Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 1 of 103
Found at i:8790 original size:6 final size:6
Alignment explanation
Indices: 8755--8789 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
8745 GAATATGGAA
*
8755 TAGGGG TAGGGT TAGGGG TAGGGG TAGGGG T-GGGG
1 TAGGGG TAGGGG TAGGGG TAGGGG TAGGGG TAGGGG
8790 GGTGAATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.14, C:0.00, G:0.66, T:0.20
Consensus pattern (6 bp):
TAGGGG
Found at i:8855 original size:2 final size:2
Alignment explanation
Indices: 8848--8873 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8838 ATACATCTTA
8848 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
8874 GTCTACTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10282 original size:3 final size:3
Alignment explanation
Indices: 10274--10307 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
10264 TCAAGTGAAG
10274 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10308 CTAGGCTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11073 original size:51 final size:51
Alignment explanation
Indices: 10998--11101 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 51
10988 AAAGGAAAAG
*
10998 AAGAAAAGAGAGGCACTACTCATATATCTACTCTGATATTCATTAATTCCA
1 AAGAAAAGAGAGGCACTACTCATATATCTACTCTGATATTCATTAATACCA
* *
11049 AAGAAACA-AGAGGCAGTAGTCATATATCTACTCTGATATTCATTAATACCA
1 AAGAAA-AGAGAGGCACTACTCATATATCTACTCTGATATTCATTAATACCA
11100 AA
1 AA
11102 ATGATGTATC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 48 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (51 bp):
AAGAAAAGAGAGGCACTACTCATATATCTACTCTGATATTCATTAATACCA
Found at i:14114 original size:18 final size:18
Alignment explanation
Indices: 14058--14134 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
14048 ATAACAATAG
*
14058 TGGTAATGGTAGTGGT-A
1 TGGTAATGGTAATGGTCA
* *
14075 GTGGTAGTGGTAATGGTAA
1 -TGGTAATGGTAATGGTCA
14094 TGGTAATGGTAATGGTCA
1 TGGTAATGGTAATGGTCA
** * *
14112 TGGTCTTGATCATGGTCA
1 TGGTAATGGTAATGGTCA
14130 TGGTA
1 TGGTA
14135 TGTATTCAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
18 48 0.98
19 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.36, T:0.35
Consensus pattern (18 bp):
TGGTAATGGTAATGGTCA
Found at i:14133 original size:6 final size:6
Alignment explanation
Indices: 14058--14115 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
14048 ATAACAATAG
* * *
14058 TGGTAA TGGTAG TGGTAG TGGTAG TGGTAA TGGTAA TGGTAA TGGTAA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
*
14106 TGGTCA TGGT
1 TGGTAA TGGT
14116 CTTGATCATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.24, C:0.02, G:0.40, T:0.34
Consensus pattern (6 bp):
TGGTAA
Found at i:18009 original size:19 final size:21
Alignment explanation
Indices: 17985--18023 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17975 ATTTAAAAAT
17985 ATTA-TTTTTTAT-AATTTTA
1 ATTATTTTTTTATCAATTTTA
18004 ATTATTTTTTTATCAATTTT
1 ATTATTTTTTTATCAATTTT
18024 TGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTTTTTTATCAATTTTA
Found at i:18712 original size:22 final size:22
Alignment explanation
Indices: 18682--18738 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
18672 TAATCACCGT
*
18682 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCATTAC
*
18704 GTGATTAG-TTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
18725 GTGACTAGTTTTTA
1 GTGACTAGTTTTTA
18739 TACATTGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:18798 original size:23 final size:23
Alignment explanation
Indices: 18772--18931 Score: 117
Period size: 26 Copynumber: 6.6 Consensus size: 23
18762 GCAATGTCTA
18772 AGTCACGCAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* *
18795 AGTCACGCAATACCTTACTAACA
1 AGTCACGCAATGCCTTACTAACT
*
18818 AATCACGCAATGCC-TA-TCAACT
1 AGTCACGCAATGCCTTACT-AACT
* * *
18840 AGTCATGCAATACCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--TAACT
* * *
18866 AGTCATGCAATGGCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--TAACT
*
18892 AGTCACGCAATGCCTTATTAAAAACT
1 AGTCACGCAATGCCTTACT---AACT
*
18918 AGTTACGCAATGCC
1 AGTCACGCAATGCC
18932 CAAAGTTAGT
Statistics
Matches: 112, Mismatches: 16, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 16 0.14
23 35 0.31
26 60 0.54
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:18865 original size:26 final size:26
Alignment explanation
Indices: 18836--18931 Score: 129
Period size: 26 Copynumber: 3.7 Consensus size: 26
18826 AATGCCTATC
*
18836 AACTAGTCATGCAATACCTTATCAGA
1 AACTAGTCATGCAATGCCTTATCAGA
*
18862 AACTAGTCATGCAATGGCTTATCAGA
1 AACTAGTCATGCAATGCCTTATCAGA
* * *
18888 AACTAGTCACGCAATGCCTTATTAAA
1 AACTAGTCATGCAATGCCTTATCAGA
* *
18914 AACTAGTTACGCAATGCC
1 AACTAGTCATGCAATGCC
18932 CAAAGTTAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (26 bp):
AACTAGTCATGCAATGCCTTATCAGA
Found at i:18992 original size:26 final size:26
Alignment explanation
Indices: 18957--19010 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
18947 AATACCTATC
*
18957 AACTAATCACGCAATGTCTTATCAAA
1 AACTAATCACGCAATGCCTTATCAAA
* *
18983 AACTAGTCACGTAATGCCTTATCAAA
1 AACTAATCACGCAATGCCTTATCAAA
19009 AA
1 AA
19011 TTTATCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (26 bp):
AACTAATCACGCAATGCCTTATCAAA
Found at i:19025 original size:37 final size:37
Alignment explanation
Indices: 18975--19047 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
18965 ACGCAATGTC
*
18975 TTATCAAAAACTAGTCACGTAATGCCTTATCAAAAAT
1 TTATCAAAAACTAGTCACGCAATGCCTTATCAAAAAT
* *
19012 TTATCAGAAACTAGTCATGCAATGCCTTATCAAAAA
1 TTATCAAAAACTAGTCACGCAATGCCTTATCAAAAA
19048 CTAGTCACGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (37 bp):
TTATCAAAAACTAGTCACGCAATGCCTTATCAAAAAT
Found at i:19048 original size:26 final size:26
Alignment explanation
Indices: 19012--19086 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
19002 TATCAAAAAT
* *
19012 TTATCAGAAACTAGTCATGCAATGCC
1 TTATCAAAAACTAGTCACGCAATGCC
*
19038 TTATCAAAAACTAGTCACGCAATGTC
1 TTATCAAAAACTAGTCACGCAATGCC
19064 TTATCAAAAA-TCAGTCACGCAAT
1 TTATCAAAAACT-AGTCACGCAAT
19087 ACTCAAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 1 0.02
26 44 0.98
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.27
Consensus pattern (26 bp):
TTATCAAAAACTAGTCACGCAATGCC
Found at i:19103 original size:21 final size:21
Alignment explanation
Indices: 19078--19128 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19068 CAAAAATCAG
*
19078 TCACGCAATACTCAAATTCAA
1 TCACGCAATACTCAAAGTCAA
* * *
19099 TCACGTAATATTCAAAGTCAG
1 TCACGCAATACTCAAAGTCAA
*
19120 TCATGCAAT
1 TCACGCAAT
19129 GCCTAAAAAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (21 bp):
TCACGCAATACTCAAAGTCAA
Found at i:33035 original size:17 final size:16
Alignment explanation
Indices: 33013--33047 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
33003 ATTATAAAAC
33013 AAAAAATTAATATTTTA
1 AAAAAATTAAT-TTTTA
33030 AAAAAATTAATTTTTA
1 AAAAAATTAATTTTTA
33046 AA
1 AA
33048 TTATTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAATTAATTTTTA
Found at i:33211 original size:17 final size:17
Alignment explanation
Indices: 33138--33211 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
33128 TTAATTATAT
33138 ATTATAA-AATATTTTAA
1 ATTATAATAATA-TTTAA
* *
33155 ATT-TAAAAATTAATTAA
1 ATTATAATAA-TATTTAA
* * *
33172 A-AATATTAATATTTTA
1 ATTATAATAATATTTAA
*
33188 ATCATAATAATATTTAA
1 ATTATAATAATATTTAA
33205 ATTATAA
1 ATTATAA
33212 ATTAAATTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
16 9 0.21
17 32 0.74
18 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATAATAATATTTAA
