Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 127 of 433
Found at i:38892601 original size:86 final size:85
Alignment explanation
Indices: 38892449--38892610 Score: 220
Period size: 86 Copynumber: 1.9 Consensus size: 85
38892439 AACTCGTACA
* *
38892449 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
38892514 CTTACACGAAATCAAATACG
66 CTTACACGAAATCAAATACG
* * * * *
38892534 ATGCTAATGTCCCAGACATGGTCTTACGTGTAAATCATAA-GTCGATGCCAAC-GTCCCATACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGT-AATCA-AATATCGATGCC-ACTGTCCCAGACAG
38892597 GGTCTTACACGAAA
63 GGTCTTACACGAAA
38892611 AAACATATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 27 0.40
86 36 0.54
87 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
CTTACACGAAATCAAATACG
Found at i:38895747 original size:18 final size:17
Alignment explanation
Indices: 38895688--38895748 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
38895678 ATATCTTGGT
38895688 TGAGCTCGCATG-TTTGA
1 TGAGCTCGCA-GCTTTGA
* * *
38895705 TGAGCTTGCAACTTTGGT
1 TGAGCTCGCAGCTTT-GA
*
38895723 TGTGCTCGCAGCTTTCGA
1 TGAGCTCGCAGCTTT-GA
38895741 TGAGCTCG
1 TGAGCTCG
38895749 TAGTTGTGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (17 bp):
TGAGCTCGCAGCTTTGA
Found at i:38895810 original size:18 final size:18
Alignment explanation
Indices: 38895763--38895810 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
38895753 TGTGTTTGAT
*
38895763 CTCACAACTCTGGATGAG
1 CTCACAACTTTGGATGAG
* *
38895781 CTCACAAGTTTGGATGGG
1 CTCACAACTTTGGATGAG
*
38895799 CTCGCAACTTTG
1 CTCACAACTTTG
38895811 CGACCTGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (18 bp):
CTCACAACTTTGGATGAG
Found at i:38901304 original size:14 final size:14
Alignment explanation
Indices: 38901285--38901315 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38901275 AAGATTCATA
38901285 ATCGACCAATTAAC
1 ATCGACCAATTAAC
38901299 ATCGACCAATTAAC
1 ATCGACCAATTAAC
38901313 ATC
1 ATC
38901316 AAGATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (14 bp):
ATCGACCAATTAAC
Found at i:38906020 original size:40 final size:40
Alignment explanation
Indices: 38905976--38906125 Score: 230
Period size: 40 Copynumber: 3.8 Consensus size: 40
38905966 ATAACCACAA
*
38905976 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATTTGGTAACTT
38906016 GCACAATTGCCTTCGGGTCTTAGCCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATTTGGTAACTT
* *** *
38906056 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATTTGGTAACTT
38906096 GCACGAA-TGCCTTCGGGTCTTAGCCCGGAT
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGAT
38906126 ATAATCACTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 101 0.98
41 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATTTGGTAACTT
Found at i:38906126 original size:40 final size:40
Alignment explanation
Indices: 38905960--38906163 Score: 223
Period size: 40 Copynumber: 5.1 Consensus size: 40
38905950 CGGGATTCAA
* * *
38905960 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAGC
* *** *
38906000 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAGC
* *** *
38906040 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAGC
38906080 CCGGATATAACAACTAGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
38906120 CCGGATATAATC-ACTAGCATAAATGCCTTCGAGACTTAGC
1 CCGGATATAA-CAACTAGCACAATTGCCTTCGGGTCTTAGC
38906160 CCGG
1 CCGG
38906164 GTATCATTCA
Statistics
Matches: 145, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.01
40 140 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAGC
Found at i:38911256 original size:43 final size:44
Alignment explanation
Indices: 38911196--38911278 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 44
38911186 TCTCAATTCA
*
38911196 TCATTTCATATTTCATTTCTCATCTTTGCCATTTCAATATTTTC
1 TCATCTCATATTTCATTTCTCATCTTTGCCATTTCAATATTTTC
* *
38911240 TCATCTCATA-TTCATTTTTCATCTTTTCCATTTCAATAT
1 TCATCTCATATTTCATTTCTCATCTTTGCCATTTCAATAT
38911279 CAATCATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 27 0.75
44 9 0.25
ACGTcount: A:0.22, C:0.23, G:0.01, T:0.54
Consensus pattern (44 bp):
TCATCTCATATTTCATTTCTCATCTTTGCCATTTCAATATTTTC
Found at i:38912480 original size:3 final size:3
Alignment explanation
Indices: 38912474--38912550 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
38912464 TTTTTATAAC
38912474 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38912522 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38912551 ACTATTATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:38914778 original size:13 final size:14
Alignment explanation
Indices: 38914760--38914792 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
38914750 CTATAGGGGA
38914760 CACATGGT-TGTGT
1 CACATGGTATGTGT
38914773 CACATGGTCATGTGT
1 CACATGGT-ATGTGT
38914788 CACAT
1 CACAT
38914793 ACCGTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
15 10 0.56
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (14 bp):
CACATGGTATGTGT
Found at i:38928458 original size:71 final size:71
Alignment explanation
Indices: 38928377--38928520 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
38928367 AACCTAATCC
38928377 TCAAGAATATTTATATTTATCCTTTTAACATGCAATAAATTTCAATGCTTTCTTATCTTAATCAT
1 TCAAGAATATTTATATTTATCCTTTTAACATGCAATAAATTTCAATGCTTTCTTATCTTAATCAT
38928442 GCATGT
66 GCATGT
38928448 TCAAGAATATTTATATTTATCCTTTTAACATGCAATAAATTTCAATGCTTTCTTATCTTAATCAT
1 TCAAGAATATTTATATTTATCCTTTTAACATGCAATAAATTTCAATGCTTTCTTATCTTAATCAT
38928513 GCATGT
66 GCATGT
38928519 TC
1 TC
38928521 GATAAACGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (71 bp):
TCAAGAATATTTATATTTATCCTTTTAACATGCAATAAATTTCAATGCTTTCTTATCTTAATCAT
GCATGT
Found at i:38928568 original size:59 final size:59
Alignment explanation
Indices: 38928476--38928596 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
38928466 ATCCTTTTAA
38928476 CATGCAATAAATTTCAATGCTTTCTTATCTTAATCATGCATGTTCGATAAACGTATATT
1 CATGCAATAAATTTCAATGCTTTCTTATCTTAATCATGCATGTTCGATAAACGTATATT
*
38928535 CATGCAATAAATTTCACTGCTTTCTTATCTTAATCATGCATGTTCGATAAACGTATATT
1 CATGCAATAAATTTCAATGCTTTCTTATCTTAATCATGCATGTTCGATAAACGTATATT
38928594 CAT
1 CAT
38928597 ATTCCTAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (59 bp):
CATGCAATAAATTTCAATGCTTTCTTATCTTAATCATGCATGTTCGATAAACGTATATT
Found at i:38936479 original size:22 final size:22
Alignment explanation
Indices: 38936454--38936498 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38936444 TTTGGTGTAG
38936454 TAGATTAAACTAGTTTTTGCAC
1 TAGATTAAACTAGTTTTTGCAC
38936476 TAGATTAAACTAGTTTTTGCAC
1 TAGATTAAACTAGTTTTTGCAC
38936498 T
1 T
38936499 TTAGGAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TAGATTAAACTAGTTTTTGCAC
Found at i:38938628 original size:47 final size:46
Alignment explanation
Indices: 38938516--38938641 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 46
38938506 GGGGTAAGGT
**
38938516 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTTGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTAATA
* * *
38938562 GCCGATG-CACGTCCCAGACAT-GTCTTACA-TTAGCACTTGTCTCAATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CAC--ATCT-AATA
38938609 -CCGATGCCATGTCCCAGACATGGTCTTACACTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTG
38938642 GCTCTCATGA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
43 2 0.03
44 11 0.17
45 13 0.20
46 16 0.24
47 15 0.23
48 8 0.12
49 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTAATA
Found at i:38943281 original size:14 final size:14
Alignment explanation
Indices: 38943262--38943289 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38943252 TAGAGACTTC
38943262 AATGGTATTTAACA
1 AATGGTATTTAACA
38943276 AATGGTATTTAACA
1 AATGGTATTTAACA
38943290 TGGCCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
AATGGTATTTAACA
Found at i:38944191 original size:54 final size:54
Alignment explanation
Indices: 38944132--38944264 Score: 212
Period size: 54 Copynumber: 2.5 Consensus size: 54
38944122 TCTTACGGCA
** * *
38944132 GGATTACCAGTCTAGGCTAAATTTCCCGTAGTAGTAACTTATAGAGCAATGTCG
1 GGATTACCAGTCTAGGCTAAATCCCCCATAGTAGTAACTCATAGAGCAATGTCG
*
38944186 GGATTACCAGTCTAGGCTAAATCCCCCATAGTAGTAACTCATATAGCAATGTCG
1 GGATTACCAGTCTAGGCTAAATCCCCCATAGTAGTAACTCATAGAGCAATGTCG
*
38944240 GGATTACTAGTCTAGGCTAAATCCC
1 GGATTACCAGTCTAGGCTAAATCCC
38944265 TCTTAATGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (54 bp):
GGATTACCAGTCTAGGCTAAATCCCCCATAGTAGTAACTCATAGAGCAATGTCG
Found at i:38947486 original size:137 final size:135
Alignment explanation
Indices: 38947162--38947444 Score: 361
Period size: 137 Copynumber: 2.1 Consensus size: 135
38947152 GAGAACATAG
* * * * * **
38947162 ATATAATTAATATGTGAATTTGATTCATATA-AAATATTAATTGTATAGATTTGACTGAATTTAT
1 ATATAATTATTATATGAATTTGATT-A-ATACAAA-ATTAATTGCATATATTTTACCAAATTTAT
* ** *
38947226 TAATATAAATAATTATATTAATTAATTTCGGTCAAAATATAAAGACATGAAAATTAATATTCTTT
63 TAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAGACATGAAAATTAATATTATTT
*
38947291 TGGAAAGA
128 TAGAAAGA
* *
38947299 ATATAATTATTATATGAATTTGATTCATACAAAATTTTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTATTATATGAATTTGATTAATACAAAA--TTAATTGCATATATTTTACCAAATTTATT
* *
38947364 AATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGATATGGAAATTAATATTATTT
64 AATATAAACAATTATATTAATTAATTTCAATCAAAATAT-AAAGACATGAAAATTAATATTATTT
38947429 TAGAAAGA
128 TAGAAAGA
38947437 ATATAATT
1 ATATAATT
38947445 TCTTTTTTTA
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
135 4 0.03
136 3 0.02
137 84 0.66
138 37 0.29
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (135 bp):
ATATAATTATTATATGAATTTGATTAATACAAAATTAATTGCATATATTTTACCAAATTTATTAA
TATAAACAATTATATTAATTAATTTCAATCAAAATATAAAGACATGAAAATTAATATTATTTTAG
AAAGA
Found at i:38947509 original size:20 final size:20
Alignment explanation
Indices: 38947484--38947531 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
