Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_pilon, whole genome shotgun sequence
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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 29
Found at i:3727941 original size:8 final size:8
Alignment explanation
Indices: 3727928--3727968 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3727918 CTCATTTTCA
3727928 GAGAATTT
1 GAGAATTT
3727936 GAGAATTT
1 GAGAATTT
*
3727944 -AGAGTTT
1 GAGAATTT
*
3727951 GGGAATTT
1 GAGAATTT
3727959 GAGAATTT
1 GAGAATTT
3727967 GA
1 GA
3727969 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:3728668 original size:127 final size:128
Alignment explanation
Indices: 3728049--3728903 Score: 1501
Period size: 128 Copynumber: 6.7 Consensus size: 128
3728039 ACTATTCACA
*
3728049 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
3728114 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
3728177 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
3728242 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
3728305 TGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
3728370 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
3728433 TGAAGGCGTGTTCTCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCA-T----TA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
3728493 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACTTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
3728556 TGAAGGCTCG-TCCCGGGGGCGCACCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
3728620 TTATGTCACTCATGTCCCTCGGAGACACTATTTATATCAGTACCTATTATTTCTCAAGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
3728683 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT-TTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
3728747 TTATGTCACTCATGTCCCTCGGAGACACTATTCATATCAGTACTTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
3728810 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATT-TTTTGTCAGATAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
3728874 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
3728904 GATGGATTGT
Statistics
Matches: 695, Mismatches: 26, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
122 44 0.06
123 73 0.11
127 253 0.36
128 325 0.47
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:3729338 original size:34 final size:34
Alignment explanation
Indices: 3729299--3729405 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
3729289 TAAGTTGAAA
* *
3729299 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
3729333 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
3729367 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
3729401 TTTAA
1 TTTAA
3729406 AAATATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:3729955 original size:21 final size:21
Alignment explanation
Indices: 3729925--3729996 Score: 103
Period size: 21 Copynumber: 3.4 Consensus size: 21
3729915 TATGGTATAA
*
3729925 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
3729946 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
3729967 AACCCTGCGGGCTTA-GAATGT
1 AACCCTGCGGGC-TAGGAATGT
3729988 AACCCTGCG
1 AACCCTGCG
3729997 AAGATGGCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
20 3 0.06
21 39 0.83
22 5 0.11
ACGTcount: A:0.22, C:0.26, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:3730048 original size:21 final size:21
Alignment explanation
Indices: 3730001--3730044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3729991 CCTGCGAAGA
*
3730001 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
3730022 TGGCATATGAAGTGGAGGG-T
1 TGGCATATGAACTGGAGGGCT
3730042 TGG
1 TGG
3730045 GCATGTACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.20, C:0.09, G:0.43, T:0.27
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:3731624 original size:17 final size:18
Alignment explanation
Indices: 3731604--3731638 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3731594 ATAAATTCAT
*
3731604 AATAACTTTAAA-ATAAA
1 AATAAATTTAAATATAAA
3731621 AATAAATTTAAATATAAA
1 AATAAATTTAAATATAAA
3731639 TTCATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAATTTAAATATAAA
Found at i:3733383 original size:12 final size:13
Alignment explanation
Indices: 3733365--3733398 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3733355 TATTAGAAAA
3733365 ATAAAAATTTAAT
1 ATAAAAATTTAAT
*
3733378 -TAAAAAATTAAT
1 ATAAAAATTTAAT
3733390 ATAAAAATT
1 ATAAAAATT
3733399 ATTTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAAAATTTAAT
Found at i:3738003 original size:31 final size:31
Alignment explanation
Indices: 3737967--3738026 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3737957 AACTTAAAAG
* *
3737967 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
3737998 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
3738027 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3740520 original size:228 final size:232
Alignment explanation
Indices: 3740081--3740535 Score: 634
Period size: 228 Copynumber: 2.0 Consensus size: 232
3740071 CTCCCAAGCG
* *
3740081 TCAAGGGAAGAAGGGATTTGAGAAGAAGACACTCAAACGATATGCAGGAGAGAATGATTGCCCGG
1 TCAAGGGAAGAAGGGATTTGAGAAGAAGACACTCAAACGACATGCAGGAGAGAATGAATGCCCGG
* *
3740146 ATGGTAAAGTGAGGAAGAAGCGCAAGCGCAAGCGCGGAAGACGACCCAAGGTACTGGGCAATGAC
66 ATGGTAAAGTGAGG-AGAA-CGCAAGCGCAAGCGCGGAAGACCACCCAAGCTACTGGGCAATGAC
* * * *
3740211 GGGTCTGTAAAGAAAGGATTTATTATAGAAGCAGGAGAGAGTGATTGCTTTGATGAGGATACAAC
129 GGGTCTGTAAAGAAAGGATTTAGTATAGAAGCAGGAGAGAGTAATTGCTCTGATGAGAATACAAC
*
3740276 TATGGAATCTAAGGGTAAGCGTGGAAGACCACCCAAGTT
194 TAAGGAATCTAAGGGTAAGCGTGGAAGACCACCCAAGTT
* * * * * *
3740315 TCAAGGGAAGACGGGGTTTGAGAGGAAGACACTCGAGC-AGCATGTAGGAGAGAATGAATGCCCA
1 TCAAGGGAAGAAGGGATTTGAGAAGAAGACACTCAAACGA-CATGCAGGAGAGAATGAATGCCC-
* *
3740379 GG-TGGTAAAGTGA-G-GAA-G-AAGCGCAAGCGTGGAAGGCCACCCAAGCTACTGGGCAATGAC
64 GGATGGTAAAGTGAGGAGAACGCAAGCGCAAGCGCGGAAGACCACCCAAGCTACTGGGCAATGAC
* * *
3740439 GGGTCTGTAAAGAAAGGATTTAGTATAGAAGCAGGGGAGAGTAATTGCTCTGTTGAGAATACAGC
129 GGGTCTGTAAAGAAAGGATTTAGTATAGAAGCAGGAGAGAGTAATTGCTCTGATGAGAATACAAC
* *
3740504 TAAGGAGTCTAAGGGTAAGCGTGGTAGACCAC
194 TAAGGAATCTAAGGGTAAGCGTGGAAGACCAC
3740536 GGAAGGTGCA
Statistics
Matches: 197, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
228 125 0.63
229 1 0.01
231 3 0.02
233 2 0.01
234 64 0.32
235 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (232 bp):
TCAAGGGAAGAAGGGATTTGAGAAGAAGACACTCAAACGACATGCAGGAGAGAATGAATGCCCGG
ATGGTAAAGTGAGGAGAACGCAAGCGCAAGCGCGGAAGACCACCCAAGCTACTGGGCAATGACGG
GTCTGTAAAGAAAGGATTTAGTATAGAAGCAGGAGAGAGTAATTGCTCTGATGAGAATACAACTA
AGGAATCTAAGGGTAAGCGTGGAAGACCACCCAAGTT
Found at i:3754997 original size:20 final size:20
Alignment explanation
Indices: 3754972--3755060 Score: 92
Period size: 20 Copynumber: 4.4 Consensus size: 20
3754962 AACTAAAACC
3754972 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
3754992 TGTTGCGAAAATAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
3755012 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * *
3755032 AGTTGTGAATTTAAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
3755053 TGTTGCGA
1 TGTTGCGA
3755061 GGAAATCGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
19 6 0.11
20 37 0.66
21 13 0.23
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:3757407 original size:28 final size:28
Alignment explanation
Indices: 3757348--3757407 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3757338 GGAAAATATT
**
3757348 TATATATTTTCTTTAAAAAATTTAAATT
1 TATATATTTTCTTTAAAAAATTTAAAAA
* *
3757376 TATATAATTTTTTTTACAAAA-TTAAAAA
1 TATAT-ATTTTCTTTAAAAAATTTAAAAA
3757404 TATA
1 TATA
3757408 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TATATATTTTCTTTAAAAAATTTAAAAA
Found at i:3758889 original size:29 final size:29
Alignment explanation
Indices: 3758854--3758935 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3758844 AAACTAAATT
*
3758854 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3758883 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3758912 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3758936 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3763657 original size:29 final size:29
Alignment explanation
Indices: 3763622--3763703 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3763612 AAACTAAATT
*
3763622 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3763651 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3763680 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3763704 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3767394 original size:14 final size:15
Alignment explanation
Indices: 3767375--3767421 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3767365 TATAAGGTAA
3767375 TTTTATTATAATT-T
1 TTTTATTATAATTAT
*
3767389 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
3767404 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
3767420 TT
1 TT
3767422 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 3 0.11
16 13 0.46
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:3769559 original size:64 final size:64
Alignment explanation
Indices: 3769490--3769648 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 64
3769480 TTGAAGGTGT
** ***
3769490 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
3769553 C
64 C
* * *
3769554 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
* *
3769618 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
3769649 TTTCATTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:3770396 original size:31 final size:31
Alignment explanation
Indices: 3770303--3770396 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
3770293 AGGGTCGAGG
3770303 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3770334 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
3770365 GTTTACCTAGGTTCTTCTGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3770396 G
1 G
3770397 GTCTTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3773983 original size:64 final size:64
Alignment explanation
Indices: 3773914--3774072 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
3773904 TTGAAGGTGT
** ***
3773914 ATCGATGCATTTGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
3773977 C
64 C
* * * *
3773978 ATCGATGCATAAGTAGTGTATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
* *
3774042 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
3774073 TTTCATTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 77 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:3774819 original size:31 final size:31
Alignment explanation
Indices: 3774727--3774820 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
3774717 AGGGTCGAGG
*
3774727 GTTTACCTATGTTCTTCGGGA-CATATGGACA
1 GTTTACCTATGTTCTTCGGGATC-TATGGACT
*
