Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 90 of 290
Found at i:27535615 original size:4 final size:4
Alignment explanation
Indices: 27535606--27535642 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
27535596 CCCTTTTCTA
27535606 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
27535643 CACGTTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:27539067 original size:40 final size:40
Alignment explanation
Indices: 27539012--27539209 Score: 360
Period size: 40 Copynumber: 5.0 Consensus size: 40
27539002 TGAAAAAAAA
27539012 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
27539052 TATAACCAGGTTAAGTCCCGAAGGCATTCGTGTGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
27539092 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
27539132 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
27539172 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
27539210 GTTACATCCG
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 152 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:27548608 original size:5 final size:5
Alignment explanation
Indices: 27548588--27548627 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
27548578 AAGAAGAAAG
*
27548588 AAGAA AGAGGA AAGAA AAGAA AAGAA AAGAA AAGAA AAGA
1 AAGAA A-AGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGA
27548628 GAAGGGAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:27552669 original size:23 final size:23
Alignment explanation
Indices: 27552637--27552690 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
27552627 CCTGCTAAGG
*
27552637 ACAAAACCCGAATAATCACCAGC
1 ACAAAGCCCGAATAATCACCAGC
27552660 ACAAAGCCCGAATAATCACCAGC
1 ACAAAGCCCGAATAATCACCAGC
27552683 ACAAAGCC
1 ACAAAGCC
27552691 TGCTAGGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.35, G:0.11, T:0.07
Consensus pattern (23 bp):
ACAAAGCCCGAATAATCACCAGC
Found at i:27552723 original size:39 final size:39
Alignment explanation
Indices: 27552664--27552755 Score: 139
Period size: 39 Copynumber: 2.4 Consensus size: 39
27552654 ACCAGCACAA
27552664 AGCCCGAATAATCACCAGCACAAAGCCTGCTAGGCACTT
1 AGCCCGAATAATCACCAGCACAAAGCCTGCTAGGCACTT
* * *
27552703 AGCCTGAATAATCACCAGCACAAAGTCTGCTAGGCACAT
1 AGCCCGAATAATCACCAGCACAAAGCCTGCTAGGCACTT
* *
27552742 AACCCGAACAATCA
1 AGCCCGAATAATCA
27552756 ACGACATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.15
Consensus pattern (39 bp):
AGCCCGAATAATCACCAGCACAAAGCCTGCTAGGCACTT
Found at i:27556874 original size:5 final size:5
Alignment explanation
Indices: 27556864--27556891 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27556854 TAAACTGTGA
27556864 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
27556892 GAACATACAA
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:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:27562682 original size:12 final size:13
Alignment explanation
Indices: 27562667--27562695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27562657 AATATTTAAA
27562667 ATTAATA-AAAAT
1 ATTAATATAAAAT
27562679 ATTAATATAAAAT
1 ATTAATATAAAAT
27562692 ATTA
1 ATTA
27562696 TAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAATATAAAAT
Found at i:27562766 original size:16 final size:16
Alignment explanation
Indices: 27562745--27562794 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
27562735 ATATCTAATC
27562745 ATATAATAAATTATTA
1 ATATAATAAATTATTA
27562761 ATATAAT--A-TATTA
1 ATATAATAAATTATTA
*
27562774 ATTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
27562791 ATAT
1 ATAT
27562795 TCCAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 1 0.04
16 9 0.32
17 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:27562823 original size:19 final size:18
Alignment explanation
Indices: 27562801--27562856 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
27562791 ATATTCCAAT
27562801 TTTATTTTAATAATAAATA
1 TTTA-TTTAATAATAAATA
* *
27562820 TTTATGGTAATTATAAATA
1 TTTAT-TTAATAATAAATA
27562839 --TA-TTAATAATAAATA
1 TTTATTTAATAATAAATA
27562854 TTT
1 TTT
27562857 TATAGTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 11 0.37
17 3 0.10
18 1 0.03
19 15 0.50
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTATTTAATAATAAATA
Found at i:27562866 original size:31 final size:34
Alignment explanation
Indices: 27562807--27562870 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
27562797 CAATTTTATT
* *
27562807 TTAATAATAAATATTTATGGTAATTATAAATATA
1 TTAATAATAAATATTTATGATAAGTATAAATATA
27562841 TTAATAATAAATATTT-T-AT-AGTATAAATAT
1 TTAATAATAAATATTTATGATAAGTATAAATAT
27562871 TAAAATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 1 0.04
34 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (34 bp):
TTAATAATAAATATTTATGATAAGTATAAATATA
Found at i:27564683 original size:27 final size:27
Alignment explanation
Indices: 27564644--27564695 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
27564634 CACTAGTTAA
*
27564644 TTTTTTTATATTGAG-TTTGAATTTTT
1 TTTTTTTAAATTGAGTTTTGAATTTTT
27564670 TTTTATTTAAATTGAGTTTTGAATTT
1 TTTT-TTTAAATTGAGTTTTGAATTT
27564696 GATAGCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 10 0.43
28 9 0.39
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (27 bp):
TTTTTTTAAATTGAGTTTTGAATTTTT
Found at i:27564684 original size:21 final size:21
Alignment explanation
Indices: 27564642--27564689 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
27564632 AACACTAGTT
**
27564642 AATTTTTTTATATTGAGTTTG
1 AATTTTTTTATATTGAAATTG
* *
27564663 AATTTTTTTTTATTTAAATTG
1 AATTTTTTTATATTGAAATTG
*
27564684 AGTTTT
1 AATTTT
27564690 GAATTTGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (21 bp):
AATTTTTTTATATTGAAATTG
Found at i:27569942 original size:18 final size:18
Alignment explanation
Indices: 27569914--27569957 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27569904 ACTGAAATTT
27569914 ATATGAAAATCCCAGAAGG
1 ATAT-AAAATCCCAGAAGG
* *
27569933 ATTTAAAATCCCTGAAGG
1 ATATAAAATCCCAGAAGG
27569951 ATATAAA
1 ATATAAA
27569958 GTTTCCTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:27575605 original size:16 final size:15
Alignment explanation
Indices: 27575578--27575608 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27575568 ATGAATATAG
27575578 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
*
27575593 TAAATATTTAAAAAA
1 TAAATATTAAAAAAA
27575608 T
1 T
27575609 TACTAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAATATTAAAAAAA
Found at i:27576208 original size:16 final size:17
Alignment explanation
Indices: 27576178--27576210 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27576168 CCTTTTGTAT
*
27576178 ATGCTAACAATTTTAAA
1 ATGCTAACAAGTTTAAA
27576195 ATGC-AACAAGTTTAAA
1 ATGCTAACAAGTTTAAA
27576211 GGATCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
ATGCTAACAAGTTTAAA
Found at i:27580568 original size:16 final size:15
Alignment explanation
Indices: 27580551--27580605 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
27580541 TATAAAATAT
27580551 ATTATATTAATTAT-
1 ATTATATTAATTATA
* *
27580565 A-TATGTTAAATAATA
1 ATTATATT-AATTATA
*
27580580 ATTATATATATTTATA
1 ATTATAT-TAATTATA
27580596 ATTATATTAA
1 ATTATATTAA
27580606 ATCACTAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 3 0.10
16 16 0.52
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTATATTAATTATA
Found at i:27580572 original size:30 final size:31
Alignment explanation
Indices: 27580528--27580607 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
27580518 AACCCGGCCC
27580528 AATTATATTATGTTATAA-AATATATTATAT-T
1 AATTATATTATGTTA-AATAATA-ATTATATAT
27580559 AATTATA-TATGTTAAATAATAATTATATAT
1 AATTATATTATGTTAAATAATAATTATATAT
* *
27580589 ATTTATAATTATATTAAAT
1 AATTAT-ATTATGTTAAAT
27580608 CACTAGCCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 9 0.21
30 17 0.40
31 8 0.19
32 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
AATTATATTATGTTAAATAATAATTATATAT
Found at i:27580790 original size:15 final size:16
Alignment explanation
Indices: 27580770--27580809 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
27580760 TTAGTGTATT
27580770 ATATTTTGTAAA-AAA
1 ATATTTTGTAAATAAA
27580785 ATATTTT-TAAATAAA
1 ATATTTTGTAAATAAA
*
27580800 A-ATTATGTAA
1 ATATTTTGTAA
27580810 CACTCCTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
ATATTTTGTAAATAAA
Found at i:27584499 original size:6 final size:5
Alignment explanation
Indices: 27584461--27584497 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
27584451 GGAAGATGAG
*
