Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold443
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: 318098
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:257695 original size:82 final size:81
Alignment explanation
Indices: 257561--258579 Score: 1536
Period size: 82 Copynumber: 12.4 Consensus size: 81
257551 AGTGTGACCT
* * *
257561 CTTTAAAGCCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
257626 ACAACTCCGTGGCACT
66 ACAACTCCGTGGCACC
*
257642 CTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGT
257707 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
257725 CTTTTAAGTCCACAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
257790 CACAACTTCGTGGCACC
65 CACAACTCCGTGGCACC
* **
257807 CTTTTAAGTCCACAACTCCGTGACACCCTTTTAAGTCCACAACTCCGTGGCATATCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
**
257872 CACAACTCCGTGGCATAT
65 CACAACTCCGTGGCA-CC
* *
257890 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCGTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
257955 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
257972 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
258037 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
*
258054 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCACCCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGTC
258119 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
* *
258137 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
258202 ACAACCCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
*
258219 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
258284 ATAACTCCATGGCATCT
66 ACAACTCCGTGGCA-CC
*
258301 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAA-T
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCC-TTTTAAGT
*
258365 CCATAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * *
258383 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAGACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
258448 ACAACTCCGTAGCACC
66 ACAACTCCGTGGCACC
* * * *
258464 CTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
258529 CCACAACTCTGTGGCACT
64 CCACAACTCCGTGGCACC
* *
258547 CTTTTAAAATCCACAACTCTGTGGCACCCTTTT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
258580 CAAAGCCCAC
Statistics
Matches: 866, Mismatches: 58, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
80 6 0.01
81 111 0.13
82 470 0.54
83 236 0.27
84 43 0.05
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:257756 original size:110 final size:109
Alignment explanation
Indices: 257561--258579 Score: 1553
Period size: 110 Copynumber: 9.3 Consensus size: 109
257551 AGTGTGACCT
* * *
257561 CTTTAAAGCCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
257626 ACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCATCT
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
257670 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
257735 CACAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * *
257780 CTTTTAAGACCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
** **
257845 ACAACTCCGTGGCATATCTTTTAAGTCCACAACTCCGTGGCATAT
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCC
* *
257890 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCGTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
257955 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* *
258000 CTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
258065 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCA-CC
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
*
258108 CTTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGT
1 C-TTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* *
258173 CCACAACTCCGCGGCACCCTTTTAAGTCCACAACCCCGTGGCATCC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
*
258219 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * * *
258284 ATAACTCCATGGCATCTCTTTTAAGTCCACAACTCTGTGGCA-CC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCC
*
258328 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAA-TCCATAACTCCGTGGCACCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* *
258392 CCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGACA-CC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
