Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 31 of 135
Found at i:12404240 original size:16 final size:16
Alignment explanation
Indices: 12404219--12404251 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12404209 TATTTTAACA
*
12404219 AAACCATAAAAACCCT
1 AAACCAAAAAAACCCT
12404235 AAACCAAAAAAACCCT
1 AAACCAAAAAAACCCT
12404251 A
1 A
12404252 GGGACTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.30, G:0.00, T:0.09
Consensus pattern (16 bp):
AAACCAAAAAAACCCT
Found at i:12409955 original size:32 final size:32
Alignment explanation
Indices: 12409893--12409955 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
12409883 TTAAACTTCA
* * *
12409893 AAAATTATTTTATTTAAATATAATATATATTT
1 AAAATTATTTCATTAAAATATAATACATATTT
*
12409925 AAAATTATTTCATTAAAA-ATTATTACATATT
1 AAAATTATTTCATTAAAATA-TAATACATATT
12409956 GAATATCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
AAAATTATTTCATTAAAATATAATACATATTT
Found at i:12421369 original size:20 final size:20
Alignment explanation
Indices: 12421327--12421369 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12421317 ATACCCTCAA
*
12421327 AATAATATTAGTTACTTTAT
1 AATAATATTAGATACTTTAT
*
12421347 AATAATATTGGAT-CTTTAGT
1 AATAATATTAGATACTTTA-T
12421367 AAT
1 AAT
12421370 TTCGCAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
AATAATATTAGATACTTTAT
Found at i:12429801 original size:17 final size:17
Alignment explanation
Indices: 12429779--12429813 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12429769 AGAAACTAAC
12429779 GGCTCAGTAACTAAAAT
1 GGCTCAGTAACTAAAAT
*
12429796 GGCTCAGTGACTAAAAT
1 GGCTCAGTAACTAAAAT
12429813 G
1 G
12429814 TTACAACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (17 bp):
GGCTCAGTAACTAAAAT
Found at i:12429895 original size:31 final size:29
Alignment explanation
Indices: 12429826--12429899 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
12429816 ACAACGTGAT
**
12429826 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
12429855 AACATAAGTGACTAAAACGTAATATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
12429886 AACAAAAGTGACTA
1 AACATAAGTGACTA
12429900 TTTTGGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:12438996 original size:27 final size:28
Alignment explanation
Indices: 12438940--12439000 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 28
12438930 CCCATATTAA
12438940 ATATATATATTTGATTAAAAATAAAAAATAT
1 ATATATATATTTGATTAAAAAT---AAATAT
12438971 ATATATATATTTGATTAAAAAT-AATAT
1 ATATATATATTTGATTAAAAATAAATAT
12438998 ATA
1 ATA
12439001 ATTCGGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.27
31 22 0.73
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (28 bp):
ATATATATATTTGATTAAAAATAAATAT
Found at i:12448961 original size:25 final size:25
Alignment explanation
Indices: 12448916--12448964 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12448906 GAGGCGCCAA
12448916 TGAATAAAAAAATATTAATTTTTTT
1 TGAATAAAAAAATATTAATTTTTTT
* * *
12448941 TGAATAAAATAATTTTTATTTTTT
1 TGAATAAAAAAATATTAATTTTTT
12448965 AAAAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TGAATAAAAAAATATTAATTTTTTT
Found at i:12449107 original size:27 final size:27
Alignment explanation
Indices: 12449033--12449107 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
12449023 GGGTCGGGTG
* *
12449033 GTGCCTCGTAGGGAAGCACCATTAAAA
1 GTGCCTCATAGGGAAGCGCCATTAAAA
* *
12449060 GTGACTCATA-GGAATGTGCCATTAAAA
1 GTGCCTCATAGGGAA-GCGCCATTAAAA
*
12449087 GTGCCTCATAGGGAGGCGCCA
1 GTGCCTCATAGGGAAGCGCCA
12449108 GTGGGTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.10
27 32 0.82
28 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (27 bp):
GTGCCTCATAGGGAAGCGCCATTAAAA
Found at i:12449140 original size:21 final size:22
Alignment explanation
Indices: 12449115--12449165 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
12449105 CCAGTGGGTA
*
12449115 ATTTTATATGTATATTGTAACT
1 ATTTTATATGAATATTGTAACT
* *
12449137 -TTTTGTATGAATATTGTAATT
1 ATTTTATATGAATATTGTAACT
12449158 ATTTTATA
1 ATTTTATA
12449166 ATTAATTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (22 bp):
ATTTTATATGAATATTGTAACT
Found at i:12449227 original size:27 final size:25
Alignment explanation
Indices: 12449197--12449271 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 25
12449187 TTGGATTAGT
12449197 ATTTTGTATGAATATTGTAATTTTG
1 ATTTTGTATGAATATTGTAATTTTG
* *
12449222 AAATTTTATATGAATATTGTAATATTG
1 --ATTTTGTATGAATATTGTAATTTTG
12449249 --TTTGTATGAATATTGTAACTTTT
1 ATTTTGTATGAATATTGTAA-TTTT
12449272 TGTATAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
23 17 0.40
24 3 0.07
27 23 0.53
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (25 bp):
ATTTTGTATGAATATTGTAATTTTG
Found at i:12449450 original size:15 final size:16
Alignment explanation
Indices: 12449415--12449450 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12449405 AACATAAAAG
12449415 TTTATATAATGTAACT
1 TTTATATAATGTAACT
*
12449431 TTTATATTATGTAA-T
1 TTTATATAATGTAACT
12449446 TTTAT
1 TTTAT
12449451 TTGATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTATATAATGTAACT
Found at i:12452281 original size:40 final size:40
Alignment explanation
Indices: 12452236--12452322 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
12452226 GCTATGTTTA
12452236 GCACTTAATATGAAATTC-GAGATAGCTTCAGCTATTTATG
1 GCACTTAATATGAAATTCGGA-ATAGCTTCAGCTATTTATG
* * ** * *
12452276 GCACTTAGTGTGCGATTTGGAATAGCTTCGGCTATTTATG
1 GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
*
12452316 ACACTTA
1 GCACTTA
12452323 GTGTGNNNNN
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (40 bp):
GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
Found at i:12467596 original size:18 final size:18
Alignment explanation
Indices: 12467575--12467626 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
12467565 ACCACTATGT
12467575 GGCCCAATACCATCC-TTC
1 GGCCCAATACCA-CCATTC
*
12467593 GGCCCAACACCACCATTC
1 GGCCCAATACCACCATTC
*
12467611 GGCCCAATAGCACCAT
1 GGCCCAATACCACCAT
12467627 CAATCCCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.15
Consensus pattern (18 bp):
GGCCCAATACCACCATTC
Found at i:12472459 original size:16 final size:16
Alignment explanation
Indices: 12472438--12472468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12472428 TATGTTTAAG
12472438 CGTATAAATTTGAAAC
1 CGTATAAATTTGAAAC
*
12472454 CGTATATATTTGAAA
1 CGTATAAATTTGAAA
12472469 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (16 bp):
CGTATAAATTTGAAAC
Found at i:12473828 original size:22 final size:22
Alignment explanation
Indices: 12473802--12473845 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12473792 CACTAATGAA
* *
12473802 CAGAGAGCACTAATGTGCTAAT
1 CAGAGAGCACCAACGTGCTAAT
12473824 CAGAGAGCACCAACGTGCTAAT
1 CAGAGAGCACCAACGTGCTAAT
12473846 AATTAGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (22 bp):
CAGAGAGCACCAACGTGCTAAT
Found at i:12475570 original size:46 final size:46
Alignment explanation
Indices: 12475503--12475593 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
12475493 AATTTAGTGA
* *
12475503 TCTCAAATCATTGTTCTGACACTACTGAAAATTGGGCTGTTACAAC
1 TCTCAAATCACTGTTCTGACACTACTGAAAATTAGGCTGTTACAAC
*
12475549 TCTCAAATTACTGTTCTGACACTACTGAAAATTAGGCTGTTACAA
1 TCTCAAATCACTGTTCTGACACTACTGAAAATTAGGCTGTTACAA
12475594 AGTGTTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (46 bp):
TCTCAAATCACTGTTCTGACACTACTGAAAATTAGGCTGTTACAAC
