Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 202 of 226
Found at i:63902780 original size:18 final size:17
Alignment explanation
Indices: 63902757--63902824 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
63902747 TGAGGTGCCG
63902757 TATTTTTATATTTTTATA
1 TATTTTTATATTTTTA-A
* *
63902775 TATTTTTTAAAATTTTAA
1 TA-TTTTTATATTTTTAA
63902793 TAATTTTTATATATTTTAA
1 T-ATTTTTATAT-TTTTAA
*
63902812 TATTTTAATATTT
1 TATTTTTATATTT
63902825 GTATATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.05
18 20 0.48
19 20 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTATATTTTTAA
Found at i:63902803 original size:27 final size:26
Alignment explanation
Indices: 63902758--63902833 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
63902748 GAGGTGCCGT
*
63902758 ATTTTTATATTTTTATATATTTTTTAAA
1 ATTTTAATATTTTTATATA--TTTTAAA
*
63902786 ATTTTAATAATTTTTATATATTTTAAT
1 ATTTTAAT-ATTTTTATATATTTTAAA
*
63902813 ATTTTAATATTTGTATATATT
1 ATTTTAATATTTTTATATATT
63902834 ATAATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 12 0.27
27 14 0.32
28 7 0.16
29 11 0.25
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
ATTTTAATATTTTTATATATTTTAAA
Found at i:63902851 original size:16 final size:17
Alignment explanation
Indices: 63902759--63902856 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 17
63902749 AGGTGCCGTA
*
63902759 TTTTTATATTTTTATATAT
1 TTTTTATATATTT-T-TAT
* *
63902778 TTTTTA-AAATTTTAATAA
1 TTTTTATATATTTT--TAT
*
63902796 TTTTTATATATTTTAAT
1 TTTTTATATATTTTTAT
* *
63902813 ATTTTA-ATATTTGTAT
1 TTTTTATATATTTTTAT
* *
63902829 ATATTATA-ATTTTTAT
1 TTTTTATATATTTTTAT
63902845 TTTTTATCATAT
1 TTTTTAT-ATAT
63902857 ATCACAATTA
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
16 25 0.41
17 9 0.15
18 15 0.25
19 12 0.20
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (17 bp):
TTTTTATATATTTTTAT
Found at i:63902856 original size:26 final size:26
Alignment explanation
Indices: 63902760--63902858 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
63902750 GGTGCCGTAT
* * * *
63902760 TTTTATATTTTTATATATTTTTTAAAA
1 TTTTA-ATATTTATATATATTATAATA
* *
63902787 TTTTAATAATTTTTATATATTTTAATA
1 TTTTAAT-ATTTATATATATTATAATA
*
63902814 TTTTAATATTTGTATATATTATAAT-
1 TTTTAATATTTATATATATTATAATA
* *
63902839 TTTTATTTTTTATCATATAT
1 TTTTAATATTTAT-ATATAT
63902859 CACAATTACA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.16
26 24 0.39
27 27 0.44
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTAATATTTATATATATTATAATA
Found at i:63905558 original size:26 final size:26
Alignment explanation
Indices: 63905498--63905558 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
63905488 TGGTAAGATA
*
63905498 AAATTTAAAATTTCTTTATTTTTAAT
1 AAATTTAAAATTTATTTATTTTTAAT
* *
63905524 -TATGTTAAAATTTATTTATTTTTGAT
1 AAAT-TTAAAATTTATTTATTTTTAAT
*
63905550 AAATCTAAA
1 AAATTTAAA
63905559 TAGTTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 2 0.07
26 24 0.86
27 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
AAATTTAAAATTTATTTATTTTTAAT
Found at i:63907121 original size:11 final size:11
Alignment explanation
Indices: 63907107--63907153 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
63907097 CTTTTTCAGT
63907107 TTTTTTATTTG
1 TTTTTTATTTG
*
63907118 TTTTTTATTAG
1 TTTTTTATTTG
*
63907129 -TTTTAATTTG
1 TTTTTTATTTG
*
63907139 TTTATTATTTG
1 TTTTTTATTTG
63907150 TTTT
1 TTTT
63907154 ATAATATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.77
Consensus pattern (11 bp):
TTTTTTATTTG
Found at i:63907132 original size:21 final size:21
Alignment explanation
Indices: 63907108--63907154 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
63907098 TTTTTCAGTT
* *
63907108 TTTTTATTTGTTTTTTATTAG
1 TTTTAATTTGTTTATTATTAG
*
63907129 TTTTAATTTGTTTATTATTTG
1 TTTTAATTTGTTTATTATTAG
63907150 TTTTA
1 TTTTA
63907155 TAATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (21 bp):
TTTTAATTTGTTTATTATTAG
Found at i:63907958 original size:15 final size:16
Alignment explanation
Indices: 63907938--63907968 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
63907928 ATGTTTGAAA
63907938 TGTAAAAT-TATATTT
1 TGTAAAATATATATTT
63907953 TGTAAAATATATATTT
1 TGTAAAATATATATTT
63907969 GGAATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TGTAAAATATATATTT
Found at i:63911995 original size:24 final size:24
Alignment explanation
Indices: 63911963--63912010 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
63911953 ATTAATAATT
*
63911963 ATTAAATTAAATTATTGAACCTAA
1 ATTAAATTAAATTATGGAACCTAA
63911987 ATTAAATTAAATTATGGAACCTAA
1 ATTAAATTAAATTATGGAACCTAA
63912011 GTAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (24 bp):
ATTAAATTAAATTATGGAACCTAA
Found at i:63936095 original size:112 final size:114
Alignment explanation
Indices: 63935954--63936189 Score: 404
Period size: 112 Copynumber: 2.1 Consensus size: 114
63935944 CTGCTTCTTG
63935954 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTC-AAAGGTAAAATGGTAA
1 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAAGGTAAAATGGTAA
*
63936018 AAAGATACCAAAAAC-AAAAAGAATGAACCATGGATTTAACCCCTTGGT
66 AAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
63936066 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAGGAAAGGTAAAATG
1 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTC--A--AAAGGTAAAATG
63936131 GTAAAAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
62 GTAAAAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
*
63936184 TTTTAT
1 ATTTAT
63936190 GGCCACTCTT
Statistics
Matches: 116, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
112 48 0.41
117 31 0.27
118 37 0.32
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (114 bp):
ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAAGGTAAAATGGTAA
AAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
Found at i:63942046 original size:12 final size:13
Alignment explanation
Indices: 63942029--63942058 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
63942019 TTATTTAACA
63942029 TTAATAT-AAATT
1 TTAATATAAAATT
63942041 TTAATATAAAATT
1 TTAATATAAAATT
63942054 TTAAT
1 TTAAT
63942059 TTATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATATAAAATT
Found at i:63942091 original size:28 final size:26
Alignment explanation
Indices: 63942047--63942102 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
63942037 AATTTTAATA
*
63942047 TAAAATTTTAATTTATTATTATATTTTT
1 TAAAATTTTAATATATT-TT-TATTTTT
63942075 TAAAATATTT-ATATATTTTTATTTTT
1 TAAAAT-TTTAATATATTTTTATTTTT
63942101 TA
1 TA
63942103 GAAGTAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
27 2 0.08
28 12 0.46
29 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TAAAATTTTAATATATTTTTATTTTT
Found at i:63943096 original size:9 final size:9
Alignment explanation
Indices: 63943082--63943121 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
63943072 GTAGTGATTC
*
63943082 AATTCGGTT
1 AATTCGGGT
63943091 AATTCGGGT
1 AATTCGGGT
63943100 AATTCGGGT
1 AATTCGGGT
*
63943109 AATTCGGTT
1 AATTCGGGT
63943118 AATT
1 AATT
63943122 TTTAACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:63945947 original size:22 final size:22
Alignment explanation
Indices: 63945912--63945953 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
63945902 AGAATATAAA
*
63945912 TTATAATTCATAATTATTTTTT
1 TTATAATTCATAATGATTTTTT
**
63945934 TTATAATTTTTAATGATTTT
1 TTATAATTCATAATGATTTT
63945954 ACAAAATCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATAATTCATAATGATTTTTT
Found at i:63946530 original size:51 final size:51
Alignment explanation
Indices: 63946461--63946605 Score: 177
Period size: 51 Copynumber: 2.8 Consensus size: 51
63946451 GATACCGGTT
* * *
63946461 CACATAGCAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
* * * * *
63946512 CACGTAGTAGCCTGCACATAATACTACACACGTGATCGA--AGCTATCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATA
*
63946563 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
63946606 TTCACTTTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
50 3 0.04
51 72 0.92
52 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
Found at i:63946620 original size:51 final size:50
Alignment explanation
Indices: 63946461--63946631 Score: 157
Period size: 51 Copynumber: 3.4 Consensus size: 50
63946451 GATACCGGTT
* *
63946461 CACATAGCAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATCC-ATA
* * * * **
63946512 CACGTAGTAGCCTGCACATAATACTACACACGTGATCGA--AGCTATCTGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGA-CCATCA-CTATC-CATA
* * * * *
63946563 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTTCACTTT
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATC-CATA
*
63946614 CACATAGTGGCCTACACA
1 CACATAGTAGCCTACACA
63946632 CAGTCCGTGC
Statistics
Matches: 95, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
