Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 36 of 310
Found at i:10110167 original size:19 final size:19
Alignment explanation
Indices: 10110135--10110176 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
10110125 GGGAGAAAAG
10110135 GAAAGAAAGAGGAAAGAAA
1 GAAAGAAAGAGGAAAGAAA
*
10110154 GAAAGGAAAG-GGAAGGAAA
1 GAAA-GAAAGAGGAAAGAAA
10110173 GAAA
1 GAAA
10110177 ATGAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAGGAAAGAAA
Found at i:10114512 original size:389 final size:388
Alignment explanation
Indices: 10113754--10114519 Score: 1112
Period size: 389 Copynumber: 2.0 Consensus size: 388
10113744 ATGGTCACTA
* * * * *
10113754 AACTAACTAAAAATTTGACTGAGGCAAGATCGCCTATTGAACAGTAGTATAGTTATGGTTAGACC
1 AACTAACTAAAAATTCGACTAAGGCAAGATCACCTATCGAACAGTAGTATAGTTATGGTGAGACC
10113819 GGAAATATCGTATCCACAAGGACTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCCTAA
66 GGAAATATCGTATCCACAAGGACTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCCTAA
* * *
10113884 CAATTAAGAGAATGTTTTAAACTAAGACAAATTATCTAATTAGCTAAAATTACGACAGATATTAA
131 CAATTAAGAGAATGTTTTAAACTAAAACAAATTATCTAATTAGCTAAAATTACGACAAAGATTAA
** *
10113949 AGTTGGAAAATACTTTTTAGAAAACCGATGGAAAAGACAATACCCAAGGAAGAATCCACCTAGAC
196 AGTTGGAAAATACTTTGGAGAAAACCGATGGAAAAGACAATACCCAAGGAACAATCCACCTAGAC
* * ** * *
10114014 TTCACTTATCACTTCTGAATTAGACGATTTATTCACTTGACTTAATCTGTATAAATCCCTGATTT
261 TTCACTTATCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCATAGAAATCCCTAATTT
10114079 ATGTTAATATCTCTCTCAAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCATGT
326 ATGTTAATATCTCTCTCAAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCATGT
*
10114142 AACTAACTAAAAATTCGACTTAAGGCGAGCA-CACCTATCGAACAGTAGTATAGTTATGGTGAGA
1 AACTAACTAAAAATTCGAC-TAAGGCAAG-ATCACCTATCGAACAGTAGTATAGTTATGGTGAGA
* *
10114206 CCGGAAATATCGTATCCATGAA-GAGTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCC
64 CCGGAAATATCGTATCCA-CAAGGACTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCC
* ** * * *
10114270 TAAGAATTAAG-GTGTGTTTTTAAACTAAAACTATTTATCTAATT-GACTAAGATTACGACAAAG
128 TAACAATTAAGAGAATG-TTTTAAACTAAAACAAATTATCTAATTAG-CTAAAATTACGACAAAG
* * *
10114333 A-TGAAGTTTGGAAAATACTTTGG-GAAAAACTGATGGAGAAGACAATACCCAAGGAACAATCCA
191 ATTAAAG-TTGGAAAATACTTTGGAG-AAAACCGATGGAAAAGACAATACCCAAGGAACAATCCA
* *
10114396 CCTAGACTTCACTTATTACTTCTGAATTAGATAATTTATTCACTTAACTTAATCCATAGAAATCC
254 CCTAGACTTCACTTATCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCATAGAAATCC
* * * *
10114461 CTAATTTATGTTAATATCTCTCTCGAGACTAAGAATAACTGACTTTAGGTTGATTAATT
319 CTAATTTATGTTAATATCTCTCTCAAGACTAAAAACAACTGACTCTAGGTTGATTAATT
10114520 AAAATCTCTT
Statistics
Matches: 336, Mismatches: 35, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
388 27 0.08
389 306 0.91
390 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (388 bp):
AACTAACTAAAAATTCGACTAAGGCAAGATCACCTATCGAACAGTAGTATAGTTATGGTGAGACC
GGAAATATCGTATCCACAAGGACTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCCTAA
CAATTAAGAGAATGTTTTAAACTAAAACAAATTATCTAATTAGCTAAAATTACGACAAAGATTAA
AGTTGGAAAATACTTTGGAGAAAACCGATGGAAAAGACAATACCCAAGGAACAATCCACCTAGAC
TTCACTTATCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCATAGAAATCCCTAATTT
ATGTTAATATCTCTCTCAAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCATGT
Found at i:10118878 original size:11 final size:11
Alignment explanation
Indices: 10118862--10118908 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
10118852 TTATTTACAA
10118862 AATCATATATT
1 AATCATATATT
10118873 AATCATATATT
1 AATCATATATT
** *
10118884 -ATTTTAAATTT
1 AATCATATA-TT
10118895 AATCATATATT
1 AATCATATATT
10118906 AAT
1 AAT
10118909 TCTGAAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
10 5 0.18
11 18 0.64
12 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (11 bp):
AATCATATATT
Found at i:10123661 original size:32 final size:31
Alignment explanation
Indices: 10123596--10123668 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
10123586 TGCATATACG
* * * *
10123596 TTATATATATAATAAGAACCACACATATATA
1 TTATATATAAAAAAAAAACCACACACATATA
*
10123627 TTATATATAAAAAAAAAACCCACACACATGTA
1 TTATATATAAAAAAAAAA-CCACACACATATA
*
10123659 TTAAATATAA
1 TTATATATAA
10123669 TACAACCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (31 bp):
TTATATATAAAAAAAAAACCACACACATATA
Found at i:10126125 original size:31 final size:32
Alignment explanation
Indices: 10126087--10126161 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 32
10126077 CATTAAATCT
*
10126087 AACCAAAAACAGCAAATATAGCAT-AAAATGC
1 AACCAAAAACAGCAAATATAGCATAAAAATAC
* *
10126118 AACCAAAAACAGCAAATTTCGCATAAAAAATAC
1 AACCAAAAACAGCAAATATAGCAT-AAAAATAC
10126151 AACCAAAAACA
1 AACCAAAAACA
10126162 TTAATTCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 22 0.56
33 17 0.44
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (32 bp):
AACCAAAAACAGCAAATATAGCATAAAAATAC
Found at i:10126880 original size:13 final size:14
Alignment explanation
Indices: 10126854--10126882 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10126844 ACTAATGACG
10126854 AATTAAACCATTAT
1 AATTAAACCATTAT
10126868 AATTAAA-CATTAT
1 AATTAAACCATTAT
10126881 AA
1 AA
10126883 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:10130209 original size:12 final size:12
Alignment explanation
Indices: 10130194--10130219 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10130184 ATCATCCTCT
10130194 TCATCAGATTCA
1 TCATCAGATTCA
10130206 TCATCAGATTCA
1 TCATCAGATTCA
10130218 TC
1 TC
10130220 CCTCGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:10134167 original size:34 final size:34
Alignment explanation
Indices: 10134119--10134185 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
10134109 AAATTCCTGT
10134119 GAAAAAAGTGAGCAAAGAATATGGTTTTAGTAAG
1 GAAAAAAGTGAGCAAAGAATATGGTTTTAGTAAG
10134153 GAAAAAAGCT-AGCAAAGAATATGGTTTTAGTAA
1 GAAAAAAG-TGAGCAAAGAATATGGTTTTAGTAA
10134186 ACGCCCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (34 bp):
GAAAAAAGTGAGCAAAGAATATGGTTTTAGTAAG
Found at i:10136703 original size:202 final size:202
Alignment explanation
Indices: 10136356--10136728 Score: 611
Period size: 202 Copynumber: 1.8 Consensus size: 202
10136346 ATGTTATCAA
*
10136356 ATTTGTTGCTCAATTTGCTAATGCTAGCTCATCAAATAATACATTGCAATAATAATATGAGTTAC
1 ATTTGTTGCTCAATTTGCTAATGCTAGCTCATCAAACAATACATTGCAATAATAATATGAGTTAC
**
10136421 AAATCAAATATCATCTCTACATCATCCAAACCATTACTCTATAGAGAGGACACTTCATTCCTAAC
66 AAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGAGGACACTTCATTCCTAAC
* * * *
10136486 CTATGAAGAACGGACACGCCAGAAATCCCCTTGTACTGGTGCCAACACGTTGTCCGACAATGGAG
131 CAATGAAGAACGGACAAGCCAGAAATCCCCTCGTACAGGTGCCAACACGTTGTCCGACAATGGAG
10136551 ATGTCAG
196 ATGTCAG
* *
10136558 ATTTGTTGTTCAATTTGCTAATGCTAGCTCATCAAACAATTCATTGCAATAATAATATGAGTTAC
1 ATTTGTTGCTCAATTTGCTAATGCTAGCTCATCAAACAATACATTGCAATAATAATATGAGTTAC
* * *
10136623 AAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGTGGACATTTCATTCCTAGC
66 AAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGAGGACACTTCATTCCTAAC
* **
10136688 CAATGAAGCACGGACAAGCTGGAAATCCCCTCGTACAGGTG
131 CAATGAAGAACGGACAAGCCAGAAATCCCCTCGTACAGGTG
10136729 TCGACATGGT
Statistics
Matches: 156, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
202 156 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (202 bp):
ATTTGTTGCTCAATTTGCTAATGCTAGCTCATCAAACAATACATTGCAATAATAATATGAGTTAC
AAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGAGGACACTTCATTCCTAAC
CAATGAAGAACGGACAAGCCAGAAATCCCCTCGTACAGGTGCCAACACGTTGTCCGACAATGGAG
ATGTCAG
Found at i:10139387 original size:2 final size:2
Alignment explanation
Indices: 10139380--10139436 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
10139370 TACATATACA
* *
10139380 TG TG TG TG TG TA CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
10139422 TG TG TG CG TG TG TG T
1 TG TG TG TG TG TG TG T
10139437 ACATATACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.02, C:0.04, G:0.47, T:0.47
Consensus pattern (2 bp):
TG
Found at i:10144953 original size:49 final size:49
Alignment explanation
Indices: 10144893--10145133 Score: 168
Period size: 49 Copynumber: 4.8 Consensus size: 49
10144883 GATAATAACA
* *
10144893 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTTCTTATACG
* * * *
10144942 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAG-TTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCTTATA-C-G
** ** * *
10144992 TGGCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGA-CCTCTCATCTCGG
1 T-GCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCTTAT-AC-G
* * * *
10145042 TGCCAACG-CATGTCCCAGACATGGTCTTACATGGGACCTTTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTTC-T--TAT--ACG
* *
10145096 ATGCCAATGCCATGTTCCAAACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
10145134 TCTCATCACC
Statistics
Matches: 151, Mismatches: 26, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
47 6 0.04
48 2 0.01
49 62 0.41
50 40 0.26
51 5 0.03
52 1 0.01
54 2 0.01
55 7 0.05
56 26 0.17
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCTTATACG
Found at i:10145021 original size:50 final size:49
Alignment explanation
Indices: 10144900--10145077 Score: 184
Period size: 49 Copynumber: 3.6 Consensus size: 49
10144890 ACATGCCAAA
* *
10144900 GCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCC-AT
* * *
10144949 GCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGGTGGCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGT-GCCAT
** ** *
10144999 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCA-
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAT
*
10145047 ACGCATGTCCCAGACATGGTCTTACATGGGA
1 GC-CATGTCCCAGACATGGTCTTACATGGGA
10145078 CCTTTCATAA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
48 5 0.05
49 61 0.56
50 39 0.36
