Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 101 of 349
Found at i:31502470 original size:28 final size:27
Alignment explanation
Indices: 31502434--31502487 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
31502424 AATTCAAAAA
* *
31502434 AAAATTATAAAATATTATAAAAGTCATG
1 AAAAGTATAAAAAATT-TAAAAGTCATG
*
31502462 AAAAGTATAAAAAATTTAAAATTCAT
1 AAAAGTATAAAAAATTTAAAAGTCAT
31502488 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAGTATAAAAAATTTAAAAGTCATG
Found at i:31502709 original size:18 final size:19
Alignment explanation
Indices: 31502672--31502712 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31502662 ATTTAGAATC
31502672 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
31502691 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
31502709 AAAA
1 AAAA
31502713 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:31502714 original size:31 final size:31
Alignment explanation
Indices: 31502638--31502711 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
31502628 TCAAGTTATC
*
31502638 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
31502670 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
31502700 TTAAATATAAAA
1 TTAAATATAAAA
31502712 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:31505990 original size:37 final size:37
Alignment explanation
Indices: 31505940--31506046 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
31505930 CTATGCAGCA
31505940 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
* *
31505977 GATGCACGGGGCGAAGACGATGGAGG-GAATGAGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAG-ATGGGTTGC
* *
31506014 GATGCACGGGGAGAAGGCGACGGAGGAGATGGG
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGG
31506047 ATTTTTTGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 60 0.97
38 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.50, T:0.11
Consensus pattern (37 bp):
GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
Found at i:31507043 original size:14 final size:14
Alignment explanation
Indices: 31507017--31507136 Score: 71
Period size: 14 Copynumber: 8.4 Consensus size: 14
31507007 AACCCCTATC
*
31507017 CCATAAACATTAAA
1 CCATAAACCTTAAA
*
31507031 CCCTAAACCTT-AA
1 CCATAAACCTTAAA
* **
31507044 CCATTAACCCCAAA
1 CCATAAACCTTAAA
* *
31507058 CCCTTACACCTTAAA
1 -CCATAAACCTTAAA
* * *
31507073 CTAGTTAACTCCTAAA
1 CCA-TAAAC-CTTAAA
* *
31507089 CCTTAAACCCTAAA
1 CCATAAACCTTAAA
* *
31507103 CCATATATCTTAAA
1 CCATAAACCTTAAA
31507117 CCATAAACCTTAAA
1 CCATAAACCTTAAA
*
31507131 CTATAA
1 CCATAA
31507137 TGATAATTAA
Statistics
Matches: 76, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
13 9 0.12
14 45 0.59
15 16 0.21
16 6 0.08
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.25
Consensus pattern (14 bp):
CCATAAACCTTAAA
Found at i:31507048 original size:21 final size:23
Alignment explanation
Indices: 31507024--31507073 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
31507014 ATCCCATAAA
*
31507024 CATTAAACCCTAAA-CCTTA-AC
1 CATTAAACCCCAAACCCTTACAC
31507045 CATT-AACCCCAAACCCTTACAC
1 CATTAAACCCCAAACCCTTACAC
31507067 C-TTAAAC
1 CATTAAAC
31507074 TAGTTAACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.32
21 11 0.44
22 6 0.24
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (23 bp):
CATTAAACCCCAAACCCTTACAC
Found at i:31513572 original size:24 final size:24
Alignment explanation
Indices: 31513517--31513588 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 24
31513507 GAGTCATGGT
*
31513517 CGGTAAGCTCTTACTGAGCTGATAAA
1 CGGTAAGCTC-TATTGAGCTGA-AAA
*
31513543 CAGTAAGCTCTATTGAGCTGAAAA
1 CGGTAAGCTCTATTGAGCTGAAAA
*
31513567 CGGTAAGCTTTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
31513589 CAGTAAGCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 23 0.55
25 10 0.24
26 9 0.21
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (24 bp):
CGGTAAGCTCTATTGAGCTGAAAA
Found at i:31513601 original size:24 final size:24
Alignment explanation
Indices: 31513519--31513647 Score: 99
Period size: 23 Copynumber: 5.5 Consensus size: 24
31513509 GTCATGGTCG
*
31513519 GTAAGCTCTTACTGAGCTGATAAACA
1 GTAAGCTCTTATTGAGCTG--AAACA
*
31513545 GTAAGCTC-TATTGAGCTGAAAACG
1 GTAAGCTCTTATTGAGCTG-AAACA
31513569 GTAAGCT-TTATTGAGCTG-AACA
1 GTAAGCTCTTATTGAGCTGAAACA
** ***
31513591 GTAAGCTCTT-TCAAGCTGAATTG
1 GTAAGCTCTTATTGAGCTGAAACA
* *
31513614 GTAAGCTAC--AATGAGCTGAAATA
1 GTAAGCT-CTTATTGAGCTGAAACA
31513637 GTAAGCTCTTA
1 GTAAGCTCTTA
31513648 CGAGATATGG
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
22 17 0.21
23 25 0.30
24 23 0.28
25 9 0.11
26 8 0.10
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (24 bp):
GTAAGCTCTTATTGAGCTGAAACA
Found at i:31513608 original size:46 final size:45
Alignment explanation
Indices: 31513517--31513646 Score: 127
Period size: 46 Copynumber: 2.8 Consensus size: 45
31513507 GAGTCATGGT
* *
31513517 CGGTAAGCTCTTACTGAGCTGATAAACAGTAAGCTCTATTGAGCTGAAAA
1 CGGTAAGCT-TTAATGAGCTG--AAACAGTAAGCTCT-TTAAGCTG-AAA
* *
31513567 CGGTAAGCTTTATTGAGCTG-AACAGTAAGCTCTTTCAAGCTGAAT
1 CGGTAAGCTTTAATGAGCTGAAACAGTAAGCTCTTT-AAGCTGAAA
* ** *
31513612 TGGTAAGCTACAATGAGCTGAAATAGTAAGCTCTT
1 CGGTAAGCTTTAATGAGCTGAAACAGTAAGCTCTT
31513647 ACGAGATATG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
45 20 0.29
46 31 0.44
49 10 0.14
50 9 0.13
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
CGGTAAGCTTTAATGAGCTGAAACAGTAAGCTCTTTAAGCTGAAA
Found at i:31516431 original size:47 final size:47
Alignment explanation
Indices: 31516364--31516468 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
31516354 CCCTTCGGGA
* * *
31516364 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATAAACTTTCACATCCATCACATTGGCCATTCGGC
31516411 CTTATCACATATATAAACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATAAACTTTCACATCCATCACATTGGCCATTCGGC
31516458 CTTATCACATA
1 CTTATCACATA
31516469 ATTAATACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATAAACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:31524406 original size:21 final size:20
Alignment explanation
Indices: 31524369--31524407 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31524359 ATTTAATTAC
**
31524369 TTTTTATTTAAGTAAATAGA
1 TTTTTATTTAACAAAATAGA
31524389 TTTTTATTATAACAAAATA
1 TTTTTATT-TAACAAAATA
31524408 TTAAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTTATTTAACAAAATAGA
Found at i:31524604 original size:16 final size:17
Alignment explanation
Indices: 31524563--31524604 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31524553 AAGTAAATAA
* *
31524563 AAGAAAGAAAGAAACAG
1 AAGAAGGAACGAAACAG
*
31524580 AATAAGGAACGAAACAG
1 AAGAAGGAACGAAACAG
31524597 -AGAAGGAA
1 AAGAAGGAA
31524605 GGAAGGAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.64, C:0.07, G:0.26, T:0.02
Consensus pattern (17 bp):
AAGAAGGAACGAAACAG
Found at i:31528788 original size:23 final size:22
Alignment explanation
Indices: 31528711--31528822 Score: 91
Period size: 23 Copynumber: 4.8 Consensus size: 22
31528701 GTCATGGTCG
31528711 GTAAGCTCTTACTGAGCTGACAAACA
1 GTAAGCTCTT--TGAGCT-A-AAACA
* *
31528737 GTTAGCTCTATTGAGCT-GAACA
1 GTAAGCTCT-TTGAGCTAAAACA
**
31528759 GTAAGCTCTTTCGAGCTAAATTA
1 GTAAGCTCTTT-GAGCTAAAACA
**
31528782 GTAAGCTACAATGAGCTAAAACA
1 GTAAGCT-CTTTGAGCTAAAACA
31528805 GTAAGCTCTTATGAGCTA
1 GTAAGCTCTT-TGAGCTA
31528823 TGGTGAGTCC
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
21 2 0.03
22 18 0.26
23 32 0.46
24 2 0.03
25 6 0.09
26 8 0.12
27 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (22 bp):
GTAAGCTCTTTGAGCTAAAACA
Found at i:31530930 original size:15 final size:15
Alignment explanation
Indices: 31530906--31530937 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31530896 TATGTAATTT
31530906 AATAAATAAAAACAA
1 AATAAATAAAAACAA
*
31530921 AATAAGTAAAAACAA
1 AATAAATAAAAACAA
31530936 AA
1 AA
31530938 CCATTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12
Consensus pattern (15 bp):
AATAAATAAAAACAA
Found at i:31531743 original size:29 final size:29
Alignment explanation
Indices: 31531708--31531775 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
31531698 ACCGACAAAT
* **
31531708 GAAAAGGGATAGTTTTGGCTATCAAATAC
1 GAAAAGGGATAGCTTCAGCTATCAAATAC
* *
31531737 GAAAAGGGATAGCTTCAGCTATCAATTAT
1 GAAAAGGGATAGCTTCAGCTATCAAATAC
31531766 GAAAAGGGAT
1 GAAAAGGGAT
31531776 GATGACGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (29 bp):
GAAAAGGGATAGCTTCAGCTATCAAATAC
Found at i:31531789 original size:29 final size:30
Alignment explanation
Indices: 31531760--31531982 Score: 165
Period size: 30 Copynumber: 7.5 Consensus size: 30
31531750 TTCAGCTATC
31531760 AATTATGAAAAGGGATGATGACGACCATCA
1 AATTATGAAAAGGGATGATGACGACCATCA
* *
31531790 ACA--ATGAAAAGGGATGGTGACGACCAT-T
1 A-ATTATGAAAAGGGATGATGACGACCATCA
* * * * * *
31531818 GACTATGAAAAGGGATAGCT-TCGGCTATCA
1 AATTATGAAAAGGGAT-GATGACGACCATCA
*
31531848 AATTATGAAAAGGGATGGTGACGA-CATCGA
1 AATTATGAAAAGGGATGATGACGACCATC-A
* * * * *
31531878 AA-TATGAAAAAGGATAACT-TCGGCTATCA
