Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 39 of 171
Found at i:17405477 original size:23 final size:23
Alignment explanation
Indices: 17405447--17405617 Score: 191
Period size: 23 Copynumber: 7.3 Consensus size: 23
17405437 ACAAAGTACT
17405447 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
17405470 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
17405493 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
* * *
17405518 GAGCACGA-GACGTGCTAAACAGA
1 GAGCAC-ACAAAGTGCTAATCAGA
* *
17405541 GAGCACACACAGTGCTAGTCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
17405564 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
17405587 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
17405612 GAGCAC
1 GAGCAC
17405618 GAGACGTGCT
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
22 1 0.01
23 94 0.78
25 25 0.21
26 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:17405499 original size:46 final size:47
Alignment explanation
Indices: 17405447--17405617 Score: 249
Period size: 46 Copynumber: 3.6 Consensus size: 47
17405437 ACAAAGTACT
*
17405447 GAGCACACAAAGTGCTAAT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
* * *
17405493 GAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC-ACGAAGTGCTAATCGGA
*
17405541 GAGCACACACAGTGCTAGT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
17405587 GAGCACACACAGTGCTAATAACAGAGAGCAC
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC
17405618 GAGACGTGCT
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
45 1 0.01
46 58 0.53
48 50 0.45
49 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (47 bp):
GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
Found at i:17405556 original size:94 final size:94
Alignment explanation
Indices: 17405447--17405638 Score: 366
Period size: 94 Copynumber: 2.0 Consensus size: 94
17405437 ACAAAGTACT
17405447 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
17405512 AACAGAGAGCACGAGACGTGCTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
* *
17405541 GAGCACACACAGTGCTAGTCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
17405606 AACAGAGAGCACGAGACGTGCTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
17405635 GAGC
1 GAGC
17405639 GCGCTAGTGT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (94 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
AACAGAGAGCACGAGACGTGCTAAACAGA
Found at i:17405627 original size:71 final size:71
Alignment explanation
Indices: 17405447--17405638 Score: 209
Period size: 71 Copynumber: 2.7 Consensus size: 71
17405437 ACAAAGTACT
* * *
17405447 GAGCACACAAAGTGCTAAT--CAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTA
1 GAGCACACACAGTGCTAATAACAGAGAGCACA-GACGTGCTAATCAGAGAGCACACACAGTGCTA
17405510 ATAACAGA
65 AT-ACAGA
* * *
17405518 GAGCACGAGAC-GTGCT-A-AACAGAGAGCACACACAGTGCTAGTCAGAGAGCACACGA-AGTGC
1 GAGCAC-ACACAGTGCTAATAACAGAGAGCACAGAC-GTGCTAATCAGAGAGCACAC-ACAGTGC
*
17405579 TAAT-CGGA
63 TAATACAGA
*
17405587 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAATAACAGAGAGCAC-AGACGTGCTAATCAGAGAGC
17405639 GCGCTAGTGT
Statistics
Matches: 101, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
68 3 0.03
69 14 0.14
70 3 0.03
71 75 0.74
72 6 0.06
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (71 bp):
GAGCACACACAGTGCTAATAACAGAGAGCACAGACGTGCTAATCAGAGAGCACACACAGTGCTAA
TACAGA
Found at i:17405632 original size:23 final size:22
Alignment explanation
Indices: 17405458--17405638 Score: 155
Period size: 23 Copynumber: 7.7 Consensus size: 22
17405448 AGCACACAAA
* *
17405458 GTGCTAATCAGAGAGCACACGAA
1 GTGCTAAACAGAGAGCACA-GAC
* * *
17405481 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
17405503 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
*
17405529 GTGCTAAACAGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
** *
17405551 AGTGCTAGTCAGAGAGCACACGAA
1 -GTGCTAAACAGAGAGCACA-GAC
* * *
17405575 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
17405597 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
17405623 GTGCTAAACAGAGAGC
1 GTGCTAAACAGAGAGC
17405639 GCGCTAGTGT
Statistics
Matches: 130, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
22 5 0.04
23 84 0.65
24 5 0.04
25 30 0.23
26 6 0.05
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACAGAC
Found at i:17411948 original size:23 final size:23
Alignment explanation
Indices: 17411918--17411994 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
17411908 ACAAAGTACT
17411918 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
17411941 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
17411964 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
17411989 GAGCAC
1 GAGCAC
17411995 GAGACGTGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 38 0.81
25 9 0.19
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:17411996 original size:46 final size:47
Alignment explanation
Indices: 17411918--17412015 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 47
17411908 ACAAAGTACT
* *
17411918 GAGCACACAAAGTGCTAATCAGAGAGCACACGA-A-GTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGAGAG-ACACGAGACGTGCTAAACAGA
*
17411964 GAGCACACACAGTGCTAATAACAGAGAG-CACGAGACGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAT--CAGAGAGACACGAGACGTGCTAAACAGA
17412012 GAGC
1 GAGC
17412016 GCGCTAGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
46 23 0.51
47 1 0.02
48 21 0.47
ACGTcount: A:0.40, C:0.22, G:0.27, T:0.11
Consensus pattern (47 bp):
GAGCACACAAAGTGCTAATCAGAGAGACACGAGACGTGCTAAACAGA
Found at i:17412004 original size:48 final size:46
Alignment explanation
Indices: 17411918--17412015 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 46
17411908 ACAAAGTACT
* *
17411918 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
* *
17411964 GAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACGAAGTGCTAAACAGA
17412012 GAGC
1 GAGC
17412016 GCGCTAGTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
46 18 0.40
48 26 0.58
49 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.27, T:0.11
Consensus pattern (46 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
Found at i:17412009 original size:23 final size:22
Alignment explanation
Indices: 17411929--17412015 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 22
17411919 AGCACACAAA
* *
17411929 GTGCTAATCAGAGAGCACACGAA
1 GTGCTAAACAGAGAGCACA-GAC
* * *
17411952 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
17411974 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
17412000 GTGCTAAACAGAGAGC
1 GTGCTAAACAGAGAGC
17412016 GCGCTAGTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 33 0.61
24 2 0.04
25 15 0.28
26 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.13
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACAGAC
Found at i:17413939 original size:16 final size:16
Alignment explanation
Indices: 17413898--17413931 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17413888 TTTAATGATG
*
17413898 AATTTATTAAAATATT
1 AATTTATAAAAATATT
17413914 AATTGTATAAAAATATT
1 AATT-TATAAAAATATT
17413931 A
1 A
17413932 GATTATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTTATAAAAATATT
Found at i:17414128 original size:3 final size:3
Alignment explanation
Indices: 17414122--17414150 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17414112 CAAAACACAT
17414122 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17414151 TATTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17424755 original size:16 final size:17
Alignment explanation
Indices: 17424729--17424762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17424719 TTTGAATTTA
*
17424729 TTTAAATATTTATATAT
1 TTTAAATATTTACATAT
17424746 TTTAAA-ATTTACATAT
1 TTTAAATATTTACATAT
17424762 T
1 T
17424763 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATATTTACATAT
Found at i:17428764 original size:15 final size:15
Alignment explanation
Indices: 17428744--17428774 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17428734 TTATTCTAAC
17428744 TCTTATAAGGAAAAT
1 TCTTATAAGGAAAAT
17428759 TCTTATAAGGAAAAT
1 TCTTATAAGGAAAAT
17428774 T
1 T
17428775 TTTTCTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
TCTTATAAGGAAAAT
Found at i:17429006 original size:23 final size:23
Alignment explanation
Indices: 17428968--17429030 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
17428958 TTGATTGAAA
* *
17428968 AAATATATTTTTTAAAATATTTATG
1 AAATA-ATATTTTAAAAT-TTTATC
17428993 AAA-AATATTTTAAAATTTTATC
1 AAATAATATTTTAAAATTTTATC
*
17429015 AAATAATATTTAAAAA
1 AAATAATATTTTAAAA
17429031 CCATAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.24
23 22 0.65
24 1 0.03
25 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATAATATTTTAAAATTTTATC
Found at i:17431150 original size:49 final size:49
Alignment explanation
Indices: 17431070--17431163 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
17431060 ATTTAAAAGA
* *
17431070 TTGAAAAACCTTATTCTAATAAATGACAAATAGATGAAGTGTAGTAACG