27584461 TATTT TGTTT TATTT TATTT TATTT TATTTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT T
27584498 TAATTAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:27592927 original size:12 final size:12
Alignment explanation
Indices: 27592910--27592938 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27592900 ACACGGGGTA
27592910 GGACATGGGCTG
1 GGACATGGGCTG
27592922 GGACATGGGCTG
1 GGACATGGGCTG
27592934 GGACA
1 GGACA
27592939 CGACTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.17, G:0.48, T:0.14
Consensus pattern (12 bp):
GGACATGGGCTG
Found at i:27599056 original size:25 final size:25
Alignment explanation
Indices: 27599022--27599071 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27599012 ATTGAGAAAA
27599022 CATATCTTGTCTGTTCTAAGATGTT
1 CATATCTTGTCTGTTCTAAGATGTT
27599047 CATATCTTGTCTGTTCTAAGATGTT
1 CATATCTTGTCTGTTCTAAGATGTT
27599072 TCTTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (25 bp):
CATATCTTGTCTGTTCTAAGATGTT
Found at i:27600546 original size:2 final size:2
Alignment explanation
Indices: 27600539--27600573 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27600529 AAGTTAAAAG
27600539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27600574 ATAAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27602632 original size:36 final size:33
Alignment explanation
Indices: 27602576--27602661 Score: 84
Period size: 36 Copynumber: 2.5 Consensus size: 33
27602566 GAGACTTTGA
* *
27602576 TGAATTACTTTTGTATTCCTACTTCAATTTGAAATT
1 TGAATTA-TTTTCTTTTCCTACTTCAA-TTGAAA-T
* *
27602612 TG-ATTATTCTTTCTTTTCCTATTTCCATTGAAAT
1 TGAATTA-T-TTTCTTTTCCTACTTCAATTGAAAT
27602646 TGAATTATTTTCTTTT
1 TGAATTATTTTCTTTT
27602662 ATCTTTCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 8 0.19
34 4 0.09
35 15 0.35
36 16 0.37
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (33 bp):
TGAATTATTTTCTTTTCCTACTTCAATTGAAAT
Found at i:27603078 original size:15 final size:14
Alignment explanation
Indices: 27603052--27603092 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
27603042 TATTCTAATA
*
27603052 CTATTATTATTTAT
1 CTATTTTTATTTAT
27603066 CTAATTTTTATTTAT
1 CT-ATTTTTATTTAT
*
27603081 CTATTTATATTT
1 CTATTTTTATTT
27603093 CTACTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
CTATTTTTATTTAT
Found at i:27603091 original size:14 final size:15
Alignment explanation
Indices: 27603059--27603092 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
27603049 ATACTATTAT
*
27603059 TATTTATCTAATTTT
1 TATTTATCTAATTTA
27603074 TATTTATCT-ATTTA
1 TATTTATCTAATTTA
27603088 TATTT
1 TATTT
27603093 CTACTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATCTAATTTA
Found at i:27603119 original size:15 final size:15
Alignment explanation
Indices: 27603085--27603129 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
27603075 ATTTATCTAT
27603085 TTATATTTCTACTGTTA
1 TTATATTTCTA-T-TTA
27603102 TTATATTTCTATTTA
1 TTATATTTCTATTTA
27603117 TTATATTT-TATTT
1 TTATATTTCTATTT
27603130 CTATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 1 0.04
17 11 0.39
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:27603128 original size:20 final size:20
Alignment explanation
Indices: 27603100--27603137 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27603090 TTTCTACTGT
27603100 TATTATATTTCTATTTATTA
1 TATTATATTTCTATTTATTA
*
27603120 TATTTTATTTCTATTTAT
1 TATTATATTTCTATTTAT
27603138 ATACTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTATATTTCTATTTATTA
Found at i:27603139 original size:17 final size:16
Alignment explanation
Indices: 27603085--27603139 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
27603075 ATTTATCTAT
*
27603085 TTATATTTCTACTGTTA
1 TTATATTTCTA-TTTTA
27603102 TTATATTTCTA-TTTA
1 TTATATTTCTATTTTA
27603117 TTATATTT-TATTTCTA
1 TTATATTTCTATTT-TA
27603133 TTTATAT
1 -TTATAT
27603140 ACTAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 2 0.06
15 13 0.38
16 2 0.06
17 17 0.50
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATATTTCTATTTTA
Found at i:27603148 original size:20 final size:20
Alignment explanation
Indices: 27603104--27603148 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
27603094 TACTGTTATT
*
27603104 ATATTTCTATTTATTATATT
1 ATATTTCTATTTATTATATA
*
27603124 TTATTTCTATTTA-TATACTA
1 ATATTTCTATTTATTATA-TA
27603144 ATATT
1 ATATT
27603149 ATTTTCATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTCTATTTATTATATA
Found at i:27603320 original size:25 final size:24
Alignment explanation
Indices: 27603259--27603320 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
27603249 TATAATGCTC
* * *
27603259 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATAAATTATGT
27603283 ACTTT-AATATTTTCATAAATTATGT
1 A-TTTCAA-ATTTTCATAAATTATGT
27603308 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
27603321 TTTTCACACA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTCAAATTTTCATAAATTATGT
Found at i:27605907 original size:18 final size:18
Alignment explanation
Indices: 27605884--27605919 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27605874 TAAGAATGTT
27605884 TACATTGCGAGAAAGACA
1 TACATTGCGAGAAAGACA
*
27605902 TACATTGTGAGAAAGACA
1 TACATTGCGAGAAAGACA
27605920 ACTTACTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (18 bp):
TACATTGCGAGAAAGACA
Found at i:27606146 original size:23 final size:22
Alignment explanation
Indices: 27606116--27606159 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27606106 TACATTAGAC
27606116 TGGACCCA-AGATGAATTAATTT
1 TGGACCCATAG-TGAATTAATTT
*
27606138 TGGATCCCATTGTGAATTAATT
1 TGGA-CCCATAGTGAATTAATT
27606160 CACTGCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGACCCATAGTGAATTAATTT
Found at i:27606553 original size:19 final size:19
Alignment explanation
Indices: 27606506--27606563 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
27606496 AAAATGATAA
27606506 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
27606526 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
27606545 AATCAAGTTAAAATTGTTT
1 AATCAAGTTAAAA-TGTTT
27606564 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 13 0.42
21 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:27619897 original size:43 final size:43
Alignment explanation
Indices: 27619754--27619908 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 43
27619744 GTTATCGAGA
* *
27619754 TGTGATTACATGTAAGACCATGTCTGAGATATTTGGCATTGTAT-
1 TGTGATTACATGTAAGACCATGTCTGAGACA-TTGGCATCG-ATG
* *
27619798 TG-GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTTAG
1 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATCGAT-G
*** * * *
27619841 T-TGATTTTGTGTAAGACCTTGTCTGGGACAATGGCATCGATG
1 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATCGATG
* * *
27619883 TGTGATAACATGTAAGGCCATATCTG
1 TGTGATTACATGTAAGACCATGTCTG
27619909 GGATATGGCA
Statistics
Matches: 90, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 10 0.11
43 77 0.86
44 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATCGATG
Found at i:27636992 original size:4 final size:4
Alignment explanation
Indices: 27636973--27637009 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
27636963 GTTGTAAAGT
*
27636973 TTTA TTTT TATTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
27637010 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:27648387 original size:17 final size:16
Alignment explanation
Indices: 27648347--27648383 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27648337 CTCAGATCTT
*
27648347 AAAAACAAAACATTAA
1 AAAAATAAAACATTAA
27648363 AAAAATAAAACATTAA
1 AAAAATAAAACATTAA
27648379 AAAAA
1 AAAAA
27648384 ATAACAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAATAAAACATTAA
Found at i:27648389 original size:15 final size:14
Alignment explanation
Indices: 27648345--27648389 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
27648335 ACCTCAGATC
*
27648345 TTAAAAACAAAACA
1 TTAAAAAAAAAACA
27648359 TTAAAAAAATAAAACA
1 TT-AAAAAA-AAAACA
27648375 TTAAAAAAAATAACA
1 TTAAAAAAAA-AACA
27648390 AAACACTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 8 0.30
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
TTAAAAAAAAAACA
Found at i:27654587 original size:17 final size:18
Alignment explanation
Indices: 27654565--27654609 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
27654555 TTATGAATTA
27654565 AAAAATAATTATA-AAAG
1 AAAAATAATTATACAAAG
*
27654582 AAAAATAGTTATACTAAAG
1 AAAAATAATTATAC-AAAG
*
27654601 ATAAATAAT
1 AAAAATAAT
27654610 ATGAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AAAAATAATTATACAAAG