51 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAT
Found at i:10149918 original size:75 final size:75
Alignment explanation
Indices: 10149795--10149939 Score: 290
Period size: 75 Copynumber: 1.9 Consensus size: 75
10149785 AAAAGATTGG
10149795 TGGCGACTCCCAATTTTCATTTTTTAAAGTCGACAACCTAAAAATTTTGTTTTTCAAAAAATGGT
1 TGGCGACTCCCAATTTTCATTTTTTAAAGTCGACAACCTAAAAATTTTGTTTTTCAAAAAATGGT
10149860 TTCGATAGCT
66 TTCGATAGCT
10149870 TGGCGACTCCCAATTTTCATTTTTTAAAGTCGACAACCTAAAAATTTTGTTTTTCAAAAAATGGT
1 TGGCGACTCCCAATTTTCATTTTTTAAAGTCGACAACCTAAAAATTTTGTTTTTCAAAAAATGGT
10149935 TTCGA
66 TTCGA
10149940 CAAACATCAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (75 bp):
TGGCGACTCCCAATTTTCATTTTTTAAAGTCGACAACCTAAAAATTTTGTTTTTCAAAAAATGGT
TTCGATAGCT
Found at i:10161975 original size:23 final size:23
Alignment explanation
Indices: 10161945--10161990 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
10161935 AACACTCATC
10161945 GACATGTAATCAAAGTAACCTGT
1 GACATGTAATCAAAGTAACCTGT
*
10161968 GACATGTAATCGAAGTAACCTGT
1 GACATGTAATCAAAGTAACCTGT
10161991 ACTCTATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (23 bp):
GACATGTAATCAAAGTAACCTGT
Found at i:10162110 original size:12 final size:13
Alignment explanation
Indices: 10162087--10162120 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
10162077 TTCAAATTGT
10162087 AATTCATCAGTTC
1 AATTCATCAGTTC
10162100 AATTCAT-AGTTC
1 AATTCATCAGTTC
*
10162112 AAATCATCA
1 AATTCATCA
10162121 ACTCATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (13 bp):
AATTCATCAGTTC
Found at i:10164675 original size:15 final size:16
Alignment explanation
Indices: 10164655--10164692 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
10164645 TTAATTGAAT
10164655 TAATTAATTTTAA-AA
1 TAATTAATTTTAAGAA
*
10164670 TAATTATTTTTAAGAA
1 TAATTAATTTTAAGAA
*
10164686 TATTTAA
1 TAATTAA
10164693 AAGTTGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAATTAATTTTAAGAA
Found at i:10169959 original size:22 final size:22
Alignment explanation
Indices: 10169933--10170004 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
10169923 TAGGATATGC
10169933 TATGATATGTTCTTATATGAAA
1 TATGATATGTTCTTATATGAAA
*
10169955 TATGATATGTTCTGATATG-AA
1 TATGATATGTTCTTATATGAAA
*
10169976 TATGATATGTT-TTGATATGAGA
1 TATGATATGTTCTT-ATATGAAA
10169998 TATGATA
1 TATGATA
10170005 ACCTTCATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 18 0.40
22 26 0.58
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (22 bp):
TATGATATGTTCTTATATGAAA
Found at i:10176140 original size:46 final size:45
Alignment explanation
Indices: 10175992--10176196 Score: 163
Period size: 46 Copynumber: 4.4 Consensus size: 45
10175982 TTATTGTGAG
* * *
10175992 CTAGTGTAAGACATGTCAGGGACACGTATCGGCCACATC-ATGA-GAG-
1 CTAGTGTAAGACATGTCTGGGACATGCATC-G--ACATCGA-GACGAGT
* *
10176038 CTAGTGTAAGACCATGTCTGGGACATGGCTTCGACATTGAGACGAGT
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATCGAGACGAGT
* * *
10176085 GCTAGTGTAAGACATGTGTGGGACATGCATCGGCCTCGAGACGTAAGT
1 -CTAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGACG--AGT
* *
10176133 -TAGTGTAAGACATGTCTAGGACATGCATC-AGC-TACGAGATGAGT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGA-CAT-CGAGACGAGT
10176177 C-AGTGTAAGACCATGTCTGG
1 CTAGTGTAAGA-CATGTCTGG
10176197 AGCATGGCAT
Statistics
Matches: 132, Mismatches: 15, Indels: 25
0.77 0.09 0.15
Matches are distributed among these distances:
44 12 0.09
45 15 0.11
46 62 0.47
47 26 0.20
48 17 0.13
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGACGAGT
Found at i:10183745 original size:46 final size:49
Alignment explanation
Indices: 10183689--10183809 Score: 159
Period size: 46 Copynumber: 2.6 Consensus size: 49
10183679 CGAGTGCTAG
*
10183689 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGA-CGTAAGT-TAA
1 TGTAACACATGTCTGGGACATGCATCGGCCTACGAGAGCGTAAGTGTAA
10183735 TGTAACACATGTCTGGGACATGCATCGG-CTACGAGATGCGTAAGTGTAA
1 TGTAACACATGTCTGGGACATGCATCGGCCTACGAGA-GCGTAAGTGTAA
10183784 -G--AC-CATGTCTGGGACATGGCATCGGC
1 TGTAACACATGTCTGGGACAT-GCATCGGC
10183810 ACAGATATGC
Statistics
Matches: 68, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
45 16 0.24
46 41 0.60
48 8 0.12
49 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (49 bp):
TGTAACACATGTCTGGGACATGCATCGGCCTACGAGAGCGTAAGTGTAA
Found at i:10186647 original size:29 final size:29
Alignment explanation
Indices: 10186584--10186651 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
10186574 TAATCACCCA
* *
10186584 CGCACACTCAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTACCATGCACTTTAAACT
* **
10186613 CACACACTTAGTACCATGCA-TTTCAAGTT
1 CGCACACTTAGTACCATGCACTTT-AAACT
10186642 CGCACACTTA
1 CGCACACTTA
10186652 CCTTTTTCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTACCATGCACTTTAAACT
Found at i:10186792 original size:175 final size:175
Alignment explanation
Indices: 10186472--10186799 Score: 507
Period size: 175 Copynumber: 1.9 Consensus size: 175
10186462 AACTCAAGGT
* ** *
10186472 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGCCGCACCCTTCGTGTAAATAATTTATG
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGCCGCACCCTTAATGTAAATAATTTATA
* * *
10186537 GAAAATATATATATTGGGTTGCACACATAATGTTTAGTAATCACCCACGCACACTCAGTGCCATG
66 GAAAATATATATATTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTCAGTGCCATG
*
10186602 CACTTTAAACTCACACACTTAGTACCATGCATTTCAAGTTCGCAC
131 CACTGTAAACTCACACACTTAGTACCATGCATTTCAAGTTCGCAC
*
10186647 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGCCGCACCCTTAATGTAAATAATTTAT
* * *
10186712 AG-AAA-ATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCA
65 AGAAAATATATATATTGGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTCAGTGCCA
*
10186775 TGTACTGTAAACTCACACACTTAGT
129 TGCACTGTAAACTCACACACTTAGT
10186800 GCTGTACAAT
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
174 14 0.10
175 70 0.51
176 54 0.39
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (175 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGCCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATATTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTCAGTGCCATG
CACTGTAAACTCACACACTTAGTACCATGCATTTCAAGTTCGCAC
Found at i:10186795 original size:29 final size:30
Alignment explanation
Indices: 10186761--10186832 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
10186751 ATCAACCGCG
*
10186761 CACACTTAGTGCCATGTAC-TGTAAACTCA
1 CACACTTAGTGCCATGTACATGTAAACCCA
* *
10186790 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATGTAAACCCA
10186819 CACACTTAGTGCCA
1 CACACTTAGTGCCA
10186833 ATCTCATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 29 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATGTAAACCCA
Found at i:10193528 original size:22 final size:22
Alignment explanation
Indices: 10193494--10193563 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
10193484 GATAGGGGAA
* *
10193494 GATATGCTATGATATGAAATAT
1 GATACGCTCTGATATGAAATAT
* *
10193516 GATACGTTCTGATACGAAATAT
1 GATACGCTCTGATATGAAATAT
* * *
10193538 AATATGCTCTGATATGAGATAT
1 GATACGCTCTGATATGAAATAT
10193560 GATA
1 GATA
10193564 AGCTTCAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (22 bp):
GATACGCTCTGATATGAAATAT
Found at i:10196379 original size:21 final size:19
Alignment explanation
Indices: 10196349--10196392 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
10196339 ATCGAGAACT
10196349 GTTTTAATTTAGTAATCTATG
1 GTTTTAATTTA-TAAT-TATG
* *
10196370 GTTTTTATTTATAATTCTG
1 GTTTTAATTTATAATTATG
10196389 GTTT
1 GTTT
10196393 CATTTAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.59
Consensus pattern (19 bp):
GTTTTAATTTATAATTATG
Found at i:10196811 original size:22 final size:22
Alignment explanation
Indices: 10196786--10196829 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10196776 ATGAGGGTAG
10196786 GATATGCTATGATATGAAATAC
1 GATATGCTATGATATGAAATAC
* *
10196808 GATATGCTTTGATATGAGATAC
1 GATATGCTATGATATGAAATAC
10196830 TATAACCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GATATGCTATGATATGAAATAC
Found at i:10199822 original size:12 final size:12
Alignment explanation
Indices: 10199805--10199829 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10199795 TGAATCTTGG
10199805 TGGAAAATTGCT
1 TGGAAAATTGCT
10199817 TGGAAAATTGCT
1 TGGAAAATTGCT
10199829 T
1 T
10199830 TAATGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TGGAAAATTGCT
Found at i:10204516 original size:43 final size:42
Alignment explanation
Indices: 10204462--10204575 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 42
10204452 AATAAAACAT
* * *
10204462 AATAAATAATAATATATATAATAAAATAATTTTATAATATATA
1 AATAAATAATAATATATATAATAAAACAA-TTAACAATATATA
*
10204505 ATATAAA-AATAAGGTATA-AAAATAAAACAATTAACAATATATA
1 A-ATAAATAATAA--TATATATAATAAAACAATTAACAATATATA
10204548 AA-AAATATATACATATATAATAATAAAA
1 AATAAATA-ATA-ATATAT-ATAATAAAA
10204576 ATAAACATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
41 3 0.05
42 6 0.10
43 21 0.36
44 24 0.41
45 4 0.07
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (42 bp):
AATAAATAATAATATATATAATAAAACAATTAACAATATATA
Found at i:10205556 original size:13 final size:13
Alignment explanation
Indices: 10205538--10205564 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10205528 ATGATTCGAA
10205538 GCCTGGAATCACG
1 GCCTGGAATCACG
10205551 GCCTGGAATCACG
1 GCCTGGAATCACG
10205564 G
1 G
10205565 TGTTGATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.33, T:0.15
Consensus pattern (13 bp):
GCCTGGAATCACG
Found at i:10206098 original size:4 final size:4
Alignment explanation
Indices: 10206084--10206123 Score: 71
Period size: 4 Copynumber: 9.8 Consensus size: 4
10206074 ATAACATTGA
10206084 AATT AATTT AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AA-TT AATT AATT AATT AATT AATT AATT AATT AAT