3774758 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGATCTATGGACT
*
3774789 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTATGTTCTTCGGGATCTATGGACT
3774820 G
1 G
3774821 GTCTATCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATCTATGGACT
Found at i:3778708 original size:21 final size:21
Alignment explanation
Indices: 3778683--3778726 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3778673 AACAATTAAG
3778683 ATCATATAAACATCATAAATT
1 ATCATATAAACATCATAAATT
* * *
3778704 ATCATATTAATATCGTAAATT
1 ATCATATAAACATCATAAATT
3778725 AT
1 AT
3778727 TTGATTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (21 bp):
ATCATATAAACATCATAAATT
Found at i:3778724 original size:68 final size:68
Alignment explanation
Indices: 3778615--3778749 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
3778605 CATGTAGATC
*
3778615 ATCATATAAACATCATAATTTACCATATTAATATCGTAAATTATTTGATTAATAGTATAACAATT
1 ATCATATAAACATCATAAATTACCATATTAATATCGTAAATTATTTGATTAATAGTATAACAATT
3778680 AAG
66 AAG
* * *
3778683 ATCATATAAACATCATAAATTATCATATTAATATCGTAAATTATTTGATTAATAGTTTAACAGTT
1 ATCATATAAACATCATAAATTACCATATTAATATCGTAAATTATTTGATTAATAGTATAACAATT
3778748 AA
66 AA
3778750 TATCGATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (68 bp):
ATCATATAAACATCATAAATTACCATATTAATATCGTAAATTATTTGATTAATAGTATAACAATT
AAG
Found at i:3779837 original size:16 final size:16
Alignment explanation
Indices: 3779795--3779837 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3779785 TAAATTTTGA
3779795 TTTATATATTTATATTT
1 TTTAT-TATTTATATTT
* **
3779812 TTAAAGATTTATATTT
1 TTTATTATTTATATTT
3779828 TTTATTATTT
1 TTTATTATTT
3779838 TGATACTTTA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTATTATTTATATTT
Found at i:3790953 original size:2 final size:2
Alignment explanation
Indices: 3790941--3790981 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3790931 AAGAATAAAA
3790941 AT AT A- 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
3790982 TTACAGCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3791264 original size:2 final size:2
Alignment explanation
Indices: 3791257--3791321 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
3791247 CAAGCGATTA
3791257 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
3791299 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
3791322 AATTTTAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3796205 original size:35 final size:35
Alignment explanation
Indices: 3796166--3796253 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
3796156 ATTTCATTCT
*
3796166 AAACCCCAAATTCCAAAATAATTCAATTATATTTG
1 AAACCCCAAATTCTAAAATAATTCAATTATATTTG
*
3796201 AAACCCCAAATTCTAAAATAATTCAATTATATTTT
1 AAACCCCAAATTCTAAAATAATTCAATTATATTTG
3796236 AAACCCCAAATTCTAAAA
1 AAACCCCAAATTCTAAAA
3796254 GTTTTGATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (35 bp):
AAACCCCAAATTCTAAAATAATTCAATTATATTTG
Found at i:3796431 original size:33 final size:34
Alignment explanation
Indices: 3796393--3796459 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
3796383 ATTAATATAC
*
3796393 TTAATA-ATATAAT-ATTCTTA-TTTTAATAAATAA
1 TTAATATA-ATAATAATT-TTATTTTTAAAAAATAA
3796426 TTAATATAATAATAATTTTATTTTTAAAAAATAA
1 TTAATATAATAATAATTTTATTTTTAAAAAATAA
3796460 GGGATCTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (34 bp):
TTAATATAATAATAATTTTATTTTTAAAAAATAA
Found at i:3797659 original size:35 final size:35
Alignment explanation
Indices: 3797619--3797693 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
3797609 TCTAAACCTT
* *
3797619 AAATTGAAATATTTTATAATTTTGGGTTTAAAATG
1 AAATTGAAATATTTTAGAATTTGGGGTTTAAAATG
* * * *
3797654 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAAATATTTTAGAATTTGGGGTTTAAAATG
3797689 AAATT
1 AAATT
3797694 AAGGACTGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (35 bp):
AAATTGAAATATTTTAGAATTTGGGGTTTAAAATG
Found at i:3798055 original size:2 final size:2
Alignment explanation
Indices: 3798050--3798117 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
3798040 ATATATATAT
3798050 AG AG AG AG 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 AG AG AG AG
3798092 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
3798118 TTTAGTTAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3798292 original size:28 final size:28
Alignment explanation
Indices: 3798209--3798277 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
3798199 ACAGAGAGCC
*
3798209 AGCAAGACCGGTTCAGAATAAACAAAGT
1 AGCAAGACTGGTTCAGAATAAACAAAGT
3798237 AGCAAGACTGGTTCAGAATAAACAAAGT
1 AGCAAGACTGGTTCAGAATAAACAAAGT
3798265 AGCAAGACTGGTT
1 AGCAAGACTGGTT
3798278 AAATGTAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (28 bp):
AGCAAGACTGGTTCAGAATAAACAAAGT
Found at i:3803387 original size:11 final size:11
Alignment explanation
Indices: 3803371--3803415 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
3803361 AATAATAAGT
3803371 ATTAATTAATA
1 ATTAATTAATA
3803382 ATTAATTAATA
1 ATTAATTAATA
*
3803393 ATT--TTTATA
1 ATTAATTAATA
3803402 ATTAATTAATA
1 ATTAATTAATA
3803413 ATT
1 ATT
3803416 TTTATCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.27
11 22 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:3803402 original size:20 final size:20
Alignment explanation
Indices: 3803379--3803420 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3803369 GTATTAATTA
3803379 ATAATTAATTAATAATTTTT
1 ATAATTAATTAATAATTTTT
3803399 ATAATTAATTAATAATTTTT
1 ATAATTAATTAATAATTTTT
3803419 AT
1 AT
3803421 CCAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTAATTAATAATTTTT
Found at i:3803432 original size:21 final size:20
Alignment explanation
Indices: 3803379--3803438 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3803369 GTATTAATTA
*
3803379 ATAATTAATTAATAATTTTT
1 ATAATTAAATAATAATTTTT
*
3803399 ATAATTAATTAATAATTTTT
1 ATAATTAAATAATAATTTTT
*
3803419 ATCCAA-TAAATAATTATTTT
1 AT--AATTAAATAATAATTTT
3803439 GACTAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 22 0.61
21 12 0.33
22 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTAAATAATAATTTTT
Found at i:3804059 original size:32 final size:32
Alignment explanation
Indices: 3804023--3804105 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
3804013 ACTAAGCAAT
3804023 TTCAAGTTCAAATGAT-T-TTCACTCACTTCGAG
1 TTCAAGTT-AAATG-TGTGTTCACTCACTTCGAG
**
3804055 TTCAAGTTATTTGTGTGTTCACTCACTTCGAG
1 TTCAAGTTAAATGTGTGTTCACTCACTTCGAG
**
3804087 TTCAAGTTATTTGTGTGTT
1 TTCAAGTTAAATGTGTGTT
3804106 TACTTGTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 4 0.09
32 42 0.89
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.45
Consensus pattern (32 bp):
TTCAAGTTAAATGTGTGTTCACTCACTTCGAG
Found at i:3805779 original size:22 final size:22
Alignment explanation
Indices: 3805754--3805805 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3805744 ATCATCATAA
3805754 TTATTTTTCATATATTTATTT-T
1 TTATTTTTCATAT-TTTATTTGT
*
3805776 TTATTTTTCTTATTTTATTTGT
1 TTATTTTTCATATTTTATTTGT
3805798 TT-TTTTTC
1 TTATTTTTC
3805806 TTTTTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (22 bp):
TTATTTTTCATATTTTATTTGT
Found at i:3805790 original size:9 final size:8
Alignment explanation
Indices: 3805768--3805841 Score: 53
Period size: 9 Copynumber: 8.6 Consensus size: 8
3805758 TTTTCATATA
3805768 TTTA-TTT
1 TTTATTTT
3805775 TTTATTTT
1 TTTATTTT
3805783 TCTTATTTT
1 T-TTATTTT
*
3805792 ATTTGTTTT
1 -TTTATTTT
3805801 TTT-TCTTT
1 TTTAT-TTT
*
3805809 TTTTTTCTT
1 TTTATT-TT
3805818 TTTATTCTTT
1 TTTA-T-TTT
3805828 TCTTATTTT
1 T-TTATTTT
3805837 TTTAT
1 TTTAT
3805842 ATTAGTTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
7 5 0.09
8 18 0.32
9 23 0.41
10 6 0.11
11 4 0.07
ACGTcount: A:0.09, C:0.07, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTATTTT
Found at i:3805810 original size:10 final size:10
Alignment explanation
Indices: 3805774--3805820 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
3805764 TATATTTATT
3805774 TTTTATTTTTC
1 TTTT-TTTTTC
3805785 TTATTTTATTT-
1 TT-TTTT-TTTC
*
3805796 GTTTTTTTTC
1 TTTTTTTTTC
3805806 TTTTTTTTTC
1 TTTTTTTTTC
3805816 TTTTT
1 TTTTT
3805821 ATTCTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 3 0.10
10 18 0.58
11 5 0.16
12 5 0.16
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:3805836 original size:24 final size:22
Alignment explanation
Indices: 3805757--3805839 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 22
3805747 ATCATAATTA
* *
3805757 TTTTTCATATATTTATTTTTTA-
1 TTTTTCTTAT-TTTTTTTTTTAT
* *
3805779 TTTTTCTTATTTTATTTGTT-T
1 TTTTTCTTATTTTTTTTTTTAT
*
3805800 TTTTTCTTTTTTTTTCTTTTTAT
1 TTTTTCTTATTTTTT-TTTTTAT
3805823 TCTTTTCTTATTTTTTT
1 T-TTTTCTTATTTTTTT
3805840 ATATTAGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 22 0.43
22 13 0.25
23 3 0.06
24 13 0.25
ACGTcount: A:0.11, C:0.07, G:0.01, T:0.81
Consensus pattern (22 bp):
TTTTTCTTATTTTTTTTTTTAT
Found at i:3805840 original size:19 final size:18
Alignment explanation
Indices: 3805772--3805841 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
3805762 CATATATTTA
3805772 TTTTTTATTTTTCTTATT-
1 TTTTTTATTTTT-TTATTC
* *
3805790 TTATTT-GTTTTTT-TTC
1 TTTTTTATTTTTTTATTC
*
3805806 TTTTTTTTTCTTTTTATTC
1 TTTTTTATT-TTTTTATTC
3805825 TTTTCTTATTTTTTTAT
1 TTTT-TTATTTTTTTAT
3805842 ATTAGTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.05
16 7 0.17
17 5 0.12
18 10 0.24
19 14 0.33
20 4 0.10
ACGTcount: A:0.09, C:0.07, G:0.01, T:0.83
Consensus pattern (18 bp):
TTTTTTATTTTTTTATTC
Found at i:3805969 original size:9 final size:9
Alignment explanation
Indices: 3805954--3806037 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
3805944 GCTCGTTATC
3805954 TTTATTTTGA
1 TTTATTTT-A
3805964 -TTATTTTA
1 TTTATTTTA
*
3805972 TTTATTTTTC
1 TTTA-TTTTA
3805982 TTTATTTTA
1 TTTATTTTA
3805991 -TT-TTTTA
1 TTTATTTTA
*
3805998 TTT-TTTATC
1 TTTATTT-TA
3806007 TTTATCTTTA
1 TTTAT-TTTA
*
3806017 -TT-GTTTA
1 TTTATTTTA
*
3806024 TTTATTTTC
1 TTTATTTTA
3806033 TTTAT
1 TTTAT
3806038 CGTGTTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
7 9 0.15
8 10 0.17
9 28 0.47
10 10 0.17
11 2 0.03
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3805986 original size:19 final size:19
Alignment explanation
Indices: 3805964--3806102 Score: 73
Period size: 20 Copynumber: 6.7 Consensus size: 19
3805954 TTTATTTTGA
3805964 TTATTTTATTTATTTTTCT
1 TTATTTTATTTATTTTTCT
*
3805983 TTATTTTATTT-TTTATTTT
1 TTATTTTATTTATTT-TTCT
*
3806002 TTATCTTTATCTTTATTGTTTAT
1 TTAT-TTTA--TTTATT-TTTCT
*
3806025 TTATTTTCTTTATCGTGTTTTCCTT
1 TTATTTTATTTA---T-TTTT-C-T
* *
3806050 TTTTTTTCATTTATTTTTAT
1 TTATTTT-ATTTATTTTTCT
**
3806070 TTCCTTTATTTTATTTTTCT
1 TTATTTTA-TTTATTTTTCT
* *
3806090 TCAGTTTATTTAT
1 TTATTTTATTTAT
3806103 CTTCATTGTC
Statistics
Matches: 93, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.03
19 24 0.26
20 29 0.31
22 10 0.11
