Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 15 of 19
Found at i:3213574 original size:2 final size:2
Alignment explanation
Indices: 3213567--3213601 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3213557 GTAGATAATC
3213567 AT 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 AT A
3213602 AGTTTATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3213688 original size:2 final size:2
Alignment explanation
Indices: 3213681--3213712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3213671 TCCCAATTAC
3213681 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
3213713 ATTCAGAAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3216920 original size:36 final size:36
Alignment explanation
Indices: 3216871--3216958 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
3216861 TTTACTGTGT
*
3216871 TTTCATTCAGGCTTATCCCTTGAGGACTTTGTGTTA
1 TTTCATTCAGGCTTATCCCTCGAGGACTTTGTGTTA
* * * *
3216907 TTTCCTTCGGGCTTATCTCTCGAGGACTTTGTGAGT-
1 TTTCATTCAGGCTTATCCCTCGAGGACTTTGTG-TTA
*
3216943 TTTCATTCAGGTTTAT
1 TTTCATTCAGGCTTAT
3216959 TTCTTCTGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.45
Consensus pattern (36 bp):
TTTCATTCAGGCTTATCCCTCGAGGACTTTGTGTTA
Found at i:3216970 original size:72 final size:72
Alignment explanation
Indices: 3216869--3217007 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 72
3216859 GATTTACTGT
*
3216869 GTTTTCATTCAGGCTTATCCCTTGAGGACT-T-TGTGTTATT-TCCTTCGGGCTTATCTCTCGAG
1 GTTTTCATTCAGGCTTATCCCTTCAGGACTGTCTGTGTT-TTCTCCTTC--GCTTATCTCTCGAG
3216931 GACTTTGTGA
63 GACTTTGTGA
* ** * * *
3216941 GTTTTCATTCAGGTTTATTTCTTCTGGACTGTCTGTGTTTTCTCCTTCGCTTATCTCTTGGGGAC
1 GTTTTCATTCAGGCTTATCCCTTCAGGACTGTCTGTGTTTTCTCCTTCGCTTATCTCTCGAGGAC
3217006 TT
66 TT
3217008 GCTGTGGGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
72 42 0.74
73 3 0.05
74 12 0.21
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (72 bp):
GTTTTCATTCAGGCTTATCCCTTCAGGACTGTCTGTGTTTTCTCCTTCGCTTATCTCTCGAGGAC
TTTGTGA
Found at i:3220161 original size:27 final size:26
Alignment explanation
Indices: 3220120--3220190 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
3220110 TTTTTAAATA
3220120 AAATA-ATTTTATTAAT-TTTATTATTTT
1 AAATATATTTT-TTAATATTTA--ATTTT
3220147 AAATATATTTTTTAATATTTAATTTT
1 AAATATATTTTTTAATATTTAATTTT
*
3220173 AAAAATATTTTTATAATA
1 AAATATATTTTT-TAATA
3220191 ATATAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 16 0.40
27 15 0.38
28 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
AAATATATTTTTTAATATTTAATTTT
Found at i:3220981 original size:3 final size:3
Alignment explanation
Indices: 3220973--3220999 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3220963 TGCTTAATGA
3220973 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3221000 TATGATTTTT
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):
ATT
Found at i:3221539 original size:26 final size:26
Alignment explanation
Indices: 3221476--3221530 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3221466 ATATTGTATG
**
3221476 TAAAATATG-TAATAAAATTATTATCA
1 TAAAATA-GATAATAAAATTATTAAAA
3221502 TAAAATAGATAATAAAATTATTAAAA
1 TAAAATAGATAATAAAATTATTAAAA
3221528 TAA
1 TAA
3221531 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
TAAAATAGATAATAAAATTATTAAAA
Found at i:3221586 original size:22 final size:22
Alignment explanation
Indices: 3221553--3221623 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
3221543 TAAATATATT
3221553 AATT-TTTAATTTATTTATAAAA
1 AATTATTT-ATTTATTTATAAAA
* *
3221575 AATTATTTATTTTTTTTTAAATCA
1 AATTATTTATTTATTTATAAA--A
* *
3221599 AATTA--TATTAAATTATAAAA
1 AATTATTTATTTATTTATAAAA
3221619 AATTA
1 AATTA
3221624 AAAATTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 6 0.15
22 25 0.62
23 3 0.08
24 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTATTTATTTATTTATAAAA
Found at i:3222102 original size:25 final size:27
Alignment explanation
Indices: 3222064--3222126 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
3222054 TAAATAAATT
* *
3222064 ATAAATTTTATTAAAAAATATT-T-TA
1 ATAATTTTTTTTAAAAAATATTATATA
* *
3222089 ATAATTTTTTTTAAATATTATTATATA
1 ATAATTTTTTTTAAAAAATATTATATA
*
3222116 ATAATATTTTT
1 ATAATTTTTTT
3222127 ATTTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 18 0.58
26 1 0.03
27 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATAATTTTTTTTAAAAAATATTATATA
Found at i:3222117 original size:27 final size:27
Alignment explanation
Indices: 3222069--3222148 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
3222059 AAATTATAAA
* *
3222069 TTTTATTAAAAAATATT-TTAATAAT-T
1 TTTTATT-AAATATATTAATAATAATAT
3222095 TTTT-TTAAATATTATTATATAATAATAT
1 TTTTATTAAATA-TATTA-ATAATAATAT
* *
3222123 TTTTATTTAATATATTAAAAATAATA
1 TTTTATTAAATATATTAATAATAATA
3222149 AATAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
24 4 0.09
25 6 0.13
26 4 0.09
27 15 0.33
28 10 0.22
29 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATTAAATATATTAATAATAATAT
Found at i:3222123 original size:16 final size:16
Alignment explanation
Indices: 3222102--3222139 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3222092 ATTTTTTTTA
3222102 AATATTATTATATAAT
1 AATATTATTATATAAT
* *
3222118 AATATTTTTATTTAAT
1 AATATTATTATATAAT
3222134 -ATATTA
1 AATATTA
3222140 AAAATAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTATTATATAAT
Found at i:3222147 original size:30 final size:30
Alignment explanation
Indices: 3222087--3222160 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
3222077 AAAAATATTT
* *
3222087 TAATAATTTTTTTTAAATATTATTATATAA
1 TAATAATTTTTTTTAAATATTATAAAATAA
3222117 TAAT-ATTTTTATTTAATATATTA-AAAATAA
1 TAATAATTTTT-TTTAA-ATATTATAAAATAA
*
3222147 TAAATAAATTTTTT
1 T-AATAATTTTTTT
3222161 ATTACATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 6 0.16
30 15 0.41
31 11 0.30
32 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TAATAATTTTTTTTAAATATTATAAAATAA
Found at i:3222180 original size:23 final size:24
Alignment explanation
Indices: 3222150--3222199 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3222140 AAAATAATAA
*
3222150 ATAAATTTT-TTATTACATTTAAT
1 ATAAATTTTATTATTACAATTAAT
* *
3222173 ATAAATTTTATTTTTATAATTAAT
1 ATAAATTTTATTATTACAATTAAT
3222197 ATA
1 ATA
3222200 TTAATTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAAATTTTATTATTACAATTAAT
Found at i:3222825 original size:20 final size:20
Alignment explanation
Indices: 3222787--3222847 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
3222777 ATTAAATTAT
* *
3222787 AATATAAAAATAATATATATA
1 AATATAAATAT-ATTTATATA
* **
3222808 AGTATATTTATATTTATATA
1 AATATAAATATATTTATATA
3222828 AATATAAATATATTTGATAT
1 AATATAAATATATTT-ATAT
3222848 TTGATAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATATAAATATATTTATATA
Found at i:3222854 original size:26 final size:26
Alignment explanation
Indices: 3222803--3222854 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3222793 AAAATAATAT
* *
3222803 ATATAAGTATATTTATATTTATATAA
1 ATATAAATATATTTATATTTAGATAA
3222829 ATATAAATATATTTGATATTT-GATAA
1 ATATAAATATATTT-ATATTTAGATAA
3222855 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
ATATAAATATATTTATATTTAGATAA
