Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold448
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1018568
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 171214 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:3260 original size:13 final size:13
Alignment explanation
Indices: 3242--3267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3232 TAAATTCTCA
3242 ATAGATAGATTGT
1 ATAGATAGATTGT
3255 ATAGATAGATTGT
1 ATAGATAGATTGT
3268 GACAAGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
ATAGATAGATTGT
Found at i:16204 original size:69 final size:67
Alignment explanation
Indices: 16107--16243 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 67
16097 ATTTGTTCCA
**
16107 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTTTTTAAAAGTTTACGATATATAAAAGAA
1 TTTCTTTACATGCATGCCTTTATTATTC--TTTTTTTTTCGAAAAGTTTACGATATATAAAAGAA
16172 AGAG
64 AGAG
16176 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG
1 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG
16241 AG
66 AG
16243 T
1 T
16244 ATGTCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 38 0.58
69 28 0.42
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (67 bp):
TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG
AG
Found at i:24584 original size:29 final size:29
Alignment explanation
Indices: 24542--24632 Score: 173
Period size: 29 Copynumber: 3.1 Consensus size: 29
24532 GCATGAATCA
*
24542 AAAAGTTTCTCTCTCCTACGTATATGGAT
1 AAAAGTTTCTCTCTCCTACGTATGTGGAT
24571 AAAAGTTTCTCTCTCCTACGTATGTGGAT
1 AAAAGTTTCTCTCTCCTACGTATGTGGAT
24600 AAAAGTTTCTCTCTCCTACGTATGTGGAT
1 AAAAGTTTCTCTCTCCTACGTATGTGGAT
24629 AAAA
1 AAAA
24633 ACTAGAACCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (29 bp):
AAAAGTTTCTCTCTCCTACGTATGTGGAT
Found at i:32275 original size:180 final size:180
Alignment explanation
Indices: 31973--32317 Score: 611
Period size: 180 Copynumber: 1.9 Consensus size: 180
31963 ATTGTATATT
31973 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT
1 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT
*
32038 CAGAGGTGTGCAGATTGCTAGGATTTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA
66 CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA
*
32103 ACTTAGTCATTTTTTGGCAGAATATTGCATATAGGATACCCTCATTGTAC
131 ACTTAGTCATTTTTTGGCAAAATATTGCATATAGGATACCCTCATTGTAC
*
32153 GGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT
1 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT
* * * *
32218 CAGAGGTGTGCATATTGCTAGGATGTTGATTTCCAATAATTTA-TGAAATTAATACCAGCTTTTG
66 CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAA-AAATACCAGCTTTCG
32282 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGG
130 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGG
32318 GTACTCCATT
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
179 5 0.03
180 152 0.97
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (180 bp):
GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT
CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA
ACTTAGTCATTTTTTGGCAAAATATTGCATATAGGATACCCTCATTGTAC
Found at i:32814 original size:4 final size:4
Alignment explanation
Indices: 32805--32847 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
32795 CTTTCCTCTG
* * * *
32805 CGTC CGTC CGTC CGTC CGCC CGCC CGTC TGTC TGTC CGTC CGT
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGT
32848 ACGTTTGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.26, T:0.26
Consensus pattern (4 bp):
CGTC
Found at i:32841 original size:20 final size:20
Alignment explanation
Indices: 32808--32861 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
32798 TCCTCTGCGT
* *
32808 CCGTCCGTCCGTCCGCCCGC
1 CCGTCTGTCTGTCCGCCCGC
* *
32828 CCGTCTGTCTGTCCGTCCGT
1 CCGTCTGTCTGTCCGCCCGC
* *
32848 ACGTTTGTCTGTCC
1 CCGTCTGTCTGTCC
32862 CACTTCAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.24, T:0.30
Consensus pattern (20 bp):
CCGTCTGTCTGTCCGCCCGC
Found at i:36363 original size:166 final size:164
Alignment explanation
Indices: 36086--36448 Score: 414
Period size: 166 Copynumber: 2.2 Consensus size: 164
36076 GATGTATAGC
* * * *
36086 TGTACCAATT-GGACGTAAACTTCCTGTTAAATGAGGACTTTGTTTATTATTAGCCTAAATTTTC
1 TGTACC-ATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATTAACCAAAATTTTC
* * * *
36150 AAACAAAATTTCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAA-ATTTAAACA-T
65 AAACAAAATTTCGTCAAAGAATTCTCAGCAACAATTAAACCCAGATGCTT-AATATTTAAACACT
* * *
36213 ACTTTGTGTTTAGGGATGCCAAAT-TGTGGGATATATTTT
129 A--TT-TATATAGCGATGCCAAATCT-TGGGATATATTTT
* *
36252 TGTACCATTCGGACGTCAACTTCCTATTAAATGACGATTTTGTTTATT-TTCAACCAAAATTTTC
1 TGTACCATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATT-AACCAAAATTTTC
* * * * *
36316 TAACAAACTTTCGTC-AAGGATTTTGCAGCAACAATTAAACCCAGATGCTTAATATTTTAACACT
65 AAACAAAATTTCGTCAAAGAATTCT-CAGCAACAATTAAACCCAGATGCTTAATATTTAAACACT
* * *
36380 ATTTATATAGCTATGCCATATCTTGGGATCTATTTT
129 ATTTATATAGCGATGCCAAATCTTGGGATATATTTT
*
36416 TGTACCAATCGGACGTCAACTTCCTGTTAAATG
1 TGTACCATTCGGACGTCAACTTCCTGTTAAATG
36449 TTGAATTTGC
Statistics
Matches: 168, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
164 56 0.33
165 17 0.10
166 93 0.55
167 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (164 bp):
TGTACCATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATTAACCAAAATTTTCA
AACAAAATTTCGTCAAAGAATTCTCAGCAACAATTAAACCCAGATGCTTAATATTTAAACACTAT
TTATATAGCGATGCCAAATCTTGGGATATATTTT
Found at i:40678 original size:2 final size:2
Alignment explanation
Indices: 40665--40720 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
40655 GTTTCGCTCG
* *
40665 CT CT CG CT CT CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40707 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
40721 ATAGCTTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.50, G:0.02, T:0.46
Consensus pattern (2 bp):
CT
Found at i:43628 original size:29 final size:29
Alignment explanation
Indices: 43549--43629 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
43539 TTTAATGTCA
*
43549 CTTGCTTCTTCATAATGGAGTCATCTTCC
1 CTTGCTTCTTCATAATGGAGTTATCTTCC
*
43578 CTTGCTTCTTCATAATGAAGTTATCTTCC
1 CTTGCTTCTTCATAATGGAGTTATCTTCC
43607 CTTGCTTCTTCATAATGGAGTTA
1 CTTGCTTCTTCATAATGGAGTTA
43630 ATAATCATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (29 bp):
CTTGCTTCTTCATAATGGAGTTATCTTCC
Found at i:45054 original size:20 final size:21
Alignment explanation
Indices: 45029--45069 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45019 TATCCAAATG
45029 ATTA-TTTTATGATTAT-ATTA
1 ATTATTTTTAT-ATTATGATTA
45049 ATTATTTTTATATTATGATTA
1 ATTATTTTTATATTATGATTA
45070 TAAAAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTATTTTTATATTATGATTA
Found at i:48085 original size:2 final size:2
Alignment explanation
Indices: 48073--48110 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
48063 GCGCAGGTAA
48073 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
48111 CACACACGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:51709 original size:42 final size:42
Alignment explanation
Indices: 51650--51737 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
51640 TTGGCAACAT
* *
51650 TTTAGGCCAGTTTCGGACAGAAACAAGCCAGTTCAATAAATG
1 TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG
* *
51692 TTTAGGCCAGTTTCGGACAGAAACGAGCCAATTCAAGAAATT
1 TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG
51734 TTTA
1 TTTA
51738 CATTCTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (42 bp):
TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG
Found at i:53456 original size:6 final size:6
Alignment explanation
Indices: 53445--53551 Score: 115
Period size: 6 Copynumber: 17.8 Consensus size: 6
53435 TACAGCCACC
* * * *
53445 ACTACT ACTACT ACTACC ACTACT ACTACC ACTACT CCTACT ACCACT
1 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT
* * * * * *
53493 ACTACT ACCACT ACTCCT ACTACC ACTACT ACTACT ACTCCT ATTGCT
1 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT
*
53541 ACTACA ACTAC
1 ACTACT ACTAC
53552 CCATCAATAC
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.31, C:0.40, G:0.01, T:0.28
Consensus pattern (6 bp):
ACTACT
Found at i:53466 original size:15 final size:15
Alignment explanation
Indices: 53442--53530 Score: 121
Period size: 15 Copynumber: 6.1 Consensus size: 15
53432 CTCTACAGCC
53442 ACCACTACTACTACT
1 ACCACTACTACTACT
* *
53457 ACTACCACTACTACT
1 ACCACTACTACTACT
*
53472 ACCACTACTCCTACT
1 ACCACTACTACTACT
53487 A-C-C-ACTACTACT
1 ACCACTACTACTACT
*
53499 ACCACTACTCCTACT
1 ACCACTACTACTACT
53514 ACCACTACTACTACT
1 ACCACTACTACTACT
53529 AC
1 AC
53531 TCCTATTGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
12 9 0.14
13 2 0.03
14 2 0.03
15 50 0.79
ACGTcount: A:0.31, C:0.43, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCACTACTACTACT
Found at i:53542 original size:27 final size:27
Alignment explanation
Indices: 53448--53527 Score: 151
Period size: 27 Copynumber: 3.0 Consensus size: 27
53438 AGCCACCACT
*
53448 ACTACTACTACTACCACTACTACTACC
1 ACTACTCCTACTACCACTACTACTACC
53475 ACTACTCCTACTACCACTACTACTACC
1 ACTACTCCTACTACCACTACTACTACC
53502 ACTACTCCTACTACCACTACTACTAC
1 ACTACTCCTACTACCACTACTACTAC
53528 TACTCCTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.26
Consensus pattern (27 bp):
ACTACTCCTACTACCACTACTACTACC
Found at i:62053 original size:1 final size:1
Alignment explanation
Indices: 62047--62076 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
62037 TTGCTCCCTT
62047 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
62077 ATGTCCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:62519 original size:169 final size:168
