Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 40 of 64
Found at i:6298412 original size:61 final size:57
Alignment explanation
Indices: 6298281--6298415 Score: 175
Period size: 61 Copynumber: 2.3 Consensus size: 57
6298271 CTTATTATTG
* *
6298281 AATTATAAAAATA-TTTTTTTATTATTGATAAAATAATTATAATATTTTTATATCGT
1 AATTATAAAAATATTTTTTTTATAATTGATAAAATAATTATAATATTTTTATATCAT
*
6298337 AATTATAAAAATATTTTTTTCTCATAATTGATTAAAATTATTATAATAATATTTT-TATCAT
1 AATTATAAAAATATTTTTTT-T-ATAATTGA-TAAAATAATTATAAT-AT-TTTTATATCAT
*
6298398 AATTATGAAAATATTTTT
1 AATTATAAAAATATTTTT
6298416 ATGAATATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
56 13 0.19
57 6 0.09
58 1 0.01
59 7 0.10
60 14 0.20
61 24 0.35
62 4 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (57 bp):
AATTATAAAAATATTTTTTTTATAATTGATAAAATAATTATAATATTTTTATATCAT
Found at i:6298425 original size:35 final size:36
Alignment explanation
Indices: 6298338--6298409 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
6298328 TTATATCGTA
* * *
6298338 ATTATAAAAATATTTTTTTCTCATAATTGATTAAAATT
1 ATTATAATAATA--TTTTTATCATAATTGATGAAAATT
6298376 ATTATAATAATATTTTTATCATAATT-ATGAAAAT
1 ATTATAATAATATTTTTATCATAATTGATGAAAAT
6298410 ATTTTTATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 7 0.23
36 13 0.42
38 11 0.35
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTATAATAATATTTTTATCATAATTGATGAAAATT
Found at i:6299864 original size:2 final size:2
Alignment explanation
Indices: 6299859--6299883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6299849 TTTTCATAAC
6299859 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 A
6299884 GCATATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6302179 original size:12 final size:12
Alignment explanation
Indices: 6302153--6302204 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
6302143 GCGACGAGAT
6302153 TAAAAA-TATTAA
1 TAAAAATTATT-A
6302165 TAAAAATTATTA
1 TAAAAATTATTA
** *
6302177 TAATTATGATTA
1 TAAAAATTATTA
6302189 TAAAAAATTATTA
1 T-AAAAATTATTA
6302202 TAA
1 TAA
6302205 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 19 0.59
13 13 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAAAAATTATTA
Found at i:6302243 original size:28 final size:30
Alignment explanation
Indices: 6302186--6302247 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
6302176 ATAATTATGA
*
6302186 TTATAAAAAATTATTATAATTTAAAAAATT
1 TTATAAAAAAATATTATAATTTAAAAAATT
6302216 TTATAAAAAAAT-TTAT-A-TTAAATAAATT
1 TTATAAAAAAATATTATAATTTAAA-AAATT
6302244 TTAT
1 TTAT
6302248 TAAAGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
28 10 0.33
29 4 0.13
30 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATAAAAAAATATTATAATTTAAAAAATT
Found at i:6302250 original size:14 final size:13
Alignment explanation
Indices: 6302206--6302251 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
6302196 TTATTATAAT
6302206 TTAAAAAATTTTA
1 TTAAAAAATTTTA
*
6302219 TAAAAAAATTTATA
1 TTAAAAAATTT-TA
6302233 TTAAATAAATTTTA
1 TTAAA-AAATTTTA
6302247 TTAAA
1 TTAAA
6302252 GTTGACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 10 0.34
14 13 0.45
15 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAAAAATTTTA
Found at i:6303168 original size:22 final size:19
Alignment explanation
Indices: 6303143--6303188 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 19
6303133 ATAGAAATGT
6303143 TAAATTTTAGAAATAATAAAAA
1 TAAATTTT-GAAAT-A-AAAAA
6303165 TAAAATTTTGAAATAAAAAA
1 T-AAATTTTGAAATAAAAAA
6303185 TAAA
1 TAAA
6303189 GTAAATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 6 0.26
21 1 0.04
22 6 0.26
23 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAATTTTGAAATAAAAAA
Found at i:6303170 original size:23 final size:20
Alignment explanation
Indices: 6303144--6303188 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
6303134 TAGAAATGTT
6303144 AAATTTTAGAAATAATAAAAATA
1 AAATTTT-GAAAT-A-AAAAATA
6303167 AAATTTTGAAATAAAAAATA
1 AAATTTTGAAATAAAAAATA
6303187 AA
1 AA
6303189 GTAAATCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 5 0.23
23 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATTTTGAAATAAAAAATA
Found at i:6315548 original size:20 final size:20
Alignment explanation
Indices: 6315505--6315548 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6315495 ATCGACATAT
* *
6315505 TTAAATTTTAAAATTTTTAT
1 TTAAATTATAAAATTTTTAA
6315525 TTAAATTAT-AAATTTATTAA
1 TTAAATTATAAAATTT-TTAA
6315545 TTAA
1 TTAA
6315549 TATGATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTATAAAATTTTTAA
Found at i:6316232 original size:16 final size:16
Alignment explanation
Indices: 6316202--6316241 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6316192 TTTTTTCATT
*
6316202 TTTAAA-AATATTAAA
1 TTTAAATAACATTAAA
6316217 TTTAAATAACATTAAA
1 TTTAAATAACATTAAA
*
6316233 TTCAAATAA
1 TTTAAATAA
6316242 TATTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAATAACATTAAA
Found at i:6316433 original size:21 final size:20
Alignment explanation
Indices: 6316416--6316454 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6316406 CAAAATTTTA
*
6316416 AATTTTTTTAAAAAAATTCT
1 AATTTTATTAAAAAAATTCT
*
6316436 AATTTTATTAAAGAAATTC
1 AATTTTATTAAAAAAATTC
6316455 AAAATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
AATTTTATTAAAAAAATTCT
Found at i:6316440 original size:47 final size:47
Alignment explanation
Indices: 6316375--6316477 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 47
6316365 AAATTTAATA
*
6316375 TTTAAAAAAATATAAATTTTCCT-AA-AAATTACAAAATT-TTAAATTTT
1 TTTAAAAAAATATAAATTTTACTAAAGAAATT-CAAAATTATT-AA-TTT
* *
6316422 TTTAAAAAAAT-TCTAATTTTATTAAAGAAATTCAAAATTATTAATTT
1 TTTAAAAAAATAT-AAATTTTACTAAAGAAATTCAAAATTATTAATTT
6316469 TTTAAAAAA
1 TTTAAAAAA
6316478 TAAATACTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
46 1 0.02
47 30 0.61
48 11 0.22
49 7 0.14
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (47 bp):
TTTAAAAAAATATAAATTTTACTAAAGAAATTCAAAATTATTAATTT
Found at i:6316458 original size:27 final size:26
Alignment explanation
Indices: 6316428--6316478 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
6316418 TTTTTTTAAA
6316428 AAAATT-CTAATTTTATTAAAGAAATTC
1 AAAATTACTAATTTT-TTAAA-AAATTC
*
6316455 AAAATTATTAATTTTTTAAAAAAT
1 AAAATTACTAATTTTTTAAAAAAT
6316479 AAATACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
AAAATTACTAATTTTTTAAAAAATTC
Found at i:6316766 original size:19 final size:19
Alignment explanation
Indices: 6316744--6316780 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6316734 ATTTTCTTAA
*
6316744 TTTTTAGAGTTTTTAAAAT
1 TTTTTACAGTTTTTAAAAT
*
6316763 TTTTTACATTTTTTAAAA
1 TTTTTACAGTTTTTAAAA
6316781 AATTTTGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTACAGTTTTTAAAAT
Found at i:6317046 original size:21 final size:21
Alignment explanation
Indices: 6317003--6317046 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
6316993 TTATGCCACG
6317003 AATTTGTTTTAATAATGAAAAA
1 AATTTGTTTTAATAA-GAAAAA
*
6317025 AATTTGTTTGTCATAA-AAAAA
1 AATTTGTTT-TAATAAGAAAAA
6317046 A
1 A
6317047 GTTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (21 bp):
AATTTGTTTTAATAAGAAAAA
Found at i:6328385 original size:25 final size:25
Alignment explanation
Indices: 6328326--6328386 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
6328316 TATTGATAAA
*
6328326 AATTATTATAATATTTTTATATCAT
1 AATTATTAAAATATTTTTATATCAT
* *
6328351 AATTA-GAAAATATTTTT-TCTCAT
1 AATTATTAAAATATTTTTATATCAT
6328374 AATTGATTAAAAT
1 AATT-ATTAAAAT
6328387 TATTATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 9 0.30
24 11 0.37
25 10 0.33
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (25 bp):
AATTATTAAAATATTTTTATATCAT
Found at i:6328387 original size:58 final size:58
Alignment explanation
Indices: 6328294--6328427 Score: 193
Period size: 58 Copynumber: 2.3 Consensus size: 58
6328284 CTTATTATTG
* *
6328294 AATTATAAAAATATTTTTTTATTATTGATAAAAATTATTATAAT-AT-TTTTATATCAT
1 AATTATGAAAATATTTTTTTATAATTGATAAAAATTATTATAATAATGTTTT-TATCAT
*
6328351 AATTA-GAAAATATTTTTTCTCATAATTGATTAAAATTATTATAATAATGTTTTTATCAT
1 AATTATGAAAATATTTTTT-T-ATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
6328410 AATTATGAAAATATTTTT
1 AATTATGAAAATATTTTT
6328428 ATGAATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
56 12 0.17
57 6 0.09
58 22 0.32
59 13 0.19
60 16 0.23
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
AATTATGAAAATATTTTTTTATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
Found at i:6331693 original size:23 final size:26
Alignment explanation
Indices: 6331653--6331706 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
6331643 TAAATTTATT
6331653 AAAATATTTTTTTATTATAATT-GTG
1 AAAATATTTTTTTATTATAATTAGTG
*
6331678 AAAATA-TTTTTT-TTATAATTAGTT
1 AAAATATTTTTTTATTATAATTAGTG
6331702 AAAAT
1 AAAAT
6331707 TATTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (26 bp):
AAAATATTTTTTTATTATAATTAGTG
Found at i:6331981 original size:25 final size:25
Alignment explanation
Indices: 6331953--6332004 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
6331943 CTCATAATCA
* *
6331953 ATCAAAATTATTATAATG-TCTTCCT
1 ATCAAAATTA-CAAAATGCTCTTCCT
*
6331978 ATCATAATTACAAAATGCTCTTCCT
1 ATCAAAATTACAAAATGCTCTTCCT
6332003 AT
1 AT
6332005 TATAATTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (25 bp):
ATCAAAATTACAAAATGCTCTTCCT
Found at i:6337353 original size:22 final size:19
Alignment explanation
Indices: 6337328--6337373 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 19
6337318 ATAGAAATGT
6337328 TAAATTTTAGAAATAATAAAAA
1 TAAATTTT-GAAAT-A-AAAAA
6337350 TAAAATTTTGAAATAAAAAA
1 T-AAATTTTGAAATAAAAAA
6337370 TAAA
1 TAAA
6337374 GTAAATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 6 0.26
21 1 0.04
22 6 0.26
23 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAATTTTGAAATAAAAAA
Found at i:6337355 original size:23 final size:20
Alignment explanation
Indices: 6337329--6337373 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
