Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold244
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: 697135
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 27162 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2944 original size:24 final size:24
Alignment explanation
Indices: 2917--2962 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2907 CCAACGTCCC
2917 AGACGTGGTCTTACATGCTATCCT
1 AGACGTGGTCTTACATGCTATCCT
2941 AGACGTGGTCTTACATGCTATC
1 AGACGTGGTCTTACATGCTATC
2963 TCATATCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (24 bp):
AGACGTGGTCTTACATGCTATCCT
Found at i:3023 original size:41 final size:44
Alignment explanation
Indices: 2965--3097 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 44
2955 ATGCTATCTC
* *
2965 ATATCGATGCCACTGTCCCAAACAGGGTCTTACACGAATCA-A-
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAATCACAT
* * *
3007 ATA-CGATGCCAATGTCCTAGACATGGTTTTACACGTAATCACAT
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACG-AATCACAT
*
3051 ATATCGATGCC-ATCGTCCCAGAC-GTGGTCTTACACGAGAACACAT
1 ATATCGATGCCAAT-GTCCCAGACAG-GGTCTTACACGA-ATCACAT
3096 AT
1 AT
3098 CGGAAATCCT
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
41 27 0.36
42 8 0.11
43 1 0.01
44 6 0.08
45 33 0.44
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAATCACAT
Found at i:3084 original size:45 final size:44
Alignment explanation
Indices: 2941--3086 Score: 137
Period size: 45 Copynumber: 3.4 Consensus size: 44
2931 ATGCTATCCT
* *
2941 AGACGTGGTCTTACATGCT-ATCTC-ATATCGATGCCA-CTGTCCC
1 AGACGTGGTCTTACACG-TAATCACAATATCGATGCCATC-GTCCC
* *
2984 AAACAG-GGTCTTACACG-AATCA-AATA-CGATGCCAAT-GTCCT
1 AGAC-GTGGTCTTACACGTAATCACAATATCGATGCC-ATCGTCCC
* *
3025 AGACATGGTTTTACACGTAATCACATATATCGATGCCATCGTCCC
1 AGACGTGGTCTTACACGTAATCACA-ATATCGATGCCATCGTCCC
3070 AGACGTGGTCTTACACG
1 AGACGTGGTCTTACACG
3087 AGAACACATA
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
41 24 0.29
42 12 0.15
43 14 0.17
44 6 0.07
45 26 0.32
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (44 bp):
AGACGTGGTCTTACACGTAATCACAATATCGATGCCATCGTCCC
Found at i:4011 original size:28 final size:31
Alignment explanation
Indices: 3979--4037 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
3969 TGTTTTGTTT
3979 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
4007 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
4038 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:7609 original size:9 final size:9
Alignment explanation
Indices: 7582--7624 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
7572 GAAAAAAAAT
*
7582 TCGAGTTAAT
1 TCGA-TTAAC
*
7592 TCGAATAAC
1 TCGATTAAC
7601 TCGATTAAC
1 TCGATTAAC
*
7610 TCGAATAAC
1 TCGATTAAC
7619 TCGATT
1 TCGATT
7625 CGTTTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:7613 original size:18 final size:18
Alignment explanation
Indices: 7582--7624 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
7572 GAAAAAAAAT
*
7582 TCGAGTTAATTCGAATAAC
1 TCGA-TTAACTCGAATAAC
7601 TCGATTAACTCGAATAAC
1 TCGATTAACTCGAATAAC
7619 TCGATT
1 TCGATT
7625 CGTTTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCGATTAACTCGAATAAC
Found at i:10752 original size:14 final size:16
Alignment explanation
Indices: 10719--10749 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10709 AGAATTTTTT
10719 TTATAAAAGTTATATA
1 TTATAAAAGTTATATA
10735 TTATAAAAGTTATAT
1 TTATAAAAGTTATAT
10750 TATTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTATAAAAGTTATATA
Found at i:16443 original size:11 final size:11
Alignment explanation
Indices: 16425--16459 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16415 TACCATCTTT
*
16425 TATTTATTTTG
1 TATTTATTTTA
*
16436 TTTTTATTTTA
1 TATTTATTTTA
16447 TATTTATTTTA
1 TATTTATTTTA
16458 TA
1 TA
16460 ACCTTTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:17614 original size:37 final size:37
Alignment explanation
Indices: 17567--17644 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
17557 TGGAGATAAT
17567 TTTTTTGGTTCATTTTTAATAGAATTGATTGATTTAA
1 TTTTTTGGTTCATTTTTAATAGAATTGATTGATTTAA
17604 TTTTTTGGTTCATTTTTAATAGAATTGATTGATTTAA
1 TTTTTTGGTTCATTTTTAATAGAATTGATTGATTTAA
17641 TTTT
1 TTTT
17645 AATTTTAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (37 bp):
TTTTTTGGTTCATTTTTAATAGAATTGATTGATTTAA
Found at i:19561 original size:310 final size:310
Alignment explanation
Indices: 18999--19604 Score: 1212
Period size: 310 Copynumber: 2.0 Consensus size: 310
18989 ATAAAAGTAA
18999 CATATTTTAATTCCATTCTTAATGCGTTTTTTGGATGATTAATTATGTAAATTAGTGAATTTGAT
1 CATATTTTAATTCCATTCTTAATGCGTTTTTTGGATGATTAATTATGTAAATTAGTGAATTTGAT
19064 GCTTCCAATCTTTTAAATTCATGTTTCTATACTTATGAGAGCATTTGGAAGTGAAAGAAGCAAAA
66 GCTTCCAATCTTTTAAATTCATGTTTCTATACTTATGAGAGCATTTGGAAGTGAAAGAAGCAAAA
19129 AAAACAAGCCAAAATTGAGCAAGTAAAGCTGCTTCCAGGATCCACATGGCCTGGCCATTTCCACA
131 AAAACAAGCCAAAATTGAGCAAGTAAAGCTGCTTCCAGGATCCACATGGCCTGGCCATTTCCACA
19194 CGGGTTGGTCACACGCCAATGTGCCAGCCCGTCTCGATGTCGCATCCTGTTTCCCAAACACACGG
196 CGGGTTGGTCACACGCCAATGTGCCAGCCCGTCTCGATGTCGCATCCTGTTTCCCAAACACACGG
19259 AAAAACCCAATTTTTAGGCTTTCTGAGCATTCTAAAAAGTCATAAACCAC
261 AAAAACCCAATTTTTAGGCTTTCTGAGCATTCTAAAAAGTCATAAACCAC
19309 CATATTTTAATTCCATTCTTAATGCGTTTTTTGGATGATTAATTATGTAAATTAGTGAATTTGAT
1 CATATTTTAATTCCATTCTTAATGCGTTTTTTGGATGATTAATTATGTAAATTAGTGAATTTGAT
19374 GCTTCCAATCTTTTAAATTCATGTTTCTATACTTATGAGAGCATTTGGAAGTGAAAGAAGCAAAA
66 GCTTCCAATCTTTTAAATTCATGTTTCTATACTTATGAGAGCATTTGGAAGTGAAAGAAGCAAAA
19439 AAAACAAGCCAAAATTGAGCAAGTAAAGCTGCTTCCAGGATCCACATGGCCTGGCCATTTCCACA
131 AAAACAAGCCAAAATTGAGCAAGTAAAGCTGCTTCCAGGATCCACATGGCCTGGCCATTTCCACA
19504 CGGGTTGGTCACACGCCAATGTGCCAGCCCGTCTCGATGTCGCATCCTGTTTCCCAAACACACGG
196 CGGGTTGGTCACACGCCAATGTGCCAGCCCGTCTCGATGTCGCATCCTGTTTCCCAAACACACGG
19569 AAAAACCCAATTTTTAGGCTTTCTGAGCATTCTAAA
261 AAAAACCCAATTTTTAGGCTTTCTGAGCATTCTAAA
19605 GTCTATAAAT
Statistics
Matches: 296, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
310 296 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (310 bp):
CATATTTTAATTCCATTCTTAATGCGTTTTTTGGATGATTAATTATGTAAATTAGTGAATTTGAT
GCTTCCAATCTTTTAAATTCATGTTTCTATACTTATGAGAGCATTTGGAAGTGAAAGAAGCAAAA
AAAACAAGCCAAAATTGAGCAAGTAAAGCTGCTTCCAGGATCCACATGGCCTGGCCATTTCCACA
CGGGTTGGTCACACGCCAATGTGCCAGCCCGTCTCGATGTCGCATCCTGTTTCCCAAACACACGG
AAAAACCCAATTTTTAGGCTTTCTGAGCATTCTAAAAAGTCATAAACCAC
Found at i:19686 original size:40 final size:40
Alignment explanation
Indices: 19625--19705 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
19615 ATCAATTAGA
* * *
19625 AAAATATCTAAGGGAGCACACAGAGAAGATTGAAGAAGTT
1 AAAAGATCTAAGGGAGAACACAAAGAAGATTGAAGAAGTT
*
19665 AAAAGATCTAATGGAGAACACAAAGAAGATTGAAGAAGTT
1 AAAAGATCTAAGGGAGAACACAAAGAAGATTGAAGAAGTT
19705 A
1 A
19706 CTCGAAGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17
Consensus pattern (40 bp):
AAAAGATCTAAGGGAGAACACAAAGAAGATTGAAGAAGTT
Found at i:20411 original size:14 final size:14
Alignment explanation
Indices: 20388--20418 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20378 TGTTGCGTTC
*
20388 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
20402 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
20416 TTA
1 TTA
20419 AAATCAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:23035 original size:11 final size:13
Alignment explanation
Indices: 23019--23051 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
23009 ATTTCACGGA
23019 AAAATTTTG-T-G
1 AAAATTTTGTTCG
23030 AAAATTTTGTTCG
1 AAAATTTTGTTCG
23043 AAAATTTTG
1 AAAATTTTG
23052 AAGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (13 bp):
AAAATTTTGTTCG
Found at i:23719 original size:33 final size:34
Alignment explanation
Indices: 23680--23963 Score: 198
Period size: 33 Copynumber: 7.7 Consensus size: 34
23670 TCCCCCAAGG
*
23680 GGTTGCTAAGTGCTGATTCC-CCGAATCATTGTT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
23713 GGTTGCTAAGTGCTGATTCCACTGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCG-AA--T-CAT-TG---GT
*
23755 GGTTGCTAAGTGTTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
23788 GGTTGCTAAGTGCTAATTCCACCGTAACTTAAATGTGAAAGA
1 GGTTGCTAAGTGCTGATTCCACCG-AA--T-CAT-TG---GT
23830 GGTTGCTAAGTGCTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
23863 GGTTGCTAAGTGCTAATTCCACCGTATCTTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGAATC-----AT-TG---GT
*
23906 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
*
23939 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
23964 GTAACGGATA
Statistics
Matches: 199, Mismatches: 23, Indels: 57
0.71 0.08 0.20
Matches are distributed among these distances:
33 79 0.40
34 15 0.08
35 4 0.02
36 6 0.03
37 7 0.04
38 6 0.03
39 6 0.03
40 6 0.03
41 5 0.03
42 45 0.23
43 20 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
Found at i:23939 original size:76 final size:75
Alignment explanation
Indices: 23676--23962 Score: 477
Period size: 75 Copynumber: 3.8 Consensus size: 75
23666 TGATTCCCCC
* * *
23676 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGTTGGTTGCTAAGTGCTGATTCCACTGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAAC
*
23741 TTGAATGTGA
66 TTAAATGTGA
*
