Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 37 of 250
Found at i:11138607 original size:40 final size:40
Alignment explanation
Indices: 11138530--11138608 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
11138520 AATTCATTGC
* * * * *
11138530 TTCAGTAATTTCACAGTTCAATGCAGTAGACATAACAATA
1 TTCAATAACTTCACAATTCAATGCAGTACACAAAACAATA
* *
11138570 TTCAATAACTTCACAATTCAATTCAGTACTCAAAACAAT
1 TTCAATAACTTCACAATTCAATGCAGTACACAAAACAAT
11138609 TCTATAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (40 bp):
TTCAATAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:11142307 original size:4 final size:4
Alignment explanation
Indices: 11142300--11142324 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11142290 GTTTCTTTCT
11142300 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
11142325 GCTTTAGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:11149217 original size:13 final size:12
Alignment explanation
Indices: 11149201--11149265 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 12
11149191 TTCCTGACCA
11149201 TTCTTCCTTTTTC
1 TTCTT-CTTTTTC
11149214 TTCTT-TCTTTTC
1 TTCTTCT-TTTTC
11149226 TTCTT-TTTTTC
1 TTCTTCTTTTTC
*
11149237 -TC-TCTTTATC
1 TTCTTCTTTTTC
**
11149247 AACTTC-TTTTC
1 TTCTTCTTTTTC
11149258 TTCTTCTT
1 TTCTTCTT
11149266 GTCTGTCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
9 1 0.02
10 7 0.17
11 15 0.36
12 14 0.33
13 5 0.12
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:11149226 original size:12 final size:11
Alignment explanation
Indices: 11149208--11149243 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
11149198 CCATTCTTCC
11149208 TTTTTCTTCTT
1 TTTTTCTTCTT
11149219 TCTTTTCTTCTT
1 T-TTTTCTTCTT
11149231 TTTTTCTCTCTT
1 TTTTTCT-TCTT
11149243 T
1 T
11149244 ATCAACTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:11149226 original size:22 final size:20
Alignment explanation
Indices: 11149201--11149243 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
11149191 TTCCTGACCA
*
11149201 TTCTTCCTTTTTCTTCTTTCTT
1 TTCTT-CTTTTT-TTCTCTCTT
11149223 TTCTTCTTTTTTTCTCTCTT
1 TTCTTCTTTTTTTCTCTCTT
11149243 T
1 T
11149244 ATCAACTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCTTCTTTTTTTCTCTCTT
Found at i:11150492 original size:27 final size:26
Alignment explanation
Indices: 11150453--11150562 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 26
11150443 GGAAGCGTCT
*
11150453 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
11150480 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
11150507 TGGTGGCTCTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
* * *
11150535 TGGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
11150561 TG
1 TG
11150563 ACAGCCATGC
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.69
28 17 0.23
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:11150556 original size:54 final size:54
Alignment explanation
Indices: 11150453--11150562 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
11150443 GGAAGCGTCT
*
11150453 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
* * *
11150507 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTC
11150561 TG
1 TG
11150563 ACAGCCATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
Found at i:11152697 original size:18 final size:18
Alignment explanation
Indices: 11152674--11152710 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11152664 AAGCTTCAAA
11152674 TATTGAAGGTTATTGACC
1 TATTGAAGGTTATTGACC
11152692 TATTGAAGGTTATTGACC
1 TATTGAAGGTTATTGACC
11152710 T
1 T
11152711 TTGTATGTAA
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:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (18 bp):
TATTGAAGGTTATTGACC
Found at i:11155749 original size:91 final size:91
Alignment explanation
Indices: 11155590--11155759 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 91
11155580 AACTGGTAGT
* * * * *
11155590 TCATATGCTCGACCACTGGTTTCTCCACAACATATTAGCAACTTCTATCTGCACAAATGAATGGT
1 TCATATGCTCAACAACTGGTTTATCCACAACATATTAGCAACTTCTATCTACACAAATGAATGAT
11155655 TCATCCACCAATATTCTAGTTGACAA
66 TCATCCACCAATATTCTAGTTGACAA
* * * * *
11155681 TCATATGCTCAACAAGTGGTTTATCCACAACATATTAGCAACTTTTATCTACATAGATGGATGAT
1 TCATATGCTCAACAACTGGTTTATCCACAACATATTAGCAACTTCTATCTACACAAATGAATGAT
11155746 TCATCCACCAATAT
66 TCATCCACCAATAT
11155760 ATTTATCATT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 69 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (91 bp):
TCATATGCTCAACAACTGGTTTATCCACAACATATTAGCAACTTCTATCTACACAAATGAATGAT
TCATCCACCAATATTCTAGTTGACAA
Found at i:11163725 original size:93 final size:93
Alignment explanation
Indices: 11163611--11163782 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
11163601 CGCCCATAAG
*
11163611 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTAAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
11163676 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
11163704 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
11163769 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
11163783 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:11163779 original size:46 final size:46
Alignment explanation
Indices: 11163604--11163779 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
11163594 TGTAACCCGC
* *
11163604 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
** *
11163650 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
11163700 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
11163743 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
11163780 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 28 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:11171280 original size:93 final size:93
Alignment explanation
Indices: 11171167--11171338 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
11171157 CGCCCATAAG
* *
11171167 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
11171232 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
11171260 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
11171325 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
11171339 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:11171335 original size:46 final size:46
Alignment explanation
Indices: 11171160--11171335 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
11171150 TGTAACCCGC
* * *
11171160 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
11171206 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
11171256 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
11171299 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
11171336 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:11172790 original size:13 final size:13
Alignment explanation
Indices: 11172772--11172803 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
11172762 CATATAGGCA
11172772 TGTGGCCAGCCCG
1 TGTGGCCAGCCCG
11172785 TGTGGCCAGCCCG
1 TGTGGCCAGCCCG
11172798 TGTGGC
1 TGTGGC
11172804 TCACGCGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.34, G:0.41, T:0.19
Consensus pattern (13 bp):
TGTGGCCAGCCCG
Found at i:11174621 original size:46 final size:45
Alignment explanation
Indices: 11174475--11174644 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
11174465 AACCCGCCCC
* * *
11174475 TAAGTGAACTCGACTCAACTCAAC-AGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
11174519 TAAGTGAACTCGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
11174566 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCA
11174611 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGA
11174645 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 25 0.24
45 8 0.08
46 35 0.34
47 24 0.23
48 1 0.01
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:11176456 original size:15 final size:15
Alignment explanation
Indices: 11176420--11176448 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11176410 TTGTGTGTTC
11176420 TTTA-TTTTTATTTT
1 TTTATTTTTTATTTT
11176434 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
11176449 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:11179141 original size:49 final size:49
Alignment explanation
Indices: 11179027--11179202 Score: 262
Period size: 49 Copynumber: 3.6 Consensus size: 49
11179017 TGTGAAGTCG
* * * * **
11179027 CATGTGTAGTACTAAATGCAGGCTACTACGCGTATCAGATGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCA
*
11179077 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA
*
11179126 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA
*
11179175 CATGTGTAGTACTATGTGCAGGCTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTA
11179203 TGCGTACCAG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 79 0.68
50 37 0.32
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA
Found at i:11188128 original size:23 final size:22
Alignment explanation
Indices: 11188088--11188130 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11188078 TTGAGAAAAA
*
11188088 ATTAATTTTCTATTATATTTAG
1 ATTAATTTTCTATAATATTTAG
*
11188110 ATTAATTTTTTATGAATATTT
1 ATTAATTTTCTAT-AATATTT
11188131 TATTGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTAATTTTCTATAATATTTAG
Found at i:11198940 original size:143 final size:143
Alignment explanation
Indices: 11198682--11198996 Score: 542
Period size: 143 Copynumber: 2.2 Consensus size: 143
11198672 ATAGCTTGTT
* *
11198682 TAATTTGT-CTAAGCTTAGGACACTTTAAATGCATGTATTAATTCAGACACATTGATTCTATATA
1 TAATTTGTCCTAA-CTAAAGACACTTTAAATGCATGTATTAATTCAGACACATTGATTCTATATA
* *
11198746 CTTACTAGGACACATTAAAACATGTCATAGATTAAGACAACAAATTAAATTCGGCTAGAATTAAT
65 CTTACTAAGACACATTAAAACATGTCATAGATTAAGAAAACAAATTAAATTCGGCTAGAATTAAT
11198811 TTTTATCATGAAAC
130 TTTTATCATGAAAC
*
11198825 TAATTTGTCCTAACTAAAGACACTTTAAATGCATGTATTAATTCAGACACATTGATTCTATGTAC
1 TAATTTGTCCTAACTAAAGACACTTTAAATGCATGTATTAATTCAGACACATTGATTCTATATAC
11198890 TTACTAAGACACATTAAAACATGTCATAGATTAAGAAAACAAATTAAATTCGGCTAGAATTAATT
66 TTACTAAGACACATTAAAACATGTCATAGATTAAGAAAACAAATTAAATTCGGCTAGAATTAATT
* *
11198955 TTTATCATGGAAT
131 TTTATCATGAAAC
*
11198968 TAATTTGTCCTAACTAAAGACACATTAAA
1 TAATTTGTCCTAACTAAAGACACTTTAAA
11198997 CTTTAATTAA
Statistics
Matches: 163, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
143 159 0.98
144 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (143 bp):
TAATTTGTCCTAACTAAAGACACTTTAAATGCATGTATTAATTCAGACACATTGATTCTATATAC
TTACTAAGACACATTAAAACATGTCATAGATTAAGAAAACAAATTAAATTCGGCTAGAATTAATT
TTTATCATGAAAC