1 AATTATGAAAAGGGATGA-TGACGACCATCA
*
31531907 AATTATGAAAAGGGAT-AGTGACGACCATCG
1 AATTATGAAAAGGGATGA-TGACGACCATCA
** * * *
31531937 AACAATGGAAAGAGATGGTGACGACCATCA
1 AATTATGAAAAGGGATGATGACGACCATCA
31531967 AATTATGAAAAGGGAT
1 AATTATGAAAAGGGAT
31531983 AGCTGCAGCT
Statistics
Matches: 145, Mismatches: 36, Indels: 24
0.71 0.18 0.12
Matches are distributed among these distances:
27 1 0.01
29 64 0.44
30 79 0.54
31 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (30 bp):
AATTATGAAAAGGGATGATGACGACCATCA
Found at i:31531869 original size:59 final size:60
Alignment explanation
Indices: 31531793--31532045 Score: 248
Period size: 59 Copynumber: 4.2 Consensus size: 60
31531783 ACCATCAACA
* * *
31531793 ATGAAAAGGGATGGTGACGACCATTG-ACTATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATAACTTCGGCTATCAAATT
*
31531852 ATGAAAAGGGATGGTGACGA-CATCGAAATATGAAAAAGGATAACTTCGGCTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATAACTTCGGCTATCAAATT
* * * ** * * *
31531911 ATGAAAAGGGATAGTGACGACCATCGAACAATG-GAAAGAGAT-GGTGACGACCATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAG-GATAACT-TCGGCTATCAAATT
* ** * * *
31531971 ATGAAAAGGGATAGCTG-C-AGCTGTTGAACTATGAAAAAGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGAT-GGTGACGA-CCATCGAACTATGAAAAAGGATAACTTCGGCTATCAAATT
**
31532031 ACAAAAAGGGATGGT
1 ATGAAAAGGGATGGT
31532046 TGACCCATTG
Statistics
Matches: 156, Mismatches: 30, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
58 4 0.03
59 77 0.49
60 68 0.44
61 7 0.04
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.22
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATAACTTCGGCTATCAAATT
Found at i:31549649 original size:49 final size:48
Alignment explanation
Indices: 31549577--31549752 Score: 199
Period size: 51 Copynumber: 3.5 Consensus size: 48
31549567 CTGATACGCA
* * *
31549577 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACAAACAAT-TGGTACACG
* * * *
31549626 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCCATTGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CAAA-CAATTG-GTACACG
** * *
31549677 TAGTAGGTTGCACTTAGTACTACACATGTGACTTAACAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGAC-AAACAAT-TGGTACACG
31549727 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
31549753 CGTGTACTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 29 0.28
50 36 0.34
51 40 0.38
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACAAACAATTGGTACACG
Found at i:31549750 original size:101 final size:100
Alignment explanation
Indices: 31549571--31549756 Score: 300
Period size: 101 Copynumber: 1.9 Consensus size: 100
31549561 AGCTATCTGA
*
31549571 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACGTAGTAGCCTG
1 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATACGGTACACGTAGTAGCCTG
31549636 CACTTAGTACTACACACGTGATCAAAGCCATTGAG
66 CACTTAGTACTACACACGTGATCAAAGCCATTGAG
** * * * *
31549671 TACGCATAGTAGGTTGCACTTAGTACTACACATGTGACTTAACAGTATGGTACACGTAGTAGCCT
1 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGAC-CAACAATACGGTACACGTAGTAGCCT
31549736 GCACTTAGTACTACACACGTG
65 GCACTTAGTACTACACACGTG
31549757 TACTCACAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 35 0.45
101 43 0.55
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (100 bp):
TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATACGGTACACGTAGTAGCCTG
CACTTAGTACTACACACGTGATCAAAGCCATTGAG
Found at i:31551908 original size:29 final size:29
Alignment explanation
Indices: 31551866--31551935 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
31551856 TCATCGAAAA
* * *
31551866 ATGAAAAGGTATAGTTTCGGTTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
31551895 ATGAAATGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
31551924 ATGAAAAGGGAT
1 ATGAAAAGGGAT
31551936 GGTGACGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:31551988 original size:30 final size:30
Alignment explanation
Indices: 31551924--31552114 Score: 192
Period size: 30 Copynumber: 6.4 Consensus size: 30
31551914 GCTATCGATT
* *
31551924 ATGAAAAGGGATGGTGACGACCAT-TAACA
1 ATGAAAAGGGATGGTGACGACCATCGAATA
*
31551953 ATGAAAAGGGATGGTGACGACCATCGGATA
1 ATGAAAAGGGATGGTGACGACCATCGAATA
*
31551983 ATGAAAAGGAATGGTGACGACCATCGAACT-
1 ATGAAAAGGGATGGTGACGACCATCGAA-TA
* * * * * *
31552013 ATGAAAAGGGATAAGT-TCGGCTATCAAATT
1 ATGAAAAGGGAT-GGTGACGACCATCGAATA
*
31552043 AT-AGAAAGGGATGGTGAAGACCATCGAATA
1 ATGA-AAAGGGATGGTGACGACCATCGAATA
* * * *
31552073 ATGGAAAGGGATGGTGACAACCATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAATA
31552103 ATGAAAAGGGAT
1 ATGAAAAGGGAT
31552115 AGCTCCGGCT
Statistics
Matches: 131, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
29 28 0.21
30 100 0.76
31 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACGACCATCGAATA
Found at i:31552051 original size:60 final size:57
Alignment explanation
Indices: 31551888--31552084 Score: 191
Period size: 60 Copynumber: 3.3 Consensus size: 57
31551878 AGTTTCGGTT
*
31551888 ATCGAATATGAAATGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAG-TTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
* * * * * * * *
31551946 AT-TAACAATGAAAAGGGATGGTGACGACCATCGGATAATGAAAAGGAATGGTGACGACC
1 ATCGAA-TATGAAAAGGGATAGT-TCGGCTATC-GATTATGAAAAGGGATGGTGACGACC
* *
31552005 ATCGAACTATGAAAAGGGATAAGTTCGGCTATCAAATTAT-AGAAAGGGATGGTGAAGACC
1 ATCGAA-TATGAAAAGGGAT-AGTTCGGCTATC-GATTATGA-AAAGGGATGGTGACGACC
*
31552065 ATCGAATAATGGAAAGGGAT
1 ATCGAAT-ATGAAAAGGGAT
31552085 GGTGACAACC
Statistics
Matches: 111, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
57 3 0.03
58 20 0.18
59 28 0.25
60 58 0.52
61 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (57 bp):
ATCGAATATGAAAAGGGATAGTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
Found at i:31552099 original size:60 final size:60
Alignment explanation
Indices: 31551921--31552114 Score: 216
Period size: 60 Copynumber: 3.2 Consensus size: 60
31551911 TCGGCTATCG
* * **
31551921 ATTATGAAAAGGGATGGTGACGACCAT-TAACAATGAAAAGGGATGGTGACGACCATCGG
1 ATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGGTGACGACCATCAA
* * * * * *
31551980 ATAATGAAAAGGAATGGTGACGACCATCGAACT-ATGAAAAGGGATAAGT-TCGGCTATCAA
1 ATTATGAAAAGGGATGGTGACGACCATCGAA-TAATGAAAAGGGAT-GGTGACGACCATCAA
* * *
31552040 ATTAT-AGAAAGGGATGGTGAAGACCATCGAATAATGGAAAGGGATGGTGACAACCATCAA
1 ATTATGA-AAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGGTGACGACCATCAA
31552100 ATTATGAAAAGGGAT
1 ATTATGAAAAGGGAT
31552115 AGCTCCGGCT
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
59 29 0.27
60 77 0.71
61 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.20
Consensus pattern (60 bp):
ATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGGTGACGACCATCAA
Found at i:31552124 original size:90 final size:90
Alignment explanation
Indices: 31551957--31552135 Score: 252
Period size: 90 Copynumber: 2.0 Consensus size: 90
31551947 TTAACAATGA
* * * *
31551957 AAAGGGATGGTGACGACCATCGGATAATGAAAAGGAATGGTGACGACCATCGAACTATGAAAAGG
1 AAAGGGATGGTGAAGACCATCGAATAATGAAAAGGAATGGTGACAACCATCAAACTATGAAAAGG
* *
31552022 GATAAGTTCGGCTATCAAATTATAG
66 GATAAGTCCGGCTATCAAACTATAG
* * *
31552047 AAAGGGATGGTGAAGACCATCGAATAATGGAAAGGGATGGTGACAACCATCAAATTATGAAAAGG
1 AAAGGGATGGTGAAGACCATCGAATAATGAAAAGGAATGGTGACAACCATCAAACTATGAAAAGG
*
31552112 GAT-AGCTCCGGCTGTCAAACTATA
66 GATAAG-TCCGGCTATCAAACTATA
31552136 AAAAAAGATA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 2 0.03
90 76 0.97
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (90 bp):
AAAGGGATGGTGAAGACCATCGAATAATGAAAAGGAATGGTGACAACCATCAAACTATGAAAAGG
GATAAGTCCGGCTATCAAACTATAG
Found at i:31554304 original size:29 final size:28
Alignment explanation
Indices: 31554244--31554321 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 28
31554234 AGCTTCAGCT
* * * *
31554244 ATCGATTATGTAAAAGGATGGTGATGAGC
1 ATCGAATATG-AAAAGGATAGTGACGACC
31554273 ATC-AATAATGAAAAGGGATAGTGACGACC
1 ATCGAAT-ATGAAAA-GGATAGTGACGACC
*
31554302 ATCGACTATGAAAAAGGATA
1 ATCGAATATG-AAAAGGATA
31554322 ACTTCGACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
28 6 0.15
29 28 0.70
30 6 0.15
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (28 bp):
ATCGAATATGAAAAGGATAGTGACGACC
Found at i:31554375 original size:60 final size:61
Alignment explanation
Indices: 31554283--31554441 Score: 205
Period size: 61 Copynumber: 2.6 Consensus size: 61
31554273 ATCAATAATG
* * *
31554283 AAAAGGGATAGTGACGACCATCG-ACTATGAAAAAGGATAACTTCGACTATAAAATTAT-A
1 AAAAAGGATAGTGATGACCATCGAACTATGAAAAGGGATAACTTCGACTATAAAATTATGA
* * ** *
31554342 AAAAAGGATAGTGATGTCCATCGAACTATGAAAAGGGATAGCTTCGGTTATTAAATTATGA
1 AAAAAGGATAGTGATGACCATCGAACTATGAAAAGGGATAACTTCGACTATAAAATTATGA
* * *
31554403 AAAAAGGATAGTGATGGCCATTGAACAATGAAAAGGGAT
1 AAAAAGGATAGTGATGACCATCGAACTATGAAAAGGGAT
31554442 GGTGATGACC
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 20 0.23
60 30 0.34
61 37 0.43
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (61 bp):
AAAAAGGATAGTGATGACCATCGAACTATGAAAAGGGATAACTTCGACTATAAAATTATGA