Found at i:36296 original size:37 final size:37
Alignment explanation
Indices: 36242--36362 Score: 181
Period size: 37 Copynumber: 3.3 Consensus size: 37
36232 TGATGATGGC
*
36242 TGATGATG-TTGAGGTGTGCGAGAAGGGAGTGCACACA
1 TGATGATGATTGA-GTGTGCGAGTAGGGAGTGCACACA
*
36279 TGATGATGATTGAGTGTGCGAGTAGGAAGTGCACACA
1 TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
* * *
36316 TGACGATGATGGAGTGTGCGAGTAGAGAGTGCACACA
1 TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
36353 TGATGATGAT
1 TGATGATGAT
36363 GTATGCATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
37 72 0.95
38 4 0.05
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (37 bp):
TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:47498 original size:3 final size:3
Alignment explanation
Indices: 47483--47516 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
47473 TGAGCAACAA
*
47483 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
47517 TATTTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:48935 original size:13 final size:14
Alignment explanation
Indices: 48912--48941 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
48902 ATTTAATAAC
48912 TTATAAAAAAAAAT
1 TTATAAAAAAAAAT
48926 TTAT-AAAAAAAAT
1 TTATAAAAAAAAAT
48939 TTA
1 TTA
48942 CCAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTATAAAAAAAAAT
Found at i:49193 original size:2 final size:2
Alignment explanation
Indices: 49186--49225 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
49176 NNAAGGTTAA
49186 AT AT AT AT AT AT AT A- 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
49226 CATGCAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49439 original size:3 final size:3
Alignment explanation
Indices: 49431--49455 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49421 TCAGGGAAAG
49431 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
49456 GTCAGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56547 original size:3 final size:3
Alignment explanation
Indices: 56539--56600 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
56529 CTCTACGCCT
* * *
56539 CAG CAG CAG CAG CAG CAG CAA CAG CAA CAG CAA CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
56587 CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CA
56601 AAGTCATAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.39, C:0.34, G:0.27, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:60646 original size:4 final size:4
Alignment explanation
Indices: 60637--60670 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
60627 AAAACCAAGT
60637 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA AC
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA AC
60671 GAAGTTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:61192 original size:6 final size:6
Alignment explanation
Indices: 61181--61205 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61171 GGTTTCGCAA
61181 TTCAAT TTCAAT TTCAAT TTCAAT T
1 TTCAAT TTCAAT TTCAAT TTCAAT T
61206 CCATGCATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCAAT
Found at i:73862 original size:19 final size:20
Alignment explanation
Indices: 73838--73875 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
73828 ATTTAAAAAT
73838 ATTATTTTATA-TAATTTTA
1 ATTATTTTATATTAATTTTA
*
73857 ATTATTTTTTATTAATTTT
1 ATTATTTTATATTAATTTT
73876 TGACATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTATTTTATATTAATTTTA
Found at i:74565 original size:21 final size:22
Alignment explanation
Indices: 74530--74592 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
74520 TAATTACCGT
*
74530 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCATTAC
*
74552 GTGATTAG-TTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
* *
74573 GTGACTAATTTTTAGACATT
1 GTGACTAGTTTTTAGGCATT
74593 GCGTAACTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:74605 original size:22 final size:22
Alignment explanation
Indices: 74533--74608 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
74523 TTACCGTGTG
* * *
74533 ACTAGTTTTTAGTCATTACGTG
1 ACTAATTTTTAGACATTACGTA
* * * *
74555 A-TTAGTTTTAGGCATTACGTG
1 ACTAATTTTTAGACATTACGTA
*
74576 ACTAATTTTTAGACATTGCGTA
1 ACTAATTTTTAGACATTACGTA
*
74598 ACTGATTTTTA
1 ACTAATTTTTA
74609 AGTAACGCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
ACTAATTTTTAGACATTACGTA
Found at i:74814 original size:74 final size:73
Alignment explanation
Indices: 74637--74854 Score: 278
Period size: 74 Copynumber: 3.0 Consensus size: 73
74627 TTTACTAACA
* * * *
74637 AGTCACGCAATACTTTATCAGAAACTAGTCACGTAATGTCTCATCAAAAACTAGTCACGCAATAC
1 AGTCACACAATACCTTATCAGAAACTAGTCACGCAATGTCTTATCAAAAACTAGTCACGCAATAC
*
74702 CCAAAGTT
66 CCAAAGCT
** * *
74710 AGTCACACAATGTCTTATCAGAAATTAGTCACACAATG-CTTTATCAAAAACTAGTCACGCAATA
1 AGTCACACAATACCTTATCAGAAACTAGTCACGCAATGTC-TTATCAAAAACTAGTCACGCAATA
*
74774 CCTATTAA-CT
65 CCCA--AAGCT
* * *
74784 AGTCACATAATACCTTATCAGAAACTAGTCACGCAATGTCTTATCAAAAATTAGTCACGCAATGC
1 AGTCACACAATACCTTATCAGAAACTAGTCACGCAATGTCTTATCAAAAACTAGTCACGCAATAC
74849 CCAAAG
66 CCAAAG
74855 TCAATCACGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
72 3 0.02
73 57 0.47
74 59 0.48
75 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (73 bp):
AGTCACACAATACCTTATCAGAAACTAGTCACGCAATGTCTTATCAAAAACTAGTCACGCAATAC
CCAAAGCT
Found at i:74847 original size:26 final size:26
Alignment explanation
Indices: 74637--74847 Score: 138
Period size: 26 Copynumber: 8.5 Consensus size: 26
74627 TTTACTAACA
* *
74637 AGTCACGCAAT-ACTTTATCAGAAACT
1 AGTCACGCAATGTC-TTATCAAAAACT
* *
74663 AGTCACGTAATGTCTCATCAAAAACT
1 AGTCACGCAATGTCTTATCAAAAACT
* * **
74689 AGTCACGCAA-----TACCCAAAGTT
1 AGTCACGCAATGTCTTATCAAAAACT
* * *
74710 AGTCACACAATGTCTTATCAGAAATT
1 AGTCACGCAATGTCTTATCAAAAACT
*
74736 AGTCACACAATG-CTTTATCAAAAACT
1 AGTCACGCAATGTC-TTATCAAAAACT
* * *
74762 AGTCACGCAAT-ACCTAT---TAACT
1 AGTCACGCAATGTCTTATCAAAAACT
** ** *
74784 AGTCACATAATACCTTATCAGAAACT
1 AGTCACGCAATGTCTTATCAAAAACT
*
74810 AGTCACGCAATGTCTTATCAAAAATT
1 AGTCACGCAATGTCTTATCAAAAACT
74836 AGTCACGCAATG
1 AGTCACGCAATG
74848 CCCAAAGTCA
Statistics
Matches: 142, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
21 15 0.11
22 13 0.09
23 4 0.03
25 4 0.03
26 105 0.74
27 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (26 bp):
AGTCACGCAATGTCTTATCAAAAACT
Found at i:74862 original size:21 final size:21
Alignment explanation
Indices: 74838--74891 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
74828 CAAAAATTAG
*
74838 TCACGCAATGCCCAAAGTCAA
1 TCACGCAATACCCAAAGTCAA
* *
74859 TCACGCAATATCCAAAGTCAG
1 TCACGCAATACCCAAAGTCAA
*
74880 TCACGTAATACC
1 TCACGCAATACC
74892 TAAAAACTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (21 bp):
TCACGCAATACCCAAAGTCAA
Found at i:80881 original size:20 final size:21
Alignment explanation
Indices: 80856--80895 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
80846 CTCACCCTGT
80856 CCGTCTTCCCCTCT-TCTCAC
1 CCGTCTTCCCCTCTCTCTCAC
80876 CCGTCTTCCCCTCTCTCTCA
1 CCGTCTTCCCCTCTCTCTCA
80896 GCTGCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.05, C:0.55, G:0.05, T:0.35
Consensus pattern (21 bp):
CCGTCTTCCCCTCTCTCTCAC
Found at i:81240 original size:26 final size:24
Alignment explanation
Indices: 81179--81277 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 24
81169 AAAAAAAAAT
* *
81179 TATTTATAAAATTTAAAATATTAATA
1 TATTAATATAATTT-AAATATT-ATA
*
81205 TTTTATATATAATTTAAATATTATTA
1 TATTA-ATATAATTTAAATATTA-TA
* *
81231 GTATTAATATGATTAAAATATTATAA
1 -TATTAATATAATTTAAATATTAT-A
81257 TATTAATAT--TTTAAATTATTA
1 TATTAATATAATTTAAA-TATTA
