Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 11 of 335
Found at i:3805299 original size:38 final size:38
Alignment explanation
Indices: 3805252--3805325 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
3805242 GTTATATAGA
*
3805252 ATAAGAGTAGTACTTAAATAGACAAATCTAAACAATAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
3805290 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
3805326 CAAAAGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (38 bp):
ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
Found at i:3809616 original size:5 final size:5
Alignment explanation
Indices: 3809606--3809650 Score: 74
Period size: 5 Copynumber: 9.0 Consensus size: 5
3809596 TACTTTATTA
3809606 TATAT TATAT TATAT TATAT TATAT TATAT TATA- TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
3809651 ATAAACTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 2 0.05
5 34 0.89
6 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3809651 original size:10 final size:10
Alignment explanation
Indices: 3809569--3809652 Score: 57
Period size: 10 Copynumber: 8.0 Consensus size: 10
3809559 ATGTTTAGTA
3809569 TATTATTATAT
1 TATTA-TATAT
*
3809580 TATTATATAA
1 TATTATATAT
* *
3809590 TA-AAGATACTT
1 TATTATATA--T
3809601 TATTATATAT
1 TATTATATAT
3809611 TA-TATTATAT
1 TATTA-TATAT
3809621 TA-TATTATATT
1 TATTA-TATA-T
3809632 ATATTATATAT
1 -TATTATATAT
3809643 TATTATATAT
1 TATTATATAT
3809653 AAACTAAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
9 6 0.10
10 33 0.55
11 9 0.15
12 10 0.17
13 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (10 bp):
TATTATATAT
Found at i:3810191 original size:21 final size:21
Alignment explanation
Indices: 3810133--3810193 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
3810123 AGGCACTTTA
3810133 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCG--TTTTAGGCACCTCG
* * *
3810156 TGTGTTGTATCAGGCACCTCG
1 TGTGTCGTTTTAGGCACCTCG
3810177 TGTGTCGTTTTAGGCAC
1 TGTGTCGTTTTAGGCAC
3810194 TTTATGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 26 0.81
23 6 0.19
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (21 bp):
TGTGTCGTTTTAGGCACCTCG
Found at i:3810201 original size:21 final size:21
Alignment explanation
Indices: 3810123--3810205 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
3810113 TTTATCGATC
* *
3810123 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCG--TTTT
* * * *
3810146 AGGCACCTCGTGTGTTGTATC
1 AGGCACCTCATGTGTCGTTTT
*
3810167 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTTTT
* *
3810188 AGGCACTTTATGTGTCGT
1 AGGCACCTCATGTGTCGT
3810206 ACTCTGATCA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 35 0.73
23 13 0.27
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTTTT
Found at i:3817757 original size:20 final size:19
Alignment explanation
Indices: 3817708--3817747 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3817698 TATTTCAAGC
3817708 TTTTGAAATTTGGTTTTTT
1 TTTTGAAATTTGGTTTTTT
3817727 TTTTGAAATTTGGTTTTTT
1 TTTTGAAATTTGGTTTTTT
3817746 TT
1 TT
3817748 ACTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (19 bp):
TTTTGAAATTTGGTTTTTT
Found at i:3835524 original size:2 final size:2
Alignment explanation
Indices: 3835517--3835546 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3835507 CCGTTCTCCG
3835517 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3835547 AGTATATATA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3838451 original size:12 final size:12
Alignment explanation
Indices: 3838434--3838459 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3838424 AGACATGTAA
3838434 GTTTACTAATGG
1 GTTTACTAATGG
3838446 GTTTACTAATGG
1 GTTTACTAATGG
3838458 GT
1 GT
3838460 CTTTTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (12 bp):
GTTTACTAATGG
Found at i:3846664 original size:4 final size:4
Alignment explanation
Indices: 3846655--3846679 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3846645 CAATAGAGAT
3846655 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3846680 GGAGGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3851698 original size:29 final size:29
Alignment explanation
Indices: 3851656--3851713 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3851646 CTGTCAGCAG
3851656 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3851685 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3851714 CACATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (29 bp):
ATAGTCAGGTTTGAGACTTATCTATCATT
Found at i:3853336 original size:21 final size:21
Alignment explanation
Indices: 3853312--3853351 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3853302 TCTCCATCTC
* *
3853312 CACCTCCACCACGGCCACCCT
1 CACCCCCACCACCGCCACCCT
*
3853333 CACCCCCACCCCCGCCACC
1 CACCCCCACCACCGCCACC
3853352 ACCAGCACCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.70, G:0.07, T:0.05
Consensus pattern (21 bp):
CACCCCCACCACCGCCACCCT
Found at i:3857218 original size:18 final size:18
Alignment explanation
Indices: 3857191--3857301 Score: 150
Period size: 18 Copynumber: 6.2 Consensus size: 18
3857181 TACGACCGTT
3857191 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
** *
3857209 TACGACACTATTTACGTA
1 TACGGTACTATTCACGTA
*
3857227 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
3857245 TATGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
3857263 TATGGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
3857281 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
3857299 TAC
1 TAC
3857302 AGTAGTTGGG
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 80 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:3864343 original size:18 final size:18
Alignment explanation
Indices: 3864280--3864350 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
3864270 ACCGTTTACA
* *
3864280 GTACTATTCACATATGCG
1 GTACTATTCACGTATACG
* **
3864298 GTACTATTTACGTATATA
1 GTACTATTCACGTATACG
*
3864316 GCACTATTCACGTATACG
1 GTACTATTCACGTATACG
*
3864334 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
3864351 AGTAGTTGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (18 bp):
GTACTATTCACGTATACG
Found at i:3868409 original size:11 final size:11
Alignment explanation
Indices: 3868393--3868448 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
3868383 TATTAAAATA
*
3868393 TGCCCATCCCT
1 TGCCCATACCT
*
3868404 TGCCCATACAT
1 TGCCCATACCT
3868415 TGCCCATACCT
1 TGCCCATACCT
*
3868426 TTCCCATACC-
1 TGCCCATACCT
*
3868436 TACCCATACCT
1 TGCCCATACCT
3868447 TG
1 TG
3868449 GAAAGGTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.20, C:0.45, G:0.07, T:0.29
Consensus pattern (11 bp):
TGCCCATACCT
Found at i:3870578 original size:39 final size:39
Alignment explanation
Indices: 3870535--3870658 Score: 230
Period size: 39 Copynumber: 3.2 Consensus size: 39
3870525 CGAAATCTAG
*
3870535 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
*
3870574 CTGAAGCATATAAGTGCTAAACTGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
3870613 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
3870652 CTGAAGC
1 CTGAAGC
3870659 TCATCAGAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (39 bp):
CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
Found at i:3870597 original size:21 final size:21
Alignment explanation
Indices: 3870535--3870640 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
3870525 CGAAATCTAG
3870535 CTGAAGCACATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
* **
3870556 CGGAAGC-CCGAAG-GCT-AA
