Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 136 of 143
Found at i:40398314 original size:47 final size:46
Alignment explanation
Indices: 40398254--40398354 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 46
40398244 AACATCCAAA
* * * *
40398254 CAACTAAAATAACAACCAAAACAGCAGTAAAAATAATAGAAAAATAG
1 CAACAAAAATAACAACAAAAACAGCA-CAAAAATAATAAAAAAATAG
* * *
40398301 CAACAAAAATAACAATAAAAACAGCACCAAAATAGTAAAAAAATAG
1 CAACAAAAATAACAACAAAAACAGCACAAAAATAATAAAAAAATAG
*
40398347 CACCAAAA
1 CAACAAAA
40398355 CAGAAACCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
46 23 0.50
47 23 0.50
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.11
Consensus pattern (46 bp):
CAACAAAAATAACAACAAAAACAGCACAAAAATAATAAAAAAATAG
Found at i:40398333 original size:23 final size:22
Alignment explanation
Indices: 40398259--40398354 Score: 66
Period size: 23 Copynumber: 4.2 Consensus size: 22
40398249 CCAAACAACT
* **
40398259 AAAATAACAACCAAAACAGCAGTA
1 AAAATAACAA-AAAAACAGCA-CC
* * * *
40398283 AAAATAATAGAAAAATAGCAACA
1 AAAATAACAAAAAAACAGC-ACC
40398306 AAAATAACAATAAAAACAGCACC
1 AAAATAACAA-AAAAACAGCACC
** *
40398329 AAAATAGTAAAAAAATAGCACC
1 AAAATAACAAAAAAACAGCACC
40398351 AAAA
1 AAAA
40398355 CAGAAACCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
22 15 0.26
23 26 0.45
24 17 0.29
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAATAACAAAAAAACAGCACC
Found at i:40398409 original size:22 final size:20
Alignment explanation
Indices: 40398351--40398431 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 20
40398341 AAATAGCACC
*
40398351 AAAACAGAAACCAAAATAGTA
1 AAAACA-AAACCAAAACAGTA
*
40398372 AAAA-AAAAACAAAACAGTA
1 AAAACAAAACCAAAACAGTA
*
40398391 AAAACACAACACCAAAACAGCA
1 AAAACA-AA-ACCAAAACAGTA
*
40398413 AAAAAATAATACCAAAACA
1 AAAACA-AA-ACCAAAACA
40398432 ACAATATAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.32
20 2 0.04
21 6 0.12
22 26 0.52
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (20 bp):
AAAACAAAACCAAAACAGTA
Found at i:40400150 original size:15 final size:14
Alignment explanation
Indices: 40400127--40400172 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
40400117 TAAATATCTC
40400127 AAAAA-AATTATAA
1 AAAAATAATTATAA
40400140 ATAAAATAATTAATAA
1 A-AAAATAATT-ATAA
*
40400156 AAAAATAAATATAA
1 AAAAATAATTATAA
40400170 AAA
1 AAA
40400173 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 12 0.41
16 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATAATTATAA
Found at i:40400166 original size:12 final size:12
Alignment explanation
Indices: 40400136--40400175 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40400126 CAAAAAAATT
*
40400136 ATAAATAAAATA
1 ATAAATAAAAAA
*
40400148 ATTAATAAAAAA
1 ATAAATAAAAAA
*
40400160 ATAAATATAAAA
1 ATAAATAAAAAA
40400172 ATAA
1 ATAA
40400176 TTTAAATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAAATAAAAAA
Found at i:40400174 original size:20 final size:20
Alignment explanation
Indices: 40400138--40400175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40400128 AAAAAATTAT
*
40400138 AAATAAAATAATTAATAAAA
1 AAATAAAATAATAAATAAAA
40400158 AAATAAATATAA-AAATAA
1 AAATAAA-ATAATAAATAA
40400176 TTTAAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAATAATAAATAAAA
Found at i:40401508 original size:18 final size:18
Alignment explanation
Indices: 40401467--40401510 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
40401457 GTATATTTGA
*
40401467 ATATTGGCTTCTCAATAT
1 ATATTTGCTTCTCAATAT
40401485 ATTATTTGCTT-TCAAATAT
1 A-TATTTGCTTCTC-AATAT
40401504 ATATTTG
1 ATATTTG
40401511 AAATTCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (18 bp):
ATATTTGCTTCTCAATAT
Found at i:40403605 original size:24 final size:24
Alignment explanation
Indices: 40403565--40403614 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40403555 TTTTCATGTT
40403565 TTTCATGAATATATTATATATATC
1 TTTCATGAATATATTATATATATC
* *
40403589 TTTCATG-ATGATTTTATATATCTC
1 TTTCATGAAT-ATATTATATATATC
40403613 TT
1 TT
40403615 GCCATGCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTCATGAATATATTATATATATC
Found at i:40407957 original size:3 final size:3
Alignment explanation
Indices: 40407949--40407999 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
40407939 TGGTTGTAGT
40407949 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40407997 TTA
1 TTA
40408000 AGAATAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40410744 original size:31 final size:31
Alignment explanation
Indices: 40410706--40410769 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
40410696 GAAAATCTTA
**
40410706 AAATTCAGGCTTTAATATGTG-AACAATTGCT
1 AAATTCAGGCTCCAATATG-GAAACAATTGCT
*
40410737 AAATTCAGGCTCCAATATGGAAACGATTGCT
1 AAATTCAGGCTCCAATATGGAAACAATTGCT
40410768 AA
1 AA
40410770 GTTTAAAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (31 bp):
AAATTCAGGCTCCAATATGGAAACAATTGCT
Found at i:40411931 original size:17 final size:17
Alignment explanation
Indices: 40411906--40411955 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
40411896 TTTTTTAAAA
40411906 ATTATAAATATATAAATT
1 ATTA-AAATATATAAATT
40411924 ATTAAAATA-ATAAAATT
1 ATTAAAATATAT-AAATT
40411941 ATATAAAATATATAA
1 AT-TAAAATATATAA
40411956 TTTAATTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
18 13 0.45
19 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAATATATAAATT
Found at i:40411954 original size:9 final size:9
Alignment explanation
Indices: 40411903--40411955 Score: 60
Period size: 8 Copynumber: 6.2 Consensus size: 9
40411893 TAGTTTTTTA
40411903 AAAAT-TAT
1 AAAATATAT
40411911 -AAATATAT
1 AAAATATAT
*
40411919 AAATTAT-T
1 AAAATATAT
40411927 AAAATA-AT
1 AAAATATAT
40411935 AAAATTATAT
1 AAAA-TATAT
40411945 AAAATATAT
1 AAAATATAT
40411954 AA
1 AA
40411956 TTTAATTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 4 0.11
8 14 0.37
9 14 0.37
10 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATAT
Found at i:40411957 original size:17 final size:16
Alignment explanation
Indices: 40411906--40411957 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
40411896 TTTTTTAAAA
40411906 ATTATAAATATATAAATT
1 ATTA-AAATATAT-AATT
*
40411924 ATTAAAATAATAAAATT
1 ATTAAAAT-ATATAATT
40411941 ATATAAAATATATAATT
1 AT-TAAAATATATAATT
40411958 TAATTTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAAATATATAATT
Found at i:40415632 original size:19 final size:19
Alignment explanation
Indices: 40415604--40415645 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40415594 TAAATATTAA
40415604 ATTT-ATATATGAA-TTTTG
1 ATTTGATATAT-AAGTTTTG
*
40415622 GTTTGATATATAAGTTTTG
1 ATTTGATATATAAGTTTTG
40415641 ATTTG
1 ATTTG
40415646 GTGTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (19 bp):
ATTTGATATATAAGTTTTG
Found at i:40440312 original size:4 final size:4
Alignment explanation
Indices: 40440303--40440332 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
40440293 CAAATAATCC
*
40440303 ACAT ACAT ACAT ACAT GCAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
40440333 GAAGCTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:40441321 original size:24 final size:24
Alignment explanation
Indices: 40441301--40441346 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40441291 TACTTTTTTT
*
40441301 AAAA-ATTTATTTTAATTTTTTGG
1 AAAATATTTATTTTAAATTTTTGG
40441324 AAAATATTTATTTTAATATTTTT
1 AAAATATTTATTTTAA-ATTTTT
40441347 AGTGTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AAAATATTTATTTTAAATTTTTGG
Found at i:40446342 original size:18 final size:19
Alignment explanation
Indices: 40446319--40446356 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40446309 TATAAGACTT
40446319 AAAAGAATA-AAAA-AAAGA
1 AAAAGAA-ACAAAAGAAAGA
40446337 AAAAGAAACAAAAGAAAGA
1 AAAAGAAACAAAAGAAAGA
40446356 A
1 A
40446357 TAGAAGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 11 0.61
19 6 0.33
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAGAAACAAAAGAAAGA
Found at i:40447143 original size:18 final size:18
Alignment explanation
Indices: 40447120--40447156 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40447110 TTTGTGATCA
40447120 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
40447138 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
40447156 A
1 A
40447157 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:40447360 original size:37 final size:38
Alignment explanation
Indices: 40447260--40447362 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
40447250 GACCTTGAGT
* *
40447260 CGATGAGACACTGGGTGTCATTATTTTACTTCGAATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGAATAGATC
** * ** **
40447301 CGATGAGGTACTGAGTACCACTTTACTTCGGCTAGA-C
1 CGATGAGACACTGGGTGTCACTTTACTTCGAATAGATC
40447338 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
40447363 TTGCTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 14 0.29
41 14 0.29
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGAATAGATC
Found at i:40451142 original size:11 final size:11
Alignment explanation
Indices: 40451126--40451161 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
40451116 CAACTTTTCC
40451126 ATTATATGTCT