6337319 TAGAAATGTT
6337329 AAATTTTAGAAATAATAAAAATA
1 AAATTTT-GAAAT-A-AAAAATA
6337352 AAATTTTGAAATAAAAAATA
1 AAATTTTGAAATAAAAAATA
6337372 AA
1 AA
6337374 GTAAATCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 5 0.23
23 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATTTTGAAATAAAAAATA
Found at i:6346913 original size:21 final size:21
Alignment explanation
Indices: 6346889--6346929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6346879 CCGGTGAGCC
*
6346889 TTTTGTTTCATG-GAAGCCAGG
1 TTTTGATTCATGTGAA-CCAGG
6346910 TTTTGATTCATGTGAACCAG
1 TTTTGATTCATGTGAACCAG
6346930 AAAGCTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TTTTGATTCATGTGAACCAGG
Found at i:6352372 original size:18 final size:18
Alignment explanation
Indices: 6352320--6352390 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
6352310 AAATTTAAAT
6352320 ATTTTTATATTTAATTTGAGTA
1 ATTTTTATATTTAA-TT-A--A
*
6352342 ATTTATA-ACTTTAATTAA
1 ATTTTTATA-TTTAATTAA
* *
6352360 ATTTTTATATTTAAATAT
1 ATTTTTATATTTAATTAA
6352378 ATTTTTATTATTT
1 ATTTTTA-TATTT
6352391 TGATTAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
18 21 0.50
19 6 0.14
20 1 0.02
21 3 0.07
22 11 0.26
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTTTATATTTAATTAA
Found at i:6353108 original size:22 final size:21
Alignment explanation
Indices: 6353057--6353108 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
6353047 AAATTTTGAT
6353057 TATTAAAAATTACTTAGATAA
1 TATTAAAAATTACTTAGATAA
*
6353078 -ATGATAAAATTAACTTCA-ATAA
1 TATTA-AAAATT-ACTT-AGATAA
6353100 TATTAAAAA
1 TATTAAAAA
6353109 CAACAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
20 3 0.12
21 6 0.24
22 12 0.48
23 4 0.16
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (21 bp):
TATTAAAAATTACTTAGATAA
Found at i:6356910 original size:13 final size:13
Alignment explanation
Indices: 6356892--6356917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6356882 AATCTATTTA
6356892 AATATATAAAAAT
1 AATATATAAAAAT
6356905 AATATATAAAAAT
1 AATATATAAAAAT
6356918 TAAAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:6362898 original size:18 final size:18
Alignment explanation
Indices: 6362875--6362929 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
6362865 TACTAATATT
6362875 ATATTATTATAATATAGG
1 ATATTATTATAATATAGG
* *
6362893 ATATTATTATAGTATAGT
1 ATATTATTATAATATAGG
*
6362911 ATAGTATAGTATAATATAG
1 ATA-T-TATTATAATATAG
6362930 TGTAGCATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 19 0.61
19 1 0.03
20 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (18 bp):
ATATTATTATAATATAGG
Found at i:6362915 original size:10 final size:10
Alignment explanation
Indices: 6362900--6362930 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6362890 AGGATATTAT
6362900 TATAGTATAG
1 TATAGTATAG
6362910 TATAGTATAG
1 TATAGTATAG
*
6362920 TATAATATAG
1 TATAGTATAG
6362930 T
1 T
6362931 GTAGCATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (10 bp):
TATAGTATAG
Found at i:6362918 original size:15 final size:15
Alignment explanation
Indices: 6362900--6362930 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6362890 AGGATATTAT
*
6362900 TATAGTATAGTATAG
1 TATAGTATAATATAG
6362915 TATAGTATAATATAG
1 TATAGTATAATATAG
6362930 T
1 T
6362931 GTAGCATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (15 bp):
TATAGTATAATATAG
Found at i:6363936 original size:23 final size:22
Alignment explanation
Indices: 6363910--6363974 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
6363900 TTTTCCATTT
*
6363910 TTTTTGATTT-TTTTGATTTTATA
1 TTTTTAATTTATTTT-ATTTT-TA
6363933 TTTTTAATTTATTTTATTTTTA
1 TTTTTAATTTATTTTATTTTTA
* * *
6363955 TTTTCAACTTCTTTTATTTT
1 TTTTTAATTTATTTTATTTT
6363975 ATTGATTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 19 0.51
23 14 0.38
24 4 0.11
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTAATTTATTTTATTTTTA
Found at i:6363969 original size:22 final size:23
Alignment explanation
Indices: 6363920--6363976 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
6363910 TTTTTGATTT
* *
6363920 TTTTGATTTTATATTTTTAATTTA
1 TTTT-ATTTTATATTTTCAACTTA
*
6363944 TTTTATTTT-TATTTTCAACTTC
1 TTTTATTTTATATTTTCAACTTA
6363966 TTTTATTTTAT
1 TTTTATTTTAT
6363977 TGATTTCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 6 0.21
24 4 0.14
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTATTTTATATTTTCAACTTA
Found at i:6371883 original size:50 final size:50
Alignment explanation
Indices: 6371808--6371908 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
6371798 TCAAATCGTG
6371808 ATTTTCCTTTTATAAATACCAAATGCCAAATTACATATTAACCCTAAATA
1 ATTTTCCTTTTATAAATACCAAATGCCAAATTACATATTAACCCTAAATA
* * *
6371858 ATTTTCTTTTTATAAATACCGAATGCCGAATTACATATTAACCCTAAATA
1 ATTTTCCTTTTATAAATACCAAATGCCAAATTACATATTAACCCTAAATA
6371908 A
1 A
6371909 AAGCAACAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (50 bp):
ATTTTCCTTTTATAAATACCAAATGCCAAATTACATATTAACCCTAAATA
Found at i:6372978 original size:21 final size:20
Alignment explanation
Indices: 6372949--6372994 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
6372939 AATTTTATAA
6372949 AATTAAATATTATTAAATACT
1 AATTAAATATTA-TAAATACT
* *
6372970 AATTTAATATTATAAATATT
1 AATTAAATATTATAAATACT
6372990 AATTA
1 AATTA
6372995 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTAAATATTATAAATACT
Found at i:6372986 original size:30 final size:28
Alignment explanation
Indices: 6372952--6373046 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 28
6372942 TTTATAAAAT
6372952 TAAATATTATTAAATACTAATTTAATATTA
1 TAAATATTATT-AATA-TAATTTAATATTA
* *
6372982 TAAATATTAATT-AT-TAATTAAATAATA
1 TAAATATT-ATTAATATAATTTAATATTA
*
6373009 TTAAATATT-TTAATAATATTTTAATATT-
1 -TAAATATTATTAAT-ATAATTTAATATTA
6373037 T-AATATTATT
1 TAAATATTATT
6373047 TTAGTAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
26 8 0.15
27 16 0.30
28 8 0.15
29 11 0.20
30 8 0.15
31 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
TAAATATTATTAATATAATTTAATATTA
Found at i:6373023 original size:18 final size:18
Alignment explanation
Indices: 6372940--6373046 Score: 60
Period size: 21 Copynumber: 5.8 Consensus size: 18
6372930 ATTAATCTTA
*
6372940 ATTTT-ATAAAATTAAAT
1 ATTTTAATAATATTAAAT
* *
6372957 ATTATTAAATACTAATTTAAT
1 ATT-TT-AATAAT-ATTAAAT
* *
6372978 ATTAT-A-AATATTAATT
1 ATTTTAATAATATTAAAT
6372994 ATTAATTAAATAATATTAAAT
1 ATT--TT-AATAATATTAAAT
*
6373015 ATTTTAATAATATTTTAAT
1 ATTTTAATAATA-TTAAAT
*
6373034 A-TTTAATATTATT
1 ATTTTAATAATATT
6373047 TTAGTAATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 8 0.12
17 7 0.10
18 20 0.29
19 8 0.12
20 5 0.07
21 21 0.30
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAATAATATTAAAT
Found at i:6373026 original size:48 final size:46
Alignment explanation
Indices: 6372949--6373044 Score: 106
Period size: 48 Copynumber: 2.0 Consensus size: 46
6372939 AATTTTATAA
*
6372949 AATTAAATATTATTAAATACTAATTTAATATTATAAATA-TTAATTATT
1 AATTAAATAATATTAAATACTAA-TTAATATT-TAAATATTTAA-TATT
* *
6372997 AATTAAATAATATTAAATATTTTAA-TAATATTTTAATATTTAATATT
1 AATTAAATAATATTAAATA--CTAATTAATATTTAAATATTTAATATT
6373044 A
1 A
6373045 TTTTAGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
47 10 0.24
48 29 0.69
50 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (46 bp):
AATTAAATAATATTAAATACTAATTAATATTTAAATATTTAATATT
Found at i:6373047 original size:18 final size:19
Alignment explanation
Indices: 6373002--6373049 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
6372992 TTATTAATTA
*
6373002 AATAATA-TTAAATATTTT
1 AATAATATTTTAATATTTT
6373020 AATAATATTTTAATA-TTT
1 AATAATATTTTAATATTTT
*
6373038 AATATTATTTTA
1 AATAATATTTTA
6373050 GTAATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATAATATTTTAATATTTT
Found at i:6375915 original size:15 final size:14
Alignment explanation
Indices: 6375801--6376027 Score: 73
Period size: 15 Copynumber: 14.9 Consensus size: 14
6375791 CTTGTTTTAG
6375801 GGTTTTAGGGTTTCAA
1 GGTTTTA-GGTTTC-A
* *
6375817 AGTTTTAAGGTTTTGA
1 GGTTTT-AGG-TTTCA
*
6375833 GGTTTAAGGTTTCA
1 GGTTTTAGGTTTCA
*
6375847 GGCTTTTAAGGTTTTGA
1 GG-TTTT-AGG-TTTCA
*
6375864 GGTTTTTA-CTTTCAAA
1 GG-TTTTAGGTTTC--A
***
6375880 GGTTCGGGGTTT-A
1 GGTTTTAGGTTTCA
6375893 GAGTTTTAGGATTTCA
1 G-GTTTTAGG-TTTCA
6375909 GGTTTTAGTGTTTCGA
1 GGTTTTAG-GTTTC-A
*
6375925 AGTTTTAGGGTTT-A
1 GGTTTTA-GGTTTCA
6375939 GGGTTTTAAGGTTTCA
1 -GGTTTT-AGGTTTCA
* *
6375955 GGATTTAAGGTTTTA
1 GG-TTTTAGGTTTCA
** *
6375970 GGATTTTGAATTTTAA
1 GG-TTTT-AGGTTTCA
*
6375986 GGTTTAAGGTTTCAA
1 GGTTTTAGGTTTC-A
* * *
6376001 GGTTTGAGTTTTTA
1 GGTTTTAGGTTTCA
6376015 GGTTTTGAGGTTT
1 GGTTTT-AGGTTT
6376028 TGAGATTTTT
Statistics
Matches: 156, Mismatches: 34, Indels: 43
0.67 0.15 0.18
Matches are distributed among these distances:
13 2 0.01
14 25 0.16
15 66 0.42
16 48 0.31
17 15 0.10
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.47
Consensus pattern (14 bp):
GGTTTTAGGTTTCA
Found at i:6375916 original size:23 final size:23
Alignment explanation
Indices: 6375889--6375975 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
6375879 AGGTTCGGGG
*
6375889 TTTAGAGTTTTAGGATTTCAGGT
1 TTTAGAGTTTTAGGATTTCAGGA
* * * * *
6375912 TTTAGTG-TTTCGAAGTTTTAGGG
1 TTTAGAGTTTTAGGA-TTTCAGGA
*
6375935 TTTAGGGTTTTAAGG-TTTCAGGA
1 TTTAGAGTTTT-AGGATTTCAGGA
6375958 TTTA-AGGTTTTAGGATTT
1 TTTAGA-GTTTTAGGATTT
6375976 TGAATTTTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
22 8 0.17
23 36 0.75
24 3 0.06
25 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (23 bp):
TTTAGAGTTTTAGGATTTCAGGA
Found at i:6376004 original size:8 final size:7
Alignment explanation
Indices: 6375928--6376019 Score: 51
Period size: 7 Copynumber: 12.4 Consensus size: 7
6375918 GTTTCGAAGT
*
6375928 TTTAGGG
1 TTTAAGG
*
6375935 TTTAGGG
1 TTTAAGG
6375942 TTTTAAGG
1 -TTTAAGG
*
6375950 TTTCAGG
1 TTTAAGG
6375957 ATTTAAGG
1 -TTTAAGG
*
6375965 TTTTAGG
1 TTTAAGG
*
6375972 ATTTTGAA-T
