Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006842.1 Hibiscus syriacus cultivar Beakdansim tig00017393_pilon, 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: 133982
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3808 original size:31 final size:32
Alignment explanation
Indices: 3770--3833 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
3760 TAGATGGGCT
* *
3770 CTGCGGCCCTGAGAT-TATTCTCGGGTAGGCC
1 CTGCGGCCCTAAGATGTATTCTCAGGTAGGCC
* *
3801 CTGCGGCCCTAAGATGTGTTCTTAGGTAGGCC
1 CTGCGGCCCTAAGATGTATTCTCAGGTAGGCC
3833 C
1 C
3834 GTGGCCCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.27
Consensus pattern (32 bp):
CTGCGGCCCTAAGATGTATTCTCAGGTAGGCC
Found at i:10417 original size:32 final size:32
Alignment explanation
Indices: 10377--10498 Score: 147
Period size: 32 Copynumber: 3.8 Consensus size: 32
10367 AGGAATAATG
* *
10377 GGGGCATCTTTAAAGGTTCAACATCAAATGTT
1 GGGGCATCTTTGAAGGTTCAACATTAAATGTT
10409 GGGGCATCTTTGAAGGTTCAACATTAAATGTT
1 GGGGCATCTTTGAAGGTTCAACATTAAATGTT
* * * * *
10441 GAGGCATTTTTGAAGATTCAACATTGAATATT
1 GGGGCATCTTTGAAGGTTCAACATTAAATGTT
* *
10473 GGGTCATCTTTG-GGGATTCAACATTA
1 GGGGCATCTTTGAAGG-TTCAACATTA
10499 TGATGTGAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
31 1 0.01
32 75 0.99
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (32 bp):
GGGGCATCTTTGAAGGTTCAACATTAAATGTT
Found at i:10957 original size:63 final size:65
Alignment explanation
Indices: 10792--10968 Score: 306
Period size: 64 Copynumber: 2.8 Consensus size: 65
10782 TCAATAAATA
*
10792 AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
1 AAGTTTAATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
* *
10857 AAGTTTAATTCAGA-TCAATTTCAACTTCGCAGCGAAGGATATTGGACTCAACAAACAACTTTCC
1 AAGTTTAATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
10921 -AGTTT-ATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTC
1 AAGTTTAATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTC
10969 GAAGTGACAT
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
62 7 0.07
63 38 0.36
64 48 0.45
65 13 0.12
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (65 bp):
AAGTTTAATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
Found at i:11345 original size:227 final size:226
Alignment explanation
Indices: 11052--11722 Score: 927
Period size: 227 Copynumber: 2.9 Consensus size: 226
11042 GAAATAGTAC
* *
11052 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAATGAATGG-GCCA
1 TTGGATTTCAACTTCACGAC-AAAGATATCCAATTCAAAGCTCAACTTCACAATGAA-GGAGCCA
*
11116 TCCACGATTTCAACTTCACGACGAAAGATATCGTGACATTCATATTTAGATTGGATTTCAACTTC
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTGACATTCATATTTAGATTGGATTTCAACTTC
11181 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-GAAGGAGCCATCCACGATTTCAACTT
129 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACGATTTCAACTT
11245 CACGACGAAGGATATCATGT-CATTCATCTTTAG
194 CACGACGAAGGATATCAT-TCCATTCATCTTTAG
* * *
11278 ATTGGATTTTAACTTCACGACAAAGGATATCCAATTTAAAGCTCAACTTCACAATTAAGGAGCCA
1 -TTGGATTTCAACTTCACGACAAA-GATATCCAATTCAAAGCTCAACTTCACAATGAAGGAGCCA
* *
11343 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGATTGGATTTCAACTTC
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTGACATTCATATTTAGATTGGATTTCAACTTC
* * * *
11408 ATGACGAAGGATATCCAATTCAAGGCTCAACTTCATAACGAAGGGGCCATCCACGATTTCAACTT
129 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACGATTTCAACTT
* *
11473 CACAACGAAGGATATCGTTCCATTCATCTTTAG
194 CACGACGAAGGATATCATTCCATTCATCTTTAG
* *
11506 TTGGGATTTCAACTTCACGACAAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCA
1 TT-GGATTTCAACTTCACGAC-AAAGATATCCAATTCAAAGCTCAACTTCACAATGAAGGAGCCA
* ** * **
11571 TCCATGATTTCAACTTCACGACGAAGGATATCGTGCACACAAGCAGCAATGCA-ACCCTTGGATT
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTG---ACATTCA--TATTTAGA---TTGGATT
* * * **
11635 TCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCGTGAT
121 TCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACGAT
*
11700 TTCAAATTCACGACGAAGGATAT
186 TTCAACTTCACGACGAAGGATAT
11723 GTCCCCAACG
Statistics
Matches: 392, Mismatches: 38, Indels: 20
0.87 0.08 0.04
Matches are distributed among these distances:
226 5 0.01
227 152 0.39
228 141 0.36
229 3 0.01
231 4 0.01
232 1 0.00
233 2 0.01
235 84 0.21
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (226 bp):
TTGGATTTCAACTTCACGACAAAGATATCCAATTCAAAGCTCAACTTCACAATGAAGGAGCCATC
CACGATTTCAACTTCACGACGAAGGATATCGTGACATTCATATTTAGATTGGATTTCAACTTCAC
GACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACGATTTCAACTTCA
CGACGAAGGATATCATTCCATTCATCTTTAG
Found at i:11390 original size:114 final size:114
Alignment explanation
Indices: 11052--11722 Score: 886
Period size: 114 Copynumber: 5.8 Consensus size: 114
11042 GAAATAGTAC
* * *
11052 TTGGATTTCAACTTCACAACGAAA-GATATCCAATTCAAGGCTCAACTTCACAATGAATGG-GCC
1 TTGGATTTCAACTTCACGAC-AAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA-GGAGCC
* * *
11115 ATCCACGATTTCAACTTCACGACGAAAGATATCGTGACATTCATATTTAGA
64 ATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
*
11166 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-GAAGGAGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
11230 CCACGATTTCAACTTCACGACGAAGGATATCATGTCATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
* * **
11279 TTGGATTTTAACTTCACGACAAAGGATATCCAATTTAAAGCTCAACTTCACAATTAAGGAGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
11344 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
* * * * *
11393 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCATAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
11458 CCACGATTTCAACTTCACAACGAAGGATATCGT-TCCATTCATCTTTAG-
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGT-CATTCATCTTTAGA
* *
11506 TTGGGATTTCAACTTCACGACAAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCA
1 TT-GGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
* ** * ***
11571 TCCATGATTTCAACTTCACGACGAAGGATATCGTG-CACACAAGCAGCAATGCAA
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTC-ATC-TTTA-G--A
** * *
11625 CCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGT
1 ---TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGC
** *
11690 CATCCGTGATTTCAAATTCACGACGAAGGATAT
63 CATCCACGATTTCAACTTCACGACGAAGGATAT
11723 GTCCCCAACG
Statistics