1 ATTATATGTCT
40451137 ATTATATGTCT
1 ATTATATGTCT
40451148 ATTATATGTCT
1 ATTATATGTCT
40451159 ATT
1 ATT
40451162 GGGAAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTATATGTCT
Found at i:40453023 original size:21 final size:19
Alignment explanation
Indices: 40452985--40453023 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
40452975 TTGATACAAT
*
40452985 TTATAAAATTATATTTTAG
1 TTATAAAATTATAATTTAG
40453004 TTATCAAAATTTATAATTTA
1 TTAT-AAAA-TTATAATTTA
40453024 AATGGTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TTATAAAATTATAATTTAG
Found at i:40453967 original size:18 final size:20
Alignment explanation
Indices: 40453931--40453968 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40453921 TCAAAATAAT
40453931 AAATTATATATTATCATTAAA
1 AAATTATATATTA-CATTAAA
40453952 AAATTA-ATATTA-ATTAA
1 AAATTATATATTACATTAA
40453969 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTATATATTACATTAAA
Found at i:40457104 original size:3 final size:3
Alignment explanation
Indices: 40457098--40457134 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
40457088 AACAACAGCT
* *
40457098 TGA TGA TGA TGA TGA TGA CGA CGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
40457135 CTAGAAGAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:40459436 original size:18 final size:20
Alignment explanation
Indices: 40459413--40459450 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
40459403 ATAGATTTTG
40459413 AATAAA-AATATTA-AAAAA
1 AATAAATAATATTATAAAAA
*
40459431 AATAAATAATTTTATAAAAA
1 AATAAATAATATTATAAAAA
40459451 TATTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAATAATATTATAAAAA
Found at i:40459484 original size:21 final size:20
Alignment explanation
Indices: 40459423--40459484 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
40459413 AATAAAAATA
* *
40459423 TTAAAAAAA-ATAAATAATT
1 TTAAAAAAATATTAATATTT
* *
40459442 TTATAAAAATATTTAT-TATT
1 TTAAAAAAATATTAATAT-TT
40459462 TTAAAAAAATTATTAATATTT
1 TTAAAAAAA-TATTAATATTT
40459483 TT
1 TT
40459485 TAGTGAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 8 0.24
20 14 0.42
21 10 0.30
22 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAAAATATTAATATTT
Found at i:40464386 original size:2 final size:2
Alignment explanation
Indices: 40464379--40464414 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40464369 TTGTATCGAC
40464379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40464415 GAAATAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40480080 original size:27 final size:27
Alignment explanation
Indices: 40480042--40480098 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
40480032 ATTCGATATC
40480042 AATATTTATTTATTAATGAGTTTATAA
1 AATATTTATTTATTAATGAGTTTATAA
40480069 AATATTTATTTATTAATGAGTTTATAA
1 AATATTTATTTATTAATGAGTTTATAA
40480096 AAT
1 AAT
40480099 GTAAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (27 bp):
AATATTTATTTATTAATGAGTTTATAA
Found at i:40482547 original size:14 final size:15
Alignment explanation
Indices: 40482528--40482561 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40482518 TCATTTCATG
40482528 TATTTAATTAT-TTT
1 TATTTAATTATATTT
*
40482542 TATTTAATTTTATTT
1 TATTTAATTATATTT
40482557 TATTT
1 TATTT
40482562 TAAAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTAATTATATTT
Found at i:40493480 original size:13 final size:13
Alignment explanation
Indices: 40493453--40493497 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
40493443 GGATTAAATT
* *
40493453 ATATGAAATTAAA
1 ATATTAAATTTAA
40493466 ATATTAAGA-TTAA
1 ATATTAA-ATTTAA
40493479 ATATTAAATTTAA
1 ATATTAAATTTAA
40493492 ATATTA
1 ATATTA
40493498 TACGGGGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATTAAATTTAA
Found at i:40500031 original size:23 final size:24
Alignment explanation
Indices: 40499975--40500031 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 24
40499965 CTCCTTTATC
40499975 TTAATTACTTTATAAATGGGGTTTTAA
1 TTAATTACTTTATAAA---GGTTTTAA
*
40500002 TCTAATTACTTTATAAA-GTTTTTA
1 T-TAATTACTTTATAAAGGTTTTAA
40500026 TTAATT
1 TTAATT
40500032 GGTCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 5 0.18
24 7 0.25
27 1 0.04
28 15 0.54
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTACTTTATAAAGGTTTTAA
Found at i:40502349 original size:24 final size:23
Alignment explanation
Indices: 40502314--40502358 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
40502304 GAGGGAGGAG
*
40502314 AAGAAAAAACAGAAAGGGAAATA
1 AAGAAAAAACAGAAAGAGAAATA
40502337 AAGAAAAAGACAGAAAGAGAAA
1 AAGAAAAA-ACAGAAAGAGAAA
40502359 GATTAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.02
Consensus pattern (23 bp):
AAGAAAAAACAGAAAGAGAAATA
Found at i:40505760 original size:6 final size:6
Alignment explanation
Indices: 40505749--40505773 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40505739 GCTATCTTGA
40505749 GTATAT GTATAT GTATAT GTATAT G
1 GTATAT GTATAT GTATAT GTATAT G
40505774 CGTATGTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:40510034 original size:21 final size:18
Alignment explanation
Indices: 40509991--40510113 Score: 75
Period size: 20 Copynumber: 6.1 Consensus size: 18
40509981 AAAAACCCAA
*
40509991 ATTAAATATTATAAATAATT
1 ATTAAA-ATTGTAAA-AATT
*
40510011 ATTAGATATTGTTAAAAATAT
1 ATTA-AAATTG-TAAAAAT-T
40510032 ATTAAAATTGTAAAAAGTT
1 ATTAAAATTGTAAAAA-TT
**
40510051 ATTAAAAATAATAAAACATT
1 ATT-AAAATTGTAAAA-ATT
*
40510071 ATTTAAAATTTTAAAAAATAT
1 A-TTAAAATTGT-AAAAAT-T
40510092 ATTAAAATAGTGTAAATAATT
1 ATTAAAAT--TGTAAA-AATT
40510113 A
1 A
40510114 ACAAATCAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
19 10 0.12
20 44 0.53
21 24 0.29
22 5 0.06
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (18 bp):
ATTAAAATTGTAAAAATT
Found at i:40510047 original size:20 final size:19
Alignment explanation
Indices: 40509991--40510099 Score: 83
Period size: 20 Copynumber: 5.4 Consensus size: 19
40509981 AAAAACCCAA
*
40509991 ATTAAATATTATAAATAATT
1 ATTAAA-ATTATAAAAAATT
* * *
40510011 ATTAGATATTGTTAAAAATAT
1 ATTA-AAATTATAAAAAAT-T
* *
40510032 ATTAAAATTGTAAAAAGTT
1 ATTAAAATTATAAAAAATT
* *
40510051 ATTAAAAATAATAAAACATT
1 ATT-AAAATTATAAAAAATT
*
40510071 ATTTAAAATTTTAAAAAATAT
1 A-TTAAAATTATAAAAAAT-T
40510092 ATTAAAAT
1 ATTAAAAT
40510100 AGTGTAAATA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 4 0.06
20 56 0.80
21 10 0.14
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (19 bp):
ATTAAAATTATAAAAAATT
Found at i:40510058 original size:30 final size:29
Alignment explanation
Indices: 40510022--40510099 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
40510012 TTAGATATTG
40510022 TTAAAAATATATTAAAATT-GTAAAAAGTT
1 TTAAAAATATATTAAAATTAGTAAAAA-TT
* * *
40510051 ATTAAAAATA-ATAAAACATTATTTAAAATT
1 -TTAAAAATATATTAAA-ATTAGTAAAAATT
40510081 TTAAAAAATATATTAAAAT
1 TT-AAAAATATATTAAAAT
40510100 AGTGTAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 7 0.17
30 23 0.57
31 10 0.25
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAAAATATATTAAAATTAGTAAAAATT
Found at i:40510287 original size:11 final size:11
Alignment explanation
Indices: 40510259--40510292 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40510249 ATATGATTCG
40510259 ATTAAAAAATT
1 ATTAAAAAATT
40510270 A-TAAAAAATT
1 ATTAAAAAATT
*
40510280 ATTTAAAAATT
1 ATTAAAAAATT
40510291 AT
1 AT
40510293 GAAATTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:40510343 original size:9 final size:9
Alignment explanation
Indices: 40510331--40510357 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40510321 CAATTTTCAA
40510331 ATAATTTTT
1 ATAATTTTT
40510340 ATAATTTTT
1 ATAATTTTT
40510349 ATAATTTTT
1 ATAATTTTT
40510358 TTTGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:40510431 original size:20 final size:18
Alignment explanation
Indices: 40510408--40510519 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 18
40510398 GTTTTATAGT
40510408 TTTTAATAAGTTTTTTACAA
1 TTTTAAT-A-TTTTTTACAA
*
40510428 TTTTAAAATATTTTTAACAA
1 TTTT--AATATTTTTTACAA
* *
40510448 TATTTAATCATTATTTATAA
1 T-TTTAAT-ATTTTTTACAA
*
40510468 TATTTAAT-TTTCTTACAA
1 T-TTTAATATTTTTTACAA
40510486 TTTTAAGTATTTTTTACAA
1 TTTTAA-TATTTTTTACAA
40510505 TTATTATATATTTTT
1 TT-TTA-ATATTTTT
40510520 AATATGCAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.07
18 9 0.12
19 14 0.18
20 40 0.53
21 5 0.07
22 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTAATATTTTTTACAA
Found at i:40515395 original size:14 final size:14
Alignment explanation
Indices: 40515372--40515406 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40515362 GGATTCAATG
*
40515372 TGTATATGTGTGTA
1 TGTATGTGTGTGTA
*
40515386 TGTATGTGTGTGTG
1 TGTATGTGTGTGTA
40515400 TGTATGT
1 TGTATGT
40515407 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.51
Consensus pattern (14 bp):
TGTATGTGTGTGTA
Found at i:40520327 original size:21 final size:21
Alignment explanation
Indices: 40520303--40520348 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40520293 AAAAATATTT
* *
40520303 AAAATTCAAAAAATTATATAA
1 AAAATTCAAAAAATTAAAGAA
*
40520324 AAAATTCATAAAATTAAAGAA
1 AAAATTCAAAAAATTAAAGAA
40520345 AAAA
