Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 96 of 205
Found at i:28013676 original size:16 final size:16
Alignment explanation
Indices: 28013655--28013724 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
28013645 TTGATTTGCT
* *
28013655 ATTACACCTCTATTTC
1 ATTACACCTCTAATCC
28013671 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
28013687 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28013703 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28013719 AATACA
1 ATTACA
28013725 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28013774 original size:24 final size:24
Alignment explanation
Indices: 28013742--28013792 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28013732 AAACGTGCCC
* **
28013742 TTAGTATTTATGAGTATAATATAT
1 TTAGCATTTATGAACATAATATAT
*
28013766 TTAGCATTTATTAACATAATATAT
1 TTAGCATTTATGAACATAATATAT
28013790 TTA
1 TTA
28013793 ACTTTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
TTAGCATTTATGAACATAATATAT
Found at i:28018186 original size:24 final size:24
Alignment explanation
Indices: 28018159--28018210 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28018149 TTTCTAGAAG
* **
28018159 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
28018183 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
28018207 ATTT
1 ATTT
28018211 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:28022367 original size:3 final size:3
Alignment explanation
Indices: 28022359--28022389 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
28022349 AAAATAAACC
28022359 CTT CTT CTT CTT CCTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT
28022390 AAAATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:28022374 original size:13 final size:13
Alignment explanation
Indices: 28022358--28022389 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28022348 TAAAATAAAC
28022358 CCTTCTTCTTCTT
1 CCTTCTTCTTCTT
28022371 CCTTCTTCTTCTT
1 CCTTCTTCTTCTT
28022384 -CTTCTT
1 CCTTCTT
28022390 AAAATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
CCTTCTTCTTCTT
Found at i:28022546 original size:19 final size:19
Alignment explanation
Indices: 28022524--28022585 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
28022514 ATCTTTGAAT
*
28022524 TATTGAATGATTTTAGCTC
1 TATTGAATGATTTTCGCTC
* *
28022543 TATTTGCAT-CTGTTTCGCTC
1 TA-TTGAATGAT-TTTCGCTC
28022563 TATTGAATGATTTTCGCTC
1 TATTGAATGATTTTCGCTC
28022582 TATT
1 TATT
28022586 TTCCTTCTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (19 bp):
TATTGAATGATTTTCGCTC
Found at i:28022997 original size:17 final size:17
Alignment explanation
Indices: 28022975--28023026 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
28022965 AATTTCTCAA
28022975 AGTAATAATGTAATATT
1 AGTAATAATGTAATATT
*
28022992 AGTAATAATATAATATT
1 AGTAATAATGTAATATT
*
28023009 AGTAATAACGTAATATT
1 AGTAATAATGTAATATT
28023026 A
1 A
28023027 ATAGAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (17 bp):
AGTAATAATGTAATATT
Found at i:28023453 original size:90 final size:89
Alignment explanation
Indices: 28023332--28023726 Score: 519
Period size: 90 Copynumber: 4.4 Consensus size: 89
28023322 CTTCAATTAA
* *
28023332 TTAATTTATGCTGTTGTACTATTATACTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAA-
* *
28023397 TATGGTTTAATAGACTTTTTTTTGT
65 TATAGTTTAACAGACTTTTTTTTGT
*
28023422 TTAATTTATGCTATTGTACTATTATATTAATTTAGGTTTCAATTAACTAACTTTAAAGTTTAAAG
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAA-
* *
28023487 TATAGTTTAATATACTTTTTTTTGT
65 TATAGTTTAACAGACTTTTTTTTGT
28023512 TTAATTTACACGGTTG-TACTTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAG
1 TTAATTT--A----TGCTA-TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAG
**
28023576 TTTAAATGATAACTTAACAGAC--TTTTTT-T
59 TTTAAAT-ATAGTTTAACAGACTTTTTTTTGT
* *
28023605 TTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTTTAAAGTTTAAAA
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTT-AAA
* *
28023670 TGTAGTTTAACATACTTTTTTTTGT
65 TATAGTTTAACAGACTTTTTTTTGT
***
28023695 TTAATTTATGCTGCCGTACTATTATATTAATT
1 TTAATTTATGCTATTGTACTATTATATTAATT
28023727 AATTTTTAAT
Statistics
Matches: 271, Mismatches: 21, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
87 59 0.22
88 5 0.02
89 6 0.02
90 120 0.44
91 1 0.00
92 1 0.00
93 8 0.03
94 6 0.02
95 3 0.01
96 62 0.23
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (89 bp):
TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAT
ATAGTTTAACAGACTTTTTTTTGT
Found at i:28023668 original size:183 final size:185
Alignment explanation
Indices: 28023345--28023702 Score: 578
Period size: 183 Copynumber: 1.9 Consensus size: 185
28023335 ATTTATGCTG
*** *
28023345 TTGTACTATTATACTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATGGTTTAATAG
1 TTGTACTATTATACTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATAACTTAACAG
* * *
28023410 ACTTTTTTTTGTTTAATTTATGCTATTGTACTATTATATTAATTTAGGTTTCAATTAACTAACTT
66 AC-TTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTT
* *
28023475 TAAAGTTTAAAGTATAGTTTAATATACTTTTTTTTGTTTAATTTACACGGTTGTAC
130 TAAAGTTTAAAATATAGTTTAACATACTTTTTTTTGTTTAATTTACACGGTTGTAC
*
28023531 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAA-TGATAACTTAACA
1 TTGTACTATTATACTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACT-ATAACTTAACA
28023595 GAC-TTTTTT-TTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTT
65 GACTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTT
*
28023658 TAAAGTTTAAAATGTAGTTTAACATACTTTTTTTTGTTTAATTTA
130 TAAAGTTTAAAATATAGTTTAACATACTTTTTTTTGTTTAATTTA
28023703 TGCTGCCGTA
Statistics
Matches: 160, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
183 93 0.58
184 6 0.04
185 1 0.01
186 60 0.38
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (185 bp):
TTGTACTATTATACTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATAACTTAACAG
ACTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTTT
AAAGTTTAAAATATAGTTTAACATACTTTTTTTTGTTTAATTTACACGGTTGTAC
Found at i:28030183 original size:27 final size:27
Alignment explanation
Indices: 28030162--28030226 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
28030152 TCTCGCTAGA
*
28030162 CCTATTGGCGAACTCCAGCTCGCCAAG
1 CCTACTGGCGAACTCCAGCTCGCCAAG
28030189 CCTACTGGCGAACTCCAGCTCGCCAAG
1 CCTACTGGCGAACTCCAGCTCGCCAAG
28030216 CCTACTGGCGA
1 CCTACTGGCGA
28030227 TCACAGTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.23, T:0.17
Consensus pattern (27 bp):
CCTACTGGCGAACTCCAGCTCGCCAAG
Found at i:28031678 original size:76 final size:76
Alignment explanation
Indices: 28031545--28031685 Score: 178
Period size: 76 Copynumber: 1.9 Consensus size: 76
28031535 TCAAGATGTG
* * * * ** * *
28031545 ATGATGTGATTAGTGTTACTGAAACAAGACTAGATCGGATGAATTGAGAATTTATCGATATAACA
1 ATGATGTGACTAGTGTTACTGAAACAAGACCAAATCGGAAGAACCGAAAATTAATCGATATAACA
28031610 GTTCGAACAAA
66 GTTCGAACAAA
28031621 ATGATGTGACTAGTGTTACT-AGAACAAGACCAAATCGGACAG-ACCGAAAATTAATCGATATAA
1 ATGATGTGACTAGTGTTACTGA-AACAAGACCAAATCGGA-AGAACCGAAAATTAATCGATATAA
28031684 CA
64 CA
28031686 ATTTGAACGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
75 1 0.02
76 53 0.96
77 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (76 bp):
ATGATGTGACTAGTGTTACTGAAACAAGACCAAATCGGAAGAACCGAAAATTAATCGATATAACA
GTTCGAACAAA
Found at i:28032959 original size:17 final size:15
Alignment explanation
Indices: 28032903--28032956 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
28032893 TTTTTCACGT
*
28032903 TCTCCTTCCCTTCTTTC
1 TCTCTTTCCC-TC-TTC
*
28032920 TTTCTTTCCCTCTTC
1 TCTCTTTCCCTCTTC
28032935 TCTCTTTCCCGTC-TC
1 TCTCTTTCCC-TCTTC
28032950 TCTCTTT
1 TCTCTTT
28032957 TTCTTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 21 0.64
16 4 0.12
17 8 0.24
ACGTcount: A:0.00, C:0.43, G:0.02, T:0.56
Consensus pattern (15 bp):
TCTCTTTCCCTCTTC
Found at i:28033954 original size:30 final size:30
Alignment explanation
Indices: 28033918--28033980 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28033908 ACTTATTTTA
*
28033918 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
28033948 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
28033978 TTG
1 TTG
28033981 CTTGATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:28034135 original size:13 final size:11
Alignment explanation
Indices: 28034101--28034128 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28034091 TATATATATT
28034101 TAAAAATAATA
1 TAAAAATAATA
28034112 TAAAAATAATA
1 TAAAAATAATA
28034123 TAAAAA
1 TAAAAA
28034129 ATTAATACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:28036187 original size:62 final size:61
Alignment explanation
Indices: 28036027--28036176 Score: 157
Period size: 62 Copynumber: 2.5 Consensus size: 61
28036017 TTGTTATTAA
** *
28036027 ATTTTAATAGGATTATTATTAGAA-T-AATTTAAT-AATA-AATAATAAATAATGTAATCAC
1 ATTTTAATATAATTATTATTA-AATTAAATTTAATAAAAATAATAATAAATAATGTAATCAC
* * *
28036085 ATTTTAATATAATTATTATTAAATTTAATTTAATAAAAATAATAA-AATATAATTTAATTAC
1 ATTTTAATATAATTATTATTAAATTAAATTTAATAAAAATAATAATAA-ATAATGTAATCAC
* * *
28036146 ATTTTTAATCTAATTATTTTTATATTAAATT
1 A-TTTTAATATAATTATTATTAAATTAAATT
28036177 ATATTTAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
57 2 0.03
58 20 0.26
59 8 0.10
60 5 0.06
61 17 0.22
62 25 0.32
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (61 bp):
ATTTTAATATAATTATTATTAAATTAAATTTAATAAAAATAATAATAAATAATGTAATCAC
Found at i:28036816 original size:30 final size:30
Alignment explanation
Indices: 28036781--28036838 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28036771 ATTTTATTAT
*
28036781 TTTTGTTATTATTTTAAAGGCATTTGCTAA
1 TTTTGTTATTATTTTAAAGACATTTGCTAA
*
28036811 TTTTGTTATTATTTTAGAGACATTTGCT
1 TTTTGTTATTATTTTAAAGACATTTGCT
28036839 TATTAAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (30 bp):
TTTTGTTATTATTTTAAAGACATTTGCTAA
Found at i:28039424 original size:19 final size:19
Alignment explanation
Indices: 28039391--28039491 Score: 53
Period size: 19 Copynumber: 5.3 Consensus size: 19
28039381 AGGGAAACTA
* *
28039391 GCACATATAGCGCATATTG
1 GCACATAAAGTGCATATTG
**
28039410 GCACATAAAGTGCATCCTG
1 GCACATAAAGTGCATATTG
* * * *
28039429 GCGCACAAAGCGCATACTG
1 GCACATAAAGTGCATATTG
* * *
28039448 GCACACAAAATGCA-ATCTA
1 GCACATAAAGTGCATAT-TG
* *
28039467 G-AGCATGAAGTGCATCTTG
1 GCA-CATAAAGTGCATATTG
28039486 GCACAT
1 GCACAT
28039492 GAGGTGCATC
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
18 2 0.03
19 56 0.93
20 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (19 bp):
GCACATAAAGTGCATATTG
Found at i:28039444 original size:38 final size:38
Alignment explanation
Indices: 28039399--28039509 Score: 107
Period size: 38 Copynumber: 2.9 Consensus size: 38
28039389 TAGCACATAT
28039399 AGCGCATATTGGCACATAAAGTGCATCCTGGCGCACAA
1 AGCGCATATTGGCACATAAAGTGCATCCTGGCGCACAA
* * * * * **
28039437 AGCGCATACTGGCACACAAAATGCAAT-CTAGAGCATGA
1 AGCGCATATTGGCACATAAAGTGC-ATCCTGGCGCACAA
* * * *
28039475 AGTGCATCTTGGCACATGAGGTGCATCCTGGCGCA
1 AGCGCATATTGGCACATAAAGTGCATCCTGGCGCA
28039510 TAAATGACTT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
37 2 0.04
38 51 0.93
39 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (38 bp):
AGCGCATATTGGCACATAAAGTGCATCCTGGCGCACAA
Found at i:28039492 original size:19 final size:19
Alignment explanation
Indices: 28039408--28039506 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
28039398 TAGCGCATAT
*
28039408 TGGCACATAAAGTGCATCC
1 TGGCACATGAAGTGCATCC
