Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 6 of 16
Found at i:870824 original size:16 final size:16
Alignment explanation
Indices: 870786--870846 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
870776 GATATTTATT
*
870786 TAATTTAAAAATAAAA
1 TAATATAAAAATAAAA
*
870802 -AATTATAAAATTAAAA
1 TAA-TATAAAAATAAAA
**
870818 TAATATATTAATAAAA
1 TAATATAAAAATAAAA
*
870834 TTATATAAGAAAT
1 TAATATAA-AAAT
870847 TTAGTTTCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 2 0.06
16 27 0.79
17 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TAATATAAAAATAAAA
Found at i:872188 original size:33 final size:35
Alignment explanation
Indices: 872135--872254 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 35
872125 TTATTATATG
* *
872135 AATATAATAT-ATATATATATATATA-ATTATTAA
1 AATATAATATAATATAGATATAAATATATTATTAA
*
872168 AATATAATATAATA-AGATATAAATATATTTTTAA
1 AATATAATATAATATAGATATAAATATATTATTAA
* *
872202 AAT-TTATATAAATATAAATTAATTTAAAT-T-TTATTAA
1 AATATAATAT-AATATAGA-T-A--TAAATATATTATTAA
*
872239 AATATAATAAAATATA
1 AATATAATATAATATA
872255 TAAATTATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
33 24 0.34
34 17 0.24
35 2 0.03
36 1 0.01
37 16 0.23
38 5 0.07
39 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
AATATAATATAATATAGATATAAATATATTATTAA
Found at i:872235 original size:27 final size:29
Alignment explanation
Indices: 872179--872245 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 29
872169 ATATAATATA
*
872179 ATAAGATATAAATATATTTTTAAAATTTAT
1 ATAA-ATATAAATATATATTTAAAATTTAT
*
872209 ATAAATATAAAT-TA-ATTTAAATTTTAT
1 ATAAATATAAATATATATTTAAAATTTAT
872236 -TAAAATATAA
1 AT-AAATATAA
872246 TAAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 2 0.06
29 8 0.24
30 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
ATAAATATAAATATATATTTAAAATTTAT
Found at i:872760 original size:19 final size:18
Alignment explanation
Indices: 872736--872774 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
872726 GAAATGTGAT
872736 TTTTAAAATATATAAA-ATA
1 TTTTAAAA-A-ATAAATATA
872755 TTTTAAAAAATAAATATA
1 TTTTAAAAAATAAATATA
872773 TT
1 TT
872775 AATATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAAAATAAATATA
Found at i:874876 original size:22 final size:22
Alignment explanation
Indices: 874848--874894 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
874838 CAATACAATT
874848 ACTAATATTTATTTAATATGAC
1 ACTAATATTTATTTAATATGAC
874870 ACTAATATTTATTTAATATGAC
1 ACTAATATTTATTTAATATGAC
874892 ACT
1 ACT
874895 CTTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (22 bp):
ACTAATATTTATTTAATATGAC
Found at i:874995 original size:2 final size:2
Alignment explanation
Indices: 874988--875036 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
874978 AAACAATTAA
874988 AT AT AT AT AT AT AT AT GA- AT AT AT AT AT AT AT GA- AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT -AT AT AT AT AT
875030 AT AT AT A
1 AT AT AT A
875037 CATTAGAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:875011 original size:16 final size:16
Alignment explanation
Indices: 874990--875035 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
874980 ACAATTAAAT
874990 ATATATATATATATGA
1 ATATATATATATATGA
875006 ATATATATATATATGA
1 ATATATATATATATGA
875022 ATATATATATATAT
1 ATATATATATATAT
875036 ACATTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
ATATATATATATATGA
Found at i:875157 original size:27 final size:28
Alignment explanation
Indices: 875127--875182 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
875117 AATTTTTTTA
*
875127 TTATATTCAAAAAT-AT-TTAAAATAAAT
1 TTATATT-AAAAATGATATTAAAAAAAAT
*
875154 TTATATTAAAATTGATATTAAAAAAAAT
1 TTATATTAAAAATGATATTAAAAAAAAT
875182 T
1 T
875183 ATGATGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 9 0.36
28 11 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TTATATTAAAAATGATATTAAAAAAAAT
Found at i:875184 original size:27 final size:27
Alignment explanation
Indices: 875126--875184 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
875116 AAATTTTTTT
875126 ATTATATTCAAAAATATTTAAAATAAA
1 ATTATATTCAAAAATATTTAAAATAAA
* *
875153 TTTATATT-AAAATTGATATTAAAA-AAA
1 ATTATATTCAAAAAT-AT-TTAAAATAAA
875180 ATTAT
1 ATTAT
875185 GATGATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.19
27 16 0.59
28 6 0.22
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTATATTCAAAAATATTTAAAATAAA
Found at i:880136 original size:27 final size:27
Alignment explanation
Indices: 880080--880136 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
880070 TATAAATTAT
* *
880080 TAATATATTAAAATTTATATAATTATA
1 TAATATATTAAAATATATATAATTACA
*
880107 TAATATTTTAAATATATATATAA-TACA
1 TAATATATTAAA-ATATATATAATTACA
880134 TAA
1 TAA
880137 AAATACAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATATATTAAAATATATATAATTACA
Found at i:880502 original size:19 final size:19
Alignment explanation
Indices: 880478--880539 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
880468 TTTATTTAAA
*
880478 TTTAATTATAAAAATAATT
1 TTTAATAATAAAAATAATT
*
880497 TTTAATAATTAAATATAA-T
1 TTTAATAA-TAAAAATAATT
*
880516 TTAAATAAT-AAAATAAATT
1 TTTAATAATAAAAAT-AATT
880535 TTTAA
1 TTTAA
880540 ACTTGACGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 4 0.11
18 3 0.09
19 20 0.57
20 8 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAATAATAAAAATAATT
Found at i:880506 original size:27 final size:27
Alignment explanation
Indices: 880449--880514 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
880439 ATTAATTATT
* *
880449 ATTTAATTAATAAAAATATTTTATTTAA
1 ATTTAATT-ATAAAAATAATTTATTAAA
880477 ATTTAATTATAAAAATAATTT-TTAATA
1 ATTTAATTATAAAAATAATTTATTAA-A
*
880504 A-TTAAATATAA
1 ATTTAATTATAA
880515 TTTAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.35
27 14 0.41
28 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTAATTATAAAAATAATTTATTAAA
Found at i:882433 original size:2 final size:2
Alignment explanation
Indices: 882426--882465 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
882416 GAAGAGACAA
882426 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
882466 GCATATGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:883081 original size:2 final size:2
Alignment explanation
Indices: 883069--883099 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
883059 TTCTTAGTTG
*
883069 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
883100 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:883450 original size:2 final size:2
Alignment explanation
Indices: 883443--883468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
883433 AAAATTCTTT
883443 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
883469 CACGAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:884257 original size:3 final size:3
Alignment explanation
Indices: 884249--884276 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
884239 AACTCTGCTA
884249 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
884277 TTTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:887439 original size:4 final size:4
Alignment explanation
Indices: 887430--887456 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
887420 TTTACAAATA
887430 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
887457 ATCCAATAAT