1 AAAA
40520349 CATGAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATTCAAAAAATTAAAGAA
Found at i:40527087 original size:69 final size:69
Alignment explanation
Indices: 40527011--40527291 Score: 311
Period size: 69 Copynumber: 4.1 Consensus size: 69
40527001 CTCTCGGAGG
* * * * *
40527011 GATGTTAGACTCCTAAGA-AGAGATATATCTCCAGAAAATTTATTGAAAGAGAGATCTAAATACT
1 GATGTTAGATTCTTAA-ACAGAGATATATTTTCAGAAAATTTATTGGAAGAGAGATCTAAATACT
*
40527075 CAAGT
65 CGAGT
*
40527080 GATGTTAGATTCTTAAACACG-GATATATTTTCGGAAAATTTATTGGAAGAGAGATCTAAATACT
1 GATGTTAGATTCTTAAACA-GAGATATATTTTCAGAAAATTTATTGGAAGAGAGATCTAAATACT
40527144 CGAGT
65 CGAGT
* * * * * * *
40527149 GAGGTTAAATTCTTAAACACAGATATATTTTCAAAAAAGTTATTGGAAGAGATATCTAAATGCTC
1 GATGTTAGATTCTTAAACAGAGATATATTTTCAGAAAATTTATTGGAAGAGAGATCTAAATACTC
40527214 GAGT
66 GAGT
** * *
40527218 GACATTAGATTTTTAAACACG-GATATACTTTCA-AAAATATTATTGGAAGAGAGATCTAAA-AC
1 GATGTTAGATTCTTAAACA-GAGATATATTTTCAGAAAAT-TTATTGGAAGAGAGATCTAAATA-
*
40527280 CTCGAGA
63 CTCGAGT
40527287 GATGT
1 GATGT
40527292 GAGTTCAGAG
Statistics
Matches: 179, Mismatches: 27, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
68 5 0.03
69 173 0.97
70 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (69 bp):
GATGTTAGATTCTTAAACAGAGATATATTTTCAGAAAATTTATTGGAAGAGAGATCTAAATACTC
GAGT
Found at i:40527235 original size:138 final size:138
Alignment explanation
Indices: 40527031--40527285 Score: 361
Period size: 138 Copynumber: 1.8 Consensus size: 138
40527021 TCCTAAGAAG
* * **
40527031 AGATATATCTCCAGAAAATTTATTGAAAGAGAGATCTAAATACTCAAGTGATGTTAGATTCTTAA
1 AGATATATCTCCAAAAAAGTTATTGAAAGAGAGATCTAAATACTCAAGTGACATTAGATTCTTAA
* *
40527096 ACACGGATATATTTTCGGAAAAT-TTATTGGAAGAGAGATCTAAATA-CTCGAGTGAGGTTAAAT
66 ACACGGATATACTTTC-AAAAATATTATTGGAAGAGAGATCTAAA-ACCTCGAGTGAGGTTAAAT
40527159 TCTTAAACAC
129 TCTTAAACAC
* * * * * * *
40527169 AGATATATTTTCAAAAAAGTTATTGGAAGAGATATCTAAATGCTCGAGTGACATTAGATTTTTAA
1 AGATATATCTCCAAAAAAGTTATTGAAAGAGAGATCTAAATACTCAAGTGACATTAGATTCTTAA
40527234 ACACGGATATACTTTCAAAAATATTATTGGAAGAGAGATCTAAAACCTCGAG
66 ACACGGATATACTTTCAAAAATATTATTGGAAGAGAGATCTAAAACCTCGAG
40527286 AGATGTGAGT
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 6 0.06
138 96 0.94
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (138 bp):
AGATATATCTCCAAAAAAGTTATTGAAAGAGAGATCTAAATACTCAAGTGACATTAGATTCTTAA
ACACGGATATACTTTCAAAAATATTATTGGAAGAGAGATCTAAAACCTCGAGTGAGGTTAAATTC
TTAAACAC
Found at i:40528152 original size:39 final size:39
Alignment explanation
Indices: 40528109--40528188 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
40528099 TTCTTTATAT
* * *
40528109 TTCTAAAATAT-TTAAATTTTTATTGAATGTTTGAGAAAC
1 TTCTAAAAT-TCTAAAATTTTTATTGAATGCTTGAAAAAC
*
40528148 TTCTATAATTCTAAAATTTTTATTGAATGCTTGAAAAAC
1 TTCTAAAATTCTAAAATTTTTATTGAATGCTTGAAAAAC
40528187 TT
1 TT
40528189 TTATACATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (39 bp):
TTCTAAAATTCTAAAATTTTTATTGAATGCTTGAAAAAC
Found at i:40533601 original size:13 final size:14
Alignment explanation
Indices: 40533567--40533595 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40533557 TATCGTATTT
40533567 TTAGTTAA-TTTAA
1 TTAGTTAATTTTAA
40533580 TTAGTTAATTTTAA
1 TTAGTTAATTTTAA
40533594 TT
1 TT
40533596 TTTAATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTAGTTAATTTTAA
Found at i:40536885 original size:30 final size:29
Alignment explanation
Indices: 40536812--40536889 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
40536802 CTTAAAATTA
* *
40536812 TACATGAATTTTAGTTTATTGTGTAATTTTT
1 TACATGAATTTT-GATT-TTGTGTAATTTCT
*
40536843 TACATTAATTTTGATTTTGTGTAATTTCT
1 TACATGAATTTTGATTTTGTGTAATTTCT
40536872 TACATGAAATTTTGATTT
1 TACATG-AATTTTGATTT
40536890 AATCCAATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.40
30 14 0.33
31 11 0.26
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (29 bp):
TACATGAATTTTGATTTTGTGTAATTTCT
Found at i:40545260 original size:16 final size:18
Alignment explanation
Indices: 40545239--40545282 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
40545229 ACAAAAACAA
40545239 TTAATTTAATTAT-TTT-
1 TTAATTTAATTATATTTG
*
40545255 TTAATTTGATTATATTTG
1 TTAATTTAATTATATTTG
40545273 TTAA-TTAATT
1 TTAATTTAATT
40545283 TAATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TTAATTTAATTATATTTG
Found at i:40547857 original size:69 final size:69
Alignment explanation
Indices: 40547673--40547858 Score: 232
Period size: 69 Copynumber: 2.7 Consensus size: 69
40547663 TCTTGAAATG
* * *
40547673 AGATATATCTCCAAAAAAATTATTGGAAGAGAGATCTAAATATTCCAGTAACGTTAGATTCTTAA
1 AGATATATCTCCAAAAAAATTATTGGAAGAGAGATCTAAATACTCGAGTAACATTAGATTCTTAA
40547738 ACAC
66 ACAC
* ** * * *
40547742 ATATATA-CTTTTAAAAAAATTGTTGAAAGAGAGATCTAAATACTCGAGTGAA-ATTAGATTTTT
1 AGATATATC-TCCAAAAAAATTATTGGAAGAGAGATCTAAATACTCGAGT-AACATTAGATTCTT
40547805 AAACAC
64 AAACAC
* * *
40547811 AGATATATCTCCAGAAAAATTATTGGAAGAGATATCTAAATCCTCGAG
1 AGATATATCTCCAAAAAAATTATTGGAAGAGAGATCTAAATACTCGAG
40547859 GGATGTGAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
68 1 0.01
69 93 0.96
70 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (69 bp):
AGATATATCTCCAAAAAAATTATTGGAAGAGAGATCTAAATACTCGAGTAACATTAGATTCTTAA
ACAC
Found at i:40548324 original size:18 final size:18
Alignment explanation
Indices: 40548285--40548326 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
40548275 ATATCACATA
*
40548285 ATAAATAATTTAAAAATT
1 ATAAATAATTTAAAAATC
40548303 ATAAATAATTTTAAAAA-C
1 ATAAATAA-TTTAAAAATC
40548321 ATAAAT
1 ATAAAT
40548327 GAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATAATTTAAAAATC
Found at i:40560771 original size:19 final size:19
Alignment explanation
Indices: 40560722--40560771 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
40560712 CTATCTGTAC
* *
40560722 TAAAAATTTTCAGAATTGT
1 TAAAATTTTTCAGAATTAT
*
40560741 TAAAATTGTTCA-AATTTAT
1 TAAAATTTTTCAGAA-TTAT
40560760 TAAAATTTTTCA
1 TAAAATTTTTCA
40560772 CTTATACAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (19 bp):
TAAAATTTTTCAGAATTAT
Found at i:40561512 original size:27 final size:28
Alignment explanation
Indices: 40561479--40561540 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
40561469 TTTCATGTGC
40561479 ATAATTA-CACCAAATCAAAATTCATAT
1 ATAATTACCACCAAATCAAAATTCATAT
** * *
40561506 ATAATTACTCACTGAATCGAAATTCATGT
1 ATAATTAC-CACCAAATCAAAATTCATAT
40561535 ATAATT
1 ATAATT
40561541 TTGAGATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.24
29 22 0.76
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (28 bp):
ATAATTACCACCAAATCAAAATTCATAT
Found at i:40562094 original size:11 final size:12
Alignment explanation
Indices: 40562067--40562095 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40562057 TTCAGTTTTA
40562067 AAAATTATTCTT
1 AAAATTATTCTT
40562079 AAAATTATTC-T
1 AAAATTATTCTT
40562090 AAAATT
1 AAAATT
40562096 TACAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
AAAATTATTCTT
Found at i:40566526 original size:21 final size:22
Alignment explanation
Indices: 40566500--40566547 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
40566490 GAGGAGGAAC
40566500 ATAAAAAGAAAAGAGAAAAA-A
1 ATAAAAAGAAAAGAGAAAAATA
*
40566521 AT-AAAAGAAAAGGGAAAAATA
1 ATAAAAAGAAAAGAGAAAAATA
40566542 A-AAAAA
1 ATAAAAA
40566548 TGACATCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (22 bp):
ATAAAAAGAAAAGAGAAAAATA
Found at i:40569458 original size:16 final size:16
Alignment explanation
Indices: 40569421--40569459 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
40569411 TTTACTTTAT
40569421 ATAATTAATACAAAATA
1 ATAATT-ATACAAAATA
*
40569438 A-AATTATTCAAAATA
1 ATAATTATACAAAATA
40569453 ATAATTA
1 ATAATTA
40569460 ATTAACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 9 0.45
17 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTATACAAAATA
Found at i:40579303 original size:18 final size:18
Alignment explanation
Indices: 40579282--40579339 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
40579272 TTAAATAGTT
*
40579282 TTTTTAATTTTAATAAAA
1 TTTTTAATTTTTATAAAA
* *
40579300 TTTTCAATTTTTATACAA
1 TTTTTAATTTTTATAAAA
* *
40579318 TATTTTGATTTTTTTAAAA
1 T-TTTTAATTTTTATAAAA
40579337 TTT
1 TTT
40579340 ATATTTATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTAATTTTTATAAAA
Found at i:40579386 original size:9 final size:9
Alignment explanation
Indices: 40579361--40579422 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
40579351 TTAGAAAAAA
40579361 ATATTTTTT
1 ATATTTTTT
* *
40579370 AAACTTTTT
1 ATATTTTTT
40579379 ATATTTTTT
1 ATATTTTTT
*
40579388 GA-ATTATTT
1 -ATATTTTTT
* *
40579397 ATATATTAT
1 ATATTTTTT
40579406 ATATTTTTT
1 ATATTTTTT
*
40579415 ACATTTTT
1 ATATTTTT
40579423 AAACCATATA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
8 1 0.03
9 38 0.95
10 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
ATATTTTTT
Found at i:40580080 original size:38 final size:38
Alignment explanation
Indices: 40580029--40580102 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
40580019 TCGAAGATAC
40580029 TATATATTATCTTTCAGTATTTATAATTGAGAAAATAG
1 TATATATTATCTTTCAGTATTTATAATTGAGAAAATAG