1 TTGAAAAACCTTATTCTAATAAATGACAAATAAAAGAAGTGTAGTAACG
**
17431119 TTGAAAATTCTTATTCTAATCAAAAT-A-AAATAAAAGAAGTGTAGT
1 TTGAAAAACCTTATTCTAAT--AAATGACAAATAAAAGAAGTGTAGT
17431164 TGTCAACGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 34 0.87
50 1 0.03
51 4 0.10
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.31
Consensus pattern (49 bp):
TTGAAAAACCTTATTCTAATAAATGACAAATAAAAGAAGTGTAGTAACG
Found at i:17433482 original size:21 final size:19
Alignment explanation
Indices: 17433452--17433496 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
17433442 ATCTGATGAA
17433452 AAGAAGTATATACAAAATG
1 AAGAAGTATATACAAAATG
17433471 AAGAAGTATATACAAAATG
1 AAGAAGTATATACAAAATG
17433490 AAGAAGT
1 AAGAAGT
17433497 TGGTAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.20
Consensus pattern (19 bp):
AAGAAGTATATACAAAATG
Found at i:17437862 original size:23 final size:23
Alignment explanation
Indices: 17437830--17437873 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17437820 CCTTTGGGCA
*
17437830 TACCGTTTTCCCA-TTGCCCATCG
1 TACCGGTTT-CCATTTGCCCATCG
17437853 TACCGGTTTCCATTTGCCCAT
1 TACCGGTTTCCATTTGCCCAT
17437874 ATCAGTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (23 bp):
TACCGGTTTCCATTTGCCCATCG
Found at i:17440946 original size:31 final size:29
Alignment explanation
Indices: 17440906--17440964 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
17440896 ATATTAAAAC
* *
17440906 TATATATGAATTATGGTTTAATGTGCAATTG
1 TATACATGAATTATGATTT--TGTGCAATTG
*
17440937 TATACATGAATTTTGATTTTGTGCAATT
1 TATACATGAATTATGATTTTGTGCAATT
17440965 CTTGTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (29 bp):
TATACATGAATTATGATTTTGTGCAATTG
Found at i:17441182 original size:29 final size:30
Alignment explanation
Indices: 17441150--17441208 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
17441140 TCACGTGTAT
*
17441150 AATTAC-ACCAAATTAAAATTCATGTATAC
1 AATTACAACCAAATCAAAATTCATGTATAC
**
17441179 AATTACATATTAAATCAAAATTCATGTATA
1 AATTACA-ACCAAATCAAAATTCATGTATA
17441209 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
31 19 0.76
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (30 bp):
AATTACAACCAAATCAAAATTCATGTATAC
Found at i:17443877 original size:16 final size:16
Alignment explanation
Indices: 17443856--17443889 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17443846 AATAATTTTG
17443856 ATTAATTAACTAATTT
1 ATTAATTAACTAATTT
17443872 ATTAATTAACTAATTT
1 ATTAATTAACTAATTT
17443888 AT
1 AT
17443890 AACCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTAACTAATTT
Found at i:17445912 original size:15 final size:15
Alignment explanation
Indices: 17445892--17445920 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17445882 TCTAGATCAC
17445892 AATAAATAAAAATAA
1 AATAAATAAAAATAA
17445907 AATAAATAAAAATA
1 AATAAATAAAAATA
17445921 GGGTTCGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAATAAAAATAA
Found at i:17447116 original size:3 final size:3
Alignment explanation
Indices: 17447108--17447154 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
17447098 TTGGTTGCTT
17447108 TTA 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 TTA TT
17447155 TAGTTTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17449121 original size:16 final size:17
Alignment explanation
Indices: 17449102--17449141 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
17449092 TAATTTTTTA
17449102 AAAATTATTAAAAT-AT
1 AAAATTATTAAAATAAT
*
17449118 AAAATT-TTTAAATAAT
1 AAAATTATTAAAATAAT
17449134 AAAATTAT
1 AAAATTAT
17449142 ATTTTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 14 0.67
17 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTATTAAAATAAT
Found at i:17472140 original size:29 final size:29
Alignment explanation
Indices: 17472103--17472160 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
17472093 ACCCAAAAAA
*
17472103 AATAATTTTAAGTTAAATTCATTTAATTT
1 AATAATTTTAAATTAAATTCATTTAATTT
*
17472132 AATAATTTTAAATTAAATTTATTTAATTT
1 AATAATTTTAAATTAAATTCATTTAATTT
17472161 TAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
AATAATTTTAAATTAAATTCATTTAATTT
Found at i:17473666 original size:30 final size:29
Alignment explanation
Indices: 17473630--17473917 Score: 233
Period size: 30 Copynumber: 9.8 Consensus size: 29
17473620 TTTTGGCCTC
*
17473630 AAACTTTTCAAAAATTACATTTTAACCCAT
1 AAACTTTTCCAAAATTACATTTTAACCC-T
* *
17473660 AAACTTTTCCAAAATCACATTTTGACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
* * * *
17473689 AAACTTTCCCAAAATCACATTTCAACCTTT
1 AAACTTTTCCAAAATTACATTTTAACC-CT
* *
17473719 AAACTTTTCAAAAATTACATTTTAACCCCA
1 AAACTTTTCCAAAATTACATTTTAA-CCCT
* * *
17473749 AAACTTTCCCAAAATCACATTTTGACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
*
17473778 AAAACTTTT-CAAAATTTCATTTTAACCCCT
1 -AAACTTTTCCAAAATTACATTTTAA-CCCT
* *
17473808 AAACTTTTCTAAAATTGCATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAA-CCCT
* ** * *
17473838 -AATTTTTTTAAAATCATATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACC-CT
* * ** *
17473867 GAACTCTTCCAAAATTATGTTTTGACCC-
1 AAACTTTTCCAAAATTACATTTTAACCCT
* *
17473895 AAAATTCTCCAAAACTT-CATTTT
1 AAACTTTTCCAAAA-TTACATTTT
17473918 TCGACCCTGT
Statistics
Matches: 208, Mismatches: 42, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
28 16 0.08
29 73 0.35
30 117 0.56
31 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTTCCAAAATTACATTTTAACCCT
Found at i:17473791 original size:89 final size:90
Alignment explanation
Indices: 17473630--17473836 Score: 303
Period size: 89 Copynumber: 2.3 Consensus size: 90
17473620 TTTTGGCCTC
*
17473630 AAACTTTTCAAAAATTACATTTTAA-CCCATAAACTTTTCCAAAATCACATTTTGACCCTAAACT
1 AAACTTTTCAAAAATTACATTTTAACCCCATAAACTTTCCCAAAATCACATTTTGACCCTAAACT
**
17473694 TTCCCAAAATCACATTTCAACCTTT
66 TTCCCAAAATCACATTTCAACCCCT
17473719 AAACTTTTCAAAAATTACATTTTAACCCCA-AAACTTTCCCAAAATCACATTTTGACCCTAAAAC
1 AAACTTTTCAAAAATTACATTTTAACCCCATAAACTTTCCCAAAATCACATTTTGACCCT-AAAC
* ** *
17473783 TTT-TCAAAATTTCATTTTAACCCCT
65 TTTCCCAAAATCACATTTCAACCCCT
* *
17473808 AAACTTTTCTAAAATTGCATTTTAACCCC
1 AAACTTTTCAAAAATTACATTTTAACCCC
17473837 TAATTTTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
89 96 0.90
90 11 0.10
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (90 bp):
AAACTTTTCAAAAATTACATTTTAACCCCATAAACTTTCCCAAAATCACATTTTGACCCTAAACT
TTCCCAAAATCACATTTCAACCCCT
Found at i:17473851 original size:59 final size:60
Alignment explanation
Indices: 17473630--17473883 Score: 246
Period size: 59 Copynumber: 4.3 Consensus size: 60
17473620 TTTTGGCCTC
* * * *
17473630 AAACTTTTCAAAAATTACATTTTAACCCATAAACTTTTCCAAAATCACATTTTGA-CCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCCT
* * * ** * *
17473689 AAACTTTCCCAAAATCACATTTCAACCTTTAAACTTTTCAAAAATTACATTTTAACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCCT
* * * *
17473749 AAACTTTCCCAAAATCACATTTTGA-CCCTAAAACTTTT-CAAAATTTCATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT-AAACTTTTCCAAAATTACATTTTAACCCCT
* * * ** * * *
17473808 AAACTTTTCTAAAATTGCATTTTAACCCCT-AATTTTTTTAAAATCATATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCCT
* *
17473867 GAACTCTTCCAAAATTA
1 AAACTTTTCCAAAATTA
17473884 TGTTTTGACC
Statistics
Matches: 159, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
58 6 0.04
59 115 0.72
60 38 0.24
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (60 bp):
AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCCT
Found at i:17473880 original size:89 final size:87
Alignment explanation
Indices: 17473630--17473883 Score: 301
Period size: 89 Copynumber: 2.9 Consensus size: 87
17473620 TTTTGGCCTC
*
17473630 AAACTTTTCAAAAATTACATTTTAACCCATAAACTTTTCCAAAATCACATTTTGACCCTAAACTT
1 AAACTTTTCAAAAATTACATTTTAACCCCT-AACTTTTCCAAAATCACATTTTGACCCTAAACTT
* **
17473695 TCCCAAAATCACATTTCAACCTTT
65 T-CCAAAATTACATTTCAACCCCT
* *
17473719 AAACTTTTCAAAAATTACATTTTAACCCCAAAACTTTCCCAAAATCACATTTTGACCCTAAAACT
1 AAACTTTTCAAAAATTACATTTTAACCCC-TAACTTTTCCAAAATCACATTTTGACCCT-AAACT
* * *
17473784 TTTCAAAATTTCATTTTAACCCCT
64 TTCCAAAATTACATTTCAACCCCT
* * * ** * * *
17473808 AAACTTTTCTAAAATTGCATTTTAACCCCTAATTTTTTTAAAATCATATTTTAACCTCTGAACTC
1 AAACTTTTCAAAAATTACATTTTAACCCCTAACTTTTCCAAAATCACATTTTGACC-CTAAACT-
17473873 TTCCAAAATTA
64 TTCCAAAATTA
17473884 TGTTTTGACC
Statistics
Matches: 140, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
88 24 0.17
89 109 0.78
90 7 0.05
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (87 bp):
AAACTTTTCAAAAATTACATTTTAACCCCTAACTTTTCCAAAATCACATTTTGACCCTAAACTTT
CCAAAATTACATTTCAACCCCT
Found at i:17479060 original size:6 final size:6
Alignment explanation
Indices: 17479049--17479100 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
17479039 CATGTTATCT
17479049 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC
17479097 TCCC
1 TCCC
17479101 ACTTCTTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCCTC
Found at i:17485899 original size:17 final size:17
Alignment explanation
Indices: 17485877--17485909 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17485867 TTACACCACC