* ** * *
28039427 TGGCGCACAAAGCGCATAC
1 TGGCACATGAAGTGCATCC
** *
28039446 TGGCACACAAAATGCAAT-C
1 TGGCACATGAAGTGC-ATCC
* *
28039465 TAG-AGCATGAAGTGCATCT
1 TGGCA-CATGAAGTGCATCC
*
28039484 TGGCACATGAGGTGCATCC
1 TGGCACATGAAGTGCATCC
28039503 TGGC
1 TGGC
28039507 GCATAAATGA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
18 3 0.05
19 55 0.90
20 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.19
Consensus pattern (19 bp):
TGGCACATGAAGTGCATCC
Found at i:28039745 original size:21 final size:21
Alignment explanation
Indices: 28039702--28039747 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28039692 TTTATTAGTT
*
28039702 TAATCTTAATTAAGTAAACAC
1 TAATCTTAATTAACTAAACAC
*
28039723 TAATCTTTAATTAACTTAA-AC
1 TAATC-TTAATTAACTAAACAC
28039744 TAAT
1 TAAT
28039748 GGCATCCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATCTTAATTAACTAAACAC
Found at i:28041276 original size:21 final size:19
Alignment explanation
Indices: 28041232--28041276 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
28041222 AATATTTCTT
*
28041232 ATAAATTTATTTAATTTAT
1 ATAAATTTATTTAATTTAA
*
28041251 GTAAATTTTAATTTAATTTAA
1 ATAAA-TTT-ATTTAATTTAA
28041272 ATAAA
1 ATAAA
28041277 AATAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATAAATTTATTTAATTTAA
Found at i:28052320 original size:24 final size:24
Alignment explanation
Indices: 28052291--28052339 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28052281 CGTTCTAGTC
28052291 CTTAACCTTCATCAATGAAACAGT
1 CTTAACCTTCATCAATGAAACAGT
28052315 CTTAACCTTCATCAATGAAACAGT
1 CTTAACCTTCATCAATGAAACAGT
28052339 C
1 C
28052340 AACCTATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.29
Consensus pattern (24 bp):
CTTAACCTTCATCAATGAAACAGT
Found at i:28069995 original size:18 final size:18
Alignment explanation
Indices: 28069951--28070005 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
28069941 ATTATTCAAT
*
28069951 TTTATATTTTATTTTATATA
1 TTTATA-TTTA-TTTATTTA
**
28069971 TAAATATTTATTTATTTA
1 TTTATATTTATTTATTTA
*
28069989 TTTATATTTATATATTT
1 TTTATATTTATTTATTT
28070006 GTTCGCTAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 21 0.72
19 4 0.14
20 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATATTTATTTATTTA
Found at i:28069996 original size:14 final size:14
Alignment explanation
Indices: 28069951--28070005 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 14
28069941 ATTATTCAAT
28069951 TTTATATTT-TAT-
1 TTTATATTTATATA
* *
28069963 TTTATATATAAATA
1 TTTATATTTATATA
*
28069977 -TT-TATTTATTTA
1 TTTATATTTATATA
28069989 TTTATATTTATATA
1 TTTATATTTATATA
28070003 TTT
1 TTT
28070006 GTTCGCTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 15 0.45
13 6 0.18
14 12 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:28082793 original size:42 final size:41
Alignment explanation
Indices: 28082746--28082884 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 41
28082736 GCACATAAGT
* * * *
28082746 GCTAAACGGAAACCCGTAAAGGTTAAATGAAAGCTCATAGGA
1 GCTAAACGGAAACCCATAAGGGTTAAATG-AAGCTCAAAAGA
* * *
28082788 GCTAAACGAAAACCTATAAGGGTTAATCTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAA-ATGAAGCTCAAAAGA
* *
28082830 GCTAAACTGAAACCCATTAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAA-TGAAGCTCAAAAGA
* *
28082872 GCTGAACTGAAAC
1 GCTAAACGGAAAC
28082885 TAGAAGAGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 80 0.98
43 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (41 bp):
GCTAAACGGAAACCCATAAGGGTTAAATGAAGCTCAAAAGA
Found at i:28082922 original size:20 final size:21
Alignment explanation
Indices: 28082767--28082944 Score: 105
Period size: 21 Copynumber: 8.6 Consensus size: 21
28082757 ACCCGTAAAG
*
28082767 GTTAAA-TGAAAGCTCATAGGA
1 GTTAAACTGAAA-CTCATAAGA
* *
28082788 GCTAAAC-GAAAAC-CTATAAGG
1 GTTAAACTG-AAACTC-ATAAGA
* * *
28082809 GTTAATCTGAAGCTCAAAAGA
1 GTTAAACTGAAACTCATAAGA
* * * *
28082830 GCTAAACTGAAACCCATTAGG
1 GTTAAACTGAAACTCATAAGA
* *
28082851 GTTAAACTGAAGCTCAAAAGA
1 GTTAAACTGAAACTCATAAGA
* * *
28082872 GCTGAACTGAAACT-AGAAGA
1 GTTAAACTGAAACTCATAAGA
* *
28082892 GTTAAAATGAAACTCATATGA
1 GTTAAACTGAAACTCATAAGA
* *
28082913 GTT-AACTGAAGCTCATGAGA
1 GTTAAACTGAAACTCATAAGA
* *
28082933 GCTAAACGGAAA
1 GTTAAACTGAAA
28082945 GCAAAAATGG
Statistics
Matches: 113, Mismatches: 37, Indels: 14
0.69 0.23 0.09
Matches are distributed among these distances:
20 32 0.28
21 76 0.67
22 5 0.04
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (21 bp):
GTTAAACTGAAACTCATAAGA
Found at i:28084460 original size:12 final size:13
Alignment explanation
Indices: 28084454--28084484 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28084444 TTTATTGTTC
28084454 TATTTATTTATCT
1 TATTTATTTATCT
28084467 TATTTATTTAT-T
1 TATTTATTTATCT
28084479 TATTTA
1 TATTTA
28084485 ACTTGGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTATTTATCT
Found at i:28084463 original size:4 final size:4
Alignment explanation
Indices: 28084454--28084484 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
28084444 TTTATTGTTC
28084454 TATT TATT TATCT TATT TATT TATT TATT TA
1 TATT TATT TAT-T TATT TATT TATT TATT TA
28084485 ACTTGGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:28092123 original size:25 final size:25
Alignment explanation
Indices: 28092095--28092173 Score: 140
Period size: 25 Copynumber: 3.2 Consensus size: 25
28092085 TGTAGTGGTA
28092095 AGGTGGCGGCACAGGTGTGGCAAGG
1 AGGTGGCGGCACAGGTGTGGCAAGG
28092120 AGGTGGCGGCACAGGTGTGGCAAGG
1 AGGTGGCGGCACAGGTGTGGCAAGG
* *
28092145 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCGGCACAGGTGTGGCAAGG
28092170 AGGT
1 AGGT
28092174 CAGAGGTTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.20, C:0.14, G:0.51, T:0.15
Consensus pattern (25 bp):
AGGTGGCGGCACAGGTGTGGCAAGG
Found at i:28093612 original size:26 final size:26
Alignment explanation
Indices: 28093529--28093618 Score: 117
Period size: 27 Copynumber: 3.4 Consensus size: 26
28093519 TAAAAGACTG
*
28093529 AAATACCCTCAATGGATAAAAGTATCA
1 AAATACCCTCAATGG-TAAAATTATCA
* * *
28093556 AAATACCCTCGATAAGTAAAATTATCG
1 AAATACCCTCAAT-GGTAAAATTATCA
*
28093583 AAATACCCTCAATGGTAAAATTACCA
1 AAATACCCTCAATGGTAAAATTATCA
28093609 AAATACCCTC
1 AAATACCCTC
28093619 TGTCGAAACC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 20 0.37
27 33 0.61
28 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (26 bp):
AAATACCCTCAATGGTAAAATTATCA
Found at i:28097175 original size:44 final size:42
Alignment explanation
Indices: 28096986--28097182 Score: 166
Period size: 44 Copynumber: 4.5 Consensus size: 42
28096976 TTTAATTCAA
*
28096986 TCCACTGCAAAC-TCAGGGAGATAAGATCC-GCCATCTTTAATCTGC
1 TCCACTGC-AACTTCAGGGAGATAAGA-CCTG--AT-TTGAATCTGC
* * *
28097031 TCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACCTGATT--TGAATCTGC
* * * ** *
28097075 TTCGCTGCAACCTCAGGGAGATAAGACCTGATGCG-ATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGACCTGATTTGAATCTGC
* * * *
28097116 TCTACTGCAATTTCAGAGAGATAAGATCTATGATTTGAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-C-CTGATTTGAATCTGC
28097160 TCCACTGCAACTTCAGGGAGATA
1 TCCACTGCAACTTCAGGGAGATA
28097183 GGATTATTGG
Statistics
Matches: 120, Mismatches: 25, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
41 25 0.21
42 2 0.02
43 6 0.05
44 65 0.54
45 22 0.18
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (42 bp):
TCCACTGCAACTTCAGGGAGATAAGACCTGATTTGAATCTGC
Found at i:28097202 original size:44 final size:44
Alignment explanation
Indices: 28097025--28097204 Score: 122
Period size: 44 Copynumber: 4.2 Consensus size: 44
28097015 GCCATCTTTA
* * * * *
28097025 ATCTGCTCCACTGCAACTTCAGGGGGATAAGA-C-CTGCTTACTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTATGATT--TCG
* * * * * *
28097069 ATCTGCTTCGCTGCAACCTCAGGGAGATAAGA-C-CTGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTATGATTTCG
* * *
28097110 ATCTACTCTACTGCAATTTCAGAGAGATAAGATCTATGATTT-G
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTATGATTTCG
* * *
28097153 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TATTGGTTTCG
1 -ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTA-TGATTTCG
28097198 ATCTGCT
1 ATCTGCT
28097205 TCATTGCCAA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
41 26 0.24
42 1 0.01
43 7 0.06
44 73 0.68
45 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTATGATTTCG
Found at i:28097366 original size:88 final size:88
Alignment explanation
Indices: 28097274--28097470 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 88
28097264 GGAGGCAATA
* ** ** * * * *
28097274 CTGGTGTTTTTGATCTGCTTCGTTGCCAGTACAGGAAGGTAAGATCTGCTATTTTTAACCTACTC
1 CTGGTGCTTTTGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTC
* * *
28097339 CGCT-TCTGCTTAGGGAGATAAGG
66 CACTAT-TGCTCAGGAAGATAAGG
* *
28097362 CTGGTGCTTCTGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCGACCTACTC
1 CTGGTGCTTTTGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTC
28097427 CACTATTGCTCAGGAAGATAAGG
66 CACTATTGCTCAGGAAGATAAGG
* * **
28097450 CTAGTGGTTTAAATCTGCTTC
1 CTGGTGCTTTTGATCTGCTTC
28097471 CCTACTACAT
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
88 88 0.99
89 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (88 bp):
CTGGTGCTTTTGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTC
CACTATTGCTCAGGAAGATAAGG
Found at i:28097487 original size:88 final size:88
Alignment explanation
Indices: 28097395--28098022 Score: 417
Period size: 88 Copynumber: 7.1 Consensus size: 88
28097385 TGCCAGTACA
* * *
28097395 GGAAGACAAGATCTACAATCTTCGACCTACTCCACTATTGCTCAGGAAGATAAGGCTAGTGGTTT
1 GGAAGATAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGTTT
28097460 AAATCTGCTTCCCTACTACATTG
66 AAATCTGCTTCCCTACTACATTG
* * * * * *
28097483 GGAAGATAAGATTCGT-C-GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAA
1 GGAAGATAAGA-TC-TACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAG-GCTAGT-G
* * * * * *
28097545 TTTTCAACCTAC-TCCACTGCTAC-TTAT
62 GTTTAAATCTGCTTCC-CTACTACATT-G
* * * * * *
28097572 GG-AGATAAGGTCTACAATCTTCAACATACTCCATTGCTGCTCAGGGAGATAAGGCTAGTGGCTT
1 GGAAGATAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGTTT
28097636 AAATCTGCTTCCCTACTACATTG
66 AAATCTGCTTCCCTACTACATTG
* * * * * * **
28097659 GGAAGATAAGAT-TCGCATTCTTCGATCTATTCCACTACTGCTTAGGGAGATAAGATCT-GTAAT
1 GGAAGATAAGATCT-ACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAG-GCTAGT-GG
* * * * *
28097722 TTTCAACCTAC-TCCACTACTGC-TCAG
63 TTTAAATCTGCTTCC-CTACTACAT-TG
* * ** *
28097748 GG-AGATAAGGTCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTT
1 GGAAGATAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGTTT
28097812 AAATCTGCTTCCCTACTACATTG
66 AAATCTGCTTCCCTACTACATTG
* ** * * * * * * **
28097835 GGAAGATAAGAT-TCGCCGTTTTCGATCTGCTCCACTACTGCTTAGGGTGATAAGATCT-GTAAT
1 GGAAGATAAGATCT-ACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAG-GCTAGT-GG
* * ** * *
28097898 TTTCAA-CTTAC-TCCACTGTTGC-TCAG
63 TTTAAATC-TGCTTCC-CTACTACAT-TG
* * * * *
28097924 GG-AGATAAGGTCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAAGGCTAGTGGCTT
1 GGAAGATAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGTTT
*
28097988 AAATCTGCTTCCCTACTACCTTG
66 AAATCTGCTTCCCTACTACATTG
*
28098011 GGAAAATAAGAT
1 GGAAGATAAGAT
28098023 TCACCGTCTT
Statistics
Matches: 392, Mismatches: 114, Indels: 68
0.68 0.20 0.12
Matches are distributed among these distances:
86 1 0.00
87 55 0.14
88 279 0.71
89 56 0.14