258437 CTTTTAAGACCACAACTCCGTAGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
* * * *
258502 CACAACTCTGTGGCACCCTTTTAAAATCCACAACTCTGTGGCA-CT
65 CACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCATCC
* *
258547 CTTTTAAAATCCACAACTCTGTGGCACCCTTTT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
258580 CAAAGCCCAC
Statistics
Matches: 836, Mismatches: 61, Indels: 24
0.91 0.07 0.03
Matches are distributed among these distances:
107 6 0.01
108 41 0.05
109 290 0.35
110 422 0.50
111 77 0.09
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (109 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:259146 original size:32 final size:32
Alignment explanation
Indices: 258558--259154 Score: 975
Period size: 32 Copynumber: 18.7 Consensus size: 32
258548 TTTTAAAATC
* *
258558 CACAACTCTGTGGC-ACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
258589 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258621 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
258653 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258685 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
258717 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258749 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
258781 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258813 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258845 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
258877 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
258909 CACAAGTCGGTGGCAACCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
258941 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
258973 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
259005 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
259037 CACAAGTCGGTGGCAACCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
259069 CACAAGTCGGTGGCAACCCATTTT-AAAGCCCA
1 CACAAGTCGGTGGCAACCC-TTTTCAAAGCCCA
* ** *
259101 CACGAGTCGGTGGCAATTCTTTTCAAGGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* **
259133 CATAAGTTAGTGGC-ACCCTTTT
1 CACAAGTCGGTGGCAACCCTTTT
259155 TTTTTAAAAA
Statistics
Matches: 531, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
31 22 0.04
32 505 0.95
33 4 0.01
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.19
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
Found at i:260739 original size:23 final size:23
Alignment explanation
Indices: 260709--260757 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
260699 TGACCATGCA
260709 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
260732 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
260755 TTT
1 TTT
260758 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTTTATTATGTTTCATGCATT
Found at i:260764 original size:20 final size:21
Alignment explanation
Indices: 260703--260757 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 21
260693 AGCCTTTGAC
260703 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
260724 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTATTATGTTT
260747 CATGCATTTTT
1 CATGCATTTTT
260758 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:264516 original size:2 final size:2
Alignment explanation
Indices: 264509--264535 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
264499 AATCTGAGCT
264509 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
264536 GCACGAAATG
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:266647 original size:26 final size:26
Alignment explanation
Indices: 266614--266666 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
266604 AAAGATTAAA
266614 TTTAAAAAAAAAAGTAATATGAGATC
1 TTTAAAAAAAAAAGTAATATGAGATC
266640 TTTAAAAAAAAAAGTAATATGAGATC
1 TTTAAAAAAAAAAGTAATATGAGATC
266666 T
1 T
266667 AATCGGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (26 bp):
TTTAAAAAAAAAAGTAATATGAGATC
Found at i:268834 original size:25 final size:27
Alignment explanation
Indices: 268763--268834 Score: 67
Period size: 30 Copynumber: 2.6 Consensus size: 27
268753 TGAAAACTTA
*
268763 TTTTATTATTTATTATTAAAATATTAT
1 TTTTATTATTTAATATTAAAATATTAT
*
268790 TTTATATTTAAATTTAA-A-TATGAATATTAT
1 TTT-TA-TT--ATTTAATATTA-AAATATTAT
