Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 53 of 318
Found at i:19331079 original size:21 final size:21
Alignment explanation
Indices: 19331063--19331141 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
19331053 ATATAAGGGT
* *
19331063 TGAACGGAAGCTCATAAGAGC
1 TGAACGAAAACTCATAAGAGC
* * *
19331084 TGAACGGAAACTCATAAGGGT
1 TGAACGAAAACTCATAAGAGC
* *
19331105 TAAAC-AAAAGCTCAAAAGAGC
1 TGAACGAAAA-CTCATAAGAGC
19331126 TGAACGAAAACTCATA
1 TGAACGAAAACTCATA
19331142 TGAGTTAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.85
22 4 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
TGAACGAAAACTCATAAGAGC
Found at i:19331080 original size:42 final size:42
Alignment explanation
Indices: 19331021--19331141 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
19331011 GCCCAAAGGC
*
19331021 TGAACAGAAGCATATAAGTGCTAAACAGAAACAT-ATAAGGGT
1 TGAACAGAAGCATATAAGAGCTAAACAGAAAC-TCATAAGGGT
* * *
19331063 TGAACGGAAGC-TCATAAGAGCTGAACGGAAACTCATAAGGGT
1 TGAACAGAAGCAT-ATAAGAGCTAAACAGAAACTCATAAGGGT
* * * *
19331105 TAAACAAAAGC-TCAAAAGAGCTGAAC-GAAAACTCATA
1 TGAACAGAAGCAT-ATAAGAGCTAAACAG-AAACTCATA
19331142 TGAGTTAAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 3 0.04
42 65 0.96
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
TGAACAGAAGCATATAAGAGCTAAACAGAAACTCATAAGGGT
Found at i:19331149 original size:42 final size:42
Alignment explanation
Indices: 19331070--19331159 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
19331060 GGTTGAACGG
* * *
19331070 AAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTAAACAA
1 AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
* *
19331112 AAGCTCAAAAGAGCTGAACGAAAACTCATATGAGTTAAACAT
1 AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
19331154 AAGCTC
1 AAGCTC
19331160 GTGAGAACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
Found at i:19346429 original size:26 final size:25
Alignment explanation
Indices: 19346382--19346431 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19346372 AAAATACTTT
19346382 AAAATTCTATATAAAAGATTTTTTA
1 AAAATTCTATATAAAAGATTTTTTA
19346407 AAAATTACTATATAAAA-ATTTTTTA
1 AAAATT-CTATATAAAAGATTTTTTA
19346432 CTTAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATTCTATATAAAAGATTTTTTA
Found at i:19354922 original size:6 final size:6
Alignment explanation
Indices: 19354911--19354935 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19354901 ATGCCCACTC
19354911 TGTCTT TGTCTT TGTCTT TGTCTT T
1 TGTCTT TGTCTT TGTCTT TGTCTT T
19354936 TCCCTCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TGTCTT
Found at i:19358771 original size:6 final size:6
Alignment explanation
Indices: 19358760--19358785 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19358750 AGATAATTTA
19358760 ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT AT
19358786 GTAAATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:19361107 original size:30 final size:31
Alignment explanation
Indices: 19361067--19361133 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
19361057 GTTAATAGTT
19361067 TATA-AAAATTAGATC-AAATTAAAATTT-TA
1 TATATAAAATTAGA-CAAAATTAAAATTTATA
* *
19361096 TATATAAAATTATACAAAATTAAAATTTATG
1 TATATAAAATTAGACAAAATTAAAATTTATA
19361127 TATATAA
1 TATATAA
19361134 TTACATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.15
30 20 0.61
31 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (31 bp):
TATATAAAATTAGACAAAATTAAAATTTATA
Found at i:19376674 original size:21 final size:20
Alignment explanation
Indices: 19376650--19376700 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
19376640 ATTTATAACA
* *
19376650 TATTCAATTCTCATCTCTTAC
1 TATTCAAATCTCAT-ACTTAC
*
19376671 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTAC
19376692 TATTCAAAT
1 TATTCAAAT
19376701 AGTTTTTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 11 0.42
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (20 bp):
TATTCAAATCTCATACTTAC
Found at i:19376886 original size:40 final size:38
Alignment explanation
Indices: 19376828--19376990 Score: 141
Period size: 37 Copynumber: 4.2 Consensus size: 38
19376818 GTACCCAGCA
* * *
19376828 CCTCATCGGATAATTCGAAGTAATAATTTGACACTTAGTG
1 CCTCATCGGCTAAATCGAAGTAA-AA-TTGACACTCAGTG
* *
19376868 TCTCATCGGCTAAATCGAAGT-AAATTGACACTCGGTG
1 CCTCATCGGCTAAATCGAAGTAAAATTGACACTCAGTG
* * *
19376905 CCTCATCGGCTAAACCGAAGT-AAATTGGCACCCAGTG
1 CCTCATCGGCTAAATCGAAGTAAAATTGACACTCAGTG
* ** * *
19376942 CCTCATTGAATTAATCCGAAGTAATAGATTGACACCCAGTG
1 CCTCATCGGCTAAAT-CGAAGTAA-A-ATTGACACTCAGTG
*
19376983 TCTCATCG
1 CCTCATCG
19376991 ACTCGAAGTC
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
37 53 0.52
38 8 0.08
39 2 0.02
40 19 0.19
41 19 0.19
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (38 bp):
CCTCATCGGCTAAATCGAAGTAAAATTGACACTCAGTG
Found at i:19377970 original size:14 final size:14
Alignment explanation
Indices: 19377951--19377996 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
19377941 TTCATTTACT
19377951 TATTTATTTTATTA
1 TATTTATTTTATTA
*
19377965 TATTTACTTTATTA
1 TATTTATTTTATTA
* *
19377979 T-TATATTATA-TA
1 TATTTATTTTATTA
19377991 TATTTA
1 TATTTA
19377997 CTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:19377979 original size:22 final size:22
Alignment explanation
Indices: 19377936--19378000 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
19377926 ATTTTCTTTC
19377936 TTTATT-TCATTTACTTATTTAT
1 TTTATTAT-ATTTACTTATTTAT
19377958 TTTATTATATTTACTTTATTATTAT
1 TTTATTATATTTAC-TTA-T-TTAT
*
19377983 ATTATATATATTTACTTA
1 TTTAT-TATATTTACTTA
19378001 AATATTAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 12 0.32
23 4 0.11
24 1 0.03
25 11 0.30
26 9 0.24
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTATATTTACTTATTTAT
Found at i:19377979 original size:26 final size:27
Alignment explanation
Indices: 19377945--19377999 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
19377935 CTTTATTTCA
*
19377945 TTTACTTATT-TATTTTATTATATTTAC
1 TTTACTTATTATATTATA-TATATTTAC
19377972 TTTA-TTATTATATTATATATATTTAC
1 TTTACTTATTATATTATATATATTTAC
19377998 TT
1 TT
19378000 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTATATTATATATATTTAC
Found at i:19378006 original size:26 final size:25
Alignment explanation
Indices: 19377954--19378007 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
19377944 ATTTACTTAT
* * *
19377954 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
19377979 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
19378005 TTA
1 TTA
19378008 AGTAATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:19378019 original size:26 final size:26
Alignment explanation
Indices: 19377964--19378021 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
19377954 TTATTTTATT
* * * *
19377964 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
19377990 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
19378016 ATATTT
1 ATATTT
19378022 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:19386276 original size:15 final size:16
Alignment explanation
Indices: 19386249--19386278 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19386239 AGATATTCCA
19386249 ATTTAGTCCCATTTTT
1 ATTTAGTCCCATTTTT
19386265 ATTTAG-CCCATTTT
1 ATTTAGTCCCATTTT
19386279 GGCAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTAGTCCCATTTTT
Found at i:19387747 original size:10 final size:10
Alignment explanation
Indices: 19387732--19387756 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19387722 CGTGGCATGT
19387732 AGAAGTCCTA
1 AGAAGTCCTA
19387742 AGAAGTCCTA
1 AGAAGTCCTA
19387752 AGAAG
1 AGAAG
19387757 ATAGAACATT
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:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (10 bp):
AGAAGTCCTA
Found at i:19389126 original size:17 final size:17
Alignment explanation
Indices: 19389087--19389129 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19389077 CCACAGAATT
*
19389087 TTTTTTATTTTTTTTCG
1 TTTTTTATTTTTTTACG
* *
19389104 TATTTTATTTTTTGTACT
1 TTTTTTATTTTTT-TACG
19389122 TTTTTTAT
1 TTTTTTAT
19389130 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTTTTACG
Found at i:19395458 original size:20 final size:20
Alignment explanation
Indices: 19395433--19395471 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19395423 AATATTTTTT
19395433 ATTTAA-AAAAATATTAATAA
1 ATTTAATAAAAA-ATTAATAA
19395453 ATTTAATAAAAAATTAATA
1 ATTTAATAAAAAATTAATA
19395472 GACCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTAATAAAAAATTAATAA
Found at i:19397059 original size:3 final size:3
Alignment explanation
Indices: 19397051--19397080 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19397041 TACTTCCATC
*
19397051 TAA TAA TAA TAA TAA GAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19397081 AAGGTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:19402049 original size:21 final size:22
Alignment explanation
Indices: 19402020--19402066 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
19402010 CAGAAGGAGT
*
19402020 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19402042 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19402063 GAGT
1 GAGT
19402067 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:19408698 original size:28 final size:28
Alignment explanation
Indices: 19408666--19408752 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
19408656 ATTATGAGTA
19408666 AATTTTTCATTCAACTCTTATGTGATTG
1 AATTTTTCATTCAACTCTTATGTGATTG
* * *
19408694 AATTTTACCATT--A-TGCTT-TG-AATTA
1 AATTTT-TCATTCAACT-CTTATGTGATTG
19408719 AATTTTTCATTCAACTCTTATGTGATTG
1 AATTTTTCATTCAACTCTTATGTGATTG
19408747 AATTTT
1 AATTTT
19408753 ACCATTATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
24 4 0.09
25 9 0.20
26 7 0.15
27 7 0.15
28 15 0.33
29 4 0.09
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (28 bp):
AATTTTTCATTCAACTCTTATGTGATTG
Found at i:19408744 original size:53 final size:53
Alignment explanation
Indices: 19408664--19408770 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
19408654 AAATTATGAG
19408664 TAAATTTTTCATTCAACTCTTATGTGATTGAATTTTACCATTATGCTTTGAAT