Found at i:27658372 original size:46 final size:46
Alignment explanation
Indices: 27658304--27658406 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
27658294 TATGTGCATG
*
27658304 TGAATTTAAGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
1 TGAATTT-GGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
27658351 TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
1 TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
27658397 TGAATTTGGT
1 TGAATTTGGT
27658407 AGGTTTATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 48 0.87
47 7 0.13
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (46 bp):
TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
Found at i:27667845 original size:32 final size:32
Alignment explanation
Indices: 27667809--27667871 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
27667799 CACATCTAAG
27667809 ATGAACTTGGAGAAATAGTTG-TCCAAGTTCAA
1 ATGAACTTGGAGAAATAGTTGCT-CAAGTTCAA
*
27667841 ATGAACTTGGATAAATAGTTGCTCAAGTTCA
1 ATGAACTTGGAGAAATAGTTGCTCAAGTTCA
27667872 TCTTAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (32 bp):
ATGAACTTGGAGAAATAGTTGCTCAAGTTCAA
Found at i:27667928 original size:21 final size:22
Alignment explanation
Indices: 27667887--27667928 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27667877 AACATAGTCT
*
27667887 TTTAAATAATTATATAAAATTA
1 TTTAAATAATTATAGAAAATTA
*
27667909 TTTAAA-AATTATAGAGAATT
1 TTTAAATAATTATAGAAAATT
27667929 GTATGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTAAATAATTATAGAAAATTA
Found at i:27679411 original size:46 final size:46
Alignment explanation
Indices: 27679344--27679436 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
27679334 CAAAAGTAAC
27679344 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
1 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
27679390 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
1 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
27679436 A
1 A
27679437 GGTTAGAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (46 bp):
AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
Found at i:27691410 original size:17 final size:19
Alignment explanation
Indices: 27691377--27691411 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27691367 GAATAGAATA
27691377 GAAAATAGTGTAAATTGAT
1 GAAAATAGTGTAAATTGAT
27691396 GAAAATA-TG-AAATTGA
1 GAAAATAGTGTAAATTGA
27691412 CTTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (19 bp):
GAAAATAGTGTAAATTGAT
Found at i:27692197 original size:35 final size:35
Alignment explanation
Indices: 27692151--27692230 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
27692141 GGCTCATGCC
*
27692151 CACGTCTAAGGCGA-CTTTAAAAAGGTTGGAATAGA
1 CACGTCTAAGGCAACCTTT-AAAAGGTTGGAATAGA
*
27692186 CCCGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
1 CACGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
27692221 CACGTCTAAG
1 CACGTCTAAG
27692231 ACAAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 37 0.90
36 4 0.10
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (35 bp):
CACGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
Found at i:27694501 original size:13 final size:13
Alignment explanation
Indices: 27694480--27694553 Score: 103
Period size: 13 Copynumber: 5.7 Consensus size: 13
27694470 CTTAAATTTT
27694480 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
27694493 TCTAAAGCACTTC
1 TCAAAAGCACTTC
* *
27694506 TTAAAAGCACTTT
1 TCAAAAGCACTTC
* *
27694519 TCCACAGCACTTC
1 TCAAAAGCACTTC
27694532 TCAAAAGCACTTC
1 TCAAAAGCACTTC
27694545 TCAAAAGCA
1 TCAAAAGCA
27694554 TTGCCAAACT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:27695141 original size:37 final size:37
Alignment explanation
Indices: 27695100--27695195 Score: 95
Period size: 41 Copynumber: 2.5 Consensus size: 37
27695090 TAATAAAAAA
* *
27695100 AGTGTAAGATAATATTTTTGGTACTAAAAAAATAGAT
1 AGTGTAAGATAATATTTTGGGCACTAAAAAAATAGAT
* *
27695137 AGTGTAA-ATTTAATGAAATTTTGGGCATTAAACAAATAGAT
1 AGTGTAAGA--TAAT---ATTTTGGGCACTAAAAAAATAGAT
*
27695178 AGTGTAAGATTATATTTT
1 AGTGTAAGATAATATTTT
27695196 ATCTAATTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
36 1 0.02
37 12 0.25
38 4 0.08
40 3 0.06
41 27 0.56
42 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (37 bp):
AGTGTAAGATAATATTTTGGGCACTAAAAAAATAGAT
Found at i:27695749 original size:126 final size:126
Alignment explanation
Indices: 27695524--27695775 Score: 387
Period size: 126 Copynumber: 2.0 Consensus size: 126
27695514 TATAAAAAAA
* * * *
27695524 GTCGGCATGGTGTTGAACAAAACTGACTCTTATTTAAGCATTGCCTTAGGCATACATATCCCGAC
1 GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCACTGCCTTAGGCATACATATCCCAAC
* *
27695589 TCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGT
66 CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
* * * *
27695650 GTCGGCATAGTGTTGGACAAAGCTGACTCTTATGTAAGCGCTGCCTTAGGCATCCATATCCCAAC
1 GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCACTGCCTTAGGCATACATATCCCAAC
* **
27695715 CCTTATACAAAGAGTTGGCTAAAGCTTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
66 CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
27695776 ATCAGCCCAA
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (126 bp):
GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCACTGCCTTAGGCATACATATCCCAAC
CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
Found at i:27701285 original size:13 final size:13
Alignment explanation
Indices: 27701267--27701295 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27701257 AGGAGCAATC
27701267 GTTGATCCATAGG
1 GTTGATCCATAGG
27701280 GTTGATCCATAGG
1 GTTGATCCATAGG
27701293 GTT
1 GTT
27701296 AAAGTCAGTA
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:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (13 bp):
GTTGATCCATAGG
Found at i:27707793 original size:22 final size:21
Alignment explanation
Indices: 27707723--27707794 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
27707713 TTTGCATTTT
* *
27707723 GTAGGTATAGAATAAAAGTAAC
1 GTAGATATAGGATAAAAGT-AC
* *
27707745 ATAGATAT-GAGATAAAA-TAA
1 GTAGATATAG-GATAAAAGTAC
27707765 GTAGATATAGGATAAAAGTATC
1 GTAGATATAGGATAAAAGTA-C
27707787 GTAGATAT
1 GTAGATAT
27707795 TTTTTGTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 15 0.38
21 5 0.12
22 20 0.50
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (21 bp):
GTAGATATAGGATAAAAGTAC
Found at i:27711669 original size:1 final size:1
Alignment explanation
Indices: 27711663--27711687 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
27711653 TGCCATTTGG
27711663 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
27711688 GAGTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27717818 original size:22 final size:22
Alignment explanation
Indices: 27717790--27717834 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
27717780 TTGTATGTCA
27717790 CCTTTTGGACTCACACTGAGCT
1 CCTTTTGGACTCACACTGAGCT
27717812 CCTTTTGGACTCACACTGAGCT
1 CCTTTTGGACTCACACTGAGCT
27717834 C
1 C
27717835 ATGTAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (22 bp):
CCTTTTGGACTCACACTGAGCT
Found at i:27720794 original size:13 final size:13
Alignment explanation
Indices: 27720776--27720801 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27720766 TAGTGGACGG
27720776 TTAGTGCATTCTC
1 TTAGTGCATTCTC
27720789 TTAGTGCATTCTC
1 TTAGTGCATTCTC
27720802 CCATTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAGTGCATTCTC
Found at i:27724983 original size:15 final size:15
Alignment explanation
Indices: 27724960--27724989 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27724950 GAGTTTGTCA
*
27724960 TTCATCATCTACAAC
1 TTCACCATCTACAAC
27724975 TTCACCATCTACAAC
1 TTCACCATCTACAAC
27724990 AAGTGTTTGC
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:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (15 bp):
TTCACCATCTACAAC
Found at i:27725103 original size:47 final size:47
Alignment explanation
Indices: 27725049--27725150 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
27725039 AAATTAATAA
*
27725049 AATTACCTTTAAAAAAATTCATCTCCAATTAGATAGTAAACACTTCG
1 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
27725096 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
1 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
27725143 AATTACCT
1 AATTACCT
27725151 AACTTGAGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (47 bp):
AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
Found at i:27725252 original size:54 final size:54
Alignment explanation
