Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2367.1
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: 253103
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:204 original size:24 final size:24
Alignment explanation
Indices: 154--205 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
144 AATCAAAGTC
* **
154 AAATATATTATGCTAATAAATGGT
1 AAATATATTATACTAATAAATACT
*
178 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
202 AAAT
1 AAAT
206 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5451 original size:19 final size:19
Alignment explanation
Indices: 5427--5463 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5417 TTGAAATTTC
*
5427 TCCAATTTTCGATTTCAAG
1 TCCAATTTTCGAGTTCAAG
5446 TCCAATTTTCGAGTTCAA
1 TCCAATTTTCGAGTTCAA
5464 TTACCAATCA
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:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (19 bp):
TCCAATTTTCGAGTTCAAG
Found at i:7077 original size:67 final size:67
Alignment explanation
Indices: 6964--7206 Score: 253
Period size: 66 Copynumber: 3.7 Consensus size: 67
6954 CTGTCTTGGC
* * * **
6964 AGACTACACTAGTTGCCA-AATCTGAGCTATGGTCTTACACCGTAATCCCCATATTTAATATCCT
1 AGACTACACTGGTTGTCATAA-CTGAGCTATGGTCTTACACCTTAATCCCCATATTTAACGTCCT
7028 GGT
65 GGT
* * * **
7031 AGACTACATTGGTTGTCATAACTGAGTTATGGTCTTACACCTTAATCCTCC--ATGTAGGGTCCT
1 AGACTACACTGGTTGTCATAACTGAGCTATGGTCTTACACCTTAATCC-CCATATTTAACGTCCT
*
7094 AGT
65 GGT
* * * * *
7097 AGACTACACTGGTTGCCATAGCCGAGCTATGG-CTTACCCCTTAATCCCCATGTTTAACGTCCTG
1 AGACTACACTGGTTGTCATAACTGAGCTATGGTCTTACACCTTAATCCCCATATTTAACGTCCTG
7161 GT
66 GT
* * *
7163 AGACTGCACTGATTGTCAT-AGTCGAGCTATGGTCTTACACCTTA
1 AGACTACACTGGTTGTCATAACT-GAGCTATGGTCTTACACCTTA
7207 TAACCTCTTT
Statistics
Matches: 142, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
64 2 0.01
65 14 0.10
66 72 0.51
67 50 0.35
68 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (67 bp):
AGACTACACTGGTTGTCATAACTGAGCTATGGTCTTACACCTTAATCCCCATATTTAACGTCCTG
GT
Found at i:7202 original size:132 final size:133
Alignment explanation
Indices: 6964--7206 Score: 337
Period size: 132 Copynumber: 1.8 Consensus size: 133
6954 CTGTCTTGGC
* * *
6964 AGACTACACTAGTTGCCAAATCTGAGCTATGGTCTTACACCGTAATCCCCATATTTAATATCCTG
1 AGACTACACTAGTTGCCAAAGCCGAGCTATGGTCTTACACCGTAATCCCCATATTTAACATCCTG
* * *
7029 GTAGACTACATTGGTTGTCATAACTGAGTTATGGTCTTACACCTTAATCCTCCATGTAGGGTCCT
66 GTAGACTACACTGATTGTCATAACTGAGCTATGGTCTTACACCTTAATCCTCCATGTAGGGTCCT
7094 AGT
131 AGT
* * * * * *
7097 AGACTACACTGGTTGCCATAGCCGAGCTATGG-CTTACCCCTTAATCCCCATGTTTAACGTCCTG
1 AGACTACACTAGTTGCCAAAGCCGAGCTATGGTCTTACACCGTAATCCCCATATTTAACATCCTG
* *
7161 GTAGACTGCACTGATTGTCAT-AGTCGAGCTATGGTCTTACACCTTA
66 GTAGACTACACTGATTGTCATAACT-GAGCTATGGTCTTACACCTTA
7207 TAACCTCTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
131 2 0.02
132 65 0.68
133 28 0.29
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (133 bp):
AGACTACACTAGTTGCCAAAGCCGAGCTATGGTCTTACACCGTAATCCCCATATTTAACATCCTG
GTAGACTACACTGATTGTCATAACTGAGCTATGGTCTTACACCTTAATCCTCCATGTAGGGTCCT
AGT
Found at i:12988 original size:21 final size:21
Alignment explanation
Indices: 12962--13005 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12952 AAAAAAAAGA
12962 TTAAAAAATCTTTATTCTAGG
1 TTAAAAAATCTTTATTCTAGG
*
12983 TTAAAAAATCTTTATTCTGGG
1 TTAAAAAATCTTTATTCTAGG
13004 TT
1 TT
13006 TTCGTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (21 bp):
TTAAAAAATCTTTATTCTAGG
Found at i:13828 original size:10 final size:10
Alignment explanation
Indices: 13815--13859 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
13805 GAAAAGAATG
13815 GAAAATAAAA
1 GAAAATAAAA
13825 GAAAA-AAAA
1 GAAAATAAAA
13834 GAAAATTAAAA
1 GAAAA-TAAAA
*
13845 GAACATAAAA
1 GAAAATAAAA
13855 GAAAA
1 GAAAA
13860 GAATTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 9 0.29
10 14 0.45
11 8 0.26
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:13843 original size:20 final size:20
Alignment explanation
Indices: 13815--13859 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
13805 GAAAAGAATG
13815 GAAAATAAAAGAA-AAAAAA
1 GAAAATAAAAGAACAAAAAA
*
13834 GAAAATTAAAAGAACATAAAA
1 GAAAA-TAAAAGAACAAAAAA
13855 GAAAA
1 GAAAA
13860 GAATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 8 0.35
21 10 0.43
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (20 bp):
GAAAATAAAAGAACAAAAAA
Found at i:13859 original size:15 final size:15
Alignment explanation
Indices: 13815--13862 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
13805 GAAAAGAATG
13815 GAAAATAAAAGAAAA
1 GAAAATAAAAGAAAA
* *
13830 -AAAAGAAAATTAAAA
1 GAAAATAAAA-GAAAA
*
13845 GAACATAAAAGAAAA
1 GAAAATAAAAGAAAA
13860 GAA
1 GAA
13863 TTAAATTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 8 0.31
15 11 0.42
16 7 0.27
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.08
Consensus pattern (15 bp):
GAAAATAAAAGAAAA
Found at i:21911 original size:26 final size:26
Alignment explanation
Indices: 21877--21975 Score: 128
Period size: 26 Copynumber: 3.8 Consensus size: 26
21867 TATTTTCTCG
* *
21877 AAATTTTACCGGGGGTAAAATCGTGA
1 AAATTTTACCAGGGGTAAAATCGTCA
**
21903 AAATTTTACCAGGGGTAAAATTATCA
1 AAATTTTACCAGGGGTAAAATCGTCA
* *
21929 AAATTTTACCAGTGGTAAAATTGTCA
1 AAATTTTACCAGGGGTAAAATCGTCA
*
21955 GAATTTTACCA-GGGTAAAATC
1 AAATTTTACCAGGGGTAAAATC
21976 ATAAAAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
25 8 0.12
26 56 0.88
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (26 bp):
AAATTTTACCAGGGGTAAAATCGTCA
Found at i:21960 original size:52 final size:51
Alignment explanation
Indices: 21877--21988 Score: 143
Period size: 52 Copynumber: 2.2 Consensus size: 51
21867 TATTTTCTCG
* * * *
21877 AAATTTTACCGGGGGTAAAATCGTGAAAATTTTACCAGGGGTAAAATTATCA
1 AAATTTTACCAGGGGTAAAATCGTCAAAATTTTACCA-GGGTAAAATCATAA
* * *
21929 AAATTTTACCAGTGGTAAAATTGTCAGAATTTTACCAGGGTAAAATCATAA
1 AAATTTTACCAGGGGTAAAATCGTCAAAATTTTACCAGGGTAAAATCATAA
*
21980 AAAATTTAC
1 AAATTTTAC
21989 TAAAGGTAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 20 0.38
52 32 0.62
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (51 bp):
AAATTTTACCAGGGGTAAAATCGTCAAAATTTTACCAGGGTAAAATCATAA
Found at i:21985 original size:26 final size:25
Alignment explanation
Indices: 21877--21988 Score: 116
Period size: 26 Copynumber: 4.4 Consensus size: 25
21867 TATTTTCTCG
* * *
21877 AAATTTTACCGGGGGTAAAATCGTGA
1 AAATTTTACC-AGGGTAAAATCATCA
*
21903 AAATTTTACCAGGGGTAAAATTATCA
1 AAATTTTACCA-GGGTAAAATCATCA
**
21929 AAATTTTACCAGTGGTAAAATTGTCA
1 AAATTTTACCAG-GGTAAAATCATCA
* *
21955 GAATTTTACCAGGGTAAAATCATAA
1 AAATTTTACCAGGGTAAAATCATCA
*
21980 AAAATTTAC
1 AAATTTTAC
21989 TAAAGGTAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
25 18 0.25
26 55 0.75
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (25 bp):
AAATTTTACCAGGGTAAAATCATCA
Found at i:21997 original size:51 final size:52
Alignment explanation
Indices: 21890--21997 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 52
21880 TTTTACCGGG
* * * * **
21890 GGTAAAATCGTGAAAATTTTACCAGGGGTAAAATTATCAAAATTTTACCAGT
1 GGTAAAATCGTCAAAATTTTACCAGGGGTAAAATCATAAAAAATTTACCAAA
* * *
21942 GGTAAAATTGTCAGAATTTTACCA-GGGTAAAATCATAAAAAATTTACTAAA
1 GGTAAAATCGTCAAAATTTTACCAGGGGTAAAATCATAAAAAATTTACCAAA
21993 GGTAA
1 GGTAA
21998 GATAGGGATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 26 0.55
52 21 0.45
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (52 bp):
GGTAAAATCGTCAAAATTTTACCAGGGGTAAAATCATAAAAAATTTACCAAA
Found at i:27893 original size:36 final size:36
Alignment explanation
Indices: 27846--27949 Score: 190
Period size: 36 Copynumber: 2.9 Consensus size: 36
27836 GCTAAGCTAC
*
27846 CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
*
27882 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
27918 CACTTATCACTTTTTCACTTGATCAGATAAGT
1 CACTTATCACTTTTTCACTTGATCAGATAAGT
27950 GTAGCTAAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
