Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 79 of 292
Found at i:24222866 original size:25 final size:25
Alignment explanation
Indices: 24222834--24222881 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24222824 ATACATAAAC
* * *
24222834 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
24222859 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
24222882 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:24227944 original size:21 final size:22
Alignment explanation
Indices: 24227897--24227945 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
24227887 TCCTAGGATG
*
24227897 TAAATTGAATCCAATTGAATAT
1 TAAATTGAATCAAATTGAATAT
*
24227919 GAAATTGAAT-AAATTG-ATGAT
1 TAAATTGAATCAAATTGAAT-AT
24227940 TAAATT
1 TAAATT
24227946 CATTTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 12 0.52
22 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (22 bp):
TAAATTGAATCAAATTGAATAT
Found at i:24231576 original size:25 final size:25
Alignment explanation
Indices: 24231546--24231638 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
24231536 ATTCTGACCC
24231546 ATAGCTCGTGTGAGCAAGCCCATTT
1 ATAGCTCGTGTGAGCAAGCCCATTT
* *
24231571 ATAGCTCATGTAAGC-AGACCCATTTT
1 ATAGCTCGTGTGAGCAAG-CCCA-TTT
* *****
24231597 CACAGCTCGTGTGAGCATTTTGATTT
1 -ATAGCTCGTGTGAGCAAGCCCATTT
24231623 ATAGCTCGTGTGAGCA
1 ATAGCTCGTGTGAGCA
24231639 TACATGTTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
24 2 0.04
25 32 0.60
26 6 0.11
27 13 0.25
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (25 bp):
ATAGCTCGTGTGAGCAAGCCCATTT
Found at i:24234077 original size:29 final size:29
Alignment explanation
Indices: 24234045--24234145 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
24234035 GACGAGATTA
* * *
24234045 GCACTGAGTGTGCGAGCTTGTAATGTATG
1 GCACTAAGTGTGCGAGCTTGGAATATATG
* *
24234074 GCACTAAGTGTGCGAGTTTGGACTATATG
1 GCACTAAGTGTGCGAGCTTGGAATATATG
* *
24234103 GCACTATA-TGTGCGGGCTT-GAATCACATG
1 GCACTA-AGTGTGCGAGCTTGGAAT-ATATG
24234132 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
24234146 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.07
29 55 0.92
30 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTTGGAATATATG
Found at i:24245995 original size:42 final size:42
Alignment explanation
Indices: 24245857--24246061 Score: 229
Period size: 42 Copynumber: 4.7 Consensus size: 42
24245847 AGCATCCGAA
*
24245857 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG--CG
*** * * *
24245901 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCATCCGAG
1 --CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCG-A-ACGCG
24245950 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCG
24245992 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA--CG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCG
24246032 -TCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
24246062 GCGGGTTACA
Statistics
Matches: 139, Mismatches: 13, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
39 30 0.22
40 2 0.01
42 41 0.29
43 2 0.01
44 2 0.01
45 1 0.01
46 27 0.19
47 27 0.19
48 1 0.01
49 3 0.02
50 2 0.01
51 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (42 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCG
Found at i:24249021 original size:15 final size:15
Alignment explanation
Indices: 24248983--24249026 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
24248973 CATAGTATCG
* *
24248983 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
24248998 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
24249013 TATCTTGGATTTCT
1 TATCTTGGATTTCT
24249027 TTATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:24249048 original size:30 final size:30
Alignment explanation
Indices: 24248983--24249039 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
24248973 CATAGTATCG
*
24248983 TATCTTGGGTTTCTTTATTCTGGATTTCTC
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
24249013 TATCTTGGATTTCTTTATTC-GG-TTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
24249040 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 2 0.08
30 19 0.73
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:24257716 original size:25 final size:25
Alignment explanation
Indices: 24257688--24257735 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24257678 TTATACCATG
* * *
24257688 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
24257713 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
24257736 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:24257838 original size:20 final size:20
Alignment explanation
Indices: 24257778--24257838 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
24257768 ATAAATATGG
*
24257778 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
24257798 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
24257818 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
24257838 T
1 T
24257839 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:24257915 original size:24 final size:24
Alignment explanation
Indices: 24257888--24258030 Score: 182
Period size: 24 Copynumber: 6.0 Consensus size: 24
24257878 GAGGAAGTGA
24257888 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
24257912 AAAAGGGTTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
24257936 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
24257959 AAAAGGGCTTATGCCCTAATTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
24257983 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
24258007 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
24258031 ATGATAAAGC
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
23 21 0.20
24 73 0.70
25 11 0.10
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:24257988 original size:47 final size:47
Alignment explanation
Indices: 24257888--24258016 Score: 177
Period size: 47 Copynumber: 2.7 Consensus size: 47
24257878 GAGGAAGTGA
* *
24257888 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGTTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAATTATC
* *
24257936 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCTAATTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAATTATC
* *
24257983 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCT
24258017 AGGCCTCCAG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
47 40 0.55
48 29 0.40
49 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAATTATC
Found at i:24258004 original size:71 final size:72
Alignment explanation
Indices: 24257888--24258031 Score: 195
Period size: 71 Copynumber: 2.0 Consensus size: 72
24257878 GAGGAAGTGA
* *
24257888 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGTTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAATTATCAAAAGGGTTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
24257951 CCAGTTAT
65 CCAGTTAT
* ** *
24257959 AAAAGGGCTTATGCCCTAATTATTGAAAGGGCTTT-TGCCCCAGTTATTAAAAGAGGCTAGGCCT
1 AAAAGGGCTTATGCCCCAATTATCAAAAGGG-TTTATGCCCCAGTTATCAAAAGAGGCTAGGCCT
24258023 CCAGTTAT
65 CCAGTTAT
24258031 A
1 A
24258032 TGATAAAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 49 0.77
72 15 0.23
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAATTATCAAAAGGGTTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:24258257 original size:31 final size:31
Alignment explanation
Indices: 24258222--24258285 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
24258212 CGTTTACAGT
24258222 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
24258253 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
24258284 AA
1 AA
24258286 CATGAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:24260459 original size:49 final size:49
Alignment explanation
Indices: 24260387--24260523 Score: 211
Period size: 49 Copynumber: 2.8 Consensus size: 49
24260377 TGAGGTCACG
* *
24260387 TGTGTAGTACTAAGTGTAGGCTACTATGTGTACTGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATAATTGGTCGCA
* * * *
24260436 TGTGTAGTACTAACTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATAATTGGTCGCA
*
24260485 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATA
24260524 GCTTCGACTA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATAATTGGTCGCA
Found at i:24263534 original size:15 final size:15
Alignment explanation
Indices: 24263514--24263568 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
24263504 GTATCTTGGG
24263514 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
24263529 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
24263544 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
24263559 TTTCTTTATT
1 TTTCTTTATT
24263569 TAGTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.12
15 27 0.79
16 3 0.09
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.64
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:24266167 original size:49 final size:49
Alignment explanation
Indices: 24266036--24266172 Score: 211
Period size: 49 Copynumber: 2.8 Consensus size: 49
24266026 TGAGGTCACG
* *
24266036 TGTGTAGTACTAAGTACAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
24266085 TGTGTAGTACTAAGTGCAGGATACTACATGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