90 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (88 bp):
GGAAGATAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGTTT
AAATCTGCTTCCCTACTACATTG
Found at i:28097615 original size:176 final size:176
Alignment explanation
Indices: 28097406--28098149 Score: 1070
Period size: 176 Copynumber: 4.2 Consensus size: 176
28097396 GAAGACAAGA
* * * *
28097406 TCTACAATCTTCGACCTACTCCACTATTGCTCAGGAAGATAAGGCTAGTGGTTTAAATCTGCTTC
1 TCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
*
28097471 CCTACTACATTGGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
66 CCTACTACATTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
* * *
28097536 GATCTGTAATTTTCAACCTACTCCACTGCTACTTATGGAGATAAGG
131 GATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
* * *
28097582 TCTACAATCTTCAACATACTCCATTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
1 TCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
** **
28097647 CCTACTACATTGGGAAGATAAGATTCGCATTCTTCGATCTATTCCACTACTGCTTAGGGAGATAA
66 CCTACTACATTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
*
28097712 GATCTGTAATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGG
131 GATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
**
28097758 TCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
1 TCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
* *
28097823 CCTACTACATTGGGAAGATAAGATTCGCCGTTTTCGATCTGCTCCACTACTGCTTAGGGTGATAA
66 CCTACTACATTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
* *
28097888 GATCTGTAATTTTCAACTTACTCCACTGTTGCTCAGGGAGATAAGG
131 GATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
* *
28097934 TCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
1 TCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
* * * **
28097999 CCTACTACCTTGGGAAAATAAGATTCACCGTCTTTAATCTGCTCCACTACTGCTTAGGG-GATAA
66 CCTACTACATTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
* * * *
28098063 GATCTGTAATCTTT-AACCTATTTCACTGAT-ATCCAGGGAGAT-AGG
131 GATCTGTAAT-TTTCAACCTACTCCACTGCTGCT-CAGGGAGATAAGG
* *
28098108 AT-TCACAATCTTCAACATA-TACCACTGCTG-TCCAGGGAGATA
1 -TCT-ACAATCTTCAACCTACT-CCACTACTGCT-CAGGGAGATA
28098150 GGACTTACCA
Statistics
Matches: 515, Mismatches: 47, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
174 7 0.01
175 67 0.13
176 441 0.86
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (176 bp):
TCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
CCTACTACATTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
GATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
Found at i:28097977 original size:44 final size:44
Alignment explanation
Indices: 28097512--28098790 Score: 364
Period size: 44 Copynumber: 29.2 Consensus size: 44
28097502 CTTCGATCTG
* ** *
28097512 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * *
28097556 CTCCACTGCTACTTATGGAGATAAGGTCTACAATCTTCAACATA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * **** * * *
28097600 CTCCATTGCTGCTCAGGGAGATAAGG-CTAGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * * * *
28097643 CTTCC-CTACTACATT-GGGAAGATAAGAT-TCGCATTCTTCGATCTA
1 C-TCCACTACTGC-TTAGGG-AGATAAGGTCT-ACAATCTTCAACCTA
* * ** *
28097688 TTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
*
28097732 CTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
** * **** * * *
28097776 CTCCACTGTTGCTCAGGGAGATAAGG-CTAGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * ** * * * *
28097819 CTTCC-CTACTACATT-GGGAAGATAAGAT-TCGCCGTTTTCGATCTG
1 C-TCCACTACTGC-TTAGGG-AGATAAGGTCT-ACAATCTTCAACCTA
* * ** * *
28097864 CTCCACTACTGCTTAGGGTGATAAGATCTGTAATTTTCAACTTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
** *
28097908 CTCCACTGTTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* **** * * *
28097952 CTCCACTACTGCTTAAGGAGATAAGG-CTAGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * ** * * *
28097995 CTTCC-CTACTACCTT-GGGAAAATAAGAT-TCACCGTCTTTAATCTG
1 C-TCCACTACT-GCTTAGGG-AGATAAGGTCT-ACAATCTTCAACCTA
* ** *
28098040 CTCCACTACTGCTTAGGG-GATAAGATCTGTAATCTTTAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
* * * * *
28098083 TTTCACTGA-T-ATCCAGGGAGAT-AGGAT-TCACAATCTTCAACATA
1 CTCCACT-ACTGCT-TAGGGAGATAAGG-TCT-ACAATCTTCAACCTA
* * * *
28098127 -TACCACTGCTG-TCCAGGGAGAT-AGGACTTACCATCTTCAACCTA
1 CT-CCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * * * *
28098171 TTCCACTACT-ATCCAAGGAGAT-AGGACTTACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * *
28098215 TTCCACTACTG-TCCAGAGAGAT-AGGAT-TCACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCT-ACAATCTTCAACCTA
* * ** *
28098259 TTCTACTACTG-TCTAGGGAGAT-AGAACTTACAATCTTCAACATA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * * *
28098303 TTCCACTGCTG-TCCAGGGAGAT-AGGACTTACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * * * *
28098347 TTTCACTACTG-TCCAGGGAGAT-AGGATTTATAA-CTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCTACAATCTTCAACCTA
* * * * *
28098390 TTCCACTGCT-ATCCAGGGAGAT-AGGAT-T-TAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCTACAATCTTCAACCTA
* * *
28098432 TTCTACTACT-ATCTAGGGAGAT-AGGAT-TCACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCT-ACAATCTTCAACCTA
* * * *
28098476 TTCCACTGCT-ATCTAGGGAGAT-AGGATTTACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCTACAATCTTCAACCTA
* * * * * *
28098520 TTCCACTACT-ATCCAGGGAGAT-AGGACTTACAATATTCAGCCTA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * *
28098564 TTCCACTGCTG-TCCAGGGAGAT-AGGAT-TCACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCT-ACAATCTTCAACCTA
* ** * * * *
28098608 TTCCACTGTTG-TCCAAGGAGAT-AGGACTTACAATCCTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
* * * *
28098652 TTCCACTGCTG-TCTAGGGAGAT-AGGATTTACAATATTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCTACAATCTTCAACCTA
* *
28098696 TTCCACTGCTG-TCTAGGGAGAT-AGGAT-TCACAATCTTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGG-TCT-ACAATCTTCAACCTA
* ** * * *
28098740 TTCCACTGTTG-TCCAGGGAGAT-AGGACTTACAATCCTCAACCTA
1 CTCCACTACTGCT-TAGGGAGATAAGGTC-TACAATCTTCAACCTA
*
28098784 TTCCACT
1 CTCCACT
28098791 GCTGTCCAGG
Statistics
Matches: 996, Mismatches: 182, Indels: 114
0.77 0.14 0.09
Matches are distributed among these distances:
41 3 0.00
42 37 0.04
43 120 0.12
44 774 0.78
45 62 0.06
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
Found at i:28098791 original size:44 final size:44
Alignment explanation
Indices: 28098070--28098809 Score: 992
Period size: 44 Copynumber: 16.9 Consensus size: 44
28098060 TAAGATCTGT
* * * *
28098070 AATCTTTAACCTATTTCACTGATATCCAGGGAGATAGGA-TTCAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTT-AC
* *
28098114 AATCTTCAACATATACCACTGCTGTCCAGGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* * * *
28098158 CATCTTCAACCTATTCCACTACTATCCAAGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* *
28098202 AATCTTCAACCTATTCCACTACTGTCCAGAGAGATAGGA-TTCAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTT-AC
* * * *
28098246 AATCTTCAACCTATTCTACTACTGTCTAGGGAGATAGAACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
*
28098290 AATCTTCAACATATTCCACTGCTGTCCAGGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* * * *
28098334 AATCTTCAACCTATTTCACTACTGTCCAGGGAGATAGGATTTAT
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* *
28098378 AA-CTTCAACCTATTCCACTGCTATCCAGGGAGATAGGA-TT-T
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* * * *
28098419 AATCTTCAACCTATTCTACTACTATCTAGGGAGATAGGA-TTCAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTT-AC
* * *
28098463 AATCTTCAACCTATTCCACTGCTATCTAGGGAGATAGGATTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* *
28098507 AATCTTCAACCTATTCCACTACTATCCAGGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* *
28098551 AATATTCAGCCTATTCCACTGCTGTCCAGGGAGATAGGA-TTCAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTT-AC
* *
28098595 AATCTTCAACCTATTCCACTGTTGTCCAAGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* * *
28098639 AATCCTCAACCTATTCCACTGCTGTCTAGGGAGATAGGATTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
* *
28098683 AATATTCAACCTATTCCACTGCTGTCTAGGGAGATAGGA-TTCAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTT-AC
*
28098727 AATCTTCAACCTATTCCACTGTTGTCCAGGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
*
28098771 AATCCTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA
1 AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA
28098810 TTTATAACTT
Statistics
Matches: 623, Mismatches: 62, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
41 3 0.00
42 37 0.06
43 39 0.06
44 534 0.86
45 10 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTAC
Found at i:28100108 original size:49 final size:50
Alignment explanation
Indices: 28100050--28100148 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
28100040 TTTGGTTTAT
*
28100050 TTTTTATTTTTT-GGACTCAAACAACCCTTTGCGGGTTTTCACCTTGGTC
1 TTTTTATTTTTTAGGAATCAAACAACCCTTTGCGGGTTTTCACCTTGGTC
***
28100099 TTTTTATTTTTTAGGAATCAAAGTGCCCTTTGCGGGTTTTCACCTTGGTC
1 TTTTTATTTTTTAGGAATCAAACAACCCTTTGCGGGTTTTCACCTTGGTC
28100149 CCTTCTCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 12 0.27
50 33 0.73
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (50 bp):
TTTTTATTTTTTAGGAATCAAACAACCCTTTGCGGGTTTTCACCTTGGTC
Found at i:28101039 original size:21 final size:21
Alignment explanation
Indices: 28101015--28101055 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28101005 TCACTTTCAG
28101015 TTTTTGATTTTGATTTTTTTA
1 TTTTTGATTTTGATTTTTTTA
*
28101036 TTTTTTATTTTGATTTTTTT
1 TTTTTGATTTTGATTTTTTT
28101056 GATGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTGATTTTGATTTTTTTA
Found at i:28102115 original size:25 final size:25
Alignment explanation
Indices: 28102065--28102130 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
28102055 AAGAAAATCC
*
28102065 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
*
28102090 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
28102115 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
28102131 TGTATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 3 0.08
25 23 0.64
26 5 0.14
27 5 0.14
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:28106887 original size:18 final size:18
Alignment explanation
Indices: 28106866--28106907 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
28106856 TTATAATCAC
28106866 AAAATAACAA-ATAAAAAT
1 AAAATAA-AATATAAAAAT
*
28106884 AAAATAAAATATTAAAAT
1 AAAATAAAATATAAAAAT
28106902 AAAATA
1 AAAATA
28106908 TGTTATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAATATAAAAAT
Found at i:28106906 original size:13 final size:13
Alignment explanation
Indices: 28106874--28106908 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28106864 ACAAAATAAC
28106874 AAATAAAA-A-TA
1 AAATAAAATATTA
28106885 AAATAAAATATTA
1 AAATAAAATATTA
28106898 AAATAAAATAT
1 AAATAAAATAT
28106909 GTTATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAAATATTA
Found at i:28107347 original size:27 final size:27
Alignment explanation
Indices: 28107308--28107595 Score: 247
Period size: 27 Copynumber: 10.7 Consensus size: 27
28107298 TGGGTATTAC
* * *
28107308 ACCCTCTATGGGTAAAATTACTGAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* * *
28107335 ACCATCGATGGGTAAAATTACCAAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* * * *
28107362 ACCC-CTAAAAGATAAAATTACTGAAAT
1 ACCCTC-GAAGGGTAAAATTACCGAAAT
* * **