Alignment explanation
Indices: 62175--63006 Score: 1175
Period size: 169 Copynumber: 4.9 Consensus size: 168
62165 TGCTCACGTG
* * ** * *
62175 TGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAACATTTTTAAAATATGACAATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * ** * *
62240 CCCTAGAGCCTAAACCCCTAACAAAGGGGTCAAT-AATTTTACAATTTTGGTAGAGGGCTTCATG
66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTC-ATGAATTTCACAATTTTGGTAGAGGGCCTCATG
* * * * * *
62304 GACATTATAACCAGGAATTTAGTTTTTAACAAATATATA
130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA
* *
62343 TGGGAGTAGAGAAGAAGATTTTCCAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * * **
62408 CCCTACAACCTGAACCCCATGACCGAGGGGTCATGAATTTCACAATTAAGGTAGAGGGCCTCATG
66 CCCTAGAGCCTGAACCCC-TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG
62473 GACATCATAATCATGCATTTAGTTTTAAACAAATA-AATA
130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAA-A
* * *
62512 TGGGAGTAAAGAAGAAGATTTTTTAAAGATTTAATACATTTATACTATATGGCCATATTGGCCCC
1 TGGGAGTAGAGAAGAAGATTTTCT-AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
62577 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG
65 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG
62642 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA
130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA
*
62681 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTAACTATATATATGGCCATATTGGC
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTT---TA-CTATATGGCCATATTGGC
* * *
62746 CCCACCCTACAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCCGC
62 CCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTC
* *
62811 ATGGACATCATAATCATGTATTTAGTTTTTAACAAATATAAA
127 ATGGACATCATAATCATGCATTTAGTTTTAAACAAATATAAA
62853 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA-TTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* ** * * * * *
62917 CCCTAGAGCCTGAACCCCTGAACTTGAGGCCATGAAATTCACAATTTTGGTAGAAGGCTTCATGG
66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGG
* *
62982 ACATCATAACCATGCATTCAGTTTT
131 ACATCATAATCATGCATTTAGTTTT
63007 TTCTTCACAT
Statistics
Matches: 599, Mismatches: 56, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
167 99 0.17
168 93 0.16
169 189 0.32
170 57 0.10
171 5 0.01
172 156 0.26
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (168 bp):
TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGG
ACATCATAATCATGCATTTAGTTTTAAACAAATATAAA
Found at i:63031 original size:167 final size:167
Alignment explanation
Indices: 62081--63009 Score: 1043
Period size: 169 Copynumber: 5.5 Consensus size: 167
62071 CCCCCCATGT
* ** * *
62081 CCTGAACCCCTGACCCAGAGGCCATGAATTTCACAATTAAGGTAG-AGGCGTTAGTGGACATCAT
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCA-TGGACATCAT
* ** * ** ** ** * * *
62145 AACTATTTATTCAGTTTTTT-TGCTCACGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAA
65 AACCATGCATTTAGTTTTTTCAACAAATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
** * *
62209 ACATTTTTAAAATATGACAATATTGGCCCCACCCTAGAG
130 ACA-TTTTACTATATGGCCATATTGGCCCCACCCTAGAG
* * ** * * * * *
62248 CCTAAACCCCTAACAAAGGGGTCAAT-AATTTTACAATTTTGGTAGAGGGCTTCATGGACATTAT
1 CCTGAACCCCTGACCCAGGGG-CCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCAT
* * *
62312 AACCAGGAATTTAG-TTTTT-AACAAATATATATGGGAGTAGAGAAGAAGATTTTCCAAGATTTA
65 AACCATGCATTTAGTTTTTTCAAC-AA-ATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTA
* * *
62375 ATACATTTTTACTATTTGGCCATATTGGCCCCACCCTACAA
128 ATACA-TTTTACTATATGGCCATATTGGCCCCACCCTAGAG
* * ** *
62416 CCTGAACCCCATGACCGAGGGGTCATGAATTTCACAATTAAGGTAGAGGGCCTCATGGACATCAT
1 CCTGAACCCC-TGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCAT
* * * *
62481 AATCATGCATTTAG--TTTTAAACAAATAAATATGGGAGTAAAGAAGAAGATTTTTTAAAGATTT
65 AACCATGCATTTAGTTTTTTCAACAAAT--ATATGGGAGTAGAGAAGAAGATTTTCT-AAGATTT
62544 AATACATTTATACTATATGGCCATATTGGCCCCACCCTAGAG
127 AATACATTT-TACTATATGGCCATATTGGCCCCACCCTAGAG
* *
62586 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA
* *
62651 ATCATGCATTTAG--TTTTAAACAAATATAAATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA
66 ACCATGCATTTAGTTTTTTCAACAAATAT--ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA
*
62714 TACATTTTAACTATATATATGGCCATATTGGCCCCACCCTACAG
129 TACATTTT-AC----TATATGGCCATATTGGCCCCACCCTAGAG
* *
62758 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCCGCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA
* *
62823 ATCATGTATTTAG-TTTTT-AACAAATATAAATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA
66 ACCATGCATTTAGTTTTTTCAACAAATAT--ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA
62886 TACATTTTACTATATGGCCATATTGGCCCCACCCTAGAG
129 TACATTTTACTATATGGCCATATTGGCCCCACCCTAGAG
* ** * * *
62925 CCTGAACCCCTGAACTTGAGGCCATGAAATTCACAATTTTGGTAGAAGGCTTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA
*
62990 ACCATGCATTCAGTTTTTTC
66 ACCATGCATTTAGTTTTTTC
63010 TTCACATGTG
Statistics
Matches: 665, Mismatches: 76, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
166 6 0.01
167 150 0.23
168 113 0.17
169 182 0.27
170 52 0.08
171 2 0.00
172 156 0.23
173 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (167 bp):
CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA
ACCATGCATTTAGTTTTTTCAACAAATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
CATTTTACTATATGGCCATATTGGCCCCACCCTAGAG
Found at i:64090 original size:2 final size:2
Alignment explanation
Indices: 64085--64142 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
64075 AGGTAAATAA
64085 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
64127 AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC
64143 TAATTATCGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:65239 original size:15 final size:15
Alignment explanation
Indices: 65219--65248 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65209 TTCCAGTCCG
65219 CAGCATTTCTAGAAA
1 CAGCATTTCTAGAAA
65234 CAGCATTTCTAGAAA
1 CAGCATTTCTAGAAA
65249 ATTGTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CAGCATTTCTAGAAA
Found at i:69191 original size:8 final size:8
Alignment explanation
Indices: 69180--69210 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
69170 TGAAAAGTTT
69180 ACGGACAG
1 ACGGACAG
69188 ACGGACAG
1 ACGGACAG
*
69196 ACAGACAG
1 ACGGACAG
69204 ACGGACA
1 ACGGACA
69211 AAATGTGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.26, G:0.32, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:70259 original size:161 final size:161
Alignment explanation
Indices: 69977--70318 Score: 567
Period size: 161 Copynumber: 2.1 Consensus size: 161
69967 AACATCCACA
* ** *
69977 AAGAAAATGAAAGTTAACTGCAAATATTTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
* *
70042 AAAATGGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACC
66 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC
70107 AAATTTCATTTCAATATGTTCATCCTCTGCG
131 AAATTTCATTTCAATATGTTCATCCTCTGCG
* * *
70138 AAGCAAATGAGCGGAAACTGCAAATATCTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
70203 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC
66 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC
* * *
70268 AAATTTTATTTCAATATGTTTATCCTCTGCT
131 AAATTTCATTTCAATATGTTCATCCTCTGCG
*
70299 AAGAAAATGAATGGAAACTG
1 AAGAAAATGAACGGAAACTG
70319 TTGGTAGACC
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
161 166 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (161 bp):
AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC
AAATTTCATTTCAATATGTTCATCCTCTGCG
Found at i:70617 original size:3 final size:3
Alignment explanation
Indices: 70611--70654 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
70601 AACAACAACA
* * *
70611 ACT ACT ACT TCT ACT ACT ACT ACT ACC ACT ACT ACT ACA ACT AC
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
70655 CCAACAGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
ACT
Found at i:84005 original size:24 final size:24
Alignment explanation
Indices: 83978--84030 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
83968 TGTAGAAACC
83978 TTTTTTATTT-ATTTTTCGT-TTAT
1 TTTTTTATTTCATTTTT-GTATTAT
*
84001 TTTTTTATTTCATTTTTTTATTAT
1 TTTTTTATTTCATTTTTGTATTAT
84025 TTTTTT
1 TTTTTT
84031 TTGGCTCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (24 bp):
TTTTTTATTTCATTTTTGTATTAT
Found at i:84024 original size:16 final size:16
Alignment explanation
Indices: 83980--84026 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
83970 TAGAAACCTT
*
83980 TTTTATTTATT-TTTCG
1 TTTT-TTTATTATTTCA
*
83996 TTTATTTTTTTATTTCA
1 TTT-TTTTATTATTTCA
84013 TTTTTTTATTATTT
1 TTTTTTTATTATTT
84027 TTTTTTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTTATTATTTCA
Found at i:84026 original size:11 final size:12
Alignment explanation
Indices: 83978--84030 Score: 65
Period size: 11 Copynumber: 4.5 Consensus size: 12
83968 TGTAGAAACC
83978 TTTTTTATTTA-
1 TTTTTTATTTAT
**
83989 TTTTTCGTTTAT
1 TTTTTTATTTAT
84001 TTTTTTATTTCAT
1 TTTTTTATTT-AT
84014 TTTTTTA-TTAT
1 TTTTTTATTTAT
84025 TTTTTT
1 TTTTTT
84031 TTGGCTCTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 17 0.47
12 10 0.28
13 9 0.25
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:84587 original size:2 final size:2
Alignment explanation
Indices: 84582--84621 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
84572 ATTTTTTCCG
*
84582 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
84622 AACTTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:85095 original size:20 final size:20
Alignment explanation
