Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 22 of 22
Found at i:3983776 original size:6 final size:6
Alignment explanation
Indices: 3983765--3983808 Score: 70
Period size: 6 Copynumber: 7.0 Consensus size: 6
3983755 AACATTGATT
3983765 TGATGG TGATGG TGATGG TGATGG TGATGAGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGAT--GG TGATGG TGATGG
3983809 AAGGAAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 30 0.83
8 6 0.17
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
TGATGG
Found at i:3984082 original size:10 final size:10
Alignment explanation
Indices: 3984064--3984112 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
3984054 AAGACACAAA
3984064 GAAAAGAAAT
1 GAAAAGAAAT
*
3984074 GAAATGAAAT
1 GAAAAGAAAT
*
3984084 GAAATGAAAT
1 GAAAAGAAAT
*
3984094 GGAAAGGAAA-
1 -GAAAAGAAAT
3984104 GAAAAGAAA
1 GAAAAGAAA
3984113 AGAATGACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.23
10 19 0.54
11 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.10
Consensus pattern (10 bp):
GAAAAGAAAT
Found at i:3984087 original size:15 final size:15
Alignment explanation
Indices: 3984064--3984116 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3984054 AAGACACAAA
3984064 GAAAAGAAATGAAAT
1 GAAAAGAAATGAAAT
*
3984079 GAAATGAAATGAAAT
1 GAAAAGAAATGAAAT
* *
3984094 GGAAAGGAAA-GAAAA
1 -GAAAAGAAATGAAAT
3984109 GAAAAGAA
1 GAAAAGAA
3984117 TGACTCTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 7 0.21
15 18 0.55
16 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (15 bp):
GAAAAGAAATGAAAT
Found at i:3984588 original size:2 final size:2
Alignment explanation
Indices: 3984581--3984616 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3984571 CATTGTGAAA
* *
3984581 AT AT AT AT AC AT AC 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
3984617 CATTGAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3989851 original size:21 final size:21
Alignment explanation
Indices: 3989825--3989865 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3989815 ACTAAATCTC
3989825 TTCATAATTCAAATATTACTT
1 TTCATAATTCAAATATTACTT
3989846 TTCATAATTCAAATATTACT
1 TTCATAATTCAAATATTACT
3989866 CTCGTCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
TTCATAATTCAAATATTACTT
Found at i:3990058 original size:35 final size:35
Alignment explanation
Indices: 3990005--3990076 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
3989995 TGCTTTATAT
* * *
3990005 TATTTTATCAAATAATTTTTTTAATATTTATTACA
1 TATTTTATAAAATAATTTTTATAATATTTAATACA
*
3990040 TATTTTA-AAAATATATTTTTATAATTTTTAATACA
1 TATTTTATAAAATA-ATTTTTATAATATTTAATACA
3990075 TA
1 TA
3990077 CAATACATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (35 bp):
TATTTTATAAAATAATTTTTATAATATTTAATACA
Found at i:3991616 original size:18 final size:19
Alignment explanation
Indices: 3991593--3991632 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3991583 TTATTTTTAT
3991593 AAAATAAAAAA-CAATTAA
1 AAAATAAAAAATCAATTAA
*
3991611 AAAATAAAAAATTAATTAA
1 AAAATAAAAAATCAATTAA
3991630 AAA
1 AAA
3991633 TTTTGTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAATAAAAAATCAATTAA
Found at i:3991739 original size:17 final size:17
Alignment explanation
Indices: 3991713--3991762 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
3991703 TAATATGATA
* *
3991713 TTTTATATAAATTAATT
1 TTTTAAATAAAATAATT
3991730 TTTTAAATAAAATAATT
1 TTTTAAATAAAATAATT
*
3991747 TTTAAAATAAAATAAT
1 TTTTAAATAAAATAAT
3991763 AAAATTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAATAAAATAATT
Found at i:3991796 original size:19 final size:18
Alignment explanation
Indices: 3991756--3991819 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
3991746 TTTTAAAATA
*
3991756 AAATAATAAAATTAGTAA-T
1 AAAT-ATAAAA-TAATAATT
3991775 AAATATAACAGATAAT-ATT
1 AAATATAA-A-ATAATAATT
3991794 AAA-ATAAAATAATAATT
1 AAATATAAAATAATAATT
3991811 AAATTATAA
1 AAA-TATAA
3991820 TGTAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
16 5 0.13
17 7 0.18
18 9 0.24
19 16 0.42
20 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATATAAAATAATAATT
Found at i:3991871 original size:25 final size:26
Alignment explanation
Indices: 3991843--3991893 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3991833 AAATAAAAAA
*
3991843 TTTTATCATT-AATAAATTTTTAAAT
1 TTTTATCATTAAATAAATTATTAAAT
* *
3991868 TTTTATTATTAAATATATTATTAAAT
1 TTTTATCATTAAATAAATTATTAAAT
3991894 CATTATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATCATTAAATAAATTATTAAAT
Found at i:3992550 original size:8 final size:8
Alignment explanation
Indices: 3992539--3992578 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
3992529 TTTTATTTTA
*
3992539 TATATATA
1 TATATATG
3992547 TATATATG
1 TATATATG
3992555 TATATATG
1 TATATATG
*
3992563 TATGTATG
1 TATATATG
3992571 TATATATG
1 TATATATG
3992579 GAATGGAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:3992558 original size:12 final size:12
Alignment explanation
Indices: 3992537--3992578 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3992527 GGTTTTATTT
*
3992537 TATATATATATA
1 TATATGTATATA
3992549 TATATGTATATA
1 TATATGTATATA
* *
3992561 TGTATGTATGTA
1 TATATGTATATA
3992573 TATATG
1 TATATG
3992579 GAATGGAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TATATGTATATA
Found at i:3995415 original size:2 final size:2
Alignment explanation
Indices: 3995408--3995445 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3995398 AGATACATAC
* *
3995408 AT AT AT AT AT AT AT AT AT AT AT GT AA AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3995446 AAAGATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3998901 original size:6 final size:6
Alignment explanation
Indices: 3998890--3998916 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3998880 TTTAAACATT
3998890 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
3998917 GAAATAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3999763 original size:2 final size:2
Alignment explanation
Indices: 3999756--3999796 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3999746 GCCTTTCTTT
*
3999756 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3999797 CAGAGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4002945 original size:20 final size:20
Alignment explanation
Indices: 4002922--4002962 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4002912 GCAAGGTGTT
4002922 GATAACATTTTGTAGTTTTA
1 GATAACATTTTGTAGTTTTA
4002942 GATAACATTTTGTAGTTTTA
1 GATAACATTTTGTAGTTTTA
4002962 G
1 G
4002963 TTCACGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (20 bp):
GATAACATTTTGTAGTTTTA
Found at i:4005264 original size:4 final size:4
Alignment explanation
Indices: 4005247--4005373 Score: 155
Period size: 4 Copynumber: 31.8 Consensus size: 4
4005237 GCAGGGAAGA
* * * * *
4005247 ATAT ATAC ATAT ATAT ATAT ATGT ATAT ATAT ACAT ACAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
4005295 ATAT ATGT ATAT GTAT ATAT ATAC ATAT ATAT ATAT ATAT ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
4005343 ATAT ATAT ATAT ATGT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
