Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 95 of 345
Found at i:31282436 original size:10 final size:10
Alignment explanation
Indices: 31282419--31282560 Score: 72
Period size: 10 Copynumber: 14.0 Consensus size: 10
31282409 CATTTTAACA
31282419 ATATATTATT
1 ATATATTATT
31282429 -TCATATTATT
1 AT-ATATTATT
31282439 AT-TATTTATT
1 ATATA-TTATT
31282449 ATATATTATTTTT
1 ATATATTA---TT
*
31282462 CATAAATTATT
1 -ATATATTATT
31282473 AT-TATT-TT
1 ATATATTATT
*
31282481 ACATTATTATTT
1 ATA-TATTA-TT
31282493 ATATATTATT
1 ATATATTATT
31282503 ATTATATT-TT
1 A-TATATTATT
31282513 -TACT-TGTATT
1 ATA-TAT-TATT
31282523 ATATA-T-TT
1 ATATATTATT
31282531 AT-TAATTATT
1 ATAT-ATTATT
31282541 -TATATATATT
1 ATATAT-TATT
31282551 ATATATTATT
1 ATATATTATT
31282561 TTTACATATA
Statistics
Matches: 104, Mismatches: 4, Indels: 48
0.67 0.03 0.31
Matches are distributed among these distances:
7 1 0.01
8 11 0.11
9 13 0.12
10 43 0.41
11 23 0.22
12 4 0.04
13 2 0.02
14 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
ATATATTATT
Found at i:31282438 original size:3 final size:3
Alignment explanation
Indices: 31282432--31282560 Score: 61
Period size: 3 Copynumber: 40.3 Consensus size: 3
31282422 TATTATTTCA
* *
31282432 TAT TAT TAT TATT TAT TAT ATAT TAT TTT TCAT AAAT TAT TAT TAT T-T
1 TAT TAT TAT TA-T TAT TAT -TAT TAT TAT T-AT -TAT TAT TAT TAT TAT
* * *
31282480 TA- CAT TAT TATT TAT ATAT TAT TAT TA- TAT TTT TACT T-G TAT TAT
1 TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
31282525 ATATT TAT TAAT TAT T-T ATAT ATAT TAT ATAT TAT T
1 -TA-T TAT T-AT TAT TAT -TAT -TAT TAT -TAT TAT T
31282561 TTTACATATA
Statistics
Matches: 99, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
2 7 0.07
3 59 0.60
4 32 0.32
5 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:31282454 original size:20 final size:20
Alignment explanation
Indices: 31282431--31282561 Score: 91
Period size: 20 Copynumber: 6.8 Consensus size: 20
31282421 ATATTATTTC
31282431 ATATTATTATTATTTATTAT
1 ATATTATTATTATTTATTAT
* **
31282451 ATATTATTTTTCATAAATTAT
1 ATATTATTATT-ATTTATTAT
*
31282472 -TATTATT-TTACATTATTAT
1 ATATTATTATTA-TTTATTAT
*
31282491 TTA-TA-TATTA-TTATTAT
1 ATATTATTATTATTTATTAT
* *
31282508 AT-TT-TTACT-TGTATTAT
1 ATATTATTATTATTTATTAT
31282525 ATATTTATTAATTATTTA-TAT
1 ATA-TTATT-ATTATTTATTAT
31282546 ATATTATATATTATTT
1 ATATTAT-TATTATTT
31282562 TTACATATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
17 20 0.23
18 2 0.02
19 14 0.16
20 32 0.37
21 16 0.18
22 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (20 bp):
ATATTATTATTATTTATTAT
Found at i:31282455 original size:30 final size:30
Alignment explanation
Indices: 31282419--31282552 Score: 98
Period size: 32 Copynumber: 4.3 Consensus size: 30
31282409 CATTTTAACA
31282419 ATATATTATTTCATATTATTATTATTTATT
1 ATATATTATTTCATATTATTATTATTTATT
31282449 ATATATTATTTTTCATAAATTATTATTA-TT-TT
1 ATATATTA--TTTCAT--ATTATTATTATTTATT
* * *
31282481 ACATTATTATTTATATATTATTATTATATTTTT
1 ATA-TATTATTT-CATATTATTATTAT-TTATT
* *
31282514 ACTTGTATTATAT-AT-TTATTAATTATTTA-T
1 A--TATATTATTTCATATTATT-ATTATTTATT
31282544 ATATATTAT
1 ATATATTAT
31282553 ATATTATTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
28 7 0.08
30 20 0.24
31 10 0.12
32 21 0.25
33 10 0.12
34 17 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
ATATATTATTTCATATTATTATTATTTATT
Found at i:31282487 original size:50 final size:50
Alignment explanation
Indices: 31282422--31282568 Score: 142
Period size: 51 Copynumber: 2.9 Consensus size: 50
31282412 TTTAACAATA
* *
31282422 TATTATTTCATATTATTATTATTTATTATATATTATTTTTCATAAAT-TAT
1 TATTATTTTA-ATTATTATTATATATTATATATTATTTTTCATAAATGTAT
**
31282472 TATTATTTTACATTATTATTTATATATTAT-TATTATATTTT--TACTTGTAT
1 TATTATTTTA-ATTATTA-TTATATATTATATATTAT-TTTTCATAAATGTAT
31282522 TATATATTTATTAATTATT-TATATATATTATATATTATTTTTACATA
1 TAT-TA-TT-TTAATTATTAT-TATATATTATATATTATTTTT-CATA
31282569 TATACACTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
49 3 0.04
50 29 0.36
51 30 0.37
52 14 0.17
53 3 0.04
54 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (50 bp):
TATTATTTTAATTATTATTATATATTATATATTATTTTTCATAAATGTAT
Found at i:31292902 original size:15 final size:14
Alignment explanation
Indices: 31292884--31292931 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
31292874 ATATTATAAT
31292884 TTTTATTAATTCATA
1 TTTTATTAATT-ATA
31292899 TTTTAATAATAATTATA
1 TTTT-AT--TAATTATA
31292916 TTTTATTAAATTATA
1 TTTTATT-AATTATA
31292931 T
1 T
31292932 ATTTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 1 0.03
15 12 0.41
16 4 0.14
17 7 0.24
18 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTATTAATTATA
Found at i:31293187 original size:16 final size:16
Alignment explanation
Indices: 31293166--31293229 Score: 85
Period size: 16 Copynumber: 4.0 Consensus size: 16
31293156 TGAATTACTG
*
31293166 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
* *
31293182 ATTACAATTCTATTAC
1 ATTACAACTCTATTCC
31293198 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
31293214 ATTACAA-TCCTATTCC
1 ATTACAACT-CTATTCC
31293230 TTCCCCCCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
15 1 0.02
16 41 0.98
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:31293202 original size:32 final size:32
Alignment explanation
Indices: 31293166--31293227 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
31293156 TGAATTACTG
* *
31293166 ATTACAGCTCTATTCCATTACAATTCTATTAC
1 ATTACAACTCTATTCCATTACAATCCTATTAC
31293198 ATTACAACTCTATTCCATTACAATCCTATT
1 ATTACAACTCTATTCCATTACAATCCTATT
31293228 CCTTCCCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTACAACTCTATTCCATTACAATCCTATTAC
Found at i:31295961 original size:42 final size:42
Alignment explanation
Indices: 31295896--31296016 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
31295886 AAATGGTTTT
* *
31295896 ACAAGCTGTGTATCAA-TGAAGCTCCCCATGTGAGCTTAAATG
1 ACAAGTTGTGTAT-AAGCGAAGCTCCCCATGTGAGCTTAAATG
* * * * *
31295938 GCAAGTTGTGTATAAGCGAAGCTCCCCACGTGATCTTAAGTT
1 ACAAGTTGTGTATAAGCGAAGCTCCCCATGTGAGCTTAAATG
* ** * *
31295980 ACAAGTTGTGTATCAGTAAAGCTCCCCGTGCGAGCTT
1 ACAAGTTGTGTATAAGCGAAGCTCCCCATGTGAGCTT
31296017 GCTCCTCATT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
41 2 0.03
42 61 0.97
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
ACAAGTTGTGTATAAGCGAAGCTCCCCATGTGAGCTTAAATG
Found at i:31296418 original size:15 final size:15
Alignment explanation
Indices: 31296400--31296429 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31296390 TTAAAAAAAC
*
31296400 ACATGTTATAATATA
1 ACATATTATAATATA
31296415 ACATATTATAATATA
1 ACATATTATAATATA
31296430 GTTAAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (15 bp):
ACATATTATAATATA
Found at i:31298782 original size:18 final size:19
Alignment explanation
Indices: 31298747--31298790 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
31298737 TGCATGGCAA
* *
31298747 TATAAATTCATTAGATATT
1 TATAAATTCATTAAATATG
31298766 TATAAATT-ATTAAATATG
1 TATAAATTCATTAAATATG
31298784 TATAAAT
1 TATAAAT
31298791 AAGTTGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TATAAATTCATTAAATATG
Found at i:31303862 original size:48 final size:49
Alignment explanation
Indices: 31303760--31303891 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 49
31303750 TGAAATCTTG
*
31303760 TATAAGACCATATCTGGGATATGGCATTGGTATC-G-ACACGAGATCCCA
1 TATAAGACCATATCTGGGATATGGCATTGGCATCTGTACAC-AGATCCCA
* * * * **
31303808 TGTAAGACCATATCTGGGATATGCCATTGGCATCTGTATA-AGGTTTCA
1 TATAAGACCATATCTGGGATATGGCATTGGCATCTGTACACAGATCCCA
* * *
31303856 TATAAGACCATGTCTGGGACATGGCATCGGCA-CTGT
1 TATAAGACCATATCTGGGATATGGCATTGGCATCTGT
31303892 TATTAGACTT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 4 0.06
48 63 0.90
49 1 0.01
50 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (49 bp):
TATAAGACCATATCTGGGATATGGCATTGGCATCTGTACACAGATCCCA
Found at i:31308069 original size:16 final size:16
Alignment explanation
Indices: 31308048--31308088 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
31308038 AGAGTAAATC
*
31308048 GAAAGCTCGTTGGATT
1 GAAAGCTCGTTAGATT
31308064 GAAAGCTCGTTAGATT
1 GAAAGCTCGTTAGATT
31308080 GAAAGCTCG
1 GAAAGCTCG
31308089 ACAGAGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (16 bp):
GAAAGCTCGTTAGATT
Found at i:31312306 original size:46 final size:47
Alignment explanation
Indices: 31312209--31312307 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 47
31312199 ATTTTTGTTA
* * * * *
31312209 TGGCAACTTGGCTGCATTTATAGTGGTTGAAGCACACATATCTGTTT
1 TGGCAGCTTGGCTGCATATATAGTGGTTGAACCACACATATCTGATC
* *
31312256 TGGCAGCTTGGCTGCA-ATATAGTGGCTTG-ACCACATATATTTGATC
1 TGGCAGCTTGGCTGCATATATAGTGG-TTGAACCACACATATCTGATC
31312302 TGGCAG
1 TGGCAG
31312308 TTTAAACTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 26 0.59
47 18 0.41
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (47 bp):
TGGCAGCTTGGCTGCATATATAGTGGTTGAACCACACATATCTGATC
Found at i:31312455 original size:22 final size:23
Alignment explanation
Indices: 31312416--31312458 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
31312406 TGGGTAGGAA
31312416 GTTTTCTGAAAAATTTGCATTTT
1 GTTTTCTGAAAAATTTGCATTTT
31312439 GTTTTCT--AAAATATTGCATT
1 GTTTTCTGAAAAAT-TTGCATT
31312459 GGCATAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (23 bp):
GTTTTCTGAAAAATTTGCATTTT
Found at i:31314736 original size:21 final size:21
Alignment explanation
Indices: 31314711--31314779 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
31314701 TATAATGATT
31314711 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
31314732 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
31314752 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
31314772 ATTATTAT
1 ATTATTAT
31314780 TATTAGTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:31317226 original size:20 final size:21
Alignment explanation
Indices: 31317188--31317232 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
31317178 ACAATTAATT
31317188 TTTTTTAAAAATTGAAAAT-A
1 TTTTTTAAAAATTGAAAATAA
*
31317208 TTTTTT-AAAATTGTTAAATAA
1 TTTTTTAAAAATTG-AAAATAA
31317229 TTTT
1 TTTT
31317233 AATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTTTAAAAATTGAAAATAA
Found at i:31322887 original size:3 final size:3
Alignment explanation
Indices: 31322879--31322918 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
31322869 AAATCAAAAG
31322879 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31322919 AAGATACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31323978 original size:13 final size:14
Alignment explanation
Indices: 31323950--31323983 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
31323940 ATGAGTTGCT
31323950 ATATAATATGATATA
1 ATATAATA-GATATA
31323965 ATATAATA-ATATA
1 ATATAATAGATATA
31323978 ATATAA
1 ATATAA
31323984 ATGGATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATATAATAGATATA
Found at i:31325387 original size:26 final size:26
Alignment explanation
Indices: 31325334--31325389 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
31325324 TGTTATTTAT
* * *
31325334 TTTTCCTTTCTTTCTTTTTTATTTTA
1 TTTTCCTTTCTTTCTTTTTGAATCTA
31325360 TTTT-CTTTCTTTTCTTTTTGAATCTA
1 TTTTCCTTTC-TTTCTTTTTGAATCTA
31325386 TTTT
1 TTTT
31325390 ATACATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTCCTTTCTTTCTTTTTGAATCTA
Found at i:31326011 original size:3 final size:3
Alignment explanation
Indices: 31326003--31326108 Score: 79
Period size: 3 Copynumber: 34.3 Consensus size: 3
31325993 TTTGGCTACT
* * * * * *
31326003 TTA TTA TTA -AA TTAA TTA TTT TTA ATA TTA TTA TTA CTA CTA TTT
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
31326048 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTAA TGTA CTG TTA TTC TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA T-TA
31326096 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
31326109 ACTATTAAAC
Statistics
Matches: 80, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
2 1 0.01
3 70 0.88
4 8 0.10
5 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31326051 original size:18 final size:18
Alignment explanation
Indices: 31326028--31326115 Score: 87
Period size: 18 Copynumber: 5.1 Consensus size: 18
31326018 TTATTTTTAA
31326028 TATTATTATTACTACTAT
1 TATTATTATTACTACTAT
* *
31326046 TTTTATTATTACTATTAT
1 TATTATTATTACTACTAT
*
31326064 TATTATTATTATTA--AT
1 TATTATTATTACTACTAT
* *
31326080 GTACTGTTATT-CT-CTAT
1 -TATTATTATTACTACTAT
31326097 TATTATTATTA-TACTAT
1 TATTATTATTACTACTAT
31326114 TA
1 TA
31326116 AACTGGTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.21
17 16 0.29
18 28 0.50
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTATTATTACTACTAT
Found at i:31326061 original size:27 final size:26
Alignment explanation
Indices: 31326017--31326115 Score: 89
Period size: 27 Copynumber: 3.8 Consensus size: 26
31326007 TATTAAATTA
* * *
31326017 ATTATTTTTAATATTATTATTACTACT
1 ATTATTATTATTACTATTATTACT-CT
*
31326044 ATTTTTATTATTACTATTATTA-T-T
1 ATTATTATTATTACTATTATTACTCT
*
31326068 ATTATTATTAATGTACTGTTATT-CTCT
1 ATTATTATT-AT-TACTATTATTACTCT
*
31326095 ATTATTATTATTA-TACTATTA
1 ATTATTATTATTACTATTATTA
31326116 AACTGGTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
24 14 0.24
25 4 0.07
26 13 0.22
27 28 0.47
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTATTATTATTACTATTATTACTCT
Found at i:31332900 original size:64 final size:64
Alignment explanation
Indices: 31332827--31332954 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
31332817 TCATTCATAA
* *
31332827 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGAAGAATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * *
31332891 CACATCTAGTTAGAAGAATTTGATTTATTTCGATCATAGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGAAGAATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
31332955 AGATACATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGAAGAATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:31333260 original size:44 final size:45
Alignment explanation
Indices: 31333212--31333299 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
31333202 CTTGTCTTTC
**
31333212 TGAGGTAGCAA-GAGAGCAGGTTGAAGATTGAAG-TCTTATCTTCT
1 TGAGGTAGCAAGGA-AGCAGACTGAAGATTGAAGATCTTATCTTCT
*
31333256 TGAGGTAGCAAGGAAGTAGACTGAAGATTGAAGATCTTATCTTC
1 TGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTTC
31333300 CTAAGAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 27 0.69
45 12 0.31
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (45 bp):
TGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTTCT
Found at i:31333336 original size:177 final size:176
Alignment explanation
Indices: 31333024--31333514 Score: 671
Period size: 177 Copynumber: 2.8 Consensus size: 176
31333014 GAATTCACAA
* * * *
31333024 CCTTACCTCTCTGAGGTAGCAATAAAGCAGGTTGAAGATTGAAGTCTTATCTTTTTAAGGTAGTA
1 CCTTATCTCTCTGAGGTAGCAAGAAAGCAGGTTGAAGATTGAAGTCTTATC-TTTTGAGGTAGCA
* * * * *
31333089 AGGAAGCAAACTGAAGGTTGAAGATCTCATC-TCTCTAAGCAATAGTGGAGAAGATCGAAGATGA
65 AGGAAGCAGACTGAAGATTGAAGATCTTATCTTC-CTAAGCAATAGTGGAGCAGATCGAAGATGG
* * *
31333153 CGAATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAG
129 CGAATCTTATCTTCCCGAGGTAGAAAGGGAACAGATTTTAGCCACCAG
* * *
31333201 CCTTGTCTTTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCTTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAAAGCAGGTTGAAGATTGAAGTCTTATCTT-TTGAGGTAGCA
* * *
31333266 AGGAAGTAGACTGAAGATTGAAGATCTTATCTTCCTAAG-AAGTTGTGGAGCAGATCAAAGATGG
65 AGGAAGCAGACTGAAGATTGAAGATCTTATCTTCCTAAGCAA-TAGTGGAGCAGATCGAAGATGG
*
31333330 CGAATCTTATCTTCCCGAGGTAGAAAGGGAATAGATTTTAGCCACCAG
129 CGAATCTTATCTTCCCGAGGTAGAAAGGGAACAGATTTTAGCCACCAG
* * * *
31333378 CCTTATCTCTCTGAGGTAGTAAGAAAGCATGTTAAAGATTGAATTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAAAGCAGGTTGAAGATTGAAGTCTTATCTTT-TGAGGTAGCA
* * * * *
31333443 AGGAAGCAGATTGAATATTAAAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGC
65 AGGAAGCAGACTGAAGATTGAAGATCTTATCTTCCTAAGCAATAGTGGAGCAGATCGAAGATGGC
31333508 GAATCTT
130 GAATCTT
31333515 GTCTCCCTAA
Statistics
Matches: 275, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
176 5 0.02
177 266 0.97
178 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (176 bp):
CCTTATCTCTCTGAGGTAGCAAGAAAGCAGGTTGAAGATTGAAGTCTTATCTTTTGAGGTAGCAA
GGAAGCAGACTGAAGATTGAAGATCTTATCTTCCTAAGCAATAGTGGAGCAGATCGAAGATGGCG
AATCTTATCTTCCCGAGGTAGAAAGGGAACAGATTTTAGCCACCAG
Found at i:31333514 original size:44 final size:43
Alignment explanation
Indices: 31333466--31333934 Score: 356
Period size: 44 Copynumber: 10.7 Consensus size: 43
31333456 AATATTAAAG
* * **
31333466 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAC-A
* ** * *
31333510 ATCTTGTCTCCCTAAATAGTAGTAGAGCAGATTTAAG-CCACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAC-A
* * * *
31333553 TCCTATCTTCTTATCTCCTTAAGCAGTAGTAGAGCAAATCGAAGA-CAGCGA
1 ----A---TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCA-C-A
* * *
31333604 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAG-CCACT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCACA
* * * * **
31333646 ATCCTATCTCCCTAAGCAGTAGTGGGGTAGGTTGAAGATTACA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCACA
* **
31333689 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAC-A
* * * *
31333734 ATCTTGTCTCCTTAAGCAGTAGTGGAGCAGATTTAAG-CCACC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCACA
* * **
31333776 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGA-TGAAGATTACA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATTGAAGACCACA
* * ***
31333819 GATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCAC-A
* * * * *
31333864 ATCTTGTCTCCCTAAGGAGTAGTAGAGCAGATTTAAG-CCACC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCACA
*
31333906 ATCCTATCTCCCTAAGCAGTAGTGGAGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA
31333935 TGTTGAAATC
Statistics
Matches: 330, Mismatches: 77, Indels: 38
0.74 0.17 0.09
Matches are distributed among these distances:
42 85 0.26
43 15 0.05
44 193 0.58
45 2 0.01
47 2 0.01
50 31 0.09
51 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCACA
Found at i:31333632 original size:94 final size:94
Alignment explanation
Indices: 31333467--31333654 Score: 295
Period size: 94 Copynumber: 2.0 Consensus size: 94
31333457 ATATTAAAGA
* * * *
31333467 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAATAGTAG
1 TCTTATCTCCCTAAGCAATAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAACAGTAG
31333532 TAGAGCAGATTTAAGCCACAATCCTATCT
66 TAGAGCAGATTTAAGCCACAATCCTATCT
* * *
31333561 TCTTATCTCCTTAAGCAGTAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAATAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAACAGTAG
* *
31333626 TGGAGCAGATTTAAGCCACTATCCTATCT
66 TAGAGCAGATTTAAGCCACAATCCTATCT
31333655 CCCTAAGCAG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (94 bp):
TCTTATCTCCCTAAGCAATAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAACAGTAG
TAGAGCAGATTTAAGCCACAATCCTATCT
Found at i:31333683 original size:86 final size:86
Alignment explanation
Indices: 31333470--31333934 Score: 348
Period size: 86 Copynumber: 5.3 Consensus size: 86
31333460 TTAAAGATCT
* * * * ** *
31333470 TATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAATAGTAGTAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC-AC-AATCTTATCTCCCTAAGCAGTAGTGG
*
31333535 AGCAGATTTAAG-CCACAATCCTATCTTC
64 AGCAGATTGAAGACCACAA----ATC--C
* * * * *
31333563 TTATCTCCTTAAGCAGTAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAGCAGTAGTG
1 -TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACA-C-AATCTTATCTCCCTAAGCAGTAGTG
* *
31333628 GAGCAGATTTAAG-CCAC-TATCC
63 GAGCAGATTGAAGACCACAAATCC
* * * *
31333650 TATCTCCCTAAGCAGTAGTGGGGTAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CACA-ATCTTATCTCCCTAAGCAGTAGTGG
* ** * *
31333715 AGCAGATCGAAGACGGCGAATCT
64 AGCAGATTGAAGACCACAAATCC
* * * * * *
31333738 TGTCTCCTTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACACAATCTTATCTCCCTAAGCAGTAGTGGAG
* ** * *
31333803 TAGGA-TGAAGATTACAGATCT
66 CA-GATTGAAGACCACAAATCC
* * ** * * *
31333824 TATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGAATCTTGTCTCCCTAAGGAGTAGTAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CAC-AATCTTATCTCCCTAAGCAGTAGTGG
* *
31333889 AGCAGATTTAAG-CCAC-CATCC
64 AGCAGATTGAAGACCACAAATCC
31333910 TATCTCCCTAAGCAGTAGTGGAGCA
1 TATCTCCCTAAGCAGTAGTGGAGCA
31333935 TGTTGAAATC
Statistics
Matches: 301, Mismatches: 61, Indels: 26
0.78 0.16 0.07
Matches are distributed among these distances:
85 1 0.00
86 154 0.51
87 13 0.04
88 58 0.19
89 3 0.01
94 72 0.24
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (86 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACACAATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATTGAAGACCACAAATCC
Found at i:31333728 original size:130 final size:130
Alignment explanation
Indices: 31333561--31333932 Score: 636
Period size: 130 Copynumber: 2.9 Consensus size: 130
31333551 AATCCTATCT
* * * *
31333561 TCTTATCTCCTTAAGCAGTAGTAGAGCAAATCGAAGACAGCGAATCTTGTCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAGCAGTAG
* * *
31333626 TGGAGCAGATTTAAGCCACTATCCTATCTCCCTAAGCAGTAGTGGGGTAGGTTGAAGATTACAGA
66 TGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATTACAGA
*
31333691 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCTTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAGCAGTAG
31333756 TGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATTACAGA
66 TGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATTACAGA
* * *
31333821 TCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGAATCTTGTCTCCCTAAGGAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAGCAGTAG
*