38947474 ATAATCCTAT
38947484 ATTCTTTTGGAAAGAATATA
1 ATTCTTTTGGAAAGAATATA
38947504 ATTCTTTTGGAAAGAATATA
1 ATTCTTTTGGAAAGAATATA
38947524 ATTCTTTT
1 ATTCTTTT
38947532 TTCTAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTCTTTTGGAAAGAATATA
Found at i:38947609 original size:76 final size:75
Alignment explanation
Indices: 38947508--38947653 Score: 240
Period size: 76 Copynumber: 1.9 Consensus size: 75
38947498 AATATAATTC
*
38947508 TTTTGGAAAGAATATAATTCTTTTTTCTAA-CTTTCTATTTGCCATTCTCTATTAATAAGGGAAT
1 TTTTGGAAAGAATATAATTCATTTTTCTAACCTTTC-ATTTGCC-TTCTCTATTAATAAGGGAAT
38947572 AATCCTATATTA
64 AATCCTATATTA
* *
38947584 TTTTGGAAAGAATATAATTCATTTTTCTAACCTTTCATTTGCCTTCTCTATTAATTAGGGTATAA
1 TTTTGGAAAGAATATAATTCATTTTTCTAACCTTTCATTTGCCTTCTCTATTAATAAGGGAATAA
38947649 TCCTA
66 TCCTA
38947654 ATTTTTCTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
75 25 0.38
76 36 0.55
77 5 0.08
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (75 bp):
TTTTGGAAAGAATATAATTCATTTTTCTAACCTTTCATTTGCCTTCTCTATTAATAAGGGAATAA
TCCTATATTA
Found at i:38958154 original size:46 final size:46
Alignment explanation
Indices: 38958089--38958257 Score: 150
Period size: 46 Copynumber: 3.6 Consensus size: 46
38958079 CTCTCGTAGT
* *
38958089 CGATGCAGGTACCAGACATGTCTTACACTGGCTTACGTCT-AGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TACGTCTAAGAGGC
* * * *
38958135 CGATGCATGTCCCAAACATGTCTTACACTAGC-ACCTGTCTCA-ATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTA-C-GTCTAAGAGGC
* * *
38958181 TGATGCCATGTCCCAGACATGGTCTTACATTGGCT-C-TCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTACGTC-TAA-GAGGC
*
38958229 TGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
38958258 AGCTCACAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
44 1 0.01
45 3 0.03
46 50 0.50
47 29 0.29
48 18 0.18
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTACGTCTAAGAGGC
Found at i:38961285 original size:17 final size:18
Alignment explanation
Indices: 38961263--38961297 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38961253 TGAATTGGTC
38961263 CGTGTAGGCC-ACACGGG
1 CGTGTAGGCCTACACGGG
38961280 CGTGTAGGCCTACACGGG
1 CGTGTAGGCCTACACGGG
38961298 TAGTCCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.29, G:0.40, T:0.14
Consensus pattern (18 bp):
CGTGTAGGCCTACACGGG
Found at i:38970776 original size:46 final size:45
Alignment explanation
Indices: 38970726--38970896 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 45
38970716 TGAGCATCCA
*
38970726 AACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGTCCG
* * *
38970772 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G--TCCG
* * *
38970819 AACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGTCCG
*
38970865 AGCTCGTTGAGTTGAGTCCGAGTTCACTTAGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
38970897 GGCGGGTTAA
Statistics
Matches: 104, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 56 0.54
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATGTCCG
Found at i:38970878 original size:93 final size:93
Alignment explanation
Indices: 38970719--38970889 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
38970709 GGATGGTTGA
* * **
38970719 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCAAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
38970784 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
38970812 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
38970877 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
38970890 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38982726 original size:90 final size:90
Alignment explanation
Indices: 38982568--38982737 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 90
38982558 TTGGGGTGAT
* * * * *
38982568 GAGATCCCGTATAAGACCATATCCAGGATATGGCATTGGCATCAGTATGTGTTATCATGTAAGAC
1 GAGATCCCATATAAGACCATATCCAGGACATGGCATTAGCATCAGTATGTGATACCATGTAAGAC
38982633 CATATCTGGGATATGACGTTAATAG
66 CATATCTGGGATATGACGTTAATAG
* * ** * *
38982658 GAGATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCGAGT-TGTGATCCCATGTAAGG
1 GAGATCCCATATAAGACCATATCCAGGACATGGCATTAGCATC-AGTATGTGATACCATGTAAGA
38982722 CCATATCTGGGATATG
65 CCATATCTGGGATATG
38982738 GCATTGGTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 65 0.96
91 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (90 bp):
GAGATCCCATATAAGACCATATCCAGGACATGGCATTAGCATCAGTATGTGATACCATGTAAGAC
CATATCTGGGATATGACGTTAATAG
Found at i:38985515 original size:27 final size:27
Alignment explanation
Indices: 38985484--38985584 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
38985474 TTACTCTACA
* *
38985484 GGGGTATTTTGATAATTTTACAAATCA
1 GGGGTATTTCGATAATTTTACAAATCG
* *
38985511 AGGGTATTT-TAGTAATTTTACAAATCG
1 GGGGTATTTCGA-TAATTTTACAAATCG
*
38985538 GGGGTATTTCAATAATTTTACAAATCG
1 GGGGTATTTCGATAATTTTACAAATCG
*
38985565 GGGGTATTTCGGTAATTTTA
1 GGGGTATTTCGATAATTTTA
38985585 AACAGTTTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.02
27 63 0.97
28 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCGATAATTTTACAAATCG
Found at i:38987170 original size:27 final size:27
Alignment explanation
Indices: 38987137--38987425 Score: 183
Period size: 27 Copynumber: 10.7 Consensus size: 27
38987127 CCTCAAATTG
*
38987137 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * ****
38987164 TAGAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *** *
38987191 TAGAATTACCATTTTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *****
38987218 TAGAATTACTGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * * *
38987245 CAAAATTACTAAAATGCCCTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
38987272 CAAAATTACCAAAATACCCTCGA-TCA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
38987298 GTAAAATTACCAAAATACCCTAG-TTTG
1 -TAAAATTACCAAAATACCCTCGATTTA
* * * *
38987325 TAAAATTGCTAAAATACCC-CTGGTTTG
1 TAAAATTACCAAAATACCCTC-GATTTA
* * *
38987352 TAAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
38987379 TAAAATTACCAAAATACCC-CTGATTTA
1 TAAAATTACCAAAATACCCTC-GATTTA
* *
38987406 CAAAGTTA-CAGAAATACCCT
1 TAAAATTACCA-AAATACCCT
38987426 TGACTTTCTA
Statistics
Matches: 211, Mismatches: 43, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
26 23 0.11
27 187 0.89
28 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTA
Found at i:38987359 original size:80 final size:80
Alignment explanation
Indices: 38987246--38987397 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 80
38987236 CTCGATTTAC
* * *
38987246 AAAATTACTAAAATGCCCTTGGTTTACAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
38987311 AATACCCTAGTTTGT
66 AATACCCTAGTTTGT
* ** * **
38987326 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
38987391 AATACCC
66 AATACCC
38987398 CTGATTTACA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (80 bp):
AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
AATACCCTAGTTTGT
Found at i:38987397 original size:54 final size:53
Alignment explanation
Indices: 38987273--38987507 Score: 193
Period size: 54 Copynumber: 4.3 Consensus size: 53
38987263 CTTGGTTTAC
** * *
38987273 AAAATTACCAAAATA-CCCTCGATCAGTAAAATTACCAAAATACCCTAGTTTGT
1 AAAATTACCAAAATACCCCT-GATTTGCAAAATTACCGAAATACCCTAGTTTGT
* * * * *
38987326 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCCTGATTTGCAAAATTACCGAAATACCCT-AGTTTGT
* * * * *
38987380 AAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCT
1 AAAATTACCAAAATACCCCTGATTTGCAAAATTACCGAAATACCC-T-AGTTTGT
*** ** * *
38987435 AAAAATTATGGAAATACCATTGGTTTGCAAAATTACTGAAATACCCTTAGTTTGT
1 -AAAATTACCAAAATACCCCTGATTTGCAAAATTACCGAAATACCC-TAGTTTGT
* * *
38987490 ATATTTACCAAAACACCC
1 AAAATTACCAAAATACCC
38987508 TTGTAGGATG
Statistics
Matches: 143, Mismatches: 35, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
53 35 0.24
54 59 0.41
55 11 0.08
56 38 0.27
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (53 bp):
AAAATTACCAAAATACCCCTGATTTGCAAAATTACCGAAATACCCTAGTTTGT
Found at i:38987475 original size:27 final size:27
Alignment explanation
Indices: 38987245--38987488 Score: 134
Period size: 27 Copynumber: 9.0 Consensus size: 27
38987235 CCTCGATTTA
* * *
38987245 CAAAATTACTAAAATGCCCTTGGTTTA
1 CAAAATTACTGAAATACCCTTGGTTTG
** * * **
38987272 CAAAATTACCAAAATACCCTCGATCAG
1 CAAAATTACTGAAATACCCTTGGTTTG
* ** *
38987299 TAAAATTACCAAAATACCC-TAGTTTG
1 CAAAATTACTGAAATACCCTTGGTTTG
* * * *
38987325 TAAAATTGCTAAAATACCCCTGGTTTG
1 CAAAATTACTGAAATACCCTTGGTTTG
* * ***
38987352 TAAAATTACCGAAATACCCTCAATTTG
1 CAAAATTACTGAAATACCCTTGGTTTG
* ** * * *
38987379 TAAAATTACCAAAATACCCCTGATTTA
1 CAAAATTACTGAAATACCCTTGGTTTG
* * *
38987406 CAAAGTTACAGAAATACCCTTGACTTT-
1 CAAAATTACTGAAATACCCTTG-GTTTG
*
38987433 CTAAAAATTA-TGGAAATACCATTGGTTTG
1 C--AAAATTACT-GAAATACCCTTGGTTTG
*
38987462 CAAAATTACTGAAATACCCTTAGTTTG
1 CAAAATTACTGAAATACCCTTGGTTTG
38987489 TATATTTACC
Statistics
Matches: 170, Mismatches: 40, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
26 19 0.11
27 126 0.74
28 7 0.04
29 18 0.11
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (27 bp):
CAAAATTACTGAAATACCCTTGGTTTG
Found at i:38987632 original size:27 final size:27
Alignment explanation
Indices: 38987545--38987632 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
38987535 CTATTAAGTG
38987545 AAAA-GACCGTAAAGCCCCTGTAAGGT
1 AAAATGACCGTAAAGCCCCTGTAAGGT
* *
38987571 AAAGTGACCGTAAAGCCCCTGTAGGGT
1 AAAATGACCGTAAAGCCCCTGTAAGGT
* *
38987598 AAAGTGACCGTAATA-CCCCTGTATGGT
1 AAAATGACCGTAA-AGCCCCTGTAAGGT
38987625 AAAATGAC
1 AAAATGAC
38987633 GAATATGCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 3 0.05
27 52 0.93
28 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
AAAATGACCGTAAAGCCCCTGTAAGGT
Found at i:38988464 original size:26 final size:26
Alignment explanation
Indices: 38988435--38988585 Score: 241
