Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 37 of 125
Found at i:11047931 original size:18 final size:20
Alignment explanation
Indices: 11047910--11047946 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
11047900 TTTTTGAACA
11047910 ATTTAATT-TTTT-CTTTTT
1 ATTTAATTATTTTCCTTTTT
*
11047928 ATTTATTTATTTTCCTTTT
1 ATTTAATTATTTTCCTTTT
11047947 CTTCTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTAATTATTTTCCTTTTT
Found at i:11056151 original size:7 final size:7
Alignment explanation
Indices: 11056139--11056169 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
11056129 TTAGGAGAAA
11056139 GGGGAAG
1 GGGGAAG
11056146 GGGGAAG
1 GGGGAAG
11056153 GGGGAAG
1 GGGGAAG
11056160 GGGGAAG
1 GGGGAAG
11056167 GGG
1 GGG
11056170 TAGGGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (7 bp):
GGGGAAG
Found at i:11058992 original size:41 final size:42
Alignment explanation
Indices: 11058935--11059019 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 42
11058925 TGCAATAACA
11058935 AAAAAATAAAAACAAAAA-AGAAAAATATTTTT-GGACTTTTG
1 AAAAAATAAAAACAAAAACA-AAAAATATTTTTGGGACTTTTG
* *
11058976 AAAAATTAAAAACAAAAACAAAAAATATTTTTGGGATTTTTG
1 AAAAAATAAAAACAAAAACAAAAAATATTTTTGGGACTTTTG
11059018 AA
1 AA
11059020 TTTTTTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 29 0.73
42 11 0.28
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (42 bp):
AAAAAATAAAAACAAAAACAAAAAATATTTTTGGGACTTTTG
Found at i:11065713 original size:21 final size:21
Alignment explanation
Indices: 11065689--11065732 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11065679 AATAATTTTC
11065689 TTTAA-ATATTAATTTGGAAAA
1 TTTAAGATATT-ATTTGGAAAA
* *
11065710 TTTAAGTTATTTTTTGGAAAA
1 TTTAAGATATTATTTGGAAAA
11065731 TT
1 TT
11065733 AATTTTGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTAAGATATTATTTGGAAAA
Found at i:11065925 original size:37 final size:36
Alignment explanation
Indices: 11065863--11065952 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
11065853 TTCCAAAAAT
11065863 AATATTATATTAATAGTTTAATATTAAATTAAATTA
1 AATATTATATTAATAGTTTAATATTAAATTAAATTA
* * * *
11065899 AATATGTATTTTAATAGTATT-TTATTAATTTATATTA
1 AATAT-TATATTAATAGT-TTAATATTAAATTAAATTA
*
11065936 AAGTGATTATCTTAATA
1 AA-T-ATTATATTAATA
11065953 TTAAGTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 5 0.11
37 26 0.58
38 12 0.27
39 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (36 bp):
AATATTATATTAATAGTTTAATATTAAATTAAATTA
Found at i:11068654 original size:26 final size:26
Alignment explanation
Indices: 11068563--11068660 Score: 72
Period size: 26 Copynumber: 3.8 Consensus size: 26
11068553 CGCAATTCTA
* * *
11068563 GACATGCTCATACAGCAAAAACTCTG
1 GACATGCTCATGCAGCGACAACTCTG
** * * * *
11068589 GACATATTCATGCAGCTATAATTTTG
1 GACATGCTCATGCAGCGACAACTCTG
* * *
11068615 GACAAGTTTC-TGCAGCGACAAGTCTG
1 GACATG-CTCATGCAGCGACAACTCTG
11068641 GACATGCTCATGCAGCGACA
1 GACATGCTCATGCAGCGACA
11068661 TTAGTAGTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
25 2 0.04
26 50 0.91
27 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (26 bp):
GACATGCTCATGCAGCGACAACTCTG
Found at i:11076426 original size:26 final size:26
Alignment explanation
Indices: 11076382--11076487 Score: 81
Period size: 26 Copynumber: 4.1 Consensus size: 26
11076372 ATTCTGGGCG
* **
11076382 CAATTCTGGACATGCTCATACAGCGA
1 CAATTCTAGACATATTCATACAGCGA
* *
11076408 CAACTCTAGACATATTCATGCAGCGA
1 CAATTCTAGACATATTCATACAGCGA
* * *
11076434 TAATTTTGGACA-AGTTTC-TACAGCGA
1 CAATTCTAGACATA--TTCATACAGCGA
* * *
11076460 CGATTCTAGACATACTCATGCAGCGA
1 CAATTCTAGACATATTCATACAGCGA
11076486 CA
1 CA
11076488 TTAGTAGTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
25 3 0.05
26 52 0.88
27 4 0.07
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (26 bp):
CAATTCTAGACATATTCATACAGCGA
Found at i:11081698 original size:18 final size:18
Alignment explanation
Indices: 11081663--11081698 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11081653 GTCCCCATTG
*
11081663 TTAAAAATAATAGAGAAT
1 TTAAAAATAAAAGAGAAT
*
11081681 TTAAAAATAAAAGTGAAT
1 TTAAAAATAAAAGAGAAT
11081699 AAATACTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAAAAATAAAAGAGAAT
Found at i:11082395 original size:12 final size:12
Alignment explanation
Indices: 11082364--11082397 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
11082354 ATCTCCATAA
*
11082364 GATCTTCCTCAG
1 GATCTTCTTCAG
11082376 GATCTTCTTCAG
1 GATCTTCTTCAG
11082388 GATCTTCTTC
1 GATCTTCTTC
11082398 TTCTTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (12 bp):
GATCTTCTTCAG
Found at i:11083317 original size:19 final size:19
Alignment explanation
Indices: 11083268--11083324 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
11083258 TTGTTCTAAC
* *
11083268 ATTTAATATAAAATATTAACA
1 ATTTAATA-ATAA-ATTAAAA
*
11083289 A-TTAAAAATAAATTAAAA
1 ATTTAATAATAAATTAAAA
11083307 ATTTAATAATAAATTAAA
1 ATTTAATAATAAATTAAA
11083325 TAAATTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.23
19 18 0.58
20 5 0.16
21 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTTAATAATAAATTAAAA
Found at i:11083345 original size:28 final size:28
Alignment explanation
Indices: 11083294--11083347 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
11083284 TAACAATTAA
*
11083294 AAATAAATTAAAAATTTAATAATAAATT
1 AAATAAATTAAAAATTTAAAAATAAATT
*
11083322 AAATAAATTAAGAA-TTAGAAAATAAA
1 AAATAAATTAAAAATTTA-AAAATAAA
11083348 AATTCTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (28 bp):
AAATAAATTAAAAATTTAAAAATAAATT
Found at i:11083928 original size:19 final size:20
Alignment explanation
Indices: 11083906--11083953 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
11083896 TAAACTTTTG
11083906 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
11083925 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
11083945 -TAAT-ATTAA
1 ATAATAATTAA
11083954 GAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:11084067 original size:28 final size:30
Alignment explanation
Indices: 11084019--11084077 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
11084009 GCTGTTTTAA
*
11084019 AATATTTACAGAAAAAGACAAC-TAATTTT
1 AATATTTACAGAAAAAGACAACAAAATTTT
11084048 AATATTTAC-GAAAATA-ACAACAAAATTTT
1 AATATTTACAGAAAA-AGACAACAAAATTTT
11084077 A
1 A
11084078 CAAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (30 bp):
AATATTTACAGAAAAAGACAACAAAATTTT
Found at i:11092635 original size:3 final size:3
Alignment explanation
Indices: 11092627--11092656 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11092617 CTTCGTCCAT
*
11092627 CTC CTC CTC CTC CTC CTC TTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
11092657 TTCACTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:11092657 original size:12 final size:12
Alignment explanation
Indices: 11092627--11092659 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11092617 CTTCGTCCAT
*
11092627 CTCCTCCTCCTC
1 CTCCTCTTCCTC
11092639 CTCCTCTTCCTC
1 CTCCTCTTCCTC
11092651 CTCCTCTTC
1 CTCCTCTTC
11092660 ACTTTCTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (12 bp):
CTCCTCTTCCTC
Found at i:11102306 original size:22 final size:22
Alignment explanation
Indices: 11102279--11102322 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11102269 AAACCTAAAT
11102279 TAATAAAAATAATAAATAATGA
1 TAATAAAAATAATAAATAATGA
*
11102301 TAATAATAATAATAAATAATGA
1 TAATAAAAATAATAAATAATGA
11102323 CAACTAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
TAATAAAAATAATAAATAATGA
Found at i:11106202 original size:15 final size:15
Alignment explanation
Indices: 11106178--11106213 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11106168 GAAGAAGTGG
*
11106178 AAGAAGAAGAAGGAA
1 AAGAAGAAGAAAGAA
11106193 AAGAAGAAGAAAGAA
1 AAGAAGAAGAAAGAA
*
11106208 AGGAAG
1 AAGAAG
11106214 GAAAATAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAGAA
Found at i:11106673 original size:17 final size:17
Alignment explanation
Indices: 11106653--11106699 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
11106643 CACATCCTCT
*
11106653 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* *
11106670 TTGTCACTGCATTTGCA
1 TTGTCATTGCATTTGAA
*
11106687 TTATCATTGCATT
1 TTGTCATTGCATT
11106700 GCCATTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:11108926 original size:40 final size:41
Alignment explanation
Indices: 11108861--11108937 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
11108851 TTTGTGTTGT
* *
11108861 GACATAAGGGGGTTTATTGCGACATAGACATTCTATGCCAC
1 GACATAAGGGGGTTTATTGCAACATAGACATGCTATGCCAC
*
11108902 GACAT-AGGGGGTTTGTTGCAACATAGACATGCTATG
1 GACATAAGGGGGTTTATTGCAACATAGACATGCTATG
11108938 TCGCGACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (41 bp):
GACATAAGGGGGTTTATTGCAACATAGACATGCTATGCCAC
Found at i:11117541 original size:23 final size:25
Alignment explanation
Indices: 11117514--11117560 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
11117504 AATGTTTTTA
11117514 AAATTTAAAT-CAAACA-ACTAATT
1 AAATTTAAATGCAAACATACTAATT
*
11117537 AAATTTCAATGGCAAACATACTAA
1 AAATTTAAAT-GCAAACATACTAA
11117561 GATAAAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (25 bp):
AAATTTAAATGCAAACATACTAATT
Found at i:11125787 original size:26 final size:26
Alignment explanation
Indices: 11125718--11125789 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
11125708 AGCATTACAC
* *
11125718 CCAGAATTGTCACTGCAGGAACTTGT
1 CCAGAATTGTCGCTGCATGAACTTGT
* *
11125744 TCAGAATTATCGCTGCATGAA-TATGT
1 CCAGAATTGTCGCTGCATGAACT-TGT
*
11125770 CCAGAGTTGTCGCTGCATGA
1 CCAGAATTGTCGCTGCATGA
11125790 GCAGGTCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (26 bp):