1 --TTT-AAGG
6375981 TTTAAGG
1 TTTAAGG
6375988 TTTAAGG
1 TTTAAGG
6375995 TTTCAAGG
1 TTT-AAGG
* *
6376003 TTTGAGT
1 TTTAAGG
*
6376010 TTTTAGG
1 TTTAAGG
6376017 TTT
1 TTT
6376020 TGAGGTTTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
6 2 0.03
7 42 0.63
8 19 0.28
9 3 0.04
10 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:6376109 original size:8 final size:8
Alignment explanation
Indices: 6375794--6376109 Score: 96
Period size: 8 Copynumber: 40.8 Consensus size: 8
6375784 TTAAGGTCTT
*
6375794 GTTTTAGG
1 GTTTTAAG
*
6375802 GTTTTAGG
1 GTTTTAAG
* *
6375810 GTTTCAAA
1 GTTTTAAG
6375818 GTTTTAAG
1 GTTTTAAG
*
6375826 GTTTTGAG
1 GTTTTAAG
6375834 G-TTTAAG
1 GTTTTAAG
*
6375841 G-TTTCAG
1 GTTTTAAG
6375848 GCTTTTAAG
1 G-TTTTAAG
*
6375857 GTTTTGAG
1 GTTTTAAG
*
6375865 GTTTTTA-
1 GTTTTAAG
* *
6375872 CTTTCAAAG
1 GTTT-TAAG
**
6375881 G--TTCGG
1 GTTTTAAG
*
6375887 GGTTT-AG
1 GTTTTAAG
6375894 AGTTTT-AG
1 -GTTTTAAG
* *
6375902 GATTTCAG
1 GTTTTAAG
6375910 GTTTT-AG
1 GTTTTAAG
*
6375917 TGTTTCGAA-
1 -GTTT-TAAG
6375926 GTTTT-AG
1 GTTTTAAG
* *
6375933 GGTTTAGG
1 GTTTTAAG
6375941 GTTTTAAG
1 GTTTTAAG
*
6375949 G-TTTCAG
1 GTTTTAAG
*
6375956 GATTTAAG
1 GTTTTAAG
6375964 GTTTT-AG
1 GTTTTAAG
6375971 GATTTTGAA-
1 G-TTTT-AAG
6375980 -TTTTAAG
1 GTTTTAAG
6375987 G-TTTAAG
1 GTTTTAAG
*
6375994 GTTTCAAG
1 GTTTTAAG
*
6376002 G-TTTGA-
1 GTTTTAAG
*
6376008 GTTTTTAG
1 GTTTTAAG
*
6376016 GTTTTGAG
1 GTTTTAAG
*
6376024 GTTTTGAG
1 GTTTTAAG
*
6376032 ATTTTTAA-
1 -GTTTTAAG
*
6376040 GTTTCGAA-
1 GTTT-TAAG
* **
6376048 ATTTTTGG
1 GTTTTAAG
**
6376056 GTTTTGGG
1 GTTTTAAG
*
6376064 GTTTTAGG
1 GTTTTAAG
6376072 GTTTTGAA-
1 GTTTT-AAG
6376080 GTTTTAAG
1 GTTTTAAG
*
6376088 GTTTTGAG
1 GTTTTAAG
6376096 GTTTTAAG
1 GTTTTAAG
6376104 GTTTTA
1 GTTTTA
6376110 GTTTTTTTTT
Statistics
Matches: 231, Mismatches: 50, Indels: 54
0.69 0.15 0.16
Matches are distributed among these distances:
6 6 0.03
7 59 0.26
8 152 0.66
9 12 0.05
10 2 0.01
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.48
Consensus pattern (8 bp):
GTTTTAAG
Found at i:6376116 original size:16 final size:16
Alignment explanation
Indices: 6375818--6376108 Score: 128
Period size: 16 Copynumber: 18.8 Consensus size: 16
6375808 GGGTTTCAAA
6375818 GTTTTAAGGTTTTGAG
1 GTTTTAAGGTTTTGAG
*
6375834 G-TTTAAGG-TTTCAG
1 GTTTTAAGGTTTTGAG
6375848 GCTTTTAAGGTTTTGAG
1 G-TTTTAAGGTTTTGAG
* * **
6375865 GTTTTTA-CTTTCAAAG
1 GTTTTAAGGTTT-TGAG
*** *
6375881 G-TTCGGGGTTTAGA-
1 GTTTTAAGGTTTTGAG
* *
6375895 GTTTT-AGGATTTCAG
1 GTTTTAAGGTTTTGAG
* *
6375910 GTTTT-AGTGTTTCGAA
1 GTTTTAAG-GTTTTGAG
* *
6375926 GTTTTAGGGTTTAG-G
1 GTTTTAAGGTTTTGAG
*
6375941 GTTTTAAGG-TTTCAG
1 GTTTTAAGGTTTTGAG
*
6375956 GATTTAAGGTTTT-AG
1 GTTTTAAGGTTTTGAG
*
6375971 GATTTTGAA--TTTTAAG
1 G-TTTT-AAGGTTTTGAG
**
6375987 G-TTTAAGGTTTCAAG
1 GTTTTAAGGTTTTGAG
* *
6376002 G-TTTGA-GTTTTTAG
1 GTTTTAAGGTTTTGAG
*
6376016 GTTTTGAGGTTTTGAG
1 GTTTTAAGGTTTTGAG
* * *
6376032 ATTTTTAA-GTTTCGAA
1 -GTTTTAAGGTTTTGAG
* ** *
6376048 ATTTTTGGGTTTTGGG
1 GTTTTAAGGTTTTGAG
* *
6376064 GTTTTAGGGTTTTGAA
1 GTTTTAAGGTTTTGAG
6376080 GTTTTAAGGTTTTGAG
1 GTTTTAAGGTTTTGAG
6376096 GTTTTAAGGTTTT
1 GTTTTAAGGTTTT
6376109 AGTTTTTTTT
Statistics
Matches: 206, Mismatches: 49, Indels: 40
0.70 0.17 0.14
Matches are distributed among these distances:
13 2 0.01
14 24 0.12
15 67 0.33
16 99 0.48
17 14 0.07
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.49
Consensus pattern (16 bp):
GTTTTAAGGTTTTGAG
Found at i:6378294 original size:70 final size:70
Alignment explanation
Indices: 6378154--6378308 Score: 170
Period size: 70 Copynumber: 2.2 Consensus size: 70
6378144 AAATCATAAC
* * * * * *
6378154 TCAAAAAATAAAAATGACTGAGACTGAACCATAAGTTGAAGAATAAAAATGATCAGGATTGAGTT
1 TCAAGAAATAAAAATGACTGAGACTGAACCACAAGTCGAAAAATAAAAATGATCAGGACTGAGCT
6378219 GTAAG
66 GTAAG
* * * * * *
6378224 TCGAGAAATAAGAATGACTGGGACTGAATCGCAAGTCGAAAAATAAAAATGA-CTGAGACTGAGC
1 TCAAGAAATAAAAATGACTGAGACTGAACCACAAGTCGAAAAATAAAAATGATCAG-GACTGAG-
6378288 CT-TAAG
64 CTGTAAG
6378294 TCAAGAAATAAAAAT
1 TCAAGAAATAAAAAT
6378309 ATCCGAGACT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
69 2 0.03
70 66 0.96
71 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (70 bp):
TCAAGAAATAAAAATGACTGAGACTGAACCACAAGTCGAAAAATAAAAATGATCAGGACTGAGCT
GTAAG
Found at i:6378306 original size:35 final size:34
Alignment explanation
Indices: 6378081--6378308 Score: 140
Period size: 35 Copynumber: 6.5 Consensus size: 34
6378071 ATTGAATCAC
* * *
6378081 AAGTCAAGAAATAAAGATGATTGAGACTG-AGTT
1 AAGTCAAGAAATAAAAATGACTGAGACTGAACTT
* * * * *
6378114 GCAAGTCAAGAAATAAAAACGATTGGGACTAAATCAT
1 --AAGTCAAGAAATAAAAATGACTGAGACTGAA-CTT
* * *
6378151 AACTCAAAAAATAAAAATGACTGAGACTGAACCAT
1 AAGTCAAGAAATAAAAATGACTGAGACTGAA-CTT
* * * **
6378186 AAGTTGAAG-AATAAAAATGA-TCAGGATTGAGTTGT
1 AAG-TCAAGAAATAAAAATGACTGA-GACTGAACT-T
* * * **
6378221 AAGTCGAGAAATAAGAATGACTGGGACTGAATCGC
1 AAGTCAAGAAATAAAAATGACTGAGACTGAA-CTT
*
6378256 AAGTCGAA-AAATAAAAATGACTGAGACTGAGCCTT
1 AAGTC-AAGAAATAAAAATGACTGAGACTGA-ACTT
6378291 AAGTCAAGAAATAAAAAT
1 AAGTCAAGAAATAAAAAT
6378309 ATCCGAGACT
Statistics
Matches: 145, Mismatches: 37, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
34 7 0.05
35 131 0.90
36 6 0.04
37 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (34 bp):
AAGTCAAGAAATAAAAATGACTGAGACTGAACTT
Found at i:6378328 original size:105 final size:106
Alignment explanation
Indices: 6378081--6378340 Score: 287
Period size: 105 Copynumber: 2.5 Consensus size: 106
6378071 ATTGAATCAC
* * * * *
6378081 AAGTCAAGAAATAAAGATGAT-TGAGACTGAGTTGCAAGTCAAGAAATAAAAACGATTGGGACTA
1 AAGTCAAGAAATAAAAATGATCAGAGACTTAGTTGTAAGTCAAGAAATAAAAACGACTGGGACTA
*
6378145 AATCATAACTCAAAAAATAAAAATGACTGAGACTGAACCAT
66 AATCACAACTCAAAAAATAAAAATGACTGAGACTGAACCAT
* * * *
6378186 AAGTTGAAG-AATAAAAATGATCAG-GA-TTGAGTTGTAAGTCGAGAAATAAGAATGACTGGGAC
1 AAG-TCAAGAAATAAAAATGATCAGAGACTT-AGTTGTAAGTCAAGAAATAAAAACGACTGGGAC
* * * * * *
6378248 TGAATCGCAAGTCGAAAAATAAAAATGACTGAGACTGAGCCTT
64 TAAATCACAACTCAAAAAATAAAAATGACTGAGACTGAACCAT
* * * *
6378291 AAGTCAAGAAATAAAAAT-ATCCGAGACTTAATAGTAAGTTAAGAAATAAA
1 AAGTCAAGAAATAAAAATGATCAGAGACTTAGTTGTAAGTCAAGAAATAAA
6378341 GATTATCGTG
Statistics
Matches: 126, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
104 9 0.07
105 110 0.87
106 7 0.06
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (106 bp):
AAGTCAAGAAATAAAAATGATCAGAGACTTAGTTGTAAGTCAAGAAATAAAAACGACTGGGACTA
AATCACAACTCAAAAAATAAAAATGACTGAGACTGAACCAT
Found at i:6378338 original size:70 final size:70
Alignment explanation
Indices: 6378262--6378416 Score: 161
Period size: 70 Copynumber: 2.2 Consensus size: 70
6378252 TCGCAAGTCG
* * *
6378262 AAAAATAAAAATGA-CTGAGACTGAGCCTTAAGTCAAGAAATAAAAAT-ATCCGAGACTTAATAG
1 AAAAATAAAAATGATC-GAGACTGAGCCATAAGTCAAGAAATAAAAATAATCAG-GACTGAATAG
*
6378325 TAAGTTA
64 TAAATTA
* * * * * * * *
6378332 AGAAATAAAGATTATCGTGATTGAGCCATAAGTCGAGAAATAAGAATAATCAGGACTGAATTGTA
1 AAAAATAAAAATGATCGAGACTGAGCCATAAGTCAAGAAATAAAAATAATCAGGACTGAATAGTA
6378397 AATTA
66 AATTA
*
6378402 AAAAATAAGAATGAT
1 AAAAATAAAAATGAT
6378417 TAGAATTAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
70 62 0.93
71 5 0.07
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (70 bp):
AAAAATAAAAATGATCGAGACTGAGCCATAAGTCAAGAAATAAAAATAATCAGGACTGAATAGTA
AATTA
Found at i:6378813 original size:172 final size:170
Alignment explanation
Indices: 6378417--6378813 Score: 386
Period size: 172 Copynumber: 2.3 Consensus size: 170
6378407 TAAGAATGAT
* ** * * *
6378417 TAGAATTAAATCGTAAGTCAAAAATAAAGATGATTAGGACTAAACTGCGAGTTAAGAAATAAAAA
1 TAGAATTAAGTCACAAGTAAAAAATAAAGATGA-TAGGACTAAACCGTGAG-TAAGAAATAAAAA
* ** *
6378482 CGATTGAGATTGAACTACAAGTTGAAGAGCAAAATGATCGGGACTGAGCCATTAATCAGAAAATG
64 CGATTGAGATTGAACTACAAGTCGAAGAGCAAAATGATCAAGACTGAGCCA-TAATCAAAAAATG
*
6378547 AAAATAATCAAAACTAAACCATGAGTCAAAGGAATATGATGGC
128 AAAATAATCAAAACTAAACCACGAGTCAAAGGAATATGATGGC
* * * * * *
6378590 TAGAATTGAGTCGCAAGTAAAAAATAAAGATGATCGAGACTGAATCGTGAGTCAGAAATAAAAAC
1 TAGAATTAAGTCACAAGTAAAAAATAAAGATGATAG-GACTAAACCGTGAGTAAGAAATAAAAAC
* * * *
6378655 GATT-AGGATTTAACTATAAGTCGAAGAGCAAAATGATTAAGACTGAGTTGCA-AATCAAAAAAT
65 GATTGA-GATTGAACTACAAGTCGAAGAGCAAAATGATCAAGACTGAG--CCATAATCAAAAAAT
* ** * * * * *
6378718 GAAAATGATTGATACTGAATCACGAGTCGAAGGAATATGAT-GA
127 GAAAATAATCAAAACTAAACCACGAGTCAAAGGAATATGATGGC
* * * * *
6378761 TCGGGATTAAGTTACAGGTTAAAAATAAAGATGAGTAGGACTAAACCGTGAGT
1 T-AGAATTAAGTCACAAGTAAAAAATAAAGATGA-TAGGACTAAACCGTGAGT
6378814 TAAAAAGTAA
Statistics
Matches: 181, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
171 3 0.02
172 135 0.75
173 41 0.23
174 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (170 bp):
TAGAATTAAGTCACAAGTAAAAAATAAAGATGATAGGACTAAACCGTGAGTAAGAAATAAAAACG
ATTGAGATTGAACTACAAGTCGAAGAGCAAAATGATCAAGACTGAGCCATAATCAAAAAATGAAA
ATAATCAAAACTAAACCACGAGTCAAAGGAATATGATGGC
Found at i:6378947 original size:173 final size:172
Alignment explanation
Indices: 6378705--6379073 Score: 388
Period size: 173 Copynumber: 2.1 Consensus size: 172
6378695 GACTGAGTTG
* * * *
6378705 CAAATCAAAAAATGAAAATGATTGATACTGAATCACGAGTCGAAGGAATATGATGATCGGGATTA
1 CAAATCAAAAAATGAAAATGATTGATACTGAATCACGAGTCGAAAGAATAGGATGATCAGGACTA
* ** *
6378770 AGTTACAGGTTAAAAA-TAAAGATGA-GTAGGACTAAACCGTGAGTTA-AAAAGTAAAACTGACC
66 AGTTACAAGTTAAAAATTAAA-ATGACCAAGG-CTAAACCGTGAGTCAGAAAA-TAAAA-TGACC
*
6378832 AAGATTGAACCGTAAGTTGAAAAGAAAGATGATCGAGATTAAGCCA
127 AAGATTGAACCGCAAGTTGAAAAGAAAGATGATCGAGATTAAGCCA
* * ** *
6378878 CAAATTAAAAAATGAGAATGATCTGA-ACTGAATTGCGAGTTGAAAGAATAGGATGA-CTAGGAC
1 CAAATCAAAAAATGAAAATGAT-TGATACTGAATCACGAGTCGAAAGAATAGGATGATC-AGGAC
* * * **
6378941 TAAGTTACAAGTTAAAAATTAAAATGACCAAGGTTGAACTGTGAGTCAGAAAATAAAATGACTGA
64 TAAGTTACAAGTTAAAAATTAAAATGACCAAGGCTAAACCGTGAGTCAGAAAATAAAATGACCAA
* * * * * * **
6379006 GATTGAACCGCAAGTTGAAGAGTAAGATGATTGGGACTAAACTG
129 GATTGAACCGCAAGTTGAAAAGAAAGATGATCGAGATTAAGCCA
* *
6379050 TAAATCAAGAAATGAAAATGATTG