24266134 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
24266173 GCTTCGGCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 78 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:24272599 original size:41 final size:43
Alignment explanation
Indices: 24272487--24272628 Score: 110
Period size: 42 Copynumber: 3.4 Consensus size: 43
24272477 ACATATCGTA
** ** * ** *
24272487 CAATGCCAACATCCCAGACATAGTCTTACATGCCATCACATAT
1 CAATGCCAATGTCCCAGACAGCGTCTTACACGTAATCAAATAT
* * * *
24272530 C-ATGTCACTATCCCAGACAGGGTCTTACACG-AATCAAATA-
1 CAATGCCAATGTCCCAGACAGCGTCTTACACGTAATCAAATAT
* * * * *
24272570 CGATGCTAATGTCCCAGACATCGTTTTACACGTAATCACATAT
1 CAATGCCAATGTCCCAGACAGCGTCTTACACGTAATCAAATAT
24272613 CAATGCCAATGTCCCA
1 CAATGCCAATGTCCCA
24272629 AACGTGGTCT
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
40 1 0.01
41 30 0.38
42 32 0.41
43 15 0.19
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.25
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACAGCGTCTTACACGTAATCAAATAT
Found at i:24272642 original size:43 final size:41
Alignment explanation
Indices: 24272540--24272643 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 41
24272530 CATGTCACTA
* * * *
24272540 TCCCAGACAGGGTCTTACACGAATCAAATACGATGCTAATG
1 TCCCAAACATGGTCTTACACGAATCAAATACAATGCCAATG
* * * *
24272581 TCCCAGACATCGTTTTACACGTAATCACATATCAATGCCAATG
1 TCCCAAACATGGTCTTACACG-AATCAAATA-CAATGCCAATG
*
24272624 TCCCAAACGTGGTCTTACAC
1 TCCCAAACATGGTCTTACAC
24272644 AAGAACACAT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 18 0.35
42 8 0.16
43 25 0.49
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (41 bp):
TCCCAAACATGGTCTTACACGAATCAAATACAATGCCAATG
Found at i:24274586 original size:29 final size:29
Alignment explanation
Indices: 24274552--24274611 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
24274542 TTATATCCAC
*
24274552 ATGGCCCCTTAGGCCCAAATCACATTTAT
1 ATGGCCACTTAGGCCCAAATCACATTTAT
* *
24274581 ATGGCCATTTAGGCCTAAATCACATTTAT
1 ATGGCCACTTAGGCCCAAATCACATTTAT
24274610 AT
1 AT
24274612 TCATGATCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (29 bp):
ATGGCCACTTAGGCCCAAATCACATTTAT
Found at i:24274787 original size:8 final size:8
Alignment explanation
Indices: 24274776--24274819 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
24274766 CCTTTCAACT
24274776 TTTCGGCA
1 TTTCGGCA
* *
24274784 TTTCGACT
1 TTTCGGCA
24274792 TTTCGGCA
1 TTTCGGCA
* *
24274800 TTTCAGCT
1 TTTCGGCA
24274808 TTTCGGCA
1 TTTCGGCA
24274816 TTTC
1 TTTC
24274820 AACATTTTGG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.45
Consensus pattern (8 bp):
TTTCGGCA
Found at i:24274834 original size:16 final size:16
Alignment explanation
Indices: 24274768--24274827 Score: 93
Period size: 16 Copynumber: 3.7 Consensus size: 16
24274758 TCAAGAAACC
24274768 TTTCAACTTTTCGGCA
1 TTTCAACTTTTCGGCA
*
24274784 TTTCGACTTTTCGGCA
1 TTTCAACTTTTCGGCA
*
24274800 TTTCAGCTTTTCGGCA
1 TTTCAACTTTTCGGCA
24274816 TTTCAACATTTT
1 TTTCAAC-TTTT
24274828 GGGATTTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 35 0.90
17 4 0.10
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (16 bp):
TTTCAACTTTTCGGCA
Found at i:24279105 original size:29 final size:29
Alignment explanation
Indices: 24279070--24279129 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
24279060 TTATATTCAC
*
24279070 ATGGCCCATTATGCCCAAATCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAT
*
24279099 ATGGCCCTTTAGGCCCAAATCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAT
24279128 AT
1 AT
24279130 TCATGCTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (29 bp):
ATGGCCCATTAGGCCCAAATCACATTTAT
Found at i:24279367 original size:16 final size:16
Alignment explanation
Indices: 24279341--24279400 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
24279331 GTAGCCAAAC
*
24279341 TTTCAGCTTTT-GGACA
1 TTTCGGCTTTTCGG-CA
*
24279357 TTTTGGCTTTTCGGCA
1 TTTCGGCTTTTCGGCA
* *
24279373 TTTCGGCTTTTCAGAA
1 TTTCGGCTTTTCGGCA
24279389 TTTCGGCATTTT
1 TTTCGGC-TTTT
24279401 GGGATTTGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 31 0.84
17 6 0.16
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:24279469 original size:26 final size:26
Alignment explanation
Indices: 24279433--24279485 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
24279423 GTGTGCAGTG
*
24279433 TATGTACACACCTGGTAAGCAAGCGC
1 TATGTACACACCTAGTAAGCAAGCGC
24279459 TATGTACACACCTAGTAAGCAAGCGC
1 TATGTACACACCTAGTAAGCAAGCGC
24279485 T
1 T
24279486 CTACGATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (26 bp):
TATGTACACACCTAGTAAGCAAGCGC
Found at i:24281687 original size:42 final size:43
Alignment explanation
Indices: 24281581--24281737 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
24281571 TAAATACAAT
* * * *
24281581 GCCAACGTCCCAGACATGGTCTTACATGTAATCAAACATCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAATCAAACATCGAA
* * * * *
24281624 GCCACTGTCTCAGACAGGGTCTTGCACGAAATCATACA-CGAA
1 GCCAATGTCCCAGACATGGTCTTACACGAAATCAAACATCGAA
* *
24281666 GCCAATGTCCCAGACATGGTCTTACACGTAAAACAGAA-GTC-AA
1 GCCAATGTCCCAGACATGGTCTTACACG-AAATCA-AACATCGAA
* * *
24281709 TGCCAACGTCCCAAACGTGGTCTTACACG
1 -GCCAATGTCCCAGACATGGTCTTACACG
24281738 CAAAATAGAT
Statistics
Matches: 91, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 27 0.30
43 37 0.41
44 27 0.30
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACGAAATCAAACATCGAA
Found at i:24285910 original size:27 final size:26
Alignment explanation
Indices: 24285873--24285931 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
24285863 ATATATATAT
*
24285873 ATAT-TGTTCTGGTGCCCTAGGCACA
1 ATATCTGTTCTGGTGACCTAGGCACA
* * *
24285898 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGGCACA
24285925 ATATCTG
1 ATATCTG
24285932 GCAGCTCGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGGCACA
Found at i:24302209 original size:29 final size:29
Alignment explanation
Indices: 24302151--24302210 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
24302141 TGGAATTGGT
* *
24302151 TACTCGATAACTTTCGACTTTCCTCGATC
1 TACTCGATAACTTTCGACTTTCCCCAATC
24302180 TACTCGATAACTTTCGACTTTCCCCAATC
1 TACTCGATAACTTTCGACTTTCCCCAATC
24302209 TA
1 TA
24302211 ACTCTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.37
Consensus pattern (29 bp):
TACTCGATAACTTTCGACTTTCCCCAATC
Found at i:24304070 original size:9 final size:9
Alignment explanation
Indices: 24304056--24304082 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
24304046 TTTTATTATA
24304056 TACATATTT
1 TACATATTT
24304065 TACATATTT
1 TACATATTT
24304074 TACATATTT
1 TACATATTT
24304083 AACCTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
TACATATTT
Found at i:24304516 original size:19 final size:21
Alignment explanation
Indices: 24304476--24304517 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24304466 TGTTCTTTCA
24304476 TTGCATCTTCTAGCTCCCATG
1 TTGCATCTTCTAGCTCCCATG
*
24304497 TTGCCTCTTCTA-CT-CCATG
1 TTGCATCTTCTAGCTCCCATG
24304516 TT
1 TT
24304518 TATAACACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.12, C:0.33, G:0.12, T:0.43
Consensus pattern (21 bp):
TTGCATCTTCTAGCTCCCATG
Found at i:24310349 original size:40 final size:39
Alignment explanation
Indices: 24310304--24310422 Score: 193
Period size: 40 Copynumber: 3.0 Consensus size: 39
24310294 CTCTATATAT
24310304 TGTATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
1 TGTATATCC-GGTTAAATCCCGCAGGCTTAGTGCTGGTAA
*
24310344 TGTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TGTATATCC-GGTTAAATCCCGCAGGCTTAGTGCTGGTAA
*
24310384 AGTATATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTA
1 TGTATATCCGG-TTAAATCCCGCAGGCTTAGTGCTGGTA
24310423 CTATATCCGG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
39 2 0.03
40 72 0.97
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (39 bp):
TGTATATCCGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
Found at i:24310450 original size:40 final size:40
Alignment explanation
Indices: 24310305--24310463 Score: 191
Period size: 40 Copynumber: 4.0 Consensus size: 40
24310295 TCTATATATT
*
24310305 GTATATCCAGG-TTAAATCCCGCAGGCTTAGTGCTGGTAA
1 GTATATCCGGGCTTAAATCCCGCAGGCTTAGTGCTGGTAA
*
24310344 TGTATATCCGGG-TTAAATCCCGCAGGCTTCGTGCTGGTAAA
1 -GTATATCCGGGCTTAAATCCCGCAGGCTTAGTGCTGGT-AA
24310385 GTATATCC-GGCTTAAATCCCGCAGGCTTAGTGCTGGT-A
1 GTATATCCGGGCTTAAATCCCGCAGGCTTAGTGCTGGTAA
* * * * * *
24310423 CTATATCCGGGCCTAAAGTCTCACAGGCTTTGTGCTAGTAA
1 GTATATCCGGGCTTAAA-TCCCGCAGGCTTAGTGCTGGTAA
24310464 CTGGATTCAG
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
38 8 0.08
39 9 0.09
40 85 0.81
41 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (40 bp):
GTATATCCGGGCTTAAATCCCGCAGGCTTAGTGCTGGTAA
Found at i:24310450 original size:80 final size:80
Alignment explanation
Indices: 24310305--24310463 Score: 216
Period size: 80 Copynumber: 2.0 Consensus size: 80
24310295 TCTATATATT
* * *
24310305 GTATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATGTATATCCGGGTTAAATCCCGCAGG
1 GTATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATCTATATCCGGGCTAAATCCCACAGG
*