81278 ATGTTTTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
23 5 0.08
24 5 0.08
25 11 0.18
26 28 0.46
27 12 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTAATATAATTTAAATATTATA
Found at i:81317 original size:16 final size:16
Alignment explanation
Indices: 81234--81318 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 16
81224 ATTATTAGTA
* *
81234 TTAATATGATTAAAATA
1 TTAATAT-ATTAAATTT
81251 TT-ATAATATTAATATTT
1 TTAAT-ATATTAA-ATTT
*
81268 TAAAT-TATT-AATGTT
1 TTAATATATTAAAT-TT
* *
81283 TT-ATTTATTAAATTA
1 TTAATATATTAAATTT
81298 TTAATATATTAAATTT
1 TTAATATATTAAATTT
81314 TTAAT
1 TTAAT
81319 GAGTATAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
14 4 0.07
15 11 0.20
16 30 0.56
17 7 0.13
18 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAATATATTAAATTT
Found at i:81479 original size:22 final size:22
Alignment explanation
Indices: 81328--81479 Score: 74
Period size: 25 Copynumber: 6.5 Consensus size: 22
81318 TGAGTATAAA
81328 TAAAAAATAAAAATTTATTAATATT
1 TAAAAAAT--AAA-TTATTAATATT
* ** *
81353 TTAATCATAACAATATTAA-A-T
1 TAAAAAATAA-ATTATTAATATT
* * *
81374 TATAAAATAAAATATTAATAAT
1 TAAAAAATAAATTATTAATATT
* *
81396 TAAATTATACTAAATTATTGATATT
1 TAAA--A-AATAAATTATTAATATT
** *
81421 TAAATTATTAATTATTAATATTT
1 TAAAAAATAAATTATTAATA-TT
*
81444 TAATTAATTATAAATTATTAATATT
1 TAA--AA-AATAAATTATTAATATT
81469 TAAAAAATAAA
1 TAAAAAATAAA
81480 ATAAAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
20 8 0.08
21 8 0.08
22 21 0.22
23 15 0.16
24 2 0.02
25 28 0.29
26 14 0.15
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAAAAATAAATTATTAATATT
Found at i:82602 original size:3 final size:3
Alignment explanation
Indices: 82594--82621 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
82584 AATCATTTAT
82594 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
82622 AGAGTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:83856 original size:14 final size:14
Alignment explanation
Indices: 83837--83878 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
83827 TTATTTATAT
83837 ATTATATTTGTTTA
1 ATTATATTTGTTTA
**
83851 ATTATATTTGACATA
1 ATTATATTTG-TTTA
83866 ATT-TATTTGTTTA
1 ATTATATTTGTTTA
83879 TAACATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 16 0.70
15 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (14 bp):
ATTATATTTGTTTA
Found at i:86553 original size:2 final size:2
Alignment explanation
Indices: 86548--86574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
86538 ATATATATAT
86548 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
86575 CAACATGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:88835 original size:14 final size:14
Alignment explanation
Indices: 88816--88852 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
88806 AAATAGATAA
88816 TTTTATTAATTATT
1 TTTTATTAATTATT
*
88830 TTTTATT-TTTATT
1 TTTTATTAATTATT
88843 TTTT-TTAATT
1 TTTTATTAATT
88853 TTTATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.10
13 11 0.55
14 7 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTAATTATT
Found at i:88851 original size:26 final size:26
Alignment explanation
Indices: 88816--88866 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
88806 AAATAGATAA
*
88816 TTTTATTAATTATTT-TTTATTTTTAT
1 TTTTATTAATT-TTTATATATTTTTAT
*
88842 TTTTTTTAATTTTTATATATTTTTA
1 TTTTATTAATTTTTATATATTTTTA
88867 ATATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTATTAATTTTTATATATTTTTAT
Found at i:88853 original size:16 final size:17
Alignment explanation
Indices: 88828--88868 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
88818 TTATTAATTA
88828 TTTTTT-ATTTTTAT-T
1 TTTTTTAATTTTTATAT
88843 TTTTTTAATTTTTATAT
1 TTTTTTAATTTTTATAT
*
88860 ATTTTTAAT
1 TTTTTTAAT
88869 ATAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTAATTTTTATAT
Found at i:104458 original size:108 final size:110
Alignment explanation
Indices: 104260--104480 Score: 347
Period size: 108 Copynumber: 2.0 Consensus size: 110
104250 GATGGCGGGC
* *
104260 TGACTCTTGTCTGAGTTTTCGACGCAAGCTTCCTGTCTGTCTGTCCGGTTCCAAAATGAACATTG
1 TGACACTTGTCTGAGTTTTCGACGCAAGCTTCCTGTCTGTC-GT-CGGCTCCAAAATGAACATTG
* *
104325 CCAATGAAAAAACACACTCACGGCCTTCATTGATAGCATTTATTTCA
64 CCAATGAAAAAACACACTCACGGCCTTCATTGATACCATTCATTTCA
104372 TGACACTTGTCTGAGTTTTCGACGCAAGCTTCCTGTCTGTC-T-GGCTCCAAAATGAACATTGCC
1 TGACACTTGTCTGAGTTTTCGACGCAAGCTTCCTGTCTGTCGTCGGCTCCAAAATGAACATTGCC
* * *
104435 AATGAAAAAACACACTCATGGCCTTCGTTTATACCATTCATTTCA
66 AATGAAAAAACACACTCACGGCCTTCATTGATACCATTCATTTCA
104480 T
1 T
104481 TTGCTCTCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
108 61 0.60
110 1 0.01
112 40 0.39
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (110 bp):
TGACACTTGTCTGAGTTTTCGACGCAAGCTTCCTGTCTGTCGTCGGCTCCAAAATGAACATTGCC
AATGAAAAAACACACTCACGGCCTTCATTGATACCATTCATTTCA
Found at i:128044 original size:2 final size:2
Alignment explanation
Indices: 128037--128069 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
128027 CAATGTAACC
128037 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 A
128070 CNATAGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128107 original size:2 final size:2
Alignment explanation
Indices: 128100--128145 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
128090 CAATACTAAC
* *
128100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC 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
128142 AT AT
1 AT AT
128146 TAGTCTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:136618 original size:6 final size:6
Alignment explanation
Indices: 136607--136636 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
136597 ATAACGCACC
136607 CATTTA CATTTA CATTTA CATTTA CATTTA
1 CATTTA CATTTA CATTTA CATTTA CATTTA
136637 TGGCGTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
CATTTA
Found at i:137534 original size:29 final size:29
Alignment explanation
Indices: 137501--137581 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 29
137491 CAGCTATGTG
137501 CGGTGTGGGAGTGCACATGAGCTGATGAC
1 CGGTGTGGGAGTGCACATGAGCTGATGAC
* * *
137530 CGGTGGGGGA-TTC-CA--ACCTTG-TG--
1 CGGTGTGGGAGTGCACATGAGC-TGATGAC
137553 CGGTGTGGGAGTGCACATGAGCTGATGAC
1 CGGTGTGGGAGTGCACATGAGCTGATGAC
137582 TAGTGGTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
23 9 0.24
24 2 0.05
25 6 0.16
26 4 0.11
27 6 0.16
28 2 0.05
29 9 0.24
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (29 bp):
CGGTGTGGGAGTGCACATGAGCTGATGAC
Found at i:141386 original size:29 final size:29
Alignment explanation
Indices: 141348--141409 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
141338 CTATCAAGAG
141348 TAAGCAATAATTCTTCCAAGCAAATAGTA
1 TAAGCAATAATTCTTCCAAGCAAATAGTA
141377 TAAGCAATAATTCTTCCAAGCAAATAGTA
1 TAAGCAATAATTCTTCCAAGCAAATAGTA
141406 TAAG
1 TAAG
141410 TAAAGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (29 bp):
TAAGCAATAATTCTTCCAAGCAAATAGTA
Found at i:147918 original size:12 final size:12
Alignment explanation
Indices: 147897--147927 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
147887 ACAAGCGGAT
*
147897 TATATATATATA
1 TATATGTATATA
147909 TATATGTATATA
1 TATATGTATATA
147921 TATATGT
1 TATATGT
147928 GTGAACATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TATATGTATATA
Found at i:155522 original size:62 final size:62
Alignment explanation
Indices: 155425--155545 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
155415 AACCAATCAC
* *
155425 ATGTTAGGACTTTGTTTGCTTCGGTGAGTTTAACTTATATATTTCAAGTTTAATGAGGTCAT
1 ATGTTAGGACTTTGTTTGCTGCAGTGAGTTTAACTTATATATTTCAAGTTTAATGAGGTCAT
155487 ATGTTAGGACTTTGTTTGCTGCAGTGAGTTTAACTTATATATTTCAAGTTTAATGAGGT
