Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1887
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: 86487
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3798 original size:31 final size:29
Alignment explanation
Indices: 3743--3804 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
3733 ATTCATGCTT
* *
3743 TGTTGTTGAATGAATTTTGATGTTTGTTA
1 TGTTGTTGAATGAATTATGATGTTTGATA
*
3772 TGTTGTATGATTGAATTATGCATGTTTGATA
1 TGTTGT-TGAATGAATTATG-ATGTTTGATA
3803 TG
1 TG
3805 AATTAAGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 11 0.39
31 11 0.39
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (29 bp):
TGTTGTTGAATGAATTATGATGTTTGATA
Found at i:3953 original size:13 final size:13
Alignment explanation
Indices: 3935--3962 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3925 ACAACATTCC
3935 TTGTATCGATACA
1 TTGTATCGATACA
3948 TTGTATCGATACA
1 TTGTATCGATACA
3961 TT
1 TT
3963 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:6072 original size:28 final size:28
Alignment explanation
Indices: 6032--6086 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
6022 ACACAAGCCA
6032 ATACGAATTGGTAAGGTAAACGCTACCT
1 ATACGAATTGGTAAGGTAAACGCTACCT
6060 ATACGAATTGGTAAGGTAAACGCTACC
1 ATACGAATTGGTAAGGTAAACGCTACC
6087 CGAAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (28 bp):
ATACGAATTGGTAAGGTAAACGCTACCT
Found at i:6590 original size:13 final size:13
Alignment explanation
Indices: 6572--6620 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
6562 CATGGGACAA
6572 TGTATCGATACAT
1 TGTATCGATACAT
6585 TGTATCGATACA-
1 TGTATCGATACAT
6597 TG-AT-GA-A-AT
1 TGTATCGATACAT
6606 TGTATCGATACAT
1 TGTATCGATACAT
6619 TG
1 TG
6621 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6593 original size:33 final size:34
Alignment explanation
Indices: 6551--6620 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
6541 TTACCGTTGT
6551 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
6584 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
6618 TTG
1 TTG
6621 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:9165 original size:45 final size:45
Alignment explanation
Indices: 9116--9210 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
9106 ATATAATTTT
* * *
9116 CTCCACCATCGGAGGCAGTCTAACCCCGTTATTATCGAGGGGATA
1 CTCCACCATCAGAGGCACTCTAACCCCGTTATTATCGAGGAGATA
* * * *
9161 CTCCACCATCAGAGGTACTTTAACCCTGTTATTTTCGAGGAGATA
1 CTCCACCATCAGAGGCACTCTAACCCCGTTATTATCGAGGAGATA
9206 CTCCA
1 CTCCA
9211 ACCCCGATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (45 bp):
CTCCACCATCAGAGGCACTCTAACCCCGTTATTATCGAGGAGATA
Found at i:9273 original size:79 final size:79
Alignment explanation
Indices: 9182--9514 Score: 379
Period size: 79 Copynumber: 4.2 Consensus size: 79
9172 GAGGTACTTT
9182 AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGATTCTATTTTTAAAATATCGATTTTCCACT
1 AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGATTCTATTTTTAAAATATCGATTTTCCACT
9247 ATCGAGGATACTCC
66 ATCGAGGATACTCC
** * ** * * * *
9261 AACCCCATTATTTTCGAGGGGATACTCCAACCTAG-TTCTTTTTTTAAAAAATCAATTTTTCACT
1 AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGATTCTATTTTTAAAATATCGATTTTCCACT
*
9325 ATCGGGGATACTCC
66 ATCGAGGATACTCC
* * * *
9339 ATCACTGTTA-TTTCGAGGAGATACTCCATCCCC-AGTTTTATTTTTAAAATATCGATTTTCCAC
1 AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGA-TTCTATTTTTAAAATATCGATTTTCCAC
* *
9402 CATCGAGGATACTCT
65 TATCGAGGATACTCC
* * * *** *
9417 AACCTTGTTATTTTCAAGGGGATACTCCAACTTTGATTCTATTTTTAAAATATCGATTTTTCA-T
1 AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGATTCTATTTTTAAAATATCGATTTTCCACT
9481 CATCG-GAGATACTCC
66 -ATCGAG-GATACTCC
* *
9496 AACCTTGTTGTTTTCGAGG
1 AACCCTGTTATTTTCGAGG
9515 GTCAAGATAG
Statistics
Matches: 207, Mismatches: 41, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
77 19 0.09
78 87 0.42
79 100 0.48
80 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (79 bp):
AACCCTGTTATTTTCGAGGAGATACTCCAACCCCGATTCTATTTTTAAAATATCGATTTTCCACT
ATCGAGGATACTCC
Found at i:16745 original size:47 final size:47
Alignment explanation
Indices: 16655--16745 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
16645 TCGAAGATGC
** * *
16655 GAAGAATGACAATGTGCTAATTCATGGCTAGCGACATTAGACTTGAA
1 GAAGAATGACAATGTGCTAAGACAAGGCTAGCGACAATAGACTTGAA
* * *
16702 GAAGAATGCCAATGTGCTGAGACAAGGCTAGCGACAATGGACTT
1 GAAGAATGACAATGTGCTAAGACAAGGCTAGCGACAATAGACTT
16746 AGGAATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (47 bp):
GAAGAATGACAATGTGCTAAGACAAGGCTAGCGACAATAGACTTGAA
Found at i:16821 original size:49 final size:49
Alignment explanation
Indices: 16755--17175 Score: 218
Period size: 49 Copynumber: 8.9 Consensus size: 49
16745 TAGGAATTTT
*
16755 AAAGATGCCAATATGCTAATTCAAGGCCAACGATATCGGACTTAAAGATG
1 AAAG-TGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
** * * * *
16805 AAAGTGCCAATATGCTAATTCAAGGCCAGTGACATTGGTCTTAACGA-C
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* ** * * *
16853 AAGGTGCCAATATATTGATTCAAGGCCAACAATATTGGGC-T-----T-
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * *** ** *
16895 --A-TGCCAATGTGCTGATTCAAAGCCGGTGACCTTGGTCTTAAAGATG
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
*
16941 ACGAAGGCGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