Found at i:27893 original size:43 final size:42
Alignment explanation
Indices: 27802--27929 Score: 128
Period size: 36 Copynumber: 3.1 Consensus size: 42
27792 TTACGTATGG
* *
27802 TCACTTATCATTTGTC-CCTGATCAGATAAGTGTAGCTAAGC-TA
1 TCACTTATCATTTGTCACTTGATCAGATAAGTATAGC--A-CTTA
* *
27845 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAACACTTA
1 TCACTTATCA-TTTGTCACTTGATCAGATAAGTATAGCACTTA
27888 TCAC---T--TTT-TCACTTGATCAGATAAGTATAGCACTTA
1 TCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTTA
27924 TCACTT
1 TCACTT
27930 TTTCACTTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
36 31 0.42
37 3 0.04
40 1 0.01
42 1 0.01
43 15 0.20
44 6 0.08
45 17 0.23
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (42 bp):
TCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTTA
Found at i:33648 original size:49 final size:49
Alignment explanation
Indices: 33595--33693 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
33585 ACATATGGAA
* *
33595 ATTCATAATTCATGTATATATCAATACAAAACATACACACTCAAAGTTT
1 ATTCATAATTCATGTATATATCAATACAAAACATAAACACTCAAAATTT
33644 ATTCATAATTCATGTATATATCAATACAAAACATAAACACTCAAAATTT
1 ATTCATAATTCATGTATATATCAATACAAAACATAAACACTCAAAATTT
33693 A
1 A
33694 ATCACACGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.32
Consensus pattern (49 bp):
ATTCATAATTCATGTATATATCAATACAAAACATAAACACTCAAAATTT
Found at i:37059 original size:20 final size:20
Alignment explanation
Indices: 37031--37124 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
37021 AATGCTATAT
* *
37031 AGAGGCACCGTAGTTCAAA-C
1 AGAGACACCGAAG-TCAAATC
*
37051 AGAGACACCGAAGTGAAATC
1 AGAGACACCGAAGTCAAATC
37071 AGAGACACCGAAGTGCAAA-C
1 AGAGACACCGAAGT-CAAATC
* *
37091 AGAGAAACCGAAGTGAAATC
1 AGAGACACCGAAGTCAAATC
37111 AGAGACACCGAAGT
1 AGAGACACCGAAGT
37125 GCAATCTCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 7 0.11
20 54 0.84
21 3 0.05
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.10
Consensus pattern (20 bp):
AGAGACACCGAAGTCAAATC
Found at i:37090 original size:40 final size:40
Alignment explanation
Indices: 37031--37128 Score: 160
Period size: 40 Copynumber: 2.5 Consensus size: 40
37021 AATGCTATAT
* * * *
37031 AGAGGCACCGTAGTTCAAACAGAGACACCGAAGTGAAATC
1 AGAGACACCGAAGTGCAAACAGAGAAACCGAAGTGAAATC
37071 AGAGACACCGAAGTGCAAACAGAGAAACCGAAGTGAAATC
1 AGAGACACCGAAGTGCAAACAGAGAAACCGAAGTGAAATC
37111 AGAGACACCGAAGTGCAA
1 AGAGACACCGAAGTGCAA
37129 TCTCATACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (40 bp):
AGAGACACCGAAGTGCAAACAGAGAAACCGAAGTGAAATC
Found at i:37125 original size:20 final size:20
Alignment explanation
Indices: 37050--37130 Score: 128
Period size: 20 Copynumber: 4.0 Consensus size: 20
37040 GTAGTTCAAA
37050 CAGAGACACCGAAGTGAAAT
1 CAGAGACACCGAAGTGAAAT
37070 CAGAGACACCGAAGTGCAAA-
1 CAGAGACACCGAAGTG-AAAT
*
37090 CAGAGAAACCGAAGTGAAAT
1 CAGAGACACCGAAGTGAAAT
*
37110 CAGAGACACCGAAGTGCAAT
1 CAGAGACACCGAAGTGAAAT
37130 C
1 C
37131 TCATACAAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (20 bp):
CAGAGACACCGAAGTGAAAT
Found at i:44070 original size:19 final size:18
Alignment explanation
Indices: 44046--44099 Score: 83
Period size: 17 Copynumber: 3.0 Consensus size: 18
44036 ATTGATTTAT
44046 TAATTTTTTTTAAAATTA
1 TAATTTTTTTTAAAATTA
*
44064 CTAATTTATTTTAAAA-TA
1 -TAATTTTTTTTAAAATTA
44082 TAATTTTTTTTAAAATTA
1 TAATTTTTTTTAAAATTA
44100 ATATCGTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 14 0.44
18 4 0.12
19 14 0.44
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTTTTTTAAAATTA
Found at i:50572 original size:9 final size:8
Alignment explanation
Indices: 50540--50569 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
50530 TAAATATTAT
50540 TTAAAATA
1 TTAAAATA
50548 TTAAAATA
1 TTAAAATA
50556 TTAAAATA
1 TTAAAATA
50564 TTAAAA
1 TTAAAA
50570 ATAGAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TTAAAATA
Found at i:55773 original size:19 final size:18
Alignment explanation
Indices: 55738--55781 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
55728 TTTTAATTTA
* *
55738 AAAATATTAAACCATAAT
1 AAAATATTAAACAATAAC
*
55756 AAAATATTAAAATAATAAC
1 AAAATATT-AAACAATAAC
55775 AAAATAT
1 AAAATAT
55782 AATATTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATATTAAACAATAAC
Found at i:56151 original size:117 final size:117
Alignment explanation
Indices: 56012--56238 Score: 271
Period size: 117 Copynumber: 1.9 Consensus size: 117
56002 ACTAGAACTT
* * * * * *
56012 CTATCACACGCGTATATGTGTGGAAACCA-AAGATTTAGAATATAAATATGT-GTTTAACTAT-A
1 CTATCACACCCATATATGTGTGGAAACCACAA-ATTTAGAACACAAATATGTACTTTAA-AATCA
* *
56074 GCATACAATAAACAATAAAATGTATGGTTTGAAACTAATTAATCATAAAGAAATC
64 -CATACAATAAACAATAAAACGTATGGTTTGAAACTAATTAATAATAAAGAAATC
* * * *
56129 CTATCACACCCATATGTGTGTGGAAATCACAAATTTAGAACACAAATGTTTACTTTAAAATCACA
1 CTATCACACCCATATATGTGTGGAAACCACAAATTTAGAACACAAATATGTACTTTAAAATCACA
* * *
56194 TACAATAAATAATGAAACGTATGGTTTGAAGCTAATTAATAATAA
66 TACAATAAACAATAAAACGTATGGTTTGAAACTAATTAATAATAA
56239 TGATGAAATA
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
117 84 0.91
118 8 0.09
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (117 bp):
CTATCACACCCATATATGTGTGGAAACCACAAATTTAGAACACAAATATGTACTTTAAAATCACA
TACAATAAACAATAAAACGTATGGTTTGAAACTAATTAATAATAAAGAAATC
Found at i:57371 original size:15 final size:15
Alignment explanation
Indices: 57351--57387 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
57341 AAATATTAAA
57351 ATAATATTAAAATGT
1 ATAATATTAAAATGT
*
57366 ATAATATTAATATGT
1 ATAATATTAAAATGT
57381 AT-ATATT
1 ATAATATT
57388 TTCTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
ATAATATTAAAATGT
Found at i:60097 original size:18 final size:19
Alignment explanation
Indices: 60076--60118 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
60066 TAGAAATTCC
*
60076 AAAATTTAT-ATTTTTTAA
1 AAAATTTATAAATTTTTAA
60094 AAAA-TTATAAATTTTTAA
1 AAAATTTATAAATTTTTAA
60112 AAAATTT
1 AAAATTT
60119 CCAAAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATTTATAAATTTTTAA
Found at i:60161 original size:7 final size:8
Alignment explanation
Indices: 60140--60165 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
60130 ATAAAGAAAG
60140 TTAAAAAT
1 TTAAAAAT
60148 TTAAAAAT
1 TTAAAAAT
60156 TTAAAAAT
1 TTAAAAAT
60164 TT
1 TT
60166 TCTAAAATAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAAAT
Found at i:65965 original size:10 final size:10
Alignment explanation
Indices: 65950--65979 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
65940 ATGCAAAATT
65950 AAGAAAGAAA
1 AAGAAAGAAA
*
65960 AAGAAAGAGA
1 AAGAAAGAAA
65970 AAGAAAGAAA
1 AAGAAAGAAA
65980 TAGAGAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:65972 original size:16 final size:16
Alignment explanation
Indices: 65951--65994 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
65941 TGCAAAATTA
65951 AGAAAGAAA-AAGAAAG
1 AGAAAGAAAGAA-AAAG
*
65967 AGAAAGAAAGAAATAG
1 AGAAAGAAAGAAAAAG
*
65983 AGAAAGGAAGAA
1 AGAAAGAAAGAA
65995 CCACACACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAG
Found at i:66472 original size:13 final size:13
Alignment explanation
Indices: 66430--66472 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
66420 AAATATTCAA
66430 TGTGAAATTGAAT
1 TGTGAAATTGAAT
* *
66443 TGTGTATATTCAA-
1 TGTG-AAATTGAAT
66456 TGTGAAATTGAAT
1 TGTGAAATTGAAT
66469 TGTG
1 TGTG
66473 TTGTATTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (13 bp):
TGTGAAATTGAAT
Found at i:66484 original size:26 final size:26
Alignment explanation
Indices: 66422--66473 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
66412 AAAAATTGAA
66422 ATATTCAATGTGAAATTGAATTGTGT
1 ATATTCAATGTGAAATTGAATTGTGT
66448 ATATTCAATGTGAAATTGAATTGTGT
1 ATATTCAATGTGAAATTGAATTGTGT
66474 TGTATTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (26 bp):
ATATTCAATGTGAAATTGAATTGTGT
Found at i:76205 original size:30 final size:30
Alignment explanation