24310370 CTTCGTGCTGGTAAA
66 CTTCGTGCTAGTAAA
*
24310385 GTATATCC-GGCTTAAATCCCGCAGGCTTAGTGCTGGT-A-CTATATCCGGGCCTAAAGTCTCAC
1 GTATATCCAGG-TTAAATCCCGCAGGCTTAGTGCTGGTAATCTATATCCGGG-CTAAA-TCCCAC
*
24310447 AGGCTTTGTGCTAGTAA
63 AGGCTTCGTGCTAGTAA
24310464 CTGGATTCAG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
78 10 0.14
79 7 0.10
80 53 0.76
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (80 bp):
GTATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATCTATATCCGGGCTAAATCCCACAGG
CTTCGTGCTAGTAAA
Found at i:24331678 original size:55 final size:53
Alignment explanation
Indices: 24331593--24331760 Score: 248
Period size: 54 Copynumber: 3.1 Consensus size: 53
24331583 TTTCCTTTTT
* *
24331593 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG-TTATCCTTGCCTTATA
1 GAACTCATCAATGCCATG-CTTGACATGGTCTTACATGATT-TCCTTGCCTTATA
24331647 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCATCAATGCCATG-CTTGACATGGTCTTACATGATTTCCTTGCCTTATA
* *
24331702 GAACTTATCAATGCCATGCTTTAGCATGGTCTTACATGATTTCCTTGCCTTATA
1 GAACTCATCAATGCCATGCTTGA-CATGGTCTTACATGATTTCCTTGCCTTATA
24331756 GAACT
1 GAACT
24331761 TTTCGGGATC
Statistics
Matches: 106, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
53 4 0.04
54 52 0.49
55 48 0.45
56 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (53 bp):
GAACTCATCAATGCCATGCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
Found at i:24333628 original size:21 final size:23
Alignment explanation
Indices: 24333587--24333628 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
24333577 ATAATAAACC
*
24333587 AAATAAAATATTATGAAAAATAA
1 AAATAAAATATTATAAAAAATAA
24333610 AAATAAAAT-TT-TAAAAAAT
1 AAATAAAATATTATAAAAAAT
24333629 TAGAACATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATAAAATATTATAAAAAATAA
Found at i:24335899 original size:40 final size:40
Alignment explanation
Indices: 24335855--24336036 Score: 244
Period size: 39 Copynumber: 4.6 Consensus size: 40
24335845 GTTCAAAACA
* * ** * *
24335855 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATTG
* *
24335895 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATTG
* *
24335935 CCTTCGGG-CTTAGCCCGGGTATCATAGCTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATTG
*
24335974 CCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATTG
24336013 CCTTC-GGACTTAGCCCGGATATCA
1 CCTTCGGGACTTAGCCCGGATATCA
24336037 CTTGAACATT
Statistics
Matches: 128, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 2 0.02
39 86 0.67
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:24337905 original size:15 final size:15
Alignment explanation
Indices: 24337882--24337919 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
24337872 TTATATATAC
*
24337882 ATAATATTA-TTTCAA
1 ATAAAATTAGTTTC-A
24337897 ATAAAATTAGTTTCA
1 ATAAAATTAGTTTCA
24337912 ATAAAATT
1 ATAAAATT
24337920 TAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAAATTAGTTTCA
Found at i:24338151 original size:17 final size:17
Alignment explanation
Indices: 24338129--24338183 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
24338119 AAATACACTC
24338129 TCTCTTTGATCTCCTAT
1 TCTCTTTGATCTCCTAT
24338146 TCTCTTTGATCTCCTAT
1 TCTCTTTGATCTCCTAT
* *
24338163 TCTCTTTGTTCT-TTAT
1 TCTCTTTGATCTCCTAT
24338179 TCTCT
1 TCTCT
24338184 GTCTTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 8 0.22
17 28 0.78
ACGTcount: A:0.09, C:0.27, G:0.05, T:0.58
Consensus pattern (17 bp):
TCTCTTTGATCTCCTAT
Found at i:24342517 original size:47 final size:47
Alignment explanation
Indices: 24342398--24342553 Score: 231
Period size: 47 Copynumber: 3.3 Consensus size: 47
24342388 TACATGATAG
24342398 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
24342447 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
* * * * * *
24342494 TATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
24342541 TAAATGTGATAAG
1 TATATGTGATAAG
24342554 TCCCGAAGGG
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 54 0.55
49 45 0.45
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:24345996 original size:31 final size:31
Alignment explanation
Indices: 24345958--24346036 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
24345948 TTTAACGGTT
24345958 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
24345989 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
24346020 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
24346037 ACTGTAAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:24346107 original size:42 final size:42
Alignment explanation
Indices: 24346060--24346151 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
24346050 TGGCCCTTAG
* ** *
24346060 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
24346102 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
24346144 GCCCATTT
1 GCCCATTT
24346152 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:24346367 original size:26 final size:26
Alignment explanation
Indices: 24346296--24346444 Score: 248
Period size: 26 Copynumber: 5.8 Consensus size: 26
24346286 CCTCTTTAAT
* *
24346296 AACTGGGGCA-AATCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCAATA
24346321 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
24346346 AACTGGGGCATAAGCCCTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
24346372 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
24346398 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
24346424 AACTGGGGCATAAGCCTTTTT
1 AACTGGGGCATAAGCCCTTTT
24346445 GCACTTCCTC
Statistics
Matches: 118, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 33 0.28
26 85 0.72
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:24347307 original size:27 final size:27
Alignment explanation
Indices: 24347246--24347309 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
24347236 GGCATATTCA
24347246 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
24347273 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
24347300 TCTTTTTACC
1 TCATTTTACC
24347310 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:24347393 original size:27 final size:27
Alignment explanation
Indices: 24347363--24347470 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
24347353 GTAAATCTAC
24347363 AAACGAAGGGTATTTTAGTAATTTTGT
1 AAACGAAGGGTATTTTAGTAATTTTGT
* *
24347390 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACGAAGGGTATTT-TAGTAATTTTGT
* *
24347416 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 A-AACG--AAGGGTATTTTAGTAATTTTGT
** * *
24347446 AAATTAGGGGTATTTTGGTAATTTT
1 AAACGAAGGGTATTTTAGTAATTTT
24347471 ACAAATTGAG
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.03
27 40 0.62
28 3 0.05
29 18 0.28
30 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.44
Consensus pattern (27 bp):
AAACGAAGGGTATTTTAGTAATTTTGT
Found at i:24347544 original size:26 final size:26
Alignment explanation
Indices: 24347425--24347548 Score: 149
Period size: 27 Copynumber: 4.7 Consensus size: 26
24347415 TAGAAAGTCA
* ** *
24347425 AGGGTATTTTTGTAATTTTGTAAATT
1 AGGGTATTTTGGTAATTTTACAAACT
*
24347451 AGGGGTATTTTGGTAATTTTACAAATT
1 A-GGGTATTTTGGTAATTTTACAAACT
* * *
24347478 GAGGGTATTTCGGTAATTTCACAAACC
1 -AGGGTATTTTGGTAATTTTACAAACT
24347505 AGTGGTATTTTGGTAATTTTACAAACT
1 AG-GGTATTTTGGTAATTTTACAAACT
24347532 AGGGTATTTTGGTAATT
1 AGGGTATTTTGGTAATT
24347549 CTACCCTATA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.21
27 66 0.78
28 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACT
Found at i:24347564 original size:80 final size:81
Alignment explanation
Indices: 24347427--24347581 Score: 206
Period size: 80 Copynumber: 1.9 Consensus size: 81
24347417 GAAAGTCAAG
* ** * * * *
24347427 GGTATTTTTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGT
24347492 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
**
24347508 GGTATTTTGGTAATTTTACAAACTA-GGGTATTTTGGTAATTCTACCCTATAG-GGGTATTTCAG
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTA-CAAATAGAGGGTATTTCAG
24347571 TAATTTCACAA
65 TAATTTCACAA
24347582 TTGAGGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
80 39 0.61
81 25 0.39
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:24347588 original size:27 final size:26
Alignment explanation
Indices: 24347447--24347588 Score: 101
Period size: 27 Copynumber: 5.3 Consensus size: 26
24347437 TAATTTTGTA
*
24347447 AATTAGGGGTATTTTGGTAATTTTAC
1 AATTAGGGGTATTTTGGTAATTTCAC
*
24347473 AAATT-GAGGGTATTTCGGTAATTTCAC
1 -AATTAG-GGGTATTTTGGTAATTTCAC
** * *
24347500 AAACCAGTGGTATTTTGGTAATTTTAC
1 -AATTAGGGGTATTTTGGTAATTTCAC
*
24347527 AAACTA-GGGTATTTTGGTAA-TTCTAC
1 -AATTAGGGGTATTTTGGTAATTTC-AC
** **
24347553 CCTATAGGGGTATTTCAGTAATTTCAC
1 AAT-TAGGGGTATTTTGGTAATTTCAC
24347580 AATTGAGGG
1 AATT-AGGG
24347589 TAAAACGATA
Statistics
Matches: 91, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.02
26 19 0.21
27 66 0.73
28 4 0.04
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (26 bp):
AATTAGGGGTATTTTGGTAATTTCAC
Found at i:24347614 original size:27 final size:27
Alignment explanation
Indices: 24347584--24347667 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
24347574 TTTCACAATT
*
