Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 15 of 85
Found at i:4909859 original size:7 final size:7
Alignment explanation
Indices: 4909847--4909882 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
4909837 TGCAAATCGC
4909847 TTTTTAT
1 TTTTTAT
4909854 TTTTTAT
1 TTTTTAT
4909861 TTTTTAT
1 TTTTTAT
4909868 TTTTTAT
1 TTTTTAT
4909875 TTTTTAT
1 TTTTTAT
4909882 T
1 T
4909883 AATCATTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:4909890 original size:21 final size:21
Alignment explanation
Indices: 4909847--4909890 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4909837 TGCAAATCGC
** *
4909847 TTTTTATTTTTTATTTTTTAT
1 TTTTTATTTTTTATTAATCAT
4909868 TTTTTATTTTTTATTAATCAT
1 TTTTTATTTTTTATTAATCAT
4909889 TT
1 TT
4909891 CCAAACTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTATTTTTTATTAATCAT
Found at i:4910322 original size:17 final size:19
Alignment explanation
Indices: 4910284--4910327 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
4910274 GGGCCACAAA
4910284 GCCCAAAACCAAATTCAGTG
1 GCCC-AAACCAAATTCAGTG
4910304 GCCCAAACCAAA-T-AGTG
1 GCCCAAACCAAATTCAGTG
4910321 GCCCAAA
1 GCCCAAA
4910328 ATTGATCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 1 0.04
19 8 0.33
20 4 0.17
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (19 bp):
GCCCAAACCAAATTCAGTG
Found at i:4924184 original size:7 final size:7
Alignment explanation
Indices: 4924172--4924207 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
4924162 TGCAAATCGC
4924172 TTTTTAT
1 TTTTTAT
4924179 TTTTTAT
1 TTTTTAT
4924186 TTTTTAT
1 TTTTTAT
4924193 TTTTTAT
1 TTTTTAT
4924200 TTTTTAT
1 TTTTTAT
4924207 T
1 T
4924208 AATCATTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:4924215 original size:21 final size:21
Alignment explanation
Indices: 4924172--4924215 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4924162 TGCAAATCGC
** *
4924172 TTTTTATTTTTTATTTTTTAT
1 TTTTTATTTTTTATTAATCAT
4924193 TTTTTATTTTTTATTAATCAT
1 TTTTTATTTTTTATTAATCAT
4924214 TT
1 TT
4924216 CCAAACTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTATTTTTTATTAATCAT
Found at i:4924647 original size:17 final size:19
Alignment explanation
Indices: 4924609--4924652 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
4924599 GGGCCACAAA
4924609 GCCCAAAACCAAATTCAGTG
1 GCCC-AAACCAAATTCAGTG
4924629 GCCCAAACCAAA-T-AGTG
1 GCCCAAACCAAATTCAGTG
4924646 GCCCAAA
1 GCCCAAA
4924653 ATTGATCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 1 0.04
19 8 0.33
20 4 0.17
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (19 bp):
GCCCAAACCAAATTCAGTG
Found at i:4925550 original size:35 final size:35
Alignment explanation
Indices: 4925509--4925585 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
4925499 AAAATGTTTC
4925509 CTTTGTATGTATTTATACCTTAAAAATTAATATTT
1 CTTTGTATGTATTTATACCTTAAAAATTAATATTT
4925544 CTTTGTATGTATTTATACCTTAAAAATTAATATTT
1 CTTTGTATGTATTTATACCTTAAAAATTAATATTT
4925579 C-TTGTAT
1 CTTTGTAT
4925586 ATTTTTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 6 0.14
35 36 0.86
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (35 bp):
CTTTGTATGTATTTATACCTTAAAAATTAATATTT
Found at i:4926631 original size:71 final size:72
Alignment explanation
Indices: 4926551--4926693 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
4926541 ACTCGAAAAA
4926551 TTCGAAAAAAAATTCGAAAGTTAACTTTATTTTTAAAATAACTTTTATTAAAAAAATCATA-TTT
1 TTCGAAAAAAAATTCGAAAGTTAACTTTATTTTTAAAATAACTTTTATTAAAAAAATCATATTTT
4926615 TAAATTT
66 TAAATTT
4926622 TTCGAAAAAAAATTCGAAAGTTAACTTTATTTTTAAAATAACTTTTATTAAAAAAATCATATTTT
1 TTCGAAAAAAAATTCGAAAGTTAACTTTATTTTTAAAATAACTTTTATTAAAAAAATCATATTTT
4926687 TAAATTT
66 TAAATTT
4926694 AATATATTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 61 0.86
72 10 0.14
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (72 bp):
TTCGAAAAAAAATTCGAAAGTTAACTTTATTTTTAAAATAACTTTTATTAAAAAAATCATATTTT
TAAATTT
Found at i:4944527 original size:63 final size:63
Alignment explanation
Indices: 4944428--4944553 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
4944418 AATCTGAACT
4944428 CTTCCTCATCCTTTCTACGATACCCTAGGTAAAGAAATGGTTAAGTGGTATCCTAAATGCTAA
1 CTTCCTCATCCTTTCTACGATACCCTAGGTAAAGAAATGGTTAAGTGGTATCCTAAATGCTAA
* *
4944491 CTTCCTCGTCCTTTCTATGATACCCTAGGTAAAGAAATGGTTAAGTGGTATCCTAAATGCTAA
1 CTTCCTCATCCTTTCTACGATACCCTAGGTAAAGAAATGGTTAAGTGGTATCCTAAATGCTAA
4944554 AAGGGTCAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (63 bp):
CTTCCTCATCCTTTCTACGATACCCTAGGTAAAGAAATGGTTAAGTGGTATCCTAAATGCTAA
Found at i:4946289 original size:17 final size:17
Alignment explanation
Indices: 4946262--4946295 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4946252 AAAAAATGTG
4946262 TCAATTAATT-ATAATT
1 TCAATTAATTAATAATT
4946278 TCAATCTAATTAATAATT
1 TCAAT-TAATTAATAATT
4946296 AATTCTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TCAATTAATTAATAATT
Found at i:4946709 original size:19 final size:18
Alignment explanation
Indices: 4946670--4946709 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4946660 TTAAAGTAGT
* *
4946670 ATTAGGTAAAAATGATTA
1 ATTAGGTAAAAAGGATAA
4946688 ATTAGGTAAAAAGGACTAA
1 ATTAGGTAAAAAGGA-TAA
4946707 ATT
1 ATT
4946710 GTAAAAGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (18 bp):
ATTAGGTAAAAAGGATAA
Found at i:4946818 original size:36 final size:36
Alignment explanation
Indices: 4946769--4946842 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
4946759 ATTGAAATGC
4946769 AAATTAATGTACTTAGATGGTATTTATACCATATGA
1 AAATTAATGTACTTAGATGGTATTTATACCATATGA
*
4946805 AAATTAATTTACTTAGATGGTATTTATACCATATGA
1 AAATTAATGTACTTAGATGGTATTTATACCATATGA
4946841 AA
1 AA
4946843 GGTTAATGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (36 bp):
AAATTAATGTACTTAGATGGTATTTATACCATATGA
Found at i:4948915 original size:23 final size:23
Alignment explanation
Indices: 4948884--4948959 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
4948874 AGTGTTATTG
4948884 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
4948907 TTCAGTGGTAGCTACGGCTCCGT
1 ATCAGTGGTAGCTTCGGCTACAT
4948930 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4948953 ATCAGTG
1 ATCAGTG
4948960 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4955283 original size:8 final size:8
Alignment explanation
Indices: 4955270--4955294 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4955260 TATGCCCATC
4955270 TACCAAGA
1 TACCAAGA
4955278 TACCAAGA
1 TACCAAGA
4955286 TACCAAGA
1 TACCAAGA
4955294 T
1 T
4955295 GCCCGTCTAC
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:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (8 bp):
TACCAAGA
Found at i:4956208 original size:30 final size:31
Alignment explanation
Indices: 4956160--4956219 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
4956150 AAACATTTTA
* * *
4956160 TTTTCCCCCACAATTTTTATTTCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
4956190 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
4956220 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:4959616 original size:16 final size:16
Alignment explanation
Indices: 4959597--4959642 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
4959587 TAAGATGGAA
*
4959597 AGGGAGTAAAAGTTTT
1 AGGGAGTAAAAATTTT
**
4959613 AGGG-G-AAAAATTGG
1 AGGGAGTAAAAATTTT
4959627 AGGGAGTAAAAATTTT
1 AGGGAGTAAAAATTTT
4959643 TGAGGAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (16 bp):
AGGGAGTAAAAATTTT
Found at i:4959877 original size:9 final size:9
Alignment explanation
Indices: 4959863--4959899 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
4959853 TATAGTTTAA
4959863 TATTCGAAT
1 TATTCGAAT
4959872 TATTCGAAT
1 TATTCGAAT
*
4959881 TATTCGAGT
1 TATTCGAAT
4959890 TATTCGAAT
1 TATTCGAAT
4959899 T
1 T
4959900 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:4979848 original size:69 final size:69
Alignment explanation
Indices: 4979736--4979964 Score: 307
Period size: 69 Copynumber: 3.3 Consensus size: 69
4979726 GAGAGTTTTT
* * * * * * * *
4979736 CTCTCGTTAATTGTCTTGGAGGTTGCGGCTCTTCGTCTACGAACCTTAATATTATAGTTAGGAGC
1 CTCTCGCTAACTGTTTTGGAGGTTGCGACTCTTCGCCTGCGAACCTTAATATTATAGCTGGGAGC
4979801 TTTG
66 TTTG
*
4979805 CTCTCGCTAACTATTTTGGAGGTTGCGACTCTTCGCCTGCGAACCTTAATATTATAGCTGGGAGC
1 CTCTCGCTAACTGTTTTGGAGGTTGCGACTCTTCGCCTGCGAACCTTAATATTATAGCTGGGAGC
4979870 TTTG
66 TTTG
* * * * * *
4979874 CTCTCGCTAACTGCTTTGGAGGTTG-TAGCTCTTCGCCTGTGAACCTTAATGTTACAACTGGGAG
1 CTCTCGCTAACTGTTTTGGAGGTTGCGA-CTCTTCGCCTGCGAACCTTAATATTATAGCTGGGAG
4979938 CTTTG
65 CTTTG
4979943 CTCTCGCTAACTGTTTTGGAGG
1 CTCTCGCTAACTGTTTTGGAGG
4979965 GTTCGGGTAA
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 1 0.01
69 141 0.99
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (69 bp):
CTCTCGCTAACTGTTTTGGAGGTTGCGACTCTTCGCCTGCGAACCTTAATATTATAGCTGGGAGC
TTTG
Found at i:4980226 original size:139 final size:140
Alignment explanation
Indices: 4979975--4980253 Score: 551
