Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 134 of 318
Found at i:41496387 original size:16 final size:16
Alignment explanation
Indices: 41496366--41496399 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41496356 CTTCTCAGAC
41496366 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
41496382 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
41496398 AC
1 AC
41496400 CACTGAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.06, T:0.18
Consensus pattern (16 bp):
ACTCCTAGAACAAATA
Found at i:41497653 original size:17 final size:17
Alignment explanation
Indices: 41497631--41497680 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
41497621 TATCAAGATA
41497631 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
*
41497648 AATATTAAGATAATAACTTT
1 AATATT-AGAT--TAAATTT
*
41497668 AATATTAAATTAA
1 AATATTAGATTAA
41497681 TAAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 3 0.11
20 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATTAGATTAAATTT
Found at i:41497740 original size:36 final size:35
Alignment explanation
Indices: 41497671--41497741 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
41497661 TAACTTTAAT
*
41497671 ATTAAATTAATAAAATACTATTAAGAAAGTATTAC
1 ATTAAATTAATAAAATACTATTAAGAAAATATTAC
*
41497706 ATTAAATTTAATATTAA-ACTATTAA-AATAATATTAC
1 ATTAAA-TTAATA-AAATACTATTAAGAA-AATATTAC
41497742 TTTTGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 21 0.68
37 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAGAAAATATTAC
Found at i:41501701 original size:13 final size:13
Alignment explanation
Indices: 41501668--41501711 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
41501658 TTTAATTGAA
*
41501668 AAATTAATGTAGTT
1 AAATTAAT-TAATT
*
41501682 AAGTTAATTAATT
1 AAATTAATTAATT
*
41501695 AAATTAATTATTT
1 AAATTAATTAATT
41501708 AAAT
1 AAAT
41501712 AAATAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:41504308 original size:33 final size:35
Alignment explanation
Indices: 41504271--41504347 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 35
41504261 TAAGGTAATA
*
41504271 TAATATTATACCTGTTTTTTATTTT-TTTC-AATT
1 TAATATTATAACTGTTTTTTATTTTATTTCAAATT
*
41504304 TAATATTATAACTTTTTTTTATTTTAGTTTCAAATT
1 TAATATTATAACTGTTTTTTATTTTA-TTTCAAATT
41504340 TATATATT
1 TA-ATATT
41504348 TAAATGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 23 0.61
35 4 0.11
36 6 0.16
37 5 0.13
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (35 bp):
TAATATTATAACTGTTTTTTATTTTATTTCAAATT
Found at i:41506057 original size:20 final size:21
Alignment explanation
Indices: 41506014--41506066 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
41506004 TAGATATTAA
41506014 TAAAAAA-ATAAA--AATCTT
1 TAAAAAATATAAATTAATCTT
*
41506032 TTAAAAATATAAATTAAT-TT
1 TAAAAAATATAAATTAATCTT
*
41506052 TAAAAAGTATAAATT
1 TAAAAAATATAAATT
41506067 TTTGGACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 15 0.52
21 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAATATAAATTAATCTT
Found at i:41507725 original size:16 final size:16
Alignment explanation
Indices: 41507706--41507739 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41507696 AAGATGTATT
41507706 AAAAATAAATTTTATA
1 AAAAATAAATTTTATA
*
41507722 AAAAATGAATTTTATA
1 AAAAATAAATTTTATA
41507738 AA
1 AA
41507740 TTGTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAAATAAATTTTATA
Found at i:41509555 original size:5 final size:5
Alignment explanation
Indices: 41509545--41509598 Score: 87
Period size: 5 Copynumber: 11.4 Consensus size: 5
41509535 TTATGTTTTA
41509545 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-T ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
41509593 A-TAT AT
1 ATTAT AT
41509599 AAACTAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.04
4 6 0.13
5 38 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:41510781 original size:47 final size:48
Alignment explanation
Indices: 41510730--41510833 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 48
41510720 TGTCGGATAT
* * * * * *
41510730 TGTTACTGTTTC-AGGTTCGTTCTAATGAGGTACTGTGTGTATCGTAC
1 TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
*
41510777 TGTTACTG-TTCTAGATTTGTTCCAATGAAGTACTCTGTGTACCATAC
1 TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
*
41510824 TGCTACTGTT
1 TGTTACTGTT
41510834 ACTGTTACTG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 3 0.06
47 43 0.91
48 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (48 bp):
TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
Found at i:41511116 original size:18 final size:18
Alignment explanation
Indices: 41511037--41511141 Score: 95
Period size: 18 Copynumber: 5.9 Consensus size: 18
41511027 ACCAATCAAT
*
41511037 TGATTGATACTGAATAAC
1 TGATTGTTACTGAATAAC
* * * *
41511055 TTATTATTATTGAATAAT
1 TGATTGTTACTGAATAAC
41511073 TGATTGTTACTGAATAAC
1 TGATTGTTACTGAATAAC
* *
41511091 TGACTGTTACTGAATAAA
1 TGATTGTTACTGAATAAC
* * * *
41511109 TAATTGTT-TTGATTGAC
1 TGATTGTTACTGAATAAC
*
41511126 TGATTGTTAATGAATA
1 TGATTGTTACTGAATA
41511142 TTACTGATTA
Statistics
Matches: 65, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
17 12 0.18
18 53 0.82
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (18 bp):
TGATTGTTACTGAATAAC
Found at i:41516441 original size:23 final size:22
Alignment explanation
Indices: 41516407--41516480 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
41516397 AAAGTGAATG
41516407 GAATTATATTAAATTGAAAATAT
1 GAATTA-ATTAAATTGAAAATAT
41516430 -ATAGTTAATT-AATT-AAAATAT
1 GA-A-TTAATTAAATTGAAAATAT
*
41516451 GAATTAATTGAAAATTGAAAA-GT
1 GAATTAATT--AAATTGAAAATAT
41516474 GAATTAA
1 GAATTAA
41516481 ATACCCTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
20 6 0.14
21 8 0.19
22 6 0.14
23 16 0.37
24 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (22 bp):
GAATTAATTAAATTGAAAATAT
Found at i:41516457 original size:16 final size:16
Alignment explanation
Indices: 41516436--41516469 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
41516426 ATATATAGTT
41516436 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
41516452 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
41516468 AA
1 AA
41516470 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:41516726 original size:47 final size:47
Alignment explanation
Indices: 41516654--41516760 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 47
41516644 CTGTTACCGT
* * * * * *
41516654 TACTGTTACTATTTCAGATTCGTTCCGATGAGTTACTGTGTGTATCA
1 TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
* *
41516701 TACTGTTACTGTTCCGGATTTGTTCCCATGAGGTACTCTGTGTACCA
1 TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
*
41516748 TACTGCTACTGTT
1 TACTGTTACTGTT
41516761 ACTGTTACTG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (47 bp):
TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
Found at i:41517014 original size:18 final size:18
Alignment explanation
Indices: 41516964--41517069 Score: 81
Period size: 18 Copynumber: 5.9 Consensus size: 18
41516954 AACTGATCAG
* *
41516964 TTGATTGATACTGTATAA
1 TTGATTGTTACTGAATAA
* *
41516982 CTT-ATTATTATTGAATAA
1 -TTGATTGTTACTGAATAA
41517000 TTGATTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* *
41517018 CTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* * * *
41517036 ATAATTGTT-CTGATTGA
1 TTGATTGTTACTGAATAA
* *
41517053 CTGATTGTTAATGAATA
1 TTGATTGTTACTGAATA
41517070 TTACTGATTG
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
17 15 0.22
18 50 0.75
19 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (18 bp):
TTGATTGTTACTGAATAA
Found at i:41517033 original size:36 final size:36
Alignment explanation
Indices: 41516964--41517069 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 36
41516954 AACTGATCAG
* * * * *
41516964 TTGATTGATACTGTATAACTTATTATTATTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* *
41517000 TTGATTGTTACTGAATAACTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* * * *
41517036 ATAATTGTT-CTGATTGACTGATTGTTAATGAATA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATA
41517070 TTACTGATTG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 21 0.36
36 37 0.64
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (36 bp):
TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
Found at i:41517068 original size:35 final size:36
Alignment explanation
Indices: 41516993--41517069 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 36
41516983 TTATTATTAT
* * *
41516993 TGAATAATTGATTGTTACTGAATAACTGACTGTTAC
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
* * *
41517029 TGAATAAATAATTGTT-CTGATTGACTGATTGTTAA
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
41517064 TGAATA
1 TGAATA
41517070 TTACTGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 21 0.60
36 14 0.40
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (36 bp):
TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
Found at i:41523761 original size:21 final size:21
Alignment explanation
Indices: 41523735--41523779 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
41523725 CGAGATGTGA
41523735 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
41523756 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
41523777 AAC
1 AAC
41523780 TCTGGACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (21 bp):
AACATATCATGGATACGATCT
Found at i:41526275 original size:43 final size:42
Alignment explanation
Indices: 41526174--41526280 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 42
41526164 ATGTGGTTAT
* * *