Found at i:12476149 original size:14 final size:15
Alignment explanation
Indices: 12476130--12476162 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12476120 ATATTCTAGA
12476130 AAAAAATATAAAT-T
1 AAAAAATATAAATAT
*
12476144 AAAAAATATGAATAT
1 AAAAAATATAAATAT
12476159 AAAA
1 AAAA
12476163 TTTACAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAAATATAAATAT
Found at i:12476504 original size:19 final size:20
Alignment explanation
Indices: 12476465--12476504 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12476455 TATATTTTTA
*
12476465 ATTTTTAATTTAAATTTAAT
1 ATTTTTAATTTAAATTAAAT
*
12476485 ATTTTTATTTTAAA-TAAAT
1 ATTTTTAATTTAAATTAAAT
12476504 A
1 A
12476505 AAATTACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTAATTTAAATTAAAT
Found at i:12477601 original size:23 final size:22
Alignment explanation
Indices: 12477575--12477644 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
12477565 TTTATTTTAG
12477575 AAAATAAAAATTAAATAAATGTT
1 AAAATAAAAATTAAA-AAATGTT
*
12477598 AAAAT--AAGTTAAAAAATGTT
1 AAAATAAAAATTAAAAAATGTT
* *
12477618 AAGTACAAAAATTAAGAAAAT-TT
1 AA-AATAAAAATTAA-AAAATGTT
12477641 AAAA
1 AAAA
12477645 AAATTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 9 0.24
21 8 0.21
22 1 0.03
23 15 0.39
24 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAATAAAAATTAAAAAATGTT
Found at i:12482961 original size:23 final size:24
Alignment explanation
Indices: 12482935--12482984 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
12482925 TGGAATTTGA
* *
12482935 TGAAAC-GTATAAGTTAAATTGTT
1 TGAAACTGTAAAAGTTAAATTGCT
12482958 TG-AACTGTAAAAGTTAAATTGCT
1 TGAAACTGTAAAAGTTAAATTGCT
12482981 TGAA
1 TGAA
12482985 CAGGTTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 19 0.83
24 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (24 bp):
TGAAACTGTAAAAGTTAAATTGCT
Found at i:12486389 original size:17 final size:16
Alignment explanation
Indices: 12486352--12486393 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12486342 CCTTTATGTA
*
12486352 ATTTTATTTTTTTAAT
1 ATTTTATATTTTTAAT
12486368 ATTTTATATTTTTAAGT
1 ATTTTATATTTTTAA-T
*
12486385 CTTTTATAT
1 ATTTTATAT
12486394 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTATATTTTTAAT
Found at i:12498687 original size:18 final size:16
Alignment explanation
Indices: 12498650--12498700 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
12498640 AAATTATAAA
12498650 AAATTAATATAAAAAC
1 AAATTAATATAAAAAC
*
12498666 AAATTAATTTAACAATAC
1 AAATTAATATAA-AA-AC
*
12498684 AAA-TAAAATAAATAAC
1 AAATTAATATAAA-AAC
12498700 A
1 A
12498701 TGTAAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.52
17 9 0.31
18 5 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATTAATATAAAAAC
Found at i:12506770 original size:24 final size:24
Alignment explanation
Indices: 12506738--12506788 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12506728 AATGTGAAGT
12506738 TTAGTTACTACTCAAAACAATTAC
1 TTAGTTACTACTCAAAACAATTAC
12506762 TTAGTTACTACTCAAAACAATTAC
1 TTAGTTACTACTCAAAACAATTAC
12506786 TTA
1 TTA
12506789 CTGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAGTTACTACTCAAAACAATTAC
Found at i:12509771 original size:3 final size:3
Alignment explanation
Indices: 12509763--12509805 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
12509753 GTCTCACATG
*
12509763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12509806 TTCTGATTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:12510633 original size:18 final size:18
Alignment explanation
Indices: 12510610--12510649 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12510600 TTATTATTTT
*
12510610 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
12510628 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
12510646 TAAA
1 TAAA
12510650 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:12510656 original size:19 final size:19
Alignment explanation
Indices: 12510620--12510670 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
12510610 TAAAATTTAC
*
12510620 TATTAAAATAAAAT-TTAAA
1 TATT-AAATAAATTATTAAA
12510639 TATTAAATAAATTATTAAA
1 TATTAAATAAATTATTAAA
*
12510658 -AAT-AATAAATTAT
1 TATTAAATAAATTAT
12510671 ATTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATAAATTATTAAA
Found at i:12510708 original size:28 final size:26
Alignment explanation
Indices: 12510678--12510773 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
12510668 TATATTAATT
*
12510678 ATATTAATAATTTATTATATGACTAA
1 ATATAAATAATTTATTATATGACTAA
* * **
12510704 ATATAAATAATTAAATAAGTATGTTTAATA
1 ATATAAATAATT-TATTA-TATGACT-A-A
12510734 ATATTAAAATAATTTATTATATGACTAA
1 ATA-T-AAATAATTTATTATATGACTAA
12510762 ATATAAATAATT
1 ATATAAATAATT
12510774 AAATACGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
26 19 0.35
27 4 0.07
28 9 0.16
29 2 0.04
30 9 0.16
31 4 0.07
32 8 0.15
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATAAATAATTTATTATATGACTAA
Found at i:12510737 original size:30 final size:30
Alignment explanation
Indices: 12510703--12510795 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
12510693 TATATGACTA
12510703 AATATAAATAATTAAATAAGTATGTTTAAT
1 AATATAAATAATTAAATAAGTATGTTTAAT
* * **
12510733 AATATTAAAATAATT-TATTA-TATGACT-A-
1 AATA-T-AAATAATTAAATAAGTATGTTTAAT
*
12510761 AATATAAATAATTAAATACGTATGTTTAAT
1 AATATAAATAATTAAATAAGTATGTTTAAT
12510791 AATAT
1 AATAT
12510796 TAAAAAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
26 8 0.17
27 3 0.06
28 9 0.19
29 2 0.04
30 14 0.29
31 4 0.08
32 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
AATATAAATAATTAAATAAGTATGTTTAAT
Found at i:12510757 original size:58 final size:58
Alignment explanation
Indices: 12510683--12510800 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
12510673 TAATTATATT
12510683 AATAATTTATTATATGACTAAATATAAATAATTAAATAAGTATGTTTAATAATATTAA
1 AATAATTTATTATATGACTAAATATAAATAATTAAATAAGTATGTTTAATAATATTAA
*
12510741 AATAATTTATTATATGACTAAATATAAATAATTAAATACGTATGTTTAATAATATTAA
1 AATAATTTATTATATGACTAAATATAAATAATTAAATAAGTATGTTTAATAATATTAA
12510799 AA
1 AA
12510801 AATATAATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (58 bp):
AATAATTTATTATATGACTAAATATAAATAATTAAATAAGTATGTTTAATAATATTAA
Found at i:12510784 original size:28 final size:27
Alignment explanation
Indices: 12510678--12510784 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 27
12510668 TATATTAATT
* * *
12510678 ATATTAATAATTTATTA-TATGACTAA
1 ATATAAATAATTAAATAGTATGACTAA
**
12510704 ATATAAATAATTAAATAAGTATGTTTAATA
1 ATATAAATAATTAAAT-AGTATGACT-A-A
* *
12510734 ATATTAAAATAATTTATTA-TATGACTAA
1 ATA-T-AAATAATTAAATAGTATGACTAA
12510762 ATATAAATAATTAAATACGTATG
1 ATATAAATAATTAAATA-GTATG
12510785 TTTAATAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
26 24 0.39
27 2 0.03
28 13 0.21
29 2 0.03
30 9 0.15
31 2 0.03
32 10 0.16
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (27 bp):
ATATAAATAATTAAATAGTATGACTAA
Found at i:12512152 original size:29 final size:28
Alignment explanation
Indices: 12512120--12512177 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
12512110 AAAGAATTTG
*
12512120 TCAT-TTATACTAAATATTATATAATAAAA
1 TCATATTATA-TAAATATTA-AAAATAAAA
*
12512149 TCATATTATATTAATATTAAAAATAAAA
1 TCATATTATATAAATATTAAAAATAAAA
12512177 T
1 T
12512178 AAATAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 12 0.46
30 5 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (28 bp):
TCATATTATATAAATATTAAAAATAAAA