23 14 0.15
24 2 0.02
25 7 0.08
26 4 0.04
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTTATTTATTTTTCT
Found at i:3805992 original size:15 final size:15
Alignment explanation
Indices: 3805968--3806105 Score: 65
Period size: 15 Copynumber: 9.1 Consensus size: 15
3805958 TTTTGATTAT
3805968 TTTA-TTTATTTTTC
1 TTTATTTTATTTTTC
3805982 TTTATTTTA--TTT-
1 TTTATTTTATTTTTC
*
3805994 TTTA-TTT-TTTATC
1 TTTATTTTATTTTTC
*
3806007 TTTATCTTTATTGTTTA
1 TTTAT-TTTATT-TTTC
* *
3806024 TTTATTTTCTTTATC
1 TTTATTTTATTTTTC
* *
3806039 GTGTTTTCCTTTTTTTTTC
1 -T-TTAT--TTTATTTTTC
*
3806058 ATTTATTTT-TATTTCC
1 -TTTATTTTAT-TTTTC
3806074 TTTATTTTATTTTTC
1 TTTATTTTATTTTTC
* * *
3806089 TTCAGTTTATTTATC
1 TTTATTTTATTTTTC
3806104 TT
1 TT
3806106 CATTGTCTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
11 3 0.03
12 6 0.06
13 7 0.07
14 4 0.04
15 36 0.38
16 16 0.17
17 10 0.11
18 3 0.03
19 9 0.10
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTTTTC
Found at i:3806016 original size:26 final size:26
Alignment explanation
Indices: 3805949--3806037 Score: 119
Period size: 26 Copynumber: 3.4 Consensus size: 26
3805939 ATTTTGCTCG
3805949 TTATCTTTATTTTGATTATTTTATTTAT
1 TTATCTTTATTTT-ATT-TTTTATTTAT
*
3805977 TTTTCTTTATTTTATTTTTTATTT-T
1 TTATCTTTATTTTATTTTTTATTTAT
*
3806002 TTATCTTTATCTTTATTGTTTATTTAT
1 TTATCTTTAT-TTTATTTTTTATTTAT
3806029 TT-TCTTTAT
1 TTATCTTTAT
3806038 CGTGTTTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
25 10 0.18
26 28 0.50
27 6 0.11
28 12 0.21
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (26 bp):
TTATCTTTATTTTATTTTTTATTTAT
Found at i:3806056 original size:53 final size:53
Alignment explanation
Indices: 3805949--3806090 Score: 132
Period size: 51 Copynumber: 2.7 Consensus size: 53
3805939 ATTTTGCTCG
* **
3805949 TTATCTTTATTTTGATTATTTTATTTATTTTTCTTTATTTTATTTTTTATTTT
1 TTATCTTTATTTTGATTAGTTTATTTATTTTTCTTTATCGTATTTTTTATTTT
*
3806002 TTATCTTTATCTTT-ATT-GTTTATTTA-TTTTCTTTATCGTGTTTTCCTT-TTTT
1 TTATCTTTAT-TTTGATTAGTTTATTTATTTTTCTTTATCGTATTTT--TTATTTT
* **
3806054 TT-TCATTTATTTTTATTTCCTTTATTTTATTTTTCTT
1 TTATC-TTTATTTTGA-TTAGTTTA-TTTATTTTTCTT
3806091 CAGTTTATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
51 20 0.27
52 20 0.27
53 17 0.23
54 7 0.09
55 4 0.05
56 7 0.09
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (53 bp):
TTATCTTTATTTTGATTAGTTTATTTATTTTTCTTTATCGTATTTTTTATTTT
Found at i:3806715 original size:18 final size:18
Alignment explanation
Indices: 3806673--3806722 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3806663 GTTTCAGATT
* *
3806673 CAGATTTCAATT-CTTGA
1 CAGATTCCAATTCCTTCA
*
3806690 CCGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
3806708 CAGATTCCAATTCCT
1 CAGATTCCAATTCCT
3806723 CATAAACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:3812650 original size:60 final size:60
Alignment explanation
Indices: 3812581--3812768 Score: 175
Period size: 60 Copynumber: 3.1 Consensus size: 60
3812571 TACATGTTCT
* * * ** *
3812581 CAAAGTATGACCCTCATTTTAAACTGGTCCCTAAAATTTT-AATTGTTTCAATTTCATCCT
1 CAAACTATGACCATCATTTTAAATTGGTCCCTAAAATTTTGAA-CATTTCAATTTCATCCC
* * * * *
3812641 TAAACTATGACTATCATTTTAAATTAGT-CCTTAAATGTTTGAACATTTCATTTTCATCCC
1 CAAACTATGACCATCATTTTAAATTGGTCCCTAAAAT-TTTGAACATTTCAATTTCATCCC
* * * * * *
3812701 CAAACTATAACCTTCATTCTAAATTGGTCCCTAAACTTTTTGAACATTCCAATTTTAT-CC
1 CAAACTATGACCATCATTTTAAATTGGTCCCTAAA-ATTTTGAACATTTCAATTTCATCCC
3812761 CAAACTAT
1 CAAACTAT
3812769 ATGTGTATAC
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
59 7 0.07
60 70 0.69
61 24 0.24
62 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
CAAACTATGACCATCATTTTAAATTGGTCCCTAAAATTTTGAACATTTCAATTTCATCCC
Found at i:3812978 original size:59 final size:58
Alignment explanation
Indices: 3812893--3813058 Score: 183
Period size: 60 Copynumber: 2.8 Consensus size: 58
3812883 TATTTAGATG
* * * *
3812893 AATTTGGGGATGGAATTGGAAGATTTAAAAG-TTAGGGACCAATTTAGAAAGAGGAT-AGT
1 AATTTAGGGAT-GAATT-GAATATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAATCA-T
* * *
3812952 AATTTAGGGATGAACTTAGAATATTTAAAAGTTTAAAGACTAATTTAGAATGAGAATCAT
1 AATTTAGGGATGAA-TT-GAATATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAATCAT
*
3813012 AATATAGGGATGAAGTTGAAATATTTAAAAGTTTAAGGACCAATTTA
1 AATTTAGGGATGAA-TTG-AATATTTAAAAGTTTAAGGACCAATTTA
3813059 AAATAAAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
58 3 0.03
59 25 0.27
60 62 0.68
61 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (58 bp):
AATTTAGGGATGAATTGAATATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAATCAT
Found at i:3813022 original size:60 final size:60
Alignment explanation
Indices: 3812915--3813058 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 60
3812905 GAATTGGAAG
* * *
3812915 ATTTAAAAG-TTAGGGACCAATTTAGAAAGAGGATAGTAATTTAGGGATGAACTT-AGAAT
1 ATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAATAGTAATATAGGGATGAACTTGA-AAT
* * * *
3812974 ATTTAAAAGTTTAAAGACTAATTTAGAATGAGAATCA-TAATATAGGGATGAAGTTGAAAT
1 ATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAAT-AGTAATATAGGGATGAACTTGAAAT
3813034 ATTTAAAAGTTTAAGGACCAATTTA
1 ATTTAAAAGTTTAAGGACCAATTTA
3813059 AAATAAAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 9 0.12
60 62 0.85
61 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.31
Consensus pattern (60 bp):
ATTTAAAAGTTTAAGGACCAATTTAGAAAGAGAATAGTAATATAGGGATGAACTTGAAAT
Found at i:3813303 original size:2 final size:2
Alignment explanation
Indices: 3813296--3813357 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3813286 CCTCGTATTA
3813296 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
3813338 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3813358 TCTATTATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3813674 original size:23 final size:25
Alignment explanation
Indices: 3813618--3813680 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
3813608 TGTTATAGTT
*
3813618 AATTTATAAAATTTT-AGTAGAATG
1 AATTTATAAAATTTTAAGTAGAACG
3813642 AA--TATAAAATTTTAAG-AG-ACG
1 AATTTATAAAATTTTAAGTAGAACG
*
3813663 AATTTATAAAATTGTAAG
1 AATTTATAAAATTTTAAG
3813681 GATAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.12
22 13 0.38
23 15 0.44
24 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.37
Consensus pattern (25 bp):
AATTTATAAAATTTTAAGTAGAACG
Found at i:3822210 original size:15 final size:16
Alignment explanation
Indices: 3822190--3822219 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3822180 TAGATATTAA
3822190 TTTTAAA-ATTTATTT
1 TTTTAAATATTTATTT
3822205 TTTTAAATATTTATT
1 TTTTAAATATTTATT
3822220 CATCAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAATATTTATTT
Found at i:3836611 original size:23 final size:23
Alignment explanation
Indices: 3836580--3836671 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 23
3836570 CACCACAGCT
* *
3836580 CGTATAAATACACCGAAGTGCCG
1 CGTAAAAATACACCGAAGTGCCA
* * * *
3836603 CTTAGAAATGCACCGTAGTGCCA
1 CGTAAAAATACACCGAAGTGCCA
* * *
3836626 CGTATAATTACACCAAAGTGCCA
1 CGTAAAAATACACCGAAGTGCCA
* *
3836649 CGTAAAAATGCACCGTAGTGCCA
1 CGTAAAAATACACCGAAGTGCCA
3836672 TATAATGTCC
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CGTAAAAATACACCGAAGTGCCA
Found at i:3836638 original size:46 final size:46
Alignment explanation
Indices: 3836580--3836671 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3836570 CACCACAGCT
* * * *
3836580 CGTATAAATACACCGAAGTGCCGCTTAGAAATGCACCGTAGTGCCA
1 CGTATAAATACACCAAAGTGCCACGTAAAAATGCACCGTAGTGCCA
*
3836626 CGTATAATTACACCAAAGTGCCACGTAAAAATGCACCGTAGTGCCA
1 CGTATAAATACACCAAAGTGCCACGTAAAAATGCACCGTAGTGCCA
3836672 TATAATGTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (46 bp):
CGTATAAATACACCAAAGTGCCACGTAAAAATGCACCGTAGTGCCA
Found at i:3838130 original size:64 final size:63
Alignment explanation
Indices: 3838059--3838198 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
3838049 TCCCTAACGA
* * * *
3838059 TGCATCGATGTACTACTTGTGCATCGGTGCA-TAAAATACATTCGATGTTTGTATT-TTAAGAGG
1 TGCATCGATGCACTACTTATGCATCGATGCACT-AAATACATTCGATGTTTGT-TTATT-AGAGA
3838122 G
63 G
** * *
3838123 TGCATCGATGCACTACTTATGCATCGATGCACTACTTGCATTCGATGTTTGTTTATTTGAGAG
1 TGCATCGATGCACTACTTATGCATCGATGCACTAAATACATTCGATGTTTGTTTATTAGAGAG
3838186 TGCATCGATGCAC
1 TGCATCGATGCAC
3838199 ATTGAATATG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 19 0.29
64 46 0.70
65 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (63 bp):
TGCATCGATGCACTACTTATGCATCGATGCACTAAATACATTCGATGTTTGTTTATTAGAGAG
Found at i:3838147 original size:19 final size:19
Alignment explanation
Indices: 3838123--3838159 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3838113 TTTAAGAGGG
3838123 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
3838142 TGCATCGATGCACTACTT
1 TGCATCGATGCACTACTT
3838160 GCATTCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:3838218 original size:65 final size:64
Alignment explanation
Indices: 3838097--3838219 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 64
3838087 GCATAAAATA
* *
3838097 CATTCGATGTTTGTATTTTAAGAGGGTGCATCGATGCACTACTTATGCATCGATGCACTACTTG
1 CATTCGATGTTTGTATTTTAAGAGAGTGCATCGATGCACTACATATGCATCGATGCACTACTTG
*
3838161 CATTCGATGTTTGT-TTATT-TGAGAGTGCATCGATGCACATTGA-ATATGCATCGATGCAC
1 CATTCGATGTTTGTATT-TTAAGAGAGTGCATCGATGCAC--T-ACATATGCATCGATGCAC
3838220 ACAACCCAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
63 19 0.37
64 16 0.31
65 16 0.31
66 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAGAGAGTGCATCGATGCACTACATATGCATCGATGCACTACTTG
Found at i:3841178 original size:20 final size:20
Alignment explanation
Indices: 3841153--3841214 Score: 106
Period size: 20 Copynumber: 3.0 Consensus size: 20
3841143 GGTTAGACAT
3841153 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
3841173 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCT-G
*
3841194 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
3841214 G
1 G
3841215 ACAATCTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.15, C:0.29, G:0.40, T:0.16
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:3841190 original size:21 final size:21
Alignment explanation
Indices: 3841153--3841214 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
3841143 GGTTAGACAT
3841153 GGGGGAATCGGTACCCCCT-G
1 GGGGGAATCGGTACCCCCTGG
3841173 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
3841194 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
3841215 ACAATCTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.15, C:0.29, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:3843527 original size:37 final size:37
Alignment explanation
Indices: 3843485--3843562 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
3843475 TTTGAGTCGT
* ** * *
3843485 GTCGGATCGGATCGGGTGAAGGATGTATATTTTTAGG
1 GTCGGATCAGATCCAGTGAAGGATGTAAAATTTTAGG