40580067 TATATATTATCTTTCAGTATTTATAATTGAGAAAAT
1 TATATATTATCTTTCAGTATTTATAATTGAGAAAAT
40580103 CAAATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (38 bp):
TATATATTATCTTTCAGTATTTATAATTGAGAAAATAG
Found at i:40583935 original size:18 final size:18
Alignment explanation
Indices: 40583910--40583949 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
40583900 TTTGAATCGA
40583910 ATTTTTTTAAAAAATTTAC
1 ATTTTTTTAAAAAATTT-C
*
40583929 ATTTTTTTAAATAATTTC
1 ATTTTTTTAAAAAATTTC
40583947 ATT
1 ATT
40583950 ATAAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTTTAAAAAATTTC
Found at i:40591005 original size:15 final size:15
Alignment explanation
Indices: 40590973--40591013 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
40590963 TATTTTTTTG
*
40590973 TATTATTAA-ATT-A
1 TATTATTAACTTTAA
*
40590986 TATTATTACCTTTAA
1 TATTATTAACTTTAA
40591001 TATTATTAACTTT
1 TATTATTAACTTT
40591014 GAACTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 8 0.35
14 2 0.09
15 13 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTAACTTTAA
Found at i:40591242 original size:35 final size:34
Alignment explanation
Indices: 40591169--40591254 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
40591159 AATTTAGTTA
* *
40591169 TTTTTATATCATAAATA-CTTTTTTTCTATTTTCAC
1 TTTTTAT-T-ATAAATATCTTATTTTCCATTTTCAC
40591204 TTTTTATTATAAATATCTTATTTTCCATTTT-ATTC
1 TTTTTATTATAAATATCTTATTTTCCATTTTCA--C
*
40591239 TTTTTATTATGAATAT
1 TTTTTATTATAAATAT
40591255 TTTTCATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
33 8 0.18
34 14 0.31
35 23 0.51
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.62
Consensus pattern (34 bp):
TTTTTATTATAAATATCTTATTTTCCATTTTCAC
Found at i:40596619 original size:13 final size:13
Alignment explanation
Indices: 40596601--40596627 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40596591 TAAAATGTAA
40596601 TCATATAAAATAT
1 TCATATAAAATAT
40596614 TCATATAAAATAT
1 TCATATAAAATAT
40596627 T
1 T
40596628 TAGGGATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATATAAAATAT
Found at i:40601613 original size:15 final size:17
Alignment explanation
Indices: 40601588--40601620 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40601578 TAACATGTTT
40601588 TTTTAAATATTT-ATTA
1 TTTTAAATATTTAATTA
40601604 TTTT-AATATTTAATTA
1 TTTTAAATATTTAATTA
40601620 T
1 T
40601621 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAATATTTAATTA
Found at i:40604424 original size:25 final size:25
Alignment explanation
Indices: 40604396--40604448 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40604386 TATTATCTAT
**
40604396 TATTTAAATATTTTAGTTTGATATA
1 TATTTAAATATTGGAGTTTGATATA
***
40604421 TATTTTGGTATTGGAGTTTGATATA
1 TATTTAAATATTGGAGTTTGATATA
40604446 TAT
1 TAT
40604449 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (25 bp):
TATTTAAATATTGGAGTTTGATATA
Found at i:40607758 original size:20 final size:20
Alignment explanation
Indices: 40607735--40607777 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40607725 AAAATTAACG
*
40607735 AAATTTAGAAAA-AAAAAATC
1 AAATTAAGAAAAGAAAAAA-C
40607755 AAATTAAGAAAAGAAAAAAC
1 AAATTAAGAAAAGAAAAAAC
40607775 AAA
1 AAA
40607778 AAAATCCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (20 bp):
AAATTAAGAAAAGAAAAAAC
Found at i:40616290 original size:4 final size:4
Alignment explanation
Indices: 40616268--40616299 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
40616258 TTTCGAGCAA
40616268 AATC AA-C AATC AA-C AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AATC AATC AA
40616300 AATTTCACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.23
4 20 0.77
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (4 bp):
AATC
Found at i:40635102 original size:34 final size:32
Alignment explanation
Indices: 40635043--40635110 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
40635033 TTATTCATGA
*
40635043 TTTTTTTAATTATTTAATATCATTTTAGTAAT
1 TTTTTTTAATTATTTAATATAATTTTAGTAAT
*
40635075 TTTTTTTATATTA-TTAATACATAATTTTCGTAAT
1 TTTTTTTA-ATTATTTAAT--ATAATTTTAGTAAT
40635109 TT
1 TT
40635111 ATTTATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 13 0.42
33 4 0.13
34 14 0.45
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (32 bp):
TTTTTTTAATTATTTAATATAATTTTAGTAAT
Found at i:40646077 original size:19 final size:19
Alignment explanation
Indices: 40646053--40646092 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40646043 ATAATCGGAT
*
40646053 AATATTGAATCTTC-TATAA
1 AATATTAAAT-TTCTTATAA
40646072 AATATTAAATTTCTTATAA
1 AATATTAAATTTCTTATAA
40646091 AA
1 AA
40646093 CTATCTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATTAAATTTCTTATAA
Found at i:40647114 original size:13 final size:13
Alignment explanation
Indices: 40647096--40647142 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
40647086 CACGATATGA
40647096 GTAAAAAATTTAT
1 GTAAAAAATTTAT
*
40647109 GTAAAAAATATAT
1 GTAAAAAATTTAT
*
40647122 TTATAAATAATTTAT
1 GTA-AAA-AATTTAT
40647137 GTAAAA
1 GTAAAA
40647143 TACAAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 14 0.50
14 6 0.21
15 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
GTAAAAAATTTAT
Found at i:40653650 original size:20 final size:20
Alignment explanation
Indices: 40653625--40653666 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40653615 ATATTTGAAA
40653625 TGAAATGAAAAGCTTCATAC
1 TGAAATGAAAAGCTTCATAC
40653645 TGAAATGAAAAGCTTCATAC
1 TGAAATGAAAAGCTTCATAC
40653665 TG
1 TG
40653667 CTATTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (20 bp):
TGAAATGAAAAGCTTCATAC
Found at i:40663851 original size:28 final size:24
Alignment explanation
Indices: 40663817--40663881 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 24
40663807 TGATGTTTAA
40663817 TTTTTTTTAAATAGTCGAATTTGAT
1 TTTTTTTTAAATAGTCG-ATTTGAT
* *
40663842 TATTAATTTTTCAAAGAGTTGATTTGAT
1 T-TT--TTTTT-AAATAGTCGATTTGAT
40663870 TTTTTTTTAAAT
1 TTTTTTTTAAAT
40663882 GTTGTAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
24 3 0.09
25 6 0.18
26 2 0.06
27 2 0.06
28 13 0.39
29 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTTTTTTAAATAGTCGATTTGAT
Found at i:40663885 original size:23 final size:23
Alignment explanation
Indices: 40663800--40663885 Score: 57
Period size: 28 Copynumber: 3.4 Consensus size: 23
40663790 TTGTTTTAAG
* *
40663800 TTAAAT-TTGATGTTTAATTTTTT
1 TTAAATGTTGAT-TTGATTTTTTT
*
40663823 TTAAATAGTCGAATTTGATTATTAATTT
1 TTAAAT-GTTG-ATTTGATT-TT--TTT
*
40663851 TTCAAAGAGTTGATTTGATTTTTTT
1 TT-AAA-TGTTGATTTGATTTTTTT
40663876 TTAAATGTTG
1 TTAAATGTTG
40663886 TAGTATAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
23 10 0.20
24 3 0.06
25 11 0.22
26 4 0.08
27 2 0.04
28 13 0.27
29 6 0.12
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (23 bp):
TTAAATGTTGATTTGATTTTTTT
Found at i:40665299 original size:21 final size:23
Alignment explanation
Indices: 40665251--40665301 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
40665241 CATTTAAATT
40665251 ATAAAAATAATCTAAGTTTGATA
1 ATAAAAATAATCTAAGTTTGATA
*
40665274 ATAAAATTAATCTAAGTTT-A-A
1 ATAAAAATAATCTAAGTTTGATA
40665295 ATAAAAA
1 ATAAAAA
40665302 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 1 0.04
23 18 0.69
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (23 bp):
ATAAAAATAATCTAAGTTTGATA
Found at i:40665302 original size:23 final size:22
Alignment explanation
Indices: 40665243--40665302 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
40665233 TAAAGGTGCA
40665243 TTTAAATTATAAAAATAATCTAAG
1 TTTAAA-TA-AAAAATAATCTAAG
*
40665267 TTTGATAAT-AAAATTAATCTAAG
1 TTT-A-AATAAAAAATAATCTAAG
40665290 TTTAAATAAAAAA
1 TTTAAATAAAAAA
40665303 AAAAAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 3 0.10
22 5 0.16
23 16 0.52
24 3 0.10
25 2 0.06
26 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (22 bp):
TTTAAATAAAAAATAATCTAAG
Found at i:40669868 original size:15 final size:15
Alignment explanation
Indices: 40669829--40669858 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40669819 TTTGAACCAG
40669829 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
40669844 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
40669859 GAGAGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:40676583 original size:29 final size:28
Alignment explanation
Indices: 40676548--40676736 Score: 129
Period size: 29 Copynumber: 6.5 Consensus size: 28
40676538 GGGGGGGGAC
*
40676548 AAAATGGTAAATTTGATGAAATCGGGGTT
1 AAAATGGTAATTTTG-TGAAATCGGGGTT
40676577 AAAATGG-AATTTTG-GAAGATTCAGGGG-T
1 AAAATGGTAATTTTGTGAA-A-TC-GGGGTT
*
40676605 AAAATGGTAATTTTAGGTGAAATCGAGGTT
1 AAAATGGTAATTTT--GTGAAATCGGGGTT
* * * * * *
40676635 AAAATGG-GATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTGTGAA-ATCGGGGTT
40676663 AAAATGGTAATTTTAGGTGAAATCGGGGTT
1 AAAATGGTAATTTT--GTGAAATCGGGGTT
* *
40676693 AAAAATGG-AATTTTG-GAAAATTTGGGGGT
1 -AAAATGGTAATTTTGTG-AAA-TCGGGGTT
*
40676722 AAAATGATAATTTTG
1 AAAATGGTAATTTTG
40676737 GGTGAAATTA
Statistics
Matches: 126, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
26 3 0.02
27 6 0.05
28 38 0.30
29 41 0.33
30 22 0.17
31 13 0.10