28107389 ACCCCCAAAGGGTAAAATTACTAAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
**
28107416 ATTCTCGAAGGGTAAAATTACCGAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* * * **
28107443 ATCCACGAAAGGTAAAACAACCGAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* *
28107470 ACCCCCGAAGGGTAAAATTACCAAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* * * *
28107497 ACCCTGGATGGGTAAAACTATCGAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
* * *
28107524 ACTCTCGAAGGGTAAAATTATCAAAAT
1 ACCCTCGAAGGGTAAAATTACCGAAAT
*
28107551 TCCCTC-AATGGGTAAAATTACCGAAAT
1 ACCCTCGAA-GGGTAAAATTACCGAAAT
* *
28107578 ACCCCCGTAGGGTAAAAT
1 ACCCTCGAAGGGTAAAAT
28107596 AATTGTTGTA
Statistics
Matches: 208, Mismatches: 49, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
26 3 0.01
27 203 0.98
28 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (27 bp):
ACCCTCGAAGGGTAAAATTACCGAAAT
Found at i:28109055 original size:26 final size:27
Alignment explanation
Indices: 28109019--28109078 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
28109009 CCTACAGTAG
28109019 TTTCAGAATATCATAACATATATCA-A
1 TTTCAGAATATCATAACATATATCAGA
* *
28109045 TTTCAGAATATCATAGCATGTATCAGA
1 TTTCAGAATATCATAACATATATCAGA
28109072 TTT-AGAA
1 TTTCAGAA
28109079 CGCTTACAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (27 bp):
TTTCAGAATATCATAACATATATCAGA
Found at i:28125048 original size:40 final size:40
Alignment explanation
Indices: 28125000--28125200 Score: 269
Period size: 40 Copynumber: 5.0 Consensus size: 40
28124990 TTATTCTCTA
*
28125000 AATGCATATACGTGCCCCTGTTTGTACTTCGATACCCCTG
1 AATGCATATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* **
28125040 AATACATATGTGTGCCCCTGTTTGTACTTCGGTACCCCTG
1 AATGCATATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
28125080 AATGCACATACATGCCCTTGTTTGTACTTCGGTACCCTTG
1 AATGCATATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
*
28125120 AATGC-TCATTCGTGCCCCTGTTTGTACTTCGGTACCCCTG
1 AATGCAT-ATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * **
28125160 AATGCACATACGTGCCCCTGTTTATACTTCAATACCCCTG
1 AATGCATATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
28125200 A
1 A
28125201 GTAGGGGTGA
Statistics
Matches: 138, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (40 bp):
AATGCATATACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:28125077 original size:20 final size:20
Alignment explanation
Indices: 28125054--28125159 Score: 65
Period size: 20 Copynumber: 5.3 Consensus size: 20
28125044 CATATGTGTG
28125054 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * * *
28125074 CCCCTGAATGCACATAC-ATG
1 CCCCTGTTTGTAC-TTCGGTA
*
28125094 CCCTTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* ** *
28125114 CCCTTGAATGCT-CATTC-GTG
1 CCCCTGTTTG-TAC-TTCGGTA
28125134 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
28125154 CCCCTG
1 CCCCTG
28125160 AATGCACATA
Statistics
Matches: 60, Mismatches: 20, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
19 6 0.10
20 48 0.80
21 6 0.10
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.35
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:28125135 original size:80 final size:80
Alignment explanation
Indices: 28125000--28125200 Score: 298
Period size: 80 Copynumber: 2.5 Consensus size: 80
28124990 TTATTCTCTA
*
28125000 AATGCATATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATACATATGTGTGCCCCTGTTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATACATATGTGTGCCCCTGTTTGT
28125065 ACTTCGGTACCCCTG
66 ACTTCGGTACCCCTG
* * * * *
28125080 AATGCACATACATGCCCTTGTTTGTACTTCGGTACCCTTGAATGC-TCAT-TCGTGCCCCTGTTT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATACAT-ATGT-GTGCCCCTGTTT
28125143 GTACTTCGGTACCCCTG
64 GTACTTCGGTACCCCTG
* *
28125160 AATGCACATACGTGCCCCTGTTTATACTTCAATACCCCTGA
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGA
28125201 GTAGGGGTGA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 2 0.02
80 105 0.98
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (80 bp):
AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATACATATGTGTGCCCCTGTTTGT
ACTTCGGTACCCCTG
Found at i:28125489 original size:19 final size:19
Alignment explanation
Indices: 28125465--28125508 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28125455 TAAAAGCAAC
28125465 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
28125484 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
28125503 ACAACA
1 ACAACA
28125509 AAAATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:28127928 original size:4 final size:4
Alignment explanation
Indices: 28127919--28127973 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
28127909 CAGCAAAGAT
28127919 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
28127967 ATAC ATA
1 ATAC ATA
28127974 TATATAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:28129020 original size:21 final size:21
Alignment explanation
Indices: 28128954--28129025 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 21
28128944 TGAGAGATTA
28128954 AAGGAGGAAGAAATACAGTGT
1 AAGGAGGAAGAAATACAGTGT
28128975 AAGGA--AATGAATGATGGATCAGTGT
1 AAGGAGGAA-GAA--AT--A-CAGTGT
28129000 AAGGAGGAAGAAATACAGTGT
1 AAGGAGGAAGAAATACAGTGT
28129021 AAGGA
1 AAGGA
28129026 AAGGAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 16 0.37
22 3 0.07
24 3 0.07
25 11 0.26
26 3 0.07
27 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.33, T:0.17
Consensus pattern (21 bp):
AAGGAGGAAGAAATACAGTGT
Found at i:28129146 original size:14 final size:14
Alignment explanation
Indices: 28129127--28129160 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28129117 CGGAGGACCA
28129127 GAGGTGGATCGGTG
1 GAGGTGGATCGGTG
*
28129141 GAGGTGGATTGGTG
1 GAGGTGGATCGGTG
28129155 GAGGTG
1 GAGGTG
28129161 AAGGTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.59, T:0.24
Consensus pattern (14 bp):
GAGGTGGATCGGTG
Found at i:28129279 original size:29 final size:30
Alignment explanation
Indices: 28129237--28129296 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
28129227 TTTGTTTTAA
28129237 ATGTAGTGCATTTTAAAAAT-AAAAAATAT
1 ATGTAGTGCATTTTAAAAATAAAAAAATAT
*
28129266 ATGTAGTGTATTTTAAAAATAAAAAAATAT
1 ATGTAGTGCATTTTAAAAATAAAAAAATAT
28129296 A
1 A
28129297 GTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (30 bp):
ATGTAGTGCATTTTAAAAATAAAAAAATAT
Found at i:28131799 original size:27 final size:27
Alignment explanation
Indices: 28131769--28131820 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
28131759 TTCCTTTCCT
*
28131769 TAGATCGCCACAAAGGCTTCCATTTCA
1 TAGATCGCCACAAAGGCATCCATTTCA
** *
28131796 TAGATTTCCAGAAAGGCATCCATTT
1 TAGATCGCCACAAAGGCATCCATTT
28131821 TCTGGTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (27 bp):
TAGATCGCCACAAAGGCATCCATTTCA
Found at i:28135835 original size:13 final size:14
Alignment explanation
Indices: 28135802--28135838 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
28135792 AAAAAGGCAA
28135802 TTAATAAATAAAAT
1 TTAATAAATAAAAT
28135816 TCT-ATAAA-AAAAT
1 T-TAATAAATAAAAT
28135829 TTAATAAATA
1 TTAATAAATA
28135839 GATAGGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.05
13 11 0.55
14 7 0.35
15 1 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAATAAATAAAAT
Found at i:28144061 original size:24 final size:24
Alignment explanation
Indices: 28144002--28144064 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
28143992 ATATTAGACT
* * *
28144002 AAAAATTATTATAAAAAAATTAAA
1 AAAAATAATTTTAAAAAAATAAAA
**
28144026 AATCATAATTTTAAAAAAATAAAA
1 AAAAATAATTTTAAAAAAATAAAA
*
28144050 AAAAATATTTTTAAA
1 AAAAATAATTTTAAA
28144065 TATGTATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAATAATTTTAAAAAAATAAAA
Found at i:28144612 original size:37 final size:37
Alignment explanation
Indices: 28144565--28144638 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
28144555 ATTATTTGAG
*
28144565 AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
1 AAAGAATTTAAGGGATAATTAAGCCTTAATTTAAGTA
28144602 AAAGAATTTAAGGGATAATTAAGCCTTAATTTAAGTA
1 AAAGAATTTAAGGGATAATTAAGCCTTAATTTAAGTA
28144639 GTGGGACGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (37 bp):
AAAGAATTTAAGGGATAATTAAGCCTTAATTTAAGTA
Found at i:28145681 original size:21 final size:21
Alignment explanation
Indices: 28145655--28145711 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28145645 TGGGTGGATT
* *
28145655 AGCTCTCACGAGCTTCTATTC
1 AGCTCTTACGAGCTTCTATTA
*
28145676 AGCTCTTACGAGATTCTATTA
1 AGCTCTTACGAGCTTCTATTA
*
28145697 AGCTCTTATGAGCTT
1 AGCTCTTACGAGCTT
28145712 TTGTTGGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTATTA
Found at i:28147475 original size:20 final size:20
Alignment explanation
Indices: 28147450--28147595 Score: 93
Period size: 20 Copynumber: 7.3 Consensus size: 20
28147440 ATGCATTTAC
*
28147450 GGGCACCGAAGTACAAACAG
1 GGGCACCGAAGTACAATCAG
* * *
28147470 GGGCA-CGTATGTGCATTCAG
1 GGGCACCG-AAGTACAATCAG
*
28147490 GGGTACCGAAGTACAATCAG
1 GGGCACCGAAGTACAATCAG
*** * *
28147510 GGGCACATTTA-TACATTTAG
1 GGGCAC-CGAAGTACAATCAG
*
28147530 GGGTACCGAAGTACAATCAG
1 GGGCACCGAAGTACAATCAG
* * *
28147550 GGGCA-CGTATGTGCATTCAG
1 GGGCACCG-AAGTACAATCAG
*
28147570 GGGTACCGAAGTACAAAT-AG
1 GGGCACCGAAGTAC-AATCAG
28147590 GGGCAC
1 GGGCAC
28147596 GTTTGTGCAT
Statistics
Matches: 90, Mismatches: 29, Indels: 14
0.68 0.22 0.11
Matches are distributed among these distances:
19 5 0.06
20 78 0.87
21 7 0.08
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (20 bp):
GGGCACCGAAGTACAATCAG
Found at i:28147498 original size:40 final size:40
Alignment explanation
Indices: 28147436--28147648 Score: 257
Period size: 40 Copynumber: 5.3 Consensus size: 40
28147426 TCAAGAGCAT
* * * *
28147436 GTATATGCATTTACGGGCACCGAAGTACAAACAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
*
28147476 GTATGTGCATTCAGGGGTACCGAAGTACAATCAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* * * * * *
28147516 ATTTATACATTTAGGGGTACCGAAGTACAATCAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
*
28147556 GTATGTGCATTCAGGGGTACCGAAGTACAAATAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* * * * *
28147596 GTTTGTGCATTCAGAGGTGCTGAAGTACAAACAAGGGCA-
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
28147635 GCTATGTGCATTCA
1 G-TATGTGCATTCA
28147649 CACAATAATT
Statistics
Matches: 148, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 147 0.99
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (40 bp):
GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
Found at i:28147621 original size:120 final size:120
Alignment explanation
Indices: 28147405--28147634 Score: 300
Period size: 120 Copynumber: 1.9 Consensus size: 120
28147395 ATATAATGTT
* * *
28147405 TTTAGAGGTACCATAGTATAATCAAGAGCATGTATATGCATTTACGGGCACCGAAGTACAAACAG
1 TTTAGAGGTACCATAGTACAATCAAGAGCACGTATATGCATTCACGGGCACCGAAGTACAAACAG
* * *
28147470 GGGCACGTATGTGCATTCAGGGGTACCGAAGTACAATCAGGGGCACATTTATACA
66 GGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAAGGGCACATTTATACA
* * * * * * *
28147525 TTTAGGGGTACCGA-AGTACAATCAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAATA
1 TTTAGAGGTACC-ATAGTACAATCAAGAGCACGTATATGCATTCACGGGCACCGAAGTACAAACA
* * *
28147589 GGGGCACGTTTGTGCATTCAGAGGTGCTGAAGTACAAACAAGGGCA
65 GGGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAAGGGCA
28147635 GCTATGTGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
120 92 0.99
121 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (120 bp):
