Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 140 of 328
Found at i:40813334 original size:13 final size:14
Alignment explanation
Indices: 40813318--40813359 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40813308 TTTCAATTTT
40813318 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
40813331 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
40813346 ATTTTAAATAATAT
1 ATTTT-AATAATAT
40813360 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:40813344 original size:16 final size:16
Alignment explanation
Indices: 40813322--40813358 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40813312 AATTTTATTT
40813322 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
40813339 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
40813354 TAATA
1 TAATA
40813359 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:40815761 original size:20 final size:19
Alignment explanation
Indices: 40815727--40815766 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
40815717 CATTTCAATT
*
40815727 TCATTTATCATTTCACATG
1 TCATTTATCAATTCACATG
*
40815746 TCATTTAATCAATTCATATG
1 TCATTT-ATCAATTCACATG
40815766 T
1 T
40815767 TTATAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (19 bp):
TCATTTATCAATTCACATG
Found at i:40817154 original size:63 final size:63
Alignment explanation
Indices: 40817044--40817163 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 63
40817034 TCAAGTTGTG
* *
40817044 TAACTCACTATTTGTGATTTAGGGTCACATGAGGTAGGGACATGGGCGTGTGTCCAGACTGTT
1 TAACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTT
* * *
40817107 TAACTCACTATTTGTGATTTAGTGTCATATG-GGTCATAGACACGGGCGTGTGTCCAG
1 TAACTCACTATTTGTGATTTAGGGTCACATGAGGT-AGAGACACGGGCGTGTGTCCAG
40817164 GTTGTGTGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (63 bp):
TAACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTT
Found at i:40818317 original size:22 final size:21
Alignment explanation
Indices: 40818269--40818319 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
40818259 ATAAACTATT
40818269 ACTATTTTAGGGAAAAATAAC
1 ACTATTTTAGGGAAAAATAAC
* * * *
40818290 AATATTTTAGAGTAACAATATC
1 ACTATTTTAG-GGAAAAATAAC
40818312 ACTATTTT
1 ACTATTTT
40818320 CGCCTGGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
ACTATTTTAGGGAAAAATAAC
Found at i:40820374 original size:46 final size:46
Alignment explanation
Indices: 40820324--40820499 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
40820314 TGGTTGAGCA
40820324 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40820370 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40820415 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40820463 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40820500 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40820480 original size:93 final size:93
Alignment explanation
Indices: 40820321--40820492 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40820311 GGATGGTTGA
* *
40820321 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40820386 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40820414 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40820479 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
40820493 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40827889 original size:46 final size:46
Alignment explanation
Indices: 40827839--40828014 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
40827829 TGGTTGAGCA
40827839 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40827885 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40827930 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40827978 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40828015 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40827995 original size:93 final size:93
Alignment explanation
Indices: 40827836--40828007 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40827826 GGATGGTTGA
* *
40827836 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40827901 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40827929 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40827994 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
40828008 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40834799 original size:46 final size:46
Alignment explanation
Indices: 40834749--40834924 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
40834739 TGGTTGAGCA
40834749 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40834795 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40834840 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40834888 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40834925 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40834905 original size:93 final size:93
Alignment explanation
Indices: 40834746--40834917 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40834736 GGATGGTTGA
* *
40834746 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40834811 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40834839 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40834904 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
40834918 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40842330 original size:46 final size:46
Alignment explanation
Indices: 40842280--40842455 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
40842270 TGGTTGAGCA
40842280 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
40842326 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GAAG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40842371 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40842419 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40842456 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40842436 original size:93 final size:93
Alignment explanation
Indices: 40842277--40842448 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40842267 GGATGGTTGA
* *
40842277 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40842342 TGAGTCCGAGTTCGTGAGAAGTAACTAG
66 TGAGTCCGAGTTCGTGAGAAGTAACTAG
*
40842370 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40842435 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
40842449 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGAAGTAACTAG
Found at i:40845565 original size:23 final size:23
Alignment explanation
Indices: 40845538--40845582 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40845528 TTGTATTAAT
40845538 TTACTAAATTAAACTTAAAAATG
1 TTACTAAATTAAACTTAAAAATG
* *
40845561 TTACTAAATTTATCTTAAAAAT
1 TTACTAAATTAAACTTAAAAAT
40845583 TATAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
TTACTAAATTAAACTTAAAAATG
Found at i:40850336 original size:2 final size:2
Alignment explanation
Indices: 40850329--40850367 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40850319 TAAATCAATC
40850329 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40850368 GTTAGTATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40850545 original size:24 final size:25
Alignment explanation
Indices: 40850502--40850583 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
40850492 TAGCTCGAGA
* *
40850502 GAGCTTACCGATATTCAGCTCGTAT
1 GAGCTTACTGTTATTCAGCTCGTAT
*
40850527 GAGCTTA-TGTTATTCAGCTTGTAT
1 GAGCTTACTGTTATTCAGCTCGTAT
* *
40850551 GAGTTTACTGTTACTCAGCTCGTAT
1 GAGCTTACTGTTATTCAGCTCGTAT
*
40850576 AAGCTTAC
1 GAGCTTAC
40850584 CGATTACAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 20 0.42
25 28 0.58
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGCTCGTAT
Found at i:40858939 original size:39 final size:39
Alignment explanation
Indices: 40858859--40858940 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
40858849 ATGCAAGACA
* *
40858859 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTATG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCATG
* *
40858898 CTGGAAATGTGTCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCATG
40858937 CTGG
1 CTGG
40858941 TGCTGGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCATG
Found at i:40862935 original size:52 final size:49
Alignment explanation
Indices: 40862877--40863088 Score: 182
Period size: 52 Copynumber: 4.2 Consensus size: 49
40862867 GACGGAAAAT
*
40862877 ATGTGATATGTGCTTCCGTAAAAGACCATAGCTGGGCTATGGCATCGGTACA
1 ATGTGATATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT--A
* * * *
40862929 ATGTGAT-TCGAGTTCCCGTATAAGACCATAGCTGGGTTATAGCATCGGTGTG
1 ATGTGATAT-GTGTT-CCGTATAAGACCATAGCTGGGCTATGGCATC-G-GTA
* * * *
40862981 ATGTGATAATATGACTCCGTATAAGACCATATCTGGGATATGGCATCGGT-