32 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGTGAAATCGGGGTT
Found at i:40676635 original size:58 final size:58
Alignment explanation
Indices: 40676548--40676744 Score: 272
Period size: 58 Copynumber: 3.4 Consensus size: 58
40676538 GGGGGGGGAC
* * **
40676548 AAAATGGTAAATTT-GATGAAATCGGGGTTAAAATGGAATTTTGGAAGATTCAGGGGT
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGATTTGGGGGT
* * *
40676605 AAAATGGTAATTTTAGGTGAAATCGAGGTTAAAATGGGATTTAGGGAAG-TTTGGGGGT
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTAAAATGGAATTT-TGGAAGATTTGGGGGT
*
40676663 AAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTTGGGGGT
1 AAAATGGTAATTTTAGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAGATTTGGGGGT
* *
40676722 AAAATGATAATTTTGGGTGAAAT
1 AAAATGGTAATTTTAGGTGAAAT
40676745 TAAGGGTCAA
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
57 13 0.11
58 64 0.52
59 46 0.37
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTAGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGATTTGGGGGT
Found at i:40678396 original size:14 final size:14
Alignment explanation
Indices: 40678368--40678405 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
40678358 CCAATTAGCC
40678368 TTTGTAATTTAGACA
1 TTTGTAA-TTAGACA
*
40678383 TTTGTAATTGGACA
1 TTTGTAATTAGACA
40678397 TTT-TAATTA
1 TTTGTAATTA
40678406 AATTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.24
14 9 0.43
15 7 0.33
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTGTAATTAGACA
Found at i:40678425 original size:17 final size:17
Alignment explanation
Indices: 40678403--40678510 Score: 128
Period size: 17 Copynumber: 6.3 Consensus size: 17
40678393 GACATTTTAA
* *
40678403 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
40678420 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
* * *
40678438 TTAAACTCAAATTAAAT
1 TTAAATTTAAAATAAAT
*
40678455 TTAAATTTAAAATAAAC
1 TTAAATTTAAAATAAAT
*
40678472 TTAAATTTAAAACAAAT
1 TTAAATTTAAAATAAAT
40678489 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
40678506 TTAAA
1 TTAAA
40678511 ATGGGTTTGG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
16 3 0.04
17 58 0.76
18 15 0.20
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:40678458 original size:6 final size:6
Alignment explanation
Indices: 40678419--40678482 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
40678409 TTATAATAAT
* * *
40678419 TTTAAA TTTGAAA -ATAAA TTTAAA CTCAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40678466 -ATAAA CTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
40678483 ACAAATTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 11 0.24
6 32 0.70
7 3 0.07
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:40678460 original size:23 final size:23
Alignment explanation
Indices: 40678433--40678482 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
40678423 AATTTGAAAA
*
40678433 TAAATTTAAACTCAAA-TTAAATT
1 TAAATTTAAAAT-AAACTTAAATT
40678456 TAAATTTAAAATAAACTTAAATT
1 TAAATTTAAAATAAACTTAAATT
40678479 TAAA
1 TAAA
40678483 ACAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATTTAAAATAAACTTAAATT
Found at i:40679491 original size:36 final size:36
Alignment explanation
Indices: 40679450--40679521 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
40679440 CTCCATTGGG
40679450 ACCTCAACCAGTTCTTTCATCAACTCGAACGTCTCT
1 ACCTCAACCAGTTCTTTCATCAACTCGAACGTCTCT
40679486 ACCTCAACCAGTTCTTTCATCAACTCGAACGTCTCT
1 ACCTCAACCAGTTCTTTCATCAACTCGAACGTCTCT
40679522 TCTCGGACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.36, G:0.08, T:0.31
Consensus pattern (36 bp):
ACCTCAACCAGTTCTTTCATCAACTCGAACGTCTCT
Found at i:40684339 original size:76 final size:77
Alignment explanation
Indices: 40684213--40684368 Score: 269
Period size: 76 Copynumber: 2.0 Consensus size: 77
40684203 GCTCTACTCG
*
40684213 AAACAAAAATTATCCGAATTCGAAATGATTAAAACAAGTAGCATAAAAGAACCAAAAAAT-AAAA
1 AAACAAAAATTATCCGAATTCGAAATAATTAAAACAAGTAGCATAAAAGAACCAAAAAATGAAAA
*
40684277 AGATAATTACTA
66 AGATAATTACCA
* *
40684289 AAACAAAAATTATCCGAGTTCGAAATAATTAGAACAAGTAGCATAAAAGAACCAAAAAATGAAAA
1 AAACAAAAATTATCCGAATTCGAAATAATTAAAACAAGTAGCATAAAAGAACCAAAAAATGAAAA
40684354 AGATAATTACCA
66 AGATAATTACCA
40684366 AAA
1 AAA
40684369 GCGTGGGTGA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 57 0.76
77 18 0.24
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (77 bp):
AAACAAAAATTATCCGAATTCGAAATAATTAAAACAAGTAGCATAAAAGAACCAAAAAATGAAAA
AGATAATTACCA
Found at i:40694134 original size:31 final size:29
Alignment explanation
Indices: 40694066--40694146 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 29
40694056 ATAACTATAA
40694066 AAAATT-TTAATAAAT-AAAAA-AT-ATAT
1 AAAATTATTAA-AAATAAAAAATATAATAT
*
40694092 AAAATTATTAAATATTAAAATAATATAATAT
1 AAAATTATTAAA-AATAAAA-AATATAATAT
40694123 AAATATT-TTAAAAATAAAAAATAT
1 AAA-ATTATTAAAAATAAAAAATAT
40694147 GGATGAGCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 7 0.15
27 6 0.13
28 3 0.07
29 7 0.15
30 8 0.17
31 12 0.26
32 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATTATTAAAAATAAAAAATATAATAT
Found at i:40695114 original size:17 final size:16
Alignment explanation
Indices: 40695092--40695163 Score: 72
Period size: 17 Copynumber: 4.3 Consensus size: 16
40695082 ACCCAATAGG
40695092 ATTTAAATCTATTTTAA
1 ATTTAAATCTA-TTTAA
* *
40695109 ATTTAAGTTTATATTAA
1 ATTTAAATCTAT-TTAA
* *
40695126 GTTTAAATCTATTGAGA
1 ATTTAAATCTATTTA-A
*
40695143 ATTTAAATTTATTTAA
1 ATTTAAATCTATTTAA
40695159 ATTTA
1 ATTTA
40695164 TAATATTCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
16 9 0.20
17 35 0.80
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (16 bp):
ATTTAAATCTATTTAA
Found at i:40695131 original size:34 final size:33
Alignment explanation
Indices: 40695092--40695163 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
40695082 ACCCAATAGG
* *
40695092 ATTTAAATCTATTTTA-AATTTAAGTTTATATTAA
1 ATTTAAATCTA-TTGAGAATTTAAATTTAT-TTAA
*
40695126 GTTTAAATCTATTGAGAATTTAAATTTATTTAA
1 ATTTAAATCTATTGAGAATTTAAATTTATTTAA
40695159 ATTTA
1 ATTTA
40695164 TAATATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (33 bp):
ATTTAAATCTATTGAGAATTTAAATTTATTTAA
Found at i:40696087 original size:30 final size:30
Alignment explanation
Indices: 40695962--40696222 Score: 133
Period size: 30 Copynumber: 8.7 Consensus size: 30
40695952 AAAGGTCCCA
* * * *
40695962 AAACTATCCAAAAATCACATTTTGGCCGCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * * *
40695992 GAA-TTTCTCTAGAAATTATATTTTGACCCCT
1 AAACTTTC-C-AAAAATTACATTTTGACCCCC
* * * * * *
40696023 AAAATATCTAAAAATCATATTTTGACCCCT
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* *
40696053 AAACTTTCTAAAAATTACATTTTTACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * * *
40696083 AAAC-TTCACAAAAAATACATTTTCACTCTC
1 AAACTTTC-CAAAAATTACATTTTGACCCCC
*
40696113 GAACTTT-CAAAAATT-CTATTATTGA-CCCC
1 AAACTTTCCAAAAATTAC-ATT-TTGACCCCC
* * ** *
40696142 AAACTTCCCAAAAATTGCATGGTCACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * * *
40696172 GAAC-TTCCAAAAATTCCCTTTTTGA-CCCT
1 AAACTTTCCAAAAATT-ACATTTTGACCCCC
40696201 AAA-TTTCCAAAAATTACCATTT
1 AAACTTTCCAAAAATTA-CATTT
40696223 AACCCCTGAA
Statistics
Matches: 173, Mismatches: 45, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
28 1 0.01
29 55 0.32
30 94 0.54
31 20 0.12
32 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.32
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCCCC
Found at i:40696154 original size:59 final size:57
Alignment explanation
Indices: 40696054--40696403 Score: 160
Period size: 58 Copynumber: 6.0 Consensus size: 57
40696044 TTGACCCCTA
* * * * *
40696054 AACTTTCTAAAAATTACATTTTTACCCCCAAACTTCACAAAAAATACATTTTCACTCTCG
1 AACTTTC-AAAAATT-CATTTTGA-CCCCAAACTTCCCAAAAATTACATTTTCACCCCCG
* **
40696114 AACTTTCAAAAATTCTATTATTGACCCCAAACTTCCCAAAAATTGCATGGTCACCCCCG
1 AACTTTCAAAAATTC-ATT-TTGACCCCAAACTTCCCAAAAATTACATTTTCACCCCCG
* * * * * *
40696173 AACTTCCAAAAATTCCCTTTTTGACCCTAAA-TTTCCAAAAATTACCA-TTTAACCCCTG
1 AACTTTCAAAAATT--CATTTTGACCCCAAACTTCCCAAAAATTA-CATTTTCACCCCCG
* * * * ** *
40696231 AA-TGTTCTAAAATTCTTTTTTGACCTCAAAATTTTCAAAAATTACCATTTT-ACCCTCG
1 AACT-TTCAAAAATTC-ATTTTGACCCCAAACTTCCCAAAAATTA-CATTTTCACCCCCG
* * * ** * * *
40696289 GA-TGTCCAAAAATTCCATTTTTTACCCCGGACCTCCCAAAAA-TACCATTTT-ACTCTCG
1 AACT-TTCAAAAATT-CA-TTTTGACCCCAAACTTCCCAAAAATTA-CATTTTCACCCCCG
* * ** **
40696347 AA-TATCCAAAAATTACATTTTTACCCTGAACTTTTCAAAAATTACCATTTT-ACCCCC
1 AACT-TTCAAAAATT-CATTTTGACCCCAAACTTCCCAAAAATTA-CATTTTCACCCCC
40696404 AGATGTCCAA
Statistics
Matches: 231, Mismatches: 47, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.00
57 32 0.14
58 102 0.44
59 83 0.36
60 12 0.05
61 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (57 bp):
AACTTTCAAAAATTCATTTTGACCCCAAACTTCCCAAAAATTACATTTTCACCCCCG
Found at i:40696208 original size:29 final size:29
Alignment explanation
Indices: 40696176--40696488 Score: 90
Period size: 29 Copynumber: 10.8 Consensus size: 29
40696166 ACCCCCGAAC
*
40696176 TTCCAAAAATTCCCTTTTTGACCCTAAAT
1 TTCCAAAAATTACCTTTTTGACCCTAAAT
* * *
40696205 TTCCAAAAATTACC-ATTTAACCCCTGAAT
1 TTCCAAAAATTACCTTTTTGA-CCCTAAAT
* * *
