Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015242.1 Kokia drynarioides strain JFW-HI SEQ_130287, whole genome shotgun sequence
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: 157169
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 279 characters in sequence are not A, C, G, or T
Found at i:1822 original size:30 final size:29
Alignment explanation
Indices: 1751--1985 Score: 260
Period size: 30 Copynumber: 8.0 Consensus size: 29
1741 TATCCCAGAG
*
1751 ACCCCGAAAC-TCCAAAAATTTCATTTTT
1 ACCCCGAAACTTCCAAAAATTCCATTTTT
1779 ACCCTCG-AACTTCCAAAAATTCCATTTTT
1 ACCC-CGAAACTTCCAAAAATTCCATTTTT
1808 GACCCCGAAACTTCCAAAAATTCCATTTTT
1 -ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
1838 AACCTCGAAACTTTCAAAAATTCCATTTTT
1 -ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
1868 AACACCGAAACTTTCAAAAATTCCATTTTT
1 -ACCCCGAAACTTCCAAAAATTCCATTTTT
* *
1898 ACCCCAAAACTTCCAAAAAATCCATTTTT
1 ACCCCGAAACTTCCAAAAATTCCATTTTT
* * * *
1927 ACCCTC-AAACATCCAAAATTTCTATTATTG
1 ACCC-CGAAACTTCCAAAAATTCCATT-TTT
* **
1957 ACCTCGAAACTTTTAAAAATTACCATTTT
1 ACCCCGAAACTTCCAAAAATT-CCATTTT
1986 GTCCCCGGAT
Statistics
Matches: 178, Mismatches: 21, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
28 7 0.04
29 67 0.38
30 100 0.56
31 4 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
ACCCCGAAACTTCCAAAAATTCCATTTTT
Found at i:1876 original size:60 final size:58
Alignment explanation
Indices: 1753--1985 Score: 256
Period size: 59 Copynumber: 4.0 Consensus size: 58
1743 TCCCAGAGAC
* *
1753 CCCGAAAC-TCCAAAAATTTCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTGA
1 CCCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTT-A
*
1810 CCCCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTAA
1 -CCCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTT-A
* * * *
1870 CACCGAAACTTTCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAAATCCATTTTTA
1 C-CCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTA
* * * * * * **
1928 CCCTCAAACATCCAAAATTTCTATTATTGACCTCGAAACTTTTAAAAATTACCATTTT
1 CCC-GAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATT-CCATTTT
1986 GTCCCCGGAT
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
57 2 0.01
58 28 0.19
59 65 0.44
60 54 0.36
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
CCCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTA
Found at i:2012 original size:88 final size:89
Alignment explanation
Indices: 1755--1985 Score: 265
Period size: 89 Copynumber: 2.6 Consensus size: 89
1745 CCAGAGACCC
* * * * *
1755 CGAAAC-TCCAAAAATTTCATT-TTTACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCCGAA
1 CGAAACATCCAAAAATTCCATTATTAACAC-CGAAACTTTCAAAAATTCCATTTTT-ACCCCAAA
*
1817 ACTTCCAAAAATTCCATTTTTAACCT
64 ACTTCCAAAAAATCCATTTTTAACCT
* * *
1843 CGAAACTTTCAAAAATTCCATTTTTAACACCGAAACTTTCAAAAATTCCATTTTTACCCCAAAAC
1 CGAAACATCCAAAAATTCCATTATTAACACCGAAACTTTCAAAAATTCCATTTTTACCCCAAAAC
*
1908 TTCCAAAAAATCCATTTTTACCCT
66 TTCCAAAAAATCCATTTTTAACCT
* * * *
1932 C-AAACATCCAAAATTTCTATTATTGAC-CTCGAAACTTTTAAAAATTACCATTTT
1 CGAAACATCCAAAAATTCCATTATTAACAC-CGAAACTTTCAAAAATT-CCATTTT
1986 GTCCCCGGAT
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
87 1 0.01
88 42 0.34
89 54 0.44
90 26 0.21
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (89 bp):
CGAAACATCCAAAAATTCCATTATTAACACCGAAACTTTCAAAAATTCCATTTTTACCCCAAAAC
TTCCAAAAAATCCATTTTTAACCT
Found at i:2032 original size:88 final size:88
Alignment explanation
Indices: 1786--2034 Score: 249
Period size: 88 Copynumber: 2.8 Consensus size: 88
1776 TTTACCCTCG
* * * *
1786 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTT
1 AACTTTCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAAATCCA-TTTTAACCTCGAAACTC
* *
1851 TCAAAAATTCCATTTTTAACACCGA
64 TCAAAATTTCCATTATTAACACCGA
*
1876 AACTTTCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAATCCATTTTTACCCTC-AAACATC
1 AACTTTCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAATCCA-TTTTAACCTCGAAAC-TC
* *
1940 -CAAAATTTCTATTATTGAC-CTCGA
64 TCAAAATTTCCATTATTAACAC-CGA
* ** * **
1964 AACTTTTAAAAATTACCATTTTGT-CCCC-GGA-TGTCCAAAAACTCCATTTCGACCTCGAAACT
1 AACTTTCAAAAATT-CCATTTT-TACCCCAAAACT-TCCAAAAAATCCATTTTAACCTCGAAACT
2026 CTCAAAATT
63 CTCAAAATT
2035 ACCCTTTTAC
Statistics
Matches: 136, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
87 11 0.08
88 59 0.43
89 44 0.32
90 22 0.16
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (88 bp):
AACTTTCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAATCCATTTTAACCTCGAAACTCTC
AAAATTTCCATTATTAACACCGA
Found at i:2051 original size:29 final size:28
Alignment explanation
Indices: 2019--2136 Score: 80
Period size: 28 Copynumber: 4.1 Consensus size: 28
2009 ATTTCGACCT
*
2019 CGAAACTCTCAAAATTACCCTTTTACCCC
1 CGAAA-TCTCAAAATTACCATTTTACCCC
* * * *
2048 CGAATGTCTAAAAATT-CAAATTTTAACCC
1 CGAA-ATCTCAAAATTAC-CATTTTACCCC
* *
2077 C-AAATTTTCCCAAAATTACCACTTTACCCC
1 CGAAA---TCTCAAAATTACCATTTTACCCC
*
2107 CGAGAAT-TCAAAATTACCATTTTATCCC
1 CGA-AATCTCAAAATTACCATTTTACCCC
2135 CG
1 CG
2137 GGTATTCGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 17
0.68 0.14 0.17
Matches are distributed among these distances:
28 23 0.34
29 23 0.34
30 17 0.25
31 2 0.03
32 2 0.03
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.30
Consensus pattern (28 bp):
CGAAATCTCAAAATTACCATTTTACCCC
Found at i:2463 original size:96 final size:96
Alignment explanation
Indices: 2361--2547 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 96
2351 AAAGCTTTAA
* *
2361 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCGAAA-ATTCGTGCATTAACTTACTAGGTGC
1 AATCGAGGCAATATTTC-ATTATCTTCGA-TTCT-GAAATATT-GCGCATTAACTTACTAGGTGC
**
2422 AATTTTTCTTCAAATCGAAATAATCAAATACCCTT
62 AACCTTTCTTCAAATCGAAATAATCAAATACCCTT
* *
2457 AATCGAGGCAATGTTTCATTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCATTATCTTCGATTCTGAAATATTGCGCATTAACTTACTAGGTGCAACC
* *
2522 TTTCTTCAAATCGATATAATCGAATA
66 TTTCTTCAAATCGAAATAATCAAATA
