Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 115 of 182
Found at i:35132192 original size:69 final size:69
Alignment explanation
Indices: 35132106--35132243 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
35132096 GTAAATCAGA
35132106 GTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTAGAAATATGGGCAATGCTAGTGGT
1 GTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTAGAAATATGGGCAATGCTAGTGGT
35132171 GGTC
66 GGTC
* *
35132175 GTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATATGGGCAATGCTGGTGGT
1 GTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTAGAAATATGGGCAATGCTAGTGGT
35132240 GGTC
66 GGTC
35132244 AGAGAGGATC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (69 bp):
GTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTAGAAATATGGGCAATGCTAGTGGT
GGTC
Found at i:35132629 original size:105 final size:106
Alignment explanation
Indices: 35132447--35132656 Score: 386
Period size: 105 Copynumber: 2.0 Consensus size: 106
35132437 TAAGACTTTA
* *
35132447 CCTATTGAGTCTACTGAGTTTGTAATTCGGGTGTCAAATCCCTTGGGTCGTTATGTGCTTGTCGA
1 CCTATTGAGTCTACTGAGTTTGTAATTCGGGTGTCAAATCCCTTGGGTCGTCACGTGCTTGTCGA
*
35132512 CAAAGTGTGTAAGAAATGTCCCCTGG-GAATTCGAGGTTCT
66 CAAAGTGTGTAAGAAATGTCCCCTGGAAAATTCGAGGTTCT
35132552 CCTATTGAGTCTACTGAGTTTGTAATTCGGGTGTCAAATCCCTTGGGTCGTCACGTGCTTGTCGA
1 CCTATTGAGTCTACTGAGTTTGTAATTCGGGTGTCAAATCCCTTGGGTCGTCACGTGCTTGTCGA
35132617 CAAAGTGTGTAAGAAATGTCCCCTGGAAAATTCGAGGTTC
66 CAAAGTGTGTAAGAAATGTCCCCTGGAAAATTCGAGGTTC
35132657 CTATTTTCCG
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 89 0.88
106 12 0.12
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
CCTATTGAGTCTACTGAGTTTGTAATTCGGGTGTCAAATCCCTTGGGTCGTCACGTGCTTGTCGA
CAAAGTGTGTAAGAAATGTCCCCTGGAAAATTCGAGGTTCT
Found at i:35137930 original size:40 final size:40
Alignment explanation
Indices: 35137875--35138083 Score: 418
Period size: 40 Copynumber: 5.2 Consensus size: 40
35137865 TATGTGCATA
35137875 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
35137915 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
35137955 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
35137995 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
35138035 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
35138075 GCATTCGTG
1 GCATTCGTG
35138084 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 169 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:35146068 original size:3 final size:3
Alignment explanation
Indices: 35146053--35146105 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
35146043 AGGATTCTTG
*
35146053 TGA TGA TGG TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
35146101 TGA TG
1 TGA TG
35146106 TAGAAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:35149850 original size:50 final size:50
Alignment explanation
Indices: 35149762--35150004 Score: 414
Period size: 50 Copynumber: 4.8 Consensus size: 50
35149752 ATTTGGGTAA
* *
35149762 AGAGATCCCATGTAAGACCATGTCTGGGACGTGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
35149812 AGAGGTCCCATGTAAGACCATGTCTGGGACATGTCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
35149862 AGAGGTCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
35149912 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
35149962 AGGACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 A-GAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
35150005 TGTTATTATC
Statistics
Matches: 183, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
50 145 0.79
51 38 0.21
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:35153211 original size:42 final size:43
Alignment explanation
Indices: 35153164--35153321 Score: 187
Period size: 42 Copynumber: 3.7 Consensus size: 43
35153154 CAAATAAAAG
** * *
35153164 CGCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAGAACA-AAA
1 CGCCGCTAAAGAAAATGTTCTTTAGCGGCGCTTAGAAAAGAAA
*
35153206 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAGAAA
1 CGCCGCTAAAGAAAATGTTCTTTAGCGGCGCTTAGAAAAGAAA
* *
35153249 TGCCGCTAAA-AAAATGTTCTTTAGTGGCGCTTTA-AAAAGAAA
1 CGCCGCTAAAGAAAATGTTCTTTAGCGGCGC-TTAGAAAAGAAA
* * *
35153291 CGACGCTAAAGACAATGCTCTTTTAGCGGCG
1 CGCCGCTAAAGAAAATGTTC-TTTAGCGGCG
35153322 TTTATTCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
42 70 0.69
43 22 0.22
44 9 0.09
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAGAAAATGTTCTTTAGCGGCGCTTAGAAAAGAAA
Found at i:35153708 original size:21 final size:21
Alignment explanation
Indices: 35153681--35153730 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35153671 TTTTGGCGTG
*
35153681 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
*
35153702 TTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
35153723 CTCTGCTT
1 CTCTGCTT
35153731 TAAGTTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.38, G:0.18, T:0.40
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:35159282 original size:55 final size:54
Alignment explanation
Indices: 35159187--35159336 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
35159177 CTACTTTGTT
* ** * *
35159187 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
35159241 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
35159296 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
35159337 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:35159299 original size:27 final size:27
Alignment explanation
Indices: 35159159--35159336 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
35159149 TAAATTGTAC
35159159 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
35159186 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
35159212 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
35159240 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
35159268 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
35159295 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
35159322 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35159337 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:35159300 original size:82 final size:81
Alignment explanation
Indices: 35159160--35159315 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
35159150 AAATTGTACA
* * * *
35159160 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
35159225 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
35159241 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
35159304 TGTGCGAGTTGA
63 TGTGCGAATTGA
35159316 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:35166405 original size:27 final size:26
Alignment explanation
Indices: 35166374--35166551 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
35166364 TAAATTGTAC
35166374 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
35166401 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
35166427 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
35166455 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
35166483 GGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
35166510 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
35166537 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35166552 GACTCGATAT
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:35166490 original size:82 final size:81
Alignment explanation
Indices: 35166375--35166530 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35166365 AAATTGTACA
*
35166375 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
35166439 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
35166456 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
35166521 TGCGAGTTGA
65 TGCGAATTGA
35166531 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35166542 original size:82 final size:81
Alignment explanation
Indices: 35166371--35166551 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
35166361 GATTAAATTG
*
35166371 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
35166436 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
35166452 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
35166516 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35166534 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35166552 GACTCGATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35168817 original size:25 final size:25
Alignment explanation
Indices: 35168774--35168856 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
35168764 GCCCTCTCTC
**
35168774 GAGCCATATAATGACAAGCTCATAT
1 GAGCCATATAATGGGAAGCTCATAT
* * *
35168799 GAGCCATGTAATGGGAAGCTTATTT
1 GAGCCATATAATGGGAAGCTCATAT
* *** *
35168824 GGGTTGTATAATGGGAAGCTCATAA
1 GAGCCATATAATGGGAAGCTCATAT
35168849 GAGCCATA
1 GAGCCATA
35168857 ATCAAGAAGC
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCATAT
Found at i:35168927 original size:73 final size:72