Indices: 76171--76231 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
76161 GGTGTACAAC
76171 TTCTGTAGTATGTAGCGTTATTCACAATAG
1 TTCTGTAGTATGTAGCGTTATTCACAATAG
76201 TTCTGTAGTATGTAGCGTTATTCACAATAG
1 TTCTGTAGTATGTAGCGTTATTCACAATAG
76231 T
1 T
76232 GAAATTCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (30 bp):
TTCTGTAGTATGTAGCGTTATTCACAATAG
Found at i:76996 original size:26 final size:26
Alignment explanation
Indices: 76966--77021 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
76956 AAATTTCTCG
*
76966 AAATTTTACTAG-GGGTAAAATTGTCA
1 AAATTTTA-TAGAGAGTAAAATTGTCA
* *
76992 AAATTTTATCGAGAGTAAAATTGTCT
1 AAATTTTATAGAGAGTAAAATTGTCA
77018 AAAT
1 AAAT
77022 CAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (26 bp):
AAATTTTATAGAGAGTAAAATTGTCA
Found at i:80729 original size:33 final size:33
Alignment explanation
Indices: 80648--80732 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
80638 AATTTCTCCA
*
80648 TAAAAGTAAATAAAA-AGAACAAAAATAAAATC
1 TAAAACTAAATAAAAGAGAACAAAAATAAAATC
* * *
80680 TAAACCTTAAGAAAAGAGAACAAAAA-AAAA-C
1 TAAAACTAAATAAAAGAGAACAAAAATAAAATC
80711 TAAAGACTAAATATAAAGAGAA
1 TAAA-ACTAAATA-AAAGAGAA
80733 AATTATACAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
31 5 0.12
32 20 0.47
33 18 0.42
ACGTcount: A:0.68, C:0.08, G:0.09, T:0.14
Consensus pattern (33 bp):
TAAAACTAAATAAAAGAGAACAAAAATAAAATC
Found at i:93676 original size:40 final size:40
Alignment explanation
Indices: 93621--93700 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
93611 ACACCGTACA
**
93621 AGGTTTTATACGAACGTAGATGTAGATCTCTGTTATATTG
1 AGGTTTTATACGAACGTAGATGTAGATCTCCATTATATTG
93661 AGGTTTTATACGAACGTAGATGTAGATCTCCATTATATTG
1 AGGTTTTATACGAACGTAGATGTAGATCTCCATTATATTG
93701 GTCCGATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (40 bp):
AGGTTTTATACGAACGTAGATGTAGATCTCCATTATATTG
Found at i:107297 original size:3 final size:3
Alignment explanation
Indices: 107289--107313 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
107279 CTCTTAGCTT
107289 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
107314 AGATTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:114839 original size:331 final size:331
Alignment explanation
Indices: 114236--114851 Score: 973
Period size: 331 Copynumber: 1.9 Consensus size: 331
114226 ATTGCCTGGA
114236 CAAAAATAGTCTCAGCATCCTTAGGCATCACGTCAACCTATGTCACGCCACACAATATCTATGGT
1 CAAAAATAGTCTCAGCATCCTTAGGCATCACGTCAACCTATGTCACGCCACACAATATCTATGGT
114301 GCGACACAACATGTATTTTCTTCATTGTGTCATTCATTTCGTGCTTTGACGTCCTAGGAAGCTTA
66 GCGACACAACATGTATTTTCTTCATTGTGTCATTCATTTCGTGCTTTGACGTCCTAGGAAGCTTA
*** * * *
114366 CGTGTCACTCATTCCTTGCTTCCACATCAATTGGGTCTTTAATTTTTTATTCTACACACTCAATT
131 CACATCACTCATTCCTTGCTTCCACATCAATTGGCTCTTTAATTCTTTATCCTACACACTCAATT
* * * *
114431 AAACATATTAATACTACCAAAGGCTCGTGTCGGTCTAATGGGTCACAACACTTATAAAATGTGTT
196 AAAAATATTAATACTACCAAAGGCTCATCTCGGCCTAATGGGTCACAACACTTATAAAATGTGTT
* *
114496 AAAAATCACTTATTTTTCTAATATTTAATCATAAGGCCTAAATATCGAAAATGTAATATAAAATG
261 AAAAAGCACTTATTTTACTAATATTTAATCATAAGGCCTAAATATCGAAAATGTAATATAAAATG
114561 CAATAT
326 CAATAT
** * * * * *
114567 CAAAAATAGTCTTGGCATCCTTGGGCATCATGTCAACTTGTGTCATGCCACACAATATCTATGGT
1 CAAAAATAGTCTCAGCATCCTTAGGCATCACGTCAACCTATGTCACGCCACACAATATCTATGGT
* * * *
114632 GTGACACAACATGTATTTTCTTCCTTGTGTCATTCATTTTGTGCTTTGACGTCCTAGGAAGCTTG
66 GCGACACAACATGTATTTTCTTCATTGTGTCATTCATTTCGTGCTTTGACGTCCTAGGAAGCTTA
* *
114697 CACATCACTCGTTCCTTGCTTCCACATCAATTAGGCT-TTTAATTCTTTATCCTATACACTCAAT
131 CACATCACTCATTCCTTGCTTCCACATCAATT-GGCTCTTTAATTCTTTATCCTACACACTCAAT
* *
114761 TAAAAATATTAGTACTACCTAAGGCTCATCTCGGCCTAATGGGTCACAACACTTATAAAATGTGT
195 TAAAAATATTAATACTACCAAAGGCTCATCTCGGCCTAATGGGTCACAACACTTATAAAATGTGT
114826 TAAAAAGCACTTATTTTACTAATATT
260 TAAAAAGCACTTATTTTACTAATATT
114852 ATACACTTTT
Statistics
Matches: 257, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
331 254 0.99
332 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (331 bp):
CAAAAATAGTCTCAGCATCCTTAGGCATCACGTCAACCTATGTCACGCCACACAATATCTATGGT
GCGACACAACATGTATTTTCTTCATTGTGTCATTCATTTCGTGCTTTGACGTCCTAGGAAGCTTA
CACATCACTCATTCCTTGCTTCCACATCAATTGGCTCTTTAATTCTTTATCCTACACACTCAATT
AAAAATATTAATACTACCAAAGGCTCATCTCGGCCTAATGGGTCACAACACTTATAAAATGTGTT
AAAAAGCACTTATTTTACTAATATTTAATCATAAGGCCTAAATATCGAAAATGTAATATAAAATG
CAATAT
Found at i:117348 original size:15 final size:16
Alignment explanation
Indices: 117323--117355 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
117313 ACACTCTAAA
*
117323 AAAATTAAAATGAAAT
1 AAAATTAAAATAAAAT
117339 AAAA-TAAAATAAAAT
1 AAAATTAAAATAAAAT
117354 AA
1 AA
117356 TAAAAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATTAAAATAAAAT
Found at i:118439 original size:15 final size:14
Alignment explanation
Indices: 118421--118450 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
118411 TTTGTATTCC
118421 ATCTTTTTTTTCTGT
1 ATCTTTTTTTT-TGT
118436 ATCTTTTTTTTTGT
1 ATCTTTTTTTTTGT
118450 A
1 A
118451 AACATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (14 bp):
ATCTTTTTTTTTGT
Found at i:119274 original size:44 final size:44
Alignment explanation
Indices: 119208--119296 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
119198 AACTTCAGGG
* *
119208 TAGTGGCTTCAATCTGCTCCACTACAACTTTAGGGAGATAAGAT
1 TAGTGGCTTCAATCTGCCCCACTACAACTTCAGGGAGATAAGAT
119252 TAGTGGCTTCAATCTGCCCCACTACAACTTCAGGGAGATAAGAT
1 TAGTGGCTTCAATCTGCCCCACTACAACTTCAGGGAGATAAGAT
119296 T
1 T
119297 TGTCATAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
TAGTGGCTTCAATCTGCCCCACTACAACTTCAGGGAGATAAGAT
Found at i:119334 original size:50 final size:51
Alignment explanation
Indices: 119280--119397 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 51
119270 CCACTACAAC
119280 TTCAGGGAGATAAGATTTGTCATAATG-A-CTTCAATCCATCCCACCGCAAA
1 TTCAGGGAGATAAGATTTGTCAT-ATGTAGCTTCAATCCATCCCACCGCAAA
* * * * * * *
119330 TTCAGGG-GTATAGGATTTGTGATCTGTAGCTTCAATCTATTCCACTGCAAT
1 TTCAGGGAG-ATAAGATTTGTCATATGTAGCTTCAATCCATCCCACCGCAAA
*
119381 TTCAGGGAAATAAGATT
1 TTCAGGGAGATAAGATT
119398 CACATATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
49 3 0.05
50 20 0.36
51 32 0.58
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (51 bp):
TTCAGGGAGATAAGATTTGTCATATGTAGCTTCAATCCATCCCACCGCAAA
Found at i:124583 original size:15 final size:16
Alignment explanation
Indices: 124558--124590 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
124548 AATACTCTAA
*
124558 AAAATTAAAATGAAAT
1 AAAATTAAAATAAAAT
124574 AAAA-TAAAATAAAAT
1 AAAATTAAAATAAAAT
124589 AA
1 AA
124591 TAAAAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATTAAAATAAAAT
Found at i:124764 original size:21 final size:23
Alignment explanation
Indices: 124740--124783 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
124730 TTGGTGAAAA
124740 GAAAATAAGAATAA-AAA-AATT
1 GAAAATAAGAATAACAAATAATT
*
124761 GAAAATAATAATAACAAATAATT
1 GAAAATAAGAATAACAAATAATT
124784 AAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (23 bp):
GAAAATAAGAATAACAAATAATT
Found at i:124766 original size:76 final size:76
Alignment explanation
Indices: 124686--124839 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
124676 ATGAATAAAC
*** *
124686 AAAATAATAATAACAAATAATAAAATAAATAAATAAACAAAGGCTTGGTGAAAAGAAAATAAGAA
1 AAAATAATAATAACAAATAATAAAATAAATAAATAAACAAAGGCGAAGCGAAAAGAAAATAAGAA
124751 TAAAAAAATTG
66 TAAAAAAATTG
*
124762 AAAATAATAATAACAAATAATTAAATAAATAAATAAACAAAGGCGAAGCGAAAAGAAAATAAGAA
1 AAAATAATAATAACAAATAATAAAATAAATAAATAAACAAAGGCGAAGCGAAAAGAAAATAAGAA
124827 TAAAAAAATTG
66 TAAAAAAATTG
124838 AA
1 AA
124840 TATAGCCACT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (76 bp):
AAAATAATAATAACAAATAATAAAATAAATAAATAAACAAAGGCGAAGCGAAAAGAAAATAAGAA
TAAAAAAATTG
Found at i:134614 original size:41 final size:41
Alignment explanation
Indices: 134520--134675 Score: 149
Period size: 41 Copynumber: 3.8 Consensus size: 41
134510 TATGAAATTC
* * **
