Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 171 of 190
Found at i:28173485 original size:80 final size:79
Alignment explanation
Indices: 28173352--28173596 Score: 328
Period size: 80 Copynumber: 3.1 Consensus size: 79
28173342 CTTAAATATT
* * * * * *
28173352 ATGGTTTGCTGAACTTTGTTGTCTGATATTTTTTTGCTGAATGGTATTATATGATATTGGGAGGT
1 ATGGTTTGCTGAACCTTGTTGTATGATATTATTTTGTTGAATGGTATTGTATGATATTGGG-GGC
28173417 TGAATCGTATGCTGA
65 TGAATCGTATGCTGA
* * * * *
28173432 ATGGTTTGCTAAACCTTATTGTATGATATTGTATTATTGAATGGTATTGTATGATATTGAGGGGC
1 ATGGTTTGCTGAACCTTGTTGTATGATATTATTTTGTTGAATGGTATTGTATGATATTG-GGGGC
*
28173497 TGAATCATATGCTGA
65 TGAATCGTATGCTGA
* * *
28173512 ATGGTTTGCTGAACCTTGTTGTTTGATATTATTTTGTTGAATGATTTTGTATGATATTAGGGGGC
1 ATGGTTTGCTGAACCTTGTTGTATGATATTATTTTGTTGAATGGTATTGTATGATATT-GGGGGC
28173577 TGAATCGTATGCTGA
65 TGAATCGTATGCTGA
28173592 ATGGT
1 ATGGT
28173597 GTATCTGATC
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 140 0.98
81 3 0.02
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (79 bp):
ATGGTTTGCTGAACCTTGTTGTATGATATTATTTTGTTGAATGGTATTGTATGATATTGGGGGCT
GAATCGTATGCTGA
Found at i:28175062 original size:21 final size:21
Alignment explanation
Indices: 28175038--28175084 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28175028 GAGCAACAAC
*
28175038 AGCAATGAATTGATGACCAAG
1 AGCAATGAATTAATGACCAAG
** *
28175059 AGCAATGCCTTAATGACCAAT
1 AGCAATGAATTAATGACCAAG
28175080 AGCAA
1 AGCAA
28175085 AGACTTGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
AGCAATGAATTAATGACCAAG
Found at i:28178635 original size:18 final size:19
Alignment explanation
Indices: 28178606--28178643 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28178596 TAAATTTAAT
28178606 ATAAAAATAAATACAAAAA
1 ATAAAAATAAATACAAAAA
*
28178625 ATAAAAA-AAATAGAAAAA
1 ATAAAAATAAATACAAAAA
28178643 A
1 A
28178644 GGTAAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (19 bp):
ATAAAAATAAATACAAAAA
Found at i:28178641 original size:10 final size:9
Alignment explanation
Indices: 28178606--28178674 Score: 52
Period size: 9 Copynumber: 7.8 Consensus size: 9
28178596 TAAATTTAAT
28178606 ATAAAAATAA
1 ATAAAAA-AA
*
28178616 ATACAAAAA
1 ATAAAAAAA
28178625 ATAAAAAAA
1 ATAAAAAAA
*
28178634 AT-AGAAAA
1 ATAAAAAAA
***
28178642 A-AGGTAAA
1 ATAAAAAAA
**
28178650 CGAAAAAAA
1 ATAAAAAAA
28178659 ATAAAAAAA
1 ATAAAAAAA
28178668 ATAAAAA
1 ATAAAAA
28178675 TGAGTAAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
8 10 0.22
9 30 0.65
10 6 0.13
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:28181871 original size:26 final size:25
Alignment explanation
Indices: 28181838--28181890 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
28181828 ACACGAAATG
28181838 AAAATATAATATA-AAAATAATTTTAA
1 AAAATATAA-ATACAAAATAA-TTTAA
*
28181864 AAAATATAAATACAATATAATTTAA
1 AAAATATAAATACAAAATAATTTAA
28181889 AA
1 AA
28181891 GTTTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAATATAAATACAAAATAATTTAA
Found at i:28181988 original size:21 final size:22
Alignment explanation
Indices: 28181963--28182009 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
28181953 ATAAATTGTA
28181963 ATATAATAATT-TTT-ATATTTT
1 ATATAAT-ATTATTTCATATTTT
28181984 ATAT-ATATTATTTCATATTTT
1 ATATAATATTATTTCATATTTT
28182005 ATATA
1 ATATA
28182010 TTAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 5 0.22
21 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATAATATTATTTCATATTTT
Found at i:28182197 original size:17 final size:18
Alignment explanation
Indices: 28182163--28182201 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28182153 TCGTTTTATA
*
28182163 TTTTTGGTTTGAATTGAC
1 TTTTTGGTTTGAACTGAC
*
28182181 TTTTTTGTTTG-ACTGAC
1 TTTTTGGTTTGAACTGAC
28182198 TTTT
1 TTTT
28182202 GTGGAGGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.13, C:0.08, G:0.18, T:0.62
Consensus pattern (18 bp):
TTTTTGGTTTGAACTGAC
Found at i:28187767 original size:11 final size:9
Alignment explanation
Indices: 28187729--28187759 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28187719 GGACCCCATA
28187729 TTAACAATAT
1 TTAA-AATAT
28187739 TTAAAATAT
1 TTAAAATAT
28187748 TTAAAATAT
1 TTAAAATAT
28187757 TTA
1 TTA
28187760 TTAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAAAATAT
Found at i:28188195 original size:17 final size:17
Alignment explanation
Indices: 28188170--28188212 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28188160 TGGTTCTCAT
28188170 ATTAAAAAAAATTATGA
1 ATTAAAAAAAATTATGA
* *
28188187 ATTATAAAAAATTTTGA
1 ATTAAAAAAAATTATGA
28188204 A--AAAAAAAA
1 ATTAAAAAAAA
28188213 ACTCAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
17 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
ATTAAAAAAAATTATGA
Found at i:28188496 original size:23 final size:23
Alignment explanation
Indices: 28188444--28188496 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
28188434 GAGTCTCATA
* *
28188444 AAAAAATTTTTAATAATAAATAT
1 AAAAAAGTTTGAATAATAAATAT
*
28188467 ATGAAAAGTTTGAA-AATAAAATAT
1 A-AAAAAGTTTGAATAAT-AAATAT
28188491 AAAAAA
1 AAAAAA
28188497 CAAATGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
AAAAAAGTTTGAATAATAAATAT
Found at i:28189328 original size:18 final size:18
Alignment explanation
Indices: 28189305--28189339 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28189295 TAGTTCAATG
28189305 TTTTTTAATTTTTTAATA
1 TTTTTTAATTTTTTAATA
*
28189323 TTTTTTATTTTTTTAAT
1 TTTTTTAATTTTTTAAT
28189340 TATTGATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTAATTTTTTAATA
Found at i:28189601 original size:18 final size:18
Alignment explanation
Indices: 28189565--28189603 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28189555 TTTTTAATAA
**
28189565 ATAAGTTATAAATTTAAT
1 ATAAGTTATAAATAAAAT
*
28189583 ATAAGTTATCAATAAAAT
1 ATAAGTTATAAATAAAAT
28189601 ATA
1 ATA
28189604 TTATATGCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
ATAAGTTATAAATAAAAT
Found at i:28192348 original size:34 final size:34
Alignment explanation
Indices: 28192305--28192374 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
28192295 ATTCTGGGAC
* *
28192305 ATAGACTTCATTTTGGTCGTACTGTTTCTCATTT
1 ATAGACTTCATTTTGATCATACTGTTTCTCATTT
*
28192339 ATAGACTTCATTTTGATCATATTGTTTCTCATTT
1 ATAGACTTCATTTTGATCATACTGTTTCTCATTT
28192373 AT
1 AT
28192375 GATATTGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.51
Consensus pattern (34 bp):
ATAGACTTCATTTTGATCATACTGTTTCTCATTT
Found at i:28197999 original size:23 final size:25
Alignment explanation
Indices: 28197973--28198018 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
28197963 AATATATACT
*
28197973 AAATCATATTA-AAA-ATCATGCAA
1 AAATCATAATAGAAATATCATGCAA
28197996 AAATCATAATAGAAATATCATGC
1 AAATCATAATAGAAATATCATGC
28198019 TAACAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (25 bp):
AAATCATAATAGAAATATCATGCAA
Found at i:28198092 original size:13 final size:13
Alignment explanation
Indices: 28198057--28198096 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
28198047 AAAATCATAC
28198057 CAAAAATATCAT-
1 CAAAAATATCATG
*
28198069 -AATAA-ATCATG
1 CAAAAATATCATG
28198080 CAAAAATATCATG
1 CAAAAATATCATG
28198093 CAAA
1 CAAA
28198097 TATTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
10 5 0.22
11 4 0.17
12 4 0.17
13 10 0.43
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (13 bp):
CAAAAATATCATG
Found at i:28198117 original size:20 final size:20
Alignment explanation
Indices: 28198089--28198126 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28198079 GCAAAAATAT
28198089 CATGCAAATATTTAATAAAC
1 CATGCAAATATTTAATAAAC
*
28198109 CATGGAAATATTTAATAA
1 CATGCAAATATTTAATAA
28198127 TAAATCATGC
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:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (20 bp):
CATGCAAATATTTAATAAAC
Found at i:28202592 original size:29 final size:29
Alignment explanation
Indices: 28202553--28202616 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
28202543 TGCATGGATG