23751 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAAC
23816 TTAAATGTGA
66 TTAAATGTGA
* *
23826 AAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAAC
23891 TTTAAATGTGA
66 -TTAAATGTGA
*
23902 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAA-TCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCT-AATTCCACCG
23963 AGTAACGGAT
Statistics
Matches: 200, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
75 132 0.66
76 66 0.33
77 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAAC
TTAAATGTGA
Found at i:27046 original size:3 final size:3
Alignment explanation
Indices: 27040--27109 Score: 113
Period size: 3 Copynumber: 23.3 Consensus size: 3
27030 TTTCCTTTTG
* *
27040 TTA TTA TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
27088 TCA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
27110 CATTTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:27266 original size:10 final size:10
Alignment explanation
Indices: 27245--27273 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
27235 TTGTTTATGG
27245 TTTTATTATT
1 TTTTATTATT
27255 TTTT-TTATT
1 TTTTATTATT
27264 TTTTATTATT
1 TTTTATTATT
27274 AATTCTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTATTATT
Found at i:31578 original size:14 final size:14
Alignment explanation
Indices: 31555--31585 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31545 TTTTGAGTTC
*
31555 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
31569 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
31583 TTA
1 TTA
31586 AAATCAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:34058 original size:22 final size:22
Alignment explanation
Indices: 34018--34073 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
34008 TAAACAAAAT
*
34018 TTTATATGTTTTTAGTTTTAT-A
1 TTTATAT-TTTATAGTTTTATAA
34040 TTTATATTTTATAGTTTTTATAA
1 TTTATATTTTATAG-TTTTATAA
34063 TTT-TATTTTAT
1 TTTATATTTTAT
34074 TTAATAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.19
22 21 0.68
23 4 0.13
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTATATTTTATAGTTTTATAA
Found at i:34069 original size:28 final size:28
Alignment explanation
Indices: 34026--34092 Score: 52
Period size: 28 Copynumber: 2.4 Consensus size: 28
34016 ATTTTATATG
34026 TTTTTAGTTTTATATTTATATTTTATA-G
1 TTTTTAGTTTTATATTT-TATTTTATATG
*
34054 TTTTTA-TAATTT-TATTTTATTTAATAAT-
1 TTTTTAGT--TTTATATTTTATTTTAT-ATG
34082 TCTTTTAGTTT
1 T-TTTTAGTTT
34093 CATGGTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
27 8 0.25
28 15 0.47
29 8 0.25
30 1 0.03
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.69
Consensus pattern (28 bp):
TTTTTAGTTTTATATTTTATTTTATATG
Found at i:34072 original size:29 final size:29
Alignment explanation
Indices: 34016--34073 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
34006 TTTAAACAAA
*
34016 ATTTTATATGTTTTTAGTTTTATATTTAT
1 ATTTTATATGTTTTTAATTTTATATTTAT
34045 ATTTTATA-GTTTTTATAATTTTAT-TTTAT
1 ATTTTATATG-TTTT-TAATTTTATATTTAT
34074 TTAATAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 17 0.65
30 8 0.31
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (29 bp):
ATTTTATATGTTTTTAATTTTATATTTAT
Found at i:34076 original size:17 final size:18
Alignment explanation
Indices: 34038--34082 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
34028 TTTAGTTTTA
34038 TATTTAT-ATTTTATAGT
1 TATTTATAATTTTATAGT
*
34055 T-TTTATAATTTTAT-TT
1 TATTTATAATTTTATAGT
34071 TATTTAATAATT
1 TATTT-ATAATT
34083 CTTTTAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
18 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTATAATTTTATAGT
Found at i:34189 original size:24 final size:25
Alignment explanation
Indices: 34157--34208 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
34147 GTTGATTTGT
* * *
34157 TTTTCTAATTTTATATTTTT-AATA
1 TTTTATAATTATAAATTTTTGAATA
34181 TTTTATAATTATAAATTTTTGAATA
1 TTTTATAATTATAAATTTTTGAATA
34206 TTT
1 TTT
34209 AAAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTATAATTATAAATTTTTGAATA
Found at i:34218 original size:24 final size:24
Alignment explanation
Indices: 34171--34218 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34161 CTAATTTTAT
* *
34171 ATTTTTAATATTTTATAATTATAA
1 ATTTTTAATATTTTAAAATAATAA
34195 ATTTTTGAATA-TTTAAAATAATAA
1 ATTTTT-AATATTTTAAAATAATAA
34219 TCAAGTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTTTAATATTTTAAAATAATAA
Found at i:46314 original size:20 final size:19
Alignment explanation
Indices: 46262--46315 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
46252 TAGATATTCT
*
46262 AAATATTTATTATTTGATTA
1 AAATATTTA-AATTTGATTA
* * *
46282 AAAGATGTGAATTTGGATTA
1 AAATATTTAAATTT-GATTA
46302 AAATATTTAAATTT
1 AAATATTTAAATTT
46316 ATCTATTACA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (19 bp):
AAATATTTAAATTTGATTA
Found at i:48935 original size:21 final size:21
Alignment explanation
Indices: 48909--48950 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48899 TTTGCCTAAG
* *
48909 ATGTGACTTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
48930 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
48951 TGTTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.40
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:51487 original size:32 final size:32
Alignment explanation
Indices: 51446--51510 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
51436 AACTAGCAAG
51446 TGATACGGATGAATGGAACAGGATCATAAAAT
1 TGATACGGATGAATGGAACAGGATCATAAAAT
51478 TGATACGGATGAATGGAACAGGATCATAAAAT
1 TGATACGGATGAATGGAACAGGATCATAAAAT
51510 T
1 T
51511 TGTCTAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (32 bp):
TGATACGGATGAATGGAACAGGATCATAAAAT
Found at i:53452 original size:64 final size:64
Alignment explanation
Indices: 53327--53456 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
53317 GCGAGCATCC
* * * * **
53327 TGATCGGTAGTGATCCTGCATGTGTTGCGGACATACCGAAGCTTTTTGTAAGCGTTTTGTTATA
1 TGATCAGTAGTAATCCTGCATGTGTTGCGGACATACCGAAGCTCTTTGTAAGCATCCTGTTATA
53391 TGATCAGTAGTAATCCTGCATGTGTTGCGGACATACCGCAA-CTCTTTGTGAA-CATCCTGTTAT
1 TGATCAGTAGTAATCCTGCATGTGTTGCGGACATACCG-AAGCTCTTTGT-AAGCATCCTGTTAT
53454 A
64 A
53455 TG
1 TG
53457 GCTTTCCGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
64 54 0.93
65 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (64 bp):
TGATCAGTAGTAATCCTGCATGTGTTGCGGACATACCGAAGCTCTTTGTAAGCATCCTGTTATA
Found at i:53550 original size:24 final size:25
Alignment explanation
Indices: 53523--53569 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
53513 GAGCTTCTGA
*
53523 TTAATGGATCTTCA-GAGCTTCCCG
1 TTAAAGGATCTTCATGAGCTTCCCG
* *
53547 TTAAAGGCTCTTTATGAGCTTCC
1 TTAAAGGATCTTCATGAGCTTCC
53570 TTATTTAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (25 bp):
TTAAAGGATCTTCATGAGCTTCCCG
Found at i:53569 original size:25 final size:24
Alignment explanation
Indices: 53537--53600 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
53527 TGGATCTTCA
53537 GAGCTTCCCGTTA-AAGGCTCTTTAT
1 GAGCTTCCC-TTATAAGGCTC-TTAT
*
53562 GAGCTT-CCTTATTTAGGCTCTTAT
1 GAGCTTCCCTTA-TAAGGCTCTTAT
53586 GAGCTTCCCATTATA
1 GAGCTTCCC-TTATA
53601 CAGCCCGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 3 0.09
24 12 0.36
25 15 0.45
26 3 0.09
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (24 bp):
GAGCTTCCCTTATAAGGCTCTTAT
Found at i:60146 original size:64 final size:64
Alignment explanation
Indices: 60043--60166 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
60033 ATCCTAATCA
* * *
60043 GTAGTTATCCTGCATGTGTTGCGAACATACCGCAGCTCTTTGTAAGCGTCCTATTATATGATCG
1 GTAGTAATCCTGCACGTGTTGCGAACATACCGCAACTCTTTGTAAGCGTCCTATTATATGATCG
* * * *
60107 GTAGTAATCCTGCACGTGTTGCGGACATACCGTAACTCTTTGTCAGTGTCCTATTATATG
1 GTAGTAATCCTGCACGTGTTGCGAACATACCGCAACTCTTTGTAAGCGTCCTATTATATG
60167 GCTCTCTGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (64 bp):
GTAGTAATCCTGCACGTGTTGCGAACATACCGCAACTCTTTGTAAGCGTCCTATTATATGATCG
Found at i:60351 original size:25 final size:25
Alignment explanation
Indices: 60323--60403 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
60313 GCCCGGATAT
*
60323 GCTTCCTGTTACATGGCTCATATGA
1 GCTTCCTGTTACATGGCTCAAATGA
* * ** *
60348 GCTTCCCGTTATACAGCCCAAAT-A
1 GCTTCCTGTTACATGGCTCAAATGA
* * *
60372 TGCTTCTTGTTACATGACTCACATGA
1 -GCTTCCTGTTACATGGCTCAAATGA
60398 GCTTCC
1 GCTTCC
60404 CGTTCTATGG
Statistics
Matches: 39, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
24 1 0.03
25 37 0.95
26 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.33
Consensus pattern (25 bp):
GCTTCCTGTTACATGGCTCAAATGA
Found at i:60357 original size:50 final size:50
Alignment explanation
Indices: 60287--60407 Score: 179
Period size: 50 Copynumber: 2.4 Consensus size: 50
60277 TCCTGATTTA
* * **
60287 GGCTCTTATAAGCTTCCCGTTATACAGCCCGGATATGCTTCCTGTTACAT
1 GGCTCATATGAGCTTCCCGTTATACAGCCCAAATATGCTTCCTGTTACAT
*
60337 GGCTCATATGAGCTTCCCGTTATACAGCCCAAATATGCTTCTTGTTACAT
1 GGCTCATATGAGCTTCCCGTTATACAGCCCAAATATGCTTCCTGTTACAT
* *
60387 GACTCACATGAGCTTCCCGTT
1 GGCTCATATGAGCTTCCCGTT
60408 CTATGGTTCG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (50 bp):
GGCTCATATGAGCTTCCCGTTATACAGCCCAAATATGCTTCCTGTTACAT
