Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 128 of 410
Found at i:38551822 original size:47 final size:47
Alignment explanation
Indices: 38551753--38552002 Score: 401
Period size: 47 Copynumber: 5.3 Consensus size: 47
38551743 CCCTTCGGGA
* * * * * *
38551753 CTTATCACATTTATACACTTTCACATCCATCGCATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38551800 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38551847 CTTATCACATATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38551894 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38551941 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38551988 CTTATCACATATATA
1 CTTATCACATATATA
38552003 TATCTCATAC
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 192 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38551831 original size:25 final size:25
Alignment explanation
Indices: 38551803--38551881 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
38551793 ACTCGGCCTT
*
38551803 ATCACATATATACACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
* * * *
38551828 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACTTTC-ACATTC
38551850 ATCACATATATGCACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
38551875 ATCACAT
1 ATCACAT
38551882 GGGCCATTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.12
24 6 0.15
25 18 0.45
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACTTTCACATTC
Found at i:38557869 original size:10 final size:10
Alignment explanation
Indices: 38557856--38557895 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
38557846 AAAAAAGAAA
38557856 AAAGAAAAAC
1 AAAGAAAAAC
38557866 AAAGAAGCAAAC
1 AAAGAA--AAAC
38557878 AAAGAAAAAC
1 AAAGAAAAAC
38557888 AAATGAAA
1 AAA-GAAA
38557896 TAGAAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 13 0.48
11 4 0.15
12 10 0.37
ACGTcount: A:0.75, C:0.10, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAC
Found at i:38557903 original size:22 final size:21
Alignment explanation
Indices: 38557843--38557895 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
38557833 GTGCAAATTT
* *
38557843 ACAAAAAAAGAAAAAAGAAAA
1 ACAAAGAAACAAAAAAGAAAA
*
38557864 ACAAAGAAGCAAACAAAGAAAA
1 ACAAAGAAACAAA-AAAGAAAA
38557886 ACAAATGAAA
1 ACAAA-GAAA
38557896 TAGAAAAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 10 0.38
22 13 0.50
23 3 0.12
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.02
Consensus pattern (21 bp):
ACAAAGAAACAAAAAAGAAAA
Found at i:38560112 original size:44 final size:44
Alignment explanation
Indices: 38560064--38560187 Score: 101
Period size: 44 Copynumber: 3.0 Consensus size: 44
38560054 CATTTAATTA
38560064 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
1 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
* * **
38560108 ATTATC-ATTCATAA--A-A-CA-AACAATCATTTA---AT--TA-
1 ATTATCTA-TCTTAATCATATCATACCCCT-ATTTAGCCATAATAC
*
38560142 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCGTAATAC
1 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
38560186 AT
1 AT
38560188 CCCATTACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 28
0.61 0.10 0.30
Matches are distributed among these distances:
34 11 0.19
35 3 0.05
36 1 0.02
37 3 0.05
38 7 0.12
39 6 0.11
40 7 0.12
41 2 0.04
42 1 0.02
43 3 0.05
44 13 0.23
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (44 bp):
ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
Found at i:38560158 original size:78 final size:78
Alignment explanation
Indices: 38560029--38560187 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 78
38560019 TTCAAAATTT
38560029 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
1 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
38560094 TTTAGCCATAATA
66 TTTAGCCATAATA
38560107 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
1 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
*
38560172 TTTAGCCGTAATA
66 TTTAGCCATAATA
38560185 CAT
1 CAT
38560188 CCCATTACAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (78 bp):
CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
TTTAGCCATAATA
Found at i:38561643 original size:16 final size:17
Alignment explanation
Indices: 38561622--38561655 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38561612 AAAATTTAAT
38561622 AAAAGTCCATTTA-AAA
1 AAAAGTCCATTTACAAA
*
38561638 AAAAGTTCATTTACAAA
1 AAAAGTCCATTTACAAA
38561655 A
1 A
38561656 TACAAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAGTCCATTTACAAA
Found at i:38561700 original size:17 final size:18
Alignment explanation
Indices: 38561671--38561705 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38561661 GCCCAAATAC
38561671 AAAAACCTAAAAGCCTAA
1 AAAAACCTAAAAGCCTAA
38561689 AAAAACCT-AAAGCCTAA
1 AAAAACCTAAAAGCCTAA
38561706 TGGCCCACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAACCTAAAAGCCTAA
Found at i:38561917 original size:14 final size:16
Alignment explanation
Indices: 38561895--38561931 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
38561885 AAAGAAAAAA
*
38561895 AACAAAAGCAGA-AAC
1 AACAGAAGCAGAGAAC
38561910 -ACAGAAGCAGAGAAC
1 AACAGAAGCAGAGAAC
38561925 AACAGAA
1 AACAGAA
38561932 CAAAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (16 bp):
AACAGAAGCAGAGAAC
Found at i:38563520 original size:34 final size:34
Alignment explanation
Indices: 38563482--38563550 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
38563472 AATAAGAAAA
38563482 TCTCATTCATAAAATTTAATTTAGATAGTGATAT
1 TCTCATTCATAAAATTTAATTTAGATAGTGATAT
38563516 TCTCATTCATAAAATTTAATTTAGATAGTGATAT
1 TCTCATTCATAAAATTTAATTTAGATAGTGATAT
38563550 T
1 T
38563551 TTCAATGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (34 bp):
TCTCATTCATAAAATTTAATTTAGATAGTGATAT
Found at i:38566441 original size:12 final size:12
Alignment explanation
Indices: 38566424--38566450 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38566414 AGATTTATGT
38566424 TCATAGTTCGGG
1 TCATAGTTCGGG
38566436 TCATAGTTCGGG
1 TCATAGTTCGGG
38566448 TCA
1 TCA
38566451 ATTAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (12 bp):
TCATAGTTCGGG
Found at i:38574641 original size:23 final size:25
Alignment explanation
Indices: 38574611--38574665 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
38574601 CAATTAACTT
38574611 TTAAAGATCGAA-TT-AAAGGTAAA
1 TTAAAGATCGAATTTAAAAGGTAAA
38574634 TTAAAGATCGAATTTTTAAAAGGTAAA
1 TTAAAGATCGAA--TTTAAAAGGTAAA
38574661 TTAAA
1 TTAAA
38574666 AAGTTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.43
26 2 0.07
27 14 0.50
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.31
Consensus pattern (25 bp):
TTAAAGATCGAATTTAAAAGGTAAA
Found at i:38574883 original size:26 final size:26
Alignment explanation
Indices: 38574850--38574949 Score: 74
Period size: 26 Copynumber: 3.6 Consensus size: 26
38574840 ATAATTATAT
38574850 TAATAATTTTATTAAATTATATTTAA
1 TAATAATTTTATTAAATTATATTTAA
* * * * *
38574876 TAATAATTATGTTAAAATATGGTTCAA
1 TAATAATTTTATTAAATTAT-ATTTAA
* *
38574903 TTATTTATTATTTTTATTAAATTATTTTTAA
1 -TA---A-TAATTTTATTAAATTATATTTAA
*
38574934 TAATAATCTTATTAAA
1 TAATAATTTTATTAAA
38574950 ATTTAATAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
26 28 0.51
27 5 0.09
28 2 0.04
30 2 0.04
31 5 0.09
32 13 0.24
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (26 bp):
TAATAATTTTATTAAATTATATTTAA
Found at i:38575098 original size:44 final size:46
Alignment explanation
Indices: 38575044--38575138 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
38575034 ATTACAACAT
* *
38575044 CATTCTATTCAACCAAACACAAGAA-TAC-TATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTTATTACAGCTCTATTC
***
38575088 CATTCCATTCAACCAAACAGTTGAATTTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAA-TTACTTATTACAGCTCTATTC
38575135 CATT
1 CATT
38575139 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 21 0.49
46 3 0.07
47 19 0.44
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (46 bp):
CATTCCATTCAACCAAACACAAGAATTACTTATTACAGCTCTATTC
Found at i:38575141 original size:16 final size:16
Alignment explanation
Indices: 38575120--38575174 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
38575110 GAATTTACTT
38575120 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
38575136 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
38575152 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
38575168 ATTACAG
1 ATTACAG
38575175 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:38576568 original size:15 final size:16
Alignment explanation
Indices: 38576527--38576561 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38576517 ATATATTTAC
*
38576527 TTATTATATAAGTATA
1 TTATTAAATAAGTATA
38576543 TTATTAAATAA-TATA
1 TTATTAAATAAGTATA
38576558 TTAT
1 TTAT
38576562 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAAATAAGTATA
Found at i:38576681 original size:2 final size:2
Alignment explanation