41526174 ATGTAAGACCATGTCTGGGACATCAACATCGTATTTGATTCG
1 ATGTAAGACCATGTCTGGGACATCAACATCGTATATGAATAG
* * *
41526216 -TGTAAGACCCTCTCTGGGACAGTC-GCATCG-ATATGAGATAG
1 ATGTAAGACCATGTCTGGGACA-TCAACATCGTATATGA-ATAG
41526257 AATGTAAGACCATGTCTGGGACAT
1 -ATGTAAGACCATGTCTGGGACAT
41526281 TGGCATTGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
40 5 0.09
41 26 0.49
42 3 0.06
43 19 0.36
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (42 bp):
ATGTAAGACCATGTCTGGGACATCAACATCGTATATGAATAG
Found at i:41530465 original size:27 final size:27
Alignment explanation
Indices: 41530300--41530483 Score: 122
Period size: 27 Copynumber: 6.9 Consensus size: 27
41530290 TTACCCTATA
* * *
41530300 AGGGTATTTCAGTAATTTTAC-ACTACA
1 AGGGTATTTCGGTAATTTTACAAAT-CG
* * * *
41530327 ATGGTATTTCGATAATTATACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
41530354 GGGGTATTTCAGTAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
41530381 -GGGTATTTTGGTAGTTTCACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
41530407 AGGATATTTCGATAATTTCACAAAT-T
1 AGGGTATTTCGGTAATTTTACAAATCG
**
41530433 AGGGGTATTTCGGTAATTTTACAACCCG
1 A-GGGTATTTCGGTAATTTTACAAATCG
***
41530461 AGGGTATTTTAATAATTTTACAA
1 AGGGTATTTCGGTAATTTTACAA
41530484 GTCAGGGGTC
Statistics
Matches: 119, Mismatches: 34, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
26 21 0.18
27 95 0.80
28 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:41538025 original size:45 final size:45
Alignment explanation
Indices: 41537976--41538145 Score: 147
Period size: 45 Copynumber: 3.9 Consensus size: 45
41537966 AGGATTTTCG
* *
41537976 ATATGTGTTTTCGTGTAAGACCACGTCAGGGACATTGGCATCGAT
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* * * * *
41538021 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGACATCG-T
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* *
41538065 AT-T-TGATTT-GTGTAAGACC-CTGTCTGGGATAGTGGCATCG--
1 ATATGTGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGAT
* * ** * *
41538105 ACATGAGATAGCATGTAAGACCATGTCTGGGACATTGGCAT
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCAT
41538146 TGTATGATAT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 26 0.26
42 7 0.07
43 25 0.25
44 3 0.03
45 37 0.37
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (45 bp):
ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
Found at i:41550588 original size:15 final size:16
Alignment explanation
Indices: 41550554--41550593 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41550544 TATATATTCT
41550554 TTTTATTTTAAATTAG
1 TTTTATTTTAAATTAG
*
41550570 TTTTATTTTAATTTA-
1 TTTTATTTTAAATTAG
*
41550585 TTTTCTTTT
1 TTTTATTTT
41550594 CCCAAATCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTATTTTAAATTAG
Found at i:41563887 original size:19 final size:17
Alignment explanation
Indices: 41563863--41563897 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
41563853 AATACTCAAA
41563863 TATTTATTATGGTATGAGG
1 TATTTATT-TGGT-TGAGG
41563882 TATTTATTTGGTTGAG
1 TATTTATTTGGTTGAG
41563898 ATATGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (17 bp):
TATTTATTTGGTTGAGG
Found at i:41566175 original size:29 final size:29
Alignment explanation
Indices: 41566112--41566179 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41566102 TAATCAACCG
41566112 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41566141 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41566170 CGCACACTTA
1 CGCACACTTA
41566180 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41566291 original size:174 final size:174
Alignment explanation
Indices: 41566001--41566328 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
41565991 AACTCAAGGT
* * *
41566001 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
41566066 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
41566131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
41566175 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
*
41566240 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
41566305 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
41566329 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41566320 original size:29 final size:28
Alignment explanation
Indices: 41566281--41566356 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
41566271 CTTAATAATC
41566281 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
41566311 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
41566340 AACCCGCACACTTAGTG
1 AACCCGCACACTTAGTG
41566357 TCAATCTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.79
30 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Found at i:41570082 original size:40 final size:40
Alignment explanation
Indices: 41570031--41570461 Score: 713
Period size: 40 Copynumber: 10.8 Consensus size: 40
41570021 CATTTGAATG
41570031 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41570071 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41570111 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41570151 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41570190 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41570230 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
41570270 ATATCCGGGATAAGACTCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
41570310 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41570350 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
41570390 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
** * *
41570430 ATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
41570462 TTGTGGTTAT
Statistics
Matches: 368, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
39 41 0.11
40 326 0.89
41 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:41581773 original size:26 final size:27
Alignment explanation
Indices: 41581743--41581812 Score: 108
Period size: 26 Copynumber: 2.7 Consensus size: 27
41581733 TTCATCTAAT
* *
41581743 AGGCATAACAGCCATTTTATCACACAG
1 AGGCATAATAGTCATTTTATCACACAG
41581770 -GGCATAATAGTCA-TTTATCACACAG
1 AGGCATAATAGTCATTTTATCACACAG
41581795 AGGCATAATAGTCATTTT
1 AGGCATAATAGTCATTTT
41581813 GTCAATTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 12 0.31
26 24 0.62
27 3 0.08
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (27 bp):
AGGCATAATAGTCATTTTATCACACAG
Found at i:41583596 original size:29 final size:29
Alignment explanation
Indices: 41583533--41583600 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41583523 TAATCAACCA
41583533 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41583562 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41583591 CGCACACTTA
1 CGCACACTTA
41583601 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41583720 original size:173 final size:173
Alignment explanation
Indices: 41583423--41583748 Score: 528
Period size: 173 Copynumber: 1.9 Consensus size: 173
41583413 AACTCAAGGT
* * *
41583423 ACTTACCTTTTCCGCTGTCCAAATTGGACTCAGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCAGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * *
41583488 GAAAATATATACTGGGTTGCGCACATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGCA
66 GAAAATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
41583553 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
41583596 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCAGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * * *
41583661 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACAC-TAGTGCCATGT
66 GAAAATATATACTGGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
41583725 ACTTTAAACTCGCACACTTAGTGC
130 ACTTTAAACTCACACACTTAGTGC
41583749 TGTACAATTT
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
173 111 0.79
174 29 0.21
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCAGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41583738 original size:28 final size:30
Alignment explanation
Indices: 41583702--41583779 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
41583692 CTTAATAATC
41583702 AACCGCGCACAC-TAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41583731 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41583760 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41583780 ATCTCATGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 5 0.12
28 8 0.19
29 28 0.67
30 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.24
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41585673 original size:39 final size:40
Alignment explanation
Indices: 41585624--41585795 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
41585614 GCTCCTCGTT
* *
41585624 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGTTTTAGTAACTCGCA
*
41585664 C-AATGCCTTCGGGACATAACCCGGTTTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTTTAGTAACTCGCA
* * * *
41585703 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTTTAGTAACTCGCA
* * * ** *
41585743 CAAAGGCCTTCGGGGCTTAACCCAGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGTTTTAGTAACTCGCA
41585783 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41585796 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 36 0.31
40 77 0.65
41 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGTTTTAGTAACTCGCA
Found at i:41585857 original size:41 final size:41
Alignment explanation
Indices: 41585780--41585857 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41585770 TTTGTATCTC
* * *
41585780 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41585821 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41585858 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41594465 original size:29 final size:29