1 TAAATTTTTCATTCAACTCTTATGTGATTGAATTTTACCATTATGCTTTGAAT
19408717 TAAATTTTTCATTCAACTCTTATGTGATTGAATTTTACCATTATGCTTTGAAT
1 TAAATTTTTCATTCAACTCTTATGTGATTGAATTTTACCATTATGCTTTGAAT
19408770 T
1 T
19408771 TTATTAAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (53 bp):
TAAATTTTTCATTCAACTCTTATGTGATTGAATTTTACCATTATGCTTTGAAT
Found at i:19414242 original size:22 final size:22
Alignment explanation
Indices: 19414202--19414243 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19414192 TTAAAGTGTA
19414202 AATATAAAAATTTTGAAGGGCC
1 AATATAAAAATTTTGAAGGGCC
*
19414224 AATAGTAAATATTTT-AAGGG
1 AATA-TAAAAATTTTGAAGGG
19414244 TGGAATGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (22 bp):
AATATAAAAATTTTGAAGGGCC
Found at i:19414479 original size:28 final size:27
Alignment explanation
Indices: 19414434--19414487 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
19414424 GATGTTGATG
19414434 ATATTTTATAATTATTTAATTGAGATAA
1 ATATTTTATAATTATTTAA-TGAGATAA
*
19414462 ATATTATTTTAATT-TTTAATGAGATA
1 ATATT-TTATAATTATTTAATGAGATA
19414488 TTTTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 10 0.42
29 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (27 bp):
ATATTTTATAATTATTTAATGAGATAA
Found at i:19414512 original size:11 final size:10
Alignment explanation
Indices: 19414490--19414523 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
19414480 ATGAGATATT
19414490 TTATTATTTA
1 TTATTATTTA
19414500 TTATTATTTTA
1 TTATTA-TTTA
19414511 TTATTAATTTA
1 TTATT-ATTTA
19414522 TT
1 TT
19414524 TAATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 15 0.68
12 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:19416286 original size:40 final size:40
Alignment explanation
Indices: 19416169--19416306 Score: 159
Period size: 40 Copynumber: 3.5 Consensus size: 40
19416159 CTCGAGAATA
* ** *
19416169 TAAAGTGAATAGGATTCGTTCCTGATTCACTATAATACCT
1 TAAAGTGAATAGGATTTGTTCCTGATTCACTATGGTAACT
* * *
19416209 CAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATT
1 TAAAGTGAATAGGATTTGTTCCTGATTCACTATGGTAACT
* * *
19416249 TAAAGTGAATAGGATTTATTCCTAATTCACTACGGTAACT
1 TAAAGTGAATAGGATTTGTTCCTGATTCACTATGGTAACT
* * *
19416289 TAAGGCGGATAGGATTTG
1 TAAAGTGAATAGGATTTG
19416307 ACCTGAAAAG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (40 bp):
TAAAGTGAATAGGATTTGTTCCTGATTCACTATGGTAACT
Found at i:19416372 original size:79 final size:79
Alignment explanation
Indices: 19416284--19416502 Score: 305
Period size: 79 Copynumber: 2.8 Consensus size: 79
19416274 TTCACTACGG
* * * *
19416284 TAACTTAAGGCGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTACGGTTACATGATAT
1 TAACCTAAGGTGGATAGGATTTGACCTGAAAAAGGTAATCCTGATTCGCTACGGTTACATGATAC
*
19416349 ATGATTCATTATGG
66 ATGATTCATTATGA
* *
19416363 TAGCCTAAGGTGGATAGGATTTGACCTGAAAAAGGTAATCCTGATTCGCTACGGTTACACGATAC
1 TAACCTAAGGTGGATAGGATTTGACCTGAAAAAGGTAATCCTGATTCGCTACGGTTACATGATAC
*
19416428 ATGATTCCTTATGA
66 ATGATTCATTATGA
* * * * * *
19416442 TAACTTAAGATGGGTAGGATTTGACCT-AAAAAGGTAATCCTGATTCACTACAGCTACATGA
1 TAACCTAAGGTGGATAGGATTTGACCTGAAAAAGGTAATCCTGATTCGCTACGGTTACATGA
19416503 GATGCGACTC
Statistics
Matches: 124, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 30 0.24
79 94 0.76
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (79 bp):
TAACCTAAGGTGGATAGGATTTGACCTGAAAAAGGTAATCCTGATTCGCTACGGTTACATGATAC
ATGATTCATTATGA
Found at i:19416972 original size:57 final size:56
Alignment explanation
Indices: 19416871--19417037 Score: 151
Period size: 57 Copynumber: 3.0 Consensus size: 56
19416861 GTAAACGAAT
* * * * * * *
19416871 TTGAAATG-CATTGAAGTGAATTGTGTGTAATTGGTATAATCTTATTGGTTGATAA
1 TTGATATGTCATTGAAATGAATTATGTGTAAATGGTATAACCTTATAGATTGATAA
19416926 GTTGATATGTCATTGAAATGAATTATGT-TCAAATGGTATAACCTTATAGATTGATAA
1 -TTGATATGTCATTGAAATGAATTATGTGT-AAATGGTATAACCTTATAGATTGATAA
* * ** * * *
19416983 TGGGATATTTCATTGAAATGTGTTAAT-TGTAATTGGTATAATCTTATGGATTGAT
1 T-TGATATGTCATTGAAATGAATT-ATGTGTAAATGGTATAACCTTATAGATTGAT
19417038 GTTAGAATAT
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
56 9 0.10
57 80 0.87
58 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (56 bp):
TTGATATGTCATTGAAATGAATTATGTGTAAATGGTATAACCTTATAGATTGATAA
Found at i:19417054 original size:57 final size:53
Alignment explanation
Indices: 19416896--19417055 Score: 133
Period size: 57 Copynumber: 2.8 Consensus size: 53
19416886 GTGAATTGTG
19416896 TGTAATTGGTATAATCTTATTGG-TTGATAAGTTGATATGTCATTGAAATGAATTA
1 TGTAATTGGTATAATCTTA-TGGATTGAT--GTTGATATGTCATTGAAATGAATTA
* * * * * * **
19416951 TGTTCAAATGGTATAACCTTATAGATTGATAATGGGATATTTCATTGAAATGTGTTAA
1 TG-T-AATTGGTATAATCTTATGGATTGAT-GT-TGATATGTCATTGAAATGAATT-A
*
19417009 TTGTAATTGGTATAATCTTATGGATTGATGTTAGAATATGACATTGA
1 -TGTAATTGGTATAATCTTATGGATTGATGTT-G-ATATGTCATTGA
19417056 GGTAAGCTAT
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
55 2 0.02
56 7 0.09
57 69 0.84
58 2 0.02
59 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (53 bp):
TGTAATTGGTATAATCTTATGGATTGATGTTGATATGTCATTGAAATGAATTA
Found at i:19421447 original size:2 final size:2
Alignment explanation
Indices: 19421442--19421468 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19421432 ATATATATAT
19421442 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
19421469 AAACACCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19440834 original size:12 final size:12
Alignment explanation
Indices: 19440817--19440842 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19440807 TTTAAACTTC
19440817 AATAAATATTCA
1 AATAAATATTCA
19440829 AATAAATATTCA
1 AATAAATATTCA
19440841 AA
1 AA
19440843 CTTTAATTAA
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAATATTCA
Found at i:19442599 original size:14 final size:14
Alignment explanation
Indices: 19442560--19442588 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19442550 TAGCTAAAAC
19442560 TACCACTTATCACT
1 TACCACTTATCACT
19442574 TACCACTTATCACT
1 TACCACTTATCACT
19442588 T
1 T
19442589 GTCACTGATC
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:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (14 bp):
TACCACTTATCACT
Found at i:19442635 original size:37 final size:37
Alignment explanation
Indices: 19442584--19442668 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
19442574 TACCACTTAT
*
19442584 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
19442621 CACTTATCATTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
19442658 CACTTATCACT
1 CACTTATCACT
19442669 TGTCACTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (37 bp):
CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:19445344 original size:52 final size:48
Alignment explanation
Indices: 19445325--19445517 Score: 259
Period size: 46 Copynumber: 4.0 Consensus size: 48
19445315 TGACAAGTGG
* *
19445325 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19445371 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
19445423 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
19445469 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19445517 A
1 A
19445518 GAGATAAGTG
Statistics
Matches: 132, Mismatches: 7, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
46 87 0.66
48 1 0.01
52 44 0.33
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:19445380 original size:98 final size:98
Alignment explanation
Indices: 19445254--19445516 Score: 449
Period size: 98 Copynumber: 2.7 Consensus size: 98
19445244 CCGGATTTGA
*
19445254 ATACTT-T-TGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTG
1 ATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTG
*
19445317 ACAAGTGGAAAGTGATAAGTAATAGCTTCGGCT
66 ACAAGTGAAAAGTGATAAGTAATAGCTTCGGCT
**
19445350 ATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTG
1 ATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTG
*
19445415 ACAAGTGAAAAGTGATAAGTGATAGCTTCGGCT
66 ACAAGTGAAAAGTGATAAGTAATAGCTTCGGCT
* *
19445448 ATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAG
1 ATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTG
19445513 ACAA
66 ACAA
19445517 AGAGATAAGT
Statistics
Matches: 156, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
96 6 0.04
97 1 0.01
98 149 0.96
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (98 bp):
ATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTG
ACAAGTGAAAAGTGATAAGTAATAGCTTCGGCT
Found at i:19445541 original size:37 final size:37
Alignment explanation
Indices: 19445491--19445673 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
19445481 GATAGCTTTA
* *
19445491 GCTACACTTATCTGATCAAGAGACAAAGAGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19445528 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19445565 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
19445602 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
19445639 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19445674 ATCATACGTA
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.08
36 4 0.03
37 125 0.89
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:19447002 original size:58 final size:59
Alignment explanation
Indices: 19446925--19447043 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
19446915 CATGTGAACA
19446925 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
19446984 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
19447042 TG
1 TG
19447044 ATTTCGTGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 55 0.92
59 5 0.08
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (59 bp):
TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:19447034 original size:28 final size:28
Alignment explanation
Indices: 19446944--19447034 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
19446934 GTGATTCCGT
19446944 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
19446972 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
19447001 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
19447030 GTAAG
1 GTAAG
19447035 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:19447057 original size:49 final size:49
Alignment explanation
Indices: 19446985--19447078 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