Indices: 38576669--38576710 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38576659 ATTAAGTTAT
38576669 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38576710 T
1 T
38576711 GGTTTAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38576801 original size:20 final size:18
Alignment explanation
Indices: 38576775--38576818 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 18
38576765 ACGAAAAGCA
38576775 GGAAAAGAAAGAAAGAAAG
1 GGAAAAGAAAG-AAGAAAG
38576794 GAGAAAAGAAAGAAGAAAG
1 G-GAAAAGAAAGAAGAAAG
38576813 GGAAAA
1 GGAAAA
38576819 TTGAAGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
GGAAAAGAAAGAAGAAAG
Found at i:38577431 original size:2 final size:2
Alignment explanation
Indices: 38577424--38577455 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38577414 TTATTATTTA
38577424 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
38577456 GTAGTAGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38577679 original size:21 final size:19
Alignment explanation
Indices: 38577641--38577679 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
38577631 AAAATTGTGA
*
38577641 TTATTGTGAAATTGAATAT
1 TTATTGTGAAAGTGAATAT
38577660 TTATTAGTGAAAAGTGAATA
1 TTATT-GTG-AAAGTGAATA
38577680 GAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (19 bp):
TTATTGTGAAAGTGAATAT
Found at i:38577713 original size:19 final size:20
Alignment explanation
Indices: 38577691--38577738 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
38577681 AATTATATTG
*
38577691 AATTGAAAAAAATAT-AGTT
1 AATTGAAAAAAATATGAATT
*
38577710 AATT-AATTAAAATATGAATT
1 AATTGAA-AAAAATATGAATT
38577730 AATTGAAAA
1 AATTGAAAA
38577739 CTAGAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTGAAAAAAATATGAATT
Found at i:38578163 original size:18 final size:18
Alignment explanation
Indices: 38578110--38578177 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
38578100 AAAGATCGAC
*
38578110 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-TTGAT
* *
38578129 TGTTACTGTATATTTGAT
1 TGTTACTGAATAATTGAT
*
38578147 T-TTCACTGAATAATTGAC
1 TGTT-ACTGAATAATTGAT
*
38578165 TGTTACTGGATAA
1 TGTTACTGAATAA
38578178 CCGATCAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.05
18 25 0.62
19 13 0.32
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:38587245 original size:17 final size:17
Alignment explanation
Indices: 38587220--38587253 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38587210 AGTTCCATCT
*
38587220 TTTTTTTTTCAATTTTA
1 TTTTATTTTCAATTTTA
*
38587237 TTTTATTTTTAATTTTA
1 TTTTATTTTCAATTTTA
38587254 ACTTTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTCAATTTTA
Found at i:38593044 original size:16 final size:17
Alignment explanation
Indices: 38593018--38593050 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
38593008 ATTTTTCATG
*
38593018 TTATTATTAAATCATTC
1 TTATTATTAAAGCATTC
38593035 TTATTA-TAAAGCATTC
1 TTATTATTAAAGCATTC
38593051 ACACGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATTATTAAAGCATTC
Found at i:38594583 original size:13 final size:13
Alignment explanation
Indices: 38594565--38594589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38594555 TCCAATTAAG
38594565 GGCACACGGCCGA
1 GGCACACGGCCGA
38594578 GGCACACGGCCG
1 GGCACACGGCCG
38594590 TGTGCTAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.40, T:0.00
Consensus pattern (13 bp):
GGCACACGGCCGA
Found at i:38596975 original size:27 final size:29
Alignment explanation
Indices: 38596939--38597062 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
38596929 AAGTCTACAT
* * *
38596939 ACATGCATATGGCCCACTGGGCCC-AA-C
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
38596966 TCATTCATATGGCCCATTAGTCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
38596995 ACATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
38597024 ACATTCATATGGCCCATTATGCCAAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
38597053 ACATCCATAT
1 ACATTCATAT
38597063 TCATGCTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 19 0.23
28 2 0.02
29 62 0.75
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:38601545 original size:13 final size:13
Alignment explanation
Indices: 38601527--38601555 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38601517 AACAAAATAG
38601527 GAAATAAAAGAAA
1 GAAATAAAAGAAA
38601540 GAAATAAAAGAAA
1 GAAATAAAAGAAA
38601553 GAA
1 GAA
38601556 GAGAAGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
GAAATAAAAGAAA
Found at i:38609299 original size:30 final size:30
Alignment explanation
Indices: 38609263--38609324 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
38609253 CACATAGGAT
38609263 AGGAAGAGTTCAAGGATTTCTTCGACTTCG
1 AGGAAGAGTTCAAGGATTTCTTCGACTTCG
*
38609293 AGGAAGAGTTCAGGGATTTCTTCGACTTCG
1 AGGAAGAGTTCAAGGATTTCTTCGACTTCG
38609323 AG
1 AG
38609325 TGGTTGAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
AGGAAGAGTTCAAGGATTTCTTCGACTTCG
Found at i:38616683 original size:27 final size:27
Alignment explanation
Indices: 38616645--38616698 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38616635 CTATTTATAG
*
38616645 GCATAAGAAGTATGAATGAAGTAGAGA
1 GCATAAGAAGTATAAATGAAGTAGAGA
38616672 GCATAAGAAGTATAAATGAAGTAGAGA
1 GCATAAGAAGTATAAATGAAGTAGAGA
38616699 TCTACTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.19
Consensus pattern (27 bp):
GCATAAGAAGTATAAATGAAGTAGAGA
Found at i:38622649 original size:22 final size:22
Alignment explanation
Indices: 38622623--38622685 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
38622613 GTTTAACTAA
38622623 GATTTAAAGTTTATTAAATTAG
1 GATTTAAAGTTTATTAAATTAG
38622645 GATTTAGAA--TT-TT-AATTAG
1 GATTTA-AAGTTTATTAAATTAG
* **
38622664 GGTTTAGTGTTTATTAAATTAG
1 GATTTAAAGTTTATTAAATTAG
38622686 TGTTTTAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
19 11 0.33
20 4 0.12
21 4 0.12
22 12 0.36
23 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (22 bp):
GATTTAAAGTTTATTAAATTAG
Found at i:38622696 original size:23 final size:23
Alignment explanation
Indices: 38622658--38622707 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
38622648 TTAGAATTTT
38622658 AATTAGGGTTTAGTG-TTTATTA
1 AATTAGGGTTTAGTGTTTTATTA
* *
38622680 AATTAGTGTTTTAGTGTTTTATTT
1 AATTAG-GGTTTAGTGTTTTATTA
38622704 AATT
1 AATT
38622708 TTTATGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (23 bp):
AATTAGGGTTTAGTGTTTTATTA
Found at i:38622723 original size:18 final size:19
Alignment explanation
Indices: 38622688--38622726 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
38622678 TAAATTAGTG
38622688 TTTTAGTGTTTTATTTAAT
1 TTTTAGTGTTTTATTTAAT
38622707 TTTTA-TGTGTTTA-TTAAT
1 TTTTAGTGT-TTTATTTAAT
38622725 TT
1 TT
38622727 GTGTTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTAGTGTTTTATTTAAT
Found at i:38626676 original size:22 final size:22
Alignment explanation
Indices: 38626651--38626692 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38626641 ACCCTAAACT
*
38626651 ATAAACCCTAAACTCTTAAATC
1 ATAAACCCTAAAATCTTAAATC
38626673 ATAAACCCTAAAATCTTAAA
1 ATAAACCCTAAAATCTTAAA
38626693 AATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAACCCTAAAATCTTAAATC
Found at i:38636751 original size:14 final size:15
Alignment explanation
Indices: 38636734--38636797 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 15
38636724 TATTTTATAA
38636734 GGTTTAGGGTATT-G
1 GGTTTAGGGTATTAG
* *
38636748 GGTTTTGAGT-TTAG
1 GGTTTAGGGTATTAG
* **
38636762 GATTTAGTTTA-TAG
1 GGTTTAGGGTATTAG
*
38636776 GGTTTAGGGTATTGG
1 GGTTTAGGGTATTAG
38636791 GGTTTAG
1 GGTTTAG
38636798 TCTATTGGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
13 2 0.05
14 26 0.70
15 9 0.24
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (15 bp):
GGTTTAGGGTATTAG
Found at i:38637106 original size:84 final size:83
Alignment explanation
Indices: 38636991--38637183 Score: 228
Period size: 84 Copynumber: 2.3 Consensus size: 83
38636981 AAAATGCCAC
*
38636991 AAAATATGATAAATTGAATGAAAACAGCGTCGTTCTACTTGG-AGGGATAGTGGAGTTAGTGGCA
1 AAAATATGAGAAATTGAATGAAAACAGCGTCGTTCTACTTGGCAGGG-TAGTGGAGTTAGTGGCA
*
38637055 CTAAGTCATAAACGCTGCT
65 CTAACTCATAAACGCTGCT
* * * * * *
38637074 AAAAGTATGAGAAATTGTATGGAAAC-GTCGTCGTTTTATTTGGCATGGTAGTGGATTTAGTGGC
1 AAAA-TATGAGAAATTGAATGAAAACAG-CGTCGTTCTACTTGGCAGGGTAGTGGAGTTAGTGGC
* * *
38637138 GCTATCTTATAAACGCTGCT
64 ACTAACTCATAAACGCTGCT
*
38637158 AAAAATATGAGAAACTGAATGAAAAC
1 -AAAATATGAGAAATTGAATGAAAAC
38637184 TACATTAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
83 5 0.05
84 80 0.87
85 7 0.08
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (83 bp):
AAAATATGAGAAATTGAATGAAAACAGCGTCGTTCTACTTGGCAGGGTAGTGGAGTTAGTGGCAC
TAACTCATAAACGCTGCT
Found at i:38637196 original size:84 final size:84
Alignment explanation
Indices: 38637038--38637246 Score: 197
Period size: 84 Copynumber: 2.5 Consensus size: 84
38637028 CTTGGAGGGA