Alignment explanation
Indices: 35168837--35169017 Score: 193
Period size: 73 Copynumber: 2.5 Consensus size: 72
35168827 TTGTATAATG
* **
35168837 GGAAGCT-CATAAGAGCCATAATCAAGAAGCTCATGCGAGCCAATAACGGGTAGCTCCGAAGAGC
1 GGAAGCTCCA-AAGAGCCATAATCAAGAAGCTCAAGCGAGCC-ATAACAAGTAGCTCCGAAGAGC
35168901 CATTAATCA
64 CATTAATCA
* * * * * *
35168910 GGAAGCTCCAAATAGCCATTTATCGAGAAGTTCAAGCGAGCCATATCAAGTAGCTCCGGAGAGCC
1 GGAAGCTCCAAAGAGCCA-TAATCAAGAAGCTCAAGCGAGCCATAACAAGTAGCTCCGAAGAGCC
*
35168975 ATTAATTA
65 ATTAATCA
* * *
35168983 GGGAGCTCACAAAGAGCCTTTAATCAGGAAGCTCA
1 GGAAGCTC-CAAAGAGCC-ATAATCAAGAAGCTCA
35169018 CGAAGAGCCA
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
73 47 0.54
74 40 0.46
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (72 bp):
GGAAGCTCCAAAGAGCCATAATCAAGAAGCTCAAGCGAGCCATAACAAGTAGCTCCGAAGAGCCA
TTAATCA
Found at i:35169015 original size:26 final size:26
Alignment explanation
Indices: 35168969--35169043 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
35168959 GTAGCTCCGG
* * *
35168969 AGAGCCATTAATTAGGGAGCTCACAA
1 AGAGCCTTTAATCAGGAAGCTCACAA
*
35168995 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCTTTAATCAGGAAGCTCACAA
* *
35169021 AGAGCCATATAA-CAGGACGCTCA
1 AGAGCC-TTTAATCAGGAAGCTCA
35169044 TAAGAGCTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAGCCTTTAATCAGGAAGCTCACAA
Found at i:35173452 original size:40 final size:39
Alignment explanation
Indices: 35173390--35173688 Score: 379
Period size: 40 Copynumber: 7.5 Consensus size: 39
35173380 AAGCCAAGTA
* * * *
35173390 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATG
* *
35173429 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATG
35173469 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATG
* *
35173509 CCTTCGGGACTTAGCCCGGATATAGCAGCTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATG
*
35173549 CCTTCGGGACTTAGCCCGGATATAGTAGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATG
* * *
35173589 CTTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATG
35173629 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACT--CGCACAAATG
35173670 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
35173689 TTATCATCCA
Statistics
Matches: 233, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
39 13 0.06
40 191 0.82
41 25 0.11
42 4 0.02
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATG
Found at i:35192448 original size:94 final size:94
Alignment explanation
Indices: 35192263--35192440 Score: 311
Period size: 94 Copynumber: 1.9 Consensus size: 94
35192253 CAAAGTCTCC
* * * *
35192263 CATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGG
1 CATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACAGAG
35192328 CTTCAATACTGATGCCGTTCATTTCTAAA
66 CTTCAATACTGATGCCGTTCATTTCTAAA
*
35192357 CATGTTACAGGGATCGACTACACTGACCTTTGCGCATTACGACTTGGATATCTCCCTGCACAGAG
1 CATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACAGAG
35192422 CTTCAATACTGATGCCGTT
66 CTTCAATACTGATGCCGTT
35192441 TGTTTCTATA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 79 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (94 bp):
CATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACAGAG
CTTCAATACTGATGCCGTTCATTTCTAAA
Found at i:35193553 original size:40 final size:40
Alignment explanation
Indices: 35193457--35193553 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 40
35193447 GCTCCTCGTT
* * *
35193457 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGATTATAGTAACTCGCA
35193497 CAAATGCCTTCGGGACTTAACCCTGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GATTATAGTAACTCGCA
*
35193537 CAAATGCCATCGGGACT
1 CAAATGCCTTCGGGACT
35193554 CGGGACTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 49 0.94
41 3 0.06
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGATTATAGTAACTCGCA
Found at i:35193575 original size:47 final size:47
Alignment explanation
Indices: 35193506--35193596 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
35193496 ACAAATGCCT
* *
35193506 TCGGGACTTAACCCTGATTTAGTAACTCGCACAAATGCCATCGGGAC
1 TCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATCGGGAC
* *
35193553 TCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGG
1 TCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATCGG
35193597 ATCTTAGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (47 bp):
TCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCATCGGGAC
Found at i:35193959 original size:16 final size:16
Alignment explanation
Indices: 35193938--35193969 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35193928 TTGAGCTTAA
35193938 TTAAACAAATAAATTG
1 TTAAACAAATAAATTG
35193954 TTAAACAAATAAATTG
1 TTAAACAAATAAATTG
35193970 ATTTAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
TTAAACAAATAAATTG
Found at i:35197300 original size:29 final size:29
Alignment explanation
Indices: 35197268--35197409 Score: 169
Period size: 29 Copynumber: 4.9 Consensus size: 29
35197258 GGCTATCGAT
35197268 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
35197297 TATG-AAAGGGATGGTGACGACCATCGAAT
1 TATGAAAAGGGATGGTGACGACCATC-AAC
* ** * * *
35197326 TATGAAAAGGGATAGTTTCGGCTATCAAT
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
35197355 TATGAAAAGGGGTGGTGATGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
35197384 TATGAAAAGAGATGGTGACAACCATC
1 TATGAAAAGGGATGGTGACGACCATC
35197410 GTGATTACAC
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 21 0.23
29 56 0.60
30 16 0.17
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:35197390 original size:87 final size:88
Alignment explanation
Indices: 35197244--35197410 Score: 273
Period size: 87 Copynumber: 1.9 Consensus size: 88
35197234 AACCAAATGC
* *
35197244 AAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATG-AAAGGGA
1 AAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGAGA
*
35197308 TGGTGACGACCATCGAATTATGA
66 TGGTGACAACCATCGAATTATGA
* * *
35197331 AAAGGGATAGTTTCGGCTATCAATTATGAAAAGGGGTGGTGATGACCATCAACTATGAAAAGAGA
1 AAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGAGA
35197396 TGGTGACAACCATCG
66 TGGTGACAACCATCG
35197411 TGATTACACT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 53 0.73
88 20 0.27
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.22
Consensus pattern (88 bp):
AAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGAGA
TGGTGACAACCATCGAATTATGA
Found at i:35198096 original size:24 final size:24
Alignment explanation
Indices: 35198065--35198122 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
35198055 TGAATATGAT
*
35198065 TTTGGTATGGTCATTTTTGTAGAA
1 TTTGGTATGGTCATTTTGGTAGAA
35198089 TTTGGTATGGTCATTTTGGTAGAA
1 TTTGGTATGGTCATTTTGGTAGAA
35198113 TTTGGTATGG
1 TTTGGTATGG
35198123 AAATTGGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.03, G:0.29, T:0.48
Consensus pattern (24 bp):
TTTGGTATGGTCATTTTGGTAGAA
Found at i:35201236 original size:20 final size:20
Alignment explanation
Indices: 35201208--35201256 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
35201198 TAATTGAAGA
*
35201208 AAATCTGATATTGAGTTATG
1 AAATGTGATATTGAGTTATG
*
35201228 AAATGTGATATTGGGTTATG
1 AAATGTGATATTGAGTTATG
35201248 AAATGTGAT
1 AAATGTGAT
35201257 TTTATGGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (20 bp):
AAATGTGATATTGAGTTATG
Found at i:35215607 original size:79 final size:80
Alignment explanation
Indices: 35215505--35215768 Score: 376
Period size: 79 Copynumber: 3.3 Consensus size: 80
35215495 GCTCCTCGTT
* * * **
35215505 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
35215568 GGATTTAGTAACTCGCA
64 GGATTTAGTAACTCGCA
35215585 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
35215649 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
*
35215664 CAAATGACTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
* * * *
35215728 ATATGGTCACTTAGCA
66 ATTTAGTAAC-TCGCA
35215744 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35215769 CATCATTCAA
Statistics
Matches: 169, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
78 3 0.02
79 132 0.78
80 34 0.20
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
ATTTAGTAACTCGCA
Found at i:35215768 original size:40 final size:40
Alignment explanation
Indices: 35215505--35215768 Score: 317
Period size: 40 Copynumber: 6.7 Consensus size: 40
35215495 GCTCCTCGTT
* *
35215505 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
35215545 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
35215585 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* *
35215624 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCGCA
* *
35215664 CAAATGACTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
35215703 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