1 CTGAAGCACATAAGTGCTAAA
*
3870574 CTGAAGCATATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
**
3870595 CTGAAGC-CCGAAG-GCT-AA
1 CTGAAGCACATAAGTGCTAAA
*
3870613 CTGAAGCATATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
*
3870634 CGGAAGC
1 CTGAAGC
3870641 CCGAAGGCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
18 17 0.26
19 12 0.18
20 13 0.20
21 23 0.35
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (21 bp):
CTGAAGCACATAAGTGCTAAA
Found at i:3870616 original size:18 final size:18
Alignment explanation
Indices: 3870558--3870658 Score: 85
Period size: 18 Copynumber: 5.3 Consensus size: 18
3870548 GTGCTAAACG
3870558 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
***
3870576 GAAGCATATAAGTGCTAAACT
1 GAAGC-CCGAAG-GCT-AACT
3870597 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
*** *
3870615 GAAGCATATAAGTGCTAAACG
1 GAAGC-CCGAAG-GCT-AACT
3870636 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
3870654 GAAGC
1 GAAGC
3870659 TCATCAGAGC
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 22 0.35
19 12 0.19
20 12 0.19
21 17 0.27
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (18 bp):
GAAGCCCGAAGGCTAACT
Found at i:3870675 original size:78 final size:78
Alignment explanation
Indices: 3870517--3870681 Score: 242
Period size: 78 Copynumber: 2.1 Consensus size: 78
3870507 ACATCGTGAT
* *
3870517 CTGAAACCCGAAATCTAGCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGCA
1 CTGAAACCCGAAAGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGCA
*
3870582 TATAAGTGCTAAA
66 TATAAGAGCTAAA
* * *
3870595 CTGAAGCCCGAAGGCTAACTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGC-
1 CTGAAACCCGAAAGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGCA
* *
3870659 TCATCAGAGCTGAA
66 T-ATAAGAGCTAAA
3870673 CTGAAACCC
1 CTGAAACCC
3870682 CAAAAGGGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 1 0.01
78 76 0.99
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (78 bp):
CTGAAACCCGAAAGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGCA
TATAAGAGCTAAA
Found at i:3872801 original size:13 final size:14
Alignment explanation
Indices: 3872785--3872820 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3872775 CAATCTCATA
3872785 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
3872798 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
3872811 TCTC-ATTTCA
1 TCTCAATTTCA
3872821 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:3872810 original size:18 final size:19
Alignment explanation
Indices: 3872772--3872812 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3872762 TTGGTTATGT
3872772 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
3872791 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
3872809 TTTC
1 TTTC
3872813 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:3873002 original size:21 final size:21
Alignment explanation
Indices: 3872976--3873060 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
3872966 TGATCAGTAT
*
3872976 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
3872997 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
3873018 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
3873040 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
3873061 TTGGTAAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:3873026 original size:23 final size:22
Alignment explanation
Indices: 3872974--3873048 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
3872964 CCTGATCAGT
** *
3872974 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
3872995 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
3873016 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
3873039 ATACGACACA
1 ATACGACACA
3873049 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:3873372 original size:15 final size:15
Alignment explanation
Indices: 3873347--3873404 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
3873337 TCATATATAT
3873347 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
*
3873363 TATAAATTCAATTAA
1 TATAAATTCAATCAA
* *
3873378 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3873393 TATAAATTCAAT
1 TATAAATTCAAT
3873405 AAAACAGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3873389 original size:30 final size:28
Alignment explanation
Indices: 3873350--3873408 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
3873340 TATATATTAT
3873350 ATAATTCAATCAATATAAATTCAATTAAA
1 ATAATTCAATCAATATAAATTCAA-TAAA
3873379 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
3873408 A
1 A
3873409 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:3873567 original size:2 final size:2
Alignment explanation
Indices: 3873560--3873611 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
3873550 ATATCTCATT
* *
3873560 CA CA CA CA CA CA CA CA CA TA CA CA TA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3873602 CA CA CA CA CA
1 CA CA CA CA CA
3873612 TATATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.46, G:0.00, T:0.04
Consensus pattern (2 bp):
CA
Found at i:3873616 original size:2 final size:2
Alignment explanation
Indices: 3873611--3873656 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
3873601 ACACACACAC
*
3873611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3873652 AT AT A
1 AT AT A
3873657 ATTCAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3874867 original size:25 final size:24
Alignment explanation
Indices: 3874821--3874868 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3874811 ACTTAACTTC
***
3874821 ATAAATATTTTTAATTTTTTTTTA
1 ATAAATATTTTTAATCCATTTTTA
3874845 ATAAATATTTTCTAATCCATTTTT
1 ATAAATATTTT-TAATCCATTTTT
3874869 CAGAAACGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (24 bp):
ATAAATATTTTTAATCCATTTTTA
Found at i:3880033 original size:2 final size:2
Alignment explanation
Indices: 3880026--3880063 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3880016 GAGAAAAAGT
3880026 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3880064 AGTGGATGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3881737 original size:5 final size:6
Alignment explanation
Indices: 3881723--3881747 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3881713 ATCATTCATC
3881723 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
3881748 TTAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:3884305 original size:10 final size:11
Alignment explanation
Indices: 3884285--3884309 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3884275 CAATCGTCCA
3884285 TTTCTTTTTTT
1 TTTCTTTTTTT
3884296 TTTCTTTTTTT
1 TTTCTTTTTTT
3884307 TTT
1 TTT
3884310 TATGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3885589 original size:18 final size:20
Alignment explanation
Indices: 3885563--3885604 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3885553 ATTTCATATT
*
3885563 ATTTTAAAG-AAAGCCAA-A
1 ATTTAAAAGTAAAGCCAATA
*
3885581 ATTTAAAAGTAAAGTCAATA
1 ATTTAAAAGTAAAGCCAATA
3885601 ATTT
1 ATTT
3885605 TTAAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTTAAAAGTAAAGCCAATA
Found at i:3889674 original size:53 final size:53
Alignment explanation
Indices: 3889533--3889683 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3889523 ACAAGTGTGC
* **
3889533 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
3889586 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
3889639 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
3889684 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:3897191 original size:53 final size:53