* * ** * * * * *
38637038 TAGTGGAGTTAGTGGCACTAAGTCATAAACGCTGCTAAAAGTATGAGAAATTGTATGGAAACGTC
1 TAGTGGAATTAGTGGCGCTATCTTATAAACGCTGCTAAAAATATGAGAAACTGAATGAAAACGTC
* ** * *
38637103 GTCGTTTTATTTGGCATGG
66 ATCAATTTATGTGGCACGG
*
38637122 TAGTGGATTTAGTGGCGCTATCTTATAAACGCTGCTAAAAATATGAGAAACTGAATGAAAAC-TA
1 TAGTGGAATTAGTGGCGCTATCTTATAAACGCTGCTAAAAATATGAGAAACTGAATGAAAACGT-
* *
38637186 CATTAATTTATGTGGTACGG
65 CATCAATTTATGTGGCACGG
* * * *
38637206 T-TTAGGAATTAGTGGCGCTATCTTAGAAATGCTGCAAAAAA
1 TAGT-GGAATTAGTGGCGCTATCTTATAAACGCTGCTAAAAA
38637247 AGTGAATTAC
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
83 2 0.02
84 100 0.98
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (84 bp):
TAGTGGAATTAGTGGCGCTATCTTATAAACGCTGCTAAAAATATGAGAAACTGAATGAAAACGTC
ATCAATTTATGTGGCACGG
Found at i:38640329 original size:3 final size:3
Alignment explanation
Indices: 38640323--38640361 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
38640313 TTAAGCTTTA
38640323 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38640362 GTTTGTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38640814 original size:13 final size:13
Alignment explanation
Indices: 38640796--38640825 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38640786 CCACATAATA
38640796 CATAAATATATAT
1 CATAAATATATAT
38640809 CATAAATATATAT
1 CATAAATATATAT
38640822 CATA
1 CATA
38640826 TCATAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:38640839 original size:9 final size:9
Alignment explanation
Indices: 38640827--38640905 Score: 56
Period size: 9 Copynumber: 9.0 Consensus size: 9
38640817 TATATCATAT
*
38640827 CATAAGTTA
1 CATAACTTA
38640836 CATAACTTA
1 CATAACTTA
38640845 CATAA--TA
1 CATAACTTA
*
38640852 CATAA-ATA
1 CATAACTTA
* ** *
38640860 TATGTCATA
1 CATAACTTA
38640869 TCATAACTTA
1 -CATAACTTA
38640879 CATAACTTA
1 CATAACTTA
*
38640888 CAAAACTTA
1 CATAACTTA
*
38640897 CTTAACTTA
1 CATAACTTA
38640906 TGTAATACAT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
7 7 0.12
8 4 0.07
9 40 0.71
10 5 0.09
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:38640917 original size:43 final size:43
Alignment explanation
Indices: 38640809--38640917 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
38640799 AAATATATAT
* * * *
38640809 CATAAATATATATCATATCATAAGTTACATAACTTACATAATA
1 CATAAATATATGTAATATCATAACTTACATAACTTACAAAATA
*
38640852 CATAAATATATGTCATATCATAACTTACATAACTTACAAAACTTA
1 CATAAATATATGTAATATCATAACTTACATAACTTACAAAA--TA
* *
38640897 CTTAACT-TATGTAATA-CATAA
1 CATAAATATATGTAATATCATAA
38640918 ATATACACTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 43 0.74
44 8 0.14
45 7 0.12
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.35
Consensus pattern (43 bp):
CATAAATATATGTAATATCATAACTTACATAACTTACAAAATA
Found at i:38644710 original size:40 final size:40
Alignment explanation
Indices: 38644664--38644794 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
38644654 CGGAATATAA
*
38644664 CCGGATATAATCACGT-GCACAAATGTCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
38644704 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
38644744 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38644784 CCGGATATAAT
1 CCGGATATAAT
38644795 TTCCAGCATA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38644808 original size:40 final size:40
Alignment explanation
Indices: 38644664--38644820 Score: 122
Period size: 40 Copynumber: 4.0 Consensus size: 40
38644654 CGGAATATAA
* ** * * *
38644664 CCGGATATAATCACGTGCACAAATGTCTTCGGGTCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
* ** *
38644704 CCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAAC
* *
38644744 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
*** * *
38644784 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTA
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTA
38644821 GCGGATATCA
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 6 0.06
40 88 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
Found at i:38649823 original size:40 final size:40
Alignment explanation
Indices: 38649696--38649825 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
38649686 ATGCTGGAAA
* *
38649696 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
38649736 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
38649776 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
38649816 TTATATCCGG
1 TTATATCCGG
38649826 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:38660504 original size:40 final size:40
Alignment explanation
Indices: 38660377--38660506 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
38660367 ATGCTGGAAA
* *
38660377 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
38660417 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
38660457 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
38660497 TTATATCCGG
1 TTATATCCGG
38660507 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:38664971 original size:13 final size:14
Alignment explanation
Indices: 38664955--38664983 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38664945 TTATAAATAT
38664955 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
38664968 TTATAATGGTTTAA
1 TTATAATGGTTTAA
38664982 TT
1 TT
38664984 TGTTATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:38665445 original size:21 final size:21
Alignment explanation
Indices: 38665393--38665447 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
38665383 ACTTAGAGCG
* *
38665393 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAGCAGCGAGAGAGGCA
*
38665414 GCGGCAGCAGCGAGAGAGGCA
1 GAGGCAGCAGCGAGAGAGGCA
38665435 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
38665448 TGGCAGCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.49, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGAGAGGCA
Found at i:38665853 original size:43 final size:42
Alignment explanation
Indices: 38665806--38665937 Score: 138
Period size: 43 Copynumber: 3.1 Consensus size: 42
38665796 AAAATTAGTG
* * *
38665806 GCGTTTATTAAAAAAGCGACGCTAAAAGTCATGGCTTTTAGCA
1 GCGTTTATTAAAAAA-CGCCGCTAAAAGCCATGACTTTTAGCA
* * * *
38665849 GCGTTTGTGAAAAAAATGCCGCTAAAAGCCATGACTTTTAGCG
1 GCGTTTAT-TAAAAAACGCCGCTAAAAGCCATGACTTTTAGCA
*** *
38665892 GCGCTTCCCTAACAAACGCCGCTAAAAGCCATGACTTTTAGCA
1 GCG-TTTATTAAAAAACGCCGCTAAAAGCCATGACTTTTAGCA
38665935 GCG
1 GCG
38665938 CTTTTCTTAC
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
43 65 0.89
44 8 0.11
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
GCGTTTATTAAAAAACGCCGCTAAAAGCCATGACTTTTAGCA
Found at i:38665939 original size:43 final size:43
Alignment explanation
Indices: 38665825--38665954 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 43
38665815 AAAAAAGCGA
* * * * ** * *
38665825 CGCTAAAAGTCATGGCTTTTAGCAGCGTTTGTGAAAAAAATGC
1 CGCTAAAAGCCATGACTTTTAGCAGCGCTTCTCTAACAAACGC
* *
38665868 CGCTAAAAGCCATGACTTTTAGCGGCGCTTCCCTAACAAACGC
1 CGCTAAAAGCCATGACTTTTAGCAGCGCTTCTCTAACAAACGC
* *
38665911 CGCTAAAAGCCATGACTTTTAGCAGCGCTTTTCTTACAAACGC
1 CGCTAAAAGCCATGACTTTTAGCAGCGCTTCTCTAACAAACGC
38665954 C
1 C
38665955 ATGCCGCTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
CGCTAAAAGCCATGACTTTTAGCAGCGCTTCTCTAACAAACGC
Found at i:38668314 original size:15 final size:15
Alignment explanation
Indices: 38668293--38668344 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
38668283 GGGTTTTTAA
38668293 GGTTTTATTAATTAG
1 GGTTTTATTAATTAG
* *
38668308 AGTTTTATTAATAAG
1 GGTTTTATTAATTAG
38668323 GGTTTTATTAATTAG
1 GGTTTTATTAATTAG
38668338 GGTTTTA
1 GGTTTTA
38668345 CATACTCGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
GGTTTTATTAATTAG
Found at i:38672115 original size:18 final size:18
Alignment explanation
Indices: 38672094--38672144 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
38672084 TTTCAATCTC
*
38672094 ATTTTTCTTCTTTTCATT
1 ATTTTTCTTCTTTTCATA
*
38672112 ATTTTTTTTCTTTTTCATA
1 ATTTTTCTTC-TTTTCATA
38672131 ATCTTTCTCTTCTT
1 AT-TTT-TCTTCTT
38672145 CTTTCTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.33
19 9 0.33
20 5 0.19
21 4 0.15
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTCTTCTTTTCATA
Found at i:38672117 original size:19 final size:20
Alignment explanation
Indices: 38672095--38672144 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
38672085 TTCAATCTCA
*
38672095 TTTTTCTTCTTTTCATTAT-
1 TTTTTCTTCTTTTCATAATC
38672114 TTTTT-TTCTTTTTCATAATC
1 TTTTTCTTC-TTTTCATAATC
*
38672134 TTTCTCTTCTT
1 TTTTTCTTCTT
38672145 CTTTCTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.12
19 14 0.54
20 6 0.23
21 3 0.12
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTCTTTTCATAATC
Found at i:38672142 original size:39 final size:42
Alignment explanation
Indices: 38672076--38672165 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 42
38672066 GATCAAGTTC
* * *
38672076 TTTTTCTTTTTCAATCTCATTTTTCTTC-T-TTTCATTATTT