Found at i:11207603 original size:46 final size:45
Alignment explanation
Indices: 11207550--11207725 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
11207540 TGGTTGAGCA
11207550 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
11207596 TCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
11207643 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
11207689 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11207726 GCGGGTTCAT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11207706 original size:93 final size:93
Alignment explanation
Indices: 11207547--11207717 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
11207537 GGATGGTTGA
* * *
11207547 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11207612 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
11207640 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11207705 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
11207718 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:11210703 original size:15 final size:15
Alignment explanation
Indices: 11210666--11210734 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
11210656 ATCTTGGGTT
* *
11210666 TCTTTATCCTAGATC
1 TCTTTATTCTGGATC
11210681 TCTTTATTCTGGATC
1 TCTTTATTCTGGATC
* *
11210696 TCTTTATTCTGGGTT
1 TCTTTATTCTGGATC
* *
11210711 TCTCTA-TCTTGGATT
1 TCTTTATTC-TGGATC
11210726 TCTTTATTC
1 TCTTTATTC
11210735 GGTTTTCTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.12, T:0.55
Consensus pattern (15 bp):
TCTTTATTCTGGATC
Found at i:11213184 original size:46 final size:45
Alignment explanation
Indices: 11213134--11213309 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
11213124 TGGTTGAGCA
11213134 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
11213180 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
11213227 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
11213273 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11213310 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11213290 original size:93 final size:93
Alignment explanation
Indices: 11213131--11213301 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
11213121 GGATGGTTGA
* *
11213131 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11213196 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
11213224 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11213289 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
11213302 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:11218340 original size:21 final size:21
Alignment explanation
Indices: 11218316--11218358 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11218306 TATTAAATAA
11218316 AAAAATATAATAGATTATATG
1 AAAAATATAATAGATTATATG
** *
11218337 AAAAATATTTTATATTATATG
1 AAAAATATAATAGATTATATG
11218358 A
1 A
11218359 TATTTGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATATAATAGATTATATG
Found at i:11225010 original size:17 final size:18
Alignment explanation
Indices: 11224990--11225023 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11224980 ATTATTTCTC
11224990 TTTTTATTTTTT-TTTTA
1 TTTTTATTTTTTATTTTA
11225007 TTTTTATTTTTTATTTT
1 TTTTTATTTTTTATTTT
11225024 TCATTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTATTTTTTATTTTA
Found at i:11226965 original size:23 final size:22
Alignment explanation
Indices: 11226923--11226967 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
11226913 AAATAAGTCA
* *
11226923 AGTATAATAATATAATATAAAT
1 AGTATAATAATAAAAGATAAAT
11226945 AGTATATATAATAAAAGATAAAT
1 AGTATA-ATAATAAAAGATAAAT
11226968 TTTTTATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
AGTATAATAATAAAAGATAAAT
Found at i:11227093 original size:26 final size:26
Alignment explanation
Indices: 11227034--11227095 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
11227024 CCAATTTTAA
* *
11227034 AAATTATATAATAAGTAATTTAAAAT
1 AAATAATATAATAAGTAATATAAAAT
*
11227060 AAACAATATAATAA-T-ATATAAATAT
1 AAATAATATAATAAGTAATATAAA-AT
11227085 GAAATAATATA
1 -AAATAATATA
11227096 GGAAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 6 0.20
25 3 0.10
26 21 0.70
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
AAATAATATAATAAGTAATATAAAAT
Found at i:11227233 original size:15 final size:16
Alignment explanation
Indices: 11227209--11227259 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
11227199 TATATAGTAA
*
11227209 AATATAATATGTAATA-
1 AATAT-ATATGAAATAG
11227225 AATATATAT-AAATAG
1 AATATATATGAAATAG
*
11227240 AATATA-ATGAAATAT
1 AATATATATGAAATAG
11227255 AATAT
1 AATAT
11227260 GATAAGGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.19
15 20 0.65
16 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
AATATATATGAAATAG
Found at i:11227387 original size:35 final size:40
Alignment explanation
Indices: 11227307--11227387 Score: 91
Period size: 41 Copynumber: 2.1 Consensus size: 40
11227297 AGTATTCTAC
* * *
11227307 ATATAAAAATACAGTAACATAAATAGTATATAATATATTAC
1 ATATAAAAAAACAG-AACATAAATAGTATATAATATATAAA
11227348 ATATAAAAAAACAG-A-ATAAATA-TATAT-ATA-ATAAA
1 ATATAAAAAAACAGAACATAAATAGTATATAATATATAAA
11227383 ATATA
1 ATATA
11227388 TAATAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 8 0.22
36 3 0.08
37 5 0.14
38 7 0.19
39 1 0.03
41 13 0.35
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.30
Consensus pattern (40 bp):
ATATAAAAAAACAGAACATAAATAGTATATAATATATAAA
Found at i:11244098 original size:53 final size:52
Alignment explanation
Indices: 11244035--11244186 Score: 189
Period size: 53 Copynumber: 2.9 Consensus size: 52
11244025 GTATTTTTCA
* * *
11244035 ATTTGTAAGACACAATACTGTCAGTCTTGAACAAAATTGTTTAATTATCTTTT
1 ATTTGTAAGACACAATATTGTC-GTCTTGAACAAAATAGTTTAATTATCTATT
* * *
11244088 ATTTGTAAGACAGAATGTTGTCGGTCTTGAACAAAATCA-TTTAATTATGTATT
1 ATTTGTAAGACACAATATTGTC-GTCTTGAACAAAAT-AGTTTAATTATCTATT
* *
11244141 ATTTGCAAGACCCAATATTGTCGATCTTGAACAAAATAGTTTAATT
1 ATTTGTAAGACACAATATTGTCG-TCTTGAACAAAATAGTTTAATT
11244187 TTTTTTTTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.02
53 83 0.98
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (52 bp):
ATTTGTAAGACACAATATTGTCGTCTTGAACAAAATAGTTTAATTATCTATT
Found at i:11248403 original size:20 final size:20
Alignment explanation
Indices: 11248380--11248417 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11248370 TCAATTTTAA
* *
11248380 TTTTAAATTTAAAAAATCAC
1 TTTTAAACTAAAAAAATCAC
11248400 TTTTAAACTAAAAAAATC
1 TTTTAAACTAAAAAAATC
11248418 TGACATTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTTAAACTAAAAAAATCAC
Found at i:11255265 original size:14 final size:14
Alignment explanation
Indices: 11255246--11255290 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
11255236 ACAAAAGGGG
11255246 AAAAAAGA-AAAGA
1 AAAAAAGAGAAAGA
11255259 AAGAAAAGAGAAAGA
1 AA-AAAAGAGAAAGA
*
11255274 AAAAAAG-GAAGGA
1 AAAAAAGAGAAAGA
11255287 AAAA
1 AAAA
11255291 CAAAAAGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 11 0.38
14 11 0.38
15 7 0.24
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAGA
Found at i:11255265 original size:15 final size:15
Alignment explanation
Indices: 11255246--11255279 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11255236 ACAAAAGGGG
11255246 AAAAAAGA-AAAGAA
1 AAAAAAGAGAAAGAA
*
11255260 AGAAAAGAGAAAGAA
1 AAAAAAGAGAAAGAA
11255275 AAAAA
1 AAAAA
11255280 GGAAGGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAAGAA
Found at i:11255270 original size:16 final size:15
Alignment explanation
Indices: 11255248--11255280 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
11255238 AAAAGGGGAA
11255248 AAAAGA-AAAGAAAG
1 AAAAGAGAAAGAAAG
11255262 AAAAGAGAAAGAAA-
1 AAAAGAGAAAGAAAG
11255276 AAAAG
1 AAAAG
11255281 GAAGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAGAAAG
Found at i:11255279 original size:23 final size:24
Alignment explanation
Indices: 11255245--11255289 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
11255235 AACAAAAGGG
11255245 GAAAAAAGAAAA-GAAAGAAAAGA
1 GAAAAAAGAAAAGGAAAGAAAAGA
*
11255268 GAAAGAAA-AAAAGGAAGGAAAA
1 GAAA-AAAGAAAAGGAAAGAAAA
11255290 ACAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAAAGGAAAGAAAAGA
Found at i:11257408 original size:15 final size:15
Alignment explanation
Indices: 11257388--11257417 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11257378 CATTTTATTT
*
11257388 ATATTAGGATAATTA
1 ATATTAAGATAATTA
11257403 ATATTAAGATAATTA
1 ATATTAAGATAATTA
11257418 TTAGGATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:11257461 original size:10 final size:10
Alignment explanation
Indices: 11257442--11257473 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
11257432 ATTTAGGATT
11257442 TTAT-TTTAA
1 TTATCTTTAA
11257451 TTATCTTTAA
1 TTATCTTTAA
11257461 TTATCTTTAA
1 TTATCTTTAA
11257471 TTA
1 TTA
11257474 AATATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:11264793 original size:99 final size:99
Alignment explanation
Indices: 11264617--11264813 Score: 290
Period size: 99 Copynumber: 2.0 Consensus size: 99
11264607 TAATTTCTAA
* *
11264617 GAATGTGTTGGGCTGAGTAACCGGGTGAGGTGCTTGGGTTGTCATCTCTCTTCGCTTCAAAAGGT
1 GAATGTGCTGGGCTGAGTAACCGGGTGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGGT
* * *
11264682 TCGATATGTTCCT-AGGAATAATAAAAAAATTAG
66 ACGATATATTCCTAAGGAAAAATAAAAAAATTAG
*
11264715 GAATGTGCTGGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGG
1 GAATGTGCTGGGCTGAGTAACC-GGGTGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGG
* *
11264780 TAC-AGTATATTCCTAAGTAAAAATAAATAAATTA
65 TACGA-TATATTCCTAAGGAAAAATAAAAAAATTA
11264814 AATTAAAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 22 0.25
99 50 0.57
100 16 0.18
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (99 bp):
GAATGTGCTGGGCTGAGTAACCGGGTGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGGT
ACGATATATTCCTAAGGAAAAATAAAAAAATTAG
Found at i:11265442 original size:15 final size:15
Alignment explanation
Indices: 11265422--11265451 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11265412 CATTTTATTT
*
11265422 ATATTAGGATAATTA
1 ATATTAAGATAATTA
11265437 ATATTAAGATAATTA
1 ATATTAAGATAATTA
11265452 TTAGGATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:11278899 original size:19 final size:19
Alignment explanation
Indices: 11278857--11278917 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
11278847 TATATCATAT
11278857 CATATCATATCTAAGATT-
1 CATATCATATCTAAGATTG
11278875 -ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