134520 GAGATAGCTTCGACTAT-TAATGACACTTAGTGTGTGATTT
1 GAGATAGCTTCGGCTATATAATGGCACTTAGTGTGTGAGAT
*
134560 G-GAATAGCTTCGGCTATAT-ATGGCACTTAGTGTGCGAGACT
1 GAG-ATAGCTTCGGCTATATAATGGCACTTAGTGTGTGAGA-T
* *
134601 GAGATAGCTTCGGCTATCTAA-GTCACTTAGTGTGTGAGAT
1 GAGATAGCTTCGGCTATATAATGGCACTTAGTGTGTGAGAT
* * * * *
134641 TATAATAGCTTCAGCTATATGATGGCAATTAGTGT
1 GA-GATAGCTTCGGCTATATAATGGCACTTAGTGT
134676 ATGAAACATT
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.01
40 32 0.34
41 49 0.52
42 12 0.13
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (41 bp):
GAGATAGCTTCGGCTATATAATGGCACTTAGTGTGTGAGAT
Found at i:134628 original size:81 final size:83
Alignment explanation
Indices: 134520--134675 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 83
134510 TATGAAATTC
* * *
134520 GAGATAGCTTCGACTATTAATGACACTTAGTGTGTGA-TTTGGAATAGCTTCGGCTATAT-ATGG
1 GAGATAGCTTCGACTATTAATGACACTTAGTGTGTGAGATTAGAATAGCTTCAGCTATATGATGG
*
134583 CACTTAGTGTGCGAGACT
66 CAATTAGTGTGCGAGACT
* * *
134601 GAGATAGCTTCGGCTATCTAA-GTCACTTAGTGTGTGAGATTATAATAGCTTCAGCTATATGATG
1 GAGATAGCTTCGACTAT-TAATGACACTTAGTGTGTGAGATTAGAATAGCTTCAGCTATATGATG
134665 GCAATTAGTGT
65 GCAATTAGTGT
134676 ATGAAACATT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 31 0.48
82 21 0.32
83 13 0.20
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (83 bp):
GAGATAGCTTCGACTATTAATGACACTTAGTGTGTGAGATTAGAATAGCTTCAGCTATATGATGG
CAATTAGTGTGCGAGACT
Found at i:135361 original size:24 final size:22
Alignment explanation
Indices: 135334--135563 Score: 88
Period size: 22 Copynumber: 10.0 Consensus size: 22
135324 ATGTGGCTAT
135334 TTTTATATGTTATAATGCTGTCCA
1 TTTTA-ATG-TATAATGCTGTCCA
*
135358 TTTTAA-GCATATTGATGCTGTCCA
1 TTTTAATG--TA-TAATGCTGTCCA
* * *
135382 ATTTGATGTATAATGCTGTTCA
1 TTTTAATGTATAATGCTGTCCA
* * * *
135404 ATTTGA-GCATATTAAAGCTATCCA
1 TTTTAATG--TA-TAATGCTGTCCA
*
135428 ATTTAATGTATAATGCTGTCCA
1 TTTTAATGTATAATGCTGTCCA
* * *
135450 TTTTGA-GTATATTGATGTTGCCCA
1 TTTTAATGTATA---ATGCTGTCCA
* * * *
135474 ATTTGATGTATAACGTTGTCCA
1 TTTTAATGTATAATGCTGTCCA
* * * *
135496 TTTGAGTATATTGATGCTGTCCA
1 TTTTAATGTA-TAATGCTGTCCA
* * *
135519 ATTTGATGTATAATGTTGTCCA
1 TTTTAATGTATAATGCTGTCCA
* * *
135541 ATTTGATGTATAAATGTTGTCCA
1 TTTTAATGTAT-AATGCTGTCCA
135564 AAACAGCGTA
Statistics
Matches: 159, Mismatches: 34, Indels: 27
0.72 0.15 0.12
Matches are distributed among these distances:
21 6 0.04
22 65 0.41
23 34 0.21
24 47 0.30
25 7 0.04
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (22 bp):
TTTTAATGTATAATGCTGTCCA
Found at i:135397 original size:46 final size:46
Alignment explanation
Indices: 135344--135546 Score: 264
Period size: 46 Copynumber: 4.4 Consensus size: 46
135334 TTTTATATGT
*
135344 TATAATGCTGTCCATTTTAAGCATATTGATGCTGTCCAATTTGATG
1 TATAATGCTGTCCATTTTGAGCATATTGATGCTGTCCAATTTGATG
* * * * * *
135390 TATAATGCTGTTCAATTTGAGCATATTAAAGCTATCCAATTTAATG
1 TATAATGCTGTCCATTTTGAGCATATTGATGCTGTCCAATTTGATG
* * *
135436 TATAATGCTGTCCATTTTGAGTATATTGATGTTGCCCAATTTGATG
1 TATAATGCTGTCCATTTTGAGCATATTGATGCTGTCCAATTTGATG
* * *
135482 TATAACGTTGTCCA-TTTGAGTATATTGATGCTGTCCAATTTGATG
1 TATAATGCTGTCCATTTTGAGCATATTGATGCTGTCCAATTTGATG
* *
135527 TATAATGTTGTCCAATTTGA
1 TATAATGCTGTCCATTTTGA
135547 TGTATAAATG
Statistics
Matches: 135, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
45 42 0.31
46 93 0.69
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (46 bp):
TATAATGCTGTCCATTTTGAGCATATTGATGCTGTCCAATTTGATG
Found at i:135400 original size:22 final size:22
Alignment explanation
Indices: 135372--135564 Score: 169
Period size: 22 Copynumber: 8.5 Consensus size: 22
135362 AAGCATATTG
135372 ATGCTGTCCAATTTGATGTATA
1 ATGCTGTCCAATTTGATGTATA
*
135394 ATGCTGTTCAATTTGA-GCATATTA
1 ATGCTGTCCAATTTGATG--TA-TA
* * *
135418 AAGCTATCCAATTTAATGTATA
1 ATGCTGTCCAATTTGATGTATA
*
135440 ATGCTGTCCATTTTGA-GTATA
1 ATGCTGTCCAATTTGATGTATA
* *
135461 TTGATGTTGCCCAATTTGATGTATA
1 ---ATGCTGTCCAATTTGATGTATA
* *
135486 ACGTTGTCC-ATTTGA-GTATA
1 ATGCTGTCCAATTTGATGTATA
135506 TTGATGCTGTCCAATTTGATGTATA
1 ---ATGCTGTCCAATTTGATGTATA
*
135531 ATGTTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTAT-A
*
135554 ATGTTGTCCAA
1 ATGCTGTCCAA
135565 AACAGCGTAG
Statistics
Matches: 140, Mismatches: 17, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.04
21 12 0.09
22 56 0.40
23 23 0.16
24 33 0.24
25 11 0.08
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (22 bp):
ATGCTGTCCAATTTGATGTATA
Found at i:145614 original size:18 final size:18
Alignment explanation
Indices: 145591--145625 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
145581 TAAAAGGTCG
*
145591 ATTAAAATTTGGTTAAGT
1 ATTAAAATTTGATTAAGT
145609 ATTAAAATTTGATTAAG
1 ATTAAAATTTGATTAAG
145626 AAATTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (18 bp):
ATTAAAATTTGATTAAGT
Found at i:146694 original size:46 final size:45
Alignment explanation
Indices: 146626--146788 Score: 184
Period size: 45 Copynumber: 3.6 Consensus size: 45
146616 ACAGGAAATG
*
146626 CCATGGTTGAAAAATACCATGGCATTATACACAAAACGAGAAAGA
1 CCATAGTTGAAAAATACCATGGCATTATACACAAAACGAGAAAGA
* * *
146671 CCATGGTTGAAAAAATACCATGGCATTATACCCAAAATGAGAAAGA
1 CCATAGTTG-AAAAATACCATGGCATTATACACAAAACGAGAAAGA
* * * * * * *
146717 CCGTAGTTGAAAGATACTATGGCATTAAATACGAAAC-AAATAAGA
1 CCATAGTTGAAAAATACCATGGCATTATACACAAAACGAGA-AAGA
* *
146762 CCATAGTTGAAAGATACTATGGCATTA
1 CCATAGTTGAAAAATACCATGGCATTA
146789 CATCGATAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 2 0.02
45 60 0.58
46 41 0.40
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (45 bp):
CCATAGTTGAAAAATACCATGGCATTATACACAAAACGAGAAAGA
Found at i:146807 original size:45 final size:43
Alignment explanation
Indices: 146626--146827 Score: 154
Period size: 45 Copynumber: 4.5 Consensus size: 43
146616 ACAGGAAATG
* * * * *
146626 CCATGGTTGAAAAATACCATGGCATTATACA-CAAAACGAGAAAGA
1 CCATAGTTGAAAGATACTATGGCATTA-A-ATCGAAATGA-AAAGA
* * * ** *
146671 CCATGGTTGAAAAAATACCATGGCATTATACCCAAAATGAGAAAGA
1 CCATAGTTG-AAAGATACTATGGCATTA-AATCGAAATGA-AAAGA
* **
146717 CCGTAGTTGAAAGATACTATGGCATTAAATACGAAACAAATAAGA
1 CCATAGTTGAAAGATACTATGGCATTAAAT-CGAAATGAA-AAGA
*
146762 CCATAGTTGAAAGATACTATGGCATTACATCGATAATGAACAAGA
1 CCATAGTTGAAAGATACTATGGCATTAAATCGA-AATGAA-AAGA
**
146807 CCATAGTTTTAAGATACTATG
1 CCATAGTTGAAAGATACTATG
146828 ACACCACTTC
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
44 5 0.04
45 89 0.66
46 40 0.30
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (43 bp):
CCATAGTTGAAAGATACTATGGCATTAAATCGAAATGAAAAGA
Found at i:149043 original size:27 final size:27
Alignment explanation
Indices: 149005--149347 Score: 288
Period size: 27 Copynumber: 12.7 Consensus size: 27
148995 ATTTTACCAA
*
149005 CGGGGGTATTTCGGTCATTTTACCCTT
1 CGGGGGTATTTCGATCATTTTACCCTT
**
149032 CGGGGGTATTTCGGCCATTTTACCCTAT
1 CGGGGGTATTTCGATCATTTTACCCT-T
* ** * *
149060 -AGGGGTATTTTAATCATTTTATCATAT
1 CGGGGGTATTTCGATCATTTTACCCT-T
149087 --GGGGTATTTCGATCATTTTACCCTT
1 CGGGGGTATTTCGATCATTTTACCCTT
*
149112 CAGGGGTATTTC-AGTCATTTTACCAC-T
1 CGGGGGTATTTCGA-TCATTTTACC-CTT
** * *
149139 CAAGGGTATTTCGATCATTTTCCCCAT
1 CGGGGGTATTTCGATCATTTTACCCTT
*
149166 CGGGGGTATTTCGGTCATTTTA-CCTT
1 CGGGGGTATTTCGATCATTTTACCCTT
* * **
149192 ATGGGGGTATTTCAATCATTTTATCCAAT
1 -CGGGGGTATTTCGATCATTTTA-CCCTT
* *
149221 -GGTGGTATTTCGGTCATTTTACCCTT
1 CGGGGGTATTTCGATCATTTTACCCTT
* * *
149247 TGGGGCTATTTCGATCATTTTATCCC-G
1 CGGGGGTATTTCGATCATTTTA-CCCTT
* *
149274 CAGGGGTATTTCGATCATTTTACCCCT
1 CGGGGGTATTTCGATCATTTTACCCTT
** * * *
149301 CAAGGGCATTTTGATCATTTTACCTTT
1 CGGGGGTATTTCGATCATTTTACCCTT
*
149328 CTGGGGTATTTCGATCATTT
1 CGGGGGTATTTCGATCATTT
149348 ACGCATGAAT
Statistics
Matches: 257, Mismatches: 46, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.00
26 31 0.12
27 217 0.84
28 6 0.02
29 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (27 bp):
CGGGGGTATTTCGATCATTTTACCCTT
Found at i:149203 original size:81 final size:79