* *
3843522 GTCGGATCAGATCCAGTGAAGGGTGTAAAATTTTCGG
1 GTCGGATCAGATCCAGTGAAGGATGTAAAATTTTAGG
3843559 GTCG
1 GTCG
3843563 CCAACCGACC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.12, G:0.36, T:0.29
Consensus pattern (37 bp):
GTCGGATCAGATCCAGTGAAGGATGTAAAATTTTAGG
Found at i:3843664 original size:21 final size:23
Alignment explanation
Indices: 3843613--3843666 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
3843603 CATGGTTGCT
3843613 AGATTTA-TGTGAATGTCATTTA
1 AGATTTATTGTGAATGTCATTTA
*
3843635 TG-TTGTATTGT-AATG-CATTTA
1 AGATT-TATTGTGAATGTCATTTA
3843656 AGATTTATTGT
1 AGATTTATTGT
3843667 TCGTCTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 15 0.56
22 9 0.33
23 3 0.11
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.50
Consensus pattern (23 bp):
AGATTTATTGTGAATGTCATTTA
Found at i:3845111 original size:2 final size:2
Alignment explanation
Indices: 3845104--3845181 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
3845094 AGCTTTTGTT
3845104 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
3845146 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
3845182 ATTAGAATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3845570 original size:2 final size:2
Alignment explanation
Indices: 3845563--3845587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3845553 TTAAAAGAAT
3845563 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 T
3845588 GATCATACAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3846003 original size:23 final size:24
Alignment explanation
Indices: 3845963--3846007 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3845953 TATATAATTT
3845963 TAAAAAATAATTAGATAATTAAAA
1 TAAAAAATAATTAGATAATTAAAA
3845987 TAAAACAA-AATTA-ATAATTAA
1 TAAAA-AATAATTAGATAATTAA
3846008 GATATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 10 0.50
25 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
TAAAAAATAATTAGATAATTAAAA
Found at i:3846096 original size:3 final size:3
Alignment explanation
Indices: 3846088--3846113 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3846078 TACCGAAGTA
3846088 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
3846114 ATTATTGTTT
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3852758 original size:888 final size:880
Alignment explanation
Indices: 3850882--3854046 Score: 3190
Period size: 855 Copynumber: 3.6 Consensus size: 880
3850872 GAATAATGTG
* * * * * * *
3850882 CTGGAGAATTCCCTTTTTGATGCAAATA-CTGAACTTGGAGGACTGAGGGTACAA-TTGAAGAAC
1 CTGGAGAATTCCCTTTGTGATGCAAA-AGCTGAACTTGAAGGATTGAGGG-AAAAGCTAAAG-AG
* * *
3850945 T-TAGAAAATTCGTGCCTGCAGCTTAGTGATGAGAAGTCTGGCCTGATAACAC-GAAGAGGAA-G
63 TGTAGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAG-AGA-GAAGG
* ** * *
3851007 TTTGATTTCTGAGTTGAATGTCAGTCAGAAAAGACTGGAAGATTTCGGA-AAACTATATCAGCGC
126 TTTGATTTCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTT-GGAGAAAAGATATCAGGGA
** * * *
3851071 TTAGAAGAAAAATATGTGGACCTGGAGATAGAGAGAGAATCAACAG-TTCGTGAAGTAGAAGAGC
190 TTAGAAGAAAAATATGTGGGTCTGGAGAAAGAGAGAGAATCAACTGCTTCATGAAGTAGAAGAGC
* *
3851135 TACAAAAGTCACTAGATGCTGAAAAACAAGAACATGCTAGTGTTGTGAAATTGAATGAAACCCGA
255 TACAAAAGTCACTAGATGCTGAAAAGCAAGAACATGCTAGT-TTGTGAAGTTGAATGAAACCCGA
* * * * * * *
3851200 GTTA-TTGCTATGGAATCTCAGATTCATTTTCTGCAAGGGGAAAGTGTGTGCAGGAAGAAAGAAT
319 ATTACTT-CTATGGAATCTCAAATCCATTTTCTACAAGGGGAAAGTCTAT-CAGAAAGAAAGAAT
* * * * * * * *
3851264 ATGAAGAGGAATTGGACAGGTCCATTATTTCTCATGTAGAAACCTTCATCTTGCAAAAATGTGCT
382 ATGAAGAGCAACTGGACAGG-CCATGAGTGCTCATGTAGAAACCTTCATCTTGCAGAAATGCGCA
* * * *
3851329 CAAGATCTGGAAGAGAAGAATTTATCCCTACTGCTTGAATGTAGGAAACTCCTGGAAGCCTCCAA
446 CAAGATCTGGAAGAGAAGAATTTATCCCTA-TGATTGAGTGTAGGAAGCTCTTGGAAGCCTCCAA
** * * *
3851394 ATTAT-C-TGAA--A-TC-GAATTGAAGC-TGGAAAATTCCAAAAAGGAGATGGAGGTAAAATCC
510 ATTATCCAAAAATTATTCTGAATTGGAGCTTGG-AAATTCCAAAAA-CAGATGGAGATAAAATCC
* * * * * *
3851452 TTATTTGATCAAATTGCCATAATGAGAACGGGGCTTTATAAGATGTCGAGGACCCTTGAGATTGA
573 TTATTTGATCAAATTACCGTAATGAGGATGGGGCTTTATCAGATGTCGAGGACTCTTGAGATTGA
* * * *
3851517 ---TGTCCATGGTTATGATGATATGATCAAACAAGATCAAAT-AATTCTTGACTGTATATTTGCC
638 TGTTGTCCATGGTTATGATGATATAATCAAACGAGA-CAAATCAGTTCTTGACTGTATATTTGGC
* *
3851578 AGGCTCCAAAAGATGCAAAACTCACATT-TAAAGTCTCTGGATGAAAATCAGCAGTTCATAATTG
702 AGGCTCCAAAAGATGCAAAATTCAC-TTCTAAAGTCTCTGGATGAAAATCAGCAATTCATAATTG
* ** *
3851642 AAAATTCAGTTCTTATTGAATTGCTTGGGA-AACTGAAACTTGAGGCAAAAAATCTTGCTACAGA
766 AGAATTCAGTTCTTATTGGTTTGCTT-GGACAACTGAAACTTGAGGCAGAAAATCTTGCTACAGA
* *
3851706 GAAGAATTCACTGCACCGGGAGTTGAAGGTTCAGTCTGAGCA-GTTCTCAGAA
830 GAAAAATTCACTGCA-CAGGAGTTGAAGGTTCAGTCTGAGCAGGTT-TCAGAA
* * * * * * * * *
3851758 TTGGAGACTTCCCTTTTTAAAGCAAATGCTGAGCTTGAA-G-TGTCAGGAGCAAAGCTAAAGAGC
1 CTGGAGAATTCCCTTTGTGATGCAAAAGCTGAACTTGAAGGAT-TGAGG-GAAAAGCTAAAGAG-
* * **
3851821 T-TGGAAAGTTCATGCCTGCTGCTTGGCAATGAGAAGTCTGGCCTGATAACACAGAGAGAAGGTT
63 TGTAGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGAGAAGGTT
* * * ** *
3851885 TGATTTCTGACTTGAATGTTAGTCGGAAAAGGCTGGCGGACTTGGAGAAAAGATATCAGGGATTA
128 TGATTTCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTTGGAGAAAAGATATCAGGGATTA
* * * **
3851950 GAAGAAAAAAATGTGGGGCTGGAGAAAGAGAGAGAGTTGA-TGCTTCATGAAGTAGAAGAGCTAC
193 GAAGAAAAATATGTGGGTCTGGAGAAAGAGAGAGAATCAACTGCTTCATGAAGTAGAAGAGCTAC
* * * * * * *
3852014 AAAAGTCACTAAATGCAGAGAAGCAAGAACATGCTAGATTTGTGAGGTCGAATGAAGCCCAAATT
258 AAAAGTCACTAGATGCTGAAAAGCAAGAACATGCTAG-TTTGTGAAGTTGAATGAAACCCGAATT
* * *
3852079 TCTTCTCTGGAATCTCAAATCCATTTTCTAGAAGGGGAAAGTCTATGCAGAAAGAAAGAATATGA
322 ACTTCTATGGAATCTCAAATCCATTTTCTACAAGGGGAAAGTCTAT-CAGAAAGAAAGAATATGA
* * * * * *
3852144 GGAGCAACTGGACAAGGCTATGAGTGCTCATGTAGAAACCTTCGTTTTGCAGAGATGTGCACAAG
386 AGAGCAACTGGAC-AGGCCATGAGTGCTCATGTAGAAACCTTCATCTTGCAGAAATGCGCACAAG
* * *
3852209 ATCTGGAAGAGAAGAATTTGTCCCTATTGATTGAGTGTAGGAAGCTCTTTGAAGCCTCCAAACTA
450 ATCTGGAAGAGAAGAATTTATCCCTA-TGATTGAGTGTAGGAAGCTCTTGGAAGCCTCCAAATTA
* * * *
3852274 TCCAAAAAATTTATTTCTGAACTGGAGCTTGGTAATTCCGGAAAACAGATGAAGATAAAATCCTT
514 TCC-AAAAA-TTA-TTCTGAATTGGAGCTTGGAAATTCC-AAAAACAGATGGAGATAAAATCCTT
* * * ** * *
3852339 ATCTGATCAAATTACTGTACTGAGGATGGGGCTCCATCAGATGTTGAGGACTCTCGAGATTGATG
575 ATTTGATCAAATTACCGTAATGAGGATGGGGCTTTATCAGATGTCGAGGACTCTTGAGATTGATG
* * * * *
3852404 TTGTGCATGGTTATGATGAGATAATCAAACGAGACCAATCAGTTCTTGATTTTATATTTGGCAGG
640 TTGTCCATGGTTATGATGATATAATCAAACGAGACAAATCAGTTCTTGACTGTATATTTGGCAGG
*
3852469 CTCCAAAAGATGCAAAATTCACTTCTAAAGTCTCTGGATGAAAATCAGCAATTCACAATTGAGAA
705 CTCCAAAAGATGCAAAATTCACTTCTAAAGTCTCTGGATGAAAATCAGCAATTCATAATTGAGAA
* *
3852534 TTCAGTTCTTATTGGTTTGCTTGGACAACTCAAACTTGAGGCAGAAAGTCTTGCTACAGAGAAAA
770 TTCAGTTCTTATTGGTTTGCTTGGACAACTGAAACTTGAGGCAGAAAATCTTGCTACAGAGAAAA
* *
3852599 ATTTATTGCACAAGGAGTTGAAGGTTCAGT-TCGAGCAGGTTTCAGAA
835 ATTCACTGCAC-AGGAGTTGAAGGTTCAGTCT-GAGCAGGTTTCAGAA
* *
3852646 CTGGAGACTTCCCTTTGTGATGCAAAAGCTGAACTTGAAGGATTGAGGGAAAAGCTAAAGAGTGC
1 CTGGAGAATTCCCTTTGTGATGCAAAAGCTGAACTTGAAGGATTGAGGGAAAAGCTAAAGAGTGT
* * * * * * *
3852711 AGAAAACTCATGCCTTCTGCTTGGTGCTGAGAAGTTTGGCTTGATAACTCAGAGAGAAGGTTTGC
66 AGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGAGAAGGTTTGA
* * * * * *
3852776 TTTCTGAGTTGAATGTCAATCAGGAAAGGCTGAAAGATTTTGAAAAAAGATACCAGGGATTAGAA
131 TTTCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTTGGAGAAAAGATATCAGGGATTAGAA
* * * * *
3852841 GAAAAATATGTCGGTCTGGAGAAAGAAAGGGAATCAAC-ACTTCATGAAGTACAAGAGCTACAAA
196 GAAAAATATGTGGGTCTGGAGAAAGAGAGAGAATCAACTGCTTCATGAAGTAGAAGAGCTACAAA
* * *
3852905 AGTCACTAGATGCTGAAATGCAAAAACATGCTAGTTCTGTGAAGTTGAATGAAACCCGAGTTACT
261 AGTCACTAGATGCTGAAAAGCAAGAACATGCTAGTT-TGTGAAGTTGAATGAAACCCGAATTACT
* * *
3852970 TCCATGGAGTCCCAAATCCATTTTCTACAAGGGG--A----A-C------------T-T-----G
325 TCTATGGAATCTCAAATCCATTTTCTACAAGGGGAAAGTCTATCAGAAAGAAAGAATATGAAGAG
* * * * * *
3853010 --AC---A-AGGCCATG-GATGCTCATGTAGAATCCTTCGTTTTGAAGAGATGCACACAAGATCT
390 CAACTGGACAGGCCATGAG-TGCTCATGTAGAAACCTTCATCTTGCAGAAATGCGCACAAGATCT
* * * *
3853068 GGAAGAGAAGAATTTATCCCTATCACTTGAGTGTAGGAAGCTCTTGAAAGCCTCCACATTATCTG
454 GGAAGAGAAGAATTTATCCCTATGA-TTGAGTGTAGGAAGCTCTTGGAAGCCTCCAAATTATC-C
* *
3853133 AAAAACTTATCTCTGAATTGGAGCTTGGGAATTCCCAAAAACAGATGGAGATAAAGTCCTTATTT
517 AAAAA-TTAT-TCTGAATTGGAGCTTGGAAATT-CCAAAAACAGATGGAGATAAAATCCTTATTT
* * * *
3853198 GATCAAATTTCCGTATTGAGGATGAGACTTTATCAGATGTCGAGGACTCTTGAGATTGATGCTT-
579 GATCAAATTACCGTAATGAGGATGGGGCTTTATCAGATGTCGAGGACTCTTGAGATTGATG-TTG
* * * * * * *
3853262 TCCATGGTTATGATTATACAATCAGA-GAAGATAAATCAGCTCTTGACAGTATATTTGGTA-GCT
643 TCCATGGTTATGATGATATAATCAAACG-AGACAAATCAGTTCTTGACTGTATATTTGGCAGGC-
* * *
3853325 TCCAAAAGATGCAAAATTCACTTCTAAAATCTCTGGATGAAAATCATCAATTCATACTTGAGAAT
706 TCCAAAAGATGCAAAATTCACTTCTAAAGTCTCTGGATGAAAATCAGCAATTCATAATTGAGAAT
** * * *
3853390 TTGGTTCTTATTGGTTTGCTT-GAGCAACTGAAACTTGAGGCTGAAAATCTTGCAACA-ACAAAC
771 TCAGTTCTTATTGGTTTGCTTGGA-CAACTGAAACTTGAGGCAGAAAATCTTGCTACAGAGAAA-
* * * *
3853453 TATTCACTGCATCAGGAGTTGACGGTTCAGTCTGAGAAGTTTTCAGAA
834 AATTCACTGCA-CAGGAGTTGAAGGTTCAGTCTGAGCAGGTTTCAGAA
* * * * * *
3853501 CTGGAGAATTCCCTTTGTGATTCAAATGTTGAACTTGAAGGATT-AAGGAAAAGTGTAAAGAGTT
1 CTGGAGAATTCCCTTTGTGATGCAAAAGCTGAACTTGAAGGATTGAGGGAAAAG-CTAAAGAGTG
* * ** * * *
3853565 TAGAAAATACATGCATGCTGCTTGGTGATGAGAAGT-TGGGTTTGCTAACACAGAGAGAATGCTT
65 TAGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCT-GGCCTGATAACACAGAGAGAAGGTTT
* * *
3853629 GATATCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTTGGAGAAAAGATGTCAGGAATTAG
129 GATTTCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTTGGAGAAAAGATATCAGGGATTAG
* * * * * ** *
3853694 AAGAAAAACATGTGGTTCTGGAGAAAGAGAGAGATTC-AGTGTTTTGTGAAGTAGAAGAACTA-A
194 AAGAAAAATATGTGGGTCTGGAGAAAGAGAGAGAATCAACTGCTTCATGAAGTAGAAGAGCTACA
* *
3853757 AAGGGTTC-CTAGATGCTGAAAAGCAAGAATATGCTAGTTTTGTGAAGTTGAATGAAACCCG-AT
259 AA-AG-TCACTAGATGCTGAAAAGCAAGAACATGCTAG-TTTGTGAAGTTGAATGAAACCCGAAT
* * * * *
3853820 CTACTTCTATGGAATCTCAGATCCATTTTCTACAAGGGGAAAGTCTGCTCATAAGGAAAGAATAC
321 -TACTTCTATGGAATCTCAAATCCATTTTCTACAAGGGGAAAGTCT-ATCAGAAAGAAAGAATAT
* * *
3853885 GAAGAGGAACTGGACAAGGCCATGAATGCTCATGTAGAAAACTTCATCTTGCAGAAATGCGCACA
384 GAAGAGCAACTGGAC-AGGCCATGAGTGCTCATGTAGAAACCTTCATCTTGCAGAAATGCGCACA
* * * * * * *
3853950 AAATCTAG-A-AG-ATAATTTCT-CCTGGTGCTTGAGTGTAGGAAGCTCTTGGAAGCCT-CTAAT
448 AGATCTGGAAGAGAAGAATTTATCCCT-ATGATTGAGTGTAGGAAGCTCTTGGAAGCCTCCAAAT
* *
3854010 TAT-CAGAAGAACTTATCTCCGAATTGGAGCTGGGAAA
512 TATCCA-AA-AA-TTAT-TCTGAATTGGAGCTTGGAAA
3854047 GTCTGCTCAT
Statistics
Matches: 1883, Mismatches: 313, Indels: 179
0.79 0.13 0.08
Matches are distributed among these distances:
854 27 0.01
855 683 0.36
856 10 0.01
857 2 0.00
860 2 0.00
862 1 0.00
863 1 0.00
867 1 0.00
868 1 0.00
875 16 0.01
876 403 0.21
877 8 0.00
879 2 0.00
880 1 0.00
881 2 0.00
882 4 0.00
883 33 0.02
884 31 0.02
885 89 0.05
886 11 0.01
887 15 0.01