40696234 GTT-CTAAAATT-CTTTTTTGACCTCAAAAT
1 -TTCCAAAAATTACCTTTTTGACC-CTAAAT
* * **
40696263 TTTCAAAAATTACCATTTT-ACCCTCGGAT
1 TTCCAAAAATTACCTTTTTGACCCT-AAAT
* * ** **
40696292 GTCCAAAAATT-CCATTTTTTACCCCGGACC
1 TTCCAAAAATTACC-TTTTTGA-CCCTAAAT
* * * *
40696322 TCCCAAAAA-TACCATTTT-ACTCTCGAAT
1 TTCCAAAAATTACCTTTTTGACCCT-AAAT
* * *
40696350 ATCCAAAAATTACATTTTT-ACCCTGAACT
1 TTCCAAAAATTACCTTTTTGACCCT-AAAT
* * * *
40696379 TTTCAAAAATTACCATTTT-ACCCCCAGAT
1 TTCCAAAAATTACCTTTTTGA-CCCTAAAT
* * * * **
40696408 GTCCAAAATTTACCATTTTAACCCCGAAT
1 TTCCAAAAATTACCTTTTTGACCCTAAAT
* ** * *
40696437 ATCCAAAAATTATATTTTT-ACCCTCGAGT
1 TTCCAAAAATTACCTTTTTGACCCT-AAAT
* *
40696466 GTCCAAAAATTACCATTTT-ACCC
1 TTCCAAAAATTACCTTTTTGACCC
40696489 CTCTAGCATC
Statistics
Matches: 207, Mismatches: 61, Indels: 32
0.69 0.20 0.11
Matches are distributed among these distances:
27 2 0.01
28 26 0.13
29 154 0.74
30 22 0.11
31 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACCTTTTTGACCCTAAAT
Found at i:40696297 original size:116 final size:116
Alignment explanation
Indices: 40696177--40696488 Score: 294
Period size: 116 Copynumber: 2.7 Consensus size: 116
40696167 CCCCCGAACT
* ** * * *
40696177 TCCAAAAATTCCCTTTTTGACCCTAAATTTCCAAAAATTACCATTTAACCC-CTGAATGTTCTAA
1 TCCAAAAATTCCCTTTTTAACCCCGAATTTCCAAAAATTACCATTTAACCCTC-GAATATCCAAA
* * *
40696241 AATT-CTTTTTTGA-CCTCAAAATTTTCAAAAATTACCATTTTACCCTCGGATG
65 AATTACATTTTT-ACCCT-AAAATTTTCAAAAATTACCATTTTACCCCCAGATG
* * ** * * *
40696293 TCCAAAAATTCCATTTTTTACCCCGGACCTCCCAAAAA-TACCATTTTACTCTCGAATATCCAAA
1 TCCAAAAATTCCCTTTTTAACCCC-GAATTTCCAAAAATTACCATTTAACCCTCGAATATCCAAA
* *
40696357 AATTACATTTTTACCCTGAACTTTTCAAAAATTACCATTTTACCCCCAGATG
65 AATTACATTTTTACCCTAAAATTTTCAAAAATTACCATTTTACCCCCAGATG
* * * * * * * *
40696409 TCCAAAATTTACCATTTTAACCCCGAATATCCAAAAATTA-TATTTTTACCCTCGAGTGTCCAAA
1 TCCAAAAATTCCCTTTTTAACCCCGAATTTCCAAAAATTACCA-TTTAACCCTCGAATATCCAAA
40696473 AATTACCA-TTTTACCC
65 AATTA-CATTTTTACCC
40696489 CTCTAGCATC
Statistics
Matches: 159, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
115 10 0.06
116 128 0.81
117 21 0.13
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (116 bp):
TCCAAAAATTCCCTTTTTAACCCCGAATTTCCAAAAATTACCATTTAACCCTCGAATATCCAAAA
ATTACATTTTTACCCTAAAATTTTCAAAAATTACCATTTTACCCCCAGATG
Found at i:40696301 original size:58 final size:57
Alignment explanation
Indices: 40696177--40696476 Score: 234
Period size: 58 Copynumber: 5.2 Consensus size: 57
40696167 CCCCCGAACT
* * *
40696177 TCCAAAAATTCCCTTTTTGACCCTAAATTTCCAAAAATTACCATTTAACCC-CTGAATG
1 TCCAAAAATT-CCTTTTTTACCCGAAATTTCCAAAAATTACCATTTTACCCTC-GAATG
* * * * *
40696235 TTCTAAAATT-CTTTTTTGACCTCAAAATTTTCAAAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATTCCTTTTTT-ACC-CGAAATTTCCAAAAATTACCATTTTACCCTCGAATG
* ** * * *
40696293 TCCAAAAATTCCATTTTTTACCCCGGACCTCCCAAAAA-TACCATTTTACTCTCGAATA
1 TCCAAAAATTCC-TTTTTTA-CCCGAAATTTCCAAAAATTACCATTTTACCCTCGAATG
* * * * *
40696351 TCCAAAAATTACATTTTTACCCTGAACTTTTCAAAAATTACCATTTTACCC-CCAGATG
1 TCCAAAAATTCCTTTTTTACCC-GAAATTTCCAAAAATTACCATTTTACCCTCGA-ATG
* * * * * *
40696409 TCCAAAATTTACCATTTTAACCCCG-AATATCCAAAAATTA-TATTTTTACCCTCGAGTG
1 TCCAAAAATT-CCTTTTTTA-CCCGAAATTTCCAAAAATTACCA-TTTTACCCTCGAATG
40696467 TCCAAAAATT
1 TCCAAAAATT
40696477 ACCATTTTAC
Statistics
Matches: 192, Mismatches: 37, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
56 9 0.05
57 22 0.11
58 128 0.67
59 22 0.11
60 11 0.06
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.35
Consensus pattern (57 bp):
TCCAAAAATTCCTTTTTTACCCGAAATTTCCAAAAATTACCATTTTACCCTCGAATG
Found at i:40696479 original size:58 final size:59
Alignment explanation
Indices: 40696266--40696489 Score: 241
Period size: 58 Copynumber: 3.9 Consensus size: 59
40696256 TCAAAATTTT
* **
40696266 CAAAAATTACCATTTTACCCTCG-GATGTCCAAAAATT-CCATTTTTTACCCCGGACCTCC
1 CAAAAATTACCATTTTACCCTCGAGATGTCCAAAAATTACCA-TTTTTACCCCGAATAT-C
* * * * *
40696325 CAAAAA-TACCATTTTACTCTCGA-ATATCCAAAAATTA-CATTTTTACCCTGAACTTTT
1 CAAAAATTACCATTTTACCCTCGAGATGTCCAAAAATTACCATTTTTACCCCGAA-TATC
* * *
40696382 CAAAAATTACCATTTTACCC-CCAGATGTCCAAAATTTACCATTTTAACCCCGAATATC
1 CAAAAATTACCATTTTACCCTCGAGATGTCCAAAAATTACCATTTTTACCCCGAATATC
*
40696440 CAAAAATTA-TATTTTTACCCTCGAG-TGTCCAAAAATTACCA-TTTTACCCC
1 CAAAAATTACCA-TTTTACCCTCGAGATGTCCAAAAATTACCATTTTTACCCC
40696490 TCTAGCATCC
Statistics
Matches: 138, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
57 28 0.20
58 88 0.64
59 22 0.16
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCTCGAGATGTCCAAAAATTACCATTTTTACCCCGAATATC
Found at i:40696485 original size:87 final size:87
Alignment explanation
Indices: 40696266--40696489 Score: 255
Period size: 87 Copynumber: 2.6 Consensus size: 87
40696256 TCAAAATTTT
*
40696266 CAAAAATTACCA-TTTTACCCTCG-GATGTCCAAAAATT-CCATTTTTTA-CCCCGGACCTCCCA
1 CAAAAATTA-CATTTTTACCCTCGAG-TGTCCAAAAATTACCA--TTTTACCCCCAGACCTCCCA
*
40696327 AAAATACCATTTTACTCTCGAATATC
62 AAAATACCATTTTACTCCCGAATATC
* * * **
40696353 CAAAAATTACATTTTTACCCT-GAACTTTTCAAAAATTACCATTTTACCCCCAGATGT-CCAAAA
1 CAAAAATTACATTTTTACCCTCG-AGTGTCCAAAAATTACCATTTTACCCCCAGACCTCCCAAAA
*
40696416 TTTACCATTTTAAC-CCCGAATATC
65 -ATACCATTTT-ACTCCCGAATATC
*
40696440 CAAAAATTATATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCC
1 CAAAAATTACATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCC
40696490 TCTAGCATCC
Statistics
Matches: 117, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
86 14 0.12
87 97 0.83
88 6 0.05
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (87 bp):
CAAAAATTACATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCCCAGACCTCCCAAAAA
TACCATTTTACTCCCGAATATC
Found at i:40696503 original size:29 final size:29
Alignment explanation
Indices: 40696266--40696506 Score: 156
Period size: 29 Copynumber: 8.3 Consensus size: 29
40696256 TCAAAATTTT
* *
40696266 CAAAAATTACCATTTTACCCTCG-GATGTC
1 CAAAAATTACCATTTTACCCCCGAG-TATC
* * *
40696295 CAAAAATT-CCATTTTTTACCCCGGACCT-CC
1 CAAAAATTACCA--TTTTACCCCCGA-GTATC
* * *
40696325 CAAAAA-TACCATTTTACTCTCGAATATC
1 CAAAAATTACCATTTTACCCCCGAGTATC
* * * *
40696353 CAAAAATTA-CATTTTTA-CCCTGAACTTTT
1 CAAAAATTACCA-TTTTACCCCCG-AGTATC
*
40696382 CAAAAATTACCATTTTACCCCC-AGATGTC
1 CAAAAATTACCATTTTACCCCCGAG-TATC
* * *
40696411 CAAAATTTACCATTTTAACCCCGAATATC
1 CAAAAATTACCATTTTACCCCCGAGTATC
* * *
40696440 CAAAAATTA-TATTTTTACCCTCGAGTGTC
1 CAAAAATTACCA-TTTTACCCCCGAGTATC
* *
40696469 CAAAAATTACCATTTTACCCCTCTAGCATC
1 CAAAAATTACCATTTTACCCC-CGAGTATC
40696499 CAAAAATT
1 CAAAAATT
40696507 GCATTTTTAA
Statistics
Matches: 162, Mismatches: 34, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 25 0.15
29 96 0.59
30 39 0.24
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAGTATC
Found at i:40706532 original size:7 final size:7
Alignment explanation
Indices: 40706517--40706555 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
40706507 TGGGGTTCGG
40706517 GATTCAA
1 GATTCAA
*
40706524 GATTTAA
1 GATTCAA
40706531 GATTCAA
1 GATTCAA
*
40706538 GATTTAA
1 GATTCAA
40706545 GATTCAA
1 GATTCAA
40706552 GATT
1 GATT
40706556 TTGAGTTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (7 bp):
GATTCAA
Found at i:40706564 original size:14 final size:14
Alignment explanation
Indices: 40706517--40706556 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
40706507 TGGGGTTCGG
40706517 GATTCAAGATTTAA
1 GATTCAAGATTTAA
40706531 GATTCAAGATTTAA
1 GATTCAAGATTTAA
40706545 GATTCAAGATTT
1 GATTCAAGATTT
40706557 TGAGTTCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (14 bp):
GATTCAAGATTTAA
Found at i:40707380 original size:16 final size:17
Alignment explanation
Indices: 40707356--40707404 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
40707346 AATTTTATTC
*
40707356 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
*
40707372 TTATAAATTATAAAATA
1 TTATAAATTATAAAATT
*
40707389 CT-TAAATTA-AAAATT
1 TTATAAATTATAAAATT
40707404 T
1 T
40707405 ACTATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:40709486 original size:29 final size:29
Alignment explanation
Indices: 40709448--40709523 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
40709438 AGGGAAAAAG
40709448 GGGGTCAAAAATG-AAGTTTCGA-AGAATTT
1 GGGGTC-AAAATGTAA-TTTCGAGAGAATTT
* *
40709477 GGGGTTAAAATGTAATTTCGAGAGAATTC
1 GGGGTCAAAATGTAATTTCGAGAGAATTT
** *
40709506 AAGATCAAAATGTAATTT
1 GGGGTCAAAATGTAATTT
40709524 TAGGAAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTCGAGAGAATTT
Found at i:40709623 original size:29 final size:30
Alignment explanation
Indices: 40709510--40709731 Score: 218
Period size: 30 Copynumber: 7.5 Consensus size: 30
40709500 GAATTCAAGA
* *
40709510 TCAAAATGTAATTTTAGGAAAGTTTAAGGG
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
* * *
40709540 TCAAAATGTGACTTTAGGAAAGTTTAAGGGG
1 TCAAAATGTAATTTTGGGAAAGTTT-AGGGG
* * * * *
40709571 TTAAAA-GTGATTTCGAGAAGGTTT-GGGG
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
* **
40709599 TCAAAATGTGATTTTGGGAAAGTTT-GGTC
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
*
40709628 TCAAAATGTAATTTTGGGAAAGTTTAAGGG
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
