Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 66 of 438
Found at i:17233108 original size:17 final size:17
Alignment explanation
Indices: 17233083--17233125 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
17233073 TTCTTGTGCC
* *
17233083 AAAAATAAAAGGTTTTG
1 AAAATTAAAAGATTTTG
17233100 AAAATTAAAAAGATTTTG
1 AAAATT-AAAAGATTTTG
17233118 AAAATTAA
1 AAAATTAA
17233126 GTGACTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAATTAAAAGATTTTG
Found at i:17233116 original size:18 final size:18
Alignment explanation
Indices: 17233089--17233125 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17233079 TGCCAAAAAT
*
17233089 AAAAGGTTTTGAAAATTA
1 AAAAGATTTTGAAAATTA
17233107 AAAAGATTTTGAAAATTA
1 AAAAGATTTTGAAAATTA
17233125 A
1 A
17233126 GTGACTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (18 bp):
AAAAGATTTTGAAAATTA
Found at i:17233455 original size:20 final size:19
Alignment explanation
Indices: 17233426--17233491 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
17233416 AAATTACCAA
* *
17233426 AAAAAATCAAGATAATTTT
1 AAAAATTCAAAATAATTTT
17233445 CAAAAATTCAAAATAACTTTT
1 -AAAAATTCAAAATAA-TTTT
17233466 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
17233484 AAAAATTC
1 AAAAATTC
17233492 TAATTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 19 0.46
20 13 0.32
21 4 0.10
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:17233531 original size:18 final size:18
Alignment explanation
Indices: 17233484--17233531 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
17233474 AAATATTTAT
* *
17233484 AAAAATTCTAATTTTTAA
1 AAAAATTCTAAATTTCAA
*
17233502 AAAAATTATAAATTTCAA
1 AAAAATTCTAAATTTCAA
*
17233520 AAAAAATCTAAA
1 AAAAATTCTAAA
17233532 AAATATATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTCTAAATTTCAA
Found at i:17236833 original size:13 final size:13
Alignment explanation
Indices: 17236815--17236878 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
17236805 TTTAGCATTA
*
17236815 ACTTTTGAAAATT
1 ACTTTTGAAAAGT
*
17236828 ACTTTTAAAAAGT
1 ACTTTTGAAAAGT
* * *
17236841 -GTTGTGAAAAAT
1 ACTTTTGAAAAGT
*
17236853 ACTTTTGAGAAGT
1 ACTTTTGAAAAGT
*
17236866 ATTTTTGAAAAGT
1 ACTTTTGAAAAGT
17236879 TTGATTTAAG
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
12 8 0.21
13 30 0.79
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (13 bp):
ACTTTTGAAAAGT
Found at i:17236876 original size:25 final size:25
Alignment explanation
Indices: 17236817--17236876 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
17236807 TAGCATTAAC
17236817 TTTTGAAAATTACTTTTAAAAAGTG
1 TTTTGAAAATTACTTTTAAAAAGTG
* * * * *
17236842 TTGTGAAAAATACTTTTGAGAAGTAT
1 TTTTGAAAATTACTTTTAAAAAGT-G
17236868 TTTTGAAAA
1 TTTTGAAAA
17236877 GTTTGATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTTGAAAATTACTTTTAAAAAGTG
Found at i:17242838 original size:40 final size:40
Alignment explanation
Indices: 17242597--17242824 Score: 379
Period size: 40 Copynumber: 5.7 Consensus size: 40
17242587 TATTCGGATG
* *
17242597 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
17242637 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
17242676 ATATCCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
17242716 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
17242756 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
17242796 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
17242825 AGCAAGTAGC
Statistics
Matches: 177, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
39 36 0.20
40 141 0.80
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:17242838 original size:120 final size:119
Alignment explanation
Indices: 17242597--17242857 Score: 375
Period size: 119 Copynumber: 2.2 Consensus size: 119
17242587 TATTCGGATG
* *
17242597 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* * *
17242662 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACT
66 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGAATTTGAGCAAGTTACT
* *
17242716 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACTGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
17242780 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
64 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGAATTTGAGCAAGTTA-CT
* * *
17242836 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
17242858 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
118 2 0.02
119 63 0.49
120 63 0.49
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGAATTTGAGCAAGTTACT
Found at i:17247712 original size:25 final size:25
Alignment explanation
Indices: 17247684--17247731 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17247674 CTAAAATAGG
17247684 ATTTGTGAACTCGACT-AACTCGATA
1 ATTTGTG-ACTCGACTCAACTCGATA
* *
17247709 ATTTTTGACTCGATTCAACTCGA
1 ATTTGTGACTCGACTCAACTCGA
17247732 CTCGATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (25 bp):
ATTTGTGACTCGACTCAACTCGATA
Found at i:17248126 original size:42 final size:43
Alignment explanation
Indices: 17248067--17248166 Score: 175
Period size: 42 Copynumber: 2.3 Consensus size: 43
17248057 TTATTTGAAA
*
17248067 AAACGCCACTAAAGGTCATGGCCTTTAGCGGCGCTTTT-CCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
17248109 AAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
17248152 AAACGCCGCTAAAGG
1 AAACGCCGCTAAAGG
17248167 CGCTTTTCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 36 0.67
43 18 0.33
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:17248176 original size:27 final size:27
Alignment explanation
Indices: 17248138--17248189 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
17248128 GGCCTTTAGC
17248138 GGCGCTTTTCCCACAAACGCCGCTAAA
1 GGCGCTTTTCCCACAAACGCCGCTAAA
*
17248165 GGCGCTTTTCCCACGAACGCCGCTA
1 GGCGCTTTTCCCACAAACGCCGCTA
17248190 TAGGTCATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.19
Consensus pattern (27 bp):
GGCGCTTTTCCCACAAACGCCGCTAAA
Found at i:17248208 original size:70 final size:69
Alignment explanation
Indices: 17248096--17248234 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 69
17248086 GGCCTTTAGC
17248096 GGCGCTTTTCCACAAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAACGCCGC
1 GGCGCTTTTCCACAAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAACGCCGC
17248161 TAAA
66 TAAA
* *
17248165 GGCGCTTTTCCCACGAACGCCGCTATAGGTCATGGCCTTTAGCGGCGTTTTTCCCACAAACGCCG
1 GGCGCTTTT-CCACAAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAACGCCG
17248230 CTAAA
65 CTAAA
17248235 ACGCCGCTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 9 0.13
70 58 0.87
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.24
Consensus pattern (69 bp):
GGCGCTTTTCCACAAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCACAAACGCCGC
TAAA
Found at i:17248432 original size:19 final size:19
Alignment explanation
Indices: 17248387--17248433 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
17248377 ATCAAATTAA
*
17248387 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
17248406 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
17248425 AATAAAAAT
1 AATAAAAAT
17248434 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:17252833 original size:3 final size:3
Alignment explanation
Indices: 17252827--17252870 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
17252817 TTTTCTCTTT
17252827 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17252871 TACTAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17253205 original size:24 final size:24
Alignment explanation
Indices: 17253178--17253232 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
17253168 CCTTTAACCC
* *
17253178 TAAAACCC-ATACGCACCTAAATCT
1 TAAAACCCTAAAC-CACATAAATCT
*
17253202 T-AAACCCTAAACCACATAACTCT
1 TAAAACCCTAAACCACATAAATCT
17253225 TAAAACCC
1 TAAAACCC
17253233 CAACTCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.20
Consensus pattern (24 bp):
TAAAACCCTAAACCACATAAATCT
Found at i:17253603 original size:7 final size:7
Alignment explanation
Indices: 17253591--17253647 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
17253581 CCCATGGCCA
17253591 TTAAACC
1 TTAAACC
17253598 TTAAACC
1 TTAAACC
*
17253605 ATAAAACC
1 -TTAAACC
*
17253613 CTAAACC
1 TTAAACC
* *
17253620 ATAGACC
1 TTAAACC
**
17253627 TTAAATA
1 TTAAACC
17253634 TTAAACC
1 TTAAACC
17253641 TTAAACC
1 TTAAACC
17253648 CCAAAATAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (7 bp):
TTAAACC
Found at i:17253611 original size:15 final size:15
Alignment explanation
Indices: 17253588--17253647 Score: 70
Period size: 14 Copynumber: 4.1 Consensus size: 15
17253578 ACACCCATGG
17253588 CCATTAAACCTTAAA
1 CCATTAAACCTTAAA
* *
17253603 CCATAAAACCCTAAA
1 CCATTAAACCTTAAA
*
17253618 CCA-TAGACCTTAAA
1 CCATTAAACCTTAAA
*
17253632 -TATTAAACCTTAAA
1 CCATTAAACCTTAAA
17253646 CC
1 CC
17253648 CCAAAATAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 1 0.03
14 18 0.51
15 16 0.46
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (15 bp):
CCATTAAACCTTAAA
Found at i:17253809 original size:16 final size:15