11278893 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
11278912 CATATC
1 CATATC
11278918 CTTAAAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.41
19 24 0.59
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
CATATCATATCTAAGATTG
Found at i:11279472 original size:87 final size:87
Alignment explanation
Indices: 11279308--11279472 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 87
11279298 ACAATACAGA
* *
11279308 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTGTGTCTTCG
1 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
* *
11279373 ATTTTCTCCTTGTGAACACAAG
66 ATCTGCTCCTTGTGAACACAAG
* * * * *
11279395 GATGCCAAATCATCTTGGATCTGCTTCAGTA-AAATCATC-TGAAGGTCAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAA-CA-CGTGAAAGCCAAATCTGCTATGTCTT
* *
11279458 TAATCTGCTTCTTGT
64 CAATCTGCTCCTTGT
11279473 AAACTTATGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.05
87 61 0.94
88 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (87 bp):
GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
ATCTGCTCCTTGTGAACACAAG
Found at i:11279994 original size:205 final size:205
Alignment explanation
Indices: 11279546--11280294 Score: 1177
Period size: 205 Copynumber: 3.7 Consensus size: 205
11279536 CTGTTTCTTT
11279546 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
1 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
*
11279611 AAACCAAATCAACTATGCCTTCGATTTGTTCCTTGTAAGCACAAGGATACC-AACCATCTTGGAT
66 AAACCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* * * * *
11279675 CCGTTTCAG--T---CATCTGAAGGTTAGATCTACTATGTATCTGCTCTCCGTCAAAATCGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
*
11279735 GCCAAACTTC
196 GCCAGACTTC
* *
11279745 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
* * * *
11279810 AAGCTAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTTGAT
66 AAACCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
* *
11279875 CTACTTCAGTATAAACATCTGAAGGTTAGATCTGTTATGTATCTGCTCTCCGTCGAAATGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
*
11279940 GGCAGACTTC
196 GCCAGACTTC
* * * *
11279950 GATTTGTTCTCTGACAATACAGAGATGCCAAATCAACTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
* * * *
11280015 AAGCCAAATTAGCTATGTCTTCGATTTGTTCATTGTAAGCACAAGGATACCAAACCATCTTGGAT
66 AAACCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
11280080 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
11280145 GCCAGACTTC
196 GCCAGACTTC
* *
11280155 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATTTTAGATTTGCTTCAGCGTAAGCACGCGA
1 GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
* * * *
11280220 AAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGGT
66 AAACCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
11280285 CTTGCTTCAG
131 C-TGCTTCAG
11280295 CCAGATCTGC
Statistics
Matches: 506, Mismatches: 37, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
199 110 0.22
200 18 0.04
202 1 0.00
205 369 0.73
206 8 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (205 bp):
GATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGCGA
AAACCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
GCCAGACTTC
Found at i:11285268 original size:20 final size:20
Alignment explanation
Indices: 11285243--11285288 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11285233 ATTGGGCCTT
11285243 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
11285263 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
11285282 GCCCATA
1 GCCCATA
11285289 ACAGAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:11285921 original size:16 final size:16
Alignment explanation
Indices: 11285900--11285930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11285890 TACAAATGCC
11285900 GGCTTTTCGACTTTTT
1 GGCTTTTCGACTTTTT
*
11285916 GGCTTTTCGGCTTTT
1 GGCTTTTCGACTTTT
11285931 ACCGATCTAG
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:0.03, C:0.19, G:0.23, T:0.55
Consensus pattern (16 bp):
GGCTTTTCGACTTTTT
Found at i:11287712 original size:15 final size:15
Alignment explanation
Indices: 11287675--11287703 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11287665 TTTTTCTATC
11287675 TAATAATAATAATTA
1 TAATAATAATAATTA
11287690 TAATAATAATAATT
1 TAATAATAATAATT
11287704 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:11297843 original size:40 final size:40
Alignment explanation
Indices: 11297696--11298025 Score: 173
Period size: 40 Copynumber: 8.4 Consensus size: 40
11297686 CAAATCAAGT
* * * *
11297696 ATTAGCGGTG-TTTTT-CAAAAAGCGTCGCTGTAGATTGAGC
1 ATTAGCGGCGCTTTTTAAAAAAAGC--CGCTATAGATCGAGC
* ** * *
11297736 ATTAGCGGCGCTTTTTGAAAATTGCCTCTATAGATTGAGC
1 ATTAGCGGCGCTTTTTAAAAAAAGCCGCTATAGATCGAGC
* * * *
11297776 ATTAGTGGAGCTTTTCAAAAAATGCCGCTATAGATCGAGC
1 ATTAGCGGCGCTTTTTAAAAAAAGCCGCTATAGATCGAGC
* * * **
11297816 ATTAGCGGCGCTTTTTAAAAAAAGCCGCAAAAAAATTAAGC
1 ATTAGCGGCGCTTTTTAAAAAAAGCCGC-TATAGATCGAGC
* * * * **** * *
11297857 A-CAACGTCGTCGTTTT--ATGTTG-AGCTTTAG-T-G-GC
1 ATTAGCGGCG-CTTTTTAAAAAAAGCCGCTATAGATCGAGC
11297891 ATTAGCGGCGC-TTTTAGAAAAACA-CCGCTATAGATCGAGC
1 ATTAGCGGCGCTTTTTA-AAAAA-AGCCGCTATAGATCGAGC
* * *
11297931 ATTAGCGGTGCTTTTTGAAAAACA-TCGCTATAGATCGAGC
1 ATTAGCGGCGCTTTTT-AAAAAAAGCCGCTATAGATCGAGC
* * ** *
11297971 ATTA-CTGGCACTTTTTAAAAAACGCCGCTATAGGCCGACC
1 ATTAGC-GGCGCTTTTTAAAAAAAGCCGCTATAGATCGAGC
11298011 ATTAGCGGCGCTTTT
1 ATTAGCGGCGCTTTT
11298026 CACAAAACGC
Statistics
Matches: 215, Mismatches: 57, Indels: 36
0.70 0.19 0.12
Matches are distributed among these distances:
33 4 0.02
34 4 0.02
35 5 0.02
36 2 0.01
37 7 0.03
38 3 0.01
39 9 0.04
40 148 0.69
41 27 0.13
42 6 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTTAAAAAAAGCCGCTATAGATCGAGC
Found at i:11298040 original size:195 final size:196
Alignment explanation
Indices: 11297721--11298159 Score: 587
Period size: 196 Copynumber: 2.2 Consensus size: 196
11297711 CAAAAAGCGT
* * *** * * *
11297721 CGCTGTAGATTGAGCATTAGCGGCGCTTTTTGAAAATTGCCTCTATAGATTGAGCATTAGTGGAG
1 CGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTACTGGAG
* * * *
11297786 CTTTTCAAAAAATGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAAAAGCCGC-AAAAAA
66 CTTTTCAAAAAACGCCGCTATAGACCGACCATTAGCGGCGCTTTTCAAAAAAAGCCGCAAAAAAA
*
11297850 ATTAAGCACAACG-TCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTAGAAAAAC
131 ATTAAGCACAACGCT-GTCGTTTTATGTTGAGCTTTAGTGGCATTAACGGCGCTTTTAGAAAAAC
11297914 AC
195 AC
* *
11297916 CGCTATAGATCGAGCATTAGCGGTGCTTTTTGAAAAACATCGCTATAGATCGAGCATTACTGGCA
1 CGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTACTGG-A
* * * *
11297981 -CTTTTTAAAAAACGCCGCTATAGGCCGACCATTAGCGGCGCTTTTCACAAAACGCCGCAAAAAA
65 GCTTTTCAAAAAACGCCGCTATAGACCGACCATTAGCGGCGCTTTTCAAAAAAAGCCGCAAAAAA
* * * *
11298045 AATTAAGCACAGCGCTGTCGTTTTATGTTGAGCTTTAGTGGCATTAATGGCGCTTTTTGAAAAAT
130 AATTAAGCACAACGCTGTCGTTTTATGTTGAGCTTTAGTGGCATTAACGGCGCTTTTAGAAAAAC
*
11298110 GC
195 AC
*** *
11298112 CGCTATAGATCGAGCATTAGCGGCGCTTTGAAAAAAACGCCGCTATAG
1 CGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCTATAG
11298160 GCCAATCATT
Statistics
Matches: 211, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
195 103 0.49
196 107 0.51
197 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (196 bp):
CGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTACTGGAG
CTTTTCAAAAAACGCCGCTATAGACCGACCATTAGCGGCGCTTTTCAAAAAAAGCCGCAAAAAAA
ATTAAGCACAACGCTGTCGTTTTATGTTGAGCTTTAGTGGCATTAACGGCGCTTTTAGAAAAACA
C
Found at i:11298188 original size:40 final size:40
Alignment explanation
Indices: 11298093--11298192 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
11298083 TGGCATTAAT
* * *
11298093 GGCGCTTTTTGAAAAATGCCGCTATAGATCGAGCATTAGC
1 GGCGCTTTTTGAAAAACGCCGCTATAGACCAAGCATTAGC
*** * *
11298133 GGCGCTTTGAAAAAAACGCCGCTATAGGCCAATCATTAGC
1 GGCGCTTTTTGAAAAACGCCGCTATAGACCAAGCATTAGC
*
11298173 GGTGCTTTTTGAAAAACGCC
1 GGCGCTTTTTGAAAAACGCC
11298193 ACAGAAAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (40 bp):
GGCGCTTTTTGAAAAACGCCGCTATAGACCAAGCATTAGC
Found at i:11298278 original size:155 final size:156
Alignment explanation
Indices: 11297932--11298295 Score: 468
Period size: 155 Copynumber: 2.3 Consensus size: 156
11297922 AGATCGAGCA
** **
11297932 TTAGCGGTGCTTTTTGAAAAACATCGCTATAGATCGAGCATTA-CTGGCACTTTTTAAAAAACGC
1 TTAGC-GTGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGC-GGCACTTTGAAAAAAACGC
* * * *
11297996 CGCTATAGGCCGACCATTAGCGGCGCTTTTCACAAAACGCCGCAAAAAAAATTAAGCACAGCGCT
64 CGCTATAGGCCAACCATTAGCGGCGCTTTTCACAAAACGCCACAAAAAAAATTAAGCACAACGCC
* *
11298061 GTCGTTTTATGTTGAGCTTTAGTGGCAT
129 ATCATTTTATGTTGAGCTTTAGTGGCAT
* * * *
11298089 TAATG-GCGCTTTTTGAAAAATGCCGCTATAGATCGAGCATTAGCGGCGCTTTGAAAAAAACGCC
1 TTA-GCGTGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCACTTTGAAAAAAACGCC
* * * *
11298153 GCTATAGGCCAATCATTAGCGGTGCTTTTTGA-AAAACGCCAC-AGAAAAATTAAGCACAACGCC
65 GCTATAGGCCAACCATTAGCGGCGC-TTTTCACAAAACGCCACAAAAAAAATTAAGCACAACGCC
11298216 ATCATTTTATGTTGAGCTTTAGT-GCAT
129 ATCATTTTATGTTGAGCTTTAGTGGCAT
* *
11298243 TTAGCAGTGCTTTTTGAAAAACGCCGCTATAGATCGAGCTTTAGTGGCACTTT
1 TTAGC-GTGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCACTTT
11298296 ATCACGCCGC
Statistics
Matches: 178, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
153 1 0.01
154 6 0.03
155 81 0.46
156 81 0.46
157 8 0.04
158 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (156 bp):
TTAGCGTGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCACTTTGAAAAAAACGCCG
CTATAGGCCAACCATTAGCGGCGCTTTTCACAAAACGCCACAAAAAAAATTAAGCACAACGCCAT
CATTTTATGTTGAGCTTTAGTGGCAT
Found at i:11299147 original size:17 final size:18
Alignment explanation
Indices: 11299125--11299158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11299115 TACTAATTTT
11299125 AATATA-TTAAAATTATC
1 AATATAGTTAAAATTATC
*
11299142 AATATAGTTTAAATTAT
1 AATATAGTTAAAATTAT
11299159 TTAAGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATAGTTAAAATTATC
Found at i:11299541 original size:40 final size:40
Alignment explanation
Indices: 11299497--11299580 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
11299487 AAAATTATAA
* * * *
11299497 AAAAGTCAAGCATTAGCGGTGTTTATGATAAAAACGCCAC
1 AAAAGACAAGCAATAGCAGCGTTTATGATAAAAACGCCAC
*
11299537 AAAAGACAAGTAATAGCAGCGTTTATGATAAAAACGCCAC
1 AAAAGACAAGCAATAGCAGCGTTTATGATAAAAACGCCAC
11299577 AAAA
1 AAAA
11299581 AATCAAGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (40 bp):
AAAAGACAAGCAATAGCAGCGTTTATGATAAAAACGCCAC
