Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 28 of 30
Found at i:4338093 original size:22 final size:23
Alignment explanation
Indices: 4338049--4338093 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
4338039 ATTTTCATGG
*
4338049 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
4338072 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAACATTTGCATAAT
4338094 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:4339793 original size:8 final size:8
Alignment explanation
Indices: 4339780--4339805 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4339770 ACCAAGGGAA
4339780 AAGGTGTG
1 AAGGTGTG
4339788 AAGGTGTG
1 AAGGTGTG
4339796 AAGGTGTG
1 AAGGTGTG
4339804 AA
1 AA
4339806 AGAGCAACTT
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:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (8 bp):
AAGGTGTG
Found at i:4342845 original size:30 final size:30
Alignment explanation
Indices: 4342809--4342868 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
4342799 GGGTGACAAC
* *
4342809 GTATTAAGGGGGAGAGTTTGTATAAATTTT
1 GTATTAAGGGGGAGAGCTTGCATAAATTTT
4342839 GTATTAAGGGGGAGAGCTTGCATAAATTTT
1 GTATTAAGGGGGAGAGCTTGCATAAATTTT
4342869 TGGTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (30 bp):
GTATTAAGGGGGAGAGCTTGCATAAATTTT
Found at i:4343995 original size:13 final size:13
Alignment explanation
Indices: 4343977--4344002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4343967 TACACCAAGT
4343977 ATGTATCGATACA
1 ATGTATCGATACA
4343990 ATGTATCGATACA
1 ATGTATCGATACA
4344003 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4344000 original size:32 final size:33
Alignment explanation
Indices: 4343959--4344022 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
4343949 TAGCCAAACT
**
4343959 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
4343991 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
4344023 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:4346280 original size:22 final size:23
Alignment explanation
Indices: 4346236--4346280 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
4346226 ATTTTCATGG
*
4346236 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
4346259 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAACATTTGCATAAT
4346281 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:4347981 original size:8 final size:8
Alignment explanation
Indices: 4347968--4347993 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4347958 ACCAAGGGAA
4347968 AAGGTGTG
1 AAGGTGTG
4347976 AAGGTGTG
1 AAGGTGTG
4347984 AAGGTGTG
1 AAGGTGTG
4347992 AA
1 AA
4347994 AGAGCAACTT
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:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (8 bp):
AAGGTGTG
Found at i:4351183 original size:21 final size:21
Alignment explanation
Indices: 4351150--4351190 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4351140 CTAAGTAAAA
4351150 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
4351171 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
4351191 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:4351256 original size:21 final size:20
Alignment explanation
Indices: 4351227--4351283 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
4351217 AAAATCCTGA
**
4351227 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
4351247 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
4351268 ATAGTATCGATACACA
1 AAAGTATCGATACACA
4351284 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:4351354 original size:53 final size:53
Alignment explanation
Indices: 4351271--4351407 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
4351261 AGATTGCATA
* *
4351271 GTATCGATACACACAAATATGTATCGATACAGGACATTGGTAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
4351325 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
4351378 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
4351408 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:4351451 original size:10 final size:10
Alignment explanation
Indices: 4351432--4351462 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4351422 ATCTCATTTT
4351432 TCACTGTTCA
1 TCACTGTTCA
*
4351442 TCACTATTCA
1 TCACTGTTCA
4351452 TCACTGTTCA
1 TCACTGTTCA
4351462 T
1 T
4351463 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:4351573 original size:13 final size:13
Alignment explanation
Indices: 4351555--4351593 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4351545 TCGCTATTCA
4351555 TGTATCGATACAT
1 TGTATCGATACAT
*
4351568 TGTATCGATACAG
1 TGTATCGATACAT
4351581 TGTATCGATACAT
1 TGTATCGATACAT
4351594 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4351707 original size:20 final size:20
Alignment explanation
Indices: 4351664--4351707 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4351654 TTCAAATGCA
* *
4351664 TGTATCGATACATTATAATT
1 TGTATCGATACATTAGAATG
* *
4351684 TGTATCGATACATTGGAGTG
1 TGTATCGATACATTAGAATG
4351704 TGTA
1 TGTA
4351708 AGTACAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTAGAATG
Found at i:4354054 original size:42 final size:42
Alignment explanation
Indices: 4353946--4354043 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
4353936 TTAGTCTGTT
* * * ** *
4353946 TGTCAACTTTGACCCTGGAGATTTTTTTACCCTCAGTCTGCT
1 TGTCAGCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCC
4353988 TGTCAGCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCC
1 TGTCAGCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCC
*
4354030 TGTCGGCTTTGACC
1 TGTCAGCTTTGACC
4354044 TTGAAGACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (42 bp):
TGTCAGCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCC
Found at i:4354068 original size:42 final size:42
Alignment explanation
Indices: 4353922--4354068 Score: 127
Period size: 42 Copynumber: 3.5 Consensus size: 42
4353912 AAACTTCTGG
* * * ** * *
4353922 AGACTTTCTTTCCTTTAGTCTGTTTGTCAACTTTGACCCTGG
1 AGACTTTTTTTCCCTCAGTCTGCCTGTCAGCTTTGACCCTGA
*
4353964 AGA-TTTTTTTACCCTCAGTCTGCTTGTCAGCTTTGACCCT-A
1 AGACTTTTTTT-CCCTCAGTCTGCCTGTCAGCTTTGACCCTGA
** * * *
4354005 GAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCTTGA
1 -AGACTTTTTTTCCCTCAGTCTGCCTGTCAGCTTTGACCCTGA
* *
4354048 AGACTTTTTTTTCCTTAGTCT
1 AGACTTTTTTTCCCTCAGTCT
4354069 ACCTATCGCT
Statistics
Matches: 84, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
41 6 0.07
42 73 0.87
43 5 0.06
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (42 bp):
AGACTTTTTTTCCCTCAGTCTGCCTGTCAGCTTTGACCCTGA
Found at i:4354080 original size:26 final size:27
Alignment explanation
Indices: 4354057--4354107 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
4354047 AAGACTTTTT
4354057 TTTCCTTAGTCTACCTATC-GCTTTCC
1 TTTCCTTAGTCTACCTATCGGCTTTCC
*
4354083 TTTCCTTAGTCTGCCTATCGGCTTT
1 TTTCCTTAGTCTACCTATCGGCTTT
4354108 GACTCTAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTCCTTAGTCTACCTATCGGCTTTCC
Found at i:4354384 original size:126 final size:125
Alignment explanation
Indices: 4354184--4354415 Score: 297
Period size: 126 Copynumber: 1.8 Consensus size: 125
4354174 AGTGTGCTTG
* * **
4354184 TCGGTTTTAACCCTAGAGACTTTTCACCCTTAGTCTGCATGTTGGCTTTGACCCCAGAGACTTTC
1 TCGGCTTTAACCCTAGAGACTTTCCACCCTTAGTCTGCATGCCGGCTTTGACCCCAGAGACTTTC
* *
4354249 CTTCCCTTAGTCTGCTTGTCAG-CTTCAACCCTAGAGACTTTCCTTGCCCTAGTCTTTCTA
66 CTACCCTTAGTCTGCCTGTCAGTCTT-AACCCTAGAGACTTTCCTTGCCCTAGTCTTTCTA
* * * ** *
4354309 TCGGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTTTGTC-TGCCGGCTTTGACCCTGGATACTT
1 TCGGCTTTAACCCTAGAGACTTTCC-ACCCTTAGTCTG-CATGCCGGCTTTGACCCCAGAGACTT
* *
4354373 TTCTACCCTTAGTCTGCCTGTCAGTCTTGACCCTAGAGACTTT
64 TCCTACCCTTAGTCTGCCTGTCAGTCTTAACCCTAGAGACTTT
4354416 TCTACCCTCA
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
125 22 0.24
126 64 0.71
127 4 0.04
ACGTcount: A:0.16, C:0.30, G:0.17, T:0.37
Consensus pattern (125 bp):
TCGGCTTTAACCCTAGAGACTTTCCACCCTTAGTCTGCATGCCGGCTTTGACCCCAGAGACTTTC
CTACCCTTAGTCTGCCTGTCAGTCTTAACCCTAGAGACTTTCCTTGCCCTAGTCTTTCTA
Found at i:4354434 original size:42 final size:43
Alignment explanation
Indices: 4354077--4354448 Score: 268
Period size: 42 Copynumber: 8.9 Consensus size: 43
4354067 CTACCTATCG
** * *
4354077 CTTTCCTTTCCTTAGTCTGCCTATC-GGCTTTGACTCTAGAGA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* * * * *
4354119 CTTAT-CTTCCCTTAGTTTGCCTATC--GATGTTGA-CCTTGAAGA
1 CTT-TCCTACCCTTAGTCTGCCTGTCAGGCT-TTGACCCTAG-AGA
* * * * *