*
17485877 AACAGAAGTCTTTGCAA
1 AACAGAAGCCTTTGCAA
17485894 AACAGAAGCCTTTGCA
1 AACAGAAGCCTTTGCA
17485910 TTGTCCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (17 bp):
AACAGAAGCCTTTGCAA
Found at i:17490447 original size:19 final size:18
Alignment explanation
Indices: 17490420--17490467 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
17490410 ATATAATACC
* *
17490420 GAAATAAAATCAAAACAAT
1 GAAAAAAAAT-AAAAAAAT
17490439 GAAAAAAAAGTAAAAAAAT
1 GAAAAAAAA-TAAAAAAAT
17490458 -AAAAAAAATA
1 GAAAAAAAATA
17490468 GCAGTAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
19 15 0.58
20 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (18 bp):
GAAAAAAAATAAAAAAAT
Found at i:17502846 original size:5 final size:5
Alignment explanation
Indices: 17502835--17502866 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17502825 TTGTAGCTAA
17502835 GTTTT -TTTT -TTTT GTTTT GTTTT GTTTT GTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTT
17502867 AGGTTAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
GTTTT
Found at i:17504709 original size:27 final size:24
Alignment explanation
Indices: 17504676--17504745 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 24
17504666 ACCCAAACTC
17504676 ATTTATTGAAATTTTTAATTTTTA
1 ATTTATTGAAATTTTTAATTTTTA
* *
17504700 ATTTAATATTTAATATTTTTATAATTTTTT
1 A-TT--TATTGAA-A-TTTT-TAATTTTTA
17504730 ATTTATTGAAATTTTT
1 ATTTATTGAAATTTTT
17504746 TATATAGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
24 2 0.05
25 6 0.16
26 1 0.03
27 12 0.32
28 1 0.03
29 6 0.16
30 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (24 bp):
ATTTATTGAAATTTTTAATTTTTA
Found at i:17504746 original size:27 final size:27
Alignment explanation
Indices: 17504676--17504749 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 27
17504666 ACCCAAACTC
17504676 ATTTATTGAAA--TTTT-TAATTTTTA
1 ATTTATTGAAATTTTTTATAATTTTTA
** *
17504700 ATTTAATATTTAATATTTTTATAATTTTTT
1 ATTT-AT-TGAAAT-TTTTTATAATTTTTA
17504730 ATTTATTGAAATTTTTTATA
1 ATTTATTGAAATTTTTTATA
17504750 TAGTCATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 4 0.10
25 2 0.05
26 3 0.08
27 8 0.21
28 4 0.10
29 6 0.15
30 12 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
ATTTATTGAAATTTTTTATAATTTTTA
Found at i:17504978 original size:98 final size:98
Alignment explanation
Indices: 17504866--17505047 Score: 258
Period size: 98 Copynumber: 1.9 Consensus size: 98
17504856 TGGTGTCAAC
* * * *
17504866 CATTGGGTGCCAAACACCCAAAAAATTATTTTTTTTATTCGTAGTTTTTTGG-TGTCAATCATTA
1 CATTGGATGACAAACACCCAAAAAATTA-GTTTTTTATTCATAGTTTTTTGGATGTCAATCATTA
* *
17504930 TTTGTCAAACACCCAAAAAAAAGATGATGTAGGT
65 CTTGCCAAACACCCAAAAAAAAGATGATGTAGGT
* * * *
17504964 CATTGGATGACAAACACCTAAAAATTTAGTTTTTTATTCATATTTTTTTGGATGTCAGTCATTAC
1 CATTGGATGACAAACACCCAAAAAATTAGTTTTTTATTCATAGTTTTTTGGATGTCAATCATTAC
17505029 TTGCCAAACACCCAAAAAA
66 TTGCCAAACACCCAAAAAA
17505048 TTATTTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 20 0.27
98 53 0.73
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (98 bp):
CATTGGATGACAAACACCCAAAAAATTAGTTTTTTATTCATAGTTTTTTGGATGTCAATCATTAC
TTGCCAAACACCCAAAAAAAAGATGATGTAGGT
Found at i:17509877 original size:28 final size:24
Alignment explanation
Indices: 17509844--17509909 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 24
17509834 TTTTTTATAT
17509844 ATTATTTAAAAATAAGAAATATAATTAA
1 ATTATTTAAAAAT-AGAAAT-T--TTAA
*
17509872 ATTATTTAATAAATATAAATTTTAA
1 ATTATTTAA-AAATAGAAATTTTAA
*
17509897 ATTATTAAAAAAT
1 ATTATTTAAAAAT
17509910 TTATTCTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.11
25 12 0.34
27 1 0.03
28 14 0.40
29 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTATTTAAAAATAGAAATTTTAA
Found at i:17510375 original size:19 final size:20
Alignment explanation
Indices: 17510339--17510377 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17510329 AAGTATGAGA
17510339 TTTAAGATTTAGGATTCAAG
1 TTTAAGATTTAGGATTCAAG
17510359 TTTAAG-TTTAAGG-TTCAAG
1 TTTAAGATTT-AGGATTCAAG
17510378 GGTTCGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (20 bp):
TTTAAGATTTAGGATTCAAG
Found at i:17511461 original size:17 final size:16
Alignment explanation
Indices: 17511439--17511484 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
17511429 GGTTGAATCA
17511439 TCAAACTTCAAAATGAT
1 TCAAACTT-AAAATGAT
*
17511456 TCAAACTTGAAATGAT
1 TCAAACTTAAAATGAT
*
17511472 ACAAACTTTAAAA
1 TCAAAC-TTAAAA
17511485 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (16 bp):
TCAAACTTAAAATGAT
Found at i:17511470 original size:16 final size:17
Alignment explanation
Indices: 17511439--17511484 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
17511429 GGTTGAATCA
17511439 TCAAACTTCAAAATGAT
1 TCAAACTTCAAAATGAT
*
17511456 TCAAACTT-GAAATGAT
1 TCAAACTTCAAAATGAT
* *
17511472 ACAAACTTTAAAA
1 TCAAACTTCAAAA
17511485 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (17 bp):
TCAAACTTCAAAATGAT
Found at i:17512623 original size:26 final size:27
Alignment explanation
Indices: 17512593--17512661 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
17512583 TCAAAATTCG
17512593 AATACATATAAATGTA-TTTTTAAAAA
1 AATACATATAAATGTATTTTTTAAAAA
**
17512619 AATACATATAAATGTATTTTTTTTAAA
1 AATACATATAAATGTATTTTTTAAAAA
17512646 AATACATATAAATGTA
1 AATACATATAAATGTA
17512662 GTACATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 16 0.40
27 24 0.60
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
AATACATATAAATGTATTTTTTAAAAA
Found at i:17513511 original size:3 final size:3
Alignment explanation
Indices: 17513505--17513529 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17513495 GTCGTCGTGG
17513505 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
17513530 TATGGTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:17515538 original size:23 final size:23
Alignment explanation
Indices: 17515507--17515550 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17515497 AAAATTTAAC
*
17515507 AAATAAAAATAAAAATATTAAAA
1 AAATAAAAATAAAAAGATTAAAA
*
17515530 AAATTAAAATAAAAAGATTAA
1 AAATAAAAATAAAAAGATTAA
17515551 TTTCTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (23 bp):
AAATAAAAATAAAAAGATTAAAA
Found at i:17515888 original size:20 final size:20
Alignment explanation
Indices: 17515829--17515877 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
17515819 AGCCCTAGTC
17515829 CTTTTAAAATAGAAAATTTT
1 CTTTTAAAATAGAAAATTTT
17515849 CTTTTAAAATAGAAAATTTT
1 CTTTTAAAATAGAAAATTTT
17515869 C-TTTAAAAT
1 CTTTTAAAAT
17515878 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
CTTTTAAAATAGAAAATTTT
Found at i:17522077 original size:27 final size:27
Alignment explanation
Indices: 17522039--17522093 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17522029 AAAAATCTAA
17522039 TTATTTAGTGCGTTTTCGGACACTACC
1 TTATTTAGTGCGTTTTCGGACACTACC
17522066 TTATTTAGTGCGTTTTCGGACACTACC
1 TTATTTAGTGCGTTTTCGGACACTACC
17522093 T
1 T
17522094 AAATCTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (27 bp):
TTATTTAGTGCGTTTTCGGACACTACC
Found at i:17530502 original size:21 final size:20
Alignment explanation
Indices: 17530478--17530517 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17530468 AGAGAGAAAG
* *
17530478 AAAGTGAAAGAAAAGGAAAAT
1 AAAGGGAAA-AAAAAGAAAAT
17530499 AAAGGGAAAAAAAAGAAAA
1 AAAGGGAAAAAAAAGAAAA
17530518 GGGAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (20 bp):
AAAGGGAAAAAAAAGAAAAT
Found at i:17546102 original size:61 final size:61
Alignment explanation
Indices: 17545985--17546105 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
17545975 TAAATGCTCT
* * *
17545985 ATTTATATTAGATATTATAATTATTTAACTTTATTTTTTATCAAATTTAAATTTAGATACC
1 ATTTATATTAGATATTATAATTATTAAACTTTATTTCTTACCAAATTTAAATTTAGATACC
* *
17546046 ATTTATACTTAGATATTGTAATTATTAAATTTTA-TTCTTACCAAA-TTAATATTTAGATAC
1 ATTTATA-TTAGATATTATAATTATTAAACTTTATTTCTTACCAAATTTAA-ATTTAGATAC
17546106 GACTTTGTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 4 0.08
61 26 0.49
62 23 0.43
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.50
Consensus pattern (61 bp):
ATTTATATTAGATATTATAATTATTAAACTTTATTTCTTACCAAATTTAAATTTAGATACC
Found at i:17548331 original size:22 final size:22
Alignment explanation
Indices: 17548301--17548365 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
17548291 AGATGAAATC
*
17548301 TTTATTTTTTAATTTAATTTAA-
1 TTTAATTTTT-ATTTAATTTAAT
*
17548323 TTTAATTTTTACTTAATGTTAAT
1 TTTAATTTTTATTTAAT-TTAAT
17548346 TTTAAATTTTTTATTTAATT
1 TTT-AA-TTTTTATTTAATT
17548366 AAAAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.17
22 13 0.36
23 3 0.08
24 3 0.08
25 11 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTAATTTTTATTTAATTTAAT
Found at i:17548333 original size:17 final size:18
Alignment explanation
Indices: 17548313--17548354 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
17548303 TATTTTTTAA
17548313 TTTAATTTAAT-TTAATT
1 TTTAATTTAATGTTAATT
*
17548330 TTT-ACTTAATGTTAATT
1 TTTAATTTAATGTTAATT
*
17548347 TTAAATTT