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:890366 original size:2 final size:2
Alignment explanation
Indices: 890359--890384 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
890349 TTTTGTTGTA
890359 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
890385 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:890603 original size:18 final size:18
Alignment explanation
Indices: 890577--890612 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
890567 ATAATTTTAA
* *
890577 ATTTTAATATTTATAATT
1 ATTTAAATATTAATAATT
890595 ATTTAAATATTAATAATT
1 ATTTAAATATTAATAATT
890613 GTACCTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAATATTAATAATT
Found at i:893981 original size:3 final size:3
Alignment explanation
Indices: 893973--894009 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
893963 TGCTTATATT
893973 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 A
894010 ATGCACATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:894491 original size:4 final size:4
Alignment explanation
Indices: 894476--894517 Score: 66
Period size: 4 Copynumber: 10.0 Consensus size: 4
894466 CATGTAATAT
894476 TAAA TGAAA TAAA TAAA GTAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA
894518 ACACATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:894574 original size:21 final size:22
Alignment explanation
Indices: 894541--894581 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
894531 AAAATTTACT
*
894541 AAAATTAGTTTAAAACTAAATC
1 AAAATAAGTTTAAAACTAAATC
894563 AAAATAAG-TTAAAACTAAA
1 AAAATAAGTTTAAAACTAAA
894582 AGTGTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAATAAGTTTAAAACTAAATC
Found at i:894983 original size:29 final size:29
Alignment explanation
Indices: 894946--895004 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
894936 AATATATCAA
* * *
894946 ATAATTTTTATAATATAAATTCAGTACTT
1 ATAAATTTTATAATAAAAATTCAATACTT
*
894975 ATAAATTTTATATTAAAAATTCAATACTT
1 ATAAATTTTATAATAAAAATTCAATACTT
895004 A
1 A
895005 ATTTTTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (29 bp):
ATAAATTTTATAATAAAAATTCAATACTT
Found at i:948112 original size:3 final size:3
Alignment explanation
Indices: 948104--948143 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
948094 GGATATTTAT
948104 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
948144 AAAGAGAAAT
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:948415 original size:3 final size:3
Alignment explanation
Indices: 948407--948445 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
948397 CATGGCTTAG
948407 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
948446 AATTGTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:952357 original size:16 final size:15
Alignment explanation
Indices: 952330--952363 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
952320 ATTTTAAAAA
*
952330 ATTAAATATATTTAT
1 ATTAAATATATTAAT
952345 ATTAAATTATATTAAT
1 ATTAAA-TATATTAAT
952361 ATT
1 ATT
952364 TTATGCTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAAATATATTAAT
Found at i:954069 original size:11 final size:9
Alignment explanation
Indices: 954035--954114 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 9
954025 ATATTTTTGT
*
954035 TATATTTATT
1 TATATTTA-A
* *
954045 TATTTTTAT
1 TATATTTAA
954054 TATATTATAA
1 TATATT-TAA
954064 TAATATTTAA
1 T-ATATTTAA
954074 TATATTT--
1 TATATTTAA
954081 TATATTTATA
1 TATATTTA-A
*
954091 TAAATTTTAA
1 TATA-TTTAA
954101 TATA-TTAA
1 TATATTTAA
954109 TA-ATTT
1 TATATTT
954115 TTATTATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
7 8 0.14
8 8 0.14
9 12 0.21
10 21 0.36
11 9 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATATTTAA
Found at i:954091 original size:22 final size:21
Alignment explanation
Indices: 954034--954173 Score: 57
Period size: 20 Copynumber: 6.9 Consensus size: 21
954024 TATATTTTTG
*
954034 TTATATT-TATTTAT-TTTTA
1 TTATATTATATTTATATTTAA
* *
954053 TTATATTATAATAATATTTAA
1 TTATATTATATTTATATTTAA
* *
954074 TATATTTTATATTTATA-TAAA
1 T-TATATTATATTTATATTTAA
* * * *
954095 TTTTAATATATTAATAATTTTTA
1 TTATATTATATTTAT-A-TTTAA
* *
954118 TTATA-TAAATTT-TA--AAA
1 TTATATTATATTTATATTTAA
954135 TATATATT-TATATTATATTTTAA
1 T-TATATTATAT-TTATA-TTTAA
954158 TTAT-TTA-ATTTATATT
1 TTATATTATATTTATATT
954174 ACCATCATAT
Statistics
Matches: 87, Mismatches: 20, Indels: 28
0.64 0.15 0.21
Matches are distributed among these distances:
17 2 0.02
18 6 0.07
19 12 0.14
20 23 0.26
21 15 0.17
22 20 0.23
23 9 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTATATTTATATTTAA
Found at i:954093 original size:27 final size:27
Alignment explanation
Indices: 954053--954151 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
954043 TTTATTTTTA
954053 TTATATTATAAT-AATATTTAATATATT
1 TTATATTATAATAAAT-TTTAATATATT
954080 TTATATT-TATATAAATTTTAATATATT
1 TTATATTATA-ATAAATTTTAATATATT
* *
954107 AATAATTTTTATTATATAAATTTTAAAATATATAT
1 --TTA-TATTA-TA-ATAAATTTT--AATATAT-T
954142 TTATATTATA
1 TTATATTATA
954152 TTTTAATTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
26 2 0.03
27 20 0.34
28 3 0.05
29 2 0.03
30 3 0.05
31 2 0.03
32 16 0.28
33 2 0.03
34 7 0.12
35 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATTATAATAAATTTTAATATATT
Found at i:954106 original size:20 final size:19
Alignment explanation
Indices: 954061--954123 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
954051 TATTATATTA
*
954061 TAATAATATTTAATATA-TT
1 TAAT-ATATTTAATAAATTT
954080 T--TATATTTATATAAATTT
1 TAATATATTTA-ATAAATTT
*
954098 TAATATA-TTAATAATTTT
1 TAATATATTTAATAAATTT
*
954116 TATTATAT
1 TAATATAT
954124 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 7 0.19
17 5 0.14
18 16 0.44
19 4 0.11
20 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATATTTAATAAATTT
Found at i:954111 original size:18 final size:17
Alignment explanation
Indices: 954064--954132 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
954054 TATATTATAA
*
954064 TAATATTTAATATATTT
1 TAATATTTAATAAATTT
954081 T-ATATTTATATAAATTT
1 TAATATTTA-ATAAATTT
954098 TAATATATTAAT-AATTT
1 TAATAT-TTAATAAATTT
954115 T--TA-TTATATAAATTT
1 TAATATTTA-ATAAATTT
954130 TAA
1 TAA
954133 AATATATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 8 0.18
16 7 0.16
17 15 0.34
18 6 0.14
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATATTTAATAAATTT
Found at i:954115 original size:34 final size:33
Alignment explanation
Indices: 954035--954152 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 33
954025 ATATTTTTGT
* * * **
954035 TATATTTATTTATTTTTATTATAT-TATAATAA
1 TATATTAATATATTTTTATTATATAAATTTTAA
954067 TAT-TTAATATATTTTATATTTATATAAATTTTAA
1 TATATTAATATATTTT-TA-TTATATAAATTTTAA
954101 TATATTAATA-ATTTTTATTATATAAATTTTAA
1 TATATTAATATATTTTTATTATATAAATTTTAA
*
954133 -A-A-T-ATATATTTATATTATAT
1 TATATTAATATATTTTTATTATAT
954153 TTTAATTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
28 3 0.04
29 13 0.17
30 1 0.01
31 11 0.15
32 20 0.27
33 8 0.11
34 13 0.17
35 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATTAATATATTTTTATTATATAAATTTTAA
Found at i:954124 original size:20 final size:20
Alignment explanation
Indices: 954019--954124 Score: 58
Period size: 19 Copynumber: 5.0 Consensus size: 20
954009 AAATTTGATA
*
954019 ATTAATATATTTTTGTTATAT