*
28202553 AATAC-ATATGTTAGTGATGCTAGATTAA
1 AATACAATATGTTAGTGATGCTAGAATAA
28202581 AATACAATATGTTAGTGATGCTAGAATAA
1 AATACAATATGTTAGTGATGCTAGAATAA
28202610 AATACAA
1 AATACAA
28202617 CACATAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (29 bp):
AATACAATATGTTAGTGATGCTAGAATAA
Found at i:28203656 original size:18 final size:18
Alignment explanation
Indices: 28203619--28203657 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28203609 AAACTTAATC
*
28203619 AATTTTATTTTTTGTTAA
1 AATTTTATTTTTTGTGAA
28203637 AATTTTATTTTTAT-TGAA
1 AATTTTATTTTT-TGTGAA
28203655 AAT
1 AAT
28203658 ATATCTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
AATTTTATTTTTTGTGAA
Found at i:28204125 original size:33 final size:33
Alignment explanation
Indices: 28204087--28204158 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
28204077 ACTTTCATTA
* *
28204087 AAATTTCATCTAAATTATTTCATCATTTAGGTT
1 AAATTTCATCTAAATTATTCCACCATTTAGGTT
28204120 AAATTTCATCTAAATTATTCCACCATTTAGGTT
1 AAATTTCATCTAAATTATTCCACCATTTAGGTT
28204153 AAATTT
1 AAATTT
28204159 AGAGAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.46
Consensus pattern (33 bp):
AAATTTCATCTAAATTATTCCACCATTTAGGTT
Found at i:28210177 original size:34 final size:36
Alignment explanation
Indices: 28210119--28210188 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
28210109 ATAATCTTAT
*
28210119 ATAAATAAATATAATTATACAATTACATAATAATTA
1 ATAAATAAATATAATCATACAATTACATAATAATTA
* *
28210155 ATAAAT-AA-ATAATCATATAATTACATTATAATTA
1 ATAAATAAATATAATCATACAATTACATAATAATTA
28210189 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 23 0.74
35 2 0.06
36 6 0.19
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAAATAAATATAATCATACAATTACATAATAATTA
Found at i:28210312 original size:24 final size:23
Alignment explanation
Indices: 28210285--28210343 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 23
28210275 TTAATACTAA
28210285 AATAAATTTAATATAATTTAATAT
1 AATAAATTTAATATAATTT-ATAT
*
28210309 AATAAATTT--TATAA-TTGTAT
1 AATAAATTTAATATAATTTATAT
28210329 AATAAA-TTAAT-TAAT
1 AATAAATTTAATATAAT
28210344 AAATAACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 3 0.10
22 5 0.16
24 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATAAATTTAATATAATTTATAT
Found at i:28210366 original size:22 final size:22
Alignment explanation
Indices: 28210327--28210376 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
28210317 TTATAATTGT
**
28210327 ATAATAAATTAATTAATAAATAA
1 ATAA-AAATTAAAAAATAAATAA
* *
28210350 CTAAAAATTAAAAAATACATAA
1 ATAAAAATTAAAAAATAAATAA
28210372 ATAAA
1 ATAAA
28210377 CAATGCATTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAAAATTAAAAAATAAATAA
Found at i:28214054 original size:5 final size:5
Alignment explanation
Indices: 28214044--28214094 Score: 59
Period size: 5 Copynumber: 10.4 Consensus size: 5
28214034 ATTATCTGCC
** * *
28214044 ATATT ATATT ATCCT ATACT ATATT ATATT ATATT ATACT ATATT AT-TT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
28214093 AT
1 AT
28214095 TTCATTTGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:28214069 original size:20 final size:20
Alignment explanation
Indices: 28214044--28214094 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
28214034 ATTATCTGCC
*
28214044 ATATTATATTATCCTATACT
1 ATATTATATTATACTATACT
*
28214064 ATATTATATTATATTATACT
1 ATATTATATTATACTATACT
28214084 ATATTAT-TTAT
1 ATATTATATTAT
28214095 TTCATTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTATATTATACTATACT
Found at i:28214552 original size:19 final size:20
Alignment explanation
Indices: 28214528--28214567 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28214518 AGGGAATCAA
28214528 GAAAAA-TTTTGGAATTTTT
1 GAAAAATTTTTGGAATTTTT
*
28214547 GAAAAATTTTTGGGATTTTT
1 GAAAAATTTTTGGAATTTTT
28214567 G
1 G
28214568 CATTTTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (20 bp):
GAAAAATTTTTGGAATTTTT
Found at i:28215155 original size:22 final size:21
Alignment explanation
Indices: 28215130--28215180 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
28215120 TAGATAAGTT
28215130 TTTTTAAATAATAAAAAATATA
1 TTTTTAAATAATAAAAAA-ATA
* ** *
28215152 TTTTTAAGTTTTCAAAAAATA
1 TTTTTAAATAATAAAAAAATA
28215173 TTTTTAAA
1 TTTTTAAA
28215181 AAAATCCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTTAAATAATAAAAAAATA
Found at i:28216859 original size:33 final size:33
Alignment explanation
Indices: 28216786--28216879 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
28216776 CATGATGATT
* * * * *
28216786 GCTAACTATTATAACCCGCTAGTCAGAGCCTTAT
1 GCTAACTACTATCACCCGTTAG-CAGGGCCTTAC
*
28216820 GCTAACTACTATCACCTGTTAGCAGGGCCTTAC
1 GCTAACTACTATCACCCGTTAGCAGGGCCTTAC
*
28216853 GTTAACTACTATCACCCGTTAGCAGGG
1 GCTAACTACTATCACCCGTTAGCAGGG
28216880 TCGTATGATC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 34 0.65
34 18 0.35
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (33 bp):
GCTAACTACTATCACCCGTTAGCAGGGCCTTAC
Found at i:28219900 original size:28 final size:27
Alignment explanation
Indices: 28219866--28219945 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
28219856 ACAAAATCAT
* *
28219866 CACTTGTAAGATTTTAACCAATCTTTTG
1 CACTTGTAAGATTTCAA-CAATCATTTG
* * *
28219894 CCCTTGTAA-AATTCAAAAATCATTTG
1 CACTTGTAAGATTTCAACAATCATTTG
28219920 CACTTGTAAGATTTCAAACAATCATT
1 CACTTGTAAGATTTC-AACAATCATT
28219946 CTTAACCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 16 0.38
27 9 0.21
28 17 0.40
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (27 bp):
CACTTGTAAGATTTCAACAATCATTTG
Found at i:28219919 original size:26 final size:28
Alignment explanation
Indices: 28219866--28219945 Score: 92
Period size: 26 Copynumber: 2.9 Consensus size: 28
28219856 ACAAAATCAT
* * * *
28219866 CACTTGTAAGATTTTAACCAATCTTTTG
1 CACTTGTAAGAATTCAAACAATCATTTG
*
28219894 CCCTTGTAA-AATTCAAA-AATCATTTG
1 CACTTGTAAGAATTCAAACAATCATTTG
*
28219920 CACTTGTAAGATTTCAAACAATCATT
1 CACTTGTAAGAATTCAAACAATCATT
28219946 CTTAACCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 16 0.37
27 12 0.28
28 15 0.35
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (28 bp):
CACTTGTAAGAATTCAAACAATCATTTG
Found at i:28223715 original size:17 final size:16
Alignment explanation
Indices: 28223673--28223715 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
28223663 AAAAGAGGTA
*
28223673 AAAATTATAATTAAGT
1 AAAATTATAATTAAAT
28223689 AAAATATATAATATAAAT
1 AAAAT-TATAAT-TAAAT
*
28223707 AGAATTATA
1 AAAATTATA
28223716 GAAGTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
AAAATTATAATTAAAT
Found at i:28231378 original size:38 final size:38
Alignment explanation
Indices: 28231301--28231380 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
28231291 TAGAACAAAA
* *
28231301 ATCATAGTAAACCCTTTAGTGTAATGGGATAAAAGTAT
1 ATCATAGTAAACCCTTTAGTGCAATGAGATAAAAGTAT
28231339 ATCATAGT-AACCCGTTTTA-TGCAATGAGATAGAAA-TAT
1 ATCATAGTAAACCC--TTTAGTGCAATGAGATA-AAAGTAT
28231377 ATCA
1 ATCA
28231381 CTGATGGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 5 0.14
38 25 0.68
39 7 0.19
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (38 bp):
ATCATAGTAAACCCTTTAGTGCAATGAGATAAAAGTAT
Found at i:28235694 original size:2 final size:2
Alignment explanation
Indices: 28235687--28235715 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28235677 ATGAAACTTC
28235687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28235716 AAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28235860 original size:10 final size:10
Alignment explanation
Indices: 28235845--28235884 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
28235835 TTGATTATTC
28235845 ATATACATAT
1 ATATACATAT
28235855 ATATACATAT
1 ATATACATAT
*
28235865 ACATACATAT
1 ATATACATAT
*
28235875 ATATATATAT
1 ATATACATAT
28235885 GGATAGATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATACATAT
Found at i:28235865 original size:16 final size:16
Alignment explanation
Indices: 28235844--28235881 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28235834 ATTGATTATT