1 TTTAATTT
17548355 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATTTAATGTTAATT
Found at i:17548367 original size:23 final size:22
Alignment explanation
Indices: 17548304--17548365 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
17548294 TGAAATCTTT
17548304 ATTTTTTAATTTAATTTAATTTA
1 ATTTTTT-ATTTAATTTAATTTA
*
17548327 A-TTTTTACTTAATGTTAATTTTAA
1 ATTTTTTATTTAAT-TTAA-TTT-A
17548351 ATTTTTTATTTAATT
1 ATTTTTTATTTAATT
17548366 AAAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 6 0.18
22 9 0.27
23 4 0.12
24 3 0.09
25 11 0.33
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTTTATTTAATTTAATTTA
Found at i:17548467 original size:23 final size:23
Alignment explanation
Indices: 17548428--17548472 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17548418 AGTTGATACA
*
17548428 TAAAATGATAACATAATAAAATT
1 TAAAATAATAACATAATAAAATT
*
17548451 TAAAATAATTAAC-TAATTAAAT
1 TAAAATAA-TAACATAATAAAAT
17548473 AACTAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAATAATAACATAATAAAATT
Found at i:17559250 original size:19 final size:18
Alignment explanation
Indices: 17559202--17559252 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
17559192 ATTTTATATA
17559202 ATTTTATTTT-TATATTTT
1 ATTTTATTTTATATA-TTT
*
17559220 TTTTTAATTTTTATATATTT
1 ATTTT-A-TTTTATATATTT
17559240 ATTTCTATTTTAT
1 ATTT-TATTTTAT
17559253 GATTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 11 0.41
21 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTATTTTATATATTT
Found at i:17560304 original size:14 final size:14
Alignment explanation
Indices: 17560287--17560321 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
17560277 TACAATATCC
17560287 AAATAATAATAATA
1 AAATAATAATAATA
*
17560301 AAATAATAGTAATA
1 AAATAATAATAATA
*
17560315 TAATAAT
1 AAATAAT
17560322 GAAACGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:17568364 original size:17 final size:17
Alignment explanation
Indices: 17568342--17568378 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17568332 CGTATAATAT
17568342 AATAAACATATT-TAAAA
1 AATAAACAT-TTATAAAA
17568359 AATAAACATTTATAAAA
1 AATAAACATTTATAAAA
17568376 AAT
1 AAT
17568379 TAATTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAACATTTATAAAA
Found at i:17575566 original size:6 final size:6
Alignment explanation
Indices: 17575555--17575583 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17575545 AAAGCAAGGC
17575555 TATGAT TATGAT TATGAT TATGAT TATGA
1 TATGAT TATGAT TATGAT TATGAT TATGA
17575584 ACTCCATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
TATGAT
Found at i:17577397 original size:16 final size:16
Alignment explanation
Indices: 17577372--17577410 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
17577362 TATTATTAAA
17577372 TAATTAATTATATTAT
1 TAATTAATTATATTAT
*
17577388 TAATTTATTATATTAT
1 TAATTAATTATATTAT
17577404 TAATTAA
1 TAATTAA
17577411 ACTATTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTAATTATATTAT
Found at i:17577409 original size:20 final size:19
Alignment explanation
Indices: 17577358--17577410 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
17577348 TTTAATACTA
*
17577358 AATATATTATTAAATAATT
1 AATATATTATTAATTAATT
17577377 AAT-TA-TATT-ATTAATTT
1 AATATATTATTAATTAA-TT
*
17577394 ATTATATTATTAATTAA
1 AATATATTATTAATTAA
17577411 ACTATTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 8 0.29
18 4 0.14
19 7 0.25
20 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATATTATTAATTAATT
Found at i:17577416 original size:20 final size:18
Alignment explanation
Indices: 17577360--17577410 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 18
17577350 TAATACTAAA
*
17577360 TATATTATTAAATAATTAAT
1 TATATTATTAATTAA-T-AT
17577380 TATATTATTAATT--TAT
1 TATATTATTAATTAATAT
17577396 TATATTATTAATTAA
1 TATATTATTAATTAA
17577411 ACTATTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 15 0.54
17 1 0.04
20 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTATTAATTAATAT
Found at i:17580241 original size:2 final size:2
Alignment explanation
Indices: 17580236--17580279 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17580226 GAGTGTGTGT
17580236 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17580278 GA
1 GA
17580280 AACATAGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17582799 original size:13 final size:13
Alignment explanation
Indices: 17582772--17582810 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
17582762 AAATAATGTT
*
17582772 AAAATAACTATATA
1 AAAATAA-TAAATA
17582786 AAAATAATAAATA
1 AAAATAATAAATA
17582799 AAAATATATAAA
1 AAAATA-ATAAA
17582811 ATTATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAATAATAAATA
Found at i:17583165 original size:20 final size:19
Alignment explanation
Indices: 17583137--17583175 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17583127 TTCTTATATT
* *
17583137 TTTCGAAAATTTTTATTAAA
1 TTTCCAAAATCTTT-TTAAA
17583157 TTTCCAAAATCTTTTTAAA
1 TTTCCAAAATCTTTTTAAA
17583176 AAATTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTCCAAAATCTTTTTAAA
Found at i:17583787 original size:21 final size:19
Alignment explanation
Indices: 17583729--17583787 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 19
17583719 TACTTGTAAT
*
17583729 TTATA-TATATTTTTAT-A
1 TTATATTATATATTTATAA
*
17583746 TTATATTGATAT-TTTAAAA
1 TTATATT-ATATATTTATAA
17583765 TTCATAATTATATATTTATAA
1 TT-AT-ATTATATATTTATAA
17583786 TT
1 TT
17583788 TTATAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 7 0.21
20 6 0.18
21 11 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATATTATATATTTATAA
Found at i:17584918 original size:33 final size:33
Alignment explanation
Indices: 17584850--17584935 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
17584840 AAATGATAAC
* * * * *
17584850 AACAAAATAGTAACAATATAATAGTGAAATTGT
1 AACAAAATAGTAAAAAAACAACAGTGAAATAGT
17584883 AACAAAATAGTAAAAAAACAACA-TGAAAATAGT
1 AACAAAATAGTAAAAAAACAACAGTG-AAATAGT
* *
17584916 AACAAAACAATAAAAAAACA
1 AACAAAATAGTAAAAAAACA
17584936 GCAATTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 2 0.04
33 43 0.96
ACGTcount: A:0.65, C:0.09, G:0.08, T:0.17
Consensus pattern (33 bp):
AACAAAATAGTAAAAAAACAACAGTGAAATAGT
Found at i:17584933 original size:22 final size:22
Alignment explanation
Indices: 17584886--17584933 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
17584876 AAATTGTAAC
**
17584886 AAAATAGTAAAAAAACAACATG
1 AAAATAGTAAAAAAACAACAAA
* *
17584908 AAAATAGTAACAAAACAATAAA
1 AAAATAGTAAAAAAACAACAAA
17584930 AAAA
1 AAAA
17584934 CAGCAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAATAGTAAAAAAACAACAAA
Found at i:17586791 original size:14 final size:14
Alignment explanation
Indices: 17586772--17586800 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17586762 CCGATGACCG
17586772 AAGCTTGGCCAGGC
1 AAGCTTGGCCAGGC
17586786 AAGCTTGGCCAGGC
1 AAGCTTGGCCAGGC
17586800 A
1 A
17586801 TGAGGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (14 bp):
AAGCTTGGCCAGGC
Found at i:17587445 original size:29 final size:29
Alignment explanation
Indices: 17587381--17587603 Score: 200
Period size: 29 Copynumber: 7.7 Consensus size: 29
17587371 TGTTTTATTT
* * * *
17587381 AAAAATTACAATTTTGACCCCAAACTTTTCC
1 AAAAATTACCATTTTGCCCCCGAAC--ATCC
17587412 -AAAATTACCATTTTGCCCCCGAACATCC
1 AAAAATTACCATTTTGCCCCCGAACATCC
***
17587440 AAAAATTACCATTTTGCCTTTGAACATCC
1 AAAAATTACCATTTTGCCCCCGAACATCC
* * *
17587469 AAAAATTACCATTTTGCTCTCGAATATCC
1 AAAAATTACCATTTTGCCCCCGAACATCC
* * * ** *
17587498 AACAATTACCATTTTGACTCTAAACTTTTCC
1 AAAAATTACCATTTTGCCCCCGAAC--ATCC
* *
17587529 -AAAATTACCATTTTTCCCCCAAACATCC
1 AAAAATTACCATTTTGCCCCCGAACATCC
**
17587557 AAAAATTACCATTTTG-CCCCGAGTATCC
1 AAAAATTACCATTTTGCCCCCGAACATCC
*
17587585 AAAAATCACCATTTTGCCC
1 AAAAATTACCATTTTGCCC
17587604 TCAAATTTCC
Statistics
Matches: 156, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
28 30 0.19
29 83 0.53
30 40 0.26
31 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATTACCATTTTGCCCCCGAACATCC
Found at i:17587484 original size:58 final size:58
Alignment explanation
Indices: 17587412--17587603 Score: 226
Period size: 58 Copynumber: 3.3 Consensus size: 58
17587402 AAACTTTTCC
*
17587412 AAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTGCCTTTGAACATCCA
1 AAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTGCCTCTGAACATCCA
* * * * * * *
17587470 AAAATTACCATTTTGCTCTCGAATATCCAACAATTACCATTTTGACTCTAAACTTTTCC-
1 AAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTGCCTCTGAAC--ATCCA
* * * **
17587529 AAAATTACCATTTTTCCCCCAAACATCCAAAAATTACCATTTTGCC-CCGAGTATCCA
1 AAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTGCCTCTGAACATCCA
*
17587586 AAAATCACCATTTTGCCC
1 AAAATTACCATTTTGCCC
17587604 TCAAATTTCC
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
56 3 0.03
57 16 0.15
58 48 0.44
59 39 0.36
60 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTGCCTCTGAACATCCA
Found at i:17587533 original size:88 final size:87
Alignment explanation