10206124 CTCCTTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:10208044 original size:27 final size:27
Alignment explanation
Indices: 10207993--10208050 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
10207983 AGTCCAACGA
* *
10207993 GACATTAAACACAAGATAGCCTGATGG
1 GACATTAAACACAAGATAGCATGATAG
* *
10208020 GACATTAAACACGAGATAGTATGATAG
1 GACATTAAACACAAGATAGCATGATAG
10208047 GACA
1 GACA
10208051 CTGAACAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (27 bp):
GACATTAAACACAAGATAGCATGATAG
Found at i:10208057 original size:27 final size:27
Alignment explanation
Indices: 10207993--10208057 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
10207983 AGTCCAACGA
* * *
10207993 GACATTAAACACAAGATAGCCTGATGG
1 GACACTAAACACAAGATAGCATGATAG
* * *
10208020 GACATTAAACACGAGATAGTATGATAG
1 GACACTAAACACAAGATAGCATGATAG
*
10208047 GACACTGAACA
1 GACACTAAACA
10208058 GGGGATGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (27 bp):
GACACTAAACACAAGATAGCATGATAG
Found at i:10218755 original size:17 final size:16
Alignment explanation
Indices: 10218731--10218767 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
10218721 TATTTTATTT
10218731 ATATATATATTATTAC
1 ATATATATATTATTAC
*
10218747 ATATCATATATTATTAT
1 ATAT-ATATATTATTAC
10218764 ATAT
1 ATAT
10218768 TATTCCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATATATTATTAC
Found at i:10218765 original size:10 final size:10
Alignment explanation
Indices: 10218708--10218803 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 10
10218698 ATCACATCAT
10218708 TTATAT-TTCA
1 TTATATATT-A
*
10218718 TTATATTTTA
1 TTATATATTA
10218728 TTTATATATATA
1 -TTATATAT-TA
*
10218740 TTAT-TACATA
1 TTATATA-TTA
*
10218750 TCATATATTA
1 TTATATATTA
10218760 TTATATATTA
1 TTATATATTA
*
10218770 TTCCCTATATTA
1 TT--ATATATTA
* *
10218782 TCTTTCT-TTA
1 T-TATATATTA
10218792 TTATATATTA
1 TTATATATTA
10218802 TT
1 TT
10218804 TCATTATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 36 0.54
11 17 0.25
12 10 0.15
13 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATTA
Found at i:10223731 original size:44 final size:44
Alignment explanation
Indices: 10223668--10223755 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
10223658 TTAAACAACC
10223668 GCTCTTGGAGTAAGAAACTACTATGCTGTTCATTAACACTTTGA
1 GCTCTTGGAGTAAGAAACTACTATGCTGTTCATTAACACTTTGA
10223712 GCTCTTGGAG-AAGGAAACTACTATGCTGTTCATTAACACTTTGA
1 GCTCTTGGAGTAA-GAAACTACTATGCTGTTCATTAACACTTTGA
10223756 AGGCCCCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (44 bp):
GCTCTTGGAGTAAGAAACTACTATGCTGTTCATTAACACTTTGA
Found at i:10231120 original size:219 final size:219
Alignment explanation
Indices: 10230736--10231309 Score: 881
Period size: 219 Copynumber: 2.6 Consensus size: 219
10230726 GGCTAAAGCA
* * * * *
10230736 TAGCAGATTTGACCTTT-AGGTGTTTACGCTGAAGCATATCCAAGATGATTTGGCATCTCTGTAT
1 TAGCAGATTTG-GCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTAT
* * * * *
10230800 TGTCAGGGAACAAATCGAAAAAACAGATTT-GCAATCACCATATTCGACGGAGAGCAGATCGAAG
65 TGTCAGAGAACAAATCGAAGAAACAGATTTGGC-ATCTCCATATTCGATGGAGAGCAGATCAAAG
10230864 AATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTTG
129 AATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTTG
**
10230929 TGTTTACAAGGAGCAGATCGAAGAAG
194 CATTTACAAGGAGCAGATCGAAGAAG
*
10230955 TAGCAGATTTGGCTTTCACGTGTTTGCGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTATT
1 TAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTATT
10231020 GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCAAAGAC
66 GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCAAAGA-
*
10231085 ATAGCAGATCTAACCTTCGGATG-TTTTGTATCGAAGCAGATCCAAGATGATTTGGCATCCTTGC
130 ATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTTGC
*
10231149 ATTTACAAGGAGCAGATCGAAGACG
195 ATTTACAAGGAGCAGATCGAAGAAG
* * *
10231174 TAGGAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATTTAAGATGATTTGGCATCTCTGAATT
1 TAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTATT
* * *
10231239 GTTAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATT-G-TCAGAGAGCAGATCAAAG-
66 GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGAT-GGAGAGCAGATCAAAGA
10231301 ATAGCAGAT
130 ATAGCAGAT
10231310 TTGGTGTCTC
Statistics
Matches: 329, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
216 9 0.03
217 1 0.00
218 20 0.06
219 274 0.83
220 25 0.08
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (219 bp):
TAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTATT
GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCAAAGAA
TAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTTGCA
TTTACAAGGAGCAGATCGAAGAAG
Found at i:10231382 original size:132 final size:131
Alignment explanation
Indices: 10231220--10231581 Score: 571
Period size: 132 Copynumber: 2.7 Consensus size: 131
10231210 GATTTAAGAT
* *
10231220 GATTTGGCATCTCTGAATTGTTAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTGTC
1 GATTTGGCGTCTCTGTATTGTTAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTGTC
* * *
10231285 AGAGAGCAGATCAAAGATAGCAGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGC
66 AGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGC
10231350 A
131 A
* *
10231351 GATTTGGCGGTCTCTGTATTGTTAGATAACAAATCGAAGAAATAGATTTGGCATCTCTATATTGT
1 GATTTGGC-GTCTCTGTATTGTTAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTGT
* *
10231416 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTGAGAGAGTAGATCAAAGATAG
65 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAG
10231481 CA
130 CA
* * * * *
10231483 GATTTGGCGTCTCTGTATTGTCAGAGAGCATATCGAAGATAGCAGATTTGGCATCTCTGTATTGT
1 GATTTGGCGTCTCTGTATTGTTAGAGAACAAATCGAAGA-AACAGATTTGGCATCTCTATATTGT
*
10231548 CAGAGAGCAGATCGAAGATAACAGATTTGGCGTC
65 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTC
10231582 CCTGAGTGTG
Statistics
Matches: 212, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
131 35 0.17
132 177 0.83
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (131 bp):
GATTTGGCGTCTCTGTATTGTTAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTGTC
AGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGC
A
Found at i:10231601 original size:44 final size:44
Alignment explanation
Indices: 10231220--10231581 Score: 485
Period size: 44 Copynumber: 8.2 Consensus size: 44
10231210 GATTTAAGAT
* * * * * *
10231220 GATTTGGCATCTCTGAATTGTTAGAGAACAAATCGAAGA-AACA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* * *
10231263 GATTTGGCATCTCTATATTGTCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
*
10231307 GATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* * * * **
10231351 GATTTGGCGGTCTCTGTATTGTTAGATAACAAATCGAAGA-AATA
1 GATTTGGC-GTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* *
10231395 GATTTGGCATCTCTATATTGTCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* * *
10231439 GATTTGGCGTCTCTGTATTGTGAGAGAGTAGATCAAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
*
10231483 GATTTGGCGTCTCTGTATTGTCAGAGAGCATATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* *
10231527 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
10231571 GATTTGGCGTC
1 GATTTGGCGTC
10231582 CCTGAGTGTG
Statistics
Matches: 277, Mismatches: 39, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
43 58 0.21
44 192 0.69
45 27 0.10
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
Found at i:10236727 original size:22 final size:21
Alignment explanation
Indices: 10236682--10236727 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
10236672 AATTATATCT
* *
10236682 TTTAAATATTATCATCTAGAG
1 TTTAAATATGAACATCTAGAG
*
10236703 TTTAAATATGAACTATCTAGGG
1 TTTAAATATGAAC-ATCTAGAG
10236725 TTT
1 TTT
10236728 TCATGTACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (21 bp):
TTTAAATATGAACATCTAGAG
Found at i:10241241 original size:103 final size:103
Alignment explanation
Indices: 10241068--10241258 Score: 253
Period size: 103 Copynumber: 1.9 Consensus size: 103
10241058 AAAAATTAAT
* **
10241068 AGTGTGTTGGGCTAAGTAACTAGGGTGGGGTGCTTGGGTTGTCATTCCACTTCGAGTCAAAAAGA
1 AGTGTGTTGGGCTAAGTAACTAGGGTAGGGTGCTTGCATTGTCATTCCACTTCGAGTCAAAAAGA
* *
10241133 ACAAAACATTTTTAAACAAAAAATAATAATAAATTAGG
66 ACAAAAAATTCTTAAACAAAAAATAATAATAAATTAGG
* *
10241171 AGTGTGTTGGGCTGAGTAACT-GAGGTATGGTGCTTGCATTGTCATTCCACTTC-ACGT-AAAAA
1 AGTGTGTTGGGCTAAGTAACTAG-GGTAGGGTGCTTGCATTGTCATTCCACTTCGA-GTCAAAAA
**
10241233 GGGCCAAAAAATTCTTAAACAAAAAA
64 -GAACAAAAAATTCTTAAACAAAAAA
10241259 ATATAAAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
102 7 0.09
103 69 0.91
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (103 bp):
AGTGTGTTGGGCTAAGTAACTAGGGTAGGGTGCTTGCATTGTCATTCCACTTCGAGTCAAAAAGA
ACAAAAAATTCTTAAACAAAAAATAATAATAAATTAGG
Found at i:10245204 original size:41 final size:41
Alignment explanation
Indices: 10245106--10245224 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 41
10245096 GTGTGATTCA
* *
10245106 TGTAAGACCATGTCTGGGACATTGGCA-CCAAAGTGAGAAAACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATA-T--GAAAACG
*
10245149 TGTAAGACCATGTCTGGGACATTGGCATCGTATATG-ATACG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-ATATGAAAACG
* *
10245190 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATG
10245225 TGATAGCATT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
40 5 0.07
41 32 0.46
42 1 0.01
43 27 0.39
44 2 0.03
45 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAAAACG
Found at i:10253654 original size:139 final size:139
Alignment explanation
Indices: 10253483--10253744 Score: 427
Period size: 139 Copynumber: 1.9 Consensus size: 139
10253473 CTTTTGCCCC
* *
10253483 TATGCTCGTAAAATGATTTTCATTCAATTTCTTTGCACTTTAAGCCAAGCTGAATCATTTTCACA
1 TATGCTCGTAAAATGATTTTCATTCAATTTCTTTACACTTTAAGCCAAGCTGAATCATCTTCACA
* *