50 3 0.03
51 89 0.94
52 3 0.03
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATCCATA
Found at i:63952009 original size:22 final size:23
Alignment explanation
Indices: 63951972--63952014 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
63951962 AGTAACCGTT
63951972 GTGCCAAGAAAGAGAC-AAAGTC
1 GTGCCAAGAAAGAGACTAAAGTC
63951994 GTGCCAAG-AAGCAGACTAAAG
1 GTGCCAAGAAAG-AGACTAAAG
63952015 CATTACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.44, C:0.19, G:0.28, T:0.09
Consensus pattern (23 bp):
GTGCCAAGAAAGAGACTAAAGTC
Found at i:63953489 original size:14 final size:14
Alignment explanation
Indices: 63953467--63953517 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
63953457 TATACAATAT
63953467 ATAAAAATATTCTC
1 ATAAAAATATTCTC
* *
63953481 ATAATAATA-T-TG
1 ATAAAAATATTCTC
*
63953493 ATAAAAATACTCTC
1 ATAAAAATATTCTC
*
63953507 ATAATAATATT
1 ATAAAAATATT
63953518 TTTTACTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 18 0.62
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (14 bp):
ATAAAAATATTCTC
Found at i:63953496 original size:26 final size:26
Alignment explanation
Indices: 63953467--63953517 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
63953457 TATACAATAT
*
63953467 ATAAAAATATTCTCATAATAATATTG
1 ATAAAAATACTCTCATAATAATATTG
63953493 ATAAAAATACTCTCATAATAATATT
1 ATAAAAATACTCTCATAATAATATT
63953518 TTTTACTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAAAAATACTCTCATAATAATATTG
Found at i:63953670 original size:23 final size:23
Alignment explanation
Indices: 63953644--63953690 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
63953634 TAATTACTTG
63953644 TAATATCAACTCCGTCAGAGATT
1 TAATATCAACTCCGTCAGAGATT
63953667 TAATATCAACTCCGTCAGAGATT
1 TAATATCAACTCCGTCAGAGATT
63953690 T
1 T
63953691 TAAGTAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (23 bp):
TAATATCAACTCCGTCAGAGATT
Found at i:63954820 original size:56 final size:56
Alignment explanation
Indices: 63954751--63954871 Score: 161
Period size: 56 Copynumber: 2.2 Consensus size: 56
63954741 GTGTCCATGC
* * * * *
63954751 CCGTGTGAATATACTGACTTGGGACACATGGCCAAGCCACACGCCCATGTGCTAAG
1 CCGTGTGAGTATACTGACTTAGGACACATAGCCAAACCACACACCCATGTGCTAAG
* * * *
63954807 CCGTGTGAGTATACTGCCTTAGGTCATATAGCCAAACCACACACCCGTGTGCTAAG
1 CCGTGTGAGTATACTGACTTAGGACACATAGCCAAACCACACACCCATGTGCTAAG
63954863 CCGTGTGAG
1 CCGTGTGAG
63954872 CAATTTGAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (56 bp):
CCGTGTGAGTATACTGACTTAGGACACATAGCCAAACCACACACCCATGTGCTAAG
Found at i:63962352 original size:56 final size:56
Alignment explanation
Indices: 63962290--63962401 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
63962280 CCAATATGAA
* * *
63962290 TATACTGACTTGGGACACACGACCAAGCCACACGCCCGTGTGCTAAGCCGTGTGAG
1 TATACTGACTTAGGACACACGACCAAACCACACACCCGTGTGCTAAGCCGTGTGAG
** * *
63962346 TATACTGACTTAGTTCACACGGCCAAACCACACACCCGTGTGCTAAGCCGTTTGAG
1 TATACTGACTTAGGACACACGACCAAACCACACACCCGTGTGCTAAGCCGTGTGAG
63962402 CAATTTAAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (56 bp):
TATACTGACTTAGGACACACGACCAAACCACACACCCGTGTGCTAAGCCGTGTGAG
Found at i:63965690 original size:30 final size:30
Alignment explanation
Indices: 63965656--63965717 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
63965646 GTCCAACAAT
63965656 AATTAA-ATAAACAATTAAAACATTTA-TAAA
1 AATTAATATAAA-AATTAAAA-ATTTATTAAA
*
63965686 AATTAATATAAAATTTAAAAATTTATTAAA
1 AATTAATATAAAAATTAAAAATTTATTAAA
63965716 AA
1 AA
63965718 ATGTATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.17
30 19 0.66
31 5 0.17
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
AATTAATATAAAAATTAAAAATTTATTAAA
Found at i:63967090 original size:17 final size:17
Alignment explanation
Indices: 63967065--63967114 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
63967055 TTTAGGGTTT
*
63967065 TTAGGTTTAAGGTTTTG
1 TTAGTTTTAAGGTTTTG
* *
63967082 TTAGTTTTAGGGTTTAG
1 TTAGTTTTAAGGTTTTG
*
63967099 GT-GTTTTAAGGTTTTG
1 TTAGTTTTAAGGTTTTG
63967115 GGTATTTTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.54
Consensus pattern (17 bp):
TTAGTTTTAAGGTTTTG
Found at i:63967191 original size:17 final size:17
Alignment explanation
Indices: 63967161--63967216 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
63967151 GTTTTAAGGG
63967161 TTTTATAGGTTTAGGGAT
1 TTTTAT-GGTTTAGGGAT
*
63967179 TTTTATGGTTTAGGGCT
1 TTTTATGGTTTAGGGAT
* *
63967196 CCTTATAGGGTTTAGGGAT
1 --TTTTATGGTTTAGGGAT
63967215 TT
1 TT
63967217 GAGATAGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.38
18 6 0.19
19 14 0.44
ACGTcount: A:0.18, C:0.05, G:0.29, T:0.48
Consensus pattern (17 bp):
TTTTATGGTTTAGGGAT
Found at i:63968479 original size:21 final size:21
Alignment explanation
Indices: 63968424--63968480 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
63968414 TAAAATAGGC
63968424 CACATGGTC-GTGTGAATGGGT
1 CACATGG-CAGTGTGAATGGGT
* * *
63968445 TAGATGGCTA-TGTGGATGGGT
1 CACATGGC-AGTGTGAATGGGT
63968466 CACATGGCAGTGTGA
1 CACATGGCAGTGTGA
63968481 GCAAACTGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.21, C:0.12, G:0.39, T:0.28
Consensus pattern (21 bp):
CACATGGCAGTGTGAATGGGT
Found at i:63981361 original size:44 final size:43
Alignment explanation
Indices: 63981210--63981379 Score: 181
Period size: 43 Copynumber: 4.0 Consensus size: 43
63981200 AACTTGTACA
* * *
63981210 ATGCCATCGTCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATA-CG
* *
63981253 ATGCC-ACTGTCCCAGACAAGGTCTTACACG-AAATCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAATCAAATACG
*
63981295 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATA-G
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAA--TCAAATACG
* *
63981339 ATGCCAACGTCTCAGA-AGTGGTCTTACACGT-AATCACATAC
1 ATGCCAACGTCCCAGACA-TGGTCTTACACGTAAATCAAATAC
63981380 CGGAATCCTA
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
41 6 0.06
42 29 0.27
43 39 0.36
44 28 0.26
45 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATACG
Found at i:63987771 original size:8 final size:8
Alignment explanation
Indices: 63987754--63987789 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
63987744 TTTTTAGTTC
63987754 AAAAAAAG
1 AAAAAAAG
*
63987762 AAAGAAAG
1 AAAAAAAG
63987770 AAAAAAAG
1 AAAAAAAG
*
63987778 AAAAGAAG
1 AAAAAAAG
63987786 AAAA
1 AAAA
63987790 GATGATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:63987841 original size:18 final size:21
Alignment explanation
Indices: 63987794--63987845 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
63987784 AGAAAAGATG
63987794 ATAATTATTAATATATAATTAT
1 ATAATTA-TAATATATAATTAT
63987816 ATACATTATAATATATATATTA-
1 ATA-ATTATAATATATA-ATTAT
*
63987838 ATTATTAT
1 ATAATTAT
63987846 CAACTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 14 0.52
23 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTATAATATATAATTAT
Found at i:63988435 original size:25 final size:25
Alignment explanation
Indices: 63988399--63988459 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
63988389 CTCCTAAATT
* *
63988399 TTAATTTAATTATCTAATTTTTTA-A
1 TTAATTAAATTAT-TAATATTTTATA
*
63988424 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
63988449 TTAATTAAATT
1 TTAATTAAATT
63988460 TTTGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:63991556 original size:14 final size:14
Alignment explanation
Indices: 63991537--63991563 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63991527 TTGGTCTAGT
63991537 TGAACTGAACCGAG
1 TGAACTGAACCGAG
63991551 TGAACTGAACCGA
1 TGAACTGAACCGA
63991564 CCAAGAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:63998632 original size:24 final size:23
Alignment explanation
Indices: 63998605--63998659 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
63998595 ATGAAACAAT
63998605 ACATTTTAAGAAAAGCTCAAATTC
1 ACATTTTAA-AAAAGCTCAAATTC
** *
63998629 ACATTTTTAATCAGGCTCAAATTC
1 ACA-TTTTAAAAAAGCTCAAATTC
63998653 ACATTTT
1 ACATTTT
63998660 TAATCAGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.63
25 6 0.22
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ACATTTTAAAAAAGCTCAAATTC
Found at i:63998660 original size:24 final size:24
Alignment explanation
Indices: 63998619--63998667 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
63998609 TTTAAGAAAA
63998619 GCTCAAATTCACATTTTTAATCAG
1 GCTCAAATTCACATTTTTAATCAG
63998643 GCTCAAATTCACATTTTTAATCAG
1 GCTCAAATTCACATTTTTAATCAG
63998667 G
1 G
63998668 TAAAGATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (24 bp):
GCTCAAATTCACATTTTTAATCAG
Found at i:64001661 original size:4 final size:4
Alignment explanation
Indices: 64001652--64001723 Score: 137
Period size: 4 Copynumber: 18.2 Consensus size: 4
64001642 ATCTAAGCCC
64001652 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
64001700 CATA CATA CATA CATA C-TA CATA C