Found at i:66928 original size:9 final size:9
Alignment explanation
Indices: 66914--66943 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
66904 GCTTAATCAA
66914 TTTTTTTAT
1 TTTTTTTAT
66923 TTTTTTTAT
1 TTTTTTTAT
*
66932 TTTTTTTGT
1 TTTTTTTAT
66941 TTT
1 TTT
66944 CTTCTCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:67558 original size:23 final size:23
Alignment explanation
Indices: 67505--67569 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
67495 AAAACAATGC
* * *
67505 ATAAAAATCCATAAATTATTCCAA
1 ATAAAAATCAATAAA-AACTCCAA
67529 A-ACAAAATCAATAAAAACTCCAA
1 ATA-AAAATCAATAAAAACTCCAA
*
67552 ATAAAAAT-AATAATAACT
1 ATAAAAATCAATAAAAACT
67570 TTAACGGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 9 0.26
23 13 0.37
24 13 0.37
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAAAAATCAATAAAAACTCCAA
Found at i:71979 original size:20 final size:19
Alignment explanation
Indices: 71946--72005 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
71936 AATCTAAAAT
*
71946 CTCAAATCCTAAACCTTAAA
1 CTCAAA-CCCAAACCTTAAA
* *
71966 CTCAAACCCCAAACATCAAA
1 CTCAAA-CCCAAACCTTAAA
**
71986 AACAAACCCAAACCTTAAA
1 CTCAAACCCAAACCTTAAA
72005 C
1 C
72006 CCCAAACCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (19 bp):
CTCAAACCCAAACCTTAAA
Found at i:73695 original size:113 final size:112
Alignment explanation
Indices: 73462--73682 Score: 358
Period size: 113 Copynumber: 2.0 Consensus size: 112
73452 TAAAAATAAG
* *
73462 GATAGATTACACCCATGATCACTCTAAAATAGGGTTTGTCCTATTTTGGCCACTCCATATTTTTT
1 GATAAATTACACCCATGATCACTCTAAAATAGGGTCTGTCCTATTTTGGCCACTCCATA-TTTTT
* * *
73527 TTCTTAATTTAGTCACTCTAAATAAGATAATTGTGCGAATTAGTCACG
65 TTCTTAATTTAGTCACTCTAAATAAAATAATTGTGCAAATTAGTCACC
*
73575 GATAAATTACACCCATGATCACTCTAAAATAGGGTCTGTCCTATTTTGGTCACT-C-TA-TTTTT
1 GATAAATTACACCCATGATCACTCTAAAATAGGGTCTGTCCTATTTTGGCCACTCCATATTTTTT
73637 TCTTAATTTAGTCACTCTAAATAAAATAATTGTGCAAATTAGTCAC
66 TCTTAATTTAGTCACTCTAAATAAAATAATTGTGCAAATTAGTCAC
73683 TACTATTAAA
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
109 49 0.48
111 2 0.02
112 1 0.01
113 51 0.50
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
GATAAATTACACCCATGATCACTCTAAAATAGGGTCTGTCCTATTTTGGCCACTCCATATTTTTT
TCTTAATTTAGTCACTCTAAATAAAATAATTGTGCAAATTAGTCACC
Found at i:76180 original size:154 final size:150
Alignment explanation
Indices: 75835--76262 Score: 576
Period size: 154 Copynumber: 2.8 Consensus size: 150
75825 TTACTTTCAA
* *
75835 TAAAAATACACACTAAATTAATACATTTCAAACATAATGTGCTAAAATAATGTAAAA-TAATAAA
1 TAAAAA-ACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAA-AAA
* * * * *
75899 ATATGAAAATAATATAT-TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAATAGT
64 AT-T-AAAA-AATATATATTTT-TTAAAAGTAATAAAATTCGGGAAAAAAATACGAACATAGAGC
*
75963 CGAAATAAGGATTTTTTTAATTTATT
125 CGAAATAAGGATTTTTTTAACTTATT
*
75989 TAAAAAGCACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
*
76054 TAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGGATAAAAAATACGAACATAGGGCCGAA
66 TAAAAAATA-TATATTTTTTAAAAGTAATAAAATTCGGGA-AAAAAATACGAACATAGAGCCGAA
76119 ATAATGG-TTTTTTTAAAACTTATT
129 ATAA-GGATTTTTTT--AACTTATT
* * *
76143 TAAAAAATACACTAAATTAATACATTTAAAATATAATGTACTAAAATAATGTAAAATAAAAAAAT
1 TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
* * *
76208 TAGAAAATATTATATTTTTTAAAAATAATAAAATTCGAG-AAAAAATACGAACATA
66 TAAAAAATA-TATATTTTTTAAAAGTAATAAAATTCGGGAAAAAAATACGAACATA
76263 AGGCTAAAAT
Statistics
Matches: 249, Mismatches: 18, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
150 4 0.02
151 27 0.11
152 52 0.21
153 54 0.22
154 112 0.45
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.31
Consensus pattern (150 bp):
TAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAAAATTAAAAAAT
TAAAAAATATATATTTTTTAAAAGTAATAAAATTCGGGAAAAAAATACGAACATAGAGCCGAAAT
AAGGATTTTTTTAACTTATT
Found at i:76514 original size:18 final size:17
Alignment explanation
Indices: 76487--76520 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
76477 TTGTCAGTTT
*
76487 TTTTTTTTTTTCCAAGCC
1 TTTTTCTTTTT-CAAGCC
76505 TTTTTCTTTTTCAAGC
1 TTTTTCTTTTTCAAGC
76521 TAAGCCACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTCTTTTTCAAGCC
Found at i:77079 original size:5 final size:5
Alignment explanation
Indices: 77069--77094 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
77059 ATGTTTCTTT
77069 TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG T
77095 GCAATGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:78698 original size:17 final size:17
Alignment explanation
Indices: 78676--78715 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
78666 AAAGAGATAA
78676 AATTTTTAATTTAAT-TT
1 AATTTTT-ATTTAATGTT
78693 AATTTTTATTTAATGTT
1 AATTTTTATTTAATGTT
78710 AATTTT
1 AATTTT
78716 AAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
AATTTTTATTTAATGTT
Found at i:79143 original size:20 final size:20
Alignment explanation
Indices: 79120--79157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
79110 TAATAGTTGC
*
79120 TTTAAGTTAATAAAACTAAG
1 TTTAAGATAATAAAACTAAG
*
79140 TTTAAGATAATTAAACTA
1 TTTAAGATAATAAAACTA
79158 GATTAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTAAGATAATAAAACTAAG
Found at i:89164 original size:14 final size:15
Alignment explanation
Indices: 89138--89166 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
89128 GAGTCATAAA
89138 ACAAAAGAGAAAAAT
1 ACAAAAGAGAAAAAT
89153 ACAAAA-AGAAAAAT
1 ACAAAAGAGAAAAAT
89167 GTTGAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (15 bp):
ACAAAAGAGAAAAAT
Found at i:91839 original size:67 final size:67
Alignment explanation
Indices: 91731--91866 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
91721 GGGAATGGAA
91731 CAGGTAATTTTGTTGAGTCTGTTTCTGCTAAATGCAAAGATAATGCAATGGATTACATGTGATGT
1 CAGGTAATTTTGTTGAGTCTGTTTCTGCTAAATGCAAAGATAATGCAATGGATTACATGTGATGT
91796 TC
66 TC
*
91798 CAGGTAATTTTGTTGAGTCTGTTTCTGCTAAATTCAAAGATAATGCAATGGATTACATGTGATGT
1 CAGGTAATTTTGTTGAGTCTGTTTCTGCTAAATGCAAAGATAATGCAATGGATTACATGTGATGT
91863 TC
66 TC
91865 CA
1 CA
91867 TTAATACACA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (67 bp):
CAGGTAATTTTGTTGAGTCTGTTTCTGCTAAATGCAAAGATAATGCAATGGATTACATGTGATGT
TC
Found at i:96015 original size:10 final size:10
Alignment explanation
Indices: 96000--96024 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
95990 CATTGGTTCC
96000 ATGTGGAGTA
1 ATGTGGAGTA
96010 ATGTGGAGTA
1 ATGTGGAGTA
96020 ATGTG
1 ATGTG
96025 ATACATACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.32
Consensus pattern (10 bp):
ATGTGGAGTA
Found at i:99171 original size:17 final size:17
Alignment explanation
Indices: 99149--99199 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
99139 CAAACTTAAT
* *
99149 ATTTAAAAATTATTTTC
1 ATTTAAATATCATTTTC
99166 ATTTAAATATCATTTTC
1 ATTTAAATATCATTTTC
99183 ATTTAAATATCATTTTC
1 ATTTAAATATCATTTTC
99200 GTTTGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAAATATCATTTTC
Found at i:99548 original size:16 final size:16
Alignment explanation
Indices: 99527--99578 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
99517 TTTGGTTCTC
99527 TGTATTGAATTAGAGG
1 TGTATTGAATTAGAGG
*
99543 TGTATTGGATTAGAGG
1 TGTATTGAATTAGAGG
*
99559 TGTAATGGAA-TAGAGG
1 TGT-ATTGAATTAGAGG
99575 TGTA
1 TGTA
99579 ATATAATAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 1 0.03
16 27 0.84
17 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGAATTAGAGG
Found at i:99586 original size:16 final size:16
Alignment explanation
Indices: 99537--99587 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
99527 TGTATTGAAT
* * *
99537 TAGAGGTGTATTGGAT
1 TAGAGGTGTAATAGAA
*
99553 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATAGAA
*
99569 TAGAGGTGTAATATAA
1 TAGAGGTGTAATAGAA
99585 TAG
1 TAG
99588 CAAATCAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (16 bp):
TAGAGGTGTAATAGAA
Found at i:105045 original size:19 final size:19
Alignment explanation
Indices: 105023--105059 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
105013 GGTGTTTTCC
105023 TTTTTTATATTCATTTTTG
1 TTTTTTATATTCATTTTTG
*
105042 TTTTTTATATTTATTTTT
1 TTTTTTATATTCATTTTT
105060 ATTTCGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTTTATATTCATTTTTG
Found at i:105309 original size:43 final size:43
Alignment explanation
Indices: 105229--105315 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
105219 ACCGGCGGGC
* *
105229 GGCGCGGTGGCCGACTGCCGGACCTAAGGCCGAAAATCGGATT
1 GGCGCGGTGGCCGACGGCCGGACCTAAGACCGAAAATCGGATT
* *
105272 GGCGCGGTGGCCGACGGCCGGACTTTAGACC-AGAAATCGGATT
1 GGCGCGGTGGCCGACGGCCGGACCTAAGACCGA-AAATCGGATT
105315 G
1 G
105316 CCCAAAAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (43 bp):
GGCGCGGTGGCCGACGGCCGGACCTAAGACCGAAAATCGGATT
Found at i:112255 original size:6 final size:6
Alignment explanation
Indices: 112246--112292 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
112236 AAAAAAAAGG
*
112246 AAAAAC AAAAA- AAAAAC -AAAAC AAAATC AAAAATC AAAAATC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA-C AAAAA-C AAAAA
112293 AATCGAAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 10 0.28
6 13 0.36
7 13 0.36