1 A--AA-GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * ** * *
16993 AAGGTGCCAATGTGCTGATTCAAGGCCGGCGACATTGG-------GCT-
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * ** * * *
17034 --CGTGCCAATGTGCTGATTCGGGGCTAACGACATTGGTCTTAAAGATG
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * * *
17081 AATGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATG
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * * * *
17130 AAGGTGCCAATATGCTGATTTAAGCCCAGCGATATTGGGCTTAAAG
1 AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAG
17176 GTGCCACGGA
Statistics
Matches: 283, Mismatches: 64, Indels: 49
0.71 0.16 0.12
Matches are distributed among these distances:
39 55 0.19
40 1 0.00
42 2 0.01
45 1 0.00
46 2 0.01
47 1 0.00
48 31 0.11
49 148 0.52
50 6 0.02
52 36 0.13
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
AAAGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATG
Found at i:16981 original size:91 final size:87
Alignment explanation
Indices: 16809--16986 Score: 212
Period size: 91 Copynumber: 2.0 Consensus size: 87
16799 AAGATGAAAG
* * * *
16809 TGCCAATATGCTAATTCAAGGCCAGTGACATTGGTCTTAACGACAAGGTGCCAATATATTGATTC
1 TGCCAATATGCTAATTCAAAGCCAGTGACATTGGTCTTAACGACAAGGCGCCAATATACTAATTC
*
16874 AAGGCCAACAATATTGGGCTTA
66 AAGGCCAACAATATTGGACTTA
* * * * * *
16896 TGCCAATGTGCTGATTCAAAGCCGGTGACCTTGGTCTTAAAGATGACGAAGGCGCCAATATGCTA
1 TGCCAATATGCTAATTCAAAGCCAGTGACATTGGTCTT--A-ACGAC-AAGGCGCCAATATACTA
*
16961 ATTCAAGGCCAACGATATTGGACTTA
62 ATTCAAGGCCAACAATATTGGACTTA
16987 AAGATGAAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
87 33 0.44
89 1 0.01
90 4 0.05
91 37 0.49
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (87 bp):
TGCCAATATGCTAATTCAAAGCCAGTGACATTGGTCTTAACGACAAGGCGCCAATATACTAATTC
AAGGCCAACAATATTGGACTTA
Found at i:17147 original size:137 final size:137
Alignment explanation
Indices: 16759--17170 Score: 475
Period size: 137 Copynumber: 3.0 Consensus size: 137
16749 AATTTTAAAG
* * * * * *
16759 ATGCCAATATGCTAATTCAAGGCCAACGATATCGGACTTAAAGATGAAAGTGCCAATATGCTAAT
1 ATGCCAATGTGCTGATTCAAAGCCAACGACATTGGTCTTAAAGATGAAAGTGCCAATATGCTAAT
** * * ** * *
16824 TCAAGGCCAGTGACATTGGTCTTAACGA-CAAGGTGCCAATATATTGATTCAAGGCCAACAATAT
66 TCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
*
16888 TGGGCTT
131 TGGGCTC
*** * *
16895 ATGCCAATGTGCTGATTCAAAGCCGGTGACCTTGGTCTTAAAGATGACGAAGGCGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAAGCCAACGACATTGGTCTTAAAGATGA--AA-GTGCCAATATGCT
* * * *
16960 AATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCGGCGA
63 AATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
*
17025 CATTGGGCTC
128 TATTGGGCTC
* *** * * * *
17035 GTGCCAATGTGCTGATTCGGGGCTAACGACATTGGTCTTAAAGATGAATGTGCCAATGTGCTGAT
1 ATGCCAATGTGCTGATTCAAAGCCAACGACATTGGTCTTAAAGATGAAAGTGCCAATATGCTAAT
* *
17100 TCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTTAAGCCCAGCGATAT
66 TCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
17165 TGGGCT
131 TGGGCT
17171 TAAAGGTGCC
Statistics
Matches: 227, Mismatches: 45, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
136 37 0.16
137 77 0.34
138 3 0.01
139 38 0.17
140 72 0.32
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (137 bp):
ATGCCAATGTGCTGATTCAAAGCCAACGACATTGGTCTTAAAGATGAAAGTGCCAATATGCTAAT
TCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGGCTC
Found at i:17215 original size:34 final size:33
Alignment explanation
Indices: 17175--17357 Score: 133
Period size: 34 Copynumber: 5.5 Consensus size: 33
17165 TGGGCTTAAA
* *
17175 GGTGCCACGGAATTGTGGACTTATAGGAAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAGGAAAAAG
* * *
17208 GGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAG
1 GG-TGCCACGGAGTTGTGGACTT-AAAGGAAAAAG
*
17243 GGTGCCACGGAGTCGTGGACTTAAA--AAAAA-
1 GGTGCCACGGAGTTGTGGACTTAAAGGAAAAAG
* * *
17273 AGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-
1 GGTGCCACGGAGTTGTGGAC-TT-AAAGGAAAAAG
** ** *
17307 GGTAACACAAAATTGTGGACTTAAAAGGAAAAA-
1 GGTGCCACGGAGTTGTGGACTT-AAAGGAAAAAG
* * *
17340 GATGCCACAGACTTGTGG
1 GGTGCCACGGAGTTGTGG
17358 GCTTTTGAGG
Statistics
Matches: 119, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
30 17 0.14
31 6 0.05
32 3 0.03
33 30 0.25
34 52 0.44
35 11 0.09
ACGTcount: A:0.37, C:0.13, G:0.32, T:0.19
Consensus pattern (33 bp):
GGTGCCACGGAGTTGTGGACTTAAAGGAAAAAG
Found at i:17278 original size:30 final size:32
Alignment explanation
Indices: 17244--17305 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
17234 AGGGAAAAGG
17244 GTGCCACGGAGTCGTGGAC-TTAAAAA-AAAA
1 GTGCCACGGAGTCGTGGACTTTAAAAAGAAAA
* *
17274 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 GTGCCACGGAGTCGTGGACTTTAAAAAGAAAA
17306 AGGTAACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 17 0.61
31 7 0.25
32 4 0.14
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (32 bp):
GTGCCACGGAGTCGTGGACTTTAAAAAGAAAA
Found at i:17290 original size:64 final size:64
Alignment explanation
Indices: 17172--17361 Score: 193
Period size: 64 Copynumber: 2.9 Consensus size: 64
17162 TATTGGGCTT
** * *
17172 AAAGGTGCCACGGAATTGTGGACTTATAGGAAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
1 AAAGGTGCCACGGAATTGTGGACTTA-A--AAAAAAAGATGCCACGGAGTTGTGGGCTTAAAA-A
17237 GAA
62 GAA
* * *