19446975 AGTGATATGT
*
19446985 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGACTATGGCATCGGTAA
* *
19447034 GTGATATGTGATTTCGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGACTATGGCATCG
19447079 AGAAAACGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGACTATGGCATCGGTAA
Found at i:19450284 original size:52 final size:48
Alignment explanation
Indices: 19450265--19450457 Score: 250
Period size: 46 Copynumber: 4.0 Consensus size: 48
19450255 TGACAAGTGG
* * *
19450265 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
19450311 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-A---A
* * *
19450363 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
* *
19450409 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
19450457 A
1 A
19450458 GAGATAAGTG
Statistics
Matches: 130, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
46 86 0.66
48 1 0.01
52 43 0.33
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
Found at i:19450319 original size:98 final size:98
Alignment explanation
Indices: 19450199--19450456 Score: 462
Period size: 98 Copynumber: 2.6 Consensus size: 98
19450189 TTTGAGTACT
*
19450199 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19450264 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
19450297 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19450362 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
19450395 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
19450457 AGAGATAAGT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 153 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:19450481 original size:37 final size:37
Alignment explanation
Indices: 19450431--19450613 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
19450421 GATAGCTTTA
* *
19450431 GCTACACTTATCTGATCAAGAGACAAAGAGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19450468 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19450505 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
19450542 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
19450579 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19450614 ATCATACGTA
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.08
36 4 0.03
37 125 0.89
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:19453732 original size:3 final size:3
Alignment explanation
Indices: 19453724--19453748 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19453714 TCATGCACGT
19453724 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
19453749 GGGAATGCAT
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:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:19468501 original size:24 final size:26
Alignment explanation
Indices: 19468453--19468502 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
19468443 AATTACATGT
* *
19468453 ATTATAAAATAACTACAAATTTATTA
1 ATTATAAAATAACAACAAATATATTA
19468479 ATTATAAAA-AA-AACAAATATATTA
1 ATTATAAAATAACAACAAATATATTA
19468503 TAAGTTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 2 0.09
26 9 0.41
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTATAAAATAACAACAAATATATTA
Found at i:19468529 original size:24 final size:23
Alignment explanation
Indices: 19468502--19468547 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19468492 CAAATATATT
*
19468502 ATAAGTTTCATTATTTAAAAAAAC
1 ATAAATTTCATT-TTTAAAAAAAC
*
19468526 ATAAATTTTATTTTTAAAAAAA
1 ATAAATTTCATTTTTAAAAAAA
19468548 ATCTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATTTCATTTTTAAAAAAAC
Found at i:19475537 original size:29 final size:29
Alignment explanation
Indices: 19475495--19475554 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
19475485 TTGACTGTAT
*
19475495 TGCAGTTTATTGTTCATAAACCCTTTAAA
1 TGCAGTTTATTGTTCATAAACCCTTCAAA
19475524 TGCAGTTTATTGTTCATAAACCCTTCAAA
1 TGCAGTTTATTGTTCATAAACCCTTCAAA
19475553 TG
1 TG
19475555 ATGAAAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (29 bp):
TGCAGTTTATTGTTCATAAACCCTTCAAA
Found at i:19479356 original size:28 final size:28
Alignment explanation
Indices: 19479322--19479382 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
19479312 AATGTTTATC
19479322 TTCTTTTCTTAATTGTTCCTTAAATTTA
1 TTCTTTTCTTAATTGTTCCTTAAATTTA
19479350 TTCTTTTCTTAATTGTTCCTTAAATTTA
1 TTCTTTTCTTAATTGTTCCTTAAATTTA
19479378 TTCTT
1 TTCTT
19479383 AAATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.62
Consensus pattern (28 bp):
TTCTTTTCTTAATTGTTCCTTAAATTTA
Found at i:19486529 original size:20 final size:20
Alignment explanation
Indices: 19486504--19486541 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19486494 TTAAACCGTC
*
19486504 GTTTATTATTTTATTATTCG
1 GTTTATCATTTTATTATTCG
19486524 GTTTATCATTTTATTATT
1 GTTTATCATTTTATTATT
19486542 ATTTGTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (20 bp):
GTTTATCATTTTATTATTCG
Found at i:19487056 original size:42 final size:42
Alignment explanation
Indices: 19487010--19487097 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
19487000 GCGACAGCCT
**
19487010 TGATGACGATCAACTCCAAGGCAGCGACAGCCATAATGACGA
1 TGATGACGATCAACTCCAAAACAGCGACAGCCATAATGACGA
* * * * *
19487052 TGATGACGATCTACTCCAAAACAGCGACTGGCATGATGACGG
1 TGATGACGATCAACTCCAAAACAGCGACAGCCATAATGACGA
19487094 TGAT
1 TGAT
19487098 CATGATTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (42 bp):
TGATGACGATCAACTCCAAAACAGCGACAGCCATAATGACGA
Found at i:19491608 original size:19 final size:21
Alignment explanation
Indices: 19491564--19491610 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
19491554 ATTGAGTGGT
19491564 TAATTAGACTTTAATTAAGTA
1 TAATTAGACTTTAATTAAGTA
*
19491585 AAATTAG-C-TTAATTAAG-A
1 TAATTAGACTTTAATTAAGTA
19491603 GTAATTAG
1 -TAATTAG
19491611 TGGAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 1 0.04
21 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATTAGACTTTAATTAAGTA
Found at i:19491810 original size:21 final size:22
Alignment explanation
Indices: 19491780--19491820 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19491770 TATTATTATT
*
19491780 ATATTGTAAT-TTATATTAATG
1 ATATTATAATATTATATTAATG
*
19491801 ATATTATAATATTATTTTAA
1 ATATTATAATATTATATTAA
19491821 CAATTGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
ATATTATAATATTATATTAATG
Found at i:19491876 original size:24 final size:23
Alignment explanation
Indices: 19491848--19491895 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
19491838 TAAATACATG
*
19491848 TGTAATA-AATTAAATACATATACT
1 TGTAATACAACTAAATA-AT-TACT
19491872 TGTAATACAACTAAATAATTACT
1 TGTAATACAACTAAATAATTACT
19491895 T
1 T
19491896 AAAATATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 9 0.41
25 8 0.36
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (23 bp):
TGTAATACAACTAAATAATTACT
Found at i:19491939 original size:5 final size:5
Alignment explanation
Indices: 19491922--19491968 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
19491912 TTATTAAATG
*
19491922 ATATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT ATATT ATAT
1 ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT ATATT ATAT
19491969 AAATAAGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 26 0.70
6 7 0.19
7 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:19491959 original size:12 final size:12
Alignment explanation
Indices: 19491922--19491969 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
19491912 TTATTAAATG
19491922 ATATTAT-TATT
1 ATATTATATATT
19491933 ATATTATAGTATATT
1 ATA-T-TA-TATATT
19491948 ATATTATATATT
1 ATATTATATATT
19491960 ATATTATATA
1 ATATTATATA
19491970 AATAAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
11 3 0.09
12 17 0.52
13 4 0.12
14 2 0.06
15 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATATTATATATT
Found at i:19492045 original size:13 final size:13
Alignment explanation
Indices: 19492029--19492054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19492019 AGAACAGGGG
19492029 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
19492042 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
19492055 GGGAGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:19493316 original size:18 final size:19
Alignment explanation
Indices: 19493295--19493333 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19493285 ATATAGATAT
19493295 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
19493313 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
19493332 AT
1 AT
19493334 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:19493672 original size:39 final size:40
Alignment explanation
Indices: 19493561--19493672 Score: 102
Period size: 39 Copynumber: 2.8 Consensus size: 40
19493551 CGACCTCGAG
* * *
19493561 TCGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA-AATATTACTTCGGATAGAC
** ** * * *
19493602 TCGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAC
*
19493641 T-GATGAGACACTGGGTGTCAAATATTGCTTCG
1 TCGATGAGACACTGGGTGTCAAATATTACTTCG
19493673 AACTATCCGA
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 17 0.31
39 19 0.35
40 1 0.02
41 17 0.31
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAC
Found at i:19493840 original size:18 final size:19
Alignment explanation
Indices: 19493819--19493859 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19493809 AATGAAATGA
19493819 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
19493837 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
19493856 GAAA
1 GAAA
19493860 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:19494885 original size:20 final size:20
Alignment explanation
Indices: 19494847--19494885 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19494837 GGAAGAAATT
** *
19494847 TATATATTTTTTAATTTTTC
1 TATATATTTTAAAACTTTTC
19494867 TATATATTTTAAAACTTTT
1 TATATATTTTAAAACTTTT
19494886 AATAACTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATATTTTAAAACTTTTC
Found at i:19497478 original size:77 final size:77
Alignment explanation
Indices: 19497351--19497506 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
19497341 ACTGGAAATG