1 ATGTGAT-ATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
* * * *
40863031 ATGT--TATGTGATCCGTATAAGACCATGGCAGGGCTATGGCTTCGGT-
1 ATGTGATATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
*
40863077 ATGTGATGTGTG
1 ATGTGATATGTG
40863089 ACAATGTGAA
Statistics
Matches: 132, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
46 34 0.26
47 4 0.03
48 6 0.05
50 4 0.03
51 5 0.04
52 45 0.34
53 30 0.23
54 4 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
ATGTGATATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
Found at i:40863069 original size:46 final size:46
Alignment explanation
Indices: 40862996--40863086 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
40862986 ATAATATGAC
* * *
40862996 TCCGTATAAGACCATATCTGGGATATGGCATCGGTATGTTATGTGA
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
* * *
40863042 TCCGTATAAGACCATGGCAGGGCTATGGCTTCGGTATGTGATGTG
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTG
40863087 TGACAATGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
Found at i:40865707 original size:25 final size:25
Alignment explanation
Indices: 40865674--40865893 Score: 136
Period size: 25 Copynumber: 8.9 Consensus size: 25
40865664 GGTTTCTCAC
*
40865674 AAGATTAGCCACAAAGGCTTTTCAT
1 AAGAATAGCCACAAAGGCTTTTCAT
*
40865699 AGGAATAGCCACAAAGG-TTTTCCAT
1 AAGAATAGCCACAAAGGCTTTT-CAT
* *
40865724 ATA-ATATA-CCATAAAGGCTTTCCA-
1 A-AGA-ATAGCCACAAAGGCTTTTCAT
* **
40865748 AAAAATA-CCACAAA-AATGTTTCAT
1 AAGAATAGCCACAAAGGCT-TTTCAT
*
40865772 AAGATTAGCCACAAAGGC-TTTC-T
1 AAGAATAGCCACAAAGGCTTTTCAT
* * * *
40865795 AGATAATACACCACAAATGCTTCTCAT
1 A-AGAATA-GCCACAAAGGCTTTTCAT
* *
40865822 AAGATTAGCCACAAAGGCTTTCCA-
1 AAGAATAGCCACAAAGGCTTTTCAT
* * *
40865846 AATAATATGCCAAAAAGGTTTTTCAT
1 AAGAATA-GCCACAAAGGCTTTTCAT
* *
40865872 AAGATTAGCCATAAAGG-TTTTC
1 AAGAATAGCCACAAAGGCTTTTC
40865894 TAGATAATCC
Statistics
Matches: 148, Mismatches: 32, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 16 0.11
24 29 0.20
25 82 0.55
26 18 0.12
27 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (25 bp):
AAGAATAGCCACAAAGGCTTTTCAT
Found at i:40865829 original size:50 final size:49
Alignment explanation
Indices: 40865667--40865901 Score: 194
Period size: 50 Copynumber: 4.8 Consensus size: 49
40865657 TTACAAGGGT
* * * *
40865667 TTCTCACAAGATTAGCCACAAAGGCTTTTCATAG-GAATA-GCCACAAAGG
1 TTCTCATAAGATTAGCCACAAAGGC-TTTC-TAGATAATACGCCAAAAATG
* * * * *
40865716 TTTTCCATATA-ATATA-CCATAAAGGCTTTCCAAAAAATAC-CACAAAAATG
1 TTCT-CATA-AGAT-TAGCCACAAAGGCTTTCTAGATAATACGC-CAAAAATG
* *
40865766 TT-TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCACAAATG
1 TTCTCATAAGATTAGCCACAAAGGCTTTCTAGATAATACGCCAAAAATG
* * * *
40865814 CTTCTCATAAGATTAGCCACAAAGGCTTTCCAAATAATATGCCAAAAAGG
1 -TTCTCATAAGATTAGCCACAAAGGCTTTCTAGATAATACGCCAAAAATG
* * *
40865864 TTTTTCATAAGATTAGCCATAAAGGTTTTCTAGATAAT
1 -TTCTCATAAGATTAGCCACAAAGGCTTTCTAGATAAT
40865902 CCATTTTTAC
Statistics
Matches: 150, Mismatches: 25, Indels: 21
0.77 0.13 0.11
Matches are distributed among these distances:
47 3 0.02
48 34 0.23
49 16 0.11
50 94 0.63
51 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (49 bp):
TTCTCATAAGATTAGCCACAAAGGCTTTCTAGATAATACGCCAAAAATG
Found at i:40868273 original size:29 final size:29
Alignment explanation
Indices: 40868241--40868308 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
40868231 ATACTATTAT
*
40868241 TATTTATATAATTTTTAT-TTATCTATTTA
1 TATTTATATAATTATTATATT-TCTATTTA
* *
40868270 TATTTCTACT-ATTATTATATTTCTATTTC
1 TATTTATA-TAATTATTATATTTCTATTTA
40868299 TATTTATATA
1 TATTTATATA
40868309 CTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 28 0.88
30 3 0.09
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTATATAATTATTATATTTCTATTTA
Found at i:40868282 original size:23 final size:23
Alignment explanation
Indices: 40868232--40868300 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
40868222 GTTATTCTAA
*
40868232 TACTATTATTAT-TTATATAATTTT
1 TACTATTATTATATT-TAT-ATTTC
*
40868256 TA-T-TTA-TCTATTTATATTTC
1 TACTATTATTATATTTATATTTC
*
40868276 TACTATTATTATATTTCTATTTC
1 TACTATTATTATATTTATATTTC
40868299 TA
1 TA
40868301 TTTATATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.16
21 6 0.16
22 8 0.22
23 15 0.41
24 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (23 bp):
TACTATTATTATATTTATATTTC
Found at i:40868446 original size:3 final size:3
Alignment explanation
Indices: 40868438--40868601 Score: 163
Period size: 3 Copynumber: 54.3 Consensus size: 3
40868428 TTTAAAACTT
40868438 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
40868486 TTA TTA TTA TTA TTA -TA TTTA TGTA TCA ATA TCA TTA TT- TTT TTA
1 TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * * * *
40868531 TT- TTT TTA TATA TTA TTA TCA TTA TTA TTA TTA CTA TTA GTA CTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40868576 TTA TTC TTT TCTA TTA TTA TTT TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA T
40868602 ATTTATTTAT
Statistics
Matches: 134, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
2 6 0.04
3 118 0.88
4 10 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40870788 original size:19 final size:20
Alignment explanation
Indices: 40870749--40870791 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
40870739 TCTCTTTTTA
*
40870749 CATT-CATTTCATGCATCTG
1 CATTGCATTTCATGCATATG
40870768 CATTGCATTTCAT-CATATG
1 CATTGCATTTCATGCATATG
40870787 CATTG
1 CATTG
40870792 AATGTCACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
CATTGCATTTCATGCATATG
Found at i:40872593 original size:40 final size:40
Alignment explanation
Indices: 40872465--40872616 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
40872455 ATAAGCATGT
* * *
40872465 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-CA
* ** *
40872505 GCACGAA-TGCCTTCGGGTCTTAGCCTGGATATAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* **
40872545 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* * *
40872585 GCATAATTGTCTTCGGGGT-TTAGCCCAGATAT
1 GCACAATTGCCTTC-GGGTCTTAGCCCGGATAT
40872617 CATTTCTCAT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 83 0.91
41 6 0.07
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
Found at i:40877446 original size:18 final size:19
Alignment explanation
Indices: 40877418--40877453 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
40877408 ACCTTGAGAC
40877418 CAAAAATAATAATAAAAAT
1 CAAAAATAATAATAAAAAT
40877437 CAAAAA-AATAATAAAAA
1 CAAAAATAATAATAAAAA
40877454 AATAAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (19 bp):
CAAAAATAATAATAAAAAT
Found at i:40878919 original size:45 final size:44
Alignment explanation
Indices: 40878811--40879080 Score: 145
Period size: 44 Copynumber: 6.1 Consensus size: 44
40878801 AGCCACCAGC
* * * * * *
40878811 CTTATTTCCCTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAGT
* *
40878855 CTTATCTTTTTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAG-T
* * * *
40878900 CTTATCTCTCTGAGATAGC-AGTGGAGTAGATCGAATACGA--CAAAT
1 CTTATCTCTCTGAGGTAGCAAG-GGAGTAGA-CTAA-A-GATTGAAGT
* * * ** ***** *
40878945 CTTATCT-TCCCGAGGTAGC-AGAGGAGCAGATTTTAGCCACCAGC
1 CTTATCTCT-CTGAGGTAGCAAG-GGAGTAGACTAAAGATTGAAGT
* * * *
40878989 CTTATTTCCCTGAGGTAGCAAGGGAGTAGGCTAAAGATTGCAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAGT
* * ** *
40879033 CTTATCTTTCTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAG-T
40879078 CTT
1 CTT
40879081 GTATTCCTGA
Statistics
Matches: 167, Mismatches: 48, Indels: 21
0.71 0.20 0.09
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 101 0.60
45 56 0.34
46 5 0.03
47 1 0.01
48 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTGAGGTAGCAAGGGAGTAGACTAAAGATTGAAGT
Found at i:40879149 original size:45 final size:43
Alignment explanation
Indices: 40878998--40879195 Score: 125
Period size: 44 Copynumber: 4.5 Consensus size: 43
40878988 CCTTATTTCC
** * *
40878998 CTGAGGTAGCAAGGGAGTAGGCTAAAGATTGCAG-TCTTATCTTT
1 CTGAGGTAGCAATAGAGCAGGCT-AAGATTGAAGATCTTATC-TT
* * * *
40879042 CTGAGGTAGCAA-AGGAACAGACTGAAGATTGAAGATCTTGTATT
1 CTGAGGTAGCAATA-GAGCAGGCT-AAGATTGAAGATCTTATCTT
* * *
40879086 CCTGA-GCAGCAATAGAGCAGGCTACGGATTGTAGATCTTATCTT
1 -CTGAGGTAGCAATAGAGCAGGCTA-AGATTGAAGATCTTATCTT
* * ** *
40879130 CATGAGGTAGCAATAGAGCAGATCGAAGA-TGGCGAATCTTATCTC
1 C-TGAGGTAGCAATAGAGCAG-GCTAAGATTGAAG-ATCTTATCTT
*
40879175 CATGAGGTAGCAATGGAGCAG
1 C-TGAGGTAGCAATAGAGCAG
40879196 ATTTAAGCCA
Statistics
Matches: 122, Mismatches: 23, Indels: 17
0.75 0.14 0.10
Matches are distributed among these distances:
43 2 0.02
44 63 0.52
45 55 0.45
46 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (43 bp):