31333886 TAGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAG
66 TGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAG
31333933 CATGTTGAAA
Statistics
Matches: 229, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 229 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (130 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTAAGCAGTAG
TGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATTACAGA
Found at i:31334092 original size:88 final size:88
Alignment explanation
Indices: 31333948--31334684 Score: 804
Period size: 88 Copynumber: 8.4 Consensus size: 88
31333938 TGAAATCCAT
* * * * ** *
31333948 AATTCATATATCCTTAAAG-TTCTAGTGGAGTAGATTGAAGCTACAAATCTTTTCTCCCTAAAAT
1 AATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAAT
* ** *
31334012 GGCACTAAAGCGGCTCAAAGCCAC
65 GGCATTGGAGCGGCTCGAAGCCAC
* * *
31334036 AATTTGTATCAT-CTTGAAGTTTCAGCGAAGTATATCAAAGCTACAAATCTCTTCTCCCTAAAAT
1 AATTCGTATC-TCCTTGAAGTTTCAGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAAT
* *
31334100 GGTATTGGAGCGCCTCGAAGCCAC
65 GGCATTGGAGCGGCTCGAAGCCAC
* ** * **
31334124 AATTCGTATCTCCTTGAAGTTCCAATGGAGTAGATCGAAA-CTACAAATCTCTTCTCCTTGTAAT
1 AATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATC-AAAGCTACAAATCTCTTCTCCCTAAAAT
* * * *
31334188 GGAATTAGAGTGGCTCGAAGCCAT
65 GGCATTGGAGCGGCTCGAAGCCAC
* * * ** *
31334212 AATTCATATCTCCTTAAAGTTCCAGCGGAGTAGATTGAAGTTACAAATCTCTTCTCCCTAAAATG
1 AATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATG
*
31334277 GCATTGGAGTGGCTCGAAGCCAC
66 GCATTGGAGCGGCTCGAAGCCAC
* * * *
31334300 AATTCGTATCTCCTTGAAG-TTCTAGCGGAGTAGATCAAAACTAAAAATCTCTTCTCCTTTAAAT
1 AATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAAT
*
31334364 GGCATTGGAGTGGCTCGAAGCCAC
65 GGCATTGGAGCGGCTCGAAGCCAC
* * * *
31334388 AATTCGTATCTCCTTAAAG-CTCTAGCGGAGTAGATTTAAA-CTACAAATCTTTTTCTCCCTAAA
1 AATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGA-TCAAAGCTACAAATC-TCTTCTCCCTAAA
* * *
31334451 ATGGCATTAGAGCAGCTCAAAGCCAC
63 ATGGCATTGGAGCGGCTCGAAGCCAC
* * * * *
31334477 AATTCGTATCTTCTTGAAGTTTCAGCGAAGTATATCGAAGCTACAAATCTCTTCTCCCTGAAATG
1 AATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATG
* *
31334542 GCATTGGAGCAGCTCGAAGCCAT
66 GCATTGGAGCGGCTCGAAGCCAC
* * *
31334565 AATTCTTATCTCCTTGAAG-TTCTAGCGGAGTAGATCAAAGCTACAAGTCTCTTCTCCCTGAAAT
1 AATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAAT
*
31334629 GGCATTGGAACGGCTCGAAGCCAC
65 GGCATTGGAGCGGCTCGAAGCCAC
* * * * *
31334653 AATTCTTATCTCCCTAAAGTTGCAGTGGAGTA
1 AATTCGTATCTCCTTGAAGTTTCAGCGGAGTA
31334685 TATTGAATCT
Statistics
Matches: 548, Mismatches: 89, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
87 8 0.01
88 458 0.84
89 80 0.15
90 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (88 bp):
AATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATG
GCATTGGAGCGGCTCGAAGCCAC
Found at i:31334162 original size:44 final size:43
Alignment explanation
Indices: 31334114--31334402 Score: 111
Period size: 44 Copynumber: 6.6 Consensus size: 43
31334104 TTGGAGCGCC
31334114 TCGAAGCCACAATTCGTATCTCCTTGAAGTTCCAATGGAGTAGA
1 TCGAAGCCACAATTC-TATCTCCTTGAAGTTCCAATGGAGTAGA
* * ** * * *
31334158 TCGAAACTACAAATCTCT-TCTCCTTGTAA--TGGAATTAGAGTGGC
1 TCGAAGCCAC-AAT-TCTATCTCCTTG-AAGTTCCAA-TGGAGTAGA
* * **
31334202 TCGAAGCCATAATTCATATCTCCTTAAAGTTCCAGCGGAGTAGA
1 TCGAAGCCACAATTC-TATCTCCTTGAAGTTCCAATGGAGTAGA
* ** * * * ** * * *
31334246 TTGAAGTTACAAATCTCT-TCTCCCTAAAATGGCATTGGAGTGGC
1 TCGAAGCCAC-AAT-TCTATCTCCTTGAAGTTCCAATGGAGTAGA
* **
31334290 TCGAAGCCACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGA
1 TCGAAGCCACAATTC-TATCTCCTTGAAGTTCCAATGGAGTAGA
* * * * * * ** * * *
31334334 TCAAAACTAAAAATCTCT-TCTCCTTTAAATGGCATTGGAGTGGC
1 TCGAAGC-CACAAT-TCTATCTCCTTGAAGTTCCAATGGAGTAGA
31334378 TCGAAGCCACAATTCGTATCTCCTT
1 TCGAAGCCACAATTC-TATCTCCTT
31334403 AAAGCTCTAG
Statistics
Matches: 169, Mismatches: 60, Indels: 32
0.65 0.23 0.12
Matches are distributed among these distances:
42 6 0.04
43 18 0.11
44 122 0.72
45 17 0.10
46 6 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
TCGAAGCCACAATTCTATCTCCTTGAAGTTCCAATGGAGTAGA
Found at i:31334560 original size:44 final size:44
Alignment explanation
Indices: 31334441--31334667 Score: 136
Period size: 44 Copynumber: 5.2 Consensus size: 44
31334431 CAAATCTTTT
* * * *
31334441 TCTCCCTAAAATGGCATTAGAGCAGCTCAAAGCCACAATTCGTA
1 TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCACAATTCTTA
* * * ** ** * * ** * *
31334485 TCTTCTTGAAGTTTCAGCGAAGTATATCGAAGCTACAAATCTCT-
1 TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCACAATTCT-TA
*
31334529 TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCATAATTCTTA
1 TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCACAATTCTTA
* * * ** * * * * *
31334573 TCTCCTTGAAGT-TCTAGCGGAGTAGATCAAAGCTACAAGTCTCT-
1 TCTCCCTGAAATGGC-ATTGGAGCAGCTCGAAGCCACAATTCT-TA
* *
31334617 TCTCCCTGAAATGGCATTGGAACGGCTCGAAGCCACAATTCTTA
1 TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCACAATTCTTA
31334661 TCTCCCT
1 TCTCCCT
31334668 AAAGTTGCAG
Statistics
Matches: 123, Mismatches: 54, Indels: 12
0.65 0.29 0.06
Matches are distributed among these distances:
43 3 0.02
44 117 0.95
45 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
TCTCCCTGAAATGGCATTGGAGCAGCTCGAAGCCACAATTCTTA
Found at i:31334726 original size:51 final size:51
Alignment explanation
Indices: 31334657--31334883 Score: 203
Period size: 51 Copynumber: 4.7 Consensus size: 51
31334647 AGCCACAATT
* * *
31334657 CTTATCTCCCTAAAGTTGCAGTGGAGTATATTGAATCTAGAAATCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
* * * * * *
31334708 CTTATCTCGCTGAAGTTGCAGTGGAGCAGACTGAAGATAG---T---GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
*
31334753 CTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
* * **
31334804 CTTATCTCCCTGAAGTTGTAGTGGGGTA-AGTTGAAG-T-----T-ACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTGAAGCTAGAAATCACAAAC
* *
31334848 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
31334884 AAAGTAGATC
Statistics
Matches: 143, Mismatches: 25, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
44 34 0.24
45 39 0.27
48 2 0.01
50 2 0.01
51 66 0.46
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (51 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
Found at i:31334772 original size:45 final size:44
Alignment explanation
Indices: 31334708--31334922 Score: 173
Period size: 45 Copynumber: 4.7 Consensus size: 44
31334698 AATCACAAAC
*
31334708 CTTATCTCGCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGT-AAT
* * * * *
31334753 CTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG---T----AAT
* * * * * *
31334804 CTTATCTCCCTGAAGTTGTAGTGGGGTA-AGTTGAAGTTA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATAGTAA-T
*
31334848 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGTAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTA-AT
* * *
31334893 CTCATCTCCTTGAAGTTGCAATGGAGCAGA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA
31334923 TTAAGCTACA
Statistics
Matches: 136, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
43 2 0.01
44 31 0.23
45 65 0.48
46 1 0.01
48 1 0.01
50 1 0.01
51 35 0.26
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAT
Found at i:31334820 original size:96 final size:95
Alignment explanation
Indices: 31334651--31334883 Score: 299
Period size: 96 Copynumber: 2.4 Consensus size: 95
31334641 GCTCGAAGCC
* * * *
31334651 ACAATTCTTATCTCCCTAAAGTTGCAGTGGAGTATATTGAATCTAGAAATCACAAACCTTATCTC
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAACCTTATCTC
*
31334716 GCTGAAGTTGCAGTGGAGC-AGACTGAAGAT
66 CCTGAAGTTGCAGTGGAGCAAG-CTGAAGAT
* *
31334746 AGTGAA-TCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAACCTTATC
1 A--CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAACCTTATC
* * * * *
31334810 TCCCTGAAGTTGTAGTGGGGTAAGTTGAAGTT
64 TCCCTGAAGTTGCAGTGGAGCAAGCTGAAGAT
* *
31334842 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
31334884 AAAGTAGATC
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
94 2 0.02
95 35 0.29
96 78 0.66
97 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (95 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTAGAAATCACAAACCTTATCTC
CCTGAAGTTGCAGTGGAGCAAGCTGAAGAT
Found at i:31335642 original size:21 final size:20
Alignment explanation
Indices: 31335613--31335661 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
31335603 AAGGTTACTG
*
31335613 TTTTTTTTTCTTTTCTTTCT
1 TTTTTTTTTATTTTCTTTCT
31335633 TTTTTATTTTATTTTCTTTCT
1 TTTTT-TTTTATTTTCTTTCT
31335654 TTTCTTTT
1 TTT-TTTT
31335662 CGAATCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTATTTTCTTTCT
Found at i:31336328 original size:3 final size:3
Alignment explanation
Indices: 31336320--31336514 Score: 114
Period size: 3 Copynumber: 64.3 Consensus size: 3
31336310 TTTGGCTACT
* * * * *
31336320 TTA TTA TTA -AA TTAA TTA TTT TTA ATA TTA TTA TTA TTA CTA TTT
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
31336365 TTA TTA TTA CTA CTA CTA CTA CTA TTA TTA TTA TTAA CTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA
* *
31336412 TTC TTA TTA GTA -TA TTA TTA TT- TCCTA TT- TT- TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA
* ** * * *
31336454 TTG TTA TTA ACA TATA TTA TTA TTAA TGTA CTG TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA
31336502 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
31336515 ACTATTAAAC
Statistics
Matches: 152, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
2 10 0.07
3 127 0.84
4 11 0.07
5 4 0.03
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:31336791 original size:21 final size:21
Alignment explanation
Indices: 31336765--31336814 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
31336755 TATTACTATT
31336765 ATTAATATCATCGCCATTATG
1 ATTAATATCATCGCCATTATG
*
31336786 ATTAATATCATCGTCATTATG
1 ATTAATATCATCGCCATTATG
31336807 ATTAATAT
1 ATTAATAT
31336815 TATTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (21 bp):
ATTAATATCATCGCCATTATG
Found at i:31358619 original size:59 final size:59
Alignment explanation
Indices: 31358547--31358663 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
31358537 GAGAGGTTGT
* *
31358547 CTTTTCTAACTCCTCCTCAATAGCTTTTGCTTTATCTACAGTGAATCCTTCAATCACGA
1 CTTTTCTAACTCCTCATCAATAGCTTTTACTTTATCTACAGTGAATCCTTCAATCACGA
* *
31358606 CTTTTCTAACTCCTCATCAATAGCTTTTACTTTATCTACAGTGACTCCTTCAGTCACG
1 CTTTTCTAACTCCTCATCAATAGCTTTTACTTTATCTACAGTGAATCCTTCAATCACG
31358664 GGGTCAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (59 bp):
CTTTTCTAACTCCTCATCAATAGCTTTTACTTTATCTACAGTGAATCCTTCAATCACGA
Found at i:31380531 original size:29 final size:28
Alignment explanation
Indices: 31380499--31380604 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 28
31380489 ATAATATGAT
31380499 TTGGGCCTAATGGGCCATATGAATGAGAA
1 TTGGGCCTAATGGGCCATATGAAT-AGAA