35215744 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35215769 CATCATTCAA
Statistics
Matches: 192, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
38 4 0.02
39 63 0.33
40 111 0.58
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:35222601 original size:27 final size:27
Alignment explanation
Indices: 35222563--35222617 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
35222553 CTTGACTTAG
35222563 TTAATTTTTAATTTTATAAATAAGGTT
1 TTAATTTTTAATTTTATAAATAAGGTT
35222590 TTAATTTTTAATTTTATAAATAAGGTT
1 TTAATTTTTAATTTTATAAATAAGGTT
35222617 T
1 T
35222618 ACTTTTGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
TTAATTTTTAATTTTATAAATAAGGTT
Found at i:35232233 original size:88 final size:88
Alignment explanation
Indices: 35232139--35232316 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
35232129 CTGTGTACTA
*
35232139 GTCGTTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAA
1 GTCGTTTTAAAAATCATATCTTGAGTTTCATAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAA
35232204 ACTAGACTCATGTGCCCATCTAT
66 ACTAGACTCATGTGCCCATCTAT
35232227 GTCGTTTTAAAAATCATATCTTGAGTTTCATAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAA
1 GTCGTTTTAAAAATCATATCTTGAGTTTCATAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAA
35232292 ACTAGACTCATGTGCCCATCTAT
66 ACTAGACTCATGTGCCCATCTAT
35232315 GT
1 GT
35232317 ATTTTTTTCT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (88 bp):
GTCGTTTTAAAAATCATATCTTGAGTTTCATAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAA
ACTAGACTCATGTGCCCATCTAT
Found at i:35232451 original size:57 final size:57
Alignment explanation
Indices: 35232361--35232473 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
35232351 TACAGTTTAT
*
35232361 TAGTCAAAGTCTCCCATGTTGCAGGGGTTGACTACACTGACCTTTGCCCATTACGAA
1 TAGTCAAAGTCTCCCATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGAA
*
35232418 TAGTCAAAGTCTCCCATGTTGCAGGGGTCGACTACACTGACCTTTTCCCATTACGA
1 TAGTCAAAGTCTCCCATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGA
35232474 CTTGGATATC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (57 bp):
TAGTCAAAGTCTCCCATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGAA
Found at i:35233557 original size:27 final size:27
Alignment explanation
Indices: 35233527--35233704 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
35233517 ATATTGAGTC
* *
35233527 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
35233554 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
35233581 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
35233609 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
35233636 CGCACACTTACTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
35233663 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
35233690 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35233705 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:35237810 original size:37 final size:37
Alignment explanation
Indices: 35237755--35237857 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
35237745 GGAAATATAT
35237755 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
** *
35237792 TCCGGGTAAGACTTGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
35237829 CCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
35237858 GGACTATTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:35242511 original size:28 final size:29
Alignment explanation
Indices: 35242429--35242518 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
35242419 CAAGCATGAC
*
35242429 TATAAATGTGAATTGGGTCT-GATGGGCCA
1 TATAAATGTGAATTGGGCCTAG-TGGGCCA
* *
35242458 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATAAATGTGAATTGGGCCTAGTGGGCCA
*
35242487 TATAAATAT-AATTGGGCCTAGTGGGCCA
1 TATAAATGTGAATTGGGCCTAGTGGGCCA
35242515 TATA
1 TATA
35242519 TAGGTATGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
28 21 0.39
29 33 0.61
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (29 bp):
TATAAATGTGAATTGGGCCTAGTGGGCCA
Found at i:35250261 original size:26 final size:27
Alignment explanation
Indices: 35250231--35250308 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 27
35250221 GCCAACACAC
35250231 CAATATCGCAGCAAAGCTGCCAGTAAT
1 CAATATCGCAGCAAAGCTGCCAGTAAT
*
35250258 -AATATCGCAGCAAAGTTGCCAGT-AT
1 CAATATCGCAGCAAAGCTGCCAGTAAT
* *
35250283 CAGTAACGCAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
35250309 CAGTATATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.04
26 42 0.93
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (27 bp):
CAATATCGCAGCAAAGCTGCCAGTAAT
Found at i:35250312 original size:26 final size:26
Alignment explanation
Indices: 35250237--35250340 Score: 109
Period size: 26 Copynumber: 4.0 Consensus size: 26
35250227 ACACCAATAT
* * *
35250237 CGCAGCAAAGCTGCCAGTAATAATAT
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
35250263 CGCAGCAAAGTTGCCAGTATCAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
35250289 CGCAGCAAAGCTGCCAGTAACAGTATA
1 CGCAGCAAAGCTGCCAGTAACAGTA-A
* ** **
35250316 TGTGGCAAAGCCACCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
35250341 TATGTGGCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
26 44 0.68
27 21 0.32
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:35250332 original size:27 final size:27
Alignment explanation
Indices: 35250293--35250361 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
35250283 CAGTAACGCA
**
35250293 GCAAAGCTGCCAGTAACAGTATATGTG
1 GCAAAGCCACCAGTAACAGTATATGTG
35250320 GCAAAGCCACCAGTAACAGTATATGTG
1 GCAAAGCCACCAGTAACAGTATATGTG
*
35250347 GCAAAGCCACTAGTA
1 GCAAAGCCACCAGTA
35250362 TAGTACACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (27 bp):
GCAAAGCCACCAGTAACAGTATATGTG
Found at i:35254443 original size:30 final size:30
Alignment explanation
Indices: 35254409--35254469 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35254399 TCCTTAACTC
35254409 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
35254439 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
35254469 A
1 A
35254470 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:35265758 original size:21 final size:21
Alignment explanation
Indices: 35265725--35265779 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
35265715 AAAATAGGGC
35265725 ACACGCCCGTGTGGAAAGGTA
1 ACACGCCCGTGTGGAAAGGTA
* * *
35265746 ACACTCCCATGTGGAAGGGTA
1 ACACGCCCGTGTGGAAAGGTA
35265767 ACACGCCCGTGTG
1 ACACGCCCGTGTG
35265780 ACTATTTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.16
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAAGGTA
Found at i:35274431 original size:19 final size:19
Alignment explanation
Indices: 35274395--35274433 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35274385 CCTAAAATTC
35274395 TCACTATTTTACACACTTA
1 TCACTATTTTACACACTTA
*
35274414 TCACTTATTTTGCA-ACTTA
1 TCAC-TATTTTACACACTTA
35274433 T
1 T
35274434 GCAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (19 bp):
TCACTATTTTACACACTTA
Found at i:35279741 original size:2 final size:2
Alignment explanation
Indices: 35279736--35279760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35279726 ACACACACAT
35279736 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
35279761 AAGAACTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35285328 original size:18 final size:19
Alignment explanation
Indices: 35285292--35285338 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
35285282 ATAGTCCATT
35285292 CATGAACCTAATGATTAAGTA
1 CATGAACCTAA-GATTAAG-A
35285313 -ATGAACCTAA-ATTAAGA
1 CATGAACCTAAGATTAAGA
35285330 CATGAACCT
1 CATGAACCT
35285339 TCTAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
20 10 0.40
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.26
Consensus pattern (19 bp):
CATGAACCTAAGATTAAGA
Found at i:35285802 original size:13 final size:13
Alignment explanation
Indices: 35285784--35285812 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35285774 CGGCTAACCT
35285784 ACATAATTAAATA
1 ACATAATTAAATA
35285797 ACATAATTAAATA
1 ACATAATTAAATA
35285810 ACA
1 ACA
35285813 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:35286070 original size:10 final size:10
Alignment explanation
Indices: 35286037--35286082 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
35286027 AAAAAGGAAT
*
35286037 GAGCTGAAAC
1 GAGCTAAAAC
*
35286047 GAGCTAAATTC
1 GAGCTAAA-AC
35286058 GAGCTAAAAC
1 GAGCTAAAAC
35286068 GAGCTAAAAC
1 GAGCTAAAAC
35286078 GAGCT
1 GAGCT
35286083 CAAGTGAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:35287221 original size:21 final size:21
Alignment explanation
Indices: 35287174--35287225 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
35287164 CTCTTTTTCT
* **
35287174 TTTCTCTTTCAATTTCTTTTC
1 TTTCTTTTTCAATTTCTTGCC