19497351 TATGATGCAATTAACTATGTTTATTATTTACTAATGCACATATTTAACTGTTATATGTTCCTGAC
1 TATGATGCAATTAACTATGTTTATTATTTACTAATGCACATATTTAACTGTTATATGTTCCTGAC
19497416 TAGAACATGTTA
66 TAGAACATGTTA
19497428 TATGATGCAATTAACTATGTTTATTATTTACTAATGCACATATTTAACTGTTATATGTTCCTGAC
1 TATGATGCAATTAACTATGTTTATTATTTACTAATGCACATATTTAACTGTTATATGTTCCTGAC
19497493 TAGAACATGTTA
66 TAGAACATGTTA
19497505 TA
1 TA
19497507 ATATTTTTTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (77 bp):
TATGATGCAATTAACTATGTTTATTATTTACTAATGCACATATTTAACTGTTATATGTTCCTGAC
TAGAACATGTTA
Found at i:19497503 original size:24 final size:24
Alignment explanation
Indices: 19497476--19497559 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
19497466 CATATTTAAC
19497476 TGTTATATGTTCCTGACTAGAACA
1 TGTTATATGTTCCTGACTAGAACA
* ** *
19497500 TGTTATAATATTTTTTGCACATATTTAAC-
1 TGTTAT-AT-GTTCCTG-AC-TA--GAACA
19497529 TGTTATATGTTCCTGACTAGAACA
1 TGTTATATGTTCCTGACTAGAACA
19497553 TGTTATA
1 TGTTATA
19497560 ATATTTTTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
23 3 0.07
24 13 0.29
25 4 0.09
26 6 0.13
27 6 0.13
28 4 0.09
29 6 0.13
30 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (24 bp):
TGTTATATGTTCCTGACTAGAACA
Found at i:19497519 original size:53 final size:53
Alignment explanation
Indices: 19497462--19497567 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
19497452 TATTTACTAA
19497462 TGCACATATTTAACTGTTATATGTTCCTGACTAGAACATGTTATAATATTTTT
1 TGCACATATTTAACTGTTATATGTTCCTGACTAGAACATGTTATAATATTTTT
19497515 TGCACATATTTAACTGTTATATGTTCCTGACTAGAACATGTTATAATATTTTT
1 TGCACATATTTAACTGTTATATGTTCCTGACTAGAACATGTTATAATATTTTT
19497568 CGAAATCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (53 bp):
TGCACATATTTAACTGTTATATGTTCCTGACTAGAACATGTTATAATATTTTT
Found at i:19498609 original size:3 final size:3
Alignment explanation
Indices: 19498603--19498796 Score: 135
Period size: 3 Copynumber: 64.7 Consensus size: 3
19498593 AATGAAAACG
* * * *
19498603 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA GTG GTA A-A A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
19498649 ATA CTA ATG ATA ATA ATA AGA ATA TTA ATA ATA GTA TTA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
19498697 ATA ATA GTA ATA GAAA ATA AAA ATA AAA ATA AT- ATA GTA ATA GTA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
19498742 ATA ATA ATG GTA ATA ATAA ATA AGA ATA ATA ACA ATA ATA CA-A ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA ATA
19498788 ATAA ATA AT
1 AT-A ATA AT
19498797 CTAAAGTTTG
Statistics
Matches: 145, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
2 7 0.05
3 129 0.89
4 9 0.06
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:19498701 original size:12 final size:12
Alignment explanation
Indices: 19498575--19498781 Score: 87
Period size: 12 Copynumber: 17.6 Consensus size: 12
19498565 AACATGGCAA
* *
19498575 AATAAAAATGAC
1 AATAATAATGAT
*
19498587 AATAATAATGAAA
1 AATAATAATG-AT
*
19498600 ACGATAATAATAAT
1 A--ATAATAATGAT
* *
19498614 AATGATAATAAT
1 AATAATAATGAT
* *
19498626 AATAATAGTGGT
1 AATAATAATGAT
*
19498638 AA-AA-AATAAT
1 AATAATAATGAT
*
19498648 AATACTAATGAT
1 AATAATAATGAT
19498660 AATAATAA-GAAT
1 AATAATAATG-AT
*
19498672 ATTAATAATAGTATT
1 AATAATAAT-G-A-T
19498687 AATAATAATGAT
1 AATAATAATGAT
* *
19498699 AATAGTAATAGAA
1 AATAATAAT-GAT
19498712 AATAA-AA--AT
1 AATAATAATGAT
*
19498721 AAAAATAAT-AT
1 AATAATAATGAT
*
19498732 AGTAAT-A-G-T
1 AATAATAATGAT
*
19498741 AATAATAATGGT
1 AATAATAATGAT
19498753 AATAATAA--AT
1 AATAATAATGAT
* * *
19498763 AAGAATAATAAC
1 AATAATAATGAT
19498775 AATAATA
1 AATAATA
19498782 CAAATAATAA
Statistics
Matches: 147, Mismatches: 30, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
9 11 0.07
10 17 0.12
11 11 0.07
12 77 0.52
13 9 0.06
14 5 0.03
15 17 0.12
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (12 bp):
AATAATAATGAT
Found at i:19498985 original size:14 final size:14
Alignment explanation
Indices: 19498960--19498995 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
19498950 GAAAGAAAAT
19498960 ATAATAATAATAGTA
1 ATAAT-ATAATAGTA
19498975 ATAATATAATAGTA
1 ATAATATAATAGTA
19498989 ATAATAT
1 ATAATAT
19498996 TAAGAAGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
ATAATATAATAGTA
Found at i:19499110 original size:3 final size:3
Alignment explanation
Indices: 19498960--19499095 Score: 73
Period size: 3 Copynumber: 45.3 Consensus size: 3
19498950 GAAAGAAAAT
* * * * *
19498960 ATA ATA ATA ATA GTA ATA AT- ATA ATA GTA ATA ATA TTA AGA AGGGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA
* * * * *
19499006 ATA ATA AT- ATA TTA GATA GTAA ATA TTA ATA ATA ATA ATA ACA GTA
1 ATA ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
19499052 ATA A-A A-A ATG ATA ATA GTG ATA TTA GTA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19499096 CAATGTATTA
Statistics
Matches: 99, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
2 8 0.08
3 84 0.85
4 4 0.04
5 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19499801 original size:125 final size:126
Alignment explanation
Indices: 19499636--19499894 Score: 335
Period size: 128 Copynumber: 2.0 Consensus size: 126
19499626 TCCAATACGG
**
19499636 AATATTGCCTCATTTTAATTTAAGAAAACATAGATGAAATTTCAAAAGGATATTTTGA-ACTTT-
1 AATATTGCCTCATTTTAATTTAAGAAAACATAGATGAAATTTCAAAAGGATA-TTCCATA-TTTC
* * * *
19499699 TGTCGAATG-AAAAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCAAACACAA
64 AGTAGAATGAAAAAATCAAAACCCAACACGATTGGGCACGATCTCTCAAACTCCCAAACACAA
* ** * * *
19499761 AATATTGCCTCTTTTTAATTTAAGAAAAGGTGGATGAAATTTCACAAGGGTATTCCATATTTCAG
1 AATATTGCCTCATTTTAATTTAAGAAAACATAGATGAAATTTCAAAAGGATATTCCATATTTCAG
* *
19499826 TAGAATGAAAAAAAATCAAAACCCAACACGATTGGGCACGATCTCTCAAACTTCCAAACACGA
66 TAGAATG--AAAAAATCAAAACCCAACACGATTGGGCACGATCTCTCAAACTCCCAAACACAA
19499889 AATATT
1 AATATT
19499895 TCCTTATGTT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
124 6 0.05
125 54 0.47
128 55 0.48
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (126 bp):
AATATTGCCTCATTTTAATTTAAGAAAACATAGATGAAATTTCAAAAGGATATTCCATATTTCAG
TAGAATGAAAAAATCAAAACCCAACACGATTGGGCACGATCTCTCAAACTCCCAAACACAA
Found at i:19500303 original size:18 final size:18
Alignment explanation
Indices: 19500280--19500321 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
19500270 ATAGTTAAAA
19500280 TAATAATAACAG-AAATAG
1 TAATAATAA-AGTAAATAG
*
19500298 TAATAATAATGTAAATAG
1 TAATAATAAAGTAAATAG
19500316 TAATAA
1 TAATAA
19500322 AAATAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (18 bp):
TAATAATAAAGTAAATAG
Found at i:19500314 original size:12 final size:12
Alignment explanation
Indices: 19500299--19500353 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
19500289 CAGAAATAGT
*
19500299 AATAATAATGTA
1 AATAATAATGAA
* *
19500311 AATAGTAATAAA
1 AATAATAATGAA
*
19500323 AATAATAACGAA
1 AATAATAATGAA
* *
19500335 AATAGTAATGAT
1 AATAATAATGAA
19500347 AATAATA
1 AATAATA
19500354 TCTAATAGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (12 bp):
AATAATAATGAA
Found at i:19500320 original size:24 final size:24
Alignment explanation
Indices: 19500293--19500353 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
19500283 TAATAACAGA
* *
19500293 AATAGTAATAATAATGTAAATAGT
1 AATAGTAATAATAACGAAAATAGT
**
19500317 AATAAAAATAATAACGAAAATAGT
1 AATAGTAATAATAACGAAAATAGT
19500341 AAT-GATAATAATA
1 AATAG-TAATAATA
19500354 TCTAATAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.28
Consensus pattern (24 bp):
AATAGTAATAATAACGAAAATAGT
Found at i:19500327 original size:42 final size:42
Alignment explanation
Indices: 19500268--19500349 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
19500258 GATAGTAAAA
*
19500268 AAATAGTTAAAATAATAATAAC-AGAAATAGTAATAATAATGT
1 AAATAGTTAAAAAAATAATAACGA-AAATAGTAATAATAATGT
*
19500310 AAATAG-TAATAAAAATAATAACGAAAATAGTAATGATAAT
1 AAATAGTTAA-AAAAATAATAACGAAAATAGTAATAATAAT
19500350 AATATCTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 3 0.08
42 32 0.89
43 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (42 bp):
AAATAGTTAAAAAAATAATAACGAAAATAGTAATAATAATGT
Found at i:19523366 original size:46 final size:44
Alignment explanation
Indices: 19523290--19523495 Score: 150
Period size: 46 Copynumber: 4.5 Consensus size: 44
19523280 GTGCCGATGC
* **
19523290 CATGTCCCAGACAGGTCTTACACTGACACATGTAACCGT-GCTGACG
1 CATGTCCCAGACATGTCTTACACTGACACA--T-ACCGTAGCCAACG
*
19523336 CATGTCCCAGACATGTCTTACACT-AGCACATCCCGTAGCCAACG
1 CATGTCCCAGACATGTCTTACACTGA-CACATACCGTAGCCAACG
* * * * *
19523380 CATGTCCCAGACATGTCTGACATTGGCTAACAT-CTCG-AGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGAC--ACATAC-CGTA-GCCAACG
* * * ** *
19523426 CATGTCCCAGACATGTCTTACACTGGATCTCATACTGTGGCTGATG
1 CATGTCCCAGACATGTCTTACACT-GA-CACATACCGTAGCCAACG
*
19523472 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
19523496 AGCCCTTGCC
Statistics
Matches: 132, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
43 4 0.03
44 29 0.22
45 3 0.02
46 93 0.70
47 2 0.02
48 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGACACATACCGTAGCCAACG
Found at i:19530408 original size:101 final size:101
Alignment explanation
Indices: 19530233--19530434 Score: 395
Period size: 101 Copynumber: 2.0 Consensus size: 101
19530223 TGAACAGTGT
19530233 AAGAAATTTAACATTTACTTAAGTCATATAATAATCATAGTAACTTGTAAATCACTAAATAATAA
1 AAGAAATTTAACATTTACTTAAGTCATATAATAATCATAGTAACTTGTAAATCACTAAATAATAA
*
19530298 TAGTTGTCATTCATATATATACATTCGAGCTTTAAA
66 TACTTGTCATTCATATATATACATTCGAGCTTTAAA
19530334 AAGAAATTTAACATTTACTTAAGTCATATAATAATCATAGTAACTTGTAAATCACTAAATAATAA
1 AAGAAATTTAACATTTACTTAAGTCATATAATAATCATAGTAACTTGTAAATCACTAAATAATAA
19530399 TACTTGTCATTCATATATATACATTCGAGCTTTAAA
66 TACTTGTCATTCATATATATACATTCGAGCTTTAAA
19530435 CTTTAACTTC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (101 bp):
AAGAAATTTAACATTTACTTAAGTCATATAATAATCATAGTAACTTGTAAATCACTAAATAATAA
TACTTGTCATTCATATATATACATTCGAGCTTTAAA
Found at i:19532213 original size:13 final size:13
Alignment explanation
Indices: 19532195--19532219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19532185 TTCTTGCCTT
19532195 TTTCTTTATTTCA
1 TTTCTTTATTTCA
19532208 TTTCTTTATTTC