Found at i:31554382 original size:30 final size:31
Alignment explanation
Indices: 31554341--31554473 Score: 92
Period size: 30 Copynumber: 4.4 Consensus size: 31
31554331 ATAAAATTAT
* *
31554341 AAAAAAGGATAGTGATGTCCATCGAACTATG
1 AAAAAGGGATAGTGATGTCCATCAAACTATG
*** * * *
31554372 -AAAAGGGATAGCTTCGGT-TATTAAATTATG
1 AAAAAGGGATAG-TGATGTCCATCAAACTATG
* * ** *
31554402 AAAAAAGGATAGTGATGGCCATTGAACAATG
1 AAAAAGGGATAGTGATGTCCATCAAACTATG
* * *
31554433 -AAAAGGGATGGTGATGACCATCAAAATATG
1 AAAAAGGGATAGTGATGTCCATCAAACTATG
31554463 AAAAAGGGATA
1 AAAAAGGGATA
31554474 ATTTCAGCTA
Statistics
Matches: 73, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
30 43 0.59
31 30 0.41
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAAAGGGATAGTGATGTCCATCAAACTATG
Found at i:31554463 original size:61 final size:61
Alignment explanation
Indices: 31554283--31554473 Score: 167
Period size: 61 Copynumber: 3.2 Consensus size: 61
31554273 ATCAATAATG
* * * * * * *
31554283 AAAAGGGATAGTGACGACCATCG-ACTATGAAAAAGGATAACTTCGACTAT-AAAATTAT-A
1 AAAAAGGATAGTGATGGCCATCGAACAATGAAAAGGGATAGCTTCGACCATCAAAA-TATGA
* * *** * *
31554342 AAAAAGGATAGTGATGTCCATCGAACTATGAAAAGGGATAGCTTCGGTTATTAAATTATGA
1 AAAAAGGATAGTGATGGCCATCGAACAATGAAAAGGGATAGCTTCGACCATCAAAATATGA
* *
31554403 AAAAAGGATAGTGATGGCCATTGAACAATGAAAAGGGAT-GGTGAT-GACCATCAAAATATGA
1 AAAAAGGATAGTGATGGCCATCGAACAATGAAAAGGGATAGCT--TCGACCATCAAAATATGA
*
31554464 AAAAGGGATA
1 AAAAAGGATA
31554474 ATTTCAGCTA
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 20 0.18
60 28 0.26
61 60 0.55
62 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (61 bp):
AAAAAGGATAGTGATGGCCATCGAACAATGAAAAGGGATAGCTTCGACCATCAAAATATGA
Found at i:31554531 original size:30 final size:30
Alignment explanation
Indices: 31554464--31554532 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
31554454 CAAAATATGA
* *
31554464 AAAAGGGATAATTTCAGCTATCGAACTATG
1 AAAAGGGATAACTTCAGCTATCGAACTACG
* * * * *
31554494 AATAGGGATAACTTCAGTTGTTGAATTACG
1 AAAAGGGATAACTTCAGCTATCGAACTACG
31554524 AAAAGGGAT
1 AAAAGGGAT
31554533 GGGTCAACCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (30 bp):
AAAAGGGATAACTTCAGCTATCGAACTACG
Found at i:31556259 original size:18 final size:18
Alignment explanation
Indices: 31556218--31556259 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31556208 TCACTTTTTC
*
31556218 AATCATCCCTCATCCCTT
1 AATCATCCCTCATCCATT
*
31556236 ATTCATCCCTCA-CTCATT
1 AATCATCCCTCATC-CATT
31556254 AATCAT
1 AATCAT
31556260 TCTCTCCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (18 bp):
AATCATCCCTCATCCATT
Found at i:31562525 original size:28 final size:28
Alignment explanation
Indices: 31562469--31562598 Score: 113
Period size: 28 Copynumber: 4.7 Consensus size: 28
31562459 GGGGACAAAG
* *
31562469 CTGTAAAATCTAAAAAAAATAAGGTTAAAT
1 CTGTAAAATCT--AAAAAATAAGGGTAAAA
* *
31562499 TTGTAAAATCTAAAAAATAGGGGTAAAA
1 CTGTAAAATCTAAAAAATAAGGGTAAAA
* *
31562527 CTATAAAATCT-AAAAA-AAGGCT-AAA
1 CTGTAAAATCTAAAAAATAAGGGTAAAA
* * * *
31562552 CTATCAAATATGAAAAATAAGGGTAAAA
1 CTGTAAAATCTAAAAAATAAGGGTAAAA
* *
31562580 CTATAAAATCTGAAAAATA
1 CTGTAAAATCTAAAAAATA
31562599 GGGAACACAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
25 12 0.14
26 9 0.11
27 10 0.12
28 43 0.51
30 10 0.12
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (28 bp):
CTGTAAAATCTAAAAAATAAGGGTAAAA
Found at i:31562601 original size:27 final size:27
Alignment explanation
Indices: 31562502--31562601 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
31562492 GTTAAATTTG
*
31562502 TAAAATCTAAAAAATAGGGGTAAAACTA
1 TAAAATCTGAAAAATA-GGGTAAAACTA
* *
31562530 TAAAATCT-AAAAAAAGGCT-AAACTA
1 TAAAATCTGAAAAATAGGGTAAAACTA
* *
31562555 TCAAATATGAAAAATAAGGGTAAAACTA
1 TAAAATCTGAAAAAT-AGGGTAAAACTA
31562583 TAAAATCTGAAAAATAGGG
1 TAAAATCTGAAAAATAGGG
31562602 AACACATGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
25 12 0.20
26 8 0.13
27 14 0.23
28 27 0.44
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.21
Consensus pattern (27 bp):
TAAAATCTGAAAAATAGGGTAAAACTA
Found at i:31565975 original size:56 final size:56
Alignment explanation
Indices: 31565889--31566147 Score: 356
Period size: 56 Copynumber: 4.6 Consensus size: 56
31565879 ACCTGGAAGT
* * * *
31565889 ATATGTGACTTCGATACATGTGTGCGAGTAAGTCCACGTTTCATACGTTGGCATCG
1 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGCATCG
* * * *
31565945 ATATGTGACTCCGATATATGTGTGTGAGTAAGTCCACGTTTCATATGTTGGCATCG
1 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGCATCG
* *
31566001 ATATGTGACTCTGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGAATCG
1 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGCATCG
* * *
31566057 ATATGTGACTCTGATATATGTGTGCAAGTAAGACCACATTTTATACGTTGGCATCG
1 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGCATCG
* * * * *
31566113 ATATGTGATTTCGATATGTGTTTACGAGTAAGACC
1 ATATGTGACTCCGATATATGTGTGCGAGTAAGACC
31566148 CTGTTTGGGA
Statistics
Matches: 183, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 183 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (56 bp):
ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTCATACGTTGGCATCG
Found at i:31575506 original size:29 final size:29
Alignment explanation
Indices: 31575473--31575532 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
31575463 CACATATGTA
*
31575473 ATAAGAGTAATTAGAAGTTATTATTTACT
1 ATAAGAGTAATTACAAGTTATTATTTACT
31575502 ATAAGAGTAATTACAAGTTATTATTTACT
1 ATAAGAGTAATTACAAGTTATTATTTACT
31575531 AT
1 AT
31575533 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (29 bp):
ATAAGAGTAATTACAAGTTATTATTTACT
Found at i:31576992 original size:15 final size:15
Alignment explanation
Indices: 31576972--31577002 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31576962 GTCATGTAAG
31576972 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
31576987 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
31577002 T
1 T
31577003 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:31577192 original size:17 final size:17
Alignment explanation
Indices: 31577159--31577197 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
31577149 TAAGCTTTTG
31577159 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
31577176 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
31577193 ATTTT
1 ATTTT
31577198 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:31577963 original size:15 final size:15
Alignment explanation
Indices: 31577939--31577968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31577929 TGGAGATCGA
*
31577939 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
31577954 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
31577969 CAAGAAGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:31580027 original size:15 final size:15
Alignment explanation
Indices: 31580007--31580037 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31579997 GTCATGTAAG
31580007 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
31580022 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
31580037 T
1 T
31580038 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:31580227 original size:17 final size:17
Alignment explanation
Indices: 31580194--31580232 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
31580184 TAAGCTTTTG
31580194 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
31580211 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
31580228 ATTTT
1 ATTTT
31580233 CCACAGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:31581811 original size:30 final size:30
Alignment explanation
Indices: 31581735--31581813 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
31581725 AAGTTGTAAA
*
31581735 TTTAGTCCTTATACTTT--ATTTGATCAAT
1 TTTAGTCCTTATACTTTCAAATTGATCAAT
* * * *
31581763 TTTAGTCC-TGTGCTTTTCAAATTGGTCACT
1 TTTAGTCCTTATAC-TTTCAAATTGATCAAT
31581793 TTTAGTCCTTATACTTTCAAA
1 TTTAGTCCTTATACTTTCAAA
31581814 AATTAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
27 3 0.08
28 11 0.28
30 23 0.57
31 3 0.08
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTAGTCCTTATACTTTCAAATTGATCAAT
Found at i:31582770 original size:29 final size:29
Alignment explanation
Indices: 31582724--31582782 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
31582714 GCCATTTGAA
*
31582724 CATATTTGCTAAGTATTTATATCAAAATT
1 CATATTTGCTAAGCATTTATATCAAAATT
*
31582753 CATATTTGCTAAGCATTTATATCAACATT
1 CATATTTGCTAAGCATTTATATCAAAATT
31582782 C
1 C
31582783 TTTTGACAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (29 bp):
CATATTTGCTAAGCATTTATATCAAAATT
Found at i:31597734 original size:20 final size:20
Alignment explanation
Indices: 31597699--31597761 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
31597689 GATCTCCGAT
*
31597699 TTTC-TTTTCTTT-GTTTTCA
1 TTTCATTTT-TTTAGTTTTTA
31597718 TTTCATTTTTTTAGTTTCTTA
1 TTTCATTTTTTTAGTTT-TTA
* *
31597739 TTTTATTTTTTTATTTTTTA
1 TTTCATTTTTTTAGTTTTTA
31597759 TTT
1 TTT
31597762 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 7 0.18