888 531 0.28
889 8 0.00
890 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (880 bp):
CTGGAGAATTCCCTTTGTGATGCAAAAGCTGAACTTGAAGGATTGAGGGAAAAGCTAAAGAGTGT
AGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGAGAAGGTTTGA
TTTCTGAGTTGAATGTCAGTCAGAAAAGGCTGGAAGATTTGGAGAAAAGATATCAGGGATTAGAA
GAAAAATATGTGGGTCTGGAGAAAGAGAGAGAATCAACTGCTTCATGAAGTAGAAGAGCTACAAA
AGTCACTAGATGCTGAAAAGCAAGAACATGCTAGTTTGTGAAGTTGAATGAAACCCGAATTACTT
CTATGGAATCTCAAATCCATTTTCTACAAGGGGAAAGTCTATCAGAAAGAAAGAATATGAAGAGC
AACTGGACAGGCCATGAGTGCTCATGTAGAAACCTTCATCTTGCAGAAATGCGCACAAGATCTGG
AAGAGAAGAATTTATCCCTATGATTGAGTGTAGGAAGCTCTTGGAAGCCTCCAAATTATCCAAAA
ATTATTCTGAATTGGAGCTTGGAAATTCCAAAAACAGATGGAGATAAAATCCTTATTTGATCAAA
TTACCGTAATGAGGATGGGGCTTTATCAGATGTCGAGGACTCTTGAGATTGATGTTGTCCATGGT
TATGATGATATAATCAAACGAGACAAATCAGTTCTTGACTGTATATTTGGCAGGCTCCAAAAGAT
GCAAAATTCACTTCTAAAGTCTCTGGATGAAAATCAGCAATTCATAATTGAGAATTCAGTTCTTA
TTGGTTTGCTTGGACAACTGAAACTTGAGGCAGAAAATCTTGCTACAGAGAAAAATTCACTGCAC
AGGAGTTGAAGGTTCAGTCTGAGCAGGTTTCAGAA
Found at i:3855731 original size:252 final size:251
Alignment explanation
Indices: 3855281--3856026 Score: 1102
Period size: 252 Copynumber: 3.0 Consensus size: 251
3855271 CTGGAGACTG
* *
3855281 TGATCTTCAAAACAAGGAGATTGAAAGTATTCGTCAGGCTAATCAGAAA-TATGAGG-TCGAGTT
1 TGATCTTCAAAATAAGGAGATTGAAAGCATTCGTCAGGCTAATCAGAAACT-TGAGGCT-GAGTT
* * * * *
3855344 ATCAAAATTGCACGAGGAACTTGAAGAAAGGAAACATAGGGAGGAGAGTTCGAGTGTGGAACTAC
64 ATCGAAATTGCACGAGGAACTTGAAGAATGGAAACATAGGGAGGAGAATTTGAGTGTTGAACTAC
* *
3855409 AAAAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCACTGTTTGGTGAGCTACAA
129 AAAAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTATTTGGTGAGCTACAA
* * *
3855474 ATTTCTGCATTCCGTGAAGCATTGCTAGAAGAGAAGGCTTGTGAGCTCAATGCAGAATT
194 ATTTCTGC-TTCCGTGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCAATACAGAACT
* *
3855533 TGATGTTCAAAATAAGGAGATTGAAAGCATTCGTCAGGCTAATCAGAAACTTGAGGCTGAATTAT
1 TGATCTTCAAAATAAGGAGATTGAAAGCATTCGTCAGGCTAATCAGAAACTTGAGGCTGAGTTAT
* * * *
3855598 CGAAATTGCATGAGGAACTTGAAGAATGGAAACATAGGGAGAAGACTTTGAGGGTTGAACTACAA
66 CGAAATTGCACGAGGAACTTGAAGAATGGAAACATAGGGAGGAGAATTTGAGTGTTGAACTACAA
* *
3855663 AAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTTTTTAGTGAGCTACAAAT
131 AAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTATTTGGTGAGCTACAAAT
*
3855728 TTCTGCTTTCCGTGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCAATACTGAACT
196 TTCTGC-TTCCGTGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCAATACAGAACT
* * * **
3855785 TGATCTTCAAAATAAGGAGATTGATAGCATTTGTCAGACTAATCAGAAACTTCTGGCTGAGTTAT
1 TGATCTTCAAAATAAGGAGATTGAAAGCATTCGTCAGGCTAATCAGAAACTTGAGGCTGAGTTAT
* * * * *
3855850 TGAAATCGCACAAAGAACTTGAAGAATGGAAACATAGGGAGGAGAATTTGCA-TGTTGAACTACG
66 CGAAATTGCACGAGGAACTTGAAGAATGGAAACATAGGGAGGAGAATTTG-AGTGTTGAACTACA
** *
3855914 AAAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACCACATTATTTGGTGAGCTACAGA
130 AAAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTATTTGGTGAGCTACAAA
*
3855979 TTTCTGCTGTCCATGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCA
195 TTTCTGCT-TCCGTGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCA
3856027 GAACGGAATG
Statistics
Matches: 448, Mismatches: 42, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
251 1 0.00
252 444 0.99
253 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (251 bp):
TGATCTTCAAAATAAGGAGATTGAAAGCATTCGTCAGGCTAATCAGAAACTTGAGGCTGAGTTAT
CGAAATTGCACGAGGAACTTGAAGAATGGAAACATAGGGAGGAGAATTTGAGTGTTGAACTACAA
AAGGAAAGAAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTATTTGGTGAGCTACAAAT
TTCTGCTTCCGTGAAGCATTGCTTGAAGAGAAGGCTTGTGAGCTCAATACAGAACT
Found at i:3859716 original size:2 final size:2
Alignment explanation
Indices: 3859709--3859738 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3859699 TTTATTGTAT
3859709 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
3859739 ATGGAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3861899 original size:18 final size:18
Alignment explanation
Indices: 3861873--3861912 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3861863 TTGTTTTGAA
*
3861873 AACCGGACCGACCAGTTC
1 AACCAGACCGACCAGTTC
3861891 AACCAGACCGACCAGTTC
1 AACCAGACCGACCAGTTC
3861909 AACC
1 AACC
3861913 GGGAACCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.17, T:0.10
Consensus pattern (18 bp):
AACCAGACCGACCAGTTC
Found at i:3863854 original size:14 final size:14
Alignment explanation
Indices: 3863835--3863864 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3863825 CATTTAAGGA
*
3863835 AAAATATATTAATT
1 AAAATAGATTAATT
3863849 AAAATAGATTAATT
1 AAAATAGATTAATT
3863863 AA
1 AA
3863865 TTTCTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AAAATAGATTAATT
Found at i:3866213 original size:313 final size:311
Alignment explanation
Indices: 3865585--3866728 Score: 1677
Period size: 313 Copynumber: 3.7 Consensus size: 311
3865575 TTGAAGTTTA
* * * *
3865585 TAATGAAGAATTTCTTTTGATCCTTTGCTTCACAGGAGTTCGATAAGAATCCCGCTTCGTCTCTT
1 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
*
3865650 TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTCTTCTGCTGCTGCTTTAACTCCATTTCC
66 TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTCTT-T-CTGCTGCTTTAACTTCATTTCC
* * *
3865715 TCGTTTTTCTTCTTTGATTTTTACTTTCTCAAGCAATTTACGTCGTCGATTGCATAATAGAGTGA
129 TTGTTTTTCTTCTTTGATTTTT-CCTTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGA
* *
3865780 AGAAACTATTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAAGCAGTAG
193 AGAAACTGTTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAAGCAGTCG
3865845 GGTAGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAG-TTTT
258 GGTAGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAGTTTTT
* *
3865898 TAATGAAGATTTTCATTTGATCCTTTGCTTCACAGGGGTTAGATAAGAATCCCGCTTCGTCGCTT
1 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
* *
3865963 TCAGCTGCCTTTCTGTGTTTTTCGCTTCAGGTAACTTCTTCTGCTGCTGCTTTAACTTCATTTCC
66 TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTCTT-T-CTGCTGCTTTAACTTCATTTCC
* *
3866028 TTGTTTTTCTTCTTTGATTTTTTCCTTCTCAATCAATTTTCGTCGTCAATTGCATAATAGAGTGA
129 TTGTTTTTCTTCTTTGA-TTTTTCCTTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGA
3866093 AGAAACTGTTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAA-CAGTCG
193 AGAAACTGTTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAAGCAGTCG
3866157 GGTAGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAGTTTTT
258 GGTAGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAGTTTTT
3866211 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
1 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
**
3866276 TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTC-TTCTGCTGCTTTATTTTCA-TTCCTT
66 TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTCTTTCTGCTGCTTTAACTTCATTTCCTT
3866339 GTTTTTCTTCTTTGATTTTTCCTTTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGAAG
131 GTTTTTCTTCTTTGATTTTTCC-TTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGAAG
* *
3866404 AAACTGTTTTCTCTCTG-TTTTTC-TCTTATGTTTCTTAGTTTTAGTTGTTATGAAGCAGTCGGG
195 AAACTGTTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAAGCAGTCGGG
* * *
3866467 TGGAGGAGAGTGAATTTTATCATATCACATTCAAAAAACTAATGCAGTTTTTTTTAAGTTTT
260 TAGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAG-------T---TTTT
* * * * *
3866529 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTCGATAAGAATCTCTCTTAGTCCCTT
1 TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
* * *
3866594 TTAGCTGCCTTTCTGTGTTGTTCCACTTCAGGTACCTTCTTT-T-C-G----AATTTCAGTTT-C
66 TCAGCTGCCTTTCTGTGTT-TTCCACTTCAGGTAACTTCTTTCTGCTGCTTTAACTTCA-TTTCC
* * * ** *
3866651 TTGTTTTTCTTTTTTGATCTGTCGCTTCTCAAGCAATTTACGTCGTCAATTGCATTGTAGAGCGA
129 TTGTTTTTCTTCTTTGATTTTTC-CTTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGA
3866716 AGAAACTGTTTTC
193 AGAAACTGTTTTC
3866729 TCTTATGTTT
Statistics
Matches: 770, Mismatches: 42, Indels: 37
0.91 0.05 0.04
Matches are distributed among these distances:
307 30 0.04
308 65 0.08
309 77 0.10
310 15 0.02
311 1 0.00
312 55 0.07
313 342 0.44
314 76 0.10
315 4 0.01
317 1 0.00
318 83 0.11
319 19 0.02
320 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (311 bp):
TAATGAAGATTTTCCTTTGATCCTTTGCTTCACAGGAGTTAGATAAGAATCCCGCTTCGTCGCTT
TCAGCTGCCTTTCTGTGTTTTCCACTTCAGGTAACTTCTTTCTGCTGCTTTAACTTCATTTCCTT
GTTTTTCTTCTTTGATTTTTCCTTCTCAAGCAATTTACGTCGTCAATTGCATAATAGAGTGAAGA
AACTGTTTTCGCTCTGTTTTTTCTTCTTATGTTTCTTAATTTTAGTTGTTATGAAGCAGTCGGGT
AGAGGAGAGTGAATTTTATCCTATCAAATTCAAAAAACTAATGCAGTTTTT
Found at i:3871591 original size:27 final size:28
Alignment explanation
Indices: 3871521--3871592 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 28
3871511 ACTGATCATC
*
3871521 AAAAATTAAATA-CTTAATTATAGAATA
1 AAAAATTAAATATCATAATTATAGAATA
* * **
3871548 AGAAACTAAATAT-ATAATTAT-TTATA
1 AAAAATTAAATATCATAATTATAGAATA
3871574 AAAAATTAAATATCATAAT
1 AAAAATTAAATATCATAAT
3871593 ATATGTAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTAAATATCATAATTATAGAATA
Found at i:3874079 original size:28 final size:28
Alignment explanation
Indices: 3874025--3874079 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
3874015 CCTTGTTTAC
* * *
3874025 ATTATACCATCAAGTAAGTGCTTGAAAT
1 ATTATACCATCAAGCAAGTACTAGAAAT
* *
3874053 ATTATACCGTCAAGCCAGTACTAGAAA
1 ATTATACCATCAAGCAAGTACTAGAAA
3874080 ACAATAGTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (28 bp):
ATTATACCATCAAGCAAGTACTAGAAAT
Found at i:3877765 original size:2 final size:2
Alignment explanation
Indices: 3877758--3877819 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
3877748 TTAATCTTTC
3877758 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
*
3877800 AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3877820 TAATATGACT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3877946 original size:19 final size:19
Alignment explanation
Indices: 3877924--3877962 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3877914 TAAAGTAATG
*
3877924 AAATTAAATAAATTAAAAT
1 AAATCAAATAAATTAAAAT
**
3877943 AAATCGCATAAATTAAAAT
1 AAATCAAATAAATTAAAAT
3877962 A
1 A
3877963 TAAAATAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
AAATCAAATAAATTAAAAT
Found at i:3879348 original size:136 final size:135
Alignment explanation
Indices: 3879190--3879666 Score: 598
Period size: 139 Copynumber: 3.5 Consensus size: 135
3879180 AGTTTTTCAG
* *
3879190 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTGGAAATGTTG
3879255 ATCCTCAAAAGAGGTATCGTTGATTCAATTTCATATTGATGAATTAAGGCAAAGTTGAACAAGTT
66 ATCCTCAAAAGAGGTATCGTTGATTCAA-TTCATATTGATGAATTAAGGCAAAGTTGAACAAGTT
3879320 CTTCTC
130 CTTCTC
* * * * * *
3879326 ATTATGAACTTCCTCTTTCTCTTCAGATGAGTTCTTCTCATTGTGAACTCCTTCTAGAAATGCTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTGGAAATGTTG
* * *
