTTATTTTA
1 -ATTTTAATTTTA
3444506 CATGTAGACA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 19 0.39
22 17 0.35
23 2 0.04
24 11 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTAATTTTAATTTTTATTT
Found at i:3450069 original size:46 final size:46
Alignment explanation
Indices: 3450002--3450094 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
3449992 CCACTGAGAG
3450002 AAGATTTTTCTTCATACCTAGGACATGGTAGACATTTTAGAGTGAC
1 AAGATTTTTCTTCATACCTAGGACATGGTAGACATTTTAGAGTGAC
3450048 AAGATTTTTCTTCATACCTAGGACATGGTAGACATTTTAGAGTGAC
1 AAGATTTTTCTTCATACCTAGGACATGGTAGACATTTTAGAGTGAC
3450094 A
1 A
3450095 CCTCGGTATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (46 bp):
AAGATTTTTCTTCATACCTAGGACATGGTAGACATTTTAGAGTGAC
Found at i:3454066 original size:46 final size:47
Alignment explanation
Indices: 3453891--3454290 Score: 635
Period size: 47 Copynumber: 8.6 Consensus size: 47
3453881 ATTCATGAAT
* ** ** *
3453891 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
3453938 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
3453985 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
* *
3454032 TTGGACAGCAT-TATGTAACAAATTGGGCAACATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
* *
3454078 TTGGACAGCAT-TATGTAACAAATTGGGCAACTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
3454124 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
3454171 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
* *
3454217 TTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
*
3454264 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
3454291 TTCAACTCAT
Statistics
Matches: 334, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
46 134 0.40
47 200 0.60
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTATGCATCAAAA
Found at i:3454140 original size:93 final size:94
Alignment explanation
Indices: 3453891--3454290 Score: 635
Period size: 93 Copynumber: 4.3 Consensus size: 94
3453881 ATTCATGAAT
* ** **
3453891 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3453956 ACAAATTGGGCAGCATTTAGGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
3453985 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
* *
3454049 ACAAATTGGGCAACATTTAAGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
* * *
3454078 TTGGACAGCAT-TATGTAACAAATTGGGCAACTTTTATGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3454142 ATAAATTGGGCAGCATTTATGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
* *
3454171 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATAAATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3454235 ATAAATTGGGCAGCATTTATGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
*
3454264 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
3454291 TTCAACTCAT
Statistics
Matches: 287, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
92 43 0.15
93 177 0.62
94 67 0.23
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (94 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
ACAAATTGGGCAGCATTTATGCATCAAAA
Found at i:3455197 original size:43 final size:43
Alignment explanation
Indices: 3455131--3455246 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
3455121 AACTCGTACA
* *
3455131 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
*
3455174 ATGCC-ACTGTCCCAGACAG-GGTCTTAGACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
*
3455217 ATGCCAACGTCCCAAACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
3455247 ATGATTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
42 4 0.06
43 56 0.89
44 3 0.05
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:3455507 original size:15 final size:16
Alignment explanation
Indices: 3455475--3455507 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3455465 AGTGGGAGAA
3455475 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
3455492 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
3455507 T
1 T
3455508 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:3460311 original size:15 final size:16
Alignment explanation