268820 TTTTATTATTTAATA
1 TTTTATTATTTAATA
268835 ACAATTTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
26 6 0.16
27 4 0.11
28 4 0.11
29 6 0.16
30 12 0.32
31 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTTATTATTTAATATTAAAATATTAT
Found at i:275037 original size:23 final size:22
Alignment explanation
Indices: 274989--275042 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
274979 ATATAAAAGC
*
274989 AATAATAAGATTTTCATATATT
1 AATAATAATATTTTCATATATT
*
275011 AATAAATAATATTTTTAT-TATT
1 AAT-AATAATATTTTCATATATT
275033 AAATAATAAT
1 -AATAATAAT
275043 TTCAGTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATAATAATATTTTCATATATT
Found at i:275662 original size:2 final size:2
Alignment explanation
Indices: 275655--275689 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
275645 ATTGCTCTTT
275655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
275690 TAAATAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:275908 original size:25 final size:25
Alignment explanation
Indices: 275878--275929 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
275868 TTTATACAAA
* *
275878 AGAAAATTATAAATGTATGAAATTG
1 AGAAAATTATAAATGAAAGAAATTG
*
275903 AGAAAATTATGAATGAAAGAAATTG
1 AGAAAATTATAAATGAAAGAAATTG
275928 AG
1 AG
275930 CATTATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (25 bp):
AGAAAATTATAAATGAAAGAAATTG
Found at i:276019 original size:50 final size:50
Alignment explanation
Indices: 275960--276097 Score: 222
Period size: 50 Copynumber: 2.8 Consensus size: 50
275950 GGTGGAAAGT
* *
275960 ACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGATGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
276010 ACCTTTGACAATAGAGGGATGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
276060 ACCTTTGACAATAGAGAAAGGTAGCCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
276098 TCTAAGTATA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:280543 original size:50 final size:50
Alignment explanation
Indices: 280468--280579 Score: 181
Period size: 50 Copynumber: 2.2 Consensus size: 50
280458 GGTGGAAAGT
* *
280468 ACCTTTGACAATAGAGAGAGGTGGCCATAATTATTGACGATTTTTCACCA
1 ACCTTTGACAATAAAGAGAGGTGGCCATAATTATTGACGATTCTTCACCA
280518 ACCTTTGACAATAAA-AGGAGGTGGCCATAATTATTGACGATTCTTCACCA
1 ACCTTTGACAATAAAGA-GAGGTGGCCATAATTATTGACGATTCTTCACCA
*
280568 ACCTTTTACAAT
1 ACCTTTGACAAT
280580 GGAGAAAGGT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.02
50 57 0.98
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (50 bp):
ACCTTTGACAATAAAGAGAGGTGGCCATAATTATTGACGATTCTTCACCA
Found at i:280590 original size:50 final size:49
Alignment explanation
Indices: 280468--280605 Score: 170
Period size: 50 Copynumber: 2.8 Consensus size: 49
280458 GGTGGAAAGT
* *
280468 ACCTTTGACAATAGAGAGAGGTGGCCATAATTATTGACGATTTTTCACCA
1 ACCTTTGACAAT-GAGAAAGGTGGCCATAATTATTGACGATTCTTCACCA
*
280518 ACCTTTGACAAT-AAAAGGAGGTGGCCATAATTATTGACGATTCTTCACCA
1 ACCTTTGACAATGAGAA--AGGTGGCCATAATTATTGACGATTCTTCACCA
* * * *
280568 ACCTTTTACAATGGAGAAAGGTGGACATCATTGTTGAC
1 ACCTTTGACAAT-GAGAAAGGTGGCCATAATTATTGAC
280606 TCTAAGTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
48 2 0.03
50 71 0.93
52 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (49 bp):
ACCTTTGACAATGAGAAAGGTGGCCATAATTATTGACGATTCTTCACCA
Found at i:281205 original size:22 final size:24
Alignment explanation
Indices: 281180--281227 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
281170 GAATTGAATT
281180 AAATTA-TT-ATTTAATAATAAAA
1 AAATTATTTAATTTAATAATAAAA
*
281202 AAATTATTTAAATTTAATTATAAAA
1 AAATTATTT-AATTTAATAATAAAA
281227 A
1 A
281228 TATAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
25 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTATTTAATTTAATAATAAAA
Found at i:281702 original size:26 final size:27
Alignment explanation
Indices: 281673--281748 Score: 73
Period size: 32 Copynumber: 2.6 Consensus size: 27
281663 TAATATGAAT
*
281673 ATATCAAATATTTTAAAATTTAAAT-A
1 ATATAAAATATTTTAAAATTTAAATAA
*
281699 ATATAAATTATTAATGTATTAAAATTTATATAA
1 ATATAAA--A-T-AT-T-TTAAAATTTAAATAA
281732 ATATAAAATATTTTAAA
1 ATATAAAATATTTTAAA
281749 TAAAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
26 6 0.15
27 5 0.12