Period size: 26 Copynumber: 5.8 Consensus size: 26
38988425 GAGGAAGTGC
38988435 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
38988461 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
38988487 AAAAGGGCTTATGCCCCAGTTTAACG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
38988513 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
38988539 AAAAAGGGTTTATGCCCCAGTTTACCG
1 -AAAAGGGCTTATGCCCCAGTTTACCG
38988566 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
38988586 ATTAAAGAGG
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
25 10 0.09
26 82 0.71
27 23 0.20
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:38988806 original size:42 final size:42
Alignment explanation
Indices: 38988730--38988819 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
38988720 TAGTCTCCCC
* ** ** *
38988730 AAATAGGCTTGCATACATTTATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
38988772 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
38988814 AAATGG
1 AAATGG
38988820 CCTATAGTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:38988889 original size:31 final size:31
Alignment explanation
Indices: 38988848--38988922 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
38988838 TACAGTAAAG
*
38988848 GCTTCAGCCCAGTGAAATAATTTATGAAAAA
1 GCTTCGGCCCAGTGAAATAATTTATGAAAAA
* * * *
38988879 GCTTTGGCCCAGTGATATGATTTATGAAAAG
1 GCTTCGGCCCAGTGAAATAATTTATGAAAAA
*
38988910 GCTTCGACCCAGT
1 GCTTCGGCCCAGT
38988923 AATCGTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (31 bp):
GCTTCGGCCCAGTGAAATAATTTATGAAAAA
Found at i:38992693 original size:47 final size:46
Alignment explanation
Indices: 38992620--38992795 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
38992610 ATTTGTGTGT
* *
38992620 GAGCTAGTGTAAGACATGTCTGGGACATACATCGGCCACCTT-ATG-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA--TTGAGGAA
*
38992666 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGGCAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATTGAGG-AA
38992714 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-TTGAGACGTAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAG--G-AA
*
38992762 G-GC-AGTGTAAGACATGTCTGAGACATGCATCGGC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
38992796 TGCGAGATGA
Statistics
Matches: 116, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
45 2 0.02
46 57 0.49
47 33 0.28
48 24 0.21
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGGAA
Found at i:38992769 original size:46 final size:45
Alignment explanation
Indices: 38992625--38992888 Score: 220
Period size: 47 Copynumber: 5.7 Consensus size: 45
38992615 TGTGTGAGCT
*
38992625 AGTGTAAGACATGTCTGGGACAT-ACATCGGCCACCTT-ATGAG-AGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGG---CCTTGA-GAGAAGCC
* *
38992671 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG-GCAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTTGAGAG--A-AGCC
*
38992719 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGACGTAAGGC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCTTGAGA-G-AAGCC
* * *
38992765 AGTGTAAGACATGTCTGAGACAT-GCATCGG-CTGCGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCT-TGAGA-GA-AGCC
* * *
38992811 AGTGTAAGAACATGTTTGGGACATGGCATC-GACTTGAGATATGAGCC
1 AGTGTAAG-ACATGTCTGGGACATGGCATCGGCCTTGAGAGA--AGCC
*
38992858 AGTTTAAGACAATGTCTGGGACATGGCATCG
1 AGTGTAAGAC-ATGTCTGGGACATGGCATCG
38992889 ACACCTTATC
Statistics
Matches: 182, Mismatches: 19, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
44 1 0.01
45 7 0.04
46 73 0.40
47 75 0.41
48 26 0.14
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGGCCTTGAGAGAAGCC
Found at i:38992835 original size:93 final size:94
Alignment explanation
Indices: 38992667--38992888 Score: 238
Period size: 93 Copynumber: 2.4 Consensus size: 94
38992657 ACCTTATGAG
* * * *** *
38992667 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGGCAAGAG-CTAGTGTAAGACA
1 AGCCAGTGTAAGACAATGTCTGAGACATGGCATCGGC-TGCGAGATGATAGTC-AGTGTAAGACA
* *
38992730 TGTCTGGGACAT-GCATCGGCCTTGAGACGTA
64 TGTCTGGGACATGGCATC-GACTTGAGACATA
*
38992761 AGGCAGTGTAAGAC-ATGTCTGAGACAT-GCATCGGCTGCGAGATGATAGTCAGTGTAAGAACAT
1 AGCCAGTGTAAGACAATGTCTGAGACATGGCATCGGCTGCGAGATGATAGTCAGTGTAAG-ACAT
* * *
38992824 GTTTGGGACATGGCATCGACTTGAGATATG
65 GTCTGGGACATGGCATCGACTTGAGACATA
* *
38992854 AGCCAGTTTAAGACAATGTCTGGGACATGGCATCG
1 AGCCAGTGTAAGACAATGTCTGAGACATGGCATCG
38992889 ACACCTTATC
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
91 1 0.01
92 22 0.21
93 48 0.45
94 30 0.28
95 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (94 bp):
AGCCAGTGTAAGACAATGTCTGAGACATGGCATCGGCTGCGAGATGATAGTCAGTGTAAGACATG
TCTGGGACATGGCATCGACTTGAGACATA
Found at i:38992877 original size:140 final size:141
Alignment explanation
Indices: 38992625--38992888 Score: 352
Period size: 140 Copynumber: 1.9 Consensus size: 141
38992615 TGTGTGAGCT
* ** *
38992625 AGTGTAAGACATGTCTGGGACATACATCGGCCACCTTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGAGACATACATCGGCCACCAGATGAGAGCCAGTGTAAGAACATGTCTGG
* * *
38992690 GACATGGCATCGGCATTGAGGCAAGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTG
66 GACATGGCATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTTG
38992754 AGACGTAAGGC
131 AGACGTAAGGC
* ** * * * *
38992765 AGTGTAAGACATGTCTGAGACATGCATCGGCTGCGAGATGATAGTCAGTGTAAGAACATGTTTGG
1 AGTGTAAGACATGTCTGAGACATACATCGGCCACCAGATGAGAGCCAGTGTAAGAACATGTCTGG
* * *
38992830 GACATGGCATCGAC-TTGAGATATGAGCCAGTTTAAGACAATGTCTGGGACATGGCATCG
66 GACATGGCATCGACATTGAGACAAGAGCCAGTGTAAGAC-ATGTCTGGGACATGGCATCG
38992889 ACACCTTATC
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
139 19 0.18
140 80 0.76
141 6 0.06
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGAGACATACATCGGCCACCAGATGAGAGCCAGTGTAAGAACATGTCTGG
GACATGGCATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTTG
AGACGTAAGGC
Found at i:38995334 original size:40 final size:40
Alignment explanation
Indices: 38995260--38995480 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
38995250 AACCCAAGTA
* *
38995260 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
38995299 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
38995339 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
38995379 CCTTC-GGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
38995418 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
38995458 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
38995481 CATTCGAATA
Statistics
Matches: 170, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 50 0.29
40 117 0.69
41 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:38995397 original size:79 final size:80
Alignment explanation
Indices: 38995260--38995480 Score: 376
Period size: 79 Copynumber: 2.8 Consensus size: 80
38995250 AACCCAAGTA
* * *
38995260 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
38995323 GTCAATAGCACAAAAG
65 GTCAATAGCACAAAAG
38995339 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC-GGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
38995403 TCAATAGCACAAATG
66 TCAATAGCACAAAAG
38995418 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
38995481 CATTCGAATA
Statistics
Matches: 135, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
79 90 0.67
80 44 0.33
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCAATAGCACAAAAG
Found at i:38995471 original size:119 final size:119
Alignment explanation
Indices: 38995260--38995480 Score: 365
Period size: 119 Copynumber: 1.9 Consensus size: 119
38995250 AACCCAAGTA
* * *
38995260 CCTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
38995325 CAATAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
66 CAATAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
38995379 CCTTC-GGACTTAGCCCGGATATAGTCAA-TAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAG-CCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
38995442 GTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
64 GTCAATAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
38995481 CATTCGAATA
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
118 7 0.07
119 85 0.89
120 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (119 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CAATAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:39000328 original size:13 final size:13
Alignment explanation
Indices: 39000310--39000337 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39000300 GCTCAGCAAG
39000310 GACACGCCCGTGT
1 GACACGCCCGTGT
39000323 GACACGCCCGTGT
1 GACACGCCCGTGT
39000336 GA
1 GA
39000338 GTCGTGCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:39009578 original size:2 final size:2
Alignment explanation
Indices: 39009571--39009601 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39009561 GTATACTAAC
39009571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39009602 CATCAATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39015456 original size:53 final size:53
Alignment explanation
Indices: 39015274--39015480 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 53
39015264 ATTAGAGTTT
* * * * * *
39015274 AAGGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * *
39015328 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
39015383 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
39015436 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
39015481 TAAAAAGGAA
Statistics
Matches: 123, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 46 0.37
54 37 0.30
55 40 0.33
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:39029286 original size:11 final size:11
Alignment explanation
Indices: 39029250--39029305 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
39029240 ACAGGTATGT
39029250 ATGATATGCAC
1 ATGATATGCAC
* *
39029261 ATGACATG--T
1 ATGATATGCAC
39029270 ATGATATGCAC