Indices: 3460279--3460311 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3460269 AGTGGGAGAA
3460279 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
3460296 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
3460311 T
1 T
3460312 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:3467670 original size:6 final size:6
Alignment explanation
Indices: 3467655--3467732 Score: 54
Period size: 6 Copynumber: 12.5 Consensus size: 6
3467645 TGAAATGATA
* * *
3467655 TTTT-T TTTTCT TTTTCT TTTTCT TTTTGAT TCTTT-T ATTCCT TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT T-TTTCT TTTTCT TTTTCT
3467702 TTATTCT TTTTCT TATTCTCT TTCTTCT TTT
1 TT-TTCT TTTTCT T-TT-TCT TT-TTCT TTT
3467733 AACCCTAGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
5 9 0.15
6 29 0.49
7 13 0.22
8 8 0.14
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:3480714 original size:16 final size:17
Alignment explanation
Indices: 3480675--3480727 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
3480665 TTTTTAAAAA
* *
3480675 AATATTTTAAAAAATAT
1 AATATTTTTACAAATAT
3480692 AATATTTTTACAAATAT
1 AATATTTTTACAAATAT
*
3480709 -ATATTTTTACAAAGAT
1 AATATTTTTACAAATAT
3480725 AAT
1 AAT
3480728 GAATTTTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTTTTACAAATAT
Found at i:3480716 original size:17 final size:16
Alignment explanation
Indices: 3480686--3480726 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3480676 ATATTTTAAA
3480686 AAATATAATATTTTTAC
1 AAATATAA-ATTTTTAC
*
3480703 AAATATATATTTTTAC
1 AAATATAAATTTTTAC
*
3480719 AAAGATAA
1 AAATATAA
3480727 TGAATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATATAAATTTTTAC
Found at i:3480781 original size:3 final size:3
Alignment explanation
Indices: 3480773--3480798 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3480763 CCCCTTTAAA
3480773 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
3480799 TATTTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3483302 original size:18 final size:17
Alignment explanation
Indices: 3483276--3483313 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3483266 CACTCTAGAC
*
3483276 ATATTTTTTAATATTTTT
1 ATATATTTTAA-ATTTTT
3483294 ATATATTTTAAATTTTT
1 ATATATTTTAAATTTTT
3483311 ATA
1 ATA
3483314 ACATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATATTTTAAATTTTT
Found at i:3483580 original size:9 final size:9
Alignment explanation
Indices: 3483568--3483605 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3483558 GTGTTATACG
3483568 TTTTATATA
1 TTTTATATA
*
3483577 TTTT-TAGA
1 TTTTATATA
*
3483585 TTTTATTTA
1 TTTTATATA
3483594 TTTTATATA
1 TTTTATATA
3483603 TTT
1 TTT
3483606 GGACAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTATATA
Found at i:3485848 original size:11 final size:11
Alignment explanation
Indices: 3485829--3485858 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3485819 AATGCATTGC
3485829 TAATATTTTTT
1 TAATATTTTTT
*
3485840 TATTATTTTTT
1 TAATATTTTTT
3485851 TAATATTT
1 TAATATTT
3485859 CAAAAAGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TAATATTTTTT
Found at i:3485938 original size:30 final size:32
Alignment explanation
Indices: 3485897--3485984 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
3485887 TAGAAACAGT
3485897 ACATA-AA-TCTTAAAAGTTAACAATGAC-A-
1 ACATAGAAGTCTTAAAAGTTAACAATGACAAC
**
3485925 ACATAGAAGTCTTAAAAGTTTAA-AAAAACAAC
1 ACATAGAAGTCTTAAAAG-TTAACAATGACAAC
* *
3485957 ACAAAGTAAGTCTTGAAAGTTAACAATG
1 ACATAG-AAGTCTTAAAAGTTAACAATG
3485985 GTAGAACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 13 0.28
31 5 0.11
32 9 0.19
33 13 0.28
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (32 bp):
ACATAGAAGTCTTAAAAGTTAACAATGACAAC
Found at i:3487213 original size:23 final size:22
Alignment explanation
Indices: 3487185--3487248 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3487175 AACACGAAAT
* *
3487185 TTTGTGAAACCTTTGTGGCGTAA
1 TTTGTGAAGCCTTTGTGGCAT-A
* *
3487208 TTTGTGACGCCTTTGTAGCATA
1 TTTGTGAAGCCTTTGTGGCATA
3487230 TTCTGTGAAGCCTTTGTGG
1 TT-TGTGAAGCCTTTGTGG