2548 TCTTTTTCCC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
96 67 0.85
97 12 0.15
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTTCATTATCTTCGATTCTGAAATATTGCGCATTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCAAATACCCTT
Found at i:10173 original size:11 final size:11
Alignment explanation
Indices: 10172--10231 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
10162 ATTTATTTTA
*
10172 AATTTAGATTT
1 AATTTAAATTT
*
10183 ATTTTAAATTT
1 AATTTAAATTT
*
10194 GAATTTAAATTA
1 -AATTTAAATTT
10206 AATTTAAATTT
1 AATTTAAATTT
*
10217 ATTTTCAAAATTT
1 AATTT--AAATTT
10230 AA
1 AA
10232 AAGATTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 23 0.59
12 9 0.23
13 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:10177 original size:6 final size:6
Alignment explanation
Indices: 10157--10217 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
10147 ACCGGACCCC
* * * *
10157 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10203 -TTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
10218 TTTTCAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 12 0.27
6 32 0.73
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:10182 original size:17 final size:17
Alignment explanation
Indices: 10157--10232 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
10147 ACCGGACCCC
10157 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
10174 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* **
10191 TTTGAATTTAAATTAAA
1 TTTAAATTTATTTTAAA
10208 TTTAAATTTATTTTCAAAA
1 TTTAAATTTATTTT--AAA
10227 TTTAAA
1 TTTAAA
10233 AGATTATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 40 0.82
19 9 0.18
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:10968 original size:3 final size:3
Alignment explanation
Indices: 10960--10999 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
10950 TTAATAGCAT
*
10960 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
11000 ATAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12168 original size:30 final size:29
Alignment explanation
Indices: 12132--12299 Score: 117
Period size: 30 Copynumber: 5.7 Consensus size: 29
12122 CCTTAGAGGT
12132 CCCTAAACTGTCCAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTATATTTTGAC
* **
12162 CCCTAAACTTCTCCAAAATTCCATTCTTGAC
1 CCCTAAACTTC-CAAAAATTATATT-TTGAC
* * *
12193 CCTTAAACTAT-CAAAAATTACTTTTTTAAC
1 CCCTAAACT-TCCAAAAATTA-TATTTTGAC
* * * *
12223 CTC-GAACTTTCAAAAATTCTAATTTTGAC
1 CCCTAAACTTCCAAAAATTAT-ATTTTGAC
* * * *
12252 CTCAAAACTTTCAAAAATTACCATTTT-AC
1 CCCTAAACTTCCAAAAATTA-TATTTTGAC
*
12281 CCCTGAACTTCCAAAAATT
1 CCCTAAACTTCCAAAAATT
12300 CCGATTTTAA
Statistics
Matches: 108, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
28 2 0.02
29 40 0.37
30 50 0.46
31 15 0.14
32 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTATATTTTGAC
Found at i:12230 original size:29 final size:31
Alignment explanation
Indices: 12197--12272 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
12187 CTTGACCCTT
* *
12197 AAACTATCAAAAATTACT-TTTTTAACCTC-
1 AAACTTTCAAAAATTACTAATTTTAACCTCA
* *
12226 GAACTTTCAAAAATT-CTAATTTTGACCTCA
1 AAACTTTCAAAAATTACTAATTTTAACCTCA
12256 AAACTTTCAAAAATTAC
1 AAACTTTCAAAAATTAC
12273 CATTTTACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 22 0.56
30 14 0.36
31 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.36
Consensus pattern (31 bp):
AAACTTTCAAAAATTACTAATTTTAACCTCA
Found at i:12290 original size:29 final size:30
Alignment explanation
Indices: 12144--12358 Score: 115
Period size: 30 Copynumber: 7.2 Consensus size: 30
12134 CTAAACTGTC
* *
12144 CAAAAATTA-TATTTTGACCCCTAAACTTCT
1 CAAAAATTACCATTTTGACCCCTGAACTT-T
* * * *
12174 CCAAAATT-CCATTCTTGACCCTTAAACTAT
1 CAAAAATTACCATT-TTGACCCCTGAACTTT
** * *
12204 CAAAAATTACTTTTTTAACCTC-GAACTTT
1 CAAAAATTACCATTTTGACCCCTGAACTTT
* * **
12233 CAAAAATT-CTAATTTTGACCTCAAAACTTT
1 CAAAAATTAC-CATTTTGACCCCTGAACTTT
*
12263 CAAAAATTACCATTTT-ACCCCTGAACTTC
1 CAAAAATTACCATTTTGACCCCTGAACTTT
* * *
12292 CAAAAATT-CCGATTTTAACCTCGGAAC-TT
1 CAAAAATTACC-ATTTTGACCCCTGAACTTT
* *
12321 CTGAAAATTATCATTTT-ACCGCC-GAACTTCT
1 C-AAAAATTACCATTTTGACC-CCTGAACTT-T
*
12352 AAAAAAT
1 CAAAAAT
12359 CTATTTTTGA
Statistics
Matches: 143, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
28 3 0.02
29 53 0.37
30 68 0.48
31 19 0.13
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (30 bp):
CAAAAATTACCATTTTGACCCCTGAACTTT
Found at i:12307 original size:59 final size:58
Alignment explanation
Indices: 12144--12365 Score: 166
Period size: 59 Copynumber: 3.8 Consensus size: 58
12134 CTAAACTGTC
* * * * *
12144 CAAAAATTA-TATTTTGACCCCTAAACTTCTCCAAAATTCCATTCTTGACC-CTTAAACTAT
1 CAAAAATTACCATTTT-ACCCCTGAACTTC-CAAAAATTCCATT-TTGACCTC-AAAACTTT
** * * *
12204 CAAAAATTACTTTTTTA-ACCTCGAACTTTCAAAAATTCTAATTTTGACCTCAAAACTTT
1 CAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATTC-CATTTTGACCTCAAAACTTT
* **
12263 CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCGATTTTAACCTCGGAAC-TT
1 CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCC-ATTTTGACCTCAAAACTTT
* * * * *
12321 CTGAAAATTATCATTTTACCGCC-GAACTTCTAAAAAATCTATTTT
1 C-AAAAATTACCATTTTACC-CCTGAACTTCCAAAAATTCCATTTT
12366 TGATCCCGAT
Statistics
Matches: 133, Mismatches: 21, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
58 8 0.06
59 96 0.72
60 24 0.18
61 5 0.04
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTGACCTCAAAACTTT
Found at i:12321 original size:30 final size:28
Alignment explanation
Indices: 12216--12365 Score: 97
Period size: 29 Copynumber: 5.1 Consensus size: 28
12206 AAAATTACTT
* *
12216 TTTTAACCTCGAACTTTCAAAAATTCTAA
1 TTTTAACCTCGAACTTCCAAAAATTC-CA
* * *
12245 TTTTGACCTCAAAACTTTCAAAAATTACCA
1 TTTTAACCTC-GAACTTCCAAAAATT-CCA
*
12275 TTTT-ACCCCTGAACTTCCAAAAATTCCGA
1 TTTTAACCTC-GAACTTCCAAAAATTCC-A
** *
12304 TTTTAACCTCGGAACTTCTGAAAATTATCA
1 TTTTAACCTC-GAACTTCCAAAAATT-CCA
* * * *
12334 TTTT-ACCGCCGAACTTCTAAAAAATCTA
1 TTTTAACC-TCGAACTTCCAAAAATTCCA
12362 TTTT
1 TTTT