CTGAGGTAGCAATAGAGCAGGCTAAGATTGAAGATCTTATCTT
Found at i:40879239 original size:44 final size:44
Alignment explanation
Indices: 40879167--40879284 Score: 110
Period size: 44 Copynumber: 2.7 Consensus size: 44
40879157 GATGGCGAAT
* * * ** * * *
40879167 CTTATCTCCATGAGGTAGCAATGGAGCAGATTTAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATCGAAACCACAAAC
* * * **
40879211 CTTATCTCCCTGAAGTTGCAGTGAAGCAGGTCGAAATTACAAAC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATCGAAACCACAAAC
*
40879255 CTTATCTCCCTGAAGTTGCATTGGAGCAGA
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGA
40879285 CTGAAGATAG
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAATGGAGCAGATCGAAACCACAAAC
Found at i:40879335 original size:45 final size:45
Alignment explanation
Indices: 40879210--40879692 Score: 142
Period size: 44 Copynumber: 10.8 Consensus size: 45
40879200 AAGCCACCAG
* *
40879210 CCTTATCTCCCTGAAGTTGCAGT-GAAGCAGGTCGAA-ATTACAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTGAAGATTACAAA
* * *
40879254 CCTTATCTCCCTGAAGTTGCATTGGAGCAGACTGAAGA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATTA-CAAA
* * * *
40879299 TCTTATTTCCCTGAAGATGCAGTGGAACAGATTGAAGCTATAAATAAACAGA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG--AT---T--ACAAA
* * * * *
40879351 TCTTATCTCTCTGAA-TTGCAGTAGAGCAGA-T---CA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATTA-CAAA
* * * * * **
40879391 CTTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTGAAG-TAACAGG
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATTACAAA
* * * * * * ** * *
40879435 TCTTATCTTCTTGAGGTAGCAG-GGAAGCAGATTTAAG-CCACCAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTGAAGATTACAAA
* * * * * *
40879479 CCTTATCTCCCTGAAATTACAGTGGAGCA-AGTTG-ACATTGCCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGA-TTGAAGATT-ACAAA
* * * * * * *
40879524 CCTTATCTCCCTAAAGTTGTAGTGGAGCA-A--GAAAATAAACGAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT-TACAAA
* * * * * *
40879567 TCTTATCTCTCTGAAGTTGTAGTGGAGCA-AGTTGAAG-TCACGAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGA-TTGAAGATTACAAA
* * * *
40879611 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAA-ATTATCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATTA-CAAA
* * * * * *
40879656 TCTTATCTCCTTGAAGTTTCAGCGGAATAGATCGAAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG
40879693 CTACAAATCT
Statistics
Matches: 321, Mismatches: 86, Indels: 62
0.68 0.18 0.13
Matches are distributed among these distances:
39 1 0.00
40 14 0.04
41 14 0.04
42 2 0.01
43 37 0.12
44 117 0.36
45 101 0.31
46 3 0.01
47 1 0.00
50 1 0.00
51 13 0.04
52 16 0.05
53 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (45 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATTACAAA
Found at i:40879630 original size:44 final size:45
Alignment explanation
Indices: 40879479--40879648 Score: 170
Period size: 44 Copynumber: 3.8 Consensus size: 45
40879469 AAGCCACCAG
* ** * *
40879479 CCTTATCTCCCTGAAATTACAGTGGAGCAAGTTGACATTGC-C-AA
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGA-AATACACGAA
* * * *
40879523 TCCTTATCTCCCTAAAGTTGTAGTGGAGCAAG--AAAATAAACGAG
1 -CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAATACACGAA
* * *
40879567 TCTTATCTCTCTGAAGTTGTAGTGGAGCAAGTTGAAGT-CACGAA
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAATACACGAA
*
40879611 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAAT
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAAT
40879649 TATCAATTCT
Statistics
Matches: 101, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.02
43 30 0.30
44 39 0.39
45 30 0.30
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (45 bp):
CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAATACACGAA
Found at i:40879639 original size:87 final size:88
Alignment explanation
Indices: 40879480--40879639 Score: 227
Period size: 88 Copynumber: 1.8 Consensus size: 88
40879470 AGCCACCAGC
*
40879480 CTTATCTCCCTGAAATTACAGTGGAGCAAGTTGACATTGCCAATCCTTATCTCCCTAAAGTTGTA
1 CTTATCTCCCTGAAATTACAGTGGAGCAAGTTGACAGTGCCAATCCTTATCTCCCTAAAGTTGTA
40879545 GTGGAGCAAGAAAATAAACGAGT
66 GTGGAGCAAGAAAATAAACGAGT
* * ** *
40879568 CTTATCTCTCTGAAGTTGTAGTGGAGCAAGTTGA-AGT-CACGAA-CCTTATCTCCCTGAAGTTG
1 CTTATCTCCCTGAAATTACAGTGGAGCAAGTTGACAGTGC-C-AATCCTTATCTCCCTAAAGTTG
40879630 TAGTGGAGCA
64 TAGTGGAGCA
40879640 GGTTGAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
86 1 0.02
87 31 0.48
88 32 0.50
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (88 bp):
CTTATCTCCCTGAAATTACAGTGGAGCAAGTTGACAGTGCCAATCCTTATCTCCCTAAAGTTGTA
GTGGAGCAAGAAAATAAACGAGT
Found at i:40880132 original size:15 final size:15
Alignment explanation
Indices: 40880105--40880142 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
40880095 TTTGTTTTTG
40880105 TTTTTATTTATTT-A
1 TTTTTATTTATTTCA
40880119 TTTTTATTTCATTTCA
1 TTTTTATTT-ATTTCA
40880135 -TTTTATTT
1 TTTTTATTT
40880143 TAATTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 12 0.55
16 1 0.05
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTATTTCA
Found at i:40880722 original size:15 final size:14
Alignment explanation
Indices: 40880696--40880782 Score: 70
Period size: 15 Copynumber: 6.0 Consensus size: 14
40880686 TATTCTAATA
*
40880696 CTATTATTATTTAT
1 CTATTTTTATTTAT
40880710 CTAATTTTTATTTAT
1 CT-ATTTTTATTTAT
* *
40880725 CTATTTATATTTCT
1 CTATTTTTATTTAT
*
40880739 ACTATTATTATATT-T
1 -CTATTTTTAT-TTAT
40880754 CTATTTATTATATT-T
1 CTATTT-TTAT-TTAT
*
40880769 CTATTTGTATTTAT
1 CTATTTTTATTTAT
40880783 ATACTAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.03
14 21 0.34
15 36 0.59
16 2 0.03
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.64
Consensus pattern (14 bp):
CTATTTTTATTTAT
Found at i:40880735 original size:29 final size:28
Alignment explanation
Indices: 40880668--40880782 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 28
40880658 ATTGCTATTA
*
40880668 TTATTATGTTTCTATTGTTATTCTAATACTA-
1 TTATTAT-TTTCTATTTTTATT-T-AT-CTAT
40880699 TTATTATTTATCTAATTTTTATTTATCTAT
1 TTATTATTT-TCT-ATTTTTATTTATCTAT
*
40880729 TTA-TATTTCTACTATTATTATATT-TCTAT
1 TTATTATTT-T-CTATTTTTAT-TTATCTAT
*
40880758 TTATTATATTTCTATTTGTATTTAT
1 TTATTAT-TTTCTATTTTTATTTAT
40880783 ATACTAATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
28 2 0.03
29 33 0.46
30 15 0.21
31 13 0.18
32 8 0.11
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (28 bp):
TTATTATTTTCTATTTTTATTTATCTAT
Found at i:40880751 original size:17 final size:15
Alignment explanation
Indices: 40880729--40880774 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
40880719 ATTTATCTAT
40880729 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
40880746 TTATATTTCTATTTA
1 TTATATTTCTATTTA
40880761 TTATATTTCTATTT
1 TTATATTTCTATTT
40880775 GTATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 11 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:40880772 original size:44 final size:44
Alignment explanation
Indices: 40880668--40880797 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
40880658 ATTGCTATTA
40880668 TTATTATGTTTCTATTGTTATTCTAATACTATTATTATTTATCTAAT
1 TTATTAT-TTTCTATT-TTATT-TAATACTATTATTATTTATCTAAT
*
40880715 TT-TTATTTATCTATTTATATTT-CTACTATTATTATATT-TCT-AT
1 TTATTATTT-TCTATTT-TATTTAATACTATTATTAT-TTATCTAAT
*
40880758 TTATTATATTTCTATTTGTATTTATATACTAATATTATTT
1 TTATTAT-TTTCTATTT-TATTTA-ATACTATTATTATTT
40880798 TCATTATTAG
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
43 4 0.06
44 31 0.43
45 10 0.14
46 25 0.35
47 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (44 bp):
TTATTATTTTCTATTTTATTTAATACTATTATTATTTATCTAAT
Found at i:40880919 original size:3 final size:3
Alignment explanation
Indices: 40880911--40881070 Score: 161
Period size: 3 Copynumber: 53.7 Consensus size: 3
40880901 TTTAAAACTT
40880911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40880959 TTA TTA TTA -TA TT- TCTA TT- TATA TATA TGTA TCA ATA TCA TTA TT-
1 TTA TTA TTA TTA TTA T-TA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA
* *
40881004 TTA TT- TTA TT- TTT TTA TATA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40881048 TTA CTA TTA GTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
40881071 TTCTATTCTT
Statistics
Matches: 133, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
2 10 0.08
3 111 0.83
4 12 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:40882511 original size:18 final size:18
Alignment explanation
Indices: 40882485--40882519 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40882475 GAGATCTATA
40882485 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTTCTTTTCTTT
* *