Alignment explanation
Indices: 3897050--3897200 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3897040 ACAAGTGTGC
* **
3897050 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
3897103 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
3897156 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
3897201 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:3899336 original size:46 final size:46
Alignment explanation
Indices: 3899284--3899459 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
3899274 TGGTCGAGCA
*
3899284 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * * * *
3899330 TTCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTTACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-ACG
* *
3899377 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
3899423 CCCGAGCTCGTTTAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3899460 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 64 0.62
47 28 0.27
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:3899440 original size:93 final size:93
Alignment explanation
Indices: 3899281--3899451 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
3899271 GGATGGTCGA
* * **
3899281 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
*
3899346 TGAGTCTGAGTTCGTGAGATGTTACTAG
66 TGAGTCCGAGTTCGTGAGATGTTACTAG
* * *
3899374 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAGCTCGTTTAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
3899439 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3899452 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTTACTAG
Found at i:3902304 original size:16 final size:17
Alignment explanation
Indices: 3902269--3902313 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3902259 TCTAATTTTT
3902269 TAAAATTATATAATATA
1 TAAAATTATATAATATA
3902286 TAAAATTAATATAATATA
1 TAAAATT-ATATAATATA
3902304 -AAATATTATA
1 TAAA-ATTATA
3902314 AACTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTATATAATATA
Found at i:3902371 original size:21 final size:21
Alignment explanation
Indices: 3902347--3902386 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3902337 TTCGAACTTA
3902347 AACATTTAAGATCCGAGCTTG
1 AACATTTAAGATCCGAGCTTG
3902368 AACATTTAAGATCCGAGCT
1 AACATTTAAGATCCGAGCT
3902387 CAGTCCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AACATTTAAGATCCGAGCTTG
Found at i:3915644 original size:42 final size:42
Alignment explanation
Indices: 3915597--3915681 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
3915587 GGAATGGCCA
* *
3915597 TAATTATAAAGTTTGGTGGGACCACTATCTTATAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
*
3915639 TAATTATAAAGTTTGGTGGGACAAGTATCTTACAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
3915681 T
1 T
3915682 TAATAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (42 bp):
TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
Found at i:3918008 original size:33 final size:31
Alignment explanation
Indices: 3917944--3918012 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
3917934 CTTGAATAAA
*
3917944 AAAATACTTAAATTCAAAATAATATAAATCT
1 AAAATACTTAAATTCAAAATAAAATAAATCT
*
3917975 AAAATGACTTAAATCTCAAAATAGAAAT-GATCT
1 AAAAT-ACTTAAAT-TCAAAATA-AAATAAATCT
3918008 AAAAT
1 AAAAT
3918013 CAATCTAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.15
32 8 0.24
33 17 0.52
34 3 0.09
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (31 bp):
AAAATACTTAAATTCAAAATAAAATAAATCT
Found at i:3918103 original size:23 final size:23
Alignment explanation
Indices: 3918077--3918121 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3918067 AACTCAAATT
*
3918077 TTTTAAAATAAAGTTGTGGATTC
1 TTTTAAAATAAAATTGTGGATTC
* *
3918100 TTTTAAAGTAAAATTTTGGATT
1 TTTTAAAATAAAATTGTGGATT
3918122 TAAATTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TTTTAAAATAAAATTGTGGATTC
Found at i:3924684 original size:14 final size:14
Alignment explanation
Indices: 3924665--3924692 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3924655 CTGCTTTCTA
3924665 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
3924679 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
3924693 CTGACAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
AATTTGTTTTAAGG
Found at i:3931685 original size:18 final size:19
Alignment explanation
Indices: 3931646--3931697 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3931636 TTTATTTATA
3931646 ATTACAAATTAAA-TACATT
1 ATTA-AAATTAAATTACATT
*
3931665 ATTAAAATTAAATTAGA-T
1 ATTAAAATTAAATTACATT
3931683 ATTTAAAATATAAAT
1 A-TTAAAAT-TAAAT
3931698 AACAGTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTAAAATTAAATTACATT
Found at i:3931873 original size:11 final size:12
Alignment explanation
Indices: 3931836--3931874 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3931826 ATATTATTTT
*
3931836 TTATTTTAAAAA
1 TTATTTTAAATA
3931848 TTATTTTAAAGTA
1 TTATTTTAAA-TA
3931861 TT-TTTTAAATA
1 TTATTTTAAATA
3931872 TTA
1 TTA
3931875 AATTTATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 4 0.17
12 17 0.71
13 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTATTTTAAATA
Found at i:3932362 original size:19 final size:20
Alignment explanation
Indices: 3932337--3932380 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3932327 TAGATTTCAA
3932337 AATAATTTATTA-GT-ATATT
1 AATAA-TTATTATGTGATATT
*
3932356 TATAATTATTATGTGATATT
1 AATAATTATTATGTGATATT
3932376 AATAA
1 AATAA
3932381 AAATTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AATAATTATTATGTGATATT
Found at i:3932861 original size:22 final size:22
Alignment explanation
Indices: 3932819--3932860 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3932809 ATGTTTAGCT
*
3932819 GAAAATTATAAAAATAGTTTTA
1 GAAAATTAAAAAAATAGTTTTA
*
3932841 GAAAA-TAAAAAAATATTTTT
1 GAAAATTAAAAAAATAGTTTT
3932861 TTAAATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
GAAAATTAAAAAAATAGTTTTA
Found at i:3952162 original size:6 final size:6
Alignment explanation
Indices: 3952151--3952176 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3952141 CCCCTCCTTG
3952151 AGTCTC AGTCTC AGTCTC AGTCTC AG
1 AGTCTC AGTCTC AGTCTC AGTCTC AG
3952177 ATTTACCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (6 bp):
AGTCTC
Found at i:3966030 original size:29 final size:28
Alignment explanation
Indices: 3965998--3966074 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 28
3965988 AAAATAAAAA
3965998 TTAATAAAAGTTATAAAAAT-TATTAAATT
1 TTAATAAAA-TTATAAAAATAT-TTAAATT
3966027 TTAATAAAATAATATAAAAATATTTAAATT
1 TTAATAAAAT--TATAAAAATATTTAAATT
* *
3966057 TTATTAAAAATTAGAAAA
1 TTAAT-AAAATTATAAAA
3966075 TCTTTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 1 0.02
29 15 0.36
30 20 0.48
31 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
TTAATAAAATTATAAAAATATTTAAATT
Found at i:3966045 original size:30 final size:30
Alignment explanation
Indices: 3966009--3966065 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3965999 TAATAAAAGT
3966009 TATAAAAAT-TATTAAATTTTAATAAAATAA
1 TATAAAAATAT-TTAAATTTTAATAAAATAA
*
3966039 TATAAAAATATTTAAATTTTATTAAAA
1 TATAAAAATATTTAAATTTTAATAAAA
3966066 ATTAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATAAAAATATTTAAATTTTAATAAAATAA
Found at i:3966178 original size:22 final size:23
Alignment explanation
Indices: 3966150--3966208 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 23
3966140 TATAAAGTCG
3966150 AAAGAAAATTATAAAAAAATGT-
1 AAAGAAAATTATAAAAAAATGTA
**
3966172 AAAG-AAA-TAT-AAAATTTGTA