1 CAAATCAAAAAATGAAAATGATTG
6379074 GGACTAAATC
Statistics
Matches: 160, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
171 2 0.01
172 59 0.37
173 85 0.53
174 14 0.09
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (172 bp):
CAAATCAAAAAATGAAAATGATTGATACTGAATCACGAGTCGAAAGAATAGGATGATCAGGACTA
AGTTACAAGTTAAAAATTAAAATGACCAAGGCTAAACCGTGAGTCAGAAAATAAAATGACCAAGA
TTGAACCGCAAGTTGAAAAGAAAGATGATCGAGATTAAGCCA
Found at i:6379106 original size:35 final size:34
Alignment explanation
Indices: 6379028--6379106 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 34
6379018 AGTTGAAGAG
* **
6379028 TAAGATGATTGGGACTAAACTGTAAATCAAGAAA
1 TAAGATGATTGGGACTAAACTATAAAAAAAGAAA
* *
6379062 TGAAAATGATTGGGACTAAA-TCATAAGAAAAAGGAA
1 T-AAGATGATTGGGACTAAACT-ATAA-AAAAAGAAA
6379098 TAAGATGAT
1 TAAGATGAT
6379107 CAAGATTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
34 2 0.06
35 27 0.75
36 7 0.19
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.23
Consensus pattern (34 bp):
TAAGATGATTGGGACTAAACTATAAAAAAAGAAA
Found at i:6379277 original size:35 final size:35
Alignment explanation
Indices: 6379231--6379301 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
6379221 TACAAATTAG
*
6379231 AAAATAAAAATGATTGGGATTGAACCACT-AGTCAA
1 AAAATAAAAATGATTGAGATTGAACCA-TAAGTCAA
6379266 AAAATAAAAATGATTGAGATTGAACCATAAGTCAA
1 AAAATAAAAATGATTGAGATTGAACCATAAGTCAA
6379301 A
1 A
6379302 GAGCAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (35 bp):
AAAATAAAAATGATTGAGATTGAACCATAAGTCAA
Found at i:6379315 original size:34 final size:35
Alignment explanation
Indices: 6379231--6379322 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 35
6379221 TACAAATTAG
* *
6379231 AAAATAAAAATGATTGGGATTGAACCACTAGTCAA
1 AAAAGAAAAATGATTGAGATTGAACCACTAGTCAA
*
6379266 AAAATAAAAATGATTGAGATTGAACCA-TAAGTC-A
1 AAAAGAAAAATGATTGAGATTGAACCACT-AGTCAA
* * *
6379300 AAGAGCAAAATGATTGAAATTGA
1 AAAAGAAAAATGATTGAGATTGA
6379323 GCAGCAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
34 21 0.41
35 30 0.59
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (35 bp):
AAAAGAAAAATGATTGAGATTGAACCACTAGTCAA
Found at i:6379705 original size:173 final size:173
Alignment explanation
Indices: 6379437--6379831 Score: 429
Period size: 173 Copynumber: 2.3 Consensus size: 173
6379427 ATCGTGAGTC
* * * * *
6379437 AAAAAATAAAAATGA-ATAGGATTGAATTGCAAGTCAAAGAGTAAGATGATCGAGACTGAGTCAC
1 AAAAAATAAAAATGACA-AGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAGCCAC
* * * * * * * *
6379501 AAATCAAGAAATGAAAATGGTCAGAACTGAACTACGAGTCGAAGGAATAGGATGATTGAAATTGA
65 AAATCAAAAAATGAAAATGCTCAGAACTGAACCACGAGCCAAAGGAATAGGATGATCGAAACTAA
*
6379566 GTCACAAATAAAAAATAAAGATGATCGGTACTAAACCACAAG-TT
130 GTCACAAATAAAAAAT-AAGATGATCGGGACTAAACCACAAGTTT
* * *
6379610 AAAAAGTAAAAATGACAAGGATTGAATCGTAAGTCAAAAAGTAAGGTGACCAAGACTGAGCCACA
1 AAAAAATAAAAATGACAAGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAGCCACA
* * * * * *
6379675 AGTCAAAAAATTAAAATGACT-GGGACTGAACCATGAGCCAAAGGAATAGGATGATCGAGACTAA
66 AATCAAAAAATGAAAATG-CTCAGAACTGAACCACGAGCCAAAGGAATAGGATGATCGAAACTAA
* *** * * *
6379739 TTTGTAAGTAAAAAATAAGATGATTGGGACTAAACCACGAGTTT
130 GTCACAAATAAAAAATAAGATGATCGGGACTAAACCACAAGTTT
* * *
6379783 AAAAAATAAAAACGATC-AGGATTGAATCGCAAGTCAAAGATTAAGATGA
1 AAAAAATAAAAATGA-CAAGGATTGAATCGCAAGTCAAAAAGTAAGATGA
6379832 ATGAAATTGA
Statistics
Matches: 182, Mismatches: 36, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
172 22 0.12
173 157 0.86
174 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.20
Consensus pattern (173 bp):
AAAAAATAAAAATGACAAGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAGCCACA
AATCAAAAAATGAAAATGCTCAGAACTGAACCACGAGCCAAAGGAATAGGATGATCGAAACTAAG
TCACAAATAAAAAATAAGATGATCGGGACTAAACCACAAGTTT
Found at i:6379866 original size:173 final size:173
Alignment explanation
Indices: 6379437--6379992 Score: 424
Period size: 173 Copynumber: 3.2 Consensus size: 173
6379427 ATCGTGAGTC
* * * * * **
6379437 AAAAAATAAAAATGA-ATAGGATTGAATTGCAAGTCAAAGAGTAAGATGATCGAGACTGAGTCAC
1 AAAAAATAAAAACGACA-AGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAACCAC
* * * * * * * * * * * * *
6379501 AAATCAAGAAATGAAAATG-GTCAGAACTGAACTACGAGTCGAAGGAATAGGATGATTGAAATTG
65 AAATCAAAAAATAAAAATGACTGAG-ACTAAACCACGAGCCAAAAGAATAGGATGATCGAGACTA
*** * *
6379565 AGTCACAAATAAAAAATAAAGATGATCGGTACTAAACCACAAGTT
129 AGTTGTAAGTAAAAAATAAAGATGATCGGGACTAAACCACAAGTT
* * * * *
6379610 AAAAAGTAAAAATGACAAGGATTGAATCGTAAGTCAAAAAGTAAGGTGACCAAGACTGAGCCACA
1 AAAAAATAAAAACGACAAGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAACCACA
* * * * * * *
6379675 AGTCAAAAAATTAAAATGACTGGGACTGAACCATGAGCCAAAGGAATAGGATGATCGAGACTAAT
66 AATCAAAAAATAAAAATGACTGAGACTAAACCACGAGCCAAAAGAATAGGATGATCGAGACTAAG
* *
6379740 TTGTAAGTAAAAAAT-AAGATGATTGGGACTAAACCACGAGTTT
131 TTGTAAGTAAAAAATAAAGATGATCGGGACTAAACCACAAG-TT
* * ** * * *
6379783 AAAAAATAAAAACGATC-AGGATTGAATCGCAAGTCAAAGATTAAGATGAATGAA-ATTGAATCG
1 AAAAAATAAAAACGA-CAAGGATTGAATCGCAAGTCAAAAAGTAAGATG-ACCAAGACTGAACCA
* * * * * * * * *
6379846 TAAATCAATAAATAAAAATGATTGAGATTAAATCACGAGCTAAAATAATAGGATTATCGAGATTA
64 CAAATCAAAAAATAAAAATGACTGAGACTAAACCACGAGCCAAAAGAATAGGATGATCGAGACTA
* * * * * * *
6379911 AGTTGTAAGTTAATAATAAAGATGATCGAGACTGAA-TAGCTAGTC
129 AGTTGTAAGTAAAAAATAAAGATGATCGGGACTAAACCA-CAAGTT
* *
6379956 AAAAAATAAAAATGACCAA-GATTGAATCGTAAGTCAA
1 AAAAAATAAAAACGA-CAAGGATTGAATCGCAAGTCAA
6379993 GAAATAAAAA
Statistics
Matches: 306, Mismatches: 69, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
172 22 0.07
173 258 0.84
174 26 0.08
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (173 bp):
AAAAAATAAAAACGACAAGGATTGAATCGCAAGTCAAAAAGTAAGATGACCAAGACTGAACCACA
AATCAAAAAATAAAAATGACTGAGACTAAACCACGAGCCAAAAGAATAGGATGATCGAGACTAAG
TTGTAAGTAAAAAATAAAGATGATCGGGACTAAACCACAAGTT
Found at i:6380018 original size:35 final size:35
Alignment explanation
Indices: 6379925--6380005 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
6379915 GTAAGTTAAT
* * * *
6379925 AATAAAGATGATCGAGACTGAATAGCT-AGTCAAAA
1 AATAAAAATGACCAAGACTGAATCG-TAAGTCAAAA
* *
6379960 AATAAAAATGACCAAGATTGAATCGTAAGTCAAGA
1 AATAAAAATGACCAAGACTGAATCGTAAGTCAAAA
6379995 AATAAAAATGA
1 AATAAAAATGA
6380006 TGAAGGCTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (35 bp):
AATAAAAATGACCAAGACTGAATCGTAAGTCAAAA
Found at i:6380052 original size:139 final size:139
Alignment explanation
Indices: 6379837--6380111 Score: 320
Period size: 139 Copynumber: 2.0 Consensus size: 139
6379827 GATGAATGAA
* * * * *
6379837 ATTGAATCGTAAATCAATAAATAAAAATGATTGAGATTAAATCACGAGCTAAAATAATAGGATTA
1 ATTGAATCGTAAATCAAGAAATAAAAATGATTGAGACTAAATCACAAGCTAAAAGAATAGGATGA
* * * ** * * *
6379902 TCGAGATTAAGTTGTAAGTTAATAATAAAGATGATCGAGACTGAATAGCTAGTCAAAAAATAAAA
66 TCGAAACTAAGTCGTAAGCCAAAAATAAAGATGATCGAGACTGAATAGCGAATCAAAAAATAAAA
*
6379967 ATGACCAAG
131 AAGACCAAG
* * *
6379976 ATTGAATCGTAAGTCAAGAAATAAAAATGA-TGAAGGCTGAATCACAAGCTAAAAGAATAGGATG
1 ATTGAATCGTAAATCAAGAAATAAAAATGATTG-AGACTAAATCACAAGCTAAAAGAATAGGATG
* * * * *
6380040 A-CGAAAACTAAGTCGTAGGCCAAAAATAAATATGATTGGGACTGAATTGCGAATCAAAAAATAA
65 ATCG-AAACTAAGTCGTAAGCCAAAAATAAAGATGATCGAGACTGAATAGCGAATCAAAAAATAA
6380104 AAAAGACC
129 AAAAGACC
6380112 GGGATTAAAC
Statistics
Matches: 112, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
138 4 0.04
139 108 0.96
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (139 bp):
ATTGAATCGTAAATCAAGAAATAAAAATGATTGAGACTAAATCACAAGCTAAAAGAATAGGATGA
TCGAAACTAAGTCGTAAGCCAAAAATAAAGATGATCGAGACTGAATAGCGAATCAAAAAATAAAA
AAGACCAAG
Found at i:6381343 original size:23 final size:23
Alignment explanation
Indices: 6381317--6381380 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
6381307 CTTAAACTTG
6381317 GCTTAAAGTACCAGCTAATCTAA
1 GCTTAAAGTACCAGCTAATCTAA
* ** * *
6381340 GCTT-GAGTGTCGGCTAATCTAG
1 GCTTAAAGTACCAGCTAATCTAA
* *
6381362 GTTTAAAGTCCCAGCTAAT
1 GCTTAAAGTACCAGCTAAT
6381381 TTGGGCTTGG
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (23 bp):
GCTTAAAGTACCAGCTAATCTAA
Found at i:6381415 original size:22 final size:22
Alignment explanation
Indices: 6381372--6381443 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
6381362 GTTTAAAGTC
* *
6381372 CCAGCTAATTTGGGCTTGGGTG
1 CCAGCTAATTCGGGCTTAGGTG
* *
6381394 CCAGTTAATTCGGGTTTAGGTG
1 CCAGCTAATTCGGGCTTAGGTG
** *
6381416 TTAACTAA-TCTGGGCTTAGGTG
1 CCAGCTAATTC-GGGCTTAGGTG
6381438 CCAGCT
1 CCAGCT
6381444 TATCTAAACT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (22 bp):
CCAGCTAATTCGGGCTTAGGTG
Found at i:6388540 original size:8 final size:8
Alignment explanation
Indices: 6388527--6388747 Score: 104
Period size: 8 Copynumber: 28.5 Consensus size: 8
6388517 TTAAGGTCTC
6388527 GTTTTAGG
1 GTTTTAGG
*
6388535 GTTTTAAG
1 GTTTTAGG
6388543 GTTTTAGG
1 GTTTTAGG
***
6388551 GTTTTTCA
1 GTTTTAGG
*
6388559 ATTTT-GG
1 GTTTTAGG
*
6388566 ATTTTAGG
1 GTTTTAGG
* *
6388574 GTATTAAG
1 GTTTTAGG
6388582 GTTTTA-G
1 GTTTTAGG
*
6388589 GTTTCA-G
1 GTTTTAGG
*
6388596 GCTTTAGG
1 GTTTTAGG
6388604 G-TTTAGAG
1 GTTTTAG-G
6388612 GTTTTAGG
1 GTTTTAGG
*
6388620 CTTTGTA--
1 GTTT-TAGG
*
6388627 GTTTTACG
1 GTTTTAGG
*
6388635 GTTTTAAG
1 GTTTTAGG
6388643 GTTTTAGG
1 GTTTTAGG
* *
6388651 ATTTT-GA
1 GTTTTAGG
* *
6388658 ATTTTATG
1 GTTTTAGG
6388666 G-TTTAGG
1 GTTTTAGG
* *
6388673 GTTTCAAG
1 GTTTTAGG
6388681 GTTTTAGG
1 GTTTTAGG
*
6388689 TTTTTA-G
1 GTTTTAGG
6388696 GTTTTAGG
1 GTTTTAGG
6388704 GTTTT-GAG
1 GTTTTAG-G
* *
6388712 ATTTTAGA
1 GTTTTAGG
*
6388720 G-TTTCGAG
1 GTTTTAG-G
*
6388728 GTTTTTGG
1 GTTTTAGG
*
6388736 GTCTTAGG
1 GTTTTAGG
6388744 GTTT
1 GTTT
6388748 CGAGGTTTTA
Statistics
Matches: 159, Mismatches: 40, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
6 2 0.01
7 47 0.30
8 98 0.62
9 12 0.08
ACGTcount: A:0.17, C:0.04, G:0.29, T:0.50
Consensus pattern (8 bp):
GTTTTAGG
Found at i:6388548 original size:16 final size:16
Alignment explanation
Indices: 6388527--6388819 Score: 120
Period size: 16 Copynumber: 17.8 Consensus size: 16