4354161 CTTTCCTTCCCTTAGTGTGCTTGTC-GGTTTTAACCCTAGAGA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* * * *
4354203 CTTTTC-ACCCTTAGTCTGCATGT-TGGCTTTGACCCCAGAGA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* * **
4354244 CTTTCCTTCCCTTAGTCTGCTTGTCA-GCTTCAACCCTAGAGA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* ** *
4354286 CTTTCCTTGCCC-TAGTCTTTCTATC-GGCTTTGACCCTAGAGA
1 CTTTCC-TACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* * * * * *
4354328 CTTTCCTTCCCTTAGTTTGTCTG-CCGGCTTTGACCCTGGATA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* *
4354370 CTTTTCTACCCTTAGTCTGCCTGTCAGTC-TTGACCCTAGAGA
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
* * * *
4354412 CTTTTCTACCCTCAGTCTGCCTGT-TGGCTATGACCCT
1 CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCT
4354449 GAAGACTGCC
Statistics
Matches: 265, Mismatches: 50, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
41 46 0.17
42 205 0.77
43 14 0.05
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (43 bp):
CTTTCCTACCCTTAGTCTGCCTGTCAGGCTTTGACCCTAGAGA
Found at i:4354972 original size:24 final size:24
Alignment explanation
Indices: 4354936--4354982 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4354926 TATTCGGTAT
*
4354936 AAAATATAATAATAAGTAGAAATTG
1 AAAATATAATAATAA-TAAAAATTG
4354961 AAAA-ATAATAATAATAAAAATT
1 AAAATATAATAATAATAAAAATT
4354983 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (24 bp):
AAAATATAATAATAATAAAAATTG
Found at i:4355355 original size:39 final size:38
Alignment explanation
Indices: 4355312--4355387 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
4355302 ACCAAACGTG
*
4355312 GGCAGC-ATGGGAGA-AAAGCTATGCAATGAAGAACATGTA
1 GGCAGCAATGGGAGACAAAGC-AT-CAA-GAAGAAAATGTA
4355351 GGCAGCAATGGGAGACAAAGCATCAAGAAGAAAATGT
1 GGCAGCAATGGGAGACAAAGCATCAAGAAGAAAATGT
4355388 GTCCAGCACA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 10 0.29
39 9 0.26
40 10 0.29
41 5 0.15
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (38 bp):
GGCAGCAATGGGAGACAAAGCATCAAGAAGAAAATGTA
Found at i:4355656 original size:16 final size:16
Alignment explanation
Indices: 4355637--4355673 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4355627 CACGGCAATG
*
4355637 TGAAAGAGCAGCAACA
1 TGAAAGAACAGCAACA
*
4355653 TGAAAGAACAGCAACG
1 TGAAAGAACAGCAACA
4355669 TGAAA
1 TGAAA
4355674 ACAGCCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.24, T:0.08
Consensus pattern (16 bp):
TGAAAGAACAGCAACA
Found at i:4355860 original size:47 final size:47
Alignment explanation
Indices: 4355811--4356090 Score: 230
Period size: 47 Copynumber: 6.0 Consensus size: 47
4355801 AGCCTTCTCT
* * * *
4355811 AGCTTCGATGGCAATAGCAGCTTCCACAAGCAACCGACAGCAACTCT
1 AGCTTCCATGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
* * **
4355858 AGCTTCCACTAGCAGCAGCAGCTTCCACGAGCAACCGACAATAACTCC
1 AGCTTCCA-TGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
* * * *
4355906 AGCTTCCATAGTC-GCAGTAGCTTCCATGAGCAACC-ATCAGCAACTCC
1 AGCTTCCAT-GGCAACAGCAGCTTCCACGAGCAACCGA-CAGCAACTCC
* * * * *
4355953 AGCTTCCATGGTAGCAGCAACTTCCACGAGCAACTGGCAGCAACTCC
1 AGCTTCCATGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
*** * * *
4356000 A-CGAGCA---CAGCAGCAGCTTCCACGAGCAACCGGCAGTAACTCC
1 AGCTTCCATGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
* * * * * *
4356043 AGCTTCCATGGTAATAGTAGCTTCCACGAGCAACTGGCAGCAATTCC
1 AGCTTCCATGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
4356090 A
1 A
4356091 CAAGCAACCA
Statistics
Matches: 186, Mismatches: 38, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
43 33 0.18
44 3 0.02
46 5 0.03
47 104 0.56
48 41 0.22
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.17
Consensus pattern (47 bp):
AGCTTCCATGGCAACAGCAGCTTCCACGAGCAACCGACAGCAACTCC
Found at i:4356003 original size:22 final size:22
Alignment explanation
Indices: 4355966--4356040 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
4355956 TTCCATGGTA
4355966 GCAGCAACTTCCACGAGCAACTG
1 GCAGCAACTTCCACGAGCAAC-G
*
4355989 GCAGCAAC-TCCACGAGC-ACA
1 GCAGCAACTTCCACGAGCAACG
*
4356009 GCAGCAGCTTCCACGAGCAACCG
1 GCAGCAACTTCCACGAGCAA-CG
*
4356032 GCAGTAACT
1 GCAGCAACT
4356041 CCAGCTTCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.16
21 11 0.25
22 10 0.23
23 16 0.36
ACGTcount: A:0.31, C:0.36, G:0.23, T:0.11
Consensus pattern (22 bp):
GCAGCAACTTCCACGAGCAACG
Found at i:4356048 original size:90 final size:89
Alignment explanation
Indices: 4355826--4356104 Score: 281
Period size: 90 Copynumber: 3.1 Consensus size: 89
4355816 CGATGGCAAT
* * * *
4355826 AGCAGCTTCCACAAGCAACCGACAGCAACTCTAGCTTCCACTAGCAGCAGCAGCTTCCACGAGCA
1 AGCAGCTTCCACGAGCAACCGACAGCAACTCCAGCTTCCA-TGGTAGCAGCAGCTTCCACGAGCA
* * ** ***
4355891 ACCGACAATAACTCCAGCTTCCATAGTCGC
65 ACTGGCAGCAACTCCA-CAAGCA-A---GC
* * *
4355921 AGTAGCTTCCATGAGCAACC-ATCAGCAACTCCAGCTTCCATGGTAGCAGCAACTTCCACGAGCA
1 AGCAGCTTCCACGAGCAACCGA-CAGCAACTCCAGCTTCCATGGTAGCAGCAGCTTCCACGAGCA
*
4355985 ACTGGCAGCAACTCCACGAGCACAGC
65 ACTGGCAGCAACTCCACAAGCA-AGC
* * ** *
4356011 AGCAGCTTCCACGAGCAACCGGCAGTAACTCCAGCTTCCATGGTAATAGTAGCTTCCACGAGCAA
1 AGCAGCTTCCACGAGCAACCGACAGCAACTCCAGCTTCCATGGTAGCAGCAGCTTCCACGAGCAA
* *
4356076 CTGGCAGCAATTCCACAAGCAACC
66 CTGGCAGCAACTCCACAAGCAAGC
4356100 AGCAG
1 AGCAG
4356105 TAACTCCATG
Statistics
Matches: 156, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
89 7 0.04
90 77 0.49
93 4 0.03
94 34 0.22
95 34 0.22
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.16
Consensus pattern (89 bp):
AGCAGCTTCCACGAGCAACCGACAGCAACTCCAGCTTCCATGGTAGCAGCAGCTTCCACGAGCAA
CTGGCAGCAACTCCACAAGCAAGC
Found at i:4359040 original size:20 final size:20
Alignment explanation
Indices: 4359015--4359068 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
4359005 CATTACAAGC
*
4359015 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTAACTT
4359035 ATGTATCGATACATTAACTT
1 ATGTATCGATACATTAACTT
*
4359055 ACTATATCGATACA
1 A-TGTATCGATACA
4359069 AATTGTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:4362481 original size:19 final size:19
Alignment explanation
Indices: 4362438--4362509 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
4362428 TGCCAGTTTA
**
4362438 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
4362458 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
*
4362477 ATGTATCGATACAAAGCATA-
1 ATGTATCGATACAATG-A-AC
4362497 ATGTATCGATACA
1 ATGTATCGATACA
4362510 TCTAGGTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:4363171 original size:25 final size:24
Alignment explanation
Indices: 4363132--4363189 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
4363122 CTAGGAATTT
*
4363132 ATGCATG-A-ATGAAGTATCGAGG
1 ATGCATGAACATGAAGTATCGAGA
4363154 ATGCATGGAACATGAAGTATCGAGA
1 ATGCAT-GAACATGAAGTATCGAGA
4363179 ATGCATGAACA
1 ATGCATGAACA
4363190 AGGGCTATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.19
23 1 0.03
24 6 0.19
25 19 0.59
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (24 bp):
ATGCATGAACATGAAGTATCGAGA
Found at i:4363914 original size:32 final size:35
Alignment explanation
Indices: 4363833--4363925 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 35
4363823 AATTGTTTAC
* *
4363833 CTTT-AAGGCTAAGGTATAACCT-TACAACCTTAT
1 CTTTCAAGGCTAAGATAGAACCTCTACAACCTTAT
4363866 CTTTTACAATGGCTAAGATAGAACCTCTAC-A-C-TAT
1 C-TTT-CAA-GGCTAAGATAGAACCTCTACAACCTTAT
4363901 CTTTCAAGGCTAAGATAGAACCTCT
1 CTTTCAAGGCTAAGATAGAACCTCT
4363926 CAATCACTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
32 18 0.34
33 4 0.08
34 6 0.11
35 4 0.08
36 3 0.06
37 15 0.28
38 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (35 bp):
CTTTCAAGGCTAAGATAGAACCTCTACAACCTTAT
Found at i:4364400 original size:14 final size:14
Alignment explanation
Indices: 4364381--4364459 Score: 68
Period size: 14 Copynumber: 6.2 Consensus size: 14
4364371 TTAATGTATC
4364381 GATACATGAACAGT
1 GATACATGAACAGT
4364395 GATACAT-AA-A-T
1 GATACATGAACAGT
4364406 -AGTA-ATGAACAGT
1 GA-TACATGAACAGT
4364419 GATACATGAAC--T
1 GATACATGAACAGT
*
4364431 G-T-GATGAACAGT
1 GATACATGAACAGT
*
4364443 GATACATGAACTGT
1 GATACATGAACAGT
4364457 GAT
1 GAT
4364460 GAACAGTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
10 9 0.17
11 6 0.12
12 6 0.12
13 6 0.12
14 25 0.48
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (14 bp):
GATACATGAACAGT
Found at i:4364418 original size:24 final size:24
Alignment explanation
Indices: 4364386--4364466 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