Alignment explanation
Indices: 17253754--17253810 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 15
17253744 ATATGATGTT
* *
17253754 TTTTGGGGTTTAAGG
1 TTTTAGGGTTTATGG
* *
17253769 TTTTAGGGGTTATAG
1 TTTTAGGGTTTATGG
*
17253784 -TTTAGTGTTTATGG
1 TTTTAGGGTTTATGG
17253798 TTTTTAGGGTTTA
1 -TTTTAGGGTTTA
17253811 AGGGTTATAG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
14 11 0.34
15 11 0.34
16 10 0.31
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.53
Consensus pattern (15 bp):
TTTTAGGGTTTATGG
Found at i:17253946 original size:40 final size:40
Alignment explanation
Indices: 17253872--17254063 Score: 278
Period size: 40 Copynumber: 4.8 Consensus size: 40
17253862 TTATATGACC
* *
17253872 TTTAGCGGCGTTTTGACCATAAACGCCACTATTGCTCTGGT
1 TTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCTGGT
*
17253913 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGTT
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
* *
17253953 TTTAGCGGCGTTTTCCCAAAAACGCCGCTATTGCTCTAGTT
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT-GGT
**
17253994 TTTAGCGGCGTTTTACCAAAAACGCCATTATTGCTCTGGTT
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGG-T
*
17254035 TTTAGCGGTG-TTTACCAAAAACGCCGCTA
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTA
17254064 ATGTACAATT
Statistics
Matches: 138, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
40 77 0.56
41 61 0.44
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (40 bp):
TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
Found at i:17254007 original size:81 final size:81
Alignment explanation
Indices: 17253872--17254063 Score: 289
Period size: 81 Copynumber: 2.4 Consensus size: 81
17253862 TTATATGACC
* *
17253872 TTTAGCGGCGTTTTGACCATAAACGCCACTATTGCTCTGGTTTTAGCGGCGTTTTACCAAAAACG
1 TTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCTGGTTTTAGCGGCGTTTTACCAAAAACG
*
17253937 CCGCTATTGCTCT-GTT
65 CCACTATTGCTCTGGTT
* *
17253953 TTTAGCGGCGTTTTCCCAAAAACGCCGCTATTGCTCTAGTTTTTAGCGGCGTTTTACCAAAAACG
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT-GGTTTTAGCGGCGTTTTACCAAAAACG
*
17254018 CCATTATTGCTCTGGTT
65 CCACTATTGCTCTGGTT
*
17254035 TTTAGCGGTG-TTTACCAAAAACGCCGCTA
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTA
17254064 ATGTACAATT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 20 0.20
81 69 0.68
82 12 0.12
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (81 bp):
TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGTTTTAGCGGCGTTTTACCAAAAACGC
CACTATTGCTCTGGTT
Found at i:17254107 original size:12 final size:12
Alignment explanation
Indices: 17254092--17254117 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17254082 GTTTTTTGAT
17254092 AAAACGCCGCTA
1 AAAACGCCGCTA
17254104 AAAACGCCGCTA
1 AAAACGCCGCTA
17254116 AA
1 AA
17254118 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:17255895 original size:13 final size:13
Alignment explanation
Indices: 17255876--17255914 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
17255866 TTTTCTCTCA
*
17255876 ATTTTACAAAAAT
1 ATTTTACTAAAAT
*
17255889 GTTTTACTAAAAT
1 ATTTTACTAAAAT
17255902 ATTTTACTAAAAT
1 ATTTTACTAAAAT
17255915 TATGATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTTTACTAAAAT
Found at i:17257703 original size:34 final size:33
Alignment explanation
Indices: 17257665--17257773 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 33
17257655 TTTCTACTGA
* *
17257665 ATTGATCTATTATAAGAATATTA-TTCGTTACTAT
1 ATTGATCTATTATAAGCATATTATTTC--TACCAT
*
17257699 ATTGAAT-TGTTATAAGCATATTGATTTCTACCAT
1 ATTG-ATCTATTATAAGCATATT-ATTTCTACCAT
* * * * *
17257733 ATTGTTCTATTAAAAGCATATTAAATGCTACCGT
1 ATTGATCTATTATAAGCATATT-ATTTCTACCAT
17257767 ATTGATC
1 ATTGATC
17257774 CGTTTTGAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
33 1 0.02
34 53 0.88
35 3 0.05
36 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (33 bp):
ATTGATCTATTATAAGCATATTATTTCTACCAT
Found at i:17258872 original size:15 final size:16
Alignment explanation
Indices: 17258828--17258866 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
17258818 TTGTTTAACA
*
17258828 TTAATTAATATAAA--
1 TTAATTAAAATAAATC
17258842 TTAATTAAAATAAATC
1 TTAATTAAAATAAATC
17258858 TTAATTAAA
1 TTAATTAAA
17258867 TTAATCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATTAAAATAAATC
Found at i:17258882 original size:21 final size:20
Alignment explanation
Indices: 17258833--17258886 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
17258823 TAACATTAAT
*
17258833 TAATATAAATT-AATTAAAA
1 TAATATTAATTAAATTAAAA
* *
17258852 TAAATCTTAATTAAATTAATCA
1 T-AATATTAATTAAATTAA-AA
17258874 TAATATTAATTAA
1 TAATATTAATTAA
17258887 CATAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 8 0.29
21 17 0.61
22 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATATTAATTAAATTAAAA
Found at i:17259742 original size:23 final size:23
Alignment explanation
Indices: 17259715--17259760 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17259705 TTCTTTCTAT
*
17259715 TTTCTAT-TTTCTTTGATGTTTTC
1 TTTCTATCTTTCTTT-ATATTTTC
*
17259738 TTTCTTTCTTTCTTTATATTTTC
1 TTTCTATCTTTCTTTATATTTTC
17259761 ATTTTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTCTATCTTTCTTTATATTTTC
Found at i:17265803 original size:18 final size:18
Alignment explanation
Indices: 17265780--17265820 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
17265770 GCTCCATATG
*
17265780 AACTTGCCTGTTCAAAAT
1 AACTTGCCTATTCAAAAT
17265798 AACTTGCCTATTCAAAAT
1 AACTTGCCTATTCAAAAT
17265816 AACTT
1 AACTT
17265821 TAGGGGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (18 bp):
AACTTGCCTATTCAAAAT
Found at i:17269560 original size:49 final size:51
Alignment explanation
Indices: 17269425--17269572 Score: 246
Period size: 52 Copynumber: 2.9 Consensus size: 51
17269415 CCCTTGTAGT
*
17269425 CAAAGCTACCTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
17269476 CAAAGCTATCTTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATC-TTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
* *
17269528 CAAA-CTATC-TCTTCTCAAAGTGGCCTTTACATAGTACCACACTTG
1 CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTG
17269573 AGTCATTAGT
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
49 34 0.37
51 14 0.15
52 45 0.48
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (51 bp):
CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
Found at i:17272059 original size:69 final size:70
Alignment explanation
Indices: 17271969--17272103 Score: 191
Period size: 69 Copynumber: 1.9 Consensus size: 70
17271959 CTCTATATGC
* * *
17271969 CAGGTCTAGTCCTAGTTTCGAGGCCTACATGAAAAGTTAAACACTATGG-GGGTGAGCTTATGAA
1 CAGGTCTAGTCCTAATTTCGAGGCCTACATGAAAAGTTAAACACTACGGAGGGTAAGCTTATGAA
17272033 AATGA
66 AATGA
* * * * *
17272038 CAGGTCTGGTCTTAATTTCGAGGCTTACCTGAAAAGTTAAACACTACGGAGGGTAAGCTTGTGAA
1 CAGGTCTAGTCCTAATTTCGAGGCCTACATGAAAAGTTAAACACTACGGAGGGTAAGCTTATGAA
17272103 A
66 A
17272104 GCTTAGTGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
69 43 0.75
70 14 0.25
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (70 bp):
CAGGTCTAGTCCTAATTTCGAGGCCTACATGAAAAGTTAAACACTACGGAGGGTAAGCTTATGAA
AATGA
Found at i:17273828 original size:21 final size:22
Alignment explanation
Indices: 17273770--17273833 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
17273760 CGGGGATAAT
*
17273770 TTAAAAACTATTTAAAGAT-CCA
1 TTAAAAA-TATTTAAAAATACCA
**
17273792 TTAAAAATATGGAAAAATACC-
1 TTAAAAATATTTAAAAATACCA
* *
17273813 TTTAAAATATTTAAAATTACC
1 TTAAAAATATTTAAAAATACC
17273834 CTAAATTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 25 0.74
22 9 0.26
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAAAAATATTTAAAAATACCA
Found at i:17275397 original size:47 final size:47
Alignment explanation
Indices: 17275279--17275452 Score: 173
Period size: 45 Copynumber: 3.8 Consensus size: 47
17275269 GGGATATTTG
* *
17275279 GGCATCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCAAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAA
* * *
17275327 TG--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--A
* **
17275372 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAA
* *
17275420 CGC--CC-AGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
17275453 TATGGGCGGG
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
43 6 0.06
45 31 0.29
46 30 0.28
47 29 0.27
48 6 0.06
50 6 0.06
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAA
Found at i:17278382 original size:15 final size:15
Alignment explanation
Indices: 17278362--17278430 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
17278352 GTATCTTGGG
17278362 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
17278377 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
17278392 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
17278407 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
17278422 TTTCTTTAT
1 TTTCTTTAT
17278431 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:17278431 original size:30 final size:30