1 ATGTTAGGACTTTGTTTGCTGCAGTGAGTTTAACTTATATATTTCAAGTTTAATGAGGT
155546 ATTTTATTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (62 bp):
ATGTTAGGACTTTGTTTGCTGCAGTGAGTTTAACTTATATATTTCAAGTTTAATGAGGTCAT
Found at i:159230 original size:92 final size:92
Alignment explanation
Indices: 159073--159257 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
159063 TTGTTCTACC
159073 TGTCTGCAGGCTATAAGGCCACAGCCATTAGGTGTAGCTGCATAATTCCAGTGCATATTTTGGAT
1 TGTCTGCAGGCTATAAGGCCACAGCCATTAGGTGTAGCTGCATAATTCCAGTGCATATTTTGGAT
159138 CTATAACCAATGATCTTACACCATGTT
66 CTATAACCAATGATCTTACACCATGTT
* * *
159165 TGTCTGCAGGCTATAAGGCCACAGCCATTGGGTTTAGCTGCATAATTCCAGTGCTTATTTTGGAT
1 TGTCTGCAGGCTATAAGGCCACAGCCATTAGGTGTAGCTGCATAATTCCAGTGCATATTTTGGAT
*
159230 CTATAACCGATGATCTTACACCATGTT
66 CTATAACCAATGATCTTACACCATGTT
159257 T
1 T
159258 CCTAAATTTC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (92 bp):
TGTCTGCAGGCTATAAGGCCACAGCCATTAGGTGTAGCTGCATAATTCCAGTGCATATTTTGGAT
CTATAACCAATGATCTTACACCATGTT
Found at i:160052 original size:2 final size:2
Alignment explanation
Indices: 160045--160073 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
160035 AACCAAACGA
160045 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
160074 AGACTTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:163739 original size:45 final size:44
Alignment explanation
Indices: 163684--163791 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 44
163674 AAAATATGTG
* *
163684 ACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTGTT
1 ACACG-CATGTACAAAAACCTATGACAAGCCATGGTTAACGTGTT
* * *
163729 ACACGTCATGTACAAAAACCTGTGACAAGCCGTGGTTAGCGTGTT
1 ACACG-CATGTACAAAAACCTATGACAAGCCATGGTTAACGTGTT
*
163774 ACACGCTATATACAAAAA
1 ACACGC-ATGTACAAAAA
163792 TATGTGACAC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (44 bp):
ACACGCATGTACAAAAACCTATGACAAGCCATGGTTAACGTGTT
Found at i:163746 original size:69 final size:69
Alignment explanation
Indices: 163615--163755 Score: 196
Period size: 69 Copynumber: 2.0 Consensus size: 69
163605 CTATGATATT
* * * *
163615 ACACGCCATGTACAAAAACCTGTGACAAGCTATGGTTAGTGTGTTACACGCTATATATAAAAATA
1 ACACGCCATGTACAAAAACCTATGACAAGCTATGGTTACTGTGTTACACGCTATATACAAAAACA
163680 TGTG
66 TGTG
*
163684 ACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACT-TGTTACACG-TCATGTACAAAAA
1 ACACGCCATGTACAAAAACCTATGACAAGCTATGGTT-ACTGTGTTACACGCT-ATATACAAAAA
*
163747 CCTGTG
64 CATGTG
163753 ACA
1 ACA
163756 AGCCGTGGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
68 1 0.02
69 61 0.95
70 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (69 bp):
ACACGCCATGTACAAAAACCTATGACAAGCTATGGTTACTGTGTTACACGCTATATACAAAAACA
TGTG
Found at i:163798 original size:45 final size:45
Alignment explanation
Indices: 163684--163807 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 45
163674 AAAATATGTG
* * * * * *
163684 ACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTGTT
1 ACACGTCATATACAAAAACATGTGACAAGCCATGGTTAACGTGTT
* * * *
163729 ACACGTCATGTACAAAAACCTGTGACAAGCCGTGGTTAGCGTGTT
1 ACACGTCATATACAAAAACATGTGACAAGCCATGGTTAACGTGTT
* *
163774 ACACG-CTATATACAAAAATATGTGACACGCCATG
1 ACACGTC-ATATACAAAAACATGTGACAAGCCATG
163808 TATAAAAACT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 1 0.01
45 66 0.99
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (45 bp):
ACACGTCATATACAAAAACATGTGACAAGCCATGGTTAACGTGTT
Found at i:163815 original size:114 final size:113
Alignment explanation
Indices: 163613--163893 Score: 445
Period size: 114 Copynumber: 2.5 Consensus size: 113
163603 CGCTATGATA
* *
163613 TTACACGCCATGTACAAAAACCTGTGACAAGCTATGGTTAGTGTGTTACACGCTATATATAAAAA
1 TTACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAG-GTGTTACACGCTATATACAAAAA
163678 TATGTGACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTG
65 TATGTGACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTG
* *
163727 TTACACGTCATGTACAAAAACCTGTGACAAGCCGTGGTTAGCGTGTTACACGCTATATACAAAAA
1 TTACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAG-GTGTTACACGCTATATACAAAAA
* * **
163792 TATGTGACACGCCATGTATAAAAACTTATGACAAGCTATGGTTAGGTTG
65 TATGTGACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTG
* *
163841 TTACACGCCATGTACAAAAACTTGTAACAAGCCATGGTTAGGTTGTTACACGC
1 TTACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGG-TGTTACACGC
163894 CATGTTGAAA
Statistics
Matches: 153, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 1 0.01
114 152 0.99
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (113 bp):
TTACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGGTGTTACACGCTATATACAAAAAT
ATGTGACACGCCATGTACAAAAACCTATGACAAGCTATGGTTAACTTG
Found at i:163849 original size:45 final size:45
Alignment explanation
Indices: 163798--163898 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
163788 AAAATATGTG
* * *
163798 ACACGCCATGTATAAAAACTTATGACAAGCTATGGTTAGGTTGTT
1 ACACGCCATGTACAAAAACTTATAACAAGCCATGGTTAGGTTGTT
*
163843 ACACGCCATGTACAAAAACTTGTAACAAGCCATGGTTAGGTTGTT
1 ACACGCCATGTACAAAAACTTATAACAAGCCATGGTTAGGTTGTT
163888 ACACGCCATGT
1 ACACGCCATGT
163899 TGAAAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (45 bp):
ACACGCCATGTACAAAAACTTATAACAAGCCATGGTTAGGTTGTT
Found at i:163875 original size:69 final size:69
Alignment explanation
Indices: 163721--163876 Score: 181
Period size: 69 Copynumber: 2.3 Consensus size: 69
163711 AGCTATGGTT
* * * * *
163721 AACTTGTTACACGTCATGTACAAAAACCTGTGACAAGCCGTGGTTAGCGTGTTACACGCTATATA
1 AACTTGTAACACGCCATGTACAAAAACCTATGACAAGCCATGGTTAGCGTGTTACACGCCATATA
163786 CAAA
66 CAAA
* * * * *
163790 AA-TATGTGACACGCCATGTATAAAAACTTATGACAAGCTATGGTTAG-GTTGTTACACGCCATG
1 AACT-TGTAACACGCCATGTACAAAAACCTATGACAAGCCATGGTTAGCG-TGTTACACGCCATA
163853 TACAAA
64 TACAAA
*
163859 AACTTGTAACAAGCCATG
1 AACTTGTAACACGCCATG
163877 GTTAGGTTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
68 2 0.03
69 70 0.96
70 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (69 bp):
AACTTGTAACACGCCATGTACAAAAACCTATGACAAGCCATGGTTAGCGTGTTACACGCCATATA
CAAA
Found at i:163954 original size:57 final size:58
Alignment explanation
Indices: 163880--163995 Score: 200
Period size: 57 Copynumber: 2.0 Consensus size: 58
163870 AGCCATGGTT
163880 AGGTTGTTACACGCCATGTTGAAAA-AAAATATTGTTGTTACACGCCATGGTT-AAAAA
1 AGGTTGTTACACGCCATGTTGAAAATAAAATATTGTTGTTACACGCCAT-GTTGAAAAA
*
163937 AGGTTGTTACACGCCATGTTGAAAATAAAATATTGTTGTTACACGTCATGTTGAAAAA
1 AGGTTGTTACACGCCATGTTGAAAATAAAATATTGTTGTTACACGCCATGTTGAAAAA
163995 A
1 A
163996 TATTATTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 28 0.50
58 28 0.50
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (58 bp):
AGGTTGTTACACGCCATGTTGAAAATAAAATATTGTTGTTACACGCCATGTTGAAAAA
Found at i:163961 original size:26 final size:27
Alignment explanation
Indices: 163879--163994 Score: 101
Period size: 32 Copynumber: 4.0 Consensus size: 27
163869 AAGCCATGGT
163879 TAGGTTGTTACACGCCATGTTGAAAAAAAA
1 TAGGTTGTTACACGCCATGTTG---AAAAA
*
163909 TATTGTTGTTACACGCCATGGTT-AAAAA
1 TA-GGTTGTTACACGCCAT-GTTGAAAAA
163937 -AGGTTGTTACACGCCATGTTGAAAATAAAA
1 TAGGTTGTTACACGCCATGTTG---A-AAAA
* *
163967 TATTGTTGTTACACGTCATGTTGAAAAA
1 TA-GGTTGTTACACGCCATGTTGAAAAA
163995 ATATTATTGT
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
25 3 0.04
26 15 0.21
27 1 0.01
28 9 0.12
29 2 0.03
30 6 0.08
31 16 0.22
32 21 0.29
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (27 bp):
TAGGTTGTTACACGCCATGTTGAAAAA
Found at i:163995 original size:29 final size:29
Alignment explanation
Indices: 163882--164034 Score: 152
Period size: 29 Copynumber: 5.2 Consensus size: 29
163872 CCATGGTTAG