1 AAAGAAAATTATAAAAAAATGTA
*
3966192 AAAAAAAATTATAAAAA
1 AAAGAAAATTATAAAAA
3966209 TTATCATACT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 6 0.20
22 7 0.23
23 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAGAAAATTATAAAAAAATGTA
Found at i:3971747 original size:2 final size:2
Alignment explanation
Indices: 3971740--3971768 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3971730 TCAGTGCTTT
3971740 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 T
3971769 TTGAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3973104 original size:18 final size:19
Alignment explanation
Indices: 3973067--3973104 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3973057 TTATTCTGAA
*
3973067 TTTGAATGCGTAAAGCACG
1 TTTGAATGCGAAAAGCACG
*
3973086 TTTGAAT-CGAAAAGTACG
1 TTTGAATGCGAAAAGCACG
3973104 T
1 T
3973105 ATTTATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (19 bp):
TTTGAATGCGAAAAGCACG
Found at i:3990242 original size:25 final size:25
Alignment explanation
Indices: 3990208--3990457 Score: 256
Period size: 25 Copynumber: 10.4 Consensus size: 25
3990198 GACCTCAGCA
3990208 TGCTCTCTGAT-TATTAGCACG-CTAG
1 TGCTCTCTGATAT-TTAGCACGTC-AG
*
3990233 TGCTCTCTGA-ATATTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGTCAG
*
3990258 TGCTCTCTGAT-TATTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGTCAG
* **
3990283 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
3990305 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
3990330 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
*
3990355 TGCTCTCTGATATTTAGCATGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* * *
3990380 CGGTCTTTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
3990405 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
3990427 TGCTCTCTG-TA--TAGCACTTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
3990449 TGCTCTCTG
1 TGCTCTCTG
3990458 TTCATTAGTG
Statistics
Matches: 196, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
22 52 0.27
23 2 0.01
24 1 0.01
25 140 0.71
26 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (25 bp):
TGCTCTCTGATATTTAGCACGTCAG
Found at i:3990308 original size:72 final size:72
Alignment explanation
Indices: 3990232--3990415 Score: 219
Period size: 72 Copynumber: 2.5 Consensus size: 72
3990222 TAGCACGCTA
3990232 GTGCTCTCTGA-ATATTAGCACGCCAGTGCTCTCTGAT-TATTAGCACGCCAGTGCTCTCTGATT
1 GTGCTCTCTGATAT-TTAGCACGCCAGTGCTCTCTGATAT-TTAGCACGCCAGTGCTCTCTGATT
3990295 AGCACATTT
64 AGCACATTT
* *
3990304 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATATT
1 GTGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATATTTAGCACGCCAGTGCTCTCTG--A-T
** **
3990369 TAGCATGTCA
63 TAGCACATTT
* * * *
3990379 GCGGTCTTTGATATTTAGCACGTCAGTGCTCTCTGAT
1 GTGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGAT
3990416 TAGCACATTT
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
72 53 0.54
73 3 0.03
74 1 0.01
75 41 0.42
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (72 bp):
GTGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATTAG
CACATTT
Found at i:3990425 original size:122 final size:119
Alignment explanation
Indices: 3990208--3990465 Score: 346
Period size: 122 Copynumber: 2.1 Consensus size: 119
3990198 GACCTCAGCA
*
3990208 TGCTCTCTGATTATTAGCACGCTAGTGCTCTCTGAATATTAGCACGCCAGTGCTCTCTGATTATT
1 TGCTCTCTGATTATTAGCACGCTAGTGCTCTCTGAATATTAGCACGCCAGCGCTCTCTGATTATT
3990273 AGCACGCCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGTCAG
66 AGCACGCCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTG-TA--TAGCACGTCAG
* * * *
3990330 TGCTCTCTGA-TATTTAGCACG-TCAGTGCTCTCTG-ATATTTAGCATGTCAGCGGTCTTTGA-T
1 TGCTCTCTGATTA-TTAGCACGCT-AGTGCTCTCTGAATA-TTAGCACGCCAGCGCTCTCTGATT
* *
3990391 ATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTGTATAGCACTTCAG
63 A-TTAGCACGCCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTGTATAGCACGTCAG
3990449 TGCTCTCTG-TTCATTAG
1 TGCTCTCTGATT-ATTAG
3990466 TGCATAATAA
Statistics
Matches: 123, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
119 24 0.20
120 1 0.01
121 10 0.08
122 88 0.72
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (119 bp):
TGCTCTCTGATTATTAGCACGCTAGTGCTCTCTGAATATTAGCACGCCAGCGCTCTCTGATTATT
AGCACGCCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTGTATAGCACGTCAG
Found at i:3997952 original size:27 final size:27
Alignment explanation
Indices: 3997921--3997974 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3997911 TTTTATACGT
*
3997921 TATAAATTA-TATAGTATATAAAAATAA
1 TATAAATTATTATA-AATATAAAAATAA
*
3997948 TATAAATTATTATAAATTTAAAAATAA
1 TATAAATTATTATAAATATAAAAATAA
3997975 ATCAAACTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TATAAATTATTATAAATATAAAAATAA
Found at i:4000165 original size:2 final size:2
Alignment explanation
Indices: 4000158--4000193 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4000148 TTTTACATGC
4000158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4000194 TGGTTTTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4009447 original size:22 final size:22
Alignment explanation
Indices: 4009367--4009436 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
4009357 TTCATGCAAG
4009367 TCATTGAATAGTTT-AAAGTTT
1 TCATTGAATAGTTTAAAAGTTT
*
4009388 TCGTTGAATAGTTTAAAAGTTT
1 TCATTGAATAGTTTAAAAGTTT
4009410 TCATTGAATAGTTTAAAAGTTT
1 TCATTGAATAGTTTAAAAGTTT
4009432 TCATT
1 TCATT
4009437 TAAATTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 13 0.28
22 33 0.72
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (22 bp):
TCATTGAATAGTTTAAAAGTTT
Found at i:4025696 original size:12 final size:12
Alignment explanation
Indices: 4025681--4025711 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4025671 TTCTCTTTTA
4025681 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
4025693 TTTTTCTTTCTC
1 TTTTTCTTTCCC
4025705 TTTTTCT
1 TTTTTCT
4025712 CCCCTGCTTC
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:4025812 original size:16 final size:16
Alignment explanation
Indices: 4025791--4025821 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4025781 TTTATTATTT
4025791 TATTAACATAATATAA
1 TATTAACATAATATAA
*
4025807 TATTAATATAATATA
1 TATTAACATAATATA
4025822 TTAAAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:4027739 original size:18 final size:19
Alignment explanation
Indices: 4027716--4027753 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4027706 TTTAAACTAA
*
4027716 ATTTAACTCCCT-AATTTC
1 ATTTAAATCCCTAAATTTC
4027734 ATTTAAATCCCTAAATTTC
1 ATTTAAATCCCTAAATTTC
4027753 A
1 A
4027754 AATTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAATCCCTAAATTTC
Found at i:4028649 original size:24 final size:24
Alignment explanation
Indices: 4028622--4028708 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
4028612 TAGCTCTTCG
*
4028622 GAGCTACCCGTTATTGGCTCGTAT
1 GAGCTTCCCGTTATTGGCTCGTAT
* *
4028646 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGTAT
* * *
4028670 GAGCTTCCCGTTATATAGCCCGGAT
1 GAGCTTCCCGTTAT-TGGCTCGTAT
*
4028695 AAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
4028709 ATGACTCGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.06
24 26 0.51
25 22 0.43
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGTAT
Found at i:4031251 original size:50 final size:50
Alignment explanation
Indices: 4031176--4031452 Score: 446
Period size: 50 Copynumber: 5.5 Consensus size: 50
4031166 CCATGGCAAC
* *
4031176 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4031226 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