1 TTTCTTTATTTC
19532220 TTTTGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTATTTCA
Found at i:19532300 original size:19 final size:19
Alignment explanation
Indices: 19532276--19532314 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19532266 AATACTTATT
*
19532276 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
19532295 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
19532314 T
1 T
19532315 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:19532364 original size:15 final size:15
Alignment explanation
Indices: 19532338--19532399 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
19532328 TACACTTGTC
19532338 TTTTAT-TTATTATA
1 TTTTATATTATTATA
19532352 TTTTATATTATTATA
1 TTTTATATTATTATA
* *
19532367 -TTAATA-TAATATA
1 TTTTATATTATTATA
*
19532380 CTTTA-ATTATTATTA
1 TTTTATATTATTA-TA
19532395 TTTTA
1 TTTTA
19532400 CTTATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.18
14 18 0.46
15 14 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATATTATTATA
Found at i:19532404 original size:15 final size:14
Alignment explanation
Indices: 19532338--19532410 Score: 51
Period size: 14 Copynumber: 5.0 Consensus size: 14
19532328 TACACTTGTC
19532338 TTTTATTTATTA-TA
1 TTTTA-TTATTATTA
19532352 TTTTA-TATTATTA
1 TTTTATTATTATTA
* * *
19532365 TATTAATATAATATA
1 TTTTATTATTAT-TA
*
19532380 CTTTAATTATTATTA
1 -TTTTATTATTATTA
19532395 TTTTACTTATATATTA
1 TTTTA-TTAT-TATTA
19532411 AGTAAATACA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 14 0.30
15 8 0.17
16 13 0.28
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:19532895 original size:3 final size:3
Alignment explanation
Indices: 19532876--19533091 Score: 126
Period size: 3 Copynumber: 72.3 Consensus size: 3
19532866 AATAGGTAAA
* * * *
19532876 AAT AAT -AT AAT AGT AAT AAT AAC AAT -AT AAT AAT AGT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
19532922 AAT AGT AAT AAT AAT AAT AAT -AT ATT TAT AAT TAT AAT AAT AGTT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * * *
19532967 AAT GAT AAT AAA AAT AAT AGT AA- AGAA AAG AA- AAGT AA- AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA-T AAT AA-T AAT
* * *
19533012 AAC GAT AAT AACG AAT -AT AAGT AAT AAT AAT AAT AAT AAT GAA- AAT
1 AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT
* *
19533058 AA- AAGT AAT AAT AAT AGT GAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19533092 TATTAAATTA
Statistics
Matches: 161, Mismatches: 35, Indels: 34
0.70 0.15 0.15
Matches are distributed among these distances:
2 17 0.11
3 128 0.80
4 16 0.10
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19532907 original size:38 final size:38
Alignment explanation
Indices: 19532865--19532940 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 38
19532855 ATTTAAAGAG
19532865 TAATAGGTAAAAATAATATAATAGTAATAATAACAATATAA
1 TAATA-GTAAAAA-AA-ATAATAGTAATAATAACAATATAA
* *
19532906 TAATAGTAATAAAAATAATAGTAATAATAATAATA
1 TAATAGTAAAAAAAATAATAGTAATAATAACAATA
19532941 ATATATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 20 0.61
39 2 0.06
40 6 0.18
41 5 0.15
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (38 bp):
TAATAGTAAAAAAAATAATAGTAATAATAACAATATAA
Found at i:19547603 original size:23 final size:23
Alignment explanation
Indices: 19547573--19547616 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19547563 GTCTCATATA
* *
19547573 TTATTTATTTTACATTGTTTTAT
1 TTATTTATTTTAAATTCTTTTAT
19547596 TTATTTATTTTAAATTCTTTT
1 TTATTTATTTTAAATTCTTTT
19547617 TATATGTTAT
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:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTTATTTTAAATTCTTTTAT
Found at i:19547626 original size:23 final size:23
Alignment explanation
Indices: 19547569--19547651 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
19547559 AATTGTCTCA
* *
19547569 TATATTATTTATTTTACATTGTTT
1 TATA-TATTTATTTTAAATTCTTT
*
19547593 TATTTATTTATTTTAAATTCTTT
1 TATATATTTATTTTAAATTCTTT
* *
19547616 T-TATATGTTATTTCTGAATTGTTAT
1 TATATAT-TTATTT-TAAATTCTT-T
*
19547641 TATAAATTTAT
1 TATATATTTAT
19547652 ATATATGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.08
23 24 0.50
24 10 0.21
25 6 0.12
26 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (23 bp):
TATATATTTATTTTAAATTCTTT
Found at i:19547635 original size:24 final size:23
Alignment explanation
Indices: 19547592--19547644 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
19547582 TTACATTGTT
19547592 TTATT-TAT-TTATTTTAAATTC
1 TTATTATATGTTATTTTAAATTC
* * *
19547613 TTTTTATATGTTATTTCTGAATTG
1 TTATTATATGTTATTT-TAAATTC
19547637 TTATTATA
1 TTATTATA
19547645 AATTTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 6 0.24
24 12 0.48
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (23 bp):
TTATTATATGTTATTTTAAATTC
Found at i:19547671 original size:25 final size:25
Alignment explanation
Indices: 19547644--19547734 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 25
19547634 TTGTTATTAT
* *
19547644 AAATTTATATATATGGTTTATTCTTA
1 AAATTTTTATATATTGTTTATT-TTA
* * *
19547670 AAATTTTTTTATAGATTATTTATTTTC
1 AAA--TTTTTATATATTGTTTATTTTA
19547697 AAATTTTTATATATTGTTTATTTTA
1 AAATTTTTATATATTGTTTATTTTA
*
19547722 AACACTTTTATAT
1 AA-ATTTTTATAT
19547735 TTTTACATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 21 0.40
26 12 0.23
27 5 0.09
28 15 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
AAATTTTTATATATTGTTTATTTTA
Found at i:19549865 original size:8 final size:8
Alignment explanation
Indices: 19549852--19549882 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19549842 ATTTAAGTAA
19549852 ATATTATT
1 ATATTATT
19549860 ATATTATT
1 ATATTATT
*
19549868 AAATTATT
1 ATATTATT
19549876 ATATTAT
1 ATATTAT
19549883 ATTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATTATT
Found at i:19549900 original size:49 final size:48
Alignment explanation
Indices: 19549811--19549903 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
19549801 ATAATATACA
* *
19549811 TATATTAGTAAATATTATATATTTACTTATAATTTAAGTAAATATTAT
1 TATATTAGTAAATATTATATATTTAATTATAATTAAAGTAAATATTAT
*
19549859 TATATTATTAAATTATTATATTATATTAATTA-AA-TAAAGTAAATA
1 TATATTAGTAAA-TATTATA-TAT-TTAATTATAATTAAAGTAAATA
19549904 AATTAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
48 11 0.28
49 17 0.44
50 5 0.13
51 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (48 bp):
TATATTAGTAAATATTATATATTTAATTATAATTAAAGTAAATATTAT
Found at i:19550072 original size:5 final size:4
Alignment explanation
Indices: 19550024--19550117 Score: 52
Period size: 4 Copynumber: 22.8 Consensus size: 4
19550014 ATAATAAACA
* *
19550024 AAAG AAAC ATAAG AAAG AAAA AAAG -AAG -AAG AACAG AATAG AAACG
1 AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AA-AG AA-AG AAA-G
* **
19550070 AAAG AAA- ACAGG GGAG AAAG AAAG AAAGG AAA- AAGAG AAAG AAAG AAA
1 AAAG AAAG A-AAG AAAG AAAG AAAG AAA-G AAAG AA-AG AAAG AAAG AAA
19550118 AGGGAGAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
3 9 0.13
4 40 0.57
5 21 0.30
ACGTcount: A:0.69, C:0.04, G:0.24, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:19550112 original size:25 final size:24
Alignment explanation
Indices: 19550034--19550117 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
19550024 AAAGAAACAT
* *
19550034 AAGAAAGAAAAAAAGAAGAAGA-A
1 AAGAAAGAAAGAAAGAAAAAGAGA
* *
19550057 CAGAATAGAAACGAAAGAAAACAG-GG
1 AAGAA-AGAAA-GAAAGAAAA-AGAGA
*
19550083 GAGAAAGAAAGAAAGGAAAAAGAGA
1 AAGAAAGAAAGAAA-GAAAAAGAGA
19550108 AAGAAAGAAA
1 AAGAAAGAAA
19550118 AGGGAGAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.08
24 11 0.23
25 27 0.56
26 6 0.12
ACGTcount: A:0.69, C:0.04, G:0.26, T:0.01
Consensus pattern (24 bp):
AAGAAAGAAAGAAAGAAAAAGAGA
Found at i:19551080 original size:40 final size:40
Alignment explanation
Indices: 19550982--19551097 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 40
19550972 CCTTCTCGAG
*
19550982 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTA-AAGA
1 AATT-AAAGTGGATAGGATTTATTCCTGATTCACTATAAGA
19551022 AATTAAAGT-GAGTAGGATTTATTCCTGATTCACTATAA-A
1 AATTAAAGTGGA-TAGGATTTATTCCTGATTCACTATAAGA
* *
19551061 TATATAAAGTGGATAGGATTTGTTCCTGATTCACTAT
1 AAT-TAAAGTGGATAGGATTTATTCCTGATTCACTAT
19551098 GGTAACTCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
38 1 0.01
39 31 0.45
40 35 0.51
41 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (40 bp):
AATTAAAGTGGATAGGATTTATTCCTGATTCACTATAAGA
Found at i:19551117 original size:40 final size:38
Alignment explanation
Indices: 19550987--19551121 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 38
19550977 TCGAGAATTA
* *
19550987 AAAGTGAATAGGATTTATTCCTGATTCACTAAAGAAATT
1 AAAGTGAATAGGATTTATTCCTGATTCACTATAGTAA-T
* *
19551026 AAAGTGAGTAGGATTTATTCCTGATTCACTATAAATATAT
1 AAAGTGAATAGGATTTATTCCTGATTCACTAT-AGTA-AT
* * *
19551066 AAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
1 AAAGTGAATAGGATTTATTCCTGATTCACTATAGTAA-T
*
19551105 CAAGGTGAATAGGATTT
1 -AAAGTGAATAGGATTT
19551122 TCCCTAAATG
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 33 0.41
40 46 0.57
41 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (38 bp):
AAAGTGAATAGGATTTATTCCTGATTCACTATAGTAAT
Found at i:19558183 original size:25 final size:22
Alignment explanation
Indices: 19558155--19558207 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
19558145 TTAAATAAGA
19558155 ATAAGACAAGTTTAAAATAATATAT
1 ATAAGA-AA-TTTAAAATAA-ATAT
19558180 ATAAAGAAATTTAAAATAAATAT
1 AT-AAGAAATTTAAAATAAATAT
19558203 -TAAGA
1 ATAAGA
19558208 GGCTCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.15
22 1 0.04
23 4 0.15
24 10 0.37
25 4 0.15
26 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (22 bp):
ATAAGAAATTTAAAATAAATAT
Found at i:19558196 original size:24 final size:23
Alignment explanation
Indices: 19558165--19558262 Score: 76
Period size: 24 Copynumber: 4.1 Consensus size: 23
19558155 ATAAGACAAG
*
19558165 TTTAAAATAATATATATAAAGAAA
1 TTTAAAATAA-ATATGTAAAGAAA
**
19558189 TTTAAAATAAATAT-T-AAGAGG
1 TTTAAAATAAATATGTAAAGAAA
* *
19558210 CTCAAAATAATAATATGTAAAAGAAA
1 TTTAAAAT-A-AATATGT-AAAGAAA
19558236 -TTAAAATAAATAATGTATAAGAAA