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (6 bp):
AAAAAC
Found at i:113181 original size:7 final size:8
Alignment explanation
Indices: 113167--113214 Score: 80
Period size: 8 Copynumber: 6.0 Consensus size: 8
113157 GAAAAAAATG
113167 ATGAAAAA
1 ATGAAAAA
113175 ATG-AAAA
1 ATGAAAAA
113182 ATGAAAAAA
1 ATG-AAAAA
113191 ATGAAAAA
1 ATGAAAAA
113199 ATGAAAAA
1 ATGAAAAA
113207 ATGAAAAA
1 ATGAAAAA
113215 GTAAAAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
ATGAAAAA
Found at i:113182 original size:9 final size:9
Alignment explanation
Indices: 113140--113214 Score: 86
Period size: 9 Copynumber: 8.6 Consensus size: 9
113130 CTTTGAGTCA
113140 AAAAAAATG
1 AAAAAAATG
**
113149 ATGAAAATG
1 AAAAAAATG
113158 AAAAAAATG
1 AAAAAAATG
113167 ATGAAAAAATG
1 A--AAAAAATG
113178 --AAAAATG
1 AAAAAAATG
113185 AAAAAAATG
1 AAAAAAATG
113194 -AAAAAATG
1 AAAAAAATG
113202 -AAAAAATG
1 AAAAAAATG
113210 AAAAA
1 AAAAA
113215 GTAAAAATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
7 7 0.12
8 16 0.28
9 26 0.46
11 8 0.14
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (9 bp):
AAAAAAATG
Found at i:113188 original size:6 final size:7
Alignment explanation
Indices: 113171--113223 Score: 54
Period size: 7 Copynumber: 7.0 Consensus size: 7
113161 AAAATGATGA
113171 AAAAATG
1 AAAAATG
113178 AAAAATG
1 AAAAATG
113185 AAAAAAATG
1 --AAAAATG
113194 AAAAAATG
1 -AAAAATG
113202 AAAAAATG
1 -AAAAATG
113210 AAAAA-G
1 AAAAATG
113216 TAAAAATG
1 -AAAAATG
113224 GAGAGGCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.02
7 17 0.40
8 17 0.40
9 7 0.17
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:113221 original size:16 final size:15
Alignment explanation
Indices: 113170--113221 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
113160 AAAAATGATG
113170 AAAAAATGAAAAATGA
1 AAAAAATGAAAAAT-A
*
113186 AAAAAATGAAAAAATG
1 AAAAAATG-AAAAATA
113202 AAAAAATGAAAAAGTA
1 AAAAAATGAAAAA-TA
113218 AAAA
1 AAAA
113222 TGGAGAGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 5 0.16
16 21 0.66
17 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAATGAAAAATA
Found at i:117614 original size:50 final size:50
Alignment explanation
Indices: 117153--117830 Score: 432
Period size: 50 Copynumber: 13.6 Consensus size: 50
117143 GCAGTGGAAC
* * ** *
117153 AGATTGAAGCTACAACAGC-AGATCTCACTTCCCTAACATTGCAA-TCAAA
1 AGATTGAAGCTACAACGGCGA-ATCTTACTTCCCCGACATTGCAACTGAAA
* * * * * ** * *
117202 AGATTGATGCCACAACGGCGAATCTTA-TTTCCAGGCGGTGC-AGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACT-GAAA
* * * * *
117251 AGATTGAAGCTACAAAAGCCG-ATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTAC-AACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * * * * **
117301 AGATTGAAGCTACAACAGCGGATCTTAC-TCTCCTAGCGTTGC-AGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-CATTGCAACT-GAAA
* * * * * *
117351 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * * * *
117401 AGATTGAAGTTACAACAGCAAATCTTACTTCCCAGGCA-TGCAA-TGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACT-GAAA
* * * * *
117450 AGATTAAAGCTACAACGGTGAATCTCACTT-CCCGACATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * * * *
117499 AGATTGAAGCTACAACGGCAAATCTTATTTCCCAGGCAGTGCAGC-GAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * *
117548 CAGATTGAAGCCACAATGGCGAATCTTACTTCCCCGACATTGCAACTCAAA
1 -AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * * *
117599 AGATTGAAGCCACAATGGCGAATCTTACTT-TCCAAGCGA-TGCAGC-GAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-C-ATTGCAACTGAAA
* * ** *
117648 CAGATTGAAGCTATAACGGTGAATCTCGCTTCCCCGACATTGCAACTCAAA
1 -AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * * * * * *
117699 AGATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAATGCAGCGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* * * *** *
117749 AGATTGAAGCTACGACAGTGAATCTCGTTTCCCCGACATTGCAAGT-AAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
* *
117798 TAGATTAAAGCTACGACGGCGAATCTTACTTCC
1 -AGATTGAAGCTACAACGGCGAATCTTACTTCC
117831 TGAAATTGTA
Statistics
Matches: 475, Mismatches: 130, Indels: 47
0.73 0.20 0.07
Matches are distributed among these distances:
47 1 0.00
48 15 0.03
49 125 0.26
50 317 0.67
51 17 0.04
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAACTGAAA
Found at i:117829 original size:100 final size:99
Alignment explanation
Indices: 117124--117830 Score: 728
Period size: 100 Copynumber: 7.1 Consensus size: 99
117114 NNNNNAGCGG
* * *
117124 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGC-AGATCTCACTTCCCT
1 ATCTTAC-TTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGA-ATCTCACTTCCCC
* * * *
117187 AACATTGCAATCAAAAGATTGATGCCACAACGGCGA
64 GACATTGCAATTAAAAGATTGAAGCTACAACGGCGA
* * * * *
117223 ATCTTA-TTTCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAAAAGCCG-ATCTTACTTCCCTG
1 ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAG-CGAATCTCACTTCCCCG
* *
117286 ACATTGCAATTAAAAAGATTGAAGCTACAACAGCGG
65 ACATTGCAATT-AAAAGATTGAAGCTACAACGGCGA
* * * * * * *
117322 ATCTTACTCTCCTA-GCGTTGCAGTGGAGCAGATTGAAGCTACAACAGCGGATCTTACTTTCCTG
1 ATCTTACT-TCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCG
* * *
117386 ACATTGCAATTAAAAAGATTGAAGTTACAACAGCAA
65 ACATTGCAATT-AAAAGATTGAAGCTACAACGGCGA
* * * *
117422 ATCTTACTTCCCAGGC-ATGCAATGGAACAGATTAAAGCTACAACGGTGAATCTCACTT-CCCGA
1 ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGA
*
117485 CATTGCAATTTAAAAGATTGAAGCTACAACGGCAA
66 CATTGCAA-TTAAAAGATTGAAGCTACAACGGCGA
* * * * ** *
117520 ATCTTATTTCCCAGGC-AGTGCAGCGAAACAGATTGAAGCCACAATGGCGAATCTTACTTCCCCG
1 ATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCG
* * *
117584 ACATTGCAACTCAAAAGATTGAAGCCACAATGGCGA
65 ACATTGCAA-TTAAAAGATTGAAGCTACAACGGCGA
* * * * * * * *
117620 ATCTTACTTTCCAAGCGATGCAGCGAAACAGATTGAAGCTATAACGGTGAATCTCGCTTCCCCGA
1 ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGA
* * *
117685 CATTGCAACTCAAAAGATTGAAGCCACAATGGCGA
66 CATTGCAA-TTAAAAGATTGAAGCTACAACGGCGA
* * * * **
117720 ATCTTACTTCCCAGGCAATGCAGCGGAACAGATTGAAGCTACGACAGTGAATCTCGTTTCCCCGA
1 ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGA
* * *
117785 CATTGCAAGTAAATAGATTAAAGCTACGACGGCGA
66 CATTGCAATTAAA-AGATTGAAGCTACAACGGCGA
117820 ATCTTACTTCC
1 ATCTTACTTCC
117831 TGAAATTGTA
Statistics
Matches: 526, Mismatches: 69, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
97 4 0.01
98 103 0.20
99 111 0.21
100 304 0.58
101 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (99 bp):
ATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGA
CATTGCAATTAAAAGATTGAAGCTACAACGGCGA
Found at i:118553 original size:132 final size:132
Alignment explanation
Indices: 118074--118531 Score: 792
Period size: 132 Copynumber: 3.5 Consensus size: 132
118064 AGCTACGAAT
118074 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
*
118139 AGTGGAGAAGCAGATTTAAGCCATTTGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
66 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
118204 TG
131 TG
* *
118206 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTTCCAATAC
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
*
118271 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAACAGTAGTGGAGTAGGTTGAAGAT
66 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
*
118336 TA
131 TG
* *
118338 CAGATTCTGTTACCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAATCTTATCTTCCCAATAC
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
* *
118403 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGGGGAGTAGGTCGAAGAT
66 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
118468 TG
131 TG
* * *
118470 CAGATTCTGTCACCTTAAACAGTAGTGGAGCAGATCGAAGATGCG-GAATCTTATCTTTCCAA
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG-GTGAATCTTATCTTCCCAA
118532 GGTAGTAGGG
Statistics
Matches: 307, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
132 307 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
TG
Found at i:120700 original size:22 final size:23
Alignment explanation
Indices: 120617--120700 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
120607 TAATTGCTCT
* *
120617 TATATATATGTATATTTTTTGTA
1 TATATATATATATACTTTTTGTA
* *
120640 TATATATACATATA-TTTTTTTA
1 TATATATATATATACTTTTTGTA
* *
120662 TATACTTACATACATACTTTTTGTA
1 TATA--TATATATATACTTTTTGTA
*
120687 -ATATATATGTATAC
1 TATATATATATATAC
120701 ATATACACTT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 19 0.40
23 12 0.25
24 10 0.21
25 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (23 bp):
TATATATATATATACTTTTTGTA
Found at i:128861 original size:19 final size:21
Alignment explanation
Indices: 128837--128878 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
128827 TGTTACTTTA
128837 ATTTTTATAC-TTAT-TTTTT
1 ATTTTTATACTTTATGTTTTT
128856 ATTTTTATACTTTATGTTTTT
1 ATTTTTATACTTTATGTTTTT
128877 AT
1 AT
128879 ATACATGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
20 4 0.19
21 7 0.33
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTATACTTTATGTTTTT
Found at i:129099 original size:4 final size:4
Alignment explanation
Indices: 129090--129135 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