*
28235844 CATATACATATATATA
1 CATATACATACATATA
28235860 CATATACATACATATA
1 CATATACATACATATA
*
28235876 TATATA
1 CATATA
28235882 TATGGATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
CATATACATACATATA
Found at i:28237441 original size:12 final size:12
Alignment explanation
Indices: 28237399--28237442 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
28237389 TTTGATATAT
28237399 TTTTTATATAGACA
1 TTTTTA-ATAGA-A
*
28237413 TTTTTAATAAAA
1 TTTTTAATAGAA
*
28237425 ATTTTAATAGAA
1 TTTTTAATAGAA
28237437 TTTTTA
1 TTTTTA
28237443 TTGTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 4 0.15
14 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (12 bp):
TTTTTAATAGAA
Found at i:28244456 original size:84 final size:84
Alignment explanation
Indices: 28244313--28244484 Score: 317
Period size: 84 Copynumber: 2.0 Consensus size: 84
28244303 TCCTGTTATG
*
28244313 AACAATGTCTCACCCTACCCATATCAGTCTTCTCTACAACTATCTTACTCATCAATATATCAATA
1 AACAATGTCTCACCCTACCCATATCAGTCTTCTCTACAACCATCTTACTCATCAATATATCAATA
28244378 TGTTCTCATATATAACCTA
66 TGTTCTCATATATAACCTA
*
28244397 AACAATGTCTCACCCTACCCATATCAGTCTTCTCTACAACCATCTTACTCATCAGTATATCAATA
1 AACAATGTCTCACCCTACCCATATCAGTCTTCTCTACAACCATCTTACTCATCAATATATCAATA
*
28244462 TGTTCTCATATATAGCCTA
66 TGTTCTCATATATAACCTA
28244481 AACA
1 AACA
28244485 TTCAACCCCC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (84 bp):
AACAATGTCTCACCCTACCCATATCAGTCTTCTCTACAACCATCTTACTCATCAATATATCAATA
TGTTCTCATATATAACCTA
Found at i:28246017 original size:26 final size:26
Alignment explanation
Indices: 28245979--28246063 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
28245969 TGGGAAGAGG
*
28245979 AAAAATGAAAAATGGAAAA-AAAAAT
1 AAAAATGAAAAATGAAAAAGAAAAAT
*
28246004 AAAAATTGAGAAATGAAAAAGAAAAA-
1 AAAAA-TGAAAAATGAAAAAGAAAAAT
* *
28246030 AATGAAA-AAAAAATGTAAAAAGAGAAAAA
1 AA--AAATGAAAAATG-AAAAAGA-AAAAT
28246059 AAAAA
1 AAAAA
28246064 AACTCAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
25 5 0.10
26 20 0.41
27 15 0.31
28 7 0.14
29 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (26 bp):
AAAAATGAAAAATGAAAAAGAAAAAT
Found at i:28246063 original size:40 final size:40
Alignment explanation
Indices: 28245986--28246063 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
28245976 AGGAAAAATG
**
28245986 AAAAATGGAAAAAAAAATAAAAATTGAGAAATGAAAAAGAA
1 AAAAATGGAAAAAAAAATAAAAA-TGAGAAAAAAAAAAGAA
28246027 AAAAAT-GAAAAAAAAATGTAAAAA-GAGAAAAAAAAAA
1 AAAAATGGAAAAAAAAA--TAAAAATGAGAAAAAAAAAA
28246064 AACTCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 21 0.64
41 6 0.18
42 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (40 bp):
AAAAATGGAAAAAAAAATAAAAATGAGAAAAAAAAAAGAA
Found at i:28246064 original size:27 final size:26
Alignment explanation
Indices: 28245996--28246065 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
28245986 AAAAATGGAA
*
28245996 AAAAAAATAAAAATTGAGAAATGAAAAAG
1 AAAAAAATAAAAA---AAAAATGAAAAAG
*
28246025 AAAAAAATGAAAAAAAAATGTAAAAAG
1 AAAAAAATAAAAAAAAAATG-AAAAAG
*
28246052 AGAAAAA-AAAAAAA
1 AAAAAAATAAAAAAA
28246066 CTCAAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 12 0.33
27 12 0.33
29 12 0.33
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (26 bp):
AAAAAAATAAAAAAAAAATGAAAAAG
Found at i:28246780 original size:71 final size:71
Alignment explanation
Indices: 28246591--28246784 Score: 228
Period size: 71 Copynumber: 2.7 Consensus size: 71
28246581 TGGTTGACAC
* * * *
28246591 AACCTATGTATTGTGATCAAATGATGGAAATAATGTGAATCAGTGGACAAAATTCATGGCTAATG
1 AACCTATGAATGGTGATCAAATGATGGAAATAATGTGAATCAGTGGACGAAATTCATGGCTAATA
28246656 CTAAGA
66 CTAAGA
* ** * * *
28246662 AACCTATGAGTTCTGATCAAATGATGAAAATAATGTGGATCAGTGGACGAAATTCATGGCTAGTA
1 AACCTATGAATGGTGATCAAATGATGGAAATAATGTGAATCAGTGGACGAAATTCATGGCTAATA
*
28246727 CTGAGA
66 CTAAGA
* * * * *
28246733 AGCC-AGTGAATGGTGATCAAATGATGGAATTAATGTAAATTATTGGACGAAA
1 AACCTA-TGAATGGTGATCAAATGATGGAAATAATGTGAATCAGTGGACGAAA
28246785 CACATAACTT
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
70 1 0.01
71 102 0.99
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (71 bp):
AACCTATGAATGGTGATCAAATGATGGAAATAATGTGAATCAGTGGACGAAATTCATGGCTAATA
CTAAGA
Found at i:28247392 original size:16 final size:17
Alignment explanation
Indices: 28247361--28247393 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28247351 CTCACAAATG
28247361 TGAATCTTGAAATCTTA
1 TGAATCTTGAAATCTTA
*
28247378 TGAATC-TGAATTCTTA
1 TGAATCTTGAAATCTTA
28247394 CGAAGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
TGAATCTTGAAATCTTA
Found at i:28247546 original size:15 final size:15
Alignment explanation
Indices: 28247526--28247570 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
28247516 CCTTATGAAT
28247526 CTTTGAATTGTAAAC
1 CTTTGAATTGTAAAC
*
28247541 CTTTGAATTGCAAAC
1 CTTTGAATTGTAAAC
28247556 CTTTG-ATTGTCAAAC
1 CTTTGAATTGT-AAAC
28247571 TCAAATTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (15 bp):
CTTTGAATTGTAAAC
Found at i:28247729 original size:44 final size:43
Alignment explanation
Indices: 28247641--28248094 Score: 336
Period size: 44 Copynumber: 10.6 Consensus size: 43
28247631 GTCGATGAGC
** * * * *
28247641 TTTATTTTTCAAAGTTATTGAGCTTTTGATTAGATGAGCATTA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
* **
28247684 TTTATGTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAATTTTA
1 TTTAT-TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
* * * * **
28247728 TTTATTTTTTTAAAGTCGTTAAGCCTTTAATTAGAAAAGTCTTTA
1 TTTA-TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAG-CTTTA
* * *
28247773 --T-TTTTT-AAAATCGTTGAGCCTCTGTTTAGAGGAG-TCATA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT-TTA
* * * * * *
28247812 TTTACTTTTTCAAAAGTCATTGAACTTTTGATTAGAGAAGCCTTA
1 TTTA-TTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
** * *
28247857 TTTA-TTTTCTAAGAGTTATTGAGCCTCTTATTAGAAGAGC----
1 TTTATTTTTC-AA-AGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
* * * * **
28247897 CTTGTTTTTCAAAGTCATTGAGCCTCTG-TTAAAATAGCTTTA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
* * * *
28247939 TTTATTTTCCAAAGTCGTTGAGCCCCTGTTTAGAGGAGCTTTG
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
* * * *
28247982 TTTAATTTCCAAAGTCGTTGAGCCTTTAATTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
** *
28248025 TTTATTTTTCCAGGGTCATTGAGCCTCTGATTAGAGGAGCTTTA
1 TTTATTTTT-CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
28248069 TTTATTTTCTCAAAGTCGTTGAGCCT
1 TTTATTTT-TCAAAGTCGTTGAGCCT
28248095 TTATTTAAAA
Statistics
Matches: 319, Mismatches: 72, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
38 9 0.03
39 16 0.05
40 25 0.08
41 11 0.03
42 23 0.07
43 72 0.23
44 130 0.41
45 33 0.10
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (43 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTA
Found at i:28247858 original size:84 final size:83
Alignment explanation
Indices: 28247641--28247859 Score: 192
Period size: 84 Copynumber: 2.6 Consensus size: 83
28247631 GTCGATGAGC
* * * *
28247641 TTTATTTTTCAAAGTTATTGAGCTTTTGATTAGATG-AGCATTATTTATGTTTTCAAAGTTGTTG
1 TTTATTTTTCAAAGTCATTGAACTTTTGATTAGA-GAAGCATTA--T-T-TTTTCAAAATCGTTG
**
28247705 AGCCTCTGATTAGAGGAATTTTA
61 AGCCTCTGATTAGAGGAATCATA
* * * * * *
28247728 TTTATTTTTTTAAAGTCGTT-AAGCCTTTAATTAGAAAAGTCTTTATTTTTT-AAAATCGTTGAG
1 TTTA-TTTTTCAAAGTCATTGAA-CTTTTGATTAGAGAAG-CATTATTTTTTCAAAATCGTTGAG
* *
28247791 CCTCTGTTTAGAGGAGTCATA
63 CCTCTGATTAGAGGAATCATA
*
28247812 TTTACTTTTTCAAAAGTCATTGAACTTTTGATTAGAGAAGCCTTATTT
1 TTTA-TTTTTC-AAAGTCATTGAACTTTTGATTAGAGAAGCATTATTT
28247860 ATTTTCTAAG
Statistics
Matches: 105, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
84 43 0.41
85 25 0.24
86 3 0.03
87 6 0.06
88 24 0.23
89 4 0.04
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (83 bp):
TTTATTTTTCAAAGTCATTGAACTTTTGATTAGAGAAGCATTATTTTTTCAAAATCGTTGAGCCT
CTGATTAGAGGAATCATA
Found at i:28249878 original size:22 final size:22
Alignment explanation