1 CATA CATA CATA CATA CATA CATA C
64001724 TTATTCCTCC
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 3 0.04
4 64 0.96
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:64002133 original size:42 final size:42
Alignment explanation
Indices: 64002086--64002173 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
64002076 ATCTAATTCA
64002086 AACTCAAATTAAAATCAATTCACATATAAATTTCATGCCAAT
1 AACTCAAATTAAAATCAATTCACATATAAATTTCATGCCAAT
64002128 AACTCAAATTAAAATCAATTCACATATAAATTTCATGCCAAT
1 AACTCAAATTAAAATCAATTCACATATAAATTTCATGCCAAT
64002170 AACT
1 AACT
64002174 TTCTAATACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (42 bp):
AACTCAAATTAAAATCAATTCACATATAAATTTCATGCCAAT
Found at i:64005842 original size:20 final size:21
Alignment explanation
Indices: 64005795--64005845 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
64005785 GTATCATGGT
64005795 CTTTGCTT-CTTCTTTACTTA
1 CTTTGCTTACTTCTTTACTTA
* *
64005815 CTCT-CTTACTTGTTTACTTA
1 CTTTGCTTACTTCTTTACTTA
64005835 -TTTGCTTACTT
1 CTTTGCTTACTT
64005846 AAATAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.59
Consensus pattern (21 bp):
CTTTGCTTACTTCTTTACTTA
Found at i:64008309 original size:58 final size:60
Alignment explanation
Indices: 64008244--64008361 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 60
64008234 ATCACTTTAA
* *
64008244 TATTAAATTAATATAACACTTATC-A-AGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAACACTTATCTATAGATAAATATTAAATTAAATTTAATATTAAATC
* * *
64008302 TATTAAATTAATAGAATATTTATCTTATATAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAATTAATAGAACACTTATC---TATAGATAAATATTAAATTAAATTTAATATTAA
64008362 GATGATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
58 21 0.42
62 1 0.02
63 28 0.56
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAATTAATAGAACACTTATCTATAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:64008843 original size:10 final size:10
Alignment explanation
Indices: 64008828--64008856 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
64008818 AAAAATATCA
64008828 AATTAATTTT
1 AATTAATTTT
64008838 AATTAATTTT
1 AATTAATTTT
64008848 AATTAATTT
1 AATTAATTT
64008857 GACTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTAATTTT
Found at i:64009228 original size:49 final size:49
Alignment explanation
Indices: 64009169--64009262 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
64009159 CAATTTACTT
*
64009169 ATTGAAAACTCCTTATTGTATACTCTTTACGAAAAAAATTCATCCCATG
1 ATTGAAAACTCCTTACTGTATACTCTTTACGAAAAAAATTCATCCCATG
*
64009218 ATTGAAAACTCCTTACTGTATACTCTTTACGAAAATAATTCATCC
1 ATTGAAAACTCCTTACTGTATACTCTTTACGAAAAAAATTCATCC
64009263 ATCTGTTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (49 bp):
ATTGAAAACTCCTTACTGTATACTCTTTACGAAAAAAATTCATCCCATG
Found at i:64010949 original size:16 final size:16
Alignment explanation
Indices: 64010928--64010959 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
64010918 TAAAATGTTA
64010928 ACTTGGAAATATGATT
1 ACTTGGAAATATGATT
64010944 ACTTGGAAATATGATT
1 ACTTGGAAATATGATT
64010960 TATTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
ACTTGGAAATATGATT
Found at i:64013017 original size:25 final size:25
Alignment explanation
Indices: 64012979--64013068 Score: 101
Period size: 25 Copynumber: 3.6 Consensus size: 25
64012969 GACTCACCAA
**
64012979 AAAGGCTTCCCAAGTAAATTGCCAC
1 AAAGGCTTTACAAGTAAATTGCCAC
* *
64013004 AAAGGCTTTACAAGTGACTTGCCAC
1 AAAGGCTTTACAAGTAAATTGCCAC
* *
64013029 AAAGGCTTCT-GAAGTAAATCGCCAC
1 AAAGGCTT-TACAAGTAAATTGCCAC
*
64013054 AAAGGCTTTATAAGT
1 AAAGGCTTTACAAGT
64013069 GACTCGTGTA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.96
26 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (25 bp):
AAAGGCTTTACAAGTAAATTGCCAC
Found at i:64016179 original size:16 final size:16
Alignment explanation
Indices: 64016158--64016189 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64016148 GGCAATACCC
*
64016158 TGGGCGTACTCTTTCT
1 TGGGCGTAATCTTTCT
64016174 TGGGCGTAATCTTTCT
1 TGGGCGTAATCTTTCT
64016190 CTGCTTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.22, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGCGTAATCTTTCT
Found at i:64016554 original size:13 final size:13
Alignment explanation
Indices: 64016536--64016560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64016526 CAATTAGATG
64016536 ATATTGTTAATTC
1 ATATTGTTAATTC
64016549 ATATTGTTAATT
1 ATATTGTTAATT
64016561 TAAACATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATATTGTTAATTC
Found at i:64022935 original size:22 final size:21
Alignment explanation
Indices: 64022905--64023024 Score: 105
Period size: 22 Copynumber: 5.5 Consensus size: 21
64022895 TACACCATAC
*
64022905 TAGAAAGCACCATAGTGCTAAA
1 TAGAGAGCACCA-AGTGCTAAA
64022927 TAGAGAGCACCAAAGTGCTAAA
1 TAGAGAGCACC-AAGTGCTAAA
* * * *
64022949 TAGAGAGCACTAAAATGCCAAG
1 TAGAGAGCAC-CAAGTGCTAAA
**
64022971 TAGAGAGCACCGAAGTGCTGGA
1 TAGAGAGCACC-AAGTGCTAAA
* *
64022993 TAGAGAGCATCGAAGTGCTAGA
1 TAGAGAGCA-CCAAGTGCTAAA
*
64023015 CAGAGAGCAC
1 TAGAGAGCAC
64023025 TAAAGTGTTG
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
21 1 0.01
22 77 0.96
23 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (21 bp):
TAGAGAGCACCAAGTGCTAAA
Found at i:64023030 original size:22 final size:22
Alignment explanation
Indices: 64022918--64023031 Score: 113
Period size: 22 Copynumber: 5.2 Consensus size: 22
64022908 AAAGCACCAT
*
64022918 AGTGCTAAATAGAGAGCACCAA
1 AGTGCTAAATAGAGAGCACTAA
64022940 AGTGCTAAATAGAGAGCACTAA
1 AGTGCTAAATAGAGAGCACTAA
* * * **
64022962 AATGCCAAGTAGAGAGCACCGA
1 AGTGCTAAATAGAGAGCACTAA
** *
64022984 AGTGCTGGATAGAGAGCA-TCGA
1 AGTGCTAAATAGAGAGCACT-AA
* *
64023006 AGTGCTAGACAGAGAGCACTAA
1 AGTGCTAAATAGAGAGCACTAA
64023028 AGTG
1 AGTG
64023032 TTGAATCCAT
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 74 0.99
23 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (22 bp):
AGTGCTAAATAGAGAGCACTAA
Found at i:64024033 original size:11 final size:11
Alignment explanation
Indices: 64024005--64024036 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
64023995 TATTAATTTA
64024005 TTATAATTAAC
1 TTATAATTAAC
64024016 -T-TAATTAAC
1 TTATAATTAAC
64024025 TTATAATTAAC
1 TTATAATTAAC
64024036 T
1 T
64024037 AAACTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATAATTAAC
Found at i:64026315 original size:20 final size:20
Alignment explanation
Indices: 64026290--64026328 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
64026280 GGGCCCTCAC
*
64026290 GCCTGTGTGTGCCCGTGTGT
1 GCCTGTGTGTACCCGTGTGT
64026310 GCCTGTGTGTACCCGTGTG
1 GCCTGTGTGTACCCGTGTG
64026329 GCCCACACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.03, C:0.26, G:0.38, T:0.33
Consensus pattern (20 bp):
GCCTGTGTGTACCCGTGTGT
Found at i:64026316 original size:8 final size:10
Alignment explanation
Indices: 64026294--64026332 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
64026284 CCTCACGCCT
64026294 GTGTGTGCCC
1 GTGTGTGCCC
*
64026304 GTGTGTGCCT
1 GTGTGTGCCC
*
64026314 GTGTGTACCC
1 GTGTGTGCCC
64026324 GTGTG-GCCC
1 GTGTGTGCCC
64026333 ACACTGCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 3 0.12
10 22 0.88
ACGTcount: A:0.03, C:0.28, G:0.38, T:0.31
Consensus pattern (10 bp):
GTGTGTGCCC
Found at i:64028954 original size:41 final size:39
Alignment explanation
Indices: 64028902--64029010 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 39
64028892 ACTTCGAGTT
* **
64028902 GATGAGACACTGGGTGTTAATTTATTACTTCAGATTAATTC
1 GATGAGACACTGGGTGTCAA-TTATTACTTCAGATT-AGCC
* * *
64028943 GATGAGGCACTGGGTGCCAA-T-TTACTTCAGCTTAGCC
1 GATGAGACACTGGGTGTCAATTATTACTTCAGATTAGCC
64028980 GATGAGACACTGGGTGTCAACTTATTACTTC
1 GATGAGACACTGGGTGTCAA-TTATTACTTC
64029011 GAATCATCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
37 20 0.35
38 11 0.19
39 2 0.04
40 7 0.12
41 17 0.30
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAATTATTACTTCAGATTAGCC
Found at i:64029788 original size:21 final size:21
Alignment explanation
Indices: 64029764--64029803 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
64029754 CTAGGTTGAT
*
64029764 TATTTTAACATGTTTTGAAGG
1 TATTTGAACATGTTTTGAAGG
* *
64029785 TATTTGATCGTGTTTTGAA
1 TATTTGAACATGTTTTGAA
64029804 TTGGTTGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (21 bp):
TATTTGAACATGTTTTGAAGG
Found at i:64037333 original size:39 final size:39
Alignment explanation
Indices: 64037289--64037367 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
64037279 AGAAAATTTC
* *
64037289 AAATCAAGTTAGGATGATAAAATATGATTCGTCAACTCG
1 AAATCAAGTTAGGATAATAAAATAGGATTCGTCAACTCG
*
64037328 AAATCATGTTAGGATAATAAAATAGGATTCGTCAACTCG
1 AAATCAAGTTAGGATAATAAAATAGGATTCGTCAACTCG
64037367 A
1 A
64037368 TTAATTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (39 bp):
AAATCAAGTTAGGATAATAAAATAGGATTCGTCAACTCG