1 TTTAAAATAAAT-ATGTA-AAGAAA
19558260 TTT
1 TTT
19558263 TAAAGTGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
21 10 0.17
22 2 0.03
23 13 0.22
24 22 0.37
25 8 0.14
26 4 0.07
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (23 bp):
TTTAAAATAAATATGTAAAGAAA
Found at i:19558247 original size:26 final size:26
Alignment explanation
Indices: 19558213--19558405 Score: 74
Period size: 26 Copynumber: 7.4 Consensus size: 26
19558203 TAAGAGGCTC
19558213 AAAAT-AATAATATGTAAAAGAAATT
1 AAAATAAATAATATGTAAAAGAAATT
*
19558238 AAAATAAAT-A-ATGTATAAGAAATTTT
1 AAAATAAATAATATGTAAAAGAAA--TT
* * * * * *
19558264 AAAGTGAATAACATGCAAAATAATTT
1 AAAATAAATAATATGTAAAAGAAATT
** * ** **
19558290 AAACCAAGTAATACATATAAA-ACTTT
1 AAAATAAATAATATGTA-AAAGAAATT
* * ** *
19558316 AAAATAGATGATATACACAAAG-ATTT
1 AAAATAAATAATATGTA-AAAGAAATT
* *
19558342 AAAATAAATCATATGTAAAAAAAAACTT
1 AAAATAAATAATATGT-AAAAGAAA-TT
* *
19558370 AAAATAATTAATATGTAAAAGTAATAT
1 AAAATAAATAATATGTAAAAGAAAT-T
19558397 AAAA-AAATA
1 AAAATAAATA
19558406 CATAATATAT
Statistics
Matches: 121, Mismatches: 36, Indels: 21
0.68 0.20 0.12
Matches are distributed among these distances:
24 11 0.09
25 6 0.05
26 63 0.52
27 17 0.14
28 24 0.20
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAATAAATAATATGTAAAAGAAATT
Found at i:19562644 original size:44 final size:44
Alignment explanation
Indices: 19562619--19562893 Score: 175
Period size: 44 Copynumber: 6.2 Consensus size: 44
19562609 GCTATTAGCT
*
19562619 TTATCTCCCTGAGGTAGCAAGAGAGCAGGCTGAAGATTGTAGTC
1 TTATCTCCCTGAGGTAGCAAGAGAGCAGACTGAAGATTGTAGTC
* * *
19562663 TTATCTTCCTGAGGTAGCAAG-GAAGTAGACTGAAGATTGAAGATC
1 TTATCTCCCTGAGGTAGCAAGAG-AGCAGACTGAAGATTGTAG-TC
* * * * * *
19562708 TTATCTCCCTGAGATAGC-AGTGGAGTAGA-TCGAAGATGGCGAATC
1 TTATCTCCCTGAGGTAGCAAG-AGAGCAGACT-GAAGATTG-TAGTC
** * * * * ***** *
19562753 TTATCTTTAC-GAGCTAGCAGGGGAGCAGA-TTATAGCCACCAGCC
1 TTATC-TCCCTGAGGTAGCAAGAGAGCAGACTGA-AGATTGTAGTC
* **
19562797 TTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTC
1 TTATCTCCCTGAGGTAGCAAGAGAGCAGACTGAAGATTGTAGTC
* * *
19562841 TTATCTTCCTAAGGTAGCAAG-GAAACAGACTGAAGATTGTAGATC
1 TTATCTCCCTGAGGTAGCAAGAG-AGCAGACTGAAGATTGTAG-TC
19562886 TTATCTCC
1 TTATCTCC
19562894 TTAAGCAGTA
Statistics
Matches: 176, Mismatches: 42, Indels: 25
0.72 0.17 0.10
Matches are distributed among these distances:
43 4 0.02
44 101 0.57
45 66 0.38
46 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAGGTAGCAAGAGAGCAGACTGAAGATTGTAGTC
Found at i:19562726 original size:89 final size:89
Alignment explanation
Indices: 19562619--19562893 Score: 254
Period size: 89 Copynumber: 3.1 Consensus size: 89
19562609 GCTATTAGCT
*
19562619 TTATCTCCCTGAGGTAGCAAGAGAGCAGGCTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAG
1 TTATCTCCCTGAGGTAGCAAGAGAGCAGGATGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAG
*
19562684 GAAGTAGACTGAAGATTGAAGATC
66 GAAGCAGACTGAAGATTGAAGATC
* * * * * * * *
19562708 TTATCTCCCTGAGATAGC-AGTGGAGTA-GATCGAAGATGGCGAATCTTATCTTTAC-GAGCTAG
1 TTATCTCCCTGAGGTAGCAAG-AGAGCAGGAT-GAAGATTG-TAGTCTTATC-TTCCTGAGGTAG
* * * ***** *
19562770 CAGGGGAGCAGA-TTATAGCCACCAG-CC
62 CAAGGAAGCAGACTGA-AGATTGAAGATC
* * *
19562797 TTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAG
1 TTATCTCCCTGAGGTAGCAAGAGAGCAGGATGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAG
* *
19562862 GAAACAGACTGAAGATTGTAGATC
66 GAAGCAGACTGAAGATTGAAGATC
19562886 TTATCTCC
1 TTATCTCC
19562894 TTAAGCAGTA
Statistics
Matches: 135, Mismatches: 41, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
87 3 0.02
88 30 0.22
89 68 0.50
90 31 0.23
91 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (89 bp):
TTATCTCCCTGAGGTAGCAAGAGAGCAGGATGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAG
GAAGCAGACTGAAGATTGAAGATC
Found at i:19562920 original size:44 final size:43
Alignment explanation
Indices: 19562883--19563558 Score: 154
Period size: 44 Copynumber: 15.6 Consensus size: 43
19562873 AAGATTGTAG
*
19562883 ATCTTATCTCCTTAAGCAGTAGTGGAGCAAATAGAAGACAATGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGA-AATGA
* * ** ** **
19562927 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCA-CC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATGA
* **
19562969 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGGCT-GAAGATTACA-G-
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-AATAGAAGA--A-ATGA
* * * * * *
19563013 ATCTAATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGACGATGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGA-AATGA
* * * * * ** ** **
19563057 ATTTTATCTCCTTAAGCAATAGTGGAGTAGATTTAAGCCA-CC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATGA
* * * **
19563099 ATCCTATCTCTCTAAGCAGTAGTGGAGTAGGCT-GAAGATTACA-G-
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-AATAGAAGA--A-ATGA
* * ***
19563143 ATCTTATTTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGA-AATGA
* * * * ** * **
19563187 ATCTTTTCTCTCTAAGCAGTAGTGGAGTAGATTTAAGCAA-CC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATGA
* * * * ** *
19563229 ATCCTAACTCTCTAAACAGTAGTGGAATATGATA-AAGATTACA-G-
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-AATAGAAGA--A-ATGA
* * * *
19563273 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGA-AATGA
* * * ** ** **
19563317 ATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTTAAGCTA-CC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATGA
* * * * **
19563359 ATCCTATCTCCCTAAGTAGTAGTGAAGTAGGCT-GAAGATTACA-G-
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-AATAGAAGA--A-ATGA
* * **
19563403 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCA-AAGACAGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAAT-AGAAGA-AATGA
* ** * *
19563447 ATCTTATCTCCCTAAACAGTAGT--AG--AATAGATTTAAGTCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGA-AGAAATGA
* * ** * *
19563487 CCATCCTATCTCCCTAAGCAGTAGTGGAGTATGTTGAAG-ATTGCAA
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATG--A
19563533 ATCTTATCTCCCTAAGCAGTAGTGGA
1 ATCTTATCTCCCTAAGCAGTAGTGGA
19563559 ACAGATTTAA
Statistics
Matches: 471, Mismatches: 122, Indels: 78
0.70 0.18 0.12
Matches are distributed among these distances:
39 1 0.00
40 6 0.01
41 1 0.00
42 137 0.29
43 25 0.05
44 293 0.62
45 4 0.01
46 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATAGAAGAAATGA
Found at i:19562985 original size:86 final size:86
Alignment explanation
Indices: 19562883--19563604 Score: 464
Period size: 86 Copynumber: 8.3 Consensus size: 86
19562873 AAGATTGTAG
* * * *
19562883 ATCTTATCTCCTTAAGCAGTAGTGGAGCAAATAGAAGACAATGAATCTTGTCTCCCTAAGCAGTA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGACAA-GAATCTTATCTCCCTAAGCAGTA
* *
19562948 GTGGAGCAGATTTAAG-CCACC
65 GTGGAGTAGATTGAAGACCACC
* * * *
19562969 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGGCT-GAAGATTACAG-ATCTAATCTCCCTAGGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GATAGAAGA-CA-AGAATCTTATCTCCCTAAGCAG
* * **
19563032 TAGTGGAGTAGATCGAAGACGATGA
63 TAGTGGAGTAGATTGAAGACCA-CC
* * * ** * ** * *
19563057 ATTTTATCTCCTTAAGCAATAGTGGAGTAGATTTAAG-CCACCATCCTATCTCTCTAAGCAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGACAAGAATCTTATCTCCCTAAGCAGTAG
** ** *
19563121 TGGAGTAGGCTGAAGATTACAG
66 TGGAGTAGATTGAAGACCAC-C
* * * * ** * *
19563143 ATCTTATTTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGAATCTTTTCTCTCTAAGCAGTA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGAC-AAGAATCTTATCTCCCTAAGCAGTA
* *
19563208 GTGGAGTAGATTTAAG-CAACC
65 GTGGAGTAGATTGAAGACCACC
* * * * * *
19563229 ATCCTAACTCTCTAAACAGTAGTGGAATATGATA-AAGATTACAG-ATCTTATCTCCCTAAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GATAGAAGA-CA-AGAATCTTATCTCCCTAAGCAG
* * * *
19563292 TAGTGGAGCAGATCGAAGACGACGA
63 TAGTGGAGTAGATTGAAGACCAC-C
* ** * ** * *
19563317 ATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTTAAG-CTACCATCCTATCTCCCTAAGTAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGACAAGAATCTTATCTCCCTAAGCAGTAG
* ** ** *
19563381 TGAAGTAGGCTGAAGATTACAG
66 TGGAGTAGATTGAAGACCAC-C
* * * *
19563403 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCA-AAGACAGCGAATCTTATCTCCCTAAACAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGAT-AGAAGACA-AGAATCTTATCTCCCTAAGCAGT
* * * *
19563467 AGTAGAATAGATTTAAG-TCACC
64 AGTGGAGTAGATTGAAGACCACC
* *
19563489 ATCCTATCTCCCTAAGCAGTAGTGGAGTATG-TTGAAGATTGC-A-AATCTTATCTCCCTAAGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GATAGAAGA---CAAGAATCTTATCTCCCTAAGCA
** * *
19563551 GTAGTGGAACAGATTTAAG-CCAAC
62 GTAGTGGAGTAGATTGAAGACCACC
* **
19563575 ATCCTATCTCCCTAAGCAGCGGTGGAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAG
19563605 GTTGAAATCA
Statistics
Matches: 487, Mismatches: 124, Indels: 51
0.74 0.19 0.08
Matches are distributed among these distances:
85 3 0.01
86 343 0.70
87 24 0.05
88 116 0.24
89 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (86 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGACAAGAATCTTATCTCCCTAAGCAGTAG
TGGAGTAGATTGAAGACCACC
Found at i:19563015 original size:130 final size:130
Alignment explanation
Indices: 19562870--19563604 Score: 963
Period size: 130 Copynumber: 5.7 Consensus size: 130
19562860 AGGAAACAGA
** * * * * * *
19562870 CTGAAGATTGTAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATAGAAGACAATGAATCTTGTC
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
* *
19562935 TCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCTTATCTCCCTAAGCAGTAGTGGAGTAGG
66 TCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGG
* * * * *
19563000 CTGAAGATTACAGATCTAATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGACGATGAATTTTATC
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
* * *
19563065 TCCTTAAGCAATAGTGGAGTAGATTTAAGCCACCATCCTATCTCTCTAAGCAGTAGTGGAGTAGG
66 TCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGG
* * * *
19563130 CTGAAGATTACAGATCTTATTTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGAATCTTTTC
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
* * * * * * *
19563195 TCTCTAAGCAGTAGTGGAGTAGATTTAAGCAACCATCCTAACTCTCTAAACAGTAGTGGAATATG