1 ATTAATA-ATTTTTATTATAT
* *
954040 -TTATTTATTTTTATTATAT
1 ATTAATAATTTTTATTATAT
*
954059 -TATAATAATATTTAATATATTTTAT
1 AT-TAAT-A-ATTT--T-TATTATAT
*
954084 ATTTATATAAATTTTA--ATAT
1 A-TTA-ATAATTTTTATTATAT
954104 ATTAATAATTTTTATTATAT
1 ATTAATAATTTTTATTATAT
954124 A
1 A
954125 AATTTTAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 23
0.67 0.09 0.24
Matches are distributed among these distances:
18 9 0.14
19 16 0.25
20 16 0.25
22 6 0.09
23 1 0.02
24 1 0.02
25 10 0.15
26 3 0.05
27 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTAATAATTTTTATTATAT
Found at i:954140 original size:18 final size:18
Alignment explanation
Indices: 954064--954141 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 18
954054 TATATTATAA
* *
954064 TAATATTTA-ATATATTT
1 TAATATATATATAAATTT
*
954081 T-ATATTTATATAAATTT
1 TAATATATATATAAATTT
954098 TAATATAT-TA-ATAATTT
1 TAATATATATATA-AATTT
954115 T--TAT-TATATAAATTT
1 TAATATATATATAAATTT
*
954130 TAAAATATATAT
1 TAATATATATAT
954142 TTATATTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.02
15 11 0.22
16 9 0.18
17 19 0.38
18 10 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATATATATAAATTT
Found at i:959580 original size:21 final size:22
Alignment explanation
Indices: 959554--959610 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
959544 TATAAATTTA
959554 TATATTA-TTAATAAATAAAAT
1 TATATTATTTAATAAATAAAAT
*
959575 TATATTATTTTATAAA-AAAAT
1 TATATTATTTAATAAATAAAAT
959596 T-TA-TATTTAATAAAT
1 TATATTATTTAATAAAT
959611 TGATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 10 0.31
20 2 0.06
21 13 0.41
22 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTATTTAATAAATAAAAT
Found at i:959599 original size:22 final size:25
Alignment explanation
Indices: 959547--959602 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 25
959537 AATATCATAT
959547 AAATTTATA-TATTATTAATAAATA
1 AAATTTATATTATTATTAATAAATA
959571 AAA-TTATATTATT-TT-ATAAA-A
1 AAATTTATATTATTATTAATAAATA
959592 AAATTTATATT
1 AAATTTATATT
959603 TAATAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.13
22 12 0.40
23 7 0.23
24 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATTTATATTATTATTAATAAATA
Found at i:960510 original size:21 final size:22
Alignment explanation
Indices: 960469--960532 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 22
960459 TAAAAATTAA
* *
960469 TAATA-TTAAATTTTAA-ATTT
1 TAATATTTAAATTATAATTTTT
960489 TAATATTTATAATT-T-ATTTTT
1 TAATATTTA-AATTATAATTTTT
* *
960510 TTATTTTTAAATTATAATTTTT
1 TAATATTTAAATTATAATTTTT
960532 T
1 T
960533 TACAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 10 0.28
21 15 0.42
22 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TAATATTTAAATTATAATTTTT
Found at i:961082 original size:16 final size:18
Alignment explanation
Indices: 961061--961101 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
961051 AAAATATATA
961061 AATA-TTAAT-ATAAAAT
1 AATATTTAATAATAAAAT
961077 AATATTTTAATAATAAAAT
1 AATA-TTTAATAATAAAAT
961096 AA-ATTT
1 AATATTT
961102 TCGAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 3 0.14
18 6 0.27
19 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTTAATAATAAAAT
Found at i:961088 original size:18 final size:18
Alignment explanation
Indices: 961058--961102 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
961048 ATAAAAATAT
*
961058 ATAAATATTAAT-ATAAA
1 ATAAATTTTAATAATAAA
961075 ATAATATTTTAATAATAAA
1 ATAA-ATTTTAATAATAAA
961094 ATAAATTTT
1 ATAAATTTT
961103 CGAATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTTTAATAATAAA
Found at i:961551 original size:27 final size:27
Alignment explanation
Indices: 961513--961568 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
961503 AGTTCCGTCG
*
961513 CTTCTCTTTCTCCCACATCTGTTGAAT
1 CTTCTCTTTCTCCCAAATCTGTTGAAT
*
961540 CTTCTCTTTCTCCTAAATCTGTTGAAT
1 CTTCTCTTTCTCCCAAATCTGTTGAAT
961567 CT
1 CT
961569 ACATAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.30, G:0.07, T:0.46
Consensus pattern (27 bp):
CTTCTCTTTCTCCCAAATCTGTTGAAT
Found at i:961870 original size:2 final size:2
Alignment explanation
Indices: 961865--961893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
961855 CGTGTGTATC
961865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
961894 GCAATCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:962505 original size:28 final size:29
Alignment explanation
Indices: 962447--962514 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
962437 TTAACCCTCC
* *
962447 AAAATAT-TTATTTTTTTTAATTTATATA
1 AAAATATATTATTTTTTTAAAATTATATA
*
962475 AAATTA-ATTATTTTTCTTAAAATTATA-A
1 AAAATATATTATTTTT-TTAAAATTATATA
962503 AAAATATATTAT
1 AAAATATATTAT
962515 AATTATCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
AAAATATATTATTTTTTTAAAATTATATA
Found at i:962513 original size:29 final size:28
Alignment explanation
Indices: 962447--962514 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
962437 TTAACCCTCC
* * *
962447 AAAATAT-TTATTTTTTTTAATTTATAT
1 AAAATATATTATTTTTTTAAAATTATAA
962474 AAAAT-TAATTATTTTTCTTAAAATTATAA
1 AAAATAT-ATTATTTTT-TTAAAATTATAA
962503 AAAATATATTAT
1 AAAATATATTAT
962515 AATTATCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 5 0.15
28 8 0.24
29 19 0.56
30 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAATATATTATTTTTTTAAAATTATAA
Found at i:963717 original size:24 final size:25
Alignment explanation
Indices: 963680--963732 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
963670 TTAAATTTTT
963680 TGTTGTAATACACTCTAGCAATATA
1 TGTTGTAATACACTCTAGCAATATA
* *
963705 TGTT-TAATGCACTTTAGCAATATA
1 TGTTGTAATACACTCTAGCAATATA
963729 TGTT
1 TGTT
963733 CTTTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (25 bp):
TGTTGTAATACACTCTAGCAATATA
Found at i:964243 original size:32 final size:30
Alignment explanation
Indices: 964205--964269 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
964195 TACGACATAA
964205 AAAAATAAT-TAAAATAT-AATATAATATAATAT
1 AAAAATAATAT-AAATATGAA-ATAA-A-AATAT
964237 AAAAATAATATAAATATGAAATAAAAATAT
1 AAAAATAATATAAATATGAAATAAAAATAT
964267 AAA
1 AAA
964270 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.26
31 1 0.03
32 19 0.61
33 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATAATATAAATATGAAATAAAAATAT
Found at i:964502 original size:34 final size:34
Alignment explanation
Indices: 964416--964506 Score: 87
Period size: 37 Copynumber: 2.6 Consensus size: 34
964406 TTGATAATTT
* *
964416 AAATTGATTTAATTTAAATTATTATTTAAATAATA
1 AAATTAATTTAATTT-AATTATAATTTAAATAATA
*
964451 AAATGTTTATTTAAATTTAATTATAAATATT-AATAA-A
1 AAA--TTAATTT-AATTTAATTAT-AAT-TTAAATAATA
964488 AAATTAATTTAATTTAATT
1 AAATTAATTTAATTTAATT
964507 TTTATTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
34 9 0.19
35 9 0.19
37 16 0.33
38 12 0.25
39 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (34 bp):
AAATTAATTTAATTTAATTATAATTTAAATAATA
Found at i:964539 original size:40 final size:40
Alignment explanation
Indices: 964493--964588 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 40
964483 ATAAAAAATT
** *
964493 AATTTAATTTAATTTTTATTATTTTAAATAATAATTTT-AA
1 AATTTAATTTAATTAAT-TTAATTTAAATAATAATTTTAAA
* * **
964533 ATTTTAAAATTAATTAATTTAATTTAAATAATTTTTTTAAA
1 AATTT-AATTTAATTAATTTAATTTAAATAATAATTTTAAA
