Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_128
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: 185367
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:14984 original size:29 final size:28
Alignment explanation
Indices: 14952--15058 Score: 101
Period size: 29 Copynumber: 3.8 Consensus size: 28
14942 ATAATATGAT
14952 TTGGGCCTAATGGGCCATATGAATGAGAA
1 TTGGGCCTAATGGGCCATATGAAT-AGAA
* * * *
14981 TTGGGCTTAGTGGGCCATAAGAGTATGAA
1 TTGGGCCTAATGGGCCATATGAATA-GAA
* *
15010 CTGGGCC-AGATGGGCCATTTGAATA-AGA
1 TTGGGCCTA-ATGGGCCATATGAATAGA-A
*
15038 TTGGGCCTAGTGGGCCATATG
1 TTGGGCCTAATGGGCCATATG
15059 CATGTATGTA
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.02
28 19 0.31
29 41 0.67
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.25
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAATAGAA
Found at i:16377 original size:48 final size:48
Alignment explanation
Indices: 16295--16479 Score: 156
Period size: 48 Copynumber: 3.8 Consensus size: 48
16285 ATACTAGGGT
* * * *
16295 TATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATCGGCATTTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATATA
* * * * **
16343 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-ATCCTCGA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGA-CATATA
* * * * * * *
16391 CATGTGGGCTAGTGTAAAACTATGTTTGGAACATGGCATCGACACCGATA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACA--TATA
* * *
16441 TATGAAAGCCAGTGTAAGACCATGTATGGGACATGGCAT
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCAT
16480 TGGCCTCGAC
Statistics
Matches: 104, Mismatches: 29, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
48 72 0.69
49 1 0.01
50 31 0.30
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATATA
Found at i:16473 original size:98 final size:96
Alignment explanation
Indices: 16296--16504 Score: 274
Period size: 98 Copynumber: 2.2 Consensus size: 96
16286 TACTAGGGTT
* * * * ** * *
16296 ATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTAAG
1 ATGTGGGCTAGTGTAAAACCATATTTGGAACATGGCATCGACAGATATATGAAAGCCAGTGTAAG
* *
16361 ACCATGTCTGGGACATGGCATCATCCTCGAC
66 ACCATGTATGGGACATGGCATCAGCCTCGAC
* *
16392 ATGTGGGCTAGTGTAAAACTATGTTTGGAACATGGCATCGACACCGATATATGAAAGCCAGTGTA
1 ATGTGGGCTAGTGTAAAACCATATTTGGAACATGGCATCGACA--GATATATGAAAGCCAGTGTA
**
16457 AGACCATGTATGGGACATGGCATTGGCCTCGAC
64 AGACCATGTATGGGACATGGCATCAGCCTCGAC
16490 ATGTGGGCTAGTGTA
1 ATGTGGGCTAGTGTA
16505 TGTAGCACCC
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 37 0.38
98 60 0.62
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (96 bp):
ATGTGGGCTAGTGTAAAACCATATTTGGAACATGGCATCGACAGATATATGAAAGCCAGTGTAAG
ACCATGTATGGGACATGGCATCAGCCTCGAC
Found at i:18741 original size:48 final size:48
Alignment explanation
Indices: 18632--18857 Score: 197
Period size: 48 Copynumber: 4.6 Consensus size: 48
18622 GGGGCGTTAC
* * *
18632 AGTGTAAGACCATGTTTGGAACATGGCATCAGCACCGATATATGAGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGGCA--TATATATGAGAGCT
* *
18682 AGTGGAAGACCATGTTTGGAACATGGCATCGGCATTTATATGAGAGCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGGCATATATATGAGAGCT
* * ** * * *
18730 AGTGTAAGACCATGTCTAGG-ACATGGCATCGGCCTCGACATGTGGGCT
1 AGTGTAAGACCATGT-TTGGAACATGGCATCGGCATATATATGAGAGCT
* * * * *
18778 AATGTAAGGCCATGTTTGGAACATGGCATTGGCACCAATATATAAGAGCCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGGCA--TATATATGAGAG-CT
* *
18829 -GTGTAAGACCGTGTCTAGG-ACATGGCATC
1 AGTGTAAGACCATGT-TTGGAACATGGCATC
18858 CACATCTTAC
Statistics
Matches: 140, Mismatches: 30, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
47 3 0.02
48 72 0.51
49 3 0.02
50 57 0.41
51 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGAACATGGCATCGGCATATATATGAGAGCT
Found at i:22710 original size:13 final size:13
Alignment explanation
Indices: 22692--22716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22682 TAAACATTTC
22692 AAATCATATTAAT
1 AAATCATATTAAT
22705 AAATCATATTAA
1 AAATCATATTAA
22717 AACCAATACA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATCATATTAAT
Found at i:34005 original size:17 final size:17