CCAGAATTGTCGCTGCATGAACTTGT
Found at i:11130778 original size:37 final size:37
Alignment explanation
Indices: 11130737--11130824 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
11130727 TTCCTGGGTA
* *
11130737 CAATTGAAGAATACTTATGCAATGATAGT-TCTGGATG
1 CAATTGAAGAATACTTATGCAACGACAGTCT-TGGATG
* *
11130774 CAATTTAAAGAATATTTATGCAACGACAGTCTTGGATG
1 CAA-TTGAAGAATACTTATGCAACGACAGTCTTGGATG
11130812 CAATCTGAA-AATA
1 CAAT-TGAAGAATA
11130825 TTCCTACGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
37 8 0.19
38 34 0.79
39 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (37 bp):
CAATTGAAGAATACTTATGCAACGACAGTCTTGGATG
Found at i:11130793 original size:38 final size:38
Alignment explanation
Indices: 11130743--11130815 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
11130733 GGTACAATTG
* *
11130743 AAGAATACTTATGCAATGATAGT-TCTGGATGCAATTTA
1 AAGAATACTTATGCAACGACAGTCT-TGGATGCAATTTA
*
11130781 AAGAATATTTATGCAACGACAGTCTTGGATGCAAT
1 AAGAATACTTATGCAACGACAGTCTTGGATGCAAT
11130816 CTGAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 30 0.97
39 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (38 bp):
AAGAATACTTATGCAACGACAGTCTTGGATGCAATTTA
Found at i:11139320 original size:3 final size:3
Alignment explanation
Indices: 11139303--11139393 Score: 52
Period size: 3 Copynumber: 32.0 Consensus size: 3
11139293 GCTACAATCA
* * *
11139303 AAT AAT AAC AA- AAT AAT AA- AAT AAT AGT -AT CA- AAT AAT AAT ACA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
11139347 ACT -AT GAT AAT AAT AGT AAT -AT GAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
11139391 AAT
1 AAT
11139394 TATTACTAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
2 9 0.13
3 56 0.81
4 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11139383 original size:17 final size:17
Alignment explanation
Indices: 11139303--11139384 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
11139293 GCTACAATCA
* * *
11139303 AATAATAACAAAATAAT
1 AATAATAATAATATGAT
* *
11139320 AA-AATAATAGTATCA-
1 AATAATAATAATATGAT
11139335 AATAATAATACAACTATGAT
1 AATAATAAT--AA-TATGAT
*
11139355 AATAATAGTAATATGAT
1 AATAATAATAATATGAT
11139372 AATAATAATAATA
1 AATAATAATAATA
11139385 ATAAATAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
15 2 0.04
16 15 0.29
17 20 0.38
18 3 0.06
19 4 0.08
20 8 0.15
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (17 bp):
AATAATAATAATATGAT
Found at i:11139652 original size:20 final size:18
Alignment explanation
Indices: 11139629--11139679 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
11139619 GAAGTGCTAG
11139629 AAATAAATAAAAAGTAAAA
1 AAATAAATAAAAAG-AAAA
11139648 TAAATAAATAAAAAAGAAAA
1 -AAATAAAT-AAAAAGAAAA
*
11139668 ACATAAATAAAA
1 AAATAAATAAAA
11139680 TTAAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 12 0.41
21 6 0.21
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAATAAAAAGAAAA
Found at i:11141319 original size:49 final size:50
Alignment explanation
Indices: 11141260--11141368 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
11141250 GGGGATTGGC
* * *
11141260 ATTGTTGTTTTATC-CACTTCACTACAACTTC-AGGAAGATAGGACTTGAT
1 ATTGTAGTTTTATCTCACTCCACTACAACTTCAAGG-AGATAAGACTTGAT
** * *
11141309 ATTGTAGTTTTATCTTGCTCCACTACATCTTCAAGGAGATAAGACTTGCT
1 ATTGTAGTTTTATCTCACTCCACTACAACTTCAAGGAGATAAGACTTGAT
*
11141359 AATGTAGTTT
1 ATTGTAGTTT
11141369 CAATCCAACC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 13 0.26
50 34 0.68
51 3 0.06
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (50 bp):
ATTGTAGTTTTATCTCACTCCACTACAACTTCAAGGAGATAAGACTTGAT
Found at i:11141408 original size:100 final size:100
Alignment explanation
Indices: 11141279--11141854 Score: 433
Period size: 100 Copynumber: 5.8 Consensus size: 100
11141269 TTATCCACTT
* * * * * * *
11141279 CACTACAACTTCAGGAAG-ATAGGACTTGATATTGTAGTTTTATCTTGCTCCACTACATCTTCAA
1 CACTGCAACTTCAGG-GGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAA
*
11141343 GGAGATAAGACTTGCTAATGTAGTTTCAATCCAACC
65 GGAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
* ** *
11141379 CACTGTAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCT-CTGTCGCAACTTCAA
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACT-GCATCTTCAA
* * * * * * * *
11141443 AGAGATAAAGATTTTCTACTATAGTTTTAATCTGATC
65 GGAGAT-AAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * *
11141480 C-TTACAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTCCACTGCATCTTCAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
** * ** * * * *
11141544 GAGATAAGTTTTTCTTCTATAGCTTCAATCAGACT
66 GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * *
11141579 CATTGCAACTTCAGGGGTATATGATTTGATTTTGTAGCTTCATCTTACTCTATTGCATCTTCAAA
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
* **
11141644 GAGATAAGACTTGCTTATGTAACTTCAATCCGACC
66 GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * * * * * *
11141679 TACTGTAATTTCAAGGGTGTCGGATTTGACGTTGTAGCTTCATCTTGTTCTACTGCAACTT-TAG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
* * * * * *
11141743 AGAGATAAAAATTTGCTATTGTAGTTTTAATCTGA-T
66 -GAGAT-AAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * *
11141779 CTCTGCAACTTCATGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGCATCTGCAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
*
11141844 GAGATCAGACT
66 GAGATAAGACT
11141855 CGTTGTTTGT
Statistics
Matches: 366, Mismatches: 102, Indels: 17
0.75 0.21 0.04
Matches are distributed among these distances:
99 31 0.08
100 289 0.79
101 46 0.13
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (100 bp):
CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
Found at i:11141722 original size:200 final size:199
Alignment explanation
Indices: 11141282--11141838 Score: 491
Period size: 200 Copynumber: 2.8 Consensus size: 199
11141272 TCCACTTCAC
* * * * ** * * * *
11141282 TACAACTTCAGGAAGATAGGACTTGATATTGTAGTTTTATCTTGCTCCACTACATCTTCAAGGAG
1 TACAACTTCAGGGATATAGGATTTAACGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAGGGAG
* * * * * *
11141347 ATAAGACTTGCTAATGTAGTTTCAATCCA-ACCCACTGTAACTTCAGGGGTATAGGATTTGATGT
66 ATAAGATTTGCT-TTGTAGTTTCAAT-CAGACTCATTGCAACTTCAGGGGTATAAGATTTGATGT
* * * * * * ** * *
11141411 TGTAGCTTCATCTTGCTCTGTCGCAACTTCAAAGAGATAAAGATTTTCTACTATAGTTTTAATCT
129 TGTAGCTTCATCTTACTCTATTGCATCTTCAAAGAGATAAAGACTTGCTACTATAACTTCAATCC
11141476 GATCCT
194 GATCCT
* * *
11141482 TACAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTCCACTGCATCTTCAGGGAG
1 TACAACTTCAGGGATATAGGATTTAACGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAGGGAG
* * * * * *
11141547 ATAAGTTTTTCTTCTATAGCTTCAATCAGACTCATTGCAACTTCAGGGGTATATGATTTGATTTT
66 ATAAGATTTGCTT-TGTAGTTTCAATCAGACTCATTGCAACTTCAGGGGTATAAGATTTGATGTT
*
11141612 GTAGCTTCATCTTACTCTATTGCATCTTCAAAGAGAT-AAGACTTGCTTA-TGTAACTTCAATCC
130 GTAGCTTCATCTTACTCTATTGCATCTTCAAAGAGATAAAGACTTGC-TACTATAACTTCAATCC
11141675 GA-CC-
194 GATCCT
* * * * * * * *
11141679 TACTGTAATTTCAAGGG-TGTCGGATTTGACGTTGTAGCTTCATCTTGTTCTACTGCAACTTTAG
1 TAC---AACTTC-AGGGATATAGGATTTAACGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAG
* * * * * *
11141743 AGAGATAAAAATTTGCTATTGTAGTTTTAATCTGA-TC-TCTGCAACTTCATGGATATAAGATTT
62 GGAGAT-AAGATTTGCT-TTGTAGTTTCAATCAGACTCAT-TGCAACTTCAGGGGTATAAGATTT
* *
11141806 GATGTTGTAGCTTCATCTTACTCCACTGCATCT
124 GATGTTGTAGCTTCATCTTACTCTATTGCATCT
11141839 GCAGGGAGAT
Statistics
Matches: 289, Mismatches: 58, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
197 3 0.01
198 2 0.01
199 21 0.07
200 239 0.83
201 23 0.08
202 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (199 bp):
TACAACTTCAGGGATATAGGATTTAACGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAGGGAG
ATAAGATTTGCTTTGTAGTTTCAATCAGACTCATTGCAACTTCAGGGGTATAAGATTTGATGTTG
TAGCTTCATCTTACTCTATTGCATCTTCAAAGAGATAAAGACTTGCTACTATAACTTCAATCCGA
TCCT
Found at i:11141835 original size:50 final size:50
Alignment explanation
Indices: 11141484--11141845 Score: 164
Period size: 50 Copynumber: 7.2 Consensus size: 50
11141474 CTGATCCTTA
* * * *
11141484 CAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTCCACTG
1 CAACTTCAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
* * * ** * ** *
11141534 CATCTTCAGGGAGATAAGTTTTTCT-TCTATAGCTTCAATCAGACT-CATTG
1 CAACTTCAGGGATATAAGATTTGATGT-TGTAGCTTC-ATCTTACTCCACTG
* * * * *
11141584 CAACTTCAGGGGTATATGATTTGATTTTGTAGCTTCATCTTACTCTATTG
1 CAACTTCAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
* ** * * * * ** *
11141634 CATCTTCAAAGAGATAAGACTTGCT-TATGTAACTTCAATCCGAC-CTACTG
1 CAACTTCAGGGATATAAGATTTGATGT-TGTAGCTTC-ATCTTACTCCACTG
* * * ** * ** *
11141684 TAATTTCAAGGG-TGTCGGATTTGACGTTGTAGCTTCATCTTGTTCTACTG
1 CAACTTC-AGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
* * * * * * * *
11141734 CAACTTTAGAGAGATA-AAAATTTGCTATTGTAGTTTTAATCTGA-T-CTCTG
1 CAACTTCAG-G-GATATAAGATTTGATGTTGTAG-CTTCATCTTACTCCACTG
*
11141784 CAACTTCATGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
1 CAACTTCAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
* *
11141834 CATCTGCAGGGA
1 CAACTTCAGGGA
11141846 GATCAGACTC
Statistics
Matches: 216, Mismatches: 80, Indels: 32
0.66 0.24 0.10
Matches are distributed among these distances:
48 11 0.05
49 29 0.13
50 142 0.66
51 27 0.12
52 7 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (50 bp):
CAACTTCAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTG
Found at i:11142158 original size:50 final size:50
Alignment explanation
Indices: 11142019--11142158 Score: 131
Period size: 50 Copynumber: 2.8 Consensus size: 50
11142009 ATTTTCATCC
* * *
11142019 GATCCACTGTAACTTCAGGGATATAGGATTCGAG-GTTGTAGCTTCATCTT