Alignment explanation
Indices: 41594402--41594469 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41594392 TAATCAACCG
41594402 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41594431 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41594460 CGCACACTTA
1 CGCACACTTA
41594470 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41594581 original size:174 final size:174
Alignment explanation
Indices: 41594291--41594618 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
41594281 AACTCAAGGT
* *
41594291 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
41594356 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
41594421 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
41594465 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
41594530 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
41594595 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
41594619 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41594610 original size:29 final size:30
Alignment explanation
Indices: 41594571--41594649 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
41594561 CTTAATAATC
41594571 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41594601 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41594630 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41594650 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41598373 original size:40 final size:40
Alignment explanation
Indices: 41598322--41598913 Score: 1033
Period size: 40 Copynumber: 14.8 Consensus size: 40
41598312 CATTTAAATG
41598322 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598362 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598402 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41598442 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598482 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598522 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41598562 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41598602 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598642 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
41598682 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
41598722 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
41598762 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
41598802 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
41598842 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
** * *
41598882 ATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
41598914 TTGTGGTTAT
Statistics
Matches: 526, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 2 0.00
40 523 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:41606872 original size:29 final size:29
Alignment explanation
Indices: 41606809--41606876 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41606799 TAATCAACCG
41606809 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41606838 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41606867 CGCACACTTA
1 CGCACACTTA
41606877 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41606988 original size:174 final size:174
Alignment explanation
Indices: 41606698--41607025 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
41606688 AACTCAAGGT
* *
41606698 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
41606763 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
41606828 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
41606872 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
41606937 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
41607002 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
41607026 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41607017 original size:29 final size:30
Alignment explanation
Indices: 41606978--41607056 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
41606968 CTTAATAATC
41606978 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41607008 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41607037 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41607057 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41610113 original size:23 final size:22
Alignment explanation
Indices: 41610081--41610135 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
41610071 ACCAATCCAA
*
41610081 TTCAACATATTT-TCAAGATAGA-
1 TTCATCATATTTAT-AAGATA-AC
41610103 TTCATGCATATTTATAAGATAAC
1 TTCAT-CATATTTATAAGATAAC
41610126 TTCATCATAT
1 TTCATCATAT
41610136 ACCAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 10 0.34
23 18 0.62
24 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCATCATATTTATAAGATAAC
Found at i:41613806 original size:31 final size:29
Alignment explanation
Indices: 41613743--41613806 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
41613733 CAAACGAACT
**
41613743 ATTTTTTAAAATTATAAAAAATAATTTTA
1 ATTTTTTAAAATTATAAAAAATAATTAAA
*
41613772 ATTTTTTATAAATTTATAAAATATAATTAAA
1 ATTTTTTA-AAA-TTATAAAAAATAATTAAA
41613803 ATTT
1 ATTT
41613807 ATAAGAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 3 0.10
31 19 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTTTAAAATTATAAAAAATAATTAAA
Found at i:41628386 original size:25 final size:25
Alignment explanation
Indices: 41628356--41628408 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
41628346 TTAAAAAAAG
41628356 TATGAATTTATCATAAGT-ATTTTCT
1 TATGAATTTATCATAA-TCATTTTCT
41628381 TATGAATTTATCATAATCATTTTCT
1 TATGAATTTATCATAATCATTTTCT
41628406 TAT
1 TAT
41628409 AGCACTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (25 bp):
TATGAATTTATCATAATCATTTTCT
Found at i:41642242 original size:47 final size:47
Alignment explanation
Indices: 41642188--41642284 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
41642178 TCGAAAACGT
41642188 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
1 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
41642235 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
1 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
41642282 TAA
1 TAA
41642285 AAACCAATGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (47 bp):
TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
Found at i:41646280 original size:12 final size:12
Alignment explanation
Indices: 41646263--41646337 Score: 93
Period size: 12 Copynumber: 6.2 Consensus size: 12
41646253 CTCTCTGTAT
41646263 TTACTTATATTA
1 TTACTTATATTA
41646275 TTACTTATATTA
1 TTACTTATATTA
41646287 TTACTTATATTA
1 TTACTTATATTA
41646299 TTA-TTACTATTA
1 TTACTTA-TATTA
*
41646311 TCA-TTATGATTTA
1 TTACTTAT-A-TTA
41646324 TTACTT-TATTA
1 TTACTTATATTA
41646335 TTA
1 TTA
41646338 TCATTATTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.18
12 39 0.68
13 6 0.11
14 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (12 bp):
TTACTTATATTA
Found at i:41646288 original size:3 final size:3
Alignment explanation
Indices: 41646270--41646346 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
41646260 TATTTACTTA
* *
41646270 TAT TAT TACT TA- TAT TAT TACT TA- TAT TAT TAT TAC TAT TAT CAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
41646315 TAT GATT TAT TAC T-T TAT TAT TAT CAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
41646347 CTGCCATTGT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
2 5 0.09
3 45 0.78
4 8 0.14
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:41646300 original size:15 final size:13
Alignment explanation
Indices: 41646263--41646317 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 13
41646253 CTCTCTGTAT
41646263 TTAC-TTATATTA
1 TTACTTTATATTA
41646275 TTAC-TTATATTA
1 TTACTTTATATTA
41646287 TTACTTATATTATTA
1 TTACTT-TA-TATTA
41646302 TTACTATTATCATTA
1 TTACT-TTAT-ATTA
41646317 T
1 T
41646318 GATTTATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 16 0.42
13 1 0.03
14 3 0.08
15 17 0.45
16 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (13 bp):
TTACTTTATATTA
Found at i:41646344 original size:27 final size:25
Alignment explanation
Indices: 41646267--41646344 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 25
41646257 CTGTATTTAC
41646267 TTATATTATTACTTATATTATTA-C-
1 TTATATTATTACTT-TATTATTATCA
*
41646291 TTATATTATTA--TTACTATTATCA
1 TTATATTATTACTTTATTATTATCA
41646314 TTATGATTTATTACTTTATTATTATCA
1 TTAT-A-TTATTACTTTATTATTATCA
41646341 TTAT
1 TTAT
41646345 TACTGCCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
21 7 0.15
22 2 0.04
23 4 0.09
24 12 0.26
25 6 0.13
27 15 0.33
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATATTATTACTTTATTATTATCA
Found at i:41646346 original size:12 final size:11
Alignment explanation
Indices: 41646267--41646346 Score: 76
Period size: 12 Copynumber: 7.0 Consensus size: 11
41646257 CTGTATTTAC
41646267 TTATATTATTA
1 TTATATTATTA
41646278 CTTATATTATTA
1 -TTATATTATTA
41646290 CTTATATTATTA
1 -TTATATTATTA
*
41646302 TTACTATTATCA
1 TTA-TATTATTA
41646314 TTATGA-T-TTA
1 TTAT-ATTATTA
41646324 TTACT-TTATTA
1 TTA-TATTATTA
41646335 TTATCATTATTA
1 TTAT-ATTATTA
41646347 CTGCCATTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
10 7 0.12
11 12 0.20
12 40 0.68
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (11 bp):
TTATATTATTA
Found at i:41646366 original size:3 final size:3
Alignment explanation
Indices: 41646057--41646112 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
41646047 ACTATTATGC
* *
41646057 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