Matches: 499, Mismatches: 43, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
112 2 0.00
113 111 0.22
114 295 0.59
115 1 0.00
116 1 0.00
121 87 0.17
122 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (114 bp):
TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
Found at i:12224 original size:84 final size:84
Alignment explanation
Indices: 11942--12224 Score: 304
Period size: 84 Copynumber: 3.4 Consensus size: 84
11932 GATTATATTC
* * * ** * *
11942 AGCTCAAGGCAAGAATGGTTATCTTTC-ATTAAAGACCTTCGAGTTTGATTACATTCAGCACAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
* * *
12006 GGCATATCAAATTTATA-TCAT
66 GGCACAT--TATTTGTAGT-AT
* * *
12027 AACTCAAGGCTAGAAGGGATATCTGTCAAC-AAAGACCTTCAAGTTCGATTACATTCAGCTCAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
*
12091 GGCACATTATTTGCAGCT-T
66 GGCACATTATTTGTAG-TAT
* * * *
12110 AGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
*
12175 GACACATTATTTGTAGTAT
66 GGCACATTATTTGTAGTAT
* * *
12194 AGCTCAAGGCGAGAAGGGTTATATGTCAACA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACA
12225 GGAAACTGCT
Statistics
Matches: 166, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
83 32 0.19
84 73 0.44
85 60 0.36
86 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (84 bp):
AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
GGCACATTATTTGTAGTAT
Found at i:12253 original size:84 final size:84
Alignment explanation
Indices: 12029--12255 Score: 228
Period size: 84 Copynumber: 2.7 Consensus size: 84
12019 TATATCATAA
* * * * * * *
12029 CTCAAGGCTAGAAGGGATATCTGTCAAC-AAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
12093 CACATTATTTGCAGCTTAG
66 CACATTATTTGCAGCTTAG
* * * *
12112 CTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGA
1 CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
*
12177 CACATTATTTGTAG-TATAG
66 CACATTATTTGCAGCT-TAG
* * * * * * *
12196 CTCAAGGCGAGAAGGGTTATATGTCAACAGGAA-A-CTGCTGAGTTCGATTCCATTCAGCTC
1 CTCAAGGCAAGAAGAGCTATATGCCAACA-AAAGACCTGC-AAGTTCGATTACATTCAGCTC
12256 GATGACATAT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
83 28 0.23
84 91 0.75
85 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (84 bp):
CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
CACATTATTTGCAGCTTAG
Found at i:13859 original size:14 final size:14
Alignment explanation
Indices: 13827--13861 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13817 TGTTTTTATT
13827 TTATTTTATTTTAG
1 TTATTTTATTTTAG
* *
13841 GTATTTTATTTTCG
1 TTATTTTATTTTAG
13855 TTATTTT
1 TTATTTT
13862 CAATTTGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (14 bp):
TTATTTTATTTTAG
Found at i:17859 original size:14 final size:15
Alignment explanation
Indices: 17840--17884 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
17830 GGGTTTGGAG
17840 AACATAAACGAACA-
1 AACATAAACGAACAT
*
17854 AACATAAATGAACAT
1 AACATAAACGAACAT
*
17869 AA-ACAAACGAACAT
1 AACATAAACGAACAT
17883 AA
1 AA
17885 ATGAACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.64, C:0.18, G:0.07, T:0.11
Consensus pattern (15 bp):
AACATAAACGAACAT
Found at i:17903 original size:24 final size:24
Alignment explanation
Indices: 17839--17895 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
17829 CGGGTTTGGA
*
17839 GAACATAAACGAACAAACATAAAT
1 GAACATAAACGAACGAACATAAAT
*
17863 GAACATAAACAAACGAACATAAAT
1 GAACATAAACGAACGAACATAAAT
17887 GAACATAAA
1 GAACATAAA
17896 TGATCGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.63, C:0.16, G:0.09, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACGAACATAAAT
Found at i:19701 original size:16 final size:19
Alignment explanation
Indices: 19680--19721 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
19670 AATATTCTCA
19680 GTAATC-CTATTCCC-C-G
1 GTAATCTCTATTCCCACTG
*
19696 GTAATCTTTATTCCCACTG
1 GTAATCTCTATTCCCACTG
19715 GTAATCT
1 GTAATCT
19722 TACATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 1 0.05
19 8 0.36
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (19 bp):
GTAATCTCTATTCCCACTG
Found at i:19709 original size:17 final size:19
Alignment explanation
Indices: 19687--19722 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19677 TCAGTAATCC
19687 TATTCCC-C-GGTAATCTT
1 TATTCCCACTGGTAATCTT
19704 TATTCCCACTGGTAATCTT
1 TATTCCCACTGGTAATCTT
19723 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (19 bp):
TATTCCCACTGGTAATCTT
Found at i:20001 original size:2 final size:2
Alignment explanation
Indices: 19996--20514 Score: 294
Period size: 2 Copynumber: 257.0 Consensus size: 2
19986 TATGTGTGTG
19996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
20080 TA TA TA TA TA CA CT- TA TC TA TA TA CT- TA T- TT TCA TA CA TCA
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA T-A TA TA T-A
* * *
20121 TA CA TA TA TA CT- TA TG TA TA GTT TA TA TA TA TA CTA TA TA GT-
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA
* * * * *
20163 TA TA T- TT TCA TA GTT TA TA GTT TA TA TA TT TA TA CTA TA TA GTT
1 TA TA TA TA T-A TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA
* * *
20207 TA TA TA CT- TA TA CTT TA TA TA TG TA CT- TT 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
* * * *
20248 TA T- TCA TA CT- TA TG TA CA TA CA TCA TA CA TA TA CT- TA TA TA
1 TA TA T-A TA -TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA
* * *
20289 TA TT TA TA TT TA TA -A TT 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
20330 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA CTA -A 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
* * * * * *
20371 CT- TA TA TA TA TA CA CA TCA TA CA TA TG TA CA TA CA T- TA T- TA
1 -TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
20412 -A TCA -A TGA TA TA T- TA -A TA T- TA TG TG CA TA CA TCA TG TA
1 TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
20450 TA AA TA CA TA TA TCA T- TGA TCA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA T-A T-A TA TA TA TA TA TA TA TA TA TA
20491 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
20515 CATAAGTGGA
Statistics
Matches: 401, Mismatches: 64, Indels: 104
0.70 0.11 0.18
Matches are distributed among these distances:
1 24 0.06
2 339 0.85
3 38 0.09
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20180 original size:15 final size:14
Alignment explanation
