Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 9 of 168
Found at i:2554592 original size:44 final size:45
Alignment explanation
Indices: 2554543--2554629 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
2554533 ATATTTTGAA
*
2554543 TATTTTGATATTATTTTATGTAAAAAAATAGAAA-TTT-TTTGAGT
1 TATTTTGATATTATTTAATGTAAAAAAATA-AAAGTTTATTTGAGT
*
2554587 TATTTTGATATTATTTAATGTAATAAAATAAAAGTTTATTTGA
1 TATTTTGATATTATTTAATGTAAAAAAATAAAAGTTTATTTGA
2554630 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 31 0.79
45 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTAATGTAAAAAAATAAAAGTTTATTTGAGT
Found at i:2554632 original size:25 final size:25
Alignment explanation
Indices: 2554597--2554689 Score: 168
Period size: 25 Copynumber: 3.7 Consensus size: 25
2554587 TATTTTGATA
* *
2554597 TTATTTAATGTAATAAAATAAAAGT
1 TTATTTGATGTAATAAAATAGAAGT
2554622 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
2554647 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
2554672 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
2554690 ACCCTAACTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:2554741 original size:30 final size:30
Alignment explanation
Indices: 2554705--2554800 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
2554695 AACTTAATTT
2554705 AACCCTAAACCCTAACCTAAATTAATTAAA
1 AACCCTAAACCCTAACCTAAATTAATTAAA
* *
2554735 AACCCTAACCCCTAACCTAAATTAATTACA
1 AACCCTAAACCCTAACCTAAATTAATTAAA
* *
2554765 AA-CCTTAACCCTAACCTAATTTAATTAAA
1 AACCCTAAACCCTAACCTAAATTAATTAAA
2554794 AACCCTA
1 AACCCTA
2554801 CACCATTAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 25 0.43
30 33 0.57
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (30 bp):
AACCCTAAACCCTAACCTAAATTAATTAAA
Found at i:2554745 original size:29 final size:29
Alignment explanation
Indices: 2554705--2555240 Score: 271
Period size: 29 Copynumber: 19.3 Consensus size: 29
2554695 AACTTAATTT
*
2554705 AACCCTAAACCCTAACCTAAATTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
* *
2554735 AACCCTAACCCCTAACCTAAATTAATTACA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
*
2554765 AACCTTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
2554794 AACCCT-A--C--ACC--A-TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
2554816 AACCCTAACCTTAACCTAATTTAATTACA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
2554845 AATCCTAAACCCT----T-A---ACTTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
2554867 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
2554896 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* * ****
2554925 AACCCTAAACCCTAAACCTTAAACCCCTAAACCCTA
1 AACCCT-AACCCT-AACC-T-AA---TTTAATTAAA
*
2554961 AACCCTAAAGCTCTAACCCTAACCTAATTTAATTAAA
1 AACCCT-AA-CCCTAA-CC-----TAATTTAATTAAA
** *
2554998 AACCCTAACCC-AATTTAATTTATTTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
2555026 AACCCTAACGCTAA--T--TGTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
2555051 ACCCCTAA----A--CT--CTTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* **
2555073 AATCCTAACATTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
2555102 AACCCTAAACCCT----T-A---ACTTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
2555124 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
2555153 AACCCT-A----AA-CT--CTTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
*
2555175 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
2555204 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
2555233 AACTCTAA
1 AACCCTAA
2555241 ACCTTTAACT
Statistics
Matches: 393, Mismatches: 52, Indels: 123
0.69 0.09 0.22
Matches are distributed among these distances:
21 23 0.06
22 56 0.14
23 4 0.01
24 5 0.01
25 19 0.05
26 6 0.02
27 6 0.02
28 28 0.07
29 141 0.36
30 59 0.15
31 4 0.01
32 1 0.00
33 2 0.01
34 2 0.01
35 2 0.01
36 17 0.04
37 15 0.04
40 2 0.01
41 1 0.00
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:2554817 original size:22 final size:20
Alignment explanation
Indices: 2554785--2554830 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
2554775 CTAACCTAAT
2554785 TTAA-TTAAAAACCCTACACC
1 TTAACTTAAAAACCCTA-ACC
2554805 ATTAACTTAAAAACCCTAACC
1 -TTAACTTAAAAACCCTAACC
2554826 TTAAC
1 TTAAC
2554831 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 7 0.29
22 12 0.50
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:2554825 original size:51 final size:50
Alignment explanation
Indices: 2554756--2555211 Score: 412
Period size: 51 Copynumber: 8.9 Consensus size: 50
2554746 CTAACCTAAA
* * * *
2554756 TTAA-TTACAAACCTTAACCCTAACCTAATTTAATTAAAAACCCTACACC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC
* *
2554805 ATTAACTTAAAAACCCTAACCTTAACCTAATTTAATTACAAATCCTAAACCC
1 -TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAA-CC
2554857 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCT-AACC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC
* ***** * * *
2554906 TTAACCTAATTTAATTAAAAACCCTAAACCCTAA---ACCTT-AAACCCCTAAACCC
1 TTAACTTAA---AAACCCTAA-CCTTAA-CCTAATTTA-ATTAAAAACCCTAAA-CC
* * * * * *
2554959 TAAACCCT-AAAGCTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCC
1 TTAA-CTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC
* * * *
2555009 AATTTAATTTATTTAAA----AACCCTAACGCTAATTGTAATTAAAACCCCTAAACTC
1 ---TTAACTTA--AAAACCCTAACCTTAAC-CTAATT-TAATTAAAAACCCTAAAC-C
* *
2555063 TTAACTTAAAAATCCTAACATTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAA-CC
2555114 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACTC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAAC-C
2555165 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
2555212 CCCTAACCTA
Statistics
Matches: 334, Mismatches: 42, Indels: 59
0.77 0.10 0.14
Matches are distributed among these distances:
48 5 0.01
49 17 0.05
50 15 0.04
51 225 0.67
52 24 0.07
53 37 0.11
54 9 0.03
55 2 0.01
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.29
Consensus pattern (50 bp):
TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC
Found at i:2554936 original size:7 final size:7
Alignment explanation
Indices: 2554924--2554982 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
2554914 ATTTAATTAA
2554924 AAACCCT
1 AAACCCT
2554931 AAACCCT
1 AAACCCT
*
2554938 AAACCTT
1 AAACCCT
2554945 AAACCCCT
1 AAA-CCCT
2554953 AAACCCT
1 AAACCCT
2554960 AAACCCT
1 AAACCCT
*
2554967 AAAGCTCT
1 AAA-CCCT
2554975 -AACCCT
1 AAACCCT
2554981 AA
1 AA
2554983 CCTAATTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 3 0.07
7 33 0.73
8 9 0.20
ACGTcount: A:0.42, C:0.39, G:0.02, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:2554954 original size:22 final size:22
Alignment explanation
Indices: 2554927--2554982 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2554917 TAATTAAAAA
*
2554927 CCCTAAACCCTAAACCTTAAAC
1 CCCTAAACCCTAAACCCTAAAC
*
2554949 CCCTAAACCCTAAACCCTAAAG
1 CCCTAAACCCTAAACCCTAAAC
*
2554971 CTCT-AACCCTAA
1 CCCTAAACCCTAA
2554983 CCTAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.39, C:0.41, G:0.02, T:0.18
Consensus pattern (22 bp):
CCCTAAACCCTAAACCCTAAAC
Found at i:2555122 original size:22 final size:20
Alignment explanation
Indices: 2555093--2555189 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 20
2555083 TTAACCTAAT
2555093 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
2555114 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
2555134 TTAACCTAATTTAATTAAAAACCCTAAACTC
1 TTAA-C--------TTAAAAACCCT-AAC-C
2555165 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
2555185 TTAAC
1 TTAAC
2555190 CTAATTTAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
20 12 0.19
21 10 0.16
22 22 0.34
29 11 0.17
30 4 0.06
31 5 0.08
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:2555247 original size:21 final size:21
Alignment explanation
Indices: 2555223--2555266 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2555213 CCTAACCTAA
*
2555223 TTTAA-TTAAAAACTCTAAACC
1 TTTAACTTAAAAACCCT-AACC
2555244 TTTAACTTAAAAACCCTAACC
1 TTTAACTTAAAAACCCTAACC
2555265 TT
1 TT
2555267 AACGTAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTAACTTAAAAACCCTAACC
Found at i:2555254 original size:102 final size:102
Alignment explanation
Indices: 2554834--2555269 Score: 437
Period size: 102 Copynumber: 4.3 Consensus size: 102
2554824 CCTTAACCTA
* *
2554834 ATTTAATTACAAATCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAC
1 ATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAC
*
2554899 CCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC
66 CCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
* * * * * * * *
2554936 -CTAAACCTT-AAACCCCTAAACCCTAAACCCT-AAAGCTCTAACCCTAACCTAATTTAATTAAA
1 ATTTAA--TTAAAAACCCTAAACCCTTAA-CTTAAAAACCCTAACCTTAACCTAATTTAATTAAA
** *
2554998 AACCCTAACCC-AATTTAATTTATTTAAAAACCCT-AACGC
63 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAC-C
* * * *
2555037 TAATTGTAATTAAAACCCCTAAACTCTTAACTTAAAAATCCTAACATTAACCTAATTTAATTAAA
1 --ATT-TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAA
* ***** *
2555102 AACCCTAAACCCTTAACTTAA---AAACCCTAA-CCTTAACC
63 AACCCT-AACCC-TAACCTAATTTAATTAAAAACCCTAAACC
*