12366 TGATCCCGAT
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
28 7 0.07
29 47 0.48
30 42 0.43
31 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (28 bp):
TTTTAACCTCGAACTTCCAAAAATTCCA
Found at i:12415 original size:59 final size:60
Alignment explanation
Indices: 12321--12483 Score: 167
Period size: 59 Copynumber: 2.8 Consensus size: 60
12311 CTCGGAACTT
*
12321 CTGAAA-ATTATCATTTTACCGCCGAACT-TCTAAAAAATCTATTTTTGATCCCGATTTTC
1 CTGAAAGATTATCATTTTACCCCCGAA-TGTCTAAAAAATCTATTTTTGATCCCGATTTTC
* * * * * *
12380 CT-AAAGATTACCATTTTACCCCCGAATGTC-CAAAAATTTCGTTTTTGATCCTGATTTTT
1 CTGAAAGATTATCATTTTACCCCCGAATGTCTAAAAAATCT-ATTTTTGATCCCGATTTTC
* * *
12439 TTGAAAG-TTATCGTTTTACCCCCGAGTGTCTAAAAATATC-ATTTT
1 CTGAAAGATTATCATTTTACCCCCGAATGTCTAAAAA-ATCTATTTT
12484 AACCCCGAAC
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
58 11 0.13
59 63 0.75
60 8 0.10
61 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (60 bp):
CTGAAAGATTATCATTTTACCCCCGAATGTCTAAAAAATCTATTTTTGATCCCGATTTTC
Found at i:13903 original size:18 final size:19
Alignment explanation
Indices: 13865--13903 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
13855 GAAATGAGGT
*
13865 ATGATATCGATAAAGTTCA
1 ATGATATCGACAAAGTTCA
*
13884 ATGATATC-ACAAATTTCA
1 ATGATATCGACAAAGTTCA
13902 AT
1 AT
13904 ACGTGACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (19 bp):
ATGATATCGACAAAGTTCA
Found at i:14706 original size:13 final size:14
Alignment explanation
Indices: 14681--14709 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
14671 TATAAATATT
14681 TTTAAATATTTTAA
1 TTTAAATATTTTAA
14695 TTTAAA-ATTTTAA
1 TTTAAATATTTTAA
14708 TT
1 TT
14710 ATTTTCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAATATTTTAA
Found at i:22291 original size:29 final size:31
Alignment explanation
Indices: 22248--22325 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 31
22238 GGGCTCCAAC
**
22248 ATATATAATATATATATTTGTGAGTTTTG-TT
1 ATATAT-ATATATATATGCGTGAGTTTTGATT
*
22279 ATATATA-ATATATATGCGTGGGTTTTGATT
1 ATATATATATATATATGCGTGAGTTTTGATT
22309 ATATATATATATATATG
1 ATATATATATATATATG
22326 GTTCTTGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.40
30 10 0.24
31 15 0.36
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (31 bp):
ATATATATATATATATGCGTGAGTTTTGATT
Found at i:25836 original size:2 final size:2
Alignment explanation
Indices: 25829--25868 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25819 TTAGATAAAT
25829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25869 CCATAACACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27808 original size:19 final size:21
Alignment explanation
Indices: 27784--27825 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27774 TATTATGTAG
*
27784 TTTTT-AATT-TTATGTTTTT
1 TTTTTAAATTATTATATTTTT
27803 TTTTTAAATTATTATATTTTT
1 TTTTTAAATTATTATATTTTT
27824 TT
1 TT
27826 AATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTAAATTATTATATTTTT
Found at i:28508 original size:18 final size:17
Alignment explanation
Indices: 28485--28545 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
28475 TATTTCCTTT
*
28485 AAATTTATCTTAAAATTA
1 AAATTTAT-TTAAATTTA
*
28503 AAATTTAATTTAAGTTTA
1 AAATTT-ATTTAAATTTA
28521 AAA-TTATTTTCAAATTTA
1 AAATTTA-TTT-AAATTTA
28539 AAATTTA
1 AAATTTA
28546 AAATAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.03
17 5 0.14
18 25 0.69
19 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTTATTTAAATTTA
Found at i:29301 original size:17 final size:17
Alignment explanation
Indices: 29279--29327 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
29269 CGGTTTTCAT
29279 AATATTTATTAATAATA
1 AATATTTATTAATAATA
**
29296 AATATTTATTTTTAAT-
1 AATATTTATTAATAATA
*
29312 AATA-ATATTAATAATA
1 AATATTTATTAATAATA
29328 TTAATGAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTATTAATAATA
Found at i:29325 original size:9 final size:9
Alignment explanation
Indices: 29311--29344 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29301 TTATTTTTAA
29311 TAATAATAT
1 TAATAATAT
29320 TAATAATAT
1 TAATAATAT
*
29329 TAATGAATAA
1 TAAT-AATAT
29339 TAATAA
1 TAATAA
29345 AAAAACGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
TAATAATAT
Found at i:30333 original size:29 final size:29
Alignment explanation
Indices: 30289--30558 Score: 307
Period size: 29 Copynumber: 9.2 Consensus size: 29
30279 CCCCGAAGGT
30289 CCCGAAACTTCCAAAAATCCCATTTTGAC
1 CCCGAAACTTCCAAAAATCCCATTTTGAC
* * *
30318 CTCGAAACTTCCAAAAATTCCATTTTTACC
1 CCCGAAACTTCCAAAAATCCCATTTTGA-C
30348 CCCG-AACTTCCAAAAATCCCATTTTTTGAC
1 CCCGAAACTTCCAAAAATCCCA--TTTTGAC
* * *
30378 CTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCCGAAACTTCCAAAAATCCCATTTTGAC
*
30407 CCTCG-AACTTCCAAAAATCCAATTTTGAC
1 CC-CGAAACTTCCAAAAATCCCATTTTGAC
* *
30436 CCCGAAACTGCCAAAAATTCCATTTT-AC
1 CCCGAAACTTCCAAAAATCCCATTTTGAC
*
30464 CCCTG-AACTTCCAAAAATCCAATTTTGAC
1 CCC-GAAACTTCCAAAAATCCCATTTTGAC
* *
30493 CCCAAAACTTCCAAAAATCCCATTTTTAC
1 CCCGAAACTTCCAAAAATCCCATTTTGAC
**
30522 CCTC-AAACTTTAAAAAAAATCCCATTTTGAC
1 CC-CGAAAC-TT-CCAAAAATCCCATTTTGAC
30553 CCCGAA
1 CCCGAA
30559 TTTTCTCAAA
Statistics
Matches: 203, Mismatches: 25, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
28 25 0.12
29 123 0.61
30 14 0.07
31 41 0.20
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.28
Consensus pattern (29 bp):
CCCGAAACTTCCAAAAATCCCATTTTGAC
Found at i:30570 original size:60 final size:58
Alignment explanation
Indices: 30294--30558 Score: 372
Period size: 60 Copynumber: 4.5 Consensus size: 58
30284 AAGGTCCCGA
* *
30294 AACTTCCAAAAATCCCATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
*
30352 AACTTCCAAAAATCCCATTTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCA--TTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* *
30412 AACTTCCAAAAATCCAATTTTGACCCCGAAACTGCCAAAAATTCCA-TTTTACCC-CTG
1 AACTTCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTC-G
* * * *
30469 AACTTCCAAAAATCCAATTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