* *
31380528 TTGGGCCTAGTGGGCCATAAGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATA-GAA
* *
31380557 CTGGGCC-AGATGGGCCATTTGAATA-AGA
1 TTGGGCCTA-ATGGGCCATATGAATAGA-A
*
31380585 TTGGG-CTAGTGGGCCATATG
1 TTGGGCCTAATGGGCCATATG
31380605 CATGTATGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
27 12 0.19
28 8 0.12
29 44 0.69
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAATAGAA
Found at i:31380554 original size:58 final size:56
Alignment explanation
Indices: 31380491--31380602 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 56
31380481 GCATGAATAT
** *
31380491 AATATGATTTGGGCCTA-ATGGGCCATATGAATGAGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAACTGGGCC-AGATGGGCCATATGAATAAG-ATTGGG-CTAGTGGGCCATAAG
*
31380549 AATATGAACTGGGCCAGATGGGCCATTTGAATAAGATTGGGCTAGTGGGCCATA
1 AATATGAACTGGGCCAGATGGGCCATATGAATAAGATTGGGCTAGTGGGCCATA
31380603 TGCATGTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 13 0.27
57 7 0.14
58 29 0.59
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.25
Consensus pattern (56 bp):
AATATGAACTGGGCCAGATGGGCCATATGAATAAGATTGGGCTAGTGGGCCATAAG
Found at i:31380909 original size:27 final size:26
Alignment explanation
Indices: 31380862--31380918 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
31380852 AAAACCGTAA
* * * *
31380862 TAAGGGAAAAATTATCGAAATGCCCT
1 TAAGGGAAAAATTACCAAAATACCCC
31380888 TAAGGGAAAAAATTACCAAAATACCCC
1 TAAGGG-AAAAATTACCAAAATACCCC
31380915 TAAG
1 TAAG
31380919 TGTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (26 bp):
TAAGGGAAAAATTACCAAAATACCCC
Found at i:31384997 original size:29 final size:28
Alignment explanation
Indices: 31384965--31385071 Score: 117
Period size: 29 Copynumber: 3.8 Consensus size: 28
31384955 ATAATATGAT
31384965 TTGGGCCTAATGGGCCATATGAATGAGAA
1 TTGGGCCTAATGGGCCATATGAAT-AGAA
*
31384994 TTGGGCCTAATGGGCCATAAGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATA-GAA
* * * * *
31385023 CTAGGCCAAATGGGCCATTTGAATA-AGT
1 TTGGGCCTAATGGGCCATATGAATAGA-A
*
31385051 TTGGGCCTAGTGGGCCATATG
1 TTGGGCCTAATGGGCCATATG
31385072 CATATATGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 17 0.27
29 46 0.72
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAATAGAA
Found at i:31386579 original size:30 final size:31
Alignment explanation
Indices: 31386503--31386585 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
31386493 TCAGTCTCGA
*
31386503 CATAT-ACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
31386533 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
31386564 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
31386586 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 18 0.35
31 33 0.65
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:31387197 original size:27 final size:27
Alignment explanation
Indices: 31387134--31387189 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
31387124 GGGCATATTC
31387134 GTCA-TTTACCATACAGGGGTATTACG
1 GTCACTTTACCATACAGGGGTATTACG
*
31387160 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCACTTTACCATACAGGGG-TATTACG
31387187 GTC
1 GTC
31387190 TTTTTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGTATTACG
Found at i:31387356 original size:56 final size:55
Alignment explanation
Indices: 31387228--31387358 Score: 149
Period size: 56 Copynumber: 2.4 Consensus size: 55
31387218 TTTCATCCTA
* * *
31387228 CAAGGGTGTTTTGGTAA-ATTTATAAACCAAGGGTATTTTAGTAATTTTGTAAAG
1 CAAGGGTATTTTGGTAATTTTTAGAAACCAAGGGTATTTTAGTAATTTTGTAAAG
* * * * *
31387282 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTTAGAAA-CCAAGGGTATTTTAGTAATTTTGTAAAG
*
31387338 TAAGGGTATTTTGGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
31387359 ACAAATTGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
54 12 0.19
55 9 0.15
56 41 0.66
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (55 bp):
CAAGGGTATTTTGGTAATTTTTAGAAACCAAGGGTATTTTAGTAATTTTGTAAAG
Found at i:31387364 original size:27 final size:27
Alignment explanation
Indices: 31387229--31387479 Score: 150
Period size: 27 Copynumber: 9.3 Consensus size: 27
31387219 TTCATCCTAC
* * * **
31387229 AAGGGTGTTTTGGTAAATTTATAAACC
1 AAGGGTATTTTGGTAATTTTACAAATT
* ** **
31387256 AAGGGTATTTTAGTAATTTTGTAAAGC
1 AAGGGTATTTTGGTAATTTTACAAATT
* * * *
31387283 AATGGTATTTCT-ATAATTTTTAGAAAGTC
1 AAGGGTATTT-TGGTAA-TTTTACAAA-TT
* **
31387312 AAGGGTATTTTTGTAATTTTGTAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
31387339 AAGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
* ** * *
31387366 GAGGGTAGCTCGGTAATTTTACAAA-C
1 AAGGGTATTTTGGTAATTTTACAAATT
* *
31387392 CAGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAATT
* * **
31387420 AGGGGTATTTTGGTAATTCTAC-CCTAT
1 AAGGGTATTTTGGTAATTTTACAAAT-T
* *
31387447 AAGGGTATTTTAGTAATTTCAC-AATT
1 AAGGGTATTTTGGTAATTTTACAAATT
*
31387473 GAGGGTA
1 AAGGGTA
31387480 AAACGGTAAT
Statistics
Matches: 176, Mismatches: 41, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
26 9 0.05
27 137 0.78
28 17 0.10
29 13 0.07
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAATT
Found at i:31387435 original size:54 final size:54
Alignment explanation
Indices: 31387236--31387437 Score: 174
Period size: 54 Copynumber: 3.7 Consensus size: 54
31387226 TACAAGGGTG
* * * * * *
31387236 TTTTGGTAAATTTATAAACCAAGGGTATTTTAGTAATTTTGTAAAGCAATGGTA
1 TTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTGTAAACCAGTGGTA
* * * * **
31387290 TTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATTAAG-GGTA
1 TTT-TGGTAA-TTTTACAAACT-AAGGGTATTTTGGTAATTTTGTAAA-CCAGTGGTA
* * ** * **
31387346 TTTTGGTAATTTTACAAATTGAGGGTAGCTCGGTAATTTTACAAACCAGTGGTA
1 TTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTGTAAACCAGTGGTA
*
31387400 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATT
1 TTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAATT
31387438 CTACCCTATA
Statistics
Matches: 115, Mismatches: 27, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
53 2 0.02
54 60 0.52
55 18 0.16
56 34 0.30
57 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTGTAAACCAGTGGTA
Found at i:31387488 original size:26 final size:26
Alignment explanation
Indices: 31387458--31387560 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 26
31387448 AGGGTATTTT
*
31387458 AGTAATTT-CACAATTGAGGGTAAAAC
1 AGTAATTTGCA-AATCGAGGGTAAAAC
* *
31387484 GGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAA-TTTGCAAATCGAGGGTAAAAC
* * *
31387511 AGTAATTCTGTAAATCAAGAGTAAAAC
1 AGTAATT-TGCAAATCGAGGGTAAAAC
**
31387538 AGTAATTCTATAAATCGAGGGTA
1 AGTAATT-TGCAAATCGAGGGTA
31387561 CTTTGGTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
26 6 0.09
27 58 0.89
28 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (26 bp):
AGTAATTTGCAAATCGAGGGTAAAAC
Found at i:31387506 original size:27 final size:27
Alignment explanation
Indices: 31387473--31387560 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
31387463 TTTCACAATT
* *
31387473 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
31387500 GAGGGTAAAACAGTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* * *
31387527 AAGAGTAAAACAGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
31387554 GAGGGTA
1 GAGGGTA
31387561 CTTTGGTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTGTAAATC
Found at i:31389938 original size:31 final size:31
Alignment explanation
Indices: 31389895--31389977 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
31389885 TCAGTCTCGA
*
31389895 CATAT-ACTGGGCCCAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
31389925 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
31389956 CATATCA-TTGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
31389978 ACTGTAAGCG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 19 0.38
31 31 0.62
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:31390213 original size:25 final size:25
Alignment explanation
Indices: 31390185--31390266 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
31390175 TAGAGGCCTA
31390185 CCCTCTTTTAAT-AACTGGGGCAAAG
1 CCCT-TTTTAATAAACTGGGGCAAAG
*
31390210 CCCTTTTTGATAAACTGGGGCAAAG
1 CCCTTTTTAATAAACTGGGGCAAAG
*** *
31390235 CCCTTTTCGGTAAACTGGGGCATAG
1 CCCTTTTTAATAAACTGGGGCAAAG
31390260 CCCTTTT
1 CCCTTTT
31390267 AGCACTTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 6 0.12
25 46 0.88
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.30
Consensus pattern (25 bp):
CCCTTTTTAATAAACTGGGGCAAAG
Found at i:31390723 original size:27 final size:28
Alignment explanation
Indices: 31390664--31390715 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
31390654 ATATTCATCA
31390664 TTTA-CCATACAGGGGTATTACGGTCAC
1 TTTACCCATACAGGGGTATTACGGTCAC
31390691 TTTACCCA-ACAGGGGCT-TTACGGTC
1 TTTACCCATACAGGGG-TATTACGGTC
31390716 TTTTTACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (28 bp):
TTTACCCATACAGGGGTATTACGGTCAC
Found at i:31390882 original size:56 final size:54
Alignment explanation
Indices: 31390762--31390963 Score: 194
Period size: 54 Copynumber: 3.7 Consensus size: 54
31390752 TACAAGGGTG
* * * *
31390762 TTTTGGTAAATTTATAAACCAAGGGTATTTTAGTAATTTTGTAAAGC-AATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAA-CTAGTGGTA
* * * * *
31390816 TTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATTAGGGGTA
1 TTT-TGGTAA-TTTTACAAA-TCAAGGGTATTTTAGTAATTTTGTAAACTAGTGGTA
* ** ***
31390872 TTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACTAGTGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACTAGTGGTA
*
31390926 TTTTGGTAATTTTACAAA-CTATGGGTATTTTAGTAATT
1 TTTTGGTAATTTTACAAATC-AAGGGTATTTTAGTAATT
31390964 CTACCCTTAA
Statistics
Matches: 120, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
54 67 0.56
55 17 0.14
56 36 0.30
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACTAGTGGTA
Found at i:31390962 original size:27 final size:27
Alignment explanation
Indices: 31390755--31390995 Score: 168
Period size: 27 Copynumber: 8.9 Consensus size: 27
31390745 TTCATCCTAC
* * * * *
31390755 AAGGGTGTTTTGGTAAATTTATAAACC
1 AAGGGTATTTTAGTAATTTTACAAACT
**
31390782 AAGGGTATTTTAGTAATTTTGTAAAGC-
1 AAGGGTATTTTAGTAATTTTACAAA-CT
* * *
31390809 AATGGTATTTCTA-TAATTTTTAGAAAGT
1 AAGGGTATTT-TAGTAA-TTTTACAAACT
* ** *
31390837 CAAGGGTATTTTTGTAATTTTGTAAATT
1 -AAGGGTATTTTAGTAATTTTACAAACT
* * *
31390865 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTACAAACT
** *
31390892 AAGGGTATTTCGGTAATTTCACAAACT
1 AAGGGTATTTTAGTAATTTTACAAACT
*
31390919 -AGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTAGTAATTTTACAAACT
* * *
31390946 ATGGGTATTTTAGTAATTCTAC--CCTT
1 AAGGGTATTTTAGTAATTTTACAAAC-T
*
31390972 AAGGGTATTTTAGTAATTTCACAA
1 AAGGGTATTTTAGTAATTTTACAA
31390996 TCGAGGGTAA
Statistics
Matches: 173, Mismatches: 30, Indels: 21
0.77 0.13 0.09
Matches are distributed among these distances:
25 1 0.01
26 22 0.13
27 118 0.68
28 20 0.12