* *
35287195 TCTCTTTTTCATTTTCTTGCC
1 TTTCTTTTTCAATTTCTTGCC
35287216 TTTCTTTTTC
1 TTTCTTTTTC
35287226 CACTCTCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTTCAATTTCTTGCC
Found at i:35294505 original size:18 final size:18
Alignment explanation
Indices: 35294482--35294527 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
35294472 TGTGTTACAT
35294482 ACATAATATATAAAAATA
1 ACATAATATATAAAAATA
*
35294500 ACATAATATATAAGAATA
1 ACATAATATATAAAAATA
35294518 ACATAATATA
1 ACATAATATA
35294528 AAATATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (18 bp):
ACATAATATATAAAAATA
Found at i:35307297 original size:39 final size:39
Alignment explanation
Indices: 35307254--35307373 Score: 177
Period size: 39 Copynumber: 3.1 Consensus size: 39
35307244 CCCGGTACCA
* * *
35307254 TTCCAACACGTAGCCTGCGGACTTCAAGTCTGGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT
*
35307293 TTCCAGCACATAGCCTGTGGACTTCAAGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT
* * *
35307332 TTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT
35307371 TTC
1 TTC
35307374 AAATACCATG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT
Found at i:35308687 original size:21 final size:21
Alignment explanation
Indices: 35308662--35308702 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35308652 CGTCAATTTC
35308662 AATTCATACTT-TTCAACCATG
1 AATTC-TACTTATTCAACCATG
35308683 AATTCTACTTATTCAACCAT
1 AATTCTACTTATTCAACCAT
35308703 CATTTAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTCTACTTATTCAACCATG
Found at i:35311850 original size:45 final size:45
Alignment explanation
Indices: 35311640--35311857 Score: 263
Period size: 45 Copynumber: 5.0 Consensus size: 45
35311630 CTGAATTCAT
* * *
35311640 TCACCGGCATT-TCA-CCTGCTAGGCT-AAAAGCCC-GATA-TCATT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCAAAGGCCCAAATAGT-ATC
* * *
35311682 TCACCGGCATTATAGCTTGCTAGGCTCAAA-GCCC-GATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGT-ATC
* **
35311725 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCTGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
35311770 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
*
35311815 TCACCGGCATTATAGCCTGCTAGCCTCAAAGGCCCAAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTA
35311858 CTGTACGATA
Statistics
Matches: 161, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
42 12 0.07
43 53 0.33
44 6 0.04
45 89 0.55
46 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
Found at i:35318319 original size:65 final size:65
Alignment explanation
Indices: 35318215--35318412 Score: 378
Period size: 65 Copynumber: 3.0 Consensus size: 65
35318205 CCATGAAAAT
* *
35318215 TTAGCTAGCCCTTGCTGTAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
1 TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
35318280 TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
1 TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
35318345 TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
1 TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
35318410 TTA
1 TTA
35318413 AAGTGTGAAA
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 131 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (65 bp):
TTAGCTAGCCCTTGTTGCAGAGAAATTTTGCATATTGATGATTTTGTGAAAAATGGACTAAATTG
Found at i:35318922 original size:85 final size:86
Alignment explanation
Indices: 35318763--35318922 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 86
35318753 AACTGAATTA
* * * **
35318763 TCGTGTAAGACCGTGTCTGGGACACAGGCATCGATTTGAGATTTATGTGTAAGACCATGTCCGGG
1 TCGTATAAGACCCTGTATGGGACACAGGCATCGATTTGAGATTTACATGTAAGACCATGTCCGGG
35318828 ACATCGACATCATATCTGATT
66 ACATCGACATCATATCTGATT
* *
35318849 TCGTATAAGACCCTGTATGGGACAGAGGCATCGATTTTGA-A-TTACATGTAAGACCATGTCTGG
1 TCGTATAAGACCCTGTATGGGACACAGGCATCGA-TTTGAGATTTACATGTAAGACCATGTCCGG
*
35318912 GACGTCGACAT
65 GACATCGACAT
35318923 TGTACCTGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 29 0.45
86 31 0.48
87 5 0.08
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (86 bp):
TCGTATAAGACCCTGTATGGGACACAGGCATCGATTTGAGATTTACATGTAAGACCATGTCCGGG
ACATCGACATCATATCTGATT
Found at i:35355702 original size:47 final size:47
Alignment explanation
Indices: 35355648--35355892 Score: 274
Period size: 47 Copynumber: 5.1 Consensus size: 47
35355638 TTAGGATTTT
* *
35355648 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
*
35355695 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--TGTGTATATAT--GTGATAAGGCCGAATGGCCA
** ** * *
35355746 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
* * *
35355793 ATGTGATGAATGTGAACATGCGTAATATATGAGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTG-A-ATGTGT-ATATATGTGATAAGGCCGAATGGCCA
** * * *
35355843 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCAAATGGCTA
1 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
35355890 ATG
1 ATG
35355893 CGAAATGTGT
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
47 73 0.44
48 4 0.02
49 18 0.11
50 37 0.22
51 34 0.20
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
Found at i:35355878 original size:97 final size:97
Alignment explanation
Indices: 35355648--35355892 Score: 323
Period size: 97 Copynumber: 2.5 Consensus size: 97
35355638 TTAGGATTTT
** * *
35355648 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
*
35355713 TGTATATATATGCGTGATAAGGCCGAATGGCCA
66 TGTATATATAT-CGAGATAAGGCCGAATGGCCA
** * * *
35355746 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
*
35355811 TGCGTA-ATATAT-GAGATAAGGTCGAATGGCCA
66 T--GTATATATATCGAGATAAGGCCGAATGGCCA
* * *
35355843 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCAAATGGCTAATG
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCAAATG
35355893 CGAAATGTGT
Statistics
Matches: 127, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
97 61 0.48
98 57 0.45
99 6 0.05
100 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (97 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
TGTATATATATCGAGATAAGGCCGAATGGCCA
Found at i:35356002 original size:46 final size:46
Alignment explanation
Indices: 35355866--35356002 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
35355856 GAACATGTAT
* *
35355866 ATATGTGGTAAGGCCAAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
35355912 TTATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
35355958 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATG
35356003 TGTATATATA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:35358069 original size:68 final size:68
Alignment explanation
Indices: 35357932--35358088 Score: 192
Period size: 68 Copynumber: 2.3 Consensus size: 68
35357922 TTAACTGTGA
* * * *
35357932 AATC-AACAGATTCGGACAGCTACATTTACTAAATAAAACAGCATATATGGTAGTGCATCGAACA
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAGTGCATCGAACA
35357996 ATG
66 ATG
* * * * *
35357999 AATTTAACACATTCGGACAGCTACATTTACCAAATAAAATAGCATAAATGAT-GATGCTTTGAAT
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAG-TGCATCGAAC
*
35358063 AGTG
65 AATG
*
35358067 AATCTAACACATTCGAACAGCT
1 AATCTAACACATTCGGACAGCT
35358089 TAATTTTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
67 4 0.05
68 72 0.95
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (68 bp):
AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAGTGCATCGAACA
ATG
Found at i:35361277 original size:40 final size:41
Alignment explanation
Indices: 35361082--35361263 Score: 225
Period size: 40 Copynumber: 4.6 Consensus size: 41
35361072 AATGATGTCT
* * *
35361082 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-ATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAATCC
* *
35361122 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAATCC
*
35361162 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCC
*
35361201 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCC
*
35361241 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
35361264 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (41 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCC
Found at i:35361285 original size:79 final size:79
Alignment explanation
Indices: 35361132--35361296 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
35361122 GGACTAAGAT
* **
35361132 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
35361197 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
35361211 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* * *
35361274 TATAT-CTGGTTAAATT
63 TAAATCCGGGTTAAATC
35361290 CCGAAGG
1 CCGAAGG
35361297 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 50 0.68
80 22 0.30
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:35373686 original size:51 final size:50
Alignment explanation
Indices: 35373498--35373691 Score: 241