4005374 CGAGTGAACA
Statistics
Matches: 105, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 105 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:4005266 original size:14 final size:14
Alignment explanation
Indices: 4005247--4005374 Score: 115
Period size: 14 Copynumber: 9.6 Consensus size: 14
4005237 GCAGGGAAGA
4005247 ATATATACATATAT
1 ATATATACATATAT
*
4005261 ATATAT--ATGTAT
1 ATATATACATATAT
*
4005273 ATATATACATACAT
1 ATATATACATATAT
*
4005287 ATATAT--GTATAT
1 ATATATACATATAT
* *
4005299 ATGTAT--ATGTAT
1 ATATATACATATAT
4005311 ATATATACATATAT
1 ATATATACATATAT
* *
4005325 ATATATATATATAC
1 ATATATACATATAT
* *
4005339 ATACATATATATAT
1 ATATATACATATAT
* *
4005353 ATATGTATATATAT
1 ATATATACATATAT
4005367 ATATATAC
1 ATATATAC
4005375 GAGTGAACAC
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
12 29 0.32
14 63 0.68
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:4008676 original size:2 final size:2
Alignment explanation
Indices: 4008669--4008696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4008659 ATACTTTGTA
4008669 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
4008697 TATCTGTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4012093 original size:3 final size:3
Alignment explanation
Indices: 4012087--4012129 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
4012077 AGGAGCCATA
4012087 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4012130 TAGGTTCTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4027846 original size:2 final size:2
Alignment explanation
Indices: 4027839--4027863 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4027829 TTTTCCACAA
4027839 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
4027864 AATATATACT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4028455 original size:2 final size:2
Alignment explanation
Indices: 4028448--4028478 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4028438 AGTATTTATC
4028448 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 T
4028479 CAAATAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4039087 original size:297 final size:290
Alignment explanation
Indices: 4038255--4039109 Score: 1330
Period size: 286 Copynumber: 2.9 Consensus size: 290
4038245 ACATATCAGG
* ** ** *
4038255 TAACTCACAAGAAAAGCAAACACCTAAAATTGTTTTAAGTGGTTACAAGTT-AAAATGAATACAG
1 TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAATACAG
* * * *
4038319 ATAATTAACACAAAACCCGAA-AAATACTTAAATGTTGTGTTACGCAGGCCACAATGCAGAGAGC
66 ATAATTAACACAAAA-GCAAACAAATACTTAAATGTTGTGTTATGCATGCCACAATGCAGAGAGC
4038383 CTTCCTCCAATAGCCAAAAGAAAAACTTGAAAAACAAGGTAGCACTGTTAAATATAGCTTATGAT
130 CTTCCTCCAATAGCC-AAAGAAAAACTTGAAAAACAAGGTAGCACTGTTAAATATAGCTTATGAT
*
4038448 TGTGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTTCATAAGCACTCAAACTCATC
194 TGTGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTCCATAAGCACTCAAACTCATC
4038513 CCCTGCAACTATAATGTACTGGGTAGCACTGT
259 CCCTGCAACTATAATGTACTGGGTAGCACTGT
*
4038545 TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAATACAA
1 TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAATACAG
* * *
4038610 ATAATTAACACAAAAGCAAACAAATACGTAAA-----TGTTATGTATGCCACAATACAGAGAGCC
66 ATAATTAACACAAAAGCAAACAAATACTTAAATGTTGTGTTATGCATGCCACAATGCAGAGAGCC
*
4038670 TTCCTCCAATAGCCAAAGGAAAAACTTGAAAAACAAGGCAGCACTGTTAAATATAGCTTATGATT
131 TTCCTCCAATAGCCAAA-GAAAAACTTGAAAAACAAGGTAGCACTGTTAAATATAGCTTATGATT
4038735 GTGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTCCATAAGCACTCAAACTCATCC
195 GTGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTCCATAAGCACTCAAACTCATCC
4038800 CCTGCAACTATAATGTACTGGGTAGCACTGT
260 CCTGCAACTATAATGTACTGGGTAGCACTGT
*
4038831 TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAAAACAG
1 TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAATACAG
4038896 ATAATTAACA-AAAAGCAAACAAATACTTAAAAATTAAATGTTGTGTTATGCATGCCACAATGCA
66 ATAATTAACACAAAAGCAAACAAATAC-------TTAAATGTTGTGTTATGCATGCCACAATGCA
* * *
4038960 GACAGCCTTCCTCCAATAGCCAAAGAAGAAACTTGAAAAACAAGTTAGCATTGTTAAATATAGCT
124 GAGAGCCTTCCTCCAATAGCCAAAGAA-AAACTTGAAAAACAAGGTAGCACTGTTAAATATAGCT
* * * *
4039025 TATGATTATGTTATGTGCTAATGGAGAACATCTAGTTAGCACAAGACTGTCCATGAGCACTCAAA
188 TATGATTGTGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTCCATAAGCACTCAAA
*
4039090 CTCATCCCCTGCATCTATAA
253 CTCATCCCCTGCAACTATAA
4039110 CATACGGGGT
Statistics
Matches: 519, Mismatches: 30, Indels: 25
0.90 0.05 0.04
Matches are distributed among these distances:
285 19 0.04
286 252 0.49
290 48 0.09
291 37 0.07
292 4 0.01
296 3 0.01
297 156 0.30
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (290 bp):
TAACTCACAAAAAAAGCAAATTCCTAAAGCTGTTTTAAGTGCTTACAAGTTAAAAATGAATACAG
ATAATTAACACAAAAGCAAACAAATACTTAAATGTTGTGTTATGCATGCCACAATGCAGAGAGCC
TTCCTCCAATAGCCAAAGAAAAACTTGAAAAACAAGGTAGCACTGTTAAATATAGCTTATGATTG
TGTTATGTGCTAATGAAGAACATCTAGTTAGCACAAGACCGTCCATAAGCACTCAAACTCATCCC
CTGCAACTATAATGTACTGGGTAGCACTGT
Found at i:4041864 original size:3 final size:3
Alignment explanation
Indices: 4041856--4041889 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4041846 CGTCAACCAA
* *
4041856 CTT CTT CTT CTT CTT CTT CTC CTT GTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4041890 ATTTGGCACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:4046621 original size:2 final size:2
Alignment explanation
Indices: 4046614--4046641 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4046604 TCAATTCTAA
4046614 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
4046642 TGTATACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4048035 original size:6 final size:6
Alignment explanation
Indices: 4048024--4048048 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4048014 AGTATTTAGC
4048024 GTCAGA GTCAGA GTCAGA GTCAGA G
1 GTCAGA GTCAGA GTCAGA GTCAGA G
4048049 ACGCTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GTCAGA
Found at i:4053240 original size:3 final size:3
Alignment explanation
Indices: 4053232--4053261 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4053222 ATCTAGCAAA
4053232 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4053262 TGCATGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4053744 original size:2 final size:2
Alignment explanation
Indices: 4053739--4053776 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4053729 TATATGCATA
4053739 TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4053777 ATTGCACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4056882 original size:3 final size:3
Alignment explanation
Indices: 4056874--4056899 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4056864 ATATTATGAT
4056874 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
4056900 GTAAATAAAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4059440 original size:6 final size:6
Alignment explanation
Indices: 4059431--4059496 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
4059421 TTCGAATTAT
*
4059431 TTTAAA TTTAAA TTTAAA -TT-AA -TTAAT TTTAAA TTATTAAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -T-TT-AAA TTTAAA