3487249 TCTGGTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (22 bp):
TTTGTGAAGCCTTTGTGGCATA
Found at i:3489815 original size:89 final size:89
Alignment explanation
Indices: 3489664--3489841 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
3489654 CTCCAACATG
3489664 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3489729 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3489753 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3489818 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3489842 CTATCATAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (89 bp):
AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
CATTTAACAACCTAACCATTCCAA
Found at i:3495504 original size:74 final size:74
Alignment explanation
Indices: 3495377--3495514 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 74
3495367 ACCAATTTTA
* * *
3495377 TTTTACTTTAATATTTTGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAAGTCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATG-AAGGCTTCTT
3495442 CCATCGTGTT
65 CCATCGTGTT
** *
3495452 TTTTA-TTTAATAATTCGACCGAAAGGT-ATCTATTAGGGGTAAAAGTGGAAATGAAGGCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGA-AGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTT
3495515 ATAGATGACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
73 10 0.18
74 41 0.73
75 5 0.09
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTTC
CATCGTGTT
Found at i:3495645 original size:7 final size:7
Alignment explanation
Indices: 3495633--3495675 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
3495623 ATGTTAGAAA
3495633 TTTAAAT
1 TTTAAAT
3495640 TTTAAATT
1 TTTAAA-T
3495648 TTTAAATTT
1 TTTAAA--T
3495657 TTTAAAT
1 TTTAAAT
*
3495664 TTTAAAA
1 TTTAAAT
3495671 TTTAA
1 TTTAA
3495676 GTTTAATTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 18 0.55
8 7 0.21
9 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:3495652 original size:8 final size:8
Alignment explanation
Indices: 3495633--3495673 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
3495623 ATGTTAGAAA
3495633 TTTAAA-T
1 TTTAAATT
3495640 TTTAAATT
1 TTTAAATT
3495648 TTTAAATTT
1 TTTAAA-TT
3495657 TTTAAATT
1 TTTAAATT
*
3495665 TTAAAATT
1 TTTAAATT
3495673 T
1 T
3495674 AAGTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
7 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTAAATT
Found at i:3495661 original size:17 final size:17
Alignment explanation
Indices: 3495639--3495673 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3495629 GAAATTTAAA
*
3495639 TTTTAAATTTTTAAATT
1 TTTTAAATTTTAAAATT
3495656 TTTTAAATTTTAAAATT
1 TTTTAAATTTTAAAATT
3495673 T
1 T
3495674 AAGTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTTAAAATT
Found at i:3498343 original size:62 final size:65
Alignment explanation
Indices: 3498238--3498379 Score: 184
Period size: 62 Copynumber: 2.2 Consensus size: 65
3498228 TACAAGTTTA
* * * *
3498238 TTGAGCTGAACTTAATATTATGAATTTCATATATATATGTGGTTCGAATATATA-TT-CAAGTT-
1 TTGAGCTGAACTTAATAGTATGAATTTCATATACATATATGGTTCGAATAT-TAGTTACAAATTC
3498300 C
65 C
* *
3498301 TTGAGCTGAATTTAAT-GTATGAATTTTATATACATATATGGTTCGAATATTAGTTACAAATTCC
1 TTGAGCTGAACTTAATAGTATGAATTTCATATACATATATGGTTCGAATATTAGTTACAAATTCC
*
3498365 TTGAGCTGAAGTTAA
1 TTGAGCTGAACTTAA
3498380 AGTTGTGAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 2 0.03
62 32 0.46
63 20 0.29
64 15 0.22
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (65 bp):
TTGAGCTGAACTTAATAGTATGAATTTCATATACATATATGGTTCGAATATTAGTTACAAATTCC
Found at i:3498584 original size:41 final size:40
Alignment explanation
Indices: 3498527--3498640 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
3498517 TGAGATTTTT
3498527 AGACTTTACGTCTAGCATGCTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTGAAATATTTC
3498568 AGACTTTACGTCTAGCAGACTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAG-CTTAATGCCGGTGAAATATTTC
* *
3498609 AGACCTTACGTCTAGCAGGTTTAATGCCGGTG
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTG
3498641 TATTGAATCA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
40 1 0.01
41 67 0.97
42 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (40 bp):
AGACTTTACGTCTAGCAGCTTAATGCCGGTGAAATATTTC
Found at i:3503697 original size:2 final size:2
Alignment explanation
Indices: 3503690--3503716 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3503680 TTATAACCGA
3503690 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3503717 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3504085 original size:41 final size:41
Alignment explanation
Indices: 3504051--3504170 Score: 186
Period size: 41 Copynumber: 2.9 Consensus size: 41
3504041 ACTGGCACTT
* * * *
3504051 AGCCTGCTAGACATAAAGTTTGAAATATTTCACTGGCGTCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
3504092 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
* *
3504133 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCGGCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCA
3504171 ATAAACCTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:3520604 original size:3 final size:3
Alignment explanation
Indices: 3520542--3520584 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3520532 CAAGATATAG
3520542 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3520585 CTTATTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3521323 original size:13 final size:13
Alignment explanation
Indices: 3521307--3521333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3521297 AAAAAAGGGT
3521307 ATAAAACAAAATA
1 ATAAAACAAAATA
3521320 ATAAAACAAAATA
1 ATAAAACAAAATA
3521333 A
1 A
3521334 AATGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAACAAAATA
Found at i:3522227 original size:132 final size:132
Alignment explanation
Indices: 3522084--3522551 Score: 697
Period size: 132 Copynumber: 3.5 Consensus size: 132
3522074 TTACTTCCCT
* * *
3522084 ACTATCTTGGGAAGATAAGATTCACCGTATTTGATCTGCTCCACTACTACTTAGGGAT-ACAGAA
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGG-TGACAGAA
*
3522148 TCTACAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGG-TTCAAATCTGCTT
65 TCTGCAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT-AAATCTGCTT
*
3522212 CTCG
129 CTCC
* * *
3522216 ACTATCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCATTACTGCTTAGGGTGACAGAAT
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAAT
* * * * *
3522281 CTGTAATCTTCGACCTACTCTACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
3522346 CC
131 CC
* * * * *
3522348 AATGTCTTGGGAAGATAAAATTTACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAAT
* *
3522413 CTGCAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGATTCT
66 CTGCAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
3522478 CC
131 CC
* * *
3522480 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAAAAT
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAAT
3522545 CTGCAAT
66 CTGCAAT
3522552 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 301 0.99
133 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (132 bp):
ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAAT
CTGCAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:3522825 original size:100 final size:100
Alignment explanation
Indices: 3522652--3523215 Score: 925
Period size: 100 Copynumber: 5.7 Consensus size: 100
3522642 NNNNNNNNNN
* *
3522652 AATCTGTTCTGCTGCATCGCCTGGGACGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
3522717 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
66 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
* *
3522752 AATCTGTTCTGCTGCATCGCCTGGGATGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
3522817 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
66 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
* * *
3522852 AATCTGTTCCGCTGCATCACCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGAATTAC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
*
3522917 AATGTCGAGGAAGGGAGATTCGCCGTCGTAGCTTC
66 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
* *