Indices: 85070--85107 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
85060 GCTTAAGTAC
85070 CTGGTTGAAGAATGTTTCAA
1 CTGGTTGAAGAATGTTTCAA
*
85090 CTGGTTGAAGACTGTTTC
1 CTGGTTGAAGAATGTTTC
85108 TTTACAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (20 bp):
CTGGTTGAAGAATGTTTCAA
Found at i:92455 original size:3 final size:3
Alignment explanation
Indices: 92449--92474 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
92439 GATGATGATG
92449 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
92475 GATTATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:94364 original size:44 final size:44
Alignment explanation
Indices: 94315--94403 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
94305 TGCCCACAAT
94315 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC
1 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC
94359 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC
1 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC
94403 T
1 T
94404 CATTTCTAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (44 bp):
TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC
Found at i:96933 original size:10 final size:11
Alignment explanation
Indices: 96909--96934 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
96899 GTTGTTGGGA
96909 TTTTTGTTTGT
1 TTTTTGTTTGT
96920 TTTTTGTTTGT
1 TTTTTGTTTGT
96931 TTTT
1 TTTT
96935 ATTTTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTGTTTGT
Found at i:110756 original size:13 final size:13
Alignment explanation
Indices: 110738--110769 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
110728 ATCATAAAGA
*
110738 TTTATTTATTTTT
1 TTTATTTATTTAT
110751 TTTATTTATTTAT
1 TTTATTTATTTAT
110764 TTTATT
1 TTTATT
110770 CGTGACGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:119595 original size:18 final size:18
Alignment explanation
Indices: 119572--119608 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
119562 TTGGGGGGAT
119572 GGTCACATTTAAATAAGA
1 GGTCACATTTAAATAAGA
119590 GGTCACATTTAAATAAGA
1 GGTCACATTTAAATAAGA
119608 G
1 G
119609 ATGTTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (18 bp):
GGTCACATTTAAATAAGA
Found at i:120865 original size:165 final size:166
Alignment explanation
Indices: 120435--121145 Score: 1176
Period size: 166 Copynumber: 4.3 Consensus size: 166
120425 GGTATTTTTC
* * * *** * *
120435 AAAAATCTTCTTCTCAAAAACTATTAGGCCGGTAAAGCTTAAACTT-GTGTGGAGGCATCATCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATCCTCAG
* * * *
120499 GTAGTGTAGATTCAAGTTTGTTCAATTCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGGGGG
65 GAAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGG
120564 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
120601 AAAAATTTTCTTCTCAAAAACTATTTGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
120666 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
120731 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATC-TTT
*
120768 AAAAAT-TTCTT-TTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* * *
120831 AAGTGTTTATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGGGGGA
66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
120896 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
120932 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGTAAGCATCCTCATG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* *
120997 TAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTTGGGGA
66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
121062 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
121098 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
121146 NGGGGTTATA
Statistics
Matches: 512, Mismatches: 29, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
164 9 0.02
165 151 0.29
166 343 0.67
167 9 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:120903 original size:331 final size:333
Alignment explanation
Indices: 120430--121145 Score: 1197
Period size: 331 Copynumber: 2.2 Consensus size: 333
120420 TTGTTGGTAT
* * * *** *
120430 TTTTCAAAAATCTTCTTCTCAAAAACTATTAGGCCGGTAAAGCTTAAACTT-GTGTGGAGGCATC
1 TTTT-AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATC
* * *
120494 ATCAGGTAGTGTAGATTCAAGTTTGTTCAATTCATGGTCCCCGGGGGTTGGGTGGGGCCACAATT
64 ATCAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATT
*
120559 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTA
129 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTA
*
120624 TTTGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCA
194 TTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCA
120689 AATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATAT
259 AATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATAT
120754 AGAGAAAATC
324 AGAGAAAATC
* *
120764 TTTTAAAAAT-TTCTT-TTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCT
1 TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCAT
**
120827 CAGGAAGTGTTTATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG
66 CAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG
120892 GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
131 GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
* * * *
120957 AGGCCAGAAAAGCTCAAATTAAAATGTAAGCATCCTCATGTAGTGTTGATTCAAGTTTGTTCAAA
196 AGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCAAA
*
121022 TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAG
261 TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAG
121087 AGAAAATC
326 AGAAAATC
121095 -TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
1 TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
121146 NGGGGTTATA
Statistics
Matches: 357, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
330 11 0.03
331 297 0.83
332 39 0.11
333 6 0.02
334 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (333 bp):
TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCAT
CAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG
GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
AGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCAAA
TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAG
AGAAAATC
Found at i:130207 original size:20 final size:21
Alignment explanation
Indices: 130165--130214 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
130155 AGTATGTTGG
**
130165 TTTTTTTTGTTTTTGTTTAGT
1 TTTTTTTTGGCTTTGTTTAGT
*
130186 TTTTTTTTGGCTTT-TTTCGT
1 TTTTTTTTGGCTTTGTTTAGT
130206 TTTTCTTTT
1 TTTT-TTTT
130215 TTTTTGAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80
Consensus pattern (21 bp):
TTTTTTTTGGCTTTGTTTAGT
Found at i:141950 original size:2 final size:2
Alignment explanation
Indices: 141943--141996 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
141933 CCGCAAACAA
141943 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
141985 AC AC AC AC AC AC
1 AC AC AC AC AC AC
141997 TTAATTTGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:145754 original size:4 final size:4
Alignment explanation
Indices: 145745--145774 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
145735 GTTACCCTGT
145745 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
145775 TGTCACGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.23, T:0.27
Consensus pattern (4 bp):
TCCG
Found at i:146507 original size:165 final size:164
Alignment explanation
Indices: 146304--146698 Score: 564
Period size: 165 Copynumber: 2.4 Consensus size: 164
146294 AGTAGCTACG
* * * * *
146304 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
* *
146369 TCATCCTGGGAGTC-AAATAGTAGCAG-AAAATTGACGTTTATCACTAAAAAAAAACAAACATTG
66 TCATCCAGGGAGTCAAAAT-GTAGCAGAAAAATTGACGTTTATCACT--AAAAAAA-AAACATAG
*
146432 ATCCAAGAGCTCCTATTATGATTTAATGGATAGACA-A
127 ATCCAAGAACTCCTATTATGATTTAATGGATAGACACA
* *
146469 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTTAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
*
146534 TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTTAAAAAAAAACATAGATCC
66 TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTAAAAAAAAAACATAGATCC
* *
146599 TAGAACTCCTTTTATGATTTAATGGATAGACACA
131 AAGAACTCCTATTATGATTTAATGGATAGACACA
* * * *
146633 TCATATCTTGGGATATGAAAGGAACTGTTCCATAGATGTGCATTAAGGTTTTGAAAAA-TTAAAT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAAT
146697 TT
65 TT
146699 AACCCTGAGG
Statistics
Matches: 208, Mismatches: 18, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
163 40 0.19
164 63 0.30
165 82 0.39
166 23 0.11
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (164 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTAAAAAAAAAACATAGATCC
AAGAACTCCTATTATGATTTAATGGATAGACACA
Found at i:146697 original size:164 final size:163
Alignment explanation
Indices: 146335--146698 Score: 536
Period size: 164 Copynumber: 2.2 Consensus size: 163
146325 GGGCTGTCCT
*
146335 ATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCTGGGAGTCAAATAGTAGCAGAAAAT
1 ATAGATGTGCAATAAGGTTTTAAAAA-TTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAAT
* *
146400 TGACGTTTATCACTAAAAAAAAACAAACATTGATCCAAGAGCTCCTATTATGATTTAATGGATAG
65 TGACGTTTATCACT-AAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATAG
* * *
146465 ACAATCATATCTTGGGATATGATAGGGACTGTTCT
129 ACAATCATATCTTGGGATATGAAAGGAACTGTTCC
* *
146500 ATAGATGTGCAGTAAGGTTTTTAAAATTTAAATTTCATCCAGGGAGTCAAA-ATGTAGCAGAAAA
1 ATAGATGTGCAATAAGG-TTTTAAAAATTAAATTTCATCCAGGGAGTCAAATA-GTAGCAG-AAA
* * *
146564 ATTGACGTTTATCACT-TAAAAAA-AAACATAGATCCTAGAACTCCTTTTATGATTTAATGGATA
63 ATTGACGTTTATCACTAAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATA
146627 GACACATCATATCTTGGGATATGAAAGGAACTGTTCC