Alignment explanation
Indices: 33967--34004 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
33957 AACTTGTCCC
33967 CTTTTATATATATTTTG
1 CTTTTATATATATTTTG
*
33984 CTTTTATTTATATTTT-
1 CTTTTATATATATTTTG
34000 CTTTT
1 CTTTT
34005 TCGGGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (17 bp):
CTTTTATATATATTTTG
Found at i:41274 original size:3 final size:3
Alignment explanation
Indices: 41266--41328 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
41256 ATTGGCTTAT
41266 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
41313 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
41329 TAAAATCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:50313 original size:26 final size:27
Alignment explanation
Indices: 50284--50343 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
50274 CCACATATAT
*
50284 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
50310 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
50337 ATATCTG
1 ATATCTG
50344 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:53051 original size:12 final size:12
Alignment explanation
Indices: 53034--53081 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
53024 TGTCATTAAC
53034 ATATAAAACCAA
1 ATATAAAACCAA
*
53046 ATATAAAACTTTAA
1 ATATAAAAC--CAA
53060 CATATAAAACCAA
1 -ATATAAAACCAA
53073 ATATAAAAC
1 ATATAAAAC
53082 TTTACTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
ATATAAAACCAA
Found at i:53067 original size:27 final size:27
Alignment explanation
Indices: 53029--53085 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
53019 CAGTATGTCA
53029 TTAACATATAAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
53056 TTAACATATAAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
53083 TTA
1 TTA
53086 CTCCCACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (27 bp):
TTAACATATAAAACCAAATATAAAACT
Found at i:69737 original size:35 final size:35
Alignment explanation
Indices: 69626--69771 Score: 150
Period size: 35 Copynumber: 4.2 Consensus size: 35
69616 GTTATCTACT
* * *
69626 GGTCCTTCAGGGCGACACCGTGTAAATGGTATACA
1 GGTCCTTCAAGGCGACACCGTGTAAATGCTATATA
* * * * *
69661 AGTCCATCGAGGCGACACCGTGTAAATGGTATAAA
1 GGTCCTTCAAGGCGACACCGTGTAAATGCTATATA
*
69696 GCTCCTTCAAGGCGACACCGTGTAAATGCTATATA
1 GGTCCTTCAAGGCGACACCGTGTAAATGCTATATA
** * **
69731 GGTCCTTTGAGGTGACATTGTGTAAATGGC-ATATA
1 GGTCCTTCAAGGCGACACCGTGTAAAT-GCTATATA
69766 GGTCCT
1 GGTCCT
69772 ACGGGGCAAC
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 91 0.98
36 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (35 bp):
GGTCCTTCAAGGCGACACCGTGTAAATGCTATATA
Found at i:84704 original size:40 final size:39
Alignment explanation
Indices: 84656--84738 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
84646 CGGGATTTAA
*
84656 CCGGATATAGCT-ACTCGCTCGAA-TGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCAC-AATTG-CTTCGGGACATAGC
* *
84696 CCGGATATAGTAACTCGCACAATTGCTTTGGGACTTAGC
1 CCGGATATAGTAACTCGCACAATTGCTTCGGGACATAGC
84735 CCGG
1 CCGG
84739 TTATCATCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 19 0.50
40 19 0.50
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAATTGCTTCGGGACATAGC
Found at i:86011 original size:16 final size:17
Alignment explanation
Indices: 85990--86023 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
85980 ACATGAGAGC
*
85990 CTTTCT-TTTTTTTTTT
1 CTTTCTCTTTTCTTTTT
86006 CTTTCTCTTTTCTTTTT
1 CTTTCTCTTTTCTTTTT
86023 C
1 C
86024 ATCATCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
CTTTCTCTTTTCTTTTT
Found at i:92644 original size:40 final size:40
Alignment explanation
Indices: 92596--92679 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
92586 CGGGATTTAA
*
92596 CCGGATATAGCT-ACTCGCTCGAA-TGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCAC-AATTGCCTTCGGGACATAGC
*
92636 CCGGATATAGTAACTCGCACAATTGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAATTGCCTTCGGGACATAGC
92676 CCGG
1 CCGG
92680 TTATCATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 3 0.08
40 37 0.93