2555140 TAATTTAATTAAAAACCCTAAACTCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAA
1 --ATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAA
*
2555205 ACCCTAACCCTAACCTAATTTAATTAAAAACTCTAAACC
64 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
2555244 -TTTAACTTAAAAACCCT-AA-CCTTAAC
1 ATTTAA-TTAAAAACCCTAAACCCTTAAC
2555270 GTAATGTTAG
Statistics
Matches: 272, Mismatches: 43, Indels: 40
0.77 0.12 0.11
Matches are distributed among these distances:
100 16 0.06
101 36 0.13
102 125 0.46
103 21 0.08
104 61 0.22
105 7 0.03
107 6 0.02
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (102 bp):
ATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAC
CCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
Found at i:2556766 original size:126 final size:125
Alignment explanation
Indices: 2556455--2556832 Score: 566
Period size: 126 Copynumber: 3.0 Consensus size: 125
2556445 CCCAATCATG
*
2556455 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
2556520 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* *
2556579 CTACTGTAGCAAAAGCGC--AC-TGACGAGGCTGCGATTTCAAAAATTCTTCTCAAATAGCATCC
1 CTACTGTAGCAAAAGCGCGTCCATGA-G-GGC-GCGATTTCACAAATTCTTCTCAAATAGCATCC
* * *
2556641 TGCTAGAAGCGATTTTATACTATTTGCTCAGAATCGTCAAAAAAATAATTATTTCTTCCGTGAT
63 TGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCATGAC
2556705 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *** *
2556770 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
2556830 CTA
1 CTA
2556833 AAAACCCTTA
Statistics
Matches: 227, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
121 2 0.01
122 2 0.01
123 3 0.01
124 85 0.37
125 24 0.11
126 103 0.45
127 3 0.01
128 2 0.01
129 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:2561008 original size:20 final size:20
Alignment explanation
Indices: 2560983--2561023 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2560973 ATGTTGCCAT
2560983 TTATTGTCCTTGAGAGGTAG
1 TTATTGTCCTTGAGAGGTAG
2561003 TTATTGTCCTTGAGAGGTAG
1 TTATTGTCCTTGAGAGGTAG
2561023 T
1 T
2561024 CAACTAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (20 bp):
TTATTGTCCTTGAGAGGTAG
Found at i:2562454 original size:76 final size:76
Alignment explanation
Indices: 2562328--2562477 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
2562318 GCTAGTCTTC
* * * *
2562328 AAGAAACTCAATAATGATTCCGATACTCAAGCAACCGGCAGTCAAGAAGCTTTATCTCAGACTGT
1 AAGAAACTCAACAATGATTCCGATACTCAAGCAACCGACAGTCAAGAAGCTTCATCACAGACTGT
2562393 CTGAAAGTTGG
66 CTGAAAGTTGG
* ** ** * * *
2562404 AAGAAACTCGACAATGATTTGGATACTTGAGCAACTGACAGTCGAGAAGCTTCATCACAGTCTGT
1 AAGAAACTCAACAATGATTCCGATACTCAAGCAACCGACAGTCAAGAAGCTTCATCACAGACTGT
2562469 CTGAAAGTT
66 CTGAAAGTT
2562478 AATAACTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (76 bp):
AAGAAACTCAACAATGATTCCGATACTCAAGCAACCGACAGTCAAGAAGCTTCATCACAGACTGT
CTGAAAGTTGG
Found at i:2564192 original size:16 final size:16
Alignment explanation
Indices: 2564160--2564197 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2564150 AACCCTTTAA
2564160 AAATTA-TAAAGATAT
1 AAATTATTAAAGATAT
2564175 AAATTATTAAA-ATGAT
1 AAATTATTAAAGAT-AT
2564191 AAATTAT
1 AAATTAT
2564198 ATTTTTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (16 bp):
AAATTATTAAAGATAT
Found at i:2567205 original size:103 final size:103
Alignment explanation
Indices: 2567018--2567210 Score: 273
Period size: 103 Copynumber: 1.9 Consensus size: 103
2567008 AAGAAAGTAT
* *
2567018 ATTAATTTGGCATAAAAACGAAAAATAGTTTGAACTTTGAGGCTTATATAAGAAAATAGAAAAGA
1 ATTAATTTGGCATAAAAACGAAAAAAAATTTGAACTTTGAGGCTTATATAAGAAAATAGAAAAGA
*
2567083 CCCATTTCAAGTTTGAAGCTTGAAACCAGAAACAGAGA
66 CCCATTTCAAGTTTAAAGCTTGAAACCAGAAACAGAGA
* * * * *
2567121 ATTATTTTGGCATAAACAC-AACAAAAAATTTGAACTTTGAGGCTTATATAAGCAAATGGAGAAG
1 ATTAATTTGGCATAAAAACGAA-AAAAAATTTGAACTTTGAGGCTTATATAAGAAAATAGAAAAG
*
2567185 ACACGA-TTCAAGTTTAAAGCTTGAAA
65 AC-CCATTTCAAGTTTAAAGCTTGAAA
2567211 TTCAATTACC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
102 2 0.03
103 75 0.95
104 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (103 bp):
ATTAATTTGGCATAAAAACGAAAAAAAATTTGAACTTTGAGGCTTATATAAGAAAATAGAAAAGA
CCCATTTCAAGTTTAAAGCTTGAAACCAGAAACAGAGA
Found at i:2570256 original size:195 final size:195
Alignment explanation
Indices: 2569917--2570312 Score: 756
Period size: 195 Copynumber: 2.0 Consensus size: 195
2569907 AAATTTAAGT
2569917 ATCTATATGGGGATGTATTTGTACCCGATACTCATCCCATAACCAAATAACATAGGTTAGTTATT
1 ATCTATATGGGGATGTATTTGTACCCGATACTCATCCCATAACCAAATAACATAGGTTAGTTATT
2569982 GGTAATAGTACCATGGAGGCCCATGAATTATGATTTAGATTGCATATTGAACCATTTATTCAAAA
66 GGTAATAGTACCATGGAGGCCCATGAATTATGATTTAGATTGCATATTGAACCATTTATTCAAAA
*
2570047 AATGAGTAAATTAGTCTTTGAACATTAGATCAAAGAGTAAACCGTTCCTTTTTATTAAAAATTCC
131 AATGAGTAAATTAGTCTTTGAACATTACATCAAAGAGTAAACCGTTCCTTTTTATTAAAAATTCC
* *
2570112 ATCTATGTGGGGATGTATTTGTACCCGATACTCATCCCATAACTAAATAACATAGGTTAGTTATT
1 ATCTATATGGGGATGTATTTGTACCCGATACTCATCCCATAACCAAATAACATAGGTTAGTTATT
2570177 GGTAATAGTACCATGGAGGCCCATGAATTATGATTTAGATTGCATATTGAACCATTTATTCAAAA
66 GGTAATAGTACCATGGAGGCCCATGAATTATGATTTAGATTGCATATTGAACCATTTATTCAAAA
*
2570242 AATGAGTAAATTAGTCTTTGAACATTACATGAAAGAGTAAACCGTTCCTTTTTATTAAAAATTCC
131 AATGAGTAAATTAGTCTTTGAACATTACATCAAAGAGTAAACCGTTCCTTTTTATTAAAAATTCC
2570307 ATCTAT
1 ATCTAT
2570313 TTTTACTGTT
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 197 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (195 bp):
ATCTATATGGGGATGTATTTGTACCCGATACTCATCCCATAACCAAATAACATAGGTTAGTTATT
GGTAATAGTACCATGGAGGCCCATGAATTATGATTTAGATTGCATATTGAACCATTTATTCAAAA
AATGAGTAAATTAGTCTTTGAACATTACATCAAAGAGTAAACCGTTCCTTTTTATTAAAAATTCC
Found at i:2578537 original size:11 final size:11
Alignment explanation
Indices: 2578523--2578562 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2578513 TATTTTTTAT
2578523 TATTTTACTAC
1 TATTTTACTAC
*
2578534 TATTTTACTAT
1 TATTTTACTAC
* *
2578545 TATGTTCCTAC
1 TATTTTACTAC
2578556 TATTTTA
1 TATTTTA
2578563 TTATTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (11 bp):
TATTTTACTAC
Found at i:2578545 original size:22 final size:22
Alignment explanation
Indices: 2578512--2578570 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
2578502 CTTTTTTTTG
2578512 CTATTTT-TTATTATTTTACTA
1 CTATTTTATTATTATTTTACTA
* * *
2578533 CTATTTTACTATTATGTTCCTA
1 CTATTTTATTATTATTTTACTA
2578555 CTATTTTATTATTATT
1 CTATTTTATTATTATT
2578571 GTTTAGATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.63
Consensus pattern (22 bp):
CTATTTTATTATTATTTTACTA
Found at i:2581639 original size:14 final size:14
Alignment explanation
Indices: 2581620--2581654 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2581610 TGACATTTTT
* *
2581620 TTCTAATGATATTA
1 TTCTAACGATACTA
2581634 TTCTAACGATACTA
1 TTCTAACGATACTA
2581648 TTCTAAC
1 TTCTAAC
2581655 ATGTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:2582913 original size:14 final size:14
Alignment explanation
Indices: 2582894--2582922 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2582884 TGGAACAAAC
2582894 TTTGTAATATAAAT
1 TTTGTAATATAAAT
2582908 TTTGTAATATAAAT
1 TTTGTAATATAAAT
2582922 T
1 T
2582923 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:2582950 original size:62 final size:62
Alignment explanation
Indices: 2582865--2583094 Score: 370
Period size: 62 Copynumber: 3.7 Consensus size: 62
2582855 CAACATTATA
* * *
2582865 ACATTACAAGATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* * *
2582927 ACATTACAATATTAAAAATTGGAACAAAATTTGTAATATAAATTTTTTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
2582989 ACATTACAACATTAAAAATTAGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* * *
2583051 ACATTATAACATTAAAACTTGGAGCAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
2583095 AGGTACATTG
Statistics
Matches: 155, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 155 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.37
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:2588603 original size:22 final size:22
Alignment explanation
Indices: 2588573--2588640 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
2588563 TATGCACTAT
2588573 TAAACAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAAAGTGC
* *
2588595 TATATAGAGAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAA-GTGC
* *
2588617 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAAAGTGC
2588639 TA
1 TA
2588641 CTAATCGGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 3 0.08
22 33 0.87
23 2 0.05
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:2588670 original size:25 final size:25
Alignment explanation
Indices: 2588621--2588670 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2588611 ATGTGCTAAA
* * *
2588621 CGGAGAGCACTAATGTGCTACTAAT
1 CGGAGAGCACTAACGTGATAATAAT
*
2588646 CGGAGAGTACTAACGTGATAATAAT
1 CGGAGAGCACTAACGTGATAATAAT
2588671 TAGAGAGCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (25 bp):
CGGAGAGCACTAACGTGATAATAAT
Found at i:2589371 original size:34 final size:35
Alignment explanation
Indices: 2589332--2589401 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
2589322 TAATTAACTA
*
2589332 TACTATCTCATTTTCCACATCAAATTTCTAT-TAT