Found at i:12525427 original size:19 final size:18
Alignment explanation
Indices: 12525378--12525417 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
12525368 GTAAATTTTA
12525378 TTAT-ATAATTTAATAAT
1 TTATAATAATTTAATAAT
12525395 TTATAATAATTTAATAAAT
1 TTATAATAATTTAAT-AAT
12525414 TTAT
1 TTAT
12525418 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAATAATTTAATAAT
Found at i:12526080 original size:1 final size:1
Alignment explanation
Indices: 12526074--12526111 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
12526064 ATTTTCACCC
12526074 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12526112 ATAGCTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12529016 original size:38 final size:38
Alignment explanation
Indices: 12528974--12529046 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
12528964 CAGTCACCAA
*
12528974 CGTTATTGAAAAGTGACAAATCAATCACTCATTAATAT
1 CGTTATCGAAAAGTGACAAATCAATCACTCATTAATAT
* *
12529012 CGTTATCGAAAAGTTACAAATCAGTCACTCATTAA
1 CGTTATCGAAAAGTGACAAATCAATCACTCATTAA
12529047 CATTTTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (38 bp):
CGTTATCGAAAAGTGACAAATCAATCACTCATTAATAT
Found at i:12531082 original size:5 final size:5
Alignment explanation
Indices: 12531063--12531153 Score: 53
Period size: 6 Copynumber: 17.4 Consensus size: 5
12531053 ATTATATTAT
* *
12531063 AAAGA TAAAGTA AAAGAA AAAGA AATAGA AAAGA AGGAGA GAAAGA AACGA
1 AAAGA -AAAG-A AAAG-A AAAGA AA-AGA AAAGA A-AAGA -AAAGA AAAGA
* * *
12531114 AACAGA AAAGG AAAG- AAAGG GAAGA AAA-A AAAG- AAAGA AA
1 AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
12531154 GAAGGAGAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
4 12 0.18
5 26 0.38
6 28 0.41
7 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:12531516 original size:18 final size:18
Alignment explanation
Indices: 12531493--12531530 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12531483 TTTGTATGAA
12531493 AATATAAGATTGACTGTG
1 AATATAAGATTGACTGTG
12531511 AATATAAGATTGACTGTG
1 AATATAAGATTGACTGTG
12531529 AA
1 AA
12531531 GAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (18 bp):
AATATAAGATTGACTGTG
Found at i:12531861 original size:24 final size:24
Alignment explanation
Indices: 12531834--12531880 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12531824 ATTGAAATGG
12531834 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
12531858 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
12531881 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:12532929 original size:11 final size:11
Alignment explanation
Indices: 12532913--12532939 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12532903 ACGGGCAAAG
12532913 ATAATTTTACT
1 ATAATTTTACT
12532924 ATAATTTTACT
1 ATAATTTTACT
12532935 ATAAT
1 ATAAT
12532940 GGGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAATTTTACT
Found at i:12533019 original size:18 final size:17
Alignment explanation
Indices: 12532987--12533020 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12532977 CTACACCCCA
12532987 AACCCCAAAAAGTAAAG
1 AACCCCAAAAAGTAAAG
*
12533004 AACCCTCAAAACGTAAA
1 AACCC-CAAAAAGTAAA
12533021 CACAAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.26, G:0.09, T:0.09
Consensus pattern (17 bp):
AACCCCAAAAAGTAAAG
Found at i:12537224 original size:2 final size:2
Alignment explanation
Indices: 12537217--12537257 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12537207 TCATTTCAGG
12537217 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12537258 TAAGATATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12540242 original size:19 final size:19
Alignment explanation
Indices: 12540215--12540258 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
12540205 TATTTTTAAG
12540215 AAATCTACCAAACAACAAA
1 AAATCTACCAAACAACAAA
*
12540234 AAATTTACCAAACAACAAA
1 AAATCTACCAAACAACAAA
12540253 AAATCT
1 AAATCT
12540259 TTTACGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (19 bp):
AAATCTACCAAACAACAAA
Found at i:12540346 original size:14 final size:14
Alignment explanation
Indices: 12540310--12540348 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12540300 TCAAAAAAAT
12540310 AAATTATTTTCTAA
1 AAATTATTTTCTAA
* *
12540324 AAATCATTTTCTGA
1 AAATTATTTTCTAA
*
12540338 AAGTTATTTTC
1 AAATTATTTTC
12540349 AATGAAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (14 bp):
AAATTATTTTCTAA
Found at i:12540875 original size:16 final size:16
Alignment explanation
Indices: 12540851--12540882 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12540841 TTCGCCTGTC
*
12540851 AACATACATACATACA
1 AACACACATACATACA
12540867 AACACACATACATACA
1 AACACACATACATACA
12540883 TATAAGAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (16 bp):
AACACACATACATACA
Found at i:12547356 original size:21 final size:22
Alignment explanation
Indices: 12547331--12547386 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
12547321 AAATCATTAA
12547331 TTTAAAAAATTGT-TAGAAATT
1 TTTAAAAAATTGTATAGAAATT
*
12547352 TTTAAAAAATTTGTATTGAAATT
1 TTTAAAAAA-TTGTATAGAAATT
*
12547375 TATTAATAAATT
1 T-TTAAAAAATT
12547387 TAGGAAGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.30
22 4 0.13
23 10 0.33
24 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTAAAAAATTGTATAGAAATT
Found at i:12547986 original size:25 final size:25
Alignment explanation
Indices: 12547958--12548005 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12547948 ATGCTTTATC
*
12547958 ATTTT-AAATTTTTATATTTTTTAAA
1 ATTTTGAAATTTTAAT-TTTTTTAAA
12547983 ATTTTGAAATTTTAATTTTTTTA
1 ATTTTGAAATTTTAATTTTTTTA
12548006 CCAACATCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTGAAATTTTAATTTTTTTAAA
Found at i:12565280 original size:44 final size:44
Alignment explanation
Indices: 12565217--12565368 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 44
12565207 ATTTTTATTG
* *
12565217 ATTTTTTAAATTAAAAAAAAACTGAAATATCTTTAAATAATGTA
1 ATTTTTTAAAATATAAAAAAACTGAAATATCTTTAAATAATGTA
* *** *** **
12565261 ATTTTTTAAAATATAAAAAATTATTTTTATAAT-TTCCGCAGGA-G-A
1 ATTTTTTAAAATATAAAAAA--ACTGAAAT-ATCTT-TAAATAATGTA
* *
12565306 CTTTTTTAAATTA-AAAAAAACTGAAATATCTTTAAATAATGTA
1 ATTTTTTAAAATATAAAAAAACTGAAATATCTTTAAATAATGTA
12565349 ATTTTTTAAAATATAAAAAA
1 ATTTTTTAAAATATAAAAAA
12565369 TTATTTTTAT
Statistics
Matches: 76, Mismatches: 24, Indels: 16
0.66 0.21 0.14
Matches are distributed among these distances:
41 4 0.05
42 7 0.09
43 12 0.16
44 30 0.39
45 12 0.16
46 7 0.09
47 4 0.05
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (44 bp):
ATTTTTTAAAATATAAAAAAACTGAAATATCTTTAAATAATGTA
Found at i:12565331 original size:88 final size:89
Alignment explanation
Indices: 12565218--12565396 Score: 351
Period size: 88 Copynumber: 2.0 Consensus size: 89
12565208 TTTTTATTGA
12565218 TTTTTTAAATTAAAAAAAAACTGAAATATCTTTAAATAATGTAATTTTTTAAAATATAAAAAATT
1 TTTTTTAAATTAAAAAAAAACTGAAATATCTTTAAATAATGTAATTTTTTAAAATATAAAAAATT
12565283 ATTTTTATAATTTCCGCAGGAGAC
66 ATTTTTATAATTTCCGCAGGAGAC
12565307 TTTTTTAAATT-AAAAAAAACTGAAATATCTTTAAATAATGTAATTTTTTAAAATATAAAAAATT
1 TTTTTTAAATTAAAAAAAAACTGAAATATCTTTAAATAATGTAATTTTTTAAAATATAAAAAATT
12565371 ATTTTTATAATTTCCGCAGGAGAC
66 ATTTTTATAATTTCCGCAGGAGAC
12565395 TT
1 TT
12565397 AAAAGTTTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 79 0.88
89 11 0.12
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (89 bp):
TTTTTTAAATTAAAAAAAAACTGAAATATCTTTAAATAATGTAATTTTTTAAAATATAAAAAATT