1 ATGATATGCAC
*
39029281 ATGATATG--T
1 ATGATATGCAC
39029290 ATGATATGCAC
1 ATGATATGCAC
39029301 ATGAT
1 ATGAT
39029306 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39029305 original size:20 final size:20
Alignment explanation
Indices: 39029245--39029305 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
39029235 GATAAACAGG
39029245 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
*
39029265 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
39029285 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
39029305 T
1 T
39029306 GTAATCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:39029380 original size:23 final size:23
Alignment explanation
Indices: 39029354--39029520 Score: 280
Period size: 23 Copynumber: 7.1 Consensus size: 23
39029344 GAGGAATGAA
39029354 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
39029377 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39029400 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
39029424 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
39029448 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
39029471 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39029494 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
39029518 AAA
1 AAA
39029521 AGAGGCTAGG
Statistics
Matches: 139, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
23 71 0.51
24 68 0.49
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:39029432 original size:24 final size:23
Alignment explanation
Indices: 39029353--39029527 Score: 269
Period size: 24 Copynumber: 7.4 Consensus size: 23
39029343 GGAGGAATGA
39029353 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
39029376 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
39029399 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
39029422 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
39029446 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
39029470 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
39029494 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
39029518 AAAAGAGGCT
1 AAAAG-GGCT
39029528 AGGCCTCCAT
Statistics
Matches: 144, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
23 66 0.46
24 74 0.51
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:39029445 original size:47 final size:46
Alignment explanation
Indices: 39029354--39029527 Score: 267
Period size: 47 Copynumber: 3.7 Consensus size: 46
39029344 GAGGAATGAA
*
39029354 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
*
39029400 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT-T
*
39029448 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
*
39029494 AAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCT
1 -AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCT
39029528 AGGCCTCCAT
Statistics
Matches: 117, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
46 22 0.19
47 64 0.55
48 27 0.23
49 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:39029764 original size:30 final size:31
Alignment explanation
Indices: 39029728--39029790 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
39029718 AATTTACAGT
39029728 AAAGGCTTCGGCCCAGTAATATGAAAT-TGA
1 AAAGGCTTCGGCCCAGTAATATGAAATGTGA
**
39029758 AAAGGCTTCGGCCCAGTGTTATGAAATGTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATGTGA
39029789 AA
1 AA
39029791 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATGTGA
Found at i:39037305 original size:25 final size:25
Alignment explanation
Indices: 39037276--39037323 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39037266 CTATAACATG
* * *
39037276 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39037301 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39037324 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39037426 original size:20 final size:20
Alignment explanation
Indices: 39037366--39037426 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
39037356 ATAAACAGGG
*
39037366 TATGTATGATATACACATGA
1 TATGTATGATATGCACATGA
*
39037386 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
39037406 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
39037426 T
1 T
39037427 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:39037502 original size:24 final size:24
Alignment explanation
Indices: 39037475--39037579 Score: 158
Period size: 24 Copynumber: 4.4 Consensus size: 24
39037465 GAGGAAGTGA
*
39037475 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
39037499 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39037523 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
39037546 AAAAGGGCTTTTTCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39037570 AAAAGAGGCT
1 AAAAG-GGCT
39037580 AGGCCTCCTG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
23 22 0.30
24 48 0.65
25 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39037550 original size:47 final size:47
Alignment explanation
Indices: 39037476--39037572 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
39037466 AGGAAGTGAA
*
39037476 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
39037523 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTTCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
39037570 AAA
1 AAA
39037573 AGAGGCTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:39037821 original size:31 final size:31
Alignment explanation
Indices: 39037786--39037849 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
39037776 CGTTTACAGT
*
39037786 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATGTGA
* **
39037817 AAAGGCTTTGGCCCAGTGTTATGAAATGTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATGTGA
39037848 AA
1 AA
39037850 TGTGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATGTGA
Found at i:39039135 original size:43 final size:41
Alignment explanation
Indices: 39039073--39039200 Score: 125
Period size: 42 Copynumber: 3.0 Consensus size: 41
39039063 TGCCAACTAT
* * *
39039073 TTGAGATATCGTGTAAGACCGTGTCTGGGACATAGGCCTCGA
1 TTGAGATTTCGTATAAGACC-TGTCTGGGACATAGGCATCGA
* *
39039115 TTGAGATTTACGTATAAGACCATGTATGGGACATCGGCATCGTA
1 TTGAGATTT-CGTATAAGACC-TGTCTGGGACATAGGCATCG-A
* *
39039159 TCT--GATTTCGTATAAGACTCTGTCTAGGACAGAGGCATCGA
1 T-TGAGATTTCGTATAAGAC-CTGTCTGGGACATAGGCATCGA
39039200 T
1 T
39039201 ATTGAATTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.03
42 34 0.47
43 33 0.46
44 2 0.03
45 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (41 bp):
TTGAGATTTCGTATAAGACCTGTCTGGGACATAGGCATCGA
Found at i:39044993 original size:28 final size:29
Alignment explanation
Indices: 39044934--39044994 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
39044924 TCTCTGTAAA
* *
39044934 ATTTAGTTTTGTTTTCTTTCGTTATTAGG
1 ATTTAGATTTGTTTTCTTTCGTTATTACG
*
39044963 ATTTAGATTT-TTTTCTTT-GTTCTTATCG
1 ATTTAGATTTGTTTTCTTTCGTTATTA-CG
39044991 ATTT
1 ATTT
39044995 CAAGAGATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 13 0.46
29 9 0.32
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (29 bp):
ATTTAGATTTGTTTTCTTTCGTTATTACG
Found at i:39049545 original size:27 final size:28
Alignment explanation
Indices: 39049489--39049558 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
39049479 AAATTTGTAC
39049489 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39049517 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39049544 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39049559 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:39057455 original size:27 final size:28
Alignment explanation
Indices: 39057399--39057468 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
39057389 AAATTTGTAC
39057399 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39057427 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39057454 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39057469 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:39059983 original size:40 final size:40
Alignment explanation
Indices: 39059928--39060096 Score: 189
Period size: 40 Copynumber: 4.2 Consensus size: 40
39059918 TGAATGATAC
* *
39059928 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
* * *
39059968 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATCATAT
* * * *
39060008 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
* * * *
39060048 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GATCATAT
39060089 CC-GGCTAA
1 CCGGGCTAA
39060097 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 97 0.92
41 8 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
Found at i:39060095 original size:80 final size:80
Alignment explanation
Indices: 39059928--39060096 Score: 216
Period size: 80 Copynumber: 2.1 Consensus size: 80
39059918 TGAATGATAC
* * * *
39059928 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
*
39059993 TGCGAGTTGTTATAT
66 TGCGAGTGGTTATAT
* * *
39060008 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGC-ATTC
**
39060072 GTGCTTGTGGATTATAT
65 GTGCGAGTGG-TTATAT
39060089 CC-GGCTAA
1 CCGGGCTAA
39060097 ATTCCGAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 66 0.86
81 11 0.14
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTGGTTATAT
Found at i:39061162 original size:23 final size:25
Alignment explanation
Indices: 39061136--39061183 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
39061126 ACAGCATCAG
39061136 TATTGAAGCCCTGT-ACA-GGGAGA
1 TATTGAAGCCCTGTAACATGGGAGA
39061159 TATTGAAGCCCTGTAACATGGGAGA
1 TATTGAAGCCCTGTAACATGGGAGA
39061184 CTTTAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
24 3 0.13
25 6 0.26
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (25 bp):
TATTGAAGCCCTGTAACATGGGAGA
Found at i:39075648 original size:35 final size:35
Alignment explanation
Indices: 39075609--39075681 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