964574 AATTTAATTATAATT
1 AATTTAATT-TAATT
964589 CAATAGGTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
40 24 0.55
41 20 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (40 bp):
AATTTAATTTAATTAATTTAATTTAAATAATAATTTTAAA
Found at i:964564 original size:14 final size:14
Alignment explanation
Indices: 964542--964582 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
964532 AATTTTAAAA
*
964542 TTAATTAATTTAAT
1 TTAAATAATTTAAT
*
964556 TTAAATAATTT-TT
1 TTAAATAATTTAAT
964569 TTAAA-AATTTAAT
1 TTAAATAATTTAAT
964582 T
1 T
964583 ATAATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 5 0.22
13 8 0.35
14 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATAATTTAAT
Found at i:964565 original size:22 final size:20
Alignment explanation
Indices: 964515--964565 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
964505 TTTTTATTAT
964515 TTTAAATAA-TAATTTTAAA
1 TTTAAATAATTAATTTTAAA
964534 TTTTAAAATTAATTAA-TTT-AA
1 -TTT-AAA-TAATTAATTTTAAA
964555 TTTAAATAATT
1 TTTAAATAATT
964566 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.18
19 3 0.11
20 6 0.21
21 5 0.18
22 6 0.21
23 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAATAATTAATTTTAAA
Found at i:966299 original size:237 final size:237
Alignment explanation
Indices: 965884--966351 Score: 756
Period size: 237 Copynumber: 2.0 Consensus size: 237
965874 TCATTTCTAG
* * * *
965884 CGACTTGGTTTTGATGTAGTTTCTTTGATCTGAATGTGTTGATACCGTTTTGAACTCAATAAAGT
1 CGACTTGATTTTGATGTAGTTTCTTTGATCTGAAGGTATTGATACCGTTTTGAACTCAACAAAGT
* * * * *
965949 TGTCTTACAGTGACACTGAGTAATATCTCTAAGAAAGAGAAATAATGACTTGGTTCAAGAAGTTG
66 TGTCTTACAGTGACACTGACTAATATCTCTAAGAAAGAAAAATAATGACTTGATACAAGAAGCTG
*
966014 AAGCCAGGCTAAATCCTTTAATTATAGTTGACTGCATAGATCGTTAGTAAACTAAGCAGGTACAT
131 AAGCCAGGCTAAATCCTTTAATTATAGTTGACTGCATAGATCGTTAGTAAACTAAGCAGATACAT
* *
966079 GAAACTATCAAGAGAGAAATTATCTTCCCAATGAATGTTGTA
196 GAAACTATCAAGAGAGAAATCACCTTCCCAATGAATGTTGTA
* *
966121 CGACTTGATTTTTATGTAGTTTCTTTGATCTGAAGGTATTGATACTGTTTTGAACTCAACAAAGT
1 CGACTTGATTTTGATGTAGTTTCTTTGATCTGAAGGTATTGATACCGTTTTGAACTCAACAAAGT
* * *
966186 TGTCTTGCAGTGACAGTGACTAATATCTCTAAGAAAGAAAAATAATGACTTGATACAAGTAGCTG
66 TGTCTTACAGTGACACTGACTAATATCTCTAAGAAAGAAAAATAATGACTTGATACAAGAAGCTG
* * *
966251 AAGCCGGGCTAAATCCTTTAATTATAGTTGACTGCATAGATGGTTAGTAAACTAAGTAGATACAT
131 AAGCCAGGCTAAATCCTTTAATTATAGTTGACTGCATAGATCGTTAGTAAACTAAGCAGATACAT
966316 GAAACTATCAAGAGAGAAATCACCTTCCCAATGAAT
196 GAAACTATCAAGAGAGAAATCACCTTCCCAATGAAT
966352 TTAGTCGGTC
Statistics
Matches: 211, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
237 211 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (237 bp):
CGACTTGATTTTGATGTAGTTTCTTTGATCTGAAGGTATTGATACCGTTTTGAACTCAACAAAGT
TGTCTTACAGTGACACTGACTAATATCTCTAAGAAAGAAAAATAATGACTTGATACAAGAAGCTG
AAGCCAGGCTAAATCCTTTAATTATAGTTGACTGCATAGATCGTTAGTAAACTAAGCAGATACAT
GAAACTATCAAGAGAGAAATCACCTTCCCAATGAATGTTGTA
Found at i:966788 original size:7 final size:7
Alignment explanation
Indices: 966776--966800 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
966766 GATTGTAAAA
966776 TAAAATT
1 TAAAATT
966783 TAAAATT
1 TAAAATT
966790 TAAAATT
1 TAAAATT
966797 TAAA
1 TAAA
966801 TCTAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:974125 original size:22 final size:21
Alignment explanation
Indices: 974073--974126 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
974063 AATAAAAATT
* *
974073 TTAATTTAAAAATTTATATAA
1 TTAATTTAAAAATCTATAAAA
* *
974094 TATAAATTAATAATCTATTAAAA
1 T-TAATTTAAAAATCTA-TAAAA
974117 TTAATTTAAA
1 TTAATTTAAA
974127 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 1 0.04
22 19 0.76
23 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAATTTAAAAATCTATAAAA
Found at i:975683 original size:19 final size:17
Alignment explanation
Indices: 975650--975690 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
975640 ATTTTAAATG
*
975650 TTTTAATTTTAATTTAT
1 TTTTAATTTTAATTTAA
975667 TTTTATATTTATAATTTAA
1 TTTTA-ATTT-TAATTTAA
975686 TTTTA
1 TTTTA
975691 GTTTATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 4 0.19
19 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTAATTTAA
Found at i:976270 original size:24 final size:23
Alignment explanation
Indices: 976225--976276 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
976215 AATTAATTAA
976225 ATAT-ATTTTTATATTAATATTT
1 ATATAATTTTTATATTAATATTT
976247 ATATAATTTTTAATAATTAA-ATTT
1 ATATAATTTTT-AT-ATTAATATTT
*
976271 AAATAA
1 ATATAA
976277 AAATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 11 0.42
25 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATAATTTTTATATTAATATTT
Found at i:977585 original size:20 final size:20
Alignment explanation
Indices: 977560--977603 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
977550 AAATTTAAAC
977560 TAAT-AACCTAATTGAAAAAT
1 TAATAAACCTAATT-AAAAAT
*
977580 TAATAAAACCTAATTAAAATT
1 TAAT-AAACCTAATTAAAAAT
977601 TAA
1 TAA
977604 AATCAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 9 0.43
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (20 bp):
TAATAAACCTAATTAAAAAT
Found at i:977677 original size:14 final size:15
Alignment explanation
Indices: 977638--977680 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 15
977628 AAATTAAAAA
977638 AATTAATATCAA-TT
1 AATTAATATCAATTT
977652 --TTAATATCAATTT
1 AATTAATATCAATTT
977665 AATTAAT-TCAATTT
1 AATTAATATCAATTT
977679 AA
1 AA
977681 AGTTTAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.38
13 2 0.08
14 9 0.35
15 5 0.19
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATATCAATTT
Found at i:977693 original size:27 final size:25
Alignment explanation
Indices: 977638--977726 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 25
977628 AAATTAAAAA
* *
977638 AATTAATATCAATTTTAATATCAATTT
1 AATTAAT-TCAATTTAAAT-TTAATTT
977665 AATTAATTCAATTTAAAGTTTAATGTT
1 AATTAATTCAATTTAAA-TTTAAT-TT
* * *
977692 AATAAATTTTAATATTAAATTTAATTA
1 AATTAA-TTCAAT-TTAAATTTAATTT
977719 AATTAATT
1 AATTAATT
977727 TTTAATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 15 0.29
27 21 0.40
28 11 0.21
29 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTAATTCAATTTAAATTTAATTT
Found at i:977728 original size:27 final size:26
Alignment explanation
Indices: 977660--977738 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
977650 TTTTAATATC
*
977660 AATTTAATTAA-TTCAATTTAAAGTTT
1 AATTTAATTAATTTTAATTTAAA-TTT
*
977686 AATGTTAATAAATTTTAATATTAAATTT
1 AAT-TTAATTAATTTTAAT-TTAAATTT
*
977714 AATTAAATTAATTTTTAATTTAAAT
1 AATTTAATTAA-TTTTAATTTAAAT
977739 AAATTAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
26 3 0.07
27 19 0.42
28 18 0.40
29 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (26 bp):
AATTTAATTAATTTTAATTTAAATTT
Found at i:977730 original size:16 final size:17
Alignment explanation
Indices: 977711--977743 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
977701 TAATATTAAA
*
977711 TTTAA-TTAAATTAATT
1 TTTAATTTAAATAAATT
977727 TTTAATTTAAATAAATT
1 TTTAATTTAAATAAATT
977744 AATCCCATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATAAATT
Found at i:977733 original size:21 final size:20
Alignment explanation
Indices: 977683--977746 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
977673 CAATTTAAAG