128 GACA-ATCATATCTTGGGATATGAAAGGAACTGTTCC
*
146664 ATAGATGTGCATTAAGGTTTTGAAAAATTAAATTT
1 ATAGATGTGCAATAAGGTTTT-AAAAATTAAATTT
146699 AACCCTGAGG
Statistics
Matches: 181, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
163 44 0.24
164 64 0.35
165 46 0.25
166 27 0.15
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (163 bp):
ATAGATGTGCAATAAGGTTTTAAAAATTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATT
GACGTTTATCACTAAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATAGAC
AATCATATCTTGGGATATGAAAGGAACTGTTCC
Found at i:146894 original size:135 final size:135
Alignment explanation
Indices: 146746--147044 Score: 367
Period size: 134 Copynumber: 2.2 Consensus size: 135
146736 GATGCCCTTT
* *
146746 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATT-CGTGCA
1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAG-GCA
* * * * * *
146809 CTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTCGATGCCCC
64 CTTCCTGTTCAA-GGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCC
146874 TTGACA-C
128 TTGACATC
* *
146881 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC
1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC
* ** *
146945 TTGCTGTTTGAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
65 TTCCTGTTCAAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCCTT
147010 GACATC
130 GACATC
* *
147016 -AGAAACATGAATATATATGGGTT-AGGGGT
1 AAGGAACAAGAATATATAT-GGTTAAGGGGT
147045 CATGATTATA
Statistics
Matches: 142, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
133 1 0.01
134 74 0.52
135 62 0.44
136 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT
TCCTGTTCAAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCCTTG
ACATC
Found at i:157152 original size:2 final size:2
Alignment explanation
Indices: 157145--157193 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
157135 GTCAGAGCGG
157145 AT AT 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 AT AT
157187 AT AT AT A
1 AT AT AT A
157194 CGGCCCGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:159382 original size:21 final size:21
Alignment explanation
Indices: 159356--159400 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
159346 GTAAAACGTA
159356 TGCAACAAATGCGAGAGCTCG
1 TGCAACAAATGCGAGAGCTCG
**
159377 TGCAACGTATGCGAGAGCTCG
1 TGCAACAAATGCGAGAGCTCG
159398 TGC
1 TGC
159401 GAAGCTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (21 bp):
TGCAACAAATGCGAGAGCTCG
Found at i:179723 original size:67 final size:67
Alignment explanation
Indices: 179650--179783 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
179640 TAAAATATAC
*
179650 ACAAATCATACAGGGTAAGTGATATATAAAAATAT-GAACAAAATATATACACGGGGCATAAAAT
1 ACAAATCATACAGGGTAAGTGATATATAAAAATATAG-ACAAAATATATACACGGAGCATAAAAT
179714 TCT
65 TCT
*
179717 ACAAATCATACAGGGTAAGTGATTTATAAAAATATAGACAAAATATATACACGGAGCATAAAATT
1 ACAAATCATACAGGGTAAGTGATATATAAAAATATAGACAAAATATATACACGGAGCATAAAATT
179782 CT
66 CT
179784 GTAACAGTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 63 0.98
68 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (67 bp):
ACAAATCATACAGGGTAAGTGATATATAAAAATATAGACAAAATATATACACGGAGCATAAAATT
CT
Found at i:181310 original size:30 final size:31
Alignment explanation
Indices: 181270--181332 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
181260 TTCAAAGTGT
*
181270 TTTTCCGAGCCTG-CGGAAAGGCCCGAGAAG
1 TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG
*
181300 TTTTCAGAGCCTGCCGGAAAGGCCTGAGAAG
1 TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG
181331 TT
1 TT
181333 GCAATTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (31 bp):
TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG
Found at i:182771 original size:48 final size:48
Alignment explanation
Indices: 182683--182775 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
182673 TGTCATATGA
* *
182683 AAAACCAAAACAACGTAAAAATTAAGGTGGCATATACAAAACATTTTG
1 AAAACAAAAACAACGTAAAAATTAAGGTGACATATACAAAACATTTTG
* * **
182731 AAAACAAAAACAATGTAAAATTTACTGTGACATA-AGCAAAACATT
1 AAAACAAAAACAACGTAAAAATTAAGGTGACATATA-CAAAACATT
182776 AAGGAGGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.03
48 37 0.97
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (48 bp):
AAAACAAAAACAACGTAAAAATTAAGGTGACATATACAAAACATTTTG
Found at i:183911 original size:38 final size:38
Alignment explanation
Indices: 183868--183953 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
183858 TGAGGGTGGT
* * *
183868 AGCAGACATAATTTGACCTA-TTGTGGGTTTAGGGTAGC
1 AGCAGACATAATCTGACCTACTT-TGGGTTCAGAGTAGC
*
183906 AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGT
1 AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGC
183944 AGCAGACATA
1 AGCAGACATA
183954 TCCTGAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 41 0.95
39 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (38 bp):
AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGC
Found at i:185713 original size:108 final size:108
Alignment explanation
Indices: 185505--185791 Score: 283
Period size: 108 Copynumber: 2.7 Consensus size: 108
185495 TTATCAAACC
* * * * *
185505 CAAACTTTGCATTTTTTCAATGTTGGGCACATTTGAGAGTTCCGGAGAACTTCTAGCTTTTTTAA
1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA
* * ** *
185570 GAGTAA-TTGAATTAGAATCTGTTTGTGGTTTTCTTATCAACAT
66 GAG-AACGTGAATTAAAATCTGTTTGTGGTGCTCTTATCAACAA
* * * * * *
185613 CAAACTTCGCATTGTTTCAATTTTTGACACTTTTGAGAGCTCCGGACAACTCCTAGCTTTTTTAA
1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA
** *
185678 GAGAACGTGTTTTAAAATCTGATGTT-T-GTGCTCTTATTAACAA
66 GAGAACGTGAATTAAAATCTG-T-TTGTGGTGCTCTTATCAACAA
** * * * * * *
185721 CAAACAACGCTTTTTTTCAATGTCGGGCACTTTTGAGAGATCTGGAAAACTCCTAACTTTTCTAG
1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA
185786 GAGAAC
66 GAGAAC
185792 AGGTGTTAGA
Statistics
Matches: 145, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
107 2 0.01
108 139 0.96
109 2 0.01
110 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (108 bp):
CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA
GAGAACGTGAATTAAAATCTGTTTGTGGTGCTCTTATCAACAA
Found at i:186492 original size:33 final size:33
Alignment explanation
Indices: 186455--186555 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
186445 TGGTTATTAT
186455 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC
1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC
* *
186488 TTTTTTTAATTTGTCTTGTTTTATCAGGTTTTC
1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC
* * *
186521 TATTTTCAATTCGGCTTATTTTATCAGGTTTTC
1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC
186554 TT
1 TT
186556 CCGAAAAGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.14, C:0.12, G:0.13, T:0.61
Consensus pattern (33 bp):
TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC
Found at i:186494 original size:18 final size:18
Alignment explanation
Indices: 186473--186526 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 18
186463 ATTTGGCTTG
186473 TTTTATCAGGTTTTCTTT
1 TTTTATCAGGTTTTCTTT
*
186491 TTTTA--A--TTTGTCTTG
1 TTTTATCAGGTTT-TCTTT
186506 TTTTATCAGGTTTTCTATT
1 TTTTATCAGGTTTTCT-TT
186525 TT
1 TT
186527 CAATTCGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 1 0.04
17 1 0.04
18 8 0.29
19 6 0.21
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67
Consensus pattern (18 bp):
TTTTATCAGGTTTTCTTT
Found at i:186945 original size:24 final size:24
Alignment explanation
Indices: 186918--186995 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
186908 TCTCTTCTTT
* *
186918 ATTTTCATCGGTCATTTTCTGTTC
1 ATTTTCATCGGTCATTTGCTGTCC
* *
186942 ATTTTCATTGGTCGTTTGCTGTCC
1 ATTTTCATCGGTCATTTGCTGTCC
* * * *
186966 ATTTCCATCGTTCGTTTGCTGTCT
1 ATTTTCATCGGTCATTTGCTGTCC
186990 ATTTTC
1 ATTTTC
186996 GTCTGCTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.15, T:0.53
Consensus pattern (24 bp):
ATTTTCATCGGTCATTTGCTGTCC
Found at i:201804 original size:16 final size:16
Alignment explanation
Indices: 201780--201815 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
201770 AAAGAAGTAT
*
201780 GACGGACGGAAACACG
1 GACGCACGGAAACACG
*
201796 GACGCACGGACACACG
1 GACGCACGGAAACACG
201812 GACG
1 GACG
201816 GACGCCCGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.36, T:0.00
Consensus pattern (16 bp):
GACGCACGGAAACACG
Found at i:207185 original size:161 final size:161
Alignment explanation
Indices: 206895--207185 Score: 374
Period size: 161 Copynumber: 1.8 Consensus size: 161
206885 GGAACATCCA
* * * * *
206895 CAAAGAAAATGAACGTAAACTGCAAATATTTGGAATTTTTTTAAGTCAAAGGGGCATAACTCTGT
1 CAAAGAAAATGAACGGAAACTGCAAATACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTGT
* * *
206960 CCAAAATTGCTCTATCATAACCAAAATTAAACTTGACCTAGATATTATTTAAAAAATTCTGTATA
66 CCAAAATTGCTCTATCATAACCAAAATCAAACTTGACCTAGATATTATATAAAAAATCCTGTATA
207025 CCAAATTTTATATCAATATGTGCACCCTCTG
131 CCAAATTTTATATCAATATGTGCACCCTCTG
** * *
207056 CAAAGAAAATGAGTGGAAACTGCAAATAACTT-GAATTTTTCTATGTCCAAGAGCCATAACTCTG
1 CAAAGAAAATGAACGGAAACTGCAAAT-ACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTG
* * * *
207120 TCCAAAATTGCT-TGATCGT-ACCAAATATCCAACTTGACCTAGATATTATCATGATAAA-CCTG
65 TCCAAAATTGCTCT-ATCATAACCAAA-ATCAAACTTGACCTAGATATTAT-ATAAAAAATCCTG
207182 TATA
127 TATA
207186 AACAACTATC
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
160 7 0.06
161 95 0.86
162 8 0.07
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (161 bp):
CAAAGAAAATGAACGGAAACTGCAAATACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTGT
CCAAAATTGCTCTATCATAACCAAAATCAAACTTGACCTAGATATTATATAAAAAATCCTGTATA
CCAAATTTTATATCAATATGTGCACCCTCTG