4364376 GTATCGATAC
* *
4364386 ATGAACAGTGATACAT-AAATAGTA
1 ATGAACAGTGATACATGAACT-GTG
4364410 ATGAACAGTGATACATGAACTGTG
1 ATGAACAGTGATACATGAACTGTG
4364434 ATGAACAGTGATACATGAACTGTG
1 ATGAACAGTGATACATGAACTGTG
4364458 ATGAACAGT
1 ATGAACAGT
4364467 AATGTATCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
24 51 0.94
25 3 0.06
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (24 bp):
ATGAACAGTGATACATGAACTGTG
Found at i:4368393 original size:13 final size:13
Alignment explanation
Indices: 4368375--4368400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4368365 TACAGCAAGT
4368375 ATGTATCGATACA
1 ATGTATCGATACA
4368388 ATGTATCGATACA
1 ATGTATCGATACA
4368401 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4370658 original size:21 final size:21
Alignment explanation
Indices: 4370625--4370669 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
4370615 TTGCAAGTTG
*
4370625 AAATAAAGAAGTTGGCTAAAGA
1 AAATAAAGAAGTTAGCT-AAGA
*
4370647 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
4370667 AAA
1 AAA
4370670 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4372491 original size:15 final size:15
Alignment explanation
Indices: 4372471--4372501 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4372461 TAAAAATGTC
*
4372471 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4372486 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4372501 C
1 C
4372502 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4374737 original size:21 final size:20
Alignment explanation
Indices: 4374713--4374759 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
4374703 AAATCTTTTG
4374713 CAAAATACTT-ATTCTTCACTT
1 CAAAATACTTCATTCTTCA--T
* *
4374734 CAAATTACTTCATTTTTCAT
1 CAAAATACTTCATTCTTCAT
4374754 CAAAAT
1 CAAAAT
4374760 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (20 bp):
CAAAATACTTCATTCTTCAT
Found at i:4385344 original size:23 final size:23
Alignment explanation
Indices: 4385309--4385353 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4385299 ACCTCACAAT
*
4385309 TTCTTCAAGAATTATACCCCAAC
1 TTCTTCAAGAATTATAACCCAAC
*
4385332 TTCTT-AAGAAATTGTAACCCAA
1 TTCTTCAAG-AATTATAACCCAA
4385354 GGTTGAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (23 bp):
TTCTTCAAGAATTATAACCCAAC
Found at i:4385778 original size:20 final size:20
Alignment explanation
Indices: 4385753--4385812 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4385743 GTTGGGCATA
4385753 ATGTATCAATACATTTCATT
1 ATGTATCAATACATTTCATT
* *
4385773 ATGTATTAATACAATGTCCA--
1 ATGTATCAATAC-AT-TTCATT
*
4385793 ATGTATCGATACATTTCATT
1 ATGTATCAATACATTTCATT
4385813 TAGGGTAGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 21 0.68
21 2 0.06
22 3 0.10
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACATTTCATT
Found at i:4385879 original size:19 final size:20
Alignment explanation
Indices: 4385834--4385886 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
4385824 CTGCCAATTT
**
4385834 CATGTATCGATACACTTGAG
1 CATGTATCGATACACAAGAG
*
4385854 TATGTATCGATACA-AAGAG
1 CATGTATCGATACACAAGAG
*
4385873 CATGTATCGGTACA
1 CATGTATCGATACA
4385887 TTGTATTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACACAAGAG
Found at i:4385898 original size:32 final size:33
Alignment explanation
Indices: 4385856--4385920 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
4385846 CACTTGAGTA
* *
4385856 TGTATCGATACAAAG-AGCATGTATCGGTACAT
1 TGTATCGATACAAAGCAGAATGTATCGATACAT
* *
4385888 TGTATTGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAAAGCAGAATGTATCGATACAT
4385921 CTAGATGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAAAGCAGAATGTATCGATACAT
Found at i:4395675 original size:2 final size:2
Alignment explanation
Indices: 4395670--4395707 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4395660 AATTCATTAA
4395670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4395708 GTACACACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4400578 original size:10 final size:10
Alignment explanation
Indices: 4400563--4400604 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
4400553 ATTAAATTAA
4400563 TTTATATATT
1 TTTATATATT
*
4400573 TTTATAAATT
1 TTTATATATT
*
4400583 TTTATATA-A
1 TTTATATATT
4400592 TTTATAT-TT
1 TTTATATATT
4400601 TTTA
1 TTTA
4400605 ATTTGATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 11 0.41
10 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTATATATT
Found at i:4400627 original size:22 final size:22
Alignment explanation
Indices: 4400588--4400629 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4400578 AAATTTTTAT
4400588 ATAATTTATATTTTTTAATTTG
1 ATAATTTATATTTTTTAATTTG
*
4400610 ATAA-TTATTTTTTATTAATT
1 ATAATTTATATTTT-TTAATT
4400630 ATTTACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATAATTTATATTTTTTAATTTG
Found at i:4401627 original size:14 final size:14
Alignment explanation
Indices: 4401608--4401638 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4401598 TGAAACTTCT
4401608 TTTTCTTTATATCG
1 TTTTCTTTATATCG
4401622 TTTTCTTTATATCG
1 TTTTCTTTATATCG
4401636 TTT
1 TTT
4401639 CAAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTCTTTATATCG
Found at i:4401663 original size:2 final size:2
Alignment explanation
Indices: 4401656--4401696 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4401646 GAAAAGGAAA
4401656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4401697 GTTTTCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4401913 original size:60 final size:60
Alignment explanation
Indices: 4401820--4401935 Score: 223
Period size: 60 Copynumber: 1.9 Consensus size: 60
4401810 CACTAGGCAG
*
4401820 TCATTCCAAGAAATGTCATAGCAAAGATCATTAATCAAGGACTATATATATATATATATA
1 TCATTCCAAGAAATGTCATAGCAAAGATCATTAATCAAGGAATATATATATATATATATA
4401880 TCATTCCAAGAAATGTCATAGCAAAGATCATTAATCAAGGAATATATATATATATA
1 TCATTCCAAGAAATGTCATAGCAAAGATCATTAATCAAGGAATATATATATATATA
4401936 CATACACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (60 bp):
TCATTCCAAGAAATGTCATAGCAAAGATCATTAATCAAGGAATATATATATATATATATA
Found at i:4402058 original size:2 final size:2
Alignment explanation
Indices: 4401921--4402047 Score: 110
Period size: 2 Copynumber: 63.5 Consensus size: 2
4401911 TAATCAAGGA
* * * *
4401921 AT AT AT AT AT AT AT AC AT AC AC AT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
4401963 AT AT AT AT AC AT AC AC AT AT AT AT AT CT AT AT AT AT AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
4402005 AC AC AC AC AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4402047 A
1 A
4402048 CACGTATATA
Statistics
Matches: 107, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:4405283 original size:16 final size:18
Alignment explanation
Indices: 4405256--4405294 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
4405246 ATTTAAAGGG
4405256 GATAATATCGAAAT-AAT
1 GATAATATCGAAATCAAT
4405273 GATAA-ATCGAAATCAAT
1 GATAATATCGAAATCAAT
4405290 G-TAAT
1 GATAAT
4405295 CAACATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (18 bp):
GATAATATCGAAATCAAT
Found at i:4409444 original size:17 final size:17
Alignment explanation
Indices: 4409422--4409459 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4409412 TGATTAGTTT
*
4409422 GTTGGCAACTAGTTTAG
1 GTTGGCAACCAGTTTAG
*
4409439 GTTGGCATCCAGTTTAG
1 GTTGGCAACCAGTTTAG
4409456 GTTG
1 GTTG
4409460 ACATCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (17 bp):
GTTGGCAACCAGTTTAG
Found at i:4409464 original size:17 final size:17
Alignment explanation
Indices: 4409432--4409466 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4409422 GTTGGCAACT
*
4409432 AGTTTAGGTTGGCATCC
1 AGTTTAGGTTGACATCC
4409449 AGTTTAGGTTGACATCC
1 AGTTTAGGTTGACATCC
4409466 A
1 A
4409467 ATTTCTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (17 bp):
AGTTTAGGTTGACATCC
Found at i:4409747 original size:9 final size:10
Alignment explanation
Indices: 4409733--4409793 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
4409723 AGGTTCAACT
4409733 AAAAAAAGA-
1 AAAAAAAGAG
4409742 AAAAAAAGAG
1 AAAAAAAGAG
4409752 AAAAAAAAGAG
1 -AAAAAAAGAG
*
4409763 AAAGAAAATAG
1 AAA-AAAAGAG
* *
4409774 AGAAGAAATAG
1 A-AAAAAAGAG
*
4409785 AAACAAAGA
1 AAAAAAAGA
4409794 TGTAGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 24 0.55
12 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:4409753 original size:11 final size:11
Alignment explanation
Indices: 4409733--4409777 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