17240 AAGGGTGCCACGGAGTCGTGGACTTAAAAAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAATTGTGGACTTAAAAAAAAAGATGCCACGGAGTTGTGGGC-TTAAAAAGAA
** ** * *
17304 AAAGGTAACACAAAATTGTGGACTTAAAAGGAAAAAGATGCCACAGACTTGTGGGCTT
1 AAAGGTGCCACGGAATTGTGGACTTAAAA--AAAAAGATGCCACGGAGTTGTGGGCTT
17362 TTGAGGGTTT
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
64 42 0.41
65 12 0.12
66 8 0.08
67 17 0.17
68 23 0.23
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (64 bp):
AAAGGTGCCACGGAATTGTGGACTTAAAAAAAAAGATGCCACGGAGTTGTGGGCTTAAAAAGAA
Found at i:17386 original size:28 final size:28
Alignment explanation
Indices: 17342--17569 Score: 269
Period size: 28 Copynumber: 8.0 Consensus size: 28
17332 AGGAAAAAGA
* *
17342 TGCCACAGACTTGTGGGCTTTTGAGGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
* *
17370 TTCCACTGACTTTTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
*
17398 TGCCACTGACTTGTGGGTTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
* * *
17426 TGCCACTAACTTGTGGGCTTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG--AAGGT
17456 TGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
* *
17484 TGCCACTGACTTGTGGGC-TTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG--AAGGT
* * * *
17513 TGCCACTGACCTGTGGCCTTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG--AAGGT
17543 TGCCACTGACTTGTGGGCTTTTGAAGG
1 TGCCACTGACTTGTGGGCTTTTGAAGG
17570 GTGAAGAATG
Statistics
Matches: 174, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
27 4 0.02
28 94 0.54
29 19 0.11
30 57 0.33
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGT
Found at i:17478 original size:58 final size:58
Alignment explanation
Indices: 17334--17567 Score: 321
Period size: 56 Copynumber: 4.1 Consensus size: 58
17324 GACTTAAAAG
* * * *
17334 GAAAAAGATGCCACAGACTTGTGGGCTTTTGAGGGTTTCCACTGACTTTTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTT
* * * *
17392 G--AAGGTTGCCACTGACTTGTGGGTTTTTGAAGGTTGCCACTAACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTT
17448 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-TTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTT
* * * *
17505 GAAAAAGATGCCACTGACCTGTGGCCTTTTGAAAAAGATGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTT
17565 GAA
1 GAA
17568 GGGTGAAGAA
Statistics
Matches: 155, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
56 48 0.31
57 32 0.21
58 48 0.31
59 21 0.14
60 6 0.04
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (58 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTT
Found at i:17553 original size:87 final size:86
Alignment explanation
Indices: 17372--17569 Score: 308
Period size: 87 Copynumber: 2.3 Consensus size: 86
17362 TTGAGGGTTT
* * * * *
17372 CCACTGACTTTTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGTTTTTGAAGGTTGCCACTAACT
1 CCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGTCTTTGAAAGATGCCACTAACC
*
17437 TGTGGGCTTTTGAAAAAGATG
66 TGTGGCCTTTTGAAAAAGATG
*
17458 CCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGG-CTTTGAAAAAGATGCCACTGA
1 CCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGTCTTTG--AAAGATGCCACTAA
17522 CCTGTGGCCTTTTGAAAAAGATG
64 CCTGTGGCCTTTTGAAAAAGATG
17545 CCACTGACTTGTGGGCTTTTGAAGG
1 CCACTGACTTGTGGGCTTTTGAAGG
17570 GTGAAGAATG
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
85 4 0.04
86 42 0.41
87 57 0.55
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (86 bp):
CCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGTCTTTGAAAGATGCCACTAACC
TGTGGCCTTTTGAAAAAGATG
Found at i:19027 original size:20 final size:19
Alignment explanation
Indices: 18994--19082 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 19
18984 ATCCGGACCC
*
18994 TTTTTTG-TTGTTGTTGTCT
1 TTTTTTGTTTTTTGTTGT-T
19013 TTTTTTGTTTTTTGTTGTT
1 TTTTTTGTTTTTTGTTGTT
* *
19032 GTTGTT-TTTTTT-TTGTT
1 TTTTTTGTTTTTTGTTGTT
* *
19049 TTGTTTGTTTGTT-TT-TT
1 TTTTTTGTTTTTTGTTGTT
19066 TTTTTTGTTTTATTGTT
1 TTTTTTGTTTT-TTGTT
19083 TTTGCGGAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 19 0.33
18 15 0.26
19 14 0.25
20 9 0.16
ACGTcount: A:0.01, C:0.01, G:0.17, T:0.81
Consensus pattern (19 bp):
TTTTTTGTTTTTTGTTGTT
Found at i:19030 original size:26 final size:25
Alignment explanation
Indices: 18994--19082 Score: 108
Period size: 26 Copynumber: 3.4 Consensus size: 25
18984 ATCCGGACCC
18994 TTTTTTGTTGTTGTTGTCTTTTTTTG
1 TTTTTTGTTGTTGTTGT-TTTTTTTG
19020 TTTTTTGTTGTTGTTGTTTTTTTT-
1 TTTTTTGTTGTTGTTGTTTTTTTTG
*
19044 TTGTTTTGTTTGTTTGTTTTTTTTTTTTG
1 TT-TTTTG-TTG-TTG-TTGTTTTTTTTG
19073 TTTTATTGTT
1 TTTT-TTGTT
19083 TTTGCGGAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
24 2 0.04
25 12 0.21
26 20 0.36
27 3 0.05
28 14 0.25
29 5 0.09
ACGTcount: A:0.01, C:0.01, G:0.17, T:0.81
Consensus pattern (25 bp):
TTTTTTGTTGTTGTTGTTTTTTTTG
Found at i:19084 original size:13 final size:13
Alignment explanation
Indices: 18994--19084 Score: 80
Period size: 13 Copynumber: 6.8 Consensus size: 13
18984 ATCCGGACCC
18994 TTTTTTGTTGTTGT
1 TTTTTTGTT-TTGT
*
19008 TGTCTTT-TTTTG-
1 T-TTTTTGTTTTGT
19020 TTTTTTGTTGTTGT
1 TTTTTTGTT-TTGT
*
19034 TGTTTTTTTTTTGT
1 T-TTTTTGTTTTGT
19048 TTTGTTTG-TTTGT
1 TTT-TTTGTTTTGT
*
19061 TTTTTTTTTTTGT
1 TTTTTTGTTTTGT
*
19074 TTTATTGTTTT
1 TTTTTTGTTTT