Found at i:64041309 original size:36 final size:36
Alignment explanation
Indices: 64041259--64041327 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
64041249 CAAAGGCTAC
64041259 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
* * *
64041295 AATTAGAAGTTGTATACAATTGGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
64041328 TTAAATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
Found at i:64046426 original size:36 final size:36
Alignment explanation
Indices: 64046374--64046442 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
64046364 CAAAGGCTAC
64046374 AATTAAAAGTTATATACAATTAGAACTCTAAGACAT
1 AATTAAAAGTTATATACAATTAGAACTCTAAGACAT
* * *
64046410 AATTAGAAGTTGTATACAATTGGAACTCTAAGA
1 AATTAAAAGTTATATACAATTAGAACTCTAAGA
64046443 TTAAATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (36 bp):
AATTAAAAGTTATATACAATTAGAACTCTAAGACAT
Found at i:64050737 original size:82 final size:82
Alignment explanation
Indices: 64050600--64050764 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
64050590 CACTCAAGTC
*
64050600 TCCCATGTAAAAGCACTTATTTTCAAAGTTTATGGTGGTGTTATAAGTTGCAATTGTTGCATCTT
1 TCCCATGTAAAAGCACTTATTTTCAAAGTTTATAGTGGTGTTATAAGTTGCAATTGTTGCATCTT
64050665 ACTTAGTAACAAAGATG
66 ACTTAGTAACAAAGATG
*
64050682 TCCCATGTAAAAGCACTTATTTTCAAAGTTTATAGTGGTGTTATATGTTGCAATTGTTGCATCTT
1 TCCCATGTAAAAGCACTTATTTTCAAAGTTTATAGTGGTGTTATAAGTTGCAATTGTTGCATCTT
64050747 ACTTAGTAACAAAGATG
66 ACTTAGTAACAAAGATG
64050764 T
1 T
64050765 TAGAGATTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (82 bp):
TCCCATGTAAAAGCACTTATTTTCAAAGTTTATAGTGGTGTTATAAGTTGCAATTGTTGCATCTT
ACTTAGTAACAAAGATG
Found at i:64051927 original size:21 final size:21
Alignment explanation
Indices: 64051903--64051945 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
64051893 TAGTTTTTTC
64051903 CCCTAAAAATTTTCCCCAAAT
1 CCCTAAAAATTTTCCCCAAAT
* ***
64051924 CCCTTATTTTTTTCCCCAAAT
1 CCCTAAAAATTTTCCCCAAAT
64051945 C
1 C
64051946 AAAATCCCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (21 bp):
CCCTAAAAATTTTCCCCAAAT
Found at i:64056833 original size:43 final size:43
Alignment explanation
Indices: 64056750--64056834 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
64056740 TTTGATATGG
*
64056750 TCTTTAGCAGCGCTTCTACTAAAAACACCGCTATAGAACATGA
1 TCTTTAGCAGCGCTTCTACTAAAAACACCGCTAAAGAACATGA
** ** * * *
64056793 TCTTTAGTGGCGCTTCTTGTAAAAATACTGCTAAATAACATG
1 TCTTTAGCAGCGCTTCTACTAAAAACACCGCTAAAGAACATG
64056835 CTTCTCATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (43 bp):
TCTTTAGCAGCGCTTCTACTAAAAACACCGCTAAAGAACATGA
Found at i:64056967 original size:43 final size:43
Alignment explanation
Indices: 64056852--64056968 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
64056842 TAAAAACGAT
* * *
64056852 GCTAAAGATCATGTTCCTTAGCGGCGTTTGTAGGAGAAGCGCC
1 GCTAAAGATCATGTTCTTTAGCGGCGTTTTTAGGAGAAGCACC
*
64056895 GCTAAAGATCATGTTCTTTAGCGGCGTTTTTAGGAGAATCACC
1 GCTAAAGATCATGTTCTTTAGCGGCGTTTTTAGGAGAAGCACC
* * *
64056938 GCTAAAGGTCATGTTCTTTAACGGTGTTTTT
1 GCTAAAGATCATGTTCTTTAGCGGCGTTTTT
64056969 CCACATAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
GCTAAAGATCATGTTCTTTAGCGGCGTTTTTAGGAGAAGCACC
Found at i:64059828 original size:11 final size:11
Alignment explanation
Indices: 64059814--64059857 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
64059804 AGATAAATAT
64059814 TATTTTATTAA
1 TATTTTATTAA
*
64059825 TATTTTAATGATA
1 TATTTT-ATTA-A
*
64059838 TATTTTATTAT
1 TATTTTATTAA
64059849 TATTTTATT
1 TATTTTATT
64059858 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:64062828 original size:17 final size:17
Alignment explanation
Indices: 64062806--64062848 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
64062796 TTAGATTATC
64062806 GGAAGCTTGATTGGGTT
1 GGAAGCTTGATTGGGTT
64062823 GGAAGCTTGATTGGGTT
1 GGAAGCTTGATTGGGTT
64062840 GGAAGCTTG
1 GGAAGCTTG
64062849 TCGGAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.19, C:0.07, G:0.42, T:0.33
Consensus pattern (17 bp):
GGAAGCTTGATTGGGTT
Found at i:64074668 original size:43 final size:43
Alignment explanation
Indices: 64074621--64074765 Score: 209
Period size: 43 Copynumber: 3.3 Consensus size: 43
64074611 ATCCAAAGTT
* *
64074621 TTATGTAAGTTATGATATGATTTATAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
*
64074664 TTATGTAAGTTATAATATGATATATATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGT-A-TTATGTAAG
* * *
64074709 TAATGTAATTTATGATATGATATATATTTATGTATAATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
*
64074752 TTCTGTAAGTTATG
1 TTATGTAAGTTATG
64074766 TAAGTTATGA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
43 49 0.54
44 2 0.02
45 39 0.43
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (43 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
Found at i:64074669 original size:9 final size:9
Alignment explanation
Indices: 64074646--64074774 Score: 81
Period size: 9 Copynumber: 14.8 Consensus size: 9
64074636 TATGATTTAT
64074646 AGTTATGT-
1 AGTTATGTA
64074654 A-TTATGTA
1 AGTTATGTA
64074662 AGTTATGTA
1 AGTTATGTA
*
64074671 AGTTATAATA
1 AGTTAT-GTA
* * *
64074681 TGATATAT-
1 AGTTATGTA
*
64074689 ATTTATGTA
1 AGTTATGTA
64074698 AGTTATGTA
1 AGTTATGTA
*
64074707 AGTAATGTA
1 AGTTATGTA
*
64074716 ATTTATGATA
1 AGTTATG-TA
* * *
64074726 TGATATAT-
1 AGTTATGTA
*
64074734 ATTTATGT-
1 AGTTATGTA
*
64074742 A-TAATGTA
1 AGTTATGTA
*
64074750 AGTTCTGTA
1 AGTTATGTA
64074759 AGTTATGTA
1 AGTTATGTA
64074768 AGTTATG
1 AGTTATG
64074775 ATCCAAAGTT
Statistics
Matches: 91, Mismatches: 23, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
7 11 0.12
8 12 0.13
9 57 0.63
10 11 0.12
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.47
Consensus pattern (9 bp):
AGTTATGTA
Found at i:64074705 original size:52 final size:51
Alignment explanation
Indices: 64074645--64074773 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 51
64074635 ATATGATTTA
64074645 TAGTTATGTATTATGTAAGTTATGTAAGTTATAATATGATATATATTTATG
1 TAGTTATGTATTATGTAAGTTATGTAAGTTATAATATGATATATATTTATG
* * *
64074696 TA---A-G--TTATGTAAGTAATGTAATTTATGATATGATATATATTTATG
1 TAGTTATGTATTATGTAAGTTATGTAAGTTATAATATGATATATATTTATG
* *
64074741 TA-TAATGTAAGTTCTGTAAGTTATGTAAGTTAT
1 TAGTTATGT-A-TTATGTAAGTTATGTAAGTTAT
64074774 GATCCAAAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
45 40 0.62
47 2 0.03
48 2 0.03
51 2 0.03
52 19 0.29
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (51 bp):
TAGTTATGTATTATGTAAGTTATGTAAGTTATAATATGATATATATTTATG
Found at i:64074864 original size:53 final size:54
Alignment explanation
Indices: 64074755--64074869 Score: 205
Period size: 53 Copynumber: 2.1 Consensus size: 54
64074745 ATGTAAGTTC
* *
64074755 TGTAAGTTATGTAAGTTATGATCCAAAGTTTTTTTTTTATTTTTTAAATGTTTA
1 TGTAAGTTATGTAAATTATGATCCAAAGTTTTTTTTTTATTCTTTAAATGTTTA
64074809 TGTAAGTTATGTAAATTATGATCCAAAG-TTTTTTTTTATTCTTTAAATGTTTA
1 TGTAAGTTATGTAAATTATGATCCAAAGTTTTTTTTTTATTCTTTAAATGTTTA
64074862 TGTAAGTT
1 TGTAAGTT
64074870 TTGATTATCA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 32 0.54
54 27 0.46
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.54
Consensus pattern (54 bp):
TGTAAGTTATGTAAATTATGATCCAAAGTTTTTTTTTTATTCTTTAAATGTTTA
Found at i:64074899 original size:13 final size:13
Alignment explanation
Indices: 64074881--64074907 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64074871 TGATTATCAT
64074881 CTTTAAATTTTAA
1 CTTTAAATTTTAA
64074894 CTTTAAATTTTAA
1 CTTTAAATTTTAA
64074907 C
1 C
64074908 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:64075360 original size:35 final size:35
Alignment explanation
Indices: 64075318--64075389 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
64075308 AATTCTATGA
64075318 AAATTTAAACTTTA-AAACTAAATATAA-AAATTAAT
1 AAATTTAAA-TTTAGAAACTAAA-ATAATAAATTAAT
**
64075353 AAATTTAAATTTAGAATTTAAAATAATAAATTAAT
1 AAATTTAAATTTAGAAACTAAAATAATAAATTAAT
64075388 AA
1 AA
64075390 CACAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (35 bp):
AAATTTAAATTTAGAAACTAAAATAATAAATTAAT
Found at i:64075942 original size:72 final size:71
Alignment explanation
Indices: 64075861--64076078 Score: 201
Period size: 71 Copynumber: 3.1 Consensus size: 71
64075851 AAATGGTTCC
* * * *
64075861 ACTTAATATCAGAAGTCAATAAGTTGAACTAAATTAAACTTTTTAAAAATTCATAATTGAACAAA
1 ACTTAATATCA-AACTCAATAAATTGAACTAAATTAAACTTTTTAAAAATTCATAATTAAATAAA
*
64075926 CGTTTTT
65 CGATTTT
* ** * * * *
64075933 ACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGC-TTCTGAAAATGT-ATAACTAAATAA
1 ACTTAATATCAAA-CTCAATAAATTGAACTAAATTAAACTTTTTAAAAAT-TCATAATTAAATAA
* *
64075996 ACGGTTTC
64 ACGATTTT
* * **
64076004 GC-TAATATCAAAACTTAATAAATTGAACTAAATT-AACATTTTTAAAAACACATAATTAAATAA
1 ACTTAATATC-AAACTCAATAAATTGAACTAAATTAAAC-TTTTTAAAAATTCATAATTAAATAA
64076067 ACGATTTT
64 ACGATTTT
64076075 ACTT
1 ACTT
64076079 GATAATTAAT
Statistics