20 14 0.37
21 17 0.45
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTCATTTTTTTAGTTTTTA
Found at i:31597752 original size:8 final size:8
Alignment explanation
Indices: 31597739--31597776 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
31597729 TAGTTTCTTA
31597739 TTTTATTT
1 TTTTATTT
31597747 TTTTATTT
1 TTTTATTT
*
31597755 TTTATTTTT
1 TTT-TATTT
31597764 TTTTATTT
1 TTTTATTT
31597772 TTTTA
1 TTTTA
31597777 CTAAAAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:31598287 original size:12 final size:12
Alignment explanation
Indices: 31598270--31598294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31598260 GTTCATGGTG
31598270 TCGTGTCCTAAC
1 TCGTGTCCTAAC
31598282 TCGTGTCCTAAC
1 TCGTGTCCTAAC
31598294 T
1 T
31598295 TACGGGATGT
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGTGTCCTAAC
Found at i:31598727 original size:16 final size:16
Alignment explanation
Indices: 31598703--31598734 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31598693 TAATTAAAAA
*
31598703 TTTATAAAATATATAT
1 TTTAAAAAATATATAT
31598719 TTTAAAAAATATATAT
1 TTTAAAAAATATATAT
31598735 ATACATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAAAATATATAT
Found at i:31599483 original size:13 final size:13
Alignment explanation
Indices: 31599423--31599483 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
31599413 TAAACCAAAT
31599423 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
31599436 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
31599449 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
31599462 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
31599475 TTTTTAAAA
1 TTTTCAAAA
31599484 ACATTGCCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:31601976 original size:20 final size:20
Alignment explanation
Indices: 31601938--31601976 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31601928 GCCGACGGCT
* *
31601938 GGTGGCCGGAGTGGACGGAC
1 GGTGGCCCGACTGGACGGAC
*
31601958 GGTGGCCCGACTGGCCGGA
1 GGTGGCCCGACTGGACGGA
31601977 GAAAAGGAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.51, T:0.10
Consensus pattern (20 bp):
GGTGGCCCGACTGGACGGAC
Found at i:31602610 original size:51 final size:50
Alignment explanation
Indices: 31602491--31602880 Score: 241
Period size: 51 Copynumber: 7.6 Consensus size: 50
31602481 TTTTAATATC
* *
31602491 AAACTGTTTCATATA-T-TTTACTTATTATAATTTTTTTATATTA-TTTATTT
1 AAACTGTTTTATATATTATTTA-TT-TTA-AATTTTTATATATTAGTTTATTT
* * * *
31602541 GAAA-TAGTGTTATATATTATTTATTTTAGACTTTTTACATATTAGTTCATTT
1 -AAACT-GTTTTATATATTATTTATTTTA-AATTTTTATATATTAGTTTATTT
* * * *
31602593 AAACTGTTTTATGTATTATATATTTAAAATTACTTTATAAATTA-TTTATTT
1 AAACTGTTTTATATATTATTTATTTTAAATT--TTTATATATTAGTTTATTT
* * *
31602644 CAAATTGTTTTATGCT-TTATTTATTTTAATTTTTTTATATATT-GTTTATTTT
1 -AAACTGTTTTAT-ATATTATTTATTTTAA-ATTTTTATATATTAGTTTA-TTT
*
31602696 AAACT-TTTTCATAAATTATTTATTTTAAATTGTTT-TATTATTA-TTTA-TT
1 AAACTGTTTT-ATATATTATTTATTTTAAATT-TTTATA-TATTAGTTTATTT
** * * **
31602745 -ATGTATTTTAAACTATTATCCATTTTAAATTTTTTATATATTA-TTTATTTT
1 AAACTGTTTTATA-TATTATTTATTTTAAA-TTTTTATATATTAGTTTA-TTT
* * * * *
31602796 AAACTGTTATATATATTGTTTATTTTGAATTTTATATATATATATTATTTTTTT
1 AAACTGTTTTATATATTATTTATTTTAAATTTT-TATATAT-TA--GTTTATTT
* *
31602850 AAACCG-TTTGTATATTATTTATTTTAAATTT
1 AAACTGTTTTATATATTATTTATTTTAAATTT
31602881 CTTTTTACAT
Statistics
Matches: 264, Mismatches: 46, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
48 4 0.02
49 31 0.12
50 20 0.08
51 117 0.44
52 53 0.20
53 28 0.11
54 8 0.03
55 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (50 bp):
AAACTGTTTTATATATTATTTATTTTAAATTTTTATATATTAGTTTATTT
Found at i:31602640 original size:103 final size:102
Alignment explanation
Indices: 31602525--31602744 Score: 234
Period size: 103 Copynumber: 2.2 Consensus size: 102
31602515 TTATAATTTT
*
31602525 TTTAT-ATTATTTATTTGAAATAGTGTTAT-ATATTATTTATTTTAGA-CTTTTTACATATTAGT
1 TTTATAATTATTTATTTCAAATAGTGTTATGAT-TTATTTATTTTA-ATCTTTTTACATATT-GT
**
31602587 TCA-TTTAAACTGTTTT-ATGTATTATATATTTAAAATTAC
63 TCATTTTAAACT-TTTTCATAAATTATATATTTAAAATTAC
* * * * * *
31602626 TTTATAAATTATTTATTTCAAATTGTTTTATGCTTTATTTATTTTAATTTTTTTATATATTGTTT
1 TTTAT-AATTATTTATTTCAAATAGTGTTATGATTTATTTATTTTAATCTTTTTACATATTGTTC
* * **
31602691 ATTTTAAACTTTTTCATAAATTATTTATTTTAAATTGT
65 ATTTTAAACTTTTTCATAAATTATATATTTAAAATTAC
*
31602729 TTTATTATTATTTATT
1 TTTATAATTATTTATT
31602745 ATGTATTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
101 5 0.05
102 19 0.19
103 74 0.75
104 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (102 bp):
TTTATAATTATTTATTTCAAATAGTGTTATGATTTATTTATTTTAATCTTTTTACATATTGTTCA
TTTTAAACTTTTTCATAAATTATATATTTAAAATTAC
Found at i:31602655 original size:26 final size:26
Alignment explanation
Indices: 31602502--31603048 Score: 323
Period size: 26 Copynumber: 21.5 Consensus size: 26
31602492 AACTGTTTCA
* * *
31602502 TATATTTTACTTATTAT-AATT-TTT
1 TATATATTATTTATTTTAAATTGTTT
* * *
31602526 T-TATATTATTTATTTGAAATAGTGT
1 TATATATTATTTATTTTAAATTGTTT
* *
31602551 TATATATTATTTATTTTAGACT-TTT
1 TATATATTATTTATTTTAAATTGTTT
* * *
31602576 TACATATTAGTTCA-TTTAAACTGTTT
1 TATATATTA-TTTATTTTAAATTGTTT
* * * **
31602602 TATGTATTATATATTTAAAATTACTT
1 TATATATTATTTATTTTAAATTGTTT
* *
31602628 TATAAATTATTTATTTCAAATTGTTT
1 TATATATTATTTATTTTAAATTGTTT
* *
31602654 TATGCT-TTATTTATTTT-AATTTTTT
1 TAT-ATATTATTTATTTTAAATTGTTT
*
31602679 TATATATTGTTTATTTTAAACTT-TTT
1 TATATATTATTTATTTTAAA-TTGTTT
* *
31602705 CATAAATTATTTATTTTAAATTGTTT
1 TATATATTATTTATTTTAAATTGTTT
*
31602731 TAT-TATTATTTA--TT--ATGTATTT
1 TATATATTATTTATTTTAAAT-TGTTT
* **
31602753 TAAACTATTATCCATTTTAAATT-TTT
1 TATA-TATTATTTATTTTAAATTGTTT
* *
31602779 TATATATTATTTATTTTAAACTGTTA
1 TATATATTATTTATTTTAAATTGTTT
* * *
31602805 TATATATTGTTTATTTTGAATTTTATAT
1 TATATATTATTTATTTTAAATTGT-T-T
**
31602833 ATATATATTATTT-TTTTAAACCG-TT
1 -TATATATTATTTATTTTAAATTGTTT
* *
31602858 TGTATATTATTTATTTTAAATTTCTTTT
1 TATATATTATTTATTTTAAA-TT-GTTT
* * * * *
31602886 TACATGTTATTTATCTTAAAACTCTTT
1 TATATATTATTTAT-TTTAAATTGTTT
* * *
31602913 T-T-T-TTATGTATTTTAAAGTG-TC
1 TATATATTATTTATTTTAAATTGTTT
*
31602935 TATTATATTATTTATGTTAAATT-TCTT
1 TA-TATATTATTTATTTTAAATTGT-TT
* * * * *
31602962 TGTATGTTATTTATTTTCATTTCTTT
1 TATATATTATTTATTTTAAATTGTTT
*
31602988 TACATATTATTTATTTTAAATTG-TT
1 TATATATTATTTATTTTAAATTGTTT
* * *
31603013 T-TATACTATTT-CTTCAAATTGTTT
1 TATATATTATTTATTTTAAATTGTTT
31603037 TATATATTATTT
1 TATATATTATTT
31603049 TGCTTCGTTT
Statistics
Matches: 393, Mismatches: 94, Indels: 71
0.70 0.17 0.13
Matches are distributed among these distances:
21 2 0.01
22 8 0.02
23 27 0.07
24 42 0.11
25 89 0.23
26 176 0.45
27 11 0.03
28 22 0.06
29 16 0.04
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (26 bp):
TATATATTATTTATTTTAAATTGTTT
Found at i:31604287 original size:18 final size:18
Alignment explanation
Indices: 31604264--31604300 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31604254 ATGTCGTTCC
31604264 TATCCATACTTGTATCGT
1 TATCCATACTTGTATCGT
31604282 TATCCATACTTGTATCGT
1 TATCCATACTTGTATCGT
31604300 T
1 T
31604301 CTCCCCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (18 bp):
TATCCATACTTGTATCGT
Found at i:31609121 original size:7 final size:7
Alignment explanation
Indices: 31609109--31609142 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31609099 AATCTGAGTA
31609109 TAACATT
1 TAACATT
31609116 TAACATT
1 TAACATT
31609123 TAACATT
1 TAACATT
31609130 TAACATT
1 TAACATT
31609137 TAACAT
1 TAACAT
31609143 GTTTTGTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TAACATT
Found at i:31609904 original size:32 final size:32
Alignment explanation
Indices: 31609863--31609990 Score: 229
Period size: 32 Copynumber: 4.0 Consensus size: 32
31609853 TATAACTATA
31609863 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
31609895 CTACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
31609927 CAACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
31609959 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
31609991 ATTTTTTATG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:31621528 original size:39 final size:39
Alignment explanation
Indices: 31621452--31621578 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
31621442 TATGAGATTG
31621452 AAAATATCCGGACATGAGGTCC-CAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
*
31621490 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
* * ** *
31621529 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
31621568 AAAATATCCGG
1 AAAATATCCGG
31621579 GTTAAAGACC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 21 0.26
39 59 0.74
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
Found at i:31621592 original size:78 final size:75
Alignment explanation
Indices: 31621451--31621604 Score: 184
Period size: 78 Copynumber: 2.0 Consensus size: 75
31621441 GTATGAGATT
* * *
31621451 GAAAATATCCGGACATGAGGTCCCAGGCTATATGCTAGAAAAATATCCGGACATGAGATCCGCAG
1 GAAAATATCCGGACATGAGGTCCCAGGCTACATGCTAGAAAAATATCCGGACATAAGACCCGCAG