Found at i:11300260 original size:34 final size:35
Alignment explanation
Indices: 11300184--11300262 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
11300174 AAGAAGTTAG
*
11300184 TCATTTTAATTTATACATTTTTTTAAGGAAAACAA
1 TCATTCTAATTTATACATTTTTTTAAGGAAAACAA
11300219 TCATTCTAATTTATACATTTTTTTAAGGAAAACAA
1 TCATTCTAATTTATACATTTTTTTAAGGAAAACAA
*
11300254 T-GTTCTAAT
1 TCATTCTAAT
11300263 ATAATCTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 7 0.17
35 35 0.83
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (35 bp):
TCATTCTAATTTATACATTTTTTTAAGGAAAACAA
Found at i:11302510 original size:29 final size:29
Alignment explanation
Indices: 11302466--11302541 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
11302456 ATGACGGTAT
*
11302466 AAAGTAAAAGTAAGTTAATTTTATTTTTAA
1 AAAGTAAGA-TAAGTTAATTTTATTTTTAA
*
11302496 TAAGTAAGATAAGTTAATTTTATTTTTAA
1 AAAGTAAGATAAGTTAATTTTATTTTTAA
*
11302525 AAAGTAAGATAATTTAA
1 AAAGTAAGATAAGTTAA
11302542 ATGATATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (29 bp):
AAAGTAAGATAAGTTAATTTTATTTTTAA
Found at i:11302602 original size:18 final size:18
Alignment explanation
Indices: 11302579--11302624 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
11302569 ATATATGAAA
*
11302579 TATTAATTTAAATGTAAG
1 TATTAATTTAAATATAAG
*
11302597 TATTAATTTAAATATAAT
1 TATTAATTTAAATATAAG
11302615 TATTTAATTT
1 TA-TTAATTT
11302625 GATATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTAATTTAAATATAAG
Found at i:11304327 original size:25 final size:24
Alignment explanation
Indices: 11304249--11304328 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 24
11304239 AGACTTGCTG
*
11304249 TATTTTATT-TATATCTTTATATTT
1 TATTTTATTCTATATTTTTAT-TTT
* * *
11304273 AATCTAATTCT-TATTATTTA-TTT
1 TATTTTATTCTATATT-TTTATTTT
11304296 TAGTTTTGATTCTATATTTTTATTTT
1 TA-TTTT-ATTCTATATTTTTATTTT
11304322 TATTTTA
1 TATTTTA
11304329 ATATTTAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
23 4 0.09
24 12 0.28
25 18 0.42
26 9 0.21
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTTTATTCTATATTTTTATTTT
Found at i:11304725 original size:85 final size:85
Alignment explanation
Indices: 11304579--11304812 Score: 287
Period size: 85 Copynumber: 2.8 Consensus size: 85
11304569 TAAAATTTTT
* * *
11304579 TTAAAGGTCATGTTTTTTA-TCAGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG-CTTTTAGT
1 TTAAAGGTCATGTTATTTAGT-GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTC-TTTAG-
* * * *
11304642 GGA-GTTTGTGGTAAAAGCGCCG
63 CGACGTTGGTGGGAAAAGCGCCA
* * *
11304664 TTAAAAGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGTCTTTAGCGA
1 TTAAAGGTCATGTTATTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGA
11304729 CGTTGGTGGGAAAAGCGCCA
66 CGTTGGTGGGAAAAGCGCCA
* * *
11304749 CTAAAGGTCATGTTATTTAGCGGCGTTTGTGGG-AAAGCGCCTCTAAAGGTCATGTTCTTTAGCG
1 TTAAAGGTCATGTTATTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG-TCTTTAGCG
11304813 GCATTTTTTT
Statistics
Matches: 130, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
84 21 0.16
85 107 0.82
86 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (85 bp):
TTAAAGGTCATGTTATTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGA
CGTTGGTGGGAAAAGCGCCA
Found at i:11304811 original size:42 final size:43
Alignment explanation
Indices: 11304580--11304814 Score: 282
Period size: 42 Copynumber: 5.5 Consensus size: 43
11304570 AAAATTTTTT
* * *
11304580 TAAAGGTCATGTTTTTTATCAGCGTTTGTGGGAAAAGCGCCGT-
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCC-TC
* * * *
11304623 TAAAGGTCATGCT-TTTAGTGGAGTTTGTGGTAAAAGCGCCGT-
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCC-TC
* * * *
11304665 TAAAAGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGCGTCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCTC
* * *
11304708 TAAAGGTCATG-TCTTTAGCGACGTTGGTGGGAAAAGCGCCAC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCTC
*
11304750 TAAAGGTCATGTTATTTAGCGGCGTTTGTGGG-AAAGCGCCTC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCTC
11304792 TAAAGGTCATGTTCTTTAGCGGC
1 TAAAGGTCATGTTCTTTAGCGGC
11304815 ATTTTTTTAC
Statistics
Matches: 166, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
42 103 0.62
43 63 0.38
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCTC
Found at i:11305080 original size:38 final size:38
Alignment explanation
Indices: 11305036--11305169 Score: 117
Period size: 38 Copynumber: 3.3 Consensus size: 38
11305026 TTTAATTTGT
*
11305036 AAATATGTTGTGCACCCACAACAAGTGGTAGTAATTGC
1 AAATATGTTGTTCACCCACAACAAGTGGTAGTAATTGC
* *
11305074 AAATATGTGGTTCGA-CCACAAACCAAGTGGCGGTTTGTTTAATTTGC
1 AAATATGTTGTTC-ACCCAC-AA-CAAGT---GG-TAG--TAA-TTGC
* *
11305121 AAATTTGTTGTTCACCCACAACAAGTGGTAATAATTGC
1 AAATATGTTGTTCACCCACAACAAGTGGTAGTAATTGC
11305159 AAATATTGTTG
1 AAATA-TGTTG
11305170 GAAAAAATTC
Statistics
Matches: 76, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
38 23 0.30
39 11 0.14
40 5 0.07
41 1 0.01
42 2 0.03
43 2 0.03
44 2 0.03
45 5 0.07
46 6 0.08
47 19 0.25
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (38 bp):
AAATATGTTGTTCACCCACAACAAGTGGTAGTAATTGC
Found at i:11305137 original size:85 final size:85
Alignment explanation
Indices: 11305009--11305164 Score: 258
Period size: 85 Copynumber: 1.8 Consensus size: 85
11304999 TTTGCTCATG
* *
11305009 AACCAAGTGACAGTTTGTTTAATTTGTAAATATGTTGTGCACCCACAACAAGTGGTAGTAATTGC
1 AACCAAGTGACAGTTTGTTTAATTTGCAAATATGTTGTGCACCCACAACAAGTGGTAATAATTGC
11305074 AAATATGTGGTTCGACCACA
66 AAATATGTGGTTCGACCACA
* * * *
11305094 AACCAAGTGGCGGTTTGTTTAATTTGCAAATTTGTTGTTCACCCACAACAAGTGGTAATAATTGC
1 AACCAAGTGACAGTTTGTTTAATTTGCAAATATGTTGTGCACCCACAACAAGTGGTAATAATTGC
11305159 AAATAT
66 AAATAT
11305165 TGTTGGAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (85 bp):
AACCAAGTGACAGTTTGTTTAATTTGCAAATATGTTGTGCACCCACAACAAGTGGTAATAATTGC
AAATATGTGGTTCGACCACA
Found at i:11312336 original size:6 final size:6
Alignment explanation
Indices: 11312318--11312460 Score: 96
Period size: 6 Copynumber: 23.3 Consensus size: 6
11312308 AAGAAGCATT
* *
11312318 ATCAGA A-CTAGA ATCAGA ATCAGA ACCAGA ATCAGA ATCAGA ATTAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
11312366 ATCAGA ATTAG- TTGACAAA ATCAGA ATCAAA ATCAGT ATCAGGTA A-CAGA
1 ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * * *
11312416 ATCAAA ATCAGA ATCAGT ATTAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
11312461 GTGAATGCAA
Statistics
Matches: 104, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
5 6 0.06
6 88 0.85
7 7 0.07
8 3 0.03
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:11312391 original size:31 final size:31
Alignment explanation
Indices: 11312353--11312460 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 31
11312343 CCAGAATCAG
* * * *
11312353 AATCAGAATTAGAATCAGAATTAGTTGACAA
1 AATCAGAATCAGAATCAGTATTAGGTAACAA
* * *
11312384 AATCAGAATCAAAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGTATTAGGTAACAA
* *
11312415 AATCAAAATCAGAATCAGTATTAGGTAACAG
1 AATCAGAATCAGAATCAGTATTAGGTAACAA
*
11312446 AATCAAAATCAGAAT
1 AATCAGAATCAGAAT
11312461 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGTATTAGGTAACAA
Found at i:11312634 original size:27 final size:26
Alignment explanation
Indices: 11312592--11312693 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
11312582 GCTCAGTTAT
* *
11312592 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
11312619 CAGATATTGTGGCAGAGCCACTAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
11312645 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
11312673 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
11312694 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.11
27 51 0.77
28 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:11312676 original size:54 final size:53
Alignment explanation
Indices: 11312592--11312694 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
11312582 GCTCAGTTAT
* * * *
11312592 CAGATATTGTGACAGAGTCACCAGATACAGATATTGTGGCAGAGCCACTAGAA
1 CAGATATTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCACTAGAA
* *
11312645 CAGATATTTGTGGCATAGCCACCAGAAACAGATAATGTGGCAAAGCCACT
1 CAGATA-TTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCACT
11312695 TAACAGAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 6 0.14
54 37 0.86
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (53 bp):
CAGATATTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCACTAGAA
Found at i:11312719 original size:54 final size:54
Alignment explanation
Indices: 11312610--11312711 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
11312600 GTGACAGAGT
* * * ** *
11312610 CACCAGATACAGATATTGTGGCAGAGCCACTAGAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCAAAGC
*
11312664 CACCAGAAACAGATAATGTGGCAAAGCCACT-TAACAGA-ATACGTGGCA
1 CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCA
11312712 CAAAGCCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 8 0.19
53 6 0.14
54 28 0.67
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (54 bp):
CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCAAAGC
Found at i:11312888 original size:22 final size:22
Alignment explanation
Indices: 11312863--11312916 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
11312853 TGGCACACAA
*
11312863 CCATAATCAGGTTGACACAGAG
1 CCATAATCAGGTTGACACAAAG
*
11312885 CCAT-ATGTAGGTTGACACAAAG
1 CCATAAT-CAGGTTGACACAAAG
11312907 CCATAATCAG
1 CCATAATCAG
11312917 AAGGCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
CCATAATCAGGTTGACACAAAG
Found at i:11314732 original size:46 final size:46
Alignment explanation
Indices: 11314665--11314840 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
11314655 TGTAACCCGC
*
11314665 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * *
11314711 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCATATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC---GGAC--GTTCGCAT
* * *
11314761 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
11314804 CCATAAGTGAATTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
11314841 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 60 0.57
47 24 0.23
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:11314844 original size:93 final size:93
Alignment explanation
Indices: 11314672--11314844 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
11314662 CGCCCATAAG
* *
11314672 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