29 12 0.07
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTACAAACT
Found at i:31390962 original size:54 final size:54
Alignment explanation
Indices: 31390730--31390963 Score: 177
Period size: 54 Copynumber: 4.3 Consensus size: 54
31390720 TACCTATTAG
* ** * * * * *
31390730 GGGTATTTTAGTCATTTCATCCTACAAG-GGTGTTTTGGTAAATTTATAAACCAA
1 GGGTATTTTAGTAATTTCA-CAAACTAGTGGTATTTTGGTAATTTTACAAACTAA
*** * * * *
31390784 GGGTATTTTAGTAATTTTGTAAAGC-AATGGTATTTCT-ATAATTTTTAGAAAGTCAA
1 GGGTATTTTAGTAATTTCACAAA-CTAGTGGTATTT-TGGTAA-TTTTACAAACT-AA
* *** * * *
31390840 GGGTATTTTTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTAGTAATTTCACAAACTAGTGGTATTTTGGTAATTTTACAAACTAA
** *
31390894 GGGTATTTCGGTAATTTCACAAACTAGTGGTATTTTGGTAATTTTACAAACTAT
1 GGGTATTTTAGTAATTTCACAAACTAGTGGTATTTTGGTAATTTTACAAACTAA
31390948 GGGTATTTTAGTAATT
1 GGGTATTTTAGTAATT
31390964 CTACCCTTAA
Statistics
Matches: 142, Mismatches: 31, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
53 2 0.01
54 87 0.61
55 18 0.13
56 35 0.25
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.43
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTCACAAACTAGTGGTATTTTGGTAATTTTACAAACTAA
Found at i:31390962 original size:81 final size:80
Alignment explanation
Indices: 31390841--31390995 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 80
31390831 GAAAGTCAAG
* ** * * * *
31390841 GGTATTTTTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTAC-AATTAAGGGTATTTCAGT
31390906 AATTTCACAAACTAGT
65 AATTTCACAAACTAGT
* ** *
31390922 GGTATTTTGGTAATTTTACAAACTATGGGTATTTTAGTAATTCTACCCTTAAGGGTATTTTAGTA
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACAATTAAGGGTATTTCAGTA
31390987 ATTTCACAA
66 ATTTCACAA
31390996 TCGAGGGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 24 0.38
81 39 0.62
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (80 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACAATTAAGGGTATTTCAGTA
ATTTCACAAACTAGT
Found at i:31391030 original size:27 final size:27
Alignment explanation
Indices: 31390994--31391083 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
31390984 GTAATTTCAC
** *
31390994 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
31391021 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* *
31391048 AATCAAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
31391075 AATCGAGGG
1 AATCGAGGG
31391084 CACTTTGGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:31401511 original size:38 final size:39
Alignment explanation
Indices: 31401455--31401537 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 39
31401445 TGAAAAATTA
* *
31401455 TTCTTCAGGAAACAAATCATTTATTTCAACTTCAT-TTG
1 TTCTTTAGGAAACAAATCATTTATTTCAACTTCATCTAG
*
31401493 TTCTTTAGGAAACGAATCATTTATTTCAACTTCATCTAG
1 TTCTTTAGGAAACAAATCATTTATTTCAACTTCATCTAG
31401532 TTCTTT
1 TTCTTT
31401538 GGTATTGGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (39 bp):
TTCTTTAGGAAACAAATCATTTATTTCAACTTCATCTAG
Found at i:31410344 original size:28 final size:28
Alignment explanation
Indices: 31410280--31410410 Score: 104
Period size: 28 Copynumber: 4.6 Consensus size: 28
31410270 CACGAACGTA
* *
31410280 TCGCACACTAAGTGCCATCCTAGAT-GT
1 TCGCACACTAAGTGCCATCCTCGATAAT
*
31410307 CTTGCACACTAAGTGCCATCCTCGATAAT
1 -TCGCACACTAAGTGCCATCCTCGATAAT
* * * * * **
31410336 TCGCTCACTAAGAGGCATTTCTGGATGTT
1 TCGCACACTAAGTGCCA-TCCTCGATAAT
* * *
31410365 TCACACACTAAGTACCATCCTCAATAACT
1 TCGCACACTAAGTGCCATCCTCGATAA-T
31410394 T-GCACACTAAGTGCCAT
1 TCGCACACTAAGTGCCAT
31410411 TTTAAAAATT
Statistics
Matches: 77, Mismatches: 23, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
28 55 0.71
29 22 0.29
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (28 bp):
TCGCACACTAAGTGCCATCCTCGATAAT
Found at i:31410412 original size:57 final size:57
Alignment explanation
Indices: 31410280--31410412 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 57
31410270 CACGAACGTA
* * * *
31410280 TCGCACACTAAGTGCCA-TCCTAGATGTCTTGCACACTAAGTGCCATCCTCGATAAT
1 TCGCACACTAAGTGCCATTTCTAGATGTCTTACACACTAAGTACCATCCTCAATAAT
* * * *
31410336 TCGCTCACTAAGAGGCATTTCTGGATGT-TTCACACACTAAGTACCATCCTCAATAACT
1 TCGCACACTAAGTGCCATTTCTAGATGTCTT-ACACACTAAGTACCATCCTCAATAA-T
31410394 T-GCACACTAAGTGCCATTT
1 TCGCACACTAAGTGCCATTT
31410413 TAAAAATTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 16 0.25
57 45 0.71
58 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (57 bp):
TCGCACACTAAGTGCCATTTCTAGATGTCTTACACACTAAGTACCATCCTCAATAAT
Found at i:31415273 original size:18 final size:18
Alignment explanation
Indices: 31415250--31415293 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
31415240 AGTGTGGTAC
*
31415250 GCCGTGTGGTAATAATA-G
1 GCCGTGTGGAAATAA-AGG
31415268 GCCGTGTGGAAATAAAGG
1 GCCGTGTGGAAATAAAGG
31415286 GCCGTGTG
1 GCCGTGTG
31415294 ATTGACGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.23
Consensus pattern (18 bp):
GCCGTGTGGAAATAAAGG
Found at i:31420329 original size:16 final size:16
Alignment explanation
Indices: 31420295--31420329 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31420285 TGTATGTATC
*
31420295 TGTGAACCCTATAATA
1 TGTGAACCCTATAACA
*
31420311 TGTGAACCCTATCACA
1 TGTGAACCCTATAACA
31420327 TGT
1 TGT
31420330 TGTAAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (16 bp):
TGTGAACCCTATAACA
Found at i:31422895 original size:26 final size:26
Alignment explanation
Indices: 31422866--31422915 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31422856 TCTCATCCCT
31422866 ATTTTACCCCCAGTAAAATTTTGATG
1 ATTTTACCCCCAGTAAAATTTTGATG
**
31422892 ATTTTACCCTTAGTAAAATTTTGA
1 ATTTTACCCCCAGTAAAATTTTGA
31422916 GAAAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (26 bp):
ATTTTACCCCCAGTAAAATTTTGATG
Found at i:31423196 original size:23 final size:24
Alignment explanation
Indices: 31423170--31423215 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
31423160 TATCCATTTC
31423170 ATTCATTTC-TA-TTCAAACAAGCA
1 ATTCATTTCTTATTTC-AACAAGCA
31423193 ATTCATTTCTTATTTCAACAAGC
1 ATTCATTTCTTATTTCAACAAGC
31423216 TAGCAGAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 9 0.43
25 3 0.14
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (24 bp):
ATTCATTTCTTATTTCAACAAGCA
Found at i:31432120 original size:28 final size:29
Alignment explanation
Indices: 31432065--31432122 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
31432055 GATTCTAAAA
* * **
31432065 GGTTTCTAGTTGAGTCATAAAAGTTAGAG
1 GGTTTCTAGTTAAGCCATAAAAACTAGAG
31432094 GGTTT-TAGTTAAGCCATAAAAACTAGAG
1 GGTTTCTAGTTAAGCCATAAAAACTAGAG
31432122 G
1 G
31432123 AAGGTTCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (29 bp):
GGTTTCTAGTTAAGCCATAAAAACTAGAG
Found at i:31442553 original size:123 final size:123
Alignment explanation
Indices: 31442301--31442554 Score: 266
Period size: 123 Copynumber: 2.1 Consensus size: 123
31442291 TTTTTAGTTT
* *
31442301 AATAAAAAAATGATAATTATTAATATATAATTATATCCATTATAATATATATTAATTATTATCAA
1 AATAATAAGATGATAATTATTAATATATAATTATATCCATTATAATATATATTAATTATTATCAA
* ** * ** ***
31442366 CTCTATATAGAATTAGGATTAGTTTTAATTTAATCATATTTTATTTGACATTTTTTTT
66 CTCTACATAGAATTAGGATTAGTTTTAATTTAATCATATTTTAAATGAAATTAATAGC
* *
31442424 AATAATAAGATGATAATCT-TTAATATATAATTATATCTATTATAATTTATATATTAATTTTTAT
1 AATAATAAGATGATAAT-TATTAATATATAATTATATCCATTATAA--TATATATTAATTATTAT
* * **
31442488 CAA-TTTAGCATAGAATTAGGATTAG-TTT-ATTTTATTTTATTTTTAAAT-AAATTAATAGC
63 CAACTCTA-CATAGAATTAGGATTAGTTTTAATTTAATCATA-TTTTAAATGAAATTAATAGC
*
31442547 ATTAATAA
1 AATAATAA
31442555 TTTAATATGT
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
123 60 0.56
124 13 0.12
125 35 0.32
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (123 bp):
AATAATAAGATGATAATTATTAATATATAATTATATCCATTATAATATATATTAATTATTATCAA
CTCTACATAGAATTAGGATTAGTTTTAATTTAATCATATTTTAAATGAAATTAATAGC
Found at i:31444054 original size:30 final size:30
Alignment explanation
Indices: 31443996--31444054 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31443986 AGTTTTCAGG
* *
31443996 ATCCACACGGGCAGGGCACACGGCCATGTA
1 ATCCACACGGGCAGGCCACACAGCCATGTA
31444026 ATCCACACGGGCAGGCCACA-AGCTCATGT
1 ATCCACACGGGCAGGCCACACAGC-CATGT
31444055 GCCAGCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.27, C:0.34, G:0.27, T:0.12
Consensus pattern (30 bp):
ATCCACACGGGCAGGCCACACAGCCATGTA
Found at i:31445172 original size:22 final size:21
Alignment explanation
Indices: 31445135--31445177 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31445125 TAATTTAACC
31445135 ATTTTTATTTTATTTCATTTT
1 ATTTTTATTTTATTTCATTTT
*
31445156 ATTTTTGTTTTAGTTTCATTTT
1 ATTTTTATTTTA-TTTCATTTT
31445178 TAATTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
ATTTTTATTTTATTTCATTTT
Found at i:31448098 original size:30 final size:30
Alignment explanation
Indices: 31448057--31448114 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31448047 GTTTTTGATC
* * *
31448057 CACATGGCCTGGCCACACGGGTGTGTGGAG
1 CACACGGCCTGGCAACACGGGGGTGTGGAG
*
31448087 CACACGGCCTGGCAACATGGGGGTGTGG
1 CACACGGCCTGGCAACACGGGGGTGTGG
31448115 GAGAAGCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.41, T:0.16
Consensus pattern (30 bp):
CACACGGCCTGGCAACACGGGGGTGTGGAG
Found at i:31448534 original size:16 final size:18
Alignment explanation
Indices: 31448506--31448544 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
31448496 ATACTTATAT
31448506 TTTTAATTTTTTACATA-
1 TTTTAATTTTTTACATAC
*
31448523 TTTTAA-TTTTTATATAC
1 TTTTAATTTTTTACATAC
31448540 TTTTA
1 TTTTA
31448545 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATTTTTTACATAC
Found at i:31448543 original size:17 final size:16
Alignment explanation
Indices: 31448500--31448554 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
31448490 ATTCTTATAC
31448500 TTATAT-TTTTAATTTT
1 TTATATATTTTAA-TTT
*
31448516 TTACATATTTTAATTT
1 TTATATATTTTAATTT
31448532 TTATATACTTTTATTATTT
1 TTATATA-TTTTA--ATTT
31448551 TTAT
1 TTAT
31448555 TTTGCTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 14 0.42
17 11 0.33
19 8 0.24
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATATTTTAATTT
Found at i:31448658 original size:14 final size:14
Alignment explanation
Indices: 31448639--31448669 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31448629 TATCATTGAG
31448639 TTTATTATTATTAT
1 TTTATTATTATTAT
*
31448653 TTTATTATTTTTAT
1 TTTATTATTATTAT
31448667 TTT
1 TTT
31448670 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:31448674 original size:6 final size:6
Alignment explanation
Indices: 31448639--31448726 Score: 54
Period size: 6 Copynumber: 14.3 Consensus size: 6
31448629 TATCATTGAG
* * * * * *
31448639 TTTATT ATTATT ATT-TT ATTATT TTTATT TTTATTT TTTATC TTTCTC
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT
* *
31448687 TTTAAT TTT-GT TTTAGTTGT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTA--T-T TTTATT TTTATT TTTATT TT