4409723 AGGTTCAACT
4409733 AAAAAA-AGAA
1 AAAAAAGAGAA
4409743 AAAAAAGAGAA
1 AAAAAAGAGAA
4409754 AAAAAAGAGAA
1 AAAAAAGAGAA
4409765 AGAAAATAGAGAA
1 A-AAAA-AGAGAA
4409778 GAAATAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.19
11 16 0.50
12 4 0.12
13 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:4409764 original size:22 final size:23
Alignment explanation
Indices: 4409733--4409777 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
4409723 AGGTTCAACT
4409733 AAAAAAAGAAA-AAAA-AGAGAA
1 AAAAAAAGAAAGAAAATAGAGAA
4409754 AAAAAAGAGAAAGAAAATAGAGAA
1 AAAAAA-AGAAAGAAAATAGAGAA
4409778 GAAATAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 4 0.19
24 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAAAGAAAGAAAATAGAGAA
Found at i:4411600 original size:89 final size:89
Alignment explanation
Indices: 4411486--4411655 Score: 283
Period size: 89 Copynumber: 1.9 Consensus size: 89
4411476 TTTTTTCATC
*
4411486 GGGATACTCTAACCCTATTCCTCCGATGG-GATACTCCAA-CCTCGCTTTTAAACACATCAAAGT
1 GGGACACTCTAACCCTATTCCTCCGA-GGAGATACTCCAACCCT-GCTTTTAAACACATCAAAGT
4411549 TTAAATCTTATTCTCACTCATCATTG
64 TTAAATCTTATTCTCACTCATCATTG
4411575 GGGACACTCTAA-CCTCATTCCTCCGAGGAGATACTCCAACCCTGCTTTTAAACACATCAAAGTT
1 GGGACACTCTAACCCT-ATTCCTCCGAGGAGATACTCCAACCCTGCTTTTAAACACATCAAAGTT
4411639 TAAATCTTATTCTCACT
65 TAAATCTTATTCTCACT
4411656 TAAATTGTCA
Statistics
Matches: 77, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
88 5 0.06
89 69 0.90
90 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (89 bp):
GGGACACTCTAACCCTATTCCTCCGAGGAGATACTCCAACCCTGCTTTTAAACACATCAAAGTTT
AAATCTTATTCTCACTCATCATTG
Found at i:4413197 original size:18 final size:19
Alignment explanation
Indices: 4413174--4413217 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4413164 TTCTAGAGTT
*
4413174 TGTATC-TATATAAGTTAA
1 TGTATCATACATAAGTTAA
4413192 TGTATCAATACATAAGTTAA
1 TGTATC-ATACATAAGTTAA
4413212 TGTATC
1 TGTATC
4413218 GATGCATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (19 bp):
TGTATCATACATAAGTTAA
Found at i:4419125 original size:2 final size:2
Alignment explanation
Indices: 4419120--4419149 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4419110 AATAAAAGAA
4419120 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4419150 CTTACTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4427613 original size:2 final size:2
Alignment explanation
Indices: 4427608--4427651 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4427598 TTATTGTGTG
4427608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4427649 TA T
1 TA T
4427652 TTGATTGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4435851 original size:18 final size:19
Alignment explanation
Indices: 4435824--4435861 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4435814 TATCAAATAT
*
4435824 TAACAAAATA-ATAGTAAA
1 TAACAAAATAGAAAGTAAA
*
4435842 TAACACAATAGAAAGTAAA
1 TAACAAAATAGAAAGTAAA
4435861 T
1 T
4435862 CAAAGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (19 bp):
TAACAAAATAGAAAGTAAA
Found at i:4436870 original size:11 final size:11
Alignment explanation
Indices: 4436830--4436869 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
4436820 AAAAAAATAT
4436830 ATATTATGTAA
1 ATATTATGTAA
4436841 ATATTATGTAA
1 ATATTATGTAA
4436852 ATATTAT-TAA
1 ATATTATGTAA
4436862 ATAATTAT
1 AT-ATTAT
4436870 TTAATTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
ATATTATGTAA
Found at i:4437557 original size:19 final size:20
Alignment explanation
Indices: 4437533--4437588 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4437523 TGTATCGATA
* *
4437533 CATTGTATCAATACATG-TT
1 CATTGTATCGATACATGCAT
*
4437552 CATTGTATTGATACATGCAT
1 CATTGTATCGATACATGCAT
*
4437572 AATTGTATCGATACATG
1 CATTGTATCGATACATG
4437589 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
CATTGTATCGATACATGCAT
Found at i:4437656 original size:13 final size:13
Alignment explanation
Indices: 4437638--4437662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4437628 CATGGCATAT
4437638 TGTATCGATACAA
1 TGTATCGATACAA
4437651 TGTATCGATACA
1 TGTATCGATACA
4437663 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4441874 original size:79 final size:80
Alignment explanation
Indices: 4441724--4441895 Score: 217
Period size: 79 Copynumber: 2.2 Consensus size: 80
4441714 ACCGAGACTA
* * * * *
4441724 GAGTATCCCCGATTATGAAAAATCGGTGTTTTAGAAATAAAAATTGGGGTTGGAGTATCCCTTCG
1 GAGTATCCCCGATTATGAAAAATCGATATTTTAGAAATAAAAATCGGGGTTGGAGTATCCCCTCA
4441789 AAAATAATAGGG-TTG
66 AAAATAA-AGGGATTG
* *
4441804 GAGTATCTCTGATTAT-AGAAAATCGATATTTT-GAAA-ATAAAATCGGGGTTGGAGTATCCCCT
1 GAGTATCCCCGATTATGA-AAAATCGATATTTTAGAAATA-AAAATCGGGGTTGGAGTATCCCCT
*
4441866 CAAAAATAACGGGATTG
64 CAAAAATAAAGGGATTG
4441883 GAGTATCCCCGAT
1 GAGTATCCCCGAT
4441896 GAAATAACGG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
78 4 0.05
79 49 0.62
80 26 0.33
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (80 bp):
GAGTATCCCCGATTATGAAAAATCGATATTTTAGAAATAAAAATCGGGGTTGGAGTATCCCCTCA
AAAATAAAGGGATTG
Found at i:4441883 original size:28 final size:28
Alignment explanation
Indices: 4441840--4441920 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
4441830 TATTTTGAAA
4441840 ATAAAAT--CGGGGTTGGAGTATCCCCTC
1 ATAAAATAACGGGGTTGGAGTATCCCC-C
* *
4441867 A-AAAATAACGGGATTGGAGTATCCCCG
1 ATAAAATAACGGGGTTGGAGTATCCCCC
*
4441894 ATGAAATAACGGGGTTGGAGTA-CCCCC
1 ATAAAATAACGGGGTTGGAGTATCCCCC
4441921 GATTATGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 5 0.11
27 6 0.13
28 35 0.76
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (28 bp):
ATAAAATAACGGGGTTGGAGTATCCCCC
Found at i:4441982 original size:109 final size:109
Alignment explanation
Indices: 4441840--4442041 Score: 332
Period size: 109 Copynumber: 1.9 Consensus size: 109
4441830 TATTTTGAAA
* *
4441840 ATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGAAATAACG
1 ATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGAAACAACA
*
4441905 GGGTTGGAGTACCCCCGATTATGAAAAAAATAATATTTTTCGAT
66 GGGTTGGAGTACCCCCAATTATGAAAAAAATAATATTTTTCGAT
* * *
4441949 ATAAAGTCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAACAACA
1 ATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGAAACAACA
* *
4442014 GGGTTGGAGTATCCCCAATTGTGAAAAA
66 GGGTTGGAGTACCCCCAATTATGAAAAA
4442042 TTGGTGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 85 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (109 bp):
ATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGAAACAACA
GGGTTGGAGTACCCCCAATTATGAAAAAAATAATATTTTTCGAT
Found at i:4441996 original size:28 final size:28
Alignment explanation
Indices: 4441956--4442029 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
4441946 GATATAAAGT
*
4441956 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-CATGAAACAA
*
4441984 CGGGGTTGGAGTATCCCCGATGAAACAA
1 CGGGGTTGGAGTATCCCCCATGAAACAA
*
4442012 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
4442030 AATTGTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAACAA
Found at i:4442124 original size:51 final size:51
Alignment explanation
Indices: 4442016--4442133 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
4442006 AAACAACAGG
* ** *
4442016 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGAAAATAAAATCGGA
* * * * *
4442067 GGTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGTAAATGGAACTGGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGAAAAT-AAAATCGGA
4442119 -TTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
4442134 GGTGAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 50 0.89
52 6 0.11
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGAAAATAAAATCGGA
Found at i:4444438 original size:16 final size:16
Alignment explanation
Indices: 4444417--4444483 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
4444407 AAAATGCCTG
**
4444417 AATGTATCGATACATT
1 AATGTATCGATACAGC
*
4444433 AATGTATCGATAAGAGC
1 AATGTATCGAT-ACAGC
4444450 AATGTATCGATACAATGC
1 AATGTATCGATAC-A-GC
4444468 AAAATGTATCGATACA
1 --AATGTATCGATACA
4444484 TCTGGGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 12 0.29
17 14 0.33
18 2 0.05
19 1 0.02
20 13 0.31
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (16 bp):
AATGTATCGATACAGC
Found at i:4448835 original size:13 final size:13
Alignment explanation
Indices: 4448817--4448843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4448807 ACATTATGCT
4448817 TTGTATCGATACA
1 TTGTATCGATACA