* *
40709658 TCAAAATATAATTTTGGAAAAGTTTAGGGG
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
* ***
40709688 TC-ATATGTAATTTTAAAAAAGTTTAGGGG
1 TCAAAATGTAATTTTGGGAAAGTTTAGGGG
*
40709717 TCAAAATATAATTTT
1 TCAAAATGTAATTTT
40709732 TAAAGAAAAT
Statistics
Matches: 160, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.06
29 66 0.41
30 76 0.47
31 9 0.06
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGGAAAGTTTAGGGG
Found at i:40709659 original size:59 final size:60
Alignment explanation
Indices: 40709510--40709723 Score: 220
Period size: 59 Copynumber: 3.6 Consensus size: 60
40709500 GAATTCAAGA
* * *
40709510 TCAAAATGTAATTTTAGGAAAGTTTAAGGGTCAAAATGTGACTTTAGGAAAGTTTAAGGGG
1 TCAAAATGTAATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTTGGGAAAGTTT-AGGGG
* * ** * * **
40709571 TTAAAA-GTGATTTCGAGAAGGTTT-GGGGTCAAAATGTGATTTTGGGAAAGTTT-GGTC
1 TCAAAATGTAATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTTGGGAAAGTTTAGGGG
** * * *
40709628 TCAAAATGTAATTTTGGGAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGG
1 TCAAAATGTAATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTTGGGAAAGTTTAGGGG
* * *
40709688 TC-ATATGTAATTTTAAAAAAGTTTAGGGGTCAAAAT
1 TCAAAATGTAATTTTAAGAAAGTTTAAGGGTCAAAAT
40709724 ATAATTTTTA
Statistics
Matches: 123, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
57 7 0.06
58 14 0.11
59 80 0.65
60 17 0.14
61 5 0.04
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (60 bp):
TCAAAATGTAATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTTGGGAAAGTTTAGGGG
Found at i:40710806 original size:6 final size:6
Alignment explanation
Indices: 40710795--40710834 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40710785 GTAAATGGAC
**
40710795 AATTTA AATTTA AA-TTA AAAATA AATTTA AATTTA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT
40710835 GATTTATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:40711850 original size:30 final size:29
Alignment explanation
Indices: 40711815--40712155 Score: 273
Period size: 30 Copynumber: 11.5 Consensus size: 29
40711805 AATTTGGGGA
40711815 TCAAAATGTAATTTTAGGAAAGTTTGAGGG
1 TCAAAATGTAATTTTAGGAAAGTTT-AGGG
* *
40711845 TCAAAATGTGACTTTAGGAAAGTTTAAGGGG
1 TCAAAATGTAATTTTAGGAAAGTTT-A-GGG
* * * *
40711876 TTAAAATGTGATTTT-GAGAAGGTTTGGGG
1 TCAAAATGTAATTTTAG-GAAAGTTTAGGG
* **
40711905 TCAAAATGTGATTTTAGGAAAGTTTAGTC
1 TCAAAATGTAATTTTAGGAAAGTTTAGGG
* * *
40711934 TCAAAATGTAATCTCA-AAAAGTTTAGGG
1 TCAAAATGTAATTTTAGGAAAGTTTAGGG
*
40711962 ATTAAAA-GTTAATTTT-GGAAAAGTTTAGGG
1 -TCAAAATG-TAATTTTAGG-AAAGTTTAGGG
* * *
40711992 TTTAAAATCTAATTTTAGAAAAGTTTAAGGG
1 -TCAAAATGTAATTTTAGGAAAGTTT-AGGG
* * *
40712023 TTAAGATATAATTTT-GGAAAAGTTTAGGGG
1 TCAAAATGTAATTTTAGG-AAAGTTTA-GGG
40712053 TCAAAATGTAATTTT-GGAAAAGTTTAAGGG
1 TCAAAATGTAATTTTAGG-AAAGTTT-AGGG
* * *
40712083 TTAAAATGTAATTTT-GGAAAACTTTAAGG
1 TCAAAATGTAATTTTAGG-AAAGTTTAGGG
* **
40712112 TTAAAATGTAATTTTAAAAAAGTTTAGGG
1 TCAAAATGTAATTTTAGGAAAGTTTAGGG
*
40712141 TCAAAATATAATTTT
1 TCAAAATGTAATTTT
40712156 TAAAAAGCTA
Statistics
Matches: 257, Mismatches: 40, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
28 10 0.04
29 90 0.35
30 128 0.50
31 29 0.11
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
TCAAAATGTAATTTTAGGAAAGTTTAGGG
Found at i:40712160 original size:29 final size:29
Alignment explanation
Indices: 40711787--40712184 Score: 265
Period size: 30 Copynumber: 13.5 Consensus size: 29
40711777 AAACAGAGCC
* *
40711787 TAAAATG-AAGTTTCGAAAAA-TTTGGGGAT
1 TAAAATGTAA-TTTTGAAAAAGTTTAGGG-T
* *
40711816 CAAAATGTAATTTT-AGGAAAGTTTGAGGGT
1 TAAAATGTAATTTTGA-AAAAGTTT-AGGGT
* * * *
40711846 CAAAATGTGACTTT-AGGAAAGTTTAAGGGGT
1 TAAAATGTAATTTTGA-AAAAGTTT-A-GGGT
* * * *
40711877 TAAAATGTGATTTTGAGAAGGTTTGGGGT
1 TAAAATGTAATTTTGAAAAAGTTTAGGGT
* * * **
40711906 CAAAATGTGATTTT-AGGAAAGTTTAGTCT
1 TAAAATGTAATTTTGA-AAAAGTTTAGGGT
* * *
40711935 CAAAATGTAA-TCTCAAAAAGTTTAGGGAT
1 TAAAATGTAATTTTGAAAAAGTTTAGGG-T
*
40711964 TAAAA-GTTAATTTTGGAAAAGTTTAGGGTT
1 TAAAATG-TAATTTTGAAAAAGTTTAGGG-T
*
40711994 TAAAATCTAATTTT-AGAAAAGTTTAAGGGT
1 TAAAATGTAATTTTGA-AAAAGTTT-AGGGT
* * *
40712024 TAAGATATAATTTTGGAAAAGTTTAGGGGT
1 TAAAATGTAATTTTGAAAAAGTTTA-GGGT
* *
40712054 CAAAATGTAATTTTGGAAAAGTTTAAGGGT
1 TAAAATGTAATTTTGAAAAAGTTT-AGGGT
* * *
40712084 TAAAATGTAATTTTGGAAAACTTTAAGGT
1 TAAAATGTAATTTTGAAAAAGTTTAGGGT
*
40712113 TAAAATGTAATTTTAAAAAAGTTTAGGGT
1 TAAAATGTAATTTTGAAAAAGTTTAGGGT
* * * *
40712142 CAAAATATAATTTTTAAAAAG-CTAGGGGT
1 TAAAATGTAATTTTGAAAAAGTTTA-GGGT
*
40712171 TAAAATATAATTTT
1 TAAAATGTAATTTT
40712185 TAAAGAAAAT
Statistics
Matches: 305, Mismatches: 46, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.05
29 121 0.40
30 136 0.45
31 31 0.10
32 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
TAAAATGTAATTTTGAAAAAGTTTAGGGT
Found at i:40712317 original size:17 final size:17
Alignment explanation
Indices: 40712284--40712333 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
40712274 TTTTAGGTTT
* *
40712284 TAAATTTTAATTCATTG
1 TAAATTTAAATTTATTG
*
40712301 TAAGTTTAAATTTATTG
1 TAAATTTAAATTTATTG
*
40712318 TAAATTTAAACTTATT
1 TAAATTTAAATTTATT
40712334 TGGAGCTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTG
Found at i:40714357 original size:30 final size:30
Alignment explanation
Indices: 40714334--40714406 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
40714324 TTGACTTTTG
*
40714334 AACTTTCTAAAAATAACATTTTGACCCCTA
1 AACTTTCCAAAAATAACATTTTGACCCCTA
**
40714364 AACTTTCCAAAAATAACATTTTGACCCCCG
1 AACTTTCCAAAAATAACATTTTGACCCCTA
40714394 AAC-TTCCAAAAAT
1 AACTTTCCAAAAAT
40714407 TCCATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 10 0.25
30 30 0.75
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.29
Consensus pattern (30 bp):
AACTTTCCAAAAATAACATTTTGACCCCTA
Found at i:40714427 original size:59 final size:58
Alignment explanation
Indices: 40714364--40714737 Score: 306
Period size: 59 Copynumber: 6.4 Consensus size: 58
40714354 TTGACCCCTA
* *
40714364 AACTTTCCAAAAATAACATTTTGACCCCCGAACTTCCAAAAATTCCATTTTTAACCTTG
1 AACTTTCCAAAAATACCATTTT-ACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * * * * *
40714423 AACTTT-TAAAAACTACCATTTTAGCCTCAAACTTCCAAAAATTCTATTTTTGACCTCG
1 AACTTTCCAAAAA-TACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
40714481 AACTTTTCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCACTTTTAACCCCG
1 AACTTTCCAAAAA-TACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * * * * * **
40714540 AAATTTCTACAAATTACCATTTTACCCCCGAGCTTTCAAAAATTCTATTTTTAAACCTTA
1 AACTTTCCA-AAAATACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTT-AACCTCG
* * * * ** * * *
40714600 AAATTTCTGAAAATTACTATTTTACCCCCAGATGTT-CAAAGATTCC-TTTTTGA-CTCCA
1 AACTTTC-CAAAAATACCATTTTACCCCC-GAACTTCCAAAAATTCCATTTTTAACCT-CG
* * * * * *
40714658 AACTTTCCAAAATTACCATTTTACCCTCGAACTTTCAAAAATTCCTTTTTTACCCCCG
1 AACTTTCCAAAAATACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
40714716 AAGTGTCCAAAATTACCATTTT
1 AACTTTCCAAAAATACCATTTT
40714738 GCTCCCGGGT
Statistics
Matches: 256, Mismatches: 49, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
56 4 0.02
57 29 0.11
58 75 0.29
59 103 0.40
60 40 0.16
61 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (58 bp):
AACTTTCCAAAAATACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:40714583 original size:29 final size:29
Alignment explanation
Indices: 40714333--40714737 Score: 213
Period size: 29 Copynumber: 13.8 Consensus size: 29
40714323 TTTGACTTTT
* *
40714333 GAACTTTCTAAAAA-TAACATTTTGACCCCT
1 GAACTTTC-AAAAATTACCATTTT-ACCCCC
* *
40714363 AAACTTTCCAAAAA-TAACATTTTGACCCCC
1 GAACTTT-CAAAAATTACCATTTT-ACCCCC
* * **
40714393 GAACTTCCAAAAATT-CCATTTTTAACCTT
1 GAACTTTCAAAAATTACCA-TTTTACCCCC
* * * *
40714422 GAACTTTTAAAAACTACCATTTTAGCCTC
1 GAACTTTCAAAAATTACCATTTTACCCCC
* * * *
40714451 AAACTTCCAAAAATT-CTATTTTTGA-CCTC
1 GAACTTTCAAAAATTACCA-TTTT-ACCCCC
*
40714480 GAACTTTTCAAAAATTACCATTTTACCCTC
1 GAAC-TTTCAAAAATTACCATTTTACCCCC
* *
40714510 GAACTTCCAAAAATT-CCACTTTTAACCCC
1 GAACTTTCAAAAATTACCA-TTTTACCCCC
* *
40714539 GAAATTTCTACAAATTACCATTTTACCCCC
1 GAACTTTC-AAAAATTACCATTTTACCCCC
* * * **
40714569 GAGCTTTCAAAAATT-CTATTTTTAAACCTT
1 GAACTTTCAAAAATTACCA-TTTT-ACCCCC
* * * *
40714599 AAAATTTCTGAAAATTACTATTTTACCCCC
1 GAACTTTC-AAAAATTACCATTTTACCCCC
* * *
40714629 -AGA-TGTTCAAAGATT-CCTTTTTGA-CTCC
1 GA-ACT-TTCAAAAATTACCATTTT-ACCCCC
* * *
40714657 AAACTTTCCAAAATTACCATTTTACCCTC
1 GAACTTTCAAAAATTACCATTTTACCCCC
*
40714686 GAACTTTCAAAAATT-CCTTTTTTACCCCC
1 GAACTTTCAAAAATTACC-ATTTTACCCCC
* * *
40714715 GAAGTGTCCAAAATTACCATTTT
1 GAACTTTCAAAAATTACCATTTT
40714738 GCTCCCGGGT
Statistics
Matches: 290, Mismatches: 60, Indels: 51
0.72 0.15 0.13
Matches are distributed among these distances:
28 27 0.09
29 144 0.50
30 100 0.34
31 16 0.06
32 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
GAACTTTCAAAAATTACCATTTTACCCCC
Found at i:40714744 original size:29 final size:28
Alignment explanation
Indices: 40714663--40714765 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 28
40714653 CTCCAAACTT
* *
40714663 TCCAAAATTACCATTTTACCCTCGAACTT