Indices: 17587441--17587600 Score: 230
Period size: 88 Copynumber: 1.8 Consensus size: 87
17587431 CGAACATCCA
**** * * *
17587441 AAAATTACCATTTTGCCTTTGAACATCCAAAAATTACCATTTTGCTCTCGAATATCCAACAATTA
1 AAAATTACCATTTTGCCCCCAAACATCCAAAAATTACCATTTTGC-CCCGAATATCCAAAAATCA
17587506 CCATTTTGACTCTAAACTTTTCC
65 CCATTTTGACTCTAAACTTTTCC
* *
17587529 AAAATTACCATTTTTCCCCCAAACATCCAAAAATTACCATTTTGCCCCGAGTATCCAAAAATCAC
1 AAAATTACCATTTTGCCCCCAAACATCCAAAAATTACCATTTTGCCCCGAATATCCAAAAATCAC
17587594 CATTTTG
66 CATTTTG
17587601 CCCTCAAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
87 23 0.37
88 40 0.63
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (87 bp):
AAAATTACCATTTTGCCCCCAAACATCCAAAAATTACCATTTTGCCCCGAATATCCAAAAATCAC
CATTTTGACTCTAAACTTTTCC
Found at i:17587628 original size:29 final size:30
Alignment explanation
Indices: 17587582--17587649 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
17587572 GCCCCGAGTA
* *
17587582 TCCAAAAATCACCATTTTGCCCTCAAA-TT
1 TCCAAAAGTCACCATTTTGACCTCAAATTT
17587611 TCCAAAAGTCA-CATTTTTGACCTCAAATTT
1 TCCAAAAGTCACCA-TTTTGACCTCAAATTT
17587641 TCCAAAAGT
1 TCCAAAAGT
17587650 TCGATTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 22 0.63
30 11 0.31
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (30 bp):
TCCAAAAGTCACCATTTTGACCTCAAATTT
Found at i:17596497 original size:16 final size:16
Alignment explanation
Indices: 17596451--17596497 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
17596441 AAAAAATATT
17596451 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
17596468 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
17596484 TATATTTTTTATTT
1 TATATTTTTTATTT
17596498 ATTGTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:17609825 original size:3 final size:3
Alignment explanation
Indices: 17609817--17609850 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
17609807 AATCCCAATA
17609817 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
17609851 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:17610472 original size:22 final size:20
Alignment explanation
Indices: 17610422--17610472 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
17610412 CAAAAAAAAT
*
17610422 AAAAAAACAATAAGAAAATA
1 AAAAAAACAATAAGAAAACA
17610442 AGAACAAAACAATAAGAAGCAACA
1 A-AA-AAAACAATAAGAA--AACA
17610466 AAAAAAA
1 AAAAAAA
17610473 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 2 0.08
22 17 0.65
23 2 0.08
24 4 0.15
ACGTcount: A:0.76, C:0.10, G:0.08, T:0.06
Consensus pattern (20 bp):
AAAAAAACAATAAGAAAACA
Found at i:17612357 original size:2 final size:2
Alignment explanation
Indices: 17612352--17612377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17612342 CATTTTTAAA
17612352 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17612378 TATTAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17619421 original size:12 final size:13
Alignment explanation
Indices: 17619383--17619423 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17619373 ATTAATTTGT
17619383 AAAATCTATAATTA
1 AAAATCT-TAATTA
*
17619397 AAAATCTTTATTA
1 AAAATCTTAATTA
17619410 AAAATC-TAATTA
1 AAAATCTTAATTA
17619422 AA
1 AA
17619424 CTCTGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATCTTAATTA
Found at i:17625522 original size:17 final size:16
Alignment explanation
Indices: 17625500--17625532 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
17625490 TCATTGAGCT
17625500 AAAGAAAGGAAGAAAGA
1 AAAGAAAGG-AGAAAGA
17625517 AAAGAAAGGAGAAAGA
1 AAAGAAAGGAGAAAGA
17625533 GGAAAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAGAAAGGAGAAAGA
Found at i:17629945 original size:35 final size:34
Alignment explanation
Indices: 17629893--17629968 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
17629883 GAAACTTTTA
*** * *
17629893 TTTTAATTTTTAGTGTATTTGATATATTATATTT
1 TTTTAATTTTTAGTGTATAAAATATAATATATAT
**
17629927 TTTTAATTTGTTTTTGTATAAAATATAATATATAT
1 TTTTAATTT-TTAGTGTATAAAATATAATATATAT
17629962 TTTTAAT
1 TTTTAAT
17629969 ACGAACGGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (34 bp):
TTTTAATTTTTAGTGTATAAAATATAATATATAT
Found at i:17631582 original size:18 final size:17
Alignment explanation
Indices: 17631559--17631592 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17631549 AATTGTTTTT
*
17631559 CATGCATGCACATTCATA
1 CATGCATACAC-TTCATA
17631577 CATGCATACACTTCAT
1 CATGCATACACTTCAT
17631593 GCATTACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (17 bp):
CATGCATACACTTCATA
Found at i:17637499 original size:3 final size:3
Alignment explanation
Indices: 17637491--17637548 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
17637481 TTGGGCTTCA
* * * * * * *
17637491 CTT CTT CTT CTT CTT CCT CTT CAT CTT CTT CTC CTT CAT CAT CAT CAT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
17637539 CTT CTT CTT C
1 CTT CTT CTT C
17637549 ATCTCCCTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.09, C:0.38, G:0.00, T:0.53
Consensus pattern (3 bp):
CTT
Found at i:17637517 original size:15 final size:15
Alignment explanation
Indices: 17637493--17637568 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 15
17637483 GGGCTTCACT
*
17637493 TCTTCTTCTTCTTCC
1 TCTTCATCTTCTTCC
17637508 TCTTCATCTTCTT-C
1 TCTTCATCTTCTTCC
* * *
17637522 TCCTTCATCATCATCA
1 T-CTTCATCTTCTTCC
*
17637538 TCTTCTTCTTCATCTCCC
1 TCTTCATCTTC-T-T-CC
17637556 TCTTCATCATTCT
1 TCTTCATC-TTCT
17637569 CGCTTCCTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
14 2 0.04
15 30 0.65
16 1 0.02
17 1 0.02
18 9 0.20
19 3 0.07
ACGTcount: A:0.11, C:0.38, G:0.00, T:0.51
Consensus pattern (15 bp):
TCTTCATCTTCTTCC
Found at i:17637519 original size:21 final size:21
Alignment explanation
Indices: 17637493--17637551 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
17637483 GGGCTTCACT
* *
17637493 TCTTCTTCTTCTTCCTCTTCA
1 TCTTCTTCTTCTTCATCATCA
*
17637514 TCTTCTTCTCCTTCATCATCA
1 TCTTCTTCTTCTTCATCATCA
*
17637535 TCATCTTCTTCTTCATC
1 TCTTCTTCTTCTTCATC
17637552 TCCCTCTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTTCTTCTTCTTCATCATCA
Found at i:17648043 original size:17 final size:16
Alignment explanation
Indices: 17648023--17648070 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
17648013 CTTTTTCAAT
17648023 AATTAAAAAATATATAA
1 AATTAAAAAATAT-TAA
**
17648040 AATTATTAAATATTAA
1 AATTAAAAAATATTAA
*
17648056 AATAAAATAAATATT
1 AATTAAA-AAATATT
17648071 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAAAAAATATTAA
Found at i:17654699 original size:6 final size:6
Alignment explanation
Indices: 17654681--17654710 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17654671 TCCTCCATTT
17654681 CTCTCC C-CTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
17654711 AACAATTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (6 bp):
CTCTCC
Found at i:17655931 original size:32 final size:31
Alignment explanation
Indices: 17655895--17655982 Score: 76
Period size: 32 Copynumber: 2.8 Consensus size: 31
17655885 GAATTAATTT
*
17655895 ATATTTTATGATCATTATATTAAACTATTTAA
1 ATATTTTATGATCATTATATTAAAAT-TTTAA
17655927 ATATTATT-T-A-CTATTATACTTAAAATTTTAA
1 ATATT-TTATGATC-ATTATA-TTAAAATTTTAA
*
17655958 A-ATATTTATGCATAATTATATTAAA
1 ATAT-TTTATG-ATCATTATATTAAA
17655983 TTAATTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
30 5 0.11
31 15 0.33
32 17 0.37
33 9 0.20
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (31 bp):
ATATTTTATGATCATTATATTAAAATTTTAA
Found at i:17665358 original size:16 final size:16
Alignment explanation
Indices: 17665299--17665360 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 16
17665289 ATAATTTCAG
17665299 TAATTCAAATTTA-AA
1 TAATTCAAATTTATAA
*
17665314 TAACTCATAATTTAAATCAA
1 TAATTCA-AATTT--AT-AA
17665334 TATATTCAAATTTATAA
1 TA-ATTCAAATTTATAA
17665351 TAATTCAAAT
1 TAATTCAAAT
17665361 CAACGTAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.15
16 13 0.33
17 4 0.10
18 3 0.08
20 9 0.23
21 4 0.10
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTCAAATTTATAA
Found at i:17667255 original size:4 final size:4
Alignment explanation
Indices: 17667248--17667278 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
17667238 ATTTTTACGC
*
17667248 ACAT ACAT ACAT ACAA ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
17667279 GAATGCTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (4 bp):
ACAT
Found at i:17667269 original size:16 final size:16
Alignment explanation
Indices: 17667248--17667278 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17667238 ATTTTTACGC
17667248 ACATACATACATACAA
1 ACATACATACATACAA
17667264 ACATACATACATACA
1 ACATACATACATACA
17667279 GAATGCTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (16 bp):
ACATACATACATACAA
Found at i:17673817 original size:3 final size:3
Alignment explanation
Indices: 17673809--17673834 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17673799 ACTGGACCAC
17673809 CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CC