Found at i:3223293 original size:13 final size:13
Alignment explanation
Indices: 3223277--3223319 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3223267 AAAATATTAA
3223277 AAATTAATTAAAT
1 AAATTAATTAAAT
*
3223290 AAATTAAATAAAT
1 AAATTAATTAAAT
3223303 AAA--AATTAAA-
1 AAATTAATTAAAT
3223313 AAATTAA
1 AAATTAA
3223320 AAATTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.12
11 6 0.23
12 2 0.08
13 15 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAATTAAAT
Found at i:3223308 original size:15 final size:15
Alignment explanation
Indices: 3223274--3223324 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3223264 TAAAAAATAT
*
3223274 TAAAAATTAATTAAA
1 TAAAAATTAAATAAA
3223289 T--AAATTAAATAAA
1 TAAAAATTAAATAAA
3223302 TAAAAATTAAA-AAA
1 TAAAAATTAAATAAA
3223316 TTAAAAATT
1 -TAAAAATT
3223325 TATACTATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 12 0.38
14 3 0.09
15 17 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTAAATAAA
Found at i:3223314 original size:8 final size:8
Alignment explanation
Indices: 3223282--3223322 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
3223272 ATTAAAAATT
3223282 AATTAAATA
1 AATTAAA-A
3223291 AATTAAATA
1 AATTAAA-A
3223300 AA-T-AAA
1 AATTAAAA
3223306 AATTAAAA
1 AATTAAAA
3223314 AATTAAAA
1 AATTAAAA
3223322 A
1 A
3223323 TTTATACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 13 0.43
9 11 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATTAAAA
Found at i:3223367 original size:30 final size:29
Alignment explanation
Indices: 3223321--3223378 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
3223311 AAAAATTAAA
*
3223321 AATTTATACTATCAATACATA-CTAATATT
1 AATTTATACAATCAATACA-AGCTAATATT
3223350 AATTTATACAAATCAATACAAGCTAATAT
1 AATTTATAC-AATCAATACAAGCTAATAT
3223379 GAGTAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (29 bp):
AATTTATACAATCAATACAAGCTAATATT
Found at i:3223517 original size:2 final size:2
Alignment explanation
Indices: 3223510--3223536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3223500 CAAATAGATG
3223510 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3223537 CATTTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3227742 original size:22 final size:22
Alignment explanation
Indices: 3227716--3227784 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
3227706 TATATTTATA
3227716 TAAAAATAAA-AAAATTAATTTT
1 TAAAAATAAATAAAA-TAATTTT
* *
3227738 TAAAATTAAATAAAATAATTAAT
1 TAAAAATAAATAAAATAATT-TT
*
3227761 T-AATATAAAATAAAAATAATTTT
1 TAAAAAT-AAAT-AAAATAATTTT
3227784 T
1 T
3227785 TATATAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 17 0.45
23 12 0.32
24 9 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATAAATAAAATAATTTT
Found at i:3227789 original size:23 final size:23
Alignment explanation
Indices: 3227725--3227791 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
3227715 ATAAAAATAA
* *
3227725 AAAAATTAATTTTTAAAATTAAAT
1 AAAAA-TAATTTTTAATATAAAAT
*
3227749 -AAAATAATTAATTAATATAAAAT
1 AAAAATAATT-TTTAATATAAAAT
*
3227772 AAAAATAATTTTTTATATAA
1 AAAAATAATTTTTAATATAA
3227792 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.14
23 22 0.61
24 9 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATAATTTTTAATATAAAAT
Found at i:3227882 original size:17 final size:17
Alignment explanation
Indices: 3227862--3227907 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3227852 TTTATCAATC
3227862 ATTAATAATTATTAAAT
1 ATTAATAATTATTAAAT
3227879 ATTAATAAAATT-TTAAAT
1 ATTAAT--AATTATTAAAT
*
3227897 ATAAAT-ATTAT
1 ATTAATAATTAT
3227908 AATTATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 6 0.24
18 11 0.44
19 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAATAATTATTAAAT
Found at i:3227896 original size:18 final size:19
Alignment explanation
Indices: 3227868--3227903 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3227858 AATCATTAAT
*
3227868 AATTATTAAATATTAATAA
1 AATTATTAAATATAAATAA
3227887 AATT-TTAAATATAAATA
1 AATTATTAAATATAAATA
3227904 TTATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATTAAATATAAATAA
Found at i:3227918 original size:24 final size:24
Alignment explanation
Indices: 3227874--3227922 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3227864 TAATAATTAT
*
3227874 TAAATATTAATAAAATTTTAAATA
1 TAAATATTAATAAAATATTAAATA
*
3227898 TAAATATT-ATAATTATATTAAATA
1 TAAATATTAATAA-AATATTAAATA
3227922 T
1 T
3227923 GTTATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAATATTAATAAAATATTAAATA
Found at i:3227919 original size:18 final size:20
Alignment explanation
Indices: 3227898--3227939 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3227888 ATTTTAAATA
3227898 TAAATA-TTA-TAATTATAT
1 TAAATAGTTATTAATTATAT
3227916 TAAATATGTTATTAATTATAT
1 TAAATA-GTTATTAATTATAT
3227937 TAA
1 TAA
3227940 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAATAGTTATTAATTATAT
Found at i:3227972 original size:13 final size:14
Alignment explanation
Indices: 3227942--3227974 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3227932 TATATTAATT
*
3227942 TATTTTATATTTAT
1 TATTTTATATTTAA
3227956 TATTTTAT-TTTAA
1 TATTTTATATTTAA
3227969 TATTTT
1 TATTTT
3227975 TTAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:3228003 original size:48 final size:48
Alignment explanation
Indices: 3227904--3228012 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
3227894 AATATAAATA
* **
3227904 TTATAATTATA-TTAAATATGTTATTAATTATATTAATTTATTTTATAT
1 TTAT-ATTATATTTTAATATGTTATTAATTATATTAATTTATGATATAT
* * * * *
3227952 TTATTATTTTATTTTAATAT-TTTTTAATTATTTTTATTTATGATATTT
1 TTA-TATTATATTTTAATATGTTATTAATTATATTAATTTATGATATAT
3228000 TTATATTATATTT
1 TTATATTATATTT
3228013 AGAAGCGGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
47 9 0.18
48 33 0.66
49 8 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (48 bp):
TTATATTATATTTTAATATGTTATTAATTATATTAATTTATGATATAT
Found at i:3228007 original size:26 final size:24
Alignment explanation
Indices: 3227951--3228013 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
3227941 TTATTTTATA
3227951 TTTATTA-TTTTATTTTAATATTT
1 TTTATTATTTTTATTTTAATATTT
*
3227974 TTTAATTATTTTTATTTATGATATTT
1 TTT-ATTATTTTTATTT-TAATATTT
*
3228000 TTATATTATATTTA
1 TT-TATTATTTTTA
3228014 GAAGCGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 3 0.09
24 4 0.12
25 8 0.24
26 18 0.53
27 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATTATTTTTATTTTAATATTT
Found at i:3228011 original size:39 final size:39
Alignment explanation
Indices: 3227936--3228012 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
3227926 ATTAATTATA
*
3227936 TTAATTTATTTTATATTTATTATTTTATTTTAATATTTT
1 TTAATTTATTTTATATTTATTATTTTATATTAATATTTT
3227975 TTAA-TTATTTT-TATTTATGATATTTTTATATT-ATATTT
1 TTAATTTATTTTATATTTAT--TA-TTTTATATTAATATTT
3228013 AGAAGCGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
37 7 0.21
38 7 0.21
39 12 0.35
40 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (39 bp):
TTAATTTATTTTATATTTATTATTTTATATTAATATTTT
Found at i:3233135 original size:22 final size:21
Alignment explanation
Indices: 3233107--3233169 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