4059478 -TTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
4059497 AATCAATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
4 6 0.12
5 7 0.14
6 29 0.57
7 3 0.06
8 3 0.06
9 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4059461 original size:21 final size:21
Alignment explanation
Indices: 4059432--4059499 Score: 91
Period size: 21 Copynumber: 3.0 Consensus size: 21
4059422 TCGAATTATT
4059432 TTAAATTTAAATTTAAATTAA
1 TTAAATTTAAATTTAAATTAA
*
4059453 TTAATTTTAAATTATTAAAATTTAA
1 TTAAATTTAAA-T-TT-AAA-TTAA
4059478 TTAAATTTAAATTTAAATTAA
1 TTAAATTTAAATTTAAATTAA
4059499 T
1 T
4059500 CAATTAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 15 0.37
22 4 0.10
23 4 0.10
24 4 0.10
25 14 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATTTAAATTTAAATTAA
Found at i:4059479 original size:14 final size:14
Alignment explanation
Indices: 4059438--4059497 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 14
4059428 TATTTTAAAT
4059438 TTAAATTTAAATTAA
1 TTAAATTTAAATT-A
*
4059453 TTAATTTTAAATTA
1 TTAAATTTAAATTA
4059467 TTAAAATTT-AATTAAA
1 TT-AAATTTAAATT--A
4059483 TTTAAATTTAAATTA
1 -TTAAATTTAAATTA
4059498 ATCAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 7 0.18
15 18 0.47
16 7 0.18
17 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTTAAATTA
Found at i:4059685 original size:3 final size:3
Alignment explanation
Indices: 4059677--4059712 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4059667 AAACTCTTAA
*
4059677 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4059713 TTGGTGTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4072096 original size:2 final size:2
Alignment explanation
Indices: 4072089--4072117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4072079 AGAGAAACAC
4072089 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4072118 CTAAAAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4075647 original size:15 final size:15
Alignment explanation
Indices: 4075627--4075656 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4075617 CCCCCCCCCC
4075627 CCCCCAAAAAAAAAA
1 CCCCCAAAAAAAAAA
4075642 CCCCCAAAAAAAAAA
1 CCCCCAAAAAAAAAA
4075657 TGTTCAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (15 bp):
CCCCCAAAAAAAAAA
Found at i:4075651 original size:16 final size:16
Alignment explanation
Indices: 4075626--4075656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4075616 CCCCCCCCCC
*
4075626 CCCCCCAAAAAAAAAA
1 CCCCCAAAAAAAAAAA
4075642 CCCCCAAAAAAAAAA
1 CCCCCAAAAAAAAAA
4075657 TGTTCAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCCCAAAAAAAAAAA
Found at i:4078091 original size:2 final size:2
Alignment explanation
Indices: 4078084--4078119 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4078074 CTGATGGGAC
* *
4078084 AT AT AT AT AT AT AT AT AT AT AT AA AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4078120 GGTAGAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4078308 original size:3 final size:3
Alignment explanation
Indices: 4078300--4078338 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4078290 AATTTCACAA
4078300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4078339 CAGGAGGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4079277 original size:2 final size:2
Alignment explanation
Indices: 4079270--4079302 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4079260 CATGCATCTT
4079270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4079303 GTAAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4080716 original size:2 final size:2
Alignment explanation
Indices: 4080709--4080735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4080699 TCCCTTTCTT
4080709 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4080736 AACTGCTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4084803 original size:13 final size:13
Alignment explanation
Indices: 4084785--4084831 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
4084775 ATTAATTTTT
4084785 AAATAAATTATTA
1 AAATAAATTATTA
4084798 AAATAATATTAATTTA
1 AAATAA-ATT-A-TTA
*
4084814 AAATAAATTATCA
1 AAATAAATTATTA
4084827 AAATA
1 AAATA
4084832 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 4 0.13
16 9 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:4084808 original size:30 final size:30
Alignment explanation
Indices: 4084774--4084843 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
4084764 ATTAATGTGC
* *
4084774 TATTAATTTTTAAATAAATTATTAAAATAA
1 TATTAATTTTAAAATAAATTATCAAAATAA
*
4084804 TATTAA-TTTAAAATAAATTATCAAAATAT
1 TATTAATTTTAAAATAAATTATCAAAATAA
4084833 TATT-ATTTTAA
1 TATTAATTTTAA
4084844 TATGTTTACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.81
30 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTAATTTTAAAATAAATTATCAAAATAA
Found at i:4084814 original size:16 final size:15
Alignment explanation
Indices: 4084775--4084823 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
4084765 TTAATGTGCT
*
4084775 ATTAATTTTTAAATAA
1 ATTAA-TTTAAAATAA
4084791 ATT-A-TTAAAATAA
1 ATTAATTTAAAATAA
4084804 TATTAATTTAAAATAA
1 -ATTAATTTAAAATAA
4084820 ATTA
1 ATTA
4084824 TCAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 8 0.28
14 3 0.10
15 6 0.21
16 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATTTAAAATAA
Found at i:4085134 original size:22 final size:20
Alignment explanation
Indices: 4085097--4085141 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
4085087 ATTATAAATA
*
4085097 TAAAAATAGTTTTTTATTAT
1 TAAAAATAGTTTTTTATAAT
*
4085117 TAAAAATTATTTTATTTATAAT
1 TAAAAA-TAGTTT-TTTATAAT
4085139 TAA
1 TAA
4085142 TGATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAAAATAGTTTTTTATAAT
Found at i:4085225 original size:13 final size:13
Alignment explanation
Indices: 4085188--4085230 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
4085178 TATTATTTTA
*
4085188 AAAGATTTAATTT
1 AAAGTTTTAATTT
**
4085201 AATTTGTTTAATTT
1 AAAGT-TTTAATTT
4085215 AAAGTTTTAATTT
1 AAAGTTTTAATTT
4085228 AAA
1 AAA
4085231 TTATAATCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (13 bp):
AAAGTTTTAATTT
Found at i:4085280 original size:24 final size:23
Alignment explanation
Indices: 4085224--4085281 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
4085214 TAAAGTTTTA
4085224 ATTTAAATTATAATCGTTTAATT
1 ATTTAAATTATAATCGTTTAATT
* *
4085247 ATTAAGAATTGTAATCGTTTAATT
1 ATTTA-AATTATAATCGTTTAATT
4085271 ATTTTAAATTA
1 A-TTTAAATTA
4085282 AGGGTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.14
24 22 0.76
25 3 0.10
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (23 bp):
ATTTAAATTATAATCGTTTAATT
Found at i:4085282 original size:31 final size:31
Alignment explanation
Indices: 4085247--4085309 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
4085237 TCGTTTAATT
** *
4085247 ATTAAGAATTGTAATCGTTTAATTATTTTAA
1 ATTAAGAATTGTAATAATCTAATTATTTTAA
**
4085278 ATTAAGGGTTGTAATAATCTAATTATTTTAA
1 ATTAAGAATTGTAATAATCTAATTATTTTAA
4085309 A
1 A
4085310 AATTATCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTAAGAATTGTAATAATCTAATTATTTTAA
Found at i:4085392 original size:17 final size:17