129080 TAATTTCAAG
*
129090 TTAT TTA- TT-T TTAT CTTACT TCAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT -TTA-T TTAT TTAT TTAT TTAT TTAT TTAT TT
129136 CCTTGCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 4 0.11
4 26 0.72
5 5 0.14
6 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:132773 original size:2 final size:2
Alignment explanation
Indices: 132766--132800 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
132756 TGGGAAGGGG
132766 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
132801 CTCTTTGTTA
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:140181 original size:6 final size:6
Alignment explanation
Indices: 140172--140196 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
140162 TTTGGATTTT
140172 GAAAAC GAAAAC GAAAAC GAAAAC G
1 GAAAAC GAAAAC GAAAAC GAAAAC G
140197 GGAGTCGCCA
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:0.64, C:0.16, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAC
Found at i:144279 original size:27 final size:27
Alignment explanation
Indices: 144241--144293 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
144231 GCATCATTCA
* *
144241 AAGAAGAACCCAAGACAGCAGCATCTG
1 AAGAAGAACCCAAGACACCAACATCTG
144268 AAGAAGAACCCAAGACACCAACATCT
1 AAGAAGAACCCAAGACACCAACATCT
144294 CTAGCTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (27 bp):
AAGAAGAACCCAAGACACCAACATCTG
Found at i:146164 original size:16 final size:15
Alignment explanation
Indices: 146143--146174 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
146133 TATTCAGTAA
146143 CCCATTTCCCCCTTTT
1 CCCATTT-CCCCTTTT
146159 CCCATTTCCCCTTTT
1 CCCATTTCCCCTTTT
146174 C
1 C
146175 GACATTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (15 bp):
CCCATTTCCCCTTTT
Found at i:146180 original size:16 final size:15
Alignment explanation
Indices: 146145--146187 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
146135 TTCAGTAACC
*
146145 CATTTCCCCCTTTTCC
1 CATTT-CCCCTTTTCA
146161 CATTTCCCCTTTTCGA
1 CATTTCCCCTTTTC-A
146177 CATTTCTCCCT
1 CATTTC-CCCT
146188 AACCTAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.09, C:0.44, G:0.02, T:0.44
Consensus pattern (15 bp):
CATTTCCCCTTTTCA
Found at i:146393 original size:11 final size:11
Alignment explanation
Indices: 146377--146414 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
146367 TGATGTCTTT
146377 TGTTTATAATC
1 TGTTTATAATC
146388 TGTTTATAATC
1 TGTTTATAATC
*
146399 TTCTTTATAATC
1 -TGTTTATAATC
146411 TGTT
1 TGTT
146415 GTTGTTGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (11 bp):
TGTTTATAATC
Found at i:146407 original size:12 final size:12
Alignment explanation
Indices: 146379--146411 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
146369 ATGTCTTTTG
*
146379 TTTATAATC-TG
1 TTTATAATCTTC
146390 TTTATAATCTTC
1 TTTATAATCTTC
146402 TTTATAATCT
1 TTTATAATCT
146412 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTATAATCTTC
Found at i:146502 original size:58 final size:59
Alignment explanation
Indices: 146402--146513 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 59
146392 TATAATCTTC
* * *
146402 TTTATAATCTGTTGTTGTTGCCTTACTAATGTTGCCTTACAGTTCCCTTTGTTTAGCTG
1 TTTATAATATGTCGTTGTTGCCTTACTAATGTTGCCTTACAGTTCCATTTGTTTAGCTG
* * *
146461 TTTATAATATGTCGTTGTTTCC-TCCTATTGTTGCCTTACAGTTCCATTTGTTT
1 TTTATAATATGTCGTTGTTGCCTTACTAATGTTGCCTTACAGTTCCATTTGTTT
146514 CGTTGTTGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 28 0.60
59 19 0.40
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.51
Consensus pattern (59 bp):
TTTATAATATGTCGTTGTTGCCTTACTAATGTTGCCTTACAGTTCCATTTGTTTAGCTG
Found at i:146904 original size:13 final size:13
Alignment explanation
Indices: 146886--146996 Score: 132
Period size: 13 Copynumber: 8.2 Consensus size: 13
146876 ATTTTTAATG
146886 TAATATACTGTTT
1 TAATATACTGTTT
*
146899 TAATATATTGTTT
1 TAATATACTGTTT
*
146912 TAATATACTATTAT
1 TAATATACTGTT-T
* *
146926 AAATATACTTTTT
1 TAATATACTGTTT
*
146939 TAATATATTGTTT
1 TAATATACTGTTT
146952 TAATATACTGTTAT
1 TAATATACTGTT-T
146966 ATATATATACTGTTT
1 -TA-ATATACTGTTT
*
146981 TAATATAATGTTT
1 TAATATACTGTTT
146994 TAA
1 TAA
146997 CTTTTAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
13 57 0.68
14 14 0.17
15 3 0.04
16 10 0.12
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:146939 original size:27 final size:26
Alignment explanation
Indices: 146886--146996 Score: 89
Period size: 27 Copynumber: 4.1 Consensus size: 26
146876 ATTTTTAATG
* *
146886 TAATATACTGTTTTAATATATTGTTT
1 TAATATACTATTTAAATATATTGTTT
146912 TAATATACTATTATAAATATACTT-TTT
1 TAATATACTATT-TAAATATA-TTGTTT
* * * *
146939 TAATATATTGTTTTAATATACTGTTAT
1 TAATATACTATTTAAATATATTGTT-T
* * *
146966 ATATATATACTGTTTTAATATAATGTTT
1 -TA-ATATACTATTTAAATATATTGTTT
146994 TAA
1 TAA
146997 CTTTTAATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.01
26 21 0.30
27 23 0.32
28 5 0.07
29 21 0.30
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (26 bp):
TAATATACTATTTAAATATATTGTTT
Found at i:146942 original size:40 final size:41
Alignment explanation
Indices: 146886--146996 Score: 179
Period size: 40 Copynumber: 2.7 Consensus size: 41
146876 ATTTTTAATG
146886 TAATATACTGTTTTAATATATTGTTTTAATATACTATTATA
1 TAATATACTGTTTTAATATATTGTTTTAATATACTATTATA
* *
146927 -AATATACTTTTTTAATATATTGTTTTAATATACTGTTATA
1 TAATATACTGTTTTAATATATTGTTTTAATATACTATTATA
*
146967 TATATATACTGTTTTAATATAATGTTTTAA
1 TA-ATATACTGTTTTAATATATTGTTTTAA
146997 CTTTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 38 0.59
41 1 0.02
42 25 0.39
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (41 bp):
TAATATACTGTTTTAATATATTGTTTTAATATACTATTATA
Found at i:149172 original size:9 final size:9
Alignment explanation
Indices: 149156--149210 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
149146 GGTTGCAAAA
149156 AGGACGATG
1 AGGACGATG
*
149165 AAGACGATG
1 AGGACGATG
149174 AGGACGATG
1 AGGACGATG
* *
149183 ACGACGTTG
1 AGGACGATG
149192 AGGACGATG
1 AGGACGATG
*
149201 AGGATGATG
1 AGGACGATG
149210 A
1 A
149211 TGTTTCTTCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.40, T:0.15
Consensus pattern (9 bp):
AGGACGATG
Found at i:162059 original size:93 final size:93
Alignment explanation
Indices: 161947--162133 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 93
161937 TAATAATGAC
161947 AAATGGTTTGTTTGAATGAATAACCTCAATTTTATTTATTTATTTATGATATATCTATATTTATA
1 AAATGGTTTGTTTGAATGAATAACCTCAATTTTATTTATTTATTTATGATATATCTATATTTATA
162012 TTAAAAATTAAAATAAAAAATAAAACCA
66 TTAAAAATTAAAATAAAAAATAAAACCA
162040 AAATGGGTTTG-TTGAATGAATAACCTCAATTTTATTTATTTATTTATGATATATCTATATTTAT
1 AAAT-GGTTTGTTTGAATGAATAACCTCAATTTTATTTATTTATTTATGATATATCTATATTTAT
162104 ATTAAAAATTAAAATAAAAAATAAAACCA
65 ATTAAAAATTAAAATAAAAAATAAAACCA
162133 A
1 A
162134 TGGTGTCGTC
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
93 87 0.94
94 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.41
Consensus pattern (93 bp):
AAATGGTTTGTTTGAATGAATAACCTCAATTTTATTTATTTATTTATGATATATCTATATTTATA
TTAAAAATTAAAATAAAAAATAAAACCA
Found at i:163261 original size:35 final size:35
Alignment explanation
Indices: 163215--163285 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
163205 TTATCAACGG
163215 CACATTCACATCTCACATCTGTTGATTGCACAACA
1 CACATTCACATCTCACATCTGTTGATTGCACAACA
163250 CACATTCACATCTCACATCTGTTGATTGCACAACA
1 CACATTCACATCTCACATCTGTTGATTGCACAACA
163285 C
1 C
163286 TTTCAACAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.28
Consensus pattern (35 bp):
CACATTCACATCTCACATCTGTTGATTGCACAACA
Found at i:165296 original size:13 final size:13
Alignment explanation
Indices: 165278--165307 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
165268 ATACTCAAAA
165278 TTTTTAAAAATAT
1 TTTTTAAAAATAT
*
165291 TTTTTAAAAGTAT
1 TTTTTAAAAATAT
165304 TTTT
1 TTTT
165308 ACTCAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTTAAAAATAT
Found at i:171606 original size:21 final size:21
Alignment explanation
Indices: 171582--171622 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
171572 ATAACCACAT
*
171582 CTCCACAAAATCTTCAACAAC
1 CTCCACAAAATCCTCAACAAC
*
171603 CTCCACTAAATCCTCAACAA
1 CTCCACAAAATCCTCAACAA
171623 TTTTGCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (21 bp):
CTCCACAAAATCCTCAACAAC
Found at i:172731 original size:8 final size:8
Alignment explanation
Indices: 172718--172746 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
172708 ATGAAAAACT
172718 ATTTTCTG
1 ATTTTCTG
172726 ATTTTCTG
1 ATTTTCTG
172734 ATTTTCTG
1 ATTTTCTG
172742 ATTTT
1 ATTTT
172747 GTAACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (8 bp):
ATTTTCTG
Found at i:177365 original size:12 final size:12
Alignment explanation
Indices: 177343--177372 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
177333 TATAGGCACG
177343 TACATAACATACA
1 TACA-AACATACA
177356 TACAAACATACA
1 TACAAACATACA
177368 TACAA
1 TACAA
177373 GACAGATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (12 bp):
TACAAACATACA
Found at i:187216 original size:13 final size:13
Alignment explanation
Indices: 187198--187223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187188 ATTGAAAACA