1 TCCAAAATTACCATTTTACCC-CGAAGTA
* * *
40714692 TCAAAAATT-CCTTTTTTACCCCCGAAGTG
1 TCCAAAATTACC-ATTTTA-CCCCGAAGTA
* *
40714721 TCCAAAATTACCATTTTGCTCCCG-GGTA
1 TCCAAAATTACCATTTTAC-CCCGAAGTA
*
40714749 TCCAAAATT-GCATTTTA
1 TCCAAAATTACCATTTTA
40714766 TCCTGTCTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.10
28 14 0.24
29 34 0.58
30 5 0.08
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCGAAGTA
Found at i:40716931 original size:6 final size:6
Alignment explanation
Indices: 40716920--40716959 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40716910 GTAAATGGAT
**
40716920 AATTTA AATTTA AA-TTA AAAATA AATTTA AATTTA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT
40716960 CATTTATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:40720966 original size:17 final size:17
Alignment explanation
Indices: 40720934--40720967 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40720924 TGAGATTTTT
*
40720934 TTTGAATTTATATTAAG
1 TTTGAATTAATATTAAG
*
40720951 TTTGAATTAATTTTAAG
1 TTTGAATTAATATTAAG
40720968 ATTTATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTGAATTAATATTAAG
Found at i:40720977 original size:17 final size:17
Alignment explanation
Indices: 40720957--40721019 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
40720947 TAAGTTTGAA
40720957 TTAATTTTAAGATTT-AT
1 TTAATTTTAA-ATTTAAT
* **
40720974 TTAAATTTAAATTTGTT
1 TTAATTTTAAATTTAAT
40720991 TTGAA-TTTAAATTTAAT
1 TT-AATTTTAAATTTAAT
*
40721008 TTAATTTAAAAT
1 TTAATTTTAAAT
40721020 GGTTTTAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.16
17 30 0.79
18 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTAATTTTAAATTTAAT
Found at i:40721025 original size:33 final size:33
Alignment explanation
Indices: 40720957--40721045 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
40720947 TAAGTTTGAA
* * *
40720957 TTAATTTTAAGATTT-ATTTAAATTTAAATTTGTT
1 TTAAATTTAA-ATTTAATTT-AATTTAAAATGGTT
*
40720991 TTGAATTTAAATTTAATTTAATTTAAAATGGTT
1 TTAAATTTAAATTTAATTTAATTTAAAATGGTT
* *
40721024 TTAAACTTAAACTTAAATTTAA
1 TTAAATTTAAA-TTTAATTTAA
40721046 AATGTCCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
33 25 0.54
34 21 0.46
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (33 bp):
TTAAATTTAAATTTAATTTAATTTAAAATGGTT
Found at i:40721747 original size:3 final size:3
Alignment explanation
Indices: 40721741--40721778 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
40721731 TAATAACTTT
40721741 TAA TAA TAA TAA CTAA TAA TAA TAA TAA T-A TAA -AA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
40721779 AAAAAGAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:40721749 original size:16 final size:16
Alignment explanation
Indices: 40721728--40721768 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
40721718 ACATTAATGG
**
40721728 TAATAATAACTTTTAA
1 TAATAATAACTAATAA
40721744 TAATAATAACTAATAA
1 TAATAATAACTAATAA
40721760 TAATAATAA
1 TAATAATAA
40721769 TATAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATAACTAATAA
Found at i:40721777 original size:16 final size:16
Alignment explanation
Indices: 40721728--40721778 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
40721718 ACATTAATGG
***
40721728 TAATAATAACTTTTAA
1 TAATAATAACTAAAAA
*
40721744 TAATAATAACTAATAA
1 TAATAATAACTAAAAA
40721760 TAATAATAA-TATAAAA
1 TAATAATAACTA-AAAA
40721776 TAA
1 TAA
40721779 AAAAAGAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 2 0.06
16 29 0.94
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAACTAAAAA
Found at i:40722827 original size:30 final size:30
Alignment explanation
Indices: 40722786--40723084 Score: 359
Period size: 30 Copynumber: 10.0 Consensus size: 30
40722776 CCCTAAATTG
*
40722786 TCCAGAAATTACATTTTAACCCAAAAACTTT
1 TCCA-AAATTACATTTTAACCCCAAAACTTT
* **
40722817 TCCTAAATTACATTTTAACCTTAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
*
40722847 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* *
40722877 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* * *
40722907 ACCAAAATTCCATTTTAACCCCGAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* *
40722937 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
*
40722967 TCCATAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* ** *
40722997 TCCAAAATTATATTTTGTCCCTAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* * * *
40723027 TCTAAAATTATATTTTGACCCCGAAAC-TT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* *
40723056 TCAAAAATTACCATTTT-ACCCCTAAACTT
1 TCCAAAATTA-CATTTTAACCCCAAAACTT
40723085 CCCTAAATCT
Statistics
Matches: 233, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.09
30 210 0.90
31 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTAACCCCAAAACTTT
Found at i:40723120 original size:59 final size:57
Alignment explanation
Indices: 40723057--40723257 Score: 165
Period size: 59 Copynumber: 3.4 Consensus size: 57
40723047 CCGAAACTTT
*
40723057 CAAAAATTACCATTTTACCCCTAAACTTCCCTAAATCTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCC-AAAT-TCATTTTTAACCCCGATTTCAC
* * * * * * * ** * **
40723116 CAAAACTTATCGTTTT-CCCTTCGAATTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCC-AAA-TTCATTTTTAACCCCGATTTCAC
* * *
40723175 CAAAATTTACCATTTTGTTCCCC-AAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCA-TTT-TACCCCTAAACTTTCCAAATT-CATTTTTAACCCCGATTTCAC
40723233 CAAAAATTACCATTTTACCCCTAAA
1 CAAAAATTACCATTTTACCCCTAAA
40723258 AACCCAAATT
Statistics
Matches: 106, Mismatches: 29, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
56 5 0.05
57 6 0.06
58 17 0.16
59 63 0.59
60 11 0.10
61 1 0.01
62 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.38
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAATTCATTTTTAACCCCGATTTCAC
Found at i:40735090 original size:68 final size:68
Alignment explanation
Indices: 40734973--40735418 Score: 730
Period size: 68 Copynumber: 6.5 Consensus size: 68
40734963 ATCATTTCCA
* *
40734973 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735038 GTC
66 GTC
* * *
40735041 ATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCCGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735106 GTC
66 GTC
* * *
40735109 ATCCTCTTGAAATTGAAGTAAAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735174 GTC
66 GTC
*
40735177 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735242 GTC
66 GTC
* * * *
40735245 GTCCTCTTGAAATTGAAGTAAAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735310 GTC
66 GTC
* *
40735313 ATCCCCTTGAAATTGAAGTAGACTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
40735378 GTC
66 GTC
* *
40735381 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCT
40735419 ACCCAGTAAG
Statistics
Matches: 349, Mismatches: 28, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
68 337 0.97
69 12 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:40741304 original size:41 final size:40
Alignment explanation
Indices: 40741256--40741368 Score: 108
Period size: 38 Copynumber: 2.9 Consensus size: 40
40741246 TCGACCTCGA
40741256 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
* * ** * *
40741296 ATTCGATGAGATACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
* *
40741334 GCCGATGAGACACTGGGTGTCACTT-TATTACTTCG
1 GTCGATGAGACACTGGGTGTCA-TTATTTTACTTCG
40741369 AACTATCCGA
Statistics
Matches: 55, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
37 11 0.20
38 17 0.31
39 4 0.07
40 11 0.20
41 12 0.22
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
Found at i:40741379 original size:40 final size:39
Alignment explanation
Indices: 40741258--40741392 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 39
40741248 GACCTCGAGT
* * *
40741258 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATA-GATT
1 CGATGAGACACTGGGTGTCACT-TTTTACTTC-GA-ACTATC
* ** * *
40741299 CGATGAGATACTGGGTACCAC--TTTACTTCG-GCTAGGC
1 CGATGAGACACTGGGTGTCACTTTTTACTTCGAACTA-TC
40741336 CGATGAGACACTGGGTGTCACTTTATTACTTCGAACTATC
1 CGATGAGACACTGGGTGTCACTTT-TTACTTCGAACTATC
*
40741376 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
40741393 CCATTCTGGT
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
36 1 0.01
37 19 0.26
38 8 0.11
39 1 0.01
40 25 0.34
41 20 0.27
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCACTTTTTACTTCGAACTATC
Found at i:40743055 original size:3 final size:3
Alignment explanation
Indices: 40743049--40743089 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
40743039 TAATAACTTT
40743049 TAA TAA TAA TAA CTAA TAA TAA TAA TAA TAA T-A TAA -AA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40743090 AAAAAGAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:40743057 original size:16 final size:16
Alignment explanation
Indices: 40743036--40743089 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
40743026 ACATTAATGG
**
40743036 TAATAATAACTTTTAA
1 TAATAATAACTAATAA
40743052 TAATAATAACTAATAA
1 TAATAATAACTAATAA
40743068 TAATAATAA-TAAT-A
1 TAATAATAACTAATAA
40743082 TAA-AATAA
1 TAATAATAA
40743090 AAAAAGAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 4 0.11
16 23 0.64
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAACTAATAA
Done.