977683 TTTAATGTTAATAAATTTTAATA
1 TTTAAT-TTAATAAA--TTAATA
* *
977706 TTAAATTTAATTAAATTAATT
1 TTTAATTTAA-TAAATTAATA
977727 TTTAATTTAAATAAATTAAT
1 TTTAATTT-AATAAATTAAT
977747 CCCATCGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 21 0.58
22 6 0.17
23 9 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTAATTTAATAAATTAATA
Found at i:984831 original size:7 final size:7
Alignment explanation
Indices: 984819--984863 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
984809 GAGTCTAATG
984819 TTTCTTT
1 TTTCTTT
984826 TTTCTTT
1 TTTCTTT
984833 TTTCTTT
1 TTTCTTT
984840 TTTCTTT
1 TTTCTTT
984847 TTTCTTT
1 TTTCTTT
984854 TTTCTTT
1 TTTCTTT
984861 TTT
1 TTT
984864 TCATCATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTCTTT
Found at i:985446 original size:27 final size:27
Alignment explanation
Indices: 985416--985472 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
985406 TAAGATAAAA
* *
985416 ATAAATTTTGATTTA-ATTTAAATAATT
1 ATAAATTTTAATTTATAATTAAA-AATT
985443 ATAAATTTTAATTTATAATTAAAAATT
1 ATAAATTTTAATTTATAATTAAAAATT
985470 ATA
1 ATA
985473 TCAAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAAATTTTAATTTATAATTAAAAATT
Found at i:985460 original size:20 final size:21
Alignment explanation
Indices: 985427--985469 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
985417 TAAATTTTGA
*
985427 TTTAATTTAAATAATTATAAAT
1 TTTAATTT-AATAATTAAAAAT
985449 TTTAATTT-ATAATTAAAAAT
1 TTTAATTTAATAATTAAAAAT
985469 T
1 T
985470 ATATCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATTTAATAATTAAAAAT
Found at i:986530 original size:19 final size:17
Alignment explanation
Indices: 986490--986522 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
986480 TCAATTCAAT
986490 TAATTTTTTTAATTTTG
1 TAATTTTTTTAATTTTG
986507 TAATTATTTTT-ATTTT
1 TAATT-TTTTTAATTTT
986523 TTTCAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TAATTTTTTTAATTTTG
Found at i:987841 original size:2 final size:2
Alignment explanation
Indices: 987834--987862 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
987824 CTAGTTGAAG
987834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
987863 ACCACCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:991509 original size:18 final size:21
Alignment explanation
Indices: 991466--991510 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
991456 AAATTTAATG
*
991466 TAATTAGAATTGAAAAGATAA
1 TAATTAGAATTGAAAAAATAA
991487 TAATTA-AATT-AAAAAAT-A
1 TAATTAGAATTGAAAAAATAA
991505 TAATTA
1 TAATTA
991511 TTAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 4 0.17
21 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
TAATTAGAATTGAAAAAATAA
Found at i:991776 original size:19 final size:18
Alignment explanation
Indices: 991752--991787 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
991742 AAAATTTATG
991752 ATTTATATATTTATATTAA
1 ATTTATATATTT-TATTAA
991771 ATTTATATATTTTATTA
1 ATTTATATATTTTATTA
991788 TATAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTATATATTTTATTAA
Found at i:991837 original size:13 final size:13
Alignment explanation
Indices: 991821--991880 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
991811 TATAAAATAT
991821 TTATATATTTATA
1 TTATATATTTATA
*
991834 TTATATTTTTATA
1 TTATATATTTATA
*
991847 CTATATAATATTATA
1 TTATAT-AT-TTATA
* *
991862 -AATAATTTTTATA
1 TTAT-ATATTTATA
991875 TTATAT
1 TTATAT
991881 CTTATCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
13 24 0.65
14 6 0.16
15 7 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:991861 original size:28 final size:26
Alignment explanation
Indices: 991822--991880 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
991812 ATAAAATATT
*
991822 TATATATTTAT-ATTATATTTTTATAC
1 TATATATTTATAAATA-ATTTTTATAC
*
991848 TATATAATATTATAAATAATTTTTATAT
1 TATAT-AT-TTATAAATAATTTTTATAC
991876 TATAT
1 TATAT
991881 CTTATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 18 0.64
29 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATATTTATAAATAATTTTTATAC
Found at i:994383 original size:16 final size:16
Alignment explanation
Indices: 994350--994383 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
994340 AGAAGAGAAA
* *
994350 TGCTATAAAATTTTCT
1 TGCTATAAAATATGCT
994366 TGCTATAAAATATGCT
1 TGCTATAAAATATGCT
994382 TG
1 TG
994384 ATGCATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TGCTATAAAATATGCT
Found at i:997188 original size:2 final size:2
Alignment explanation
Indices: 997181--997230 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
997171 TTTACCGTTA
997181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
997223 AT AT AT AT
1 AT AT AT AT
997231 TTGGTTAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1007700 original size:21 final size:22
Alignment explanation
Indices: 1007662--1007712 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1007652 AAGTGGTTAC
* *
1007662 ATTTTTTTTAAATTAAATAAATA
1 ATTTTTATTAAA-TAAATAAAAA
1007685 ATTTTTATTAAA-AAATAAAAA
1 ATTTTTATTAAATAAATAAAAA
*
1007706 ATATTTA
1 ATTTTTA
1007713 AAAATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
23 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTTATTAAATAAATAAAAA
Found at i:1008115 original size:23 final size:23
Alignment explanation
Indices: 1008057--1008115 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1008047 ATTTAAACTT
* *
1008057 AAATCTATTTAAATCTAAACTAA
1 AAATCTAATTAAACCTAAACTAA
* *
1008080 AAGTC-CATCTAAACCTAAACTAA
1 AAATCTAAT-TAAACCTAAACTAA
1008103 AAATCTAATTAAA
1 AAATCTAATTAAA
1008116 ACAAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 1 0.04
23 25 0.89
24 2 0.07
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATCTAATTAAACCTAAACTAA
Found at i:1009865 original size:4 final size:4
Alignment explanation
Indices: 1009858--1009884 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1009848 TGTGTATATA
1009858 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1009885 TTTCATACGC
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1014824 original size:19 final size:19
Alignment explanation
Indices: 1014782--1014824 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1014772 AGAAAGTTAT
*
1014782 ATTATAATATGTAACTTTA
1 ATTATAATATGTAACTCTA
*
1014801 GTTATAATATGTAACTCTA
1 ATTATAATATGTAACTCTA
1014820 ATTAT
1 ATTAT
1014825 GTAACATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTATAATATGTAACTCTA
Found at i:1014870 original size:26 final size:26
Alignment explanation
Indices: 1014841--1014891 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1014831 TTAAATGTTA
*
1014841 ATGTAAATTTCAT-TATAATATATAAC
1 ATGTAAATTT-ATGCATAATATATAAC
*
1014867 ATGTAACTTTATGCATAATATATAA
1 ATGTAAATTTATGCATAATATATAA
1014892 AATTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (26 bp):
ATGTAAATTTATGCATAATATATAAC
Found at i:1016091 original size:37 final size:37
Alignment explanation
Indices: 1016011--1016092 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
1016001 TGAATGTTGG
* * *
1016011 AATATAA-CTTAAATATATTTTATTAATATAATAAAT
1 AATATAATATTAAATATATATAATTAATATAATAAAT
*
1016047 -TTAATAATATTAAATATGATATAATT-ATATAATAAAT
1 AAT-ATAATATTAAATAT-ATATAATTAATATAATAAAT
1016084 AATATAATA
1 AATATAATA
1016093 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
35 1 0.03
36 4 0.11