4031276 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4031326 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
** *
4031376 AAGTGATAAGTGATAGCTTCAACTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
4031427 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
4031453 CTGATCAATG
Statistics
Matches: 210, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 188 0.90
51 22 0.10
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:4031470 original size:31 final size:31
Alignment explanation
Indices: 4031432--4031490 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
4031422 ATGGCAAGTA
4031432 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4031463 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
4031491 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:4031498 original size:46 final size:46
Alignment explanation
Indices: 4031445--4031536 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
4031435 AGTGGTAGCT
* *
4031445 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
4031491 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
4031537 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:4031540 original size:31 final size:31
Alignment explanation
Indices: 4031492--4031560 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4031482 ACCTGATCAT
* * *
4031492 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
4031523 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
4031554 CGGCTAC
1 CGGCTAC
4031561 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:4036538 original size:33 final size:32
Alignment explanation
Indices: 4036501--4036569 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
4036491 ATCAATTAAG
*
4036501 TAATCATAATAATTTAATATAAAA-CTATAATAA
1 TAATCATAATAATAT-ATATAAAACCTA-AATAA
*
4036534 TAATCATTATAATATATATAAAACCTAAATAA
1 TAATCATAATAATATATATAAAACCTAAATAA
4036566 -AATC
1 TAATC
4036570 TTTGATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.12
32 13 0.39
33 16 0.48
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (32 bp):
TAATCATAATAATATATATAAAACCTAAATAA
Found at i:4042033 original size:33 final size:32
Alignment explanation
Indices: 4041996--4042064 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
4041986 ATCAATTAAG
* *
4041996 TAATCATAATATTTTAATATAAAA-CTATAATAA
1 TAATCATAATAATAT-ATATAAAACCTA-AATAA
*
4042029 TAATCATTATAATATATATAAAACCTAAATAA
1 TAATCATAATAATATATATAAAACCTAAATAA
4042061 -AATC
1 TAATC
4042065 TTTGATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.12
32 13 0.41
33 15 0.47
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (32 bp):
TAATCATAATAATATATATAAAACCTAAATAA
Found at i:4043197 original size:11 final size:11
Alignment explanation
Indices: 4043181--4043205 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4043171 GATTTTAATA
4043181 TTAAATTATTT
1 TTAAATTATTT
4043192 TTAAATTATTT
1 TTAAATTATTT
4043203 TTA
1 TTA
4043206 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAAATTATTT
Found at i:4047590 original size:55 final size:53
Alignment explanation
Indices: 4047400--4047654 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 53
4047390 ACGCGGGTAC
* * * * *
4047400 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGT-A---T-CCTTTTGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* *
4047449 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
* * * *
4047502 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGG-AACATTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAAC-CTTGCCTTAT-G-AA
* * **
4047557 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* * * *
4047610 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTAACCTT
4047655 AAACTCTAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
49 34 0.20
52 2 0.01
53 47 0.28
54 14 0.08
55 71 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
Found at i:4047591 original size:108 final size:110
Alignment explanation
Indices: 4047447--4047647 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
4047437 ATCCTTTTGA
* *
4047447 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
4047510 -TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
* * *
4047555 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
4047620 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
4047648 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 27 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
Found at i:4050571 original size:30 final size:31
Alignment explanation
Indices: 4050537--4050605 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
4050527 TGGCCCAAGA
* * *
4050537 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
4050567 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
*
4050597 GCAAATATT
1 GTAAATATT
4050606 TTAAGGGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (31 bp):
GTAAATATTAAAAAGTTGAAGGACTAATAGT
Found at i:4050584 original size:29 final size:30
Alignment explanation
Indices: 4050537--4050604 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4050527 TGGCCCAAGA
* * *
4050537 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
4050567 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAGT
*
4050597 GCAAATAT
1 GTAAATAT
4050605 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:4052803 original size:46 final size:46
Alignment explanation
Indices: 4052751--4052982 Score: 295
Period size: 46 Copynumber: 5.0 Consensus size: 46
4052741 GTGTGCTCTC
* *
4052751 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* **
4052797 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*
4052843 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *** *
4052889 TAACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
** * * * *
4052935 TGGCA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
4052981 TG
1 TG
4052983 TCAAAGATAA
Statistics
Matches: 167, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:4053284 original size:16 final size:17
Alignment explanation
Indices: 4053263--4053295 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4053253 ATGATGGAGC
4053263 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4053279 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4053296 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:4054386 original size:25 final size:25
Alignment explanation
Indices: 4054358--4054405 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4054348 GACCTCAGCA
4054358 TGCTCTCTGATTACTAGCACATTAG
1 TGCTCTCTGATTACTAGCACATTAG
*
4054383 TGCTCTCTGATTATTAGCACATT
1 TGCTCTCTGATTACTAGCACATT
4054406 CAGCACATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (25 bp):
TGCTCTCTGATTACTAGCACATTAG
Found at i:4055757 original size:30 final size:31
Alignment explanation
Indices: 4055723--4055789 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
4055713 TGGCCCAAGA
*
4055723 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATACTCAAAATTTGAAGGACTAATAGT
* *
4055753 GTAAAT-GTGAAAATTTGAAGGACTAATAGT
1 GTAAATACTCAAAATTTGAAGGACTAATAGT
*
4055783 GCAAATA
1 GTAAATA
4055790 TTTTAAGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAAATACTCAAAATTTGAAGGACTAATAGT
Found at i:4060254 original size:46 final size:46
Alignment explanation
Indices: 4060188--4060465 Score: 389
Period size: 46 Copynumber: 6.0 Consensus size: 46
4060178 GTGTGCTCTC
** *
4060188 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
** * *
4060234 TGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