28 2 0.05
29 3 0.07
30 3 0.07
31 2 0.05
32 12 0.29
33 8 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATAAAATATTTTAAAATTTAAATAA
Found at i:283685 original size:13 final size:13
Alignment explanation
Indices: 283669--283735 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 13
283659 TCCCACACTT
283669 TCCTTTTCCTTTC
1 TCCTTTTCCTTTC
*
283682 TCCTTTTTCTTTC
1 TCCTTTTCCTTTC
*
283695 AATCTTTTTCTCTTTC
1 --TCCTTTTC-CTTTC
*
283711 T-CTTTT-CTTGC
1 TCCTTTTCCTTTC
283722 T-C-TTTCCTTTC
1 TCCTTTTCCTTTC
283733 TCC
1 TCC
283736 CCCAACTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.07
11 11 0.26
12 1 0.02
13 16 0.37
14 1 0.02
15 6 0.14
16 5 0.12
ACGTcount: A:0.03, C:0.33, G:0.01, T:0.63
Consensus pattern (13 bp):
TCCTTTTCCTTTC
Found at i:284706 original size:19 final size:19
Alignment explanation
Indices: 284658--284707 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
284648 AGTGGATTTA
284658 ATTT-TAATTGATAAAAAGC
1 ATTTATAATT-ATAAAAAGC
*
284677 A--TATAATTTATAAAAATC
1 ATTTATAA-TTATAAAAAGC
284695 ATTTATAATTATA
1 ATTTATAATTATA
284708 TATACAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 8 0.31
20 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (19 bp):
ATTTATAATTATAAAAAGC
Found at i:285153 original size:2 final size:2
Alignment explanation
Indices: 285148--285180 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
285138 CACACTCACG
285148 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
285181 ATTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:288839 original size:33 final size:33
Alignment explanation
Indices: 288797--288860 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
288787 ACTGTTAAGT
* *
288797 CCATCGATATTGATCCTTGCATGAAAAAGATGC
1 CCATCGATATTAATCCTTACATGAAAAAGATGC
288830 CCATCGATATTAATCCTTACATGAAAAAGAT
1 CCATCGATATTAATCCTTACATGAAAAAGAT
288861 CGATCCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (33 bp):
CCATCGATATTAATCCTTACATGAAAAAGATGC
Found at i:290385 original size:24 final size:26
Alignment explanation
Indices: 290334--290391 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
290324 TGGGTGGCTA
*
290334 GTCAACAAAAACCACCCTTTGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
*
290360 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
290384 GTCAACAA
1 GTCAACAA
290392 TGGTGGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAACCACCCTATGTGTTT
Found at i:290420 original size:27 final size:27
Alignment explanation
Indices: 290381--290446 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
290371 CCACCATGTG
*
290381 TTTGTCAACAATGGTGGTTAC-TTTGTA
1 TTTGTCAAAAATGGTGGTT-CTTTTGTA
* *
290408 TTTGTCAAAAATGGTGGTTCTTTTTTG
1 TTTGTCAAAAATGGTGGTTCTTTTGTA
290435 TTTGTCAAAAAT
1 TTTGTCAAAAAT
290447 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 34 0.97
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTCTTTTGTA
Found at i:290463 original size:28 final size:27
Alignment explanation
Indices: 290379--290468 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
290369 AGCCACCATG
* * *
290379 TGTTTGTCAACAATGGTGGTTACTT-TG
1 TGTTTGTCAAAAATGATGGTT-CTTGTT
* * *
290406 TATTTGTCAAAAATGGTGGTTCTTTTT
1 TGTTTGTCAAAAATGATGGTTCTTGTT
*
290433 TGTTTGTCAAAAATTATGG--CTTG-T
1 TGTTTGTCAAAAATGATGGTTCTTGTT
290457 TGTTTGTCAAAA
1 TGTTTGTCAAAA
290469 TTGGTGGCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
24 13 0.24
25 3 0.05
26 3 0.05
27 36 0.65
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGGTTCTTGTT
Found at i:290476 original size:24 final size:24
Alignment explanation
Indices: 290408--290477 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
290398 TTACTTTGTA
* *
290408 TTTGTCAAAAATGGTGGTTCTTTTTTG
1 TTTGTCAAAATTGGTGG--C-TTGTTG
*
290435 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
290459 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
290478 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 16 0.43
25 1 0.03
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:293051 original size:21 final size:22
Alignment explanation
Indices: 293022--293067 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
293012 TGTTCAGACA
* *
293022 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