Indices: 20157--20226 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
20147 ATATATACTA
20157 TATAG-TTATATTT
1 TATAGTTTATATTT
20170 TCATAGTTTATAGTTT
1 T-ATAGTTTATA-TTT
* *
20186 ATATA-TTTATACTA
1 -TATAGTTTATATTT
*
20200 TATAGTTTATATACT
1 TATAGTTTATAT-TT
*
20215 TATACTTTATAT
1 TATAGTTTATAT
20227 ATGTACTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 5 0.11
14 11 0.24
15 22 0.49
16 6 0.13
17 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (14 bp):
TATAGTTTATATTT
Found at i:20225 original size:7 final size:7
Alignment explanation
Indices: 20137--20210 Score: 53
Period size: 7 Copynumber: 10.6 Consensus size: 7
20127 TATACTTATG
20137 TATAGTT
1 TATAGTT
*
20144 TATA-TA
1 TATAGTT
* *
20150 TATACTA
1 TATAGTT
20157 TATAG-T
1 TATAGTT
*
20163 TATATTT
1 TATAGTT
20170 TCATAGTT
1 T-ATAGTT
20178 TATAGTT
1 TATAGTT
*
20185 TATATATT
1 TATA-GTT
* *
20193 TATACTA
1 TATAGTT
20200 TATAGTT
1 TATAGTT
20207 TATA
1 TATA
20211 TACTTATACT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
6 9 0.17
7 32 0.60
8 12 0.23
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (7 bp):
TATAGTT
Found at i:24023 original size:22 final size:24
Alignment explanation
Indices: 23996--24049 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
23986 TTTTTCATTG
23996 AAAAACCG-AT-AAACCGAACCGA
1 AAAAACCGTATCAAACCGAACCGA
24018 AAAAACCGCATTATCAAACCGAACCGA
1 AAAAACCG---TATCAAACCGAACCGA
24045 AAAAA
1 AAAAA
24050 TCGGTTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 8 0.30
26 2 0.07
27 17 0.63
ACGTcount: A:0.56, C:0.26, G:0.11, T:0.07
Consensus pattern (24 bp):
AAAAACCGTATCAAACCGAACCGA
Found at i:47357 original size:11 final size:11
Alignment explanation
Indices: 47341--47365 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47331 AGGAAATGCG
47341 GGTTAATATAC
1 GGTTAATATAC
47352 GGTTAATATAC
1 GGTTAATATAC
47363 GGT
1 GGT
47366 GTTATCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:47753 original size:20 final size:19
Alignment explanation
Indices: 47716--47776 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
47706 ATATCGATCC
*
47716 AAAATGAT-ATACCAGGTAA
1 AAAATGATAAAACC-GGTAA
47735 AAATATGATAAAACCGGTAA
1 AAA-ATGATAAAACCGGTAA
47755 GAAAATGATAAAACCGGTAA
1 -AAAATGATAAAACCGGTAA
47775 AA
1 AA
47777 CGTTACCGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 26 0.68
21 7 0.18
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:47835 original size:180 final size:182
Alignment explanation
Indices: 47519--47990 Score: 648
Period size: 181 Copynumber: 2.6 Consensus size: 182
47509 GATCCAAATT
* * * * *
47519 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAAACCAGTATTG-AAATGA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGA-TAAAACCGGTA-TGAAAATGA
* * * * * *
47583 TAAAACTGGTAAAGCGCTA-CGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
64 TAAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACT
* *
47647 TCGTGAATTTAAAAGA-AAGCAGTTTTAAG-TCCTATAAAGTGTCGATACTTTTA
129 TCGTGAATTTAAAAGAGAAGCAGTTTT-AGCGCCTATAAAGTGTCGATACTTTAA
* * *
47700 AAAAATATATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTAAGAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
* * * *
47765 AAACCGGTAAAACGTTACCGAATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
47829 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* ** *
47881 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAAAAGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
*
47946 AAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
47991 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
179 1 0.00
180 65 0.25
181 191 0.74
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:47933 original size:20 final size:20
Alignment explanation
Indices: 47910--47948 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47900 ACGATATAAC
47910 AGGTA-AAAATATGATAAAAA
1 AGGTATAAAA-ATGATAAAAA
*
47930 AGGTATCAAAATGATAAAA
1 AGGTATAAAAATGATAAAA
47949 CCGGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (20 bp):
AGGTATAAAAATGATAAAAA
Found at i:50153 original size:21 final size:21
Alignment explanation
Indices: 50127--50191 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
50117 AAGACAATCA
*
50127 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
50148 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
50169 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
50190 AG
1 AG
50192 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:50267 original size:33 final size:33
Alignment explanation
Indices: 50225--50290 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
50215 AAATAGATGG
*
50225 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
50258 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
50291 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:52104 original size:19 final size:19
Alignment explanation
Indices: 52080--52128 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
52070 AATGTAGGGT
52080 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
52099 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
52118 TAATTTTGTAT
1 TAATTTTGTAT
52129 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:52588 original size:200 final size:200
Alignment explanation
Indices: 52246--54000 Score: 2710
Period size: 200 Copynumber: 8.9 Consensus size: 200
52236 CAATATGGCC
* *
52246 AACAGGGTGCAACCATAAAGTGTCGAACCATATAT-AAAAGTGTCGATCCCAAAAACTTCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
52310 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
52375 GAATATGTCTAAATAATGTGTCGACAGTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
52440 TGGAA
196 TGGAA
52445 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
52510 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
52575 AAATATGTCTAAATAATTTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
52640 TGGAA
196 TGGAA
* *
52645 AACATGGTGCAACCATAAAGTGTCGATCCATATA-ACAAAAGTATCGATCCCAAAAACATCGAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATA-AAAAGTGTCGATCCCAAAAACATCGAAA
*
52709 ACCAAAAGTACAATGTAATATGTAATTTTTTAATCTAACCGGTACAAGTATACCGGTTTTATGAG
65 ACCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
*
52774 AGAATATGTCTAAATAATGTGTCGACAGTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
52839 ATGGAA
195 ATGGAA
* * *