17673835 AATGATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:17676110 original size:101 final size:101
Alignment explanation
Indices: 17675899--17676098 Score: 240
Period size: 101 Copynumber: 2.0 Consensus size: 101
17675889 TTTTTTAATT
* * * * *
17675899 TAGAAAAATAAGTCGTTTTTGAAGAGTGTGTGAAAGTACGTTCAGTTGCGCACTCTTTCTGCATA
1 TAGAGAAATAAGTCGTTTTTAAAGAGTGTGTGAAAGCACGTCCAGTTGCGCACTCTTTCTGCACA
* ** *
17675964 GCTAGTGTAAAAGCATGCTCATTTTTTTTTTAAAAA
66 GCTAATGTAAAAGCACACTCATTTTTTTTCTAAAAA
* * * *
17676000 TAGAGAAATAGGTCGTTTTTAAAGTGTGTGTGAAAGCACGTCCAGTTGGGCGCGT-TTTCTGCAC
1 TAGAGAAATAAGTCGTTTTTAAAGAGTGTGTGAAAGCACGTCCAGTTGCGCAC-TCTTTCTGCAC
* * *
17676064 AGTTAATGTAAAAGTACACTTATTTTTTTTCTAAA
65 AGCTAATGTAAAAGCACACTCATTTTTTTTCTAAA
17676099 TTTAAGGAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 81 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.36
Consensus pattern (101 bp):
TAGAGAAATAAGTCGTTTTTAAAGAGTGTGTGAAAGCACGTCCAGTTGCGCACTCTTTCTGCACA
GCTAATGTAAAAGCACACTCATTTTTTTTCTAAAAA
Found at i:17681082 original size:20 final size:20
Alignment explanation
Indices: 17681054--17681094 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17681044 AATGACATTA
* *
17681054 TTAATATAATAAATATTTTT
1 TTAAAATAACAAATATTTTT
17681074 TTAAAATAACAAATATTTTT
1 TTAAAATAACAAATATTTTT
17681094 T
1 T
17681095 CAATCACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAAATAACAAATATTTTT
Found at i:17682260 original size:6 final size:6
Alignment explanation
Indices: 17682251--17682285 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
17682241 AAAGAGGGGT
17682251 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
17682286 AAGTCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:17684550 original size:18 final size:17
Alignment explanation
Indices: 17684527--17684564 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
17684517 CTTTACTTTT
*
17684527 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACAC-GA
17684545 ATTTTATTTTAACACGA
1 ATTTTATTTTAACACGA
17684562 ATT
1 ATT
17684565 CTAGTCACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTTATTTTAACACGA
Found at i:17684577 original size:17 final size:17
Alignment explanation
Indices: 17684557--17684590 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17684547 TTTATTTTAA
17684557 CACGAATTCTAGTCACC
1 CACGAATTCTAGTCACC
17684574 CACGAATTCTAGTCACC
1 CACGAATTCTAGTCACC
17684591 TAATTCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (17 bp):
CACGAATTCTAGTCACC
Found at i:17688482 original size:16 final size:15
Alignment explanation
Indices: 17688443--17688491 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
17688433 TTAATTTGAC
*
17688443 TTATTTTTATGTTTA
1 TTATTTTTATATTTA
*
17688458 TAATATTTTATATTATA
1 TTAT-TTTTATATT-TA
17688475 TTATTTTTATATATTA
1 TTATTTTTATAT-TTA
17688491 T
1 T
17688492 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.11
16 19 0.68
17 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTTATATTTA
Found at i:17693394 original size:2 final size:2
Alignment explanation
Indices: 17693382--17693412 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17693372 ATAGAATTAA
*
17693382 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17693413 GTCAAGGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17694799 original size:80 final size:80
Alignment explanation
Indices: 17694572--17694805 Score: 278
Period size: 81 Copynumber: 2.9 Consensus size: 80
17694562 TACAATGGTT
* * * * * *
17694572 GTTGGTTAAACCAACCAGAGCTGAGCTCACTTTCGCAGTTTAACCGCTAAGCACTGGGTGCCAGG
1 GTTGGTTAATCCAACTAGAGCTGAGCTCACTTTTGCAGTTTATCCGCTAGGCACTGGGTGCCATG
* *
17694637 ATTTGACGGATTATTC
66 AATTGAC-GATAATTC
* * *
17694653 GTTGGTTAATCCAATTAGAGCTGAGCTCACTTCTGCTA-TTTATCTGCTAGGCACTGGGTGCCAT
1 GTTGGTTAATCCAACTAGAGCTGAGCTCACTTTTGC-AGTTTATCCGCTAGGCACTGGGTGCCAT
17694717 GAATTGACGA-AATTC
65 GAATTGACGATAATTC
* *
17694732 GTTGGTTAATCCAACTAAAGCT-AGGCTCACTTATTGCGGTTTATCCGCTAGGCA-TCGGGTGCC
1 GTTGGTTAATCCAACTAGAGCTGA-GCTCACTT-TTGCAGTTTATCCGCTAGGCACT-GGGTGCC
17694795 ATGAATTGACG
63 ATGAATTGACG
17694806 GATTTGGTTG
Statistics
Matches: 132, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 33 0.25
80 37 0.28
81 60 0.45
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAGCTGAGCTCACTTTTGCAGTTTATCCGCTAGGCACTGGGTGCCATG
AATTGACGATAATTC
Found at i:17700969 original size:29 final size:29
Alignment explanation
Indices: 17700877--17700985 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 29
17700867 TTTGGACATC
*
17700877 CGGGGGTAAAATGGTAATTTTTGAAAGTTT
1 CGGGGTTAAAAT-GTAATTTTTGAAAGTTT
* * *
17700907 CGAGGTTAAAAT-TGAATTTTAGGAAGTTT
1 CGGGGTTAAAATGT-AATTTTTGAAAGTTT
17700936 CGGGGTTAAAATGTAATTTTTGAAAGTTT
1 CGGGGTTAAAATGTAATTTTTGAAAGTTT
* * *
17700965 AGGGGTAAAAATGTCATTTTT
1 CGGGGTTAAAATGTAATTTTT
17700986 ACCCTCGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 55 0.82
30 11 0.16
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.39
Consensus pattern (29 bp):
CGGGGTTAAAATGTAATTTTTGAAAGTTT
Found at i:17701014 original size:28 final size:29
Alignment explanation
Indices: 17700982--17701167 Score: 116
Period size: 29 Copynumber: 6.4 Consensus size: 29
17700972 AAAATGTCAT
17700982 TTTTACCCTCGAATTTCCAAAAATT-CCA
1 TTTTACCCTCGAATTTCCAAAAATTACCA
* *
17701010 TTTTAACCTCGAAACTT-CAAAAATTACCA
1 TTTTACCCTCG-AATTTCCAAAAATTACCA
* * ** *
17701039 TTTTACCCTCGGATGTCCAAAAGCT-CCGTT
1 TTTTACCCTCGAATTTCCAAAAATTACC--A
* * *
17701069 TTTTA-TCTCGATTTTCTAAAAATTACCA
1 TTTTACCCTCGAATTTCCAAAAATTACCA
* * *
17701097 TTTTACCCTCGGATATCC-AAAA-TATCA
1 TTTTACCCTCGAATTTCCAAAAATTACCA
* *
17701124 TTTTTAGCCC-CAAAATTTCCCAAAATTACCA
1 -TTTTA-CCCTC-GAATTTCCAAAAATTACCA
*
17701155 TTTTTGCCCTCGA
1 -TTTTACCCTCGA
17701168 GAGTCTAAAA
Statistics
Matches: 116, Mismatches: 29, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
27 4 0.03
28 37 0.32
29 50 0.43
30 15 0.13
31 10 0.09
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTTACCCTCGAATTTCCAAAAATTACCA
Found at i:17701041 original size:58 final size:57
Alignment explanation
Indices: 17700982--17701167 Score: 153
Period size: 58 Copynumber: 3.2 Consensus size: 57
17700972 AAAATGTCAT
* *
17700982 TTTTACCCTCGAATTTCCAAAAATTCCATTTTAACCTCGAAACTTCAAAAATTACCA
1 TTTTACCCTCGAATATCCAAAAATTCCATTTTAACCTCGAAATTTCAAAAATTACCA
* * ** * * * *
17701039 TTTTACCCTCGGATGTCCAAAAGCTCCGTTTTTTATCTCG-ATTTTCTAAAAATTACCA
1 TTTTACCCTCGAATATCCAAAAATTCC-ATTTTAACCTCGAAATTTC-AAAAATTACCA
* * * * *
17701097 TTTTACCCTCGGATATCC-AAAATAT-CATTTTTAGCCCCAAAATTTCCCAAAATTACCA
1 TTTTACCCTCGAATATCCAAAAAT-TCCA-TTTTAACCTCGAAATTT-CAAAAATTACCA
*
17701155 TTTTTGCCCTCGA
1 -TTTTACCCTCGA
17701168 GAGTCTAAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
57 37 0.37
58 52 0.52
59 11 0.11
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (57 bp):
TTTTACCCTCGAATATCCAAAAATTCCATTTTAACCTCGAAATTTCAAAAATTACCA
Found at i:17706158 original size:15 final size:15
Alignment explanation
Indices: 17706138--17706172 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17706128 ACGTGTTATC
17706138 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
17706153 AAAAAAAAGAGAAAG
1 AAAAAAAAGAAAAAG
17706168 AAAAA
1 AAAAA
17706173 TGGGTCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:17707101 original size:39 final size:38
Alignment explanation
Indices: 17707058--17707174 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 38
17707048 GATTCAGTGA
17707058 ATAAAAGAAAAGAAAAAAAGAAGAAGAAAAAAGAAAAAG
1 ATAAAAGAAAAGAAAAAAAGAAGAA-AAAAAAGAAAAAG
* *
17707097 ATAAAAGAAAAGAAAAGAAGAAGAAAAAAAAGATAAAG
1 ATAAAAGAAAAGAAAAAAAGAAGAAAAAAAAGAAAAAG
* *
17707135 ATAAAGATAAAAGAAAAGAAAAAAAGAAAGAAAAAGAAAA
1 ATAAA-AGAAAAG-AAA-AAAAGAAGAAA-AAAAAGAAAA
17707175 GGAGAGGTCG
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
38 17 0.25
39 30 0.44
40 3 0.04
41 9 0.13
42 9 0.13
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (38 bp):
ATAAAAGAAAAGAAAAAAAGAAGAAAAAAAAGAAAAAG
Found at i:17707110 original size:44 final size:44
Alignment explanation
Indices: 17707060--17707174 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 44
17707050 TTCAGTGAAT
*
17707060 AAAAGAAAAGAAAAAAAGAAGAAGAAAAAAGAAAAAGATAAAAG
1 AAAAGAAAAGAAAAAAAGAAAAAGAAAAAAGAAAAAGATAAAAG
* *
17707104 AAAAGAAAAGAAGAAGAAA-AAAAAG-ATAAAGATAAAGATAAAAG
1 AAAAGAAAAGAA-AA-AAAGAAAAAGAAAAAAGAAAAAGATAAAAG
*
17707148 AAAAGAAAA-AAAGAAAGAAAAAGAAAA
1 AAAAGAAAAGAAAAAAAGAAAAAGAAAA
17707175 GGAGAGGTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
41 3 0.05
42 7 0.11
43 4 0.06
44 38 0.61
45 7 0.11
46 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (44 bp):
AAAAGAAAAGAAAAAAAGAAAAAGAAAAAAGAAAAAGATAAAAG
Found at i:17707134 original size:6 final size:5
Alignment explanation
Indices: 17707060--17707175 Score: 89
Period size: 5 Copynumber: 22.0 Consensus size: 5
17707050 TTCAGTGAAT
*
17707060 AAAAG AAAAG AAAAA AAGAAG AAGAA- AAAAG AAAAAG ATAAAAG AAAAG
1 AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG -AAAAG --AAAAG AAAAG
17707109 AAAAG AAGAAG AAAA- AAAAG ATAAAG ATAAAG ATAAAAG AAAAG -AAA-