Period size: 50 Copynumber: 3.9 Consensus size: 50
35373488 TAGCCAAAGC
*
35373498 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA--TGCAACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTG-AACCAAT
* * *
35373547 TATCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG-ACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAACC-AAT
* * * * *
35373597 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAACCAA-T
* *
35373648 TATCGGGTATACATAGTAGCCTGCACTTAGTACTACACACGTGA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
35373692 CCTCACAATA
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
49 39 0.31
50 44 0.35
51 42 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAACCAAT
Found at i:35373686 original size:101 final size:99
Alignment explanation
Indices: 35373511--35373694 Score: 280
Period size: 101 Copynumber: 1.8 Consensus size: 99
35373501 CTGGTACGCA
* *
35373511 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCTAGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCGAGTACACATAGTAGCCTGCACTTA
35373576 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* * * *
35373610 TAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGTTATCGGGTATACATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATCGAGTACACATAGTAGCCTGCAC
35373674 TTAGTACTACACACGTGACCT
63 TTAGTACTACACACGTGACCT
35373695 CACAATAGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
99 26 0.34
100 4 0.05
101 46 0.61
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCGAGTACACATAGTAGCCTGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:35376204 original size:25 final size:25
Alignment explanation
Indices: 35376173--35376239 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
35376163 AATCAAAATG
* * *
35376173 AGAATCAGAATCAGAATCAGGTGAT
1 AGAATCAAAATCAGAATCAGGTAAC
* *
35376198 AGAATCAAAATCGGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGGTAAC
*
35376223 AGAATCAAAATTAGAAT
1 AGAATCAAAATCAGAAT
35376240 GTGAATGTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAATCAAAATCAGAATCAGGTAAC
Found at i:35376426 original size:26 final size:26
Alignment explanation
Indices: 35376356--35376429 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
35376346 CAGCATGGCT
* ** *
35376356 ACCAGAATAGATATTGTGATAGAGTC
1 ACCAGAACAGATATTGTGGCAGAGCC
35376382 ACCAGATACAGATATTGTGGCAGAGCC
1 ACCAGA-ACAGATATTGTGGCAGAGCC
*
35376409 ACCAGAACAGATAATGTGGCA
1 ACCAGAACAGATATTGTGGCA
35376430 AAACCACTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGGCAGAGCC
Found at i:35376436 original size:26 final size:27
Alignment explanation
Indices: 35376381--35376436 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
35376371 GTGATAGAGT
* * *
35376381 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAAAC
35376408 CACCAGA-ACAGATAATGTGGCAAAAC
1 CACCAGATACAGATAATGTGGCAAAAC
35376434 CAC
1 CAC
35376437 TTAAAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAAAC
Found at i:35377208 original size:6 final size:6
Alignment explanation
Indices: 35377187--35377265 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
35377177 TGTTAGAACT
* * *
35377187 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * *
35377236 AGTATC AGGTAA-C AGAGTC AGAATT AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
35377266 GTGAATGCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
5 2 0.04
6 46 0.82
7 6 0.11
8 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:35377232 original size:25 final size:25
Alignment explanation
Indices: 35377199--35377265 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
35377189 AATCAAAATG
*
35377199 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
35377224 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
35377249 AGAGTCAGAATTAGAAT
1 AGAATCAGAATCAGAAT
35377266 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:35377453 original size:26 final size:27
Alignment explanation
Indices: 35377383--35377460 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 27
35377373 AGCATGGCTG
* * *
35377383 CCAGAATAGATATTGTGACAGAG-TCA
1 CCAGAACAGATATTGTGGCAGAGCCCA
35377409 CCAGATACAGATATTGTGGCAGAGCCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCCA
* *
35377437 CCAGAA-AGATAATGTGGCAAAGCC
1 CCAGAACAGATATTGTGGCAGAGCC
35377461 ACTTAACAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 21 0.47
27 17 0.38
28 7 0.16
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATTGTGGCAGAGCCCA
Found at i:35377655 original size:22 final size:22
Alignment explanation
Indices: 35377624--35377685 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
35377614 AATACGTTTA
*
35377624 GCACACAGCCATAATCAGGTTG
1 GCACAAAGCCATAATCAGGTTG
* *
35377646 GCACAGAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTG
* *
35377668 GCGCAAACCCATAATCAG
1 GCACAAAGCCATAATCAG
35377686 AAGGCTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTG
Found at i:35378151 original size:27 final size:27
Alignment explanation
Indices: 35378121--35378544 Score: 580
Period size: 27 Copynumber: 15.7 Consensus size: 27
35378111 ATGGTGATTT
* * *
35378121 TACCCCACAAGGGTATCTCGATAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* * * *
35378148 TACCCTGCAGGGGTATTTCGATATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
35378175 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
** * **
35378202 TGTCCTATAAGGGTATTTTAGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* *
35378229 TACCCTAC-AGGAGTATTTCGATATTTC
1 TACCCTACAAGG-GTATTTCGGTAATTC
* *
35378256 TACCCTATAAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
35378283 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
*
35378310 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* * * *
35378337 TACCCTACAGGGGTATTTCGATATTTT
1 TACCCTACAAGGGTATTTCGGTAATTC
*
35378364 TACCCTACAAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
35378391 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
*
35378418 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* * *
35378445 TACCCTACAGGGGTATTTCGGTATTTT
1 TACCCTACAAGGGTATTTCGGTAATTC
*
35378472 TACCCTACAAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
*
35378499 TACCCTACAAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
35378526 TACCCTACAAGGGTATTTC
1 TACCCTACAAGGGTATTTC
35378545 AATAATTTTG
Statistics
Matches: 357, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
26 3 0.01
27 351 0.98
28 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
TACCCTACAAGGGTATTTCGGTAATTC
Found at i:35378282 original size:108 final size:108
Alignment explanation
Indices: 35378121--35378544 Score: 668
Period size: 108 Copynumber: 3.9 Consensus size: 108
35378111 ATGGTGATTT
* * * * * * *
35378121 TACCCCACAAGGGTATCTCGATAATTCTACCCTGCAGGGGTATTTCGATATTTCTACCCTACAAG
1 TACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
** * **
35378186 GGTATTTCGGTAATTCTGTCCTATAAGGGTATTTTAGTAATTC
66 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTC
* *
35378229 TACCCTACAGGAGTATTTCGATATTTCTACCCTATAAGGGTATTTCGGTATTTCTACCCTACAAG
1 TACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
*
35378294 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTC
66 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTC
*
35378337 TACCCTACAGGGGTATTTCGATATTTTTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
1 TACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
*
35378402 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTC
66 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTC
* *
35378445 TACCCTACAGGGGTATTTCGGTATTTTTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
1 TACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
*
35378510 GGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
66 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTC
35378545 AATAATTTTG
Statistics
Matches: 295, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 295 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (108 bp):
TACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAG
GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTC
Found at i:35378656 original size:26 final size:27
Alignment explanation
Indices: 35378583--35378766 Score: 146
Period size: 27 Copynumber: 6.9 Consensus size: 27
35378573 GTAATTCTGT
* *
35378583 AAATCGGGGGTACTTTGA-TAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTAC
*
35378610 AAGTCGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
35378637 AAATCGA-GTTATTTCAGTAATTTTGC
1 AAATCGAGGGTATTTCAGTAATTTTAC
*
35378663 AAA-CTGAGGGTATTTCGGTAATTTTAC
1 AAATC-GAGGGTATTTCAGTAATTTTAC
* * * ** *
35378690 AAATCAAGGATGTTTGGGTAATTTTAT
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
35378717 AAA-CTGGGGGTACTTT-GGTAATTTTAC