ATTTTTATAATTTCCGCAGGAGAC
Found at i:12574833 original size:27 final size:27
Alignment explanation
Indices: 12574803--12574859 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
12574793 TTTATATACA
12574803 AATACA-TTTATACAACTAATATTAATT
1 AATACACTTTATACAA-TAATATTAATT
* * **
12574830 AATATACTTTTTGTAATAATATTAATT
1 AATACACTTTATACAATAATATTAATT
12574857 AAT
1 AAT
12574860 TTTAATAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (27 bp):
AATACACTTTATACAATAATATTAATT
Found at i:12583022 original size:19 final size:20
Alignment explanation
Indices: 12583000--12583065 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
12582990 TTGAAAGAGC
*
12583000 TTATAAAAATT-ATATAAAA
1 TTATAAAAATTCATACAAAA
*
12583019 TTATAAAAATTCATACAAAC
1 TTATAAAAATTCATACAAAA
*
12583039 TTAT-AAAATTCTTA-AAAA
1 TTATAAAAATTCATACAAAA
*
12583057 GTATAAAAA
1 TTATAAAAA
12583066 AATTTATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 6 0.15
19 24 0.60
20 10 0.25
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
TTATAAAAATTCATACAAAA
Found at i:12583027 original size:9 final size:9
Alignment explanation
Indices: 12583000--12583065 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
12582990 TTGAAAGAGC
12583000 TTATAAAAA
1 TTATAAAAA
12583009 TTATATAAAA
1 TTATA-AAAA
12583019 TTATAAAAA
1 TTATAAAAA
*
12583028 TTCATACAAAC
1 TT-ATA-AAAA
12583039 TTAT-AAAA
1 TTATAAAAA
*
12583047 TTCTTAAAAA
1 TT-ATAAAAA
*
12583057 GTATAAAAA
1 TTATAAAAA
12583066 AATTTATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 5 0.11
9 18 0.38
10 19 0.40
11 5 0.11
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:12583042 original size:20 final size:19
Alignment explanation
Indices: 12582999--12583046 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
12582989 ATTGAAAGAG
*
12582999 CTTATAAAAATTATATAAA
1 CTTATAAAAATTATACAAA
*
12583018 ATTATAAAAATTCATACAAA
1 CTTATAAAAATT-ATACAAA
12583038 CTTATAAAA
1 CTTATAAAA
12583047 TTCTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
CTTATAAAAATTATACAAA
Found at i:12590350 original size:1 final size:1
Alignment explanation
Indices: 12590344--12590370 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
12590334 CATTTGCTTC
12590344 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
12590371 ACATAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12594680 original size:19 final size:19
Alignment explanation
Indices: 12594645--12594682 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12594635 GATATAATCA
*
12594645 TCAATAATAAATGATAAAT
1 TCAATAATAAATAATAAAT
12594664 TCAATAA-AAATAAATAAAT
1 TCAATAATAAAT-AATAAAT
12594683 GATGATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
TCAATAATAAATAATAAAT
Found at i:12604385 original size:9 final size:9
Alignment explanation
Indices: 12604371--12604421 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
12604361 GTAGTGATTC
12604371 AATTCGGGT
1 AATTCGGGT
12604380 AATTCGGGT
1 AATTCGGGT
*
12604389 AATTCAGGT
1 AATTCGGGT
12604398 AATTCGGGT
1 AATTCGGGT
*
12604407 AATTCGGTT
1 AATTCGGGT
12604416 AATTCG
1 AATTCG
12604422 ACTAATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (9 bp):
AATTCGGGT
Found at i:12604427 original size:27 final size:27
Alignment explanation
Indices: 12604371--12604428 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
12604361 GTAGTGATTC
*
12604371 AATTCGGGTAATTCGGGTAATTCAGGT
1 AATTCGGGTAATTCGGGTAATTCAGCT
*
12604398 AATTCGGGTAATTCGGTTAATTC-GACT
1 AATTCGGGTAATTCGGGTAATTCAG-CT
12604425 AATT
1 AATT
12604429 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (27 bp):
AATTCGGGTAATTCGGGTAATTCAGCT
Found at i:12605736 original size:17 final size:18
Alignment explanation
Indices: 12605714--12605748 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12605704 TTTCGTTAAA
12605714 TAAATAATT-TAAATTAT
1 TAAATAATTATAAATTAT
*
12605731 TAAATATTTATAAATTAT
1 TAAATAATTATAAATTAT
12605749 ACTAAATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATTATAAATTAT
Found at i:12617591 original size:27 final size:27
Alignment explanation
Indices: 12617561--12617615 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12617551 AAAGCTGGTG
*
12617561 CAGCAGCAGCCACCCCAGGGTTAAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
* *
12617588 CAGCAGCAGCAACTCCAGGGTTGAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
12617615 C
1 C
12617616 CACTCCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (27 bp):
CAGCAGCAGCAACCCCAGGGTTAAACC
Found at i:12618598 original size:6 final size:6
Alignment explanation
Indices: 12618589--12618658 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
12618579 CTCCTCTTCC
** * * ** *
12618589 TCCTCT TCCTCT TCCAGT TCCACT TCCTCT TCTTCT TCAACC TCCTCT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
*
12618637 T-CTACT TCCTCT TCCACT TCCT
1 TCCT-CT TCCTCT TCCTCT TCCT
12618659 GTAGTTGCTG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
5 2 0.04
6 45 0.92
7 2 0.04
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (6 bp):
TCCTCT
Found at i:12618655 original size:12 final size:12
Alignment explanation
Indices: 12618593--12618658 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
12618583 TCTTCCTCCT
12618593 CTTCCTCTTCCA
1 CTTCCTCTTCCA
* * *
12618605 GTTCCACTTCCT
1 CTTCCTCTTCCA
* *
12618617 CTTCTTCTTCAA
1 CTTCCTCTTCCA
* *
12618629 CCTCCTCTTCTA
1 CTTCCTCTTCCA
12618641 CTTCCTCTTCCA
1 CTTCCTCTTCCA
12618653 CTTCCT
1 CTTCCT
12618659 GTAGTTGCTG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (12 bp):
CTTCCTCTTCCA
Found at i:12618656 original size:18 final size:18
Alignment explanation
Indices: 12618593--12618656 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
12618583 TCTTCCTCCT
* *
12618593 CTTCCTCTTCCAGTTCCA
1 CTTCCTCTTCTACTTCCA
* *
12618611 CTTCCTCTTCTTCTTCAA
1 CTTCCTCTTCTACTTCCA
* *
12618629 CCTCCTCTTCTACTTCCT
1 CTTCCTCTTCTACTTCCA
*
12618647 CTTCCACTTC
1 CTTCCTCTTC
12618657 CTGTAGTTGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (18 bp):
CTTCCTCTTCTACTTCCA
Found at i:12620948 original size:17 final size:17
Alignment explanation
Indices: 12620911--12620958 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
12620901 GAATTTAGAA
*
12620911 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
12620927 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
12620944 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
12620959 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:12632459 original size:22 final size:21
Alignment explanation
Indices: 12632434--12632478 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
12632424 AATAGAATAA
12632434 ATTTAATATTA-ATTTTGAATTT
1 ATTTAATATTACA-TTT-AATTT
*
12632456 ATTTAATTTTACATTTAATTT
1 ATTTAATATTACATTTAATTT
12632477 AT
1 AT
12632479 CAAATACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTAATATTACATTTAATTT
Found at i:12632471 original size:16 final size:17
Alignment explanation
Indices: 12632433--12632477 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
12632423 TAATAGAATA
12632433 AATTTAATATTAATTTTG
1 AATTTAAT-TTAATTTTG
12632451 AATTT-ATTTAATTTT-
1 AATTTAATTTAATTTTG
12632466 ACATTTAATTTA
1 A-ATTTAATTTA
12632478 TCAAATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.48
17 7 0.28
18 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTAATTTAATTTTG
Found at i:12639772 original size:31 final size:32
Alignment explanation