163882 GTTGTTACACGCCATGTTGAAAAAAAATATT
1 GTTGTTACACGCCATGTTG--AAAAAATATT
*
163913 GTTGTTACACGCCATGGTT--AAAAA-A-G
1 GTTGTTACACGCCAT-GTTGAAAAAATATT
163939 GTTGTTACACGCCATGTTGAAAATAAAATATT
1 GTTGTTACACGCCATGTTG--AA-AAAATATT
*
163971 GTTGTTACACGTCATGTTGAAAAAATATT
1 GTTGTTACACGCCATGTTGAAAAAATATT
* * * * *
164000 ATTGTTACACGACATATTCAAAAACATTTT
1 GTTGTTACACGCCATGTTGAAAAA-ATATT
164030 GTTGT
1 GTTGT
164035 GCTTTAATGT
Statistics
Matches: 104, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.03
26 15 0.14
27 1 0.01
28 5 0.05
29 29 0.28
30 14 0.13
31 16 0.15
32 21 0.20
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (29 bp):
GTTGTTACACGCCATGTTGAAAAAATATT
Found at i:164818 original size:2 final size:2
Alignment explanation
Indices: 164802--164855 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
164792 AAAGAGAGGG
* *
164802 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
164844 TA TA TA TA TA TA
1 TA TA TA TA TA TA
164856 GCTTTTTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:171072 original size:16 final size:16
Alignment explanation
Indices: 171051--171085 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
171041 TATGTTATGA
171051 TTCCTGCTATTGTGAT
1 TTCCTGCTATTGTGAT
* *
171067 TTCCTGTTATTTTGAT
1 TTCCTGCTATTGTGAT
171083 TTC
1 TTC
171086 AATCTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.57
Consensus pattern (16 bp):
TTCCTGCTATTGTGAT
Found at i:180664 original size:18 final size:18
Alignment explanation
Indices: 180638--180672 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
180628 GCCAATTGCC
*
180638 TAAATCAGTAACCAGTAA
1 TAAAACAGTAACCAGTAA
180656 TAAAACAGTAACCAGTA
1 TAAAACAGTAACCAGTA
180673 CCCTCTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.20
Consensus pattern (18 bp):
TAAAACAGTAACCAGTAA
Found at i:181218 original size:84 final size:83
Alignment explanation
Indices: 181113--181275 Score: 254
Period size: 84 Copynumber: 2.0 Consensus size: 83
181103 TCTTGAAGTG
* * * * *
181113 TCAGATTGTGGTGCAGGTGATCAGAGAGTGCTAATTCGTACAGTGAACAAACAAAAAACTACTGT
1 TCAGACTGTGATGCAGGTGATCAGAGAGCGCTAATTCGCACAGTGAACAAAC-AAAAACTACCGT
181178 TGAATTAGGCTTACCAGCA
65 TGAATTAGGCTTACCAGCA
* *
181197 TCAGACTGTGATGCAGGTGATCAGAGGGCGCTAATTCGCATAGTGAACAAACAAAAACTACCGTT
1 TCAGACTGTGATGCAGGTGATCAGAGAGCGCTAATTCGCACAGTGAACAAACAAAAACTACCGTT
181262 GAATTAGGCTTACC
66 GAATTAGGCTTACC
181276 GACAAGAAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 26 0.36
84 46 0.64
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (83 bp):
TCAGACTGTGATGCAGGTGATCAGAGAGCGCTAATTCGCACAGTGAACAAACAAAAACTACCGTT
GAATTAGGCTTACCAGCA
Found at i:186399 original size:2 final size:2
Alignment explanation
Indices: 186392--186447 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
186382 AACTTTTAAC
186392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
186433 TA -A TA TA GTA TA TA T
1 TA TA TA TA -TA TA TA T
186448 GCACGTAGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:188538 original size:17 final size:18
Alignment explanation
Indices: 188505--188544 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
188495 ATGTAGACAC
188505 ATAAATTAAAATAAATAA
1 ATAAATTAAAATAAATAA
*
188523 ATAAATT-AATTAAATAA
1 ATAAATTAAAATAAATAA
188540 ATAAA
1 ATAAA
188545 AAAAAATCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATTAAAATAAATAA
Found at i:195198 original size:29 final size:29
Alignment explanation
Indices: 195166--195222 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
195156 TATTTCTAGC
195166 AATCATAATTACTCGTTATATTTAATTAT
1 AATCATAATTACTCGTTATATTTAATTAT
* *
195195 AATCATAATTATTGGTTATATTTAATTA
1 AATCATAATTACTCGTTATATTTAATTA
195223 GTGTCTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (29 bp):
AATCATAATTACTCGTTATATTTAATTAT
Found at i:198598 original size:12 final size:12
Alignment explanation
Indices: 198583--198622 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
198573 TTTTTCTCTA
198583 TTATTTATTTTT
1 TTATTTATTTTT
*
198595 TTATTCATTTTGT
1 TTATTTATTTT-T
*
198608 TTATATATTTTT
1 TTATTTATTTTT
198620 TTA
1 TTA
198623 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:198673 original size:2 final size:2
Alignment explanation
Indices: 198666--198712 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
198656 TGTCCAAGCN
*
198666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
198709 -T AT A
1 AT AT A
198713 GTGCTAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:207709 original size:8 final size:8
Alignment explanation
Indices: 207696--207720 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
207686 GGTGCAGGAG
207696 GGAAATGT
1 GGAAATGT
207704 GGAAATGT
1 GGAAATGT
207712 GGAAATGT
1 GGAAATGT
207720 G
1 G
207721 AAGAGCCGCC
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:0.40, T:0.24
Consensus pattern (8 bp):
GGAAATGT
Found at i:210084 original size:86 final size:87
Alignment explanation
Indices: 209939--210116 Score: 331
Period size: 86 Copynumber: 2.1 Consensus size: 87
209929 GATCCTTTCG
*
209939 AGATAGTAATGGTCCACTCAACCATGTTCTCGACAGAGAAATTAAATGAGGGAAGGACTCCTTTA
1 AGATAGCAATGGTCCACTCAACCATGTTCTCGACAGAGAAATTAAATGAGGGAAGGACTCCTTTA
210004 TTTTCTAATTGCAGGTTGCAA-
66 TTTTCTAATTGCAGGTTGCAAT
*
210025 AGATAGCAATGGTCCACTCAACCATGTTCTCGACAGAGAATTTAAATGAGGGAAGGACTCCTTTA
1 AGATAGCAATGGTCCACTCAACCATGTTCTCGACAGAGAAATTAAATGAGGGAAGGACTCCTTTA
210090 TTTTCTAATTGCAGGTTGCAAT
66 TTTTCTAATTGCAGGTTGCAAT
210112 AGATA
1 AGATA
210117 TACTGAAAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 84 0.94
87 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (87 bp):
AGATAGCAATGGTCCACTCAACCATGTTCTCGACAGAGAAATTAAATGAGGGAAGGACTCCTTTA
TTTTCTAATTGCAGGTTGCAAT
Found at i:221337 original size:24 final size:24
Alignment explanation
Indices: 221275--221356 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
221265 CAACTAAGAG
** *
221275 AGAAGAGCAGAGTCCAACCAAGGT
1 AGAAGAGCAGTTTCCAACCAAAGT
* * ** *
221299 AGCAGAGGAACTTCCTACCAAAGT
1 AGAAGAGCAGTTTCCAACCAAAGT
*
221323 AGAAGAGCAGTTTCCAACCACAGT
1 AGAAGAGCAGTTTCCAACCAAAGT
*
221347 AGAGGAGCAG
1 AGAAGAGCAG
221357 CATGGTTTGG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAGAGCAGTTTCCAACCAAAGT
Found at i:231867 original size:20 final size:20
Alignment explanation
Indices: 231837--231899 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
231827 ATATTATTAT
231837 TAAAA-TAAAATATATAATA
1 TAAAATTAAAATATATAATA
231856 TAAAATTAAAATA-A-AATA
1 TAAAATTAAAATATATAATA
231874 TAAAAAATTAAAATTTATATAATA
1 T--AAAATTAAAA--TATATAATA
231898 TA
1 TA
231900 GATAAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
18 5 0.14
19 6 0.16
20 17 0.46
22 3 0.08
23 1 0.03
24 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATTAAAATATATAATA
Found at i:231876 original size:7 final size:7
Alignment explanation
Indices: 231841--231922 Score: 52
Period size: 7 Copynumber: 12.3 Consensus size: 7
231831 TATTATTAAA
231841 ATAAAAT
1 ATAAAAT
*
231848 ATATAAT
1 ATAAAAT
231855 ATAAAAT
1 ATAAAAT
231862 -T-AAA-
1 ATAAAAT
231866 ATAAAAT
1 ATAAAAT
*
231873 ATAAAAA
1 ATAAAAT
231880 ATTAAAATTT
1 A-TAAAA--T
*
231890 ATATAAT
1 ATAAAAT
*
231897 AT-AGAT
1 ATAAAAT
231903 A-AAAAT
1 ATAAAAT
231909 -TAAAAT
1 ATAAAAT
231915 -TAAAAT
1 ATAAAAT
231921 AT
1 AT
231923 TATATATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
5 4 0.07
6 21 0.36
7 23 0.40
8 5 0.09
9 4 0.07
10 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (7 bp):
ATAAAAT
Found at i:231926 original size:27 final size:26
Alignment explanation
Indices: 231856--231926 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