39075599 ACACATTCTT
*
39075609 TATTCTCGTCAGATCACTCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
39075644 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
39075679 TAT
1 TAT
39075682 ATCACATACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:39091016 original size:53 final size:54
Alignment explanation
Indices: 39090887--39091087 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
39090877 ACACGGGTAC
* * * * * *
39090887 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---T-CCTT-TTGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCTTGCCTTATAGTAA
*
39090936 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTAT-G-AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGTAA
* ** * * *
39090989 CTCACCAATGCCATACCTTGGCATGGTCTTACATGGGACTTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAC-CTTGCCTTATAGTAA
*
39091044 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTG
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTA-CCTTG
39091088 AACCCTAATG
Statistics
Matches: 125, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
49 35 0.28
52 1 0.01
53 44 0.35
54 6 0.05
55 38 0.30
56 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCTTGCCTTATAGTAA
Found at i:39098178 original size:16 final size:16
Alignment explanation
Indices: 39098159--39098189 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39098149 CTTCTTCACT
39098159 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39098175 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39098190 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:39098195 original size:20 final size:20
Alignment explanation
Indices: 39098156--39098195 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39098146 AAACTTCTTC
* *
39098156 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
39098176 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
39098196 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:39098509 original size:53 final size:54
Alignment explanation
Indices: 39098380--39098580 Score: 211
Period size: 53 Copynumber: 3.8 Consensus size: 54
39098370 AGATGGGTAC
* * * * * *
39098380 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---T-CCTT-TTGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCTTGCCTTATAGTAA
*
39098429 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTAT-G-AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGTAA
* * *
39098482 CTCACCAATGCCATGCCTTGGCATGGTCTTACATAGG-ACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GGTACC-TTGCCTTATAGTAA
*
39098537 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTG
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTA-CCTTG
39098581 AACCCTAATG
Statistics
Matches: 129, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
49 35 0.27
52 2 0.02
53 43 0.33
54 10 0.08
55 37 0.29
56 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCTTGCCTTATAGTAA
Found at i:39107324 original size:32 final size:32
Alignment explanation
Indices: 39107283--39107349 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
39107273 TACTCAATTG
*
39107283 AATTTCCGTACATACCTGTACCATCTCGTACC
1 AATTTCCGTACATACCTGTACCATATCGTACC
* *
39107315 AATTTCCGTACATTCCTGTACCATATTGTACC
1 AATTTCCGTACATACCTGTACCATATCGTACC
39107347 AAT
1 AAT
39107350 CTCATATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (32 bp):
AATTTCCGTACATACCTGTACCATATCGTACC
Found at i:39107491 original size:42 final size:42
Alignment explanation
Indices: 39107415--39107576 Score: 198
Period size: 42 Copynumber: 3.9 Consensus size: 42
39107405 TTACTCGGGA
** * * * * *
39107415 ATCTCGCAGGCTAAGTGCCAATACGTAGCTGAAGCTAACTCA
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTCG
* * *
39107457 ATCACGCACACTAAGTGCCAATGCATAGTCGAAGCTATCTTG
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTCG
* * *
39107499 ATCTCACACACTAAGTGCTAATGCATAGCCGAAGCTATCCCG
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTCG
*
39107541 ATCTCGCATACTAAGTGCCAATGCATAGCCGAAGCT
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCT
39107577 CTCTTAAATA
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTCG
Found at i:39115349 original size:42 final size:42
Alignment explanation
Indices: 39115261--39115349 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
39115251 TCATTTACTT
* * *
39115261 GATGCCATAGTCCAACTATGGTCTTACACGAAGTCTCACATG
1 GATGCCATAGTCCAACTATGGTCTTACACGAAATCACACATC
* *
39115303 GATGCCAT-GTCCCAAAC-ATGGTCTTATACGAAATCACATATC
1 GATGCCATAGT-CC-AACTATGGTCTTACACGAAATCACACATC
39115345 GATGC
1 GATGC
39115350 AGATGCCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.05
42 35 0.88
43 3 0.08
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
GATGCCATAGTCCAACTATGGTCTTACACGAAATCACACATC
Found at i:39115374 original size:48 final size:48
Alignment explanation
Indices: 39115303--39115426 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 48
39115293 GTCTCACATG
* * * *
39115303 GATGCCATGTCCCAAACATGGTCTTATACGAAATCACATATCGATGCA
1 GATGCCATATCCCAAATATGGTCTTACACGAAATCACATATCGATCCA
* * ** * *
39115351 GATGCCATATCCTAGATATGGTCTTACACGGGATCTCATATCGATCCC
1 GATGCCATATCCCAAATATGGTCTTACACGAAATCACATATCGATCCA
*
39115399 GATGCCATATCCCAAATATGGTCCTACA
1 GATGCCATATCCCAAATATGGTCTTACA
39115427 TGTATCACAA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGCCATATCCCAAATATGGTCTTACACGAAATCACATATCGATCCA
Found at i:39115480 original size:37 final size:36
Alignment explanation
Indices: 39115400--39115655 Score: 332
Period size: 37 Copynumber: 7.0 Consensus size: 36
39115390 ATCGATCCCG
* ** *
39115400 ATGCCATATCCCAAATATGGTCCTACATGTATCACA
1 ATGCCATAGCCCAGCTATGGTCTTACATGTATCACA
* *
39115436 ATGCCATAGCCTAGCTATGGTCTTACATGTCATCACG
1 ATGCCATAGCCCAGCTATGGTCTTACATGT-ATCACA
*
39115473 ATGCCATAGCCCAGCTATGGTCTTACACGTATCACA
1 ATGCCATAGCCCAGCTATGGTCTTACATGTATCACA
*
39115509 ATGCCATAGCCCAGCTATGGTCTTACATGTCATCACG
1 ATGCCATAGCCCAGCTATGGTCTTACATGT-ATCACA
* **
39115546 ATGCCATAACCCAGCTATGGTCTTACACATATCACA
1 ATGCCATAGCCCAGCTATGGTCTTACATGTATCACA
* *
39115582 ATGCCATAGACCAGCTATGGTCTTACATGTCATCACG
1 ATGCCATAGCCCAGCTATGGTCTTACATGT-ATCACA
* * *
39115619 ATGCCATAGCCGAGCTATGATCTTACACGTACTCACA
1 ATGCCATAGCCCAGCTATGGTCTTACATGTA-TCACA
39115656 TGTATTGCCA
Statistics
Matches: 191, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
36 91 0.48
37 100 0.52
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (36 bp):
ATGCCATAGCCCAGCTATGGTCTTACATGTATCACA
Found at i:39115517 original size:73 final size:72
Alignment explanation
Indices: 39115398--39115655 Score: 399
Period size: 73 Copynumber: 3.5 Consensus size: 72
39115388 ATATCGATCC
* ** * *
39115398 CGATGCCATATCCCAAATATGGTCCTACATGTATCACAATGCCATAGCCTAGCTATGGTCTTACA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTATCACAATGCCATAGCC-AGCTATGGTCTTACA
39115463 TGTCATCA
65 TGTCATCA
39115471 CGATGCCATAGCCCAGCTATGGTCTTACACGTATCACAATGCCATAGCCCAGCTATGGTCTTACA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTATCACAATGCCATAG-CCAGCTATGGTCTTACA
39115536 TGTCATCA
65 TGTCATCA
* *
39115544 CGATGCCATAACCCAGCTATGGTCTTACACATATCACAATGCCATAGACCAGCTATGGTCTTACA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTATCACAATGCCATAG-CCAGCTATGGTCTTACA
39115609 TGTCATCA
65 TGTCATCA
* *
39115617 CGATGCCATAGCCGAGCTATGATCTTACACGTACTCACA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTA-TCACA
39115656 TGTATTGCCA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
73 164 0.96
74 7 0.04
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (72 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGTATCACAATGCCATAGCCAGCTATGGTCTTACAT
GTCATCA
Found at i:39117312 original size:2 final size:2
Alignment explanation
Indices: 39117305--39117345 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39117295 GAGACTAGTC
39117305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39117346 CATGTCATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39121584 original size:32 final size:32
Alignment explanation
Indices: 39121542--39121608 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
39121532 AATACTCAAT
39121542 AATTTCCGTACATACCTGTACCATATCGTACC
1 AATTTCCGTACATACCTGTACCATATCGTACC
* * *
39121574 AATTTTCGTACATACGTGTACCATATTGTACC
1 AATTTCCGTACATACCTGTACCATATCGTACC
39121606 AAT
1 AAT
39121609 CTCATATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (32 bp):
AATTTCCGTACATACCTGTACCATATCGTACC
Found at i:39121745 original size:42 final size:42
Alignment explanation
Indices: 39121673--39121842 Score: 214
Period size: 42 Copynumber: 4.0 Consensus size: 42
39121663 GTTACTTGGG
* * * * *
39121673 AATCTCGTAGACTAAGTGCCAATACGTAGCCGAAGCTAACTC
1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTC
* *
39121715 AATCACGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTT
1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTC
* * * * *
39121757 GATCTCGCACGCTAAGTGCTAATGCATAGTCGAAGCTATCCC
1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTC
* *
39121799 AATCTCGCACACTAAATGCCAATGCATAGCAGAAGCTATCTC
1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTC
39121841 AA
1 AA
39121843 ATATTTTCAT
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 107 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (42 bp):
AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTC
Found at i:39124781 original size:17 final size:18
Alignment explanation
Indices: 39124739--39124787 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39124729 AGTTGAAAAG
39124739 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39124758 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39124775 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39124788 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39125773 original size:40 final size:39
Alignment explanation