Alignment explanation
Indices: 17278353--17278440 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
17278343 CATAGTATCG
* * * *
17278353 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
17278383 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
17278413 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
17278441 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:17280934 original size:47 final size:47
Alignment explanation
Indices: 17280816--17280989 Score: 184
Period size: 45 Copynumber: 3.8 Consensus size: 47
17280806 GGGATATTTG
*
17280816 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAT
* *
17280864 -G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA-T
*
17280907 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGC-AAT
* * *
17280956 CGC--CTGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
17280990 TATGGGCGGG
Statistics
Matches: 108, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 30 0.28
46 29 0.27
47 30 0.28
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAT
Found at i:17280985 original size:46 final size:44
Alignment explanation
Indices: 17280821--17280994 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 44
17280811 ATTTGGGCAT
*
17280821 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
* * *
17280865 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAC---G
17280910 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 ---CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACG
*
17280958 CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17280995 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 6 0.05
44 2 0.02
45 31 0.28
46 33 0.30
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
Found at i:17286506 original size:16 final size:17
Alignment explanation
Indices: 17286487--17286533 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
17286477 TACCGATTTC
17286487 TCTTTCA-TCTTTTCCT
1 TCTTTCATTCTTTTCCT
*
17286503 TC-TTCATTGTTTTCCT
1 TCTTTCATTCTTTTCCT
* *
17286519 TTTTTCTTTCTTTTC
1 TCTTTCATTCTTTTC
17286534 TATCAGCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.68
Consensus pattern (17 bp):
TCTTTCATTCTTTTCCT
Found at i:17288917 original size:39 final size:39
Alignment explanation
Indices: 17288870--17288949 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
17288860 TATTTATTTT
17288870 ACTTAGTTTAAAATCTTAGTTTTTAATCACCCTCTTCAA
1 ACTTAGTTTAAAATCTTAGTTTTTAATCACCCTCTTCAA
17288909 ACTTAGTTTAAAATCTTAGTTTTTAATCACCCTCTTCAA
1 ACTTAGTTTAAAATCTTAGTTTTTAATCACCCTCTTCAA
17288948 AC
1 AC
17288950 AAAATATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (39 bp):
ACTTAGTTTAAAATCTTAGTTTTTAATCACCCTCTTCAA
Found at i:17291324 original size:29 final size:29
Alignment explanation
Indices: 17291291--17291454 Score: 265
Period size: 29 Copynumber: 5.7 Consensus size: 29
17291281 ATAAACGATC
* *** *
17291291 TCGCAGACTTAGTGCCATGCGATTTAAGC
1 TCGCACACTTAGTGCCATATAATTTAAGT
*
17291320 TCGCACACATAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
*
17291349 TTGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17291378 TCGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17291407 TCGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17291436 TCGCACACTTAGTGCCATA
1 TCGCACACTTAGTGCCATA
17291455 CCTTCCAAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 126 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATATAATTTAAGT
Found at i:17291470 original size:58 final size:58
Alignment explanation
Indices: 17291292--17291481 Score: 229
Period size: 58 Copynumber: 3.3 Consensus size: 58
17291282 TAAACGATCT
* *** * * * **
17291292 CGCAGACTTAGTGCCATGCGATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTCAAGCC
* * **
17291350 TGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTCAAGCC
**
17291408 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATA-CCTTCCAAGCC
1 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATT-CAAGCC
17291466 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
17291482 ATCTTGTCAC
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
57 2 0.02
58 116 0.98
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (58 bp):
CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTCAAGCC
Found at i:17291470 original size:87 final size:87
Alignment explanation
Indices: 17291292--17291481 Score: 256
Period size: 87 Copynumber: 2.2 Consensus size: 87
17291282 TAAACGATCT
* * * *
17291292 CGCAGACTTAGTGCCATGCGATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACAC
1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
* **
17291357 TTAGTGCCATATAATTTAAGTT
66 TTAGTGCCATATAATTCAAGCC
* * *
17291379 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTCGCACAC
1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
**
17291444 TTAGTGCCATA-CCTTCCAAGCC
66 TTAGTGCCATATAATT-CAAGCC
17291466 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
17291482 ATCTTGTCAC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
86 2 0.02
87 88 0.98
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (87 bp):
CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
TTAGTGCCATATAATTCAAGCC
Found at i:17299364 original size:29 final size:29
Alignment explanation
Indices: 17299329--17299492 Score: 274
Period size: 29 Copynumber: 5.7 Consensus size: 29
17299319 ATAAACGATC
*** *
17299329 TCGCACACTTAGTGCCATGCGATTTAAGC
1 TCGCACACTTAGTGCCATATAATTTAAGT
*
17299358 TCGCACACATAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
*
17299387 TTGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17299416 TCGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17299445 TCGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATATAATTTAAGT
17299474 TCGCACACTTAGTGCCATA
1 TCGCACACTTAGTGCCATA
17299493 CCTTCCAAGC
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 127 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATATAATTTAAGT
Found at i:17299508 original size:87 final size:87
Alignment explanation
Indices: 17299330--17299519 Score: 265
Period size: 87 Copynumber: 2.2 Consensus size: 87
17299320 TAAACGATCT
* * *
17299330 CGCACACTTAGTGCCATGCGATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACAC
1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
* **
17299395 TTAGTGCCATATAATTTAAGTT
66 TTAGTGCCATATAATTCAAGCC
* * *
17299417 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTCGCACAC
1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
**
17299482 TTAGTGCCATA-CCTTCCAAGCC
66 TTAGTGCCATATAATT-CAAGCC
17299504 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
17299520 ATCTTGTCAC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
86 2 0.02
87 89 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (87 bp):
CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC
TTAGTGCCATATAATTCAAGCC
Found at i:17303734 original size:42 final size:42
Alignment explanation
Indices: 17303670--17303762 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 42
17303660 TTTGACTTGT
*
17303670 CAGCAGGTTAAGGCTGAGCATCAGTTACCTTC-GGCTTTGCTG
1 CAGCCGGTTAAGGCTGAGCATCAGTTACCTTCAGG-TTTGCTG
*
17303712 CAGCCGGTTAAGGTTGAGCATCAGTTACCTTCAGGTTTGCTG
1 CAGCCGGTTAAGGCTGAGCATCAGTTACCTTCAGGTTTGCTG
17303754 CAG-CGGTTA
1 CAGCCGGTTA
17303763 TGATTCTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
41 6 0.12
42 40 0.83
43 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (42 bp):
CAGCCGGTTAAGGCTGAGCATCAGTTACCTTCAGGTTTGCTG
Found at i:17305340 original size:15 final size:16
Alignment explanation
Indices: 17305320--17305352 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17305310 CTACTAATTT
*
17305320 CTCTTTCA-TCTTTTC
1 CTCTTTCACTATTTTC
17305335 CTCTTTCACTATTTTC
1 CTCTTTCACTATTTTC
17305351 CT
1 CT
17305353 TTTTTCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (16 bp):
CTCTTTCACTATTTTC
Found at i:17307734 original size:23 final size:23
Alignment explanation
Indices: 17307699--17307742 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17307689 CCTTTTTCAC
* *
17307699 TTTTGTTTTATTATAAAATAACT
1 TTTTATTTAATTATAAAATAACT
*
17307722 TTTTATTTAATTATAATATAA
1 TTTTATTTAATTATAAAATAA
17307743 AATTAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTATTTAATTATAAAATAACT
Found at i:17311550 original size:13 final size:12
Alignment explanation
Indices: 17311528--17311578 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
17311518 ATAAGTCTTC
17311528 AAAAAT-AAATA
1 AAAAATAAAATA
17311539 GAAAAATAAAATA
1 -AAAAATAAAATA
17311552 AAAAATAATAAT-
1 AAAAATAA-AATA
*
17311564 AATAATAAAATA
1 AAAAATAAAATA
17311576 AAA
1 AAA
17311579 GGACTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 23 0.68
13 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:17313437 original size:4 final size:4
Alignment explanation
Indices: 17313430--17313495 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
17313420 AGAGGAGGGG
* * *
17313430 GAAA GAAA GGGAAA GAAA GAGA -AAA GAAA GAAA GAAA -AGA GAAG GAAA