Alignment explanation
Indices: 148993--149347 Score: 317
Period size: 81 Copynumber: 4.4 Consensus size: 79
148983 GCTATAACAG
* * * * *
148993 TCATTTTA-CCAACGGGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCGGCCATTTTACC-
1 TCATTTTACCCATCGGGGGTATTTCGATCATTTTACCCTT-AGGGGTATTTCAGTCATTTTACCA
**
149056 CTATAGGGGTATTTTAA
65 CTA-A-GGGTATTTCGA
* **
149073 TCATTTTA-TCATATGGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCAGTCATTTTACCA
1 TCATTTTACCCATCGGGGGTATTTCGATCATTTTACCCTT-AGGGGTATTTCAGTCATTTTACCA
149137 CTCAAGGGTATTTCGA
65 CT-AAGGGTATTTCGA
* * *
149153 TCATTTTCCCCATCGGGGGTATTTCGGTCATTTTA-CCTTATGGGGGTATTTCAATCATTTTATC
1 TCATTTTACCCATCGGGGGTATTTCGATCATTTTACCCTTA--GGGGTATTTCAGTCATTTTA-C
* * *
149217 CAAT-GGTGGTATTTCGG
63 CACTAAG-GGTATTTCGA
* * * **
149234 TCATTTTACCCTTTGGGGCTATTTCGATCATTTTATCCCGCAGGGGTATTTC-GATCATTTTACC
1 TCATTTTACCCATCGGGGGTATTTCGATCATTTTA-CCCTTAGGGGTATTTCAG-TCATTTTACC
* * *
149298 CCTCAAGGGCATTTTGA
64 ACT-AAGGGTATTTCGA
** *
149315 TCATTTTACCTTTCTGGGGTATTTCGATCATTT
1 TCATTTTACCCATCGGGGGTATTTCGATCATTT
149348 ACGCATGAAT
Statistics
Matches: 226, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
79 1 0.00
80 79 0.35
81 137 0.61
82 6 0.03
83 3 0.01
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (79 bp):
TCATTTTACCCATCGGGGGTATTTCGATCATTTTACCCTTAGGGGTATTTCAGTCATTTTACCAC
TAAGGGTATTTCGA
Found at i:152450 original size:3 final size:3
Alignment explanation
Indices: 152442--153303 Score: 1706
Period size: 3 Copynumber: 287.3 Consensus size: 3
152432 TACTTTTCTG
* *
152442 TTC TTC TTC TTC TTC TTA TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152490 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152538 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152586 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152634 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152682 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152730 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152778 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152826 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152874 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152922 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
152970 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153018 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153066 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153114 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153162 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153210 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153258 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
153304 ATCATTAACC
Statistics
Matches: 855, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 855 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:161386 original size:15 final size:16
Alignment explanation
Indices: 161362--161403 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
161352 TTAAACTATA
161362 TAAAATTAAATAT-TAT
1 TAAAA-TAAATATGTAT
161378 TAAAATAAA-ATGTAT
1 TAAAATAAATATGTAT
161393 T-AAATAAATAT
1 TAAAATAAATAT
161404 AATGATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.38
15 10 0.42
16 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAATAAATATGTAT
Found at i:171210 original size:9 final size:9
Alignment explanation
Indices: 171185--171277 Score: 50
Period size: 9 Copynumber: 10.4 Consensus size: 9
171175 ATGTTTTGAA
*
171185 AAAAAATAT
1 AAAATATAT
171194 AAAA-ATAT
1 AAAATATAT
171202 AAAATATAT
1 AAAATATAT
* * *
171211 ATACATTTAC
1 A-AAATATAT
*
171221 AAAA-AAATT
1 AAAATATA-T
*
171230 GAAAATTTAT
1 -AAAATATAT
171240 -AAATATAT
1 AAAATATAT
171248 -AAATATAT
1 AAAATATAT
* *
171256 ATAATAAAT
1 AAAATATAT
*
171265 AAAATAAAT
1 AAAATATAT
171274 AAAA
1 AAAA
171278 ATTTATAGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
8 24 0.37
9 29 0.45
10 11 0.17
11 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAATATAT
Found at i:171243 original size:8 final size:8
Alignment explanation
Indices: 171232--171310 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
171222 AAAAAATTGA
171232 AAATTTAT
1 AAATTTAT
*
171240 AAATATAT
1 AAATTTAT
*
171248 AAATATAT
1 AAATTTAT
**
171256 ATAATAAAT
1 A-AATTTAT
**
171265 AAAATAAAT
1 -AAATTTAT
171274 AAAAATTTAT
1 -AA-ATTTAT
*
171284 AGATTTAT
1 AAATTTAT
*
171292 AGATTTAT
1 AAATTTAT
171300 AAATTTAT
1 AAATTTAT
171308 AAA
1 AAA
171311 AATATATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
8 40 0.65
9 17 0.27
10 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
AAATTTAT
Found at i:171279 original size:44 final size:44
Alignment explanation
Indices: 171186--171284 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
171176 TGTTTTGAAA
* * **
171186 AAAAATATAAAAATATAAAATATATATACATTTACAAAAAAATT
1 AAAAATTTATAAATATAAAATATATATACATAAACAAAAAAATT
* *
171230 GAAAATTTATAAATATATAAATATATATA-ATAAATAAAATAAA-T
1 AAAAATTTATAAATATA-AAATATATATACATAAACAAAA-AAATT
171274 AAAAATTTATA
1 AAAAATTTATA
171285 GATTTATAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 32 0.70
45 14 0.30
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (44 bp):
AAAAATTTATAAATATAAAATATATATACATAAACAAAAAAATT
Found at i:172781 original size:5 final size:5
Alignment explanation
Indices: 172771--172795 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
172761 AAATTACATG
172771 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
172796 CTACATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:174965 original size:29 final size:29
Alignment explanation
Indices: 174919--174976 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
174909 TCGTCCTTCC
174919 TTTTCCATTTTTAATAAATGGCCCAATAT
1 TTTTCCATTTTTAATAAATGGCCCAATAT
* **
174948 TTTTCCCTTTTTGCTAAATGGCCCAATAT
1 TTTTCCATTTTTAATAAATGGCCCAATAT
174977 GTTTATGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTTCCATTTTTAATAAATGGCCCAATAT
Found at i:176669 original size:5 final size:5
Alignment explanation
Indices: 176654--176704 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
176644 AAATTTAACG
* * * *
176654 TTCTT TCCTT TTCTT TTCTC TTCTT TTCTT GTCTT TTTTCT TTC-T TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT-T TTCTT TTCTT
176704 T
1 T
176705 CTTCTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 4 0.11
5 29 0.81
6 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (5 bp):
TTCTT
Found at i:176679 original size:15 final size:15
Alignment explanation
Indices: 176661--176712 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
176651 ACGTTCTTTC
176661 CTTTTCTTTTCTCTT
1 CTTTTCTTTTCTCTT
* *
176676 CTTTTCTTGTCTTTT
1 CTTTTCTTTTCTCTT
* *
176691 TTCTTTCTTTCTTTCTT
1 CT-TTTCTTT-TCTCTT
176708 CTTTT
1 CTTTT
176713 TTGTTCTGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 14 0.50
16 9 0.32
17 5 0.18
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (15 bp):
CTTTTCTTTTCTCTT
Found at i:176679 original size:20 final size:21
Alignment explanation
Indices: 176654--176712 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
176644 AAATTTAACG
176654 TTCTTTCCTTTTCTTTTCTC-
1 TTCTTTCCTTTTCTTTTCTCT
* * *
176674 TTCTTTTCTTGTCTTTTTTCT
1 TTCTTTCCTTTTCTTTTCTCT
*
176695 TTCTTTCTTTCTTCTTTT
1 TTCTTTCCTT-TTCTTTT
176713 TTGTTCTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 17 0.55
21 8 0.26
22 6 0.19
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (21 bp):
TTCTTTCCTTTTCTTTTCTCT
Found at i:176694 original size:12 final size:11
Alignment explanation
Indices: 176654--176714 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 11
176644 AAATTTAACG
176654 TTCTTTCCTTTT
1 TTCTTT-CTTTT
176666 CTT-TTCTCTTCTT
1 -TTCTT-TCTT-TT
176679 TTCTTGTCTTTT
1 TTCTT-TCTTTT
176691 TTCTTTCTTTCT
1 TTCTTTCTTT-T
176703 TTC-TTCTTTT
1 TTCTTTCTTTT
176713 TT
1 TT
176715 GTTCTGATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.07
11 11 0.26