Period size: 139 Copynumber: 2.0 Consensus size: 140
4979965 GTTCGGGTAA
4979975 AAATATAGGCCCAAAATATGGGTTTGGGCAAAAAATAAGGCCTGTTTAGAAAACGGGACTGGCAT
1 AAATATAGGCCCAAAATATGGGTTTGGGCAAAAAATAAGGCCTGTTTAGAAAACGGGACTGGCAT
4980040 CAGGTAAAACTTTTTTAGCCCGGGCTCAGCCCTAATTATATATTAAATATATATTTTATTTTTAA
66 CAGGTAAAACTTTTTTAGCCCGGGCTCAGCCCTAATTATATATTAAATATATATTTTATTTTTAA
4980105 TCAAATATAC
131 TCAAATATAC
4980115 AAATATAGGCCC-AAATATGGGTTTGGGCAAAAAATAAGGCCTGTTTAGAAAACGGGACTGGCAT
1 AAATATAGGCCCAAAATATGGGTTTGGGCAAAAAATAAGGCCTGTTTAGAAAACGGGACTGGCAT
4980179 CAGGTAAAACTTTTTTAGCCCGGGCTCAGCCCTAATTATATATTAAATATATATTTTATTTTTAA
66 CAGGTAAAACTTTTTTAGCCCGGGCTCAGCCCTAATTATATATTAAATATATATTTTATTTTTAA
4980244 TCAAATATAC
131 TCAAATATAC
4980254 TTTTTAAAAT
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 127 0.91
140 12 0.09
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (140 bp):
AAATATAGGCCCAAAATATGGGTTTGGGCAAAAAATAAGGCCTGTTTAGAAAACGGGACTGGCAT
CAGGTAAAACTTTTTTAGCCCGGGCTCAGCCCTAATTATATATTAAATATATATTTTATTTTTAA
TCAAATATAC
Found at i:4980488 original size:20 final size:19
Alignment explanation
Indices: 4980443--4980488 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
4980433 TTACCTAAGC
*
4980443 CCGGCCAAACTCGGTCCGT
1 CCGGCCAAACCCGGTCCGT
4980462 CCTGGCCAAACCCGGTCCGT
1 CC-GGCCAAACCCGGTCCGT
4980482 GCCGGCC
1 -CCGGCC
4980489 CATGATCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.13, C:0.46, G:0.28, T:0.13
Consensus pattern (19 bp):
CCGGCCAAACCCGGTCCGT
Found at i:4981875 original size:20 final size:19
Alignment explanation
Indices: 4981830--4981875 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
4981820 TTACCTAAGC
*
4981830 CCGGCCAAACTCGGTCCGT
1 CCGGCCAAACCCGGTCCGT
4981849 CCTGGCCAAACCCGGTCCGT
1 CC-GGCCAAACCCGGTCCGT
4981869 GCCGGCC
1 -CCGGCC
4981876 CATGATCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.13, C:0.46, G:0.28, T:0.13
Consensus pattern (19 bp):
CCGGCCAAACCCGGTCCGT
Found at i:4988102 original size:25 final size:25
Alignment explanation
Indices: 4988064--4988111 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4988054 CAAGCGAGCC
4988064 ATATCAAGAAGCTCACAAAGAGCAT
1 ATATCAAGAAGCTCACAAAGAGCAT
* * *
4988089 ATATCAGGACGCTCATAAAGAGC
1 ATATCAAGAAGCTCACAAAGAGC
4988112 TACGGTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.17
Consensus pattern (25 bp):
ATATCAAGAAGCTCACAAAGAGCAT
Found at i:4988210 original size:64 final size:64
Alignment explanation
Indices: 4988086--4988214 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 64
4988076 TCACAAAGAG
* * * * * * *
4988086 CATATATCAGGACGCTCATAAAGAGCTACGGTATATCCGTATTATATGTAGGATTCATACCGAT
1 CATATAACAGGACGCTCACAAAGAGCTACGATATATCCGTAATACATGCAGGAGTCATACCGAT
*
4988150 CATATAACAGGACGCTCACAAAGAGCTGCGATATGA-CCGTAATACATGCAGG-GTCAATACCGA
1 CATATAACAGGACGCTCACAAAGAGCTACGATAT-ATCCGTAATACATGCAGGAGTC-ATACCGA
4988213 T
64 T
4988214 C
1 C
4988215 GAGATACTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.04
64 52 0.95
65 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (64 bp):
CATATAACAGGACGCTCACAAAGAGCTACGATATATCCGTAATACATGCAGGAGTCATACCGAT
Found at i:5008640 original size:37 final size:38
Alignment explanation
Indices: 5008593--5008690 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 38
5008583 CTACAAAAGA
*
5008593 AATATTAAATTAAATTTAATATTAAGAAAATCACT-TT
1 AATATTAAATTAAATTAAATATTAAGAAAATCACTATT
* * ** * *
5008630 AATATTAAATT-AATAAAATACTATTAAAATGATTATT
1 AATATTAAATTAAATTAAATATTAAGAAAATCACTATT
5008667 AA-ATTAAATTAAATTAAATATTAA
1 AATATTAAATTAAATTAAATATTAA
5008691 ATCTATTAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
36 24 0.49
37 25 0.51
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (38 bp):
AATATTAAATTAAATTAAATATTAAGAAAATCACTATT
Found at i:5008644 original size:11 final size:11
Alignment explanation
Indices: 5008628--5008692 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
5008618 GAAAATCACT
5008628 TTAATATTAAA
1 TTAATATTAAA
5008639 TTAATA--AAA
1 TTAATATTAAA
*
5008648 -TACTATTAAAA
1 TTAATATT-AAA
* *
5008659 TGATTATTAAA
1 TTAATATTAAA
5008670 TTAA-ATTAAA
1 TTAATATTAAA
5008680 TTAAATATTAAA
1 TT-AATATTAAA
5008692 T
1 T
5008693 CTATTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 8 0.19
11 16 0.37
12 12 0.28
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:5008647 original size:25 final size:26
Alignment explanation
Indices: 5008608--5008656 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
5008598 TAAATTAAAT
5008608 TTAATATTAAGAAAATCACT-TTAATA
1 TTAATATTAAGAAAAT-ACTATTAATA
*
5008634 TTAA-ATTAATAAAATACTATTAA
1 TTAATATTAAGAAAATACTATTAA
5008657 AATGATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAATATTAAGAAAATACTATTAATA
Found at i:5008833 original size:138 final size:139
Alignment explanation
Indices: 5008668--5008945 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 139
5008658 ATGATTATTA
5008668 AATTAAATTAAATTAAATATTAAATCTATTAAAATAATAATATTTTTAAAATAGTTAATCTGAAA
1 AATTAAATTAAATTAAATATTAAATCTATTAAAATAATAATATTTTTAAAATAGTTAATCTGAAA
5008733 TCAAATTCTCTAGTAGAGTCTCAGTAGAATTATAATTCTTTCACTACTCAACCACTAAAGAACCA
66 TCAAATTCTCTAGTAGAGTCTCAGTAGAATTATAATTCTTTCACTACTCAACCACTAAAGAACCA
5008798 TCGTTCCCG
131 TCGTTCCCG
5008807 AATTAAATT-AATTAAATATTAAATCTATTAAAATAATAATATTTTTAAAATAGTTAATCTGAAA
1 AATTAAATTAAATTAAATATTAAATCTATTAAAATAATAATATTTTTAAAATAGTTAATCTGAAA
5008871 TCAAATTCTCTAGTAGAGTCTCAGTAGAATTATAATTCTTTCACTACTCAACCACTAAAGAACCA
66 TCAAATTCTCTAGTAGAGTCTCAGTAGAATTATAATTCTTTCACTACTCAACCACTAAAGAACCA
5008936 TCGTTCCCG
131 TCGTTCCCG
5008945 A
1 A
5008946 CCATTTTCTG
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
138 130 0.94
139 9 0.06
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (139 bp):
AATTAAATTAAATTAAATATTAAATCTATTAAAATAATAATATTTTTAAAATAGTTAATCTGAAA
TCAAATTCTCTAGTAGAGTCTCAGTAGAATTATAATTCTTTCACTACTCAACCACTAAAGAACCA
TCGTTCCCG
Found at i:5019240 original size:38 final size:38
Alignment explanation
Indices: 5019195--5019273 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
5019185 AGCACAAGGC
5019195 TCTAAAAACAGTCTCGACTCTTTCAGGTACATGCACAA
1 TCTAAAAACAGTCTCGACTCTTTCAGGTACATGCACAA
5019233 TCTAAAAACAGTCTCGACTCTTTCAGGTACATGCACAA
1 TCTAAAAACAGTCTCGACTCTTTCAGGTACATGCACAA
5019271 TCT
1 TCT
5019274 TTATTATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (38 bp):
TCTAAAAACAGTCTCGACTCTTTCAGGTACATGCACAA
Found at i:5019829 original size:15 final size:15
Alignment explanation
Indices: 5019806--5019874 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
5019796 CAGCAAAACC
*
5019806 GCCGGAGAAGGAGGA
1 GCCGAAGAAGGAGGA
*
5019821 GCCGAAGAAGGAAGA
1 GCCGAAGAAGGAGGA
* * *
5019836 ACCCAAGAAAGAGGA
1 GCCGAAGAAGGAGGA
*
5019851 GCCCAAGAAGGAGGA
1 GCCGAAGAAGGAGGA
5019866 GCCGAAGAA
1 GCCGAAGAA
5019875 AGAAGAACCC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.43, C:0.17, G:0.39, T:0.00
Consensus pattern (15 bp):
GCCGAAGAAGGAGGA
Found at i:5019888 original size:15 final size:15
Alignment explanation
Indices: 5019825--5019965 Score: 93
Period size: 15 Copynumber: 8.8 Consensus size: 15
5019815 GGAGGAGCCG
*
5019825 AAGAAGGAAGAACCC
1 AAGAAAGAAGAACCC
* *
5019840 AAGAAAGAGGAGCCC
1 AAGAAAGAAGAACCC
* * * *
5019855 AAGAAGGAGGAGCCG
1 AAGAAAGAAGAACCC
5019870 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
* *
5019885 AAGAAGGAAGAGGAGCCA
1 AAGAAAGAAGA--A-CCC
5019903 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
*
5019918 AAGAAGGAAGAGGAACCC
1 AAG-A--AAGAAGAACCC
* *
5019936 AAGAAGGAAGAGGAGCCA
1 AAGAAAGAAGA--A-CCC
5019954 AAGAAAGAAGAA
1 AAGAAAGAAGAA
5019966 GAGAAACAGC
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
15 56 0.57
16 3 0.03
17 3 0.03
18 37 0.37
ACGTcount: A:0.53, C:0.15, G:0.32, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAGAACCC
Found at i:5019895 original size:18 final size:18
Alignment explanation
Indices: 5019869--5019967 Score: 96
Period size: 18 Copynumber: 5.7 Consensus size: 18
5019859 AGGAGGAGCC
*
5019869 GAAGAAAGAAGAACCCAA
1 GAAGGAAGAAGAACCCAA
* *
5019887 GAAGGAAG-AGGAGCC-A
1 GAAGGAAGAAGAACCCAA
*
5019903 -AAGAAAGAAGAACCCAA
1 GAAGGAAGAAGAACCCAA
*
5019920 GAAGGAAGAGGAACCCAA
1 GAAGGAAGAAGAACCCAA
* * *
5019938 GAAGGAAGAGGAGCCAAA
1 GAAGGAAGAAGAACCCAA
*
5019956 GAAAGAAGAAGA
1 GAAGGAAGAAGA
5019968 GAAACAGCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.09
16 6 0.09
17 6 0.09
18 48 0.73
ACGTcount: A:0.56, C:0.13, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAGAACCCAA
Found at i:5019907 original size:33 final size:33
Alignment explanation
Indices: 5019825--5019946 Score: 148
Period size: 33 Copynumber: 3.9 Consensus size: 33
5019815 GGAGGAGCCG
* *
5019825 AAGAAGGAAGA--A-CCCAAGAAAGAGGAGCCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
*
5019855 AAGAA-G--GAGGAGCCGAAGAAAGAAGAACCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
*
5019885 AAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
* *
5019918 AAGAAGGAAGAGGAACCCAAGAAGGAAGA