Indices: 27725185--27725287 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
27725175 TACTTAATTC
* *
27725185 AAATTGTAATTAATG-GTAAAAAAGATGTTT-TTTCTTCTCAAATAACAATGAATA
1 AAATAGTAATTAATGAG-AAAAAAGAT-TTTCTTTCTTATCAAATAACAATGAATA
** *
27725239 AAATAGTAATTAATGAGCGAAAATATTTTCTTTCTTATCAAATAACAAT
1 AAATAGTAATTAATGAGAAAAAAGATTTTCTTTCTTATCAAATAACAAT
27725288 TAACAATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.07
54 38 0.90
55 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (54 bp):
AAATAGTAATTAATGAGAAAAAAGATTTTCTTTCTTATCAAATAACAATGAATA
Found at i:27733600 original size:20 final size:20
Alignment explanation
Indices: 27733575--27733614 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27733565 TTTTTTTTAC
27733575 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
27733595 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
27733615 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:27733619 original size:16 final size:18
Alignment explanation
Indices: 27733570--27733614 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
27733560 AAAAGTTTTT
* *
27733570 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
27733588 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
27733608 TTTATAT
1 TTTATAT
27733615 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:27736473 original size:14 final size:14
Alignment explanation
Indices: 27736454--27736480 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27736444 AGAAAAACTT
27736454 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
27736468 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
27736481 AGGTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:27742520 original size:39 final size:39
Alignment explanation
Indices: 27742476--27742600 Score: 196
Period size: 39 Copynumber: 3.2 Consensus size: 39
27742466 AACCCGAAAT
* *
27742476 TATATTACCAGCACAAAGCCTGCGGGACTTTAGCTCGGA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGA
*
27742515 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGA
* *
27742554 TACATTTCCAGCACAAAGCCTGCGGGACTTTATCCCGGA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGA
*
27742593 TACATTTC
1 TATATTTC
27742601 TAGTGTCTTG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGA
Found at i:27748342 original size:261 final size:261
Alignment explanation
Indices: 27747878--27748401 Score: 1030
Period size: 261 Copynumber: 2.0 Consensus size: 261
27747868 TATCAAAATT
27747878 TTCATGCAACCTTCCTATCATAATATAGACCATACCACAATATTAAAATAAATTTTCTTTCTAAC
1 TTCATGCAACCTTCCTATCATAATATAGACCATACCACAATATTAAAATAAATTTTCTTTCTAAC
*
27747943 TCGGATTTGTGGTTACAAAATTACTATTTCGATTTCACTGAAAATAAGTCATTACAATGTAAGTA
66 TCGGATTTGTGGCTACAAAATTACTATTTCGATTTCACTGAAAATAAGTCATTACAATGTAAGTA
27748008 ACTCTATAAAATTGAATAAAAGAGAGAAATAATGAAGTAAAAGGAAATACTGAAAGACTGGACTA
131 ACTCTATAAAATTGAATAAAAGAGAGAAATAATGAAGTAAAAGGAAATACTGAAAGACTGGACTA
27748073 TTTTGTATTCATTGTATGCTTTAACAGCACAAAGATAGAATTTATATAATGACAAGGAATGATTA
196 TTTTGTATTCATTGTATGCTTTAACAGCACAAAGATAGAATTTATATAATGACAAGGAATGATTA
27748138 A
261 A
27748139 TTCATGCAACCTTCCTATCATAATATAGACCATACCACAATATTAAAATAAATTTTCTTTCTAAC
1 TTCATGCAACCTTCCTATCATAATATAGACCATACCACAATATTAAAATAAATTTTCTTTCTAAC
27748204 TCGGATTTGTGGCTACAAAATTACTATTTCGATTTCACTGAAAATAAGTCATTACAATGTAAGTA
66 TCGGATTTGTGGCTACAAAATTACTATTTCGATTTCACTGAAAATAAGTCATTACAATGTAAGTA
27748269 ACTCTATAAAATTGAATAAAAGAGAGAAATAATGAAGTAAAAGGAAATACTGAAAGACTGGACTA
131 ACTCTATAAAATTGAATAAAAGAGAGAAATAATGAAGTAAAAGGAAATACTGAAAGACTGGACTA
*
27748334 TTTTGTATTCATTGTATGCTTTAACAGTACAAAGATAGAATTTATATAATGACAAGGAATGATTA
196 TTTTGTATTCATTGTATGCTTTAACAGCACAAAGATAGAATTTATATAATGACAAGGAATGATTA
27748399 A
261 A
27748400 TT
1 TT
27748402 GTTGCTAACT
Statistics
Matches: 261, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 261 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (261 bp):
TTCATGCAACCTTCCTATCATAATATAGACCATACCACAATATTAAAATAAATTTTCTTTCTAAC
TCGGATTTGTGGCTACAAAATTACTATTTCGATTTCACTGAAAATAAGTCATTACAATGTAAGTA
ACTCTATAAAATTGAATAAAAGAGAGAAATAATGAAGTAAAAGGAAATACTGAAAGACTGGACTA
TTTTGTATTCATTGTATGCTTTAACAGCACAAAGATAGAATTTATATAATGACAAGGAATGATTA
A
Found at i:27763974 original size:22 final size:23
Alignment explanation
Indices: 27763924--27763975 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
27763914 ATGTTTTTAC
*
27763924 TTTTATTTTACTTTAGGACTACT
1 TTTTATTTTACTTTAAGACTACT
*
27763947 TTTTATTTTTCTTTAAG-CTTA-T
1 TTTTATTTTACTTTAAGAC-TACT
27763969 TTTTATT
1 TTTTATT
27763976 AGGATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTATTTTACTTTAAGACTACT
Found at i:27767788 original size:44 final size:43
Alignment explanation
Indices: 27767738--27767891 Score: 138
Period size: 43 Copynumber: 3.6 Consensus size: 43
27767728 TATGTGTTTT
27767738 CGTGTAAGACCACGTCTGGGACATTGGCATC-AACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGAA-TT-TGATTTA
* * * *
27767782 CGTGTAATACTATGTCTGGGACATCT-GCATCGTATTTGATTT-
1 CGTGTAAGACCACGTCTGGGACAT-TGGCATCGAATTTGATTTA
* * * *
27767824 CGTATAAGACC-CTATCTGGGACAGTGGCATCGATATTTGA-CTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGA-ATTTGATTTA
* *
27767867 CATGTAAGACCACGTTTGGGACATT
1 CGTGTAAGACCACGTCTGGGACATT
27767892 CGTATTGTAC
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
41 1 0.01
42 24 0.28
43 30 0.35
44 29 0.34
45 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGAATTTGATTTA
Found at i:27775695 original size:16 final size:16
Alignment explanation
Indices: 27775658--27775689 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27775648 TATGCTTAAG
*
27775658 TATATATTTTGATTAT
1 TATATGTTTTGATTAT
27775674 TATATGTTTTGATTAT
1 TATATGTTTTGATTAT
27775690 GTTATGCTTA
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:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
TATATGTTTTGATTAT
Found at i:27794802 original size:56 final size:56
Alignment explanation
Indices: 27794735--27794861 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 56
27794725 GCCCCTATGG
**
27794735 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGTTGTGTGA
1 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCCGTGTGA
* * * * * **
27794791 GTATACTGACTTGGGTCACACGGCCAAGCTACATGCCCATGTGCTAAGCCGTGTGA
1 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCCGTGTGA
* *
27794847 GCATTCTGACTTGTG
1 GTATACTGACTTGTG
27794862 CTCTTTAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (56 bp):
GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCCGTGTGA
Found at i:27795990 original size:25 final size:26
Alignment explanation
Indices: 27795947--27796020 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
27795937 ATGAGATATA
* *
27795947 AACAGTAAGCTCCTTCGAGCTGAA-T
1 AACAGTAAGCTCATACGAGCTGAAGT
*
27795972 AACAGTAAGCTCATACGAG-TTAAGT
1 AACAGTAAGCTCATACGAGCTGAAGT
* *
27795997 ATCAGTAAGCTCATAAGAGCTGAA
1 AACAGTAAGCTCATACGAGCTGAA
27796021 ATCGTTAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 3 0.07
25 35 0.85
26 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (26 bp):
AACAGTAAGCTCATACGAGCTGAAGT
Found at i:27796162 original size:20 final size:19
Alignment explanation
Indices: 27796137--27796174 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
27796127 TGGAAATTAC
27796137 TCAATTCACAAACATATAAT
1 TCAATTCA-AAACATATAAT
*
27796157 TCAATTTAAAACATATAA
1 TCAATTCAAAACATATAA
27796175 ATGTACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
TCAATTCAAAACATATAAT
Found at i:27799883 original size:7 final size:7
Alignment explanation
Indices: 27799871--27799939 Score: 50
Period size: 7 Copynumber: 10.0 Consensus size: 7
27799861 ACCCAAACTG
27799871 TAAGGTT
1 TAAGGTT
27799878 TAAGGTT
1 TAAGGTT
* *
27799885 TGAGATT
1 TAAGGTT
*
27799892 TAAAGTT
1 TAAGGTT
*
27799899 TAAAGTT
1 TAAGGTT
*
27799906 TAGGGTT
1 TAAGGTT
*
27799913 TGA-GTT
1 TAAGGTT
27799919 TAAGGTT
1 TAAGGTT
* *
27799926 CAAGATT
1 TAAGGTT
*
27799933 TTAGGTT
1 TAAGGTT
27799940 CAGGGTTCAT
Statistics
Matches: 46, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
6 5 0.11
7 41 0.89
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (7 bp):
TAAGGTT
Found at i:27799935 original size:28 final size:28
Alignment explanation
Indices: 27799875--27799937 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
27799865 AAACTGTAAG
* *
27799875 GTTTAAGGTTTGAGATTTAAAGTTTAAA
1 GTTTAGGGTTTGAGATTTAAAGTTCAAA
*
27799903 GTTTAGGGTTTGAG-TTTAAGGTTCAAGA
1 GTTTAGGGTTTGAGATTTAAAGTTCAA-A
*
27799931 TTTTAGG
1 GTTTAGG
27799938 TTCAGGGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (28 bp):