37 25 0.68
38 7 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (37 bp):
AATATAATATTAAATATATATAATTAATATAATAAAT
Found at i:1016471 original size:27 final size:27
Alignment explanation
Indices: 1016441--1016596 Score: 86
Period size: 27 Copynumber: 5.4 Consensus size: 27
1016431 AATTATGCTT
**
1016441 TTAAATTTATGTTATAAATATAAATTA
1 TTAAATTTATAATATAAATATAAATTA
* *
1016468 TTAAATATATAATATAAATATATATTA
1 TTAAATTTATAATATAAATATAAATTA
* *
1016495 --AAATTTAAATAATAAAAATTATTAATATA
1 TTAAATTT--ATAATATAAA-TATAAAT-TA
*
1016524 TTAAAATTT-TAA-ATAAATAAAAATTA
1 TT-AAATTTATAATATAAATATAAATTA
1016550 TTTTAAATATTATTACAACATGATAAAATATAAATTA
1 --TTAAAT-TTA-T---A-AT-AT-AAATATAAATTA
1016587 TTAAATTTAT
1 TTAAATTTAT
1016597 TTTTTATTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
25 5 0.05
26 2 0.02
27 41 0.42
28 13 0.13
29 5 0.05
30 1 0.01
32 6 0.06
33 2 0.02
34 4 0.04
35 6 0.06
36 2 0.02
37 11 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
TTAAATTTATAATATAAATATAAATTA
Found at i:1016505 original size:18 final size:18
Alignment explanation
Indices: 1016482--1016538 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 18
1016472 ATATATAATA
1016482 TAAATATATATTAAAATT
1 TAAATATATATTAAAATT
1016500 TAAATA-ATA--AAAA-T
1 TAAATATATATTAAAATT
*
1016514 T-ATTAATATATTAAAATTT
1 TAAAT-ATATATTAAAA-TT
1016533 TAAATA
1 TAAATA
1016539 AATAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 13
0.67 0.04 0.29
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 7 0.23
17 7 0.23
18 6 0.20
19 3 0.10
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATATATTAAAATT
Found at i:1016525 original size:32 final size:34
Alignment explanation
Indices: 1016487--1016551 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1016477 TAATATAAAT
1016487 ATATATTAAAA-TTTAAAT-AATAAAAATTATTA
1 ATATATTAAAATTTTAAATAAATAAAAATTATTA
1016519 ATATATTAAAATTTTAAATAAATAAAAATTATT
1 ATATATTAAAATTTTAAATAAATAAAAATTATT
1016552 TTAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.35
33 7 0.23
34 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATATTAAAATTTTAAATAAATAAAAATTATTA
Found at i:1016529 original size:17 final size:16
Alignment explanation
Indices: 1016487--1016548 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
1016477 TAATATAAAT
* *
1016487 ATATATTAAAATTTAA
1 ATATATAAAAATTTTA
1016503 ATA-ATAAAAATTATTA
1 ATATATAAAAATT-TTA
*
1016519 ATATATTAAAATTTTAA
1 ATATATAAAAATTTT-A
*
1016536 ATAAATAAAAATT
1 ATATATAAAAATT
1016549 ATTTTAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.21
16 10 0.26
17 20 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATAAAAATTTTA
Found at i:1017197 original size:29 final size:30
Alignment explanation
Indices: 1017165--1017223 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1017155 AACAATTTAT
*
1017165 GCATA-ATGAAAATTTAAATTTTTTATTAA
1 GCATACATGAAAATTCAAATTTTTTATTAA
* *
1017194 GCATACGTGAAAATTCAAATTTTTTCTTAA
1 GCATACATGAAAATTCAAATTTTTTATTAA
1017224 TTTAATTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (30 bp):
GCATACATGAAAATTCAAATTTTTTATTAA
Found at i:1017732 original size:15 final size:15
Alignment explanation
Indices: 1017712--1017741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1017702 AAAATTAAAA
*
1017712 AATATTTTTATATTT
1 AATATTTATATATTT
1017727 AATATTTATATATTT
1 AATATTTATATATTT
1017742 TTTAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATATTTATATATTT
Found at i:1017815 original size:15 final size:15
Alignment explanation
Indices: 1017760--1017829 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
1017750 TTTTAATTAT
*
1017760 TTAATATAAATATAAA
1 TTAA-ATAAATTTAAA
* *
1017776 TTAATTTAATTTAAA
1 TTAAATAAATTTAAA
*
1017791 TT-AATAAAATTTAAT
1 TTAAAT-AAATTTAAA
1017806 TTAAATAAA-TTAAA
1 TTAAATAAATTTAAA
*
1017820 TCAAATAAAT
1 TTAAATAAAT
1017830 AATTTGATGA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 14 0.33
15 22 0.51
16 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATAAATTTAAA
Found at i:1017820 original size:20 final size:20
Alignment explanation
Indices: 1017771--1017820 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1017761 TAATATAAAT
1017771 ATAAATT-AATTTAATTTAA
1 ATAAATTAAATTTAATTTAA
* *
1017790 ATTAATAAAATTTAATTTAA
1 ATAAATTAAATTTAATTTAA
1017810 ATAAATTAAAT
1 ATAAATTAAAT
1017821 CAAATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTAAATTTAATTTAA
Found at i:1018273 original size:14 final size:15
Alignment explanation
Indices: 1018246--1018274 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1018236 TAATATTTAA
1018246 TTTAATATTATAATT
1 TTTAATATTATAATT
1018261 TTTAATA-TATAATT
1 TTTAATATTATAATT
1018275 AAGGGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATATTATAATT
Found at i:1018275 original size:20 final size:19
Alignment explanation
Indices: 1018221--1018275 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1018211 TATAGTAGTT
*
1018221 TTTTTAATA-AAAATATAA
1 TTTTTAATATAAATTATAA
* *
1018239 TATTTAATTTAATATTATAA
1 TTTTTAATATAA-ATTATAA
1018259 TTTTTAATATATAATTA
1 TTTTTAATATA-AATTA
1018276 AGGGATGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.24
19 2 0.07
20 19 0.66
21 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAATATAAATTATAA
Found at i:1018476 original size:14 final size:14
Alignment explanation
Indices: 1018459--1018488 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1018449 TGGTAATTTT
*
1018459 AATATAATTATATA
1 AATATAATAATATA
1018473 AATATAATAATATA
1 AATATAATAATATA
1018487 AA
1 AA
1018489 ATTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAATAATATA
Found at i:1018483 original size:22 final size:23
Alignment explanation
Indices: 1018458--1018501 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1018448 ATGGTAATTT
*
1018458 TAATAT-AATTATATAAATATAA
1 TAATATAAATTATAAAAATATAA
1018480 TAATATAAAATTATAAAAATAT
1 TAATAT-AAATTATAAAAATAT
1018502 GATATGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAATTATAAAAATATAA
Found at i:1019504 original size:8 final size:8
Alignment explanation
Indices: 1019504--1019562 Score: 59
Period size: 8 Copynumber: 7.4 Consensus size: 8
1019494 ATATTAAAAT
1019504 AATATTAA
1 AATATTAA
1019512 AATATTAA
1 AATATTAA
1019520 AATATTAA
1 AATATTAA
1019528 AAT-TTATA
1 AATATTA-A
1019536 TAATA-TAA
1 -AATATTAA
*
1019544 ATTATTAA
1 AATATTAA
* *
1019552 TATTTTAA
1 AATATTAA
1019560 AAT
1 AAT
1019563 TTATATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.14
8 31 0.74
9 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AATATTAA
Found at i:1019560 original size:32 final size:32
Alignment explanation
Indices: 1019502--1019590 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 32
1019492 AAATATTAAA
*
1019502 ATAATATTAAAATATTAAAATATTAAAATTTAT
1 ATAATA-TAAATTATTAAAATATTAAAATTTAT
* *
1019535 ATAATATAAATTATTAATATTTTAAAATTTAT
1 ATAATATAAATTATTAAAATATTAAAATTTAT
* *
1019567 ATAAATATATAATTTTTTAAATAT
1 AT-AATATA-AATTATTAAAATAT
1019591 AATTATCACA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 25 0.53
33 12 0.26
34 10 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATAATATAAATTATTAAAATATTAAAATTTAT
Found at i:1020394 original size:4 final size:4
Alignment explanation
Indices: 1020385--1020449 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