TTTAGAGGTACCATAGTACAATCAAGAGCACGTATATGCATTCACGGGCACCGAAGTACAAACAG
GGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAAGGGCACATTTATACA
Found at i:28161610 original size:40 final size:39
Alignment explanation
Indices: 28161579--28161788 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
28161569 GGACTAAGAT
* *
28161579 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28161619 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28161659 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
28161699 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
28161739 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28161778 CCGAAGGCATT
1 CCGAAGGCATT
28161789 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28161742 original size:120 final size:120
Alignment explanation
Indices: 28161526--28161788 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
28161516 TTGAATGCTG
* *
28161526 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28161590 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28161646 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
28161709 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28161765 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28161789 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28161808 original size:79 final size:80
Alignment explanation
Indices: 28161579--28161823 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
28161569 GGACTAAGAT
* * * * * * * ** *
28161579 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
28161642 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
28161659 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
28161724 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
28161739 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
28161803 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
28161817 CCGAAGG
1 CCGAAGG
28161824 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:28168936 original size:101 final size:101
Alignment explanation
Indices: 28168748--28168934 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 101
28168738 GAACATGTTG
* * *
28168748 GGCTGAGTAACCGGGGTACGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTT
1 GGCTGAGTAACCGGGGTACGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTAGATATGTC
*
28168813 CTTAAGAAAAAAATATAATAAATTAGGAGTCTACTA
66 CTAAAGAAAAAAATATAATAAATTAGGAGTCTACTA
** * *
28168849 GGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTTTCTTCGTGTCAAAAGGTTCAGTATAT-
1 GGCTGAGTAACCGGGGTACGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTT-AG-ATATG
28168913 TCCTAAAGCATAAAAAATATAA
64 TCCTAAAG-A-AAAAAATATAA
28168935 ATAATAAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
101 52 0.70
102 7 0.09
103 4 0.05
104 11 0.15
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (101 bp):
GGCTGAGTAACCGGGGTACGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTAGATATGTC
CTAAAGAAAAAAATATAATAAATTAGGAGTCTACTA
Found at i:28168951 original size:23 final size:22
Alignment explanation
Indices: 28168924--28168979 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
28168914 CCTAAAGCAT
* *
28168924 AAAAAATATAAATAATAAATAA
1 AAAAAATATAAATAAAAAAGAA
28168946 ATAAAAATCA-AAATAAAAAAGAA
1 A-AAAAAT-ATAAATAAAAAAGAA
28168969 AAAAAATATAA
1 AAAAAATATAA
28168980 TTTGGGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 18 0.62
24 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAAATATAAATAAAAAAGAA
Found at i:28171543 original size:843 final size:842
Alignment explanation
Indices: 28169875--28171562 Score: 2973
Period size: 843 Copynumber: 2.0 Consensus size: 842
28169865 TATTGAGATA
28169875 ATTATTAAGGATTATTTTTAGGATTTTATTTTATTTATCTTTATTATCTTCAATTAAATGTATTT
1 ATTATTAAGGATTATTTTTAGGATTTTATTTTATTTATCTTTATTATCTTCAATTAAATGTATTT
* *
28169940 ATCTTTTAGGAATTTAAGTAGGATTAGACTATCTCCCCTAGCACTATAAATAGGGGGTGAAGTGA
66 ATCTTTTAGGAATTTAAGTAGGAATAGACTATCTCCCCTAGCACTATAAATAGGGGGTGAAATGA
* *
28170005 CTCAAAAGAGATCACTCTTTTTCTATAAACACTCTGTCCCCAAAATTCTAGGCTTTTGTTCTTCT
131 CTCAAAAGAGATCACTCTTTTTCTATAAACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
*
28170070 CATATTTCCTTTCAATAAAATCTCTATTGTTATTTTATTTATTTTCTTTTCTACCACAACTATGA
196 CATATTTCCTTTCAATAAAATCTCTATTGTTATTTTATTTATTTTCTTTTCTACCACAACCATGA
28170135 GCCACTAAACCCATCTAGCTGAAGGTTGTCGAAAATCCCTGAAAGGGTTCATGAGGCTTAGAATC
261 GCCACTAAACCCATCTAGCTGAAGGTTGTCGAAAATCCCTGAAAGGGTTCATGAGGCTTAGAATC
* * *
28170200 TGTACTTAGCCTTCTTAACGAGTATTCATCGTTTCTTCGCACTACAGGGCTAACGCTTCCGTCCA
326 TGTACTTAGCCTTCTCAACGAGTATTCATCGTTTCTCCGCACTACAGGGCTAACACTTCCGTCCA
*
28170265 TGTCCCTTGAGAAGTAAGCTTTTCAACGTATGCAAAGGCGGCCGCTTTGTATGTTTTGGAAAGGT
391 TGTCCCTTGAGAAGTAAGATTTTCAACGTATGCAAAGGCGGCCGCTTTGTATGTTTTGGAAAGGT
* * *
28170330 TGCACAGTCGGTTCGTTAGCTTACTGCTCTAGAGGTTGGCGAGCCCAAGAGACAAAATGGCGTGG
456 TGCACAGTCGGTTCGTTAGCTTACTGCGCCAGAGGTTGGCGAGCCCAAGAGACAAAATGGAGTGG
*
28170395 GATTCACCATTGAGAAGCGCTGATGTAGCATAAGACGATCCCACAAAAGCGATTGTTGGCTAGAG
521 GATTCACCATTGAGAAGCGCTGATCTAGCATAAGACGATCCCACAAAAGCGATTGTTGGCTAGAG
* ** * *
28170460 TTAGGTTCCACCAAATCGTAAGTCCAAATCCTTGGAGCTAGTGGTTGTAGGCATCCTCTTCCACT
586 TCAGGTTCCACCAAATCACAAGTCCAAATCCTTGGAACTAGTGGTCGTAGGCATCCTCTTCCACT
* *
28170525 ATATCCGGCTTATTCAGTTTGGGAAGGATCATCTAAAAGCTGAGGATTGAACCCAAGGCGGAACG
651 ATAACCGGCTTATTCAGTTTGGGAAGGATCATCTAAAAGCTGAGGATTGAACCCAAGGCGAAACG
28170590 AGACAACTGGAGGCTGGAATCTCCCATAAAAATTTCCTTTCTCTCAACTCTATTTTTAATTTCTC
716 AGACAACTGGAGGCTGGAATCTCCCATAAAAATTTCCTTTCTCTCAACTCTATTTTTAATTTCTC
* * *
28170655 TAATTTTTGATTCAATATTCTTAATTCTGTTTTTATTTTATTTTTCGTTTTCAAATCCAAAC
781 TAATTTTCGATTCAATATTCTTAATTCTATTTTTATTTTATTTTTCGTCTTCAAATCCAAAC
*
28170717 ATTATTAAGGATTATTTTTAGGATTTTATTTTATTTATGTTTATTTATCTTCAATTAAATGTATT
1 ATTATTAAGGATTATTTTTAGGATTTTATTTTATTTATCTTTA-TTATCTTCAATTAAATGTATT
28170782 TATCTTTTAGGAATTTAAGTAGGAATAGACTATCTCCCCTAGCACTATAAATAGGGGGTGAAATG
65 TATCTTTTAGGAATTTAAGTAGGAATAGACTATCTCCCCTAGCACTATAAATAGGGGGTGAAATG
* *
28170847 ACTCAAAAGAGATCACTCTTTTTCTGTAAACACTTTCTCCCCAAAAGTCTAGGCTTTTGTTCTTC
130 ACTCAAAAGAGATCACTCTTTTTCTATAAACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTC
*
28170912 TCATATTTCCTTTCAATAAAATCTCTATTGTTATTTTATTTATTTTCTTTTCTACCCCAACCATG
195 TCATATTTCCTTTCAATAAAATCTCTATTGTTATTTTATTTATTTTCTTTTCTACCACAACCATG
28170977 AGCCACTAAACCCATCTAGCTGAAGGTTGTCGAAAATCCCTGAAAGGGTTCATGAGGCTTAGAAT
260 AGCCACTAAACCCATCTAGCTGAAGGTTGTCGAAAATCCCTGAAAGGGTTCATGAGGCTTAGAAT
*
28171042 CTGTACTTAGCCTTCTCAACGAGTATTCATCGTTTCTCCGCACTA-AGGGGCTGACACTTCCGTC
325 CTGTACTTAGCCTTCTCAACGAGTATTCATCGTTTCTCCGCACTACA-GGGCTAACACTTCCGTC
* *
28171106 CATGTCCCTTGAGAAGTAAGATTTTCAACGTATGCAAAGGCGGTCGCTTTGTATGTTTTGGGAAG
389 CATGTCCCTTGAGAAGTAAGATTTTCAACGTATGCAAAGGCGGCCGCTTTGTATGTTTTGGAAAG
* *
28171171 GTTGCACAGTCTGTTCGTTAGCTTACTGCGCCAGAGGTTGGCGATCCCAAGAGACAAAATGGAGT
454 GTTGCACAGTCGGTTCGTTAGCTTACTGCGCCAGAGGTTGGCGAGCCCAAGAGACAAAATGGAGT
* *
28171236 GGGATTCACCATTGAGAAGCGTTTATCTAGCATAAGACGATCCCACAAAAGCGATTGTTGGCTAG
519 GGGATTCACCATTGAGAAGCGCTGATCTAGCATAAGACGATCCCACAAAAGCGATTGTTGGCTAG
* * *
28171301 AGTCAGGTTCCACCAAATCACAAGTCTAAATTCTTGGAACTGGTGGTCGTAGGCATCCTCTTCCA
584 AGTCAGGTTCCACCAAATCACAAGTCCAAATCCTTGGAACTAGTGGTCGTAGGCATCCTCTTCCA
* *
28171366 CTATAACTGGCTTATTCAGTTTGGTAAGGATCATCTAAAAGCTGAGGATTGAACCCAAGGCGAAA
649 CTATAACCGGCTTATTCAGTTTGGGAAGGATCATCTAAAAGCTGAGGATTGAACCCAAGGCGAAA
* *
28171431 CGAGACAACTGGAGGCTGGAATCTCCCATAAGAATTTCTTTTCTCTCAACTCTATTTTTAATTTC
714 CGAGACAACTGGAGGCTGGAATCTCCCATAAAAATTTCCTTTCTCTCAACTCTATTTTTAATTTC
*
28171496 TCTAATTTTCGATTCAATATTCTTAATTCTATTTTTATTTTATTTTTCGTCTTCAGATCCAAAC
779 TCTAATTTTCGATTCAATATTCTTAATTCTATTTTTATTTTATTTTTCGTCTTCAAATCCAAAC
28171560 ATT
1 ATT
28171563 TAATTCTATT
Statistics
Matches: 802, Mismatches: 42, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
842 43 0.05
843 759 0.95
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (842 bp):
ATTATTAAGGATTATTTTTAGGATTTTATTTTATTTATCTTTATTATCTTCAATTAAATGTATTT
ATCTTTTAGGAATTTAAGTAGGAATAGACTATCTCCCCTAGCACTATAAATAGGGGGTGAAATGA
CTCAAAAGAGATCACTCTTTTTCTATAAACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
CATATTTCCTTTCAATAAAATCTCTATTGTTATTTTATTTATTTTCTTTTCTACCACAACCATGA
GCCACTAAACCCATCTAGCTGAAGGTTGTCGAAAATCCCTGAAAGGGTTCATGAGGCTTAGAATC
TGTACTTAGCCTTCTCAACGAGTATTCATCGTTTCTCCGCACTACAGGGCTAACACTTCCGTCCA
TGTCCCTTGAGAAGTAAGATTTTCAACGTATGCAAAGGCGGCCGCTTTGTATGTTTTGGAAAGGT
TGCACAGTCGGTTCGTTAGCTTACTGCGCCAGAGGTTGGCGAGCCCAAGAGACAAAATGGAGTGG
GATTCACCATTGAGAAGCGCTGATCTAGCATAAGACGATCCCACAAAAGCGATTGTTGGCTAGAG
TCAGGTTCCACCAAATCACAAGTCCAAATCCTTGGAACTAGTGGTCGTAGGCATCCTCTTCCACT
ATAACCGGCTTATTCAGTTTGGGAAGGATCATCTAAAAGCTGAGGATTGAACCCAAGGCGAAACG
AGACAACTGGAGGCTGGAATCTCCCATAAAAATTTCCTTTCTCTCAACTCTATTTTTAATTTCTC
TAATTTTCGATTCAATATTCTTAATTCTATTTTTATTTTATTTTTCGTCTTCAAATCCAAAC
Found at i:28181537 original size:21 final size:21
Alignment explanation
Indices: 28181511--28181565 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
28181501 AACAGTGGTG
*
28181511 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
28181532 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
28181553 GCGGTGAGATTAG
1 GCGGTGAGATTAG
28181566 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:28185499 original size:16 final size:16
Alignment explanation
Indices: 28185460--28185500 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
28185450 TTCTCCATTC
28185460 CCATCTCCCCTCTTCCA
1 CCAT-TCCCCTCTTCCA
*
28185477 TCATTCCCCTCTTCCA
1 CCATTCCCCTCTTCCA
*
28185493 CCGTTCCC
1 CCATTCCC
28185501 TCCTCCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.56, G:0.02, T:0.32
Consensus pattern (16 bp):
CCATTCCCCTCTTCCA
Found at i:28185544 original size:60 final size:59
Alignment explanation
Indices: 28185480--28185662 Score: 223
Period size: 60 Copynumber: 3.1 Consensus size: 59
28185470 TCTTCCATCA
* *
28185480 TTCCCCTCTTCCACCGTTCCCTCCTCCCATTTCCTATTCCCATGCAATACCCATTCCAAT
1 TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCC-AT
* * * *
28185540 TT-CCC-ATTCCACCGTGCCGTCCTCCCATTTCCCATTCCCAT-C--TCCCCTCTTCCAT
1 TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCC-ATTCCAT
28185595 CGATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCCAT
1 ---TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATT-CCAT
28185658 TTCCC
1 TTCCC
28185663 ATTTCCCATT
Statistics
Matches: 103, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
55 6 0.06
56 4 0.04
57 1 0.01
58 34 0.33
59 6 0.06
60 41 0.40
61 1 0.01
62 2 0.02
63 8 0.08
ACGTcount: A:0.14, C:0.49, G:0.05, T:0.32
Consensus pattern (59 bp):
TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCAT
Found at i:28185573 original size:28 final size:28
Alignment explanation
Indices: 28185538--28185637 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
28185528 ACCCATTCCA
*
28185538 ATTTCCCATTCCACCGTGCCGTCCTCCC
1 ATTTCCCATTCCACCGTGCCCTCCTCCC
* * *
28185566 ATTTCCCATTCCCATC-TCCCCTCTTCCATC
1 ATTTCCCATT-CCACCGTGCCCTCCTCC--C
* *
28185596 GATTCCCCTCTTCCACCGTGCCCTCCTCCC
1 -ATTTCCC-ATTCCACCGTGCCCTCCTCCC
28185626 ATTTCCCATTCC
1 ATTTCCCATTCC
28185638 CATGCAATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 22 0.40
29 10 0.18
30 2 0.04
31 10 0.18
32 11 0.20
ACGTcount: A:0.11, C:0.51, G:0.06, T:0.32
Consensus pattern (28 bp):
ATTTCCCATTCCACCGTGCCCTCCTCCC
Found at i:28185660 original size:118 final size:118
Alignment explanation
Indices: 28185448--28185665 Score: 393