Indices: 39125605--39125775 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
39125595 AGAAATTGAA
* *
39125605 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
39125645 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
39125685 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
39125725 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
39125765 TGATATCCGGG
1 TGATATCCGGG
39125776 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:39133792 original size:40 final size:39
Alignment explanation
Indices: 39133624--39133794 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
39133614 AGAAATTGAA
* *
39133624 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
39133664 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
39133704 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
39133744 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
39133784 TGATATCCGGG
1 TGATATCCGGG
39133795 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:39136415 original size:29 final size:28
Alignment explanation
Indices: 39136345--39136419 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
39136335 ATACTCGATT
* *
39136345 TCGCACACTTAGTGCCATGCGATTTAGC
1 TCGCACACTTAGTGCCATGCCATTGAGC
* ** *
39136373 CCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGCCATT-GAGC
39136402 TCGCACACTTAGTGCCAT
1 TCGCACACTTAGTGCCAT
39136420 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (28 bp):
TCGCACACTTAGTGCCATGCCATTGAGC
Found at i:39136436 original size:29 final size:29
Alignment explanation
Indices: 39136403--39136476 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
39136393 CCTTCGAGCT
39136403 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
39136432 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39136461 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39136477 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:39144244 original size:29 final size:29
Alignment explanation
Indices: 39144210--39144284 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
39144200 TACTCGATTT
*
39144210 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
39144239 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
39144268 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
39144285 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:39144301 original size:29 final size:29
Alignment explanation
Indices: 39144268--39144341 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
39144258 CCTTCGAGCT
39144268 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
39144297 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39144326 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39144342 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:39148958 original size:116 final size:116
Alignment explanation
Indices: 39148662--39148961 Score: 528
Period size: 116 Copynumber: 2.6 Consensus size: 116
39148652 GTGTTGCTTC
* * *
39148662 CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTGGACGGTCATAATAATCTTTTGATTTCG
1 CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTAGACGGTTATAATAATCTTTTGATTTCT
* *
39148727 TTGAATAGGAATGATAGGGTTTACTCATTGTCCTCTTTCTTGAATCTCTAA
66 TTGAAGAGGAATGATAGGGTTTACTCATTGTCCTCTTTCTTGAATATCTAA
39148778 CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTAGACGGTTATAATAATCTTTTGATTTCT
1 CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTAGACGGTTATAATAATCTTTTGATTTCT
39148843 TTGAAGAGGAATGATAGGGTTTACTCATTGTCCTCTTTCTTGAATATCTAA
66 TTGAAGAGGAATGATAGGGTTTACTCATTGTCCTCTTTCTTGAATATCTAA
* * *
39148894 CCACGATCTCTGTTAGAATACCCCAACTGAAGCTGTCAGATGGTTATAATAATCTTTTGATTTCT
1 CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTAGACGGTTATAATAATCTTTTGATTTCT
39148959 TTG
66 TTG
39148962 CTAAGTTCTT
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 176 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (116 bp):
CCACGATCTCTGTTAGAATACCCCAACTGAAGTTGTTAGACGGTTATAATAATCTTTTGATTTCT
TTGAAGAGGAATGATAGGGTTTACTCATTGTCCTCTTTCTTGAATATCTAA
Found at i:39151824 original size:2 final size:2
Alignment explanation
Indices: 39151817--39151845 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39151807 TTTCTTGATC
39151817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39151846 TCAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39155741 original size:46 final size:45
Alignment explanation
Indices: 39155645--39155817 Score: 133
Period size: 46 Copynumber: 3.7 Consensus size: 45
39155635 CATATCCATG
* *
39155645 CCGATGCCATGTACCAGACATGGTCTTACACT-GACACATCAT--GT-A
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTC-TCATAAGTGA
* * *
39155690 CCCGATGCATGTCCCAAACATTTCTTACACTAGCTCTCGTCTCAA-T-A
1 -CCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC--AT-AAGTGA
* * *
39155737 CCGATGCAATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGG
1 CCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GTGA
39155785 CCGATGCATGTCCCAGACATGTCTTACACTAGC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC
39155818 ACACATATCA
Statistics
Matches: 103, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
43 2 0.02
44 11 0.11
45 16 0.16
46 26 0.25
47 26 0.25
48 22 0.21
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTGA
Found at i:39155762 original size:92 final size:94
Alignment explanation
Indices: 39155645--39155817 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
39155635 CATATCCATG
* *
39155645 CCGATGCCATGTACCAGACATGGTCTTACACT-G-ACACATCATGTACCCGATGCATGTCCCAAA
1 CCGATGCAATGTACCAGACATGGTCTTACACTGGCACACATAATGTACCCGATGCATGTCCCAAA
*
39155708 CATTTCTTACACTAGCTCTCGTCTCAATA
66 CATGTCTTACACTAGCTCTCGTCTCAATA
* * ** *
39155737 CCGATGCAATGT-CCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAG
1 CCGATGCAATGTACC-AGACATGGTCTTACACTGGCACACATAATGTACCCGATGCATGTCCCAA
39155801 ACATGTCTTACACTAGC
65 ACATGTCTTACACTAGC
39155818 ACACATATCA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 2 0.03
92 28 0.40
93 1 0.01
94 39 0.56
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (94 bp):
CCGATGCAATGTACCAGACATGGTCTTACACTGGCACACATAATGTACCCGATGCATGTCCCAAA
CATGTCTTACACTAGCTCTCGTCTCAATA
Found at i:39164515 original size:67 final size:65
Alignment explanation
Indices: 39164318--39164524 Score: 176
Period size: 67 Copynumber: 3.2 Consensus size: 65
39164308 ATATAGTTTG
* * * * * *
39164318 GCTCTCTTGTAC-ACATGGTG-AACAC-TCAGTACCACCCATGTGACCTAGCCA-ATTTAT-CTC
1 GCTCTCTTGT-CTACATGGTGCTACACAT-AGAACCACGCATGCGACCTAGCTACATATATCCT-
39164378 GTA
63 GTA
* * *
39164381 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCTG
1 GCTCTCTTGTCTACATGGTG--CTACACATAGAACCACGCATGCGACCTAGCTACATATATCCTG
39164446 TA
64 TA
* * *
39164448 GCTCTCTTGTCTACATGGTG-TACACATAGTATCAC-CATGCGACCTAGCTACATCATAATGGCT
1 GCTCTCTTGTCTACATGGTGCTACACATAGAACCACGCATGCGACCTAGCTACAT-AT-AT--CC
39164511 TGTA
62 TGTA
39164515 GCTCTCTTGT
1 GCTCTCTTGT
39164525 ACACATGATG
Statistics
Matches: 119, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 36 0.30
64 12 0.10
65 2 0.02
66 22 0.18
67 44 0.37
68 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGCTACACATAGAACCACGCATGCGACCTAGCTACATATATCCTGTA
Found at i:39166734 original size:46 final size:45
Alignment explanation
Indices: 39166541--39166856 Score: 257
Period size: 46 Copynumber: 6.8 Consensus size: 45
39166531 AGGGTATAAT
* * * * *
39166541 GCCGATGCCATGTCCCAAACGTGGTCTTACACTGGCTCTCA-CGTTAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATC-TGAG
** * * * *
39166588 GTTGATGCCATGTCCTAGACATGGTCTTACACTGATCTCATGTATCTG-T
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACT-AGCTC-T-CATCTGAG
* *
39166637 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCATGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATC-TG-AG
*
39166683 CCCGATGCATGTCCCAGACATGTCTTACACTAGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCT-GAG
* *
39166729 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCT-GAG
* * *
39166775 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTGAG
39166823 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
39166857 ACACATATCA
Statistics
Matches: 224, Mismatches: 29, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
44 13 0.06
45 19 0.08
46 72 0.32
47 57 0.25
48 28 0.12
49 32 0.14
50 2 0.01
51 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTGAG
Found at i:39166826 original size:94 final size:92
Alignment explanation
Indices: 39166541--39166856 Score: 319
Period size: 94 Copynumber: 3.4 Consensus size: 92
39166531 AGGGTATAAT
* * * ** *
39166541 GCCGATGCCATGTCCCAAACGTGGTCTTACACTGGCTCTCA-CGTTAAGTTGATGCCATGTCCTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATC--TAAGCCGATGCCATGTCCCA
* *
39166605 GACATGGTCTTACACTGATCTCATGTATCTG
64 GACATGGTCTTACACTGCTCTCA--TATGTG
* * *
39166636 TGCCGATGCCATGTCCCAGACATGGTCTTACACT-GACACATCATGT-ACCCGATG-CATGTCCC
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTC-TCATCTAAGCCGATGCCATGTCCC
* *
39166698 AGACAT-GTCTTACACTAGCT-TACATCTCGAG
63 AGACATGGTCTTACACT-GCTCT-CATAT-GTG
39166729 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCT-AA-GCCGATGCCATGTCCCA
39166792 GACATGGTCTTACACTGGCTCTCATAATGTG
64 GACATGGTCTTACACT-GCTCTCAT-ATGTG
39166823 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
39166857 ACACATATCA
Statistics
Matches: 188, Mismatches: 18, Indels: 30
0.80 0.08 0.13
Matches are distributed among these distances:
89 5 0.03
90 12 0.06
91 16 0.09
92 15 0.08
93 26 0.14
94 69 0.37
95 8 0.04
96 34 0.18
97 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (92 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTAAGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGCTCTCATATGTG
Found at i:39166828 original size:140 final size:140
Alignment explanation
Indices: 39166591--39166856 Score: 385
Period size: 140 Copynumber: 1.9 Consensus size: 140