4448830 TTGTATCGATACA
1 TTGTATCGATACA
4448843 T
1 T
4448844 GTTCATTGGA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4450693 original size:13 final size:13
Alignment explanation
Indices: 4450675--4450700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4450665 CAATTTTTTG
4450675 TGTATCGATACAT
1 TGTATCGATACAT
4450688 TGTATCGATACAT
1 TGTATCGATACAT
4450701 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4453098 original size:21 final size:21
Alignment explanation
Indices: 4453074--4453120 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4453064 TTTGATGCTG
4453074 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
4453094 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
4453115 ATTTTG
1 ATTTTG
4453121 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4453259 original size:13 final size:13
Alignment explanation
Indices: 4453241--4453279 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4453231 ATAATCACCC
*
4453241 TGTATCGATACAG
1 TGTATCGATACAA
4453254 TGTATCGATACAA
1 TGTATCGATACAA
4453267 TGTATCGATACAA
1 TGTATCGATACAA
4453280 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4453290 original size:20 final size:20
Alignment explanation
Indices: 4453265--4453343 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
4453255 GTATCGATAC
4453265 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4453285 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
4453310 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
4453330 CATGTATCGATACA
1 AATGTATCGATACA
4453344 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:4455370 original size:15 final size:15
Alignment explanation
Indices: 4455350--4455380 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4455340 ATTTCGTTTG
*
4455350 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4455365 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4455380 G
1 G
4455381 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4457213 original size:21 final size:21
Alignment explanation
Indices: 4457184--4457228 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4457174 AAGTTTTCAT
*
4457184 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4457204 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4457226 TTT
1 TTT
4457229 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4459465 original size:13 final size:13
Alignment explanation
Indices: 4459447--4459472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4459437 CAATTTTTTG
4459447 TGTATCGATACAT
1 TGTATCGATACAT
4459460 TGTATCGATACAT
1 TGTATCGATACAT
4459473 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4460232 original size:19 final size:18
Alignment explanation
Indices: 4460191--4460231 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4460181 TAATGGCCCT
* * *
4460191 AAAATGATGAAATTTGCC
1 AAAAAGATGAAATTTACA
4460209 AAAAAGATGAAATTTACA
1 AAAAAGATGAAATTTACA
4460227 AAAAA
1 AAAAA
4460232 AATCCTAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (18 bp):
AAAAAGATGAAATTTACA
Found at i:4461793 original size:164 final size:163
Alignment explanation
Indices: 4461591--4461977 Score: 544
Period size: 164 Copynumber: 2.3 Consensus size: 163
4461581 TTAATTACCA
* * * *
4461591 TTAAATTAGTTTTAAAAAATTCATTTATTTTCATTAGTTTCTCATTTTTCCTTAAAATTTTCCAA
1 TTAAATCAATTTTAAAAAATT-ATTTATTTTCATTAGTTTTTCATTTTTCCTTGAAATTTTCCAA
* *
4461656 TTAT-AAAAAAATGAGTCTT-CTATTTCATAAATGTTTTTAGGGGGATTTTTCTCGATTTAAAAT
65 TTATCAAAAAAATGAGT-TTCCTATTTCATAAATG-TTTTAGGGGGATTTTTCTCAAATTAAAAT
4461719 TTTTAAAATTCATCTAACATTGTCATTAGACTCCCT
128 TTTTAAAATTCATCTAACATTGTCATTAGACTCCCT
* * * *
4461755 TTAAATCAATTTTGAGAAAATTATTTATTTTCATTAGTTTTTCATTTTTTCTTGAAATTTTTCTA
1 TTAAATCAATTTT-AAAAAATTATTTATTTTCATTAGTTTTTCATTTTTCCTTGAAATTTTCCAA
* * *
4461820 TTTTCGAAAAACTGAGTTTCCTATTTCATAAATGTTTTAGGGGGATTTTTCTCAAATTAAAATTT
65 TTATCAAAAAAATGAGTTTCCTATTTCATAAATGTTTTAGGGGGATTTTTCTCAAATTAAAATTT
* *
4461885 TTAAAATTCATGTAACATTGTCATTAGACTCCTT
130 TTAAAATTCATCTAACATTGTCATTAGACTCCCT
* * *
4461919 TTAAATTAGTTTTAAAAAATTTATTTATTTTCATAAGTTTTTCATTTTTTCCTTGAAAT
1 TTAAATCAATTTTAAAAAA-TTATTTATTTTCATTAGTTTTTCA-TTTTTCCTTGAAAT
4461978 GACCTTATTT
Statistics
Matches: 198, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
163 5 0.03
164 149 0.75
165 44 0.22
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (163 bp):
TTAAATCAATTTTAAAAAATTATTTATTTTCATTAGTTTTTCATTTTTCCTTGAAATTTTCCAAT
TATCAAAAAAATGAGTTTCCTATTTCATAAATGTTTTAGGGGGATTTTTCTCAAATTAAAATTTT
TAAAATTCATCTAACATTGTCATTAGACTCCCT
Found at i:4463257 original size:20 final size:20
Alignment explanation
Indices: 4463232--4463269 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4463222 GATACAGTTG
*
4463232 GTGAATATATCGATACATAA
1 GTGAATATATCCATACATAA
*
4463252 GTGAATGTATCCATACAT
1 GTGAATATATCCATACAT
4463270 GTCTCAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
GTGAATATATCCATACATAA
Found at i:4469374 original size:77 final size:78
Alignment explanation
Indices: 4469230--4469378 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 78
4469220 CAACCCCGGT
* * * * * *
4469230 TTTATTTCTAAAACATCGATTTTTCACCATCAAGGATACTCCAATCCTGTTGCTTTCGAGGGGAT
1 TTTATTCCCAAAACATCGATTTTCCACCATCAAGGATACTCCAACCCTATTACTTTCGAGGGGAT
4469295 ACTCCAAACCCGA
66 ACTCCAAACCCGA
* * *
4469308 TTTATTCCCAAAACATCGATTTTCCACCATC-GGGATACTCCAACCCTATTATTTTTGAGGGGAT
1 TTTATTCCCAAAACATCGATTTTCCACCATCAAGGATACTCCAACCCTATTACTTTCGAGGGGAT
4469372 ACTCCAA
66 ACTCCAA
4469379 CCCTGTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
77 34 0.55
78 28 0.45
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (78 bp):
TTTATTCCCAAAACATCGATTTTCCACCATCAAGGATACTCCAACCCTATTACTTTCGAGGGGAT
ACTCCAAACCCGA
Found at i:4471969 original size:13 final size:13
Alignment explanation
Indices: 4471948--4471977 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4471938 CGATACATGG
*
4471948 TACATTGTATCGA
1 TACAATGTATCGA
4471961 TACAATGTATCGA
1 TACAATGTATCGA
4471974 TACA
1 TACA
4471978 TTGCTTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:4478761 original size:13 final size:13
Alignment explanation
Indices: 4478743--4478778 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4478733 GCATTCTCTA
*
4478743 TATCGATACATTG
1 TATCGATACAGTG
*
4478756 TATCGATATAGTG
1 TATCGATACAGTG
4478769 TATCGATACA
1 TATCGATACA
4478779 AGGGGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:4479779 original size:18 final size:17
Alignment explanation
Indices: 4479752--4479785 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4479742 CAAAGAGGGC
*
4479752 TCGATTCCTCGAAACAT
1 TCGATTCCTCAAAACAT
4479769 TCGAGTTCCTCAAAACA
1 TCGA-TTCCTCAAAACA
4479786 AAGCCACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (17 bp):
TCGATTCCTCAAAACAT
Found at i:4481210 original size:13 final size:13
Alignment explanation
Indices: 4481192--4481216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4481182 ATAATGCACA
4481192 GTATCGATACATT
1 GTATCGATACATT
4481205 GTATCGATACAT
1 GTATCGATACAT
4481217 GACCACTGTA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:4481337 original size:32 final size:33
Alignment explanation
Indices: 4481296--4481363 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
4481286 CCTTAACTAT
4481296 TTGTATCGATACAT-A-CAAGATATATCGATACA
1 TTGTATCGATACATGACCAA-ATATATCGATACA
*
4481328 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATATATCGATACA
4481361 TTG
1 TTG
4481364 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATATATCGATACA
Found at i:4481960 original size:19 final size:20
Alignment explanation
Indices: 4481936--4481987 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
4481926 TAGCTAAACT
4481936 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
4481955 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
4481976 TGTATCGATACA
1 TGTATCGATACA
4481988 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:4488163 original size:13 final size:13
Alignment explanation
Indices: 4488145--4488169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4488135 CATTTTTCTT
4488145 TGTATCGATACAC
1 TGTATCGATACAC
4488158 TGTATCGATACA
1 TGTATCGATACA
4488170 GGAGGATTAT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:4490725 original size:19 final size:19
Alignment explanation
Indices: 4490701--4490765 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
4490691 TAGCCAAACT
4490701 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