19085 TGCGGAGGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
11 4 0.06
12 6 0.10
13 30 0.48
14 12 0.19
15 11 0.17
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.81
Consensus pattern (13 bp):
TTTTTTGTTTTGT
Found at i:22705 original size:52 final size:52
Alignment explanation
Indices: 22620--22744 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
22610 ATATGAAAAG
* *
22620 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
22672 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
22724 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
22745 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:22757 original size:52 final size:50
Alignment explanation
Indices: 22620--22764 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
22610 ATATGAAAAG
* *
22620 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
22672 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
22724 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
22765 ATATATCGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:22834 original size:33 final size:33
Alignment explanation
Indices: 22797--22863 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22787 AGTAGCTTGA
22797 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
22830 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
22863 A
1 A
22864 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:22837 original size:13 final size:13
Alignment explanation
Indices: 22819--22843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22809 CAAAAAAATA
22819 TGTATCGATACAT
1 TGTATCGATACAT
22832 TGTATCGATACA
1 TGTATCGATACA
22844 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23715 original size:169 final size:172
Alignment explanation
Indices: 23422--23808 Score: 444
Period size: 169 Copynumber: 2.2 Consensus size: 172
23412 ATTTTGCAAT
* * * * * * * *
23422 GTGCCACTGTGCAGATTCAAGGCCTGCAACACTGGTCTTAAAGATGATGAGGATAAAGAGTGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGAGAAAGAGCGATA
*
23487 AAAGGACCAATACGTTAATTCACGGCCAACAATATTGGGTTTAAAGATGAGAAAAAGGAT-AAAA
66 AAAGGACCAATACGTTAATTCACGGCCAACAATATTGGGCTTAAAGATGAGAAAAAGGATGAAAA
* * *
23551 T-AGCCAATATGC-GGCTAGCGATATTGGACTTAAAGAT-AAAG
131 TGAGCCAAT-T-CAGGCCAGCGACATTGAACTTAAAGATGAAAG
*
23592 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGATGAGAAA-AGCGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGAGAAAGAGCGATA
* * * * **
23656 AAGATG-CCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
66 AA-AGGACCAATACGTTAATTCACGGCCAACAATATTGGGCTTAAAGATGAGAAAAAGGATGAAA
* ** *
23720 ATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAG
130 ATGAGCCAATTC-AGGCCAGCGACATTGAACTTAAAGAT-G-AAAG
* * *
23766 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
23809 GTCCCAATGT
Statistics
Matches: 183, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
169 59 0.32
170 55 0.30
171 25 0.14
174 44 0.24
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (172 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGAGAAAGAGCGATA
AAAGGACCAATACGTTAATTCACGGCCAACAATATTGGGCTTAAAGATGAGAAAAAGGATGAAAA
TGAGCCAATTCAGGCCAGCGACATTGAACTTAAAGATGAAAG
Found at i:23892 original size:49 final size:48
Alignment explanation
Indices: 23718--24044 Score: 296
Period size: 43 Copynumber: 6.8 Consensus size: 48
23708 AAAAGGATGT
* * * * *
23718 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA---AGAA-GTGC
* *
23770 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTCC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAAGTGC
* ** *
23813 CAATGTGCTGATTCAAGGCCAGTTACATTGGACTTAAAGAAGAAGTTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAAG-TGC
23862 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAAGTGC
* * * *
23905 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAA-GTGC
* *
23954 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGGATGT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GA-AG-AA-G-TGC
* *
24009 CAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
24045 GAAGGGTTGC
Statistics
Matches: 233, Mismatches: 24, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
43 70 0.30
44 1 0.00
45 1 0.00
46 11 0.05
48 1 0.00
49 69 0.30
50 3 0.01
51 1 0.00
52 34 0.15
53 1 0.00
54 5 0.02
55 36 0.15
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAAGTGC
Found at i:23902 original size:92 final size:92
Alignment explanation
Indices: 23718--23992 Score: 442
Period size: 92 Copynumber: 3.0 Consensus size: 92
23708 AAAAGGATGT
* *
23718 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATT
*
23783 CAAGGCCAGCTATATTGGACTTAAAGGTCC
63 CAAGGCCAGCGATATTGGACTTAAAGGTCC
* *
23813 CAATGTGCTGATTCAAGGCCAGTTACATTGGACTTAAAGAAGAAGTTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* *
23878 GGCCAGCGATATTGGACTTGAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTCC
*
23905 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
23970 GGCCAGCGATATTGGGCTTAAAG
66 GGCCAGCGATATTGGACTTAAAG
23993 ATGAGAGAAA
Statistics
Matches: 168, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
92 130 0.77
95 38 0.23
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGGTCC
Found at i:24043 original size:55 final size:49
Alignment explanation
Indices: 23660--24044 Score: 317
Period size: 49 Copynumber: 7.8 Consensus size: 49