24347584 GAGGGTAAAAC-GATAATTTTGTAAATC
1 GAGGGTAAAACAG-TAATTCTGTAAATC
24347611 GAGGGTAAAACAGTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* * * *
24347638 AAAGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
24347665 GAG
1 GAG
24347668 CGTACTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTGTAAATC
Found at i:24352935 original size:700 final size:700
Alignment explanation
Indices: 24351596--24352990 Score: 2493
Period size: 700 Copynumber: 2.0 Consensus size: 700
24351586 ATTTTACAGT
*
24351596 TTTAGTAGAGAAGGCAAAGATCATTGAGGATGTGAAACGCGCTGAGAGCCAGAATCGTGAGAAGG
1 TTTAGTAGAGAAGGCAAAGATCATTGAGGATGTGAAACGCGCTGAAAGCCAGAATCGTGAGAAGG
24351661 ATAAGGGGAGAAACAAGAGGGTTTGGAAGCCCTCAAGTTCAGCTATGGGGTCTAAGAAAAAGGCC
66 ATAAGGGGAGAAACAAGAGGGTTTGGAAGCCCTCAAGTTCAGCTATGGGGTCTAAGAAAAAGGCC
*
24351726 AGAGTTGATGGGCCAGCTAGAGTTGGGGCATTTGTTGCCACATTTGGGTTACAATCTTGTACTAT
131 AGAGTTGATGGGCCAGCTAGAGTTGGGGCACTTGTTGCCACATTTGGGTTACAATCTTGTACTAT
* *
24351791 TTGTGGTTAGCGCCATCAGGGCGAGTGTTGGGTATAGATAGGGTATGTTTTAGGTGTGGATCTAT
196 TTATGGTTAGCGCCATCAGGGCGAGTGCTGGGTATAGATAGGGTATGTTTTAGGTGTGGATCTAT
*
24351856 GGAGCACCGTATTAGGGATTGTTCACAGAGGCCAGATCAGATGCCAATTTCTGGTAGAGGTACTG
261 GGAGCACCGTATTAGGGATTGTCCACAGAGGCCAGATCAGATGCCAATTTCTGGTAGAGGTACTG
24351921 TTCAGCCGCAGAGAGCTTTTCAGCCAGAGGTGGAAATGGTATGGGTTGTGGTCGTGGGGTATCGG
326 TTCAGCCGCAGAGAGCTTTTCAGCCAGAGGTGGAAATGGTATGGGTTGTGGTCGTGGGGTATCGG
* * *
24351986 GCAGAGGTCCTGGTCATACTGAGGCTAGGCAACTGGCATTGGTTTATGTTGCACATAGCCGAGAG
391 GCAGAGGTCCTGGTCATACTGAGGCTAGGCAACTAGCACTGGTTTATGCTGCACATAGCCGAGAG
* *
24352051 GACTGAGACACCCCAGATGTTATTATGGGTATGTTATTTATCCACTATGTACCTTACACTGCATT
456 GACTGAGACACCCCAGATGTTATTATAGGTACGTTATTTATCCACTATGTACCTTACACTGCATT
* *
24352116 TATTGATGTTGGTTCTACGTACTCTTATATAACATGCACTGTGTCTGAGACTTTGGGTGTGGTAT
521 GATTGATGTTGGTTCTACGTACTCTTATATAACATGCACTGTGTCTGAGACTTTAGGTGTGGTAT
* *
24352181 GTGAAAACACAACGAGTGAGATTACTGTGTTAAGTCCATTAGGGCAGTCAATACGAGTGAACAAA
586 GTGAAAACACAACGAGTAAGATTACTATGTTAAGTCCATTAGGGCAGTCAATACGAGTGAACAAA
*
24352246 TTGTTTAAAGATGTACCCTTAGAGGTTCAAGGAAAAATCTCTTTAGCTGA
651 TTGTTTAAAGATGTACCCTCAGAGGTTCAAGGAAAAATCTCTTTAGCTGA
*
24352296 TTTAGTAGAGAAGGCAAAGATCGTTGAGGATGTGAAACGCGCTGAAAGCCAGAATCGTGAGAAGG
1 TTTAGTAGAGAAGGCAAAGATCATTGAGGATGTGAAACGCGCTGAAAGCCAGAATCGTGAGAAGG
*
24352361 ATAAGGGGAGAAACAAGAGGGTTTGGGAGCCCTCAAGTTCAGCTATGGGGTCTAAGAAAAAGGCC
66 ATAAGGGGAGAAACAAGAGGGTTTGGAAGCCCTCAAGTTCAGCTATGGGGTCTAAGAAAAAGGCC
*
24352426 AGAGTTGATGGGCCAGCTAGAGTTGGGGCACTTGTTGCCACATTTGGGTTACATTCTTGTACTAT
131 AGAGTTGATGGGCCAGCTAGAGTTGGGGCACTTGTTGCCACATTTGGGTTACAATCTTGTACTAT
* *
24352491 TTATGGTTAGTGCCATCAGGGCGAGTGCTGGGTATAGATGGGGTATGTTTTAGGTGTGGATCTAT
196 TTATGGTTAGCGCCATCAGGGCGAGTGCTGGGTATAGATAGGGTATGTTTTAGGTGTGGATCTAT
*
24352556 GGAGCACCGTATTAGGGATTGTCCACAGAGGCCGGATCAGATGCCAATTTCTGGTAGAGGTACTG
261 GGAGCACCGTATTAGGGATTGTCCACAGAGGCCAGATCAGATGCCAATTTCTGGTAGAGGTACTG
24352621 TTCAGCCGCAGAGAGCTTTTCAGCCAGAGGTGGAAATGGTATGGGTTGTGGTCGTGGGGTATCGG
326 TTCAGCCGCAGAGAGCTTTTCAGCCAGAGGTGGAAATGGTATGGGTTGTGGTCGTGGGGTATCGG
* * * *
24352686 GCAGAGGTCTTGGTCATACTGAGGCTAGGCAGCTAGCACTGGTTTATGCTGCACATAGCTGAGGG
391 GCAGAGGTCCTGGTCATACTGAGGCTAGGCAACTAGCACTGGTTTATGCTGCACATAGCCGAGAG
* *
24352751 GACTGAGACGCCCCAGATGTTATTATAGGTACGTTCTTTATCCACTATGTACCTTACACTGCATT
456 GACTGAGACACCCCAGATGTTATTATAGGTACGTTATTTATCCACTATGTACCTTACACTGCATT
* *
24352816 GATTGATGTTGGTTCTACGTACTCTTATATAGCATGCACTGTGTCTGAGACTTTAGGTGTGGTTT
521 GATTGATGTTGGTTCTACGTACTCTTATATAACATGCACTGTGTCTGAGACTTTAGGTGTGGTAT
* * *
24352881 GTGAAAACACAATGAGTAAGGTTACTATGTTAAGTCCATTAGGGTAGTCAATACGAGTGAACAAA
586 GTGAAAACACAACGAGTAAGATTACTATGTTAAGTCCATTAGGGCAGTCAATACGAGTGAACAAA
*
24352946 TTGTTTAAAGATGTACCCTCAGAGGTTCAAGGAAAAATCTTTTTA
651 TTGTTTAAAGATGTACCCTCAGAGGTTCAAGGAAAAATCTCTTTA
24352991 ATTGACTTGA
Statistics
Matches: 662, Mismatches: 33, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
700 662 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (700 bp):
TTTAGTAGAGAAGGCAAAGATCATTGAGGATGTGAAACGCGCTGAAAGCCAGAATCGTGAGAAGG
ATAAGGGGAGAAACAAGAGGGTTTGGAAGCCCTCAAGTTCAGCTATGGGGTCTAAGAAAAAGGCC
AGAGTTGATGGGCCAGCTAGAGTTGGGGCACTTGTTGCCACATTTGGGTTACAATCTTGTACTAT
TTATGGTTAGCGCCATCAGGGCGAGTGCTGGGTATAGATAGGGTATGTTTTAGGTGTGGATCTAT
GGAGCACCGTATTAGGGATTGTCCACAGAGGCCAGATCAGATGCCAATTTCTGGTAGAGGTACTG
TTCAGCCGCAGAGAGCTTTTCAGCCAGAGGTGGAAATGGTATGGGTTGTGGTCGTGGGGTATCGG
GCAGAGGTCCTGGTCATACTGAGGCTAGGCAACTAGCACTGGTTTATGCTGCACATAGCCGAGAG
GACTGAGACACCCCAGATGTTATTATAGGTACGTTATTTATCCACTATGTACCTTACACTGCATT
GATTGATGTTGGTTCTACGTACTCTTATATAACATGCACTGTGTCTGAGACTTTAGGTGTGGTAT
GTGAAAACACAACGAGTAAGATTACTATGTTAAGTCCATTAGGGCAGTCAATACGAGTGAACAAA
TTGTTTAAAGATGTACCCTCAGAGGTTCAAGGAAAAATCTCTTTAGCTGA
Found at i:24359901 original size:32 final size:32
Alignment explanation
Indices: 24359858--24359920 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
24359848 CACTGGAATG
* *
24359858 GAATAAGGCTGTAATAAAATAGAGTTGTAATA
1 GAATAAAGCTGTAATAAAATAGAGCTGTAATA
* **
24359890 GAATAAAGCTGTAGTGGAATAGAGCTGTAAT
1 GAATAAAGCTGTAATAAAATAGAGCTGTAAT
24359921 GAGTAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (32 bp):
GAATAAAGCTGTAATAAAATAGAGCTGTAATA
Found at i:24359902 original size:16 final size:16
Alignment explanation
Indices: 24359858--24359920 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
24359848 CACTGGAATG
*
24359858 GAATAAGGCTGTAATA
1 GAATAAAGCTGTAATA
* * *
24359874 AAATAGAGTTGTAATA
1 GAATAAAGCTGTAATA
* *
24359890 GAATAAAGCTGTAGTG
1 GAATAAAGCTGTAATA
*
24359906 GAATAGAGCTGTAAT
1 GAATAAAGCTGTAAT
24359921 GAGTAATTCA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (16 bp):
GAATAAAGCTGTAATA
Found at i:24360156 original size:26 final size:26
Alignment explanation
Indices: 24360127--24360178 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
24360117 AATAAATAAT
* *
24360127 TTAACCATATTTTAATATA-ATTATTA
1 TTAAACATACTTTAATA-ACATTATTA
*
24360153 TTAAATATACTTTAATAACATTATTA
1 TTAAACATACTTTAATAACATTATTA
24360179 ATATAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAAACATACTTTAATAACATTATTA
Found at i:24368331 original size:56 final size:55
Alignment explanation
Indices: 24368261--24368387 Score: 182
Period size: 56 Copynumber: 2.3 Consensus size: 55
24368251 ACCTGGAAGC
24368261 ATATGTGATCCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
1 ATATGTGAT-CCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
* * * * *
24368317 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTTATGCGTTGGCATTG
1 ATATGTGA-TCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
24368373 ATATGTGATTCCGAT
1 ATATGTGA-TCCGAT
24368388 GTGTTTACGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 63 0.98
57 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (55 bp):
ATATGTGATCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
Found at i:24371688 original size:29 final size:29
Alignment explanation
Indices: 24371655--24371786 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
24371645 GTGACGAGAT
*
24371655 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
24371684 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
24371713 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
24371742 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
24371771 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24371787 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:24378927 original size:29 final size:29
Alignment explanation
Indices: 24378894--24379025 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
24378884 GTGACGAGAT
*
24378894 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
24378923 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
24378952 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
24378981 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
24379010 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24379026 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:24386646 original size:29 final size:29
Alignment explanation
Indices: 24386613--24386744 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
24386603 GTGACGAGAT
*
24386613 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
24386642 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
24386671 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
24386700 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
24386729 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24386745 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:24393105 original size:56 final size:55
Alignment explanation
Indices: 24393035--24393161 Score: 182
Period size: 56 Copynumber: 2.3 Consensus size: 55
24393025 ACCTGGAAGC
24393035 ATATGTGATCCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
1 ATATGTGAT-CCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
* * * * *
24393091 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACATTTTATGCGTTGGCATTG
1 ATATGTGA-TCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
24393147 ATATGTGATTCCGAT
1 ATATGTGA-TCCGAT
24393162 GTGTTTACGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 63 0.98