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGA
5019947 GGAGCCAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
27 2 0.03
29 2 0.03
30 25 0.32
31 1 0.01
33 49 0.62
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (33 bp):
AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
Found at i:5019949 original size:51 final size:51
Alignment explanation
Indices: 5019824--5019965 Score: 179
Period size: 51 Copynumber: 2.9 Consensus size: 51
5019814 AGGAGGAGCC
* * * * *
5019824 GAAGAAGGAAGAACCCAAG-A--AAGAGGAGCCCAAG-AAGGAGGAGCC--
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
5019869 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
* *
5019920 GAAGGAAGAGGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAA
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAA
5019966 GAGAAACAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
45 18 0.21
46 1 0.01
48 13 0.15
49 8 0.10
51 44 0.52
ACGTcount: A:0.53, C:0.15, G:0.32, T:0.00
Consensus pattern (51 bp):
GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
Found at i:5028508 original size:23 final size:22
Alignment explanation
Indices: 5028456--5028508 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
5028446 TCCTTGTCTT
* * *
5028456 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTCTCCAA
* *
5028478 CTTATTTTCTCTTCTTTCTCCAA
1 TTTCTTTTCT-TTCTTTCTCCAA
5028501 TTTCTTTT
1 TTTCTTTT
5028509 TCACTTTTCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTCTCCAA
Found at i:5028538 original size:18 final size:18
Alignment explanation
Indices: 5028501--5028539 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5028491 CTTTCTCCAA
* * *
5028501 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
5028519 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
5028537 TTT
1 TTT
5028540 TACTCTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:5041489 original size:19 final size:19
Alignment explanation
Indices: 5041465--5041516 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
5041455 TCATATCTTT
5041465 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
*
5041484 TAAGATTACATATCATATC
1 TAAGATTGCATATCATATC
5041503 TAAGATTGCATATC
1 TAAGATTGCATATC
5041517 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:5044109 original size:26 final size:26
Alignment explanation
Indices: 5044061--5044110 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5044051 TTAAATAAAC
*
5044061 AGTTAATAGAATCAGTCGATCAAATT
1 AGTTAATAGAATCAGTAGATCAAATT
5044087 AGTTAATAGAATCAGTTAG-TCAAA
1 AGTTAATAGAATCAG-TAGATCAAA
5044111 CTAGCTACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (26 bp):
AGTTAATAGAATCAGTAGATCAAATT
Found at i:5046945 original size:26 final size:26
Alignment explanation
Indices: 5046878--5046945 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
5046868 TGGCTTGTCA
5046878 ATTTAAGATCGTAGCCCGACTCGCTG
1 ATTTAAGATCGTAGCCCGACTCGCTG
** * *
5046904 ATTTAAGATCACAGCCCGATTTGCTG
1 ATTTAAGATCGTAGCCCGACTCGCTG
*
5046930 ATTTAAGATTGTAGCC
1 ATTTAAGATCGTAGCC
5046946 TAATACTTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (26 bp):
ATTTAAGATCGTAGCCCGACTCGCTG
Found at i:5046990 original size:54 final size:54
Alignment explanation
Indices: 5046929--5047134 Score: 261
Period size: 54 Copynumber: 3.8 Consensus size: 54
5046919 CCGATTTGCT
* * * * *
5046929 GATTTAAGATTGTAGCCTAATACTTACAAGATTTTTCAAATCTTGTGGCTCGCC
1 GATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTTGTGGCTCGTC
* * *
5046983 GATTTAAGATCACAACCTTATACTTACAAGA-TTTTCTGAATCTTGTGGCTTGTC
1 GATTTAAGATCGCAGCCTTATACTTACAAGATTTTTC-GAATCTTGTGGCTCGTC
* * *
5047037 AATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTTGTGACTCATC
1 GATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTTGTGGCTCGTC
* * * *
5047091 GATTTAATATCGCAGCCTCATACTTAAAATATTTTTCGAATCTT
1 GATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTT
5047135 ACAATTTGCC
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.04
54 121 0.92
55 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (54 bp):
GATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTTGTGGCTCGTC
Found at i:5047150 original size:108 final size:107
Alignment explanation
Indices: 5046922--5047151 Score: 246
Period size: 108 Copynumber: 2.1 Consensus size: 107
5046912 TCACAGCCCG
* * * *
5046922 ATTTGCTGATTTAAGATTGTAGCCTAATACTTACAAGATTTTTCAAATCTTGTGGCTCGCCGATT
1 ATTTGCT-ATTTAAGATCGCAGCCTAATACTTACAAGATTTTTCAAATCTTGTGACTCACCGATT
* * ***
5046987 TAAGATCACAACCTTATACTTACAAGATTTTCTGAATCTTGTG
65 TAAGATCACAACCTCATACTTAAAAGATTTTCTGAATCTTACA
** * * * *
5047030 GCTTGTCAATTTAAGATCGCAGCCTTATACTTACAAGATTTTTCGAATCTTGTGACTCATCGATT
1 ATTTG-CTATTTAAGATCGCAGCCTAATACTTACAAGATTTTTCAAATCTTGTGACTCACCGATT
* * * *
5047095 TAATATCGCAGCCTCATACTTAAAATATTTT-TCGAATCTTACA
65 TAAGATCACAACCTCATACTTAAAAGATTTTCT-GAATCTTACA
5047138 ATTTGCCTATTTAA
1 ATTTG-CTATTTAA
5047152 TATTCAAGAT
Statistics
Matches: 97, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
107 1 0.01
108 95 0.98
109 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (107 bp):
ATTTGCTATTTAAGATCGCAGCCTAATACTTACAAGATTTTTCAAATCTTGTGACTCACCGATTT
AAGATCACAACCTCATACTTAAAAGATTTTCTGAATCTTACA
Found at i:5047362 original size:22 final size:23
Alignment explanation
Indices: 5047337--5047420 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
5047327 AATTGACGTA
* *
5047337 ATTTTTA-AGTACAGTTCGTAGT
1 ATTTTTACAGTACAGTCCGCAGT
**
5047359 ATTTTTACAGTGTAGTCCGCAGT
1 ATTTTTACAGTACAGTCCGCAGT
** * * *
5047382 ATTTTTACAACACTGTTCGCATT
1 ATTTTTACAGTACAGTCCGCAGT
*
5047405 ATTTTTACAATACAGT
1 ATTTTTACAGTACAGT
5047421 TTGAAATAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 7 0.15
23 41 0.85
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.43
Consensus pattern (23 bp):
ATTTTTACAGTACAGTCCGCAGT
Found at i:5047519 original size:23 final size:24
Alignment explanation
Indices: 5047493--5047547 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
5047483 CATAACTCCT
5047493 TGAATTTTTGCTGTACAGCTCG-C
1 TGAATTTTTGCTGTACAGCTCGTC
*
5047516 TGAATTTTTGTTGTACAGCTCGTC
1 TGAATTTTTGCTGTACAGCTCGTC
5047540 T-AATTTTT
1 TGAATTTTT
5047548 CTATATACGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (24 bp):
TGAATTTTTGCTGTACAGCTCGTC
Found at i:5047888 original size:19 final size:20
Alignment explanation
Indices: 5047861--5047898 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5047851 AGTATGTCAT
5047861 CTAGCTCGCCA-CTTCGCTC
1 CTAGCTCGCCATCTTCGCTC
*
5047880 CTAGTTCGCCATCTTCGCT
1 CTAGCTCGCCATCTTCGCT
5047899 AGCTTGCCAC
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:0.11, C:0.42, G:0.16, T:0.32
Consensus pattern (20 bp):
CTAGCTCGCCATCTTCGCTC
Found at i:5055924 original size:10 final size:9
Alignment explanation
Indices: 5055909--5055956 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
5055899 CCGTGTCAAT
5055909 ATTTTAAAAA
1 ATTTT-AAAA
5055919 ATTTTAAAA
1 ATTTTAAAA
*
5055928 ATCTT-AAA
1 ATTTTAAAA
5055936 ATTTTAAAA
1 ATTTTAAAA
*
5055945 ATGATTAAAA
1 AT-TTTAAAA
5055955 AT
1 AT
5055957 AACATCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 7 0.21
9 13 0.39
10 13 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:5056075 original size:10 final size:11
Alignment explanation
Indices: 5056045--5056100 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 11
5056035 GAGCGATTTC
5056045 TTAAATAATTA
1 TTAAATAATTA
5056056 TTAAATAATT-
1 TTAAATAATTA
*
5056066 TTAAAAAATTA
1 TTAAATAATTA
*
5056077 TTTAAA-AGTTA
1 -TTAAATAATTA
*
5056088 TT-AAGAATTA
1 TTAAATAATTA
5056098 TTA
1 TTA
5056101 TAAATTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 2 0.05
10 17 0.45
11 14 0.37
12 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (11 bp):
TTAAATAATTA
Found at i:5060408 original size:34 final size:36
Alignment explanation
Indices: 5060365--5060455 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 36
5060355 AGAAAATAAG
*
5060365 TTTGGTTTTGTGTTTAGATATTCGAGTAATGGTTTTTGGT
1 TTTGGTTTTGTGTTTAGATATTCGACTAATGG---TT-GT
5060405 TTTGGTTTTGTGTTTAGATATTCGACTAATGG-T-T
1 TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTGT
5060439 TTTGGTTGTTTGTGTTT
1 TTTGG-T-TTTGTGTTT
5060456 TTTTTTTGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
34 6 0.12
35 1 0.02
36 10 0.21
40 31 0.65
ACGTcount: A:0.13, C:0.03, G:0.26, T:0.57
Consensus pattern (36 bp):
TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTGT
Found at i:5060409 original size:40 final size:40
Alignment explanation
Indices: 5060365--5060445 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
5060355 AGAAAATAAG
*
5060365 TTTGGTTTTGTGTTTAGATATTCGAGTAATGGTTTTTGGT
1 TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTTTTGGT
5060405 TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTTTTGGT
1 TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTTTTGGT
5060445 T
1 T
5060446 GTTTGTGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.15, C:0.04, G:0.26, T:0.56