52845 AACATGGTGCAACCATAAAGTGTCGATTCATATATAGAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
52910 CCAAAAGTGCAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
52975 GAATATGTCTAAATAATGTGTCGACACTTTATTAGTTTGTGTCGATATTTGTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
53040 TGGAA
196 TGGAA
* **
53045 AACAGGATGTGACCATAAAGTGTCGATCCATATA-ACAAAAGTGTCGATCCCAAAAACATCGAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATA-AAAAGTGTCGATCCCAAAAACATCGAAA
*
53109 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
65 ACCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
53174 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
53239 ATGGAA
195 ATGGAA
* * *
53245 AACATGGTGCAATCATAAAGTGTCGATCCATATATAGAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
53310 CCAAAAGTACAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* * *
53375 GAATATGTCTAAATAATGTGTCGACACTTTGTTAGTTTGTGACGATATTTGTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
53440 TGGAA
196 TGGAA
* *
53445 AACAGGGTGCAACCATAAAGTGTCGATCC-----CAAAAA----C-AT--CGAAAAC--C-AAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
** * * * * * ** * * *
53495 GTATAATGTA-ATATGTAATTTTTCAA--TCT-AACCGGT-ACAAGT---A-TA-CCGGTT-TTA
66 CCA-AAAGTACA-ATGTAATATGT-AATTTTTCAATC--TAACCGGTACAAGTATACCGGTTTTA
53549 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGA
126 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGA
53614 ATGAATGGAA
191 ATGAATGGAA
* *
53624 AACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAGAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
53689 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
53754 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
53819 TGGAA
196 TGGAA
* *
53824 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAGAACGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
53889 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* * * *
53954 GAAT-TGGTATATAAT-ATGTATCGACACTGTTTAATGTTT-TGTCGATA
131 GAATAT-GTCTA-AATAATGTGTCGACACTTTTTTA-GTTTGTGTCGATA
54001 CTAATTTAAA
Statistics
Matches: 1425, Mismatches: 92, Indels: 77
0.89 0.06 0.05
Matches are distributed among these distances:
179 103 0.07
180 3 0.00
181 2 0.00
182 1 0.00
184 6 0.00
185 12 0.01
186 16 0.01
187 2 0.00
188 7 0.00
189 2 0.00
190 2 0.00
191 7 0.00
192 2 0.00
193 16 0.01
194 12 0.01
195 7 0.00
197 1 0.00
198 1 0.00
199 40 0.03
200 1174 0.82
201 9 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:52702 original size:21 final size:21
Alignment explanation
Indices: 52661--52702 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52651 GTGCAACCAT
* *
52661 AAAGTGTCGATCCATATAACA
1 AAAGTATCGATCCATAAAACA
52682 AAAGTATCGATCCCA-AAAACA
1 AAAGTATCGAT-CCATAAAACA
52703 TCGAAAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (21 bp):
AAAGTATCGATCCATAAAACA
Found at i:53102 original size:21 final size:21
Alignment explanation
Indices: 53061--53102 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53051 ATGTGACCAT
*
53061 AAAGTGTCGATCCATATAACA
1 AAAGTGTCGATCCATAAAACA
53082 AAAGTGTCGATCCCA-AAAACA
1 AAAGTGTCGAT-CCATAAAACA
53103 TCGAAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.19
Consensus pattern (21 bp):
AAAGTGTCGATCCATAAAACA
Found at i:54509 original size:21 final size:21
Alignment explanation
Indices: 54483--54527 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54473 AAGATATTAA
*
54483 TTTATAAAAGTATCTATCCTT
1 TTTATAAAAGTATCTATACTT
*
54504 TTTATAAAAGTGTCTATACTT
1 TTTATAAAAGTATCTATACTT
54525 TTT
1 TTT
54528 TCACTGTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTATAAAAGTATCTATACTT
Found at i:59236 original size:32 final size:33
Alignment explanation
Indices: 59200--59262 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
59190 TCGAATTACA
59200 TAGTCCAACATCC-AAACATAATTAAAAAATGT
1 TAGTCCAACATCCAAAACATAATTAAAAAATGT
59232 TAGTCCAACATCCAAAACATAATTAAAAAAT
1 TAGTCCAACATCCAAAACATAATTAAAAAAT
59263 ATCATGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (33 bp):
TAGTCCAACATCCAAAACATAATTAAAAAATGT
Found at i:59568 original size:68 final size:68
Alignment explanation
Indices: 59344--59672 Score: 319
Period size: 68 Copynumber: 4.9 Consensus size: 68
59334 AATTTTGAAA
* * * * *
59344 TAAATAATAATCGAGTGATCAAAACATAAATTAGATAATATATAGGTGACCAAATAGGTAGTTTA
1 TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAGTTTA
*
59409 TCT
66 CCT
* * * * * * * * *
59412 TAAATAAAAAT-ATAT-AT--TAA-TTATATTAGATAATATATAAGTAACCAAATAGGTTTGTTT
1 TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACCAAATA-GATAGTTT
* *
59472 ATCA
65 ACCT
* * * * * *
59476 TACATAATAATCGAGTAACCAAAACATAAATTAAATAATATATAAGTGATCAAATAGATAGTTTA
1 TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAGTTTA
59541 CCT
66 CCT
* *
59544 TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACAAAATAGATAATTTA
1 TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAGTTTA
*
59609 CCC
66 CCT
* * * * *
59612 TAAATAATAATTAAA-GAACCAAAATATAAATTAAATAATATATAACTGAACAAATAGATAG
1 TAAATAATAATCAAATG-ATCAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAG
59673 GGCATTTTTG
Statistics
Matches: 210, Mismatches: 44, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
63 27 0.13
64 20 0.10
65 1 0.00
66 3 0.01
67 2 0.01
68 131 0.62
69 26 0.12
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (68 bp):
TAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAGTTTA
CCT
Found at i:59651 original size:136 final size:132
Alignment explanation
Indices: 59343--59672 Score: 340
Period size: 132 Copynumber: 2.5 Consensus size: 132
59333 TAATTTTGAA
** * * * * * *
59343 ATAAATAATAATCGAGTGATCAAAACATAAATTAGATAATATATAGGTGACCAAATAGGTAGTTT
1 ATAAATAATAATAAAGTAACCAAAACATAAATTAAATAATATATAAGTGAACAAATAGATAGTTT
* * * * * * * * **
59408 ATCTTAAATAAAAATATATATTAATTATATTAGATAATATATAAGTAACCAAATAGGTTTGTTTA
66 ACCTTAAATAAAAATAAATATAAAATAAATTAAATAATATATAAGTAACAAAATAGGATAATTTA
*
59473 TC
131 CC
* ** *
59475 ATACATAATAATCGAGTAACCAAAACATAAATTAAATAATATATAAGTGATCAAATAGATAGTTT
1 ATAAATAATAATAAAGTAACCAAAACATAAATTAAATAATATATAAGTGAACAAATAGATAGTTT
* *
59540 ACCTTAAATAATAATCAAATGATCAAAACATAAATTAAATAATATATAAGTGACAAAATA-GATA
66 ACCTTAAATAAAAAT-AAAT-AT--AAA-ATAAATTAAATAATATATAAGTAACAAAATAGGATA
59604 ATTTACC
126 ATTTACC
* * *
59611 CTAAATAATAATTAAAG-AACCAAAATATAAATTAAATAATATATAACTGAACAAATAGATAG