3879391 ATCCTCAAAAGCGGTGTCGTTGATTCAACTTCATATGTGATGAATTAAGGCAATGTTGAACAAGT
66 ATCCTCAAAAGAGGTATCGTTGATTCAA-TTCATAT-TGATGAATTAAGGCAAAGTTGAACAAGT
3879456 TCTTCTC
129 TCTTCTC
* * *
3879463 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACT-TTCTCTGAAAATATT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCT-TCTGGAAATGTT
* ** * * * * * * ** * *
3879527 GATCTTCAGGAGAGGTTCTTCTTTCATTCAACTCTATAGGTGATGAATCAAGTTAAGGTCGAACA
65 GATCCTCAAAAGAGG-T-ATCGTTGATTCAATTC-ATA-TTGATGAATTAAGGCAAAGTTGAACA
3879592 AGTTCTTCTC
126 AGTTCTTCTC
* *
3879602 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTTATTATGAACTTTCTT-TGGAAATGTT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAAC-TCCTTCTGGAAATGTT
3879666 G
65 G
3879667 GTGTTGATCT
Statistics
Matches: 297, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
136 94 0.32
137 98 0.33
138 3 0.01
139 99 0.33
140 2 0.01
141 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (135 bp):
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTGGAAATGTTG
ATCCTCAAAAGAGGTATCGTTGATTCAATTCATATTGATGAATTAAGGCAAAGTTGAACAAGTTC
TTCTC
Found at i:3879494 original size:137 final size:137
Alignment explanation
Indices: 3879190--3879650 Score: 606
Period size: 137 Copynumber: 3.4 Consensus size: 137
3879180 AGTTTTTCAG
* * *
3879190 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTAGAAATGTTG
*
3879255 ATCCTCAAAAGAGGTATCGTTGATTCAATTTCATAT-TGATGAATTAAGGCAAAGTTGAACAAGT
66 ATCCTCAAAAGAGGTATCGTTGATTCAACTTCATATGTGATGAATTAAGGCAAAGTTGAACAAGT
3879319 TCTTCTC
131 TCTTCTC
* * * * *
3879326 ATTATGAACTTCCTCTTTCTCTTCAGATGAGTTCTTCTCATTGTGAACTCCTTCTAGAAATGCTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTAGAAATGTTG
* * *
3879391 ATCCTCAAAAGCGGTGTCGTTGATTCAACTTCATATGTGATGAATTAAGGCAATGTTGAACAAGT
66 ATCCTCAAAAGAGGTATCGTTGATTCAACTTCATATGTGATGAATTAAGGCAAAGTTGAACAAGT
3879456 TCTTCTC
131 TCTTCTC
* *
3879463 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACT--TTCTCTGAAAATAT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCT-AG-AAATGT
* ** * * * * * ** * *
3879526 TGATCTTCAGGAGAGGTTCTTCTTTCATTCAAC-TCTATAGGTGATGAATCAAGTTAAGGTCGAA
64 TGATCCTCAAAAGAGG-T-ATCGTTGATTCAACTTC-ATATGTGATGAATTAAGGCAAAGTTGAA
3879590 CAAGTTCTTCTC
126 CAAGTTCTTCTC
*
3879602 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTTATTATGAACT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACT
3879651 TTCTTTGGAA
Statistics
Matches: 289, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
135 4 0.01
136 94 0.33
137 95 0.33
138 3 0.01
139 93 0.32
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (137 bp):
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTATGAACTCCTTCTAGAAATGTTG
ATCCTCAAAAGAGGTATCGTTGATTCAACTTCATATGTGATGAATTAAGGCAAAGTTGAACAAGT
TCTTCTC
Found at i:3879758 original size:83 final size:82
Alignment explanation
Indices: 3879631--3879814 Score: 262
Period size: 83 Copynumber: 2.2 Consensus size: 82
3879621 TCTTCAGATG
* * * * * *
3879631 AGTTTTTCTTATTATGAACTTTCTTTGGAAATGTTGGTGTTGATCTATCTCCTTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTTC-TTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA
*
3879696 TCGAGCAAAAGGTTGAACA
65 TCAAGC-AAAGGTTGAACA
*
3879715 AGTTCTTCTCATTATGAACTCTTC-TGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
1 AGTTCTTCTCATTATGAACT-TTCTTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA
3879779 TCAAGCAAAGGTTGAACA
65 TCAAGCAAAGGTTGAACA
3879797 AGTTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
3879815 TTTTTCTTCC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
82 30 0.33
83 40 0.44
84 18 0.20
85 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (82 bp):
AGTTCTTCTCATTATGAACTTTCTTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAAT
CAAGCAAAGGTTGAACA
Found at i:3879891 original size:121 final size:122
Alignment explanation
Indices: 3879715--3880116 Score: 596
Period size: 121 Copynumber: 3.3 Consensus size: 122
3879705 AGGTTGAACA
*
3879715 AGTTCTTCTCATTATGAACTCT-TCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
* *
3879779 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTTTTCTTCCTCTTTAGATG
66 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* * * *
3879835 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
** * *
3879900 TTGAGCAAAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTC-TCCTTCTTCAGATG
66 TCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATG
* * * * *
3879958 AGTTCTTCTTATTATGAAC-TCCTCTGGAAAAGTTGATGATGATCTATCGCTTTATGTGATAGAA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
3880022 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
66 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* *
3880079 AGTTCTTCTCATTATGAACTTTCTCTAGAAATGTTGAT
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
3880117 CCATCGATCA
Statistics
Matches: 248, Mismatches: 28, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
120 21 0.08
121 105 0.42
122 90 0.36
123 32 0.13
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (122 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAA
TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
Found at i:3879922 original size:204 final size:205
Alignment explanation
Indices: 3879566--3879944 Score: 627
Period size: 204 Copynumber: 1.9 Consensus size: 205
3879556 AACTCTATAG
**
3879566 GTGATGAATCAAGTTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
1 GTGATGAATCAAGCAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* * * *
3879631 AGTTTTTCTTATTATGAACTTTCTTTGGAAATGTTGGTGTTGATCTATCTCCTTCTGTGATAGAG
66 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAG
*
3879696 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTGGAAAAGTTGATGCTGATCT
131 TCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTGGAAAAGTTGATGCTGATCT
3879760 ATCTCTTTCT
196 ATCTCTTTCT
* * *
3879770 GTGATAGAATCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTTTTCTTCCTCTTTAGAT
1 GTGAT-GAATCAAGCAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
3879834 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGA
65 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGA
* *
3879899 GTTGAGCAAAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTCT
130 GTCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCT
3879945 CCTTCTTCAG
Statistics
Matches: 161, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
204 119 0.74
205 42 0.26
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (205 bp):
GTGATGAATCAAGCAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAG
TCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTGGAAAAGTTGATGCTGATCT
ATCTCTTTCT
Found at i:3880127 original size:102 final size:102
Alignment explanation
Indices: 3880021--3880225 Score: 358
Period size: 102 Copynumber: 2.0 Consensus size: 102
3880011 ATGTGATAGA
3880021 ATCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
1 ATCAAGCTAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
* * *
3880085 TCTCATTATGAACTTTCTCTAGAAATGTTGATCCATCG
65 TCTCATTACGAACTTTATCTAGAAATGTTGACCCATCG
3880123 ATCAAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
1 ATCAAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
*
3880188 CTCATTACGAACTTTATCTGGAAATGTTGACCCATCG
66 CTCATTACGAACTTTATCTAGAAATGTTGACCCATCG
3880225 A
1 A
3880226 ATGATGGATC
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 95 0.97
103 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (102 bp):
ATCAAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
CTCATTACGAACTTTATCTAGAAATGTTGACCCATCG
Found at i:3884447 original size:71 final size:72
Alignment explanation
Indices: 3884331--3884465 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 72
3884321 AGTATAATAA
*
3884331 ATTAGTTGAATATTATCCATAAAGCCAGGGCGATTAACAAATTGCTTTAG-GGGATAACTCAAGC
1 ATTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACAAATTGCTTTAGTGGGATAACTCAAGC
3884395 ATAACAG
66 ATAACAG
* * * *
3884402 ATTAGCTGAATATTATCCATAAATCCGGGGCTATTAACCAATTGCTTTAGTGGGATAACTCAAG
1 ATTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACAAATTGCTTTAGTGGGATAACTCAAG
3884466 TTTTATTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
71 45 0.78
72 13 0.22
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (72 bp):
ATTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACAAATTGCTTTAGTGGGATAACTCAAGC
ATAACAG
Found at i:3888472 original size:46 final size:46
Alignment explanation
Indices: 3888385--3888472 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
3888375 AGGTATAAAT
*
3888385 CCTAACCTCATGATTTCTAGTTCCATGCTTTATTTATAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCCATGCTTTATTTAGAAAAATTAA
* *
3888431 CCTAA-CTGCATGATTTCTAGTTCCATGCTTTGTTTCGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCCATGCTTTATTTAGAAAAA
3888473 AATGAAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (46 bp):
CCTAACCTCATGATTTCTAGTTCCATGCTTTATTTAGAAAAATTAA
Found at i:3889798 original size:2 final size:2
Alignment explanation
Indices: 3889791--3889823 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3889781 TTAATCTTTC
3889791 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
3889824 CACACACACA
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:3894985 original size:23 final size:23
Alignment explanation
Indices: 3894958--3895027 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
3894948 GTCAGCACAG
* *
3894958 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAATTGCACCGAAGTGC
*
3894981 CTCATAGAATTGCACCGCAGTGC
1 CTCATAGAATTGCACCGAAGTGC
* * *
3895004 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGAAGTGC
3895027 C
1 C
3895028 ATATAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (23 bp):
CTCATAGAATTGCACCGAAGTGC
Found at i:3895215 original size:103 final size:103
Alignment explanation
Indices: 3895044--3895364 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
3895034 TAATGTCCAT
* *
3895044 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGTTCAAGTACGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
3895109 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3895147 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
3895212 GACTTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3895250 AAGGACCACATATTATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
3895315 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3895353 AAGGACCACATA
1 AAGGACCACATA
3895365 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3899312 original size:23 final size:23
Alignment explanation
Indices: 3899285--3899354 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
3899275 GTCAGCACAG
*
3899285 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* *
3899308 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* * *
3899331 GC-CGTAGAATTGCACCGTAGTGC