10253548 ACTATAG-CATCCAACAATTCCACTAAATCACACTTTTATGACAAATTTATAACTTTTACAATTT
66 ACTATAGAAACCCAA-AATTCCACTAAATCACACTTTTATGACAAATTTATAACTTTTACAATTT
10253612 CTTTGCACTT
130 CTTTGCACTT
* *
10253622 TATGCTCGTAAAATGATTTTCATTCAATTTCTTTACACTTTAAGCCTAGCTGAATCATCTTCATA
1 TATGCTCGTAAAATGATTTTCATTCAATTTCTTTACACTTTAAGCCAAGCTGAATCATCTTCACA
* * *
10253687 ACTGTAGAAACCCAAAATTCCACTAAATTACACTTTTATGACAAATTTATAATTTTTA
66 ACTATAGAAACCCAAAATTCCACTAAATCACACTTTTATGACAAATTTATAACTTTTA
10253745 TAAATTAGTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
139 108 0.96
140 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (139 bp):
TATGCTCGTAAAATGATTTTCATTCAATTTCTTTACACTTTAAGCCAAGCTGAATCATCTTCACA
ACTATAGAAACCCAAAATTCCACTAAATCACACTTTTATGACAAATTTATAACTTTTACAATTTC
TTTGCACTT
Found at i:10257876 original size:28 final size:26
Alignment explanation
Indices: 10257827--10257879 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
10257817 ACACATACTT
10257827 AGCCTTATATTCATGTAGTTCATATA
1 AGCCTTATATTCATGTAGTTCATATA
* *
10257853 AGCCTATATATTTCATTTATTTCATAT
1 AGCCT-TATA-TTCATGTAGTTCATAT
10257880 TTTAGTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 4 0.17
28 14 0.61
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
AGCCTTATATTCATGTAGTTCATATA
Found at i:10259562 original size:31 final size:32
Alignment explanation
Indices: 10259497--10259576 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 32
10259487 TCCATATATG
* * *
10259497 CATATACATTATATATATAATCAAGAGCCACA
1 CATATATATTATATATATAATCAAAACCCACA
10259529 CATATATATTATATATATAA-CAAAACCCACA
1 CATATATATTATATATATAATCAAAACCCACA
*
10259560 CATATGTATTATATATA
1 CATATATATTATATATA
10259577 ATACAACCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 25 0.57
32 19 0.43
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (32 bp):
CATATATATTATATATATAATCAAAACCCACA
Found at i:10265549 original size:32 final size:32
Alignment explanation
Indices: 10265508--10265570 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
10265498 TTTGCAAGAG
10265508 CTCGATCAAATTTTACACCATTAGCGACTATA
1 CTCGATCAAATTTTACACCATTAGCGACTATA
10265540 CTCGATCAAATTTTACACCATTAGCGACTAT
1 CTCGATCAAATTTTACACCATTAGCGACTAT
10265571 GTAATCACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (32 bp):
CTCGATCAAATTTTACACCATTAGCGACTATA
Found at i:10269017 original size:20 final size:20
Alignment explanation
Indices: 10268980--10269024 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10268970 AGGGACTAAA
* * *
10268980 ATGAAAAGTTGTACAATTTG
1 ATGAAAAATTCTAAAATTTG
*
10269000 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
10269020 ATGAA
1 ATGAA
10269025 TACATCTGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:10273345 original size:14 final size:14
Alignment explanation
Indices: 10273326--10273353 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10273316 AACTTGTTTG
10273326 ACCAGTTGAAATGT
1 ACCAGTTGAAATGT
10273340 ACCAGTTGAAATGT
1 ACCAGTTGAAATGT
10273354 GCCATTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ACCAGTTGAAATGT
Found at i:10273587 original size:39 final size:39
Alignment explanation
Indices: 10273541--10273620 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
10273531 AGCATGTATT
*
10273541 TTGACAGGTTTATGGTGGTATTTATAGTTCATATTTTGG
1 TTGACAGGTTTATGGTGGTATTTATAGATCATATTTTGG
* *
10273580 TTGACAGGTTTGTGGTGGTATTTATAGATGATATTTTGG
1 TTGACAGGTTTATGGTGGTATTTATAGATCATATTTTGG
10273619 TT
1 TT
10273621 TACTCTCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.49
Consensus pattern (39 bp):
TTGACAGGTTTATGGTGGTATTTATAGATCATATTTTGG
Found at i:10285375 original size:46 final size:45
Alignment explanation
Indices: 10285318--10285544 Score: 178
Period size: 46 Copynumber: 4.9 Consensus size: 45
10285308 GGGTTATTGT
* * *
10285318 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATCATGA-
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACA-GA-GAC
* * **
10285364 GAGCCAGTGTAAGACCATGTCTAGGACATGGCTTCGG-TATTGAGAC
1 GAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCACAGAGAC
* * *
10285410 GAATGCTAGTGTAAGACATGTCTAGAACATGCATCGGCCTC-GAGAC
1 G-A-GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACAGAGAC
* * * *
10285456 GTAAGTCAGTGTAAGACATGTCTAGGACATGCATCAGCTAC-GAGAT
1 G--AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACAGAGAC
*
10285502 GAGTCAGTGTAAGACCATGTCT-GGAACATGGCATCGG-CACAGA
1 GAGCCAGTGTAAGA-CATGTCTAGG-ACAT-GCATCGGCCACAGA
10285545 TATGCTAGTG
Statistics
Matches: 148, Mismatches: 22, Indels: 22
0.77 0.11 0.11
Matches are distributed among these distances:
44 15 0.10
45 15 0.10
46 71 0.48
47 30 0.20
48 17 0.11
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACAGAGAC
Found at i:10287101 original size:73 final size:74
Alignment explanation
Indices: 10286982--10287131 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 74
10286972 CTAGTGAAAG
* * * *
10286982 TATGGGTCTAGCTGTACATGCCATAATTGTATATTGATAGTGTGACAACTTCTGACGTTTATAAA
1 TATGGGTCTAGCTATACATGCCACAACTATATATTGATAGTGTGACAACTTCTGACGTTTATAAA
10287047 -ATTATTTT
66 TATTATTTT
* * **
10287055 TATGGGTGTAGCTATACATGCCACAACTATATATTTATAGTGTGACAACTTCTTCCGTTTATAAA
1 TATGGGTCTAGCTATACATGCCACAACTATATATTGATAGTGTGACAACTTCTGACGTTTATAAA
*
10287120 TTTTATTTT
66 TATTATTTT
10287129 TAT
1 TAT
10287132 ATAGTAAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 57 0.85
74 10 0.15
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (74 bp):
TATGGGTCTAGCTATACATGCCACAACTATATATTGATAGTGTGACAACTTCTGACGTTTATAAA
TATTATTTT
Found at i:10288060 original size:27 final size:27
Alignment explanation
Indices: 10288030--10288275 Score: 271
Period size: 27 Copynumber: 9.1 Consensus size: 27
10288020 AGTACTCCCA
*
10288030 ATTTATAGAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
* *
10288057 ATTTACAGAATTATCGTTTTACCCTCA
1 ATTTACAGAATTACCGTTTTACCCTCG
** * *
10288084 ATTTTTAAAATTACCATTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
* **
10288111 ATTTACAGAATTACCATTTTACCCTTA
1 ATTTACAGAATTACCGTTTTACCCTCG
** *
10288138 ATTTACAGAATTACTATTTTACCCTTG
1 ATTTACAGAATTACCGTTTTACCCTCG
10288165 ATTTACAGAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCG
** * *
10288192 ATTTGTAAAATTACCGTTTTACCCTTG
1 ATTTACAGAATTACCGTTTTACCCTCG
*
10288219 ATTTACAGAATTACTAG-TTTACCCTC-
1 ATTTACAGAATTAC-CGTTTTACCCTCG
* * *
10288245 AGTTTACAAAATTATCGTTTTACCCTTG
1 A-TTTACAGAATTACCGTTTTACCCTCG
10288273 ATT
1 ATT
10288276 GTGAAATTAC
Statistics
Matches: 183, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 179 0.98
28 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
ATTTACAGAATTACCGTTTTACCCTCG
Found at i:10288121 original size:81 final size:81
Alignment explanation
Indices: 10288030--10288275 Score: 307
Period size: 81 Copynumber: 3.0 Consensus size: 81
10288020 AGTACTCCCA
* **
10288030 ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCAATTTTTAAAAT
1 ATTTATAGAATTACCGTTTTACCCTTGATTTACAGAATTATCGTTTTACCCTCAATTTACAAAAT
*
10288095 TACCATTTTACCCTCG
66 TACCGTTTTACCCTCG
* * * * ** *
10288111 ATTTACAGAATTACCATTTTACCCTTAATTTACAGAATTA-CTATTTTACCCTTGATTTACAGAA
1 ATTTATAGAATTACCGTTTTACCCTTGATTTACAGAATTATC-GTTTTACCCTCAATTTACAAAA
10288175 TTACCGTTTTACCCTCG
65 TTACCGTTTTACCCTCG
* * * *
10288192 ATTTGTAAAATTACCGTTTTACCCTTGATTTACAGAATTACTAG-TTTACCCTCAGTTTACAAAA
1 ATTTATAGAATTACCGTTTTACCCTTGATTTACAGAATTA-TCGTTTTACCCTCAATTTACAAAA
* *
10288256 TTATCGTTTTACCCTTG
65 TTACCGTTTTACCCTCG
10288273 ATT
1 ATT
10288276 GTGAAATTAC
Statistics
Matches: 138, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
80 1 0.01
81 137 0.99
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (81 bp):
ATTTATAGAATTACCGTTTTACCCTTGATTTACAGAATTATCGTTTTACCCTCAATTTACAAAAT
TACCGTTTTACCCTCG
Found at i:10288310 original size:27 final size:27
Alignment explanation
Indices: 10288280--10288475 Score: 257
Period size: 27 Copynumber: 7.3 Consensus size: 27
10288270 TTGATTGTGA
* *
10288280 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
10288307 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
10288334 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
10288361 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
10288388 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
10288415 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
10288442 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
10288469 AATTACC
1 AATTACC
10288476 ATTTTGCCCC
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:10288719 original size:27 final size:26
Alignment explanation
Indices: 10288675--10288760 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
10288665 GGAGGAAGCG
* *
10288675 TTCTGGTGGCTATGCCACAAATATCTA
1 TTCTGGTGGCTCTACCAC-AATATCTA
*
10288702 TTCTGGTGGCTCTACCACAATATCTG
1 TTCTGGTGGCTCTACCACAATATCTA
* ** * *
10288728 TATCTGGTGACTCTGTCACGATATCTG
1 T-TCTGGTGGCTCTACCACAATATCTA
10288755 TTCTGG
1 TTCTGG
10288761 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 13 0.25
27 38 0.75
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
TTCTGGTGGCTCTACCACAATATCTA
Found at i:10288887 original size:6 final size:6
Alignment explanation
Indices: 10288878--10289064 Score: 154
Period size: 6 Copynumber: 30.8 Consensus size: 6
10288868 TTGCATTCAC
* *
10288878 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
10288927 -TTACTA ATACTG ATTCTG ATTTTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * * *
10288975 ATTCTG -TCACCTA ATTTTG ATTTTG ATTCTG ATTCT- ATTACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
10289024 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
10289065 CATTTTGGTT
Statistics
Matches: 148, Mismatches: 17, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
5 12 0.08
6 122 0.82
7 11 0.07
8 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:10288940 original size:30 final size:30
Alignment explanation