4490720 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
4490733 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
4490754 TGTATCGATACA
1 TGTATCGATACA
4490766 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:4490737 original size:13 final size:13
Alignment explanation
Indices: 4490719--4490744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4490709 TACACAAAAT
4490719 ATGTATCGATACA
1 ATGTATCGATACA
4490732 ATGTATCGATACA
1 ATGTATCGATACA
4490745 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4490742 original size:32 final size:33
Alignment explanation
Indices: 4490701--4490765 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
4490691 TAGCCAAACT
4490701 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
4490733 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
4490766 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:4496347 original size:19 final size:21
Alignment explanation
Indices: 4496323--4496363 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
4496313 GAAATTTTCT
4496323 AGAATGTAT-GATACAT-TGA
1 AGAATGTATCGATACATCTGA
4496342 AGAATGTATCGATACATCTGA
1 AGAATGTATCGATACATCTGA
4496363 A
1 A
4496364 AAACCCAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AGAATGTATCGATACATCTGA
Found at i:4496410 original size:13 final size:13
Alignment explanation
Indices: 4496392--4496430 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4496382 ACAATATTCT
4496392 TTGTATCGATACA
1 TTGTATCGATACA
*
4496405 TTGTATCGACACA
1 TTGTATCGATACA
4496418 TTGTATCGATACA
1 TTGTATCGATACA
4496431 AGGGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4497755 original size:280 final size:280
Alignment explanation
Indices: 4497254--4497815 Score: 1070
Period size: 280 Copynumber: 2.0 Consensus size: 280
4497244 GCTTTTCTTA
*
4497254 GTAACGCTCGTCTCGAGCATAATGATAGCAATGAAGTAGTTGCTATTCATTCCTACCTCATGGGT
1 GTAACGCTCGTCTCGAGCATAACGATAGCAATGAAGTAGTTGCTATTCATTCCTACCTCATGGGT
4497319 CAAGACTTGATCCTAACCCCCTCCATTCTAGCCGACACACTAAACATGCCGTATAAAAGAGAGAC
66 CAAGACTTGATCCTAACCCCCTCCATTCTAGCCGACACACTAAACATGCCGTATAAAAGAGAGAC
*
4497384 CAAAGAGGGGACGGCTCTTCGTAACACTAGAGTTCCTTTAAATAAAGCCACTCGCCTTCCACCTC
131 CAAAGAGGGGACGACTCTTCGTAACACTAGAGTTCCTTTAAATAAAGCCACTCGCCTTCCACCTC
*
4497449 ATGATCGTTACCTTCACCTTCTCATAACCTATATCTTTCGACTGTTCGGCACCCAATACTCAACC
196 ATGATCGTTACCTTCACCTTCTCATAACCTATATCTTCCGACTGTTCGGCACCCAATACTCAACC
*
4497514 CTCAATAACTCCGATTACTG
261 CTCAATAACTCCAATTACTG
4497534 GTAACGCTCGTCTCGAGCATAACGATAGCAATGAAGTAGTTGCTATTCATTCCTACCTCATGGGT
1 GTAACGCTCGTCTCGAGCATAACGATAGCAATGAAGTAGTTGCTATTCATTCCTACCTCATGGGT
* *
4497599 CAAGACTTGATCCTAACTCCCTCCATTCTAGCCGACACACTAAACATGCCGTATAAAGGAGAGAC
66 CAAGACTTGATCCTAACCCCCTCCATTCTAGCCGACACACTAAACATGCCGTATAAAAGAGAGAC
4497664 CAAAGAGGGGACGACTCTTCGTAACACTAGAGTTCCTTTAAATAAAGCCACTCGCCTTCCACCTC
131 CAAAGAGGGGACGACTCTTCGTAACACTAGAGTTCCTTTAAATAAAGCCACTCGCCTTCCACCTC
4497729 ATGATCGTTACCTTCACCTTCTCATAACCTATATCTTCCGACTGTTCGGCACCCAATACTCAACC
196 ATGATCGTTACCTTCACCTTCTCATAACCTATATCTTCCGACTGTTCGGCACCCAATACTCAACC
4497794 CTCAATAACTCCAATTACTG
261 CTCAATAACTCCAATTACTG
4497814 GT
1 GT
4497816 GGCTTCACAT
Statistics
Matches: 276, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
280 276 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (280 bp):
GTAACGCTCGTCTCGAGCATAACGATAGCAATGAAGTAGTTGCTATTCATTCCTACCTCATGGGT
CAAGACTTGATCCTAACCCCCTCCATTCTAGCCGACACACTAAACATGCCGTATAAAAGAGAGAC
CAAAGAGGGGACGACTCTTCGTAACACTAGAGTTCCTTTAAATAAAGCCACTCGCCTTCCACCTC
ATGATCGTTACCTTCACCTTCTCATAACCTATATCTTCCGACTGTTCGGCACCCAATACTCAACC
CTCAATAACTCCAATTACTG
Found at i:4500456 original size:162 final size:162
Alignment explanation
Indices: 4500284--4500740 Score: 743
Period size: 162 Copynumber: 2.8 Consensus size: 162
4500274 TTAATTCAAT
* * * * *
4500284 TTAATTTTATTTATTTTCGAAAATACCATTTCATATCCTAAGGGAAGCCCAAAAGGATACAAAAG
1 TTAATTTTATTTATTTTTGAAAATACCATTTCATATCCTAATGGAAGCCCGAAAGAATACGAAAG
*
4500349 GTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGACTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
* *
4500414 ATTAGAATTTATCCCAATAATACCAATTTCAG
131 ATTAGAATTTATCCCAATAATACCAATATAAG
* ** *
4500446 TTAATTTTATTTGTTTTTGAAAATACCATTTTGTATCCTAATGGAAGCCCGAAAGAATATGAAAG
1 TTAATTTTATTTATTTTTGAAAATACCATTTCATATCCTAATGGAAGCCCGAAAGAATACGAAAG
*
4500511 GTTTTTGAAATCTTTTATACCCCTACGGAAGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
4500576 ATTAGAATTTATCCCAATAATACCAATATAAG
131 ATTAGAATTTATCCCAATAATACCAATATAAG
* * *
4500608 TTAATTTTATTTATTTTTGAAAATACCATTTCATACCCTAATAGAAGCCCGAAAGAATAGGAAAG
1 TTAATTTTATTTATTTTTGAAAATACCATTTCATATCCTAATGGAAGCCCGAAAGAATACGAAAG
* * *
4500673 GTTTTTGAAATCTTTTATATCCCTACGAATGCCCATAAGAATATAAAAGATTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
4500738 ATT
131 ATT
4500741 GTTTTCTTTT
Statistics
Matches: 272, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 272 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (162 bp):
TTAATTTTATTTATTTTTGAAAATACCATTTCATATCCTAATGGAAGCCCGAAAGAATACGAAAG
GTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
ATTAGAATTTATCCCAATAATACCAATATAAG
Found at i:4504054 original size:50 final size:50
Alignment explanation
Indices: 4503920--4504055 Score: 186
Period size: 50 Copynumber: 2.7 Consensus size: 50
4503910 TTTGCCTGTG
* * *
4503920 TGTATCGATACATTGA-CAATGTATCGATACATCTCAGTAAAATACTTAGA
1 TGTATCGATACATTGATCAATGTATCGATACAT-TTAGTAAAAAACTCAGA
4503970 TGTATCGATACATTGATCAATGTATCGATACATTTAGTAAAAAA-TCCAGA
1 TGTATCGATACATTGATCAATGTATCGATACATTTAGTAAAAAACT-CAGA
* * *
4504020 TGTATTGATACATTAATAAATGTATCGATACATTTA
1 TGTATCGATACATTGATCAATGTATCGATACATTTA
4504056 TCATTGTATT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
49 1 0.01
50 61 0.78
51 16 0.21
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (50 bp):
TGTATCGATACATTGATCAATGTATCGATACATTTAGTAAAAAACTCAGA
Found at i:4504074 original size:20 final size:20
Alignment explanation
Indices: 4504019--4504074 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4504009 AAAAATCCAG
*
4504019 ATGTATTGATACATTAATAA
1 ATGTATTGATACATTTATAA
* *
4504039 ATGTATCGATACATTTATCA
1 ATGTATTGATACATTTATAA
*
4504059 TTGTATTGATACATTT
1 ATGTATTGATACATTT
4504075 CCTTGGCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATTGATACATTTATAA
Found at i:4504999 original size:13 final size:13
Alignment explanation
Indices: 4504981--4505006 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4504971 ACAATCCTTC
4504981 ATGTATCGATACA
1 ATGTATCGATACA
4504994 ATGTATCGATACA
1 ATGTATCGATACA
4505007 TTTCACTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4505073 original size:13 final size:13
Alignment explanation
Indices: 4505055--4505081 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4505045 TACAATGAGC
4505055 ATGTATCGATACA
1 ATGTATCGATACA
4505068 ATGTATCGATACA
1 ATGTATCGATACA
4505081 A
1 A
4505082 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4513016 original size:19 final size:19
Alignment explanation
Indices: 4512992--4513107 Score: 139
Period size: 19 Copynumber: 6.7 Consensus size: 19
4512982 TTTCAACAAT
4512992 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
4513011 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
4513025 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
4513043 TTGTATCGATACAAAAGTG
1 TTGTATCGATACATAAGTG
4513062 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
4513076 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
4513094 TTGTATCGATACAT
1 TTGTATCGATACAT
4513108 TGTATCGATA
Statistics
Matches: 84, Mismatches: 1, Indels: 24
0.77 0.01 0.22
Matches are distributed among these distances:
13 22 0.26
15 4 0.05
17 4 0.05
19 54 0.64
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:4513030 original size:13 final size:13
Alignment explanation
Indices: 4513012--4513036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4513002 ACATAAGTGT
4513012 TGTATCGATACAA
1 TGTATCGATACAA
4513025 TGTATCGATACA
1 TGTATCGATACA
4513037 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4513030 original size:32 final size:32
Alignment explanation
Indices: 4512993--4513056 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4512983 TTCAACAATT
4512993 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4513025 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4513057 AAGTGTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:4513068 original size:51 final size:51
Alignment explanation