Indices: 28249836--28249878 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28249826 TTTTGGTATT
28249836 TTTATTATTTTTATTTATTCTA
1 TTTATTATTTTTATTTATTCTA
*
28249858 TTTATTTATTTTTCTTT-TTCT
1 TTTA-TTATTTTTATTTATTCT
28249879 TGTATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTATTTTTATTTATTCTA
Found at i:28254540 original size:23 final size:22
Alignment explanation
Indices: 28254506--28254560 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
28254496 TTTTAATTAG
28254506 AATTT-ATAAAAT-AATTTTATT
1 AATTTAATAAAATAAATTTTA-T
28254527 AATTTAATATAAATAAATTTTAT
1 AATTTAATA-AAATAAATTTTAT
*
28254550 AATATAATAAA
1 AATTTAATAAA
28254561 CTAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 5 0.17
23 13 0.43
24 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAATAAAATAAATTTTAT
Found at i:28254649 original size:29 final size:29
Alignment explanation
Indices: 28254596--28254652 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
28254586 ATTATTATTA
* **
28254596 TTATTATATAATAAATTAATTAATAAATT
1 TTATTATATAATAAACTAAGAAATAAATT
*
28254625 TTATTATTTAATAAACTAAGAAATAAAT
1 TTATTATATAATAAACTAAGAAATAAAT
28254653 AAATTTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TTATTATATAATAAACTAAGAAATAAATT
Found at i:28258059 original size:30 final size:30
Alignment explanation
Indices: 28258000--28258059 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28257990 TATTTAATTA
* * * *
28258000 TTTAATTATATATATTTATATAATGATATT
1 TTTAAATATATATATTTAAAAAATAATATT
*
28258030 TTTAAATATTTATATTTAAAAAATAATATT
1 TTTAAATATATATATTTAAAAAATAATATT
28258060 CTATATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTAAATATATATATTTAAAAAATAATATT
Found at i:28258066 original size:21 final size:21
Alignment explanation
Indices: 28258034--28258086 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
28258024 GATATTTTTA
28258034 AATATTTATA-TTTAAAAAAT
1 AATATTTATATTTTAAAAAAT
28258054 AATATTCTATATTTTAAAAAAT
1 AATATT-TATATTTTAAAAAAT
28258076 AATATTT-TATT
1 AATATTTATATT
28258087 AATTTTAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.32
21 5 0.16
22 16 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTATATTTTAAAAAAT
Found at i:28260984 original size:22 final size:22
Alignment explanation
Indices: 28260959--28261028 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
28260949 TTTTAGATAT
28260959 CATAGACGAAATTAGCAGGTAA
1 CATAGACGAAATTAGCAGGTAA
* * *
28260981 CATATATTGGAAGA-TAACA--TAA
1 CATAGA--CGAA-ATTAGCAGGTAA
28261003 CATAGACGAAATTAGCAGGTAA
1 CATAGACGAAATTAGCAGGTAA
28261025 CATA
1 CATA
28261029 TATTGGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
22 20 0.56
24 7 0.19
25 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (22 bp):
CATAGACGAAATTAGCAGGTAA
Found at i:28261008 original size:44 final size:44
Alignment explanation
Indices: 28260959--28261057 Score: 198
Period size: 44 Copynumber: 2.2 Consensus size: 44
28260949 TTTTAGATAT
28260959 CATAGACGAAATTAGCAGGTAACATATATTGGAAGATAACATAA
1 CATAGACGAAATTAGCAGGTAACATATATTGGAAGATAACATAA
28261003 CATAGACGAAATTAGCAGGTAACATATATTGGAAGATAACATAA
1 CATAGACGAAATTAGCAGGTAACATATATTGGAAGATAACATAA
28261047 CATAGACGAAA
1 CATAGACGAAA
28261058 GGAAGGACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (44 bp):
CATAGACGAAATTAGCAGGTAACATATATTGGAAGATAACATAA
Found at i:28261047 original size:22 final size:22
Alignment explanation
Indices: 28260978--28261050 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
28260968 AATTAGCAGG
28260978 TAACATATATTGGAAGATAACA
1 TAACATATATTGGAAGATAACA
* * *
28261000 TAACATAGA--CGAA-ATTAGCA
1 TAACATATATTGGAAGA-TAACA
28261020 GGTAACATATATTGGAAGATAACA
1 --TAACATATATTGGAAGATAACA
28261044 TAACATA
1 TAACATA
28261051 GACGAAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 1 0.03
20 7 0.18
22 23 0.59
24 7 0.18
25 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (22 bp):
TAACATATATTGGAAGATAACA
Found at i:28268944 original size:30 final size:31
Alignment explanation
Indices: 28268904--28268969 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
28268894 CAACAGAGCA
28268904 AAACACAGCCTCCAGTTGAATGCAAAAAGAT
1 AAACACAGCCTCCAGTTGAATGCAAAAAGAT
28268935 AAACA-AGCCTCCAGTTGAATGCAAAAAGAT
1 AAACACAGCCTCCAGTTGAATGCAAAAAGAT
28268965 AAACA
1 AAACA
28268970 TACTCATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (31 bp):
AAACACAGCCTCCAGTTGAATGCAAAAAGAT
Found at i:28269949 original size:2 final size:2
Alignment explanation
Indices: 28269942--28269970 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28269932 CAGATTACAA
28269942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28269971 AAGACTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28270119 original size:77 final size:77
Alignment explanation
Indices: 28270027--28270177 Score: 293
Period size: 77 Copynumber: 2.0 Consensus size: 77
28270017 AAGTTATTGA
28270027 TATACCATCCAAATAATAAAATTATGAAAATACAACAGTTCAAAACTATGCATACATAGCCCAAA
1 TATACCATCCAAATAATAAAATTATGAAAATACAACAGTTCAAAACTATGCATACATAGCCCAAA
28270092 ATCATAACCCTG
66 ATCATAACCCTG
*
28270104 TATACCATCCAAATAATAAAATTATGAAAATATAACAGTTCAAAACTATGCATACATAGCCCAAA
1 TATACCATCCAAATAATAAAATTATGAAAATACAACAGTTCAAAACTATGCATACATAGCCCAAA
28270169 ATCATAACC
66 ATCATAACC
28270178 ATTAATCAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (77 bp):
TATACCATCCAAATAATAAAATTATGAAAATACAACAGTTCAAAACTATGCATACATAGCCCAAA
ATCATAACCCTG
Found at i:28271989 original size:15 final size:15
Alignment explanation
Indices: 28271959--28272002 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28271949 AAAAATAAAA
*
28271959 TAAAATAATTTAATT
1 TAAAATAATTGAATT
* *
28271974 TTAAATAATTGGATT
1 TAAAATAATTGAATT
28271989 TAAAATTAATTGAA
1 TAAAA-TAATTGAA
28272003 CTTACAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TAAAATAATTGAATT
Found at i:28272946 original size:57 final size:56
Alignment explanation
Indices: 28272821--28272942 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 56
28272811 TAGCAGAGGA
* *
28272821 AAATTTAAATTTTAATTTAATTAATTTATATAATTATTTTTAAAAATAATATATAAT
1 AAATTTAAATTTTAATTT-ATTAATTTATATAATTATTTTTAAAAATAACATATAAC
* *
28272878 AAATTTTAATTTTAATTT-TTAATTTATATAATTATTTTTATAAAATAACATCTAAC
1 AAATTTAAATTTTAATTTATTAATTTATATAATTATTTTTA-AAAATAACATATAAC
*
28272934 GAATTTAAA
1 AAATTTAAA
28272943 ATTTGAATCC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 22 0.38
56 19 0.33
57 17 0.29
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (56 bp):
AAATTTAAATTTTAATTTATTAATTTATATAATTATTTTTAAAAATAACATATAAC
Found at i:28272961 original size:56 final size:55
Alignment explanation
Indices: 28272846--28272965 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 55
28272836 TTTAATTAAT
* * * * ** *
28272846 TTATATAATTATTTTTAAAAATAATATATAATAAATTTTAATTTTAATTTTTAAT
1 TTATATAATTATTTTTAAAAATAACATATAACAAATTTAAATTTGAATTCCTAAC
* *
28272901 TTATATAATTATTTTTATAAAATAACATCTAACGAATTTAAAATTTGAA-TCCTAAC
1 TTATATAATTATTTTTA-AAAATAACATATAACAAATTT-AAATTTGAATTCCTAAC
28272957 TTATATAAT
1 TTATATAAT
28272966 CTTTTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
55 17 0.31
56 30 0.56
57 7 0.13
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (55 bp):
TTATATAATTATTTTTAAAAATAACATATAACAAATTTAAATTTGAATTCCTAAC
Found at i:28273042 original size:23 final size:23
Alignment explanation
Indices: 28273016--28273061 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28273006 ATAATAGAGG
28273016 GGTGATCTAAATTAAGTCGTAAT
1 GGTGATCTAAATTAAGTCGTAAT
*
28273039 GGTGATCTAAATTAAGTTGTAAT
1 GGTGATCTAAATTAAGTCGTAAT
28273062 AGATCTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (23 bp):
GGTGATCTAAATTAAGTCGTAAT
Found at i:28275903 original size:19 final size:18
Alignment explanation
Indices: 28275860--28275903 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
28275850 ATATAAAATA
28275860 TATTTTTTAATTTTTAATT
1 TATTTTTTAATTTTTAA-T
*
28275879 TATTTTTT-ATTATTTGAT
1 TATTTTTTAATT-TTTAAT
28275897 TATTTTT
1 TATTTTT