23650 GCGATAAAGA
* * * *
23660 TGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT--G---AAGG
* * * **
23714 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT-G--AAGG
* * *
23767 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* ** * * * *
23810 TCCCAATGTGCTGATTCAAGGCCAGTTACATTGGACTTAAAGAAGAAGT
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* *
23859 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* * *
23902 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
*
23951 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT----G-AAGG
*
24005 ATGTCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 -TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
24045 GAAGGGTTGC
Statistics
Matches: 277, Mismatches: 35, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
43 75 0.27
44 1 0.00
47 1 0.00
48 2 0.01
49 80 0.29
52 34 0.12
53 7 0.03
54 5 0.02
55 72 0.26
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
Found at i:24085 original size:32 final size:31
Alignment explanation
Indices: 24037--24111 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 31
24027 CCAGCGATAT
*
24037 TGGGC-TTAGAAGGGTTGCCACTGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
24067 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
24099 TGGGCTTTAGAAG
1 TGGGCTTTAGAAG
24112 AAAAAGAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 5 0.12
31 7 0.17
32 30 0.71
ACGTcount: A:0.17, C:0.16, G:0.37, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:24210 original size:29 final size:30
Alignment explanation
Indices: 24146--24218 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
24136 GCTTACAAAA
* * *
24146 GAAAAAGAGTGCCACGGAGTTGTCGACTTT
1 GAAAAAGAGTGCCACCGACTTGTCGACTTC
* * *
24176 GGAAAAGA-TGCCACCGACTTGTGGGCTTC
1 GAAAAAGAGTGCCACCGACTTGTCGACTTC
*
24205 GAAAAAGGGTGCCA
1 GAAAAAGAGTGCCA
24219 TTGATTTGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (30 bp):
GAAAAAGAGTGCCACCGACTTGTCGACTTC
Found at i:24254 original size:27 final size:27
Alignment explanation
Indices: 24184--24270 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
24174 TTGGAAAAGA
* *
24184 TGCCACCGACTTGTGGGCTTCGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTG---AAGGG
* * *
24214 TGCCATTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
*
24241 TGCCACTGACTTGTGGACTTTTGAAGGG
1 TGCCACTGACTTGTGGGC-TTTGAAGGG
24269 TG
1 TG
24271 AGGAATGTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 19 0.40
28 10 0.21
30 18 0.38
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.31
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:25706 original size:1 final size:1
Alignment explanation
Indices: 25700--25805 Score: 86
Period size: 1 Copynumber: 106.0 Consensus size: 1
25690 TCCGGACCTA
* * * * * * * *
25700 TTTTTTTGTTTTTTTTGTTTGTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTGTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
25765 GTTTTTGTTGTTTTTTTTTGTTTTCTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25806 GTGGAGGATG
Statistics
Matches: 77, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (1 bp):
T
Found at i:25715 original size:10 final size:10
Alignment explanation
Indices: 25700--25803 Score: 111
Period size: 10 Copynumber: 9.7 Consensus size: 10
25690 TCCGGACCTA
25700 TTTTTTTGTT
1 TTTTTTTGTT
*
25710 TTTTTTGTTTGT
1 TTTTTT-TGT-T
25722 TTTTTTTGTT
1 TTTTTTTGTT
25732 TTTTTTTGTT
1 TTTTTTTGTT
25742 TTTGTTTT-TT
1 TTT-TTTTGTT
25752 TGTTTTTTGTTTT
1 T-TTTTTTG--TT
25765 GTTTTTGTTGTT
1 -TTTTT-TTGTT
25777 TTTTTTTGTT
1 TTTTTTTGTT
*
25787 TTCTTTTGTT
1 TTTTTTTGTT
25797 TTTTTTT
1 TTTTTTT
25804 TTGTGGAGGA
Statistics
Matches: 81, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
10 47 0.58
11 15 0.19
12 9 0.11
13 6 0.07
14 4 0.05
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:25743 original size:29 final size:28
Alignment explanation
Indices: 25700--25799 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 28
25690 TCCGGACCTA
*
25700 TTTTTTTGTTTTTTTTGTTTGTTTTTTTTG
1 TTTTTTT-TTGTTTTTG-TTGTTTTTTTTG
*
25730 TTTTTTTTTGTTTTTGTT-TTTTTGTT-
1 TTTTTTTTTGTTTTTGTTGTTTTTTTTG
*
25756 TTTTGTTTTGTTTTTGTTGTTTTTTTTTG
1 TTTTTTTTTGTTTTTGTTG-TTTTTTTTG
*
25785 TTTTCTTTTGTTTTT
1 TTTTTTTTTGTTTTT
25800 TTTTTTGTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 17 0.27
27 7 0.11
28 9 0.15
29 22 0.35
30 7 0.11
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (28 bp):
TTTTTTTTTGTTTTTGTTGTTTTTTTTG
Found at i:25750 original size:45 final size:44
Alignment explanation
Indices: 25700--25807 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 44
25690 TCCGGACCTA
*
25700 TTTTTTTGTTTTTTTTGTTTGTTTTTTTTGTTTTTTTTTGTTTT-
1 TTTTTTT-TTTTTTTTGTTTGTTTTTGTTGTTTTTTTTTGTTTTC
*
25744 TGTTTTTTTGTTTTTTGTTTTGTTTTTGTTGTTTTTTTTTGTTTTC
1 T-TTTTTTTTTTTTTTG-TTTGTTTTTGTTGTTTTTTTTTGTTTTC
25790 TTTTGTTTTTTTTTTTGT
1 TTTT-TTTTTTTTTTTGT
25808 GGAGGATGCC
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
44 9 0.16
45 36 0.63
46 12 0.21
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (44 bp):
TTTTTTTTTTTTTTTGTTTGTTTTTGTTGTTTTTTTTTGTTTTC
Found at i:25771 original size:55 final size:52
Alignment explanation
Indices: 25701--25805 Score: 158
Period size: 55 Copynumber: 2.0 Consensus size: 52