1 GAAA GAAA --GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
17313478 GAAA G--A GAAA GGAAA GAA
1 GAAA GAAA GAAA -GAAA GAA
17313496 GAAGAGAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
2 2 0.04
3 4 0.08
4 35 0.71
5 4 0.08
6 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:17313460 original size:15 final size:14
Alignment explanation
Indices: 17313430--17313500 Score: 70
Period size: 15 Copynumber: 4.9 Consensus size: 14
17313420 AGAGGAGGGG
**
17313430 GAAAGAAAGGGAAA
1 GAAAGAAAAAGAAA
17313444 GAAAGAGAAAAGAAA
1 GAAAGA-AAAAGAAA
*
17313459 GAAAGAAAAGAGAAG
1 GAAAGAAAA-AGAAA
*
17313474 GAAAGAAAGAGAAA
1 GAAAGAAAAAGAAA
*
17313488 GGAAAGAAGAAGA
1 -GAAAGAAAAAGA
17313501 GAGGAAGAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
14 13 0.28
15 34 0.72
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAA
Found at i:17313464 original size:19 final size:19
Alignment explanation
Indices: 17313440--17313495 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
17313430 GAAAGAAAGG
17313440 GAAAGAAAGAGAAAAGAAA
1 GAAAGAAAGAGAAAAGAAA
*
17313459 GAAAGAAA-AG---AGAAG
1 GAAAGAAAGAGAAAAGAAA
*
17313474 GAAAGAAAGAGAAAGGAAA
1 GAAAGAAAGAGAAAAGAAA
17313493 GAA
1 GAA
17313496 GAAGAGAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
18 2 0.07
19 14 0.47
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAGAAAAGAAA
Found at i:17313469 original size:34 final size:34
Alignment explanation
Indices: 17313431--17313503 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
17313421 GAGGAGGGGG
17313431 AAAGA-AAGGGAAAGAAAGAGAAAAGAAAGAAAGA
1 AAAGAGAA-GGAAAGAAAGAGAAAAGAAAGAAAGA
*
17313465 AAAGAGAAGGAAAGAAAGAGAAAGGAAAG-AAGA
1 AAAGAGAAGGAAAGAAAGAGAAAAGAAAGAAAGA
*
17313498 AGAGAG
1 AAAGAG
17313504 GAAGAGCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 9 0.25
34 25 0.69
35 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (34 bp):
AAAGAGAAGGAAAGAAAGAGAAAAGAAAGAAAGA
Found at i:17313508 original size:14 final size:14
Alignment explanation
Indices: 17313449--17313520 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 14
17313439 GGAAAGAAAG
*
17313449 AGAAAAGA-AAGAA
1 AGAAAAGAGAGGAA
17313462 AGAAAAGAGAAGGAA
1 AGAAAAGAG-AGGAA
*
17313477 AGAAAGAGAAAGGAA
1 AGAAA-AGAGAGGAA
17313492 AGAAGAAGAGAGGAA
1 AGAA-AAGAGAGGAA
* *
17313507 GAGCAAGGAGAGGA
1 -AGAAAAGAGAGGA
17313521 GCTAGGTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.16
15 34 0.69
16 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.36, T:0.00
Consensus pattern (14 bp):
AGAAAAGAGAGGAA
Found at i:17313508 original size:25 final size:24
Alignment explanation
Indices: 17313429--17313515 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
17313419 AAGAGGAGGG
17313429 GGAAAGAAAGGGAAAGAA-AGAGAAA
1 GGAAAGAAA-GGAAAGAAGA-AGAAA
* *
17313454 AGAAAGAAAGAAAAG-AGAAGGAAA
1 GGAAAGAAAGGAAAGAAGAA-GAAA
* *
17313478 GAAAGAGAAAGGAAAGAAGAAGAGA
1 GGAA-AGAAAGGAAAGAAGAAGAAA
*
17313503 GGAAGAGCAAGGA
1 GGAA-AGAAAGGA
17313516 GAGGAGCTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.04
24 12 0.24
25 32 0.64
26 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.36, T:0.00
Consensus pattern (24 bp):
GGAAAGAAAGGAAAGAAGAAGAAA
Found at i:17321137 original size:20 final size:19
Alignment explanation
Indices: 17321114--17321249 Score: 69
Period size: 18 Copynumber: 7.3 Consensus size: 19
17321104 AAAATAAAAG
17321114 TAAAAATTATAGAAAAATAT
1 TAAAAATTATA-AAAAATAT
*
17321134 T--AAATTTTAATAAAA-AT
1 TAAAAATTATAA-AAAATAT
17321151 TAGAAAATTA-AAAAAATCAT
1 TA-AAAATTATAAAAAAT-AT
* *
17321171 AAAAAATATATATAAAAT-T
1 TAAAAAT-TATAAAAAATAT
17321190 GTAAAAATT-TATAAAAAT-T
1 -TAAAAATTATA-AAAAATAT
*
17321209 TTAAAA-TA-AAAAAATAT
1 TAAAAATTATAAAAAATAT
*
17321226 ATAGAAA-TATAGAAAAATA-
1 -TAAAAATTATA-AAAAATAT
17321245 TAAAA
1 TAAAA
17321250 TTTTATAAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
16 6 0.07
17 7 0.08
18 32 0.35
19 16 0.18
20 24 0.26
21 6 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAAATTATAAAAAATAT
Found at i:17321215 original size:18 final size:20
Alignment explanation
Indices: 17321172--17321214 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
17321162 AAAAATCATA
17321172 AAAAATATATATAAAATTGT
1 AAAAATATATATAAAATTGT
* *
17321192 AAAAATTTATA-AAAATTTT
1 AAAAATATATATAAAATTGT
17321211 AAAA
1 AAAA
17321215 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATATATATAAAATTGT
Found at i:17321249 original size:28 final size:28
Alignment explanation
Indices: 17321211--17321294 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
17321201 TAAAAATTTT
*
17321211 AAAATAAAAAAATATATAGAAATATAGA
1 AAAATATAAAAATATATAGAAATATAGA
* * *
17321239 AAAATATAAAATTTTATA-AAGTCATAAGA
1 AAAATATAAAAATATATAGAAAT-AT-AGA
* * *
17321268 AAATTATAAAAACTGTAAAGAAATATA
1 AAAATATAAAAA-TATATAGAAATATA
17321295 AAATTCTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.07
28 17 0.40
29 14 0.33
30 6 0.14
31 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (28 bp):
AAAATATAAAAATATATAGAAATATAGA
Found at i:17321316 original size:20 final size:20
Alignment explanation
Indices: 17321267--17321318 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
17321257 AAGTCATAAG
17321267 AAAATTATAAAAACTGTAAA
1 AAAATTATAAAAACTGTAAA
* *
17321287 GAAA-TATAAAATTCT-TAAA
1 AAAATTATAAAA-ACTGTAAA
17321306 AAAATTATAAAAA
1 AAAATTATAAAAA
17321319 TTATTGTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATTATAAAAACTGTAAA
Found at i:17321317 original size:10 final size:9
Alignment explanation
Indices: 17321114--17321322 Score: 77
Period size: 10 Copynumber: 22.1 Consensus size: 9
17321104 AAAATAAAAG
17321114 TAAAAATTA
1 TAAAAATTA
*
17321123 TAGAAAAATA
1 TA-AAAATTA
**
17321133 TTAAATTTTAA
1 -TAAAAATT-A
17321144 TAAAAATTA
1 TAAAAATTA
*
17321153 -GAAAATTA
1 TAAAAATTA
* *
17321161 AAAAAATCA
1 TAAAAATTA
17321170 TAAAAAATATA
1 T-AAAAAT-TA
*
17321181 TATAAAATTG
1 TA-AAAATTA
17321191 TAAAAATTTA
1 TAAAAA-TTA
17321201 TAAAAATT-
1 TAAAAATTA
*
17321209 TTAAAA-TA
1 TAAAAATTA
*
17321217 AAAAAATATA
1 TAAAAAT-TA
*
17321227 TAGAAA-TA
1 TAAAAATTA
*
17321235 TAGAAAAATA
1 TA-AAAATTA
*
17321245 T-AAAATTT
1 TAAAAATTA
* *
17321253 TATAAAGTCA
1 TA-AAAATTA
17321263 TAAGAAAATTA
1 T-A-AAAATTA
* *
17321274 TAAAAACTG
1 TAAAAATTA
*
17321283 TAAAGAAATA
1 TAAA-AATTA
*
17321293 TAAAATTCTTA
1 TAAAA--ATTA
*
17321304 AAAAAATTA
1 TAAAAATTA
17321313 TAAAAATTA
1 TAAAAATTA
17321322 T
1 T
17321323 TGTACCAAAA
Statistics
Matches: 145, Mismatches: 36, Indels: 38
0.66 0.16 0.17
Matches are distributed among these distances:
7 1 0.01
8 26 0.18
9 40 0.28
10 55 0.38
11 23 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:17321950 original size:95 final size:98
Alignment explanation
Indices: 17321766--17321953 Score: 231
Period size: 98 Copynumber: 1.9 Consensus size: 98
17321756 TGTCAAAGGG
* * *
17321766 TTTTTTTGATGCATTTTGACAGTTGAAATACCAAATTGAGTGCACAAAAAAAAAGAGTAGGGGCT
1 TTTTTTTGATGCATTTTGAAACTTGAAATACCAAATTGAGTGCACAAAAAAAAAGAGTAGGAGCT
* * *
17321831 TAATTGCTTTTTTTGAAAGAGTTTAAAGGTCTT
66 TAATTGATTTTTTTAAAAAAGTTTAAAGGTCTT
* * * * *
17321864 TTTTTTTTATGCATTTTGAAACTTTAAGTACCCAATTGAGTGC-C-AAAAAAAA-AGTAGGAGTT
1 TTTTTTTGATGCATTTTGAAACTTGAAATACCAAATTGAGTGCACAAAAAAAAAGAGTAGGAGCT
*
17321926 TAGTT-ATTTTTTTAAAAAAAGTTTAAAG
66 TAATTGATTTTTTT-AAAAAAGTTTAAAG
17321954 ACTTTTTATA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
94 7 0.09
95 24 0.31
96 8 0.10
97 1 0.01
98 37 0.48
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (98 bp):
TTTTTTTGATGCATTTTGAAACTTGAAATACCAAATTGAGTGCACAAAAAAAAAGAGTAGGAGCT
TAATTGATTTTTTTAAAAAAGTTTAAAGGTCTT
Found at i:17322168 original size:17 final size:17
Alignment explanation
Indices: 17322146--17322180 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17322136 CTAAGGAGGT
17322146 AAGTGTATTTTACAGTA
1 AAGTGTATTTTACAGTA
* *
17322163 AAGTGTTTTTTACCGTA
1 AAGTGTATTTTACAGTA
17322180 A
1 A
17322181 TAAAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (17 bp):
AAGTGTATTTTACAGTA
Found at i:17325765 original size:32 final size:34
Alignment explanation
Indices: 17325729--17325793 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
17325719 TAACAGTGGT
*
17325729 ACTGGGCCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
17325761 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATA
17325794 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:17328395 original size:22 final size:22
Alignment explanation
Indices: 17328360--17328416 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
17328350 CTCCTGAAAC
17328360 AGGGGC-ACACGCCCATATGGA
1 AGGGGCGACACGCCCATATGGA
*
17328381 AGGGGCGAGACGCCCATATGGA
1 AGGGGCGACACGCCCATATGGA
*
17328403 AGGGGCGACTCGCC
1 AGGGGCGACACGCC
17328417 TATGTGGCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.25, C:0.28, G:0.39, T:0.09
Consensus pattern (22 bp):
AGGGGCGACACGCCCATATGGA
Found at i:17329765 original size:49 final size:47
Alignment explanation
Indices: 17329709--17329890 Score: 181
Period size: 49 Copynumber: 3.7 Consensus size: 47