57 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (55 bp):
ATATGTGATCCGATATATATGTGCAAGTAAGACCACATTTTATACGTTGCCATCG
Found at i:24404890 original size:25 final size:25
Alignment explanation
Indices: 24404842--24404890 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
24404832 AAATTGAAGA
*
24404842 TATTGTAGATAGTATATTCTGAAAC
1 TATTGTAGATAGTATATGCTGAAAC
*
24404867 TATTGTAGGTAGTATACTGC-GAAA
1 TATTGTAGATAGTATA-TGCTGAAA
24404891 ACACTCTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (25 bp):
TATTGTAGATAGTATATGCTGAAAC
Found at i:24416704 original size:28 final size:27
Alignment explanation
Indices: 24416672--24416761 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 27
24416662 CACATACCTA
24416672 TATATGGCCCACTAGGCCCAATCACATT
1 TATATGGCCCA-TAGGCCCAATCACATT
* * *
24416700 TATATAGACCATTATGCCCAAATCACATT
1 TATATGGCCCA-TAGGCCC-AATCACATT
24416729 TATATGGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCAT-AGGCCCAA-TCACATT
24416758 TATA
1 TATA
24416762 GTCATGCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 18 0.35
29 34 0.65
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (27 bp):
TATATGGCCCATAGGCCCAATCACATT
Found at i:24429768 original size:27 final size:27
Alignment explanation
Indices: 24429730--24429798 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
24429720 AAACTTGTAC
24429730 AGCACTAAGTGTGCGAGTTTGATCA-AT
1 AGCACTAAGTGTGCGAG-TTGATCATAT
*
24429757 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATCATAT
24429784 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
24429799 GACTCACTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATCATAT
Found at i:24429809 original size:27 final size:27
Alignment explanation
Indices: 24429730--24429810 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
24429720 AAACTTGTAC
* *
24429730 AGCACTAAGTGTGCGAGTTTGA-TCA-AT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
24429757 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
24429784 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
24429811 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:24437181 original size:32 final size:29
Alignment explanation
Indices: 24437084--24437187 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
24437074 GATTGAATCA
* * * *
24437084 AAATTAATATTTCATATATACATTTAAATC
1 AAATTAAAATTT-ATATATAAAATTATATC
*
24437114 ACAATCAAAATTTTATATATAAAATTATATC
1 A-AATTAAAA-TTTATATATAAAATTATATC
*
24437145 AAATTAAAATTTATATATCAAAATTATATATT
1 AAATTAAAATTTATATAT-AAAA-T-TATATC
24437177 AAATTAAAATT
1 AAATTAAAATT
24437188 AATGTACAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
29 9 0.15
30 12 0.19
31 22 0.35
32 19 0.31
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTAAAATTTATATATAAAATTATATC
Found at i:24437954 original size:15 final size:15
Alignment explanation
Indices: 24437934--24437965 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24437924 TTGATTTAGC
*
24437934 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTACTT
24437949 TTTCTTTTTTTACTT
1 TTTCTTTTTTTACTT
24437964 TT
1 TT
24437966 ATTTGCTTAA
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:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTTACTT
Found at i:24443511 original size:18 final size:18
Alignment explanation
Indices: 24443483--24443523 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
24443473 TAATTAAAAT
24443483 GTTAA-TTTTTAAATGTG
1 GTTAATTTTTTAAATGTG
24443500 GTTAATTTTTTAAATGTG
1 GTTAATTTTTTAAATGTG
24443518 G-TAATT
1 GTTAATT
24443524 ACATGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (18 bp):
GTTAATTTTTTAAATGTG
Found at i:24443578 original size:12 final size:12
Alignment explanation
Indices: 24443549--24443583 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
24443539 TATACTTCGT
*
24443549 AATATTTTTTTA
1 AATATTTTTATA
24443561 AA-ATTTTTATA
1 AATATTTTTATA
24443572 AATATTTTTATA
1 AATATTTTTATA
24443584 TTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATATTTTTATA
Found at i:24443711 original size:121 final size:122
Alignment explanation
Indices: 24443563--24443783 Score: 390
Period size: 121 Copynumber: 1.8 Consensus size: 122
24443553 TTTTTTTAAA
24443563 ATTTTTATAAATATTTTTATATTTTTTAATTTATTTTTTAGTGTGACATATAATATAAATAATAC
1 ATTTTTATAAATATTTTTATATTTTTTAATTTATTTTTTAGTGTGACATATAATATAAATAATAC
*
24443628 CATATCAGCATAAATTGTATATGGAATGTTGCATATAATACAAGTATACTTTGTGAT
66 CATATCAGCATAAATTGTACATGGAATGTTGCATATAATACAAGTATACTTTGTGAT
* * *
24443685 ATTTTTTTAAA-ATTTTTATATTTTTTAATTTATTTTTTGGTGTGACATATAATATAAATAATAT
1 ATTTTTATAAATATTTTTATATTTTTTAATTTATTTTTTAGTGTGACATATAATATAAATAATAC
*
24443749 CATATCAGTATAAATTGTACATGGAATGTTGCATA
66 CATATCAGCATAAATTGTACATGGAATGTTGCATA
24443784 AGTTGTGGGC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 84 0.89
122 10 0.11
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (122 bp):
ATTTTTATAAATATTTTTATATTTTTTAATTTATTTTTTAGTGTGACATATAATATAAATAATAC
CATATCAGCATAAATTGTACATGGAATGTTGCATATAATACAAGTATACTTTGTGAT
Found at i:24445591 original size:19 final size:20
Alignment explanation
Indices: 24445550--24445599 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
24445540 TTTTAATATT
* *
24445550 ATATTAATATATTATTTAAA
1 ATATAAATATATTATATAAA
24445570 ATATAAATA-ATTATATACAA
1 ATATAAATATATTATATA-AA
24445590 TATATAAATA
1 -ATATAAATA
24445600 ATTCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 10 0.38
21 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAAATATATTATATAAA
Found at i:24445596 original size:21 final size:20
Alignment explanation
Indices: 24445549--24445602 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
24445539 TTTTTAATAT
* *
24445549 TATATTAATATATTATTTAAA
1 TATATAAATA-ATTATATAAA
24445570 -ATATAAATAATTATATACAA
1 TATATAAATAATTATATA-AA
24445590 TATATAAATAATT
1 TATATAAATAATT
24445603 CAAAAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 10 0.34
21 12 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAAATAATTATATAAA
Found at i:24448112 original size:39 final size:39
Alignment explanation
Indices: 24448068--24448145 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
24448058 AATTAATCTT
*
24448068 TATTACTTAGTATATAAGGAAATTGAAAGTGGATGGAGA
1 TATTACTTAATATATAAGGAAATTGAAAGTGGATGGAGA
24448107 TATTACTTAATATATAAGGAAATTGAAAGTGGATGGAGA
1 TATTACTTAATATATAAGGAAATTGAAAGTGGATGGAGA
24448146 GATAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (39 bp):
TATTACTTAATATATAAGGAAATTGAAAGTGGATGGAGA
Found at i:24449577 original size:10 final size:10
Alignment explanation
Indices: 24449550--24449580 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
24449540 GGGTTAGGTG
*
24449550 ATATATATAT
1 ATATATAAAT
24449560 ATATATAAAT
1 ATATATAAAT
24449570 ATATATAAAT
1 ATATATAAAT
24449580 A
1 A
24449581 GATGTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATAAAT
Found at i:24450606 original size:35 final size:35
Alignment explanation
Indices: 24450550--24450629 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
24450540 ATAAATGTTT
* *
24450550 TACTGGCTCAACGAAGTGACACCATGGAAATCATC
1 TACTGGCTCAACGAAGCGACACCATGAAAATCATC
* * * **
24450585 TACTGGCTCTATGAAGCGACACTATGAAAATGGTC
1 TACTGGCTCAACGAAGCGACACCATGAAAATCATC
*
24450620 TACTGACTCA
1 TACTGGCTCA
24450630 GTAGAGTCGA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (35 bp):
TACTGGCTCAACGAAGCGACACCATGAAAATCATC
Found at i:24451074 original size:28 final size:28
Alignment explanation
Indices: 24451034--24451108 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
24451024 GAAAAGGGAA
*
24451034 GTCCACTAAGGACTATCTTAGGTGAAAT
1 GTCCACTAAGGACTATCTTAGATGAAAT
* * *
24451062 GTCCACCAAGGACTATCTTATATGGAAT
1 GTCCACTAAGGACTATCTTAGATGAAAT
24451090 GTCCACTAAGGACTATCTT
1 GTCCACTAAGGACTATCTT
24451109 GACAACTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (28 bp):
GTCCACTAAGGACTATCTTAGATGAAAT
Found at i:24451133 original size:30 final size:27
Alignment explanation
Indices: 24451030--24451135 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 27
24451020 GCTAGAAAAG
**
24451030 GGAA-GTCCACTAAGGACTATCTTAGGT
1 GGAATGTCCAC-AAGGACTATCTTAAAT
* *
24451057 GAAATGTCCACCAAGGACTATCTTATAT
1 GGAATGTCCA-CAAGGACTATCTTAAAT
24451085 GGAATGTCCACTAAGGACTATCTTGACAACT
1 GGAATGTCCAC-AAGGACTATCTT-A-AA-T
* *
24451116 GGAATGTTCTCAAGGACTAT
1 GGAATGTCCACAAGGACTAT
24451136 TTGTTTTGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.06
28 40 0.61
29 2 0.03
30 10 0.15
31 10 0.15
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (27 bp):
GGAATGTCCACAAGGACTATCTTAAAT
Found at i:24456582 original size:40 final size:40
Alignment explanation
Indices: 24456527--24456736 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
24456517 AACATTGGAA
24456527 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
24456567 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
24456607 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
24456647 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
24456686 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
24456727 CTATATCCGG
1 ATATATCCGG
24456737 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:24464718 original size:40 final size:40