231846 ATATATAATA
* *
231856 TAAAATTAAAATAAAATATAAAAAAT
1 TAAAATTAAAATAATATAGAAAAAAT
* *
231882 TAAAATTTATATAATATAGATAAAAAT
1 TAAAATTAAAATAATATAGA-AAAAAT
*
231909 TAAAATTAAAATATTATA
1 TAAAATTAAAATAATATA
231927 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
TAAAATTAAAATAATATAGAAAAAAT
Found at i:231980 original size:18 final size:17
Alignment explanation
Indices: 231962--232017 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
231952 AAATAAAAAT
231962 AATATATAAAATTATAA
1 AATATATAAAATTATAA
* *
231979 TAAAAAATAAAA--ATAA
1 -AATATATAAAATTATAA
*
231995 AATATATAACATTA-AA
1 AATATATAAAATTATAA
232011 AATATAT
1 AATATAT
232018 TTAAAAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 8 0.26
16 13 0.42
17 1 0.03
18 9 0.29
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATATAAAATTATAA
Found at i:232002 original size:25 final size:25
Alignment explanation
Indices: 231956--232003 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
231946 TTAAAAAAAT
*
231956 AAAAATAATATATAAAATTATAATA
1 AAAAATAATAAATAAAATTATAATA
231981 AAAAATAA-AAATAAAATATATAA
1 AAAAATAATAAATAAAAT-TATAA
232004 CATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAATAATAAATAAAATTATAATA
Found at i:232003 original size:33 final size:32
Alignment explanation
Indices: 231937--232000 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
231927 TATTTTTTAA
*
231937 AAAATTATATTAAAAAAATAAAAATAATATAT
1 AAAATTATAATAAAAAAATAAAAATAATATAT
*
231969 AAAATTATAAT-AAAAAATAAAAATAAAATAT
1 AAAATTATAATAAAAAAATAAAAATAATATAT
232000 A
1 A
232001 TAACATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (32 bp):
AAAATTATAATAAAAAAATAAAAATAATATAT
Found at i:232063 original size:13 final size:13
Alignment explanation
Indices: 231952--232063 Score: 52
Period size: 13 Copynumber: 8.4 Consensus size: 13
231942 TATATTAAAA
231952 AAAT-AAAAATA-
1 AAATAAAAAATAT
* *
231963 ATATATAAAAT-T
1 AAATAAAAAATAT
*
231975 ATAATAAAAAATAA
1 A-AATAAAAAATAT
*
231989 AAATAAAATATAT
1 AAATAAAAAATAT
*
232002 AACATTAAAAATAT
1 AA-ATAAAAAATAT
** *
232016 ATTTAAAAGATGAT
1 AAATAAAAAAT-AT
*
232030 ATTATATAAAAAT-T
1 A-AATA-AAAAATAT
232044 AATAATAAAAAATAT
1 -A-AATAAAAAATAT
232059 AAATA
1 AAATA
232064 TATTAAACTT
Statistics
Matches: 75, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
11 3 0.04
12 6 0.08
13 30 0.40
14 22 0.29
15 9 0.12
16 5 0.07
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (13 bp):
AAATAAAAAATAT
Found at i:232715 original size:22 final size:23
Alignment explanation
Indices: 232690--232735 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
232680 TATAAATCAA
*
232690 ATATTATAA-TATTATTTTTCTT
1 ATATTATAATTATTATTTTACTT
* *
232712 ATATTTTAATTATTGTTTTACTT
1 ATATTATAATTATTATTTTACTT
232735 A
1 A
232736 CATATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
ATATTATAATTATTATTTTACTT
Found at i:232796 original size:15 final size:15
Alignment explanation
Indices: 232765--232815 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
232755 TTATTTTCTC
*
232765 TATAATTATATTGTT
1 TATAATTATATTATT
232780 TATAATTATATTATT
1 TATAATTATATTATT
* ** *
232795 TACAATTGCATTATC
1 TATAATTATATTATT
232810 TATAAT
1 TATAAT
232816 CACATTGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (15 bp):
TATAATTATATTATT
Found at i:233938 original size:17 final size:17
Alignment explanation
Indices: 233916--233950 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
233906 GAGAGAGAGC
233916 AAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAACAAA
* *
233933 AAAAAAAAGAAAAGAAA
1 AAAAAAAAAAAAACAAA
233950 A
1 A
233951 CAAGAGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAACAAA
Found at i:238413 original size:33 final size:33
Alignment explanation
Indices: 238371--238434 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
238361 TTCACCAAGT
*
238371 GATGTTGTGGAAGAAAGCACTTCGGCTTCTCAG
1 GATGTTGTGGAAGAAAGCACATCGGCTTCTCAG
238404 GATGTTGTGGAAGAAAGCACATCGGCTTCTC
1 GATGTTGTGGAAGAAAGCACATCGGCTTCTC
238435 GGGAAATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (33 bp):
GATGTTGTGGAAGAAAGCACATCGGCTTCTCAG
Found at i:240588 original size:27 final size:27
Alignment explanation
Indices: 240535--240588 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
240525 AATTTTAAAA
* *
240535 TTTATAAAAATGAAATTATAAATTTTT
1 TTTAAAAAAATGAAATTATAAAATTTT
* *
240562 TTTAAAAAAAT-AAATTGTAAAAATTT
1 TTTAAAAAAATGAAATTATAAAATTTT
240588 T
1 T
240589 AAAATTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTAAAAAAATGAAATTATAAAATTTT
Found at i:258743 original size:13 final size:14
Alignment explanation
Indices: 258720--258748 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
258710 ACAACGGCTA
258720 GCGCGGCGCCCACT
1 GCGCGGCGCCCACT
258734 GCGC-GCGCCCACT
1 GCGCGGCGCCCACT
258747 GC
1 GC
258749 CTCTGATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.07, C:0.52, G:0.34, T:0.07
Consensus pattern (14 bp):
GCGCGGCGCCCACT
Found at i:260295 original size:2 final size:2
Alignment explanation
Indices: 260288--260321 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
260278 ATCCATTCTT
260288 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
260322 CGTCTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:269393 original size:21 final size:21
Alignment explanation
Indices: 269363--269402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
269353 ACAACCCCGT
*
269363 ATCCTTTCCCATATCTCCTTA
1 ATCCTCTCCCATATCTCCTTA
*
269384 ATCCTCTCCCTTATCTCCT
1 ATCCTCTCCCATATCTCCT
269403 CAATTGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (21 bp):
ATCCTCTCCCATATCTCCTTA
Found at i:269486 original size:23 final size:24
Alignment explanation
Indices: 269440--269487 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
269430 ATAAGAAATT
269440 CTTTAGAAAAGGATTAGCCAATCC
1 CTTTAGAAAAGGATTAGCCAATCC
* *
269464 CTTTAGAAATGG-TTAGCCGATCC
1 CTTTAGAAAAGGATTAGCCAATCC
269487 C
1 C
269488 AACCCAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (24 bp):
CTTTAGAAAAGGATTAGCCAATCC
Found at i:319419 original size:14 final size:14
Alignment explanation
Indices: 319400--319431 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
319390 GAAAGTACGT
319400 AATATCAGCATAAA
1 AATATCAGCATAAA
319414 AATATCAGCATAAA
1 AATATCAGCATAAA
319428 AATA
1 AATA
319432 ACAACTAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (14 bp):
AATATCAGCATAAA
Found at i:340646 original size:122 final size:122
Alignment explanation
Indices: 340426--340668 Score: 357
Period size: 122 Copynumber: 2.0 Consensus size: 122
340416 GGATACTAAC
*
340426 AACAGTCCTATTAGTGACTCCATGATGCATTATTAGTCTTATAAATTCTTCATCTCTACCTCAAA
1 AACAGTCCTATTAGTGACTCCATGATGCATTACTAGTCTTATAAATTCTTCATCTCTACCTCAAA
*
340491 TGCCTCTATAGTACGATTTATCACAATTAAATAAGTTTGCAAACTTT-AACCAGGTGAA
66 TGCCTCTATAGTACGATTTATCACAATTAAATAAGTATG-AAACTTTCAA-CAGGTGAA
* * *
340549 AACAGTCCTATTAGTGACTCCATGTTGCATTACTAGTCTTAT-GATTCTTCATCTCTGCCTCAAA
1 AACAGTCCTATTAGTGACTCCATGATGCATTACTAGTCTTATAAATTCTTCATCTCTACCTCAAA
* ** *
340613 TGCCTCTATAGTATGA-TTAGTGGCAATTGAATAAGTATGAAACTTTCAACAGGTGA
66 TGCCTCTATAGTACGATTTA-TCACAATTAAATAAGTATGAAACTTTCAACAGGTGA
340669 CTTATCCAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
121 17 0.16
122 52 0.48
123 40 0.37
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (122 bp):
AACAGTCCTATTAGTGACTCCATGATGCATTACTAGTCTTATAAATTCTTCATCTCTACCTCAAA
TGCCTCTATAGTACGATTTATCACAATTAAATAAGTATGAAACTTTCAACAGGTGAA
Found at i:343361 original size:15 final size:15
Alignment explanation
Indices: 343337--343370 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
343327 CAGATTAAAA