41646103 TAT TAT TAT T
1 TAT TAT TAT T
41646113 TATCGTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:41646434 original size:20 final size:19
Alignment explanation
Indices: 41646405--41646452 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
41646395 CTTATTTTAT
* *
41646405 TTTATTTATTCTTCACTCA
1 TTTATATATTATTCACTCA
* *
41646424 CTTTATATATTATTTACTTA
1 -TTTATATATTATTCACTCA
41646444 TTTATATAT
1 TTTATATAT
41646453 ACACATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATATTATTCACTCA
Found at i:41652801 original size:30 final size:30
Alignment explanation
Indices: 41652765--41652825 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41652755 TTTAACCTCT
41652765 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
41652795 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
41652825 A
1 A
41652826 AAAAATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (30 bp):
ATACATAGATTGTATTCTACACAATCTACC
Found at i:41658595 original size:14 final size:14
Alignment explanation
Indices: 41658576--41658609 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
41658566 ATGACGTTAA
41658576 GGTGTGGCAATGGC
1 GGTGTGGCAATGGC
41658590 GGTGTGGCAATGGC
1 GGTGTGGCAATGGC
41658604 GGTGTG
1 GGTGTG
41658610 CATGTCTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.53, T:0.24
Consensus pattern (14 bp):
GGTGTGGCAATGGC
Found at i:41659951 original size:36 final size:35
Alignment explanation
Indices: 41659902--41659998 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 35
41659892 CAAAAAACAC
*
41659902 ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
1 ACACA-CAAATGCTCATAAGAGCTAATACATCCAAA
* * **
41659938 ACACACTAAATGCTTATAAGAGCTAATCCATCTGAA
1 ACACAC-AAATGCTCATAAGAGCTAATACATCCAAA
* *
41659974 ACACACCAATAGCTCAGAAGAGCTA
1 ACACACAAAT-GCTCATAAGAGCTA
41659999 GTCCAATCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 4 0.08
36 47 0.92
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (35 bp):
ACACACAAATGCTCATAAGAGCTAATACATCCAAA
Found at i:41666882 original size:42 final size:43
Alignment explanation
Indices: 41666836--41666924 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
41666826 TGGGACATCA
* * *
41666836 GCATC-ATATTTGATTTCGTGTAAGACCCTATCTAGGACAG-TG
1 GCATCGATATTTGATTACATGTAAGACCATATCTAGGAC-GTTG
*
41666878 GCATCGATATTTGATTACATGTAAGACCATGTCTAGGACGTTG
1 GCATCGATATTTGATTACATGTAAGACCATATCTAGGACGTTG
41666921 GCAT
1 GCAT
41666925 TGTACGATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 6 0.15
43 35 0.85
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (43 bp):
GCATCGATATTTGATTACATGTAAGACCATATCTAGGACGTTG
Found at i:41668823 original size:12 final size:12
Alignment explanation
Indices: 41668789--41668824 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
41668779 TATACATCAT
41668789 ATTGACTGTTCG
1 ATTGACTGTTCG
*
41668801 ATTGAAATGTTCG
1 ATTG-ACTGTTCG
41668814 ATTGACTGTTC
1 ATTGACTGTTC
41668825 AATTTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (12 bp):
ATTGACTGTTCG
Found at i:41673819 original size:39 final size:40
Alignment explanation
Indices: 41673728--41673946 Score: 258
Period size: 39 Copynumber: 5.5 Consensus size: 40
41673718 ATGATGTCCA
*
41673728 GGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT-TCCG
*
41673767 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATTCCG
41673807 GGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCG
* *
41673846 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCG
* *
41673885 GGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-TCCG
*
41673925 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
41673947 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 89 0.56
40 59 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCG
Found at i:41673861 original size:78 final size:80
Alignment explanation
Indices: 41673728--41673946 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 80
41673718 ATGATGTCCA
* * * * *
41673728 GGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCATTTGT
1 GGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCATTTGT
*
41673790 GCGAGATACTAATTCCG
64 GCGAGATACTAAATCCG
*
41673807 GGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGT
1 GGCTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCATTTGT
*
41673868 GCGAGTTACTAAATCCG
64 GCGAGATACTAAATCCG
* *
41673885 GGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
41673947 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 9, Indels: 17
0.82 0.06 0.11
Matches are distributed among these distances:
78 46 0.38
79 53 0.43
80 22 0.18
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGC
GAGATACTAAATCCG
Found at i:41673968 original size:79 final size:79
Alignment explanation
Indices: 41673776--41673979 Score: 213
Period size: 79 Copynumber: 2.6 Consensus size: 79
41673766 GGACTAAGAT
** * *
41673776 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT
*
41673839 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** *
41673854 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACT
*
41673918 -ATAACCGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
* * *
41673934 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
41673980 TACGTGATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 37 0.34
79 47 0.43
80 25 0.23
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:41681220 original size:40 final size:40
Alignment explanation
Indices: 41680994--41681255 Score: 310
Period size: 39 Copynumber: 6.7 Consensus size: 40
41680984 TTGAATGATG
*
41680994 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAA-A
* * *
41681033 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
41681073 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
41681112 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
41681151 TCCGGGCTAAG-CCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
41681190 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AA
*
41681231 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41681256 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
39 129 0.64
40 59 0.29
41 12 0.06
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:41682681 original size:29 final size:30
Alignment explanation
Indices: 41682642--41682720 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
41682632 CTTAATAATC
41682642 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41682672 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41682701 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41682721 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41692584 original size:43 final size:41
Alignment explanation
Indices: 41692488--41692586 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 41
41692478 TATGGATATG
* *
41692488 TGATTTCATGTAAAACCATGTCTGGGAAATTGGCATTGTAT
1 TGATTTCATGTAAAACCATGTCGGGGAAATTGGCATCGTAT
* * * *
41692529 TGAGATTACATGTAAGATCATGTCGGGGACATTGGCATCGTTAAT
1 T--GATTTCATGTAAAACCATGTCGGGGAAATTGGCATCG-T-AT
41692574 TGATTTCATGTAA
1 TGATTTCATGTAA
41692587 CACTCTATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 1 0.02
43 42 0.89
44 1 0.02
45 3 0.06
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (41 bp):
TGATTTCATGTAAAACCATGTCGGGGAAATTGGCATCGTAT
Found at i:41696308 original size:35 final size:35
Alignment explanation
Indices: 41696269--41696336 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
41696259 ATTTTCACAG
*
41696269 AATCATGCAATCATATCATATACCTCAAAATAAAC
1 AATCATGCAATCATATCATAGACCTCAAAATAAAC
41696304 AATCATGCAATCATATCATAGACCTCAAAATAA
1 AATCATGCAATCATATCATAGACCTCAAAATAA
41696337 TCATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (35 bp):
AATCATGCAATCATATCATAGACCTCAAAATAAAC
Found at i:41700130 original size:27 final size:27
Alignment explanation
Indices: 41700100--41700249 Score: 108
Period size: 27 Copynumber: 5.5 Consensus size: 27
41700090 CATAGGGGTC
*
41700100 AAACAATCATCTTACCATAAAAGGGCA
1 AAACAATCATTTTACCATAAAAGGGCA
* * *
41700127 AAACAAACATTTTACCACATAA-GGCAA
1 AAACAATCATTTTACCATAAAAGGGC-A
*
41700154 AAACAGTCATTTTACCCCAT-AAAGGGCA
1 AAACAATCATTTTA--CCATAAAAGGGCA
* *
41700182 AAATAATCATTTTACC-TCATAAGGGCA
1 AAACAATCATTTTACCAT-AAAAGGGCA
* * * ** *
41700209 GAATAGTCATTTTACCCCATAAGGGCA
1 AAACAATCATTTTACCATAAAAGGGCA
* *
41700236 AAATAGTCATTTTA
1 AAACAATCATTTTA
41700250 TCGATTATGG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 74 0.73
28 15 0.15
29 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.25
Consensus pattern (27 bp):
AAACAATCATTTTACCATAAAAGGGCA
Found at i:41700193 original size:55 final size:55
Alignment explanation
Indices: 41700114--41700249 Score: 186
Period size: 55 Copynumber: 2.5 Consensus size: 55
41700104 AATCATCTTA
* *
41700114 CCATAAAAGGGCAAAACAAACATTTTACCACATAA-GGCAAAAACAGTCATTTTACC
1 CCAT-AAAGGGCAAAATAATCATTTTACCACATAAGGGC-AAAACAGTCATTTTACC
* * *
41700170 CCATAAAGGGCAAAATAATCATTTTACCTCATAAGGGCAGAATAGTCATTTTACC
1 CCATAAAGGGCAAAATAATCATTTTACCACATAAGGGCAAAACAGTCATTTTACC
*
41700225 CCAT-AAGGGCAAAATAGTCATTTTA
1 CCATAAAGGGCAAAATAATCATTTTA
41700250 TCGATTATGG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
54 20 0.27
55 46 0.63
56 7 0.10
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (55 bp):
CCATAAAGGGCAAAATAATCATTTTACCACATAAGGGCAAAACAGTCATTTTACC
Found at i:41706964 original size:39 final size:39
Alignment explanation
Indices: 41706919--41707088 Score: 232
Period size: 39 Copynumber: 4.3 Consensus size: 39
41706909 GGACTTTAAC
** * *
41706919 CCGGATATTTTTCCAGCACGTAGCCTGCGAACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * * *
41706958 CTGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
41706997 CCGGATATTTTTCCTGCATAAAGCCTGCGGACCTTATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
41707036 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
41707075 CCGGATATATTTTC
1 CCGGATAT-TTTTC
41707089 AATCTCATAC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 107 0.96
40 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:41714886 original size:39 final size:39
Alignment explanation
Indices: 41714843--41715011 Score: 250
Period size: 39 Copynumber: 4.3 Consensus size: 39
41714833 GGACTTTAAC
* ** *
41714843 CCGGATATTTTTCCAGTACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
41714882 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
41714921 CCGGATATTTTT-CAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
41714959 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
41714998 CGGGATATATTTTC
1 CCGGATAT-TTTTC
41715012 AATCTCATAC
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
38 36 0.31
39 76 0.65
40 5 0.04
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:41714949 original size:77 final size:77
Alignment explanation
Indices: 41714843--41715012 Score: 250
Period size: 77 Copynumber: 2.2 Consensus size: 77
41714833 GGACTTTAAC
* * *
41714843 CCGGATATTTTTCCAGTACGTAGCCTGCGGACCTCAAGTCCGGATATATTTCTAGCATATAGCCT
1 CCGGATATTTTT-CAGCACATAGCCTGCGGACCTCAAGTCCGGATATATTTCCAGCATATAGCCT
*
41714908 GCGGATCTCATGT
65 GCGGACCTCATGT
* * *
41714921 CCGGATATTTTTCAGCATATAGCCTGCGGACCTCATGTCCGGATATTTTTCCAGCATATAGCCTG
1 CCGGATATTTTTCAGCACATAGCCTGCGGACCTCAAGTCCGGATATATTTCCAGCATATAGCCTG
41714986 CGGACCTCATGT
66 CGGACCTCATGT
*
41714998 CGGGATATATTTTCA
1 CCGGATAT-TTTTCA
41715013 ATCTCATACA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 65 0.78
78 18 0.22
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (77 bp):
CCGGATATTTTTCAGCACATAGCCTGCGGACCTCAAGTCCGGATATATTTCCAGCATATAGCCTG
CGGACCTCATGT
Found at i:41718630 original size:29 final size:28
Alignment explanation
Indices: 41718594--41718671 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
41718584 TCATGAGATT
41718594 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
41718624 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
41718651 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
41718672 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:41718948 original size:173 final size:174
Alignment explanation
Indices: 41718624--41718950 Score: 557
Period size: 173 Copynumber: 1.9 Consensus size: 174
41718614 AAATTGTACA
* *
41718624 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
41718689 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
*
41718754 TTTTGGACAGCGGAGAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
41718798 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
41718863 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
41718927 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
41718951 ACCTTGAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
173 79 0.55
174 64 0.45
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:41755065 original size:21 final size:21
Alignment explanation
Indices: 41755008--41755071 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
41754998 ATGCTTTTTA
*
41755008 TAGCAAAT-ACAGACCATGCT
1 TAGCAAATAACAGATCATGCT
*
41755028 TAGCAAATAACATATCATGCT
1 TAGCAAATAACAGATCATGCT
** * *
41755049 TAGCTTATAATAGATCACGCT
1 TAGCAAATAACAGATCATGCT
41755070 TA
1 TA
41755072 ACATATGACA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 8 0.22
21 28 0.78
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (21 bp):
TAGCAAATAACAGATCATGCT
Found at i:41770080 original size:47 final size:47
Alignment explanation
Indices: 41770026--41770344 Score: 521
Period size: 47 Copynumber: 6.7 Consensus size: 47
41770016 TTAGGATTCT
* *
41770026 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAGTGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41770073 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41770120 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41770167 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
41770214 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
* * * * *
41770263 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
41770310 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41770345 TCCCGAAGGG
Statistics
Matches: 256, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
47 210 0.82
49 46 0.18
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:41770308 original size:143 final size:141
Alignment explanation
Indices: 41770026--41770344 Score: 530
Period size: 143 Copynumber: 2.2 Consensus size: 141
41770016 TTAGGATTCT
*
41770026 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAGTGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
41770091 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGG
* *
41770156 CCTAATGGCCG
131 CCGAATGGCCA
*
41770167 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
41770232 TGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
66 TG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
*
41770297 GGCCGAGTGGCCA
129 GGCCGAATGGCCA
* *
41770310 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAG
41770345 TCCCGAAGGG
Statistics
Matches: 165, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
141 65 0.39
143 100 0.61
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (141 bp):
ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGG
CCGAATGGCCA
Found at i:41781033 original size:37 final size:37
Alignment explanation
Indices: 41780983--41781061 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41780973 TTATTACGAA
* * *
41780983 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41781020 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41781057 GTCTT
1 GTCTT
41781062 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41781456 original size:49 final size:49
Alignment explanation
Indices: 41781180--41781477 Score: 403
Period size: 47 Copynumber: 6.1 Consensus size: 49
41781170 CCCTTCGGGA
* * * *
41781180 CTTATCACAT-T-TATACACTTTCACATCCATCAC-GCTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATC-GGCCATTAGGC
* * *
41781227 CCTGTCAC--ATATATACACTTTCACATTCATCAAATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41781274 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41781321 CCTATCACATATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41781372 CTTATCACATATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41781425 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41781474 CTTA
1 CTTA
41781478 CTGTCATTTC
Statistics
Matches: 228, Mismatches: 14, Indels: 16
0.88 0.05 0.06
Matches are distributed among these distances:
46 1 0.00
47 86 0.38
48 1 0.00
49 45 0.20
51 45 0.20
53 50 0.22
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41781926 original size:23 final size:23
Alignment explanation
Indices: 41781884--41781934 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
41781874 TGAAACTAGA
* *
41781884 CTCATTCAGCTTTAATTTCATGT
1 CTCATTCAGCTCTAATTTCAAGT
41781907 CTCATTCAGCCTCTAA-TTCAAGT
1 CTCATTCAG-CTCTAATTTCAAGT
41781930 C-CATT
1 CTCATT
41781935 AATTTATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (23 bp):
CTCATTCAGCTCTAATTTCAAGT
Found at i:41784604 original size:40 final size:40
Alignment explanation
Indices: 41784559--41784715 Score: 224
Period size: 40 Copynumber: 3.9 Consensus size: 40
41784549 CGAATACACG
* * *
41784559 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * *
41784599 ACACCAGCACGAATGCTCTTCGGAACTTATCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
41784639 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
41784679 TCACTAGCATGAATGCTCTTCGGGACTTAGCCTGGAT
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
41784716 TTAGTAACTC
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:41784740 original size:40 final size:41
Alignment explanation
Indices: 41784572--41784833 Score: 168
Period size: 40 Copynumber: 6.6 Consensus size: 41
41784562 CCAGCATGAT
* * *
41784572 TGCTCTTCGGGACCTAGCCCGGA--TA-TAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATTTAGTAAC-TC-GCACAAA
* * ** * * **
41784612 TGCTCTTCGGAACTTATCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA
** * * **
41784652 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA
* *
41784692 TGCTCTTCGGGACTTAGCCTGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA
* *
41784733 TGC-CTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA
* * * * *
41784772 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA
1 TGCTCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAA
*
41784813 -GC-CTTCGGGACTTACCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
41784834 CATCATTCGA
Statistics
Matches: 185, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.17
40 124 0.67
41 23 0.12
42 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (41 bp):
TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA
Found at i:41784740 original size:80 final size:80
Alignment explanation
Indices: 41784572--41784753 Score: 215
Period size: 80 Copynumber: 2.3 Consensus size: 80
41784562 CCAGCATGAT
* * *
41784572 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAACTTATCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
* **
41784637 CATCACTAGCATGAA
66 CATAACTAGCACCAA
* * * * * *