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAATTGCCTTCGGGACATAGC
Found at i:93954 original size:16 final size:18
Alignment explanation
Indices: 93933--93967 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
93923 ACATGAGAGC
93933 CTTTCT-TTTT-TTTTTT
1 CTTTCTCTTTTCTTTTTT
93949 CTTTCTCTTTTCTTTTTT
1 CTTTCTCTTTTCTTTTTT
93967 C
1 C
93968 ATCATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTCTCTTTTCTTTTTT
Found at i:96595 original size:17 final size:17
Alignment explanation
Indices: 96573--96611 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
96563 TTTGAAAAGG
96573 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
* *
96590 AAAACAATTGAGTCTTA
1 AAAACAAATGAATCTTA
96607 AAAAC
1 AAAAC
96612 TTAATAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:102860 original size:40 final size:40
Alignment explanation
Indices: 102815--103044 Score: 354
Period size: 40 Copynumber: 5.8 Consensus size: 40
102805 CAAGCTCAAT
* * *
102815 TGCCTTCGGGTCTTAACCC-GAGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGA-TATATCAACTCGCACAAA
* *
102855 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
102895 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
102935 TGCCTTCGGGACTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
102975 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
* *
103015 TTCCTTCGGGTTTTAGCCCGGATATATCAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA
103045 TTGCTCATGC
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 174 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
Found at i:104367 original size:13 final size:13
Alignment explanation
Indices: 104349--104373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104339 TTTCATTTGC
104349 TTTCTTTTATTCT
1 TTTCTTTTATTCT
104362 TTTCTTTTATTC
1 TTTCTTTTATTC
104374 ATTAAATCCC
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTATTCT
Found at i:110948 original size:40 final size:40
Alignment explanation
Indices: 110903--111172 Score: 441
Period size: 40 Copynumber: 6.8 Consensus size: 40
110893 CAAGCTCAAT
* * * *
110903 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
* *
110943 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
* *
110983 TGCCTTCGGGTCTTAGCCTGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
111023 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
111063 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
111103 TGCCTTCGGGTTTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
111143 TGCCTTCGGGTTTTAGCCCGGATATATCAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA
111173 TTGCTCATGC
Statistics
Matches: 217, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
Found at i:125755 original size:40 final size:40
Alignment explanation
Indices: 125672--125887 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
125662 CAACCAAGTA
** *
125672 CCTTCGGGGTTTAG-CCGGATATAGCT-ACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
125710 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
125750 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
125790 CCTTCGGGACTTAGCCCGGATATAATAACTCGCATAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
125830 CCTTCGGG-CTTAGCCC-GAAATTAGTCACTTGCACAGATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
125869 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
125888 TTATCATCCG
Statistics
Matches: 157, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 16 0.10
39 40 0.25
40 100 0.64
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:129943 original size:40 final size:40
Alignment explanation
Indices: 129873--130029 Score: 226
Period size: 40 Copynumber: 4.0 Consensus size: 40
129863 CCTCATAATT
* *** *
129873 CTAGCATGAATGC-CTTCGAGGTTTAACCCGGATATATCA
1 CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATATCA
129912 CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATATCA
*
129952 CTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATATCA
* * *
129992 CTAGCACGAATGCTCTTCGGAACTTAGTCTGGATATAT
1 CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATAT
130030 AACTCTCAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 12 0.11
40 97 0.89
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
CTAGCACGAATGCTCTTCGAAACTTAGCCCGGATATATCA
Found at i:131535 original size:46 final size:46
Alignment explanation
Indices: 131467--131602 Score: 191
Period size: 46 Copynumber: 3.0 Consensus size: 46
131457 TATATATACA
* * *
131467 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
131513 CATCTCATACATGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * * *
131559 TATCTCATACACATTCCGCATTAGCCATTCGGCCTTACCACATA
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATA
131603 AATACATGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:131637 original size:47 final size:47
Alignment explanation
Indices: 131577--131865 Score: 362
Period size: 47 Copynumber: 6.1 Consensus size: 47
131567 ACACATTCCG
* * *
131577 CATTAGCCATTCGGCCTTACCACATAAATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* *
131624 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* * **
131671 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* **
131718 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* * *
131765 CATTAGCCATTCGGCCTTATCCCGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT----CACATATATACATGTTCACATTCATCA
* * ** *
131816 CATTTGCCATTCGGCCTTATCTCATATATACACATTCGCATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
131863 CAT
1 CAT
131866 AAAATCCTAA
Statistics
Matches: 216, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
47 175 0.81
51 41 0.19
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
Found at i:131866 original size:25 final size:25
Alignment explanation
Indices: 131792--131866 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
131782 TATCCCGCAT
** *
131792 ATATATACAGGTTCACATTCATCAC
1 ATATATACACATTCGCATTCATCAC
* * *
131817 AT-T-TGC-CATTCGGCCTT-ATCTC
1 ATATATACACATTC-GCATTCATCAC
131839 ATATATACACATTCGCATTCATCAC
1 ATATATACACATTCGCATTCATCAC
131864 ATA
1 ATA
131867 AAATCCTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
22 9 0.25
23 6 0.17
24 7 0.19
25 14 0.39
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (25 bp):
ATATATACACATTCGCATTCATCAC
Found at i:134636 original size:26 final size:25
Alignment explanation
Indices: 134607--134666 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
134597 TAATTAGTAT
*
134607 AAAATATTAATAATTCAAT-AAATTGA
1 AAAAT-TTAATAATTAAATGAAATT-A
* *
134633 AAAATTAAATGATTAAATGAAATTA
1 AAAATTTAATAATTAAATGAAATTA
134658 AAAATTTAA
1 AAAATTTAA
134667 GAGAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (25 bp):
AAAATTTAATAATTAAATGAAATTA
Found at i:136103 original size:53 final size:53
Alignment explanation
Indices: 135922--136128 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 53
135912 ATTAGGGTCT
* * * * * * *
135922 AAGGATATCAAGTAAGACCATGCCAATG-CATGGCATTGGTAAGTTTTACAATGC
1 AAGGATACCATGTAAGACCATGCCAA-GACATGGCAATGATAAG-TTCATAAGGC
* * * * * *
135976 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTATGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGAT-AAGT-TCATAAGGC
** * * *
136031 AAATATCCCATGTAAGACCATGCCAAGGCATGGCAATGATGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCATAAGGC
* *
136084 AAGGATACCATGGAAGACCATGTCAAGACATGGCAATGATAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTT
136129 TAAAAAGGAA
Statistics
Matches: 124, Mismatches: 26, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
53 47 0.38
54 37 0.30
55 40 0.32
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCATAAGGC
Found at i:136144 original size:53 final size:54
Alignment explanation
Indices: 135933--136150 Score: 190
Period size: 53 Copynumber: 4.1 Consensus size: 54
135923 AGGATATCAA
* * * * * * * * *
135933 GTAAGACCATGCCAATG-CATGGCATTGGTAAGTTTTACAATGCAAGGAAATCAT
1 GTAAGACCATGTCAA-GACATGGCAATGATAAGTTTAATAAGGCAAAGATACCAT
* * * * * *
135987 GTAAGACCATGTCAAGACATGGCATTGATAAACTATGATAAGGCAAATATCCCAT
1 GTAAGACCATGTCAAGACATGGCAATGAT-AAGTTTAATAAGGCAAAGATACCAT
* * * * *
136042 GTAAGACCATGCCAAGGCATGGCAATGATGAG-TTCATAAGGCAAGGATACCAT