11314737 ATGAGCTCATATGCCTAGTTACATCTCA
66 ACGAGCTCAGATGCCTAGTTACATCTCA
* *
11314765 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAATTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
11314830 ACGAGTTCGGATGCC
66 ACGAGCTCAGATGCC
11314845 CAAATATCCC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCAGATGCCTAGTTACATCTCA
Found at i:11317260 original size:30 final size:30
Alignment explanation
Indices: 11317217--11317305 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
11317207 CAAATATAAC
11317217 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
11317246 GAGAAACCCAGAATAAAGAAAT-CTAGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
11317276 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
11317306 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 10 0.21
30 35 0.73
31 3 0.06
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:11317265 original size:15 final size:15
Alignment explanation
Indices: 11317217--11317296 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
11317207 CAAATATAAC
*
11317217 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
11317231 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
11317246 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
11317261 AAGAAATCTAGAATA
1 AAGAAATCCAGAATA
* *
11317276 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
11317291 AAGAAA
1 AAGAAA
11317297 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:11317305 original size:15 final size:15
Alignment explanation
Indices: 11317228--11317305 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
11317218 AGAAAACCGA
*
11317228 ATAAAGAAATCCAAG
1 ATAAAGAAACCCAAG
*
11317243 ATAGAGAAACCC-AG
1 ATAAAGAAACCCAAG
* *
11317257 AATAAAGAAA-TCTAG
1 -ATAAAGAAACCCAAG
* * *
11317272 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
11317288 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
11317303 ATA
1 ATA
11317306 CGATACTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.90
16 2 0.04
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:11318016 original size:26 final size:27
Alignment explanation
Indices: 11317977--11318171 Score: 216
Period size: 27 Copynumber: 7.3 Consensus size: 27
11317967 GATATTACAA
* *
11317977 GGTATCTCGGTAATTCCACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTATAGG
* *
11318004 GGTATTT-AGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTATAGG
11318030 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTATAGG
*
11318057 GGTATTTCGGTAATTCTACCCTATATG
1 GGTATTTCGGTAATTCTACCCTATAGG
* **
11318084 GGTATTTCGGTAATTTTA-CAAACTAGG
1 GGTATTTCGGTAATTCTACCCTA-TAGG
* * **
11318111 GGTATTTTGGTAATTTTA-CAAACTAGG
1 GGTATTTCGGTAATTCTACCCTA-TAGG
* * *
11318138 GGTATTTTGGTAATTCTATCCTACAGG
1 GGTATTTCGGTAATTCTACCCTATAGG
11318165 GGTATTT
1 GGTATTT
11318172 TAGTAATTTC
Statistics
Matches: 149, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
26 25 0.17
27 122 0.82
28 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTATAGG
Found at i:11318214 original size:27 final size:27
Alignment explanation
Indices: 11318188--11318354 Score: 208
Period size: 27 Copynumber: 6.2 Consensus size: 27
11318178 TTTCATAATT
*
11318188 GAGGGTAAAATGGTAATTTTGTAAATT
1 GAGGGTAAAATGGTAATTTTGTAAATC
*** *
11318215 GAGGGTAAAACACTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
*
11318242 GAGGGTAAAATGGTAATTTTTTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
11318269 GAGGGTAAAATGGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
* * * * *
11318296 GAGGGTGAAACGGTAATTCTATAAATT
1 GAGGGTAAAATGGTAATTTTGTAAATC
* **
11318323 GAGGGTAAAATGGTAATTCTACAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
11318350 GAGGG
1 GAGGG
11318355 CATTTCAATA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 120 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTTTGTAAATC
Found at i:11318292 original size:81 final size:81
Alignment explanation
Indices: 11318188--11318354 Score: 253
Period size: 81 Copynumber: 2.1 Consensus size: 81
11318178 TTTCATAATT
* *
11318188 GAGGGTAAAATGGTAATTTTGTAAATTGAGGGTAAAACACTAATTCTGTAAATCGAGGGTAAAAT
1 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACACTAATTCTATAAATCGAGGGTAAAAT
* **
11318253 GGTAATTTTTTAAATC
66 GGTAATTCTACAAATC
* ** *
11318269 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTATAAATTGAGGGTAAAAT
1 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACACTAATTCTATAAATCGAGGGTAAAAT
11318334 GGTAATTCTACAAATC
66 GGTAATTCTACAAATC
11318350 GAGGG
1 GAGGG
11318355 CATTTCAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (81 bp):
GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACACTAATTCTATAAATCGAGGGTAAAAT
GGTAATTCTACAAATC
Found at i:11318448 original size:27 final size:26
Alignment explanation
Indices: 11318407--11318613 Score: 216
Period size: 27 Copynumber: 7.7 Consensus size: 26
11318397 TAGAAAGTCA
* ** *
11318407 AGGGTATTTTTGTAATTTTGTAAATC
1 AGGGTATTTTGGTAATTTTACAAACC
* **
11318433 AGGGATATTTCGGTAATTTTACAAATTA
1 AGGG-TATTTTGGTAATTTTACAAA-CC
** *
11318461 AGGGTATTTCAGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
* *
11318487 AGTGGTATTTCGGTAATTTCACAAACC
1 AG-GGTATTTTGGTAATTTTACAAACC
*
11318514 AGGGGTATTTTGATAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
*
11318541 AGGGGTATTTTGGTAATTTTACAAACT
1 A-GGGTATTTTGGTAATTTTACAAACC
*
11318568 AGAGGTATTTTGGTAATTTTACAAATC
1 AG-GGTATTTTGGTAATTTTACAAACC
11318595 AGGGGTATTTTGGTAATTT
1 A-GGGTATTTTGGTAATTT
11318614 GGTAAAGTAT
Statistics
Matches: 158, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.04
27 144 0.91
28 7 0.04
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:11318496 original size:54 final size:54
Alignment explanation
Indices: 11318334--11318613 Score: 240
Period size: 54 Copynumber: 5.1 Consensus size: 54
11318324 AGGGTAAAAT
* * * * ** **
11318334 GGTAATTCTACAAATCGAGGGCATTTCAATAATTTTGTAAACCAATGGTATTTC
1 GGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTATTTC
** * ** ** * *
11318388 TATAATTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATCAGGGATATTTC
1 GGTAA-TTTTACAAA-TCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTATTTC
* * *
11318444 GGTAATTTTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTC
1 GGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTATTTC
* * * * *
11318498 GGTAATTTCACAAACCAGGGGTATTT-TGATAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAATCAAGGGTATTTCAG-TAATTTTACAAACCAGGGGTATTTC
* ** * *
11318552 GGTAATTTTACAAA-CTAGAGGTATTTTGGTAATTTTACAAATCAGGGGTATTTT
1 GGTAATTTTACAAATCAAG-GGTATTTCAGTAATTTTACAAACCAGGGGTATTTC
11318606 GGTAATTT
1 GGTAATTT
11318614 GGTAAAGTAT
Statistics
Matches: 183, Mismatches: 38, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
53 3 0.02
54 130 0.71
55 16 0.09
56 34 0.19
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (54 bp):
GGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTATTTC
Found at i:11318531 original size:81 final size:81
Alignment explanation
Indices: 11318432--11318613 Score: 238
Period size: 81 Copynumber: 2.2 Consensus size: 81
11318422 TTTTGTAAAT
* * ** *
11318432 CAGGGATATTTCGGTAATTTTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTT
1 CAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTCACAAACCAGAGGTATTT
11318497 CGGTAATTTCACAAAC
66 CGGTAATTTCACAAAC
* * ** * *
11318513 CAGGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGAGGTATTT
1 CAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTCACAAACCAGAGGTATTT
* * *
11318578 TGGTAATTTTACAAAT
66 CGGTAATTTCACAAAC
11318594 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
11318614 GGTAAAGTAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
CAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTCACAAACCAGAGGTATTT
CGGTAATTTCACAAAC
Found at i:11320131 original size:12 final size:12
Alignment explanation
Indices: 11320096--11320186 Score: 55
Period size: 12 Copynumber: 7.2 Consensus size: 12
11320086 TTTTTCTTTG
11320096 TATATTATT-TA
1 TATATTATTATA
11320107 T-TA-TATTATTA
1 TATATTATTA-TA
11320118 TATATTATTATA
1 TATATTATTATA
11320130 TAT-TGTATTACCTA
1 TATAT-TATTA--TA
* *
11320144 CATTTTATTATATA
1 TATATTA-T-TATA
*
11320158 TATATTATTTTA
1 TATATTATTATA
11320170 TATATTACTTATCA
1 TATATTA-TTAT-A
11320184 TAT
1 TAT
11320187 TGCTTATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
9 4 0.06
10 2 0.03
11 5 0.08
12 22 0.35
13 9 0.14
14 17 0.27
15 2 0.03
16 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (12 bp):
TATATTATTATA
Found at i:11329463 original size:26 final size:26
Alignment explanation
Indices: 11329428--11329479 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11329418 AATGTGAAAG
*
11329428 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11329454 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11329480 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:11329603 original size:105 final size:104
Alignment explanation
Indices: 11329351--11329780 Score: 712
Period size: 104 Copynumber: 4.2 Consensus size: 104
11329341 TGTATATAAA
** * *
11329351 AGGGGTTGCTGTGTGCTGATT-CCCGATTT-ATGGGTGGTGCTATGTGCG-TGATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
11329413 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
11329453 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
11329518 TTGAAATG-AAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGTGAAA-GGGGGTTGCTATGTGCTGATT-CCCCG
11329558 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
11329623 TTGAAA--TGAAATGGGGGTTGCTATGTGCTGATTCCCCG
66 TTGAAATGTGAAA-GGGGGTTGCTATGTGCTGATTCCCCG
*
11329661 AGGGGTTGCTAAGTGCTGATTCCCCG-GTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
11329725 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
11329765 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11329781 GATATCCATT
Statistics
Matches: 311, Mismatches: 8, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
102 62 0.20
103 63 0.20
104 109 0.35
105 77 0.25
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:11329676 original size:26 final size:26
Alignment explanation
Indices: 11329636--11329686 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11329626 AAATGAAATG
*
11329636 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11329662 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
11329687 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:11329725 original size:207 final size:206