1 GATCCACTGCAACTTCAAGGATATAGGATTTG-GTGTTGTAGCTTCATCTT
* * * * * * * * **
11142069 GCTCAACTACGACTTCAAGGAGATAAGATTTGCTATTGTATTTTCAAT-TT
1 GATCCACTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTC-ATCTT
11142119 GATCCACTGCAACTTCAAGGATATAGGATTTGGTGTTGTA
1 GATCCACTGCAACTTCAAGGATATAGGATTTGGTGTTGTA
11142159 CTGATAGATC
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
50 65 0.97
51 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (50 bp):
GATCCACTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTT
Found at i:11142158 original size:100 final size:100
Alignment explanation
Indices: 11141954--11142148 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
11141944 GGATTTGACA
* * **
11141954 TTGTAGCGTCATCTTGCTCCACTGCATCTTCGGGGAGACAAGATTTGCTATCGTAATTTTCATCC
1 TTGTAGCGTCATCTTGCTCAACTACATCTTCAAGGAGACAAGATTTGCTATCGTAATTTTCATCC
* *
11142019 GATCCACTGTAACTTCAGGGATATAGGATTCGAGG
66 GATCCACTGCAACTTCAAGGATATAGGATTCGAGG
* * *
11142054 TTGTAGCTTCATCTTGCTCAACTACGA-CTTCAAGGAGATAAGATTTGCTATTGT-ATTTTCAAT
1 TTGTAGCGTCATCTTGCTCAACTAC-ATCTTCAAGGAGACAAGATTTGCTATCGTAATTTTC-AT
**
11142117 TTGATCCACTGCAACTTCAAGGATATAGGATT
64 CCGATCCACTGCAACTTCAAGGATATAGGATT
11142149 TGGTGTTGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 6 0.07
100 75 0.91
101 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (100 bp):
TTGTAGCGTCATCTTGCTCAACTACATCTTCAAGGAGACAAGATTTGCTATCGTAATTTTCATCC
GATCCACTGCAACTTCAAGGATATAGGATTCGAGG
Found at i:11144931 original size:13 final size:13
Alignment explanation
Indices: 11144909--11144947 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11144899 TGGGTATTGG
11144909 GTTATTTGTAATT
1 GTTATTTGTAATT
* *
11144922 GTTCTTTGTATTT
1 GTTATTTGTAATT
*
11144935 TTTATTTGTAATT
1 GTTATTTGTAATT
11144948 CATTTGTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (13 bp):
GTTATTTGTAATT
Found at i:11158939 original size:34 final size:35
Alignment explanation
Indices: 11158887--11158960 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 35
11158877 TTAGTAAGCA
*
11158887 TTGTCATCACATTCCCA-TTGTCATTACATTTTAG
1 TTGTCATCACATTCCCATTTGTCATTACAATTTAG
** * *
11158921 TTGTCATTGCATTTCCATTTGTCATTATAATTTAG
1 TTGTCATCACATTCCCATTTGTCATTACAATTTAG
11158956 -TGTCA
1 TTGTCA
11158961 GAGCATTGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (35 bp):
TTGTCATCACATTCCCATTTGTCATTACAATTTAG
Found at i:11160064 original size:26 final size:26
Alignment explanation
Indices: 11160035--11160093 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
11160025 GGAACTTATT
* * *
11160035 CAGAATTATCGCTGCATGAATATGTC
1 CAGAATTATCGCTACATGAACAGGTC
* * *
11160061 CAGAGTTGTCGCTACATGAGCAGGTC
1 CAGAATTATCGCTACATGAACAGGTC
11160087 CAGAATT
1 CAGAATT
11160094 GCGCCTAGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (26 bp):
CAGAATTATCGCTACATGAACAGGTC
Found at i:11161964 original size:3 final size:3
Alignment explanation
Indices: 11161947--11162043 Score: 64
Period size: 3 Copynumber: 34.0 Consensus size: 3
11161937 GCTACTATCA
* * *
11161947 AAT AAT AAC AA- AAT AAT AA- AAT AAT AGT -AT CA- AAT AAT AAT ACA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
11161991 ACT -AT GAT AAT AAT AGT AAT -AT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11162037 AAAT AAT
1 -AAT AAT
11162044 TATTACTAGC
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
2 9 0.12
3 62 0.83
4 4 0.05
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11162002 original size:17 final size:17
Alignment explanation
Indices: 11161980--11162022 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
11161970 ATAGTATCAA
11161980 ATAATAATA-CAACTATG
1 ATAATAATAGCAA-TATG
*
11161997 ATAATAATAGTAATATG
1 ATAATAATAGCAATATG
11162014 ATAATAATA
1 ATAATAATA
11162023 ATAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (17 bp):
ATAATAATAGCAATATG
Found at i:11162027 original size:17 final size:17
Alignment explanation
Indices: 11161947--11162043 Score: 76
Period size: 16 Copynumber: 5.7 Consensus size: 17
11161937 GCTACTATCA
* * *
11161947 AATAATAACAAAATAAT
1 AATAATAATAATATGAT
* *
11161964 AA-AATAATAGTATCA-
1 AATAATAATAATATGAT
11161979 AATAATAATACAACTATGAT
1 AATAATAAT--AA-TATGAT
*
11161999 AATAATAGTAATATGAT
1 AATAATAATAATATGAT
11162016 AATAATAATAATA--AT
1 AATAATAATAATATGAT
11162031 AATAATAAATAAT
1 AATAAT-AATAAT
11162044 TATTACTAGC
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
15 10 0.15
16 21 0.32
17 20 0.30
18 3 0.05
19 4 0.06
20 8 0.12
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (17 bp):
AATAATAATAATATGAT
Found at i:11162312 original size:20 final size:18
Alignment explanation
Indices: 11162289--11162339 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
11162279 GAAGTGCTAG
11162289 AAATAAATAAAAAGTAAAA
1 AAATAAATAAAAAG-AAAA
11162308 TAAATAAATAAAAAAGAAAA
1 -AAATAAAT-AAAAAGAAAA
*
11162328 ACATAAATAAAA
1 AAATAAATAAAA
11162340 TTAAGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 12 0.41
21 6 0.21
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAATAAAAAGAAAA
Found at i:11162563 original size:30 final size:30
Alignment explanation
Indices: 11162529--11162585 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11162519 TTGCAAAACG
*
11162529 AATAAAATCAAAT-GGGCAAAATTAAAATAA
1 AATAAAAT-AAATAGGACAAAATTAAAATAA
*
11162559 AATAAAATAAATAGGACTAAATTAAAA
1 AATAAAATAAATAGGACAAAATTAAAA
11162586 CAAGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (30 bp):
AATAAAATAAATAGGACAAAATTAAAATAA
Found at i:11164063 original size:100 final size:100
Alignment explanation
Indices: 11163941--11164516 Score: 514
Period size: 100 Copynumber: 5.8 Consensus size: 100
11163931 TTATCCACTT
* * * * *
11163941 CACTGCAACTTCAGGAAG-ATAGGACTTGATATTGTAGTTTTATCTTGCTCCACTGCATCTTCAA
1 CACTGCAACTTCAGG-GGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAA
*
11164005 GGAGATAAGACTTGCTAATGTAGTTTCAATCCAACC
65 GGAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
** *
11164041 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCT-CTGTCGCAACTTCAA
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACT-GCATCTTCAA
* * * * * * *
11164105 AGAGATAAAGATTTTCTACTGTAGTTTTAATCTGATC
65 GGAGAT-AAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * *
11164142 C-TTGCAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTCCACTGCATCTTCAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
* * ** * * * *
11164206 GAGATAAGATTTTCTTCTATAGCTTCAATCAGACT
66 GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * *
11164241 CATTGCAACTTCAGGGGTATATGATTTGATTTTGTAGCTTCATCTTACTCTATTGCATCTTCAAA
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
* **
11164306 GAGATAAGACTTGCTTATGTAACTTCAATCCGACC
66 GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * * * ** * *
11164341 TACTGCAATTTCAAGGGTGTAGGATTTGACGTTGTAGCTTCATCTTGTTCTGCTGCAACTT-TAG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
* * * * * *
11164405 AGAGATAAAAATTTGCTATTGTAGTTTTAATCTGA-T
66 -GAGAT-AAGACTTGCTAATGTAGTTTCAATCCGACC
* * * * *
11164441 CTCTGCAACTTCATGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGCATCTTCAAG
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
*
11164506 GAGATCAGACT
66 GAGATAAGACT
11164517 CGCTGTTTGT
Statistics
Matches: 378, Mismatches: 90, Indels: 17
0.78 0.19 0.04
Matches are distributed among these distances:
99 31 0.08
100 299 0.79
101 48 0.13
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (100 bp):
CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTTCAAG
GAGATAAGACTTGCTAATGTAGTTTCAATCCGACC
Found at i:11164385 original size:300 final size:300
Alignment explanation
Indices: 11163944--11164510 Score: 807
Period size: 300 Copynumber: 1.9 Consensus size: 300
11163934 TCCACTTCAC
* * * *
11163944 TGCAACTTCAGGAAGATAGGACTTGATATTGTAGTTTTATCTTGCTCCACTGCATCTTCAAGGAG
1 TGCAACTTCAGGAAGATAGGACTTGATATTGTAGCTTCATCTTACTCCACTGCATCTTCAAAGAG
** * *
11164009 ATAAGACTTGCTAATGTAGTTTCAATCCAACCCACTGCAACTTCAGGGGTATAGGATTTGATGTT
66 ATAAGACTTGCTAATGTAACTTCAATCCAACCCACTGCAACTTCAAGGGTATAGGATTTGACGTT
* *
11164074 GTAGCTTCATCTTGCTCTG-TCGCAACTTCAAAGAGATAAAGATTTTCTACTGTAGTTTTAATCT
131 GTAGCTTCATCTTGCTCTGCT-GCAACTTCAAAGAGATAAAAATTTGCTACTGTAGTTTTAATCT
* *
11164138 GATC-CTTGCAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTCCACTGCATCTT
195 GATCTC-TGCAACTTCAGGGATATAAGATTTAATGTTGTAACTTCATCTTACTCCACTGCATCTT
*
11164202 CAGGGAGATAAGATTTTCTTCTATAGCTTCAATCAGACTCAT
259 CAAGGAGATAAGATTTTCTTCTATAGCTTCAATCAGACTCAT
* * * * * *
11164244 TGCAACTTCAGG-GGTATATGATTTGATTTTGTAGCTTCATCTTACTCTATTGCATCTTCAAAGA
1 TGCAACTTCAGGAAG-ATAGGACTTGATATTGTAGCTTCATCTTACTCCACTGCATCTTCAAAGA
* * * * *
11164308 GATAAGACTTGCTTATGTAACTTCAATCCGACCTACTGCAATTTCAAGGGTGTAGGATTTGACGT
65 GATAAGACTTGCTAATGTAACTTCAATCCAACCCACTGCAACTTCAAGGGTATAGGATTTGACGT
* * * *
11164373 TGTAGCTTCATCTTGTTCTGCTGCAACTTTAGAGAGATAAAAATTTGCTATTGTAGTTTTAATCT
130 TGTAGCTTCATCTTGCTCTGCTGCAACTTCAAAGAGATAAAAATTTGCTACTGTAGTTTTAATCT
* * *
11164438 GATCTCTGCAACTTCATGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGCATCTTC
195 GATCTCTGCAACTTCAGGGATATAAGATTTAATGTTGTAACTTCATCTTACTCCACTGCATCTTC
11164503 AAGGAGAT
260 AAGGAGAT
11164511 CAGACTCGCT
Statistics
Matches: 233, Mismatches: 31, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
299 1 0.00
300 230 0.99
301 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (300 bp):
TGCAACTTCAGGAAGATAGGACTTGATATTGTAGCTTCATCTTACTCCACTGCATCTTCAAAGAG
ATAAGACTTGCTAATGTAACTTCAATCCAACCCACTGCAACTTCAAGGGTATAGGATTTGACGTT
GTAGCTTCATCTTGCTCTGCTGCAACTTCAAAGAGATAAAAATTTGCTACTGTAGTTTTAATCTG
ATCTCTGCAACTTCAGGGATATAAGATTTAATGTTGTAACTTCATCTTACTCCACTGCATCTTCA
AGGAGATAAGATTTTCTTCTATAGCTTCAATCAGACTCAT