3522952 AATCTGTTCCGCTGCATCGCCT-AGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTTC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
* **
3523016 AATGTCGAGGAAGTGAGATTCACCGTCGTAGCTTC
66 AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
* *
3523051 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTGC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
* *
3523116 AATGTCGAGGAAGTGAG-TTTCGCTGTCGTAGCTTC
66 AATGTCGAGGAAGGGAGATTT-GCCGTCGTAGCTTC
* * *
3523151 AATTTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTGGCTTCGATCTTTTGAATTGC
1 AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
3523216 TAGGGAAGCA
Statistics
Matches: 439, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
99 96 0.22
100 343 0.78
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (100 bp):
AATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTGAATTGC
AATGTCGAGGAAGGGAGATTTGCCGTCGTAGCTTC
Found at i:3523200 original size:50 final size:50
Alignment explanation
Indices: 3522656--3523200 Score: 231
Period size: 50 Copynumber: 10.9 Consensus size: 50
3522646 NNNNNNAATC
* * * *
3522656 TGTTCTGCTGCATCGCCTGGGACGTAAGATTCACCGTTGTGGCTTCGATCT
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT-T
**** * ** * * * *
3522707 T-TTGAATTGCAAT-GTC-GAGGAAGGGAGATTTGCCGTCGTAGCTTCAATC
1 TGTTCCGCTGC-ATCGCCTG-GGAAGTAAGATTCGCCGTTGTGGCTTCAATT
* * * *
3522756 TGTTCTGCTGCATCGCCTGGGATGTAAGATTCACCGTTGTGGCTTCGATCT
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT-T
**** * ** * * * *
3522807 T-TTGAATTGCAAT-GTC-GAGGAAGGGAGATTTGCCGTCGTAGCTTCAATC
1 TGTTCCGCTGC-ATCGCCTG-GGAAGTAAGATTCGCCGTTGTGGCTTCAATT
* *
3522856 TGTTCCGCTGCATCACCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT-T
**** * * ** * * *
3522907 T-TTGAATTACAAT-GTC-GAGGAAGGGAGATTCGCCGTCGTAGCTTCAATC
1 TGTTCCGCTGC-ATCGCCTG-GGAAGTAAGATTCGCCGTTGTGGCTTCAATT
* * *
3522956 TGTTCCGCTGCATCGCCT-AGAAGTAAGATTCACCGTTGTGGCTTCGATCT
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT-T
**** * * * * * * *
3523006 T-TTGAATTTCAAT-GTC-GAGGAAGTGAGATTCACCGTCGTAGCTTCAATC
1 TGTTCCGCTGC-ATCGCCTG-GGAAGTAAGATTCGCCGTTGTGGCTTCAATT
3523055 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAAT-T
**** * * * * * *
3523106 T-TTGAATTGCAAT-GTC-GAGGAAGTGAGTTTCGCTGTCGTAGCTTCAATT
1 TGTTCCGCTGC-ATCGCCTG-GGAAGTAAGATTCGCCGTTGTGGCTTCAATT
*
3523155 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTGGCTTC
1 TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTC
3523201 GATCTTTTGA
Statistics
Matches: 340, Mismatches: 124, Indels: 61
0.65 0.24 0.12
Matches are distributed among these distances:
49 49 0.14
50 275 0.81
51 16 0.05
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (50 bp):
TGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATT
Found at i:3523287 original size:95 final size:95
Alignment explanation
Indices: 3523143--3523692 Score: 744
Period size: 95 Copynumber: 5.8 Consensus size: 95
3523133 TTTCGCTGTC
* * * * * * * *
3523143 GTAGCTTCAATTTGTTCCGCTGCATCGCCT-GGGAAGTAAGATTCGCTGTTGTGGCTTCGATCTT
1 GTAGCTTCAATCTGTTCCACTGCAAC-ACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
* * *
3523207 TTGAATTGCTAGGGAAGCAAGATCCGCTGCT
65 TTTAACTGCCAGGGAAGCAAGATCCGCTGCT
* * * *
3523238 GTAGCTTCAATCCGTTTCACTGCAACACTAGGAAAATAAGATCCGCTGTTGTAACTTCAATCTTT
1 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
* *
3523303 TTAACTGCCGGGGAAGCAAGATCCGCTGTT
66 TTAACTGCCAGGGAAGCAAGATCCGCTGCT
*
3523333 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTTTAGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
* *
3523398 TTAACTACCGGGGAAGCAAGATCCGCTGCT
66 TTAACTGCCAGGGAAGCAAGATCCGCTGCT
** ** *
3523428 GTAGCTTCAATCTGTTCCACTATAATGCTAGGAAAGTAAGATCCGCTGTTGTAGTTTCAATCTTT
1 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
*
3523493 TTAACTGTCAGGGAAGCAAGATCCGCTGCT
66 TTAACTGCCAGGGAAGCAAGATCCGCTGCT
* * * *
3523523 GTAGCTTCAATCCGTTTCACTACAACACTAGGAAAATAAGATCCGCTGTTGTAGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
* *
3523588 TTAATTGCCAGGGAAGTAAGATCCGCTGCT
66 TTAACTGCCAGGGAAGCAAGATCCGCTGCT
* * *