1 ATAAATAATAA-TAAAGTAACCAAAACATAAATTAAATAATATATAAGTGAACAAATAGATAG
59673 GGCATTTTTG
Statistics
Matches: 165, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
132 71 0.43
133 3 0.02
134 2 0.01
136 60 0.36
137 29 0.18
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (132 bp):
ATAAATAATAATAAAGTAACCAAAACATAAATTAAATAATATATAAGTGAACAAATAGATAGTTT
ACCTTAAATAAAAATAAATATAAAATAAATTAAATAATATATAAGTAACAAAATAGGATAATTTA
CC
Found at i:80611 original size:39 final size:39
Alignment explanation
Indices: 80566--80805 Score: 182
Period size: 40 Copynumber: 5.8 Consensus size: 39
80556 AACCAAATGG
80566 TTTATTTCCTTTTACAAAACA-ATAAAATAAATACAACGA
1 TTTATTTCCTTTTACAAAACAGA-AAAATAAATACAACGA
*
80605 TTTATTTCCTTTTACAAAACAGAAAAATTAAATCCAACGA
1 TTTATTTCCTTTTACAAAACAGAAAAA-TAAATACAACGA
*
80645 TTTATTTCCTTTTACAAAGCAGAAAAATAAAATCAAACAGTTTATTTCGA
1 TTTATTTCCTTTTACAAAACAGAAAAAT-AAAT---ACA----A---CGA
* * * * * *
80695 TTTATTTTCTTTTACAAAATAGGAAATTAAATCCAACTA
1 TTTATTTCCTTTTACAAAACAGAAAAATAAATACAACGA
* * *
80734 TTTATTTCCTTTTTACAATATATG-AAAACAAATACAACGA
1 TTTATTTCC-TTTTACAAAACA-GAAAAATAAATACAACGA
* *
80774 TTTATTT-TTTTATATAAAACATG-AAAATAAAT
1 TTTATTTCCTTT-TACAAAACA-GAAAAATAAAT
80806 CAAACAATTT
Statistics
Matches: 164, Mismatches: 21, Indels: 32
0.76 0.10 0.15
Matches are distributed among these distances:
38 3 0.02
39 52 0.32
40 72 0.44
41 1 0.01
42 1 0.01
43 2 0.01
46 2 0.01
47 1 0.01
49 4 0.02
50 26 0.16
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (39 bp):
TTTATTTCCTTTTACAAAACAGAAAAATAAATACAACGA
Found at i:80737 original size:129 final size:127
Alignment explanation
Indices: 80566--80901 Score: 389
Period size: 129 Copynumber: 2.6 Consensus size: 127
80556 AACCAAATGG
* * * *
80566 TTTATTTCCTTTTACAAAACAATAAAATAAATACAACGATTTATTTCCTTTTACAAAACA-GAAA
1 TTTATTTCCTTTTACAAAATAAGAAATTAAAT-CAACTATTTATTTCCTTTTACAAAACATG-AA
* *
80630 AATTAAATCCAACGATTTATTTCCTTT-TACAAAGCA-GAAAAATAAAATCAAACAGTTTATTTC
64 AATTAAATCCAACGATTTATTT-CTTTATACAAAACATG-AAAAT-AAATCAAACAATTTATTTC
80693 GA
126 GA
* * * *
80695 TTTATTTTCTTTTACAAAATAGGAAATTAAATCCAACTATTTATTTCCTTTTTACAATATATGAA
1 TTTATTTCCTTTTACAAAATAAGAAATTAAAT-CAACTATTTATTTCC-TTTTACAAAACATGAA
* * * * *
80760 AA-CAAATACAACGATTTATTTTTTTATATAAAACATGAAAATAAATCAAACAATTTGTTTCGA
64 AATTAAATCCAACGATTTATTTCTTTATACAAAACATGAAAATAAATCAAACAATTTATTTCGA
* *
80823 TTTA-TTCCTTTTACAAAATAAGAAATTAAATCAA-TGATTTATTTCTTTTTACAAACCATGAAA
1 TTTATTTCCTTTTACAAAATAAGAAATTAAATCAACT-ATTTATTTCCTTTTACAAAACATGAAA
*
80886 ATT-AATCAAACGATTT
65 ATTAAATCCAACGATTT
80902 GTAACCCCCT
Statistics
Matches: 176, Mismatches: 25, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
125 27 0.15
126 12 0.07
127 25 0.14
128 26 0.15
129 70 0.40
130 15 0.09
131 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.38
Consensus pattern (127 bp):
TTTATTTCCTTTTACAAAATAAGAAATTAAATCAACTATTTATTTCCTTTTACAAAACATGAAAA
TTAAATCCAACGATTTATTTCTTTATACAAAACATGAAAATAAATCAAACAATTTATTTCGA
Found at i:80883 original size:86 final size:89
Alignment explanation
Indices: 80733--80903 Score: 224
Period size: 86 Copynumber: 2.0 Consensus size: 89
80723 AAATCCAACT
* * *
80733 ATTTATTTCCTTTTTACAATATATGAAAACAAATACAACGATTTATTTTTTTATATAAAACATGA
1 ATTTATTTCCTTTTTACAAAATAAGAAAACAAATACAACGATTTATTTTTTTATACAAAACATGA
80798 AAATAAATCAAACAATTTGTTTCG
66 AAATAAATCAAACAATTTGTTTCG
** * *
80822 ATTTA-TTCC-TTTTACAAAATAAGAAATTAAAT-CAATGATTTATTTCTTTT-TACAAACCATG
1 ATTTATTTCCTTTTTACAAAATAAGAAAACAAATACAACGATTTATTT-TTTTATACAAAACATG
* *
80883 AAAATTAATCAAACGATTTGT
65 AAAATAAATCAAACAATTTGT
80904 AACCCCCTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 40 0.56
87 23 0.32
88 4 0.06
89 5 0.07
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (89 bp):
ATTTATTTCCTTTTTACAAAATAAGAAAACAAATACAACGATTTATTTTTTTATACAAAACATGA
AAATAAATCAAACAATTTGTTTCG
Found at i:82454 original size:7 final size:7
Alignment explanation
Indices: 82430--82467 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
82420 GGTCAAAGGA
82430 GGTCAAC
1 GGTCAAC
82437 GGTC-AC
1 GGTCAAC
82443 GGTCAAC
1 GGTCAAC
*
82450 AGTCAAC
1 GGTCAAC
82457 GGTCAAC
1 GGTCAAC
82464 GGTC
1 GGTC
82468 GAGTCGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:82478 original size:5 final size:5
Alignment explanation
Indices: 82464--82496 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
82454 AACGGTCAAC
*
82464 GGTCG AGTCG GGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
82497 AGACCGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:82489 original size:14 final size:15
Alignment explanation
Indices: 82464--82496 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
82454 AACGGTCAAC
82464 GGTCGAGTCGGGTCG
1 GGTCGAGTCGGGTCG
82479 GGTCG-GTCGGGTCG
1 GGTCGAGTCGGGTCG
82493 GGTC
1 GGTC
82497 AGACCGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (15 bp):
GGTCGAGTCGGGTCG
Found at i:82504 original size:19 final size:19
Alignment explanation
Indices: 82463--82505 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
82453 CAACGGTCAA
* **
82463 CGGTCGAGTCGGGTCGGGT
1 CGGTCGAGTCGGGTCAGAC
*
82482 CGGTCGGGTCGGGTCAGAC
1 CGGTCGAGTCGGGTCAGAC
82501 CGGTC
1 CGGTC
82506 AAAACTGGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.26, G:0.49, T:0.19
Consensus pattern (19 bp):
CGGTCGAGTCGGGTCAGAC
Found at i:83571 original size:39 final size:39
Alignment explanation
Indices: 83528--83714 Score: 202
Period size: 39 Copynumber: 4.8 Consensus size: 39
83518 CAAAGTAGAG
83528 AAATAAATTATACGATTTATTTCCTTTTACAAAACAGAA
1 AAATAAATTATACGATTTATTTCCTTTTACAAAACAGAA
* * *
83567 AAATAAATTCTACGATTTATTTCCTTTTACAAAATAGGA
1 AAATAAATTATACGATTTATTTCCTTTTACAAAACAGAA
* *
83606 AAATAAATCTA-ACGATTTATTTTCTTATACAAAACA-AGA
1 AAATAAAT-TATACGATTTATTTCCTTTTACAAAACAGA-A
* * * * *
83645 AACTAAATTCA-ACGATTTGTTTCATTTTCCAAAATAGAA
1 AAATAAATT-ATACGATTTATTTCCTTTTACAAAACAGAA
* *
83684 AAATAAA-TATGAAGATTTATTTTCTTTTACA
1 AAATAAATTAT-ACGATTTATTTCCTTTTACA
83715 GATAGAATCA
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 116 0.96
40 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (39 bp):
AAATAAATTATACGATTTATTTCCTTTTACAAAACAGAA
Found at i:83621 original size:78 final size:77
Alignment explanation
Indices: 83518--83714 Score: 245
Period size: 78 Copynumber: 2.5 Consensus size: 77
83508 AGGTAAATTT
* * * *