Alignment explanation
Indices: 24464663--24464872 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
24464653 AACATTGGAA
24464663 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
24464703 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
24464743 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
24464783 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
24464822 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
24464863 CTATATCCGG
1 ATATATCCGG
24464873 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:24476262 original size:168 final size:168
Alignment explanation
Indices: 24475983--24476285 Score: 464
Period size: 168 Copynumber: 1.8 Consensus size: 168
24475973 ATATTTATAA
* * *
24475983 AAAATTTAATATTTAATTAAATTGTAAAATATGTTTATTTTCCTTTGATTTTGACACATAAATTA
1 AAAATTTAATATTTAATTAAATTATAAAATATATTTATTTTCCTTTGATTGTGACACATAAATTA
*
24476048 AGAATAAATAAATAAATTTATATATTATAAAATAAATTACCAATATATTGATATTATC-TTATAT
66 AGAATAAATAAATAAATTTATACATTATAAAATAAATTACCAATATATTGATATTATCTTTATAT
24476112 ATATAATATTAATATCACACATTTAATTTTTATTAATT
131 ATATAATATTAATATCACACATTTAATTTTTATTAATT
* * * * *
24476150 AAAATTTGATGTTTAATTTAATTATAAAATATATTTATTTTTCTTTGAGTTGTGACATATAAATT
1 AAAATTTAATATTTAATTAAATTATAAAATATATTTATTTTCCTTTGA-TTGTGACACATAAATT
* * * * *
24476215 AAGAATAAATAAGTAAATTTATACATTATAGATTAGATTATCAATATATTGATATTATCTTTATA
65 AAGAATAAATAAATAAATTTATACATTATAAAATAAATTACCAATATATTGATATTATCTTTATA
24476280 TATATA
130 TATATA
24476286 CACATTTTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
167 42 0.35
168 67 0.56
169 11 0.09
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (168 bp):
AAAATTTAATATTTAATTAAATTATAAAATATATTTATTTTCCTTTGATTGTGACACATAAATTA
AGAATAAATAAATAAATTTATACATTATAAAATAAATTACCAATATATTGATATTATCTTTATAT
ATATAATATTAATATCACACATTTAATTTTTATTAATT
Found at i:24476556 original size:15 final size:15
Alignment explanation
Indices: 24476529--24476569 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
24476519 ATAATGTCAC
24476529 ATTAATATAATA-TTA
1 ATTAAT-TAATATTTA
24476544 TATTAATTAATATTTA
1 -ATTAATTAATATTTA
24476560 ATTAA-TAATA
1 ATTAATTAATA
24476570 CTTTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAATTAATATTTA
Found at i:24476578 original size:15 final size:14
Alignment explanation
Indices: 24476535--24476578 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
24476525 TCACATTAAT
*
24476535 ATAATATTATATTA
1 ATAATATTTTATTA
*
24476549 ATTAATATTTAATTA
1 A-TAATATTTTATTA
24476564 ATAATACTTTTATTA
1 ATAATA-TTTTATTA
24476579 TTATCACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATATTTTATTA
Found at i:24476954 original size:2 final size:2
Alignment explanation
Indices: 24476947--24476989 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
24476937 TTTTAAAGTT
24476947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24476989 T
1 T
24476990 GGCATAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24477807 original size:42 final size:42
Alignment explanation
Indices: 24477731--24477810 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
24477721 AACTATGGGG
* *
24477731 ACTTCTACCTATACATCCTGTGCGATATATCGATACAATTCC
1 ACTTCTACCTATACATCCTGTGAGATATACCGATACAATTCC
* * *
24477773 ACTTCTACCTATACATCTTGTGAGTTGTACCGATACAA
1 ACTTCTACCTATACATCCTGTGAGATATACCGATACAA
24477811 GTCTATATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (42 bp):
ACTTCTACCTATACATCCTGTGAGATATACCGATACAATTCC
Found at i:24478223 original size:16 final size:16
Alignment explanation
Indices: 24478202--24478236 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
24478192 GTCATAGCCT
24478202 TTGTAAAAGATAAAAA
1 TTGTAAAAGATAAAAA
* *
24478218 TTGTAAATGATAAACA
1 TTGTAAAAGATAAAAA
24478234 TTG
1 TTG
24478237 CAAACGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.31
Consensus pattern (16 bp):
TTGTAAAAGATAAAAA
Found at i:24480421 original size:34 final size:34
Alignment explanation
Indices: 24480383--24480451 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
24480373 ACATTAATTG
24480383 AATACACAGCCTATA-CTCAAACATGCTATTTGTC
1 AATACACAGCCTATATC-CAAACATGCTATTTGTC
* *
24480417 AATACATAGCTTATATCCAAACATGCTATTTGTC
1 AATACACAGCCTATATCCAAACATGCTATTTGTC
24480451 A
1 A
24480452 CAAGTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (34 bp):
AATACACAGCCTATATCCAAACATGCTATTTGTC
Found at i:24480741 original size:28 final size:29
Alignment explanation
Indices: 24480665--24480742 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
24480655 AAAAGAAGTT
24480665 TAAAATTAAAAACTA-AAT-TAAAATTAAAA
1 TAAAA-TAAAAAC-ACAATGTAAAATTAAAA
* * * *
24480694 TAAAGTAAAAAGAGATTGTAAAA-TAAAA
1 TAAAATAAAAACACAATGTAAAATTAAAA
*
24480722 TAAAATAAAACCACAATGTAA
1 TAAAATAAAAACACAATGTAA
24480743 CAAAGCTCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.03
28 29 0.74
29 9 0.23
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.23
Consensus pattern (29 bp):
TAAAATAAAAACACAATGTAAAATTAAAA
Found at i:24481634 original size:21 final size:20
Alignment explanation
Indices: 24481610--24481648 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24481600 GAATATTTTG
24481610 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATA-ATTATGA
*
24481631 ATGTTTGATGATAATTAT
1 ATGTTTAATGATAATTAT
24481649 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAATTATGA
Found at i:24485259 original size:38 final size:38
Alignment explanation
Indices: 24485217--24485293 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
24485207 GCCTAAAGTT
24485217 AGCTGAGAAAGATAAGATTTAGAATGCAAGACCGAGTA
1 AGCTGAGAAAGATAAGATTTAGAATGCAAGACCGAGTA
24485255 AGCTGAGAAAGATAAGATTTAGAATGCAAGACCGAGTA
1 AGCTGAGAAAGATAAGATTTAGAATGCAAGACCGAGTA
24485293 A
1 A
24485294 TATAGCTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.18
Consensus pattern (38 bp):
AGCTGAGAAAGATAAGATTTAGAATGCAAGACCGAGTA
Found at i:24493188 original size:18 final size:20
Alignment explanation
Indices: 24493154--24493191 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
24493144 AAAAGGTGTA
24493154 AAATATGTGGTAAAAATGTG
1 AAATATGTGGTAAAAATGTG
24493174 AAATAT-TGG-AAAAATGTG
1 AAATATGTGGTAAAAATGTG
24493192 GGCTGCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (20 bp):
AAATATGTGGTAAAAATGTG
Found at i:24496438 original size:17 final size:19
Alignment explanation
Indices: 24496396--24496439 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24496386 ATGAAATTTT
*
24496396 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
24496415 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
24496433 AA-TATTA
1 AATTATTA
24496440 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:24500872 original size:40 final size:40
Alignment explanation
Indices: 24500827--24500994 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
24500817 CGGAATATAA
*
24500827 CCGGATATAATCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACT-AGCACAAATGCCTTCGGGTCTTAGC
* * * *
24500867 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
24500907 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * * *
24500947 CCGGATATAATTTCCAGCATAATTGTCTTCGCGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
24500987 CCGGATAT
1 CCGGATAT
24500995 CATTCAATTT
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 104 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:24500977 original size:80 final size:80
Alignment explanation
Indices: 24500843--24500994 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 80
24500833 ATAATCATGT
* * *
24500843 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGCGACTTAGCC
24500908 CGGATATAGCCACTA
66 CGGATATAGCCACTA
* * ** * *
24500923 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGCGACTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGCGACTTAG
24500986 CCCGGATAT
64 CCCGGATAT
24500995 CATTCAATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
79 3 0.05
80 58 0.95
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGCGACTTAGCC
CGGATATAGCCACTA
Found at i:24504068 original size:61 final size:61
Alignment explanation
Indices: 24503973--24504096 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
24503963 CGTACGCCTA
24503973 TGTGCAAGAAAGGGGATTGTTTTGTTTCTTGGTTCTTACCTATATTTTTCAAGAATTAATT
1 TGTGCAAGAAAGGGGATTGTTTTGTTTCTTGGTTCTTACCTATATTTTTCAAGAATTAATT
24504034 TGTGCAAGAAAGGGGATTGTTTTGTTTCTTGGTTCTTACCTATATTTTTCAAGAATTAATT
1 TGTGCAAGAAAGGGGATTGTTTTGTTTCTTGGTTCTTACCTATATTTTTCAAGAATTAATT
24504095 TG
1 TG
24504097 AGTTTTTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (61 bp):
TGTGCAAGAAAGGGGATTGTTTTGTTTCTTGGTTCTTACCTATATTTTTCAAGAATTAATT
Found at i:24508069 original size:5 final size:5
Alignment explanation
Indices: 24508059--24508095 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
24508049 TCGAGCCAAA
24508059 AATTT AATTT AATTT AATATT -A-TT AATTT AATTT AAT
1 AATTT AATTT AATTT AAT-TT AATTT AATTT AATTT AAT
24508096 ATTATTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 1 0.03
5 24 0.83
6 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:24508086 original size:19 final size:19
Alignment explanation