25691 CCGGACCTAT
*
25701 TTTTTTGTTTTTTTTGTT-TGTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTTGTTGT-TTTTTTTTGTTTTCTTTTGTTTTT-TTTTTTTG
25754 TTTTTTGTTTTGTTTTTGTTGTTTTTTTTTGTTTTCTTTTGTTTTTTTTTTT
1 TTTTTTG-TTT-TTTTTGTTGTTTTTTTTTGTTTTCTTTTGTTTTTTTTTTT
25806 GTGGAGGATG
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
53 7 0.15
54 9 0.19
55 31 0.65
56 1 0.02
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (52 bp):
TTTTTTGTTTTTTTTGTTGTTTTTTTTTGTTTTCTTTTGTTTTTTTTTTTTG
Found at i:35509 original size:10 final size:10
Alignment explanation
Indices: 35494--35520 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35484 ATGTATCAAG
35494 CAAAAACAAA
1 CAAAAACAAA
35504 CAAAAACAAA
1 CAAAAACAAA
35514 CAAAAAC
1 CAAAAAC
35521 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:39713 original size:52 final size:51
Alignment explanation
Indices: 39635--39783 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 51
39625 CGAAATATGA
39635 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGAC
* * * *
39687 AAATTTGCCTGCATATATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGAC
* **
39739 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
39784 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGAC
Found at i:39790 original size:13 final size:13
Alignment explanation
Indices: 39772--39796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39762 CAAAGATCAG
39772 TGTATCGATACAA
1 TGTATCGATACAA
39785 TGTATCGATACA
1 TGTATCGATACA
39797 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:39874 original size:33 final size:33
Alignment explanation
Indices: 39837--39903 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
39827 AGTAGCTTGA
39837 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
39870 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
39903 A
1 A
39904 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:39877 original size:13 final size:13
Alignment explanation
Indices: 39859--39883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39849 CAAAAAAATA
39859 TGTATCGATACAT
1 TGTATCGATACAT
39872 TGTATCGATACA
1 TGTATCGATACA
39884 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49164 original size:33 final size:33
Alignment explanation
Indices: 49122--49187 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
49112 AAATTCCCAG
*
49122 ATGTATCGATACAAAGATTAATGTATCAATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
** *
49155 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
49188 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCAATACA
Found at i:49334 original size:21 final size:20
Alignment explanation
Indices: 49308--49346 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
49298 GTTGGGACCT
*
49308 TGTATCTATACATTCTGGAAA
1 TGTATCGATACATT-TGGAAA
49329 TGTATCGATACATTTGGA
1 TGTATCGATACATTTGGA
49347 CAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTGGAAA
Found at i:50305 original size:29 final size:30
Alignment explanation
Indices: 50253--50339 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 30
50243 AGAAGAAGAC
*
50253 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 GCCATCAACTTGTGT--GCTTTTGAAAGGGTT
50285 G-CATCAACTTGTGTGCTTTTG-AA-GGTT
1 GCCATCAACTTGTGTGCTTTTGAAAGGGTT
** *
50312 GCCATTGACTTGTGGGCTTTTGAAAGGG
1 GCCATCAACTTGTGTGCTTTTGAAAGGG
50340 GTGTCACCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 5 0.10
28 19 0.40
29 9 0.19
30 2 0.04
31 12 0.25
32 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.34
Consensus pattern (30 bp):
GCCATCAACTTGTGTGCTTTTGAAAGGGTT
Found at i:50390 original size:34 final size:34
Alignment explanation
Indices: 50352--50699 Score: 137
Period size: 34 Copynumber: 10.9 Consensus size: 34
50342 GTCACCGACT
*
50352 TGTGGGCTTACAA-GAAAAAGGGATGCCACAGAGG
1 TGTGGGCTTAAAAGGAAAAA-GGATGCCACAGAGG
* *
50386 TGTGGGCTTAAAAGGGAAAAGGTTGCCACAGA-G
1 TGTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
* * * * *
50419 TCATGGACTTAAAAAG-AAAAGG-TGCCACGGAGT
1 T-GTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
* * *
50452 TGTGGACTTAAAA-G-----GG-TGCCACGGAGT
1 TGTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
* *
50479 TGTGGACTTAAAAGGAAAAA-GAGTGCCAC-GAAGT
1 TGTGGGCTTAAAAGGAAAAAGGA-TGCCACAG-AGG
* * * *
50513 TATGGACTTAAAA-G-----GG-TGCCACGGAGT
1 TGTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
* * ** *
50540 TGTGGACTTAAAAGGAAAAA-GAGTTCCATGGAGT
1 TGTGGGCTTAAAAGGAAAAAGGA-TGCCACAGAGG
* * *
50574 TGTGAGCTTAAAAGGAAAAA-GAGTGCTACAGAGT
1 TGTGGGCTTAAAAGGAAAAAGGA-TGCCACAGAGG
* *
50608 TGTGGGCTTAAAAGGAAAAAAGG-TGCCACGGAGT
1 TGTGGGCTTAAAAGG-AAAAAGGATGCCACAGAGG
* *
50642 TGTGGACTTAAAA-G-----GG-TGCCACAGAGT
1 TGTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
* *
50669 TGTGGACTTAAAAGGAAAAA-AATGCCACAGA
1 TGTGGGCTTAAAAGGAAAAAGGATGCCACAGA
50700 CTTATGGGCT
Statistics
Matches: 258, Mismatches: 25, Indels: 63
0.75 0.07 0.18
Matches are distributed among these distances:
27 72 0.28
28 4 0.02
29 1 0.00
31 1 0.00
32 21 0.08
33 21 0.08
34 127 0.49
35 10 0.04
36 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (34 bp):
TGTGGGCTTAAAAGGAAAAAGGATGCCACAGAGG
Found at i:50472 original size:27 final size:27
Alignment explanation
Indices: 50435--50554 Score: 152