1 GTAAGACCATGTCAAGACATGGCAATGATAAGTTTAATAAGGCAAAGATACCAT
* * *
136095 GGAAGACCATGTCAAGACATGGCAATGATAAGTTTAAAAAGG-AAAGATACCCT
1 GTAAGACCATGTCAAGACATGGCAATGATAAGTTTAATAAGGCAAAGATACCAT
136148 GTA
1 GTA
136151 TCCTTAGTAT
Statistics
Matches: 130, Mismatches: 31, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
53 56 0.43
54 33 0.25
55 41 0.32
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (54 bp):
GTAAGACCATGTCAAGACATGGCAATGATAAGTTTAATAAGGCAAAGATACCAT
Found at i:138668 original size:49 final size:49
Alignment explanation
Indices: 138596--138784 Score: 220
Period size: 49 Copynumber: 3.8 Consensus size: 49
138586 TGAGGTCACG
* *
138596 TGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * *
138645 TGTGTAGTACTAAGTGCAGGCTACT--GTGCATACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTG--TACCAGATAA-T-TGGTCGCA
* *
138696 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
138745 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
138785 CTTCGGCTAC
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 3 0.03
49 72 0.62
50 2 0.02
51 37 0.32
53 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:138766 original size:100 final size:100
Alignment explanation
Indices: 138591--138778 Score: 313
Period size: 100 Copynumber: 1.9 Consensus size: 100
138581 TATTGTGAGG
* *
138591 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGTCGAATGTGTAGTACT
*
138656 AAGTGCAGGCTACTGTGCATACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCATACCCGAAAACTGTGA
* *
138691 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGAATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGTCGAATGTGTAGTACT
* *
138756 AAGTGTAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCATACC
138779 AGATAACTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGTCGAATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCCGAAAACTGTGA
Found at i:141869 original size:22 final size:20
Alignment explanation
Indices: 141830--141876 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
141820 TGTAAAGTTG
141830 ATAATAATTAATATATATT-
1 ATAATAATTAATATATATTA
141849 ATAATAGATATAATTATATATTA
1 ATAATA-AT-TAA-TATATATTA
141872 ATAAT
1 ATAAT
141877 TATCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 3 0.12
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATAATTAATATATATTA
Found at i:146234 original size:40 final size:40
Alignment explanation
Indices: 146179--146436 Score: 378
Period size: 40 Copynumber: 6.5 Consensus size: 40
146169 TGGATGATAA
** * *
146179 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
146219 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
146259 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
146299 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
146339 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
146379 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
146419 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
146437 TACTTGGCTT
Statistics
Matches: 204, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
39 16 0.08
40 188 0.92
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:148516 original size:27 final size:27
Alignment explanation
Indices: 148478--148530 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
148468 AGTACCTTAC
148478 GTTCTAATTTAGGTGGCTCCTCGATTA
1 GTTCTAATTTAGGTGGCTCCTCGATTA
148505 GTTCTAATTTAGGTGGCTCCTCGATT
1 GTTCTAATTTAGGTGGCTCCTCGATT
148531 GACGCTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (27 bp):
GTTCTAATTTAGGTGGCTCCTCGATTA
Found at i:152907 original size:10 final size:10
Alignment explanation
Indices: 152894--152933 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
152884 TCGAAAAATG
152894 ATCAAAATTA
1 ATCAAAATTA
152904 ATCAAAATTA
1 ATCAAAATTA
*
152914 ATTATAAATTA
1 ATCA-AAATTA
*
152925 ATTAAAATT
1 ATCAAAATT
152934 CAACACGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (10 bp):
ATCAAAATTA
Found at i:153797 original size:47 final size:47
Alignment explanation
Indices: 153696--153806 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 47
153686 CACAGTAATG