Indices: 12639737--12639802 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
12639727 TTTTTTAGTT
*
12639737 AAATTT-ACTCATCAACCTTTT-AAAAAGAGTC
1 AAATTTGACT-ATCAACCTTTTGAAAAAGAATC
* *
12639768 AAATTTGACTATTAGCCTTTTGAAAAAGAATC
1 AAATTTGACTATCAACCTTTTGAAAAAGAATC
12639800 AAA
1 AAA
12639803 ATGATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (32 bp):
AAATTTGACTATCAACCTTTTGAAAAAGAATC
Found at i:12655005 original size:20 final size:20
Alignment explanation
Indices: 12654982--12655020 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12654972 AATAAATACC
*
12654982 AAAAAATTATTTTAAAAATT
1 AAAAAAGTATTTTAAAAATT
12655002 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
12655021 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAAAAGTATTTTAAAAATT
Found at i:12655132 original size:20 final size:19
Alignment explanation
Indices: 12655109--12655153 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12655099 AATAAATACC
*
12655109 AAAAATTTATTTTAAAAATT
1 AAAAATGTATTTT-AAAATT
* *
12655129 AAAAAAGTGTTTTAAAATT
1 AAAAATGTATTTTAAAATT
12655148 AAAAAT
1 AAAAAT
12655154 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAAATGTATTTTAAAATT
Found at i:12655171 original size:29 final size:26
Alignment explanation
Indices: 12655120--12655174 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 26
12655110 AAAATTTATT
12655120 TTAAAAATTAAAAAAGTGTTTTAAAA
1 TTAAAAATTAAAAAAGTGTTTTAAAA
*
12655146 TTAAAAATAATAAAAAATGTATTTTAAAA
1 TTAAAAAT--TAAAAAA-GTGTTTTAAAA
12655175 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
28 7 0.28
29 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (26 bp):
TTAAAAATTAAAAAAGTGTTTTAAAA
Found at i:12655191 original size:17 final size:17
Alignment explanation
Indices: 12655169--12655215 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
12655159 AAAATGTATT
*
12655169 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
12655186 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
12655203 ATAAATATATTTA
1 TTAAAAATATTTA
12655216 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:12667332 original size:23 final size:23
Alignment explanation
Indices: 12667305--12667380 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
12667295 AGTGTTATTG
12667305 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
12667328 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12667351 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12667374 ATCAGTG
1 ATCAGTG
12667381 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:12667552 original size:38 final size:37
Alignment explanation
Indices: 12667510--12667582 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
12667500 ATGTATGGAA
* *
12667510 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
12667548 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
12667583 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:12669286 original size:28 final size:28
Alignment explanation
Indices: 12669246--12669304 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
12669236 AAATTTAACT
12669246 TACCATTATTTCACACATAAGGTAAGCA
1 TACCATTATTTCACACATAAGGTAAGCA
12669274 TACCATTATTTCACACATAAGGTAAGCA
1 TACCATTATTTCACACATAAGGTAAGCA
12669302 TAC
1 TAC
12669305 AAATATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (28 bp):
TACCATTATTTCACACATAAGGTAAGCA
Found at i:12669311 original size:28 final size:28
Alignment explanation
Indices: 12669252--12669312 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
12669242 AACTTACCAT
* *
12669252 TATTTCACACATAAGGTAAGCATACCAT
1 TATTTCACACATAAGGTAAGCATACAAA
12669280 TATTTCACACATAAGGTAAGCATACAAA
1 TATTTCACACATAAGGTAAGCATACAAA
12669308 TATTT
1 TATTT
12669313 ATCCAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (28 bp):
TATTTCACACATAAGGTAAGCATACAAA
Found at i:12677231 original size:6 final size:6
Alignment explanation
Indices: 12677222--12677246 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12677212 GTAATAATAA
12677222 TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT T
12677247 ATACAACTAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:12677984 original size:75 final size:76
Alignment explanation
Indices: 12677876--12678030 Score: 258
Period size: 75 Copynumber: 2.0 Consensus size: 76
12677866 GATATATATT
*
12677876 TAAATATATCTGGGTGTTCTTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAA
1 TAAATATATCTGGGTG-T-GTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAA
12677941 TTTTAATTTTTTA
64 TTTTAATTTTTTA
* *
12677954 TAAATATATCTGGGTG-GTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTTGATGTTTTGAATT
1 TAAATATATCTGGGTGTGTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAATT
12678018 TTAATTTTTTA
66 TTAATTTTTTA
12678029 TA
1 TA
12678031 CATCCTAGCA
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
75 58 0.78
78 16 0.22
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.59
Consensus pattern (76 bp):
TAAATATATCTGGGTGTGTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAATT
TTAATTTTTTA
Found at i:12678221 original size:36 final size:36
Alignment explanation
Indices: 12678174--12678245 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12678164 ACTCGTTGGT
12678174 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
1 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
12678210 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
1 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
12678246 TTATAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (36 bp):
ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
Found at i:12679422 original size:28 final size:28
Alignment explanation
Indices: 12679390--12679445 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12679380 TCTCATCCAT
12679390 ACACTTGATAAACACCCTTATCATTGCC
1 ACACTTGATAAACACCCTTATCATTGCC
12679418 ACACTTGATAAACACCCTTATCATTGCC
1 ACACTTGATAAACACCCTTATCATTGCC
12679446 TTCAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (28 bp):
ACACTTGATAAACACCCTTATCATTGCC
Found at i:12681513 original size:31 final size:31
Alignment explanation
Indices: 12681464--12681524 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
12681454 ACTCGATGAT
12681464 TTACACTATTGTAGTCCGTATGAATCATATG
1 TTACACTATTGTAGTCCGTATGAATCATATG
*
12681495 TTACACTGTTGT-GATCCGTATGAATCATAT
1 TTACACTATTGTAG-TCCGTATGAATCATAT
12681525 ATTGTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
TTACACTATTGTAGTCCGTATGAATCATATG
Found at i:12696620 original size:13 final size:14
Alignment explanation
Indices: 12696602--12696630 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12696592 TCTTCTACTC
12696602 TACTCACATG-ATT
1 TACTCACATGTATT
12696615 TACTCACATGTATT
1 TACTCACATGTATT
12696629 TA
1 TA
12696631 AGATTTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TACTCACATGTATT
Found at i:12708729 original size:16 final size:16
Alignment explanation
Indices: 12708699--12708743 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
12708689 AAATATCGAT
12708699 ATCAA-ATATTATAATG
1 ATCAATATATT-TAATG
*
12708715 TTCAATATATTTAATG
1 ATCAATATATTTAATG
12708731 AT--ATATATTTAAT
1 ATCAATATATTTAAT
12708744 AGTACAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
ATCAATATATTTAATG
Found at i:12717092 original size:28 final size:28
Alignment explanation
Indices: 12717052--12717106 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
12717042 TTTTTCAAAG
12717052 TTAGAATAGGAGATCCCGAAATCATTCA