66 TCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGG
* * *
19563260 ATAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATTTTATC
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
* * *
19563325 TCCCTAAGCAGTAGTGGAGTAGATTTAAGCTACCATCCTATCTCCCTAAGTAGTAGTGAAGTAGG
66 TCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGG
* *
19563390 CTGAAGATTACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGAC-AGCGAATCTTAT
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CGAATCTTAT
* * * * *
19563454 CTCCCTAAACAGTAGTAGAATAGATTTAAGTCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAT
65 CTCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAG
19563519 G
130 G
* * * * ** * * *
19563520 TTGAAGATTGCAAATCTTATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCAAC--ATCCTATC
1 CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
**
19563583 TCCCTAAGCAGCGGTGGAGTAG
66 TCCCTAAGCAGTAGTGGAGTAG
19563605 GTTGAAATCA
Statistics
Matches: 527, Mismatches: 76, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
128 24 0.05
129 1 0.00
130 501 0.95
131 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (130 bp):
CTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATC
TCCCTAAGCAGTAGTGGAGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGG
Found at i:19563626 original size:216 final size:216
Alignment explanation
Indices: 19563187--19563628 Score: 511
Period size: 216 Copynumber: 2.0 Consensus size: 216
19563177 AAGACGGCGA
* * ** * *
19563187 ATCTTTTCTCTCTAAGCAGTAGTGGAGTAGATTTAAGCAACCATCCTAACTCTCTAAACAGTAGT
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGCAACAATCCTAACTCCCTAAACAGTAGT
* * * * *
19563252 GGAATATGATAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
66 AGAATATGATAAAGATCACACATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
* ** * * * *
19563317 ATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTTAAGCTACCATCCTATCTCCCTAAGTAGTAGT
131 ATCTTATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCAACATCCTATCTCCCTAAGCAGCAGT
*
19563382 GAAGTAGGCTGAAGATTACAG
196 GAAGTAGGCTGAAGATAACAG
* * *
19563403 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACAGCGAATCTTATCTCCCTAAACAGTA
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAG-CAAC-AATCCTAACTCCCTAAACAGTA
* * * *
19563468 GTAGAATA-GATTTAAG-TCAC-CATCCTATCTCCCTAAGCAGTAGTGGAGTATG-TTGAAGATT
64 GTAGAATATGA-TAAAGATCACACATCCTATCTCCCTAAGCAGTAGTGGAGCA-GATCGAAGA-C
19563529 G-CAAATCTTATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCAACATCCTATCTCCCTAAGCA
126 GACAAATCTTATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCAACATCCTATCTCCCTAAGCA
* * *
19563593 GCGGTGGAGTAGGTTGAA-ATCAAC-G
191 GCAGTGAAGTAGGCTGAAGAT-AACAG
19563618 ATTCTTATCTC
1 A-TCTTATCTC
19563629 CTTAAAGTTT
Statistics
Matches: 190, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
215 4 0.02
216 147 0.77
217 10 0.05
218 29 0.15
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (216 bp):
ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGCAACAATCCTAACTCCCTAAACAGTAGT
AGAATATGATAAAGATCACACATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
ATCTTATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCAACATCCTATCTCCCTAAGCAGCAGT
GAAGTAGGCTGAAGATAACAG
Found at i:19563845 original size:44 final size:44
Alignment explanation
Indices: 19563797--19564046 Score: 130
Period size: 44 Copynumber: 5.5 Consensus size: 44
19563787 AGACACCAAT
*
19563797 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTA-TTAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-TAGTGAAC
* * * * *
19563841 CTTATCT-CTTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAGTGAAC
* * * * *
19563885 CTCATCTCCCTGAAGTTGTAGTGG-GTCAGATTAAAGCTACAAATCACAAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAA---A-TAGT--GAA-C
* * * * **
19563936 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTA-CGAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAGTGAAC
* * * * * ** *
19563980 CTTATCTCTCTAAAGTTGCAATGGAGTAGACTAAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAGTGAAC
*
19564025 CTTATCTCTCTGAAGTTGCAGT
1 CTTATCTCCCTGAAGTTGCAGT
19564047 AGAACCGATT
Statistics
Matches: 154, Mismatches: 39, Indels: 25
0.71 0.18 0.11
Matches are distributed among these distances:
43 22 0.14
44 54 0.35
45 42 0.27
47 1 0.01
48 3 0.02
50 2 0.01
51 29 0.19
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAGTGAAC
Found at i:19563886 original size:88 final size:88
Alignment explanation
Indices: 19563709--19563919 Score: 239
Period size: 88 Copynumber: 2.4 Consensus size: 88
19563699 AGCCAAAAAC
* * * * *
19563709 CTCATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAATTACAAGTCTTATCTTCTTGAAGTTACAA
1 CTCATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAAGCCTTATCTTCTTGAAGTTACAA
* *
19563774 TGGAGCGGACTGAAGACACCAAT
66 TGGAACAGACTGAAGACACCAAT
* * *
19563797 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTATTAA-CCTTATC-TCTTGAAGTTGCA
1 CTCATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTA-CAAGCCTTATCTTCTTGAAGTTACA
* * **
19563860 GTGGAACAGACTGAAGATAGTGAAT
65 ATGGAACAGACTGAAGACA-CCAAT
*
19563885 CTCATCTCCCTGAAGTTGTAGTGG-GTCAGATTAAA
1 CTCATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAA
19563920 GCTACAAATC
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
87 28 0.27
88 74 0.71
89 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (88 bp):
CTCATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAAGCCTTATCTTCTTGAAGTTACAA
TGGAACAGACTGAAGACACCAAT
Found at i:19563970 original size:139 final size:140
Alignment explanation
Indices: 19563797--19564069 Score: 341
Period size: 140 Copynumber: 2.0 Consensus size: 140
19563787 AGACACCAAT
* ** * *
19563797 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTATTAACCTTATCTCT-TGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATTACGAACCTTATCTCTCTAAAGTTGCAA
* ** * * **
19563861 TGGAACAGACTGAAGATAGTGAATCTCATCTCCCTGAAGTTGTAGTGGGTCAGATTAAAGCTACA
66 TGGAACAGACTAAAGATAGCAAATCTCATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCTACA
19563926 AATCACAAGC
131 AATCACAAGC
* * **
19563936 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACGAGTCTTATCTCTCTAAAGTTGCAA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATTACGAACCTTATCTCTCTAAAGTTGCAA
** * * * *
19564001 TGGAGTAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAACCGATTAAAGCTATA
66 TGGAACAGACTAAAGATAGCAAATCTCATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCTACA
19564066 AATC
131 AATC
19564070 CTATACCTCT
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
139 46 0.41
140 65 0.59
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (140 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATTACGAACCTTATCTCTCTAAAGTTGCAA
TGGAACAGACTAAAGATAGCAAATCTCATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCTACA
AATCACAAGC
Found at i:19564060 original size:45 final size:44
Alignment explanation
Indices: 19563936--19564092 Score: 145
Period size: 44 Copynumber: 3.5 Consensus size: 44
19563926 AATCACAAGC
* * * * * *
19563936 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACGAGT
1 CTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGATACAAAT
* * * *
19563980 CTTATCTCTCTAAAGTTGCAATGGAGTAGACTAAAGATAGCAAAT
1 CTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGATA-CAAAT
* * * * *
19564025 CTTATCTCTCTGAAGTTGCAGTAGAACCGATTAAAGCTATAAAT
1 CTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGATACAAAT
*
19564069 CCTATAC-CTCTAAAGTTGCAGTAG
1 CTTAT-CTCTCTAAAGTTGCAGTAG
19564093 GTCGGATCAA
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
44 55 0.61
45 35 0.39
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGATACAAAT
Found at i:19564168 original size:227 final size:220
Alignment explanation
Indices: 19563697--19564271 Score: 536
Period size: 227 Copynumber: 2.5 Consensus size: 220
19563687 AGAGCGACTC
* * *
19563697 GAAGCCAAAAACCTCATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAA-TTACAAGTCTTATCT-
1 GAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTT-AAAGTTACAAGTCTTATCTC
* * * * * *
19563760 TCTTGAAGTTACAATGGAGCGGACTGAAGACA-CCAATCTTATCTCCCTGAAGTTGCAGTGGAGC
65 TC-TAAAGTTACAATGGAGCAGACTGAAGAAAGCAAATCTTATCT-CCTGAAGTTGCAGTAGAAC
* * * * * *
19563824 AGATTAAAATTATTAACCTTATCTCTTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTCA
128 AGATTAAAACTATAAACCTTACCTCTTAAAGTTGCAGTGGAACAAACTGAACATAGTGAATCTCA
*
19563889 TCTCCCTGAAGTTGTAGTGGGTCAGATT
193 TCTCCCTGAAGTTGTAGCGGGTCAGATT
* *
19563917 AAAGCTACAAATCACAAGCCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACGAGTCT
1 GAAGC--C--A-CA-AA-CCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACAAGTCT
* * * *
19563982 TATCTCTCTAAAGTTGCAATGGAGTAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGT
59 TATCTCTCTAAAGTTACAATGGAGCAGACTGAAGAAAGCAAATCTTATCTC-CTGAAGTTGCAGT
* * * *
19564047 AGAACCGATTAAAGCTATAAATCCTATACCTC-TAAAGTTGCAGTAGGTCGGATCAAACCT-ACC
123 AGAACAGATTAAAACTATAAA-CCT-TACCTCTTAAAGTTGC---A-GT-GGAACAAA-CTGAAC
* * *
19564110 ATGGTGAATCTTATCTCCTTGAAGTTGTAGCGGAGT-AGATT
180 ATAGTGAATCTCATCTCCCTGAAGTTGTAGCGG-GTCAGATT
* * * * *
19564151 GAAGCCACAAACCTTATC-CTCGTGAAGTTGCAGTGGGGCAAGTTGAAGTTACAAGTCTTATCTC
1 GAAGCCACAAACCTTATCTC-CCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACAAGTCTTATCTC
* ** * *
19564215 CCTGAAA-TTACTGTGGAGCAGATTGAAGAAAGCAGATCTTATCTCCTTGAAGTTGCA
65 TCT-AAAGTTACAATGGAGCAGACTGAAGAAAGCAAATCTTATCTCC-TGAAGTTGCA
19564272 ATGGAGCAGA
Statistics
Matches: 288, Mismatches: 44, Indels: 39
0.78 0.12 0.11
Matches are distributed among these distances:
220 4 0.01
222 1 0.00
224 1 0.00
225 1 0.00
226 7 0.02
227 156 0.54
228 46 0.16
229 13 0.05
230 6 0.02
232 2 0.01
233 2 0.01
234 45 0.16
235 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (220 bp):
GAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAGTTACAAGTCTTATCTCT
CTAAAGTTACAATGGAGCAGACTGAAGAAAGCAAATCTTATCTCCTGAAGTTGCAGTAGAACAGA
TTAAAACTATAAACCTTACCTCTTAAAGTTGCAGTGGAACAAACTGAACATAGTGAATCTCATCT
CCCTGAAGTTGTAGCGGGTCAGATT
Found at i:19566084 original size:27 final size:26
Alignment explanation