Found at i:208853 original size:14 final size:14
Alignment explanation
Indices: 208836--208865 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
208826 TAATGTTTCC
*
208836 CACGAAATGCTTCA
1 CACGAAATGCTACA
208850 CACGAAATGCTACA
1 CACGAAATGCTACA
208864 CA
1 CA
208866 GTTTACACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.30, G:0.13, T:0.17
Consensus pattern (14 bp):
CACGAAATGCTACA
Found at i:210475 original size:21 final size:21
Alignment explanation
Indices: 210446--210550 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
210436 GCTACACGCT
* *
210446 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
*
210467 CGCTGAACGGTTTACATGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
210488 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* * *
210509 CGCTAAACGATATACACGAAA
1 CGCTGAACGGTTTACACGAAA
* *
210530 TGCTGAATGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
210551 TGTTTCTCGC
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:210769 original size:21 final size:21
Alignment explanation
Indices: 210743--210888 Score: 118
Period size: 21 Copynumber: 7.0 Consensus size: 21
210733 TACAAGATAA
* *
210743 ACGATAGGATAGGATTTATGC
1 ACGATAGGATAGGATTAACGC
*
210764 ACGATAGGATAGCATTAACGC
1 ACGATAGGATAGGATTAACGC
* * * *
210785 ACGATAGAACAGTA-TACATGC
1 ACGATAGGATAGGATTA-ACGC
*
210806 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTAACGC
* *
210827 ACGATAGGACAGTA-TACACGC
1 ACGATAGGATAGGATTA-ACGC
* *
210848 ACGATATGATAGGATTGATC-C
1 ACGATAGGATAGGATT-AACGC
* *
210869 ACGATAGGAAAGGATAAACG
1 ACGATAGGATAGGATTAACG
210889 ATGTTCATGA
Statistics
Matches: 96, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
20 6 0.06
21 85 0.89
22 4 0.04
23 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (21 bp):
ACGATAGGATAGGATTAACGC
Found at i:210860 original size:42 final size:42
Alignment explanation
Indices: 210762--210877 Score: 162
Period size: 42 Copynumber: 2.8 Consensus size: 42
210752 TAGGATTTAT
* * *
210762 GCACGATAGGATAGCATTAACGCACGATAGAACAGTATACAT
1 GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC
*
210804 GCACGAAAGGATAGGATTAACGCACGATAGGACAGTATACAC
1 GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC
* *
210846 GCACGATATGATAGGATTGATC-CACGATAGGA
1 GCACGATAGGATAGGATT-AACGCACGATAGGA
210878 AAGGATAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (42 bp):
GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC
Found at i:210872 original size:63 final size:63
Alignment explanation
Indices: 210743--210888 Score: 152
Period size: 63 Copynumber: 2.3 Consensus size: 63
210733 TACAAGATAA
* * * * *
210743 ACGATAGGATAGGATTTATGCACGATAGGATAGCATTAACGCACGATAGAACAGTATACATGC
1 ACGATAGGATAGGATTAACGCACGATAGGACAGCATTAACGCACGATAGAACAGGATACATCC
* * * **
210806 ACGAAAGGATAGGATTAACGCACGATAGGACAGTA-TACACGCACGATATG-ATAGGATTGATCC
1 ACGATAGGATAGGATTAACGCACGATAGGACAGCATTA-ACGCACGATA-GAACAGGATACATCC
* *
210869 ACGATAGGAAAGGATAAACG
1 ACGATAGGATAGGATTAACG
210889 ATGTTCATGA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
62 2 0.03
63 65 0.96
64 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (63 bp):
ACGATAGGATAGGATTAACGCACGATAGGACAGCATTAACGCACGATAGAACAGGATACATCC
Found at i:211866 original size:21 final size:21
Alignment explanation
Indices: 211842--211925 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
211832 CGATAAACCT
211842 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
211863 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * *
211884 AACAGTA-TACACGCACGATAG
1 GATAGGATTA-ACGCACGATAG
* *
211905 GATAGAATTAACACACGATAG
1 GATAGGATTAACGCACGATAG
211926 AACAGTTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:211899 original size:42 final size:45
Alignment explanation
Indices: 211852--211969 Score: 161
Period size: 42 Copynumber: 2.7 Consensus size: 45
211842 GATAGGATTA
*
211852 ACGCACGATAGGATAGGATTAACGCACGATAGAACAG-T-AT-AC
1 ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC
* *
211894 ACGCACGATAGGATAGAATTAACACACGATAGAACAGTTAATAAT
1 ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC
* * *
211939 ACGCACGATACGATAGGATTGATACACGATA
1 ACGCACGATAGGATAGGATTAACACACGATA
211970 CGATAGGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 35 0.53
43 1 0.02
44 2 0.03
45 28 0.42
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (45 bp):
ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC
Found at i:212462 original size:124 final size:124
Alignment explanation
Indices: 212216--212589 Score: 662
Period size: 124 Copynumber: 3.0 Consensus size: 124
212206 TCAATATGTC
212216 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTATTAATATTTTTATTGGTTTCA
1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCAC---ATTAATATTTTTATTGGTTTCA
*
212281 GAGAATACGATGT-AAAAATACTAACTGTAAATAAACCTGTGATTATTTACATTGATAATTT
63 GAGAATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT
212342 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
212407 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT
66 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT
*
212466 GGTTTTTCAGTATTCGGCGGGATTTGTTTTCTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
* *
212531 AATACGATGTAAAAAATATTTGCTGTAAATAAACCTGT-ATTTATTTACATTGATAATTT
66 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGA-TTATTTACATTGATAATTT
212590 TGAAAGTTAT
Statistics
Matches: 242, Mismatches: 4, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
123 36 0.15
124 166 0.69
126 40 0.17
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (124 bp):
GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT
Found at i:223809 original size:24 final size:24
Alignment explanation
Indices: 223768--223814 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
223758 GAAATGCCTC
223768 TAATTGTACCGTGAACAATTAGTA
1 TAATTGTACCGTGAACAATTAGTA
* * *
223792 TAATTGTTCCTTGGACAATTAGT
1 TAATTGTACCGTGAACAATTAGT
223815 CTACAAGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (24 bp):
TAATTGTACCGTGAACAATTAGTA
Found at i:224453 original size:16 final size:16
Alignment explanation
Indices: 224431--224474 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
224421 AAGTGTGAAG
*
224431 GACGGACACACGGAC-
1 GACGGACACACAGACA
*
224446 GCACGGACCCACAGACA
1 G-ACGGACACACAGACA
224463 GACGGACACACA
1 GACGGACACACA
224475 AGGGTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.36, C:0.36, G:0.27, T:0.00
Consensus pattern (16 bp):
GACGGACACACAGACA
Found at i:226094 original size:13 final size:13
Alignment explanation
Indices: 226078--226102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226068 TATAATATTG
226078 ATATATGATTTAC
1 ATATATGATTTAC
226091 ATATATGATTTA
1 ATATATGATTTA
226103 ATTTACATGG
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATATATGATTTAC
Found at i:241851 original size:2 final size:2
Alignment explanation
Indices: 241844--241877 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
241834 TACCCTAGAT
*
241844 TA TA TA TA TA TA TA TA TG 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
241878 CACTTACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:253726 original size:2 final size:2
Alignment explanation
Indices: 253719--253761 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
253709 NNNNNNNNNN
253719 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
253761 T
1 T
253762 GTTCATCCGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:254180 original size:112 final size:112
Alignment explanation
Indices: 253983--254205 Score: 392
Period size: 112 Copynumber: 2.0 Consensus size: 112
253973 AGTTTTGTTC
* *
253983 GTTTGTGTATATCTAATTAAAGTCTATTTTTTGTCCAACTTAAGAAAACCCATGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA
*
254048 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
* * *
254095 GTTTGTGTATATCTAATTAAAGTTTATTGTTTGTCGAACTAAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA
254160 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
254206 CGTCAGGGTT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:255118 original size:17 final size:16
Alignment explanation
Indices: 255078--255118 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
255068 GCCGTGGGCG
*
255078 TTTTTTTT-TTTTGTT
1 TTTTTTTTCTTTTCTT
255093 TTTTTTTTCTTCTTCTT
1 TTTTTTTTCTT-TTCTT
255110 TTTTTTTTC
1 TTTTTTTTC
255119 CATTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (16 bp):
TTTTTTTTCTTTTCTT
Found at i:255232 original size:11 final size:11
Alignment explanation
Indices: 255216--255256 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
255206 TTTTTTAATT
255216 GCTTAAAGGTG
1 GCTTAAAGGTG
*
255227 GCTTAAAGGTA
1 GCTTAAAGGTG
255238 GCTTAAAGGTG
1 GCTTAAAGGTG
255249 GCTTAAAG
1 GCTTAAAG
255257 AAGTTTGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (11 bp):
GCTTAAAGGTG
Found at i:255413 original size:11 final size:11
Alignment explanation
Indices: 255397--255435 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
255387 TAAAGATCGT
255397 CTTTAAGCTAC
1 CTTTAAGCTAC
*
255408 CTTTAAAC-AC
1 CTTTAAGCTAC
*
255418 CTTTAAGCTAT
1 CTTTAAGCTAC
255429 CTTTAAG
1 CTTTAAG
255436 GAGGACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:269300 original size:11 final size:11
Alignment explanation
Indices: 269284--269308 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
269274 AATATCCTTT
269284 ATTTACACATA
1 ATTTACACATA
269295 ATTTACACATA
1 ATTTACACATA
269306 ATT
1 ATT
269309 ATATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTACACATA
Found at i:287216 original size:12 final size:12
Alignment explanation
Indices: 287199--287240 Score: 75