1 AAATC-GAGGGTA-TTTCAGTAATTTTAC
* *
35378744 AACT-GGGGGTATTTCAGTAATTT
1 AAATCGAGGGTATTTCAGTAATTT
35378767 GGTAAACTAA
Statistics
Matches: 128, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
25 4 0.03
26 41 0.32
27 79 0.62
28 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
AAATCGAGGGTATTTCAGTAATTTTAC
Found at i:35378672 original size:53 final size:53
Alignment explanation
Indices: 35378601--35378766 Score: 165
Period size: 53 Copynumber: 3.1 Consensus size: 53
35378591 GGTACTTTGA
* * *
35378601 TAATTTTAC-AAGTCGAGGGTATTTCAGTAATTTTACAAATCGAGTTATTTCAG
1 TAATTTTACAAACT-GAGGGTATTTCGGTAATTTTACAAATCGAGATATTTCAG
* * * **
35378654 TAATTTTGCAAACTGAGGGTATTTCGGTAATTTTACAAATCAAGGATGTTTGGG
1 TAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGA-GATATTTCAG
* * * * * *
35378708 TAATTTTATAAACTGGGGGTACTTT-GGTAATTTTACAACTGGGGGTATTTCAG
1 TAATTTTACAAACTGAGGGTA-TTTCGGTAATTTTACAAATCGAGATATTTCAG
35378761 TAATTT
1 TAATTT
35378767 GGTAAACTAA
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
53 47 0.52
54 41 0.45
55 3 0.03
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (53 bp):
TAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGAGATATTTCAG
Found at i:35378774 original size:27 final size:25
Alignment explanation
Indices: 35378707--35378766 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
35378697 GGATGTTTGG
*
35378707 GTAATTTTATAAACTGGGGGTACTTTG
1 GTAA-TTT-TAAACTGGGGGTACTTTA
35378734 GTAATTTTACAACTGGGGGTA-TTTCA
1 GTAATTTTA-AACTGGGGGTACTTT-A
35378760 GTAATTT
1 GTAATTT
35378767 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 21 0.70
27 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
GTAATTTTAAACTGGGGGTACTTTA
Found at i:35387492 original size:48 final size:48
Alignment explanation
Indices: 35387421--35387639 Score: 244
Period size: 48 Copynumber: 4.5 Consensus size: 48
35387411 GTGCTAGAGG
***
35387421 AAGACCATGTCTGGGACATGGCATCGGCCACCTTATGAGAGCCAGTGT
1 AAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGT
* * * * **
35387469 AAGACCATGTCTAGGACATGGCATCGG-CATTGAGACGAGAGATAGTGT
1 AAGACCATGTCTGGGACATGGCATCGGCCA-CGACATGAGAGCCAGTGT
* * * *
35387517 AAGACCATGTTTGGGACATGGCATCAGCCTCGACATGAGAGCTAGTGT
1 AAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGT
* * *
35387565 AAGACCATGTCTGGGGCATGGCATCAGCCTCGACATGTA-AGCCAGTGT
1 AAGACCATGTCTGGGACATGGCATCGGCCACGACATG-AGAGCCAGTGT
*
35387613 AAGACCATGTCTGGGGCATTGGCATCG
1 AAGACCATGTCTGGGACA-TGGCATCG
35387640 ACAATTTCAC
Statistics
Matches: 147, Mismatches: 20, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
47 2 0.01
48 136 0.93
49 9 0.06
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (48 bp):
AAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGT
Found at i:35390939 original size:30 final size:30
Alignment explanation
Indices: 35390905--35390965 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35390895 CTCCCGAGCC
35390905 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
35390935 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
35390965 T
1 T
35390966 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:35392953 original size:29 final size:27
Alignment explanation
Indices: 35392935--35393004 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
35392925 ATATTAAGTC
35392935 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
35392962 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
35392990 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
35393005 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:35392998 original size:28 final size:28
Alignment explanation
Indices: 35392935--35393032 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
35392925 ATATTAAGTC
*
35392935 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
35392962 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
35392990 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
35393019 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35393033 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:35397671 original size:51 final size:51
Alignment explanation
Indices: 35397612--35397714 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
35397602 TTTCCGTCTC
35397612 TTTGCTATCAAATACATACGCAAGGTATGTTTCACACCCCTTTTTCACATA
1 TTTGCTATCAAATACATACGCAAGGTATGTTTCACACCCCTTTTTCACATA
35397663 TTTGCTATCAAATACATACGCAAGGTATGTTTCACACCCCTTTTTCACATA
1 TTTGCTATCAAATACATACGCAAGGTATGTTTCACACCCCTTTTTCACATA
35397714 T
1 T
35397715 CTCTGAGCGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (51 bp):
TTTGCTATCAAATACATACGCAAGGTATGTTTCACACCCCTTTTTCACATA
Found at i:35410745 original size:17 final size:17
Alignment explanation
Indices: 35410723--35410757 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35410713 ATTATAAAAT
*
35410723 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
35410740 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
35410757 C
1 C
35410758 TTTCTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:35411199 original size:19 final size:19
Alignment explanation
Indices: 35411134--35411205 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 19
35411124 CTCATATTAA
*
35411134 ATATATATTTAATATATAAA-
1 ATATATATTTGAT-TA-AAAT
*
35411154 AAATATATTTGATTAAAAAT
1 ATATATATTTGATT-AAAAT
35411174 AAAATATATATTTGATTAAAAT
1 ---ATATATATTTGATTAAAAT
35411196 ATATATATTT
1 ATATATATTT
35411206 AATATATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 14 0.32
20 12 0.27
22 5 0.11
23 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATATATATTTGATTAAAAT
Found at i:35411203 original size:23 final size:23
Alignment explanation
Indices: 35411149--35411194 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35411139 TATTTAATAT
*
35411149 ATAAAAAATATATTTGATTAAAA
1 ATAAAATATATATTTGATTAAAA
35411172 ATAAAATATATATTTGATTAAAA
1 ATAAAATATATATTTGATTAAAA
35411195 TATATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
ATAAAATATATATTTGATTAAAA
Found at i:35411819 original size:18 final size:18
Alignment explanation
Indices: 35411798--35411832 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35411788 TTATTTCGTG
*
35411798 TTTTGAATTTAGATTTTT
1 TTTTCAATTTAGATTTTT
*
35411816 TTTTCAGTTTAGATTTT
1 TTTTCAATTTAGATTTT
35411833 GAAAATAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTCAATTTAGATTTTT
Found at i:35412438 original size:18 final size:18
Alignment explanation
Indices: 35412417--35412472 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
35412407 GAAATATTTA
*
35412417 TTTTAATAT-TTTTAGTAT
1 TTTTAATATATTATA-TAT
*
35412435 TTTTGATATATTATATAT
1 TTTTAATATATTATATAT
*
35412453 TTTTAAAATATATATATAT
1 TTTTAATATAT-TATATAT
35412472 T
1 T
35412473 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTTAATATATTATATAT
Found at i:35413039 original size:31 final size:28
Alignment explanation
Indices: 35412967--35413040 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 28
35412957 CGCTGCACTC
*
35412967 TTTTGAAATTTAATTTTTATATTTTTTA
1 TTTTAAAATTTAATTTTTATATTTTTTA
*
35412995 TTTTCAAGAATTTAATTTTTTTTAATTTTTATA
1 TTTT-AA-AATTTAA-TTTTTAT-ATTTTT-TA
*
35413028 TTTTTAAATTTAA
1 TTTTAAAATTTAA
35413041 GTCTGACGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 7 0.18
31 13 0.34
32 7 0.18
33 6 0.16
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTAAAATTTAATTTTTATATTTTTTA
Found at i:35416042 original size:39 final size:40
Alignment explanation
Indices: 35415985--35416098 Score: 151
Period size: 39 Copynumber: 2.9 Consensus size: 40
35415975 ATTTACATGG
* * *
35415985 TAATCATATTCACTTTTAAGCATATATCACATTACAT-ATA
1 TAATCATA-TAACATTTAAGCATATATCACAATACATCATA
*
35416025 TAATCATATAACATTTAATCATATATCACAATAC-TCATA
1 TAATCATATAACATTTAAGCATATATCACAATACATCATA
* *
35416064 TAATCACATAACATTCAAGCATATATCACAATACA
1 TAATCATATAACATTTAAGCATATATCACAATACA
35416099 CAAAAACATG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.02
39 56 0.86
40 8 0.12
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (40 bp):
TAATCATATAACATTTAAGCATATATCACAATACATCATA
Found at i:35416175 original size:15 final size:15
Alignment explanation
Indices: 35416133--35416175 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
35416123 GCATAATGGT
*
35416133 CACAT-TTCATATAAA
1 CACATATTCATA-ATA
35416148 CACATA-TCATAATA
1 CACATATTCATAATA
35416162 CACATATTCATAAT
1 CACATATTCATAAT
35416176 TTAAGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (15 bp):
CACATATTCATAATA
Found at i:35424028 original size:7 final size:7
Alignment explanation
Indices: 35424016--35424041 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35424006 TCCCTTCCCA
35424016 TCCCACC
1 TCCCACC
35424023 TCCCACC
1 TCCCACC
35424030 TCCCACC
1 TCCCACC
35424037 TCCCA
1 TCCCA
35424042 TCTACCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCACC
Found at i:35424790 original size:5 final size:5
Alignment explanation
Indices: 35424780--35424806 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35424770 CTCGAAATTT
35424780 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
35424807 GAACGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:35431925 original size:18 final size:19
Alignment explanation
Indices: 35431886--35431928 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
35431876 ATTTATAATT
*
35431886 TAAAAAATATTAATTACTA
1 TAAAAAATATTAAGTACTA
35431905 TAAAAAATATT-AGTA-TGA
1 TAAAAAATATTAAGTACT-A
35431923 TAAAAA
1 TAAAAA
35431929 TAATTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 10 0.45
19 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAAAATATTAAGTACTA
Found at i:35436460 original size:25 final size:25
Alignment explanation
Indices: 35436432--35436479 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
35436422 ACTGTGTTCA
* *
35436432 CCAGGCAAGTTGCCAACTGGGTTTG
1 CCAGGCAAGGTGCCAACAGGGTTTG
* *
35436457 CCAGTCAAGGTGCGAACAGGGTT
1 CCAGGCAAGGTGCCAACAGGGTT
35436480 CGCTGGTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (25 bp):
CCAGGCAAGGTGCCAACAGGGTTTG
Found at i:35439245 original size:27 final size:28
Alignment explanation
Indices: 35439179--35439247 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
35439169 GAAGATGAAG
* * *
35439179 AGGAAAAAAAGAA-AAATAAAGAGAGAA
1 AGGAAAAAAATAAGAAAGAAAGAGAAAA
***
35439206 AGGAAAGTGATAAGAAAGAAAGA-AAAA
1 AGGAAAAAAATAAGAAAGAAAGAGAAAA
35439233 AGGAAAAAAATAAGA
1 AGGAAAAAAATAAGA
35439248 GTGTGGGAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (28 bp):
AGGAAAAAAATAAGAAAGAAAGAGAAAA
Found at i:35446006 original size:44 final size:44
Alignment explanation
Indices: 35445958--35446053 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
35445948 ATATCTCAAG
*
35445958 GTCCATGTTTATAACATGGCAATTAAGGAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
*
35446002 GTCCATGTTTATAACATGGCAATTAATAAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
35446046 GTACCATG
1 GT-CCATG
35446054 GTTGATCCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
Found at i:35446170 original size:50 final size:50
Alignment explanation
Indices: 35446071--35446316 Score: 314
Period size: 50 Copynumber: 4.9 Consensus size: 50
35446061 CATGTCAACA
35446071 CGAGATGAGAGGTCCCATGTAAGA-CATGTCTGGGATATGGCATTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* * *
35446120 CGAGATGAGAGGTCCCATGTAGGACCATGTCTGGGATATGGCGTTTGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* * *
35446170 CAAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* ** * ** * *
35446220 CAAGATGAGAGGTCCCCCGTAAGACCATGTTTGGGGCATGGCATGGGCAT
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
* ** * *
35446270 CGATATGAGAACTCCCATGTAAGATCATATCTGGGATATGGCATTGG
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGG
35446317 TAGTACAGGA
Statistics
Matches: 170, Mismatches: 26, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 23 0.14
50 147 0.86
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAC
Found at i:35451510 original size:3 final size:3
Alignment explanation
Indices: 35451504--35451553 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
35451494 TTTAATAGTC
* * * * *
35451504 GAA GAA GAA GAA GAA GAA GAA GGA GAT GAT GAA GAA CAA GAA CAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
35451552 GA
1 GA
35451554 GGAATTTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.60, C:0.04, G:0.32, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:35451928 original size:46 final size:46
Alignment explanation
Indices: 35451860--35451950 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
35451850 GTGGTTACTG
* *
35451860 TTGTTTAAGAGTGTATTTTATATACTTCTCTAGAATGTTGATTTTC
1 TTGTTTAAGAGTGTAGTATATATACTTCTCTAGAATGTTGATTTTC
*
35451906 TTGTTTAAGAGTGTAGTATATATACTTCTCTAGAATGTTGTTTTT
1 TTGTTTAAGAGTGTAGTATATATACTTCTCTAGAATGTTGATTTT
35451951 TTTTTGTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (46 bp):
TTGTTTAAGAGTGTAGTATATATACTTCTCTAGAATGTTGATTTTC
Found at i:35461755 original size:21 final size:21
Alignment explanation
Indices: 35461714--35461755 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
35461704 CAATTATTTA
*
35461714 AATTAAAATAAATTAAATAAT
1 AATTAAAATAAAGTAAATAAT
*
35461735 AATTCAAAA-AAAGTAATTAAT
1 AATT-AAAATAAAGTAAATAAT
35461756 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTAAAATAAAGTAAATAAT
Found at i:35462549 original size:27 final size:27
Alignment explanation
Indices: 35462519--35462575 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
35462509 GTGAGCTAGC
* *
35462519 GTACACCAATAGGTTTGGCGAGTTCGT
1 GTACACCAAAAGGTCTGGCGAGTTCGT
*
35462546 GTACACCAAAAGGTCTGGCGAGTTTGT
1 GTACACCAAAAGGTCTGGCGAGTTCGT
35462573 GTA
1 GTA
35462576 TAAACAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (27 bp):
GTACACCAAAAGGTCTGGCGAGTTCGT
Found at i:35466042 original size:31 final size:31
Alignment explanation
Indices: 35466007--35466068 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
35465997 AAGTAACTTA
35466007 ATCAGTGATTGTCCAACGACCTTGTCATAAG
1 ATCAGTGATTGTCCAACGACCTTGTCATAAG
* *
35466038 ATCAGTGCTTGTCCAACGACCTTGTCGTAAG
1 ATCAGTGATTGTCCAACGACCTTGTCATAAG
35466069 TGTGTTACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (31 bp):
ATCAGTGATTGTCCAACGACCTTGTCATAAG
Found at i:35473704 original size:24 final size:24
Alignment explanation
Indices: 35473676--35473727 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
35473666 TTCATAGGTC
* *
35473676 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
35473700 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
35473724 AAAT
1 AAAT
35473728 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:35475989 original size:23 final size:23
Alignment explanation
Indices: 35475963--35476017 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
35475953 ATTACTAGTA
* *
35475963 TATTATGTT-TATAATTTTATTTT
1 TATTTTGTTGTATAAATTT-TTTT
*
35475986 TATTTTATTGTATAAATTTTTTT
1 TATTTTGTTGTATAAATTTTTTT
35476009 TATTTTGTT
1 TATTTTGTT
35476018 ATTTTTGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (23 bp):
TATTTTGTTGTATAAATTTTTTT
Found at i:35476716 original size:14 final size:14
Alignment explanation
Indices: 35476697--35476734 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35476687 TGTAAGTCTT
35476697 AACCCTAAA-TATTA
1 AACCCTAAACTA-TA
35476711 AACCCTAAACTATA
1 AACCCTAAACTATA
*
35476725 AAACCTAAAC
1 AACCCTAAAC
35476735 CCCAAACTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAACTATA
Found at i:35476856 original size:21 final size:22
Alignment explanation
Indices: 35476831--35476884 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
35476821 CGTAAACATT
**
35476831 AACCATAAATTTTAAACCC-TA
1 AACCATAAACATTAAACCCGTA
35476852 AACCATAAACATTAAACCCGTA
1 AACCATAAACATTAAACCCGTA
*
35476874 AACCACAAACA
1 AACCATAAACA
35476885 ACAACCACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.19
Consensus pattern (22 bp):
AACCATAAACATTAAACCCGTA
Found at i:35482299 original size:11 final size:11
Alignment explanation
Indices: 35482280--35482315 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35482270 CATCTCGTCC
35482280 GAATTCTTGGT
1 GAATTCTTGGT
*
35482291 GAATCCTTGGT
1 GAATTCTTGGT
*
35482302 GAATTTTTGGT
1 GAATTCTTGGT
35482313 GAA
1 GAA
35482316 GGTGCCTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (11 bp):
GAATTCTTGGT
Found at i:35485360 original size:5 final size:6
Alignment explanation
Indices: 35485345--35485392 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
35485335 AAGAAGTCTA
*
35485345 AAAAAT AAAAAT AAAACAACT AAAAA- CAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT -AAA-AA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAA
35485393 CTGAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 21 0.58
7 5 0.14
8 5 0.14
9 1 0.03
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:35486910 original size:3 final size:3
Alignment explanation
Indices: 35486904--35486948 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
35486894 ATATGAAACC
35486904 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35486949 CAAACTAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35489720 original size:3 final size:3
Alignment explanation
Indices: 35489712--35489762 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
35489702 GTAATAACAG
*
35489712 TAA TAA TAA AAA TAA TAAA TAA TAAA TAA TAAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA T-AA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA
35489758 TAA TA
1 TAA TA
35489763 GGGGAGGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 4 0.10
3 28 0.68