Found at i:11164770 original size:50 final size:50
Alignment explanation
Indices: 11163941--11164812 Score: 152
Period size: 50 Copynumber: 17.6 Consensus size: 50
11163931 TTATCCACTT
* * * * * * *
11163941 CACTGCAACTTCAGGAAGATAGGACTTGATATTGTAGTTTTATCTTGCTC
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATCTTGCTC
* * * * * * ***
11163991 CACTGCATCTTCAAGGAGATAAGACTTGCTAATGTAGTTTCAATCCAAC-C
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTC-ATCTTGCTC
* * * *
11164041 CACTGCAACTTCAGGG-GTATAGGATTTGATGTTGTAGCTTCATCTTGCT-
1 CACTACAACTTCAGGGAG-ATAAGATTTGCTATTGTAGCTTCATCTTGCTC
** * ** * * * * *
11164090 CTGTCGCAACTTCAAAGAGATAAAGATTTTCTACTGTAGTTTTAATC-TGATC
1 CACT-ACAACTTCAGGGAGAT-AAGATTTGCTATTGTAG-CTTCATCTTGCTC
* * * * ** * *
11164142 C-TTGCAACTTCAGGGATATATGATTTAATGTTGTAACTTCATCTTGCTC
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATCTTGCTC
* * * * *
11164191 CACTGCATCTTCAGGGAGATAAGATTTTCT-TCTATAGCTTCAATC-AGACT-
1 CACTACAACTTCAGGGAGATAAGATTTGCTAT-TGTAGCTTC-ATCTTG-CTC
* * * * * *
11164241 CATTGCAACTTCAGGG-GTATATGATTTGATTTTGTAGCTTCATCTTACTC
1 CACTACAACTTCAGGGAG-ATAAGATTTGCTATTGTAGCTTCATCTTGCTC
* * * * ** * * *
11164291 TATTGCATCTTCAAAGAGATAAGACTTGCT-TATGTAACTTCAATC-CGAC-C
1 CACTACAACTTCAGGGAGATAAGATTTGCTAT-TGTAGCTTC-ATCTTG-CTC
* * * * * * *
11164341 TACTGCAATTTCAAGGGTG-TAGGATTTGAC-GTTGTAGCTTCATCTTGTTC
1 CACTACAACTTC-AGGGAGATAAGATTTG-CTATTGTAGCTTCATCTTGCTC
** * * * * * * *
11164391 TGCTGCAACTTTAGAGAGATAAAAATTTGCTATTGTAGTTTTAATC-TGAT-
1 CACTACAACTTCAGGGAGAT-AAGATTTGCTATTGTAG-CTTCATCTTGCTC
* * * * * * *
11164441 CTCTGCAACTTCATGGATATAAGATTTGATGTTGTAGCTTCATCTTACTC
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATCTTGCTC
* * * * * * * ** * *
11164491 CACTGCATCTTCAAGGAGATCAGACTCGCTGTTTGTAATTTCA--TTCCAAC
1 CACTACAACTTCAGGGAGATAAGATTTGCT-ATTGTAGCTTCATCTTGC-TC
* * * * * *
11164541 CTA-TGAAAACTTCGGGGGGACT-AGAATTG-TCA-T-T---TT-AT-TCGCTT
1 C-ACT-ACAACTTCAGGGAGA-TAAGATTTGCT-ATTGTAGCTTCATCTTGCTC
* * * * *
11164585 CACTACAACCTCAAGAAGATAGGATTTGAC-ATTGTAGCGTCATCTTGCTC
1 CACTACAACTTCAGGGAGATAAGATTTG-CTATTGTAGCTTCATCTTGCTC
* * * * ** * *
11164635 CACTGCATCTTC-GAGGAGACAAGATTTGCTATCGTAATTTTCATC-CGATC
1 CACTACAACTTCAG-GGAGATAAGATTTGCTATTGT-AGCTTCATCTTGCTC
* * * * ***
11164685 CACTGCAACTTCAGGGATATAGGATTCGAGGTTGTAGCTTCATCTTGCTC
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATCTTGCTC
* ** *
11164735 AACTACAACTTCAGGGAGATAAGATTTGCTATTGTATTTTCAAT-TTGATC
1 CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTC-ATCTTGCTC
* * * *
11164785 CACTGCAACTTCAAGGATATAGGATTTG
1 CACTACAACTTCAGGGAGATAAGATTTG
11164813 GTGTTGTACT
Statistics
Matches: 579, Mismatches: 188, Indels: 110
0.66 0.21 0.13
Matches are distributed among these distances:
42 1 0.00
43 16 0.03
44 4 0.01
45 5 0.01
48 12 0.02
49 68 0.12
50 376 0.65
51 85 0.15
52 12 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (50 bp):
CACTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATCTTGCTC
Found at i:11164820 original size:100 final size:100
Alignment explanation
Indices: 11164616--11164810 Score: 277
Period size: 100 Copynumber: 1.9 Consensus size: 100
11164606 GGATTTGACA
* * *
11164616 TTGTAGCGTCATCTTGCTCCACTGCATCTTCGAGGAGACAAGATTTGCTATCGTAATTTTCATCC
1 TTGTAGCGTCATCTTGCTCAACTACAACTTCGAGGAGACAAGATTTGCTATCGTAATTTTCATCC
*
11164681 GATCCACTGCAACTTCAGGGATATAGGATTCGAGG
66 GATCCACTGCAACTTCAAGGATATAGGATTCGAGG
* * *
11164716 TTGTAGCTTCATCTTGCTCAACTACAACTTC-AGGGAGATAAGATTTGCTATTGT-ATTTTCAAT
1 TTGTAGCGTCATCTTGCTCAACTACAACTTCGA-GGAGACAAGATTTGCTATCGTAATTTTC-AT
**
11164779 TTGATCCACTGCAACTTCAAGGATATAGGATT
64 CCGATCCACTGCAACTTCAAGGATATAGGATT
11164811 TGGTGTTGTA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 7 0.08
100 77 0.92
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (100 bp):
TTGTAGCGTCATCTTGCTCAACTACAACTTCGAGGAGACAAGATTTGCTATCGTAATTTTCATCC
GATCCACTGCAACTTCAAGGATATAGGATTCGAGG
Found at i:11167613 original size:13 final size:13
Alignment explanation
Indices: 11167591--11167629 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11167581 TGGGTATTGG
11167591 GTTATTTGTAATT
1 GTTATTTGTAATT
* *
11167604 GTTCTTTGTATTT
1 GTTATTTGTAATT
*
11167617 TTTATTTGTAATT
1 GTTATTTGTAATT
11167630 CATTTGTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (13 bp):
GTTATTTGTAATT
Found at i:11172996 original size:17 final size:17
Alignment explanation
Indices: 11172974--11173011 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
11172964 AGTTTTTAAA
*
11172974 CATTTTTATTGT-GCTTG
1 CATTTTAATTGTCG-TTG
11172991 CATTTTAATTGTCGTTG
1 CATTTTAATTGTCGTTG
11173008 CATT
1 CATT
11173012 CATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (17 bp):
CATTTTAATTGTCGTTG
Found at i:11178654 original size:3 final size:3
Alignment explanation
Indices: 11178637--11178694 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
11178627 GTTACAATCA
* * * *
11178637 AAT AAT AAC AA- AAT AAT AAA AAT AAT AGT AACA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
11178682 AAT AAT AAAT AAT
1 AAT AAT -AAT AAT
11178695 TATTACTAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:11178675 original size:22 final size:23
Alignment explanation
Indices: 11178637--11178689 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
11178627 GTTACAATCA
11178637 AATAATAACAAAATAATAAAAAT
1 AATAATAACAAAATAATAAAAAT
* *
11178660 AATAGTAAC-AAATAATAATAAT
1 AATAATAACAAAATAATAAAAAT
11178682 AATAATAA
1 AATAATAA
11178690 ATAATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAATAACAAAATAATAAAAAT
Found at i:11178679 original size:19 final size:19
Alignment explanation
Indices: 11178637--11178694 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
11178627 GTTACAATCA
* * *
11178637 AATAATAACAAAATAATAAA
1 AATAATAATAACA-AATAAT
*
11178657 AATAATAGTAACAAATAAT
1 AATAATAATAACAAATAAT
*
11178676 AATAATAATAATAAATAAT
1 AATAATAATAACAAATAAT
11178695 TATTACTAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAATAACAAATAAT
Found at i:11178939 original size:4 final size:4
Alignment explanation
Indices: 11178930--11178978 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
11178920 GAAGTTCTAG
* *
11178930 AAAT AAAT AAAT -AAT -AAT AAAT -AAT AAAT AAAA AGAAA AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
11178976 AAA
1 AAA
11178979 ATTAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
3 9 0.22
4 27 0.68
5 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:11178950 original size:10 final size:11
Alignment explanation
Indices: 11178931--11178978 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
11178921 AAGTTCTAGA
11178931 AATAAATAAAT
1 AATAAATAAAT
11178942 AAT-AATAAAT
1 AATAAATAAAT
11178952 AATAAATAAA-
1 AATAAATAAAT
*
11178962 AAGAAA-AAAT
1 AATAAATAAAT
11178972 AAATAAA
1 -AATAAA
11178979 ATTAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 3 0.09
10 15 0.47
11 14 0.44
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:11178957 original size:17 final size:17
Alignment explanation
Indices: 11178928--11178979 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
11178918 TAGAAGTTCT
*
11178928 AGAAATAAATAAATAATA
1 AGAAAT-AATAAATAAAA
*
11178946 ATAAATAATAAATAAAA
1 AGAAATAATAAATAAAA
*
11178963 AGAAAAAATAAATAAAA
1 AGAAATAATAAATAAAA
11178980 TTAAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
AGAAATAATAAATAAAA
Found at i:11181941 original size:48 final size:48
Alignment explanation
Indices: 11181870--11181984 Score: 212
Period size: 48 Copynumber: 2.4 Consensus size: 48
11181860 AAGGTGGAAG
11181870 TATATGGCAGTTTATCTGTATTAATGTGACATTGTTGACGATTCTGAT
1 TATATGGCAGTTTATCTGTATTAATGTGACATTGTTGACGATTCTGAT
*
11181918 TATATGGCTGTTTATCTGTATTAATGTGACATTGTTGACGATTCTGAT
1 TATATGGCAGTTTATCTGTATTAATGTGACATTGTTGACGATTCTGAT
11181966 TATATGGCAGTTTTATCTG
1 TATATGGCAG-TTTATCTG
11181985 CGACTCTGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
48 56 0.88
49 8 0.12
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.45
Consensus pattern (48 bp):
TATATGGCAGTTTATCTGTATTAATGTGACATTGTTGACGATTCTGAT
Found at i:11186342 original size:40 final size:40
Alignment explanation
Indices: 11186296--11186385 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
11186286 GAAGCTATTC
* *
11186296 TAACTTGTTTGCAAAAAATTTTGAAGTG-TTAAAATGATTT
1 TAACTTGATTG-AAAAAATTTTGAAGTGTTTAAAATCATTT
* ** **
11186336 TGACTTGATTGAAATCATTTTGACTTGTTTAAAATCATTT
1 TAACTTGATTGAAAAAATTTTGAAGTGTTTAAAATCATTT
11186376 TAACTTGATT
1 TAACTTGATT
11186386 TTACAATTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 12 0.29
40 29 0.71
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (40 bp):
TAACTTGATTGAAAAAATTTTGAAGTGTTTAAAATCATTT
Found at i:11186355 original size:20 final size:20
Alignment explanation
Indices: 11186324--11186385 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
11186314 TTTTGAAGTG
*
11186324 TTAAAATGATTTTGACTTGA
1 TTAAAATCATTTTGACTTGA
* *
11186344 TTGAAATCATTTTGACTTGT
1 TTAAAATCATTTTGACTTGA
*
11186364 TTAAAATCATTTTAACTTGA
1 TTAAAATCATTTTGACTTGA
11186384 TT
1 TT
11186386 TTACAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTGACTTGA
Found at i:11188669 original size:24 final size:25
Alignment explanation
Indices: 11188638--11188701 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 25
11188628 ACAAAATTAT
*
11188638 CTCA-TACGAGCCCAGATAGGTTAG
1 CTCATTACGAGCCCAGATAAGTTAG
*
11188662 CTC-TTACGAGCCTAGATAAGTTAG
1 CTCATTACGAGCCCAGATAAGTTAG
11188686 CTCATT-CGAGCCCAGA
1 CTCATTACGAGCCCAGA
11188702 CAGAGTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (25 bp):
CTCATTACGAGCCCAGATAAGTTAG
Found at i:11188701 original size:48 final size:49