Indices: 10288878--10289064 Score: 215
Period size: 30 Copynumber: 6.4 Consensus size: 30
10288868 TTGCATTCAC
* *
10288878 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATACTG
10288909 ATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
*
10288939 ATTCTGATTTTGATTCTG----T--TACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* **
10288963 ATTCTGATTCTGATTCTGTCACCTAATTTTG
1 ATTCTGATTCTGATTCTGTTA-CTAATACTG
* * *
10288994 ATTTTGATTCTGATTCTATTACTAATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
10289024 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
10289054 ATTCTGATTCT
1 ATTCTGATTCT
10289065 CATTTTGGTT
Statistics
Matches: 134, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
24 22 0.16
26 1 0.01
29 1 0.01
30 69 0.51
31 41 0.31
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:10289018 original size:85 final size:85
Alignment explanation
Indices: 10288878--10289064 Score: 329
Period size: 85 Copynumber: 2.2 Consensus size: 85
10288868 TTGCATTCAC
*
10288878 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATACTGATTC
*
10288943 TGATTTTGATTCTGTTACTG
66 TGATTCTGATTCTGTTACTG
* * *
10288963 ATTCTGATTCTGATTCTGTCACCTAATTTTGATTTTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATACTGATTC
10289028 TGATTCTGATTCTGTTACTG
66 TGATTCTGATTCTGTTACTG
10289048 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
10289065 CATTTTGGTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 97 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (85 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATACTGATTC
TGATTCTGATTCTGTTACTG
Found at i:10292625 original size:41 final size:41
Alignment explanation
Indices: 10292551--10292851 Score: 455
Period size: 41 Copynumber: 7.4 Consensus size: 41
10292541 GCGTTTTTCT
*
10292551 TAAAACGCCGC-AAAAGA-CAGAGCATTAGTGGCGCTTTCGG
1 TAAAACGCCGCTAAAA-ACCAGAGCATTAGCGGCGCTTTCGG
* *
10292591 TAAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTCGA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* *
10292632 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGT
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* *
10292673 TAAAGCGCCGCTAAAAACCAGAGCATTAGCGACGCTTTCGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
*
10292714 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGTGCTTTCGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* *
10292755 TAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGT
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* *
10292796 TAAAACGCCGCTAAAAACCAGAGCA-TAGCGACGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
*
10292836 TAAAACGTCGCTAAAA
1 TAAAACGCCGCTAAAA
10292852 GTCATATAAC
Statistics
Matches: 238, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 39 0.16
41 199 0.84
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (41 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
Found at i:10293289 original size:25 final size:25
Alignment explanation
Indices: 10293260--10293313 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
10293250 GTGATTTTGA
10293260 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCATTTGTTGAACT
10293285 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCATTTGTTGAACT
10293310 ATGT
1 ATGT
10293314 ATAATTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (25 bp):
ATGTGGAATTAGCATTTGTTGAACT
Found at i:10293933 original size:15 final size:15
Alignment explanation
Indices: 10293913--10293943 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10293903 TTTAATTTAG
*
10293913 AAGATAAATGTATAT
1 AAGATAAATATATAT
10293928 AAGATAAATATATAT
1 AAGATAAATATATAT
10293943 A
1 A
10293944 TAAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:10305402 original size:129 final size:131
Alignment explanation
Indices: 10305260--10305507 Score: 322
Period size: 129 Copynumber: 1.9 Consensus size: 131
10305250 ACTGGGCAAA
* *
10305260 TTAGCGACGTTTTTTAAAAAAACCCCGCTAAAAGTACAGGTCTCTAGCGGCGTTTTTTATAAAAG
1 TTAGCGACGTTTTTTAAAAAAACCCCACTAAAAGTACAGGTCTCTAGCGACGTTTTTTATAAAAG
*
10305325 CGCCGCTAAAGGTCCTGA-TCTCTAGCGGCG-TTTTT-TAAAAAAGCGCCGCTAAAAGTACAGGT
66 CGCCGCTAAAGGT-CTGAGTCTCTAGCGGCGTTTTTTCTAAAAAAACGCCGCTAAAAGTACAGGT
10305387 AT
130 AT
* * * * * * * * *
10305389 TTAGCGGCGTTTTTTATAAGAGCGCCACTAAAGGTCCTGGTCTTTAGCGACGTTTTTTATAAAAG
1 TTAGCGACGTTTTTTAAAAAAACCCCACTAAAAGTACAGGTCTCTAGCGACGTTTTTTATAAAAG
* * * *
10305454 CGCCGCTAAAGGTCTTAGTCTTTAGCGGTGTTTTTTCTAAAAAAATGCCGCTAA
66 CGCCGCTAAAGGTCTGAGTCTCTAGCGGCGTTTTTTCTAAAAAAACGCCGCTAA
10305508 GTTTTGTGGC
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
128 3 0.03
129 77 0.77
130 5 0.05
131 15 0.15
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (131 bp):
TTAGCGACGTTTTTTAAAAAAACCCCACTAAAAGTACAGGTCTCTAGCGACGTTTTTTATAAAAG
CGCCGCTAAAGGTCTGAGTCTCTAGCGGCGTTTTTTCTAAAAAAACGCCGCTAAAAGTACAGGTA
T
Found at i:10305464 original size:43 final size:43
Alignment explanation
Indices: 10305260--10305495 Score: 274
Period size: 43 Copynumber: 5.5 Consensus size: 43
10305250 ACTGGGCAAA
* * * * * * *
10305260 TTAGCGACGTTTTTTAAAAAAACCCCGCTAAAAGTACAGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* *
10305303 CTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGATCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * * * * *
10305346 CTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTAT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* *
10305389 TTAGCGGCGTTTTTTATAAGAGCGCCACTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * *
10305432 TTAGCGACGTTTTTTATAAAAGCGCCGCTAAAGGTCTTAGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* *
10305475 TTAGCGGTGTTTTTTCTAAAA
1 TTAGCGGCGTTTTTTATAAAA
10305496 AAATGCCGCT
Statistics
Matches: 162, Mismatches: 31, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
Found at i:10305478 original size:86 final size:86
Alignment explanation
Indices: 10305260--10305495 Score: 323
Period size: 86 Copynumber: 2.7 Consensus size: 86
10305250 ACTGGGCAAA
* * *
10305260 TTAGCGACGTTTTTTAAAAAAACCCCGCTAAAAGTACAGGTCTCTAGCGGCGTTTTTTATAAAAG
1 TTAGCGACGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCGGCGTTTTTTATAAAAG
*
10305325 CGCCGCTAAAGGTCCTGATCT
66 CGCCACTAAAGGTCCTGATCT
* * * *
10305346 CTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTATTTAGCGGCGTTTTTTATAAGAG
1 TTAGCGACGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCGGCGTTTTTTATAAAAG
*
10305411 CGCCACTAAAGGTCCTGGTCT
66 CGCCACTAAAGGTCCTGATCT
* * * *
10305432 TTAGCGACGTTTTTTATAAAAGCGCCGCTAAAGGT-CTTA-GTCTTTAGCGGTGTTTTTTCTAAA
1 TTAGCGACGTTTTTTAAAAAAGCGCCGCTAAAAGTAC--AGGTCTTTAGCGGCGTTTTTTATAAA
10305495 A
64 A
10305496 AAATGCCGCT
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.01
86 129 0.98
87 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (86 bp):
TTAGCGACGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCGGCGTTTTTTATAAAAG
CGCCACTAAAGGTCCTGATCT
Found at i:10308188 original size:20 final size:20
Alignment explanation
Indices: 10308151--10308193 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
10308141 AAGGACTATA
10308151 TTGTATAAGTTGTAAAATAG
1 TTGTATAAGTTGTAAAATAG
* *
10308171 TTGT-TAAGTATGTGAAATTG
1 TTGTATAAGT-TGTAAAATAG
10308191 TTG
1 TTG
10308194 GAATTTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGTATAAGTTGTAAAATAG
Found at i:10308848 original size:46 final size:46
Alignment explanation
Indices: 10308724--10308850 Score: 152
Period size: 46 Copynumber: 2.7 Consensus size: 46
10308714 AGAGCTAGTC
* * *
10308724 CAGTGTAAGATCATGTCTAGGACATGGCATTGGCATTGAGATGAGTA
1 CAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATCGAGATGAGTA
*
10308771 CTAGTGTAAGACATGTCTGGGACAT-GCATCGGC-TACGAGATGTGT-
1 C-AGTGTAAGACATGTCTGGGACATGGCATCGGCAT-CGAGATGAGTA
*
10308816 CAGTGTAAAACCATGTCTGGGACATGGCATCGGCA
1 CAGTGTAAGA-CATGTCTGGGACATGGCATCGGCA
10308851 CAGATATGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
44 8 0.11
45 16 0.23
46 23 0.33
47 14 0.20
48 9 0.13
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
CAGTGTAAGACATGTCTGGGACATGGCATCGGCATCGAGATGAGTA
Found at i:10315311 original size:22 final size:22
Alignment explanation
Indices: 10315277--10315346 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
10315267 ATAGGGGTAA
* *
10315277 GATATGCTATGATATGAAATAT
1 GATACGCTCTGATATGAAATAT
* **
10315299 GATACGTTCTGATGCGAAATAT
1 GATACGCTCTGATATGAAATAT
* * * *
10315321 AATATGCTCTAATATGAGATAT
1 GATACGCTCTGATATGAAATAT
10315343 GATA
1 GATA
10315347 AGCTTCAATA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (22 bp):
GATACGCTCTGATATGAAATAT
Found at i:10316258 original size:22 final size:23
Alignment explanation
Indices: 10316223--10316274 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
10316213 ATGTAAGCTT
*
10316223 TGTTTGTACAAAATTATGTGTTA
1 TGTTTATACAAAATTATGTGTTA
10316246 TGTTTATA-AAAATTATGTGTTA
1 TGTTTATACAAAATTATGTGTTA
10316268 TGTTTAT
1 TGTTTAT
10316275 GATCCGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (23 bp):
TGTTTATACAAAATTATGTGTTA
Found at i:10318626 original size:22 final size:22
Alignment explanation
Indices: 10318573--10318632 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
10318563 ATGGGGGTAG
*
10318573 GATATGCTATGATATGAAATAC
1 GATATGCTTTGATATGAAATAC
*
10318595 GATATGCTTTGATATGAGATAC
1 GATATGCTTTGATATGAAATAC
10318617 GATAAT-CTTTGATATG
1 GAT-ATGCTTTGATATG
10318633 TTATATGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (22 bp):
GATATGCTTTGATATGAAATAC
Found at i:10319494 original size:10 final size:11
Alignment explanation
Indices: 10319469--10319495 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10319459 CCCTGCATAT
10319469 TTTTTGAAAAG
1 TTTTTGAAAAG
10319480 TTTTTGAAAAG
1 TTTTTGAAAAG
10319491 TTTTT
1 TTTTT
10319496 TCTGCCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (11 bp):