12 18 0.42
13 11 0.26
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:182974 original size:20 final size:20
Alignment explanation
Indices: 182946--182994 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
182936 TTTTATCTTG
* *
182946 ATTTTATTTGATTTCAATCA
1 ATTTGATTTGATTTCAAACA
*
182966 ATTTGATTTGATTTTAAACA
1 ATTTGATTTGATTTCAAACA
*
182986 AATTGATTT
1 ATTTGATTT
182995 AATTGCTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (20 bp):
ATTTGATTTGATTTCAAACA
Found at i:183463 original size:22 final size:23
Alignment explanation
Indices: 183418--183466 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
183408 GATATTTTAA
*
183418 ATATAAATTATTTATTTTATTTT
1 ATATAAATTACTTATTTTATTTT
183441 ATATAAA-TACTTA-TTTATATTT
1 ATATAAATTACTTATTTTAT-TTT
183463 ATAT
1 ATAT
183467 TTGTTCGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATAAATTACTTATTTTATTTT
Found at i:184562 original size:52 final size:52
Alignment explanation
Indices: 184500--184605 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
184490 TTATGAATAG
184500 TTGTGTCCTTTGAAATATAGACATCTCTTTAATTTTATATTACAATATTTCT
1 TTGTGTCCTTTGAAATATAGACATCTCTTTAATTTTATATTACAATATTTCT
184552 TTGTGTCCTTTGAAATATAGACATCTCTTTAATTTTATATTACAATATTTCT
1 TTGTGTCCTTTGAAATATAGACATCTCTTTAATTTTATATTACAATATTTCT
184604 TT
1 TT
184606 CTTTTTTCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (52 bp):
TTGTGTCCTTTGAAATATAGACATCTCTTTAATTTTATATTACAATATTTCT
Found at i:184746 original size:21 final size:22
Alignment explanation
Indices: 184722--184765 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
184712 TACTTTATAT
184722 AATATATA-TAGTATATAATAA
1 AATATATATTAGTATATAATAA
* *
184743 AATATATATTATTATATATTAA
1 AATATATATTAGTATATAATAA
184765 A
1 A
184766 TAACAACAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATATTAGTATATAATAA
Found at i:186383 original size:7 final size:7
Alignment explanation
Indices: 186371--186396 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
186361 TAGAATTGAA
186371 ATTTTAT
1 ATTTTAT
186378 ATTTTAT
1 ATTTTAT
186385 ATTTTAT
1 ATTTTAT
186392 ATTTT
1 ATTTT
186397 TCTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTAT
Found at i:186519 original size:20 final size:21
Alignment explanation
Indices: 186472--186519 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
186462 TAGTTAAAGT
*
186472 TTTTTTTTTCTATTTTTTGAA
1 TTTTTTATTCTATTTTTTGAA
*
186493 TGTTTTATTC-ATTTTTTGAA
1 TTTTTTATTCTATTTTTTGAA
186513 TTTTTTA
1 TTTTTTA
186520 ATTTAGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTTATTCTATTTTTTGAA
Found at i:186643 original size:29 final size:28
Alignment explanation
Indices: 186611--186667 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
186601 TTGCAATTTC
* *
186611 TAGAATTTAAATACTTTTTTCATTTTTTA
1 TAGAATTTAAATA-TTATTTAATTTTTTA
* *
186640 TAGATTTTATATATTATTTAATTTTTTA
1 TAGAATTTAAATATTATTTAATTTTTTA
186668 AATTGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
TAGAATTTAAATATTATTTAATTTTTTA
Found at i:187771 original size:29 final size:29
Alignment explanation
Indices: 187725--187784 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
187715 GTTAATGATT
*
187725 TATAAAAATTAAATC-AAATTAAAATTTCA
1 TATAAAAATTAAATCAAAATCAAAA-TTCA
*
187754 TATATAAAATTACA-CAAAATCAAAATTCA
1 TATA-AAAATTAAATCAAAATCAAAATTCA
187783 TA
1 TA
187785 ATTGTGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (29 bp):
TATAAAAATTAAATCAAAATCAAAATTCA
Found at i:188097 original size:43 final size:42
Alignment explanation
Indices: 188032--188294 Score: 339
Period size: 43 Copynumber: 6.1 Consensus size: 42
188022 CGCTATTATC
* *
188032 AACGCTGCTATAGATCATGACCTTTAGCGGCGCTTTTCCTACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCC-ACA
*
188075 AACGCCGCTATAGATCAAGACCTTTAGCGGCTCTTTCTCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTT-TCCACA
188118 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACA
* **
188161 AACGCCGCTATAGATCAAGACCTTTAGAGGCATTTTTTCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGC-GCTTTTCCACA
* * **
188204 AACGCCGCTATAGCTCGAGACCTTTAGCAACGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACA
* * * *
188247 AACGCCGCTATAGAACAA-ACCTTTAGCGACGCTTCTCGCAAA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTC-CACA
188289 AACGCC
1 AACGCC
188295 ACTAAAAACA
Statistics
Matches: 195, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 30 0.15
43 157 0.81
44 7 0.04
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (42 bp):
AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACA
Found at i:188177 original size:86 final size:86
Alignment explanation
Indices: 188032--188274 Score: 373
Period size: 86 Copynumber: 2.8 Consensus size: 86
188022 CGCTATTATC
* * *
188032 AACGCTGCTATAGATCATGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAGATCAAGACC
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
188097 TTTAGCGGC-TCTTTCTCCACA
66 TTTAGCGGCAT-TTTCTCCACA
188118 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
* *
188183 TTTAGAGGCATTTTTTCCACA
66 TTTAGCGGCATTTTCTCCACA
* * ** *
188204 AACGCCGCTATAGCTCGAGACCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGAACAA-ACC
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
188268 TTTAGCG
66 TTTAGCG
188275 ACGCTTCTCG
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
85 9 0.06
86 135 0.93
87 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (86 bp):
AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
TTTAGCGGCATTTTCTCCACA
Found at i:190755 original size:48 final size:49
Alignment explanation
Indices: 190699--190798 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
190689 GAAAGTGACT
* *
190699 TCAAAATTGATCCTATA-TTCATCATTTGTTATCTCCAATGCATTGAGG
1 TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
* *
190747 TCAAAATTGATCCTATATTTGATCTTTTGCTATCTCCAAGGCATTGAGG
1 TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
190796 TCA
1 TCA
190799 TTTCAATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 17 0.36
49 30 0.64
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (49 bp):
TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
Found at i:195867 original size:41 final size:40
Alignment explanation
Indices: 195822--195923 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
195812 TGATTCAGTA
195822 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
195863 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
195904 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
195924 AGCGCTAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 2 0.04
41 51 0.93
42 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:195938 original size:41 final size:41
Alignment explanation
Indices: 195822--195938 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
195812 TGATTCAGTA
* * * * *
195822 CACCGGCACTTAGCCTGCTAGACA-TATAGTCTGAAATATTT
1 CACCGGCAATAAGCCTGCTAGACACTA-AGCCTGAAGTGTTT
* * * *
195863 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
*
195904 CACCGGCAATAAGCCTGCTA-AGCGCTAAGCCTGAA
1 CACCGGCAATAAGCCTGCTAGA-CACTAAGCCTGAA
195939 AATCTCAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
Found at i:199129 original size:19 final size:19
Alignment explanation
Indices: 199105--199153 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
199095 TAAAATTATA
199105 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
199125 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
199144 ATTTTTATTT
1 ATTTTTATTT
199154 GTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:199558 original size:43 final size:43
Alignment explanation
Indices: 199504--199586 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
199494 CTAATTAATC
* ** *
199504 TAAAACCTAAACCTTTAACCCATATCCCCTAAACCCTAAATTA
1 TAAAACATAAACCCCTAACCCATAACCCCTAAACCCTAAATTA
* * *
199547 TAAAACATAAACCCCTAACCCCTAACCCTTAAACCTTAAA
1 TAAAACATAAACCCCTAACCCATAACCCCTAAACCCTAAA