31448727 CTCTTCAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
5 9 0.13
6 46 0.69
7 7 0.10
9 5 0.07
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:31448690 original size:19 final size:20
Alignment explanation
Indices: 31448649--31448695 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
31448639 TTTATTATTA
* *
31448649 TTATTTTATTATTTTTATTT
1 TTATTTTATTATCTTTATCT
*
31448669 TTATTTT-TTATCTTTCTCT
1 TTATTTTATTATCTTTATCT
31448688 TTAATTTT
1 TT-ATTTT
31448696 GTTTTAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (20 bp):
TTATTTTATTATCTTTATCT
Found at i:31450172 original size:47 final size:45
Alignment explanation
Indices: 31450104--31450466 Score: 234
Period size: 47 Copynumber: 7.8 Consensus size: 45
31450094 GATTCATACA
* *
31450104 CCAGTGCAAGACATGTCTGGGACATGCTTCGGCTACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGC-ACATTATGAGAG
* * * * *
31450150 CCAGTGTAAGATCATGTTTGGGAGATGGCATCGGCATC-TAGACGAGGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-CAT-TATGAGAG
* * * * *
31450198 CTAGTGTAAGACATGTCTAGGACATGCATCAGCCATATTATGAGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GGCACATTATGAGAG
* ** *
31450244 CCAATGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACA-TTATGAGAG
* * *
31450292 CCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGG---C-ACATTATGAGAG
* * * * * *
31450339 CTAGTGTAAGACGTGTTTGGGACACGCATCGGCTAAGATT-T--GTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGC--ACATTATGAGAG
* * **
31450383 CCAATGTAAGACATGTTTGGGACATGCATCAACACGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCA--CAT-TATGAGAG
*
31450431 CCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
31450467 ATATATCCCA
Statistics
Matches: 243, Mismatches: 50, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
42 1 0.00
44 31 0.13
45 3 0.01
46 37 0.15
47 90 0.37
48 58 0.24
49 13 0.05
50 10 0.04
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCACATTATGAGAG
Found at i:31450272 original size:94 final size:94
Alignment explanation
Indices: 31450104--31450466 Score: 308
Period size: 94 Copynumber: 3.9 Consensus size: 94
31450094 GATTCATACA
* * * * * * *
31450104 CCAGTGCAAGACATGTCTGGGACATGCTTCGGCTACATTATGAGAGCCAGTGTAAGATCATGTTT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAATGTAAGACCATGTCT
* *
31450169 GGGAGATGGCATCGGCATC-TAGACGAGGG
66 GGGACATGGCATCGGCA-CAGAGACGAGGG
* * * *
31450198 CTAGTGTAAGACATGTCTAGGACATGCATCAGCCATATTATGAGTGCCAATGTAAGACCATGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAATGTAAGACCATGTCT
* *
31450263 GGGACATGGCATCGGCACAGAGATGAGTG
66 GGGACATGGCATCGGCACAGAGACGAGGG
* * * * * * *
31450292 CCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATAGCTAGTGTAAGA-CGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAG-C-C-ACATTATGAGAGCCAATGTAAGACCATG
* * * *** *
31450354 TTTGGGACA-CGCATCGGC-TA-AGATTTGTG
63 TCTGGGACATGGCATCGGCACAGAGACGAGGG
* * * * *
31450383 CCAATGTAAGACATGTTTGGGACATGCATCAACACGCATATATGAGAGCCAGTGTAAGACCATGT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGC-CACAT-TATGAGAGCCAATGTAAGACCATGT
*
31450448 CTAGGACATGGCATCGGCA
64 CTGGGACATGGCATCGGCA
31450467 ATATATCCCA
Statistics
Matches: 214, Mismatches: 45, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
89 2 0.01
90 2 0.01
91 35 0.16
92 15 0.07
93 19 0.09
94 124 0.58
95 13 0.06
96 2 0.01
97 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (94 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAATGTAAGACCATGTCT
GGGACATGGCATCGGCACAGAGACGAGGG
Found at i:31450342 original size:141 final size:136
Alignment explanation
Indices: 31450111--31450466 Score: 369
Period size: 141 Copynumber: 2.5 Consensus size: 136
31450101 ACACCAGTGC
* * * * *
31450111 AAGACATGTCTGGGACATGCTTCGGCTACATTATGAGAGCCAGTGTAAGATCATGTTTGGGAGAT
1 AAGACATGTCTGGGACATGCATCGGC-ACAATATGAGAGCCAGTGTAAGACCATGTCTGGGACAT
* * * *
31450176 GGCATCGGCATCTAGACGAGGGCTAGTGTAAGACATGTCTAGGACATGCATCAGC-CATATTATG
65 GGCATCGGCA-CTAGACGAGAGCTAGTGTAAGACATGTCTAGGACACGCATCAGCTAAGATT-T-
31450240 AGTGCCAATGT
127 -GTGCCAATGT
* * *
31450251 AAGACCATGTCTGGGACATGGCATCGGCACAGAGATGAGTGCCAGAGTAAGA-CATGTCTGGGAC
1 AAGA-CATGTCTGGGACAT-GCATCGGCACA-ATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
* * * * *
31450315 AT-GCATCGGC-CTCGACAGAGATAGCTAGTGTAAGACGTGTTTGGGACACGCATCGGCTAAGAT
63 ATGGCATCGGCACTAGAC-GAG--AGCTAGTGTAAGACATGTCTAGGACACGCATCAGCTAAGAT
31450378 TTGTGCCAATGT
125 TTGTGCCAATGT
* ** *
31450390 AAGACATGTTTGGGACATGCATCAACACGCATATATGAGAGCCAGTGTAAGACCATGTCTAGGAC
1 AAGACATGTCTGGGACATGCATCGGCA--CA-ATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
31450455 ATGGCATCGGCA
63 ATGGCATCGGCA
31450467 ATATATCCCA
Statistics
Matches: 180, Mismatches: 24, Indels: 22
0.80 0.11 0.10
Matches are distributed among these distances:
137 7 0.04
138 18 0.10
139 36 0.20
140 25 0.14
141 67 0.37
142 27 0.15
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (136 bp):
AAGACATGTCTGGGACATGCATCGGCACAATATGAGAGCCAGTGTAAGACCATGTCTGGGACATG
GCATCGGCACTAGACGAGAGCTAGTGTAAGACATGTCTAGGACACGCATCAGCTAAGATTTGTGC
CAATGT
Found at i:31454597 original size:16 final size:16
Alignment explanation
Indices: 31454578--31454612 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31454568 TGAAATGCCG
* *
31454578 AAATGCCGAAAAGTCA
1 AAATGCAGAAAAGCCA
31454594 AAATGCAGAAAAGCCA
1 AAATGCAGAAAAGCCA
31454610 AAA
1 AAA
31454613 GTTTAGCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.09
Consensus pattern (16 bp):
AAATGCAGAAAAGCCA
Found at i:31454597 original size:24 final size:23
Alignment explanation
Indices: 31454570--31454614 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31454560 GTAAAAGTTG
* *
31454570 AAATGCCGAAATGCCGAAAAGTCA
1 AAATGCAGAAAAGCC-AAAAGTCA
31454594 AAATGCAGAAAAGCCAAAAGT
1 AAATGCAGAAAAGCCAAAAGT
31454615 TTAGCTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.11
Consensus pattern (23 bp):
AAATGCAGAAAAGCCAAAAGTCA
Found at i:31461049 original size:9 final size:8
Alignment explanation
Indices: 31461027--31461058 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
31461017 GTTGTAATGC
31461027 CCAAAAAT
1 CCAAAAAT
31461035 CCAAAAAT
1 CCAAAAAT
31461043 CCAAAAAT
1 CCAAAAAT
*
31461051 CCTAAAAT
1 CCAAAAAT
31461059 TTTGAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.59, C:0.25, G:0.00, T:0.16
Consensus pattern (8 bp):
CCAAAAAT
Found at i:31462593 original size:29 final size:29
Alignment explanation
Indices: 31462557--31462636 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
31462547 TGAATGTGAC
*
31462557 TGGGCCTAATGGGCCATATATAA-GTGATT
1 TGGGCCTAATGGGCCATATATAATATGA-T
*
31462586 TGGGCCTAAAGAGG-C-TATATGAATATGAT
1 TGGGCCTAATG-GGCCATATAT-AATATGAT
* *
31462615 TGGGCTTAATGGGCCAGATATA
1 TGGGCCTAATGGGCCATATATA
31462637 GGTATGTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
28 7 0.17
29 25 0.61
30 9 0.22
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATATAATATGAT
Found at i:31466995 original size:14 final size:14
Alignment explanation
Indices: 31466976--31467002 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31466966 AGTGGTCCAG
31466976 TTGAACTGAACTGA
1 TTGAACTGAACTGA
31466990 TTGAACTGAACTG
1 TTGAACTGAACTG
31467003 GCCAAGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (14 bp):
TTGAACTGAACTGA
Found at i:31472822 original size:22 final size:22
Alignment explanation
Indices: 31472797--31472841 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
31472787 TGATAACCTG
*
31472797 AAAACTGTGACTTCAATAATAA
1 AAAACCGTGACTTCAATAATAA
*
31472819 AAAACCGTTACTTCAATAATAA
1 AAAACCGTGACTTCAATAATAA
31472841 A
1 A
31472842 CCGTACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAACCGTGACTTCAATAATAA
Found at i:31480984 original size:27 final size:27
Alignment explanation
Indices: 31480924--31480984 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
31480914 CATACATATC
** * *
31480924 ATAGGGGCATATTAGTCATTTTACCAC
1 ATAGGGGCATAACAGTCATTTCACCAA
*
31480951 ATAGGGGCATAACAGTCATTTCATCAA
1 ATAGGGGCATAACAGTCATTTCACCAA
*
31480978 ATTGGGG
1 ATAGGGG
31480985 TCTAGGTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (27 bp):
ATAGGGGCATAACAGTCATTTCACCAA
Found at i:31483168 original size:113 final size:113
Alignment explanation
Indices: 31483029--31483253 Score: 441
Period size: 113 Copynumber: 2.0 Consensus size: 113
31483019 TTTAATCCCT
*
31483029 AATTTGAAATTTCATTCAAAATCACTTAGCAAATGTCGTTTATCTAACAACAACTATTTATTTTC
1 AATTTGAAATTTCATTCAAAATCACTTAACAAATGTCGTTTATCTAACAACAACTATTTATTTTC
31483094 TACCATCAAACATCAAAATACATACACATTCATCAATGGTAAAACCCA
66 TACCATCAAACATCAAAATACATACACATTCATCAATGGTAAAACCCA
31483142 AATTTGAAATTTCATTCAAAATCACTTAACAAATGTCGTTTATCTAACAACAACTATTTATTTTC
1 AATTTGAAATTTCATTCAAAATCACTTAACAAATGTCGTTTATCTAACAACAACTATTTATTTTC
31483207 TACCATCAAACATCAAAATACATACACATTCATCAATGGTAAAACCC
66 TACCATCAAACATCAAAATACATACACATTCATCAATGGTAAAACCC
31483254 TAGACTTTTA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (113 bp):
AATTTGAAATTTCATTCAAAATCACTTAACAAATGTCGTTTATCTAACAACAACTATTTATTTTC
TACCATCAAACATCAAAATACATACACATTCATCAATGGTAAAACCCA
Found at i:31493550 original size:22 final size:21
Alignment explanation
Indices: 31493524--31493566 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31493514 ATTCTCGAAT
31493524 TATTG-TTGCACATCATTAAAAA
1 TATTGATTGCA-A-CATTAAAAA
*
31493546 TATTGATTGTAACATTAAAAA
1 TATTGATTGCAACATTAAAAA
31493567 CACTAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (21 bp):
TATTGATTGCAACATTAAAAA
Found at i:31498219 original size:43 final size:43
Alignment explanation
Indices: 31498166--31498322 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 43
31498156 TGTGTTCTCA
31498166 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
* * * ** *
31498209 TGTAAAACCACGTCTGAGATGTTGGCATTAATATGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
* *** * * *
31498252 AGTAAGACCTTATTTAGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGATATGTGATTACG
* * *
31498295 TGTAAGTCCACGTCTGGAACATTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
31498323 TGTACGATAT
Statistics
Matches: 84, Mismatches: 28, Indels: 4
0.72 0.24 0.03
Matches are distributed among these distances:
43 83 0.99
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
Found at i:31504955 original size:46 final size:46
Alignment explanation
Indices: 31504906--31505085 Score: 222
Period size: 46 Copynumber: 3.9 Consensus size: 46
31504896 TACCCTAACA
*
31504906 CATCTCGTA-GCCGATGCATGCCCCAGACATGTCTTACACTAGCT-T
1 CATCTC-TAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
*
31504951 ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
1 -CATCTCTAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
* * * * *
31504998 CGTCTCAATGTCGATGTCATGTCCTAGACATGTTCTTACACTAGCTCT
1 CATCTCTAGGCCGATG-CATGTCCCAGACATG-TCTTACACTAGCTCT
*
31505046 CATAATCT-GGCCGATGCATGTCCCAGACATGTCTTACACT