1 -CTCATAGAAATGCACCGAAGTGC
3899354 C
1 C
3899355 ATATAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCATAGAAATGCACCGAAGTGC
Found at i:3899542 original size:103 final size:103
Alignment explanation
Indices: 3899375--3899691 Score: 580
Period size: 103 Copynumber: 3.1 Consensus size: 103
3899365 GTCCATAAGT
* *
3899375 ACCACATATCATTCCTAAAGAATCATATACATATGCCAAGGATCAAGTACGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
* *
3899440 TCACGCATGTTCCAAATAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
3899478 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
3899543 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
* *
3899581 ACCACATATCATTCCTTAAGAATCATATACATATTCCAAGGATCAAGTATGTGTCTCACCATACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
3899646 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
3899684 ACCACATA
1 ACCACATA
3899692 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:3900908 original size:21 final size:21
Alignment explanation
Indices: 3900869--3900908 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3900859 TTTTGTTCGT
* *
3900869 TTGAAGGGGTATCGGTTCCTA
1 TTGAAGGGGTACCGATTCCTA
*
3900890 TTGAATGGGTACCGATTCC
1 TTGAAGGGGTACCGATTCC
3900909 CCTTGCCCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCTA
Found at i:3907556 original size:22 final size:23
Alignment explanation
Indices: 3907499--3907579 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 23
3907489 AGGTATATCA
*
3907499 AATATATAATTTTAAGTAAAATA-T
1 AATAT-TAATTTTAAG-AATATATT
3907523 AATATAAATAATTTTAA-AATATATT
1 AATAT---TAATTTTAAGAATATATT
*
3907548 ACTATTAA-TTTAAGAATATATT
1 AATATTAATTTTAAGAATATATT
*
3907570 AATATCAATT
1 AATATTAATT
3907580 AATGTCATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
21 5 0.10
22 17 0.35
23 1 0.02
24 10 0.21
25 5 0.10
26 10 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AATATTAATTTTAAGAATATATT
Found at i:3909531 original size:74 final size:74
Alignment explanation
Indices: 3909410--3909556 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 74
3909400 CACAAAAGCA
* *
3909410 CCGAGCAACCTTGGAAATCATCCGGCACATCTCAGCACGCGATCACAAAAGAATAAATCGATAAC
1 CCGAGCAACCTCGGAAATCATCCGGCACATCTCAGCACGAGATCACAAAAGAATAAATCGATAAC
3909475 AAGTTTATT
66 AAGTTTATT
* * ** *
3909484 CCGAGCAACCTCGTAAATCATCCGGCACATTTCTTCACGAGATCACAAAGGAATAAATCGATAAC
1 CCGAGCAACCTCGGAAATCATCCGGCACATCTCAGCACGAGATCACAAAAGAATAAATCGATAAC
3909549 AAGTTTAT
66 AAGTTTAT
3909557 CCCTACAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (74 bp):
CCGAGCAACCTCGGAAATCATCCGGCACATCTCAGCACGAGATCACAAAAGAATAAATCGATAAC
AAGTTTATT
Found at i:3927516 original size:31 final size:31
Alignment explanation
Indices: 3927478--3927541 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3927468 TGATCATTAT
3927478 TTATAGGATGTGATGAAATAAAAACTGAAAC
1 TTATAGGATGTGATGAAATAAAAACTGAAAC
3927509 TTATAGGATGTGATGAAATAAAAACTGAAAC
1 TTATAGGATGTGATGAAATAAAAACTGAAAC
3927540 TT
1 TT
3927542 TTTATTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (31 bp):
TTATAGGATGTGATGAAATAAAAACTGAAAC
Found at i:3928816 original size:2 final size:2
Alignment explanation
Indices: 3928809--3928846 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3928799 CTTAATTAGC
3928809 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
3928847 TTATTTGTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3941111 original size:161 final size:161
Alignment explanation
Indices: 3940899--3941227 Score: 631
Period size: 161 Copynumber: 2.0 Consensus size: 161
3940889 GATCAATATA
3940899 TTCTTATCAACAATCAATGCAAAGGAAACAAAGAAGGATGATCTAAATTTGCGAAGGAAAAAAGG
1 TTCTTATCAACAATCAATGCAAAGGAAACAAAGAAGGATGATCTAAATTTGCGAAGGAAAAAAGG
3940964 ACCATTCAGTTAGGGCTTTTGGGTCTAGTATTTCTTAACAAATAAACAAACCATGAGTACAACAA
66 ACCATTCAGTTAGGGCTTTTGGGTCTAGTATTTCTTAACAAATAAACAAACCATGAGTACAACAA
*
3941029 TGAAACTCAAATACTAGCACATGGGGAAGAT
131 TGAAACTCAAATACTAGCACATGGGCAAGAT
*
3941060 TTCTTATCAACAATCAATGCAAAGGAAACAAAGAAGGATGATCTCAATTTGCGAAGGAAAAAAGG
1 TTCTTATCAACAATCAATGCAAAGGAAACAAAGAAGGATGATCTAAATTTGCGAAGGAAAAAAGG
*
3941125 ACCATTCAGTTAGGGCTTTTGGGTCTAGTATTTCTTAACAAATAAACAAACCATGAGTACGACAA
66 ACCATTCAGTTAGGGCTTTTGGGTCTAGTATTTCTTAACAAATAAACAAACCATGAGTACAACAA
3941190 TGAAACTCAAATACTAGCACATGGGCAAGAT
131 TGAAACTCAAATACTAGCACATGGGCAAGAT
3941221 TTCTTAT
1 TTCTTAT
3941228 TCAGTCATCT
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 165 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (161 bp):
TTCTTATCAACAATCAATGCAAAGGAAACAAAGAAGGATGATCTAAATTTGCGAAGGAAAAAAGG
ACCATTCAGTTAGGGCTTTTGGGTCTAGTATTTCTTAACAAATAAACAAACCATGAGTACAACAA
TGAAACTCAAATACTAGCACATGGGCAAGAT
Found at i:3941864 original size:40 final size:40
Alignment explanation
Indices: 3941813--3942194 Score: 584
Period size: 40 Copynumber: 9.3 Consensus size: 40
3941803 TCCAAGTTCG
*
3941813 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
3941853 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* *
3941895 CGTTGCGATAGTTGAAAATTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCG-AAGTTCGCGTTGCGATTTTCCAAATT
3941936 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
3941976 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
*
3942018 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
**
3942058 CGTTGCGATAGTTAAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
* *
3942098 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTTTTCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA--TTTTCCAAATT
* *
3942140 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
3942182 CGTTGCGATAGTC
1 CGTTGCGATAGTC
3942195 CAAAATCGCA
Statistics
Matches: 316, Mismatches: 18, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
40 153 0.48
41 31 0.10
42 119 0.38
43 13 0.04
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:3942040 original size:82 final size:81
Alignment explanation
Indices: 3941813--3942194 Score: 588
Period size: 82 Copynumber: 4.7 Consensus size: 81
3941803 TCCAAGTTCG
* *
3941813 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
3941878 GCGATTTATTCCAAATT
66 GCGATTT-TTCCAAATT
* *
3941895 CGTTGCGATAGTTGAAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 CGTTGCGATAGTCG-AAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
3941960 TGCGA-TTTTCCAAATT
65 TGCGATTTTTCCAAATT
*
3941976 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
3942041 TTGCGA-TTTTCCAAATT
64 TTGCGATTTTTCCAAATT
** *
3942058 CGTTGCGATAGTTAAAGTTCGCGTTGCGATTTTCCAAATTCGTTACGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
*
3942123 GCGATTTTTTCAAAATT
66 GCGA-TTTTTCCAAATT
* *
3942140 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTC
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTC
3942195 CAAAATCGCA
Statistics
Matches: 277, Mismatches: 16, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
80 50 0.18
81 26 0.09
82 127 0.46
83 54 0.19
84 20 0.07
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (81 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTTTCCAAATT
Found at i:3942109 original size:122 final size:122
Alignment explanation
Indices: 3941813--3942194 Score: 629
Period size: 122 Copynumber: 3.1 Consensus size: 122
3941803 TCCAAGTTCG
* *
3941813 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
* *
3941878 GCGATTTATTCCAAATTCGTTGCGATAGTTGAAAATTCGCGTTGCGATTTTCCAAATT
66 GCGATTTATTCCAAATTCGTTGCGATAGTCG-AAGTTCGCGTTGCGATTTTCCAAATT
3941936 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
*
3942001 GCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
66 GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
** *
3942058 CGTTGCGATAGTTAAAGTTCGCGTTGCGATTTTCCAAATTCGTTACGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
* * * *
3942123 GCGATTTTTTCAAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
66 GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
3942182 CGTTGCGATAGTC
1 CGTTGCGATAGTC
3942195 CAAAATCGCA
Statistics
Matches: 243, Mismatches: 14, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
122 129 0.53
123 94 0.39
124 20 0.08
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (122 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:3943083 original size:21 final size:21
Alignment explanation
Indices: 3942907--3943113 Score: 162
Period size: 21 Copynumber: 10.0 Consensus size: 21
3942897 CGTTGCGATT
*
3942907 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
3942926 TTGGAATAAATCGTAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
3942949 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
3942968 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
3942991 AAT-GACTATCGCAA--CGAAC
1 -TTGGACTATCGCAACGCGAAC
*
3943010 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
3943033 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
3943052 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
3943073 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
3943094 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
3943114 TATGTAAATC
Statistics
Matches: 146, Mismatches: 26, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.01
19 38 0.26
21 80 0.55
23 26 0.18
24 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:3943098 original size:42 final size:42
Alignment explanation
Indices: 3942910--3943088 Score: 301
Period size: 42 Copynumber: 4.3 Consensus size: 42
3942900 TGCGATTTTG
*
3942910 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
3942952 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACAAT-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC-TTC
*
3942994 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
3943036 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
3943076 GACTATCGCAACG
1 GACTATCGCAACG
3943089 CGAACTTGGA
Statistics
Matches: 130, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
40 32 0.25
41 2 0.02
42 95 0.73
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:3943113 original size:42 final size:41
Alignment explanation
Indices: 3942910--3943113 Score: 270
Period size: 42 Copynumber: 4.9 Consensus size: 41
3942900 TGCGATTTTG
* *
3942910 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
3942952 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACAAT-
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC-TTC
3942994 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
3943036 GACTATCGCAACGAATTTGGAA-AATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
* *
3943076 GACTATCGCAACGCGAACTTGGACT-ATCGCAATGCGAA
1 GACTATCGCAA--CGAACTTGGAATAATCGCAACGCGAA
3943114 TATGTAAATC
Statistics
Matches: 149, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
40 29 0.19
41 1 0.01
42 118 0.79
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
Found at i:3946753 original size:21 final size:21
Alignment explanation