*
153696 TAGATAAACTGCCACTTAATAATATTGTGAACAAGCCACCACTTTTG
1 TAGATAAACTGCCACTTAATAATATTGTGAACAAGCCACCACTTTTC
* * * ** *
153743 AAAATAAACTGCCACTCT-ATAATATTGTGTATGAGCCACCATTTTTC
1 TAGATAAACTGCCACT-TAATAATATTGTGAACAAGCCACCACTTTTC
*
153790 TAGATAAACTACCACTT
1 TAGATAAACTGCCACTT
153807 CGTCCTCCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
46 1 0.02
47 51 0.96
48 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (47 bp):
TAGATAAACTGCCACTTAATAATATTGTGAACAAGCCACCACTTTTC
Found at i:155652 original size:25 final size:25
Alignment explanation
Indices: 155618--155687 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
155608 CTCTTTTAAT
* *
155618 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
155643 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
155668 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
155688 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:156617 original size:27 final size:28
Alignment explanation
Indices: 156587--156800 Score: 126
Period size: 27 Copynumber: 7.9 Consensus size: 28
156577 GTAAATCTAC
* *
156587 AAACCAAGGGCATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTTAT
* *
156614 AAACCGAA-GGTATTTCTA-TGATTTTTT
1 AAACC-AAGGGTATTTCTAGTAATTTTAT
*
156641 AAAGTCAAGGGTATTTCT-GTAATTTTAT
1 AAA-CCAAGGGTATTTCTAGTAATTTTAT
* * *
156669 AAATCAAGGGTATTT-TGGTAATTTTACA
1 AAACCAAGGGTATTTCTAGTAATTTTA-T
* * *
156697 AAACC-AGTGGTATTT-TGGTAATTTCAC
1 AAACCAAG-GGTATTTCTAGTAATTTTAT
* *
156724 AAACC-AGTGGTATTT-TGGTAATTTTAC
1 AAACCAAG-GGTATTTCTAGTAATTTTAT
* * * *
156751 AAACTAGGGGTATTT-TGGTAATTTTAC
1 AAACCAAGGGTATTTCTAGTAATTTTAT
* * *
156778 AAACTAGGGGTATTT-TGGTAATT
1 AAACCAAGGGTATTTCTAGTAATT
156801 CTATCCTATA
Statistics
Matches: 165, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.01
27 118 0.72
28 46 0.28
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (28 bp):
AAACCAAGGGTATTTCTAGTAATTTTAT
Found at i:156693 original size:55 final size:53
Alignment explanation
Indices: 156563--156800 Score: 187
Period size: 55 Copynumber: 4.4 Consensus size: 53
156553 ATTTCATCCT
* * * * * * **
156563 ACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGCATTTTAGTAATTTTGTAA
1 ACAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAA
* * ** *
156616 ACCGAA-GGTATTTCT-ATGATTTTTTAAAGTCAAGGGTATTTCT-GTAATTTTATAA
1 A-C-AAGGGTATTT-TGGTAATTTTACAAA-TCAAGGGTATTT-TGGTAATTTTACAA
* * *
156671 ATCAAGGGTATTTTGGTAATTTTACAAAACCAGTGGTATTTTGGTAATTTCACAA
1 A-CAAGGGTATTTTGGTAATTTTACAAATCAAG-GGTATTTTGGTAATTTTACAA
* *
156726 ACCAGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAA
1 ACAAG-GGTATTTTGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAA
*
156780 ACTAGGGGTATTTTGGTAATT
1 AC-AAGGGTATTTTGGTAATT
156801 CTATCCTATA
Statistics
Matches: 148, Mismatches: 25, Indels: 23
0.76 0.13 0.12
Matches are distributed among these distances:
53 1 0.01
54 62 0.42
55 84 0.57
56 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
ACAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAA
Found at i:156813 original size:54 final size:54
Alignment explanation
Indices: 156649--156829 Score: 186
Period size: 54 Copynumber: 3.3 Consensus size: 54
156639 TTAAAGTCAA
* * * * * *
156649 GGGTATTTCT-GTAATTTTATAAATCAAGGGTATTTTGGTAATTTTACAAAACCAG
1 GGGTATTT-TGGTAATTTCACAAACCAGGGGTATTTTGGTAATTCTAC-AAACTAG
* * *
156704 TGGTATTTTGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTCTACAAACTAG
* * **
156758 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCTA-TAG
1 GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTCTA-CAAACTAG
**
156812 GGGTATTTCAGTAATTTC
1 GGGTATTTTGGTAATTTC
156830 GCAATTGAGG
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 66 0.62
55 41 0.38
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTCTACAAACTAG
Found at i:156819 original size:27 final size:27
Alignment explanation
Indices: 156649--156800 Score: 200
Period size: 27 Copynumber: 5.6 Consensus size: 27
156639 TTAAAGTCAA
* *
156649 GGGTATTTCT-GTAATTTTATAAA-TCAA
1 GGGTATTT-TGGTAATTTTACAAACT-AG
*
156676 GGGTATTTTGGTAATTTTACAAAACCAG