Alignment explanation
Indices: 4085367--4085401 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4085357 TTTTAAAATT
4085367 AATTATAATTATTTTAA
1 AATTATAATTATTTTAA
*
4085384 AATTTTAATTATTTTAA
1 AATTATAATTATTTTAA
4085401 A
1 A
4085402 TTGCTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTATAATTATTTTAA
Found at i:4085554 original size:39 final size:39
Alignment explanation
Indices: 4085470--4085556 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
4085460 ATTACAACTT
* * *
4085470 AAATTTT-AAAATAATTAAACTATTACAACCTTTAATTT
1 AAATTTTAAAAATAATTAAACAATTACAACCTTAAATTA
* *
4085508 AAATTTTAAAAATAATTAGACAATTACAA-GTTAAATTA
1 AAATTTTAAAAATAATTAAACAATTACAACCTTAAATTA
4085546 AAAGTTTTAAA
1 AAA-TTTTAAA
4085557 TAAATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 16 0.38
39 26 0.62
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (39 bp):
AAATTTTAAAAATAATTAAACAATTACAACCTTAAATTA
Found at i:4085683 original size:17 final size:18
Alignment explanation
Indices: 4085638--4085684 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
4085628 TTTTTAATAA
4085638 TAAAAACTACTATTATATT
1 TAAAAA-TACTATTATATT
*
4085657 TATAATAATATTATTA-ATT
1 TA-AA-AATACTATTATATT
4085676 TAAAAATAC
1 TAAAAATAC
4085685 CAACATAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.17
18 2 0.08
19 7 0.29
20 9 0.38
21 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAATACTATTATATT
Found at i:4085715 original size:27 final size:25
Alignment explanation
Indices: 4085677--4085727 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
4085667 TTATTAATTT
4085677 AAAAATACCAACATAATCATATAACTA
1 AAAAATACCAACATAAT-A-ATAACTA
*
4085704 AAAAATATCAACATAATAATAACT
1 AAAAATACCAACATAATAATAACT
4085728 TTGATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 1 0.04
27 16 0.70
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATACCAACATAATAATAACTA
Found at i:4085850 original size:19 final size:19
Alignment explanation
Indices: 4085826--4085863 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4085816 TGTAAGAATA
*
4085826 GCTAAAATTTTTAACGATT
1 GCTAAAACTTTTAACGATT
*
4085845 GCTAAAGCTTTTAACGATT
1 GCTAAAACTTTTAACGATT
4085864 TTAAATTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (19 bp):
GCTAAAACTTTTAACGATT
Found at i:4085999 original size:13 final size:13
Alignment explanation
Indices: 4085981--4086032 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
4085971 AAACTAGCAA
4085981 TATTTTAAAAATT
1 TATTTTAAAAATT
*
4085994 TATTTTAAATTAAAGT
1 TATTTT-AA--AAATT
*
4086010 TATTTTAAGAATT
1 TATTTTAAAAATT
4086023 TA-TTTAAAAA
1 TATTTTAAAAA
4086033 CTAAAGTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 7 0.22
13 11 0.34
14 2 0.06
15 2 0.06
16 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (13 bp):
TATTTTAAAAATT
Found at i:4086816 original size:34 final size:34
Alignment explanation
Indices: 4086772--4086912 Score: 158
Period size: 34 Copynumber: 4.1 Consensus size: 34
4086762 AAAAACCACA
* *
4086772 AAATCACCCATTTAATCAACAATGGTAAACTACC
1 AAATCTCCCATTTAATCAACAATGGCAAACTACC
* *
4086806 AAATCTCCCATTTAGTCAACAATGACAAACTACC
1 AAATCTCCCATTTAATCAACAATGGCAAACTACC
* * * *
4086840 AAATCAT-CAATTTAATCAACAATAGCAAATTATC
1 AAATC-TCCCATTTAATCAACAATGGCAAACTACC
* * * *
4086874 AAATCTCCCATTTAGTCAATAATGGCAAACCAAC
1 AAATCTCCCATTTAATCAACAATGGCAAACTACC
4086908 AAATC
1 AAATC
4086913 AATGGCAAAC
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
33 1 0.01
34 86 0.98
35 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.25
Consensus pattern (34 bp):
AAATCTCCCATTTAATCAACAATGGCAAACTACC
Found at i:4086854 original size:68 final size:68
Alignment explanation
Indices: 4086764--4086913 Score: 194
Period size: 68 Copynumber: 2.2 Consensus size: 68
4086754 GGTTTGGTAA
* * *
4086764 AAACC-ACAAAATCACCCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAGTCAACAA
1 AAACCAAC-AAATCACCAATTTAATCAACAATAGCAAACTACCAAATCTCCCATTTAGTCAACAA
4086828 TGAC
65 TGAC
* * * * * *
4086832 AAACTACCAAATCATCAATTTAATCAACAATAGCAAATTATCAAATCTCCCATTTAGTCAATAAT
1 AAACCAACAAATCACCAATTTAATCAACAATAGCAAACTACCAAATCTCCCATTTAGTCAACAAT
*
4086897 GGC
66 GAC
4086900 AAACCAACAAATCA
1 AAACCAACAAATCA
4086914 ATGGCAAACT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
68 68 0.99
69 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.23
Consensus pattern (68 bp):
AAACCAACAAATCACCAATTTAATCAACAATAGCAAACTACCAAATCTCCCATTTAGTCAACAAT
GAC
Found at i:4091038 original size:19 final size:19
Alignment explanation
Indices: 4090995--4091048 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
4090985 TGCACAGTAT
4090995 CGTATACGTGAATAGTACC
1 CGTATACGTGAATAGTACC
* *
4091014 CATATATGTGAATAGTACC
1 CGTATACGTGAATAGTACC
* *
4091033 TGTATACGTAAATAGT
1 CGTATACGTGAATAGT
4091049 GCATTGACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (19 bp):
CGTATACGTGAATAGTACC
Found at i:4091390 original size:34 final size:34
Alignment explanation
Indices: 4091345--4091588 Score: 296
Period size: 34 Copynumber: 7.2 Consensus size: 34
4091335 GGTTTGATAA
* * *
4091345 AAACTATCAAATCACTAATTTAATTAACAATGAC
1 AAACTACCAAATCACTCATTTAATCAACAATGAC
* *
4091379 AAACTACCAAATCTCTCATTTAGTCAACAATGAC
1 AAACTACCAAATCACTCATTTAATCAACAATGAC
* **
4091413 AAACTAACAAATCAC-CATTTAATCAACAATGGT
1 AAACTACCAAATCACTCATTTAATCAACAATGAC
* * * *
4091446 AAACTATCAAATCTCCCATTTAGTCAACAATGAC
1 AAACTACCAAATCACTCATTTAATCAACAATGAC
*
4091480 AAA-TCACCAAATCACTCATTTGATCAACAATGAC
1 AAACT-ACCAAATCACTCATTTAATCAACAATGAC
* * *
4091514 AAACTACCAAATCTCCCATTTAGTCAACAATGAC
1 AAACTACCAAATCACTCATTTAATCAACAATGAC
*
4091548 AAA-TCACCAAATCACTCATTTGATCAACAATGAC
1 AAACT-ACCAAATCACTCATTTAATCAACAATGAC
4091582 AAACTAC
1 AAACTAC
4091589 TAAACCACCA
Statistics
Matches: 177, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
33 30 0.17
34 145 0.82
35 2 0.01
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (34 bp):
AAACTACCAAATCACTCATTTAATCAACAATGAC
Found at i:4091528 original size:68 final size:68
Alignment explanation
Indices: 4091352--4091588 Score: 370
Period size: 68 Copynumber: 3.5 Consensus size: 68
4091342 TAAAAACTAT
* * *
4091352 CAAATCACTAATTTAATTAACAATGACAAACTACCAAATCTCTCATTTAGTCAACAATGACAAA-
1 CAAATCACTCATTTAATCAACAATGACAAACTACCAAATCTCCCATTTAGTCAACAATGACAAAT
*
4091416 CTAA
66 C-AC
** *
4091420 CAAATCAC-CATTTAATCAACAATGGTAAACTATCAAATCTCCCATTTAGTCAACAATGACAAAT
1 CAAATCACTCATTTAATCAACAATGACAAACTACCAAATCTCCCATTTAGTCAACAATGACAAAT
4091484 CAC
66 CAC
*
4091487 CAAATCACTCATTTGATCAACAATGACAAACTACCAAATCTCCCATTTAGTCAACAATGACAAAT
1 CAAATCACTCATTTAATCAACAATGACAAACTACCAAATCTCCCATTTAGTCAACAATGACAAAT
4091552 CAC
66 CAC
*
4091555 CAAATCACTCATTTGATCAACAATGACAAACTAC
1 CAAATCACTCATTTAATCAACAATGACAAACTAC
4091589 TAAACCACCA
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
67 58 0.37
68 98 0.63
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.25
Consensus pattern (68 bp):
CAAATCACTCATTTAATCAACAATGACAAACTACCAAATCTCCCATTTAGTCAACAATGACAAAT
CAC
Found at i:4095806 original size:3 final size:3
Alignment explanation
Indices: 4095798--4095824 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4095788 CATGTACTAA