1 TACTATCTCATTTTCCACACCAAATTTCTATGTAT
2589366 TACTATCTCATTTTCCACACCAAATTTCTATGTAT
1 TACTATCTCATTTTCCACACCAAATTTCTATGTAT
2589401 T
1 T
2589402 TCACTTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.29, C:0.24, G:0.01, T:0.46
Consensus pattern (35 bp):
TACTATCTCATTTTCCACACCAAATTTCTATGTAT
Found at i:2589592 original size:2 final size:2
Alignment explanation
Indices: 2589585--2589609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2589575 TATTTCACAC
2589585 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2589610 TACTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2591056 original size:34 final size:34
Alignment explanation
Indices: 2591018--2591175 Score: 165
Period size: 34 Copynumber: 4.6 Consensus size: 34
2591008 TTCTAATATG
* *
2591018 ATATGACGTTCTGATATGATATATGTTTATGAAA
1 ATATGACATTCTGATATGATATATGTTTCTGAAA
* * * * *
2591052 ATATGAAATTATGATCTGGTATATGTTTCTGGAA
1 ATATGACATTCTGATATGATATATGTTTCTGAAA
* * * *
2591086 ATATGACATTTTGATCTGGTATATGTTTCTGGAA
1 ATATGACATTCTGATATGATATATGTTTCTGAAA
* * *
2591120 ATATGACATTTTGATTTGATATATGTTTCT-AGTA
1 ATATGACATTCTGATATGATATATGTTTCTGA-AA
*
2591154 ATGTGACATTCTGATATGATAT
1 ATATGACATTCTGATATGATAT
2591176 TCGTATATGT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
34 107 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (34 bp):
ATATGACATTCTGATATGATATATGTTTCTGAAA
Found at i:2591143 original size:68 final size:68
Alignment explanation
Indices: 2591018--2591175 Score: 199
Period size: 68 Copynumber: 2.3 Consensus size: 68
2591008 TTCTAATATG
* * *
2591018 ATATGACGTTCTGATATGATATATGTTTATGAAAATATGAAATTATGATCTGGTATATGTTTCTG
1 ATATGACATTCTGATATGATATATGTTTATGAAAATATGAAATTATGATCTGATATATGTTTCTA
2591083 GAA
66 GAA
* * * * * * * *
2591086 ATATGACATTTTGATCTGGTATATGTTTCTGGAAATATGACATTTTGATTTGATATATGTTTCTA
1 ATATGACATTCTGATATGATATATGTTTATGAAAATATGAAATTATGATCTGATATATGTTTCTA
*
2591151 GTA
66 GAA
*
2591154 ATGTGACATTCTGATATGATAT
1 ATATGACATTCTGATATGATAT
2591176 TCGTATATGT
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (68 bp):
ATATGACATTCTGATATGATATATGTTTATGAAAATATGAAATTATGATCTGATATATGTTTCTA
GAA
Found at i:2594342 original size:13 final size:14
Alignment explanation
Indices: 2594318--2594355 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2594308 TGTTTCACTG
2594318 AAAATGACTTTC-GA
1 AAAATGA-TTTCTGA
2594332 AAAATGATTTCTGA
1 AAAATGATTTCTGA
*
2594346 AAAATAATTT
1 AAAATGATTT
2594356 TATTGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:2594990 original size:25 final size:25
Alignment explanation
Indices: 2594951--2595000 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2594941 ACATATTAAA
2594951 TAATTTATTAGATAATAATTTATAT
1 TAATTTATTAGATAATAATTTATAT
**
2594976 TAATTATATTA-ATAATTTTTTATAT
1 TAATT-TATTAGATAATAATTTATAT
2595001 GATTAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TAATTTATTAGATAATAATTTATAT
Found at i:2596784 original size:30 final size:30
Alignment explanation
Indices: 2596750--2596855 Score: 121
Period size: 30 Copynumber: 3.5 Consensus size: 30
2596740 TTTAAAATAT
2596750 ATATATTTTTATGTTTAAAATATATATTAA
1 ATATATTTTTATGTTTAAAATATATATTAA
*
2596780 ATATATATATTTATGTTTAAAATATACTAGTTTA
1 ATATAT-T-TTTATGTTTAAAATATA-TA-TTAA
* *
2596814 A-GT-TTTTTATGTTTAAAATATATA-TAT
1 ATATATTTTTATGTTTAAAATATATATTAA
2596841 ATATA-TTTTATGTTT
1 ATATATTTTTATGTTT
2596856 TAGTTTTAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.03
28 11 0.17
29 2 0.03
30 23 0.35
31 2 0.03
32 18 0.28
33 3 0.05
34 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.55
Consensus pattern (30 bp):
ATATATTTTTATGTTTAAAATATATATTAA
Found at i:2596793 original size:32 final size:30
Alignment explanation
Indices: 2596748--2596855 Score: 118
Period size: 32 Copynumber: 3.6 Consensus size: 30
2596738 CGTTTAAAAT
2596748 ATATATATTTTTATGTTTAAAATATATATTAA
1 ATATATA-TTTTATGTTTAAAATATATATT-A
2596780 ATATATATATTTATGTTTAAAATATACTAGTT-
1 ATATATAT-TTTATGTTTAAAATATA-TA-TTA
*
2596812 -TA-AGTTTTTTATGTTTAAAATATATA-T-
1 ATATA-TATTTTATGTTTAAAATATATATTA
2596839 ATATATATTTTATGTTT
1 ATATATATTTTATGTTT
2596856 TAGTTTTAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
27 1 0.01
28 13 0.19
29 3 0.04
30 18 0.26
31 5 0.07
32 24 0.35
33 2 0.03
34 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.55
Consensus pattern (30 bp):
ATATATATTTTATGTTTAAAATATATATTA
Found at i:2596813 original size:21 final size:20
Alignment explanation
Indices: 2596776--2596818 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2596766 AAAATATATA
*
2596776 TTAAATATATATATTTATGT
1 TTAAATATATATATTTAAGT
2596796 TTAAA-ATATACTAGTTTAAGT
1 TTAAATATATA-TA-TTTAAGT
2596817 TT
1 TT
2596819 TTTATGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (20 bp):
TTAAATATATATATTTAAGT
Found at i:2596869 original size:12 final size:13
Alignment explanation
Indices: 2596846--2596874 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2596836 TATATATATA
2596846 TTTTATGTTTTAG
1 TTTTATGTTTTAG
2596859 TTTTA-GTTTTAG
1 TTTTATGTTTTAG
2596871 TTTT
1 TTTT
2596875 TTTATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (13 bp):
TTTTATGTTTTAG
Found at i:2597072 original size:9 final size:9
Alignment explanation
Indices: 2597058--2597092 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2597048 TTTTGTTACA
2597058 ACAATTAAT
1 ACAATTAAT
2597067 ACAATT-A-
1 ACAATTAAT
2597074 ACAATTAAT
1 ACAATTAAT
2597083 ACAATTAAT
1 ACAATTAAT
2597092 A
1 A
2597093 ATTTGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.25
8 2 0.08
9 16 0.67
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2597078 original size:16 final size:16
Alignment explanation
Indices: 2597057--2597095 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2597047 ATTTTGTTAC
2597057 AACAATTAATACAATT
1 AACAATTAATACAATT
2597073 AACAATTAATACAATT
1 AACAATTAATACAATT
*
2597089 AATAATT
1 AACAATT
2597096 TGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:2597186 original size:16 final size:16
Alignment explanation
Indices: 2597165--2597206 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2597155 AATAATTTGA
*
2597165 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2597181 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2597197 TAGTTTTAAT
1 TAATTTTAAT
2597207 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2599719 original size:2 final size:2
Alignment explanation
Indices: 2599652--2599704 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2599642 ACACACACAG
*
2599652 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2599694 AT AT AT AT AT A
1 AT AT AT AT AT A
2599705 AGTTTCAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2602331 original size:21 final size:20
Alignment explanation
Indices: 2602296--2602334 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2602286 AATTATAAAC
*
2602296 TATAAAAATATATATGTACA
1 TATAAAAAAATATATGTACA
2602316 TATAAGAAAAATATATGTA
1 TATAA-AAAAATATATGTA
2602335 TGTGTAAAAG
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:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TATAAAAAAATATATGTACA
Found at i:2604466 original size:88 final size:89
Alignment explanation
Indices: 2604354--2604688 Score: 453
Period size: 88 Copynumber: 3.8 Consensus size: 89
2604344 CGCTAGCGAT
* * * * *
2604354 ATAAAATTTGCTGCCTTCAGCTTTAATCTACTCCGCTACAATGCCAAGA-AAAATAAGACTCGCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACGCCAAGAGAAAAGAAGACTCGCT
* *
2604418 ATCTTCAGTCTTAACGCCAAGGAG
66 GTCTTCTGTCTTAACGCCAAGGAG
* * *
2604442 AGAAGATTCGCTGCCTTCAGCTTTAATTTGCTCCGCTACAACGCC-AGGGAAAAGAAGACTCGCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACGCCAAGAGAAAAGAAGACTCGCT
* * * *
2604506 GTCTTCTTTCTTAAGGTCAGGGAG
66 GTCTTCTGTCTTAACGCCAAGGAG
* * **
2604530 ATAAGATTCGCTACCTTTAGCTTTAATCTGCTCCATTACAACGCC-AGAGAAAAGAAGACTCGCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACGCCAAGAGAAAAGAAGACTCGCT
*
2604594 GTCTTCTGTCTTAACGCTAAGGAG
66 GTCTTCTGTCTTAACGCCAAGGAG
* *
2604618 ATAAAATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAATGCCAA-AGAAAAGAAGACTCGCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACGCCAAGAGAAAAGAAGACTCGCT
2604682 GTCTTCT
66 GTCTTCT
2604689 TCAAACTATT
Statistics
Matches: 213, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
87 2 0.01
88 210 0.99
89 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (89 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACGCCAAGAGAAAAGAAGACTCGCT
GTCTTCTGTCTTAACGCCAAGGAG
Found at i:2613716 original size:3 final size:3
Alignment explanation
Indices: 2613708--2613825 Score: 74
Period size: 3 Copynumber: 39.3 Consensus size: 3
2613698 AATTTTAATC
* ** * * * **
2613708 ATT ATT ATT ACT CCT ATT ACT ATT ATT TTT ATT ATT ACT CGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
2613756 ATT TTT ATT TTT ACT ACT ATT ATT ATT ATC ATT ATT ATC GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
2613804 ATT ATT AAT ATC ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
2613826 GTTACTCATT
Statistics
Matches: 86, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2613745 original size:27 final size:26
Alignment explanation
Indices: 2613709--2613793 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 26