Indices: 24508062--24508102 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
24508052 AGCCAAAAAT
24508062 TTAATTTAATTTAATATTA
1 TTAATTTAATTTAATATTA
24508081 TTAATTTAATTTAATATTA
1 TTAATTTAATTTAATATTA
24508100 TTA
1 TTA
24508103 CATGGTCCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATTTAATTTAATATTA
Found at i:24510782 original size:43 final size:43
Alignment explanation
Indices: 24510683--24510849 Score: 171
Period size: 43 Copynumber: 3.9 Consensus size: 43
24510673 CATATAACTC
* * * * *
24510683 ATACAATGCC-ATATCCCAGATATGGTCTTGCATGTTATCAC-
1 ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
* *
24510724 ATATCAATGCTAATGTCCCAAACATGGTCTTACACG-AATTCA-A
1 ATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAA-TCACA
* * **
24510767 ATAACGATGCCAATGTCCCAGGCATCATCTTACACGTAATCACA
1 AT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
*
24510811 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAT
1 ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
24510850 TACATCTCGG
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 3 0.03
42 7 0.07
43 85 0.84
44 6 0.06
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
Found at i:24513403 original size:14 final size:15
Alignment explanation
Indices: 24513379--24513408 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
24513369 GGATATCAAA
24513379 ACATGAATTAAGAAC
1 ACATGAATTAAGAAC
24513394 ACAT-AATTAAGAAC
1 ACATGAATTAAGAAC
24513408 A
1 A
24513409 AGTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (15 bp):
ACATGAATTAAGAAC
Found at i:24520642 original size:30 final size:30
Alignment explanation
Indices: 24520606--24520765 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
24520596 GACAAGATTG
* * * * *
24520606 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
24520636 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
24520664 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24520693 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24520723 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24520752 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
24520766 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:24520734 original size:59 final size:57
Alignment explanation
Indices: 24520606--24520765 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
24520596 GACAAGATTG
* * * * * *
24520606 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
24520664 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
24520723 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
24520766 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:24528507 original size:30 final size:30
Alignment explanation
Indices: 24528471--24528630 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
24528461 GACAAGATTG
* * * * *
24528471 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
24528501 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
24528529 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24528558 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24528588 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
24528617 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
24528631 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:24528599 original size:59 final size:57
Alignment explanation
Indices: 24528471--24528630 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
24528461 GACAAGATTG
* * * * * *
24528471 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
24528529 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
24528588 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
24528631 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:24538106 original size:40 final size:40
Alignment explanation
Indices: 24538032--24538185 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
24538022 CCGCACCAAG
* * * * * *
24538032 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
24538072 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
** * *
24538112 GCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * *
24538152 GTCC-TCGGGACTTAGCCCGGATATCACAATTTGC
1 G-CCTTCGGGTCTTAGCCCGGATATAACAACTTGC
24538186 TCATGCACAC
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 91 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:24541266 original size:31 final size:31
Alignment explanation
Indices: 24541231--24541294 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
24541221 CCTTTTCATG
24541231 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
24541262 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
24541293 TT
1 TT
24541295 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:24541537 original size:24 final size:24
Alignment explanation
Indices: 24541486--24541604 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
24541476 GCTTTATCAT
*
24541486 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
24541511 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
24541535 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
24541558 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
24541582 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
24541605 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:24541565 original size:47 final size:48
Alignment explanation
Indices: 24541486--24541604 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
24541476 GCTTTATCAT
*
24541486 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
24541535 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
24541582 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
24541605 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:24541679 original size:20 final size:20
Alignment explanation
Indices: 24541654--24541714 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
24541644 TTATGATTAC
24541654 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
24541674 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
24541694 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
24541714 A
1 A
24541715 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:24541789 original size:25 final size:25
Alignment explanation
Indices: 24541757--24541804 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24541747 ATACATAAAC
* * *
24541757 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
24541782 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
24541805 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:24543373 original size:27 final size:27
Alignment explanation
Indices: 24543045--24543362 Score: 390
Period size: 27 Copynumber: 11.8 Consensus size: 27
24543035 GGGTATTTTA
* *
24543045 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
24543072 GTAATTTTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
24543099 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
24543126 GTAATTCTGTAAATCGAGGGTGAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
24543153 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
24543180 ATAATTATGTAAATCG-GGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
24543206 GTAATTATGTAAAT-TAGGGGTAAAACG
1 GTAATTCTGTAAATCGA-GGGTAAAACG
* * **
24543233 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
24543260 GTAATTCTGTAAA-CTGAGGGTAAAACA
1 GTAATTCTGTAAATC-GAGGGTAAAACG
24543287 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
24543314 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
24543341 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
24543363 CTTTGGTAAT
Statistics
Matches: 256, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
26 23 0.09
27 231 0.90
28 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:24543386 original size:27 final size:27
Alignment explanation
Indices: 24543313--24543563 Score: 188
Period size: 27 Copynumber: 9.3 Consensus size: 27
24543303 AGGGTAAAAC
* ****
24543313 GGTAATTTTACAAATCGAGGGTAAAAC
1 GGTAATTTTACAAATTGAGGGTATTTT
* * * *
24543340 GGTAATTCTATAAATCGAGGGTACTTT
1 GGTAATTTTACAAATTGAGGGTATTTT
* *
24543367 GGTAATTTTACAAGTTGAGGGTATTTC
1 GGTAATTTTACAAATTGAGGGTATTTT
** ** * *
24543394 AATAATTTTACAGGTGGAGGGTATTTC
1 GGTAATTTTACAAATTGAGGGTATTTT
* *
24543421 AGTAATTTCACAAATT-AGGGGTATTTT
1 GGTAATTTTACAAATTGA-GGGTATTTT
* *
24543448 GGTAATTTTACAAACTAAGGGTATTTT
1 GGTAATTTTACAAATTGAGGGTATTTT
* *
24543475 GATAATTTTACAAACT-AGGGGTATTTT
1 GGTAATTTTACAAATTGA-GGGTATTTT
* **
24543502 GGTAATTTTATAAA-CCATGGGTATTTT
1 GGTAATTTTACAAATTGA-GGGTATTTT
*
24543529 AGTAATTTTACAAA--GCAGGGTATTTT
1 GGTAATTTTACAAATTG-AGGGTATTTT
24543555 GGTAATTTT
1 GGTAATTTT
24543564 GTAAACCAAA
Statistics
Matches: 185, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
26 19 0.10
27 165 0.89
28 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
GGTAATTTTACAAATTGAGGGTATTTT
Found at i:24543497 original size:81 final size:80
Alignment explanation
Indices: 24543358--24543563 Score: 209
Period size: 81 Copynumber: 2.5 Consensus size: 80
24543348 TATAAATCGA
* ** ** ** *
24543358 GGGTACTTTGGTAATTTTACAAGTTGAGGGTATTTCAATAATTTTACAGGTGGAGGGTATTTCAG
1 GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGATAATTTTACAACTAGAGGGTATTTCAG