Alignment explanation
Indices: 11188609--11188701 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 49
11188599 TTCCGAAAAC
*
11188609 TTAGCTCATACAAGCCTAGACAAAATTATCTCATACGAGCCCAGATAGG
1 TTAGCTCATACAAGCCTAGACAAAATTAGCTCATACGAGCCCAGATAGG
* * * * *
11188658 TTAGCTCTTACGAGCCTAGA-TAAGTTAGCTCATTCGAGCCCAGA
1 TTAGCTCATACAAGCCTAGACAAAATTAGCTCATACGAGCCCAGA
11188702 CAGAGTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 20 0.53
49 18 0.47
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (49 bp):
TTAGCTCATACAAGCCTAGACAAAATTAGCTCATACGAGCCCAGATAGG
Found at i:11192500 original size:32 final size:32
Alignment explanation
Indices: 11192454--11192520 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
11192444 TGTAATAGAG
*
11192454 GGAGTTTTTTTTCTTTTCGAATAAGATTGAGA
1 GGAGGTTTTTTTCTTTTCGAATAAGATTGAGA
*
11192486 GGAGGTTTTTTTCTTTTTGAATAAGATTGAGA
1 GGAGGTTTTTTTCTTTTCGAATAAGATTGAGA
11192518 GGA
1 GGA
11192521 TTCTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.45
Consensus pattern (32 bp):
GGAGGTTTTTTTCTTTTCGAATAAGATTGAGA
Found at i:11192857 original size:20 final size:21
Alignment explanation
Indices: 11192809--11192857 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
11192799 GTTCGTATTT
*
11192809 TTTATTATTATTCATATTTAA
1 TTTATTATTATTCACATTTAA
*
11192830 TTGT-TTATT-TTGACATTTAA
1 TT-TATTATTATTCACATTTAA
11192850 TTTATTAT
1 TTTATTAT
11192858 CTTGTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 7 0.29
22 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTATTATTATTCACATTTAA
Found at i:11193553 original size:20 final size:19
Alignment explanation
Indices: 11193528--11193565 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11193518 TAATTGATTA
*
11193528 ATATTATTGCCATTATTATG
1 ATATTATTACCA-TATTATG
11193548 ATATTATTACCATATTAT
1 ATATTATTACCATATTAT
11193566 TTGTTACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
ATATTATTACCATATTATG
Found at i:11198714 original size:44 final size:43
Alignment explanation
Indices: 11198652--11198737 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 43
11198642 ACACTTCGCT
* * *
11198652 TAAAAAAAGGTTTGAGTTGAAAACCTGAAAGGGCGGCTCAAAC
1 TAAAAAAAAGTTTAAGTTGAAAACCTGAAAGGGCAGCTCAAAC
11198695 TAAAAAAAAGTTTCAAGTTGAAAACCTGAAAGGGCAGCTCAAA
1 TAAAAAAAAGTTT-AAGTTGAAAACCTGAAAGGGCAGCTCAAA
11198738 TTAGCAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 12 0.31
44 27 0.69
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (43 bp):
TAAAAAAAAGTTTAAGTTGAAAACCTGAAAGGGCAGCTCAAAC
Found at i:11199793 original size:49 final size:49
Alignment explanation
Indices: 11199720--11200229 Score: 375
Period size: 49 Copynumber: 10.4 Consensus size: 49
11199710 CATAGAGTTT
* * * * *
11199720 GAAGAAGGATAGGTTAAAATCGCAACGGCGAACCTAACATCC-TAAAATC
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACA-CCTTAAAATC
* * * * * *
11199769 GAAGAGGGAAAGGTTAAAGCCGCAATGGCGGACCTTACACCTTAAAA-C
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* ** *
11199817 TGAAGAGGGATAGGTTGAAG-CTGCAACGACGAACCTAACACCCAAAAAATT
1 -GAAGAGGGATAGGTTGAAGTC-GCAACGACGGACCTAACA-CCTTAAAATC
* * * * * * * * *
11199868 GAAAAGGGAAAGATTGAAGTCGTAATGACGGATCTTACACCCTAAAACC
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* * *
11199917 AAAGAGGGATAGGTTGAAGTCGCAACAACGGATCTAACACCTTAAAATC
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* * * * ** * *
11199966 AAAGAGGGATAGATTGAAGCCGTAACGATAGATCTAACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* * * * *
11200015 AAAGAGGAAAAGGTTGAAGTCGCAACGACGGACCTTACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* * *
11200064 GAAGAGGGATAGGTTGAAGTCGCAATGACGGACCTAACACCCTAAAACAC
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAA-TC
* * * * * * * *
11200114 GACGAGGGAAAGATTGAAGTCACAACGAAGGATCTTACACCTTAAAATA
1 GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
* * * * * * *
11200163 AAAGAGGAACAGGTTGAAG-CGTGACCG-TGGACCTAATACCTTAAAA-C
1 GAAGAGGGATAGGTTGAAGTCG-CAACGACGGACCTAACACCTTAAAATC
* *
11200210 TAATGAGGGATAGATTGAAG
1 GAA-GAGGGATAGGTTGAAG
11200230 CCACGACGGC
Statistics
Matches: 360, Mismatches: 92, Indels: 19
0.76 0.20 0.04
Matches are distributed among these distances:
47 2 0.01
48 33 0.09
49 251 0.70
50 73 0.20
51 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (49 bp):
GAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
Found at i:11207752 original size:19 final size:20
Alignment explanation
Indices: 11207717--11207773 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
11207707 CTATTCTGAC
*
11207717 TTGTTTGAAAAACATTTTGAA
1 TTGTTT-AAAATCATTTTGAA
* *
11207738 TTG-TTAAAATGATTTTGAC
1 TTGTTTAAAATCATTTTGAA
11207757 TTGTTTAAAATCATTTT
1 TTGTTTAAAATCATTTT
11207774 AACTTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 14 0.45
20 14 0.45
21 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (20 bp):
TTGTTTAAAATCATTTTGAA
Found at i:11207766 original size:20 final size:20
Alignment explanation
Indices: 11207713--11207789 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
11207703 GGAGCTATTC
*
11207713 TGACTTGTTTGAAAAACATTT
1 TGACTTGTTT-AAAATCATTT
* *
11207734 TGAATTG-TTAAAATGATTT
1 TGACTTGTTTAAAATCATTT
11207753 TGACTTGTTTAAAATCATTT
1 TGACTTGTTTAAAATCATTT
*
11207773 TAACTTGATTTTAAAAT
1 TGACTTG--TTTAAAAT
11207790 TGTTTCAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
19 14 0.30
20 19 0.40
21 6 0.13
22 8 0.17
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (20 bp):
TGACTTGTTTAAAATCATTT
Found at i:11212109 original size:9 final size:9
Alignment explanation
Indices: 11212095--11212209 Score: 54
Period size: 9 Copynumber: 12.1 Consensus size: 9
11212085 TTCTAGAAAC
11212095 TTTTAAATT
1 TTTTAAATT
*
11212104 TTTTAACTT
1 TTTTAAATT
11212113 CTTTATATAATT
1 -TTT-TA-AATT
*
11212125 TTTAGAAATTT
1 TTT-TAAA-TT
11212136 TTTTGAAA-T
1 TTTT-AAATT
11212145 TTTTAGAATT
1 TTTTA-AATT
* *
11212155 TTTGAAAAT
1 TTTTAAATT
*
11212164 TTATAAA-T
1 TTTTAAATT
**
11212172 TTTGGAATT
1 TTTTAAATT
*
11212181 TTTATAAATA
1 TTT-TAAATT
*
11212191 TTTTGAATT
1 TTTTAAATT
*
11212200 TTTGAAATT
1 TTTTAAATT
11212209 T
1 T
11212210 ATTTTGAATT
Statistics
Matches: 79, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
8 6 0.08
9 39 0.49
10 16 0.20
11 15 0.19
12 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (9 bp):
TTTTAAATT
Found at i:11212158 original size:18 final size:18
Alignment explanation
Indices: 11212121--11212202 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 18
11212111 TTCTTTATAT
11212121 AATTTTTAGAAATTTTTTTGA
1 AATTTTTAG-AA--TTTTTGA
11212142 AATTTTTAGAATTTTTGAA
1 AATTTTTAGAATTTTTG-A
* *
11212161 AATTTATA-AA-TTTTGG
1 AATTTTTAGAATTTTTGA
*
11212177 AATTTTTATAAATATTTTG-
1 AATTTTTA-GAAT-TTTTGA
11212196 AATTTTT
1 AATTTTT
11212203 GAAATTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
16 7 0.13
17 5 0.09
18 10 0.19
19 15 0.28
20 7 0.13
21 9 0.17
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
AATTTTTAGAATTTTTGA
Found at i:11217596 original size:23 final size:24
Alignment explanation
Indices: 11217562--11217606 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
11217552 CCAATTAAGG
*
11217562 AATTATTGTTT-AGATTTAATTCT
1 AATTATTGTTTAAAATTTAATTCT
11217585 AATTATCT-TTTAAAATTTAATT
1 AATTAT-TGTTTAAAATTTAATT
11217607 TGGATCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (24 bp):
AATTATTGTTTAAAATTTAATTCT
Found at i:11225141 original size:51 final size:51
Alignment explanation
Indices: 11225065--11225302 Score: 244
Period size: 51 Copynumber: 4.6 Consensus size: 51
11225055 CTATAAACGA
*
11225065 AAAGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
1 AAAGATTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
* * * *
11225116 AAAGATTCGGTGTCTAAGTGTCATCGTGAGTAAATGAATTCTTTACGGATT
1 AAAGATTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
* * * * * *
11225167 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAATT
1 AAAGATTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
* * * * * * * * *
11225218 AAAGGTCCGATGACTCAGTGTCATCGTTAGTATATGAATTCCTATATGAAAT
1 AAAGATTCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGACT
* *
11225270 AAGAGGTTCGATGACTATA-TGTCATCGTTAGTA
1 AA-AGATTCGATGACTA-AGTGTCATCGTGAGTA
11225303 TTAAACGAAA
Statistics
Matches: 161, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
51 123 0.76
52 11 0.07
53 26 0.16
54 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (51 bp):
AAAGATTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
Found at i:11225255 original size:102 final size:104
Alignment explanation
Indices: 11225072--11225302 Score: 279
Period size: 102 Copynumber: 2.2 Consensus size: 104
11225062 CGAAAAGATC
* * * * * *
11225072 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACTAAAGATTCGGTGTCTAAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAACTAAAGATCCGATGACTAAGTGT
* * *
11225137 CATCGTGAGTAAATGAATT-CTTTACGGATTAA-AGGTT
66 CATCGTGAGTAAATGAATTCCTATACGAAATAAGAGGTT
* * * *
11225174 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAATTAAAGGTCCGATGACTCAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAACTAAAGATCCGATGACTAAGTGT
* * *
11225239 CATCGTTAGTATATGAATTCCTATATGAAATAAGAGGTT
66 CATCGTGAGTAAATGAATTCCTATACGAAATAAGAGGTT
*
11225278 CGATGACTATA-TGTCATCGTTAGTA
1 CGATGACTA-AGTGTCATCGTGAGTA
11225303 TTAAACGAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
102 72 0.66
103 9 0.08
104 27 0.25
105 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (104 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAACTAAAGATCCGATGACTAAGTGT
CATCGTGAGTAAATGAATTCCTATACGAAATAAGAGGTT