*
31621516 GCTATATGCTA
66 GCT-TACGCTA
* * * **
31621527 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCC-CAGGCTACATGCTAGAAAAATATCCGGACAT-AAGACCCG
31621591 CAGGCTTACGCTA
63 CAGGCTTACGCTA
31621604 G
1 G
31621605 TAATGTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
76 4 0.06
77 26 0.39
78 36 0.55
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (75 bp):
GAAAATATCCGGACATGAGGTCCCAGGCTACATGCTAGAAAAATATCCGGACATAAGACCCGCAG
GCTTACGCTA
Found at i:31629517 original size:39 final size:39
Alignment explanation
Indices: 31629465--31629592 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
31629455 TATGAGATTG
31629465 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
*
31629504 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
* * * **
31629543 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
31629582 AAAATATCCGG
1 AAAATATCCGG
31629593 GTTAAAGACC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
Found at i:31629606 original size:78 final size:76
Alignment explanation
Indices: 31629464--31629618 Score: 195
Period size: 78 Copynumber: 2.0 Consensus size: 76
31629454 GTATGAGATT
* * *
31629464 GAAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGCA
1 GAAAATATCCGGACATGAGATCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
*
31629529 GGCTATATGCTA
66 GGCT-TACGCTA
* * * **
31629541 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGATCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACCCG
31629605 CAGGCTTACGCTA
64 CAGGCTTACGCTA
31629618 G
1 G
31629619 TAATGTATTC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 12 0.18
78 55 0.82
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGATCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:31644554 original size:53 final size:55
Alignment explanation
Indices: 31644496--31644608 Score: 124
Period size: 56 Copynumber: 2.1 Consensus size: 55
31644486 GATGTTTCCA
* * *
31644496 TTTTTAAAGATCAATAA-AGACAAAA-T-TTAATAGTTGAGTGACCATTTTATAAC
1 TTTTTAAAGATCAATAATA-AAAAAATTATTAATAATTAAGTGACCATTTTATAAC
* * * *
31644549 TTTTTACAGTTTAATAATAAAAAAATTTATTAATAATTAAGTGATCATTTTATAAC
1 TTTTTAAAGATCAATAATAAAAAAA-TTATTAATAATTAAGTGACCATTTTATAAC
31644605 TTTT
1 TTTT
31644609 CACAATTGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
53 19 0.39
54 1 0.02
55 1 0.02
56 28 0.57
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (55 bp):
TTTTTAAAGATCAATAATAAAAAAATTATTAATAATTAAGTGACCATTTTATAAC
Found at i:31653629 original size:21 final size:21
Alignment explanation
Indices: 31653596--31653635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31653586 CAAAACAATG
* *
31653596 TAGTTTTGCCTTTTAACTTAA
1 TAGTTGTGACTTTTAACTTAA
31653617 TAGTTGTGACTTTTAACTT
1 TAGTTGTGACTTTTAACTT
31653636 TAGAAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (21 bp):
TAGTTGTGACTTTTAACTTAA
Found at i:31657637 original size:16 final size:15
Alignment explanation
Indices: 31657618--31657647 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
31657608 TAATATTTCG
31657618 TTTAATATTTTATTTA
1 TTTAATA-TTTATTTA
31657634 TTTAATATTTATTT
1 TTTAATATTTATTT
31657648 CTTCAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATATTTATTTA
Found at i:31657734 original size:18 final size:19
Alignment explanation
Indices: 31657711--31657755 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
31657701 ATATATTGTC
31657711 TATTATTACTATC-ATTAT
1 TATTATTACTATCTATTAT
*
31657729 TATTATT-TTATCTATTAT
1 TATTATTACTATCTATTAT
31657747 TATTTATTA
1 TA-TTATTA
31657756 TATATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTACTATCTATTAT
Found at i:31661694 original size:20 final size:19
Alignment explanation
Indices: 31661657--31661697 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
31661647 CGCCTTCTTT
*
31661657 TTTGCATTCATCCCATGCA
1 TTTGCATTCATCACATGCA
*
31661676 TTTGCATTACATCATATGCA
1 TTTGCATT-CATCACATGCA
31661696 TT
1 TT
31661698 AAATTTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTGCATTCATCACATGCA
Found at i:31669467 original size:44 final size:44
Alignment explanation
Indices: 31669402--31669739 Score: 213
Period size: 44 Copynumber: 7.7 Consensus size: 44
31669392 GTCATCATGG
* * *
31669402 CGAATCTTATCTCCCTAAAGTTATAGCGGAGCAGATTAAAGTCA
1 CGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
* * *
31669446 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
1 CGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
* * ** *
31669490 -TAGATCTTATCTCACTGAAGTTACAGTGGAATAGATCAAAGAT-A
1 CGA-ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TCA
* * * * *
31669534 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAAG-CTA
1 -CGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTC-A
** * * * *
31669579 TAAACCTTATCTCCCTGAAGTTACAGT-GAGCAGGTTGAAGTTA
1 CGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
* * * * *
31669622 C-AAGTCTCATCTTCCTGAAGTTGCAGTGGAGCAGAGTAAAG-AA
1 CGAA-TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
* * * * * * * *
31669665 GGAAAATCTTATCTCCCTAAAGTTGCGGTAGAGTAGATTGAAGCCA
1 CG--AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
* **
31669711 CAAATCCCATAC-CCCTGAAGTTACAGTGG
1 CGAATCTTAT-CTCCCTGAAGTTACAGTGG
31669740 GATAGATTGA
Statistics
Matches: 224, Mismatches: 56, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
42 2 0.01
43 32 0.14
44 123 0.55
45 63 0.28
46 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
CGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCA
Found at i:31669688 original size:132 final size:133
Alignment explanation
Indices: 31669404--31669752 Score: 338
Period size: 132 Copynumber: 2.6 Consensus size: 133
31669394 CATCATGGCG
** ** * * * *
31669404 AATCTTATCTCCCTAAAGTTATAGCGGAGCAGATTAAAGTCACGAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGTCACAAACCTTATCTCCCTGAAGTTA
* * *
31669469 CAGTGGAGCAGATTGAAGTTATAGATCTTATCTCACTGAAGTTACAGTGGAATAGATCAAAGATA
66 CAGTGGAGCAGATTGAAGTTAAAGATCTCATCTCACTGAAGTTACAGTGGAACAGATCAAAGATA
*
31669534 GCA
131 GAA
* * *
31669537 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAAG-CTATAAACCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGTC-ACAAACCTTATCTCCCTGAAGTT
* * *
31669601 ACAGT-GAGCAGGTTGAAGTTACAAG-TCTCATCTTC-CTGAAGTTGCAGTGGAGCAGAGT-AAA
65 ACAGTGGAGCAGATTGAAGTTA-AAGATCTCATC-TCACTGAAGTTACAGTGGAACAGA-TCAAA
31669662 GA-AGGAA
127 GATA-GAA
* * * * * *
31669669 AATCTTATCTCCCTAAAGTTGCGGTAGAGTAGATTGAAGCCACAAATCC-CATAC-CCCTGAAGT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGTCACAAA-CCTTAT-CTCCCTGAAGT
*
31669732 TACAGTGG-GATAGATTGAAGT
64 TACAGTGGAG-CAGATTGAAGT
31669753 CATCTATTAT
Statistics
Matches: 178, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
131 1 0.01
132 102 0.57
133 75 0.42
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (133 bp):
AATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGTCACAAACCTTATCTCCCTGAAGTTA
CAGTGGAGCAGATTGAAGTTAAAGATCTCATCTCACTGAAGTTACAGTGGAACAGATCAAAGATA
GAA
Found at i:31671291 original size:15 final size:16
Alignment explanation
Indices: 31671259--31671298 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
31671249 AAAGCACTGT
31671259 TTTATTTAATATTTTA
1 TTTATTTAATATTTTA
31671275 TTTATTTAATA-TTTA
1 TTTATTTAATATTTTA
*
31671290 TTTCTTTAA
1 TTTATTTAA
31671299 CCATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTAATATTTTA
Found at i:31671378 original size:18 final size:18
Alignment explanation
Indices: 31671357--31671396 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
31671347 ATATATTGTC
31671357 TATTATTACTATC-ATTAT
1 TATTATT-CTATCTATTAT
*
31671375 TATTATTTTATCTATTAT
1 TATTATTCTATCTATTAT
31671393 TATT
1 TATT
31671397 TATTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTCTATCTATTAT
Found at i:31671403 original size:18 final size:17
Alignment explanation
Indices: 31671366--31671401 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
31671356 CTATTATTAC
31671366 TATCATTATTATTATTT
1 TATCATTATTATTATTT
31671383 TATCTATTATTATTTATTT
1 TATC-ATTATTA-TTATTT
31671402 ATATATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TATCATTATTATTATTT
Found at i:31673899 original size:10 final size:10
Alignment explanation
Indices: 31673869--31673902 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31673859 TTAGTTTAGA
31673869 TTTAGTTTTC
1 TTTAGTTTTC
*
31673879 TATAGGTTTTC
1 TTTA-GTTTTC
31673890 TTTAGTTTTC
1 TTTAGTTTTC
31673900 TTT
1 TTT
31673903 GCCATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:31675511 original size:15 final size:17
Alignment explanation
Indices: 31675493--31675524 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
31675483 TAGCATAATT
31675493 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
31675508 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
31675525 CCAGTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:31682146 original size:20 final size:20
Alignment explanation
Indices: 31682095--31682146 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
31682085 GAAATGAAAA