343337 TTTAAAATTTAAGAT
1 TTTAAAATTTAAGAT
* *
343352 TTTAATATTTGAGAT
1 TTTAAAATTTAAGAT
343367 TTTA
1 TTTA
343371 GTTGATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TTTAAAATTTAAGAT
Found at i:347412 original size:2 final size:2
Alignment explanation
Indices: 347397--347450 Score: 81
Period size: 2 Copynumber: 26.0 Consensus size: 2
347387 AAACGCATGA
*
347397 AG AG AG CAG CAG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG
1 AG AG AG -AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
347441 AG AG AG AG AG
1 AG AG AG AG AG
347451 GAGGGGAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 44 0.90
3 5 0.10
ACGTcount: A:0.48, C:0.06, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:347469 original size:1 final size:1
Alignment explanation
Indices: 347453--347487 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
347443 AGAGAGAGGA
* *
347453 GGGGAGGGGGGNGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
347488 ATGGGTGGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.94, T:0.00
Consensus pattern (1 bp):
G
Found at i:347750 original size:2 final size:2
Alignment explanation
Indices: 347743--347794 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
347733 CAAGTTGCAT
* *
347743 AG AG AG AG AG CG AG AG AG AG AG AA AG AG AG ATG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG
347786 AG AG AG AG A
1 AG AG AG AG A
347795 AGGGGGGGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:347956 original size:15 final size:15
Alignment explanation
Indices: 347938--347985 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
347928 TTCCTTTTTA
347938 CCTTCAACTTTTTCC
1 CCTTCAACTTTTTCC
* *
347953 CCTTTCATCCTTTTT-G
1 CC-TTCA-ACTTTTTCC
347969 CCTTCAACTTTTTCC
1 CCTTCAACTTTTTCC
347984 CC
1 CC
347986 CCTCCCCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 6 0.23
17 6 0.23
ACGTcount: A:0.10, C:0.40, G:0.02, T:0.48
Consensus pattern (15 bp):
CCTTCAACTTTTTCC
Found at i:347967 original size:31 final size:31
Alignment explanation
Indices: 347924--347985 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
347914 ATTTGTTCTT
*
347924 TTTCTTCCTTTTTACCTTCAACTTTTTCCCC
1 TTTCATCCTTTTTACCTTCAACTTTTTCCCC
*
347955 TTTCATCCTTTTTGCCTTCAACTTTTTCCCC
1 TTTCATCCTTTTTACCTTCAACTTTTTCCCC
347986 CCTCCCCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.10, C:0.35, G:0.02, T:0.53
Consensus pattern (31 bp):
TTTCATCCTTTTTACCTTCAACTTTTTCCCC
Found at i:356438 original size:18 final size:18
Alignment explanation
Indices: 356415--356450 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
356405 GAAAACACAA
356415 GATCCAGAAATATTTAAG
1 GATCCAGAAATATTTAAG
356433 GATCCAGAAATATTTAAG
1 GATCCAGAAATATTTAAG
356451 AACATCATCT
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:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GATCCAGAAATATTTAAG
Found at i:364733 original size:36 final size:36
Alignment explanation
Indices: 364693--364765 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
364683 GACAACTTAC
364693 CAACTCTCTGTCTATTCTATCCCAACTCTGTTCCTT
1 CAACTCTCTGTCTATTCTATCCCAACTCTGTTCCTT
* *
364729 CAACTCTCTGTTTATTCTATCCTAACTCTGTTCCTT
1 CAACTCTCTGTCTATTCTATCCCAACTCTGTTCCTT
364765 C
1 C
364766 CAGTGTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.16, C:0.34, G:0.05, T:0.44
Consensus pattern (36 bp):
CAACTCTCTGTCTATTCTATCCCAACTCTGTTCCTT
Found at i:383608 original size:33 final size:33
Alignment explanation
Indices: 383566--383631 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
383556 TTTTAAATAC
*
383566 GTGCATCGATATGTTTATTACATTTATTACATG
1 GTGCATCGATATGTTTATTACATCTATTACATG
383599 GTGCATCGATATGTTTATTACATCTATTACATG
1 GTGCATCGATATGTTTATTACATCTATTACATG
383632 ACAAGTCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (33 bp):
GTGCATCGATATGTTTATTACATCTATTACATG
Found at i:386508 original size:50 final size:51
Alignment explanation
Indices: 386420--386524 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 51
386410 TCTTGGTTTT
386420 ATTTATTTCAGACACAAAACTTTTTAATTACAATGAAGAATTCTTGTATTC
1 ATTTATTTCAGACACAAAACTTTTTAATTACAATGAAGAATTCTTGTATTC
386471 ATTTATTTCAGACAC-AAACTTTTTAATTACAATGAAGAATTCTTGTATTC
1 ATTTATTTCAGACACAAAACTTTTTAATTACAATGAAGAATTCTTGTATTC
386521 ATTT
1 ATTT
386525 GTTTTATTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 39 0.72
51 15 0.28
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (51 bp):
ATTTATTTCAGACACAAAACTTTTTAATTACAATGAAGAATTCTTGTATTC
Found at i:389824 original size:27 final size:27
Alignment explanation
Indices: 389793--389856 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
389783 ACATTGGGTG
*
389793 TTAGGATGGTCTTGAATTATAGTTTGA
1 TTAGGATAGTCTTGAATTATAGTTTGA
*
389820 TTAGGATAGTCTTGAATTGTAGTTTGA
1 TTAGGATAGTCTTGAATTATAGTTTGA
389847 TTAGGATAGT
1 TTAGGATAGT
389857 TTAATTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.44
Consensus pattern (27 bp):
TTAGGATAGTCTTGAATTATAGTTTGA
Found at i:389858 original size:14 final size:14
Alignment explanation
Indices: 389811--389858 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
389801 GTCTTGAATT
389811 ATAGTTTGATTAGG
1 ATAGTTTGATTAGG
389825 ATAGTCTTGAATT--G
1 ATAGT-TTG-ATTAGG
389839 -TAGTTTGATTAGG
1 ATAGTTTGATTAGG
389852 ATAGTTT
1 ATAGTTT
389859 AATTCTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 3 0.10
12 3 0.10
13 5 0.17
14 12 0.41
15 3 0.10
16 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (14 bp):
ATAGTTTGATTAGG
Found at i:407226 original size:31 final size:30
Alignment explanation
Indices: 407191--407255 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
407181 TTTCAAAAGC
* * *
407191 AAATTAATTGAATTCTCATAAAAAATAATCA
1 AAATTAATCGAATTATAATAAAAAA-AATCA
* *
407222 AAATTGATCGAATTATAATAAAAAAAATCG
1 AAATTAATCGAATTATAATAAAAAAAATCA
407252 AAAT
1 AAAT
407256 CAACTTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (30 bp):
AAATTAATCGAATTATAATAAAAAAAATCA
Found at i:407358 original size:21 final size:20
Alignment explanation
Indices: 407303--407356 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
407293 CAATTTTAGT
**
407303 TATATTTT-AAAAATATTAA
1 TATATTTTAAAAAATAAAAA
* *
407322 TATAATTTATATAAATAAAAA
1 TATATTTTA-AAAAATAAAAA
407343 TATATTTTAAAAAA
1 TATATTTTAAAAAA
407357 ATTAGTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 7 0.26
20 4 0.15
21 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATTTTAAAAAATAAAAA
Found at i:415066 original size:2 final size:2
Alignment explanation
Indices: 415061--415095 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
415051 ACTCTCTGTT
*
415061 TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
415096 GCCTTTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:415136 original size:2 final size:2
Alignment explanation
Indices: 415131--415169 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
415121 TTTTTTCCTT
415131 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
415170 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:415271 original size:2 final size:2
Alignment explanation
Indices: 415264--415302 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
415254 TCCTTTTCGT
415264 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
415303 TGGGTTTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:419019 original size:2 final size:2
Alignment explanation
Indices: 419012--419063 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
419002 AAACAGCTCG
* *
419012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
419054 AT AT AT AT AT
1 AT AT AT AT AT