Indices: 3946729--3946771 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3946719 AATCCTAGCT
*
3946729 TCCAACCCCAAAATTC-CTAAA
1 TCCAAACCCAAAA-TCACTAAA
*
3946750 TCCAAACCCTAAATCACTAAA
1 TCCAAACCCAAAATCACTAAA
3946771 T
1 T
3946772 TCCCCACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (21 bp):
TCCAAACCCAAAATCACTAAA
Found at i:3947100 original size:2 final size:2
Alignment explanation
Indices: 3947095--3947131 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3947085 TTTGGTCAAT
3947095 TA TA 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 TA TA T
3947132 GAGATAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3958921 original size:15 final size:16
Alignment explanation
Indices: 3958903--3958935 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3958893 AATTTTCAAG
3958903 TTTTTAAAT-ATAATA
1 TTTTTAAATAATAATA
*
3958918 TTTTTATATAATAATA
1 TTTTTAAATAATAATA
3958934 TT
1 TT
3958936 AATTGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAAATAATAATA
Found at i:3966872 original size:21 final size:21
Alignment explanation
Indices: 3966848--3966887 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3966838 TATAATTGTA
3966848 ATAAAATAAAATAAAATAAAC
1 ATAAAATAAAATAAAATAAAC
* * *
3966869 ATAATATAATATAATATAA
1 ATAAAATAAAATAAAATAA
3966888 TATAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAAATAAAATAAAATAAAC
Found at i:3966898 original size:5 final size:5
Alignment explanation
Indices: 3966832--3966898 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
3966822 CAACGGTAAT
* * * * *
3966832 TATAA TTATAA TTGTAA TAAAA TAAAA TAAAA TA-AA CATAA TATAA TATAA
1 TATAA -TATAA -TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
3966883 TATAA TATAA TATAA T
1 TATAA TATAA TATAA T
3966899 CGAGCTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
4 3 0.05
5 42 0.76
6 10 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:3969338 original size:2 final size:2
Alignment explanation
Indices: 3969294--3969327 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3969284 TTTTTAAAGA
3969294 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
3969328 TAGTAATATA
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:3984161 original size:20 final size:20
Alignment explanation
Indices: 3984129--3984166 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3984119 TCACTAACTT
*
3984129 TGTAAAAAGAAAAGGAAAAC
1 TGTAAAAAGAAAAAGAAAAC
3984149 TGTAAACAA-AAAAAGAAA
1 TGTAAA-AAGAAAAAGAAA
3984167 GAAGGAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (20 bp):
TGTAAAAAGAAAAAGAAAAC
Found at i:3990921 original size:38 final size:36
Alignment explanation
Indices: 3990862--3990965 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 36
3990852 TTTTCGGGTT
3990862 GGGTCGGG-TTTTTTAAGTGTGATATTCAGGTCGATTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCG--TC
3990899 GGGTCGGGTTTTTTTAAGTGTGATATTCA-G--GTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGTC
* * *
3990932 GGGTCAGGTTTTTTAAAGTGTGATATTCGGGTCG
1 GGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCG
3990966 GGTTTGGGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
33 28 0.47
34 1 0.02
35 1 0.02
36 1 0.02
37 9 0.15
38 20 0.33
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (36 bp):
GGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGTC
Found at i:3997998 original size:23 final size:23
Alignment explanation
Indices: 3997972--3998040 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3997962 CACCACAGCT
*
3997972 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
3997995 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
3998018 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3998041 TATAAGGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4002988 original size:23 final size:23
Alignment explanation
Indices: 4002962--4003030 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
4002952 CACCACAGCT
*
4002962 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
4002985 CGTAGAATTGCAACGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
4003008 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4003031 TTTAAGGTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4006354 original size:15 final size:15
Alignment explanation
Indices: 4006331--4006360 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4006321 ATCTGGGTGT
4006331 AGAGAAGTTCTAGAA
1 AGAGAAGTTCTAGAA
*
4006346 AGAGCAGTTCTAGAA
1 AGAGAAGTTCTAGAA
4006361 GACTAGGTTG
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:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (15 bp):
AGAGAAGTTCTAGAA
Found at i:4009123 original size:22 final size:22
Alignment explanation
Indices: 4009095--4009188 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
4009085 AATTTGGAAA
* *
4009095 ATCGCAACGACAATTATAGACT
1 ATCGCAACGACAACTGTAGACT
*
4009117 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
4009139 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
4009158 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
4009180 ATCGCAACG
1 ATCGCAACG
4009189 CGAAATGGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 2 0.04
22 40 0.70
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:4009162 original size:41 final size:41
Alignment explanation
Indices: 4009117--4009207 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
4009107 ATTATAGACT
*
4009117 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAACCGAA-ATGGAAA
*
4009158 ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAAC-CGAAATGGAAA
4009200 ATCGCAAC
1 ATCGCAAC
4009208 GCGAAATGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 28 0.61
42 14 0.30
43 4 0.09
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (41 bp):
ATCGCAACAACAACTGTAGACTATCGCAACCGAAATGGAAA
Found at i:4010122 original size:12 final size:13
Alignment explanation
Indices: 4010105--4010133 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4010095 CTTAATTACA
4010105 AAAATTAAAA-TT
1 AAAATTAAAATTT
4010117 AAAATTAAAATTT
1 AAAATTAAAATTT
4010130 AAAA
1 AAAA
4010134 ATTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:4012258 original size:152 final size:152
Alignment explanation
Indices: 4011978--4012281 Score: 590
Period size: 152 Copynumber: 2.0 Consensus size: 152
4011968 TCCTTCGTCG
4011978 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
4012043 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
4012108 TGAAATCCAATGTTGTTTGTGA
131 TGAAATCCAATGTTGTTTGTGA
4012130 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
* *
4012195 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
4012260 TGAAATCCAATGTTGTTTGTGA
131 TGAAATCCAATGTTGTTTGTGA
4012282 GCACGATATC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (152 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
TGAAATCCAATGTTGTTTGTGA
Found at i:4012412 original size:170 final size:170
Alignment explanation
Indices: 4012130--4012610 Score: 917
Period size: 170 Copynumber: 2.8 Consensus size: 170
4012120 TTGTTTGTGA
*
4012130 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
*
4012195 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
4012260 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
4012300 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
*
4012365 ATGAAACTGGGAAGCCCCTTCGTTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
4012430 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
*
4012470 TGAAGTTGAAATCGTTGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
*
4012535 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
4012600 TGAAATCCAAT
131 TGAAATCCAAT
4012611 CTTCAGTAAA
Statistics
Matches: 305, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 305 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (170 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
Found at i:4012478 original size:46 final size:44
Alignment explanation
Indices: 4012426--4012525 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
4012416 TTTCGCTGTA
* * *
4012426 AAGTTGAAATCCAATGTTGTTTGTGAG-CACGATATCCTTCGTCGTG
1 AAGTTGAAAT-CAATGATGTTT-CGAGTC-CAATATCCTTCGTCGTG
**
4012472 AAGTTGAAATCGTTGATGTTTCGAGTCCAATATCCTTCGTCGTG
1 AAGTTGAAATCAATGATGTTTCGAGTCCAATATCCTTCGTCGTG
4012516 AAGTTGAAAT
1 AAGTTGAAAT
4012526 TGGCTCTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 29 0.60
45 9 0.19
46 10 0.21
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (44 bp):
AAGTTGAAATCAATGATGTTTCGAGTCCAATATCCTTCGTCGTG
Found at i:4013492 original size:9 final size:10
Alignment explanation
Indices: 4013477--4013503 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4013467 AACATTTTTC
4013477 TCTTTTTTGT
1 TCTTTTTTGT
4013487 TCTTTTTTGT
1 TCTTTTTTGT
4013497 TCTTTTT
1 TCTTTTT
4013504 CTTTTTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (10 bp):
TCTTTTTTGT
Found at i:4020255 original size:39 final size:39
Alignment explanation
Indices: 4020201--4020280 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
4020191 TTAACAGTAG
* *
4020201 ATGCAGCTTTCCCTTTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
4020240 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
4020279 AT
1 AT
4020281 ACTCCGGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:4022921 original size:17 final size:18
Alignment explanation
Indices: 4022899--4022941 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
4022889 AAAAGTTAGT
*
4022899 AAAAAAATAAAC-AAATA
1 AAAAAAATAAACGAAAGA
4022916 AAAAAAAT-AACGAAAGA
1 AAAAAAATAAACGAAAGA
4022933 AAAAAAATA
1 AAAAAAATA
4022942 CAAAAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (18 bp):
AAAAAAATAAACGAAAGA
Found at i:4023735 original size:12 final size:13
Alignment explanation
Indices: 4023718--4023746 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4023708 CTTAATTACA
4023718 AAAATTAAAA-TT
1 AAAATTAAAATTT
4023730 AAAATTAAAATTT
1 AAAATTAAAATTT
4023743 AAAA
1 AAAA
4023747 ATTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:4033405 original size:23 final size:23
Alignment explanation
Indices: 4033379--4033446 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
4033369 ATTATTATAT
*
4033379 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
4033402 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
4033425 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
4033447 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:4043041 original size:21 final size:21
Alignment explanation
Indices: 4043015--4043054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4043005 CCCCCTTTAA
*
4043015 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
4043036 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
4043055 CTGGGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Done.