*
31682095 GAAGGAAAGAAACAGAGTA-
1 GAAGGAAAGAAACAGAGAAG
* *
31682114 GCATGAAACGAAACAGAGAAG
1 GAAGGAAA-GAAACAGAGAAG
*
31682135 GAAGGAAGGAAA
1 GAAGGAAAGAAA
31682147 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.56, C:0.08, G:0.33, T:0.04
Consensus pattern (20 bp):
GAAGGAAAGAAACAGAGAAG
Found at i:31682602 original size:13 final size:13
Alignment explanation
Indices: 31682584--31682610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31682574 AAGAAATTAG
31682584 TATTAAATGTAAA
1 TATTAAATGTAAA
31682597 TATTAAATGTAAA
1 TATTAAATGTAAA
31682610 T
1 T
31682611 TAGTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TATTAAATGTAAA
Found at i:31683551 original size:18 final size:18
Alignment explanation
Indices: 31683528--31683679 Score: 180
Period size: 18 Copynumber: 8.4 Consensus size: 18
31683518 TAAATAAAGG
* * *
31683528 TACTGAATAACTCACTGC
1 TACTGAATAAATGACTGT
* *
31683546 TACTGAATAATTAACTGT
1 TACTGAATAAATGACTGT
*
31683564 TACTGAATAAATGACTAT
1 TACTGAATAAATGACTGT
*
31683582 TACTGAATAAATGATTGT
1 TACTGAATAAATGACTGT
31683600 TACTGAATAAATGACTGT
1 TACTGAATAAATGACTGT
31683618 TACTGAATAAATGACTGT
1 TACTGAATAAATGACTGT
** *
31683636 TACTGAATAACCGACTAT
1 TACTGAATAAATGACTGT
* *
31683654 TACTGAACAATTGA-TCGT
1 TACTGAATAAATGACT-GT
31683672 TACTGAAT
1 TACTGAAT
31683680 GATATTGATA
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
17 1 0.01
18 115 0.99
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
TACTGAATAAATGACTGT
Found at i:31685707 original size:52 final size:52
Alignment explanation
Indices: 31685650--31685751 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
31685640 TCTCTGTCGA
* * *
31685650 AATTCTCCTAAAATTCTCCATTTTTCTTTTTGT-CATCTTCCCTTTCTTGAGT
1 AATTCTCCTAAAATTCTCCATTTTTATTTTTATCCCT-TTCCCTTTCTTGAGT
31685702 AATTCTCCTAAAATTCTCCATTTTTATTTTTATCCCTTTCCCTTTCTTGA
1 AATTCTCCTAAAATTCTCCATTTTTATTTTTATCCCTTTCCCTTTCTTGA
31685752 TTATTGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 44 0.96
53 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (52 bp):
AATTCTCCTAAAATTCTCCATTTTTATTTTTATCCCTTTCCCTTTCTTGAGT
Found at i:31711930 original size:87 final size:88
Alignment explanation
Indices: 31711822--31711984 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 88
31711812 GGATGTCAAC
* *
31711822 TTAACTTAATACATTTATTAAGGTTAAGTTTATAGTAAATAGTGAAAATTGAATTATAGAGGAAC
1 TTAACTTAATACATTTATTAAGGTTAAGTTTATAATAAATAGTGAAAATTGAATTATAGAAGAAC
31711887 TCAACATCCATTTGTGTCTACTT
66 TCAACATCCATTTGTGTCTACTT
* ** *
31711910 TTAA-TTAATATATTTATTAAGGTTTTGTTTATAATATATAGTGAAAATTGAATTATAGAAGAAC
1 TTAACTTAATACATTTATTAAGGTTAAGTTTATAATAAATAGTGAAAATTGAATTATAGAAGAAC
31711974 TCAACATCCAT
66 TCAACATCCAT
31711985 CAATGTTGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 65 0.94
88 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (88 bp):
TTAACTTAATACATTTATTAAGGTTAAGTTTATAATAAATAGTGAAAATTGAATTATAGAAGAAC
TCAACATCCATTTGTGTCTACTT
Found at i:31714334 original size:2 final size:2
Alignment explanation
Indices: 31714327--31714356 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31714317 AAAACACCAA
31714327 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
31714357 TAAGAACAAA
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:31717900 original size:28 final size:28
Alignment explanation
Indices: 31717868--31717980 Score: 165
Period size: 28 Copynumber: 4.1 Consensus size: 28
31717858 CATGCCAGAC
* * *
31717868 AAAGGAAGTCTTTATGGCCATCTATGAA
1 AAAGGAAGCCTTTGTGGCGATCTATGAA
31717896 AAAGGAAGCCTTTGTGGCGATCTATGAA
1 AAAGGAAGCCTTTGTGGCGATCTATGAA
* * *
31717924 AAATGAAGTCTTTGTGGCAATCTATGAA
1 AAAGGAAGCCTTTGTGGCGATCTATGAA
31717952 AAAGGAAGCCTTTGTGGCGATCTAT-AA
1 AAAGGAAGCCTTTGTGGCGATCTATGAA
31717979 AA
1 AA
31717981 TAAAAAAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 4 0.05
28 72 0.95
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (28 bp):
AAAGGAAGCCTTTGTGGCGATCTATGAA
Found at i:31717958 original size:56 final size:55
Alignment explanation
Indices: 31717872--31717980 Score: 191
Period size: 56 Copynumber: 2.0 Consensus size: 55
31717862 CCAGACAAAG
*
31717872 GAAGTCTTTATGGCCATCTATGAAAAAGGAAGCCTTTGTGGCGATCTATGAAAAAT
1 GAAGTCTTTATGGCAATCTATGAAAAAGGAAGCCTTTGTGGCGATCTAT-AAAAAT
*
31717928 GAAGTCTTTGTGGCAATCTATGAAAAAGGAAGCCTTTGTGGCGATCTATAAAA
1 GAAGTCTTTATGGCAATCTATGAAAAAGGAAGCCTTTGTGGCGATCTATAAAA
31717981 TAAAAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 4 0.08
56 47 0.92
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (55 bp):
GAAGTCTTTATGGCAATCTATGAAAAAGGAAGCCTTTGTGGCGATCTATAAAAAT
Found at i:31720588 original size:18 final size:18
Alignment explanation
Indices: 31720565--31720602 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31720555 ACTACTCATC
*
31720565 GTTGTGGACGAACCACTA
1 GTTGTGGACAAACCACTA
*
31720583 GTTGTGGATAAACCACTA
1 GTTGTGGACAAACCACTA
31720601 GT
1 GT
31720603 AATAAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (18 bp):
GTTGTGGACAAACCACTA
Found at i:31720760 original size:21 final size:21
Alignment explanation
Indices: 31720720--31720765 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
31720710 ACACTGTGGT
*
31720720 TAAACCACTCAAATGGTATGGA
1 TAAACCACTCAAATGATAT-GA
31720742 TAAACCACTC-AATGATATGA
1 TAAACCACTCAAATGATATGA
31720762 TAAA
1 TAAA
31720766 TTGCTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (21 bp):
TAAACCACTCAAATGATATGA
Found at i:31731718 original size:30 final size:30
Alignment explanation
Indices: 31731684--31731742 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31731674 TCTTCCTTTA
31731684 TTAATTCCCTT-AAAATAATAAAAAAATAAT
1 TTAATT-CCTTAAAAATAATAAAAAAATAAT
* * *
31731714 TTAATTCTTTAAAAATTATAAAAATATAA
1 TTAATTCCTTAAAAATAATAAAAAAATAA
31731743 GTTATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (30 bp):
TTAATTCCTTAAAAATAATAAAAAAATAAT
Found at i:31733931 original size:15 final size:15
Alignment explanation
Indices: 31733911--31733948 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31733901 TGCTTATCAT
31733911 TTTTATTTGGA-TTTA
1 TTTTATTT-GATTTTA
*
31733926 TTTTATTTTATTTTA
1 TTTTATTTGATTTTA
31733941 TTTTATTT
1 TTTTATTT
31733949 TTAAGGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTATTTGATTTTA
Found at i:31733932 original size:5 final size:5
Alignment explanation
Indices: 31733922--31733949 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31733912 TTTATTTGGA
31733922 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
31733950 TAAGGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:31742955 original size:50 final size:49
Alignment explanation
Indices: 31742831--31743020 Score: 227
Period size: 50 Copynumber: 3.8 Consensus size: 49
31742821 GTAGACAAGG
* * * * * *
31742831 TTATCTGGTACGCATAGTAGCCTGCACATAGTACTATACATGCGACCAA
1 TTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAA
* *
31742880 TTATCCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AA
** *
31742930 CCATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAA
1 TTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA
* * *
31742980 GTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 -TTATCTGATACACATAGTAGCCTGCACTTAGTACTACACA
31743021 TGCGACCTCA
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
49 39 0.32
50 45 0.38
51 36 0.30
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAA
Found at i:31743028 original size:101 final size:99
Alignment explanation
Indices: 31742833--31743028 Score: 257
Period size: 101 Copynumber: 2.0 Consensus size: 99
31742823 AGACAAGGTT
* * * * * *
31742833 ATCTGGTACGCATAGTAGCCTGCACATAGTACTATACATGCGACCAATTATCCGATACACGTAGT
1 ATCTGATACACATAGTAGCCTGCACATAGTACTACACACGCGACAAATTATCCGATACACATAGT
*
31742898 AGCCTGCACTTAGTACTACACACGTGACCTAACC
66 AGCCTGCACTTAGTACTACACACGCGACCTAACC
* * * * *
31742932 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATA
1 ATCTGATACACATAGTAGCCTGCACATAGTACTACACACGCGA-CAAA-TTATCCGATACACATA
*
31742997 GTAGCCTGCACTTAGTACTACACATGCGACCT
64 GTAGCCTGCACTTAGTACTACACACGCGACCT
31743029 CACAATAGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 37 0.45
100 3 0.04
101 42 0.51
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (99 bp):
ATCTGATACACATAGTAGCCTGCACATAGTACTACACACGCGACAAATTATCCGATACACATAGT
AGCCTGCACTTAGTACTACACACGCGACCTAACC
Found at i:31748749 original size:46 final size:46
Alignment explanation
Indices: 31748699--31748827 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
31748689 TGATTGAGCA
*
31748699 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
31748745 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
31748791 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31748828 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:31756230 original size:46 final size:46
Alignment explanation
Indices: 31756180--31756308 Score: 206
Period size: 46 Copynumber: 2.8 Consensus size: 46
31756170 TGATTGAGCA
* *
31756180 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