GTTTAGGGTTTGAGATTTAAAGTTCAAA
Found at i:27800679 original size:48 final size:44
Alignment explanation
Indices: 27800587--27800682 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 44
27800577 AAGTGAAAAT
*
27800587 TATTAAATTATTTTTATTTATATTAATTATTTAAAATATATAAA
1 TATTAAATTATTTATATTTATATTAATTATTTAAAATATATAAA
* * * *
27800631 TATTAAATTAATTTATATTTTGTATATAATTATATTACATTATTTAAA
1 TATTAAATT-ATTTATA-TTTATAT-TAATTAT-TTAAAATATATAAA
27800679 TATT
1 TATT
27800683 TTATGTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 9 0.21
45 6 0.14
46 6 0.14
47 7 0.16
48 15 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (44 bp):
TATTAAATTATTTATATTTATATTAATTATTTAAAATATATAAA
Found at i:27800696 original size:33 final size:33
Alignment explanation
Indices: 27800622--27800720 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
27800612 ATTATTTAAA
27800622 ATATATAA--ATATTAAATTAATTT--ATATTTT
1 ATATATAATTATATTAAATT-ATTTAAATATTTT
* *
27800652 GTATATAATTATATTACATTATTTAAATATTTT
1 ATATATAATTATATTAAATTATTTAAATATTTT
* * * *
27800685 ATGTATTATTATGTTAAATTATTTAAATATTAT
1 ATATATAATTATATTAAATTATTTAAATATTTT
27800718 ATA
1 ATA
27800721 ACTTAATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 7 0.12
31 4 0.07
32 9 0.16
33 36 0.64
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (33 bp):
ATATATAATTATATTAAATTATTTAAATATTTT
Found at i:27803068 original size:25 final size:25
Alignment explanation
Indices: 27803040--27803099 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
27803030 AGGTGACTGG
*
27803040 ATGCATAGATCCTAAATACTGCTGC
1 ATGCATAGATCCTAAATACTGCTAC
**
27803065 ATGCATAGATCCTAAATGGTGCTAC
1 ATGCATAGATCCTAAATACTGCTAC
27803090 ATGCATAGAT
1 ATGCATAGAT
27803100 AGTGTTACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (25 bp):
ATGCATAGATCCTAAATACTGCTAC
Found at i:27809572 original size:4 final size:4
Alignment explanation
Indices: 27809563--27809587 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27809553 GTAAATATAA
27809563 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
27809588 CAGTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:27811113 original size:23 final size:21
Alignment explanation
Indices: 27811079--27811136 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
27811069 TTATCCAAAC
* *
27811079 AAAAAATATAAATAATAATCCTA
1 AAAAAATTTAAATAAAAAT--TA
*
27811102 AAAAAATTTAAAACAAAAATTA
1 AAAAAATTT-AAATAAAAATTA
27811124 AAAAAATTTAAAT
1 AAAAAATTTAAAT
27811137 CAAACTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 8 0.27
24 8 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTTAAATAAAAATTA
Found at i:27812225 original size:38 final size:37
Alignment explanation
Indices: 27812166--27812249 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
27812156 ATATAATAAT
* **
27812166 AATTTTAATGGATTTATGATAATGACT-ATTATTT-TA
1 AATTTTAATAGATTTATGATAACCA-TAATTATTTATA
27812202 AATTTTAATAGATAATTATGATAACCATAATTATTTATA
1 AATTTTAATAGAT--TTATGATAACCATAATTATTTATA
27812241 AATTTTAAT
1 AATTTTAAT
27812250 TACCCACCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 12 0.29
37 1 0.02
38 17 0.41
39 11 0.27
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (37 bp):
AATTTTAATAGATTTATGATAACCATAATTATTTATA
Found at i:27817073 original size:23 final size:24
Alignment explanation
Indices: 27817047--27817147 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 24
27817037 TTGATGAACA
*
27817047 GTAAGCTCTAATGAGCT-AAAATG
1 GTAAGCTCTAATGAGCTGAAAACG
27817070 GTAAGCTCT-ATCGAGCTGAACAA--
1 GTAAGCTCTAAT-GAGCTGAA-AACG
*
27817093 -TAAGCTCATAA-GAGTTG-AAACG
1 GTAAGCTC-TAATGAGCTGAAAACG
* *
27817115 GTAAGCTCCAATGAGCTGAAAACA
1 GTAAGCTCTAATGAGCTGAAAACG
27817139 GTAAGCTCT
1 GTAAGCTCT
27817148 TACGAGTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
20 2 0.03
21 1 0.02
22 16 0.25
23 27 0.43
24 15 0.24
25 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (24 bp):
GTAAGCTCTAATGAGCTGAAAACG
Found at i:27817131 original size:45 final size:44
Alignment explanation
Indices: 27817041--27817171 Score: 120
Period size: 45 Copynumber: 2.8 Consensus size: 44
27817031 CCTGAGTTGA
* * * *
27817041 TGAACAGTAAGCTCTAATGAGCTAAAATGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTAA-GAGTTGAAACGGTAAGCTCAATCGAGC
*
27817086 TGAACAATAAGCTCATAAGAGTTGAAACGGTAAGCTCCAAT-GAGC
1 TGAACAGTAAGCTC-TAAGAGTTGAAACGGTAAGCT-CAATCGAGC
*
27817131 TGAAAACAGTAAGCTCTTACGAGTTGATACATCGGTAAGCT
1 TG--AACAGTAAGCTC-TAAGAGTTGA-A-A-CGGTAAGCT
27817172 TATACGAACT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
45 34 0.48
46 6 0.08
47 20 0.28
48 1 0.01
49 1 0.01
50 9 0.13
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (44 bp):
TGAACAGTAAGCTCTAAGAGTTGAAACGGTAAGCTCAATCGAGC
Found at i:27827405 original size:33 final size:33
Alignment explanation
Indices: 27827354--27827433 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
27827344 TCACAAGTGT
*
27827354 TCATCACATGTTAGTCATTTTACAAATACATGAAA
1 TCATC-CAT-TTATTCATTTTACAAATACATGAAA
27827389 TCATCCATTTATTCATTTTACAAATACATGAAA
1 TCATCCATTTATTCATTTTACAAATACATGAAA
27827422 TCATCCATTTAT
1 TCATCCATTTAT
27827434 ACAATACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 36 0.82
34 3 0.07
35 5 0.11
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (33 bp):
TCATCCATTTATTCATTTTACAAATACATGAAA
Found at i:27827667 original size:23 final size:23
Alignment explanation
Indices: 27827637--27827719 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
27827627 CTGATGAACA
27827637 GTAAGCTCTAATGAGCTAAAATG
1 GTAAGCTCTAATGAGCTAAAATG
*
27827660 GTAAGCTCT-ATCGAGCTGAACA-G
1 GTAAGCTCTAAT-GAGCT-AAAATG
* * *
27827683 G-AAGCT-TATACGAGCTGAAATA
1 GTAAGCTCTA-ATGAGCTAAAATG
*
27827705 GTAGGCTCTAATGAG
1 GTAAGCTCTAATGAG
27827720 ATGAAAACAG
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
21 3 0.07
22 13 0.28
23 25 0.54
24 5 0.11
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (23 bp):
GTAAGCTCTAATGAGCTAAAATG
Found at i:27832648 original size:43 final size:43
Alignment explanation
Indices: 27832601--27832717 Score: 191
Period size: 43 Copynumber: 2.7 Consensus size: 43
27832591 TGTCACATAT
27832601 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCAT-ATAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAAT-A
* *
27832644 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGTAATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAATA
*
27832687 TGATGCCAATGTCCCAGACATGGTCTTACAC
1 CGATGCCAATGTCCCAGACATGGTCTTACAC
27832718 ATAATCACAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 68 0.97
44 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAATA
Found at i:27833568 original size:14 final size:14
Alignment explanation
Indices: 27833545--27833577 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
27833535 CTAGGTGATG
27833545 AAAT-TTGAAAGAA
1 AAATGTTGAAAGAA
27833558 AAATGTTGAAAGAA
1 AAATGTTGAAAGAA
27833572 AAATGT
1 AAATGT
27833578 CTTTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (14 bp):
AAATGTTGAAAGAA
Found at i:27837963 original size:21 final size:20
Alignment explanation
Indices: 27837939--27837977 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27837929 AAACTTGTAT
27837939 ATCTATCAACAAACATTCATA
1 ATCTATCAACAAAC-TTCATA
*
27837960 ATCTATCAAGAAACTTCA
1 ATCTATCAACAAACTTCA
27837978 AAATACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (20 bp):
ATCTATCAACAAACTTCATA
Found at i:27843354 original size:46 final size:44
Alignment explanation
Indices: 27843252--27843379 Score: 123
Period size: 46 Copynumber: 2.8 Consensus size: 44
27843242 ACATTATGAG
* * *
27843252 AGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGACA
1 AGCCAGTGTAA-AACATGTCTAGGACAT-GCATCGGCATCGAGACA
* * *
27843298 AGTGCTAGTGTAAAACATGTCTTGGACATGCATCGGCCTCGAGACGTA
1 A--GCCAGTGTAAAACATGTCTAGGACATGCATCGGCATCGAGAC--A
* *
27843346 AGCCAGTGTAAGACATGTCTAGGACA-ACATCGGC
1 AGCCAGTGTAAAACATGTCTAGGACATGCATCGGC
27843380 TACGAGATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
45 7 0.10
46 38 0.55
47 14 0.20
48 10 0.14
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (44 bp):
AGCCAGTGTAAAACATGTCTAGGACATGCATCGGCATCGAGACA
Found at i:27844595 original size:21 final size:22
Alignment explanation
Indices: 27844556--27844596 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
27844546 TCGAATTGGT
27844556 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
27844578 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
27844597 GTGTCAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.44, G:0.29, T:0.17