1 CAT-CTCTAGGCCGATGCATGTCCCAGACATGTCTTACACT
31505086 GGCACACAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
45 1 0.01
46 61 0.53
47 29 0.25
48 23 0.20
49 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.29
Consensus pattern (46 bp):
CATCTCTAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
Found at i:31505058 original size:94 final size:92
Alignment explanation
Indices: 31504917--31505085 Score: 252
Period size: 94 Copynumber: 1.8 Consensus size: 92
31504907 ATCTCGTAGC
*
31504917 CGATGCATGCCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGATGCATGTCCCAGACAT
1 CGATGCATGCCCCAGACATGTCTTACACTAGCTTACATATCGAGGCCGATGCATGTCCCAGACAT
31504982 GTCTTACACTAGCTCTCGTCTCAATGT
66 GTCTTACACTAGCTCTCGTCTCAATGT
* * *
31505009 CGATGTCATGTCCTAGACATGTTCTTACACTAGCTCT-CATAATC-TGGCCGATGCATGTCCCAG
1 CGATG-CATGCCCCAGACATG-TCTTACACTAGCT-TACAT-ATCGAGGCCGATGCATGTCCCAG
31505072 ACATGTCTTACACT
62 ACATGTCTTACACT
31505086 GGCACACAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
92 5 0.07
93 13 0.19
94 48 0.70
95 3 0.04
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (92 bp):
CGATGCATGCCCCAGACATGTCTTACACTAGCTTACATATCGAGGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCGTCTCAATGT
Found at i:31508649 original size:118 final size:118
Alignment explanation
Indices: 31508441--31508678 Score: 413
Period size: 118 Copynumber: 2.0 Consensus size: 118
31508431 CCAAAATTTG
31508441 CTCTTACTGAACTTGGCGTATAACTGCATATCTCTCAAGGTTTGTAAAACCATTCTCAAATGCTC
1 CTCTTACTGAACTTGGCGTATAACTGCATATCTCTCAAGGTTTGTAAAACCATTCTCAAATGCTC
31508506 CGCAAGCTCACTCTCATCACTCGAATAAATCAAAATGTCATCAATAAAGACAA
66 CGCAAGCTCACTCTCATCACTCGAATAAATCAAAATGTCATCAATAAAGACAA
* * *
31508559 CTCTTACTGAACTTGGTGTGTAACTGCATATCTTTCAAGGTTTGTAAAACCATTCTCAAATGCTC
1 CTCTTACTGAACTTGGCGTATAACTGCATATCTCTCAAGGTTTGTAAAACCATTCTCAAATGCTC
** * *
31508624 CGCGTGCTCACTCTCATCACTCGAATAAATCAATATGTCATCGATAAAGACAA
66 CGCAAGCTCACTCTCATCACTCGAATAAATCAAAATGTCATCAATAAAGACAA
31508677 CT
1 CT
31508679 AAGAACTTAT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (118 bp):
CTCTTACTGAACTTGGCGTATAACTGCATATCTCTCAAGGTTTGTAAAACCATTCTCAAATGCTC
CGCAAGCTCACTCTCATCACTCGAATAAATCAAAATGTCATCAATAAAGACAA
Found at i:31512795 original size:45 final size:47
Alignment explanation
Indices: 31512587--31512807 Score: 163
Period size: 50 Copynumber: 4.7 Consensus size: 47
31512577 GTATAATGCT
* * * *
31512587 GATGCCATGTCCCAGATATGGTCTTACACTGGATCATC-CATCAAGT--C
1 GATGCCATGTCCCAGACATGGTCTTACACTGCA-CA-CATATC-TGTGCC
* * * * *
31512634 GATGCCACGTCCCAAACATGGTCTTACACTG-ACTATCGAAAT-TGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGCAC-A-C-ATATCTG-TGCC
* * *
31512683 GACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCTGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACT-G--CACACATATCTGTGCC
*
31512733 GATGCCATGTCCCAGACATGGTCTTACACTG-ACACATTTC-GTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGCACACATATCTGT-GCC
31512779 GATG-CATGTCCCAGACAT-GTCTTACACTG
1 GATGCCATGTCCCAGACATGGTCTTACACTG
31512808 GCTTACAACT
Statistics
Matches: 143, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
44 11 0.08
45 17 0.12
46 19 0.13
47 28 0.20
48 2 0.01
49 27 0.19
50 34 0.24
51 3 0.02
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGCACACATATCTGTGCC
Found at i:31517418 original size:12 final size:12
Alignment explanation
Indices: 31517403--31517438 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
31517393 GCAAAAAGAG
31517403 ATGCAAGAACAA
1 ATGCAAGAACAA
* *
31517415 ATGCAAGCACAG
1 ATGCAAGAACAA
31517427 ATGCAAGAACAA
1 ATGCAAGAACAA
31517439 CTAGCTAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.08
Consensus pattern (12 bp):
ATGCAAGAACAA
Found at i:31520204 original size:12 final size:11
Alignment explanation
Indices: 31520153--31520204 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 11
31520143 ACAAAAGTAT
31520153 AAAAATAAAAA
1 AAAAATAAAAA
31520164 AAAAATAAAAA
1 AAAAATAAAAA
*
31520175 TAAAAAGAAGAATGA
1 -AAAAATAA-AA--A
31520190 AAACAATAAAAA
1 AAA-AATAAAAA
31520202 AAA
1 AAA
31520205 GGTCATAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.32
12 11 0.32
13 2 0.06
14 5 0.15
15 5 0.15
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:31522138 original size:134 final size:133
Alignment explanation
Indices: 31521921--31522163 Score: 360
Period size: 134 Copynumber: 1.8 Consensus size: 133
31521911 AGATGGCGAA
* * * *
31521921 TCTTATCTTCCCGAGGTAGTAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCGGAGGTAGCA
1 TCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCGAAGGTAGCA
* **
31521986 AGGGAACAGGCTGCAGATTGTAGATCTTATCTCCCTGAGACAGCAGTGGGGCGGATAAAAAATGG
66 AGGGAACAGCCTAAAGATTGTAG-TCTTATCTCCCTGAGACAGCAGTGGGGCGGATAAAAAATGG
31522051 TGAT
130 TGAT
* * *
31522055 TCTTATCTTTCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCTAAGGTAGTA
1 TCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCGAAGGTAGCA
* * *
31522120 AGGGAGCAGCCTAAAGATTGTAGTCTTATCTTCCTGAGGCAGCA
66 AGGGAACAGCCTAAAGATTGTAGTCTTATCTCCCTGAGACAGCA
31522164 AGGAAGCAGA
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
133 19 0.20
134 77 0.80
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (133 bp):
TCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCGAAGGTAGCA
AGGGAACAGCCTAAAGATTGTAGTCTTATCTCCCTGAGACAGCAGTGGGGCGGATAAAAAATGGT
GAT
Found at i:31522148 original size:44 final size:45
Alignment explanation
Indices: 31522100--31522196 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 45
31522090 AGCCACCAGC
* * * *
31522100 CTTATCTCCCTAAGGTAGTAAGGGAGCAGCCTAAAGATTGTAG-T
1 CTTATCTCCCTAAGGCAGCAAGGAAGCAGACTAAAGATTGTAGAT
* * * *
31522144 CTTATCTTCCTGAGGCAGCAAGGAAGCAGACTGAAGTTTGTAGAT
1 CTTATCTCCCTAAGGCAGCAAGGAAGCAGACTAAAGATTGTAGAT
*
31522189 CCTATCTC
1 CTTATCTC
31522197 TCTCAGATAG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
44 35 0.83
45 7 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCTAAGGCAGCAAGGAAGCAGACTAAAGATTGTAGAT
Found at i:31522312 original size:173 final size:174
Alignment explanation
Indices: 31521977--31522372 Score: 519
Period size: 173 Copynumber: 2.3 Consensus size: 174
31521967 TTATCTCTCG
* * * * *
31521977 GAGGTAGCAAGGGAA-CAGGCTGCAGATTGTAGATCTTATCTCCCTGAGACAGCAGTGGGGCGGA
1 GAGGTAGCAA-GGAAGCAGACTGAAGATTGTAGATCCTATCTCCCTCAGACAGCAGTGGGGCAGA
* *
31522041 TAAAAAATGGTGATTCTTATCTTTCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATC
65 TAAAAAATGGTGA----TATCTTACCGAGCTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATC
*
31522106 TCCCTAAGGTAGTAAGGGAGCAGCCTAAAGATTGTAGTCTTATCTTCCT
126 TCCCTAAGGTAGCAAGGGAGCAGCCTAAAGATTGTAGTCTTATCTTCCT
* * * *
31522155 GAGGCAGCAAGGAAGCAGACTGAAGTTTGTAGATCCTATCTCTCTCAGATAGCAGTGGGGCAGAT
1 GAGGTAGCAAGGAAGCAGACTGAAGATTGTAGATCCTATCTCCCTCAGACAGCAGTGGGGCAGAT
**
31522220 TGAAAATGGTGA-ATCTTACCGAGCTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCT
66 AAAAAATGGTGATATCTTACCGAGCTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCT
* * *
31522284 GAGGTAGCAAGGGAGCAAG-CTGAAGATTGTAGTCTTATCTTCTT
131 AAGGTAGCAAGGGAGC-AGCCTAAAGATTGTAGTCTTATCTTCCT
* * * * *
31522328 GAGGTAGCAAGAAAGTAGACTGAAGATGGTACATCTTATCTCCCT
1 GAGGTAGCAAGGAAGCAGACTGAAGATTGTAGATCCTATCTCCCT
31522373 AAAGTTGCAG
Statistics
Matches: 191, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
173 124 0.65
174 2 0.01
177 4 0.02
178 61 0.32
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (174 bp):
GAGGTAGCAAGGAAGCAGACTGAAGATTGTAGATCCTATCTCCCTCAGACAGCAGTGGGGCAGAT
AAAAAATGGTGATATCTTACCGAGCTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCCT
AAGGTAGCAAGGGAGCAGCCTAAAGATTGTAGTCTTATCTTCCT
Found at i:31523447 original size:39 final size:39
Alignment explanation
Indices: 31523391--31523555 Score: 258
Period size: 39 Copynumber: 4.2 Consensus size: 39
31523381 CTGGCAATTT
** * *
31523391 GCCTGCTAGGTATAAACCCCAACTTAACACCGGCACGAG
1 GCCTGCTAGGTATAAACCTAAATTTATCACCGGCACGAG
*
31523430 GCCTGCTAGGTACAAACCTAAATTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTAAATTTATCACCGGCACGAG
*
31523469 GCCTGCTAGGTATAAACCTTAATTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTAAATTTATCACCGGCACGAG
* *
31523508 GCCTGCTAGGTATAAACCTGAATTTATCACTGGCACGAG
1 GCCTGCTAGGTATAAACCTAAATTTATCACCGGCACGAG
31523547 GCCTGCTAG
1 GCCTGCTAG
31523556 ACATTAAGTC
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 117 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTAAATTTATCACCGGCACGAG
Found at i:31526021 original size:44 final size:43
Alignment explanation
Indices: 31525973--31526233 Score: 159
Period size: 44 Copynumber: 5.9 Consensus size: 43
31525963 TATCTCTCTA
* *
31525973 AGGTAGCAAGAGAGTAGGTTGAAGATTGTAGTCTCATCTTCCTG
1 AGGTAGCAAG-GAGCAGATTGAAGATTGTAGTCTCATCTTCCTG
* * * *
31526017 AGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCTCCCTA
1 AGGTAGCAAGG-AGCAGATTGAAGATTGTAG-TCTCATCTTCCTG
* * * * * * * *
31526062 AGCAGTAG--TGGAGTAGATAGAAGATGGCGAATCTTATCTTCTTG
1 AG--GTAGCAAGGAGCAGATTGAAGATTG-TAGTCTCATCTTCCTG
* ** ***** * *
31526106 AGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATC-TCTCTG
1 AGGTAGCA-AGGAGCAGATTGAAGATTGTAGTCTCATCTTC-CTG
*
31526150 AGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTCATCTTCCTG
1 AGGTAGCAAG-GAGCAGATTGAAGATTGTAGTCTCATCTTCCTG
* *
31526194 AGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
1 AGGTAGCAAGG-AGCAGATTGAAGATTGTAG-TCTCATCT
31526234 CCCTAAGCAG
Statistics
Matches: 160, Mismatches: 44, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
42 4 0.03
43 5 0.03
44 113 0.71
45 34 0.21
47 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (43 bp):
AGGTAGCAAGGAGCAGATTGAAGATTGTAGTCTCATCTTCCTG
Found at i:31526223 original size:177 final size:177
Alignment explanation
Indices: 31525927--31526543 Score: 918
Period size: 177 Copynumber: 3.5 Consensus size: 177
31525917 CTGCCACACC
* *
31525927 TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGTAGGT
1 TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
31525992 TGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
66 TGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
31526057 CCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
131 CCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
*
31526104 TGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
1 TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
31526169 TGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
66 TGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
31526234 CCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
131 CCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
* * * *
31526281 TGAGGTTGTAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAG-GAAACAGG
1 TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAG-AGCAGG
* * * * * * *
31526345 CTGAAGATTATAGTCTCATCTTCCTGAGGTAGCAAGGGAGGAGACTAAAGATTGTAGATTTTATC