Consensus pattern (40 bp):
TTTGGTTTTGTGTTTAGATATTCGACTAATGGTTTTTGGT
Found at i:5063741 original size:27 final size:28
Alignment explanation
Indices: 5063702--5063773 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
5063692 ATAAAAAATA
5063702 ACCAAAATATTATAAATTTTT-TTATTT
1 ACCAAAATATTATAAATTTTTATTATTT
*
5063729 ATCAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAA--ATTTTTATTATTT
5063759 ACCAAAATA-TATAAA
1 ACCAAAATATTATAAA
5063774 AAAAAAACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 15 0.38
29 11 0.28
30 14 0.35
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTATTATTT
Found at i:5063914 original size:27 final size:27
Alignment explanation
Indices: 5063821--5063921 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 27
5063811 GCCTGATCAG
* * * *
5063821 GCCAATGGCATTGGTGGCACCAAAGGT
1 GCCAAAGGTATTGGCGGCACCAATGGT
***
5063848 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAAAGGTATTGGCGGCACCAATGGT
*
5063875 GCCAAAGGTATTGGCAGCACCAATGGT
1 GCCAAAGGTATTGGCGGCACCAATGGT
5063902 GCCATACA-G-ATTGGCGGCAC
1 GCCA-A-AGGTATTGGCGGCAC
5063922 TACTTGTGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 59 0.95
28 2 0.03
29 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.17
Consensus pattern (27 bp):
GCCAAAGGTATTGGCGGCACCAATGGT
Found at i:5064020 original size:11 final size:11
Alignment explanation
Indices: 5064004--5064043 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
5063994 GGTGTTGCGG
5064004 AAAAGAAGAGA
1 AAAAGAAGAGA
5064015 AAAAG-AGAGA
1 AAAAGAAGAGA
*
5064025 AAGAGAAGAGA
1 AAAAGAAGAGA
5064036 AAAAGAAG
1 AAAAGAAG
5064044 GTATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:5064033 original size:21 final size:20
Alignment explanation
Indices: 5064003--5064041 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5063993 AGGTGTTGCG
5064003 GAAAAGAAGAGAAAAAGAGA
1 GAAAAGAAGAGAAAAAGAGA
5064023 GAAAGAGAAGAGAAAAAGA
1 GAAA-AGAAGAGAAAAAGA
5064042 AGGTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAAAAGAAGAGAAAAAGAGA
Found at i:5073526 original size:15 final size:16
Alignment explanation
Indices: 5073500--5073529 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5073490 AATAAAAATA
5073500 TATTATTTTTATATTT
1 TATTATTTTTATATTT
5073516 TATTA-TTTTATATT
1 TATTATTTTTATATT
5073530 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:5073652 original size:480 final size:480
Alignment explanation
Indices: 5072746--5073692 Score: 1128
Period size: 480 Copynumber: 2.0 Consensus size: 480
5072736 TATTGCTTCG
** * * *
5072746 AATCAATTCAGCCATTGCAATGCCTGCAAGTTGAAAAAAAAGTTAGTAAAAAAATCGTATTTCGG
1 AATCAATGAAGCCATTGCAATGCCTGCAAGTTCAAAAAAAAATTAGTAAAAAAACCGTATTTCGG
* * * *
5072811 CCATTTATTCGTATTTTTTTCTGCGCATTTTATTCCTTTAAAAATATCATAATTCCTAATTTTAT
66 CCATTTATTCGTACTATTTTCTCCGAATTTTATTCCTTTAAAAATATCATAATTCCTAATTTTAT
* * *
5072876 ATTTTTACATTCTTTCACTGCATAATGTTTGAAATTTATTAATCGAGTTTGTTATTTAAATTAAT
131 ATTTTTACATTATTTCACTACATAATGTTTGAAATTTATTAATCGAGTGTGTTATTTAAATTAAT
* * * ***
5072941 TTGCTGTAAAAACTTAACCCTTACCCCTGTCCTTTGTTCGTATAATTTTCTTTAATTTTTATTAC
196 AT-CTGTAAAAA--TAACCCTTACCCATGCCCTTTGTTCGTATAATTTTCCCGAATTTTTATTAC
* *
5073006 TTTAAATAAAAAATATTATTCTCCTATTTTATTGTTTTAAATTATTTCAGAACATTTTCTTTGAA
258 TTTAAATAAAAAATATTATTCTCATATTTTATTATTTTAAATTATTTCAGAACATTTTCTTT-AA
* * * *
5073071 ATATTTTGTATTAATTGTTTCTGAATTTTAAAAAAGTTAGTAATACACTCTTACTTCTGCCATTT
322 ATATTATGAATTAATTATTTCTGAATTTTAAAAAAGTTACTAATACACTCTTACTTCTGCCATTT
* * *
5073136 GTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATTAACTTAGT-CTTTTATAAT
387 GTTCGTAATTTTTTATCCGCATTTTATTACTTTAAAAAATATC-TTAA-TTAGTAATTTTATAAT
5073200 TTTACATTATTTCAGTGCATAATGCTTGATT
450 TTTACATTATTTCAGTGCATAATGCTTGATT
* * * * *
5073231 AATCAATGAAGCCATTTCGATGCCTGCAATTTCAAAAAAAAATTAGTAAAAAACCCTTATTTCGG
1 AATCAATGAAGCCATTGCAATGCCTGCAAGTTCAAAAAAAAATTAGTAAAAAAACCGTATTTCGG
* * *
5073296 CCATTTATTCGTACTATTTTC-CCGAATTTTATTACTTTCAATAAAAATATCATATTTTCTAATT
66 CCATTTATTCGTACTATTTTCTCCGAATTTTATT-CCTT---TAAAAATATCATAATTCCTAATT
* * * ** *
5073360 TTAT-TATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAA
127 TTATAT-TTTTACATTATTTCACTACATAATGTTTGAAATTTATTAATCGAGTGTGTTATTTAAA
* ** *
5073424 -TAA-AT-T-TAAAAA-AGCCCCTTATTCATGCCCTTTGTTCGTATTATTTTCCCGAA-TTTTAT
191 TTAATATCTGTAAAAATA-ACCCTTACCCATGCCCTTTGTTCGTATAATTTTCCCGAATTTTTAT
* * * * * *
5073483 TACTTTCAATAAAAATATATTATTTTTATATTTTATTATTTTATATTATTTCAGTACATTTTGTT
255 TACTTTAAATAAAAA-ATATTATTCTCATATTTTATTATTTTAAATTATTTCAGAACATTTTCTT
* * *
5073548 T-CA-ATTAT-AATTAATTATTTCTGAAATTTTTTTAAAAATTTACTAATACACTCTTACTTC-G
319 TAAATATTATGAATTAATTATTTCTG-AA--TTTTAAAAAAGTTACTAATACACTCTTACTTCTG
* * **
5073609 ACCATTTGTTCGTAATTTTTTATCCGTATTTTATTATTTTAAAAAATATCTTAATTTTTAATTTT
381 -CCATTTGTTCGTAATTTTTTATCCGCATTTTATTACTTTAAAAAATATCTTAATTAGTAATTTT
5073674 ATAATTTTACATTATTTCA
445 ATAATTTTACATTATTTCA
5073693 ATTTATTATG
Statistics
Matches: 392, Mismatches: 58, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
477 13 0.03
478 9 0.02
479 29 0.07
480 95 0.24
481 73 0.19
483 6 0.02
484 11 0.03
485 77 0.20
486 1 0.00
487 4 0.01
488 74 0.19
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (480 bp):
AATCAATGAAGCCATTGCAATGCCTGCAAGTTCAAAAAAAAATTAGTAAAAAAACCGTATTTCGG
CCATTTATTCGTACTATTTTCTCCGAATTTTATTCCTTTAAAAATATCATAATTCCTAATTTTAT
ATTTTTACATTATTTCACTACATAATGTTTGAAATTTATTAATCGAGTGTGTTATTTAAATTAAT
ATCTGTAAAAATAACCCTTACCCATGCCCTTTGTTCGTATAATTTTCCCGAATTTTTATTACTTT
AAATAAAAAATATTATTCTCATATTTTATTATTTTAAATTATTTCAGAACATTTTCTTTAAATAT
TATGAATTAATTATTTCTGAATTTTAAAAAAGTTACTAATACACTCTTACTTCTGCCATTTGTTC
GTAATTTTTTATCCGCATTTTATTACTTTAAAAAATATCTTAATTAGTAATTTTATAATTTTACA
TTATTTCAGTGCATAATGCTTGATT
Found at i:5074092 original size:3 final size:3
Alignment explanation
Indices: 5074084--5074174 Score: 52
Period size: 3 Copynumber: 31.3 Consensus size: 3
5074074 CTTCCTTCCC
* * *
5074084 TCT TCT TCT TCT TCT TCT T-T TTT TC- TCT TCT CCT T-T CCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
5074128 CCT TCTT TCTT TCGT TTT TCT TC- TCT T-T TCCT TC- TCT TCT TCT TCT
1 TCT TC-T TC-T TC-T TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT
5074174 T
1 T
5074175 TCTTTCTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
2 12 0.17
3 46 0.67
4 11 0.16
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5074122 original size:47 final size:50
Alignment explanation
Indices: 5074054--5074167 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 50
5074044 AAAATATTAC
* *
5074054 CTTTTTTT-TCTTTTCTTTTCCTTCCTTCCCTC-TTC-TTC-TTCTTCTT
1 CTTTTTTTCTCTTCTCCTTTCCTTCCTTCCCTCTTTCTTTCGTTCTTCTT
* * *
5074100 CTTTTTTTCTCTTCTCCTTTCCTTCTTTCCTTCTTTCTTTCGTTTTTCTT
1 CTTTTTTTCTCTTCTCCTTTCCTTCCTTCCCTCTTTCTTTCGTTCTTCTT
5074150 CTCTTTTCCTTCTCTTCT
1 CT-TTTT--TTCTCTTCT
5074168 TCTTCTTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
46 8 0.14
47 20 0.36
48 3 0.05
49 3 0.05
50 9 0.16
51 4 0.07
53 9 0.16
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (50 bp):
CTTTTTTTCTCTTCTCCTTTCCTTCCTTCCCTCTTTCTTTCGTTCTTCTT
Found at i:5074158 original size:37 final size:39
Alignment explanation
Indices: 5074104--5074224 Score: 138
Period size: 37 Copynumber: 3.0 Consensus size: 39
5074094 CTTCTTCTTT
*
5074104 TTTTCTCTTCTCCTTTCCTTCTTTCCTTCTTTCTTTC-G
1 TTTTCTCTTCTCTTTTCCTTCTTTCCTTCTTTCTTTCTG
*
5074142 TTTT-TCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTT
1 TTTTCTCTTCTCTTTTCCTTCT-TTC--CTTCTTTCTTTC-TG
*
5074184 TTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTTCTTTCT
1 TTTTCTCTTCT-CTTTTCC-TTCTTTCCTTC-TTTCTTTCT
5074225 CTCTCCTTCT
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
37 16 0.23
38 7 0.10
40 12 0.17
42 9 0.13
43 14 0.20
44 9 0.13
45 4 0.06
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (39 bp):
TTTTCTCTTCTCTTTTCCTTCTTTCCTTCTTTCTTTCTG
Found at i:5074173 original size:48 final size:50
Alignment explanation
Indices: 5074070--5074217 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 50
5074060 TTTCTTTTCT
* * * *
5074070 TTTCCTTCCTTCCCTC-TTC-TTC-TTCTTCTTCTTTTTTTCTCTTCTCC
1 TTTCCTTCTTTCCTTCTTTCTTTCGTTTTTCTTCTTCTTTTCTCTTCTCC
5074117 TTTCCTTCTTTCCTTCTTTCTTTCGTTTTTCTTC-TCTTTTC-CTTCT-C
1 TTTCCTTCTTTCCTTCTTTCTTTCGTTTTTCTTCTTCTTTTCTCTTCTCC
* * *
5074164 -TT-CTTC-TTCTTTCTTTCTTT--TTTTCTCTTC-TCCTTTCCCTT-T-C
1 TTTCCTTCTTTCCTTCTTTCTTTCGTTTT-TCTTCTTCTTTTCTCTTCTCC
5074207 TTTCCTTCTTT
1 TTTCCTTCTTT
5074218 TCTTTCTCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
42 4 0.05
43 13 0.15
44 18 0.21
45 8 0.09
46 4 0.05
47 15 0.17
48 8 0.09
49 9 0.10
50 8 0.09
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.66
Consensus pattern (50 bp):
TTTCCTTCTTTCCTTCTTTCTTTCGTTTTTCTTCTTCTTTTCTCTTCTCC
Found at i:5074216 original size:34 final size:35
Alignment explanation
Indices: 5074170--5074237 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
5074160 TCTCTTCTTC
*
5074170 TTCTTTCTTTCTTTT-TTTCTCTTCTCCTT-TCCCT