1 TTAGAATAGGAGATCCCGAAATCATTCA
12717080 TTAGAATAGGAGATCCCGAAATCATTC
1 TTAGAATAGGAGATCCCGAAATCATTC
12717107 TCGCCTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
TTAGAATAGGAGATCCCGAAATCATTCA
Found at i:12718331 original size:26 final size:24
Alignment explanation
Indices: 12718283--12718333 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
12718273 TTTAAAATAC
* *
12718283 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
12718307 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
12718333 T
1 T
12718334 AAAAGATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:12719508 original size:22 final size:19
Alignment explanation
Indices: 12719483--12719540 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
12719473 AATAACAACA
12719483 AAATAATAGCAACATAATAGTG
1 AAATAATAGC-A-A-AATAGTG
*
12719505 AAATAGTAGCAAAATAGTG
1 AAATAATAGCAAAATAGTG
*
12719524 AAAAAATAAG-AAAATAG
1 AAATAAT-AGCAAAATAG
12719541 CAACAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 19 0.59
20 3 0.09
21 1 0.03
22 9 0.28
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATAATAGCAAAATAGTG
Found at i:12719539 original size:30 final size:28
Alignment explanation
Indices: 12719505--12719560 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
12719495 CATAATAGTG
* *
12719505 AAATAGTAGCAAAATAGTGAAAAAATAAGA
1 AAATAGCAACAAAATA--GAAAAAATAAGA
12719535 AAATAGCAACAAAATAGAAAAAATAA
1 AAATAGCAACAAAATAGAAAAAATAA
12719561 CAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
30 14 0.58
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.14
Consensus pattern (28 bp):
AAATAGCAACAAAATAGAAAAAATAAGA
Found at i:12719577 original size:20 final size:20
Alignment explanation
Indices: 12719534--12719586 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
12719524 AAAAAATAAG
*
12719534 AAAATAGCAACAAAATAGAA
1 AAAATAACAACAAAATAGAA
*
12719554 AAAATAACAATAAAATA-AA
1 AAAATAACAACAAAATAGAA
*
12719573 TAAAAAAACAACAA
1 -AAAATAACAACAA
12719587 TTTTTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAATAACAACAAAATAGAA
Found at i:12719838 original size:34 final size:35
Alignment explanation
Indices: 12719773--12719840 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
12719763 ATATTTTTCT
* * *
12719773 TTAATAATATATTATATTAATTAATTAATTAAATA
1 TTAATAATATATTATAATAATAAAATAATTAAATA
12719808 TTAA-AATATATTATAAATAATAAAAT-ATTAAAT
1 TTAATAATATATTAT-AATAATAAAATAATTAAAT
12719841 CAATCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TTAATAATATATTATAATAATAAAATAATTAAATA
Found at i:12724292 original size:19 final size:21
Alignment explanation
Indices: 12724249--12724297 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
12724239 GATAATTTCT
*
12724249 TAAAGTTAACTAATCAAAATG
1 TAAACTTAACTAATCAAAATG
*
12724270 TAAACTTAA-TAAT-AAATTG
1 TAAACTTAACTAATCAAAATG
12724289 TAAACTTAA
1 TAAACTTAA
12724298 ATATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 14 0.54
20 4 0.15
21 8 0.31
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (21 bp):
TAAACTTAACTAATCAAAATG
Found at i:12725429 original size:13 final size:13
Alignment explanation
Indices: 12725413--12725437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12725403 AAATATTTTT
12725413 TAAAAATAAAAAA
1 TAAAAATAAAAAA
12725426 TAAAAATAAAAA
1 TAAAAATAAAAA
12725438 TATTTTTAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:12734005 original size:21 final size:21
Alignment explanation
Indices: 12733979--12734021 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12733969 TATTAAACGT
12733979 ATAATTTCTACATGCATACGC
1 ATAATTTCTACATGCATACGC
12734000 ATAATTTCTACATGCATACGC
1 ATAATTTCTACATGCATACGC
12734021 A
1 A
12734022 GGGAAGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (21 bp):
ATAATTTCTACATGCATACGC
Found at i:12766207 original size:23 final size:24
Alignment explanation
Indices: 12766180--12766226 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
12766170 AACTAAGGTC
12766180 ACATGC-AT-AAGCAACACTAAAAA
1 ACATGCTATAAAGCAA-ACTAAAAA
12766203 ACATGCTATAAAAGCAAACTAAAA
1 ACATGCTAT-AAAGCAAACTAAAA
12766227 TTTCTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 7 0.33
26 6 0.29
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (24 bp):
ACATGCTATAAAGCAAACTAAAAA
Found at i:12767353 original size:26 final size:26
Alignment explanation
Indices: 12767324--12767400 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
12767314 ATTGAATTTT
*
12767324 ATTTTAAATATAGATTATATATTTAA
1 ATTTTAAATATAGTTTATATATTTAA
12767350 ATTTGT--A-AT-GTTTATAT-TTTAA
1 ATTT-TAAATATAGTTTATATATTTAA
*
12767372 TATTTAAAATATAGTTTATATATTTAA
1 -ATTTTAAATATAGTTTATATATTTAA
12767399 AT
1 AT
12767401 ATAATGTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
22 5 0.12
23 11 0.26
24 3 0.07
25 3 0.07
26 14 0.33
27 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
ATTTTAAATATAGTTTATATATTTAA
Found at i:12767389 original size:19 final size:19
Alignment explanation
Indices: 12767362--12767403 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12767352 TTGTAATGTT
*
12767362 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTT-AAA
12767381 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
12767400 TATA
1 TATA
12767404 ATGTTTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATAGTTTATATATTTAAA
Found at i:12779717 original size:29 final size:29
Alignment explanation
Indices: 12779666--12779721 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12779656 AATCTACCCC
* * *
12779666 AAAATCTTGATTTTTAAGTTATCCTCACT
1 AAAATCTTGATCTTCAAGCTATCCTCACT
*
12779695 AAAATCTTTATCTTCAAGCTATCCTCA
1 AAAATCTTGATCTTCAAGCTATCCTCA
12779722 AATGATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAATCTTGATCTTCAAGCTATCCTCACT
Found at i:12788126 original size:167 final size:169
Alignment explanation
Indices: 12787848--12788184 Score: 547
Period size: 167 Copynumber: 2.0 Consensus size: 169
12787838 CATGATTGGC
12787848 ATAACACAAGAAAGACAGAGAAAAAGTGAGAAAATGTGTGTCAAAATCTGACACATTTACATATA
1 ATAACACAAGAAAGACAGAGAAAAAGTGAGAAAATGTGTGTCAAAATCTGACACATTTACATATA
*
12787913 TATAGAAAAGACAAACATATAAATATCGGGTATGCGGTCAGTCAGATTGTTGTTTTGCAAGAACC
66 TATAGAAAAGACAAACATATAAATATAGGGTATGCGGTCAGTCAGATTGTTGTTTTGCAAGAACC
12787978 TAGAAGACT-CGAAGAACCAGGTCAGGTATGGAAAATCAA
131 TAGAAGA-TGCGAAGAACCAGGTCAGGTATGGAAAATCAA
* *
12788017 ATAACAC-A-AAAGACAGAGAAAAA-TGGAGAAAATGTGTGTCAGATTCTGACACATTTACATAT
1 ATAACACAAGAAAGACAGAGAAAAAGT-GAGAAAATGTGTGTCAAAATCTGACACATTTACATAT
* *
12788079 ATATAGAAAAGACAAACATATAAATATAGGGTATGCGGTCGGTCAGATTGTTGTTTTGTAAGAAC
65 ATATAGAAAAGACAAACATATAAATATAGGGTATGCGGTCAGTCAGATTGTTGTTTTGCAAGAAC
* * * *
12788144 CTAGAAGATGCGAAGAATCGGGTTAGGTATGGAGAATCAA
130 CTAGAAGATGCGAAGAACCAGGTCAGGTATGGAAAATCAA
12788184 A
1 A
12788185 ACAAGTTCAC
Statistics
Matches: 157, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
166 2 0.01
167 147 0.94
168 1 0.01
169 7 0.04
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (169 bp):
ATAACACAAGAAAGACAGAGAAAAAGTGAGAAAATGTGTGTCAAAATCTGACACATTTACATATA
TATAGAAAAGACAAACATATAAATATAGGGTATGCGGTCAGTCAGATTGTTGTTTTGCAAGAACC
TAGAAGATGCGAAGAACCAGGTCAGGTATGGAAAATCAA
Found at i:12791810 original size:14 final size:15
Alignment explanation
Indices: 12791790--12791827 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12791780 GTAGCTGATC
*
12791790 CAAAATTGGATAAAT
1 CAAAATTGAATAAAT
12791805 -AAAATTTGAATAAAT
1 CAAAA-TTGAATAAAT