**
30527 AACTTTAAAAAAAATCCCATTTTGACCCCGAA
1 AAC-TT-CCAAAAATCCCATTTTGACCCCGAA
30559 TTTTCTCAAA
Statistics
Matches: 188, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
56 1 0.01
57 52 0.28
58 55 0.29
59 3 0.02
60 77 0.41
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:30599 original size:28 final size:29
Alignment explanation
Indices: 30565--30627 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
30555 CGAATTTTCT
*
30565 CAAAATTA-CCGTTTCACCCCCGAGAATC
1 CAAAATTATCAGTTTCACCCCCGAGAATC
* **
30593 CAAAATTATCATTTTTTCCCCCGAGAATC
1 CAAAATTATCAGTTTCACCCCCGAGAATC
30622 CGAAAA
1 C-AAAA
30628 GTCTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.28
29 17 0.59
30 4 0.14
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (29 bp):
CAAAATTATCAGTTTCACCCCCGAGAATC
Found at i:41325 original size:20 final size:20
Alignment explanation
Indices: 41280--41332 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
41270 AATTTGTTAG
41280 AAAT-ATTATTAAATAATATA
1 AAATAATTA-TAAATAATATA
*
41300 ATATAATTATAAATAA-AGTA
1 AAATAATTATAAATAATA-TA
*
41320 AAATAAATATAAA
1 AAATAATTATAAA
41333 AGAGTAAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 23 0.82
21 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAATAATTATAAATAATATA
Found at i:41408 original size:21 final size:21
Alignment explanation
Indices: 41374--41413 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41364 AGAATATATA
41374 AAAAATATATTTATTATATTGT
1 AAAAATATATTTATT-TATTGT
*
41396 AAAATTATA-TTATTTATT
1 AAAAATATATTTATTTATT
41414 TTACCTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
AAAAATATATTTATTTATTGT
Found at i:44263 original size:141 final size:141
Alignment explanation
Indices: 44078--44360 Score: 521
Period size: 141 Copynumber: 2.0 Consensus size: 141
44068 TATGGAAAGT
44078 TGCTAGATATGATTTCGGGGTTTTTATTAAAATAATAAGAAAAATAAAATTAAATTACAAAATGA
1 TGCTAGATATGATTTCGGGGTTTTTATTAAAATAATAAGAAAAATAAAATTAAATTACAAAATGA
44143 TATAAGTTAGAAATCACTTGCCAAAATTGTATGAAAGCTACGGTAATTTTTGGGTATACATTTAA
66 TATAAGTTAGAAATCACTTGCCAAAATTGTATGAAAGCTACGGTAATTTTTGGGTATACATTTAA
44208 AAAAATTGGTG
131 AAAAATTGGTG
* ** * *
44219 TGCTAGATTTGATTTCGGGGTTTTTATTAAAATAATGTGAAAAATAAAATTAATTTTCAAAATGA
1 TGCTAGATATGATTTCGGGGTTTTTATTAAAATAATAAGAAAAATAAAATTAAATTACAAAATGA
44284 TATAAGTTAGAAATCACTTGCCAAAATTGTATGAAAGCTACGGTAATTTTTGGGTATACATTTAA
66 TATAAGTTAGAAATCACTTGCCAAAATTGTATGAAAGCTACGGTAATTTTTGGGTATACATTTAA
44349 AAAAATTGGTG
131 AAAAATTGGTG
44360 T
1 T
44361 CGTATAAACA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 137 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (141 bp):
TGCTAGATATGATTTCGGGGTTTTTATTAAAATAATAAGAAAAATAAAATTAAATTACAAAATGA
TATAAGTTAGAAATCACTTGCCAAAATTGTATGAAAGCTACGGTAATTTTTGGGTATACATTTAA
AAAAATTGGTG
Found at i:48378 original size:44 final size:44
Alignment explanation
Indices: 48315--48528 Score: 241
Period size: 44 Copynumber: 4.9 Consensus size: 44
48305 AGATTAACAA
* * * * * *
48315 TTTATCTGCAAATTTTGTTGTGTATCCATAGCCTAATGACATAT
1 TTTATCTACAAATTTTGTTGTGCATCCACAACCTAGTGACAGAT
* * *
48359 TTTATCTGCAAATTTTGTTGTGTATCCACAACCTAGTGGCAGAT
1 TTTATCTACAAATTTTGTTGTGCATCCACAACCTAGTGACAGAT
* * * *
48403 TTTATCTACGAATTTTGCTATGCATCCACAACCTATTGACA-AT
1 TTTATCTACAAATTTTGTTGTGCATCCACAACCTAGTGACAGAT
* * * *
48446 TTTCACCTACAAATTTTGTTGTGCACCCACAACCCAGTGATAGAT
1 TTT-ATCTACAAATTTTGTTGTGCATCCACAACCTAGTGACAGAT
* *
48491 TTTATCTTCAAATTTTGTTGTGCATCCATAACCTAGTG
1 TTTATCTACAAATTTTGTTGTGCATCCACAACCTAGTG
48529 GCAGTTTATT
Statistics
Matches: 143, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.03
44 133 0.93
45 5 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (44 bp):
TTTATCTACAAATTTTGTTGTGCATCCACAACCTAGTGACAGAT
Found at i:48723 original size:109 final size:110
Alignment explanation
Indices: 48512--48731 Score: 291
Period size: 109 Copynumber: 2.0 Consensus size: 110
48502 ATTTTGTTGT
* * ****
48512 GCATCCATAACCTAGTGGCAGTTTATTTGCAAACCAATGGTGGTTAAACCTCAACCCGGTGTATA
1 GCATCCATAACCTAGTGGCAGTTTATCTGCAAACCAATGGTGGTTAAACCACAACCCAAAATATA
* *
48577 AGGATGTTTGAGTTTAGGGGAACTACCAGTGAAGTGTGTAGTGGA
66 AGGATGTTTGAGTTCAGGGGAACTACCAATGAAGTGTGTAGTGGA
* *
48622 GCATCCATAAACC-AG-GGTAGTTTATCTGCAAACCAGTGGTGGTTAAACCACAACCCAAAATAT
1 GCATCCAT-AACCTAGTGGCAGTTTATCTGCAAACCAATGGTGGTTAAACCACAACCCAAAATAT
* * * *
48685 AAGGATGTTTGAGTTCAGGGGGACTCCCAATTAGGTGTGTAGTGGA
65 AAGGATGTTTGAGTTCAGGGGAACTACCAATGAAGTGTGTAGTGGA
48731 G
1 G
48732 TTGGGTAGGA
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
109 81 0.85
110 10 0.11
111 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (110 bp):
GCATCCATAACCTAGTGGCAGTTTATCTGCAAACCAATGGTGGTTAAACCACAACCCAAAATATA
AGGATGTTTGAGTTCAGGGGAACTACCAATGAAGTGTGTAGTGGA
Found at i:49602 original size:29 final size:31
Alignment explanation
Indices: 49557--49617 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
49547 GAGGGTGGGA
*
49557 TGGGAGGAGAGTAAAAGTTTT-AGGGGAAAG
1 TGGGAGGAGAATAAAAGTTTTGAGGGGAAAG
49587 TGGGA-GAGAATAAAAGTTTTGAGGGGAAAG
1 TGGGAGGAGAATAAAAGTTTTGAGGGGAAAG
49617 T
1 T
49618 AAAAAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (31 bp):
TGGGAGGAGAATAAAAGTTTTGAGGGGAAAG
Found at i:49682 original size:18 final size:18
Alignment explanation
Indices: 49659--49695 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49649 TATAGTTTGA
49659 TATTTG-GTCTATTCGAAT
1 TATTTGAGT-TATTCGAAT
49677 TATTTGAGTTATTCGAAT
1 TATTTGAGTTATTCGAAT
49695 T
1 T
49696 CAAAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (18 bp):
TATTTGAGTTATTCGAAT
Found at i:49762 original size:18 final size:18
Alignment explanation
Indices: 49741--49775 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49731 AAGAATTTTG
*
49741 AATTGACTCGAATAACTC
1 AATTAACTCGAATAACTC
49759 AATTAACTCGAATAACT
1 AATTAACTCGAATAACT
49776 TGAATCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
AATTAACTCGAATAACTC
Found at i:50949 original size:21 final size:20
Alignment explanation