83518 CAAAGTAGAGAAATAAATTATACGATTTATTTCCTTTTACAAAAC-AGAAAAATAAATTCTACGA
1 CAAAATAGAAAAATAAATTA-ACGATTTATTTTCTTTTACAAAACAAG-AAAATAAATTCAACGA
*
83582 TTTATTTCCTTTTA
64 TTTATTTCATTTTA
* * *
83596 CAAAATAGGAAAATAAATCTAACGATTTATTTTCTTATACAAAACAAGAAACTAAATTCAACGAT
1 CAAAATAGAAAAATAAAT-TAACGATTTATTTTCTTTTACAAAACAAGAAAATAAATTCAACGAT
* *
83661 TTGTTTCATTTTC
65 TTATTTCATTTTA
83674 CAAAATAGAAAAATAAATATGAA-GATTTATTTTCTTTTACA
1 CAAAATAGAAAAATAAAT-T-AACGATTTATTTTCTTTTACA
83715 GATAGAATCA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 97 0.94
79 6 0.06
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (77 bp):
CAAAATAGAAAAATAAATTAACGATTTATTTTCTTTTACAAAACAAGAAAATAAATTCAACGATT
TATTTCATTTTA
Found at i:83837 original size:58 final size:57
Alignment explanation
Indices: 83772--84162 Score: 398
Period size: 58 Copynumber: 6.8 Consensus size: 57
83762 AAGTTTCCCT
* * *
83772 AGAAAATAAATTTAACAATTTATTTCTTTTAACAAA-ATAGAATCATTTAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTT-TCTT-ACAAAGTTAGAATCATTTAAGATTCTCA
* * * * * *
83830 AGAAAATAAATTTAACAATTTATTTATTTTTA-AATGATAGAATCATCTACGATTCTCA
1 AGAAAATAAATTCAACAATTTA-TT-TTCTTACAAAGTTAGAATCATTTAAGATTCTCA
** * ** * *
83888 AGAAAATAAATTTGATAATTTAATTTTCTTACAAAGTTAG--TCATTCCATATTTTCA
1 AGAAAATAAATTCAACAATTT-ATTTTCTTACAAAGTTAGAATCATTTAAGATTCTCA
* * *
83944 AGAAAATAAATTCAACAATATATTTCCCTAACAAAGTTAGAATCATTTAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTT-TCTTACAAAGTTAGAATCATTTAAGATTCTCA
* * *
84002 AGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAAAATCATTCAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTTT-CTTACAAAGTTAGAATCATTTAAGATTCTCA
* *
84060 A-AGAAATAAATTCAACAATTTATTTTCCTTAC-AAGTTTTGAATCATTTAAGATTCTTA
1 AGA-AAATAAATTCAACAATTTATTTT-CTTACAAAG-TTAGAATCATTTAAGATTCTCA
* * *
84118 AGGAAATAAATTCAACAATATATTTCCCTTACAAAGTTAGAATCA
1 AGAAAATAAATTCAACAATTTATTT-TCTTACAAAGTTAGAATCA
84163 ACGCAAGATT
Statistics
Matches: 280, Mismatches: 39, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
55 4 0.01
56 39 0.14
57 10 0.04
58 216 0.77
59 10 0.04
60 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (57 bp):
AGAAAATAAATTCAACAATTTATTTTCTTACAAAGTTAGAATCATTTAAGATTCTCA
Found at i:84058 original size:172 final size:173
Alignment explanation
Indices: 83772--84162 Score: 456
Period size: 172 Copynumber: 2.3 Consensus size: 173
83762 AAGTTTCCCT
* * ** *
83772 AGAAAATAAATTTAACAATTTATTTCTTTTAACAAA-ATAGAATCATTTAAGATTCTCAAGAAAA
1 AGAAAATAAATTCAACAATATATTTC-CCTAACAAAGTTAGAATCATTTAAGATTCTCAAGAAAA
* ** * * *
83836 TAAATTTAACAATTTATTTATTTTTAAATGATAGAATCATCTACGATTCTC-AAGAAAATAAATT
65 TAAATTCAACAATTTATTTATCCTTAAAAGATAAAATCATCTAAGATTCTCAAAG-AAATAAATT
** * * * *
83900 TGATAATTTAATTTT-CTTACAAAG-TT-AGTCATTCCATATT-TTCA
129 CAACAATTT-ATTTTCCTTAC-AAGTTTGAATCATTCAAGATTCTT-A
*
83944 AGAAAATAAATTCAACAATATATTTCCCTAACAAAGTTAGAATCATTTAAGATTCTCAAGGAAAT
1 AGAAAATAAATTCAACAATATATTTCCCTAACAAAGTTAGAATCATTTAAGATTCTCAAGAAAAT
*
84009 AAATTCAACAATTTATTT-TCCTTACAAAGTTAAAATCAT-TCAAGATTCTCAAAGAAATAAATT
66 AAATTCAACAATTTATTTATCCTTA-AAAGATAAAATCATCT-AAGATTCTCAAAGAAATAAATT
*
84072 CAACAATTTATTTTCCTTACAAGTTTTGAATCATTTAAGATTCTTA
129 CAACAATTTATTTTCCTTACAAG-TTTGAATCATTCAAGATTCTTA
* *
84118 AGGAAATAAATTCAACAATATATTTCCCTTACAAAGTTAGAATCA
1 AGAAAATAAATTCAACAATATATTTCCCTAACAAAGTTAGAATCA
84163 ACGCAAGATT
Statistics
Matches: 188, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
171 20 0.11
172 107 0.57
173 5 0.03
174 54 0.29
175 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (173 bp):
AGAAAATAAATTCAACAATATATTTCCCTAACAAAGTTAGAATCATTTAAGATTCTCAAGAAAAT
AAATTCAACAATTTATTTATCCTTAAAAGATAAAATCATCTAAGATTCTCAAAGAAATAAATTCA
ACAATTTATTTTCCTTACAAGTTTGAATCATTCAAGATTCTTA
Found at i:84642 original size:14 final size:13
Alignment explanation
Indices: 84617--84661 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
84607 GGCCAAAGGT
*
84617 TATATAATAATAA
1 TATATAACAATAA
84630 TACTATAACAATAA
1 TA-TATAACAATAA
84644 TATCATGAACAATAA
1 TAT-AT-AACAATAA
84659 TAT
1 TAT
84662 GATTAAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 11 0.39
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (13 bp):
TATATAACAATAA
Found at i:84869 original size:14 final size:14
Alignment explanation
Indices: 84848--84887 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
84838 AAAAAAGGCA
**
84848 AATCACCATGTGCT
1 AATCACCATGCACT
*
84862 AGTCACCATGCACT
1 AATCACCATGCACT
84876 AATCACCATGCA
1 AATCACCATGCA
84888 TTTTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.23
Consensus pattern (14 bp):
AATCACCATGCACT
Found at i:87532 original size:15 final size:14
Alignment explanation
Indices: 87500--87526 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87490 AGAAAAAGGA
87500 ACAGTACAAAAAAG
1 ACAGTACAAAAAAG
87514 ACAGTACAAAAAA
1 ACAGTACAAAAAA
87527 ATACAGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.11, T:0.07
Consensus pattern (14 bp):
ACAGTACAAAAAAG
Found at i:89016 original size:14 final size:15
Alignment explanation
Indices: 88991--89021 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
88981 TGGCGGCGCT
88991 GCTAAGAGCCATCGG
1 GCTAAGAGCCATCGG
89006 GCTAA-AGCCATCGG
1 GCTAAGAGCCATCGG
89020 GC
1 GC
89022 GATCAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (15 bp):
GCTAAGAGCCATCGG
Found at i:90345 original size:10 final size:10
Alignment explanation
Indices: 90326--90370 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
90316 TTTTTTATTA
*
90326 ATATTATAAT
1 ATATTTTAAT
90336 ATATTTTAAT
1 ATATTTTAAT
*
90346 AT-TTTTCAT
1 ATATTTTAAT
90355 ATATTTTAAT
1 ATATTTTAAT
*
90365 TTATTT
1 ATATTT
90371 ATTTATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTAAT
Found at i:91410 original size:16 final size:16
Alignment explanation
Indices: 91391--91421 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91381 ATGTTATCAT
*
91391 TATATTTTAGTTATTA
1 TATATTTTAGATATTA
91407 TATATTTTAGATATT
1 TATATTTTAGATATT
91422 TATTTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TATATTTTAGATATTA
Found at i:94679 original size:12 final size:12
Alignment explanation
Indices: 94662--94688 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
94652 CTTAAAATGC
94662 ATGTATGCATGT
1 ATGTATGCATGT
94674 ATGTATGCATGT
1 ATGTATGCATGT
94686 ATG
1 ATG
94689 CATGTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (12 bp):