17329699 ATACATCAAG
*
17329709 GCCGATGCCATGTCCCAAACAGGTCTTACACCAGCTCTCACTTATATGT
1 GCCGATGCCATGTCCCAAACAGGTCTTACACTAGCT-TCACTTATA-GT
* *
17329758 GTCGATGCCATGTCTCAAACAGGTCTTACACTAGCTTGCATATCTTA-AG-
1 GCCGATGCCATGTCCCAAACAGGTCTTACACTAGCTT-C--A-CTTATAGT
* * *
17329807 GCCGATGCCGTGTCCCAGATAGGTCTTACACTAGCTTTCA-TCTATAGGT
1 GCCGATGCCATGTCCCAAACAGGTCTTACACTAGC-TTCACT-TATA-GT
* * *
17329856 GCCAATGCCATGTCCCAGAGAGGTCTTACACTAGC
1 GCCGATGCCATGTCCCAAACAGGTCTTACACTAGC
17329891 ACACACAACA
Statistics
Matches: 113, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
45 1 0.01
46 2 0.02
47 2 0.02
48 2 0.02
49 97 0.86
50 3 0.03
51 2 0.02
52 4 0.04
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAAACAGGTCTTACACTAGCTTCACTTATAGT
Found at i:17329864 original size:98 final size:98
Alignment explanation
Indices: 17329706--17329890 Score: 255
Period size: 98 Copynumber: 1.9 Consensus size: 98
17329696 TCCATACATC
* * *
17329706 AAGGCCGATGCCATGTCCCAAACAGGTCTTACACCAGCTCTCACTTATATGTGTCGATGCCATGT
1 AAGGCCGATGCCATGTCCCAAACAGGTCTTACACCAGCTCTCACTTATAGGTGCCAATGCCATGT
*
17329771 CTCAAACAGGTCTTACACTAGCTTGCATATCTT
66 CCCAAACAGGTCTTACACTAGCTTGCATATCTT
* * * * *
17329804 AAGGCCGATGCCGTGTCCCAGATAGGTCTTACACTAGCTTTCA-TCTATAGGTGCCAATGCCATG
1 AAGGCCGATGCCATGTCCCAAACAGGTCTTACACCAGCTCTCACT-TATAGGTGCCAATGCCATG
* *
17329868 TCCCAGAGAGGTCTTACACTAGC
65 TCCCAAACAGGTCTTACACTAGC
17329891 ACACACAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
97 1 0.01
98 74 0.99
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (98 bp):
AAGGCCGATGCCATGTCCCAAACAGGTCTTACACCAGCTCTCACTTATAGGTGCCAATGCCATGT
CCCAAACAGGTCTTACACTAGCTTGCATATCTT
Found at i:17336216 original size:28 final size:28
Alignment explanation
Indices: 17336185--17336270 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
17336175 AGCGTTCCAT
17336185 TTTTCTTATTTTATCAGTTTCTTCATTC
1 TTTTCTTATTTTATCAGTTTCTTCATTC
* * *
17336213 TTTTCTTGTTCCT-CCA-TTTC-T--TT-
1 TTTTCTTATT-TTATCAGTTTCTTCATTC
17336236 TTTTCTTATTTTATCAGTTTCTTCATTC
1 TTTTCTTATTTTATCAGTTTCTTCATTC
17336264 TTTTCTT
1 TTTTCTT
17336271 GTTCCTCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
22 1 0.02
23 11 0.24
24 6 0.13
25 1 0.02
26 1 0.02
27 6 0.13
28 18 0.40
29 1 0.02
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTCTTATTTTATCAGTTTCTTCATTC
Found at i:17336240 original size:51 final size:51
Alignment explanation
Indices: 17336184--17336286 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
17336174 TAGCGTTCCA
17336184 TTTTTCTTATTTTATCAGTTTCTTCATTCTTTTCTTGTTCCTCCATTTCTT
1 TTTTTCTTATTTTATCAGTTTCTTCATTCTTTTCTTGTTCCTCCATTTCTT
17336235 TTTTTCTTATTTTATCAGTTTCTTCATTCTTTTCTTGTTCCTCCATTTCTT
1 TTTTTCTTATTTTATCAGTTTCTTCATTCTTTTCTTGTTCCTCCATTTCTT
17336286 T
1 T
17336287 CCCCCTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.10, C:0.21, G:0.04, T:0.65
Consensus pattern (51 bp):
TTTTTCTTATTTTATCAGTTTCTTCATTCTTTTCTTGTTCCTCCATTTCTT
Found at i:17338176 original size:28 final size:28
Alignment explanation
Indices: 17338111--17338211 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
17338101 ATAGTGAATC
*
17338111 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
17338140 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17338168 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
17338198 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17338212 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17346091 original size:28 final size:28
Alignment explanation
Indices: 17346026--17346126 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
17346016 ATAGTGAATC
*
17346026 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
17346055 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17346083 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
17346113 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17346127 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17350830 original size:38 final size:35
Alignment explanation
Indices: 17350772--17350889 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 35
17350762 TCAATCATGC
17350772 ACTGGGCC-ATAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGA-AG-CCTTTTCATATTTCATATTT-AT--T
17350811 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
17350842 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
17350873 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
17350890 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 10 0.13
40 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:17350833 original size:31 final size:31
Alignment explanation
Indices: 17350795--17350889 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
17350785 CCTTTTCATA
*
17350795 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
17350826 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
17350857 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
17350888 TT
1 TT
17350890 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:17351485 original size:25 final size:25
Alignment explanation
Indices: 17351439--17351486 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17351429 TTATAATATG
* * * *
17351439 AAAATGACCGTTTTGCCTCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
17351464 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
17351487 GTTTATGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:17351555 original size:20 final size:20
Alignment explanation
Indices: 17351530--17351585 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
17351520 TAAATATGGT
17351530 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
17351550 ATGTATAATATGCACATGAT
1 ATGTATGATATGCACATGAA
17351570 ATGTATGATATGCACA
1 ATGTATGATATGCACA
17351586 AGAGGTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:17351707 original size:47 final size:49
Alignment explanation
Indices: 17351640--17351733 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 49
17351630 AGGAAGTGAA
*
17351640 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
*
17351687 AAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
17351734 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 20 0.48
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:17351729 original size:25 final size:24
Alignment explanation
Indices: 17351639--17351733 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
17351629 GAGGAAGTGA
17351639 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
17351662 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
17351686 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
17351710 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
17351734 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 22 0.34
24 31 0.48
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:17351960 original size:31 final size:31
Alignment explanation
Indices: 17351925--17352019 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
17351915 CGTTTACAGT
17351925 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
17351956 AAAGGCTTCGGCCCAGAAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
17351987 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
17352018 AA
1 AA
17352020 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:17354358 original size:13 final size:14
Alignment explanation
Indices: 17354337--17354365 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17354327 TGAAAAATGG
17354337 ATTAGAAAATATTT
1 ATTAGAAAATATTT
17354351 ATTA-AAAATATTT
1 ATTAGAAAATATTT
17354364 AT
1 AT
17354366 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:17355751 original size:15 final size:15
Alignment explanation
Indices: 17355728--17355775 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
17355718 TATCAAATTT
17355728 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
17355743 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
17355758 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
17355772 ATAT
1 ATAT
17355776 AATATATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:17356378 original size:21 final size:21
Alignment explanation
Indices: 17356330--17356381 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
17356320 ATGTGTCATA
*
17356330 TTTCAGGCACCTTGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
***
17356351 CAGCAGGCACCTCGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
17356372 TTTCAGGCAC
1 TTTCAGGCAC
17356382 TTATGTGTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (21 bp):
TTTCAGGCACCTCGTGTGTCG
Found at i:17363774 original size:43 final size:42
Alignment explanation
Indices: 17363719--17363889 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 42
17363709 ATATCGTACA
17363719 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCACATATTG
1 ATGCCAACATCCCAGACGTGGTCTTACATG-AATCACATATTG
* * *
17363762 ATGCC-ACTATCCCAGAC-TGGGTCTGACATGAATCA-AAAATG
1 ATGCCAAC-ATCCCAGACGT-GGTCTTACATGAATCACATATTG
* ** * * ** *
17363803 ATGCCGATGTCTCAGACATGGTCTTACACAAAATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACA-TGAATCACATATTG