3233097 TGAAAATAAA
3233107 AAATTATAAATATTTAAATTT
1 AAATTATAAATATTTAAATTT
*
3233128 AAATTTATTAAATA-TTATATTT
1 AAA-TTA-TAAATATTTAAATTT
* *
3233150 AAATTATAATTATATAAATT
1 AAATTATAAATATTTAAATT
3233170 AATTGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 5 0.14
21 11 0.31
22 13 0.37
23 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATAAATATTTAAATTT
Found at i:3233542 original size:3 final size:3
Alignment explanation
Indices: 3233536--3233569 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3233526 CATCATCATC
3233536 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3233570 CTATCTTAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3233667 original size:4 final size:4
Alignment explanation
Indices: 3233660--3233710 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
3233650 CAGCAGGCTG
* *
3233660 AGAA AGAA GGAA GAGAA AGAA A-AA AGAA A-AA AGAA AGAA GGAA AG-A
1 AGAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
3233706 AGAA A
1 AGAA A
3233711 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 9 0.23
4 27 0.69
5 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3233685 original size:7 final size:7
Alignment explanation
Indices: 3233675--3233713 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
3233665 GAAGGAAGAG
3233675 AAAGAAA
1 AAAGAAA
3233682 AAAGAAA
1 AAAGAAA
3233689 AAAGAAA
1 AAAGAAA
*
3233696 GAAGGAAA
1 -AAAGAAA
*
3233704 GAAGAAA
1 AAAGAAA
3233711 AAA
1 AAA
3233714 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:3233784 original size:11 final size:11
Alignment explanation
Indices: 3233765--3233802 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3233755 ATATTAATAA
3233765 TTTAT-TTTAT
1 TTTATGTTTAT
3233775 TTTATGTTTATT
1 TTTATGTTTA-T
*
3233787 TTTATGTATAT
1 TTTATGTTTAT
3233798 TTTAT
1 TTTAT
3233803 TTTGTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 10 0.40
12 10 0.40
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (11 bp):
TTTATGTTTAT
Found at i:3236077 original size:13 final size:13
Alignment explanation
Indices: 3236012--3236077 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
3236002 TAAAATATAA
3236012 TTATTTTATCATTTT
1 TTATTTTA--ATTTT
*
3236027 TATATTTTTAAATTT
1 T-TA-TTTTAATTTT
*
3236042 TTATTTTAATTTA
1 TTATTTTAATTTT
* **
3236055 ATATGATAATTTT
1 TTATTTTAATTTT
3236068 TTATTTTAAT
1 TTATTTTAAT
3236078 AATATTAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
13 24 0.62
14 2 0.05
15 6 0.15
16 2 0.05
17 5 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:3236421 original size:32 final size:33
Alignment explanation
Indices: 3236362--3236447 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 33
3236352 AATAATTAAA
* * *
3236362 ATAT-AATAAAAATATATAAATATTTAAAATTT
1 ATATAAATATAAATATATTAATATTTAAAATTG
3236394 ATA-AAATATAAATA-ATTAATATATTAAAATTG
1 ATATAAATATAAATATATTAATAT-TTAAAATTG
3236426 ATATAAATATAAAATATATTAA
1 ATATAAATAT-AAATATATTAA
3236448 ACGTAATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 7 0.15
32 23 0.50
33 6 0.13
34 5 0.11
35 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
ATATAAATATAAATATATTAATATTTAAAATTG
Found at i:3236438 original size:17 final size:18
Alignment explanation
Indices: 3236375--3236440 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
3236365 TAATAAAAAT
*
3236375 ATATAAATATTTAAAATTT
1 ATATAAATA-TTAAAATTA
3236394 ATA-AAATA-T-AAA-TA
1 ATATAAATATTAAAATTA
*
3236408 AT-TAATATATTAAAATTG
1 ATATAA-ATATTAAAATTA
3236426 ATATAAATA-TAAAAT
1 ATATAAATATTAAAAT
3236441 ATATTAAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
14 5 0.13
15 6 0.15
16 2 0.05
17 9 0.23
18 11 0.28
19 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATAAATATTAAAATTA
Found at i:3238377 original size:2 final size:2
Alignment explanation
Indices: 3238370--3238404 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3238360 AATAGGATAC
3238370 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 T
3238405 GTAATGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3240245 original size:15 final size:13
Alignment explanation
Indices: 3240227--3240268 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
3240217 ATTAAATAAA
3240227 TAAATTTATATTATT
1 TAAATTTA-ATT-TT
3240242 TAAATTTAATTTT
1 TAAATTTAATTTT
*
3240255 T-AATTTAAATTT
1 TAAATTTAATTTT
3240267 TA
1 TA
3240269 TATCAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 11 0.44
13 3 0.12
14 3 0.12
15 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTTAATTTT
Found at i:3240265 original size:13 final size:14
Alignment explanation
Indices: 3240227--3240267 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
3240217 ATTAAATAAA
*
3240227 TAAATTTATATTATT
1 TAAATTTAAATT-TT
3240242 TAAATTT-AATTTT
1 TAAATTTAAATTTT
3240255 T-AATTTAAATTTT
1 TAAATTTAAATTTT
3240268 ATATCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.21
13 9 0.38
14 3 0.12
15 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAAATTTAAATTTT
Found at i:3240462 original size:23 final size:23
Alignment explanation
Indices: 3240421--3240487 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 23
3240411 AAATAAAAAT
* **
3240421 TTTAATTATTATATTTAATATTA
1 TTTAATTTTTATAAATAATATTA
3240444 TTTAATTTTTATAAATAATATATTA
1 TTTAATTTTTATAAAT-A-ATATTA
* * *
3240469 ATTAATTTTAAAAAATAAT
1 TTTAATTTTTATAAATAAT
3240488 TTAAAAGCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 15 0.42
24 2 0.06
25 19 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAATTTTTATAAATAATATTA
Found at i:3240473 original size:25 final size:25
Alignment explanation
Indices: 3240438--3240487 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3240428 ATTATATTTA
* * *
3240438 ATATTATTTAATTTTTATAAATAAT
1 ATATTAATTAATTTTAAAAAATAAT
3240463 ATATTAATTAATTTTAAAAAATAAT
1 ATATTAATTAATTTTAAAAAATAAT
3240488 TTAAAAGCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATATTAATTAATTTTAAAAAATAAT
Found at i:3241659 original size:12 final size:13
Alignment explanation
Indices: 3241639--3241676 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3241629 AAATATTTTT
*
3241639 ATATTTATATTTA
1 ATATATATATTTA
3241652 A-ATATATATTTA
1 ATATATATATTTA
*
3241664 ATATAAATATTTA
1 ATATATATATTTA
3241677 GTCAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATTTA
Found at i:3242245 original size:22 final size:22
Alignment explanation
Indices: 3242200--3242241 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3242190 TTTATTGGAT
* *
3242200 AATAAGATTTATCATATTTATA
1 AATAAGAATTATAATATTTATA
3242222 AATAAGAATTATAAT-TTTAT
1 AATAAGAATTATAATATTTAT
3242242 TAAAAGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AATAAGAATTATAATATTTATA
Found at i:3242276 original size:75 final size:71
Alignment explanation
Indices: 3242135--3242279 Score: 184
Period size: 73 Copynumber: 2.0 Consensus size: 71
3242125 TATTAATACA
* * * *
3242135 ATTTATCATATATAAATAAAAGTTCTAATTATATTGAAATATTTGGTTAAATAAATTTATTGGAT
1 ATTTATCATATATAAATAAAAGTTATAATTATATTAAAAGATTTGGGTAAATAAATTTATTGGAT
3242200 AATAAG
66 AATAAG
*
3242206 ATTTATCATATTTATAAATAAGAA-TTATAATTTTATTAAAAGACTTTGGGTAAATAAAATTTAT
1 ATTTATCATA--TATAAATAA-AAGTTATAATTATATTAAAAGA-TTTGGGTAAAT-AAATTTAT