4095798 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
4095825 GAGAATTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4099985 original size:1 final size:1
Alignment explanation
Indices: 4099974--4100019 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
4099964 GGAAAGACAG
* * * *
4099974 AAAACAAAAAAAAAACAAAACAAAAAAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4100020 GAAGAATTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4099995 original size:16 final size:15
Alignment explanation
Indices: 4099974--4100019 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
4099964 GGAAAGACAG
4099974 AAAACAAAAAAAAAA
1 AAAACAAAAAAAAAA
4099989 CAAAAC--AAAAAAAA
1 -AAAACAAAAAAAAAA
4100003 AAAACAAAAAAAAAA
1 AAAACAAAAAAAAAA
4100018 AA
1 AA
4100020 GAAGAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.18
14 8 0.29
15 10 0.36
16 5 0.18
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAAAAA
Found at i:4100002 original size:18 final size:17
Alignment explanation
Indices: 4099974--4100019 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
4099964 GGAAAGACAG
*
4099974 AAAACAAAAAAAAAACA
1 AAAAAAAAAAAAAAACA
4099991 AAACAAAAAAAAAAAACA
1 AAA-AAAAAAAAAAAACA
4100009 AAAAAAAAAAA
1 AAAAAAAAAAA
4100020 GAAGAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAACA
Found at i:4100019 original size:13 final size:13
Alignment explanation
Indices: 4099981--4100019 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
4099971 CAGAAAACAA
4099981 AAAAAAAACAAAAC
1 AAAAAAAA-AAAAC
4099995 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
4100008 AAAAAAAAAAAA
1 AAAAAAAAAAAA
4100020 GAAGAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:4100636 original size:2 final size:2
Alignment explanation
Indices: 4100629--4100660 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4100619 CACAGAGGCG
4100629 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4100661 ATGGTAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4102521 original size:4 final size:4
Alignment explanation
Indices: 4102512--4102541 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4102502 ATTTAGGATT
4102512 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
4102542 GCAAATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:4102940 original size:3 final size:3
Alignment explanation
Indices: 4102932--4102965 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4102922 GCAAACAGAC
4102932 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4102966 TTCTTCCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4105937 original size:6 final size:6
Alignment explanation
Indices: 4105926--4105959 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4105916 AATTAAACTA
* *
4105926 TGTCTG TGTCTG TGTCCG TGTCCG TGTCCG TGTC
1 TGTCCG TGTCCG TGTCCG TGTCCG TGTCCG TGTC
4105960 TGTCCTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.32, T:0.41
Consensus pattern (6 bp):
TGTCCG
Found at i:4105946 original size:12 final size:12
Alignment explanation
Indices: 4105926--4105962 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4105916 AATTAAACTA
*
4105926 TGTCTGTGTCTG
1 TGTCCGTGTCTG
*
4105938 TGTCCGTGTCCG
1 TGTCCGTGTCTG
4105950 TGTCCGTGTCTG
1 TGTCCGTGTCTG
4105962 T
1 T
4105963 CCTTATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.32, T:0.43
Consensus pattern (12 bp):
TGTCCGTGTCTG
Found at i:4105974 original size:6 final size:6
Alignment explanation
Indices: 4105962--4106002 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
4105952 TCCGTGTCTG
* * *
4105962 TCCTTA TCTTTA TCTTTA TCCTTA TCCTTA TCCTTG TCCTT
1 TCCTTA TCCTTA TCCTTA TCCTTA TCCTTA TCCTTA TCCTT
4106003 TTCATTCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.56
Consensus pattern (6 bp):
TCCTTA
Found at i:4108884 original size:2 final size:2
Alignment explanation
Indices: 4108877--4108916 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4108867 GAGCATGTTT
4108877 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4108917 ACTAGGCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4112260 original size:23 final size:22
Alignment explanation
Indices: 4112206--4112260 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
4112196 TAATTAAAAA
4112206 ATTTTTAAA-TAAAAATATTAT
1 ATTTTTAAATTAAAAATATTAT
*
4112227 ATTTTAAAAATTAAAAAATAATTAT
1 ATTTT-TAAATT-AAAAAT-ATTAT
4112252 -TTTTTAAAT
1 ATTTTTAAAT
4112261 GTATTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 5 0.18
22 3 0.11
23 5 0.18
24 10 0.36
25 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTTAAATTAAAAATATTAT
Found at i:4113528 original size:12 final size:12
Alignment explanation
Indices: 4113497--4113530 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4113487 TTACTCGTTA
4113497 ATTATTTATTTT
1 ATTATTTATTTT
4113509 -TTATTTTATTTT
1 ATTA-TTTATTTT
4113521 ATTATTTATT
1 ATTATTTATT
4113531 CTTAAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTATTTATTTT
Found at i:4116287 original size:38 final size:35
Alignment explanation
Indices: 4116232--4116301 Score: 86
Period size: 38 Copynumber: 1.9 Consensus size: 35
4116222 TGTTCAACAC
* *
4116232 ATTGAATATTAATAGATTTCAAATCTATCTTTTTAAA
1 ATTGAATATGAAAAGATTTCAAA--TATCTTTTTAAA
*
4116269 ATTGACATATGAAAAGATTTTAAATATCTTTTT
1 ATTGA-ATATGAAAAGATTTCAAATATCTTTTT
4116302 CTTGTGGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 9 0.31
37 5 0.17
38 15 0.52
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (35 bp):
ATTGAATATGAAAAGATTTCAAATATCTTTTTAAA
Found at i:4119104 original size:29 final size:29
Alignment explanation
Indices: 4119059--4119147 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
4119049 TATTAATTAT
* *
4119059 TTAAAAATCAAAGATGGACACTTGGGCAC
1 TTAAAAATCAAATATGGGCACTTGGGCAC
4119088 TTAAAAATCAAATATGGGCACTTGGGCAC
1 TTAAAAATCAAATATGGGCACTTGGGCAC
*
4119117 TTAAAAATCAAATATGGGCACTTGGACAC
1 TTAAAAATCAAATATGGGCACTTGGGCAC
4119146 TT
1 TT
4119148 GGGACACTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (29 bp):
TTAAAAATCAAATATGGGCACTTGGGCAC
Found at i:4119197 original size:17 final size:18
Alignment explanation
Indices: 4119175--4119209 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
4119165 ATTAAAGATG
4119175 TAATTATATT-TTTATTT
1 TAATTATATTATTTATTT
4119192 TAATTATATTATTTATTT
1 TAATTATATTATTTATTT
4119210 ATTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTATATTATTTATTT
Found at i:4122222 original size:15 final size:15
Alignment explanation
Indices: 4122189--4122235 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
4122179 TTAGTTTTAT
*
4122189 TAAATT-TTTATATAA
1 TAAATTATTT-TATAG
4122204 TAAATATATTTT-TAG
1 TAAAT-TATTTTATAG
4122219 TAAATTATTTTATAG
1 TAAATTATTTTATAG
4122234 TA
1 TA
4122236 GCAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 17 0.61
16 2 0.07
17 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
TAAATTATTTTATAG
Found at i:4132099 original size:2 final size:2
Alignment explanation
Indices: 4132092--4132117 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4132082 TTGTACTCAG