293044 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
293065 AGT
1 AGT
293068 TTCAATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:294981 original size:24 final size:26
Alignment explanation
Indices: 294930--294987 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
294920 TGGGTGGCTA
*
294930 GTCAACAAAAACCACCCTTTGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
*
294956 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
294980 GTCAACAA
1 GTCAACAA
294988 TGGTGGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAACCACCCTATGTGTTT
Found at i:295016 original size:27 final size:27
Alignment explanation
Indices: 294977--295042 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
294967 CCACCATGTG
*
294977 TTTGTCAACAATGGTGGTTAC-TTTGTA
1 TTTGTCAAAAATGGTGGTT-CTTTTGTA
* *
295004 TTTGTCAAAAATGGTGGTTCTTTTTTG
1 TTTGTCAAAAATGGTGGTTCTTTTGTA
295031 TTTGTCAAAAAT
1 TTTGTCAAAAAT
295043 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 34 0.97
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTCTTTTGTA
Found at i:295059 original size:28 final size:27
Alignment explanation
Indices: 294975--295064 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
294965 AGCCACCATG
* * *
294975 TGTTTGTCAACAATGGTGGTTACTT-TG
1 TGTTTGTCAAAAATGATGGTT-CTTGTT
* * *
295002 TATTTGTCAAAAATGGTGGTTCTTTTT
1 TGTTTGTCAAAAATGATGGTTCTTGTT
*
295029 TGTTTGTCAAAAATTATGG--CTTG-T
1 TGTTTGTCAAAAATGATGGTTCTTGTT
295053 TGTTTGTCAAAA
1 TGTTTGTCAAAA
295065 TTGGTGGCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
24 13 0.24
25 3 0.05
26 3 0.05
27 36 0.65
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGGTTCTTGTT
Found at i:295072 original size:24 final size:24
Alignment explanation
Indices: 295004--295073 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
294994 TTACTTTGTA
* *
295004 TTTGTCAAAAATGGTGGTTCTTTTTTG
1 TTTGTCAAAATTGGTGG--C-TTGTTG
*
295031 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
295055 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
295074 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 16 0.43
25 1 0.03
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:297025 original size:2 final size:2
Alignment explanation
Indices: 297018--297055 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
297008 GCTATGATCA
297018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
297056 GCAGAGTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297378 original size:58 final size:58
Alignment explanation
Indices: 297308--297424 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
297298 GAGAACGCTC
297308 ACATTTTTCATTTTCTTCAAAATAAAAAAATCACTCTTGAGATTTCAAGATTTATTAA
1 ACATTTTTCATTTTCTTCAAAATAAAAAAATCACTCTTGAGATTTCAAGATTTATTAA
297366 ACATTTTTCATTTTCTTCAAAATAAAAAAATCACTCTTGAGATTTCAAGATTTATTAA
1 ACATTTTTCATTTTCTTCAAAATAAAAAAATCACTCTTGAGATTTCAAGATTTATTAA
297424 A
1 A
297425 ACGTTAATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (58 bp):
ACATTTTTCATTTTCTTCAAAATAAAAAAATCACTCTTGAGATTTCAAGATTTATTAA
Found at i:297413 original size:28 final size:28
Alignment explanation
Indices: 297323--297413 Score: 67
Period size: 28 Copynumber: 3.2 Consensus size: 28
297313 TTTCATTTTC
297323 TTCAAAATAAAAAAATCACTCTTGAGAT
1 TTCAAAATAAAAAAATCACTCTTGAGAT
* * ** * * * **
297351 TTCAAGATTTATTAAA-CATTTTTCATTTT
1 TTCAA-AATAAAAAAATCACTCTTGA-GAT
297380 CTTCAAAATAAAAAAATCACTCTTGAGAT
1 -TTCAAAATAAAAAAATCACTCTTGAGAT
297409 TTCAA
1 TTCAA
297414 GATTTATTAA
Statistics
Matches: 41, Mismatches: 18, Indels: 8
0.61 0.27 0.12
Matches are distributed among these distances:
28 16 0.39
29 14 0.34
30 11 0.27
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.37
Consensus pattern (28 bp):
TTCAAAATAAAAAAATCACTCTTGAGAT
Found at i:299161 original size:25 final size:25
Alignment explanation
Indices: 299125--299175 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
299115 TCATGAGATA
299125 AGTGAGAGCTATGATCAATATATAT
1 AGTGAGAGCTATGATCAATATATAT
*
299150 AGTGAGATCTATGATCAATATATAT
1 AGTGAGAGCTATGATCAATATATAT
299175 A
1 A
299176 TATATATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (25 bp):
AGTGAGAGCTATGATCAATATATAT
Found at i:302517 original size:28 final size:29