Period size: 27 Copynumber: 4.2 Consensus size: 27
50425 ACTTAAAAAG
50435 AAAA-GGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
50461 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
50488 AAAAGGAAAAAGAGTGCCACGAAGTTATGGACTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGACTT
50522 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
50549 AAAAGG
1 AAAAGG
50555 AAAAAGAGTT
Statistics
Matches: 82, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.05
27 51 0.62
28 2 0.02
33 2 0.02
34 23 0.28
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:50528 original size:61 final size:61
Alignment explanation
Indices: 50402--50696 Score: 357
Period size: 61 Copynumber: 4.8 Consensus size: 61
50392 CTTAAAAGGG
* ** *
50402 AAAAGGTTGCCACAGAGTCATGGACTTAAAAAG-AAAAG-GTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * *
50461 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTATGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * *
50522 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTTCCATGGAGTTGT-GAGCTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGA-CTT
* *
50583 AAAAGGAAAAAGAGTGCTACAGAGTTGTGGGCTTAAAAGGAAAAA-AGGTGCCACGGAGTTGTGG
1 AAAA-G-----G-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGA-GTGCCACGGAGTTGTGG
50647 ACTT
58 ACTT
*
50651 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAA-AATGCCAC
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCAC
50697 AGACTTATGG
Statistics
Matches: 205, Mismatches: 19, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
59 28 0.14
60 13 0.06
61 108 0.53
62 2 0.01
67 3 0.01
68 49 0.24
69 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:50618 original size:68 final size:68
Alignment explanation
Indices: 50522--50689 Score: 201
Period size: 68 Copynumber: 2.6 Consensus size: 68
50512 TTATGGACTT
* * * *
50522 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAAGAGTTCCATGGAGTTGT-GAGCTTAA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAAG-GTGCCACGGAGTTGTGGA-CTTAA
50585 AAGGA
64 AAGGA
* *
50590 AAAAGAGTGCTACAGAGTTGTGGGCTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAA
50655 -G-
66 GGA
50656 ----G-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAA
50690 ATGCCACAGA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
61 31 0.34
62 1 0.01
67 1 0.01
68 49 0.54
69 8 0.09
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.20
Consensus pattern (68 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAA
GGA
Found at i:50620 original size:27 final size:27
Alignment explanation
Indices: 50590--50682 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 27
50580 CTTAAAAGGA
* *
50590 AAAAGAGTGCTACAGAGTTGTGGGCTT
1 AAAAGAGTGCCACAGAGTTGTGGACTT
*
50617 AAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAA-G-----AG-TGCCACAGAGTTGTGGACTT
*
50651 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGACTT
50678 AAAAG
1 AAAAG
50683 GAAAAAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 28 0.52
28 2 0.04
33 3 0.06
34 21 0.39
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.20
Consensus pattern (27 bp):
AAAAGAGTGCCACAGAGTTGTGGACTT
Found at i:50683 original size:27 final size:27
Alignment explanation
Indices: 50624--50683 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
50614 CTTAAAAGGA
* *
50624 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
50651 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
50678 AAAAGG
1 AAAAGG
50684 AAAAAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGACTT
Found at i:50724 original size:28 final size:28
Alignment explanation
Indices: 50691--50767 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
50681 AGGAAAAAAA
* *
50691 TGCCACAGACTTATGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
50719 TGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
50747 TGCCACTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
50768 GAAAAAGATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGT
Found at i:50733 original size:61 final size:61
Alignment explanation
Indices: 50590--50734 Score: 148
Period size: 61 Copynumber: 2.4 Consensus size: 61
50580 CTTAAAAGGA
* * * * * * * *
50590 AAAAGAGTGCTACAGAGTTGTGGGCTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGACTTGTGGACTTAAAAGGAAAAAAGATGCCACAGACTTATGGACTT
* *
50651 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAA-ATGCCACAGACTTATGGGCTTT
1 AAAAGGGTGCCACAGACTTGTGGACTTAAAAGGAAAAAAGATGCCACAGACTTATGGAC-TT
** * *
50712 TGAAGGTTGCCACTGACTTGTGG
1 AAAAGGGTGCCACAGACTTGTGG
50735 GCTTTTGAAG
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
60 14 0.20
61 56 0.80
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (61 bp):
AAAAGGGTGCCACAGACTTGTGGACTTAAAAGGAAAAAAGATGCCACAGACTTATGGACTT
Found at i:51035 original size:21 final size:21
Alignment explanation
Indices: 50988--51045 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
50978 AAAATTTATC
*
50988 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
51009 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
51030 CAAATGTATCGATACA
1 CAAATGTATCGATACA
51046 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:51174 original size:13 final size:13
Alignment explanation