1 TTTTTCTTTTTCAATATCATTTCTCTTCTTCTTTCATTACTT
*
38672116 TTTTTCTTTTTC-ATAATC-TTTCTCTTCTTCTTTCTTTACTT
1 TTTTTCTTTTTCAAT-ATCATTTCTCTTCTTCTTTCATTACTT
38672157 TTTTTCTTT
1 TTTTTCTTT
38672166 CACACACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
39 10 0.23
40 15 0.35
41 18 0.42
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (42 bp):
TTTTTCTTTTTCAATATCATTTCTCTTCTTCTTTCATTACTT
Found at i:38680138 original size:39 final size:39
Alignment explanation
Indices: 38680094--38680221 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
38680084 TTTGAGATTG
*
38680094 AAAATATCCGGACATGAGGTCCGTAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
38680133 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * *
38680172 AATATATCCGGACTTGAGGTCCGCAGGCTACATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
38680211 AAAATATCCGG
1 AAAATATCCGG
38680222 GTTAAAGACC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:38680235 original size:39 final size:39
Alignment explanation
Indices: 38680113--38680239 Score: 132
Period size: 39 Copynumber: 3.3 Consensus size: 39
38680103 GGACATGAGG
* **
38680113 TCCGTAGGCTATATGCTGGAAAAATATCC-GGACATGAGA
1 TCCGCAGGCTATATGCTGGAAAAATATCCGGGTTA-GAGA
* * * *
38680152 TCCGCAGGCTATATGCTAGAAATATATCCGGACTT-GAGG
1 TCCGCAGGCTATATGCTGGAAAAATATCCGG-GTTAGAGA
* *
38680191 TCCGCAGGCTACATGCTGGAAAAATATCCGGGTTAAAGA
1 TCCGCAGGCTATATGCTGGAAAAATATCCGGGTTAGAGA
*
38680230 CCCGCAGGCT
1 TCCGCAGGCT
38680240 TACGCTAGTA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.03
39 68 0.96
40 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (39 bp):
TCCGCAGGCTATATGCTGGAAAAATATCCGGGTTAGAGA
Found at i:38680235 original size:78 final size:76
Alignment explanation
Indices: 38680093--38680247 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 76
38680083 GTTTGAGATT
* * * *
38680093 GAAAATATCCGGACATGAGGTCCGTAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGCA
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
*
38680158 GGCTATATGCTA
66 GGCT-TACGCTA
* **
38680170 GAAATATATCCGGACTTGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACCCG
38680234 CAGGCTTACGCTA
64 CAGGCTTACGCTA
38680247 G
1 G
38680248 TAATGTATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 12 0.18
78 56 0.82
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:38685423 original size:39 final size:39
Alignment explanation
Indices: 38685379--38685505 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
38685369 TTTGAGATTG
38685379 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
38685418 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * * *
38685457 AATATATCTGGACTTGAGGTCCGCAGGCTACATGCTGG-
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
38685495 AAAATATCCGG
1 AAAATATCCGG
38685506 GTTAAAGACC
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 9 0.12
39 69 0.88
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:38689989 original size:8 final size:8
Alignment explanation
Indices: 38689978--38690024 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
38689968 AAAATTAGAA
38689978 AAAAATAT
1 AAAAATAT
*
38689986 AAAAAAAT
1 AAAAATAT
38689994 AAAAATTAT
1 AAAAA-TAT
38690003 AAAATATAT
1 AAAA-ATAT
*
38690012 AGAAATAT
1 AAAAATAT
38690020 AAAAA
1 AAAAA
38690025 AATTATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 20 0.61
9 12 0.36
10 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:38690019 original size:10 final size:9
Alignment explanation
Indices: 38689979--38690035 Score: 50
Period size: 8 Copynumber: 6.6 Consensus size: 9
38689969 AAATTAGAAA
38689979 AAAATATA-
1 AAAATATAT
*
38689987 AAAAAATA-
1 AAAATATAT
38689995 AAAAT-TAT
1 AAAATATAT
38690003 AAAATATAT
1 AAAATATAT
38690012 AGAAATATA-
1 A-AAATATAT
*
38690021 AAAAAATTAT
1 AAAATA-TAT
38690031 AAAAT
1 AAAAT
38690036 TTTATAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.05
8 20 0.50
9 7 0.17
10 11 0.28
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAATATAT
Found at i:38690374 original size:27 final size:28
Alignment explanation
Indices: 38690329--38690384 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
38690319 TTTTTTCCTA
* * *
38690329 ATTTTTAATAAATTTTAAT-TTTTTTAT
1 ATTTTTAATAAAATGTAATAATTTTTAT
*
38690356 ATTTTTATTAAAATGTAATAATTTTTAT
1 ATTTTTAATAAAATGTAATAATTTTTAT
38690384 A
1 A
38690385 AAATTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTTTTAATAAAATGTAATAATTTTTAT
Found at i:38690532 original size:84 final size:84
Alignment explanation
Indices: 38690443--38690596 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
38690433 TTAATTGTAA
* * * *
38690443 TTTTTTGAAAAATTTTAAGGGTCTTTTTGATGTATTTTGAAAGTTCAAAT-ATCCAATTAAGTGA
1 TTTTTTGAAAAAGTTTAAGGGTCTTTTTGATGCATTTTGAAAATTCAAATGCT-CAATTAAGTGA
38690507 AAAAAAAAGCTTAGTTGCTT
65 AAAAAAAAGCTTAGTTGCTT
* * *
38690527 TTTTTTGAACAAGTTTAAGGGTCTTTTTGATGCATTTTGAAAATTCAAGTGCTCAATTAAGTGTA
1 TTTTTTGAAAAAGTTTAAGGGTCTTTTTGATGCATTTTGAAAATTCAAATGCTCAATTAAGTGAA
38690592 AAAAA
66 AAAAA
38690597 GAGAGGAGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
84 61 0.98
85 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (84 bp):
TTTTTTGAAAAAGTTTAAGGGTCTTTTTGATGCATTTTGAAAATTCAAATGCTCAATTAAGTGAA
AAAAAAAGCTTAGTTGCTT
Found at i:38694608 original size:46 final size:46
Alignment explanation
Indices: 38694459--38694631 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
38694449 TCACTTGTGT
* * * *
38694459 GAGCTAGTGTAAGACATGCCTGGGGA-ATGCATCGGCCA-C-ATTATGA
1 GAGCCAGTGTAAGACATGTCT-GGGACATGCATCGG-CATCGA-GACGA
* *
38694505 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGA
* * * *
38694553 GTGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-A
*
38694600 -AGCCAGTGTAAGAGATGTCTGGGACATGCATC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC
38694632 AGCTATGAGA
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
46 59 0.55
47 24 0.22
48 23 0.21
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGA
Found at i:38698326 original size:28 final size:27
Alignment explanation
Indices: 38698263--38698332 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
38698253 ATAGTGAGTC
38698263 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
38698290 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
38698318 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38698333 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:38705969 original size:29 final size:28
Alignment explanation
Indices: 38705937--38706039 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
38705927 GTGACGAGAT
* *
38705937 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
38705966 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
38705995 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
38706024 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
38706040 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:38708510 original size:27 final size:27
Alignment explanation
Indices: 38708492--38708561 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
38708482 ATAGTGAGTC
38708492 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
38708519 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
38708547 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
38708562 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:38714720 original size:46 final size:46
Alignment explanation
Indices: 38714584--38714754 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
38714574 TCGACTAGTC
* * * * *
38714584 GCTAGTGTAGGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGA
1 GCTACTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGA
* * * * * *
38714630 GCTAGTGTAAGACCATGTCTAGGACATGGAATCGGCATTGAGACGAGT
1 GCTACTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAGA
*
38714678 GCTACTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGACGTA-A
1 GCTACTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGA
* *
38714724 GCCACTGTAAGAGATGTCTGGGACATGCATC
1 GCTACTGTAAGACATGTCTGGGACATGCATC
38714755 AGCTATGAGA
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
46 53 0.52
47 26 0.25
48 22 0.22
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTACTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGA
Found at i:38722274 original size:28 final size:28
Alignment explanation
Indices: 38722234--38722306 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
38722224 GTTCAAATTG
* *
38722234 TATAGCACTAAGTGTGCAAGTTTGATTA
1 TATAGCACTAAGTGTGCAAGTTCGACTA
* *
38722262 TATAGCACTAAGTGTACGAGTTCGACTA
1 TATAGCACTAAGTGTGCAAGTTCGACTA
38722290 T-TAAGCACTAAGTGTGC
1 TAT-AGCACTAAGTGTGC
38722307 GGGCTTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCAAGTTCGACTA
Found at i:38724798 original size:46 final size:45
Alignment explanation
Indices: 38724691--38724864 Score: 138
Period size: 44 Copynumber: 3.9 Consensus size: 45