6388517 TTAAGGTCTC
6388527 GTTTTAGGGTTTTAAG
1 GTTTTAGGGTTTTAAG
6388543 GTTTTAGGGTTTTTCAATTTTG
1 GTTTTAGGG-TTTT-AA----G
*
6388565 GATTTTAGGGTATTAAG
1 G-TTTTAGGGTTTTAAG
*
6388582 GTTTTA-GG-TTTCAG
1 GTTTTAGGGTTTTAAG
*
6388596 GCTTTAGGG-TTTAGAG
1 GTTTTAGGGTTTTA-AG
*
6388612 GTTTTAGGCTTTGT-A-
1 GTTTTAGGGTTT-TAAG
*
6388627 GTTTTACGGTTTTAAG
1 GTTTTAGGGTTTTAAG
*
6388643 GTTTTAGGATTTTGAATTTTATG
1 GTTTTAGG-----G--TTTTAAG
*
6388666 G-TTTAGGGTTTCAAG
1 GTTTTAGGGTTTTAAG
*
6388681 GTTTTA-GGTTTTTAG
1 GTTTTAGGGTTTTAAG
*
6388696 GTTTTAGGGTTTTGAG
1 GTTTTAGGGTTTTAAG
* * **
6388712 ATTTTAGAGTTTCGAG
1 GTTTTAGGGTTTTAAG
* *
6388728 GTTTTTGGGTCTT-AG
1 GTTTTAGGGTTTTAAG
* * *
6388743 GGTTTCGAGGTTTTAAA
1 GTTTTAG-GGTTTTAAG
**
6388760 GTTTT-GAGGTTACGAA-
1 GTTTTAG-GGTT-TTAAG
**
6388776 GTTTTAATGTTTTAAG
1 GTTTTAGGGTTTTAAG
* **
6388792 ATTTTAGGGTTTTGGG
1 GTTTTAGGGTTTTAAG
6388808 GTTTTAGGGTTT
1 GTTTTAGGGTTT
6388820 CGAGATTTTA
Statistics
Matches: 209, Mismatches: 41, Indels: 54
0.69 0.13 0.18
Matches are distributed among these distances:
14 10 0.05
15 46 0.22
16 105 0.50
17 16 0.08
18 3 0.01
21 3 0.01
22 11 0.05
23 15 0.07
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.49
Consensus pattern (16 bp):
GTTTTAGGGTTTTAAG
Found at i:6388640 original size:69 final size:66
Alignment explanation
Indices: 6388529--6388708 Score: 161
Period size: 69 Copynumber: 2.6 Consensus size: 66
6388519 AAGGTCTCGT
* * *
6388529 TTTAGGGTTTTAAGGTTTTAGGGTTTTTCAATTTT-GGATTTTAGGGTATTAAGG-TTTT-AGGT
1 TTTAGGG-TTTAAGGTTTTA-GGTTTTT-AGTTTTAGG-TTTTAAGGT-TTAAGGATTTTGA-AT
6388591 TTCA-GG
60 TTCATGG
* *
6388597 CTTTAGGGTTTAGAGGTTTTAGGCTTTGTAGTTTTACGGTTTTAAGGTTTTAGGATTTTGAATTT
1 -TTTAGGGTTTA-AGGTTTTAGG-TTTTTAGTTTTA-GGTTTTAAGGTTTAAGGATTTTGAATTT
*
6388662 TATGG
62 CATGG
6388667 TTTAGGGTTTCAAGGTTTTAGGTTTTTAGGTTTTAGGGTTTT
1 TTTAGGGTTT-AAGGTTTTAGGTTTTTA-GTTTTA-GGTTTT
6388709 GAGATTTTAG
Statistics
Matches: 94, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
68 21 0.22
69 67 0.71
70 6 0.06
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (66 bp):
TTTAGGGTTTAAGGTTTTAGGTTTTTAGTTTTAGGTTTTAAGGTTTAAGGATTTTGAATTTCATG
G
Found at i:6388717 original size:31 final size:30
Alignment explanation
Indices: 6388528--6388742 Score: 102
Period size: 31 Copynumber: 7.0 Consensus size: 30
6388518 TAAGGTCTCG
*
6388528 TTTTAGGGTTTTAAGGTTTTAGGGTTTTTCA-A
1 TTTTA-GGTTTTTAGGTTTTAGGG-TTTT-AGA
* * * *
6388560 TTTT-GGATTTTAGGGTATTAAGGTTTTAGG
1 TTTTAGGTTTTTA-GGTTTTAGGGTTTTAGA
* * * *
6388590 TTTCAGG-CTTTAGGGTTTAGAGGTTTTAGGC
1 TTTTAGGTTTTTAGGTTTTAG-GGTTTTA-GA
*
6388621 TTTGTA-G-TTTTACGGTTTTAAGGTTTTAGGA
1 TTT-TAGGTTTTTA-GGTTTTAGGGTTTTA-GA
** * *
6388652 TTTT-GAATTTTATGG-TTTAGGGTTTCAAGG
1 TTTTAGGTTTTTA-GGTTTTAGGGTTT-TAGA
6388682 TTTTAGGTTTTTAGGTTTTAGGGTTTTGAGA
1 TTTTAGGTTTTTAGGTTTTAGGGTTTT-AGA
** * *
6388713 TTTTAGAGTTTCGAGGTTTTTGGGTCTTAG
1 TTTTAG-GTTTTTAGGTTTTAGGGTTTTAG
6388743 GGTTTCGAGG
Statistics
Matches: 140, Mismatches: 29, Indels: 29
0.71 0.15 0.15
Matches are distributed among these distances:
29 6 0.04
30 41 0.29
31 65 0.46
32 28 0.20
ACGTcount: A:0.18, C:0.04, G:0.28, T:0.50
Consensus pattern (30 bp):
TTTTAGGTTTTTAGGTTTTAGGGTTTTAGA
Found at i:6388730 original size:24 final size:23
Alignment explanation
Indices: 6388703--6388756 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
6388693 TAGGTTTTAG
*
6388703 GGTTTTGAGATTTTAGAGTTTCGA
1 GGTTTTG-GATCTTAGAGTTTCGA
* *
6388727 GGTTTTTGGGTCTTAGGGTTTCGA
1 GG-TTTTGGATCTTAGAGTTTCGA
6388751 GGTTTT
1 GGTTTT
6388757 AAAGTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.65
25 5 0.19
ACGTcount: A:0.13, C:0.06, G:0.33, T:0.48
Consensus pattern (23 bp):
GGTTTTGGATCTTAGAGTTTCGA
Found at i:6388743 original size:40 final size:40
Alignment explanation
Indices: 6388686--6388770 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
6388676 TCAAGGTTTT
* * *
6388686 AGGTTTTTAGGTTTTAGGGTTTTGAGATTTTAGAGTTTCG
1 AGGTTTTTAGGTCTTAGGGTTTCGAGATTTTAAAGTTTCG
* * *
6388726 AGGTTTTTGGGTCTTAGGGTTTCGAGGTTTTAAAGTTTTG
1 AGGTTTTTAGGTCTTAGGGTTTCGAGATTTTAAAGTTTCG
6388766 AGGTT
1 AGGTT
6388771 ACGAAGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.16, C:0.04, G:0.32, T:0.48
Consensus pattern (40 bp):
AGGTTTTTAGGTCTTAGGGTTTCGAGATTTTAAAGTTTCG
Found at i:6388770 original size:24 final size:24
Alignment explanation
Indices: 6388743--6388788 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6388733 TGGGTCTTAG
* *
6388743 GGTTTCGAGGTTTTAAAGTTTTGA
1 GGTTACGAAGTTTTAAAGTTTTGA
*
6388767 GGTTACGAAGTTTTAATGTTTT
1 GGTTACGAAGTTTTAAAGTTTT
6388789 AAGATTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.48
Consensus pattern (24 bp):
GGTTACGAAGTTTTAAAGTTTTGA
Found at i:6388828 original size:16 final size:16
Alignment explanation
Indices: 6388790--6388829 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6388780 TAATGTTTTA
*
6388790 AGATTTTAGGGTTTTG
1 AGATTTTAGGGTTTCG
* *
6388806 GGGTTTTAGGGTTTCG
1 AGATTTTAGGGTTTCG
6388822 AGATTTTA
1 AGATTTTA
6388830 ATGTTTTAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.33, T:0.47
Consensus pattern (16 bp):
AGATTTTAGGGTTTCG
Found at i:6388835 original size:24 final size:24
Alignment explanation
Indices: 6388739--6388837 Score: 60
Period size: 24 Copynumber: 4.1 Consensus size: 24
6388729 TTTTTGGGTC
* *
6388739 TTAGGGTTTCGAGGTTTTAAAGTT
1 TTAGGGTTTCGAGATTTTAATGTT
*
6388763 TT-GAGGTTACGA-AGTTTTAATGTT
1 TTAG-GGTTTCGAGA-TTTTAATGTT
* * * * ***
6388787 TTAAGATTT-TAGGGTTTTGGGGTT
1 TTAGGGTTTCGA-GATTTTAATGTT
6388811 TTAGGGTTTCGAGATTTTAATGTT
1 TTAGGGTTTCGAGATTTTAATGTT
6388835 TTA
1 TTA
6388838 AAGTTTCATT
Statistics
Matches: 51, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
23 2 0.04
24 48 0.94
25 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.27, T:0.48
Consensus pattern (24 bp):
TTAGGGTTTCGAGATTTTAATGTT
Found at i:6395571 original size:19 final size:20
Alignment explanation
Indices: 6395549--6395599 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6395539 GGGTTTATAG
*
6395549 TTTATGGTTTCATAAA-TGA
1 TTTAAGGTTTCATAAAGTGA
*
6395568 TTTAAGGTTT-AAAAAGTGA
1 TTTAAGGTTTCATAAAGTGA
*
6395587 TTTAGGGTTTCAT
1 TTTAAGGTTTCAT
6395600 GGGTGGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 21 0.81
20 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTAAGGTTTCATAAAGTGA
Found at i:6401559 original size:14 final size:15
Alignment explanation
Indices: 6401531--6401561 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6401521 TTTTTCCTCA
6401531 AAATTTTCTTTCTTC
1 AAATTTTCTTTCTTC
6401546 AAATTTTC-TTCTTC
1 AAATTTTCTTTCTTC
6401560 AA
1 AA
6401562 CTTCCTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTTCTTTCTTC
Found at i:6404100 original size:20 final size:20
Alignment explanation
Indices: 6404075--6404122 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
6404065 TAATCTTCTT
6404075 GATTCTTTCACTTAGCTTAG
1 GATTCTTTCACTTAGCTTAG
6404095 GATTCTTTCACTTAGCTTAG
1 GATTCTTTCACTTAGCTTAG
6404115 GATTCTTT
1 GATTCTTT
6404123 TGGATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (20 bp):
GATTCTTTCACTTAGCTTAG
Found at i:6407426 original size:27 final size:25
Alignment explanation
Indices: 6407396--6407496 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 25
6407386 TGGAGCTTGA
*
6407396 AAAAGAATGAAAAAAAAAGTCAAATAG
1 AAAAGAA-GAAAAAAAAAATCAAA-AG
* *
6407423 AAAA-AAGAAAAGAAAAAATGAAAGG
1 AAAAGAAGAAAA-AAAAAATCAAAAG
* *
6407448 AAAAGAAAGAAAAAGAAAAACTGAAAGG
1 AAAAG-AAGAAAAA-AAAAA-TCAAAAG
6407476 AAAAGAAAAGAAAAAGAAAAA
1 AAAAG--AAGAAAAA-AAAAA
6407497 GCAATAAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
25 10 0.15
26 12 0.18
27 16 0.25
28 12 0.18
29 15 0.23
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (25 bp):
AAAAGAAGAAAAAAAAAATCAAAAG
Found at i:6407439 original size:6 final size:6
Alignment explanation
Indices: 6407424--6407497 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
6407414 GTCAAATAGA
* * *
6407424 AAAAAG -AAAAG AAAAA- ATGAAAG GAAAAG --AAAG AAAAAG AAAAAC
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** *
6407469 TGAAAG GAAAAG -AAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
6407498 CAATAAAGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 4 0.08
5 11 0.21
6 38 0.72
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:6407461 original size:28 final size:29
Alignment explanation
Indices: 6407425--6407496 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 29
6407415 TCAAATAGAA
6407425 AAAAG-AAAAGAAAAAATGAAAGGAAAAG
1 AAAAGAAAAAGAAAAAATGAAAGGAAAAG
*
6407453 -AAAGAAAAAGAAAAACTGAAAGGAAAAG
1 AAAAGAAAAAGAAAAAATGAAAGGAAAAG
6407481 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
6407497 GCAATAAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 4 0.10
28 22 0.54
29 15 0.37
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (29 bp):
AAAAGAAAAAGAAAAAATGAAAGGAAAAG
Found at i:6407557 original size:37 final size:40
Alignment explanation
Indices: 6407477--6407557 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 40
6407467 ACTGAAAGGA
* *
6407477 AAAGAAAAGAAAAAGAAAAAGCAATAAAGTGGTGAAAACC
1 AAAGAAAAGAAAAAGAAAAAGCAATAAAGTGGTCAAAAAC
6407517 AAAGAAAAGAAGAAA-AAAAAG-AA-AAA-TGAG-CAAAAAC
1 AAAGAAAAGAA-AAAGAAAAAGCAATAAAGTG-GTCAAAAAC
6407554 AAAG
1 AAAG
6407558 TTTAGAGGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
37 11 0.30
38 4 0.11
39 2 0.05
40 17 0.46
41 3 0.08
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.05
Consensus pattern (40 bp):
AAAGAAAAGAAAAAGAAAAAGCAATAAAGTGGTCAAAAAC
Found at i:6412586 original size:19 final size:19
Alignment explanation
Indices: 6412549--6412587 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6412539 CACTATTTGT
**
6412549 AGGCTAAAATGTAACAATC
1 AGGCTAAAAAATAACAATC
*
6412568 AGGCTAAAAAATAATAATC
1 AGGCTAAAAAATAACAATC
6412587 A
1 A
6412588 ATGTCTGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.21
Consensus pattern (19 bp):