12791820 CAAAATTG
1 CAAAATTG
12791828 TGCTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 4 0.20
15 12 0.60
16 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (15 bp):
CAAAATTGAATAAAT
Found at i:12798103 original size:29 final size:30
Alignment explanation
Indices: 12798056--12798115 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
12798046 TTTTACATTT
* *
12798056 AGAATTTAGTTCTTTTACTTTT-ATTTTCA
1 AGAATTTAGTTCTTCTACTTTTCATATTCA
12798085 AGAATTTAG-TCTCTCTACTTTTCATATTCA
1 AGAATTTAGTTCT-TCTACTTTTCATATTCA
12798115 A
1 A
12798116 AAATGTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 17 0.63
30 7 0.26
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (30 bp):
AGAATTTAGTTCTTCTACTTTTCATATTCA
Found at i:12806976 original size:15 final size:16
Alignment explanation
Indices: 12806946--12806984 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
12806936 TCACGAAAAT
12806946 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
12806963 ATAATTTA-TATTTTA
1 ATAATTTATTATTTTA
12806978 ATAATTT
1 ATAATTT
12806985 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:12811730 original size:3 final size:3
Alignment explanation
Indices: 12811722--12811755 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12811712 AAACAATTCG
12811722 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
12811756 TTGTTTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:12816101 original size:13 final size:14
Alignment explanation
Indices: 12816074--12816111 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
12816064 TTAAATTTAT
12816074 TTTTTTATAAATAA
1 TTTTTTATAAATAA
*
12816088 TTTTTT-TAATTAA
1 TTTTTTATAAATAA
12816101 TTTTATTATAA
1 TTTT-TTATAA
12816112 CTTCTCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 8 0.38
15 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTATAAATAA
Found at i:12819096 original size:17 final size:17
Alignment explanation
Indices: 12819059--12819106 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
12819049 GAATTTATAA
*
12819059 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
12819075 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
12819092 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
12819107 AAAATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:12820273 original size:49 final size:49
Alignment explanation
Indices: 12820216--12820314 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
12820206 ACTGAAAATA
*
12820216 GACTCATTAAGGAATCTATACATATAAATTATAACAAATAATTCCTTCT
1 GACTCATTAAGGAATCTATACATACAAATTATAACAAATAATTCCTTCT
12820265 GACTCATTAAGGAATCTATACATACAAATTATAACAAATAATTCCTTCT
1 GACTCATTAAGGAATCTATACATACAAATTATAACAAATAATTCCTTCT
12820314 G
1 G
12820315 TACAATTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (49 bp):
GACTCATTAAGGAATCTATACATACAAATTATAACAAATAATTCCTTCT
Found at i:12821303 original size:45 final size:46
Alignment explanation
Indices: 12821194--12821317 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
12821184 GTGATAAGTG
*
12821194 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
12821240 GCTACACTTATCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
12821285 GCTACACTTATCTGATCAAG-GA-CAAGTGATAAG
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAG
12821318 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 1 0.01
45 21 0.28
46 42 0.57
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
Found at i:12828665 original size:18 final size:19
Alignment explanation
Indices: 12828630--12828670 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
12828620 TATAATTTTA
*
12828630 AAAAAATATATAACACA-T
1 AAAAAATATATAAAACATT
12828648 AAAAAATACTA-AAAACATT
1 AAAAAATA-TATAAAACATT
12828667 AAAA
1 AAAA
12828671 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAAATATATAAAACATT
Found at i:12851657 original size:13 final size:13
Alignment explanation
Indices: 12851639--12851663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12851629 GGGTATAGTA
12851639 AAATATTAAAAAT
1 AAATATTAAAAAT
12851652 AAATATTAAAAA
1 AAATATTAAAAA
12851664 AAAAGTATAT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATTAAAAAT
Found at i:12854702 original size:90 final size:90
Alignment explanation
Indices: 12854086--12854690 Score: 942
Period size: 90 Copynumber: 6.7 Consensus size: 90
12854076 GTGGACCCAT
* * *
12854086 GGTTTGTGCATTGACTAGAGCAGGAGAAACAGTTTGCAT-GCTAGTAGCTGAGCCAGTTGAAGGG
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAG-TAGAAGCTGAGCCAGTTGAAGGG
* * *
12854150 ATCCCTGAAGCAGTGGAAGGCGGCAA
65 ATCCCTGAAGCAGTAGAACGCTGCAA
* * *
12854176 GGTTTGTGCATTGCCTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGGAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
* *
12854241 TCCCTGAAGCAGTGGAAGGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * * * *
12854266 GGTTTGTGCATTGACTGCAGCAAGTGAAACAGTTTGCATAGTAGAAGTTGAGCTACTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
12854331 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* *
12854356 AGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGTTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
12854421 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
*
12854446 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGAA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
*
12854511 TCCCTGAAGCAGTAGAAAGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * *
12854536 TGTTTGCGCATTGACTACAGCAGGTGAAACAATTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
12854601 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
** * * *
12854626 TATTTGTGCATTAACTACAGCGGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
12854691 GACCAGAAGC
Statistics
Matches: 477, Mismatches: 37, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
90 477 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (90 bp):
GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
TCCCTGAAGCAGTAGAACGCTGCAA
Found at i:12863357 original size:16 final size:16
Alignment explanation
Indices: 12863338--12863368 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12863328 AATTCAAGTA
12863338 AACCCATAACCTAAAT
1 AACCCATAACCTAAAT
12863354 AACCCATAACCTAAA
1 AACCCATAACCTAAA
12863369 ACAAGATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (16 bp):
AACCCATAACCTAAAT
Found at i:12870413 original size:42 final size:42
Alignment explanation
Indices: 12870165--12870405 Score: 365
Period size: 42 Copynumber: 5.7 Consensus size: 42
12870155 TTAAATCATT
*
12870165 ATCTCCATCATCCTTAGCTTTCCTACTAGAAGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* ** *
12870207 ATCTCCATCATCCTTAGTTTTCCTACTAGTTGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
12870249 ATCTCCATCATTCTTAGCTTTCCTACTAGAGGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
12870291 ACCTCCATCATCCTCAGCTTTCCTACTAGACGATCTAATACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* *
12870333 ATCTCCGTCATCCTTAGCTTTCCTACCAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
12870375 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
12870406 AGCCTAGTGC
Statistics
Matches: 178, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 178 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.34
Consensus pattern (42 bp):
ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
Found at i:12871980 original size:116 final size:118
Alignment explanation
Indices: 12871843--12872076 Score: 429