*
3242270 TTGATAATAA
61 TGGATAATAA
3242280 ATAAAAAGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
71 10 0.16
73 24 0.38
74 12 0.19
75 17 0.27
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (71 bp):
ATTTATCATATATAAATAAAAGTTATAATTATATTAAAAGATTTGGGTAAATAAATTTATTGGAT
AATAAG
Found at i:3243097 original size:21 final size:21
Alignment explanation
Indices: 3243073--3243114 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3243063 TTGTATGATC
* *
3243073 TTTTTATTATT-TTAAATAAT
1 TTTTTATAATTATAAAATAAT
3243093 TTTTTATAATTATAAAATAAT
1 TTTTTATAATTATAAAATAAT
3243114 T
1 T
3243115 AATACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTATAATTATAAAATAAT
Found at i:3243950 original size:50 final size:50
Alignment explanation
Indices: 3243895--3243989 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
3243885 ATAAAATTTG
* *
3243895 AAATTTTATATTATTTTAAATATTTAATATAAAAGCAATTGATAAACTTA
1 AAATTTTATATCATTTTAAATATTTAATATAAAAACAATTGATAAACTTA
*
3243945 AAATTTTATATCATTTTAAATATTTAATATAAAAATAATTGATAA
1 AAATTTTATATCATTTTAAATATTTAATATAAAAACAATTGATAA
3243990 TTTATGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (50 bp):
AAATTTTATATCATTTTAAATATTTAATATAAAAACAATTGATAAACTTA
Found at i:3244036 original size:16 final size:17
Alignment explanation
Indices: 3244010--3244052 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
3244000 AAATCAACTT
3244010 AAATATAAAATTATAA-A
1 AAAT-TAAAATTATAATA
3244027 AAATTAAAATTATAATA
1 AAATTAAAATTATAATA
3244044 AATATTAAA
1 AA-ATTAAA
3244053 TAATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTAAAATTATAATA
Found at i:3248903 original size:79 final size:80
Alignment explanation
Indices: 3248781--3248938 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 80
3248771 GATCTTTATA
*
3248781 TTATTTTAGAATAGTTAGAGAGTAGATTAGATTCATTCAGTGAGGATAAATATGTTAATAGCCAG
1 TTATTTTAGAATAGTTA-AGAGTAGAATAGATTCATTCAGTGAGGATAAATATGTTAATAGCCAG
*
3248846 TAGAAAACTCATAATT
65 TAGAAAACTAATAATT
* *
3248862 TTATTTTAGAATTGTT-AGAGTAGAATAGATTCATTCAGTGAGTATAAATATGTTAATAGCCAGT
1 TTATTTTAGAATAGTTAAGAGTAGAATAGATTCATTCAGTGAGGATAAATATGTTAATAGCCAGT
3248926 AGAAAACTAATAA
66 AGAAAACTAATAA
3248939 AGGACTAGCT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 58 0.79
81 15 0.21
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.35
Consensus pattern (80 bp):
TTATTTTAGAATAGTTAAGAGTAGAATAGATTCATTCAGTGAGGATAAATATGTTAATAGCCAGT
AGAAAACTAATAATT
Found at i:3258159 original size:27 final size:26
Alignment explanation
Indices: 3258121--3258180 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
3258111 GATTTGATTT
*
3258121 TTTTTAATATTAAAA-AAATAAAAAATA
1 TTTTTAAAATTAAAATAAAT--AAAATA
3258148 TTTTTAAAATTAAAATTAAATAAAATA
1 TTTTTAAAATTAAAA-TAAATAAAATA
3258175 TTTTTA
1 TTTTTA
3258181 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 26 0.87
29 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTTTAAAATTAAAATAAATAAAATA
Found at i:3264455 original size:27 final size:26
Alignment explanation
Indices: 3264425--3264475 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
3264415 TCATAATTAT
* *
3264425 ATTTAAAATATTAAATATTTATATAAA
1 ATTTAAAATATAAAAAATTT-TATAAA
3264452 ATTTAAAATATAAAAAATTTTATA
1 ATTTAAAATATAAAAAATTTTATA
3264476 CTATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTAAAATATAAAAAATTTTATAAA
Found at i:3264463 original size:16 final size:16
Alignment explanation
Indices: 3264444--3264493 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3264434 ATTAAATATT
3264444 TATATAAAATTTAAAA
1 TATATAAAATTTAAAA
* * *
3264460 TATAAAAAATTTTATAC
1 TATATAAAA-TTTAAAA
*
3264477 TATATAAATTTTAAAA
1 TATATAAAATTTAAAA
3264493 T
1 T
3264494 TTTTATATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAAAATTTAAAA
Found at i:3264484 original size:26 final size:27
Alignment explanation
Indices: 3264428--3264502 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 27
3264418 TAATTATATT
* * *
3264428 TAAAATATTAAATATTTATATAAAATT
1 TAAAATATAAAAAATTTATATAAAATA
**
3264455 TAAAATATAAAAAATTT-TATACTATA
1 TAAAATATAAAAAATTTATATAAAATA
* * **
3264481 TAAATTTTAAAATTTTTATATA
1 TAAAATATAAAAAATTTATATA
3264503 TTATATATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAATATAAAAAATTTATATAAAATA
Found at i:3264506 original size:7 final size:7
Alignment explanation
Indices: 3264496--3264548 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
3264486 TTTAAAATTT
3264496 TTATATA
1 TTATATA
3264503 TTATATA
1 TTATATA
3264510 -TATTAATA
1 TTA-T-ATA
3264518 TTATATA
1 TTATATA
3264525 TTATATA
1 TTATATA
3264532 TTAT-T-
1 TTATATA
3264537 TT-TATA
1 TTATATA
3264543 TTATAT
1 TTATAT
3264549 TCATATCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 5 0.12
7 25 0.62
8 4 0.10
9 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:3264515 original size:25 final size:24
Alignment explanation
Indices: 3264465--3264532 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 24
3264455 TAAAATATAA
* *
3264465 AAAATTTTATACTA-TATAAATTTT
1 AAAATTTTATA-TATTATATATATT
3264489 AAAATTTTTATATATTATATATATT
1 AAAA-TTTTATATATTATATATATT
*
3264514 --AATATTATATATTATATAT
1 AAAATTTTATATATTATATAT
3264533 TATTTTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 16 0.41
23 2 0.05
24 6 0.15
25 15 0.38
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
AAAATTTTATATATTATATATATT
Found at i:3264542 original size:18 final size:20
Alignment explanation
Indices: 3264496--3264548 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 20
3264486 TTTAAAATTT
3264496 TTATATATTATATATATTAATA
1 TTATATA-T-TATATATTAATA
3264518 TTATATATTATATATT-AT-
1 TTATATATTATATATTAATA
*
3264536 TTTTATATTATAT
1 TTATATATTATAT
3264549 TCATATCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.40
19 2 0.07
20 8 0.27
21 1 0.03
22 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATATTATATATTAATA
Found at i:3266622 original size:17 final size:17
Alignment explanation
Indices: 3266580--3266636 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
3266570 TATTTTTAAT
*
3266580 ATATATTT-AAATATATA
1 ATATATTTAAAAAATA-A
* *
3266597 ATTTTTTTAAAAAATAA
1 ATATATTTAAAAAATAA
3266614 ATATATTTAAATTAAATAA
1 ATATATTTAAA--AAATAA
3266633 ATAT
1 ATAT
3266637 TTATATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 16 0.50
18 6 0.19
19 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTTAAAAAATAA
Found at i:3266637 original size:17 final size:17
Alignment explanation
Indices: 3266616--3266660 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3266606 AAAAATAAAT
3266616 ATATTTAAATTAAATAA
1 ATATTTAAATTAAATAA
* * *
3266633 ATATTTATATTTAATAT
1 ATATTTAAATTAAATAA
*
3266650 TTATTTAAATT
1 ATATTTAAATT
3266661 CGTATAATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAAATTAAATAA
Found at i:3267098 original size:3 final size:3
Alignment explanation
Indices: 3267090--3267128 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3267080 TTAATCGTTC
*
3267090 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3267129 TAATCCTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3270644 original size:3 final size:3
Alignment explanation