40882503 TTTTGTTTTTTTTTCTT
1 TTTTCTTTTCTTTTCTT
40882520 GTTAAATATA
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:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTT
Found at i:40884024 original size:12 final size:12
Alignment explanation
Indices: 40883994--40884018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40883984 GAACAAACAT
40883994 AAAATTATAAAA
1 AAAATTATAAAA
40884006 AAAATTATAAAA
1 AAAATTATAAAA
40884018 A
1 A
40884019 TTATTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:40884029 original size:7 final size:7
Alignment explanation
Indices: 40884017--40884053 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
40884007 AAATTATAAA
40884017 AATTATT
1 AATTATT
40884024 AATTATT
1 AATTATT
40884031 AATTATT
1 AATTATT
40884038 AATTATT
1 AATTATT
*
40884045 AGTTATT
1 AATTATT
40884052 AA
1 AA
40884054 AAATTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (7 bp):
AATTATT
Found at i:40887408 original size:63 final size:64
Alignment explanation
Indices: 40887281--40887408 Score: 179
Period size: 63 Copynumber: 2.0 Consensus size: 64
40887271 ATGCCATTAT
*
40887281 TTTGTGACATGATTATCGAGTAAATATTTTTAAAAAAATTAGAAGGTTACATCAACAAATTTTAA
1 TTTGTGACATGATTATCGAGTAAATA-TTTTAAAAAAATTAGAAGCTTACATCAACAAATTTTAA
* * * *
40887346 TTTGTGAGATGATTATCGAGTAAGTA-TTTAAAAAAATTAGAA-CTTCGCATCAACAATTTTTAA
1 TTTGTGACATGATTATCGAGTAAATATTTTAAAAAAATTAGAAGCTT-ACATCAACAAATTTTAA
40887409 CGGTATTAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 2 0.04
63 31 0.54
65 24 0.42
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (64 bp):
TTTGTGACATGATTATCGAGTAAATATTTTAAAAAAATTAGAAGCTTACATCAACAAATTTTAA
Found at i:40887783 original size:21 final size:21
Alignment explanation
Indices: 40887759--40887805 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
40887749 TGAAGAAAGC
40887759 AAAGGAAGATT-ACAAAGAAAT
1 AAAGGAA-ATTCACAAAGAAAT
* * *
40887780 AAAGCAACTTCCCAAAGAAAT
1 AAAGGAAATTCACAAAGAAAT
40887801 AAAGG
1 AAAGG
40887806 TAAGCGTTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (21 bp):
AAAGGAAATTCACAAAGAAAT
Found at i:40889288 original size:2 final size:2
Alignment explanation
Indices: 40889281--40889320 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40889271 AAATTAGTCC
40889281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40889321 CTTAAATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40893981 original size:17 final size:17
Alignment explanation
Indices: 40893941--40893980 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
40893931 AAAAACAGTT
40893941 AAAAAAATTAAAAATAC
1 AAAAAAATTAAAAATAC
40893958 AAAAAAATT-AAAATAC
1 AAAAAAATTAAAAATAC
40893974 AAAAAAA
1 AAAAAAA
40893981 AACACTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAATTAAAAATAC
Found at i:40894111 original size:12 final size:12
Alignment explanation
Indices: 40894090--40894136 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
40894080 CTCCTTCTCC
*
40894090 TTCTTCTCTTCT
1 TTCTTTTCTTCT
40894102 TTCTTTTCTTC-
1 TTCTTTTCTTCT
*
40894113 TTC--TCCTTCT
1 TTCTTTTCTTCT
40894123 TTCTTTTCTTCT
1 TTCTTTTCTTCT
40894135 TT
1 TT
40894137 TCCTTCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 3 0.10
12 18 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:40894123 original size:21 final size:21
Alignment explanation
Indices: 40894089--40894178 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
40894079 ACTCCTTCTC
40894089 CTTCTTCT-CTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
40894109 CTTCTTCTCCTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
40894130 CTTCTTTTCCTTCTTTATTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
40894151 CCTCTTCTCCTTATTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
40894172 CTTCTTC
1 CTTCTTC
40894179 CCGAAATGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 8 0.13
21 54 0.87
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTCTTCTCCTTCTTTCTTTT
Found at i:40894332 original size:20 final size:20
Alignment explanation
Indices: 40894306--40894355 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
40894296 ACCACCAGTC
40894306 CAGCTTTTTTTTTTCAAATTT
1 CAGCTTTTTTTTTTC-AATTT
*
40894327 -AGC-TTTTTTTTTCAGTTT
1 CAGCTTTTTTTTTTCAATTT
40894345 CAGCTTTTTTT
1 CAGCTTTTTTT
40894356 CAGCTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 9 0.35
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.64
Consensus pattern (20 bp):
CAGCTTTTTTTTTTCAATTT
Found at i:40895267 original size:20 final size:20
Alignment explanation
Indices: 40895242--40895309 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
40895232 TTTAAGATAC
40895242 AACAATTATTACTATTTTTT
1 AACAATTATTACTATTTTTT
* *
40895262 AACAATCTTTTA-TAATTTTT
1 AACAAT-TATTACTATTTTTT
* * *
40895282 AATAATT-CTACGATTTTTT
1 AACAATTATTACTATTTTTT
40895301 -ACAA-TATTA
1 AACAATTATTA
40895310 TACAATTTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 7 0.19
20 18 0.49
21 4 0.11
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (20 bp):
AACAATTATTACTATTTTTT
Found at i:40895378 original size:26 final size:28
Alignment explanation
Indices: 40895343--40895403 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
40895333 TTTTTATAGT
40895343 TTTTTAAATTC-TAATATA-TTTTTAAA
1 TTTTTAAATTCATAATATATTTTTTAAA
* *
40895369 TTTTTAAATTCAATTATATATTTTTTTAA
1 TTTTTAAATTC-ATAATATATTTTTTAAA
40895398 TTTTTA
1 TTTTTA
40895404 TAGTTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.37
28 6 0.20
29 13 0.43
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTAAATTCATAATATATTTTTTAAA
Found at i:40896380 original size:27 final size:27
Alignment explanation
Indices: 40896332--40896383 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40896322 CGATATCATA
*
40896332 AATAGTTTGATGAGACATTAAACATGG
1 AATAGTTTGATGAGACACTAAACATGG
* *
40896359 AATAGTTTGATGGGACGCTAAACAT
1 AATAGTTTGATGAGACACTAAACAT
40896384 CATCTAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (27 bp):
AATAGTTTGATGAGACACTAAACATGG
Found at i:40897166 original size:30 final size:29
Alignment explanation
Indices: 40897132--40897197 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
40897122 CCCAGCCACC
40897132 CCCAATCC-AGATAAAAATTTATAAACCCAA
1 CCCAATCCGA-ATAAAAATTTAT-AACCCAA
*
40897162 CCCAATTCGAATAAAAATTTATAACCCAA
1 CCCAATCCGAATAAAAATTTATAACCCAA
*
40897191 TCCAATC
1 CCCAATC
40897198 TAAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.38
30 19 0.59
31 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (29 bp):
CCCAATCCGAATAAAAATTTATAACCCAA
Found at i:40899482 original size:54 final size:54
Alignment explanation
Indices: 40899423--40899531 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
40899413 TTAGTGAAAC
*
40899423 TGTGAAATTGGTTTGAAATTAAGATGATTCATGTTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
40899477 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
40899531 T
1 T
40899532 ATTTGATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (54 bp):
TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
Found at i:40899523 original size:27 final size:26
Alignment explanation
Indices: 40899439--40899529 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 26
40899429 ATTGGTTTGA
*
40899439 AATTAAGATGATTCATGTTATTATATG
1 AATTAA-ATGATTCATGATATTATATG
* * * * *
40899466 AATTAAATGAGT-GTGAAATTGGTTTG
1 AATTAAATGATTCATGATATT-ATATG
*
40899492 AAATTAAGATGATTCATGCTATTATATG
1 -AATTAA-ATGATTCATGATATTATATG
40899520 AATTAAATGA
1 AATTAAATGA
40899530 GTATTTGATT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
25 5 0.10
26 12 0.25
27 18 0.38
28 8 0.17
29 5 0.10
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (26 bp):
AATTAAATGATTCATGATATTATATG
Found at i:40900162 original size:26 final size:30
Alignment explanation
Indices: 40900106--40900162 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
40900096 TAAATTGATT
**
40900106 AAATGTTGATTGATTATGTGAATGACACTG
1 AAATGTTGATTGATTATGTGAACAACACTG
40900136 AAATGTTGATT-A-TATGT-AACAAC-CTG
1 AAATGTTGATTGATTATGTGAACAACACTG
40900162 A
1 A
40900163 TTTTGGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 5 0.20
29 1 0.04
30 11 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (30 bp):
AAATGTTGATTGATTATGTGAACAACACTG
Found at i:40901281 original size:17 final size:19
Alignment explanation
Indices: 40901239--40901282 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40901229 ATGAAATTTT
*
40901239 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
40901258 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
40901276 AA-TATTA
1 AATTATTA
40901283 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:40903104 original size:28 final size:28