**
24543423 TAATTTCACAAATTAG
65 TAATTTCACAAACCAG
**
24543439 GGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTGATAATTTTACAAACTAG-GGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGATAATTTTAC-AACTAGAGGGTATTTCA
* * *
24543503 GTAATTTTATAAACCAT
64 GTAATTTCACAAACCAG
* *
24543520 GGGTATTTTAGTAATTTTACAAAGC-AGGGTATTTTGGTAATTTT
1 GGGTATTTTGGTAATTTTACAAA-CTAGGGTATTTTGATAATTTT
24543564 GTAAACCAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
80 18 0.17
81 83 0.79
82 4 0.04
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.41
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGATAATTTTACAACTAGAGGGTATTTCAGT
AATTTCACAAACCAG
Found at i:24545422 original size:6 final size:6
Alignment explanation
Indices: 24545413--24545445 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
24545403 AAGAAAATTG
*
24545413 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
24545446 AATAGGAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:24552975 original size:26 final size:26
Alignment explanation
Indices: 24552939--24553000 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
24552929 ACATATTTTC
*
24552939 TCAAAATTTTA-CTAGGGGTAAGA-TCG
1 TCAAAATTTTATC-AGGGGTAA-ATTCA
24552965 TCAAAATTTTATCAGGGGTAAATTCA
1 TCAAAATTTTATCAGGGGTAAATTCA
24552991 TCAAAATTTT
1 TCAAAATTTT
24553001 TTTGGTGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 1 0.03
26 31 0.94
27 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (26 bp):
TCAAAATTTTATCAGGGGTAAATTCA
Found at i:24558797 original size:40 final size:40
Alignment explanation
Indices: 24558738--24558959 Score: 349
Period size: 40 Copynumber: 5.6 Consensus size: 40
24558728 ATTCGGATTG
24558738 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24558778 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
24558818 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24558858 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24558898 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
24558938 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
24558960 TACTTGGTTT
Statistics
Matches: 171, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 16 0.09
40 155 0.91
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:24566893 original size:40 final size:40
Alignment explanation
Indices: 24566834--24567050 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
24566824 GGATTGATAA
24566834 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
24566873 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
24566913 CCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
* *
24566954 -CGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
24566993 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
24567033 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
24567051 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 27 0.17
40 135 0.83
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:24570416 original size:25 final size:25
Alignment explanation
Indices: 24570379--24570448 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
24570369 CTCTTTTAAT
*
24570379 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
24570404 AATTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
24570429 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
24570449 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:24570521 original size:20 final size:21
Alignment explanation
Indices: 24570496--24570543 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
24570486 AAATGAATAC
*
24570496 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
24570516 ATCATGTGCATATCATATCAA
1 ATCATGTGCATATCATATCAA
24570537 ATCATGT
1 ATCATGT
24570544 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:24571780 original size:21 final size:22
Alignment explanation
Indices: 24571754--24571794 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
24571744 AAGAAAGAAA
24571754 AAGAAAA-GACTA-ATCCTAAAG
1 AAGAAAATGAC-ACATCCTAAAG
24571775 AAGAAAATGACACATCCTAA
1 AAGAAAATGACACATCCTAA
24571795 GTCCCTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (22 bp):
AAGAAAATGACACATCCTAAAG
Found at i:24573833 original size:6 final size:6
Alignment explanation
Indices: 24573815--24573927 Score: 81
Period size: 6 Copynumber: 18.3 Consensus size: 6
24573805 AAGAAACATT
*
24573815 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAGGA GA-CAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-GA -ATCAGA ATCAGA
* * * *
24573864 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCGGT ATCAGGTA A-CAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
24573914 ATCAAA ATCAGA AT
1 ATCAGA ATCAGA AT
24573928 GTGAATGCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
5 6 0.07
6 65 0.77
7 10 0.12
8 3 0.04
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:24573860 original size:25 final size:25
Alignment explanation
Indices: 24573829--24573924 Score: 99
Period size: 25 Copynumber: 3.8 Consensus size: 25
24573819 GAACTAGAAT
*
24573829 CAGAATCAGAATCAGAATTAGG-AGA
1 CAGAATCAGAATCAGAATCAGGTA-A
*
24573854 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
* *
24573879 CAGAATCAAAATCAGAATC-GGTAT
1 CAGAATCAGAATCAGAATCAGGTAA
*
24573903 CAGGTAA-CAGAATCAAAATCAG
1 CA-G-AATCAGAATCAGAATCAG
24573925 AATGTGAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
24 6 0.10
25 50 0.83
26 4 0.07
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:24573892 original size:31 final size:31
Alignment explanation
Indices: 24573857--24573927 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
24573847 TAGGAGACAG
24573857 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
*
24573888 AATCAGAATCGGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
24573919 AATCAGAAT
1 AATCAGAAT
24573928 GTGAATGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:24574359 original size:27 final size:27
Alignment explanation
Indices: 24574329--24574577 Score: 383
Period size: 27 Copynumber: 9.3 Consensus size: 27
24574319 GGGGCAAAAT
* * *
24574329 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24574356 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24574383 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
24574410 GGTCATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24574437 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
24574464 GGTTATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24574491 GGTAATTCTAACCTAC-AGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24574517 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
24574544 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
24574571 GGTAATT
1 GGTAATT
24574578 TCACAAAGTA
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
26 23 0.11
27 181 0.89
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:24574620 original size:27 final size:27
Alignment explanation
Indices: 24574532--24574687 Score: 125
Period size: 27 Copynumber: 5.8 Consensus size: 27
24574522 TTCTACCCTA
* * **
24574532 CAAGGGTATTTCGGTAATTCTACCCTA-
1 CAAGGGTATTTTGGTAATTTTA-CAAAC
* * *
24574559 CAAGGGTATTTCGGTAATTTCACAAAG
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
24574586 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** *
24574613 CAATGGTATTTTGGTAATTTTATTGAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
24574640 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
**
24574667 CAAGGGTATTTCAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
24574688 TTACATTGAG
Statistics
Matches: 103, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
26 2 0.02
27 101 0.98
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:24574621 original size:54 final size:54
Alignment explanation
Indices: 24574559--24574686 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
24574549 TTCTACCCTA
24574559 CAAGGGTATTTCGGTAATTTCACAAAGTAG-GGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTCACAAA-TAGAGGGTATTTTGGTAATTTTACAAAC
* * * *** * **
24574613 CAATGGTATTTTGGTAATTTTATTGATCGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTCACAAATAGAGGGTATTTTGGTAATTTTACAAAC
*
24574667 CAAGGGTATTTCAGTAATTT
1 CAAGGGTATTTCGGTAATTT
24574687 TTTACATTGA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 2 0.03
54 59 0.97
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (54 bp):
CAAGGGTATTTCGGTAATTTCACAAATAGAGGGTATTTTGGTAATTTTACAAAC
Found at i:24574699 original size:54 final size:54
Alignment explanation
Indices: 24574589--24574728 Score: 147
Period size: 54 Copynumber: 2.6 Consensus size: 54
24574579 CACAAAGTAG
** * ** *
24574589 GGGTATTTTGGTAATTTTACAAACCAATGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATTCATCGA
*
24574643 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT-TTACATTGA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATT-CATCGA
*** * * *
24574697 GGGTAAAATGGTAATTCTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTA
24574729 AGACGGTAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 2 0.03
54 70 0.97
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATTCATCGA
Done.