4060280 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* *
4060326 TGACGA-GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGA-TATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
4060372 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * * *
4060418 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
4060464 TG
1 TG
4060466 TCAAAGATAA
Statistics
Matches: 213, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
45 2 0.01
46 210 0.99
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:4060345 original size:92 final size:91
Alignment explanation
Indices: 4060188--4060460 Score: 438
Period size: 92 Copynumber: 3.0 Consensus size: 91
4060178 GTGTGCTCTC
** * * *
4060188 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAATGAGTAAGA
4060253 CCATAGTTGAAAGATACCATGGCAACG
65 CCATAGTTGAAAGATACCATGGCAACG
*
4060280 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATGAGTAAGA
*
4060345 CCATGGTTGAAAGATACCATGGCAACG
65 CCATAGTTGAAAGATACCATGGCAACG
4060372 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG-AAATGAGTAAGA
* *
4060437 CCATAGTTGAAAGACACTATGGCA
65 CCATAGTTGAAAGATACCATGGCA
4060461 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
91 2 0.01
92 165 0.98
93 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (91 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAGTAAGAC
CATAGTTGAAAGATACCATGGCAACG
Found at i:4062519 original size:4 final size:4
Alignment explanation
Indices: 4062510--4062588 Score: 52
Period size: 4 Copynumber: 19.2 Consensus size: 4
4062500 TCCCTTTTTA
* ** * **
4062510 TTTC TTTC TTTC TTTC CTTC TTTC TTTC TCAC GTTTGC TCTC TGTT- AGTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC T-TTC TTTC
* *
4062560 TTTC TATA TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
4062589 CACGTTTGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
3 1 0.02
4 49 0.89
5 4 0.07
6 1 0.02
ACGTcount: A:0.05, C:0.25, G:0.05, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:4062625 original size:14 final size:14
Alignment explanation
Indices: 4062606--4062636 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4062596 GCTCTCTTTC
4062606 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
4062620 TATTCTTTATTCAT
1 TATTCTTTACTCAT
4062634 TAT
1 TAT
4062637 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:4063270 original size:16 final size:17
Alignment explanation
Indices: 4063249--4063281 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4063239 ATGATGGAGC
4063249 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4063265 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4063282 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:4070655 original size:2 final size:2
Alignment explanation
Indices: 4070650--4070679 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4070640 TCCTTTTTTA
4070650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4070680 TAATCACCTA
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):
AT
Found at i:4070760 original size:30 final size:30
Alignment explanation
Indices: 4070724--4070783 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4070714 ATGCATGCAT
4070724 GCATATGAAATTGTTACGGCTCCATGCCGA
1 GCATATGAAATTGTTACGGCTCCATGCCGA
4070754 GCATATGAAATTGTTACGGCTCCATGCCGA
1 GCATATGAAATTGTTACGGCTCCATGCCGA
4070784 ACCCATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (30 bp):
GCATATGAAATTGTTACGGCTCCATGCCGA
Found at i:4077595 original size:17 final size:19
Alignment explanation
Indices: 4077559--4077596 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
4077549 TCTTAACAAT
*
4077559 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTCTAA
4077578 AATTC-AAAT-ATTTCTAA
1 AATTCAAAATAATTTCTAA
4077595 AA
1 AA
4077597 ATTCCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATAATTTCTAA
Found at i:4077677 original size:40 final size:41
Alignment explanation
Indices: 4077619--4077697 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
4077609 ATATTTTTAA
*
4077619 AATATATATAAAAATTAAATATTCTAAAA-AAAATCTAATG
1 AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
* *
4077659 AATATATA-AAAAAGTTAAAAATTTTAAAAGAAATTCTAA
1 AATATATATAAAAA-TTAAAAATTCTAAAAGAAAATCTAA
4077698 AGTAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 5 0.15
40 21 0.62
41 8 0.24
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (41 bp):
AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
Found at i:4081583 original size:2 final size:2
Alignment explanation
Indices: 4081563--4081607 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
4081553 TAATGAAATT
*
4081563 TA TA TG TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4081605 TA T
1 TA T
4081608 TCCAGGAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4081635 original size:3 final size:3
Alignment explanation
Indices: 4081629--4081660 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4081619 AAAAAGGAAA
4081629 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4081661 GAAGGAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4088278 original size:64 final size:66
Alignment explanation
Indices: 4088174--4088305 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 66
4088164 TCCACGATGG
4088174 AACAGGAAAAAAATGGATGACACCCATTCTTGATTACAATGTTC-TTTAAGGATAATTCGACAAA
1 AACAGGAAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAA
4088238 C
66 C
*
4088239 AACAGG-AAAAAAT-GATTGACACCCATTCTTGATTGCAATGTTCTTTTAAGGATAATTCGACAA
1 AACAGGAAAAAAATGGA-TGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAA
4088302 AC
65 AC
4088304 AA
1 AA
4088306 GGAGGAAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
63 2 0.03
64 33 0.52
65 29 0.45
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (66 bp):
AACAGGAAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAA
C
Found at i:4089928 original size:46 final size:46
Alignment explanation
Indices: 4089875--4089989 Score: 169
Period size: 46 Copynumber: 2.5 Consensus size: 46
4089865 GACGGTTTGG
* *
4089875 CTCGAATTATTTATTTAAATTAATCTATAAATTTAA-TCTGGATTGA
1 CTCGAATTATTTATTTAAATTAATCTATAAACTTAATTC-AGATTGA
* * *
4089921 CTCGAATTATTTACTTAAACTAATCTATAAACTTAATTCAGTTTGA
1 CTCGAATTATTTATTTAAATTAATCTATAAACTTAATTCAGATTGA
4089967 CTCGAATTATTTATTTAAATTAA
1 CTCGAATTATTTATTTAAATTAA
4089990 CCGTTGAGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 59 0.97
47 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (46 bp):
CTCGAATTATTTATTTAAATTAATCTATAAACTTAATTCAGATTGA
Found at i:4091588 original size:16 final size:16
Alignment explanation
Indices: 4091567--4091602 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4091557 TTATATATGG
* *
4091567 ATTTTACTTTTATTTT
1 ATTTTACCTATATTTT
4091583 ATTTTACCTATATTTT
1 ATTTTACCTATATTTT
4091599 ATTT
1 ATTT
4091603 AAATAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTACCTATATTTT
Found at i:4092945 original size:18 final size:18
Alignment explanation
Indices: 4092922--4092957 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4092912 TCAAGACTTA
* *
4092922 TAATTTGGTTGATTCGGT
1 TAATTTGGATAATTCGGT
4092940 TAATTTGGATAATTCGGT
1 TAATTTGGATAATTCGGT
4092958 CAAATGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (18 bp):
TAATTTGGATAATTCGGT
Found at i:4094725 original size:11 final size:11
Alignment explanation
Indices: 4094709--4094740 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
4094699 TAGGATTATA
4094709 TTTTAATTTTT
1 TTTTAATTTTT
4094720 TTTTAA-TTTT
1 TTTTAATTTTT