187198 ATTTTTAGGAAAT
1 ATTTTTAGGAAAT
187211 ATTTTTAGGAAAT
1 ATTTTTAGGAAAT
187224 TTGTCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTTTAGGAAAT
Found at i:187300 original size:17 final size:19
Alignment explanation
Indices: 187274--187308 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
187264 CTAAACAACA
187274 AAAAATATAAATT-TTTTC
1 AAAAATATAAATTATTTTC
187292 AAAAA-ATAAATTATTTT
1 AAAAATATAAATTATTTT
187309 TTAAAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATATAAATTATTTTC
Found at i:187997 original size:22 final size:23
Alignment explanation
Indices: 187955--187998 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
187945 AAAATTAAAT
* *
187955 TGTAATTTTTACAATAGTAAAAA
1 TGTAATTTTTACAAGAATAAAAA
187978 TGTAATTTTTA-AAGAATAAAA
1 TGTAATTTTTACAAGAATAAAA
187999 TCAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (23 bp):
TGTAATTTTTACAAGAATAAAAA
Found at i:194943 original size:94 final size:95
Alignment explanation
Indices: 194816--195009 Score: 381
Period size: 94 Copynumber: 2.1 Consensus size: 95
194806 TGTATTTAAG
194816 AAATTAAAACCTTTATATTTATAAATATAATGATATAATTTTTTTATACTTTATTGGACTCTAGT
1 AAATTAAAACCTTTATATTTATAAATATAATGATATAATTTTTTTATACTTTATTGGACTCTAGT
194881 TTTTATTTAAACTTTAAATTCATATTTTTA
66 TTTTATTTAAACTTTAAATTCATATTTTTA
194911 AAATTAAAACCTTT-TATTTATAAATATAATGATATAATTTTTTTATACTTTATTGGACTCTAGT
1 AAATTAAAACCTTTATATTTATAAATATAATGATATAATTTTTTTATACTTTATTGGACTCTAGT
194975 TTTTATTTAAACTTTAAATTCATATTTTTA
66 TTTTATTTAAACTTTAAATTCATATTTTTA
195005 AAATT
1 AAATT
195010 TAATGTAAAT
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 85 0.86
95 14 0.14
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (95 bp):
AAATTAAAACCTTTATATTTATAAATATAATGATATAATTTTTTTATACTTTATTGGACTCTAGT
TTTTATTTAAACTTTAAATTCATATTTTTA
Found at i:196163 original size:2 final size:2
Alignment explanation
Indices: 196156--196180 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
196146 TAAGGAGGAC
196156 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
196181 GGGGGGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:198139 original size:20 final size:20
Alignment explanation
Indices: 198095--198132 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
198085 AAAATTGTAG
198095 TAAAA-TAAACAAAACGAAA
1 TAAAATTAAACAAAACGAAA
*
198114 TAAAATTAAATAAAACGAA
1 TAAAATTAAACAAAACGAA
198133 TAGAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (20 bp):
TAAAATTAAACAAAACGAAA
Found at i:198555 original size:16 final size:18
Alignment explanation
Indices: 198522--198563 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
198512 TATGTGTTAC
198522 AAATTACATAATATATAA
1 AAATTACATAATATATAA
198540 AAATTACATAATATA-AA
1 AAATTACATAATATATAA
*
198557 ATATTAC
1 AAATTAC
198564 TTGTAATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTACATAATATATAA
Found at i:209403 original size:8 final size:8
Alignment explanation
Indices: 209390--209415 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
209380 TAAAAACAAT
209390 TAAAGATA
1 TAAAGATA
209398 TAAAGATA
1 TAAAGATA
209406 TAAAGATA
1 TAAAGATA
209414 TA
1 TA
209416 TTCATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (8 bp):
TAAAGATA
Found at i:209650 original size:3 final size:3
Alignment explanation
Indices: 209644--209689 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
209634 GTAGTAGTAG
209644 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
209690 TTTAGCCCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:210983 original size:11 final size:11
Alignment explanation
Indices: 210969--211002 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
210959 CTTAGAACAA
210969 TATTAGGTGAG
1 TATTAGGTGAG
210980 TATTAGGTGAG
1 TATTAGGTGAG
210991 TATTAGGTGAG
1 TATTAGGTGAG
211002 T
1 T
211003 CTCTACCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (11 bp):
TATTAGGTGAG
Found at i:215148 original size:22 final size:22
Alignment explanation
Indices: 215109--215150 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
215099 TCCTGAATTC
*
215109 TTTAAGGATGAAATTATTGAAA
1 TTTAAGGATGAAAATATTGAAA
215131 TTTAA-GATGAAAAATATTGA
1 TTTAAGGATG-AAAATATTGA
215151 TGTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (22 bp):
TTTAAGGATGAAAATATTGAAA
Found at i:218196 original size:2 final size:2
Alignment explanation
Indices: 218189--218219 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
218179 ACTTCTTTCA
218189 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 T
218220 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:218224 original size:2 final size:2
Alignment explanation
Indices: 218219--218257 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
218209 TCTCTCTCTC
*
218219 TA TA TA TA TA TA TA TA TA TA TG T- TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
218258 GTCTTATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:221723 original size:26 final size:25
Alignment explanation
Indices: 221668--221723 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
221658 CGCCTAATAT
*
221668 GAAAACTTAAAATATTTTATGCTAA
1 GAAAAATTAAAATATTTTATGCTAA
221693 GAAAAATTAAAATATTTTATGCTAA
1 GAAAAATTAAAATATTTTATGCTAA
221718 GAAAAA
1 GAAAAA
221724 AATTATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (25 bp):
GAAAAATTAAAATATTTTATGCTAA
Found at i:223480 original size:16 final size:16
Alignment explanation
Indices: 223459--223494 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
223449 TTCTATTGTC
*
223459 TATATTTTTTTATAGA
1 TATATTTTTATATAGA
*
223475 TATATTTTTATCTAGA
1 TATATTTTTATATAGA
223491 TATA
1 TATA
223495 CAAGATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TATATTTTTATATAGA
Found at i:227313 original size:19 final size:18
Alignment explanation
Indices: 227276--227314 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
227266 AATTTGAATC
* *
227276 AAAACAGAAAATTTTGGA
1 AAAACAGAAAAATTGGGA
227294 AAAACATGAAAAATTGGGA
1 AAAACA-GAAAAATTGGGA
227313 AA
1 AA
227315 CAAGAGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAACAGAAAAATTGGGA
Found at i:235583 original size:12 final size:12
Alignment explanation
Indices: 235566--235595 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
235556 AGCCACACGC
235566 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
235578 CCGTGTGCTAGG
1 CCGTGTGCCAGG
235590 CCGTGT
1 CCGTGT
235596 AACTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:236567 original size:35 final size:35
Alignment explanation
Indices: 236457--236649 Score: 136
Period size: 35 Copynumber: 5.5 Consensus size: 35
236447 ACATCATCAG
* * * *
236457 TCCAACCATAACACGCCAGATGCTCATACGAG-TCAA
1 TCCAACCAAAACACACCA-TTGCTCATAAGAGCT-AA
** * *
236493 TCCCTCCAAAACACACCAAATGCTCACAAGAGCTAA
1 TCCAACCAAAACACACC-ATTGCTCATAAGAGCTAA
* *
236529 TCCAACCAAAACACACCATTTCTCATAAGAGCTTA
1 TCCAACCAAAACACACCATTGCTCATAAGAGCTAA
* * * *
236564 TCCAATCGAAACAAACCATTGCTCATAAGAGCTCA
1 TCCAACCAAAACACACCATTGCTCATAAGAGCTAA
** * * * * *
236599 TCCAACTGAAATACGCCAGTGCACATAAGAGTTAA
1 TCCAACCAAAACACACCATTGCTCATAAGAGCTAA
* * *
236634 TTCAATCGAAACACAC
1 TCCAACCAAAACACAC
236650 TAGACAAAGA
Statistics
Matches: 124, Mismatches: 31, Indels: 5
0.77 0.19 0.03
Matches are distributed among these distances:
35 81 0.65
36 41 0.33
37 2 0.02
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.19
Consensus pattern (35 bp):
TCCAACCAAAACACACCATTGCTCATAAGAGCTAA
Found at i:237119 original size:28 final size:27
Alignment explanation
Indices: 237088--237152 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
237078 TTCATTTTCA
*
237088 AAATTTACATAATTTCCCCAAATTCATC
1 AAATTAAC-TAATTTCCCCAAATTCATC
* *
237116 AAATTAACTATTTTTCCCAAATTCATC
1 AAATTAACTAATTTCCCCAAATTCATC
237143 AAATTAACTA
1 AAATTAACTA
237153 TTTTTCCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATTAACTAATTTCCCCAAATTCATC
Found at i:237186 original size:33 final size:27
Alignment explanation
Indices: 237104--237159 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
237094 ACATAATTTC
237104 CCCAAATTCATCAAATTAACTATTTTT
1 CCCAAATTCATCAAATTAACTATTTTT
237131 CCCAAATTCATCAAATTAACTATTTTT
1 CCCAAATTCATCAAATTAACTATTTTT
237158 CC
1 CC
237160 GAAGTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (27 bp):
CCCAAATTCATCAAATTAACTATTTTT
Found at i:237206 original size:28 final size:28
Alignment explanation
Indices: 237167--237277 Score: 213
Period size: 28 Copynumber: 4.0 Consensus size: 28
237157 TCCGAAGTCA
237167 AAATTCATCAAATTCACTATCAAACCCC
1 AAATTCATCAAATTCACTATCAAACCCC
237195 AAATTCATCAAATTCACTATCAAACCCC
1 AAATTCATCAAATTCACTATCAAACCCC
*
237223 AAATTTATCAAATTCACTATCAAACCCC
1 AAATTCATCAAATTCACTATCAAACCCC
237251 AAATTCATCAAATTCACTATCAAACCC
1 AAATTCATCAAATTCACTATCAAACCC
237278 TAAAATTTTG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 81 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (28 bp):
AAATTCATCAAATTCACTATCAAACCCC
Found at i:244834 original size:35 final size:35
Alignment explanation
Indices: 244776--244892 Score: 155
Period size: 35 Copynumber: 3.3 Consensus size: 35
244766 AATCCCTTCA
* *
244776 AAACACACCAAATGCTCACAAGAGCTAATCCAACCG
1 AAACACACC-AGTGCTCATAAGAGCTAATCCAACCG