199587 CCCCAACCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (43 bp):
TAAAACATAAACCCCTAACCCATAACCCCTAAACCCTAAATTA
Found at i:199599 original size:21 final size:22
Alignment explanation
Indices: 199563--199630 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 22
199553 ATAAACCCCT
*
199563 AACCCCTAACCCTTAAACCTTA
1 AACCCCTAACCCTTAAACCATA
*
199585 AACCCC-AACCTTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
* * *
199606 AA-CCATAAACCATAAACCATA
1 AACCCCTAACCCTTAAACCATA
199627 AACC
1 AACC
199631 ATAAACCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 2 0.05
21 29 0.76
22 7 0.18
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:199607 original size:7 final size:7
Alignment explanation
Indices: 199597--199653 Score: 96
Period size: 7 Copynumber: 8.1 Consensus size: 7
199587 CCCCAACCTT
199597 TAAACCA
1 TAAACCA
199604 TAAACCA
1 TAAACCA
199611 TAAACCA
1 TAAACCA
199618 TAAACCA
1 TAAACCA
199625 TAAACCA
1 TAAACCA
199632 TAAACCA
1 TAAACCA
* *
199639 TAATCCC
1 TAAACCA
199646 TAAACCA
1 TAAACCA
199653 T
1 T
199654 CGGAGTAACC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:200449 original size:14 final size:14
Alignment explanation
Indices: 200417--200465 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
200407 AATGGTATCA
*
200417 CCTAAACCTAAAAC
1 CCTAAACCAAAAAC
* * * *
200431 TCTAAATCATATAC
1 CCTAAACCAAAAAC
200445 CCTAAACCAAAAAC
1 CCTAAACCAAAAAC
200459 CCTAAAC
1 CCTAAAC
200466 TACAGTGATA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCAAAAAC
Found at i:200692 original size:40 final size:41
Alignment explanation
Indices: 200648--200724 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
200638 TTAAATCCCT
* * *
200648 GAGCATTAGTGGCACTTT-TTAGAAAACGCCGCTAAAAAAA
1 GAGCATTAGCGGCACTTTCTCAAAAAACGCCGCTAAAAAAA
* *
200688 GAGCATTAGCGGCGCTTTCTCAAAAAATGCCGCTAAA
1 GAGCATTAGCGGCACTTTCTCAAAAAACGCCGCTAAA
200725 GCCTTGAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 16 0.52
41 15 0.48
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCGGCACTTTCTCAAAAAACGCCGCTAAAAAAA
Found at i:200738 original size:42 final size:41
Alignment explanation
Indices: 200688--200808 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 41
200678 GCTAAAAAAA
* * **
200688 GAGCATTAGCGGCGCTTTCTCAAAAAATGCCGCTAAAGCCTT
1 GAGCATTAGCGGCGCTTCCTC-AAAAACGCCGCTAAAGCCCC
* * *
200730 GAGCATTAGCGGCGCCTCCTCAGAAACGCCACTAAAGCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
* *
200771 AAGCATTAGCGACGCTTCCTCAAAAACGCCGCTAAAGC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGC
200809 TCGCCTCCTC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 48 0.72
42 19 0.28
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
Found at i:200855 original size:68 final size:68
Alignment explanation
Indices: 200742--200874 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 68
200732 GCATTAGCGG
*
200742 CGCCTCCTCAGAAACGCCACTAAAGCCCCAAGCATTAGCGACGCTTC-CTCAAAAACGCCGCTAA
1 CGCCTCCTCAAAAACGCCACTAAAGCCCCAAGCATTAGCGACGCTTCTC-CAAAAACGCCGCTAA
200806 AGCT
65 AGCT
* * * * * * *
200810 CGCCTCCTCAAAAATGTCGCTATAGCCCCGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAA
1 CGCCTCCTCAAAAACGCCACTAAAGCCCCAAGCATTAGCGACGCTTCTCCAAAAACGCCGCTAAA
200875 TCCCTAGCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 55 0.98
69 1 0.02
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.17
Consensus pattern (68 bp):
CGCCTCCTCAAAAACGCCACTAAAGCCCCAAGCATTAGCGACGCTTCTCCAAAAACGCCGCTAAA
GCT
Found at i:200874 original size:109 final size:108
Alignment explanation
Indices: 200710--200914 Score: 250
Period size: 109 Copynumber: 1.9 Consensus size: 108
200700 CGCTTTCTCA
** *
200710 AAAAATGCCGCTAAAGCCTTGAGCATTAGCGGCGCCTCCTCAGAAACGCCACTAAAGCCCCAAGC
1 AAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCGCCTCCTCAAAAACGCCACTAAA-CCCCAAGC
*
200775 ATTAGCGACGCTTCCTCAAAAACGCCGCTAAAGCTCGCCTCCTC
65 ATTAGCGACGCTTCATCAAAAACGCCGCTAAAGCTCGCCTCCTC
* * ** * * *
200819 AAAAATGTCGCTATAGCCCCGAGCATTAGCGGCG-CTTTTCCAAAAACGCCGCTAAATCCCTAGC
1 AAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCGCCTCCT-CAAAAACGCCACTAAACCCCAAGC
* * * *
200883 ATTAGCGGCGCTTTATTAAAACCGCCGCTAAA
65 ATTAGCGACGCTTCATCAAAAACGCCGCTAAA
200915 TCCCTGAAAC
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
108 36 0.45
109 44 0.55
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (108 bp):
AAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCGCCTCCTCAAAAACGCCACTAAACCCCAAGCA
TTAGCGACGCTTCATCAAAAACGCCGCTAAAGCTCGCCTCCTC
Found at i:200890 original size:40 final size:40
Alignment explanation
Indices: 200840--200919 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
200830 TATAGCCCCG
200840 AGCATTAGCGGCGCTTT-TCCAAAAACGCCGCTAAATCCCT
1 AGCATTAGCGGCGCTTTAT-CAAAAACGCCGCTAAATCCCT
* *
200880 AGCATTAGCGGCGCTTTATTAAAACCGCCGCTAAATCCCT
1 AGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAATCCCT
200920 GAAACCTCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (40 bp):
AGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAATCCCT
Found at i:207620 original size:16 final size:16
Alignment explanation
Indices: 207599--207633 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
207589 AACTTAAACC
207599 ACCCGATAGATTTCGA
1 ACCCGATAGATTTCGA
207615 ACCCGATAGATTTCGA
1 ACCCGATAGATTTCGA
207631 ACC
1 ACC
207634 AATTCGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (16 bp):
ACCCGATAGATTTCGA
Found at i:207702 original size:3 final size:3
Alignment explanation
Indices: 207694--207737 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
207684 GGTGAGGTGG
207694 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
207738 ATAGTGGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:209563 original size:11 final size:11
Alignment explanation
Indices: 209547--209612 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
209537 TCCGCCTTGT
209547 TTTTTAAATAA
1 TTTTTAAATAA
209558 TTTTT-AAT--
1 TTTTTAAATAA
209566 TTTTTAAATAA
1 TTTTTAAATAA
*
209577 ATTTT--ATAA
1 TTTTTAAATAA
209586 TTTTCT--ATAA
1 TTTT-TAAATAA
*
209596 ATTTTAAATAA
1 TTTTTAAATAA
209607 TTTTTA
1 TTTTTA
209613 TTCTTTTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 5 0.11
9 11 0.24
10 11 0.24
11 18 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAATAA
Found at i:209570 original size:19 final size:21
Alignment explanation
Indices: 209546--209611 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 21
209536 TTCCGCCTTG
209546 TTTTTTAAAT-AATTTT-TAA
1 TTTTTTAAATAAATTTTATAA
209565 TTTTTTAAATAAATTTTATAA
1 TTTTTTAAATAAATTTTATAA
*
209586 TTTTCT--ATAAATTTTAAATAA
1 TTTTTTAAATAAATTTT--ATAA
209607 TTTTT
1 TTTTT
209612 ATTCTTTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 19 0.46
20 6 0.15
21 16 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAAATAAATTTTATAA
Found at i:209579 original size:20 final size:20
Alignment explanation
Indices: 209546--209611 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
209536 TTCCGCCTTG
209546 TTTTTTAAATAATTTT-TAA
1 TTTTTTAAATAATTTTATAA
209565 TTTTTTAAATAAATTTTATAA
1 TTTTTTAAAT-AATTTTATAA
* *
209586 TTTTCTATA-AATTTTAAATAA
1 TTTTTTAAATAATTTT--ATAA
209607 TTTTT
1 TTTTT
209612 ATTCTTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 16 0.40
20 6 0.15
21 18 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAATAATTTTATAA
Found at i:209608 original size:10 final size:10
Alignment explanation
Indices: 209548--209610 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
209538 CCGCCTTGTT
209548 TTTTAAATAA
1 TTTTAAATAA
* *
209558 TTTTTAAT-T
1 TTTTAAATAA
209567 TTTTAAATAAA
1 TTTTAAAT-AA
209578 TTTT--ATAA
1 TTTTAAATAA
**
209586 TTTTCTATAAA
1 TTTTAAAT-AA
209597 TTTTAAATAA
1 TTTTAAATAA
209607 TTTT
1 TTTT
209611 TATTCTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
8 6 0.14
9 9 0.21
10 15 0.36
11 12 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:209992 original size:29 final size:30