38724681 GCTATACACC
* ** * * * *
38724691 TAAAA-TGAGTAAGACAATAACTGAAAGATGTTATGACTTCA-GAA
1 TAAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGGCATAATG-A
* * * *
38724735 TAAAA-TAAGTAAGACCATAGTTGGAAGATGCTATAGCATAATGG
1 TAAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGGCATAATGA
* ** *
38724779 TAAAAGATGAGTAAGACCATAGTTAAAAGACACTATGGCATCATGA
1 TAAAAG-TGAGTAAGACCATAGTTGAAAGATGCTATGGCATAATGA
** * *
38724825 TGGAAGTGAGTAAGACCATGGCTGAAAGATGCTATGGCAT
1 TAAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGGCAT
38724865 CCTTTGAAAG
Statistics
Matches: 101, Mismatches: 26, Indels: 5
0.77 0.20 0.04
Matches are distributed among these distances:
44 36 0.36
45 30 0.30
46 35 0.35
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.24
Consensus pattern (45 bp):
TAAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGGCATAATGA
Found at i:38728187 original size:27 final size:27
Alignment explanation
Indices: 38728157--38728209 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
38728147 TGGTAAGGAG
* *
38728157 GTTCACTAGTGTTTTTGGTGAGCTAGT
1 GTTCACTAGTGTGTTTGGTGAACTAGT
38728184 GTTCACTAGTGTGTTTGGTGAACTAG
1 GTTCACTAGTGTGTTTGGTGAACTAG
38728210 GGGTTCGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.42
Consensus pattern (27 bp):
GTTCACTAGTGTGTTTGGTGAACTAGT
Found at i:38737662 original size:2 final size:2
Alignment explanation
Indices: 38737655--38737692 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
38737645 ATTGAAAGGG
*
38737655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38737693 GTGTTAAAGT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38738471 original size:2 final size:2
Alignment explanation
Indices: 38738464--38738493 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38738454 ATTGAAAGGG
*
38738464 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38738494 GTGTTAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38747420 original size:28 final size:28
Alignment explanation
Indices: 38747350--38747450 Score: 96
Period size: 28 Copynumber: 3.5 Consensus size: 28
38747340 ATAGTGGATC
* *
38747350 CGCACACTTAGTGCTATATGTATTC-AGCT
1 CGCACACTTAGTGCTATA--TAATCAAACT
*
38747379 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38747407 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
38747437 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38747451 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.07
28 21 0.34
29 17 0.28
30 19 0.31
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38747443 original size:30 final size:28
Alignment explanation
Indices: 38747380--38747450 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
38747370 TATTCAGCTT
* *
38747380 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATACAATCAAACCC
* *
38747408 GCACACTTAGTGCTGTACAATTTTAAACCC
1 GCACACTTAGTGCTATACAA--TCAAACCC
38747438 GCACACTTAGTGC
1 GCACACTTAGTGC
38747451 CAATCTTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 18 0.49
30 19 0.51
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (28 bp):
GCACACTTAGTGCTATACAATCAAACCC
Found at i:38752507 original size:12 final size:12
Alignment explanation
Indices: 38752490--38752521 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38752480 TTATTAAAAC
38752490 TACTTTTATTTT
1 TACTTTTATTTT
38752502 TACTTTTATTTT
1 TACTTTTATTTT
*
38752514 TATTTTTA
1 TACTTTTA
38752522 GCAGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (12 bp):
TACTTTTATTTT
Found at i:38756711 original size:27 final size:27
Alignment explanation
Indices: 38756679--38756989 Score: 410
Period size: 27 Copynumber: 11.5 Consensus size: 27
38756669 AGTACTCCCA
*
38756679 ATTTATAGAATTACCGTTTTACCCTC-
1 ATTTACAGAATTACCGTTTTACCCTCG
* *
38756705 AGGTTATAGAATTACCGTTTTACCCTCG
1 A-TTTACAGAATTACCGTTTTACCCTCG
38756733 ATTTACAGAATTACCGTTTTACCCTC-
1 ATTTACAGAATTACCGTTTTACCCTCG
**
38756759 AGTTTACAGAATTACTATTTTACCCTCG
1 A-TTTACAGAATTACCGTTTTACCCTCG
* * *
38756787 ATTTACAGAATTATCGTTTTACCCCCA
1 ATTTACAGAATTACCGTTTTACCCTCG
* *
38756814 ATTTACATAATTACCGTTTTACCCCCG
1 ATTTACAGAATTACCGTTTTACCCTCG
* *
38756841 ATTTACATAATTATCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
*
38756868 ATTTACAAAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
*
38756895 ATTTACAGAATTACCATTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
* * *
38756922 ATTTATAGAATTACTGTTTTACCCTTG
1 ATTTACAGAATTACCGTTTTACCCTCG
* *
38756949 ATTTACAGAATTACTGTTTTACCCCCG
1 ATTTACAGAATTACCGTTTTACCCTCG
*
38756976 ATTTACAAAATTAC
1 ATTTACAGAATTAC
38756990 TAAAATACCT
Statistics
Matches: 254, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
26 2 0.01
27 250 0.98
28 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (27 bp):
ATTTACAGAATTACCGTTTTACCCTCG
Found at i:38758255 original size:25 final size:25
Alignment explanation
Indices: 38758227--38758298 Score: 126
Period size: 25 Copynumber: 2.9 Consensus size: 25
38758217 TTATACCATG
* *
38758227 AAAATGACCGTTTTACCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38758252 AAAATGACCATTATACCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38758277 AAAATGACCATTATACCCCTAG
1 AAAATGACCATTATACCCCTAG
38758299 AGTTTATGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38758368 original size:20 final size:20
Alignment explanation
Indices: 38758343--38758421 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
38758333 TAAATATGGT
*
38758343 ATGTATGAGATGCACATGAC
1 ATGTATGATATGCACATGAC
38758363 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
38758383 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
38758403 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
38758422 TGTAATCATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:38758403 original size:11 final size:11
Alignment explanation
Indices: 38758367--38758422 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
38758357 CATGACATGT
38758367 ATGATATGCAC
1 ATGATATGCAC
* *
38758378 ATGACATG--T
1 ATGATATGCAC
38758387 ATGATATGCAC
1 ATGATATGCAC
*
38758398 ATGATATG--T
1 ATGATATGCAC
38758407 ATGATATGCAC
1 ATGATATGCAC
38758418 ATGAT
1 ATGAT
38758423 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:38758499 original size:24 final size:24
Alignment explanation
Indices: 38758472--38758614 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
38758462 GAGGAAGTGA
38758472 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38758496 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38758520 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
38758543 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * * *
38758567 GAAAGGGCTTTTACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
38758591 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38758615 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
23 23 0.21
24 75 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:38758565 original size:47 final size:47
Alignment explanation
Indices: 38758472--38758614 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
38758462 GAGGAAGTGA
38758472 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
38758520 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * * *
38758567 GAAAGGGCTTTTACCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
38758615 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 42 0.48
48 34 0.39
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:38758588 original size:71 final size:72
Alignment explanation
Indices: 38758472--38758615 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
38758462 GAGGAAGTGA
* *
38758472 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATCAAAAGAGGC-TAGGCCT
38758535 CCAGTTAT
65 CCAGTTAT
** * *
38758543 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTACCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATCAAAAGAGGCTAGGCCTC
38758608 CAGTTAT
66 CAGTTAT
38758615 A
1 A
38758616 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 53 0.82
72 12 0.18
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:38758841 original size:31 final size:31
Alignment explanation
Indices: 38758806--38758869 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
38758796 CGTTTACAGT
38758806 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
38758837 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38758868 AA
1 AA
38758870 CATGAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38761726 original size:40 final size:40
Alignment explanation
Indices: 38761641--38761791 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
38761631 AATTGAATGA
* * *
38761641 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGATA-TAC
* * *
38761681 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGGCTAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGAT--ATAC
*