41784652 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCTGGATT
1 TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
* *
41784717 TAGTAACTCGCACCAA
66 CA-TAACTAGCACCAA
41784733 TGC-CTTCGGG-CTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
41784754 ATTAGTATCT
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 11 0.13
80 64 0.74
81 12 0.14
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.25
Consensus pattern (80 bp):
TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
CATAACTAGCACCAA
Found at i:41785178 original size:29 final size:29
Alignment explanation
Indices: 41785139--41785217 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
41785129 CTTAATAATC
*
41785139 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
41785169 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
41785198 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41785218 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:41787181 original size:37 final size:37
Alignment explanation
Indices: 41787120--41787198 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41787110 TTATTACGAA
* * *
41787120 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
41787157 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
41787194 GTCTT
1 GTCTT
41787199 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:41787492 original size:49 final size:49
Alignment explanation
Indices: 41787316--41787707 Score: 634
Period size: 49 Copynumber: 8.1 Consensus size: 49
41787306 CCCTTCGGGA
* * * * * *
41787316 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGTCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41787363 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41787410 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41787461 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41787510 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41787559 CTTATCAC--GTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41787606 CTTATCACATATATATAAACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41787655 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41787704 CTTA
1 CTTA
41787708 CTGTCATTTC
Statistics
Matches: 323, Mismatches: 14, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
46 1 0.00
47 88 0.27
49 187 0.58
51 47 0.15
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41787605 original size:145 final size:146
Alignment explanation
Indices: 41787316--41787707 Score: 632
Period size: 145 Copynumber: 2.7 Consensus size: 146
41787306 CCCTTCGGGA
* * * * * * * *
41787316 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGTCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
41787377 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATACACTTTCACATTC
66 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--A-ATATATACACTTTCACATTC
41787442 ATCACATCGGCCATTAGGC
128 ATCACATCGGCCATTAGGC
41787461 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
41787526 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-GTATATACACTTTCACATTCATC
66 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATC
41787590 ACATCGGCCATTAGGC
131 ACATCGGCCATTAGGC
*
41787606 CTTATCACATATATATAAACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
41787671 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
66 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41787708 CTGTCATTTC
Statistics
Matches: 233, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
145 149 0.64
146 1 0.00
147 36 0.15
149 47 0.20
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (146 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATC
ACATCGGCCATTAGGC
Found at i:41791994 original size:28 final size:28
Alignment explanation
Indices: 41791962--41792025 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
41791952 ATTTACTAGA
*
41791962 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
41791990 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41792018 ATACCCCT
1 ATACCCCT
41792026 TGGGTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41792205 original size:29 final size:28
Alignment explanation
Indices: 41792142--41792205 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
41792132 CTAGTGGCTA
* *
41792142 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
41792170 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
41792199 TGTCACA
1 TGCCACA
41792206 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:41792673 original size:19 final size:19
Alignment explanation
Indices: 41792649--41792687 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41792639 TTTTAATTAT
* *
41792649 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
41792668 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
41792687 T
1 T
41792688 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:41796237 original size:47 final size:47
Alignment explanation
Indices: 41796184--41796524 Score: 520
Period size: 47 Copynumber: 7.2 Consensus size: 47
41796174 AATTCTAAAT
41796184 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
41796231 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
41796278 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
41796326 TGTGATAAGGCCTAATGGCCGATGTGCTGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* * *
41796375 TGTGATAAGGCTTAATGGCCGATGTGAAGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
41796422 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * *
41796469 TGTGACAAGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
41796516 TGTGATAAG
1 TGTGATAAG
41796525 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 180 0.67
48 45 0.17
49 44 0.16
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:41796698 original size:37 final size:37
Alignment explanation
Indices: 41796642--41796720 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41796632 TCGAGCTCTA
* * *
41796642 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41796679 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41796716 AAGAC
1 AAGAC
41796721 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41803928 original size:28 final size:28
Alignment explanation
Indices: 41803892--41803956 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
41803882 ATTTACTATA
*
41803892 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* * *
41803920 ATAGCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41803948 ATACCCCTA
1 ATACCCCTA
41803957 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41804103 original size:28 final size:28
Alignment explanation
Indices: 41804062--41804116 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41804052 AGGAAGCATC
*
41804062 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTT
41804090 CTGGTGGC-ATTGCCACAAAATATCTGT
1 CTGGTGGCTA-TGCCACAAAATATCTGT
41804117 ATCTAGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (28 bp):
CTGGTGGCTATGCCACAAAATATCTGTT
Found at i:41804602 original size:19 final size:19
Alignment explanation
Indices: 41804578--41804616 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41804568 TTTTAATTAT
* *
41804578 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
41804597 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
41804616 T
1 T
41804617 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:41805834 original size:30 final size:30
Alignment explanation
Indices: 41805800--41805860 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41805790 TCCTTAACTC
41805800 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41805830 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41805860 A
1 A
41805861 GGCTCGGGAA
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:41806926 original size:18 final size:18
Alignment explanation
Indices: 41806890--41807041 Score: 229
Period size: 18 Copynumber: 8.6 Consensus size: 18
41806880 AATCATATCT
*
41806890 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
41806909 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
41806927 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
41806944 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
41806962 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
*
41806979 TCTAAGATTGCAATGATA
1 TCTAAGATTGCAATCATA
*
41806997 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
41807014 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
41807032 TCTAAGATTG
1 TCTAAGATTG
41807042 TATTATATCT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
17 47 0.39
18 63 0.52
19 11 0.09
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:41806948 original size:35 final size:35
Alignment explanation
Indices: 41806890--41807076 Score: 293
Period size: 35 Copynumber: 5.3 Consensus size: 35
41806880 AATCATATCT
41806890 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
41806927 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
41806962 TCTAAGATTGTATCATATCTAAGATTGCAATGATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
41806997 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* * * * *
41807032 TCTAAGATTGTATTATATCTAGGATTGTATCTCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
41807068 TCTAAGATT
1 TCTAAGATT
41807077 TGCTTTAACG
Statistics
Matches: 142, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
35 119 0.84
36 13 0.09
37 10 0.07
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:41807425 original size:205 final size:205
Alignment explanation
Indices: 41807066--41807737 Score: 1092
Period size: 205 Copynumber: 3.3 Consensus size: 205