2613699 ATTTTAATCA
2613709 TTATTATTACTCCTATTACTATTATTT
1 TTATTATTACTCCTATTA-TATTATTT
*
2613736 TTATTATTACTCGTA-T-TATTATTT
1 TTATTATTACTCCTATTATATTATTT
* * **
2613760 TTATTTTTACTACTATTATTATTATCA
1 TTATTATTACTCCTATTA-TATTATTT
2613787 TTATTAT
1 TTATTAT
2613794 CGTTATTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 20 0.42
25 1 0.02
26 1 0.02
27 26 0.54
ACGTcount: A:0.27, C:0.11, G:0.01, T:0.61
Consensus pattern (26 bp):
TTATTATTACTCCTATTATATTATTT
Found at i:2614081 original size:13 final size:13
Alignment explanation
Indices: 2614052--2614089 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2614042 TTTATTTACA
*
2614052 TTATTATTA-TGT
1 TTATTATTATTTT
*
2614064 TTATTTTTATTTT
1 TTATTATTATTTT
2614077 TTATTATTATTTT
1 TTATTATTATTTT
2614090 CTTAGAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:2620645 original size:140 final size:140
Alignment explanation
Indices: 2620384--2620679 Score: 323
Period size: 140 Copynumber: 2.1 Consensus size: 140
2620374 ATAGTTTGTA
* * * *
2620384 GAAGACAGCGAGTCTTCTTTTCCCTGGCGTTATAGCGAAGCATATTAAAACTCAAGACAGCGAAT
1 GAAGGCAGCGAATCTTCTTTTCCCTGGCGTTACAGCGAAGCAGATTAAAACTCAAGACAGCGAAT
* **
2620449 CTTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCCCTGACATTGTAGCAGAGCA
66 ATTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCAATGACATTGTAGCAGAGCA
*
2620514 GATTAAAATT
131 GATTAAAACT
** *
2620524 GAAGGCAGCGAATCTTCTTTTCTCC-GGCGTTACAGCGGAA-CAGATTAAAGTTGAAGACAGCGA
1 GAAGGCAGCGAATCTTCTTTTC-CCTGGCGTTACAGC-GAAGCAGATTAAAACTCAAGACAGCGA
* * * * **
2620587 ATATTATCT-TTTTGACGTTAAGACTA-AAG-CTAGCGAGTCTTCTTTTCAATGCCGTTGTAGTG
64 ATATTATCTCCTTAG-CGTTAAGAC-AGAAGAC-AGCGAGTCTTCTTTTCAATGACATTGTAGCA
* *
2620649 GAGTAGATTAAAGCT
126 GAGCAGATTAAAACT
* *
2620664 GAAAGCAGCAAATCTT
1 GAAGGCAGCGAATCTT
2620680 ATATCCCTGG
Statistics
Matches: 130, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
139 4 0.03
140 120 0.92
141 6 0.05
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (140 bp):
GAAGGCAGCGAATCTTCTTTTCCCTGGCGTTACAGCGAAGCAGATTAAAACTCAAGACAGCGAAT
ATTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCAATGACATTGTAGCAGAGCA
GATTAAAACT
Found at i:2622506 original size:265 final size:259
Alignment explanation
Indices: 2622039--2622559 Score: 970
Period size: 265 Copynumber: 2.0 Consensus size: 259
2622029 AGATCCAGTA
2622039 TTGGGTATTAATTTTGAAAGGGGAATGTCTAATTCAAGTCAAGGGAGAACATGTGTTCGAAGACT
1 TTGGGTATTAATTTTGAAAGGGGAATGTCTAATTCAAGTCAAGGGAGAACATGTGTTCGAAGACT
2622104 TCGGCATACGCTGATGTTACATAATCCTCAATTGGTCTTCTTCATGGAGACAAATTAGAAGTCAT
66 TCGGCATACGCTGATGTTACATAATCCTCAATTGGTCTTCTTCATGGAGACAAATTAGAAGTCAT
* *
2622169 ATGGAAAGAGTTCGAAGAAGTTGTGGTTTTGTTAATGGTATTAATGTAGAATCAATTGGTTCTAG
131 ATGAAAAGAGTTCGAAGAAGTTGTGGTTTTGTTAATGGTATTAATGTAGAATCAATTGGTTCTAA
2622234 AGGTGGACTATGGTTGGCATGGAATGGGTACACTAATATTTTACTTCAAAACTTTTCAAAAGTG
196 AGGTGGACTATGGTTGGCATGGAATGGGTACACTAATATTTTACTTCAAAACTTTTCAAAAGTG
2622298 TTGGGTATTAATTTTGAAAGGGGAATGTCTAATTCAAGTCAAGGAAGGGAGAACATGTGTTCGAA
1 TTGGGTATTAATTTTGAAAGGGGAATGTCTAATTCAAGTC----AAGGGAGAACATGTGTTCGAA
2622363 GACTTCGGCATACGCTGATGTTACATAATCCTCAATTGGTCTTCTTCATGGAGACAACAATTAGA
62 GACTTCGGCATACGCTGATGTTACATAATCCTCAATTGGTCTTCTTCATGGAGAC-A-AATTAGA
2622428 AGTCATATGAAAAGAGTTCGAAGAAGTTGTGGTTTTGTTAATGGTATTAATGTAGAATCAATTGG
125 AGTCATATGAAAAGAGTTCGAAGAAGTTGTGGTTTTGTTAATGGTATTAATGTAGAATCAATTGG
2622493 TTCTAAAGGTGGACTATGGTTGGCATGGAATGGGTACACTAATATTTTACTTCAAAACTTTTCAA
190 TTCTAAAGGTGGACTATGGTTGGCATGGAATGGGTACACTAATATTTTACTTCAAAACTTTTCAA
2622558 AA
255 AA
2622560 AAGGCATATT
Statistics
Matches: 254, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
259 40 0.16
263 76 0.30
264 1 0.00
265 137 0.54
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (259 bp):
TTGGGTATTAATTTTGAAAGGGGAATGTCTAATTCAAGTCAAGGGAGAACATGTGTTCGAAGACT
TCGGCATACGCTGATGTTACATAATCCTCAATTGGTCTTCTTCATGGAGACAAATTAGAAGTCAT
ATGAAAAGAGTTCGAAGAAGTTGTGGTTTTGTTAATGGTATTAATGTAGAATCAATTGGTTCTAA
AGGTGGACTATGGTTGGCATGGAATGGGTACACTAATATTTTACTTCAAAACTTTTCAAAAGTG
Found at i:2636580 original size:42 final size:42
Alignment explanation
Indices: 2636479--2636603 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 42
2636469 CGCTTACAGA
* **
2636479 AAAAAACGCCGCT-AAAGATCATGTTCTTTAGCGGTGCTTAGG
1 AAAAAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCACTTAGG
* *
2636521 AAGAAAACGCTGCTAAAAGTAATGTTCTATAGCGGCACTT-GG
1 AA-AAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTAGG
* * *
2636563 TCAAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTA
1 -AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTA
2636604 TTTCACAAAC
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
42 37 0.54
43 28 0.41
44 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTAGG
Found at i:2637075 original size:21 final size:20
Alignment explanation
Indices: 2637051--2637115 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
2637041 GCTTCTATCG
2637051 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGC-GCCT
*
2637072 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTG-CGCCT
*
2637093 CTGCTTCCCTCGCTGTCGCCT
1 CTGCTTCTCTCGCTG-CGCCT
2637114 CT
1 CT
2637116 ACTTTAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.02, C:0.43, G:0.20, T:0.35
Consensus pattern (20 bp):
CTGCTTCTCTCGCTGCGCCT
Found at i:2641478 original size:7 final size:7
Alignment explanation
Indices: 2641460--2641499 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
2641450 TTAGCCTCTC
2641460 CATTTTT
1 CATTTTT
2641467 C-TTTTT
1 CATTTTT
2641473 CATTTTT
1 CATTTTT
2641480 CA-TTTT
1 CATTTTT
2641486 CATTTTT
1 CATTTTT
2641493 CATTTTT
1 CATTTTT
2641500 TTTTGACTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:2641478 original size:13 final size:13
Alignment explanation
Indices: 2641460--2641499 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
2641450 TTAGCCTCTC
2641460 CATTTTTCTTTTT
1 CATTTTTCTTTTT
*
2641473 CATTTTTCATTTT
1 CATTTTTCTTTTT
2641486 CATTTTTCATTTTT
1 CATTTTTC-TTTTT
2641500 TTTTGACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.72
Consensus pattern (13 bp):
CATTTTTCTTTTT
Found at i:2641483 original size:20 final size:20
Alignment explanation
Indices: 2641463--2641499 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2641453 GCCTCTCCAT
2641463 TTTTC-TTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
2641482 TTTTCATTTTTCATTTTT
1 TTTTCATTTTTCATTTTT
2641500 TTTTGACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:2642341 original size:6 final size:6
Alignment explanation
Indices: 2642330--2642367 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
2642320 TGACCTCTCC
2642330 TTTTCT TTTTCT TTTTCTT TTTTCT TCTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTC-T TTTTCT T-TTTCT TTTTCT
2642368 CCTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:2642353 original size:13 final size:13
Alignment explanation
Indices: 2642330--2642365 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
2642320 TGACCTCTCC
2642330 TTTTC-TTTTTCT
1 TTTTCTTTTTTCT
2642342 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
2642355 TCTTTCTTTTT
1 T-TTTCTTTTT
2642366 CTCCTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:2642366 original size:13 final size:12
Alignment explanation
Indices: 2642330--2642367 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
2642320 TGACCTCTCC
2642330 TTTTCTTTTTCT
1 TTTTCTTTTTCT
2642342 TTTTCTTTTTTCT
1 TTTTC-TTTTTCT
2642355 TCTTTCTTTTTCT
1 T-TTTCTTTTTCT
2642368 CCTATTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 15 0.62
14 4 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:2642409 original size:11 final size:10
Alignment explanation
Indices: 2642392--2642417 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2642382 TGATTGATTG
2642392 ATTTTTTTTT
1 ATTTTTTTTT
2642402 ATTTTTTTTT
1 ATTTTTTTTT
2642412 ATTTTT
1 ATTTTT
2642418 GATTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:2642422 original size:17 final size:15
Alignment explanation
Indices: 2642393--2642439 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
2642383 GATTGATTGA
2642393 TTTTTTTTTATTTTT
1 TTTTTTTTTATTTTT
2642408 TTTTATTTTTGATTTTT
1 TTTT-TTTTT-ATTTTT
2642425 TCTTCTTTTTT-TTTT
1 T-TT-TTTTTTATTTT
2642440 GAGTCTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 7 0.25
18 7 0.25
19 1 0.04
ACGTcount: A:0.06, C:0.04, G:0.02, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTATTTTT
Found at i:2643189 original size:17 final size:18
Alignment explanation
Indices: 2643157--2643193 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2643147 TCTACACAGT
2643157 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
2643175 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
2643192 AT
1 AT
2643194 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:2645739 original size:18 final size:18
Alignment explanation
Indices: 2645716--2645752 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2645706 CGCACGAGGA
2645716 AGGATTAGCACCCTCGAT
1 AGGATTAGCACCCTCGAT
2645734 AGGATTAGCACCCTCGAT
1 AGGATTAGCACCCTCGAT
2645752 A
1 A