4 9 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:35489733 original size:7 final size:7
Alignment explanation
Indices: 35489712--35489747 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
35489702 GTAATAACAG
35489712 TAAT-AA
1 TAATAAA
35489718 TAA-AAA
1 TAATAAA
35489724 TAATAAA
1 TAATAAA
35489731 TAATAAA
1 TAATAAA
35489738 TAATAAA
1 TAATAAA
35489745 TAA
1 TAA
35489748 AATAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 8 0.29
7 20 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAATAAA
Found at i:35489741 original size:23 final size:24
Alignment explanation
Indices: 35489713--35489760 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
35489703 TAATAACAGT
35489713 AATAATAAA-AATAAT-AAATAATA
1 AATAATAAATAA-AATAAAATAATA
35489736 AATAATAAATAAAATAAAATAATA
1 AATAATAAATAAAATAAAATAATA
35489760 A
1 A
35489761 TAGGGGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (24 bp):
AATAATAAATAAAATAAAATAATA
Found at i:35496238 original size:23 final size:24
Alignment explanation
Indices: 35496200--35496257 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
35496190 AAACAAAAGA
* * *
35496200 AAAATTAAAATGTAAAAATTAAAT
1 AAAATAAAAATATAAAAATGAAAT
*
35496224 TAAA-AAAAATATAAAAATGAAAT
1 AAAATAAAAATATAAAAATGAAAT
35496247 AAAATAAAAAT
1 AAAATAAAAAT
35496258 GGATAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (24 bp):
AAAATAAAAATATAAAAATGAAAT
Found at i:35501091 original size:15 final size:15
Alignment explanation
Indices: 35501071--35501104 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
35501061 CAATTCGAAT
35501071 ATACGATTGGTGTAA
1 ATACGATTGGTGTAA
*
35501086 ATACGATTGTTGTAA
1 ATACGATTGGTGTAA
35501101 ATAC
1 ATAC
35501105 CCTTTTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (15 bp):
ATACGATTGGTGTAA
Found at i:35501239 original size:21 final size:21
Alignment explanation
Indices: 35501192--35501239 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35501182 ACTTTATAAC
35501192 TCAAAA-AATTATAAAAAGTT
1 TCAAAAGAATTATAAAAAGTT
*
35501212 TCGAAAGAATATATAAAAA-TT
1 TCAAAAGAAT-TATAAAAAGTT
*
35501233 TTAAAAG
1 TCAAAAG
35501240 CATAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (21 bp):
TCAAAAGAATTATAAAAAGTT
Found at i:35505829 original size:41 final size:41
Alignment explanation
Indices: 35505779--35505860 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
35505769 TTGTAAAGTT
*
35505779 GTTATTTTATTTATTTAACTTTTATATATTCTCCCTATATA
1 GTTATTTTATTTATTTAACTTTTATATATTCTCACTATATA
35505820 GTTATTTTATTTATTTAACTTTTATATATTCTCACTATATA
1 GTTATTTTATTTATTTAACTTTTATATATTCTCACTATATA
35505861 TATACTATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (41 bp):
GTTATTTTATTTATTTAACTTTTATATATTCTCACTATATA
Found at i:35506036 original size:10 final size:10
Alignment explanation
Indices: 35506021--35506055 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
35506011 AATGTTCATA
35506021 TTATTTATTG
1 TTATTTATTG
35506031 TTATTTATTG
1 TTATTTATTG
*
35506041 TTA-TTATTA
1 TTATTTATTG
35506050 TTATTT
1 TTATTT
35506056 TATTCGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (10 bp):
TTATTTATTG
Found at i:35506539 original size:82 final size:83
Alignment explanation
Indices: 35506422--35506588 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 83
35506412 AAACTAAACA
*
35506422 TTTATAATTTCAAAATGTCGTATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT
1 TTTATAATTTCAAAATGTCGCATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT
35506487 -AAGGCAATGTTTGATGC
66 AAAGGCAATGTTTGATGC
35506504 TTTATAATTTCAAAATGTCGCATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT
1 TTTATAATTTCAAAATGTCGCATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT
35506569 AAAGGCAATGTTTGATGC
66 AAAGGCAATGTTTGATGC
35506587 TT
1 TT
35506589 AAGAACTTCG
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 64 0.77
83 19 0.23
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (83 bp):
TTTATAATTTCAAAATGTCGCATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT
AAAGGCAATGTTTGATGC
Found at i:35506624 original size:83 final size:82
Alignment explanation
Indices: 35506430--35506616 Score: 270
Period size: 82 Copynumber: 2.3 Consensus size: 82
35506420 CATTTATAAT
* *
35506430 TTCAAAATGTCGTATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTTAAGGCAAT
1 TTCAAAATGTCGAACCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTTAAGGCAAT
* * *
35506495 GTTTGATGCTTTATAAT
66 GTTTGATGCTTAAGAAC
* *
35506512 TTCAAAATGTCGCATCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTTAAAGGCAA
1 TTCAAAATGTCGAACCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTT-AAGGCAA
35506577 TGTTTGATGCTTAAGAAC
65 TGTTTGATGCTTAAGAAC
35506595 TTCGAGAAAT-T-GAACCCTAACT
1 TTC-A-AAATGTCGAACCCTAACT
35506617 CATTGGATTC
Statistics
Matches: 96, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
82 56 0.58
83 34 0.35
84 2 0.02
85 4 0.04
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (82 bp):
TTCAAAATGTCGAACCCTAACTTACTGGATGTGATATTTTGTTATCCTGATTTTTTTAAGGCAAT
GTTTGATGCTTAAGAAC
Found at i:35507529 original size:9 final size:10
Alignment explanation
Indices: 35507505--35507565 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
35507495 ACAATAATTG
35507505 AAAAATTCATT
1 AAAAATT-ATT
35507516 AAAAATTA-T
1 AAAAATTATT
*
35507525 AAAAATAATT
1 AAAAATTATT
*
35507535 AAAAATTA-G
1 AAAAATTATT
*
35507544 AAATA-TATT
1 AAAAATTATT
35507553 AAAAATTA-T
1 AAAAATTATT
35507562 AAAA
1 AAAA
35507566 TCGATTCAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 2 0.05
9 21 0.51
10 11 0.27
11 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAAATTATT
Found at i:35507553 original size:18 final size:19
Alignment explanation
Indices: 35507500--35507565 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
35507490 ATTCAACAAT
*
35507500 AATT-GAAAAATTCATTAAA
1 AATTAGAAAAA-TAATTAAA
*
35507519 AATTATAAAAATAATTAAA
1 AATTAGAAAAATAATTAAA
*
35507538 AATTAGAAATAT-ATTAAA
1 AATTAGAAAAATAATTAAA
*
35507556 AATTATAAAA
1 AATTAGAAAA
35507566 TCGATTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 14 0.35
19 21 0.52
20 5 0.12
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTAGAAAAATAATTAAA
Found at i:35508619 original size:42 final size:42
Alignment explanation
Indices: 35508560--35508643 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
35508550 CACAAGGGAA
35508560 AAATTACACAAATTAAATATAAATTGTATATCTCACTAAATT
1 AAATTACACAAATTAAATATAAATTGTATATCTCACTAAATT
*
35508602 AAATTACACAAATTAAATATAAATTGTATATCTCATTAAATT
1 AAATTACACAAATTAAATATAAATTGTATATCTCACTAAATT
35508644 TCCCTGCACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (42 bp):
AAATTACACAAATTAAATATAAATTGTATATCTCACTAAATT
Found at i:35509232 original size:54 final size:54
Alignment explanation
Indices: 35509162--35509274 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
35509152 AGTATCATAT
35509162 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
35509216 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
35509270 ATTAT
1 ATTAT
35509275 ATATTTTAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
Found at i:35509294 original size:16 final size:16
Alignment explanation
Indices: 35509273--35509314 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35509263 TTATTAAATT
*
35509273 ATATATTTTAATTATA
1 ATATATTTTAATAATA
35509289 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
35509304 AT-TATGTTTAA
1 ATATAT-TTTAA
35509315 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:35509299 original size:15 final size:15
Alignment explanation
Indices: 35509264--35509305 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35509254 TTAAGAATTT
*
35509264 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35509278 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35509292 TATTTAATAATAAT
1 TATTTAATTATAAT
35509306 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35509540 original size:45 final size:43
Alignment explanation
Indices: 35509440--35509549 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
35509430 TTTTCCATTA
35509440 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
35509479 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
35509524 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
35509550 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:35509551 original size:16 final size:16
Alignment explanation
Indices: 35509530--35509582 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
35509520 GATTTGCTAT
*
35509530 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
35509546 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
35509562 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35509578 TACAC
1 TACAC
35509583 TTCGTCACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Done.