Found at i:11232354 original size:51 final size:51
Alignment explanation
Indices: 11232270--11232501 Score: 271
Period size: 51 Copynumber: 4.6 Consensus size: 51
11232260 CTATAAACGA
*
11232270 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
11232321 AATGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGA-T
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
11232371 -----TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * **
11232417 AAAGGTCCGATGACTCAGTGTCATCATGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
11232469 AAGAGGTCTGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
11232502 TTAAACGAAA
Statistics
Matches: 156, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
45 41 0.26
46 1 0.01
50 1 0.01
51 77 0.49
52 10 0.06
53 25 0.16
54 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:11232416 original size:45 final size:45
Alignment explanation
Indices: 11232278--11232416 Score: 170
Period size: 45 Copynumber: 3.0 Consensus size: 45
11232268 GAAAAGGTCT
* **
11232278 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAATGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCC---A-TGATGGAT--TCC
* * *
11232329 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTCC
11232374 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
11232417 AAAGGTCCGA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 43 0.54
47 3 0.04
51 33 0.42
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (45 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTCC
Found at i:11232447 original size:96 final size:96
Alignment explanation
Indices: 11232278--11232455 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 96
11232268 GAAAAGGTCT
* * *
11232278 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAATGGTCCGATGACTAAGTGTC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAAGGTCCGATGACTAAGTGTC
*
11232343 ATCGTGAGTAAATGAATCCTTTACGGATTCC
66 ATCATGAGTAAATGAATCCTTTACGGATTCC
* *
11232374 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCGATGACTCAGTGTC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAAGGTCCGATGACTAAGTGTC
*
11232439 ATCATGAGTATATGAAT
66 ATCATGAGTAAATGAAT
11232456 TCCTATATGG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (96 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAAGGTCCGATGACTAAGTGTC
ATCATGAGTAAATGAATCCTTTACGGATTCC
Found at i:11260621 original size:21 final size:20
Alignment explanation
Indices: 11260572--11260621 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
11260562 TTGATAATTC
11260572 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
11260590 TTAAATT-TTATAATTTATATA
1 TT-AATTATTATAA-TTATAAA
11260611 TTAATTATTAT
1 TTAATTATTAT
11260622 CAAAAGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 5 0.19
20 7 0.27
21 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:11265153 original size:12 final size:12
Alignment explanation
Indices: 11265136--11265161 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11265126 TATTATTATG
11265136 ATGAATGCTATT
1 ATGAATGCTATT
11265148 ATGAATGCTATT
1 ATGAATGCTATT
11265160 AT
1 AT
11265162 TATTTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:11267126 original size:5 final size:5
Alignment explanation
Indices: 11267116--11267159 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
11267106 TTGCAACAAG
* * *
11267116 ATTTT ATTTT ACTAT A-TTT ATTTT ATTTT ATTTT GTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
11267160 TAGTTTAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:11267557 original size:3 final size:3
Alignment explanation
Indices: 11267537--11267570 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
11267527 ATATACGAAA
* *
11267537 TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11267571 GTTGTTGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11273540 original size:13 final size:12
Alignment explanation
Indices: 11273512--11273546 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
11273502 TATAAACAGT
11273512 ATCCTAAAAATA
1 ATCCTAAAAATA
*
11273524 ATCCTAAATATTA
1 ATCCTAAA-AATA
11273537 ATCCTAAAAA
1 ATCCTAAAAA
11273547 AATAAAGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (12 bp):
ATCCTAAAAATA
Found at i:11276454 original size:16 final size:16
Alignment explanation
Indices: 11276433--11276463 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11276423 CATACCTTGT
*
11276433 AGAAAATAATCACAAC
1 AGAAAATAAACACAAC
11276449 AGAAAATAAACACAA
1 AGAAAATAAACACAA
11276464 AGGATAATAT
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:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (16 bp):
AGAAAATAAACACAAC
Found at i:11281619 original size:17 final size:17
Alignment explanation
Indices: 11281589--11281629 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
11281579 AAACTAAAAT
11281589 GAATGCAACGACAATTAA
1 GAATGCAACGACAA-TAA
11281607 -AATGCAA-GCACAATAA
1 GAATGCAACG-ACAATAA
11281623 GAATGCA
1 GAATGCA
11281630 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (17 bp):
GAATGCAACGACAATAA
Found at i:11281757 original size:45 final size:45
Alignment explanation
Indices: 11281697--11281797 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
11281687 TGCTTTGGTT
11281697 TTCTTTTTCTTCTTTTTCGAGCGCTCTTTCTCGTCATGGTGTTTC
1 TTCTTTTTCTTCTTTTTCGAGCGCTCTTTCTCGTCATGGTGTTTC
11281742 TTCTTTTTCTTCTTTTTCGAGCGCTCTTTCTCGTCATGGTGTTTC
1 TTCTTTTTCTTCTTTTTCGAGCGCTCTTTCTCGTCATGGTGTTTC
11281787 TTCTTTTTCTT
1 TTCTTTTTCTT
11281798 TTCCTTGTGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.04, C:0.24, G:0.14, T:0.58
Consensus pattern (45 bp):
TTCTTTTTCTTCTTTTTCGAGCGCTCTTTCTCGTCATGGTGTTTC
Found at i:11293980 original size:18 final size:18
Alignment explanation
Indices: 11293954--11293992 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11293944 GGAACTAATC
* *
11293954 TTGAGAGAATAGAGAGAA
1 TTGAAAGAATAGAGAAAA
*
11293972 TTGAAAGAATGGAGAAAA
1 TTGAAAGAATAGAGAAAA
11293990 TTG
1 TTG
11293993 GATTTGAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (18 bp):
TTGAAAGAATAGAGAAAA
Found at i:11299749 original size:27 final size:27
Alignment explanation
Indices: 11299701--11299774 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
11299691 AGTTTATCTT
* *
11299701 TTACAAGCCCAAAT-AGAATATCGCTC
1 TTACGAGCCAAAATCAGAATATCGCTC
* * *
11299727 TTACGAGCCAGAATCAGAATATCGTTT
1 TTACGAGCCAAAATCAGAATATCGCTC
* *
11299754 TTATGAGCCAAAATCAAAATA
1 TTACGAGCCAAAATCAGAATA
11299775 CTCCTCCAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 11 0.28
27 28 0.72
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (27 bp):
TTACGAGCCAAAATCAGAATATCGCTC
Found at i:11302322 original size:12 final size:12
Alignment explanation
Indices: 11302305--11302345 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
11302295 TTTAAAGAGT
11302305 ATAAAATAAAAG
1 ATAAAATAAAAG
*
11302317 ATAAAATAAAAT
1 ATAAAATAAAAG
*
11302329 AGAAAATAAAAG
1 ATAAAATAAAAG
11302341 -TAAAA
1 ATAAAA
11302346 GTTTGAGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:11302327 original size:17 final size:17
Alignment explanation
Indices: 11302305--11302345 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
11302295 TTTAAAGAGT
11302305 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
11302322 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
11302339 AGTAAAA
1 A-TAAAA
11302346 GTTTGAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:11307003 original size:24 final size:25
Alignment explanation
Indices: 11306962--11307010 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
11306952 ACAATAATTT
11306962 TTTTTCTTCTTTTCTTTTCTCTTTC
1 TTTTTCTTCTTTTCTTTTCTCTTTC
*
11306987 TTTTTC-TCATTTT-TTTTCTTTTTC
1 TTTTTCTTC-TTTTCTTTTCTCTTTC
11307011 AAGTGACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCTTCTTTTCTTTTCTCTTTC
Found at i:11307009 original size:10 final size:11
Alignment explanation
Indices: 11306959--11307009 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
11306949 ATAACAATAA
11306959 TTTTTTTTCTTC
1 TTTTTTTTC-TC
11306971 TTTTCTTTTCTC
1 TTTT-TTTTCTC
11306983 TTTCTTTTTCTC
1 TTT-TTTTTCTC
11306995 ATTTTTTTTCT-
1 -TTTTTTTTCTC
11307006 TTTT
1 TTTT
11307010 CAAGTGACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.11
12 23 0.64
13 9 0.25
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:11308671 original size:15 final size:16
Alignment explanation
Indices: 11308637--11308672 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
11308627 AAACGTATTC
11308637 ATATCACAATATCATA
1 ATATCACAATATCATA
*
11308653 ATATCACAA-ATCATG
1 ATATCACAATATCATA
11308668 ATATC
1 ATATC
11308673 CATATTCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATCACAATATCATA
Found at i:11325925 original size:18 final size:16
Alignment explanation
Indices: 11325892--11325924 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11325882 TACATTGCTA
11325892 ATATAAAAAATATATT
1 ATATAAAAAATATATT
*
11325908 ATAT-ATAAATATATT
1 ATATAAAAAATATATT
11325923 AT
1 AT
11325925 TTCGGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAAAATATATT
Found at i:11326153 original size:69 final size:69
Alignment explanation
Indices: 11326039--11326168 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
11326029 ATCGAATGAT
* * *
11326039 AATTAGATCGGTTTAATCGGTTAATTAGGTTTTAATCAAATTATGAACACCCTTACACTTCCATA
1 AATTAGATCGGTTTAATCAGTTAATTAGGTTTTAATCAAACTATGAACACCCCTACACTTCCATA
11326104 ATCG
66 ATCG
* * *
11326108 AATTAGATCGGTTTGA-CTAGTTAATTCGGTTTTAATCGAACTATGAACACCCCTACACTTC
1 AATTAGATCGGTTTAATC-AGTTAATTAGGTTTTAATCAAACTATGAACACCCCTACACTTC
11326169 TATATGTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 53 0.98