2645753 CGCCCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (18 bp):
AGGATTAGCACCCTCGAT
Found at i:2647890 original size:16 final size:17
Alignment explanation
Indices: 2647858--2647897 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2647848 CTTGCTGTAA
2647858 TGGGC-TTGTTTGGATT
1 TGGGCTTTGTTTGGATT
*
2647874 TGGGCTTTGTTT-TATT
1 TGGGCTTTGTTTGGATT
2647890 TGGG-TTTG
1 TGGGCTTTG
2647898 GCATTTGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.05, C:0.05, G:0.35, T:0.55
Consensus pattern (17 bp):
TGGGCTTTGTTTGGATT
Found at i:2649375 original size:9 final size:9
Alignment explanation
Indices: 2649342--2649730 Score: 438
Period size: 9 Copynumber: 43.7 Consensus size: 9
2649332 TTAAAACGCC
2649342 AGTTATGT-
1 AGTTATGTA
2649350 A-TTATGT-
1 AGTTATGTA
2649357 A-TTATGTA
1 AGTTATGTA
2649365 AG-TACTGTA
1 AGTTA-TGTA
2649374 AGTTATGTA
1 AGTTATGTA
2649383 AGTTATGTA
1 AGTTATGTA
2649392 AGTTATGTA
1 AGTTATGTA
*
2649401 AGTTATTTA
1 AGTTATGTA
*
2649410 ATTTATGTA
1 AGTTATGTA
2649419 AGTTATGTA
1 AGTTATGTA
2649428 AGTTATGTA
1 AGTTATGTA
*
2649437 AGTTA-CTA
1 AGTTATGTA
*
2649445 CATTTATGTA
1 -AGTTATGTA
2649455 AGTTATGTA
1 AGTTATGTA
* *
2649464 AGATATTTA
1 AGTTATGTA
*
2649473 ATTTATGTA
1 AGTTATGTA
2649482 AGTTATGTA
1 AGTTATGTA
*
2649491 AGTTATTTA
1 AGTTATGTA
*
2649500 ATTTATGTA
1 AGTTATGTA
2649509 AGTTATGTA
1 AGTTATGTA
*
2649518 AGTTGCT-TA
1 AGTT-ATGTA
*
2649527 ATTTATGTA
1 AGTTATGTA
2649536 AGTTATGTA
1 AGTTATGTA
*
2649545 AGTTATTTA
1 AGTTATGTA
*
2649554 ATTTATGTA
1 AGTTATGTA
2649563 AGTTATGTA
1 AGTTATGTA
2649572 AGTTATGTA
1 AGTTATGTA
*
2649581 AGTTATTTA
1 AGTTATGTA
*
2649590 ATTTATGTA
1 AGTTATGTA
2649599 AGTTATGTA
1 AGTTATGTA
2649608 AGTTACT-TA
1 AGTTA-TGTA
*
2649617 ATTTATGTA
1 AGTTATGTA
2649626 AGTTATGTA
1 AGTTATGTA
* *
2649635 AGATATTTA
1 AGTTATGTA
* *
2649644 ATTTTTGTA
1 AGTTATGTA
2649653 AGTTATGTA
1 AGTTATGTA
2649662 AGTTACT-TA
1 AGTTA-TGTA
*
2649671 ATTTATGTA
1 AGTTATGTA
2649680 AGTTATGTA
1 AGTTATGTA
*
2649689 AGTTATTTA
1 AGTTATGTA
* *
2649698 ATTTTTGTA
1 AGTTATGTA
2649707 AGTTATGTA
1 AGTTATGTA
2649716 A-TTAATGTA
1 AGTT-ATGTA
2649725 AGTTAT
1 AGTTAT
2649731 TTAATTTGTG
Statistics
Matches: 319, Mismatches: 48, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
7 13 0.04
8 11 0.03
9 286 0.90
10 9 0.03
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (9 bp):
AGTTATGTA
Found at i:2654292 original size:14 final size:14
Alignment explanation
Indices: 2654275--2654354 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
2654265 ATCTAAACTG
2654275 TAAACCATAAACCC
1 TAAACCATAAACCC
*
2654289 TAAAATCATAAACCC
1 T-AAACCATAAACCC
* *
2654304 TTAA-CATATAACCT
1 TAAACCATA-AACCC
*
2654318 TAAACCTTAAACCC
1 TAAACCATAAACCC
* * *
2654332 -CAACCTTTAAACCA
1 TAAACC-ATAAACCC
2654346 TAAACCATA
1 TAAACCATA
2654355 GACCAAATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
13 8 0.16
14 23 0.45
15 20 0.39
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:2654341 original size:21 final size:20
Alignment explanation
Indices: 2654313--2654351 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2654303 CTTAACATAT
*
2654313 AACCTTAAACCTTAAACCCC
1 AACCTTAAACCATAAACCCC
2654333 AACCTTTAAACCATAAACC
1 AACC-TTAAACCATAAACC
2654352 ATAGACCAAA
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:0.44, C:0.36, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCTTAAACCATAAACCCC
Found at i:2654798 original size:210 final size:209
Alignment explanation
Indices: 2654417--2654877 Score: 473
Period size: 210 Copynumber: 2.2 Consensus size: 209
2654407 GGTTAAGACC
* * ** * *
2654417 AAAACTCTGCATTTTGGTTAAGATATTTTCCGGCGCTTTAATACTATGCTTTAGCGGCGATTTCT
1 AAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGC-TT--GGC-ATGATTTAGCGGCG-TTTTT
* * ** * ** * * * *
2654482 CG-T-GGACGCCACTAATTCCAGTATACATCAAGACTTAAACGCTGCGTTTTTGTTAATATATTT
61 TGATATG-CGCCACTAATAACAGTACACATCAAGACAAAAACGCTGCGTTTTGGTTAACAAATGT
* *
2654545 TGCGACGCTTCTCAAAAAGCGCCGCAAATAATATGCTTTAGCGGCGT-TCCCCCATAAGCGCCAC
125 TGCGACGCTTCTCAAAAAGCGCCGCAAATAATATACCTTAGCGGCGTGT-CCCC-TAAGCGCCAC
*
2654609 TAAGTCTAATATACCTCATGAA
188 TAAGTCTAATATACCTCAAGAA
*
2654631 AAAACTCTGCGTTTTGG-TGAGCATATTTTGCGGCGCTTGGCATGATTTAGCGGCGTTTTTTGAT
1 AAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGCTTGGCATGATTTAGCGGCGTTTTTTGAT
* * * *
2654695 ATGCGCCACTAATAACTGTACACATCAAGACAAAAACGTTGCGTTTTGGTTACCAAATGTTGCGG
65 ATGCGCCACTAATAACAGTACACATCAAGACAAAAACGCTGCGTTTTGGTTAACAAATGTTGCGA
* * * * ** * *
2654760 CGCTTCTCTGAAAA-CGCCGCTAATAGTATACCTTAGCGGCGTGTTCCCTTTGTGCCACTAATTC
130 CGCTTCTC-AAAAAGCGCCGCAAATAATATACCTTAGCGGCGTGTCCCCTAAGCGCCACTAAGTC
* *
2654824 TAGTATACCTCAAGAC
194 TAATATACCTCAAGAA
*
2654840 CAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
1 AAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
2654878 CCCAAAAAAC
Statistics
Matches: 204, Mismatches: 37, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
209 62 0.30
210 101 0.50
211 7 0.03
213 5 0.02
214 29 0.14
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (209 bp):
AAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTGGCATGATTTAGCGGCGTTTTTTGATA
TGCGCCACTAATAACAGTACACATCAAGACAAAAACGCTGCGTTTTGGTTAACAAATGTTGCGAC
GCTTCTCAAAAAGCGCCGCAAATAATATACCTTAGCGGCGTGTCCCCTAAGCGCCACTAAGTCTA
ATATACCTCAAGAA
Found at i:2655245 original size:112 final size:112
Alignment explanation
Indices: 2654984--2655269 Score: 306
Period size: 112 Copynumber: 2.5 Consensus size: 112
2654974 AGGATAGTTT
* * * * ** *
2654984 GCGGCGTTTTTCCATAAGCGCCA-TAAATTCTAACATACCTCTAGACAAAACTCTGCGTTTTGGT
1 GCGGCGTTTTTTCATAAGCGCCACT-AATTCTAATATACATCAAGACAAAACAATGCGTTTTCGT
** *
2655048 TAACATATGTTGCGGCGCTTTTTGTAAGCGCCGCTAATACTTCCTTTA
65 TAACATATGTTGCGGCGCTTTCGGCAAGCGCCGCTAATACTTCCTTTA
** * * * ** * *
2655096 GCGGCGGGTTTTCGTAAGCGTCGCTAACGCTAATATACAGCGAGACAAAACAATGCGTTTTCGTT
1 GCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACATCAAGACAAAACAATGCGTTTTCGTT
* *
2655161 AAGAT-TTTTGCGGCGCTTTCGGCAATGCGCCGCTAATACTTCCTTTA
66 AACATATGTTGCGGCGCTTTCGGCAA-GCGCCGCTAATACTTCCTTTA
* * * *
2655208 GCGGCGTTTTTTCATAAACGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCATTTT
1 GCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACATCAAGA-CAAAACAATGCGTTTT
2655270 GATCTTCAGA
Statistics
Matches: 138, Mismatches: 33, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
111 16 0.12
112 107 0.78
113 15 0.11
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (112 bp):
GCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACATCAAGACAAAACAATGCGTTTTCGTT
AACATATGTTGCGGCGCTTTCGGCAAGCGCCGCTAATACTTCCTTTA
Found at i:2655566 original size:30 final size:29
Alignment explanation
Indices: 2655525--2655582 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2655515 TAATAAATAA
2655525 AAAATATATAAA-AGTATAAAATTAAAATT
1 AAAATATATAAATA-TATAAAATTAAAATT
*
2655554 AAAATAATATAAATATTTAAAATTAAAAT
1 AAAAT-ATATAAATATATAAAATTAAAAT
2655583 AATATGGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 20 0.77
31 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATATATAAATATATAAAATTAAAATT
Found at i:2655573 original size:24 final size:22
Alignment explanation
Indices: 2655539--2655587 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
2655529 TATATAAAAG
2655539 TATAAAATTAAAATTAAAATAA
1 TATAAAATTAAAATTAAAATAA
2655561 TATAAATATTTAAAATTAAAATAA
1 TATAAA-A-TTAAAATTAAAATAA
2655585 TAT
1 TAT
2655588 GGAGAGGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 6 0.24
23 1 0.04
24 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAAAATTAAAATTAAAATAA
Found at i:2667338 original size:16 final size:16
Alignment explanation
Indices: 2667317--2667373 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
2667307 TTTGGTTCGC
*
2667317 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2667333 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2667349 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
2667365 TGTAATGGA
1 TGTAATGGA
2667374 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:2667640 original size:18 final size:17
Alignment explanation
Indices: 2667619--2667653 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2667609 TTATTATTAA
*
2667619 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2667637 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2667654 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2671714 original size:15 final size:15
Alignment explanation
Indices: 2671694--2671725 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2671684 TTAGCATTTG
2671694 TTAATTGAGGTAAAA
1 TTAATTGAGGTAAAA
2671709 TTAATTGAGGTAAAA
1 TTAATTGAGGTAAAA
2671724 TT
1 TT
2671726 TGAAGGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (15 bp):
TTAATTGAGGTAAAA
Found at i:2675388 original size:23 final size:24
Alignment explanation
Indices: 2675326--2675388 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
2675316 TCATTAATAT
*
2675326 TGTTCGTGAACATGTTTAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* * * **
2675350 TGTTCATAAACGTGTTCGTTTA-A
1 TGTTCGTGAACATGTTCAATTATA
2675373 TGTTCGTGAACATGTT
1 TGTTCGTGAACATGTT
2675389 TGATTAAGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:2675395 original size:23 final size:23