Indices: 3270636--3270685 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3270626 CATGCGTTTA
3270636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3270684 AA
1 AA
3270686 ATGTTTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3273054 original size:23 final size:23
Alignment explanation
Indices: 3273028--3273071 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3273018 ATATAATTAT
3273028 TTTTAAAATT-AATATTTAATAAA
1 TTTTAAAATTAAATA-TTAATAAA
*
3273051 TTTTAAATTTAAATATTAATA
1 TTTTAAAATTAAATATTAATA
3273072 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAAAATTAAATATTAATAAA
Found at i:3273377 original size:2 final size:2
Alignment explanation
Indices: 3273370--3273397 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3273360 AAAGATTTCA
3273370 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
3273398 TAAACTAAGA
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:3275129 original size:17 final size:17
Alignment explanation
Indices: 3275075--3275132 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
3275065 CTATTTTTTA
3275075 ATTTAAAA-AT-AA-AT
1 ATTTAAAATATAAATAT
3275089 ATTT--AATATAAATAT
1 ATTTAAAATATAAATAT
*
3275104 -TTATGAAATATAAATAT
1 ATT-TAAAATATAAATAT
3275121 ATTTAAAATATA
1 ATTTAAAATATA
3275133 TATTTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
12 2 0.06
13 2 0.06
14 8 0.22
15 3 0.08
17 19 0.53
18 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTAAAATATAAATAT
Found at i:3275146 original size:21 final size:22
Alignment explanation
Indices: 3275122--3275172 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
3275112 TATAAATATA
3275122 TTTAAAA-TATATATTTTTATT
1 TTTAAAATTATATATTTTTATT
3275143 TTTAAAATTATATATTTTTATT
1 TTTAAAATTATATATTTTTATT
3275165 TATTAAAA
1 T-TTAAAA
3275173 AAAGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.25
22 15 0.54
23 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAAAATTATATATTTTTATT
Found at i:3276420 original size:2 final size:2
Alignment explanation
Indices: 3276413--3276451 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3276403 GTTTTACTAG
3276413 AT AT AT 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 AT AT AT A
3276452 CACCCTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3281029 original size:11 final size:11
Alignment explanation
Indices: 3281013--3281037 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3281003 AAGGAAAGAG
3281013 TATAAATTTGA
1 TATAAATTTGA
3281024 TATAAATTTGA
1 TATAAATTTGA
3281035 TAT
1 TAT
3281038 CCTCCGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
TATAAATTTGA
Found at i:3281394 original size:17 final size:18
Alignment explanation
Indices: 3281350--3281385 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
3281340 TTAATTATAA
3281350 AAAATATAATTATTAATAT
1 AAAA-ATAATTATTAATAT
3281369 AAAAATAATT-TTAATAT
1 AAAAATAATTATTAATAT
3281386 GTAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATAATTATTAATAT
Found at i:3286230 original size:21 final size:21
Alignment explanation
Indices: 3286201--3286242 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3286191 AAATAATATC
3286201 AATATAATTAAAAATTTATTAA
1 AATATAATTAAAAA-TTATTAA
3286223 AATA-AATTAAAAATTATTAA
1 AATATAATTAAAAATTATTAA
3286243 TAAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAATTAAAAATTATTAA
Found at i:3286234 original size:20 final size:20
Alignment explanation
Indices: 3286201--3286256 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
3286191 AAATAATATC
3286201 AATATAATTAAAAATTTATTAA
1 AATA-AATT-AAAATTTATTAA
*
3286223 AATAAATTAAAAATTATTAA
1 AATAAATTAAAATTTATTAA
*
3286243 TA-AAATATAAAATT
1 AATAAAT-TAAAATT
3286257 AAAAAAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 18 0.60
21 4 0.13
22 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTAAAATTTATTAA
Found at i:3290674 original size:25 final size:26
Alignment explanation
Indices: 3290641--3290693 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
3290631 TAGTCGAAAG
3290641 TTTTAAAAGTAATATC-TTTTTTTAT
1 TTTTAAAAGTAATATCTTTTTTTTAT
3290666 TTTTAAAAGTAATATCTTTTTTTTAT
1 TTTTAAAAGTAATATCTTTTTTTTAT
3290692 TT
1 TT
3290694 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTAAAAGTAATATCTTTTTTTTAT
Found at i:3299598 original size:23 final size:24
Alignment explanation
Indices: 3299557--3299613 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3299547 TAAAATTTTG
* * *
3299557 TTAATATTTATATATTAAATTTAA
1 TTAATAATTAAATATTAAATATAA
*
3299581 -TATTAATTAAATATTAAATATAA
1 TTAATAATTAAATATTAAATATAA
3299604 TTAATAATTA
1 TTAATAATTA
3299614 TCGAAGACGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATAATTAAATATTAAATATAA
Found at i:3299604 original size:17 final size:15
Alignment explanation
Indices: 3299557--3299607 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
3299547 TAAAATTTTG
3299557 TTAATATTT-ATAT-A
1 TTAA-ATTTAATATAA
3299571 TTAAATTTAATATTAA
1 TTAAATTTAATA-TAA
3299587 TTAAATATTAAATATAA
1 TTAAAT-TT-AATATAA
3299604 TTAA
1 TTAA
3299608 TAATTATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.12
14 7 0.22
15 1 0.03
16 7 0.22
17 9 0.28
18 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAATTTAATATAA
Found at i:3302615 original size:13 final size:14
Alignment explanation
Indices: 3302597--3302625 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3302587 GTTTTGACCC
3302597 AAAAAAAA-GAAAA
1 AAAAAAAAGGAAAA
3302610 AAAAAAAAGGAAAA
1 AAAAAAAAGGAAAA
3302624 AA
1 AA
3302626 CTTAGCTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGAAAA
Found at i:3302959 original size:3 final size:3
Alignment explanation
Indices: 3302951--3302982 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
3302941 CGTTTACTTG
3302951 TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT T
3302983 TAAATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3303986 original size:17 final size:16
Alignment explanation
Indices: 3303964--3304012 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3303954 TTGTATATTT
3303964 TATTTATATCAAAATTA
1 TATTTATAT-AAAATTA
* **
3303981 TATTTAAATAATTTTA
1 TATTTATATAAAATTA
3303997 TAATTTATATAAAATT
1 T-ATTTATATAAAATT
3304013 TAAATTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTATATAAAATTA
Found at i:3304038 original size:25 final size:25
Alignment explanation
Indices: 3303979--3304046 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
3303969 ATATCAAAAT
*
3303979 TATATTTAAATAATTTTATAATTTATA
1 TATATTTAAAT--TATTATAATTTATA
*
3304006 TAAAATTTAAATTATTAT-ATTTATAA
1 T-ATATTTAAATTATTATAATTTAT-A
*
3304032 TATATTTATATTATT
1 TATATTTAAATTATT
3304047 TTTATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 18 0.51
26 7 0.20
27 1 0.03
28 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATTTAAATTATTATAATTTATA
Found at i:3304050 original size:22 final size:22
Alignment explanation
Indices: 3304018--3304059 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3304008 AAATTTAAAT
3304018 TATTATATTTATAATATATTTA
1 TATTATATTTATAATATATTTA
* *
3304040 TATTATTTTTATATTATATT
1 TATTATATTTATAATATATT
3304060 AATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTATATTTATAATATATTTA
Found at i:3304052 original size:17 final size:17