Matches: 113, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
69 2 0.02
70 24 0.21
71 54 0.48
72 33 0.29
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (71 bp):
ACTTAATATCAAACTCAATAAATTGAACTAAATTAAACTTTTTAAAAATTCATAATTAAATAAAC
GATTTT
Found at i:64078894 original size:25 final size:25
Alignment explanation
Indices: 64078860--64078907 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
64078850 GGATAGGATT
64078860 TTGTTAAATGAAATGAA-AAAAATAA
1 TTGTTAAATGAAAT-AATAAAAATAA
64078885 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
64078908 TGAGCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:64079382 original size:41 final size:40
Alignment explanation
Indices: 64079297--64079383 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
64079287 CTTTGCGGTG
* * * *
64079297 TTTTTCTCATAGCACCGCTAATGCTTAACCTTTTACGGTG
1 TTTTTCTCATAGAACCGCTAATGCTTAACCTATTACGATA
* *
64079337 TTTTTCTCATA-AACGCTGCTACTGCTTTACCTATTACGATA
1 TTTTTCTCATAGAAC-C-GCTAATGCTTAACCTATTACGATA
64079378 TTTTTC
1 TTTTTC
64079384 CGTTAGCGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.05
40 12 0.31
41 25 0.64
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (40 bp):
TTTTTCTCATAGAACCGCTAATGCTTAACCTATTACGATA
Found at i:64081130 original size:3 final size:3
Alignment explanation
Indices: 64081117--64081151 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
64081107 AAATTAGTTA
*
64081117 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
64081152 AAAGGATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64086938 original size:283 final size:284
Alignment explanation
Indices: 64086426--64086978 Score: 1036
Period size: 283 Copynumber: 2.0 Consensus size: 284
64086416 ATCAAGATAC
*
64086426 TCCCTTTTGCTCTTGTAACATCTGGGTCATGCGATGTTCGAATTGAGTTTGCAACTTTTTCATCT
1 TCCCTTTTGCTCTTGTAACATCTGGGTCATGCGATGTTCGAATTGAGTTTGCAACTTTTTCATAT
* *
64086491 CTTTTTGTAACAACTCGACCAAAGGATCATTCTCTCTTTTTTGCTCATCCTCTTCATTTTTACTA
66 CTTTTAGTAACAACTCGACCAAAGGATCATTCTCTCTTTTTTGCTCATCCTCTTCAGTTTTACTA
*
64086556 GTTTGGGATCTAGTGATTGGCATGGTATCTGTGAAAAAATCACACAAACAAGAACAAGAAAGAAA
131 GTTTGGGATCTAGTGATCGGCATGGTATCTGTGAAAAAATCACACAAACAAGAACAAGAAAGAAA
64086621 AAATAATAATAACCTCACTCGTTAGCTCTCAAAAGAATAACTCTCTGAATGATTCAAAACTTGTA
196 AAATAATAATAACCTCACTCGTTAGCTCTCAAAAGAATAACTCTCTGAATGATTCAAAACTTGTA
64086686 AATATGTTTGGAGAGGGTTACTAA
261 AATATGTTTGGAGAGGGTTACTAA
64086710 TCCC-TTTGCTCTTGTAACATCTGGGTCATGCGATGTTCGAATTGAGTTTGCAACTTTTTCATAT
1 TCCCTTTTGCTCTTGTAACATCTGGGTCATGCGATGTTCGAATTGAGTTTGCAACTTTTTCATAT
*
64086774 CTTTTAGTAACAACTCGACCAAAGGATCGTTCTCTCTTTTTTGCTCATCCTCTTCAGTTTTACTA
66 CTTTTAGTAACAACTCGACCAAAGGATCATTCTCTCTTTTTTGCTCATCCTCTTCAGTTTTACTA
*
64086839 GTTTGGGATCTAGTGATCGGCATGGTATCTGTGAAAAAATCACACAAACAGGAACAAGAAAGAAA
131 GTTTGGGATCTAGTGATCGGCATGGTATCTGTGAAAAAATCACACAAACAAGAACAAGAAAGAAA
*
64086904 AAATAATAATAACCTCACTCGTTAGCTCTCAAAAGAATAACTCTCTGAATGATTCAGAACTTGTA
196 AAATAATAATAACCTCACTCGTTAGCTCTCAAAAGAATAACTCTCTGAATGATTCAAAACTTGTA
64086969 AATATGTTTG
261 AATATGTTTG
64086979 TAAAGTGTTT
Statistics
Matches: 262, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
283 258 0.98
284 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (284 bp):
TCCCTTTTGCTCTTGTAACATCTGGGTCATGCGATGTTCGAATTGAGTTTGCAACTTTTTCATAT
CTTTTAGTAACAACTCGACCAAAGGATCATTCTCTCTTTTTTGCTCATCCTCTTCAGTTTTACTA
GTTTGGGATCTAGTGATCGGCATGGTATCTGTGAAAAAATCACACAAACAAGAACAAGAAAGAAA
AAATAATAATAACCTCACTCGTTAGCTCTCAAAAGAATAACTCTCTGAATGATTCAAAACTTGTA
AATATGTTTGGAGAGGGTTACTAA
Found at i:64087522 original size:31 final size:32
Alignment explanation
Indices: 64087458--64087522 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
64087448 GGCAAATTAC
64087458 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
64087490 AAGAGTAATTGAATCCTAATAAAAA-TCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
64087521 AA
1 AA
64087523 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:64087899 original size:11 final size:11
Alignment explanation
Indices: 64087885--64087911 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
64087875 GTATAAGTAG
64087885 ATTAAAAGTTA
1 ATTAAAAGTTA
64087896 ATTAAAAGTTA
1 ATTAAAAGTTA
64087907 ATTAA
1 ATTAA
64087912 TGCCAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (11 bp):
ATTAAAAGTTA
Found at i:64091234 original size:28 final size:28
Alignment explanation
Indices: 64091188--64091464 Score: 315
Period size: 28 Copynumber: 9.9 Consensus size: 28
64091178 AACACGTCGA
* * * **
64091188 GAAAGAATGAGCCTCTGTGACGAACTGT
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
* *
64091216 GAAAGAATAAGTCTTTGTGGCGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
* * * *
64091244 GAAAGAATAAGTCTTTGTGGTGAAGTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
* *
64091272 GAAATAATAAGCCTTTGTGGCAAACTAC
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
*
64091300 GAAAGAATAAGCCTTTGTGGTGAACTAC
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
*
64091328 GAAAGAATAAGCCTTTGTGGCAAACTAC
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
*
64091356 GAAAGAATAAGCCTTTGTGGTGAACTAC
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
* *
64091384 GAAAGAATAAGCCTTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAC
* *
64091412 GAAAGAATAAG-CTTTGTTGGCAAACTAT
1 GAAAGAATAAGCCTTTG-TGGCGAACTAC
* * * *
64091440 GGAAG-ATTAGCTTTTGTGGTGAACT
1 GAAAGAATAAGCCTTTGTGGCGAACT
64091465 CTGTATGAAG
Statistics
Matches: 219, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
27 16 0.07
28 203 0.93
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (28 bp):
GAAAGAATAAGCCTTTGTGGCGAACTAC
Found at i:64092064 original size:78 final size:78
Alignment explanation
Indices: 64091899--64092054 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
64091889 GACACTCACT
64091899 GTGATAGATAGTGGATGATGAAATAAGAGAAACTGGCGGTGATGAACTACCTGGCACTTTACGAA
1 GTGATAGATAGTGGATGATGAAATAAGAGAAACTGGCGGTGATGAACTACCTGGCACTTTACGAA
64091964 AATGATTACTAAG
66 AATGATTACTAAG
64091977 GTGATAGATAGTGGATGATGAAATAAGAGAAACTGGCGGTGATGAACTACCTGGCACTTTACGAA
1 GTGATAGATAGTGGATGATGAAATAAGAGAAACTGGCGGTGATGAACTACCTGGCACTTTACGAA
64092042 AATGATTACTAAG
66 AATGATTACTAAG
64092055 TTATAAGATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (78 bp):
GTGATAGATAGTGGATGATGAAATAAGAGAAACTGGCGGTGATGAACTACCTGGCACTTTACGAA
AATGATTACTAAG
Found at i:64107452 original size:3 final size:3
Alignment explanation
Indices: 64107444--64107507 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
64107434 TGGCCGAACC
64107444 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* *
64107492 GGT GGT AGT GAT GGT G
1 GGT GGT GGT GGT GGT G
64107508 ATCGGTCATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.03, C:0.00, G:0.64, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:64108358 original size:7 final size:7
Alignment explanation
Indices: 64108346--64108373 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
64108336 TCTGTTGAAG
64108346 AGAAAAA
1 AGAAAAA
64108353 AGAAAAA
1 AGAAAAA
64108360 AGAAAAA
1 AGAAAAA
64108367 AGAAAAA
1 AGAAAAA
64108374 TAATTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:64111282 original size:56 final size:56
Alignment explanation
Indices: 64111196--64111305 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
64111186 AATGGTTTTC
64111196 TCCACTATTTTCGTACCACAAACTACTTCGAGTATGGGTCGAACTAATCCGAATTA
1 TCCACTATTTTCGTACCACAAACTACTTCGAGTATGGGTCGAACTAATCCGAATTA
64111252 TCCACTATTTTCGTACCACAAACTACTTCGAGTATGGGTCGAACTAATCCGAAT
1 TCCACTATTTTCGTACCACAAACTACTTCGAGTATGGGTCGAACTAATCCGAAT
64111306 CATACACAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (56 bp):
TCCACTATTTTCGTACCACAAACTACTTCGAGTATGGGTCGAACTAATCCGAATTA
Found at i:64114619 original size:20 final size:20
Alignment explanation
Indices: 64114582--64114662 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
64114572 ATAGATGTAT
** *
64114582 AACAGGGGCACCGTAGTGCG
1 AACAGGGGCACCAAAGTGCA
* *
64114602 AACAGGGACACCAAAGTGTA
1 AACAGGGGCACCAAAGTGCA
*
64114622 TACAGGGGCACCAAAGTGCA
1 AACAGGGGCACCAAAGTGCA
* *
64114642 AATAGGGGCATCAAAGTGCA
1 AACAGGGGCACCAAAGTGCA
64114662 A
1 A
64114663 GTCTTGTACA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.21, G:0.31, T:0.11
Consensus pattern (20 bp):
AACAGGGGCACCAAAGTGCA
Found at i:64114640 original size:40 final size:41
Alignment explanation
Indices: 64114577--64114659 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
64114567 GCATCATAGA
** *
64114577 TGTATAACAGGGGCACCGTAGTGCGAACAGGGACACCAAAG
1 TGTATAACAGGGGCACCAAAGTGCAAACAGGGACACCAAAG
* * *
64114618 TGTAT-ACAGGGGCACCAAAGTGCAAATAGGGGCATCAAAG
1 TGTATAACAGGGGCACCAAAGTGCAAACAGGGACACCAAAG
64114658 TG
1 TG
64114660 CAAGTCTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.14
Consensus pattern (41 bp):
TGTATAACAGGGGCACCAAAGTGCAAACAGGGACACCAAAG