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (69 bp):
AATTAGATCGGTTTAATCAGTTAATTAGGTTTTAATCAAACTATGAACACCCCTACACTTCCATA
ATCG
Found at i:11331906 original size:25 final size:23
Alignment explanation
Indices: 11331869--11331938 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
11331859 TTATCTAGTC
**
11331869 ATATAATGAATTATTAATATAATT
1 ATATAATTTATTATTAATA-AATT
11331893 AATATAATTTATTATTTTAATAAATT
1 -ATATAATTTATTA--TTAATAAATT
*
11331919 ATTTAATATTATT-TTAATAA
1 ATATAAT-TTATTATTAATAA
11331939 TAAATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.18
25 17 0.44
26 9 0.23
27 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
ATATAATTTATTATTAATAAATT
Found at i:11332509 original size:21 final size:20
Alignment explanation
Indices: 11332485--11332527 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11332475 ATCCAAATAT
11332485 AAAAAAAATTAATTTTTCAAA
1 AAAAAAAATT-ATTTTTCAAA
* * *
11332506 AAAATATATTATTTTTTAAA
1 AAAAAAAATTATTTTTCAAA
11332526 AA
1 AA
11332528 TCAATTTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAAAATTATTTTTCAAA
Found at i:11334774 original size:18 final size:18
Alignment explanation
Indices: 11334751--11334793 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
11334741 ACACACATTG
11334751 CTAATTGTTTTAACAACA
1 CTAATTGTTTTAACAACA
11334769 CTAATTGTTTTAACAACA
1 CTAATTGTTTTAACAACA
11334787 CTAATTG
1 CTAATTG
11334794 CTACTAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (18 bp):
CTAATTGTTTTAACAACA
Found at i:11334835 original size:27 final size:28
Alignment explanation
Indices: 11334767--11334835 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
11334757 GTTTTAACAA
* *
11334767 CACTAATTGTTTTAACAACACTAATTGC
1 CACTAACTGTTTTAACAACACTAACTGC
* * * * *
11334795 TACTAACAGCTTTACCAAC-TTAACTGC
1 CACTAACTGTTTTAACAACACTAACTGC
11334822 CACTAACTGTTTTA
1 CACTAACTGTTTTA
11334836 TACCTTTTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (28 bp):
CACTAACTGTTTTAACAACACTAACTGC
Found at i:11343266 original size:15 final size:15
Alignment explanation
Indices: 11343246--11343275 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11343236 TTTTATCAAA
11343246 ATATTATAAGAGTTG
1 ATATTATAAGAGTTG
11343261 ATATTATAAGAGTTG
1 ATATTATAAGAGTTG
11343276 GCATCCGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
ATATTATAAGAGTTG
Found at i:11344178 original size:272 final size:272
Alignment explanation
Indices: 11343692--11344227 Score: 1063
Period size: 272 Copynumber: 2.0 Consensus size: 272
11343682 AGTTGTAAGT
11343692 AAAGATATTTGGTTGAAGGCCCCTTCCACACATTTCATGAAGAAGCTCGTTGGCTGTATCTAGCT
1 AAAGATATTTGGTTGAAGGCCCCTTCCACACATTTCATGAAGAAGCTCGTTGGCTGTATCTAGCT
11343757 CCCCACATTTACAAAGGCCATCAACAAGTGCAGTATAAGTCACAACATTTGGTATAAGCCCCATT
66 CCCCACATTTACAAAGGCCATCAACAAGTGCAGTATAAGTCACAACATTTGGTATAAGCCCCATT
11343822 TGCACCATCTGATTATGGAGGGAAAAGGCCTTTTTCATTTCACCTGCCTTGCAATAACCATCAAT
131 TGCACCATCTGATTATGGAGGGAAAAGGCCTTTTTCATTTCACCTGCCTTGCAATAACCATCAAT
*
11343887 AAGTGCTGTGTATGTAAATTCATCGAGTTCCAACCCTCTTCCAAGCATTTCTTGAAAGACATTAC
196 AAGTGCTGTGTATGTAAATTCATCGAGTTCCAACCCTCTTCCAAACATTTCTTGAAAGACATTAC
11343952 AAGCATTTCTTG
261 AAGCATTTCTTG
11343964 AAAGATATTTGGTTGAAGGCCCCTTCCACACATTTCATGAAGAAGCTCGTTGGCTGTATCTAGCT
1 AAAGATATTTGGTTGAAGGCCCCTTCCACACATTTCATGAAGAAGCTCGTTGGCTGTATCTAGCT
11344029 CCCCACATTTACAAAGGCCATCAACAAGTGCAGTATAAGTCACAACATTTGGTATAAGCCCCATT
66 CCCCACATTTACAAAGGCCATCAACAAGTGCAGTATAAGTCACAACATTTGGTATAAGCCCCATT
11344094 TGCACCATCTGATTATGGAGGGAAAAGGCCTTTTTCATTTCACCTGCCTTGCAATAACCATCAAT
131 TGCACCATCTGATTATGGAGGGAAAAGGCCTTTTTCATTTCACCTGCCTTGCAATAACCATCAAT
11344159 AAGTGCTGTGTATGTAAATTCATCGAGTTCCAACCCTCTTCCAAACATTTCTTGAAAGACATTAC
196 AAGTGCTGTGTATGTAAATTCATCGAGTTCCAACCCTCTTCCAAACATTTCTTGAAAGACATTAC
11344224 AAGC
261 AAGC
11344228 TTCTGTCATC
Statistics
Matches: 263, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 263 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (272 bp):
AAAGATATTTGGTTGAAGGCCCCTTCCACACATTTCATGAAGAAGCTCGTTGGCTGTATCTAGCT
CCCCACATTTACAAAGGCCATCAACAAGTGCAGTATAAGTCACAACATTTGGTATAAGCCCCATT
TGCACCATCTGATTATGGAGGGAAAAGGCCTTTTTCATTTCACCTGCCTTGCAATAACCATCAAT
AAGTGCTGTGTATGTAAATTCATCGAGTTCCAACCCTCTTCCAAACATTTCTTGAAAGACATTAC
AAGCATTTCTTG
Found at i:11348963 original size:23 final size:25
Alignment explanation
Indices: 11348936--11348981 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11348926 CTAATTAGGA
11348936 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
11348959 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
11348982 TAGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:11355394 original size:20 final size:19
Alignment explanation
Indices: 11355369--11355413 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
11355359 GTTATTTTTT
*
11355369 AAAAAAATGAAAAAAGTTAA
1 AAAAAAATGAAAAAA-TCAA
*
11355389 AAAAAATTGAAAAAATCAA
1 AAAAAAATGAAAAAATCAA
11355408 AAAAAA
1 AAAAAA
11355414 TTATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAAAAATGAAAAAATCAA
Found at i:11355415 original size:19 final size:20
Alignment explanation
Indices: 11355369--11355415 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
11355359 GTTATTTTTT
*
11355369 AAAAAAA-TGAAAAAAGTTA
1 AAAAAAATTGAAAAAAGTCA
11355388 AAAAAAATTGAAAAAA-TCA
1 AAAAAAATTGAAAAAAGTCA
11355407 AAAAAAATT
1 AAAAAAATT
11355416 ATTATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAAAAATTGAAAAAAGTCA
Found at i:11355448 original size:13 final size:13
Alignment explanation
Indices: 11355426--11355459 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11355416 ATTATATTTA
11355426 TTTT-TTTTCATT
1 TTTTATTTTCATT
11355438 TTTTATTTTCATT
1 TTTTATTTTCATT
*
11355451 TTTCATTTT
1 TTTTATTTT
11355460 TAGTTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTTCATT
Found at i:11355494 original size:16 final size:17
Alignment explanation
Indices: 11355463--11355504 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
11355453 TCATTTTTAG
*
11355463 TTTTAGTTTTAGTTTCA
1 TTTTATTTTTAGTTTCA
11355480 TTTTATTTTTA-TTTCA
1 TTTTATTTTTAGTTTCA
11355496 TTTTATTTT
1 TTTTATTTT
11355505 ATTATGCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTAGTTTCA
Found at i:11355498 original size:5 final size:5
Alignment explanation
Indices: 11355438--11355507 Score: 50
Period size: 5 Copynumber: 12.4 Consensus size: 5
11355428 TTTTTTCATT
*
11355438 TTTTA TTTTCA TTTTTCA TTTTTA GTTTTA GTTTTA GTTTCA TTTTA TTTTTA
1 TTTTA TTTT-A -TTTT-A -TTTTA -TTTTA -TTTTA -TTTTA TTTTA -TTTTA
*
11355491 TTTCA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
11355508 ATGCATTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
5 23 0.40
6 23 0.40
7 11 0.19
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:11356429 original size:17 final size:17
Alignment explanation
Indices: 11356406--11356443 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11356396 TATTTTGTTC
*
11356406 GAAAAAAA-GAGAAAAA
1 GAAAAAAACAAGAAAAA
11356422 GAAAAAAATCAAGAAAAA
1 GAAAAAAA-CAAGAAAAA
11356440 GAAA
1 GAAA
11356444 TTGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
GAAAAAAACAAGAAAAA
Found at i:11357553 original size:23 final size:25
Alignment explanation
Indices: 11357527--11357572 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11357517 CCAATTAGAG
11357527 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
11357550 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
11357573 TGAATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:11358736 original size:131 final size:131
Alignment explanation
Indices: 11358581--11358849 Score: 493
Period size: 131 Copynumber: 2.1 Consensus size: 131
11358571 CATTGTTAAT
* *
11358581 ATTTTAATATATAAAAAATAAATTTTAAATATTTTTTAAGTAATTAATCAAAGAAGGGAAAGTAT
1 ATTTTGATATATAAAAAATAAATTTTAAATATTTTTTAAGTAATTAATCAAAAAAGGGAAAGTAT
*
11358646 CATGTGTTGGAAGGGTGAAAACGTAATTGAGCTGTCAAAGGTGCTTTTGGGATGGAAAAGCTAAA
66 CATGTGTTGGAAGGGTGAAAACGTAATTGAGCTGTCAAAGGTGCTTTTGGGATGGAAAAACTAAA
11358711 A
131 A
11358712 ATTTTGATATATAAAAAATAAATTTTAAATATTTTTTAAGTAATTAATCAAAAAAGGGAAAGTAT
1 ATTTTGATATATAAAAAATAAATTTTAAATATTTTTTAAGTAATTAATCAAAAAAGGGAAAGTAT
* *
11358777 CATGTGTTGGAGGGGTGAAAACGTAATTGAGCTGTCAAAGGTGCTTTTGGGATGGAAAAATTAAA
66 CATGTGTTGGAAGGGTGAAAACGTAATTGAGCTGTCAAAGGTGCTTTTGGGATGGAAAAACTAAA
11358842 A
131 A
11358843 ATTTTGA
1 ATTTTGA
11358850 CTTCTCCATT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (131 bp):
ATTTTGATATATAAAAAATAAATTTTAAATATTTTTTAAGTAATTAATCAAAAAAGGGAAAGTAT
CATGTGTTGGAAGGGTGAAAACGTAATTGAGCTGTCAAAGGTGCTTTTGGGATGGAAAAACTAAA
A
Found at i:11363259 original size:13 final size:13
Alignment explanation
Indices: 11363234--11363300 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
11363224 GTTGGTAAAA
*
11363234 AAAGTTAACGGTC
1 AAAGTCAACGGTC
*
11363247 AAAGTCAATGGTC
1 AAAGTCAACGGTC
*
11363260 AAAGTCAACGATC
1 AAAGTCAACGGTC
* * *
11363273 AAGGTTAACGGTT
1 AAAGTCAACGGTC
* *
11363286 AATGTCAATGGTC
1 AAAGTCAACGGTC
11363299 AA
1 AA
11363301 TGAGTCGATC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:11365002 original size:13 final size:13
Alignment explanation
Indices: 11364973--11365005 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11364963 CTCATTTGAT
*
11364973 TCTCTTT-TCTTC
1 TCTCTTTCTCTCC
11364985 TCTCTTTCTCTCC
1 TCTCTTTCTCTCC
11364998 TCTCTTTC
1 TCTCTTTC
11365006 AATTGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (13 bp):
TCTCTTTCTCTCC
Found at i:11365105 original size:24 final size:24
Alignment explanation
Indices: 11365078--11365133 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
11365068 TCTATAGCTT