* * *
17363846 ATGCCAACGTCCCAGACGTGGTCTTACACGAGAACACATATTG
1 ATGCCAACATCCCAGACGTGGTCTTACATGA-ATCACATATTG
17363889 A
1 A
17363890 AAATCCTAGG
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
41 24 0.24
42 16 0.16
43 61 0.60
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACATGAATCACATATTG
Found at i:17373863 original size:140 final size:141
Alignment explanation
Indices: 17373583--17373886 Score: 343
Period size: 140 Copynumber: 2.2 Consensus size: 141
17373573 GGGTGTTACA
* * * *
17373583 CCCAGGCATGGTCTTACACTGGGTCAT-CCATCAA-GTCGATGCTATGTCCCAGACATGGTCTTA
1 CCCAGACAT-GTCTTACACTGGCTTATGTCA-CAAGGTCGATGCTATGTCCCAGACATGGTCTTA
**
17373646 CACTAACTCTCACATATCTGTGCCGATGTCATGTCCCAGACGTGGTCTTACACAGACACATCTCG
64 CACTAACTCT-ACATATCAATGCCGATGTCATGTCCCAGACGTGGTCTTACACAGACACATCTCG
17373711 TAGCCGATGCATGT
128 TAGCCGATGCATGT
*
17373725 CTCAGACATGTCTTACACTGGCTTATGTCACAAGGTCGATGC-ATGTCCCAGACAT-GTCTTACA
1 CCCAGACATGTCTTACACTGGCTTATGTCACAAGGTCGATGCTATGTCCCAGACATGGTCTTACA
* * * * * * * * *
17373788 CTAGCTCT-CGTCTCAATGCTGATGTCATGTCCCAGA-GATGGTCTTACACTGGCTC-CCTTAAT
66 CTAACTCTACATATCAATGCCGATGTCATGTCCCAGACG-TGGTCTTACACAGACACATC-T--C
*
17373850 GTGGCCGATGCATGT
127 GTAGCCGATGCATGT
17373865 CCCAGACATGTCTTACACTGGC
1 CCCAGACATGTCTTACACTGGC
17373887 ACACAAATAA
Statistics
Matches: 138, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
137 2 0.01
138 38 0.28
140 50 0.36
141 31 0.22
142 17 0.12
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (141 bp):
CCCAGACATGTCTTACACTGGCTTATGTCACAAGGTCGATGCTATGTCCCAGACATGGTCTTACA
CTAACTCTACATATCAATGCCGATGTCATGTCCCAGACGTGGTCTTACACAGACACATCTCGTAG
CCGATGCATGT
Found at i:17373864 original size:47 final size:45
Alignment explanation
Indices: 17373583--17373886 Score: 176
Period size: 46 Copynumber: 6.5 Consensus size: 45
17373573 GGGTGTTACA
* * *
17373583 CCCAGGCATGGTCTTACACTGGGTCATC-CATCAA-GTCGATGCTATGT
1 CCCAGACAT-GTCTTACACTGGCTC-TCGC-TCAATGCCGATGC-ATGT
** * **
17373630 CCCAGACATGGTCTTACACTAACTCTCACATATCTGTGCCGATGTCATGT
1 CCCAGACAT-GTCTTACACTGGCTCTCGC---TCAATGCCGATG-CATGT
* * *
17373680 CCCAGACGTGGTCTTACACAGACACATCTCG-T--A-GCCGATGCATGT
1 CCCAGACAT-GTCTTACACTG--GC-TCTCGCTCAATGCCGATGCATGT
* * * * *
17373725 CTCAGACATGTCTTACACTGGCT-TATGTCACAAGGTCGATGCATGT
1 CCCAGACATGTCTTACACTGGCTCT-CG-CTCAATGCCGATGCATGT
* *
17373771 CCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATGTCATGT
1 CCCAGACATGTCTTACACTGGCTCTCG-CTCAATGCCGATG-CATGT
* *
17373818 CCCAGAGATGGTCTTACACTGGCTC-C-CTTAATGTGGCCGATGCATGT
1 CCCAGACAT-GTCTTACACTGGCTCTCGCTCAA--T-GCCGATGCATGT
17373865 CCCAGACATGTCTTACACTGGC
1 CCCAGACATGTCTTACACTGGC
17373887 ACACAAATAA
Statistics
Matches: 206, Mismatches: 31, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
40 1 0.00
41 2 0.01
42 1 0.00
44 10 0.05
45 17 0.08
46 65 0.32
47 51 0.25
48 20 0.10
49 4 0.02
50 28 0.14
51 1 0.00
52 2 0.01
53 4 0.02
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (45 bp):
CCCAGACATGTCTTACACTGGCTCTCGCTCAATGCCGATGCATGT
Found at i:17375269 original size:28 final size:27
Alignment explanation
Indices: 17375238--17375321 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 27
17375228 GTTACCATAT
* *
17375238 ACAGATAATTGTGGCAGGGCCATCAGAA
1 ACAGATATTTGTGGCAGAGCCA-CAGAA
17375266 ACAGATATTTGTGGCAGAGCCACTAGAA
1 ACAGATATTTGTGGCAGAGCCAC-AGAA
*
17375294 ACAAATATTTGTGGCAGAGCCACCAGAA
1 ACAGATATTTGTGGCAGAGCCA-CAGAA
17375322 CGCTTCCTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
27 1 0.02
28 49 0.96
29 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (27 bp):
ACAGATATTTGTGGCAGAGCCACAGAA
Found at i:17377983 original size:27 final size:28
Alignment explanation
Indices: 17377953--17378022 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
17377943 ATAGTGAGTC
* *
17377953 CGCACACCTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17377980 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17378008 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17378023 GTACAAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:17380770 original size:37 final size:37
Alignment explanation
Indices: 17380728--17380808 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
17380718 CGGGGTTTTA
* *
17380728 ACCCGGATAAAATCTCCACACGTGGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
* *
17380765 ACCCGGACAGAATCTCCATACGTAGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
17380802 ACCCGGA
1 ACCCGGA
17380809 ATATATTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (37 bp):
ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
Found at i:17381038 original size:48 final size:48
Alignment explanation
Indices: 17380927--17381048 Score: 172
Period size: 48 Copynumber: 2.5 Consensus size: 48
17380917 CACATTTGAT
* * * *
17380927 CATTCGACTTTACCAAATATACATCTCTCATACATATTTCATATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATCTCATATTAGC
* *
17380975 CATTTGGCTTTACCACATATACATATCTCATACATGTCTCATATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATCTCATATTAGC
* *
17381023 CATTCGGCTTTACCACACATATATAT
1 CATTCGGCTTTACCACATATACATAT
17381049 ATTTACCTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (48 bp):
CATTCGGCTTTACCACATATACATATCTCATACATATCTCATATTAGC
Found at i:17387116 original size:46 final size:46
Alignment explanation
Indices: 17387063--17387238 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
17387053 TATTTGGGCA
17387063 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
17387109 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* *
17387156 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
17387202 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17387239 GCAGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 66 0.59
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:17387218 original size:93 final size:93
Alignment explanation
Indices: 17387059--17387230 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
17387049 GGGATATTTG
* * *
17387059 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAG
17387124 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
17387152 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAG
17387217 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
17387231 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:17394242 original size:28 final size:28
Alignment explanation
Indices: 17394206--17394275 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
17394196 ACGGCCTGAC
17394206 ACATGCCCGTGTCCCTCACACAGCCATG
1 ACATGCCCGTGTCCCTCACACAGCCATG
* **
17394234 ACATACCCGTGTCCCTCACATGGCCATG
1 ACATGCCCGTGTCCCTCACACAGCCATG
17394262 ACATGCCCGTGTCC
1 ACATGCCCGTGTCC
17394276 TAGCCCGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (28 bp):
ACATGCCCGTGTCCCTCACACAGCCATG
Found at i:17395340 original size:50 final size:50
Alignment explanation
Indices: 17395221--17395452 Score: 184
Period size: 47 Copynumber: 4.9 Consensus size: 50
17395211 ATAAGGTGTA
* * * * *
17395221 ATGCCGATACCACGTCCCAGACATAGTCTTACACTGGCTTATC-CA--T-C
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC-TCTCACATCTCC
* * *
17395268 AAGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCC
** * *
17395318 ATGTTGATGCCATGTCCTAGACATGGTCTTACACT-G---ACACATCT-C
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCC
* * * *
17395363 GTAGCCGATG-CATGTCCCAGACAT-GTGTTACACTAGCTCT--CGTCTCA
1 AT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCC
* * *
17395410 ATGCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCTCA
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA
17395453 TCATGTGGTC
Statistics
Matches: 146, Mismatches: 25, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
44 9 0.06
45 16 0.11
46 25 0.17
47 48 0.33
48 13 0.09
49 2 0.01
50 33 0.23
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (50 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCC
Found at i:17398725 original size:16 final size:16
Alignment explanation
Indices: 17398688--17398726 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
17398678 AAAATTTATT
17398688 AATT-TTTTATGAAAA
1 AATTATTTTATGAAAA
*
17398703 ATTTTATTTTATGAAAA
1 A-ATTATTTTATGAAAA
17398720 AATTATT
1 AATTATT
17398727 AAAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
AATTATTTTATGAAAA
Found at i:17399505 original size:28 final size:26
Alignment explanation
Indices: 17399452--17399506 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
17399442 TACTGGGACA
*
17399452 TTTTTTTCTAATATGATACCTCTATT
1 TTTTTTTCTAATATGATACCTATATT
* *
17399478 TTTTTTTACTCAATTTGATACTTATATT
1 TTTTTTT-CT-AATATGATACCTATATT
17399506 T
1 T
17399507 GACAAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 2 0.08
28 15 0.62
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTTTTCTAATATGATACCTATATT
Found at i:17406485 original size:21 final size:21
Alignment explanation
Indices: 17406459--17406499 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17406449 AGACAAGCGA
* *