Period size: 12 Copynumber: 3.4 Consensus size: 12
287189 AGGTTTGAAT
287199 AAAAAAAAAAAC
1 AAAAAAAAAAAC
287211 AAAAAAAAAAAC
1 AAAAAAAAAAAC
287223 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
287236 AAAAA
1 AAAAA
287241 CAATACACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:287217 original size:13 final size:13
Alignment explanation
Indices: 287199--287240 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
287189 AGGTTTGAAT
287199 AAAAAAAAAAAC-
1 AAAAAAAAAAACA
287211 AAAAAAAAAAACA
1 AAAAAAAAAAACA
*
287224 AAACAAAAAAACA
1 AAAAAAAAAAACA
287237 AAAA
1 AAAA
287241 CAATACACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:294059 original size:201 final size:200
Alignment explanation
Indices: 293714--294114 Score: 784
Period size: 201 Copynumber: 2.0 Consensus size: 200
293704 GATTGAATCT
*
293714 CCTATAAATCTCTAACCGTAATATTTCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC
1 CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC
293779 AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT
66 AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT
293844 GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA
131 GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA
293909 ACGTA
196 ACGTA
293914 NCCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGA
1 -CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGA
293979 CAATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGT
65 CAATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGT
294044 TGGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCA
130 TGGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCA
294109 AACGTA
195 AACGTA
294115 TCATCCTGCA
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 199 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (200 bp):
CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC
AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT
GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA
ACGTA
Found at i:297038 original size:17 final size:17
Alignment explanation
Indices: 297016--297056 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
297006 CAAATGAAAG
*
297016 AATTTTCAAATGATTTA
1 AATTTTAAAATGATTTA
*
297033 AATTTTAAAATGTTTTA
1 AATTTTAAAATGATTTA
*
297050 AAATTTA
1 AATTTTA
297057 GATATTCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
AATTTTAAAATGATTTA
Found at i:303525 original size:66 final size:66
Alignment explanation
Indices: 303455--303592 Score: 258
Period size: 66 Copynumber: 2.1 Consensus size: 66
303445 TGTAAAATAT
303455 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT
303520 C
66 C
* *
303521 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTATTGTTTCTTTTTCACTTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT
303586 C
66 C
303587 TTATTA
1 TTATTA
303593 TTCTTTTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.49
Consensus pattern (66 bp):
TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT
C
Found at i:304401 original size:69 final size:69
Alignment explanation
Indices: 304290--304502 Score: 374
Period size: 69 Copynumber: 3.1 Consensus size: 69
304280 ACAGTCTTTA
304290 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT
1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT
304355 TCTT
66 TCTT
*
304359 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCT-TCGGTTTCTTTTTCACTT
1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAT-TGTTTCTTTTTCACTT
304423 TTCTT
65 TTCTT
* * *
304428 CTTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTT
1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT
304493 TCTT
66 TCTT
304497 ATTATT
1 ATTATT
304503 CTTTTTTTTT
Statistics
Matches: 136, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.01
69 135 0.99
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.49
Consensus pattern (69 bp):
ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT
TCTT
Found at i:320380 original size:51 final size:52
Alignment explanation
Indices: 320262--320394 Score: 232
Period size: 51 Copynumber: 2.6 Consensus size: 52
320252 AAAGAAACCG
* * *
320262 TAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAAAAAAAACAA
1 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA
320314 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT-AAAAAAACAA
1 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA
320365 TAGAATAACAAGAGGGTCTTCCGTTGAAAA
1 TAGAATAACAAGAGGGTCTTCCGTTGAAAA
320395 AGAAAAACAA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 40 0.51
52 38 0.49
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (52 bp):
TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA
Found at i:322193 original size:30 final size:30
Alignment explanation
Indices: 322154--322217 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
322144 AAATATGAAA
*
322154 AAAATCGAAT-ATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAAGTACGACTTAAC
*
322183 AAAATACGAATGATTTTAAGTACGACTTAAC
1 AAAAT-CGAATGATTCTAAGTACGACTTAAC
322214 AAAA
1 AAAA
322218 ACCTTTCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (30 bp):
AAAATCGAATGATTCTAAGTACGACTTAAC
Found at i:322992 original size:30 final size:30
Alignment explanation
Indices: 322953--323016 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
322943 AAAAGATGAA
322953 AAAATCGAAT-ATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAGGTACGACTTAAC
* *
322982 AAAATACGAATGATTTTAGGTATGACTTAAC
1 AAAAT-CGAATGATTCTAGGTACGACTTAAC
323013 AAAA
1 AAAA
323017 ACCTTTTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 19 0.63
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (30 bp):
AAAATCGAATGATTCTAGGTACGACTTAAC
Found at i:323637 original size:21 final size:21
Alignment explanation
Indices: 323613--323653 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
323603 AAAAATAAAG
*
323613 AAAAAGAAAAAATATAATAAT
1 AAAAAGAAAAAATAGAATAAT
*
323634 AAAAAGAAACAATAGAATAA
1 AAAAAGAAAAAATAGAATAA
323654 CAAGAGGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAAGAAAAAATAGAATAAT
Found at i:326474 original size:15 final size:15
Alignment explanation
Indices: 326444--326483 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
326434 ATGTGACCAG
326444 ATAAATACTG-TTTT
1 ATAAATACTGTTTTT
*
326458 ATAACTACTGTTTTT
1 ATAAATACTGTTTTT
326473 ATAAATACTGT
1 ATAAATACTGT
326484 CTAAACATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (15 bp):
ATAAATACTGTTTTT
Found at i:326550 original size:14 final size:14
Alignment explanation
Indices: 326531--326562 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
326521 AGTATCTACA
326531 TTTATACAGAAAAT
1 TTTATACAGAAAAT
326545 TTTATACAGAAAAT
1 TTTATACAGAAAAT
326559 TTTA
1 TTTA
326563 CCAAAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (14 bp):
TTTATACAGAAAAT
Found at i:328842 original size:65 final size:66
Alignment explanation
Indices: 328735--328869 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 66
328725 CAGAGAGCAG
328735 TCAGTCTACAGTCAGGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGG
1 TCAGTCTACAGTC--GAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGG
328800 GAC
64 GAC
* *
328803 TCAGTCTACAGTC-AGGATGACGTCATGGGTTTTCCCCATAAGGTCATACGAGGTCAAGGTGGGA
1 TCAGTCTACAGTCGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGGGA
328867 C
66 C
328868 TC
1 TC
328870 TACAGTCAGG
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
65 52 0.80
68 13 0.20
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (66 bp):
TCAGTCTACAGTCGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGGGA
C
Found at i:329116 original size:59 final size:59
Alignment explanation
Indices: 329024--329220 Score: 306
Period size: 59 Copynumber: 3.3 Consensus size: 59
329014 ACTCAAAGGA
* *
329024 TTAGTTCACATAGCAACAGTTGAAGGATGATACCATACATATCTACTGTCAGGGTCACC
1 TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC
* * * *
329083 TTAGTTCTCATAGCAACAGTTG-AGCGATGATACCATAAATATTTACTGACAGGGTCACC
1 TTAGTTCACAGAGCAACAGTTGAAG-GATGATACCATAAATATCTACTGTCAGGGTCACC
* *
329142 TTAGTTCTCAGAGCAACAGTTGAAGGATGATACCATAAATATCAACTGTCAGGGTCACC
1 TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC
329201 TTAGTTCACAGAGCAACAGT
1 TTAGTTCACAGAGCAACAGT
329221 CAAGGGAGGG
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
58 2 0.02
59 123 0.97
60 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (59 bp):
TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC
Found at i:334538 original size:40 final size:40
Alignment explanation
Indices: 334492--334639 Score: 161
Period size: 40 Copynumber: 3.9 Consensus size: 40
334482 CAGATACCTC
334492 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT
1 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT
334532 GATTCTAATGATGTTCG----AT-T-A--ATCAGATAT-TT
1 GATTCTAATGATGTTCGATTTATCTGATTATCAGAT-TCTT
* * * * *
334564 GATTCTGATGATGTTAGATTTATTTCATTATCAGATACTT
1 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT
* *
334604 TATTTTAATGATGTTCGATTTATCTGATTATCAGAT
1 GATTCTAATGATGTTCGATTTATCTGATTATCAGAT
334640 ACCTTGTTGC
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
32 24 0.27
33 1 0.01
34 1 0.01
35 1 0.01
36 4 0.04
37 1 0.01
38 1 0.01
40 56 0.63
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (40 bp):
GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT
Found at i:334558 original size:32 final size:31
Alignment explanation
Indices: 334517--334583 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
334507 CGATTTATCT
*
334517 GATTATCAGAT-TCTTGATTCTAATGATGTTC
1 GATTATCAGATAT-TTGATTCTAATGATGTTA