4132092 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
4132118 ACAATAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4134145 original size:29 final size:28
Alignment explanation
Indices: 4134103--4134157 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4134093 AAACTTTATT
4134103 AAAAAAAATCAAAAGACTTTTTTATTAA
1 AAAAAAAATCAAAAGACTTTTTTATTAA
**
4134131 AAAAAAGAATCAAAAGGTTTTTTTATT
1 AAAAAA-AATCAAAAGACTTTTTTATT
4134158 TAAGATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAAAAAATCAAAAGACTTTTTTATTAA
Found at i:4134235 original size:20 final size:19
Alignment explanation
Indices: 4134204--4134241 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4134194 AATAAAATTA
4134204 TTTATTTATTTTTAATATT
1 TTTATTTATTTTTAATATT
*
4134223 TTTATTATATTTTTGATAT
1 TTTATT-TATTTTTAATAT
4134242 AAAATTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTATTTTTAATATT
Found at i:4139468 original size:18 final size:18
Alignment explanation
Indices: 4139431--4139464 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4139421 TTTATTTTTA
4139431 AAAATTAAGTAAAAATAT
1 AAAATTAAGTAAAAATAT
*
4139449 AAAATT-AGTAACAATA
1 AAAATTAAGTAAAAATA
4139465 ATAACTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATTAAGTAAAAATAT
Found at i:4141645 original size:15 final size:16
Alignment explanation
Indices: 4141627--4141656 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4141617 TATGATGATG
4141627 AAATTTTT-TTATTTT
1 AAATTTTTATTATTTT
4141642 AAATTTTTATTATTT
1 AAATTTTTATTATTT
4141657 AGCGTGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
AAATTTTTATTATTTT
Found at i:4142685 original size:103 final size:102
Alignment explanation
Indices: 4142467--4142777 Score: 484
Period size: 103 Copynumber: 3.1 Consensus size: 102
4142457 ATCCTTCAAA
* * * *
4142467 TATG-AACCAAATACTTTGGATCTACAAAGGAGATGGCGTAAACTCAGACAGCCATCGGCAGACA
1 TATGAAACCGAATACTATGTATCTACAAAAGAGATGGCGTAAACTCAGACAGCCATCGGCAGACA
4142531 GACATTCCATTAGGCCACCAAGTTCCAGTATTTAGGC
66 GACATTCCATTAGGCCACCAAGTTCCAGTATTTAGGC
* *
4142568 TATGAAACCGAATACTATGTATCTACAAAAGCGATGGCGTAAACTCAGACAGCCATTGGCAGACA
1 TATGAAACCGAATACTATGTATCTACAAAAGAGATGGCGTAAACTCAGACAGCCATCGGCAGAC-
**
4142633 AGACATTCCATTAGGCCACCAAGAACCAGT-TTTGAGGC
65 AGACATTCCATTAGGCCACCAAGTTCCAGTATTT-AGGC
* *
4142671 TATGAAACCGAATACTATGTATCTACAAAAGTGATGACGTAAACTCAGACAGCCATCGGCAG-CA
1 TATGAAACCGAATACTATGTATCTACAAAAGAGATGGCGTAAACTCAGACAGCCATCGGCAGACA
*
4142735 GACATTCCACTAGGCCACCAAGTTCCAGTATTTAGGC
66 GACATTCCATTAGGCCACCAAGTTCCAGTATTTAGGC
4142772 TATGAA
1 TATGAA
4142778 GAGTGACTAC
Statistics
Matches: 192, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
101 41 0.21
102 60 0.31
103 91 0.47
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (102 bp):
TATGAAACCGAATACTATGTATCTACAAAAGAGATGGCGTAAACTCAGACAGCCATCGGCAGACA
GACATTCCATTAGGCCACCAAGTTCCAGTATTTAGGC
Found at i:4146131 original size:76 final size:76
Alignment explanation
Indices: 4146005--4146158 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
4145995 CACTTAAAAT
4146005 TTCAAGTCAATCCTATATCCCTCTCACATTATCTAGAATATTGTCTTCTACAATAGTTATAATGG
1 TTCAAGTCAATCCTATATCCCTCTCACATTATCTAGAATATTGTCTTCTACAATAGTTATAATGG
4146070 TAGAAATATTA
66 TAGAAATATTA
4146081 TTCAAGTCAATCCTATATCCCTCTCACATTATCTAGAATATTGTCTTCTACAATAGTTATAATGG
1 TTCAAGTCAATCCTATATCCCTCTCACATTATCTAGAATATTGTCTTCTACAATAGTTATAATGG
4146146 TAGAAATATTA
66 TAGAAATATTA
4146157 TT
1 TT
4146159 TTTATCAAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (76 bp):
TTCAAGTCAATCCTATATCCCTCTCACATTATCTAGAATATTGTCTTCTACAATAGTTATAATGG
TAGAAATATTA
Found at i:4163018 original size:160 final size:160
Alignment explanation
Indices: 4162747--4163048 Score: 480
Period size: 160 Copynumber: 1.9 Consensus size: 160
4162737 GATTGTACAG
* * ** *
4162747 GTTGTGACTGAGACTGGTTAGGTTGGAATTGTGACTCTATGGATTAGGATTGATGCTGTGTTTAA
1 GTTGTGACTAAGACTGGTTAGGTTGGAATTGTGACTCTATAGATTAGGACCGACGCTGTGTTTAA
* *
4162812 GTTTGGGTACGTTGGGTAGGCAAAACTAGTGTTTGTAAAAGCTGCTGTTCAAGTAGAAAGCTGTC
66 GTTTAGGTACGTTGGGTAGGCAAAACCAGTGTTTGTAAAAGCTGCTGTTCAAGTAGAAAGCTGTC
*
4162877 CCTATCCTTATCAAGTAGAAAGCTATATAA
131 CCTATACTTATCAAGTAGAAAGCTATATAA
* *
4162907 GTTGTGACTAAGACTGGTTAGGTTGGAATTGTGACTCTGTAGATT-GAGACCGACGCTGTGTTTG
1 GTTGTGACTAAGACTGGTTAGGTTGGAATTGTGACTCTATAGATTAG-GACCGACGCTGTGTTTA
* *
4162971 AGTTTAGGTAGGTTGGGTAGGCAAAACCAGTGTTTGTAAAGGCTGCTGTTCAAGTAGAAAGCTGT
65 AGTTTAGGTACGTTGGGTAGGCAAAACCAGTGTTTGTAAAAGCTGCTGTTCAAGTAGAAAGCTGT
4163036 CCCTATACTTATC
130 CCCTATACTTATC
4163049 TTCTACTAGT
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
159 1 0.01
160 128 0.99
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.33
Consensus pattern (160 bp):
GTTGTGACTAAGACTGGTTAGGTTGGAATTGTGACTCTATAGATTAGGACCGACGCTGTGTTTAA
GTTTAGGTACGTTGGGTAGGCAAAACCAGTGTTTGTAAAAGCTGCTGTTCAAGTAGAAAGCTGTC
CCTATACTTATCAAGTAGAAAGCTATATAA
Found at i:4165706 original size:15 final size:15
Alignment explanation
Indices: 4165686--4165715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4165676 CTAATATTCT
4165686 CACCTAACACACCAC
1 CACCTAACACACCAC
*
4165701 CACCTAACGCACCAC
1 CACCTAACACACCAC
4165716 TTAATATTCT
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:0.37, C:0.53, G:0.03, T:0.07
Consensus pattern (15 bp):
CACCTAACACACCAC
Found at i:4165721 original size:40 final size:40
Alignment explanation
Indices: 4165661--4165753 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
4165651 AAAAAATACT
4165661 CACCTAACACACCACCTAATATTCTCACCTAACACACCAC
1 CACCTAACACACCACCTAATATTCTCACCTAACACACCAC
* *
4165701 CACCTAACGCACCACTTAATATTCTCACCTAACACACCAC
1 CACCTAACACACCACCTAATATTCTCACCTAACACACCAC
4165741 CACCTAACACACC
1 CACCTAACACACC
4165754 TAACATACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.37, C:0.45, G:0.01, T:0.17
Consensus pattern (40 bp):
CACCTAACACACCACCTAATATTCTCACCTAACACACCAC
Found at i:4169421 original size:2 final size:2
Alignment explanation
Indices: 4169414--4169465 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
4169404 AATGCCCCTC
*
4169414 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4169456 CT CT CT -T CT C
1 CT CT CT CT CT C
4169466 ATGGACATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4171843 original size:6 final size:6
Alignment explanation
Indices: 4171832--4171858 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4171822 CCAAACAAAC
4171832 ACCATA ACCATA ACCATA ACCATA ACC
1 ACCATA ACCATA ACCATA ACCATA ACC
4171859 CCAGCCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCATA
Found at i:4176532 original size:92 final size:94
Alignment explanation
Indices: 4176366--4176538 Score: 201
Period size: 93 Copynumber: 1.9 Consensus size: 94
4176356 TGATATAAAG
* * * ***
4176366 TTTATTATTTTTAATGTTAATGTAAAATTAAAAGTACGAAAATAAAGAGATTTAATGTAAGTTTT
1 TTTATTATTTTTAAGGTTAATGAAAAATTAAAAGTACGAAAATAAAGAAATTTAATGTAAACCTT
*
4176431 AACT-CTTTTTATTTAGCAAATAAATTTA
66 AACTATTTTTTATTTAGCAAATAAATTTA
* **
4176459 TTTATT-TTTTTAAGGTTAATGAAAAATTAGAAATTTTGAAAATAAA-ACAATTTAA-GTAAACC
1 TTTATTATTTTTAAGGTTAATGAAAAATTA-AAAGTACGAAAATAAAGA-AATTTAATGTAAACC
*
4176521 TTAATTATTTTTTATTTA
64 TTAACTATTTTTTATTTA