419064 GAAAAACTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:419443 original size:7 final size:7
Alignment explanation
Indices: 419399--419442 Score: 70
Period size: 7 Copynumber: 6.1 Consensus size: 7
419389 AACTAGACGA
419399 AGGCTTTC
1 AGGC-TTC
419407 AGGCTTC
1 AGGCTTC
419414 AGGCTTC
1 AGGCTTC
419421 AGGCTTC
1 AGGCTTC
419428 AGGCTTC
1 AGGCTTC
*
419435 AAGCTTC
1 AGGCTTC
419442 A
1 A
419443 ACCTGCCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
7 31 0.89
8 4 0.11
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (7 bp):
AGGCTTC
Found at i:445331 original size:17 final size:16
Alignment explanation
Indices: 445301--445340 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
445291 ATTAATTAAA
*
445301 AAAATTAAATTATAAT
1 AAAATAAAATTATAAT
445317 AAAATAAAATATATAAT
1 AAAATAAAAT-TATAAT
445334 AAAATAA
1 AAAATAA
445341 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAAAATTATAAT
Found at i:446559 original size:8 final size:8
Alignment explanation
Indices: 446546--446581 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
446536 TATATNAAAT
446546 AAATAATA
1 AAATAATA
446554 AAATAATA
1 AAATAATA
446562 AAATAATAA
1 AAATAAT-A
446571 AAATAATA
1 AAATAATA
446579 AAA
1 AAA
446582 AAATGAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:446567 original size:20 final size:18
Alignment explanation
Indices: 446542--446585 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
446532 ATCCTATATN
446542 AAATAAATAATAAAATAATA
1 AAATAAAT-A-AAAATAATA
446562 AAAT-AATAAAAATAATA
1 AAATAAATAAAAATAATA
446579 AAA-AAAT
1 AAATAAAT
446586 GAATGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.65
18 1 0.04
19 3 0.13
20 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAATAATA
Found at i:448321 original size:75 final size:74
Alignment explanation
Indices: 448121--448348 Score: 318
Period size: 74 Copynumber: 3.1 Consensus size: 74
448111 CACTGTGACA
* * * * * *
448121 CCAAACCCTTTGTTTTGGGCACTTA-ATAT--TGCTGAAATTGGCGCTGCAGCCAGAATGGAATC
1 CCAAACTCTCTGTTTTGGG-ACTTACAT-TGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAAC
** *
448183 TCGCCGTAGCG
64 TCGCCGCGGCC
448194 CCAAACTCTCTGTTTTGGGACTTACATTGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAACTC
1 CCAAACTCTCTGTTTTGGGACTTACATTGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAACTC
448259 GCCGCGGCC
66 GCCGCGGCC
448268 CCAAACTCTCTGTTTTGGGACTTGACATTGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAACT
1 CCAAACTCTCTGTTTTGGGACTT-ACATTGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAACT
*
448333 CGCCGCGGCT
65 CGCCGCGGCC
448343 CCAAAC
1 CCAAAC
448349 ATGCTTTGTT
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
72 6 0.04
73 19 0.13
74 60 0.43
75 56 0.40
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (74 bp):
CCAAACTCTCTGTTTTGGGACTTACATTGCTGCTGAATTTGGCGCTGCAGCCAAAATGAAAACTC
GCCGCGGCC
Found at i:468567 original size:24 final size:24
Alignment explanation
Indices: 468521--468567 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
468511 TGGACTATCC
* **
468521 CTTCTCATCGATTAATATTGAAAG
1 CTTCTAATCGATTAATACCGAAAG
*
468545 CTTCTAATTGATTAATACCGAAA
1 CTTCTAATCGATTAATACCGAAA
468568 TTGAAAAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (24 bp):
CTTCTAATCGATTAATACCGAAAG
Found at i:474885 original size:21 final size:21
Alignment explanation
Indices: 474859--474900 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
474849 AAACATTGAG
474859 TAAGTCACAAGTCTCTGTTCC
1 TAAGTCACAAGTCTCTGTTCC
474880 TAAGTCACAAGTCTCTGTTCC
1 TAAGTCACAAGTCTCTGTTCC
474901 CTGTATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (21 bp):
TAAGTCACAAGTCTCTGTTCC
Found at i:479445 original size:27 final size:27
Alignment explanation
Indices: 479394--479566 Score: 120
Period size: 27 Copynumber: 6.4 Consensus size: 27
479384 AACACTCAGA
*
479394 GGTGTTCTAAGTC-TGGAAGCGCCCAGG
1 GGTGTTCCAAG-CATGGAAGCGCCCAGG
* * **
479421 GGTTTTCCAAGCATGGAAGTGCCCAAA
1 GGTGTTCCAAGCATGGAAGCGCCCAGG
** * *
479448 GGTGTTCCAAGCACAGAAGCACCCAAG
1 GGTGTTCCAAGCATGGAAGCGCCCAGG
* * * **
479475 GATATTCCAAGCATAGAATTGCCCAGG
1 GGTGTTCCAAGCATGGAAGCGCCCAGG
* *
479502 GGTGTTCTAAGCGA-GGAAGCGTCCAGG
1 GGTGTTCCAAGC-ATGGAAGCGCCCAGG
* *
479529 GGTGTTCCGAG--TGCGAAAGCGTCCAGG
1 GGTGTTCCAAGCATG-G-AAGCGCCCAGG
479556 GGTGTTCCAAG
1 GGTGTTCCAAG
479567 TGCGAAAGCA
Statistics
Matches: 113, Mismatches: 28, Indels: 10
0.75 0.19 0.07
Matches are distributed among these distances:
25 1 0.01
26 2 0.02
27 109 0.96
28 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (27 bp):
GGTGTTCCAAGCATGGAAGCGCCCAGG
Found at i:479568 original size:27 final size:27
Alignment explanation
Indices: 479497--479601 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
479487 ATAGAATTGC
* * * *
479497 CCAGGGGTGTTCTAAGCGAGGAAGCGT
1 CCAGGGGTGTTCCAAGTGCGAAAGCGT
*
479524 CCAGGGGTGTTCCGAGTGCGAAAGCGT
1 CCAGGGGTGTTCCAAGTGCGAAAGCGT
*
479551 CCAGGGGTGTTCCAAGTGCGAAAGC-A
1 CCAGGGGTGTTCCAAGTGCGAAAGCGT
*
479577 CCTAAGGGTGTTCCAAGTGCAGAAA
1 CC-AGGGGTGTTCCAAGTGC-GAAA
479602 CGCCCTAAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 2 0.03
27 62 0.91
28 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.36, T:0.18
Consensus pattern (27 bp):
CCAGGGGTGTTCCAAGTGCGAAAGCGT
Found at i:479608 original size:28 final size:27
Alignment explanation
Indices: 479528--479610 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
479518 AAGCGTCCAG
* * *
479528 GGGTGTTCCGAGTGCGAAAGCGTCC-AG
1 GGGTGTTCCAAGTGCGAAA-CGCCCTAA
479555 GGGTGTTCCAAGTGCGAAA-GCACCTAA
1 GGGTGTTCCAAGTGCGAAACGC-CCTAA
479582 GGGTGTTCCAAGTGCAGAAACGCCCTAA
1 GGGTGTTCCAAGTGC-GAAACGCCCTAA
479610 G
1 G
479611 TGTGGAAACG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 34 0.69
28 10 0.20
29 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.34, T:0.18
Consensus pattern (27 bp):
GGGTGTTCCAAGTGCGAAACGCCCTAA
Found at i:479644 original size:27 final size:27
Alignment explanation
Indices: 479613--479671 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
479603 GCCCTAAGTG
*
479613 TGGAAACGTCCAAAG-GTGTTCTAAGCA
1 TGGAAACG-CCAAAGAGTGTTCCAAGCA
* *
479640 TGGAAGCGCCCAAGAGTGTTCCAAGCA
1 TGGAAACGCCAAAGAGTGTTCCAAGCA
479667 TGGAA
1 TGGAA
479672 GTGTCTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (27 bp):
TGGAAACGCCAAAGAGTGTTCCAAGCA
Found at i:479717 original size:27 final size:28
Alignment explanation
Indices: 479682--479741 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
479672 GTGTCTAAGT
*
479682 TGTTTCAAGCGC-GAAAGTGCCAAGGGG
1 TGTTCCAAGCGCAGAAAGTGCCAAGGGG
* * *
479709 TGTTCCAAGCTCAGAAAGTGTCTAGGGG
1 TGTTCCAAGCGCAGAAAGTGCCAAGGGG
479737 TGTTC
1 TGTTC
479742 TAAGTGTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.25
Consensus pattern (28 bp):
TGTTCCAAGCGCAGAAAGTGCCAAGGGG
Found at i:484473 original size:79 final size:80
Alignment explanation
Indices: 484374--484532 Score: 275
Period size: 79 Copynumber: 2.0 Consensus size: 80
484364 TTTTCATATG
*
484374 AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGGTTGAATGTTTATCTTTCTTTGG
1 AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGGTTGAAAGTTTATCTTTCTTTGG
484439 ATAATTAAGTTTGGT
66 ATAATTAAGTTTGGT
* * *
484454 AAGAGATAA-GTTTTTAAAATACACCAATAATTACAAGTTTGGTTGAAAGTTTATCTTTGTTTGG
1 AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGGTTGAAAGTTTATCTTTCTTTGG
484518 ATAATTAAGTTTGGT
66 ATAATTAAGTTTGGT
484533 TAAATGTCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 66 0.88
80 9 0.12
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (80 bp):
AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGGTTGAAAGTTTATCTTTCTTTGG
ATAATTAAGTTTGGT
Done.