Alignment explanation
Indices: 2675326--2675395 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2675316 TCATTAATAT
*
2675326 TGTTCGTGAACATGTTTAATTATA
1 TGTTCGTGAACATGTTTGATTA-A
* * * * *
2675350 TGTTCATAAACGTGTTCGTTTAA
1 TGTTCGTGAACATGTTTGATTAA
2675373 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTTGATTAA
2675396 GTTAAATGAA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTTGATTAA
Found at i:2679290 original size:23 final size:23
Alignment explanation
Indices: 2679226--2679290 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
2679216 ATAATTAGTA
* *
2679226 ATAAATATTATGTGA-TTTTATT
1 ATAAATATTATTTAATTTTTATT
* *
2679248 A-AAATTAGTA-TAAATATTTTATT
1 ATAAA-TATTATTTAAT-TTTTATT
2679271 ATAAATATTATTTAATTTTT
1 ATAAATATTATTTAATTTTT
2679291 CGAATAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
21 4 0.12
22 5 0.16
23 16 0.50
24 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (23 bp):
ATAAATATTATTTAATTTTTATT
Found at i:2679806 original size:21 final size:20
Alignment explanation
Indices: 2679776--2679829 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
2679766 ATTCTAAAAA
*
2679776 ATAAAAAATTTATAAAAATAC
1 ATAAATAATTTAT-AAAATAC
*
2679797 ATAAATAA-TTATAAAATAT
1 ATAAATAATTTATAAAATAC
2679816 ATATAATAAATTTA
1 ATA-AAT-AATTTA
2679830 CATCATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 7 0.25
21 9 0.32
22 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATAATTTATAAAATAC
Found at i:2680040 original size:2 final size:2
Alignment explanation
Indices: 2680033--2680109 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
2680023 AACTAGTGGT
* *
2680033 TA TA TA TA TC TA TA TA TC 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
2680075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2680110 TTCTCCAGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2685501 original size:2 final size:2
Alignment explanation
Indices: 2685496--2685521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2685486 TGTTTAAAAC
2685496 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2685522 TATTAAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2698493 original size:25 final size:25
Alignment explanation
Indices: 2698459--2698537 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
2698449 TAGGGATTAT
2698459 CGATTCTCAGCTCGTATAAGCTTAC
1 CGATTCTCAGCTCGTATAAGCTTAC
2698484 CGATAT-TCAGCTCGTA-AGAGCTTAC
1 CGAT-TCTCAGCTCGTATA-AGCTTAC
* *
2698509 CGATTCTTAGCTCG-ATGAGCTTAC
1 CGATTCTCAGCTCGTATAAGCTTAC
2698533 CGATT
1 CGATT
2698538 TACAACTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
24 15 0.31
25 32 0.67
26 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (25 bp):
CGATTCTCAGCTCGTATAAGCTTAC
Found at i:2698547 original size:49 final size:50
Alignment explanation
Indices: 2698459--2698574 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 50
2698449 TAGGGATTAT
* * *
2698459 CGATTCTCAGCTCGTATAAGCTTACCGATATTCAGCTCGTAAGAGCTTAC
1 CGATTCTTAGCTCGTATAAGCTTACCGATATTCAACTCGTAAGAGCATAC
* *
2698509 CGATTCTTAGCTCG-ATGAGCTTACCGAT-TTACAACTCGTGAGAGCATAC
1 CGATTCTTAGCTCGTATAAGCTTACCGATATT-CAACTCGTAAGAGCATAC
*
2698558 TGATT-TATAGCTCGTAT
1 CGATTCT-TAGCTCGTAT
2698575 GGCCATACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
48 3 0.05
49 39 0.68
50 15 0.26
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (50 bp):
CGATTCTTAGCTCGTATAAGCTTACCGATATTCAACTCGTAAGAGCATAC
Found at i:2698571 original size:25 final size:25
Alignment explanation
Indices: 2698477--2698572 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
2698467 AGCTCGTATA
* *
2698477 AGCTTACCGATATT-CAGCTCGTAAG
1 AGCTTACCGAT-TTATAGCTCGTGAG
2698502 AGCTTACCGATTCT-TAGCTC--GATG
1 AGCTTACCGATT-TATAGCTCGTGA-G
* *
2698526 AGCTTACCGATTTACAACTCGTGAG
1 AGCTTACCGATTTATAGCTCGTGAG
* *
2698551 AGCATACTGATTTATAGCTCGT
1 AGCTTACCGATTTATAGCTCGT
2698573 ATGGCCATAC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
23 2 0.03
24 18 0.31
25 36 0.62
26 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCTTACCGATTTATAGCTCGTGAG
Found at i:2704013 original size:16 final size:17
Alignment explanation
Indices: 2703992--2704044 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2703982 AAATTTCAAG
2703992 AATTAAATT-AAAATAA
1 AATTAAATTAAAAATAA
*
2704008 AATTAATTTAAAAATAA
1 AATTAAATTAAAAATAA
* * * *
2704025 ATTTTAATTGAACATAA
1 AATTAAATTAAAAATAA
2704042 AAT
1 AAT
2704045 AAAAACAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTAAATTAAAAATAA
Found at i:2705625 original size:23 final size:23
Alignment explanation
Indices: 2705590--2705634 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2705580 TGGAGTATAA
* *
2705590 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
2705613 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
2705635 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:2706270 original size:42 final size:42
Alignment explanation
Indices: 2706218--2706485 Score: 423
Period size: 42 Copynumber: 6.4 Consensus size: 42
2706208 CAGTGCCTAT
*
2706218 CAGGTTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
2706260 CAGGCTTAATGCAGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
2706302 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
2706344 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
2706386 CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
2706428 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
2706469 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
2706486 TACTGAATCG
Statistics
Matches: 209, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
40 3 0.01
41 30 0.14
42 176 0.84
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:2706448 original size:126 final size:124
Alignment explanation
Indices: 2706218--2706528 Score: 423
Period size: 126 Copynumber: 2.5 Consensus size: 124
2706208 CAGTGCCTAT
* * *
2706218 CAGGTTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATG-CAGGTGAAATA
1 CAGGCTTAATGCCGGTGAAATAAT-TCAGACTTTACGTCTAGCAGGCTTAATGCCA-GTGAAACA
* *
2706282 ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
64 ATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAC-ATATCAGACTATACGTCTAG
2706344 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAA
1 CAGGCTTAATGCCGGTGAAATAA-TTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAA
* *
2706409 TATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTAG
65 TATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATATCAGACTATACGTCTAG
* * * * *
2706469 CAGGC-TAAGTGCCGGTGTACTGAA-TCGGGCTTTAAGTCTAGCAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAAAT-AATTCAGACTTTACGTCTAGCAGGCTTAA-TGCCAGTGAA
2706529 TCTGTTTAAA
Statistics
Matches: 168, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
123 3 0.02
124 32 0.19
125 32 0.19
126 98 0.58
127 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (124 bp):
CAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAAT
ATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATATCAGACTATACGTCTAG
Found at i:2718091 original size:3 final size:3
Alignment explanation
Indices: 2718083--2718119 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2718073 ATCTACTAAT
2718083 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2718120 CTAGCGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2719399 original size:67 final size:67
Alignment explanation
Indices: 2719310--2719440 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 67
2719300 ACCTTAATAT
**
2719310 GTTGAGTGTAGGCAAATCCCTATCGTCAAAAACATCATTTACCAAAATGTGAAAGCCTTTGTGGG
1 GTTGAGTGTAGGCAAATCCCTATCAACAAAAACATCATTTACCAAAATGTGAAAGCCTTTGTGGG
2719375 AC
66 AC
* * * * *
2719377 GTTGAGTTTAGGGAAATCCCTATCAACGAAAGCATCATTTACCGAAATGTGAAAGCCTTTGTGG
1 GTTGAGTGTAGGCAAATCCCTATCAACAAAAACATCATTTACCAAAATGTGAAAGCCTTTGTGG
2719441 ATGTTCTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (67 bp):
GTTGAGTGTAGGCAAATCCCTATCAACAAAAACATCATTTACCAAAATGTGAAAGCCTTTGTGGG
AC
Found at i:2719756 original size:29 final size:29
Alignment explanation
Indices: 2719716--2719774 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
2719706 TGGCTTCCAA
* *
2719716 AAGTTATATGGACGCCCTT-GTGGCTATCT
1 AAGTTATATGGAC-ACCTTCGTAGCTATCT
2719745 AAGTTA-ATTGGACACCTTCGTAGCTATCT
1 AAGTTATA-TGGACACCTTCGTAGCTATCT
2719774 A
1 A
2719775 TTGATCAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (29 bp):
AAGTTATATGGACACCTTCGTAGCTATCT
Found at i:2727859 original size:3 final size:3
Alignment explanation
Indices: 2727851--2727887 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2727841 AGAACGACAG
2727851 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2727888 ATGGATGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2728915 original size:30 final size:29
Alignment explanation
Indices: 2728855--2728923 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2728845 AAATAAAAAA
* *
2728855 AAAT-AGTCACTAAACTTTGAAAAGTTAC
1 AAATCAGTCACTAAACTTTGAAAAATAAC
2728883 AAATCAGTCACTAAACTTTAGAAAAATAAC
1 AAATCAGTCACTAAACTTT-GAAAAATAAC
2728913 AAA-CTAGTCAC
1 AAATC-AGTCAC
2728924 CAACAACCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 4 0.11