41807056 TTGTATCTCA
* * * * * *
41807066 CATCTAAGATTTGCTTTAACGTAAGCACGTGAAATCCAAATCAGCTATGTCTTCGATTTGCTCCT
1 CATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCT
* *
41807131 TGTAAGCACAAGGATGCCAAACCATATTGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCT
66 TGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCT
* * *
41807196 GCCATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGA
131 GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGA
41807261 GATGACAAAT
196 GATGACAAAT
* *
41807271 CATCTTAGATTTGCTTCATCATAAATACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCT
1 CATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCT
* *
41807336 TGTAAGCACAAGGATACAAAACCATCTTGGATCTACTTCAGCATAAACATCTGAAGGTGAGATCT
66 TGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCT
*
41807401 GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAAA
131 GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGA
*
41807466 GACGACAAAT
196 GATGACAAAT
* * * * *
41807476 CATCTTATATTTGCTTTAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCAT
1 CATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCT
* *
41807541 TGTAAGCACAATGATACCAAACCATCTTGGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCT
66 TGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCT
* *
41807606 GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCTATTTGTTCTCTGACAATACAGA
131 GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGA
*
41807671 GATGAAAAAT
196 GATGACAAAT
*
41807681 CATCTTAGATTTGCTTCATTGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGAT
1 CATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGAT
41807738 CTACTCTCTG
Statistics
Matches: 429, Mismatches: 38, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 429 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (205 bp):
CATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCT
TGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCT
GCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGA
GATGACAAAT
Found at i:41807822 original size:44 final size:44
Alignment explanation
Indices: 41807728--41807822 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
41807718 AAATCAGCTA
* *
41807728 TGTCTTCGATCTACTCTCTGCCAATACAGAGATGCCAAATCTGG
1 TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
* * *
41807772 TATCTTCGATCTGCTCTCTGACAATACAGAGATGCCGAATCTGC
1 TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
41807816 TGTCTTC
1 TGTCTTC
41807823 AACTTGTTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (44 bp):
TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
Found at i:41807881 original size:44 final size:43
Alignment explanation
Indices: 41807827--41808336 Score: 310
Period size: 44 Copynumber: 11.6 Consensus size: 43
41807817 GTCTTCAACT
* * *
41807827 TGTTCCCTGTAAACACAGGGATACCATGCTGAAATCTTCGATC
1 TGTTCCCTATAAACACAGGGATGCCATGCTGATATCTTCGATC
* * * * *
41807870 TGCTTCGCTGTAAGCACA-GGAGTGTCA-GATCT-ATTATCTTCGATA
1 TG-TTCCCTATAAACACAGGGA-TGCCATG--CTGA-TATCTTCGATC
* * *
41807915 TGTTCCATATAAACACAGGGATGCCAAAT-CTGCTATCTTC-AAC
1 TGTTCCCTATAAACACAGGGATGCC--ATGCTGATATCTTCGATC
* *
41807958 TTGTTCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATC
1 -TGTTCCCTATAAACACAGGGATGCCATGCTGATATCTTCGATC
* * * * * * *
41808002 GGTTACGCTGTAAGCACA-GGAGTGTCA-GATTTGTTATCTTCGATC
1 TGTT-CCCTATAAACACAGGGA-TGCCATG--CTGATATCTTCGATC
* * *
41808047 TGTTCCCTATAAATACAGGGATGCCAAAT-CTGCTATCTTC-AAC
1 TGTTCCCTATAAACACAGGGATGCC--ATGCTGATATCTTCGATC
* * *
41808090 TTGTTCCCTATAAACATAGGGATGCCATGCTGAAATCCTCGATC
1 -TGTTCCCTATAAACACAGGGATGCCATGCTGATATCTTCGATC
* * * * *
41808134 TGCTTCGCTGTAAGCACA-GGAGTGTCA-GATCTGTTATCTTCGATC
1 TG-TTCCCTATAAACACAGGGA-TGCCATG--CTGATATCTTCGATC
* * * *
41808179 TATTCCCTATAAACACAGGGATGCCAAAT-CCGCTATCTTC-AAC
1 TGTTCCCTATAAACACAGGGATGCC--ATGCTGATATCTTCGATC
*
41808222 TTGTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATC
1 -TGTTCCCTATAAACACAGGGATGCCATGCTGATATCTTCGATC
* * * * * * *
41808266 TGCTTCGCTCTAAGCATAGGAATGTCA-GATCTGCTATCTTCGATC
1 TG-TTCCCTATAAACACAGGGATGCCATG--CTGATATCTTCGATC
41808311 TGTTCCCTATAAACACAGGGATGCCA
1 TGTTCCCTATAAACACAGGGATGCCA
41808337 AATCTTGTTT
Statistics
Matches: 351, Mismatches: 78, Indels: 75
0.70 0.15 0.15
Matches are distributed among these distances:
42 6 0.02
43 51 0.15
44 227 0.65
45 64 0.18
46 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
TGTTCCCTATAAACACAGGGATGCCATGCTGATATCTTCGATC
Found at i:41808011 original size:132 final size:132
Alignment explanation
Indices: 41807766--41808341 Score: 895
Period size: 132 Copynumber: 4.4 Consensus size: 132
41807756 GAGATGCCAA
* * * * * * * *
41807766 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCGAATCTGCTGTCTTCAACTTGT
1 ATCTGTTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGT
* * *
41807830 TCCCTGTAAACACAGGGATACCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
65 TCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
41807895 CAG
130 CAG
* * *
41807898 ATCTATTATCTTCGATATGTTCCATATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
*
41807963 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATC-GGTTACGCTGTAAGCACAGGAGTGT
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTT-CGCTGTAAGCACAGGAGTGT
41808027 CAG
130 CAG
* *
41808030 ATTTGTTATCTTCGATCTGTTCCCTATAAATACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
*
41808095 CCCTATAAACATAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
41808160 AG
131 AG
* *
41808162 ATCTGTTATCTTCGATCTATTCCCTATAAACACAGGGATGCCAAATCCGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* * * *
41808227 CCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTCTAAGCATAGGAATGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
41808292 AG
131 AG
*
41808294 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
41808342 TGTTTCTTTG
Statistics
Matches: 407, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
131 4 0.01
132 400 0.98
133 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
AG
Found at i:41809258 original size:21 final size:21
Alignment explanation
Indices: 41809232--41809287 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
41809222 TGGCCTCTCC
*
41809232 ATTTTTCTTCTTTCTCTTTTTT
1 ATTTTTCTT-TTTATCTTTTTT
*
41809254 ATTTTTCTTTTTATTTTTTTT
1 ATTTTTCTTTTTATCTTTTTT
*
41809275 ATTTATTTTTTTT
1 ATTT-TTCTTTTT
41809288 CCTTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (21 bp):
ATTTTTCTTTTTATCTTTTTT
Found at i:41809285 original size:13 final size:12
Alignment explanation
Indices: 41809248--41809287 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
41809238 CTTCTTTCTC
41809248 TTTTTTATTTTT
1 TTTTTTATTTTT
*
41809260 CTTTTTATTTTT
1 TTTTTTATTTTT
41809272 TTTATTTATTTTT
1 TTT-TTTATTTTT
41809285 TTT
1 TTT
41809288 CCTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTATTTTT
Found at i:41809293 original size:21 final size:21
Alignment explanation
Indices: 41809232--41809302 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
41809222 TGGCCTCTCC
*
41809232 ATTTTTCTTCTTTCTCTTTTTT
1 ATTTTTCTTTTTTC-CTTTTTT
*
41809254 ATTTTTCTTTTTAT-TTTTTTT
1 ATTTTTCTTTTT-TCCTTTTTT
41809275 ATTTATT-TTTTTTCCTTTTCTT
1 ATTT-TTCTTTTTTCCTTTT-TT
*
41809297 TTTTTT
1 ATTTTT
41809303 TTGAAATAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.02
21 21 0.51
22 18 0.44
23 1 0.02
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (21 bp):
ATTTTTCTTTTTTCCTTTTTT
Found at i:41809298 original size:15 final size:15
Alignment explanation
Indices: 41809242--41809302 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
41809232 ATTTTTCTTC
*
41809242 TTTCTCTTTT-TTATT
1 TTTC-CTTTTATTTTT
*
41809257 TTTCTTTTTATTTTT
1 TTTCCTTTTATTTTT
*
41809272 TTT--ATTTATTTTT
1 TTTCCTTTTATTTTT
*
41809285 TTTCCTTTTCTTTTT
1 TTTCCTTTTATTTTT
41809300 TTT
1 TTT
41809303 TTGAAATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 12 0.32
14 4 0.11
15 22 0.58
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCCTTTTATTTTT
Found at i:41815007 original size:23 final size:23
Alignment explanation
Indices: 41814981--41815025 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41814971 TGGGTATGTG
*
41814981 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
41815004 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
41815026 ATCAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:41823182 original size:30 final size:30
Alignment explanation
Indices: 41823146--41823214 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
41823136 TCACCAGGGG
*
41823146 ACACACGGCCATGTAACATGACCATGTGTC
1 ACACACGGCCATGTAACAAGACCATGTGTC
41823176 ACACACGGCCATGTAACAAGACCATGTGTC
1 ACACACGGCCATGTAACAAGACCATGTGTC
41823206 ACACACGGC
1 ACACACGGC
41823215 TGAGACACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (30 bp):
ACACACGGCCATGTAACAAGACCATGTGTC
Found at i:41823189 original size:17 final size:17
Alignment explanation
Indices: 41823167--41823214 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
41823157 TGTAACATGA
41823167 CCATGTGTCACACACGG
1 CCATGTGTCACACACGG
* *
41823184 CCA--TGT-A-ACAAGA
1 CCATGTGTCACACACGG
41823197 CCATGTGTCACACACGG
1 CCATGTGTCACACACGG
41823214 C
1 C
41823215 TGAGACACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 8
0.66 0.11 0.23
Matches are distributed among these distances:
13 7 0.30
14 1 0.04
15 6 0.26
16 1 0.04
17 8 0.35
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (17 bp):
CCATGTGTCACACACGG
Found at i:41824139 original size:48 final size:48