*
11365078 GACCACCACCGAGTCG-CGGACGTG
1 GACCACCACCGAGTCGTC-GACATG
* *
11365102 GACCACTATCGAGTCGTCGACATG
1 GACCACCACCGAGTCGTCGACATG
11365126 GACCACCA
1 GACCACCA
11365134 TTGAGCCACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.27, T:0.12
Consensus pattern (24 bp):
GACCACCACCGAGTCGTCGACATG
Found at i:11367294 original size:32 final size:30
Alignment explanation
Indices: 11367234--11367294 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 30
11367224 TGTTCTTTAG
11367234 ATGTGAAACTATAGACTTTGAAAATATAGAA
1 ATGTGAAACTATAGA-TTTGAAAATATAGAA
11367265 ATGTGAAAACTATAG-TTTGTAAAACTATAG
1 ATGTG-AAACTATAGATTTG-AAAA-TATAG
11367295 GAAACTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 14 0.52
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (30 bp):
ATGTGAAACTATAGATTTGAAAATATAGAA
Found at i:11372788 original size:21 final size:20
Alignment explanation
Indices: 11372747--11372792 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
11372737 TTATATTTTC
* *
11372747 TATTATTAATAATAAAATAT
1 TATTATTTATTATAAAATAT
11372767 TATTATTTATTATAATAATAT
1 TATTATTTATTATAA-AATAT
11372788 TATTA
1 TATTA
11372793 ATTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTTATTATAAAATAT
Found at i:11372801 original size:21 final size:20
Alignment explanation
Indices: 11372747--11372801 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
11372737 TTATATTTTC
11372747 TATT-ATTAATAATAAAATAT
1 TATTAATTAAT-ATAAAATAT
* *
11372767 TATTATTTATTATAATAATAT
1 TATTAATTAATATAA-AATAT
11372788 TATTAATTAATATA
1 TATTAATTAATATA
11372802 TCTTTTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATTAATATAAAATAT
Found at i:11379574 original size:13 final size:14
Alignment explanation
Indices: 11379537--11379571 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
11379527 CATAGCATCA
11379537 TATAAAAATTTGGC
1 TATAAAAATTTGGC
*
11379551 TATAAAAATTTGGG
1 TATAAAAATTTGGC
11379565 TATAAAA
1 TATAAAA
11379572 TTTTAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (14 bp):
TATAAAAATTTGGC
Found at i:11403517 original size:17 final size:17
Alignment explanation
Indices: 11403478--11403543 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
11403468 CTATAGTATA
* *
11403478 ATTGTCCTTGCATTATT
1 ATTGTCATTGCATTTTT
*
11403495 AATGTCATTGCATTTTT
1 ATTGTCATTGCATTTTT
** * **
11403512 ATTGTCGCTGCATCTAC
1 ATTGTCATTGCATTTTT
11403529 ATTGTCATTGCATTT
1 ATTGTCATTGCATTT
11403544 CCATATATAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:11414668 original size:22 final size:23
Alignment explanation
Indices: 11414643--11414685 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11414633 TATATGTCCA
11414643 TTAAATAATATAATTT-CATGCT
1 TTAAATAATATAATTTGCATGCT
*
11414665 TTAATTAATATAATTTGCATG
1 TTAAATAATATAATTTGCATG
11414686 ACCCACTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (23 bp):
TTAAATAATATAATTTGCATGCT
Found at i:11415263 original size:87 final size:87
Alignment explanation
Indices: 11415117--11415285 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 87
11415107 TGATGAACAA
* * * *
11415117 TATGCATATTTGGAATGTAAATGATGAATATGAAATGAAATGTGTATTGAGAATAAAAAAAATGA
1 TATGCATATATGGAATGAAAATGATGAATATGAAATGAAAAGTGTATTAAGAAT-AAAAAAATGA
11415182 GATATAAATATG-ACAATGATAG
65 GATATAAATATGTACAATGATAG
*
11415204 TATGCATATATGGAATGAAAATGATGGATATGAAATGAAAAGTGTATTAAGAATAAAAAAATGAG
1 TATGCATATATGGAATGAAAATGATGAATATGAAATGAAAAGTGTATTAAGAATAAAAAAATGAG
*
11415269 ATATGAATATGTACAAT
66 ATATAAATATGTACAAT
11415286 AATAATGGCA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 21 0.28
87 54 0.72
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (87 bp):
TATGCATATATGGAATGAAAATGATGAATATGAAATGAAAAGTGTATTAAGAATAAAAAAATGAG
ATATAAATATGTACAATGATAG
Found at i:11418382 original size:156 final size:156
Alignment explanation
Indices: 11418098--11418410 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 156
11418088 CAAGCTACAA
11418098 GAGCCACATGAGCTGGACCATTCCACACGGCTAAACCACATGGACATGTGACCCACAAGGGTTGA
1 GAGCCACATGAGCTGGACCATTCCACACGGCTAAACCACATGGACATGTGACCCACAAGGGTTGA
*
11418163 ACCATTCCACATGGCTAGACCACGGACGTGTGGGAGGCCATGTCGCTTTCATGGGATTACACACC
66 ACCATTCCACATGGCCAGACCACGGACGTGTGGGAGGCCATGTCGCTTTCATGGGATTACACACC
11418228 GAATTGCGAAAAATCACAAATTTCAG
131 GAATTGCGAAAAATCACAAATTTCAG
11418254 GAGCCACATGAGCTGGACCATTCCACACGGCTAAACCACATGGACATGTGACCCACAAGGGTTGA
1 GAGCCACATGAGCTGGACCATTCCACACGGCTAAACCACATGGACATGTGACCCACAAGGGTTGA
*
11418319 ACCATTCCACATGGCCAGACCACGGACGTGTGGTAGGCCATGTCGCTTTCATGGGATTACACACC
66 ACCATTCCACATGGCCAGACCACGGACGTGTGGGAGGCCATGTCGCTTTCATGGGATTACACACC
11418384 GAATTGCGAAAAATCACAAATTTCAG
131 GAATTGCGAAAAATCACAAATTTCAG
11418410 G
1 G
11418411 TTTTCAGACA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (156 bp):
GAGCCACATGAGCTGGACCATTCCACACGGCTAAACCACATGGACATGTGACCCACAAGGGTTGA
ACCATTCCACATGGCCAGACCACGGACGTGTGGGAGGCCATGTCGCTTTCATGGGATTACACACC
GAATTGCGAAAAATCACAAATTTCAG
Found at i:11429139 original size:160 final size:160
Alignment explanation
Indices: 11428875--11429200 Score: 573
Period size: 160 Copynumber: 2.0 Consensus size: 160
11428865 TGCTAGGCCG
*
11428875 TGTGTCCACTGCACTAAGTTTTGAAATGGCACACAGTCGTGTGACTGCCTGTGTCTCAGGCCGTA
1 TGTGTCCACTACACTAAGTTTTGAAATGGCACACAGTCGTGTGACTGCCTGTGTCTCAGGCCGTA
* *
11428940 TGCTGCCTAAAATGCTTCTAAAATAATTCATTCAATCATCATTCCTTGCATAATAAGATACACCA
66 TGCTACCTAAAATGCTTCTAAAACAATTCATTCAATCATCATTCCTTGCATAATAAGATACACCA
*
11429005 AAACTAGACTAAGATTCTATGCTCAAAACA
131 AAACTAGACTAAGATTCTATGCTAAAAACA
*
11429035 TGTGTCCACTACACTAAGTTTTGAAATGGCACACGGTTC-TGTGACTGCCTGTGTCTCAGGCCGT
1 TGTGTCCACTACACTAAGTTTTGAAATGGCACACAG-TCGTGTGACTGCCTGTGTCTCAGGCCGT
*
11429099 ATGCTACCTAAATTGCTTCTAAAACAATTCATTCAATCATCATTCCTTGCATAATAAGATACACC
65 ATGCTACCTAAAATGCTTCTAAAACAATTCATTCAATCATCATTCCTTGCATAATAAGATACACC
*
11429164 AAAACTAGACTAAGATTCTATGTTAAAAACA
130 AAAACTAGACTAAGATTCTATGCTAAAAACA
11429195 TGTGTC
1 TGTGTC
11429201 GAAACCATTT
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
160 156 0.99
161 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (160 bp):
TGTGTCCACTACACTAAGTTTTGAAATGGCACACAGTCGTGTGACTGCCTGTGTCTCAGGCCGTA
TGCTACCTAAAATGCTTCTAAAACAATTCATTCAATCATCATTCCTTGCATAATAAGATACACCA
AAACTAGACTAAGATTCTATGCTAAAAACA
Found at i:11430140 original size:30 final size:28
Alignment explanation
Indices: 11430045--11430232 Score: 114
Period size: 30 Copynumber: 6.4 Consensus size: 28
11430035 AAGGAAAAAA
* *
11430045 AGGGGTCAAAATGAAATTTTGGAAAGTTT
1 AGGGGTCAAATTGAATTTTTGGAAA-TTT
* *
11430074 AGGGGTTAAATTTAAGTTTTTAGGAAGA--T
1 AGGGGTCAAATTGAA-TTTTT-GGAA-ATTT
*
11430103 CGGGGTCAAATTCGAATTTTTGGAAATTT
1 AGGGGTCAAATT-GAATTTTTGGAAATTT
* *
11430132 CAGGGGTCAAAACTT-AATTTTTAGAAAGTTC
1 -AGGGGTC-AAA-TTGAATTTTTGGAAA-TTT
* * *
11430163 ATGAGTCAAAACAT-AATTTTTGGAAAGTTT
1 AGGGGTC-AAA-TTGAATTTTTGGAAA-TTT
* *
11430193 AGGGGTCAAATCTAAATTTTTTGATAATTT
1 AGGGGTCAAAT-TGAATTTTTGGA-AATTT
11430223 AGGGGTCAAA
1 AGGGGTCAAA
11430233 ACATAATTTT
Statistics
Matches: 127, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 33 0.26
30 75 0.59
31 11 0.09
32 3 0.02
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (28 bp):
AGGGGTCAAATTGAATTTTTGGAAATTT
Found at i:11430187 original size:60 final size:59
Alignment explanation
Indices: 11430117--11430271 Score: 179
Period size: 60 Copynumber: 2.6 Consensus size: 59
11430107 GTCAAATTCG
*
11430117 AATTTTTGGAAATTTCAGGGGTCAAAACTTAATTTTTAGA-AAGTTCATGAGTCAAAACAT
1 AATTTTTGGAAATTT-AGGGGTCAAAACTTAATTTTTAGATAA-TTCAGGAGTCAAAACAT
* * * * *
11430177 AATTTTTGGAAAGTTTAGGGGTCAAATCTAAATTTTTTGATAATTTAGGGGTCAAAACAT
1 AATTTTTGGAAA-TTTAGGGGTCAAAACTTAATTTTTAGATAATTCAGGAGTCAAAACAT
* *
11430237 AATTTTT-GAATAGTTAGGAGGTCAAAACATAATTT
1 AATTTTTGGAA-ATTTAGG-GGTCAAAACTTAATTT
11430272 CTAAATAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
59 8 0.10
60 68 0.84
61 5 0.06
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (59 bp):
AATTTTTGGAAATTTAGGGGTCAAAACTTAATTTTTAGATAATTCAGGAGTCAAAACAT
Found at i:11430213 original size:90 final size:90
Alignment explanation
Indices: 11430104--11430271 Score: 236
Period size: 90 Copynumber: 1.9 Consensus size: 90
11430094 TAGGAAGATC
* * *
11430104 GGGGTCAAATTCGAATTTTTGGA-AATTTCAGGGGTCAAAACTTAATTTTTAGAA-AGTTCATGA
1 GGGGTCAAATTCAAATTTTTGGATAATTT-AGGGGTCAAAACATAATTTTT-GAATAGTT-AGGA
11430167 -GTCAAAACATAATTTTTGGAAAGTTTA
63 GGTCAAAACATAATTTTTGGAAAGTTTA
*
11430194 GGGGTCAAA-TCTAAATTTTTTGATAATTTAGGGGTCAAAACATAATTTTTGAATAGTTAGGAGG
1 GGGGTCAAATTC-AAATTTTTGGATAATTTAGGGGTCAAAACATAATTTTTGAATAGTTAGGAGG
11430258 TCAAAACATAATTT
65 TCAAAACATAATTT
11430272 CTAAATAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
89 8 0.11
90 57 0.81
91 5 0.07
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (90 bp):
GGGGTCAAATTCAAATTTTTGGATAATTTAGGGGTCAAAACATAATTTTTGAATAGTTAGGAGGT
CAAAACATAATTTTTGGAAAGTTTA
Found at i:11430241 original size:30 final size:29
Alignment explanation
Indices: 11430117--11430271 Score: 161
Period size: 30 Copynumber: 5.2 Consensus size: 29
11430107 GTCAAATTCG
*
11430117 AATTTTTGGAAATTTCAGGGGTCAAAACTT
1 AATTTTTGGAAATTT-AGGGGTCAAAACAT
* * * *
11430147 AATTTTTAGAAAGTTCATGAGTCAAAACAT
1 AATTTTTGGAAA-TTTAGGGGTCAAAACAT
*
11430177 AATTTTTGGAAAGTTTAGGGGTCAAATC-T
1 AATTTTTGGAAA-TTTAGGGGTCAAAACAT
*
11430206 AAATTTTTTGATAATTTAGGGGTCAAAACAT
1 -AATTTTTGGA-AATTTAGGGGTCAAAACAT
*
11430237 AATTTTT-GAATAGTTAGGAGGTCAAAACAT
1 AATTTTTGGAA-ATTTAGG-GGTCAAAACAT
11430267 AATTT
1 AATTT
11430272 CTAAATAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
28 1 0.01
29 9 0.08
30 91 0.86
31 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAATTTAGGGGTCAAAACAT
Done.