4176539 TTATCAAACA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
92 31 0.47
93 35 0.53
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (94 bp):
TTTATTATTTTTAAGGTTAATGAAAAATTAAAAGTACGAAAATAAAGAAATTTAATGTAAACCTT
AACTATTTTTTATTTAGCAAATAAATTTA
Found at i:4181027 original size:21 final size:20
Alignment explanation
Indices: 4181003--4181189 Score: 73
Period size: 21 Copynumber: 9.2 Consensus size: 20
4180993 AAGTTTTTGG
4181003 ATTTAAGGTATAAAGTTTAAA
1 ATTTAAGGT-TAAAGTTTAAA
* *
4181024 ATTTAAAGTTTAAGATTTAGAA
1 ATTTAAGGTTAAAG-TTTA-AA
* * *
4181046 ATTAAAGTTTTAAGGTTTAAA
1 ATTTAAG-GTTAAAGTTTAAA
* *
4181067 ATTTAAAGTTTTAAGTTTCAAA
1 ATTT-AAGGTTAAAGTTT-AAA
* * * *
4181089 GGTTTAACGTTTAAGGTTTAAT
1 -ATTTAA-GGTTAAAGTTTAAA
4181111 ATTT-A----AAA-TTTAAA
1 ATTTAAGGTTAAAGTTTAAA
* * *
4181125 GTTT-AGGATTTAAGTTAAAA
1 ATTTAAGG-TTAAAGTTTAAA
* *
4181145 AATTAAGGTTAAATTTTAAA
1 ATTTAAGGTTAAAGTTTAAA
* *
4181165 ATTTAAGGTTTAAAATTTAAG
1 ATTTAAGG-TTAAAGTTTAAA
4181186 ATTT
1 ATTT
4181190 TGTAGTTTAG
Statistics
Matches: 123, Mismatches: 28, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
14 9 0.07
15 2 0.02
19 2 0.02
20 28 0.23
21 45 0.37
22 21 0.17
23 16 0.13
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (20 bp):
ATTTAAGGTTAAAGTTTAAA
Found at i:4181028 original size:7 final size:7
Alignment explanation
Indices: 4181013--4181129 Score: 87
Period size: 7 Copynumber: 16.3 Consensus size: 7
4181003 ATTTAAGGTA
4181013 TAAAGTT
1 TAAAGTT
*
4181020 TAAAATT
1 TAAAGTT
4181027 TAAAGTT
1 TAAAGTT
4181034 T-AAGATT
1 TAAAG-TT
*
4181041 TAGAA-AT
1 TA-AAGTT
4181048 TAAAGTTT
1 TAAAG-TT
*
4181056 TAAGGTT
1 TAAAGTT
*
4181063 TAAAATT
1 TAAAGTT
4181070 TAAAGTT
1 TAAAGTT
*
4181077 TTAAGTT
1 TAAAGTT
4181084 TCAAAGGTT
1 T-AAA-GTT
*
4181093 TAACGTT
1 TAAAGTT
*
4181100 TAAGGTT
1 TAAAGTT
4181107 TAATA-TT
1 TAA-AGTT
*
4181114 TAAAATT
1 TAAAGTT
4181121 TAAAGTT
1 TAAAGTT
4181128 TA
1 TA
4181130 GGATTTAAGT
Statistics
Matches: 87, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
6 6 0.07
7 66 0.76
8 9 0.10
9 6 0.07
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (7 bp):
TAAAGTT
Found at i:4181057 original size:22 final size:22
Alignment explanation
Indices: 4181018--4181117 Score: 100
Period size: 22 Copynumber: 4.6 Consensus size: 22
4181008 AGGTATAAAG
4181018 TTTAAAATTTAAAG-TTTAAGA
1 TTTAAAATTTAAAGTTTTAAGA
*
4181039 TTTAGAAA-TTAAAGTTTTAAGG
1 TTTA-AAATTTAAAGTTTTAAGA
4181061 TTTAAAATTTAAAGTTTTAAG-
1 TTTAAAATTTAAAGTTTTAAGA
* * *
4181082 TTTCAAAGGTTTAACG-TTTAAGG
1 TTT-AAA-ATTTAAAGTTTTAAGA
*
4181105 TTTAATATTTAAA
1 TTTAAAATTTAAA
4181118 ATTTAAAGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
21 21 0.31
22 37 0.55
23 9 0.13
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (22 bp):
TTTAAAATTTAAAGTTTTAAGA
Found at i:4181170 original size:20 final size:21
Alignment explanation
Indices: 4181112--4181189 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
4181102 AGGTTTAATA
*
4181112 TTTAAAATTTAAAGTTT-AGG
1 TTTAAAATTTAAAATTTAAGG
* * *
4181132 ATTT-AAGTTAAAAAATTAAGG
1 -TTTAAAATTTAAAATTTAAGG
*
4181153 -TTAAATTTTAAAATTTAAGG
1 TTTAAAATTTAAAATTTAAGG
*
4181173 TTTAAAATTTAAGATTT
1 TTTAAAATTTAAAATTT
4181190 TGTAGTTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 23 0.51
21 20 0.44
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTAAAATTTAAAATTTAAGG
Found at i:4181525 original size:7 final size:7
Alignment explanation
Indices: 4181513--4181579 Score: 52
Period size: 7 Copynumber: 10.0 Consensus size: 7
4181503 GAGGTTCAAA
4181513 ATTTAAG
1 ATTTAAG
4181520 ATTTAAG
1 ATTTAAG
* *
4181527 GTTTGAG
1 ATTTAAG
4181534 -TTTAA-
1 ATTTAAG
*
4181539 AGTTTAAA
1 A-TTTAAG
*
4181547 ATTTAAA
1 ATTTAAG
4181554 ATTTAAG
1 ATTTAAG
4181561 ATTT--G
1 ATTTAAG
*
4181566 AGTTAAG
1 ATTTAAG
4181573 ATTTAAG
1 ATTTAAG
4181580 GTTTGGAGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
5 4 0.08
6 4 0.08
7 40 0.82
8 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.43
Consensus pattern (7 bp):
ATTTAAG
Found at i:4181551 original size:27 final size:28
Alignment explanation
Indices: 4181500--4181552 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
4181490 GGGTTTAGGA
*
4181500 TTTGAGGTTCAAAATTTAAGATTTAAGG
1 TTTGAGGTTCAAAATTTAAAATTTAAGG
* *
4181528 TTTGA-GTTTAAAGTTTAAAATTTAA
1 TTTGAGGTTCAAAATTTAAAATTTAA
4181553 AATTTAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (28 bp):
TTTGAGGTTCAAAATTTAAAATTTAAGG
Found at i:4182132 original size:16 final size:15
Alignment explanation
Indices: 4182113--4182154 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4182103 AGGCGAGTAA
*
4182113 AATTAATTTCGAGTTG
1 AATT-ATTTCAAGTTG
4182129 AATTATTTCAAGTT-
1 AATTATTTCAAGTTG
4182143 AAGTTATTTCAA
1 AA-TTATTTCAA
4182155 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 18 0.75
16 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (15 bp):
AATTATTTCAAGTTG
Found at i:4184164 original size:158 final size:154
Alignment explanation
Indices: 4183873--4184401 Score: 474
Period size: 158 Copynumber: 3.4 Consensus size: 154
4183863 GTTATAATAT
* * * * * * *
4183873 AAAATTACT-AAAATACTCTTAGGATATACTTTCGACGTGAAAGTATTCTAATAACCCTAAAAGA
1 AAAATTA-TGAAAATACTCCTAAGATATACATTCGACATAAAAGTATTCCAATAACCCTAAAAAA
** * * * * *
4183937 CTTAAAAATGATCATAAATGAGATTAACCTATCTTAAATGC-CTACTTTTGGCATAAAAGCATCC
65 CTTAAAAATGATTGTAAATGGGA-TAACCTATCATAAATGCACAAC-TTTGGCATAAAAACATCT
4184001 CAATGACAACTTATAACTCAATTTTTTAAA
128 CAATGACAACTTA-AACTCAA--TTTTAAA
* * * *
4184031 AAAATTATGAAAATACTCCTAAAATAAACCTTCGACATAAAAGTATCCCAATAACCCTAAAAAAC
1 AAAATTATGAAAATACTCCTAAGATATACATTCGACATAAAAGTATTCCAATAACCCTAAAAAAC
* * * *
4184096 TTAAAAATGATTGTAAATGGGATGAACTTATCCTAAATGCACAACTTTGGCATAAAAACATTTTA
66 TTAAAAATGATTGTAAATGGGAT-AACCTATCATAAATGCACAACTTTGGCATAAAAACATCTCA
* **
4184161 ATGACAACTTGAGACTCAATTTTAGC
130 ATGACAACTT-AAACTCAATTTTAAA
* ** * * * *
4184187 AAAATTATGAACATAC-CCTTGGATATACATTCAACATGAAAGTATT-CAGGTAACTCTAAAAGA
1 AAAATTATGAAAATACTCCTAAGATATACATTCGACATAAAAGTATTCCA-ATAACCCTAAAA-A
* * * * * *
4184250 CCTT-GAAATGATTGTAAATAGGACTAACCTATCATAAATGCATATCTTTAGCATAAAAACATCT
64 ACTTAAAAATGATTGTAAATGGGA-TAACCTATCATAAATGCACAACTTTGGCATAAAAACATCT
* * * ** *
4184314 CAGTGACAGCCTAAGACTTGATTCTAAA
128 CAATGACAACTTAA-ACTCAATTTTAAA
* * * * *
4184342 AAATTTATGAAAATATTCCTAAGATATACTTTCGACATAAAAATATTCCGATAACCCTAA
1 AAAATTATGAAAATACTCCTAAGATATACATTCGACATAAAAGTATTCCAATAACCCTAA
4184402 TAGATATTAA
Statistics
Matches: 296, Mismatches: 65, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
154 3 0.01
155 111 0.38
156 57 0.19
157 3 0.01
158 118 0.40
159 4 0.01
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (154 bp):
AAAATTATGAAAATACTCCTAAGATATACATTCGACATAAAAGTATTCCAATAACCCTAAAAAAC
TTAAAAATGATTGTAAATGGGATAACCTATCATAAATGCACAACTTTGGCATAAAAACATCTCAA
TGACAACTTAAACTCAATTTTAAA
Found at i:4186315 original size:21 final size:22
Alignment explanation
Indices: 4186291--4186343 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
4186281 AGTTTCAGAT
*
4186291 TTTGAGTTTTGAA-GTTCAAGG
1 TTTGAGGTTTGAAGGTTCAAGG
*
4186312 TTTG-GGTTTCAAGGTTCAAGG