*
334548 GATTAATCAGATATTTGATTCTGATGATGTTA
1 GATT-ATCAGATATTTGATTCTAATGATGTTA
334580 GATT
1 GATT
334584 TATTTCATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 4 0.12
32 27 0.84
33 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (31 bp):
GATTATCAGATATTTGATTCTAATGATGTTA
Found at i:334640 original size:40 final size:41
Alignment explanation
Indices: 334548--334663 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 41
334538 AATGATGTTC
* *
334548 GATTAATCAGATA-TTTGATTCTGATGATGTTAGATTTATTT
1 GATT-ATCAGATACTTTGATTCTAATGATGTTAGATTTATCT
* * *
334589 CATTATCAGATACTTT-ATTTTAATGATGTTCGATTTATCT
1 GATTATCAGATACTTTGATTCTAATGATGTTAGATTTATCT
* *
334629 GATTATCAGATACCTTG-TTGCTAACGATGTTAGAT
1 GATTATCAGATACTTTGATT-CTAATGATGTTAGAT
334664 ATATATAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 44 0.71
41 18 0.29
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (41 bp):
GATTATCAGATACTTTGATTCTAATGATGTTAGATTTATCT
Found at i:335451 original size:62 final size:62
Alignment explanation
Indices: 335375--335498 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
335365 GGTTCTTAAC
* *
335375 AACTTAACAATGAAATTACTACACTGAACTATACTAGAACTATTGAAATGAACAATACTCAA
1 AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA
* *
335437 AACTTAACAATGAAATTACTACATTTAACTATACTAAAACTACTGAAATGAACAATACTCAA
1 AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA
335499 TCTACTTAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (62 bp):
AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA
Found at i:335494 original size:24 final size:24
Alignment explanation
Indices: 335467--335513 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
335457 ACATTTAACT
335467 ATACTAAAACTACTGAAATGAACA
1 ATACTAAAACTACTGAAATGAACA
* * * *
335491 ATACTCAATCTACTTAACTGAAC
1 ATACTAAAACTACTGAAATGAAC
335514 TGCGATACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (24 bp):
ATACTAAAACTACTGAAATGAACA
Found at i:335562 original size:24 final size:24
Alignment explanation
Indices: 335535--335601 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
335525 TGATCTAAAG
* *
335535 AATACTGAAACTGCTGAACTGAAC
1 AATACTAAAACTACTGAACTGAAC
*
335559 AATAGTAAAACTACTGAACTGAAC
1 AATACTAAAACTACTGAACTGAAC
* *
335583 AATGCTAAGACTACTGAAC
1 AATACTAAAACTACTGAAC
335602 AATGAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (24 bp):
AATACTAAAACTACTGAACTGAAC
Found at i:336007 original size:16 final size:16
Alignment explanation
Indices: 335986--336017 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
335976 TTTCATGTCA
*
335986 TTCAGGTCTTTGGTAT
1 TTCAGGTCTTTAGTAT
336002 TTCAGGTCTTTAGTAT
1 TTCAGGTCTTTAGTAT
336018 GTCCCATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.50
Consensus pattern (16 bp):
TTCAGGTCTTTAGTAT
Found at i:346579 original size:102 final size:103
Alignment explanation
Indices: 346397--346644 Score: 372
Period size: 104 Copynumber: 2.4 Consensus size: 103
346387 TTTTAGAAAA
* ** *
346397 AAAGTTGGTTAAACATTGTGTATATCAAACAGACCTGTTTTGCAACAGTTGAGAATAAATCTGTA
1 AAAGTTGGTTAAACATTGTG--TATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTA
* *
346462 AAAATATTGTTTACTTTACATGTACAT-AAAAAAGAACAT
64 AAAATATTGTGTACTTCACATGTACATAAAAAAAGAACAT
* *
346501 TAAGTTGGTTAAACATTGTGTATCAAACATACTTGTTTTGCAACAGTAAAAAATAAATCTGTAAA
1 AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTAAA
*
346566 GATATTGTGTACTTCACATGTACATAAAAAAAAGAACAT
66 AATATTGTGTACTTCACATGTACAT-AAAAAAAGAACAT
*
346605 AAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTG
1 AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTG
346645 TAAAGATATT
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
102 62 0.48
104 68 0.52
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (103 bp):
AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTAAA
AATATTGTGTACTTCACATGTACATAAAAAAAGAACAT
Found at i:346812 original size:178 final size:176
Alignment explanation
Indices: 346521--347136 Score: 905
Period size: 176 Copynumber: 3.5 Consensus size: 176
346511 AAACATTGTG
* * * * *
346521 TATCAAACATACTTGTTTTGCAACAGT--AAAAAATAAATCTG-----TAAAGATATTGTGTACT
1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAATTACAGATACTGTGTACT
346579 TCACATGTACATAAAAAAAAGAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTT
66 TCACATGTACAT---AAAAA-AACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTT
346644 GTAAAGATATTGTGTACTTCAATGTACATAAAAAAAACCCATAAAGTTGGT
127 GTAAAGATATTGTGTACTTCAATGTACAT-AAAAAAACCCATAAAGTTGGT
*
346695 TATCAAACATTCCTGTTTTGCACCAGTAAAAAAAATAAATCTGAAAAGTTACAGATACTGTGTAC
1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAA-TTACAGATACTGTGTAC
* *
346760 TTCACATGTACATAAAAAACCATTAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA
65 TTCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA
346825 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT
130 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT
* * *
346872 AATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAAAAAAT-TACAAAATTACAGATACTGTGTAC
1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCT-GAAAATTACAGATACTGTGTAC
* *
346936 TTCACATGTTCATAAAAAAACATAAAGTGGGTTAAACATTGTTTATCAAACATACCTGTTTTGTA
65 TTCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA
347001 AAGATATTGTGTACTTC-ATGTACATAAAAAAA-CCATAAAGTTGGT
130 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT
* * * *
347046 TATCAAACATACATGTTTTGCAGCAGT--AAAATATAAATCTGCAAAATTACAGATACTGTGAAC
1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTG-AAAATTACAGATACTGTGTAC
* *
347109 TTCACATGTACATGAAAAACCATAAAGT
65 TTCACATGTACATAAAAAAACATAAAGT
347137 TTAATATTCA
Statistics
Matches: 406, Mismatches: 25, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
172 9 0.02
173 46 0.11
174 61 0.15
175 15 0.04
176 110 0.27
177 62 0.15
178 71 0.17
179 5 0.01
182 27 0.07
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (176 bp):
TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAATTACAGATACTGTGTACT
TCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTAA
AGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT
Found at i:354101 original size:2 final size:2
Alignment explanation
Indices: 354094--354126 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
354084 ATTTGTATTC
354094 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
354127 TTCATTCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:367631 original size:2 final size:2
Alignment explanation
Indices: 367624--367655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
367614 AGACTGAAAA
367624 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
367656 ATGCTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:370655 original size:16 final size:16
Alignment explanation
Indices: 370616--370657 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
370606 TGGAGTGCAC
370616 ACACACACACATACAT
1 ACACACACACATACAT
*
370632 ACATACACACATACGA-
1 ACACACACACATAC-AT
370648 ACACACACAC
1 ACACACACAC
370658 GCACGGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.50, C:0.38, G:0.02, T:0.10
Consensus pattern (16 bp):
ACACACACACATACAT
Found at i:377650 original size:27 final size:27
Alignment explanation
Indices: 377598--377651 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
377588 CTTGATTATC
**
377598 GCTCAACCAAAACACAATTACCCACTG
1 GCTCAACCAAAACACAATTAAACACTG
377625 GCTCAACCAAAACACAATTAAACACTG
1 GCTCAACCAAAACACAATTAAACACTG
377652 CAGTTTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15
Consensus pattern (27 bp):
GCTCAACCAAAACACAATTAAACACTG
Found at i:389623 original size:14 final size:15
Alignment explanation
Indices: 389604--389641 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
389594 AAAATATAAC
389604 TAATATGTAAA-CTG
1 TAATATGTAAATCTG
389618 TAATATGTAAATCTG
1 TAATATGTAAATCTG
389633 --ATATGTAAA
1 TAATATGTAAA
389642 ACATTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 11 0.48
15 3 0.13
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (15 bp):
TAATATGTAAATCTG
Found at i:402136 original size:4 final size:4
Alignment explanation
Indices: 402127--402183 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
402117 CTATGTAACA
402127 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
402175 AGAT AGAT A
1 AGAT AGAT A
402184 CGAAGAAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:404213 original size:2 final size:2
Alignment explanation
Indices: 404208--404261 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
404198 TATTATGTGT
404208 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
404250 GA GA GA GA GA GA
1 GA GA GA GA GA GA
404262 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:409468 original size:2 final size:2
Alignment explanation
Indices: 409461--409494 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
409451 TTATAAATAA
409461 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
409495 GACCTGTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:410582 original size:17 final size:17
Alignment explanation
Indices: 410560--410592 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
410550 AACTCTCAGT
410560 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
410577 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
410593 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:416671 original size:18 final size:18
Alignment explanation
Indices: 416649--416689 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
416639 ACAATATATT
416649 CTCTCTCTTTTTCTCT-A
1 CTCTCTCTTTTTCTCTCA
416666 -TCTCTCTTTTTCTCTCA
1 CTCTCTCTTTTTCTCTCA
416683 CTCTCTC
1 CTCTCTC