Alignment explanation
Indices: 11329351--11329780 Score: 724
Period size: 207 Copynumber: 2.1 Consensus size: 206
11329341 TGTATATAAA
** *
11329351 AGGGGTTGCTGTGTGCTGATTCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCGATTTATGGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
*
11329416 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAT
66 GAAA-GTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAG
11329481 TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATG-AAAAGGGGGGTTGCTATGT
130 TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTAAAA-GGGGGTTGCTATGT
11329545 GCTGATTCCCCCG
194 GCTGATTCCCCCG
*
11329558 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATT-CCCGATTT-ATGGGTGGTGCTAAGTGCG-TGATCCACCATATC
11329622 TTTGAAA-TGAAATGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
63 TTTGAAAGTGAAA-GGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
*
11329686 G-GTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTAT
127 GAGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTAAAAGGGGGTTGCTAT
11329750 GTGCTGATTCCCCCG
192 GTGCTGATTCCCCCG
11329765 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11329781 GATATCCATT
Statistics
Matches: 212, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
207 112 0.53
208 63 0.30
209 36 0.17
210 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.31
Consensus pattern (206 bp):
AGGGGTTGCTAAGTGCTGATTCCCGATTTATGGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAAGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAGT
TCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTAAAAGGGGGTTGCTATGTGC
TGATTCCCCCG
Found at i:11329832 original size:71 final size:72
Alignment explanation
Indices: 11329699--11329850 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
11329689 TCATTGGTGG
* *
11329699 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
11329764 GAGGGGT
66 GAGGGGT
***
11329771 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
11329835 GAGGGGT
66 GAGGGGT
11329842 TGCTAAGTG
1 TGCTAAGTG
11329851 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:11335960 original size:14 final size:15
Alignment explanation
Indices: 11335936--11335964 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11335926 ACGGAAAATT
11335936 TTCGTAAAAATTTCG
1 TTCGTAAAAATTTCG
11335951 TTCG-AAAAATTTCG
1 TTCGTAAAAATTTCG
11335965 ACGTTTGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
TTCGTAAAAATTTCG
Found at i:11341119 original size:26 final size:26
Alignment explanation
Indices: 11341084--11341135 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11341074 AATGTGAAAG
*
11341084 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11341110 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11341136 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:11341325 original size:26 final size:26
Alignment explanation
Indices: 11341290--11341340 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11341280 AAATGAAAAG
*
11341290 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11341316 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
11341341 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:11341359 original size:102 final size:102
Alignment explanation
Indices: 11341009--11341429 Score: 662
Period size: 102 Copynumber: 4.2 Consensus size: 102
11340999 TTGTATATAA
** *
11341009 AGGGGTTGCTGTGTGCTGATTCCCGATT-A-TGGTGGTGCTATGTGCG-TGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTT
*
11341071 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
11341109 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATT-CCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
11341174 TTGAAATG-AAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGTAAAA-GGGGGTTGCTATGTGCTGATT-CCCCG
*
11341214 AGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTTCTAAGTGCGATATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
11341279 GAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 GAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
11341315 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATC-T
1 AGGGGTTGCTAAGTGCTGATT-CCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
11341379 TGAAATGTGAAAGGGGG-T--TATGTGCTGATTCCCCG
65 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
11341414 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11341430 GATATCCATT
Statistics
Matches: 304, Mismatches: 8, Indels: 19
0.92 0.02 0.06
Matches are distributed among these distances:
99 33 0.11
100 19 0.06
101 40 0.13
102 70 0.23
103 52 0.17
104 63 0.21
105 27 0.09
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
GAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:11341370 original size:205 final size:200
Alignment explanation
Indices: 11341009--11341429 Score: 670
Period size: 205 Copynumber: 2.1 Consensus size: 200
11340999 TTGTATATAA
** *
11341009 AGGGGTTGCTGTGTGCTGATTCCCGATTATGGTGGTGCTATGTGCGTGATCCACCATATCTTTGA
1 AGGGGTTGCTAAGTGCTGATTCCCGATTATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGA
* *
11341074 AATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTT
66 AATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAGTT
11341139 CATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATG-AAAAGGGGGGTTGCTATGTGC
131 CATTGGTGGTGCTAAGTGCGATATCCACCATATC-TTGAAATGTAAAA-GGGGG-T--TATGTGC
11341203 TGATTCCCCCG
191 TGATT-CCCCG
*
11341214 AGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTTCTAAGTGCGAT-ATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCGATT-A-TGGTGGTGCTAAGTGCG-TGATCCACCATATCTT
11341278 TGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCG-
63 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGA
*
11341341 GTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTGAAATGTGAAAGGGGGTTATGTGCTG
128 GTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTGAAATGTAAAAGGGGGTTATGTGCTG
11341406 ATTCCCCG
193 ATTCCCCG
11341414 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11341430 GATATCCATT
Statistics
Matches: 205, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
200 21 0.10
201 12 0.06
203 1 0.00
204 13 0.06
205 65 0.32
206 56 0.27
207 36 0.18
208 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (200 bp):
AGGGGTTGCTAAGTGCTGATTCCCGATTATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGA
AATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAGTT
CATTGGTGGTGCTAAGTGCGATATCCACCATATCTTGAAATGTAAAAGGGGGTTATGTGCTGATT
CCCCG
Found at i:11341461 original size:67 final size:70
Alignment explanation
Indices: 11341353--11341499 Score: 205
Period size: 67 Copynumber: 2.1 Consensus size: 70
11341343 TCATTGGTGG
*
11341353 TGCTAAGTGCGATATCCACCATATCTTGAAATGTGAAAGGGGG-T-TATGTGCTGATT-CCCCGA
1 TGCTAAGTGCGATATCCACCATATCTTGAAATGTAAAAGGGGGTTCTATGTGCTGATTCCCCCGA
11341415 GGGGT
66 GGGGT
**
11341420 TGCTAAGTGCGATATCCATTGTATAT-TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCC
1 TGCTAAGTGCGATATCCA--CCATATCTTGAAATGTAAAAGGGGGTT-CTATGTGCTGATTCCCC
11341483 CGAGGGGT
63 CGAGGGGT
11341491 TGCTAAGTG
1 TGCTAAGTG
11341500 ATGATTCCCC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
67 26 0.37
68 9 0.13
69 4 0.06
70 12 0.17
71 20 0.28
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (70 bp):
TGCTAAGTGCGATATCCACCATATCTTGAAATGTAAAAGGGGGTTCTATGTGCTGATTCCCCCGA
GGGGT
Found at i:11345373 original size:44 final size:44
Alignment explanation
Indices: 11345322--11345893 Score: 743
Period size: 44 Copynumber: 13.0 Consensus size: 44
11345312 TCACCGGTGA
* * *
11345322 CAGATTTGGCATCTCTGTATTGTCAGAGAGTC-GATCAAAGGTGAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAG-CAGATCGAAGAT-AG
* * * * * *
11345367 -AAATTTGGCGTCTCCGTATTGACAGAGAGTAGATCAAATATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
*
11345410 CAGATTTGGCGTCTTTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11345454 CAGATTTGGCATCTCTGTATTGTCAGAGAGCAGGTTGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
11345498 TAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * * *
11345542 TAGATTTGGCGTCTTTGTATTGTTAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
*
11345586 CAGATTTGGCGTCTCTGTATTTTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11345630 CAGATTTGGCGTCTTTGTATTGTCCGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * * * *
11345674 CAGATTTTGCGTCTCTATATTTTCAGAGAGAAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
**
11345718 TGGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * * * *
11345762 CAGATTTGGCGTCTCTTTATTTTTAGAGAGAAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
11345806 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGGTCGAGGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11345850 CAGATTTTGCGTCTCTGTACTGTCAGAGACCAGATTCGAAGATA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGA-TCGAAGATA
11345894 ACCGATCTGG
Statistics
Matches: 456, Mismatches: 68, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
43 2 0.00
44 446 0.98
45 8 0.02
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
Found at i:11347557 original size:28 final size:27
Alignment explanation
Indices: 11347474--11347562 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 27
11347464 TTTTTCTTTG
11347474 TATATTATTTATTATATTATTATATATTATTA
1 TATATTA-TT-TTATA-TATTAT-TATTA-TA
* *
11347506 TATATTATATTACCTACATT-TTATTATA
1 TATATTATTTTA--TATATTATTATTATA
*
11347534 TATATTATTTTATATATTACTTATCATA
1 TATATTATTTTATATATTA-TTATTATA
11347562 T
1 T
11347563 TGTTTATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
26 5 0.10
28 21 0.44
29 5 0.10
30 4 0.08
31 4 0.08
32 9 0.19
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTATTTTATATATTATTATTATA
Found at i:11347562 original size:14 final size:12
Alignment explanation
Indices: 11347474--11347581 Score: 70
Period size: 12 Copynumber: 9.1 Consensus size: 12
11347464 TTTTTCTTTG
11347474 TATATTATT-TA
1 TATATTATTATA
11347485 T-TA-TATTATTA
1 TATATTATTA-TA
11347496 TATATTATTATA
1 TATATTATTATA
11347508 TAT-TATATTACCTA
1 TATAT-TATTA--TA
* *
11347522 CATTTTATTATA
1 TATATTATTATA
*
11347534 TATATTATTTTA
1 TATATTATTATA
11347546 TATATTACTTATCA
1 TATATTA-TTAT-A
11347560 TAT-TGT-TTATA
1 TATAT-TATTATA
11347571 T-TATTA-TATA
1 TATATTATTATA
11347581 T
1 T
11347582 TTCGTTTATG
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
9 4 0.05
10 9 0.11
11 8 0.10
12 34 0.43
13 9 0.11
14 14 0.18