Found at i:64115576 original size:18 final size:18
Alignment explanation
Indices: 64115555--64115590 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64115545 TCAAAAACAT
64115555 AAAAATTACAAGAAACGA
1 AAAAATTACAAGAAACGA
64115573 AAAAATTACAAGAAACGA
1 AAAAATTACAAGAAACGA
64115591 GATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAATTACAAGAAACGA
Found at i:64117166 original size:27 final size:27
Alignment explanation
Indices: 64117136--64117190 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
64117126 GTATACGCCA
64117136 TAGGATAAAAGTAAATGAATTTAAATC
1 TAGGATAAAAGTAAATGAATTTAAATC
64117163 TAGGATAAAAGTAAATGAATTTAAATC
1 TAGGATAAAAGTAAATGAATTTAAATC
64117190 T
1 T
64117191 TTTGGTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.31
Consensus pattern (27 bp):
TAGGATAAAAGTAAATGAATTTAAATC
Found at i:64118228 original size:14 final size:14
Alignment explanation
Indices: 64118209--64118237 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
64118199 GGCTTTTTCC
64118209 ATGGTTAACAACTA
1 ATGGTTAACAACTA
64118223 ATGGTTAACAACTA
1 ATGGTTAACAACTA
64118237 A
1 A
64118238 CATGTCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ATGGTTAACAACTA
Found at i:64123681 original size:39 final size:40
Alignment explanation
Indices: 64123636--64123813 Score: 202
Period size: 39 Copynumber: 4.5 Consensus size: 40
64123626 ACATGTTTTA
*
64123636 AGTATTGTGATATATGCTTAAATGTTATGAGATTATATGT
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* * *
64123676 A-TATTGTGATATATGCTTGAGTATTATGTGATTATATG-
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* * * *
64123714 AGTATTGTAATATATACTTAAATGTTATGTGATTACAT-A
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
** *
64123753 AGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGT
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
***
64123793 A-TAACATGATATATGCTTAAA
1 AGTATTGTGATATATGCTTAAA
64123814 AGTGATTATG
Statistics
Matches: 113, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 110 0.97
40 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (40 bp):
AGTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
Found at i:64128011 original size:43 final size:43
Alignment explanation
Indices: 64127960--64128178 Score: 266
Period size: 43 Copynumber: 5.1 Consensus size: 43
64127950 AAAAATGCCG
* *
64127960 CTAAAGAACATGACCTTTAGCGGCGCTTTTATCAAAAATGCCT
1 CTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCT
*
64128003 CTAGAGAACATGACCTTTAGCGGCGCTTTT-TCACAAACGCCGT
1 CTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC-T
*
64128046 -TAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCG
1 CTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCT
* * ** *
64128088 CTATAGAGA-ATGACTTTTAGCGGCTTTTTTTTCACAAACG-CT
1 CTAAAGA-ACATGACCTTTAGCGGCGCTTTTATCACAAACGCCT
* * * *
64128130 GCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAGACGCCG
1 -CTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCT
64128174 CTAAA
1 CTAAA
64128179 AGTGCCGTTC
Statistics
Matches: 149, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
42 39 0.26
43 108 0.72
44 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
CTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCT
Found at i:64128101 original size:85 final size:86
Alignment explanation
Indices: 64127956--64128176 Score: 311
Period size: 85 Copynumber: 2.6 Consensus size: 86
64127946 ATGAAAAAAT
* * *
64127956 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAAAAATGCCTCTAGAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAGAGAACATGACCTTT
64128021 AGCGGC-GCTTTTTCACAAAC
66 AGCGGCTGCTTTTTCACAAAC
* * *
64128041 GCCGTTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGAGA-ATGACTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAGAGA-ACATGACCTT
**
64128105 TAGCGGCTTTTTTTTCACAAAC
65 TAGCGGCTGCTTTTTCACAAAC
* * * *
64128127 GCTGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAGACGCCGCTA
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTA
64128177 AAAGTGCCGT
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
85 63 0.52
86 58 0.48
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (86 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAGAGAACATGACCTTT
AGCGGCTGCTTTTTCACAAAC
Found at i:64134372 original size:50 final size:51
Alignment explanation
Indices: 64134224--64134453 Score: 202
Period size: 50 Copynumber: 4.5 Consensus size: 51
64134214 CGATCTTGTA
* * * * *
64134224 TAAGACCATGTCTGGGACATGGCATCGACACCGAAG-TGTGA-G--CTAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATGATGAGAGGTCCCA-TG
** * *
64134272 TAAGACCATGTCTGGGACATGGCATTGGCATTATTGAAATTATGAGAGGTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC---ACCG--ATGATGAGAGGTCCCATG
* **
64134328 TAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATGATGAGAGGTCCCATG
* **
64134378 TAAGACCATGTCTGGGACATGGCATGGGCACCGATG-TGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATGATGAGAGGTCCCATG
* * *
64134428 TAAGACCATATCTGAGATATGGCATT
1 TAAGACCATGTCTGGGACATGGCATT
64134454 AGCAGTACAG
Statistics
Matches: 146, Mismatches: 26, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
48 27 0.18
50 76 0.52
51 4 0.03
53 3 0.02
54 4 0.03
55 1 0.01
56 30 0.21
57 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (51 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGATGATGAGAGGTCCCATG
Found at i:64138929 original size:21 final size:20
Alignment explanation
Indices: 64138872--64138929 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
64138862 ATTATGGTTA
64138872 TTATGTTATCTTTAAATCAT
1 TTATGTTATCTTTAAATCAT
* ** **
64138892 ATAACTTATACGATAAATCAT
1 TTATGTTAT-CTTTAAATCAT
64138913 GTTATGTTATCTTTAAA
1 -TTATGTTATCTTTAAA
64138930 GTACCATAAT
Statistics
Matches: 26, Mismatches: 10, Indels: 3
0.67 0.26 0.08
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
TTATGTTATCTTTAAATCAT
Found at i:64140310 original size:40 final size:39
Alignment explanation
Indices: 64140278--64140353 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
64140268 TGGGAATAGG
* *
64140278 ATAACTTGGGGGAAATT-GGGGAAAATAATTTGGGGAACA
1 ATAACTTGAGGGAAATTGGGGGAAAAGAATTT-GGGAACA
*
64140317 ATAACTTGAGGGAAATTGGGGGAAAAGAAGTTGGGAA
1 ATAACTTGAGGGAAATTGGGGGAAAAGAATTTGGGAA
64140354 ATTGGGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 21 0.64
40 12 0.36
ACGTcount: A:0.39, C:0.04, G:0.36, T:0.21
Consensus pattern (39 bp):
ATAACTTGAGGGAAATTGGGGGAAAAGAATTTGGGAACA
Found at i:64140312 original size:14 final size:14
Alignment explanation
Indices: 64140293--64140331 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
64140283 TTGGGGGAAA
*
64140293 TTGGGGAAAATAAT
1 TTGGGGAAAATAAC
64140307 TTGGGGAACAATAAC
1 TTGGGGAA-AATAAC
64140322 TTGAGGGAAA
1 TTG-GGGAAA
64140332 TTGGGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 9 0.41
16 5 0.23
ACGTcount: A:0.41, C:0.05, G:0.31, T:0.23
Consensus pattern (14 bp):
TTGGGGAAAATAAC
Found at i:64140707 original size:42 final size:41
Alignment explanation
Indices: 64140636--64140716 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
64140626 TTAATACATA
* *
64140636 TTTGCGGTGTTTGGACCAAAAACGCCACTATTGTTCAACTT
1 TTTGCGGCGTTTGGACCAAAAACGCCACTATTGCTCAACTT
*
64140677 TTTGCGGCGTTTGGAGCCAAAAATGCCACTATTGCTCAAC
1 TTTGCGGCGTTTGGA-CCAAAAACGCCACTATTGCTCAAC
64140717 CTAATTAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 14 0.39
42 22 0.61
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
TTTGCGGCGTTTGGACCAAAAACGCCACTATTGCTCAACTT
Found at i:64141392 original size:7 final size:7
Alignment explanation
Indices: 64141380--64141597 Score: 138
Period size: 7 Copynumber: 30.7 Consensus size: 7
64141370 AACACTGAAT
*
64141380 CATAAAA
1 CATAAAC
64141387 CATAAAC
1 CATAAAC
64141394 CATAAAC
1 CATAAAC
64141401 CATAAAC
1 CATAAAC
64141408 CATAAAC
1 CATAAAC
64141415 CATAAAC
1 CATAAAC
*
64141422 CCTAAATC
1 CATAAA-C
*
64141430 TC-TAACC
1 -CATAAAC
*
64141437 CTTAAAC
1 CATAAAC
**
64141444 TTTAAAC
1 CATAAAC
**
64141451 C-CCAAC
1 CATAAAC
*
64141457 GCTTAAAC
1 -CATAAAC
64141465 CATAAAC
1 CATAAAC
64141472 CATAAAC
1 CATAAAC
64141479 CATAAAC
1 CATAAAC
64141486 CATAAAC
1 CATAAAC
*
64141493 CATAATC
1 CATAAAC
*
64141500 CCTAAACC
1 CATAAA-C
*
64141508 CATAATC
1 CATAAAC
64141515 CATAAAC
1 CATAAAC
**
64141522 TTTAAA-
1 CATAAAC
64141528 -ATAGTAAC
1 CATA--AAC
*
64141536 TCCTAAAC
1 -CATAAAC
*
64141544 CTTAAAC
1 CATAAAC
*
64141551 CTTAAAC
1 CATAAAC
*
64141558 CCTAAAC
1 CATAAAC
* *
64141565 TATATAC
1 CATAAAC
*
64141572 CCTAAAC
1 CATAAAC
64141579 CATAAAC
1 CATAAAC
*
64141586 CCTAAAC
1 CATAAAC
*
64141593 TATAA
1 CATAA
64141598 TGATAATTAA
Statistics
Matches: 167, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
5 2 0.01
6 4 0.02
7 143 0.86
8 15 0.09
9 1 0.01
10 2 0.01
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (7 bp):