38761722 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGATATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGATATAC
*
38761761 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
38761792 ACGTGATTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
39 5 0.05
40 82 0.90
41 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGATATAC
Found at i:38761805 original size:40 final size:40
Alignment explanation
Indices: 38761677--38761807 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 40
38761667 TATGCTGGAA
* * *
38761677 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * *
38761717 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TG
*
38761757 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
38761797 ATTATATCCGG
1 ATTATATCCGG
38761808 TTATATTCCG
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 72 0.96
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:38763529 original size:42 final size:42
Alignment explanation
Indices: 38763424--38763581 Score: 194
Period size: 42 Copynumber: 3.7 Consensus size: 42
38763414 ACCAATGTCG
* * * *
38763424 TATCCTAGATACGGTCTTACA-TATAATCTCATATCAATGCCAA
1 TATCCCAGATATGGTCTTACACGA-AGTCTCATATCAATGCC-A
* * *
38763467 TAGCCCAGCTATGGTCTTACACGAAGTCTCATATCGATGCCA
1 TATCCCAGATATGGTCTTACACGAAGTCTCATATCAATGCCA
* *
38763509 TATCCCAGATATGGTCTTACATGAAGTCTTATATCAATGCCA
1 TATCCCAGATATGGTCTTACACGAAGTCTCATATCAATGCCA
38763551 TATCCCAGATATGGTCTTACACGTAA-TCTCA
1 TATCCCAGATATGGTCTTACACG-AAGTCTCA
38763582 GTAACCCTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 64 0.65
43 34 0.34
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (42 bp):
TATCCCAGATATGGTCTTACACGAAGTCTCATATCAATGCCA
Found at i:38763544 original size:85 final size:84
Alignment explanation
Indices: 38763424--38763581 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 84
38763414 ACCAATGTCG
* *
38763424 TATCCTAGATACGGTCTTACATATAATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTACAC
1 TATCCCAGATACGGTCTTACATATAATCTCATATCAATGCC-ATAGCCCAGATATGGTCTTACAC
38763489 G-AAGTCTCATATCGATGCCA
65 GTAA-TCTCATATCGATGCCA
* * * *
38763509 TATCCCAGATATGGTCTTACATGA-AGTCTTATATCAATGCCATATCCCAGATATGGTCTTACAC
1 TATCCCAGATACGGTCTTACAT-ATAATCTCATATCAATGCCATAGCCCAGATATGGTCTTACAC
38763573 GTAATCTCA
65 GTAATCTCA
38763582 GTAACCCTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
84 27 0.42
85 37 0.57
86 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (84 bp):
TATCCCAGATACGGTCTTACATATAATCTCATATCAATGCCATAGCCCAGATATGGTCTTACACG
TAATCTCATATCGATGCCA
Found at i:38769555 original size:46 final size:46
Alignment explanation
Indices: 38769488--38769708 Score: 299
Period size: 46 Copynumber: 4.8 Consensus size: 46
38769478 TGTAACCCGC
* *
38769488 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
38769534 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* * *
38769584 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
38769626 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
38769672 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
38769709 TGCCCAAATA
Statistics
Matches: 154, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 2 0.01
44 2 0.01
45 26 0.17
46 83 0.54
47 26 0.17
48 2 0.01
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:38772131 original size:29 final size:29
Alignment explanation
Indices: 38772092--38772179 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
38772082 CAAAGATAAC
*
38772092 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
38772121 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
38772150 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
38772180 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:38772150 original size:15 final size:15
Alignment explanation
Indices: 38772092--38772170 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
38772082 CAAAGATAAC
*
38772092 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
38772106 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
38772121 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
38772135 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
38772150 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
38772165 AAGAAA
1 AAGAAA
38772171 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:38772179 original size:15 final size:15
Alignment explanation
Indices: 38772103--38772179 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
38772093 AGAAAACCGA
38772103 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
38772118 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
38772132 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
38772146 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
38772162 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
38772177 ATA
1 ATA
38772180 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:38778992 original size:25 final size:25
Alignment explanation
Indices: 38778964--38779014 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
38778954 TGTGTTTTAA
38778964 TGATTTATGAAGAAACATGAGAGTT
1 TGATTTATGAAGAAACATGAGAGTT
* *
38778989 TGATTTATGAAGGAATATGAGAGTT
1 TGATTTATGAAGAAACATGAGAGTT
38779014 T
1 T
38779015 AAAGGATGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (25 bp):
TGATTTATGAAGAAACATGAGAGTT
Found at i:38781142 original size:40 final size:40
Alignment explanation
Indices: 38781097--38781247 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
38781087 ATAATCACGT
38781097 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
* *
38781137 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTC
* * **
38781177 GCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATTTC-C
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
** * *
38781216 AGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 -GCACGAATGCCTTCGGGTCTTAGCCCGGATA
38781248 TCATTCAATT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 84 0.91
41 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
Found at i:38783130 original size:40 final size:39
Alignment explanation
Indices: 38782963--38783132 Score: 150
Period size: 40 Copynumber: 4.3 Consensus size: 39
38782953 AGAAATTGAA
* *
38782963 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
38783003 TTATATCCGGGTTAAGACCCGAAGG-AATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
38783042 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
38783082 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
38783122 TGATATCCGGG
1 TGATATCCGGG
38783133 TAAAGTCCCG
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 24 0.23
40 72 0.69
41 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:38791056 original size:39 final size:40
Alignment explanation
Indices: 38790998--38791098 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
38790988 AAATTGAATG
* *
38790998 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
38791037 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
38791077 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
38791099 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:38791091 original size:40 final size:40
Alignment explanation
Indices: 38790998--38791174 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 40
38790988 AAATTGAATG
* * * * *
38790998 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38791037 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38791077 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
38791117 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
*
38791157 ATATCCGGG-TAAGTCCCG
1 ATATCCGGGCTAAGACCCG
38791175 TTGGCCTTGG
Statistics
Matches: 117, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 40 0.34
40 75 0.64
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:38800371 original size:17 final size:16
Alignment explanation
Indices: 38800353--38800395 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
38800343 AATGGTTTGT
38800353 TTTAATTAACTAATTG
1 TTTAATTAACTAATTG
* *
38800369 TTTAATCTAATTAACTG
1 TTTAAT-TAACTAATTG
38800386 ATTTAATTAA
1 -TTTAATTAA
38800396 AGCAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (16 bp):
TTTAATTAACTAATTG
Found at i:38800612 original size:21 final size:21
Alignment explanation
Indices: 38800586--38800637 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
38800576 TAATCCTCAG
38800586 TTGAATTAATCAAAATTTCTT
1 TTGAATTAATCAAAATTTCTT
*
38800607 TTGAATTAATCGAAATTTCTT
1 TTGAATTAATCAAAATTTCTT
*
38800628 TCTTAATTAA
1 T-TGAATTAA
38800638 AACCCCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (21 bp):
TTGAATTAATCAAAATTTCTT
Found at i:38803333 original size:12 final size:11
Alignment explanation
Indices: 38803298--38803369 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
38803288 TATGTCTTTC
38803298 AAAATAAAATAAT
1 AAAAT-AAA-AAT
**
38803311 AAAATTGAAAT
1 AAAATAAAAAT
38803322 GAAAATAAAAAT