Alignment explanation
Indices: 40903072--40903140 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
40903062 GCGTAGATCA
40903072 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
40903100 CGAAATTACCCCTAAAGAGCATAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
40903128 CGATA-TACCCCTA
1 CGAAATTACCCCTA
40903141 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:40904734 original size:48 final size:49
Alignment explanation
Indices: 40904627--40904761 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 49
40904617 CTTGTGTGCT
* * *
40904627 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AG-TA-TGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTGAGAGCC
*
40904673 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTGAGAGCC
* * ** *
40904721 AGTTTAAGACATGTTTACTACATGCATCGGCCTCGCGATAT
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATAT
40904762 ACAAGCTAGT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
46 31 0.40
47 2 0.03
48 42 0.55
49 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTGAGAGCC
Found at i:40904792 original size:48 final size:48
Alignment explanation
Indices: 40904627--40904777 Score: 155
Period size: 48 Copynumber: 3.2 Consensus size: 48
40904617 CTTGTGTGCT
** * * *
40904627 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AG-TATGA-GAGCC
1 AGTGTAAGACATGTCTACGACATGCATCGGCCTCGAGATAT-ACAAGCC
* **
40904673 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTACGACATGCATCGGCCTCGAGATATACAAGCC
* * * * *
40904721 AGTTTAAGACATGTTTACTACATGCATCGGCCTCGCGATATACAAGCT
1 AGTGTAAGACATGTCTACGACATGCATCGGCCTCGAGATATACAAGCC
40904769 AGTGTAAGA
1 AGTGTAAGA
40904778 TCTGTCTGAG
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
46 31 0.35
47 2 0.02
48 55 0.62
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTACGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:40904874 original size:49 final size:49
Alignment explanation
Indices: 40904812--40904937 Score: 184
Period size: 49 Copynumber: 2.6 Consensus size: 49
40904802 TGTAGTGTAT
40904812 CAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CTA-TAGATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTC-ACTAGATGAAAGC
* * *
40904861 CAGTGTAAAACCTGTCTGGGACATGGCATCGGCCTCACTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCACTAGATGAAAGC
40904910 CAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
40904938 GTTGGTATCT
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
48 2 0.03
49 53 0.76
50 15 0.21
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCACTAGATGAAAGC
Found at i:40914615 original size:15 final size:15
Alignment explanation
Indices: 40914580--40914638 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
40914570 AAGAGTGAGA
**
40914580 AGTAAAATTTTAGAA
1 AGTAAAATTTTAGGG
40914595 AGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
* *
40914610 A-TTAAATTTAAGGG
1 AGTAAAATTTTAGGG
*
40914624 GGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
40914639 GAAAATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (15 bp):
AGTAAAATTTTAGGG
Found at i:40932951 original size:19 final size:19
Alignment explanation
Indices: 40932913--40932970 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
40932903 TCTTTATATA
* *
40932913 TTATAAAT-TTTGGAATTT
1 TTATAAATATTTTGTATTT
40932931 TTATAAATATTTTGTATTT
1 TTATAAATATTTTGTATTT
40932950 TTGA-AAATTATTTT-TATTT
1 TT-ATAAA-TATTTTGTATTT
40932969 TT
1 TT
40932971 TGTAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 8 0.23
19 20 0.57
20 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATAAATATTTTGTATTT
Found at i:40932951 original size:20 final size:19
Alignment explanation
Indices: 40932928--40932971 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
40932918 AATTTTGGAA
40932928 TTTTTATAAA-TATTTTGTAT
1 TTTTTA-AAATTATTTT-TAT
*
40932948 TTTTGAAAATTATTTTTAT
1 TTTTTAAAATTATTTTTAT
40932967 TTTTT
1 TTTTT
40932972 GTAATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTAAAATTATTTTTAT
Found at i:40932977 original size:19 final size:19
Alignment explanation
Indices: 40932927--40932977 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
40932917 AAATTTTGGA
* *
40932927 ATTTTTATAAATATTTTGT
1 ATTTTTGTAATTATTTTGT
*
40932946 ATTTTTGAAAATTATTTT-T
1 ATTTTTG-TAATTATTTTGT
40932965 ATTTTTTGTAATT
1 A-TTTTTGTAATT
40932978 TATGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
ATTTTTGTAATTATTTTGT
Found at i:40937089 original size:18 final size:18
Alignment explanation
Indices: 40937053--40937098 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
40937043 ATTCGAAAAA
40937053 AATTCGAGTTAACTTAAAT
1 AATTCGA-TTAACTTAAAT
40937072 AATTCGATTAA-TTCAAAT
1 AATTCGATTAACTT-AAAT
*
40937090 AACTCGATT
1 AATTCGATT
40937099 CGTTTAACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (18 bp):
AATTCGATTAACTTAAAT
Found at i:40943072 original size:27 final size:27
Alignment explanation
Indices: 40943042--40943095 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
40943032 TTTGGATCAT
40943042 CACCCTATTGTAATCTATGGAGTAAAA
1 CACCCTATTGTAATCTATGGAGTAAAA
40943069 CACCCTATTGTAATCTATGGAGTAAAA
1 CACCCTATTGTAATCTATGGAGTAAAA
40943096 GAAGATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (27 bp):
CACCCTATTGTAATCTATGGAGTAAAA
Found at i:40944127 original size:19 final size:18
Alignment explanation
Indices: 40944097--40944146 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40944087 ATATGAATTG
*
40944097 AAAAATAAATATTCACATAT
1 AAAAAT-AATATTCAC-TAA
* *
40944117 AAAAATTATATTTACTAA
1 AAAAATAATATTCACTAA
40944135 AAAAATAATATT
1 AAAAATAATATT
40944147 TACAACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 7 0.27
20 6 0.23
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATAATATTCACTAA
Found at i:40944600 original size:16 final size:16
Alignment explanation
Indices: 40944576--40944606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40944566 ATATATCGAT
40944576 AAATATAAAAAAATTA
1 AAATATAAAAAAATTA
*
40944592 AAATTTAAAAAAATT
1 AAATATAAAAAAATT
40944607 CAACCCAAAT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAAAAAAATTA
Found at i:40944845 original size:21 final size:21
Alignment explanation
Indices: 40944819--40944859 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40944809 TAGCATGAGT
40944819 GTTGATGTGGCAAGTTAACTA
1 GTTGATGTGGCAAGTTAACTA
*
40944840 GTTGATGTGGCCAGTTAACT
1 GTTGATGTGGCAAGTTAACT
40944860 TGCCACTTTG
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:0.24, C:0.12, G:0.29, T:0.34
Consensus pattern (21 bp):
GTTGATGTGGCAAGTTAACTA
Found at i:40946113 original size:10 final size:10
Alignment explanation
Indices: 40946100--40946125 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40946090 TTAATATTAT
40946100 TTATTATTTA
1 TTATTATTTA
40946110 TTATTATTTA
1 TTATTATTTA
40946120 TTATTA
1 TTATTA
40946126 CTAATAGTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTATTTA
Found at i:40946487 original size:11 final size:11
Alignment explanation
Indices: 40946473--40946506 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40946463 TTTCTCTTAT
*
40946473 TCTTCTTTTTC
1 TCTTCTTCTTC
*
40946484 TCTTCTTCTCC
1 TCTTCTTCTTC
40946495 TCTTCTTCTTC
1 TCTTCTTCTTC
40946506 T
1 T
40946507 TCTACTGTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:40954607 original size:21 final size:22
Alignment explanation
Indices: 40954583--40954637 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
40954573 TAAAGTAACT
40954583 ATTTATTATATATTACATA-AA
1 ATTTATTATATATTACATATAA
* *
40954604 ATTTCATTTATATTTTACATATAT
1 ATTT-A-TTATATATTACATATAA
40954628 ATTT-TTATAT
1 ATTTATTATAT
40954638 GCATGCGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 13 0.45
24 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTATTATATATTACATATAA
Found at i:40955148 original size:6 final size:6
Alignment explanation
Indices: 40955137--40955164 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40955127 CCCCCTACTA
40955137 CACAGG CACAGG CACAGG CACAGG CACA
1 CACAGG CACAGG CACAGG CACAGG CACA
40955165 ACCATGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.29, T:0.00
Consensus pattern (6 bp):
CACAGG
Found at i:40960596 original size:3 final size:3
Alignment explanation
Indices: 40960588--40960629 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
40960578 CAAGGTGATT
*
40960588 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40960630 CACCTCCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:40961907 original size:10 final size:10
Alignment explanation