Alignment explanation
Indices: 3304032--3304068 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3304022 ATATTTATAA
3304032 TATATTTATATT-ATTTT
1 TATA-TTATATTAATTTT
3304049 TATATTATATTAATTTT
1 TATATTATATTAATTTT
3304066 TAT
1 TAT
3304069 TATATTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTATATTAATTTT
Found at i:3304080 original size:17 final size:16
Alignment explanation
Indices: 3304018--3304074 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
3304008 AAATTTAAAT
* **
3304018 TATTATATTTATAATA
1 TATTATATTAATTTTA
*
3304034 TATTTATATTATTTTTA
1 TA-TTATATTAATTTTA
3304051 TATTATATTAATTTT-
1 TATTATATTAATTTTA
3304066 TATTATATT
1 TATTATATT
3304075 CGAATTACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 9 0.26
16 14 0.40
17 12 0.34
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATATTAATTTTA
Found at i:3315509 original size:19 final size:18
Alignment explanation
Indices: 3315433--3315538 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 18
3315423 AAATTATTAA
3315433 TATTTATAATTAAATTTA-
1 TATTTA-AATTAAATTTAT
* ** *
3315451 AATAAAAATTAATTTTAT
1 TATTTAAATTAAATTTAT
*
3315469 TA-TT-AATTAAA-TAAT
1 TATTTAAATTAAATTTAT
*
3315484 AATTTAAATTAAATTTAT
1 TATTTAAATTAAATTTAT
3315502 TCATTTAAATATAAAATTT-T
1 T-ATTTAAAT-T-AAATTTAT
*
3315522 TATTTATATTAAATTTA
1 TATTTAAATTAAATTTA
3315539 ACTAATAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
15 4 0.06
16 8 0.12
17 23 0.34
18 8 0.12
19 15 0.22
20 3 0.04
21 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTAAATTAAATTTAT
Found at i:3319804 original size:48 final size:50
Alignment explanation
Indices: 3319739--3319836 Score: 173
Period size: 48 Copynumber: 2.0 Consensus size: 50
3319729 TAATATTTGA
3319739 ATTTGCATAGACTTGAGTCAATATATATATATATATATATTTATTTATTT
1 ATTTGCATAGACTTGAGTCAATATATATATATATATATATTTATTTATTT
*
3319789 ATTTG-ATAGAC-TGAGTCAATATATATATATATATTTATTTATTTATTT
1 ATTTGCATAGACTTGAGTCAATATATATATATATATATATTTATTTATTT
3319837 GATGCATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 36 0.77
49 6 0.13
50 5 0.11
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (50 bp):
ATTTGCATAGACTTGAGTCAATATATATATATATATATATTTATTTATTT
Found at i:3320006 original size:2 final size:2
Alignment explanation
Indices: 3319999--3320049 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3319989 TAAGGATTTG
*
3319999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3320041 AT AT AT AT A
1 AT AT AT AT A
3320050 GAAGCATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3320148 original size:12 final size:13
Alignment explanation
Indices: 3320116--3320153 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3320106 AAAAATAGGT
*
3320116 TAATTTTTTAAAA
1 TAATTATTTAAAA
*
3320129 TAATTATTTAAAT
1 TAATTATTTAAAA
3320142 TAA-TATTTAAAA
1 TAATTATTTAAAA
3320154 AATAAATCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTATTTAAAA
Found at i:3321265 original size:42 final size:42
Alignment explanation
Indices: 3321179--3321313 Score: 220
Period size: 42 Copynumber: 3.2 Consensus size: 42
3321169 AAATGGAAAT
* * *
3321179 AAGGCATATTCGAAGCGTGTGAGCAGT--AAAAAAGCTAAAT
1 AAGGCATATTTGAAGCGTGTGAACAGTAAAAAAAAGCTAAAC
3321219 AAGGCATATTTGAAGCGTGTGAACAGTAAAAAAAAGCTAAAC
1 AAGGCATATTTGAAGCGTGTGAACAGTAAAAAAAAGCTAAAC
3321261 AAGGCATATTTGAAGCGTGTGAACAGTAAAAAAAAAGCTAAAC
1 AAGGCATATTTGAAGCGTGTGAACAGT-AAAAAAAAGCTAAAC
3321304 AAGGCATATT
1 AAGGCATATT
3321314 GCGAGGTTAA
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
40 25 0.28
42 39 0.44
43 25 0.28
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (42 bp):
AAGGCATATTTGAAGCGTGTGAACAGTAAAAAAAAGCTAAAC
Found at i:3321640 original size:16 final size:16
Alignment explanation
Indices: 3321616--3321659 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3321606 AAAATAAAAA
3321616 AATTAAAATAAAATTT
1 AATTAAAATAAAATTT
* *
3321632 AATTCAAATTAAATTT
1 AATTAAAATAAAATTT
*
3321648 -ATTAAATTAAAA
1 AATTAAAATAAAA
3321660 AAATAATTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAATAAAATTT
Found at i:3322163 original size:2 final size:2
Alignment explanation
Indices: 3322156--3322190 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3322146 CAAACCTTTT
*
3322156 TG TG TG TG TT 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 T
3322191 TGATACATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:3322834 original size:22 final size:22
Alignment explanation
Indices: 3322792--3322833 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
3322782 TTACATGTAA
3322792 GCCAGCCAGCCTGAGAGTTTTG
1 GCCAGCCAGCCTGAGAGTTTTG
3322814 GCCAG-CAGCCTGAGAGTTTT
1 GCCAGCCAGCCTGAGAGTTTT
3322834 TAAGTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (22 bp):
GCCAGCCAGCCTGAGAGTTTTG
Found at i:3323872 original size:40 final size:39
Alignment explanation
Indices: 3323827--3323951 Score: 128
Period size: 39 Copynumber: 3.2 Consensus size: 39
3323817 ATTTTTTCTC
*
3323827 ATTAAATGTACAATATGATAAAAATAAAAAAAAATATTTG
1 ATTAAATGTACAATATGATAAAAAT-AAAAAATATATTTG
* *
3323867 ATTAAATTGATAGAAAAT-A-AAAAATAAAAAATATATTTG
1 ATTAAA-TG-TACAATATGATAAAAATAAAAAATATATTTG
* ** * * *
3323906 ATCAAACATTCGATATGATACAAATAAAAAATATATTTG
1 ATTAAATGTACAATATGATAAAAATAAAAAATATATTTG
3323945 ATTAAAT
1 ATTAAAT
3323952 TGATAGAGCT
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
37 4 0.06
38 1 0.01
39 42 0.62
40 12 0.18
41 3 0.04
42 6 0.09
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (39 bp):
ATTAAATGTACAATATGATAAAAATAAAAAATATATTTG
Found at i:3325981 original size:15 final size:15
Alignment explanation
Indices: 3325961--3326001 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3325951 AAAGATTAAA
3325961 ATTTATATTTA-ATTT
1 ATTTAT-TTTATATTT
3325976 ATTTATTTTATATTT
1 ATTTATTTTATATTT
*
3325991 -TTAATTTTATA
1 ATTTATTTTATA
3326002 ATAATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTTATATTT
Found at i:3326202 original size:185 final size:185
Alignment explanation
Indices: 3325878--3326228 Score: 494
Period size: 185 Copynumber: 1.9 Consensus size: 185
3325868 AAGTTTATAT
* * * *
3325878 TAAATTATTTTATTTTTAATATTTTAATTTTTTTATTAATTTTAAAAAATAAAATACATTTATTT
1 TAAATTATTTTATTTTTAAAATTTTAATTTTTTCATTAATTTAAAAAAATAAAATACATTTACTT
* * * * *
3325943 CATATAAAAAAGATTAAAATTTATATTTAATTTATTTATTTTATATTTTTAATTTTATAATAATA
66 CAAACAAAAAACATTAAAATTTACATTAAATTTATTTATTTTATATTTTTAATTTTATAATAATA
*
3326008 TTAAAAATAATAAATTTTATATTAATTTGATATAATATGTAAGTGGAATAAAAAA
131 TTAAAAATAATAAACTTTATATTAATTTGATATAATATGTAAGTGGAATAAAAAA
*
3326063 TAAATTCTTTTATTTTTAAAATTTTAA-TTTTTCATTAATCTTAAAAAAAT-AAATATC-TTTAC
1 TAAATTATTTTATTTTTAAAATTTTAATTTTTTCATTAAT-TTAAAAAAATAAAATA-CATTTAC
** * * *
3326125 TTCAAACAAGGCAACATTGAAATTTACATTAAATTTATTTATCTTTATATTTTTAATTTTTTATT
64 TTCAAACAA-AAAACATTAAAATTTACATTAAATTTATTTAT-TTTATATTTTTAATTTTATAAT
3326190 AATATT-AAAATAATAAACTTTATATTAATTTGATATAAT
127 AATATTAAAAATAATAAACTTTATATTAATTTGATATAAT
3326229 TTATGGATAG
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
184 27 0.18
185 93 0.64
186 26 0.18
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (185 bp):
TAAATTATTTTATTTTTAAAATTTTAATTTTTTCATTAATTTAAAAAAATAAAATACATTTACTT