TTTTTGAAAAG
Found at i:10320301 original size:25 final size:25
Alignment explanation
Indices: 10320273--10320328 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
10320263 AAGAGTCACC
10320273 TCATTCCCTATACTCAAACCATCTA
1 TCATTCCCTATACTCAAACCATCTA
10320298 TCATTCCCTATACTCAAACCATCTA
1 TCATTCCCTATACTCAAACCATCTA
10320323 TCATTC
1 TCATTC
10320329 TACCAAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.34
Consensus pattern (25 bp):
TCATTCCCTATACTCAAACCATCTA
Found at i:10322216 original size:12 final size:12
Alignment explanation
Indices: 10322199--10322223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10322189 TGAATCTTGG
10322199 TGGAAAATTGCT
1 TGGAAAATTGCT
10322211 TGGAAAATTGCT
1 TGGAAAATTGCT
10322223 T
1 T
10322224 CAATGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TGGAAAATTGCT
Found at i:10326352 original size:50 final size:50
Alignment explanation
Indices: 10326274--10326372 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
10326264 AGGCAGTTCA
*
10326274 TGCGTGGATCTTGTCAGCAAGTCGTCACAAATCAGGTGTGTAACTGACAG
1 TGCGTGGATCTTGTCAGCAAGTCATCACAAATCAGGTGTGTAACTGACAG
10326324 TGCGTGGATCTTGTCAGCAAGTCATCACAAATCAGGTGTGTAACTGACA
1 TGCGTGGATCTTGTCAGCAAGTCATCACAAATCAGGTGTGTAACTGACA
10326373 CCCTTTCATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (50 bp):
TGCGTGGATCTTGTCAGCAAGTCATCACAAATCAGGTGTGTAACTGACAG
Found at i:10326624 original size:28 final size:28
Alignment explanation
Indices: 10326592--10326656 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
10326582 ATTTACTAGA
*
10326592 ATACCCCTATGTATGCAAAATTACAATT
1 ATACCCCTATGTATGCAAAATGACAATT
* **
10326620 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACAATT
10326648 ATACCCCTA
1 ATACCCCTA
10326657 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACAATT
Found at i:10326803 original size:28 final size:29
Alignment explanation
Indices: 10326762--10326824 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
10326752 AGGAAGCGTC
*
10326762 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
10326790 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
10326819 CTGGTG
1 CTGGTG
10326825 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:10326835 original size:29 final size:28
Alignment explanation
Indices: 10326772--10326835 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
10326762 CTGGTGGCTA
* *
10326772 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
10326800 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
10326829 TGTCACA
1 TGCCACA
10326836 TTTTTTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:10327312 original size:19 final size:19
Alignment explanation
Indices: 10327288--10327326 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10327278 TTTTAATTAT
* *
10327288 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
10327307 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
10327326 T
1 T
10327327 ATGACGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:10327938 original size:11 final size:10
Alignment explanation
Indices: 10327910--10327943 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
10327900 AGCCTGTAAG
10327910 TATTCTGAAT
1 TATTCTGAAT
*
10327920 TTTTCTGAAT
1 TATTCTGAAT
10327930 ATATTCTGAAT
1 -TATTCTGAAT
10327941 TAT
1 TAT
10327944 CTGTTTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:10334471 original size:28 final size:28
Alignment explanation
Indices: 10334439--10334503 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
10334429 ATTTACTAGA
* *
10334439 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATACAAAATGACCATT
* *
10334467 ATACCCCTATGTATACTAAATGACCTTT
1 ATACCCCTATGTATACAAAATGACCATT
10334495 ATACCCCTA
1 ATACCCCTA
10334504 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATACAAAATGACCATT
Found at i:10334650 original size:28 final size:29
Alignment explanation
Indices: 10334609--10334671 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
10334599 AGGAAGCGTC
*
10334609 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
10334637 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
10334666 CTGGTG
1 CTGGTG
10334672 ACTTTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:10335159 original size:19 final size:19
Alignment explanation
Indices: 10335135--10335173 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10335125 GTTTAATTAT
* *
10335135 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
10335154 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
10335173 T
1 T
10335174 ATGACGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:10341977 original size:17 final size:17
Alignment explanation
Indices: 10341946--10341978 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10341936 CTAATATATG
*
10341946 TATATATTGTATATTTA
1 TATATATTATATATTTA
10341963 TATATATTATATATTT
1 TATATATTATATATTT
10341979 TTAATGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATATTATATATTTA
Found at i:10342307 original size:3 final size:3
Alignment explanation
Indices: 10342293--10342376 Score: 59
Period size: 3 Copynumber: 27.3 Consensus size: 3
10342283 GTATTTTTAC
*
10342293 TAT TAT TGT TAT TAT TAT TAT TAT T-T TAT T-T TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
10342337 T-T TTT GTAT ATAT TAT TCAT CCTAT CAT TAT TA- TAT TAT T
1 TAT TAT -TAT -TAT TAT T-AT --TAT TAT TAT TAT TAT TAT T
10342377 TTTACGACTG
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 8 0.12
3 45 0.68
4 10 0.15
5 2 0.03
6 1 0.02
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:10342350 original size:23 final size:23
Alignment explanation
Indices: 10342304--10342350 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10342294 ATTATTGTTA
*
10342304 TTATTATTATTATTTTATTTTAT
1 TTATTATTATTATTTTATTATAT
*
10342327 TTATTATTATT-TTTTGTATATAT
1 TTATTATTATTATTTTAT-TATAT
10342350 T
1 T
10342351 ATTCATCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTATTATTATTTTATTATAT
Found at i:10342353 original size:26 final size:23
Alignment explanation
Indices: 10342295--10342341 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
10342285 ATTTTTACTA
10342295 TTATTGTTA-TTATTATTATTATT
1 TTATT-TTATTTATTATTATTATT
10342318 TTATTTTATTTATTATTATT-TT
1 TTATTTTATTTATTATTATTATT
10342340 TT
1 TT
10342342 GTATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
TTATTTTATTTATTATTATTATT
Found at i:10354883 original size:75 final size:75
Alignment explanation
Indices: 10354790--10354928 Score: 224
Period size: 75 Copynumber: 1.9 Consensus size: 75
10354780 TTCTGTTTTC
* * *
10354790 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTTAAGACACGTTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTT
10354855 GGTCTTTCAA
66 GGTCTTTCAA
** *
10354865 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
10354929 CTGTTTTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTT
GGTCTTTCAA
Found at i:10355026 original size:90 final size:88
Alignment explanation
Indices: 10354865--10355081 Score: 230
Period size: 88 Copynumber: 2.5 Consensus size: 88
10354855 GGTCTTTCAA
*
10354865 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCTATTTTCAATTTC
*
10354930 TGTTTTTTCAATTTATATTTTTC
66 TATTTTTTCAATTTATATTTTTC
* * * *
10354953 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGTCT-TGGCTCACGTGCTGAGCTATTTTCAA-
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GCTGAGCTATTTTCAAT
* * *
10355016 TTC-ATATTTTT-AATGTCTGTTTTT-
63 TTCTAT-TTTTTCAATTTATATTTTTC
* * **
10355040 AAAGATTCAATTCATATTGCGAGAAATGAGTTGAG-CTCAGGA
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
10355082 TCATATACTG
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
87 7 0.07
88 77 0.72
89 8 0.07
90 15 0.14
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCTATTTTCAATTTC
TATTTTTTCAATTTATATTTTTC
Found at i:10357200 original size:35 final size:35
Alignment explanation
Indices: 10357154--10357226 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
10357144 TGGACTCGGC
* *
10357154 ATTCGAAGAATCACCTTGGACCTCAGACTATTCTT
1 ATTCGAAGAATCAACTTGGACCTCAGACTATTATT
* *
10357189 ATTCGAAGAATCAACTTGGACCTCGGATTATTATT
1 ATTCGAAGAATCAACTTGGACCTCAGACTATTATT
10357224 ATT
1 ATT
10357227 TTTAATTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (35 bp):
ATTCGAAGAATCAACTTGGACCTCAGACTATTATT
Found at i:10364623 original size:30 final size:30
Alignment explanation
Indices: 10364577--10364670 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
10364567 TTTTATTATG
*
10364577 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
10364608 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
10364638 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
10364668 CCA
1 CCA
10364671 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:10364632 original size:15 final size:15
Alignment explanation
Indices: 10364587--10364664 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
10364577 CCAATATCTC
10364587 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
10364602 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
10364617 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
10364632 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
10364647 GATACCCATATCTTT
1 GATACCCATATCTTT
10364662 GAT
1 GAT
10364665 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:10380560 original size:3 final size:3
Alignment explanation
Indices: 10380552--10380626 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
10380542 GTAATAAAGG
* *
10380552 AAT AAT AAT CAT AAT AAT AAT AATT AAT AAC AA- ATAT AAT GAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A-AT AAT -AAT AAT
* * *
10380599 AAC AGT AAT AAT AAT AAAG AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT
10380627 TAAAAATGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