Alignment explanation
Indices: 302484--302548 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
302474 AAATGTCACC
302484 TTTTGTATTTGTC-AAATATGGTGGTT-T
1 TTTTGTATTTGTCAAAATATGGTGGTTAT
302511 TCTTTGTATTTGTCAAAATATGGTGGTTAT
1 T-TTTGTATTTGTCAAAATATGGTGGTTAT
302541 TTTTGTAT
1 TTTTGTAT
302549 GTAAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 1 0.03
28 12 0.34
29 20 0.57
30 2 0.06
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (29 bp):
TTTTGTATTTGTCAAAATATGGTGGTTAT
Found at i:302554 original size:26 final size:28
Alignment explanation
Indices: 302485--302586 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 28
302475 AATGTCACCT
302485 TTTGTATTTGTC-AAATATGGTGGTTTTC
1 TTTGTA-TTGTCAAAATATGGTGGTTTTC
302513 TTTGTATTTGTCAAAATATGGTGGTTATT-
1 TTTGTA-TTGTCAAAATATGGTGGTT-TTC
* *
302542 TTTGTA-TGT-AAAAAATGGTGG-CTT-
1 TTTGTATTGTCAAAATATGGTGGTTTTC
*
302566 GTTGT-TTGTCAAAAT-TGGTGG
1 TTTGTATTGTCAAAATATGGTGG
302587 CTAATTTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
24 15 0.23
25 4 0.06
26 11 0.17
27 3 0.05
28 12 0.18
29 19 0.29
30 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.48
Consensus pattern (28 bp):
TTTGTATTGTCAAAATATGGTGGTTTTC
Found at i:302579 original size:24 final size:24
Alignment explanation
Indices: 302519--302588 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
302509 TTTCTTTGTA
* *
302519 TTTGTCAAAATATGGTGGTTATTTTTG
1 TTTGTCAAAA-ATGGTGG--CTTGTTG
* *
302546 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
302570 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
302589 AATTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 21 0.58
26 7 0.19
27 8 0.22
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:304731 original size:21 final size:22
Alignment explanation
Indices: 304702--304747 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
304692 TTTTCAGACA
** *
304702 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
304724 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
304745 AGT
1 AGT
304748 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:306686 original size:28 final size:30
Alignment explanation
Indices: 306654--306718 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
306644 AAATGCCACC
306654 CTTTGTATTTGTC-AAATATGGTGGTT-TT
1 CTTTGTATTTGTCAAAATATGGTGGTTATT
306682 CTTTGTATTTGTCAAAATATGGTGGTTATT
1 CTTTGTATTTGTCAAAATATGGTGGTTATT
306712 -TTTGTAT
1 CTTTGTAT
306719 GTAAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 13 0.37
29 20 0.57
30 2 0.06
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (30 bp):
CTTTGTATTTGTCAAAATATGGTGGTTATT
Found at i:306724 original size:26 final size:28
Alignment explanation
Indices: 306654--306756 Score: 96
Period size: 29 Copynumber: 3.9 Consensus size: 28
306644 AAATGCCACC
306654 CTTTGTATTTGTC-AAATATGGTGGTTTT
1 CTTTGTA-TTGTCAAAATATGGTGGTTTT
306682 CTTTGTATTTGTCAAAATATGGTGGTTATT
1 CTTTGTA-TTGTCAAAATATGGTGGTT-TT
* *
306712 -TTTGTA-TGT-AAAAAATGGTGG-CTT
1 CTTTGTATTGTCAAAATATGGTGGTTTT
*
306736 -GTTGT-TTGTCAAAAT-TGGTGG
1 CTTTGTATTGTCAAAATATGGTGG
306757 CTAATTTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
24 15 0.22
25 4 0.06
26 11 0.16
27 3 0.04
28 13 0.19
29 19 0.28
30 2 0.03
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (28 bp):
CTTTGTATTGTCAAAATATGGTGGTTTT
Found at i:306749 original size:24 final size:24
Alignment explanation
Indices: 306689--306758 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
306679 TTTCTTTGTA
* *
306689 TTTGTCAAAATATGGTGGTTATTTTTG
1 TTTGTCAAAA-ATGGTGG--CTTGTTG
* *
306716 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
306740 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
306759 AATTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 21 0.58
26 7 0.19
27 8 0.22
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:308438 original size:15 final size:15
Alignment explanation
Indices: 308418--308451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
308408 CATTCTTTGA
*
308418 ATCACCATCAGTATC
1 ATCACCAACAGTATC
308433 ATCACCAACAGTATC
1 ATCACCAACAGTATC
308448 ATCA
1 ATCA
308452 TATCTACCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24
Consensus pattern (15 bp):