1 TTCTTTCCTTCTTTTCTTTCTC-TCTCCTTCTCCCT
5074204 TTCTTTCCTTCTTTTCTTTCTCTCTCCTTCTCCC
1 TTCTTTCCTTCTTTTCTTTCTCTCTCCTTCTCCC
5074238 CCCCCACCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (35 bp):
TTCTTTCCTTCTTTTCTTTCTCTCTCCTTCTCCCT
Found at i:5074219 original size:72 final size:74
Alignment explanation
Indices: 5074083--5074235 Score: 190
Period size: 80 Copynumber: 2.0 Consensus size: 74
5074073 CCTTCCTTCC
*
5074083 CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTCTTTCCTTCTTTCTTTCGTTTT-T
1 CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCC-TC-TT-CTTCTTTCCTTCGTTTTCT
*
5074147 CTTCTCTTTTCCTT
63 -TTCTC-TCTCCTT
5074161 CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCC-C-T-TTCTTTCCTTC-TTTTCTT
1 CTCTTCTTCTTC-TTC-TTCTTTTTTTCTCTTCTCCTTTCCTCTTCTTCTTTCCTTCGTTTTCTT
5074222 TCTCTCTCCTT
64 TCTCTCTCCTT
5074233 CTC
1 CTC
5074236 CCCCCCCACC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
72 9 0.13
73 9 0.13
74 11 0.16
76 1 0.01
78 13 0.19
79 3 0.04
80 24 0.34
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.65
Consensus pattern (74 bp):
CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTCTTCTTCTTTCCTTCGTTTTCTTTC
TCTCTCCTT
Found at i:5074228 original size:75 final size:76
Alignment explanation
Indices: 5074083--5074229 Score: 208
Period size: 78 Copynumber: 1.9 Consensus size: 76
5074073 CCTTCCTTCC
* *
5074083 CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTCTTTCCTTCTTTCTTTCGTTTTTC
1 CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCC-TCTTTCCTTCCTTCTTTC-TCTTTC
5074148 TTCTCTTTTCCTT
64 TTCTCTTTTCCTT
*
5074161 CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCC-CTTTCTTTCCTTCTTT-TCTTTC
1 CTCTTCTTCTTC-TTC-TTCTTTTTTTCTCTTCTCCTTTCCTCTTTCCTTCCTTCTTTCTCTTTC
5074224 TCTCTC
64 T-TCTC
5074230 CTTCTCCCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
76 6 0.10
77 4 0.06
78 26 0.41
79 3 0.05
80 24 0.38
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (76 bp):
CTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTCTTTCCTTCCTTCTTTCTCTTTCTT
CTCTTTTCCTT
Found at i:5074231 original size:19 final size:19
Alignment explanation
Indices: 5074143--5074234 Score: 54
Period size: 19 Copynumber: 5.1 Consensus size: 19
5074133 TTTCTTTCGT
*
5074143 TTTTC-TTCTCTTTTCCTTC
1 TTTTCTTTCTC-TCTCCTTC
* * *
5074162 TCTTC-TTCTTCTTTCTTTC
1 TTTTCTTTC-TCTCTCCTTC
5074181 TTTT-TTTCTCTTCTCC-T-
1 TTTTCTTTCTC-TCTCCTTC
**
5074198 TTCCCTTTCT-T-TCCTTC
1 TTTTCTTTCTCTCTCCTTC
5074215 TTTTCTTTCTCTCTCCTTC
1 TTTTCTTTCTCTCTCCTTC
5074234 T
1 T
5074235 CCCCCCCCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
15 3 0.05
16 2 0.04
17 10 0.18
18 9 0.16
19 30 0.54
20 2 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTCTTTCTCTCTCCTTC
Found at i:5074342 original size:27 final size:27
Alignment explanation
Indices: 5074265--5074335 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
5074255 CCTATTATGG
* *
5074265 CATTGGTGCCGCCAATGGTTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGAAC
5074292 CATTGGTGCCGCCAATGGCTTTGGAAC
1 CATTGGTGCCGCCAATGGCTTTGGAAC
*
5074319 CTTTGGTGCCGCCAATG
1 CATTGGTGCCGCCAATG
5074336 CCATTGGCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGAAC
Found at i:5074454 original size:28 final size:29
Alignment explanation
Indices: 5074392--5074463 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 29
5074382 AGGTTTTTTT
5074392 TTAT-ATATTTTGGTAAATAATGAAAATAA
1 TTATAATATTTTGGTAAATAA-GAAAATAA
5074421 TTATAATATTTTGGTAAATAA-AAAA-AA
1 TTATAATATTTTGGTAAATAAGAAAATAA
5074448 GTTATAATATTTTGGT
1 -TTATAATATTTTGGT
5074464 TATTTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 4 0.10
30 16 0.39
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (29 bp):
TTATAATATTTTGGTAAATAAGAAAATAA
Found at i:5074652 original size:17 final size:17
Alignment explanation
Indices: 5074626--5074667 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
5074616 GCTTGACGAT
*
5074626 AAATAGTATAATGACAC
1 AAATAATATAATGACAC
5074643 AAATAATATAATGACAC
1 AAATAATATAATGACAC
5074660 ATAATAAT
1 A-AATAAT
5074668 CTCACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (17 bp):
AAATAATATAATGACAC
Found at i:5076179 original size:6 final size:6
Alignment explanation
Indices: 5076163--5076193 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
5076153 AAAGGCAACA
5076163 AAGAGTG AAGATG AAGATG AAGATG AAGATG
1 AAGA-TG AAGATG AAGATG AAGATG AAGATG
5076194 CATTACAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
AAGATG
Found at i:5078509 original size:31 final size:31
Alignment explanation
Indices: 5078454--5078515 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5078444 GTAAGGGTTA
* *
5078454 ATTTTATTTTTTAATATTATTTAATATTTTT
1 ATTTCATTTTTTAATATTAATTAATATTTTT
5078485 ATTTCATTTTTGTAAT-TTAATTAATATTTTT
1 ATTTCATTTTT-TAATATTAATTAATATTTTT
5078516 TATAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (31 bp):
ATTTCATTTTTTAATATTAATTAATATTTTT
Found at i:5078526 original size:31 final size:31
Alignment explanation
Indices: 5078459--5078526 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
5078449 GGTTAATTTT
* * *
5078459 ATTTTTTAATATTATTTAATATTTTTATTTC
1 ATTTTTTAATATTAATTAATATTTTTATATA
5078490 ATTTTTGTAAT-TTAATTAATATTTTT-TATA
1 ATTTTT-TAATATTAATTAATATTTTTATATA
5078520 ATTTTTT
1 ATTTTTT
5078527 TATAACAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 8 0.24
31 20 0.61
32 4 0.12
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (31 bp):
ATTTTTTAATATTAATTAATATTTTTATATA
Found at i:5082551 original size:20 final size:18
Alignment explanation
Indices: 5082512--5082557 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5082502 TTATGTCAAG
*
5082512 TGTGTATCTTAACCCTTA
1 TGTGTATCCTAACCCTTA
5082530 TGTGTATCCTAACCCTTA
1 TGTGTATCCTAACCCTTA
*
5082548 TATGTATCCT
1 TGTGTATCCT
5082558 TTTTCCACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTGTATCCTAACCCTTA
Found at i:5085657 original size:37 final size:39
Alignment explanation
Indices: 5085607--5085712 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 39
5085597 TTTAAAGTAA
5085607 TAAATTGACACCCAATGTCTCATCGACTAAACCG-A-AG
1 TAAATTGACACCCAATGTCTCATCGACTAAACCGAAGAG
* * * * *
5085644 TAAATTGGCACCCAATGCCTCATCAAATTAATCCGAAGTAG
1 TAAATTGACACCCAATGTCTCATC-GACTAAACCGAAG-AG
* *
5085685 TAAATTGAAACCCAGTGTCTCATCGACT
1 TAAATTGACACCCAATGTCTCATCGACT
5085713 CGAAGTTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
37 22 0.41
38 7 0.13
39 1 0.02
40 2 0.04
41 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (39 bp):
TAAATTGACACCCAATGTCTCATCGACTAAACCGAAGAG
Found at i:5086561 original size:8 final size:9
Alignment explanation
Indices: 5086545--5086606 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
5086535 CTTGCATTTC
5086545 TTCTTTCTT
1 TTCTTTCTT
5086554 TT-TTTCTT
1 TTCTTTCTT
5086562 TTCTTTCTT
1 TTCTTTCTT
* *
5086571 TCCTTTCAGT
1 TTCTTTC-TT
5086581 TTCGTTT-TGT
1 TTC-TTTCT-T
5086591 TTCTTTCTT
1 TTCTTTCTT
5086600 TCTCTTT
1 T-TCTTT
5086607 TTATTTCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.19
9 19 0.44
10 13 0.30
11 3 0.07
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.73
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:5086703 original size:34 final size:35
Alignment explanation
Indices: 5086633--5086718 Score: 81
Period size: 37 Copynumber: 2.4 Consensus size: 35
5086623 TTATATTTAC
*
5086633 TTTATTATTATATTATATATATTTACTTAATTCTTAAGGT
1 TTTA-TATTATA--ATATATATTTACTTAA-TCTTAA-AT
*
5086673 TTTATATTATAATATATATTT-TTTAA-CTTAAAT
1 TTTATATTATAATATATATTTACTTAATCTTAAAT
5086706 TTTATA--ATAATAT
1 TTTATATTATAATAT
5086719 TAAACCTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
31 7 0.16
33 7 0.16
34 5 0.11
36 4 0.09
37 10 0.23
39 7 0.16
40 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (35 bp):
TTTATATTATAATATATATTTACTTAATCTTAAAT
Found at i:5088670 original size:13 final size:13
Alignment explanation
Indices: 5088652--5088717 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
5088642 TAGATTTTTC
5088652 CTAAATATTATCA
1 CTAAATATTATCA
5088665 CTAAATA--AT-A
1 CTAAATATTATCA
*
5088675 TTAAATATTATCA
1 CTAAATATTATCA
*
5088688 CTAAATA--AT-T
1 CTAAATATTATCA
5088698 CTAAATATTATCA
1 CTAAATATTATCA
5088711 CTAAATA
1 CTAAATA
5088718 ATACAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 14 0.33
11 4 0.09
12 4 0.09
13 21 0.49
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:5088683 original size:23 final size:24
Alignment explanation
Indices: 5088652--5088720 Score: 124
Period size: 23 Copynumber: 3.0 Consensus size: 24
5088642 TAGATTTTTC
5088652 CTAAATATTATCACTAAATAATAT
1 CTAAATATTATCACTAAATAATAT
5088676 -TAAATATTATCACTAAATAAT-T
1 CTAAATATTATCACTAAATAATAT
5088698 CTAAATATTATCACTAAATAATA
1 CTAAATATTATCACTAAATAATA
5088721 CAAAATTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.02
23 42 0.98
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.38
Consensus pattern (24 bp):
CTAAATATTATCACTAAATAATAT