31756226 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* *
31756272 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31756309 GCGGGTTACA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 2 0.03
46 76 0.97
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
Found at i:31773938 original size:26 final size:26
Alignment explanation
Indices: 31773902--31773954 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
31773892 TATCTCATAG
*
31773902 TACGAGACTCGGATAATGTTCCCGTC
1 TACGAGACTCGAATAATGTTCCCGTC
*
31773928 TACGAGACTCGAATAATGTTCCTGTC
1 TACGAGACTCGAATAATGTTCCCGTC
31773954 T
1 T
31773955 CTTTCTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (26 bp):
TACGAGACTCGAATAATGTTCCCGTC
Found at i:31776814 original size:22 final size:22
Alignment explanation
Indices: 31776772--31776814 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31776762 TGTGATATGT
*
31776772 GTAATACTATGGCAAGGCCATG
1 GTAATACTATGGCAAGACCATG
*
31776794 GTAATA-TATGTGTAAGACCAT
1 GTAATACTATG-GCAAGACCAT
31776815 AGTTTGGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (22 bp):
GTAATACTATGGCAAGACCATG
Found at i:31780088 original size:46 final size:44
Alignment explanation
Indices: 31779988--31780095 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
31779978 TGTCTTTGAC
** * * * *
31779988 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
*
31780032 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
31780078 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
31780096 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:31785381 original size:6 final size:6
Alignment explanation
Indices: 31785372--31785404 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31785362 GGCGTGGAGA
*
31785372 TGGAGG TGGAAG TGGAAG TGGAAG TGGAAG TGG
1 TGGAAG TGGAAG TGGAAG TGGAAG TGGAAG TGG
31785405 TAGCAGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.55, T:0.18
Consensus pattern (6 bp):
TGGAAG
Found at i:31788527 original size:18 final size:18
Alignment explanation
Indices: 31788504--31788541 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31788494 CCAAACAGGG
31788504 GTTTTCCAAACATTCACA
1 GTTTTCCAAACATTCACA
*
31788522 GTTTTCCAAACATTCGCA
1 GTTTTCCAAACATTCACA
31788540 GT
1 GT
31788542 CCTTGCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (18 bp):
GTTTTCCAAACATTCACA
Found at i:31793397 original size:19 final size:19
Alignment explanation
Indices: 31793351--31793398 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
31793341 GTATATATTT
*
31793351 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGAAGA
*
31793369 TAAATCTTATTTAGGAAGA
1 TAAATTTTATTTAGGAAGA
31793388 TAAATTTTATT
1 TAAATTTTATT
31793399 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (19 bp):
TAAATTTTATTTAGGAAGA
Found at i:31797321 original size:19 final size:19
Alignment explanation
Indices: 31797275--31797322 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
31797265 GTATATATTT
*
31797275 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGAAGA
*
31797293 TAAATCTTATTTAGGAAGA
1 TAAATTTTATTTAGGAAGA
31797312 TAAATTTTATT
1 TAAATTTTATT
31797323 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (19 bp):
TAAATTTTATTTAGGAAGA
Found at i:31814140 original size:18 final size:18
Alignment explanation
Indices: 31814117--31814159 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31814107 CTTCAATGTG
31814117 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
31814135 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
31814153 TAATTAA
1 TAATTAA
31814160 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:31815152 original size:53 final size:53
Alignment explanation
Indices: 31815072--31815178 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
31815062 TGATTAAAGA
* *
31815072 GTCGCTTCTAGCATCTCTCGTAGAATTTAACACTTGAATATATTCAATGTTAT
1 GTCGCTTCAAGCATCTCTCGTAGAATTTAACACTTGAATATATTCAATATTAT
*
31815125 GTCGCTTGAAGCATCTCTCGTAGAATTTAACACTTGAATATATTCAATATTAT
1 GTCGCTTCAAGCATCTCTCGTAGAATTTAACACTTGAATATATTCAATATTAT
31815178 G
1 G
31815179 CTATAACTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (53 bp):
GTCGCTTCAAGCATCTCTCGTAGAATTTAACACTTGAATATATTCAATATTAT
Found at i:31819028 original size:22 final size:22
Alignment explanation
Indices: 31818976--31819029 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
31818966 TTTTTTATGC
* * *
31818976 ATTTAAAATTATAATTGTAATT
1 ATTTATAATTAAAATTATAATT
31818998 ATATT-TAATTAAAATTATAATT
1 AT-TTATAATTAAAATTATAATT
*
31819020 GTTTATAATT
1 ATTTATAATT
31819030 CAATACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTATAATTAAAATTATAATT
Found at i:31819039 original size:28 final size:27
Alignment explanation
Indices: 31818980--31819039 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
31818970 TTATGCATTT
* *
31818980 AAAATTATAATTGTAATTATATTTAATT
1 AAAATTATAATTGT-ATTATATTCAATC
31819008 AAAATTATAATTGT-TTATAATTCAATAC
1 AAAATTATAATTGTATTAT-ATTCAAT-C
31819036 AAAA
1 AAAA
31819040 ATATGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
AAAATTATAATTGTATTATATTCAATC
Found at i:31822751 original size:11 final size:11
Alignment explanation
Indices: 31822721--31822759 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
31822711 CACAAATTAT
*
31822721 TATTATTTTACA
1 TATTATTTT-TA
31822733 TCATTATTTTTA
1 T-ATTATTTTTA
31822745 TATTATTTTTA
1 TATTATTTTTA
31822756 TATT
1 TATT
31822760 TTTACTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 14 0.56
12 3 0.12
13 8 0.32
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:31822792 original size:19 final size:18
Alignment explanation
Indices: 31822737--31822796 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
31822727 TTTACATCAT
*
31822737 TATTTTTATATTATTTTTA
1 TATTTTTA-ATTATTTATA
* *
31822756 TATTTTTACTTGTATTATA
1 TATTTTTAATTAT-TTATA
31822775 TATTTATTAATTATTTATA
1 TATTT-TTAATTATTTATA
31822794 TAT
1 TAT
31822797 ATTGTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.09
19 25 0.74
20 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTTTAATTATTTATA
Found at i:31823095 original size:19 final size:19
Alignment explanation
Indices: 31823073--31823132 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
31823063 TTATTATTTA
31823073 TTTATTTATTATGTATTAT
1 TTTATTTATTATGTATTAT
**
31823092 TTTACTTTAAAATG-A-TAT
1 TTTA-TTTATTATGTATTAT
* *
31823110 TTT-TATATTATGTGTTAT
1 TTTATTTATTATGTATTAT
31823128 TTTAT
1 TTTAT
31823133 AAATTCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 6 0.19
18 12 0.39
19 6 0.19
20 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTATTTATTATGTATTAT
Found at i:31823461 original size:33 final size:33
Alignment explanation
Indices: 31823413--31823489 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
31823403 CATTGATATT
31823413 GTATTACTCTTTTTGTATATCATGCATTATTTAA
1 GTATTACT-TTTTTGTATATCATGCATTATTTAA
*
31823447 TTATTACTTTTTTGTATATCATGCATTATTTAA
1 GTATTACTTTTTTGTATATCATGCATTATTTAA
31823480 GTATTACTTT
1 GTATTACTTT
31823490 GTATGTTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 34 0.83
34 7 0.17
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (33 bp):
GTATTACTTTTTTGTATATCATGCATTATTTAA
Found at i:31824986 original size:20 final size:20
Alignment explanation
Indices: 31824963--31825001 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31824953 AATCTACGAG
31824963 TATTGGTTTTA-TTTTATTTT
1 TATT-GTTTTATTTTTATTTT
*
31824983 TATTTTTTTATTTTTATTT
1 TATTGTTTTATTTTTATTT
31825002 GGTTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (20 bp):
TATTGTTTTATTTTTATTTT
Found at i:31824991 original size:14 final size:14
Alignment explanation
Indices: 31824974--31825001 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31824964 ATTGGTTTTA
31824974 TTTTATTTTTATTT
1 TTTTATTTTTATTT
31824988 TTTTATTTTTATTT
1 TTTTATTTTTATTT
31825002 GGTTAAGTTT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:31826126 original size:19 final size:20
Alignment explanation
Indices: 31826095--31826148 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
31826085 GGTTCTTTTG
* *
31826095 TGAAATTTAATGCACATG-A
1 TGAAATGTAATGCAAATGCA
*
31826114 TGCAATGTAATGCAAATGCA
1 TGAAATGTAATGCAAATGCA
31826134 TGAAATG-AATGCAAA
1 TGAAATGTAATGCAAA
31826149 AAGAAAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGCA
Found at i:31830853 original size:30 final size:30
Alignment explanation
Indices: 31830819--31830878 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31830809 ATTTAATACG
31830819 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
31830849 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
31830879 GGCTCAGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:31882552 original size:39 final size:39
Alignment explanation
Indices: 31882431--31882535 Score: 183
Period size: 39 Copynumber: 2.7 Consensus size: 39
31882421 GAGATTGGAA
31882431 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
31882470 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
* * *
31882509 ATATCTGGACTTGAGGTCCGCAGGCTA