AGGCTAAAAAATAACAATC
Found at i:6423081 original size:19 final size:20
Alignment explanation
Indices: 6423057--6423095 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6423047 TAGCTATTTG
6423057 GATTTTAA-CAAATAAATCC
1 GATTTTAACCAAATAAATCC
6423076 GATTTTAATCCAAATAAATC
1 GATTTTAA-CCAAATAAATC
6423096 ATAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
GATTTTAACCAAATAAATCC
Found at i:6424841 original size:20 final size:21
Alignment explanation
Indices: 6424816--6424857 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6424806 GGTTCAGCAT
* *
6424816 TGAAATG-ATTTTGATTAATG
1 TGAAATGAATATTCATTAATG
6424836 TGAAATGAATATTCATTAATG
1 TGAAATGAATATTCATTAATG
6424857 T
1 T
6424858 AGAATATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (21 bp):
TGAAATGAATATTCATTAATG
Found at i:6431061 original size:11 final size:12
Alignment explanation
Indices: 6431044--6431072 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6431034 GTGTTGCCTT
6431044 ATTTTTCTTTTC
1 ATTTTTCTTTTC
6431056 -TTTTTCTTTTC
1 ATTTTTCTTTTC
6431067 ATTTTT
1 ATTTTT
6431073 TGATTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTCTTTTC
Found at i:6431135 original size:3 final size:3
Alignment explanation
Indices: 6431127--6431161 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6431117 ATTTTTTGTG
6431127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6431162 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6431137 original size:30 final size:29
Alignment explanation
Indices: 6431081--6431137 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
6431071 TTTGATTTGA
* * *
6431081 TTTAATTATTTTTGTTTTGTTGTTATTTT
1 TTTAATTATTTTTGTGTTATTATTATTTT
*
6431110 TTTACTTATTTTTTGTGTTATTATTATT
1 TTTAATTA-TTTTTGTGTTATTATTATT
6431138 ATTATTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.74
Consensus pattern (29 bp):
TTTAATTATTTTTGTGTTATTATTATTTT
Found at i:6433358 original size:7 final size:7
Alignment explanation
Indices: 6433327--6433391 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
6433317 TTTATTAAAC
6433327 TTAATTT
1 TTAATTT
*
6433334 TTACTTT
1 TTAATTT
6433341 TATATAGTTT
1 T-TA-A-TTT
6433351 TT-ATTT
1 TTAATTT
6433357 TTAATTT
1 TTAATTT
*
6433364 TTACATAT
1 TTA-ATTT
*
6433372 ATAATTT
1 TTAATTT
6433379 TT-ATTT
1 TTAATTT
6433385 TTAATTT
1 TTAATTT
6433392 ATATATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
6 11 0.24
7 23 0.50
8 7 0.15
9 1 0.02
10 4 0.09
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.68
Consensus pattern (7 bp):
TTAATTT
Found at i:6433380 original size:28 final size:28
Alignment explanation
Indices: 6433327--6433406 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
6433317 TTTATTAAAC
* *
6433327 TTAATTTTTACTTTTATATAGTTTTTATTT
1 TTAATTTTTAC--ATATATAATTTTTATTT
6433357 TTAATTTTTACATATATAATTTTTATTT
1 TTAATTTTTACATATATAATTTTTATTT
* *
6433385 TTAATTTATATATATATGAATT
1 TTAATTTTTACATATAT-AATT
6433407 AAATATTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 30 0.67
29 4 0.09
30 11 0.24
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (28 bp):
TTAATTTTTACATATATAATTTTTATTT
Found at i:6434074 original size:16 final size:16
Alignment explanation
Indices: 6434034--6434075 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6434024 ATATTTCATA
6434034 TATATTTTATAAATAT
1 TATATTTTATAAATAT
*
6434050 TATAATTTA-AAATAAT
1 TATATTTTATAAAT-AT
*
6434066 TTTATTTTAT
1 TATATTTTAT
6434076 GTTATGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTTATAAATAT
Found at i:6434173 original size:20 final size:20
Alignment explanation
Indices: 6434143--6434188 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
6434133 TTAAATTAAG
*
6434143 TTAAAAAATT-CAAATCCTT
1 TTAAAAAATTCCAAATCATT
*
6434162 TTAAAGAAATTCCATATCATT
1 TTAAA-AAATTCCAAATCATT
6434183 TTAAAA
1 TTAAAA
6434189 GATTTAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 6 0.26
21 12 0.52
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (20 bp):
TTAAAAAATTCCAAATCATT
Found at i:6435441 original size:14 final size:16
Alignment explanation
Indices: 6435415--6435450 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
6435405 ATTATTTAAC
6435415 ATTTATAAAAATTTA-
1 ATTTATAAAAATTTAT
6435430 ATTTAT-AAAATTTAT
1 ATTTATAAAAATTTAT
6435445 ATTTAT
1 ATTTAT
6435451 TTAACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATAAAAATTTAT
Found at i:6435532 original size:33 final size:32
Alignment explanation
Indices: 6435468--6435537 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
6435458 TAATGAAATT
6435468 TAATAAAATGTAAATTTATTAGTTTATATATAA
1 TAATAAAATGTAAATTTATTAGTTTATATAT-A
* * *
6435501 TAATAAAATTTATTATTTATTATTTTA-ATATA
1 TAATAAAATGTA-AATTTATTAGTTTATATATA
6435533 TAATA
1 TAATA
6435538 GTAATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 15 0.45
34 12 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TAATAAAATGTAAATTTATTAGTTTATATATA
Found at i:6435550 original size:35 final size:34
Alignment explanation
Indices: 6435468--6435550 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
6435458 TAATGAAATT
* *
6435468 TAATAAAATGTA-AATTTATTAGTTTATATATAA
1 TAATAAAATATATTATTTATTAGTTTATATATAA
* *
6435501 TAATAAAATTTATTATTTATTATTTTAATATATAA
1 TAATAAAATATATTATTTATTAGTTT-ATATATAA
* *
6435536 TAGTAATATATATTA
1 TAATAAAATATATTA
6435551 AATAAAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 11 0.26
34 11 0.26
35 20 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (34 bp):
TAATAAAATATATTATTTATTAGTTTATATATAA
Found at i:6435698 original size:1 final size:1
Alignment explanation
Indices: 6435692--6435732 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
6435682 AATCTAAGGT
6435692 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6435733 CTTTTAGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6441195 original size:27 final size:27
Alignment explanation
Indices: 6441153--6441281 Score: 110
Period size: 27 Copynumber: 4.9 Consensus size: 27
6441143 TGACTTTCTT
*
6441153 CAAATCCATTCGAATGTAACCTTGTTC
1 CAAATCCATTCAAATGTAACCTTGTTC
6441180 CAAATCCATTCAAATGTAACCTTG-T-
1 CAAATCCATTCAAATGTAACCTTGTTC
* *** *
6441205 C-AAT--TTTTTGATG--GCCTTGACTTTCTC
1 CAAATCCATTCAAATGTAACCTTG----T-TC
6441232 CAAATCCATTCAAATGTAACCTTGTTC
1 CAAATCCATTCAAATGTAACCTTGTTC
6441259 CAAATCCATTCAAATGTAACCTT
1 CAAATCCATTCAAATGTAACCTT
6441282 ATCAATTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 5 0.06
22 5 0.06
24 3 0.04
25 1 0.01
26 2 0.03
27 49 0.62
28 4 0.05
30 5 0.06
32 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (27 bp):
CAAATCCATTCAAATGTAACCTTGTTC
Found at i:6441263 original size:79 final size:79
Alignment explanation
Indices: 6441132--6441328 Score: 331
Period size: 79 Copynumber: 2.5 Consensus size: 79
6441122 TTGCCCATTC
* *
6441132 TTTGATGGCCCTGACTTTCTTCAAATCCATTCGAATGTAACCTTGTTCCAAATCCATTCAAATGT
1 TTTGATGGCCCTGACTTTCTCCAAATCCATTCAAATGTAACCTTGTTCCAAATCCATTCAAATGT
* *
6441197 AACCTTGTCAATTT
66 AACCTTATCAATTA
*
6441211 TTTGATGGCCTTGACTTTCTCCAAATCCATTCAAATGTAACCTTGTTCCAAATCCATTCAAATGT
1 TTTGATGGCCCTGACTTTCTCCAAATCCATTCAAATGTAACCTTGTTCCAAATCCATTCAAATGT
6441276 AACCTTATCAATTA
66 AACCTTATCAATTA
* *
6441290 TTTGATGGCCCTAACTTTCTCTAAATCCATTCAAATGTA
1 TTTGATGGCCCTGACTTTCTCCAAATCCATTCAAATGTA
6441329 TCTATGTTTG
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 110 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (79 bp):
TTTGATGGCCCTGACTTTCTCCAAATCCATTCAAATGTAACCTTGTTCCAAATCCATTCAAATGT
AACCTTATCAATTA
Found at i:6443267 original size:11 final size:11
Alignment explanation
Indices: 6443253--6443278 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6443243 TTTAATATTG
6443253 AAAAAAAGAAA
1 AAAAAAAGAAA
6443264 AAAAAAAGAAA
1 AAAAAAAGAAA
6443275 AAAA
1 AAAA
6443279 GAGAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:6443268 original size:10 final size:10
Alignment explanation
Indices: 6443253--6443286 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6443243 TTTAATATTG
6443253 AAAAAAAGAAA
1 AAAAAAAG-AA
6443264 AAAAAAAGAA
1 AAAAAAAGAA
*
6443274 AAAAAGAGAA
1 AAAAAAAGAA
6443284 AAA
1 AAA
6443287 TTAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:6443763 original size:12 final size:12
Alignment explanation
Indices: 6443748--6443773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6443738 ACACAAAACC
6443748 AAATAAAAAAAT
1 AAATAAAAAAAT
6443760 AAATAAAAAAAT
1 AAATAAAAAAAT
6443772 AA
1 AA
6443774 CAGTCTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:6444526 original size:13 final size:12
Alignment explanation
Indices: 6444510--6444595 Score: 52
Period size: 12 Copynumber: 7.1 Consensus size: 12
6444500 ATAAAGTAGG
6444510 ATAATAACTAAAA
1 ATAATAA-TAAAA
6444523 ATAATAATAAAA
1 ATAATAATAAAA
* *
6444535 AT-GTAAAAAATA
1 ATAATAATAAA-A
*
6444547 ATAATAATAACA
1 ATAATAATAAAA
*
6444559 AT-CTAA-AAAA
1 ATAATAATAAAA
* *
6444569 GTGATAATAACAA
1 ATAATAATAA-AA
*
6444582 TAAAATAATAAAA
1 -ATAATAATAAAA
6444595 A
1 A
6444596 AATTTCCCTG
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
10 4 0.07
11 12 0.22
12 16 0.29
13 16 0.29
14 7 0.13
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:6444554 original size:24 final size:25
Alignment explanation
Indices: 6444522--6444578 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
6444512 AATAACTAAA
*
6444522 AATAATAATAAAAATGTAAAAAA-T
1 AATAATAATAAAAATCTAAAAAAGT
*
6444546 AATAATAATAACAATCTAAAAAAGT
1 AATAATAATAAAAATCTAAAAAAGT
*
6444571 GATAATAA
1 AATAATAA
6444579 CAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (25 bp):
AATAATAATAAAAATCTAAAAAAGT
Found at i:6445017 original size:30 final size:31
Alignment explanation
Indices: 6444918--6445018 Score: 88
Period size: 30 Copynumber: 3.4 Consensus size: 31
6444908 CTAAATCCTC
* * *
6444918 CAAACCGTAAAA-CTAAGACCTTAAACCTTTT
1 CAAACCCTAAAATCAAAAACCTTAAA-CTTTT
***
6444949 -AAACCCTAAAATCAAAAACC-T-AA-TCCC
1 CAAACCCTAAAATCAAAAACCTTAAACTTTT
*
6444976 CAAACCTTAAAATC-AAAACCTTAAACTTTT