Period size: 118 Copynumber: 1.8 Consensus size: 118
28185438 ATACAATGCA
*
28185448 ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCATTTC
1 ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTC
*
28185513 CTATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
66 CCATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
28185566 ATTTC-CCATTCCCATCTCCCCTCTTCCATCGATTCCCCTCTTCCACCGTGCCCTCCTCCCATTT
1 ATTTCTCCATTCCCATCTCCCCTCTTCCATC-ATTCCCCTCTTCCACCGTGCCCTCCTCCCATTT
*
28185630 CCCATTCCCATGCAATACCCATTCCCATTTCCCATT
65 CCCATTCCCATGCAATACCCATTCCAATTTCCCATT
28185666 TCCCATTCCC
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
117 25 0.26
118 71 0.74
ACGTcount: A:0.15, C:0.48, G:0.04, T:0.33
Consensus pattern (118 bp):
ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTC
CCATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
Found at i:28185663 original size:7 final size:6
Alignment explanation
Indices: 28185622--28185684 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
28185612 CGTGCCCTCC
* * *
28185622 TCCCATT TCCCAT TCCCA- TGCAAT ACCCAT TCCCATT TCCCATT TCCCAT
1 TCCCA-T TCCCAT TCCCAT TCCCAT TCCCAT TCCCA-T TCCCA-T TCCCAT
28185672 TCCCAT TCCCAT T
1 TCCCAT TCCCAT T
28185685 ATCAACAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
5 3 0.06
6 27 0.56
7 18 0.38
ACGTcount: A:0.19, C:0.44, G:0.02, T:0.35
Consensus pattern (6 bp):
TCCCAT
Found at i:28190053 original size:9 final size:9
Alignment explanation
Indices: 28190004--28190072 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
28189994 CAATAAATGC
*
28190004 TATAAATAT
1 TATAAAAAT
*
28190013 TATTAAAATT
1 TA-TAAAAAT
28190023 TAATAAAAAT
1 T-ATAAAAAT
*
28190033 TA-AAATA-
1 TATAAAAAT
28190040 T-TAAAAAT
1 TATAAAAAT
*
28190048 TATAAAAAA
1 TATAAAAAT
28190057 TATAAAAAT
1 TATAAAAAT
*
28190066 TGTAAAA
1 TATAAAA
28190073 TAAAATATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
7 5 0.11
8 5 0.11
9 23 0.49
10 13 0.28
11 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (9 bp):
TATAAAAAT
Found at i:28190055 original size:18 final size:18
Alignment explanation
Indices: 28190034--28190226 Score: 63
Period size: 19 Copynumber: 9.9 Consensus size: 18
28190024 AATAAAAATT
28190034 AAAATATTAAAAATTATAA
1 AAAATA-TAAAAATTATAA
*
28190053 AAAATATAAAAATTGTAAAA
1 AAAATATAAAAA-T-TATAA
*
28190073 TAAAATATAAAAAATTTTAA
1 -AAAATAT-AAAAATTATAA
** *
28190093 AATTTTATCAAAATCT-TAA
1 AA-AATATAAAAAT-TATAA
28190112 AAAACTAT-AAAATCTATAGA
1 AAAA-TATAAAAAT-TATA-A
* *
28190132 AATATAAAAAAAGTTAT-A
1 AAAATATAAAAA-TTATAA
* * * *
28190150 AAATTTTATAAAGTCATAA
1 AAAATATA-AAAATTATAA
28190169 GAAAATTATACAAAATGTA-AA
1 -AAAA-TATA-AAAAT-TATAA
* *
28190190 GAAATAT-AAATTTCATAAA
1 AAAATATAAAAATT-AT-AA
28190209 AAAATTATAAAAATTATA
1 AAAA-TATAAAAATTATA
28190227 GTACCAAAAG
Statistics
Matches: 128, Mismatches: 25, Indels: 42
0.66 0.13 0.22
Matches are distributed among these distances:
16 1 0.01
17 5 0.04
18 21 0.16
19 39 0.30
20 33 0.26
21 23 0.18
22 6 0.05
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAATATAAAAATTATAA
Found at i:28190055 original size:25 final size:26
Alignment explanation
Indices: 28189956--28190063 Score: 78
Period size: 25 Copynumber: 4.0 Consensus size: 26
28189946 CCCATGCATT
*
28189956 TATTAAAAATTAGAAAAAGAATTATAAAA
1 TATTAAAAATTA-ATAAA-AA-TATAAAA
* * **
28189985 AATT-AAAATCAATAAATGCTATAAATA
1 TATTAAAAATTAATAAA-AATATAAA-A
*
28190012 TTATTAAAATTTAATAAAAAT-TAAAA
1 -TATTAAAAATTAATAAAAATATAAAA
28190038 TATTAAAAATT-ATAAAAAATATAAAA
1 TATTAAAAATTAAT-AAAAATATAAAA
28190064 ATTGTAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
24 2 0.03
25 16 0.26
26 12 0.19
27 9 0.15
28 10 0.16
29 13 0.21
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
TATTAAAAATTAATAAAAATATAAAA
Found at i:28190075 original size:23 final size:22
Alignment explanation
Indices: 28190049--28190095 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28190039 ATTAAAAATT
28190049 ATAAAAAATATAAAAATTGTAAA
1 ATAAAAAATA-AAAAATTGTAAA
* *
28190072 ATAAAATATAAAAAATTTTAAA
1 ATAAAAAATAAAAAATTGTAAA
28190094 AT
1 AT
28190096 TTTATCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAAAAATAAAAAATTGTAAA
Found at i:28190112 original size:29 final size:28
Alignment explanation
Indices: 28190072--28190178 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 28
28190062 AAATTGTAAA
* *
28190072 ATAAAAT-ATAAAAAATTTTAAAATTTT
1 ATAAAATCTTAAAAAATTATAAAATTTT
* *
28190099 ATCAAAATCTTAAAAAACTATAAAA-TCT
1 AT-AAAATCTTAAAAAATTATAAAATTTT
* *
28190127 ATAGAAATATAAAAAAAGTTATAAAATTTT
1 ATA-AAATCTTAAAAAA-TTATAAAATTTT
* *
28190157 ATAAAGTCATAAGAAAATTATA
1 ATAAAATCTTAA-AAAATTATA
28190179 CAAAATGTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
27 3 0.05
28 20 0.32
29 30 0.48
30 9 0.15
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAAAATCTTAAAAAATTATAAAATTTT
Found at i:28190154 original size:58 final size:58
Alignment explanation
Indices: 28190033--28190199 Score: 148
Period size: 58 Copynumber: 2.9 Consensus size: 58
28190023 TAATAAAAAT
* * * * *
28190033 TAAAATATTA-AAAATTATAA-AAAA-TATAAAAATTGTAAA-ATAAAATATAAAAAATTT
1 TAAAATTTTATAAAATCATAAGAAAACTATAAAAA-TCTAAAGA-AATATA-AAAAAATTA
* *
28190090 TAAAATTTTATCAAAATCTTAA-AAAACTAT-AAAATCTATAGAAATATAAAAAAAGTTA
1 TAAAATTTTAT-AAAATCATAAGAAAACTATAAAAATCTAAAGAAATATAAAAAAA-TTA
* * *
28190148 TAAAATTTTATAAAGTCATAAGAAAATTATACAAAATGTAAAGAAATATAAA
1 TAAAATTTTATAAAATCATAAGAAAACTATA-AAAATCTAAAGAAATATAAA
28190200 TTTCATAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
57 23 0.26
58 29 0.32
59 17 0.19
60 21 0.23
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (58 bp):
TAAAATTTTATAAAATCATAAGAAAACTATAAAAATCTAAAGAAATATAAAAAAATTA
Found at i:28190425 original size:36 final size:36
Alignment explanation
Indices: 28190359--28190430 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
28190349 GTCGTTAATA
* **
28190359 TTTTTATGATTTTTATAAAATTTTACAATTTTTTAT
1 TTTTTAAGATTTTTATAAAAAATTACAATTTTTTAT
28190395 TTTTTAAGATTTTTATAAAAAATT-CTAATTTTTTAT
1 TTTTTAAGATTTTTATAAAAAATTAC-AATTTTTTAT
28190431 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTTTAAGATTTTTATAAAAAATTACAATTTTTTAT
Found at i:28190455 original size:31 final size:29
Alignment explanation
Indices: 28190393--28190472 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
28190383 ACAATTTTTT
* *
28190393 ATTTTTTAAGATTTTTATAAAAAATTCTA
1 ATTTTTTAAAATTTTTATAAAAAATTATA
* *
28190422 ATTTTTTATAAATTTTTATTAAAATTTAATA
1 ATTTTTTA-AAATTTTTATAAAAAATT-ATA
*
28190453 ATTTTTCTAAAGTTTATTAT
1 ATTTTT-TAAAATTT-TTAT
28190473 TTATTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 8 0.19
30 15 0.36
31 13 0.31
32 6 0.14
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTTTTTAAAATTTTTATAAAAAATTATA
Found at i:28190609 original size:92 final size:94
Alignment explanation
Indices: 28190510--28190686 Score: 250
Period size: 93 Copynumber: 1.9 Consensus size: 94
28190500 ATAAGAGTAG
* * ** *
28190510 GGGCTTAATTGCTTTTTT-GAAAAATTTTGAGGGTCTTTTTTATACATTTTGAAAGTTCAAGTAC
1 GGGCTTAATTGCTTTTTTCGAAAAAGTTTGAGGGCCTTTTAGATACATTTTGAAAATTCAAGTAC
*
28190574 CCAATTGAGT-TAAAAAAAAGAAAAGAAA
66 CCAATTGAGTGCAAAAAAAAGAAAAGAAA
* * *
28190602 GGGCTTAATTGCTTTTTTCGAAGAAGTTTGAGGGCCTTTTAGATGCATTTTGAAAATTCAAGTGC
1 GGGCTTAATTGCTTTTTTCGAAAAAGTTTGAGGGCCTTTTAGATACATTTTGAAAATTCAAGTAC
*
28190667 TCAATTGAGTGCAAAAAAAA
66 CCAATTGAGTGCAAAAAAAA
28190687 AAGTTTGAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 18 0.25
93 47 0.64
94 8 0.11
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (94 bp):
GGGCTTAATTGCTTTTTTCGAAAAAGTTTGAGGGCCTTTTAGATACATTTTGAAAATTCAAGTAC
CCAATTGAGTGCAAAAAAAAGAAAAGAAA
Found at i:28197275 original size:25 final size:26
Alignment explanation
Indices: 28197226--28197275 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
28197216 CTTTTTCTTT
* *
28197226 TCTTTTCATTTTTAGTTTAGGTTTTC
1 TCTTTTCATTTTTAGGTTAGATTTTC
*
28197252 TCTTTTC-TTTTTAGGTTATATTTT
1 TCTTTTCATTTTTAGGTTAGATTTT
28197276 AATTTTGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (26 bp):
TCTTTTCATTTTTAGGTTAGATTTTC
Found at i:28198523 original size:33 final size:32
Alignment explanation
Indices: 28198450--28198540 Score: 121
Period size: 34 Copynumber: 2.8 Consensus size: 32
28198440 TATGGGTTTT
* *
28198450 GGTGTTATATATATAATATATATTTAAGTGCATG
1 GGTGTTATATGTAT-ATATATATTT-GGTGCATG
*
28198484 GATGTTATATGTATGATATATATTTGGTGCATG
1 GGTGTTATATGTAT-ATATATATTTGGTGCATG
28198517 GGTGTTATATGTATA-ATATATTTG
1 GGTGTTATATGTATATATATATTTG
28198541 CGTGGGTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
31 9 0.17
32 1 0.02
33 20 0.38
34 22 0.42
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (32 bp):
GGTGTTATATGTATATATATATTTGGTGCATG
Found at i:28207612 original size:10 final size:11
Alignment explanation
Indices: 28207597--28207647 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 11
28207587 TTTATTAAGA
28207597 TAAATTTT-AT
1 TAAATTTTGAT
28207607 TAAATTTTGAT
1 TAAATTTTGAT
28207618 AATAAATTTT-AT
1 --TAAATTTTGAT
28207630 TAAATTTTGAT
1 TAAATTTTGAT
*
28207641 AAAATTT
1 TAAATTT
28207648 AAACCAATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 16 0.44
11 10 0.28
12 2 0.06
13 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (11 bp):
TAAATTTTGAT
Found at i:28207623 original size:23 final size:23
Alignment explanation
Indices: 28207596--28207642 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28207586 ATTTATTAAG
28207596 ATAAATTTTATTAAATTTTGATA
1 ATAAATTTTATTAAATTTTGATA
28207619 ATAAATTTTATTAAATTTTGATA
1 ATAAATTTTATTAAATTTTGATA
28207642 A
1 A
28207643 AATTTAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATAAATTTTATTAAATTTTGATA
Found at i:28214321 original size:50 final size:50
Alignment explanation
Indices: 28214207--28214341 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
28214197 AAAGTGATGG
* * * *
28214207 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGAAAGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCAGAAAGAAAGA
* * * * ***
28214257 TCGCATGTGGAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCAGAAAGAAAGA
*
28214307 TCACGTGTGTAGTACTATGTGAAGGCTACTGCGTG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
28214342 TATTGAATGA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCAGAAAGAAAGA
Found at i:28215262 original size:15 final size:15
Alignment explanation
Indices: 28215250--28215291 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
28215240 TGGTATGGAG
*
28215250 TGGATTGGAATGGTA
1 TGGAATGGAATGGTA
28215265 TGGAATGGAATGGTA
1 TGGAATGGAATGGTA
28215280 TGGAATGGAATG
1 TGGAATGGAATG
28215292 AAATAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (15 bp):
TGGAATGGAATGGTA
Found at i:28215267 original size:5 final size:5
Alignment explanation
Indices: 28215244--28215291 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
28215234 TATAATTGGT
* * * *
28215244 ATGGA GTGGA TTGGA ATGGT ATGGA ATGGA ATGGT ATGGA ATGGA ATG
1 ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATG
28215292 AAATAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (5 bp):
ATGGA
Found at i:28226795 original size:20 final size:20
Alignment explanation
Indices: 28226740--28226797 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
28226730 TATATAAATA
*
28226740 TACCCCTGATCGCACTTACG
1 TACCCCTGATCGTACTTACG
* *
28226760 TGCCCCT-ATTGTACTT-CGG
1 TACCCCTGATCGTACTTAC-G
28226779 TACCCCTGATCGTACTTAC