ATGTATGCATGT
Found at i:94716 original size:20 final size:20
Alignment explanation
Indices: 94691--94737 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
94681 CATGTATGCA
*
94691 TGTGTGTGCGTGTGCGTGTG
1 TGTGTGTGCGCGTGCGTGTG
94711 TGTGTGTGCGCGTGCGTGTG
1 TGTGTGTGCGCGTGCGTGTG
94731 TGTGTGT
1 TGTGTGT
94738 TACTCATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.00, C:0.11, G:0.49, T:0.40
Consensus pattern (20 bp):
TGTGTGTGCGCGTGCGTGTG
Found at i:100348 original size:20 final size:20
Alignment explanation
Indices: 100323--100376 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
100313 GACCAACAAA
100323 TTCGCAACACGAATTCCAAT
1 TTCGCAACACGAATTCCAAT
* *
100343 TTCGCAACAC-AGTTTCTAAT
1 TTCGCAACACGA-ATTCCAAT
*
100363 TTCGCAACGCGAAT
1 TTCGCAACACGAAT
100377 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (20 bp):
TTCGCAACACGAATTCCAAT
Found at i:100423 original size:20 final size:20
Alignment explanation
Indices: 100400--100451 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
100390 TGCGATTTTC
*
100400 CAAATTTGCAACGCGATAGT
1 CAAATTTGCAACGCGAGAGT
**
100420 CAAATTCACAACGCGAGAGT
1 CAAATTTGCAACGCGAGAGT
100440 CAAATTTGCAAC
1 CAAATTTGCAAC
100452 TGAATTTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTTGCAACGCGAGAGT
Found at i:100463 original size:19 final size:19
Alignment explanation
Indices: 100439--100489 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
100429 AACGCGAGAG
*
100439 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
100458 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
100477 TCAAATTCGCAAC
1 TCAAATTCGCAAC
100490 AGGTTTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:101256 original size:12 final size:12
Alignment explanation
Indices: 101235--101268 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
101225 ACCACATTTC
*
101235 CAATACCAAACA
1 CAATATCAAACA
101247 CAATATCAAACA
1 CAATATCAAACA
*
101259 CAATCTCAAA
1 CAATATCAAA
101269 ACCCACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:101440 original size:24 final size:24
Alignment explanation
Indices: 101394--101447 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
101384 GTATTCGAAA
*
101394 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATAACCGGAC
* *
101418 TTTGATCTTGGTCAATAATCGGAT
1 TTTGATCTTGGTCAATAACCGGAC
101442 TTTGAT
1 TTTGAT
101448 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATAACCGGAC
Found at i:102542 original size:14 final size:14
Alignment explanation
Indices: 102523--102554 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
102513 CAGTAGCCAT
102523 GGATGCTAACAATG
1 GGATGCTAACAATG
102537 GGATGCTAACAATG
1 GGATGCTAACAATG
102551 GGAT
1 GGAT
102555 ACTGCCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (14 bp):
GGATGCTAACAATG
Found at i:103746 original size:18 final size:18
Alignment explanation
Indices: 103723--103758 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
103713 AAGCAAAAGG
*
103723 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
103741 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
103759 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:104913 original size:39 final size:39
Alignment explanation
Indices: 104870--104995 Score: 243
Period size: 39 Copynumber: 3.2 Consensus size: 39
104860 TCCGATGCTC
*
104870 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
104909 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
104948 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
104987 ATCAAAATC
1 ATCAAAATC
104996 TACAACTTGA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
Found at i:105284 original size:20 final size:20
Alignment explanation
Indices: 105259--105345 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 20
105249 CAGAAAATTA
*
105259 CGTTGCGAATTTAACTTTCG
1 CGTTGCGAATTTGACTTTCG
*
105279 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTTTCG
** * *
105299 C--AACG--CTT-A-TTTCA
1 CGTTGCGAATTTGACTTTCG
105313 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
105333 CGTTGCGAATTTG
1 CGTTGCGAATTTG
105346 TACCTTCAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
14 4 0.08
15 1 0.02
16 4 0.08
18 4 0.08
19 1 0.02
20 36 0.72
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:107003 original size:21 final size:21
Alignment explanation
Indices: 106926--107015 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 21
106916 GGCGGGACCA
*
106926 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * * *
106947 CTTCAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* *
106968 TTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
106989 CTTGAACGATAAGAGGCGCCT
1 CTTGAACGATGAGAGGGGCCT
107010 CTTGAA
1 CTTGAA
107016 TAATGATAGG
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.98
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:107197 original size:4 final size:4
Alignment explanation
Indices: 107165--107210 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
107155 GGGCCGCTGA
* * * *
107165 AAAT AAAT TAAT ATAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
107211 TGCCGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:109477 original size:22 final size:22
Alignment explanation
Indices: 109445--109486 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
109435 GAGATAGACG
*
109445 GATTTCGTCGGAAATGGGGATA
1 GATTTCATCGGAAATGGGGATA
*
109467 GATTTCATCGGAGATGGGGA
1 GATTTCATCGGAAATGGGGA
109487 CGGATGTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.38, T:0.26
Consensus pattern (22 bp):
GATTTCATCGGAAATGGGGATA
Found at i:109642 original size:20 final size:20
Alignment explanation
Indices: 109617--109676 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
109607 GCGTAAAAAC
109617 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
* **
109637 ATTTGACTATCACGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
* *
109657 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
109677 TTTACATATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTTGCGTTGCGA
Found at i:109661 original size:40 final size:40
Alignment explanation
Indices: 109617--109740 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 40
109607 GCGTAAAAAC
109617 ATTTGACTTTTGCGTTGCGAATTTGACTATCACGTTGCGA
1 ATTTGACTTTTGCGTTGCGAATTTGACTATCACGTTGCGA