1 -AAAATAAAAAT
*
38803334 CAAAAGAAAAA-
1 -AAAATAAAAAT
*
38803345 AAAAAAAAAAT
1 AAAATAAAAAT
38803356 AAAAT-AAAAT
1 AAAATAAAAAT
38803366 AAAA
1 AAAA
38803370 ATAGGAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
10 18 0.37
11 7 0.14
12 19 0.39
13 5 0.10
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:38803342 original size:17 final size:17
Alignment explanation
Indices: 38803308--38803370 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
38803298 AAAATAAAAT
* * *
38803308 AATAAAATTGAAATGAA
1 AATAAAAATAAAAAGAA
*
38803325 AATAAAAATCAAAAGAA
1 AATAAAAATAAAAAGAA
* *
38803342 AA-AAAAAAAAAAATAA
1 AATAAAAATAAAAAGAA
38803358 AAT-AAAATAAAAA
1 AATAAAAATAAAAA
38803371 TAGGAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 22 0.58
17 16 0.42
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (17 bp):
AATAAAAATAAAAAGAA
Found at i:38803371 original size:6 final size:6
Alignment explanation
Indices: 38803318--38803372 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
38803308 AATAAAATTG
* * *
38803318 AAATGA AAATAA AAATCA AAAGAA AAA-AA AAA-AA AAAT-A AAAT-A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
38803362 AAATAA AAATA
1 AAATAA AAATA
38803373 GGAATAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 20 0.47
6 23 0.53
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:38808167 original size:39 final size:40
Alignment explanation
Indices: 38808067--38808249 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
38808057 TCGAATGATG
* * *
38808067 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
38808107 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
*
38808147 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * *
38808186 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
** *
38808227 -CCGGGCTTCGTCCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
38808250 TGAGTGAGTC
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 33 0.28
40 75 0.64
41 9 0.08
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:38808231 original size:79 final size:81
Alignment explanation
Indices: 38808067--38808251 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
38808057 TCGAATGATG
* * *
38808067 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
38808131 CGTGCGAGTTAATAAA
66 CGTGCGAGTCAATAAA
* **
38808147 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
38808209 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATA-AA
** *
38808227 -CCGGGCTTCGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38808252 AGTGAGTCGT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATAAA
Found at i:38811970 original size:17 final size:17
Alignment explanation
Indices: 38811948--38811994 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
38811938 ATAAAAGGGT
38811948 TTGTTTTAATTAACTAA
1 TTGTTTTAATTAACTAA
* *
38811965 TTGTTTTAACTAATTAA
1 TTGTTTTAATTAACTAA
* *
38811982 CTGATTTAATTAA
1 TTGTTTTAATTAA
38811995 AGGAAAGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (17 bp):
TTGTTTTAATTAACTAA
Found at i:38817125 original size:100 final size:100
Alignment explanation
Indices: 38816899--38817390 Score: 604
Period size: 100 Copynumber: 4.9 Consensus size: 100
38816889 TAGCCGAAGC
* * * *
38816899 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACGTA-
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACGTAG
* *
38816963 TAGCCTGTACTTAGTACTACACACGTGA-CCTAA-C
66 TAGCCTGCACTTAGTACTACACACGTGATCC-AAGT
* * * * * * *
38816997 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACACAT
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACGT
* * *
38817062 AGCAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
64 AGTAGCCTGCACTTAGTACTACACACGTGATCCAAGT
* * * ** * *
38817097 TATTC-GGTACACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGT
1 TA-TCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCAGGTACACGT
*
38817161 AGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
64 AGTAGCCTGCACTTAGTACTACACACGTGATCCAAGT
** *
38817198 TATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCA-GTACACGTA
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTAT-CAGGTACACGTA
*
38817262 GTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
65 GTAGCCTGCACTTAGTACTACACACGTGATCCAAGT
*
38817298 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCTA-GTACACGTA
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATC-AGGTACACGTA
38817362 GTAGCCTGCACTTAGTACTACACACGTGA
65 GTAGCCTGCACTTAGTACTACACACGTGA
38817391 CCTCACAATA
Statistics
Matches: 345, Mismatches: 39, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
98 39 0.11
99 42 0.12
100 197 0.57
101 67 0.19
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACGTAG
TAGCCTGCACTTAGTACTACACACGTGATCCAAGT
Found at i:38817171 original size:150 final size:150
Alignment explanation
Indices: 38816893--38817385 Score: 742
Period size: 150 Copynumber: 3.3 Consensus size: 150
38816883 CACTTGTAGC
* * *
38816893 CGAAGCTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATAC
1 CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTAC
* *
38816958 ACG-TATAGCCTGTACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCA
66 ACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCA
38817022 CTTAGTACTACACACGTGAT
131 CTTAGTACTACACACGTGAT
* *
38817042 CGAAGTTATCAGGTACACATAGCAGCCTGCACTTAGTACTACACATGCGACCAATTATTCGGTAC
1 CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTAC
38817107 ACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCA
66 ACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCA
38817172 CTTAGTACTACACACGTGAT
131 CTTAGTACTACACACGTGAT
** *
38817192 CGAAGTTATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTAC
1 CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTAC
* * * ** * * * *
38817257 ACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGC
66 ACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTGATACACGTAGTAGCCTGC
*
38817322 ACTTAGTACTACACATGTGA-
130 ACTTAGTACTACACACGTGAT
* *
38817342 CCAA-TTATCTA-GTACACGTAGTAGCCTGCACTTAGTACTACACA
1 CGAAGTTATC-AGGTACACATAGTAGCCTGCACTTAGTACTACACA
38817386 CGTGACCTCA
Statistics
Matches: 315, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
149 98 0.31
150 179 0.57
151 38 0.12
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (150 bp):
CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTAC
ACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCA
CTTAGTACTACACACGTGAT
Found at i:38817359 original size:250 final size:248
Alignment explanation
Indices: 38816900--38817393 Score: 733
Period size: 250 Copynumber: 2.0 Consensus size: 248
38816890 AGCCGAAGCT
* * * *
38816900 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACGTATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGATACACATATA
* * *
38816965 GCCTGTACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTAC
66 GCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACACGTAGTAGCCTGCACTTAGTAC
38817030 TACACACGTGATCGAAGTTATCAGGTACACATAGCAGCCTGCACTTAGTACTACACATGCGACCA
131 TACACACGTGATCGAAGTTATCAGGTACACATAGCAGCCTGCACTTAGTACTACACATGCGACCA
* *
38817095 ATTATTCGGTACACGTTGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
196 ATTATTCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * * * **
38817148 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTATGCATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCAGATACACATA
* **
38817213 GTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCAG-TACACGTAGTAGCCTGCACTTA
64 -TAGCCTGCACTTAGTACTACACACGCGACCTAACCAT-CAGATACACGTAGTAGCCTGCACTTA
* * *
38817276 GTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTG
127 GTACTACACACGTGATCGAAGTTATCAGGTACACATAGCAGCCTGCACTTAGTACTACACATGCG
38817341 ACCAATTA-TCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
192 ACCAATTATTC-AGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
38817394 CACAATAGCT
Statistics
Matches: 220, Mismatches: 21, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
248 39 0.18
249 5 0.02
250 147 0.67
251 29 0.13
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (248 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGATACACATATA
GCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACACGTAGTAGCCTGCACTTAGTAC
TACACACGTGATCGAAGTTATCAGGTACACATAGCAGCCTGCACTTAGTACTACACATGCGACCA
ATTATTCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:38821460 original size:20 final size:20
Alignment explanation
Indices: 38821435--38821473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38821425 TCACATTTGC
* *
38821435 TGAATTTGGCATATAATTGT
1 TGAATTTAGCATACAATTGT
38821455 TGAATTTAGCATACAATTG
1 TGAATTTAGCATACAATTG
38821474 CTTATCTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
TGAATTTAGCATACAATTGT
Found at i:38824546 original size:42 final size:42
Alignment explanation