1 TACCCCTGATCGTACTTAC
28226798 ATGCCCTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 14 0.47
21 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.16, T:0.31
Consensus pattern (20 bp):
TACCCCTGATCGTACTTACG
Found at i:28226818 original size:39 final size:39
Alignment explanation
Indices: 28226740--28226834 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
28226730 TATATAAATA
* * *
28226740 TACCCCTGATCGCACTTACGTGCCCCTATTGTACTTCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTATACATCGG
* * *
28226779 TACCCCTGATCGTACTTACATGCCCTTGTTATACATCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTATACATCGG
* * *
28226818 TACTCTTGATAGCACTT
1 TACCCCTGATCGCACTT
28226835 TCGTGTCGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.34
Consensus pattern (39 bp):
TACCCCTGATCGCACTTACATGCCCCTATTATACATCGG
Found at i:28236380 original size:29 final size:29
Alignment explanation
Indices: 28236343--28236398 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
28236333 ATAATAGTAC
28236343 GTAATAATAATATATAA-AAAGTTAAAATAA
1 GTAATAATAA-A-ATAACAAAGTTAAAATAA
*
28236373 GTAA-AATAAAATAACAAATTTAAAAT
1 GTAATAATAAAATAACAAAGTTAAAAT
28236399 GAATAAGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 5 0.21
30 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (29 bp):
GTAATAATAAAATAACAAAGTTAAAATAA
Found at i:28239739 original size:28 final size:28
Alignment explanation
Indices: 28239707--28239774 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
28239697 ATGAATAGGA
* *
28239707 AATTTCATTAAGTTATTTTA-GACTCATT
1 AATTTAATTAAGTTATTTTAGGA-TAATT
*
28239735 AATTTAATTAGGTTATTTTAGGATAATT
1 AATTTAATTAAGTTATTTTAGGATAATT
28239763 AATTTAATTAAG
1 AATTTAATTAAG
28239775 ATTTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (28 bp):
AATTTAATTAAGTTATTTTAGGATAATT
Found at i:28241428 original size:11 final size:11
Alignment explanation
Indices: 28241412--28241448 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
28241402 AATTATGAAC
28241412 TTACCATTTCA
1 TTACCATTTCA
28241423 TTACCATTTCA
1 TTACCATTTCA
*
28241434 TTACCTTTTC-
1 TTACCATTTCA
28241444 TTACC
1 TTACC
28241449 CGTTTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.49
Consensus pattern (11 bp):
TTACCATTTCA
Found at i:28241437 original size:22 final size:22
Alignment explanation
Indices: 28241412--28241457 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28241402 AATTATGAAC
28241412 TTACCATTTCATTA-CCATTTCA
1 TTACCATTTC-TTACCCATTTCA
* *
28241434 TTACCTTTTCTTACCCGTTTCA
1 TTACCATTTCTTACCCATTTCA
28241456 TT
1 TT
28241458 TGCATAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (22 bp):
TTACCATTTCTTACCCATTTCA
Found at i:28246276 original size:23 final size:23
Alignment explanation
Indices: 28246250--28246293 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28246240 TGAATTAAAG
28246250 AGCAAATACAGACATAGATGCGT
1 AGCAAATACAGACATAGATGCGT
* **
28246273 AGCAGATACAGATTTAGATGC
1 AGCAAATACAGACATAGATGC
28246294 ATAATAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (23 bp):
AGCAAATACAGACATAGATGCGT
Found at i:28250666 original size:14 final size:14
Alignment explanation
Indices: 28250647--28250687 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
28250637 CAATCAATAG
28250647 ATTTTTTGTGTATT
1 ATTTTTTGTGTATT
28250661 ATTTTTTGTGTATT
1 ATTTTTTGTGTATT
28250675 ATTTTTTGT-TATT
1 ATTTTTTGTGTATT
28250688 CTTAACTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (14 bp):
ATTTTTTGTGTATT
Found at i:28267705 original size:10 final size:10
Alignment explanation
Indices: 28267690--28267715 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28267680 CCCCGTCAAA
28267690 AGTTTCCTAT
1 AGTTTCCTAT
28267700 AGTTTCCTAT
1 AGTTTCCTAT
28267710 AGTTTC
1 AGTTTC
28267716 ACAATCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (10 bp):
AGTTTCCTAT
Found at i:28279386 original size:5 final size:6
Alignment explanation
Indices: 28279338--28279385 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
28279328 TAAGTCTAAG
**
28279338 AAAATA AAAATAA AACAACTA AAAGCA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAATA AAAATA AAA
28279386 TCAATTGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 25 0.71
7 4 0.11
8 5 0.14
9 1 0.03
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:28280651 original size:26 final size:26
Alignment explanation
Indices: 28280624--28280678 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
28280614 ACTTAGCTAT
*
28280624 AATAAAATAATAATGAAGGGAAAAATA
1 AATAAAATAA-AATAAAGGGAAAAATA
* *
28280651 AATAAAATAAAATAAATGGAAAACTA
1 AATAAAATAAAATAAAGGGAAAAATA
28280677 AA
1 AA
28280679 AGTACTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (26 bp):
AATAAAATAAAATAAAGGGAAAAATA
Found at i:28280740 original size:3 final size:3
Alignment explanation
Indices: 28280732--28280759 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28280722 CAGTAAAACA
28280732 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28280760 TGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28297863 original size:10 final size:10
Alignment explanation
Indices: 28297848--28297915 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
28297838 CTCAATCAAT
28297848 TTTTTTTCTC
1 TTTTTTTCTC
*
28297858 TTTTTTATGT-
1 TTTTTT-TCTC
*
28297868 TTTTTCTTTTC
1 TTTTT-TTCTC
28297879 TTTTCTTT-TC
1 TTTT-TTTCTC
**
28297889 TTTTTTTCGA
1 TTTTTTTCTC
*
28297899 TTTTTTTATC
1 TTTTTTTCTC
28297909 TTTTTTT
1 TTTTTTT
28297916 AGATTAAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 3 0.07
10 33 0.72
11 9 0.20
12 1 0.02
ACGTcount: A:0.04, C:0.12, G:0.03, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:28302389 original size:53 final size:53
Alignment explanation
Indices: 28302318--28302424 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
28302308 TTGATTTAAG
28302318 TATGATTGTGGTTTATCTTGATCTAAATAAATAATTCATTTCAATTAAGTACT
1 TATGATTGTGGTTTATCTTGATCTAAATAAATAATTCATTTCAATTAAGTACT
*
28302371 TATGATTGTGGTTTATCTTGATCTAAATAAATAATTCCTTTCAATTAAGTACT
1 TATGATTGTGGTTTATCTTGATCTAAATAAATAATTCATTTCAATTAAGTACT
28302424 T
1 T
28302425 CTAGTATTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (53 bp):
TATGATTGTGGTTTATCTTGATCTAAATAAATAATTCATTTCAATTAAGTACT
Found at i:28311457 original size:18 final size:19
Alignment explanation
Indices: 28311434--28311486 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
28311424 AATCGTGTCG
28311434 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCATTA
*
28311452 TTCATTTAC-AAATCATTA
1 TTCATTTTCAAAATCATTA
*
28311470 TTCAATTTCAAAA-CATT
1 TTCATTTTCAAAATCATT
28311487 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCATTTTCAAAATCATTA
Found at i:28318043 original size:7 final size:7
Alignment explanation
Indices: 28318033--28318133 Score: 96
Period size: 7 Copynumber: 14.4 Consensus size: 7
28318023 AAAAATAATG
28318033 GAGAATT
1 GAGAATT
28318040 GAGAATT
1 GAGAATT
*
28318047 AAGAATT
1 GAGAATT
*
28318054 GAGGATT
1 GAGAATT
*
28318061 -AGGGATT
1 GA-GAATT
* *
28318068 GGGGATT
1 GAGAATT
*
28318075 GAGCATT
1 GAGAATT
28318082 GAGAATT
1 GAGAATT
28318089 GAGAATT
1 GAGAATT
28318096 GAGAATT
1 GAGAATT
*
28318103 GAAAATT
1 GAGAATT
*
28318110 GAAAATT
1 GAGAATT
*
28318117 GAAAATT
1 GAGAATT
*
28318124 GAAAATT
1 GAGAATT
28318131 GAG
1 GAG
28318134 GAATGAATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
6 1 0.01
7 82 0.99
ACGTcount: A:0.43, C:0.01, G:0.29, T:0.28
Consensus pattern (7 bp):
GAGAATT
Found at i:28318140 original size:14 final size:15
Alignment explanation
Indices: 28318079--28318147 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 15
28318069 GGGATTGAGC
*
28318079 ATTGAGAATTGAG-A
1 ATTGAAAATTGAGAA
*
28318093 ATTGAGAATTGA-AA
1 ATTGAAAATTGAGAA
28318107 ATTGAAAATTGA-AA
1 ATTGAAAATTGAGAA
*
28318121 ATTGAAAATTGAGGA
1 ATTGAAAATTGAGAA
*
28318136 A-TGAATATTGAG
1 ATTGAAAATTGAG
28318148 TATTTGGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
14 48 0.96
15 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (15 bp):
ATTGAAAATTGAGAA
Found at i:28318140 original size:21 final size:21
Alignment explanation
Indices: 28318079--28318146 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
28318069 GGGATTGAGC
* *
28318079 ATTGAGAATTGAGAATTGAGA
1 ATTGAAAATTGAGAATTGAAA
*
28318100 ATTGAAAATTGAAAATTGAAA
1 ATTGAAAATTGAGAATTGAAA
*
28318121 ATTGAAAATTGAGGAA-TGAAT
1 ATTGAAAATTGA-GAATTGAAA
28318142 ATTGA
1 ATTGA
28318147 GTATTTGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (21 bp):
ATTGAAAATTGAGAATTGAAA
Found at i:28318972 original size:26 final size:25
Alignment explanation
Indices: 28318925--28318973 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
28318915 ACCCATAAAA
* * *
28318925 ACCCACAAAATGCCTAAGCCCACTC
1 ACCCACAAAATCCCAAAACCCACTC
28318950 ACCCACCAAAATCCCAAAACCCAC
1 ACCCA-CAAAATCCCAAAACCCAC
28318974 CAACCATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.41, C:0.47, G:0.04, T:0.08
Consensus pattern (25 bp):
ACCCACAAAATCCCAAAACCCACTC
Found at i:28320618 original size:6 final size:6
Alignment explanation
Indices: 28320607--28320653 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
28320597 AAATATATAC
28320607 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
28320654 GTGTTGAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
CTTTTT
Found at i:28328081 original size:62 final size:61
Alignment explanation
Indices: 28327970--28328095 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 61
28327960 ATATTATTTA
*
28327970 GATCATTATAGAAAACATGCACTGCACCCTTCGGTATTCAACTTAATCAATTAAATTAGTT
1 GATCATTATAGAAAACATGCACTGCACCCTTCAGTATTCAACTTAATCAATTAAATTAGTT
* * *
28328031 GATCATTATGGAACACATGCATTGCACCCCTTCAGTATTCAACTTAATCAATTAAATTAGTT
1 GATCATTATAGAAAACATGCACTGCA-CCCTTCAGTATTCAACTTAATCAATTAAATTAGTT
28328093 GAT
1 GAT
28328096 AAAGCCCAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 23 0.38
62 37 0.62
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (61 bp):
GATCATTATAGAAAACATGCACTGCACCCTTCAGTATTCAACTTAATCAATTAAATTAGTT
Found at i:28330118 original size:3 final size:3
Alignment explanation
Indices: 28330105--28330154 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
28330095 GTTAATTAAT
*
28330105 TTA TCA 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
28330153 TT
1 TT
28330155 GTCATTAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28330615 original size:16 final size:16
Alignment explanation
Indices: 28330591--28330621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28330581 ATTTTTATGC
28330591 TTTAGTTATTTATTCA
1 TTTAGTTATTTATTCA
*
28330607 TTTATTTATTTATTC
1 TTTAGTTATTTATTC
28330622 GCTATGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTAGTTATTTATTCA
Found at i:28330942 original size:111 final size:111
Alignment explanation
Indices: 28330748--28331286 Score: 887
Period size: 111 Copynumber: 4.9 Consensus size: 111
28330738 AGGAAAATTT
*
28330748 TTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
1 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
*
28330813 GATTTTTTCTCGTTCAACCAAAGAGCTAAATATCCTTTTAAAAAAA
66 GATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
28330859 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
1 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
*
28330924 GATTTTTTCTCGTTCAACCAAAGAGCTAAATATCCTTTTAAAAAAA
66 GATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
28330970 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