Indices: 40961892--40961917 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40961882 GCAAATTCAA
40961892 AAAAAAAAAT
1 AAAAAAAAAT
40961902 AAAAAAAAAT
1 AAAAAAAAAT
40961912 AAAAAA
1 AAAAAA
40961918 GCCCCCAAAA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:40971942 original size:18 final size:17
Alignment explanation
Indices: 40971902--40971935 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40971892 ATGTGTACAA
*
40971902 ATAATATATATATGTAT
1 ATAATATATATATGAAT
40971919 ATAATA-ATATATGAAT
1 ATAATATATATATGAAT
40971935 A
1 A
40971936 CTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATAATATATATATGAAT
Found at i:40973014 original size:40 final size:40
Alignment explanation
Indices: 40972892--40973029 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
40972882 ACCTCGAGTC
*
40972892 GATGAGACACTGGGTGTCAATTTATTACTTC-AGATATAT-T
1 GATGAGACACTGGATGTCAATTTATTACTTCGA-AT-TATCT
* * ** * *
40972932 CGATGAGGCACT-GAGTGCCAA---ATTACTTCGGTTTAGCC
1 -GATGAGACACTGGA-TGTCAATTTATTACTTCGAATTATCT
40972970 GATGAGACACTGGATGTCAATTTATTACTTCGAATTATCT
1 GATGAGACACTGGATGTCAATTTATTACTTCGAATTATCT
* *
40973010 GATGAGGCACTGGGTGTCAA
1 GATGAGACACTGGATGTCAA
40973030 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
37 17 0.23
38 11 0.15
40 32 0.43
41 15 0.20
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
GATGAGACACTGGATGTCAATTTATTACTTCGAATTATCT
Found at i:40976751 original size:35 final size:35
Alignment explanation
Indices: 40976724--40976890 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
40976714 CATGGCAAAG
40976724 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
40976759 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
*
40976794 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGC
** ** * *
40976834 TAAGAAATGTAGGTATGACATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGC
**
40976869 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
40976891 TCAATGAGGA
Statistics
Matches: 116, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.01
35 83 0.72
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.24
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:40976814 original size:40 final size:40
Alignment explanation
Indices: 40976735--40976850 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
40976725 GTGAAATGTA
40976735 GGTATGGTATTATCCATACTGAGCTGTGAAA--T--GTA-
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
40976770 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
* * **
40976810 GGTAT--TATCAAATCCATACTGAGTTAAGAAATGTAGGTAT
1 GGTATGGTAT--TATCCATACTGAGCTGTGAAATGTAGGTAT
40976850 G
1 G
40976851 ACATTTCCCA
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
35 31 0.44
37 1 0.01
38 3 0.04
39 3 0.04
40 32 0.46
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (40 bp):
GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
Found at i:40976862 original size:75 final size:74
Alignment explanation
Indices: 40976724--40976894 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 74
40976714 CATGGCAAAG
** **
40976724 TGTGAAATGTAGGTATGGTA-TT---ATCCATACTGAGCTGTGAAATGTAGGTATGGTATTATCC
1 TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGCTAAGAAATGTAGGTATGACATTATCC
*
40976785 ATACTGAGC
66 ATACCGAGC
*
40976794 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGACATT-TC
1 TGTGAAATGTAGGTATGGTATT-TCAAATCCATACTGAGCTAAGAAATGTAGGTATGACATTAT-
*
40976858 CCATACCGAGT
64 CCATACCGAGC
**
40976869 TGAAAAATGTAGGTATGGTATTTCAA
1 TGTGAAATGTAGGTATGGTATTTCAA
40976895 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 20 0.23
71 1 0.01
72 1 0.01
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (74 bp):
TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGCTAAGAAATGTAGGTATGACATTATCC
ATACCGAGC
Found at i:40979286 original size:43 final size:43
Alignment explanation
Indices: 40979236--40979322 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
40979226 TCATATTTGA
40979236 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
* * *
40979279 TTTCTCATCTCATATTCATTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
40979322 T
1 T
40979323 AATCATATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.02, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:40982439 original size:12 final size:12
Alignment explanation
Indices: 40982418--40982472 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
40982408 GCCATTTCTG
* *
40982418 CTTCTCCATCAC
1 CTTCTTCATCAT
40982430 CTTCTTCATCAT
1 CTTCTTCATCAT
* *
40982442 CATCATCATCAT
1 CTTCTTCATCAT
* *
40982454 CTTCTTCTTCTT
1 CTTCTTCATCAT
40982466 CTTCTTC
1 CTTCTTC
40982473 TTCTTCTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (12 bp):
CTTCTTCATCAT
Found at i:40982459 original size:3 final size:3
Alignment explanation
Indices: 40982453--40982480 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40982443 ATCATCATCA
40982453 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
40982481 TAAGTAGGGC
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:40989627 original size:20 final size:19
Alignment explanation
Indices: 40989602--40989640 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40989592 TTAACAACCA
40989602 TAAAATAAAAATAATCAAAT
1 TAAAATAAAAAT-ATCAAAT
*
40989622 TAAAATATAAATATCAAAT
1 TAAAATAAAAATATCAAAT
40989641 ATGTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAATAAAAATATCAAAT
Found at i:40994119 original size:19 final size:19
Alignment explanation
Indices: 40994095--40994131 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40994085 TTTTATTAAT
*
40994095 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
40994114 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
40994132 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:40997541 original size:7 final size:7
Alignment explanation
Indices: 40997529--40997601 Score: 76
Period size: 7 Copynumber: 10.4 Consensus size: 7
40997519 AAAATATTTT
40997529 AGAATTG
1 AGAATTG
40997536 AGAATTG
1 AGAATTG
40997543 AGAATTG
1 AGAATTG
* *
40997550 AAAATTA
1 AGAATTG
*
40997557 AGAATTA
1 AGAATTG
*
40997564 AGGATT-
1 AGAATTG
40997570 ACGAATTG
1 A-GAATTG
40997578 AGAATTG
1 AGAATTG
*
40997585 AGGATTG
1 AGAATTG
*
40997592 AGTATTG
1 AGAATTG
40997599 AGA
1 AGA
40997602 TAAAAAGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
6 1 0.02
7 54 0.96
8 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (7 bp):
AGAATTG
Found at i:40997598 original size:21 final size:21
Alignment explanation
Indices: 40997529--40997601 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
40997519 AAAATATTTT
*
40997529 AGAATTGAGAATTGAGAATTG
1 AGAATTGAGAATTGAGGATTG
* * *
40997550 AAAATTAAGAATTAAGGATT-
1 AGAATTGAGAATTGAGGATTG
40997570 ACGAATTGAGAATTGAGGATTG
1 A-GAATTGAGAATTGAGGATTG
*
40997592 AGTATTGAGA
1 AGAATTGAGA
40997602 TAAAAAGAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (21 bp):
AGAATTGAGAATTGAGGATTG
Found at i:40998113 original size:65 final size:65
Alignment explanation
Indices: 40998042--40998228 Score: 243
Period size: 65 Copynumber: 2.9 Consensus size: 65
40998032 TATAAGATAA
* * * * *
40998042 ATAATTTGTGTATTTATATTTGGTATTTAAATATCTTATTGAATTATAATCATATTTGTTTTAAT
1 ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATATTTATTTTAAT
* * * *
40998107 ATAATTTGTATATTTATAACTCATATTTAAATATTTTATTAAATTATAATAATATTTATTTTAAT
1 ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATATTTATTTTAAT
* * *
40998172 ATAATTTGTAG-ATTTGTAATTGACATTAAAATATTTTATTGAATTATAATAAT-TTTA
1 ATAATTTGT-GTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATATTTA
40998229 ATAAAATTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
64 4 0.04
65 101 0.96
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (65 bp):
ATAATTTGTGTATTTATAATTGATATTTAAATATTTTATTGAATTATAATAATATTTATTTTAAT
Found at i:40998222 original size:18 final size:20
Alignment explanation
Indices: 40998190--40998228 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40998180 TAGATTTGTA
40998190 ATTGACATTAAAAT-ATTTT
1 ATTGACATTAAAATAATTTT
*
40998209 ATTGA-ATTATAATAATTTT
1 ATTGACATTAAAATAATTTT
40998228 A
1 A
40998229 ATAAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTGACATTAAAATAATTTT
Found at i:40999264 original size:136 final size:137
Alignment explanation
Indices: 40999020--40999293 Score: 532
Period size: 136 Copynumber: 2.0 Consensus size: 137
40999010 AGCCCATTCA
40999020 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
40999085 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCC
40999149 CATTTGG
131 CATTTGG
40999156 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
*
40999221 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