2 1 0.02
3 48 0.83
4 9 0.16
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:10380590 original size:19 final size:21
Alignment explanation
Indices: 10380551--10380653 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 21
10380541 AGTAATAAAG
10380551 GAATAATAATCATAATAATAAT
1 GAATAATAA-CATAATAATAAT
10380573 -AATTAATAACA-AAT-ATAAT
1 GAA-TAATAACATAATAATAAT
10380592 GAATAATAACAGTAATAATAAT
1 GAATAATAACA-TAATAATAAT
* * *
10380614 AAAGAAT-A-ATAATTAAAAAT
1 GAATAATAACATAA-TAATAAT
*
10380634 GAATAAATAA-ATAAAAATAA
1 GAAT-AATAACATAATAATAA
10380654 AGGGTAAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
19 16 0.24
20 14 0.21
21 15 0.23
22 21 0.32
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (21 bp):
GAATAATAACATAATAATAAT
Found at i:10380607 original size:16 final size:14
Alignment explanation
Indices: 10380538--10380626 Score: 64
Period size: 13 Copynumber: 6.6 Consensus size: 14
10380528 CAACCAACAA
* *
10380538 AATAGTAATAAAGG
1 AATAATAATAAAGT
*
10380552 AATAATAAT-CA-T
1 AATAATAATAAAGT
*
10380564 AATAATAAT-AATT
1 AATAATAATAAAGT
* *
10380577 AATAACAA-ATA-T
1 AATAATAATAAAGT
10380589 AATGAATAATAACAGT
1 AAT-AATAATAA-AGT
10380605 AATAATAATAAAG-
1 AATAATAATAAAGT
10380618 AATAATAAT
1 AATAATAAT
10380627 TAAAAATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
12 14 0.23
13 23 0.38
14 11 0.18
15 9 0.15
16 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (14 bp):
AATAATAATAAAGT
Found at i:10380775 original size:78 final size:77
Alignment explanation
Indices: 10380646--10380802 Score: 242
Period size: 78 Copynumber: 2.0 Consensus size: 77
10380636 ATAAATAAAT
* * * * *
10380646 AAAAATAAAGGGTAAAAGGCGAAACCGACTATATGAAGGGTGGTCGATCGGAAGGAAGGGCAACA
1 AAAAATAAAGGGGAAAAGGCGAAACCGAATATATGAAAGGTGGTCAATCGGAAGAAAGGGCAACA
10380711 GTGGACCGAGGC
66 GTGGACCGAGGC
* *
10380723 NAAAAATAAAGGGGAAAAGGGGAAACCGAATATATGAAAGGTGGTTAATCGGAAGAAAGGGCAAC
1 -AAAAATAAAGGGGAAAAGGCGAAACCGAATATATGAAAGGTGGTCAATCGGAAGAAAGGGCAAC
10380788 AGTGGACCGAGGC
65 AGTGGACCGAGGC
10380801 AA
1 AA
10380803 GGGTGGGTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 2 0.03
78 70 0.97
ACGTcount: A:0.42, C:0.12, G:0.34, T:0.11
Consensus pattern (77 bp):
AAAAATAAAGGGGAAAAGGCGAAACCGAATATATGAAAGGTGGTCAATCGGAAGAAAGGGCAACA
GTGGACCGAGGC
Found at i:10380986 original size:20 final size:19
Alignment explanation
Indices: 10380956--10381011 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
10380946 GGAGATGGGA
10380956 GAAAGGAAAAGAAAGAGGAAG
1 GAAA-GAAAAGAAAG-GGAAG
10380977 GAAAGAAAAGAAAGGGAAG
1 GAAAGAAAAGAAAGGGAAG
10380996 GAAAGAAAAAGAAAGG
1 GAAAG-AAAAGAAAGG
10381012 AAAGAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.29
20 20 0.59
21 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAGAAAGGGAAG
Found at i:10381022 original size:15 final size:15
Alignment explanation
Indices: 10380961--10381022 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
10380951 TGGGAGAAAG
* *
10380961 GAAAAGAAAGAGGAA
1 GAAAGGAAAGAAGAA
* *
10380976 GGAAAGAAAAGAA-AG
1 -GAAAGGAAAGAAGAA
* *
10380991 GGAAGGAAAGAAAAA
1 GAAAGGAAAGAAGAA
10381006 GAAAGGAAAGAAGAA
1 GAAAGGAAAGAAGAA
10381021 GA
1 GA
10381023 GAAAGACAGC
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 10 0.28
15 17 0.47
16 9 0.25
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
GAAAGGAAAGAAGAA
Found at i:10385239 original size:387 final size:388
Alignment explanation
Indices: 10384518--10385281 Score: 1117
Period size: 387 Copynumber: 2.0 Consensus size: 388
10384508 ATGGTCGCTA
* *
10384518 AACTAACTAAAAATTCGACTAAGGCAAGATCACCTATCGAACAGTAGTATAGTTATGGTTAGACC
1 AACTAACTAAAAATTCGACTAAGGCAAGAGCACCTATCGAACAGTAGTATAGTTATGGTGAGACC
* * *
10384583 GGAAATATCGTATCCACAAGGACTAAAAGTACTAGTAATTACTATCTTTTTATTATCTAGCCTAA
66 GAAAATATCGTATCCACAAGAACTAAAAGTACTAGTAATTACTATCTTTTGATTATCTAGCCTAA
* * *
10384648 CAATTAAGAGAATGTTTTAAAATAAGACTAATTATCTAATGAACTAAAATTACGATAGAGATTAA
131 CAATTAAGAGAATGTTTTAAAATAAAAATAATTATCTAATGAACTAAAATTACGATAAAGATTAA
** ** * *
10384713 AGTTGGAAAATACTTTTTAGAAAACTGATGGAAAAGACAATACCCAAGGAAGAATCCATATAGAC
196 AGTTGGAAAATACTTTGGAGAAAACAAATGGAAAAGACAATACCCAAGGAAAAATCCACATAGAC
* * * *
10384778 TTCACTTATCACTTCTGAATTAGACGATTTATTCACTTGACTTAATCCGTATAAATCCCTGATTT
261 TTCACTTATCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCGTAAAAATCCCTAATTT
10384843 ATGTTAATATCTCTCTCGAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCGTGT
326 ATGTTAATATCTCTCTCGAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCGTGT
* * *
10384906 AACTAACTAAAAATTCGAATTAAGGCAAGCGCACCTTTCGAACAGTAGTATAGTTATGGTGAGAC
1 AACTAACTAAAAATTCG-ACTAAGGCAAGAGCACCTATCGAACAGTAGTATAGTTATGGTGAGAC
** *
10384971 CGAAAATATCGTATCCATGAGAAGTAAAAGTACTAGTAATTACTATCTTTTGATTATCTAGCCTA
65 CGAAAATATCGTATCCACAAGAACTAAAAGTACTAGTAATTACTATCTTTTGATTATCTAGCCTA
** * * *
10385036 A-AATTAA-AGTGTGTTTTTAAAATAAAAATATTTATCTAATTAACTAAGATTACGA-AAAGA-T
130 ACAATTAAGAGAATG-TTTTAAAATAAAAATAATTATCTAATGAACTAAAATTACGATAAAGATT
* * *
10385097 GAAGTTTGGAAAATACTTTGG-GAGAAACAAATGGAGAAGACAATACCCAAGGAAAAATCCACCT
194 AAAG-TTGGAAAATACTTTGGAGA-AAACAAATGGAAAAGACAATACCCAAGGAAAAATCCACAT
*
10385161 AGACTTCACTTAGT-ACTTCTGAATTAGACAATTTATTCACTTAACTTAATTCGTAAAAATCCCT
257 AGACTTCACTTA-TCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCGTAAAAATCCCT
* * *
10385225 AATTTATTTTAATATCTCTCTCGAGACTAAGAACAACTGACTTTAGGTTGATTAATT
321 AATTTATGTTAATATCTCTCTCGAGACTAAAAACAACTGACTCTAGGTTGATTAATT
10385282 AAAATCTCTT
Statistics
Matches: 335, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
386 6 0.02
387 167 0.50
388 60 0.18
389 102 0.30
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (388 bp):
AACTAACTAAAAATTCGACTAAGGCAAGAGCACCTATCGAACAGTAGTATAGTTATGGTGAGACC
GAAAATATCGTATCCACAAGAACTAAAAGTACTAGTAATTACTATCTTTTGATTATCTAGCCTAA
CAATTAAGAGAATGTTTTAAAATAAAAATAATTATCTAATGAACTAAAATTACGATAAAGATTAA
AGTTGGAAAATACTTTGGAGAAAACAAATGGAAAAGACAATACCCAAGGAAAAATCCACATAGAC
TTCACTTATCACTTCTGAATTAGACAATTTATTCACTTAACTTAATCCGTAAAAATCCCTAATTT
ATGTTAATATCTCTCTCGAGACTAAAAACAACTGACTCTAGGTTGATTAATTGATGATCGTGT
Found at i:10388212 original size:11 final size:10
Alignment explanation
Indices: 10388186--10388262 Score: 58
Period size: 11 Copynumber: 8.0 Consensus size: 10
10388176 AGGAGGGAAG
* *
10388186 AAGAAAGGGT
1 AAGAAAGAGA
10388196 AAGAAAGAGCA
1 AAGAAAGAG-A
10388207 AAG-AA-AGA
1 AAGAAAGAGA
10388215 AAGAAGAGAGA
1 AAGAA-AGAGA
10388226 AAG-AA-AGA
1 AAGAAAGAGA
10388234 AAGAAA-A-A
1 AAGAAAGAGA
*
10388242 AAGGAAGAGA
1 AAGAAAGAGA
10388252 AGAGAAAGAGA
1 A-AGAAAGAGA
10388263 GGGGGGTTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
8 16 0.29
9 8 0.15
10 14 0.25
11 17 0.31
ACGTcount: A:0.66, C:0.01, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAAGAGA
Found at i:10388213 original size:4 final size:4
Alignment explanation
Indices: 10388206--10388260 Score: 58
Period size: 4 Copynumber: 13.2 Consensus size: 4
10388196 AAGAAAGAGC
* *
10388206 AAAG AAAG AAAG -AAG AGAG AAAG AAAG AAAG AAAA AAAGG AAGAG AAGAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AA-AG AA-AG
10388256 AAAG A
1 AAAG A
10388261 GAGGGGGGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
3 3 0.07
4 30 0.68
5 10 0.23
6 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:10388216 original size:15 final size:14
Alignment explanation
Indices: 10388186--10388260 Score: 66
Period size: 15 Copynumber: 5.3 Consensus size: 14
10388176 AGGAGGGAAG
* *
10388186 AAGAAAGGGTAAGA
1 AAGAAAGAGAAAGA
10388200 AAGAGCAA-AGAAAGA
1 AAGA--AAGAGAAAGA
10388215 AAGAAGAGAGAAAGA
1 AAGAA-AGAGAAAGA
10388230 AAGAAAGA-AAA-A
1 AAGAAAGAGAAAGA
*
10388242 AAGGAAGAGAAGAGA
1 AAGAAAGAGAA-AGA
10388257 AAGA
1 AAGA
10388261 GAGGGGGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 8 0.16
13 6 0.12
14 9 0.18
15 25 0.50
16 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (14 bp):
AAGAAAGAGAAAGA
Found at i:10388228 original size:19 final size:19
Alignment explanation
Indices: 10388196--10388239 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
10388186 AAGAAAGGGT
10388196 AAGAAAGAGCAAAGAAAGA
1 AAGAAAGAGCAAAGAAAGA
10388215 AAGAAGAGAG-AAAGAAAGA
1 AAGAA-AGAGCAAAGAAAGA
10388234 AAGAAA
1 AAGAAA
10388240 AAAAGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.00
Consensus pattern (19 bp):
AAGAAAGAGCAAAGAAAGA
Found at i:10388235 original size:23 final size:22
Alignment explanation
Indices: 10388200--10388260 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 22
10388190 AAGGGTAAGA
*
10388200 AAGAGCAAAGAAAGAAAGAAGAGAG
1 AAGAG-AAAGAAAGAAA-AAAAG-G
10388225 AA-AGAAAGAAAGAAAAAAAGG
1 AAGAGAAAGAAAGAAAAAAAGG
10388246 AAGAGAAGAGAAAGA
1 AAGAGAA-AGAAAGA
10388261 GAGGGGGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.09
22 8 0.24
23 18 0.55
24 2 0.06
25 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.30, T:0.00
Consensus pattern (22 bp):
AAGAGAAAGAAAGAAAAAAAGG
Found at i:10396040 original size:22 final size:22
Alignment explanation
Indices: 10396008--10396069 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
10395998 AAAATCATAT
*
10396008 ATTAATCATATATTATTTT-AA
1 ATTAATTATATATTATTTTGAA
10396029 ATTTAATTATATATTAATTTTGAA
1 A-TTAATTATATATT-ATTTTGAA
*
10396053 ATAAATTA-ATATTATTT
1 ATTAATTATATATTATTT
10396070 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 17 0.47
23 11 0.31
24 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTAATTATATATTATTTTGAA
Found at i:10398019 original size:7 final size:7
Alignment explanation
Indices: 10398009--10398123 Score: 80
Period size: 7 Copynumber: 16.1 Consensus size: 7
10397999 TTTTTATTTT
10398009 TATATTA
1 TATATTA
10398016 TATATTA
1 TATATTA
10398023 TATAATTA
1 TAT-ATTA
10398031 T-T-TTA
1 TATATTA
10398036 TATATTA
1 TATATTA
10398043 CTCATATTA
1 -T-ATATTA
*
10398052 TTTA-TA