CAAACAAAAAACATTAAAATTTACATTAAATTTATTTATTTTATATTTTTAATTTTATAATAATA
TTAAAAATAATAAACTTTATATTAATTTGATATAATATGTAAGTGGAATAAAAAA
Found at i:3326911 original size:4 final size:4
Alignment explanation
Indices: 3326902--3326937 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
3326892 GAACATGCAC
* *
3326902 AAAT AAAT AAAT AAAT AAAT AAAT AATT AATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3326938 CAAGCAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:3327635 original size:5 final size:5
Alignment explanation
Indices: 3327625--3327687 Score: 60
Period size: 5 Copynumber: 13.2 Consensus size: 5
3327615 TAAATTTATA
* * * *
3327625 TAATT TGATT TAATT TAATT TAATT T-TTT TAA-T AAATT TAAAT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT
*
3327673 TAATA T-ATT TAATT T
1 TAATT TAATT TAATT T
3327688 TTTTTATAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
4 9 0.20
5 36 0.80
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:3327655 original size:19 final size:19
Alignment explanation
Indices: 3327633--3327691 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
3327623 TATAATTTGA
3327633 TTTAATTTAATTTAATTTT
1 TTTAATTTAATTTAATTTT
* **
3327652 TTTAA-TAAATTTAAATTAA
1 TTTAATTTAATTT-AATTTT
*
3327671 TTTAATAT-ATTTAATTTT
1 TTTAATTTAATTTAATTTT
3327689 TTT
1 TTT
3327692 TATAATTTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATTTAATTTAATTTT
Found at i:3327672 original size:28 final size:28
Alignment explanation
Indices: 3327632--3327685 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3327622 ATATAATTTG
* * *
3327632 ATTTAATTTAATTTAATTTTTTTAATAA
1 ATTTAAATTAATTTAATATATTTAATAA
3327660 ATTTAAATTAATTTAATATATTTAAT
1 ATTTAAATTAATTTAATATATTTAAT
3327686 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTAAATTAATTTAATATATTTAATAA
Found at i:3327693 original size:19 final size:18
Alignment explanation
Indices: 3327641--3327696 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
3327631 GATTTAATTT
3327641 AATTTAATTTTTTTAATA
1 AATTTAATTTTTTTAATA
**
3327659 AATTTAAATTAATTTAATA
1 AATTT-AATTTTTTTAATA
* *
3327678 TATTTAATTTTTTTTATA
1 AATTTAATTTTTTTAATA
3327696 A
1 A
3327697 TTTCAAACTC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTAATTTTTTTAATA
Found at i:3328010 original size:2 final size:2
Alignment explanation
Indices: 3328003--3328031 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3327993 GCAGATAAGC
3328003 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 T
3328032 GCAGTGTTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3329456 original size:224 final size:224
Alignment explanation
Indices: 3329049--3329498 Score: 690
Period size: 224 Copynumber: 2.0 Consensus size: 224
3329039 GTTGATGTGA
*
3329049 TTTTACATATTAATTATCTTATAATTATAAAAAAAATTATGTTAAATAATTAAAAGATCACGCAA
1 TTTTACATATTAATTATCTTATAATTATAAAAAAAATTATGTTAAATAATGAAAAGATCACGCAA
* ** *
3329114 ATAAATATCACATTATATAAAAATATATTAAATAAAATTTCATTATATCTATTTATATAAAAATA
66 AT-AATATCACATTACATAAAAATATATTAAATAAAAAATCATTATATCTATTTACATAAAAATA
* * *
3329179 AAAAATTACTAATTAAAAACAACTATTATCAAAATATAAGTTAACAATTTATTATAAAACTTTTT
130 AAAAATTACTAATTAAAAACAAATATTATCAAAATATAAGTTAACAATTTATTATAAAACCTTTA
3329244 AAGAAAAAAAAAATCACAAAACCATTTTGAG
195 AAG-AAAAAAAAATCACAAAACCATTTTGAG
* *
3329275 TTTTACATGTTAATTATCTTATAATTATAAAAAAAAATTATGTTAAATAATGAAAAGATCATGCA
1 TTTTACATATTAATTATCTTATAATTAT-AAAAAAAATTATGTTAAATAATGAAAAGATCACGCA
*
3329340 AAT-ATATCACATTACATAAAAATATTTTAAATAAAAAATC-TTATATCTATTTACATAAAAATA
65 AATAATATCACATTACATAAAAATATATTAAATAAAAAATCATTATATCTATTTACATAAAAATA
* * * *
3329403 AAAAATTACTAATTAAAAAGAAATATTATCAAAATGTGAGTT-ACAATTTTATTATAAGACCTTT
130 AAAAATTACTAATTAAAAACAAATATTATCAAAATATAAGTTAACAA-TTTATTATAAAACCTTT
* *
3329467 AAAGAACAAAAAATCACAAAATCATTTTGAG
194 AAAGAAAAAAAAATCACAAAACCATTTTGAG
3329498 T
1 T
3329499 AATTTGACAA
Statistics
Matches: 205, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
223 30 0.15
224 78 0.38
225 33 0.16
226 27 0.13
227 37 0.18
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (224 bp):
TTTTACATATTAATTATCTTATAATTATAAAAAAAATTATGTTAAATAATGAAAAGATCACGCAA
ATAATATCACATTACATAAAAATATATTAAATAAAAAATCATTATATCTATTTACATAAAAATAA
AAAATTACTAATTAAAAACAAATATTATCAAAATATAAGTTAACAATTTATTATAAAACCTTTAA
AGAAAAAAAAATCACAAAACCATTTTGAG
Found at i:3330603 original size:13 final size:13
Alignment explanation
Indices: 3330585--3330609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3330575 TCTCAAAGTT
3330585 GAAAAGAAAAAAC
1 GAAAAGAAAAAAC
3330598 GAAAAGAAAAAA
1 GAAAAGAAAAAA
3330610 TTCTTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAAC
Found at i:3332670 original size:87 final size:82
Alignment explanation
Indices: 3332513--3332683 Score: 227
Period size: 87 Copynumber: 2.0 Consensus size: 82
3332503 TTGTAGAGGT
*
3332513 AGGTATTTTTATCAGTAGATCAACAAACTTACGATATTCTCTGGTAAGAAATGTTTTTACATGTT
1 AGGTATTTTTATCAGTAGACCAACAAACTTACGATATTCTCTGGTAAGAAATGTTTTTACATGTT
3332578 AAATATATTAATTAGAC
66 AAATATATTAATTAGAC
* *
3332595 AGGTATTTTTATCAGTAGACCAACAAAAGTTACTTAACGATATTTTCTGGTGAG-AATGTTTTTA
1 AGGTATTTTTATCAGTAGACCAAC--AA---ACTT-ACGATATTCTCTGGTAAGAAATGTTTTTA
* * *
3332659 CTTGTTAAATATGTTATTTAGAC
60 CATGTTAAATATATTAATTAGAC
3332682 AG
1 AG
3332684 TTTATTAATC
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
82 23 0.30
84 2 0.03
87 36 0.47
88 16 0.21
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (82 bp):
AGGTATTTTTATCAGTAGACCAACAAACTTACGATATTCTCTGGTAAGAAATGTTTTTACATGTT
AAATATATTAATTAGAC
Found at i:3337381 original size:19 final size:18
Alignment explanation
Indices: 3337357--3337402 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
3337347 CAGAGAAGGT
3337357 AAGTTGAAGTACCGCACTA
1 AAGTTGAAGTACC-CACTA
*
3337376 AAGTTGGAAGTACCCATTA
1 AAGTT-GAAGTACCCACTA
3337395 AAGTTGAA
1 AAGTTGAA
3337403 CTGAAGCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (18 bp):
AAGTTGAAGTACCCACTA
Found at i:3338920 original size:17 final size:19
Alignment explanation
Indices: 3338898--3338936 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3338888 ATTAATATAA
3338898 AATATCAT-AT-TAAATTT
1 AATATCATAATATAAATTT
3338915 AATATCATAATATAAATTT
1 AATATCATAATATAAATTT
3338934 AAT
1 AAT
3338937 TATAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATCATAATATAAATTT
Found at i:3338947 original size:19 final size:19
Alignment explanation
Indices: 3338908--3338974 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
3338898 AATATCATAT
3338908 TAAATTTAA-TATCATAA-TA
1 TAAATTTAATTAT-A-AATTA
3338927 TAAATTTAATTATAAATTA
1 TAAATTTAATTATAAATTA
3338946 TAAATAATTAATT-T-AATTAA
1 TAAAT--TTAATTATAAATT-A
3338966 TAAATTTAA
1 TAAATTTAA
3338975 ATACAACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.14
19 21 0.49
20 10 0.23
21 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTTAATTATAAATTA
Found at i:3338971 original size:13 final size:13
Alignment explanation
Indices: 3338926--3338974 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3338916 ATATCATAAT
3338926 ATAAATTTAATT-
1 ATAAATTTAATTA
*
3338938 ATAAATTATAAATA
1 ATAAATT-TAATTA
*
3338952 ATTAATTTAATTA
1 ATAAATTTAATTA
3338965 ATAAATTTAA
1 ATAAATTTAA