CATAAAC
Found at i:64141948 original size:40 final size:41
Alignment explanation
Indices: 64141917--64142045 Score: 106
Period size: 40 Copynumber: 3.2 Consensus size: 41
64141907 TTTGATAAAA
*
64141917 CGCCGTTAAAGCTCGATCTATAGAGGCA-TTTTACAAAGAG
1 CGCCGCTAAAGCTCGATCTATAGAGGCATTTTTACAAAGAG
** *
64141957 CGCCGCTAATTCTCGATCTATAGCGGCATTTTT-C-AAGTAG
1 CGCCGCTAAAGCTCGATCTATAGAGGCATTTTTACAAAG-AG
* * * * * *
64141997 CGCCACTAATGCTCAACCTATA-ACGGCGTTTTT-CAAAAAG
1 CGCCGCTAAAGCTCGATCTATAGA-GGCATTTTTACAAAGAG
*
64142037 CACCGCTAA
1 CGCCGCTAA
64142046 TGCCACTAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
39 3 0.04
40 63 0.88
41 6 0.08
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (41 bp):
CGCCGCTAAAGCTCGATCTATAGAGGCATTTTTACAAAGAG
Found at i:64142046 original size:40 final size:40
Alignment explanation
Indices: 64141941--64142048 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
64141931 GATCTATAGA
* * * * * *
64141941 GGCATTTTACAAAGAGCGCCGCTAATTCTCGATCTATAGC
1 GGCATTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAAC
** *
64141981 GGCATTTTTCAAGTAGCGCCACTAATGCTCAACCTATAAC
1 GGCATTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAAC
* *
64142021 GGCGTTTTTCAAAAAGCACCGCTAATGC
1 GGCATTTTTCAAAAAGCGCCGCTAATGC
64142049 CACTAGTGCT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (40 bp):
GGCATTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAAC
Found at i:64142160 original size:40 final size:40
Alignment explanation
Indices: 64142098--64142190 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
64142088 TTTTGTGGAA
* * *
64142098 TTTTTCAAAAAGCGCTGTTAATGGTCGACCTATAGCGACG
1 TTTTTCAAAAAGCGCAGCTAATGCTCGACCTATAGCGACG
* ** **
64142138 TTTTTCAAAAAGCGCAGCTAATGCTTGATTTATAGCGGTG
1 TTTTTCAAAAAGCGCAGCTAATGCTCGACCTATAGCGACG
64142178 TTTTTCAAAAAGC
1 TTTTTCAAAAAGC
64142191 ATCGCTAATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCAGCTAATGCTCGACCTATAGCGACG
Found at i:64142244 original size:153 final size:153
Alignment explanation
Indices: 64142002--64142354 Score: 428
Period size: 153 Copynumber: 2.3 Consensus size: 153
64141992 AGTAGCGCCA
* * * * **
64142002 CTAATGCTCAACCTATAACGGCGTTTTTCAAAAAGCACCGCTAATGCCACTAGTGCTCAACATAA
1 CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCATCGCTAATGCCACTAAAGCTCAACATAA
* * ***
64142067 AACGAGGCATTGTGCTTAAGTTTTTGTG-GA-ATTTTTCAAAAAGCGCTGTTAATGGTCGACCTA
66 AACGAGACATTGTACTTAAGTTTTT-TGCGACATTTTTCAAAAAGC-CAACTAATGGTCGACCTA
*
64142130 TAGCGACGTTTTTCAAAAAGCGCAG
129 TAGCGACGCTTTTCAAAAAGCGCAG
* * * *
64142155 CTAATGCTTGATTTATAGCGGTGTTTTTCAAAAAGCATCGCTAATGCCACTAAAGCTCAACATAT
1 CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCATCGCTAATGCCACTAAAGCTCAACATAA
* * * *
64142220 AATGACGACATTGTACTTAA-TTTTTTGCGACGTTTTTCAAAAAGCCAACTAATTGTTGACCTAT
66 AACGA-GACATTGTACTTAAGTTTTTTGCGACATTTTTCAAAAAGCCAACTAATGGTCGACCTAT
*
64142284 AGCGGCGCTTTTCAAAAAGCGCAG
130 AGCGACGCTTTTCAAAAAGCGCAG
*
64142308 CTAATGCTCGATCTATAGCGACGTTTTTCGAAAAGAGC-T-GCTAATGC
1 CTAATGCTCGATCTATAGCGGCGTTTTTC-AAAA-AGCATCGCTAATGC
64142355 TCAATCTATA
Statistics
Matches: 170, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
152 2 0.01
153 135 0.79
154 30 0.18
155 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (153 bp):
CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCATCGCTAATGCCACTAAAGCTCAACATAA
AACGAGACATTGTACTTAAGTTTTTTGCGACATTTTTCAAAAAGCCAACTAATGGTCGACCTATA
GCGACGCTTTTCAAAAAGCGCAG
Found at i:64142324 original size:40 final size:40
Alignment explanation
Indices: 64142250--64142406 Score: 174
Period size: 40 Copynumber: 4.0 Consensus size: 40
64142240 TTTTTTGCGA
* * *
64142250 CGTTTTTCAAAAAGC-CAACTAATTG-TTGACCTATAGCGG
1 CGTTTTTCAAAAAGCGCAGCTAA-TGCTCGATCTATAGCGG
* *
64142289 CGCTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGCGA
1 CGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGCGG
* * * *
64142329 CGTTTTTCGAAAAGAGCTGCTAATGCTCAATCTATAGCGG
1 CGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGCGG
* * * *
64142369 CGTTTTTCAGAAAGCGCCGTTAATGTTCGATCTATAGC
1 CGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGC
64142407 AACATTTTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 16 0.16
40 82 0.84
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGCGG
Found at i:64152432 original size:36 final size:36
Alignment explanation
Indices: 64152392--64152474 Score: 130
Period size: 37 Copynumber: 2.3 Consensus size: 36
64152382 AGAAGAAATT
*
64152392 TTCTAATTAAGACTTAAATTTTTTTAATTTCATTTG
1 TTCTATTTAAGACTTAAATTTTTTTAATTTCATTTG
* *
64152428 TTCTATTTAAATATTTAAATTTTTTTAATTTCATTTG
1 TTCTATTT-AAGACTTAAATTTTTTTAATTTCATTTG
64152465 TTCTATTTAA
1 TTCTATTTAA
64152475 ATATTTATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 9 0.21
37 34 0.79
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (36 bp):
TTCTATTTAAGACTTAAATTTTTTTAATTTCATTTG
Found at i:64152446 original size:37 final size:37
Alignment explanation
Indices: 64152405--64152481 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
64152395 TAATTAAGAC
64152405 TTAAATTTTTTTAATTTCATTTGTTCTATTTAAATAT
1 TTAAATTTTTTTAATTTCATTTGTTCTATTTAAATAT
64152442 TTAAATTTTTTTAATTTCATTTGTTCTATTTAAATAT
1 TTAAATTTTTTTAATTTCATTTGTTCTATTTAAATAT
64152479 TTA
1 TTA
64152482 TGTTAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (37 bp):
TTAAATTTTTTTAATTTCATTTGTTCTATTTAAATAT
Found at i:64166025 original size:21 final size:21
Alignment explanation
Indices: 64166001--64166042 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64165991 TCGCTATTTA
64166001 CATTAAAAATTAATCTTTATC
1 CATTAAAAATTAATCTTTATC
*
64166022 CATTAAAAATTAATTTTTATC
1 CATTAAAAATTAATCTTTATC
64166043 TCACATTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
CATTAAAAATTAATCTTTATC
Found at i:64166262 original size:94 final size:92
Alignment explanation
Indices: 64165924--64166262 Score: 277
Period size: 94 Copynumber: 3.7 Consensus size: 92
64165914 ACTCACTTCT
* * *
64165924 ACTATTTTCATTAAAAAGTTAATTTTAATCACACATTCATTAGAGAATACTCTCATAGCTCACAT
1 ACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACAT
* ** * *
64165989 TTTCGCTATTTACA--TTAAAA-ATTAA
66 TTAC-CTATAAACAGGTCAAAATTTTAA
* * * * *
64166014 TCT-TTATCCATTAAAAA-TTAATTTTTATCTCACATT-AGCT-G-TAATACACTTCCAT-GCTC
1 ACTATT-TTCATTAAAAAGTTAATTTTAATCTCACATTGA-CTAGAGAATACTC-T-CATAGCTC
* * * *
64166073 ACACTTACCCTATAAATAAGTGTCAAATTTTTTAT
62 ACATTTA-CCTATAAA-CAG-GTCAAA-ATTTTAA
* * * * * *
64166108 A-TATTTTAATT-AAAAGTTAATTTTAATCTCACATTGACTCGAGAACACCCCCATATCTCACAT
1 ACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACAT
*
64166171 TTACCATATAAACAGGTGAAAATCTTTAA
66 TTACC-TATAAACAGGTCAAAAT-TTTAA
*
64166200 ACTATTTTTATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCAC
1 ACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCAC
64166263 GTATTCATTA
Statistics
Matches: 192, Mismatches: 36, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
87 6 0.03
88 17 0.09
89 25 0.13
90 12 0.06
91 1 0.01
92 18 0.09
93 41 0.21
94 67 0.35
95 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (92 bp):
ACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACAT
TTACCTATAAACAGGTCAAAATTTTAA
Found at i:64166282 original size:69 final size:69
Alignment explanation
Indices: 64166200--64166368 Score: 214
Period size: 70 Copynumber: 2.4 Consensus size: 69
64166190 AAATCTTTAA
* * * * *
64166200 ACTATTTTTATTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACGT
1 ACTATTTTAATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAATACTATAATAACTCACGT
64166265 ATTC
66 ATTC
* * * *
64166269 ATTATTTTAATTAAAAAAGTTAGTTTTAACCCCACATTGACTAGAGAATACTATAATAACTCACT
1 ACTATTTTAATT-AAAAAGTTAATTTTAATCCCACATTGACTAGAGAATACTATAATAACTCACG
64166334 TATTC
65 TATTC
* * *
64166339 GCTATTTTCATTAAAAA-TTAATTTGAATCC
1 ACTATTTTAATTAAAAAGTTAATTTTAATCC
64166369 TTCACTGGCT
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
68 10 0.12
69 15 0.18
70 59 0.70
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (69 bp):
ACTATTTTAATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAATACTATAATAACTCACGT
ATTC
Found at i:64166986 original size:93 final size:93
Alignment explanation
Indices: 64166760--64166987 Score: 368
Period size: 93 Copynumber: 2.5 Consensus size: 93
64166750 TTTTAGCCCC
*
64166760 TTAAAAAGTTAATTTTTATCCCACATTGGCTAGAATACACTCCCATGCTCACACATACCCTATAA
1 TTAAAAAGTTAATTTTTATCCCACATTGGCTAGAATACACTTCCATGCTCACACATACCCTATAA
*
64166825 ATACGTGTCAATTTCTTCTCTATTTTTA
66 ATACGTGCCAATTTCTTCTCTATTTTTA
* *
64166853 TTAAAAAGTTAATTTTTATTCCACATTGGCTAGAATACACTTCCATGCTCACACATACCTTATAA
1 TTAAAAAGTTAATTTTTATCCCACATTGGCTAGAATACACTTCCATGCTCACACATACCCTATAA
64166918 ATACGTGCCAATTTCTTCTCTATTTTTA
66 ATACGTGCCAATTTCTTCTCTATTTTTA
* * * *
64166946 TTAAAAAATTAA-TTTTAGTCCCACATTGACTACAAAACACTT