1 AAAAG AA-AAG AAAAG AAAAG A-AAAG A-AAAG --AAAAG AAAAG AAAAG
17707156 AAAAG -AAAG AAAAAG AAAAG
1 AAAAG AAAAG -AAAAG AAAAG
17707176 GAGAGGTCGA
Statistics
Matches: 95, Mismatches: 3, Indels: 26
0.77 0.02 0.21
Matches are distributed among these distances:
4 16 0.17
5 38 0.40
6 31 0.33
7 9 0.09
8 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:17708722 original size:39 final size:39
Alignment explanation
Indices: 17708674--17708816 Score: 135
Period size: 39 Copynumber: 3.7 Consensus size: 39
17708664 TCATCAACCA
* *
17708674 ATCTCTTACCCCGAGCCTAGGGCAGATTGAAGCCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTAAAGCCATTTG
* * * * * ****
17708713 ATCTTTTACCCCGAGCTTGGGGCAGATCATCA-TCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTA-AAGCCATTTG
* *
17708752 ATCTCTTGCTCCGAGCCTGGGGCAGATTAAAGCCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTAAAGCCATTTG
* *
17708791 ATCTTTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGA
17708817 CCACCTTCAA
Statistics
Matches: 76, Mismatches: 26, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
38 1 0.01
39 74 0.97
40 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTAAAGCCATTTG
Found at i:17708785 original size:78 final size:78
Alignment explanation
Indices: 17708652--17708833 Score: 301
Period size: 78 Copynumber: 2.3 Consensus size: 78
17708642 TGCAGTGGAA
*
17708652 TGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGAAGCCATTTGATCT
1 TGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTAAAGCCATTTGATCT
17708717 TTTACCCCGAGCT
66 TTTACCCCGAGCT
* * *
17708730 TGGGGCAGATCATCATCAACCAATCTCTTGCTCCGAGCCTGGGGCAGATTAAAGCCATTTGATCT
1 TGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTAAAGCCATTTGATCT
17708795 TTTACCCCGAGCT
66 TTTACCCCGAGCT
* * *
17708808 TGGGGCAGACCACCTTCAACCAATCT
1 TGGGGCAGATCATCATCAACCAATCT
17708834 ACTACCCTGA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (78 bp):
TGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTAAAGCCATTTGATCT
TTTACCCCGAGCT
Found at i:17709235 original size:209 final size:209
Alignment explanation
Indices: 17708923--17709764 Score: 1100
Period size: 209 Copynumber: 4.0 Consensus size: 209
17708913 TACCAACTCG
* * ** * *
17708923 AGGCTCAAAGCGAGCAAATCTTCAAACCCCAGCTTTTTGATGAGATACTGAGAAGTAGGTCAAAG
1 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* * *
17708988 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACTAAATTTGTCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * * * * *
17709053 TACAGAGAAGCAAATTGAAACAAGCGATACGGTCATCTTTCTGATGAGATACTGAGAAGTAGTCC
131 TACAGAGAAGCAGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGTCC
*
17709118 AAATCAATGAAACA
196 AAATCAATAAAACA
*
17709132 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAG
1 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
17709197 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTTGTCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * ** *
17709262 TACAGAGAAGCGGATTGAAACAAGTAATGCGGTCATCTTCCTGATGAGATACTAAGAAGTAGAT-
131 TACAGAGAAGCAGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAG-TC
17709326 CAAATCAATAAAACA
195 CAAATCAATAAAACA
17709341 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
1 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
17709406 CAATAAAATAGTTAGCTTCCTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * * *
17709471 TACAAAGAAGCAGATTAAAACAAGCGATGCGGTTATCTTCCTGATGAGATACTGAGAAGAAGACC
131 TACAGAGAAGCAGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGTCC
* *
17709536 AAATC---AAACCC
196 AAATCAATAAAACA
* * * ** * * * * *
17709547 ACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTAATAAGACACTGAGAAGTAGGTCGAAG
1 AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* * ** * * * *
17709612 TAAT-AAATGGTTAACTTCCCAATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAA
66 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* ** * * * * *
17709676 CACAGAGAAGTGGATCAAAACAAGTGATGCGATCATCTTCCTGATGAGACACTAAGAAGAAGGCC
131 TACAGAGAAGCAGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGTCC
*
17709741 AAATCAATAAAACC
196 AAATCAATAAAACA
*
17709755 AGACTCAAAG
1 AGGCTCAAAG
17709765 ACTATGGTGA
Statistics
Matches: 560, Mismatches: 68, Indels: 11
0.88 0.11 0.02
Matches are distributed among these distances:
205 110 0.20
206 62 0.11
208 11 0.02
209 376 0.67
210 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (209 bp):
AGGCTCAAAGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
TACAGAGAAGCAGATTAAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGTCC
AAATCAATAAAACA
Found at i:17710100 original size:6 final size:6
Alignment explanation
Indices: 17710072--17710148 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
17710062 GGCCCAACAG
* * * *
17710072 AATTTG AATTTA AGTTT- ATTTTA AATTTA AATTGGA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA
* * *
17710119 -ATCATA AATTTA AGTTTA AATTCA AATTTA
1 AAT-TTA AATTTA AATTTA AATTTA AATTTA
17710149 TTTGAATAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 40 0.74
7 7 0.13
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:17710149 original size:29 final size:30
Alignment explanation
Indices: 17710093--17710149 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
17710083 AAGTTTATTT
*
17710093 TAAATTTAAATTGGAAATTTAAATTTATCA
1 TAAATTTAAATTGGAAATTCAAATTTATCA
* *
17710123 TAAATTTAAGTT-TAAATTCAAATTTAT
1 TAAATTTAAATTGGAAATTCAAATTTAT
17710150 TTGAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (30 bp):
TAAATTTAAATTGGAAATTCAAATTTATCA
Found at i:17710781 original size:16 final size:17
Alignment explanation
Indices: 17710760--17710791 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17710750 ATGTTTATTG
17710760 CTATCA-TTATTATTAA
1 CTATCATTTATTATTAA
17710776 CTATCATTTATTATTA
1 CTATCATTTATTATTA
17710792 TTACTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
CTATCATTTATTATTAA
Found at i:17711923 original size:30 final size:29
Alignment explanation
Indices: 17711887--17712118 Score: 215
Period size: 29 Copynumber: 7.9 Consensus size: 29
17711877 CCCTGAAGGT
* *
17711887 CCCTAAACTGTCTAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTACATTTTGAC
17711917 CCCTAAACTTCTC-AAAATTACATCTTTGAC
1 CCCTAAACTTC-CAAAAATTACAT-TTTGAC
* *
17711947 CCCAAAACTTCCAAAAATTACATCTTT-AA
1 CCCTAAACTTCCAAAAATTACAT-TTTGAC
* * *
17711976 CCTTGAAACTTCC-AAAATTCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTACA-TTTTGAC
*
17712006 CCCAAAACTTCCAAAAATTACATTTT-AC
1 CCCTAAACTTCCAAAAATTACATTTTGAC
* *
17712034 CCCTAAATTTTCAAAAATTACAATTTTGA-
1 CCCTAAACTTCCAAAAATTAC-ATTTTGAC
*
17712063 CCCTAAAACTTCCAAAAATTACATTTTTA-
1 CCCT-AAACTTCCAAAAATTACATTTTGAC
* * *
17712092 CCCTCGAACTTTCAAAAATTCCATTTT
1 CCCT-AAACTTCCAAAAATTACATTTT
17712119 TGGTCCCGAG
Statistics
Matches: 171, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
28 20 0.12
29 76 0.44
30 75 0.44
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTGAC
Found at i:17711961 original size:29 final size:29
Alignment explanation
Indices: 17711891--17712118 Score: 212
Period size: 30 Copynumber: 7.8 Consensus size: 29
17711881 GAAGGTCCCT
* * *
17711891 AAACTGTCTAAAAATTATATTTTGACCCCT
1 AAACT-TCCAAAAATTACATTTTGACCCCA
17711921 AAACTTCTC-AAAATTACATCTTTGACCCCA
1 AAACTTC-CAAAAATTACAT-TTTGACCCCA
* ***
17711951 AAACTTCCAAAAATTACATCTTTAACCTTG
1 AAACTTCCAAAAATTACAT-TTTGACCCCA
* *
17711981 AAACTTCC-AAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACA-TTTTGACCCCA
*
17712010 AAACTTCCAAAAATTACATTTT-ACCCCT
1 AAACTTCCAAAAATTACATTTTGACCCCA
* * *
17712038 AAATTTTCAAAAATTACAATTTTGACCCTA
1 AAACTTCCAAAAATTAC-ATTTTGACCCCA
*
17712068 AAACTTCCAAAAATTACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTGACCC-CA
* * *
17712097 GAACTTTCAAAAATTCCATTTT
1 AAACTTCCAAAAATTACATTTT
17712119 TGGTCCCGAG
Statistics
Matches: 166, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
28 20 0.12
29 72 0.43
30 74 0.45
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCCA
Found at i:17712120 original size:59 final size:59
Alignment explanation
Indices: 17711891--17712120 Score: 261
Period size: 59 Copynumber: 3.9 Consensus size: 59
17711881 GAAGGTCCCT
* * * *
17711891 AAACTGTCTAAAAATTATATTTTGACCCCTAAACTTCTC-AAAATTACATCTTTGACCCCA
1 AAACT-TCCAAAAATTACATTTTTACCCCTAAACTT-TCAAAAATTACATTTTTGACCCCA
* * * * * *
17711951 AAACTTCCAAAAATTACATCTTTAACCTTGAAAC-TTCCAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTTACCCCT-AAACTTTCAAAAATTACATTTTTGACCCCA
* * *
17712010 AAACTTCCAAAAATTACA-TTTTACCCCTAAATTTTCAAAAATTACAATTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTACATTTTTGACCCCA
* *
17712068 AAACTTCCAAAAATTACATTTTTA-CCCTCGAACTTTCAAAAATTCCATTTTTG
1 AAACTTCCAAAAATTACATTTTTACCCCT-AAACTTTCAAAAATTACATTTTTG
17712121 GTCCCGAGGC
Statistics
Matches: 143, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
57 3 0.02
58 51 0.36
59 80 0.56
60 9 0.06
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTACATTTTTGACCCCA
Found at i:17712167 original size:59 final size:59