66 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCC
40999286 CATTTGG
131 CATTTGG
40999293 G
1 G
40999294 GAGACTACTC
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
136 114 0.84
137 22 0.16
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCC
CATTTGG
Found at i:40999578 original size:25 final size:26
Alignment explanation
Indices: 40999550--40999605 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
40999540 CATTTAGGTC
**
40999550 AATTTAAC-CCTAGGGGTATTTCAGT
1 AATTTAACACCTAGGGGTATAACAGT
**
40999575 AATTTTGCACCTAGGGGTATAACAGT
1 AATTTAACACCTAGGGGTATAACAGT
40999601 AATTT
1 AATTT
40999606 TCCATACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (26 bp):
AATTTAACACCTAGGGGTATAACAGT
Found at i:41001079 original size:26 final size:26
Alignment explanation
Indices: 41001050--41001185 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
41001040 CATGATATTC
*
41001050 TTATAATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
41001076 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
41001102 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
41001128 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
41001154 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
41001180 TTATCA
1 TTATCA
41001186 ATTTGTATCA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:41003643 original size:160 final size:160
Alignment explanation
Indices: 41003371--41003676 Score: 447
Period size: 160 Copynumber: 1.9 Consensus size: 160
41003361 CAGAAATTGA
* *
41003371 TTACAATGCTTTTTTTTTCTTTGAACAAAATTTGTTCATTCATTTTTTTTTTTGTATTTCATTTG
1 TTACAATGCTTTTTTTTTCTTT-AACAAAATCTATTCATTCATTTTTTTTTTTGTATTTCATTTG
* * * *
41003436 TATTTTTCACTATCTACTAACATTCATATAGTGGAAAAATTGCTACTTTAAGCT-TTACATCAAA
65 TATTTGTCACCATCTACTAACAATCATATAGTGGAAAAATAGCTACTTTAAG-TGTTACATCAAA
41003500 TACCAATTACAATTTCTCTAGCGATGGAACTT
129 TACCAATTACAATTTCTCTAGCGATGGAACTT
41003532 TTACAATGCTTCTTTTTTTC-TTATACAAAATCTATTCATTCA-TTTTTTTTTTGTATTTCATTT
1 TTACAATGCTT-TTTTTTTCTTTA-ACAAAATCTATTCATTCATTTTTTTTTTTGTATTTCATTT
* * * ** *
41003595 GTATTTGTCGCCGTTTACTAACAATCATATAGTGGAAAAATAGCTACTTTAAGTGTTATGTCAAG
64 GTATTTGTCACCATCTACTAACAATCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAA
41003660 TACCAATTACAATTTCT
129 TACCAATTACAATTTCT
41003677 TTGCCGATTG
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
159 1 0.01
160 92 0.71
161 29 0.22
162 8 0.06
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (160 bp):
TTACAATGCTTTTTTTTTCTTTAACAAAATCTATTCATTCATTTTTTTTTTTGTATTTCATTTGT
ATTTGTCACCATCTACTAACAATCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAATA
CCAATTACAATTTCTCTAGCGATGGAACTT
Found at i:41006684 original size:94 final size:94
Alignment explanation
Indices: 41006535--41007019 Score: 371
Period size: 94 Copynumber: 5.2 Consensus size: 94
41006525 AAATCCGTTG
* * * * *
41006535 CAACTTCAGGGGTATAAGATTTATAGCTTCATCTTGCTTCACTGCATCTTTAGGGAGATAAAATT
1 CAACTTCAGGGGTATAAGATTTATAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
* *
41006600 CGCCATTATAGCTTCAATTTGACCCACTA
66 CGCCATTGTAGCTTCAATCTGACCCACTA
* * * * * *
41006629 CAACTTCAAGGGTATACGATTTATAACTTTATTTTACTCCACTACAACTTCAGGGAGATAAGATT
1 CAACTTCAGGGGTATAAGATTTATAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
* * * * * * *
41006694 CACTATGGTAACTTTAATCTGACCCATTG
66 CGCCATTGTAGCTTCAATCTGACCCACTA
* * * * *
41006723 CAACTTTAGGGGTATAAGGTTTATAGCTTTATCTTGGTCCATTGCAACTTCAGAGAGATAAGATT
1 CAACTTCAGGGGTATAAGATTTATAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
* *
41006788 CGCCATTGTAGTTTCAATCT-ATTCCACTA
66 CGCCATTGTAGCTTCAATCTGA-CCCACTA
* * * * * * * * * * * *
41006817 AAACTTTAAGGATATAAGGTTTGTAGCTTTGTCTTGCTCTACTGCAACTTTAAGGATATAAGACT
1 CAACTTCAGGGGTATAAGATTTATAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
* ** * * *
41006882 CGCAATTGTAATTTCATTCCGACCCACTG
66 CGCCATTGTAGCTTCAATCTGACCCACTA
* * * * * * *
41006911 TAACATCAGGGGTATAGGAATTGTAGCTTTAATC-TGATCCACTGCAAC-TCTAGGGATATAAGA
1 CAACTTCAGGGGTATAAGATTTATAGCTTT-ATCTTGCTCCACTGCAACTTC-AGGGAGATAAGA
*
41006974 -T-----TTGTAGCTTC-ATCTTACACCACTA
64 TTCGCCATTGTAGCTTCAATCTGAC-CCACTA
41006999 CAACTTCAGGGAG-ATAAGATT
1 CAACTTCAGGG-GTATAAGATT
41007020 CGCTAGGTAA
Statistics
Matches: 303, Mismatches: 82, Indels: 18
0.75 0.20 0.04
Matches are distributed among these distances:
87 4 0.01
88 28 0.09
89 1 0.00
93 3 0.01
94 264 0.87
95 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (94 bp):
CAACTTCAGGGGTATAAGATTTATAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATT
CGCCATTGTAGCTTCAATCTGACCCACTA
Found at i:41007065 original size:93 final size:94
Alignment explanation
Indices: 41006937--41007138 Score: 284
Period size: 93 Copynumber: 2.2 Consensus size: 94
41006927 GGAATTGTAG
* *
41006937 CTTTAATCTGATCCACTGCAACTCTAGGGATATAAGATTTGTAGCTTCAT-CTTACACCACTACA
1 CTTTAATCTGACCCACTGCAACTCTAGGGAGATAAGATTTGTAGCTTCATCCTT-CACCACTACA
* *
41007001 ACTTCAGGGAGATAAGATTCGCTA-GGTAA
65 ACTTCAAGGAGATAAAATTCGCTATGGTAA
* * * *
41007030 CTTTAATCAGACCCACTGCAACT-TCAGTGAGATAAGATTTGTAGCTTCATCCTTCTCCACTGCA
1 CTTTAATCTGACCCACTGCAACTCT-AGGGAGATAAGATTTGTAGCTTCATCCTTCACCACTACA
41007094 ACTTCAAGGAGATAAAATTCGCTATGGTAA
65 ACTTCAAGGAGATAAAATTCGCTATGGTAA
*
41007124 CTTCAATCTGACCCA
1 CTTTAATCTGACCCA
41007139 TTGTAAATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
92 1 0.01
93 74 0.77
94 21 0.22
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (94 bp):
CTTTAATCTGACCCACTGCAACTCTAGGGAGATAAGATTTGTAGCTTCATCCTTCACCACTACAA
CTTCAAGGAGATAAAATTCGCTATGGTAA
Found at i:41007106 original size:44 final size:44
Alignment explanation
Indices: 41006948--41007108 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 44
41006938 TTTAATCTGA
* *
41006948 TCCACTGCAAC-TCTAGGGATATAAGATTTGTAGCTTCAT-CTTAC
1 TCCACTGCAACTTC-AAGGAGATAAGATTTGTAGCTTCATCCTT-C
* * * * * ***
41006992 ACCACTACAACTTCAGGGAGATAAGATTCGCTAGGTAACTTTAATCAGAC
1 TCCACTGCAACTTCAAGGAGATAAGATT---T--GTAGC-TTCATCCTTC
41007042 -CCACTGCAACTTC-AGTGAGATAAGATTTGTAGCTTCATCCTTC
1 TCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCTTCATCCTTC
41007085 TCCACTGCAACTTCAAGGAGATAA
1 TCCACTGCAACTTCAAGGAGATAA
41007109 AATTCGCTAT
Statistics
Matches: 91, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
43 6 0.07
44 46 0.51
45 4 0.04
46 1 0.01
47 1 0.01
48 1 0.01
49 27 0.30
50 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
TCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCATCCTTC
Found at i:41010748 original size:38 final size:38
Alignment explanation
Indices: 41010682--41010754 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
41010672 ACCAGTTTGG
*
41010682 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTAA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTAA
* * *
41010720 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGT
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGCAAAGT
41010755 GGTACCCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTAA
Found at i:41010812 original size:41 final size:38
Alignment explanation
Indices: 41010719--41010815 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 38
41010709 AGCAAAGTTA
*
41010719 ACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAGTG
1 ACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTG
** ** * *
41010756 GTACCCAGTACCTCATCGAATCTATCCGAAGTAACAGTATG
1 ACACCCAGTGTCTCATCGAACCTAGCCGAAGTAA-AG--TG
41010797 ACACCCAGTGTCTCATCGA
1 ACACCCAGTGTCTCATCGA
41010816 CTCGAGGTCG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
37 14 0.31
38 12 0.27
39 2 0.04
41 17 0.38
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (38 bp):
ACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTG
Found at i:41011871 original size:16 final size:17
Alignment explanation
Indices: 41011839--41011872 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41011829 AATCCTTAGT
*
41011839 TTTCTCTTTTATCTTTC
1 TTTCCCTTTTATCTTTC
41011856 TTTCCCTTTT-TCTTTC
1 TTTCCCTTTTATCTTTC
41011872 T
1 T
41011873 CTTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCCTTTTATCTTTC
Found at i:41015809 original size:24 final size:24
Alignment explanation
Indices: 41015759--41015835 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
41015749 AACTTTTTCG
* *
41015759 TCTTCACCTCAACCCTTGTAC-TGA
1 TCTTCACCTCAACCCTCGT-CTTCA
*
41015783 TCTTCACCTCGACCCTCGTCTTCA
1 TCTTCACCTCAACCCTCGTCTTCA
* * *
41015807 TCTTCATCTCTATCCC-CGTCTTCG
1 TCTTCACCTC-AACCCTCGTCTTCA
41015831 TCTTC
1 TCTTC
41015836 GTCTCCATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.91
25 3 0.07
ACGTcount: A:0.13, C:0.42, G:0.08, T:0.38
Consensus pattern (24 bp):