1 ATATCCGGACATGAGATCCGCAGGCTA
31882536 CGTGCTGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (39 bp):
ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
Found at i:31882785 original size:2 final size:2
Alignment explanation
Indices: 31882780--31882817 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31882770 TATATATATA
*
31882780 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31882818 CGAATGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:31888639 original size:9 final size:9
Alignment explanation
Indices: 31888625--31888872 Score: 210
Period size: 9 Copynumber: 28.4 Consensus size: 9
31888615 TATTTAAGTA
*
31888625 TTATGTAAG
1 TTATATAAG
*
31888634 TTATGTAAG
1 TTATATAAG
*
31888643 TTATGATATG
1 TTAT-ATAAG
* *
31888653 ATATAT-AT
1 TTATATAAG
*
31888661 TTATGTAAG
1 TTATATAAG
*
31888670 TTATAT-AT
1 TTATATAAG
*
31888678 TTATCTAAG
1 TTATATAAG
31888687 TTATATAAG
1 TTATATAAG
31888696 ---T-TAAG
1 TTATATAAG
* *
31888701 TTATGTAAA
1 TTATATAAG
*
31888710 TTATGTAAG
1 TTATATAAG
31888719 TTATAT-AG
1 TTATATAAG
31888727 TTATCA-AAG
1 TTAT-ATAAG
*
31888736 TTATATCAG
1 TTATATAAG
31888745 TTATATAAG
1 TTATATAAG
31888754 TTATATAAG
1 TTATATAAG
*
31888763 TTATGTAAG
1 TTATATAAG
31888772 TTATATAAG
1 TTATATAAG
*
31888781 TTATAT-AT
1 TTATATAAG
*
31888789 TTATCTAAG
1 TTATATAAG
31888798 TTATATAAG
1 TTATATAAG
*
31888807 TTATGTAAG
1 TTATATAAG
*
31888816 TTATGTAAG
1 TTATATAAG
*
31888825 TTATAT-AT
1 TTATATAAG
*
31888833 TTATCTAAG
1 TTATATAAG
31888842 TTATATAAG
1 TTATATAAG
*
31888851 TTATGTAAG
1 TTATATAAG
* *
31888860 TTTTGTAAG
1 TTATATAAG
31888869 TTAT
1 TTAT
31888873 GTTAAATATT
Statistics
Matches: 194, Mismatches: 33, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
5 4 0.02
6 1 0.01
8 30 0.15
9 153 0.79
10 6 0.03
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (9 bp):
TTATATAAG
Found at i:31888696 original size:53 final size:54
Alignment explanation
Indices: 31888625--31888874 Score: 268
Period size: 53 Copynumber: 4.8 Consensus size: 54
31888615 TATTTAAGTA
* * * * * *
31888625 TTATGTAAGTTATGTAAGTTATGATATGATATAT-ATTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGTAAGTTATATAG
* *
31888678 TTATCTAAGTTATATAAG---T--TAAGTTATGTAAATTATGTAAGTTATATAG
1 TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGTAAGTTATATAG
* *
31888727 TTATCAAAGTTATATCAGTTAT-ATAAGTTATATAAGTTATGTAAGTTATATAAG
1 TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGTAAGTTATAT-AG
* * * * *
31888781 TTATAT-ATTTATCTAAGTTAT-ATAAGTTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGTAAGTTATATAG
* *
31888833 TTATCTAAGTTATATAAGTTATG-TAAGTTTTGTAAGTTATGT
1 TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGT
31888875 TAAATATTTA
Statistics
Matches: 167, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
48 7 0.04
49 33 0.20
50 1 0.01
52 7 0.04
53 113 0.68
54 6 0.04
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (54 bp):
TTATCTAAGTTATATAAGTTATGATAAGTTATATAAGTTATGTAAGTTATATAG
Found at i:31888713 original size:23 final size:23
Alignment explanation
Indices: 31888678--31888747 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
31888668 AGTTATATAT
*
31888678 TTATCTAAGTTATATAAGTTAAG
1 TTATCTAAATTATATAAGTTAAG
* *
31888701 TTATGTAAATTATGTAAGTTATATAG
1 TTATCTAAATTATATAAG-T-TA-AG
*
31888727 TTATC-AAAGTTATATCAGTTA
1 TTATCTAAA-TTATATAAGTTA
31888748 TATAAGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
23 15 0.41
24 3 0.08
25 6 0.16
26 13 0.35
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
TTATCTAAATTATATAAGTTAAG
Found at i:31888867 original size:44 final size:44
Alignment explanation
Indices: 31888625--31888872 Score: 281
Period size: 44 Copynumber: 5.7 Consensus size: 44
31888615 TATTTAAGTA
* * * *
31888625 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAG
1 TTATATAAGTTATGTAAGTTATG-TAAGTTATATATTTATCTAAG
* * * * * *
31888670 TTATAT-ATTTATCTAAGTTATATAAG-T-TA-AGTTATGTAAA
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
* * ** * *
31888710 TTATGTAAGTTATAT-AGTTATCAAAGTTATATCAGTTATATAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAG
*
31888754 TTATATAAGTTATGTAAGTTATATAAGTTATATATTTATCTAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
31888798 TTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
*
31888842 TTATATAAGTTATGTAAGTTTTGTAAGTTAT
1 TTATATAAGTTATGTAAGTTATGTAAGTTAT
31888873 GTTAAATATT
Statistics
Matches: 175, Mismatches: 22, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
40 23 0.13
41 9 0.05
42 3 0.02
43 3 0.02
44 117 0.67
45 20 0.11
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (44 bp):
TTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
Found at i:31889004 original size:15 final size:15
Alignment explanation
Indices: 31888984--31889068 Score: 95
Period size: 14 Copynumber: 5.9 Consensus size: 15
31888974 GTAAGTTGCG
31888984 AATTAAATAATATTT
1 AATTAAATAATATTT
31888999 AATTAAATAATATTT
1 AATTAAATAATATTT
* *
31889014 -ATAAAATTAT-TTT
1 AATTAAATAATATTT
*
31889027 AATTAAATAATATTG
1 AATTAAATAATATTT
** *
31889042 AAAAAAATTAT-TTT
1 AATTAAATAATATTT
31889056 AATTAAATAATAT
1 AATTAAATAATAT
31889069 ACATGTCGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
13 3 0.05
14 26 0.47
15 26 0.47
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:31889027 original size:28 final size:29
Alignment explanation
Indices: 31888996--31889068 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
31888986 TTAAATAATA
* *
31888996 TTTAATTAAATAATATT-TATAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
31889024 TTTAATTAAATAATATTGAAAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
31889053 TTTAATTAAATAATAT
1 TTTAATTAAATAATAT
31889069 ACATGTCGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TTTAATTAAATAATATTGAAAAAAATTAT
Found at i:31889274 original size:24 final size:24
Alignment explanation
Indices: 31889242--31889288 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31889232 TTAACTTAAA
* *
31889242 TGATAAAACGGACGATAATATTTG
1 TGATAAAACAGACGAGAATATTTG
31889266 TGATAAAACAGACGAGAATATTT
1 TGATAAAACAGACGAGAATATTT
31889289 CAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (24 bp):
TGATAAAACAGACGAGAATATTTG
Found at i:31889543 original size:64 final size:64
Alignment explanation
Indices: 31889336--31889533 Score: 360
Period size: 64 Copynumber: 3.1 Consensus size: 64
31889326 ATATTTTATT
* *
31889336 AAATATTTGTATATTAGATGGGATATATAATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
*
31889400 AAATATTTGTATATTAGATGGGACATATTATATTAATGAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
*
31889464 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
31889528 AAATAT
1 AAATAT
31889534 AGAAATATTA
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 129 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:31890332 original size:40 final size:40
Alignment explanation
Indices: 31890288--31890390 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
31890278 AAACAGATTA
*
31890288 AAAAAGCAAAAAGCAAAAAGCAATTGTTACTTATAAACGC
1 AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
* *
31890328 AAAAAGAAAAAAGAAAAAAGCAACTGTTACTTATAAACGC
1 AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
31890368 AAAAAGCAAAAAGCAAAAAGCAA
1 AAAAAGCAAAAAGCAAAAAGCAA
31890391 ATCTATAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.61, C:0.14, G:0.13, T:0.13
Consensus pattern (40 bp):
AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
Found at i:31890385 original size:6 final size:7
Alignment explanation
Indices: 31890366--31890391 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31890356 ACTTATAAAC
31890366 GCAAAAA
1 GCAAAAA
31890373 GCAAAAA
1 GCAAAAA
31890380 GCAAAAA
1 GCAAAAA
31890387 GCAAA
1 GCAAA
31890392 TCTATAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:31890742 original size:21 final size:21
Alignment explanation
Indices: 31890701--31890743 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31890691 GAAATAAGTC
* *
31890701 AAATATTTATAAACTCTTAAA
1 AAATAATTAAAAACTCTTAAA
31890722 AAATAATTAAAAA-TCTCTAAA
1 AAATAATTAAAAACTCT-TAAA
31890743 A
1 A
31890744 TAAAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAATTAAAAACTCTTAAA
Found at i:31893768 original size:13 final size:13
Alignment explanation
Indices: 31893750--31893783 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31893740 ACCCAAATAC
31893750 CCTAAACTTTAAA
1 CCTAAACTTTAAA
*
31893763 CCTAAATTTTAAA
1 CCTAAACTTTAAA
31893776 CTCTAAAC
1 C-CTAAAC
31893784 CCTAATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
CCTAAACTTTAAA
Found at i:31893922 original size:19 final size:19
Alignment explanation
Indices: 31893898--31893940 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
31893888 CCTTACCTTA
31893898 AAACCATATATAATACTCT
1 AAACCATATATAATACTCT
31893917 AAACCATATATAATACTCT
1 AAACCATATATAATACTCT
31893936 AAACC
1 AAACC
31893941 TGTACTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (19 bp):
AAACCATATATAATACTCT
Done.