4094730 TTTTAATTTTT
1 TTTTAATTTTT
4094741 ATCTAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:4096760 original size:27 final size:28
Alignment explanation
Indices: 4096695--4096763 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
4096685 AATGAGATTG
*
4096695 GCACTAAGTGTGCGAGTTTAATTGTATA
1 GCACTAAGTGTGCGAGTTGAATTGTATA
*
4096723 GCACTAAGTGTGCGAGTTGACTAT-TA-A
1 GCACTAAGTGTGCGAGTTGAAT-TGTATA
4096750 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4096764 GACTTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 15 0.39
28 22 0.58
29 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTGAATTGTATA
Found at i:4096772 original size:27 final size:27
Alignment explanation
Indices: 4096695--4096773 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
4096685 AATGAGATTG
* * *
4096695 GCACTAAGTGTGCGAGTTTAAT-TGTATA
1 GCACTAAGTGTGCGACTTGACTAT-TA-A
*
4096723 GCACTAAGTGTGCGAGTTGACTATTAA
1 GCACTAAGTGTGCGACTTGACTATTAA
4096750 GCACTAAGTGTGCGGACTT-ACTAT
1 GCACTAAGTGTGC-GACTTGACTAT
4096774 ATATTTTCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 19 0.41
28 26 0.57
29 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTGACTATTAA
Found at i:4104494 original size:27 final size:28
Alignment explanation
Indices: 4104429--4104497 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
4104419 AATGAGATTG
*
4104429 GCACTAAGTGTGCGAGTTTAATTGTATA
1 GCACTAAGTGTGCGAGTTGAATTGTATA
*
4104457 GCACTAAGTGTGCGAGTTGACTAT-TA-A
1 GCACTAAGTGTGCGAGTTGAAT-TGTATA
4104484 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4104498 GACTTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 15 0.39
28 22 0.58
29 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTGAATTGTATA
Found at i:4104506 original size:27 final size:27
Alignment explanation
Indices: 4104429--4104507 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
4104419 AATGAGATTG
* * *
4104429 GCACTAAGTGTGCGAGTTTAAT-TGTATA
1 GCACTAAGTGTGCGACTTGACTAT-TA-A
*
4104457 GCACTAAGTGTGCGAGTTGACTATTAA
1 GCACTAAGTGTGCGACTTGACTATTAA
4104484 GCACTAAGTGTGCGGACTT-ACTAT
1 GCACTAAGTGTGC-GACTTGACTAT
4104508 ATATTTTCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 19 0.41
28 26 0.57
29 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTGACTATTAA
Found at i:4108485 original size:20 final size:20
Alignment explanation
Indices: 4108457--4108494 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4108447 TTTAATTAAT
*
4108457 TTAGCTTAATTAACTTAAAC
1 TTAGCTTAATTAAATTAAAC
*
4108477 TTAGTTTAATTAAATTAA
1 TTAGCTTAATTAAATTAA
4108495 GCTAACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAGCTTAATTAAATTAAAC
Found at i:4114521 original size:12 final size:12
Alignment explanation
Indices: 4114504--4114538 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4114494 GAAAAGAAGC
*
4114504 TATATATATAGA
1 TATATATATACA
*
4114516 TATATATACACA
1 TATATATATACA
4114528 TATATATATAC
1 TATATATATAC
4114539 TGTTGGATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (12 bp):
TATATATATACA
Found at i:4116971 original size:2 final size:2
Alignment explanation
Indices: 4116964--4116994 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4116954 ACATGCGTAA
4116964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4116995 ATCATATTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4117970 original size:107 final size:108
Alignment explanation
Indices: 4117859--4118074 Score: 398
Period size: 107 Copynumber: 2.0 Consensus size: 108
4117849 AAAAAAAAAA
*
4117859 ATTAGTTTAACAAAATAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
*
4117924 ACTTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
*
4117966 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
4118031 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
4118074 A
1 A
4118075 CGTGTTTTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 92 0.88
108 13 0.12
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:4128710 original size:16 final size:16
Alignment explanation
Indices: 4128680--4128727 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
4128670 GAAAATTAAT
4128680 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
4128695 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
4128712 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
4128727 A
1 A
4128728 CTTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:4128726 original size:11 final size:11
Alignment explanation
Indices: 4128671--4128741 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
4128661 ATAGCTTAAG
*
4128671 AAAATTAATAT
1 AAAATTAAAAT
4128682 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
4128694 AATAA-T-AATT
1 AA-AATTAAAAT
*
4128704 AAAAAT-AAAT
1 AAAATTAAAAT
4128714 AAAATTAAAAT
1 AAAATTAAAAT
*
4128725 AAACTTAAAAT
1 AAAATTAAAAT
*
4128736 ATAATT
1 AAAATT
4128742 TCTTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:4132376 original size:21 final size:21
Alignment explanation
Indices: 4132352--4132429 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 21
4132342 TCAGTATACT
*
4132352 ACACATAAAGTGCCTAAAATG
1 ACACATAAAGTGCCTAAAACG
* * *
4132373 ACAC--GAGGTGCCTAATACG
1 ACACATAAAGTGCCTAAAACG
** *
4132392 ACACACGAGGTGCCTGAAATACG
1 ACACATAAAGTGCCT-AAA-ACG
4132415 ACACATAAAGTGCCT
1 ACACATAAAGTGCCT
4132430 GATCGATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 15 0.33
21 13 0.29
22 2 0.04
23 15 0.33
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (21 bp):
ACACATAAAGTGCCTAAAACG
Found at i:4132385 original size:19 final size:20
Alignment explanation
Indices: 4132361--4132411 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
4132351 TACACATAAA
4132361 GTGCCTAAAATG-ACACGAG
1 GTGCCTAAAATGAACACGAG
* *
4132380 GTGCCTAATACGACACACGAG
1 GTGCCTAAAATGA-ACACGAG
*
4132401 GTGCCTGAAAT
1 GTGCCTAAAAT
4132412 ACGACACATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
21 15 0.60
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (20 bp):
GTGCCTAAAATGAACACGAG
Found at i:4132416 original size:23 final size:21
Alignment explanation
Indices: 4132373--4132419 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 21
4132363 GCCTAAAATG
4132373 ACACGAGGTGCCTAATACGAC
1 ACACGAGGTGCCTAATACGAC
4132394 ACACGAGGTGCCTGAAATACGAC
1 ACACGAGGTGCCT--AATACGAC
4132417 ACA
1 ACA
4132420 TAAAGTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.54
23 11 0.46
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (21 bp):
ACACGAGGTGCCTAATACGAC
Found at i:4132431 original size:23 final size:22
Alignment explanation
Indices: 4132347--4132429 Score: 66
Period size: 23 Copynumber: 3.9 Consensus size: 22
4132337 CCTGATCAGT
*
4132347 ATACTACACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
* * *
4132369 A-ATGACAC--GAGGTGCCT-A
1 ATACGACACATAAAGTGCCTAA
** *
4132387 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCT-AA
4132410 ATACGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
4132430 GATCGATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.04
19 13 0.27
21 14 0.29
22 1 0.02
23 18 0.38
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAA
Found at i:4132622 original size:13 final size:13
Alignment explanation
Indices: 4132604--4132648 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
4132594 CAATTCATAC
4132604 AATTATTCACATT
1 AATTATTCACATT
4132617 AATTA-TCAC---
1 AATTATTCACATT
4132626 AATTATTTCACATT
1 AATTA-TTCACATT
4132640 AATTATTCA
1 AATTATTCA
4132649 ATTCAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
9 5 0.19
11 4 0.15