29 15 0.42
30 17 0.47
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (29 bp):
AAATCAGTCACTAAACTTTGAAAAATAAC
Found at i:2729010 original size:20 final size:20
Alignment explanation
Indices: 2728965--2729003 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2728955 AGACGCTGAT
2728965 GTGGCATGTTAACTAGCCAAA
1 GTGG-ATGTTAACTAGCCAAA
*
2728986 TTGGATGTTAACTAGCCA
1 GTGGATGTTAACTAGCCA
2729004 TGGTGGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGGATGTTAACTAGCCAAA
Found at i:2729046 original size:3 final size:3
Alignment explanation
Indices: 2729038--2729067 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2729028 CTAGCTACTG
2729038 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2729068 AATAGAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2729746 original size:21 final size:21
Alignment explanation
Indices: 2729710--2729751 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2729700 GTCCGACGTG
*
2729710 GCTAGTTAACTAGCCATGTCA
1 GCTAGTTAACTAGCCACGTCA
2729731 GCTAGTTAA-TAGGCCACGTCA
1 GCTAGTTAACTA-GCCACGTCA
2729752 TCTATCCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
GCTAGTTAACTAGCCACGTCA
Found at i:2738475 original size:33 final size:33
Alignment explanation
Indices: 2738403--2738475 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
2738393 AAGTTATCAC
* * *
2738403 ACTATTTTTTTACCCCCATTTTCATCTGGTTTG
1 ACTATTTTTTTACCCCCATTTTCATCTAGTGTA
2738436 ACTATTTTTTTACCCCCATTTTCATCTAGTGTA
1 ACTATTTTTTTACCCCCATTTTCATCTAGTGTA
*
2738469 AGTATTT
1 ACTATTT
2738476 GCAACTATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.51
Consensus pattern (33 bp):
ACTATTTTTTTACCCCCATTTTCATCTAGTGTA
Found at i:2748377 original size:3 final size:3
Alignment explanation
Indices: 2748369--2748422 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
2748359 TTAATTTTCC
* *
2748369 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAC TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
2748414 TAT T-T TAT T
1 TAT TAT TAT T
2748423 TTCATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:2748435 original size:6 final size:6
Alignment explanation
Indices: 2748369--2748437 Score: 59
Period size: 6 Copynumber: 11.2 Consensus size: 6
2748359 TTAATTTTCC
* * * *
2748369 TATTAT TATTAT TATTAT TATTAT TATTATT TATTTT TACTATTT TA-TTT
1 TATTTT TATTTT TATTTT TATTTT TATT-TT TATTTT TA-T-TTT TATTTT
*
2748419 TATTTT CATTTT TATTTT T
1 TATTTT TATTTT TATTTT T
2748438 GCAGGAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
5 5 0.09
6 40 0.71
7 6 0.11
8 5 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (6 bp):
TATTTT
Found at i:2753200 original size:17 final size:16
Alignment explanation
Indices: 2753180--2753230 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
2753170 ATTTTAATAG
2753180 ATTTAATATTAAATTTA
1 ATTTAATATT-AATTTA
*
2753197 ATTTAATACTTATTTTA
1 ATTTAATA-TTAATTTA
2753214 ATATTAA-ATTTAATTTA
1 AT-TTAATA-TTAATTTA
2753231 CTAATTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAATATTAATTTA
Found at i:2753238 original size:29 final size:29
Alignment explanation
Indices: 2753181--2753238 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2753171 TTTTAATAGA
*
2753181 TTTAATATTAAATTTAATTTAATACTTAT
1 TTTAATATTAAATTTAATTTAATAATTAT
*
2753210 TTTAATATTAAATTTAATTTACTAATTAT
1 TTTAATATTAAATTTAATTTAATAATTAT
2753239 CTTGTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAATATTAAATTTAATTTAATAATTAT
Found at i:2771967 original size:18 final size:18
Alignment explanation
Indices: 2771944--2771979 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2771934 CTCTTTTGTA
* *
2771944 TTTGGGTTTGTAATTTTT
1 TTTGGGTCTATAATTTTT
2771962 TTTGGGTCTATAATTTTT
1 TTTGGGTCTATAATTTTT
2771980 GGACTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.19, T:0.64
Consensus pattern (18 bp):
TTTGGGTCTATAATTTTT
Found at i:2772474 original size:89 final size:88
Alignment explanation
Indices: 2772365--2772775 Score: 446
Period size: 89 Copynumber: 4.5 Consensus size: 88
2772355 AGAGGTATAG
* * * *
2772365 GATTTGTCGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATGAGAGTTGTTATCTTTAACCTGC
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTTATCTTCAATCTGC
2772430 TCCACTGCAACTTCAGGGAGATAA
65 TCCACTGCAACTTCAGGGAGATAA
* * * *
2772454 GGTTTGTAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAATTCTG
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTATCTTCAA-TCTG
2772519 CTCCACTGCAACTTCAGGGAGATAA
64 CTCCACTGCAACTTCAGGGAGATAA
* * * * * * * * *
2772544 TGTCTGTAACTTGTAGCTTTAATTTGTTTCATTGCAAATTCAGGGA-AGTAAGATTCTCATCTTT
1 -----G--ATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA-TAAGATTGTTATCTTC
** * *
2772608 AATCTTTTCCACTACAACTTCAGAGAGATAA
58 AATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * *
2772639 GATTTATAGATTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGTTATCTTCAGTCTGC
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTTATCTTCAATCTGC
2772704 TCCACTGCAACTTCAGGGAGATAA
65 TCCACTGCAACTTCAGGGAGATAA
* *
2772728 GATTTGTCGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
2772776 CACCATAATA
Statistics
Matches: 259, Mismatches: 51, Indels: 25
0.77 0.15 0.07
Matches are distributed among these distances:
88 36 0.14
89 124 0.48
90 29 0.11
95 26 0.10
96 8 0.03
97 36 0.14
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (88 bp):
GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTTATCTTCAATCTGCT
CCACTGCAACTTCAGGGAGATAA
Found at i:2772482 original size:44 final size:44
Alignment explanation
Indices: 2772248--2772775 Score: 402
Period size: 44 Copynumber: 11.7 Consensus size: 44
2772238 CTTCAATCCA
* * * *
2772248 CTCCACTGCAACTTTAGGGAGATGAGA-TCG-ATGACTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTA-G-CTTTAATCTG
* * * * *
2772292 CTCCACTGCAACTTTAGAGAGATAAGATTTGTAACCAAATTTAGTCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-AGC---TTTAATCTG
* * * * * *
2772340 AC-CCATTGTAACTTTAGAGG-TATAGGATTTGTCGCTTTAATCTG
1 -CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTTAATCTG
* * * *
2772384 CTCCACTGCAACTTCAGGGAGATGAGAGTTGTTATCTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
*
2772429 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * * *
2772473 CTCTACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAATTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAA-TCTG
* *
2772519 CTCCACTGCAACTTCAGGGAGATAATGTCTGTAACTTGTAGCTTTAATTTG
1 CTCCACTGCAACTTCAGGGAGATAA-----G--ATTTGTAGCTTTAATCTG
* * * * * * *
2772570 TTTCATTGCAAATTCAGGGA-AGTAAGATTCT-CATCTTTAATCTT
1 CTCCACTGCAACTTCAGGGAGA-TAAGATT-TGTAGCTTTAATCTG
* * * * * *
2772614 TTCCACTACAACTTCAGAGAGATAAGATTTATAGATTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * * *
2772658 CTCTACTGCAACTTCAGAGAGATAAGATTTGTTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
*
2772703 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
*
2772747 CTCCACTGCAACTTCAGGGAAATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
2772776 CACCATAATA
Statistics
Matches: 381, Mismatches: 78, Indels: 50
0.75 0.15 0.10
Matches are distributed among these distances:
43 4 0.01
44 195 0.51
45 87 0.23
46 28 0.07
47 2 0.01
48 29 0.08
49 2 0.01
50 1 0.00
51 23 0.06
52 7 0.02
53 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
Found at i:2774643 original size:63 final size:63
Alignment explanation
Indices: 2774566--2774688 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
2774556 TTGTTAACAC
* * *
2774566 TAGGTAACATAATAAAACACATATTGATAGTTTAGATACCATATTGGACATTTTATGAAAATA
1 TAGGTAACATAATAAAACACATATTCATAGTTTAGATACCACATTGGACATGTTATGAAAATA
2774629 TAGGT-ACTATAATAAAACACATATTCATAGTTTAGATACCACATTGGACATGTTATGAAA
1 TAGGTAAC-ATAATAAAACACATATTCATAGTTTAGATACCACATTGGACATGTTATGAAA
2774689 GTGCATGTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (63 bp):
TAGGTAACATAATAAAACACATATTCATAGTTTAGATACCACATTGGACATGTTATGAAAATA
Found at i:2789164 original size:22 final size:22
Alignment explanation
Indices: 2789122--2789164 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2789112 AAAAATTATC
* *
2789122 AAAATATTAATATATTTTTAAT
1 AAAATATTAAGATATTCTTAAT
2789144 AAAATATTAAGA-ATTACTTAA
1 AAAATATTAAGATATT-CTTAA
2789165 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATATTAAGATATTCTTAAT
Found at i:2789231 original size:12 final size:13
Alignment explanation
Indices: 2789206--2789234 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2789196 TAAATTTATA
2789206 TTTGAAGCTAGTG
1 TTTGAAGCTAGTG
2789219 TTTGAAG-TAGTG
1 TTTGAAGCTAGTG
2789231 TTTG
1 TTTG
2789235 GGACTAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (13 bp):
TTTGAAGCTAGTG
Found at i:2791015 original size:22 final size:22
Alignment explanation
Indices: 2790986--2791034 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2790976 GTAAACTAGA
*
2790986 ATTTTTTTTAA-TGGTTATAAG
1 ATTTTTTTTAATTGCTTATAAG
2791007 ATTTTTTTTAATTGCTTATAAG
1 ATTTTTTTTAATTGCTTATAAG
2791029 ATTTTT
1 ATTTTT
2791035 GAAATAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTTTTTTTAATTGCTTATAAG
Found at i:2797526 original size:7 final size:7
Alignment explanation