1 TTAAAAAGTTAATTTTTA-TCCCACATTGGCTAGAATACACTT
64166988 TCATATTTGT
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
92 5 0.04
93 120 0.96
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (93 bp):
TTAAAAAGTTAATTTTTATCCCACATTGGCTAGAATACACTTCCATGCTCACACATACCCTATAA
ATACGTGCCAATTTCTTCTCTATTTTTA
Found at i:64171051 original size:5 final size:6
Alignment explanation
Indices: 64171036--64171061 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
64171026 TTATATTCTC
64171036 CCCCCA CCCCCA CCCCCA CCCCCA CC
1 CCCCCA CCCCCA CCCCCA CCCCCA CC
64171062 AATGCCTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:64173253 original size:27 final size:28
Alignment explanation
Indices: 64173196--64173253 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
64173186 TTTTAGTGGG
* *
64173196 AAAATTAATTTCTCTCTACAGGAAAACA
1 AAAATTAACTTCTCTCTACAAGAAAACA
64173224 AAAACTTAACTTCTCTCT-CAAGAAAA-A
1 AAAA-TTAACTTCTCTCTACAAGAAAACA
64173251 AAA
1 AAA
64173254 GAAGAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 11 0.41
29 12 0.44
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.26
Consensus pattern (28 bp):
AAAATTAACTTCTCTCTACAAGAAAACA
Found at i:64180687 original size:17 final size:17
Alignment explanation
Indices: 64180650--64180689 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
64180640 AATCAACCCT
*
64180650 GCGAACCCCTATTGCTG
1 GCGAACCCCTATTGCTA
**
64180667 GCGAACCCCTATTTTTA
1 GCGAACCCCTATTGCTA
64180684 GCGAAC
1 GCGAAC
64180690 TCTAGCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (17 bp):
GCGAACCCCTATTGCTA
Found at i:64182116 original size:18 final size:18
Alignment explanation
Indices: 64182095--64182144 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
64182085 TTTGCATAAA
*
64182095 TAACACAGTTCACCAAAT
1 TAACACAGTTCACAAAAT
* *
64182113 TAACATAGTTCGCAAAAT
1 TAACACAGTTCACAAAAT
*
64182131 TAACACAATTCACA
1 TAACACAGTTCACA
64182145 TTATTATAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (18 bp):
TAACACAGTTCACAAAAT
Found at i:64184939 original size:7 final size:6
Alignment explanation
Indices: 64184924--64184955 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
64184914 CATTTCTAGG
64184924 TCATTT TCATTTT TCATTT TCATTT TCATTT T
1 TCATTT TCA-TTT TCATTT TCATTT TCATTT T
64184956 GAAGAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TCATTT
Found at i:64185043 original size:58 final size:58
Alignment explanation
Indices: 64184930--64185065 Score: 185
Period size: 58 Copynumber: 2.4 Consensus size: 58
64184920 TAGGTCATTT
* *
64184930 TCATTTTTC-ATTTTCATTTTC-ATTTTGAAGAAAACATATTCATTTCCAAATGTTTC
1 TCATTTCTCTATTTTCATTTTCAATTTGGAAGAAAACATATTCATTTCCAAATGTTTC
64184986 -CATTTCTCTATTTTCATTTTCAATTTGGTAA-AAACCACAT-TTCATTTCCAAATGTTTC
1 TCATTTCTCTATTTTCATTTTCAATTTGG-AAGAAA--ACATATTCATTTCCAAATGTTTC
64185044 TCATTTCTCTA-TTTCATTTTCA
1 TCATTTCTCTATTTTCATTTTCA
64185066 TTGATCAATG
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
55 7 0.10
56 12 0.17
57 8 0.11
58 31 0.43
59 14 0.19
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (58 bp):
TCATTTCTCTATTTTCATTTTCAATTTGGAAGAAAACATATTCATTTCCAAATGTTTC
Found at i:64202171 original size:22 final size:22
Alignment explanation
Indices: 64202143--64202190 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
64202133 TGATTGATTA
*
64202143 GGATATTCTATAGCGTTTTAAG
1 GGATATTCTATAGCATTTTAAG
* * *
64202165 GGATATTTTATGGTATTTTAAG
1 GGATATTCTATAGCATTTTAAG
64202187 GGAT
1 GGAT
64202191 TGATTAGGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (22 bp):
GGATATTCTATAGCATTTTAAG
Found at i:64202194 original size:54 final size:52
Alignment explanation
Indices: 64202072--64202200 Score: 150
Period size: 52 Copynumber: 2.4 Consensus size: 52
64202062 TTCAAAGCTC
* * *
64202072 TATTTTTAGAGATTGATTAGGATATTTTATAGGATTTATGACATATTTATGG
1 TATTTTAAGAGATTGATTAGGATATTCTATAGGATTTAAGACATATTTATGG
* ** * **
64202124 GATTTTAATTGATTGATTAGGATATTCTATAGCGTTTTAAGGGATATTTTATGG
1 TATTTTAAGAGATTGATTAGGATATTCTATAG-GATTTAAGACATA-TTTATGG
*
64202178 TATTTTAAGGGATTGATTAGGAT
1 TATTTTAAGAGATTGATTAGGAT
64202201 TTTATGGGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
52 27 0.43
53 9 0.14
54 27 0.43
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (52 bp):
TATTTTAAGAGATTGATTAGGATATTCTATAGGATTTAAGACATATTTATGG
Found at i:64205157 original size:43 final size:43
Alignment explanation
Indices: 64205105--64205190 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
64205095 ATTAGTGCAA
*
64205105 CAATTAAATGAATGATATTCTAGGATCTTTAGCTATATTAGTG
1 CAATTAAATGAATGATATTCTAGGATCTTTAGCTATACTAGTG
* *
64205148 CAATTAAATGAATGGTATTCTAGGATCTTTAGCTGTACTAGTG
1 CAATTAAATGAATGATATTCTAGGATCTTTAGCTATACTAGTG
64205191 GATGTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (43 bp):
CAATTAAATGAATGATATTCTAGGATCTTTAGCTATACTAGTG
Found at i:64208983 original size:24 final size:24
Alignment explanation
Indices: 64208949--64209025 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
64208939 CATTTTAATA
64208949 GCCTTTATGGCATATTCTGATTTG
1 GCCTTTATGGCATATTCTGATTTG
* *
64208973 GCCTTTGTGGCAT-TT-TG--TTC
1 GCCTTTATGGCATATTCTGATTTG
* *
64208993 GCC-TTATGGCATATTCTAATTTA
1 GCCTTTATGGCATATTCTGATTTG
64209016 GCCTTTATGG
1 GCCTTTATGG
64209026 TATTCTAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 8 0.19
20 7 0.16
21 1 0.02
22 2 0.05
23 7 0.16
24 18 0.42
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (24 bp):
GCCTTTATGGCATATTCTGATTTG
Found at i:64209083 original size:20 final size:20
Alignment explanation
Indices: 64209041--64209088 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
64209031 TAGTATGGCA
* * *
64209041 TTTGTGGCATCCTGTTGGTC
1 TTTGTGGCATCCTGCTAGCC
*
64209061 TTTGTGGCATTCTGCTAGCC
1 TTTGTGGCATCCTGCTAGCC
*
64209081 TTTATGGC
1 TTTGTGGC
64209089 GTATTCTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.08, C:0.21, G:0.27, T:0.44
Consensus pattern (20 bp):
TTTGTGGCATCCTGCTAGCC
Found at i:64217723 original size:8 final size:8
Alignment explanation
Indices: 64217710--64217734 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
64217700 GGGGGTCAAT
64217710 TTGTTAAA
1 TTGTTAAA
64217718 TTGTTAAA
1 TTGTTAAA
64217726 TTGTTAAA
1 TTGTTAAA
64217734 T
1 T
64217735 GTTTAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTTAAA
Found at i:64221089 original size:19 final size:19
Alignment explanation
Indices: 64221065--64221116 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
64221055 CATGTTCAAA
*
64221065 ATTTTAATACAATTTAATC
1 ATTTTAATACAAATTAATC
* *
64221084 ATTTT-ATAAAAATTAATT
1 ATTTTAATACAAATTAATC
*
64221102 ATTTTATTACAAATT
1 ATTTTAATACAAATT
64221117 CTATCGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTAATACAAATTAATC
Found at i:64222459 original size:25 final size:25
Alignment explanation
Indices: 64222425--64222474 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
64222415 AAGAGGAGGT
64222425 GAGTCAAATTGACTACTTAAGTACC
1 GAGTCAAATTGACTACTTAAGTACC
64222450 GAGTCAAATTGACTACTTAAGTACC
1 GAGTCAAATTGACTACTTAAGTACC
64222475 AAGCTCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (25 bp):
GAGTCAAATTGACTACTTAAGTACC
Found at i:64226358 original size:22 final size:22
Alignment explanation
Indices: 64226274--64226345 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
64226264 ATTGTTCAAA
* **
64226274 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
64226296 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
64226318 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
64226340 CATGAG
1 CATGAG
64226346 GGTTTAGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:64254654 original size:16 final size:16
Alignment explanation
Indices: 64254620--64254668 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
64254610 ACCTTAAAAG
**
64254620 ATTAAATA-TGTACCA
1 ATTAAATATTGTTTCA
64254635 ATTAAATATTGTTTCA
1 ATTAAATATTGTTTCA
* *
64254651 ATTAATTATAGTTTCA
1 ATTAAATATTGTTTCA
64254667 AT
1 AT
64254669 ACGTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTAAATATTGTTTCA
Found at i:64255746 original size:22 final size:22
Alignment explanation
Indices: 64255712--64255755 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
64255702 CAAATTTATG
* *
64255712 AAAATTTATTATAAAAATAATT
1 AAAATTCAATATAAAAATAATT
**
64255734 AAAATTCAATATATTAATAATT
1 AAAATTCAATATAAAAATAATT
64255756 TAAGTGAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTCAATATAAAAATAATT
Found at i:64255765 original size:28 final size:27
Alignment explanation
Indices: 64255734--64255788 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
64255724 AAAAATAATT
*
64255734 AAAATTCAA-TATATTAATAATTTAAGTG
1 AAAATT-AATTAT-TTAATAATTAAAGTG
*
64255762 AAAATTAATTATTTTATAATTAAAGTG
1 AAAATTAATTATTTAATAATTAAAGTG
64255789 TGAATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTAATTATTTAATAATTAAAGTG
Done.