Alignment explanation
Indices: 17711989--17712272 Score: 172
Period size: 59 Copynumber: 4.8 Consensus size: 59
17711979 TGAAACTTCC
* * * ** * *
17711989 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTA-CATTTTACCC-CTA-AATTTTCA
1 AAAATTCCATTTTTGATCCCGAAA-TTTTAAAAATTACCATTTTACCCTC-AGAATATCCA
* * * ** *
17712047 AAAATTACAATTTTGA-CCCTAAAACTTCCAAAAATTA-CATTTTTACCCTC-GAACT-TTCA
1 AAAATTCCATTTTTGATCCC-GAAA-TTTTAAAAATTACCA-TTTTACCCTCAGAA-TATCCA
* ** *
17712106 AAAATTCCATTTTTGGTCCCGAGGCTTTTAAAAATTTCCATTTTACCCTCAG-ATATCCA
1 AAAATTCCATTTTTGATCCCGA-AATTTTAAAAATTACCATTTTACCCTCAGAATATCCA
** * * * *
17712165 AAAGCTCCATTTTTTACCCCGAAATTTTAAAAATTAGCATTTTACCC-CCGAATATCCA
1 AAAATTCCATTTTTGATCCCGAAATTTTAAAAATTACCATTTTACCCTCAGAATATCCA
** * ** *
17712223 AAAATTTTATTTTTGATCTCGATTTTTCTAAAAATTACCGTTTTACCCTC
1 AAAATTCCATTTTTGATCCCGAAATTT-TAAAAATTACCATTTTACCCTC
17712273 GGATGTCTAA
Statistics
Matches: 179, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
57 5 0.03
58 79 0.44
59 86 0.48
60 9 0.05
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTGATCCCGAAATTTTAAAAATTACCATTTTACCCTCAGAATATCCA
Found at i:17712177 original size:117 final size:114
Alignment explanation
Indices: 17711941--17712327 Score: 264
Period size: 117 Copynumber: 3.3 Consensus size: 114
17711931 AAATTACATC
* * * *
17711941 TTTGACCCCAAAACTTCCAAAAATTACATCTTTAACCTTGAAAC-TTCCAAAATTCCATTTTTAA
1 TTTGACCCCAAAACTTCCAAAAATTACAT-TTTACCCTCG-AACTTTCAAAAATTCCATTTTTGA
* * ** * * * * * *
17712005 CCCCAAAACTTCCAAAAA-TTACATTTTACCC-CTAAATTTTCAAAAATTACAAT
64 TCCC-GAACTTTTAAAAATTTCCATTTTACCCTC-AGA-TATCCAAAAGT-CCAT
* *
17712058 TTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGGT
1 TTTGACCCCAAAACTTCCAAAAATTACA-TTTTACCCTCGAACTTTCAAAAATTCCATTTTTGAT
*
17712123 CCCGAGGCTTTTAAAAATTTCCATTTTACCCTCAGATATCCAAAAGCTCCATT
65 CCCGA-ACTTTTAAAAATTTCCATTTTACCCTCAGATATCCAAAAG-TCCA-T
* * ** * * **
17712176 TTTTACCCCGAAA-TTTTAAAAATTAGCATTTTACCCCCGAA-TATCCAAAAATTTTATTTTTGA
1 TTTGACCCCAAAACTTCCAAAAATTA-CATTTTACCCTCGAACT-TTCAAAAATTCCATTTTTGA
* ** * * * * *
17712239 TCTCGATTTTTCTAAAAATTACCGTTTTACCCTCGGATGTCTAAAATGT-CAT
64 TCCCGAACTTT-TAAAAATTTCCATTTTACCCTCAGATATCCAAAA-GTCCAT
* * **
17712291 TTTAACCCTAAATTTTCCAAAAATTAACATTTTACCC
1 TTTGACCCCAAAACTTCCAAAAATT-ACATTTTACCC
17712328 CTGAGAGTCC
Statistics
Matches: 216, Mismatches: 41, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
115 10 0.05
116 29 0.13
117 146 0.68
118 30 0.14
119 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (114 bp):
TTTGACCCCAAAACTTCCAAAAATTACATTTTACCCTCGAACTTTCAAAAATTCCATTTTTGATC
CCGAACTTTTAAAAATTTCCATTTTACCCTCAGATATCCAAAAGTCCAT
Found at i:17728322 original size:29 final size:28
Alignment explanation
Indices: 17728290--17728421 Score: 76
Period size: 31 Copynumber: 4.5 Consensus size: 28
17728280 AAAAATAGAC
17728290 TTTTGGAAAGTTTTGGGGTAAAATGGTAA
1 TTTTGGAAAG-TTTGGGGTAAAATGGTAA
* *
17728319 TTTTTGGTGAAA--TCGAGGTCAAAAATGG-AA
1 -TTTT-G-GAAAGTTTGGGGT--AAAATGGTAA
*
17728349 TTTTGGAAAGTTTGAGGATAAAATGGTAA
1 TTTTGGAAAGTTTG-GGGTAAAATGGTAA
* * *
17728378 TTTTTGGTGAAA-TTAGGGTTAAAAATAG-AA
1 -TTTT-G-GAAAGTTTGGGGT-AAAATGGTAA
17728408 TTTTGGAAAGTTTG
1 TTTTGGAAAGTTTG
17728422 AGGTCAGAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
27 8 0.10
28 12 0.15
29 17 0.21
30 17 0.21
31 18 0.22
32 8 0.10
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
TTTTGGAAAGTTTGGGGTAAAATGGTAA
Found at i:17728367 original size:118 final size:113
Alignment explanation
Indices: 17728143--17728438 Score: 364
Period size: 118 Copynumber: 2.6 Consensus size: 113
17728133 GGGTAAGAAT
* * *
17728143 GTAATTTTTGGTGAAACGGGGTTAAAAATGGGA-TTTAGAAAGTTTGGGGGTAAGAATGTAATTT
1 GTAATTTTTGGTGAAACAGGGTTAAAAAT-AGATTTTGGAAAGTTTGGGGGTAAGAATGTAATTT
**
17728207 TGGTGAAATCGGGTTTAAATGGAATTTTGGAAAGTTCAAGGATAAAATA
65 TGGTGAAATCGGGTAAAAATGGAATTTTGGAAAGTTCAAGGATAAAATA
* *
17728256 GTAATTTTTGGTGAAACCAGGGTCAAAAATAGACTTTTGGAAAGTTTTGGGGTAA-AATGGTAAT
1 GTAATTTTTGGTGAAA-CAGGGTTAAAAATAGA-TTTTGGAAAGTTTGGGGGTAAGAAT-GTAA-
** *
17728320 TTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGATAAAATG
62 TTTTGGTGAAATCG-GGT-AAAAATGGAATTTTGGAAAGTTCAAGGATAAAATA
* * * *
17728374 GTAATTTTTGGTGAAATTAGGGTTAAAAATAGAATTTTGGAAAGTTT-GAGGTCAGAATATAATT
1 GTAATTTTTGGTGAAA-CAGGGTTAAAAATAG-ATTTTGGAAAGTTTGGGGGTAAGAATGTAATT
17728438 T
64 T
17728439 ATGAATAGTT
Statistics
Matches: 158, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
113 18 0.11
114 14 0.09
115 22 0.14
116 17 0.11
117 11 0.07
118 75 0.47
119 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (113 bp):
GTAATTTTTGGTGAAACAGGGTTAAAAATAGATTTTGGAAAGTTTGGGGGTAAGAATGTAATTTT
GGTGAAATCGGGTAAAAATGGAATTTTGGAAAGTTCAAGGATAAAATA
Found at i:17728401 original size:30 final size:31
Alignment explanation
Indices: 17728308--17728401 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
17728298 AGTTTTGGGG
*
17728308 TAAAATGGTAATTTTTGGTGAAA-TCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATTAGAGGT
* * *
17728338 CAAAAATGG-AA-TTTT-G-GAAAGTTTGAGGA
1 -TAAAATGGTAATTTTTGGTGAAA-TTAGAGGT
17728367 TAAAATGGTAATTTTTGGTGAAATTAG-GGT
1 TAAAATGGTAATTTTTGGTGAAATTAGAGGT
17728397 TAAAA
1 TAAAA
17728402 ATAGAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 11 0.22
30 13 0.25
31 11 0.22
32 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (31 bp):
TAAAATGGTAATTTTTGGTGAAATTAGAGGT
Found at i:17728410 original size:30 final size:31
Alignment explanation
Indices: 17728250--17728411 Score: 78
Period size: 30 Copynumber: 5.5 Consensus size: 31
17728240 GTTCAAGGAT
** *
17728250 AAAATAGTAATTTTTGGTGAAACCAGGGTCA
1 AAAATAGTAATTTTTGGTGAAATTAGGGTTA
* * *
17728281 AAAATAG--ACTTTT-G-GAAAGTTTTGGGGT-
1 AAAATAGTAATTTTTGGTGAAA--TTAGGGTTA
* * *
17728309 AAAATGGTAATTTTTGGTGAAA-TCGAGGTCA
1 AAAATAGTAATTTTTGGTGAAATTAG-GGTTA
* * *
17728340 AAAAT-GGAA-TTTT-G-GAAAGTTTGAGGAT-
1 AAAATAGTAATTTTTGGTGAAA-TTAG-GGTTA
*
17728368 AAAATGGTAATTTTTGGTGAAATTAGGGTTA
1 AAAATAGTAATTTTTGGTGAAATTAGGGTTA
17728399 AAAATAG-AATTTT
1 AAAATAGTAATTTT
17728412 GGAAAGTTTG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
27 8 0.08
28 13 0.13
29 22 0.23
30 23 0.24
31 23 0.24
32 8 0.08
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (31 bp):
AAAATAGTAATTTTTGGTGAAATTAGGGTTA
Found at i:17728421 original size:59 final size:58
Alignment explanation
Indices: 17728143--17728424 Score: 313
Period size: 59 Copynumber: 4.9 Consensus size: 58
17728133 GGGTAAGAAT
** * * * *
17728143 GTAATTTTTGGTGAAACGGGGTTAAAAATGGGA-TTTAGAAAGTTTGGGGGTAAGAAT-
1 GTAATTTTTGGTGAAATAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGATAA-AATG
* * ** *
17728200 GTAA-TTTTGGTGAAATCGGGTT-TAAATGGAATTTTGGAAAGTTCAAGGATAAAATA
1 GTAATTTTTGGTGAAATAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGATAAAATG
* * * * *
17728256 GTAATTTTTGGTGAAACCAGGGTCAAAAATAGACTTTTGGAAAGTTTTG-GGGTAAAATG
1 GTAATTTTTGGTGAAA-TAGGGTTAAAAATGGAATTTTGGAAAG-TTTGAGGATAAAATG
* *
17728315 GTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGATAAAATG
1 GTAATTTTTGGTGAAATAG-GGTTAAAAATGGAATTTTGGAAAGTTTGAGGATAAAATG
*
17728374 GTAATTTTTGGTGAAATTAGGGTTAAAAATAGAATTTTGGAAAGTTTGAGG
1 GTAATTTTTGGTGAAA-TAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGG
17728425 TCAGAATATA
Statistics
Matches: 189, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
55 10 0.05
56 35 0.19
57 15 0.08
58 9 0.05
59 116 0.61
60 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GTAATTTTTGGTGAAATAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGATAAAATG
Found at i:17729197 original size:15 final size:15
Alignment explanation
Indices: 17729177--17729209 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17729167 TTCTTAAAAC
*
17729177 AAAATCCAGATCTGG
1 AAAATCCAAATCTGG
17729192 AAAATCCAAATCTGG
1 AAAATCCAAATCTGG
17729207 AAA
1 AAA
17729210 TTTCTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (15 bp):
AAAATCCAAATCTGG
Found at i:17730505 original size:17 final size:17
Alignment explanation
Indices: 17730485--17730547 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
17730475 TTTTAAATGT
17730485 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
17730502 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
17730518 ATTTAAAGTTAATTCAA
1 ATTTAAATTTAAAACAA
*
17730535 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
17730548 TTCAAGTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:17730513 original size:33 final size:32
Alignment explanation
Indices: 17730468--17730546 Score: 79
Period size: 33 Copynumber: 2.5 Consensus size: 32
17730458 TTTTAAGTTT
* ** *
17730468 CAAA-TTATTTTAAATGTATTTAAATTTAAAA
1 CAAACTTAATTTAAATAAATTTAAAGTTAAAA
* **
17730499 CAAATTTAAATTTAAATAAATTTAAAGTTAATT
1 CAAACTT-AATTTAAATAAATTTAAAGTTAAAA
17730532 CAAACTTAATTTAAA
1 CAAACTTAATTTAAA
17730547 ATTCAAGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 4 0.10
32 10 0.26
33 25 0.64
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
CAAACTTAATTTAAATAAATTTAAAGTTAAAA
Done.