* *
244812 AAACACGCCAGTGCTCATAAGAGCTAATCCAACTG
1 AAACACACCAGTGCTCATAAGAGCTAATCCAACCG
* *
244847 AAACACACCATTGC-CTATAAGAGCTAATTCAACCG
1 AAACACACCAGTGCTC-ATAAGAGCTAATCCAACCG
244882 AAACACACCAG
1 AAACACACCAG
244893 ACAGAGAGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
34 1 0.01
35 62 0.87
36 8 0.11
ACGTcount: A:0.42, C:0.31, G:0.13, T:0.15
Consensus pattern (35 bp):
AAACACACCAGTGCTCATAAGAGCTAATCCAACCG
Found at i:252829 original size:15 final size:14
Alignment explanation
Indices: 252804--252834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
252794 GCAACCCAAT
252804 TTTTATTTTTATTA
1 TTTTATTTTTATTA
252818 TTTTATTATTTATTA
1 TTTTATT-TTTATTA
252833 TT
1 TT
252835 ATTTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:252835 original size:18 final size:17
Alignment explanation
Indices: 252806--252839 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
252796 AACCCAATTT
252806 TTATTTTTATTATTTTA
1 TTATTTTTATTATTTTA
252823 TTATTTATTATTATTTT
1 TTATTT-TTATTATTTT
252840 TCTTTACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTTATTATTTTA
Found at i:252877 original size:19 final size:19
Alignment explanation
Indices: 252826--252879 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
252816 TATTTTATTA
252826 TTTATTA-TTATT--TTTC
1 TTTATTATTTATTACTTTC
252842 TTTACTTTATTTATTACTTTC
1 TTTA--TTATTTATTACTTTC
252863 TTTATTATTTATTACTT
1 TTTATTATTTATTACTT
252880 ATTTGGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 4 0.12
18 3 0.09
19 18 0.55
21 8 0.24
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTATTTATTACTTTC
Found at i:253894 original size:97 final size:97
Alignment explanation
Indices: 253728--253921 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
253718 CATGTTGGGC
*
253728 TGAGTAACCGAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATATTCCT
1 TGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATATTCCT
253793 AAAGCATAAAAAAAAGAGAAAAAAAGAAAAAA
66 AAAGCATAAAAAAAAGAGAAAAAAAGAAAAAA
*
253825 TGAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATATTCCT
1 TGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATATTCCT
253890 AAAGCATAAAAAAAAGAGAAAAAAAGAAAAAA
66 AAAGCATAAAAAAAAGAGAAAAAAAGAAAAAA
253922 AATTTGGGGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (97 bp):
TGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATATTCCT
AAAGCATAAAAAAAAGAGAAAAAAAGAAAAAA
Found at i:268483 original size:2 final size:2
Alignment explanation
Indices: 268478--268568 Score: 91
Period size: 2 Copynumber: 45.5 Consensus size: 2
268468 AGATAAAATT
*
268478 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
268520 A- AG GG ATG -G A- AG CAG CAG TTG AG A- AG AG AG AG AG AG AG AG
1 AG AG AG A-G AG AG AG -AG -AG -AG AG AG AG AG AG AG AG AG AG AG
268560 AG AG AG AG A
1 AG AG AG AG A
268569 ACATACAGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
1 4 0.05
2 65 0.86
3 7 0.09
ACGTcount: A:0.46, C:0.02, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:269231 original size:21 final size:21
Alignment explanation
Indices: 269190--269233 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
269180 AATTATTGAA
*
269190 ATTTAATTTAAATCTATTTTT
1 ATTTAATTTAAATCTAATTTT
* *
269211 ATTTAATTTAATTTTAATTTT
1 ATTTAATTTAAATCTAATTTT
269232 AT
1 AT
269234 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTTAAATCTAATTTT
Found at i:272263 original size:26 final size:26
Alignment explanation
Indices: 272233--272290 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
272223 CATATCAATT
272233 AGCTCACAAAGAGCC-TTTAATCGGGA
1 AGCTCACAAAGAGCCATTTAA-CGGGA
272259 AGCTCACAAAGAGCCATTTAACGGGA
1 AGCTCACAAAGAGCCATTTAACGGGA
*
272285 TGCTCA
1 AGCTCA
272291 TAAGAGTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (26 bp):
AGCTCACAAAGAGCCATTTAACGGGA
Found at i:275111 original size:41 final size:41
Alignment explanation
Indices: 275063--275210 Score: 176
Period size: 41 Copynumber: 3.6 Consensus size: 41
275053 TACCCGAAGT
** *
275063 TATTATAATTTTGCACACTAAGTGCCTTACCTAGCCAAAGC
1 TATTATAATTCCGCACACTAAGTGCCTTACATAGCCAAAGC
* * *
275104 TATTATAATTCCACACACTAAGTGCCTTACATAGTCGAAGC
1 TATTATAATTCCGCACACTAAGTGCCTTACATAGCCAAAGC
* * *
275145 TATTATAATTCCCCACACTAAGTGCCATATATAGCCAAAGC
1 TATTATAATTCCGCACACTAAGTGCCTTACATAGCCAAAGC
275186 TATTCCA-AATT--GCACACTAAGTGCC
1 TATT--ATAATTCCGCACACTAAGTGCC
275211 ATTAATAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
40 13 0.14
41 75 0.81
42 4 0.04
43 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (41 bp):
TATTATAATTCCGCACACTAAGTGCCTTACATAGCCAAAGC
Found at i:275170 original size:82 final size:80
Alignment explanation
Indices: 275057--275228 Score: 204
Period size: 82 Copynumber: 2.1 Consensus size: 80
275047 ATCATATACC
* *** * *
275057 CGAAGTTATTATAATTTTGCACACTAAGTGCCTTACCTAGCCAAAGCTATT-ATAATTCCACACA
1 CGAAGCTATTATAATTCCCCACACTAAGTGCCATACATAGCCAAAGCTATTCA-AATT--ACACA
*
275121 CTAAGTGCC-TTACATAGT
63 CTAAGTGCCATTA-ATAAT
* *
275139 CGAAGCTATTATAATTCCCCACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATTGCACACT
1 CGAAGCTATTATAATTCCCCACACTAAGTGCCATACATAGCCAAAGCTATT-CAAATTACACACT
275204 AAGTGCCATTAATAAT
65 AAGTGCCATTAATAAT
275220 CGAAGCTAT
1 CGAAGCTAT
275229 CTCGAATTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
81 26 0.33
82 47 0.60
83 4 0.05
84 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (80 bp):
CGAAGCTATTATAATTCCCCACACTAAGTGCCATACATAGCCAAAGCTATTCAAATTACACACTA
AGTGCCATTAATAAT
Found at i:275226 original size:40 final size:41
Alignment explanation
Indices: 275057--275228 Score: 158
Period size: 41 Copynumber: 4.2 Consensus size: 41
275047 ATCATATACC
* ** * *
275057 CGAAGTTATTATAATTTTGCACACTAAGTGCC-TTACCTAGC
1 CGAAGCTATTATAA-TTCCCACACTAAGTGCCATTACATAGT
*
275098 CAAAGCTATTATAATTCCACACACTAAGTGCC-TTACATAGT
1 CGAAGCTATTATAATTCC-CACACTAAGTGCCATTACATAGT
* *
275139 CGAAGCTATTATAATTCCCCACACTAAGTGCCA-TATATAGC
1 CGAAGCTATTATAATT-CCCACACTAAGTGCCATTACATAGT
* * *
275180 CAAAGCTATTCCA-AATT-GCACACTAAGTGCCATTA-ATAAT
1 CGAAGCTATT--ATAATTCCCACACTAAGTGCCATTACATAGT
275220 CGAAGCTAT
1 CGAAGCTAT
275229 CTCGAATTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
40 27 0.24
41 77 0.69
42 6 0.05
43 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (41 bp):
CGAAGCTATTATAATTCCCACACTAAGTGCCATTACATAGT
Found at i:279733 original size:17 final size:17
Alignment explanation
Indices: 279711--279748 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
279701 ATATTTTATT
*
279711 ATTTACAGGAATGGGTC
1 ATTTACAGGAATGGGCC
*
279728 ATTTACCGGAATGGGCC
1 ATTTACAGGAATGGGCC
279745 ATTT
1 ATTT
279749 CCCCGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (17 bp):
ATTTACAGGAATGGGCC
Found at i:280446 original size:26 final size:26
Alignment explanation
Indices: 280410--280471 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
280400 CGGCCCGTCC
* * *
280410 TATTTTTAAAATAAACATTAAAAAAT
1 TATTTTAAAAATAAAAAATAAAAAAT
280436 TATTTTAAAAATAAAAAATAAAAAAT
1 TATTTTAAAAATAAAAAATAAAAAAT
280462 TATTTTAAAA
1 TATTTTAAAA
280472 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAATAAAAAAT
Found at i:281174 original size:10 final size:10
Alignment explanation
Indices: 281159--281192 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
281149 ATAACACAAA
281159 TATAAAAAAT
1 TATAAAAAAT
281169 TATAAAAAA-
1 TATAAAAAAT
*
281178 TATAAAAATT
1 TATAAAAAAT
281188 TATAA
1 TATAA
281193 TTGTTGGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:281180 original size:19 final size:19
Alignment explanation
Indices: 281156--281192 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
281146 TCCATAACAC
281156 AAATATAAAAAATTATAAA
1 AAATATAAAAAATTATAAA
*
281175 AAATATAAAAATTTATAA
1 AAATATAAAAAATTATAA
281193 TTGTTGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATAAAAAATTATAAA
Found at i:290111 original size:32 final size:32
Alignment explanation
Indices: 290075--290138 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
290065 AGCTTTTTGT
290075 AACGACTCAGTTTTCAGTGGTGTCGAAAATAG
1 AACGACTCAGTTTTCAGTGGTGTCGAAAATAG
290107 AACGACTCAGTTTTCAGTGGTGTCGAAAATAG
1 AACGACTCAGTTTTCAGTGGTGTCGAAAATAG
290139 TAGTTTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (32 bp):
AACGACTCAGTTTTCAGTGGTGTCGAAAATAG
Found at i:292692 original size:44 final size:44
Alignment explanation
Indices: 292641--293254 Score: 346
Period size: 44 Copynumber: 13.8 Consensus size: 44
292631 TAATTTCAAC
* ** * *
292641 CTGCTCCACTGCAACTTTAATGAGATAAGATTTGTAGATTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * * * ** *
292685 CTACTCCACTGTAGCTTCAGGGAGATAAAATTTGTAGCTCCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * *
292729 CTGCTCCACTGCAACTTCAGGGAGATAAGGCCTATAGCTTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * *
292773 CTGCTCTACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAA-
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * * * *
292816 CTTGCTCTACTGCAATTTTAGGGAGATAAGACTCGTAACTTCAA-
1 C-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * * *
292860 CTTGCTCCACTACAAATTCAGGGAGATAAG-GTT-T-GCTATGAT
1 C-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