39166581 ACGTTAAGTT
* **
39166591 GATGCCATGTCCTAGACATGGTCTTACACTGATCTCATGTATCTGTGCCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGATCTCA-GTATCAATGCCGATGCCATGTCCCAGA
*
39166656 CATGGTCTTACACTGACACATCATGTACCCGATGCATGTCCCAGACATGTCTTACACTAGCTTAC
65 CATGGTCTTACACTGACACATAATGTACCCGATGCATGTCCCAGACATGTCTTACACTAGCTTAC
39166721 ATCTCGAGGCC
130 ATCTCGAGGCC
* *
39166732 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCA-TCTCAATGCCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACT-GATCTCAGTATCAATGCCGATGCCATGTCCCAGA
* * **
39166794 CATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTAGC
65 CATGGTCTTACACT-G-ACACATAATGTACCCGATGCATGTCCCAGACATGTCTTACACTAGC
39166857 ACACATATCA
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
138 37 0.33
139 11 0.10
140 60 0.54
141 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (140 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGATCTCAGTATCAATGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTGACACATAATGTACCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACA
TCTCGAGGCC
Found at i:39182714 original size:28 final size:28
Alignment explanation
Indices: 39182674--39182728 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
39182664 TAAGTAAGGA
39182674 AACTTTATCATTATTATGTGTGGAATGC
1 AACTTTATCATTATTATGTGTGGAATGC
39182702 AACTTTATCATTATTATGTGTGGAATG
1 AACTTTATCATTATTATGTGTGGAATG
39182729 ATTGATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (28 bp):
AACTTTATCATTATTATGTGTGGAATGC
Found at i:39182994 original size:48 final size:48
Alignment explanation
Indices: 39182858--39183127 Score: 265
Period size: 48 Copynumber: 5.6 Consensus size: 48
39182848 TATGTTTGCT
* * * **
39182858 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCC
* * * * * *
39182906 ATTGTAAGA-CATGTCTGGGACATGGCATCAGCCAA-ATTATGGGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATC-GACAATGTTATGAGAGCC
* * * *
39182953 AATGTAAGACCATGTTTGGAACATAGCATCAACAATGTTATGCGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCC
* **
39183001 AGTGTAAGACCATATTTGGAACATGGCATCGGTAATGTTATGAGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCC
* * * * *
39183049 TGTGTAAGATCATGTTTGGAACATGGCATCGGCAATGTTACGAAAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCC
** ** *
39183097 AGAATAAGACCATGCCTGGGACATGGCATCG
1 AGTGTAAGACCATGTTTGGAACATGGCATCG
39183128 GCATTGAGAC
Statistics
Matches: 187, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
47 42 0.22
48 145 0.78
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCC
Found at i:39183128 original size:48 final size:48
Alignment explanation
Indices: 39182862--39183232 Score: 219
Period size: 48 Copynumber: 7.8 Consensus size: 48
39182852 TTTGCTAGTG
* * ** * * * *
39182862 TAAGACCATGTCTGGGACATGGCATCGACCACATTATGAGAGCCATTG
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
* * * ** * *
39182910 TAAGA-CATGTCTGGGACATGGCATCAGCCAA-ATTATGGGAGCCAATG
1 TAAGACCATGTCTGGGACATGGCATC-GGCAATGTTACGAAAGCCAGTA
* * * ** * ** *
39182957 TAAGACCATGTTTGGAACATAGCATCAACAATGTTATGCGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
* * * * * * * *
39183005 TAAGACCATATTTGGAACATGGCATCGGTAATGTTATGAGAGCCTGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
* * * *
39183053 TAAGATCATGTTTGGAACATGGCATCGGCAATGTTACGAAAGCCAGAA
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
* * ** * *
39183101 TAAGACCATGCCTGGGACATGGCATCGGCATTGAGACGAAAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
* * * * * ** * **
39183149 CAAGACCATGTCTAGGACATGTCATCAGC-CTCGACATGTGAGCCAGTA
1 TAAGACCATGTCTGGGACATGGCATCGGCAAT-GTTACGAAAGCCAGTA
*
39183197 TAAGACCATGTCTGGGACATGGCATCGGTAAT-TTAC
1 TAAGACCATGTCTGGGACATGGCATCGGCAATGTTAC
39183233 CCTCTTGTGT
Statistics
Matches: 260, Mismatches: 58, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
47 44 0.17
48 215 0.83
49 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCAATGTTACGAAAGCCAGTA
Found at i:39183927 original size:21 final size:21
Alignment explanation
Indices: 39183903--39183943 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39183893 TGGTTATTTG
39183903 TGTTTG-TGCTTGGATTGGTTA
1 TGTTTGATG-TTGGATTGGTTA
*
39183924 TGTTTGATGTTGTATTGGTT
1 TGTTTGATGTTGGATTGGTT
39183944 GGTGCAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.10, C:0.02, G:0.32, T:0.56
Consensus pattern (21 bp):
TGTTTGATGTTGGATTGGTTA
Found at i:39186124 original size:12 final size:12
Alignment explanation
Indices: 39186107--39186135 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39186097 CGAGACCTTG
39186107 GATTTACCTCTA
1 GATTTACCTCTA
39186119 GATTTACCTCTA
1 GATTTACCTCTA
39186131 GATTT
1 GATTT
39186136 TAGGGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (12 bp):
GATTTACCTCTA
Found at i:39188527 original size:16 final size:16
Alignment explanation
Indices: 39188502--39188532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39188492 TTTAAGTGAA
39188502 TTGAAATACTATATGT
1 TTGAAATACTATATGT
*
39188518 TTGAATTACTATATG
1 TTGAAATACTATATG
39188533 ATATGGTTAT
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:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
TTGAAATACTATATGT
Found at i:39190440 original size:21 final size:23
Alignment explanation
Indices: 39190414--39190475 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
39190404 ATCAGTATAT
39190414 GACACATAAAGTGCCT-AAA-AC
1 GACACATAAAGTGCCTGAAATAC
** *
39190435 GACACACGAGGTGCCTGAAATAC
1 GACACATAAAGTGCCTGAAATAC
39190458 GACACATAAAGTGCCTGA
1 GACACATAAAGTGCCTGA
39190476 TCAGTAAAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 13 0.39
22 3 0.09
23 17 0.52
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (23 bp):
GACACATAAAGTGCCTGAAATAC
Found at i:39193842 original size:40 final size:39
Alignment explanation
Indices: 39193674--39193844 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
39193664 AGAAATTGAA
* *
39193674 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
39193714 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
39193754 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
39193794 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
39193834 TGATATCCGGG
1 TGATATCCGGG
39193845 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:39195338 original size:22 final size:22
Alignment explanation
Indices: 39195313--39195357 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39195303 CTTTCTATTC
* *
39195313 TCTTTTCTCTATTCTTTTTGTT
1 TCTTTTCTCTACTCTGTTTGTT
*
39195335 TCTTTTCTTTACTCTGTTTGTT
1 TCTTTTCTCTACTCTGTTTGTT
39195357 T
1 T
39195358 TATTCAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.04, C:0.18, G:0.07, T:0.71
Consensus pattern (22 bp):
TCTTTTCTCTACTCTGTTTGTT
Found at i:39201638 original size:21 final size:21
Alignment explanation
Indices: 39201614--39201661 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
39201604 GACACATAAA
39201614 GTGCCTAAAAAGACACACGAG
1 GTGCCTAAAAAGACACACGAG
* * *
39201635 GTGCCTGATACGACACACGAG
1 GTGCCTAAAAAGACACACGAG
39201656 GTGCCT
1 GTGCCT
39201662 GAAATACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (21 bp):
GTGCCTAAAAAGACACACGAG
Found at i:39201662 original size:21 final size:22
Alignment explanation
Indices: 39201625--39201674 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
39201615 TGCCTAAAAA
39201625 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
39201646 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
39201669 GACACA
1 GACACA
39201675 TAAAGCCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:39203264 original size:18 final size:18
Alignment explanation
Indices: 39203227--39203265 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39203217 CTCTATTCTT
* *
39203227 TTTGTTTCTTTTCTTTAC
1 TTTGTTTCTTTTATTCAC
*
39203245 TTTGTTTGTTTTATTCAC
1 TTTGTTTCTTTTATTCAC
39203263 TTT
1 TTT
39203266 AGTTACTAAT
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:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTGTTTCTTTTATTCAC
Found at i:39207127 original size:28 final size:29
Alignment explanation
Indices: 39207072--39207129 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
39207062 GCTTGTAAAC
39207072 TTTAAGTTAATTTTCAAACTTTAAAACAT
1 TTTAAGTTAATTTTCAAACTTTAAAACAT
39207101 TTTAA-TTAAATTTTCAAACTTT-AAACAT
1 TTTAAGTT-AATTTTCAAACTTTAAAACAT
39207129 T
1 T
39207130 ATTGCTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTAAGTTAATTTTCAAACTTTAAAACAT
Found at i:39210638 original size:63 final size:63
Alignment explanation
Indices: 39210539--39210667 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 63
39210529 CAACCTGATT
*
39210539 TATAACTTAAATTTTGTAACTCAAACTCTATTAAGATGCGCCTCATT-CTCGATGGGATAAGAA
1 TATAACTTAAATTTGGTAACTCAAACTCTATTAAGATGCGCCTCATTCCT-GATGGGATAAGAA
* *
39210602 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAACTCAAACTCTATTAAGATGCGCCTCATTCCTGATGGGATAAGAA
39210665 TAT
1 TAT
39210668 CTCCATGTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 60 0.97
64 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (63 bp):
TATAACTTAAATTTGGTAACTCAAACTCTATTAAGATGCGCCTCATTCCTGATGGGATAAGAA
Found at i:39211702 original size:35 final size:35
Alignment explanation
Indices: 39211645--39211718 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
39211635 AGACTAAGAG
39211645 GATTGAAGACCAGGGGGAGTATGGAAAGTGATTCA
1 GATTGAAGACCAGGGGGAGTATGGAAAGTGATTCA
*
39211680 GATTGAAGGCCATGGGGG-GTATGGAAAGTGATTCA
1 GATTGAAGACCA-GGGGGAGTATGGAAAGTGATTCA
39211715 GATT
1 GATT
39211719 CAAATTGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 32 0.86
36 5 0.14
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (35 bp):
GATTGAAGACCAGGGGGAGTATGGAAAGTGATTCA
Found at i:39212238 original size:44 final size:44
Alignment explanation
Indices: 39212190--39212278 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