Alignment explanation
Indices: 209923--209993 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
209913 CGAATATAAT
*
209923 AAATATATTTTTTTAATTTTATTAATTTTA
1 AAATAAATTTTTTTAATTTTATTAATTTTA
* * *
209953 AAAT-ACTTTTTTATTATTTT-TTATTTTTA
1 AAATAAATTTTTT-TAATTTTATTAATTTTA
209982 AAATAAATTTTT
1 AAATAAATTTTT
209994 GGTGTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
AAATAAATTTTTTTAATTTTATTAATTTTA
Found at i:212126 original size:21 final size:22
Alignment explanation
Indices: 212096--212138 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
212086 GTGCTTTCTA
*
212096 TAAAATGAGC-TAGAACATATT
1 TAAAAGGAGCATAGAACATATT
212117 TAAAAGGAGCTATAGAACATAT
1 TAAAAGGAGC-ATAGAACATAT
212139 GTAGATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (22 bp):
TAAAAGGAGCATAGAACATATT
Found at i:217022 original size:32 final size:32
Alignment explanation
Indices: 216980--217055 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
216970 AAAATAAATT
* *
216980 ATGAAAAGTTACGAATGTGAAAAGACTTGAAT
1 ATGAAAAGTTACGAATGCGAAAAGACTTGAAG
** *
217012 AT-AAAGAGTTAATAATGCGAAGAGACTTGAAG
1 ATGAAA-AGTTACGAATGCGAAAAGACTTGAAG
217044 ATGAAAAGTTAC
1 ATGAAAAGTTAC
217056 ACACATGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 3 0.08
32 30 0.83
33 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (32 bp):
ATGAAAAGTTACGAATGCGAAAAGACTTGAAG
Found at i:217146 original size:37 final size:38
Alignment explanation
Indices: 217064--217151 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 38
217054 ACACACATGC
* * *
217064 ATGAATAGTCACAACTCCTATAGTATTTAAGTTATGTAA
1 ATGAATAGTCACAACTCC-ATAGCATTTAAGTGATATAA
*
217103 ATGAATAGTCACAACTCC-TAGCATTT-AGTGATATAG
1 ATGAATAGTCACAACTCCATAGCATTTAAGTGATATAA
217139 ATAGAATAGTCAC
1 AT-GAATAGTCAC
217152 TTACAACTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 9 0.20
37 17 0.39
39 18 0.41
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (38 bp):
ATGAATAGTCACAACTCCATAGCATTTAAGTGATATAA
Found at i:221664 original size:36 final size:39
Alignment explanation
Indices: 221578--221664 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
221568 ACACGCATGC
* * *
221578 ATGAATAGTCACAACTCCTATAGTATTTAAGTTATGTAA
1 ATGAATAGTCACAACTCCTATAGCATTTAAGTGATATAA
*
221617 ATGAATAGTCACAACTCCTA-A-CATTT-AGTGATATAG
1 ATGAATAGTCACAACTCCTATAGCATTTAAGTGATATAA
221653 ATGAATAGTCAC
1 ATGAATAGTCAC
221665 TTACAACTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 19 0.43
37 4 0.09
38 1 0.02
39 20 0.45
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (39 bp):
ATGAATAGTCACAACTCCTATAGCATTTAAGTGATATAA
Found at i:223355 original size:26 final size:26
Alignment explanation
Indices: 223325--223374 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
223315 TTCAAATTGT
223325 TAAATATACGTTACATGAAATGAAAC
1 TAAATATACGTTACATGAAATGAAAC
223351 TAAATATACGTTACATGAAATGAA
1 TAAATATACGTTACATGAAATGAA
223375 CATAGCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (26 bp):
TAAATATACGTTACATGAAATGAAAC
Found at i:227696 original size:126 final size:126
Alignment explanation
Indices: 227548--227844 Score: 443
Period size: 126 Copynumber: 2.4 Consensus size: 126
227538 AGTGTTAATT
* * * *
227548 TAAAA-AAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATATCGAGAAG
* * ** *
227612 ACGTTTCTGAGTAAATAGTGTCAAAAACGCTTTAAGCGGGATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAATAC
* * * *
227673 TGAAAGAAGCTCCCATGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATATCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATATCGAGAAG
*
227738 ATGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAATAC
66 ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAATAC
* *
227799 TAAAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCACCTG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
227845 TTTGGCCTGA
Statistics
Matches: 152, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
125 4 0.03
126 148 0.97
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATATCGAGAAG
ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAATAC
Found at i:231379 original size:18 final size:18
Alignment explanation
Indices: 231353--231395 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
231343 GACTAGAAAA
* * *
231353 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
231371 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
231389 AGGATAC
1 AGGATAC
231396 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:233864 original size:30 final size:30
Alignment explanation
Indices: 233828--233891 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
233818 AAAAAAAAAT
*
233828 TCTCAAATTTCTCCCTAAATTTCTTAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
*
233858 TCTCAAATTTCTCCTTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
233888 TCTC
1 TCTC
233892 TTTAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (30 bp):
TCTCAAATTTCTCCCTAAATTTCTCAAAGC
Found at i:237364 original size:126 final size:126
Alignment explanation
Indices: 237138--237409 Score: 377
Period size: 126 Copynumber: 2.2 Consensus size: 126
237128 TAAGGCCAAA
* * *
237138 CAGGAACTACTGTAGAAAAGGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
1 CAGGAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTATCATCAATTTTGCTGACAATGC
* * ** *
237203 ATCTTGCTTGAAGTGTTTTTGACACTATTTATTCAGAACCGTC-TTCTTAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTATTCAGAAAAGTCTTTC-CAAAATTATTTTTT
* * * *
237264 TAGGAACTATTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTATCAGT-AATTTTGCTGACAGTG
1 CAGGAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTATCA-TCAATTTTGCTGACAATG
*
237328 CATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAAGTCTTTCCAAAATTATTTTTT
65 CATCCTGCTTGAAGCGTTTTTGACACTATTTATTCAGAAAAGTCTTTCCAAAATTATTTTTT
* *
237390 CAGAAACTAGTATAGAAAAA
1 CAGGAACTACTATAGAAAAA
237410 AACCAAAATC
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
126 124 0.97
127 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (126 bp):
CAGGAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTATCATCAATTTTGCTGACAATGC
ATCCTGCTTGAAGCGTTTTTGACACTATTTATTCAGAAAAGTCTTTCCAAAATTATTTTTT
Found at i:238512 original size:58 final size:58
Alignment explanation
Indices: 238450--238562 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
238440 GGATTTGGAT
*
238450 TTTCCCTACTTACCAAGCTTCTCTCTTGTACCTCTTCTTTTGCTTATATAAATATAAC
1 TTTCCCTACGTACCAAGCTTCTCTCTTGTACCTCTTCTTTTGCTTATATAAATATAAC
*
238508 TTTCCCTACGTACCGAGCTTCTCTCTTGTACCTCTTCTTTTGCTTATATAAATAT
1 TTTCCCTACGTACCAAGCTTCTCTCTTGTACCTCTTCTTTTGCTTATATAAATAT
238563 TACATATATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.45
Consensus pattern (58 bp):
TTTCCCTACGTACCAAGCTTCTCTCTTGTACCTCTTCTTTTGCTTATATAAATATAAC
Found at i:247174 original size:15 final size:14
Alignment explanation
Indices: 247150--247179 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
247140 TTGTAATAAC
247150 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
247164 AAAAGAAAAAAGAAA
1 AAAA-AAAAAAGAAA
247179 A
1 A
247180 CAGGGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:248430 original size:93 final size:93
Alignment explanation
Indices: 248271--248456 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
248261 TTTTTTATAT
248271 TTTCAAATATGTTTTGAAAGTGTTTGTTATTCTATAAGTTCTCTCATTTATTTATTCTTTTAGGA
1 TTTCAAATATGTTTTGAAAGTGTTTGTTATTCTATAAGTTCTCTCATTTATTTATTCTTTTAGGA
248336 ATTTGGTTAAATTTTAAATTAAAAATAA
66 ATTTGGTTAAATTTTAAATTAAAAATAA
*
248364 TTTCAAATATGTTTTGAAAGTTTTTGTTATTCTATAAGTTCTCTCATTTATTTATTCTTTTAGGA
1 TTTCAAATATGTTTTGAAAGTGTTTGTTATTCTATAAGTTCTCTCATTTATTTATTCTTTTAGGA
248429 ATTTGGTTAAATTTTAAATTAAAAATAA
66 ATTTGGTTAAATTTTAAATTAAAAATAA
248457 ATTTTAAGAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.51
Consensus pattern (93 bp):
TTTCAAATATGTTTTGAAAGTGTTTGTTATTCTATAAGTTCTCTCATTTATTTATTCTTTTAGGA
ATTTGGTTAAATTTTAAATTAAAAATAA
Done.