65 TTGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATC
* * * * * *
31526410 TCCCTAAGCAGTAGTGTAGCAGATCGAAGATGGCAAATATTATCTTCC
130 TCCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
* * * * * *
31526458 CGAGGTAGCAAGGGAGCAAATTTTAGCCACTAGTCTCATCT-TCCTGTA-GTAGCAAGGGAGCAG
1 TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCT-CTG-AGGTAGCAAGAGAGCAG
*
31526521 AG-TGAAGATTGTAGATCTTATCT
64 -GTTGAAGATTGTAG-TCTCATCT
31526544 CCCTAAGCAG
Statistics
Matches: 404, Mismatches: 30, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
176 2 0.00
177 392 0.97
178 10 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (177 bp):
TGAGGTAGCAAGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
TGAAGATTGTAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGTAGATCTGATCT
CCCTAAGCAGTAGTGGAGTAGATAGAAGATGGCGAATCTTATCTTCT
Found at i:31526716 original size:133 final size:132
Alignment explanation
Indices: 31526359--31526716 Score: 423
Period size: 133 Copynumber: 2.7 Consensus size: 132
31526349 AGATTATAGT
* * *
31526359 CTCATCTTCCTGAGGTAGCAAGGGAGGAGACT-AAAGATTGTAGATTTTATCTCCCTAAGCAGTA
1 CTCATCTTCCTTAGGTAGCAAGGGAGCAGACTGAAA-ATTGTAGATCTTATCTCCCTAAGCAGTA
* * * *
31526423 GTGTAGCAGATCGAAGATGGCAAATATTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCAC
65 GTGGAGCAGATCGAAGATGGCGAA-CTTATCTTCCCAAGGTAGCAAGGGAGCAAATTTTAGCCAC
*
31526488 TAGT
129 TAGC
* * *
31526492 CTCATCTTCCTGTA-GTAGCAAGGGAGCAGAGTGAAGATTGTAGATCTTATCTCCCTAAGCAGTT
1 CTCATCTTCCT-TAGGTAGCAAGGGAGCAGACTGAAAATTGTAGATCTTATCTCCCTAAGCAGTA
* * * *
31526556 GTGGAGCAGATCGAAGATGGCGAAACTTATTTTCCCAAGGTAGCAGGGGAGCAGATTTTTGCCAC
65 GTGGAGCAGATCGAAGATGGCG-AACTTATCTTCCCAAGGTAGCAAGGGAGCAAATTTTAGCCAC
31526621 TAGC
129 TAGC
* * * * * * * *
31526625 CTTATCTTTCTTAGGTAGCAATGGAGTAGACTGAAAATTATAGATCTTATCTCCCTGACGTAGCA
1 CTCATCTTCCTTAGGTAGCAAGGGAGCAGACTGAAAATTGTAGATCTTATCTCCCT-AAGCAGTA
* * *
31526690 GTGGAGTAGATCGAAGACGGTGAACTT
65 GTGGAGCAGATCGAAGATGGCGAACTT
31526717 TAGCAATGAA
Statistics
Matches: 191, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
132 2 0.01
133 161 0.84
134 28 0.15
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
CTCATCTTCCTTAGGTAGCAAGGGAGCAGACTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGATGGCGAACTTATCTTCCCAAGGTAGCAAGGGAGCAAATTTTAGCCACTA
GC
Found at i:31527148 original size:16 final size:17
Alignment explanation
Indices: 31527123--31527154 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31527113 AGTGATAAAT
31527123 AAACCAAAAATAAATTA
1 AAACCAAAAATAAATTA
31527140 AAACC-AAAATAAATT
1 AAACCAAAAATAAATT
31527155 TTTTTAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (17 bp):
AAACCAAAAATAAATTA
Found at i:31532868 original size:38 final size:39
Alignment explanation
Indices: 31532777--31532868 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
31532767 AGGTACCTTT
* *
31532777 TGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCA-ACA
*
31532817 TGGTGTGTAGGGTT-GAGTGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTGGA-TGGGTCGATTATATCCCCAACA
*
31532855 TGGTGTGTTGGGTT
1 TGGTGTGTAGGGTT
31532869 AGTCGGAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 15 0.32
39 2 0.04
40 30 0.64
ACGTcount: A:0.14, C:0.13, G:0.36, T:0.37
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCAACA
Found at i:31538847 original size:13 final size:13
Alignment explanation
Indices: 31538831--31538866 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31538821 TTTCTTTTTC
*
31538831 TTTCTTCTCTATT
1 TTTCTTCTCCATT
31538844 TTTCTTCTCCATT
1 TTTCTTCTCCATT
31538857 TTTCTTCTCC
1 TTTCTTCTCC
31538867 TTTGATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCTTCTCCATT
Found at i:31542219 original size:3 final size:3
Alignment explanation
Indices: 31542211--31542254 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
31542201 GATAATACTA
31542211 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31542255 GGGTTAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31548149 original size:21 final size:22
Alignment explanation
Indices: 31548125--31548165 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31548115 ATAATTTTTA
31548125 GAAAA-TAAATAATAAAAAAGT
1 GAAAATTAAATAATAAAAAAGT
31548146 GAAAATTAAATAATAAAAAA
1 GAAAATTAAATAATAAAAAA
31548166 TTAAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
GAAAATTAAATAATAAAAAAGT
Found at i:31548172 original size:22 final size:21
Alignment explanation
Indices: 31548126--31548172 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
31548116 TAATTTTTAG
31548126 AAAATAAATAATAAAAAAGTGA
1 AAAATAAATAATAAAAAAGT-A
* *
31548148 AAATTAAATAATAAAAAATTA
1 AAAATAAATAATAAAAAAGTA
31548169 AAAA
1 AAAA
31548173 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAATAAATAATAAAAAAGTA
Found at i:31553892 original size:4 final size:4
Alignment explanation
Indices: 31553883--31553909 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31553873 ATCCTTTTCT
31553883 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
31553910 GCATGGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:31556070 original size:22 final size:23
Alignment explanation
Indices: 31556035--31556081 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
31556025 CTTGTGATCT
31556035 TTTATCTTTATAAATTAGCATTA
1 TTTATCTTTATAAATTAGCATTA
31556058 TTTATC-TTATAAATTAGCATTA
1 TTTATCTTTATAAATTAGCATTA
31556080 TT
1 TT
31556082 AGAAGGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTATCTTTATAAATTAGCATTA
Found at i:31558500 original size:14 final size:13
Alignment explanation
Indices: 31558460--31558503 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
31558450 TATAATGATA
31558460 TTATTGTATGTTAT
1 TTATTGTAT-TTAT
*
31558474 TAATTGTA-TTAT
1 TTATTGTATTTAT
31558486 TTATTGTATTATAT
1 TTATTGTATT-TAT
31558500 TTAT
1 TTAT
31558504 GTGTTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
13 1 0.04
14 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (13 bp):
TTATTGTATTTAT
Found at i:31573934 original size:21 final size:22
Alignment explanation
Indices: 31573909--31573966 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
31573899 CGTAAGGTAA
31573909 CACACGACAGTGTGACAG-AGG
1 CACACGACAGTGTGACAGCAGG
* *
31573930 CACACGCCCGTGTGA-AGCAGG
1 CACACGACAGTGTGACAGCAGG
* * *
31573951 GACACGGCTGTGTGAC
1 CACACGACAGTGTGAC
31573967 CAGACCGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.26, C:0.28, G:0.34, T:0.12
Consensus pattern (22 bp):
CACACGACAGTGTGACAGCAGG
Found at i:31575363 original size:37 final size:37
Alignment explanation
Indices: 31575313--31575400 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
31575303 TCGGTTGAAC
* *
31575313 TAGCTCTTATGAGCATCTGGTGTGTTATCGGGTGGAT
1 TAGCTCTTATGAGCATCTAGCGTGTTATCGGGTGGAT
31575350 TAGCTCTTATGAGCATCTAGCGTGTTATCGGGTGGAT
1 TAGCTCTTATGAGCATCTAGCGTGTTATCGGGTGGAT
31575387 TAGCTCTTATGAGC
1 TAGCTCTTATGAGC
31575401 GATTGGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (37 bp):
TAGCTCTTATGAGCATCTAGCGTGTTATCGGGTGGAT
Found at i:31577264 original size:13 final size:13
Alignment explanation
Indices: 31577246--31577306 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
31577236 CATTGGGTGG
31577246 AAAATGAATATAT
1 AAAATGAATATAT
*
31577259 AAAATGATTATAT
1 AAAATGAATATAT
* * **
31577272 GAATTGGTTATAT
1 AAAATGAATATAT
31577285 GGAAAATGAATATAT
1 --AAAATGAATATAT
31577300 AAAATGA
1 AAAATGA
31577307 TAATATGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 29 0.76
15 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (13 bp):
AAAATGAATATAT
Found at i:31577288 original size:41 final size:41
Alignment explanation
Indices: 31577243--31577367 Score: 191
Period size: 41 Copynumber: 3.1 Consensus size: 41
31577233 GTTCATTGGG
*
31577243 TGGAAAATGAATATATAAAATGATTATATGAATTGGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGGTTATA
* **
31577284 TGGAAAATGAATATATAAAATGATAATATGAATCAATTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGGTTATA
*
31577325 TGG-AAATG-ATATATAGAATGATTATATGAATCGGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGGTTATA
31577364 TGGA
1 TGGA
31577368 TAGATATTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
39 30 0.40
40 5 0.07
41 40 0.53
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (41 bp):
TGGAAAATGAATATATAAAATGATTATATGAATCGGTTATA
Found at i:31577337 original size:13 final size:13
Alignment explanation
Indices: 31577261--31577367 Score: 60
Period size: 13 Copynumber: 8.1 Consensus size: 13
31577251 GAATATATAA
31577261 AATGATTATAT-G
1 AATGATTATATGG
*
31577273 AATTGGTTATATGG
1 AA-TGATTATATGG
* **
31577287 AAAATGAATATATAA
1 --AATGATTATATGG
*
31577302 AATGATAATAT-G
1 AATGATTATATGG
*
31577314 AATCAATTATATGG
1 AAT-GATTATATGG
*
31577328 AAATGA-TATATAG
1 -AATGATTATATGG
31577341 AATGATTATAT-G
1 AATGATTATATGG
*
31577353 AATCGGTTATATGG
1 AAT-GATTATATGG
31577367 A
1 A
31577368 TAGATATTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
12 14 0.19
13 41 0.57
14 5 0.07
15 10 0.14
16 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.36
Consensus pattern (13 bp):
AATGATTATATGG
Found at i:31577338 original size:26 final size:27
Alignment explanation
Indices: 31577301--31577352 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
31577291 TGAATATATA
31577301 AAATGATAATAT-GAATCAATTATATGG
1 AAATGATAATATAGAAT-AATTATATGG
*
31577328 AAATGAT-ATATAGAATGATTATATG
1 AAATGATAATATAGAATAATTATATG
31577353 AATCGGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (27 bp):
AAATGATAATATAGAATAATTATATGG
Found at i:31584736 original size:27 final size:28
Alignment explanation
Indices: 31584674--31584736 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
31584664 GTTTTAACCC
*
31584674 ATTAAAA-TTTTAACTATTTTACCCTTG
1 ATTAAAATTTTTAACAATTTTACCCTTG
* *
31584701 A-TAACATTTTTTACAATTTTACCCTT-
1 ATTAAAATTTTTAACAATTTTACCCTTG
31584727 ATTAAAATTT
1 ATTAAAATTT
31584737 CTATAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTAAAATTTTTAACAATTTTACCCTTG
Found at i:31587511 original size:19 final size:19
Alignment explanation
Indices: 31587477--31587515 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
31587467 GATTTCGTAC
*
31587477 TTTGGCCCATTTTCTCCGTT
1 TTTGGCCCAGTTTCT-CGTT
31587497 TTTGGCCC-GTTTCTCGTT
1 TTTGGCCCAGTTTCTCGTT
31587515 T
1 T
31587516 CTTTCGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.03, C:0.28, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTGGCCCAGTTTCTCGTT
Found at i:31599623 original size:32 final size:32
Alignment explanation
Indices: 31599582--31599645 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31599572 CATCCTCATC
31599582 AGTCATACCATGTGCATATACTTTGTGTGAGT
1 AGTCATACCATGTGCATATACTTTGTGTGAGT
31599614 AGTCATACCATGTGCATATACTTTGTGTGAGT
1 AGTCATACCATGTGCATATACTTTGTGTGAGT
31599646 TTGTTCCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (32 bp):
AGTCATACCATGTGCATATACTTTGTGTGAGT
Done.