Indices: 4512992--4513106 Score: 221
Period size: 51 Copynumber: 2.3 Consensus size: 51
4512982 TTTCAACAAT
*
4512992 TTGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTGTTGTATCGATACAATGTATCGATACATAAGTG
4513043 TTGTATCGATACAAAAGTGTTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTGTTGTATCGATACAATGTATCGATACATAAGTG
4513094 TTGTATCGATACA
1 TTGTATCGATACA
4513107 TTGTATCGAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGTATCGATACAAAAGTGTTGTATCGATACAATGTATCGATACATAAGTG
Found at i:4513080 original size:32 final size:32
Alignment explanation
Indices: 4513044--4513121 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
4513034 ACATAAGTGT
4513044 TGTATCGATACAAAAGTGTTGTATCGATACAA
1 TGTATCGATACAAAAGTGTTGTATCGATACAA
* *
4513076 TGTATCGATACATAAGTGTTGTATCGATACAT
1 TGTATCGATACAAAAGTGTTGTATCGATACAA
4513108 TGTATCGATACAAA
1 TGTATCGATACAAA
4513122 GCTACTGCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAAGTGTTGTATCGATACAA
Found at i:4513081 original size:13 final size:13
Alignment explanation
Indices: 4513063--4513120 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
4513053 ACAAAAGTGT
4513063 TGTATCGATACAA
1 TGTATCGATACAA
4513076 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
4513091 GTGTTGTATCGATACAT
1 ----TGTATCGATACAA
4513108 TGTATCGATACAA
1 TGTATCGATACAA
4513121 AGCTACTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 23 0.62
15 2 0.05
17 1 0.03
19 11 0.30
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4513161 original size:20 final size:20
Alignment explanation
Indices: 4513136--4513202 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
4513126 CTGCCAAGGA
4513136 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
4513156 AATGTATCG----A-TA--C
1 AATGTATCGATACATTACTC
4513169 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
4513189 AATGTATCGATACA
1 AATGTATCGATACA
4513203 ATGTATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 24 0.60
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:4513173 original size:13 final size:13
Alignment explanation
Indices: 4513155--4513215 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
4513145 ATACATTACT
4513155 CAATGTATCGATA
1 CAATGTATCGATA
4513168 CAATGTATCGATA
1 CAATGTATCGATA
4513181 C-AT-TA-C--T-
1 CAATGTATCGATA
4513188 CAATGTATCGATA
1 CAATGTATCGATA
4513201 CAATGTATCGATA
1 CAATGTATCGATA
4513214 CA
1 CA
4513216 TTGATCTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 2 0.05
10 2 0.05
11 2 0.05
12 3 0.07
13 29 0.69
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:4513178 original size:33 final size:33
Alignment explanation
Indices: 4513136--4513235 Score: 166
Period size: 33 Copynumber: 3.0 Consensus size: 33
4513126 CTGCCAAGGA
4513136 AATGTATCGATACATTACTCAATGTATCGATAC
1 AATGTATCGATACATTACTCAATGTATCGATAC
4513169 AATGTATCGATACATTACTCAATGTATCGATAC
1 AATGTATCGATACATTACTCAATGTATCGATAC
**
4513202 AATGTATCGATACATTGA-TCTTTGTATCGATAC
1 AATGTATCGATACATT-ACTCAATGTATCGATAC
4513235 A
1 A
4513236 TCTGGGAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (33 bp):
AATGTATCGATACATTACTCAATGTATCGATAC
Found at i:4513266 original size:51 final size:51
Alignment explanation
Indices: 4513203--4513338 Score: 229
Period size: 51 Copynumber: 2.7 Consensus size: 51
4513193 TATCGATACA
4513203 ATGTATCGATACATTGATCTTTGTATCGATACATCTGGGAATTTTACCCAG
1 ATGTATCGATACATTGATCTTTGTATCGATACATCTGGGAATTTTACCCAG
*
4513254 ATGTATCGATACATTGATCTTCGTATCGATACATCTGGGAATTTTACCCAG
1 ATGTATCGATACATTGATCTTTGTATCGATACATCTGGGAATTTTACCCAG
**
4513305 ATGTATCGATACATT-ACTCAATGTATCGATACAT
1 ATGTATCGATACATTGA-TCTTTGTATCGATACAT
4513339 GCAGGCAAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 1 0.01
51 79 0.99
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (51 bp):
ATGTATCGATACATTGATCTTTGTATCGATACATCTGGGAATTTTACCCAG
Found at i:4514233 original size:20 final size:20
Alignment explanation
Indices: 4514188--4514233 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
4514178 GTTAACAGCC
*
4514188 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
4514208 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
4514229 CATGT
1 CATGT
4514234 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:4516665 original size:52 final size:52
Alignment explanation
Indices: 4516602--4516730 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
4516592 CACTGACCTT
* *
4516602 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
* * *
4516654 TGTATTAATACATACAGGCAAATTTGCCCAGATGTATCAATATACTATGAAA
1 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
*
4516706 TGTATCGATACATGCAGGCAAATTT
1 TGTATCAATACATGCAGGCAAATTT
4516731 TCATATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
Found at i:4539469 original size:9 final size:8
Alignment explanation
Indices: 4539455--4539503 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 8
4539445 TTTCTTACCT
4539455 AAAAAAACC
1 AAAAAAA-C
*
4539464 AAAAAAATA
1 AAAAAAA-C
4539473 AAAAAAAC
1 AAAAAAAC
4539481 AAAAAAAAC
1 -AAAAAAAC
*
4539490 AAACAAAC
1 AAAAAAAC
4539498 AAAAAA
1 AAAAAA
4539504 GAGGTCCAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 12 0.35
9 22 0.65
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:4539476 original size:17 final size:17
Alignment explanation
Indices: 4539454--4539503 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
4539444 CTTTCTTACC
*
4539454 TAAAAAAACCAAAAAAA
1 TAAAAAAAACAAAAAAA
4539471 TAAAAAAAACAAAAAAA
1 TAAAAAAAACAAAAAAA
*
4539488 -ACAAACAAACAAAAAA
1 TA-AAAAAAACAAAAAA
4539504 GAGGTCCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 1 0.03
17 29 0.97
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.04
Consensus pattern (17 bp):
TAAAAAAAACAAAAAAA
Found at i:4540995 original size:119 final size:116
Alignment explanation
Indices: 4540782--4541330 Score: 504
Period size: 119 Copynumber: 4.6 Consensus size: 116
4540772 AGTGGCATTT
* * * * * *
4540782 TTTCAAAGCCTACAAGTCAGTGGTATACCCTTTCAAAGCCCACACAAGTCGGTGGTAACTCTTTT
1 TTTCAAAGCCCACAAGTCAGTGGCAT--CTTTTCAAAG-CC-CACAAGTCAGTGG-CA-TCTCTT
* * *
4540847 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG-CC-TACAAGTCAGTGGCATAC-CC
60 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCA-ACTCC
*
4540902 TTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTC-
* **
4540967 AAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTC-GATGGCAACTAT
61 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAG-TGGCAACTCC
* ** * * * *
4541023 TTTCAAAGCTCATGAGTCAGTAGCATCTTTTCAAGAGACCACAAGTTAGTGGCATACCTTTTCAA
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAA-AGCCCACAAGTCAGTGGCAT--CTCTTCAA
* *
4541088 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCT
63 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCC
* * *
4541142 TTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAAGCCCATAAGTCAGTGGCA-CCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCATCTC-TTCAAA
* * *
4541206 GCCCACACAAGTCGGTGGCATCTCTTTTCAATG-CC-CACAAGTCAGTGGC-AC-CC
64 G-CC-CACAAGTCAGTGGCA-C-CCTTTCAAAGCCCACACAAGTCAGTGGCAACTCC
* * * ** * *
4541259 TTTCACAGCCCACAAGTCAGTGGTACCCCTTCAAAGCTCACAAGTCAGTGGCATCCCCATTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTC-TTCAAA
4541324 GCCCACA
64 GCCCACA
4541331 CAAGTCGGTG
Statistics
Matches: 363, Mismatches: 45, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
116 24 0.07
117 47 0.13
118 39 0.11
119 162 0.45
120 37 0.10
121 32 0.09
122 20 0.06
123 1 0.00
124 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (116 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGC
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCC
Found at i:4541028 original size:89 final size:88
Alignment explanation
Indices: 4540758--4541313 Score: 532
Period size: 89 Copynumber: 6.3 Consensus size: 88
4540748 TCATCTCTTT
* * * * *
4540758 AAAGCTCACAGGTCAGTGGCATTTTTTCAAAGCCTACAAGTCAGTGGTATACCCTTTCAAAGCCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG--CACCCTTTCAAAGCCC
* *
4540823 ACACAAGTCGGTGGTAACTCTTTTC
64 ACACAAGTCGATGGCAACTCTTTTC
*
4540848 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCTACAAGTCAGTGGCATACCCTTTCAAAGCCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC--ACCCTTTCAAAGCCC
*
4540913 ACACAAGTCGGTGGCAACTCTTTTC
64 ACACAAGTCGATGGCAACTCTTTTC
* *
4540938 AAAGCCCACAAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
*
4541003 CACAAGTCGATGGCAACTATTTTC
65 CACAAGTCGATGGCAACTCTTTTC
* ** * * * *