TCTTCACCTCAACCCTCGTCTTCA
Found at i:41018297 original size:17 final size:18
Alignment explanation
Indices: 41018277--41018310 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41018267 AATGAATTGT
*
41018277 TTTATTGTAT-AAATTAA
1 TTTATTGAATGAAATTAA
41018294 TTTATTGAATGAAATTA
1 TTTATTGAATGAAATTA
41018311 TTAATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTATTGAATGAAATTAA
Found at i:41018707 original size:21 final size:21
Alignment explanation
Indices: 41018681--41018745 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
41018671 GATTTGGGTG
*
41018681 GTTCAGCTCTGACGAGCTTCT
1 GTTCAGCTCTCACGAGCTTCT
* *
41018702 GTTCAGCTTTCACAAGCTTCT
1 GTTCAGCTCTCACGAGCTTCT
* * * *
41018723 ATTCAGCTGTTATGAGCTTCT
1 GTTCAGCTCTCACGAGCTTCT
41018744 GT
1 GT
41018746 CATCATGTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (21 bp):
GTTCAGCTCTCACGAGCTTCT
Found at i:41022816 original size:8 final size:8
Alignment explanation
Indices: 41022783--41022831 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
41022773 TAAATAAGAA
41022783 ATAATAATT
1 ATAATAA-T
41022792 ATAATAAT
1 ATAATAAT
*
41022800 TTAATAAT
1 ATAATAAT
41022808 ATAATAAT
1 ATAATAAT
**
41022816 AT-ATGTT
1 ATAATAAT
41022823 ATAATAAT
1 ATAATAAT
41022831 A
1 A
41022832 ATAGAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
7 5 0.15
8 21 0.64
9 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (8 bp):
ATAATAAT
Found at i:41030702 original size:20 final size:20
Alignment explanation
Indices: 41030652--41030704 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
41030642 ACGACTGCAG
* * *
41030652 CACACGGGCATGTTCCAGGC
1 CACACGGGCGTGTCCCAAGC
*
41030672 CACACGAGCGTGTCCCAAGC
1 CACACGGGCGTGTCCCAAGC
41030692 CACACGGGCGTGT
1 CACACGGGCGTGT
41030705 GCCCCTATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.36, G:0.30, T:0.13
Consensus pattern (20 bp):
CACACGGGCGTGTCCCAAGC
Found at i:41032539 original size:17 final size:17
Alignment explanation
Indices: 41032507--41032551 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41032497 TAGAATTTTT
* *
41032507 TTTTTAAAATTTTATAA
1 TTTTTAAAAATATATAA
41032524 TTTTTAAAAATATATAA
1 TTTTTAAAAATATATAA
**
41032541 AATTTAAAAAT
1 TTTTTAAAAAT
41032552 TTTTTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAATATATAA
Found at i:41032552 original size:27 final size:28
Alignment explanation
Indices: 41032511--41032564 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
41032501 ATTTTTTTTT
* *
41032511 TAAAATTTTATAA-TTTTTAAAAATATA
1 TAAAATTTAAAAATTTTTTAAAAATATA
*
41032538 TAAAATTTAAAAATTTTTTACAAATAT
1 TAAAATTTAAAAATTTTTTAAAAATAT
41032565 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAATTTAAAAATTTTTTAAAAATATA
Found at i:41034637 original size:21 final size:20
Alignment explanation
Indices: 41034598--41034637 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41034588 ACATAAATAC
* *
41034598 TAGTTATTATTTAACATATA
1 TAGTTATTAATTAAAATATA
41034618 TAGTTATATAATTAAAATAT
1 TAGTTAT-TAATTAAAATAT
41034638 TTTGTGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TAGTTATTAATTAAAATATA
Found at i:41037126 original size:36 final size:36
Alignment explanation
Indices: 41037086--41037156 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
41037076 AGGAATGAGG
41037086 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
1 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
*
41037122 CAGTCCAAAATCTATTCTCAAATTACGGAATCTTA
1 CAGTCCAAAATCTATTCTCAAACTACGGAATCTTA
41037157 CATTGGAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (36 bp):
CAGTCCAAAATCTATTCTCAAACTACGGAATCTTAA
Found at i:41045453 original size:13 final size:13
Alignment explanation
Indices: 41045435--41045460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41045425 CACTTTTAAA
41045435 TTTTAAAAATTAT
1 TTTTAAAAATTAT
41045448 TTTTAAAAATTAT
1 TTTTAAAAATTAT
41045461 AAACAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAAAATTAT
Found at i:41047923 original size:2 final size:2
Alignment explanation
Indices: 41047916--41047952 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41047906 CATTGGTAGA
41047916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41047953 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41049268 original size:6 final size:6
Alignment explanation
Indices: 41049257--41049291 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
41049247 AGGGAGCAAC
*
41049257 TTCCTA TTCCTA TTCCTA TTCCCA TTCCTA TTCCT
1 TTCCTA TTCCTA TTCCTA TTCCTA TTCCTA TTCCT
41049292 CCCTCATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.37, G:0.00, T:0.49
Consensus pattern (6 bp):
TTCCTA
Found at i:41049492 original size:26 final size:26
Alignment explanation
Indices: 41049444--41049498 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
41049434 ATTATATCTT
* *
41049444 TTTATTACTTTAATGTCATATTAATAA
1 TTTATTACTTTAATATCAAATTAA-AA
*
41049471 TTTATTA-TTTAATATTAAATTAAAA
1 TTTATTACTTTAATATCAAATTAAAA
41049496 TTT
1 TTT
41049499 TTGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTACTTTAATATCAAATTAAAA
Found at i:41049548 original size:41 final size:43
Alignment explanation
Indices: 41049464--41049549 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 43
41049454 TAATGTCATA
* * *
41049464 TTAATAATTTATTATTTAATATTAAATTAAAATTTTTGAATAAT
1 TTAATAATTTA-TAATTAATATTAAATGAAAATTTTTAAATAAT
* *
41049508 TTAATAATTTA-AATTAAT-TTAAGTGAAATTTTTTAAATAAT
1 TTAATAATTTATAATTAATATTAAATGAAAATTTTTAAATAAT
41049549 T
1 T
41049550 ATTAAGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 20 0.54
42 6 0.16
44 11 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (43 bp):
TTAATAATTTATAATTAATATTAAATGAAAATTTTTAAATAAT
Found at i:41054622 original size:3 final size:3
Alignment explanation
Indices: 41054616--41054670 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
41054606 CATTTAACAG
* * *
41054616 AGA AGA AGA AGA AGA AGA GGA AGA AGA AGG AGA AGA AGA A-A AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
41054663 AGA AGA AG
1 AGA AGA AG
41054671 CAGCAGCAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41056504 original size:33 final size:34
Alignment explanation
Indices: 41056443--41056507 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
41056433 CAAATCCATC
**
41056443 ATCTCCTGAATGGGAAACGAACTTGAAAATGATT
1 ATCTCCTGAACAGGAAACGAACTTGAAAATGATT
41056477 ATCTCCTGAACAGGAAAC-AACTTGAAAATGA
1 ATCTCCTGAACAGGAAACGAACTTGAAAATGA
41056508 CACTTATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (34 bp):
ATCTCCTGAACAGGAAACGAACTTGAAAATGATT
Found at i:41056706 original size:12 final size:13
Alignment explanation
Indices: 41056680--41056704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41056670 TTATTTAATT
41056680 TTTATAAAAAAAA
1 TTTATAAAAAAAA
41056693 TTTATAAAAAAA
1 TTTATAAAAAAA
41056705 TTGAATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTATAAAAAAAA
Found at i:41057786 original size:30 final size:30
Alignment explanation
Indices: 41057752--41057844 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
41057742 AATTTTACTG
41057752 TTTAATTGATCTATTAGCTATATATGTTCT
1 TTTAATTGATCTATTAGCTATATATGTTCT
* * * * *
41057782 TTTAA-T-A-ATA-GAGATA-AAATTTTACT
1 TTTAATTGATCTATTAGCTATATATGTT-CT
41057808 GTTTAATTGATCTATTAGCTATATCA-GTTCT
1 -TTTAATTGATCTATTAGCTATAT-ATGTTCT
41057839 TTTAAT
1 TTTAAT
41057845 AATAGAGATG
Statistics
Matches: 45, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
25 5 0.11
26 6 0.13
27 7 0.16
28 2 0.04
29 2 0.04
30 13 0.29
31 6 0.13
32 3 0.07
33 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTAATTGATCTATTAGCTATATATGTTCT
Found at i:41057812 original size:57 final size:57
Alignment explanation
Indices: 41057740--41057853 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
41057730 TTTATTACTA
41057740 AAAATTTTACTGTTTAATTGATCTATTAGCTATAT-ATGTTCTTTTAATAATAGAGAT
1 AAAATTTTACTGTTTAATTGATCTATTAGCTATATCA-GTTCTTTTAATAATAGAGAT
41057797 AAAATTTTACTGTTTAATTGATCTATTAGCTATATCAGTTCTTTTAATAATAGAGAT
1 AAAATTTTACTGTTTAATTGATCTATTAGCTATATCAGTTCTTTTAATAATAGAGAT
41057854 GAATGAAACT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 55 0.98
58 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (57 bp):
AAAATTTTACTGTTTAATTGATCTATTAGCTATATCAGTTCTTTTAATAATAGAGAT
Found at i:41061261 original size:7 final size:7
Alignment explanation
Indices: 41061249--41061276 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
41061239 GCTGGGCATT
41061249 GAAATTG
1 GAAATTG
41061256 GAAATTG
1 GAAATTG
41061263 GAAATTG
1 GAAATTG
41061270 GAAATTG
1 GAAATTG
41061277 CAAAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
GAAATTG
Done.