Alignment explanation
Indices: 41824079--41824210 Score: 160
Period size: 48 Copynumber: 2.8 Consensus size: 48
41824069 TCAATCAATA
* *
41824079 AGTAGCTATACCATGGCCTGAAGCCAAATCAAGGTAACTTATCCCCAG-
1 AGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCAT-CCCAGT
* * * *
41824127 AGTACCTATACCATGGCTTGTAGCCAAATCAAGGTAACTCATCTCTGT
1 AGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCATCCCAGT
* *
41824175 AATACCTATACCATGG-CTCGAAGCGAAATCAAGGTA
1 AGTACCTATACCATGGCCT-GAAGCCAAATCAAGGTA
41824211 TAATTCGCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
47 4 0.06
48 68 0.94
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (48 bp):
AGTACCTATACCATGGCCTGAAGCCAAATCAAGGTAACTCATCCCAGT
Found at i:41830221 original size:26 final size:26
Alignment explanation
Indices: 41830186--41830235 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
41830176 AAGGGAAAGA
41830186 AAAAAAAGTCGACTAAGTCTTCGGAG
1 AAAAAAAGTCGACTAAGTCTTCGGAG
41830212 AAAAAAAGTCGACTAAGTCTTCGG
1 AAAAAAAGTCGACTAAGTCTTCGG
41830236 TTCCACCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (26 bp):
AAAAAAAGTCGACTAAGTCTTCGGAG
Found at i:41838442 original size:25 final size:25
Alignment explanation
Indices: 41838414--41838466 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
41838404 AAAAAAATCA
* *
41838414 TGATTAAAGAACTAGTGAATTTACC
1 TGATTAAAGAAATAGTAAATTTACC
41838439 TGATTAAAGAAATAGTAAATTTACC
1 TGATTAAAGAAATAGTAAATTTACC
41838464 TGA
1 TGA
41838467 GAGATAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (25 bp):
TGATTAAAGAAATAGTAAATTTACC
Found at i:41839048 original size:43 final size:42
Alignment explanation
Indices: 41839001--41839126 Score: 180
Period size: 43 Copynumber: 3.0 Consensus size: 42
41838991 CAGCGTCAAG
41839001 ACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAC
1 ACCAGGACCTTTAGCGGCGCTTTT-TAAAAAACGCCGCTAAAC
* * *
41839044 ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCACGAAAG
1 ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAC
* * *
41839086 ACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTAA
1 ACCAGGACCTTTAGCGGCGC-TTTTTAAAAAACGCCGCTAA
41839127 TTTGCCCAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 32 0.43
43 42 0.57
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAC
Found at i:41839486 original size:21 final size:21
Alignment explanation
Indices: 41839424--41839488 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
41839414 GTTCTGTTTT
*
41839424 GCCTCCCTCGCTGCTGCCTCT
1 GCCTCCCTCGCTGCTGCCTCC
41839445 GCCTCCCTCGCTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
*
41839466 GCCTCCCTCGCTGCTGACTCC
1 GCCTCCCTCGCTGCTGCCTCC
41839487 GC
1 GC
41839489 TCTAAGTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.02, C:0.54, G:0.20, T:0.25
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCC
Found at i:41844832 original size:15 final size:15
Alignment explanation
Indices: 41844812--41844840 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41844802 ACAATTTTGA
41844812 AATAAAACGTACCTT
1 AATAAAACGTACCTT
41844827 AATAAAACGTACCT
1 AATAAAACGTACCT
41844841 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:41846293 original size:20 final size:19
Alignment explanation
Indices: 41846264--41846325 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
41846254 ATAAGCTTAA
41846264 AAATTTAGGAATGTAATTT
1 AAATTTAGGAATGTAATTT
** *
41846283 AAATGTTAGGAA-AAACATTAA
1 AAAT-TTAGGAATGTA-ATT-T
41846304 AAATTTAGGAATGTAA-TT
1 AAATTTAGGAATGTAATTT
41846322 AAAT
1 AAAT
41846326 GTTAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 18 0.55
21 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.34
Consensus pattern (19 bp):
AAATTTAGGAATGTAATTT
Found at i:41849136 original size:15 final size:15
Alignment explanation
Indices: 41849116--41849147 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41849106 AAATAATAAT
*
41849116 TTATATATATTTATC
1 TTATATACATTTATC
41849131 TTATATACATTTATC
1 TTATATACATTTATC
41849146 TT
1 TT
41849148 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:41849297 original size:18 final size:19
Alignment explanation
Indices: 41849253--41849303 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
41849243 CCAAACTTTA
**
41849253 AACCCCAAAACCATTCAGT
1 AACCCCAAAACCAACCAGT
41849272 AACCCCAAAACCAACCA-T
1 AACCCCAAAACCAACCAGT
* *
41849290 AACTCCAAGACCAA
1 AACCCCAAAACCAA
41849304 ACTATAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.47, C:0.39, G:0.04, T:0.10
Consensus pattern (19 bp):
AACCCCAAAACCAACCAGT
Found at i:41850211 original size:41 final size:39
Alignment explanation
Indices: 41850165--41850259 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 39
41850155 GTTATATGAC
* *
41850165 TTTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCG-CACTAATGCTCT-GT
* *
41850206 TTTTAGCAGTGTTTTACCAAAAGCGCACTAATGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCACTAATGCTCTGT
*
41850245 TTTTAGCGACGTTTT
1 TTTTAGCGGCGTTTT
41850260 TTGTAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 14 0.30
40 11 0.23
41 22 0.47
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCACTAATGCTCTGT
Found at i:41850322 original size:38 final size:41
Alignment explanation
Indices: 41850231--41850330 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
41850221 ACCAAAAGCG
* * *
41850231 CACTAATGCTCTGTTTTTAGCGACGTTTTTTGTAAAAAATGC
1 CACTATTGCTCTGTTTTTAGCGACGATTTTTGT-AAAAACGC
* *
41850273 CACTGTTGCTCTGTTTTTAGCGGC-ATTTTT-T-AAAACGC
1 CACTATTGCTCTGTTTTTAGCGACGATTTTTGTAAAAACGC
41850311 CACTATTGCTCTGTATTTTA
1 CACTATTGCTCTGT-TTTTA
41850331 AAATTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 19 0.37
39 5 0.10
40 1 0.02
41 5 0.10
42 21 0.41
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (41 bp):
CACTATTGCTCTGTTTTTAGCGACGATTTTTGTAAAAACGC
Found at i:41853676 original size:39 final size:39
Alignment explanation
Indices: 41853622--41853712 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
41853612 TGCATGGTAT
* * *
41853622 TGGAAAAATATCCAGACTTGAAGTCCGCAGGCTTTA-TGC
1 TGGAAATATATCCAGACTTAAAGTCCGCAGGC-TAAGTGC
41853661 TGGAAATATATCCAGACTTAAAGTCCGCAGGCTAAGTGC
1 TGGAAATATATCCAGACTTAAAGTCCGCAGGCTAAGTGC
41853700 TGGAAATATATCC
1 TGGAAATATATCC
41853713 GGGCTAAGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
38 2 0.04
39 46 0.96
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (39 bp):
TGGAAATATATCCAGACTTAAAGTCCGCAGGCTAAGTGC
Found at i:41859455 original size:39 final size:39
Alignment explanation
Indices: 41859412--41859504 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
41859402 TGCATGGTAT
* * * *
41859412 TGGAAAAATATCCGGACTTGAAGTCCGCATGCTTTA-TGC
1 TGGAAATATATCCGGACTTAAAGTCCGCAGGC-TAAGTGC
41859451 TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
1 TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
41859490 TGGAAATATATCCGG
1 TGGAAATATATCCGG
41859505 GCTAAGTCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.04
39 47 0.96
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (39 bp):
TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
Found at i:41859529 original size:39 final size:39
Alignment explanation
Indices: 41859486--41859673 Score: 268
Period size: 39 Copynumber: 4.8 Consensus size: 39
41859476 CGCAGGCTAA
* *
41859486 GTGCTGGAAATATATCCGGGCTAAGTCCCGAAGGCATTC
1 GTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTC
*
41859525 GTGCTGGTATTATATCCGGGCTAAGTCCTGAAGGCATTC
1 GTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTC
** *
41859564 GTGCTGGTGCTATATCCGGGCTAAGTCCCAAAGGCATTC
1 GTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTC
** *
41859603 GTGCTGGCGTTATATCCGAGCTAAGTCCCGAAGGCATTC
1 GTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTC
*
41859642 GTACTGGTATTATATCCGGGCTTAAAGTCCCG
1 GTGCTGGTATTATATCCGGGC-T-AAGTCCCG
41859674 TATGCTTTGT
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 123 0.93
40 1 0.01
41 8 0.06
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (39 bp):
GTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTC
Found at i:41859541 original size:78 final size:78
Alignment explanation
Indices: 41859448--41859672 Score: 222
Period size: 78 Copynumber: 2.9 Consensus size: 78
41859438 GCATGCTTTA
* *
41859448 TGCTGGAAATATATCCGGACTTAAAGTCC-GCAGGC-TAAGTGCTGGAAATATATCCGGGCTAAG
1 TGCTGGAATTATATCCGGAC-T-AAGTCCTGAAGGCATAAGTGCTGGAAATATATCCGGGCTAAG
*
41859511 TCCCGAAGGCATTCG
64 TCCCAAAGGCATTCG
* * ** ***
41859526 TGCTGGTATTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGCTATATCCGGGCTAAGTC
1 TGCTGGAATTATATCCGGACTAAGTCCTGAAGGCATAAGTGCTGGAAATATATCCGGGCTAAGTC
41859591 CCAAAGGCATTCG
66 CCAAAGGCATTCG
** * ** * * *
41859604 TGCTGGCGTTATATCC-GAGCTAAGTCCCGAAGGCATTCGTACTGGTATTATATCCGGGCTTAAA
1 TGCTGGAATTATATCCGGA-CTAAGTCCTGAAGGCATAAGTGCTGGAAATATATCCGGGC-T-AA
41859668 GTCCC
63 GTCCC
41859673 GTATGCTTTG
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
76 6 0.05
77 7 0.06
78 104 0.83
79 1 0.01
80 7 0.06
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (78 bp):
TGCTGGAATTATATCCGGACTAAGTCCTGAAGGCATAAGTGCTGGAAATATATCCGGGCTAAGTC
CCAAAGGCATTCG
Found at i:41862662 original size:21 final size:21
Alignment explanation
Indices: 41862638--41862687 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
41862628 GCTTGCGAGC
41862638 TGCTCAAATCAAGTAATAAGG
1 TGCTCAAATCAAGTAATAAGG
41862659 TGCTCAAATCAAGTAATAAGG
1 TGCTCAAATCAAGTAATAAGG
*
41862680 TACTCAAA
1 TGCTCAAA
41862688 CATGGCTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (21 bp):
TGCTCAAATCAAGTAATAAGG
Done.