4541027 AAAGCTCATGAGTCAGTAGCATCTTTTCAAGAGACCACAAGTTAGTGGCATACCTTTTCAAAG-C
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAA-AGCCCACAAGTCAGTGGC--ACCCTTTCAAAGCC
*
4541091 C-CACAAGTC-AGTGGC-AC-CCTTTC
63 CACACAAGTCGA-TGGCAACTCTTTTC
* *
4541114 AAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTCTTCAAAA
1 AAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGCCCACAAGTCAGTGGCACCCT-TTC-AAA
* *
4541178 G-CC-CATAAGTC-AGTGGC-AC-CCTTTC
60 GCCCACACAAGTCGA-TGGCAACTCTTTTC
* * *
4541203 AAAGCCCACACAAGTCGGTGGCATCTCTTTTCAATGCCCACAAGTCAGTGGCACCCTTTCACAG-
1 AAAG-CC-CACAAGTCAGTGGCA--TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* **
4541267 CC-CACAAGTC-AGTGG-TAC-CCCTTC
62 CCACACAAGTCGA-TGGCAACTCTTTTC
*
4541291 AAAGCTCACAAGTCAGTGGCATC
1 AAAGCCCACAAGTCAGTGGCATC
4541314 CCCATTCAAA
Statistics
Matches: 414, Mismatches: 36, Indels: 38
0.85 0.07 0.08
Matches are distributed among these distances:
84 2 0.00
86 14 0.03
87 10 0.02
88 39 0.09
89 180 0.43
90 131 0.32
91 38 0.09
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (88 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
ACAAGTCGATGGCAACTCTTTTC
Found at i:4541112 original size:208 final size:207
Alignment explanation
Indices: 4540841--4541342 Score: 751
Period size: 208 Copynumber: 2.4 Consensus size: 207
4540831 CGGTGGTAAC
*
4540841 TCTTTTCAAAGCCCACAAGTCAGTGGCAT--CTTTTCAAAGCCTACAAGTCAGTGGCATACCCTT
1 TCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTCAAAGCCCACAAGTCAGTGGC--ACCCTT
4540904 TCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAA
64 TCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAA
* *
4540969 AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTCGATGGCAACTATTTTCAAAGCTC
129 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGATGGCAACTATTTTCAAAGCCC
**
4541034 ATGAGTCAGTAGCA
194 ACAAGTCAGTAGCA
* *
4541048 TCTTTTCAAGAGACCACAAGTTAGTGGCATACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCTTTTCAA-AGCCCACAAGTCAGTGGCATACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
4541113 CAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAA
65 CAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAA
* * * * *
4541178 GCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCATCTCTTTTCAATGCCCA
130 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGATGGCAACTATTTTCAAAGCCCA
*
4541243 CAAGTCAGTGGCA
195 CAAGTCAGTAGCA
* * * ** * *
4541256 CCCTTTCACAGCCCACAAGTCAGTGG--TACCCCTTCAAAGCTCACAAGTCAGTGGCATCCCCAT
1 TCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTCAAAGCCCACAAGTCAGTGGCA--CCCTT
4541319 TCAAAGCCCACACAAGTCGGTGGC
64 TCAAAGCCCACACAAGTCGGTGGC
4541343 CTCAAAGCCC
Statistics
Matches: 268, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
205 27 0.10
207 52 0.19
208 164 0.61
210 25 0.09
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (207 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
AAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAAG
CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGATGGCAACTATTTTCAAAGCCCAC
AAGTCAGTAGCA
Found at i:4541366 original size:25 final size:25
Alignment explanation
Indices: 4541319--4541367 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4541309 GCATCCCCAT
*
4541319 TCAAAGCCCACACAAGTCGGTGGCC
1 TCAAAGCCCACACAAGTCAGTGGCC
* *
4541344 TCAAAGCCCACATAAGTTAGTGGC
1 TCAAAGCCCACACAAGTCAGTGGC
4541368 ACCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (25 bp):
TCAAAGCCCACACAAGTCAGTGGCC
Found at i:4541547 original size:48 final size:48
Alignment explanation
Indices: 4541444--4541609 Score: 203
Period size: 48 Copynumber: 3.5 Consensus size: 48
4541434 AAGTCTGATA
* * * * *
4541444 TCGCTGGCATTGAATCAGCATATTG-GCACCTTT--ATTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
4541489 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* * * *
4541537 TTGCTAGCCTTGAATCAGCACATTGTCCATTTTTCCCTTAGCTCGATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* **
4541585 TCGTTGGCCTTGAATTGGCACATTG
1 TCGCTGGCCTTGAATCAGCACATTG
4541610 GCATTCCTCT
Statistics
Matches: 104, Mismatches: 14, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
45 23 0.22
46 6 0.06
48 75 0.72
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
Found at i:4544657 original size:17 final size:17
Alignment explanation
Indices: 4544635--4544691 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
4544625 CCATTTCATA
4544635 CTTTTTCTTTTTTTTTT
1 CTTTTTCTTTTTTTTTT
* *
4544652 CTTTTTCTTTCTTTCTT
1 CTTTTTCTTTTTTTTTT
** * *
4544669 CTTCATCTTCTTTCTTT
1 CTTTTTCTTTTTTTTTT
4544686 CTTTTT
1 CTTTTT
4544692 TACCTAACTT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTTTCTTTTTTTTTT
Found at i:4545797 original size:20 final size:20
Alignment explanation
Indices: 4545772--4545962 Score: 121
Period size: 20 Copynumber: 8.5 Consensus size: 20
4545762 ACCCAGATGC
*
4545772 ATCGATATATTTTTCAATGT
1 ATCGATACATTTTTCAATGT
* * *
4545792 ATCGATACATGTGTGAATGT
1 ATCGATACATTTTTCAATGT
4545812 ATCGATACATTTTTCAATGT
1 ATCGATACATTTTTCAATGT
4545832 ATCGATACATTCTGTCATTTTACCGAGATGT
1 ATCGATACA-----T--TTTT--C-A-ATGT
* * *
4545863 ATCGATACATGTATGAATGT
1 ATCGATACATTTTTCAATGT
*
4545883 ATCGATACAATTTTCAATGT
1 ATCGATACATTTTTCAATGT
4545903 ATCGATGCATTCTATTTTTTTCCCAGATGT
1 ATCGAT--A--C-A--TTTTT--CA-ATGT
4545933 ATCGATACATTTTTCAATGT
1 ATCGATACATTTTTCAATGT
4545953 ATCGATACAT
1 ATCGATACAT
4545963 CTAGCTAAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
20 82 0.61
21 3 0.02
22 1 0.01
23 5 0.04
24 3 0.02
25 3 0.02
26 2 0.01
27 8 0.06
28 1 0.01
29 3 0.02
30 11 0.08
31 13 0.10
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
ATCGATACATTTTTCAATGT
Found at i:4545863 original size:71 final size:70
Alignment explanation
Indices: 4545707--4545962 Score: 259
Period size: 71 Copynumber: 3.6 Consensus size: 70
4545697 AAAGTCACAT
* * * ** * * *
4545707 TTTTACCTAGATATATCGATACATGTATGAATGTATCGATACATTCTGTCTTTTTACCCAGATGC
1 TTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATT-TTTCAATGTA-TC-GATAC
4545772 A-TCGATATA
63 ATTC--TATA
* *
4545781 TTTT--TCA-ATGTATCGATACATGTGTGAATGTATCGATACATTTTTCAATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATT
*
4545843 CTGTCA
66 CTAT-A
* * *
4545849 TTTTACCGAGATGTATCGATACATGTATGAATGTATCGATACAATTTTCAATGTATCGATGCATT
1 TTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATT
*
4545914 CTATT
66 CTATA
* * * *
4545919 TTTTTCCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACAT
4545963 CTAGCTAAAA
Statistics
Matches: 153, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
67 2 0.01
68 10 0.07
69 3 0.02
70 45 0.29
71 88 0.58
72 1 0.01
74 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (70 bp):
TTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATT
CTATA
Found at i:4545882 original size:91 final size:91
Alignment explanation
Indices: 4545720--4545913 Score: 255
Period size: 91 Copynumber: 2.1 Consensus size: 91
4545710 TACCTAGATA
* * * * * *
4545720 TATCGATACATGTATGAATGTATCGATACATTCTGTCTTTTTACCCAGATGCATCGATATATTTT
1 TATCGATACATTTATCAATGTATCGATACATTCTGTCATTTTACCCAGATGCATCGATACATGTA
*
4545785 TCAATGTATCGATAC-ATGTGTGAATG
66 TCAATGTATCGATACAAT-TGTCAATG
* * *
4545811 TATCGATACATTTTTCAATGTATCGATACATTCTGTCATTTTACCGAGATGTATCGATACATGTA
1 TATCGATACATTTATCAATGTATCGATACATTCTGTCATTTTACCCAGATGCATCGATACATGTA
* *
4545876 TGAATGTATCGATACAATTTTCAATG
66 TCAATGTATCGATACAATTGTCAATG
*
4545902 TATCGATGCATT
1 TATCGATACATT
4545914 CTATTTTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 87 0.98
92 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (91 bp):
TATCGATACATTTATCAATGTATCGATACATTCTGTCATTTTACCCAGATGCATCGATACATGTA
TCAATGTATCGATACAATTGTCAATG
Found at i:4549216 original size:19 final size:19
Alignment explanation
Indices: 4549172--4549223 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4549162 CAGTTTCATG
** *
4549172 TATCGATACAATTGTCCATG
1 TATCGATACAA-TGAACATA
4549192 TATCGATACAATGAACATA
1 TATCGATACAATGAACATA
*
4549211 TATCGATATAATG
1 TATCGATACAATG
4549224 TATCGATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (19 bp):
TATCGATACAATGAACATA
Found at i:4553173 original size:15 final size:17
Alignment explanation
Indices: 4553155--4553186 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4553145 TGTTCATCAA
4553155 CTTC-TTTTGGA-ACTT
1 CTTCATTTTGGACACTT
4553170 CTTCATTTTGGACACTT
1 CTTCATTTTGGACACTT
4553187 TCATCTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (17 bp):
CTTCATTTTGGACACTT
Done.