Indices: 50924--50964 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
50914 TTATGCTTTC
50924 TTTTGAATTTTTATATTTTTA
1 TTTTGAATTTTT-TATTTTTA
50945 TTTTGAATTTTTTATTTTTA
1 TTTTGAATTTTTTATTTTTA
50965 AATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTGAATTTTTTATTTTTA
Found at i:50963 original size:15 final size:15
Alignment explanation
Indices: 50936--50974 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
50926 TTGAATTTTT
*
50936 ATATTTTTATTTTGA
1 ATATTTTTATTTTAA
50951 AT-TTTTTATTTTTAA
1 ATATTTTTA-TTTTAA
50966 ATATTTTTA
1 ATATTTTTA
50975 AATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATATTTTTATTTTAA
Found at i:50983 original size:11 final size:10
Alignment explanation
Indices: 50957--50984 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
50947 TTGAATTTTT
50957 TATTTTTAAA
1 TATTTTTAAA
50967 TATTTTTAAA
1 TATTTTTAAA
50977 TATTTTTA
1 TATTTTTA
50985 TTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:50989 original size:19 final size:20
Alignment explanation
Indices: 50956--51000 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
50946 TTTGAATTTT
50956 TTATTTTTAAATATTTTTAAA
1 TTATTTTTAAATA-TTTTAAA
*
50977 -TATTTTT-ATTATTTTAAA
1 TTATTTTTAAATATTTTAAA
50995 TTATTT
1 TTATTT
51001 GTTTTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTAAATATTTTAAA
Found at i:57033 original size:45 final size:45
Alignment explanation
Indices: 56839--57023 Score: 316
Period size: 45 Copynumber: 4.1 Consensus size: 45
56829 TTCTTCTTCA
56839 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
1 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
*
56884 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAA
1 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
56929 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
1 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
* * * * *
56974 TCTTCGTTTTCTTCTACAGGATATAATGATTCCATCAAAGGATAC
1 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
57019 TCTTC
1 TCTTC
57024 ATCATCTTCT
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (45 bp):
TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
Found at i:63204 original size:31 final size:31
Alignment explanation
Indices: 63147--63205 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
63137 TGATCAAATT
*
63147 AAAGTATAGGTCCTAATACTACAATTTACAC
1 AAAGTATAGGTCCTAATACTAAAATTTACAC
63178 AAAGTATAAGGT-CTAATAGC-AAAATTTA
1 AAAGTAT-AGGTCCTAATA-CTAAAATTTA
63206 ACCTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (31 bp):
AAAGTATAGGTCCTAATACTAAAATTTACAC
Found at i:79995 original size:166 final size:160
Alignment explanation
Indices: 79689--80000 Score: 405
Period size: 166 Copynumber: 1.9 Consensus size: 160
79679 TATATGATTG
* **
79689 TCAAATCTCAAAATCTAAAATATCTTCATAGCAAAACTCACATAATTCTTATGTATAATTTTAAT
1 TCAAATATCAAAATCTAAAATATCTTCATAGCAAAACTCACATAATTCAAATGTATAATTTTAAT
* * * *
79754 AGTCTTAGGAAAAAAAGAGATTTGGCCTTTCAAATTAGTAGTGCAGAAAATTTACAGAGTCAGAT
66 AGTCATAGGAAAAAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAATTCACAGAGTCAGAT
79819 TTTGAAGAGTTGAAATCAAGCATACAATTT
131 TTTGAAGAGTTGAAATCAAGCATACAATTT
* * *
79849 TCAAATATCAAATTCTAAGAATATTTTTCATTGCAAAAAACTCACATAATTCAAACT-TATAATT
1 TCAAATATCAAAATCTAA-AATA-TCTTCATAGC--AAAACTCACATAATTCAAA-TGTATAATT
* *
79913 TTAATGAAGTCATA-TAAAATAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAATTCACAT
61 TTAAT--AGTCATAGGAAAA-AAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAATTCACAG
*
79977 ATTCA-ATTTTGTAAGAGTTGAAAT
123 AGTCAGATTTTG-AAGAGTTGAAAT
80001 TAAATGAATG
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
160 16 0.12
161 4 0.03
162 8 0.06
164 29 0.22
165 11 0.08
166 62 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (160 bp):
TCAAATATCAAAATCTAAAATATCTTCATAGCAAAACTCACATAATTCAAATGTATAATTTTAAT
AGTCATAGGAAAAAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAATTCACAGAGTCAGAT
TTTGAAGAGTTGAAATCAAGCATACAATTT
Found at i:92054 original size:2 final size:2
Alignment explanation
Indices: 92049--92076 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
92039 AAATATTCCA
92049 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
92077 GATGTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101800 original size:5 final size:5
Alignment explanation
Indices: 101790--101816 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
101780 ACAGGTTGTC
101790 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
101817 ATAAATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:107101 original size:12 final size:12
Alignment explanation
Indices: 107063--107131 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
107053 CAACTTAATT
107063 GAACATGTTCAC
1 GAACATGTTCAC
* **
107075 GAATAT-TAAAC
1 GAACATGTTCAC
107086 GAACATGTTCAC
1 GAACATGTTCAC
* * *
107098 GAACAT-ATAATT
1 GAACATGTTCA-C
107110 GAACATGTTCAC
1 GAACATGTTCAC
107122 GAACAATGTT
1 GAAC-ATGTT
107132 AATGAATAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
11 10 0.24
12 24 0.59
13 7 0.17
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (12 bp):
GAACATGTTCAC
Found at i:107118 original size:24 final size:23
Alignment explanation
Indices: 107040--107126 Score: 106
Period size: 23 Copynumber: 3.7 Consensus size: 23
107030 TAATGTTCAC
107040 GAACATGTTCATTC-AAC-TTAATT
1 GAACATGTTCA--CGAACATTAATT
* **
107063 GAACATGTTCACGAATATTAAAC
1 GAACATGTTCACGAACATTAATT
107086 GAACATGTTCACGAACATATAATT
1 GAACATGTTCACGAACAT-TAATT
107110 GAACATGTTCACGAACA
1 GAACATGTTCACGAACA
107127 ATGTTAATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 32 0.58
24 20 0.36
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (23 bp):
GAACATGTTCACGAACATTAATT
Found at i:107188 original size:12 final size:12
Alignment explanation
Indices: 107171--107206 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
107161 CAATAAATAC
107171 ATAAACGAGCTT
1 ATAAACGAGCTT
**
107183 ATAAACGAGCCA
1 ATAAACGAGCTT
107195 ATAAACGAGCTT
1 ATAAACGAGCTT