Indices: 38824487--38824572 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
38824477 GAGTATACTG
*
38824487 ACTTCATTTCAATTTCCACACTAGGGGACACACAGCCGTGTA
1 ACTTCATTTCAATTTCCACACTAGGGGACACACAGCCGCGTA
38824529 ACTTCATTTCAATTTCCACACTAGGGGACACACAGCCGCGTA
1 ACTTCATTTCAATTTCCACACTAGGGGACACACAGCCGCGTA
38824571 AC
1 AC
38824573 ATGTTCGTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (42 bp):
ACTTCATTTCAATTTCCACACTAGGGGACACACAGCCGCGTA
Found at i:38826948 original size:28 final size:29
Alignment explanation
Indices: 38826836--38826960 Score: 189
Period size: 29 Copynumber: 4.3 Consensus size: 29
38826826 GAAAGCATGA
*
38826836 ATATGAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
38826865 ATATGAATGTGATTTTGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
38826894 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
38826923 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
38826951 ATATGTATGT
1 ATATGAATGT
38826961 ATGTAGACTT
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 23 0.26
29 64 0.74
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:38828394 original size:41 final size:40
Alignment explanation
Indices: 38828344--38828489 Score: 211
Period size: 41 Copynumber: 3.6 Consensus size: 40
38828334 ATCTCAAATC
*
38828344 GCACACTAAGTTCCATATATAGCCGAAGCTATCTCGATCTT
1 GCACACTAAGTGCCATATATAGCCGAAGCTATCT-GATCTT
* *
38828385 GCACACTAAGTGCCATATATAGTCGTAGCTATCTTGATCTT
1 GCACACTAAGTGCCATATATAGCCGAAGCTATC-TGATCTT
* *
38828426 GCACACTAAGTGCCATATATAGCCAAAGCTATCATGATCTC
1 GCACACTAAGTGCCATATATAGCCGAAGCTATC-TGATCTT
*
38828467 GCACACTAAGTGCCACATATAGC
1 GCACACTAAGTGCCATATATAGC
38828490 TGATTTGTCG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 94 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (40 bp):
GCACACTAAGTGCCATATATAGCCGAAGCTATCTGATCTT
Found at i:38835472 original size:40 final size:41
Alignment explanation
Indices: 38835407--38835555 Score: 194
Period size: 40 Copynumber: 3.7 Consensus size: 41
38835397 TACTCGATAT
* * *
38835407 CTCGTACACTAAGTGCCGTACATAGCTGAAGCTATCTC-AA
1 CTCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGAA
* * * *
38835447 ATCGCACACTAAGTGGCATATATAGCTGAAGCTATATCGAT
1 CTCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGAA
* * *
38835488 CTCGCACACGAAGTGCCATAT-TAGCCGAAGCTATCTCGAC
1 CTCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGAA
38835528 CTCGCACACTAAGTGCCATATATAGCTG
1 CTCGCACACTAAGTGCCATATATAGCTG
38835556 CTTTGTCATC
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
40 68 0.74
41 24 0.26
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (41 bp):
CTCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGAA
Found at i:38835567 original size:81 final size:81
Alignment explanation
Indices: 38835405--38835555 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
38835395 AATACTCGAT
* * * * *
38835405 ATCTCGTACACTAAGTGCCGTACATAGCTGAAGCTATCTCAAATCGCACACTAAGTGGCATATAT
1 ATCTCGCACACGAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATAT
38835470 AGCTGAAGCTATATCG
66 AGCTGAAGCTATATCG
* **
38835486 ATCTCGCACACGAAGTGCCATA-TTAGCCGAAGCTATCTCGACCTCGCACACTAAGTGCCATATA
1 ATCTCGCACACGAAGTGCCATACATAGCCGAAGCTATCTC-AAATCGCACACTAAGTGCCATATA
38835550 TAGCTG
65 TAGCTG
38835556 CTTTGTCATC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 15 0.25
81 46 0.75
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (81 bp):
ATCTCGCACACGAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATAT
AGCTGAAGCTATATCG
Found at i:38839950 original size:46 final size:46
Alignment explanation
Indices: 38839890--38840254 Score: 577
Period size: 46 Copynumber: 7.9 Consensus size: 46
38839880 TTTCTGTCAT
* * * *
38839890 GTTGCCATGTTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
38839936 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
**
38839982 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
* * * *
38840028 GTTGCCATTGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
*
38840074 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
**
38840120 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
**
38840166 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
**
38840212 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
38840255 TAGAGAGCAC
Statistics
Matches: 301, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 301 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
Found at i:38842348 original size:16 final size:16
Alignment explanation
Indices: 38842329--38842367 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38842319 AATTTTTCCC
*
38842329 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
*
38842345 TTTTTTCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
38842361 TCTTTCC
1 TTTTTCC
38842368 CCTGCTCTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:38842428 original size:16 final size:16
Alignment explanation
Indices: 38842393--38842434 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
38842383 GTTTCATCCT
38842393 TTTTTCTTTTTCTATTC
1 TTTTTC-TTTTCTATTC
38842410 TTTTTCTTTT-TATTCC
1 TTTTTCTTTTCTATT-C
*
38842426 TTTTACTTT
1 TTTTTCTTT
38842435 AATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 13 0.57
17 6 0.26
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTCTATTC
Found at i:38845295 original size:34 final size:34
Alignment explanation
Indices: 38845252--38845320 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
38845242 TTTAGAAAGA
*
38845252 AAGAATTTCTATCGACACATTTATATACCAAATC
1 AAGAATTTCTATCGACACATGTATATACCAAATC
38845286 AAGAATTTCTATCGACACATGTATATACCAAATC
1 AAGAATTTCTATCGACACATGTATATACCAAATC
38845320 A
1 A
38845321 TGATCCATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (34 bp):
AAGAATTTCTATCGACACATGTATATACCAAATC
Found at i:38845693 original size:18 final size:18
Alignment explanation
Indices: 38845670--38845723 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
38845660 AAATTAGTAA
38845670 TGAAGAGGAAGAAGATCC
1 TGAAGAGGAAGAAGATCC
*
38845688 TGAAGAGGAAGAGGA-CC
1 TGAAGAGGAAGAAGATCC
* *
38845705 TAGAGGAGGAAGAATATCC
1 T-GAAGAGGAAGAAGATCC
38845724 CAATGAAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 25 0.83
19 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.35, T:0.11
Consensus pattern (18 bp):
TGAAGAGGAAGAAGATCC
Found at i:38847096 original size:13 final size:13
Alignment explanation
Indices: 38847078--38847111 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
38847068 TTGTTTAGTG
38847078 TTTAATTATTGCA
1 TTTAATTATTGCA
38847091 TTTAATTATTGCA
1 TTTAATTATTGCA
38847104 TTTCAATT
1 TTT-AATT
38847112 TTTTTAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (13 bp):
TTTAATTATTGCA
Found at i:38847500 original size:21 final size:21
Alignment explanation
Indices: 38847462--38847501 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38847452 CCAATGCCAT
**
38847462 TTTAGGGTTTTAGTTTAGTAG
1 TTTAGGGTTTTAACTTAGTAG
*
38847483 TTTAGGTTTTTAACTTAGT
1 TTTAGGGTTTTAACTTAGT
38847502 TTATTTTATT
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:0.20, C:0.03, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTAGGGTTTTAACTTAGTAG
Found at i:38851254 original size:27 final size:27
Alignment explanation
Indices: 38851211--38851286 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
38851201 TGAACACGCT
** *
38851211 AGAAATTGGAAGCCTTTGTGGTGATATA
1 AGAAA-TGGAAGCCTTTGTGGCAATACA
*
38851239 AGAAATGGAAGCCTTTGTGGCAATCCA
1 AGAAATGGAAGCCTTTGTGGCAATACA
* *
38851266 AAAAATGGAAACCTTTGTGGC
1 AGAAATGGAAGCCTTTGTGGC
38851287 GAATTAAGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 37 0.88
28 5 0.12
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (27 bp):
AGAAATGGAAGCCTTTGTGGCAATACA
Found at i:38856682 original size:52 final size:52
Alignment explanation
Indices: 38856550--38856777 Score: 185
Period size: 52 Copynumber: 4.6 Consensus size: 52
38856540 ATAAGTTGAC
* * * * * *
38856550 GATGCCATGTCCCAGACATGGTCTTATACTGGCTATC--AT-CAT-CGAGGCA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATAC-ATGCT
*
38856599 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATACGTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATACATGCT
* * * * * * *
38856651 GATGCCATGTCCCAGACGTAGTCTTATACTAG--CAC--A-A-CT-CTTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATACAT-GCT
* *
38856697 GATG-CATGTCCCAAACAT-GTATTACACTAGCTCTCGTATATATACATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATACATGCT
* *
38856747 GATTCCATGTCCCAGACATGGTCTTATACTA
1 GATGCCATGTCCCAGACATGGTCTTACACTA
38856778 CCACAACTCT
Statistics
Matches: 139, Mismatches: 26, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
44 10 0.07
45 14 0.10
46 9 0.06
47 1 0.01
48 2 0.01
49 35 0.25
50 8 0.06
51 17 0.12
52 42 0.30
53 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (52 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATACATGCT
Done.