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:27848246 original size:21 final size:21
Alignment explanation
Indices: 27848220--27848270 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
27848210 AAGATCATTT
*
27848220 AACAAAACTT-GTATATCTATC
1 AACAAAACTTCATA-ATCTATC
27848241 AAC-AAACATTCATAATCTATC
1 AACAAAAC-TTCATAATCTATC
27848262 AA-AAAACTT
1 AACAAAACTT
27848271 TAAAATACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.23
21 18 0.69
22 2 0.08
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (21 bp):
AACAAAACTTCATAATCTATC
Found at i:27851031 original size:28 final size:28
Alignment explanation
Indices: 27850992--27851079 Score: 121
Period size: 27 Copynumber: 3.3 Consensus size: 28
27850982 TGGAGGAAGC
27850992 GTTT-TGGTGGCTCTGCCACAAATATCT
1 GTTTCTGGTGGCTCTGCCACAAATATCT
27851019 GTTTCTGGTGGCTCTGCCA-AAATATCT
1 GTTTCTGGTGGCTCTGCCACAAATATCT
* * *
27851046 GTATCTGGTGACTCTGTCAC-AATATCT
1 GTTTCTGGTGGCTCTGCCACAAATATCT
27851073 G-TTCTGG
1 GTTTCTGG
27851080 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.09
27 36 0.65
28 14 0.25
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.38
Consensus pattern (28 bp):
GTTTCTGGTGGCTCTGCCACAAATATCT
Found at i:27853617 original size:25 final size:25
Alignment explanation
Indices: 27853589--27853644 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
27853579 TAAAGTGTTA
* *
27853589 CAATGAAACACTTCAGGAAGTATTT
1 CAATGAAACACTCCAGGAACTATTT
*
27853614 CAATGAAACTCTCCAGGAACTATTT
1 CAATGAAACACTCCAGGAACTATTT
*
27853639 CGATGA
1 CAATGA
27853645 TCGTATCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (25 bp):
CAATGAAACACTCCAGGAACTATTT
Found at i:27859734 original size:26 final size:26
Alignment explanation
Indices: 27859699--27859750 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
27859689 AATGTGAAAG
*
27859699 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
27859725 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
27859751 TTCAGCGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:27866652 original size:30 final size:30
Alignment explanation
Indices: 27866589--27866653 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
27866579 ATTTCCGAGC
*
27866589 TTGGGGACAAAAGTGTAATTATGCAAAAGT
1 TTGGGGACAAAAGTGTAATTATGCAAAAAT
* * *
27866619 TTGGGGGCAAAATTGTAATT-TTCAAAAAAT
1 TTGGGGACAAAAGTGTAATTATGC-AAAAAT
27866649 TTGGG
1 TTGGG
27866654 TGGTGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (30 bp):
TTGGGGACAAAAGTGTAATTATGCAAAAAT
Found at i:27875341 original size:50 final size:50
Alignment explanation
Indices: 27875266--27875372 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
27875256 CCTTATCACC
* *
27875266 AAGGCTTCCCAAATAATATGCCACATAGACTTTTCA-AGTAACAAGCCACA
1 AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGA-TAACAAGCCACA
** * * *
27875316 AAGGCTTCTGAAATAATACGCCACATAGGCCTTTCAGATAACTATCCACA
1 AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGATAACAAGCCACA
27875366 AAGGCTT
1 AAGGCTT
27875373 TTTTGGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (50 bp):
AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGATAACAAGCCACA
Found at i:27875657 original size:20 final size:20
Alignment explanation
Indices: 27875632--27875672 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27875622 AGATAGGGGC
27875632 ACATGCCCGTGTGGCCTGGG
1 ACATGCCCGTGTGGCCTGGG
*
27875652 ACATGCCCGTGTGGCTTGGG
1 ACATGCCCGTGTGGCCTGGG
27875672 A
1 A
27875673 TATGGCCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.27, G:0.39, T:0.22
Consensus pattern (20 bp):
ACATGCCCGTGTGGCCTGGG
Found at i:27880229 original size:41 final size:41
Alignment explanation
Indices: 27880172--27880258 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
27880162 TCTCTTTGCT
27880172 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
1 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
*
27880213 TCTTTTCAACTTTAGTTTGCAACTTTATTCAGAGGTAACTA
1 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
27880254 TCTTT
1 TCTTT
27880259 CTCTTTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (41 bp):
TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
Found at i:27887983 original size:55 final size:55
Alignment explanation
Indices: 27887865--27887983 Score: 123
Period size: 55 Copynumber: 2.2 Consensus size: 55
27887855 TTTGGTAGGT
* * * * *
27887865 TCGACCACGGGTGTTAGACACGGGCGTGTCGCACGCCCGTGCTATTTTATCAGGT
1 TCGACCACGGGTCTTACACACGGGCATGTCGCACGCCCGTGCTATTTTATAAGGC
* * * * * *
27887920 TCGCCCACGGTTCTTACACACGGGCATGTCGTATGCCCGTGTTGTTTTGA-AAGGC
1 TCGACCACGGGTCTTACACACGGGCATGTCGCACGCCCGTGCTATTTT-ATAAGGC
27887975 TCGACCACG
1 TCGACCACG
27887984 ACCATATCGC
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
55 50 0.98
56 1 0.02
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.26
Consensus pattern (55 bp):
TCGACCACGGGTCTTACACACGGGCATGTCGCACGCCCGTGCTATTTTATAAGGC
Found at i:27914138 original size:49 final size:49
Alignment explanation
Indices: 27914084--27914308 Score: 263
Period size: 49 Copynumber: 4.5 Consensus size: 49
27914074 CTGGTACGCT
* * * *
27914084 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACA
*
27914133 TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACA
* * ** * * **
27914182 TAGTAGCCTGTACTTAGTACTACACACATGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACA
* * *
27914232 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT-TTCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCG-GTACACA
27914283 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
27914309 TGCAACCTCA
Statistics
Matches: 149, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 76 0.51
50 41 0.28
51 31 0.21
52 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACA
Found at i:27914257 original size:99 final size:101
Alignment explanation
Indices: 27914084--27914308 Score: 287
Period size: 99 Copynumber: 2.3 Consensus size: 101
27914074 CTGGTACGCT
* *** ** * *
27914084 TAGTAGCCTGCACATAGTACTACACATGCGACC-AATTATCCGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
27914148 AGTACTACACACATGA-C-CAATTATCCG-GTACACA
66 AGTACTACACACATGATCACAATT-TCCGAGTACACA
* *
27914182 TAGTAGCCTGTACTTAGTACTACACACATGACCTAACCATCTGATACATGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
* * * *
27914247 AGTACTACACACGTGATCACAGTTTTCGAGTACGCA
66 AGTACTACACACATGATCACAATTTCCGAGTACACA
27914283 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
27914309 TGCAACCTCA
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
98 28 0.26
99 41 0.38
100 4 0.04
101 35 0.32
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
AGTACTACACACATGATCACAATTTCCGAGTACACA
Found at i:27916380 original size:15 final size:15
Alignment explanation
Indices: 27916352--27916415 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
27916342 AGAAAACCGA
*
27916352 ATAAAGAAATCCAAG
1 ATAAAGAAACCCAAG
* *
27916367 ATAGAGAAACCCAAA
1 ATAAAGAAACCCAAG
* * *
27916382 ATAAAAAAAACCTAG
1 ATAAAGAAACCCAAG
27916397 AGTAAAGAAACCCAAG
1 A-TAAAGAAACCCAAG
27916413 ATA
1 ATA
27916416 CGATACTATG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 25 0.68
16 12 0.32
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.11
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:27916385 original size:30 final size:31
Alignment explanation
Indices: 27916351--27916411 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
27916341 AAGAAAACCG
* * *
27916351 AATAAAGAAATCCAAGA-TAGAGAAACCCAA
1 AATAAAAAAAACCAAGAGTAAAGAAACCCAA
*
27916381 AATAAAAAAAACCTAGAGTAAAGAAACCCAA
1 AATAAAAAAAACCAAGAGTAAAGAAACCCAA
27916412 GATACGATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.62, C:0.16, G:0.11, T:0.10
Consensus pattern (31 bp):
AATAAAAAAAACCAAGAGTAAAGAAACCCAA
Found at i:27919238 original size:27 final size:27
Alignment explanation
Indices: 27919214--27919445 Score: 286
Period size: 27 Copynumber: 8.6 Consensus size: 27
27919204 TTAGTTTACC
*
27919214 AAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
27919241 AAATCACAAAAATACCCCTGGTTT-TA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
27919267 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCCTGGTTTATA
*
27919294 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
27919321 AAATTACTAAAATACCCATGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
27919348 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
27919375 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
27919402 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTATA
**
27919429 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
27919446 TCGACCTGTA
Statistics
Matches: 177, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 22 0.12
27 155 0.88
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:27919333 original size:54 final size:54
Alignment explanation
Indices: 27919214--27919446 Score: 317
Period size: 54 Copynumber: 4.3 Consensus size: 54
27919204 TTAGTTTACC
* * * *
27919214 AAATTACCAAAATACCCTTGGTTTATAAAATCACAAAAATACCCCTGGTTT-TA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* *
27919267 AAATTACCAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* * *
27919321 AAATTACTAAAATACCCATGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* * * *
27919375 AAATTA-TCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACT-AAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
*
27919429 AAATTACTGAAATACCCT
1 AAATTACTAAAATACCCT
27919447 CGACCTGTAA
Statistics
Matches: 160, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
53 48 0.30
54 111 0.69
55 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:27919456 original size:54 final size:54
Alignment explanation
Indices: 27919214--27919472 Score: 258
Period size: 54 Copynumber: 4.8 Consensus size: 54
27919204 TTAGTTTACC
* * * * * *
27919214 AAATTACCAAAATACCCTTGGTTTATAAAATCACAAAAATACCCCTGGTTT-TA
1 AAATTACTAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * **
27919267 AAATTACCAAAATACCCT-TAGTTTACAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATACCCTCGA-TTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * *
27919321 AAATTACTAAAATACCCAT-GGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACTAAAATACCC-TCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * *
27919375 AAATTA-TCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACT-AAAATACCCTCGA-TTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* ** **
27919429 AAATTACTGAAATACCCTCGACCTGTAAAATTATTAAAATACCC
1 AAATTACTAAAATACCCTCGATTTGTAAAATTACCAAAATACCC
27919473 TCAACTTGTA
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
53 46 0.26
54 126 0.72
55 4 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACTAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:27919456 original size:81 final size:78
Alignment explanation
Indices: 27919214--27919506 Score: 273
Period size: 81 Copynumber: 3.7 Consensus size: 78
27919204 TTAGTTTACC
* * * * * *
27919214 AAATTACCAAAATACCCTTGGTTTATAAAATCACAAAAATACCCCTGGTTTTAAAATTACCAAAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTTAAAATTACCAAAA
* * *
27919279 TACCCTTAGTTTACA
66 TACCCTGACTGT--A
* * * *
27919294 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCATGGTTTATAAAATTACCAAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTT-TAAAATTACCAAA
**
27919359 ATACCCTTGGTTTGTA
65 ATACCC-T-GACTGTA
* * **
27919375 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTT-TAAAATTACCAAA
27919440 ATACCCTCGACCTGTA
65 ATACCCT-GA-CTGTA
** ** * *
27919456 AAATTATTAAAATA-CCCTCAACTTGTAAAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTGATTT
27919507 ACAGAATTAT
Statistics
Matches: 182, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
80 52 0.29
81 127 0.70
82 1 0.01
83 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (78 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTTAAAATTACCAAAA
TACCCTGACTGTA
Found at i:27919459 original size:27 final size:27
Alignment explanation
Indices: 27919293--27919500 Score: 147
Period size: 27 Copynumber: 7.7 Consensus size: 27
27919283 CTTAGTTTAC
* **
27919293 AAAATTACCAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
** *
27919320 AAAATTACTAAAATACCCAT-GGTTTAT
1 AAAATTACTAAAATACCC-TCGACTTGT
* * **
27919347 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* *
27919374 AAAATTA-TCAAAATACCC-CTAGTTTGT
1 AAAATTACT-AAAATACCCTCGA-CTTGT
* *
27919401 AAAATTACCAAAATACCC-CTGATTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
* * *
27919428 GAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* *
27919455 AAAATTATTAAAATACCCTCAACTTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* *
27919482 AAAATTACCAAAGTACCCT
1 AAAATTACTAAAATACCCT
27919501 TGATTTACAG
Statistics
Matches: 150, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.01
27 147 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGACTTGT
Found at i:27919568 original size:27 final size:27
Alignment explanation
Indices: 27919538--27919867 Score: 439
Period size: 27 Copynumber: 12.3 Consensus size: 27
27919528 CGATTTAAAA
27919538 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
27919565 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
27919592 AATTATC-AGAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
* *
27919619 AATTACCGGAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
27919646 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
27919673 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
27919700 AATTACCGAAATATCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
27919727 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
27919754 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
27919781 AATTATCGAAATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
27919808 AATTACTAAAATACCCCTATAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
27919835 AATTATCGAGATA-CCTTTTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
27919861 AATTACC
1 AATTACC
27919868 ATTTTGCCCC
Statistics
Matches: 266, Mismatches: 35, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
26 16 0.06
27 250 0.94
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:27920347 original size:22 final size:22
Alignment explanation
Indices: 27920294--27920358 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
27920284 TTAAAGCCTT
* * *
27920294 CTGATTATGGCTTTGTGTCAAC
1 CTGATAATGGCTCTGTGCCAAC
*
27920316 CT-ACATATGGCTCTGTGCCAAC
1 CTGATA-ATGGCTCTGTGCCAAC
* *
27920338 CTGATAATGGTTGTGTGCCAA
1 CTGATAATGGCTCTGTGCCAA
27920359 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATAATGGCTCTGTGCCAAC
Found at i:27920547 original size:27 final size:27
Alignment explanation
Indices: 27920517--27920618 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
27920507 ATTCTGTTAA
* *
27920517 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
27920544 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
27920571 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
27920598 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
27920619 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 52 0.78
28 7 0.10
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:27920804 original size:25 final size:25
Alignment explanation
Indices: 27920766--27920822 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
27920756 TTCTAATTTT
*
27920766 TGATTCTGTTACCTGATACTGATTC
1 TGATTCTGTCACCTGATACTGATTC
*
27920791 TGATTCTGTCACCTGATTCTGATTC
1 TGATTCTGTCACCTGATACTGATTC
27920816 TGATTCT
1 TGATTCT
27920823 AGTTCTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.46
Consensus pattern (25 bp):
TGATTCTGTCACCTGATACTGATTC
Found at i:27922579 original size:49 final size:49
Alignment explanation
Indices: 27922520--27922744 Score: 281
Period size: 49 Copynumber: 4.5 Consensus size: 49
27922510 CTGGTACGCA
* * * *
27922520 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACAAG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
*
27922569 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
** * * *
27922618 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACAAG
* * * *
27922668 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA-
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTAC-AAG
27922719 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
27922745 TGCAACCTCA
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
49 77 0.50
50 42 0.27
51 34 0.22
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
Found at i:27922696 original size:99 final size:100
Alignment explanation
Indices: 27922507--27922744 Score: 311
Period size: 98 Copynumber: 2.4 Consensus size: 100
27922497 TAGCCAAAGC
* * * * **
27922507 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACAAGTAG
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCAGTACAAGTAG
27922572 TAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
66 TAGCCTGCACTTAGTACTACACACGTGATCACAAT
* * * *
27922605 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCAT-CTGATACATGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-AACCATCCAG-TACAAGT
*