1 TTTGAGGTTTGAAGGTTCAAGG
4186333 TTTGAGGTTTG
1 TTTGAGGTTTG
4186344 CAATCGAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 16 0.59
22 5 0.19
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.43
Consensus pattern (22 bp):
TTTGAGGTTTGAAGGTTCAAGG
Found at i:4186378 original size:21 final size:21
Alignment explanation
Indices: 4186353--4186426 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
4186343 GCAATCGAGG
* *
4186353 TTTAGGGTTTTAAGTTTTGGA
1 TTTAGAGTTTAAAGTTTTGGA
* * *
4186374 TTTAGAGTTTGAAGTTTAGAA
1 TTTAGAGTTTAAAGTTTTGGA
* *
4186395 TTTAAAGTTTAAAGTTTTAGA
1 TTTAGAGTTTAAAGTTTTGGA
4186416 TTTAGAGTTTA
1 TTTAGAGTTTA
4186427 GGGATTAAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (21 bp):
TTTAGAGTTTAAAGTTTTGGA
Found at i:4186391 original size:14 final size:13
Alignment explanation
Indices: 4186374--4186426 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
4186364 AAGTTTTGGA
4186374 TTTAGAGTTTGAAG
1 TTTAGAGTTT-AAG
*
4186388 TTTAGAATTTAAAG
1 TTTAGAGTTT-AAG
* *
4186402 TTTAAAGTTTTAG
1 TTTAGAGTTTAAG
4186415 ATTTAGAGTTTA
1 -TTTAGAGTTTA
4186427 GGGATTAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
13 2 0.06
14 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
TTTAGAGTTTAAG
Found at i:4186445 original size:20 final size:20
Alignment explanation
Indices: 4186420--4186458 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4186410 TTTAGATTTA
*
4186420 GAGTTTAGGGATTAAGGTTG
1 GAGTTTAGCGATTAAGGTTG
*
4186440 GAGTTTAGCGTTTAAGGTT
1 GAGTTTAGCGATTAAGGTT
4186459 AAGATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.36, T:0.38
Consensus pattern (20 bp):
GAGTTTAGCGATTAAGGTTG
Found at i:4186619 original size:14 final size:14
Alignment explanation
Indices: 4186602--4186646 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
4186592 TAAGATTTGA
*
4186602 GGTTACGAGTTAAG
1 GGTTAAGAGTTAAG
*
4186616 GGTTAAG-GTTAAA
1 GGTTAAGAGTTAAG
*
4186629 GGTTAAGGGTTAAG
1 GGTTAAGAGTTAAG
4186643 GGTT
1 GGTT
4186647 CGAGGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.29, C:0.02, G:0.38, T:0.31
Consensus pattern (14 bp):
GGTTAAGAGTTAAG
Found at i:4186620 original size:7 final size:7
Alignment explanation
Indices: 4186610--4186646 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
4186600 GAGGTTACGA
4186610 GTTAAGG
1 GTTAAGG
4186617 GTTAA-G
1 GTTAAGG
*
4186623 GTTAAAG
1 GTTAAGG
4186630 GTTAAGG
1 GTTAAGG
4186637 GTTAAGG
1 GTTAAGG
4186644 GTT
1 GTT
4186647 CGAGGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (7 bp):
GTTAAGG
Found at i:4186621 original size:27 final size:27
Alignment explanation
Indices: 4186591--4186646 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
4186581 AGTTTGAGGT
** *
4186591 TTAAGATTTGAGGTTACGAGTTAAGGG
1 TTAAGATTAAAGGTTAAGAGTTAAGGG
* *
4186618 TTAAGGTTAAAGGTTAAGGGTTAAGGG
1 TTAAGATTAAAGGTTAAGAGTTAAGGG
4186645 TT
1 TT
4186647 CGAGGTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (27 bp):
TTAAGATTAAAGGTTAAGAGTTAAGGG
Found at i:4186653 original size:14 final size:13
Alignment explanation
Indices: 4186610--4186646 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4186600 GAGGTTACGA
4186610 GTTAAGGGTTAAG
1 GTTAAGGGTTAAG
*
4186623 GTTAAAGGTTAAGG
1 GTTAAGGGTTAA-G
4186637 GTTAAGGGTT
1 GTTAAGGGTT
4186647 CGAGGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (13 bp):
GTTAAGGGTTAAG
Found at i:4190609 original size:21 final size:22
Alignment explanation
Indices: 4190567--4190654 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
4190557 CAAAAACCAA
4190567 AAAAAAAAGAAGCAAAAAAAAG-
1 AAAAAAAA-AAGCAAAAAAAAGC
** **
4190589 ACTAAAAAAAGCAAAGCAAAGC
1 AAAAAAAAAAGCAAAAAAAAGC
*
4190611 AAAAAAAAAAGCAAAATAAAGC
1 AAAAAAAAAAGCAAAAAAAAGC
*
4190633 AAAGAAAAAAGAGAAAAAAAAA
1 AAA-AAAAAA-AGCAAAAAAAA
4190655 CTCTGATGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 11 0.21
22 27 0.51
23 6 0.11
24 9 0.17
ACGTcount: A:0.77, C:0.08, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAGCAAAAAAAAGC
Found at i:4190650 original size:32 final size:33
Alignment explanation
Indices: 4190580--4190654 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
4190570 AAAAAGAAGC
*
4190580 AAAAAAAAGACTAAAAAAAGCAAAGCAAAGCAA
1 AAAAAAAAGACTAAAAAAAGCAAAGCAAAGAAA
* *
4190613 AAAAAAAAG-C-AAAATAAAGCAAAGAAAAAAGAGA
1 AAAAAAAAGACTAAAA-AAAGCAAAG--CAAAGAAA
4190647 AAAAAAAA
1 AAAAAAAA
4190655 CTCTGATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.11
32 10 0.28
33 9 0.25
34 13 0.36
ACGTcount: A:0.77, C:0.08, G:0.12, T:0.03
Consensus pattern (33 bp):
AAAAAAAAGACTAAAAAAAGCAAAGCAAAGAAA
Found at i:4190977 original size:17 final size:16
Alignment explanation
Indices: 4190955--4191007 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
4190945 ATCGGATAAA
*
4190955 TCAAGTAATGTTTGTAT
1 TCAAGTAATATTT-TAT
*
4190972 TCAAGTAATATATTA-
1 TCAAGTAATATTTTAT
4190987 TCAAGTAATATTTATAT
1 TCAAGTAATATTT-TAT
4191004 TCAA
1 TCAA
4191008 ATCTAACTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 12 0.39
16 4 0.13
17 15 0.48
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (16 bp):
TCAAGTAATATTTTAT
Found at i:4190992 original size:15 final size:14
Alignment explanation
Indices: 4190972--4191001 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4190962 ATGTTTGTAT
4190972 TCAAGTAATATATTA
1 TCAAGTAATAT-TTA
4190987 TCAAGTAATATTTA
1 TCAAGTAATATTTA
4191001 T
1 T
4191002 ATTCAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TCAAGTAATATTTA
Found at i:4191874 original size:20 final size:21
Alignment explanation
Indices: 4191851--4191890 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4191841 TCTACTATAA
4191851 AGTA-AACAAACTTTAAAAAT
1 AGTATAACAAACTTTAAAAAT
* *
4191871 AGTATTACAAATTTTAAAAA
1 AGTATAACAAACTTTAAAAA
4191891 ATTAATAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
AGTATAACAAACTTTAAAAAT
Found at i:4193467 original size:16 final size:16
Alignment explanation
Indices: 4193405--4193459 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
4193395 TCGAGCCCTA
* *
4193405 AAAAAGCTCAAACTCG
1 AAAAAGCCCAAACCCG
*
4193421 -AAAAGACCCGAACCCG
1 AAAAAG-CCCAAACCCG
*
4193437 AATAAGCCCAAACCCG
1 AAAAAGCCCAAACCCG
4193453 AAAAAGC
1 AAAAAGC
4193460 TCGAACCCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 5 0.16
16 22 0.71
17 4 0.13
ACGTcount: A:0.49, C:0.31, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAGCCCAAACCCG
Found at i:4198580 original size:28 final size:28
Alignment explanation
Indices: 4198539--4198593 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4198529 AAATAAACAT
*
4198539 TTTTTCTCTAGTTCAGTTTTATCAATTC
1 TTTTTCTCTAGTTCAATTTTATCAATTC
*
4198567 TTTTTCTCTGGTTCAATTTTATCAATT
1 TTTTTCTCTAGTTCAATTTTATCAATT
4198594 ACTTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTTTCTCTAGTTCAATTTTATCAATTC
Found at i:4199091 original size:2 final size:2
Alignment explanation
Indices: 4199084--4199116 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4199074 CATTCATTCT
4199084 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4199117 TTTAAAATGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.