1020375 TGGTGAAAAC
* *
1020385 AGAA AGAA AGAA AGAA AGAA A-AA ATGAA AGAA AGAA AGAA AGAG AG-G
1 AGAA AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA
*
1020432 AGAA AAAA AGGAA AGAA A
1 AGAA AGAA A-GAA AGAA A
1020450 AAAATTTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
3 6 0.11
4 41 0.77
5 6 0.11
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:1020536 original size:33 final size:33
Alignment explanation
Indices: 1020468--1020539 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 33
1020458 TATATGGGTA
* *
1020468 TTTATATTATTTTTTTATATTTAAAATATGATAT
1 TTTATATAAATTTTTTATATTTAAAATAT-ATAT
1020502 TTTATATAAATTTTTTATATATTAATAAT-T-TAT
1 TTTATATAAATTTTTTATAT-TTAA-AATATATAT
1020535 TTTAT
1 TTTAT
1020540 TTCATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 8 0.24
34 18 0.53
35 5 0.15
36 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
TTTATATAAATTTTTTATATTTAAAATATATAT
Found at i:1020584 original size:21 final size:21
Alignment explanation
Indices: 1020537--1020605 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1020527 TAATTTATTT
* *
1020537 TATTTCATATATATATATATA
1 TATTTTATATATACATATATA
1020558 TATTTTATATATACATATAT-
1 TATTTTATATATACATATATA
** *
1020578 TCGTTT-TATATGCATAT-TA
1 TATTTTATATATACATATATA
1020597 T-TTTTATAT
1 TATTTTATAT
1020606 TATATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 4 0.10
19 14 0.35
20 4 0.10
21 18 0.45
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (21 bp):
TATTTTATATATACATATATA
Found at i:1020587 original size:19 final size:17
Alignment explanation
Indices: 1020546--1020605 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1020536 TTATTTCATA
*
1020546 TATATATATATATATTT
1 TATATATACATATATTT
1020563 TATATATACATATATTCGT
1 TATATATACATATATT--T
* *
1020582 TTTATATGCATATTATTT
1 TATATATACATA-TATTT
1020600 T-TATAT
1 TATATAT
1020606 TATATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 20 0.54
18 2 0.05
19 11 0.30
20 4 0.11
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (17 bp):
TATATATACATATATTT
Found at i:1020594 original size:48 final size:46
Alignment explanation
Indices: 1020504--1020619 Score: 108
Period size: 46 Copynumber: 2.4 Consensus size: 46
1020494 TATGATATTT
* * * *
1020504 TATATAAATTTTTTATATATTAATAATTTATTTTATTTCATA-TATA
1 TATATATATATTTTATATA-TAATAATTCATTTTATTGCATATTATA
* *
1020550 TATATATATATTTTATATATACATATATTCGTTTTATATGCATATTATT
1 TATATATATATTTTATATATA-ATA-ATTCATTTTAT-TGCATATTATA
* *
1020599 TTTATATTATATTTTAAATAT
1 TATATA-TATATTTTATATAT
1020620 TTTTTATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
45 2 0.04
46 20 0.35
47 9 0.16
48 5 0.09
49 8 0.14
50 13 0.23
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (46 bp):
TATATATATATTTTATATATAATAATTCATTTTATTGCATATTATA
Found at i:1020874 original size:12 final size:11
Alignment explanation
Indices: 1020855--1020902 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 11
1020845 TCTATGGGAG
1020855 AGAAAAAAAAA
1 AGAAAAAAAAA
1020866 AGTAAAAAAAAAAA
1 AG---AAAAAAAAA
1020880 AGAAAAAAGAAA
1 AGAAAAAA-AAA
1020892 AGAAAAAAAAA
1 AGAAAAAAAAA
1020903 GGAGAGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.33
12 11 0.33
14 11 0.33
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:1020876 original size:14 final size:13
Alignment explanation
Indices: 1020857--1020902 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
1020847 TATGGGAGAG
1020857 AAAAAAAAAAGTAA
1 AAAAAAAAAAG-AA
1020871 AAAAAAAAAAG-A
1 AAAAAAAAAAGAA
*
1020883 AAAAAGAAAAGAA
1 AAAAAAAAAAGAA
1020896 AAAAAAA
1 AAAAAAA
1020903 GGAGAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 11 0.38
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:1020919 original size:22 final size:21
Alignment explanation
Indices: 1020857--1020903 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1020847 TATGGGAGAG
1020857 AAAA-AAAAAAGTAAAAAAAAA
1 AAAAGAAAAAAG-AAAAAAAAA
1020878 AA-AGAAAAAAGAAAAGAAAAA
1 AAAAGAAAAAAGAAAA-AAAAA
1020899 AAAAG
1 AAAAG
1020904 GAGAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAAGAAAAAAAAA
Found at i:1020919 original size:27 final size:26
Alignment explanation
Indices: 1020851--1020924 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 26
1020841 AACATCTATG
1020851 GGAGAGAAAAAAAAAAGTAAAAAAAAA
1 GGAGAGAAAAAAAAAAG-AAAAAAAAA
*
1020878 --AAAGAAAAAAGAAAAGAAAAAAAAA
1 GGAGAGAAAAAA-AAAAGAAAAAAAAA
*
1020903 GGAGAGAGAAATAAAAAGAAAA
1 GGAGAGA-AAAAAAAAAGAAAA
1020925 GTTAATGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 18 0.45
26 5 0.12
27 13 0.32
28 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (26 bp):
GGAGAGAAAAAAAAAAGAAAAAAAAA
Found at i:1021464 original size:12 final size:11
Alignment explanation
Indices: 1021440--1021474 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
1021430 TTTATTTGAT
1021440 AAAAAAG-AAA
1 AAAAAAGAAAA
1021450 AAAAAAGAAAGA
1 AAAAAAGAAA-A
1021462 AAAAAAGAAAA
1 AAAAAAGAAAA
1021473 AA
1 AA
1021475 TTTATACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.30
11 5 0.22
12 11 0.48
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1022587 original size:21 final size:21
Alignment explanation
Indices: 1022563--1022610 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1022553 TATTCGTATC
1022563 ATGTTCATGTTATTTTTTA-TT
1 ATGTTCAT-TTATTTTTTATTT
*
1022584 ATGTTTTATTTATTTTTTATTT
1 ATG-TTCATTTATTTTTTATTT
1022606 ATGTT
1 ATGTT
1022611 GTGTTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (21 bp):
ATGTTCATTTATTTTTTATTT
Found at i:1022596 original size:11 final size:11
Alignment explanation
Indices: 1022572--1022610 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1022562 CATGTTCATG
*
1022572 TTATTTTTTA-
1 TTATGTTTTAT
1022582 TTATGTTTTAT
1 TTATGTTTTAT
*
1022593 TTATTTTTTAT
1 TTATGTTTTAT
1022604 TTATGTT
1 TTATGTT
1022611 GTGTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (11 bp):
TTATGTTTTAT
Found at i:1023903 original size:21 final size:22
Alignment explanation
Indices: 1023856--1023899 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1023846 ATTATAATAA
**
1023856 ATAAATTAATAAATTTAATTTT
1 ATAAATTAATAAATTTAAAATT
1023878 ATAAA-TAAT-AATTTAAAATT
1 ATAAATTAATAAATTTAAAATT
1023898 AT
1 AT
1023900 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 4 0.20
22 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTAATAAATTTAAAATT
Found at i:1024575 original size:10 final size:10
Alignment explanation
Indices: 1024562--1024594 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1024552 AATACTTTAA
1024562 AATGTTCTAG
1 AATGTTCTAG
1024572 AATGTTCTAG
1 AATGTTCTAG
*
1024582 AATATTCTAG
1 AATGTTCTAG
1024592 AAT
1 AAT
1024595 ATCGTGGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (10 bp):
AATGTTCTAG
Found at i:1024620 original size:40 final size:39
Alignment explanation
Indices: 1024586--1024685 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 39
1024576 TTCTAGAATA
1024586 TTCTAGAATATCGTGGAAGGCTCTGGAAGATTCTAAAACG
1 TTCTAGAATAT-GTGGAAGGCTCTGGAAGATTCTAAAACG
1024626 TTCTAGAATAT-TGTGAGAGGCTCTGGAAGATTCTAAAACG
1 TTCTAGAATATGTG-GA-AGGCTCTGGAAGATTCTAAAACG
1024666 TTCTAGAATAATGTGGAAGG
1 TTCTAGAAT-ATGTGGAAGG
1024686 TTCTAGAACT
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 46 0.82
41 4 0.07