ATCACCAACAGTATC
Found at i:310550 original size:2 final size:2
Alignment explanation
Indices: 310543--310581 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
310533 TCCCATGAAC
310543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310582 TCATGTACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:311299 original size:17 final size:17
Alignment explanation
Indices: 311255--311300 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
311245 AATTTCAATA
311255 AAAAATAAATATTAAAT
1 AAAAATAAATATTAAAT
* *
311272 -ATAATAAATATTGAAT
1 AAAAATAAATATTAAAT
*
311288 AAAAATACATATT
1 AAAAATAAATATT
311301 TAGTTATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATAAATATTAAAT
Found at i:312091 original size:25 final size:27
Alignment explanation
Indices: 312062--312115 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
312052 ATCAAAGCTC
*
312062 ATATTTATTAT-A-ATTAATTATAATA
1 ATATTTATTATGACAATAATTATAATA
312087 ATATTTATTATGATCAATAATTATAATA
1 ATATTTATTATGA-CAATAATTATAATA
312115 A
1 A
312116 ACATAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
28 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTTATTATGACAATAATTATAATA
Found at i:312457 original size:20 final size:18
Alignment explanation
Indices: 312434--312469 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
312424 TTAAATATTG
312434 AATAAAT-AAT-TTTAAT
1 AATAAATAAATATTTAAT
312450 AATAAATAAATATTTAAT
1 AATAAATAAATATTTAAT
312468 AA
1 AA
312470 GTGATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATAAATATTTAAT
Found at i:313026 original size:27 final size:27
Alignment explanation
Indices: 312996--313068 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
312986 AAATGATTAC
312996 AAATATAATATATATAAAAAATATTTA
1 AAATATAATATATATAAAAAATATTTA
* ** * *
313023 AAAT-TTATATAATATAATTATTATTTT
1 AAATATAATAT-ATATAAAAAATATTTA
313050 AAATATAAT-TATAATAAAA
1 AAATATAATATAT-ATAAAA
313069 TAAAATATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
26 7 0.20
27 25 0.71
28 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATATAATATATATAAAAAATATTTA
Found at i:314378 original size:67 final size:67
Alignment explanation
Indices: 314270--314406 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
314260 ATTTTTGCAA
314270 ATAAATTAGGCACTCTTTATGATTTATTGTCATAATTATATATTTTAAGCTTACTCTATATATAT
1 ATAAATTAGGCACTCTTTATGATTTATTGTCATAATTATATATTTTAAGCTTACTCTATATATAT
314335 AT
66 AT
314337 ATAAATTAGGCACTCTTTATGATTTATTGTCATAATTATATATTTTAAGCTTACTCTATATATAT
1 ATAAATTAGGCACTCTTTATGATTTATTGTCATAATTATATATTTTAAGCTTACTCTATATATAT
314402 AT
66 AT
314404 ATA
1 ATA
314407 TATATATATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (67 bp):
ATAAATTAGGCACTCTTTATGATTTATTGTCATAATTATATATTTTAAGCTTACTCTATATATAT
AT
Found at i:314453 original size:2 final size:2
Alignment explanation
Indices: 314393--314436 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
314383 AAGCTTACTC
314393 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
314435 TA
1 TA
314437 CAAAAACACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:314572 original size:13 final size:13
Alignment explanation
Indices: 314554--314578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314544 CTTAATAACA
314554 TTAAAAAAATAAT
1 TTAAAAAAATAAT
314567 TTAAAAAAATAA
1 TTAAAAAAATAA
314579 CATATGTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TTAAAAAAATAAT
Found at i:317112 original size:17 final size:17
Alignment explanation
Indices: 317060--317113 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
317050 TGAATGTCTC
317060 AAAATTTATAT-AATA-
1 AAAATTTATATAAATAT
*
317075 CAAA-TTAT-TAATATAT
1 AAAATTTATATAA-ATAT
317091 CAAAATTTATATAAATAT
1 -AAAATTTATATAAATAT
317109 AAAAT
1 AAAAT
317114 ATCTAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
17 8 0.26
18 8 0.26
19 3 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:317155 original size:20 final size:20
Alignment explanation
Indices: 317130--317169 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
317120 ACATGATTAT
*
317130 GATACTATATAAATATACGA
1 GATACTATATAAATACACGA
317150 GATACTATATAAATACACGA
1 GATACTATATAAATACACGA
317170 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
GATACTATATAAATACACGA
Done.