15 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (12 bp):
TATATTATTATA
Found at i:11347615 original size:17 final size:17
Alignment explanation
Indices: 11347593--11347626 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11347583 TCGTTTATGA
* *
11347593 ATTTTATTATATGTTAT
1 ATTTTACTATATATTAT
11347610 ATTTTACTATATATTAT
1 ATTTTACTATATATTAT
11347627 CTCTTACATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTACTATATATTAT
Found at i:11349802 original size:48 final size:48
Alignment explanation
Indices: 11349731--11349827 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
11349721 TAGACTTAGT
11349731 ACCTATTTTGGAGGAGTATACGACCTTGCTTCACTGCCCAAAAATTCA
1 ACCTATTTTGGAGGAGTATACGACCTTGCTTCACTGCCCAAAAATTCA
11349779 ACCTATTTTGGAGGAGTATACGACCTTGCTTCACTGCCCAAAAATTCA
1 ACCTATTTTGGAGGAGTATACGACCTTGCTTCACTGCCCAAAAATTCA
11349827 A
1 A
11349828 GGTAACAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (48 bp):
ACCTATTTTGGAGGAGTATACGACCTTGCTTCACTGCCCAAAAATTCA
Found at i:11356269 original size:48 final size:48
Alignment explanation
Indices: 11356194--11356771 Score: 958
Period size: 48 Copynumber: 12.0 Consensus size: 48
11356184 CAAGACAAAT
*
11356194 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
11356242 ATATATATATGTGGTAAAGCCGTATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
11356290 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
11356338 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
11356386 ATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
11356434 ATATATATATGTGGTAAAGCCGTATGGCTAATGTGAAATATTTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
11356482 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
11356530 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
11356578 ATATATATATGTGGTAAAGCCGTATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
11356626 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
11356674 ATATGTATATGTGGTAAAGCCGAATGGATAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
11356722 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
11356770 AT
1 AT
11356772 GTGTGTATAT
Statistics
Matches: 492, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 492 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:11362378 original size:44 final size:44
Alignment explanation
Indices: 11362328--11362857 Score: 756
Period size: 44 Copynumber: 12.0 Consensus size: 44
11362318 TCACCGGTGA
*
11362328 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGGT-G
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11362371 ACAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATTGAAGATAA
1 -CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
*
11362416 CAGATTTGGCGTCTCCGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11362460 CAAATTTGGCGTCTCTGTATTGTTAGACAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11362504 TAGATTTGGCGTCTCTGTATTATCAGAGAGCATATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11362548 TAGATTTGCCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * *
11362592 CAGATTTGGCGTCTTTGTATTGTTAGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* * * *
11362636 CAGATTTGACGTCTCTGTATTGTTAGAGAGAAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
** *
11362680 TGGATTTGGCGTCTTTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
11362724 CAGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
* *
11362768 CGGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAGGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
** *
11362812 CAGATTTGGTATCTCTGTATTGTCAGAGACCAGATTCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGA-TCGAAGATAG
11362857 C
1 C
11362858 CAATTTGACA
Statistics
Matches: 431, Mismatches: 53, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
44 421 0.98
45 10 0.02
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.29
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
Found at i:11364463 original size:21 final size:21
Alignment explanation
Indices: 11364438--11364519 Score: 62
Period size: 24 Copynumber: 3.7 Consensus size: 21
11364428 TACGTACATT
*
11364438 TTATTATATATATTATTT-TA
1 TTATTATATATATTGTTTATA
11364458 TATATTACTTATCATATTGTTTATA
1 T-TATTA--TAT-ATATTGTTTATA
11364483 TTATTATATAT-TTCGTTTATGAA
1 TTATTATATATATT-GTTTAT--A
11364506 TT-TTATTATATATT
1 TTATTA-TATATATT
11364520 ATATTTTACC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
20 3 0.06
21 13 0.25
22 6 0.12
23 11 0.22
24 15 0.29
25 3 0.06
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
TTATTATATATATTGTTTATA
Found at i:11364469 original size:16 final size:17
Alignment explanation
Indices: 11364377--11364462 Score: 58
Period size: 15 Copynumber: 5.2 Consensus size: 17
11364367 TATAAAAGTG
*
11364377 TATATATTATTTT-TCTT
1 TATATATTATTTTAT-TA
*
11364394 TGTATATTA-TTTATTA
1 TATATATTATTTTATTA
*
11364410 TAT-TATTA-TATATTA
1 TATATATTATTTTATTA
*
11364425 TAT-TACGTACATTTTATTA
1 TATATA--T-TATTTTATTA
11364444 TATATATTATTTTA-TA
1 TATATATTATTTTATTA
11364460 TAT
1 TAT
11364463 TACTTATCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
15 16 0.29
16 11 0.20
17 16 0.29
18 2 0.04
19 9 0.16
20 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATATTATTTTATTA
Found at i:11364474 original size:14 final size:12
Alignment explanation
Indices: 11364396--11364493 Score: 64
Period size: 12 Copynumber: 8.1 Consensus size: 12
11364386 TTTTTCTTTG
11364396 TATATTATT-TA
1 TATATTATTATA
11364407 TTATATTATTATA
1 -TATATTATTATA
11364420 TAT-TATATTACGTA
1 TATAT-TATTA--TA
* *
11364434 CATTTTATTATA
1 TATATTATTATA
*
11364446 TATATTATTTTA
1 TATATTATTATA
11364458 TATATTACTTATCA
1 TATATTA-TTAT-A
11364472 TAT-TGT-TTATA
1 TATAT-TATTATA
11364483 T-TATTA-TATA
1 TATATTATTATA
11364493 T
1 T
11364494 TTCGTTTATG
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
10 7 0.10
11 4 0.06
12 39 0.55
13 6 0.08
14 14 0.20
15 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (12 bp):
TATATTATTATA
Found at i:11364897 original size:16 final size:19
Alignment explanation
Indices: 11364862--11364898 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
11364852 GTAGGTTAAA
11364862 TTTTCATAGATTATTTGTT
1 TTTTCATAGATTATTTGTT
11364881 TTTTCAT-G-TTA-TTGTT
1 TTTTCATAGATTATTTGTT
11364897 TT
1 TT
11364899 ACATATTCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 1 0.06
19 7 0.39
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (19 bp):
TTTTCATAGATTATTTGTT
Found at i:11367993 original size:27 final size:27
Alignment explanation
Indices: 11367946--11368142 Score: 184
Period size: 27 Copynumber: 7.3 Consensus size: 27
11367936 TTAGTTTACT
*
11367946 AAATTACC-AAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
11367972 ACATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
*
11367999 AAATTACCAAAATA-CCCTCAGTTTATA
1 AAATTACCAAAATACCCCT-GGTTTATA
* *
11368026 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* ** * *
11368053 AAATTACCAAAATACCTCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTATA
* ** *
11368080 AAATTACCGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTATA
* ***
11368107 AAATTACCAAAGTACCCCCAATTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
11368134 AAATTACCA
1 AAATTACCA
11368143 TTTTACCCTC
Statistics
Matches: 141, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
26 14 0.10
27 121 0.86
28 6 0.04
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:11368023 original size:54 final size:54
Alignment explanation
Indices: 11367946--11368142 Score: 238
Period size: 54 Copynumber: 3.7 Consensus size: 54
11367936 TTAGTTTACT
*** *
11367946 AAATTACC-AAATACCCTTGGTTTATAACATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCCTGGTTTGTA
* *
11367999 AAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCCTGGTTTGTA
* * * **
11368053 AAATTACCAAAATA-CCTCTAATTTGTGAAATTACCGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCTC-AATTTATAAAATTACCAAAATACCCCT-GGTTTGTA
* *
11368107 AAATTACCAAAGTACCCCCAATTTATAAAATTACCA
1 AAATTACCAAAATACCCTCAATTTATAAAATTACCA
11368143 TTTTACCCTC
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 15 0.12
54 106 0.85
55 3 0.02
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:11368078 original size:81 final size:81
Alignment explanation
Indices: 11367938--11368142 Score: 245
Period size: 81 Copynumber: 2.5 Consensus size: 81
11367928 AGAATACTTT
* **
11367938 AGTTTACT-AAATTACC-AAATACCCTTGGTTTATAACATTACCAAAATACCCCTGGTTTGTAAA
1 AGTTTA-TAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAATTTGTAAA
11368001 ATTACCAAAATACCCTC
65 ATTACCAAAATACCCTC
* * *
11368018 AGTTTATAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCTCTAATTTGTGAAA
1 AGTTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAATTTGTAAAA
*
11368083 TTACCGAAATACCCTC
66 TTACCAAAATACCCTC
* * * ****
11368099 -GACTTGTAAAATTACCAAAGTACCCCCAATTTATAAAATTACCA
1 AG-TTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCA
11368143 TTTTACCCTC
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 15 0.14
81 91 0.85
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (81 bp):
AGTTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAATTTGTAAAA
TTACCAAAATACCCTC
Found at i:11368157 original size:27 final size:27
Alignment explanation
Indices: 11367946--11368166 Score: 164
Period size: 27 Copynumber: 8.2 Consensus size: 27
11367936 TTAGTTTACT
* *
11367946 AAATTACCAAA-TACCCTTGGTTTATA
1 AAATTACCAAAGTACCCTCGATTTATA
* * * *
11367972 ACATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAGTACCCTC-GATTTATA
*
11367999 AAATTACCAAAATACCCTC-AGTTTATA
1 AAATTACCAAAGTACCCTCGA-TTTATA
* * * *
11368026 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAGTACCCTCGATTTATA
* * * *
11368053 AAATTACCAAAATA-CCTCTAATTTGTG
1 AAATTACCAAAGTACCCTC-GATTTATA
* *
11368080 AAATTACCGAAA-TACCCTCGACTTGTA
1 AAATTACC-AAAGTACCCTCGATTTATA
* *
11368107 AAATTACCAAAGTACCCCCAATTTATA
1 AAATTACCAAAGTACCCTCGATTTATA
*** *
11368134 AAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAGTACCCTCGATTTATA
11368161 AAATTA
1 AAATTA
11368167 TTGAAATACC
Statistics
Matches: 160, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
26 16 0.10
27 136 0.85
28 8 0.05
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAGTACCCTCGATTTATA
Found at i:11368164 original size:54 final size:53
Alignment explanation
Indices: 11367966--11368166 Score: 206
Period size: 54 Copynumber: 3.7 Consensus size: 53
11367956 ATACCCTTGG
* * * *