3338975 ATACAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 7 0.23
13 18 0.58
14 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAAATTTAATTA
Found at i:3339955 original size:44 final size:42
Alignment explanation
Indices: 3339891--3339972 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 42
3339881 GGCAAATTTT
3339891 TTAAATTTTTATTAATATTTAAATAATAATAATTTTTAAATCAAA
1 TTAAATTTTTATTAATATTTAAATAA-AA-AA-TTTTAAATCAAA
3339936 TTAAA-TTTTATTTAA-ATTTAAATAAAAAATTTTAAAT
1 TTAAATTTTTA-TTAATATTTAAATAAAAAATTTTAAAT
3339973 TTTTTAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
41 8 0.22
42 2 0.06
43 2 0.06
44 15 0.42
45 9 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
TTAAATTTTTATTAATATTTAAATAAAAAATTTTAAATCAAA
Found at i:3340334 original size:3 final size:3
Alignment explanation
Indices: 3340328--3340364 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3340318 ATTATATAAG
3340328 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3340365 GGAATCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3341156 original size:15 final size:16
Alignment explanation
Indices: 3341117--3341156 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3341107 CGATAAATTT
3341117 AATTTAT-ATTAAATA
1 AATTTATAATTAAATA
*
3341132 TATTTA-AATTAAA-A
1 AATTTATAATTAAATA
3341146 AATTTATAATT
1 AATTTATAATT
3341157 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTATAATTAAATA
Found at i:3341209 original size:20 final size:20
Alignment explanation
Indices: 3341184--3341247 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
3341174 ATTTGAATTA
3341184 TTATTTAAATAAAAATATTT
1 TTATTTAAATAAAAATATTT
** * *
3341204 TTATTTAAATTTAATTATTA
1 TTATTTAAATAAAAATATTT
*
3341224 ATA-TTAATATAAAAATATTT
1 TTATTTAA-ATAAAAATATTT
3341244 TTAT
1 TTAT
3341248 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTTAAATAAAAATATTT
Found at i:3341257 original size:40 final size:40
Alignment explanation
Indices: 3341169--3341271 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
3341159 AATTTAATTA
* *
3341169 ATTTGATTTGAATTATT-AT-TTAA-ATAAAAATATTTTT
1 ATTTAATTTTAATTATTAATATTAATATAAAAATATTTTT
*
3341206 ATTTAAATTTAATTATTAATATTAATATAAAAATATTTTT
1 ATTTAATTTTAATTATTAATATTAATATAAAAATATTTTT
* * *
3341246 ATATT-ATTTTAAATAATAAAATTAAT
1 AT-TTAATTTTAATTATTAATATTAAT
3341272 TTTTAAATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
37 14 0.25
38 2 0.04
39 4 0.07
40 33 0.60
41 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (40 bp):
ATTTAATTTTAATTATTAATATTAATATAAAAATATTTTT
Found at i:3344415 original size:2 final size:2
Alignment explanation
Indices: 3344408--3344434 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3344398 TGTCCTTTTA
3344408 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3344435 CATTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3348143 original size:10 final size:10
Alignment explanation
Indices: 3348128--3348162 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3348118 GTGATAGATT
3348128 AAAATATATA
1 AAAATATATA
3348138 AAAATATATA
1 AAAATATATA
3348148 TAAAAT-TATA
1 -AAAATATATA
3348158 AAAAT
1 AAAAT
3348163 TTAAAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATATATA
Found at i:3348744 original size:2 final size:2
Alignment explanation
Indices: 3348700--3348729 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3348690 GCTAAAATCC
*
3348700 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3348730 AATGCCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3349668 original size:12 final size:12
Alignment explanation
Indices: 3349651--3349696 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
3349641 TATTTAAATT
3349651 AATAATTATAAA
1 AATAATTATAAA
3349663 AATAATTAT-AA
1 AATAATTATAAA
*
3349674 AATTATT-TAAA
1 AATAATTATAAA
3349685 AA-AATTA-AAA
1 AATAATTATAAA
3349695 AA
1 AA
3349697 ACATCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 9 0.30
11 12 0.40
12 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATTATAAA
Found at i:3349695 original size:20 final size:18
Alignment explanation
Indices: 3349646--3349695 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
3349636 TTATTTATTT
*
3349646 AAATTAATAATTATAAAA
1 AAATTAAAAATTATAAAA
3349664 ATAATTATAAAATTATTTAAAA
1 A-AATTA-AAAATTA--TAAAA
3349686 AAATTAAAAA
1 AAATTAAAAA
3349696 AACATCACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
19 5 0.19
20 10 0.37
21 5 0.19
22 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAAAATTATAAAA
Found at i:3353154 original size:50 final size:51
Alignment explanation
Indices: 3353078--3353179 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 51
3353068 ATGGAAAGAC
*
3353078 AGCTTTCTACTCCCCCACTCAATGCAAAACAAACCCATTATTTAAAGATAT
1 AGCTTTCTACTCCCCCACTCAATGCAAAACAAACCCATGATTTAAAGATAT
* *
3353129 AGCTTTCTACT-TCCCACTCATTGCAAAACAAACCCATGATTTAAAGATAT
1 AGCTTTCTACTCCCCCACTCAATGCAAAACAAACCCATGATTTAAAGATAT
3353179 A
1 A
3353180 CATATACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 37 0.77
51 11 0.23
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.28
Consensus pattern (51 bp):
AGCTTTCTACTCCCCCACTCAATGCAAAACAAACCCATGATTTAAAGATAT
Found at i:3358162 original size:2 final size:2
Alignment explanation
Indices: 3358155--3358187 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3358145 AGACAAAACT
3358155 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
3358188 GTGATAACTT
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
Found at i:3358237 original size:6 final size:6
Alignment explanation
Indices: 3358223--3358270 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
3358213 AGTTTTTACC
*
3358223 TTCTCT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
3358270 T
1 T
3358271 CGAGAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:3359394 original size:23 final size:21
Alignment explanation
Indices: 3359367--3359424 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3359357 AAGTTATTTG
3359367 TATATTAATATAATTAATAATAT
1 TATATTAAT-TAATT-ATAATAT
*
3359390 TATATTAATTAATTATATTAT
1 TATATTAATTAATTATAATAT
*
3359411 TTTATT-ATT-ATTAT
1 TATATTAATTAATTAT
3359425 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 11 0.33
22 5 0.15
23 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTAATTAATTATAATAT
Found at i:3359410 original size:18 final size:19
Alignment explanation
Indices: 3359367--3359410 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3359357 AAGTTATTTG
3359367 TATATTA-ATATAATTAAT
1 TATATTATATATAATTAAT
*
3359385 AATATTATAT-TAATTAAT
1 TATATTATATATAATTAAT
3359403 TATATTAT
1 TATATTAT
3359411 TTTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATTATATATAATTAAT
Found at i:3359416 original size:8 final size:8
Alignment explanation
Indices: 3359405--3359446 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
3359395 TAATTAATTA
3359405 TATTATTT
1 TATTATTT
3359413 TATTATTAT
1 TATTATT-T
*
3359422 TATTTTTT
1 TATTATTT
3359430 TATT-TTT
1 TATTATTT
3359437 TA-TATTT
1 TATTATTT
3359444 TAT
1 TAT
3359447 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
6 1 0.03
7 10 0.33
8 12 0.40
9 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Done.