1 TATATTA
10398058 TATATTA
1 TATATTA
10398065 TATATTA
1 TATATTA
* *
10398072 TTTCCACATA
1 TAT--A-TTA
*
10398082 TATACTTT
1 TATA-TTA
10398090 TATATTA
1 TATATTA
10398097 TATATTA
1 TATATTA
10398104 TAT-TTA
1 TATATTA
10398110 T-T-TTA
1 TATATTA
10398115 TATTATTA
1 TA-TATTA
10398123 T
1 T
10398124 GTCATTTTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
5 9 0.10
6 10 0.11
7 40 0.45
8 18 0.20
9 7 0.08
10 4 0.05
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:10398036 original size:20 final size:19
Alignment explanation
Indices: 10398008--10398123 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 19
10397998 ATTTTTATTT
*
10398008 TTATATTATATATTATATAA
1 TTATTTTATATATTATAT-A
10398028 TTATTTTATATATTACTCATA
1 TTATTTTATATATTA-T-ATA
10398049 TTATTTATATATATTATATA
1 TTATTT-TATATATTATATA
* * *
10398069 TTATTTCCACATA-TATACTT
1 TTATTT-TATATATTATA-TA
*
10398089 TTATATTATATATTATAT-
1 TTATTTTATATATTATATA
10398107 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
10398124 GTCATTTTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
18 9 0.11
19 15 0.19
20 37 0.46
21 9 0.11
22 11 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTATATATTATATA
Found at i:10398052 original size:29 final size:26
Alignment explanation
Indices: 10398002--10398072 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 26
10397992 TGCTTTATTT
10398002 TTATTTT-TATATTATATATTATATAA
1 TTATTTTATATATTATATATTAT-TAA
*
10398028 TTATTTTATATATTACTCATATTATTTA
1 TTATTTTATATATTA-T-ATATTATTAA
*
10398056 TATATATTATATATTAT
1 T-TATTTTATATATTAT
10398073 TTCCACATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 7 0.18
27 7 0.18
28 5 0.13
29 20 0.51
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATATTATATATTATTAA
Found at i:10398116 original size:16 final size:18
Alignment explanation
Indices: 10398092--10398140 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
10398082 TATACTTTTA
*
10398092 TATTATATATTA-TAT-T
1 TATTTTATATTATTATGT
10398108 TATTTTATATTATTATGT
1 TATTTTATATTATTATGT
* *
10398126 CATTTTATACTATTA
1 TATTTTATATTATTA
10398141 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 14 0.50
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTTTATATTATTATGT
Found at i:10409473 original size:46 final size:47
Alignment explanation
Indices: 10409405--10409494 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 47
10409395 ACAAGATCCA
**
10409405 AGATGATTTGACATTCTTGTGCTTACAAGGAA-CAAATCGAAGACAT
1 AGATGATTTGACATTCACGTGCTTACAAGGAAGCAAATCGAAGACAT
* * * * *
10409451 AGATGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGA
1 AGATGATTTGACATTCACGTGCTTACAAGGAAGCAAATCGAAGA
10409495 TGATTTCTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 26 0.72
47 10 0.28
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (47 bp):
AGATGATTTGACATTCACGTGCTTACAAGGAAGCAAATCGAAGACAT
Found at i:10411211 original size:7 final size:7
Alignment explanation
Indices: 10411201--10411315 Score: 81
Period size: 7 Copynumber: 17.1 Consensus size: 7
10411191 TTTTTATTTT
10411201 TATATTA
1 TATATTA
10411208 TATATTA
1 TATATTA
10411215 TATAATTA
1 TAT-ATTA
10411223 T-T-TTA
1 TATATTA
10411228 TATATTA
1 TATATTA
10411235 CTCATATTA
1 -T-ATATTA
*
10411244 TTTA-TA
1 TATATTA
10411250 TATATTA
1 TATATTA
10411257 TATATTA
1 TATATTA
10411264 T-T-TTCA
1 TATATT-A
*
10411270 CATA-TA
1 TATATTA
10411276 TACT-TT-
1 TA-TATTA
10411282 TATATTA
1 TATATTA
10411289 TATATTA
1 TATATTA
10411296 TAT-TTA
1 TATATTA
10411302 T-T-TTA
1 TATATTA
10411307 TATTATTA
1 TA-TATTA
10411315 T
1 T
10411316 GTCATTTTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
5 12 0.14
6 18 0.20
7 41 0.47
8 11 0.12
9 6 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:10411228 original size:20 final size:19
Alignment explanation
Indices: 10411200--10411315 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 19
10411190 ATTTTTATTT
*
10411200 TTATATTATATATTATATAA
1 TTATTTTATATATTATAT-A
10411220 TTATTTTATATATTACTCATA
1 TTATTTTATATATTA-T-ATA
10411241 TTATTTATATATATTATATA
1 TTATTT-TATATATTATATA
* *
10411261 TTATTTTCACATA-TATACTT
1 TTATTTT-ATATATTATA-TA
*
10411281 TTATATTATATATTATAT-
1 TTATTTTATATATTATATA
10411299 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
10411316 GTCATTTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
18 9 0.11
19 16 0.19
20 38 0.46
21 9 0.11
22 11 0.13
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTATATATTATATA
Found at i:10411244 original size:29 final size:26
Alignment explanation
Indices: 10411194--10411315 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 26
10411184 TGCTTTATTT
10411194 TTATTTT-TATATTATATATTATATAA
1 TTATTTTATATATTATATATTAT-TAA
*
10411220 TTATTTTATATATTACTCATATTATTTA
1 TTATTTTATATATTA-T-ATATTATTAA
* *
10411248 TATATATTATATATTAT-T-TTCA-CATA
1 T-TATTTTATATATTATATATT-ATTA-A
* *
10411274 TATACTTT-TATATTATATATTA-TAT
1 T-TATTTTATATATTATATATTATTAA
10411299 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
10411316 GTCATTTTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
24 5 0.06
25 13 0.17
26 25 0.32
27 9 0.12
28 5 0.06
29 20 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATATTATATATTATTAA
Found at i:10411322 original size:18 final size:17
Alignment explanation
Indices: 10411289--10411332 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
10411279 TTTTATATTA
*
10411289 TATATTA-TATTTATTT
1 TATATTATTATTCATTT
10411305 TATATTATTATGTCATTT
1 TATATTATTAT-TCATTT
*
10411323 TATACTATTA
1 TATATTATTA
10411333 AATATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 14 0.58
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TATATTATTATTCATTT
Found at i:10411666 original size:17 final size:17
Alignment explanation
Indices: 10411609--10411666 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
10411599 TTTAAACCAT
*
10411609 TATATTTTATATTTTTA
1 TATATTATATATTTTTA
*
10411626 TATAATTAT-TATTCTTA
1 TAT-ATTATATATTTTTA
10411643 TA-A--ATATATTTTTA
1 TATATTATATATTTTTA
10411657 TATATTATAT
1 TATATTATAT
10411667 CATTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 2 0.06
17 16 0.48
18 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:10414782 original size:5 final size:5
Alignment explanation
Indices: 10414772--10414796 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10414762 TTTTTAATTC
10414772 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
10414797 CCCAGGTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:10416801 original size:14 final size:13
Alignment explanation
Indices: 10416760--10416800 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
10416750 GTCTGAACTG
*
10416760 ATTATTATACAAAA
1 ATTATT-TAAAAAA
10416774 ATTATTTAAAAAA
1 ATTATTTAAAAAA
10416787 ATTATTTAAAAAA
1 ATTATTTAAAAAA
10416800 A
1 A
10416801 AAAATAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTATTTAAAAAA
Found at i:10417189 original size:11 final size:11
Alignment explanation
Indices: 10417175--10417215 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
10417165 TGTTTTCTTC
10417175 CTATTTTGCTA
1 CTATTTTGCTA
*
10417186 CTATTTTACTA
1 CTATTTTGCTA
* *
10417197 TTATGTTGCTA
1 CTATTTTGCTA
10417208 CTATTTTG
1 CTATTTTG
10417216 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:10417468 original size:12 final size:12
Alignment explanation
Indices: 10417438--10417470 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10417428 TATATATTTT
10417438 AAAATT-ATATA
1 AAAATTAATATA
10417449 AAAA-TAATATA
1 AAAATTAATATA
10417460 AAAATTAATAT
1 AAAATTAATAT
10417471 GGGNTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:10419786 original size:33 final size:31
Alignment explanation
Indices: 10419708--10419793 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
10419698 AACCCTTCAT
* *
10419708 GCATTAAATCCAACCAAAAACAGCAAATATA
1 GCATAAAATACAACCAAAAACAGCAAATATA
* * *
10419739 GCATAAAATGCAACCAAAAACAGTAAATTTA
1 GCATAAAATACAACCAAAAACAGCAAATATA
10419770 GCATAAAAAATACAACCAAAAACA
1 GCAT--AAAATACAACCAAAAACA
10419794 TTAATTCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 31 0.65
33 17 0.35
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.15
Consensus pattern (31 bp):
GCATAAAATACAACCAAAAACAGCAAATATA
Found at i:10420052 original size:21 final size:21
Alignment explanation
Indices: 10420028--10420068 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10420018 GCTGCCATCA
*
10420028 CTGCTGCCTCTGCCTCTCTCG
1 CTGCTGCCGCTGCCTCTCTCG
10420049 CTGCTGCCGCTGCCTCTCTC
1 CTGCTGCCGCTGCCTCTCTC
10420069 TGTTGCCTCC
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:0.00, C:0.49, G:0.20, T:0.32
Consensus pattern (21 bp):
CTGCTGCCGCTGCCTCTCTCG
Found at i:10420513 original size:13 final size:14
Alignment explanation
Indices: 10420487--10420515 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10420477 ACTAATGACG
10420487 AATTAAACCATTAT
1 AATTAAACCATTAT
10420501 AATTAAA-CATTAT
1 AATTAAACCATTAT
10420514 AA
1 AA
10420516 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:10420704 original size:17 final size:16
Alignment explanation
Indices: 10420682--10420720 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
10420672 AAAATATTAT
10420682 TTAATAGTAGAAAGTAA
1 TTAATAGTAGAAAG-AA
* *
10420699 TTAATATTTGAAAGAA
1 TTAATAGTAGAAAGAA
10420715 TTAATA
1 TTAATA
10420721 AATTCATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (16 bp):
TTAATAGTAGAAAGAA
Found at i:10429714 original size:12 final size:12
Alignment explanation
Indices: 10429697--10429736 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
10429687 CAGAGAATAG
*
10429697 AGAAGAAAAGAA
1 AGAAGAAAAAAA
10429709 AGAAGAAAAAAA
1 AGAAGAAAAAAA
10429721 ATGAA-AAAAAAA
1 A-GAAGAAAAAAA
10429733 AGAA
1 AGAA
10429737 CTGGAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AGAAGAAAAAAA
Done.