17406459 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17406480 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17406500 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:17410572 original size:18 final size:18
Alignment explanation
Indices: 17410550--17410589 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17410540 AAAGAAAGGG
*
17410550 AAAAAAGAAATACAGAAAT
1 AAAAAAGAAA-AAAGAAAT
17410569 AAAAAAGAAAAAAGAAAT
1 AAAAAAGAAAAAAGAAAT
17410587 AAA
1 AAA
17410590 TATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAGAAAAAAGAAAT
Found at i:17410756 original size:18 final size:18
Alignment explanation
Indices: 17410742--17410779 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
17410732 ATGAATTTTA
17410742 GTCTGGCTATCAATTGTT
1 GTCTGGCTATCAATTGTT
17410760 GTCTGGCTATCAATTGTT
1 GTCTGGCTATCAATTGTT
17410778 GT
1 GT
17410780 TATCTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (18 bp):
GTCTGGCTATCAATTGTT
Found at i:17411002 original size:19 final size:19
Alignment explanation
Indices: 17410965--17411005 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17410955 AAAGAAAGGG
*
17410965 AAAAAAGAAATACAGAAAT
1 AAAAAAGAAATAAAGAAAT
17410984 AAAAAAGAAA-AAAGAAAAT
1 AAAAAAGAAATAAAG-AAAT
17411003 AAA
1 AAA
17411006 TATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.07
Consensus pattern (19 bp):
AAAAAAGAAATAAAGAAAT
Found at i:17413575 original size:21 final size:21
Alignment explanation
Indices: 17413539--17413599 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
17413529 CTCTTGAAGC
*
17413539 AGGGC-ACACACCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
* *
17413559 AGGGCAACATGCCCGTGCGGA
1 AGGGCAACACGCCCGTGTGGA
*
17413580 AGGGCAGCACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
17413600 TCATTATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.21, C:0.30, G:0.39, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:17414941 original size:48 final size:47
Alignment explanation
Indices: 17414887--17415101 Score: 227
Period size: 46 Copynumber: 4.6 Consensus size: 47
17414877 AAGCTGACGC
* * * * *
17414887 CATGTCCCAGATAGGTCTTACACTAGCTTTTATATCGTGAGGTCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTTATATC-TAAGGCCGATG
* * * *
17414935 CATGTCCCAGACATGTCTTACACTAGCTCTTGTCTC-AATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTTATATCTAAGGCCGATG
* * **
17414981 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCTCAAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTTATATCT-AAGGCCGATG
* * * ** *
17415029 CATGTCCCAAACATGTCTTACACTAGCTTTCAT-GCTGTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTTATATCTAAGGCCGATG
17415075 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
17415102 ACACATATCA
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
46 68 0.49
47 2 0.01
48 68 0.49
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTTTATATCTAAGGCCGATG
Found at i:17415002 original size:94 final size:94
Alignment explanation
Indices: 17414887--17415101 Score: 249
Period size: 94 Copynumber: 2.3 Consensus size: 94
17414877 AAGCTGACGC
* * ** * * *
17414887 CATGTCCCAGATAGGTCTTACACTAGCTTTTATATCGT-GAGGTCAATGCATGTCCCAGACATGT
1 CATGTCCCAGACAAGTCTTACACTAGCTTAAATATC-TCAAGGCCAATGCATGTCCCAAACATGT
17414951 CTTACACTAGCTCTTGTC-T-CAAT-GCCGATG
65 CTTACACTAG--CTT-TCATGCAATGGCCGATG
* *
17414981 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCTCAAGGCCGATGCATGTCCCAAACATGTC
1 CATGTCCCAGACAAGTCTTACACTAGCTTAAATATCTCAAGGCCAATGCATGTCCCAAACATGTC
** *
17415046 TTACACTAGCTTTCATGCTGTGGCTGATG
66 TTACACTAGCTTTCATGCAATGGCCGATG
*
17415075 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACAAGTCTTACACTAGC
17415102 ACACATATCA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
91 2 0.02
92 4 0.04
93 3 0.03
94 94 0.91
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (94 bp):
CATGTCCCAGACAAGTCTTACACTAGCTTAAATATCTCAAGGCCAATGCATGTCCCAAACATGTC
TTACACTAGCTTTCATGCAATGGCCGATG
Found at i:17422449 original size:10 final size:10
Alignment explanation
Indices: 17422434--17422458 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17422424 CTCATTTGGA
17422434 ATACTACCGG
1 ATACTACCGG
17422444 ATACTACCGG
1 ATACTACCGG
17422454 ATACT
1 ATACT
17422459 CAATAGCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (10 bp):
ATACTACCGG
Found at i:17422569 original size:49 final size:49
Alignment explanation
Indices: 17422492--17422611 Score: 170
Period size: 49 Copynumber: 2.4 Consensus size: 49
17422482 ATGTCGACGT
*
17422492 CATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAG-GCCGATGC
1 CATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGCG-GTGCCGATGC
* * * *
17422542 CATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCGGTGTCGATGC
1 CATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGGTGCCGATGC
17422591 CATGTCCCAGACAGGTCTTAC
1 CATGTCCCAGACAGGTCTTAC
17422612 TCTGACACAC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.78
50 13 0.20
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (49 bp):
CATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGGTGCCGATGC
Found at i:17425011 original size:21 final size:22
Alignment explanation
Indices: 17424985--17425025 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17424975 CACTTGACAT
17424985 AGGGGC-ACACGCCCGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
17425006 AGGGGCAACACGCCCGTGTG
1 AGGGGCAACACGCCCGTGTG
17425026 ACCAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.29, G:0.44, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:17426217 original size:47 final size:50
Alignment explanation
Indices: 17426146--17426272 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 50
17426136 AATGCTGACA
* *
17426146 CCATGTCCCAGACATGGTCTTACACTGGCTCA-TGTC-TC-AAGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCATTGTCACCGAAGTCGACG
* * *
17426193 CTATGTCCCAGACATGGTCTTACACTGACT-ATTGTCACCGAGGTCGACG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCATTGTCACCGAAGTCGACG
*
17426242 CCATGTCCCAGACATGGTCTTACACTAGCTC
1 CCATGTCCCAGACATGGTCTTACACTGGCTC
17426273 TCGCATATCT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.01
47 32 0.47
48 1 0.01
49 34 0.50
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCATTGTCACCGAAGTCGACG
Found at i:17426258 original size:49 final size:47
Alignment explanation
Indices: 17426146--17426267 Score: 165
Period size: 47 Copynumber: 2.6 Consensus size: 47
17426136 AATGCTGACA
* * *
17426146 CCATGTCCCAGACATGGTCTTACACTGGCTCATGTCTCAAGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCATGTCCCAAGTCGACG
* *
17426193 CTATGTCCCAGACATGGTCTTACACTGACT-ATTGTCACCGAGGTCGACG
1 CCATGTCCCAGACATGGTCTTACACTGACTCA-TGTC-CC-AAGTCGACG
17426242 CCATGTCCCAGACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
17426268 AGCTCTCGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 1 0.02
47 32 0.48
48 1 0.02
49 32 0.48
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
CCATGTCCCAGACATGGTCTTACACTGACTCATGTCCCAAGTCGACG
Found at i:17426428 original size:46 final size:45
Alignment explanation
Indices: 17426377--17426506 Score: 129
Period size: 47 Copynumber: 2.8 Consensus size: 45
17426367 ACCTTACGAG
* *
17426377 GTCGATGCATGTCCCAGACACATCTTACACTAGCTCTCGTCTCAAT-T
1 GTCGATGCATGTCCCAGACACGTCTTACACTAGCTCTC--AT-AATAT
* * *
17426424 -TCGATGCCATGTCCCAGGCATGGTCTTACAGTAGCTCTCATAATAT
1 GTCGATG-CATGTCCCAGACA-CGTCTTACACTAGCTCTCATAATAT
* *
17426470 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GTC-GATGCATGTCCCAGACACGTCTTACACTAGCTC
17426507 ACAATAGCCC
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
45 3 0.04
46 22 0.32
47 25 0.36
48 19 0.28
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (45 bp):
GTCGATGCATGTCCCAGACACGTCTTACACTAGCTCTCATAATAT
Found at i:17432123 original size:23 final size:23
Alignment explanation
Indices: 17432088--17432132 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
17432078 ATAGCTATGA
*
17432088 AACAACAATAAAACAACACCAAT
1 AACAACAACAAAACAACACCAAT
* * *
17432111 AACAACACCAAAATAGCACCAA
1 AACAACAACAAAACAACACCAA
17432133 AAACCTGCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.29, G:0.02, T:0.07
Consensus pattern (23 bp):
AACAACAACAAAACAACACCAAT
Found at i:17439653 original size:127 final size:129
Alignment explanation
Indices: 17439512--17439743 Score: 339
Period size: 127 Copynumber: 1.8 Consensus size: 129
17439502 AATATAAAAT
*
17439512 AAACTAATCCTAATTCTATTGTAAA-TTGATAAAAATTAATATATGA-ATTATAATAGATATAAT
1 AAACTAATCCTAATTCTA-TATAAAGTTGATAAAAATTAATATAT-ATATTATAATAGATATAAT
17439575 TATATATTAA-AGATTATCATC-TTATTATTAAA-AAAAAATTATCAAATAAAATATGATTAAAT
64 TATATATTAATA-ATTATCATCTTTATTATTAAACAAAAAATTATCAAATAAAATATGATTAAAT
17439637 TA
128 TA
* * * *
17439639 AAACTAATCTTAATTCTATATAAAGTTGATAATAATTAATATATATATTATACTGGATATAATTA
1 AAACTAATCCTAATTCTATATAAAGTTGATAAAAATTAATATATATATTATAATAGATATAATTA
*
17439704 TATATTAATAATTATCATCTTTTTTATTAAACCAAAAAAT
66 TATATTAATAATTATCATCTTTATTATTAAA-CAAAAAAT
17439744 ATTTATTCTA
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