1 GGGTATTTTGGTAATTTTAC-AAACTAG
* * *
156704 TGGTATTTTGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
156731 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
156758 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
156785 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
156801 CTATCCTATA
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
26 1 0.01
27 91 0.80
28 22 0.19
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:156851 original size:26 final size:27
Alignment explanation
Indices: 156822--156923 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
156812 GGGTATTTCA
* *
156822 GTAATTTCG-CAATTGAGGGTAAAACG
1 GTAATTTCGTAAATCGAGGGTAAAACG
*
156848 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTTCGTAAATCGAGGGTAAAACG
** *
156875 GTAATTTTATAAATCGAGGGTAAAACA
1 GTAATTTCGTAAATCGAGGGTAAAACG
*
156902 GTAA-TTCTGTAAATCAAGGGTA
1 GTAATTTC-GTAAATCGAGGGTA
156924 CTTTGGTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 10 0.15
27 56 0.85
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (27 bp):
GTAATTTCGTAAATCGAGGGTAAAACG
Found at i:156866 original size:27 final size:27
Alignment explanation
Indices: 156836--156923 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
156826 TTTCGCAATT
156836 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
*
156863 GAGGGTAAAACGGTAATTTTATAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
* *
156890 GAGGGTAAAACAGTAATTCTGTAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
*
156917 AAGGGTA
1 GAGGGTA
156924 CTTTGGTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (27 bp):
GAGGGTAAAACGGTAATTTTGTAAATC
Found at i:156932 original size:54 final size:54
Alignment explanation
Indices: 156836--156948 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
156826 TTTCGCAATT
* * * *
156836 GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTTTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTTTACAAATC
**** *
156890 GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTACTTTGGTAATTTTACAAGTC
1 GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTTTACAAATC
156944 GAGGG
1 GAGGG
156949 CATTTTAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (54 bp):
GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTTTACAAATC
Found at i:163310 original size:15 final size:15
Alignment explanation
Indices: 163290--163322 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
163280 TAAAGTTGAT
*
163290 ACTTTACTTTGATCA
1 ACTTTACTTAGATCA
163305 ACTTTACTTAGATCA
1 ACTTTACTTAGATCA
163320 ACT
1 ACT
163323 CTAATACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (15 bp):
ACTTTACTTAGATCA
Found at i:175298 original size:43 final size:43
Alignment explanation
Indices: 175251--175333 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
175241 ATCAGAATCG
* * *
175251 TATTTGATTTCGTACAAGACCCTGTCTGGGACAG-TGGCATCAA
1 TATTTGATTGCATACAAGACCATGTCTGGGAC-GTTGGCATCAA
**
175294 TATTTGATTGCATGTAAGACCATGTCTGGGACGTTGGCAT
1 TATTTGATTGCATACAAGACCATGTCTGGGACGTTGGCAT
175334 TGTACAAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
TATTTGATTGCATACAAGACCATGTCTGGGACGTTGGCATCAA
Found at i:180375 original size:37 final size:36
Alignment explanation
Indices: 180322--180400 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
180312 TGAATGTGAC
* *
180322 TGGGCCTACTGGGCCATATAAATGTGAATTGGGTGTAA
1 TGGGCCTACTGGGCCATATAAATAT-AATTGGG-CTAA
*
180360 TGGGCCTA-TGGGCCATATGAATATAATTGGGCTAA
1 TGGGCCTACTGGGCCATATAAATATAATTGGGCTAA
180395 TGGGCC
1 TGGGCC
180401 AGATACAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 9 0.24
36 7 0.18
37 14 0.37
38 8 0.21
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (36 bp):
TGGGCCTACTGGGCCATATAAATATAATTGGGCTAA
Found at i:183605 original size:10 final size:10
Alignment explanation
Indices: 183571--183597 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
183561 AATAGCCATG
183571 TTAAGGTATA
1 TTAAGGTATA
183581 TTAAGGTATA
1 TTAAGGTATA
183591 TTAAGGT
1 TTAAGGT
183598 CATTTAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (10 bp):
TTAAGGTATA
Done.