28275904 AATATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TATTTTTTAATTTTTAAT
Found at i:28276985 original size:11 final size:11
Alignment explanation
Indices: 28276968--28277008 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
28276958 ATGTGGATGA
28276968 AATTTTAAAAT
1 AATTTTAAAAT
*
28276979 TATTTTAAAGAT
1 AATTTTAAA-AT
28276991 AATTTTTAAAAT
1 AA-TTTTAAAAT
28277003 AATTTT
1 AATTTT
28277009 TGATTGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 12 0.46
12 7 0.27
13 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:28277004 original size:12 final size:12
Alignment explanation
Indices: 28276970--28277009 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
28276960 GTGGATGAAA
*
28276970 TTTTAAAATTA-
1 TTTTAAAATAAT
28276981 TTTTAAAGATAAT
1 TTTTAAA-ATAAT
28276994 TTTTAAAATAAT
1 TTTTAAAATAAT
28277006 TTTT
1 TTTT
28277010 GATTGAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.27
12 12 0.46
13 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
TTTTAAAATAAT
Found at i:28277528 original size:24 final size:25
Alignment explanation
Indices: 28277469--28277530 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
28277459 TTTATAATAT
** *
28277469 TTTTATTTTTATTTTATTTAATTTA
1 TTTTATTTAAATTTTATTTAATTCA
*
28277494 TTTTATGTAAATTTTATTT-ATTCA
1 TTTTATTTAAATTTTATTTAATTCA
28277518 TTTTATTTAAATT
1 TTTTATTTAAATT
28277531 AATTTTTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTATTTAAATTTTATTTAATTCA
Found at i:28277537 original size:29 final size:30
Alignment explanation
Indices: 28277473--28277537 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
28277463 TAATATTTTT
* *
28277473 ATTTTTATTTTATTTAATTTATTTTATGTA
1 ATTTTTATTTTATTCAATTTATTTAATGTA
* *
28277503 AATTTTA-TTTATTCATTTTATTTAAAT-TA
1 ATTTTTATTTTATTCAATTTATTT-AATGTA
28277532 ATTTTT
1 ATTTTT
28277538 TGTTAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
ATTTTTATTTTATTCAATTTATTTAATGTA
Found at i:28285601 original size:23 final size:23
Alignment explanation
Indices: 28285560--28285622 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
28285550 TAAATATATT
*
28285560 TTACTTATTTAA--ACATTTTTA
1 TTACTTGTTTAATTACATTTTTA
*
28285581 TTA-TT-TTATAGTTACATTTTTA
1 TTACTTGTT-TAATTACATTTTTA
28285603 TTACTTGTTTAATTACATTT
1 TTACTTGTTTAATTACATTT
28285623 ATTAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.06
20 4 0.11
21 3 0.09
22 12 0.34
23 12 0.34
24 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (23 bp):
TTACTTGTTTAATTACATTTTTA
Found at i:28288416 original size:47 final size:46
Alignment explanation
Indices: 28288320--28288415 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 46
28288310 ATTTTACAAG
*
28288320 TTTTATTTCTAAATTTTTCACCATTTGAGCTAATTTAGAAATTTCT
1 TTTTATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTTCT
28288366 TTTTGATTTCTAAATTTTTCACCATTT-AGGCCAATTTAGAAA-TTCT
1 TTTT-ATTTCTAAATTTTTCACCATTTGA-GCCAATTTAGAAATTTCT
28288412 TTTT
1 TTTT
28288416 TTTTTTATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
46 13 0.28
47 34 0.72
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (46 bp):
TTTTATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTTCT
Found at i:28289075 original size:26 final size:26
Alignment explanation
Indices: 28289002--28289075 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
28288992 AATTTGGGAC
* **
28289002 AAATTTAAAAAAATTTC-TCACCTAA
1 AAATTTTAAAAAATTTCATCATTTAA
* *
28289027 GAATTTTATAAAAATTT-ACCATTTAA
1 AAATTTTA-AAAAATTTCATCATTTAA
*
28289053 AAATTTTAAAATATTTCATCATT
1 AAATTTTAAAAAATTTCATCATT
28289076 AGATAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
25 13 0.34
26 25 0.66
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (26 bp):
AAATTTTAAAAAATTTCATCATTTAA
Found at i:28289124 original size:17 final size:17
Alignment explanation
Indices: 28289102--28289139 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28289092 TTTTCAAAAA
*
28289102 TTTTATTTTATTTTATT
1 TTTTATATTATTTTATT
28289119 TTTTATATTATTTTATT
1 TTTTATATTATTTTATT
28289136 TTTT
1 TTTT
28289140 CTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATATTATTTTATT
Found at i:28289461 original size:19 final size:19
Alignment explanation
Indices: 28289437--28289480 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28289427 AAAAAATCTT
*
28289437 TTTTTTCTTCAGAT-TTCTC
1 TTTTTTCCTCA-ATCTTCTC
*
28289456 TTTTTTCCTCACTCTTCTC
1 TTTTTTCCTCAATCTTCTC
28289475 TTTTTT
1 TTTTTT
28289481 TTCCTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.07, C:0.25, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTTCCTCAATCTTCTC
Found at i:28289909 original size:18 final size:18
Alignment explanation
Indices: 28289880--28289917 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
28289870 CCAATTTTCT
28289880 TTAAATTCTAACTTCAAAC
1 TTAAATTCTAACTT-AAAC
28289899 TTAAA-TCTAACTTAAAC
1 TTAAATTCTAACTTAAAC
28289916 TT
1 TT
28289918 TATAGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATTCTAACTTAAAC
Found at i:28290236 original size:44 final size:44
Alignment explanation
Indices: 28290172--28290647 Score: 459
Period size: 44 Copynumber: 11.0 Consensus size: 44
28290162 AAAACCCTTT
* * * *
28290172 TAAATAGAGGCTC--CATACTTTTGAGAAATAAATAAAGCTCATC
1 TAAACAGAGGCTCAACA-ACTTTTGAAAAATAAATAAGGCTCTTC
* * * *
28290215 TAAGCAGAGGCTTAACGACTTTTGAAAAGTAAATAAGGCTTCTT-
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGC-TCTTC
* * *
28290259 TAAACAGAGGCTCAACAATTTTTGAAAAGTAAATAAGGCTCATC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* * ** *
28290303 TAAGCAAAGGCTCAATGATTTTTGAAAAATAAATAAGGCT-TATC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCT-TC
* * * * *
28290347 CAAATAGAGGTTCAACAACTTTTGAAAAGTAAATAAGGCTCTTT
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* * * * **
28290391 TAAATAGAAGCTCAATAACTTTTGAAAAGTAAATAAATCTCTTC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* * * *
28290435 TAAATAGAGGCTC-ACAACTTTTAAAAAATAAATAAAGCTCCTC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* *
28290478 TAAACAGAGGCTC-ACAACTTTTGAAAAATAAACAAGGCTCTTT
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* * * * * * *
28290521 TAAACAGAAGCTCAATAAC-TTTAAAAAATACATAAAGCCCCTC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* *
28290564 TAAATAGAGGCTCAATAAC-TTTGAAAAATAAATAAGGCTCTTC
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
* *
28290607 TAAACAAAGGCTC-ACAAC-TTTGAAAAATAAATAAAGCTCTT
1 TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTT
28290648 TGACAATTAT
Statistics
Matches: 358, Mismatches: 68, Indels: 15
0.81 0.15 0.03
Matches are distributed among these distances:
42 26 0.07
43 151 0.42
44 176 0.49
45 5 0.01
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (44 bp):
TAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAGGCTCTTC
Found at i:28292018 original size:16 final size:15
Alignment explanation
Indices: 28292015--28292095 Score: 67
Period size: 16 Copynumber: 5.1 Consensus size: 15
28292005 TTCTTTATTT
28292015 TTTTTAATTTTTTTCA
1 TTTTT-ATTTTTTTCA
*
28292031 TTTCTCATTTTTTTCA
1 TTT-TTATTTTTTTCA
28292047 TTTTTATTTTTTTCTTCA
1 TTTTTA--TTTTT-TTCA
28292065 TTTTTCA-TTTTTTC-
1 TTTTT-ATTTTTTTCA
*
28292079 TTTATCATTTTTTTCA
1 TTT-TTATTTTTTTCA
28292095 T
1 T
28292096 CCATTATTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
14 4 0.07
15 13 0.24
16 21 0.39
17 6 0.11
18 9 0.17
19 1 0.02
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTTTTCA
Found at i:28292040 original size:26 final size:25
Alignment explanation
Indices: 28291986--28292044 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
28291976 CTCGTTTTAT
* *
28291986 ATTTTTTTTTATTTTTTCATTCTTT
1 ATTTTTTTTAATTTTTTCATTCTTC
28292011 ATTTTTTTTAATTTTTTTCATT-TCTC
1 ATTTTTTTTAA-TTTTTTCATTCT-TC
28292037 ATTTTTTT
1 ATTTTTTT
28292045 CATTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (25 bp):
ATTTTTTTTAATTTTTTCATTCTTC
Found at i:28292041 original size:25 final size:25
Alignment explanation
Indices: 28291988--28292095 Score: 84