42 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (39 bp):
TTCTAGAATATGTGGAAGGCTCTGGAAGATTCTAAAACG
Found at i:1028284 original size:10 final size:10
Alignment explanation
Indices: 1028269--1028381 Score: 61
Period size: 10 Copynumber: 11.3 Consensus size: 10
1028259 AACACTTTGA
1028269 AATGTTCTAG
1 AATGTTCTAG
*
1028279 AATGTTCTGG
1 AATGTTCTAG
1028289 AATGTTCTAG
1 AATGTTCTAG
* *
1028299 AAT-ATCGTGG
1 AATGTTC-TAG
* * *
1028309 AAGGCTCTGG
1 AATGTTCTAG
1028319 AA-GATTCTAG
1 AATG-TTCTAG
1028329 AATGTTCTAG
1 AATGTTCTAG
* * *
1028339 AATATTGTGG
1 AATGTTCTAG
* * *
1028349 GAGGTTCTGG
1 AATGTTCTAG
1028359 AA-GATTCTAG
1 AATG-TTCTAG
*
1028369 AACGTTCTAG
1 AATGTTCTAG
1028379 AAT
1 AAT
1028382 AATGTGGAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
9 4 0.05
10 71 0.90
11 4 0.05
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (10 bp):
AATGTTCTAG
Found at i:1028292 original size:20 final size:20
Alignment explanation
Indices: 1028272--1028400 Score: 75
Period size: 20 Copynumber: 6.5 Consensus size: 20
1028262 ACTTTGAAAT
*
1028272 GTTCTAGAATGTTCTGGAAT
1 GTTCTAGAATGTTCTGGAAG
*
1028292 GTTCTAGAAT-ATCGTGGAAG
1 GTTCTAGAATGTTC-TGGAAG
* * * *
1028312 GCTCTGGAA-GATTCTAGAAT
1 GTTCTAGAATG-TTCTGGAAG
* * *
1028332 GTTCTAGAATATTGTGGGAG
1 GTTCTAGAATGTTCTGGAAG
* * *
1028352 GTTCTGGAA-GATTCTAGAAC
1 GTTCTAGAATG-TTCTGGAAG
** *
1028372 GTTCTAGAATAATGTGGAAG
1 GTTCTAGAATGTTCTGGAAG
1028392 GTTCTAGAA
1 GTTCTAGAA
1028401 CTTTATGGAG
Statistics
Matches: 77, Mismatches: 26, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
19 2 0.03
20 73 0.95
21 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTCTAGAATGTTCTGGAAG
Found at i:1028332 original size:40 final size:39
Alignment explanation
Indices: 1028283--1028392 Score: 157
Period size: 40 Copynumber: 2.7 Consensus size: 39
1028273 TTCTAGAATG
*
1028283 TTCTGGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATAT-GTGGAAGGCTCTGGAAGA
* *
1028323 TTCTAGAATGTTCTAGAATATTGTGGGAGGTTCTGGAAGA
1 TTCTAGAATGTTCTAGAATA-TGTGGAAGGCTCTGGAAGA
*
1028363 TTCTAGAACGTTCTAGAATAATGTGGAAGG
1 TTCTAGAATGTTCTAGAAT-ATGTGGAAGG
1028393 TTCTAGAACT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (39 bp):
TTCTAGAATGTTCTAGAATATGTGGAAGGCTCTGGAAGA
Found at i:1028646 original size:14 final size:16
Alignment explanation
Indices: 1028616--1028647 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1028606 TCATTTGGAG
1028616 GAGGTATAGAGGAAGA
1 GAGGTATAGAGGAAGA
1028632 GAGGTA-AGA-GAAGA
1 GAGGTATAGAGGAAGA
1028646 GA
1 GA
1028648 ATAATAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (16 bp):
GAGGTATAGAGGAAGA
Found at i:1029501 original size:13 final size:14
Alignment explanation
Indices: 1029453--1029502 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
1029443 TAAAATATTT
*
1029453 TTATTAA-ATTTAA
1 TTATTAATATATAA
*
1029466 TTATAAAATATATAA
1 TTAT-TAATATATAA
1029481 TTATTAATATA-AA
1 TTATTAATATATAA
*
1029494 TTTTTAATA
1 TTATTAATA
1029503 GTTTTTAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 14 0.45
14 8 0.26
15 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATTAATATATAA
Found at i:1032262 original size:39 final size:41
Alignment explanation
Indices: 1032163--1032272 Score: 107
Period size: 39 Copynumber: 2.7 Consensus size: 41
1032153 CCCCCTCCCC
*
1032163 CTCCTCCTCCATCTCCACCACCACCACCACTACCAGTTTATT
1 CTCCTCCTCCACCTCCACCACCACCACCAC-ACCAGTTTATT
* * * * * *
1032205 CACCTCCTTCGCCGCCACCACCACCTCC-C-CCGGTTTATT
1 CTCCTCCTCCACCTCCACCACCACCACCACACCAGTTTATT
* * *
1032244 CTCCACCTCCACCTCCACCTCCGCCACCA
1 CTCCTCCTCCACCTCCACCACCACCACCA
1032273 TCCCCACCCC
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
39 29 0.56
41 1 0.02
42 22 0.42
ACGTcount: A:0.17, C:0.55, G:0.05, T:0.22
Consensus pattern (41 bp):
CTCCTCCTCCACCTCCACCACCACCACCACACCAGTTTATT
Found at i:1032297 original size:15 final size:15
Alignment explanation
Indices: 1032259--1032317 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1032249 CCTCCACCTC
*
1032259 CACCTCCGCCACCAT
1 CACCTCCCCCACCAT
* *
1032274 CCCCACCCCCACCAT
1 CACCTCCCCCACCAT
* *
1032289 CACCTCCCCCGCCTT
1 CACCTCCCCCACCAT
*
1032304 CACCTCCACCACCA
1 CACCTCCCCCACCA
1032318 ACTTATCCAT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.19, C:0.66, G:0.03, T:0.12
Consensus pattern (15 bp):
CACCTCCCCCACCAT
Found at i:1032346 original size:39 final size:39
Alignment explanation
Indices: 1032285--1032382 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 39
1032275 CCCACCCCCA
* * * * * *
1032285 CCATCACCTCCCCCGCCTTCACCTCCACCACCAACTTAT
1 CCATCACCACCTCCACCGTCACCACCACCACCAACTTAC
*
1032324 CCATCACCACCTCCACCGTCACCACCACCACCTACTTAC
1 CCATCACCACCTCCACCGTCACCACCACCACCAACTTAC
* *
1032363 CCATCGCCACCTCCTCCGTC
1 CCATCACCACCTCCACCGTC
1032383 CCCCCCGCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.20, C:0.57, G:0.04, T:0.18
Consensus pattern (39 bp):
CCATCACCACCTCCACCGTCACCACCACCACCAACTTAC
Found at i:1038533 original size:11 final size:11
Alignment explanation
Indices: 1038517--1038545 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1038507 GATTAGGAGT
1038517 ATAATAACAGA
1 ATAATAACAGA
1038528 ATAATAACAGA
1 ATAATAACAGA
1038539 ATAATAA
1 ATAATAA
1038546 TTTAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (11 bp):
ATAATAACAGA
Found at i:1038768 original size:33 final size:33
Alignment explanation
Indices: 1038726--1038806 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
1038716 TCTGGCACGG
1038726 CTGATGCATAAGGCAGTGACTGCAATGACATCC
1 CTGATGCATAAGGCAGTGACTGCAATGACATCC
1038759 CTGATGCATAAGGCAGTGACTGCAATGACATCC
1 CTGATGCATAAGGCAGTGACTGCAATGACATCC
1038792 CTGATGCATAAGGCA
1 CTGATGCATAAGGCA
1038807 AAGTCTGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (33 bp):
CTGATGCATAAGGCAGTGACTGCAATGACATCC
Found at i:1042441 original size:24 final size:24
Alignment explanation
Indices: 1042409--1042461 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1042399 AACATTGACT
1042409 CAGAAACATGTTAACTAATGAAGA
1 CAGAAACATGTTAACTAATGAAGA
1042433 CAGAAACATGTTAACTAATGAAGA
1 CAGAAACATGTTAACTAATGAAGA
1042457 CAGAA
1 CAGAA
1042462 CCAAAAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (24 bp):
CAGAAACATGTTAACTAATGAAGA
Found at i:1044447 original size:4 final size:4
Alignment explanation
Indices: 1044438--1044487 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
1044428 ACTAAGCAAA
1044438 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1044485 AAA
1 AAA
1044488 AGGCTGCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.07
4 42 0.93
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1045321 original size:13 final size:13
Alignment explanation
Indices: 1045298--1045335 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1045288 TATATAATTT
1045298 TAAAT-TATTATA
1 TAAATATATTATA
1045310 TAAATATATTATA
1 TAAATATATTATA
* *
1045323 TATATATAATATA
1 TAAATATATTATA
1045336 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATATTATA
Found at i:1053302 original size:2 final size:2
Alignment explanation
Indices: 1053295--1053326 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1053285 TGGCCACCAA
1053295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1053327 TTGGCATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.