Period size: 116 Copynumber: 2.0 Consensus size: 118
12871833 CAAAATAGTA
12871843 TGAAACTTATTATTTTTAATATTAATGTGAAACCAAATGTAGCGAGATAAATAAAATGTAATGGA
1 TGAAACTTATTATTTTTAATATTAATGTGAAACCAAATGTAGCGAGATAAATAAAATGTAATGGA
12871908 AGTTTTAATTTCTTATATAAAAATTTATCA-AAAATATTATATGAAATAAATTT
66 AGTTTTAATTTCTTATATAAAAATTTAT-ATAAAATATTATATGAAATAAATTT
12871961 TGAAACTTA-T-TTTTTAATATTAATGTGAAACCAAATGTAGCGAGATAAATAAAATGTAATGGA
1 TGAAACTTATTATTTTTAATATTAATGTGAAACCAAATGTAGCGAGATAAATAAAATGTAATGGA
*
12872024 AGTTTTAATTTCTTATATAAAAATTTATATCAAATATTATATGAAATAAATTT
66 AGTTTTAATTTCTTATATAAAAATTTATATAAAATATTATATGAAATAAATTT
12872077 ATTTACTTTT
Statistics
Matches: 114, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
115 1 0.01
116 103 0.90
117 1 0.01
118 9 0.08
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (118 bp):
TGAAACTTATTATTTTTAATATTAATGTGAAACCAAATGTAGCGAGATAAATAAAATGTAATGGA
AGTTTTAATTTCTTATATAAAAATTTATATAAAATATTATATGAAATAAATTT
Found at i:12875051 original size:30 final size:30
Alignment explanation
Indices: 12875017--12875079 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12875007 ACTTAACAAG
*
12875017 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
12875047 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
12875077 CAA
1 CAA
12875080 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:12879867 original size:28 final size:30
Alignment explanation
Indices: 12879835--12879891 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
12879825 ATGATTTAGG
* *
12879835 TATTATATTGGATAT-TT-TCAAAGTACAA
1 TATTAAATCGGATATCTTATCAAAGTACAA
*
12879863 TATTAAATCGGATATCTTATGAAAGTACA
1 TATTAAATCGGATATCTTATCAAAGTACA
12879892 TGTACCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.54
29 2 0.08
30 9 0.38
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
TATTAAATCGGATATCTTATCAAAGTACAA
Found at i:12885152 original size:11 final size:10
Alignment explanation
Indices: 12885123--12885155 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
12885113 TGAATTTTTT
12885123 AAATTATAAA
1 AAATTATAAA
12885133 AAATT-TAAA
1 AAATTATAAA
12885142 AAAGTTATAAA
1 AAA-TTATAAA
12885153 AAA
1 AAA
12885156 ATATTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 7 0.33
11 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAATTATAAA
Found at i:12887357 original size:24 final size:23
Alignment explanation
Indices: 12887301--12887358 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
12887291 GTTTGTTTAT
*
12887301 TTAAAT-TAATTTATAAATATTAA
1 TTAAATAT-ATTTATAAACATTAA
*
12887324 ATAAATATATTTATAAACATATAA
1 TTAAATATATTTATAAACAT-TAA
12887348 TTAAATATATT
1 TTAAATATATT
12887359 CGTGTCAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAATATATTTATAAACATTAA
Found at i:12887810 original size:22 final size:24
Alignment explanation
Indices: 12887770--12887815 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
12887760 CAATAATTTT
12887770 TTTGTATTTGCATTATACT-CTAA
1 TTTGTATTTGCATTATACTACTAA
12887793 TTTG-ATTTGCAATT-TACTACTAA
1 TTTGTATTTGC-ATTATACTACTAA
12887816 CACAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTGTATTTGCATTATACTACTAA
Found at i:12889371 original size:24 final size:23
Alignment explanation
Indices: 12889341--12889415 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 23
12889331 GGGGTTAAAA
*
12889341 TTAAAATTTATATTTTTATGATAG
1 TTAAAATTTATATTTTTATCAT-G
* *
12889365 TTAAAATGTA-A-TTTTATCATT
1 TTAAAATTTATATTTTTATCATG
* *
12889386 TTAATAATTTATATTTTTATAATT
1 TTAA-AATTTATATTTTTATCATG
12889410 TTAAAA
1 TTAAAA
12889416 AAGTTAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 4 0.09
24 22 0.51
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (23 bp):
TTAAAATTTATATTTTTATCATG
Found at i:12889412 original size:16 final size:17
Alignment explanation
Indices: 12889373--12889412 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
12889363 AGTTAAAATG
12889373 TAATTTTATCATTTTAA
1 TAATTTTATCATTTTAA
*
12889390 TAA-TTTAT-ATTTTTA
1 TAATTTTATCATTTTAA
12889405 TAATTTTA
1 TAATTTTA
12889413 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTATCATTTTAA
Found at i:12891518 original size:9 final size:9
Alignment explanation
Indices: 12891506--12891533 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12891496 TTTTATTACA
12891506 ACAATTAAT
1 ACAATTAAT
12891515 ACAATTAAT
1 ACAATTAAT
12891524 ACAATTAAT
1 ACAATTAAT
12891533 A
1 A
12891534 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:12891574 original size:68 final size:68
Alignment explanation
Indices: 12891465--12891685 Score: 419
Period size: 68 Copynumber: 3.3 Consensus size: 68
12891455 TTGGGCAAAA
12891465 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
1 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
12891530 AAT
66 AAT
12891533 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
1 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
12891598 AAT
66 AAT
12891601 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATT
1 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
12891664 AAT
66 AAT
*
12891667 AATTTGATAATTTTACTAA
1 AATTTGATAAATTTACTAA
12891686 CAATTAATTT
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.18
67 1 0.01
68 124 0.82
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
AAT
Found at i:12891586 original size:9 final size:9
Alignment explanation
Indices: 12891574--12891601 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12891564 TTTTATTACA
12891574 ACAATTAAT
1 ACAATTAAT
12891583 ACAATTAAT
1 ACAATTAAT
12891592 ACAATTAAT
1 ACAATTAAT
12891601 A
1 A
12891602 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:12891695 original size:16 final size:16
Alignment explanation
Indices: 12891674--12891715 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
12891664 AATAATTTGA
*
12891674 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
12891690 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
12891706 TAGTTTTAAT
1 TAATTTTAAT
12891716 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:12891699 original size:22 final size:22
Alignment explanation
Indices: 12891689--12891749 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
12891679 TTACTAACAA
* * **
12891689 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAACT
*
12891711 TTAATTTTATTAAAAAATAACT
1 TTAATTTTAATAAAAAATAACT
*
12891733 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
12891750 CGGGCCGGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAACT
Found at i:12892191 original size:94 final size:94
Alignment explanation
Indices: 12892030--12892215 Score: 363
Period size: 94 Copynumber: 2.0 Consensus size: 94
12892020 CATTGGGTCG
12892030 TATATTATGACATATTAGTTCAAGAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTGGCCCA
1 TATATTATGACATATTAGTTCAAGAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTGGCCCA
12892095 AGAGTAAATACTCAAAAATTAAGGGGTGT
66 AGAGTAAATACTCAAAAATTAAGGGGTGT
*
12892124 TATATTATGACATATTAGTTCAAGAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTGCCCA
1 TATATTATGACATATTAGTTCAAGAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTGGCCCA
12892189 AGAGTAAATACTCAAAAATTAAGGGGT
66 AGAGTAAATACTCAAAAATTAAGGGGT
12892216 TAAAGTGTAA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (94 bp):
TATATTATGACATATTAGTTCAAGAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTGGCCCA
AGAGTAAATACTCAAAAATTAAGGGGTGT
Done.