Indices: 19566047--19566134 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 26
19566037 TTCTGAATTG
* * *
19566047 TTATTATAAATTTATATATATATGGT
1 TTATTTTAAATTTTTATATATATGAT
* * *
19566073 TTATTCTTAAATTTTTTTATAGATTAT
1 TTATT-TTAAATTTTTATATATATGAT
19566100 TTATTTTCAAATTTTTATATAT-TG-T
1 TTATTTT-AAATTTTTATATATATGAT
*
19566125 CTATTTTAAA
1 TTATTTTAAA
19566135 CACTTTTATA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
24 3 0.06
25 7 0.14
26 8 0.16
27 32 0.64
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (26 bp):
TTATTTTAAATTTTTATATATATGAT
Found at i:19566129 original size:25 final size:26
Alignment explanation
Indices: 19566086--19566145 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
19566076 TTCTTAAATT
* * *
19566086 TTTTTATAGATTATTTATTTTCAA-A
1 TTTTTATATATTATCTATTTTAAACA
*
19566111 TTTTTATATATTGTCTATTTTAAACA
1 TTTTTATATATTATCTATTTTAAACA
*
19566137 CTTTTATAT
1 TTTTTATAT
19566146 TTTTACATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTTATATATTATCTATTTTAAACA
Found at i:19569071 original size:131 final size:131
Alignment explanation
Indices: 19568898--19569144 Score: 413
Period size: 131 Copynumber: 1.9 Consensus size: 131
19568888 TCATTCAAAA
* * * *
19568898 ATTCTTCAAAACGAAGGCGAGATTCGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGG
1 ATTCTCCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGG
* *
19568963 GTTGCAATTTCGCGTTTGTTCGAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
66 GTTGCAATTTCGAGTTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
19569028 G
131 G
19569029 ATTCTCCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGG
1 ATTCTCCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGG
* * *
19569094 GTTGCAATTTCGAGTTTGTTCAAAATAATCGAGTATCCCTTTAAAATTTCA
66 GTTGCAATTTCGAGTTTGTTCAAAATAATCGAATATCACTTCAAAATTTCA
19569145 ATAATTTAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 107 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (131 bp):
ATTCTCCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGG
GTTGCAATTTCGAGTTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
G
Found at i:19570991 original size:29 final size:31
Alignment explanation
Indices: 19570916--19570993 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 31
19570906 ATTTTTTAAA
19570916 ATTTGAAAAATA-AAAAATACATATAAAAATT
1 ATTT-AAAAATATAAAAATACATATAAAAATT
19570947 ATTTATAAAA-ATTAAAAAT-CAT-T-AAAATT
1 ATTTA-AAAATA-TAAAAATACATATAAAAATT
19570976 ATTTAAAAATTATAAAAA
1 ATTTAAAAA-TATAAAAA
19570994 ATATAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
28 4 0.10
29 17 0.40
30 4 0.10
31 11 0.26
32 6 0.14
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (31 bp):
ATTTAAAAATATAAAAATACATATAAAAATT
Found at i:19574527 original size:141 final size:141
Alignment explanation
Indices: 19574272--19574557 Score: 511
Period size: 141 Copynumber: 2.0 Consensus size: 141
19574262 TAGGTGAGAG
*
19574272 GGTTCTTGTTTGGCGGCTTATACTTTAATAACATTTCCAGGTTTTTTCTCTTCTTTTTTGGCTGT
1 GGTTCTTGTTTGGCGGCTCATACTTTAATAACATTTCCAGGTTTTTTCTCTTCTTTTTTGGCTGT
*
19574337 CCCACTGCTAACTGCTTAATTAGTCGGTCAGCTCCTTTCTAAAATAAGATATATAGAAGATGTAA
66 CCCACTGCTAACTACTTAATTAGTCGGTCAGCTCCTTTCTAAAATAAGATATATAGAAGATGTAA
19574402 TAAAAAAATTTA
131 T-AAAAAATTTA
*
19574414 GGTTCTTGTTTGGCGGCTCATACTTTAATAACATTTCCAGGTTTTTT-TGTTCTTTTTTGGCTGT
1 GGTTCTTGTTTGGCGGCTCATACTTTAATAACATTTCCAGGTTTTTTCTCTTCTTTTTTGGCTGT
*
19574478 CCCACTGCTAACTACTTAATTAGTCGGTCAGCTCCTTTCTAAAATAAGATATATAGAGGATGTAA
66 CCCACTGCTAACTACTTAATTAGTCGGTCAGCTCCTTTCTAAAATAAGATATATAGAAGATGTAA
*
19574543 TAAAAAATTTT
131 TAAAAAATTTA
19574554 GGTT
1 GGTT
19574558 GGTTAAAATT
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
140 13 0.09
141 80 0.58
142 46 0.33
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (141 bp):
GGTTCTTGTTTGGCGGCTCATACTTTAATAACATTTCCAGGTTTTTTCTCTTCTTTTTTGGCTGT
CCCACTGCTAACTACTTAATTAGTCGGTCAGCTCCTTTCTAAAATAAGATATATAGAAGATGTAA
TAAAAAATTTA
Found at i:19574635 original size:17 final size:17
Alignment explanation
Indices: 19574596--19574638 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
19574586 TAAGTAAAAA
19574596 TGTAATTTTATTATTTT
1 TGTAATTTTATTATTTT
**
19574613 AATAATTTATATT-TTTT
1 TGTAATTT-TATTATTTT
19574630 TGTAATTTT
1 TGTAATTTT
19574639 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
TGTAATTTTATTATTTT
Found at i:19575021 original size:28 final size:27
Alignment explanation
Indices: 19574990--19575107 Score: 84
Period size: 28 Copynumber: 4.3 Consensus size: 27
19574980 CATAAAAATG
19574990 TTATAAAAAATTAAAAATATATATAAA
1 TTATAAAAAATTAAAAATATATATAAA
** *
19575017 CTTATAAAACCTATAAAAAT-TATAAAAA
1 -TTATAAAAAAT-TAAAAATATATATAAA
*
19575045 CTTATAATAAATTATACAAATAGTA-A-AAA
1 -TTATAAAAAATTA-A-AAATA-TATATAAA
*
19575074 --ATAAAACATATTAAAAATATTTATAAA
1 TTATAAAA-A-ATTAAAAATATATATAAA
19575101 TTATAAA
1 TTATAAA
19575108 TATTATAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
25 1 0.01
26 11 0.15
27 7 0.10
28 30 0.42
29 19 0.27
30 1 0.01
31 2 0.03
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (27 bp):
TTATAAAAAATTAAAAATATATATAAA
Found at i:19575035 original size:10 final size:10
Alignment explanation
Indices: 19575009--19575060 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
19574999 ATTAAAAATA
*
19575009 TATATAAACT
1 TATAAAAACT
*
19575019 TAT-AAAACC
1 TATAAAAACT
19575028 TATAAAAA-T
1 TATAAAAACT
19575037 TATAAAAACT
1 TATAAAAACT
19575047 TATAATAAA-T
1 TATAA-AAACT
19575057 TATA
1 TATA
19575061 CAAATAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 15 0.42
10 18 0.50
11 3 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (10 bp):
TATAAAAACT
Found at i:19575040 original size:9 final size:9
Alignment explanation
Indices: 19574973--19575185 Score: 105
Period size: 9 Copynumber: 22.9 Consensus size: 9
19574963 ATTTCCTCAT
*
19574973 TAAAAATCA
1 TAAAAATTA
19574982 TAAAAATGTTA
1 TAAAAA--TTA
*
19574993 TAAAAAAT-
1 TAAAAATTA
19575001 TAAAAATATA
1 TAAAAAT-TA
*
19575011 TATAAACTTA
1 TA-AAAATTA
**
19575021 TAAAACCTA
1 TAAAAATTA
19575030 TAAAAATTA
1 TAAAAATTA
19575039 TAAAAACTTA
1 TAAAAA-TTA
19575049 TAATAAATTA
1 TAA-AAATTA
*
19575059 TACAAA-TA
1 TAAAAATTA
19575067 GTAAAAA--A
1 -TAAAAATTA
19575075 TAAAACA-TA
1 TAAAA-ATTA
*
19575084 TTAAAAATATT
1 -TAAAAAT-TA
*
19575095 TATAAATTA
1 TAAAAATTA
*
19575104 TAAATATTA
1 TAAAAATTA
* *
19575113 TAAAAAATC
1 TAAAAATTA
** *
19575122 TAGTAA-TC
1 TAAAAATTA
*
19575130 TAATAATTA
1 TAAAAATTA
*
19575139 TCAATAATTA
1 T-AAAAATTA
*
19575149 TAAAACTTA
1 TAAAAATTA
19575158 TAAAAATTA
1 TAAAAATTA
*
19575167 GAAGAAATTA
1 TAA-AAATTA
19575177 TGAAAAATT
1 T-AAAAATT
19575186 GTAATTTTAT
Statistics
Matches: 161, Mismatches: 26, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.03
8 17 0.11
9 73 0.45
10 48 0.30
11 18 0.11
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:19575103 original size:17 final size:16
Alignment explanation
Indices: 19575083--19575116 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19575073 AATAAAACAT
19575083 ATTAAAAATATTTATAA
1 ATTAAAAATA-TTATAA
*
19575100 ATTATAAATATTATAA
1 ATTAAAAATATTATAA
19575116 A
1 A
19575117 AAATCTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAAAATATTATAA
Found at i:19575701 original size:17 final size:17
Alignment explanation
Indices: 19575676--19575718 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19575666 TTAACTACCT
19575676 TTTTATAATTTCTAATG
1 TTTTATAATTTCTAATG
* * *
19575693 TTTTCTAATTTTTAATAA
1 TTTTATAATTTCTAAT-G
19575711 TTTTATAA
1 TTTTATAA
19575719 GTTTTTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATAATTTCTAATG
Found at i:19575764 original size:19 final size:17
Alignment explanation
Indices: 19575740--19575783 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
19575730 ATTCAATAGA
19575740 AATTTTTGTAAGTTTATAT
1 AATTTTT-TAAGTTT-TAT
19575759 AATTTTATT-AGTTTTAT
1 AATTTT-TTAAGTTTTAT
19575776 AATTTTTT
1 AATTTTTT
19575784 TAAGATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 5 0.21
19 7 0.29
20 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
AATTTTTTAAGTTTTAT
Found at i:19578883 original size:24 final size:24
Alignment explanation
Indices: 19578851--19578897 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
19578841 ATTTACTTTT
*
19578851 CCTTGATAAATTTTTTGTAATATA
1 CCTTGATAAACTTTTTGTAATATA
19578875 CCTTGATAAACTTTTTGTAATAT
1 CCTTGATAAACTTTTTGTAATAT
19578898 TGAAACCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (24 bp):
CCTTGATAAACTTTTTGTAATATA
Found at i:19580812 original size:13 final size:13
Alignment explanation
Indices: 19580796--19580825 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19580786 AGTGCTGCAA
19580796 AAAAATGCTTATG
1 AAAAATGCTTATG
*
19580809 AAAAATGCTTTTG
1 AAAAATGCTTATG
19580822 AAAA
1 AAAA
19580826 GCTTGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (13 bp):
AAAAATGCTTATG
Found at i:19582422 original size:16 final size:18
Alignment explanation
Indices: 19582385--19582419 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19582375 AATACTAAGA
19582385 ATTT-TATTAAATTATAT
1 ATTTATATTAAATTATAT
19582402 ATTTATATTAAATTATAT
1 ATTTATATTAAATTATAT
19582420 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTAAATTATAT
Found at i:19582431 original size:16 final size:17
Alignment explanation
Indices: 19582392--19582437 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
19582382 AGAATTTTAT
* *
19582392 TAAATTATATATTTATAT
1 TAAATTATAT-TTAATAA
19582410 TAAATTATATTTAATAA
1 TAAATTATATTTAATAA
19582427 T-AATTAT-TTTA
1 TAAATTATATTTA
19582438 GATTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 6 0.23
18 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATATTTAATAA
Found at i:19582433 original size:26 final size:25
Alignment explanation
Indices: 19582404--19582460 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
19582394 AATTATATAT
19582404 TTATATTAAATTATATTTAATAATAA
1 TTATATTAAATTATATTTAATAAT-A
* * * *
19582430 TTATTTTAGATTATATTTTATAGTA
1 TTATATTAAATTATATTTAATAATA
19582455 TTATAT
1 TTATAT
19582461 ATTATGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATATTAAATTATATTTAATAATA
Done.