1 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
* ** *
28331035 GA-TTTTTCTCGTTCAACCAAATAGCCAAATATCC-TTCCAAAAAT
66 GATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
*
28331079 TTCAAAATAAGGCAATG-TTTGCGTTTGAAAACTT-GAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTCAAAATAAGGCAATGTTTTGCGTTTGGAAA-TTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
28331142 CGATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
65 CGATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
* * *
28331189 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAATGTGCCCTAATGTGCTGGGTTT
1 -TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
28331253 CGA---TTTCTCGTTTAACCAAATAGCCAAATATCCT
65 CGATTTTTTCTCGTTCAACCAAATAGCTAAATATCCT
28331287 CTTGAATTTC
Statistics
Matches: 406, Mismatches: 16, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
108 74 0.18
109 57 0.14
110 37 0.09
111 222 0.55
112 16 0.04
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (111 bp):
TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
GATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAA
Found at i:28331172 original size:219 final size:221
Alignment explanation
Indices: 28330747--28331286 Score: 903
Period size: 219 Copynumber: 2.5 Consensus size: 221
28330737 GAGGAAAATT
*
28330747 TTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * *
28330812 CGATTTTTTCTCGTTCAACCAAAGAGCTAAATATCCTTTTAAAAAAATTCAAAATAAGGCAATGT
66 CGA-TTTTTCTCGTTCAACCAAATAGCCAAATATCC-TTCAAAAAAATTCAAAATAAGGCAATGT
*
28330877 TTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCTCGTTCAAC
129 TTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCTCGTTCAAC
28330942 CAAAGAGCTAAATATCCTTTTAAAAAAA
194 CAAAGAGCTAAATATCCTTTTAAAAAAA
28330970 -TTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
28331034 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTTCAAAATAAGGCAATG-TT
66 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCAAAAAAATTCAAAATAAGGCAATGTTT
28331098 TGCGTTTGAAAACTT-GAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCTCGTTCAACC
131 TGCGTTTGAAAA-TTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCTCGTTCAACC
*
28331162 AAATAGCTAAATATCCTTTTAAAAAAA
195 AAAGAGCTAAATATCCTTTTAAAAAAA
* * *
28331189 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAATGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
28331253 CGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCT
28331287 CTTGAATTTC
Statistics
Matches: 303, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
217 30 0.10
219 114 0.38
220 63 0.21
221 30 0.10
222 66 0.22
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (221 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCAAAAAAATTCAAAATAAGGCAATGTTT
TGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCTCGTTCAACCA
AAGAGCTAAATATCCTTTTAAAAAAA
Found at i:28331889 original size:26 final size:26
Alignment explanation
Indices: 28331860--28331912 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28331850 TAAGTGGGAG
28331860 TGAGAAGTTAGTCCTTCGTGAGGTTT
1 TGAGAAGTTAGTCCTTCGTGAGGTTT
28331886 TGAGAAGTTAGTCCTTCGTGAGGTTT
1 TGAGAAGTTAGTCCTTCGTGAGGTTT
28331912 T
1 T
28331913 CACCTCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.40
Consensus pattern (26 bp):
TGAGAAGTTAGTCCTTCGTGAGGTTT
Found at i:28343863 original size:101 final size:101
Alignment explanation
Indices: 28343051--28343843 Score: 1153
Period size: 101 Copynumber: 7.9 Consensus size: 101
28343041 AAACCATAGT
* * * *
28343051 TTGCAATTTAAAAGATTGAAGCCACAACGGCAAATCTTA-CTT-CCAAGCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
*
28343114 ATTGAAGCTACAACGGCGAATCTCGCTTCCTAGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
*
28343150 TTCCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
28343215 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
* *
28343251 TTGCAACTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCAATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
* *
28343316 ATTGAAGCTACAATGGCGAATCTCGCTTCCTAGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
* * * *
28343352 TTGCAACTCAAAAGATTGAGGCCACAACGGTGAATCTTACCTTCCCAGGCAATGCAGCAGAACAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
*
28343417 ATTGAAGCTACAACAGTGAATCTCGCTTCCTAGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
* * * * * *
28343453 TTGCAACTCAAAAGATTGAGGCCACAACGGCGAATCTTACATTCCCAGGGGATACAGCGAAACAA
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
* *
28343518 ATTGAAGCTACAACGGCGAATCTCACTTCCTAGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
*
28343554 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCAATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
* * *
28343619 ATTGAAGCTGCAACAGTGAATCTCGCTTCCTCGACA
66 ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
* *
28343655 TTGCAACTCAAAAGATTAAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGC-GAAGCA
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAA-CA
* * **
28343719 AATTGAAG-TCACAACGGTGAATCTTGCTTCCCCGACA
65 GATTGAAGCT-ACAACGGTGAATCTCGCTTCCTAGACA
* * ** * ** * *
28343756 TTGCAATTTAAAACATTGAGGCCACAACGGCGAATCTTACCTTCTTAGGTGATATAGTGGAATAG
1 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
*
28343821 ATTGAAGCCACAACGGTGAATCT
66 ATTGAAGCTACAACGGTGAATCT
28343844 TCCTTCCCCG
Statistics
Matches: 628, Mismatches: 60, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
99 35 0.06
100 7 0.01
101 583 0.93
102 3 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (101 bp):
TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGCGGAACAG
ATTGAAGCTACAACGGTGAATCTCGCTTCCTAGACA
Found at i:28346449 original size:109 final size:109
Alignment explanation
Indices: 28346258--28346901 Score: 1015
Period size: 109 Copynumber: 5.9 Consensus size: 109
28346248 GAGGAAAATT
* *
28346258 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGATTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
28346323 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
66 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
*
28346367 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGATTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
28346432 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
66 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
28346476 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * **
28346541 CGATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 TGA-TTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
** * * **
28346586 AATCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCAAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
28346651 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCATTCCAAAAA
66 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
* * * *
28346695 TTTCAAAATAAGGCAATTTTTTGCGTTTAAAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * ** *
28346760 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAT
66 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
* * *
28346804 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
28346868 TGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCT
28346902 CTTGAATTTC
Statistics
Matches: 493, Mismatches: 41, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
106 29 0.06
108 24 0.05
109 341 0.69
110 99 0.20
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAA
Found at i:28346636 original size:219 final size:218
Alignment explanation
Indices: 28346258--28346901 Score: 1060
Period size: 219 Copynumber: 3.0 Consensus size: 218
28346248 GAGGAAAATT
* *
28346258 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGATTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * **
28346323 TGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTTCAAAATAAGGCAATGTTT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTT
* *
28346388 TGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGATTTTGATTTTTCTCGTTCAACCAA
131 TGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCAACCAA
28346453 ATAGCCAAATATCCTTCCAAAAA
196 ATAGCCAAATATCCTTCCAAAAA
28346476 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
**
28346541 CGATTTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAATCAAAATAAGGCAATGTT
66 CGA-TTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGGCAATGTT
* **
28346606 TTGTGTTTGGAAATTCAAGAAAACGTGCCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCAACCA
130 TTGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCAACCA
*
28346671 AATAGCCAAATATCATTCCAAAAA
195 AATAGCCAAATATCCTTCCAAAAA
* * * *
28346695 TTTCAAAATAAGGCAATTTTTTGCGTTTAAAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
28346760 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTT
* * *
28346825 TGCGTTTGGAAATTTGAG-GAACGTGCCCTAATGTGTTGGGTTTTGA--TTTCTCGTTTAACCAA
131 TGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCAACCAA
28346887 ATAGCCAAATATCCT
196 ATAGCCAAATATCCT
28346902 CTTGAATTTC
Statistics
Matches: 397, Mismatches: 28, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
215 29 0.07
217 26 0.07
218 139 0.35
219 203 0.51
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (218 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTT
TGCGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCAACCAA
ATAGCCAAATATCCTTCCAAAAA
Found at i:28349191 original size:18 final size:18
Alignment explanation
Indices: 28349152--28349275 Score: 61
Period size: 18 Copynumber: 6.6 Consensus size: 18
28349142 TTTAGGTGGG
* *
28349152 GGTGCTGGTGGA-GGCTTT
1 GGTGGTGGTGGAGGGC-TA
28349170 GGTGGTGGTGGAGGGCTA
1 GGTGGTGGTGGAGGGCTA
* * * *
28349188 GGTGGCGGTGGTGGTCTTGGG
1 GGTGGTGGTGGAGGGC-T--A
* *
28349209 GGTGGTGGGGGAGGAGGATTA
1 GGTGGTGGTGGA-G-GG-CTA
* * *
28349230 GGTGGTGGAGGAGGTCTT
1 GGTGGTGGTGGAGGGCTA
* *
28349248 GGGGGTGGTGGAGGCCTA
1 GGTGGTGGTGGAGGGCTA
28349266 GGTGGTGGTG
1 GGTGGTGGTG
28349276 CGGGAGGAGG
Statistics
Matches: 78, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
18 49 0.63
19 5 0.06
20 1 0.01
21 20 0.26
22 1 0.01
23 2 0.03
ACGTcount: A:0.09, C:0.06, G:0.60, T:0.25
Consensus pattern (18 bp):
GGTGGTGGTGGAGGGCTA
Found at i:28349192 original size:30 final size:30
Alignment explanation
Indices: 28349098--28349192 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
28349088 TGGTGGTCTA
* * *
28349098 GGTGGTGGTTTTGGTGGTGGTGGAGGCACT
1 GGTGGAGGATTTGGTGGTGGTGGAGGCGCT
** * * *
28349128 GGTGGAGGAGGTGGT-TTAGGTGGGGGTGCT
1 GGTGGAGGATTTGGTGGT-GGTGGAGGCGCT
*
28349158 GGTGGAGGCTTTGGTGGTGGTGGAGG-GCT
1 GGTGGAGGATTTGGTGGTGGTGGAGGCGCT
28349187 AGGTGG
1 -GGTGG
28349193 CGGTGGTGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
29 4 0.08
30 44 0.90
31 1 0.02
ACGTcount: A:0.08, C:0.05, G:0.58, T:0.28
Consensus pattern (30 bp):
GGTGGAGGATTTGGTGGTGGTGGAGGCGCT
Found at i:28349215 original size:42 final size:42
Alignment explanation
Indices: 28349169--28349258 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
28349159 GTGGAGGCTT
* * * * *
28349169 TGGTGGTGGTGGAGGGCTAGGTGGCGGTGGTGGTCTTGGGGG
1 TGGTGGGGGAGGAGGACTAGGTGGCGGAGGAGGTCTTGGGGG
* *
28349211 TGGTGGGGGAGGAGGATTAGGTGGTGGAGGAGGTCTTGGGGG
1 TGGTGGGGGAGGAGGACTAGGTGGCGGAGGAGGTCTTGGGGG
28349253 TGGTGG
1 TGGTGG
28349259 AGGCCTAGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.09, C:0.04, G:0.62, T:0.24
Consensus pattern (42 bp):
TGGTGGGGGAGGAGGACTAGGTGGCGGAGGAGGTCTTGGGGG
Done.