Found at i:5088759 original size:18 final size:18
Alignment explanation
Indices: 5088736--5088784 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
5088726 TTTAAAAATC
*
5088736 AAATTTAAACTAGAGATT
1 AAATTTAAACTAAAGATT
*
5088754 AAATTTAAACTAAAGTTT
1 AAATTTAAACTAAAGATT
*
5088772 AAGTTTAAACTAA
1 AAATTTAAACTAA
5088785 TTACAGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTAAACTAAAGATT
Found at i:5090349 original size:111 final size:111
Alignment explanation
Indices: 5090153--5090362 Score: 323
Period size: 111 Copynumber: 1.9 Consensus size: 111
5090143 GTATAAGGAC
* * * *
5090153 TAAATTGCATATAGGGTGAAAGTTAAATTATAGATTAAAGAAAAATTTAAGGGACTAAATAAGCA
1 TAAATTGCATATAGGGTGAAAGTTAAATTATAGATTAAAGAAAAAGTAAAAGGACTAAAGAAGCA
*
5090218 ATTATGCCATTGGCATTAAATGAGGCGGCATAAGGATGAAGATATT
66 ATTATGCCATTGGCATTAAATGAGGCGACATAAGGATGAAGATATT
* * *
5090264 TAAATTGCATATTGGGTGAAAGTTGAATTATAGATTAAAGAAAAAGTAAAAGGACTAAAGAAGTA
1 TAAATTGCATATAGGGTGAAAGTTAAATTATAGATTAAAGAAAAAGTAAAAGGACTAAAGAAGCA
*
5090329 ATTATGCCATTGCTCA-TAAATGAGGCGACATAAG
66 ATTATGCCATTG-GCATTAAATGAGGCGACATAAG
5090363 TGTTTATTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
111 87 0.98
112 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (111 bp):
TAAATTGCATATAGGGTGAAAGTTAAATTATAGATTAAAGAAAAAGTAAAAGGACTAAAGAAGCA
ATTATGCCATTGGCATTAAATGAGGCGACATAAGGATGAAGATATT
Found at i:5090436 original size:5 final size:5
Alignment explanation
Indices: 5090426--5090459 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5090416 AATTATTAAG
5090426 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
5090460 ATGATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:5090514 original size:24 final size:23
Alignment explanation
Indices: 5090481--5090546 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
5090471 AAGAATAAAT
5090481 AAAAAGAAAGAAAGAAACG-AAAC
1 AAAAAGAAAGAAAGAAA-GAAAAC
*
5090504 AAAAAGAAAAGAAAGAAAGAAAAT
1 AAAAAG-AAAGAAAGAAAGAAAAC
*
5090528 AAAAAGGAAAGAAATAAAG
1 AAAAA-GAAAGAAAGAAAG
5090547 GAGAAAACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 7 0.18
24 30 0.79
25 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAGAAAGAAAGAAAAC
Found at i:5091879 original size:24 final size:24
Alignment explanation
Indices: 5091852--5091898 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5091842 ATTGAAATGG
5091852 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
5091876 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
5091899 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:5101283 original size:32 final size:33
Alignment explanation
Indices: 5101247--5101309 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 33
5101237 TGCTACATGT
5101247 TTAAA-TATTTTATTTTCT-TTCTTT-TTTTTACA
1 TTAAATTA-TTTATTTTCTATT-TTTGTTTTTACA
5101279 TTAAATTATTTATTTTCTATTTTTGTTTTTA
1 TTAAATTATTTATTTTCTATTTTTGTTTTTA
5101310 TTTTTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (33 bp):
TTAAATTATTTATTTTCTATTTTTGTTTTTACA
Found at i:5102653 original size:18 final size:18
Alignment explanation
Indices: 5102630--5102666 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5102620 ATACTAATCT
5102630 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
* *
5102648 AATACTGATATAATAGAA
1 AATACTAATAGAATAGAA
5102666 A
1 A
5102667 GAAAAGAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Found at i:5104823 original size:121 final size:121
Alignment explanation
Indices: 5104609--5104849 Score: 473
Period size: 121 Copynumber: 2.0 Consensus size: 121
5104599 TTTGTCTAGG
5104609 AAGAGCAGATCTAATTGTATTAGTGTCTATAATTGATTTCTTTTGTGTAATACTAATCGATAGGG
1 AAGAGCAGATCTAATTGTATTAGTGTCTATAATTGATTTCTTTTGTGTAATACTAATCGATAGGG
*
5104674 CCTCATTAGTAAGTGCTACAAGATCTCGTGCATTGGAACCCACGGTTATGGACCCA
66 CCTCATTAGTAAGTGCTACAAGATCTCGTGCATTGGAACCCACGATTATGGACCCA
5104730 AAGAGCAGATCTAATTGTATTAGTGTCTATAATTGATTTCTTTTGTGTAATACTAATCGATAGGG
1 AAGAGCAGATCTAATTGTATTAGTGTCTATAATTGATTTCTTTTGTGTAATACTAATCGATAGGG
5104795 CCTCATTAGTAAGTGCTACAAGATCTCGTGCATTGGAACCCACGATTATGGACCC
66 CCTCATTAGTAAGTGCTACAAGATCTCGTGCATTGGAACCCACGATTATGGACCC
5104850 GAATCCATTA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (121 bp):
AAGAGCAGATCTAATTGTATTAGTGTCTATAATTGATTTCTTTTGTGTAATACTAATCGATAGGG
CCTCATTAGTAAGTGCTACAAGATCTCGTGCATTGGAACCCACGATTATGGACCCA
Found at i:5105339 original size:18 final size:18
Alignment explanation
Indices: 5105276--5105336 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
5105266 CAAGGTCACT
5105276 ATCAATAGCGTCACTATC
1 ATCAATAGCGTCACTATC
* ** *
5105294 ATTAATAGAATCACTAGC
1 ATCAATAGCGTCACTATC
*
5105312 ATCAATATCGTCACTATC
1 ATCAATAGCGTCACTATC
5105330 ATCAATA
1 ATCAATA
5105337 TCGATATCAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:5105344 original size:15 final size:17
Alignment explanation
Indices: 5105305--5105351 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
5105295 TTAATAGAAT
*
5105305 CACTAGCATCAATATCG
1 CACTATCATCAATATCG
5105322 TCACTATCATCAATATCG
1 -CACTATCATCAATATCG
5105340 -A-TATCATCAATA
1 CACTATCATCAATA
5105352 AGAAAACCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.39
16 1 0.04
18 16 0.57
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (17 bp):
CACTATCATCAATATCG
Found at i:5109789 original size:43 final size:43
Alignment explanation
Indices: 5109713--5109802 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
5109703 AAGATCATGC
*
5109713 TTGTAGTAAAGGCGCCGCTAAACATCATATTCTATAACGACGT
1 TTGTAGTAAAGGCGCCGCTAAACAACATATTCTATAACGACGT
* * * * *
5109756 TTGTAGTCAAA-GCGCCGGTAAAGAACATGTTCTATAGCGGCGT
1 TTGTAGT-AAAGGCGCCGCTAAACAACATATTCTATAACGACGT
5109799 TTGT
1 TTGT
5109803 GAGAAAACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 37 0.93
44 3 0.08
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
TTGTAGTAAAGGCGCCGCTAAACAACATATTCTATAACGACGT
Found at i:5115103 original size:19 final size:20
Alignment explanation
Indices: 5115079--5115124 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5115069 TAAATTCTGG
5115079 AATTTTT-ATAAA-TATTTTA
1 AATTTTTGA-AAATTATTTTA
*
5115098 AATTTTTGAAAATTATTTTG
1 AATTTTTGAAAATTATTTTA
5115118 AATTTTT
1 AATTTTT
5115125 TTATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
AATTTTTGAAAATTATTTTA
Found at i:5115598 original size:19 final size:21
Alignment explanation
Indices: 5115562--5115613 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
5115552 AAATATAAAA
5115562 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTATAAATTAT
5115582 TTTG-AATTTTTGA-AAATTAT
1 TTTGAAATTTTT-ATAAATTAT
*
5115602 TTTAAAATTTTT
1 TTTGAAATTTTT
5115614 TGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.36
20 11 0.39
21 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTGAAATTTTTATAAATTAT
Found at i:5117028 original size:12 final size:12
Alignment explanation
Indices: 5117011--5117035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5117001 TAATTGGATG
5117011 TCCATTGATAAA
1 TCCATTGATAAA
5117023 TCCATTGATAAA
1 TCCATTGATAAA
5117035 T
1 T
5117036 AGATGTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCCATTGATAAA
Found at i:5119767 original size:11 final size:11
Alignment explanation
Indices: 5119751--5119808 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
5119741 GCCCGGCCCT
5119751 TATTAAATATA
1 TATTAAATATA
5119762 TATTAAATATA
1 TATTAAATATA
5119773 TA-T-AATATA
1 TATTAAATATA
5119782 TATTAAAT-TAA
1 TATTAAATAT-A
*
5119793 AATTAAAATATA
1 TATT-AAATATA
5119805 TATT
1 TATT
5119809 TGATTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.20
10 3 0.08
11 20 0.50
12 8 0.20
13 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATTAAATATA
Found at i:5119823 original size:21 final size:22
Alignment explanation
Indices: 5119756--5119828 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
5119746 GCCCTTATTA
*
5119756 AATATATATTAAA-T-ATATAT
1 AATATATATTAAATTAAAATAT
*
5119776 AATATATATTAAATTAAAATTAA
1 AATATATATTAAATTAAAA-TAT
**
5119799 AATATATATTTGATTAAAA-AT
1 AATATATATTAAATTAAAATAT
5119820 AATATATAT
1 AATATATAT
5119829 ATAATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.29
21 11 0.24
22 2 0.04
23 19 0.42
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
AATATATATTAAATTAAAATAT
Found at i:5122225 original size:64 final size:66
Alignment explanation
Indices: 5122098--5122229 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 66
5122088 ATTCTGAAGC
* * * **
5122098 TGTAGCTGGAGTTTATCATATTTTCTTATTGCCTCTGCTTCTCTCGCTGCTGCCTCTGTTTTAAG
1 TGTAGCTGGAGTTCATCATATTTTCTTATAGCCTCTGCTTCTCTCGATGCTGCCTCTACTTTAAG
5122163 T
66 T
*
5122164 TGTAGCTGGAGTTCATCAT-TTTT-TT-TGAGCCTCTGCTTCTCTTGATGCTGCCT-TCACTTTA
1 TGTAGCTGGAGTTCATCATATTTTCTTAT-AGCCTCTGCTTCTCTCGATGCTGCCTCT-ACTTTA
5122225 AGT
64 AGT
5122228 TG
1 TG
5122230 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
63 2 0.03
64 34 0.59
65 4 0.07
66 18 0.31
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (66 bp):
TGTAGCTGGAGTTCATCATATTTTCTTATAGCCTCTGCTTCTCTCGATGCTGCCTCTACTTTAAG