107207 GTTCGTGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:109625 original size:21 final size:22
Alignment explanation
Indices: 109601--109641 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
109591 TATATTCGGG
*
109601 ATTTTGGATTTTA-GATTTTAA
1 ATTTCGGATTTTATGATTTTAA
109622 ATTTCGGATTTTATGATTTT
1 ATTTCGGATTTTATGATTTT
109642 TTTTTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (22 bp):
ATTTCGGATTTTATGATTTTAA
Found at i:110354 original size:58 final size:58
Alignment explanation
Indices: 110245--110354 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
110235 TTAATATAAT
* * * *
110245 ATTTGGTATCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTGACCCA
1 ATTTGATATATGAACTCGACACTTTTTCTTAATTTGGTATCTAAACATTTTTGACCCA
* *
110303 ATTTGATATATGAACTCGATACTTTTTTTCTAATTTGGTA-CTTAAA-ATTTTT
1 ATTTGATATATGAACTCGACACTTTTTCT-TAATTTGGTATC-TAAACATTTTT
110355 TTGGACCCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
58 30 0.68
59 14 0.32
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (58 bp):
ATTTGATATATGAACTCGACACTTTTTCTTAATTTGGTATCTAAACATTTTTGACCCA
Found at i:110389 original size:60 final size:59
Alignment explanation
Indices: 110245--110416 Score: 170
Period size: 60 Copynumber: 2.9 Consensus size: 59
110235 TTAATATAAT
* *
110245 ATTTGGTATCTGAACTTGACA-CTTTTTCTTAATTTGGTA-TCT-AAACTTTTTTGACCCA
1 ATTTGGTATCTGAACTTGACATTTTTTTC-TAATTTGGTACT-TAAAATTTTTTTGACCCA
* * * * *
110303 ATTTGATATATGAACTCGATACTTTTTTTCTAATTTGGTACTTAAAATTTTTTTGGACCCG
1 ATTTGGTATCTGAACTTGACA-TTTTTTTCTAATTTGGTACTTAAAATTTTTTT-GACCCA
* * * * * *
110364 ATTTGGTACCTTAACTTGACATTTTTTCCTAATTTAGTACCTAAGATTTTTTT
1 ATTTGGTATCTGAACTTGACATTTTTTTCTAATTTGGTACTTAAAATTTTTTT
110417 TAGATTCAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
58 17 0.18
59 11 0.12
60 44 0.48
61 20 0.22
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (59 bp):
ATTTGGTATCTGAACTTGACATTTTTTTCTAATTTGGTACTTAAAATTTTTTTGACCCA
Found at i:111250 original size:18 final size:20
Alignment explanation
Indices: 111227--111266 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
111217 GTCAATTTCC
111227 AATTATAAT-ATAAAAT-TA
1 AATTATAATAATAAAATGTA
*
111245 AATTATTATAATAAAATGTA
1 AATTATAATAATAAAATGTA
111265 AA
1 AA
111267 ACTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTATAATAATAAAATGTA
Found at i:118691 original size:28 final size:28
Alignment explanation
Indices: 118643--118697 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
118633 CACATTAACA
* *
118643 AAAAATTCAAAAATTCAAAAAATAATAT
1 AAAAATTCAAAAAATCAAAAAAGAATAT
118671 AAAAATTCAAAAAAT-ATAAAAAGAATA
1 AAAAATTCAAAAAATCA-AAAAAGAATA
118698 AGATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (28 bp):
AAAAATTCAAAAAATCAAAAAAGAATAT
Found at i:119110 original size:25 final size:26
Alignment explanation
Indices: 119064--119112 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
119054 AGTTGACTTG
*
119064 GTTATTTATTGAATAATTTTAAAACA
1 GTTATTTATTGAATAATATTAAAACA
119090 GTTATTATATT-AA-AATATTAAAA
1 GTTATT-TATTGAATAATATTAAAA
119113 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 8 0.38
27 4 0.19
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (26 bp):
GTTATTTATTGAATAATATTAAAACA
Found at i:119449 original size:30 final size:31
Alignment explanation
Indices: 119389--119468 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
119379 AGACATGATA
119389 GCTCTTATTTGAGCACTTTAAAAAATGTTTG
1 GCTCTTATTTGAGCACTTTAAAAAATGTTTG
* *
119420 GCTCTTACTTGATCACTTTAAAAAA-GTTTG
1 GCTCTTATTTGAGCACTTTAAAAAATGTTTG
*
119450 GCTCTTATTTGAGTACTTT
1 GCTCTTATTTGAGCACTTT
119469 TGTAAAGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 21 0.48
31 23 0.52
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (31 bp):
GCTCTTATTTGAGCACTTTAAAAAATGTTTG
Found at i:119625 original size:43 final size:43
Alignment explanation
Indices: 119559--119650 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
119549 CTCAATTTGA
* * * *
119559 GCGTTTGTGGGGAAAGCGTCGCTAAAGATCATGTTCTATAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAACG
* *
119602 GCGTTTGTGGGAAAATCGCCGCTAGAGACCATGTTCTATAACG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAACG
119645 GCGTTT
1 GCGTTT
119651 TTCCTCATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAACG
Found at i:122805 original size:191 final size:191
Alignment explanation
Indices: 122478--123225 Score: 1239
Period size: 191 Copynumber: 3.9 Consensus size: 191
122468 TTATTCATGG
* *
122478 TGTTCATTTAATAATAGTCGAATTGATGATGATTTTGATGCCTGATCCAGTTTTTAGTGCATTCA
1 TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCATTCA
* * *
122543 TAGAATTATTTTATACGAAATATATTGTTGATTTCAACTAAGAGTATATAA-ATAAAGTGTTAAG
66 TAGAATTATTTTATACAAAATATATTGTTGATTTCAACTAGGAGTATATAATA-AAAGTGTTATG
122607 TATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCCAACTTAAGTTAATGA
130 TATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCCAACTTAAGTTAATGA
* **
122669 TGCTCATTTAATAATAGTCGAACTGATGATGATTTTGATATCTGATCCAGCTTTTAGTGCATTCA
1 TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCATTCA
* * * *
122734 TAGAATTATTTTATATAAAATATATTGTAGATTTCAACTAGGAGTAGATAGTAAAAGAT-TTATG
66 TAGAATTATTTTATACAAAATATATTGTTGATTTCAACTAGGAGTATATAATAAAAG-TGTTATG
* *
122798 TATGAAAGTGAATGGTTAGAATTAGTAAAATTATAACACCAAAATCCAACTTAAGTTAATGA
130 TATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCCAACTTAAGTTAATGA
*
122860 TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGAATTCA
1 TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCATTCA
* * *
122925 TAGAATTATTTTATACAAAATATAATGTTGATTTCAACTAGGAGTATATAATAGAAGTGTAATGT
66 TAGAATTATTTTATACAAAATATATTGTTGATTTCAACTAGGAGTATATAATAAAAGTGTTATGT
*
122990 ATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCTAACTTAAGTTAATGA
131 ATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCCAACTTAAGTTAATGA
* *
123051 TGTTCATTTAATAATTGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCTTTCA
1 TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCATTCA
* *