** * * * *
292902 CTGCTTTACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATA--A---G--ACTTGTAGCTTTAAT
* * * * * * *
292953 -TCGTTCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAGT
1 CT-GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTTAAT
* * * *
292998 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * * *
293042 CTGTTCCACTGCAACTTCAGGGAAATAAGGCTTG-A--TATGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
* * * * *
293083 TTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-CT----TGTAGCTTTAAT
* * * * * * * * *
293132 TTGTTCCACTACAACTTCAGGAAAATAAGATTTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTTAAT
* * * * * *
293177 CTACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
*
293221 CTGCTCCACTGCAACTTCAGGGGGATAAGACTTG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
293255 ATATGATCTA
Statistics
Matches: 437, Mismatches: 109, Indels: 48
0.74 0.18 0.08
Matches are distributed among these distances:
41 50 0.11
42 4 0.01
43 4 0.01
44 247 0.57
45 68 0.16
46 4 0.01
47 1 0.00
48 1 0.00
49 30 0.07
50 2 0.00
51 26 0.06
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAAT
Found at i:293055 original size:89 final size:88
Alignment explanation
Indices: 292955--293241 Score: 339
Period size: 89 Copynumber: 3.2 Consensus size: 88
292945 GCTTCAATTC
292955 GTTCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
1 GTTCCACTGCAACTTCAG-GAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
293020 AGATAAGACTAGTAACTTCAACCT
65 AGATAAGACTAGTAACTTCAACCT
** * * * * *
293044 GTTCCACTGCAACTTCAGGGAAATAAGGCTTG--AT-ATGA-TTTGCTCTACTGCAACTTCAGAG
1 GTTCCACTGCAACTTCA-GGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
* * **
293105 AGATAAGATCTGCAATTTAGCTTCAATTT
65 AGATAAGA-CT---A-GTAACTTCAACCT
* * *
293134 GTTCCACTACAACTTCAGGAAAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAAGG
1 GTTCCACTGCAACTTCAGG-AAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
293199 AGATAAGACTAGTAACTTCAACCT
65 AGATAAGACTAGTAACTTCAACCT
*
293223 GCTCCACTGCAACTTCAGG
1 GTTCCACTGCAACTTCAGG
293242 GGGATAAGAC
Statistics
Matches: 160, Mismatches: 27, Indels: 22
0.77 0.13 0.11
Matches are distributed among these distances:
85 28 0.17
86 4 0.03
87 2 0.01
89 57 0.36
90 37 0.23
92 2 0.01
93 4 0.03
94 26 0.16
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (88 bp):
GTTCCACTGCAACTTCAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGTAACTTCAACCT
Found at i:293187 original size:179 final size:179
Alignment explanation
Indices: 292818--294738 Score: 983
Period size: 179 Copynumber: 10.5 Consensus size: 179
292808 AACTTCAACT
* * * * * * *
292818 TGCTCTACTGCAATTTTAGGGAGATAAGACTCGTAACTTCAACTTGCTCCACTACAAATTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
* * *
292883 AGATAAGGTTTGCTATGATCTGCTTTACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCT
66 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAA-TT-TAGCT
*
292948 TCAAT-TCGTTCCACTGCAACTTCA-GAGAAATAAGATTTGCTATCTTCAGTC
129 TCAATCT-GTTCCACTGCAACTTCAGGA-AAATAAGATTCGCTATCTTCAGTC
*
292999 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGTTCCACTGCAACTTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
* * * *
293064 AAATAAGGCTTGATATGATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTAGCTTC
66 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTAGCTTC
* * *
293129 AATTTGTTCCACTACAACTTCAGGAAAATAAGATTTGCTATCTTCAGTC
131 AATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* *
293178 TACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
* ** * * * ** * *** * ** *
293243 GGATAAGACTTGATATGATCTACTTTAGGGAGATAAGTCTTCAGTCTGCT-CCA-CTGCAACTTC
66 AGATAAGGTTTGCTATGATCTGCTCTA--CTG-CAA--CTTCAGAGAGATAAGATCTGCAA-TTT
** * * * * ** ** **
293306 AGGGAGAT-AAGACTAG-T-AACTTCAACCTGCTCCACTGCAACTTCAGAGAAATAAGGCT-TGA
125 A--G-CTTCAA-TCT-GTTCCACTGCAA-CT--T-CA--GGAAAAT-A-AG--AT-TCGCTATCT
293367 T-ATGATC
174 TCA-G-TC
* * * * * *
293374 TGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAA-TTCGTTCCACTGCAA
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-C--T-A-GTA-A-CTTCAACCT-GCTCCACTGCAA
* * * * * * *
293438 CTTCAGAGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGA-CT-
58 CTTCAGGGAGATAAGGTTTGCTA---TGA-TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
* * * * * * * * *
293501 --A-GTAACTTCAACCTGCTCCACTGTAACTTCAGGGAAATAAGGCTT-G--AT-ATGA-TC
119 CAATTTAGCTTCAATCTGTTCCACTGCAACTTCAGGAAAATAA-GATTCGCTATCTTCAGTC
* * * * *
293555 TGCTCTACTGCAACTTCAGAGAGATAAGATCT-GTAATTTAGCTTCAATCTGTTCCACTGTAACT
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTAGT-A---A-CTTCAACCTGCTCCACTGCAACT
* * * * * * * * * *
293619 TCAGGAAAATAAGATTCGCTATCTTCAGTCTACTCCACTACAACTTTA-AGGAAATAAGA-CTAG
60 TCAGGGAGATAAGGTTTGCTA---TGA-TCTGCTCTACTGCAACTTCAGA-GAGATAAGATCT-G
* * * * * * * * * *
293682 CTA-TT---TTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAG-TAACTTCA-AC
119 CAATTTAGCTTCAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* * * * * * *
293737 ATGCTCTACTGCAACTTTAGGGAGATAAAGA-T--T-GCTAT-GATCTACTCTACTGCAACTTCA
1 -TGCTCCACTGCAACTTCAGGGAGAT-AAGACTAGTAACT-TCAACCTGCTCCACTGCAACTTCA
* ** * * * * * * ** *
293797 GAGAGATAAGATCTGTTTATTTTTAACCTGTTCCACTGCAACTTCATG-GGGATCTGAAT-TGTA
63 GGGAGATAAG----GTTT-GCTATGATCTGCTCTACTGCAACTTCA-GAGAGATAAG-ATCTGCA
* * * * *
293860 ATTTGTAGCTTTAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTCGTTATCTTTAGTC
121 A-TT-TAGCTTCAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* * * * * * **
293921 TACTCTACTACAACTTTAGGGAGATAAGATCTGCAATTTATAGCTTCAATCTATTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT---A-GTA-A-CTTCAACCTGCTCCACTGCAAC
* * * * * * ** *
293986 TTTAGGGAAATAAGATTCGTTAACTTCAGTCCTGCTCCGCTGCAACTTCAGGGAGATAATG-T-T
59 TTCAGGGAGATAAGGTTTGCT-A--TGA-T-CTGCTCTACTGCAACTTCAGAGAGATAA-GATCT
* * * * * * * * * * *
294049 ----TGTGGCTTTAATATGTTTCACTGCAACTTTAGGAAGATACGATTTGTAGCCCATCTTCAAT
118 GCAATTTAGCTTCAATCTGTTCCACTGCAACTTCAGGAAAATAAGA--T-TCG-CTATCTTCAGT
*
294110 T
179 C
* ** ** * ** * * *
294111 TGCTCCACTGTAACTTTGGGGAGATAAGGTTGGTTTATTTTTAACCTGTTCCACTACAACTTCAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAG--TAACTTCAACCTGCTCCACTGCAACTTCAG
* * * * *
294176 GGAGATAAGGTTTGATATGATCTGCTCTACTGTAACCTCTGAGAGATAAGATCTGTAATTTATAG
64 GGAGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAA-TT-TAG
* * **
294241 CTTTAATCTGTTCCACTACAACTTCAGGAAAATAAGATTCATTATCTTCAGTC
127 CTTCAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* *
294294 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
** *
294359 AGATAAATTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGCAATTATAGCTT
66 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATT-TAGCTT
* * * * *
294424 CAATTTGTTCCACTGTAACTTCAGGGAAATAAGATTCACTATCTTTAGTC
130 CAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* * * *
294474 TGCTTCACTGCAACGTAAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTTAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
* * * * * *
294539 AGATAAGTTTTGCTATGATATACTCTACTGTAACTTCAAAGAGATAAGATCTGCAATTTAGCTTT
66 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTAGCTTC
* * ** *
294604 AATCTGTTCCATTGTAACTTTTGGGAAATAAGATTCGCTATCTTCAGTC
131 AATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
* * *
294653 TGCTCCACTGCAACTTTAGGGAAATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTTAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
*
294718 AAATAAGGTTTGCTATGATCT
66 AGATAAGGTTTGCTATGATCT
294739 TCAATCCATC
Statistics
Matches: 1349, Mismatches: 281, Indels: 222
0.73 0.15 0.12
Matches are distributed among these distances:
175 26 0.02
176 23 0.02
177 5 0.00
178 1 0.00
179 343 0.25
180 223 0.17
181 217 0.16
182 50 0.04
183 95 0.07
184 18 0.01
185 44 0.03
186 38 0.03
187 38 0.03
188 5 0.00
189 9 0.01
190 34 0.03
191 6 0.00
192 7 0.01
193 52 0.04
194 3 0.00
195 11 0.01
196 36 0.03
197 1 0.00
198 1 0.00
199 1 0.00
200 2 0.00
201 2 0.00
202 9 0.01
203 38 0.03
204 2 0.00
205 1 0.00
206 2 0.00
207 6 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (179 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAGGG
AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTAGCTTC
AATCTGTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTC
Found at i:293366 original size:111 final size:111
Alignment explanation
Indices: 293169--293374 Score: 358
Period size: 111 Copynumber: 1.9 Consensus size: 111
293159 AGATTTGCTA
293169 TCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCA
1 TCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCA
* **
293234 ACTTCAGGGGGATAAGACTTGATATGATCTACTTTAGGGAGATAAG
66 ACTTCAGAGAAATAAGACTTGATATGATCTACTTTAGGGAGATAAG
* *
293280 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCA
1 TCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCA
*
293345 ACTTCAGAGAAATAAGGCTTGATATGATCT
66 ACTTCAGAGAAATAAGACTTGATATGATCT
293375 GCTCTACTGC
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 89 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (111 bp):
TCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCA
ACTTCAGAGAAATAAGACTTGATATGATCTACTTTAGGGAGATAAG
Done.