Indices: 51156--51181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51146 CATTTTTCTA
51156 TGTATCGATACAT
1 TGTATCGATACAT
51169 TGTATCGATACAT
1 TGTATCGATACAT
51182 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:53672 original size:54 final size:50
Alignment explanation
Indices: 53549--53674 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 50
53539 CTCAATTCTC
* * * * *
53549 CACAATCGGGGATATTCAAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
*
53599 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAACA-CAAATTTT
53654 CACAATCGGGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
53675 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.02
51 31 0.48
54 24 0.38
55 8 0.12
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
Found at i:53688 original size:27 final size:28
Alignment explanation
Indices: 53658--53732 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 28
53648 AATTTTCACA
53658 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
53685 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
53713 -TGAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
53733 AACTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:53791 original size:51 final size:52
Alignment explanation
Indices: 53718--53836 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 52
53708 ATTTCTGAGG
* * * * * *
53718 GGATACTCCAACCCCAACTTTATTTCCAAAATATTGATTTTT-CATAATCGA
1 GGATACTCCAACCCCGACTTTATTGCCAAAACACTAATTTTTCCACAATCGA
* * * *
53769 GGATACTCCAACCCCGATTTTATTGCTAAAACCCTAATTTTTCCACAATCGC
1 GGATACTCCAACCCCGACTTTATTGCCAAAACACTAATTTTTCCACAATCGA
53821 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
53837 GTGATGATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 34 0.60
52 23 0.40
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.30
Consensus pattern (52 bp):
GGATACTCCAACCCCGACTTTATTGCCAAAACACTAATTTTTCCACAATCGA
Found at i:62189 original size:20 final size:20
Alignment explanation
Indices: 62164--62217 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
62154 GTTAGAAGCA
*
62164 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
62184 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
62204 ATGTATCGATACAA
1 ATGTATCGATACAA
62218 ACTGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:64341 original size:22 final size:24
Alignment explanation
Indices: 64311--64354 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
64301 CCTCACAATC
*
64311 TCTTCAAGA-ATTGTACCCCAAAT
1 TCTTCAAGAGATTGTAACCCAAAT
64334 TCTT-AAGAGATTGTAACCCAA
1 TCTTCAAGAGATTGTAACCCAA
64355 GGTTGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (24 bp):
TCTTCAAGAGATTGTAACCCAAAT
Found at i:64776 original size:13 final size:13
Alignment explanation
Indices: 64758--64784 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64748 ACTTTTTTCC
64758 ATGTATTGATACA
1 ATGTATTGATACA
64771 ATGTATTGATACA
1 ATGTATTGATACA
64784 A
1 A
64785 ATGTCCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:64891 original size:13 final size:13
Alignment explanation
Indices: 64873--64928 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 13
64863 TATATTGAGC
64873 ATGTATCGATAGA
1 ATGTATCGATAGA
64886 ATGTATCGATATAATGA
1 ATGTATCG--AT-A-GA
64903 GCATGTATCGATAGA
1 --ATGTATCGATAGA
64918 ATGTATCGATA
1 ATGTATCGATA
64929 CAAAGCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 19 0.51
15 4 0.11
16 2 0.05
17 4 0.11
19 8 0.22
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (13 bp):
ATGTATCGATAGA
Found at i:64895 original size:32 final size:32
Alignment explanation
Indices: 64854--64928 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
64844 ACAATTGAGT
*
64854 ATGTATCGATATATTGAGCATGTATCGATAGA
1 ATGTATCGATATAATGAGCATGTATCGATAGA
64886 ATGTATCGATATAATGAGCATGTATCGATAGA
1 ATGTATCGATATAATGAGCATGTATCGATAGA
64918 ATGTATCGATA
1 ATGTATCGATA
64929 CAAAGCATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (32 bp):
ATGTATCGATATAATGAGCATGTATCGATAGA
Found at i:64920 original size:19 final size:19
Alignment explanation
Indices: 64833--64920 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
64823 TTGCCAGTTT
* *
64833 CATGTATCGACACAATTGAG
1 CATGTATCGATATAA-TGAG
* *
64853 TATGTATCGATATATTGAG
1 CATGTATCGATATAATGAG
64872 CATGTATCG--AT-A-GA-
1 CATGTATCGATATAATGAG
64886 -ATGTATCGATATAATGAG
1 CATGTATCGATATAATGAG
*
64904 CATGTATCGATAGAATG
1 CATGTATCGATATAATG
64921 TATCGATACA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
13 8 0.15
15 4 0.07
16 1 0.02
17 4 0.07
19 27 0.49
20 11 0.20
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (19 bp):
CATGTATCGATATAATGAG
Found at i:70231 original size:13 final size:13
Alignment explanation
Indices: 70213--70239 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70203 CAATTTGTCC
70213 ATGTATCGATACA
1 ATGTATCGATACA
70226 ATGTATCGATACA
1 ATGTATCGATACA
70239 A
1 A
70240 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:72862 original size:20 final size:20
Alignment explanation
Indices: 72837--72874 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
72827 CTATAGACCC
72837 TAATTCATATCA-AACAAACA
1 TAATTCA-ATCATAACAAACA
72857 TAATTCAATCATAACAAA
1 TAATTCAATCATAACAAA
72875 TATCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
TAATTCAATCATAACAAACA
Done.