1 CAAACCCTAAAATCAAAAACCTTAAACTTTT
6445006 CAAACCCTAAAAT
1 CAAACCCTAAAAT
6445019 TCAAGCCCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
27 7 0.13
28 13 0.24
29 4 0.07
30 24 0.44
31 6 0.11
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.23
Consensus pattern (31 bp):
CAAACCCTAAAATCAAAAACCTTAAACTTTT
Found at i:6445029 original size:58 final size:59
Alignment explanation
Indices: 6444897--6445029 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 59
6444887 CTAAACCTCG
* *
6444897 AAATTGAAACCCTAAATCCTCCAAACCGTAAAACTAAGACCTTAAACCTTTTAAACCCTA
1 AAATTCAAACCCT-AATCCTCCAAACCGTAAAACTAAAACCTTAAACCTTTTAAACCCTA
* *
6444957 AAA-TCAAAAACCTAATCC-CCAAACCTTAAAA-TCAAAACCTTAAA-CTTTTCAAACCCTA
1 AAATTC-AAACCCTAATCCTCCAAACCGTAAAACT-AAAACCTTAAACCTTTT-AAACCCTA
*
6445015 AAATTCAAGCCCTAA
1 AAATTCAAACCCTAA
6445030 AACTTTCTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
57 6 0.10
58 40 0.63
59 8 0.13
60 9 0.14
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (59 bp):
AAATTCAAACCCTAATCCTCCAAACCGTAAAACTAAAACCTTAAACCTTTTAAACCCTA
Found at i:6445171 original size:14 final size:15
Alignment explanation
Indices: 6445141--6445178 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
6445131 AAACTCTAAC
6445141 CCTAAAATCTAAAAT
1 CCTAAAATCTAAAAT
*
6445156 CCTAAAAT-TCAAAT
1 CCTAAAATCTAAAAT
*
6445170 CCAAAAATC
1 CCTAAAATC
6445179 CCAAATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (15 bp):
CCTAAAATCTAAAAT
Found at i:6445175 original size:28 final size:27
Alignment explanation
Indices: 6445109--6445175 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
6445099 TTAAAAACCT
* *
6445109 AAATCCCAAAATCTAAAACTTGAAACTC
1 AAAT-CCAAAATCTAAAACCTAAAACTC
* * *
6445137 TAACCCTAAAATCTAAAATCCTAAAATTC
1 AAATCC-AAAATCTAAAA-CCTAAAACTC
6445166 AAATCCAAAA
1 AAATCCAAAA
6445176 ATCCCAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
27 2 0.07
28 17 0.57
29 11 0.37
ACGTcount: A:0.52, C:0.24, G:0.01, T:0.22
Consensus pattern (27 bp):
AAATCCAAAATCTAAAACCTAAAACTC
Found at i:6451884 original size:11 final size:11
Alignment explanation
Indices: 6451868--6451899 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
6451858 GTATAAAAAT
6451868 TATCCATTTGC
1 TATCCATTTGC
6451879 TATCCATTTGC
1 TATCCATTTGC
6451890 TATCCATTTG
1 TATCCATTTG
6451900 AGCCTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (11 bp):
TATCCATTTGC
Found at i:6453283 original size:41 final size:42
Alignment explanation
Indices: 6453237--6453331 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 42
6453227 ATATTCATAG
** *
6453237 TTGCATCACTTGCT-TGTGCATCATCAA-AGGGATATTTGCAT
1 TTGCATCACTTGCTATGTGCATCA-CAAGAAAGATATTCGCAT
* *
6453278 TTGCATCACTTG-TATTTGTATCACAAGAAAGATATTCGCAT
1 TTGCATCACTTGCTATGTGCATCACAAGAAAGATATTCGCAT
6453319 TTGCATCACTTGC
1 TTGCATCACTTGC
6453332 ATTTACACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGCATCACTTGCTATGTGCATCACAAGAAAGATATTCGCAT
Found at i:6453912 original size:88 final size:88
Alignment explanation
Indices: 6453803--6454000 Score: 220
Period size: 88 Copynumber: 2.2 Consensus size: 88
6453793 ATCGATTTTC
* * * **
6453803 TAAGACCTTCGAGAATAATTTTGA-TT-TGCAGTATTGTCCCAATTGATTTTTTATTTTTTGACT
1 TAAGACCTTCGGGAATAATTTTGATTTATG-A-TATTATCCCAATCGATTCCTTATTTTTTGACT
* ** *
6453866 TATGGTGTTGTCCCGGTTGTTTCTT
64 TATGGTGTTGTCCCAGTTAATTCTG
* * * * *
6453891 TAAGACCTCCGGGTATAATTTTGATTTATGATGTTATCCCGATCGATTCCTTATTTTTTGACTTG
1 TAAGACCTTCGGGAATAATTTTGATTTATGATATTATCCCAATCGATTCCTTATTTTTTGACTTA
6453956 TGGTGTTGTCCCAGTTAATTCTG
66 TGGTGTTGTCCCAGTTAATTCTG
* *
6453979 TAAGACCTTCGGGCATGATTTT
1 TAAGACCTTCGGGAATAATTTT
6454001 TAAGACCTTC
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
88 86 0.95
89 3 0.03
90 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (88 bp):
TAAGACCTTCGGGAATAATTTTGATTTATGATATTATCCCAATCGATTCCTTATTTTTTGACTTA
TGGTGTTGTCCCAGTTAATTCTG
Found at i:6454024 original size:22 final size:22
Alignment explanation
Indices: 6453979--6454030 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6453969 GTTAATTCTG
* *
6453979 TAAGACCTTCGGGCATGATTTT
1 TAAGACCTTCGGGCATAATCTT
*
6454001 TAAGACCTTCGGGTATAATCTT
1 TAAGACCTTCGGGCATAATCTT
*
6454023 TAAAACCT
1 TAAGACCT
6454031 CCAAGCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAGACCTTCGGGCATAATCTT
Found at i:6454392 original size:110 final size:111
Alignment explanation
Indices: 6454112--6454395 Score: 358
Period size: 110 Copynumber: 2.6 Consensus size: 111
6454102 ATCGATACTA
* * * * * * *
6454112 TAAGACCTCCAGGCATAGTTTTGATTCGTAATATTATCCCGATCGATTCTTTATTTTTTAATTTG
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCTCGATCGATTCTTTATTTTTTGACTTG
* *
6454177 TGTCGTTATCTCGGTCGATTCTGTAAGACCTCCGGGCATAATCTCT
66 TGTCATTATCCCGGTCGATTCTGTAAGACCTCCGGGCATAATCTCT
* ** *
6454223 AAAGACCTTTAGGCATAATTTTGATTCGCAGTGTTATCTTGATCGATTCTTTA-TTTTTGACTTG
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCTCGATCGATTCTTTATTTTTTGACTTG
* * *
6454287 TGGT-ATTATCCCGGTCGATTTTGTAAGACCTCTGGGTATAATCT-T
66 T-GTCATTATCCCGGTCGATTCTGTAAGACCTCCGGGCATAATCTCT
* * * *
6454332 TAAGACCTCCAGGCATAATTTTGATTCACAGTGTTATCTCAATAGATTTTTTATTTTTTGACTT
1 TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCTCGATCGATTCTTTATTTTTTGACTT
6454396 ACGGTGTTTC
Statistics
Matches: 147, Mismatches: 24, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
109 46 0.31
110 55 0.37
111 46 0.31
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.43
Consensus pattern (111 bp):
TAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTATCTCGATCGATTCTTTATTTTTTGACTTG
TGTCATTATCCCGGTCGATTCTGTAAGACCTCCGGGCATAATCTCT
Found at i:6454416 original size:36 final size:37
Alignment explanation
Indices: 6454362--6454444 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 37
6454352 TTGATTCACA
6454362 GTGTTATCTCAATAGATTTTTTATTTTTTGACTTACG
1 GTGTTATCTCAATAGATTTTTTATTTTTTGACTTACG
* *
6454399 GTGTT-TCTCAATTGATTTTTTATTTTTTGATTTACG
1 GTGTTATCTCAATAGATTTTTTATTTTTTGACTTACG
*
6454435 GTGTTGTCTC
1 GTGTTATCTC
6454445 GGTTAATTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 34 0.79
37 9 0.21
ACGTcount: A:0.17, C:0.11, G:0.16, T:0.57
Consensus pattern (37 bp):
GTGTTATCTCAATAGATTTTTTATTTTTTGACTTACG
Found at i:6454416 original size:109 final size:110
Alignment explanation
Indices: 6454191--6454417 Score: 269
Period size: 109 Copynumber: 2.1 Consensus size: 110
6454181 GTTATCTCGG
* ** *
6454191 TCGATTCTGTAAGACCTCCGGGCATAATCTCTAAAGACCTTTAGGCATAATTTTGATTCGCAGTG
1 TCGATTTTGTAAGACCTCCGGGCATAATCTCTAAAGACCTCCAGGCATAATTTTGATTCACAGTG
** * ** **
6454256 TTATCTTGATCGATTCTTTATTTTTGACTTGTGGTATTATCCCGG
66 TTATCTCAATAGATTCTTTATTTTTGACTTACGGTATTATCCCAA
* * *
6454301 TCGATTTTGTAAGACCTCTGGGTATAATCT-TTAAGACCTCCAGGCATAATTTTGATTCACAGTG
1 TCGATTTTGTAAGACCTCCGGGCATAATCTCTAAAGACCTCCAGGCATAATTTTGATTCACAGTG
* * *
6454365 TTATCTCAATAGATTTTTTATTTTTTGACTTACGGTGTT-TCTCAA
66 TTATCTCAATAGATTCTTTA-TTTTTGACTTACGGTATTATCCCAA
*
6454410 TTGATTTT
1 TCGATTTT
6454418 TTATTTTTTG
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
109 56 0.57
110 42 0.43
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (110 bp):
TCGATTTTGTAAGACCTCCGGGCATAATCTCTAAAGACCTCCAGGCATAATTTTGATTCACAGTG
TTATCTCAATAGATTCTTTATTTTTGACTTACGGTATTATCCCAA
Found at i:6454521 original size:22 final size:22
Alignment explanation
Indices: 6454473--6454521 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
6454463 TTCATGCATG
* *
6454473 ATTTCTAAGATCTTCGGGTATA
1 ATTTTTAAGACCTTCGGGTATA
6454495 ATTTTTAAGACCTTCGGGTATA
1 ATTTTTAAGACCTTCGGGTATA
6454517 ATTTT
1 ATTTT
6454522 GATTCACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTTTTAAGACCTTCGGGTATA
Found at i:6454635 original size:22 final size:22
Alignment explanation
Indices: 6454588--6454652 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
6454578 GTCGATTCTG
*
6454588 TAAGACCTTCG-GACATGATTTC
1 TAAGACCTTCGAG-CATAATTTC
6454610 TAAGACCTTCGAGCATAATCTT-
1 TAAGACCTTCGAGCATAAT-TTC
*
6454632 TAAGA-CTTCCAGGCATAATTT
1 TAAGACCTTCGA-GCATAATTT
6454653 TGATTCGCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.18
22 28 0.74
23 3 0.08
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (22 bp):
TAAGACCTTCGAGCATAATTTC
Found at i:6454654 original size:132 final size:131
Alignment explanation
Indices: 6454450--6455278 Score: 671
Period size: 132 Copynumber: 6.3 Consensus size: 131
6454440 GTCTCGGTTA
* * * * * *
6454450 ATTCTGTAAGACCTTCATG-CATGATTTCTAAGATCTTCGGGTATAATTTTTAAGACCTT-CGGG
1 ATTCTGTAAGACCTTC-GGACATGATTTCTAAGA-CCTCGAGCATAATCTTTAAGA-CTTCCAGG
* * * *
6454513 TATAATTTTGATTCACAGTGTTGTCCCAATCGATTCTTTATTTTTCAACTTACGATATTGTCCC-
63 CATAATTTTGATTCACAGTGTTATCCCGATCGATTCTTTATTTTTCAACTTACGATGTTGTCCCG
6454577 AGTCG
128 A-TCG
6454582 ATTCTGTAAGACCTTCGGACATGATTTCTAAGACCTTCGAGCATAATCTTTAAGACTTCCAGGCA
1 ATTCTGTAAGACCTTCGGACATGATTTCTAAGACC-TCGAGCATAATCTTTAAGACTTCCAGGCA
* * * * * * *
6454647 TAATTTTGATTCGCGGTATTAT-CCAATCGATTCTTTA-TTTTGAGACTTGC-AGTGTTGTCTCG
65 TAATTTTGATTCACAGTGTTATCCCGATCGATTCTTTATTTTTCA-ACTTACGA-TGTTGTCCCG
6454709 ATCG
128 ATCG
* * * * **
6454713 ATTTTGTAAGACTTTCAGG-TATGATTTTTAAGACCTCTGAGCATAATCTTTAAGACCACC-GAG
1 ATTCTGTAAGACCTTC-GGACATGATTTCTAAGACCTC-GAGCATAATCTTTAAGACTTCCAG-G
* * * * *
6454776 CATAATTTCT-ATTCGC-GATGTTATCCCGATCAATTTTTTTTATTTTTTAACTTACGATGTTAT
63 CATAATTT-TGATTCACAG-TGTTATCCCGATCGA--TTCTTTATTTTTCAACTTACGATGTTGT
6454839 CCCTG-TCG
124 CCC-GATCG
* * *
6454847 ATTCTGTAAGACCTTCGGACATGATTTCTAAGATCTCTGGGCATAATCTTTAAGACCTCCAGGCA
1 ATTCTGTAAGACCTTCGGACATGATTTCTAAGACCTC-GAGCATAATCTTTAAGACTTCCAGGCA
* * * * * ** * * *
6454912 TAATTTTGATTCGA-GGTGTTGTCCCCATTGATTTTTTATTTTTCAACTTGTGGTGTTATCTCGA
65 TAATTTTGATTC-ACAGTGTTATCCCGATCGATTCTTTATTTTTCAACTTACGATGTTGTCCCGA
6454976 TCG
129 TCG
* * * * * * ***
6454979 ATTCTATAAAACCTTCGGACATAATTTTTAAGACCTCCAGACATAATCTTTAAGAATTTTGGGCA
1 ATTCTGTAAGACCTTCGGACATGATTTCTAAGACCTCGAG-CATAATCTTTAAGACTTCCAGGCA
* * * ** * *