12 4 0.15
13 9 0.33
14 5 0.19
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATTCACATT
Found at i:4132627 original size:22 final size:23
Alignment explanation
Indices: 4132602--4132645 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4132592 CACAATTCAT
4132602 ACAATTA-TTCACATTAATTATC
1 ACAATTATTTCACATTAATTATC
4132624 ACAATTATTTCACATTAATTAT
1 ACAATTATTTCACATTAATTAT
4132646 TCAATTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (23 bp):
ACAATTATTTCACATTAATTATC
Found at i:4132861 original size:15 final size:16
Alignment explanation
Indices: 4132836--4132867 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4132826 TCATATATAT
4132836 TATATAATTCAATAAA
1 TATATAATTCAATAAA
4132852 TATA-AATTCAATAAA
1 TATATAATTCAATAAA
4132867 T
1 T
4132868 TCATCGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATAATTCAATAAA
Found at i:4143928 original size:16 final size:16
Alignment explanation
Indices: 4143898--4143945 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
4143888 GAAAATTAAT
4143898 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
4143913 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
4143930 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
4143945 A
1 A
4143946 CTTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:4143944 original size:11 final size:11
Alignment explanation
Indices: 4143889--4143959 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
4143879 ATAGCTTAAG
*
4143889 AAAATTAATAT
1 AAAATTAAAAT
4143900 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
4143912 AATAA-T-AATT
1 AA-AATTAAAAT
*
4143922 AAAAAT-AAAT
1 AAAATTAAAAT
4143932 AAAATTAAAAT
1 AAAATTAAAAT
*
4143943 AAACTTAAAAT
1 AAAATTAAAAT
*
4143954 ATAATT
1 AAAATT
4143960 TCTTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:4146593 original size:2 final size:2
Alignment explanation
Indices: 4146586--4146621 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4146576 AATTATTTTA
4146586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4146622 TTGTACATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4159405 original size:82 final size:82
Alignment explanation
Indices: 4159317--4159500 Score: 230
Period size: 82 Copynumber: 2.2 Consensus size: 82
4159307 GGGCCTTGGT
*
4159317 CCCTAAAAATAAAAA-ATTTAATTTAATCCTCTTATAAATAGAAAATTTATAAA-TATATATATA
1 CCCTAAAAATAAAAATATTTAATTTAATCCTCTTATAAATA-AAAAATTATAAATTA-ATATATA
* * ** *
4159380 GTGAAATTGTACTTTAACC
64 ATAAAATTACAATTTAACC
* * * *
4159399 TCCT-AAAATAAAAATTTTTTAATTTAGTCTTCTTATAAATAAAAAATTATAAATTAATATATAA
1 CCCTAAAAATAAAAA-TATTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATAA
4159463 TAAAATTACAATTTAACC
65 TAAAATTACAATTTAACC
4159481 CCCTAAAAATAAAAATATTT
1 CCCTAAAAATAAAAATATTT
4159501 TTGTTTAATC
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
81 10 0.12
82 42 0.49
83 34 0.40
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (82 bp):
CCCTAAAAATAAAAATATTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATAAT
AAAATTACAATTTAACC
Found at i:4159433 original size:83 final size:84
Alignment explanation
Indices: 4159317--4159538 Score: 235
Period size: 83 Copynumber: 2.7 Consensus size: 84
4159307 GGGCCTTGGT
*
4159317 CCCTAAAAATAAAAA-A--TTTAATTTAATCCTCTTATAAATAGAAAATTTATAAA-TATATATA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATA-AAAAATTATAAATTA-ATATA
* * ** *
4159378 TAGTGAAATTGTACTTTAACC
64 TAATAAAATTACAATTTAACC
* * *
4159399 TCCT-AAAATAAAAAT-TTTTTAATTTAGTCTTCTTATAAATAAAAAATTATAAATTAATATATA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATA
4159462 ATAAAATTACAATTTAACC
66 ATAAAATTACAATTTAACC
* * **
4159481 CCCTAAAAATAAAAATATTTTT-GTTTAATCCT-TTAAAAAATGATGAAATTATAAATTA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTT-ATAAAT-AAAAAATTATAAATTA
4159539 TACAAAATAA
Statistics
Matches: 116, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
81 10 0.09
82 40 0.34
83 47 0.41
84 19 0.16
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (84 bp):
CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATA
ATAAAATTACAATTTAACC
Found at i:4178772 original size:35 final size:35
Alignment explanation
Indices: 4178707--4178872 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
4178697 TCCTCATTGA
** *
4178707 AATACCATACCTACATTT-TTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
4178741 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
4178781 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
4178816 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
4178851 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
4178873 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
34 17 0.14
35 71 0.60
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:4178831 original size:75 final size:72
Alignment explanation
Indices: 4178702--4178874 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 72
4178692 GGTTTTCCTC
* * * **
4178702 ATTGAAATACCATACCTACATTTTTA-ACTCGGTATGGGAAATGCCATACCTACATTTCTTAACT
1 ATTGAAATACCATACCTACA-TTTCACACTCAGTATGGGAAATACCATACCTACATTTCACAACT
4178766 CAGTATGG
65 CAGTATGG
4178774 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACA-CTCAGTATGGGA-AATACCATACCTACATTTCACA
4178838 ACTCAGTATGG
62 ACTCAGTATGG
4178849 A-TG--ATACCATACCTACATTTCACACT
1 ATTGAAATACCATACCTACATTTCACACT
4178875 TTGCCATGGA
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
69 2 0.02
70 21 0.23
72 1 0.01
73 10 0.11
74 19 0.21
75 38 0.42
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (72 bp):
ATTGAAATACCATACCTACATTTCACACTCAGTATGGGAAATACCATACCTACATTTCACAACTC
AGTATGG
Found at i:4186260 original size:35 final size:35
Alignment explanation
Indices: 4186193--4186360 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
4186183 TCCTCATTGA
*** *
4186193 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
4186229 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
4186269 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
4186304 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
4186339 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
4186361 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:4186319 original size:75 final size:73
Alignment explanation
Indices: 4186188--4186360 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
4186178 GGTTTTCCTC
*** * * **
4186188 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
4186253 TCAGTATGG
65 TCAGTATGG
*
4186262 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
4186326 ACTCAGTATGG
63 ACTCAGTATGG
4186337 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
4186361 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:4194762 original size:20 final size:21
Alignment explanation
Indices: 4194731--4194770 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4194721 TATTCTTTTA
4194731 AAAATCTAATTTATTTAATTT
1 AAAATCTAATTTATTTAATTT
*
4194752 AAAAT-TAATTTTTTTAATT
1 AAAATCTAATTTATTTAATT
4194771 GAATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATCTAATTTATTTAATTT
Found at i:4196983 original size:44 final size:44
Alignment explanation
Indices: 4196935--4197018 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
4196925 GTAGTAATCA
*
4196935 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACCGTCCATCTAATT
4196979 TTTTATCCTTGTGTGGTTTAGATCTAAGAACCGTCCATCT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACCGTCCATCT
4197019 GGTTTTGCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (44 bp):
TTTTATCCTTGTGTGGTTTAGATCTAAGAACCGTCCATCTAATT
Done.