11367966 TTTATAACATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCCTCAG
1 TTTATAAAATTACC-AAATACCCTC-GATTTGTAAAATTACCAAAATACCCCCAA
* * * *
11368020 TTTATAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCTCTAA
1 TTTATAAAATTACC-AAATACCCTCGATTTGTAAAATTACCAAAATACCCCCAA
* * * *
11368074 TTTGTGAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCAA
1 TTTATAAAATTACC-AAATACCCTCGATTTGTAAAATTACCAAAATACCCCCAA
** **
11368128 TTTATAAAATTACCATTTTACCCTCGATTTACAAAATTA
1 TTTATAAAATTACCA-AATACCCTCGATTTGTAAAATTA
11368167 TTGAAATACC
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
53 1 0.01
54 122 0.99
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (53 bp):
TTTATAAAATTACCAAATACCCTCGATTTGTAAAATTACCAAAATACCCCCAA
Found at i:11368192 original size:27 final size:27
Alignment explanation
Indices: 11368162--11368382 Score: 232
Period size: 27 Copynumber: 8.2 Consensus size: 27
11368152 CGATTTACAA
* *
11368162 AATTATTGAAATACCTCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
11368189 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
11368216 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
11368243 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
11368270 AATTACCGAAATACCCATGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* **
11368297 AATTACCGAAATACCTTTGTAGGGT-G
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
11368323 AAAATA-TCAAAATACCCCT-TAGGGTAG
1 -AATTACT-GAAATACCCCTGTAGGGTAG
* * * * * *
11368350 AATTACCGAGATACTCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
11368377 AATTAC
1 AATTAC
11368383 CATTTTGCCC
Statistics
Matches: 164, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
26 18 0.11
27 146 0.89
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:11368220 original size:54 final size:54
Alignment explanation
Indices: 11368170--11368384 Score: 263
Period size: 54 Copynumber: 4.0 Consensus size: 54
11368160 AAAATTATTG
* ** *
11368170 AAATACCTCTGTAGGGTAGAATTATTGAAATACCCTTGTAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCA
* * * *
11368224 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCA
* * * *
11368278 AAATACCCATGTAGGGTAGAATTACCGAAATACCTTTGTAGGGT-GAAAATATCA
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG-AATTACCA
* * * *
11368332 AAATACCCCT-TAGGGTAGAATTACCGAGATACTCTTGTGGGGTAAAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCA
11368385 TTTTGCCCTA
Statistics
Matches: 137, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
53 36 0.26
54 101 0.74
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (54 bp):
AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCA
Found at i:11368509 original size:10 final size:11
Alignment explanation
Indices: 11368494--11368568 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
11368484 ATATTGTTAT
*
11368494 ACATGATA-GG
1 ACATGATATGC
11368504 ACATGATATGC
1 ACATGATATGC
11368515 ACATGATATG-
1 ACATGATATGC
**
11368525 TTATGATATGC
1 ACATGATATGC
*
11368536 ACATGGTATGC
1 ACATGATATGC
* *
11368547 -TATGATATAC
1 ACATGATATGC
* *
11368557 TCATTATATGC
1 ACATGATATGC
11368568 A
1 A
11368569 TTGGTGGGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
10 23 0.47
11 26 0.53
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:11368519 original size:21 final size:21
Alignment explanation
Indices: 11368494--11368540 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11368484 ATATTGTTAT
11368494 ACATGATAGGACATGATATGC
1 ACATGATAGGACATGATATGC
* **
11368515 ACATGATATGTTATGATATGC
1 ACATGATAGGACATGATATGC
11368536 ACATG
1 ACATG
11368541 GTATGCTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (21 bp):
ACATGATAGGACATGATATGC
Found at i:11368567 original size:21 final size:21
Alignment explanation
Indices: 11368506--11368554 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
11368496 ATGATAGGAC
*
11368506 ATGATATGCACATGATATGTT
1 ATGATATGCACATGATATGCT
*
11368527 ATGATATGCACATGGTATGCT
1 ATGATATGCACATGATATGCT
11368548 ATGATAT
1 ATGATAT
11368555 ACTCATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (21 bp):
ATGATATGCACATGATATGCT
Found at i:11368652 original size:23 final size:23
Alignment explanation
Indices: 11368601--11368672 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
11368591 GAGGAAGTGC
11368601 TAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAG-TTAT
*
11368625 CAAAAGGGCTTTGCCCCAGTTAT
1 TAAAAGGGCTTTGCCCCAGTTAT
**
11368648 TAAAAGAGGCTAGGCCTCCAGTTAT
1 TAAAAG-GGCTTTGCC-CCAGTTAT
11368673 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 9 0.21
24 25 0.60
25 8 0.19
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
TAAAAGGGCTTTGCCCCAGTTAT
Found at i:11395759 original size:64 final size:64
Alignment explanation
Indices: 11395678--11395861 Score: 196
Period size: 67 Copynumber: 2.8 Consensus size: 64
11395668 AGAAATTATG
* *
11395678 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACG-GTATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAG-ATAA
* * * * *
11395742 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
11395807 AA
63 AA
* * *
11395809 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
11395862 CGAACTATAT
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 32 0.32
68 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:11398589 original size:40 final size:40
Alignment explanation
Indices: 11398534--11398671 Score: 190
Period size: 40 Copynumber: 3.5 Consensus size: 40
11398524 TGGATGATAA
*
11398534 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
*
11398574 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* * *
11398614 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATAT
* *
11398654 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
11398672 TACTTGGCTT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 15 0.17
40 74 0.83
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:11402491 original size:11 final size:11
Alignment explanation
Indices: 11402475--11402505 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
11402465 CCTAAAACCC
11402475 TTTTATTTTCT
1 TTTTATTTTCT
11402486 TTTTATTTTCT
1 TTTTATTTTCT
11402497 TTTGTATTT
1 TTT-TATTT
11402506 GACAAGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:11413775 original size:20 final size:19
Alignment explanation
Indices: 11413665--11413776 Score: 86
Period size: 20 Copynumber: 5.8 Consensus size: 19
11413655 AATAATTACA
*
11413665 ATAAAAAT-TTATAAATATT
1 ATAAAAATATTA-AAAAATT
*
11413684 ATAAAAATATAAAAAAAATTT
1 ATAAAAATAT-TAAAAAA-TT
* *
11413705 ATAAAATTAATAAAAAATT
1 ATAAAAATATTAAAAAATT
* * *
11413724 -TAAAATTTTTAAAAACTT
1 ATAAAAATATTAAAAAATT
*
11413742 ATGAAAATCA-TAAAAATATT
1 ATAAAAAT-ATTAAAAA-ATT
11413762 ATAAAAATATTAAAA
1 ATAAAAATATTAAAA
11413777 TTGATATAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
18 15 0.21
19 22 0.30
20 25 0.34
21 11 0.15
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAAAAATATTAAAAAATT
Found at i:11413776 original size:9 final size:11
Alignment explanation
Indices: 11413665--11413773 Score: 64
Period size: 11 Copynumber: 11.1 Consensus size: 11
11413655 AATAATTACA
11413665 ATAAAAAT-TT
1 ATAAAAATATT
11413675 AT--AAATATT
1 ATAAAAATATT
*
11413684 ATAAAAATATA
1 ATAAAAATATT
*
11413695 AAAAAAAT-TT
1 ATAAAAATATT
*
11413705 AT-AAAAT-TA
1 ATAAAAATATT
11413714 ATAAAAA-ATT
1 ATAAAAATATT
11413724 -T-AAAAT-TT
1 ATAAAAATATT
* *
11413732 TTAAAAA-CTT
1 ATAAAAATATT
* *
11413742 AT-GAAA-ATC
1 ATAAAAATATT
11413751 ATAAAAATATT
1 ATAAAAATATT
11413762 ATAAAAATATT
1 ATAAAAATATT
11413773 A
1 A
11413774 AAATTGATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
8 10 0.13
9 20 0.26
10 19 0.25
11 27 0.36
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (11 bp):
ATAAAAATATT
Found at i:11414404 original size:10 final size:10
Alignment explanation
Indices: 11414389--11414610 Score: 73
Period size: 10 Copynumber: 22.9 Consensus size: 10
11414379 TTTAAATGAC
*
11414389 ATTTTTAATT
1 ATTTTTAATA
11414399 ATTTTT-ATA
1 ATTTTTAATA
11414408 ATTTATTAA-A
1 ATTT-TTAATA
11414418 ATTTTT-AT-
1 ATTTTTAATA
* *
11414426 ATTATTCATA
1 ATTTTTAATA
11414436 ATTTTT-ATAA
1 ATTTTTAAT-A
11414446 ATGTTTTAAT-
1 AT-TTTTAATA
*
11414456 ATTTTAAAT-
1 ATTTTTAATA
*
11414465 ATATTTTATTA
1 AT-TTTTAATA
*
11414476 A-TTTTATACA
1 ATTTTTA-ATA
*
11414486 AGTTTTAATA
1 ATTTTTAATA
*
11414496 ATTTGTTAA-G
1 ATTT-TTAATA
*
11414506 A--TTTACTA
1 ATTTTTAATA
*
11414514 TATTTTTTATA
1 -ATTTTTAATA
* *
11414525 ATATTTATTA
1 ATTTTTAATA
* *
11414535 GTTTTT-ATG
1 ATTTTTAATA
*
11414544 ATTTTTTAT-
1 ATTTTTAATA
11414553 ATTTTT-ATA
1 ATTTTTAATA
*
11414562 A-GTTTATATA
1 ATTTTTA-ATA
*
11414572 AATTTTAATA
1 ATTTTTAATA
11414582 TATTTTTTAA-A
1 -A-TTTTTAATA
*
11414593 AATTTTAAT-
1 ATTTTTAATA
11414602 ATTTTTAAT
1 ATTTTTAAT
11414611 TTTAATAAAT
Statistics
Matches: 159, Mismatches: 28, Indels: 51
0.67 0.12 0.21
Matches are distributed among these distances:
7 3 0.02
8 12 0.08
9 53 0.33
10 57 0.36
11 26 0.16
12 8 0.05
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:11414421 original size:19 final size:19
Alignment explanation
Indices: 11414399--11414445 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
11414389 ATTTTTAATT
11414399 ATTTTTATAATTTATT-AAA
1 ATTTTTATAA-TTATTCAAA
*
11414418 ATTTTTAT-ATTATTCATA
1 ATTTTTATAATTATTCAAA
11414436 ATTTTTATAA
1 ATTTTTATAA
11414446 ATGTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
19 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTATAATTATTCAAA
Found at i:11414458 original size:30 final size:28
Alignment explanation
Indices: 11414389--11414460 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
11414379 TTTAAATGAC
*
11414389 ATTTTTAATTATTTTTATAATTTATTAAA
1 ATTTTTAA-TATTTTCATAATTTATTAAA
11414418 ATTTTT-ATATTATTCATAATTT-TTATAA
1 ATTTTTAATATT-TTCATAATTTATTA-AA
11414446 ATGTTTTAATATTTT
1 AT-TTTTAATATTTT
11414461 AAATATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.18
28 14 0.37
29 12 0.32
30 5 0.13
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTTAATATTTTCATAATTTATTAAA
Found at i:11414558 original size:19 final size:18
Alignment explanation
Indices: 11414512--11414562 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
11414502 TAAGATTTAC
11414512 TATATTTTTTATAATATT
1 TATATTTTTTATAATATT
* *
11414530 TATTAGTTTTTATGAT-TT
1 TA-TATTTTTTATAATATT
*
11414548 TTTATATTTTTATAA
1 TATAT-TTTTTATAA
11414563 GTTTATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TATATTTTTTATAATATT
Done.