3523618 ATAGCTTCAATCTGTTCCATTGCAACGA-TAGGAAAGTAAGATCCGCTATTGTAGCTTCAATCTT
1 GTAGCTTCAATCTGTTCCACTGCAAC-ACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
3523682 TTTAATTGCCA
65 TTTAACTGCCA
3523693 TCTATGGTTT
Statistics
Matches: 403, Mismatches: 50, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
94 2 0.00
95 400 0.99
96 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (95 bp):
GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
TTAACTGCCAGGGAAGCAAGATCCGCTGCT
Found at i:3525856 original size:12 final size:12
Alignment explanation
Indices: 3525830--3525868 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3525820 TGACCTCTCC
*
3525830 TTTTTCT-TTTC
1 TTTTTCTCTTTT
3525841 TTTTTCTCTTTT
1 TTTTTCTCTTTT
3525853 TTTTTCTCTTATT
1 TTTTTCTCTT-TT
3525866 TTT
1 TTT
3525869 GAATTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 7 0.28
12 13 0.52
13 5 0.20
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:3525917 original size:7 final size:7
Alignment explanation
Indices: 3525907--3525941 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
3525897 TTGACTTTGA
3525907 TTTTTCT
1 TTTTTCT
3525914 TTTTTCT
1 TTTTTCT
3525921 TTTCCTTCT
1 TTT--TTCT
3525930 TTTTTCT
1 TTTTTCT
3525937 TTTTT
1 TTTTT
3525942 TTTATGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 19 0.73
9 7 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:3528706 original size:107 final size:106
Alignment explanation
Indices: 3528545--3528743 Score: 303
Period size: 108 Copynumber: 1.9 Consensus size: 106
3528535 TTGAAATTCA
3528545 AAAGGATATTTGACTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACG-TTCCTC
1 AAAGGATATTTGACTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTCCTC
* *
3528609 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTG
* * *
3528650 AAAGGATATTCTG-CTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTT
1 AAAGGATATT-TGACTATTTGGTTAAACGAG--AAATCGAAACCCAACACATTAGGGCACGTTTC
*
3528714 CTCGAATTTCCAAACGCAAAATATTACCTT
63 CTCGAATTTCCAAACGCAAAACATTACCTT
3528744 TATTATTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
105 26 0.31
106 2 0.02
107 27 0.32
108 29 0.35
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (106 bp):
AAAGGATATTTGACTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTG
Found at i:3529602 original size:3 final size:3
Alignment explanation
Indices: 3529540--3529582 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3529530 CAAGATATAG
3529540 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3529583 CTTATTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3530266 original size:13 final size:13
Alignment explanation
Indices: 3530248--3530274 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3530238 AAAAAAGGGT
3530248 ATAAAACAAAATA
1 ATAAAACAAAATA
3530261 ATAAAACAAAATA
1 ATAAAACAAAATA
3530274 A
1 A
3530275 AATGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAACAAAATA
Found at i:3540748 original size:13 final size:13
Alignment explanation
Indices: 3540726--3540758 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3540716 CCCCATATAC
*
3540726 AGATAAATATAAT
1 AGATACATATAAT
3540739 AGATACATATAAT
1 AGATACATATAAT
3540752 AGATACA
1 AGATACA
3540759 AATATACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (13 bp):
AGATACATATAAT
Found at i:3548236 original size:27 final size:26
Alignment explanation
Indices: 3548206--3548262 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
3548196 AATTTCGAGG
*
3548206 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
3548232 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
3548259 TTTA
1 TTTA
3548263 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:3548420 original size:22 final size:24
Alignment explanation
Indices: 3548376--3548420 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
3548366 AATTTAAAAA
3548376 ATAAAACATAATATAATATTTATC
1 ATAAAACATAATATAATATTTATC
*
3548400 ATAAAA-ATAA-ATATTATTTAT
1 ATAAAACATAATATAATATTTAT
3548421 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAACATAATATAATATTTATC
Done.