123116 TAGTATTATTTTATACAAAAATATATTGTTGATTTCAATTAGGAGTATATAATAAAAGTGTTATG
66 TAGAATTATTTTATAC-AAAATATATTGTTGATTTCAACTAGGAGTATATAATAAAAGTGTTATG
*
123181 TATGAAAGTGAATGGTTAGAATTAGTAAAACTGTAACACCCAAAT
130 TATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAAT
123226 TCGGTCTAAG
Statistics
Matches: 516, Mismatches: 37, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
190 1 0.00
191 425 0.82
192 90 0.17
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (191 bp):
TGTTCATTTAATAATAGTCGAACTGATGATGATTTTGATGCCTGATCCAGCTTTTAGTGCATTCA
TAGAATTATTTTATACAAAATATATTGTTGATTTCAACTAGGAGTATATAATAAAAGTGTTATGT
ATGAAAGTGAATGGTTAGAATTAGTAAAATTGTAACACCCAAATCCAACTTAAGTTAATGA
Found at i:123774 original size:29 final size:29
Alignment explanation
Indices: 123732--123895 Score: 195
Period size: 29 Copynumber: 5.7 Consensus size: 29
123722 TACAGATATA
* *
123732 ATAC-GATATAGTTACAAATGCAAACATG
1 ATACAGATACAGTTACAGATGCAAACATG
***
123760 ATACAGATACAGTTACAGATGTGGACATG
1 ATACAGATACAGTTACAGATGCAAACATG
*
123789 ATACATATACAGTTACAGATGCAAACATG
1 ATACAGATACAGTTACAGATGCAAACATG
* * *
123818 ATATAGATACAATTACAGATGCAAACACG
1 ATACAGATACAGTTACAGATGCAAACATG
* * * *
123847 GTACAAATACAGTTATAGATGCAAACACG
1 ATACAGATACAGTTACAGATGCAAACATG
*
123876 GTACAGATACAGTTACAGAT
1 ATACAGATACAGTTACAGAT
123896 TTAGACACAG
Statistics
Matches: 115, Mismatches: 20, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
28 4 0.03
29 111 0.97
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (29 bp):
ATACAGATACAGTTACAGATGCAAACATG
Found at i:124411 original size:53 final size:53
Alignment explanation
Indices: 124330--124720 Score: 376
Period size: 53 Copynumber: 7.3 Consensus size: 53
124320 TTATTACAGA
* * *
124330 CCATGTGTCTCAAAACATTATACACACACCCTGACACACGCTCGTGTGTCAGT
1 CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGTCAGC
* * * *
124383 TCATGTGCCGCAAAACAGTATACACACACCTTGACACACGC-C-TATGTGCTAGC
1 CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGT-C-AGC
* * * * **
124436 CCGTGTGCCTCAAAACAGTATACATACACACCGTGACACAAGCCCGTGTACCAGC
1 CCATGTGCCTCAAAACAGTATAC--ACACACCCTGACACACGCTCGTGTGTCAGC
* * * * *
124491 CCGTGTGCCTCCAAATAGTATACACACACCTTGACACACGCTCATGTGTCAGC
1 CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGTCAGC
* * * * *
124544 CCGTGTGCCTCCAAACTA-TATACACAAACCCTAACACACGCTCGTGTATCAGC
1 CCATGTGCCTCAAAAC-AGTATACACACACCCTGACACACGCTCGTGTGTCAGC
* * * * * * * * *
124597 CCGTGTTCCTCCAAATAATATGCACACACCCTAACACATGCCCGTGT-TCTAGC
1 CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGTC-AGC
* * * *
124650 CCATGTGCCTCAAAACAGTATACATACACCTTGACACATGTTCGTGTGTCAGC
1 CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGTCAGC
124703 CCATGTGCCTCAAAACAG
1 CCATGTGCCTCAAAACAG
124721 CACCATTTCG
Statistics
Matches: 282, Mismatches: 46, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
51 4 0.01
52 5 0.02
53 226 0.80
54 3 0.01
55 40 0.14
56 2 0.01
57 2 0.01
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (53 bp):
CCATGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTGTCAGC
Found at i:124651 original size:106 final size:106
Alignment explanation
Indices: 124333--124713 Score: 415
Period size: 106 Copynumber: 3.6 Consensus size: 106
124323 TTACAGACCA
* * * ** * * *
124333 TGTGTCTCAAAACATTATACACACACCCTGACACACGCTCGTGTGTCAGTTCATGTGCCGCAAAA
1 TGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTATCAGCCCGTGTGCCTCCAAA
* * *
124398 CAGTATACACACACCTTGACACACGCCTATGTGCTAGCCCG
66 TAGTATACACACACCTTGACACACGCCCATGTTCTAGCCCG
* * * *
124439 TGTGCCTCAAAACAGTATACATACACACCGTGACACAAGCCCGTGTACCAGCCCGTGTGCCTCCA
1 TGTGCCTCAAAACAGTATAC--ACACACCCTGACACACGCTCGTGTATCAGCCCGTGTGCCTCCA
*
124504 AATAGTATACACACACCTTGACACACGCTCATGTGTC-AGCCCG
64 AATAGTATACACACACCTTGACACACGCCCATGT-TCTAGCCCG
* * * *
124547 TGTGCCTCCAAACTA-TATACACAAACCCTAACACACGCTCGTGTATCAGCCCGTGTTCCTCCAA
1 TGTGCCTCAAAAC-AGTATACACACACCCTGACACACGCTCGTGTATCAGCCCGTGTGCCTCCAA
* * * * * * *
124611 ATAATATGCACACACCCTAACACATGCCCGTGTTCTAGCCCA
65 ATAGTATACACACACCTTGACACACGCCCATGTTCTAGCCCG
* * * * * *
124653 TGTGCCTCAAAACAGTATACATACACCTTGACACATGTTCGTGTGTCAGCCCATGTGCCTC
1 TGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTATCAGCCCGTGTGCCTC
124714 AAAACAGCAC
Statistics
Matches: 227, Mismatches: 42, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
105 3 0.01
106 135 0.59
108 87 0.38
109 2 0.01
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (106 bp):
TGTGCCTCAAAACAGTATACACACACCCTGACACACGCTCGTGTATCAGCCCGTGTGCCTCCAAA
TAGTATACACACACCTTGACACACGCCCATGTTCTAGCCCG
Found at i:124681 original size:159 final size:160
Alignment explanation
Indices: 124330--124720 Score: 448
Period size: 161 Copynumber: 2.4 Consensus size: 160
124320 TTATTACAGA
* * * ** *
124330 CCATGTGTCTCAAAACATTATACACACACCCTGACACACGCTCGTGTGTCAGTTCATGTGCCGCA
1 CCATGTGCCTCAAAACAGTATACACACACCTTGACACACGCTCGTGTGTCAGCCCATGTGCCTCA
* * * *
124395 AAACAGTATACACACACCTTGACACACGCCTATGTGCTAGCCCGTGTGCCTCAAAACAGTATACA
66 AAACAGTATACACAAACCCTAACACACGCCTATGTGCTAGCCCGTGTGCCTCAAAACAATATACA
* *
124460 TACACACCGTGACACAAGCCCGTGTACCAGC
131 -ACACACCCTAACACAAGCCCGTGTACCAGC
* * * * * *
124491 CCGTGTGCCTCCAAATAGTATACACACACCTTGACACACGCTCATGTGTCAGCCCGTGTGCCTCC
1 CCATGTGCCTCAAAACAGTATACACACACCTTGACACACGCTCGTGTGTCAGCCCATGTGCCTCA
* * * * *
124556 AAACTA-TATACACAAACCCTAACACACG-CT-CGTGTATCAGCCCGTGTTCCTCCAAATAATAT
66 AAAC-AGTATACACAAACCCTAACACACGCCTATGTG-CT-AGCCCGTGTGCCTCAAAACAATAT
* * * *
124618 GC-ACACACCCTAACACATGCCCGTGTTCTAGC
128 ACAACACACCCTAACACAAGCCCGTGTACCAGC
* * *
124650 CCATGTGCCTCAAAACAGTATACATACACCTTGACACATGTTCGTGTGTCAGCCCATGTGCCTCA
1 CCATGTGCCTCAAAACAGTATACACACACCTTGACACACGCTCGTGTGTCAGCCCATGTGCCTCA
124715 AAACAG
66 AAACAG
124721 CACCATTTCG
Statistics
Matches: 190, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
158 1 0.01
159 88 0.46
160 3 0.02
161 97 0.51
162 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (160 bp):
CCATGTGCCTCAAAACAGTATACACACACCTTGACACACGCTCGTGTGTCAGCCCATGTGCCTCA