27922669 AGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
64 AGTAGCCTGCACTTAGTACTACACACGTGATCACAAT
* * *
27922706 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
27922745 TGCAACCTCA
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
98 42 0.35
99 40 0.33
100 1 0.01
101 38 0.31
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (100 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCAGTACAAGTAG
TAGCCTGCACTTAGTACTACACACGTGATCACAAT
Found at i:27923908 original size:13 final size:13
Alignment explanation
Indices: 27923890--27923923 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
27923880 AAAAATTGGC
27923890 TTTTAATTTTGTA
1 TTTTAATTTTGTA
27923903 TTTTAATTTTGTA
1 TTTTAATTTTGTA
27923916 TTTTAATT
1 TTTTAATT
27923924 CATTTTACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTGTA
Found at i:27925570 original size:55 final size:55
Alignment explanation
Indices: 27925505--27925611 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
27925495 ACCATGGGTG
** * *
27925505 TTCCACACGGGCGTGTTGCACGCCCGTGTTGTTTTGGCAGGCTCGCCCACGGTTA
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGTTA
*
27925560 TTCCACACGGGCGTGTCACATGCCCGTGTTGTTTTGACAGGCTCGACCACGG
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGG
27925612 CCATGTCACA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.13, C:0.31, G:0.30, T:0.26
Consensus pattern (55 bp):
TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGTTA
Found at i:27925622 original size:55 final size:55
Alignment explanation
Indices: 27925505--27925629 Score: 162
Period size: 55 Copynumber: 2.3 Consensus size: 55
27925495 ACCATGGGTG
** * * **
27925505 TTCCACACGGGCGTGTTGCACGCCCGTGTTGTTTTGGCAGGCTCGCCCACGGTTA
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGCCA
*
27925560 TTCCACACGGGCGTGTCACATGCCCGTGTTGTTTTGACAGGCTCGACCACGGCCA
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGCCA
*
27925615 TGT-CACACGGCCGTG
1 T-TCCACACGGGCGTG
27925630 GCATTTCATC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 60 0.98
56 1 0.02
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.25
Consensus pattern (55 bp):
TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGCCA
Found at i:27931883 original size:24 final size:24
Alignment explanation
Indices: 27931808--27931887 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
27931798 ATGTTCTCAC
*
27931808 GAGCTGGAAATCAGTAAGCTAATAT
1 GAGCT-GAAATCAGTAAGCTCATAT
* **
27931833 GAACTGAGAATTGGTAAGCTC-TAAT
1 GAGCTGA-AATCAGTAAGCTCAT-AT
*
27931858 GAGCTGAAATCAATAAGCTCATAT
1 GAGCTGAAATCAGTAAGCTCATAT
27931882 GAGCTG
1 GAGCTG
27931888 TGGTGTGTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (24 bp):
GAGCTGAAATCAGTAAGCTCATAT
Found at i:27934586 original size:27 final size:27
Alignment explanation
Indices: 27934555--27934609 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
27934545 TACAGAGCAT
27934555 AAGGGCATAATCG-TCATTTTACCATAC
1 AAGGGCATAA-CGATCATTTTACCATAC
* * *
27934582 AAGGGTATTACGATCATTTTACCCTAC
1 AAGGGCATAACGATCATTTTACCATAC
27934609 A
1 A
27934610 GGGGTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGGGCATAACGATCATTTTACCATAC
Found at i:27940877 original size:103 final size:104
Alignment explanation
Indices: 27940676--27940940 Score: 410
Period size: 103 Copynumber: 2.6 Consensus size: 104
27940666 GTTGTACATA
** *
27940676 AAGGGGTTGCTGTGTGCT-ATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
27940740 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
27940779 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
27940843 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
27940882 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
27940941 AATAACGGTT
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
103 98 0.66
104 50 0.34
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:27948374 original size:76 final size:77
Alignment explanation
Indices: 27948241--27948389 Score: 266
Period size: 76 Copynumber: 1.9 Consensus size: 77
27948231 GTGCGATATC
*
27948241 CACCGTATCTTGAAATAAAAAAGGGGGTTGCTTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGC
1 CACCGTATCTTGAAATAAAAAAGGGGGTTGCTTATGTGCTGATTCCCCAAGGGGTTGCTAAGTGC
27948306 TGATTCCCAGTT
66 TGATTCCCAGTT
27948318 CACCGTATCTCTGAAAT-AAAAAGGGGGTTGC-TATGTGCTGATTCCCCAAGGGGTTGCTAAGTG
1 CACCGTATCT-TGAAATAAAAAAGGGGGTTGCTTATGTGCTGATTCCCCAAGGGGTTGCTAAGTG
27948381 CTGATTCCC
65 CTGATTCCC
27948390 CGATTAAGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
76 40 0.57
77 24 0.34
78 6 0.09
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (77 bp):
CACCGTATCTTGAAATAAAAAAGGGGGTTGCTTATGTGCTGATTCCCCAAGGGGTTGCTAAGTGC
TGATTCCCAGTT
Found at i:27948376 original size:26 final size:26
Alignment explanation
Indices: 27948341--27948390 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
27948331 AAATAAAAAG
*
27948341 GGGGTTGCTATGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
27948367 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
27948391 GATTAAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:27961105 original size:48 final size:47
Alignment explanation
Indices: 27961053--27961325 Score: 213
Period size: 48 Copynumber: 5.7 Consensus size: 47
27961043 TGATATGTGT
* * *
27961053 GCCAGTGTAAGACCATGTCTGGGACATGACGTCAGCCACAATATGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CATAATATGAGA
* * * * * * ** * *
27961101 GCCAGTGTAAAATCATGTTTGGAACATGGCATCGGGGATGTTGTGAAA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-AGCATAATATGAGA
* * * *
27961149 GCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCA-TAATATGAGA
* * * * *
27961197 GCTAGTGTAAGACCATGTCTGGGACATGGCACCAGCATTGAGACGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCA-TAATATGAGA
* * * * * * *
27961245 GCTAGTGTAAGACCATGTCTAGGACATGGTATCAGCCTTGACATGTGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CATAATATGAGA
* * *
27961293 GCCAGTGTAAGATCATGTTTGGAACATGGCATC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC
27961326 GGCAATTCAC
Statistics
Matches: 177, Mismatches: 45, Indels: 6
0.78 0.20 0.03
Matches are distributed among these distances:
47 2 0.01
48 173 0.98
49 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATAATATGAGA
Found at i:27961224 original size:96 final size:96
Alignment explanation
Indices: 27961056--27961327 Score: 300
Period size: 96 Copynumber: 2.8 Consensus size: 96
27961046 TATGTGTGCC
* * * * *
27961056 AGTGTAAGACCATGTCTGGGACATGACGTCAGCCA-CAATATGAGAGCCAGTGTAAAATCATGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTAATATGTGAGCCAGTGTAAGATCATGTT
* *
27961120 TGGAACATGGCATCGGGGATGTTGTGA-A-AGCT
65 TGGAACATGGCATCGGGCA--TTGAGACAGAGCT
* * * * *
27961152 AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAATATGTGTGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
* **
27961217 GGGACATGGCA-CCAGCATTGAGACGAGAGCT
66 GGAACATGGCATCGGGCATTGAGAC-AGAGCT
* * * * *
27961248 AGTGTAAGACCATGTCTAGGACATGGTATCAGCCTTGACATGTGAGCCAGTGTAAGATCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
27961313 GGAACATGGCATCGG
66 GGAACATGGCATCGG
27961328 CAATTCACCC
Statistics
Matches: 143, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
93 5 0.03
95 6 0.04
96 131 0.92
97 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
GGAACATGGCATCGGGCATTGAGACAGAGCT
Found at i:27962964 original size:25 final size:24
Alignment explanation
Indices: 27962920--27962967 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
27962910 ATTTGTTTTA
*
27962920 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATGATTTTAAAT
27962944 ATATTTGGTTTATTAT-ATTTTAAA
1 ATATTT-GTTT-TTATGATTTTAAA
27962968 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (24 bp):
ATATTTGTTTTTATGATTTTAAAT
Found at i:27962964 original size:26 final size:24
Alignment explanation
Indices: 27962920--27962969 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
27962910 ATTTGTTTTA
* *
27962920 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTAAAAT
27962944 ATATTTGGTTTATTATATTTTAAAAT
1 ATATTT-GTTT-TTATATTTTAAAAT
27962970 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTAAAAT
Found at i:27965159 original size:26 final size:26
Alignment explanation
Indices: 27965130--27965180 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
27965120 ATATTCGGCT
27965130 ATAACA-AATATAAATTCTAACATTTC
1 ATAACAGAATATAAATT-TAACATTTC
* *
27965156 ATAACAGCATATATATTTAACATTT
1 ATAACAGAATATAAATTTAACATTT
27965181 AACTACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAACAGAATATAAATTTAACATTTC
Done.