6455044 TAATTTTGATTCACAGTGTTATCCCGATTGATTTTTTATTTTTCGACTTGTGGTGTTGTCTCGAT
65 TAATTTTGATTCACAGTGTTATCCCGATCGATTCTTTATTTTTCAACTTACGATGTTGTCCCGAT
6455109 CG
130 CG
* * * * * * *
6455111 ATTCTATAACACCTCCGGACATGATTTCTAAAACCTCAAGGCATAAACTTTAAGACCTT-TAGGC
1 ATTCTGTAAGACCTTCGGACATGATTTCTAAGACCTCGA-GCATAATCTTTAAGA-CTTCCAGGC
* * * * ** * * * *
6455175 ATAATTTCGATTCA-TGATGTTATCCCGTTTGATTCTTTATTTTTTGACTTATGGTATTGTCCCA
64 ATAATTTTGATTCACAG-TGTTATCCCGATCGATTCTTTATTTTTCAACTTACGATGTTGTCCCG
6455239 ATCG
128 ATCG
* *
6455243 ATTCTGTAAGACC-TCTGGGCATGATTTTTAAGACCT
1 ATTCTGTAAGACCTTC-GGACATGATTTCTAAGACCT
6455279 TTAAACATAA
Statistics
Matches: 581, Mismatches: 87, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
130 10 0.02
131 108 0.19
132 353 0.61
133 6 0.01
134 95 0.16
135 9 0.02
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (131 bp):
ATTCTGTAAGACCTTCGGACATGATTTCTAAGACCTCGAGCATAATCTTTAAGACTTCCAGGCAT
AATTTTGATTCACAGTGTTATCCCGATCGATTCTTTATTTTTCAACTTACGATGTTGTCCCGATC
G
Found at i:6454764 original size:22 final size:22
Alignment explanation
Indices: 6454739--6454781 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6454729 AGGTATGATT
* *
6454739 TTTAAGACCTCTGAGCATAATC
1 TTTAAGACCACCGAGCATAATC
6454761 TTTAAGACCACCGAGCATAAT
1 TTTAAGACCACCGAGCATAAT
6454782 TTCTATTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTAAGACCACCGAGCATAATC
Found at i:6455245 original size:264 final size:262
Alignment explanation
Indices: 6454398--6455278 Score: 814
Period size: 264 Copynumber: 3.3 Consensus size: 262
6454388 TTTGACTTAC
* * * * ** * **
6454398 GGTGTT-TCTCAATTGATTTTTTATTTTTTGATTTACGGTGTTGTCTCGGTTAATTCTGTAAGAC
1 GGTGTTATCCCAATTGATTCTTTATTTTTAGACTTGTGGTGTTGTCTCGATCGATTCTGTAAGAC
* * * * * * * ** * *
6454462 CTTCATGCATGATTTCTAAGATCTTC-GGGTATAATTTTTAAGACCTTCGGGTATAATTTTGATT
66 CTTCAGGCATGATTTTTAAGA-CCTCAGAGCATAATCTTTAAGAACACCGAGCATAATTTTGATT
* * * * *
6454526 CACAGTGTTGTCCCAATCGATTCTTTATTTTTCAACTTACGATATTGTCCCAGTCGATTCTGTAA
130 CACAGTGTTATCCCGATCGATTTTTTATTTTTCAACTTACGATGTTGTCCGA-TCGATTCTGTAA
*
6454591 GACCTTCGGACATGATTTCTAAGACCTTCGA-GCATAATCTTTAAGA-CTTCCAGGCATAATTTT
194 GACCTTCGGACATGATTTCTAAGACC-TCAAGGCATAATCTTTAAGACCTT-CAGGCATAATTTT
*
6454654 GATTCGC
257 GATTC-A
* * * ** *
6454661 GGTATTAT-CCAATCGATTCTTTATTTTGAGACTTGCAGTGTTGTCTCGATCGATTTTGTAAGAC
1 GGTGTTATCCCAATTGATTCTTTATTTTTAGACTTGTGGTGTTGTCTCGATCGATTCTGTAAGAC
* * * *
6454725 TTTCAGGTATGATTTTTAAGACCTCTGAGCATAATCTTTAAGACCACCGAGCATAATTTCT-ATT
66 CTTCAGGCATGATTTTTAAGACCTCAGAGCATAATCTTTAAGAACACCGAGCATAATTT-TGATT
* * * *
6454789 CGC-GATGTTATCCCGATCAATTTTTTTTATTTTTTAACTTACGATGTTATCCCTG-TCGATTCT
130 CACAG-TGTTATCCCGATCGA--TTTTTTATTTTTCAACTTACGATGTTGT-CC-GATCGATTCT
* ** *
6454852 GTAAGACCTTCGGACATGATTTCTAAGATCTCTGGGCATAATCTTTAAGACCTCCAGGCATAATT
190 GTAAGACCTTCGGACATGATTTCTAAGACCTCAAGGCATAATCTTTAAGACCTTCAGGCATAATT
6454917 TTGATTCGA
255 TTGATTC-A
* * * * * *
6454926 GGTGTTGTCCCCATTGATTTTTTATTTTTCA-ACTTGTGGTGTTATCTCGATCGATTCTATAAAA
1 GGTGTTATCCCAATTGATTCTTTATTTTT-AGACTTGTGGTGTTGTCTCGATCGATTCTGTAAGA
* **** *
6454990 CCTTC-GGACATAATTTTTAAGACCTCCAGA-CATAATCTTTAAGAATTTTGGGCATAATTTTGA
65 CCTTCAGG-CATGATTTTTAAGACCT-CAGAGCATAATCTTTAAGAACACCGAGCATAATTTTGA
* * ** * *
6455053 TTCACAGTGTTATCCCGATTGATTTTTTATTTTTCGACTTGTGGTGTTGTCTCGATCGATTCTAT
128 TTCACAGTGTTATCCCGATCGATTTTTTATTTTTCAACTTACGATGTTGTC-CGATCGATTCTGT
* * * * * *
6455118 AACACCTCCGGACATGATTTCTAAAACCTCAAGGCATAAACTTTAAGACCTTTAGGCATAATTTC
192 AAGACCTTCGGACATGATTTCTAAGACCTCAAGGCATAATCTTTAAGACCTTCAGGCATAATTTT
6455183 GATTCA
257 GATTCA
* ** * * * * *
6455189 TGATGTTATCCCGTTTGATTCTTTATTTTTTGACTTATGGTATTGTCCCAATCGATTCTGTAAGA
1 -GGTGTTATCCCAATTGATTCTTTATTTTTAGACTTGTGGTGTTGTCTCGATCGATTCTGTAAGA
*
6455254 CC-TCTGGGCATGATTTTTAAGACCT
65 CCTTC-AGGCATGATTTTTAAGACCT
6455279 TTAAACATAA
Statistics
Matches: 501, Mismatches: 95, Indels: 43
0.78 0.15 0.07
Matches are distributed among these distances:
262 4 0.01
263 114 0.23
264 164 0.33
265 106 0.21
266 108 0.22
267 5 0.01
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (262 bp):
GGTGTTATCCCAATTGATTCTTTATTTTTAGACTTGTGGTGTTGTCTCGATCGATTCTGTAAGAC
CTTCAGGCATGATTTTTAAGACCTCAGAGCATAATCTTTAAGAACACCGAGCATAATTTTGATTC
ACAGTGTTATCCCGATCGATTTTTTATTTTTCAACTTACGATGTTGTCCGATCGATTCTGTAAGA
CCTTCGGACATGATTTCTAAGACCTCAAGGCATAATCTTTAAGACCTTCAGGCATAATTTTGATT
CA
Found at i:6455394 original size:36 final size:37
Alignment explanation
Indices: 6455311--6455394 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
6455301 ATATTATTCT
* *
6455311 GATCGATTCTTTATTTCTTAATTTGTGGTGTTATCCTA
1 GATC-ATTCTTTATTTCTTAACTTGTGGTGTTATCCCA
* *
6455349 GTTGA-TCTTTATTT-TTAAACTTGTGGTGTTATCCCA
1 GATCATTCTTTATTTCTT-AACTTGTGGTGTTATCCCA
6455385 -ATCATTCTTT
1 GATCATTCTTT
6455395 GACTTGTGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
35 4 0.11
36 31 0.82
37 1 0.03
38 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (37 bp):
GATCATTCTTTATTTCTTAACTTGTGGTGTTATCCCA
Found at i:6460372 original size:11 final size:11
Alignment explanation
Indices: 6460335--6460377 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
6460325 TAGTGTTATT
6460335 ATAAACAAATA
1 ATAAACAAATA
** * *
6460346 GCAAATAAACA
1 ATAAACAAATA
6460357 ATAAACAAATA
1 ATAAACAAATA
6460368 ATAAACAAAT
1 ATAAACAAAT
6460378 CAGTTTTAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (11 bp):
ATAAACAAATA
Found at i:6464968 original size:37 final size:37
Alignment explanation
Indices: 6464922--6464997 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
6464912 ACAAGATTTA
* *
6464922 TCACATGCTCTATTAATGAACGACTGCTTTCTTAAAG
1 TCACATGCTCTATTAATGAAAGACTACTTTCTTAAAG
*
6464959 TCACGTGCTCTATTAATGAAAGACTACTTTCTTAAAG
1 TCACATGCTCTATTAATGAAAGACTACTTTCTTAAAG
6464996 TC
1 TC
6464998 CGTTGACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (37 bp):
TCACATGCTCTATTAATGAAAGACTACTTTCTTAAAG
Found at i:6465628 original size:25 final size:25
Alignment explanation
Indices: 6465600--6465647 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
6465590 TTTATTATTT
* *
6465600 TTTTTAATTGTAATTATAATAATAA
1 TTTTTAATTATAATTACAATAATAA
6465625 TTTTTAATTATAATTACAATAAT
1 TTTTTAATTATAATTACAATAAT
6465648 TTTTATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTTAATTATAATTACAATAATAA
Found at i:6467566 original size:15 final size:14
Alignment explanation
Indices: 6467532--6467571 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
6467522 AATAAAAATA
6467532 AATAATTTAA-TTT
1 AATAATTTAATTTT
6467545 AATTAATTTAATTTT
1 AA-TAATTTAATTTT
6467560 AGATAATTTAAT
1 A-ATAATTTAAT
6467572 ACGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 8 0.33
15 13 0.54
16 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AATAATTTAATTTT
Found at i:6470587 original size:132 final size:132
Alignment explanation
Indices: 6470416--6470667 Score: 398
Period size: 132 Copynumber: 1.9 Consensus size: 132
6470406 AGAGATCGTG
* * **
6470416 AAGTATTTCAAGATATTTGAATAAGGTATGTTTACTATGCTTATGCCCAAGTTTAAGATTTCATT
1 AAGTATTTCAAGATATCTGAAGAACATATGTTTACTATGCTTATGCCCAAGTTTAAGATTTCATT
* *
6470481 ATTTGATGGAAAGAGTAATTTTACGTTATGGTAAAGT-ATGATTCAAGATTTATTAAGATCATGA
66 ATTTGATGGAAAGAGTAATTTTACGTTATGGCAAAGTAAT-ATTCAAGATCTATTAAGATCATGA
6470545 AGC
130 AGC
* * *
6470548 AAGTATTTCAAGATGTCTGAAGAACATATGTTTAGTATGCTTATGCCCAAGTTTGAGATTTCATT
1 AAGTATTTCAAGATATCTGAAGAACATATGTTTACTATGCTTATGCCCAAGTTTAAGATTTCATT
*
6470613 ATTTGATGGAAAGAGTAATTTTATGTTATGGCAAAGTAATATTCAAGATCTATTA
66 ATTTGATGGAAAGAGTAATTTTACGTTATGGCAAAGTAATATTCAAGATCTATTA
6470668 GTACAATAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
132 107 0.98
133 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (132 bp):
AAGTATTTCAAGATATCTGAAGAACATATGTTTACTATGCTTATGCCCAAGTTTAAGATTTCATT
ATTTGATGGAAAGAGTAATTTTACGTTATGGCAAAGTAATATTCAAGATCTATTAAGATCATGAA
GC
Found at i:6479813 original size:20 final size:21
Alignment explanation
Indices: 6479766--6479814 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6479756 AAGAATTTGA
6479766 AATTAATAAATTAAAATTAACT
1 AATTAA-AAATTAAAATTAACT
6479788 AA-TAAAAATTAAAACTT-A-T
1 AATTAAAAATTAAAA-TTAACT
6479807 AATTAAAA
1 AATTAAAA
6479815 TATTTAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 5 0.20
22 2 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAAAAATTAAAATTAACT
Found at i:6486096 original size:16 final size:16
Alignment explanation
Indices: 6486072--6486106 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6486062 ATACATGCTC
*
6486072 ATACCAATTATTAAGG
1 ATACCAATTATTAAAG
*
6486088 ATACTAATTATTAAAG
1 ATACCAATTATTAAAG
6486104 ATA
1 ATA
6486107 TGTTATCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (16 bp):
ATACCAATTATTAAAG
Found at i:6487919 original size:21 final size:21
Alignment explanation
Indices: 6487895--6487956 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
6487885 ACAAAAAATC
*
6487895 TAAAATATTTCACAAAATTAA
1 TAAAATATTTCACAAAATAAA
* *
6487916 TAAAACATTTAAGCAAAA-AAA
1 TAAAATATTTCA-CAAAATAAA
*
6487937 TAAGTATATTTCACAAAATA
1 TAA-AATATTTCACAAAATA
6487957 TCTTTCACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (21 bp):
TAAAATATTTCACAAAATAAA
Found at i:6493918 original size:7 final size:7
Alignment explanation
Indices: 6493903--6493936 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
6493893 CATTTTGTAT
*
6493903 TGTTGTA
1 TGTTTTA
6493910 TGTTTTA
1 TGTTTTA
6493917 TGTTTTA
1 TGTTTTA
*
6493924 TATTTTA
1 TGTTTTA
6493931 TGTTTT
1 TGTTTT
6493937 TGAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (7 bp):
TGTTTTA
Found at i:6493951 original size:14 final size:15
Alignment explanation
Indices: 6493912--6493952 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
6493902 TTGTTGTATG
*
6493912 TTTTATGTTTT-ATA
1 TTTTATGTTTTGAAA
6493926 TTTTATGTTTTTGAAA
1 TTTTATG-TTTTGAAA
6493942 TTTT-TGTTTTG
1 TTTTATGTTTTG
6493953 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
16 6 0.25
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (15 bp):
TTTTATGTTTTGAAA
Done.