AAACAGTATACACAAACCCTAACACACGCCTATGTGCTAGCCCGTGTGCCTCAAAACAATATACA
ACACACCCTAACACAAGCCCGTGTACCAGC
Found at i:127871 original size:8 final size:8
Alignment explanation
Indices: 127854--127897 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
127844 AGAGAAACCC
*
127854 AAACTGTA
1 AAACTCTA
127862 AAACTCTA
1 AAACTCTA
127870 AAACTCTA
1 AAACTCTA
127878 AAACTCTA
1 AAACTCTA
127886 AAACTCTA
1 AAACTCTA
127894 AAAC
1 AAAC
127898 AAGCTCTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (8 bp):
AAACTCTA
Found at i:130367 original size:21 final size:21
Alignment explanation
Indices: 130332--130377 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
130322 TTATTTTTTC
130332 AATTTAAACTAAAATGTTACTA
1 AATTTAAACTAAAATGTTA-TA
* *
130354 AATTTACA-TAAAATTTTATA
1 AATTTAAACTAAAATGTTATA
130374 AATT
1 AATT
130378 GTATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTTAAACTAAAATGTTATA
Found at i:130519 original size:1 final size:1
Alignment explanation
Indices: 130513--130542 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
130503 NNNNNNNNNN
130513 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
130543 GGAGGCAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:133410 original size:30 final size:30
Alignment explanation
Indices: 133356--133417 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
133346 ACTAGTTCTA
** * *
133356 GAATTTGCTACAGTAGGAGGAACAGGACTT
1 GAATTTGCTACAACAGGAGAAACAGAACTT
*
133386 GAATTTGCTACAACAGGTGAAACAGAACTT
1 GAATTTGCTACAACAGGAGAAACAGAACTT
133416 GA
1 GA
133418 GGCACTTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (30 bp):
GAATTTGCTACAACAGGAGAAACAGAACTT
Found at i:136949 original size:21 final size:21
Alignment explanation
Indices: 136904--136952 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
136894 TTAAGTTCTA
* * *
136904 AACCCTAAACTTTAGATCTTT
1 AACCCTAAACTTTAGACCATG
*
136925 AACCCTAAACTTTTGACCATG
1 AACCCTAAACTTTAGACCATG
136946 AACCCTA
1 AACCCTA
136953 CACCTTGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.31
Consensus pattern (21 bp):
AACCCTAAACTTTAGACCATG
Found at i:136965 original size:7 final size:7
Alignment explanation
Indices: 136953--136979 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
136943 ATGAACCCTA
136953 CACCTTG
1 CACCTTG
136960 CACCTTG
1 CACCTTG
136967 CACCTTG
1 CACCTTG
136974 CACCTT
1 CACCTT
136980 ACACTAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.44, G:0.11, T:0.30
Consensus pattern (7 bp):
CACCTTG
Found at i:137027 original size:21 final size:20
Alignment explanation
Indices: 137003--137048 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
136993 AAATTTAAGA
*
137003 TCTAAGCTTTAGGGTTCAAGG
1 TCTAAGC-TTAGAGTTCAAGG
*
137024 TCTAAAGCTTAGAGTTTAAGG
1 TCT-AAGCTTAGAGTTCAAGG
137045 TCTA
1 TCTA
137049 GGATCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (20 bp):
TCTAAGCTTAGAGTTCAAGG
Found at i:139229 original size:2 final size:2
Alignment explanation
Indices: 139222--139257 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
139212 AGAACACAAA
*
139222 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
139258 TTTTGAGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:144365 original size:2 final size:2
Alignment explanation
Indices: 144352--144388 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
144342 AAAGAACACA
*
144352 AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
144389 TTTGAGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:144567 original size:20 final size:20
Alignment explanation
Indices: 144542--144579 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
144532 CTACAACAAG
*
144542 AATCTCTAAGATTACAATCA
1 AATCTCTAAGATCACAATCA
144562 AATCTCTAAGATCACAAT
1 AATCTCTAAGATCACAAT
144580 GATCATACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
AATCTCTAAGATCACAATCA
Found at i:145054 original size:9 final size:10
Alignment explanation
Indices: 145023--145055 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
145013 TGAAATTAAA
145023 TTATATATTT
1 TTATATATTT
145033 TTATTATATTT
1 TTA-TATATTT
145044 TTATA-ATTT
1 TTATATATTT
145053 TTA
1 TTA
145056 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 5 0.23
11 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATATATTT
Found at i:145104 original size:28 final size:30
Alignment explanation
Indices: 145037--145104 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 30
145027 ATATTTTTAT
* *
145037 TATATTTTTATAATTTTTAAAAAATTAAAT
1 TATAATTTTATAATTTTTAAAAAATTAAAA
* * *
145067 TA-AATATTAT-ATTTTT-AGAGATTAAAA
1 TATAATTTTATAATTTTTAAAAAATTAAAA
145094 TATAATTTTAT
1 TATAATTTTAT
145105 TAATATTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 10 0.32
28 13 0.42
29 6 0.19
30 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAAAATTAAAA
Found at i:147144 original size:31 final size:31
Alignment explanation
Indices: 147108--147168 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
147098 AGGTAGTGAC
**
147108 TTAAAT-AAAATCTTTTGAATAATTCAATAAT
1 TTAAATGAAAA-CTTTCAAATAATTCAATAAT
*
147139 TTAAATGAAAACTTTCAAATAGTTCAATAA
1 TTAAATGAAAACTTTCAAATAATTCAATAA
147169 CTATTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
TTAAATGAAAACTTTCAAATAATTCAATAAT
Found at i:156218 original size:21 final size:21
Alignment explanation
Indices: 156194--156234 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
156184 GATTTAAAAA
*
156194 AAATTTTAATCGAGTGAAATG
1 AAATTTGAATCGAGTGAAATG
156215 AAATTTGAATCGAGTGAAAT
1 AAATTTGAATCGAGTGAAAT
156235 TGTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (21 bp):
AAATTTGAATCGAGTGAAATG
Found at i:156476 original size:24 final size:24
Alignment explanation
Indices: 156449--156494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
156439 TTTTCATATT
* * *
156449 TTTTAGAATTTTTTTAAATATAAG
1 TTTTAAAAATTTTATAAATATAAG
156473 TTTTAAAAATTTTATAAATATA
1 TTTTAAAAATTTTATAAATATA
156495 TTGAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTTAAAAATTTTATAAATATAAG
Done.