T
Found at i:5132504 original size:2 final size:2
Alignment explanation
Indices: 5132497--5132526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5132487 NNNNNNNNNN
5132497 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
5132527 ATTTTTCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5137858 original size:16 final size:15
Alignment explanation
Indices: 5137833--5137863 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5137823 TGATAGGTCT
5137833 CCGACGAGCTTTCAA
1 CCGACGAGCTTTCAA
5137848 CCGATCGAGCTTTCAA
1 CCGA-CGAGCTTTCAA
5137864 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (15 bp):
CCGACGAGCTTTCAA
Found at i:5157683 original size:89 final size:89
Alignment explanation
Indices: 5157522--5157687 Score: 298
Period size: 88 Copynumber: 1.9 Consensus size: 89
5157512 CAGTACACTG
* *
5157522 GAGGTGATCAAATTCAGTTAAAAACTGGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
1 GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
5157587 GAGCAAGTCAACTTCAAAGACTCA
66 GAGCAAGTCAACTTCAAAGACTCA
5157611 GAGGTGAT-AAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTTGGAGTGAGGT
1 GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTC-TGGAGTGAGGT
5157675 TGAGCAAGTCAAC
65 TGAGCAAGTCAAC
5157688 CATCATTACC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
88 42 0.57
89 32 0.43
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (89 bp):
GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
GAGCAAGTCAACTTCAAAGACTCA
Found at i:5167481 original size:133 final size:134
Alignment explanation
Indices: 5167258--5167524 Score: 527
Period size: 133 Copynumber: 2.0 Consensus size: 134
5167248 ATTTATATTT
5167258 ATTTAAATCTCTCACTGAATTAGTATTAGAAATTAACTAGACATCAATTTAATAAAAAAATACAA
1 ATTTAAATCTCTCACTGAATTAGTATTAGAAATTAACTAGACATCAATTTAATAAAAAAATACAA
5167323 AAAAATCAAATTAAATATATAATATCAAATGCAATTAAAGGATAACTATGTCTTTTATTATATAA
66 AAAAATCAAATTAAATATATAATATCAAATGCAATTAAAGGATAACTATGTCTTTTATTATATAA
5167388 AATA
131 AATA
5167392 ATTTAAATCT-TCACTGAATTAGTATTAGAAATTAACTAGACATCAATTTAATAAAAAAATACAA
1 ATTTAAATCTCTCACTGAATTAGTATTAGAAATTAACTAGACATCAATTTAATAAAAAAATACAA
5167456 AAAAATCAAATTAAATATATAATATCAAATGCAATTAAAGGATAACTATGTCTTTTATTATATAA
66 AAAAATCAAATTAAATATATAATATCAAATGCAATTAAAGGATAACTATGTCTTTTATTATATAA
5167521 AATA
131 AATA
5167525 TGCATCAAAT
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 123 0.92
134 10 0.08
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (134 bp):
ATTTAAATCTCTCACTGAATTAGTATTAGAAATTAACTAGACATCAATTTAATAAAAAAATACAA
AAAAATCAAATTAAATATATAATATCAAATGCAATTAAAGGATAACTATGTCTTTTATTATATAA
AATA
Found at i:5173520 original size:31 final size:31
Alignment explanation
Indices: 5173485--5173544 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5173475 CATATAATTT
*
5173485 AAATTGATAAATTTTAATCTCTGTACTTTTC
1 AAATTGATAAAATTTAATCTCTGTACTTTTC
* *
5173516 AAATTGGTAAAATTTAGTCTCTGTACTTT
1 AAATTGATAAAATTTAATCTCTGTACTTT
5173545 CCAAGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (31 bp):
AAATTGATAAAATTTAATCTCTGTACTTTTC
Found at i:5174092 original size:2 final size:2
Alignment explanation
Indices: 5174085--5174115 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5174075 TAAATAAATG
5174085 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 T
5174116 TAGCTAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5175211 original size:18 final size:18
Alignment explanation
Indices: 5175175--5175208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5175165 AAATATTTAC
5175175 AAATATCAAATACTAAAT
1 AAATATCAAATACTAAAT
*
5175193 AAATTTCAAATA-TAAA
1 AAATATCAAATACTAAA
5175209 ATACTCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATCAAATACTAAAT
Found at i:5176825 original size:16 final size:16
Alignment explanation
Indices: 5176804--5176837 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5176794 TCAATATCCA
* *
5176804 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
5176820 ATTATCACATTTACAC
1 ATTATCACATTTACAC
5176836 AT
1 AT
5176838 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:5177998 original size:154 final size:151
Alignment explanation
Indices: 5177708--5178516 Score: 977
Period size: 153 Copynumber: 5.4 Consensus size: 151
5177698 AACATGTTCG
* * * * * *
5177708 TATTTCAGCCATTTGTTCGTATTTTTTTCTGGATTTTATTAC-TTT-AAAAAATATACTATTTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAAATATATTATTTTC
* * *
5177771 TAATTTTATTATTTTACATTATTTTAATACACTATGTTTGAAATGTATTCATTTAGTATGTTTTT
66 T-ATTTTATTATTTTACATTA-TTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
**
5177836 TATTTAAATTTAAAAAAAAACCCT
129 TAAATAAATTT-AAAAAAAACCCT
* *
5177860 AATTTCGGCCCTTTATTCGTATTTTTTCCCAGGATTTTATTACTTTTAATAAAAATATATTATTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCC-GGATTTTATTACTTTTAA-AAAAATATATTATTT
* * *
5177925 TCGTATTTTATTATTTTACATTA-TTAGTACATTATGTTTGAAATGTACTAATTTACTGTGTTTT
64 TC-TATTTTATTATTTTACATTATTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
*
5177989 TTAAATAAATTTTTAAAAAAACCCT
128 TTAAATAAA-TTTAAAAAAAACCCT
* *
5178014 TATTTTGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTAC-TTTAAAAAAATAT-TCTATTT
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCGGATTTTATTACTTTTAAAAAAATATAT-TATTT
* *
5178077 TC-----TA--A--TTACATTATTTTAGTGCATTATGTTTGAAATGTATCCATTTAGTGTGTTTT
64 TCTATTTTATTATTTTACATTA-TTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
*
5178133 TTAAATAAATTT-AAAAAAACTCT
128 TTAAATAAATTTAAAAAAAACCCT
* * *
5178156 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAACAAAAGTATATTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAA-AAAAATATATTA-TTT
* * *
5178221 TGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAATGTGTTTT
64 TCTATTTTATTATTTTACATTA-TTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
*
5178286 TTAAATAAATTTAGTAAAAAACCCT
128 TTAAATAAATTTA-AAAAAAACCCT
* * * * **
5178311 TATTTCGGCCCTTTGTTCGTATTTTTTTCTGGATTTTAATA-ATTTAAAAAAATATACAATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAAATATATTATTTTC
*
5178375 TAATTTTATTATTTTACATTATTTTAGTACATTGTGTTTGAAATGTATTCATTTAGTGTGTTTTT
66 T-ATTTTATTATTTTACATTA-TTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
5178440 TAAATAAA-TTAAAAAAAACCCT
129 TAAATAAATTTAAAAAAAACCCT
* * * *
5178462 TATTTTGGCCATTTGTTCGTATTTTTTTTCCGGATTTTATTACTTTCAATAAAAA
1 TATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTTAA-AAAAA
5178517 ACACACTAAA
Statistics
Matches: 569, Mismatches: 59, Indels: 56
0.83 0.09 0.08
Matches are distributed among these distances:
141 13 0.02
142 48 0.08
143 12 0.02
144 51 0.09
146 2 0.00
149 2 0.00
151 31 0.05
152 65 0.11
153 157 0.28
154 100 0.18
155 53 0.09
156 34 0.06
157 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (151 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAAATATATTATTTTC
TATTTTATTATTTTACATTATTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTA
AATAAATTTAAAAAAAACCCT
Found at i:5198266 original size:16 final size:17
Alignment explanation
Indices: 5198240--5198272 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5198230 TTATTTAGAT
*
5198240 ATTTTATAATTTATAAA
1 ATTTTATAATTAATAAA
5198257 ATTTTA-AATTAATAAA
1 ATTTTATAATTAATAAA
5198273 GTTAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTATAATTAATAAA
Found at i:5200086 original size:5 final size:5
Alignment explanation
Indices: 5200076--5200101 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5200066 CGTTTTTTAA
5200076 ATTTG ATTTG ATTTG ATTTG ATTTG A
1 ATTTG ATTTG ATTTG ATTTG ATTTG A
5200102 CTCCAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (5 bp):
ATTTG
Found at i:5206531 original size:2 final size:2
Alignment explanation
Indices: 5206524--5206558 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5206514 TAGACACGCG
* *
5206524 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5206559 GAGTCCAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5207968 original size:4 final size:4
Alignment explanation
Indices: 5207959--5207984 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5207949 GATTGAACAC
5207959 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
5207985 CGTAGTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5208604 original size:3 final size:3
Alignment explanation
Indices: 5208591--5208629 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
5208581 ATTTTACTTC
5208591 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CTAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
5208630 TTCAGAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5213967 original size:28 final size:29
Alignment explanation
Indices: 5213935--5213990 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
5213925 TGAAAATATT
5213935 AAAAATTTTAAAATTAT-TTAAAAAAATA
1 AAAAATTTTAAAATTATCTTAAAAAAATA
*
5213963 AAAAATTTTAAAATTTTCTTAAAAAAAT
1 AAAAATTTTAAAATTATCTTAAAAAAAT
5213991 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAAAATTATCTTAAAAAAATA
Found at i:5214062 original size:22 final size:22
Alignment explanation
Indices: 5214032--5214073 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5214022 ATTTGGAGAT
*
5214032 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
5214054 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
5214074 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:5214094 original size:52 final size:51
Alignment explanation
Indices: 5214023--5214166 Score: 135
Period size: 52 Copynumber: 2.9 Consensus size: 51
5214013 TTAATATGGA
* * *
5214023 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
5214074 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGA-
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
* * *
5214125 ----GA-AATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAATTGA
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGA
5214167 TATTGAATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
44 25 0.30
45 11 0.13
46 2 0.02
51 4 0.05
52 31 0.38
53 9 0.11
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:5214100 original size:22 final size:22
Alignment explanation
Indices: 5214075--5214166 Score: 125
Period size: 22 Copynumber: 4.2 Consensus size: 22
5214065 ATTTGAGAGT
5214075 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTT-GAAGGAAA
* *
5214097 TTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAGGAAA
5214119 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTG-AAGGAAA
*
5214141 TTGAGAGAAATTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAGGAAA
5214163 TTGA
1 TTGA
5214167 TATTGAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
21 3 0.05
22 50 0.79
23 10 0.16
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.29
Consensus pattern (22 bp):
TTGAGAGAAATTTTGAAGGAAA
Found at i:5214134 original size:12 final size:12
Alignment explanation
Indices: 5214097--5214164 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
5214087 TGGAAGGAAA
*
5214097 TTGATAGAAATT
1 TTGAAAGAAATT
* *
5214109 TTGAAGGGAA--
1 TTGAAAGAAATT
*
5214119 TTGAGAGAAATT
1 TTGAAAGAAATT
*
5214131 TTGAAAGGAA--
1 TTGAAAGAAATT
*
5214141 TTGAGAGAAATT
1 TTGAAAGAAATT
5214153 TTGAAAGAAATT
1 TTGAAAGAAATT
5214165 GATATTGAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
10 15 0.37
12 26 0.63
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (12 bp):
TTGAAAGAAATT
Found at i:5216733 original size:2 final size:2
Alignment explanation
Indices: 5216726--5216762 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5216716 AATTAAGGGG
5216726 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5216763 GCTAATTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5228453 original size:76 final size:76
Alignment explanation
Indices: 5228325--5228474 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 76
5228315 CCCAGACTCG
* * * * *
5228325 GGTTTGATACTTTTGAAAACTTCAGTTTCTCTCTCGATGTCCATAGTTAATTCTCCCCGTCTTAC
1 GGTTTGACACATTTGAAAACTTCAGTTTCTCTCTCGATATCCATAGTCAATTCTCCCCGTCCTAC
5228390 GTCTATGGTCT
66 GTCTATGGTCT
* * *
5228401 GGTTTGACACATTTGAATACTTTAGTTTCTC-CTTCGATATCCATAGTCAATTCTCGCCGTCCTA
1 GGTTTGACACATTTGAAAACTTCAGTTTCTCTC-TCGATATCCATAGTCAATTCTCCCCGTCCTA
5228465 CGTCTATGGT
65 CGTCTATGGT
5228475 GGCCCTAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
75 1 0.02
76 64 0.98
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (76 bp):
GGTTTGACACATTTGAAAACTTCAGTTTCTCTCTCGATATCCATAGTCAATTCTCCCCGTCCTAC
GTCTATGGTCT
Found at i:5233060 original size:48 final size:47
Alignment explanation
Indices: 5233002--5233110 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 47
5232992 TATCCCAGAT
* *
5233002 ATGGTCTTACA-TGGGATCACATATTG-GTGCCGATGCAATGTCCTAGAC
1 ATGGTCTTACACTGGCA-CACATATCGAGT--CGATGCAATGTCCTAGAC
* * *
5233050 ATGGTCTTACACTGGCACTCATCTCGAGTCGATGCCATGTCCTAGAC
1 ATGGTCTTACACTGGCACACATATCGAGTCGATGCAATGTCCTAGAC
*
5233097 ATGGTTTTACACTG
1 ATGGTCTTACACTG
5233111 ACTCTCCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
47 30 0.57
48 17 0.32
49 6 0.11
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (47 bp):
ATGGTCTTACACTGGCACACATATCGAGTCGATGCAATGTCCTAGAC
Found at i:5233090 original size:47 final size:48
Alignment explanation
Indices: 5233028--5233213 Score: 196
Period size: 49 Copynumber: 3.8 Consensus size: 48
5233018 TCACATATTG
* *
5233028 GTGCCGATGCAATGTCCTAGACATGGTCTTACACTGGCACTCATC-TC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTCGTC
* * * * * *
5233075 GAGTCGATGCCATGTCCTAGACATGGTTTTACACTGACTCTCCTCTTTC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTC-GTC
* * * * *
5233124 GTGCCGATGCCATTTCCCAAACATGGTCATACACTAGCACTCCTCGGTC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTC-GTC
*
5233173 TGTGCCGATGCCATGT-CTCAGACATGGTCTTACATTGGCAC
1 -GTGCCGATGCCATGTCCT-AGACATGGTCTTACACTGGCAC
5233214 ACTCACTGCC
Statistics
Matches: 110, Mismatches: 25, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
47 38 0.35
49 40 0.36
50 32 0.29
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.29
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTCGTC
Found at i:5233150 original size:96 final size:98
Alignment explanation
Indices: 5233028--5233206 Score: 229
Period size: 96 Copynumber: 1.8 Consensus size: 98
5233018 TCACATATTG
* * * * *
5233028 GTGCCGATGCAATGTCCTAGACATGGTCTTACACTGGCACTCATC-TC-GAGTCGATGCCATGTC
1 GTGCCGATGCAATGTCCCAAACATGGTCATACACTAGCACTCATCGTCTGAGCCGATGCCATGTC
*
5233091 -CTAGACATGGTTTTACACTGACTCTCCTCTTTC
66 TC-AGACATGGTCTTACACTGACTCTCCTCTTTC
* * * *
5233124 GTGCCGATGCCATTTCCCAAACATGGTCATACACTAGCACTCCTCGGTCTGTGCCGATGCCATGT
1 GTGCCGATGCAATGTCCCAAACATGGTCATACACTAGCACTCATC-GTCTGAGCCGATGCCATGT
5233189 CTCAGACATGGTCTTACA
65 CTCAGACATGGTCTTACA
5233207 TTGGCACACT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
96 38 0.55
98 2 0.03
99 28 0.41
100 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (98 bp):
GTGCCGATGCAATGTCCCAAACATGGTCATACACTAGCACTCATCGTCTGAGCCGATGCCATGTC
TCAGACATGGTCTTACACTGACTCTCCTCTTTC
Found at i:5238674 original size:45 final size:45
Alignment explanation
Indices: 5238542--5238685 Score: 137
Period size: 45 Copynumber: 3.2 Consensus size: 45
5238532 ATAGTACTCA
* * * ** * *
5238542 GTGAAATCAGCACATAGCAACCACCTTTATACTCAACGATACCGG
1 GTGAAATCAACACATAGCAATCACCTTTATAATCATTGATATCAG
* * *
5238587 GTGAATTCATCACATAGCAATCA-CTTATATAACCATTGATATCAG
1 GTGAAATCAACACATAGCAATCACCTT-TATAATCATTGATATCAG
** * *
5238632 GTGAAATCAACACATAGCAATCACCTTTATTTTCATTAATATCCG
1 GTGAAATCAACACATAGCAATCACCTTTATAATCATTGATATCAG
*
5238677 GTGGAATCA
1 GTGAAATCA
5238686 GTACATAACA
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
44 3 0.04
45 74 0.93
46 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (45 bp):
GTGAAATCAACACATAGCAATCACCTTTATAATCATTGATATCAG
Found at i:5240428 original size:23 final size:23
Alignment explanation
Indices: 5240395--5240438 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5240385 TGAAGATTCA
*
5240395 TAATCTAAAAAGATTTTATTTTG
1 TAATCTAAAAAGATTTGATTTTG
*
5240418 TAATCTTAAAAGATTTGATTT
1 TAATCTAAAAAGATTTGATTT
5240439 GTAGATTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (23 bp):
TAATCTAAAAAGATTTGATTTTG
Found at i:5240961 original size:24 final size:26
Alignment explanation
Indices: 5240913--5240979 Score: 111
Period size: 24 Copynumber: 2.6 Consensus size: 26
5240903 AAAAATAAAA
5240913 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTT
5240940 ATTTACCAAAATATAT-AC-TTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
5240964 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
5240980 CAAAAAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 22 0.55
25 2 0.05
26 3 0.08
27 13 0.32
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:5241783 original size:21 final size:21
Alignment explanation
Indices: 5241751--5241806 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
5241741 CAAAATAATA
*
5241751 GAGGAAAAAAAAAGGGTGATG
1 GAGGGAAAAAAAAGGGTGATG
* *
5241772 TAGGG-GAAAAAAGGGTGATG
1 GAGGGAAAAAAAAGGGTGATG
5241792 GAGGGAAAAAAAAGG
1 GAGGGAAAAAAAAGG
5241807 CAGCACAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (21 bp):
GAGGGAAAAAAAAGGGTGATG
Found at i:5249024 original size:12 final size:12
Alignment explanation
Indices: 5249004--5249034 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5248994 AAAAAAATTT
*
5249004 ATACTCAAAATA
1 ATACACAAAATA
5249016 ATACACAAAATA
1 ATACACAAAATA
5249028 ATACACA
1 ATACACA
5249035 CTANNNNNNN
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:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:5249185 original size:3 final size:3
Alignment explanation
Indices: 5249177--5249238 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
5249167 NNNTCATACT
5249177 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
5249225 AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AA
5249239 TAATAATAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Done.