Indices: 2797516--2797544 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2797506 ATACAATCTC
2797516 TTTTCTT
1 TTTTCTT
2797523 TTTTCTT
1 TTTTCTT
2797530 TTTTCTT
1 TTTTCTT
2797537 TTTTCTT
1 TTTTCTT
2797544 T
1 T
2797545 ATACAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:2818037 original size:3 final size:3
Alignment explanation
Indices: 2818031--2818075 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2818021 TTTTTTCTGC
2818031 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2818076 GTTGTTGTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2819416 original size:19 final size:19
Alignment explanation
Indices: 2819394--2819432 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2819384 CAATACACTA
*
2819394 TTAAAATTA-GAATAGATAT
1 TTAAAAATATGAATA-ATAT
2819413 TTAAAAATATGAATAATAT
1 TTAAAAATATGAATAATAT
2819432 T
1 T
2819433 ACAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
TTAAAAATATGAATAATAT
Found at i:2826340 original size:21 final size:23
Alignment explanation
Indices: 2826313--2826363 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
2826303 TAAGTTTAAA
*
2826313 ATAAAAA-AATATTTAAAA-TGTT
1 ATAAAAATAA-ATTAAAAATTGTT
2826335 -TAAAAATAAATTAAAAATTGTT
1 ATAAAAATAAATTAAAAATTGTT
2826357 ATAAAAA
1 ATAAAAA
2826364 CCCTATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 13 0.52
22 6 0.24
23 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAAAAATAAATTAAAAATTGTT
Found at i:2829590 original size:24 final size:24
Alignment explanation
Indices: 2829563--2829609 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2829553 ATGTGCTTAT
2829563 AATAATATTGTTAAT-TTTTTTAAA
1 AATAA-ATTGTTAATCTTTTTTAAA
* *
2829587 AATAAATTTTTACTCTTTTTTAA
1 AATAAATTGTTAATCTTTTTTAA
2829610 TTAAAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
AATAAATTGTTAATCTTTTTTAAA
Found at i:2830328 original size:11 final size:10
Alignment explanation
Indices: 2830291--2830324 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
2830281 TAGACCCACC
2830291 AAAATTTTTA
1 AAAATTTTTA
2830301 AAAATTTTTA
1 AAAATTTTTA
2830311 AAAATTTTTA
1 AAAATTTTTA
2830321 AAAA
1 AAAA
2830325 ATTTATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:2833828 original size:21 final size:21
Alignment explanation
Indices: 2833803--2833928 Score: 94
Period size: 21 Copynumber: 6.0 Consensus size: 21
2833793 GGTACACGAT
*
2833803 CGTGTGACTGAGATACATGGT
1 CGTGTGACTGAGATACATGGC
* * * * *
2833824 TGTGT-AGCTAAGAGACACGAC
1 CGTGTGA-CTGAGATACATGGC
* *
2833845 CGTGTGACTGAGATACATAGT
1 CGTGTGACTGAGATACATGGC
*
2833866 CGTGTGGCTGAGATACATGGC
1 CGTGTGACTGAGATACATGGC
* * *
2833887 CGTGTGGCTGAGAGACA-CGC
1 CGTGTGACTGAGATACATGGC
* *
2833907 TCGTGTGACTGGGGTACATGGC
1 -CGTGTGACTGAGATACATGGC
2833929 TGTGCCAGGC
Statistics
Matches: 78, Mismatches: 23, Indels: 7
0.72 0.21 0.06
Matches are distributed among these distances:
20 3 0.04
21 72 0.92
22 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
CGTGTGACTGAGATACATGGC
Found at i:2833890 original size:42 final size:42
Alignment explanation
Indices: 2833796--2833899 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
2833786 TTCACAGGGT
* * *
2833796 ACACGATCGTGTGACTGAGATACATGGTTGTGTAGCTAAGAG
1 ACACGACCGTGTGACTGAGATACATAGTCGTGTAGCTAAGAG
* * *
2833838 ACACGACCGTGTGACTGAGATACATAGTCGTGTGGCTGAGAT
1 ACACGACCGTGTGACTGAGATACATAGTCGTGTAGCTAAGAG
* * *
2833880 ACATGGCCGTGTGGCTGAGA
1 ACACGACCGTGTGACTGAGA
2833900 GACACGCTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (42 bp):
ACACGACCGTGTGACTGAGATACATAGTCGTGTAGCTAAGAG
Found at i:2836636 original size:18 final size:18
Alignment explanation
Indices: 2836610--2836662 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2836600 GCAATAAGAA
*
2836610 AACGTTTTG-AAATTGAAT
1 AACGATTTGTAAA-TGAAT
2836628 AACGATTTGTAAATGAAT
1 AACGATTTGTAAATGAAT
* * *
2836646 AATGTTTTGGAAATGAA
1 AACGATTTGTAAATGAA
2836663 CGACATGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (18 bp):
AACGATTTGTAAATGAAT
Found at i:2837036 original size:25 final size:25
Alignment explanation
Indices: 2836990--2837054 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
2836980 CTGTCTTTGA
* *
2836990 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* * *
2837015 TAGTATATATTGATACTACTATAGA
1 TAGTATATACTGAAACTACTATAGG
2837040 TAG-ACTATACTGAAA
1 TAGTA-TATACTGAAA
2837055 ACACTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:2838657 original size:9 final size:9
Alignment explanation
Indices: 2838643--2838673 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2838633 GTTAAACGAA
2838643 TCGAGTTAT
1 TCGAGTTAT
*
2838652 TCGAGTTAA
1 TCGAGTTAT
2838661 TCGAGTTAT
1 TCGAGTTAT
2838670 TCGA
1 TCGA
2838674 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2838744 original size:9 final size:9
Alignment explanation
Indices: 2838727--2838763 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2838717 TGAGTTTTCG
2838727 AATTCGAAT
1 AATTCGAAT
*
2838736 AACTCGAAT
1 AATTCGAAT
2838745 AATTCGAAT
1 AATTCGAAT
2838754 AATTCGAAT
1 AATTCGAAT
2838763 A
1 A
2838764 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2840510 original size:32 final size:32
Alignment explanation
Indices: 2840469--2840536 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
2840459 TAGCCTATGC
2840469 ATCTCGTCAGCTTAAGACCCATGAGGCAAATT
1 ATCTCGTCAGCTTAAGACCCATGAGGCAAATT
2840501 ATCTCGTCAGCTTAAGACCCATGAGGCAAATT
1 ATCTCGTCAGCTTAAGACCCATGAGGCAAATT
2840533 ATCT
1 ATCT
2840537 GACGCATAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (32 bp):
ATCTCGTCAGCTTAAGACCCATGAGGCAAATT
Found at i:2844888 original size:18 final size:18
Alignment explanation
Indices: 2844844--2844888 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2844834 GCAATAAGAA
2844844 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
2844862 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
2844880 AATGTTTTG
1 AACGTTTTG
2844889 GAAACGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:2847030 original size:23 final size:22
Alignment explanation
Indices: 2847003--2847052 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
2846993 CAATTTTCTC
2847003 TATTTTT-TGAATTTTTTTATTTT
1 TATTTTTAT-AATTTTTTTA-TTT
2847026 TATTTTTATAATTTTTTTATTT
1 TATTTTTATAATTTTTTTATTT
2847048 TATTT
1 TATTT
2847053 AATTGAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.31
23 17 0.65
24 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TATTTTTATAATTTTTTTATTT
Found at i:2851626 original size:50 final size:51
Alignment explanation
Indices: 2851471--2851681 Score: 345
Period size: 51 Copynumber: 4.2 Consensus size: 51
2851461 TGAGTACTTT
* **
2851471 TGATCAGTGACAAGTGATAAGCAGTAG-TTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
2851521 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
2851572 TGATAAATGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAA
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
2851622 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATATGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
2851673 TGATAAGTG
1 TGATAAGTG
2851682 GTAGCTTTAG
Statistics
Matches: 150, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
50 72 0.48
51 78 0.52
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:2851639 original size:101 final size:101
Alignment explanation
Indices: 2851478--2851678 Score: 357
Period size: 101 Copynumber: 2.0 Consensus size: 101
2851468 TTTTGATCAG
*
2851478 TGACAAGTGATAAGCAGTAGTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATAAGT
1 TGACAAGTGATAAGCAGTAGTTTAGCTACACTTATCTGATCAATGATAAGTGACAAGTGATAAGT
*
2851543 GGTAGCTTTAGCTACACTTATCTGATCAGTGATAAA
66 GGTAGCTTTAGCTACACTTATATGATCAGTGATAAA
**
2851579 TGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAATGATAAGTGACAAGTGATAAGT
1 TGACAAGTGATAAGCAGTAGTTTAGCTACACTTATCTGATCAATGATAAGTGACAAGTGATAAGT
*
2851644 GGTAGCTTTAGCTGCACTTATATGATCAGTGATAA
66 GGTAGCTTTAGCTACACTTATATGATCAGTGATAA
2851679 GTGGTAGCTT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (101 bp):
TGACAAGTGATAAGCAGTAGTTTAGCTACACTTATCTGATCAATGATAAGTGACAAGTGATAAGT
GGTAGCTTTAGCTACACTTATATGATCAGTGATAAA
Found at i:2851684 original size:37 final size:37
Alignment explanation
Indices: 2851634--2851718 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
2851624 ATAAGTGACA
*
2851634 AGTGATAAGTGGTAGCTTTAGCTGCACTTATATGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATATGATC
*
2851671 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATATGATC
* *
2851708 AATGACAAGTG
1 AGTGATAAGTG
2851719 ACAAGTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATATGATC
Found at i:2860437 original size:49 final size:49
Alignment explanation
Indices: 2860380--2860480 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
2860370 AGTACCGCAT
*
2860380 TAAACATTTTATGAAAGTACAAGTACTAAATGAGATATTATCCTAAAAA
1 TAAACATTTTATGAAAGTACAAGTACCAAATGAGATATTATCCTAAAAA
2860429 TAAACATTTTATGAAAGTACAAGTACCAAATGAGATATTATCCTAAAAA
1 TAAACATTTTATGAAAGTACAAGTACCAAATGAGATATTATCCTAAAAA
2860478 TAA
1 TAA
2860481 TTTAATAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.30
Consensus pattern (49 bp):
TAAACATTTTATGAAAGTACAAGTACCAAATGAGATATTATCCTAAAAA
Done.