* *
109657 ATTTGACTTCTGTGTTGCG-ATTT-ACATATTCACGTTGCGAA
1 ATTTGACTTTTGCGTTGCGAATTTGAC-TA-TCACGTTGCG-A
* * * * * * *
109698 ATTGGA-ATTCGCGTTGCAAATTTGA-GATCGCGTTGTGA
1 ATTTGACTTTTGCGTTGCGAATTTGACTATCACGTTGCGA
109736 ATTTG
1 ATTTG
109741 TTGGTCATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
38 7 0.10
39 14 0.21
40 35 0.52
41 10 0.15
42 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (40 bp):
ATTTGACTTTTGCGTTGCGAATTTGACTATCACGTTGCGA
Found at i:110116 original size:22 final size:22
Alignment explanation
Indices: 110091--110132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
110081 TGTTATGAGA
*
110091 TAAATTTATAAAATTCTAGGGG
1 TAAATTCATAAAATTCTAGGGG
* *
110113 TAAATTCATGAAATTGTAGG
1 TAAATTCATAAAATTCTAGG
110133 AGACAAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (22 bp):
TAAATTCATAAAATTCTAGGGG
Found at i:112952 original size:23 final size:23
Alignment explanation
Indices: 112922--112965 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
112912 CAAAACATGT
112922 ATTTGTATTAAGGGCAGATTCGA
1 ATTTGTATTAAGGGCAGATTCGA
112945 ATTTGTATTAAGGGCAGATTC
1 ATTTGTATTAAGGGCAGATTC
112966 TTCAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (23 bp):
ATTTGTATTAAGGGCAGATTCGA
Found at i:113978 original size:22 final size:22
Alignment explanation
Indices: 113937--113978 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
113927 TCGGTAACGG
* *
113937 TTTTGTTATTTTTTTCTACTGA
1 TTTTGTTATTGTTTGCTACTGA
*
113959 TTTTGTTATTGTTTGGTACT
1 TTTTGTTATTGTTTGCTACT
113979 TTTATCGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTTGTTATTGTTTGCTACTGA
Found at i:116374 original size:2 final size:2
Alignment explanation
Indices: 116367--116397 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
116357 CAATAATAAT
116367 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 T
116398 TCAATTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117069 original size:2 final size:2
Alignment explanation
Indices: 117062--117088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117052 AGCAAAAGGG
117062 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 T
117089 TAAAATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:121528 original size:16 final size:16
Alignment explanation
Indices: 121507--121572 Score: 96
Period size: 16 Copynumber: 4.0 Consensus size: 16
121497 TCATTATTTA
121507 TATTATAATATATATT
1 TATTATAATATATATT
*
121523 TATTATAATATATATA
1 TATTATAATATATATT
121539 TATTATATATATATATTT
1 TATTATA-ATATATA-TT
*
121557 TATTATATTATATATT
1 TATTATAATATATATT
121573 CAGCTATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
16 24 0.53
17 13 0.29
18 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATAATATATATT
Found at i:121560 original size:5 final size:5
Alignment explanation
Indices: 121499--121569 Score: 69
Period size: 5 Copynumber: 14.4 Consensus size: 5
121489 TTTGTTCTTC
*
121499 ATTAT -TTAT ATTAT AATATAT ATT-T ATTAT AATAT ATATAT ATTAT
1 ATTAT ATTAT ATTAT -AT-TAT ATTAT ATTAT ATTAT AT-TAT ATTAT
*
121545 A-TAT A-TAT ATTTT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
121570 ATTCAGCTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
4 16 0.29
5 28 0.50
6 9 0.16
7 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:121569 original size:34 final size:32
Alignment explanation
Indices: 121505--121571 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 32
121495 CTTCATTATT
121505 TATATTATAATATATATTTATTATAATATATA
1 TATATTATAATATATATTTATTATAATATATA
*
121537 TATATTATATATATATATTTTATTATATTATATA
1 TATATTATA-ATATATA-TTTATTATAATATATA
121571 T
1 T
121572 TCAGCTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 9 0.28
33 7 0.22
34 16 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATTATAATATATATTTATTATAATATATA
Found at i:121581 original size:31 final size:33
Alignment explanation
Indices: 121514--121582 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
121504 TTATATTATA
* *
121514 ATATATATTTATTATAATATATATATATTATAT
1 ATATATATTTATTATAATATATATATATCAGAT
*
121547 ATATATATTTTATTAT-AT-TATATAT-TCAGCT
1 ATATATA-TTTATTATAATATATATATATCAGAT
121578 ATATA
1 ATATA
121583 ATATACATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.25
32 7 0.22
33 9 0.28
34 8 0.25
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (33 bp):
ATATATATTTATTATAATATATATATATCAGAT
Found at i:121582 original size:2 final size:2
Alignment explanation
Indices: 121505--121571 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
121495 CTTCATTATT
*
121505 TA TA T- TA TA -A TA TA TA TT TA T- TA TA -A TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
121542 TA TA TA TA TA TA T- TT TA T- TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
121572 TCAGCTATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
1 8 0.15
2 46 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:121587 original size:34 final size:34
Alignment explanation
Indices: 121510--121596 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
121500 TTATTTATAT
*
121510 TATAATATATATTTATTATAATATATATATATTA
1 TATAATATATATTTATTATAATATATATATACTA
*
121544 TAT-ATATATATTTTATTATATTATATAT-TCAGCTA
1 TATAATATATA-TTTATTATAATATATATAT-A-CTA
*
121579 TATAATATACATATTATT
1 TATAATATATAT-TTATT
121597 TACATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
33 8 0.18
34 20 0.44
35 6 0.13
36 11 0.24
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (34 bp):
TATAATATATATTTATTATAATATATATATACTA
Found at i:122670 original size:27 final size:28
Alignment explanation
Indices: 122634--122705 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
122624 TTTCTTTTTC
122634 TTATTATTATTTATTTAAATA-GTATAT
1 TTATTATTATTTATTTAAATATGTATAT
* * *
122661 TTATTATTATCCATATTTAATTATGTATTT
1 TTATTATTAT--TTATTTAAATATGTATAT
*
122691 TTATTATTAATTATT
1 TTATTATTATTTATT
122706 CTCATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 10 0.27
28 4 0.11
29 9 0.24
30 14 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TTATTATTATTTATTTAAATATGTATAT
Found at i:122783 original size:2 final size:2
Alignment explanation
Indices: 122776--122811 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
122766 TAATTTATGA
122776 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122812 CACTACTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.