416690 CCGCTCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.68
17 1 0.05
18 6 0.27
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.56
Consensus pattern (18 bp):
CTCTCTCTTTTTCTCTCA
Found at i:420096 original size:2 final size:2
Alignment explanation
Indices: 420091--420125 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
420081 AAATAAGACA
420091 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
420126 GCCAGCTTAC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:423018 original size:22 final size:22
Alignment explanation
Indices: 422986--423122 Score: 177
Period size: 22 Copynumber: 6.2 Consensus size: 22
422976 ACGCTACATG
*
422986 TCTCTACCCATGATGCCATGTT
1 TCTCTACCCATCATGCCATGTT
* * *
423008 TCTTTTCCCATGATGCCATGTT
1 TCTCTACCCATCATGCCATGTT
* *
423030 TGTCTACCCATCATGTCATGTT
1 TCTCTACCCATCATGCCATGTT
*
423052 TCTCTTCCCATCATGCCATGTT
1 TCTCTACCCATCATGCCATGTT
*
423074 TCTCTACCCATCATGCAATGTT
1 TCTCTACCCATCATGCCATGTT
*
423096 TCAT-TACCCATCATGCCGTGTT
1 TC-TCTACCCATCATGCCATGTT
423118 TCTCT
1 TCTCT
423123 TCTTATTAGT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
21 1 0.01
22 97 0.98
23 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTCTACCCATCATGCCATGTT
Found at i:427237 original size:2 final size:2
Alignment explanation
Indices: 427230--427265 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
427220 ATGGAAATAT
427230 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
427266 AGTAAGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:433429 original size:21 final size:21
Alignment explanation
Indices: 433405--433449 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
433395 AACAGGAAGA
*
433405 TGAAATAACACACACCATTTC
1 TGAAATAACACACACCATTGC
* *
433426 TGAAATCACACAGACCATTGC
1 TGAAATAACACACACCATTGC
433447 TGA
1 TGA
433450 TCTGAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (21 bp):
TGAAATAACACACACCATTGC
Found at i:434559 original size:15 final size:15
Alignment explanation
Indices: 434535--434581 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
434525 GATGTGTAAT
434535 TACATATTTTAGATA
1 TACATATTTTAGATA
*
434550 TACATGTTTTAGATA
1 TACATATTTTAGATA
*
434565 TACATATTTTACATA
1 TACATATTTTAGATA
434580 TA
1 TA
434582 TTAGATAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
TACATATTTTAGATA
Found at i:435128 original size:13 final size:13
Alignment explanation
Indices: 435110--435134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
435100 GCATTTTTCA
435110 AATTTTCAAATTT
1 AATTTTCAAATTT
435123 AATTTTCAAATT
1 AATTTTCAAATT
435135 CATTTTGATT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTCAAATTT
Found at i:439512 original size:22 final size:22
Alignment explanation
Indices: 439484--439526 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
439474 ACTAGAAGTG
439484 TGCCTACCATTCTGTCAACCAC
1 TGCCTACCATTCTGTCAACCAC
* *
439506 TGCCTACCATTTTGTCTACCA
1 TGCCTACCATTCTGTCAACCA
439527 TTCTGTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.09, T:0.33
Consensus pattern (22 bp):
TGCCTACCATTCTGTCAACCAC
Found at i:439526 original size:12 final size:12
Alignment explanation
Indices: 439509--439561 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
439499 CAACCACTGC
439509 CTACCATTTTGT
1 CTACCATTTTGT
*
439521 CTACCATTCTGT
1 CTACCATTTTGT
* *
439533 CAACCA--TTGC
1 CTACCATTTTGT
439543 CTACCATTTTGT
1 CTACCATTTTGT
439555 CTACCAT
1 CTACCAT
439562 GGTCTTCCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
12 26 0.79
ACGTcount: A:0.21, C:0.32, G:0.08, T:0.40
Consensus pattern (12 bp):
CTACCATTTTGT
Found at i:439527 original size:34 final size:34
Alignment explanation
Indices: 439487--439561 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
439477 AGAAGTGTGC
439487 CTACCATTCTGTCAACCACTGCCTACCATTTTGT
1 CTACCATTCTGTCAACCACTGCCTACCATTTTGT
*
439521 CTACCATTCTGTCAACCATTGCCTACCATTTTGT
1 CTACCATTCTGTCAACCACTGCCTACCATTTTGT
439555 CTACCAT
1 CTACCAT
439562 GGTCTTCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (34 bp):
CTACCATTCTGTCAACCACTGCCTACCATTTTGT
Found at i:439788 original size:36 final size:36
Alignment explanation
Indices: 439748--440005 Score: 141
Period size: 36 Copynumber: 7.2 Consensus size: 36
439738 TCTACCATTG
439748 TATCAACTGATCTGTTACTAACTATATGTATCAGTT
1 TATCAACTGATCTGTTACTAACTATATGTATCAGTT
* * * * *
439784 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT
1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT
439819 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT
1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT
* * * * *
439856 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT
1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT
439891 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT
1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT
* * * * *
439928 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT
1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT
439963 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT
1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT
440000 TATCAA
1 TATCAA
440006 TCAATCTACC
Statistics
Matches: 162, Mismatches: 30, Indels: 60
0.64 0.12 0.24
Matches are distributed among these distances:
33 12 0.07
34 9 0.06
35 9 0.06
36 102 0.63
37 9 0.06
38 9 0.06
39 12 0.07
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (36 bp):
TATCAACTGATCTGTTACTAACTATATGTATCAGTT
Found at i:439798 original size:72 final size:72
Alignment explanation
Indices: 439681--440194 Score: 913
Period size: 72 Copynumber: 7.1 Consensus size: 72
439671 CAATGTAACG
*
439681 ACTGATCTGTGACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
439746 TGTATCA
66 TGTATCA
439753 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
439818 TGTATCA
66 TGTATCA
439825 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
439890 TGTATCA
66 TGTATCA
439897 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
439962 TGTATCA
66 TGTATCA
*
439969 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCGT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
440034 TGTATCA
66 TGTATCA
* * *
440041 ACT-AGTCTGTGACTAACTATATGTATCAGCTTATCAATCAATCTACCATTCTATCTATCTACCA
1 ACTGA-TCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCA
440105 TTGTATCA
65 TTGTATCA
* * * *
440113 ACTGGTCTGTGACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTGTATCTATCTACCGT
1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
*
440178 TGTAACA
66 TGTATCA
*
440185 ACTGGTCTGT
1 ACTGATCTGT
440195 GANNNNNNNN
Statistics
Matches: 428, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
71 1 0.00
72 427 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (72 bp):
ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT
TGTATCA
Found at i:440102 original size:16 final size:16
Alignment explanation
Indices: 440081--440111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
440071 TTATCAATCA
440081 ATCTACCATTCTATCT
1 ATCTACCATTCTATCT
*
440097 ATCTACCATTGTATC
1 ATCTACCATTCTATC
440112 AACTGGTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (16 bp):
ATCTACCATTCTATCT
Found at i:447692 original size:8 final size:8
Alignment explanation
Indices: 447666--447708 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
447656 CACCTTGTCC
*
447666 GTCCGTCC
1 GTCCGTCT
447674 GTCCGTCT
1 GTCCGTCT
*
447682 GTCCGTAT
1 GTCCGTCT
*
447690 GTCTGTCT
1 GTCCGTCT
447698 GTCCGTCT
1 GTCCGTCT
447706 GTC
1 GTC
447709 TGTGCAATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.02, C:0.35, G:0.26, T:0.37
Consensus pattern (8 bp):
GTCCGTCT
Found at i:447705 original size:12 final size:12
Alignment explanation
Indices: 447661--447711 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
447651 GGAATCACCT
*
447661 TGTCCGTCCGTC
1 TGTCCGTCTGTC
*
447673 CGTCCGTCTGTC
1 TGTCCGTCTGTC
* **
447685 CGTATGTCTGTC
1 TGTCCGTCTGTC
447697 TGTCCGTCTGTC
1 TGTCCGTCTGTC
447709 TGT
1 TGT
447712 GCAATCATGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.02, C:0.33, G:0.25, T:0.39
Consensus pattern (12 bp):
TGTCCGTCTGTC
Found at i:447983 original size:146 final size:146
Alignment explanation
Indices: 447719--447986 Score: 414
Period size: 146 Copynumber: 1.8 Consensus size: 146
447709 TGTGCAATCA
*
447719 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGCTTA
1 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA
* * * *
447784 TGACCTAAGGGTGTGTCATGACCTTGACGCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGA
66 TGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGAGAAAGGTCAAGGTCACTGGCAGA
447849 AAAAGTGCAAAATTTG
131 AAAAGTGCAAAATTTG
* * *
447865 TGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTAGTTCACACAAAGATTGATTA
1 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA
* *
447930 TGA-TTAAAGGATGTGTCATGACCTTGACCCAAGGTCAATT-GAGAAAGTTCAAGGTCA
66 TGACCT-AAGGATGTGTCATGACCTTGACCCAAGGTC-ATTCGAGAAAGGTCAAGGTCA
447987 TTGTTTCAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
145 1 0.01
146 106 0.96
147 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (146 bp):
TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA
TGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGAGAAAGGTCAAGGTCACTGGCAGA
AAAAGTGCAAAATTTG
Found at i:477736 original size:15 final size:15
Alignment explanation
Indices: 477716--477745 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
477706 TGATACAATG
477716 TTGTATCAAATGATA
1 TTGTATCAAATGATA
*
477731 TTGTATCATATGATA
1 TTGTATCAAATGATA
477746 CAATATCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (15 bp):
TTGTATCAAATGATA
Done.