Period size: 25 Copynumber: 4.4 Consensus size: 25
28291978 CGTTTTATAT
* *
28291988 TTTTTTTTATTTTTTCA-TTCTTTA
1 TTTTTTTCATTTTTTCATTTCTTCA
*
28292012 TTTTTTTTAATTTTTTTCATTTC-TCA
1 -TTTTTTTCA-TTTTTTCATTTCTTCA
**
28292038 TTTTTTTCATTTTTATTTTTTTCTTCA
1 TTTTTTTCA-TTTT-TTCATTTCTTCA
*
28292065 --TTTTTCATTTTTTC-TTT-ATCA
1 TTTTTTTCATTTTTTCATTTCTTCA
28292086 TTTTTTTCAT
1 TTTTTTTCAT
28292096 CCATTATTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.04
22 3 0.04
23 10 0.14
24 4 0.06
25 28 0.40
26 16 0.23
27 6 0.09
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTTCATTTTTTCATTTCTTCA
Found at i:28292050 original size:7 final size:7
Alignment explanation
Indices: 28292024--28292090 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
28292014 TTTTTTAATT
28292024 TTTTTCA
1 TTTTTCA
*
28292031 TTTCTCA
1 TTTTTCA
28292038 TTTTTTTCA
1 --TTTTTCA
28292047 TTTTT-A
1 TTTTTCA
28292053 TTTTT--
1 TTTTTCA
*
28292058 TTCTTCA
1 TTTTTCA
28292065 TTTTTCA
1 TTTTTCA
28292072 TTTTTTC-
1 -TTTTTCA
*
28292079 TTTATCA
1 TTTTTCA
28292086 TTTTT
1 TTTTT
28292091 TTCATCCATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 4 0.08
6 11 0.23
7 21 0.44
8 6 0.12
9 6 0.12
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:28292051 original size:26 final size:27
Alignment explanation
Indices: 28291997--28292077 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 27
28291987 TTTTTTTTTA
* * *
28291997 TTTTTTCA-TTCTTTATTTTTTTTAAT
1 TTTTTTCATTTCTTCATTTTTTTCATT
28292023 TTTTTTCATTTC-TCATTTTTTTCATT
1 TTTTTTCATTTCTTCATTTTTTTCATT
*
28292049 TTTATTT-TTTTCTTCA--TTTTTCATT
1 TTT-TTTCATTTCTTCATTTTTTTCATT
28292074 TTTT
1 TTTT
28292078 CTTTATCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 1 0.02
25 12 0.25
26 26 0.54
27 9 0.19
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTCATTTCTTCATTTTTTTCATT
Found at i:28292051 original size:34 final size:34
Alignment explanation
Indices: 28292022--28292093 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
28292012 TTTTTTTTAA
28292022 TTTTT-TTCATTTCTCATTTTTTTCATTTTTATT
1 TTTTTCTTCATTTCTCATTTTTTTCATTTTTATT
* *
28292055 TTTTTCTTCATTTTTCA-TTTTTTC-TTTATCATT
1 TTTTTCTTCATTTCTCATTTTTTTCATTT-TTATT
28292088 TTTTTC
1 TTTTTC
28292094 ATCCATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 3 0.09
33 22 0.63
34 10 0.29
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTTTCTTCATTTCTCATTTTTTTCATTTTTATT
Found at i:28294114 original size:172 final size:171
Alignment explanation
Indices: 28293887--28294334 Score: 566
Period size: 172 Copynumber: 2.6 Consensus size: 171
28293877 ACAACTTTTT
* * * * * * *
28293887 TTTTTTTGAAGTTTCATTTAAATTCTTCCATTATTTGGGA-CAAATTTAAAAAAATTTCTCACCT
1 TTTTATTGAAATTTCATCTAAATTATTCTACTATTTGGGATCAAATTTAGAAAAATTTCTCACCT
* * * * * *
28293951 AGAGATTTCTTTGAAATTTTACCATTTGAAATTTCTAAGATTTTCATCCTTGGATAATTGTT-AA
66 AGAGATTTCTTTAAAAATTTACCATTTGAAATTTCTAA-AATCTCATCATTAGATAATT-TTCAA
* * * *
28294015 ATGTTTTCAACCAAAATTTTTTTATTTGGAAAAAATATAACTAC
129 ATATTTTCAAACAAAA-TTTTTAATTTGAAAAAAATATAACTAC
*
28294059 TTTTATTGAAATTTCATCTAAATTATTCTACTATTT-GGATCAAATTTAGAAAAATTTTTTCACC
1 TTTTATTGAAATTTCATCTAAATTATTCTACTATTTGGGATCAAATTTAGAAAAA-TTTCTCACC
* *
28294123 TACAGATTTCTTAAAAAATTTACCATTTGAAATTTCTATAAATCTCATCATTAGATAATTTTCAA
65 TAGAGATTTCTTTAAAAATTTACCATTTGAAATTTCTA-AAATCTCATCATTAGATAATTTTCAA
*
28294188 ATATTTTCAAACAAAATTTTTAATTTGAAAAAAATATAATTAC
129 ATATTTTCAAACAAAATTTTTAATTTGAAAAAAATATAACTAC
* * *
28294231 TTTTATTGAAATTTTATCTAAATTATTCTACAATTTGGGAT-AAATTTAGAAAAATTTCTCACAT
1 TTTTATTGAAATTTCATCTAAATTATTCTACTATTTGGGATCAAATTTAGAAAAATTTCTCACCT
* *
28294295 AGAAATTT-TATAAAAATTTACCATTT-AAATTTTCTAAAAT
66 AGAGATTTCTTTAAAAATTTACCATTTGAAA-TTTCTAAAAT
28294335 ATTCCATCAT
Statistics
Matches: 241, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
169 7 0.03
170 22 0.09
171 17 0.07
172 116 0.48
173 78 0.32
174 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (171 bp):
TTTTATTGAAATTTCATCTAAATTATTCTACTATTTGGGATCAAATTTAGAAAAATTTCTCACCT
AGAGATTTCTTTAAAAATTTACCATTTGAAATTTCTAAAATCTCATCATTAGATAATTTTCAAAT
ATTTTCAAACAAAATTTTTAATTTGAAAAAAATATAACTAC
Found at i:28294426 original size:9 final size:9
Alignment explanation
Indices: 28294414--28294470 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
28294404 TTTAAAAAAC
28294414 ATAAATAAA
1 ATAAATAAA
*
28294423 ATAACT-AA
1 ATAAATAAA
28294431 ATAAATAAA
1 ATAAATAAA
28294440 AT-AATAAA
1 ATAAATAAA
28294448 ATAAATAAA
1 ATAAATAAA
*
28294457 A-ATACTAAA
1 ATA-AATAAA
28294466 ATAAA
1 ATAAA
28294471 AATAGCTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 16 0.40
9 23 0.57
10 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAATAAA
Found at i:28294436 original size:17 final size:18
Alignment explanation
Indices: 28294414--28294470 Score: 84
Period size: 17 Copynumber: 3.3 Consensus size: 18
28294404 TTTAAAAAAC
28294414 ATAAATAAAATAACT-AA
1 ATAAATAAAATAACTAAA
28294431 ATAAATAAAATAA-TAAA
1 ATAAATAAAATAACTAAA
28294448 ATAAATAAAA-ATACTAAA
1 ATAAATAAAATA-ACTAAA
28294466 ATAAA
1 ATAAA
28294471 AATAGCTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.05
17 26 0.70
18 9 0.24
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAATAAAATAACTAAA
Found at i:28294466 original size:8 final size:8
Alignment explanation
Indices: 28294417--28294469 Score: 54
Period size: 8 Copynumber: 6.2 Consensus size: 8
28294407 AAAAAACATA
28294417 AATAAAAT
1 AATAAAAT
28294425 AACT-AAAT
1 AA-TAAAAT
28294433 AAATAAAAT
1 -AATAAAAT
28294442 AATAAAAT
1 AATAAAAT
28294450 AAATAAAAAT
1 -AAT-AAAAT
*
28294460 ACTAAAAT
1 AATAAAAT
28294468 AA
1 AA
28294470 AAATAGCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 21 0.55
9 12 0.32
10 5 0.13
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAAAAT
Found at i:28296355 original size:2 final size:2
Alignment explanation
Indices: 28296343--28296375 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28296333 AGAATATAAG
*
28296343 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28296376 AAACTCTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28298057 original size:30 final size:30
Alignment explanation
Indices: 28298022--28298087 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
28298012 ACTTTAAATC
** *
28298022 AATTAAATTTTTAAATTTTTATTTTTATTT
1 AATTAAATTTTTAAACATTTATATTTATTT
*
28298052 GATTAAATTTTTAAACATTTATATTTATTT
1 AATTAAATTTTTAAACATTTATATTTATTT
28298082 AATTAA
1 AATTAA
28298088 GCTCTTGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
AATTAAATTTTTAAACATTTATATTTATTT
Found at i:28301608 original size:22 final size:20
Alignment explanation
Indices: 28301578--28301617 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28301568 TTATAATGTG
28301578 TTTTAGTTTTACTATAATTAAA
1 TTTTAG-TTTAC-ATAATTAAA
*
28301600 TTTTTGTTTACATAATTA
1 TTTTAGTTTACATAATTA
28301618 TATACCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTAGTTTACATAATTAAA
Found at i:28302159 original size:20 final size:20
Alignment explanation
Indices: 28302130--28302172 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28302120 GACTTTAGAA
*
28302130 CAAAGTTCTTTGTCAAGCAT
1 CAAAGGTCTTTGTCAAGCAT
*
28302150 CAAAGGTCTTTGTCAAGTAT
1 CAAAGGTCTTTGTCAAGCAT
28302170 CAA
1 CAA
28302173 CATAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (20 bp):
CAAAGGTCTTTGTCAAGCAT
Found at i:28305947 original size:27 final size:27
Alignment explanation
Indices: 28305917--28305968 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28305907 TTAATTTTAG
*
28305917 TTTGATTTTTATTTTAATTTGATTTGA
1 TTTGATTTTTAGTTTAATTTGATTTGA
* *
28305944 TTTGATTTTTGGTTTAATTTTATTT
1 TTTGATTTTTAGTTTAATTTGATTT
28305969 TTTAGACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (27 bp):
TTTGATTTTTAGTTTAATTTGATTTGA
Found at i:28310355 original size:2 final size:2
Alignment explanation
Indices: 28310348--28310377 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28310338 AACCAAACAG
*