39212180 CCAAATGTGG
*
39212190 TGTAAATGTCATTAGTTTAGATGGTAAAATTGAGAAAATGGAAT
1 TGTAAATGTCATTAGTTTAGATGGTAAAATTGAAAAAATGGAAT
39212234 TGTAAATGTCATTAGTTTAGATGGTAAAATTGAAAAAATGGAAT
1 TGTAAATGTCATTAGTTTAGATGGTAAAATTGAAAAAATGGAAT
39212278 T
1 T
39212279 TATGATATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (44 bp):
TGTAAATGTCATTAGTTTAGATGGTAAAATTGAAAAAATGGAAT
Found at i:39218580 original size:46 final size:48
Alignment explanation
Indices: 39218351--39218664 Score: 224
Period size: 47 Copynumber: 6.6 Consensus size: 48
39218341 TAATATCGAA
* * *
39218351 GCCATGTCCCAAACATAGTCTTACACTAG--CTCATC-CATCAAGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAT--AGCCGAT
* * ** * * *
39218398 GCCATGTCCCAGACTTGGTCTTACACT-GACTATCAAAATCGA-GGCTGAC
1 GCCATGTCCCAGACATGGTCTTACACTAG-CTCTC-ATCTC-ATAGCCGAT
* * * * *
39218447 ACCATGTCCCAGAAATGGTCTTACATTAGCTCTCACATATCCGT-GCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCT-CATAGCCGAT
* * *
39218497 GCCATGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCATAGCCGAT
* *
39218543 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCA-ATGCAGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCATA-GCCGAT
* * * *
39218589 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCATAGCCGAT
39218637 G-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCATGTCCCAGACATGGTCTTACACTAGC
39218665 ACACAAATAA
Statistics
Matches: 209, Mismatches: 39, Indels: 39
0.73 0.14 0.14
Matches are distributed among these distances:
44 10 0.05
45 17 0.08
46 37 0.18
47 52 0.25
48 24 0.11
49 33 0.16
50 32 0.15
51 3 0.01
52 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCATAGCCGAT
Found at i:39218644 original size:94 final size:93
Alignment explanation
Indices: 39218353--39218664 Score: 296
Period size: 94 Copynumber: 3.3 Consensus size: 93
39218343 ATATCGAAGC
* *
39218353 CATGTCCCAAACATAGTCTTACACTAGCTCATC-CATCAA-GTCGATGCCATGTCCCAGACTTGG
1 CATGTCCCAGACATAGTCTTACACTAGCTC-TCTC-TCAATG-CGATGCCATGTCCCAGACATGG
* * * * **
39218416 TCTTACACTGACTATCAAAATCGAGGCTGACAC
63 TCTTACACTGACTCTCATAAT-GTGGCCGA-TG
* * * * ** *
39218449 CATGTCCCAGAAATGGTCTTACATTAGCTCTCACATATCCGTGCCGATGCCATGTCCTAGACATG
1 CATGTCCCAGACATAGTCTTACACTAGCTCT--C-TCTCAATG-CGATGCCATGTCCCAGACATG
* * *
39218514 GTCTTACACTGACACATC-TCA--TAGCCGATG
62 GTCTTACACTGACTC-TCATAATGTGGCCGATG
39218544 CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATGCAGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATAGTCTTACACTAGCTCTC-TCTCAATGC-GATGCCATGTCCCAGACATGGT
*
39218608 CTTACACTGGCTCTCATAATGTGGCCGATG
64 CTTACACTGACTCTCATAATGTGGCCGATG
39218638 CATGTCCCAGACAT-GTCTTACACTAGC
1 CATGTCCCAGACATAGTCTTACACTAGC
39218665 ACACAAATAA
Statistics
Matches: 176, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
91 3 0.02
92 40 0.23
94 50 0.28
95 14 0.08
96 30 0.17
97 1 0.01
98 2 0.01
99 34 0.19
100 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (93 bp):
CATGTCCCAGACATAGTCTTACACTAGCTCTCTCTCAATGCGATGCCATGTCCCAGACATGGTCT
TACACTGACTCTCATAATGTGGCCGATG
Found at i:39222136 original size:27 final size:27
Alignment explanation
Indices: 39222078--39222143 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
39222068 ACCCTAATAT
* * *
39222078 TGGTAAAATTACCGTAATTCCCCTCTA
1 TGGTAAAATGACCATAATACCCCTCTA
* *
39222105 GGGTAAAATGACCATAATACCCCTGTA
1 TGGTAAAATGACCATAATACCCCTCTA
*
39222132 TGGTAGAATGAC
1 TGGTAAAATGAC
39222144 GATTATGCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (27 bp):
TGGTAAAATGACCATAATACCCCTCTA
Found at i:39228761 original size:16 final size:17
Alignment explanation
Indices: 39228729--39228762 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39228719 ATATAGTGGT
*
39228729 TTGAAATGTTGACTTAA
1 TTGAAATATTGACTTAA
39228746 TTGAAATATT-ACTTAA
1 TTGAAATATTGACTTAA
39228762 T
1 T
39228763 GACTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TTGAAATATTGACTTAA
Found at i:39230516 original size:25 final size:22
Alignment explanation
Indices: 39230466--39230516 Score: 57
Period size: 25 Copynumber: 2.2 Consensus size: 22
39230456 TGTCAAATTA
*
39230466 CATTCAAACATACCAATTTGGT
1 CATTCAAACATACCAATTTGGC
*
39230488 CATTCAAAACATACCTTTATTTGGC
1 CATTC-AAACATACC--AATTTGGC
39230513 CATT
1 CATT
39230517 TCAACACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
25 10 0.42
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (22 bp):
CATTCAAACATACCAATTTGGC
Found at i:39235912 original size:40 final size:40
Alignment explanation
Indices: 39235857--39236062 Score: 333
Period size: 40 Copynumber: 5.2 Consensus size: 40
39235847 GGACTAAGAT
* * *
39235857 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
*
39235897 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
*
39235937 CCGAAGGTATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
39235977 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
** *
39236017 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
39236056 CCGAAGG
1 CCGAAGG
39236063 TACTTGGGTT
Statistics
Matches: 158, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
39 15 0.09
40 143 0.91
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:39237900 original size:11 final size:11
Alignment explanation
Indices: 39237873--39237905 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
39237863 CGACAAGTAA
39237873 ATTATTATTTT
1 ATTATTATTTT
39237884 -TTATTATTTT
1 ATTATTATTTT
39237894 ATTATTATTTT
1 ATTATTATTTT
39237905 A
1 A
39237906 ATGTCATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:39242131 original size:40 final size:40
Alignment explanation
Indices: 39242086--39242253 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
39242076 CGGAATACAA
39242086 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
39242126 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
39242166 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
39242206 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
39242246 CCGGATAT
1 CCGGATAT
39242254 CATTCAATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 102 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:39250172 original size:40 final size:40
Alignment explanation
Indices: 39250127--39250294 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39250117 CGGAATACAA
39250127 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
39250167 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
39250207 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
39250247 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
39250287 CCGGATAT
1 CCGGATAT
39250295 CATTCAATTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 100 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:39252149 original size:3 final size:3
Alignment explanation
Indices: 39252141--39252292 Score: 64
Period size: 3 Copynumber: 50.7 Consensus size: 3
39252131 ACAAAAGGGG
* * * * *
39252141 AAT AAT AAT AAT GAT AGT AAT AAT AAT AGTT ACT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * *
39252187 -CT AAGT AAAT AA- AAA AAG AA- AAT ATAT AAT -GT AAT AAA AAT AAT
1 AAT AA-T -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* ** * * *
39252231 AGAA AAT AAT AA- AAT AAT AAT AAT AGG GAT AAT AGT AA- ACAA AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
39252276 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
39252293 AAGGCAAACA
Statistics
Matches: 110, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
2 9 0.08
3 89 0.81
4 10 0.09
5 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:39252250 original size:27 final size:28
Alignment explanation
Indices: 39252203--39252255 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
39252193 AAATAAAAAA
**
39252203 AGAAAATATATAATGTAATAAAAATAAT
1 AGAAAATATATAAAATAATAAAAATAAT
*
39252231 AGAAAATA-ATAAAATAATAATAATA
1 AGAAAATATATAAAATAATAAAAATA
39252256 GGGATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (28 bp):
AGAAAATATATAAAATAATAAAAATAAT
Found at i:39252263 original size:33 final size:36
Alignment explanation
Indices: 39252226--39252291 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
39252216 TGTAATAAAA
*
39252226 ATAATAG-AAA-ATAATAA-AATAATAATAATAGGG
1 ATAATAGTAAACAAAATAATAATAATAATAATAGGG
39252259 ATAATAGTAAACAAAATAATAATAATAATAATA
1 ATAATAGTAAACAAAATAATAATAATAATAATA
39252292 AAAGGCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.24
34 3 0.10
35 6 0.21
36 13 0.45
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.26
Consensus pattern (36 bp):
ATAATAGTAAACAAAATAATAATAATAATAATAGGG
Found at i:39255743 original size:16 final size:16
Alignment explanation
Indices: 39255722--39255753 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39255712 GTAATGCCCT
39255722 AAAAATCTCGAAATCC
1 AAAAATCTCGAAATCC
39255738 AAAAATCTCGAAATCC
1 AAAAATCTCGAAATCC
39255754 TAAACTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAATCTCGAAATCC
Found at i:39257027 original size:24 final size:24
Alignment explanation
Indices: 39256978--39257028 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
39256968 ATGTATCAGC
* * * *
39256978 AAAAGCCGAAATGCTGAAATGTCG
1 AAAAGCCGAAACGCTAAAAAGCCG
39257002 AAAAGCCGAAACGCTAAAAAGCCG
1 AAAAGCCGAAACGCTAAAAAGCCG
39257026 AAA
1 AAA
39257029 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.10
Consensus pattern (24 bp):
AAAAGCCGAAACGCTAAAAAGCCG
Found at i:39257327 original size:28 final size:29
Alignment explanation
Indices: 39257263--39257327 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
39257253 GGGCCTAACG
* **
39257263 GGCCATATAAATGTGATTTGGGCCTAATA
1 GGCCATATAAAGGTGATTTGGGAATAATA
*
39257292 GGCCATATACAGGTGATTT-GGAATAATA
1 GGCCATATAAAGGTGATTTGGGAATAATA
39257320 GGCCATAT
1 GGCCATAT
39257328 GAATATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (29 bp):
GGCCATATAAAGGTGATTTGGGAATAATA
Done.