126 6 0.06
127 69 0.74
128 11 0.12
130 7 0.08
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (129 bp):
AAACTAATCCTAATTCTATATAAAGTTGATAAAAATTAATATATATATTATAATAGATATAATTA
TATATTAATAATTATCATCTTTATTATTAAACAAAAAATTATCAAATAAAATATGATTAAATTA
Found at i:17439824 original size:30 final size:30
Alignment explanation
Indices: 17439769--17439825 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17439759 CTTCTGAAAA
* ***
17439769 TATTTACAAAAAGAGGAATTTAATTTTTAT
1 TATTTACAAAAAGAGCAACCAAATTTTTAT
17439799 TATTTACAAAAAGAGCAACCAAATTTT
1 TATTTACAAAAAGAGCAACCAAATTTT
17439826 AAAAATACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (30 bp):
TATTTACAAAAAGAGCAACCAAATTTTTAT
Found at i:17448527 original size:40 final size:40
Alignment explanation
Indices: 17448472--17448551 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
17448462 CAATTCTTAA
17448472 TTCAAATACTATCTCAATGGCATTGATAATTTATTAAGGC
1 TTCAAATACTATCTCAATGGCATTGATAATTTATTAAGGC
*
17448512 TTCAAATATTATCTCAATGGCATTGATAATTTATTAAGGC
1 TTCAAATACTATCTCAATGGCATTGATAATTTATTAAGGC
17448552 ATAACCAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (40 bp):
TTCAAATACTATCTCAATGGCATTGATAATTTATTAAGGC
Found at i:17449076 original size:43 final size:42
Alignment explanation
Indices: 17449019--17449177 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
17449009 ACATATCGTA
17449019 CAATGCCAACGTCCCAGACGTGGTCTTACATGAAATCACATGT
1 CAATGCCAACGTCCCAGACGTGGTCTTACATGAAATCACAT-T
*
17449062 CAATGCC-ACTGTCCCAGACAG-GGTCTTACA-CAAATCACAATT
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATCAC-ATT
* * * * * *
17449104 ACGATGCCGATGTCCTAGACATGGTCTTAC-TCGAAATCAGATAT
1 -CAATGCCAACGTCCCAGACGTGGTCTTACAT-GAAATCACAT-T
** *
17449148 TGATGCCAACGTCCCAGATGTGGTCTTACA
1 CAATGCCAACGTCCCAGACGTGGTCTTACA
17449178 CGAGAACACA
Statistics
Matches: 93, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
42 10 0.11
43 74 0.80
44 9 0.10
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (42 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACATGAAATCACATT
Found at i:17456642 original size:29 final size:30
Alignment explanation
Indices: 17456586--17456643 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
17456576 CTTTTGAAAA
* * *
17456586 TATTTACAAAAAGTAGCATCTAATTTTTAT
1 TATTTACAAAAAGTAGCAACCAAATTTTAT
17456616 TATTTACAAAAAG-AGCAACCAAATTTTA
1 TATTTACAAAAAGTAGCAACCAAATTTTA
17456644 AAAATACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (30 bp):
TATTTACAAAAAGTAGCAACCAAATTTTAT
Found at i:17462082 original size:30 final size:30
Alignment explanation
Indices: 17462048--17462108 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
17462038 TTCCTGAGCC
17462048 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
17462078 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
17462108 T
1 T
17462109 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:17462890 original size:68 final size:68
Alignment explanation
Indices: 17462818--17462965 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 68
17462808 CATCATGTGT
* * * *
17462818 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTACAAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
17462881 TGTAG
64 TGTAG
* ** * *
17462886 ACAAGAGAGCT--ATGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCAT
1 ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCAT
17462949 GTAG
65 GTAG
17462953 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
17462966 GAGATAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
64 24 0.36
65 3 0.05
66 5 0.08
67 23 0.35
68 11 0.17
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATG
TAG
Found at i:17462922 original size:64 final size:64
Alignment explanation
Indices: 17462842--17463025 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
17462832 AGACATTATG
* * * *
17462842 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTATGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
17462906 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
17462971 AA
63 AA
* * *
17462973 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
17463026 CAAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 21 0.21
67 32 0.33
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:17472450 original size:49 final size:49
Alignment explanation
Indices: 17472284--17472463 Score: 234
Period size: 50 Copynumber: 3.6 Consensus size: 49
17472274 TGAGGTCGCA
* * * * * *
17472284 TGTGTAGTACTAAGTGCAAGCTACTAGGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* ** *
17472335 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
*
17472385 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
17472434 TGTGTAGTACTAAGTGCAGGCTACTACGTG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTG
17472464 CAGGCTACTA
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 37 0.33
50 44 0.39
51 32 0.28
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:17472464 original size:14 final size:14
Alignment explanation
Indices: 17472441--17472477 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
17472431 ACGTGTGTAG
*
17472441 TACTAAGTGCAGGC
1 TACTACGTGCAGGC
17472455 TACTACGTGCAGGC
1 TACTACGTGCAGGC
17472469 TACTACGTG
1 TACTACGTG
17472478 TACCGGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (14 bp):
TACTACGTGCAGGC
Found at i:17472471 original size:63 final size:63
Alignment explanation
Indices: 17472392--17472519 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
17472382 ACATGTGTAG
*
17472392 TACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTACTAAGTGCAGGC
1 TACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACATGTGTAGTACTAAGTGCAGGC
* * *
17472455 TACTACGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTATGTGCAGGC
1 TACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACATGTGTAGTACTAAGTGCAGGC
17472518 TA
1 TA
17472520 TTATGCGTAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (63 bp):
TACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACATGTGTAGTACTAAGTGCAGGC
Found at i:17476337 original size:19 final size:21
Alignment explanation
Indices: 17476300--17476339 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
17476290 ACTATATATA
17476300 TTAATTAGTTTTGTAAAAGTT
1 TTAATTAGTTTTGTAAAAGTT
17476321 TTAATTA-TTTT-TAAAAGTT
1 TTAATTAGTTTTGTAAAAGTT
17476340 ATAACAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TTAATTAGTTTTGTAAAAGTT
Found at i:17479120 original size:67 final size:66
Alignment explanation
Indices: 17479049--17479197 Score: 178
Period size: 67 Copynumber: 2.2 Consensus size: 66
17479039 CATCATGTGT
* **
17479049 ACAAGA-AGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GAT-ACTATGTGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATCAAGATGTGTACACCA
17479111 TGTAG
62 TGTAG
** *
17479116 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGATGTGTACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGAT-CAAGATGTGTACACCATGT
17479181 AG
65 AG
17479183 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
17479198 GATAAACTGG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
64 20 0.28
65 5 0.07
66 2 0.03
67 38 0.54
68 6 0.08
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATCAAGATGTGTACACCATGTA
G
Found at i:17481610 original size:40 final size:40
Alignment explanation
Indices: 17481508--17481691 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
17481498 AAATTGAATG
* * * * *
17481508 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
17481548 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
17481588 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
17481628 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
17481668 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
17481692 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:17481716 original size:80 final size:80
Alignment explanation
Indices: 17481550--17481736 Score: 189
Period size: 80 Copynumber: 2.3 Consensus size: 80
17481540 TGAAAATTAT
* * *
17481550 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCATT
* *
17481615 CGTGCAAGTTGTTAA
66 CGTGCAAGTTATCAA
* * * * * *
17481630 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCT-ATATCCGGGCTAAGACCCGAAGGCAT
* **
17481694 TGGTGCGGGTTATCATA
65 TCGTGCAAGTTATCA-A
* * *
17481711 A-CCGGGCTATGTCCCGAAGGCGATTG
1 ATCCGGGCTAAGACCCGAAGGCAATTG
17481737 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
79 1 0.01
80 84 0.97
81 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCATT
CGTGCAAGTTATCAA
Found at i:17486857 original size:68 final size:67
Alignment explanation
Indices: 17486785--17486934 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
17486775 CATCATGTGT
* * * *
17486785 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
17486847 ATGTAG
62 ATGTAG
** * *
17486853 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
17486918 AG
66 AG
17486920 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
17486935 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Done.