28310348 GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28310378 AAGCATTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28324279 original size:12 final size:14
Alignment explanation
Indices: 28324262--28324301 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
28324252 TTGTTCTCGA
28324262 TTTATT-TT-TTAT
1 TTTATTATTATTAT
28324274 TTTATTATTATTAT
1 TTTATTATTATTAT
28324288 TATTATTATTATTA
1 T-TTATTATTATTA
28324302 ACTCTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 2 0.08
14 5 0.20
15 12 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:28324283 original size:3 final size:3
Alignment explanation
Indices: 28324270--28324301 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28324260 GATTTATTTT
28324270 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28324302 ACTCTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28327814 original size:28 final size:29
Alignment explanation
Indices: 28327782--28327838 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
28327772 TCTGGCAAGC
*
28327782 GTCAAAACTGATATGATAAAATA-AAAAA
1 GTCAAAACTGATATAATAAAATATAAAAA
28327810 GTCAAAACTGATATAATAAAATATAAAAA
1 GTCAAAACTGATATAATAAAATATAAAAA
28327839 TATCACCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (29 bp):
GTCAAAACTGATATAATAAAATATAAAAA
Found at i:28332608 original size:16 final size:17
Alignment explanation
Indices: 28332562--28332614 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
28332552 AATATTATTT
*
28332562 TAAATATAATATAAAAT
1 TAAATATAATATAAAAA
28332579 TAAATAT-ATATAAAAA
1 TAAATATAATATAAAAA
* *
28332595 TATATATAAT-TAAATA
1 TAAATATAATATAAAAA
28332611 TAAA
1 TAAA
28332615 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATATAATATAAAAA
Found at i:28332617 original size:12 final size:14
Alignment explanation
Indices: 28332570--28332620 Score: 65
Period size: 12 Copynumber: 3.9 Consensus size: 14
28332560 TTTAAATATA
*
28332570 ATATAAAATTAAAT
1 ATATATAATTAAAT
28332584 ATATATAA--AAAT
1 ATATATAATTAAAT
28332596 ATATATAATTAAAT
1 ATATATAATTAAAT
28332610 ATA-A-AATTAAA
1 ATATATAATTAAA
28332621 AAAATAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 19 0.56
13 1 0.03
14 14 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATATAATTAAAT
Found at i:28334796 original size:26 final size:27
Alignment explanation
Indices: 28334766--28334818 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
28334756 ATGCTAAAAT
28334766 AAATACTTTTATAAAT-ATTA-AATTTA
1 AAATACTTTTA-AAATAATTATAATTTA
28334792 AAATACTTTTAAAATAATTATAATTTA
1 AAATACTTTTAAAATAATTATAATTTA
28334819 TCAAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.16
26 15 0.60
27 6 0.24
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATACTTTTAAAATAATTATAATTTA
Found at i:28334867 original size:14 final size:15
Alignment explanation
Indices: 28334842--28334873 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
28334832 AATATGAAAA
28334842 AAATTAAATGAG-AG
1 AAATTAAATGAGAAG
28334856 AAATTAAATGAGAAG
1 AAATTAAATGAGAAG
28334871 AAA
1 AAA
28334874 ATAGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (15 bp):
AAATTAAATGAGAAG
Found at i:28335086 original size:16 final size:15
Alignment explanation
Indices: 28335065--28335094 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28335055 ATTCTAATTC
28335065 TTTCTCAATTGTTTTT
1 TTTCTCAATT-TTTTT
28335081 TTTCTCAATTTTTT
1 TTTCTCAATTTTTT
28335095 ATTTAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTCTCAATTTTTTT
Found at i:28339090 original size:24 final size:22
Alignment explanation
Indices: 28339049--28339109 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
28339039 TTATTTTTAA
* *
28339049 TTAAATTTAATTTTAAATATATT
1 TTAAATTTAATATAAAAT-TATT
28339072 TTAAATATTAATATAAAATTATT
1 TTAAAT-TTAATATAAAATTATT
*
28339095 TATAATTTTTAATAT
1 T-TAA-ATTTAATAT
28339110 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 11 0.34
24 20 0.62
25 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATTTAATATAAAATTATT
Found at i:28340631 original size:19 final size:19
Alignment explanation
Indices: 28340596--28340690 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
28340586 TATTATTATT
*
28340596 TTATTACTTT-AACAATATA
1 TTATTA-TTTAAATAATATA
*
28340615 TTATTATTTAAATAATATT
1 TTATTATTTAAATAATATA
* *
28340634 TTATTGTTTTAATAAT-TA
1 TTATTATTTAAATAATATA
* * *
28340652 ATATTATTTAATAGAATGTTA
1 TTATTATTTAA-ATAAT-ATA
* *
28340673 ATATTATTTTAATAATAT
1 TTATTATTTAAATAATAT
28340691 GAATATTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 12 0.20
19 32 0.53
20 4 0.07
21 12 0.20
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (19 bp):
TTATTATTTAAATAATATA
Found at i:28340663 original size:17 final size:17
Alignment explanation
Indices: 28340641--28340703 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 17
28340631 ATTTTATTGT
28340641 TTTAATAATTAATATTA
1 TTTAATAATTAATATTA
28340658 TTTAATAGAATGTTAATATTA
1 TTTAAT--AA--TTAATATTA
28340679 TTTTAATAATATGAATATT-
1 -TTTAATAAT-T-AATATTA
28340698 TTTAAT
1 TTTAAT
28340704 CATTTTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.15
18 7 0.18
19 3 0.08
20 8 0.21
21 9 0.23
22 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAATAATTAATATTA
Found at i:28340713 original size:39 final size:39
Alignment explanation
Indices: 28340635--28340716 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
28340625 AATAATATTT
* *
28340635 TATTGTTTTAATAATTAATATTATTTAATAGAATGTTAA
1 TATTATTTTAATAATTAATATTATTTAATACAATGTTAA
* *
28340674 TATTATTTTAATAATATGAATATT-TTTAAT-CATTTTTAA
1 TATTATTTTAATAAT-T-AATATTATTTAATACAATGTTAA
28340713 TATT
1 TATT
28340717 TTCAATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 24 0.65
40 7 0.19
41 6 0.16
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (39 bp):
TATTATTTTAATAATTAATATTATTTAATACAATGTTAA
Found at i:28340855 original size:21 final size:21
Alignment explanation
Indices: 28340824--28340936 Score: 79
Period size: 21 Copynumber: 5.4 Consensus size: 21
28340814 AGATACTGTC
*
28340824 AATATAAAATA-TAACTATTTT
1 AATATTAAATATTAA-TATTTT
*
28340845 AGTATTAAATATTAATATTTT
1 AATATTAAATATTAATATTTT
* **
28340866 AATATTATTATATTAATAAATT
1 AATATTA-AATATTAATATTTT
* **
28340888 AATATTTAATATTAA-ATGCT
1 AATATTAAATATTAATATTTT
* *
28340908 ATTATTAAA-ATAAATTATTTT
1 AATATTAAATATTAA-TATTTT
*
28340929 AACATTAA
1 AATATTAA
28340937 TAAATATAGT
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
19 4 0.06
20 9 0.13
21 37 0.53
22 20 0.29
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (21 bp):
AATATTAAATATTAATATTTT
Found at i:28340871 original size:14 final size:14
Alignment explanation
Indices: 28340852--28340902 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
28340842 TTTAGTATTA
28340852 AATATTAATATTTT
1 AATATTAATATTTT
* *
28340866 AATATTATTATATT
1 AATATTAATATTTT
28340880 AATAAATTAATA-TTT
1 AAT--ATTAATATTTT
28340895 AATATTAA
1 AATATTAA
28340903 ATGCTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 15 0.48
15 5 0.16
16 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:28340879 original size:29 final size:30
Alignment explanation
Indices: 28340839--28340901 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
28340829 AAAATATAAC
*
28340839 TATT-TTAGTATTAA-ATATTAATATTTTAA
1 TATTATTAGTATTAATAAATTAATA-TTTAA
28340868 TATTATTA-TATTAATAAATTAATATTTAA
1 TATTATTAGTATTAATAAATTAATATTTAA
28340897 TATTA
1 TATTA
28340902 AATGCTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTATTAGTATTAATAAATTAATATTTAA
Found at i:28350022 original size:16 final size:17
Alignment explanation
Indices: 28349988--28350027 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28349978 TTTATCAAAT
28349988 GAAAATAAATATGAAAA
1 GAAAATAAATATGAAAA
* *
28350005 GAAAATTAA-ATGAGAA
1 GAAAATAAATATGAAAA
28350021 GAAAATA
1 GAAAATA
28350028 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (17 bp):
GAAAATAAATATGAAAA
Found at i:28354191 original size:24 final size:22
Alignment explanation
Indices: 28354150--28354210 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
28354140 TTTATTTTAA
* *
28354150 TTAAATTTAATTTTAAATATATT
1 TTAAATTTAATATAAAAT-TATT
28354173 TTAAATATTAATATAAAATTATT
1 TTAAAT-TTAATATAAAATTATT
*
28354196 TATAATTTTTAATAT
1 T-TAA-ATTTAATAT
28354211 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 11 0.34
24 20 0.62
25 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATTTAATATAAAATTATT
Found at i:28355582 original size:20 final size:21
Alignment explanation
Indices: 28355545--28355583 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28355535 GATCCGATTT
28355545 AAAATATTATTATATTAATAA
1 AAAATATTATTATATTAATAA
28355566 AAAATACTT-TTAT-TTAAT
1 AAAATA-TTATTATATTAAT
28355584 TTTAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 10 0.59
22 2 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATATTATTATATTAATAA
Found at i:28355861 original size:17 final size:16
Alignment explanation
Indices: 28355839--28355870 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28355829 ATATTATTTT
28355839 TATATTTTATTGACTAA
1 TATATTTTATT-ACTAA
28355856 TATATTTTATTACTA
1 TATATTTTATTACTA
28355871 TTTTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
TATATTTTATTACTAA
Found at i:28355975 original size:14 final size:14
Alignment explanation
Indices: 28355953--28356008 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
28355943 ACTATTTTAG
*
28355953 ATTTAAATATTAAT
1 ATTTTAATATTAAT
*
28355967 ATTTTAATATTATT
1 ATTTTAATATTAAT
*
28355981 ATATTAATAAATTAAT
1 ATTTTAAT--ATTAAT
28355997 A-TTTAATATTAA
1 ATTTTAATATTAA
28356009 ATGCTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 5 0.14
14 19 0.54
15 5 0.14
16 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTAATATTAAT
Found at i:28355987 original size:22 final size:21
Alignment explanation
Indices: 28355953--28356008 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
28355943 ACTATTTTAG
**
28355953 ATTTAAATATTAATATTTTAAT
1 ATTT-AATATTAATAAATTAAT
*
28355975 ATTATTATATTAATAAATTAAT
1 ATT-TAATATTAATAAATTAAT
28355997 ATTTAATATTAA
1 ATTTAATATTAA
28356009 ATGCTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.28
22 20 0.69
23 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATATTAATAAATTAAT
Found at i:28356070 original size:25 final size:25
Alignment explanation
Indices: 28356042--28356096 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
28356032 TTTTAACATT
28356042 AATAAATATAGTAATAAATAATTTC
1 AATAAATATAGTAATAAATAATTTC
* * *
28356067 AATATATTTATTAATAAATAATTTC
1 AATAAATATAGTAATAAATAATTTC
28356092 AATAA
1 AATAA
28356097 TTTAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
AATAAATATAGTAATAAATAATTTC
Found at i:28370272 original size:30 final size:29
Alignment explanation
Indices: 28370229--28370286 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
28370219 AAATAAAATA
28370229 AATTTTTTATTTCTTAAT-AAGGATATTTTT
1 AATTTTTTATTTC-TAATAAAGG-TATTTTT
28370259 AATTTTATT-TTTCTAATAAAGGTATTTT
1 AATTTT-TTATTTCTAATAAAGGTATTTT
28370287 ACGACACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 10 0.38
30 14 0.54
31 2 0.08
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (29 bp):
AATTTTTTATTTCTAATAAAGGTATTTTT
Found at i:28370636 original size:8 final size:8
Alignment explanation
Indices: 28370619--28370665 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
28370609 TTTAATTTTT
28370619 TATTTATA
1 TATTTATA
28370627 TATATT-TA
1 TAT-TTATA
28370635 TATTTATA
1 TATTTATA
*
28370643 TAATTATA
1 TATTTATA
*
28370651 TATTTAAA
1 TATTTATA
28370659 TATTTAT
1 TATTTAT
28370666 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 2 0.06
8 29 0.88
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:28375222 original size:16 final size:17
Alignment explanation
Indices: 28375188--28375227 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28375178 TTTATCAAAT
28375188 GAAAATAAATATGAAAA
1 GAAAATAAATATGAAAA
* *
28375205 GAAAATTAA-ATGAGAA
1 GAAAATAAATATGAAAA
28375221 GAAAATA
1 GAAAATA
28375228 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (17 bp):
GAAAATAAATATGAAAA
Found at i:28378657 original size:2 final size:2
Alignment explanation
Indices: 28378650--28378676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28378640 TGATCATAGA
28378650 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28378677 ATTAGAGTGG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28379132 original size:2 final size:2
Alignment explanation
Indices: 28379125--28379161 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28379115 TTGTTAAGAG
28379125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28379162 ATTGAAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28379458 original size:24 final size:24
Alignment explanation
Indices: 28379431--28379477 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28379421 TTTAATTTTT
28379431 AAATATATTT-TAAATATTAATATA
1 AAAT-TATTTATAAATATTAATATA
* *
28379455 AAATTATTTATAATTTTTAATAT
1 AAATTATTTATAAATATTAATAT
28379478 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTATTTATAAATATTAATATA
Found at i:28379489 original size:13 final size:13
Alignment explanation
Indices: 28379416--28379492 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
28379406 TTATTTTTAA
28379416 TTAAAT-TTAATTT
1 TTAAATATT-ATTT
28379429 TTAAATA-TA-TT
1 TTAAATATTATTT
* *
28379440 TTAAATATTAATA
1 TTAAATATTATTT
*
28379453 TAAAATTATTTATAATT
1 TTAAA-TA-TTAT--TT
*
28379470 TTTAATATTATTT
1 TTAAATATTATTT
28379483 TTAAATATTA
1 TTAAATATTA
28379493 ACCGAGACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 9 0.18
12 3 0.06
13 23 0.46
14 2 0.04
15 7 0.14
16 2 0.04
17 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATATTATTT
Found at i:28380959 original size:29 final size:28
Alignment explanation
Indices: 28380916--28380976 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 28
28380906 CATAAATATG
28380916 TTTAATATTTCAATAATAGATATTATTAT
1 TTTAATATTTCAATAATA-ATATTATTAT
*
28380945 TTTATTATTT---TAATAATATTATTAT
1 TTTAATATTTCAATAATAATATTATTAT
*
28380970 TTAAATA
1 TTTAATA
28380977 ATATTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 15 0.52
26 5 0.17
29 9 0.31
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAATATTTCAATAATAATATTATTAT
Found at i:28380968 original size:17 final size:17
Alignment explanation
Indices: 28380946--28381012 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
28380936 TATTATTATT
28380946 TTATTATTTTAATAATA
1 TTATTATTTTAATAATA
*
28380963 TTATTATTTAAATAATA
1 TTATTATTTTAATAATA
*
28380980 TTTTATTGTTTTAATAATTA
1 --TTATTATTTTAATAA-TA
*
28381000 ATATTA-TTTAATA
1 TTATTATTTTAATA
28381013 GAATGTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 23 0.55
18 4 0.10
19 13 0.31
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TTATTATTTTAATAATA
Found at i:28380984 original size:36 final size:37
Alignment explanation
Indices: 28380942--28381038 Score: 124
Period size: 36 Copynumber: 2.6 Consensus size: 37
28380932 TAGATATTAT
*
28380942 TATTTTATTATTTTAATAATATTATTATTTAA-ATAA
1 TATTTTATTATTTTAATAATATTATTATTTAATAGAA
* *
28380978 TATTTTATTGTTTTAATAATTAATATTATTTAATAGAA
1 TATTTTATTATTTTAATAA-TATTATTATTTAATAGAA
* *
28381016 TGTTAATATTATTTTAATAATAT
1 TATT-TTATTATTTTAATAATAT
28381039 GAATATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
36 18 0.35
37 12 0.24
38 8 0.16
39 13 0.25
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (37 bp):
TATTTTATTATTTTAATAATATTATTATTTAATAGAA
Found at i:28381199 original size:21 final size:21
Alignment explanation
Indices: 28381168--28381246 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
28381158 AGATACTGTC
*
28381168 AATATAAAATA-TAACTATTTT
1 AATATTAAATATTAA-TATTTT
*
28381189 AGTATTAAATATTAATATTTT
1 AATATTAAATATTAATATTTT
* **
28381210 AATATTATTATATTAATAAATT
1 AATATTA-AATATTAATATTTT
*
28381232 AATATTTAATATTAA
1 AATATTAAATATTAA
28381247 ATGCTATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 28 0.58
22 20 0.42
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
AATATTAAATATTAATATTTT
Done.